Multiple sequence alignment - TraesCS3D01G081900

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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 TraesCS3D01G081900 chr3D 100.000 7939 0 0 1 7939 41033795 41041733 0.000000e+00 14661.0
1 TraesCS3D01G081900 chr3D 89.695 3930 327 37 3495 7395 40912853 40916733 0.000000e+00 4942.0
2 TraesCS3D01G081900 chr3D 90.233 2314 158 27 475 2765 40909823 40912091 0.000000e+00 2959.0
3 TraesCS3D01G081900 chr3D 87.620 727 58 17 2811 3506 40912090 40912815 0.000000e+00 815.0
4 TraesCS3D01G081900 chr3D 92.491 293 20 2 176 466 40909457 40909749 1.230000e-112 418.0
5 TraesCS3D01G081900 chr3D 90.141 284 13 3 1 269 40909140 40909423 9.800000e-94 355.0
6 TraesCS3D01G081900 chr3D 91.509 212 14 4 7546 7757 40916873 40917080 1.010000e-73 289.0
7 TraesCS3D01G081900 chr3D 91.584 202 8 5 7747 7939 40917128 40917329 3.650000e-68 270.0
8 TraesCS3D01G081900 chr3D 77.982 109 16 7 1375 1476 599342477 599342584 2.390000e-05 62.1
9 TraesCS3D01G081900 chr3A 89.752 3103 199 66 459 3506 52819810 52822848 0.000000e+00 3858.0
10 TraesCS3D01G081900 chr3A 91.780 2798 162 36 459 3228 52725629 52728386 0.000000e+00 3831.0
11 TraesCS3D01G081900 chr3A 91.673 2798 167 34 459 3228 52771927 52774686 0.000000e+00 3816.0
12 TraesCS3D01G081900 chr3A 91.415 2749 203 21 3495 6227 52728714 52731445 0.000000e+00 3738.0
13 TraesCS3D01G081900 chr3A 91.415 2749 202 23 3495 6227 52822886 52825616 0.000000e+00 3738.0
14 TraesCS3D01G081900 chr3A 91.645 2717 196 19 3495 6197 52636982 52639681 0.000000e+00 3731.0
15 TraesCS3D01G081900 chr3A 91.240 2751 206 22 3495 6227 52775015 52777748 0.000000e+00 3712.0
16 TraesCS3D01G081900 chr3A 91.744 2592 187 18 3651 6227 52590580 52593159 0.000000e+00 3576.0
17 TraesCS3D01G081900 chr3A 93.446 2121 123 9 1115 3228 52588086 52590197 0.000000e+00 3133.0
18 TraesCS3D01G081900 chr3A 91.551 2225 166 14 4015 6227 52683099 52685313 0.000000e+00 3048.0
19 TraesCS3D01G081900 chr3A 91.330 2203 129 33 459 2636 52633780 52635945 0.000000e+00 2953.0
20 TraesCS3D01G081900 chr3A 93.989 1414 77 6 1820 3228 52681121 52682531 0.000000e+00 2134.0
21 TraesCS3D01G081900 chr3A 89.933 1341 84 28 459 1776 52679798 52681110 0.000000e+00 1681.0
22 TraesCS3D01G081900 chr3A 96.127 723 20 4 6238 6955 52639675 52640394 0.000000e+00 1173.0
23 TraesCS3D01G081900 chr3A 95.994 724 23 3 6237 6955 52593138 52593860 0.000000e+00 1171.0
24 TraesCS3D01G081900 chr3A 95.856 724 24 3 6237 6955 52731424 52732146 0.000000e+00 1166.0
25 TraesCS3D01G081900 chr3A 95.856 724 24 3 6237 6955 52777727 52778449 0.000000e+00 1166.0
26 TraesCS3D01G081900 chr3A 95.856 724 24 3 6237 6955 52825595 52826317 0.000000e+00 1166.0
27 TraesCS3D01G081900 chr3A 95.718 724 25 3 6237 6955 52685292 52686014 0.000000e+00 1160.0
28 TraesCS3D01G081900 chr3A 86.892 679 41 21 459 1117 52582168 52582818 0.000000e+00 717.0
29 TraesCS3D01G081900 chr3A 87.479 607 50 10 6954 7541 52778611 52779210 0.000000e+00 676.0
30 TraesCS3D01G081900 chr3A 87.150 607 51 11 6954 7541 52826479 52827077 0.000000e+00 664.0
31 TraesCS3D01G081900 chr3A 86.985 607 53 10 6954 7541 52686176 52686775 0.000000e+00 660.0
32 TraesCS3D01G081900 chr3A 86.985 607 53 10 6954 7541 52732308 52732907 0.000000e+00 660.0
33 TraesCS3D01G081900 chr3A 86.820 607 54 10 6954 7541 52640556 52641155 0.000000e+00 654.0
34 TraesCS3D01G081900 chr3A 87.031 586 50 10 6954 7520 52594022 52594600 8.690000e-179 638.0
35 TraesCS3D01G081900 chr3A 92.138 407 23 5 7542 7939 52595192 52595598 4.160000e-157 566.0
36 TraesCS3D01G081900 chr3A 92.138 407 23 5 7542 7939 52827693 52828099 4.160000e-157 566.0
37 TraesCS3D01G081900 chr3A 91.892 407 24 4 7542 7939 52641770 52642176 1.930000e-155 560.0
38 TraesCS3D01G081900 chr3A 91.646 407 25 5 7542 7939 52687390 52687796 9.000000e-154 555.0
39 TraesCS3D01G081900 chr3A 91.379 406 26 5 7542 7938 52733522 52733927 1.510000e-151 547.0
40 TraesCS3D01G081900 chr3A 87.224 407 26 8 7542 7939 52779825 52780214 2.630000e-119 440.0
41 TraesCS3D01G081900 chr3A 95.364 151 6 1 14 163 52633370 52633520 1.030000e-58 239.0
42 TraesCS3D01G081900 chr3A 95.364 151 6 1 14 163 52819399 52819549 1.030000e-58 239.0
43 TraesCS3D01G081900 chr3A 94.702 151 7 1 14 163 52581758 52581908 4.790000e-57 233.0
44 TraesCS3D01G081900 chr3A 94.040 151 8 1 14 163 52679388 52679538 2.230000e-55 228.0
45 TraesCS3D01G081900 chr3A 94.040 151 8 1 14 163 52725219 52725369 2.230000e-55 228.0
46 TraesCS3D01G081900 chr3A 94.040 151 8 1 14 163 52771517 52771667 2.230000e-55 228.0
47 TraesCS3D01G081900 chr3A 78.205 312 34 18 3196 3506 52774699 52774977 1.370000e-37 169.0
48 TraesCS3D01G081900 chr3A 87.333 150 14 5 3196 3345 52728399 52728543 4.930000e-37 167.0
49 TraesCS3D01G081900 chr3A 78.968 252 26 13 3255 3506 52636720 52636944 6.420000e-31 147.0
50 TraesCS3D01G081900 chrUn 92.532 1232 77 9 1153 2379 423824818 423823597 0.000000e+00 1751.0
51 TraesCS3D01G081900 chrUn 84.478 335 51 1 2848 3182 32434578 32434911 5.940000e-86 329.0
52 TraesCS3D01G081900 chr2B 77.953 381 68 15 2773 3148 6891710 6892079 2.880000e-54 224.0
