Multiple sequence alignment - TraesCS6D01G155100

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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 TraesCS6D01G155100 chr6D 100.000 5677 0 0 1 5677 131605833 131611509 0.000000e+00 10484.0
1 TraesCS6D01G155100 chr6B 95.100 2898 113 14 2117 4999 228974410 228977293 0.000000e+00 4538.0
2 TraesCS6D01G155100 chr6B 92.060 932 38 15 429 1345 228972131 228973041 0.000000e+00 1279.0
3 TraesCS6D01G155100 chr6B 92.342 666 46 5 1451 2114 228973040 228973702 0.000000e+00 942.0
4 TraesCS6D01G155100 chr6B 92.791 430 31 0 2 431 228970117 228970546 1.740000e-174 623.0
5 TraesCS6D01G155100 chr6B 88.560 507 37 10 4992 5478 228977431 228977936 3.790000e-166 595.0
6 TraesCS6D01G155100 chr6B 85.167 418 42 14 3180 3581 706519277 706518864 1.470000e-110 411.0
7 TraesCS6D01G155100 chr6B 95.294 170 6 2 5507 5675 228977935 228978103 9.380000e-68 268.0
8 TraesCS6D01G155100 chr6B 98.182 110 2 0 1346 1455 612317152 612317261 5.800000e-45 193.0
9 TraesCS6D01G155100 chr6B 97.345 113 2 1 1346 1457 207511007 207510895 2.090000e-44 191.0
10 TraesCS6D01G155100 chr6A 96.689 2054 53 12 2205 4248 169514079 169516127 0.000000e+00 3402.0
11 TraesCS6D01G155100 chr6A 94.350 761 36 4 1451 2206 169507083 169507841 0.000000e+00 1160.0
12 TraesCS6D01G155100 chr6A 95.284 721 21 7 632 1345 169506370 169507084 0.000000e+00 1131.0
13 TraesCS6D01G155100 chr6A 92.885 759 40 11 4244 4999 169522222 169522969 0.000000e+00 1090.0
14 TraesCS6D01G155100 chr6A 89.825 855 72 9 1901 2748 555436670 555437516 0.000000e+00 1083.0
15 TraesCS6D01G155100 chr6A 94.274 489 26 2 5190 5677 169523350 169523837 0.000000e+00 747.0
16 TraesCS6D01G155100 chr6A 88.372 258 27 3 3124 3381 555438331 555438585 1.990000e-79 307.0
17 TraesCS6D01G155100 chr6A 82.787 244 35 3 3380 3616 609801088 609800845 1.600000e-50 211.0
18 TraesCS6D01G155100 chr6A 89.809 157 16 0 2740 2896 555438181 555438337 9.640000e-48 202.0
19 TraesCS6D01G155100 chr4A 89.531 1003 90 9 1901 2896 545882123 545881129 0.000000e+00 1256.0
20 TraesCS6D01G155100 chr4A 87.645 259 29 3 3123 3381 545881136 545880881 1.200000e-76 298.0
21 TraesCS6D01G155100 chr4A 93.204 103 7 0 3369 3471 545879422 545879320 9.850000e-33 152.0
22 TraesCS6D01G155100 chr3A 89.232 1003 94 8 1901 2896 125442800 125443795 0.000000e+00 1242.0
23 TraesCS6D01G155100 chr3A 88.417 259 27 3 3123 3381 125443788 125444043 5.520000e-80 309.0
24 TraesCS6D01G155100 chr3A 89.583 240 20 5 2890 3126 176148239 176148002 3.320000e-77 300.0
25 TraesCS6D01G155100 chr3A 97.321 112 3 0 1346 1457 644809235 644809124 2.090000e-44 191.0
26 TraesCS6D01G155100 chr1B 87.451 1012 91 18 1895 2889 30839736 30840728 0.000000e+00 1133.0
27 TraesCS6D01G155100 chr1B 99.065 107 1 0 1346 1452 308586771 308586665 5.800000e-45 193.0
28 TraesCS6D01G155100 chr4B 89.286 672 66 5 2205 2873 97557022 97556354 0.000000e+00 837.0
29 TraesCS6D01G155100 chr4B 88.559 236 21 5 1976 2206 97557370 97557136 1.200000e-71 281.0
30 TraesCS6D01G155100 chr4B 98.182 110 2 0 1346 1455 149160513 149160404 5.800000e-45 193.0
31 TraesCS6D01G155100 chr4B 96.491 114 3 1 1346 1459 63765802 63765690 2.700000e-43 187.0
32 TraesCS6D01G155100 chr4B 90.385 52 5 0 1910 1961 97557420 97557369 1.020000e-07 69.4
33 TraesCS6D01G155100 chr5A 90.274 329 29 1 2567 2892 692369121 692369449 1.460000e-115 427.0
34 TraesCS6D01G155100 chr5A 99.083 109 1 0 1346 1454 504767939 504767831 4.490000e-46 196.0
35 TraesCS6D01G155100 chr2B 89.627 241 21 4 2894 3131 667259193 667259432 2.570000e-78 303.0
36 TraesCS6D01G155100 chr2B 97.321 112 2 1 1346 1456 646951393 646951282 7.510000e-44 189.0
37 TraesCS6D01G155100 chr7D 88.845 251 19 9 2886 3131 428711357 428711603 3.320000e-77 300.0
38 TraesCS6D01G155100 chr1D 89.540 239 21 4 2890 3124 397047789 397047551 3.320000e-77 300.0
39 TraesCS6D01G155100 chr3D 89.212 241 20 6 2890 3126 153506993 153507231 4.300000e-76 296.0
40 TraesCS6D01G155100 chr3D 96.460 113 4 0 1346 1458 67437085 67437197 2.700000e-43 187.0
41 TraesCS6D01G155100 chr3D 81.818 209 17 8 249 454 26035047 26034857 7.620000e-34 156.0
42 TraesCS6D01G155100 chr7B 88.446 251 19 9 2886 3131 446140394 446140639 1.550000e-75 294.0
43 TraesCS6D01G155100 chr2D 88.936 235 20 4 2896 3126 246704762 246704530 9.310000e-73 285.0
44 TraesCS6D01G155100 chrUn 78.198 344 51 14 1 323 297428270 297428610 1.250000e-46 198.0
