Multiple sequence alignment - TraesCS4D01G210000

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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 TraesCS4D01G210000 chr4D 100.000 4856 0 0 1 4856 361364351 361359496 0.000000e+00 8968.0
1 TraesCS4D01G210000 chr4A 94.466 2024 74 18 681 2685 103492216 103494220 0.000000e+00 3083.0
2 TraesCS4D01G210000 chr4A 95.446 1010 39 6 2894 3898 103494262 103495269 0.000000e+00 1604.0
3 TraesCS4D01G210000 chr4A 89.728 331 34 0 358 688 626279980 626280310 1.620000e-114 424.0
4 TraesCS4D01G210000 chr4A 84.140 372 41 9 1 367 626279472 626279830 1.290000e-90 344.0
5 TraesCS4D01G210000 chr4A 77.381 504 96 13 2114 2606 318039734 318039238 2.860000e-72 283.0
6 TraesCS4D01G210000 chr4B 93.700 1635 69 11 2945 4559 446734149 446732529 0.000000e+00 2418.0
7 TraesCS4D01G210000 chr4B 93.393 1332 43 15 782 2078 446736581 446735260 0.000000e+00 1930.0
8 TraesCS4D01G210000 chr4B 92.647 612 33 8 2084 2685 446734997 446734388 0.000000e+00 870.0
9 TraesCS4D01G210000 chr4B 91.597 238 20 0 4618 4855 446732182 446731945 3.620000e-86 329.0
10 TraesCS4D01G210000 chr4B 88.043 184 10 5 782 954 446767349 446767167 1.770000e-49 207.0
11 TraesCS4D01G210000 chr7D 88.133 691 67 9 2 688 122938228 122937549 0.000000e+00 808.0
12 TraesCS4D01G210000 chr7D 78.090 356 68 9 334 686 93677750 93677402 2.940000e-52 217.0
13 TraesCS4D01G210000 chr7D 90.196 51 5 0 2683 2733 104892079 104892029 3.140000e-07 67.6
14 TraesCS4D01G210000 chr7A 90.649 524 41 2 163 686 125913534 125913019 0.000000e+00 689.0
15 TraesCS4D01G210000 chr7A 88.387 155 18 0 480 634 49984805 49984651 2.310000e-43 187.0
16 TraesCS4D01G210000 chr5A 83.884 484 38 16 233 687 676907262 676907734 4.490000e-115 425.0
17 TraesCS4D01G210000 chr5A 95.349 43 2 0 2684 2726 338412378 338412420 8.720000e-08 69.4
18 TraesCS4D01G210000 chr5A 87.500 48 6 0 2684 2731 457088998 457089045 6.790000e-04 56.5
19 TraesCS4D01G210000 chr6B 82.979 188 31 1 484 671 95239359 95239173 8.360000e-38 169.0
20 TraesCS4D01G210000 chr2D 76.471 357 57 10 336 687 642983504 642983838 8.360000e-38 169.0
21 TraesCS4D01G210000 chr2D 100.000 28 0 0 639 666 547770106 547770079 9.000000e-03 52.8
22 TraesCS4D01G210000 chr2B 81.935 155 28 0 508 662 368260906 368261060 1.100000e-26 132.0
23 TraesCS4D01G210000 chr6D 98.000 50 1 0 639 688 47659465 47659416 2.410000e-13 87.9
24 TraesCS4D01G210000 chr2A 92.000 50 3 1 2678 2726 779873959 779874008 8.720000e-08 69.4
25 TraesCS4D01G210000 chr2A 90.476 42 3 1 2685 2726 6080202 6080242 2.000000e-03 54.7
26 TraesCS4D01G210000 chr7B 88.235 51 6 0 2683 2733 63558111 63558061 1.460000e-05 62.1
27 TraesCS4D01G210000 chr1A 100.000 33 0 0 4704 4736 496650015 496650047 1.460000e-05 62.1


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 TraesCS4D01G210000 chr4D 361359496 361364351 4855 True 8968.00 8968 100.00000 1 4856 1 chr4D.!!$R1 4855
1 TraesCS4D01G210000 chr4A 103492216 103495269 3053 False 2343.50 3083 94.95600 681 3898 2 chr4A.!!$F1 3217
2 TraesCS4D01G210000 chr4A 626279472 626280310 838 False 384.00 424 86.93400 1 688 2 chr4A.!!$F2 687
3 TraesCS4D01G210000 chr4B 446731945 446736581 4636 True 1386.75 2418 92.83425 782 4855 4 chr4B.!!$R2 4073
4 TraesCS4D01G210000 chr7D 122937549 122938228 679 True 808.00 808 88.13300 2 688 1 chr7D.!!$R3 686
5 TraesCS4D01G210000 chr7A 125913019 125913534 515 True 689.00 689 90.64900 163 686 1 chr7A.!!$R2 523

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
720 886 0.537143 AAAACATGGCGTGGCAGAGA 60.537 50.0 12.05 0.0 0.0 3.10 F
1922 2130 0.034960 GGAAGAAGAGGGTCAAGGGC 60.035 60.0 0.00 0.0 0.0 5.19 F
2500 2974 0.318699 GGGGCGCTGAAAAGTTTGAC 60.319 55.0 7.64 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2548 3022 0.796312 CCGACTTGCGTATTGCTTGT 59.204 50.0 0.00 0.00 46.63 3.16 R
3083 3622 0.454452 GTCGCCGGCATTCTTTCAAC 60.454 55.0 28.98 5.75 0.00 3.18 R
4159 4703 0.818296 GTCACACCGAGCTACCATCT 59.182 55.0 0.00 0.00 0.00 2.90 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
29 30 2.485122 GCCATTTGGACTTCGCGG 59.515 61.111 6.13 0.00 37.39 6.46
30 31 2.485122 CCATTTGGACTTCGCGGC 59.515 61.111 6.13 0.00 37.39 6.53
64 65 6.078456 TCATGAAGGGATATTCCAAACACT 57.922 37.500 1.92 0.00 38.64 3.55
65 66 7.206789 TCATGAAGGGATATTCCAAACACTA 57.793 36.000 1.92 0.00 38.64 2.74
67 68 6.884472 TGAAGGGATATTCCAAACACTAGA 57.116 37.500 1.92 0.00 38.64 2.43
94 97 2.094286 TGTGCTTTTGTGGACAGGTTTG 60.094 45.455 0.00 0.00 33.47 2.93
