Multiple sequence alignment - TraesCS3D01G442000

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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 TraesCS3D01G442000 chr3D 100.000 6463 0 0 1 6463 552004241 551997779 0.000000e+00 11936.0
1 TraesCS3D01G442000 chr3D 80.862 2738 354 88 1156 3814 547298354 547301000 0.000000e+00 1997.0
2 TraesCS3D01G442000 chr3D 83.172 517 74 7 3859 4363 547301003 547301518 1.640000e-125 460.0
3 TraesCS3D01G442000 chr3D 83.122 474 60 11 4786 5241 547301775 547302246 1.300000e-111 414.0
4 TraesCS3D01G442000 chr3A 93.978 3587 126 48 961 4516 688693672 688690145 0.000000e+00 5345.0
5 TraesCS3D01G442000 chr3A 80.394 2744 364 93 1156 3814 684040958 684043612 0.000000e+00 1927.0
6 TraesCS3D01G442000 chr3A 96.291 674 25 0 4574 5247 688690142 688689469 0.000000e+00 1107.0
7 TraesCS3D01G442000 chr3A 86.807 667 36 16 5288 5934 688689463 688688829 0.000000e+00 697.0
8 TraesCS3D01G442000 chr3A 89.245 530 44 9 2 526 688697093 688696572 0.000000e+00 651.0
9 TraesCS3D01G442000 chr3A 82.331 532 78 8 3859 4375 684043615 684044145 1.280000e-121 448.0
10 TraesCS3D01G442000 chr3A 92.038 314 9 6 644 951 688694252 688693949 1.670000e-115 427.0
11 TraesCS3D01G442000 chr3A 82.245 490 62 19 4774 5241 684044380 684044866 3.630000e-107 399.0
12 TraesCS3D01G442000 chr3A 86.792 106 14 0 6347 6452 688687358 688687253 1.140000e-22 119.0
13 TraesCS3D01G442000 chr3A 88.172 93 10 1 6142 6233 688688688 688688596 6.850000e-20 110.0
14 TraesCS3D01G442000 chr3B 91.392 3613 183 69 952 4507 732619521 732615980 0.000000e+00 4831.0
15 TraesCS3D01G442000 chr3B 81.077 2748 344 97 1156 3814 724737747 724740407 0.000000e+00 2032.0
16 TraesCS3D01G442000 chr3B 89.901 812 61 12 1 810 732620761 732619969 0.000000e+00 1026.0
17 TraesCS3D01G442000 chr3B 86.378 969 62 23 5288 6231 732615181 732614258 0.000000e+00 994.0
18 TraesCS3D01G442000 chr3B 96.250 560 21 0 4729 5288 732615780 732615221 0.000000e+00 918.0
19 TraesCS3D01G442000 chr3B 82.798 529 78 10 3859 4375 724740410 724740937 1.640000e-125 460.0
20 TraesCS3D01G442000 chr3B 84.110 472 59 10 4786 5241 724741185 724741656 5.950000e-120 442.0
21 TraesCS3D01G442000 chr3B 89.855 138 14 0 4575 4712 732615981 732615844 1.850000e-40 178.0
22 TraesCS3D01G442000 chr3B 82.178 202 31 5 5043 5241 175096843 175096644 1.110000e-37 169.0
23 TraesCS3D01G442000 chr3B 96.154 52 2 0 6274 6325 732613753 732613702 1.150000e-12 86.1
24 TraesCS3D01G442000 chr7D 80.879 387 52 15 4874 5241 12707764 12707381 1.060000e-72 285.0
25 TraesCS3D01G442000 chr7D 83.929 224 22 12 1156 1375 85519844 85520057 1.100000e-47 202.0
26 TraesCS3D01G442000 chr7D 94.203 69 1 1 4509 4574 236822612 236822680 1.150000e-17 102.0
27 TraesCS3D01G442000 chr4B 84.247 292 32 9 2125 2409 17357145 17357429 8.260000e-69 272.0
28 TraesCS3D01G442000 chr4B 89.855 69 6 1 6354 6422 249049291 249049358 3.210000e-13 87.9
29 TraesCS3D01G442000 chr5D 81.818 297 37 15 1009 1294 562970806 562971096 3.900000e-57 233.0
30 TraesCS3D01G442000 chr5D 90.066 151 10 5 1155 1305 562973534 562973389 2.380000e-44 191.0
31 TraesCS3D01G442000 chr5D 87.662 154 5 3 1361 1514 562973390 562973251 4.010000e-37 167.0
32 TraesCS3D01G442000 chr5D 86.928 153 6 3 1361 1513 562971101 562971239 6.710000e-35 159.0
33 TraesCS3D01G442000 chr5D 90.667 75 4 3 4503 4574 441356334 441356408 5.330000e-16 97.1
34 TraesCS3D01G442000 chr6D 90.972 144 10 3 1156 1298 32521777 32521636 2.380000e-44 191.0
35 TraesCS3D01G442000 chr1A 81.683 202 32 5 5043 5241 244562187 244561988 5.190000e-36 163.0
36 TraesCS3D01G442000 chr7B 81.188 202 33 5 5043 5241 665368491 665368292 2.410000e-34 158.0
37 TraesCS3D01G442000 chr7B 93.243 74 2 3 4507 4578 620597824 620597896 8.860000e-19 106.0
38 TraesCS3D01G442000 chr7B 92.958 71 3 2 4507 4575 744409762 744409692 1.150000e-17 102.0
39 TraesCS3D01G442000 chr6A 92.208 77 4 1 4507 4581 214565316 214565392 2.460000e-19 108.0
40 TraesCS3D01G442000 chr4D 94.030 67 4 0 4509 4575 40796886 40796820 1.150000e-17 102.0
41 TraesCS3D01G442000 chr7A 90.789 76 4 3 4508 4580 135963975 135963900 1.480000e-16 99.0
42 TraesCS3D01G442000 chr2D 90.789 76 2 3 4511 4581 267707165 267707090 5.330000e-16 97.1
43 TraesCS3D01G442000 chr2D 91.667 72 2 2 4507 4578 537496582 537496649 5.330000e-16 97.1


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 TraesCS3D01G442000 chr3D 551997779 552004241 6462 True 11936.000000 11936 100.000000 1 6463 1 chr3D.!!$R1 6462
1 TraesCS3D01G442000 chr3D 547298354 547302246 3892 False 957.000000 1997 82.385333 1156 5241 3 chr3D.!!$F1 4085
2 TraesCS3D01G442000 chr3A 688687253 688697093 9840 True 1208.000000 5345 90.474714 2 6452 7 chr3A.!!$R1 6450
3 TraesCS3D01G442000 chr3A 684040958 684044866 3908 False 924.666667 1927 81.656667 1156 5241 3 chr3A.!!$F1 4085
4 TraesCS3D01G442000 chr3B 732613702 732620761 7059 True 1338.850000 4831 91.655000 1 6325 6 chr3B.!!$R2 6324
5 TraesCS3D01G442000 chr3B 724737747 724741656 3909 False 978.000000 2032 82.661667 1156 5241 3 chr3B.!!$F1 4085

