Multiple sequence alignment - TraesCS5B01G054300

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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 TraesCS5B01G054300 chr5B 100.000 8013 0 0 1 8013 59181936 59173924 0.000000e+00 14798
1 TraesCS5B01G054300 chr5D 96.580 5321 112 32 859 6141 56470845 56465557 0.000000e+00 8754
2 TraesCS5B01G054300 chr5D 95.910 1858 52 9 6168 8013 56465238 56463393 0.000000e+00 2988
3 TraesCS5B01G054300 chr5D 84.888 536 36 18 231 748 56471371 56470863 4.320000e-137 499
4 TraesCS5B01G054300 chr5A 95.390 1844 58 13 6193 8013 44995434 44993595 0.000000e+00 2909
5 TraesCS5B01G054300 chr5A 89.814 1021 80 13 2705 3709 44999178 44998166 0.000000e+00 1288
6 TraesCS5B01G054300 chr5A 91.024 869 39 18 852 1707 45000694 44999852 0.000000e+00 1136
7 TraesCS5B01G054300 chr5A 95.070 710 22 4 4897 5594 44996791 44996083 0.000000e+00 1105
8 TraesCS5B01G054300 chr5A 88.905 685 60 9 1982 2664 44999852 44999182 0.000000e+00 830
9 TraesCS5B01G054300 chr5A 95.991 424 17 0 5718 6141 44996085 44995662 0.000000e+00 689
10 TraesCS5B01G054300 chr5A 86.756 521 52 14 4099 4607 44997767 44997252 1.510000e-156 564
11 TraesCS5B01G054300 chr5A 88.393 336 22 7 464 787 45001020 45000690 9.750000e-104 388
12 TraesCS5B01G054300 chr5A 84.345 313 45 4 4609 4919 44997127 44996817 3.630000e-78 303
13 TraesCS5B01G054300 chr5A 89.474 228 16 4 1 222 45001663 45001438 1.700000e-71 281
14 TraesCS5B01G054300 chr5A 83.516 182 15 7 257 429 45001359 45001184 1.080000e-33 156
15 TraesCS5B01G054300 chr7B 93.701 127 8 0 5586 5712 431680487 431680361 2.950000e-44 191
16 TraesCS5B01G054300 chr6D 94.915 118 6 0 5587 5704 418956987 418957104 1.370000e-42 185
17 TraesCS5B01G054300 chr6D 92.063 126 10 0 5587 5712 178859039 178858914 2.300000e-40 178
18 TraesCS5B01G054300 chr2D 92.308 130 8 2 5575 5704 71386581 71386454 4.940000e-42 183
19 TraesCS5B01G054300 chr7A 92.857 126 8 1 5587 5712 293302393 293302517 1.780000e-41 182
20 TraesCS5B01G054300 chr4A 92.000 125 10 0 5580 5704 89430794 89430918 8.260000e-40 176
21 TraesCS5B01G054300 chr4A 97.531 81 1 1 4021 4101 614251508 614251429 3.900000e-28 137
22 TraesCS5B01G054300 chr7D 89.552 134 14 0 5580 5713 26540155 26540288 3.850000e-38 171
23 TraesCS5B01G054300 chr7D 91.919 99 4 4 4006 4103 181912010 181911915 1.400000e-27 135
24 TraesCS5B01G054300 chr6B 91.200 125 11 0 5587 5711 293959106 293959230 3.850000e-38 171
25 TraesCS5B01G054300 chr4D 95.604 91 3 1 4021 4111 449455694 449455605 2.330000e-30 145
26 TraesCS5B01G054300 chrUn 92.784 97 5 2 4012 4107 23900941 23900846 1.080000e-28 139
27 TraesCS5B01G054300 chr2B 92.784 97 5 2 4012 4107 799161143 799161048 1.080000e-28 139
28 TraesCS5B01G054300 chr2B 92.784 97 5 2 4012 4107 799214299 799214204 1.080000e-28 139
29 TraesCS5B01G054300 chr2B 91.176 102 5 3 4021 4122 782178763 782178860 1.400000e-27 135
30 TraesCS5B01G054300 chr2B 89.091 110 7 5 3993 4100 41129599 41129493 1.810000e-26 132
31 TraesCS5B01G054300 chr3B 89.815 108 6 5 3997 4102 3660753 3660857 5.040000e-27 134
32 TraesCS5B01G054300 chr3B 86.087 115 11 5 4000 4111 774226093 774226205 1.410000e-22 119
33 TraesCS5B01G054300 chr1B 95.181 83 3 1 4021 4103 117222172 117222091 6.530000e-26 130
34 TraesCS5B01G054300 chr4B 89.320 103 7 4 4003 4104 607437411 607437510 8.440000e-25 126
35 TraesCS5B01G054300 chr3D 93.023 86 4 2 4021 4105 47483335 47483251 3.040000e-24 124


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 TraesCS5B01G054300 chr5B 59173924 59181936 8012 True 14798.000000 14798 100.000000 1 8013 1 chr5B.!!$R1 8012
1 TraesCS5B01G054300 chr5D 56463393 56471371 7978 True 4080.333333 8754 92.459333 231 8013 3 chr5D.!!$R1 7782
2 TraesCS5B01G054300 chr5A 44993595 45001663 8068 True 877.181818 2909 89.879818 1 8013 11 chr5A.!!$R1 8012

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
451 517 0.035056 ATTCTGGCAGAAGAACGGGG 60.035 55.000 31.17 0.00 37.69 5.73 F
1282 1514 0.240678 CATTTTGCTGCTGCGGTGTA 59.759 50.000 10.62 0.00 43.34 2.90 F