103 106 3.485463 TGGACAGGTTTGTACAGGAAG 57.515 47.619 0.00 0.00 43.26 3.46
114 117 7.176690 AGGTTTGTACAGGAAGTCCAAATAATG 59.823 37.037 0.00 0.00 38.17 1.90
126 129 6.381801 AGTCCAAATAATGCAGAAGAAAACG 58.618 36.000 0.00 0.00 0.00 3.60
134 137 2.224426 TGCAGAAGAAAACGCCTAGGAA 60.224 45.455 14.75 0.00 0.00 3.36
178 181 1.453155 GCATGTGGAATCTCAACGGT 58.547 50.000 0.00 0.00 0.00 4.83
193 196 4.452733 GGTCGAAGGCTCCACCCG 62.453 72.222 0.00 0.00 40.58 5.28
194 197 3.379445 GTCGAAGGCTCCACCCGA 61.379 66.667 0.00 0.00 40.58 5.14
195 198 3.379445 TCGAAGGCTCCACCCGAC 61.379 66.667 0.00 0.00 40.58 4.79
196 199 4.452733 CGAAGGCTCCACCCGACC 62.453 72.222 0.00 0.00 40.58 4.79
197 200 3.319198 GAAGGCTCCACCCGACCA 61.319 66.667 0.00 0.00 40.58 4.02
198 201 3.607370 GAAGGCTCCACCCGACCAC 62.607 68.421 0.00 0.00 40.58 4.16
220 223 1.067516 CCAGGGCCATGCTAAAATTCG 59.932 52.381 13.13 0.00 0.00 3.34
278 281 1.725292 GCGTCGACTGTGTGTAGAGAC 60.725 57.143 14.70 0.00 31.11 3.36
295 298 5.255710 AGAGACAGTGATGGAAACTATCG 57.744 43.478 0.00 0.00 0.00 2.92
297 300 5.000012 AGACAGTGATGGAAACTATCGAC 58.000 43.478 0.00 0.00 0.00 4.20
299 302 3.442625 ACAGTGATGGAAACTATCGACGA 59.557 43.478 0.00 0.00 0.00 4.20
309 312 2.645802 ACTATCGACGAAGCTCTTCCT 58.354 47.619 0.00 0.00 36.27 3.36
387 552 2.800544 GCTCTTTCGTTAGCACAAGACA 59.199 45.455 0.00 0.00 38.63 3.41
397 562 6.476706 TCGTTAGCACAAGACATTCATCTATG 59.523 38.462 0.00 0.00 0.00 2.23
465 630 5.020132 TCAACCAAGGAAGTCAAGGAAAAA 58.980 37.500 0.00 0.00 0.00 1.94
466 631 5.660864 TCAACCAAGGAAGTCAAGGAAAAAT 59.339 36.000 0.00 0.00 0.00 1.82
476 641 5.787380 AGTCAAGGAAAAATTGGAGCAATC 58.213 37.500 0.00 0.00 32.43 2.67
478 643 4.592351 TCAAGGAAAAATTGGAGCAATCCA 59.408 37.500 0.00 0.00 32.43 3.41
488 653 2.286872 GGAGCAATCCACACTGAGATG 58.713 52.381 0.00 0.00 0.00 2.90
605 770 1.303806 TCCGGGTCGTCATGTCTGA 60.304 57.895 0.00 0.00 0.00 3.27
631 796 4.022416 TGGCTAACCACATGACACAAATTC 60.022 41.667 0.00 0.00 42.67 2.17
641 806 6.823182 CACATGACACAAATTCTATCCCACTA 59.177 38.462 0.00 0.00 0.00 2.74
720 886 0.537143 AAAACATGGCGTGGCAGAGA 60.537 50.000 12.05 0.00 0.00 3.10
722 888 1.028330 AACATGGCGTGGCAGAGATG 61.028 55.000 12.05 0.00 0.00 2.90
723 889 2.515523 ATGGCGTGGCAGAGATGC 60.516 61.111 1.74 0.00 0.00 3.91
724 890 3.333899 ATGGCGTGGCAGAGATGCA 62.334 57.895 1.74 0.00 36.33 3.96
731 897 0.978907 TGGCAGAGATGCAGAGTGAA 59.021 50.000 2.29 0.00 36.33 3.18
752 918 2.925563 ACGTTCGCTATTTTTACTCCGG 59.074 45.455 0.00 0.00 0.00 5.14
761 929 7.066525 TCGCTATTTTTACTCCGGATCAATTTT 59.933 33.333 3.57 0.00 0.00 1.82
776 944 4.577246 TTTTTGCACGGGCCGCAC 62.577 61.111 28.71 19.25 39.59 5.34
806 974 4.589798 TCGGACCAGAAATAATATCCCGAA 59.410 41.667 0.00 0.00 40.17 4.30
807 975 4.929808 CGGACCAGAAATAATATCCCGAAG 59.070 45.833 0.00 0.00 36.86 3.79
932 1114 1.141185 CTTATCCCCTTCACCCTCCC 58.859 60.000 0.00 0.00 0.00 4.30
962 1144 3.787001 CCACCCTCCCGCTTCTCC 61.787 72.222 0.00 0.00 0.00 3.71
1041 1234 1.890979 GGCAGCATCACCTCCATCG 60.891 63.158 0.00 0.00 0.00 3.84
1045 1238 1.890979 GCATCACCTCCATCGGCAG 60.891 63.158 0.00 0.00 0.00 4.85
1335 1532 0.105142 CCTCCTCCCCCTTCGGATAA 60.105 60.000 0.00 0.00 0.00 1.75
1429 1637 0.890683 GATTGGTTTGGAGTGGGCTG 59.109 55.000 0.00 0.00 0.00 4.85
1435 1643 2.283143 TTTGGAGTGGGCTGTGCTGT 62.283 55.000 0.00 0.00 0.00 4.40
1556 1764 2.269241 GAGGCCGTGGCTTTAGCT 59.731 61.111 11.25 0.00 38.98 3.32
1658 1866 3.842869 GGTGGAGGACAGCTACTTG 57.157 57.895 0.00 0.00 44.08 3.16
1661 1869 1.066787 GTGGAGGACAGCTACTTGACC 60.067 57.143 0.00 0.00 33.83 4.02
1922 2130 0.034960 GGAAGAAGAGGGTCAAGGGC 60.035 60.000 0.00 0.00 0.00 5.19
1976 2184 1.801913 CGGACGGAAGCTTCTGACG 60.802 63.158 36.22 31.75 37.03 4.35
2001 2209 5.612865 CGAAGCAAGAAGTTGAGTTATCAC 58.387 41.667 0.00 0.00 35.46 3.06
2021 2229 2.292267 CAAGGCATTCAGGTAGCGAAT 58.708 47.619 6.29 6.29 33.33 3.34
2049 2257 1.067425 CAATGCCAAGGACATGTGTGG 60.067 52.381 1.15 9.29 0.00 4.17
2050 2258 0.405198 ATGCCAAGGACATGTGTGGA 59.595 50.000 19.35 8.40 32.54 4.02
2051 2259 0.405198 TGCCAAGGACATGTGTGGAT 59.595 50.000 19.35 0.00 32.54 3.41
2078 2286 7.987750 TTTTCCATGCTGTACAAACATACTA 57.012 32.000 9.96 0.00 34.37 1.82
2080 2288 5.106442 TCCATGCTGTACAAACATACTACG 58.894 41.667 9.96 0.22 34.37 3.51
2122 2587 5.246203 TGCTGGTGTCTGACTAAGTTTATCT 59.754 40.000 9.51 0.00 0.00 1.98
2142 2609 3.766591 TCTTGAACTGACAGGATCTCCTC 59.233 47.826 7.51 0.00 46.65 3.71
2187 2654 1.440938 TTGCACACTACAACGGTGGC 61.441 55.000 4.97 0.00 38.83 5.01