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
640 2891 0.033642 TGTGGTACGCGGTGAATTGA 59.966 50.000 12.47 0.0 45.01 2.57 F
1124 3681 0.257616 CTCCTCCTCCTCCTTCTCGT 59.742 60.000 0.00 0.0 0.00 4.18 F
1125 3682 0.705253 TCCTCCTCCTCCTTCTCGTT 59.295 55.000 0.00 0.0 0.00 3.85 F
1701 4284 1.144276 GAGCCGGAAGTAAGCCCTC 59.856 63.158 5.05 0.0 0.00 4.30 F
3263 5928 0.392595 CTCCTGTTAACCCGCTTCCC 60.393 60.000 2.48 0.0 0.00 3.97 F
4375 7078 0.907486 TTCATGCCAGCTGCTAGTCT 59.093 50.000 8.66 0.0 42.00 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2188 4803 0.247460 TGGTCGGCTTCAGATCACAG 59.753 55.0 0.00 0.0 0.00 3.66 R
2202 4817 1.742761 ATGGTCTGCTCAATTGGTCG 58.257 50.0 5.42 0.0 0.00 4.79 R
2211 4826 2.229784 CCTCCAACAAAATGGTCTGCTC 59.770 50.0 0.00 0.0 41.46 4.26 R
3637 6325 0.181587 TCACGCCTTCCCAACTGAAA 59.818 50.0 0.00 0.0 0.00 2.69 R
4951 7742 0.873312 CGAGCATCATGTCACCCTCG 60.873 60.0 0.00 0.0 36.65 4.63 R
5849 8710 0.036164 AAGCGACAAGGCACCACATA 59.964 50.0 0.00 0.0 34.64 2.29 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
37 38 4.280929 TTCGAAGATGGTCTGAAAGTCAGA 59.719 41.667 3.83 3.83 44.09 3.27
62 63 8.942338 ACCCAAGACTTCAAAAGTTTTATTTC 57.058 30.769 0.00 0.00 43.03 2.17
185 188 7.013655 TCTGAAAGTTCTCCCAAATTTTCTCAG 59.986 37.037 0.00 0.00 36.42 3.35
214 218 3.904136 AAAGCTCACTCCGAAATGTTG 57.096 42.857 0.00 0.00 0.00 3.33
219 223 3.365364 GCTCACTCCGAAATGTTGGAAAG 60.365 47.826 0.00 0.00 32.89 2.62
284 288 6.264292 TGAAATTCCTTGAATCTCAAAACCGA 59.736 34.615 0.00 0.00 35.73 4.69
292 296 2.178912 TCTCAAAACCGATCACCCAC 57.821 50.000 0.00 0.00 0.00 4.61
377 381 6.619874 GCAATGTCGAAAACGAGGAATTTCTA 60.620 38.462 0.00 0.00 34.22 2.10
406 410 2.271800 GTAAGACGCCTCCATTGTCAG 58.728 52.381 0.00 0.00 35.09 3.51
455 462 1.983224 CCCTTCACATCACCCGACT 59.017 57.895 0.00 0.00 0.00 4.18
462 469 3.771160 ATCACCCGACTGACGCCC 61.771 66.667 0.00 0.00 41.07 6.13
505 512 6.699642 AGAAATTAGATCTTCTAGCAAGACGC 59.300 38.462 0.00 3.92 42.91 5.19
516 523 1.868997 CAAGACGCTCACCGCATTT 59.131 52.632 0.00 0.00 41.76 2.32
527 534 3.223435 TCACCGCATTTCCCAAGTAAAA 58.777 40.909 0.00 0.00 0.00 1.52
555 2801 5.789710 ATACGTAAAAAGAATCACCACGG 57.210 39.130 0.00 0.00 32.52 4.94
640 2891 0.033642 TGTGGTACGCGGTGAATTGA 59.966 50.000 12.47 0.00 45.01 2.57
642 2893 0.390603 TGGTACGCGGTGAATTGAGG 60.391 55.000 12.47 0.00 0.00 3.86
667 2918 1.402259 GAGAGACAGGCGATCGAGAAA 59.598 52.381 21.57 0.00 0.00 2.52
677 2928 7.251994 ACAGGCGATCGAGAAATATTATACTC 58.748 38.462 21.57 0.00 0.00 2.59
846 3098 4.261801 AGAGACCACCACCAAATTAATCG 58.738 43.478 0.00 0.00 0.00 3.34
853 3105 0.634465 ACCAAATTAATCGGCCCCCT 59.366 50.000 0.00 0.00 0.00 4.79
854 3106 1.328279 CCAAATTAATCGGCCCCCTC 58.672 55.000 0.00 0.00 0.00 4.30
914 3171 2.819117 TTCTACTGACGCTGCCGCTG 62.819 60.000 0.00 0.00 38.22 5.18
951 3208 1.306226 ACTCCCCTTTCCCTCCTCG 60.306 63.158 0.00 0.00 0.00 4.63
952 3209 1.001760 CTCCCCTTTCCCTCCTCGA 59.998 63.158 0.00 0.00 0.00 4.04
953 3210 1.305887 TCCCCTTTCCCTCCTCGAC 60.306 63.158 0.00 0.00 0.00 4.20
954 3211 2.368011 CCCCTTTCCCTCCTCGACC 61.368 68.421 0.00 0.00 0.00 4.79
955 3212 2.368011 CCCTTTCCCTCCTCGACCC 61.368 68.421 0.00 0.00 0.00 4.46
956 3213 2.368011 CCTTTCCCTCCTCGACCCC 61.368 68.421 0.00 0.00 0.00 4.95
957 3214 2.682494 TTTCCCTCCTCGACCCCG 60.682 66.667 0.00 0.00 37.07 5.73
1102 3659 2.124151 CCCCTTTCCGGCTCCATG 60.124 66.667 0.00 0.00 0.00 3.66
1103 3660 2.124151 CCCTTTCCGGCTCCATGG 60.124 66.667 4.97 4.97 0.00 3.66
1117 3674 0.762461 CCATGGTCTCCTCCTCCTCC 60.762 65.000 2.57 0.00 0.00 4.30
1118 3675 0.264359 CATGGTCTCCTCCTCCTCCT 59.736 60.000 0.00 0.00 0.00 3.69
1119 3676 1.022903 ATGGTCTCCTCCTCCTCCTT 58.977 55.000 0.00 0.00 0.00 3.36
1120 3677 0.336737 TGGTCTCCTCCTCCTCCTTC 59.663 60.000 0.00 0.00 0.00 3.46
1121 3678 0.634465 GGTCTCCTCCTCCTCCTTCT 59.366 60.000 0.00 0.00 0.00 2.85
1122 3679 1.411074 GGTCTCCTCCTCCTCCTTCTC 60.411 61.905 0.00 0.00 0.00 2.87
1123 3680 0.548989 TCTCCTCCTCCTCCTTCTCG 59.451 60.000 0.00 0.00 0.00 4.04
1124 3681 0.257616 CTCCTCCTCCTCCTTCTCGT 59.742 60.000 0.00 0.00 0.00 4.18
1125 3682 0.705253 TCCTCCTCCTCCTTCTCGTT 59.295 55.000 0.00 0.00 0.00 3.85
1276 3833 3.077556 ATCGAGCAGGTCCGCCTT 61.078 61.111 0.00 0.00 44.18 4.35
1309 3869 2.787866 CCCTCCCTTCCTCCCTCA 59.212 66.667 0.00 0.00 0.00 3.86
1310 3870 1.690985 CCCTCCCTTCCTCCCTCAC 60.691 68.421 0.00 0.00 0.00 3.51
1311 3871 1.690985 CCTCCCTTCCTCCCTCACC 60.691 68.421 0.00 0.00 0.00 4.02
1516 4087 1.903877 GCTCAAGGTGCCTGCCTCTA 61.904 60.000 0.00 0.00 38.03 2.43
1520 4091 3.798511 GGTGCCTGCCTCTACCCC 61.799 72.222 0.00 0.00 0.00 4.95
1521 4092 2.689034 GTGCCTGCCTCTACCCCT 60.689 66.667 0.00 0.00 0.00 4.79
1526 4097 1.458588 CTGCCTCTACCCCTCCCTC 60.459 68.421 0.00 0.00 0.00 4.30
1571 4142 1.675720 CCGCCCAATTTCCACATCCC 61.676 60.000 0.00 0.00 0.00 3.85
1622 4205 3.058914 CGGCTCACTTTTTCTGTCGATTT 60.059 43.478 0.00 0.00 0.00 2.17
