Multiple sequence alignment - TraesCS4D01G033700

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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 TraesCS4D01G033700 chr4D 100.000 3431 0 0 1 3431 15424007 15427437 0.000000e+00 6336.0
1 TraesCS4D01G033700 chr4D 85.714 84 12 0 2240 2323 460712741 460712658 4.720000e-14 89.8
2 TraesCS4D01G033700 chr4D 87.931 58 4 2 1271 1327 472879842 472879897 7.950000e-07 65.8
3 TraesCS4D01G033700 chr4A 89.379 885 61 19 1501 2373 585378392 585377529 0.000000e+00 1083.0
4 TraesCS4D01G033700 chr4A 81.904 1061 92 42 428 1441 585379502 585378495 0.000000e+00 804.0
5 TraesCS4D01G033700 chr4A 84.867 489 23 13 2372 2823 585377445 585376971 2.430000e-121 446.0
6 TraesCS4D01G033700 chr4A 85.484 372 48 6 2942 3311 585376930 585376563 1.930000e-102 383.0
7 TraesCS4D01G033700 chr4A 88.136 236 8 7 95 311 585379867 585379633 2.630000e-66 263.0
8 TraesCS4D01G033700 chr4A 100.000 42 0 0 1286 1327 285485455 285485414 1.020000e-10 78.7
9 TraesCS4D01G033700 chr4B 84.081 892 92 15 1337 2187 25928548 25929430 0.000000e+00 815.0
10 TraesCS4D01G033700 chr4B 87.122 629 30 19 2236 2849 25929516 25930108 0.000000e+00 665.0
11 TraesCS4D01G033700 chr4B 83.934 610 30 32 22 582 25927183 25927773 3.920000e-144 521.0
12 TraesCS4D01G033700 chr4B 78.323 775 67 45 609 1293 25927769 25928532 1.150000e-109 407.0
13 TraesCS4D01G033700 chr4B 79.044 272 38 15 3111 3378 25930590 25930846 5.890000e-38 169.0
14 TraesCS4D01G033700 chr4B 88.000 75 9 0 2240 2314 575527427 575527501 4.720000e-14 89.8
15 TraesCS4D01G033700 chr5D 100.000 41 0 0 1288 1328 174620027 174620067 3.670000e-10 76.8
16 TraesCS4D01G033700 chr6D 92.593 54 1 2 1277 1327 49869815 49869762 1.320000e-09 75.0
17 TraesCS4D01G033700 chr6D 97.561 41 1 0 1287 1327 340947314 340947274 1.710000e-08 71.3
18 TraesCS4D01G033700 chr7A 93.750 48 3 0 1280 1327 686371305 686371352 4.750000e-09 73.1
19 TraesCS4D01G033700 chr6A 92.453 53 1 2 1277 1326 65062009 65062061 4.750000e-09 73.1
20 TraesCS4D01G033700 chr2D 92.308 52 3 1 1276 1327 527530063 527530013 4.750000e-09 73.1
21 TraesCS4D01G033700 chr3B 92.157 51 3 1 1276 1325 372246396 372246346 1.710000e-08 71.3


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 TraesCS4D01G033700 chr4D 15424007 15427437 3430 False 6336.0 6336 100.0000 1 3431 1 chr4D.!!$F1 3430
1 TraesCS4D01G033700 chr4A 585376563 585379867 3304 True 595.8 1083 85.9540 95 3311 5 chr4A.!!$R2 3216
2 TraesCS4D01G033700 chr4B 25927183 25930846 3663 False 515.4 815 82.5008 22 3378 5 chr4B.!!$F2 3356

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
992 1148 0.322322 CCCCGTGCTACCAAACAGTA 59.678 55.0 0.0 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2548 2972 0.03563 ACAGCAGCAGACCCTGAATC 60.036 55.0 0.0 0.0 34.77 2.52 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
42 43 1.070445 CGCCCCTGTCATCCATCTC 59.930 63.158 0.00 0.00 0.00 2.75
43 44 1.689243 CGCCCCTGTCATCCATCTCA 61.689 60.000 0.00 0.00 0.00 3.27
44 45 0.769873 GCCCCTGTCATCCATCTCAT 59.230 55.000 0.00 0.00 0.00 2.90
45 46 1.271271 GCCCCTGTCATCCATCTCATC 60.271 57.143 0.00 0.00 0.00 2.92
46 47 2.336891 CCCCTGTCATCCATCTCATCT 58.663 52.381 0.00 0.00 0.00 2.90
201 213 1.140804 GCCTCTCGTCTGCTTCCTC 59.859 63.158 0.00 0.00 0.00 3.71
312 339 1.065998 CCGGTGTTTCTATTTCGGGGA 60.066 52.381 0.00 0.00 34.54 4.81
335 394 1.496403 GGCCGCGGATAAGTTAGCAC 61.496 60.000 33.48 5.78 0.00 4.40
487 561 1.795286 CGCAGATTAGGGCTCGAATTC 59.205 52.381 0.00 0.00 0.00 2.17
565 645 1.442148 CGGAGGAATTCCCGTCTCC 59.558 63.158 21.22 18.78 43.63 3.71
657 737 4.689071 TCGTTTCTTTACTGTTCTGCTGA 58.311 39.130 0.00 0.00 0.00 4.26
666 746 1.869767 CTGTTCTGCTGAGTGTTCCAC 59.130 52.381 0.00 0.00 34.10 4.02
698 778 0.923911 GTTCGTGCGTGTCAAACTGC 60.924 55.000 0.00 0.00 0.00 4.40
757 855 5.182570 GCCGTAATAAACCTGGAGAAAAGTT 59.817 40.000 0.00 0.00 0.00 2.66
763 861 3.382083 ACCTGGAGAAAAGTTGTTGGT 57.618 42.857 0.00 0.00 0.00 3.67
787 889 0.535335 TCGATCCCGTCTTTCTTGGG 59.465 55.000 0.00 0.00 44.75 4.12
818 920 0.738975 TCTGATCCCGTTCACTAGCG 59.261 55.000 0.00 0.00 0.00 4.26
839 941 3.684788 CGGTAGTAATTGCTTGCTTCAGT 59.315 43.478 0.00 0.00 0.00 3.41
840 942 4.154195 CGGTAGTAATTGCTTGCTTCAGTT 59.846 41.667 0.00 0.00 0.00 3.16
841 943 5.334879 CGGTAGTAATTGCTTGCTTCAGTTT 60.335 40.000 0.00 0.00 0.00 2.66
