Multiple sequence alignment - TraesCS6A01G108000

Loading Multiple Alignment...

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 TraesCS6A01G108000 chr6A 100.000 2548 0 0 1 2548 76640023 76637476 0.000000e+00 4706.0
1 TraesCS6A01G108000 chr6A 100.000 1487 0 0 2791 4277 76637233 76635747 0.000000e+00 2747.0
2 TraesCS6A01G108000 chr6A 84.646 254 27 5 2199 2452 76637717 76637476 4.270000e-60 243.0
3 TraesCS6A01G108000 chr6A 84.646 254 27 5 2307 2548 76637825 76637572 4.270000e-60 243.0
4 TraesCS6A01G108000 chr6A 93.878 49 3 0 2791 2839 76637605 76637557 1.650000e-09 75.0
5 TraesCS6A01G108000 chr6D 87.886 2559 137 82 38 2548 60169306 60166873 0.000000e+00 2848.0
6 TraesCS6A01G108000 chr6D 86.127 1557 106 50 2791 4277 60166807 60165291 0.000000e+00 1578.0
7 TraesCS6A01G108000 chr6D 85.714 336 33 7 2212 2544 60167101 60166778 1.470000e-89 340.0
8 TraesCS6A01G108000 chr6D 91.925 161 10 3 2306 2463 60166923 60166763 5.570000e-54 222.0
9 TraesCS6A01G108000 chr6B 92.043 1860 77 31 708 2548 134000735 133998928 0.000000e+00 2549.0
10 TraesCS6A01G108000 chr6B 86.699 624 35 17 2994 3599 133998596 133998003 0.000000e+00 649.0
11 TraesCS6A01G108000 chr6B 86.705 346 34 5 2199 2544 133999169 133998836 1.450000e-99 374.0
12 TraesCS6A01G108000 chr6B 93.617 188 12 0 2791 2978 133998865 133998678 9.050000e-72 281.0
13 TraesCS6A01G108000 chr6B 83.699 319 23 14 3966 4277 133997658 133997362 1.520000e-69 274.0
14 TraesCS6A01G108000 chr6B 83.387 313 31 9 245 557 134001129 134000838 1.960000e-68 270.0
15 TraesCS6A01G108000 chr6B 84.091 264 30 5 2204 2467 133999068 133998817 1.190000e-60 244.0
16 TraesCS6A01G108000 chr6B 87.923 207 14 7 3720 3921 133997856 133997656 2.570000e-57 233.0
17 TraesCS6A01G108000 chr6B 90.476 147 14 0 2402 2548 133999170 133999024 1.210000e-45 195.0
18 TraesCS6A01G108000 chr6B 80.952 210 10 12 1 204 134002009 134001824 5.770000e-29 139.0
19 TraesCS6A01G108000 chr6B 93.878 49 3 0 2791 2839 133999057 133999009 1.650000e-09 75.0
20 TraesCS6A01G108000 chr7A 99.079 543 5 0 2791 3333 678952334 678951792 0.000000e+00 976.0
21 TraesCS6A01G108000 chr7A 83.930 1033 147 15 1118 2146 606331017 606330000 0.000000e+00 970.0
22 TraesCS6A01G108000 chr7A 91.975 162 10 2 2386 2544 678952466 678952305 1.550000e-54 224.0
23 TraesCS6A01G108000 chr7D 84.047 1028 146 14 1123 2146 525774481 525773468 0.000000e+00 974.0
24 TraesCS6A01G108000 chr7D 75.600 250 45 13 1151 1397 525989156 525988920 4.520000e-20 110.0
25 TraesCS6A01G108000 chr7B 83.965 1029 145 16 1123 2146 562409355 562408342 0.000000e+00 968.0
26 TraesCS6A01G108000 chr5A 99.468 376 2 0 2791 3166 48475561 48475186 0.000000e+00 684.0
27 TraesCS6A01G108000 chr5A 99.202 376 3 0 2791 3166 534075683 534076058 0.000000e+00 678.0
28 TraesCS6A01G108000 chr5A 92.222 180 11 2 2368 2544 48475711 48475532 7.100000e-63 252.0
29 TraesCS6A01G108000 chr5A 92.222 180 11 2 2368 2544 534075533 534075712 7.100000e-63 252.0
30 TraesCS6A01G108000 chr1D 77.710 978 176 35 1144 2103 119010761 119009808 1.040000e-155 560.0
31 TraesCS6A01G108000 chr1B 77.607 978 177 33 1144 2103 181218236 181217283 4.830000e-154 555.0
32 TraesCS6A01G108000 chr1A 77.075 1012 182 39 1144 2132 131521549 131520565 4.870000e-149 538.0
33 TraesCS6A01G108000 chr3A 79.937 638 102 22 1147 1779 384319976 384320592 3.030000e-121 446.0
34 TraesCS6A01G108000 chr3B 77.665 197 16 13 3405 3590 176424270 176424091 1.270000e-15 95.3


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 TraesCS6A01G108000 chr6A 76635747 76640023 4276 True 1602.800000 4706 92.634000 1 4277 5 chr6A.!!$R1 4276
1 TraesCS6A01G108000 chr6D 60165291 60169306 4015 True 1247.000000 2848 87.913000 38 4277 4 chr6D.!!$R1 4239
2 TraesCS6A01G108000 chr6B 133997362 134002009 4647 True 480.272727 2549 87.588182 1 4277 11 chr6B.!!$R1 4276
3 TraesCS6A01G108000 chr7A 606330000 606331017 1017 True 970.000000 970 83.930000 1118 2146 1 chr7A.!!$R1 1028
4 TraesCS6A01G108000 chr7A 678951792 678952466 674 True 600.000000 976 95.527000 2386 3333 2 chr7A.!!$R2 947
5 TraesCS6A01G108000 chr7D 525773468 525774481 1013 True 974.000000 974 84.047000 1123 2146 1 chr7D.!!$R1 1023
6 TraesCS6A01G108000 chr7B 562408342 562409355 1013 True 968.000000 968 83.965000 1123 2146 1 chr7B.!!$R1 1023
7 TraesCS6A01G108000 chr5A 48475186 48475711 525 True 468.000000 684 95.845000 2368 3166 2 chr5A.!!$R1 798