1283 1515 0.240945 ATTTTGCTGCTGCGGTGTAC 59.759 50.000 10.62 0.00 43.34 2.90 F
1561 1794 1.347707 TGGCCAAGTTCACTACAGGAG 59.652 52.381 0.61 0.00 0.00 3.69 F
2311 2563 2.237392 GGTTCTGGTCAGGTATCAGCTT 59.763 50.000 0.00 0.00 36.15 3.74 F
2996 3251 2.548480 AGATGCTTCATCACATCATGCG 59.452 45.455 9.19 0.00 44.16 4.73 F
4707 5197 0.042448 GTGCGTGTCTCGTTTGAACC 60.042 55.000 0.00 0.00 42.13 3.62 F
5615 6169 1.468127 CATTCCACAATGTAGTGCGCA 59.532 47.619 5.66 5.66 38.18 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1724 1972 1.202940 ACTCACCAAAAGGGAAGGAGC 60.203 52.381 0.00 0.00 41.15 4.70 R
2769 3021 1.068127 GGATAGGCCAAGCAAAGCATG 59.932 52.381 5.01 0.00 36.34 4.06 R
2835 3090 2.045561 TTGCTGTCGTTCCCAAAAGA 57.954 45.000 0.00 0.00 0.00 2.52 R
3512 3767 1.152830 ACGAAAACCCTGCCCACAT 59.847 52.632 0.00 0.00 0.00 3.21 R
3592 3847 0.620556 CCAGGGCAGGTGTCTGTATT 59.379 55.000 0.00 0.00 42.78 1.89 R
4886 5382 3.117512 AGGAAGTCCCAAAAGCTTCTTGA 60.118 43.478 17.53 4.09 38.77 3.02 R
6158 6712 0.613777 GCAGTAGATTATCCCCGGGG 59.386 60.000 35.80 35.80 0.00 5.73 R
7515 8378 1.315690 CACTGATGGGATCATGTGGC 58.684 55.000 0.00 0.00 38.85 5.01 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
53 59 4.759693 TGTAAGAAATTCATCTTGGCGTGT 59.240 37.500 3.14 0.00 39.87 4.49
100 106 2.477189 CGTCAACCACAACCACTTCAAC 60.477 50.000 0.00 0.00 0.00 3.18
102 108 2.752354 TCAACCACAACCACTTCAACTG 59.248 45.455 0.00 0.00 0.00 3.16
110 116 4.889409 ACAACCACTTCAACTGTTCATGAT 59.111 37.500 0.00 0.00 0.00 2.45
115 121 2.401583 TCAACTGTTCATGATCCCCG 57.598 50.000 0.00 0.00 0.00 5.73
124 130 4.408921 TGTTCATGATCCCCGTAATCTCTT 59.591 41.667 0.00 0.00 0.00 2.85
126 132 5.215252 TCATGATCCCCGTAATCTCTTTC 57.785 43.478 0.00 0.00 0.00 2.62
128 134 3.654273 TGATCCCCGTAATCTCTTTCCT 58.346 45.455 0.00 0.00 0.00 3.36
134 140 3.451178 CCCGTAATCTCTTTCCTTCTCCA 59.549 47.826 0.00 0.00 0.00 3.86
136 142 5.293560 CCGTAATCTCTTTCCTTCTCCATC 58.706 45.833 0.00 0.00 0.00 3.51
141 147 7.700022 AATCTCTTTCCTTCTCCATCTTTTG 57.300 36.000 0.00 0.00 0.00 2.44
183 189 5.842907 TCTCACCATAAGGATACACATTCG 58.157 41.667 0.00 0.00 38.69 3.34
222 228 2.543430 GCATCCAAACGCAACACAAAAT 59.457 40.909 0.00 0.00 0.00 1.82
223 229 3.002144 GCATCCAAACGCAACACAAAATT 59.998 39.130 0.00 0.00 0.00 1.82
224 230 4.210120 GCATCCAAACGCAACACAAAATTA 59.790 37.500 0.00 0.00 0.00 1.40
225 231 5.665232 CATCCAAACGCAACACAAAATTAC 58.335 37.500 0.00 0.00 0.00 1.89
228 234 4.208253 CCAAACGCAACACAAAATTACTCC 59.792 41.667 0.00 0.00 0.00 3.85
229 235 3.262135 ACGCAACACAAAATTACTCCG 57.738 42.857 0.00 0.00 0.00 4.63
315 365 0.951040 CGCACCTTTCTCCTGTCACC 60.951 60.000 0.00 0.00 0.00 4.02
318 368 2.430465 CACCTTTCTCCTGTCACCATG 58.570 52.381 0.00 0.00 0.00 3.66
321 371 3.008049 ACCTTTCTCCTGTCACCATGTAC 59.992 47.826 0.00 0.00 0.00 2.90
323 373 2.319025 TCTCCTGTCACCATGTACCA 57.681 50.000 0.00 0.00 0.00 3.25
324 374 2.179427 TCTCCTGTCACCATGTACCAG 58.821 52.381 0.00 0.00 0.00 4.00
336 388 1.093972 TGTACCAGCCAATTGCATCG 58.906 50.000 0.00 0.00 44.83 3.84
359 418 0.106894 GATGCCACCCCAGCTACTAC 59.893 60.000 0.00 0.00 0.00 2.73
364 423 2.119495 CCACCCCAGCTACTACTTCAT 58.881 52.381 0.00 0.00 0.00 2.57
365 424 2.505819 CCACCCCAGCTACTACTTCATT 59.494 50.000 0.00 0.00 0.00 2.57
369 435 3.197766 CCCCAGCTACTACTTCATTCACA 59.802 47.826 0.00 0.00 0.00 3.58
370 436 4.184629 CCCAGCTACTACTTCATTCACAC 58.815 47.826 0.00 0.00 0.00 3.82
371 437 4.322725 CCCAGCTACTACTTCATTCACACA 60.323 45.833 0.00 0.00 0.00 3.72
372 438 4.627467 CCAGCTACTACTTCATTCACACAC 59.373 45.833 0.00 0.00 0.00 3.82
373 439 5.230182 CAGCTACTACTTCATTCACACACA 58.770 41.667 0.00 0.00 0.00 3.72
412 478 5.534207 TCAAGCAAACATGATCCAAAACT 57.466 34.783 0.00 0.00 0.00 2.66
416 482 7.984050 TCAAGCAAACATGATCCAAAACTAAAA 59.016 29.630 0.00 0.00 0.00 1.52
438 504 5.718724 AAAGAAAGGCTCAAAGATTCTGG 57.281 39.130 0.00 0.00 31.14 3.86
439 505 3.087781 AGAAAGGCTCAAAGATTCTGGC 58.912 45.455 0.00 0.00 0.00 4.85
441 507 2.125773 AGGCTCAAAGATTCTGGCAG 57.874 50.000 8.58 8.58 0.00 4.85
442 508 1.632409 AGGCTCAAAGATTCTGGCAGA 59.368 47.619 14.43 14.43 0.00 4.26
