Multiple sequence alignment - TraesCS7B01G495600

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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 TraesCS7B01G495600 chr7B 100.000 4061 0 0 1 4061 746737596 746741656 0.000000e+00 7500
1 TraesCS7B01G495600 chr7B 83.165 2281 351 23 1114 3372 744259801 744257532 0.000000e+00 2054
2 TraesCS7B01G495600 chr7B 82.873 2283 354 28 1114 3372 743739205 743741474 0.000000e+00 2015
3 TraesCS7B01G495600 chr7B 82.724 2298 356 26 1104 3372 743815968 743818253 0.000000e+00 2006
4 TraesCS7B01G495600 chr7B 83.903 1988 288 18 1112 3078 744109590 744107614 0.000000e+00 1869
5 TraesCS7B01G495600 chr7B 96.285 996 35 2 1 995 493207604 493206610 0.000000e+00 1633
6 TraesCS7B01G495600 chr7B 95.892 998 39 2 1 997 34289846 34290842 0.000000e+00 1615
7 TraesCS7B01G495600 chr7B 76.977 1290 252 23 2092 3371 746527119 746525865 0.000000e+00 695
8 TraesCS7B01G495600 chr7B 77.268 981 196 22 1122 2084 746528128 746527157 5.930000e-153 551
9 TraesCS7B01G495600 chr7B 79.710 690 115 23 3374 4055 743741532 743742204 3.670000e-130 475
10 TraesCS7B01G495600 chr7B 80.587 613 108 9 3375 3984 743818312 743818916 2.860000e-126 462
11 TraesCS7B01G495600 chr7B 79.743 622 99 21 3375 3984 744257473 744256867 3.750000e-115 425
12 TraesCS7B01G495600 chr7B 76.775 521 93 17 3375 3875 744312849 744313361 2.410000e-67 267
13 TraesCS7B01G495600 chr7B 83.333 258 40 3 3117 3372 744107617 744107361 6.790000e-58 235
14 TraesCS7B01G495600 chr7B 91.818 110 9 0 998 1107 744109763 744109654 1.950000e-33 154
15 TraesCS7B01G495600 chr7B 92.079 101 8 0 996 1096 744348371 744348471 4.230000e-30 143
16 TraesCS7B01G495600 chr7A 80.741 2295 369 35 1104 3372 736341714 736343961 0.000000e+00 1722
17 TraesCS7B01G495600 chr7A 80.160 625 101 18 3375 3990 736293152 736293762 2.880000e-121 446
18 TraesCS7B01G495600 chr7A 82.143 140 23 2 1128 1266 735133488 735133626 7.130000e-23 119
19 TraesCS7B01G495600 chr2B 96.382 995 36 0 1 995 177026783 177025789 0.000000e+00 1639
20 TraesCS7B01G495600 chr2B 96.274 993 35 2 3 995 132607129 132606139 0.000000e+00 1628
21 TraesCS7B01G495600 chr7D 96.084 996 39 0 1 996 157754888 157753893 0.000000e+00 1624
22 TraesCS7B01G495600 chr2D 95.988 997 40 0 1 997 90786240 90787236 0.000000e+00 1620
23 TraesCS7B01G495600 chr2D 74.720 447 98 12 2752 3189 633216617 633217057 6.930000e-43 185
24 TraesCS7B01G495600 chr4B 95.980 995 37 3 1 995 626665248 626666239 0.000000e+00 1613
25 TraesCS7B01G495600 chr3B 95.879 995 41 0 1 995 744495115 744494121 0.000000e+00 1611
26 TraesCS7B01G495600 chr3B 95.779 995 42 0 1 995 799281119 799282113 0.000000e+00 1605
27 TraesCS7B01G495600 chr5B 82.456 1140 192 6 2135 3270 604164980 604166115 0.000000e+00 990
28 TraesCS7B01G495600 chr6A 79.197 971 127 41 2420 3372 540847200 540846287 4.490000e-169 604
29 TraesCS7B01G495600 chr3D 74.525 895 190 24 1144 2012 428246488 428247370 4.990000e-94 355
30 TraesCS7B01G495600 chr4A 72.083 1200 282 43 2092 3271 736886031 736887197 1.100000e-80 311
31 TraesCS7B01G495600 chr4A 74.517 569 127 16 2092 2651 735769177 735769736 8.780000e-57 231


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 TraesCS7B01G495600 chr7B 746737596 746741656 4060 False 7500.000000 7500 100.000000 1 4061 1 chr7B.!!$F4 4060
1 TraesCS7B01G495600 chr7B 493206610 493207604 994 True 1633.000000 1633 96.285000 1 995 1 chr7B.!!$R1 994
2 TraesCS7B01G495600 chr7B 34289846 34290842 996 False 1615.000000 1615 95.892000 1 997 1 chr7B.!!$F1 996
3 TraesCS7B01G495600 chr7B 743739205 743742204 2999 False 1245.000000 2015 81.291500 1114 4055 2 chr7B.!!$F5 2941
4 TraesCS7B01G495600 chr7B 744256867 744259801 2934 True 1239.500000 2054 81.454000 1114 3984 2 chr7B.!!$R3 2870
5 TraesCS7B01G495600 chr7B 743815968 743818916 2948 False 1234.000000 2006 81.655500 1104 3984 2 chr7B.!!$F6 2880
6 TraesCS7B01G495600 chr7B 744107361 744109763 2402 True 752.666667 1869 86.351333 998 3372 3 chr7B.!!$R2 2374
7 TraesCS7B01G495600 chr7B 746525865 746528128 2263 True 623.000000 695 77.122500 1122 3371 2 chr7B.!!$R4 2249