53 TraesCS3D01G081900 chr2B 77.690 381 68 16 2773 3148 6972122 6972490 4.820000e-52 217.0
54 TraesCS3D01G081900 chr2B 79.779 272 55 0 6661 6932 7909049 7908778 1.750000e-46 198.0
55 TraesCS3D01G081900 chr2B 82.222 225 40 0 6661 6885 8078783 8078559 2.260000e-45 195.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G081900 chr3D 41033795 41041733 7938 False 14661.000000 14661 100.000000 1 7939 1 chr3D.!!$F1 7938
1 TraesCS3D01G081900 chr3D 40909140 40917329 8189 False 1435.428571 4942 90.467571 1 7939 7 chr3D.!!$F3 7938
2 TraesCS3D01G081900 chr3A 52588086 52595598 7512 False 1816.800000 3576 92.070600 1115 7939 5 chr3A.!!$F2 6824
3 TraesCS3D01G081900 chr3A 52819399 52828099 8700 False 1705.166667 3858 91.945833 14 7939 6 chr3A.!!$F7 7925
4 TraesCS3D01G081900 chr3A 52725219 52733927 8708 False 1476.714286 3831 91.255429 14 7938 7 chr3A.!!$F5 7924
5 TraesCS3D01G081900 chr3A 52771517 52780214 8697 False 1458.142857 3816 89.388143 14 7939 7 chr3A.!!$F6 7925
6 TraesCS3D01G081900 chr3A 52679388 52687796 8408 False 1352.285714 3048 91.980286 14 7939 7 chr3A.!!$F4 7925
7 TraesCS3D01G081900 chr3A 52633370 52642176 8806 False 1351.000000 3731 90.306571 14 7939 7 chr3A.!!$F3 7925
8 TraesCS3D01G081900 chr3A 52581758 52582818 1060 False 475.000000 717 90.797000 14 1117 2 chr3A.!!$F1 1103
9 TraesCS3D01G081900 chrUn 423823597 423824818 1221 True 1751.000000 1751 92.532000 1153 2379 1 chrUn.!!$R1 1226

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
551 839 0.175302 CTGCAGTCTAGGCCTCACAG 59.825 60.000 9.68 5.58 0.00 3.66 F
1894 2220 0.307760 GACGTGGCTCACCTTTGTTG 59.692 55.000 0.00 0.00 36.63 3.33 F
1986 2315 3.425193 GTGCAAAAGAACAACATTAGCGG 59.575 43.478 0.00 0.00 0.00 5.52 F
3136 3467 0.322277 ATGTCCACTTGCAGGAGCTG 60.322 55.000 1.40 0.00 42.74 4.24 F
4173 4739 0.035056 GCTACACATGGGCCTCTGTT 60.035 55.000 4.53 3.00 0.00 3.16 F
4798 5364 0.037882 CAGTGATGACTGGTGTCGCT 60.038 55.000 4.13 0.00 45.26 4.93 F
5782 6351 0.240411 GTTGACTCACGCGTACTCCT 59.760 55.000 13.44 0.00 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2137 2466 2.482721 ACTCGTAGCCATTTTTGTTCGG 59.517 45.455 0.00 0.00 0.00 4.30 R
3112 3443 0.038892 CCTGCAAGTGGACATGTTGC 60.039 55.000 11.67 11.67 45.56 4.17 R
3561 4113 1.340889 GCCTGTTGAAAGCACATTGGA 59.659 47.619 0.00 0.00 0.00 3.53 R
4948 5514 0.036671 GTAGTTGTTCCCCACCTCCG 60.037 60.000 0.00 0.00 0.00 4.63 R
5470 6037 0.179004 ACCACGGGTGCTTGAAATCA 60.179 50.000 0.00 0.00 32.98 2.57 R
6665 7246 0.329261 AGCTTGCTGCATCACCCTTA 59.671 50.000 1.84 0.00 45.94 2.69 R
7456 8222 0.604073 CACAATGCTGATTGGCACCA 59.396 50.000 2.24 0.00 45.36 4.17 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
130 132 1.095228 CCATGAATTCGTCACGGGGG 61.095 60.000 0.00 0.00 35.86 5.40
165 167 3.062099 CACCACATCTTTATTGTCGACGG 59.938 47.826 11.62 3.65 0.00 4.79
176 178 1.732308 GTCGACGGGACACCTATCC 59.268 63.158 0.00 0.00 45.36 2.59
179 181 0.384669 CGACGGGACACCTATCCTTC 59.615 60.000 0.00 0.00 38.95 3.46
222 237 3.325135 GGACTAAGGATCCACATACCTGG 59.675 52.174 15.82 0.00 36.15 4.45
232 375 4.311613 TCCACATACCTGGGATGGATAAA 58.688 43.478 22.62 1.19 34.50 1.40
280 424 1.486726 GTTGGGATCTAGGTGACCCTG 59.513 57.143 0.00 0.00 42.67 4.45
286 430 1.195115 TCTAGGTGACCCTGACATGC 58.805 55.000 0.00 0.00 42.67 4.06
372 516 2.833943 TGTTGAGATCTAAGGCTGCTCA 59.166 45.455 0.00 0.00 34.11 4.26
379 523 3.032265 TCTAAGGCTGCTCATAGTGGA 57.968 47.619 0.00 0.00 0.00 4.02
385 529 3.713764 AGGCTGCTCATAGTGGAAGTATT 59.286 43.478 0.00 0.00 27.50 1.89
417 561 9.504710 CTAGCATCACGTATATGTTAATACCTC 57.495 37.037 10.70 0.00 0.00 3.85
441 585 9.988815 CTCCATAGTGCATAGTATCTTAAGTTT 57.011 33.333 1.63 0.00 0.00 2.66
502 790 2.281762 GGTCTAAAAGAGCGTGCGTATG 59.718 50.000 0.00 0.00 32.69 2.39
510 798 1.089481 AGCGTGCGTATGGTTGGATG 61.089 55.000 0.00 0.00 0.00 3.51
539 827 0.598065 AATCCAAAACCGCTGCAGTC 59.402 50.000 16.64 6.83 0.00 3.51
551 839 0.175302 CTGCAGTCTAGGCCTCACAG 59.825 60.000 9.68 5.58 0.00 3.66
577 865 0.609131 ACCCACATCGGCTTTTCCAG 60.609 55.000 0.00 0.00 34.01 3.86
684 976 2.104281 ACTCTAGAACCGGTGCTTGTTT 59.896 45.455 23.37 7.36 0.00 2.83
730 1022 2.557056 TGTTAGCACTCGACTTAGCACT 59.443 45.455 0.00 0.00 0.00 4.40
757 1049 2.180131 GACCAACTCTGCGCTTGCTG 62.180 60.000 9.73 0.03 40.12 4.41
790 1082 3.038280 ACATAGTGGCTGCTATACACCA 58.962 45.455 0.00 0.00 35.79 4.17
792 1084 4.103153 ACATAGTGGCTGCTATACACCATT 59.897 41.667 0.00 0.00 35.79 3.16
795 1087 3.054434 AGTGGCTGCTATACACCATTGAA 60.054 43.478 0.00 0.00 35.79 2.69
797 1089 4.157656 GTGGCTGCTATACACCATTGAAAA 59.842 41.667 0.00 0.00 33.75 2.29
798 1090 4.157656 TGGCTGCTATACACCATTGAAAAC 59.842 41.667 0.00 0.00 0.00 2.43
799 1091 4.399303 GGCTGCTATACACCATTGAAAACT 59.601 41.667 0.00 0.00 0.00 2.66
800 1092 5.105756 GGCTGCTATACACCATTGAAAACTT 60.106 40.000 0.00 0.00 0.00 2.66
801 1093 6.094881 GGCTGCTATACACCATTGAAAACTTA 59.905 38.462 0.00 0.00 0.00 2.24
802 1094 7.362574 GGCTGCTATACACCATTGAAAACTTAA 60.363 37.037 0.00 0.00 0.00 1.85
803 1095 7.698130 GCTGCTATACACCATTGAAAACTTAAG 59.302 37.037 0.00 0.00 0.00 1.85
804 1096 8.630054 TGCTATACACCATTGAAAACTTAAGT 57.370 30.769 1.12 1.12 0.00 2.24