842 944 6.086871 GGTAGTAATTGCTTGCTTCAGTTTC 58.913 40.000 0.00 0.00 0.00 2.78
843 945 6.072452 GGTAGTAATTGCTTGCTTCAGTTTCT 60.072 38.462 0.00 0.00 0.00 2.52
861 963 1.822990 TCTGGTACAACTCCACCGATC 59.177 52.381 0.00 0.00 38.70 3.69
870 972 3.992260 ACTCCACCGATCTCTTAATCG 57.008 47.619 0.00 0.00 46.28 3.34
882 984 4.860072 TCTCTTAATCGTCATGATCCGTG 58.140 43.478 0.00 0.00 35.84 4.94
891 1019 3.589988 GTCATGATCCGTGTGTTCTTCT 58.410 45.455 0.00 0.00 0.00 2.85
892 1020 4.674362 CGTCATGATCCGTGTGTTCTTCTA 60.674 45.833 0.00 0.00 0.00 2.10
895 1023 3.585862 TGATCCGTGTGTTCTTCTAAGC 58.414 45.455 0.00 0.00 0.00 3.09
918 1047 3.649986 GCGCGTGGCAAGTTGAGT 61.650 61.111 8.43 0.00 42.87 3.41
946 1078 6.494893 TGAATATGCTCTGTGTTTGTAACC 57.505 37.500 0.00 0.00 0.00 2.85
982 1114 4.015406 CCTGTGTGCCCCGTGCTA 62.015 66.667 0.00 0.00 42.00 3.49
983 1115 2.742372 CTGTGTGCCCCGTGCTAC 60.742 66.667 0.00 0.00 42.00 3.58
992 1148 0.322322 CCCCGTGCTACCAAACAGTA 59.678 55.000 0.00 0.00 0.00 2.74
1017 1178 1.072806 GCTATGAGTGGCATGGGATCA 59.927 52.381 0.00 0.00 37.87 2.92
1171 1332 4.681978 GCCTGTCGAGCAACCCGT 62.682 66.667 0.00 0.00 0.00 5.28
1208 1384 0.977395 CAGGGGAAGAAGAAGACGGT 59.023 55.000 0.00 0.00 0.00 4.83
1209 1385 0.977395 AGGGGAAGAAGAAGACGGTG 59.023 55.000 0.00 0.00 0.00 4.94
1266 1442 2.123077 CCGAGATCAGGGGAGCCT 60.123 66.667 0.00 0.00 0.00 4.58
1293 1469 5.228665 GGTTTGTTGACCTGTCTACTACTC 58.771 45.833 11.95 2.88 36.53 2.59
1294 1470 5.228665 GTTTGTTGACCTGTCTACTACTCC 58.771 45.833 11.95 0.00 36.53 3.85
1296 1472 3.075582 TGTTGACCTGTCTACTACTCCCT 59.924 47.826 11.95 0.00 36.53 4.20
1298 1474 2.241685 TGACCTGTCTACTACTCCCTCC 59.758 54.545 0.00 0.00 0.00 4.30
1300 1476 1.212441 CCTGTCTACTACTCCCTCCGT 59.788 57.143 0.00 0.00 0.00 4.69
1301 1477 2.437281 CCTGTCTACTACTCCCTCCGTA 59.563 54.545 0.00 0.00 0.00 4.02
1303 1479 4.521146 CTGTCTACTACTCCCTCCGTAAA 58.479 47.826 0.00 0.00 0.00 2.01
1304 1480 4.521146 TGTCTACTACTCCCTCCGTAAAG 58.479 47.826 0.00 0.00 0.00 1.85
1305 1481 4.225942 TGTCTACTACTCCCTCCGTAAAGA 59.774 45.833 0.00 0.00 0.00 2.52
1306 1482 5.189180 GTCTACTACTCCCTCCGTAAAGAA 58.811 45.833 0.00 0.00 0.00 2.52
1308 1484 6.320926 GTCTACTACTCCCTCCGTAAAGAAAT 59.679 42.308 0.00 0.00 0.00 2.17
1309 1485 7.500559 GTCTACTACTCCCTCCGTAAAGAAATA 59.499 40.741 0.00 0.00 0.00 1.40
1311 1487 9.512588 CTACTACTCCCTCCGTAAAGAAATATA 57.487 37.037 0.00 0.00 0.00 0.86
1312 1488 8.773033 ACTACTCCCTCCGTAAAGAAATATAA 57.227 34.615 0.00 0.00 0.00 0.98
1313 1489 8.858094 ACTACTCCCTCCGTAAAGAAATATAAG 58.142 37.037 0.00 0.00 0.00 1.73
1314 1490 7.909485 ACTCCCTCCGTAAAGAAATATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
1315 1491 7.953752 ACTCCCTCCGTAAAGAAATATAAGAG 58.046 38.462 0.00 0.00 0.00 2.85
1316 1492 6.756221 TCCCTCCGTAAAGAAATATAAGAGC 58.244 40.000 0.00 0.00 0.00 4.09
1317 1493 6.325545 TCCCTCCGTAAAGAAATATAAGAGCA 59.674 38.462 0.00 0.00 0.00 4.26
1318 1494 7.016268 TCCCTCCGTAAAGAAATATAAGAGCAT 59.984 37.037 0.00 0.00 0.00 3.79
1319 1495 7.661847 CCCTCCGTAAAGAAATATAAGAGCATT 59.338 37.037 0.00 0.00 0.00 3.56
1331 1507 9.524496 AAATATAAGAGCATTTAGATCATGGCA 57.476 29.630 0.00 0.00 34.30 4.92
1332 1508 8.734218 ATATAAGAGCATTTAGATCATGGCAG 57.266 34.615 0.00 0.00 34.30 4.85
1333 1509 3.147629 AGAGCATTTAGATCATGGCAGC 58.852 45.455 0.00 0.00 34.30 5.25
1334 1510 2.882761 GAGCATTTAGATCATGGCAGCA 59.117 45.455 0.00 0.00 31.47 4.41
1335 1511 2.621998 AGCATTTAGATCATGGCAGCAC 59.378 45.455 0.00 0.00 0.00 4.40
1338 1514 4.607955 CATTTAGATCATGGCAGCACTTG 58.392 43.478 0.00 0.00 0.00 3.16
1343 1519 3.130516 AGATCATGGCAGCACTTGATTTG 59.869 43.478 2.35 0.00 35.96 2.32
1367 1543 5.297029 GCTCCTGTCCTATGTATTGTTTTCC 59.703 44.000 0.00 0.00 0.00 3.13
1399 1575 7.939039 ACAAAATCTTGGATCTTGTGAGTAGAA 59.061 33.333 0.00 0.00 36.82 2.10
1450 1626 8.762645 ACTCATGTCCTATCTTGATCTTGTAAA 58.237 33.333 0.00 0.00 0.00 2.01
1497 1767 7.838884 ACAAGTATGTAAACTAGAAGGGAGAC 58.161 38.462 0.00 0.00 38.24 3.36
1498 1768 7.453752 ACAAGTATGTAAACTAGAAGGGAGACA 59.546 37.037 0.00 0.00 38.24 3.41
1535 1805 8.893727 AGTAATTTATGCACCTGAATAACTGTC 58.106 33.333 0.00 0.00 0.00 3.51
1538 1808 7.701539 TTTATGCACCTGAATAACTGTCATT 57.298 32.000 0.00 0.00 0.00 2.57
1589 1861 8.863872 ATTTACATACCTGATATTTGCTACCC 57.136 34.615 0.00 0.00 0.00 3.69
1623 1898 1.538047 TGCCAGATGGAAGCTTTGAC 58.462 50.000 0.00 0.00 37.39 3.18
