Multiple sequence alignment - TraesCS3A01G336700

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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 TraesCS3A01G336700 chr3A 100.000 4928 0 0 1 4928 583708477 583703550 0.000000e+00 9101.0
1 TraesCS3A01G336700 chr3A 95.960 99 3 1 4482 4579 52453100 52453002 5.110000e-35 159.0
2 TraesCS3A01G336700 chr3A 97.222 36 1 0 4856 4891 16661544 16661579 1.480000e-05 62.1
3 TraesCS3A01G336700 chr3B 92.608 2435 153 12 1172 3602 580038217 580035806 0.000000e+00 3474.0
4 TraesCS3A01G336700 chr3B 88.320 488 45 12 3600 4077 580035762 580035277 4.280000e-160 575.0
5 TraesCS3A01G336700 chr3B 85.592 583 43 12 275 818 580039378 580038798 1.540000e-159 573.0
6 TraesCS3A01G336700 chr3B 91.184 397 24 4 776 1172 580038807 580038422 3.380000e-146 529.0
7 TraesCS3A01G336700 chr3B 88.087 277 29 2 3 279 580039687 580039415 4.760000e-85 326.0
8 TraesCS3A01G336700 chr3B 87.597 129 10 6 4448 4572 580034358 580034232 1.430000e-30 145.0
9 TraesCS3A01G336700 chr5A 89.415 2069 174 21 1186 3243 270179202 270181236 0.000000e+00 2566.0
10 TraesCS3A01G336700 chr5A 86.667 450 56 4 3622 4068 270181617 270182065 3.430000e-136 496.0
11 TraesCS3A01G336700 chr5A 88.959 317 26 5 3273 3585 270181233 270181544 2.780000e-102 383.0
12 TraesCS3A01G336700 chr5A 90.960 177 15 1 996 1172 270178699 270178874 2.290000e-58 237.0
13 TraesCS3A01G336700 chr5A 95.050 101 4 1 4472 4571 561124658 561124558 1.840000e-34 158.0
14 TraesCS3A01G336700 chr5D 89.275 2070 165 27 1186 3240 209310913 209312940 0.000000e+00 2540.0
15 TraesCS3A01G336700 chr5D 87.414 437 53 2 3622 4057 209313510 209313945 7.360000e-138 501.0
16 TraesCS3A01G336700 chr5D 77.778 711 78 46 492 1160 209310067 209310739 1.010000e-96 364.0
17 TraesCS3A01G336700 chr5D 88.562 306 24 10 3289 3585 209312954 209313257 1.300000e-95 361.0
18 TraesCS3A01G336700 chr5B 88.995 2090 175 25 1172 3243 222368808 222370860 0.000000e+00 2534.0
19 TraesCS3A01G336700 chr5B 87.305 449 54 3 3622 4068 222371421 222371868 1.220000e-140 510.0
20 TraesCS3A01G336700 chr5B 88.328 317 29 6 3273 3585 222370857 222371169 1.680000e-99 374.0
21 TraesCS3A01G336700 chr5B 92.655 177 12 1 996 1172 222368324 222368499 2.280000e-63 254.0
22 TraesCS3A01G336700 chr3D 95.749 1082 41 4 1172 2251 442503949 442502871 0.000000e+00 1738.0
23 TraesCS3A01G336700 chr3D 91.523 755 56 4 2518 3271 442502577 442501830 0.000000e+00 1033.0
24 TraesCS3A01G336700 chr3D 85.987 892 83 26 275 1141 442505052 442504178 0.000000e+00 917.0
25 TraesCS3A01G336700 chr3D 92.443 397 29 1 3601 3997 442500391 442499996 2.570000e-157 566.0
26 TraesCS3A01G336700 chr3D 86.912 489 32 14 4443 4928 442499503 442499044 2.030000e-143 520.0
27 TraesCS3A01G336700 chr3D 93.429 350 20 2 3255 3602 442500784 442500436 2.630000e-142 516.0
28 TraesCS3A01G336700 chr3D 90.086 232 20 3 2248 2478 442502802 442502573 1.040000e-76 298.0
29 TraesCS3A01G336700 chr3D 96.907 97 2 1 4485 4581 515749867 515749962 1.420000e-35 161.0
30 TraesCS3A01G336700 chr3D 95.050 101 4 1 4473 4572 40745373 40745273 1.840000e-34 158.0
31 TraesCS3A01G336700 chr3D 100.000 40 0 0 2901 2940 467570101 467570140 1.900000e-09 75.0
32 TraesCS3A01G336700 chr6B 98.913 92 1 0 4488 4579 189563994 189564085 1.100000e-36 165.0
33 TraesCS3A01G336700 chr6A 98.925 93 0 1 4487 4579 125885165 125885256 1.100000e-36 165.0
34 TraesCS3A01G336700 chr7D 96.907 97 2 1 4485 4580 604327833 604327929 1.420000e-35 161.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G336700 chr3A 583703550 583708477 4927 True 9101.000000 9101 100.000000 1 4928 1 chr3A.!!$R2 4927
1 TraesCS3A01G336700 chr3B 580034232 580039687 5455 True 937.000000 3474 88.898000 3 4572 6 chr3B.!!$R1 4569
2 TraesCS3A01G336700 chr5A 270178699 270182065 3366 False 920.500000 2566 89.000250 996 4068 4 chr5A.!!$F1 3072
3 TraesCS3A01G336700 chr5D 209310067 209313945 3878 False 941.500000 2540 85.757250 492 4057 4 chr5D.!!$F1 3565
4 TraesCS3A01G336700 chr5B 222368324 222371868 3544 False 918.000000 2534 89.320750 996 4068 4 chr5B.!!$F1 3072
5 TraesCS3A01G336700 chr3D 442499044 442505052 6008 True 798.285714 1738 90.875571 275 4928 7 chr3D.!!$R2 4653