805 1097 9.727859 TGCTATACACCATTGAAAACTTAAGTA 57.272 29.630 8.92 0.00 0.00 2.24
806 1098 9.983804 GCTATACACCATTGAAAACTTAAGTAC 57.016 33.333 8.92 4.65 0.00 2.73
809 1101 7.875327 ACACCATTGAAAACTTAAGTACAGT 57.125 32.000 8.92 4.34 0.00 3.55
810 1102 7.703328 ACACCATTGAAAACTTAAGTACAGTG 58.297 34.615 8.92 14.72 0.00 3.66
811 1103 7.554835 ACACCATTGAAAACTTAAGTACAGTGA 59.445 33.333 21.97 7.01 0.00 3.41
812 1104 8.402472 CACCATTGAAAACTTAAGTACAGTGAA 58.598 33.333 21.97 9.33 0.00 3.18
813 1105 8.962679 ACCATTGAAAACTTAAGTACAGTGAAA 58.037 29.630 21.97 9.38 0.00 2.69
814 1106 9.965824 CCATTGAAAACTTAAGTACAGTGAAAT 57.034 29.630 21.97 10.68 0.00 2.17
882 1180 6.561614 GGCTATGCATGAATATTCCAATGAG 58.438 40.000 10.16 8.41 0.00 2.90
907 1218 4.104738 CCCCTTGATATAAAGGCCTCTCAA 59.895 45.833 13.05 9.80 44.69 3.02
1054 1374 1.817099 GCCAGAGCGTCCATCAAGG 60.817 63.158 0.00 0.00 39.47 3.61
1146 1466 3.938963 GCTGTATGAAAATTGACGGAGGA 59.061 43.478 0.00 0.00 0.00 3.71
1302 1622 3.873361 CAGAACCACTGCAGGTATACATG 59.127 47.826 19.93 13.10 42.25 3.21
1308 1628 4.201950 CCACTGCAGGTATACATGAAAAGC 60.202 45.833 21.10 5.82 0.00 3.51
1368 1689 6.259167 CCCTCCATTTCAAAATACAATGCATG 59.741 38.462 0.00 0.00 0.00 4.06
1537 1858 3.627577 TGCTGAAACTTCACCAGACTTTC 59.372 43.478 0.00 0.00 32.90 2.62
1601 1922 3.136626 GGAGTATACCCACTGGCATCTTT 59.863 47.826 0.00 0.00 33.59 2.52
1627 1948 3.575805 TCAAATTGGAACTTTGGCTCCT 58.424 40.909 0.00 0.00 34.95 3.69
1685 2007 1.868469 CACACCATGTGCCAAAAAGG 58.132 50.000 0.00 0.00 41.89 3.11
1756 2082 8.352752 TGCTTTCACAATAACTAGATGATACG 57.647 34.615 0.00 0.00 0.00 3.06
1768 2094 6.982852 ACTAGATGATACGTTGTCCCATAAG 58.017 40.000 0.00 0.00 0.00 1.73
1815 2141 2.842208 TGACAAAAGTGCTCCGTTTG 57.158 45.000 11.54 11.54 44.82 2.93
1820 2146 4.919677 CAAAAGTGCTCCGTTTGTTTTT 57.080 36.364 7.02 0.00 37.63 1.94
1858 2184 5.552178 AGGCTAGTGTGAAAAGGTAAGAAG 58.448 41.667 0.00 0.00 0.00 2.85
1864 2190 9.884465 CTAGTGTGAAAAGGTAAGAAGAAAATG 57.116 33.333 0.00 0.00 0.00 2.32
1894 2220 0.307760 GACGTGGCTCACCTTTGTTG 59.692 55.000 0.00 0.00 36.63 3.33
1972 2301 7.970614 GGAGGAAAATGATAGTTAGTGCAAAAG 59.029 37.037 0.00 0.00 0.00 2.27
1986 2315 3.425193 GTGCAAAAGAACAACATTAGCGG 59.575 43.478 0.00 0.00 0.00 5.52
2036 2365 9.613428 CATAGTGACATACAAAGATTTCCCTTA 57.387 33.333 0.00 0.00 0.00 2.69
2170 2499 7.484035 AATGGCTACGAGTCTTATTCATTTC 57.516 36.000 0.00 0.00 0.00 2.17
2266 2595 5.748402 TCATGGATCTATGTATTGCATCCC 58.252 41.667 17.55 0.00 38.94 3.85
2275 2604 7.546358 TCTATGTATTGCATCCCTTTGTTTTG 58.454 34.615 0.00 0.00 38.94 2.44
2286 2616 9.267084 GCATCCCTTTGTTTTGTTAATTTAAGA 57.733 29.630 0.00 0.00 0.00 2.10
2376 2706 7.860373 TGCATGATGTTTAAGTCTTGTAACAAC 59.140 33.333 15.01 13.45 34.54 3.32
2436 2766 6.750148 ACATCTCGGAATAGATTACCACTTC 58.250 40.000 0.00 0.00 33.87 3.01
2756 3087 7.984050 GGATGACATTAGATCTCTGACAAAGAA 59.016 37.037 0.00 0.00 33.37 2.52
2768 3099 8.224389 TCTCTGACAAAGAAATCAATTTGTGA 57.776 30.769 7.94 0.00 46.67 3.58
2795 3126 9.932207 ATGCAGATGTTTTCAATAAATTCAAGA 57.068 25.926 0.00 0.00 0.00 3.02
2797 3128 9.195411 GCAGATGTTTTCAATAAATTCAAGACA 57.805 29.630 0.00 0.00 0.00 3.41
2799 3130 9.398170 AGATGTTTTCAATAAATTCAAGACACG 57.602 29.630 0.00 0.00 0.00 4.49
2828 3159 4.381411 GGGCTTCAGTAAGGACATATCAC 58.619 47.826 0.00 0.00 32.98 3.06
2834 3165 8.090831 GCTTCAGTAAGGACATATCACATGATA 58.909 37.037 0.00 4.11 36.10 2.15
2946 3277 7.583024 GCATCATCTTAGATCAATGAGGGGTAT 60.583 40.741 14.68 0.00 33.15 2.73
2980 3311 4.080863 ACCCCACTAGCTAATCAAGTCAAG 60.081 45.833 0.00 0.00 0.00 3.02
3054 3385 8.147058 ACTGCATTATATCTCTGAGTACAAAGG 58.853 37.037 4.32 0.00 0.00 3.11
3112 3443 8.568732 TCGCAAAACTAGATTTTAACCTTTTG 57.431 30.769 0.00 1.01 38.50 2.44
3128 3459 2.222007 TTTGCAACATGTCCACTTGC 57.778 45.000 11.67 11.67 40.63 4.01
3136 3467 0.322277 ATGTCCACTTGCAGGAGCTG 60.322 55.000 1.40 0.00 42.74 4.24
3247 3637 1.598882 TGTGTGTGTGTGTGTGTGTT 58.401 45.000 0.00 0.00 0.00 3.32
3248 3638 1.950216 TGTGTGTGTGTGTGTGTGTTT 59.050 42.857 0.00 0.00 0.00 2.83
3281 3767 9.855021 ATAGTGTAAATCATTACCAACAAAAGC 57.145 29.630 0.00 0.00 40.61 3.51
3350 3837 3.868661 GGTTTCACAATTTCACACCCAAC 59.131 43.478 0.00 0.00 0.00 3.77
3383 3874 4.018506 TGGACCACCACATAAATCACTCAT 60.019 41.667 0.00 0.00 41.77 2.90
3416 3908 9.719355 CATGGGCCCTAAATTTAATTATTTACC 57.281 33.333 25.70 0.00 0.00 2.85
3418 3910 9.150028 TGGGCCCTAAATTTAATTATTTACCTC 57.850 33.333 25.70 0.00 0.00 3.85
3490 3994 9.458374 ACACGTTACTTCCTTATTTGAAAATTG 57.542 29.630 0.00 0.00 0.00 2.32
3510 4062 3.465871 TGTACGTTTTTACTTTCGGGCT 58.534 40.909 0.00 0.00 0.00 5.19
3529 4081 3.440522 GGCTAACAAGATTCAAGGTGGTC 59.559 47.826 0.00 0.00 0.00 4.02
3545 4097 5.701224 AGGTGGTCTTTCTCCATGTTTTAA 58.299 37.500 0.00 0.00 37.30 1.52
3593 4146 5.734720 CTTTCAACAGGCTATCCTTACTCA 58.265 41.667 0.00 0.00 41.93 3.41
3594 4147 4.737855 TCAACAGGCTATCCTTACTCAC 57.262 45.455 0.00 0.00 41.93 3.51
3595 4148 4.093743 TCAACAGGCTATCCTTACTCACA 58.906 43.478 0.00 0.00 41.93 3.58
3596 4149 4.716784 TCAACAGGCTATCCTTACTCACAT 59.283 41.667 0.00 0.00 41.93 3.21
3804 4358 3.457234 TCTAGTGCATGCCTATTGTTCG 58.543 45.455 16.68 3.83 0.00 3.95
