Multiple sequence alignment - TraesCS2A01G098300

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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 TraesCS2A01G098300 chr2A 100.000 5150 0 0 1 5150 51590752 51585603 0.000000e+00 9511
1 TraesCS2A01G098300 chr2D 92.712 2113 114 18 1792 3879 49882735 49880638 0.000000e+00 3013
2 TraesCS2A01G098300 chr2D 94.351 1186 53 9 3958 5136 49880642 49879464 0.000000e+00 1807
3 TraesCS2A01G098300 chr2D 90.842 808 52 8 922 1729 49883537 49882752 0.000000e+00 1062
4 TraesCS2A01G098300 chr2D 86.961 951 72 25 1 923 49884600 49883674 0.000000e+00 1022
5 TraesCS2A01G098300 chr2D 92.784 97 6 1 3873 3968 307490175 307490079 6.950000e-29 139
6 TraesCS2A01G098300 chr2B 94.384 1745 77 10 2145 3879 77175275 77173542 0.000000e+00 2660
7 TraesCS2A01G098300 chr2B 95.725 1193 43 6 3958 5149 77173546 77172361 0.000000e+00 1914
8 TraesCS2A01G098300 chr2B 95.067 1196 57 2 922 2116 77176467 77175273 0.000000e+00 1881
9 TraesCS2A01G098300 chr2B 83.267 753 76 22 211 923 77177346 77176604 0.000000e+00 647
10 TraesCS2A01G098300 chr2B 84.579 214 26 2 4519 4726 1678830 1678618 6.760000e-49 206
11 TraesCS2A01G098300 chr4B 86.512 215 20 5 4519 4726 391595575 391595363 1.440000e-55 228
12 TraesCS2A01G098300 chr7A 85.915 213 21 5 4521 4726 605163510 605163720 8.680000e-53 219
13 TraesCS2A01G098300 chr7A 84.507 213 26 3 4519 4725 694564749 694564538 2.430000e-48 204
14 TraesCS2A01G098300 chr7A 96.667 90 2 1 3874 3962 83936103 83936192 1.160000e-31 148
15 TraesCS2A01G098300 chr7B 85.047 214 25 2 4519 4726 654701520 654701732 1.450000e-50 211
16 TraesCS2A01G098300 chr5A 98.837 86 1 0 3876 3961 355734055 355734140 2.480000e-33 154
17 TraesCS2A01G098300 chr7D 98.824 85 1 0 3877 3961 414277683 414277599 8.930000e-33 152
18 TraesCS2A01G098300 chr3D 93.204 103 4 3 3874 3974 203684542 203684643 1.160000e-31 148
19 TraesCS2A01G098300 chr4D 97.674 86 1 1 3877 3961 28237809 28237894 4.160000e-31 147
20 TraesCS2A01G098300 chr4D 93.137 102 3 4 3864 3962 481110379 481110279 4.160000e-31 147
21 TraesCS2A01G098300 chr6D 94.737 95 2 3 3870 3961 6967925 6968019 1.490000e-30 145
22 TraesCS2A01G098300 chr6B 95.604 91 2 2 3874 3962 617177201 617177291 1.490000e-30 145


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 TraesCS2A01G098300 chr2A 51585603 51590752 5149 True 9511.0 9511 100.00000 1 5150 1 chr2A.!!$R1 5149
1 TraesCS2A01G098300 chr2D 49879464 49884600 5136 True 1726.0 3013 91.21650 1 5136 4 chr2D.!!$R2 5135
2 TraesCS2A01G098300 chr2B 77172361 77177346 4985 True 1775.5 2660 92.11075 211 5149 4 chr2B.!!$R2 4938

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
719 769 0.588252 CGCAAAATATCCGCCTGAGG 59.412 55.0 0.00 0.00 0.00 3.86 F
1173 1365 0.407139 AGGCCAAGGTTCAGAAGCAT 59.593 50.0 14.73 0.00 0.00 3.79 F
1404 1597 0.602638 ATGTTGACGCCGCTCTGAAA 60.603 50.0 0.00 0.00 0.00 2.69 F
2279 2473 0.981183 ATGTTGCTCCCGAGGTAACA 59.019 50.0 7.85 7.85 41.41 2.41 F
2728 2925 0.108585 GGTCAACAGAACTGCTCCCA 59.891 55.0 1.46 0.00 0.00 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1721 1914 0.239347 GCAACTGGTGTGCTGCTAAG 59.761 55.0 0.0 0.0 29.85 2.18 R
2726 2923 0.032403 CACTTGTGTTGCATGGGTGG 59.968 55.0 0.0 0.0 0.00 4.61 R
2727 2924 0.032403 CCACTTGTGTTGCATGGGTG 59.968 55.0 0.0 0.0 0.00 4.61 R
3943 4163 0.906282 GGTACTCCCTCCGTCCCAAA 60.906 60.0 0.0 0.0 0.00 3.28 R
4417 4637 0.804989 GTCCCGATTGCCTGTTCTTG 59.195 55.0 0.0 0.0 0.00 3.02 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
38 39 2.031508 CGCGCCTTACAAAAAGGAAAGA 60.032 45.455 0.00 0.00 39.81 2.52
43 44 4.796290 GCCTTACAAAAAGGAAAGACCAGC 60.796 45.833 7.97 0.00 39.81 4.85
153 157 2.594013 GCTGCTGGCTGCCTATCC 60.594 66.667 21.03 5.92 42.00 2.59
154 158 2.280660 CTGCTGGCTGCCTATCCG 60.281 66.667 21.03 4.36 42.00 4.18
157 161 2.280660 CTGGCTGCCTATCCGCTG 60.281 66.667 21.03 0.00 0.00 5.18
158 162 3.083349 TGGCTGCCTATCCGCTGT 61.083 61.111 21.03 0.00 0.00 4.40
160 164 1.452108 GGCTGCCTATCCGCTGTTT 60.452 57.895 12.43 0.00 0.00 2.83
169 173 1.627297 ATCCGCTGTTTCTCCCTCCC 61.627 60.000 0.00 0.00 0.00 4.30