444 510 2.422832 GGCTCAAAGATTCTGGCAGAAG 59.577 50.000 31.17 19.03 37.69 2.85
445 511 3.341823 GCTCAAAGATTCTGGCAGAAGA 58.658 45.455 31.17 21.74 37.69 2.87
446 512 3.755378 GCTCAAAGATTCTGGCAGAAGAA 59.245 43.478 31.17 12.75 37.69 2.52
449 515 2.393271 AGATTCTGGCAGAAGAACGG 57.607 50.000 31.17 0.00 37.69 4.44
450 516 1.065854 AGATTCTGGCAGAAGAACGGG 60.066 52.381 31.17 0.00 37.69 5.28
451 517 0.035056 ATTCTGGCAGAAGAACGGGG 60.035 55.000 31.17 0.00 37.69 5.73
452 518 2.747855 CTGGCAGAAGAACGGGGC 60.748 66.667 9.42 0.00 0.00 5.80
453 519 3.551496 CTGGCAGAAGAACGGGGCA 62.551 63.158 9.42 0.00 33.90 5.36
462 528 3.910627 AGAAGAACGGGGCATAGGAATAT 59.089 43.478 0.00 0.00 0.00 1.28
532 733 2.112815 CGATTTCCCTGTTCCCGGC 61.113 63.158 0.00 0.00 0.00 6.13
533 734 1.753078 GATTTCCCTGTTCCCGGCC 60.753 63.158 0.00 0.00 0.00 6.13
534 735 2.493273 GATTTCCCTGTTCCCGGCCA 62.493 60.000 2.24 0.00 0.00 5.36
541 742 3.670377 GTTCCCGGCCAACAGTGC 61.670 66.667 2.24 0.00 0.00 4.40
629 830 3.120025 GCTAGGCTGTTTTTCTTCTCTGC 60.120 47.826 0.00 0.00 0.00 4.26
660 867 2.726887 GCTAGCTAGCGATAACGGC 58.273 57.895 28.89 5.01 39.82 5.68
748 966 0.666577 GTCTTCTGACGTTGACCGGG 60.667 60.000 6.32 0.00 42.24 5.73
749 967 1.374252 CTTCTGACGTTGACCGGGG 60.374 63.158 6.32 0.00 42.24 5.73
756 974 3.728373 GTTGACCGGGGCCCTCAT 61.728 66.667 24.38 6.86 0.00 2.90
757 975 3.407967 TTGACCGGGGCCCTCATC 61.408 66.667 24.38 16.69 0.00 2.92
784 1002 4.451652 GTCCCGTCCGTCGTCGTC 62.452 72.222 0.71 0.00 37.94 4.20
789 1007 4.030452 GTCCGTCGTCGTCGGGTT 62.030 66.667 26.45 0.00 46.82 4.11
790 1008 3.286751 TCCGTCGTCGTCGGGTTT 61.287 61.111 26.45 0.00 46.82 3.27
791 1009 2.355009 CCGTCGTCGTCGGGTTTT 60.355 61.111 21.00 0.00 43.68 2.43
792 1010 1.950630 CCGTCGTCGTCGGGTTTTT 60.951 57.895 21.00 0.00 43.68 1.94
842 1060 5.744666 TTTTCTTTTTGAGAATCCGTCGT 57.255 34.783 0.00 0.00 43.65 4.34
843 1061 4.985044 TTCTTTTTGAGAATCCGTCGTC 57.015 40.909 0.00 0.00 39.44 4.20
844 1062 3.323243 TCTTTTTGAGAATCCGTCGTCC 58.677 45.455 0.00 0.00 0.00 4.79
845 1063 3.006537 TCTTTTTGAGAATCCGTCGTCCT 59.993 43.478 0.00 0.00 0.00 3.85
846 1064 3.396260 TTTTGAGAATCCGTCGTCCTT 57.604 42.857 0.00 0.00 0.00 3.36
847 1065 2.363788 TTGAGAATCCGTCGTCCTTG 57.636 50.000 0.00 0.00 0.00 3.61
848 1066 0.530744 TGAGAATCCGTCGTCCTTGG 59.469 55.000 0.00 0.00 0.00 3.61
849 1067 0.806492 GAGAATCCGTCGTCCTTGGC 60.806 60.000 0.00 0.00 0.00 4.52
850 1068 1.218316 GAATCCGTCGTCCTTGGCT 59.782 57.895 0.00 0.00 0.00 4.75
851 1069 1.079127 AATCCGTCGTCCTTGGCTG 60.079 57.895 0.00 0.00 0.00 4.85
852 1070 1.827399 AATCCGTCGTCCTTGGCTGT 61.827 55.000 0.00 0.00 0.00 4.40
853 1071 1.827399 ATCCGTCGTCCTTGGCTGTT 61.827 55.000 0.00 0.00 0.00 3.16
854 1072 2.317609 CCGTCGTCCTTGGCTGTTG 61.318 63.158 0.00 0.00 0.00 3.33
855 1073 2.317609 CGTCGTCCTTGGCTGTTGG 61.318 63.158 0.00 0.00 0.00 3.77
856 1074 1.227853 GTCGTCCTTGGCTGTTGGT 60.228 57.895 0.00 0.00 0.00 3.67
857 1075 0.818040 GTCGTCCTTGGCTGTTGGTT 60.818 55.000 0.00 0.00 0.00 3.67
900 1118 4.353437 ACCGACGCGTGTTCTCCC 62.353 66.667 20.70 0.00 0.00 4.30
901 1119 4.351938 CCGACGCGTGTTCTCCCA 62.352 66.667 20.70 0.00 0.00 4.37
980 1201 2.383527 GCGCTGTGCTAGTTTCGCT 61.384 57.895 5.84 0.00 41.73 4.93
1147 1377 1.700186 ACTTCTTCAAGGTCCACTCCC 59.300 52.381 0.00 0.00 33.37 4.30
1148 1378 1.981495 CTTCTTCAAGGTCCACTCCCT 59.019 52.381 0.00 0.00 0.00 4.20
1149 1379 1.645710 TCTTCAAGGTCCACTCCCTC 58.354 55.000 0.00 0.00 0.00 4.30
1150 1380 0.615850 CTTCAAGGTCCACTCCCTCC 59.384 60.000 0.00 0.00 0.00 4.30
1171 1401 0.544223 CTCCCCGTCTCTCTCTCTCA 59.456 60.000 0.00 0.00 0.00 3.27
1279 1511 1.870055 CTCCATTTTGCTGCTGCGGT 61.870 55.000 10.62 0.00 43.34 5.68
1280 1512 1.735198 CCATTTTGCTGCTGCGGTG 60.735 57.895 10.62 6.70 43.34 4.94
1281 1513 1.007038 CATTTTGCTGCTGCGGTGT 60.007 52.632 10.62 0.00 43.34 4.16
1282 1514 0.240678 CATTTTGCTGCTGCGGTGTA 59.759 50.000 10.62 0.00 43.34 2.90
1283 1515 0.240945 ATTTTGCTGCTGCGGTGTAC 59.759 50.000 10.62 0.00 43.34 2.90
1561 1794 1.347707 TGGCCAAGTTCACTACAGGAG 59.652 52.381 0.61 0.00 0.00 3.69
