Multiple sequence alignment - TraesCS1D01G333800

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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 TraesCS1D01G333800 chr1D 100.000 5012 0 0 1 5012 423762810 423767821 0.000000e+00 9256
1 TraesCS1D01G333800 chr1D 77.247 712 110 33 1204 1890 246937157 246937841 2.200000e-98 370
2 TraesCS1D01G333800 chr1A 86.013 2724 218 75 202 2848 520121821 520124458 0.000000e+00 2769
3 TraesCS1D01G333800 chr1A 94.530 713 29 4 4304 5012 520128790 520129496 0.000000e+00 1092
4 TraesCS1D01G333800 chr1A 91.111 765 32 12 3476 4222 520125255 520126001 0.000000e+00 1003
5 TraesCS1D01G333800 chr1A 87.442 645 57 19 2859 3488 520124591 520125226 0.000000e+00 721
6 TraesCS1D01G333800 chr1A 91.599 369 26 3 1 367 520121320 520121685 5.790000e-139 505
7 TraesCS1D01G333800 chr1A 77.195 706 125 26 1204 1890 300859827 300859139 3.660000e-101 379
8 TraesCS1D01G333800 chr1A 89.759 166 16 1 202 367 520121671 520121835 1.410000e-50 211
9 TraesCS1D01G333800 chr1B 87.545 2473 170 66 623 2998 573215343 573217774 0.000000e+00 2734
10 TraesCS1D01G333800 chr1B 91.157 1357 76 28 3057 4391 573218034 573219368 0.000000e+00 1801
11 TraesCS1D01G333800 chr1B 76.947 321 45 18 1204 1502 331146665 331146352 6.720000e-34 156
12 TraesCS1D01G333800 chr1B 88.636 132 10 3 4391 4519 573220649 573220778 6.720000e-34 156
13 TraesCS1D01G333800 chr2D 80.547 658 66 17 1 657 528804631 528805227 2.750000e-122 449
14 TraesCS1D01G333800 chr2D 82.727 330 48 5 4519 4846 3031270 3030948 8.210000e-73 285
15 TraesCS1D01G333800 chr7A 89.408 321 29 1 4519 4839 176248429 176248114 2.810000e-107 399
16 TraesCS1D01G333800 chr3D 86.604 321 36 4 4519 4839 481917270 481917583 1.030000e-91 348
17 TraesCS1D01G333800 chr3D 86.111 324 39 2 4517 4839 169426218 169426536 1.340000e-90 344
18 TraesCS1D01G333800 chr4D 86.293 321 38 2 4519 4839 173577035 173576721 1.340000e-90 344
19 TraesCS1D01G333800 chr6B 85.185 324 40 3 4517 4839 701189222 701189538 4.840000e-85 326
20 TraesCS1D01G333800 chr6B 90.756 119 4 2 1206 1324 72379517 72379406 8.690000e-33 152
21 TraesCS1D01G333800 chr6B 87.395 119 15 0 1390 1508 72379300 72379182 2.430000e-28 137
22 TraesCS1D01G333800 chr4A 83.483 333 46 6 4517 4848 726087348 726087672 8.150000e-78 302
23 TraesCS1D01G333800 chr2A 83.282 323 48 2 4517 4839 136969902 136969586 4.910000e-75 292
24 TraesCS1D01G333800 chr6A 89.076 119 13 0 1390 1508 39180723 39180605 1.120000e-31 148
25 TraesCS1D01G333800 chr6D 89.916 119 5 3 1206 1324 34999789 34999678 4.040000e-31 147
26 TraesCS1D01G333800 chr6D 87.395 119 15 0 1390 1508 34999576 34999458 2.430000e-28 137
27 TraesCS1D01G333800 chr4B 88.333 120 12 2 1 118 27529424 27529543 5.230000e-30 143


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 TraesCS1D01G333800 chr1D 423762810 423767821 5011 False 9256.000000 9256 100.000000 1 5012 1 chr1D.!!$F2 5011
1 TraesCS1D01G333800 chr1D 246937157 246937841 684 False 370.000000 370 77.247000 1204 1890 1 chr1D.!!$F1 686
2 TraesCS1D01G333800 chr1A 520121320 520129496 8176 False 1050.166667 2769 90.075667 1 5012 6 chr1A.!!$F1 5011
3 TraesCS1D01G333800 chr1A 300859139 300859827 688 True 379.000000 379 77.195000 1204 1890 1 chr1A.!!$R1 686
4 TraesCS1D01G333800 chr1B 573215343 573220778 5435 False 1563.666667 2734 89.112667 623 4519 3 chr1B.!!$F1 3896
5 TraesCS1D01G333800 chr2D 528804631 528805227 596 False 449.000000 449 80.547000 1 657 1 chr2D.!!$F1 656

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
989 1326 0.524862 GTAGGAAGGACGAACAGCGA 59.475 55.0 0.00 0.00 44.57 4.93 F
1617 2015 0.036294 GACAGGACAACCCAGTAGGC 60.036 60.0 0.00 0.00 40.58 3.93 F
1977 2395 0.366871 CGTGCATGCAGTCTTCGTAC 59.633 55.0 23.41 4.73 0.00 3.67 F
2207 2625 0.523072 CAACCGAATGCTCAACTGGG 59.477 55.0 0.00 0.00 0.00 4.45 F
3813 4666 0.673437 GCAGGGCACTTTGTAAGCAA 59.327 50.0 0.00 0.00 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2108 2526 0.394216 TCCCTGTTCATCAATGGCGG 60.394 55.0 0.00 0.0 0.00 6.13 R
3137 3940 0.387929 AGAGTGTTGAACCGAAGCGA 59.612 50.0 0.00 0.0 0.00 4.93 R
3304 4107 0.395312 ACGTACTGGACACCCCAAAG 59.605 55.0 0.00 0.0 46.07 2.77 R
3981 4845 0.034059 AAAGAGCCGGAGACTGTGTG 59.966 55.0 5.05 0.0 0.00 3.82 R
4848 9708 0.182299 TGCATGGTTCGGATGGCATA 59.818 50.0 0.00 0.0 0.00 3.14 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