1638 1913 1.502231 TTGACGAAGAGAAGCAGCAC 58.498 50.000 0.00 0.00 0.00 4.40
1648 1923 3.848301 AAGCAGCACGCCACATCCA 62.848 57.895 0.00 0.00 44.04 3.41
1679 1954 3.621268 GCATTGGCGTCAGACTATTTACA 59.379 43.478 0.00 0.00 0.00 2.41
1738 2013 3.053077 TGAACTCTTTCCCTTCCTGGAA 58.947 45.455 9.14 9.14 42.62 3.53
1742 2018 3.463704 ACTCTTTCCCTTCCTGGAAACTT 59.536 43.478 10.86 0.00 46.76 2.66
1743 2019 4.075682 CTCTTTCCCTTCCTGGAAACTTC 58.924 47.826 10.86 0.00 46.76 3.01
1750 2026 3.883489 CCTTCCTGGAAACTTCGTTTTCT 59.117 43.478 10.86 0.00 35.77 2.52
1754 2030 5.430007 TCCTGGAAACTTCGTTTTCTGTTA 58.570 37.500 0.00 0.00 35.77 2.41
1755 2031 5.295045 TCCTGGAAACTTCGTTTTCTGTTAC 59.705 40.000 0.00 0.00 35.77 2.50
1758 2034 4.968181 GGAAACTTCGTTTTCTGTTACTGC 59.032 41.667 6.80 0.00 35.77 4.40
1770 2048 6.573664 TTCTGTTACTGCTTGCAACATATT 57.426 33.333 0.00 0.00 32.13 1.28
1796 2074 2.042259 TCTGGCAGCCGCAATTCTG 61.042 57.895 10.34 0.00 41.24 3.02
1863 2141 1.066918 GTACCCGTACCCTGATGCG 59.933 63.158 0.00 0.00 0.00 4.73
1881 2159 1.674817 GCGTACTACACAGGCATGGTT 60.675 52.381 2.31 0.00 0.00 3.67
1929 2212 8.421002 GTGGTATATTTCCATGCCAATTTAAGT 58.579 33.333 3.27 0.00 41.59 2.24
1930 2213 9.647918 TGGTATATTTCCATGCCAATTTAAGTA 57.352 29.630 0.00 0.00 37.69 2.24
1948 2236 4.985538 AGTAGTACCAGAAACCATCTCG 57.014 45.455 0.00 0.00 35.73 4.04
1973 2261 1.136305 CCTGAATTGGCTGCATTCCTG 59.864 52.381 0.50 0.00 30.64 3.86
1996 2284 0.746204 TGTCTGCGTTTCTTGTGGCA 60.746 50.000 0.00 0.00 0.00 4.92
2000 2288 1.008538 GCGTTTCTTGTGGCACTGG 60.009 57.895 19.83 11.27 0.00 4.00
2057 2345 4.172512 ATGCCGCTGCCTCTGGAG 62.173 66.667 0.00 0.00 36.33 3.86
2192 2480 1.431440 CGAAGCAGTCTCCCTCTCG 59.569 63.158 0.00 0.00 0.00 4.04
2194 2482 0.892063 GAAGCAGTCTCCCTCTCGTT 59.108 55.000 0.00 0.00 0.00 3.85
2201 2492 2.577105 AGTCTCCCTCTCGTTCTTCCTA 59.423 50.000 0.00 0.00 0.00 2.94
2330 2655 2.035961 TCAACACCAAGAAGGACGAGAG 59.964 50.000 0.00 0.00 41.22 3.20
2332 2657 0.734253 CACCAAGAAGGACGAGAGCG 60.734 60.000 0.00 0.00 41.22 5.03
2333 2658 1.153745 CCAAGAAGGACGAGAGCGG 60.154 63.158 0.00 0.00 43.17 5.52
2521 2945 4.065281 GGTGGGTCTCCGTCCGTG 62.065 72.222 0.00 0.00 35.24 4.94
2531 2955 2.125673 CGTCCGTGATGGTGTCCC 60.126 66.667 0.00 0.00 39.52 4.46
2611 3035 0.390340 TCGCATTCTGTCACCTCTGC 60.390 55.000 0.00 0.00 0.00 4.26
2613 3037 1.367659 GCATTCTGTCACCTCTGCTC 58.632 55.000 0.00 0.00 0.00 4.26
2621 3061 2.139118 GTCACCTCTGCTCTGTTGTTC 58.861 52.381 0.00 0.00 0.00 3.18
2628 3068 3.461061 TCTGCTCTGTTGTTCTGTGAAG 58.539 45.455 0.00 0.00 0.00 3.02
2630 3070 2.938451 TGCTCTGTTGTTCTGTGAAGTG 59.062 45.455 0.00 0.00 0.00 3.16
2634 3074 4.832248 TCTGTTGTTCTGTGAAGTGAACT 58.168 39.130 0.00 0.00 41.99 3.01
2635 3075 5.972935 TCTGTTGTTCTGTGAAGTGAACTA 58.027 37.500 0.00 0.00 41.99 2.24
2636 3076 6.042777 TCTGTTGTTCTGTGAAGTGAACTAG 58.957 40.000 0.00 0.00 41.99 2.57
2735 3200 0.613012 AGAGTGGGATTTGGCTTGCC 60.613 55.000 4.43 4.43 0.00 4.52
2739 3204 1.072173 GTGGGATTTGGCTTGCCTTTT 59.928 47.619 13.18 0.00 0.00 2.27
2740 3205 1.072015 TGGGATTTGGCTTGCCTTTTG 59.928 47.619 13.18 0.00 0.00 2.44
2743 3208 3.069289 GGATTTGGCTTGCCTTTTGAAG 58.931 45.455 13.18 0.00 0.00 3.02
2765 3237 9.005777 TGAAGATTGGGTAGTGTAACAAATTAC 57.994 33.333 0.00 0.00 41.43 1.89
2799 3272 1.067565 TGAACCTCGATGTGCAGAGAC 60.068 52.381 0.00 0.00 36.65 3.36
2823 3296 2.191128 ACTGGTGTCAGCATTCTTCC 57.809 50.000 4.95 0.00 44.59 3.46
2824 3297 1.081892 CTGGTGTCAGCATTCTTCCG 58.918 55.000 4.95 0.00 33.86 4.30
2825 3298 0.396435 TGGTGTCAGCATTCTTCCGT 59.604 50.000 0.00 0.00 0.00 4.69
2832 3305 2.560981 TCAGCATTCTTCCGTAGTGTCA 59.439 45.455 0.00 0.00 0.00 3.58
2849 3322 0.598419 TCAGTGTGCTTCTCGTGCAG 60.598 55.000 0.00 0.00 41.41 4.41
2851 3324 1.856012 GTGTGCTTCTCGTGCAGAC 59.144 57.895 0.00 0.00 44.92 3.51
2852 3325 0.598680 GTGTGCTTCTCGTGCAGACT 60.599 55.000 8.42 0.00 46.68 3.24
2853 3326 0.104855 TGTGCTTCTCGTGCAGACTT 59.895 50.000 0.00 0.00 41.41 3.01
2854 3327 1.221414 GTGCTTCTCGTGCAGACTTT 58.779 50.000 0.00 0.00 41.41 2.66
2855 3328 1.599542 GTGCTTCTCGTGCAGACTTTT 59.400 47.619 0.00 0.00 41.41 2.27
2856 3329 2.032178 GTGCTTCTCGTGCAGACTTTTT 59.968 45.455 0.00 0.00 41.41 1.94
2857 3330 2.287915 TGCTTCTCGTGCAGACTTTTTC 59.712 45.455 0.00 0.00 35.31 2.29
2858 3331 2.545946 GCTTCTCGTGCAGACTTTTTCT 59.454 45.455 0.00 0.00 33.33 2.52
2859 3332 3.741344 GCTTCTCGTGCAGACTTTTTCTA 59.259 43.478 0.00 0.00 31.12 2.10