45 TraesCS6D01G155100 chrUn 77.616 344 53 18 1 323 297433222 297433562 2.700000e-43 187.0


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 TraesCS6D01G155100 chr6D 131605833 131611509 5676 False 10484.000000 10484 100.000000 1 5677 1 chr6D.!!$F1 5676
1 TraesCS6D01G155100 chr6B 228970117 228978103 7986 False 1374.166667 4538 92.691167 2 5675 6 chr6B.!!$F2 5673
2 TraesCS6D01G155100 chr6A 169514079 169516127 2048 False 3402.000000 3402 96.689000 2205 4248 1 chr6A.!!$F1 2043
3 TraesCS6D01G155100 chr6A 169506370 169507841 1471 False 1145.500000 1160 94.817000 632 2206 2 chr6A.!!$F2 1574
4 TraesCS6D01G155100 chr6A 169522222 169523837 1615 False 918.500000 1090 93.579500 4244 5677 2 chr6A.!!$F3 1433
5 TraesCS6D01G155100 chr6A 555436670 555438585 1915 False 530.666667 1083 89.335333 1901 3381 3 chr6A.!!$F4 1480
6 TraesCS6D01G155100 chr4A 545879320 545882123 2803 True 568.666667 1256 90.126667 1901 3471 3 chr4A.!!$R1 1570
7 TraesCS6D01G155100 chr3A 125442800 125444043 1243 False 775.500000 1242 88.824500 1901 3381 2 chr3A.!!$F1 1480
8 TraesCS6D01G155100 chr1B 30839736 30840728 992 False 1133.000000 1133 87.451000 1895 2889 1 chr1B.!!$F1 994
9 TraesCS6D01G155100 chr4B 97556354 97557420 1066 True 395.800000 837 89.410000 1910 2873 3 chr4B.!!$R3 963

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
547 2136 0.104120 TATGGGACGACCGATTGCAG 59.896 55.0 6.75 0.0 44.64 4.41 F
555 2144 0.179000 GACCGATTGCAGGATCCACT 59.821 55.0 15.82 0.0 0.00 4.00 F
1447 3054 0.107361 AAGTATTTTCGGGCGGAGGG 60.107 55.0 0.00 0.0 0.00 4.30 F
1449 3056 0.532196 GTATTTTCGGGCGGAGGGAG 60.532 60.0 0.00 0.0 0.00 4.30 F
1450 3057 0.979187 TATTTTCGGGCGGAGGGAGT 60.979 55.0 0.00 0.0 0.00 3.85 F
1451 3058 0.979187 ATTTTCGGGCGGAGGGAGTA 60.979 55.0 0.00 0.0 0.00 2.59 F
3097 6234 1.343506 GGTAGTGTTACTTCGTGCCG 58.656 55.0 0.00 0.0 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1437 3044 0.037303 TATAGTACTCCCTCCGCCCG 59.963 60.000 0.00 0.00 0.00 6.13 R
2153 4474 1.903183 GGCTTGTTCCAGTAGGAGAGT 59.097 52.381 0.00 0.00 46.74 3.24 R
2987 6115 0.593128 AAGTCGCCATGCTTCACAAC 59.407 50.000 0.00 0.00 0.00 3.32 R
3097 6234 1.086696 ATGATAAGTGCCACACGTGC 58.913 50.000 17.22 1.66 39.64 5.34 R
3182 6320 3.307242 CGGCTACAGAAGATAGCAAACAC 59.693 47.826 6.37 0.00 45.76 3.32 R
3738 8347 3.241067 TGAAATACCGTAAGAGCGCTT 57.759 42.857 13.26 8.09 43.02 4.68 R
5177 9967 0.601841 GGTGATCGTTTGTCCACCGT 60.602 55.000 0.00 0.00 39.52 4.83 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
60 61 2.202492 CTCCTTCGTCCGTCAGCG 60.202 66.667 0.00 0.00 37.95 5.18
74 75 3.379445 AGCGGGTGGACGAACGAT 61.379 61.111 0.14 0.00 35.47 3.73
120 121 3.740397 CGCTCGGGTGTGGACGTA 61.740 66.667 0.00 0.00 0.00 3.57
126 127 1.080298 GGGTGTGGACGTACTTCCG 60.080 63.158 13.28 0.00 38.69 4.30
163 164 3.000819 TCCCCCGTGCTCAATCGT 61.001 61.111 0.00 0.00 0.00 3.73
168 169 3.902063 CGTGCTCAATCGTCGCCG 61.902 66.667 0.00 0.00 0.00 6.46
199 200 2.746277 GCGTGGTTCGAGGCCAAT 60.746 61.111 5.01 0.00 42.86 3.16
228 229 4.742201 TGCCCGAGACGAAGCTGC 62.742 66.667 0.00 0.00 0.00 5.25
263 264 2.278013 CGCTCTTCGAGGCGTACC 60.278 66.667 17.12 0.00 45.34 3.34
292 293 0.325765 AGGTCCCCTCTAGCACCTTC 60.326 60.000 0.00 0.00 35.61 3.46
302 303 0.604578 TAGCACCTTCGTGTACCACC 59.395 55.000 0.00 0.00 42.39 4.61
307 308 0.395312 CCTTCGTGTACCACCACCTT 59.605 55.000 0.00 0.00 31.47 3.50
447 2035 9.233649 TCCGTTTTTATGTATGAACTTTGGTAT 57.766 29.630 0.00 0.00 0.00 2.73
494 2083 0.809241 GGATCTGCTCTGACCAAGCG 60.809 60.000 0.00 0.00 42.83 4.68
515 2104 3.299542 CGTCCCGCAAAATTCAAAATACG 59.700 43.478 0.00 0.00 0.00 3.06
521 2110 6.311690 CCCGCAAAATTCAAAATACGGTAAAT 59.688 34.615 0.00 0.00 37.74 1.40
533 2122 9.296400 CAAAATACGGTAAATGAGTTTTATGGG 57.704 33.333 0.00 0.00 32.56 4.00
547 2136 0.104120 TATGGGACGACCGATTGCAG 59.896 55.000 6.75 0.00 44.64 4.41
555 2144 0.179000 GACCGATTGCAGGATCCACT 59.821 55.000 15.82 0.00 0.00 4.00
556 2145 1.412710 GACCGATTGCAGGATCCACTA 59.587 52.381 15.82 2.77 0.00 2.74
592 2181 1.265095 CGAATCATAGGCCACACATGC 59.735 52.381 5.01 0.00 0.00 4.06
593 2182 1.265095 GAATCATAGGCCACACATGCG 59.735 52.381 5.01 0.00 0.00 4.73
632 2221 0.528017 TCGGCGCCTATCATCATCTC 59.472 55.000 26.68 0.00 0.00 2.75
645 2234 8.921205 CCTATCATCATCTCCCAAAAGAAAAAT 58.079 33.333 0.00 0.00 0.00 1.82
659 2248 5.567138 AAGAAAAATATCTTCCGCACCTG 57.433 39.130 0.00 0.00 34.60 4.00