1623 4206 4.554723 CGGCTCACTTTTTCTGTCGATTTT 60.555 41.667 0.00 0.00 0.00 1.82
1701 4284 1.144276 GAGCCGGAAGTAAGCCCTC 59.856 63.158 5.05 0.00 0.00 4.30
1702 4285 1.306226 AGCCGGAAGTAAGCCCTCT 60.306 57.895 5.05 0.00 0.00 3.69
1706 4289 1.386533 CGGAAGTAAGCCCTCTCGTA 58.613 55.000 0.00 0.00 0.00 3.43
1716 4299 2.091555 AGCCCTCTCGTAAATCTCTCCT 60.092 50.000 0.00 0.00 0.00 3.69
1717 4300 2.696187 GCCCTCTCGTAAATCTCTCCTT 59.304 50.000 0.00 0.00 0.00 3.36
1726 4309 6.472887 TCGTAAATCTCTCCTTCCAAAATGT 58.527 36.000 0.00 0.00 0.00 2.71
1753 4345 3.633986 GGGATTTTATTCTGCTCCAGGTG 59.366 47.826 0.00 0.00 31.51 4.00
1754 4346 4.273318 GGATTTTATTCTGCTCCAGGTGT 58.727 43.478 0.00 0.00 31.51 4.16
1756 4348 5.885912 GGATTTTATTCTGCTCCAGGTGTTA 59.114 40.000 0.00 0.00 31.51 2.41
1757 4349 6.377146 GGATTTTATTCTGCTCCAGGTGTTAA 59.623 38.462 0.00 0.00 31.51 2.01
1758 4350 6.817765 TTTTATTCTGCTCCAGGTGTTAAG 57.182 37.500 0.00 0.00 31.51 1.85
1759 4351 5.755409 TTATTCTGCTCCAGGTGTTAAGA 57.245 39.130 0.00 0.00 31.51 2.10
1761 4353 1.623811 TCTGCTCCAGGTGTTAAGACC 59.376 52.381 13.87 13.87 36.09 3.85
1788 4401 2.595124 TTCAGCAAAGTGAGACGACA 57.405 45.000 0.00 0.00 0.00 4.35
2148 4762 2.738587 TTGTGTTCCTTGCCTTACCA 57.261 45.000 0.00 0.00 0.00 3.25
2167 4782 5.241403 ACCATGATCTGTACCACTTTGAA 57.759 39.130 0.00 0.00 0.00 2.69
2187 4802 4.570369 TGAAATCGCCATGTATATATGCCG 59.430 41.667 6.51 6.51 30.95 5.69
2188 4803 1.934589 TCGCCATGTATATATGCCGC 58.065 50.000 7.81 4.72 29.94 6.53
2202 4817 2.467826 GCCGCTGTGATCTGAAGCC 61.468 63.158 8.60 0.00 33.24 4.35
2211 4826 2.096496 GTGATCTGAAGCCGACCAATTG 59.904 50.000 0.00 0.00 0.00 2.32
2229 4844 3.731652 TTGAGCAGACCATTTTGTTGG 57.268 42.857 0.00 0.00 42.82 3.77
2244 4859 7.093771 CCATTTTGTTGGAGGAGCTTAGTTATT 60.094 37.037 0.00 0.00 39.25 1.40
2420 5044 3.096092 TGTCAGTTCCAAAAGGCTTGTT 58.904 40.909 0.00 0.00 0.00 2.83
2477 5102 2.892852 TGTTTCCTTTCTCCCAAGCATG 59.107 45.455 0.00 0.00 0.00 4.06
2683 5323 4.202284 TGTTCACTGTCTACTACAAACCCC 60.202 45.833 0.00 0.00 37.74 4.95
2693 5340 4.950205 ACTACAAACCCCGGTATATCAG 57.050 45.455 0.00 0.00 0.00 2.90
2777 5427 8.027771 CGTTCTGAGTACTTACCTTGTCTAATT 58.972 37.037 0.00 0.00 0.00 1.40
2936 5596 6.327279 GGTAACTGTTGTATTTGCTTTCCT 57.673 37.500 2.69 0.00 0.00 3.36
2973 5633 3.010027 TGTTTGCATTATCCCCTGACAGA 59.990 43.478 3.32 0.00 0.00 3.41
3004 5666 6.150976 GTCATCATTTGTAATCTGTTGTCCCA 59.849 38.462 0.00 0.00 0.00 4.37
3026 5688 5.125417 CCATTTGTCATGTAGGTTTACTGGG 59.875 44.000 0.00 0.00 0.00 4.45
3145 5810 4.295051 GTCGGAAGAGTCTCATGCTTATC 58.705 47.826 1.94 0.00 43.49 1.75
3263 5928 0.392595 CTCCTGTTAACCCGCTTCCC 60.393 60.000 2.48 0.00 0.00 3.97
3264 5929 1.128809 TCCTGTTAACCCGCTTCCCA 61.129 55.000 2.48 0.00 0.00 4.37
3365 6037 6.166279 TCATTGTTAGTCTTACTGGAAGCTG 58.834 40.000 0.00 0.00 37.60 4.24
3367 6039 3.901844 TGTTAGTCTTACTGGAAGCTGGT 59.098 43.478 0.00 0.00 37.60 4.00
3368 6040 4.246458 GTTAGTCTTACTGGAAGCTGGTG 58.754 47.826 0.00 0.00 37.60 4.17
3369 6041 2.609747 AGTCTTACTGGAAGCTGGTGA 58.390 47.619 0.00 0.00 37.60 4.02
3372 6044 4.042187 AGTCTTACTGGAAGCTGGTGAAAT 59.958 41.667 0.00 0.00 37.60 2.17
3378 6050 6.029346 ACTGGAAGCTGGTGAAATAAAATG 57.971 37.500 0.00 0.00 37.60 2.32
3539 6224 8.206325 ACTGACATTAATGACTTTGATGCTAG 57.794 34.615 22.16 8.18 35.31 3.42
3637 6325 1.668419 GCCCTCTGTGCATAATTCGT 58.332 50.000 0.00 0.00 0.00 3.85
3883 6571 3.473923 TGCACACAGAGAACAATGAGA 57.526 42.857 0.00 0.00 0.00 3.27
3916 6604 4.735132 GGCCGAGCACTGCGTACA 62.735 66.667 0.00 0.00 0.00 2.90
4374 7077 1.012841 GTTCATGCCAGCTGCTAGTC 58.987 55.000 8.66 0.00 42.00 2.59
4375 7078 0.907486 TTCATGCCAGCTGCTAGTCT 59.093 50.000 8.66 0.00 42.00 3.24
4376 7079 0.907486 TCATGCCAGCTGCTAGTCTT 59.093 50.000 8.66 0.00 42.00 3.01
4377 7080 2.110578 TCATGCCAGCTGCTAGTCTTA 58.889 47.619 8.66 0.00 42.00 2.10
4415 7118 6.503524 TGTTTCTGTGGCATTTTCTTACTTC 58.496 36.000 0.00 0.00 0.00 3.01
4418 7121 4.216257 TCTGTGGCATTTTCTTACTTCTGC 59.784 41.667 0.00 0.00 0.00 4.26
4524 7228 6.370186 AATATTAAATACTCCCTCCGTCCC 57.630 41.667 0.00 0.00 0.00 4.46
4525 7229 2.852714 TAAATACTCCCTCCGTCCCA 57.147 50.000 0.00 0.00 0.00 4.37
4526 7230 2.191981 AAATACTCCCTCCGTCCCAT 57.808 50.000 0.00 0.00 0.00 4.00
4527 7231 3.339713 AAATACTCCCTCCGTCCCATA 57.660 47.619 0.00 0.00 0.00 2.74
4528 7232 3.339713 AATACTCCCTCCGTCCCATAA 57.660 47.619 0.00 0.00 0.00 1.90
4529 7233 3.562108 ATACTCCCTCCGTCCCATAAT 57.438 47.619 0.00 0.00 0.00 1.28
4530 7234 4.687262 ATACTCCCTCCGTCCCATAATA 57.313 45.455 0.00 0.00 0.00 0.98
4531 7235 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
4532 7236 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
4533 7237 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
4534 7238 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
4535 7239 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
4536 7240 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
4537 7241 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