2372 2839 7.801716 TTTCCGATCTTATCCAGGTATTTTG 57.198 36.000 0.00 0.00 0.00 2.44
2387 2854 5.048991 AGGTATTTTGCCTGTACTTTCGTTG 60.049 40.000 0.00 0.00 34.56 4.10
2412 2886 7.667219 TGAAGCCCCTTCATGATTATAATTCTC 59.333 37.037 0.00 0.00 44.27 2.87
2413 2887 6.488715 AGCCCCTTCATGATTATAATTCTCC 58.511 40.000 0.00 0.00 0.00 3.71
2437 2911 5.163513 GGAAATGAAATGTTTGACTCGCAT 58.836 37.500 0.00 0.00 0.00 4.73
2441 2915 4.789174 GAAATGTTTGACTCGCATTTCG 57.211 40.909 11.68 0.00 44.34 3.46
2446 2920 2.163818 TTGACTCGCATTTCGTTCCT 57.836 45.000 0.00 0.00 39.67 3.36
2450 2924 2.218603 ACTCGCATTTCGTTCCTTGTT 58.781 42.857 0.00 0.00 39.67 2.83
2464 2938 5.105473 CGTTCCTTGTTCTATACAGGAAGGA 60.105 44.000 12.18 0.00 43.38 3.36
2500 2974 0.318699 GGGGCGCTGAAAAGTTTGAC 60.319 55.000 7.64 0.00 0.00 3.18
2548 3022 4.020573 ACGTATTCTCACTGGTGGATCAAA 60.021 41.667 0.00 0.00 0.00 2.69
2584 3058 3.064931 GTCGGTTCTAGAACAAACCCAG 58.935 50.000 31.30 15.56 41.59 4.45
2622 3096 5.857517 CAGTACGTCCTCTTTCTCTTTGTAC 59.142 44.000 0.00 0.00 0.00 2.90
2638 3112 1.937223 TGTACGTTCACCACTTGCAAG 59.063 47.619 24.84 24.84 0.00 4.01
2685 3159 7.043961 TGTTGATGTAAGCACATTTGGTAAA 57.956 32.000 0.00 0.00 45.58 2.01
2687 3161 8.147058 TGTTGATGTAAGCACATTTGGTAAATT 58.853 29.630 0.00 0.00 45.58 1.82
2688 3162 8.987890 GTTGATGTAAGCACATTTGGTAAATTT 58.012 29.630 0.00 0.00 45.58 1.82
2689 3163 8.531622 TGATGTAAGCACATTTGGTAAATTTG 57.468 30.769 0.00 0.00 45.58 2.32
2690 3164 8.363390 TGATGTAAGCACATTTGGTAAATTTGA 58.637 29.630 0.00 0.00 45.58 2.69
2691 3165 9.202273 GATGTAAGCACATTTGGTAAATTTGAA 57.798 29.630 0.00 0.00 45.58 2.69
2692 3166 8.359060 TGTAAGCACATTTGGTAAATTTGAAC 57.641 30.769 0.00 0.00 31.78 3.18
2693 3167 8.200792 TGTAAGCACATTTGGTAAATTTGAACT 58.799 29.630 0.00 0.00 31.78 3.01
2694 3168 9.685828 GTAAGCACATTTGGTAAATTTGAACTA 57.314 29.630 0.00 0.00 31.78 2.24
2696 3170 9.606631 AAGCACATTTGGTAAATTTGAACTAAA 57.393 25.926 0.00 3.18 31.78 1.85
2697 3171 9.606631 AGCACATTTGGTAAATTTGAACTAAAA 57.393 25.926 0.00 0.00 31.78 1.52
2698 3172 9.644993 GCACATTTGGTAAATTTGAACTAAAAC 57.355 29.630 0.00 0.00 31.78 2.43
2700 3174 9.892130 ACATTTGGTAAATTTGAACTAAAACCA 57.108 25.926 0.00 0.89 35.77 3.67
2702 3176 7.988904 TTGGTAAATTTGAACTAAAACCACG 57.011 32.000 0.00 0.00 36.75 4.94
2703 3177 5.978322 TGGTAAATTTGAACTAAAACCACGC 59.022 36.000 0.00 0.00 33.74 5.34
2704 3178 5.403166 GGTAAATTTGAACTAAAACCACGCC 59.597 40.000 0.00 0.00 30.42 5.68
2705 3179 4.657436 AATTTGAACTAAAACCACGCCA 57.343 36.364 0.00 0.00 0.00 5.69
2706 3180 3.423996 TTTGAACTAAAACCACGCCAC 57.576 42.857 0.00 0.00 0.00 5.01
2707 3181 2.335316 TGAACTAAAACCACGCCACT 57.665 45.000 0.00 0.00 0.00 4.00
2708 3182 2.645802 TGAACTAAAACCACGCCACTT 58.354 42.857 0.00 0.00 0.00 3.16
2709 3183 3.806380 TGAACTAAAACCACGCCACTTA 58.194 40.909 0.00 0.00 0.00 2.24
2710 3184 4.391155 TGAACTAAAACCACGCCACTTAT 58.609 39.130 0.00 0.00 0.00 1.73
2711 3185 4.822896 TGAACTAAAACCACGCCACTTATT 59.177 37.500 0.00 0.00 0.00 1.40
2712 3186 5.299782 TGAACTAAAACCACGCCACTTATTT 59.700 36.000 0.00 0.00 0.00 1.40
2713 3187 5.777850 ACTAAAACCACGCCACTTATTTT 57.222 34.783 0.00 0.00 0.00 1.82
2714 3188 6.151663 ACTAAAACCACGCCACTTATTTTT 57.848 33.333 0.00 0.00 0.00 1.94
2715 3189 5.980715 ACTAAAACCACGCCACTTATTTTTG 59.019 36.000 0.00 0.00 0.00 2.44
2716 3190 3.378911 AACCACGCCACTTATTTTTGG 57.621 42.857 0.00 0.00 35.81 3.28
2717 3191 2.588620 ACCACGCCACTTATTTTTGGA 58.411 42.857 0.00 0.00 34.46 3.53
2718 3192 2.295070 ACCACGCCACTTATTTTTGGAC 59.705 45.455 0.00 0.00 34.46 4.02
2719 3193 2.580589 CACGCCACTTATTTTTGGACG 58.419 47.619 0.00 0.00 37.97 4.79
2720 3194 1.538075 ACGCCACTTATTTTTGGACGG 59.462 47.619 0.00 0.00 36.99 4.79
2721 3195 1.807742 CGCCACTTATTTTTGGACGGA 59.192 47.619 0.00 0.00 34.46 4.69
2722 3196 2.159572 CGCCACTTATTTTTGGACGGAG 60.160 50.000 0.00 0.00 34.46 4.63
2723 3197 2.163613 GCCACTTATTTTTGGACGGAGG 59.836 50.000 0.00 0.00 34.46 4.30
2724 3198 2.752903 CCACTTATTTTTGGACGGAGGG 59.247 50.000 0.00 0.00 34.46 4.30
2725 3199 3.560453 CCACTTATTTTTGGACGGAGGGA 60.560 47.826 0.00 0.00 34.46 4.20
2726 3200 4.270008 CACTTATTTTTGGACGGAGGGAT 58.730 43.478 0.00 0.00 0.00 3.85
2729 3203 5.884232 ACTTATTTTTGGACGGAGGGATTAC 59.116 40.000 0.00 0.00 0.00 1.89
2731 3205 5.703730 ATTTTTGGACGGAGGGATTACTA 57.296 39.130 0.00 0.00 0.00 1.82
2735 3209 2.242965 TGGACGGAGGGATTACTAGTGA 59.757 50.000 5.39 0.00 0.00 3.41
2744 3218 7.415765 CGGAGGGATTACTAGTGATGATGATAC 60.416 44.444 4.64 0.00 0.00 2.24