2861 3334 5.277345 GCTTCTCGTGCAGACTTTTTCTAAA 60.277 40.000 0.00 0.00 31.12 1.85
2862 3335 5.652744 TCTCGTGCAGACTTTTTCTAAAC 57.347 39.130 0.00 0.00 31.12 2.01
2863 3336 5.357257 TCTCGTGCAGACTTTTTCTAAACT 58.643 37.500 0.00 0.00 31.12 2.66
2864 3337 5.462398 TCTCGTGCAGACTTTTTCTAAACTC 59.538 40.000 0.00 0.00 31.12 3.01
2866 3339 4.272504 CGTGCAGACTTTTTCTAAACTCCA 59.727 41.667 0.00 0.00 31.12 3.86
2867 3340 5.220777 CGTGCAGACTTTTTCTAAACTCCAA 60.221 40.000 0.00 0.00 31.12 3.53
2868 3341 5.971792 GTGCAGACTTTTTCTAAACTCCAAC 59.028 40.000 0.00 0.00 31.12 3.77
2871 3344 7.147915 TGCAGACTTTTTCTAAACTCCAACAAT 60.148 33.333 0.00 0.00 31.12 2.71
2872 3345 7.168135 GCAGACTTTTTCTAAACTCCAACAATG 59.832 37.037 0.00 0.00 31.12 2.82
2873 3346 7.168135 CAGACTTTTTCTAAACTCCAACAATGC 59.832 37.037 0.00 0.00 31.12 3.56
2874 3347 6.872920 ACTTTTTCTAAACTCCAACAATGCA 58.127 32.000 0.00 0.00 0.00 3.96
2875 3348 7.327214 ACTTTTTCTAAACTCCAACAATGCAA 58.673 30.769 0.00 0.00 0.00 4.08
2876 3349 7.821846 ACTTTTTCTAAACTCCAACAATGCAAA 59.178 29.630 0.00 0.00 0.00 3.68
2877 3350 8.729805 TTTTTCTAAACTCCAACAATGCAAAT 57.270 26.923 0.00 0.00 0.00 2.32
2880 3353 6.680810 TCTAAACTCCAACAATGCAAATGAG 58.319 36.000 9.59 4.16 0.00 2.90
2881 3354 3.308438 ACTCCAACAATGCAAATGAGC 57.692 42.857 9.59 0.00 0.00 4.26
2888 3361 3.999701 TGCAAATGAGCATCGCCA 58.000 50.000 0.00 0.00 40.11 5.69
2889 3362 1.507630 TGCAAATGAGCATCGCCAC 59.492 52.632 0.00 0.00 40.11 5.01
2890 3363 1.226773 GCAAATGAGCATCGCCACC 60.227 57.895 0.00 0.00 38.61 4.61
2891 3364 1.434696 CAAATGAGCATCGCCACCC 59.565 57.895 0.00 0.00 38.61 4.61
2892 3365 1.001020 AAATGAGCATCGCCACCCA 60.001 52.632 0.00 0.00 38.61 4.51
2893 3366 1.033746 AAATGAGCATCGCCACCCAG 61.034 55.000 0.00 0.00 38.61 4.45
2894 3367 1.913951 AATGAGCATCGCCACCCAGA 61.914 55.000 0.00 0.00 38.61 3.86
2896 3369 3.315142 GAGCATCGCCACCCAGACA 62.315 63.158 0.00 0.00 0.00 3.41
2897 3370 2.359850 GCATCGCCACCCAGACAA 60.360 61.111 0.00 0.00 0.00 3.18
2898 3371 1.971167 GCATCGCCACCCAGACAAA 60.971 57.895 0.00 0.00 0.00 2.83
2899 3372 1.315257 GCATCGCCACCCAGACAAAT 61.315 55.000 0.00 0.00 0.00 2.32
2900 3373 1.176527 CATCGCCACCCAGACAAATT 58.823 50.000 0.00 0.00 0.00 1.82
2901 3374 1.133025 CATCGCCACCCAGACAAATTC 59.867 52.381 0.00 0.00 0.00 2.17
2902 3375 0.109532 TCGCCACCCAGACAAATTCA 59.890 50.000 0.00 0.00 0.00 2.57
2903 3376 1.176527 CGCCACCCAGACAAATTCAT 58.823 50.000 0.00 0.00 0.00 2.57
2904 3377 1.135315 CGCCACCCAGACAAATTCATG 60.135 52.381 0.00 0.00 0.00 3.07
2905 3378 2.170166 GCCACCCAGACAAATTCATGA 58.830 47.619 0.00 0.00 0.00 3.07
2907 3380 3.181483 GCCACCCAGACAAATTCATGATC 60.181 47.826 0.00 0.00 0.00 2.92
2909 3382 4.708421 CCACCCAGACAAATTCATGATCTT 59.292 41.667 0.00 0.00 0.00 2.40
2910 3383 5.186409 CCACCCAGACAAATTCATGATCTTT 59.814 40.000 0.00 0.00 0.00 2.52
2911 3384 6.327934 CACCCAGACAAATTCATGATCTTTC 58.672 40.000 0.00 0.00 0.00 2.62
2912 3385 6.152323 CACCCAGACAAATTCATGATCTTTCT 59.848 38.462 0.00 0.00 0.00 2.52
2913 3386 7.337689 CACCCAGACAAATTCATGATCTTTCTA 59.662 37.037 0.00 0.00 0.00 2.10
2914 3387 7.890127 ACCCAGACAAATTCATGATCTTTCTAA 59.110 33.333 0.00 0.00 0.00 2.10
2979 3704 1.200020 CGAAATCTTGGACCTTGTGCC 59.800 52.381 0.00 0.00 0.00 5.01
2999 3724 5.815740 GTGCCAAGAAGATATTTCCGTCTAA 59.184 40.000 0.00 0.00 0.00 2.10
3013 3738 3.069016 TCCGTCTAAGTGCTCAAACTCAA 59.931 43.478 0.00 0.00 0.00 3.02
3018 3743 3.951979 AAGTGCTCAAACTCAAACTCG 57.048 42.857 0.00 0.00 0.00 4.18
3053 3778 6.891624 TGATTCTTCACTGAAATCTTCGTTG 58.108 36.000 5.46 0.00 0.00 4.10
3054 3779 4.732285 TCTTCACTGAAATCTTCGTTGC 57.268 40.909 0.00 0.00 0.00 4.17
3071 3796 1.975660 TGCTGTACCTCACAAAACCC 58.024 50.000 0.00 0.00 36.48 4.11
3083 3808 3.561017 AAAACCCTGGGCCCATGGG 62.561 63.158 38.26 38.26 46.07 4.00
3116 3841 4.077184 CCCTCGCCGTGGCACTTA 62.077 66.667 16.72 0.00 42.06 2.24
3117 3842 2.047655 CCTCGCCGTGGCACTTAA 60.048 61.111 16.72 0.00 42.06 1.85
3121 3846 2.311701 CGCCGTGGCACTTAAACGA 61.312 57.895 16.72 0.00 42.06 3.85
3162 3887 4.654724 GCTTATAGGAGTCACTAAGGGGTT 59.345 45.833 0.00 0.00 0.00 4.11
3209 3936 3.938637 TTCGGCGGGCTGAGAGAGA 62.939 63.158 7.21 0.00 32.36 3.10
3210 3937 3.898509 CGGCGGGCTGAGAGAGAG 61.899 72.222 0.00 0.00 0.00 3.20
3212 3939 2.355193 GGCGGGCTGAGAGAGAGTT 61.355 63.158 0.00 0.00 0.00 3.01