679 2268 4.180946 CGGCCTCTCACCGTCTCG 62.181 72.222 0.00 0.00 45.70 4.04
680 2269 4.500116 GGCCTCTCACCGTCTCGC 62.500 72.222 0.00 0.00 0.00 5.03
681 2270 4.838486 GCCTCTCACCGTCTCGCG 62.838 72.222 0.00 0.00 40.95 5.87
966 2565 1.442148 CGCTAGCTAGGGTTGGGAC 59.558 63.158 25.54 5.33 0.00 4.46
1345 2952 7.225931 GCAAGGTAAGACCACGAATAATCATAA 59.774 37.037 0.00 0.00 41.95 1.90
1346 2953 8.548721 CAAGGTAAGACCACGAATAATCATAAC 58.451 37.037 0.00 0.00 41.95 1.89
1347 2954 8.019656 AGGTAAGACCACGAATAATCATAACT 57.980 34.615 0.00 0.00 41.95 2.24
1348 2955 8.483758 AGGTAAGACCACGAATAATCATAACTT 58.516 33.333 0.00 0.00 41.95 2.66
1349 2956 8.548721 GGTAAGACCACGAATAATCATAACTTG 58.451 37.037 0.00 0.00 38.42 3.16
1350 2957 9.095065 GTAAGACCACGAATAATCATAACTTGT 57.905 33.333 0.00 0.00 0.00 3.16
1351 2958 7.772332 AGACCACGAATAATCATAACTTGTC 57.228 36.000 0.00 0.00 0.00 3.18
1352 2959 7.327975 AGACCACGAATAATCATAACTTGTCA 58.672 34.615 0.00 0.00 0.00 3.58
1353 2960 7.987458 AGACCACGAATAATCATAACTTGTCAT 59.013 33.333 0.00 0.00 0.00 3.06
1354 2961 8.142994 ACCACGAATAATCATAACTTGTCATC 57.857 34.615 0.00 0.00 0.00 2.92
1355 2962 7.768582 ACCACGAATAATCATAACTTGTCATCA 59.231 33.333 0.00 0.00 0.00 3.07
1356 2963 8.611757 CCACGAATAATCATAACTTGTCATCAA 58.388 33.333 0.00 0.00 0.00 2.57
1357 2964 9.986833 CACGAATAATCATAACTTGTCATCAAA 57.013 29.630 0.00 0.00 32.87 2.69
1370 2977 7.614494 ACTTGTCATCAAAATGGATAAAAGGG 58.386 34.615 0.00 0.00 33.42 3.95
1371 2978 6.543430 TGTCATCAAAATGGATAAAAGGGG 57.457 37.500 0.00 0.00 33.42 4.79
1372 2979 6.259893 TGTCATCAAAATGGATAAAAGGGGA 58.740 36.000 0.00 0.00 33.42 4.81
1373 2980 6.902416 TGTCATCAAAATGGATAAAAGGGGAT 59.098 34.615 0.00 0.00 33.42 3.85
1374 2981 7.147689 TGTCATCAAAATGGATAAAAGGGGATG 60.148 37.037 0.00 0.00 33.42 3.51
1375 2982 6.902416 TCATCAAAATGGATAAAAGGGGATGT 59.098 34.615 0.00 0.00 33.42 3.06
1376 2983 8.064389 TCATCAAAATGGATAAAAGGGGATGTA 58.936 33.333 0.00 0.00 33.42 2.29
1377 2984 8.873144 CATCAAAATGGATAAAAGGGGATGTAT 58.127 33.333 0.00 0.00 0.00 2.29
1378 2985 8.477419 TCAAAATGGATAAAAGGGGATGTATC 57.523 34.615 0.00 0.00 0.00 2.24
1379 2986 8.288812 TCAAAATGGATAAAAGGGGATGTATCT 58.711 33.333 0.00 0.00 0.00 1.98
1380 2987 9.586732 CAAAATGGATAAAAGGGGATGTATCTA 57.413 33.333 0.00 0.00 0.00 1.98
1381 2988 9.813826 AAAATGGATAAAAGGGGATGTATCTAG 57.186 33.333 0.00 0.00 0.00 2.43
1382 2989 8.757307 AATGGATAAAAGGGGATGTATCTAGA 57.243 34.615 0.00 0.00 0.00 2.43
1383 2990 7.554959 TGGATAAAAGGGGATGTATCTAGAC 57.445 40.000 0.00 0.00 0.00 2.59
1384 2991 6.210784 TGGATAAAAGGGGATGTATCTAGACG 59.789 42.308 0.00 0.00 0.00 4.18
1385 2992 6.210984 GGATAAAAGGGGATGTATCTAGACGT 59.789 42.308 0.00 0.00 0.00 4.34
1386 2993 7.395489 GGATAAAAGGGGATGTATCTAGACGTA 59.605 40.741 0.00 0.00 0.00 3.57
1387 2994 8.896722 ATAAAAGGGGATGTATCTAGACGTAT 57.103 34.615 0.00 0.00 0.00 3.06
1388 2995 7.613551 AAAAGGGGATGTATCTAGACGTATT 57.386 36.000 0.00 0.00 0.00 1.89
1389 2996 7.613551 AAAGGGGATGTATCTAGACGTATTT 57.386 36.000 0.00 0.00 0.00 1.40
1390 2997 7.613551 AAGGGGATGTATCTAGACGTATTTT 57.386 36.000 0.00 0.00 0.00 1.82
1391 2998 8.716674 AAGGGGATGTATCTAGACGTATTTTA 57.283 34.615 0.00 0.00 0.00 1.52
1392 2999 8.350852 AGGGGATGTATCTAGACGTATTTTAG 57.649 38.462 0.00 0.00 0.00 1.85
1393 3000 7.949006 AGGGGATGTATCTAGACGTATTTTAGT 59.051 37.037 0.00 0.00 0.00 2.24
1394 3001 8.583296 GGGGATGTATCTAGACGTATTTTAGTT 58.417 37.037 0.00 0.00 0.00 2.24
1395 3002 9.623350 GGGATGTATCTAGACGTATTTTAGTTC 57.377 37.037 0.00 0.00 0.00 3.01
1396 3003 9.327529 GGATGTATCTAGACGTATTTTAGTTCG 57.672 37.037 0.00 0.00 0.00 3.95
1399 3006 9.317936 TGTATCTAGACGTATTTTAGTTCGAGA 57.682 33.333 0.00 0.00 0.00 4.04
1403 3010 9.317936 TCTAGACGTATTTTAGTTCGAGATACA 57.682 33.333 0.00 0.00 0.00 2.29
1406 3013 8.838365 AGACGTATTTTAGTTCGAGATACATCT 58.162 33.333 0.00 0.00 40.50 2.90
1431 3038 9.918630 CTCTTTTTATCCATTTTGATGACAAGT 57.081 29.630 0.00 0.00 37.32 3.16
1438 3045 8.915871 ATCCATTTTGATGACAAGTATTTTCG 57.084 30.769 0.00 0.00 37.32 3.46
1439 3046 7.312154 TCCATTTTGATGACAAGTATTTTCGG 58.688 34.615 0.00 0.00 37.32 4.30
1440 3047 6.531240 CCATTTTGATGACAAGTATTTTCGGG 59.469 38.462 0.00 0.00 37.32 5.14
1441 3048 4.695217 TTGATGACAAGTATTTTCGGGC 57.305 40.909 0.00 0.00 0.00 6.13
1442 3049 2.675844 TGATGACAAGTATTTTCGGGCG 59.324 45.455 0.00 0.00 0.00 6.13
1443 3050 1.444836 TGACAAGTATTTTCGGGCGG 58.555 50.000 0.00 0.00 0.00 6.13