3825 4379 6.358118 TCGTCATATTTTACTTGATGTGGC 57.642 37.500 0.00 0.00 0.00 5.01
3865 4419 8.547967 TTTCTAGCTATGTTGAACCTAACTTG 57.452 34.615 0.00 0.00 0.00 3.16
4032 4592 4.346730 TCCATTTTTCTGACATGGAGCAT 58.653 39.130 7.88 0.00 41.35 3.79
4044 4605 4.535781 ACATGGAGCATGGCTAATGTTTA 58.464 39.130 11.24 0.00 45.16 2.01
4055 4616 9.023967 GCATGGCTAATGTTTACTAAATCAAAG 57.976 33.333 0.00 0.00 38.65 2.77
4103 4669 0.751277 TTGTGCAGGTGGTGGAACAG 60.751 55.000 0.00 0.00 41.80 3.16
4161 4727 1.964448 CGTGGTGGAGAGCTACACA 59.036 57.895 14.37 0.00 46.14 3.72
4169 4735 0.105778 GAGAGCTACACATGGGCCTC 59.894 60.000 4.53 0.00 0.00 4.70
4173 4739 0.035056 GCTACACATGGGCCTCTGTT 60.035 55.000 4.53 3.00 0.00 3.16
4230 4796 7.171508 AGACGTATTATCGCAATGATGATTGTT 59.828 33.333 6.75 0.00 41.09 2.83
4314 4880 6.493458 AGTTACATGAAGCCATACAAAGGTTT 59.507 34.615 0.00 0.00 31.85 3.27
4397 4963 8.695456 AGTAATTGTTTCCTATTAGCCATTTGG 58.305 33.333 0.00 0.00 38.53 3.28
4568 5134 3.604875 TGATACGAAGGGTTCCAAGAC 57.395 47.619 0.00 0.00 0.00 3.01
4692 5258 5.001232 GGTCTAATGCACTACACAAGGAAA 58.999 41.667 0.00 0.00 0.00 3.13
4694 5260 6.821665 GGTCTAATGCACTACACAAGGAAATA 59.178 38.462 0.00 0.00 0.00 1.40
4699 5265 7.701539 ATGCACTACACAAGGAAATAATTCA 57.298 32.000 0.00 0.00 37.29 2.57
4727 5293 4.906065 ATGCAACACTATAAGCACATGG 57.094 40.909 0.00 0.00 40.14 3.66
4733 5299 3.225104 CACTATAAGCACATGGCCCAAT 58.775 45.455 0.00 0.00 46.50 3.16
4762 5328 8.241497 AGAAATGTATGCAATATGGAATGTGT 57.759 30.769 0.00 0.00 0.00 3.72
4798 5364 0.037882 CAGTGATGACTGGTGTCGCT 60.038 55.000 4.13 0.00 45.26 4.93
4800 5366 0.792640 GTGATGACTGGTGTCGCTTG 59.207 55.000 0.00 0.00 45.70 4.01
4809 5375 1.005630 GTGTCGCTTGAGTGAGGCT 60.006 57.895 0.00 0.00 34.93 4.58
4817 5383 1.053835 TTGAGTGAGGCTGACACCCA 61.054 55.000 6.92 0.00 38.82 4.51
4826 5392 1.039856 GCTGACACCCAACCATTGTT 58.960 50.000 0.00 0.00 34.14 2.83
4866 5432 2.159184 AGATACATCCGCCGCAGATATG 60.159 50.000 0.00 0.00 0.00 1.78
4867 5433 1.253100 TACATCCGCCGCAGATATGA 58.747 50.000 0.00 0.00 0.00 2.15
4948 5514 3.945285 TGGAGGTGAAGTGACAGTTTTTC 59.055 43.478 0.00 0.00 0.00 2.29
4983 5549 7.148018 GGAACAACTACATCATCAATGTCCAAT 60.148 37.037 0.00 0.00 45.78 3.16
4984 5550 7.707624 ACAACTACATCATCAATGTCCAATT 57.292 32.000 0.00 0.00 45.78 2.32
4985 5551 8.806429 ACAACTACATCATCAATGTCCAATTA 57.194 30.769 0.00 0.00 45.78 1.40
4986 5552 9.241919 ACAACTACATCATCAATGTCCAATTAA 57.758 29.630 0.00 0.00 45.78 1.40
5007 5573 2.176045 TGGTTCGTTGCTAGAGGATGA 58.824 47.619 0.00 0.00 0.00 2.92
5008 5574 2.166459 TGGTTCGTTGCTAGAGGATGAG 59.834 50.000 0.00 0.00 0.00 2.90
5035 5601 4.151335 CACATTTCTTCTCTGTCAAGGACG 59.849 45.833 0.00 0.00 34.95 4.79
5040 5606 1.924731 TCTCTGTCAAGGACGACCAT 58.075 50.000 6.71 0.00 38.94 3.55
5045 5611 1.270094 TGTCAAGGACGACCATGTCAC 60.270 52.381 6.71 0.58 40.72 3.67
5206 5772 8.713708 AACGTAGGTAGTACTCTAGGTATCTA 57.286 38.462 14.03 0.00 34.69 1.98
5237 5803 4.154015 CCAGTGTTTGACGCATCATTAAGA 59.846 41.667 0.00 0.00 33.85 2.10
5267 5833 2.746279 ATGGGTTGTGACCTTCAACA 57.254 45.000 10.21 0.00 45.75 3.33
5278 5844 6.716284 TGTGACCTTCAACAATATGGTATCA 58.284 36.000 0.00 0.00 0.00 2.15
5310 5876 0.249322 CCACATACCCGCTAAGACCG 60.249 60.000 0.00 0.00 0.00 4.79
5323 5889 4.320275 CGCTAAGACCGAATGTAGCTATGA 60.320 45.833 0.00 0.00 37.42 2.15
5435 6001 7.993101 ACACAAGGATCACATCAAAATATCTG 58.007 34.615 0.00 0.00 0.00 2.90
5439 6005 5.768662 AGGATCACATCAAAATATCTGGCAG 59.231 40.000 8.58 8.58 0.00 4.85
5454 6021 1.180029 GGCAGCAATGGTTGAGACAT 58.820 50.000 0.00 0.00 0.00 3.06
5481 6048 6.202570 GCACAAAATTTACCTGATTTCAAGCA 59.797 34.615 0.00 0.00 0.00 3.91
5513 6080 3.963374 GGTAATAACCCTACTTCCCTCGT 59.037 47.826 0.00 0.00 40.21 4.18
5518 6085 1.263356 CCCTACTTCCCTCGTTGTCA 58.737 55.000 0.00 0.00 0.00 3.58
5673 6242 4.100529 CCAAATTGCTCATAGTTGCTTCG 58.899 43.478 0.00 0.00 0.00 3.79
5684 6253 1.412710 AGTTGCTTCGGAGTGAGTTGA 59.587 47.619 0.00 0.00 0.00 3.18
5717 6286 5.789643 GCATATTCCTTTTATGCCTTGGA 57.210 39.130 4.69 0.00 43.92 3.53
5719 6288 5.509670 GCATATTCCTTTTATGCCTTGGACC 60.510 44.000 4.69 0.00 43.92 4.46
5723 6292 2.493278 CCTTTTATGCCTTGGACCACAG 59.507 50.000 0.00 0.00 0.00 3.66
5736 6305 5.546621 TGGACCACAGCTCCTTTATATAC 57.453 43.478 0.00 0.00 0.00 1.47
5737 6306 4.966168 TGGACCACAGCTCCTTTATATACA 59.034 41.667 0.00 0.00 0.00 2.29
5746 6315 7.950684 ACAGCTCCTTTATATACACATCTAGGA 59.049 37.037 0.00 0.00 0.00 2.94
5782 6351 0.240411 GTTGACTCACGCGTACTCCT 59.760 55.000 13.44 0.00 0.00 3.69
5833 6402 4.660303 TCTGGTTAGCTCATATGAACCCAT 59.340 41.667 17.76 2.17 40.59 4.00
5841 6410 5.789575 AGCTCATATGAACCCATATTCCTCT 59.210 40.000 6.90 0.00 41.83 3.69
5844 6413 2.620251 TGAACCCATATTCCTCTGCG 57.380 50.000 0.00 0.00 0.00 5.18
5883 6452 8.270137 ACCCTGGTTTCCTTATTTTGTAAATT 57.730 30.769 0.00 0.00 0.00 1.82
5912 6481 6.985645 AGATAGAATCTTGCAGTGAGATGTTC 59.014 38.462 0.16 0.00 35.76 3.18
5925 6494 7.279536 GCAGTGAGATGTTCATCTTTTATCTGA 59.720 37.037 15.16 0.00 38.29 3.27
5993 6568 7.540299 ACAAGCTAATAGAAGTGTCTCACTAC 58.460 38.462 2.80 0.00 44.62 2.73
6008 6583 5.239525 GTCTCACTACTTTCTTTTGTGCCAT 59.760 40.000 0.00 0.00 0.00 4.40