8 TraesCS7B01G495600 chr7B 744312849 744313361 512 False 267.000000 267 76.775000 3375 3875 1 chr7B.!!$F2 500
9 TraesCS7B01G495600 chr7A 736341714 736343961 2247 False 1722.000000 1722 80.741000 1104 3372 1 chr7A.!!$F3 2268
10 TraesCS7B01G495600 chr7A 736293152 736293762 610 False 446.000000 446 80.160000 3375 3990 1 chr7A.!!$F2 615
11 TraesCS7B01G495600 chr2B 177025789 177026783 994 True 1639.000000 1639 96.382000 1 995 1 chr2B.!!$R2 994
12 TraesCS7B01G495600 chr2B 132606139 132607129 990 True 1628.000000 1628 96.274000 3 995 1 chr2B.!!$R1 992
13 TraesCS7B01G495600 chr7D 157753893 157754888 995 True 1624.000000 1624 96.084000 1 996 1 chr7D.!!$R1 995
14 TraesCS7B01G495600 chr2D 90786240 90787236 996 False 1620.000000 1620 95.988000 1 997 1 chr2D.!!$F1 996
15 TraesCS7B01G495600 chr4B 626665248 626666239 991 False 1613.000000 1613 95.980000 1 995 1 chr4B.!!$F1 994
16 TraesCS7B01G495600 chr3B 744494121 744495115 994 True 1611.000000 1611 95.879000 1 995 1 chr3B.!!$R1 994
17 TraesCS7B01G495600 chr3B 799281119 799282113 994 False 1605.000000 1605 95.779000 1 995 1 chr3B.!!$F1 994
18 TraesCS7B01G495600 chr5B 604164980 604166115 1135 False 990.000000 990 82.456000 2135 3270 1 chr5B.!!$F1 1135
19 TraesCS7B01G495600 chr6A 540846287 540847200 913 True 604.000000 604 79.197000 2420 3372 1 chr6A.!!$R1 952
20 TraesCS7B01G495600 chr3D 428246488 428247370 882 False 355.000000 355 74.525000 1144 2012 1 chr3D.!!$F1 868
21 TraesCS7B01G495600 chr4A 736886031 736887197 1166 False 311.000000 311 72.083000 2092 3271 1 chr4A.!!$F2 1179
22 TraesCS7B01G495600 chr4A 735769177 735769736 559 False 231.000000 231 74.517000 2092 2651 1 chr4A.!!$F1 559

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
432 433 0.703488 TGGCATTTGGTGGAGGATGA 59.297 50.0 0.0 0.0 0.0 2.92 F
1339 1399 0.769873 AGGATAAGGCTGCATGGGAG 59.230 55.0 0.5 0.0 0.0 4.30 F
2600 2728 1.140312 ACTTCCAACCAGCCTTGAGA 58.860 50.0 0.0 0.0 0.0 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2423 2551 0.324943 TCCTCAAGTAACCAGCCTGC 59.675 55.0 0.00 0.0 0.00 4.85 R
2667 2795 0.692476 CACCATGGTGTTCTCCCTCA 59.308 55.0 32.94 0.0 40.91 3.86 R
3478 3678 0.034089 GGCCAGCTAACATCAAGGGT 60.034 55.0 0.00 0.0 0.00 4.34 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
227 228 2.030007 GCAGCCAAGTGTTTGATTAGCA 60.030 45.455 0.00 0.00 36.36 3.49
228 229 3.367703 GCAGCCAAGTGTTTGATTAGCAT 60.368 43.478 0.00 0.00 36.36 3.79
432 433 0.703488 TGGCATTTGGTGGAGGATGA 59.297 50.000 0.00 0.00 0.00 2.92
433 434 1.341285 TGGCATTTGGTGGAGGATGAG 60.341 52.381 0.00 0.00 0.00 2.90
454 455 5.191722 TGAGTATTTGGGTAGAGGAAAGCAT 59.808 40.000 0.00 0.00 0.00 3.79
566 567 9.995003 TGTTGAGTTATTTTTGAAATAGGCAAT 57.005 25.926 0.00 0.00 0.00 3.56
786 787 9.706691 CCATCTATATTGGTCGTTAACAACTAT 57.293 33.333 6.39 1.60 0.00 2.12
1008 1009 9.643693 ATTTCTTGTAGTGAATGCAAATTAAGG 57.356 29.630 0.00 0.00 32.74 2.69
1011 1012 7.615365 TCTTGTAGTGAATGCAAATTAAGGGAT 59.385 33.333 0.00 0.00 32.74 3.85
1023 1024 8.535335 TGCAAATTAAGGGATATACTGCAAAAA 58.465 29.630 0.00 0.00 34.57 1.94
1024 1025 9.546428 GCAAATTAAGGGATATACTGCAAAAAT 57.454 29.630 0.00 0.00 0.00 1.82
1031 1032 8.133024 AGGGATATACTGCAAAAATCAAACAA 57.867 30.769 0.00 0.00 0.00 2.83
1050 1051 5.767816 ACAAATACCTTCTTGTGTTGGAC 57.232 39.130 0.00 0.00 34.52 4.02
1098 1099 2.834549 TGAGATGGAGTGGGAGAAACTC 59.165 50.000 0.00 0.00 42.79 3.01
1100 1101 2.836981 AGATGGAGTGGGAGAAACTCTG 59.163 50.000 3.80 0.00 43.03 3.35
1110 1170 3.990959 GAGAAACTCTGGTCTCCCATT 57.009 47.619 0.00 0.00 40.90 3.16
1132 1192 7.114811 CCATTTCCTCTTTGTTGTAATGAAACG 59.885 37.037 0.00 0.00 0.00 3.60
1177 1237 7.416964 AGACACTGATATCTTAGCACTCTTT 57.583 36.000 3.98 0.00 0.00 2.52
1198 1258 2.167704 AAGGACCATGCCTTTTCTGGC 61.168 52.381 0.00 0.00 45.85 4.85
1241 1301 3.916061 CGTGAGCAGCTAGAGACTC 57.084 57.895 0.00 0.00 0.00 3.36
1252 1312 4.082300 CAGCTAGAGACTCTTGCAGAGAAA 60.082 45.833 31.42 4.02 45.43 2.52
1258 1318 1.869767 ACTCTTGCAGAGAAACTTGCG 59.130 47.619 16.81 0.82 45.07 4.85
1270 1330 3.694566 AGAAACTTGCGAAAAGACTTGGT 59.305 39.130 5.41 0.00 0.00 3.67
1339 1399 0.769873 AGGATAAGGCTGCATGGGAG 59.230 55.000 0.50 0.00 0.00 4.30