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
247 248 0.179062 CCTCCAATGCCGAGAAGAGG 60.179 60.000 0.00 0.0 35.34 3.69 F
479 552 0.322546 ATCAACAAGCCCTCGAACCC 60.323 55.000 0.00 0.0 0.00 4.11 F
632 722 0.684535 TTGCTCCAGATCCACGAACA 59.315 50.000 0.00 0.0 0.00 3.18 F
1114 1262 1.090728 GCAGTGCCTCCTTAAGCTTC 58.909 55.000 0.00 0.0 0.00 3.86 F
2544 3137 2.031870 TGAATGCTTAGCGCTCTCCTA 58.968 47.619 16.34 0.0 40.11 2.94 F
3213 3822 0.250124 TGCATCGTCCGGTGAGTTTT 60.250 50.000 3.76 0.0 0.00 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1402 1869 2.818130 TTGTTGAAAAGGCCTGATGC 57.182 45.000 5.69 0.0 40.16 3.91 R
2452 2999 0.240945 CACAGACGCCATGGGTTTTC 59.759 55.000 15.13 0.0 0.00 2.29 R
2572 3165 4.021719 CCAAGTGCAGAAAAGATCCAATGT 60.022 41.667 0.00 0.0 0.00 2.71 R
2883 3491 1.135944 GCGAACTACAAGAGCAAAGGC 60.136 52.381 0.00 0.0 41.61 4.35 R
3612 5297 0.179161 TTTGTGTTTGCCGTCGTTGG 60.179 50.000 0.00 0.0 0.00 3.77 R
4479 6978 0.249489 GCACGACCACTTCTGTGAGT 60.249 55.000 0.00 0.0 46.55 3.41 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
20 21 1.377333 GACCCCAGTGGCAACTAGC 60.377 63.158 2.61 0.00 44.65 3.42
119 120 1.787847 CGGCAGACGTTGATGTTCC 59.212 57.895 0.00 0.00 37.93 3.62
120 121 1.787847 GGCAGACGTTGATGTTCCG 59.212 57.895 0.00 0.00 0.00 4.30
137 138 4.717313 GGGGGACGTGGCAGTTCC 62.717 72.222 0.00 5.85 39.10 3.62
138 139 3.637273 GGGGACGTGGCAGTTCCT 61.637 66.667 12.81 0.00 39.76 3.36
143 144 0.249911 GACGTGGCAGTTCCTGAAGT 60.250 55.000 0.00 0.00 32.44 3.01
148 149 0.606673 GGCAGTTCCTGAAGTCCCAC 60.607 60.000 0.00 0.00 32.44 4.61
155 156 1.301716 CTGAAGTCCCACCACACCG 60.302 63.158 0.00 0.00 0.00 4.94
186 187 1.381327 CCTTGCCCTCCTCCTCGTA 60.381 63.158 0.00 0.00 0.00 3.43
187 188 1.677637 CCTTGCCCTCCTCCTCGTAC 61.678 65.000 0.00 0.00 0.00 3.67
188 189 1.677637 CTTGCCCTCCTCCTCGTACC 61.678 65.000 0.00 0.00 0.00 3.34
189 190 2.043248 GCCCTCCTCCTCGTACCA 60.043 66.667 0.00 0.00 0.00 3.25
242 243 4.161295 CCGCCTCCAATGCCGAGA 62.161 66.667 0.00 0.00 0.00 4.04
243 244 2.125147 CGCCTCCAATGCCGAGAA 60.125 61.111 0.00 0.00 0.00 2.87
247 248 0.179062 CCTCCAATGCCGAGAAGAGG 60.179 60.000 0.00 0.00 35.34 3.69
361 407 7.612668 GGTTTTGTTTGCTTAAACCCTTTTA 57.387 32.000 0.00 0.00 43.09 1.52
367 413 7.612677 TGTTTGCTTAAACCCTTTTAAACAGA 58.387 30.769 0.00 0.00 35.62 3.41
377 424 5.066893 ACCCTTTTAAACAGAGGTCGAAAAC 59.933 40.000 4.17 0.00 0.00 2.43
400 447 4.129737 ACCGTCCGATGCACTCCG 62.130 66.667 0.00 0.00 0.00 4.63
449 496 2.250939 CGCCCAAACGCACTTCTCA 61.251 57.895 0.00 0.00 0.00 3.27
450 497 1.576421 GCCCAAACGCACTTCTCAG 59.424 57.895 0.00 0.00 0.00 3.35
451 498 1.856265 GCCCAAACGCACTTCTCAGG 61.856 60.000 0.00 0.00 0.00 3.86
455 528 1.166531 AAACGCACTTCTCAGGTGGC 61.167 55.000 0.00 0.00 35.47 5.01
477 550 1.087501 GGATCAACAAGCCCTCGAAC 58.912 55.000 0.00 0.00 0.00 3.95
479 552 0.322546 ATCAACAAGCCCTCGAACCC 60.323 55.000 0.00 0.00 0.00 4.11
524 597 3.839432 GTCGCCTTCCTCCTCCCG 61.839 72.222 0.00 0.00 0.00 5.14
532 605 2.756283 CCTCCTCCCGCTTCGACT 60.756 66.667 0.00 0.00 0.00 4.18
564 646 1.715785 CCTCCTCTCCCATCTCCTTC 58.284 60.000 0.00 0.00 0.00 3.46
632 722 0.684535 TTGCTCCAGATCCACGAACA 59.315 50.000 0.00 0.00 0.00 3.18
662 752 2.616765 GGTTCCTCCTCTTCTTTCAGCC 60.617 54.545 0.00 0.00 0.00 4.85
672 762 1.428448 TCTTTCAGCCAATCGTCACG 58.572 50.000 0.00 0.00 0.00 4.35
723 813 3.143168 CCTCCTACCCCCTAGATCTTTCT 59.857 52.174 0.00 0.00 35.90 2.52
737 827 5.249420 AGATCTTTCTGGCAAACCTTCTAC 58.751 41.667 0.00 0.00 36.63 2.59
779 870 9.768662 AATGAACATTTGATAATTGCCCTTATC 57.231 29.630 7.92 7.92 38.20 1.75
793 884 2.615493 CCCTTATCTGACACGCCACTTT 60.615 50.000 0.00 0.00 0.00 2.66
850 969 4.695217 TCAGAATTTGTTTCCATACGCC 57.305 40.909 0.00 0.00 34.67 5.68
877 1014 8.646004 AGTGATTTAGCTAGAGATTAAGCATGA 58.354 33.333 0.00 0.00 41.32 3.07
895 1032 7.444629 AGCATGATGTATCAATATGGACAAC 57.555 36.000 0.00 0.00 40.69 3.32
926 1063 3.780804 TTTAAAGGTCACTAGCCTGCA 57.219 42.857 0.00 0.00 36.30 4.41
983 1131 8.514330 AATCGGCTTATGTTATTTCAGGTTTA 57.486 30.769 0.00 0.00 0.00 2.01
993 1141 7.419204 TGTTATTTCAGGTTTAAGTGTTTCGG 58.581 34.615 0.00 0.00 0.00 4.30