6057 6632 0.304705 GTGCCGTTGATATTCTGCCG 59.695 55.000 0.00 0.00 0.00 5.69
6153 6728 5.100943 GTCGACTACAATGTTTCCTACCTC 58.899 45.833 8.70 0.00 0.00 3.85
6332 6908 7.332430 CCATGCATACAGTTTCAAAATCATGTT 59.668 33.333 0.00 0.00 0.00 2.71
6462 7038 2.182842 GTGATGGCAGGCGTGGATC 61.183 63.158 8.72 0.00 0.00 3.36
6517 7093 4.141883 CGTACCCGACGTTGTCAG 57.858 61.111 1.30 0.00 46.86 3.51
6665 7246 1.081641 CGTACAGCGTCGGAAGTGT 60.082 57.895 0.00 0.00 35.54 3.55
6802 7383 4.771590 AAGCTCGCTTTGAAAATCATGA 57.228 36.364 0.00 0.00 31.29 3.07
6987 7731 4.864704 TTGGCTGTTTAATTCTTCCACC 57.135 40.909 0.00 0.00 0.00 4.61
6990 7734 5.826643 TGGCTGTTTAATTCTTCCACCTAT 58.173 37.500 0.00 0.00 0.00 2.57
7082 7827 1.002868 AGCCTGCTCCATGTGTGTC 60.003 57.895 0.00 0.00 0.00 3.67
7089 7834 2.750712 TGCTCCATGTGTGTCATCAATG 59.249 45.455 0.00 0.00 34.09 2.82
7167 7912 9.110617 CAAATATCGTCATATTCTCATTTGCAC 57.889 33.333 0.00 0.00 34.57 4.57
7172 7918 4.037208 GTCATATTCTCATTTGCACCCAGG 59.963 45.833 0.00 0.00 0.00 4.45
7188 7934 5.256474 CACCCAGGAAAACTGTCATATTCT 58.744 41.667 0.00 0.00 46.06 2.40
7189 7935 5.124457 CACCCAGGAAAACTGTCATATTCTG 59.876 44.000 0.00 0.00 46.06 3.02
7195 7941 9.918630 CAGGAAAACTGTCATATTCTGAAAAAT 57.081 29.630 0.00 0.00 42.42 1.82
7275 8041 2.521126 TCGTGGAGTGAATGTGACCTA 58.479 47.619 0.00 0.00 0.00 3.08
7303 8069 6.432783 TGTGAGACCTGGGTAAATTTAATGTG 59.567 38.462 0.00 0.00 0.00 3.21
7359 8125 9.761504 TTTGCAATGAAACTATTCTGAATTTGA 57.238 25.926 8.38 0.00 36.48 2.69
7385 8151 6.260700 TGTAGGGTTATCTGCAAACCATAT 57.739 37.500 18.21 7.95 46.85 1.78
7440 8206 0.248866 CCACTTTTGCACGTGAACCC 60.249 55.000 22.23 1.13 33.04 4.11
7465 8231 4.393239 AGGAATATATGCTGGTGCCAAT 57.607 40.909 0.00 0.00 38.71 3.16
7468 8234 4.157289 GGAATATATGCTGGTGCCAATCAG 59.843 45.833 0.00 0.00 38.71 2.90
7494 8260 7.148306 GCATTGTGTATTATTATCCTAACCGGG 60.148 40.741 6.32 0.00 0.00 5.73
7499 8265 7.983484 GTGTATTATTATCCTAACCGGGTATGG 59.017 40.741 6.32 7.58 0.00 2.74
7507 8273 2.789323 AACCGGGTATGGATAGGAGT 57.211 50.000 6.32 0.00 0.00 3.85
7508 8274 2.011122 ACCGGGTATGGATAGGAGTG 57.989 55.000 6.32 0.00 0.00 3.51
7513 8279 0.608640 GTATGGATAGGAGTGCCCCG 59.391 60.000 0.00 0.00 34.66 5.73
7521 8287 0.104934 AGGAGTGCCCCGAGGAATAT 60.105 55.000 0.00 0.00 34.66 1.28
7545 8311 6.870971 AACTGTGACGTTAATAATGTTGGT 57.129 33.333 0.00 0.00 0.00 3.67
7546 8312 6.870971 ACTGTGACGTTAATAATGTTGGTT 57.129 33.333 0.00 0.00 0.00 3.67
7547 8313 6.664515 ACTGTGACGTTAATAATGTTGGTTG 58.335 36.000 0.00 0.00 0.00 3.77
7586 8967 6.887626 TTGCTTACATCATCATATGCATGT 57.112 33.333 10.16 15.11 36.11 3.21
7628 9009 1.308069 GCATGCTGTGATTGGGTCGT 61.308 55.000 11.37 0.00 0.00 4.34
7757 9229 7.591006 TTCTACACGTTTCAAGGATTATGTC 57.409 36.000 0.00 0.00 0.00 3.06
7879 9351 6.072838 CGACTTAGAGTTGTGTACTAGAACCA 60.073 42.308 0.00 0.00 37.17 3.67
7900 9372 5.779771 ACCAACTGGGAAATCATGTTATGTT 59.220 36.000 0.00 0.00 41.15 2.71
7907 9388 5.221244 GGGAAATCATGTTATGTTACCAGCC 60.221 44.000 0.00 0.00 0.00 4.85
7910 9391 3.266636 TCATGTTATGTTACCAGCCACG 58.733 45.455 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 4.629092 GGACTAATCCGTGATACTTTCCC 58.371 47.826 0.00 0.00 34.48 3.97
165 167 3.698040 TGTTACTCGAAGGATAGGTGTCC 59.302 47.826 0.00 0.00 38.62 4.02
176 178 2.271800 GCAGGGATGTGTTACTCGAAG 58.728 52.381 0.00 0.00 0.00 3.79
179 181 0.249120 TGGCAGGGATGTGTTACTCG 59.751 55.000 0.00 0.00 0.00 4.18
232 375 4.899352 ATGTAGAAGCAGAAACTGGACT 57.101 40.909 0.00 0.00 31.21 3.85
315 459 2.989909 TCATACTTACGTCGTCCCTCA 58.010 47.619 0.00 0.00 0.00 3.86
320 464 4.494764 GTCACACATCATACTTACGTCGTC 59.505 45.833 0.00 0.00 0.00 4.20
400 544 8.248253 TGCACTATGGAGGTATTAACATATACG 58.752 37.037 0.00 0.00 32.85 3.06
408 552 9.769677 AGATACTATGCACTATGGAGGTATTAA 57.230 33.333 0.00 0.00 0.00 1.40
411 555 9.769677 TTAAGATACTATGCACTATGGAGGTAT 57.230 33.333 0.00 0.00 0.00 2.73
417 561 9.547753 ACAAACTTAAGATACTATGCACTATGG 57.452 33.333 10.09 0.00 0.00 2.74
486 774 1.196808 CAACCATACGCACGCTCTTTT 59.803 47.619 0.00 0.00 0.00 2.27
487 775 0.796312 CAACCATACGCACGCTCTTT 59.204 50.000 0.00 0.00 0.00 2.52
502 790 5.253330 TGGATTTGTAGACTTCATCCAACC 58.747 41.667 2.79 0.00 34.21 3.77
510 798 4.215613 AGCGGTTTTGGATTTGTAGACTTC 59.784 41.667 0.00 0.00 0.00 3.01
539 827 1.205893 GTTCTGACCTGTGAGGCCTAG 59.794 57.143 4.42 0.00 39.63 3.02
551 839 1.745489 GCCGATGTGGGTTCTGACC 60.745 63.158 0.00 0.00 45.75 4.02
684 976 6.869913 ACAAAATTCGTTGGAGTCGACTATTA 59.130 34.615 20.09 4.84 37.05 0.98
730 1022 1.398692 GCAGAGTTGGTCAAAACCCA 58.601 50.000 0.00 0.00 45.83 4.51
757 1049 1.482593 CCACTATGTCAGGGTCACCTC 59.517 57.143 0.00 0.00 46.95 3.85
795 1087 8.557029 CGGAGAAATTTCACTGTACTTAAGTTT 58.443 33.333 19.99 0.00 0.00 2.66
797 1089 6.649557 CCGGAGAAATTTCACTGTACTTAAGT 59.350 38.462 19.99 13.68 0.00 2.24
798 1090 6.402226 GCCGGAGAAATTTCACTGTACTTAAG 60.402 42.308 19.99 0.00 0.00 1.85
799 1091 5.410439 GCCGGAGAAATTTCACTGTACTTAA 59.590 40.000 19.99 0.00 0.00 1.85
800 1092 4.933400 GCCGGAGAAATTTCACTGTACTTA 59.067 41.667 19.99 0.00 0.00 2.24
801 1093 3.751698 GCCGGAGAAATTTCACTGTACTT 59.248 43.478 19.99 0.00 0.00 2.24