174 178 1.460689 TGTTTCTCCCTCCCCGTGT 60.461 57.895 0.00 0.00 0.00 4.49
292 303 1.606313 CTCGCCCCCACATTGGTTT 60.606 57.895 0.00 0.00 35.17 3.27
299 310 2.247358 CCCCACATTGGTTTGTTAGCT 58.753 47.619 0.00 0.00 35.17 3.32
308 319 1.084289 GTTTGTTAGCTAGCACCGGG 58.916 55.000 18.83 0.00 0.00 5.73
321 332 2.128507 ACCGGGATTCTCGCCTCTC 61.129 63.158 6.32 0.00 0.00 3.20
322 333 2.333225 CGGGATTCTCGCCTCTCG 59.667 66.667 0.00 0.00 40.15 4.04
323 334 2.482333 CGGGATTCTCGCCTCTCGT 61.482 63.158 0.00 0.00 39.67 4.18
325 336 1.360911 GGATTCTCGCCTCTCGTCC 59.639 63.158 0.00 0.00 39.67 4.79
326 337 1.009449 GATTCTCGCCTCTCGTCCG 60.009 63.158 0.00 0.00 39.67 4.79
340 364 3.006728 TCCGCCCGGGACAAGAAT 61.007 61.111 29.31 0.00 40.94 2.40
345 369 2.354729 CCGGGACAAGAATGGGCA 59.645 61.111 0.00 0.00 0.00 5.36
370 394 3.827898 CTCTCTCCGGCCGGTGAC 61.828 72.222 41.57 0.00 34.54 3.67
445 477 2.089980 GCAACATTCCATCAGCAGAGT 58.910 47.619 0.00 0.00 0.00 3.24
488 520 1.377333 CCGCCTGAGGAAAGGGAAC 60.377 63.158 0.65 0.00 37.84 3.62
513 545 0.960364 GACGCCATGGAGCTTTCCAA 60.960 55.000 18.40 0.00 43.83 3.53
516 548 3.677963 CCATGGAGCTTTCCAAGGT 57.322 52.632 5.56 0.00 42.10 3.50
578 627 1.774217 TGTTCCCTTCCCAGTGCCT 60.774 57.895 0.00 0.00 0.00 4.75
623 672 7.922382 TCTTCATCCTTTCTTGGTTAATCTCT 58.078 34.615 0.00 0.00 0.00 3.10
624 673 7.826252 TCTTCATCCTTTCTTGGTTAATCTCTG 59.174 37.037 0.00 0.00 0.00 3.35
632 681 1.985159 TGGTTAATCTCTGTGGCCTGT 59.015 47.619 3.32 0.00 0.00 4.00
662 711 6.005583 TCAGCACTTCTGACATCAAAATTC 57.994 37.500 0.00 0.00 46.34 2.17
690 739 4.591321 TTCTTCCCAAGGCTTACATCAT 57.409 40.909 0.00 0.00 0.00 2.45
713 763 2.051345 CGGGCGCAAAATATCCGC 60.051 61.111 10.83 0.00 46.34 5.54
719 769 0.588252 CGCAAAATATCCGCCTGAGG 59.412 55.000 0.00 0.00 0.00 3.86
727 777 0.678048 ATCCGCCTGAGGTTTCAAGC 60.678 55.000 0.00 0.00 37.41 4.01
841 895 7.619964 AGTAACCACTGAAATTAATTACCCG 57.380 36.000 0.01 0.00 32.25 5.28
908 962 0.790207 TCGATGAAGCTTGCACGTTC 59.210 50.000 2.10 0.00 0.00 3.95
917 971 0.871722 CTTGCACGTTCCCGATTTGA 59.128 50.000 0.00 0.00 37.88 2.69
984 1176 2.818132 CTTGAGGGCGCCTAGGAG 59.182 66.667 28.56 11.38 31.76 3.69
1071 1263 3.592814 TATGAGCTCGGGCGGACG 61.593 66.667 9.64 0.00 44.37 4.79
1104 1296 1.895231 GTTCGCCAAGGTCCGGTTT 60.895 57.895 0.00 0.00 0.00 3.27
1107 1299 2.909965 GCCAAGGTCCGGTTTGCA 60.910 61.111 0.00 0.00 0.00 4.08
1173 1365 0.407139 AGGCCAAGGTTCAGAAGCAT 59.593 50.000 14.73 0.00 0.00 3.79
1224 1417 8.761575 TTTCTGATAAATTTCCTTTGCATGAC 57.238 30.769 0.00 0.00 0.00 3.06
1250 1443 7.394016 TGCTCTGTTTCCTAGATATTTCACAA 58.606 34.615 0.00 0.00 0.00 3.33
1299 1492 4.948608 TTCTACTAGAACTGAGCTGTCG 57.051 45.455 0.00 0.00 0.00 4.35
1306 1499 2.029020 AGAACTGAGCTGTCGTTATGCA 60.029 45.455 0.00 0.00 0.00 3.96
1309 1502 1.657594 CTGAGCTGTCGTTATGCACAG 59.342 52.381 0.00 0.00 42.61 3.66
1361 1554 2.046280 AGTCAAGAAAGGGGGCTAGT 57.954 50.000 0.00 0.00 0.00 2.57
1404 1597 0.602638 ATGTTGACGCCGCTCTGAAA 60.603 50.000 0.00 0.00 0.00 2.69
1491 1684 4.333926 GCCTGCATGAGGTAAAGACTAAAG 59.666 45.833 0.00 0.00 44.97 1.85
1496 1689 5.582665 GCATGAGGTAAAGACTAAAGACCAG 59.417 44.000 0.00 0.00 32.28 4.00
1534 1727 7.981142 TGTTTTAAGTATGATATCCCCTACCC 58.019 38.462 0.00 0.00 0.00 3.69
1548 1741 6.448369 TCCCCTACCCACATTAGAAATATG 57.552 41.667 0.00 0.00 0.00 1.78
1558 1751 9.300681 CCCACATTAGAAATATGTACATCCAAT 57.699 33.333 12.68 0.00 34.59 3.16
1591 1784 9.362539 GTTGATAACTAACTATTTCGACTCCAA 57.637 33.333 0.00 0.00 0.00 3.53
1629 1822 4.628766 GGAAGCAAGGCAAGAATTTTCATC 59.371 41.667 0.00 0.00 0.00 2.92
1721 1914 4.965814 TCATATTTCTCTGTGATGGGAGC 58.034 43.478 0.00 0.00 0.00 4.70
1807 2001 4.351131 ACGTTCGCCTTTATTGATTTCC 57.649 40.909 0.00 0.00 0.00 3.13
1827 2021 5.957771 TCCACTAACTTCATATTCAGGCT 57.042 39.130 0.00 0.00 0.00 4.58
1836 2030 1.344953 ATATTCAGGCTGCCCGTGGA 61.345 55.000 16.57 2.71 35.76 4.02
1958 2152 1.603739 GCCAACCACTCAACCCCTC 60.604 63.158 0.00 0.00 0.00 4.30
1986 2180 8.682710 GTTCCAATTTATGTATCTGGTTTAGCA 58.317 33.333 0.00 0.00 0.00 3.49