994 1142 7.282675 TGTTATTTCAGGTTTAAGTGTTTCGGA 59.717 33.333 0.00 0.00 0.00 4.55
1114 1262 1.090728 GCAGTGCCTCCTTAAGCTTC 58.909 55.000 0.00 0.00 0.00 3.86
1145 1293 6.882458 GGTCTTTACCTAATGAACTACGTG 57.118 41.667 0.00 0.00 43.08 4.49
1149 1297 8.219105 GTCTTTACCTAATGAACTACGTGTTTG 58.781 37.037 0.00 0.00 39.30 2.93
1216 1683 8.537049 TTGAGAAAATGCCATTTGTTATTCTG 57.463 30.769 2.91 0.00 31.77 3.02
1246 1713 3.215975 TGTCATGACACATGCATATGGG 58.784 45.455 24.56 0.00 43.55 4.00
1275 1742 6.238293 CGTTCTGGAGTACGATATGTTACTGA 60.238 42.308 0.00 0.00 40.51 3.41
1330 1797 4.275196 CCATTCCTGATGCAGAATACACTG 59.725 45.833 0.00 0.00 40.43 3.66
1402 1869 4.458397 AGAAGATATCAGTTGTGCATGGG 58.542 43.478 5.32 0.00 0.00 4.00
1658 2125 4.966168 TGGTTCCTAATGCAGTGGATACTA 59.034 41.667 0.00 0.88 34.74 1.82
1698 2165 2.076863 GAACCGCTTAAGCTGTGATGT 58.923 47.619 22.97 9.18 38.49 3.06
1744 2211 9.780186 AGTAGATTAGTATATTGAAAAGGTGCC 57.220 33.333 0.00 0.00 0.00 5.01
1779 2246 4.019411 TGAAGTCATTCCAGAAGTATGCCA 60.019 41.667 0.00 0.00 34.28 4.92
1781 2248 5.121380 AGTCATTCCAGAAGTATGCCATT 57.879 39.130 0.00 0.00 0.00 3.16
1807 2274 5.782677 TTCCAAAGGTGGGTTATAGCTAA 57.217 39.130 0.00 0.00 46.01 3.09
1808 2275 5.782677 TCCAAAGGTGGGTTATAGCTAAA 57.217 39.130 0.00 0.00 46.01 1.85
1947 2414 5.664908 ACTGTCATCCTTTCTGGTCTGATAT 59.335 40.000 0.00 0.00 37.07 1.63
2003 2470 7.685304 CGTAGAATGTTTTGGTTCATACGTTAC 59.315 37.037 0.00 0.00 32.85 2.50
2027 2494 6.948309 ACCATCTTGCACCTTTACTTTCTTAT 59.052 34.615 0.00 0.00 0.00 1.73
2087 2556 9.408648 TCCCTCAGTTAATAAATCTTGGATTTC 57.591 33.333 8.51 0.00 0.00 2.17
2097 2566 4.559862 ATCTTGGATTTCTCAGGTTCGT 57.440 40.909 0.00 0.00 0.00 3.85
2209 2679 2.159226 GCTGTACCTCGTGCTCAAGTAT 60.159 50.000 0.00 0.00 0.00 2.12
2261 2803 7.844493 TTCTTAACAGGTACCTTTCTGAGTA 57.156 36.000 13.15 0.00 35.20 2.59
2340 2885 8.833231 TCTGTTCTTACTGGATTTCTACTTTG 57.167 34.615 0.00 0.00 0.00 2.77
2363 2908 7.619964 TGCCATCGATTATCGTATACTCTTA 57.380 36.000 14.47 0.00 41.35 2.10
2365 2910 8.343366 TGCCATCGATTATCGTATACTCTTATC 58.657 37.037 14.47 0.00 41.35 1.75
2412 2959 5.814705 TCCAATTTTCAGTTTTTGTTGCGAT 59.185 32.000 0.00 0.00 0.00 4.58
2413 2960 5.902981 CCAATTTTCAGTTTTTGTTGCGATG 59.097 36.000 0.00 0.00 0.00 3.84
2414 2961 5.655893 ATTTTCAGTTTTTGTTGCGATGG 57.344 34.783 0.00 0.00 0.00 3.51
2416 2963 4.582701 TTCAGTTTTTGTTGCGATGGAT 57.417 36.364 0.00 0.00 0.00 3.41
2452 2999 5.846203 ACCAAACTTGTCCATTGAATTCTG 58.154 37.500 7.05 0.00 0.00 3.02
2509 3101 7.762382 ACCATTAACAGAGTAGCTAAAATTGC 58.238 34.615 0.00 0.00 0.00 3.56
2516 3108 8.567285 ACAGAGTAGCTAAAATTGCTGTATTT 57.433 30.769 0.00 0.00 41.32 1.40
2544 3137 2.031870 TGAATGCTTAGCGCTCTCCTA 58.968 47.619 16.34 0.00 40.11 2.94
2563 3156 6.384015 TCTCCTAGAACAGATATTTTGAGCCA 59.616 38.462 0.00 0.00 0.00 4.75
2572 3165 7.118723 ACAGATATTTTGAGCCACTTTGGATA 58.881 34.615 0.00 0.00 35.51 2.59
2603 3196 6.500684 TCTTTTCTGCACTTGGTCATATTC 57.499 37.500 0.00 0.00 0.00 1.75
2606 3199 3.261580 TCTGCACTTGGTCATATTCGTG 58.738 45.455 0.00 0.00 0.00 4.35
2618 3211 5.700832 GGTCATATTCGTGCCAGATTATTGA 59.299 40.000 0.00 0.00 0.00 2.57
2619 3212 6.204688 GGTCATATTCGTGCCAGATTATTGAA 59.795 38.462 0.00 0.00 0.00 2.69
2620 3213 7.094634 GGTCATATTCGTGCCAGATTATTGAAT 60.095 37.037 0.00 0.00 0.00 2.57
2707 3300 6.119536 ACTGATGTTGCGGGAATATTTCTTA 58.880 36.000 0.00 0.00 0.00 2.10
2997 3605 1.294068 AGGGGTTCCAGAGGTATGCTA 59.706 52.381 0.00 0.00 34.83 3.49
3003 3612 6.214819 GGGGTTCCAGAGGTATGCTATTTATA 59.785 42.308 0.00 0.00 0.00 0.98
3065 3674 4.342092 AGCTAGTTGGACAATTTGCAGTTT 59.658 37.500 13.99 0.00 32.98 2.66
3159 3768 2.507110 TACGAGCTGTCAGGCAAGCC 62.507 60.000 2.02 2.02 34.17 4.35
3172 3781 2.017049 GGCAAGCCATCGACATACTTT 58.983 47.619 6.14 0.00 35.81 2.66
3203 3812 2.582052 TCCCCAAATTATGCATCGTCC 58.418 47.619 0.19 0.00 0.00 4.79
3213 3822 0.250124 TGCATCGTCCGGTGAGTTTT 60.250 50.000 3.76 0.00 0.00 2.43
3230 3839 5.242795 AGTTTTAACTCTATGCACCTGGT 57.757 39.130 0.00 0.00 32.86 4.00
3231 3840 5.246307 AGTTTTAACTCTATGCACCTGGTC 58.754 41.667 0.00 0.00 32.86 4.02
3461 5133 0.251297 TCGTCTTCCCCGGTGAGTAA 60.251 55.000 0.00 0.00 0.00 2.24
3466 5138 1.350019 CTTCCCCGGTGAGTAAAAGGT 59.650 52.381 0.00 0.00 0.00 3.50
