Multiple sequence alignment - TraesCS6D01G117400

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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 TraesCS6D01G117400 chr6D 100.000 4136 0 0 1 4136 83161432 83157297 0.000000e+00 7638.0
1 TraesCS6D01G117400 chr6D 83.748 2412 352 31 940 3325 83046957 83044560 0.000000e+00 2246.0
2 TraesCS6D01G117400 chr6D 84.573 1828 269 11 971 2793 83525237 83527056 0.000000e+00 1801.0
3 TraesCS6D01G117400 chr6D 78.000 200 28 11 126 315 83048191 83047998 1.220000e-20 111.0
4 TraesCS6D01G117400 chr6A 95.221 3264 116 16 126 3369 100229768 100226525 0.000000e+00 5127.0
5 TraesCS6D01G117400 chr6A 85.250 2644 345 27 863 3478 100738092 100740718 0.000000e+00 2680.0
6 TraesCS6D01G117400 chr6A 85.629 2498 316 17 1035 3509 100797548 100800025 0.000000e+00 2584.0
7 TraesCS6D01G117400 chr6A 84.597 2571 360 17 971 3509 100755377 100757943 0.000000e+00 2521.0
8 TraesCS6D01G117400 chr6A 85.505 2118 291 13 1048 3156 100760994 100763104 0.000000e+00 2196.0
9 TraesCS6D01G117400 chr6A 90.671 343 26 6 3346 3687 100226459 100226122 6.300000e-123 451.0
10 TraesCS6D01G117400 chr6A 92.913 127 8 1 1 126 100229932 100229806 2.540000e-42 183.0
11 TraesCS6D01G117400 chr6A 73.114 517 74 44 126 616 100358200 100357723 1.560000e-24 124.0
12 TraesCS6D01G117400 chr6A 79.747 158 22 9 126 273 100074196 100074039 5.650000e-19 106.0
13 TraesCS6D01G117400 chr6A 94.444 54 3 0 10 63 100754245 100754298 2.650000e-12 84.2
14 TraesCS6D01G117400 chr6B 96.082 2910 100 10 463 3365 158163584 158160682 0.000000e+00 4730.0
15 TraesCS6D01G117400 chr6B 85.415 2674 344 30 822 3478 159377793 159380437 0.000000e+00 2736.0
16 TraesCS6D01G117400 chr6B 84.933 2230 319 16 1034 3257 159395982 159398200 0.000000e+00 2241.0
17 TraesCS6D01G117400 chr6B 85.694 2118 280 20 1055 3159 158149775 158147668 0.000000e+00 2211.0
18 TraesCS6D01G117400 chr6B 95.467 353 10 1 126 478 158165181 158164835 3.610000e-155 558.0
19 TraesCS6D01G117400 chr6B 86.567 335 16 5 3354 3687 158153210 158152904 3.960000e-90 342.0
20 TraesCS6D01G117400 chr6B 82.792 308 34 16 3391 3687 159398357 159398656 1.480000e-64 257.0
21 TraesCS6D01G117400 chr6B 96.512 86 2 1 22 106 158165335 158165250 1.550000e-29 141.0
22 TraesCS6D01G117400 chr6B 90.323 62 4 1 126 187 159394422 159394481 3.430000e-11 80.5
23 TraesCS6D01G117400 chr3B 86.478 673 43 21 3039 3687 680860905 680860257 0.000000e+00 695.0
24 TraesCS6D01G117400 chr3B 95.272 423 19 1 3689 4110 27246645 27246223 0.000000e+00 669.0
25 TraesCS6D01G117400 chr1B 95.023 442 21 1 3696 4136 66926403 66925962 0.000000e+00 693.0
26 TraesCS6D01G117400 chr1A 94.843 446 20 3 3689 4133 548464439 548463996 0.000000e+00 693.0
27 TraesCS6D01G117400 chr3D 94.209 449 25 1 3689 4136 452585615 452586063 0.000000e+00 684.0
28 TraesCS6D01G117400 chr5D 94.209 449 23 3 3689 4136 520786673 520787119 0.000000e+00 682.0
29 TraesCS6D01G117400 chr5D 100.000 111 0 0 229 339 455825408 455825298 5.420000e-49 206.0
30 TraesCS6D01G117400 chr7B 93.722 446 27 1 3689 4133 648109955 648110400 0.000000e+00 667.0
31 TraesCS6D01G117400 chr7B 92.955 440 28 3 3689 4126 592544529 592544091 4.510000e-179 638.0
32 TraesCS6D01G117400 chr1D 93.556 450 25 4 3689 4136 482003569 482003122 0.000000e+00 667.0
33 TraesCS6D01G117400 chr3A 92.152 446 31 4 3689 4133 474564612 474565054 9.760000e-176 627.0
34 TraesCS6D01G117400 chr4A 98.485 66 1 0 3451 3516 624286076 624286011 2.610000e-22 117.0


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 TraesCS6D01G117400 chr6D 83157297 83161432 4135 True 7638.000000 7638 100.000000 1 4136 1 chr6D.!!$R1 4135