1387 1453 3.196685 GTGATCCCAGTAGAGCACTTCTT 59.803 47.826 2.86 0.00 46.95 2.52
1415 1481 9.620259 GGAGTTATGAGAAATTAGATCCAAGTT 57.380 33.333 0.00 0.00 0.00 2.66
1460 1526 5.891198 TGCAGTTTATATCCATAAGGCCAT 58.109 37.500 5.01 0.00 33.74 4.40
1461 1527 5.945784 TGCAGTTTATATCCATAAGGCCATC 59.054 40.000 5.01 0.00 33.74 3.51
1497 1563 2.812011 GAGTTGGTTCACATGTGGGTAC 59.188 50.000 25.16 18.86 0.00 3.34
1498 1564 2.441750 AGTTGGTTCACATGTGGGTACT 59.558 45.455 25.16 17.03 0.00 2.73
1501 1567 3.244582 TGGTTCACATGTGGGTACTAGT 58.755 45.455 25.16 0.00 0.00 2.57
1502 1568 4.418359 TGGTTCACATGTGGGTACTAGTA 58.582 43.478 25.16 0.00 0.00 1.82
1525 1591 5.839621 AGGACTTATTGATTCATGCAATGC 58.160 37.500 0.00 0.00 46.21 3.56
1526 1592 5.361571 AGGACTTATTGATTCATGCAATGCA 59.638 36.000 11.44 11.44 46.21 3.96
1534 1600 5.749620 TGATTCATGCAATGCAAACAAAAC 58.250 33.333 13.45 4.06 46.21 2.43
1545 1611 6.790285 ATGCAAACAAAACAATGGAAGATC 57.210 33.333 0.00 0.00 0.00 2.75
1548 1614 7.495901 TGCAAACAAAACAATGGAAGATCTTA 58.504 30.769 8.25 0.00 0.00 2.10
1549 1615 8.149647 TGCAAACAAAACAATGGAAGATCTTAT 58.850 29.630 8.25 0.00 0.00 1.73
1560 1626 3.999663 GGAAGATCTTATGAGGGATTGCG 59.000 47.826 8.25 0.00 0.00 4.85
1582 1648 5.512788 GCGTTAATGAGATGGTCAATGTTTG 59.487 40.000 0.00 0.00 39.19 2.93
1583 1649 6.029607 CGTTAATGAGATGGTCAATGTTTGG 58.970 40.000 0.00 0.00 39.19 3.28
1599 1665 4.515361 TGTTTGGTTCCTTCAACGAGTTA 58.485 39.130 0.00 0.00 35.59 2.24
1649 1736 3.084039 TGTTCATGATTTGGCAGAGTCC 58.916 45.455 0.00 0.00 0.00 3.85
1661 1748 2.810852 GGCAGAGTCCTTGTCTGAAAAG 59.189 50.000 4.28 0.32 43.65 2.27
1713 1800 4.944048 GGCAACAATACCTTTGACTGTTT 58.056 39.130 0.00 0.00 0.00 2.83
1741 1828 9.209175 ACATTTGTCTGTCTATGTTAAGAGTTC 57.791 33.333 0.00 0.00 0.00 3.01
1743 1830 5.950883 TGTCTGTCTATGTTAAGAGTTCGG 58.049 41.667 0.00 0.00 0.00 4.30
1769 1856 6.071784 AGCAACATCAACAATCTATCTGCAAA 60.072 34.615 0.00 0.00 0.00 3.68
1795 1882 6.604735 ACATCATTTACGCACCTTTATCTC 57.395 37.500 0.00 0.00 0.00 2.75
1811 1898 6.884295 CCTTTATCTCCATTCAACCACTTACA 59.116 38.462 0.00 0.00 0.00 2.41
1812 1899 7.066284 CCTTTATCTCCATTCAACCACTTACAG 59.934 40.741 0.00 0.00 0.00 2.74
1819 1906 5.352569 CCATTCAACCACTTACAGAGATGAC 59.647 44.000 0.00 0.00 0.00 3.06
1865 1952 4.098349 TGCTGCAGAATTTGAAGAAGTTGT 59.902 37.500 20.43 0.00 33.87 3.32
1873 1960 8.826710 CAGAATTTGAAGAAGTTGTGTGTACTA 58.173 33.333 0.00 0.00 0.00 1.82
1874 1961 8.827677 AGAATTTGAAGAAGTTGTGTGTACTAC 58.172 33.333 0.00 0.00 33.54 2.73
1880 1967 6.300354 AGAAGTTGTGTGTACTACATTTGC 57.700 37.500 4.72 0.00 42.24 3.68
2008 2095 2.012673 GCTCTCTACCACCTGCAATTG 58.987 52.381 0.00 0.00 0.00 2.32
2012 2099 2.821969 CTCTACCACCTGCAATTGCTTT 59.178 45.455 29.37 12.02 42.66 3.51
2016 2103 3.929094 ACCACCTGCAATTGCTTTATTG 58.071 40.909 29.37 18.10 42.66 1.90
2024 2111 4.811158 CAATTGCTTTATTGCAGTGACG 57.189 40.909 0.00 0.00 44.27 4.35
2061 2148 8.865590 TTGCCTGAAAAACTATTCAACTTAAC 57.134 30.769 0.00 0.00 38.75 2.01
2088 2205 7.429374 AGTTGAGATATCTTCAAGGATGTGA 57.571 36.000 6.70 0.00 0.00 3.58
2090 2207 7.932491 AGTTGAGATATCTTCAAGGATGTGATG 59.068 37.037 6.70 0.00 0.00 3.07
2099 2216 6.600822 TCTTCAAGGATGTGATGAAATTCCTC 59.399 38.462 0.00 0.00 35.78 3.71
2130 2247 6.039616 GCAAGTTAATTTCACTCCAACACAA 58.960 36.000 0.00 0.00 0.00 3.33
2133 2250 6.795399 AGTTAATTTCACTCCAACACAACAG 58.205 36.000 0.00 0.00 0.00 3.16
2156 2273 3.432517 TTTTGCGTGCAAAAGCAGT 57.567 42.105 24.40 0.00 46.80 4.40
2204 2321 2.554032 GACATGAACAACCTTGGTGGAG 59.446 50.000 0.00 0.00 39.71 3.86
2281 2398 5.532406 AGCAAAGCTACATCAGAAAAGTCAA 59.468 36.000 0.00 0.00 36.99 3.18
2309 2426 3.087031 AGATTGCACCTTGAATGGAGTG 58.913 45.455 0.00 0.00 0.00 3.51
2320 2446 5.593095 CCTTGAATGGAGTGACAATGATGAT 59.407 40.000 0.00 0.00 0.00 2.45
2333 2459 6.548251 TGACAATGATGATATGGCTTCACATT 59.452 34.615 0.00 0.00 31.28 2.71
2411 2539 5.816258 GGCCTTACTATCAAAGGTTACAGAC 59.184 44.000 0.00 0.00 44.56 3.51
2423 2551 5.545658 AGGTTACAGACATGCAAAATACG 57.454 39.130 0.00 0.00 0.00 3.06
2448 2576 3.691609 GGCTGGTTACTTGAGGATTCTTG 59.308 47.826 0.00 0.00 0.00 3.02