3473 5145 3.512680 CGGTGAGTAAAAGGTAGAGCAG 58.487 50.000 0.00 0.00 0.00 4.24
3524 5205 9.567776 TTTCAGATTATTTGTAACTGAAGACCA 57.432 29.630 0.00 0.00 44.45 4.02
3526 5210 8.593679 TCAGATTATTTGTAACTGAAGACCAGA 58.406 33.333 0.00 0.00 45.78 3.86
3577 5262 9.383519 CCTTACATATATTGTCTGTCAAAGTGT 57.616 33.333 0.00 0.00 39.87 3.55
3606 5291 9.747898 ATTCTATACTTTTTATGTTCCACCACA 57.252 29.630 0.00 0.00 0.00 4.17
3607 5292 9.747898 TTCTATACTTTTTATGTTCCACCACAT 57.252 29.630 0.00 0.00 40.61 3.21
3608 5293 9.747898 TCTATACTTTTTATGTTCCACCACATT 57.252 29.630 0.00 0.00 38.40 2.71
3612 5297 6.989759 ACTTTTTATGTTCCACCACATTTTCC 59.010 34.615 0.00 0.00 38.40 3.13
3620 5531 0.948678 ACCACATTTTCCCAACGACG 59.051 50.000 0.00 0.00 0.00 5.12
3653 5564 2.826128 AGGAAGTCGCTGATGTTCTGTA 59.174 45.455 0.00 0.00 0.00 2.74
3654 5565 2.924290 GGAAGTCGCTGATGTTCTGTAC 59.076 50.000 0.00 0.00 0.00 2.90
3686 5597 4.402793 GTGTAGATACCTCACATGTGGAGT 59.597 45.833 25.16 22.49 33.21 3.85
3757 5668 3.198853 GTGGTGCCTTCTAGAATTCCTCT 59.801 47.826 5.44 0.00 38.28 3.69
3758 5669 3.198635 TGGTGCCTTCTAGAATTCCTCTG 59.801 47.826 5.44 0.00 35.41 3.35
3817 5730 8.258007 TCTGGAGATTGACGAAATTGTAATAGT 58.742 33.333 0.00 0.00 0.00 2.12
3837 5750 0.539518 GTTTCTCTCCCTCTCAGCCC 59.460 60.000 0.00 0.00 0.00 5.19
3859 5772 3.118956 CGCTGAAGGTATTGAAGAGGTCT 60.119 47.826 0.00 0.00 0.00 3.85
3885 5798 0.403655 TAGGGCCACTGCACATTCAA 59.596 50.000 6.18 0.00 46.13 2.69
3912 5825 1.274447 TCAGCAGATGACCAGTGTGAG 59.726 52.381 0.00 0.00 31.12 3.51
3914 5827 2.093606 CAGCAGATGACCAGTGTGAGAT 60.094 50.000 0.00 0.00 0.00 2.75
3920 5833 1.417517 TGACCAGTGTGAGATGCAAGT 59.582 47.619 0.00 0.00 0.00 3.16
3931 5844 7.661437 AGTGTGAGATGCAAGTAAATTGAACTA 59.339 33.333 0.00 0.00 41.83 2.24
3934 5847 9.495754 GTGAGATGCAAGTAAATTGAACTATTC 57.504 33.333 0.00 0.00 41.83 1.75
4091 6055 3.808174 GCTGATACGGGAATTTACAGTCC 59.192 47.826 0.00 0.00 36.32 3.85
4105 6069 3.146104 ACAGTCCTGTTGCATAAAGCT 57.854 42.857 0.00 0.00 41.83 3.74
4115 6079 4.082300 TGTTGCATAAAGCTAATGGTGTGG 60.082 41.667 10.16 0.00 45.94 4.17
4125 6089 3.564225 GCTAATGGTGTGGGTAGTAATGC 59.436 47.826 0.00 0.00 0.00 3.56
4130 6094 2.949644 GGTGTGGGTAGTAATGCCATTC 59.050 50.000 0.00 0.00 0.00 2.67
4131 6095 3.371595 GGTGTGGGTAGTAATGCCATTCT 60.372 47.826 0.00 0.00 0.00 2.40
4152 6116 6.844696 TCTCAACTTCTTGTGTGATGTAAC 57.155 37.500 0.00 0.00 0.00 2.50
4159 6123 6.147821 ACTTCTTGTGTGATGTAACTGTATGC 59.852 38.462 0.00 0.00 0.00 3.14
4164 6128 5.118990 GTGTGATGTAACTGTATGCTCCAT 58.881 41.667 0.00 0.00 0.00 3.41
4167 6131 5.464722 GTGATGTAACTGTATGCTCCATCAG 59.535 44.000 0.00 0.00 38.21 2.90
4171 6135 6.515832 TGTAACTGTATGCTCCATCAGTATG 58.484 40.000 0.00 0.00 39.72 2.39
4173 6137 5.207110 ACTGTATGCTCCATCAGTATGTC 57.793 43.478 0.00 0.00 39.01 3.06
4174 6138 4.233005 CTGTATGCTCCATCAGTATGTCG 58.767 47.826 0.00 0.00 37.40 4.35
4220 6185 2.558313 GACGCCAGCTGCTTGTTC 59.442 61.111 8.66 0.00 38.05 3.18
4231 6196 2.287009 GCTGCTTGTTCGTGCTAGTTTT 60.287 45.455 0.00 0.00 0.00 2.43
4242 6207 5.220381 TCGTGCTAGTTTTGACTACAAGAG 58.780 41.667 0.00 0.00 37.32 2.85
4251 6216 7.215085 AGTTTTGACTACAAGAGATTACGGTT 58.785 34.615 0.00 0.00 37.32 4.44
4318 6310 6.959671 AAAATTTTGAAGCTCGTTTTGTCA 57.040 29.167 1.75 0.00 0.00 3.58
4329 6321 4.089065 GCTCGTTTTGTCATGAATTTGCTC 59.911 41.667 0.00 0.00 0.00 4.26
4330 6322 5.437289 TCGTTTTGTCATGAATTTGCTCT 57.563 34.783 0.00 0.00 0.00 4.09
4331 6323 5.830912 TCGTTTTGTCATGAATTTGCTCTT 58.169 33.333 0.00 0.00 0.00 2.85
4332 6324 6.272318 TCGTTTTGTCATGAATTTGCTCTTT 58.728 32.000 0.00 0.00 0.00 2.52
4333 6325 6.756074 TCGTTTTGTCATGAATTTGCTCTTTT 59.244 30.769 0.00 0.00 0.00 2.27
4334 6326 7.277539 TCGTTTTGTCATGAATTTGCTCTTTTT 59.722 29.630 0.00 0.00 0.00 1.94
4335 6327 7.371355 CGTTTTGTCATGAATTTGCTCTTTTTG 59.629 33.333 0.00 0.00 0.00 2.44
4336 6328 6.847956 TTGTCATGAATTTGCTCTTTTTGG 57.152 33.333 0.00 0.00 0.00 3.28
4337 6329 6.159299 TGTCATGAATTTGCTCTTTTTGGA 57.841 33.333 0.00 0.00 0.00 3.53
4338 6330 6.580788 TGTCATGAATTTGCTCTTTTTGGAA 58.419 32.000 0.00 0.00 0.00 3.53
4339 6331 7.046652 TGTCATGAATTTGCTCTTTTTGGAAA 58.953 30.769 0.00 0.00 0.00 3.13