2747 3221 9.331466 AGGGATTACTAGTGATGATGATACATT 57.669 33.333 4.64 0.00 0.00 2.71
2797 3324 8.758829 AGTATAAGGTGATTCACAGTTATGACA 58.241 33.333 22.13 9.25 35.86 3.58
2800 3329 5.620206 AGGTGATTCACAGTTATGACACAA 58.380 37.500 18.09 0.00 35.86 3.33
2814 3343 7.936847 AGTTATGACACAACCTAGTTGATCAAA 59.063 33.333 10.35 0.00 45.28 2.69
2820 3349 6.886459 ACACAACCTAGTTGATCAAATAGCAT 59.114 34.615 29.02 19.55 45.28 3.79
2829 3358 7.637229 AGTTGATCAAATAGCATGAAATCTCG 58.363 34.615 10.35 0.00 0.00 4.04
2836 3365 6.604735 AATAGCATGAAATCTCGTAACCAC 57.395 37.500 0.00 0.00 0.00 4.16
2971 3508 6.656270 TGATTAGAACAGACTCATGTTGCATT 59.344 34.615 0.00 0.00 43.32 3.56
2986 3523 4.168760 GTTGCATTCGGATCTTTCTTTGG 58.831 43.478 0.00 0.00 0.00 3.28
3006 3545 3.244735 TGGAAACCAATGTGATTCCGAGA 60.245 43.478 0.00 0.00 43.41 4.04
3010 3549 2.303022 ACCAATGTGATTCCGAGAGTGT 59.697 45.455 0.00 0.00 0.00 3.55
3032 3571 7.239773 AGTGTTGGTATGAGCCCCTATATAATT 59.760 37.037 0.00 0.00 0.00 1.40
3037 3576 5.878406 ATGAGCCCCTATATAATTCCGAG 57.122 43.478 0.00 0.00 0.00 4.63
3042 3581 4.101856 CCCCTATATAATTCCGAGGGTGT 58.898 47.826 11.66 0.00 44.78 4.16
3059 3598 5.329399 AGGGTGTTGTTTGATTTATAGGCA 58.671 37.500 0.00 0.00 0.00 4.75
3233 3772 1.371183 CCTCACTGGCAAAGTCGGA 59.629 57.895 0.00 0.00 36.83 4.55
3277 3816 0.247460 TGCTCACTACGCTCTGCAAT 59.753 50.000 0.00 0.00 0.00 3.56
3295 3834 4.096833 TGCAATGCCAATGTCTATCTGAAC 59.903 41.667 1.53 0.00 0.00 3.18
3310 3849 1.670811 CTGAACAACACACACCTCCAC 59.329 52.381 0.00 0.00 0.00 4.02
3553 4095 3.695606 ACGACATCGGGCAGCTGT 61.696 61.111 16.64 0.00 44.95 4.40
3585 4127 2.446512 GGAGAGGATCCGGCAGATT 58.553 57.895 5.98 0.00 38.67 2.40
3633 4175 1.412710 AGCAAGAAGAAGGTGACGTCA 59.587 47.619 15.76 15.76 41.72 4.35
3814 4356 2.672188 ATACGATTCACTCTCGAGCG 57.328 50.000 7.81 3.64 39.38 5.03
4040 4582 2.774439 AGTTTCCGTTGAACATGTGC 57.226 45.000 0.00 0.00 0.00 4.57
4047 4589 2.033299 CCGTTGAACATGTGCTTCAGTT 59.967 45.455 5.18 0.00 0.00 3.16
4117 4659 0.675083 TGCCTGGCTTTGAACATGTG 59.325 50.000 21.03 0.00 0.00 3.21
4118 4660 0.668401 GCCTGGCTTTGAACATGTGC 60.668 55.000 12.43 0.00 0.00 4.57
4159 4703 6.439375 TGCTAGGGTTTTGTAGTGATCTTCTA 59.561 38.462 0.00 0.00 0.00 2.10
4165 4709 7.331791 GGTTTTGTAGTGATCTTCTAGATGGT 58.668 38.462 5.84 0.00 34.53 3.55
4173 4717 3.579534 TCTTCTAGATGGTAGCTCGGT 57.420 47.619 5.84 0.00 0.00 4.69
4174 4718 3.215151 TCTTCTAGATGGTAGCTCGGTG 58.785 50.000 5.84 0.00 0.00 4.94
4204 4748 3.509575 GGTGCAAACTGGTTATGAATGGA 59.490 43.478 0.00 0.00 0.00 3.41
4207 4751 6.040842 GGTGCAAACTGGTTATGAATGGATAT 59.959 38.462 0.00 0.00 0.00 1.63
4238 4782 6.737254 TTAGTCAGCCATAAAACTTGCTAC 57.263 37.500 0.00 0.00 31.69 3.58
4258 4802 7.518161 TGCTACAAAATGTTTAGAATGTCTCG 58.482 34.615 0.00 0.00 0.00 4.04
4338 4882 6.091305 CGAGATGAGCTCACTTGAATGTTTAA 59.909 38.462 20.97 0.00 44.15 1.52
4356 4900 7.036996 TGTTTAAGCATGTTCTTGTGAATGA 57.963 32.000 0.00 0.00 34.40 2.57
4434 4991 3.772932 AGTTCAAACATGTGTTGCACTG 58.227 40.909 17.85 0.00 38.44 3.66
4475 5032 4.348461 AGGAGACGTCATCAGACCTATAGA 59.652 45.833 19.50 0.00 41.87 1.98
4476 5033 5.013704 AGGAGACGTCATCAGACCTATAGAT 59.986 44.000 19.50 0.00 41.87 1.98
4482 5039 6.369340 ACGTCATCAGACCTATAGATTCTACG 59.631 42.308 15.62 15.62 41.87 3.51
4548 5106 4.588528 ACTCAAAGGTTGTATTGGTGCAAT 59.411 37.500 0.00 0.00 37.80 3.56
4570 5128 8.518151 CAATTAATGCAACACACATTCTGTAA 57.482 30.769 0.00 0.00 38.62 2.41
4571 5129 8.641155 CAATTAATGCAACACACATTCTGTAAG 58.359 33.333 0.00 0.00 38.62 2.34
4572 5130 4.771590 ATGCAACACACATTCTGTAAGG 57.228 40.909 0.00 0.00 0.00 2.69
4573 5131 3.814625 TGCAACACACATTCTGTAAGGA 58.185 40.909 0.00 0.00 0.00 3.36
4574 5132 3.563808 TGCAACACACATTCTGTAAGGAC 59.436 43.478 0.00 0.00 0.00 3.85
4575 5133 3.058224 GCAACACACATTCTGTAAGGACC 60.058 47.826 0.00 0.00 0.00 4.46
4576 5134 3.040147 ACACACATTCTGTAAGGACCG 57.960 47.619 0.00 0.00 0.00 4.79
4577 5135 2.631062 ACACACATTCTGTAAGGACCGA 59.369 45.455 0.00 0.00 0.00 4.69
4578 5136 3.254060 CACACATTCTGTAAGGACCGAG 58.746 50.000 0.00 0.00 0.00 4.63
4579 5137 3.056821 CACACATTCTGTAAGGACCGAGA 60.057 47.826 0.00 0.00 0.00 4.04
4580 5138 3.193691 ACACATTCTGTAAGGACCGAGAG 59.806 47.826 0.00 0.00 0.00 3.20
4581 5139 3.193691 CACATTCTGTAAGGACCGAGAGT 59.806 47.826 0.00 0.00 0.00 3.24
4582 5140 4.398358 CACATTCTGTAAGGACCGAGAGTA 59.602 45.833 0.00 0.00 0.00 2.59
4583 5141 5.067936 CACATTCTGTAAGGACCGAGAGTAT 59.932 44.000 0.00 0.00 0.00 2.12