1 TraesCS6D01G117400 chr6D 83525237 83527056 1819 False 1801.000000 1801 84.573000 971 2793 1 chr6D.!!$F1 1822
2 TraesCS6D01G117400 chr6D 83044560 83048191 3631 True 1178.500000 2246 80.874000 126 3325 2 chr6D.!!$R2 3199
3 TraesCS6D01G117400 chr6A 100738092 100740718 2626 False 2680.000000 2680 85.250000 863 3478 1 chr6A.!!$F1 2615
4 TraesCS6D01G117400 chr6A 100797548 100800025 2477 False 2584.000000 2584 85.629000 1035 3509 1 chr6A.!!$F2 2474
5 TraesCS6D01G117400 chr6A 100226122 100229932 3810 True 1920.333333 5127 92.935000 1 3687 3 chr6A.!!$R3 3686
6 TraesCS6D01G117400 chr6A 100754245 100763104 8859 False 1600.400000 2521 88.182000 10 3509 3 chr6A.!!$F3 3499
7 TraesCS6D01G117400 chr6B 159377793 159380437 2644 False 2736.000000 2736 85.415000 822 3478 1 chr6B.!!$F1 2656
8 TraesCS6D01G117400 chr6B 158160682 158165335 4653 True 1809.666667 4730 96.020333 22 3365 3 chr6B.!!$R2 3343
9 TraesCS6D01G117400 chr6B 158147668 158153210 5542 True 1276.500000 2211 86.130500 1055 3687 2 chr6B.!!$R1 2632
10 TraesCS6D01G117400 chr6B 159394422 159398656 4234 False 859.500000 2241 86.016000 126 3687 3 chr6B.!!$F2 3561
11 TraesCS6D01G117400 chr3B 680860257 680860905 648 True 695.000000 695 86.478000 3039 3687 1 chr3B.!!$R2 648

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
271 739 1.079197 TCGCACAGCATACACCCTG 60.079 57.895 0.00 0.0 35.26 4.45 F
273 741 1.675310 GCACAGCATACACCCTGCA 60.675 57.895 0.00 0.0 42.15 4.41 F
1719 4151 1.604604 ACAACAACCTCAATGGGACG 58.395 50.000 0.00 0.0 41.11 4.79 F
1794 4226 0.103208 ATCGGTTAGAAGGAGCGCTG 59.897 55.000 18.48 0.0 37.86 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1233 3665 1.800805 CCAGCGAAACATCAGTGACT 58.199 50.000 0.0 0.0 0.00 3.41 R
1794 4226 3.018856 TGTGAGGTTGATGATGCCATTC 58.981 45.455 0.0 0.0 32.09 2.67 R
2884 5318 1.694696 AGGGCCTTCGAGGTCATTATC 59.305 52.381 0.0 0.0 43.30 1.75 R
3770 6573 0.402504 TAAACAGCCGACCACCCATT 59.597 50.000 0.0 0.0 0.00 3.16 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
26 27 3.906720 TGGTAAAGACTAGATGCCACC 57.093 47.619 0.00 0.00 0.00 4.61
121 150 2.674796 AATAGTTCCGACCTGCTCAC 57.325 50.000 0.00 0.00 0.00 3.51
124 191 1.733399 GTTCCGACCTGCTCACGTC 60.733 63.158 0.00 0.00 0.00 4.34
271 739 1.079197 TCGCACAGCATACACCCTG 60.079 57.895 0.00 0.00 35.26 4.45
272 740 2.753966 CGCACAGCATACACCCTGC 61.754 63.158 0.00 0.00 39.97 4.85
273 741 1.675310 GCACAGCATACACCCTGCA 60.675 57.895 0.00 0.00 42.15 4.41
415 899 3.187700 GGCCACTTACTGATCGTAGTTG 58.812 50.000 0.00 0.00 32.19 3.16
482 2232 9.378551 CACTTACTGCTGATAGGTATTTTAACA 57.621 33.333 0.00 0.00 0.00 2.41
627 2379 3.181483 CGTCCATCACAGATCACATCTCA 60.181 47.826 0.00 0.00 37.58 3.27
712 2544 4.038162 GTCAGTACCTCAGGGCATAGTAAG 59.962 50.000 0.00 0.00 35.63 2.34
861 2726 2.526304 TCACTGCTCACTACAACCAC 57.474 50.000 0.00 0.00 0.00 4.16
1233 3665 4.037222 TCACCTGCAACCAAGATAGGATA 58.963 43.478 0.00 0.00 32.86 2.59
1719 4151 1.604604 ACAACAACCTCAATGGGACG 58.395 50.000 0.00 0.00 41.11 4.79
1794 4226 0.103208 ATCGGTTAGAAGGAGCGCTG 59.897 55.000 18.48 0.00 37.86 5.18
2133 4566 5.936956 GCTGACTGCATTAAGGCTATCTTAT 59.063 40.000 13.92 0.00 42.31 1.73
2225 4658 8.607713 TGTTAACCTCTCCCTTACAAATATCAA 58.392 33.333 2.48 0.00 0.00 2.57
2264 4697 1.270907 GAGAGTTCCAGGAGCCTCAA 58.729 55.000 16.69 0.00 0.00 3.02
2409 4842 7.542130 CCTGATTGGTTATCAAAGCTAACAAAC 59.458 37.037 0.00 0.00 42.56 2.93
2634 5068 8.450578 TCAGTCCATTTATCCAATACATCAAC 57.549 34.615 0.00 0.00 0.00 3.18