4340 6332 7.011295 TGTCATGAATTTGCTCTTTTTGGAAAC 59.989 33.333 0.00 0.00 0.00 2.78
4341 6333 7.011295 GTCATGAATTTGCTCTTTTTGGAAACA 59.989 33.333 0.00 0.00 39.83 2.83
4342 6334 7.716123 TCATGAATTTGCTCTTTTTGGAAACAT 59.284 29.630 0.00 0.00 42.32 2.71
4343 6335 8.991026 CATGAATTTGCTCTTTTTGGAAACATA 58.009 29.630 0.00 0.00 42.32 2.29
4344 6336 9.729281 ATGAATTTGCTCTTTTTGGAAACATAT 57.271 25.926 0.00 0.00 42.32 1.78
4345 6337 8.991026 TGAATTTGCTCTTTTTGGAAACATATG 58.009 29.630 0.00 0.00 42.32 1.78
4346 6338 7.910441 ATTTGCTCTTTTTGGAAACATATGG 57.090 32.000 7.80 0.00 42.32 2.74
4347 6339 6.662865 TTGCTCTTTTTGGAAACATATGGA 57.337 33.333 7.80 0.00 42.32 3.41
4348 6340 6.271488 TGCTCTTTTTGGAAACATATGGAG 57.729 37.500 7.80 1.21 42.32 3.86
4349 6341 6.009589 TGCTCTTTTTGGAAACATATGGAGA 58.990 36.000 7.80 0.00 42.32 3.71
4350 6342 6.664816 TGCTCTTTTTGGAAACATATGGAGAT 59.335 34.615 7.80 0.00 42.32 2.75
4351 6343 7.833682 TGCTCTTTTTGGAAACATATGGAGATA 59.166 33.333 7.80 0.00 42.32 1.98
4352 6344 8.686334 GCTCTTTTTGGAAACATATGGAGATAA 58.314 33.333 7.80 0.00 42.32 1.75
4399 6876 3.058160 GTTCTGCTGCCGCCATGT 61.058 61.111 0.00 0.00 34.43 3.21
4401 6878 3.258228 TTCTGCTGCCGCCATGTCT 62.258 57.895 0.00 0.00 34.43 3.41
4431 6908 0.314935 AAAGTTGCAGCGGTGGATTG 59.685 50.000 17.54 0.00 0.00 2.67
4432 6909 1.526575 AAGTTGCAGCGGTGGATTGG 61.527 55.000 17.54 0.00 0.00 3.16
4439 6916 2.834505 CGGTGGATTGGCCCCATG 60.835 66.667 0.00 0.00 35.91 3.66
4450 6949 3.339547 GCCCCATGCCGTATGTTAT 57.660 52.632 0.00 0.00 34.87 1.89
4453 6952 3.150767 GCCCCATGCCGTATGTTATTAA 58.849 45.455 0.00 0.00 34.87 1.40
4481 6980 8.514330 TTATTGACAAACCAACAGAAAGTACT 57.486 30.769 0.00 0.00 0.00 2.73
4486 6985 5.354234 ACAAACCAACAGAAAGTACTCACAG 59.646 40.000 0.00 0.00 0.00 3.66
4573 7072 3.545124 AATCCTGCCGACCACGCAA 62.545 57.895 0.00 0.00 38.29 4.85
4578 7077 0.318614 CTGCCGACCACGCAATTTTT 60.319 50.000 0.00 0.00 38.29 1.94
4677 7176 9.634163 AAAGTATTATTCCACGAATTTTGTTCC 57.366 29.630 0.00 0.00 33.95 3.62
4713 7212 4.208632 GGGTGACGAGATTGGCAG 57.791 61.111 0.00 0.00 0.00 4.85
4714 7213 1.296715 GGGTGACGAGATTGGCAGT 59.703 57.895 0.00 0.00 0.00 4.40
4812 7311 9.362539 TCTATAACTCATTTTTCGTTCACCTAC 57.637 33.333 0.00 0.00 0.00 3.18
4827 7326 2.102588 CACCTACTTCAATAGGACCCCG 59.897 54.545 5.84 0.00 44.12 5.73
4830 7329 0.909623 ACTTCAATAGGACCCCGGTG 59.090 55.000 0.00 0.00 0.00 4.94
4859 7358 4.434989 CGAACGTTCGGAATTTAAGCATGA 60.435 41.667 36.53 0.00 46.30 3.07
4865 7364 4.331968 TCGGAATTTAAGCATGACAACCT 58.668 39.130 0.00 0.00 0.00 3.50
4917 7417 6.346518 CGGATTTTCATGTTTGCCAACTAAAC 60.347 38.462 2.01 0.00 38.26 2.01
4921 7421 5.590530 TCATGTTTGCCAACTAAACTTGT 57.409 34.783 2.01 0.00 40.81 3.16
4923 7423 5.126222 TCATGTTTGCCAACTAAACTTGTCA 59.874 36.000 2.01 0.00 40.81 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.827399 CTAGTTGCCACTGGGGTCGT 61.827 60.000 0.00 0.00 39.65 4.34
1 2 1.079127 CTAGTTGCCACTGGGGTCG 60.079 63.158 0.00 0.00 39.65 4.79
5 6 3.127533 GCGCTAGTTGCCACTGGG 61.128 66.667 0.00 1.05 38.78 4.45
120 121 4.717313 GGAACTGCCACGTCCCCC 62.717 72.222 0.00 0.00 36.34 5.40
137 138 1.301716 CGGTGTGGTGGGACTTCAG 60.302 63.158 0.00 0.00 0.00 3.02
138 139 1.762858 TCGGTGTGGTGGGACTTCA 60.763 57.895 0.00 0.00 0.00 3.02
143 144 3.552384 GGTGTCGGTGTGGTGGGA 61.552 66.667 0.00 0.00 0.00 4.37
148 149 1.597027 GGTGAAGGTGTCGGTGTGG 60.597 63.158 0.00 0.00 0.00 4.17
155 156 2.617274 GCAAGGCGGTGAAGGTGTC 61.617 63.158 0.00 0.00 0.00 3.67
218 219 4.489771 ATTGGAGGCGGCGGGAAG 62.490 66.667 9.78 0.00 0.00 3.46
229 230 0.813210 GCCTCTTCTCGGCATTGGAG 60.813 60.000 0.00 0.00 46.77 3.86
270 271 0.877649 CGATTCATGCTGCCGCTACT 60.878 55.000 0.70 0.00 36.97 2.57
312 355 1.073199 CGAACTGAAAGCCCACCCT 59.927 57.895 0.00 0.00 37.60 4.34
325 368 0.395173 ACAAAACCCTGCCACGAACT 60.395 50.000 0.00 0.00 0.00 3.01
361 407 0.942252 GCGGTTTTCGACCTCTGTTT 59.058 50.000 0.00 0.00 46.92 2.83
400 447 2.517450 CGCCAGATCGAAGCCGTTC 61.517 63.158 0.00 0.00 37.05 3.95
449 496 2.484287 CTTGTTGATCCGGGCCACCT 62.484 60.000 4.39 0.00 33.28 4.00
450 497 2.034999 TTGTTGATCCGGGCCACC 59.965 61.111 4.39 0.00 0.00 4.61
451 498 2.700773 GCTTGTTGATCCGGGCCAC 61.701 63.158 4.39 0.00 0.00 5.01