1444 3051 1.002201 TGACAAGTATTTTCGGGCGGA 59.998 47.619 0.00 0.00 0.00 5.54
1445 3052 1.664151 GACAAGTATTTTCGGGCGGAG 59.336 52.381 0.00 0.00 0.00 4.63
1446 3053 1.014352 CAAGTATTTTCGGGCGGAGG 58.986 55.000 0.00 0.00 0.00 4.30
1447 3054 0.107361 AAGTATTTTCGGGCGGAGGG 60.107 55.000 0.00 0.00 0.00 4.30
1448 3055 0.979187 AGTATTTTCGGGCGGAGGGA 60.979 55.000 0.00 0.00 0.00 4.20
1449 3056 0.532196 GTATTTTCGGGCGGAGGGAG 60.532 60.000 0.00 0.00 0.00 4.30
1450 3057 0.979187 TATTTTCGGGCGGAGGGAGT 60.979 55.000 0.00 0.00 0.00 3.85
1451 3058 0.979187 ATTTTCGGGCGGAGGGAGTA 60.979 55.000 0.00 0.00 0.00 2.59
1568 3175 2.291670 ACCGGGTCTATCAGTCTGTCTT 60.292 50.000 6.32 0.00 0.00 3.01
1585 3192 6.874134 GTCTGTCTTAAGTCACCACAATGTAT 59.126 38.462 1.63 0.00 0.00 2.29
1624 3231 1.760613 TCTCCAAGTGTGAAACGGACT 59.239 47.619 0.00 0.00 42.39 3.85
1627 3234 2.014128 CCAAGTGTGAAACGGACTGTT 58.986 47.619 0.00 0.00 44.59 3.16
1658 3265 4.579454 TCTAATAACGGATTCAGACGGG 57.421 45.455 0.00 0.00 0.00 5.28
1726 3337 3.181489 GGGACATCACTAGAAGTACACCG 60.181 52.174 0.00 0.00 27.72 4.94
1904 3515 8.402472 CAGTATAATGGAGCTGTCTATAGTAGC 58.598 40.741 18.07 18.07 37.71 3.58
1941 3552 2.818350 GCAGGTTGTTCTTGCATGC 58.182 52.632 11.82 11.82 46.35 4.06
2046 3659 2.413142 GGCATGCCTTGAGCTCACC 61.413 63.158 29.98 8.83 44.23 4.02
2153 4474 6.584471 TCTATAGCTAAAATCCAAACCCCA 57.416 37.500 0.00 0.00 0.00 4.96
2188 4510 6.072563 TGGAACAAGCCCTTACGTAAAATAAC 60.073 38.462 9.68 0.00 31.92 1.89
2192 4514 5.494632 AGCCCTTACGTAAAATAACATGC 57.505 39.130 9.68 3.75 0.00 4.06
2338 4775 2.426522 GCTCTGCTGGACATTACAACA 58.573 47.619 0.00 0.00 0.00 3.33
2396 4833 5.511386 AGGAATCACACCTTCTGATTTCT 57.489 39.130 0.00 0.00 38.61 2.52
2538 4975 5.366482 TGCACCATGTAATTAAGCTCCTA 57.634 39.130 0.00 0.00 0.00 2.94
2557 5000 8.982723 AGCTCCTATCTTATTAGTTCTCAACAA 58.017 33.333 0.00 0.00 0.00 2.83
2940 6067 2.690778 GCACGAAGCAATTCCGCCT 61.691 57.895 0.00 0.00 44.79 5.52
2987 6115 3.252974 ACTCGAGGATGGCAACTTTAG 57.747 47.619 18.41 0.00 37.61 1.85
3002 6130 2.226437 ACTTTAGTTGTGAAGCATGGCG 59.774 45.455 0.00 0.00 0.00 5.69
3080 6217 9.902196 CAATTTTAGTTATAAAAACGTCAGGGT 57.098 29.630 0.00 0.00 42.56 4.34
3097 6234 1.343506 GGTAGTGTTACTTCGTGCCG 58.656 55.000 0.00 0.00 0.00 5.69
3182 6320 5.237996 CACATCTTAGGCAGTACCATTCATG 59.762 44.000 0.00 0.00 43.14 3.07
3236 6374 3.977312 TCTGGGTTGCTAGCTAGACTTA 58.023 45.455 25.15 4.25 34.89 2.24
3285 6423 5.241403 TGTCAGAAATGTATGACCACCTT 57.759 39.130 8.17 0.00 43.93 3.50
3738 8347 7.252612 TGGAAGGTACTGTTTCTGATCATAA 57.747 36.000 0.00 0.00 40.86 1.90
3742 8351 5.812642 AGGTACTGTTTCTGATCATAAAGCG 59.187 40.000 6.51 4.13 37.18 4.68
3922 8531 0.170339 GCTGCGTTTGTAATGGTCCC 59.830 55.000 0.00 0.00 0.00 4.46
3949 8558 8.798975 AGGTTAAATCATAGGGTAGATCAGAA 57.201 34.615 0.00 0.00 0.00 3.02
4252 8861 5.934402 TCATCTTGACCCTCCTAACTTAC 57.066 43.478 0.00 0.00 0.00 2.34
4263 8873 7.229308 ACCCTCCTAACTTACGAAGAATTTTT 58.771 34.615 0.00 0.00 0.00 1.94
4299 8909 4.785301 CATCTTCCTCTAAAATGGCTCCA 58.215 43.478 0.00 0.00 0.00 3.86
4302 8912 6.575244 TCTTCCTCTAAAATGGCTCCAATA 57.425 37.500 0.00 0.00 0.00 1.90
4396 9006 5.466058 CAGAATTCATCAGATGCTGTAGGAC 59.534 44.000 8.44 0.00 32.61 3.85
4451 9069 7.174946 TCCTATCTTTTGACCTGTTTTTAGCTG 59.825 37.037 0.00 0.00 0.00 4.24
4678 9296 7.249858 CGTCTATTCATAGATCAGGAGTGATG 58.750 42.308 0.00 0.00 43.92 3.07
4686 9304 1.576577 TCAGGAGTGATGATGCCTGT 58.423 50.000 0.00 0.00 46.21 4.00
4697 9315 1.275856 TGATGCCTGTTTGAAATGCCC 59.724 47.619 0.00 0.00 0.00 5.36
4699 9317 2.300956 TGCCTGTTTGAAATGCCCTA 57.699 45.000 0.00 0.00 0.00 3.53
4700 9318 1.892474 TGCCTGTTTGAAATGCCCTAC 59.108 47.619 0.00 0.00 0.00 3.18
4703 9321 0.519519 TGTTTGAAATGCCCTACGCG 59.480 50.000 3.53 3.53 42.08 6.01
4720 9338 4.029809 GGCGGCCTACCCTGTGTT 62.030 66.667 12.87 0.00 0.00 3.32
4728 9346 2.747446 GCCTACCCTGTGTTTGTATGTG 59.253 50.000 0.00 0.00 0.00 3.21
4729 9347 3.809324 GCCTACCCTGTGTTTGTATGTGT 60.809 47.826 0.00 0.00 0.00 3.72
4730 9348 4.563993 GCCTACCCTGTGTTTGTATGTGTA 60.564 45.833 0.00 0.00 0.00 2.90
4731 9349 5.175859 CCTACCCTGTGTTTGTATGTGTAG 58.824 45.833 0.00 0.00 0.00 2.74
4732 9350 4.967084 ACCCTGTGTTTGTATGTGTAGA 57.033 40.909 0.00 0.00 0.00 2.59
4734 9352 4.253685 CCCTGTGTTTGTATGTGTAGAGG 58.746 47.826 0.00 0.00 0.00 3.69
4735 9353 4.262894 CCCTGTGTTTGTATGTGTAGAGGT 60.263 45.833 0.00 0.00 0.00 3.85