4538 7242 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
4539 7243 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
4540 7244 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
4541 7245 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
4542 7246 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
4543 7247 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
4544 7248 7.069569 CGTCCCATAATATAAGAGCGTTTTTG 58.930 38.462 0.00 0.00 0.00 2.44
4545 7249 7.042321 CGTCCCATAATATAAGAGCGTTTTTGA 60.042 37.037 0.00 0.00 0.00 2.69
4546 7250 8.068380 GTCCCATAATATAAGAGCGTTTTTGAC 58.932 37.037 0.00 0.00 0.00 3.18
4547 7251 7.227910 TCCCATAATATAAGAGCGTTTTTGACC 59.772 37.037 0.00 0.00 0.00 4.02
4548 7252 7.228706 CCCATAATATAAGAGCGTTTTTGACCT 59.771 37.037 0.00 0.00 0.00 3.85
4549 7253 8.283291 CCATAATATAAGAGCGTTTTTGACCTC 58.717 37.037 0.00 0.00 0.00 3.85
4550 7254 9.046296 CATAATATAAGAGCGTTTTTGACCTCT 57.954 33.333 0.00 0.00 37.44 3.69
4551 7255 7.923414 AATATAAGAGCGTTTTTGACCTCTT 57.077 32.000 6.92 6.92 42.89 2.85
4553 7257 9.614792 AATATAAGAGCGTTTTTGACCTCTTAT 57.385 29.630 19.50 19.50 46.50 1.73
4556 7260 7.923414 AAGAGCGTTTTTGACCTCTTATATT 57.077 32.000 0.00 0.00 40.75 1.28
4558 7262 9.614792 AAGAGCGTTTTTGACCTCTTATATTAT 57.385 29.630 0.00 0.00 40.75 1.28
4559 7263 9.046296 AGAGCGTTTTTGACCTCTTATATTATG 57.954 33.333 0.00 0.00 34.34 1.90
4560 7264 8.154649 AGCGTTTTTGACCTCTTATATTATGG 57.845 34.615 0.00 0.00 0.00 2.74
4561 7265 7.228706 AGCGTTTTTGACCTCTTATATTATGGG 59.771 37.037 0.00 0.00 0.00 4.00
4562 7266 7.227910 GCGTTTTTGACCTCTTATATTATGGGA 59.772 37.037 0.00 0.00 0.00 4.37
4563 7267 8.774586 CGTTTTTGACCTCTTATATTATGGGAG 58.225 37.037 0.00 0.00 0.00 4.30
4564 7268 9.067986 GTTTTTGACCTCTTATATTATGGGAGG 57.932 37.037 17.66 17.66 46.27 4.30
4565 7269 6.952605 TTGACCTCTTATATTATGGGAGGG 57.047 41.667 20.72 10.29 45.44 4.30
4566 7270 6.241223 TGACCTCTTATATTATGGGAGGGA 57.759 41.667 20.72 10.96 45.44 4.20
4567 7271 6.264528 TGACCTCTTATATTATGGGAGGGAG 58.735 44.000 20.72 0.00 45.44 4.30
4568 7272 5.604752 ACCTCTTATATTATGGGAGGGAGG 58.395 45.833 20.72 0.00 45.44 4.30
4569 7273 4.971924 CCTCTTATATTATGGGAGGGAGGG 59.028 50.000 14.11 0.00 39.67 4.30
4570 7274 5.282832 CCTCTTATATTATGGGAGGGAGGGA 60.283 48.000 14.11 0.00 39.67 4.20
4571 7275 5.854843 TCTTATATTATGGGAGGGAGGGAG 58.145 45.833 0.00 0.00 0.00 4.30
4572 7276 5.321625 TCTTATATTATGGGAGGGAGGGAGT 59.678 44.000 0.00 0.00 0.00 3.85
4601 7305 3.312828 TGCCGAAAACATTTGAATTCCG 58.687 40.909 2.27 0.00 0.00 4.30
4664 7368 7.192852 AGGCTGACTGATATTAGGGATTATG 57.807 40.000 0.00 0.00 0.00 1.90
4761 7512 3.070446 TGGGATCGTATCGCATAACCTTT 59.930 43.478 9.44 0.00 45.72 3.11
4796 7587 8.154203 TGATATATGTATCGTCCATGGTTTTGT 58.846 33.333 12.58 0.00 39.69 2.83
4910 7701 6.219417 TGTTTGAATTTGATGGTGAACTGT 57.781 33.333 0.00 0.00 0.00 3.55
4939 7730 5.355596 TCAAACAAAAATTGGCAGATCGTT 58.644 33.333 0.00 0.00 34.12 3.85
4951 7742 4.868171 TGGCAGATCGTTTATACTGACAAC 59.132 41.667 0.00 0.00 43.95 3.32
5032 7828 2.639839 TGCTTAGCAGAACTTCCCTTCT 59.360 45.455 1.39 0.00 33.32 2.85
5045 7841 9.994017 AGAACTTCCCTTCTTAGTACTAATACT 57.006 33.333 15.57 0.00 44.22 2.12
5147 7955 0.111446 TCGAAACCATCTGGCCCAAA 59.889 50.000 0.00 0.00 39.32 3.28
5372 8221 0.940126 GCTATCACAAGCATCACCCG 59.060 55.000 0.00 0.00 42.30 5.28
5427 8276 0.946221 CGGTCTCTGCAGGTTGTGTC 60.946 60.000 15.13 0.00 0.00 3.67
5492 8343 4.098807 GCAAAGAAGTAACAACCCCTGAAA 59.901 41.667 0.00 0.00 0.00 2.69
5504 8355 5.104485 ACAACCCCTGAAAGTATGGTCTATC 60.104 44.000 0.00 0.00 29.52 2.08
5538 8391 1.303282 GATCACCACCAACTCCCCC 59.697 63.158 0.00 0.00 0.00 5.40
5541 8394 2.038762 ACCACCAACTCCCCCACT 60.039 61.111 0.00 0.00 0.00 4.00
5543 8396 2.757077 CACCAACTCCCCCACTCC 59.243 66.667 0.00 0.00 0.00 3.85
5635 8488 2.542907 CGCTTGTCGGCTGGTTTGT 61.543 57.895 0.00 0.00 33.78 2.83
5653 8506 1.815613 TGTTCTTCGGCAGAGAGAGAG 59.184 52.381 0.00 0.00 31.12 3.20
5654 8507 2.088423 GTTCTTCGGCAGAGAGAGAGA 58.912 52.381 0.00 0.00 31.12 3.10
5657 8510 1.608590 CTTCGGCAGAGAGAGAGATCC 59.391 57.143 0.00 0.00 0.00 3.36
5783 8636 2.307496 AACCATCCATGAACCAGCAA 57.693 45.000 0.00 0.00 0.00 3.91
5828 8689 6.145338 ACAGTGGTAGTAGTACATGTATGC 57.855 41.667 9.18 2.77 0.00 3.14
5833 8694 5.301045 TGGTAGTAGTACATGTATGCCTGAC 59.699 44.000 9.18 3.90 0.00 3.51
5835 8696 2.890808 AGTACATGTATGCCTGACCG 57.109 50.000 9.18 0.00 0.00 4.79
5836 8697 2.384828 AGTACATGTATGCCTGACCGA 58.615 47.619 9.18 0.00 0.00 4.69
5837 8698 2.965831 AGTACATGTATGCCTGACCGAT 59.034 45.455 9.18 0.00 0.00 4.18
5849 8710 3.873910 CCTGACCGATCCTGTTTAATGT 58.126 45.455 0.00 0.00 0.00 2.71
5870 8743 3.286751 TGGTGCCTTGTCGCTTGC 61.287 61.111 0.00 0.00 0.00 4.01
5887 8760 2.839098 CTGTGGAGTTGGCAGGGT 59.161 61.111 0.00 0.00 0.00 4.34
5924 8797 6.381481 TCTCGACCGTATGTATAAACACAT 57.619 37.500 0.00 0.00 41.88 3.21
5928 8801 6.638063 TCGACCGTATGTATAAACACATAAGC 59.362 38.462 0.00 0.00 41.74 3.09