802 1094 3.008049 AGCCGGAGAAATTTCACTGTACT 59.992 43.478 19.99 14.06 0.00 2.73
803 1095 3.125316 CAGCCGGAGAAATTTCACTGTAC 59.875 47.826 19.99 12.28 0.00 2.90
804 1096 3.334691 CAGCCGGAGAAATTTCACTGTA 58.665 45.455 19.99 0.00 0.00 2.74
805 1097 2.154462 CAGCCGGAGAAATTTCACTGT 58.846 47.619 19.99 0.00 0.00 3.55
806 1098 1.135575 GCAGCCGGAGAAATTTCACTG 60.136 52.381 19.99 17.46 0.00 3.66
807 1099 1.168714 GCAGCCGGAGAAATTTCACT 58.831 50.000 19.99 6.44 0.00 3.41
808 1100 1.168714 AGCAGCCGGAGAAATTTCAC 58.831 50.000 19.99 13.54 0.00 3.18
809 1101 2.779755 TAGCAGCCGGAGAAATTTCA 57.220 45.000 19.99 0.00 0.00 2.69
810 1102 3.627577 TCATTAGCAGCCGGAGAAATTTC 59.372 43.478 5.05 10.33 0.00 2.17
811 1103 3.620488 TCATTAGCAGCCGGAGAAATTT 58.380 40.909 5.05 0.00 0.00 1.82
812 1104 3.281727 TCATTAGCAGCCGGAGAAATT 57.718 42.857 5.05 0.00 0.00 1.82
813 1105 3.144506 CATCATTAGCAGCCGGAGAAAT 58.855 45.455 5.05 0.00 0.00 2.17
814 1106 2.170397 TCATCATTAGCAGCCGGAGAAA 59.830 45.455 5.05 0.00 0.00 2.52
815 1107 1.762370 TCATCATTAGCAGCCGGAGAA 59.238 47.619 5.05 0.00 0.00 2.87
816 1108 1.342496 CTCATCATTAGCAGCCGGAGA 59.658 52.381 5.05 0.00 0.00 3.71
882 1180 1.429299 AGGCCTTTATATCAAGGGGGC 59.571 52.381 15.89 5.76 43.42 5.80
907 1218 1.006832 GGTACGAGAATGCATGCGTT 58.993 50.000 24.84 24.84 38.09 4.84
1031 1351 3.411114 ATGGACGCTCTGGCCATGG 62.411 63.158 5.51 7.63 40.72 3.66
1032 1352 1.890979 GATGGACGCTCTGGCCATG 60.891 63.158 5.51 3.24 42.22 3.66
1033 1353 1.913951 TTGATGGACGCTCTGGCCAT 61.914 55.000 5.51 0.93 44.70 4.40
1034 1354 2.526450 CTTGATGGACGCTCTGGCCA 62.526 60.000 4.71 4.71 35.91 5.36
1035 1355 1.817099 CTTGATGGACGCTCTGGCC 60.817 63.158 0.00 0.00 34.44 5.36
1046 1366 2.056223 CCTTGCCCAGCCTTGATGG 61.056 63.158 0.00 0.00 39.04 3.51
1054 1374 4.666253 TGCCTGACCTTGCCCAGC 62.666 66.667 0.00 0.00 0.00 4.85
1276 1596 1.529010 CCTGCAGTGGTTCTGGCAA 60.529 57.895 13.81 0.00 43.78 4.52
1277 1597 1.414866 TACCTGCAGTGGTTCTGGCA 61.415 55.000 13.81 0.00 43.78 4.92
1302 1622 3.004734 TGCTAGCTTGGTTTCAGCTTTTC 59.995 43.478 17.23 0.00 39.79 2.29
1308 1628 1.200948 GCCTTGCTAGCTTGGTTTCAG 59.799 52.381 17.23 0.00 0.00 3.02
1560 1881 5.172934 ACTCCGTTTATTTCGCAATACAGA 58.827 37.500 0.00 0.00 0.00 3.41
1717 2043 8.976986 ATTGTGAAAGCAAGTTCATTCTAATC 57.023 30.769 1.48 0.00 39.61 1.75
1727 2053 8.621532 TCATCTAGTTATTGTGAAAGCAAGTT 57.378 30.769 0.00 0.00 0.00 2.66
1858 2184 4.496341 CCACGTCATCAGTATGGCATTTTC 60.496 45.833 4.78 0.00 37.59 2.29
1894 2220 5.972018 GACATCATGTCACGATTGATTCTC 58.028 41.667 13.26 0.00 46.22 2.87
1942 2269 6.525629 CACTAACTATCATTTTCCTCCGGAT 58.474 40.000 3.57 0.00 0.00 4.18
1972 2301 5.235831 GGGAGTAATACCGCTAATGTTGTTC 59.764 44.000 0.00 0.00 0.00 3.18
1986 2315 5.176958 GCACACACGATTATGGGAGTAATAC 59.823 44.000 0.00 0.00 0.00 1.89
2137 2466 2.482721 ACTCGTAGCCATTTTTGTTCGG 59.517 45.455 0.00 0.00 0.00 4.30
2227 2556 6.996879 AGATCCATGATCAAGTTATCCAGTTG 59.003 38.462 0.00 0.00 41.12 3.16
2286 2616 4.015084 CCTCAGACCTCTGCAATTGATTT 58.985 43.478 10.34 0.00 43.46 2.17
2385 2715 7.145932 GAGTGTATCCAGTAAGCAAATTTGT 57.854 36.000 19.03 3.40 0.00 2.83
2436 2766 3.244814 GCATAGTGTCGATCTGCTCTTTG 59.755 47.826 0.00 0.00 0.00 2.77
2589 2919 1.766494 TGTCATGGGCATCATCCAAC 58.234 50.000 0.00 0.00 37.87 3.77
2683 3013 1.825090 TGTAACTCCAAGGCATGCAG 58.175 50.000 21.36 10.32 0.00 4.41
2756 3087 7.972832 AAACATCTGCATTCACAAATTGATT 57.027 28.000 0.00 0.00 32.84 2.57
2795 3126 1.903877 CTGAAGCCCCCATCTCGTGT 61.904 60.000 0.00 0.00 0.00 4.49
2797 3128 0.325296 TACTGAAGCCCCCATCTCGT 60.325 55.000 0.00 0.00 0.00 4.18
2799 3130 1.141858 CCTTACTGAAGCCCCCATCTC 59.858 57.143 0.00 0.00 0.00 2.75
2828 3159 7.823745 AACTTAATAGCCCCTTTGTATCATG 57.176 36.000 0.00 0.00 0.00 3.07
2834 3165 9.709387 ATTATACAAACTTAATAGCCCCTTTGT 57.291 29.630 0.00 0.00 33.79 2.83
2946 3277 4.362677 AGCTAGTGGGGTCTTTAGATCAA 58.637 43.478 0.00 0.00 0.00 2.57
2953 3284 4.536489 ACTTGATTAGCTAGTGGGGTCTTT 59.464 41.667 0.00 0.00 31.27 2.52
2980 3311 2.516225 GGTATGTGAAGGGCCCGC 60.516 66.667 18.44 13.87 0.00 6.13
3083 3414 6.206829 AGGTTAAAATCTAGTTTTGCGAGCTT 59.793 34.615 11.12 0.00 40.17 3.74
3112 3443 0.038892 CCTGCAAGTGGACATGTTGC 60.039 55.000 11.67 11.67 45.56 4.17
3128 3459 2.606725 CAGTAATCGCTTTCAGCTCCTG 59.393 50.000 0.00 0.00 39.60 3.86
3136 3467 8.923683 AGTTTAACTTACTCAGTAATCGCTTTC 58.076 33.333 0.00 0.00 32.94 2.62
3228 3615 1.598882 AACACACACACACACACACA 58.401 45.000 0.00 0.00 0.00 3.72
3229 3616 2.697431 AAACACACACACACACACAC 57.303 45.000 0.00 0.00 0.00 3.82
3230 3617 2.618709 TGAAAACACACACACACACACA 59.381 40.909 0.00 0.00 0.00 3.72
3231 3618 3.275400 TGAAAACACACACACACACAC 57.725 42.857 0.00 0.00 0.00 3.82
3232 3619 4.455877 TGTATGAAAACACACACACACACA 59.544 37.500 0.00 0.00 0.00 3.72
3233 3620 4.975788 TGTATGAAAACACACACACACAC 58.024 39.130 0.00 0.00 0.00 3.82
3234 3621 5.826601 ATGTATGAAAACACACACACACA 57.173 34.783 0.00 0.00 30.02 3.72
3235 3622 6.850823 CACTATGTATGAAAACACACACACAC 59.149 38.462 0.00 0.00 30.02 3.82
3343 3830 5.048294 GTGGTCCATTTACTAAAGTTGGGTG 60.048 44.000 0.00 0.00 0.00 4.61
3350 3837 7.931578 TTATGTGGTGGTCCATTTACTAAAG 57.068 36.000 0.00 0.00 46.20 1.85