19 20 2.882927 AGCTACAAGTGACACAACGA 57.117 45.000 8.59 0.00 0.00 3.85
21 22 2.159156 AGCTACAAGTGACACAACGACA 60.159 45.455 8.59 0.00 0.00 4.35
109 110 1.228124 TGAGTTTGCTGGAACCGGG 60.228 57.895 6.32 0.00 0.00 5.73
185 188 3.069443 ACGAACATCCATGGTTTTGCTTT 59.931 39.130 12.58 0.30 0.00 3.51
190 193 3.651803 TCCATGGTTTTGCTTTAACCG 57.348 42.857 12.58 0.00 46.44 4.44
202 205 4.698575 TGCTTTAACCGGCAATTCTTTTT 58.301 34.783 0.00 0.00 35.40 1.94
242 245 8.496707 AAGTTTTTGCTTCAAATGACTTCAAT 57.503 26.923 12.01 0.00 36.40 2.57
243 246 8.496707 AGTTTTTGCTTCAAATGACTTCAATT 57.503 26.923 0.00 0.00 33.19 2.32
367 668 1.172812 GGAGTTGCTGAAACCGGCTT 61.173 55.000 0.00 0.00 39.85 4.35
372 673 2.564721 GCTGAAACCGGCTTTGGCT 61.565 57.895 0.00 0.00 38.73 4.75
428 729 4.643387 AAGTGGGTGGCGCTGGAC 62.643 66.667 7.64 1.32 0.00 4.02
435 736 1.672356 GTGGCGCTGGACAATGACT 60.672 57.895 7.64 0.00 28.51 3.41
511 819 1.029947 TCCTCACGCGAGATGTGCTA 61.030 55.000 15.93 0.00 42.34 3.49
522 830 0.811219 GATGTGCTAGTGGCGATGCA 60.811 55.000 0.00 0.00 45.43 3.96
535 843 1.371635 GATGCACGGTGTTGGTTGC 60.372 57.895 10.24 0.00 0.00 4.17
559 867 4.974368 TTTTCTTTTGTTTCTCTGCGGA 57.026 36.364 0.00 0.00 0.00 5.54
563 871 1.497991 TTTGTTTCTCTGCGGACGAG 58.502 50.000 0.00 0.00 0.00 4.18
569 877 3.057547 CTCTGCGGACGAGAGGTGG 62.058 68.421 0.00 0.00 34.42 4.61
587 895 3.194968 GGTGGACGAGGACAAAGATTAGA 59.805 47.826 0.00 0.00 0.00 2.10
620 928 2.169561 TGGTTGTTAGCAGGCATATCGA 59.830 45.455 0.00 0.00 0.00 3.59
649 957 2.285824 GCAGGCCAGCCCAAATTTA 58.714 52.632 9.39 0.00 36.58 1.40
658 966 2.049767 CCCAAATTTAGGCCGGCGT 61.050 57.895 26.70 26.70 0.00 5.68
700 1008 9.249457 GCTGCCCAAATAAAATCTAAATAAGTC 57.751 33.333 0.00 0.00 0.00 3.01
710 1018 8.631480 AAAATCTAAATAAGTCCCGTGTTCTT 57.369 30.769 0.00 0.00 0.00 2.52
786 1095 3.181487 GCCTCCGCAAACAATATGACAAT 60.181 43.478 0.00 0.00 34.03 2.71
797 1106 5.012239 ACAATATGACAATCACAAGTGCCT 58.988 37.500 0.00 0.00 0.00 4.75
818 1127 6.126768 TGCCTAGCTGTTTATTGTCCTCTTAT 60.127 38.462 0.00 0.00 0.00 1.73
827 1136 7.550551 TGTTTATTGTCCTCTTATCAGAGCAAG 59.449 37.037 0.00 0.00 44.96 4.01
844 1181 8.894731 TCAGAGCAAGTAGTAGTAGTTTAGATG 58.105 37.037 0.00 0.00 0.00 2.90
845 1182 7.646130 CAGAGCAAGTAGTAGTAGTTTAGATGC 59.354 40.741 0.00 0.00 0.00 3.91
846 1183 7.558444 AGAGCAAGTAGTAGTAGTTTAGATGCT 59.442 37.037 7.85 7.85 0.00 3.79
869 1206 2.793278 AACAACCGCCATGAAGTTTC 57.207 45.000 0.00 0.00 0.00 2.78
872 1209 0.898326 AACCGCCATGAAGTTTCCCC 60.898 55.000 0.00 0.00 0.00 4.81
873 1210 2.406616 CCGCCATGAAGTTTCCCCG 61.407 63.158 0.00 0.00 0.00 5.73
874 1211 1.376683 CGCCATGAAGTTTCCCCGA 60.377 57.895 0.00 0.00 0.00 5.14
875 1212 0.958382 CGCCATGAAGTTTCCCCGAA 60.958 55.000 0.00 0.00 0.00 4.30
876 1213 1.253100 GCCATGAAGTTTCCCCGAAA 58.747 50.000 0.00 0.00 0.00 3.46
877 1214 1.202348 GCCATGAAGTTTCCCCGAAAG 59.798 52.381 0.00 0.00 31.87 2.62
968 1305 3.684103 TTTAAACCGTTCAGTGCACTG 57.316 42.857 36.07 36.07 45.08 3.66
977 1314 2.802816 GTTCAGTGCACTGTGTAGGAAG 59.197 50.000 38.41 16.38 44.12 3.46
985 1322 2.035449 CACTGTGTAGGAAGGACGAACA 59.965 50.000 0.00 0.00 0.00 3.18
986 1323 2.296471 ACTGTGTAGGAAGGACGAACAG 59.704 50.000 0.00 0.00 39.49 3.16
987 1324 1.000506 TGTGTAGGAAGGACGAACAGC 59.999 52.381 0.00 0.00 0.00 4.40
989 1326 0.524862 GTAGGAAGGACGAACAGCGA 59.475 55.000 0.00 0.00 44.57 4.93
1053 1417 0.814457 TCTTCCTCTCTCTGCTTCGC 59.186 55.000 0.00 0.00 0.00 4.70
1054 1418 0.529833 CTTCCTCTCTCTGCTTCGCA 59.470 55.000 0.00 0.00 36.92 5.10
1122 1486 2.639883 GATACGTGGAGGTTCGGCCC 62.640 65.000 0.00 0.00 38.26 5.80
1138 1502 1.520666 CCCAGTAAGTCCGGCGATT 59.479 57.895 9.30 2.49 0.00 3.34
1176 1540 1.762419 TGTTCGTCTCCGTTTTCTCG 58.238 50.000 0.00 0.00 35.01 4.04
1177 1541 0.433871 GTTCGTCTCCGTTTTCTCGC 59.566 55.000 0.00 0.00 35.01 5.03
1178 1542 0.313043 TTCGTCTCCGTTTTCTCGCT 59.687 50.000 0.00 0.00 35.01 4.93
1196 1563 1.978712 CTGCTGACGCTGCTTGGATG 61.979 60.000 0.00 0.00 36.97 3.51
1200 1567 2.033141 ACGCTGCTTGGATGTGCT 59.967 55.556 0.00 0.00 0.00 4.40
1201 1568 2.249557 GACGCTGCTTGGATGTGCTG 62.250 60.000 0.00 0.00 0.00 4.41
1202 1569 2.882876 GCTGCTTGGATGTGCTGG 59.117 61.111 0.00 0.00 0.00 4.85
1336 1718 2.435938 TCATCGGCGGGAACTTGC 60.436 61.111 7.21 0.00 0.00 4.01
1348 1742 1.544314 GGAACTTGCTTGTCCTCAGCT 60.544 52.381 0.00 0.00 0.00 4.24