2837 5271 7.281774 CAGCAATCATCTTACTGGTACAATTCT 59.718 37.037 0.00 0.00 38.70 2.40
2856 5290 2.235155 TCTGGCCGCACTAAACAATCTA 59.765 45.455 0.00 0.00 0.00 1.98
2884 5318 9.101655 ACTTTCTTTCCAAATTCAACATTTCTG 57.898 29.630 0.00 0.00 0.00 3.02
2915 5349 1.065418 CGAAGGCCCTATTCCAACTGT 60.065 52.381 0.00 0.00 0.00 3.55
2985 5420 6.515272 AAATTGTGTGGTCCTATGATTGTC 57.485 37.500 0.00 0.00 0.00 3.18
3030 5465 2.247111 AGGTCCAGAGTCCATCATCTCT 59.753 50.000 0.00 0.00 41.04 3.10
3096 5534 2.091885 TGCTTTCTTTGGAGTGGGAGTT 60.092 45.455 0.00 0.00 0.00 3.01
3120 5558 7.326968 TCTATATGATCAGATGGTCTTAGCG 57.673 40.000 13.11 0.00 0.00 4.26
3129 5567 6.682746 TCAGATGGTCTTAGCGAGATATTTC 58.317 40.000 0.00 0.00 36.61 2.17
3247 5696 3.304726 GCAAGAACAACAGCCCTTCTAAC 60.305 47.826 0.00 0.00 0.00 2.34
3310 5801 0.229753 CGAGTGAGCAACGTCAACAC 59.770 55.000 0.00 0.00 0.00 3.32
3328 5820 7.635973 CGTCAACACTGTGTAAGCATATTATTG 59.364 37.037 14.69 4.30 0.00 1.90
3329 5821 7.429340 GTCAACACTGTGTAAGCATATTATTGC 59.571 37.037 14.69 0.00 43.09 3.56
3409 6008 7.388776 TGATGAATGTTTCTCTTGGTAGTTGAG 59.611 37.037 0.00 0.00 0.00 3.02
3608 6212 3.636679 TGCAGTCTAGCCATCTAACTCT 58.363 45.455 0.00 0.00 0.00 3.24
3660 6265 1.295792 AACACGCGCTGAGAGAAAAA 58.704 45.000 5.73 0.00 0.00 1.94
3687 6297 5.864474 AGAAATGTCAACGAAGCTAGTACTG 59.136 40.000 5.39 0.00 0.00 2.74
3688 6298 3.570926 TGTCAACGAAGCTAGTACTGG 57.429 47.619 5.39 3.15 0.00 4.00
3690 6300 3.190744 TGTCAACGAAGCTAGTACTGGAG 59.809 47.826 10.90 0.00 0.00 3.86
3692 6302 4.394300 GTCAACGAAGCTAGTACTGGAGTA 59.606 45.833 10.90 0.00 0.00 2.59
3693 6303 5.005740 TCAACGAAGCTAGTACTGGAGTAA 58.994 41.667 10.90 0.00 31.52 2.24
3694 6304 5.474532 TCAACGAAGCTAGTACTGGAGTAAA 59.525 40.000 10.90 0.00 31.52 2.01
3695 6305 6.152323 TCAACGAAGCTAGTACTGGAGTAAAT 59.848 38.462 10.90 0.00 31.52 1.40
3696 6306 7.337689 TCAACGAAGCTAGTACTGGAGTAAATA 59.662 37.037 10.90 0.00 31.52 1.40
3697 6307 7.261829 ACGAAGCTAGTACTGGAGTAAATAG 57.738 40.000 10.90 0.00 31.52 1.73
3699 6309 6.238676 CGAAGCTAGTACTGGAGTAAATAGCA 60.239 42.308 22.31 0.00 43.42 3.49
3700 6310 7.522399 CGAAGCTAGTACTGGAGTAAATAGCAT 60.522 40.741 22.31 15.95 43.42 3.79
3702 6312 8.707796 AGCTAGTACTGGAGTAAATAGCATAA 57.292 34.615 22.31 0.00 43.42 1.90
3703 6313 9.144298 AGCTAGTACTGGAGTAAATAGCATAAA 57.856 33.333 22.31 0.00 43.42 1.40
3720 6330 7.845066 AGCATAAAACTACTACTTTACAGGC 57.155 36.000 0.00 0.00 0.00 4.85
3722 6332 8.755977 AGCATAAAACTACTACTTTACAGGCTA 58.244 33.333 0.00 0.00 0.00 3.93
3723 6333 9.032420 GCATAAAACTACTACTTTACAGGCTAG 57.968 37.037 0.00 0.00 0.00 3.42
3724 6334 9.530633 CATAAAACTACTACTTTACAGGCTAGG 57.469 37.037 0.00 0.00 0.00 3.02
3725 6335 6.541934 AAACTACTACTTTACAGGCTAGGG 57.458 41.667 0.00 0.00 0.00 3.53
3726 6336 5.204131 ACTACTACTTTACAGGCTAGGGT 57.796 43.478 0.00 0.00 0.00 4.34
3727 6337 5.587861 ACTACTACTTTACAGGCTAGGGTT 58.412 41.667 0.00 0.00 0.00 4.11
3728 6338 5.655974 ACTACTACTTTACAGGCTAGGGTTC 59.344 44.000 0.00 0.00 0.00 3.62
3729 6339 3.773667 ACTACTTTACAGGCTAGGGTTCC 59.226 47.826 0.00 0.00 0.00 3.62
3730 6340 2.627933 ACTTTACAGGCTAGGGTTCCA 58.372 47.619 0.00 0.00 0.00 3.53
3732 6342 3.396611 ACTTTACAGGCTAGGGTTCCAAA 59.603 43.478 0.00 0.00 0.00 3.28
3734 6344 4.456662 TTACAGGCTAGGGTTCCAAAAA 57.543 40.909 0.00 0.00 0.00 1.94
3764 6567 9.687210 ACCGGTTTTAAATTTTTCTCAGATAAC 57.313 29.630 0.00 0.00 0.00 1.89
3784 6587 2.035626 CCAAATGGGTGGTCGGCT 59.964 61.111 0.00 0.00 33.63 5.52
3785 6588 2.342650 CCAAATGGGTGGTCGGCTG 61.343 63.158 0.00 0.00 33.63 4.85