2518 2646 1.294041 TCCTACCATCCAATGCCACA 58.706 50.000 0.00 0.00 0.00 4.17
2548 2676 3.452627 GGAATTGCTCCTCACTTCTCCTA 59.547 47.826 0.00 0.00 41.61 2.94
2552 2680 1.681264 GCTCCTCACTTCTCCTAGAGC 59.319 57.143 0.00 0.00 38.56 4.09
2581 2709 5.070001 CCAAACCTGAAGACATTACCTTCA 58.930 41.667 0.00 0.00 45.30 3.02
2599 2727 1.202806 TCACTTCCAACCAGCCTTGAG 60.203 52.381 0.00 0.00 0.00 3.02
2600 2728 1.140312 ACTTCCAACCAGCCTTGAGA 58.860 50.000 0.00 0.00 0.00 3.27
2606 2734 2.814336 CCAACCAGCCTTGAGAAGTTAC 59.186 50.000 0.00 0.00 0.00 2.50
2624 2752 8.579006 AGAAGTTACAAATTGAGAAATGCATGA 58.421 29.630 0.00 0.00 0.00 3.07
2644 2772 7.707464 TGCATGATGCTTATGTTTATTTCCAAG 59.293 33.333 19.19 0.00 45.31 3.61
2659 2787 5.964958 TTTCCAAGGATGAGCTAAAACAG 57.035 39.130 0.00 0.00 0.00 3.16
2684 2812 0.254178 CCTGAGGGAGAACACCATGG 59.746 60.000 11.19 11.19 33.58 3.66
2710 2838 0.613260 ATGACTTGAAGGCACGGCTA 59.387 50.000 1.17 0.00 35.04 3.93
2721 2849 1.668419 GCACGGCTATCTTCCATGTT 58.332 50.000 0.00 0.00 0.00 2.71
2736 2864 3.517901 TCCATGTTGGAAGAGTATTCGGT 59.482 43.478 0.00 0.00 45.00 4.69
2767 2895 6.723298 ATCAAGGAGGTACTATTGTCAGAG 57.277 41.667 0.00 0.00 41.55 3.35
2784 2913 3.196939 AGAGCATTCATCTCTGAAGCC 57.803 47.619 0.00 0.00 44.32 4.35
2817 2946 6.738832 ATTGATGGATGCTGATATTTCTCG 57.261 37.500 0.00 0.00 0.00 4.04
2831 2965 9.098355 CTGATATTTCTCGTCTTCAAACCATTA 57.902 33.333 0.00 0.00 0.00 1.90
2871 3005 4.731929 AGTGGGGGATGAAGTATTGGTAAT 59.268 41.667 0.00 0.00 0.00 1.89
2911 3045 0.180406 GGGTATGTTGCCACGAGGAT 59.820 55.000 1.86 0.00 36.89 3.24
2915 3049 1.204146 ATGTTGCCACGAGGATAGGT 58.796 50.000 1.86 0.00 36.89 3.08
2917 3051 1.338674 TGTTGCCACGAGGATAGGTTG 60.339 52.381 1.86 0.00 36.89 3.77
2923 3057 1.831736 CACGAGGATAGGTTGGGACTT 59.168 52.381 0.00 0.00 0.00 3.01
2928 3062 4.663334 GAGGATAGGTTGGGACTTGTTTT 58.337 43.478 0.00 0.00 0.00 2.43
2943 3077 7.201875 GGGACTTGTTTTTAGAAGGAACATCAA 60.202 37.037 0.00 0.00 33.73 2.57
2991 3125 5.240403 GGTTGTCTCAGCTTCATCTTTCTTT 59.760 40.000 0.00 0.00 0.00 2.52
2992 3126 5.936686 TGTCTCAGCTTCATCTTTCTTTG 57.063 39.130 0.00 0.00 0.00 2.77
3003 3137 6.741992 TCATCTTTCTTTGTGCATCGTTAT 57.258 33.333 0.00 0.00 0.00 1.89
3045 3179 1.912043 CCCCTTGATGGTCTCACTTCT 59.088 52.381 0.00 0.00 32.17 2.85
3059 3193 3.706698 TCACTTCTCTGAGACGTTTGTG 58.293 45.455 13.47 13.26 0.00 3.33
3070 3204 6.423905 TCTGAGACGTTTGTGATTAAAAGAGG 59.576 38.462 0.00 0.00 0.00 3.69
3072 3206 6.202188 TGAGACGTTTGTGATTAAAAGAGGTC 59.798 38.462 0.00 0.00 0.00 3.85
3189 3326 1.153369 GGGATTGCGAGCTGCTACA 60.153 57.895 0.15 0.68 46.63 2.74
3216 3353 9.136323 AGTCTTTCAAGTTTTTCATTATGGAGT 57.864 29.630 0.00 0.00 0.00 3.85
3226 3363 5.708736 TTCATTATGGAGTTGCCCTTCTA 57.291 39.130 0.00 0.00 34.97 2.10
3271 3408 4.320608 TTTTTGCCATTGTCCTTGAGAC 57.679 40.909 0.00 0.00 46.51 3.36
3282 3419 4.647424 GTCCTTGAGACACTGGAGATAG 57.353 50.000 0.00 0.00 45.55 2.08
3333 3477 0.888619 TAGTGACTTCTCGCACCTGG 59.111 55.000 0.00 0.00 35.67 4.45
3334 3478 1.115930 AGTGACTTCTCGCACCTGGT 61.116 55.000 0.00 0.00 35.67 4.00
3372 3516 2.008329 GGTGCAGAAGCTCTTCATCAG 58.992 52.381 11.69 1.08 41.84 2.90
3410 3610 2.376032 GTTGTCTTCGCTGCAACTTTC 58.624 47.619 0.00 0.00 39.30 2.62
3413 3613 1.537202 GTCTTCGCTGCAACTTTCCAT 59.463 47.619 0.00 0.00 0.00 3.41
3414 3614 1.806542 TCTTCGCTGCAACTTTCCATC 59.193 47.619 0.00 0.00 0.00 3.51
3419 3619 1.973138 CTGCAACTTTCCATCGCAAG 58.027 50.000 0.00 0.00 31.10 4.01
3441 3641 1.990799 TTGCGTATGTCTCGAACCTG 58.009 50.000 0.00 0.00 0.00 4.00
3453 3653 5.047306 TGTCTCGAACCTGAATATGAAGTGT 60.047 40.000 0.00 0.00 0.00 3.55
3472 3672 3.926527 GTGTATCTCACATTTGCGAGTCA 59.073 43.478 0.00 0.00 45.51 3.41
3478 3678 4.022329 TCTCACATTTGCGAGTCAAGACTA 60.022 41.667 2.15 0.00 42.66 2.59
3484 3684 1.272490 TGCGAGTCAAGACTACCCTTG 59.728 52.381 2.15 0.00 42.66 3.61
3495 3695 3.452627 AGACTACCCTTGATGTTAGCTGG 59.547 47.826 0.00 0.00 0.00 4.85
3502 3702 0.177141 TGATGTTAGCTGGCCCGTAC 59.823 55.000 0.00 0.00 0.00 3.67
3509 3709 2.125512 CTGGCCCGTACTGCTCAC 60.126 66.667 0.00 0.00 0.00 3.51
3516 3716 0.460284 CCGTACTGCTCACCCACATC 60.460 60.000 0.00 0.00 0.00 3.06