3371 3862 9.193806 GGCCCATGAAATATATGAGTGATTTAT 57.806 33.333 0.00 0.00 0.00 1.40
3390 3881 9.719355 GGTAAATAATTAAATTTAGGGCCCATG 57.281 33.333 27.56 0.00 33.19 3.66
3489 3993 3.465871 AGCCCGAAAGTAAAAACGTACA 58.534 40.909 0.00 0.00 0.00 2.90
3490 3994 5.050431 TGTTAGCCCGAAAGTAAAAACGTAC 60.050 40.000 0.00 0.00 0.00 3.67
3493 3997 4.471157 TGTTAGCCCGAAAGTAAAAACG 57.529 40.909 0.00 0.00 0.00 3.60
3500 4052 4.015872 TGAATCTTGTTAGCCCGAAAGT 57.984 40.909 0.00 0.00 0.00 2.66
3510 4062 6.601332 AGAAAGACCACCTTGAATCTTGTTA 58.399 36.000 0.00 0.00 34.79 2.41
3545 4097 7.557719 AGCACATTGGATAGCTTACATAAACTT 59.442 33.333 0.00 0.00 32.52 2.66
3561 4113 1.340889 GCCTGTTGAAAGCACATTGGA 59.659 47.619 0.00 0.00 0.00 3.53
3593 4146 6.212187 TGCTACCAGCTCATTCTCATATATGT 59.788 38.462 12.42 0.00 42.97 2.29
3594 4147 6.637657 TGCTACCAGCTCATTCTCATATATG 58.362 40.000 6.36 6.36 42.97 1.78
3595 4148 6.864151 TGCTACCAGCTCATTCTCATATAT 57.136 37.500 0.00 0.00 42.97 0.86
3596 4149 6.864151 ATGCTACCAGCTCATTCTCATATA 57.136 37.500 0.00 0.00 42.97 0.86
3649 4203 4.999950 AGTAGTCTTTTGAGCTGTTGATGG 59.000 41.667 0.00 0.00 0.00 3.51
3705 4259 9.217278 CCATCAATTTCACCACAAAAATGATAA 57.783 29.630 0.00 0.00 30.57 1.75
3720 4274 8.551682 AGGAAATTATTAGGCCATCAATTTCA 57.448 30.769 27.70 8.90 42.93 2.69
3721 4275 9.914131 GTAGGAAATTATTAGGCCATCAATTTC 57.086 33.333 23.26 23.26 41.54 2.17
3781 4335 4.332543 CGAACAATAGGCATGCACTAGAAA 59.667 41.667 21.36 0.00 0.00 2.52
3782 4336 3.871006 CGAACAATAGGCATGCACTAGAA 59.129 43.478 21.36 0.00 0.00 2.10
3804 4358 9.722056 CTTAAGCCACATCAAGTAAAATATGAC 57.278 33.333 0.00 0.00 0.00 3.06
3875 4431 9.202273 GTATTCCATGAAAACAACAAATAAGCA 57.798 29.630 0.00 0.00 0.00 3.91
4084 4650 0.751277 CTGTTCCACCACCTGCACAA 60.751 55.000 0.00 0.00 0.00 3.33
4161 4727 6.501805 TCTGATAATATACAACAGAGGCCCAT 59.498 38.462 0.00 0.00 33.57 4.00
4230 4796 5.730550 GTGTCATCCACAGTGGTAATAAGA 58.269 41.667 19.65 6.84 43.92 2.10
4314 4880 8.768397 AGTAAGAAATATAATGTCCACCACTCA 58.232 33.333 0.00 0.00 0.00 3.41
4375 4941 7.633553 GCTTCCAAATGGCTAATAGGAAACAAT 60.634 37.037 0.00 0.00 34.14 2.71
4397 4963 7.878127 TGGCCTATGTATAAATAGTTGAGCTTC 59.122 37.037 3.32 0.00 0.00 3.86
4418 4984 8.499406 TGGTTCACTATACTAAATAATTGGCCT 58.501 33.333 3.32 0.00 0.00 5.19
4568 5134 0.914551 CTATTCTTCGCGGTGTGTCG 59.085 55.000 6.13 0.00 0.00 4.35
4634 5200 4.082300 CGATTTTCACCATGTGGGATTTCA 60.082 41.667 3.77 0.00 41.15 2.69
4641 5207 1.130373 CGGTCGATTTTCACCATGTGG 59.870 52.381 0.00 0.00 42.17 4.17
4692 5258 8.701908 ATAGTGTTGCATTGGAGATGAATTAT 57.298 30.769 0.00 0.00 0.00 1.28
4694 5260 8.523915 TTATAGTGTTGCATTGGAGATGAATT 57.476 30.769 0.00 0.00 0.00 2.17
4699 5265 5.297776 GTGCTTATAGTGTTGCATTGGAGAT 59.702 40.000 0.00 0.00 37.76 2.75
4727 5293 7.790823 ATTGCATACATTTCTAAAATTGGGC 57.209 32.000 0.00 0.00 0.00 5.36
4798 5364 1.053835 TGGGTGTCAGCCTCACTCAA 61.054 55.000 21.33 0.00 42.31 3.02
4800 5366 0.603975 GTTGGGTGTCAGCCTCACTC 60.604 60.000 21.33 4.61 36.53 3.51
4817 5383 7.739498 ACTCGTCTAATTAACAACAATGGTT 57.261 32.000 0.00 0.00 37.87 3.67
4891 5457 5.752955 GCAGCTCCTTCATCTACTAGAAAAG 59.247 44.000 0.00 0.00 0.00 2.27
4892 5458 5.395768 GGCAGCTCCTTCATCTACTAGAAAA 60.396 44.000 0.00 0.00 0.00 2.29
4939 5505 0.179001 CCCCACCTCCGAAAAACTGT 60.179 55.000 0.00 0.00 0.00 3.55
4948 5514 0.036671 GTAGTTGTTCCCCACCTCCG 60.037 60.000 0.00 0.00 0.00 4.63
4983 5549 4.811969 TCCTCTAGCAACGAACCATTAA 57.188 40.909 0.00 0.00 0.00 1.40
4984 5550 4.404394 TCATCCTCTAGCAACGAACCATTA 59.596 41.667 0.00 0.00 0.00 1.90
4985 5551 3.197766 TCATCCTCTAGCAACGAACCATT 59.802 43.478 0.00 0.00 0.00 3.16
4986 5552 2.766263 TCATCCTCTAGCAACGAACCAT 59.234 45.455 0.00 0.00 0.00 3.55
5007 5573 3.326006 TGACAGAGAAGAAATGTGGCTCT 59.674 43.478 0.00 0.00 36.44 4.09
5008 5574 3.668447 TGACAGAGAAGAAATGTGGCTC 58.332 45.455 0.00 0.00 0.00 4.70
5035 5601 6.753180 ACATAGACATATCTGTGACATGGTC 58.247 40.000 4.60 0.00 44.66 4.02
5040 5606 4.580580 AGCGACATAGACATATCTGTGACA 59.419 41.667 4.60 0.00 44.66 3.58
5045 5611 5.767269 AGTTGAGCGACATAGACATATCTG 58.233 41.667 0.00 0.00 36.29 2.90
5162 5728 3.499918 CGTTCAATGATAGCTTCCCATCC 59.500 47.826 0.00 0.00 0.00 3.51
5167 5733 4.694339 ACCTACGTTCAATGATAGCTTCC 58.306 43.478 0.00 0.00 0.00 3.46
5206 5772 2.484264 GCGTCAAACACTGGCTAAATCT 59.516 45.455 0.00 0.00 0.00 2.40
5212 5778 0.534877 TGATGCGTCAAACACTGGCT 60.535 50.000 6.04 0.00 0.00 4.75
5237 5803 4.567747 GGTCACAACCCATAACATCCTTCT 60.568 45.833 0.00 0.00 39.93 2.85
5267 5833 8.224025 TGGGTGATGTTGTAATGATACCATATT 58.776 33.333 0.00 0.00 31.59 1.28
5278 5844 4.532834 GGGTATGTGGGTGATGTTGTAAT 58.467 43.478 0.00 0.00 0.00 1.89
5310 5876 5.801350 TGTGCAACTTCATAGCTACATTC 57.199 39.130 0.00 0.00 38.04 2.67
5435 6001 1.135199 CATGTCTCAACCATTGCTGCC 60.135 52.381 0.00 0.00 0.00 4.85
5439 6005 0.889994 TGCCATGTCTCAACCATTGC 59.110 50.000 0.00 0.00 33.02 3.56
5454 6021 6.166984 TGAAATCAGGTAAATTTTGTGCCA 57.833 33.333 0.00 0.00 0.00 4.92
5470 6037 0.179004 ACCACGGGTGCTTGAAATCA 60.179 50.000 0.00 0.00 32.98 2.57
5471 6038 2.641197 ACCACGGGTGCTTGAAATC 58.359 52.632 0.00 0.00 32.98 2.17
5583 6152 1.621992 GATCGCTGGGATCTAGACCA 58.378 55.000 22.95 7.58 46.66 4.02