455 528 1.452108 GAGGGCTTGTTGATCCGGG 60.452 63.158 0.00 0.00 0.00 5.73
524 597 1.472904 GGGGCTAACCTTAGTCGAAGC 60.473 57.143 0.00 0.00 36.26 3.86
553 635 1.140652 GGAGAAGCAGAAGGAGATGGG 59.859 57.143 0.00 0.00 0.00 4.00
557 639 1.178276 GACGGAGAAGCAGAAGGAGA 58.822 55.000 0.00 0.00 0.00 3.71
564 646 1.005340 GCATGAAGACGGAGAAGCAG 58.995 55.000 0.00 0.00 0.00 4.24
632 722 4.324991 GGAGGAACCGTTGCCCGT 62.325 66.667 0.00 0.00 33.66 5.28
662 752 1.781555 GCCTGTGACGTGACGATTG 59.218 57.895 13.70 0.00 0.00 2.67
672 762 2.029844 GGTTCTGCTCGCCTGTGAC 61.030 63.158 0.00 0.00 0.00 3.67
723 813 6.325286 ACCAAAATAAAGTAGAAGGTTTGCCA 59.675 34.615 0.00 0.00 37.19 4.92
737 827 6.857777 TGTTCATTGCCAACCAAAATAAAG 57.142 33.333 0.00 0.00 36.92 1.85
779 870 4.481930 TGATTTTAAAGTGGCGTGTCAG 57.518 40.909 0.00 0.00 0.00 3.51
850 969 8.710551 CATGCTTAATCTCTAGCTAAATCACTG 58.289 37.037 0.00 0.00 38.22 3.66
877 1014 8.985315 AACTCATGTTGTCCATATTGATACAT 57.015 30.769 0.00 3.21 34.71 2.29
881 1018 7.943079 TCAAACTCATGTTGTCCATATTGAT 57.057 32.000 0.00 0.00 36.39 2.57
895 1032 7.965107 GCTAGTGACCTTTAAATCAAACTCATG 59.035 37.037 0.00 0.00 0.00 3.07
951 1088 8.128582 TGAAATAACATAAGCCGATTCATTCAC 58.871 33.333 0.00 0.00 0.00 3.18
992 1140 0.819582 CTGCCCATCCATTGTGTTCC 59.180 55.000 0.00 0.00 0.00 3.62
993 1141 1.747355 CTCTGCCCATCCATTGTGTTC 59.253 52.381 0.00 0.00 0.00 3.18
994 1142 1.843368 CTCTGCCCATCCATTGTGTT 58.157 50.000 0.00 0.00 0.00 3.32
1145 1293 3.338249 TGAGCAGAGCAGGATAACAAAC 58.662 45.455 0.00 0.00 0.00 2.93
1149 1297 7.158021 AGTATAAATGAGCAGAGCAGGATAAC 58.842 38.462 0.00 0.00 0.00 1.89
1196 1663 7.906327 ACCTACAGAATAACAAATGGCATTTT 58.094 30.769 22.26 12.05 0.00 1.82
1197 1664 7.480760 ACCTACAGAATAACAAATGGCATTT 57.519 32.000 19.39 19.39 0.00 2.32
1201 1668 6.267496 ACAACCTACAGAATAACAAATGGC 57.733 37.500 0.00 0.00 0.00 4.40
1216 1683 4.613622 GCATGTGTCATGACAACAACCTAC 60.614 45.833 29.42 14.94 43.77 3.18
1246 1713 5.338365 ACATATCGTACTCCAGAACGTTTC 58.662 41.667 0.46 0.00 39.99 2.78
1275 1742 4.142469 GCACATAATAAACCTTCAAGCCGT 60.142 41.667 0.00 0.00 0.00 5.68
1330 1797 7.275888 TGGAAATGTCATGAATAATGTAGGC 57.724 36.000 0.00 0.00 37.56 3.93
1402 1869 2.818130 TTGTTGAAAAGGCCTGATGC 57.182 45.000 5.69 0.00 40.16 3.91
1658 2125 3.170717 TCGAGGAGGGAGTAAACATTGT 58.829 45.455 0.00 0.00 0.00 2.71
1978 2445 7.959109 GGTAACGTATGAACCAAAACATTCTAC 59.041 37.037 0.00 0.00 33.28 2.59
2003 2470 5.712152 AAGAAAGTAAAGGTGCAAGATGG 57.288 39.130 0.00 0.00 0.00 3.51
2027 2494 9.226606 CCACTATAACTCCAAAACAACATAGAA 57.773 33.333 0.00 0.00 0.00 2.10
2087 2556 5.334879 CCTCCAACAATAAAACGAACCTGAG 60.335 44.000 0.00 0.00 0.00 3.35
2097 2566 3.426615 ACCATCGCCTCCAACAATAAAA 58.573 40.909 0.00 0.00 0.00 1.52
2167 2637 4.971924 AGCCCCTAACATCTCAACTCTATT 59.028 41.667 0.00 0.00 0.00 1.73
2198 2668 5.414360 TCAGAACAGATCATACTTGAGCAC 58.586 41.667 0.00 0.00 40.79 4.40
2209 2679 6.990908 ATGACCAGATATCAGAACAGATCA 57.009 37.500 5.32 0.00 0.00 2.92
2340 2885 8.561212 AGATAAGAGTATACGATAATCGATGGC 58.439 37.037 0.00 0.00 43.74 4.40
2363 2908 5.249393 ACCTGACAGGACTATTTCAACAGAT 59.751 40.000 28.56 0.00 37.67 2.90
2365 2910 4.899502 ACCTGACAGGACTATTTCAACAG 58.100 43.478 28.56 0.00 37.67 3.16
2412 2959 5.362430 AGTTTGGTAAAAGCAACTTCATCCA 59.638 36.000 0.00 0.00 35.07 3.41
2413 2960 5.842907 AGTTTGGTAAAAGCAACTTCATCC 58.157 37.500 0.00 0.00 35.07 3.51
2414 2961 6.756542 ACAAGTTTGGTAAAAGCAACTTCATC 59.243 34.615 0.00 0.00 35.07 2.92
2416 2963 6.031751 ACAAGTTTGGTAAAAGCAACTTCA 57.968 33.333 0.00 0.00 35.07 3.02
2452 2999 0.240945 CACAGACGCCATGGGTTTTC 59.759 55.000 15.13 0.00 0.00 2.29
2509 3101 8.589629 GCTAAGCATTCAAACATTCAAATACAG 58.410 33.333 0.00 0.00 0.00 2.74
2544 3137 6.071728 CCAAAGTGGCTCAAAATATCTGTTCT 60.072 38.462 0.00 0.00 0.00 3.01
2563 3156 7.363268 GCAGAAAAGATCCAATGTATCCAAAGT 60.363 37.037 0.00 0.00 0.00 2.66
2572 3165 4.021719 CCAAGTGCAGAAAAGATCCAATGT 60.022 41.667 0.00 0.00 0.00 2.71
2574 3167 4.154942 ACCAAGTGCAGAAAAGATCCAAT 58.845 39.130 0.00 0.00 0.00 3.16
2603 3196 7.379529 GGAACAATTATTCAATAATCTGGCACG 59.620 37.037 3.00 0.00 34.50 5.34