3787 6590 1.152830 AAATGGGTGGTCGGCTGTT 59.847 52.632 0.00 0.00 0.00 3.16
3788 6591 0.469144 AAATGGGTGGTCGGCTGTTT 60.469 50.000 0.00 0.00 0.00 2.83
3790 6593 0.402504 ATGGGTGGTCGGCTGTTTAA 59.597 50.000 0.00 0.00 0.00 1.52
3791 6594 0.183014 TGGGTGGTCGGCTGTTTAAA 59.817 50.000 0.00 0.00 0.00 1.52
3792 6595 1.320507 GGGTGGTCGGCTGTTTAAAA 58.679 50.000 0.00 0.00 0.00 1.52
3793 6596 1.682323 GGGTGGTCGGCTGTTTAAAAA 59.318 47.619 0.00 0.00 0.00 1.94
3815 6618 8.549338 AAAAACCCAAAATCTTCGTTGTTAAA 57.451 26.923 0.00 0.00 0.00 1.52
3816 6619 8.549338 AAAACCCAAAATCTTCGTTGTTAAAA 57.451 26.923 0.00 0.00 0.00 1.52
3817 6620 8.549338 AAACCCAAAATCTTCGTTGTTAAAAA 57.451 26.923 0.00 0.00 0.00 1.94
3840 6643 9.758651 AAAAATTAAACAGGTTTATGACAGGTC 57.241 29.630 5.53 0.00 35.27 3.85
3843 6646 3.703001 ACAGGTTTATGACAGGTCAGG 57.297 47.619 8.24 0.00 43.61 3.86
3844 6647 2.290323 ACAGGTTTATGACAGGTCAGGC 60.290 50.000 8.24 0.00 43.61 4.85
3845 6648 1.282157 AGGTTTATGACAGGTCAGGCC 59.718 52.381 8.24 0.00 43.61 5.19
3847 6650 0.251916 TTTATGACAGGTCAGGCCCG 59.748 55.000 8.24 0.00 43.61 6.13
3848 6651 2.252072 TTATGACAGGTCAGGCCCGC 62.252 60.000 8.24 0.00 43.61 6.13
3854 6657 3.712907 GGTCAGGCCCGCACCTAA 61.713 66.667 0.00 0.00 38.26 2.69
3855 6658 2.349755 GTCAGGCCCGCACCTAAA 59.650 61.111 0.00 0.00 38.26 1.85
3856 6659 2.038837 GTCAGGCCCGCACCTAAAC 61.039 63.158 0.00 0.00 38.26 2.01
3857 6660 3.124921 CAGGCCCGCACCTAAACG 61.125 66.667 0.00 0.00 38.26 3.60
3858 6661 3.315949 AGGCCCGCACCTAAACGA 61.316 61.111 0.00 0.00 38.67 3.85
3859 6662 2.124860 GGCCCGCACCTAAACGAT 60.125 61.111 0.00 0.00 0.00 3.73
3861 6664 2.178235 GCCCGCACCTAAACGATCC 61.178 63.158 0.00 0.00 0.00 3.36
3862 6665 1.881252 CCCGCACCTAAACGATCCG 60.881 63.158 0.00 0.00 0.00 4.18
3863 6666 1.153706 CCGCACCTAAACGATCCGT 60.154 57.895 0.00 0.00 43.97 4.69
3864 6667 1.143969 CCGCACCTAAACGATCCGTC 61.144 60.000 0.00 0.00 39.99 4.79
3865 6668 0.179145 CGCACCTAAACGATCCGTCT 60.179 55.000 0.00 0.00 39.99 4.18
3866 6669 1.064505 CGCACCTAAACGATCCGTCTA 59.935 52.381 0.00 0.00 39.99 2.59
3868 6671 3.714391 GCACCTAAACGATCCGTCTATT 58.286 45.455 0.00 0.00 39.99 1.73
3869 6672 4.117685 GCACCTAAACGATCCGTCTATTT 58.882 43.478 0.00 0.00 39.99 1.40
3870 6673 4.025979 GCACCTAAACGATCCGTCTATTTG 60.026 45.833 0.00 0.00 39.99 2.32
3871 6674 5.345702 CACCTAAACGATCCGTCTATTTGA 58.654 41.667 0.00 0.00 39.99 2.69
3872 6675 5.231568 CACCTAAACGATCCGTCTATTTGAC 59.768 44.000 0.00 0.00 39.99 3.18
3873 6676 4.743644 CCTAAACGATCCGTCTATTTGACC 59.256 45.833 0.00 0.00 39.99 4.02
3875 6678 1.747355 ACGATCCGTCTATTTGACCGT 59.253 47.619 0.00 0.00 42.49 4.83
3878 6681 3.242837 CGATCCGTCTATTTGACCGTGTA 60.243 47.826 0.00 0.00 42.49 2.90
3879 6682 4.556104 CGATCCGTCTATTTGACCGTGTAT 60.556 45.833 0.00 0.00 42.49 2.29
3880 6683 4.724074 TCCGTCTATTTGACCGTGTATT 57.276 40.909 0.00 0.00 42.49 1.89
3881 6684 5.075858 TCCGTCTATTTGACCGTGTATTT 57.924 39.130 0.00 0.00 42.49 1.40
3883 6686 4.865925 CCGTCTATTTGACCGTGTATTTGA 59.134 41.667 0.00 0.00 42.49 2.69
3884 6687 5.220340 CCGTCTATTTGACCGTGTATTTGAC 60.220 44.000 0.00 0.00 42.49 3.18
3885 6688 5.220340 CGTCTATTTGACCGTGTATTTGACC 60.220 44.000 0.00 0.00 42.49 4.02
3886 6689 5.640357 GTCTATTTGACCGTGTATTTGACCA 59.360 40.000 0.00 0.00 39.69 4.02
3887 6690 6.315393 GTCTATTTGACCGTGTATTTGACCAT 59.685 38.462 0.00 0.00 39.69 3.55
3888 6691 5.975693 ATTTGACCGTGTATTTGACCATT 57.024 34.783 0.00 0.00 0.00 3.16
3889 6692 8.041919 TCTATTTGACCGTGTATTTGACCATTA 58.958 33.333 0.00 0.00 0.00 1.90