4736 9354 5.046878 CCCTGTGTTTGTATGTGTAGAGGTA 60.047 44.000 0.00 0.00 0.00 3.08
4738 9356 6.757010 CCTGTGTTTGTATGTGTAGAGGTATC 59.243 42.308 0.00 0.00 0.00 2.24
4773 9391 6.071221 ACGTATCCATTGTAGAACAAGGTGTA 60.071 38.462 4.06 0.00 41.94 2.90
4806 9424 4.034048 CGCTTGTGCTAGTTATTACCTTGG 59.966 45.833 0.00 0.00 36.97 3.61
4835 9453 1.819905 CTCCGGGAGAGGAAAGAGC 59.180 63.158 19.57 0.00 40.25 4.09
4920 9539 2.766313 TGTTCTTGGATCGGACTTGTG 58.234 47.619 0.00 0.00 0.00 3.33
4926 9545 4.221924 TCTTGGATCGGACTTGTGTAATGA 59.778 41.667 0.00 0.00 0.00 2.57
4947 9566 1.070577 CGCTCACGGTAATATGCTTGC 60.071 52.381 0.00 0.00 34.97 4.01
4967 9586 5.536554 TGCGCTGATAGAGAAAAAGAAAG 57.463 39.130 9.73 0.00 0.00 2.62
4989 9608 2.226674 GGTTTGCTTCTAGCTGAACCAC 59.773 50.000 21.56 6.13 46.96 4.16
4991 9610 2.928801 TGCTTCTAGCTGAACCACAA 57.071 45.000 0.00 0.00 42.97 3.33
4999 9618 5.918608 TCTAGCTGAACCACAATTCCTATC 58.081 41.667 0.00 0.00 0.00 2.08
5002 9621 4.079558 AGCTGAACCACAATTCCTATCCAT 60.080 41.667 0.00 0.00 0.00 3.41
5003 9622 5.132648 AGCTGAACCACAATTCCTATCCATA 59.867 40.000 0.00 0.00 0.00 2.74
5006 9625 7.308830 GCTGAACCACAATTCCTATCCATAATC 60.309 40.741 0.00 0.00 0.00 1.75
5010 9629 8.275187 ACCACAATTCCTATCCATAATCTGTA 57.725 34.615 0.00 0.00 0.00 2.74
5012 9631 9.003658 CCACAATTCCTATCCATAATCTGTAAC 57.996 37.037 0.00 0.00 0.00 2.50
5052 9816 7.228706 TGAGTTTCTTCCACTCCATTTTTAGTC 59.771 37.037 0.00 0.00 40.12 2.59
5084 9848 2.338809 TCATTCCTCCACTGAACTGGT 58.661 47.619 0.00 0.00 32.50 4.00
5090 9854 2.413837 CTCCACTGAACTGGTAAACCG 58.586 52.381 0.00 0.00 39.43 4.44
5092 9856 2.171027 TCCACTGAACTGGTAAACCGTT 59.829 45.455 8.45 8.45 39.43 4.44
5096 9860 1.489649 TGAACTGGTAAACCGTTGGGA 59.510 47.619 12.07 0.00 39.43 4.37
5099 9863 4.019141 TGAACTGGTAAACCGTTGGGATAT 60.019 41.667 12.07 0.00 39.43 1.63
5106 9870 0.986019 ACCGTTGGGATATGGCAGGA 60.986 55.000 0.00 0.00 36.97 3.86
5113 9877 2.567169 TGGGATATGGCAGGAATAGACG 59.433 50.000 0.00 0.00 0.00 4.18
5128 9892 6.096564 AGGAATAGACGAGAAACTTATCGGTT 59.903 38.462 10.82 1.87 45.32 4.44
5146 9936 3.469739 GGTTTGTTTACCGACAGGAGAA 58.530 45.455 0.00 0.00 41.02 2.87
5148 9938 4.124970 GTTTGTTTACCGACAGGAGAAGT 58.875 43.478 0.00 0.00 41.02 3.01
5177 9967 7.040201 AGCTTCTGTTTATGCATTTCTGAGAAA 60.040 33.333 10.39 10.39 0.00 2.52
5178 9968 7.061557 GCTTCTGTTTATGCATTTCTGAGAAAC 59.938 37.037 10.18 8.25 0.00 2.78
5179 9969 6.602179 TCTGTTTATGCATTTCTGAGAAACG 58.398 36.000 10.18 2.77 0.00 3.60
5180 9970 5.698832 TGTTTATGCATTTCTGAGAAACGG 58.301 37.500 10.18 6.90 0.00 4.44
5181 9971 5.240623 TGTTTATGCATTTCTGAGAAACGGT 59.759 36.000 10.18 0.02 0.00 4.83
5183 9973 1.879380 TGCATTTCTGAGAAACGGTGG 59.121 47.619 10.18 0.00 0.00 4.61
5185 9975 2.095718 GCATTTCTGAGAAACGGTGGAC 60.096 50.000 10.18 0.00 0.00 4.02
5186 9976 2.992124 TTTCTGAGAAACGGTGGACA 57.008 45.000 3.02 0.00 0.00 4.02
5188 9978 2.992124 TCTGAGAAACGGTGGACAAA 57.008 45.000 0.00 0.00 0.00 2.83
5195 10007 1.223187 AACGGTGGACAAACGATCAC 58.777 50.000 0.00 0.00 0.00 3.06
5198 10010 1.821216 GGTGGACAAACGATCACCAT 58.179 50.000 6.48 0.00 46.39 3.55
5234 10047 6.651225 AGGAAGAGAAACGTTTTGATCTTAGG 59.349 38.462 24.70 0.00 0.00 2.69
5360 10173 3.130160 CTTGAAGCTGCTCCCGGC 61.130 66.667 1.00 0.00 43.89 6.13
5494 10307 2.034532 CAGTGGCAGACATGGGCA 59.965 61.111 0.00 0.00 38.62 5.36
5528 10341 3.766691 GTCGCCGCCTAGGTCCAA 61.767 66.667 11.31 0.00 43.70 3.53
5570 10383 4.410400 CTGGCCGGGTTCCTGGTC 62.410 72.222 13.86 13.86 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 1.688884 GAAGGAGCTCCCAGCCTCT 60.689 63.158 29.54 5.79 43.77 3.69
60 61 1.153628 CTCCATCGTTCGTCCACCC 60.154 63.158 0.00 0.00 0.00 4.61
141 142 1.915078 ATTGAGCACGGGGGAGAAGG 61.915 60.000 0.00 0.00 0.00 3.46
168 169 3.394836 ACGCCTTCTCTGCCTCCC 61.395 66.667 0.00 0.00 0.00 4.30
207 208 4.421479 CTTCGTCTCGGGCAGCGT 62.421 66.667 0.00 0.00 0.00 5.07
211 212 4.742201 GCAGCTTCGTCTCGGGCA 62.742 66.667 0.00 0.00 0.00 5.36
337 338 1.514087 GCCGTAGTCGTTCCCATCA 59.486 57.895 0.00 0.00 35.01 3.07
338 339 1.588139 CGCCGTAGTCGTTCCCATC 60.588 63.158 0.00 0.00 35.01 3.51
350 351 4.246206 CTCATCGCCGTCGCCGTA 62.246 66.667 0.00 0.00 35.26 4.02
359 360 2.853705 ACTAGTCTACTCCTCATCGCC 58.146 52.381 0.00 0.00 0.00 5.54
360 361 4.142773 GCATACTAGTCTACTCCTCATCGC 60.143 50.000 0.00 0.00 0.00 4.58
368 369 5.838531 ACAGGTTGCATACTAGTCTACTC 57.161 43.478 0.00 0.00 0.00 2.59