3213 3940 1.594310 GCGGGCTGAGAGAGAGTTT 59.406 57.895 0.00 0.00 0.00 2.66
3214 3941 0.818296 GCGGGCTGAGAGAGAGTTTA 59.182 55.000 0.00 0.00 0.00 2.01
3215 3942 1.204941 GCGGGCTGAGAGAGAGTTTAA 59.795 52.381 0.00 0.00 0.00 1.52
3218 3945 2.499693 GGGCTGAGAGAGAGTTTAAGCT 59.500 50.000 0.00 0.00 0.00 3.74
3221 3948 4.562552 GGCTGAGAGAGAGTTTAAGCTGTT 60.563 45.833 0.00 0.00 0.00 3.16
3231 3958 2.614983 GTTTAAGCTGTTCGTCCAACCA 59.385 45.455 0.00 0.00 33.51 3.67
3234 3961 0.670546 AGCTGTTCGTCCAACCATCG 60.671 55.000 0.00 0.00 33.51 3.84
3235 3962 1.787847 CTGTTCGTCCAACCATCGC 59.212 57.895 0.00 0.00 33.51 4.58
3240 3967 2.800736 GTCCAACCATCGCCATGC 59.199 61.111 0.00 0.00 0.00 4.06
3253 3980 3.792047 CATGCGTCACGTGCTGGG 61.792 66.667 11.67 0.48 0.00 4.45
3268 3995 0.394192 CTGGGCGCTCCATCAAGATA 59.606 55.000 16.50 0.00 46.01 1.98
3311 4038 4.279671 TCTGCATGTGTTTTCGGGTTTTAT 59.720 37.500 0.00 0.00 0.00 1.40
3314 4041 6.692486 TGCATGTGTTTTCGGGTTTTATATT 58.308 32.000 0.00 0.00 0.00 1.28
3316 4043 7.657761 TGCATGTGTTTTCGGGTTTTATATTTT 59.342 29.630 0.00 0.00 0.00 1.82
3351 4078 2.766970 TCTCGGCTTTTCGGTTTTTG 57.233 45.000 0.00 0.00 0.00 2.44
3353 4080 0.249114 TCGGCTTTTCGGTTTTTGCC 60.249 50.000 0.00 0.00 37.24 4.52
3355 4082 0.179070 GGCTTTTCGGTTTTTGCCCA 60.179 50.000 0.00 0.00 34.81 5.36
3360 4087 2.588027 TTCGGTTTTTGCCCAGTTTC 57.412 45.000 0.00 0.00 0.00 2.78
3367 4094 0.407918 TTTGCCCAGTTTCCCTAGGG 59.592 55.000 23.22 23.22 44.37 3.53
3378 4105 2.444033 TCCCTAGGGTTTGGAGGAAA 57.556 50.000 27.58 0.49 36.47 3.13
3379 4106 2.720896 TCCCTAGGGTTTGGAGGAAAA 58.279 47.619 27.58 0.00 36.47 2.29
3380 4107 3.065175 TCCCTAGGGTTTGGAGGAAAAA 58.935 45.455 27.58 0.00 36.47 1.94
3411 4138 8.700722 GGAAAAACCTTTTTGCATGAATTTTT 57.299 26.923 9.21 0.00 44.59 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 1.378882 CCAATCCGTGGCCACAGATG 61.379 60.000 30.70 23.23 41.72 2.90
43 44 1.077501 CCAATCCGTGGCCACAGAT 60.078 57.895 34.16 29.97 41.72 2.90
44 45 2.350895 CCAATCCGTGGCCACAGA 59.649 61.111 34.16 29.10 41.72 3.41
201 213 6.206829 AGACGAGAATAAAAAGGAAACAAGGG 59.793 38.462 0.00 0.00 0.00 3.95
335 394 2.996621 GGAATTCATCGGATAAGCCTCG 59.003 50.000 7.93 0.00 0.00 4.63
372 432 2.266055 GCTCTTCACTCCCCCACG 59.734 66.667 0.00 0.00 0.00 4.94
373 433 2.266055 CGCTCTTCACTCCCCCAC 59.734 66.667 0.00 0.00 0.00 4.61
438 512 0.387239 GCAACAGCAACCGTGATTCC 60.387 55.000 0.00 0.00 0.00 3.01
441 515 2.616330 CGGCAACAGCAACCGTGAT 61.616 57.895 0.00 0.00 42.01 3.06
565 645 2.391389 GCAACCGAGCCGAGGAAAG 61.391 63.158 0.00 0.00 0.00 2.62
640 720 4.672587 ACACTCAGCAGAACAGTAAAGA 57.327 40.909 0.00 0.00 0.00 2.52
641 721 4.212214 GGAACACTCAGCAGAACAGTAAAG 59.788 45.833 0.00 0.00 0.00 1.85
666 746 3.120546 ACGCACGAACTTGAATCAATCAG 60.121 43.478 0.00 0.00 39.77 2.90
698 778 5.882000 TGTCTGTCAGATTACAATCCATTGG 59.118 40.000 5.68 0.00 41.96 3.16
757 855 0.604243 CGGGATCGAACCAACCAACA 60.604 55.000 14.28 0.00 39.00 3.33
763 861 1.621814 AGAAAGACGGGATCGAACCAA 59.378 47.619 14.28 0.00 40.11 3.67
802 904 4.732106 CCGCTAGTGAACGGGATC 57.268 61.111 4.44 0.00 45.74 3.36
807 909 3.242248 GCAATTACTACCGCTAGTGAACG 59.758 47.826 4.44 0.00 34.79 3.95
818 920 5.629079 AACTGAAGCAAGCAATTACTACC 57.371 39.130 0.00 0.00 0.00 3.18
839 941 2.040939 TCGGTGGAGTTGTACCAGAAA 58.959 47.619 0.00 0.00 38.14 2.52
840 942 1.707106 TCGGTGGAGTTGTACCAGAA 58.293 50.000 0.00 0.00 38.14 3.02
841 943 1.822990 GATCGGTGGAGTTGTACCAGA 59.177 52.381 0.00 0.00 38.14 3.86
842 944 1.825474 AGATCGGTGGAGTTGTACCAG 59.175 52.381 0.00 0.00 38.14 4.00
843 945 1.822990 GAGATCGGTGGAGTTGTACCA 59.177 52.381 0.00 0.00 36.76 3.25
861 963 4.442403 CACACGGATCATGACGATTAAGAG 59.558 45.833 12.18 0.00 33.17 2.85
870 972 3.589988 AGAAGAACACACGGATCATGAC 58.410 45.455 0.00 0.00 0.00 3.06
882 984 1.666189 GCCGGATGCTTAGAAGAACAC 59.334 52.381 5.05 0.00 36.87 3.32
946 1078 3.681897 CAGGTCAACGAAGAAGAAGATGG 59.318 47.826 0.00 0.00 0.00 3.51
981 1113 5.720041 ACTCATAGCTTCCTACTGTTTGGTA 59.280 40.000 0.00 0.00 0.00 3.25
982 1114 4.532521 ACTCATAGCTTCCTACTGTTTGGT 59.467 41.667 0.00 0.00 0.00 3.67
983 1115 4.872691 CACTCATAGCTTCCTACTGTTTGG 59.127 45.833 0.00 0.00 0.00 3.28
992 1148 1.142465 CCATGCCACTCATAGCTTCCT 59.858 52.381 0.00 0.00 33.19 3.36
1026 1187 1.079543 CTCCACCAGGTTGCTCTCG 60.080 63.158 0.00 0.00 35.89 4.04
1186 1347 0.391793 GTCTTCTTCTTCCCCTGCGG 60.392 60.000 0.00 0.00 0.00 5.69