4584 5142 6.262496 CACATTCTGTAAGGACCGAGAGTATA 59.738 42.308 0.00 0.00 0.00 1.47
4585 5143 7.005296 ACATTCTGTAAGGACCGAGAGTATAT 58.995 38.462 0.00 0.00 0.00 0.86
4586 5144 7.175293 ACATTCTGTAAGGACCGAGAGTATATC 59.825 40.741 0.00 0.00 0.00 1.63
4587 5145 5.236282 TCTGTAAGGACCGAGAGTATATCG 58.764 45.833 0.00 0.00 39.86 2.92
4588 5146 4.965814 TGTAAGGACCGAGAGTATATCGT 58.034 43.478 0.00 0.00 38.50 3.73
4589 5147 4.993584 TGTAAGGACCGAGAGTATATCGTC 59.006 45.833 0.00 0.00 38.50 4.20
4590 5148 3.056588 AGGACCGAGAGTATATCGTCC 57.943 52.381 0.00 0.00 39.01 4.79
4591 5149 2.371179 AGGACCGAGAGTATATCGTCCA 59.629 50.000 13.69 0.00 40.09 4.02
4592 5150 2.743126 GGACCGAGAGTATATCGTCCAG 59.257 54.545 0.00 0.00 38.79 3.86
4593 5151 2.743126 GACCGAGAGTATATCGTCCAGG 59.257 54.545 0.00 0.00 38.50 4.45
4594 5152 2.085320 CCGAGAGTATATCGTCCAGGG 58.915 57.143 0.00 0.00 38.50 4.45
4595 5153 2.085320 CGAGAGTATATCGTCCAGGGG 58.915 57.143 0.00 0.00 35.48 4.79
4596 5154 2.448453 GAGAGTATATCGTCCAGGGGG 58.552 57.143 0.00 0.00 0.00 5.40
4610 5168 2.608759 GGGGGTGGGGATGAATGG 59.391 66.667 0.00 0.00 0.00 3.16
4611 5169 2.012210 GGGGGTGGGGATGAATGGA 61.012 63.158 0.00 0.00 0.00 3.41
4612 5170 1.589399 GGGGGTGGGGATGAATGGAA 61.589 60.000 0.00 0.00 0.00 3.53
4613 5171 0.106015 GGGGTGGGGATGAATGGAAG 60.106 60.000 0.00 0.00 0.00 3.46
4614 5172 0.926293 GGGTGGGGATGAATGGAAGA 59.074 55.000 0.00 0.00 0.00 2.87
4615 5173 1.500736 GGGTGGGGATGAATGGAAGAT 59.499 52.381 0.00 0.00 0.00 2.40
4616 5174 2.091111 GGGTGGGGATGAATGGAAGATT 60.091 50.000 0.00 0.00 0.00 2.40
4622 5468 5.965705 TGGGGATGAATGGAAGATTCAAAAT 59.034 36.000 0.00 0.00 40.84 1.82
4625 5471 7.830697 GGGGATGAATGGAAGATTCAAAATTTT 59.169 33.333 0.00 0.00 40.84 1.82
4652 5498 5.321516 CGAAAGTTTGAATCGTACCCAATC 58.678 41.667 0.00 0.00 0.00 2.67
4656 5502 4.695455 AGTTTGAATCGTACCCAATCACAG 59.305 41.667 0.00 0.00 0.00 3.66
4693 5539 4.645136 TCGGTAGAGTAAATGCAGATGAGT 59.355 41.667 0.00 0.00 0.00 3.41
4752 5598 5.163784 GCTATAATCGTCCGTGCATAGTAGA 60.164 44.000 0.00 0.00 0.00 2.59
4753 5599 3.351020 AATCGTCCGTGCATAGTAGAC 57.649 47.619 0.00 0.00 0.00 2.59
4783 5629 8.131100 GGGTTTGACAATCATGATAGTAATGTG 58.869 37.037 13.38 7.13 0.00 3.21
4784 5630 8.892723 GGTTTGACAATCATGATAGTAATGTGA 58.107 33.333 13.38 3.99 0.00 3.58
4827 5673 5.687780 ACATGAGATGGCAAACAGATATGA 58.312 37.500 0.00 0.00 33.60 2.15
4855 5701 4.442706 ACGCTTGAAAGAGAGTGAGAAAA 58.557 39.130 0.55 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 2.291741 CCCTTCATGAATAGCCTTTCGC 59.708 50.000 8.96 0.00 37.98 4.70
30 31 3.808728 TCCCTTCATGAATAGCCTTTCG 58.191 45.455 8.96 0.00 0.00 3.46
64 65 2.557924 CCACAAAAGCACAATGCCTCTA 59.442 45.455 0.00 0.00 46.52 2.43
65 66 1.342174 CCACAAAAGCACAATGCCTCT 59.658 47.619 0.00 0.00 46.52 3.69
67 68 1.069049 GTCCACAAAAGCACAATGCCT 59.931 47.619 0.00 0.00 46.52 4.75
94 97 5.880332 TCTGCATTATTTGGACTTCCTGTAC 59.120 40.000 0.00 0.00 36.82 2.90
103 106 5.060940 GCGTTTTCTTCTGCATTATTTGGAC 59.939 40.000 0.00 0.00 0.00 4.02
114 117 2.094762 TCCTAGGCGTTTTCTTCTGC 57.905 50.000 2.96 0.00 0.00 4.26
126 129 2.027100 ACCTGCAGTAGTTTTCCTAGGC 60.027 50.000 13.81 0.00 0.00 3.93
134 137 1.274447 GTACCGGACCTGCAGTAGTTT 59.726 52.381 9.46 0.00 0.00 2.66
156 159 2.267426 CGTTGAGATTCCACATGCGTA 58.733 47.619 0.00 0.00 0.00 4.42
157 160 1.078709 CGTTGAGATTCCACATGCGT 58.921 50.000 0.00 0.00 0.00 5.24
161 164 1.548719 TCGACCGTTGAGATTCCACAT 59.451 47.619 0.00 0.00 0.00 3.21
178 181 3.379445 GTCGGGTGGAGCCTTCGA 61.379 66.667 0.00 0.00 37.43 3.71
193 196 4.447342 CATGGCCCTGGGGTGGTC 62.447 72.222 16.03 0.00 37.65 4.02
196 199 2.512986 TTTAGCATGGCCCTGGGGTG 62.513 60.000 16.03 0.00 37.65 4.61
197 200 1.809939 TTTTAGCATGGCCCTGGGGT 61.810 55.000 16.03 0.21 37.65 4.95
198 201 0.398948 ATTTTAGCATGGCCCTGGGG 60.399 55.000 16.03 4.75 38.57 4.96
199 202 1.413812 GAATTTTAGCATGGCCCTGGG 59.586 52.381 8.86 8.86 0.00 4.45
200 203 1.067516 CGAATTTTAGCATGGCCCTGG 59.932 52.381 10.28 0.00 0.00 4.45
201 204 1.536709 GCGAATTTTAGCATGGCCCTG 60.537 52.381 0.00 0.46 0.00 4.45
202 205 0.746659 GCGAATTTTAGCATGGCCCT 59.253 50.000 0.00 0.00 0.00 5.19
220 223 1.060937 CTAACAGCCGCATCAACGC 59.939 57.895 0.00 0.00 0.00 4.84
278 281 4.028852 TCGTCGATAGTTTCCATCACTG 57.971 45.455 0.00 0.00 37.40 3.66
284 287 2.753452 AGAGCTTCGTCGATAGTTTCCA 59.247 45.455 0.00 0.00 37.40 3.53
295 298 4.379339 ACTATCAAGGAAGAGCTTCGTC 57.621 45.455 5.97 0.00 40.37 4.20