2019 2213 8.592105 AAACTGACAAATGGATGTTTTATGTG 57.408 30.769 0.00 0.00 32.57 3.21
2119 2313 3.377172 GCAGGCGAAGGTAATAACACATT 59.623 43.478 0.00 0.00 0.00 2.71
2120 2314 4.142469 GCAGGCGAAGGTAATAACACATTT 60.142 41.667 0.00 0.00 0.00 2.32
2121 2315 5.621329 GCAGGCGAAGGTAATAACACATTTT 60.621 40.000 0.00 0.00 0.00 1.82
2141 2335 9.773328 ACATTTTACAATCATAAAGATCACACG 57.227 29.630 0.00 0.00 35.39 4.49
2169 2363 8.268738 GTCATTGCATTTCTGTAGTTTTTGTTC 58.731 33.333 0.00 0.00 0.00 3.18
2243 2437 5.303589 GGCTGATGGGTTACTACATACTACA 59.696 44.000 0.00 0.00 0.00 2.74
2279 2473 0.981183 ATGTTGCTCCCGAGGTAACA 59.019 50.000 7.85 7.85 41.41 2.41
2281 2475 1.019805 GTTGCTCCCGAGGTAACAGC 61.020 60.000 0.00 0.00 41.41 4.40
2283 2477 1.192146 TGCTCCCGAGGTAACAGCTT 61.192 55.000 0.00 0.00 41.41 3.74
2287 2481 1.549170 TCCCGAGGTAACAGCTTCTTC 59.451 52.381 0.00 0.00 41.41 2.87
2298 2492 5.972107 AACAGCTTCTTCTACATTTGCAT 57.028 34.783 0.00 0.00 0.00 3.96
2304 2498 7.544566 CAGCTTCTTCTACATTTGCATTGATTT 59.455 33.333 4.32 0.00 0.00 2.17
2332 2526 3.959495 ACCAGGAATGAACATGCCTAT 57.041 42.857 13.35 3.49 45.28 2.57
2342 2536 8.680903 GGAATGAACATGCCTATAATCTAATGG 58.319 37.037 4.66 0.00 33.45 3.16
2437 2631 2.036217 TCTTTTTGTGATGCTTGCTGGG 59.964 45.455 0.00 0.00 0.00 4.45
2593 2788 2.028930 AGCTCAGTTTACTTGTCCCTCG 60.029 50.000 0.00 0.00 0.00 4.63
2616 2811 5.278266 CGTGGTTTTCTGATGGAGCTAAAAA 60.278 40.000 0.00 0.00 0.00 1.94
2660 2855 2.168728 CCCAGTCCTTCTACTGTAAGCC 59.831 54.545 3.56 0.00 44.45 4.35
2683 2880 6.928492 GCCTTTTTACTTCACATTCCATTTCA 59.072 34.615 0.00 0.00 0.00 2.69
2726 2923 2.262423 AAGGTCAACAGAACTGCTCC 57.738 50.000 1.46 0.57 27.57 4.70
2727 2924 0.398318 AGGTCAACAGAACTGCTCCC 59.602 55.000 1.46 0.00 0.00 4.30
2728 2925 0.108585 GGTCAACAGAACTGCTCCCA 59.891 55.000 1.46 0.00 0.00 4.37
2729 2926 1.230324 GTCAACAGAACTGCTCCCAC 58.770 55.000 1.46 0.00 0.00 4.61
2808 3006 3.744942 GGAGTTGTTTCTTACTCGGTTCC 59.255 47.826 0.00 0.00 41.30 3.62
3032 3234 8.055279 ACTAAAATGGATGGTTACTGTGATTG 57.945 34.615 0.00 0.00 0.00 2.67
3169 3371 3.005791 GGTTAGGAACTGTTGCAGCATTT 59.994 43.478 14.52 4.53 41.52 2.32
3185 3387 5.394443 GCAGCATTTTGTCCCATAAATCTCA 60.394 40.000 0.00 0.00 0.00 3.27
3213 3424 6.704512 ATATTTGTCGCAATTTTTCACACC 57.295 33.333 0.00 0.00 0.00 4.16
3215 3426 3.724508 TGTCGCAATTTTTCACACCAT 57.275 38.095 0.00 0.00 0.00 3.55
3570 3782 6.655078 AAATGTTGCAACTGAGGTTAGAAT 57.345 33.333 28.61 8.37 33.88 2.40
3601 3813 6.040166 ACAGCAGTTTGAGAAATGTCTTTCAT 59.960 34.615 0.00 0.00 42.71 2.57
3747 3959 8.044060 TCTTGAATATTGTGGTTCTTTAGCTG 57.956 34.615 0.00 0.00 0.00 4.24
3766 3978 8.547967 TTAGCTGTTTTACTCATTTCACTAGG 57.452 34.615 0.00 0.00 0.00 3.02
3819 4031 8.555361 CCTGAAGCTTTTCTATTCTATACAAGC 58.445 37.037 0.00 0.00 36.27 4.01
3842 4062 2.038426 CCCATGAAGGACTACACACACA 59.962 50.000 0.00 0.00 41.22 3.72
3874 4094 4.319477 GCAAGCGACTTAGAACACAATCAA 60.319 41.667 0.00 0.00 0.00 2.57
3875 4095 5.377358 CAAGCGACTTAGAACACAATCAAG 58.623 41.667 0.00 0.00 0.00 3.02
3876 4096 4.632153 AGCGACTTAGAACACAATCAAGT 58.368 39.130 0.00 0.00 32.33 3.16
3877 4097 5.779922 AGCGACTTAGAACACAATCAAGTA 58.220 37.500 0.00 0.00 29.89 2.24
3878 4098 5.634020 AGCGACTTAGAACACAATCAAGTAC 59.366 40.000 0.00 0.00 29.89 2.73
3879 4099 5.634020 GCGACTTAGAACACAATCAAGTACT 59.366 40.000 0.00 0.00 29.89 2.73
3880 4100 6.183359 GCGACTTAGAACACAATCAAGTACTC 60.183 42.308 0.00 0.00 29.89 2.59
3881 4101 6.308282 CGACTTAGAACACAATCAAGTACTCC 59.692 42.308 0.00 0.00 29.89 3.85
3882 4102 6.465084 ACTTAGAACACAATCAAGTACTCCC 58.535 40.000 0.00 0.00 0.00 4.30
3883 4103 6.270231 ACTTAGAACACAATCAAGTACTCCCT 59.730 38.462 0.00 0.00 0.00 4.20
3884 4104 5.153950 AGAACACAATCAAGTACTCCCTC 57.846 43.478 0.00 0.00 0.00 4.30
3885 4105 3.983044 ACACAATCAAGTACTCCCTCC 57.017 47.619 0.00 0.00 0.00 4.30
3886 4106 2.233922 ACACAATCAAGTACTCCCTCCG 59.766 50.000 0.00 0.00 0.00 4.63
3887 4107 2.233922 CACAATCAAGTACTCCCTCCGT 59.766 50.000 0.00 0.00 0.00 4.69
3888 4108 2.496470 ACAATCAAGTACTCCCTCCGTC 59.504 50.000 0.00 0.00 0.00 4.79
3889 4109 1.777941 ATCAAGTACTCCCTCCGTCC 58.222 55.000 0.00 0.00 0.00 4.79