5933 8806 8.697067 CCGTATGTATAAACACATAAGCAGTAC 58.303 37.037 0.00 0.00 41.74 2.73
5934 8807 9.459640 CGTATGTATAAACACATAAGCAGTACT 57.540 33.333 0.00 0.00 41.74 2.73
5942 8815 4.770531 ACACATAAGCAGTACTGTACCTGA 59.229 41.667 23.44 6.62 0.00 3.86
5962 8835 0.840288 TGTGGTAGGGCATCACTGGT 60.840 55.000 0.00 0.00 33.04 4.00
5963 8836 0.107654 GTGGTAGGGCATCACTGGTC 60.108 60.000 0.00 0.00 0.00 4.02
5964 8837 1.144057 GGTAGGGCATCACTGGTCG 59.856 63.158 0.00 0.00 0.00 4.79
5965 8838 1.521681 GTAGGGCATCACTGGTCGC 60.522 63.158 0.00 0.00 0.00 5.19
5966 8839 1.685765 TAGGGCATCACTGGTCGCT 60.686 57.895 0.00 0.00 0.00 4.93
5968 8841 2.821366 GGCATCACTGGTCGCTGG 60.821 66.667 0.00 0.00 0.00 4.85
5969 8842 2.265739 GCATCACTGGTCGCTGGA 59.734 61.111 0.00 0.00 0.00 3.86
5992 8865 1.153046 CCACCGAACTGTGTGGGTT 60.153 57.895 7.67 0.00 46.67 4.11
5993 8866 0.750182 CCACCGAACTGTGTGGGTTT 60.750 55.000 7.67 0.00 46.67 3.27
5995 8868 0.253610 ACCGAACTGTGTGGGTTTGA 59.746 50.000 3.93 0.00 31.65 2.69
5996 8869 0.944386 CCGAACTGTGTGGGTTTGAG 59.056 55.000 0.00 0.00 31.65 3.02
5997 8870 0.307760 CGAACTGTGTGGGTTTGAGC 59.692 55.000 0.00 0.00 31.65 4.26
5998 8871 0.668535 GAACTGTGTGGGTTTGAGCC 59.331 55.000 0.00 0.00 36.00 4.70
6000 8873 0.258774 ACTGTGTGGGTTTGAGCCTT 59.741 50.000 0.00 0.00 36.53 4.35
6001 8874 0.954452 CTGTGTGGGTTTGAGCCTTC 59.046 55.000 0.00 0.00 36.53 3.46
6002 8875 0.817634 TGTGTGGGTTTGAGCCTTCG 60.818 55.000 0.00 0.00 36.53 3.79
6008 8881 2.034066 TTTGAGCCTTCGCCCCTG 59.966 61.111 0.00 0.00 34.57 4.45
6050 8923 1.849219 GTCTCGATCGATCAACAGCAC 59.151 52.381 24.40 12.21 0.00 4.40
6053 8926 1.638467 GATCGATCAACAGCACGCC 59.362 57.895 20.52 0.00 0.00 5.68
6082 8955 7.661847 CACAAGATCTCACCTACCTTTTTAAGT 59.338 37.037 0.00 0.00 0.00 2.24
6087 8960 4.648651 TCACCTACCTTTTTAAGTGCTCC 58.351 43.478 0.00 0.00 0.00 4.70
6090 8963 5.181433 CACCTACCTTTTTAAGTGCTCCTTC 59.819 44.000 0.00 0.00 34.46 3.46
6099 8972 2.119801 AGTGCTCCTTCGATGCAAAT 57.880 45.000 0.00 0.00 38.50 2.32
6101 8974 1.097232 TGCTCCTTCGATGCAAATGG 58.903 50.000 0.00 0.00 33.48 3.16
6107 8980 3.065233 TCCTTCGATGCAAATGGATTTCG 59.935 43.478 0.00 0.00 0.00 3.46
6122 8995 3.005578 GGATTTCGTAGGCCTTCGAGTAT 59.994 47.826 29.58 25.63 37.38 2.12
6125 8998 4.460948 TTCGTAGGCCTTCGAGTATTTT 57.539 40.909 29.58 0.00 37.38 1.82
6158 9155 4.697352 AGATGTTTGGAATCCTCGTGAAAG 59.303 41.667 0.00 0.00 0.00 2.62
6201 9199 6.934083 TGCACCCTATTTTGAAGGAAAATTTC 59.066 34.615 0.00 0.00 40.73 2.17
6236 9236 9.083080 CAAACTTCTTACGATTCCTTTGTTTTT 57.917 29.630 0.00 0.00 0.00 1.94
6238 9238 8.221965 ACTTCTTACGATTCCTTTGTTTTTCT 57.778 30.769 0.00 0.00 0.00 2.52
6257 9257 0.396435 TGCGTCATCAAACACCCTCT 59.604 50.000 0.00 0.00 0.00 3.69
6258 9258 1.079503 GCGTCATCAAACACCCTCTC 58.920 55.000 0.00 0.00 0.00 3.20
6262 9262 2.028930 GTCATCAAACACCCTCTCGTCT 60.029 50.000 0.00 0.00 0.00 4.18
6271 9271 2.117051 ACCCTCTCGTCTAAATTCCCC 58.883 52.381 0.00 0.00 0.00 4.81
6272 9272 1.416772 CCCTCTCGTCTAAATTCCCCC 59.583 57.143 0.00 0.00 0.00 5.40
6286 9636 4.618378 ATTCCCCCTGGTTTGCTAATTA 57.382 40.909 0.00 0.00 0.00 1.40
6334 9686 6.542370 CCACTTCCATCCTGTATTTTTCGTAT 59.458 38.462 0.00 0.00 0.00 3.06
6366 10812 1.964933 GAAATACGAGGAGGAGGAGGG 59.035 57.143 0.00 0.00 0.00 4.30
6367 10813 0.470268 AATACGAGGAGGAGGAGGGC 60.470 60.000 0.00 0.00 0.00 5.19
6427 10873 4.996434 ATGCCCGATGCGCTAGGC 62.996 66.667 19.23 19.23 45.60 3.93
6438 10884 1.450025 GCGCTAGGCAAGTTTAAGGT 58.550 50.000 0.00 0.00 42.87 3.50
6440 10886 1.659098 CGCTAGGCAAGTTTAAGGTCG 59.341 52.381 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 5.551233 TGACTTTCAGACCATCTTCGAAAT 58.449 37.500 0.00 0.00 0.00 2.17
37 38 7.985184 GGAAATAAAACTTTTGAAGTCTTGGGT 59.015 33.333 0.00 0.00 41.91 4.51
62 63 6.442952 TCAACAACGTTTTTGAATATCCAGG 58.557 36.000 23.67 0.00 0.00 4.45
219 223 5.356470 AGATTCAACTAAGAAGCCAAGATGC 59.644 40.000 0.00 0.00 34.59 3.91
255 259 9.399403 GTTTTGAGATTCAAGGAATTTCAGTAC 57.601 33.333 10.72 9.58 41.70 2.73
259 263 6.264292 TCGGTTTTGAGATTCAAGGAATTTCA 59.736 34.615 7.78 7.78 39.99 2.69
264 268 5.181245 GTGATCGGTTTTGAGATTCAAGGAA 59.819 40.000 0.00 0.00 37.70 3.36
284 288 3.165071 GGGAAAAGAATGTGTGGGTGAT 58.835 45.455 0.00 0.00 0.00 3.06
292 296 8.380644 CGCGTATATTATAGGGAAAAGAATGTG 58.619 37.037 0.00 0.00 0.00 3.21
345 349 2.136196 TTTTCGACATTGCCGTGCCC 62.136 55.000 0.00 0.00 0.00 5.36
346 350 1.001745 GTTTTCGACATTGCCGTGCC 61.002 55.000 0.00 0.00 0.00 5.01
347 351 2.420097 GTTTTCGACATTGCCGTGC 58.580 52.632 0.00 0.00 0.00 5.34
377 381 1.808390 GGCGTCTTACGGTTGCGAT 60.808 57.895 1.25 0.00 42.82 4.58
406 410 1.192428 ACCATCCGGTGTAAGAGTCC 58.808 55.000 0.00 0.00 46.79 3.85
425 432 2.990977 TGAAGGGCCTTCATCGAGA 58.009 52.632 38.53 19.67 44.27 4.04
455 462 0.320374 CTGAGGTTTAGTGGGCGTCA 59.680 55.000 0.00 0.00 0.00 4.35
462 469 6.884280 ATTTCTTGGAACTGAGGTTTAGTG 57.116 37.500 0.00 0.00 35.58 2.74
505 512 2.107950 TACTTGGGAAATGCGGTGAG 57.892 50.000 0.00 0.00 0.00 3.51
531 538 6.183360 GCCGTGGTGATTCTTTTTACGTATTA 60.183 38.462 0.00 0.00 0.00 0.98