3533 3739 2.027377 ACATCCTCTCAGCTGAAGGTTG 60.027 50.000 30.17 30.17 0.00 3.77
3564 3770 3.172229 AGAAATCTCGCTCTTGTAGGC 57.828 47.619 0.00 0.00 0.00 3.93
3574 3780 1.192146 TCTTGTAGGCGGCAAGGAGT 61.192 55.000 13.08 0.00 42.44 3.85
3622 3828 5.735324 CAGATTTATCATCTGTCAACTGCG 58.265 41.667 4.00 0.00 40.34 5.18
3633 3839 4.572795 TCTGTCAACTGCGTGTCATTTTAA 59.427 37.500 0.00 0.00 0.00 1.52
3645 3851 8.060679 TGCGTGTCATTTTAAAATTGTGAAATG 58.939 29.630 16.21 16.21 39.58 2.32
3672 3885 4.019174 CCTTGCCAGGAAATATGAAGTGT 58.981 43.478 0.00 0.00 44.19 3.55
3682 3895 9.480053 CAGGAAATATGAAGTGTTTTTCATGTT 57.520 29.630 10.58 7.86 45.12 2.71
3747 3960 7.403231 TCTTTACCAGATTTACCATCCTCTCTT 59.597 37.037 0.00 0.00 0.00 2.85
3748 3961 8.618240 TTTACCAGATTTACCATCCTCTCTTA 57.382 34.615 0.00 0.00 0.00 2.10
3754 3967 7.281100 CAGATTTACCATCCTCTCTTAACCAAC 59.719 40.741 0.00 0.00 0.00 3.77
3756 3969 4.559862 ACCATCCTCTCTTAACCAACTG 57.440 45.455 0.00 0.00 0.00 3.16
3765 3978 4.525487 TCTCTTAACCAACTGTACGTGGAT 59.475 41.667 14.96 7.36 0.00 3.41
3801 4014 2.206576 AGAAGAGTTGCCAATCACCC 57.793 50.000 0.00 0.00 0.00 4.61
3816 4029 0.250234 CACCCGATGGAGAAAGCTGA 59.750 55.000 0.00 0.00 34.81 4.26
3836 4049 5.114764 TGACCAAAGATTGAGCATATCCA 57.885 39.130 0.00 0.00 0.00 3.41
3850 4064 6.932960 TGAGCATATCCACTCAATACAGATTG 59.067 38.462 0.00 0.00 43.39 2.67
3912 4126 1.071699 GGTAAACACCTCACCTGCTCA 59.928 52.381 0.00 0.00 0.00 4.26
3914 4128 0.532862 AAACACCTCACCTGCTCACG 60.533 55.000 0.00 0.00 0.00 4.35
3926 4140 1.659601 CTGCTCACGCTCAAAGAGATG 59.340 52.381 0.00 0.00 36.97 2.90
3928 4142 2.289010 TGCTCACGCTCAAAGAGATGAA 60.289 45.455 0.00 0.00 36.97 2.57
3929 4143 2.093467 GCTCACGCTCAAAGAGATGAAC 59.907 50.000 0.00 0.00 30.06 3.18
3930 4144 3.320626 CTCACGCTCAAAGAGATGAACA 58.679 45.455 0.00 0.00 30.06 3.18
3933 4147 4.389992 TCACGCTCAAAGAGATGAACATTC 59.610 41.667 0.00 0.00 0.00 2.67
3934 4148 4.391216 CACGCTCAAAGAGATGAACATTCT 59.609 41.667 0.00 0.00 0.00 2.40
3935 4149 4.391216 ACGCTCAAAGAGATGAACATTCTG 59.609 41.667 0.00 0.00 0.00 3.02
4035 4253 9.810545 AAAGTTTTCCTTGTTCATTTATTTCGA 57.189 25.926 0.00 0.00 32.32 3.71
4040 4258 7.737972 TCCTTGTTCATTTATTTCGAACAGA 57.262 32.000 0.00 0.00 46.88 3.41
4044 4262 6.378582 TGTTCATTTATTTCGAACAGAAGGC 58.621 36.000 0.00 0.00 42.95 4.35
4045 4263 6.206634 TGTTCATTTATTTCGAACAGAAGGCT 59.793 34.615 0.00 0.00 42.95 4.58
4050 4268 1.878953 TTCGAACAGAAGGCTTCCAC 58.121 50.000 23.09 11.15 34.26 4.02
4052 4270 1.291877 CGAACAGAAGGCTTCCACGG 61.292 60.000 23.09 12.90 0.00 4.94
4053 4271 0.034896 GAACAGAAGGCTTCCACGGA 59.965 55.000 23.09 0.00 0.00 4.69
4054 4272 0.250338 AACAGAAGGCTTCCACGGAC 60.250 55.000 23.09 0.00 0.00 4.79
4055 4273 1.376037 CAGAAGGCTTCCACGGACC 60.376 63.158 23.09 0.00 0.00 4.46
4056 4274 1.841556 AGAAGGCTTCCACGGACCA 60.842 57.895 23.09 0.00 0.00 4.02
4057 4275 1.072505 GAAGGCTTCCACGGACCAA 59.927 57.895 16.50 0.00 0.00 3.67
4058 4276 0.536460 GAAGGCTTCCACGGACCAAA 60.536 55.000 16.50 0.00 0.00 3.28
4059 4277 0.822121 AAGGCTTCCACGGACCAAAC 60.822 55.000 0.00 0.00 0.00 2.93
4060 4278 2.265904 GGCTTCCACGGACCAAACC 61.266 63.158 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
227 228 1.408702 GCCATGTGCATTTCCCGTAAT 59.591 47.619 0.00 0.00 40.77 1.89
228 229 0.814457 GCCATGTGCATTTCCCGTAA 59.186 50.000 0.00 0.00 40.77 3.18
260 261 4.038271 ACTGATCATCCTCAGCCAAAAA 57.962 40.909 0.00 0.00 45.37 1.94
432 433 5.717119 ATGCTTTCCTCTACCCAAATACT 57.283 39.130 0.00 0.00 0.00 2.12
433 434 5.652452 ACAATGCTTTCCTCTACCCAAATAC 59.348 40.000 0.00 0.00 0.00 1.89
558 559 6.610075 ATGTCAAAAACCTTCATTGCCTAT 57.390 33.333 0.00 0.00 0.00 2.57
566 567 9.695526 CTTCATCAAATATGTCAAAAACCTTCA 57.304 29.630 0.00 0.00 0.00 3.02
669 670 7.144661 GTCATGTCCATGTGTCAATTTTTGTA 58.855 34.615 7.13 0.00 39.72 2.41
670 671 5.984926 GTCATGTCCATGTGTCAATTTTTGT 59.015 36.000 7.13 0.00 39.72 2.83
786 787 1.745827 GCTGGTCCGCTGCCTTATTTA 60.746 52.381 0.00 0.00 0.00 1.40
940 941 3.650942 TGTCAGTGACCCTGGAAGTATTT 59.349 43.478 20.43 0.00 41.83 1.40
944 945 1.051812 CTGTCAGTGACCCTGGAAGT 58.948 55.000 20.43 0.00 41.83 3.01