3890 4110 0.702902 TCAAGTACTCCCTCCGTCCT 59.297 55.000 0.00 0.00 0.00 3.85
3891 4111 1.918262 TCAAGTACTCCCTCCGTCCTA 59.082 52.381 0.00 0.00 0.00 2.94
3892 4112 2.309755 TCAAGTACTCCCTCCGTCCTAA 59.690 50.000 0.00 0.00 0.00 2.69
3893 4113 3.094572 CAAGTACTCCCTCCGTCCTAAA 58.905 50.000 0.00 0.00 0.00 1.85
3894 4114 3.463048 AGTACTCCCTCCGTCCTAAAA 57.537 47.619 0.00 0.00 0.00 1.52
3895 4115 3.991683 AGTACTCCCTCCGTCCTAAAAT 58.008 45.455 0.00 0.00 0.00 1.82
3896 4116 5.134725 AGTACTCCCTCCGTCCTAAAATA 57.865 43.478 0.00 0.00 0.00 1.40
3897 4117 5.522641 AGTACTCCCTCCGTCCTAAAATAA 58.477 41.667 0.00 0.00 0.00 1.40
3898 4118 5.597594 AGTACTCCCTCCGTCCTAAAATAAG 59.402 44.000 0.00 0.00 0.00 1.73
3899 4119 4.359996 ACTCCCTCCGTCCTAAAATAAGT 58.640 43.478 0.00 0.00 0.00 2.24
3900 4120 4.161754 ACTCCCTCCGTCCTAAAATAAGTG 59.838 45.833 0.00 0.00 0.00 3.16
3901 4121 4.355549 TCCCTCCGTCCTAAAATAAGTGA 58.644 43.478 0.00 0.00 0.00 3.41
3902 4122 4.161001 TCCCTCCGTCCTAAAATAAGTGAC 59.839 45.833 0.00 0.00 0.00 3.67
3903 4123 4.161754 CCCTCCGTCCTAAAATAAGTGACT 59.838 45.833 0.00 0.00 0.00 3.41
3904 4124 5.349809 CCTCCGTCCTAAAATAAGTGACTC 58.650 45.833 0.00 0.00 0.00 3.36
3905 4125 5.105473 CCTCCGTCCTAAAATAAGTGACTCA 60.105 44.000 0.00 0.00 0.00 3.41
3906 4126 6.349243 TCCGTCCTAAAATAAGTGACTCAA 57.651 37.500 0.00 0.00 0.00 3.02
3907 4127 6.161381 TCCGTCCTAAAATAAGTGACTCAAC 58.839 40.000 0.00 0.00 0.00 3.18
3908 4128 6.014840 TCCGTCCTAAAATAAGTGACTCAACT 60.015 38.462 0.00 0.00 0.00 3.16
3909 4129 6.649557 CCGTCCTAAAATAAGTGACTCAACTT 59.350 38.462 0.00 0.00 42.89 2.66
3910 4130 7.172703 CCGTCCTAAAATAAGTGACTCAACTTT 59.827 37.037 0.00 0.00 40.77 2.66
3911 4131 8.009974 CGTCCTAAAATAAGTGACTCAACTTTG 58.990 37.037 0.00 0.00 40.77 2.77
3912 4132 8.837389 GTCCTAAAATAAGTGACTCAACTTTGT 58.163 33.333 0.00 0.00 40.77 2.83
3918 4138 8.535690 AATAAGTGACTCAACTTTGTACTAGC 57.464 34.615 0.00 0.00 40.77 3.42
3919 4139 5.793030 AGTGACTCAACTTTGTACTAGCT 57.207 39.130 0.00 0.00 0.00 3.32
3920 4140 6.163135 AGTGACTCAACTTTGTACTAGCTT 57.837 37.500 0.00 0.00 0.00 3.74
3921 4141 6.583562 AGTGACTCAACTTTGTACTAGCTTT 58.416 36.000 0.00 0.00 0.00 3.51
3922 4142 6.480320 AGTGACTCAACTTTGTACTAGCTTTG 59.520 38.462 0.00 0.00 0.00 2.77
3923 4143 6.258068 GTGACTCAACTTTGTACTAGCTTTGT 59.742 38.462 0.00 0.00 0.00 2.83
3924 4144 7.437267 GTGACTCAACTTTGTACTAGCTTTGTA 59.563 37.037 0.00 0.00 0.00 2.41
3925 4145 7.437267 TGACTCAACTTTGTACTAGCTTTGTAC 59.563 37.037 17.52 17.52 40.27 2.90
3926 4146 7.270047 ACTCAACTTTGTACTAGCTTTGTACA 58.730 34.615 21.04 21.04 45.56 2.90
3946 4166 9.781834 TTGTACAAAGTTGAGTCACTTATTTTG 57.218 29.630 5.64 8.80 35.87 2.44
3947 4167 8.402472 TGTACAAAGTTGAGTCACTTATTTTGG 58.598 33.333 12.94 0.78 35.87 3.28
3948 4168 6.805713 ACAAAGTTGAGTCACTTATTTTGGG 58.194 36.000 12.94 0.00 35.87 4.12
3949 4169 6.605594 ACAAAGTTGAGTCACTTATTTTGGGA 59.394 34.615 12.94 0.00 35.87 4.37
3950 4170 6.635030 AAGTTGAGTCACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
3951 4171 4.755123 AGTTGAGTCACTTATTTTGGGACG 59.245 41.667 0.00 0.00 33.84 4.79
3952 4172 3.670625 TGAGTCACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 33.84 4.79
3953 4173 3.325425 TGAGTCACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 33.84 4.69
3954 4174 3.933332 GAGTCACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 33.84 4.63
3955 4175 3.007635 GTCACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
3956 4176 2.026636 TCACTTATTTTGGGACGGAGGG 60.027 50.000 0.00 0.00 0.00 4.30
4042 4262 9.005318 TCAGTTTATATCCAATGGGTAAACCTA 57.995 33.333 20.94 12.95 41.11 3.08
4127 4347 1.371558 GGGTTTGCGAGAGTGAGGT 59.628 57.895 0.00 0.00 0.00 3.85
4148 4368 4.565652 GGTTGAAGAAAGAGGCTCCACATA 60.566 45.833 11.71 0.00 0.00 2.29
4234 4454 4.884668 TTGTTCCTTGTAGATTCGTCCT 57.115 40.909 0.00 0.00 0.00 3.85
4241 4461 2.167662 TGTAGATTCGTCCTGTGCTCA 58.832 47.619 0.00 0.00 0.00 4.26
4276 4496 2.672961 TAGGCTGGTTCATGACTTCG 57.327 50.000 0.00 0.00 0.00 3.79
4361 4581 8.630037 TGAAGAAGGAAAGGTTAAAATCTTGTC 58.370 33.333 0.00 0.00 27.85 3.18