1354 1748 1.020437 GCTTGTCCTCAGCTTATGCC 58.980 55.000 0.00 0.00 40.80 4.40
1356 1750 0.744414 TTGTCCTCAGCTTATGCCGC 60.744 55.000 0.00 0.00 40.80 6.53
1364 1758 3.320078 CTTATGCCGCCGTCGTCG 61.320 66.667 0.00 0.00 0.00 5.12
1365 1759 4.118995 TTATGCCGCCGTCGTCGT 62.119 61.111 0.71 0.00 35.01 4.34
1366 1760 4.541482 TATGCCGCCGTCGTCGTC 62.541 66.667 0.71 0.00 35.01 4.20
1375 1769 2.200073 CGTCGTCGTCGTCATCGTG 61.200 63.158 3.67 0.00 38.33 4.35
1508 1902 2.167281 CCTCATCTTCGTGGTCAGTCAT 59.833 50.000 0.00 0.00 0.00 3.06
1536 1933 4.152402 ACAAGCACATCGTGTTCTATGTTC 59.848 41.667 0.00 0.00 33.60 3.18
1548 1945 6.109359 GTGTTCTATGTTCCTTCTGCAGTAT 58.891 40.000 14.67 1.41 0.00 2.12
1551 1948 7.093509 TGTTCTATGTTCCTTCTGCAGTATACA 60.094 37.037 14.67 12.06 0.00 2.29
1552 1949 7.603180 TCTATGTTCCTTCTGCAGTATACAT 57.397 36.000 14.67 17.40 0.00 2.29
1553 1950 8.023021 TCTATGTTCCTTCTGCAGTATACATT 57.977 34.615 14.67 5.79 0.00 2.71
1554 1951 8.486210 TCTATGTTCCTTCTGCAGTATACATTT 58.514 33.333 14.67 2.03 0.00 2.32
1556 1953 7.759489 TGTTCCTTCTGCAGTATACATTTTT 57.241 32.000 14.67 0.00 0.00 1.94
1611 2009 0.608130 CTGATCGACAGGACAACCCA 59.392 55.000 7.01 0.00 42.39 4.51
1614 2012 1.822990 GATCGACAGGACAACCCAGTA 59.177 52.381 0.00 0.00 37.41 2.74
1617 2015 0.036294 GACAGGACAACCCAGTAGGC 60.036 60.000 0.00 0.00 40.58 3.93
1920 2334 4.025401 CCAACACTTCCACCGCGC 62.025 66.667 0.00 0.00 0.00 6.86
1921 2335 3.276091 CAACACTTCCACCGCGCA 61.276 61.111 8.75 0.00 0.00 6.09
1977 2395 0.366871 CGTGCATGCAGTCTTCGTAC 59.633 55.000 23.41 4.73 0.00 3.67
2048 2466 1.373246 CAAACAAGTGCGGCCATGG 60.373 57.895 7.63 7.63 0.00 3.66
2066 2484 3.577649 TGGCTCGTCTCAAGAACTAAG 57.422 47.619 0.00 0.00 0.00 2.18
2069 2487 3.131400 GGCTCGTCTCAAGAACTAAGGAT 59.869 47.826 0.00 0.00 0.00 3.24
2105 2523 5.860941 TCTTCTGATCAACTCATACCTCC 57.139 43.478 0.00 0.00 32.10 4.30
2106 2524 5.272402 TCTTCTGATCAACTCATACCTCCA 58.728 41.667 0.00 0.00 32.10 3.86
2108 2526 5.344743 TCTGATCAACTCATACCTCCAAC 57.655 43.478 0.00 0.00 32.10 3.77
2152 2570 2.359230 GTGGTGAGGCAGCAGGTC 60.359 66.667 0.00 0.00 42.60 3.85
2207 2625 0.523072 CAACCGAATGCTCAACTGGG 59.477 55.000 0.00 0.00 0.00 4.45
2253 2671 4.929808 GGTAACATGAAACGAGTCATCAGT 59.070 41.667 0.00 0.00 36.04 3.41
2257 2675 6.893958 ACATGAAACGAGTCATCAGTATTC 57.106 37.500 0.00 0.00 36.04 1.75
2258 2676 5.812642 ACATGAAACGAGTCATCAGTATTCC 59.187 40.000 0.00 0.00 36.04 3.01
2259 2677 4.421058 TGAAACGAGTCATCAGTATTCCG 58.579 43.478 0.00 0.00 0.00 4.30
2261 2679 4.451629 AACGAGTCATCAGTATTCCGTT 57.548 40.909 0.00 0.00 34.71 4.44
2262 2680 3.770666 ACGAGTCATCAGTATTCCGTTG 58.229 45.455 0.00 0.00 0.00 4.10
2268 2691 5.362717 AGTCATCAGTATTCCGTTGTCCATA 59.637 40.000 0.00 0.00 0.00 2.74
2277 2700 1.597663 CCGTTGTCCATAATTCGCTCC 59.402 52.381 0.00 0.00 0.00 4.70
2467 2914 1.001706 CATGAATGGAGCCATCAAGCG 60.002 52.381 1.88 0.00 35.31 4.68
2522 2969 0.911769 TGGGCCTCATTCGAACAGAT 59.088 50.000 4.53 0.00 0.00 2.90
2526 2973 1.943340 GCCTCATTCGAACAGATTCCC 59.057 52.381 0.00 0.00 0.00 3.97
2532 2979 5.953183 TCATTCGAACAGATTCCCATTTTG 58.047 37.500 0.00 0.00 0.00 2.44
2533 2980 5.709631 TCATTCGAACAGATTCCCATTTTGA 59.290 36.000 0.00 0.00 0.00 2.69
2534 2981 6.208402 TCATTCGAACAGATTCCCATTTTGAA 59.792 34.615 0.00 0.00 0.00 2.69
2535 2982 6.588719 TTCGAACAGATTCCCATTTTGAAT 57.411 33.333 0.00 0.00 35.21 2.57
2536 2983 6.194796 TCGAACAGATTCCCATTTTGAATC 57.805 37.500 5.13 5.13 45.42 2.52
2571 3022 1.279271 ACTGCCGGCTGAAATAAGACT 59.721 47.619 36.36 10.71 0.00 3.24
2643 3094 4.486090 CGCAATCCTACAGCGTCTATTAT 58.514 43.478 0.00 0.00 45.82 1.28
2685 3136 1.218316 GCCGAGGATTCACGAGGTT 59.782 57.895 0.00 0.00 0.00 3.50
2922 3506 3.127376 TGACACGATCAGATGCCATTTTG 59.873 43.478 0.00 0.00 31.91 2.44
2931 3515 3.376859 CAGATGCCATTTTGCAATGCATT 59.623 39.130 20.21 5.99 45.84 3.56
2933 3517 5.065346 CAGATGCCATTTTGCAATGCATTTA 59.935 36.000 20.21 0.00 45.84 1.40
2934 3518 4.948608 TGCCATTTTGCAATGCATTTAG 57.051 36.364 9.39 0.17 38.88 1.85
2938 3522 5.065474 GCCATTTTGCAATGCATTTAGTCAT 59.935 36.000 9.39 0.00 38.88 3.06
2940 3524 7.041644 GCCATTTTGCAATGCATTTAGTCATAT 60.042 33.333 9.39 0.00 38.88 1.78
2967 3551 2.773993 ACATTAACCCGTGGTAGGTG 57.226 50.000 0.00 0.00 37.78 4.00
3002 3776 7.062749 TGACTTTGTCAGAGTATTACAAGGT 57.937 36.000 0.00 0.00 43.47 3.50
3003 3777 6.929049 TGACTTTGTCAGAGTATTACAAGGTG 59.071 38.462 4.54 0.00 41.65 4.00