8 TraesCS6A01G108000 chr5A 534075533 534076058 525 False 465.000000 678 95.712000 2368 3166 2 chr5A.!!$F1 798
9 TraesCS6A01G108000 chr1D 119009808 119010761 953 True 560.000000 560 77.710000 1144 2103 1 chr1D.!!$R1 959
10 TraesCS6A01G108000 chr1B 181217283 181218236 953 True 555.000000 555 77.607000 1144 2103 1 chr1B.!!$R1 959
11 TraesCS6A01G108000 chr1A 131520565 131521549 984 True 538.000000 538 77.075000 1144 2132 1 chr1A.!!$R1 988
12 TraesCS6A01G108000 chr3A 384319976 384320592 616 False 446.000000 446 79.937000 1147 1779 1 chr3A.!!$F1 632

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
676 1373 0.108396 TGCCAGCAGTAGCAGTGAAA 59.892 50.0 0.0 0.0 45.49 2.69 F
784 1490 0.110956 CGTCGCAGCATCATACATGC 60.111 55.0 0.0 0.0 44.85 4.06 F
1786 2529 0.248094 GATCGTGCTCATCGACGACA 60.248 55.0 0.0 0.0 46.60 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2342 3094 1.153429 GAGTGGTATGACGGGGTGC 60.153 63.158 0.0 0.00 0.00 5.01 R
2460 3308 4.129148 GTGGTGGATCCCTGGGGC 62.129 72.222 14.0 5.39 34.77 5.80 R
3704 4705 0.179000 CCCAACATTCTCCCTCTCGG 59.821 60.000 0.0 0.00 0.00 4.63 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
31 32 0.753262 GGGAGGAGATCTGCGCTTTA 59.247 55.000 16.91 0.00 34.34 1.85
33 34 2.478831 GGAGGAGATCTGCGCTTTAAG 58.521 52.381 16.91 0.00 0.00 1.85
34 35 2.101582 GGAGGAGATCTGCGCTTTAAGA 59.898 50.000 16.91 2.65 0.00 2.10
35 36 3.380142 GAGGAGATCTGCGCTTTAAGAG 58.620 50.000 9.73 0.00 0.00 2.85
36 37 2.763448 AGGAGATCTGCGCTTTAAGAGT 59.237 45.455 9.73 0.00 0.00 3.24
76 82 1.483415 GGTGGCCAGCAATCAATCAAT 59.517 47.619 29.70 0.00 0.00 2.57
77 83 2.482490 GGTGGCCAGCAATCAATCAATC 60.482 50.000 29.70 0.36 0.00 2.67
78 84 2.166870 GTGGCCAGCAATCAATCAATCA 59.833 45.455 5.11 0.00 0.00 2.57
79 85 2.832733 TGGCCAGCAATCAATCAATCAA 59.167 40.909 0.00 0.00 0.00 2.57
80 86 3.261137 TGGCCAGCAATCAATCAATCAAA 59.739 39.130 0.00 0.00 0.00 2.69
81 87 4.080807 TGGCCAGCAATCAATCAATCAAAT 60.081 37.500 0.00 0.00 0.00 2.32
82 88 4.879545 GGCCAGCAATCAATCAATCAAATT 59.120 37.500 0.00 0.00 0.00 1.82
83 89 5.355910 GGCCAGCAATCAATCAATCAAATTT 59.644 36.000 0.00 0.00 0.00 1.82
84 90 6.127842 GGCCAGCAATCAATCAATCAAATTTT 60.128 34.615 0.00 0.00 0.00 1.82
85 91 6.745450 GCCAGCAATCAATCAATCAAATTTTG 59.255 34.615 2.59 2.59 0.00 2.44
86 92 7.247728 CCAGCAATCAATCAATCAAATTTTGG 58.752 34.615 9.18 0.00 0.00 3.28
87 93 7.094549 CCAGCAATCAATCAATCAAATTTTGGT 60.095 33.333 9.18 0.00 0.00 3.67
88 94 8.937884 CAGCAATCAATCAATCAAATTTTGGTA 58.062 29.630 9.18 0.00 0.00 3.25
89 95 9.675464 AGCAATCAATCAATCAAATTTTGGTAT 57.325 25.926 9.18 0.00 0.00 2.73
121 128 0.807667 GGTGTCGCCAGAGCATGTAG 60.808 60.000 0.00 0.00 39.83 2.74
122 129 0.108615 GTGTCGCCAGAGCATGTAGT 60.109 55.000 0.00 0.00 39.83 2.73
123 130 1.134367 GTGTCGCCAGAGCATGTAGTA 59.866 52.381 0.00 0.00 39.83 1.82
124 131 2.031870 TGTCGCCAGAGCATGTAGTAT 58.968 47.619 0.00 0.00 39.83 2.12
125 132 3.004419 GTGTCGCCAGAGCATGTAGTATA 59.996 47.826 0.00 0.00 39.83 1.47
126 133 3.826729 TGTCGCCAGAGCATGTAGTATAT 59.173 43.478 0.00 0.00 39.83 0.86
127 134 4.169508 GTCGCCAGAGCATGTAGTATATG 58.830 47.826 2.65 2.65 39.83 1.78
128 135 4.079253 TCGCCAGAGCATGTAGTATATGA 58.921 43.478 10.80 0.00 39.83 2.15
129 136 4.156739 TCGCCAGAGCATGTAGTATATGAG 59.843 45.833 10.80 0.00 39.83 2.90
130 137 4.156739 CGCCAGAGCATGTAGTATATGAGA 59.843 45.833 10.80 0.00 39.83 3.27
131 138 5.649557 GCCAGAGCATGTAGTATATGAGAG 58.350 45.833 10.80 0.00 39.53 3.20
175 185 3.722289 CGTGCATGATTGTTGATCGATTG 59.278 43.478 0.00 0.00 37.60 2.67
176 186 3.484649 GTGCATGATTGTTGATCGATTGC 59.515 43.478 0.00 2.44 37.60 3.56
177 187 3.379057 TGCATGATTGTTGATCGATTGCT 59.621 39.130 12.56 0.00 38.01 3.91
178 188 3.729217 GCATGATTGTTGATCGATTGCTG 59.271 43.478 0.00 0.00 37.60 4.41
187 197 1.677576 GATCGATTGCTGGCCATTTGA 59.322 47.619 5.51 1.46 0.00 2.69
194 204 1.338294 TGCTGGCCATTTGATTTGCTG 60.338 47.619 5.51 0.00 0.00 4.41
197 207 3.259064 CTGGCCATTTGATTTGCTGAAG 58.741 45.455 5.51 0.00 0.00 3.02
205 215 2.422597 TGATTTGCTGAAGTGGTACCG 58.577 47.619 7.57 0.00 0.00 4.02
243 907 4.619227 CCGGCCGTGGAGTGTTGT 62.619 66.667 26.12 0.00 0.00 3.32
249 913 0.320421 CCGTGGAGTGTTGTAGGTGG 60.320 60.000 0.00 0.00 0.00 4.61
257 921 1.873591 GTGTTGTAGGTGGAAGCACTG 59.126 52.381 0.00 0.00 36.26 3.66
265 929 1.880027 GGTGGAAGCACTGTAGGTTTG 59.120 52.381 0.00 0.00 0.00 2.93
272 936 1.266989 GCACTGTAGGTTTGTTGAGCC 59.733 52.381 0.00 0.00 0.00 4.70