1668 1916 7.717436 TCAAGTGTGTATTACTCATGGTTTTCA 59.283 33.333 2.22 0.00 0.00 2.69
1691 1939 3.568430 GCCGGGTTTCCCTTAATTATCTG 59.432 47.826 2.18 0.00 42.67 2.90
1786 2034 5.673337 TGCTAGCATTTTATTAGGAAGCG 57.327 39.130 14.93 0.00 0.00 4.68
1950 2199 7.330262 GTTTACATGTGGAAATTGGGATGATT 58.670 34.615 9.11 0.00 0.00 2.57
2311 2563 2.237392 GGTTCTGGTCAGGTATCAGCTT 59.763 50.000 0.00 0.00 36.15 3.74
2430 2682 8.295288 CCTATGAAATACTTCTTCCATTCATGC 58.705 37.037 8.60 0.00 37.86 4.06
2629 2881 6.910536 ATCCATCGAAATGTAAAGAGACAC 57.089 37.500 0.00 0.00 30.52 3.67
2651 2903 6.525629 CACCTGGAGTATCTTTTATAGGTGG 58.474 44.000 11.24 0.00 46.24 4.61
2673 2925 4.300189 TGCAATTAGAAAGCACAAACGT 57.700 36.364 0.00 0.00 32.55 3.99
2769 3021 6.967199 GCTGTTAGAAAGTACAAATGTATGCC 59.033 38.462 0.00 0.00 32.54 4.40
2835 3090 3.857157 ACACTGTGGGAACTGTACATT 57.143 42.857 13.09 0.00 0.00 2.71
2836 3091 3.740115 ACACTGTGGGAACTGTACATTC 58.260 45.455 13.09 2.92 0.00 2.67
2846 3101 5.278808 GGGAACTGTACATTCTTTTGGGAAC 60.279 44.000 0.00 0.00 0.00 3.62
2996 3251 2.548480 AGATGCTTCATCACATCATGCG 59.452 45.455 9.19 0.00 44.16 4.73
3035 3290 4.450053 GTGCAGAGAGGATAAAGAAGCAT 58.550 43.478 0.00 0.00 0.00 3.79
3130 3385 6.612247 TTTCTGTTTCTACAAATCGCTTCA 57.388 33.333 0.00 0.00 32.92 3.02
3370 3625 4.702131 GCCTGTGGTGATCTTTCAGTTAAT 59.298 41.667 0.00 0.00 30.85 1.40
3451 3706 6.495181 TGGCCTTTTCTCCATACACATAAAAA 59.505 34.615 3.32 0.00 0.00 1.94
3512 3767 3.847671 TCCAACATGGTAACTGTGTCA 57.152 42.857 0.00 0.00 39.03 3.58
3592 3847 4.116961 CTGTTACAACTTGTTGTCCGAGA 58.883 43.478 20.47 7.90 36.44 4.04
3775 4126 5.881447 AGACAAGTACAAGACATAGTAGCG 58.119 41.667 0.00 0.00 0.00 4.26
3922 4278 9.545105 TCATGTAAGCAAGTTTTCATTTTCATT 57.455 25.926 0.00 0.00 0.00 2.57
4383 4742 6.031751 ACTTTTTGGTAGTCTTGTTTTGCA 57.968 33.333 0.00 0.00 0.00 4.08
4486 4850 0.541296 AAAAGCTGTCAGGCATGGCT 60.541 50.000 17.44 17.44 31.00 4.75
4526 4890 9.953565 TTGTAGTGAAGGTATGCTTTATACTTT 57.046 29.630 0.00 0.00 42.30 2.66
4527 4891 9.378551 TGTAGTGAAGGTATGCTTTATACTTTG 57.621 33.333 0.00 0.00 40.44 2.77
4528 4892 9.379791 GTAGTGAAGGTATGCTTTATACTTTGT 57.620 33.333 0.00 0.00 40.44 2.83
4560 4926 8.190122 CCTTAATGTTCATGTAAGCAGCATTTA 58.810 33.333 0.00 0.00 0.00 1.40
4592 4958 0.545171 GCTACCCTTACCACCCCTTC 59.455 60.000 0.00 0.00 0.00 3.46
4667 5157 1.207329 ACTCCATTTGGTCTAGTCGCC 59.793 52.381 0.00 0.00 36.34 5.54
4707 5197 0.042448 GTGCGTGTCTCGTTTGAACC 60.042 55.000 0.00 0.00 42.13 3.62
4836 5332 5.036117 ACAGCTTTTGAGTTCTGGTAGAA 57.964 39.130 0.00 0.00 0.00 2.10
4886 5382 8.353423 AGTTGTCTGTTGGCTTATGATTAAAT 57.647 30.769 0.00 0.00 0.00 1.40
4998 5542 1.518903 GGCAAGGAAAAGCTCTGCGT 61.519 55.000 0.00 0.00 0.00 5.24
5033 5577 8.155352 GCTTCGAAAAGTTATGGAATCCCATTC 61.155 40.741 0.00 0.00 41.25 2.67
5612 6166 2.684881 CCTCCATTCCACAATGTAGTGC 59.315 50.000 0.00 0.00 38.22 4.40
5615 6169 1.468127 CATTCCACAATGTAGTGCGCA 59.532 47.619 5.66 5.66 38.18 6.09
5616 6170 1.598882 TTCCACAATGTAGTGCGCAA 58.401 45.000 14.00 0.00 38.18 4.85
5658 6212 6.674066 AGTTTGACCATACATTTAACCAACG 58.326 36.000 0.00 0.00 0.00 4.10
6142 6696 7.448748 AACCATCTTCACAAAATGTAGTACC 57.551 36.000 0.00 0.00 0.00 3.34
6143 6697 6.779860 ACCATCTTCACAAAATGTAGTACCT 58.220 36.000 0.00 0.00 0.00 3.08
6144 6698 6.655003 ACCATCTTCACAAAATGTAGTACCTG 59.345 38.462 0.00 0.00 0.00 4.00
6145 6699 6.094048 CCATCTTCACAAAATGTAGTACCTGG 59.906 42.308 0.00 0.00 0.00 4.45
6146 6700 5.556915 TCTTCACAAAATGTAGTACCTGGG 58.443 41.667 0.00 0.00 0.00 4.45
6147 6701 5.308497 TCTTCACAAAATGTAGTACCTGGGA 59.692 40.000 0.00 0.00 0.00 4.37
6148 6702 5.772393 TCACAAAATGTAGTACCTGGGAT 57.228 39.130 0.00 0.00 0.00 3.85
6149 6703 6.877668 TCACAAAATGTAGTACCTGGGATA 57.122 37.500 0.00 0.00 0.00 2.59
6150 6704 6.646267 TCACAAAATGTAGTACCTGGGATAC 58.354 40.000 0.00 0.00 0.00 2.24
6501 7348 2.560542 CAGACTCTTCTAGTGTGGCAGT 59.439 50.000 0.00 0.00 43.96 4.40
6909 7771 7.446625 GCAGATATGGGAATGTACAAGAGATTT 59.553 37.037 0.00 0.00 0.00 2.17
6961 7823 6.798427 AATGCTAGGTCAACTTCTAGATCA 57.202 37.500 0.00 0.00 36.08 2.92