297 300 4.098044 TGGTACTATCAAGGAAGAGCTTCG 59.902 45.833 4.32 0.00 40.37 3.79
299 302 4.407296 CCTGGTACTATCAAGGAAGAGCTT 59.593 45.833 0.00 0.00 0.00 3.74
309 312 5.279809 GGTCACAAACTCCTGGTACTATCAA 60.280 44.000 0.00 0.00 0.00 2.57
387 552 7.664318 TGCTATGACAAGATTGCATAGATGAAT 59.336 33.333 24.90 0.00 41.91 2.57
397 562 3.059325 GTCGGATGCTATGACAAGATTGC 60.059 47.826 0.00 0.00 32.91 3.56
476 641 3.743521 TCTGGTTTTCATCTCAGTGTGG 58.256 45.455 0.00 0.00 0.00 4.17
478 643 3.181451 TGCTCTGGTTTTCATCTCAGTGT 60.181 43.478 0.00 0.00 0.00 3.55
488 653 1.166531 ACACCGCTGCTCTGGTTTTC 61.167 55.000 0.00 0.00 35.96 2.29
530 695 1.964373 AACATTGACCGCACGACCC 60.964 57.895 0.00 0.00 0.00 4.46
716 882 2.669670 CGAACGTTCACTCTGCATCTCT 60.670 50.000 26.71 0.00 0.00 3.10
720 886 0.319900 AGCGAACGTTCACTCTGCAT 60.320 50.000 26.71 9.42 0.00 3.96
722 888 1.630148 ATAGCGAACGTTCACTCTGC 58.370 50.000 26.71 20.37 0.00 4.26
723 889 4.647291 AAAATAGCGAACGTTCACTCTG 57.353 40.909 26.71 11.88 0.00 3.35
724 890 5.924825 AGTAAAAATAGCGAACGTTCACTCT 59.075 36.000 26.71 20.52 0.00 3.24
731 897 2.925563 CCGGAGTAAAAATAGCGAACGT 59.074 45.455 0.00 0.00 0.00 3.99
776 944 4.730949 TTATTTCTGGTCCGACTACAGG 57.269 45.455 0.00 0.00 33.19 4.00
1045 1238 1.652167 GCTGGTTGGCTAGCTCTTGC 61.652 60.000 15.72 8.26 44.51 4.01
1429 1637 4.630069 ACGAGGACAAACATATTACAGCAC 59.370 41.667 0.00 0.00 0.00 4.40
1435 1643 7.837863 AGAAAGAGACGAGGACAAACATATTA 58.162 34.615 0.00 0.00 0.00 0.98
1661 1869 4.900154 GTGCGAAGGACCTCTCTG 57.100 61.111 0.00 0.00 45.47 3.35
1689 1897 4.603946 GGCATACCGAGACCCCGC 62.604 72.222 0.00 0.00 0.00 6.13
1922 2130 1.821332 GCCCAGAGAATTCCGGCAG 60.821 63.158 15.07 0.00 38.52 4.85
1976 2184 1.230324 ACTCAACTTCTTGCTTCGCC 58.770 50.000 0.00 0.00 0.00 5.54
2001 2209 1.737838 TTCGCTACCTGAATGCCTTG 58.262 50.000 0.00 0.00 0.00 3.61
2021 2229 4.359434 TGTCCTTGGCATTGTGTTAGTA 57.641 40.909 0.00 0.00 0.00 1.82
2057 2265 5.105675 TCGTAGTATGTTTGTACAGCATGGA 60.106 40.000 19.10 9.62 43.62 3.41
2058 2266 5.106442 TCGTAGTATGTTTGTACAGCATGG 58.894 41.667 19.10 8.15 43.62 3.66
2078 2286 3.119849 GCAACAGGACAGCATTATTTCGT 60.120 43.478 0.00 0.00 0.00 3.85
2080 2288 4.418392 CAGCAACAGGACAGCATTATTTC 58.582 43.478 0.00 0.00 0.00 2.17
2155 2622 1.067060 GTGTGCAACCTCCTTTTGGAC 59.933 52.381 0.00 0.29 43.49 4.02
2156 2623 1.064017 AGTGTGCAACCTCCTTTTGGA 60.064 47.619 0.00 0.00 41.36 3.53
2219 2686 2.469274 AGTGTTCTCATCAGTGCCAG 57.531 50.000 0.00 0.00 0.00 4.85
2387 2854 7.121907 GGAGAATTATAATCATGAAGGGGCTTC 59.878 40.741 0.00 0.12 40.54 3.86
2412 2886 4.158384 CGAGTCAAACATTTCATTTCCGG 58.842 43.478 0.00 0.00 0.00 5.14
2413 2887 3.603770 GCGAGTCAAACATTTCATTTCCG 59.396 43.478 0.00 0.00 0.00 4.30
2437 2911 6.349243 TCCTGTATAGAACAAGGAACGAAA 57.651 37.500 0.00 0.00 37.74 3.46
2441 2915 6.295719 TCCTTCCTGTATAGAACAAGGAAC 57.704 41.667 10.27 0.00 38.92 3.62
2446 2920 7.338710 CCTGAATTCCTTCCTGTATAGAACAA 58.661 38.462 2.27 0.00 37.74 2.83
2450 2924 4.348168 GCCCTGAATTCCTTCCTGTATAGA 59.652 45.833 2.27 0.00 0.00 1.98
2464 2938 2.158310 GCCCCTTATAAGGCCCTGAATT 60.158 50.000 24.05 0.00 45.10 2.17
2500 2974 1.905637 ACCTAAAACCCTTTGAGGCG 58.094 50.000 0.00 0.00 32.73 5.52
2548 3022 0.796312 CCGACTTGCGTATTGCTTGT 59.204 50.000 0.00 0.00 46.63 3.16
2584 3058 2.864343 ACGTACTGGCAAGCGAATTATC 59.136 45.455 11.04 0.00 0.00 1.75
2622 3096 3.354089 AATTCTTGCAAGTGGTGAACG 57.646 42.857 25.19 0.00 0.00 3.95
2685 3159 3.634910 AGTGGCGTGGTTTTAGTTCAAAT 59.365 39.130 0.00 0.00 0.00 2.32
2687 3161 2.645802 AGTGGCGTGGTTTTAGTTCAA 58.354 42.857 0.00 0.00 0.00 2.69
2688 3162 2.335316 AGTGGCGTGGTTTTAGTTCA 57.665 45.000 0.00 0.00 0.00 3.18
2689 3163 5.366829 AATAAGTGGCGTGGTTTTAGTTC 57.633 39.130 0.00 0.00 0.00 3.01
2690 3164 5.777850 AAATAAGTGGCGTGGTTTTAGTT 57.222 34.783 0.00 0.00 0.00 2.24
2691 3165 5.777850 AAAATAAGTGGCGTGGTTTTAGT 57.222 34.783 0.00 0.00 0.00 2.24
2692 3166 5.404066 CCAAAAATAAGTGGCGTGGTTTTAG 59.596 40.000 0.00 0.00 0.00 1.85
2693 3167 5.068723 TCCAAAAATAAGTGGCGTGGTTTTA 59.931 36.000 0.00 0.00 34.68 1.52
2694 3168 4.123506 CCAAAAATAAGTGGCGTGGTTTT 58.876 39.130 0.00 0.00 0.00 2.43
2695 3169 3.385111 TCCAAAAATAAGTGGCGTGGTTT 59.615 39.130 0.00 0.00 34.68 3.27
2696 3170 2.959707 TCCAAAAATAAGTGGCGTGGTT 59.040 40.909 0.00 0.00 34.68 3.67
2697 3171 2.295070 GTCCAAAAATAAGTGGCGTGGT 59.705 45.455 0.00 0.00 34.68 4.16
2698 3172 2.667171 CGTCCAAAAATAAGTGGCGTGG 60.667 50.000 0.00 0.00 34.68 4.94
2699 3173 2.580589 CGTCCAAAAATAAGTGGCGTG 58.419 47.619 0.00 0.00 34.68 5.34