278 945 4.942852 TGTAGGTTTGTTGAGCCAAATTG 58.057 39.130 0.00 0.00 36.75 2.32
313 981 1.070601 TGTGGTGTGATCACTGGTGAG 59.929 52.381 25.55 0.00 43.61 3.51
317 985 1.070758 GTGTGATCACTGGTGAGTGGT 59.929 52.381 25.55 0.00 46.90 4.16
318 986 1.070601 TGTGATCACTGGTGAGTGGTG 59.929 52.381 25.55 0.00 44.07 4.17
319 987 1.344438 GTGATCACTGGTGAGTGGTGA 59.656 52.381 18.83 0.00 44.07 4.02
320 988 1.344438 TGATCACTGGTGAGTGGTGAC 59.656 52.381 9.33 0.00 44.07 3.67
321 989 1.620819 GATCACTGGTGAGTGGTGACT 59.379 52.381 9.33 0.00 44.07 3.41
322 990 2.611473 GATCACTGGTGAGTGGTGACTG 60.611 54.545 9.33 0.00 44.07 3.51
323 991 0.250038 CACTGGTGAGTGGTGACTGG 60.250 60.000 0.00 0.00 45.26 4.00
334 1002 5.193099 AGTGGTGACTGGGCTAAATTAAT 57.807 39.130 0.00 0.00 0.00 1.40
335 1003 4.949856 AGTGGTGACTGGGCTAAATTAATG 59.050 41.667 0.00 0.00 0.00 1.90
336 1004 4.097892 GTGGTGACTGGGCTAAATTAATGG 59.902 45.833 0.00 0.00 0.00 3.16
337 1005 3.068165 GGTGACTGGGCTAAATTAATGGC 59.932 47.826 0.00 0.00 0.00 4.40
373 1041 3.394313 GTTCGAAACGCCGGAATTTAT 57.606 42.857 5.05 0.00 0.00 1.40
374 1042 3.750512 GTTCGAAACGCCGGAATTTATT 58.249 40.909 5.05 0.00 0.00 1.40
375 1043 3.661758 TCGAAACGCCGGAATTTATTC 57.338 42.857 5.05 0.00 36.08 1.75
376 1044 2.029486 TCGAAACGCCGGAATTTATTCG 59.971 45.455 5.05 11.92 39.43 3.34
416 1088 4.651867 CCAACCTGGCTCATGGAG 57.348 61.111 0.00 0.00 34.82 3.86
417 1089 1.993653 CCAACCTGGCTCATGGAGA 59.006 57.895 0.00 0.00 34.82 3.71
436 1108 0.519961 AACTCGCGTGTAAAATGCCC 59.480 50.000 14.90 0.00 37.53 5.36
464 1136 1.515736 CGTAGGCCCGAGACGTTTC 60.516 63.158 0.00 0.00 0.00 2.78
484 1160 6.414987 CGTTTCCTGTGAAGTTCTTCAAAATC 59.585 38.462 15.44 5.62 32.04 2.17
487 1163 7.403312 TCCTGTGAAGTTCTTCAAAATCAAA 57.597 32.000 15.44 1.11 32.04 2.69
488 1164 7.835822 TCCTGTGAAGTTCTTCAAAATCAAAA 58.164 30.769 15.44 0.84 32.04 2.44
490 1166 8.545420 CCTGTGAAGTTCTTCAAAATCAAAATG 58.455 33.333 15.44 0.00 32.04 2.32
493 1169 9.906111 GTGAAGTTCTTCAAAATCAAAATGAAC 57.094 29.630 15.44 0.00 34.55 3.18
494 1170 9.650539 TGAAGTTCTTCAAAATCAAAATGAACA 57.349 25.926 12.08 0.00 36.15 3.18
495 1171 9.906111 GAAGTTCTTCAAAATCAAAATGAACAC 57.094 29.630 7.57 0.00 36.15 3.32
521 1197 2.101575 TCGTCCGGCGAGAAATCG 59.898 61.111 9.30 4.58 45.68 3.34
533 1209 3.130633 CGAGAAATCGGTGGCATTATGA 58.869 45.455 0.00 0.00 0.00 2.15
539 1215 4.853924 ATCGGTGGCATTATGAAATTCC 57.146 40.909 0.00 0.00 0.00 3.01
562 1238 1.611977 CTTGGCCATCGCATGAATCAT 59.388 47.619 6.09 0.00 36.38 2.45
566 1242 2.606308 GGCCATCGCATGAATCATTCAC 60.606 50.000 0.98 0.00 43.48 3.18
569 1245 2.715749 TCGCATGAATCATTCACCCT 57.284 45.000 0.98 0.00 43.48 4.34
599 1275 1.280746 CGCGAATGGTCATGGCATC 59.719 57.895 0.00 0.00 0.00 3.91
600 1276 1.656441 GCGAATGGTCATGGCATCC 59.344 57.895 0.00 0.00 0.00 3.51
603 1279 1.152694 AATGGTCATGGCATCCCCG 60.153 57.895 0.00 0.00 35.87 5.73
604 1280 1.936767 AATGGTCATGGCATCCCCGT 61.937 55.000 0.00 0.00 35.87 5.28
605 1281 2.203209 GGTCATGGCATCCCCGTC 60.203 66.667 0.00 0.00 35.87 4.79
606 1282 2.588877 GTCATGGCATCCCCGTCG 60.589 66.667 0.00 0.00 35.87 5.12
608 1284 2.588877 CATGGCATCCCCGTCGTC 60.589 66.667 0.00 0.00 35.87 4.20
609 1285 3.080765 ATGGCATCCCCGTCGTCA 61.081 61.111 0.00 0.00 35.87 4.35
621 1318 1.024046 CGTCGTCATCCCCATGCAAA 61.024 55.000 0.00 0.00 0.00 3.68
627 1324 3.674138 CGTCATCCCCATGCAAAAGAAAG 60.674 47.826 0.00 0.00 0.00 2.62
629 1326 4.021192 GTCATCCCCATGCAAAAGAAAGAA 60.021 41.667 0.00 0.00 0.00 2.52
630 1327 4.592351 TCATCCCCATGCAAAAGAAAGAAA 59.408 37.500 0.00 0.00 0.00 2.52
659 1356 9.816354 AGAAGAAGAGATAAAATAAGAGAGTGC 57.184 33.333 0.00 0.00 0.00 4.40
660 1357 8.956533 AAGAAGAGATAAAATAAGAGAGTGCC 57.043 34.615 0.00 0.00 0.00 5.01
661 1358 8.083828 AGAAGAGATAAAATAAGAGAGTGCCA 57.916 34.615 0.00 0.00 0.00 4.92
662 1359 8.203485 AGAAGAGATAAAATAAGAGAGTGCCAG 58.797 37.037 0.00 0.00 0.00 4.85
663 1360 6.287525 AGAGATAAAATAAGAGAGTGCCAGC 58.712 40.000 0.00 0.00 0.00 4.85
664 1361 5.994250 AGATAAAATAAGAGAGTGCCAGCA 58.006 37.500 0.00 0.00 0.00 4.41
665 1362 6.054295 AGATAAAATAAGAGAGTGCCAGCAG 58.946 40.000 0.00 0.00 0.00 4.24
666 1363 3.710209 AAATAAGAGAGTGCCAGCAGT 57.290 42.857 0.00 0.00 0.00 4.40
667 1364 4.826274 AAATAAGAGAGTGCCAGCAGTA 57.174 40.909 0.00 0.00 0.00 2.74
668 1365 4.399004 AATAAGAGAGTGCCAGCAGTAG 57.601 45.455 0.00 0.00 0.00 2.57
669 1366 0.248843 AAGAGAGTGCCAGCAGTAGC 59.751 55.000 0.00 0.00 42.56 3.58