4377 4597 3.255888 TCTTGTCTGTGTAGCATCGAAGT 59.744 43.478 0.00 0.00 0.00 3.01
4394 4614 8.023706 GCATCGAAGTGTACTGATATCAAGATA 58.976 37.037 6.90 0.00 0.00 1.98
4417 4637 5.728637 AAAAAGAATGAACATGGGAGGAC 57.271 39.130 0.00 0.00 0.00 3.85
4482 4703 3.770933 AGGCTAATACGGTGAACAAGGTA 59.229 43.478 0.00 0.00 0.00 3.08
4484 4705 4.510340 GGCTAATACGGTGAACAAGGTATG 59.490 45.833 0.00 0.00 0.00 2.39
4496 4717 5.104151 TGAACAAGGTATGCCATCTGGATAA 60.104 40.000 1.54 0.00 37.39 1.75
4509 4730 3.359033 TCTGGATAAAGCAAGCAAGCAT 58.641 40.909 3.19 0.00 36.85 3.79
4547 4772 0.235926 GCAACTCAACCAGCGAAGTC 59.764 55.000 0.00 0.00 0.00 3.01
4578 4803 1.000938 CTCAAGCTGCAACTTGTTCCC 60.001 52.381 24.98 0.00 45.86 3.97
4597 4822 2.149578 CCTCAGGTTTTCTGCTGACTG 58.850 52.381 0.00 0.00 43.06 3.51
4620 4845 2.691526 ACGCCGACATTGTCCTTATCTA 59.308 45.455 11.12 0.00 0.00 1.98
4798 5023 9.886132 GTTATTTACATAGAAGAAAGACAGGGA 57.114 33.333 0.00 0.00 0.00 4.20
5045 5270 1.098050 CATTCAGCACCTTGCCCTAC 58.902 55.000 0.00 0.00 46.52 3.18
5087 5312 1.271543 CCACATGGAACCAGAAGCAGA 60.272 52.381 0.00 0.00 37.39 4.26
5126 5351 6.183361 GGACATCTTCCTCTGAGAACCATATT 60.183 42.308 6.17 0.00 41.95 1.28
5129 5354 6.240549 TCTTCCTCTGAGAACCATATTTCC 57.759 41.667 6.17 0.00 0.00 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 75 1.594310 GAGGGAGAAGCTCGCAGTT 59.406 57.895 12.96 0.00 44.32 3.16
147 151 1.069358 GAGGGAGAAACAGCGGATAGG 59.931 57.143 0.00 0.00 0.00 2.57
150 154 1.627297 GGGAGGGAGAAACAGCGGAT 61.627 60.000 0.00 0.00 0.00 4.18
151 155 2.291043 GGGAGGGAGAAACAGCGGA 61.291 63.158 0.00 0.00 0.00 5.54
153 157 2.269241 GGGGAGGGAGAAACAGCG 59.731 66.667 0.00 0.00 0.00 5.18
154 158 2.269241 CGGGGAGGGAGAAACAGC 59.731 66.667 0.00 0.00 0.00 4.40
157 161 1.003718 CACACGGGGAGGGAGAAAC 60.004 63.158 0.00 0.00 0.00 2.78
158 162 2.890766 GCACACGGGGAGGGAGAAA 61.891 63.158 0.00 0.00 0.00 2.52
235 239 2.360726 GGGCGTACCTTGTTGGGG 60.361 66.667 0.00 0.00 41.11 4.96
238 242 1.376812 GAGGGGGCGTACCTTGTTG 60.377 63.158 0.00 0.00 38.79 3.33
292 303 1.138266 GAATCCCGGTGCTAGCTAACA 59.862 52.381 17.23 0.00 0.00 2.41
299 310 2.792947 GGCGAGAATCCCGGTGCTA 61.793 63.158 0.00 0.00 0.00 3.49
308 319 1.009449 CGGACGAGAGGCGAGAATC 60.009 63.158 0.00 0.00 43.44 2.52
323 334 3.006728 ATTCTTGTCCCGGGCGGA 61.007 61.111 18.49 10.57 38.83 5.54
325 336 2.824041 CCATTCTTGTCCCGGGCG 60.824 66.667 18.49 3.88 0.00 6.13
326 337 2.440247 CCCATTCTTGTCCCGGGC 60.440 66.667 18.49 12.24 0.00 6.13
329 340 1.750399 CCTGCCCATTCTTGTCCCG 60.750 63.158 0.00 0.00 0.00 5.14
330 341 1.380380 CCCTGCCCATTCTTGTCCC 60.380 63.158 0.00 0.00 0.00 4.46
331 342 0.394899 CTCCCTGCCCATTCTTGTCC 60.395 60.000 0.00 0.00 0.00 4.02
332 343 1.034292 GCTCCCTGCCCATTCTTGTC 61.034 60.000 0.00 0.00 35.15 3.18
333 344 1.000396 GCTCCCTGCCCATTCTTGT 60.000 57.895 0.00 0.00 35.15 3.16
409 441 2.265739 GCACGTGCAGGGAGATCA 59.734 61.111 34.52 0.00 41.59 2.92
435 467 1.838715 AGGATGCAAGACTCTGCTGAT 59.161 47.619 0.00 0.00 43.07 2.90
445 477 1.139734 GCGAGACGAGGATGCAAGA 59.860 57.895 0.00 0.00 0.00 3.02
474 506 3.437049 GTCATTTCGTTCCCTTTCCTCAG 59.563 47.826 0.00 0.00 0.00 3.35
488 520 1.091771 AGCTCCATGGCGTCATTTCG 61.092 55.000 6.96 0.00 37.29 3.46
513 545 2.081585 GAAACCTCAGCCCCCAACCT 62.082 60.000 0.00 0.00 0.00 3.50
516 548 0.772124 AGAGAAACCTCAGCCCCCAA 60.772 55.000 0.00 0.00 33.16 4.12
526 561 2.179517 CGCGCGAGAGAGAAACCT 59.820 61.111 28.94 0.00 0.00 3.50
658 707 6.497640 AGCCTTGGGAAGAATTTAGAGAATT 58.502 36.000 0.00 0.00 0.00 2.17
659 708 6.084749 AGCCTTGGGAAGAATTTAGAGAAT 57.915 37.500 0.00 0.00 0.00 2.40
662 711 6.180472 TGTAAGCCTTGGGAAGAATTTAGAG 58.820 40.000 0.00 0.00 0.00 2.43
670 719 4.444876 GCTATGATGTAAGCCTTGGGAAGA 60.445 45.833 0.00 0.00 32.40 2.87
706 756 2.746472 GCTTGAAACCTCAGGCGGATAT 60.746 50.000 0.00 0.00 43.78 1.63
713 763 0.035458 AGGACGCTTGAAACCTCAGG 59.965 55.000 0.00 0.00 31.69 3.86
761 815 3.103738 CGTTAAACGTCTCCGGATACTG 58.896 50.000 16.97 12.70 36.74 2.74
838 892 2.627699 ACCTTTATGCATTTATGGCGGG 59.372 45.455 3.54 0.00 0.00 6.13
841 895 4.744631 CCGAAACCTTTATGCATTTATGGC 59.255 41.667 3.54 0.00 0.00 4.40