1293 1469 6.522054 TGCTCTTATATTTCTTTACGGAGGG 58.478 40.000 0.00 0.00 0.00 4.30
1294 1470 8.608844 AATGCTCTTATATTTCTTTACGGAGG 57.391 34.615 0.00 0.00 0.00 4.30
1305 1481 9.524496 TGCCATGATCTAAATGCTCTTATATTT 57.476 29.630 0.00 0.00 0.00 1.40
1306 1482 9.175312 CTGCCATGATCTAAATGCTCTTATATT 57.825 33.333 0.00 0.00 0.00 1.28
1308 1484 6.596888 GCTGCCATGATCTAAATGCTCTTATA 59.403 38.462 0.00 0.00 0.00 0.98
1309 1485 5.415077 GCTGCCATGATCTAAATGCTCTTAT 59.585 40.000 0.00 0.00 0.00 1.73
1311 1487 3.568853 GCTGCCATGATCTAAATGCTCTT 59.431 43.478 0.00 0.00 0.00 2.85
1312 1488 3.147629 GCTGCCATGATCTAAATGCTCT 58.852 45.455 0.00 0.00 0.00 4.09
1313 1489 2.882761 TGCTGCCATGATCTAAATGCTC 59.117 45.455 0.00 0.00 0.00 4.26
1314 1490 2.621998 GTGCTGCCATGATCTAAATGCT 59.378 45.455 0.00 0.00 0.00 3.79
1315 1491 2.621998 AGTGCTGCCATGATCTAAATGC 59.378 45.455 0.00 0.00 0.00 3.56
1316 1492 4.337274 TCAAGTGCTGCCATGATCTAAATG 59.663 41.667 0.00 0.00 0.00 2.32
1317 1493 4.529897 TCAAGTGCTGCCATGATCTAAAT 58.470 39.130 0.00 0.00 0.00 1.40
1318 1494 3.954200 TCAAGTGCTGCCATGATCTAAA 58.046 40.909 0.00 0.00 0.00 1.85
1319 1495 3.632643 TCAAGTGCTGCCATGATCTAA 57.367 42.857 0.00 0.00 0.00 2.10
1322 1498 3.444916 CAAATCAAGTGCTGCCATGATC 58.555 45.455 10.87 0.00 31.58 2.92
1323 1499 2.418197 GCAAATCAAGTGCTGCCATGAT 60.418 45.455 0.00 1.64 39.00 2.45
1324 1500 1.067425 GCAAATCAAGTGCTGCCATGA 60.067 47.619 0.00 0.00 39.00 3.07
1326 1502 3.826637 GCAAATCAAGTGCTGCCAT 57.173 47.368 0.00 0.00 39.00 4.40
1332 1508 1.200948 GGACAGGAGCAAATCAAGTGC 59.799 52.381 0.00 0.00 42.55 4.40
1333 1509 2.787994 AGGACAGGAGCAAATCAAGTG 58.212 47.619 0.00 0.00 0.00 3.16
1334 1510 4.018960 ACATAGGACAGGAGCAAATCAAGT 60.019 41.667 0.00 0.00 0.00 3.16
1335 1511 4.521146 ACATAGGACAGGAGCAAATCAAG 58.479 43.478 0.00 0.00 0.00 3.02
1338 1514 6.058183 ACAATACATAGGACAGGAGCAAATC 58.942 40.000 0.00 0.00 0.00 2.17
1343 1519 5.297029 GGAAAACAATACATAGGACAGGAGC 59.703 44.000 0.00 0.00 0.00 4.70
1367 1543 9.748708 TCACAAGATCCAAGATTTTGTTAAAAG 57.251 29.630 9.94 1.54 33.22 2.27
1399 1575 4.404394 TCATCATCATTTTGCTGAAGCCAT 59.596 37.500 0.00 0.00 41.18 4.40
1476 1706 9.668497 ATTTTGTCTCCCTTCTAGTTTACATAC 57.332 33.333 0.00 0.00 0.00 2.39
1508 1778 8.677300 ACAGTTATTCAGGTGCATAAATTACTG 58.323 33.333 19.48 19.48 41.22 2.74
1514 1784 7.701539 AATGACAGTTATTCAGGTGCATAAA 57.298 32.000 0.00 0.00 0.00 1.40
1535 1805 4.393062 ACAAGCTCGTTTCCACTGATAATG 59.607 41.667 0.00 0.00 0.00 1.90
1538 1808 3.258372 AGACAAGCTCGTTTCCACTGATA 59.742 43.478 0.00 0.00 0.00 2.15
1589 1861 3.870274 TCTGGCATTCAGAGAACATCAG 58.130 45.455 0.00 0.00 46.71 2.90
1623 1898 2.734673 GGCGTGCTGCTTCTCTTCG 61.735 63.158 0.00 0.00 45.43 3.79
1638 1913 2.903855 GGCATCCTGGATGTGGCG 60.904 66.667 31.40 11.78 41.60 5.69
1659 1934 4.634443 GGTTGTAAATAGTCTGACGCCAAT 59.366 41.667 1.52 0.00 0.00 3.16
1679 1954 2.639839 AGTTCCAGCTGTGAGTATGGTT 59.360 45.455 13.81 0.00 34.32 3.67
1742 2018 2.939756 TGCAAGCAGTAACAGAAAACGA 59.060 40.909 0.00 0.00 0.00 3.85
1743 2019 3.332761 TGCAAGCAGTAACAGAAAACG 57.667 42.857 0.00 0.00 0.00 3.60
1787 2065 4.183865 TGTCCTTCAGATACAGAATTGCG 58.816 43.478 0.00 0.00 0.00 4.85
1790 2068 6.600822 CCAACATGTCCTTCAGATACAGAATT 59.399 38.462 0.00 0.00 0.00 2.17
1796 2074 3.609853 TGCCAACATGTCCTTCAGATAC 58.390 45.455 0.00 0.00 0.00 2.24
1863 2141 2.290071 ACCAACCATGCCTGTGTAGTAC 60.290 50.000 0.00 0.00 0.00 2.73
1881 2159 0.399091 CCTGAGCTCCATAGGGACCA 60.399 60.000 12.15 0.00 38.64 4.02
1899 2177 2.558359 GGCATGGAAATATACCACTGCC 59.442 50.000 22.77 22.77 45.08 4.85
1929 2212 5.221185 GCATACGAGATGGTTTCTGGTACTA 60.221 44.000 0.00 0.00 45.04 1.82
1930 2213 4.441634 GCATACGAGATGGTTTCTGGTACT 60.442 45.833 0.00 0.00 45.04 2.73
1931 2214 3.802685 GCATACGAGATGGTTTCTGGTAC 59.197 47.826 0.00 0.00 45.04 3.34
1932 2215 3.181469 GGCATACGAGATGGTTTCTGGTA 60.181 47.826 0.00 0.92 45.90 3.25
1970 2258 1.871080 AGAAACGCAGACAGTTCAGG 58.129 50.000 0.00 0.00 0.00 3.86
1973 2261 2.286418 CCACAAGAAACGCAGACAGTTC 60.286 50.000 0.00 0.00 0.00 3.01
1996 2284 2.149383 TGGAAGTGAGCCTGCCAGT 61.149 57.895 0.00 0.00 44.77 4.00
2000 2288 0.742635 GTAGCTGGAAGTGAGCCTGC 60.743 60.000 0.00 0.00 46.86 4.85
2181 2469 1.842052 AGGAAGAACGAGAGGGAGAC 58.158 55.000 0.00 0.00 0.00 3.36
2192 2480 3.071167 ACACAGGTTCAGGTAGGAAGAAC 59.929 47.826 0.00 0.00 40.58 3.01