7109 7971 6.544928 ACAAGTTGTCAGGGATTTCTTTTT 57.455 33.333 1.64 0.00 0.00 1.94
7143 8006 4.528206 CCCCTTATCAAATAGATTTGCCCC 59.472 45.833 9.66 0.00 45.06 5.80
7182 8045 5.907197 ACTGTAGAGTGAAACAATCGTTG 57.093 39.130 0.00 0.00 41.43 4.10
7188 8051 7.592533 TGTAGAGTGAAACAATCGTTGTACTAC 59.407 37.037 4.24 0.00 44.59 2.73
7210 8073 5.324409 ACCACATCTGCCTGAAAATAAGAA 58.676 37.500 0.00 0.00 0.00 2.52
7345 8208 5.620738 TCATTTAGGCTGAGCTAGACAAT 57.379 39.130 3.72 0.00 36.64 2.71
7515 8378 2.108700 GCGTTTATTAAGCATGTGCCG 58.891 47.619 0.57 0.00 43.38 5.69
7643 8507 3.120752 CGACTTCACTGATCTTGCTTGTG 60.121 47.826 0.00 0.00 0.00 3.33
7658 8533 7.711846 TCTTGCTTGTGTGAGCTTTATTTAAA 58.288 30.769 0.00 0.00 43.11 1.52
7721 8596 9.998106 TGTAATTAGTTTTAAGAACTCTCTGCT 57.002 29.630 6.38 0.00 30.03 4.24
7775 8650 1.888512 GTTCTGCATGTCCATGTTGGT 59.111 47.619 8.91 0.00 40.80 3.67
7793 8668 6.542821 TGTTGGTCAGTCCTTTCTATCATTT 58.457 36.000 0.00 0.00 37.07 2.32
7916 8797 4.718961 AGATCTGTGCAAAACCTAACTGT 58.281 39.130 0.00 0.00 0.00 3.55
7987 8868 1.024271 TTGCACTGGAACTCAACTGC 58.976 50.000 0.00 0.00 32.52 4.40
8002 8883 4.138290 TCAACTGCCGGAATTCAAGTTAA 58.862 39.130 5.05 0.00 0.00 2.01
8003 8884 4.215399 TCAACTGCCGGAATTCAAGTTAAG 59.785 41.667 5.05 0.00 0.00 1.85
8004 8885 4.015872 ACTGCCGGAATTCAAGTTAAGA 57.984 40.909 5.05 0.00 0.00 2.10
8005 8886 4.003648 ACTGCCGGAATTCAAGTTAAGAG 58.996 43.478 5.05 0.00 0.00 2.85
8007 8888 4.394729 TGCCGGAATTCAAGTTAAGAGTT 58.605 39.130 5.05 0.00 0.00 3.01
8008 8889 4.454504 TGCCGGAATTCAAGTTAAGAGTTC 59.545 41.667 5.05 0.00 32.78 3.01
8009 8890 4.454504 GCCGGAATTCAAGTTAAGAGTTCA 59.545 41.667 5.05 0.00 34.53 3.18
8010 8891 5.123979 GCCGGAATTCAAGTTAAGAGTTCAT 59.876 40.000 5.05 0.00 34.53 2.57
8011 8892 6.675728 GCCGGAATTCAAGTTAAGAGTTCATC 60.676 42.308 5.05 0.00 34.53 2.92
8012 8893 6.595716 CCGGAATTCAAGTTAAGAGTTCATCT 59.404 38.462 7.93 0.00 41.27 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 0.537143 AGGCGTGTGGAGCAATTTGA 60.537 50.000 0.00 0.00 36.08 2.69
15 16 1.531149 CTTACAAACAGGCGTGTGGAG 59.469 52.381 13.63 8.52 36.84 3.86
22 23 5.942872 AGATGAATTTCTTACAAACAGGCG 58.057 37.500 0.00 0.00 0.00 5.52
53 59 0.681564 ACAAACCACAAACAGCCCGA 60.682 50.000 0.00 0.00 0.00 5.14
100 106 4.039730 AGAGATTACGGGGATCATGAACAG 59.960 45.833 0.00 0.00 0.00 3.16
102 108 4.608948 AGAGATTACGGGGATCATGAAC 57.391 45.455 0.00 0.00 0.00 3.18
110 116 3.705072 GAGAAGGAAAGAGATTACGGGGA 59.295 47.826 0.00 0.00 0.00 4.81
115 121 8.672815 CAAAAGATGGAGAAGGAAAGAGATTAC 58.327 37.037 0.00 0.00 0.00 1.89
124 130 4.371624 TGCTCAAAAGATGGAGAAGGAA 57.628 40.909 0.00 0.00 32.87 3.36
126 132 4.267536 TGATGCTCAAAAGATGGAGAAGG 58.732 43.478 0.00 0.00 32.87 3.46
128 134 5.503002 TCATGATGCTCAAAAGATGGAGAA 58.497 37.500 0.00 0.00 32.87 2.87
134 140 4.800023 TGGGATCATGATGCTCAAAAGAT 58.200 39.130 24.25 0.00 0.00 2.40
136 142 6.644248 TTATGGGATCATGATGCTCAAAAG 57.356 37.500 24.25 0.00 34.96 2.27
141 147 5.585445 GTGAGATTATGGGATCATGATGCTC 59.415 44.000 24.25 14.54 34.96 4.26
156 162 9.950496 GAATGTGTATCCTTATGGTGAGATTAT 57.050 33.333 0.00 0.00 34.23 1.28
183 189 6.346096 TGGATGCCTATTACTTTGTCTACAC 58.654 40.000 0.00 0.00 0.00 2.90
186 192 6.537301 CGTTTGGATGCCTATTACTTTGTCTA 59.463 38.462 0.00 0.00 0.00 2.59
194 200 3.127895 TGTTGCGTTTGGATGCCTATTAC 59.872 43.478 0.00 0.00 36.96 1.89
195 201 3.127895 GTGTTGCGTTTGGATGCCTATTA 59.872 43.478 0.00 0.00 36.96 0.98
198 204 0.878416 GTGTTGCGTTTGGATGCCTA 59.122 50.000 0.00 0.00 36.96 3.93
225 231 7.758076 TGCCATTCGAATAATACTAATACGGAG 59.242 37.037 10.97 0.00 0.00 4.63
228 234 7.062956 TGCTGCCATTCGAATAATACTAATACG 59.937 37.037 10.97 0.00 0.00 3.06
229 235 8.251750 TGCTGCCATTCGAATAATACTAATAC 57.748 34.615 10.97 0.00 0.00 1.89
315 365 2.542205 CGATGCAATTGGCTGGTACATG 60.542 50.000 7.72 0.00 45.15 3.21
318 368 0.248621 GCGATGCAATTGGCTGGTAC 60.249 55.000 7.72 0.00 45.15 3.34
321 371 0.874175 CATGCGATGCAATTGGCTGG 60.874 55.000 7.72 0.00 43.62 4.85
323 373 1.037493 ATCATGCGATGCAATTGGCT 58.963 45.000 7.72 0.00 43.62 4.75