670 1367 0.902048 AGAGAGTGCCAGCAGTAGCA 60.902 55.000 0.00 0.00 45.49 3.49
671 1368 0.459934 GAGAGTGCCAGCAGTAGCAG 60.460 60.000 0.00 0.00 45.49 4.24
672 1369 1.190833 AGAGTGCCAGCAGTAGCAGT 61.191 55.000 0.00 0.00 45.18 4.40
673 1370 1.004080 AGTGCCAGCAGTAGCAGTG 60.004 57.895 0.00 0.00 45.49 3.66
674 1371 1.004560 GTGCCAGCAGTAGCAGTGA 60.005 57.895 0.00 0.00 45.49 3.41
675 1372 0.603707 GTGCCAGCAGTAGCAGTGAA 60.604 55.000 0.00 0.00 45.49 3.18
676 1373 0.108396 TGCCAGCAGTAGCAGTGAAA 59.892 50.000 0.00 0.00 45.49 2.69
783 1489 1.454653 CTCGTCGCAGCATCATACATG 59.545 52.381 0.00 0.00 0.00 3.21
784 1490 0.110956 CGTCGCAGCATCATACATGC 60.111 55.000 0.00 0.00 44.85 4.06
917 1660 1.305381 CGACCTCCCTCACCTCCTT 60.305 63.158 0.00 0.00 0.00 3.36
928 1671 2.042435 CCTCCTTCCTCCCTCGCT 60.042 66.667 0.00 0.00 0.00 4.93
936 1679 2.277072 CTCCCTCGCTCTCCTCCA 59.723 66.667 0.00 0.00 0.00 3.86
937 1680 2.043852 TCCCTCGCTCTCCTCCAC 60.044 66.667 0.00 0.00 0.00 4.02
938 1681 3.151022 CCCTCGCTCTCCTCCACC 61.151 72.222 0.00 0.00 0.00 4.61
939 1682 2.043450 CCTCGCTCTCCTCCACCT 60.043 66.667 0.00 0.00 0.00 4.00
940 1683 1.684049 CCTCGCTCTCCTCCACCTT 60.684 63.158 0.00 0.00 0.00 3.50
941 1684 1.515020 CTCGCTCTCCTCCACCTTG 59.485 63.158 0.00 0.00 0.00 3.61
942 1685 2.125350 CGCTCTCCTCCACCTTGC 60.125 66.667 0.00 0.00 0.00 4.01
943 1686 2.654079 CGCTCTCCTCCACCTTGCT 61.654 63.158 0.00 0.00 0.00 3.91
960 1703 1.807886 CTCTTGCTTGCATCCAGCC 59.192 57.895 6.42 0.00 44.83 4.85
975 1718 2.092753 TCCAGCCACATTCTCCATTCTC 60.093 50.000 0.00 0.00 0.00 2.87
978 1721 1.752084 GCCACATTCTCCATTCTCCCC 60.752 57.143 0.00 0.00 0.00 4.81
997 1740 0.720027 CAGATCACAGCTCAACGCAG 59.280 55.000 0.00 0.00 42.61 5.18
1044 1787 4.869440 CTCGCGCTCCTGCTCCTG 62.869 72.222 5.56 0.00 36.97 3.86
1572 2315 1.258445 ACCTCGACCTCCGCTTCAAT 61.258 55.000 0.00 0.00 38.37 2.57
1585 2328 1.677217 GCTTCAATGACTTCGAGGGCT 60.677 52.381 0.67 0.00 0.00 5.19
1786 2529 0.248094 GATCGTGCTCATCGACGACA 60.248 55.000 0.00 0.00 46.60 4.35
1842 2585 2.561569 CTGAAGAAGGTGACGGTGTTT 58.438 47.619 0.00 0.00 0.00 2.83
2342 3094 4.803426 GCCACCGTCGAGCTCCAG 62.803 72.222 8.47 0.00 0.00 3.86
2460 3308 4.824166 CCGTCGTACCACTCGCCG 62.824 72.222 0.00 0.00 0.00 6.46
2484 3332 2.588877 GGATCCACCACGCCATCG 60.589 66.667 6.95 0.00 42.43 3.84
3349 4281 2.337749 AATACCTCACCTCGCGCTCG 62.338 60.000 5.56 0.00 0.00 5.03
3411 4345 9.838975 GGATTTCTTTTTCATCTCTTCTTCTTC 57.161 33.333 0.00 0.00 0.00 2.87
3418 4352 8.614469 TTTTCATCTCTTCTTCTTCCTTCTTC 57.386 34.615 0.00 0.00 0.00 2.87
3419 4353 7.552050 TTCATCTCTTCTTCTTCCTTCTTCT 57.448 36.000 0.00 0.00 0.00 2.85
3420 4354 6.934056 TCATCTCTTCTTCTTCCTTCTTCTG 58.066 40.000 0.00 0.00 0.00 3.02
3438 4372 6.831769 TCTTCTGAATTTGTTGCGAGTATTC 58.168 36.000 0.00 0.00 0.00 1.75
3458 4392 3.394719 TCGATCCACGATCTACAGAGAG 58.605 50.000 0.00 0.00 46.45 3.20
3459 4393 3.069729 TCGATCCACGATCTACAGAGAGA 59.930 47.826 0.00 0.00 46.45 3.10
3460 4394 3.431912 CGATCCACGATCTACAGAGAGAG 59.568 52.174 0.00 0.00 45.77 3.20
3461 4395 4.637276 GATCCACGATCTACAGAGAGAGA 58.363 47.826 0.00 0.00 36.27 3.10
3462 4396 4.066646 TCCACGATCTACAGAGAGAGAG 57.933 50.000 0.00 0.00 34.35 3.20
3463 4397 3.707102 TCCACGATCTACAGAGAGAGAGA 59.293 47.826 0.00 0.00 34.35 3.10
3551 4495 2.289382 TGTGTAATCTTCGAGCCTGCAA 60.289 45.455 0.00 0.00 0.00 4.08
3552 4496 2.939103 GTGTAATCTTCGAGCCTGCAAT 59.061 45.455 0.00 0.00 0.00 3.56
3555 4499 4.570772 TGTAATCTTCGAGCCTGCAATAAC 59.429 41.667 0.00 0.00 0.00 1.89
3557 4501 2.621338 TCTTCGAGCCTGCAATAACAG 58.379 47.619 0.00 0.00 37.42 3.16
3574 4518 1.421268 ACAGAATGAGTGGCACCTTCA 59.579 47.619 15.27 13.07 39.69 3.02
3599 4543 6.266323 TCTACTGCAGTAAAACATCTCGATC 58.734 40.000 25.95 0.00 0.00 3.69
3656 4652 3.921677 TCTGAACACGGGTTGATTACTC 58.078 45.455 8.36 0.00 37.36 2.59
3674 4675 1.370609 TCGTAGAGGAGACGCAGAAG 58.629 55.000 0.00 0.00 40.14 2.85
3694 4695 3.041701 CAGCGGCCAAAAAGAGCA 58.958 55.556 2.24 0.00 0.00 4.26
3704 4705 3.059393 GCCAAAAAGAGCAGCAATGAAAC 60.059 43.478 0.00 0.00 0.00 2.78
3710 4711 1.396301 GAGCAGCAATGAAACCGAGAG 59.604 52.381 0.00 0.00 0.00 3.20
3732 4733 3.181472 GGGAGAATGTTGGGCATCAATTC 60.181 47.826 0.00 0.00 36.67 2.17
3739 4740 1.382522 TGGGCATCAATTCGCTCTTC 58.617 50.000 0.00 0.00 0.00 2.87
3746 4747 2.881074 TCAATTCGCTCTTCCTTCTCG 58.119 47.619 0.00 0.00 0.00 4.04