1007 1008 8.770438 TTTGTTTGATTTTTGCAGTATATCCC 57.230 30.769 0.00 0.00 0.00 3.85
1023 1024 7.069331 TCCAACACAAGAAGGTATTTGTTTGAT 59.931 33.333 10.74 0.00 35.46 2.57
1024 1025 6.378564 TCCAACACAAGAAGGTATTTGTTTGA 59.621 34.615 10.74 0.00 35.46 2.69
1031 1032 4.345859 TCGTCCAACACAAGAAGGTATT 57.654 40.909 0.00 0.00 0.00 1.89
1050 1051 4.970003 GTGTTTTCTTCAAACCAGACATCG 59.030 41.667 0.00 0.00 43.87 3.84
1109 1169 7.323049 TCGTTTCATTACAACAAAGAGGAAA 57.677 32.000 0.00 0.00 0.00 3.13
1110 1170 6.928979 TCGTTTCATTACAACAAAGAGGAA 57.071 33.333 0.00 0.00 0.00 3.36
1132 1192 5.803967 GTCTTCCATGTCTTGCAAATGAATC 59.196 40.000 10.52 0.00 0.00 2.52
1142 1202 6.580788 AGATATCAGTGTCTTCCATGTCTTG 58.419 40.000 5.32 0.00 0.00 3.02
1177 1237 3.085952 CCAGAAAAGGCATGGTCCTTA 57.914 47.619 5.18 0.00 45.25 2.69
1198 1258 0.108472 TCTGGTCTCTGATTGCTGCG 60.108 55.000 0.00 0.00 0.00 5.18
1241 1301 3.338818 TTTCGCAAGTTTCTCTGCAAG 57.661 42.857 0.00 0.00 39.48 4.01
1252 1312 4.067972 TCTACCAAGTCTTTTCGCAAGT 57.932 40.909 0.00 0.00 39.48 3.16
1258 1318 6.337356 CAGAGGAGATCTACCAAGTCTTTTC 58.663 44.000 0.00 0.00 36.10 2.29
1270 1330 2.165357 TTGCTGCCAGAGGAGATCTA 57.835 50.000 0.00 0.00 36.10 1.98
1339 1399 4.775236 AGTTGTCAATCCTTAGAGCATCC 58.225 43.478 0.00 0.00 33.66 3.51
1387 1453 9.618890 CTTGGATCTAATTTCTCATAACTCCAA 57.381 33.333 0.00 0.00 36.87 3.53
1415 1481 6.208402 TGCAATATAGAAAACACCTCTGCAAA 59.792 34.615 0.00 0.00 0.00 3.68
1416 1482 5.709631 TGCAATATAGAAAACACCTCTGCAA 59.290 36.000 0.00 0.00 0.00 4.08
1452 1518 8.270137 TCCTTAATGTAATACTGATGGCCTTA 57.730 34.615 3.32 0.00 0.00 2.69
1460 1526 8.598916 TGAACCAACTCCTTAATGTAATACTGA 58.401 33.333 0.00 0.00 0.00 3.41
1461 1527 8.665685 GTGAACCAACTCCTTAATGTAATACTG 58.334 37.037 0.00 0.00 0.00 2.74
1497 1563 8.893219 TTGCATGAATCAATAAGTCCTACTAG 57.107 34.615 0.00 0.00 0.00 2.57
1498 1564 9.276590 CATTGCATGAATCAATAAGTCCTACTA 57.723 33.333 0.00 0.00 33.27 1.82
1501 1567 6.546772 TGCATTGCATGAATCAATAAGTCCTA 59.453 34.615 7.38 0.00 33.27 2.94
1502 1568 5.361571 TGCATTGCATGAATCAATAAGTCCT 59.638 36.000 7.38 0.00 33.27 3.85
1525 1591 9.695526 TCATAAGATCTTCCATTGTTTTGTTTG 57.304 29.630 12.24 0.00 0.00 2.93
1526 1592 9.918630 CTCATAAGATCTTCCATTGTTTTGTTT 57.081 29.630 12.24 0.00 0.00 2.83
1534 1600 6.072064 GCAATCCCTCATAAGATCTTCCATTG 60.072 42.308 12.24 11.06 0.00 2.82
1545 1611 5.991606 TCTCATTAACGCAATCCCTCATAAG 59.008 40.000 0.00 0.00 0.00 1.73
1548 1614 4.422073 TCTCATTAACGCAATCCCTCAT 57.578 40.909 0.00 0.00 0.00 2.90
1549 1615 3.904800 TCTCATTAACGCAATCCCTCA 57.095 42.857 0.00 0.00 0.00 3.86
1560 1626 6.924111 ACCAAACATTGACCATCTCATTAAC 58.076 36.000 0.00 0.00 0.00 2.01
1582 1648 4.374399 TCTGTTAACTCGTTGAAGGAACC 58.626 43.478 7.22 0.00 0.00 3.62
1583 1649 5.120363 GGATCTGTTAACTCGTTGAAGGAAC 59.880 44.000 7.22 0.00 0.00 3.62
1599 1665 6.936335 TCATGCATAACATATTCGGATCTGTT 59.064 34.615 11.73 11.73 36.64 3.16
1649 1736 3.879295 TGAAGCAGACCTTTTCAGACAAG 59.121 43.478 0.00 0.00 32.78 3.16
1661 1748 5.911752 TCATCTTCTAATCTGAAGCAGACC 58.088 41.667 0.00 0.00 43.63 3.85
1703 1790 8.050778 AGACAGACAAATGTTAAACAGTCAAA 57.949 30.769 0.00 0.00 32.25 2.69
1705 1792 8.773645 CATAGACAGACAAATGTTAAACAGTCA 58.226 33.333 0.00 0.00 32.25 3.41
1706 1793 8.774586 ACATAGACAGACAAATGTTAAACAGTC 58.225 33.333 0.00 0.00 32.25 3.51
1741 1828 4.813161 AGATAGATTGTTGATGTTGCTCCG 59.187 41.667 0.00 0.00 0.00 4.63
1743 1830 5.065602 TGCAGATAGATTGTTGATGTTGCTC 59.934 40.000 0.00 0.00 0.00 4.26
1769 1856 7.272978 AGATAAAGGTGCGTAAATGATGTAGT 58.727 34.615 0.00 0.00 0.00 2.73
1795 1882 5.352569 GTCATCTCTGTAAGTGGTTGAATGG 59.647 44.000 0.00 0.00 33.76 3.16
1811 1898 5.988561 GGAAAATATCTCTTGCGTCATCTCT 59.011 40.000 0.00 0.00 0.00 3.10
1812 1899 5.755375 TGGAAAATATCTCTTGCGTCATCTC 59.245 40.000 0.00 0.00 0.00 2.75
1819 1906 3.003068 CCTGCTGGAAAATATCTCTTGCG 59.997 47.826 2.92 0.00 34.57 4.85
1865 1952 3.659786 AGAAGCGCAAATGTAGTACACA 58.340 40.909 11.47 0.00 42.69 3.72
1873 1960 3.689161 TGCTGTTATAGAAGCGCAAATGT 59.311 39.130 11.47 0.00 42.54 2.71
1874 1961 4.277257 TGCTGTTATAGAAGCGCAAATG 57.723 40.909 11.47 0.00 42.54 2.32