2194 2482 2.972348 ACACAGGTTCAGGTAGGAAGA 58.028 47.619 0.00 0.00 0.00 2.87
2339 2664 2.045045 TTCTGCCGCCATTGGAGG 60.045 61.111 20.25 20.25 45.66 4.30
2340 2665 2.409870 GGTTCTGCCGCCATTGGAG 61.410 63.158 6.95 2.49 0.00 3.86
2341 2666 2.361104 GGTTCTGCCGCCATTGGA 60.361 61.111 6.95 0.00 0.00 3.53
2427 2849 1.180029 GCATCAAGGTGCCACTTCAT 58.820 50.000 0.00 0.00 39.18 2.57
2500 2924 3.450115 GACGGAGACCCACCCTCG 61.450 72.222 0.00 0.00 0.00 4.63
2501 2925 3.075641 GGACGGAGACCCACCCTC 61.076 72.222 0.00 0.00 36.03 4.30
2509 2933 1.153823 CACCATCACGGACGGAGAC 60.154 63.158 0.00 0.00 38.63 3.36
2548 2972 0.035630 ACAGCAGCAGACCCTGAATC 60.036 55.000 0.00 0.00 34.77 2.52
2549 2973 0.035630 GACAGCAGCAGACCCTGAAT 60.036 55.000 0.00 0.00 34.77 2.57
2550 2974 1.123861 AGACAGCAGCAGACCCTGAA 61.124 55.000 0.00 0.00 34.77 3.02
2611 3035 4.872691 AGTTCACTTCACAGAACAACAGAG 59.127 41.667 7.88 0.00 44.94 3.35
2613 3037 5.812642 ACTAGTTCACTTCACAGAACAACAG 59.187 40.000 7.88 4.70 44.94 3.16
2621 3061 4.021894 ACAGCCTACTAGTTCACTTCACAG 60.022 45.833 0.00 0.00 0.00 3.66
2628 3068 2.611518 CAGCACAGCCTACTAGTTCAC 58.388 52.381 0.00 0.00 0.00 3.18
2630 3070 1.646189 GCAGCACAGCCTACTAGTTC 58.354 55.000 0.00 0.00 0.00 3.01
2634 3074 1.511305 GACGCAGCACAGCCTACTA 59.489 57.895 0.00 0.00 0.00 1.82
2635 3075 2.262915 GACGCAGCACAGCCTACT 59.737 61.111 0.00 0.00 0.00 2.57
2636 3076 2.815647 GGACGCAGCACAGCCTAC 60.816 66.667 0.00 0.00 0.00 3.18
2735 3200 7.504924 TGTTACACTACCCAATCTTCAAAAG 57.495 36.000 0.00 0.00 0.00 2.27
2739 3204 9.005777 GTAATTTGTTACACTACCCAATCTTCA 57.994 33.333 0.00 0.00 0.00 3.02
2740 3205 8.173130 CGTAATTTGTTACACTACCCAATCTTC 58.827 37.037 0.00 0.00 0.00 2.87
2743 3208 6.676213 GCCGTAATTTGTTACACTACCCAATC 60.676 42.308 0.00 0.00 0.00 2.67
2799 3272 4.199432 AGAATGCTGACACCAGTTCTAG 57.801 45.455 0.00 0.00 42.35 2.43
2823 3296 2.320367 GAGAAGCACACTGACACTACG 58.680 52.381 0.00 0.00 0.00 3.51
2824 3297 2.287668 ACGAGAAGCACACTGACACTAC 60.288 50.000 0.00 0.00 0.00 2.73
2825 3298 1.954382 ACGAGAAGCACACTGACACTA 59.046 47.619 0.00 0.00 0.00 2.74
2832 3305 0.598680 GTCTGCACGAGAAGCACACT 60.599 55.000 0.00 0.00 37.02 3.55
2849 3322 6.978080 TGCATTGTTGGAGTTTAGAAAAAGTC 59.022 34.615 0.00 0.00 42.16 3.01
2851 3324 7.769272 TTGCATTGTTGGAGTTTAGAAAAAG 57.231 32.000 0.00 0.00 0.00 2.27
2852 3325 8.610896 CATTTGCATTGTTGGAGTTTAGAAAAA 58.389 29.630 0.00 0.00 0.00 1.94
2853 3326 7.984050 TCATTTGCATTGTTGGAGTTTAGAAAA 59.016 29.630 0.00 0.00 0.00 2.29
2854 3327 7.495901 TCATTTGCATTGTTGGAGTTTAGAAA 58.504 30.769 0.00 0.00 0.00 2.52
2855 3328 7.048629 TCATTTGCATTGTTGGAGTTTAGAA 57.951 32.000 0.00 0.00 0.00 2.10
2856 3329 6.647334 TCATTTGCATTGTTGGAGTTTAGA 57.353 33.333 0.00 0.00 0.00 2.10
2857 3330 5.346822 GCTCATTTGCATTGTTGGAGTTTAG 59.653 40.000 0.00 0.00 0.00 1.85
2858 3331 5.221402 TGCTCATTTGCATTGTTGGAGTTTA 60.221 36.000 0.00 0.00 38.12 2.01
2859 3332 4.060205 GCTCATTTGCATTGTTGGAGTTT 58.940 39.130 0.00 0.00 0.00 2.66
2861 3334 2.629137 TGCTCATTTGCATTGTTGGAGT 59.371 40.909 0.00 0.00 38.12 3.85
2862 3335 3.306917 TGCTCATTTGCATTGTTGGAG 57.693 42.857 0.00 0.00 38.12 3.86
2872 3345 1.226773 GGTGGCGATGCTCATTTGC 60.227 57.895 0.00 1.07 0.00 3.68
2873 3346 1.314534 TGGGTGGCGATGCTCATTTG 61.315 55.000 0.00 0.00 0.00 2.32
2874 3347 1.001020 TGGGTGGCGATGCTCATTT 60.001 52.632 0.00 0.00 0.00 2.32
2875 3348 1.452651 CTGGGTGGCGATGCTCATT 60.453 57.895 0.00 0.00 0.00 2.57
2876 3349 2.191375 CTGGGTGGCGATGCTCAT 59.809 61.111 0.00 0.00 0.00 2.90
2877 3350 3.002583 TCTGGGTGGCGATGCTCA 61.003 61.111 0.00 0.00 0.00 4.26
2880 3353 1.315257 ATTTGTCTGGGTGGCGATGC 61.315 55.000 0.00 0.00 0.00 3.91
2881 3354 1.133025 GAATTTGTCTGGGTGGCGATG 59.867 52.381 0.00 0.00 0.00 3.84
2882 3355 1.271871 TGAATTTGTCTGGGTGGCGAT 60.272 47.619 0.00 0.00 0.00 4.58
2883 3356 0.109532 TGAATTTGTCTGGGTGGCGA 59.890 50.000 0.00 0.00 0.00 5.54
2884 3357 1.135315 CATGAATTTGTCTGGGTGGCG 60.135 52.381 0.00 0.00 0.00 5.69
2885 3358 2.170166 TCATGAATTTGTCTGGGTGGC 58.830 47.619 0.00 0.00 0.00 5.01
2887 3360 5.909621 AAGATCATGAATTTGTCTGGGTG 57.090 39.130 0.00 0.00 0.00 4.61
2888 3361 6.251471 AGAAAGATCATGAATTTGTCTGGGT 58.749 36.000 12.53 0.00 0.00 4.51
2889 3362 6.770746 AGAAAGATCATGAATTTGTCTGGG 57.229 37.500 12.53 0.00 0.00 4.45
2890 3363 8.954350 AGTTAGAAAGATCATGAATTTGTCTGG 58.046 33.333 12.53 0.00 0.00 3.86