3748 4749 3.442625 TCAATTCGCTCTTCCTTCTCGTA 59.557 43.478 0.00 0.00 0.00 3.43
3749 4750 4.082408 TCAATTCGCTCTTCCTTCTCGTAA 60.082 41.667 0.00 0.00 0.00 3.18
3862 4863 3.339093 GGTTGGTCCCTCCCCCAG 61.339 72.222 0.00 0.00 34.77 4.45
3863 4864 2.204090 GTTGGTCCCTCCCCCAGA 60.204 66.667 0.00 0.00 34.77 3.86
3864 4865 1.850755 GTTGGTCCCTCCCCCAGAA 60.851 63.158 0.00 0.00 34.77 3.02
3865 4866 1.850755 TTGGTCCCTCCCCCAGAAC 60.851 63.158 0.00 0.00 34.77 3.01
3866 4867 2.125225 GGTCCCTCCCCCAGAACT 59.875 66.667 0.00 0.00 0.00 3.01
3867 4868 1.996187 GGTCCCTCCCCCAGAACTC 60.996 68.421 0.00 0.00 0.00 3.01
3869 4870 1.081092 TCCCTCCCCCAGAACTCAG 59.919 63.158 0.00 0.00 0.00 3.35
3870 4871 1.081092 CCCTCCCCCAGAACTCAGA 59.919 63.158 0.00 0.00 0.00 3.27
3871 4872 0.547712 CCCTCCCCCAGAACTCAGAA 60.548 60.000 0.00 0.00 0.00 3.02
3951 4956 3.691118 ACAAATCAGACATCCATTCCGTG 59.309 43.478 0.00 0.00 0.00 4.94
3954 4959 1.815421 AGACATCCATTCCGTGCGC 60.815 57.895 0.00 0.00 0.00 6.09
3998 5024 2.032894 CCTTGCTGTTGTACTTGTCGTG 60.033 50.000 0.00 0.00 0.00 4.35
3999 5025 1.577468 TGCTGTTGTACTTGTCGTGG 58.423 50.000 0.00 0.00 0.00 4.94
4000 5026 0.865769 GCTGTTGTACTTGTCGTGGG 59.134 55.000 0.00 0.00 0.00 4.61
4001 5027 1.508632 CTGTTGTACTTGTCGTGGGG 58.491 55.000 0.00 0.00 0.00 4.96
4002 5028 0.107081 TGTTGTACTTGTCGTGGGGG 59.893 55.000 0.00 0.00 0.00 5.40
4003 5029 0.107268 GTTGTACTTGTCGTGGGGGT 59.893 55.000 0.00 0.00 0.00 4.95
4004 5030 0.107081 TTGTACTTGTCGTGGGGGTG 59.893 55.000 0.00 0.00 0.00 4.61
4160 5199 4.796495 GCGGGGTAGGGGCAAGTG 62.796 72.222 0.00 0.00 0.00 3.16
4180 5219 4.760047 GTCGCTGTCGGTGCCCAT 62.760 66.667 0.00 0.00 36.13 4.00
4209 5248 4.232905 TGGAGACAGACAAGGGGG 57.767 61.111 0.00 0.00 35.01 5.40
4210 5249 1.551875 TGGAGACAGACAAGGGGGA 59.448 57.895 0.00 0.00 35.01 4.81
4211 5250 0.836400 TGGAGACAGACAAGGGGGAC 60.836 60.000 0.00 0.00 35.01 4.46
4212 5251 0.545548 GGAGACAGACAAGGGGGACT 60.546 60.000 0.00 0.00 0.00 3.85
4213 5252 0.610687 GAGACAGACAAGGGGGACTG 59.389 60.000 0.00 0.00 36.58 3.51
4214 5253 0.191064 AGACAGACAAGGGGGACTGA 59.809 55.000 0.00 0.00 34.88 3.41
4216 5255 1.298014 CAGACAAGGGGGACTGAGC 59.702 63.158 0.00 0.00 32.90 4.26
4218 5257 2.203788 ACAAGGGGGACTGAGCGA 60.204 61.111 0.00 0.00 0.00 4.93
4219 5258 2.232298 GACAAGGGGGACTGAGCGAG 62.232 65.000 0.00 0.00 0.00 5.03
4220 5259 3.394836 AAGGGGGACTGAGCGAGC 61.395 66.667 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 0.753262 TAAAGCGCAGATCTCCTCCC 59.247 55.000 11.47 0.00 0.00 4.30
13 14 2.101582 TCTTAAAGCGCAGATCTCCTCC 59.898 50.000 11.47 0.00 0.00 4.30
14 15 3.181480 ACTCTTAAAGCGCAGATCTCCTC 60.181 47.826 11.47 0.00 0.00 3.71
15 16 2.763448 ACTCTTAAAGCGCAGATCTCCT 59.237 45.455 11.47 0.00 0.00 3.69
31 32 3.021269 CAACACATGCATGCAACTCTT 57.979 42.857 26.68 11.10 0.00 2.85
76 82 7.571025 GGTCCTAGTCCTATACCAAAATTTGA 58.429 38.462 7.37 0.00 0.00 2.69
77 83 6.482308 CGGTCCTAGTCCTATACCAAAATTTG 59.518 42.308 0.00 0.00 0.00 2.32
78 84 6.408891 CCGGTCCTAGTCCTATACCAAAATTT 60.409 42.308 0.00 0.00 0.00 1.82
79 85 5.071384 CCGGTCCTAGTCCTATACCAAAATT 59.929 44.000 0.00 0.00 0.00 1.82
80 86 4.591924 CCGGTCCTAGTCCTATACCAAAAT 59.408 45.833 0.00 0.00 0.00 1.82
81 87 3.962718 CCGGTCCTAGTCCTATACCAAAA 59.037 47.826 0.00 0.00 0.00 2.44
82 88 3.052642 ACCGGTCCTAGTCCTATACCAAA 60.053 47.826 0.00 0.00 0.00 3.28
83 89 2.515429 ACCGGTCCTAGTCCTATACCAA 59.485 50.000 0.00 0.00 0.00 3.67
84 90 2.138542 ACCGGTCCTAGTCCTATACCA 58.861 52.381 0.00 0.00 0.00 3.25
85 91 2.158549 ACACCGGTCCTAGTCCTATACC 60.159 54.545 2.59 0.00 0.00 2.73
86 92 3.145286 GACACCGGTCCTAGTCCTATAC 58.855 54.545 2.59 0.00 38.12 1.47
87 93 2.224378 CGACACCGGTCCTAGTCCTATA 60.224 54.545 2.59 0.00 41.13 1.31
88 94 1.476471 CGACACCGGTCCTAGTCCTAT 60.476 57.143 2.59 0.00 41.13 2.57
89 95 0.107508 CGACACCGGTCCTAGTCCTA 60.108 60.000 2.59 0.00 41.13 2.94
90 96 1.378250 CGACACCGGTCCTAGTCCT 60.378 63.158 2.59 0.00 41.13 3.85
121 128 3.995705 ACGTACGCTCTCCTCTCATATAC 59.004 47.826 16.72 0.00 0.00 1.47
122 129 3.995048 CACGTACGCTCTCCTCTCATATA 59.005 47.826 16.72 0.00 0.00 0.86
123 130 2.809119 CACGTACGCTCTCCTCTCATAT 59.191 50.000 16.72 0.00 0.00 1.78
124 131 2.210961 CACGTACGCTCTCCTCTCATA 58.789 52.381 16.72 0.00 0.00 2.15
125 132 1.018148 CACGTACGCTCTCCTCTCAT 58.982 55.000 16.72 0.00 0.00 2.90
126 133 1.645704 GCACGTACGCTCTCCTCTCA 61.646 60.000 16.72 0.00 0.00 3.27
127 134 1.062845 GCACGTACGCTCTCCTCTC 59.937 63.158 16.72 0.00 0.00 3.20