3005 3779 7.155328 ACTTTGTCAGAGTATTACAAGGTGAG 58.845 38.462 0.00 0.00 40.55 3.51
3006 3780 6.665992 TTGTCAGAGTATTACAAGGTGAGT 57.334 37.500 0.00 0.00 0.00 3.41
3007 3781 6.268825 TGTCAGAGTATTACAAGGTGAGTC 57.731 41.667 0.00 0.00 0.00 3.36
3008 3782 5.773176 TGTCAGAGTATTACAAGGTGAGTCA 59.227 40.000 0.00 0.00 0.00 3.41
3009 3783 6.437477 TGTCAGAGTATTACAAGGTGAGTCAT 59.563 38.462 0.00 0.00 0.00 3.06
3010 3784 7.039011 TGTCAGAGTATTACAAGGTGAGTCATT 60.039 37.037 0.00 0.00 0.00 2.57
3011 3785 7.489757 GTCAGAGTATTACAAGGTGAGTCATTC 59.510 40.741 0.00 0.00 0.00 2.67
3012 3786 7.397476 TCAGAGTATTACAAGGTGAGTCATTCT 59.603 37.037 0.00 0.00 0.00 2.40
3013 3787 8.687242 CAGAGTATTACAAGGTGAGTCATTCTA 58.313 37.037 0.00 0.00 0.00 2.10
3014 3788 9.427821 AGAGTATTACAAGGTGAGTCATTCTAT 57.572 33.333 0.00 0.00 0.00 1.98
3019 3793 9.739276 ATTACAAGGTGAGTCATTCTATTTTCA 57.261 29.630 0.00 0.00 0.00 2.69
3020 3794 7.440523 ACAAGGTGAGTCATTCTATTTTCAC 57.559 36.000 0.00 0.00 35.42 3.18
3021 3795 6.998074 ACAAGGTGAGTCATTCTATTTTCACA 59.002 34.615 0.00 0.00 37.31 3.58
3022 3796 7.041098 ACAAGGTGAGTCATTCTATTTTCACAC 60.041 37.037 0.00 0.00 37.31 3.82
3023 3797 6.533730 AGGTGAGTCATTCTATTTTCACACA 58.466 36.000 0.00 0.00 37.31 3.72
3024 3798 6.652481 AGGTGAGTCATTCTATTTTCACACAG 59.348 38.462 0.00 0.00 37.31 3.66
3027 3801 6.427853 TGAGTCATTCTATTTTCACACAGGTG 59.572 38.462 0.00 0.00 46.66 4.00
3030 3804 7.285401 AGTCATTCTATTTTCACACAGGTGTTT 59.715 33.333 1.58 0.00 45.45 2.83
3032 3806 8.564574 TCATTCTATTTTCACACAGGTGTTTAC 58.435 33.333 1.58 0.00 45.45 2.01
3039 3813 6.425577 TTCACACAGGTGTTTACTACAAAC 57.574 37.500 1.58 0.00 45.45 2.93
3091 3893 6.814506 AGAAATGAGTTCTGGATTCACTTG 57.185 37.500 0.00 0.00 45.29 3.16
3103 3906 1.180907 TTCACTTGCAACAAGGCACA 58.819 45.000 11.69 0.00 44.86 4.57
3137 3940 1.029408 TTCAGCTGCACGTGGTTTGT 61.029 50.000 18.88 0.00 0.00 2.83
3259 4062 4.660938 GGGCCACGGACAAGCCTT 62.661 66.667 4.39 0.00 46.31 4.35
3260 4063 3.056328 GGCCACGGACAAGCCTTC 61.056 66.667 0.00 0.00 43.62 3.46
3301 4104 7.180229 TCCAGAAAGATAATTTTCTTTTCCCCC 59.820 37.037 20.39 10.53 44.04 5.40
3411 4214 2.813754 AGCGCAAACACTACATTGTCAT 59.186 40.909 11.47 0.00 0.00 3.06
3421 4224 4.632688 CACTACATTGTCATCATGTGCAGA 59.367 41.667 0.00 0.00 0.00 4.26
3430 4233 5.907866 TCATCATGTGCAGATGAAAATGT 57.092 34.783 28.00 10.55 46.36 2.71
3501 4346 7.428472 GCAACAAGTTACTAAAGTCTGTGAAAC 59.572 37.037 0.00 0.00 37.35 2.78
3524 4369 4.527509 TCTCTTTTGACTGAAGCTCGAT 57.472 40.909 0.00 0.00 0.00 3.59
3604 4451 3.438360 CAGTTTTCAGCTGTCGCTTTTT 58.562 40.909 14.67 0.00 46.47 1.94
3608 4455 3.619233 TTCAGCTGTCGCTTTTTAACC 57.381 42.857 14.67 0.00 46.47 2.85
3611 4458 3.003275 TCAGCTGTCGCTTTTTAACCTTG 59.997 43.478 14.67 0.00 46.47 3.61
3612 4459 2.051423 GCTGTCGCTTTTTAACCTTGC 58.949 47.619 0.00 0.00 0.00 4.01
3616 4468 4.109050 TGTCGCTTTTTAACCTTGCTTTG 58.891 39.130 0.00 0.00 0.00 2.77
3639 4491 9.562226 TTTGGGTAATGGGATTAAGGAAAAATA 57.438 29.630 0.00 0.00 0.00 1.40
3730 4583 1.435515 GCCTCTCTACTGTGGCTCG 59.564 63.158 0.00 0.00 41.72 5.03
3772 4625 7.255836 GGCTTTGTTAGATCCTACAAAAACCTT 60.256 37.037 20.91 0.00 41.96 3.50
3813 4666 0.673437 GCAGGGCACTTTGTAAGCAA 59.327 50.000 0.00 0.00 0.00 3.91
3814 4667 1.602920 GCAGGGCACTTTGTAAGCAAC 60.603 52.381 0.00 0.00 33.82 4.17
3815 4668 1.956477 CAGGGCACTTTGTAAGCAACT 59.044 47.619 0.00 0.00 33.82 3.16
3816 4669 2.030805 CAGGGCACTTTGTAAGCAACTC 60.031 50.000 0.00 0.00 33.82 3.01
3894 4757 4.152402 TCACAGAGATTTTGCTAGCGTTTC 59.848 41.667 10.77 4.54 0.00 2.78
3981 4845 2.540361 GCTTGACATGATCGGCAACATC 60.540 50.000 0.00 0.00 0.00 3.06
4045 4910 2.664081 GGAGCACAGAGGGGTGGAG 61.664 68.421 0.00 0.00 39.19 3.86
4046 4911 1.610673 GAGCACAGAGGGGTGGAGA 60.611 63.158 0.00 0.00 39.19 3.71
4079 4944 0.451135 CTACACGCAGTTTGCTTCGC 60.451 55.000 0.00 0.00 41.61 4.70
4425 9285 0.667453 TTGTGCGCTGCAGATTCAAA 59.333 45.000 20.43 3.34 40.08 2.69
4430 9290 0.109597 CGCTGCAGATTCAAACCACC 60.110 55.000 20.43 0.00 0.00 4.61
4466 9326 3.041940 CCAACTGCCGACGTGGAC 61.042 66.667 0.00 0.00 42.00 4.02
4526 9386 3.173151 TCAAGTCAGTCTTAGGGCATGA 58.827 45.455 0.00 0.00 34.66 3.07
4545 9405 0.773644 ACCAATGCATAGCCCTAGGG 59.226 55.000 24.89 24.89 38.57 3.53
4552 9412 0.326264 CATAGCCCTAGGGTGATGCC 59.674 60.000 28.96 11.17 37.65 4.40
4595 9455 7.661968 TCAGATATCAGGAAAAGTAGATTCGG 58.338 38.462 5.32 0.00 0.00 4.30