2700 3174 1.538075 CCGTCCAAAAATAAGTGGCGT 59.462 47.619 0.00 0.00 34.63 5.68
2701 3175 1.807742 TCCGTCCAAAAATAAGTGGCG 59.192 47.619 0.00 0.00 34.68 5.69
2702 3176 2.163613 CCTCCGTCCAAAAATAAGTGGC 59.836 50.000 0.00 0.00 34.68 5.01
2703 3177 2.752903 CCCTCCGTCCAAAAATAAGTGG 59.247 50.000 0.00 0.00 36.13 4.00
2704 3178 3.681593 TCCCTCCGTCCAAAAATAAGTG 58.318 45.455 0.00 0.00 0.00 3.16
2705 3179 4.586306 ATCCCTCCGTCCAAAAATAAGT 57.414 40.909 0.00 0.00 0.00 2.24
2706 3180 6.120220 AGTAATCCCTCCGTCCAAAAATAAG 58.880 40.000 0.00 0.00 0.00 1.73
2707 3181 6.069705 AGTAATCCCTCCGTCCAAAAATAA 57.930 37.500 0.00 0.00 0.00 1.40
2708 3182 5.703730 AGTAATCCCTCCGTCCAAAAATA 57.296 39.130 0.00 0.00 0.00 1.40
2709 3183 4.586306 AGTAATCCCTCCGTCCAAAAAT 57.414 40.909 0.00 0.00 0.00 1.82
2710 3184 4.533311 ACTAGTAATCCCTCCGTCCAAAAA 59.467 41.667 0.00 0.00 0.00 1.94
2711 3185 4.081309 CACTAGTAATCCCTCCGTCCAAAA 60.081 45.833 0.00 0.00 0.00 2.44
2712 3186 3.449737 CACTAGTAATCCCTCCGTCCAAA 59.550 47.826 0.00 0.00 0.00 3.28
2713 3187 3.028850 CACTAGTAATCCCTCCGTCCAA 58.971 50.000 0.00 0.00 0.00 3.53
2714 3188 2.242965 TCACTAGTAATCCCTCCGTCCA 59.757 50.000 0.00 0.00 0.00 4.02
2715 3189 2.941480 TCACTAGTAATCCCTCCGTCC 58.059 52.381 0.00 0.00 0.00 4.79
2716 3190 4.142790 TCATCACTAGTAATCCCTCCGTC 58.857 47.826 0.00 0.00 0.00 4.79
2717 3191 4.180377 TCATCACTAGTAATCCCTCCGT 57.820 45.455 0.00 0.00 0.00 4.69
2718 3192 4.767409 TCATCATCACTAGTAATCCCTCCG 59.233 45.833 0.00 0.00 0.00 4.63
2719 3193 6.865834 ATCATCATCACTAGTAATCCCTCC 57.134 41.667 0.00 0.00 0.00 4.30
2720 3194 8.354711 TGTATCATCATCACTAGTAATCCCTC 57.645 38.462 0.00 0.00 0.00 4.30
2721 3195 8.907829 ATGTATCATCATCACTAGTAATCCCT 57.092 34.615 0.00 0.00 0.00 4.20
2722 3196 9.593134 GAATGTATCATCATCACTAGTAATCCC 57.407 37.037 0.00 0.00 0.00 3.85
2723 3197 9.593134 GGAATGTATCATCATCACTAGTAATCC 57.407 37.037 0.00 0.00 0.00 3.01
2747 3221 9.690913 ACTCTGAAATTTCTGAATCATATTGGA 57.309 29.630 23.05 2.99 35.23 3.53
2768 3282 9.254133 CATAACTGTGAATCACCTTATACTCTG 57.746 37.037 11.24 0.00 32.73 3.35
2797 3324 7.112122 TCATGCTATTTGATCAACTAGGTTGT 58.888 34.615 25.62 2.42 43.23 3.32
2800 3329 8.757982 ATTTCATGCTATTTGATCAACTAGGT 57.242 30.769 25.62 7.88 0.00 3.08
2814 3343 5.918608 AGTGGTTACGAGATTTCATGCTAT 58.081 37.500 0.00 0.00 0.00 2.97
2878 3407 7.255520 CGGTTACTAGTTGCATAATCTCTACCT 60.256 40.741 0.00 0.00 0.00 3.08
2885 3414 4.952460 TCCCGGTTACTAGTTGCATAATC 58.048 43.478 0.00 0.00 0.00 1.75
2886 3415 5.121105 GTTCCCGGTTACTAGTTGCATAAT 58.879 41.667 0.00 0.00 0.00 1.28
2892 3421 3.332034 CTTGGTTCCCGGTTACTAGTTG 58.668 50.000 0.00 0.00 0.00 3.16
2895 3431 1.738030 CGCTTGGTTCCCGGTTACTAG 60.738 57.143 0.00 1.68 0.00 2.57
2913 3449 6.327177 TCTCATAGTTATCGTTTTGTTCGC 57.673 37.500 0.00 0.00 0.00 4.70
2961 3498 4.627611 AGAAAGATCCGAATGCAACATG 57.372 40.909 0.00 0.00 0.00 3.21
2971 3508 4.093472 TGGTTTCCAAAGAAAGATCCGA 57.907 40.909 0.00 0.00 42.60 4.55
2986 3523 4.003648 ACTCTCGGAATCACATTGGTTTC 58.996 43.478 0.00 0.00 0.00 2.78
3006 3545 2.263895 TAGGGGCTCATACCAACACT 57.736 50.000 0.00 0.00 0.00 3.55
3010 3549 6.126883 CGGAATTATATAGGGGCTCATACCAA 60.127 42.308 0.00 0.00 0.00 3.67
3032 3571 2.649531 AATCAAACAACACCCTCGGA 57.350 45.000 0.00 0.00 0.00 4.55
3037 3576 5.047660 TGTGCCTATAAATCAAACAACACCC 60.048 40.000 0.00 0.00 0.00 4.61
3042 3581 6.629128 CCATGTGTGCCTATAAATCAAACAA 58.371 36.000 0.00 0.00 32.38 2.83
3059 3598 0.823356 AACTTGCTTCCGCCATGTGT 60.823 50.000 0.00 0.00 34.43 3.72
3083 3622 0.454452 GTCGCCGGCATTCTTTCAAC 60.454 55.000 28.98 5.75 0.00 3.18
3084 3623 1.873165 GTCGCCGGCATTCTTTCAA 59.127 52.632 28.98 0.00 0.00 2.69
3110 3649 1.069765 TAGCCTATTCAGCTGCCGC 59.930 57.895 9.47 5.55 41.71 6.53
3233 3772 0.459585 GGTATGTCACGTCCGTGCAT 60.460 55.000 22.97 22.97 45.04 3.96
3277 3816 4.455533 GTGTTGTTCAGATAGACATTGGCA 59.544 41.667 0.00 0.00 0.00 4.92
3295 3834 1.691196 ATTGGTGGAGGTGTGTGTTG 58.309 50.000 0.00 0.00 0.00 3.33
3310 3849 1.745087 AGCCACAAGTGCGATTATTGG 59.255 47.619 0.00 0.00 0.00 3.16
3553 4095 2.935481 CTCCCTGCTCACCCCCAA 60.935 66.667 0.00 0.00 0.00 4.12
3585 4127 4.161295 CGGAAGGCGGCCATCTCA 62.161 66.667 23.09 0.00 0.00 3.27
3633 4175 1.187087 GCTCCAGGTAGTGCTGTAGT 58.813 55.000 0.00 0.00 0.00 2.73
3748 4290 1.539065 CGGCAGGCAATCCAGTACTAG 60.539 57.143 0.00 0.00 33.74 2.57
3974 4516 7.521669 AGATAATGGGAAGTTAGCTTGCTAAT 58.478 34.615 16.65 3.63 41.90 1.73
4052 4594 1.131315 GCCTGCGCCTTTTCTCTAAAG 59.869 52.381 4.18 0.00 42.41 1.85