128 135 0.961358 AAGCACGTACGCTCTCCTCT 60.961 55.000 16.72 0.00 42.89 3.69
129 136 0.523757 GAAGCACGTACGCTCTCCTC 60.524 60.000 16.72 4.43 42.89 3.71
130 137 1.507174 GAAGCACGTACGCTCTCCT 59.493 57.895 16.72 1.50 42.89 3.69
131 138 1.868251 CGAAGCACGTACGCTCTCC 60.868 63.158 16.72 0.00 42.89 3.71
153 163 3.597377 ATCGATCAACAATCATGCACG 57.403 42.857 0.00 0.00 33.65 5.34
175 185 1.066716 TCAGCAAATCAAATGGCCAGC 60.067 47.619 13.05 6.38 0.00 4.85
176 186 3.259064 CTTCAGCAAATCAAATGGCCAG 58.741 45.455 13.05 0.00 0.00 4.85
177 187 2.633967 ACTTCAGCAAATCAAATGGCCA 59.366 40.909 8.56 8.56 0.00 5.36
178 188 2.997986 CACTTCAGCAAATCAAATGGCC 59.002 45.455 0.00 0.00 0.00 5.36
187 197 1.165270 GCGGTACCACTTCAGCAAAT 58.835 50.000 13.54 0.00 0.00 2.32
194 204 2.813908 CAGCGGCGGTACCACTTC 60.814 66.667 12.74 0.00 39.03 3.01
205 215 4.789075 CCAACATGCAGCAGCGGC 62.789 66.667 11.05 11.05 46.23 6.53
209 219 2.260434 GCCACCAACATGCAGCAG 59.740 61.111 0.00 0.00 0.00 4.24
210 220 3.304721 GGCCACCAACATGCAGCA 61.305 61.111 0.00 0.00 0.00 4.41
243 907 2.320681 ACCTACAGTGCTTCCACCTA 57.679 50.000 0.00 0.00 43.09 3.08
249 913 3.304057 GCTCAACAAACCTACAGTGCTTC 60.304 47.826 0.00 0.00 0.00 3.86
257 921 4.202212 ACCAATTTGGCTCAACAAACCTAC 60.202 41.667 15.49 0.00 42.67 3.18
265 929 6.401796 CGTTACTAGTACCAATTTGGCTCAAC 60.402 42.308 15.49 8.66 42.67 3.18
272 936 6.247903 CACATGCGTTACTAGTACCAATTTG 58.752 40.000 0.91 0.00 0.00 2.32
278 945 3.184541 CACCACATGCGTTACTAGTACC 58.815 50.000 0.91 0.00 0.00 3.34
313 981 4.097892 CCATTAATTTAGCCCAGTCACCAC 59.902 45.833 0.00 0.00 0.00 4.16
316 984 3.954258 AGCCATTAATTTAGCCCAGTCAC 59.046 43.478 0.00 0.00 0.00 3.67
317 985 3.953612 CAGCCATTAATTTAGCCCAGTCA 59.046 43.478 0.00 0.00 0.00 3.41
318 986 3.319122 CCAGCCATTAATTTAGCCCAGTC 59.681 47.826 0.00 0.00 0.00 3.51
319 987 3.299503 CCAGCCATTAATTTAGCCCAGT 58.700 45.455 0.00 0.00 0.00 4.00
320 988 2.036346 GCCAGCCATTAATTTAGCCCAG 59.964 50.000 0.00 0.00 0.00 4.45
321 989 2.038659 GCCAGCCATTAATTTAGCCCA 58.961 47.619 0.00 0.00 0.00 5.36
322 990 2.319844 AGCCAGCCATTAATTTAGCCC 58.680 47.619 0.00 0.00 0.00 5.19
323 991 4.556699 CGTTAGCCAGCCATTAATTTAGCC 60.557 45.833 0.00 0.00 0.00 3.93
334 1002 2.349755 GGGTTCGTTAGCCAGCCA 59.650 61.111 4.12 0.00 44.15 4.75
335 1003 2.437895 GGGGTTCGTTAGCCAGCC 60.438 66.667 9.93 0.00 46.65 4.85
336 1004 2.818274 CGGGGTTCGTTAGCCAGC 60.818 66.667 9.93 0.00 46.65 4.85
356 1024 2.222863 ACGAATAAATTCCGGCGTTTCG 60.223 45.455 6.01 15.28 40.04 3.46
364 1032 3.371591 TCCCAACGAACGAATAAATTCCG 59.628 43.478 0.14 0.00 33.28 4.30
409 1081 1.170442 TACACGCGAGTTCTCCATGA 58.830 50.000 15.93 0.00 46.40 3.07
411 1083 2.736144 TTTACACGCGAGTTCTCCAT 57.264 45.000 15.93 0.00 46.40 3.41
413 1085 2.474032 GCATTTTACACGCGAGTTCTCC 60.474 50.000 15.93 0.00 46.40 3.71
415 1087 1.463444 GGCATTTTACACGCGAGTTCT 59.537 47.619 15.93 0.00 46.40 3.01
416 1088 1.465187 GGGCATTTTACACGCGAGTTC 60.465 52.381 15.93 0.00 46.40 3.01
417 1089 0.519961 GGGCATTTTACACGCGAGTT 59.480 50.000 15.93 0.00 46.40 3.01
484 1160 4.151070 CGATTCGACCTGTGTTCATTTTG 58.849 43.478 0.00 0.00 0.00 2.44
487 1163 2.993899 GACGATTCGACCTGTGTTCATT 59.006 45.455 13.95 0.00 0.00 2.57
488 1164 2.607187 GACGATTCGACCTGTGTTCAT 58.393 47.619 13.95 0.00 0.00 2.57
490 1166 1.347320 GGACGATTCGACCTGTGTTC 58.653 55.000 18.28 1.01 38.50 3.18
493 1169 1.516386 CCGGACGATTCGACCTGTG 60.516 63.158 21.81 9.29 39.29 3.66
494 1170 2.882876 CCGGACGATTCGACCTGT 59.117 61.111 21.81 0.00 39.29 4.00
495 1171 2.582498 GCCGGACGATTCGACCTG 60.582 66.667 21.81 17.41 39.29 4.00
515 1191 5.691754 GGAATTTCATAATGCCACCGATTTC 59.308 40.000 0.00 0.00 39.08 2.17
533 1209 1.066929 GCGATGGCCAAGTTGGAATTT 60.067 47.619 26.52 6.44 40.96 1.82
539 1215 0.527113 TTCATGCGATGGCCAAGTTG 59.473 50.000 10.96 9.61 38.85 3.16
562 1238 1.533033 TCTGCGTCTCCAGGGTGAA 60.533 57.895 0.00 0.00 33.64 3.18
566 1242 4.803426 GCGTCTGCGTCTCCAGGG 62.803 72.222 0.00 0.00 40.81 4.45
599 1275 3.161450 ATGGGGATGACGACGGGG 61.161 66.667 0.00 0.00 0.00 5.73
600 1276 2.108976 CATGGGGATGACGACGGG 59.891 66.667 0.00 0.00 0.00 5.28
603 1279 1.133025 CTTTTGCATGGGGATGACGAC 59.867 52.381 0.00 0.00 0.00 4.34
604 1280 1.004161 TCTTTTGCATGGGGATGACGA 59.996 47.619 0.00 0.00 0.00 4.20
605 1281 1.462616 TCTTTTGCATGGGGATGACG 58.537 50.000 0.00 0.00 0.00 4.35
606 1282 3.511146 TCTTTCTTTTGCATGGGGATGAC 59.489 43.478 0.00 0.00 0.00 3.06