2898 3371 9.730705 TGACAAGAAGTTAGAAAGATCATGAAT 57.269 29.630 0.00 0.00 0.00 2.57
2899 3372 8.993121 GTGACAAGAAGTTAGAAAGATCATGAA 58.007 33.333 0.00 0.00 0.00 2.57
2900 3373 8.150296 TGTGACAAGAAGTTAGAAAGATCATGA 58.850 33.333 0.00 0.00 0.00 3.07
2901 3374 8.315391 TGTGACAAGAAGTTAGAAAGATCATG 57.685 34.615 0.00 0.00 0.00 3.07
2902 3375 8.908786 TTGTGACAAGAAGTTAGAAAGATCAT 57.091 30.769 0.00 0.00 0.00 2.45
2903 3376 8.731275 TTTGTGACAAGAAGTTAGAAAGATCA 57.269 30.769 0.00 0.00 28.02 2.92
2979 3704 6.758886 AGCACTTAGACGGAAATATCTTCTTG 59.241 38.462 0.00 0.00 0.00 3.02
2982 3707 6.273825 TGAGCACTTAGACGGAAATATCTTC 58.726 40.000 0.00 0.00 0.00 2.87
2999 3724 2.158957 TCCGAGTTTGAGTTTGAGCACT 60.159 45.455 0.00 0.00 0.00 4.40
3013 3738 1.380524 ATCATCGTCGTCTCCGAGTT 58.619 50.000 0.00 0.00 45.26 3.01
3018 3743 3.109619 GTGAAGAATCATCGTCGTCTCC 58.890 50.000 0.00 0.00 38.01 3.71
3053 3778 1.880027 CAGGGTTTTGTGAGGTACAGC 59.120 52.381 0.00 0.00 41.10 4.40
3054 3779 2.504367 CCAGGGTTTTGTGAGGTACAG 58.496 52.381 0.00 0.00 41.10 2.74
3104 3829 1.495951 CTCGTTTAAGTGCCACGGC 59.504 57.895 0.00 0.00 42.35 5.68
3126 3851 4.471548 TCCTATAAGCGAGATATAGGGGC 58.528 47.826 19.84 0.00 46.64 5.80
3187 3914 3.204827 CTCAGCCCGCCGAATTGG 61.205 66.667 0.00 0.00 42.50 3.16
3190 3917 2.759973 TCTCTCAGCCCGCCGAAT 60.760 61.111 0.00 0.00 0.00 3.34
3196 3923 2.737039 GCTTAAACTCTCTCTCAGCCCG 60.737 54.545 0.00 0.00 0.00 6.13
3209 3936 2.876550 GGTTGGACGAACAGCTTAAACT 59.123 45.455 2.63 0.00 36.12 2.66
3210 3937 2.614983 TGGTTGGACGAACAGCTTAAAC 59.385 45.455 2.63 0.00 36.12 2.01
3212 3939 2.623878 TGGTTGGACGAACAGCTTAA 57.376 45.000 2.63 0.00 36.12 1.85
3213 3940 2.695359 GATGGTTGGACGAACAGCTTA 58.305 47.619 2.63 0.00 36.12 3.09
3214 3941 1.523758 GATGGTTGGACGAACAGCTT 58.476 50.000 2.63 0.00 36.12 3.74
3215 3942 0.670546 CGATGGTTGGACGAACAGCT 60.671 55.000 2.63 0.00 36.12 4.24
3218 3945 1.669760 GGCGATGGTTGGACGAACA 60.670 57.895 2.63 0.00 36.12 3.18
3221 3948 1.449423 CATGGCGATGGTTGGACGA 60.449 57.895 0.00 0.00 0.00 4.20
3234 3961 4.450122 CAGCACGTGACGCATGGC 62.450 66.667 22.23 4.01 0.00 4.40
3235 3962 3.792047 CCAGCACGTGACGCATGG 61.792 66.667 22.23 14.01 0.00 3.66
3283 4010 4.057432 CCCGAAAACACATGCAGAAAAAT 58.943 39.130 0.00 0.00 0.00 1.82
3289 4016 2.507339 AAACCCGAAAACACATGCAG 57.493 45.000 0.00 0.00 0.00 4.41
3330 4057 3.440228 CAAAAACCGAAAAGCCGAGAAA 58.560 40.909 0.00 0.00 0.00 2.52
3331 4058 2.796735 GCAAAAACCGAAAAGCCGAGAA 60.797 45.455 0.00 0.00 0.00 2.87
3332 4059 1.268845 GCAAAAACCGAAAAGCCGAGA 60.269 47.619 0.00 0.00 0.00 4.04
3333 4060 1.128513 GCAAAAACCGAAAAGCCGAG 58.871 50.000 0.00 0.00 0.00 4.63
3335 4062 1.218875 GGGCAAAAACCGAAAAGCCG 61.219 55.000 0.00 0.00 42.89 5.52
3336 4063 0.179070 TGGGCAAAAACCGAAAAGCC 60.179 50.000 0.00 0.00 41.29 4.35
3337 4064 1.217001 CTGGGCAAAAACCGAAAAGC 58.783 50.000 0.00 0.00 0.00 3.51
3338 4065 2.595124 ACTGGGCAAAAACCGAAAAG 57.405 45.000 0.00 0.00 0.00 2.27
3342 4069 0.747852 GGAAACTGGGCAAAAACCGA 59.252 50.000 0.00 0.00 0.00 4.69
3343 4070 0.249699 GGGAAACTGGGCAAAAACCG 60.250 55.000 0.00 0.00 0.00 4.44
3345 4072 2.299013 CCTAGGGAAACTGGGCAAAAAC 59.701 50.000 0.00 0.00 41.29 2.43
3346 4073 2.604139 CCTAGGGAAACTGGGCAAAAA 58.396 47.619 0.00 0.00 41.29 1.94
3347 4074 1.203125 CCCTAGGGAAACTGGGCAAAA 60.203 52.381 24.99 0.00 45.96 2.44
3351 4078 0.408309 AAACCCTAGGGAAACTGGGC 59.592 55.000 35.38 0.00 45.96 5.36
3353 4080 1.708551 TCCAAACCCTAGGGAAACTGG 59.291 52.381 35.38 28.60 38.96 4.00
3355 4082 1.993301 CCTCCAAACCCTAGGGAAACT 59.007 52.381 35.38 9.13 38.96 2.66
3360 4087 3.536075 TTTTTCCTCCAAACCCTAGGG 57.464 47.619 27.36 27.36 42.03 3.53
3379 4106 6.641169 TGCAAAAAGGTTTTTCCAACTTTT 57.359 29.167 0.00 0.00 42.91 2.27
3380 4107 6.432472 TCATGCAAAAAGGTTTTTCCAACTTT 59.568 30.769 0.00 0.00 38.23 2.66
3381 4108 5.942826 TCATGCAAAAAGGTTTTTCCAACTT 59.057 32.000 0.00 0.00 38.23 2.66
3382 4109 5.495640 TCATGCAAAAAGGTTTTTCCAACT 58.504 33.333 0.00 0.00 38.23 3.16
3383 4110 5.809719 TCATGCAAAAAGGTTTTTCCAAC 57.190 34.783 0.00 0.00 38.23 3.77
3384 4111 7.401955 AATTCATGCAAAAAGGTTTTTCCAA 57.598 28.000 0.00 0.00 38.23 3.53
3385 4112 7.401955 AAATTCATGCAAAAAGGTTTTTCCA 57.598 28.000 0.00 0.00 38.23 3.53
3386 4113 8.700722 AAAAATTCATGCAAAAAGGTTTTTCC 57.299 26.923 0.00 0.00 38.23 3.13


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

AutoCloner maintained by Alex Coulton.