4676 9536 9.539825 TCTGTTGCATAAATTAAAGCTGAAAAA 57.460 25.926 0.00 0.00 0.00 1.94
4795 9655 8.854614 AATCAATATAGATGCCTCAAACTACC 57.145 34.615 0.00 0.00 0.00 3.18
4848 9708 7.801104 TGTCACCATTGTACATATGTCCTTAT 58.199 34.615 12.68 0.00 0.00 1.73
4891 9751 2.689175 GCATTGGATCCACCCCCA 59.311 61.111 15.91 0.00 38.00 4.96
4908 9768 3.447229 CCCCCAAGACAATAACCATGAAC 59.553 47.826 0.00 0.00 0.00 3.18
4919 9780 8.706492 ACAATAACCATGAACAAAATATGCAG 57.294 30.769 0.00 0.00 0.00 4.41
4969 9830 2.356125 GCTAGAGGAGGAAATTGCACCA 60.356 50.000 3.71 0.00 0.00 4.17
4977 9838 3.356290 AGGAAATTGCACCATGTCCTAC 58.644 45.455 8.18 0.00 33.70 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.396996 GCTTGTCGTTGTGTCACTTGT 59.603 47.619 4.27 0.00 0.00 3.16
19 20 0.468029 CCCACCAGGTTGAAGCTTGT 60.468 55.000 2.10 0.00 0.00 3.16
21 22 4.929807 CCCACCAGGTTGAAGCTT 57.070 55.556 0.00 0.00 0.00 3.74
49 50 2.507944 GGCATGGTCTCCATCGCT 59.492 61.111 16.29 0.00 43.15 4.93
202 205 0.109723 AACTTTAGCCGGTTCCAGCA 59.890 50.000 1.90 0.00 0.00 4.41
275 278 6.054860 AGATTTGCAGTACTATGTTCCAGT 57.945 37.500 0.00 0.00 0.00 4.00
284 287 6.040247 CCATTGTCGTAGATTTGCAGTACTA 58.960 40.000 0.00 0.00 40.67 1.82
326 329 0.392863 CACCCCATCGAAGCACATCA 60.393 55.000 0.00 0.00 0.00 3.07
328 331 1.750399 GCACCCCATCGAAGCACAT 60.750 57.895 0.00 0.00 0.00 3.21
329 332 2.359850 GCACCCCATCGAAGCACA 60.360 61.111 0.00 0.00 0.00 4.57
358 659 2.367868 CTTGCAGCCAAAGCCGGTTT 62.368 55.000 1.90 0.00 41.25 3.27
400 701 3.814268 CCCACTTTGCCGGATGCG 61.814 66.667 5.05 0.00 45.60 4.73
424 725 3.559811 CCCAATCTCACAGTCATTGTCCA 60.560 47.826 0.00 0.00 38.16 4.02
428 729 3.630769 CCATCCCAATCTCACAGTCATTG 59.369 47.826 0.00 0.00 0.00 2.82
435 736 1.614711 GCCCCATCCCAATCTCACA 59.385 57.895 0.00 0.00 0.00 3.58
492 800 1.029947 TAGCACATCTCGCGTGAGGA 61.030 55.000 26.87 12.59 42.79 3.71
504 812 1.221566 TGCATCGCCACTAGCACAT 59.778 52.632 0.00 0.00 44.04 3.21
511 819 3.825160 AACACCGTGCATCGCCACT 62.825 57.895 0.00 0.00 38.35 4.00
522 830 0.899019 AAAAAGGCAACCAACACCGT 59.101 45.000 0.00 0.00 37.17 4.83
535 843 4.504097 CCGCAGAGAAACAAAAGAAAAAGG 59.496 41.667 0.00 0.00 0.00 3.11
559 867 1.674980 GTCCTCGTCCACCTCTCGT 60.675 63.158 0.00 0.00 0.00 4.18
563 871 0.966920 TCTTTGTCCTCGTCCACCTC 59.033 55.000 0.00 0.00 0.00 3.85
569 877 5.570234 AGAGTCTAATCTTTGTCCTCGTC 57.430 43.478 0.00 0.00 0.00 4.20
587 895 6.375455 CCTGCTAACAACCATTTGATTAGAGT 59.625 38.462 0.00 0.00 36.48 3.24
599 907 2.169561 TCGATATGCCTGCTAACAACCA 59.830 45.455 0.00 0.00 0.00 3.67
668 976 4.400567 AGATTTTATTTGGGCAGCACTCTC 59.599 41.667 0.00 0.00 0.00 3.20
679 987 9.730420 CACGGGACTTATTTAGATTTTATTTGG 57.270 33.333 0.00 0.00 0.00 3.28
700 1008 1.009389 GTCTCGCTGAAGAACACGGG 61.009 60.000 0.00 0.00 0.00 5.28
710 1018 0.530744 GGGTACATGTGTCTCGCTGA 59.469 55.000 9.11 0.00 0.00 4.26
786 1095 2.638480 AAACAGCTAGGCACTTGTGA 57.362 45.000 4.79 0.00 41.75 3.58
797 1106 8.306313 TCTGATAAGAGGACAATAAACAGCTA 57.694 34.615 0.00 0.00 0.00 3.32
818 1127 8.894731 CATCTAAACTACTACTACTTGCTCTGA 58.105 37.037 0.00 0.00 0.00 3.27
840 1177 1.003118 TGGCGGTTGTTAGAAGCATCT 59.997 47.619 0.00 0.00 39.82 2.90
844 1181 1.448985 TCATGGCGGTTGTTAGAAGC 58.551 50.000 0.00 0.00 0.00 3.86
845 1182 3.074412 ACTTCATGGCGGTTGTTAGAAG 58.926 45.455 0.00 0.00 37.57 2.85
846 1183 3.134574 ACTTCATGGCGGTTGTTAGAA 57.865 42.857 0.00 0.00 0.00 2.10
853 1190 0.898326 GGGGAAACTTCATGGCGGTT 60.898 55.000 0.00 0.00 0.00 4.44
881 1218 5.279960 GGCAAGATTTCATGGGGTAGTTTTT 60.280 40.000 0.00 0.00 0.00 1.94
882 1219 4.222810 GGCAAGATTTCATGGGGTAGTTTT 59.777 41.667 0.00 0.00 0.00 2.43
883 1220 3.769300 GGCAAGATTTCATGGGGTAGTTT 59.231 43.478 0.00 0.00 0.00 2.66
884 1221 3.011708 AGGCAAGATTTCATGGGGTAGTT 59.988 43.478 0.00 0.00 0.00 2.24
885 1222 2.582636 AGGCAAGATTTCATGGGGTAGT 59.417 45.455 0.00 0.00 0.00 2.73
886 1223 2.954318 CAGGCAAGATTTCATGGGGTAG 59.046 50.000 0.00 0.00 0.00 3.18
887 1224 2.580322 TCAGGCAAGATTTCATGGGGTA 59.420 45.455 0.00 0.00 0.00 3.69
888 1225 1.358787 TCAGGCAAGATTTCATGGGGT 59.641 47.619 0.00 0.00 0.00 4.95
889 1226 2.148446 TCAGGCAAGATTTCATGGGG 57.852 50.000 0.00 0.00 0.00 4.96
890 1227 2.223971 GCATCAGGCAAGATTTCATGGG 60.224 50.000 0.00 0.00 43.97 4.00
891 1228 3.093717 GCATCAGGCAAGATTTCATGG 57.906 47.619 0.00 0.00 43.97 3.66