4055 4597 4.617875 GCCTGCGCCTTTTCTCTA 57.382 55.556 4.18 0.00 0.00 2.43
4079 4621 2.362077 GCAAGGTTTGAGCCTTTTCTCA 59.638 45.455 0.00 0.00 45.91 3.27
4081 4623 1.688735 GGCAAGGTTTGAGCCTTTTCT 59.311 47.619 0.00 0.00 45.91 2.52
4159 4703 0.818296 GTCACACCGAGCTACCATCT 59.182 55.000 0.00 0.00 0.00 2.90
4165 4709 2.566529 CGCAGTCACACCGAGCTA 59.433 61.111 0.00 0.00 0.00 3.32
4173 4717 1.451207 AGTTTGCACCGCAGTCACA 60.451 52.632 0.00 0.00 40.61 3.58
4174 4718 1.009675 CAGTTTGCACCGCAGTCAC 60.010 57.895 0.00 0.00 40.61 3.67
4207 4751 8.189119 AGTTTTATGGCTGACTAATTTTTCCA 57.811 30.769 0.00 0.00 0.00 3.53
4221 4765 6.758254 ACATTTTGTAGCAAGTTTTATGGCT 58.242 32.000 0.00 0.00 40.26 4.75
4338 4882 3.504906 CCAGTCATTCACAAGAACATGCT 59.495 43.478 0.00 0.00 36.39 3.79
4356 4900 5.127682 GGATAAATGTTTGAAGGCATCCAGT 59.872 40.000 0.00 0.00 32.65 4.00
4434 4991 9.012161 ACGTCTCCTCCTAAAGAATATATACAC 57.988 37.037 0.00 0.00 0.00 2.90
4475 5032 4.122776 GGATGCATCTGTGAACGTAGAAT 58.877 43.478 25.28 0.00 0.00 2.40
4476 5033 3.056179 TGGATGCATCTGTGAACGTAGAA 60.056 43.478 25.28 0.00 0.00 2.10
4482 5039 4.510038 ACTTTTGGATGCATCTGTGAAC 57.490 40.909 25.28 8.88 0.00 3.18
4561 5119 5.776173 ATACTCTCGGTCCTTACAGAATG 57.224 43.478 0.00 0.00 46.00 2.67
4562 5120 6.372103 CGATATACTCTCGGTCCTTACAGAAT 59.628 42.308 0.00 0.00 32.58 2.40
4563 5121 5.699915 CGATATACTCTCGGTCCTTACAGAA 59.300 44.000 0.00 0.00 32.58 3.02
4564 5122 5.221601 ACGATATACTCTCGGTCCTTACAGA 60.222 44.000 0.00 0.00 40.37 3.41
4565 5123 4.996122 ACGATATACTCTCGGTCCTTACAG 59.004 45.833 0.00 0.00 40.37 2.74
4566 5124 4.965814 ACGATATACTCTCGGTCCTTACA 58.034 43.478 0.00 0.00 40.37 2.41
4567 5125 4.391523 GGACGATATACTCTCGGTCCTTAC 59.608 50.000 0.00 0.00 40.37 2.34
4568 5126 4.040829 TGGACGATATACTCTCGGTCCTTA 59.959 45.833 9.18 0.00 40.37 2.69
4569 5127 3.181447 TGGACGATATACTCTCGGTCCTT 60.181 47.826 9.18 0.00 40.37 3.36
4570 5128 2.371179 TGGACGATATACTCTCGGTCCT 59.629 50.000 9.18 0.00 40.37 3.85
4571 5129 2.743126 CTGGACGATATACTCTCGGTCC 59.257 54.545 1.21 1.21 40.37 4.46
4572 5130 2.743126 CCTGGACGATATACTCTCGGTC 59.257 54.545 0.00 0.00 40.37 4.79
4573 5131 2.552591 CCCTGGACGATATACTCTCGGT 60.553 54.545 0.00 0.00 40.37 4.69
4574 5132 2.085320 CCCTGGACGATATACTCTCGG 58.915 57.143 0.00 0.00 40.37 4.63
4575 5133 2.085320 CCCCTGGACGATATACTCTCG 58.915 57.143 0.00 0.00 41.77 4.04
4576 5134 2.448453 CCCCCTGGACGATATACTCTC 58.552 57.143 0.00 0.00 0.00 3.20
4577 5135 2.606751 CCCCCTGGACGATATACTCT 57.393 55.000 0.00 0.00 0.00 3.24
4593 5151 1.589399 TTCCATTCATCCCCACCCCC 61.589 60.000 0.00 0.00 0.00 5.40
4594 5152 0.106015 CTTCCATTCATCCCCACCCC 60.106 60.000 0.00 0.00 0.00 4.95
4595 5153 0.926293 TCTTCCATTCATCCCCACCC 59.074 55.000 0.00 0.00 0.00 4.61
4596 5154 3.225940 GAATCTTCCATTCATCCCCACC 58.774 50.000 0.00 0.00 0.00 4.61
4597 5155 3.902218 TGAATCTTCCATTCATCCCCAC 58.098 45.455 0.00 0.00 33.55 4.61
4598 5156 4.606476 TTGAATCTTCCATTCATCCCCA 57.394 40.909 0.00 0.00 37.79 4.96
4599 5157 5.937975 TTTTGAATCTTCCATTCATCCCC 57.062 39.130 0.00 0.00 37.79 4.81
4600 5158 8.797350 AAAATTTTGAATCTTCCATTCATCCC 57.203 30.769 1.75 0.00 37.79 3.85
4625 5471 4.529446 GGTACGATTCAAACTTTCGCAAA 58.471 39.130 0.00 0.00 36.37 3.68
4631 5477 5.533154 TGTGATTGGGTACGATTCAAACTTT 59.467 36.000 0.00 0.00 29.16 2.66
4637 5483 2.027653 TGCTGTGATTGGGTACGATTCA 60.028 45.455 0.00 0.00 0.00 2.57
4641 5487 0.391130 GCTGCTGTGATTGGGTACGA 60.391 55.000 0.00 0.00 0.00 3.43
4644 5490 1.078497 CCGCTGCTGTGATTGGGTA 60.078 57.895 5.63 0.00 0.00 3.69
4652 5498 1.061131 CGAACTTATTCCGCTGCTGTG 59.939 52.381 0.00 0.00 0.00 3.66
4656 5502 1.859080 CTACCGAACTTATTCCGCTGC 59.141 52.381 0.00 0.00 0.00 5.25
4702 5548 9.903682 CATCTTTCTTCAAAAGATTTGCTTAGA 57.096 29.630 9.67 0.00 42.52 2.10
4716 5562 6.420903 CGGACGATTATAGCATCTTTCTTCAA 59.579 38.462 0.00 0.00 0.00 2.69
4717 5563 5.920840 CGGACGATTATAGCATCTTTCTTCA 59.079 40.000 0.00 0.00 0.00 3.02
4722 5568 3.741344 GCACGGACGATTATAGCATCTTT 59.259 43.478 0.00 0.00 0.00 2.52
4752 5598 1.885887 CATGATTGTCAAACCCGTGGT 59.114 47.619 0.00 0.00 37.65 4.16
4753 5599 2.158559 TCATGATTGTCAAACCCGTGG 58.841 47.619 0.00 0.00 0.00 4.94
4757 5603 8.131100 CACATTACTATCATGATTGTCAAACCC 58.869 37.037 23.24 0.00 0.00 4.11
4795 5641 7.112122 TGTTTGCCATCTCATGTTACTCTATT 58.888 34.615 0.00 0.00 0.00 1.73
4827 5673 5.357257 TCACTCTCTTTCAAGCGTTTAGTT 58.643 37.500 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.