447 2035 4.144297 ACCGAGCCCGTATATTTAGTACA 58.856 43.478 0.00 0.00 0.00 2.90
462 2050 1.606737 GCAGATCCTTCATACCGAGCC 60.607 57.143 0.00 0.00 0.00 4.70
494 2083 3.610677 CCGTATTTTGAATTTTGCGGGAC 59.389 43.478 0.00 0.00 34.97 4.46
515 2104 5.065602 GGTCGTCCCATAAAACTCATTTACC 59.934 44.000 0.00 0.00 36.35 2.85
521 2110 1.894466 TCGGTCGTCCCATAAAACTCA 59.106 47.619 0.00 0.00 0.00 3.41
530 2119 2.264480 CTGCAATCGGTCGTCCCA 59.736 61.111 0.00 0.00 0.00 4.37
533 2122 0.876342 GGATCCTGCAATCGGTCGTC 60.876 60.000 3.84 0.00 0.00 4.20
547 2136 6.942532 TGTATGAGCATTTTTAGTGGATCC 57.057 37.500 4.20 4.20 0.00 3.36
613 2202 0.528017 GAGATGATGATAGGCGCCGA 59.472 55.000 23.20 18.26 0.00 5.54
632 2221 5.576774 GTGCGGAAGATATTTTTCTTTTGGG 59.423 40.000 0.00 0.00 36.10 4.12
645 2234 1.813859 CGTCCAGGTGCGGAAGATA 59.186 57.895 0.00 0.00 36.74 1.98
827 2417 0.323360 CGGGGGATTTGAAAGCTCCA 60.323 55.000 14.72 0.00 39.92 3.86
966 2565 1.933307 AACCCTAGGCCCCAAATCGG 61.933 60.000 2.05 0.00 0.00 4.18
1107 2712 1.153369 CATGGCGTGGTACTGGGAG 60.153 63.158 0.00 0.00 0.00 4.30
1154 2759 2.033194 CGCAGAAGGAACCCGAACC 61.033 63.158 0.00 0.00 0.00 3.62
1345 2952 7.310609 CCCCTTTTATCCATTTTGATGACAAGT 60.311 37.037 0.00 0.00 37.32 3.16
1346 2953 7.043565 CCCCTTTTATCCATTTTGATGACAAG 58.956 38.462 0.00 0.00 37.32 3.16
1347 2954 6.728164 TCCCCTTTTATCCATTTTGATGACAA 59.272 34.615 0.00 0.00 0.00 3.18
1348 2955 6.259893 TCCCCTTTTATCCATTTTGATGACA 58.740 36.000 0.00 0.00 0.00 3.58
1349 2956 6.790232 TCCCCTTTTATCCATTTTGATGAC 57.210 37.500 0.00 0.00 0.00 3.06
1350 2957 6.902416 ACATCCCCTTTTATCCATTTTGATGA 59.098 34.615 0.00 0.00 32.39 2.92
1351 2958 7.128234 ACATCCCCTTTTATCCATTTTGATG 57.872 36.000 0.00 0.00 33.80 3.07
1352 2959 9.093458 GATACATCCCCTTTTATCCATTTTGAT 57.907 33.333 0.00 0.00 0.00 2.57
1353 2960 8.288812 AGATACATCCCCTTTTATCCATTTTGA 58.711 33.333 0.00 0.00 0.00 2.69
1354 2961 8.482852 AGATACATCCCCTTTTATCCATTTTG 57.517 34.615 0.00 0.00 0.00 2.44
1355 2962 9.813826 CTAGATACATCCCCTTTTATCCATTTT 57.186 33.333 0.00 0.00 0.00 1.82
1356 2963 9.182642 TCTAGATACATCCCCTTTTATCCATTT 57.817 33.333 0.00 0.00 0.00 2.32
1357 2964 8.606830 GTCTAGATACATCCCCTTTTATCCATT 58.393 37.037 0.00 0.00 0.00 3.16
1358 2965 7.093289 CGTCTAGATACATCCCCTTTTATCCAT 60.093 40.741 0.00 0.00 0.00 3.41
1359 2966 6.210784 CGTCTAGATACATCCCCTTTTATCCA 59.789 42.308 0.00 0.00 0.00 3.41
1360 2967 6.210984 ACGTCTAGATACATCCCCTTTTATCC 59.789 42.308 0.00 0.00 0.00 2.59
1361 2968 7.229581 ACGTCTAGATACATCCCCTTTTATC 57.770 40.000 0.00 0.00 0.00 1.75
1362 2969 8.896722 ATACGTCTAGATACATCCCCTTTTAT 57.103 34.615 0.00 0.00 0.00 1.40
1363 2970 8.716674 AATACGTCTAGATACATCCCCTTTTA 57.283 34.615 0.00 0.00 0.00 1.52
1364 2971 7.613551 AATACGTCTAGATACATCCCCTTTT 57.386 36.000 0.00 0.00 0.00 2.27
1365 2972 7.613551 AAATACGTCTAGATACATCCCCTTT 57.386 36.000 0.00 0.00 0.00 3.11
1366 2973 7.613551 AAAATACGTCTAGATACATCCCCTT 57.386 36.000 0.00 0.00 0.00 3.95
1367 2974 7.949006 ACTAAAATACGTCTAGATACATCCCCT 59.051 37.037 0.00 0.00 0.00 4.79
1368 2975 8.120140 ACTAAAATACGTCTAGATACATCCCC 57.880 38.462 0.00 0.00 0.00 4.81
1369 2976 9.623350 GAACTAAAATACGTCTAGATACATCCC 57.377 37.037 0.00 0.00 0.00 3.85
1370 2977 9.327529 CGAACTAAAATACGTCTAGATACATCC 57.672 37.037 0.00 0.00 0.00 3.51
1373 2980 9.317936 TCTCGAACTAAAATACGTCTAGATACA 57.682 33.333 0.00 0.00 0.00 2.29
1377 2984 9.317936 TGTATCTCGAACTAAAATACGTCTAGA 57.682 33.333 0.00 0.00 0.00 2.43
1380 2987 8.838365 AGATGTATCTCGAACTAAAATACGTCT 58.162 33.333 0.00 8.87 41.19 4.18
1381 2988 9.105206 GAGATGTATCTCGAACTAAAATACGTC 57.895 37.037 6.16 0.00 43.29 4.34
1405 3012 9.918630 ACTTGTCATCAAAATGGATAAAAAGAG 57.081 29.630 0.00 0.00 33.42 2.85
1413 3020 7.975616 CCGAAAATACTTGTCATCAAAATGGAT 59.024 33.333 0.00 0.00 33.42 3.41
1414 3021 7.312154 CCGAAAATACTTGTCATCAAAATGGA 58.688 34.615 0.00 0.00 33.42 3.41
1415 3022 6.531240 CCCGAAAATACTTGTCATCAAAATGG 59.469 38.462 0.00 0.00 33.42 3.16
1416 3023 6.034898 GCCCGAAAATACTTGTCATCAAAATG 59.965 38.462 0.00 0.00 32.87 2.32
1417 3024 6.099341 GCCCGAAAATACTTGTCATCAAAAT 58.901 36.000 0.00 0.00 32.87 1.82
1418 3025 5.465935 GCCCGAAAATACTTGTCATCAAAA 58.534 37.500 0.00 0.00 32.87 2.44
1419 3026 4.378978 CGCCCGAAAATACTTGTCATCAAA 60.379 41.667 0.00 0.00 32.87 2.69
1420 3027 3.126171 CGCCCGAAAATACTTGTCATCAA 59.874 43.478 0.00 0.00 0.00 2.57
1421 3028 2.675844 CGCCCGAAAATACTTGTCATCA 59.324 45.455 0.00 0.00 0.00 3.07