968 1305 1.711206 GCTGTTCGTCCTTCCTACAC 58.289 55.000 0.00 0.00 0.00 2.90
977 1314 1.803519 CAGAGCTCGCTGTTCGTCC 60.804 63.158 8.37 0.00 39.67 4.79
985 1322 0.321919 TCCATTTTGCAGAGCTCGCT 60.322 50.000 24.04 7.77 0.00 4.93
986 1323 0.098376 CTCCATTTTGCAGAGCTCGC 59.902 55.000 19.33 19.33 0.00 5.03
1020 1384 1.566703 AGGAAGAGGACGGAGATGAGA 59.433 52.381 0.00 0.00 0.00 3.27
1122 1486 1.135083 ACAGAATCGCCGGACTTACTG 60.135 52.381 5.05 11.15 0.00 2.74
1196 1563 3.730761 CTCTGCAACGCCCAGCAC 61.731 66.667 0.00 0.00 36.62 4.40
1200 1567 4.704833 GAGCCTCTGCAACGCCCA 62.705 66.667 0.00 0.00 41.13 5.36
1201 1568 4.704833 TGAGCCTCTGCAACGCCC 62.705 66.667 0.00 0.00 41.13 6.13
1202 1569 3.426568 GTGAGCCTCTGCAACGCC 61.427 66.667 0.00 0.00 41.13 5.68
1318 1690 2.464459 GCAAGTTCCCGCCGATGAG 61.464 63.158 0.00 0.00 0.00 2.90
1324 1696 2.626780 GGACAAGCAAGTTCCCGCC 61.627 63.158 0.00 0.00 0.00 6.13
1325 1697 1.578206 GAGGACAAGCAAGTTCCCGC 61.578 60.000 0.00 0.00 0.00 6.13
1326 1698 0.250295 TGAGGACAAGCAAGTTCCCG 60.250 55.000 0.00 0.00 0.00 5.14
1327 1699 1.528129 CTGAGGACAAGCAAGTTCCC 58.472 55.000 0.00 0.00 0.00 3.97
1328 1700 0.877743 GCTGAGGACAAGCAAGTTCC 59.122 55.000 0.00 0.00 0.00 3.62
1356 1750 2.643790 CGATGACGACGACGACGG 60.644 66.667 22.36 6.21 44.46 4.79
1364 1758 4.710528 AAAAGAAGAACACGATGACGAC 57.289 40.909 0.00 0.00 42.66 4.34
1365 1759 5.047847 AGAAAAAGAAGAACACGATGACGA 58.952 37.500 0.00 0.00 42.66 4.20
1366 1760 5.051039 TGAGAAAAAGAAGAACACGATGACG 60.051 40.000 0.00 0.00 45.75 4.35
1367 1761 6.287107 TGAGAAAAAGAAGAACACGATGAC 57.713 37.500 0.00 0.00 0.00 3.06
1368 1762 5.466728 CCTGAGAAAAAGAAGAACACGATGA 59.533 40.000 0.00 0.00 0.00 2.92
1369 1763 5.334414 CCCTGAGAAAAAGAAGAACACGATG 60.334 44.000 0.00 0.00 0.00 3.84
1375 1769 3.187432 CGCTCCCTGAGAAAAAGAAGAAC 59.813 47.826 0.00 0.00 0.00 3.01
1410 1804 1.078848 CCTCCAGGAAGTTGCCGAG 60.079 63.158 0.00 2.98 37.39 4.63
1508 1902 0.392706 ACACGATGTGCTTGTCTCCA 59.607 50.000 0.00 0.00 36.98 3.86
1517 1911 3.262420 AGGAACATAGAACACGATGTGC 58.738 45.455 0.00 0.00 36.42 4.57
1556 1953 1.266718 GCTCGATTCAGCCACACAAAA 59.733 47.619 0.00 0.00 32.76 2.44
1560 1957 1.975363 GCAGCTCGATTCAGCCACAC 61.975 60.000 0.00 0.00 40.65 3.82
1562 1959 1.449246 AGCAGCTCGATTCAGCCAC 60.449 57.895 0.00 0.00 40.65 5.01
1611 2009 2.413142 GCTGTACCCGACGCCTACT 61.413 63.158 0.00 0.00 0.00 2.57
1614 2012 2.044650 TAGCTGTACCCGACGCCT 60.045 61.111 0.00 0.00 0.00 5.52
1617 2015 1.226211 CACGTAGCTGTACCCGACG 60.226 63.158 12.36 12.36 37.35 5.12
1920 2334 6.854892 GTCAGAATCTCAATCACAACAGTTTG 59.145 38.462 0.00 0.00 38.83 2.93
1921 2335 6.543465 TGTCAGAATCTCAATCACAACAGTTT 59.457 34.615 0.00 0.00 0.00 2.66
1977 2395 1.738099 CTGGAACAAGAGCGTCCCG 60.738 63.158 0.00 0.00 38.70 5.14
2048 2466 3.851976 TCCTTAGTTCTTGAGACGAGC 57.148 47.619 0.00 0.00 0.00 5.03
2105 2523 1.135315 CCTGTTCATCAATGGCGGTTG 60.135 52.381 0.00 0.00 0.00 3.77
2106 2524 1.176527 CCTGTTCATCAATGGCGGTT 58.823 50.000 0.00 0.00 0.00 4.44
2108 2526 0.394216 TCCCTGTTCATCAATGGCGG 60.394 55.000 0.00 0.00 0.00 6.13
2207 2625 3.764049 GCCGCTGTTGACGACGAC 61.764 66.667 0.00 0.00 0.00 4.34
2239 2657 4.451629 ACGGAATACTGATGACTCGTTT 57.548 40.909 0.00 0.00 0.00 3.60
2241 2659 3.192844 ACAACGGAATACTGATGACTCGT 59.807 43.478 0.00 0.00 0.00 4.18
2245 2663 3.857052 TGGACAACGGAATACTGATGAC 58.143 45.455 0.00 0.00 0.00 3.06
2253 2671 4.699637 AGCGAATTATGGACAACGGAATA 58.300 39.130 0.00 0.00 0.00 1.75
2257 2675 1.597663 GGAGCGAATTATGGACAACGG 59.402 52.381 0.00 0.00 0.00 4.44
2258 2676 2.540101 GAGGAGCGAATTATGGACAACG 59.460 50.000 0.00 0.00 0.00 4.10
2259 2677 2.872858 GGAGGAGCGAATTATGGACAAC 59.127 50.000 0.00 0.00 0.00 3.32
2261 2679 1.068588 CGGAGGAGCGAATTATGGACA 59.931 52.381 0.00 0.00 0.00 4.02
2262 2680 1.784525 CGGAGGAGCGAATTATGGAC 58.215 55.000 0.00 0.00 0.00 4.02
2277 2700 1.884235 AAGCTGTCAGAAAACCGGAG 58.116 50.000 9.46 0.00 0.00 4.63
2340 2781 0.686441 TCCATCCCGGTGTCCAGTAG 60.686 60.000 0.00 0.00 35.57 2.57
2342 2783 2.121832 TCCATCCCGGTGTCCAGT 59.878 61.111 0.00 0.00 35.57 4.00
2435 2882 2.236766 CCATTCATGGCCTCCTGAATC 58.763 52.381 19.48 0.00 39.47 2.52
2467 2914 1.066143 TGGGGACGATCTTGAGCTTTC 60.066 52.381 0.00 0.00 0.00 2.62
2481 2928 3.006217 ACTTACACTACGTCTTTGGGGAC 59.994 47.826 0.00 0.00 0.00 4.46
2493 2940 3.532542 GAATGAGGCCCACTTACACTAC 58.467 50.000 0.00 0.00 0.00 2.73