908 962 3.696051 AGATGTGGTGAAATCAAATCGGG 59.304 43.478 0.00 0.00 34.82 5.14
917 971 9.829507 TTTGAACAATTTAAGATGTGGTGAAAT 57.170 25.926 0.00 0.00 0.00 2.17
979 1171 1.566703 CCTCCAGGTCAGTCTCTCCTA 59.433 57.143 0.00 0.00 0.00 2.94
984 1176 1.859302 ACATCCTCCAGGTCAGTCTC 58.141 55.000 0.00 0.00 36.34 3.36
1044 1236 0.030908 CGAGCTCATACTTCCCGACC 59.969 60.000 15.40 0.00 0.00 4.79
1050 1242 1.300233 CCGCCCGAGCTCATACTTC 60.300 63.158 15.40 0.00 36.60 3.01
1071 1263 1.143401 GAACGTCCCTTCCCCGATC 59.857 63.158 0.00 0.00 0.00 3.69
1104 1296 4.771127 GACTCGGTGTCCTTTGCA 57.229 55.556 0.00 0.00 39.69 4.08
1173 1365 2.847234 ACCTGCTCGACCAACCCA 60.847 61.111 0.00 0.00 0.00 4.51
1224 1417 7.044181 TGTGAAATATCTAGGAAACAGAGCAG 58.956 38.462 0.00 0.00 0.00 4.24
1250 1443 4.263905 TGAGGCAGGGAACTTTCAATATGT 60.264 41.667 0.00 0.00 40.21 2.29
1299 1492 5.355350 AGGAGCAGTTATTTCTGTGCATAAC 59.645 40.000 0.00 0.00 38.44 1.89
1306 1499 7.168219 TGAAATACAGGAGCAGTTATTTCTGT 58.832 34.615 11.98 0.00 38.71 3.41
1309 1502 8.897752 AGAATGAAATACAGGAGCAGTTATTTC 58.102 33.333 0.00 0.00 35.60 2.17
1361 1554 3.036091 AGGTAGAGCATAAGCCCGTAAA 58.964 45.455 0.00 0.00 43.56 2.01
1404 1597 5.344743 TCTCGTCTAATCTGCCAAAAGAT 57.655 39.130 0.00 0.00 38.59 2.40
1491 1684 3.751479 ACAAAATTCCAAAGGCTGGTC 57.249 42.857 0.00 0.00 46.51 4.02
1496 1689 9.267084 TCATACTTAAAACAAAATTCCAAAGGC 57.733 29.630 0.00 0.00 0.00 4.35
1548 1741 5.824904 ATCAACTGCAGAATTGGATGTAC 57.175 39.130 23.35 0.00 0.00 2.90
1558 1751 8.869897 CGAAATAGTTAGTTATCAACTGCAGAA 58.130 33.333 23.35 5.64 42.84 3.02
1583 1776 4.991056 CCATCACCTGTTATATTGGAGTCG 59.009 45.833 0.00 0.00 0.00 4.18
1591 1784 5.380043 CTTGCTTCCCATCACCTGTTATAT 58.620 41.667 0.00 0.00 0.00 0.86
1629 1822 2.201732 CCCGTGACATATTCCAGAACG 58.798 52.381 0.00 0.00 0.00 3.95
1721 1914 0.239347 GCAACTGGTGTGCTGCTAAG 59.761 55.000 0.00 0.00 29.85 2.18
1732 1925 2.456577 ACAAGGTTTCAAGCAACTGGT 58.543 42.857 0.00 0.00 0.00 4.00
1776 1969 7.588488 TCAATAAAGGCGAACGTAAAGAAAAAG 59.412 33.333 0.00 0.00 0.00 2.27
1786 1979 3.754323 TGGAAATCAATAAAGGCGAACGT 59.246 39.130 0.00 0.00 0.00 3.99
1787 1980 4.095610 GTGGAAATCAATAAAGGCGAACG 58.904 43.478 0.00 0.00 0.00 3.95
1788 1981 5.310720 AGTGGAAATCAATAAAGGCGAAC 57.689 39.130 0.00 0.00 0.00 3.95
1807 2001 4.274459 GGCAGCCTGAATATGAAGTTAGTG 59.726 45.833 3.29 0.00 0.00 2.74
1820 2014 3.551496 CTTCCACGGGCAGCCTGAA 62.551 63.158 28.29 15.13 33.36 3.02
1827 2021 1.600636 CTTCAAGCTTCCACGGGCA 60.601 57.895 0.00 0.00 0.00 5.36
1836 2030 2.620108 GGCTTCATCCTCCTTCAAGCTT 60.620 50.000 0.00 0.00 39.57 3.74
1958 2152 6.693315 AACCAGATACATAAATTGGAACCG 57.307 37.500 0.00 0.00 33.19 4.44
1986 2180 7.274447 ACATCCATTTGTCAGTTTCATGTTTT 58.726 30.769 0.00 0.00 0.00 2.43
2019 2213 3.671702 GCAACAAATTCTCTAGCTGGCAC 60.672 47.826 0.00 0.00 0.00 5.01
2064 2258 3.748568 CACTTAAGCCAAAGTCTGAGACC 59.251 47.826 9.33 0.00 37.61 3.85
2119 2313 8.771920 ACTCGTGTGATCTTTATGATTGTAAA 57.228 30.769 0.00 0.00 35.14 2.01
2120 2314 8.032451 TGACTCGTGTGATCTTTATGATTGTAA 58.968 33.333 0.00 0.00 35.14 2.41
2121 2315 7.543756 TGACTCGTGTGATCTTTATGATTGTA 58.456 34.615 0.00 0.00 35.14 2.41
2128 2322 5.178061 TGCAATGACTCGTGTGATCTTTAT 58.822 37.500 0.00 0.00 0.00 1.40
2131 2325 3.044235 TGCAATGACTCGTGTGATCTT 57.956 42.857 0.00 0.00 0.00 2.40
2135 2329 3.187022 CAGAAATGCAATGACTCGTGTGA 59.813 43.478 0.00 0.00 0.00 3.58
2141 2335 7.649306 ACAAAAACTACAGAAATGCAATGACTC 59.351 33.333 0.00 0.00 0.00 3.36
2143 2337 7.698836 ACAAAAACTACAGAAATGCAATGAC 57.301 32.000 0.00 0.00 0.00 3.06
2243 2437 4.843728 CAACATAGTTAGGTGTCCCACAT 58.156 43.478 0.00 0.00 35.86 3.21
2255 2449 2.463752 ACCTCGGGAGCAACATAGTTA 58.536 47.619 0.00 0.00 0.00 2.24
2279 2473 6.770746 ATCAATGCAAATGTAGAAGAAGCT 57.229 33.333 0.00 0.00 0.00 3.74
2281 2475 9.199982 ACAAAATCAATGCAAATGTAGAAGAAG 57.800 29.630 0.00 0.00 0.00 2.85
2283 2477 9.545105 AAACAAAATCAATGCAAATGTAGAAGA 57.455 25.926 0.00 0.00 0.00 2.87
2298 2492 9.103861 GTTCATTCCTGGTTAAAACAAAATCAA 57.896 29.630 0.00 0.00 0.00 2.57