5597 6166 0.663688 TGCCGAGAACTAGAGATCGC 59.336 55.000 0.00 0.00 33.94 4.58
5673 6242 4.919754 GCAAATCACAATTCAACTCACTCC 59.080 41.667 0.00 0.00 0.00 3.85
5717 6286 5.950544 TGTGTATATAAAGGAGCTGTGGT 57.049 39.130 0.00 0.00 0.00 4.16
5719 6288 8.031864 CCTAGATGTGTATATAAAGGAGCTGTG 58.968 40.741 0.00 0.00 0.00 3.66
5723 6292 9.593134 CAATCCTAGATGTGTATATAAAGGAGC 57.407 37.037 0.00 0.00 0.00 4.70
5736 6305 6.539826 TGATTTGTACTGCAATCCTAGATGTG 59.460 38.462 0.00 0.00 36.89 3.21
5737 6306 6.653020 TGATTTGTACTGCAATCCTAGATGT 58.347 36.000 0.00 0.00 36.89 3.06
5746 6315 5.072741 AGTCAACCTGATTTGTACTGCAAT 58.927 37.500 0.00 0.00 36.89 3.56
5833 6402 5.304357 TGATGGAAGAATACGCAGAGGAATA 59.696 40.000 0.00 0.00 0.00 1.75
5841 6410 2.238646 AGGGTTGATGGAAGAATACGCA 59.761 45.455 0.00 0.00 0.00 5.24
5844 6413 4.236527 ACCAGGGTTGATGGAAGAATAC 57.763 45.455 0.00 0.00 40.51 1.89
5883 6452 5.420104 TCTCACTGCAAGATTCTATCTCACA 59.580 40.000 0.00 0.00 39.08 3.58
5900 6469 8.713737 TCAGATAAAAGATGAACATCTCACTG 57.286 34.615 16.12 17.42 46.75 3.66
5912 6481 9.011095 ACTGATGGCATATTCAGATAAAAGATG 57.989 33.333 20.32 0.00 41.53 2.90
5925 6494 5.894298 TGAAGACCTACTGATGGCATATT 57.106 39.130 0.00 0.00 0.00 1.28
5928 6497 3.972638 AGATGAAGACCTACTGATGGCAT 59.027 43.478 0.00 0.00 0.00 4.40
6008 6583 6.147473 TCCCATCTATAGGACCAATTGTGTA 58.853 40.000 4.43 0.00 0.00 2.90
6153 6728 6.136071 GCATGTATGTATTACCGCTTTTCTG 58.864 40.000 0.00 0.00 0.00 3.02
6251 6827 6.207691 TCAAAAGGGCTAAAGCATAATCAC 57.792 37.500 4.07 0.00 44.36 3.06
6332 6908 3.243301 CGGCTTCTTGTAGATAACCGCTA 60.243 47.826 0.00 0.00 31.07 4.26
6462 7038 5.729883 CGAGTGACTGCTTCATTATTTTTCG 59.270 40.000 0.00 0.00 36.32 3.46
6517 7093 2.673368 CGTACAATCTTTCCACCTGCTC 59.327 50.000 0.00 0.00 0.00 4.26
6665 7246 0.329261 AGCTTGCTGCATCACCCTTA 59.671 50.000 1.84 0.00 45.94 2.69
6802 7383 2.072874 TTGCAAGGCTGGGAGAAGCT 62.073 55.000 0.00 0.00 43.06 3.74
7012 7756 6.368791 GGGAAAGTAAGGTTTGAATTTGCATC 59.631 38.462 0.00 0.00 0.00 3.91
7089 7834 9.605955 GCATTGTGGGAAAAACATTTATTTTAC 57.394 29.630 0.00 0.00 31.50 2.01
7111 7856 5.845103 TGTGACAATTTTCTCATGTGCATT 58.155 33.333 0.00 0.00 0.00 3.56
7167 7912 5.500234 TCAGAATATGACAGTTTTCCTGGG 58.500 41.667 0.00 0.00 46.06 4.45
7198 7944 7.649533 TGTCAAGATCTGAAATATGCCATTT 57.350 32.000 0.00 0.00 35.22 2.32
7201 7947 6.124340 ACATGTCAAGATCTGAAATATGCCA 58.876 36.000 0.00 0.00 35.22 4.92
7237 7984 7.921214 ACTCCACGATGACAACTGTATAATAAG 59.079 37.037 0.00 0.00 0.00 1.73
7250 7997 2.298729 TCACATTCACTCCACGATGACA 59.701 45.455 0.00 0.00 0.00 3.58
7254 8001 1.902508 AGGTCACATTCACTCCACGAT 59.097 47.619 0.00 0.00 0.00 3.73
7275 8041 8.531146 CATTAAATTTACCCAGGTCTCACATTT 58.469 33.333 0.00 0.00 0.00 2.32
7303 8069 3.441222 TCACCAAATCTCACATGCACATC 59.559 43.478 0.00 0.00 0.00 3.06
7359 8125 5.329399 TGGTTTGCAGATAACCCTACAAAT 58.671 37.500 14.72 0.00 43.55 2.32
7417 8183 0.941542 TCACGTGCAAAAGTGGCTAC 59.058 50.000 11.67 0.00 38.77 3.58
7420 8186 0.869880 GGTTCACGTGCAAAAGTGGC 60.870 55.000 11.67 10.07 38.77 5.01
7440 8206 4.122776 GGCACCAGCATATATTCCTATCG 58.877 47.826 0.00 0.00 44.61 2.92
7456 8222 0.604073 CACAATGCTGATTGGCACCA 59.396 50.000 2.24 0.00 45.36 4.17
7459 8225 6.468333 AATAATACACAATGCTGATTGGCA 57.532 33.333 2.24 0.00 43.00 4.92
7465 8231 9.502091 GGTTAGGATAATAATACACAATGCTGA 57.498 33.333 0.00 0.00 0.00 4.26
7468 8234 7.148306 CCCGGTTAGGATAATAATACACAATGC 60.148 40.741 0.00 0.00 45.00 3.56
7469 8235 7.881232 ACCCGGTTAGGATAATAATACACAATG 59.119 37.037 0.00 0.00 45.00 2.82
7489 8255 2.011122 CACTCCTATCCATACCCGGT 57.989 55.000 0.00 0.00 0.00 5.28
7490 8256 0.608640 GCACTCCTATCCATACCCGG 59.391 60.000 0.00 0.00 0.00 5.73
7494 8260 0.608640 CGGGGCACTCCTATCCATAC 59.391 60.000 0.00 0.00 35.33 2.39
7499 8265 0.759436 TTCCTCGGGGCACTCCTATC 60.759 60.000 0.00 0.00 35.33 2.08
7507 8273 2.104111 CACAGTTATATTCCTCGGGGCA 59.896 50.000 0.00 0.00 0.00 5.36
7508 8274 2.367567 TCACAGTTATATTCCTCGGGGC 59.632 50.000 0.00 0.00 0.00 5.80
7521 8287 7.966246 ACCAACATTATTAACGTCACAGTTA 57.034 32.000 0.00 0.00 35.70 2.24
7541 8307 8.637986 AGCAAAGTATAACATTCTTTCAACCAA 58.362 29.630 0.00 0.00 29.02 3.67
7542 8308 8.177119 AGCAAAGTATAACATTCTTTCAACCA 57.823 30.769 0.00 0.00 29.02 3.67
7586 8967 6.070481 TGCAAAGTCTGATGGGTAGTTGTATA 60.070 38.462 0.00 0.00 0.00 1.47
7594 8975 2.025981 AGCATGCAAAGTCTGATGGGTA 60.026 45.455 21.98 0.00 0.00 3.69
7628 9009 1.739466 GAACATTCGCTCATCTTGGCA 59.261 47.619 0.00 0.00 0.00 4.92
7687 9102 5.820947 CCCTAGTCGGCTACATAAACAAAAT 59.179 40.000 0.00 0.00 0.00 1.82
7721 9136 0.879090 GTGTAGAAACCCGGCCAAAG 59.121 55.000 2.24 0.00 0.00 2.77
7741 9156 5.220416 CCTCGAACGACATAATCCTTGAAAC 60.220 44.000 0.00 0.00 0.00 2.78
7757 9229 3.948196 TGGTTTGTAAAACCTCGAACG 57.052 42.857 19.66 0.00 40.88 3.95
7879 9351 6.951198 TGGTAACATAACATGATTTCCCAGTT 59.049 34.615 0.00 0.00 46.17 3.16
7900 9372 1.764134 CCCCTATTTACGTGGCTGGTA 59.236 52.381 0.00 0.00 0.00 3.25
7907 9388 1.474498 GCCAGTCCCCCTATTTACGTG 60.474 57.143 0.00 0.00 0.00 4.49
7910 9391 2.422945 CCTTGCCAGTCCCCCTATTTAC 60.423 54.545 0.00 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.