608 1284 4.540359 TTCTTTCTTTTGCATGGGGATG 57.460 40.909 0.00 0.00 0.00 3.51
609 1285 5.565455 TTTTCTTTCTTTTGCATGGGGAT 57.435 34.783 0.00 0.00 0.00 3.85
635 1332 8.543774 TGGCACTCTCTTATTTTATCTCTTCTT 58.456 33.333 0.00 0.00 0.00 2.52
638 1335 6.765512 GCTGGCACTCTCTTATTTTATCTCTT 59.234 38.462 0.00 0.00 0.00 2.85
639 1336 6.126940 TGCTGGCACTCTCTTATTTTATCTCT 60.127 38.462 0.00 0.00 0.00 3.10
640 1337 6.051717 TGCTGGCACTCTCTTATTTTATCTC 58.948 40.000 0.00 0.00 0.00 2.75
641 1338 5.994250 TGCTGGCACTCTCTTATTTTATCT 58.006 37.500 0.00 0.00 0.00 1.98
642 1339 5.819901 ACTGCTGGCACTCTCTTATTTTATC 59.180 40.000 0.00 0.00 0.00 1.75
644 1341 5.165961 ACTGCTGGCACTCTCTTATTTTA 57.834 39.130 0.00 0.00 0.00 1.52
645 1342 4.026356 ACTGCTGGCACTCTCTTATTTT 57.974 40.909 0.00 0.00 0.00 1.82
649 1346 1.478510 GCTACTGCTGGCACTCTCTTA 59.521 52.381 0.00 0.00 36.03 2.10
650 1347 0.248843 GCTACTGCTGGCACTCTCTT 59.751 55.000 0.00 0.00 36.03 2.85
651 1348 0.902048 TGCTACTGCTGGCACTCTCT 60.902 55.000 0.00 0.00 40.48 3.10
652 1349 0.459934 CTGCTACTGCTGGCACTCTC 60.460 60.000 0.00 0.00 40.48 3.20
653 1350 1.190833 ACTGCTACTGCTGGCACTCT 61.191 55.000 0.00 0.00 41.57 3.24
654 1351 1.018226 CACTGCTACTGCTGGCACTC 61.018 60.000 0.00 0.00 41.57 3.51
655 1352 1.004080 CACTGCTACTGCTGGCACT 60.004 57.895 0.00 0.00 41.57 4.40
656 1353 0.603707 TTCACTGCTACTGCTGGCAC 60.604 55.000 0.00 0.00 41.57 5.01
657 1354 0.108396 TTTCACTGCTACTGCTGGCA 59.892 50.000 0.00 0.00 41.57 4.92
658 1355 0.519077 GTTTCACTGCTACTGCTGGC 59.481 55.000 0.00 0.00 41.57 4.85
659 1356 0.792640 CGTTTCACTGCTACTGCTGG 59.207 55.000 0.00 0.00 41.57 4.85
660 1357 0.164647 GCGTTTCACTGCTACTGCTG 59.835 55.000 0.00 0.00 42.70 4.41
661 1358 1.284982 CGCGTTTCACTGCTACTGCT 61.285 55.000 0.00 0.00 40.48 4.24
662 1359 1.130613 CGCGTTTCACTGCTACTGC 59.869 57.895 0.00 0.00 40.20 4.40
663 1360 0.666274 TCCGCGTTTCACTGCTACTG 60.666 55.000 4.92 0.00 0.00 2.74
664 1361 0.388649 CTCCGCGTTTCACTGCTACT 60.389 55.000 4.92 0.00 0.00 2.57
665 1362 1.956620 GCTCCGCGTTTCACTGCTAC 61.957 60.000 4.92 0.00 0.00 3.58
666 1363 1.736645 GCTCCGCGTTTCACTGCTA 60.737 57.895 4.92 0.00 0.00 3.49
667 1364 3.044305 GCTCCGCGTTTCACTGCT 61.044 61.111 4.92 0.00 0.00 4.24
668 1365 4.090057 GGCTCCGCGTTTCACTGC 62.090 66.667 4.92 0.00 0.00 4.40
669 1366 3.423154 GGGCTCCGCGTTTCACTG 61.423 66.667 4.92 0.00 0.00 3.66
670 1367 4.699522 GGGGCTCCGCGTTTCACT 62.700 66.667 4.92 0.00 0.00 3.41
693 1390 4.394712 AGGAGGGCCGCGTTTCAG 62.395 66.667 4.92 0.00 39.96 3.02
762 1468 0.249031 TGTATGATGCTGCGACGAGG 60.249 55.000 0.00 0.00 0.00 4.63
763 1469 1.454653 CATGTATGATGCTGCGACGAG 59.545 52.381 0.00 0.00 0.00 4.18
764 1470 1.490621 CATGTATGATGCTGCGACGA 58.509 50.000 0.00 0.00 0.00 4.20
765 1471 0.110956 GCATGTATGATGCTGCGACG 60.111 55.000 0.00 0.00 41.52 5.12
766 1472 3.742290 GCATGTATGATGCTGCGAC 57.258 52.632 0.00 0.00 41.52 5.19
791 1504 2.136878 ATGGGGGAGCTGCTACGAG 61.137 63.158 5.66 0.00 0.00 4.18
804 1517 3.420482 GGGAGGGGTCACATGGGG 61.420 72.222 0.00 0.00 0.00 4.96
889 1611 2.107141 GGAGGTCGGGATCAAGCG 59.893 66.667 0.00 0.00 0.00 4.68
890 1612 2.034048 GAGGGAGGTCGGGATCAAGC 62.034 65.000 0.00 0.00 0.00 4.01
891 1613 0.687757 TGAGGGAGGTCGGGATCAAG 60.688 60.000 0.00 0.00 0.00 3.02
917 1660 2.598467 GAGGAGAGCGAGGGAGGA 59.402 66.667 0.00 0.00 0.00 3.71
928 1671 0.979665 CAAGAGCAAGGTGGAGGAGA 59.020 55.000 0.00 0.00 0.00 3.71
936 1679 0.886563 GATGCAAGCAAGAGCAAGGT 59.113 50.000 0.00 0.00 44.88 3.50
937 1680 0.172803 GGATGCAAGCAAGAGCAAGG 59.827 55.000 0.00 0.00 44.88 3.61
938 1681 0.885879 TGGATGCAAGCAAGAGCAAG 59.114 50.000 0.00 0.00 44.88 4.01
939 1682 0.885879 CTGGATGCAAGCAAGAGCAA 59.114 50.000 0.00 0.00 44.88 3.91
940 1683 1.592400 GCTGGATGCAAGCAAGAGCA 61.592 55.000 14.61 0.00 45.92 4.26
941 1684 1.139095 GCTGGATGCAAGCAAGAGC 59.861 57.895 3.97 3.33 40.52 4.09
942 1685 0.963856 TGGCTGGATGCAAGCAAGAG 60.964 55.000 10.85 0.00 45.15 2.85
943 1686 1.075305 TGGCTGGATGCAAGCAAGA 59.925 52.632 10.85 0.00 45.15 3.02
960 1703 2.507058 TCTGGGGAGAATGGAGAATGTG 59.493 50.000 0.00 0.00 0.00 3.21
975 1718 0.742281 CGTTGAGCTGTGATCTGGGG 60.742 60.000 0.00 0.00 0.00 4.96
1572 2315 1.330655 GGATGGAGCCCTCGAAGTCA 61.331 60.000 0.00 0.00 0.00 3.41
1824 2567 2.557317 TCAAACACCGTCACCTTCTTC 58.443 47.619 0.00 0.00 0.00 2.87
1842 2585 2.741985 CGGTTGCCGCTGACATCA 60.742 61.111 0.00 0.00 41.17 3.07