324 374 1.136690 CATCATGCGATGCAATTGGC 58.863 50.000 7.72 2.42 43.62 4.52
336 388 2.629424 TAGCTGGGGTGGCATCATGC 62.629 60.000 0.00 0.00 44.08 4.06
343 402 0.178301 GAAGTAGTAGCTGGGGTGGC 59.822 60.000 0.00 0.00 0.00 5.01
359 418 7.697352 TTATGCTTTTTGTGTGTGAATGAAG 57.303 32.000 0.00 0.00 0.00 3.02
364 423 7.093354 TCTTGTTTATGCTTTTTGTGTGTGAA 58.907 30.769 0.00 0.00 0.00 3.18
365 424 6.625362 TCTTGTTTATGCTTTTTGTGTGTGA 58.375 32.000 0.00 0.00 0.00 3.58
369 435 7.042523 GCTTGATCTTGTTTATGCTTTTTGTGT 60.043 33.333 0.00 0.00 0.00 3.72
370 436 7.042590 TGCTTGATCTTGTTTATGCTTTTTGTG 60.043 33.333 0.00 0.00 0.00 3.33
371 437 6.985645 TGCTTGATCTTGTTTATGCTTTTTGT 59.014 30.769 0.00 0.00 0.00 2.83
372 438 7.410800 TGCTTGATCTTGTTTATGCTTTTTG 57.589 32.000 0.00 0.00 0.00 2.44
373 439 8.337532 GTTTGCTTGATCTTGTTTATGCTTTTT 58.662 29.630 0.00 0.00 0.00 1.94
416 482 4.021632 GCCAGAATCTTTGAGCCTTTCTTT 60.022 41.667 0.00 0.00 0.00 2.52
419 485 2.821969 TGCCAGAATCTTTGAGCCTTTC 59.178 45.455 0.00 0.00 0.00 2.62
421 487 2.040813 TCTGCCAGAATCTTTGAGCCTT 59.959 45.455 0.00 0.00 0.00 4.35
422 488 1.632409 TCTGCCAGAATCTTTGAGCCT 59.368 47.619 0.00 0.00 0.00 4.58
424 490 3.341823 TCTTCTGCCAGAATCTTTGAGC 58.658 45.455 7.75 0.00 33.13 4.26
425 491 4.142945 CGTTCTTCTGCCAGAATCTTTGAG 60.143 45.833 7.75 0.00 35.23 3.02
426 492 3.748048 CGTTCTTCTGCCAGAATCTTTGA 59.252 43.478 7.75 0.00 35.23 2.69
427 493 3.120060 CCGTTCTTCTGCCAGAATCTTTG 60.120 47.826 7.75 0.00 35.23 2.77
428 494 3.077359 CCGTTCTTCTGCCAGAATCTTT 58.923 45.455 7.75 0.00 35.23 2.52
429 495 2.616510 CCCGTTCTTCTGCCAGAATCTT 60.617 50.000 7.75 0.00 35.23 2.40
430 496 1.065854 CCCGTTCTTCTGCCAGAATCT 60.066 52.381 7.75 0.00 35.23 2.40
432 498 0.035056 CCCCGTTCTTCTGCCAGAAT 60.035 55.000 7.75 0.00 35.23 2.40
433 499 1.374947 CCCCGTTCTTCTGCCAGAA 59.625 57.895 7.00 7.00 32.50 3.02
435 501 2.747855 GCCCCGTTCTTCTGCCAG 60.748 66.667 0.00 0.00 0.00 4.85
436 502 1.558167 TATGCCCCGTTCTTCTGCCA 61.558 55.000 0.00 0.00 0.00 4.92
437 503 0.815615 CTATGCCCCGTTCTTCTGCC 60.816 60.000 0.00 0.00 0.00 4.85
438 504 0.815615 CCTATGCCCCGTTCTTCTGC 60.816 60.000 0.00 0.00 0.00 4.26
439 505 0.830648 TCCTATGCCCCGTTCTTCTG 59.169 55.000 0.00 0.00 0.00 3.02
441 507 2.640316 ATTCCTATGCCCCGTTCTTC 57.360 50.000 0.00 0.00 0.00 2.87
442 508 4.724279 AATATTCCTATGCCCCGTTCTT 57.276 40.909 0.00 0.00 0.00 2.52
444 510 8.570068 TTTTATAATATTCCTATGCCCCGTTC 57.430 34.615 0.00 0.00 0.00 3.95
446 512 9.623000 GTATTTTATAATATTCCTATGCCCCGT 57.377 33.333 0.00 0.00 0.00 5.28
532 733 1.811266 CGATCTCCGGCACTGTTGG 60.811 63.158 0.00 0.00 33.91 3.77
533 734 3.786101 CGATCTCCGGCACTGTTG 58.214 61.111 0.00 0.00 33.91 3.33
602 803 4.214332 AGAAGAAAAACAGCCTAGCGAAAG 59.786 41.667 0.00 0.00 0.00 2.62
819 1037 6.126568 ACGACGGATTCTCAAAAAGAAAAA 57.873 33.333 0.00 0.00 46.85 1.94
820 1038 5.277634 GGACGACGGATTCTCAAAAAGAAAA 60.278 40.000 0.00 0.00 46.85 2.29
821 1039 4.212636 GGACGACGGATTCTCAAAAAGAAA 59.787 41.667 0.00 0.00 46.85 2.52
823 1041 3.006537 AGGACGACGGATTCTCAAAAAGA 59.993 43.478 0.00 0.00 0.00 2.52
824 1042 3.326747 AGGACGACGGATTCTCAAAAAG 58.673 45.455 0.00 0.00 0.00 2.27
825 1043 3.396260 AGGACGACGGATTCTCAAAAA 57.604 42.857 0.00 0.00 0.00 1.94
826 1044 3.064207 CAAGGACGACGGATTCTCAAAA 58.936 45.455 0.00 0.00 0.00 2.44
827 1045 2.611971 CCAAGGACGACGGATTCTCAAA 60.612 50.000 0.00 0.00 0.00 2.69
828 1046 1.067142 CCAAGGACGACGGATTCTCAA 60.067 52.381 0.00 0.00 0.00 3.02
829 1047 0.530744 CCAAGGACGACGGATTCTCA 59.469 55.000 0.00 0.00 0.00 3.27
830 1048 0.806492 GCCAAGGACGACGGATTCTC 60.806 60.000 0.00 0.00 0.00 2.87
831 1049 1.218316 GCCAAGGACGACGGATTCT 59.782 57.895 0.00 0.00 0.00 2.40
832 1050 1.084370 CAGCCAAGGACGACGGATTC 61.084 60.000 0.00 0.00 0.00 2.52
833 1051 1.079127 CAGCCAAGGACGACGGATT 60.079 57.895 0.00 0.00 0.00 3.01
834 1052 1.827399 AACAGCCAAGGACGACGGAT 61.827 55.000 0.00 0.00 0.00 4.18
835 1053 2.504274 AACAGCCAAGGACGACGGA 61.504 57.895 0.00 0.00 0.00 4.69
836 1054 2.030562 AACAGCCAAGGACGACGG 59.969 61.111 0.00 0.00 0.00 4.79
837 1055 2.317609 CCAACAGCCAAGGACGACG 61.318 63.158 0.00 0.00 0.00 5.12