1422 3029 2.031683 CCGCCCGAAAATACTTGTCATC 59.968 50.000 0.00 0.00 0.00 2.92
1423 3030 2.014128 CCGCCCGAAAATACTTGTCAT 58.986 47.619 0.00 0.00 0.00 3.06
1424 3031 1.002201 TCCGCCCGAAAATACTTGTCA 59.998 47.619 0.00 0.00 0.00 3.58
1425 3032 1.664151 CTCCGCCCGAAAATACTTGTC 59.336 52.381 0.00 0.00 0.00 3.18
1426 3033 1.677820 CCTCCGCCCGAAAATACTTGT 60.678 52.381 0.00 0.00 0.00 3.16
1427 3034 1.014352 CCTCCGCCCGAAAATACTTG 58.986 55.000 0.00 0.00 0.00 3.16
1428 3035 0.107361 CCCTCCGCCCGAAAATACTT 60.107 55.000 0.00 0.00 0.00 2.24
1429 3036 0.979187 TCCCTCCGCCCGAAAATACT 60.979 55.000 0.00 0.00 0.00 2.12
1430 3037 0.532196 CTCCCTCCGCCCGAAAATAC 60.532 60.000 0.00 0.00 0.00 1.89
1431 3038 0.979187 ACTCCCTCCGCCCGAAAATA 60.979 55.000 0.00 0.00 0.00 1.40
1432 3039 0.979187 TACTCCCTCCGCCCGAAAAT 60.979 55.000 0.00 0.00 0.00 1.82
1433 3040 1.610086 TACTCCCTCCGCCCGAAAA 60.610 57.895 0.00 0.00 0.00 2.29
1434 3041 2.037687 TACTCCCTCCGCCCGAAA 59.962 61.111 0.00 0.00 0.00 3.46
1435 3042 1.925285 TAGTACTCCCTCCGCCCGAA 61.925 60.000 0.00 0.00 0.00 4.30
1436 3043 1.713005 ATAGTACTCCCTCCGCCCGA 61.713 60.000 0.00 0.00 0.00 5.14
1437 3044 0.037303 TATAGTACTCCCTCCGCCCG 59.963 60.000 0.00 0.00 0.00 6.13
1438 3045 2.496470 CAATATAGTACTCCCTCCGCCC 59.504 54.545 0.00 0.00 0.00 6.13
1439 3046 2.094130 GCAATATAGTACTCCCTCCGCC 60.094 54.545 0.00 0.00 0.00 6.13
1440 3047 2.826725 AGCAATATAGTACTCCCTCCGC 59.173 50.000 0.00 0.00 0.00 5.54
1441 3048 4.337145 AGAGCAATATAGTACTCCCTCCG 58.663 47.826 0.00 0.00 0.00 4.63
1442 3049 5.567823 GCAAGAGCAATATAGTACTCCCTCC 60.568 48.000 0.00 0.00 41.58 4.30
1443 3050 5.474825 GCAAGAGCAATATAGTACTCCCTC 58.525 45.833 0.00 0.00 41.58 4.30
1444 3051 4.021894 CGCAAGAGCAATATAGTACTCCCT 60.022 45.833 0.00 0.00 42.27 4.20
1445 3052 4.022242 TCGCAAGAGCAATATAGTACTCCC 60.022 45.833 0.00 0.00 45.01 4.30
1446 3053 5.122512 TCGCAAGAGCAATATAGTACTCC 57.877 43.478 0.00 0.00 45.01 3.85
1568 3175 9.161629 CTTGTGATTATACATTGTGGTGACTTA 57.838 33.333 0.00 0.00 0.00 2.24
1658 3265 7.817641 ACCAGTTTGCTTCTAGTAATTTAAGC 58.182 34.615 4.98 4.98 43.62 3.09
1726 3337 4.153986 CAAGTTCACATCATTTGCTCGAC 58.846 43.478 0.00 0.00 0.00 4.20
1904 3515 5.472478 ACCTGCAGTCTATTTATGATGCATG 59.528 40.000 13.81 0.00 42.24 4.06
2046 3659 2.096811 GCAAACATTTTGACATGCCACG 60.097 45.455 2.80 0.00 0.00 4.94
2153 4474 1.903183 GGCTTGTTCCAGTAGGAGAGT 59.097 52.381 0.00 0.00 46.74 3.24
2208 4645 4.501071 TCAAAGCTCCGACCAGTATAAAC 58.499 43.478 0.00 0.00 0.00 2.01
2211 4648 4.811969 TTTCAAAGCTCCGACCAGTATA 57.188 40.909 0.00 0.00 0.00 1.47
2212 4649 3.695830 TTTCAAAGCTCCGACCAGTAT 57.304 42.857 0.00 0.00 0.00 2.12
2220 4657 5.179045 AGCATCAATATTTCAAAGCTCCG 57.821 39.130 0.00 0.00 0.00 4.63
2263 4700 2.620115 CACTGCAGTGTGAAAGGACATT 59.380 45.455 34.04 0.00 40.96 2.71
2338 4775 4.457466 ACCTCACAGATTTTACCAACGTT 58.543 39.130 0.00 0.00 0.00 3.99
2951 6079 5.419788 TCCTCGAGTAACTAAACTTGCCATA 59.580 40.000 12.31 0.00 31.83 2.74
2987 6115 0.593128 AAGTCGCCATGCTTCACAAC 59.407 50.000 0.00 0.00 0.00 3.32
3002 6130 3.319122 ACTTGCCATCCAAACAGAAAGTC 59.681 43.478 0.00 0.00 31.94 3.01
3097 6234 1.086696 ATGATAAGTGCCACACGTGC 58.913 50.000 17.22 1.66 39.64 5.34
3182 6320 3.307242 CGGCTACAGAAGATAGCAAACAC 59.693 47.826 6.37 0.00 45.76 3.32
3738 8347 3.241067 TGAAATACCGTAAGAGCGCTT 57.759 42.857 13.26 8.09 43.02 4.68
3742 8351 8.068380 GGTCAAATATTGAAATACCGTAAGAGC 58.932 37.037 0.00 0.00 42.15 4.09
3877 8486 2.473816 CATGCGGTCATAGTGGTACTG 58.526 52.381 0.00 0.00 0.00 2.74
3908 8517 7.612633 TGATTTAACCTAGGGACCATTACAAAC 59.387 37.037 14.81 0.78 0.00 2.93
3922 8531 9.535170 TCTGATCTACCCTATGATTTAACCTAG 57.465 37.037 0.00 0.00 0.00 3.02
3949 8558 6.442244 ACCTTGCTCTTCCTTCTTAAGACTAT 59.558 38.462 4.18 0.00 0.00 2.12
3953 8562 6.042781 TGTTACCTTGCTCTTCCTTCTTAAGA 59.957 38.462 0.00 0.00 0.00 2.10
4263 8873 4.464008 AGGAAGATGCAAACAGAGTCAAA 58.536 39.130 0.00 0.00 0.00 2.69
4299 8909 7.944729 ATGAGTCACTGGTTTAGCAAATATT 57.055 32.000 0.00 0.00 0.00 1.28
4302 8912 6.655078 AAATGAGTCACTGGTTTAGCAAAT 57.345 33.333 0.00 0.00 0.00 2.32
4430 9048 6.545666 TCATCAGCTAAAAACAGGTCAAAAGA 59.454 34.615 0.00 0.00 0.00 2.52
4431 9049 6.738114 TCATCAGCTAAAAACAGGTCAAAAG 58.262 36.000 0.00 0.00 0.00 2.27
4432 9050 6.707440 TCATCAGCTAAAAACAGGTCAAAA 57.293 33.333 0.00 0.00 0.00 2.44
4433 9051 6.707440 TTCATCAGCTAAAAACAGGTCAAA 57.293 33.333 0.00 0.00 0.00 2.69