2522 2969 7.334090 TGTTTGTCAAAGATTCAAAATGGGAA 58.666 30.769 0.00 0.00 33.80 3.97
2532 2979 6.477742 GGCAGTTTTTGTTTGTCAAAGATTC 58.522 36.000 0.00 0.00 45.14 2.52
2533 2980 5.063312 CGGCAGTTTTTGTTTGTCAAAGATT 59.937 36.000 0.00 0.00 45.14 2.40
2534 2981 4.566360 CGGCAGTTTTTGTTTGTCAAAGAT 59.434 37.500 0.00 0.00 45.14 2.40
2535 2982 3.923461 CGGCAGTTTTTGTTTGTCAAAGA 59.077 39.130 0.00 0.00 45.14 2.52
2536 2983 3.061965 CCGGCAGTTTTTGTTTGTCAAAG 59.938 43.478 0.00 0.00 45.14 2.77
2537 2984 2.996621 CCGGCAGTTTTTGTTTGTCAAA 59.003 40.909 0.00 0.00 43.24 2.69
2538 2985 2.611518 CCGGCAGTTTTTGTTTGTCAA 58.388 42.857 0.00 0.00 0.00 3.18
2539 2986 1.737363 GCCGGCAGTTTTTGTTTGTCA 60.737 47.619 24.80 0.00 0.00 3.58
2540 2987 0.927537 GCCGGCAGTTTTTGTTTGTC 59.072 50.000 24.80 0.00 0.00 3.18
2587 3038 9.062524 TCTGCAGATAGTTTTAAAAACAGCTAA 57.937 29.630 13.74 0.00 0.00 3.09
2591 3042 7.274250 GCCATCTGCAGATAGTTTTAAAAACAG 59.726 37.037 28.27 10.88 40.77 3.16
2643 3094 1.437625 TGAAATCGTTGATCAGCGCA 58.562 45.000 25.04 15.05 34.98 6.09
2679 3130 3.181455 TGATGATATCCCAACCAACCTCG 60.181 47.826 0.00 0.00 0.00 4.63
2685 3136 5.890049 TGCAATATGATGATATCCCAACCA 58.110 37.500 0.00 0.00 0.00 3.67
2890 3474 9.102757 GGCATCTGATCGTGTCAAAATATATAT 57.897 33.333 0.00 0.00 36.14 0.86
2908 3492 2.028020 TGCATTGCAAAATGGCATCTGA 60.028 40.909 9.33 0.00 44.48 3.27
2911 3495 4.364415 AAATGCATTGCAAAATGGCATC 57.636 36.364 22.78 1.59 43.62 3.91
2940 3524 7.887495 ACCTACCACGGGTTAATGTTTTTATAA 59.113 33.333 0.72 0.00 37.09 0.98
2942 3526 6.151480 CACCTACCACGGGTTAATGTTTTTAT 59.849 38.462 0.72 0.00 37.09 1.40
2943 3527 5.472820 CACCTACCACGGGTTAATGTTTTTA 59.527 40.000 0.72 0.00 37.09 1.52
2995 3769 8.154203 TGTGAAAATAGAATGACTCACCTTGTA 58.846 33.333 0.00 0.00 0.00 2.41
2996 3770 6.998074 TGTGAAAATAGAATGACTCACCTTGT 59.002 34.615 0.00 0.00 0.00 3.16
2997 3771 7.041167 TGTGTGAAAATAGAATGACTCACCTTG 60.041 37.037 0.00 0.00 0.00 3.61
2998 3772 6.998074 TGTGTGAAAATAGAATGACTCACCTT 59.002 34.615 0.00 0.00 0.00 3.50
2999 3773 6.533730 TGTGTGAAAATAGAATGACTCACCT 58.466 36.000 0.00 0.00 0.00 4.00
3000 3774 6.128172 CCTGTGTGAAAATAGAATGACTCACC 60.128 42.308 0.00 0.00 0.00 4.02
3001 3775 6.428159 ACCTGTGTGAAAATAGAATGACTCAC 59.572 38.462 0.00 0.00 0.00 3.51
3002 3776 6.427853 CACCTGTGTGAAAATAGAATGACTCA 59.572 38.462 0.00 0.00 45.76 3.41
3003 3777 6.428159 ACACCTGTGTGAAAATAGAATGACTC 59.572 38.462 1.39 0.00 45.76 3.36
3005 3779 6.560253 ACACCTGTGTGAAAATAGAATGAC 57.440 37.500 1.39 0.00 45.76 3.06
3006 3780 7.581213 AAACACCTGTGTGAAAATAGAATGA 57.419 32.000 3.28 0.00 45.76 2.57
3007 3781 8.567948 AGTAAACACCTGTGTGAAAATAGAATG 58.432 33.333 3.28 0.00 45.76 2.67
3008 3782 8.691661 AGTAAACACCTGTGTGAAAATAGAAT 57.308 30.769 3.28 0.00 45.76 2.40
3009 3783 9.048446 GTAGTAAACACCTGTGTGAAAATAGAA 57.952 33.333 3.28 0.00 45.76 2.10
3010 3784 8.205512 TGTAGTAAACACCTGTGTGAAAATAGA 58.794 33.333 3.28 0.00 45.76 1.98
3011 3785 8.373048 TGTAGTAAACACCTGTGTGAAAATAG 57.627 34.615 3.28 0.00 45.76 1.73
3012 3786 8.734218 TTGTAGTAAACACCTGTGTGAAAATA 57.266 30.769 3.28 0.00 45.76 1.40
3013 3787 7.633193 TTGTAGTAAACACCTGTGTGAAAAT 57.367 32.000 3.28 0.00 45.76 1.82
3014 3788 7.040617 TGTTTGTAGTAAACACCTGTGTGAAAA 60.041 33.333 3.28 0.00 45.76 2.29
3015 3789 6.430308 TGTTTGTAGTAAACACCTGTGTGAAA 59.570 34.615 3.28 0.00 45.76 2.69
3016 3790 5.938710 TGTTTGTAGTAAACACCTGTGTGAA 59.061 36.000 3.28 0.00 45.76 3.18
3017 3791 5.489249 TGTTTGTAGTAAACACCTGTGTGA 58.511 37.500 3.28 0.00 45.76 3.58
3018 3792 6.535865 TACTGTTTGTAGTAAACACCTGTGTG 59.464 38.462 3.28 0.00 38.00 3.82
3019 3793 6.642430 TACTGTTTGTAGTAAACACCTGTGT 58.358 36.000 0.00 0.00 38.00 3.72
3020 3794 7.724305 ATACTGTTTGTAGTAAACACCTGTG 57.276 36.000 1.42 0.00 38.00 3.66
3048 3822 7.648039 TTTCTGTTACCAAGTTACCACAAAT 57.352 32.000 0.00 0.00 0.00 2.32
3054 3828 7.444487 AGAACTCATTTCTGTTACCAAGTTACC 59.556 37.037 0.00 0.00 43.45 2.85
3074 3876 3.565482 TGTTGCAAGTGAATCCAGAACTC 59.435 43.478 0.00 0.00 0.00 3.01
3091 3893 1.000938 CTTCCTTCTGTGCCTTGTTGC 60.001 52.381 0.00 0.00 0.00 4.17
3137 3940 0.387929 AGAGTGTTGAACCGAAGCGA 59.612 50.000 0.00 0.00 0.00 4.93
3259 4062 3.819368 TCTGGAAAGCAGACAAATGTGA 58.181 40.909 0.00 0.00 0.00 3.58
3260 4063 4.572985 TTCTGGAAAGCAGACAAATGTG 57.427 40.909 0.00 0.00 0.00 3.21
3301 4104 1.003233 GTACTGGACACCCCAAAGAGG 59.997 57.143 0.00 0.00 46.07 3.69