838 1056 0.818040 AACCAACAGCCAAGGACGAC 60.818 55.000 0.00 0.00 0.00 4.34
839 1057 0.817634 CAACCAACAGCCAAGGACGA 60.818 55.000 0.00 0.00 0.00 4.20
840 1058 1.101049 ACAACCAACAGCCAAGGACG 61.101 55.000 0.00 0.00 0.00 4.79
841 1059 1.111277 AACAACCAACAGCCAAGGAC 58.889 50.000 0.00 0.00 0.00 3.85
842 1060 1.110442 CAACAACCAACAGCCAAGGA 58.890 50.000 0.00 0.00 0.00 3.36
843 1061 0.104671 CCAACAACCAACAGCCAAGG 59.895 55.000 0.00 0.00 0.00 3.61
844 1062 0.823460 ACCAACAACCAACAGCCAAG 59.177 50.000 0.00 0.00 0.00 3.61
845 1063 1.270907 AACCAACAACCAACAGCCAA 58.729 45.000 0.00 0.00 0.00 4.52
846 1064 1.066573 CAAACCAACAACCAACAGCCA 60.067 47.619 0.00 0.00 0.00 4.75
847 1065 1.650825 CAAACCAACAACCAACAGCC 58.349 50.000 0.00 0.00 0.00 4.85
848 1066 1.006086 GCAAACCAACAACCAACAGC 58.994 50.000 0.00 0.00 0.00 4.40
849 1067 1.650825 GGCAAACCAACAACCAACAG 58.349 50.000 0.00 0.00 35.26 3.16
850 1068 0.108615 CGGCAAACCAACAACCAACA 60.109 50.000 0.00 0.00 34.57 3.33
851 1069 0.173708 TCGGCAAACCAACAACCAAC 59.826 50.000 0.00 0.00 34.57 3.77
852 1070 0.173708 GTCGGCAAACCAACAACCAA 59.826 50.000 0.00 0.00 34.57 3.67
853 1071 1.810532 GTCGGCAAACCAACAACCA 59.189 52.632 0.00 0.00 34.57 3.67
854 1072 1.298788 CGTCGGCAAACCAACAACC 60.299 57.895 0.00 0.00 34.57 3.77
855 1073 0.863957 CACGTCGGCAAACCAACAAC 60.864 55.000 0.00 0.00 34.57 3.32
856 1074 1.429825 CACGTCGGCAAACCAACAA 59.570 52.632 0.00 0.00 34.57 2.83
857 1075 3.102985 CACGTCGGCAAACCAACA 58.897 55.556 0.00 0.00 34.57 3.33
884 1102 4.351938 TGGGAGAACACGCGTCGG 62.352 66.667 9.86 0.56 0.00 4.79
889 1107 1.079750 GAGAGGTGGGAGAACACGC 60.080 63.158 0.00 0.00 42.23 5.34
955 1173 3.076296 CTAGCACAGCGCAACGAGC 62.076 63.158 11.47 8.04 46.13 5.03
963 1181 1.008875 TGAGCGAAACTAGCACAGCG 61.009 55.000 0.00 0.00 37.01 5.18
980 1201 2.283529 GCGAGGGGAGAAGTGGTGA 61.284 63.158 0.00 0.00 0.00 4.02
1147 1377 2.123640 GAGAGACGGGGAGGGGAG 60.124 72.222 0.00 0.00 0.00 4.30
1148 1378 2.617538 AGAGAGACGGGGAGGGGA 60.618 66.667 0.00 0.00 0.00 4.81
1149 1379 2.123640 GAGAGAGACGGGGAGGGG 60.124 72.222 0.00 0.00 0.00 4.79
1150 1380 1.152839 GAGAGAGAGACGGGGAGGG 60.153 68.421 0.00 0.00 0.00 4.30
1158 1388 1.409661 GGGGGAGTGAGAGAGAGAGAC 60.410 61.905 0.00 0.00 0.00 3.36
1223 1454 2.047560 AAGCACGCGGACCCTAAC 60.048 61.111 12.47 0.00 0.00 2.34
1279 1511 2.333926 GCAAGATGCACGTACAGTACA 58.666 47.619 11.37 0.00 44.26 2.90
1561 1794 3.106672 CGACCTCGCAGTGAGTATAAAC 58.893 50.000 10.16 0.00 43.64 2.01
1700 1948 8.202137 AGCTCTTAGGCTTAACAAATACGAATA 58.798 33.333 0.00 0.00 39.86 1.75
1706 1954 6.561519 AGGAGCTCTTAGGCTTAACAAATA 57.438 37.500 14.64 0.00 43.20 1.40
1707 1955 5.443230 AGGAGCTCTTAGGCTTAACAAAT 57.557 39.130 14.64 0.00 43.20 2.32
1724 1972 1.202940 ACTCACCAAAAGGGAAGGAGC 60.203 52.381 0.00 0.00 41.15 4.70
1786 2034 4.207165 TCAAACTCCCTGCTAATATTGCC 58.793 43.478 0.00 0.00 0.00 4.52
1950 2199 4.142359 ACGTGTGTGCCTTTTACATTGAAA 60.142 37.500 0.00 0.00 0.00 2.69
1963 2214 1.333619 AGATGACAAAACGTGTGTGCC 59.666 47.619 9.69 0.00 41.96 5.01
2148 2400 8.617290 AACTGAATTTAACTTTGGACGTAGAT 57.383 30.769 0.00 0.00 0.00 1.98
2443 2695 8.972458 TGGCTAATACATAAGTTTGATGCTTA 57.028 30.769 0.00 0.00 33.59 3.09
2629 2881 6.525629 CACCACCTATAAAAGATACTCCAGG 58.474 44.000 0.00 0.00 0.00 4.45
2673 2925 9.086758 GTAGGCCAAGTAAGAAGGTAGAATATA 57.913 37.037 5.01 0.00 0.00 0.86
2769 3021 1.068127 GGATAGGCCAAGCAAAGCATG 59.932 52.381 5.01 0.00 36.34 4.06
2835 3090 2.045561 TTGCTGTCGTTCCCAAAAGA 57.954 45.000 0.00 0.00 0.00 2.52
2836 3091 2.099098 AGTTTGCTGTCGTTCCCAAAAG 59.901 45.455 0.00 0.00 0.00 2.27
2846 3101 5.273170 TGAAGAATTTGAAGTTTGCTGTCG 58.727 37.500 0.00 0.00 0.00 4.35
2996 3251 4.921515 TCTGCACGAGTATTTGTAACAGAC 59.078 41.667 6.48 0.00 32.34 3.51
3035 3290 7.461182 AAAAGTGTACCATTTAGCAGCATAA 57.539 32.000 0.00 0.00 0.00 1.90
3130 3385 6.449635 TTCTCTACACTGCAAAAACAACAT 57.550 33.333 0.00 0.00 0.00 2.71
3370 3625 5.278758 GCACAAAAAGACCAACCTTAGCATA 60.279 40.000 0.00 0.00 0.00 3.14
3409 3664 3.009473 AGGCCACACTACATCAATTCAGT 59.991 43.478 5.01 0.00 0.00 3.41