3890 6693 6.879276 TTTGACCGTGTATTTGACCATTAA 57.121 33.333 0.00 0.00 0.00 1.40
3891 6694 5.866335 TGACCGTGTATTTGACCATTAAC 57.134 39.130 0.00 0.00 0.00 2.01
3892 6695 5.553123 TGACCGTGTATTTGACCATTAACT 58.447 37.500 0.00 0.00 0.00 2.24
3894 6697 5.553123 ACCGTGTATTTGACCATTAACTGA 58.447 37.500 0.00 0.00 0.00 3.41
3897 6700 6.093495 CCGTGTATTTGACCATTAACTGACAT 59.907 38.462 0.00 0.00 0.00 3.06
3898 6701 6.960992 CGTGTATTTGACCATTAACTGACATG 59.039 38.462 0.00 0.00 0.00 3.21
3899 6702 7.360861 CGTGTATTTGACCATTAACTGACATGT 60.361 37.037 0.00 0.00 0.00 3.21
3900 6703 7.750458 GTGTATTTGACCATTAACTGACATGTG 59.250 37.037 1.15 0.00 0.00 3.21
3902 6705 3.684908 TGACCATTAACTGACATGTGGG 58.315 45.455 1.15 0.00 0.00 4.61
3906 6709 2.871096 TTAACTGACATGTGGGTCCC 57.129 50.000 1.15 0.00 36.97 4.46
3907 6710 1.735926 TAACTGACATGTGGGTCCCA 58.264 50.000 6.47 6.47 36.97 4.37
3916 6719 2.858476 TGGGTCCCACATGGCAGT 60.858 61.111 6.47 0.00 0.00 4.40
3918 6721 2.436109 GGTCCCACATGGCAGTGT 59.564 61.111 13.48 6.55 37.82 3.55
3919 6722 1.675641 GGTCCCACATGGCAGTGTC 60.676 63.158 13.48 0.00 37.82 3.67
3922 6725 1.073722 CCCACATGGCAGTGTCTGT 59.926 57.895 13.48 1.24 37.82 3.41
3923 6726 0.324614 CCCACATGGCAGTGTCTGTA 59.675 55.000 13.48 0.00 37.82 2.74
3924 6727 1.271325 CCCACATGGCAGTGTCTGTAA 60.271 52.381 13.48 0.00 37.82 2.41
3925 6728 2.503331 CCACATGGCAGTGTCTGTAAA 58.497 47.619 13.48 0.00 37.82 2.01
3926 6729 2.226437 CCACATGGCAGTGTCTGTAAAC 59.774 50.000 13.48 0.00 37.82 2.01
3927 6730 3.141398 CACATGGCAGTGTCTGTAAACT 58.859 45.455 0.00 0.00 34.83 2.66
3932 6735 4.265893 TGGCAGTGTCTGTAAACTTTTCA 58.734 39.130 0.00 0.00 33.43 2.69
3933 6736 4.702612 TGGCAGTGTCTGTAAACTTTTCAA 59.297 37.500 0.00 0.00 33.43 2.69
3934 6737 5.184096 TGGCAGTGTCTGTAAACTTTTCAAA 59.816 36.000 0.00 0.00 33.43 2.69
3935 6738 6.096695 GGCAGTGTCTGTAAACTTTTCAAAA 58.903 36.000 0.00 0.00 33.43 2.44
3936 6739 6.588373 GGCAGTGTCTGTAAACTTTTCAAAAA 59.412 34.615 0.00 0.00 33.43 1.94
3937 6740 7.277760 GGCAGTGTCTGTAAACTTTTCAAAAAT 59.722 33.333 0.00 0.00 33.43 1.82
3938 6741 8.110002 GCAGTGTCTGTAAACTTTTCAAAAATG 58.890 33.333 0.00 0.00 33.43 2.32
3939 6742 8.110002 CAGTGTCTGTAAACTTTTCAAAAATGC 58.890 33.333 0.00 0.00 0.00 3.56
3940 6743 7.277760 AGTGTCTGTAAACTTTTCAAAAATGCC 59.722 33.333 0.00 0.00 0.00 4.40
3941 6744 7.064016 GTGTCTGTAAACTTTTCAAAAATGCCA 59.936 33.333 0.00 0.00 0.00 4.92
3942 6745 7.768120 TGTCTGTAAACTTTTCAAAAATGCCAT 59.232 29.630 0.00 0.00 0.00 4.40
3943 6746 8.275632 GTCTGTAAACTTTTCAAAAATGCCATC 58.724 33.333 0.00 0.00 0.00 3.51
3944 6747 7.984050 TCTGTAAACTTTTCAAAAATGCCATCA 59.016 29.630 0.00 0.00 0.00 3.07
3945 6748 8.140677 TGTAAACTTTTCAAAAATGCCATCAG 57.859 30.769 0.00 0.00 0.00 2.90
3946 6749 6.622833 AAACTTTTCAAAAATGCCATCAGG 57.377 33.333 0.00 0.00 38.23 3.86
3947 6750 5.294734 ACTTTTCAAAAATGCCATCAGGT 57.705 34.783 0.00 0.00 37.19 4.00
3948 6751 5.299949 ACTTTTCAAAAATGCCATCAGGTC 58.700 37.500 0.00 0.00 37.19 3.85
3949 6752 3.959535 TTCAAAAATGCCATCAGGTCC 57.040 42.857 0.00 0.00 37.19 4.46
3950 6753 2.178580 TCAAAAATGCCATCAGGTCCC 58.821 47.619 0.00 0.00 37.19 4.46
3951 6754 2.181975 CAAAAATGCCATCAGGTCCCT 58.818 47.619 0.00 0.00 37.19 4.20
3952 6755 1.856629 AAAATGCCATCAGGTCCCTG 58.143 50.000 7.02 7.02 44.86 4.45
3953 6756 0.685458 AAATGCCATCAGGTCCCTGC 60.685 55.000 8.53 0.00 43.31 4.85
3954 6757 1.866483 AATGCCATCAGGTCCCTGCA 61.866 55.000 8.53 3.60 43.31 4.41
3955 6758 1.866483 ATGCCATCAGGTCCCTGCAA 61.866 55.000 8.53 0.00 43.31 4.08
3956 6759 1.304381 GCCATCAGGTCCCTGCAAA 60.304 57.895 8.53 0.00 43.31 3.68