4434 9052 6.545666 TCTTTCATCAGCTAAAAACAGGTCAA 59.454 34.615 0.00 0.00 0.00 3.18
4435 9053 6.061441 TCTTTCATCAGCTAAAAACAGGTCA 58.939 36.000 0.00 0.00 0.00 4.02
4436 9054 6.560253 TCTTTCATCAGCTAAAAACAGGTC 57.440 37.500 0.00 0.00 0.00 3.85
4437 9055 6.547510 ACTTCTTTCATCAGCTAAAAACAGGT 59.452 34.615 0.00 0.00 0.00 4.00
4451 9069 3.594603 TCAGGGACGACTTCTTTCATC 57.405 47.619 0.00 0.00 0.00 2.92
4678 9296 1.551883 AGGGCATTTCAAACAGGCATC 59.448 47.619 1.17 0.00 0.00 3.91
4686 9304 2.176140 CCGCGTAGGGCATTTCAAA 58.824 52.632 4.92 0.00 43.84 2.69
4703 9321 3.562732 AAACACAGGGTAGGCCGCC 62.563 63.158 0.00 0.00 34.97 6.13
4708 9326 4.015872 ACACATACAAACACAGGGTAGG 57.984 45.455 0.00 0.00 0.00 3.18
4713 9331 4.894784 ACCTCTACACATACAAACACAGG 58.105 43.478 0.00 0.00 0.00 4.00
4720 9338 4.579454 GGCGATACCTCTACACATACAA 57.421 45.455 0.00 0.00 34.51 2.41
4731 9349 8.229028 TGGATACGTTAATCAGGCGATACCTC 62.229 46.154 0.00 0.00 45.91 3.85
4734 9352 4.801891 TGGATACGTTAATCAGGCGATAC 58.198 43.478 0.00 0.00 42.51 2.24
4735 9353 5.654603 ATGGATACGTTAATCAGGCGATA 57.345 39.130 0.00 0.00 42.51 2.92
4736 9354 4.537135 ATGGATACGTTAATCAGGCGAT 57.463 40.909 0.00 0.00 42.51 4.58
4738 9356 3.807622 ACAATGGATACGTTAATCAGGCG 59.192 43.478 0.00 0.00 46.43 5.52
4753 9371 4.348461 TGGTACACCTTGTTCTACAATGGA 59.652 41.667 12.06 0.00 37.48 3.41
4773 9391 4.301505 CACAAGCGGTGCTATGGT 57.698 55.556 0.00 0.00 41.36 3.55
4797 9415 3.385115 AGGAATCTCGTCCCAAGGTAAT 58.615 45.455 0.00 0.00 38.59 1.89
4835 9453 8.076714 TCTATTGAGCTTACATTTCTATTGCG 57.923 34.615 0.00 0.00 0.00 4.85
4920 9539 4.143389 GCATATTACCGTGAGCGTCATTAC 60.143 45.833 0.00 0.00 36.15 1.89
4926 9545 2.201732 CAAGCATATTACCGTGAGCGT 58.798 47.619 0.00 0.00 36.15 5.07
4947 9566 4.938226 ACCCTTTCTTTTTCTCTATCAGCG 59.062 41.667 0.00 0.00 0.00 5.18
5012 9631 9.273016 TGGAAGAAACTCACTTATTGTTAGAAG 57.727 33.333 0.00 0.00 0.00 2.85
5014 9633 8.429641 AGTGGAAGAAACTCACTTATTGTTAGA 58.570 33.333 0.00 0.00 38.44 2.10
5015 9634 8.608844 AGTGGAAGAAACTCACTTATTGTTAG 57.391 34.615 0.00 0.00 38.44 2.34
5017 9636 6.486993 GGAGTGGAAGAAACTCACTTATTGTT 59.513 38.462 5.97 0.00 44.86 2.83
5028 9792 7.290813 AGACTAAAAATGGAGTGGAAGAAACT 58.709 34.615 0.00 0.00 0.00 2.66
5052 9816 4.578105 GTGGAGGAATGATCTAAAGGCAAG 59.422 45.833 0.00 0.00 0.00 4.01
5084 9848 2.422235 CCTGCCATATCCCAACGGTTTA 60.422 50.000 0.00 0.00 0.00 2.01
5090 9854 4.327680 GTCTATTCCTGCCATATCCCAAC 58.672 47.826 0.00 0.00 0.00 3.77
5092 9856 2.567169 CGTCTATTCCTGCCATATCCCA 59.433 50.000 0.00 0.00 0.00 4.37
5096 9860 5.305644 AGTTTCTCGTCTATTCCTGCCATAT 59.694 40.000 0.00 0.00 0.00 1.78
5099 9863 2.832129 AGTTTCTCGTCTATTCCTGCCA 59.168 45.455 0.00 0.00 0.00 4.92
5106 9870 7.095270 ACAAACCGATAAGTTTCTCGTCTATT 58.905 34.615 6.74 0.00 37.87 1.73
5128 9892 4.828939 TCTACTTCTCCTGTCGGTAAACAA 59.171 41.667 0.00 0.00 0.00 2.83
5146 9936 7.065563 CAGAAATGCATAAACAGAAGCTCTACT 59.934 37.037 0.00 0.00 0.00 2.57
5148 9938 7.105588 TCAGAAATGCATAAACAGAAGCTCTA 58.894 34.615 0.00 0.00 0.00 2.43
5177 9967 0.601841 GGTGATCGTTTGTCCACCGT 60.602 55.000 0.00 0.00 39.52 4.83
5178 9968 2.159181 GGTGATCGTTTGTCCACCG 58.841 57.895 0.00 0.00 39.52 4.94
5179 9969 1.821216 ATGGTGATCGTTTGTCCACC 58.179 50.000 0.00 0.00 46.82 4.61
5180 9970 4.214545 TGTTTATGGTGATCGTTTGTCCAC 59.785 41.667 0.00 0.00 0.00 4.02
5181 9971 4.214545 GTGTTTATGGTGATCGTTTGTCCA 59.785 41.667 0.00 0.00 0.00 4.02
5183 9973 4.214545 TGGTGTTTATGGTGATCGTTTGTC 59.785 41.667 0.00 0.00 0.00 3.18
5185 9975 4.757799 TGGTGTTTATGGTGATCGTTTG 57.242 40.909 0.00 0.00 0.00 2.93
5186 9976 5.007034 TCATGGTGTTTATGGTGATCGTTT 58.993 37.500 0.00 0.00 0.00 3.60
5188 9978 4.191544 CTCATGGTGTTTATGGTGATCGT 58.808 43.478 0.00 0.00 0.00 3.73
5195 10007 5.102953 TCTCTTCCTCATGGTGTTTATGG 57.897 43.478 0.00 0.00 34.23 2.74
5198 10010 4.994852 CGTTTCTCTTCCTCATGGTGTTTA 59.005 41.667 0.00 0.00 34.23 2.01
5234 10047 2.811317 CAGACGCGTCTTGAGGGC 60.811 66.667 37.66 10.83 37.98 5.19
5360 10173 4.113815 TCGGCAAGCCCATGGGAG 62.114 66.667 36.00 22.82 37.50 4.30
5528 10341 2.555757 GTTGCCAAGAAGATGAGCAAGT 59.444 45.455 0.00 0.00 43.53 3.16
5633 10446 3.383185 TCTTGTTTTTCTCGCCCAATTGT 59.617 39.130 4.43 0.00 0.00 2.71
5636 10449 3.193479 GGATCTTGTTTTTCTCGCCCAAT 59.807 43.478 0.00 0.00 0.00 3.16
5639 10452 2.095212 GTGGATCTTGTTTTTCTCGCCC 60.095 50.000 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.