534 2780 3.432933 GCCGTGGTGATTCTTTTTACGTA 59.567 43.478 0.00 0.00 0.00 3.57
536 2782 2.224549 TGCCGTGGTGATTCTTTTTACG 59.775 45.455 0.00 0.00 0.00 3.18
555 2801 2.706890 TGTTCCCTCGAATTACCTTGC 58.293 47.619 0.00 0.00 0.00 4.01
640 2891 2.366570 GCCTGTCTCTCTCCCCCT 59.633 66.667 0.00 0.00 0.00 4.79
642 2893 1.456705 ATCGCCTGTCTCTCTCCCC 60.457 63.158 0.00 0.00 0.00 4.81
667 2918 7.033791 CCCGATTAACGCACAGAGTATAATAT 58.966 38.462 0.00 0.00 41.07 1.28
677 2928 3.808036 CCCCCGATTAACGCACAG 58.192 61.111 0.00 0.00 41.07 3.66
853 3105 3.752167 GAGGAGGAGGACGGGGGA 61.752 72.222 0.00 0.00 0.00 4.81
854 3106 4.862823 GGAGGAGGAGGACGGGGG 62.863 77.778 0.00 0.00 0.00 5.40
1095 3652 1.406860 GGAGGAGGAGACCATGGAGC 61.407 65.000 21.47 10.13 0.00 4.70
1100 3657 1.022903 AAGGAGGAGGAGGAGACCAT 58.977 55.000 0.00 0.00 0.00 3.55
1102 3659 0.634465 AGAAGGAGGAGGAGGAGACC 59.366 60.000 0.00 0.00 0.00 3.85
1103 3660 1.749286 CGAGAAGGAGGAGGAGGAGAC 60.749 61.905 0.00 0.00 0.00 3.36
1117 3674 0.241213 TCAGGCACGAGAACGAGAAG 59.759 55.000 0.00 0.00 42.66 2.85
1118 3675 0.888619 ATCAGGCACGAGAACGAGAA 59.111 50.000 0.00 0.00 42.66 2.87
1119 3676 0.171231 CATCAGGCACGAGAACGAGA 59.829 55.000 0.00 0.00 42.66 4.04
1120 3677 0.109086 ACATCAGGCACGAGAACGAG 60.109 55.000 0.00 0.00 42.66 4.18
1121 3678 0.109272 GACATCAGGCACGAGAACGA 60.109 55.000 0.00 0.00 42.66 3.85
1122 3679 0.109086 AGACATCAGGCACGAGAACG 60.109 55.000 0.00 0.00 45.75 3.95
1123 3680 1.634702 GAGACATCAGGCACGAGAAC 58.365 55.000 0.00 0.00 0.00 3.01
1124 3681 0.171231 CGAGACATCAGGCACGAGAA 59.829 55.000 0.00 0.00 0.00 2.87
1125 3682 0.960861 ACGAGACATCAGGCACGAGA 60.961 55.000 0.00 0.00 0.00 4.04
1283 3842 2.285743 AAGGGAGGGGAGGAGTGC 60.286 66.667 0.00 0.00 0.00 4.40
1284 3843 1.690985 GGAAGGGAGGGGAGGAGTG 60.691 68.421 0.00 0.00 0.00 3.51
1285 3844 1.869452 AGGAAGGGAGGGGAGGAGT 60.869 63.158 0.00 0.00 0.00 3.85
1287 3846 2.647949 GGAGGAAGGGAGGGGAGGA 61.648 68.421 0.00 0.00 0.00 3.71
1289 3848 2.040359 GGGAGGAAGGGAGGGGAG 60.040 72.222 0.00 0.00 0.00 4.30
1311 3871 3.930012 GAATCGCGGGAGGGGAGG 61.930 72.222 6.13 0.00 41.34 4.30
1355 3922 3.651480 AATTCAGCGCGCGAACTGC 62.651 57.895 37.18 16.01 41.47 4.40
1356 3923 1.122419 GAAATTCAGCGCGCGAACTG 61.122 55.000 37.18 30.20 35.15 3.16
1357 3924 1.132640 GAAATTCAGCGCGCGAACT 59.867 52.632 37.18 20.06 0.00 3.01
1571 4142 1.491274 AATTTTGGGGCAGGGCAAGG 61.491 55.000 0.00 0.00 0.00 3.61
1701 4284 6.595716 ACATTTTGGAAGGAGAGATTTACGAG 59.404 38.462 0.00 0.00 0.00 4.18
1702 4285 6.472887 ACATTTTGGAAGGAGAGATTTACGA 58.527 36.000 0.00 0.00 0.00 3.43
1726 4309 5.090139 TGGAGCAGAATAAAATCCCCAAAA 58.910 37.500 0.00 0.00 0.00 2.44
1739 4331 3.307762 GGTCTTAACACCTGGAGCAGAAT 60.308 47.826 0.00 0.00 32.44 2.40
1753 4345 8.135529 ACTTTGCTGAAAAATACTGGTCTTAAC 58.864 33.333 0.00 0.00 0.00 2.01
1754 4346 8.134895 CACTTTGCTGAAAAATACTGGTCTTAA 58.865 33.333 0.00 0.00 0.00 1.85
1756 4348 6.321181 TCACTTTGCTGAAAAATACTGGTCTT 59.679 34.615 0.00 0.00 0.00 3.01
1757 4349 5.827797 TCACTTTGCTGAAAAATACTGGTCT 59.172 36.000 0.00 0.00 0.00 3.85
1758 4350 6.017109 TCTCACTTTGCTGAAAAATACTGGTC 60.017 38.462 0.00 0.00 0.00 4.02
1759 4351 5.827797 TCTCACTTTGCTGAAAAATACTGGT 59.172 36.000 0.00 0.00 0.00 4.00
1761 4353 5.848036 CGTCTCACTTTGCTGAAAAATACTG 59.152 40.000 0.00 0.00 0.00 2.74
1788 4401 1.606889 AGGGCTCGACTTCTCCGTT 60.607 57.895 0.00 0.00 0.00 4.44
2127 4741 3.366396 TGGTAAGGCAAGGAACACAAAA 58.634 40.909 0.00 0.00 0.00 2.44
2148 4762 5.065218 GCGATTTCAAAGTGGTACAGATCAT 59.935 40.000 0.00 0.00 41.80 2.45
2187 4802 1.086634 GGTCGGCTTCAGATCACAGC 61.087 60.000 0.00 0.00 0.00 4.40
2188 4803 0.247460 TGGTCGGCTTCAGATCACAG 59.753 55.000 0.00 0.00 0.00 3.66
2202 4817 1.742761 ATGGTCTGCTCAATTGGTCG 58.257 50.000 5.42 0.00 0.00 4.79
2211 4826 2.229784 CCTCCAACAAAATGGTCTGCTC 59.770 50.000 0.00 0.00 41.46 4.26
2229 4844 7.042389 GCATTGTCAGTAATAACTAAGCTCCTC 60.042 40.741 0.00 0.00 33.48 3.71
2420 5044 2.424842 AAATGAAGGCGTCCCCAGCA 62.425 55.000 0.00 0.00 36.08 4.41
2477 5102 2.433436 AGTAACGAACTGGGAATTGGC 58.567 47.619 0.00 0.00 36.93 4.52
2649 5289 7.051623 AGTAGACAGTGAACATGGTTTTTGTA 58.948 34.615 0.00 0.00 0.00 2.41
2683 5323 3.681897 GCCAAAGAGATGCTGATATACCG 59.318 47.826 0.00 0.00 0.00 4.02
2693 5340 4.792057 GCAGTATGATTGCCAAAGAGATGC 60.792 45.833 0.00 0.00 39.69 3.91
2777 5427 4.453136 GCTTGTCCTAAAATTGACACGGTA 59.547 41.667 0.00 0.00 40.96 4.02
2936 5596 7.440523 AATGCAAACAAAACCAACTTTGTAA 57.559 28.000 0.00 0.00 46.32 2.41
3004 5666 5.944007 GTCCCAGTAAACCTACATGACAAAT 59.056 40.000 0.00 0.00 0.00 2.32
3026 5688 6.597832 AGATTATCACTGCCCACTATAGTC 57.402 41.667 1.26 0.00 0.00 2.59
3123 5788 2.663826 AAGCATGAGACTCTTCCGAC 57.336 50.000 3.68 0.00 0.00 4.79
3124 5789 3.003793 CGATAAGCATGAGACTCTTCCGA 59.996 47.826 3.68 0.00 0.00 4.55
3125 5790 3.003793 TCGATAAGCATGAGACTCTTCCG 59.996 47.826 3.68 0.00 0.00 4.30
3145 5810 4.735822 CCTAAGTAGAAGAAGCAATCGTCG 59.264 45.833 0.00 0.00 40.93 5.12