3957 6760 1.598701 GCCATCAGGTCCCTGCAAAC 61.599 60.000 8.53 0.00 43.31 2.93
3958 6761 0.038744 CCATCAGGTCCCTGCAAACT 59.961 55.000 8.53 0.00 43.31 2.66
3959 6762 1.548582 CCATCAGGTCCCTGCAAACTT 60.549 52.381 8.53 0.00 43.31 2.66
3960 6763 2.242043 CATCAGGTCCCTGCAAACTTT 58.758 47.619 8.53 0.00 43.31 2.66
3961 6764 2.452600 TCAGGTCCCTGCAAACTTTT 57.547 45.000 8.53 0.00 43.31 2.27
3962 6765 2.306847 TCAGGTCCCTGCAAACTTTTC 58.693 47.619 8.53 0.00 43.31 2.29
3963 6766 2.031120 CAGGTCCCTGCAAACTTTTCA 58.969 47.619 0.00 0.00 37.24 2.69
3964 6767 2.430332 CAGGTCCCTGCAAACTTTTCAA 59.570 45.455 0.00 0.00 37.24 2.69
3965 6768 3.103742 AGGTCCCTGCAAACTTTTCAAA 58.896 40.909 0.00 0.00 0.00 2.69
3966 6769 3.517500 AGGTCCCTGCAAACTTTTCAAAA 59.482 39.130 0.00 0.00 0.00 2.44
3967 6770 3.621268 GGTCCCTGCAAACTTTTCAAAAC 59.379 43.478 0.00 0.00 0.00 2.43
3968 6771 3.305897 GTCCCTGCAAACTTTTCAAAACG 59.694 43.478 0.00 0.00 0.00 3.60
3969 6772 2.030335 CCCTGCAAACTTTTCAAAACGC 59.970 45.455 0.00 0.00 0.00 4.84
3970 6773 2.670414 CCTGCAAACTTTTCAAAACGCA 59.330 40.909 0.00 0.00 0.00 5.24
3971 6774 3.124297 CCTGCAAACTTTTCAAAACGCAA 59.876 39.130 0.00 0.00 0.00 4.85
3972 6775 4.201802 CCTGCAAACTTTTCAAAACGCAAT 60.202 37.500 0.00 0.00 0.00 3.56
3973 6776 4.891516 TGCAAACTTTTCAAAACGCAATC 58.108 34.783 0.00 0.00 0.00 2.67
3974 6777 3.953242 GCAAACTTTTCAAAACGCAATCG 59.047 39.130 0.00 0.00 42.43 3.34
3975 6778 4.504385 CAAACTTTTCAAAACGCAATCGG 58.496 39.130 0.00 0.00 40.69 4.18
3976 6779 2.738135 ACTTTTCAAAACGCAATCGGG 58.262 42.857 0.00 0.00 40.69 5.14
3977 6780 2.100087 ACTTTTCAAAACGCAATCGGGT 59.900 40.909 0.00 0.00 40.63 5.28
3978 6781 2.409152 TTTCAAAACGCAATCGGGTC 57.591 45.000 0.00 0.00 37.30 4.46
3979 6782 0.594110 TTCAAAACGCAATCGGGTCC 59.406 50.000 0.00 0.00 37.30 4.46
3980 6783 1.211709 CAAAACGCAATCGGGTCCC 59.788 57.895 0.00 0.00 37.30 4.46
3981 6784 1.074248 AAAACGCAATCGGGTCCCT 59.926 52.632 6.29 0.00 37.30 4.20
3982 6785 1.241315 AAAACGCAATCGGGTCCCTG 61.241 55.000 6.29 0.00 37.30 4.45
3983 6786 4.778143 ACGCAATCGGGTCCCTGC 62.778 66.667 6.29 8.48 40.69 4.85
3984 6787 4.776322 CGCAATCGGGTCCCTGCA 62.776 66.667 18.17 0.00 34.39 4.41
3985 6788 2.361104 GCAATCGGGTCCCTGCAA 60.361 61.111 14.34 0.00 34.87 4.08
3986 6789 1.976474 GCAATCGGGTCCCTGCAAA 60.976 57.895 14.34 0.00 34.87 3.68
3987 6790 1.883021 CAATCGGGTCCCTGCAAAC 59.117 57.895 6.29 0.00 0.00 2.93
3988 6791 0.609131 CAATCGGGTCCCTGCAAACT 60.609 55.000 6.29 0.00 0.00 2.66
3989 6792 0.112412 AATCGGGTCCCTGCAAACTT 59.888 50.000 6.29 0.00 0.00 2.66
3990 6793 0.112412 ATCGGGTCCCTGCAAACTTT 59.888 50.000 6.29 0.00 0.00 2.66
3991 6794 0.106419 TCGGGTCCCTGCAAACTTTT 60.106 50.000 6.29 0.00 0.00 2.27
3992 6795 0.031994 CGGGTCCCTGCAAACTTTTG 59.968 55.000 6.29 0.00 41.03 2.44
3993 6796 1.408969 GGGTCCCTGCAAACTTTTGA 58.591 50.000 0.00 0.00 40.55 2.69
3994 6797 1.760029 GGGTCCCTGCAAACTTTTGAA 59.240 47.619 0.00 0.00 40.55 2.69
3995 6798 2.169561 GGGTCCCTGCAAACTTTTGAAA 59.830 45.455 0.00 0.00 40.55 2.69
3996 6799 3.369997 GGGTCCCTGCAAACTTTTGAAAA 60.370 43.478 0.00 0.00 40.55 2.29
3997 6800 4.257731 GGTCCCTGCAAACTTTTGAAAAA 58.742 39.130 5.87 0.00 40.55 1.94
4012 6815 3.765968 AAAAAGCAATCGGGTCCCT 57.234 47.368 6.29 0.00 0.00 4.20
4013 6816 1.545841 AAAAAGCAATCGGGTCCCTC 58.454 50.000 6.29 0.00 0.00 4.30
4014 6817 0.323451 AAAAGCAATCGGGTCCCTCC 60.323 55.000 6.29 0.00 0.00 4.30
4089 6892 4.148825 CCGTGGAGCTCCCTTCCG 62.149 72.222 29.95 23.37 37.54 4.30
4090 6893 3.382832 CGTGGAGCTCCCTTCCGT 61.383 66.667 29.95 0.00 37.54 4.69