3303 4106 0.682852 CGTACTGGACACCCCAAAGA 59.317 55.000 0.00 0.00 46.07 2.52
3304 4107 0.395312 ACGTACTGGACACCCCAAAG 59.605 55.000 0.00 0.00 46.07 2.77
3305 4108 0.838608 AACGTACTGGACACCCCAAA 59.161 50.000 0.00 0.00 46.07 3.28
3411 4214 4.398988 GGGTACATTTTCATCTGCACATGA 59.601 41.667 0.00 0.00 0.00 3.07
3421 4224 7.093945 GGTGTCATAGTTTGGGTACATTTTCAT 60.094 37.037 0.00 0.00 0.00 2.57
3429 4232 3.439129 GCTTGGTGTCATAGTTTGGGTAC 59.561 47.826 0.00 0.00 0.00 3.34
3430 4233 3.073209 TGCTTGGTGTCATAGTTTGGGTA 59.927 43.478 0.00 0.00 0.00 3.69
3501 4346 4.302455 TCGAGCTTCAGTCAAAAGAGAAG 58.698 43.478 0.00 0.00 40.23 2.85
3524 4369 1.506718 GACGGTCGAGCAGATCACA 59.493 57.895 15.89 0.00 0.00 3.58
3604 4451 3.076182 TCCCATTACCCAAAGCAAGGTTA 59.924 43.478 0.00 0.00 37.59 2.85
3608 4455 5.163416 CCTTAATCCCATTACCCAAAGCAAG 60.163 44.000 0.00 0.00 0.00 4.01
3611 4458 4.542697 TCCTTAATCCCATTACCCAAAGC 58.457 43.478 0.00 0.00 0.00 3.51
3612 4459 7.489239 TTTTCCTTAATCCCATTACCCAAAG 57.511 36.000 0.00 0.00 0.00 2.77
3616 4468 7.015877 GGGTATTTTTCCTTAATCCCATTACCC 59.984 40.741 0.00 0.00 34.39 3.69
3639 4491 2.408565 TCAGTTGAGAAGTTCAGGGGT 58.591 47.619 5.50 0.00 37.07 4.95
3772 4625 4.141620 GCTCCAAGGATCCAGTAGAAATGA 60.142 45.833 15.82 0.00 0.00 2.57
3813 4666 4.712476 AGTGCTGAATCAAAAGAGTGAGT 58.288 39.130 0.00 0.00 0.00 3.41
3814 4667 5.686159 AAGTGCTGAATCAAAAGAGTGAG 57.314 39.130 0.00 0.00 0.00 3.51
3815 4668 6.267817 CAAAAGTGCTGAATCAAAAGAGTGA 58.732 36.000 0.00 0.00 0.00 3.41
3816 4669 6.506464 CAAAAGTGCTGAATCAAAAGAGTG 57.494 37.500 0.00 0.00 0.00 3.51
3842 4695 7.443575 TCTGCTATTCTCTTCAGGATAATTTGC 59.556 37.037 0.00 0.00 0.00 3.68
3894 4757 2.354510 TCGGCGCCTTAGATGAAAAATG 59.645 45.455 26.68 3.04 0.00 2.32
3981 4845 0.034059 AAAGAGCCGGAGACTGTGTG 59.966 55.000 5.05 0.00 0.00 3.82
4045 4910 1.813178 GTGTAGCTGGCTCCCTTTTTC 59.187 52.381 0.00 0.00 0.00 2.29
4046 4911 1.882352 CGTGTAGCTGGCTCCCTTTTT 60.882 52.381 0.00 0.00 0.00 1.94
4079 4944 1.734477 CCGACCAACACGAGCTGAG 60.734 63.158 0.00 0.00 0.00 3.35
4274 7822 9.926427 AGGTTTCAGCCTCCTTTTCAGAAAAGA 62.926 40.741 29.90 17.72 45.83 2.52
4275 7823 5.284864 GTTTCAGCCTCCTTTTCAGAAAAG 58.715 41.667 23.82 23.82 45.78 2.27
4333 7909 3.404899 GTTCAACGATGGTCACCCTTTA 58.595 45.455 0.00 0.00 0.00 1.85
4413 9273 2.030540 CACTGGTGGTTTGAATCTGCAG 60.031 50.000 7.63 7.63 0.00 4.41
4425 9285 0.466189 CAAGCTGGTTCACTGGTGGT 60.466 55.000 0.70 0.00 0.00 4.16
4430 9290 0.040958 GTTCGCAAGCTGGTTCACTG 60.041 55.000 0.00 0.00 37.18 3.66
4526 9386 0.773644 CCCTAGGGCTATGCATTGGT 59.226 55.000 16.90 0.00 0.00 3.67
4552 9412 0.886490 GATTCTACATGGCCTGCGGG 60.886 60.000 7.41 7.41 0.00 6.13
4556 9416 6.046290 TGATATCTGATTCTACATGGCCTG 57.954 41.667 3.32 2.01 0.00 4.85
4595 9455 3.579496 AGGATCCCCCTACACCATC 57.421 57.895 8.55 0.00 45.48 3.51
4625 9485 3.141409 TTTTTCTCCCCAAGCACCC 57.859 52.632 0.00 0.00 0.00 4.61
4645 9505 8.190122 CAGCTTTAATTTATGCAACAGACCATA 58.810 33.333 0.00 0.00 0.00 2.74
4647 9507 6.208402 TCAGCTTTAATTTATGCAACAGACCA 59.792 34.615 0.00 0.00 0.00 4.02
4663 9523 8.247562 TCTGCACTTTAACTTTTTCAGCTTTAA 58.752 29.630 0.00 0.00 0.00 1.52
4664 9524 7.767261 TCTGCACTTTAACTTTTTCAGCTTTA 58.233 30.769 0.00 0.00 0.00 1.85
4665 9525 6.630071 TCTGCACTTTAACTTTTTCAGCTTT 58.370 32.000 0.00 0.00 0.00 3.51
4666 9526 6.127619 ACTCTGCACTTTAACTTTTTCAGCTT 60.128 34.615 0.00 0.00 0.00 3.74
4667 9527 5.358160 ACTCTGCACTTTAACTTTTTCAGCT 59.642 36.000 0.00 0.00 0.00 4.24
4676 9536 4.624125 GCATCCCTACTCTGCACTTTAACT 60.624 45.833 0.00 0.00 35.96 2.24
4680 9540 1.630369 TGCATCCCTACTCTGCACTTT 59.370 47.619 0.00 0.00 40.75 2.66
4701 9561 9.386010 GAATAGAAAGTAGACTCTCACTACTCA 57.614 37.037 0.00 0.00 46.29 3.41
4793 9653 1.077663 AGATGCCCCATGACAAAAGGT 59.922 47.619 0.00 0.00 0.00 3.50
4795 9655 2.173519 ACAGATGCCCCATGACAAAAG 58.826 47.619 0.00 0.00 0.00 2.27
4848 9708 0.182299 TGCATGGTTCGGATGGCATA 59.818 50.000 0.00 0.00 0.00 3.14
4891 9751 9.369904 GCATATTTTGTTCATGGTTATTGTCTT 57.630 29.630 0.00 0.00 0.00 3.01
4908 9768 5.518847 CCACAAGAAGCATCTGCATATTTTG 59.481 40.000 4.79 0.00 45.16 2.44
4919 9780 0.242017 GGCACACCACAAGAAGCATC 59.758 55.000 0.00 0.00 35.26 3.91
4944 9805 2.804933 GCAATTTCCTCCTCTAGCCTCG 60.805 54.545 0.00 0.00 0.00 4.63
4969 9830 1.480954 ACAAGCCGATTCGTAGGACAT 59.519 47.619 5.20 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.