2304 2498 5.988561 GCATGTTCATTCCTGGTTAAAACAA 59.011 36.000 9.99 0.00 0.00 2.83
2342 2536 5.733620 TCGATAACCTGGATATTGGGTAC 57.266 43.478 0.00 0.00 32.50 3.34
2437 2631 4.517285 TGTCATCCTCAAAAGGCAGATAC 58.483 43.478 0.00 0.00 43.02 2.24
2524 2719 7.297614 AGGGTAAATGCAAATATACATCCAGT 58.702 34.615 0.00 0.00 0.00 4.00
2529 2724 9.646522 AGAAAGAGGGTAAATGCAAATATACAT 57.353 29.630 0.00 0.00 0.00 2.29
2534 2729 7.888021 TCAAGAGAAAGAGGGTAAATGCAAATA 59.112 33.333 0.00 0.00 0.00 1.40
2547 2742 5.394443 CCAGAGATCTGTCAAGAGAAAGAGG 60.394 48.000 0.00 0.00 41.35 3.69
2593 2788 5.705609 TTTTAGCTCCATCAGAAAACCAC 57.294 39.130 0.00 0.00 0.00 4.16
2643 2838 7.160049 AGTAAAAAGGCTTACAGTAGAAGGAC 58.840 38.462 0.00 0.00 34.75 3.85
2660 2855 9.748708 TTCTGAAATGGAATGTGAAGTAAAAAG 57.251 29.630 0.00 0.00 0.00 2.27
2683 2880 5.743636 TGGCTGCCTAATTTCAAATTTCT 57.256 34.783 21.03 0.00 0.00 2.52
2699 2896 1.032014 TCTGTTGACCTTTTGGCTGC 58.968 50.000 0.00 0.00 45.59 5.25
2726 2923 0.032403 CACTTGTGTTGCATGGGTGG 59.968 55.000 0.00 0.00 0.00 4.61
2727 2924 0.032403 CCACTTGTGTTGCATGGGTG 59.968 55.000 0.00 0.00 0.00 4.61
2728 2925 0.396974 ACCACTTGTGTTGCATGGGT 60.397 50.000 5.31 0.00 32.79 4.51
2729 2926 0.032403 CACCACTTGTGTTGCATGGG 59.968 55.000 5.31 0.00 40.26 4.00
2792 2990 4.995487 ACAATGAGGAACCGAGTAAGAAAC 59.005 41.667 0.00 0.00 0.00 2.78
2808 3006 0.439985 CGCTGGTCAACGACAATGAG 59.560 55.000 0.00 0.00 33.68 2.90
3032 3234 4.262036 CCTCCTTAACTTGTTTTTCCTGGC 60.262 45.833 0.00 0.00 0.00 4.85
3510 3722 5.505181 TCCTGCTTCTAGGTTCTTCATTT 57.495 39.130 0.00 0.00 38.99 2.32
3570 3782 6.862209 ACATTTCTCAAACTGCTGTGTTTTA 58.138 32.000 0.00 0.00 37.98 1.52
3601 3813 7.860373 GCCTTGATCAATAATTGCATTACGTTA 59.140 33.333 8.96 0.00 0.00 3.18
3766 3978 8.421673 AAGAAGCTACCGTACATCTTAATTTC 57.578 34.615 0.00 0.00 0.00 2.17
3805 4017 4.820897 TCATGGGCGCTTGTATAGAATAG 58.179 43.478 7.64 0.00 0.00 1.73
3842 4062 8.175716 GTGTTCTAAGTCGCTTGCTTAAATTAT 58.824 33.333 2.86 0.00 0.00 1.28
3874 4094 3.463048 TTTTAGGACGGAGGGAGTACT 57.537 47.619 0.00 0.00 36.60 2.73
3875 4095 5.362143 ACTTATTTTAGGACGGAGGGAGTAC 59.638 44.000 0.00 0.00 0.00 2.73
3876 4096 5.361857 CACTTATTTTAGGACGGAGGGAGTA 59.638 44.000 0.00 0.00 0.00 2.59
3877 4097 4.161754 CACTTATTTTAGGACGGAGGGAGT 59.838 45.833 0.00 0.00 0.00 3.85
3878 4098 4.404715 TCACTTATTTTAGGACGGAGGGAG 59.595 45.833 0.00 0.00 0.00 4.30
3879 4099 4.161001 GTCACTTATTTTAGGACGGAGGGA 59.839 45.833 0.00 0.00 0.00 4.20
3880 4100 4.161754 AGTCACTTATTTTAGGACGGAGGG 59.838 45.833 0.00 0.00 33.84 4.30
3881 4101 5.105473 TGAGTCACTTATTTTAGGACGGAGG 60.105 44.000 0.00 0.00 33.84 4.30
3882 4102 5.962433 TGAGTCACTTATTTTAGGACGGAG 58.038 41.667 0.00 0.00 33.84 4.63
3883 4103 5.988310 TGAGTCACTTATTTTAGGACGGA 57.012 39.130 0.00 0.00 33.84 4.69
3884 4104 6.164176 AGTTGAGTCACTTATTTTAGGACGG 58.836 40.000 0.00 0.00 33.84 4.79
3885 4105 7.653767 AAGTTGAGTCACTTATTTTAGGACG 57.346 36.000 0.00 0.00 35.10 4.79
3886 4106 8.837389 ACAAAGTTGAGTCACTTATTTTAGGAC 58.163 33.333 0.00 0.00 35.87 3.85
3887 4107 8.974060 ACAAAGTTGAGTCACTTATTTTAGGA 57.026 30.769 0.00 0.00 35.87 2.94
3892 4112 8.989980 GCTAGTACAAAGTTGAGTCACTTATTT 58.010 33.333 0.00 0.00 35.87 1.40
3893 4113 8.368668 AGCTAGTACAAAGTTGAGTCACTTATT 58.631 33.333 0.00 0.00 35.87 1.40
3894 4114 7.897864 AGCTAGTACAAAGTTGAGTCACTTAT 58.102 34.615 0.00 0.00 35.87 1.73
3895 4115 7.286215 AGCTAGTACAAAGTTGAGTCACTTA 57.714 36.000 0.00 0.00 35.87 2.24
3896 4116 6.163135 AGCTAGTACAAAGTTGAGTCACTT 57.837 37.500 0.00 0.00 38.74 3.16
3897 4117 5.793030 AGCTAGTACAAAGTTGAGTCACT 57.207 39.130 0.00 0.00 0.00 3.41
3898 4118 6.258068 ACAAAGCTAGTACAAAGTTGAGTCAC 59.742 38.462 0.00 0.00 0.00 3.67
3899 4119 6.346096 ACAAAGCTAGTACAAAGTTGAGTCA 58.654 36.000 0.00 0.00 0.00 3.41
3900 4120 6.846325 ACAAAGCTAGTACAAAGTTGAGTC 57.154 37.500 0.00 0.00 0.00 3.36
3901 4121 7.270047 TGTACAAAGCTAGTACAAAGTTGAGT 58.730 34.615 22.60 0.00 46.22 3.41
3902 4122 7.709269 TGTACAAAGCTAGTACAAAGTTGAG 57.291 36.000 22.60 0.00 46.22 3.02
3920 4140 9.781834 CAAAATAAGTGACTCAACTTTGTACAA 57.218 29.630 3.59 3.59 40.77 2.41