4091 6894 2.579738 GTGGAGCTCCCTTCCGTC 59.420 66.667 29.95 7.78 37.54 4.79
4092 6895 2.683933 TGGAGCTCCCTTCCGTCC 60.684 66.667 29.95 2.80 37.54 4.79
4093 6896 3.471806 GGAGCTCCCTTCCGTCCC 61.472 72.222 23.19 0.00 0.00 4.46
4094 6897 3.839432 GAGCTCCCTTCCGTCCCG 61.839 72.222 0.87 0.00 0.00 5.14
4117 9441 2.203126 CGCATGGAGCTCCCTTCC 60.203 66.667 29.95 14.09 42.61 3.46
4118 9442 2.203126 GCATGGAGCTCCCTTCCG 60.203 66.667 29.95 14.06 41.15 4.30
4119 9443 3.036429 GCATGGAGCTCCCTTCCGT 62.036 63.158 29.95 3.82 41.15 4.69
4120 9444 1.144936 CATGGAGCTCCCTTCCGTC 59.855 63.158 29.95 2.66 37.54 4.79
4123 9447 3.760035 GAGCTCCCTTCCGTCGCA 61.760 66.667 0.87 0.00 0.00 5.10
4124 9448 3.296709 GAGCTCCCTTCCGTCGCAA 62.297 63.158 0.87 0.00 0.00 4.85
4126 9450 2.342279 CTCCCTTCCGTCGCAACA 59.658 61.111 0.00 0.00 0.00 3.33
4127 9451 1.738099 CTCCCTTCCGTCGCAACAG 60.738 63.158 0.00 0.00 0.00 3.16
4129 9453 2.342279 CCTTCCGTCGCAACAGGA 59.658 61.111 0.00 0.00 0.00 3.86
4130 9454 1.301401 CCTTCCGTCGCAACAGGAA 60.301 57.895 2.03 2.03 41.28 3.36
4131 9455 1.566018 CCTTCCGTCGCAACAGGAAC 61.566 60.000 0.00 0.00 38.94 3.62
4132 9456 0.878523 CTTCCGTCGCAACAGGAACA 60.879 55.000 0.00 0.00 38.94 3.18
4135 9459 2.243957 CGTCGCAACAGGAACAGCA 61.244 57.895 0.00 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 3.065371 GGTTGAAATTCGGTGGCATCTAG 59.935 47.826 0.00 0.00 0.00 2.43
26 27 2.426522 TCAGCAGGAGGTTGAAATTCG 58.573 47.619 0.00 0.00 33.43 3.34
121 150 0.040157 CCCACAACAGCAACATGACG 60.040 55.000 0.00 0.00 0.00 4.35
124 191 1.541147 CCTACCCACAACAGCAACATG 59.459 52.381 0.00 0.00 0.00 3.21
415 899 6.650390 AGTTGGTTGATGGAATAATTTGTTGC 59.350 34.615 0.00 0.00 0.00 4.17
482 2232 5.594317 GGTTGATGGAATAGGTGCAGTTATT 59.406 40.000 0.00 0.00 0.00 1.40
712 2544 3.769844 TCTGACCATTTCTCCTACCAGTC 59.230 47.826 0.00 0.00 0.00 3.51
861 2726 5.682943 TCTTTAGTTTGTTTGATCCGGTG 57.317 39.130 0.00 0.00 0.00 4.94
1233 3665 1.800805 CCAGCGAAACATCAGTGACT 58.199 50.000 0.00 0.00 0.00 3.41
1719 4151 5.249420 ACCTTAAAGAGTTCATCTGGAAGC 58.751 41.667 0.00 0.00 38.67 3.86
1794 4226 3.018856 TGTGAGGTTGATGATGCCATTC 58.981 45.455 0.00 0.00 32.09 2.67
2133 4566 5.424573 TGACAATTGGCCATGGAAATGATTA 59.575 36.000 18.40 0.99 0.00 1.75
2225 4658 5.083122 TCTCAAGGATCTGAAGTGTTCTCT 58.917 41.667 0.00 0.00 0.00 3.10
2409 4842 4.937015 CCTTGCAAAAATAACATCCCCAAG 59.063 41.667 0.00 0.00 0.00 3.61
2634 5068 2.244436 CTTTCGGACATGCACCAGCG 62.244 60.000 9.64 0.00 46.23 5.18
2837 5271 2.289756 TGTAGATTGTTTAGTGCGGCCA 60.290 45.455 2.24 0.00 0.00 5.36
2856 5290 8.791327 AAATGTTGAATTTGGAAAGAAAGTGT 57.209 26.923 0.00 0.00 0.00 3.55
2884 5318 1.694696 AGGGCCTTCGAGGTCATTATC 59.305 52.381 0.00 0.00 43.30 1.75
2915 5349 2.690653 AAACGTGCTAAGCTGGCCCA 62.691 55.000 0.00 0.00 0.00 5.36
3030 5465 4.777896 ACCTTACTGCCAATCTGTTCTCTA 59.222 41.667 0.00 0.00 0.00 2.43
3096 5534 7.112779 TCGCTAAGACCATCTGATCATATAGA 58.887 38.462 0.00 0.00 0.00 1.98
3120 5558 6.679327 ACAAGGTTTTAGCCGAAATATCTC 57.321 37.500 0.00 0.00 0.00 2.75
3129 5567 4.823790 AACAGTTACAAGGTTTTAGCCG 57.176 40.909 0.00 0.00 0.00 5.52
3247 5696 4.040829 TGGAGTACAATGATGATAGCAGGG 59.959 45.833 0.00 0.00 0.00 4.45
3328 5820 6.687604 ACCAAATAGTTACAAATTCCACAGC 58.312 36.000 0.00 0.00 0.00 4.40
3329 5821 7.881142 TGACCAAATAGTTACAAATTCCACAG 58.119 34.615 0.00 0.00 0.00 3.66
3409 6008 4.061596 GCTTATTATGTGTCCTCCTCTGC 58.938 47.826 0.00 0.00 0.00 4.26
3608 6212 2.158726 GGATAATTGCGACCCTGGGTTA 60.159 50.000 21.59 7.53 35.25 2.85
3644 6249 1.728971 CTGATTTTTCTCTCAGCGCGT 59.271 47.619 8.43 0.00 33.12 6.01