2606 3199 8.416329 ACAGGAACAATTATTCAATAATCTGGC 58.584 33.333 15.27 8.44 34.50 4.85
2723 3316 6.862209 TGTTTGCATTAGGTCCATGAAATAC 58.138 36.000 0.00 0.00 0.00 1.89
2735 3328 9.696917 AACTATTTTCTTTCTGTTTGCATTAGG 57.303 29.630 0.00 0.00 0.00 2.69
2801 3408 9.802039 AACAATGTTAACTTATCCACCTTCTAA 57.198 29.630 7.22 0.00 0.00 2.10
2859 3467 2.688958 AGCCTCACGTCTCAGTATTACC 59.311 50.000 0.00 0.00 0.00 2.85
2883 3491 1.135944 GCGAACTACAAGAGCAAAGGC 60.136 52.381 0.00 0.00 41.61 4.35
3065 3674 6.601332 ACCTGAAAAAGAGTCATTTGTAGGA 58.399 36.000 21.20 0.00 32.40 2.94
3159 3768 7.971168 GGATCTATACCAGAAAGTATGTCGATG 59.029 40.741 0.00 0.00 36.67 3.84
3172 3781 6.274436 TGCATAATTTGGGGATCTATACCAGA 59.726 38.462 0.00 0.00 35.37 3.86
3213 3822 2.426024 GTCGACCAGGTGCATAGAGTTA 59.574 50.000 3.51 0.00 0.00 2.24
3230 3839 0.739462 CCAATGCGCAGTAAGGTCGA 60.739 55.000 18.32 0.00 0.00 4.20
3231 3840 0.739462 TCCAATGCGCAGTAAGGTCG 60.739 55.000 18.32 0.00 0.00 4.79
3268 3877 1.676006 AGGAAAAACTGGTGCAGAACG 59.324 47.619 0.00 0.00 35.18 3.95
3311 4983 7.530426 AGATTTGAATAAGCACAAAAGGACT 57.470 32.000 0.00 0.00 39.01 3.85
3314 4986 9.643693 ACATTAGATTTGAATAAGCACAAAAGG 57.356 29.630 0.00 0.00 39.01 3.11
3461 5133 2.031495 ACAGTCCCTGCTCTACCTTT 57.969 50.000 0.00 0.00 34.37 3.11
3466 5138 5.663106 AGATGAATTTACAGTCCCTGCTCTA 59.337 40.000 0.00 0.00 34.37 2.43
3473 5145 6.173339 TGACAGAAGATGAATTTACAGTCCC 58.827 40.000 0.00 0.00 0.00 4.46
3522 5203 6.473455 GCTGACGATCCAAAAATAAAATCTGG 59.527 38.462 0.00 0.00 0.00 3.86
3523 5204 7.219535 CAGCTGACGATCCAAAAATAAAATCTG 59.780 37.037 8.42 0.00 0.00 2.90
3524 5205 7.094205 ACAGCTGACGATCCAAAAATAAAATCT 60.094 33.333 23.35 0.00 0.00 2.40
3526 5210 6.924111 ACAGCTGACGATCCAAAAATAAAAT 58.076 32.000 23.35 0.00 0.00 1.82
3531 5215 2.749621 GGACAGCTGACGATCCAAAAAT 59.250 45.455 23.35 0.00 0.00 1.82
3533 5217 1.347707 AGGACAGCTGACGATCCAAAA 59.652 47.619 23.35 0.00 33.33 2.44
3588 5273 6.426633 GGGAAAATGTGGTGGAACATAAAAAG 59.573 38.462 0.00 0.00 44.52 2.27
3592 5277 4.483950 TGGGAAAATGTGGTGGAACATAA 58.516 39.130 0.00 0.00 44.52 1.90
3602 5287 0.239879 CCGTCGTTGGGAAAATGTGG 59.760 55.000 0.00 0.00 0.00 4.17
3603 5288 0.386731 GCCGTCGTTGGGAAAATGTG 60.387 55.000 0.00 0.00 0.00 3.21
3604 5289 0.820074 TGCCGTCGTTGGGAAAATGT 60.820 50.000 0.00 0.00 0.00 2.71
3605 5290 0.312416 TTGCCGTCGTTGGGAAAATG 59.688 50.000 0.66 0.00 36.30 2.32
3606 5291 1.033574 TTTGCCGTCGTTGGGAAAAT 58.966 45.000 11.54 0.00 44.95 1.82
3607 5292 2.490165 TTTGCCGTCGTTGGGAAAA 58.510 47.368 11.54 2.83 44.95 2.29
3608 5293 1.030488 TGTTTGCCGTCGTTGGGAAA 61.030 50.000 10.29 10.29 45.61 3.13
3610 5295 2.181521 GTGTTTGCCGTCGTTGGGA 61.182 57.895 0.00 0.00 0.00 4.37
3612 5297 0.179161 TTTGTGTTTGCCGTCGTTGG 60.179 50.000 0.00 0.00 0.00 3.77
3620 5531 2.459934 CGACTTCCTTTTGTGTTTGCC 58.540 47.619 0.00 0.00 0.00 4.52
3653 5564 5.365895 GTGAGGTATCTACACCATTAAGGGT 59.634 44.000 5.84 5.84 43.89 4.34
3654 5565 5.365605 TGTGAGGTATCTACACCATTAAGGG 59.634 44.000 4.20 4.20 43.89 3.95
3686 5597 0.908198 AAACAGTTTGCCTGCCCAAA 59.092 45.000 0.00 0.00 45.68 3.28
3817 5730 1.270907 GGCTGAGAGGGAGAGAAACA 58.729 55.000 0.00 0.00 0.00 2.83
3837 5750 3.118956 AGACCTCTTCAATACCTTCAGCG 60.119 47.826 0.00 0.00 0.00 5.18
3859 5772 1.694150 GTGCAGTGGCCCTATATCTGA 59.306 52.381 0.00 0.00 40.13 3.27
3885 5798 3.053842 ACTGGTCATCTGCTGAATCCAAT 60.054 43.478 12.80 4.21 35.07 3.16
3912 5825 9.508567 GGAAGAATAGTTCAATTTACTTGCATC 57.491 33.333 0.00 0.00 34.66 3.91
3914 5827 8.402798 TGGAAGAATAGTTCAATTTACTTGCA 57.597 30.769 0.00 0.00 34.66 4.08
3931 5844 2.607499 TGCCACAATGGTTGGAAGAAT 58.393 42.857 0.00 0.00 40.46 2.40
3934 5847 1.066716 CCATGCCACAATGGTTGGAAG 60.067 52.381 11.47 0.00 42.11 3.46
4091 6055 5.097529 CACACCATTAGCTTTATGCAACAG 58.902 41.667 0.00 0.00 45.94 3.16
4105 6069 3.523972 TGGCATTACTACCCACACCATTA 59.476 43.478 0.00 0.00 0.00 1.90
4115 6079 6.116126 AGAAGTTGAGAATGGCATTACTACC 58.884 40.000 13.65 8.46 0.00 3.18
4125 6089 5.240183 ACATCACACAAGAAGTTGAGAATGG 59.760 40.000 0.00 0.00 37.10 3.16
4130 6094 6.258727 ACAGTTACATCACACAAGAAGTTGAG 59.741 38.462 0.00 0.00 37.10 3.02
4131 6095 6.112734 ACAGTTACATCACACAAGAAGTTGA 58.887 36.000 0.00 0.00 37.10 3.18