2008 2095 3.747099 ATGTCGTCACTGCAATAAAGC 57.253 42.857 0.00 0.00 0.00 3.51
2012 2099 8.910666 CAAAATTTTAATGTCGTCACTGCAATA 58.089 29.630 2.44 0.00 0.00 1.90
2016 2103 5.388371 GGCAAAATTTTAATGTCGTCACTGC 60.388 40.000 2.44 0.00 0.00 4.40
2061 2148 9.258826 CACATCCTTGAAGATATCTCAACTTAG 57.741 37.037 5.51 1.28 0.00 2.18
2088 2205 7.414222 AACTTGCATATGTGAGGAATTTCAT 57.586 32.000 4.29 0.00 0.00 2.57
2090 2207 9.807649 AATTAACTTGCATATGTGAGGAATTTC 57.192 29.630 4.29 0.00 0.00 2.17
2099 2216 7.537715 TGGAGTGAAATTAACTTGCATATGTG 58.462 34.615 4.29 0.00 0.00 3.21
2105 2222 5.126222 TGTGTTGGAGTGAAATTAACTTGCA 59.874 36.000 0.00 0.00 0.00 4.08
2130 2247 2.575694 TTGCACGCAAAATTGTCTGT 57.424 40.000 1.07 0.00 32.44 3.41
2156 2273 1.220749 GTCGCACCTCATAGCCCAA 59.779 57.895 0.00 0.00 0.00 4.12
2204 2321 6.100004 TCTCGAGATTTGTGAGACATAAACC 58.900 40.000 12.08 0.00 34.00 3.27
2213 2330 5.004821 CGGTAACATTCTCGAGATTTGTGAG 59.995 44.000 24.18 15.20 0.00 3.51
2281 2398 3.777106 TCAAGGTGCAATCTCTCAAGT 57.223 42.857 0.00 0.00 0.00 3.16
2309 2426 6.570672 ATGTGAAGCCATATCATCATTGTC 57.429 37.500 0.00 0.00 0.00 3.18
2320 2446 8.978874 AATGTGAACTATAATGTGAAGCCATA 57.021 30.769 0.00 0.00 0.00 2.74
2333 2459 7.685481 TCCAGAGTTTCCAAATGTGAACTATA 58.315 34.615 0.00 0.00 32.85 1.31
2411 2539 1.552226 CAGCCTGCGTATTTTGCATG 58.448 50.000 0.00 0.00 42.32 4.06
2423 2551 0.324943 TCCTCAAGTAACCAGCCTGC 59.675 55.000 0.00 0.00 0.00 4.85
2472 2600 2.094675 AGGCGCTGCAATTAACAAGAT 58.905 42.857 7.64 0.00 0.00 2.40
2548 2676 1.067295 TCAGGTTTGGGACATGCTCT 58.933 50.000 0.00 0.00 39.80 4.09
2552 2680 2.862541 TGTCTTCAGGTTTGGGACATG 58.137 47.619 0.00 0.00 41.28 3.21
2581 2709 1.140312 TCTCAAGGCTGGTTGGAAGT 58.860 50.000 0.00 0.00 0.00 3.01
2599 2727 8.746922 TCATGCATTTCTCAATTTGTAACTTC 57.253 30.769 0.00 0.00 0.00 3.01
2600 2728 9.146984 CATCATGCATTTCTCAATTTGTAACTT 57.853 29.630 0.00 0.00 0.00 2.66
2624 2752 8.537728 TCATCCTTGGAAATAAACATAAGCAT 57.462 30.769 0.00 0.00 0.00 3.79
2659 2787 2.633488 GTGTTCTCCCTCAGGTTATGC 58.367 52.381 0.00 0.00 0.00 3.14
2663 2791 1.352352 CATGGTGTTCTCCCTCAGGTT 59.648 52.381 0.00 0.00 0.00 3.50
2667 2795 0.692476 CACCATGGTGTTCTCCCTCA 59.308 55.000 32.94 0.00 40.91 3.86
2684 2812 3.062639 CGTGCCTTCAAGTCATATGTCAC 59.937 47.826 1.90 0.00 0.00 3.67
2693 2821 1.134670 AGATAGCCGTGCCTTCAAGTC 60.135 52.381 0.00 0.00 0.00 3.01
2702 2830 1.331756 CAACATGGAAGATAGCCGTGC 59.668 52.381 0.00 0.00 44.49 5.34
2721 2849 6.785337 TTTCTGATACCGAATACTCTTCCA 57.215 37.500 0.00 0.00 0.00 3.53
2725 2853 7.287927 TCCTTGATTTCTGATACCGAATACTCT 59.712 37.037 0.00 0.00 0.00 3.24
2729 2857 6.326583 ACCTCCTTGATTTCTGATACCGAATA 59.673 38.462 0.00 0.00 0.00 1.75
2736 2864 9.213777 ACAATAGTACCTCCTTGATTTCTGATA 57.786 33.333 0.00 0.00 0.00 2.15
2767 2895 2.345124 AGGGCTTCAGAGATGAATGC 57.655 50.000 0.00 0.00 0.00 3.56
2784 2913 5.944007 TCAGCATCCATCAATATCATCAAGG 59.056 40.000 0.00 0.00 0.00 3.61
2817 2946 6.739112 AGAGCACTTTTAATGGTTTGAAGAC 58.261 36.000 0.00 0.00 0.00 3.01
2850 2984 6.154645 TCTATTACCAATACTTCATCCCCCA 58.845 40.000 0.00 0.00 0.00 4.96
2871 3005 9.744125 ATACCCATGCCTTTATTATATCCTCTA 57.256 33.333 0.00 0.00 0.00 2.43
2881 3015 4.670896 GCAACATACCCATGCCTTTATT 57.329 40.909 0.00 0.00 35.39 1.40
2911 3045 6.066032 CCTTCTAAAAACAAGTCCCAACCTA 58.934 40.000 0.00 0.00 0.00 3.08
2915 3049 5.952947 TGTTCCTTCTAAAAACAAGTCCCAA 59.047 36.000 0.00 0.00 30.39 4.12
2917 3051 6.264518 TGATGTTCCTTCTAAAAACAAGTCCC 59.735 38.462 0.00 0.00 36.57 4.46
2923 3057 6.460953 GCAGGTTGATGTTCCTTCTAAAAACA 60.461 38.462 0.00 0.00 37.32 2.83
2928 3062 3.073798 TGGCAGGTTGATGTTCCTTCTAA 59.926 43.478 0.00 0.00 30.91 2.10
2943 3077 2.515901 GTGGAACCAGTGGCAGGT 59.484 61.111 9.78 0.00 42.34 4.00
2969 3103 5.824624 ACAAAGAAAGATGAAGCTGAGACAA 59.175 36.000 0.00 0.00 0.00 3.18
2971 3105 5.687828 CACAAAGAAAGATGAAGCTGAGAC 58.312 41.667 0.00 0.00 0.00 3.36
2991 3125 2.549992 GCCCCATCTATAACGATGCACA 60.550 50.000 0.00 0.00 39.51 4.57
2992 3126 2.076863 GCCCCATCTATAACGATGCAC 58.923 52.381 0.00 0.00 39.51 4.57
3003 3137 3.554934 CAAACAGCTAATGCCCCATCTA 58.445 45.455 0.00 0.00 40.80 1.98