3263 5928 3.019564 AGATCTTTTGGGCCGAGAAATG 58.980 45.455 7.95 2.14 0.00 2.32
3264 5929 3.372440 AGATCTTTTGGGCCGAGAAAT 57.628 42.857 7.95 0.00 0.00 2.17
3372 6044 9.213777 AGAGTCAGATATGGAACCTACATTTTA 57.786 33.333 0.00 0.00 0.00 1.52
3378 6050 6.716934 TCAAGAGTCAGATATGGAACCTAC 57.283 41.667 0.00 0.00 0.00 3.18
3539 6224 3.624861 CCACATCATAGGCTTCTGAACAC 59.375 47.826 0.00 0.00 0.00 3.32
3637 6325 0.181587 TCACGCCTTCCCAACTGAAA 59.818 50.000 0.00 0.00 0.00 2.69
3883 6571 1.125633 GGCCCATTCCAGAAATGCAT 58.874 50.000 0.00 0.00 42.96 3.96
3916 6604 7.118971 GTCTTGTGCTTGATCTCTTGAATTACT 59.881 37.037 0.00 0.00 0.00 2.24
4375 7078 9.743057 CCACAGAAACATTTTAACATCAAGTAA 57.257 29.630 0.00 0.00 0.00 2.24
4376 7079 7.865385 GCCACAGAAACATTTTAACATCAAGTA 59.135 33.333 0.00 0.00 0.00 2.24
4377 7080 6.701400 GCCACAGAAACATTTTAACATCAAGT 59.299 34.615 0.00 0.00 0.00 3.16
4415 7118 1.799403 CTGACAGCAGAAACTGAGCAG 59.201 52.381 2.81 0.00 45.17 4.24
4418 7121 3.247173 GTCAACTGACAGCAGAAACTGAG 59.753 47.826 1.25 0.00 45.17 3.35
4449 7152 3.617263 CCACAACTAGCTAATGAACGGAC 59.383 47.826 11.97 0.00 0.00 4.79
4512 7216 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
4516 7220 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
4517 7221 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
4518 7222 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
4519 7223 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
4520 7224 8.068380 GTCAAAAACGCTCTTATATTATGGGAC 58.932 37.037 0.00 0.00 0.00 4.46
4521 7225 7.227910 GGTCAAAAACGCTCTTATATTATGGGA 59.772 37.037 0.00 0.00 0.00 4.37
4522 7226 7.228706 AGGTCAAAAACGCTCTTATATTATGGG 59.771 37.037 0.00 0.00 0.00 4.00
4523 7227 8.154649 AGGTCAAAAACGCTCTTATATTATGG 57.845 34.615 0.00 0.00 0.00 2.74
4524 7228 9.046296 AGAGGTCAAAAACGCTCTTATATTATG 57.954 33.333 0.00 0.00 34.02 1.90
4525 7229 9.614792 AAGAGGTCAAAAACGCTCTTATATTAT 57.385 29.630 0.00 0.00 40.62 1.28
4527 7231 7.923414 AAGAGGTCAAAAACGCTCTTATATT 57.077 32.000 0.00 0.00 40.62 1.28
4530 7234 9.614792 AATATAAGAGGTCAAAAACGCTCTTAT 57.385 29.630 20.28 20.28 46.48 1.73
4532 7236 7.923414 AATATAAGAGGTCAAAAACGCTCTT 57.077 32.000 0.00 0.00 42.80 2.85
4533 7237 9.046296 CATAATATAAGAGGTCAAAAACGCTCT 57.954 33.333 0.00 0.00 37.21 4.09
4534 7238 8.283291 CCATAATATAAGAGGTCAAAAACGCTC 58.717 37.037 0.00 0.00 0.00 5.03
4535 7239 7.228706 CCCATAATATAAGAGGTCAAAAACGCT 59.771 37.037 0.00 0.00 0.00 5.07
4536 7240 7.227910 TCCCATAATATAAGAGGTCAAAAACGC 59.772 37.037 0.00 0.00 0.00 4.84
4537 7241 8.671384 TCCCATAATATAAGAGGTCAAAAACG 57.329 34.615 0.00 0.00 0.00 3.60
4538 7242 9.067986 CCTCCCATAATATAAGAGGTCAAAAAC 57.932 37.037 8.74 0.00 39.45 2.43
4539 7243 8.224720 CCCTCCCATAATATAAGAGGTCAAAAA 58.775 37.037 13.52 0.00 42.18 1.94
4540 7244 7.574750 TCCCTCCCATAATATAAGAGGTCAAAA 59.425 37.037 13.52 0.00 42.18 2.44
4541 7245 7.086260 TCCCTCCCATAATATAAGAGGTCAAA 58.914 38.462 13.52 0.00 42.18 2.69
4542 7246 6.639938 TCCCTCCCATAATATAAGAGGTCAA 58.360 40.000 13.52 1.38 42.18 3.18
4543 7247 6.241223 TCCCTCCCATAATATAAGAGGTCA 57.759 41.667 13.52 1.91 42.18 4.02
4544 7248 5.663556 CCTCCCTCCCATAATATAAGAGGTC 59.336 48.000 13.52 0.00 42.18 3.85
4545 7249 5.522892 CCCTCCCTCCCATAATATAAGAGGT 60.523 48.000 13.52 0.00 42.18 3.85
4546 7250 4.971924 CCCTCCCTCCCATAATATAAGAGG 59.028 50.000 9.60 9.60 43.16 3.69
4547 7251 5.854843 TCCCTCCCTCCCATAATATAAGAG 58.145 45.833 0.00 0.00 0.00 2.85
4548 7252 5.321625 ACTCCCTCCCTCCCATAATATAAGA 59.678 44.000 0.00 0.00 0.00 2.10
4549 7253 5.604752 ACTCCCTCCCTCCCATAATATAAG 58.395 45.833 0.00 0.00 0.00 1.73
4550 7254 5.650167 ACTCCCTCCCTCCCATAATATAA 57.350 43.478 0.00 0.00 0.00 0.98
4551 7255 6.963154 ATACTCCCTCCCTCCCATAATATA 57.037 41.667 0.00 0.00 0.00 0.86
4552 7256 5.858532 ATACTCCCTCCCTCCCATAATAT 57.141 43.478 0.00 0.00 0.00 1.28
4553 7257 5.650167 AATACTCCCTCCCTCCCATAATA 57.350 43.478 0.00 0.00 0.00 0.98
4554 7258 4.526991 AATACTCCCTCCCTCCCATAAT 57.473 45.455 0.00 0.00 0.00 1.28
4555 7259 3.980698 CAAATACTCCCTCCCTCCCATAA 59.019 47.826 0.00 0.00 0.00 1.90
4556 7260 3.050564 ACAAATACTCCCTCCCTCCCATA 60.051 47.826 0.00 0.00 0.00 2.74
4557 7261 2.294536 ACAAATACTCCCTCCCTCCCAT 60.295 50.000 0.00 0.00 0.00 4.00
4558 7262 1.082194 ACAAATACTCCCTCCCTCCCA 59.918 52.381 0.00 0.00 0.00 4.37
4559 7263 1.894699 ACAAATACTCCCTCCCTCCC 58.105 55.000 0.00 0.00 0.00 4.30
4560 7264 3.621558 CAAACAAATACTCCCTCCCTCC 58.378 50.000 0.00 0.00 0.00 4.30
4561 7265 3.017442 GCAAACAAATACTCCCTCCCTC 58.983 50.000 0.00 0.00 0.00 4.30
4562 7266 2.291605 GGCAAACAAATACTCCCTCCCT 60.292 50.000 0.00 0.00 0.00 4.20
4563 7267 2.100197 GGCAAACAAATACTCCCTCCC 58.900 52.381 0.00 0.00 0.00 4.30
4564 7268 1.743394 CGGCAAACAAATACTCCCTCC 59.257 52.381 0.00 0.00 0.00 4.30
4565 7269 2.706890 TCGGCAAACAAATACTCCCTC 58.293 47.619 0.00 0.00 0.00 4.30
4566 7270 2.871096 TCGGCAAACAAATACTCCCT 57.129 45.000 0.00 0.00 0.00 4.20
4567 7271 3.926821 TTTCGGCAAACAAATACTCCC 57.073 42.857 0.00 0.00 0.00 4.30