4152 6116 4.233005 CGACATACTGATGGAGCATACAG 58.767 47.826 0.00 0.00 37.39 2.74
4159 6123 3.801114 TCAACCGACATACTGATGGAG 57.199 47.619 0.00 0.00 37.39 3.86
4164 6128 3.572682 AGACAGTTCAACCGACATACTGA 59.427 43.478 0.00 0.00 38.74 3.41
4167 6131 4.175787 AGAGACAGTTCAACCGACATAC 57.824 45.455 0.00 0.00 0.00 2.39
4171 6135 2.540101 CACAAGAGACAGTTCAACCGAC 59.460 50.000 0.00 0.00 0.00 4.79
4173 6137 1.261619 GCACAAGAGACAGTTCAACCG 59.738 52.381 0.00 0.00 0.00 4.44
4174 6138 1.604278 GGCACAAGAGACAGTTCAACC 59.396 52.381 0.00 0.00 0.00 3.77
4217 6182 5.461078 TCTTGTAGTCAAAACTAGCACGAAC 59.539 40.000 0.00 0.00 38.66 3.95
4220 6185 5.220381 TCTCTTGTAGTCAAAACTAGCACG 58.780 41.667 0.00 0.00 38.66 5.34
4231 6196 7.211573 TCAAAAACCGTAATCTCTTGTAGTCA 58.788 34.615 0.00 0.00 0.00 3.41
4242 6207 9.796120 TCCAAATCAATATCAAAAACCGTAATC 57.204 29.630 0.00 0.00 0.00 1.75
4276 6267 5.452078 TTTTATGCCAACTGTCTCCAAAG 57.548 39.130 0.00 0.00 0.00 2.77
4318 6310 9.729281 ATATGTTTCCAAAAAGAGCAAATTCAT 57.271 25.926 0.00 0.00 0.00 2.57
4331 6323 8.748412 CCAAGTTATCTCCATATGTTTCCAAAA 58.252 33.333 1.24 0.00 0.00 2.44
4332 6324 7.893302 ACCAAGTTATCTCCATATGTTTCCAAA 59.107 33.333 1.24 0.00 0.00 3.28
4333 6325 7.410174 ACCAAGTTATCTCCATATGTTTCCAA 58.590 34.615 1.24 0.00 0.00 3.53
4334 6326 6.969043 ACCAAGTTATCTCCATATGTTTCCA 58.031 36.000 1.24 0.00 0.00 3.53
4335 6327 7.201821 CCAACCAAGTTATCTCCATATGTTTCC 60.202 40.741 1.24 0.00 0.00 3.13
4336 6328 7.339466 ACCAACCAAGTTATCTCCATATGTTTC 59.661 37.037 1.24 0.00 0.00 2.78
4337 6329 7.182060 ACCAACCAAGTTATCTCCATATGTTT 58.818 34.615 1.24 0.00 0.00 2.83
4338 6330 6.731467 ACCAACCAAGTTATCTCCATATGTT 58.269 36.000 1.24 0.00 0.00 2.71
4339 6331 6.327386 ACCAACCAAGTTATCTCCATATGT 57.673 37.500 1.24 0.00 0.00 2.29
4340 6332 5.765182 GGACCAACCAAGTTATCTCCATATG 59.235 44.000 0.00 0.00 38.79 1.78
4341 6333 5.431731 TGGACCAACCAAGTTATCTCCATAT 59.568 40.000 0.00 0.00 46.75 1.78
4342 6334 4.785914 TGGACCAACCAAGTTATCTCCATA 59.214 41.667 0.00 0.00 46.75 2.74
4343 6335 3.591527 TGGACCAACCAAGTTATCTCCAT 59.408 43.478 0.00 0.00 46.75 3.41
4344 6336 2.983192 TGGACCAACCAAGTTATCTCCA 59.017 45.455 0.00 0.00 46.75 3.86
4345 6337 3.713826 TGGACCAACCAAGTTATCTCC 57.286 47.619 0.00 0.00 46.75 3.71
4399 6876 4.261994 GCTGCAACTTTTACCATGGAAAGA 60.262 41.667 25.22 8.28 36.58 2.52
4401 6878 3.551863 CGCTGCAACTTTTACCATGGAAA 60.552 43.478 21.47 11.78 0.00 3.13
4432 6909 1.616159 AATAACATACGGCATGGGGC 58.384 50.000 0.00 0.00 39.13 5.80
4463 6962 5.584649 TCTGTGAGTACTTTCTGTTGGTTTG 59.415 40.000 0.00 0.00 0.00 2.93
4465 6964 5.353394 TCTGTGAGTACTTTCTGTTGGTT 57.647 39.130 0.00 0.00 0.00 3.67
4467 6966 5.235186 CACTTCTGTGAGTACTTTCTGTTGG 59.765 44.000 0.00 0.00 46.55 3.77
4471 6970 4.950050 ACCACTTCTGTGAGTACTTTCTG 58.050 43.478 0.00 0.00 46.55 3.02
4472 6971 4.261656 CGACCACTTCTGTGAGTACTTTCT 60.262 45.833 0.00 0.00 46.55 2.52
4477 6976 2.662700 CACGACCACTTCTGTGAGTAC 58.337 52.381 0.00 0.00 46.55 2.73
4479 6978 0.249489 GCACGACCACTTCTGTGAGT 60.249 55.000 0.00 0.00 46.55 3.41
4480 6979 0.946221 GGCACGACCACTTCTGTGAG 60.946 60.000 0.00 0.00 46.55 3.51
4481 6980 1.069090 GGCACGACCACTTCTGTGA 59.931 57.895 0.00 0.00 46.55 3.58
4573 7072 3.981211 AGAGCACATTTGACGCAAAAAT 58.019 36.364 8.65 0.00 36.90 1.82
4578 7077 1.398041 GCATAGAGCACATTTGACGCA 59.602 47.619 0.00 0.00 44.79 5.24
4652 7151 8.798402 TGGAACAAAATTCGTGGAATAATACTT 58.202 29.630 0.00 0.00 29.69 2.24
4677 7176 7.516155 CGTCACCCGTAACAAATATGAGTTATG 60.516 40.741 10.60 10.60 37.11 1.90
4787 7286 9.367444 AGTAGGTGAACGAAAAATGAGTTATAG 57.633 33.333 0.00 0.00 0.00 1.31
4788 7287 9.715121 AAGTAGGTGAACGAAAAATGAGTTATA 57.285 29.630 0.00 0.00 0.00 0.98
4797 7296 7.172019 GTCCTATTGAAGTAGGTGAACGAAAAA 59.828 37.037 0.00 0.00 41.65 1.94
4812 7311 1.200519 TCACCGGGGTCCTATTGAAG 58.799 55.000 2.12 0.00 0.00 3.02
4848 7347 9.777297 AAAATGTTTAGGTTGTCATGCTTAAAT 57.223 25.926 0.00 0.00 0.00 1.40
4884 7384 6.422400 GGCAAACATGAAAATCCGAACTAAAA 59.578 34.615 0.00 0.00 0.00 1.52
4893 7393 6.705825 AGTTTAGTTGGCAAACATGAAAATCC 59.294 34.615 6.76 0.00 38.88 3.01


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

AutoCloner maintained by Alex Coulton.