3921 4141 8.402472 CCAAAATAAGTGACTCAACTTTGTACA 58.598 33.333 0.00 0.00 40.77 2.90
3922 4142 7.860872 CCCAAAATAAGTGACTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
3923 4143 7.776030 TCCCAAAATAAGTGACTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
3924 4144 6.605594 TCCCAAAATAAGTGACTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
3925 4145 6.918022 GTCCCAAAATAAGTGACTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
3926 4146 6.238648 CGTCCCAAAATAAGTGACTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
3927 4147 5.238650 CGTCCCAAAATAAGTGACTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
3928 4148 4.755123 CGTCCCAAAATAAGTGACTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
3929 4149 4.083484 CCGTCCCAAAATAAGTGACTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
3930 4150 4.069304 CCGTCCCAAAATAAGTGACTCAA 58.931 43.478 0.00 0.00 0.00 3.02
3931 4151 3.325425 TCCGTCCCAAAATAAGTGACTCA 59.675 43.478 0.00 0.00 0.00 3.41
3932 4152 3.933332 CTCCGTCCCAAAATAAGTGACTC 59.067 47.826 0.00 0.00 0.00 3.36
3933 4153 3.307480 CCTCCGTCCCAAAATAAGTGACT 60.307 47.826 0.00 0.00 0.00 3.41
3934 4154 3.007635 CCTCCGTCCCAAAATAAGTGAC 58.992 50.000 0.00 0.00 0.00 3.67
3935 4155 2.026636 CCCTCCGTCCCAAAATAAGTGA 60.027 50.000 0.00 0.00 0.00 3.41
3936 4156 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
3937 4157 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
3938 4158 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
3939 4159 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
3940 4160 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
3941 4161 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
3942 4162 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
3943 4163 0.906282 GGTACTCCCTCCGTCCCAAA 60.906 60.000 0.00 0.00 0.00 3.28
3944 4164 1.305549 GGTACTCCCTCCGTCCCAA 60.306 63.158 0.00 0.00 0.00 4.12
3945 4165 2.361771 GGTACTCCCTCCGTCCCA 59.638 66.667 0.00 0.00 0.00 4.37
3955 4175 5.070685 ACATTCTTCTTTGTTGGGTACTCC 58.929 41.667 0.00 0.00 0.00 3.85
3956 4176 5.998363 AGACATTCTTCTTTGTTGGGTACTC 59.002 40.000 0.00 0.00 0.00 2.59
4009 4229 7.201938 ACCCATTGGATATAAACTGATTTGCAG 60.202 37.037 3.62 0.00 42.13 4.41
4042 4262 5.460646 CAAACAATTAATGCCGAGTCAGTT 58.539 37.500 0.00 0.00 0.00 3.16
4127 4347 3.795688 ATGTGGAGCCTCTTTCTTCAA 57.204 42.857 0.00 0.00 0.00 2.69
4148 4368 1.302351 GACACTCTGCAGCTGCCTT 60.302 57.895 34.64 14.06 41.18 4.35
4356 4576 3.366121 CACTTCGATGCTACACAGACAAG 59.634 47.826 0.00 0.00 0.00 3.16
4361 4581 3.854240 CAGTACACTTCGATGCTACACAG 59.146 47.826 0.00 0.00 0.00 3.66
4401 4621 4.082125 GTTCTTGTCCTCCCATGTTCATT 58.918 43.478 0.00 0.00 0.00 2.57
4417 4637 0.804989 GTCCCGATTGCCTGTTCTTG 59.195 55.000 0.00 0.00 0.00 3.02
4482 4703 2.626743 GCTTGCTTTATCCAGATGGCAT 59.373 45.455 0.00 0.00 34.44 4.40
4484 4705 2.026641 TGCTTGCTTTATCCAGATGGC 58.973 47.619 0.00 0.00 34.44 4.40
4496 4717 1.335145 AACCTGATGCTTGCTTGCTT 58.665 45.000 3.47 0.00 0.00 3.91
4509 4730 1.948104 CGTTGGTGTCTGAAACCTGA 58.052 50.000 17.64 4.29 38.60 3.86
4547 4772 1.601171 AGCTTGAGGCAGTAGCTGG 59.399 57.895 0.00 0.00 43.25 4.85
4578 4803 1.534595 GCAGTCAGCAGAAAACCTGAG 59.465 52.381 0.00 0.00 45.78 3.35
4597 4822 1.017177 TAAGGACAATGTCGGCGTGC 61.017 55.000 6.85 1.63 32.65 5.34
4620 4845 4.322567 GCCTCAAATTCAGAGAGTTCAGT 58.677 43.478 8.91 0.00 35.09 3.41
4779 5004 5.782845 ACTCTTCCCTGTCTTTCTTCTATGT 59.217 40.000 0.00 0.00 0.00 2.29
4783 5008 3.244387 GCACTCTTCCCTGTCTTTCTTCT 60.244 47.826 0.00 0.00 0.00 2.85
4784 5009 3.070748 GCACTCTTCCCTGTCTTTCTTC 58.929 50.000 0.00 0.00 0.00 2.87
4785 5010 2.439507 TGCACTCTTCCCTGTCTTTCTT 59.560 45.455 0.00 0.00 0.00 2.52
4786 5011 2.050144 TGCACTCTTCCCTGTCTTTCT 58.950 47.619 0.00 0.00 0.00 2.52
4798 5023 1.035139 CAGGCTTGGTTTGCACTCTT 58.965 50.000 0.00 0.00 0.00 2.85
5045 5270 6.259608 GTGGATTCTGACTAGGTTGAATGATG 59.740 42.308 9.88 0.00 30.41 3.07
5087 5312 2.376518 AGATGTCCTCCAAACCATGTGT 59.623 45.455 0.00 0.00 0.00 3.72
5126 5351 4.023291 GGACATGGAAATTTAGGCAGGAA 58.977 43.478 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.