4601 7305 4.022935 TCAAGCATTTGTTCACATGAGGTC 60.023 41.667 0.00 0.00 35.73 3.85
4664 7368 2.656560 ATACAAGCGGACAGAGACAC 57.343 50.000 0.00 0.00 0.00 3.67
4761 7512 9.936759 TGGACGATACATATATCATTAGCAAAA 57.063 29.630 0.00 0.00 37.63 2.44
4910 7701 4.836825 TGCCAATTTTTGTTTGAGGACAA 58.163 34.783 0.00 0.00 37.73 3.18
4939 7730 3.827876 TGTCACCCTCGTTGTCAGTATAA 59.172 43.478 0.00 0.00 0.00 0.98
4951 7742 0.873312 CGAGCATCATGTCACCCTCG 60.873 60.000 0.00 0.00 36.65 4.63
5147 7955 2.783510 TCCACTGAACCTTCCTCCTTTT 59.216 45.455 0.00 0.00 0.00 2.27
5504 8355 8.635542 GGTGGTGATCAACAATAGCAATAGCG 62.636 46.154 16.70 0.00 38.33 4.26
5538 8391 1.271543 TGTTGCATCAGAAGGGGAGTG 60.272 52.381 0.00 0.00 0.00 3.51
5541 8394 1.547675 GGTTGTTGCATCAGAAGGGGA 60.548 52.381 0.00 0.00 0.00 4.81
5543 8396 0.890683 GGGTTGTTGCATCAGAAGGG 59.109 55.000 0.00 0.00 0.00 3.95
5635 8488 2.498644 TCTCTCTCTCTGCCGAAGAA 57.501 50.000 0.00 0.00 33.37 2.52
5653 8506 2.123982 CAGCCTTGGCCCTGGATC 60.124 66.667 14.52 0.00 0.00 3.36
5654 8507 2.943265 ACAGCCTTGGCCCTGGAT 60.943 61.111 14.52 5.69 33.43 3.41
5675 8528 2.028839 CACCAATGAGCATCCAAGCAAA 60.029 45.455 0.00 0.00 36.85 3.68
5680 8533 2.658285 GGATCACCAATGAGCATCCAA 58.342 47.619 0.00 0.00 43.37 3.53
5783 8636 4.767928 GTCACTCCCGGAATAGATAGACAT 59.232 45.833 0.73 0.00 0.00 3.06
5828 8689 3.873910 ACATTAAACAGGATCGGTCAGG 58.126 45.455 0.00 0.00 0.00 3.86
5833 8694 5.007626 CACCACATACATTAAACAGGATCGG 59.992 44.000 0.00 0.00 0.00 4.18
5835 8696 5.221048 GGCACCACATACATTAAACAGGATC 60.221 44.000 0.00 0.00 0.00 3.36
5836 8697 4.644685 GGCACCACATACATTAAACAGGAT 59.355 41.667 0.00 0.00 0.00 3.24
5837 8698 4.013728 GGCACCACATACATTAAACAGGA 58.986 43.478 0.00 0.00 0.00 3.86
5849 8710 0.036164 AAGCGACAAGGCACCACATA 59.964 50.000 0.00 0.00 34.64 2.29
5870 8743 1.601759 CACCCTGCCAACTCCACAG 60.602 63.158 0.00 0.00 0.00 3.66
5924 8797 4.159693 CCACATCAGGTACAGTACTGCTTA 59.840 45.833 22.90 5.95 34.76 3.09
5928 8801 4.098044 CCTACCACATCAGGTACAGTACTG 59.902 50.000 21.44 21.44 43.08 2.74
5933 8806 1.139058 GCCCTACCACATCAGGTACAG 59.861 57.143 0.00 0.00 43.08 2.74
5934 8807 1.200519 GCCCTACCACATCAGGTACA 58.799 55.000 0.00 0.00 43.08 2.90
5935 8808 1.200519 TGCCCTACCACATCAGGTAC 58.799 55.000 0.00 0.00 43.08 3.34
5936 8809 2.047061 GATGCCCTACCACATCAGGTA 58.953 52.381 0.00 0.00 43.08 3.08
5937 8810 0.839946 GATGCCCTACCACATCAGGT 59.160 55.000 0.00 0.00 45.72 4.00
5942 8815 0.548031 CCAGTGATGCCCTACCACAT 59.452 55.000 0.00 0.00 33.53 3.21
5966 8839 2.203182 AGTTCGGTGGAGGGTCCA 59.797 61.111 0.00 0.00 45.98 4.02
5968 8841 1.004918 CACAGTTCGGTGGAGGGTC 60.005 63.158 0.00 0.00 35.13 4.46
5969 8842 1.764854 ACACAGTTCGGTGGAGGGT 60.765 57.895 7.82 0.00 43.08 4.34
5971 8844 4.361253 CACACAGTTCGGTGGAGG 57.639 61.111 7.82 0.00 43.08 4.30
5998 8871 4.452733 GACCGGTCAGGGGCGAAG 62.453 72.222 29.75 0.00 46.96 3.79
6001 8874 4.760047 CTTGACCGGTCAGGGGCG 62.760 72.222 33.06 18.59 46.96 6.13
6002 8875 3.316573 CTCTTGACCGGTCAGGGGC 62.317 68.421 37.34 13.83 46.96 5.80
6008 8881 2.572284 CCGTCCTCTTGACCGGTC 59.428 66.667 28.17 28.17 41.18 4.79
6050 8923 1.078759 GGTGAGATCTTGTGACGGCG 61.079 60.000 4.80 4.80 0.00 6.46
6053 8926 2.755655 AGGTAGGTGAGATCTTGTGACG 59.244 50.000 0.00 0.00 0.00 4.35
6082 8955 1.097232 CCATTTGCATCGAAGGAGCA 58.903 50.000 0.00 0.00 36.32 4.26
6087 8960 4.019919 ACGAAATCCATTTGCATCGAAG 57.980 40.909 8.89 0.00 0.00 3.79
6090 8963 3.849645 GCCTACGAAATCCATTTGCATCG 60.850 47.826 0.83 0.83 0.00 3.84
6099 8972 1.136305 CTCGAAGGCCTACGAAATCCA 59.864 52.381 5.16 0.00 38.05 3.41
6101 8974 2.580966 ACTCGAAGGCCTACGAAATC 57.419 50.000 5.16 0.00 38.05 2.17
6125 8998 7.461749 AGGATTCCAAACATCTTCTGTAGAAA 58.538 34.615 5.29 0.00 36.98 2.52
6131 9004 4.093998 CACGAGGATTCCAAACATCTTCTG 59.906 45.833 5.29 0.00 0.00 3.02
6132 9005 4.020218 TCACGAGGATTCCAAACATCTTCT 60.020 41.667 5.29 0.00 0.00 2.85
6133 9006 4.253685 TCACGAGGATTCCAAACATCTTC 58.746 43.478 5.29 0.00 0.00 2.87
6135 9008 3.981071 TCACGAGGATTCCAAACATCT 57.019 42.857 5.29 0.00 0.00 2.90
6158 9155 3.619929 GTGCAAAGCAATCATTTGGATCC 59.380 43.478 4.20 4.20 41.47 3.36
6236 9236 0.396435 AGGGTGTTTGATGACGCAGA 59.604 50.000 0.00 0.00 0.00 4.26
6238 9238 0.396435 AGAGGGTGTTTGATGACGCA 59.604 50.000 0.00 0.00 0.00 5.24
6257 9257 1.961133 ACCAGGGGGAATTTAGACGA 58.039 50.000 0.00 0.00 38.05 4.20
6258 9258 2.752903 CAAACCAGGGGGAATTTAGACG 59.247 50.000 0.00 0.00 38.05 4.18
6262 9262 4.405756 TTAGCAAACCAGGGGGAATTTA 57.594 40.909 0.00 0.00 38.05 1.40
6286 9636 8.938801 TGGCAATGTCCACTTAAATCATATAT 57.061 30.769 0.00 0.00 0.00 0.86
6334 9686 8.098286 TCCTCCTCGTATTTCAAAACATAGAAA 58.902 33.333 0.00 0.00 38.04 2.52
6352 9704 4.507916 TCGCCCTCCTCCTCCTCG 62.508 72.222 0.00 0.00 0.00 4.63
6401 10847 2.281761 ATCGGGCATGCCGAATCC 60.282 61.111 29.90 14.92 42.93 3.01
6421 10867 1.397343 GCGACCTTAAACTTGCCTAGC 59.603 52.381 0.00 0.00 0.00 3.42


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

AutoCloner maintained by Alex Coulton.