3027 3161 3.513119 TCAGAGAAGTGAGACCATCAAGG 59.487 47.826 0.00 0.00 40.43 3.61
3028 3162 4.462132 TCTCAGAGAAGTGAGACCATCAAG 59.538 45.833 0.00 0.00 46.52 3.02
3045 3179 6.423905 CCTCTTTTAATCACAAACGTCTCAGA 59.576 38.462 0.00 0.00 0.00 3.27
3070 3204 5.924825 ACGGAAGTGTAGTTAAAGTCATGAC 59.075 40.000 18.47 18.47 46.97 3.06
3150 3287 1.207089 CCTAGTGATCGAAGGCACCAA 59.793 52.381 11.34 2.40 34.68 3.67
3189 3326 9.971922 CTCCATAATGAAAAACTTGAAAGACTT 57.028 29.630 0.00 0.00 0.00 3.01
3216 3353 2.843730 TGCCAAGTCTATAGAAGGGCAA 59.156 45.455 27.88 17.53 41.01 4.52
3226 3363 1.831106 TGATCCACGTGCCAAGTCTAT 59.169 47.619 10.91 0.00 0.00 1.98
3265 3402 3.056536 GTGTGCTATCTCCAGTGTCTCAA 60.057 47.826 0.00 0.00 0.00 3.02
3267 3404 2.757868 AGTGTGCTATCTCCAGTGTCTC 59.242 50.000 0.00 0.00 0.00 3.36
3268 3405 2.495270 CAGTGTGCTATCTCCAGTGTCT 59.505 50.000 0.00 0.00 0.00 3.41
3270 3407 1.066573 GCAGTGTGCTATCTCCAGTGT 60.067 52.381 0.00 0.00 40.96 3.55
3271 3408 1.066645 TGCAGTGTGCTATCTCCAGTG 60.067 52.381 0.00 0.00 45.31 3.66
3273 3410 2.210961 CATGCAGTGTGCTATCTCCAG 58.789 52.381 0.00 0.00 45.31 3.86
3274 3411 1.134310 CCATGCAGTGTGCTATCTCCA 60.134 52.381 0.00 0.00 45.31 3.86
3275 3412 1.134280 ACCATGCAGTGTGCTATCTCC 60.134 52.381 0.00 0.00 45.31 3.71
3276 3413 2.322355 ACCATGCAGTGTGCTATCTC 57.678 50.000 0.00 0.00 45.31 2.75
3323 3467 3.069586 TGGAAAGATATACCAGGTGCGAG 59.930 47.826 0.76 0.00 0.00 5.03
3324 3468 3.035363 TGGAAAGATATACCAGGTGCGA 58.965 45.455 0.76 0.00 0.00 5.10
3372 3516 1.322442 ACCCTTCAAGAAAGCACAGC 58.678 50.000 0.00 0.00 33.29 4.40
3419 3619 2.735134 AGGTTCGAGACATACGCAAAAC 59.265 45.455 0.00 0.00 0.00 2.43
3427 3627 7.147897 ACACTTCATATTCAGGTTCGAGACATA 60.148 37.037 0.00 0.00 0.00 2.29
3433 3633 7.068226 TGAGATACACTTCATATTCAGGTTCGA 59.932 37.037 0.00 0.00 0.00 3.71
3462 3662 1.968493 AGGGTAGTCTTGACTCGCAAA 59.032 47.619 6.55 0.00 35.74 3.68
3472 3672 4.080863 CCAGCTAACATCAAGGGTAGTCTT 60.081 45.833 0.00 0.00 0.00 3.01
3478 3678 0.034089 GGCCAGCTAACATCAAGGGT 60.034 55.000 0.00 0.00 0.00 4.34
3484 3684 0.464452 AGTACGGGCCAGCTAACATC 59.536 55.000 4.39 0.00 0.00 3.06
3495 3695 3.702048 TGGGTGAGCAGTACGGGC 61.702 66.667 4.61 4.61 0.00 6.13
3502 3702 0.177604 GAGAGGATGTGGGTGAGCAG 59.822 60.000 0.00 0.00 0.00 4.24
3509 3709 0.907486 TTCAGCTGAGAGGATGTGGG 59.093 55.000 17.43 0.00 0.00 4.61
3516 3716 2.300152 TGTACAACCTTCAGCTGAGAGG 59.700 50.000 28.71 28.71 0.00 3.69
3533 3739 4.246458 AGCGAGATTTCTTGGAACTGTAC 58.754 43.478 0.00 0.00 0.00 2.90
3574 3780 7.039574 TGCTGATTCTTCAAATGAAAAGGATCA 60.040 33.333 6.06 6.06 42.54 2.92
3633 3839 6.297582 TGGCAAGGAAATCATTTCACAATTT 58.702 32.000 12.27 0.00 41.43 1.82
3664 3877 7.068593 TCTCCTCAAACATGAAAAACACTTCAT 59.931 33.333 0.00 0.00 44.98 2.57
3672 3885 5.445069 TGGAGTCTCCTCAAACATGAAAAA 58.555 37.500 19.82 0.00 39.64 1.94
3682 3895 3.963374 CCACAGATATGGAGTCTCCTCAA 59.037 47.826 19.82 5.73 43.02 3.02
3735 3948 3.910627 ACAGTTGGTTAAGAGAGGATGGT 59.089 43.478 0.00 0.00 0.00 3.55
3747 3960 4.811969 ATCATCCACGTACAGTTGGTTA 57.188 40.909 0.00 0.00 0.00 2.85
3748 3961 3.695830 ATCATCCACGTACAGTTGGTT 57.304 42.857 0.00 0.00 0.00 3.67
3754 3967 4.748892 AGTTCAGAATCATCCACGTACAG 58.251 43.478 0.00 0.00 0.00 2.74
3756 3969 5.000012 AGAGTTCAGAATCATCCACGTAC 58.000 43.478 0.00 0.00 0.00 3.67
3789 4002 0.394216 CTCCATCGGGTGATTGGCAA 60.394 55.000 0.68 0.68 34.93 4.52
3801 4014 2.099141 TTGGTCAGCTTTCTCCATCG 57.901 50.000 0.00 0.00 0.00 3.84
3816 4029 5.121380 AGTGGATATGCTCAATCTTTGGT 57.879 39.130 0.00 0.00 0.00 3.67
3863 4077 8.849168 TCTCTTTCTTTGTAATTGCAAATCTGA 58.151 29.630 19.96 12.32 37.66 3.27
3875 4089 8.680001 GGTGTTTACCTTTCTCTTTCTTTGTAA 58.320 33.333 0.00 0.00 43.97 2.41
3912 4126 4.391216 CAGAATGTTCATCTCTTTGAGCGT 59.609 41.667 0.00 0.00 30.24 5.07
4021 4239 6.612306 AGCCTTCTGTTCGAAATAAATGAAC 58.388 36.000 0.00 0.00 41.75 3.18
4023 4241 6.128007 GGAAGCCTTCTGTTCGAAATAAATGA 60.128 38.462 0.00 0.00 0.00 2.57
4035 4253 0.250338 GTCCGTGGAAGCCTTCTGTT 60.250 55.000 4.15 0.00 0.00 3.16
4040 4258 0.822121 GTTTGGTCCGTGGAAGCCTT 60.822 55.000 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.