2334 3086 4.459089 GACGGGGTGCTGGAGCTC 62.459 72.222 4.71 4.71 42.66 4.09
2342 3094 1.153429 GAGTGGTATGACGGGGTGC 60.153 63.158 0.00 0.00 0.00 5.01
2460 3308 4.129148 GTGGTGGATCCCTGGGGC 62.129 72.222 14.00 5.39 34.77 5.80
2463 3311 4.489771 GGCGTGGTGGATCCCTGG 62.490 72.222 9.90 0.00 34.77 4.45
3378 4310 6.210185 AGAGATGAAAAAGAAATCCAAGGTGG 59.790 38.462 0.00 0.00 39.43 4.61
3380 4312 7.727634 AGAAGAGATGAAAAAGAAATCCAAGGT 59.272 33.333 0.00 0.00 0.00 3.50
3381 4313 8.120140 AGAAGAGATGAAAAAGAAATCCAAGG 57.880 34.615 0.00 0.00 0.00 3.61
3383 4315 9.359653 AGAAGAAGAGATGAAAAAGAAATCCAA 57.640 29.630 0.00 0.00 0.00 3.53
3385 4317 9.838975 GAAGAAGAAGAGATGAAAAAGAAATCC 57.161 33.333 0.00 0.00 0.00 3.01
3387 4319 9.585369 AGGAAGAAGAAGAGATGAAAAAGAAAT 57.415 29.630 0.00 0.00 0.00 2.17
3391 4325 8.620116 AGAAGGAAGAAGAAGAGATGAAAAAG 57.380 34.615 0.00 0.00 0.00 2.27
3411 4345 4.023707 ACTCGCAACAAATTCAGAAGAAGG 60.024 41.667 0.00 0.00 37.14 3.46
3418 4352 5.203358 TCGAATACTCGCAACAAATTCAG 57.797 39.130 0.00 0.00 45.04 3.02
3419 4353 5.220586 GGATCGAATACTCGCAACAAATTCA 60.221 40.000 0.00 0.00 45.04 2.57
3420 4354 5.198274 GGATCGAATACTCGCAACAAATTC 58.802 41.667 0.00 0.00 45.04 2.17
3438 4372 3.394719 TCTCTCTGTAGATCGTGGATCG 58.605 50.000 0.34 0.00 43.17 3.69
3458 4392 6.765512 CCTCTTTTAACTCCATCCAATCTCTC 59.234 42.308 0.00 0.00 0.00 3.20
3459 4393 6.657875 CCTCTTTTAACTCCATCCAATCTCT 58.342 40.000 0.00 0.00 0.00 3.10
3460 4394 5.298026 GCCTCTTTTAACTCCATCCAATCTC 59.702 44.000 0.00 0.00 0.00 2.75
3461 4395 5.196695 GCCTCTTTTAACTCCATCCAATCT 58.803 41.667 0.00 0.00 0.00 2.40
3462 4396 4.339530 GGCCTCTTTTAACTCCATCCAATC 59.660 45.833 0.00 0.00 0.00 2.67
3463 4397 4.281657 GGCCTCTTTTAACTCCATCCAAT 58.718 43.478 0.00 0.00 0.00 3.16
3541 4485 2.938451 TCATTCTGTTATTGCAGGCTCG 59.062 45.455 0.00 0.00 37.12 5.03
3551 4495 4.263462 TGAAGGTGCCACTCATTCTGTTAT 60.263 41.667 0.00 0.00 0.00 1.89
3552 4496 3.072330 TGAAGGTGCCACTCATTCTGTTA 59.928 43.478 0.00 0.00 0.00 2.41
3555 4499 2.189594 TGAAGGTGCCACTCATTCTG 57.810 50.000 0.00 0.00 0.00 3.02
3557 4501 2.996631 AGATGAAGGTGCCACTCATTC 58.003 47.619 1.63 2.06 0.00 2.67
3574 4518 6.208988 TCGAGATGTTTTACTGCAGTAGAT 57.791 37.500 24.79 15.71 0.00 1.98
3599 4543 9.322773 AGTACACTTTTGATCATCATGTATCAG 57.677 33.333 0.00 0.00 33.83 2.90
3656 4652 0.248296 GCTTCTGCGTCTCCTCTACG 60.248 60.000 0.00 0.00 43.12 3.51
3674 4675 4.341502 TCTTTTTGGCCGCTGCGC 62.342 61.111 18.00 12.10 38.85 6.09
3694 4695 0.984230 TCCCTCTCGGTTTCATTGCT 59.016 50.000 0.00 0.00 0.00 3.91
3704 4705 0.179000 CCCAACATTCTCCCTCTCGG 59.821 60.000 0.00 0.00 0.00 4.63
3710 4711 1.851304 TTGATGCCCAACATTCTCCC 58.149 50.000 0.00 0.00 39.84 4.30
3732 4733 4.174009 TGAAATTACGAGAAGGAAGAGCG 58.826 43.478 0.00 0.00 0.00 5.03
3739 4740 6.887376 TTTCGATCTGAAATTACGAGAAGG 57.113 37.500 8.13 0.00 41.59 3.46
3859 4860 2.245159 TGTGCAGTTCTGAGTTCTGG 57.755 50.000 3.84 0.00 0.00 3.86
3861 4862 3.758755 TCATGTGCAGTTCTGAGTTCT 57.241 42.857 3.84 0.00 0.00 3.01
3862 4863 4.818534 TTTCATGTGCAGTTCTGAGTTC 57.181 40.909 3.84 0.00 0.00 3.01
3863 4864 4.037208 CCTTTTCATGTGCAGTTCTGAGTT 59.963 41.667 3.84 0.00 0.00 3.01
3864 4865 3.567164 CCTTTTCATGTGCAGTTCTGAGT 59.433 43.478 3.84 0.00 0.00 3.41
3865 4866 3.611057 GCCTTTTCATGTGCAGTTCTGAG 60.611 47.826 3.84 0.00 0.00 3.35
3866 4867 2.294233 GCCTTTTCATGTGCAGTTCTGA 59.706 45.455 3.84 0.00 0.00 3.27
3867 4868 2.608752 GGCCTTTTCATGTGCAGTTCTG 60.609 50.000 0.00 0.00 0.00 3.02
3869 4870 1.340889 TGGCCTTTTCATGTGCAGTTC 59.659 47.619 3.32 0.00 0.00 3.01
3870 4871 1.412079 TGGCCTTTTCATGTGCAGTT 58.588 45.000 3.32 0.00 0.00 3.16
3871 4872 1.274167 CATGGCCTTTTCATGTGCAGT 59.726 47.619 3.32 0.00 37.72 4.40
3930 4931 3.488047 GCACGGAATGGATGTCTGATTTG 60.488 47.826 0.00 0.00 0.00 2.32
3973 4978 1.001378 CAAGTACAACAGCAAGGTGGC 60.001 52.381 4.16 0.00 40.07 5.01
3982 4987 1.508632 CCCCACGACAAGTACAACAG 58.491 55.000 0.00 0.00 0.00 3.16
4054 5086 3.249189 GCCGGGCCCTCCATGATA 61.249 66.667 22.43 0.00 34.36 2.15
4089 5121 1.518572 CCGTCTACCCATGCGTGAC 60.519 63.158 7.72 0.00 0.00 3.67
4143 5182 4.796495 CACTTGCCCCTACCCCGC 62.796 72.222 0.00 0.00 0.00 6.13
4209 5248 4.167359 TCGCTCGCTCGCTCAGTC 62.167 66.667 0.00 0.00 0.00 3.51
4210 5249 4.172772 CTCGCTCGCTCGCTCAGT 62.173 66.667 0.00 0.00 0.00 3.41
4237 5280 0.674895 ACTTCCTCGCCATTCACAGC 60.675 55.000 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.