3410 3665 3.614092 AGGCCACACTACATCAATTCAG 58.386 45.455 5.01 0.00 0.00 3.02
3512 3767 1.152830 ACGAAAACCCTGCCCACAT 59.847 52.632 0.00 0.00 0.00 3.21
3592 3847 0.620556 CCAGGGCAGGTGTCTGTATT 59.379 55.000 0.00 0.00 42.78 1.89
3839 4194 7.094762 TGCTCTAGACCACATAACTATGTATCG 60.095 40.741 2.10 0.00 44.57 2.92
3922 4278 7.375834 TGAATAAGTCTGCTAGAAAAAGACGA 58.624 34.615 0.00 0.00 44.07 4.20
4486 4850 6.485313 CCTTCACTACAAGGTATCAACAAACA 59.515 38.462 0.00 0.00 38.58 2.83
4522 4886 9.077885 ACATGAACATTAAGGTGATTACAAAGT 57.922 29.630 0.00 0.00 0.00 2.66
4526 4890 8.673711 GCTTACATGAACATTAAGGTGATTACA 58.326 33.333 0.00 0.00 0.00 2.41
4527 4891 8.673711 TGCTTACATGAACATTAAGGTGATTAC 58.326 33.333 0.00 0.00 0.00 1.89
4528 4892 8.800370 TGCTTACATGAACATTAAGGTGATTA 57.200 30.769 0.00 0.00 0.00 1.75
4529 4893 7.629222 GCTGCTTACATGAACATTAAGGTGATT 60.629 37.037 0.00 0.00 0.00 2.57
4531 4895 5.123820 GCTGCTTACATGAACATTAAGGTGA 59.876 40.000 0.00 0.00 0.00 4.02
4532 4896 5.106197 TGCTGCTTACATGAACATTAAGGTG 60.106 40.000 0.00 0.00 0.00 4.00
4533 4897 5.009631 TGCTGCTTACATGAACATTAAGGT 58.990 37.500 0.00 0.00 0.00 3.50
4534 4898 5.565592 TGCTGCTTACATGAACATTAAGG 57.434 39.130 0.00 0.00 0.00 2.69
4546 4912 5.887598 ACAGGAATCATAAATGCTGCTTACA 59.112 36.000 0.00 0.00 0.00 2.41
4560 4926 4.322057 AAGGGTAGCAAACAGGAATCAT 57.678 40.909 0.00 0.00 0.00 2.45
4592 4958 4.080582 TCAGGTTGGTCTGTACCCAATATG 60.081 45.833 5.51 7.53 46.16 1.78
4667 5157 5.455392 CACTCATCAGCAAGTTAAAGTTGG 58.545 41.667 0.00 0.00 0.00 3.77
4836 5332 5.242838 TCTTGTCCAACAAAACAGTGAAACT 59.757 36.000 0.00 0.00 43.20 2.66
4886 5382 3.117512 AGGAAGTCCCAAAAGCTTCTTGA 60.118 43.478 17.53 4.09 38.77 3.02
4998 5542 2.557317 ACTTTTCGAAGCCTTTGACGA 58.443 42.857 0.00 0.00 0.00 4.20
5033 5577 0.109342 ATCAGCTTTCCCCATAGCCG 59.891 55.000 0.00 0.00 38.14 5.52
5452 6006 7.383687 ACAAAATTCAGACTAAGACATACGGA 58.616 34.615 0.00 0.00 0.00 4.69
5615 6169 2.280628 CTTAAATCTCGGGAAGCGCTT 58.719 47.619 25.35 25.35 0.00 4.68
5616 6170 1.207329 ACTTAAATCTCGGGAAGCGCT 59.793 47.619 2.64 2.64 0.00 5.92
5701 6255 9.990360 TGCTTATCAGTACCAATATTTTCGATA 57.010 29.630 0.00 0.00 0.00 2.92
6157 6711 1.276622 CAGTAGATTATCCCCGGGGG 58.723 60.000 39.51 27.32 46.11 5.40
6158 6712 0.613777 GCAGTAGATTATCCCCGGGG 59.386 60.000 35.80 35.80 0.00 5.73
6159 6713 0.613777 GGCAGTAGATTATCCCCGGG 59.386 60.000 15.80 15.80 0.00 5.73
6160 6714 1.348064 TGGCAGTAGATTATCCCCGG 58.652 55.000 0.00 0.00 0.00 5.73
6161 6715 2.368875 AGTTGGCAGTAGATTATCCCCG 59.631 50.000 0.00 0.00 0.00 5.73
6162 6716 3.391296 TGAGTTGGCAGTAGATTATCCCC 59.609 47.826 0.00 0.00 0.00 4.81
6163 6717 4.689612 TGAGTTGGCAGTAGATTATCCC 57.310 45.455 0.00 0.00 0.00 3.85
6164 6718 5.428253 TGTTGAGTTGGCAGTAGATTATCC 58.572 41.667 0.00 0.00 0.00 2.59
6165 6719 6.985188 TTGTTGAGTTGGCAGTAGATTATC 57.015 37.500 0.00 0.00 0.00 1.75
6166 6720 7.944729 AATTGTTGAGTTGGCAGTAGATTAT 57.055 32.000 0.00 0.00 0.00 1.28
6501 7348 7.397476 TCTCTAGATCTAAAGGAAGAACAAGCA 59.603 37.037 3.57 0.00 0.00 3.91
6961 7823 3.903090 TGAAAGTGAAAGGCCATGGAATT 59.097 39.130 18.40 5.92 0.00 2.17
7109 7971 8.553153 TCTATTTGATAAGGGGTACATCAACAA 58.447 33.333 5.34 0.00 38.16 2.83
7182 8045 3.887621 TTCAGGCAGATGTGGTAGTAC 57.112 47.619 0.00 0.00 0.00 2.73
7188 8051 5.902613 TTCTTATTTTCAGGCAGATGTGG 57.097 39.130 0.00 0.00 0.00 4.17
7210 8073 9.690913 TCATTTGAGAAAAGATCCACTTGATAT 57.309 29.630 0.00 0.00 38.98 1.63
7345 8208 5.235616 GCAACCTACAGCGTATAATGCTTAA 59.764 40.000 0.00 0.00 38.65 1.85
7515 8378 1.315690 CACTGATGGGATCATGTGGC 58.684 55.000 0.00 0.00 38.85 5.01
7701 8576 7.469537 AGCTAGCAGAGAGTTCTTAAAACTA 57.530 36.000 18.83 0.00 0.00 2.24
7721 8596 5.817816 GCCAATTCTAGAAGTTGCTAAGCTA 59.182 40.000 18.59 0.00 0.00 3.32
7775 8650 5.415701 GGTGCAAAATGATAGAAAGGACTGA 59.584 40.000 0.00 0.00 0.00 3.41
7793 8668 8.397575 TGAACTATAAAACTATGTTGGTGCAA 57.602 30.769 0.00 0.00 0.00 4.08
7987 8868 6.595716 AGATGAACTCTTAACTTGAATTCCGG 59.404 38.462 2.27 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.