3660 6265 5.482908 ACTAGCTTCGTTGACATTTCTGAT 58.517 37.500 0.00 0.00 0.00 2.90
3694 6304 9.543783 GCCTGTAAAGTAGTAGTTTTATGCTAT 57.456 33.333 8.25 0.00 0.00 2.97
3695 6305 8.755977 AGCCTGTAAAGTAGTAGTTTTATGCTA 58.244 33.333 8.25 0.00 0.00 3.49
3696 6306 7.621796 AGCCTGTAAAGTAGTAGTTTTATGCT 58.378 34.615 8.25 8.97 0.00 3.79
3697 6307 7.845066 AGCCTGTAAAGTAGTAGTTTTATGC 57.155 36.000 8.25 7.22 0.00 3.14
3699 6309 8.702819 CCCTAGCCTGTAAAGTAGTAGTTTTAT 58.297 37.037 8.25 0.00 0.00 1.40
3700 6310 7.675619 ACCCTAGCCTGTAAAGTAGTAGTTTTA 59.324 37.037 8.25 0.00 0.00 1.52
3702 6312 6.021672 ACCCTAGCCTGTAAAGTAGTAGTTT 58.978 40.000 8.04 8.04 0.00 2.66
3703 6313 5.587861 ACCCTAGCCTGTAAAGTAGTAGTT 58.412 41.667 0.00 0.00 0.00 2.24
3705 6315 5.068855 GGAACCCTAGCCTGTAAAGTAGTAG 59.931 48.000 0.00 0.00 0.00 2.57
3706 6316 4.958581 GGAACCCTAGCCTGTAAAGTAGTA 59.041 45.833 0.00 0.00 0.00 1.82
3707 6317 3.773667 GGAACCCTAGCCTGTAAAGTAGT 59.226 47.826 0.00 0.00 0.00 2.73
3708 6318 3.773119 TGGAACCCTAGCCTGTAAAGTAG 59.227 47.826 0.00 0.00 0.00 2.57
3709 6319 3.793712 TGGAACCCTAGCCTGTAAAGTA 58.206 45.455 0.00 0.00 0.00 2.24
3710 6320 2.627933 TGGAACCCTAGCCTGTAAAGT 58.372 47.619 0.00 0.00 0.00 2.66
3711 6321 3.713826 TTGGAACCCTAGCCTGTAAAG 57.286 47.619 0.00 0.00 0.00 1.85
3712 6322 4.456662 TTTTGGAACCCTAGCCTGTAAA 57.543 40.909 0.00 0.00 0.00 2.01
3713 6323 4.456662 TTTTTGGAACCCTAGCCTGTAA 57.543 40.909 0.00 0.00 0.00 2.41
3734 6344 8.905850 TCTGAGAAAAATTTAAAACCGGTAGTT 58.094 29.630 8.00 8.25 41.81 2.24
3735 6345 8.454570 TCTGAGAAAAATTTAAAACCGGTAGT 57.545 30.769 8.00 0.16 0.00 2.73
3738 6348 9.687210 GTTATCTGAGAAAAATTTAAAACCGGT 57.313 29.630 0.00 0.00 0.00 5.28
3739 6349 9.908152 AGTTATCTGAGAAAAATTTAAAACCGG 57.092 29.630 0.00 0.00 0.00 5.28
3749 6359 8.971073 CCCATTTGGTAGTTATCTGAGAAAAAT 58.029 33.333 0.00 0.00 0.00 1.82
3750 6360 8.348285 CCCATTTGGTAGTTATCTGAGAAAAA 57.652 34.615 0.00 0.00 0.00 1.94
3769 6572 0.469144 AAACAGCCGACCACCCATTT 60.469 50.000 0.00 0.00 0.00 2.32
3770 6573 0.402504 TAAACAGCCGACCACCCATT 59.597 50.000 0.00 0.00 0.00 3.16
3771 6574 0.402504 TTAAACAGCCGACCACCCAT 59.597 50.000 0.00 0.00 0.00 4.00
3790 6593 8.549338 TTTAACAACGAAGATTTTGGGTTTTT 57.451 26.923 0.00 0.00 0.00 1.94
3791 6594 8.549338 TTTTAACAACGAAGATTTTGGGTTTT 57.451 26.923 0.00 0.00 0.00 2.43
3792 6595 8.549338 TTTTTAACAACGAAGATTTTGGGTTT 57.451 26.923 0.00 0.00 0.00 3.27
3814 6617 9.758651 GACCTGTCATAAACCTGTTTAATTTTT 57.241 29.630 6.57 0.00 38.38 1.94
3815 6618 8.919145 TGACCTGTCATAAACCTGTTTAATTTT 58.081 29.630 6.57 0.00 38.38 1.82
3816 6619 8.472007 TGACCTGTCATAAACCTGTTTAATTT 57.528 30.769 6.57 0.00 38.38 1.82
3817 6620 7.176690 CCTGACCTGTCATAAACCTGTTTAATT 59.823 37.037 6.57 0.00 38.38 1.40
3818 6621 6.659242 CCTGACCTGTCATAAACCTGTTTAAT 59.341 38.462 6.57 0.00 38.38 1.40
3819 6622 6.001460 CCTGACCTGTCATAAACCTGTTTAA 58.999 40.000 6.57 0.00 38.38 1.52
3820 6623 5.556915 CCTGACCTGTCATAAACCTGTTTA 58.443 41.667 5.05 5.05 39.13 2.01
3822 6625 3.810743 GCCTGACCTGTCATAAACCTGTT 60.811 47.826 0.00 0.00 39.13 3.16
3823 6626 2.290323 GCCTGACCTGTCATAAACCTGT 60.290 50.000 0.00 0.00 39.13 4.00
3824 6627 2.359900 GCCTGACCTGTCATAAACCTG 58.640 52.381 0.00 0.00 39.13 4.00
3827 6630 1.751437 GGGCCTGACCTGTCATAAAC 58.249 55.000 0.84 0.00 39.13 2.01
3830 6633 3.628989 CGGGCCTGACCTGTCATA 58.371 61.111 5.28 0.00 40.35 2.15
3836 6639 4.715130 TAGGTGCGGGCCTGACCT 62.715 66.667 28.10 28.10 42.87 3.85
3837 6640 3.262448 TTTAGGTGCGGGCCTGACC 62.262 63.158 18.31 19.34 39.60 4.02
3838 6641 2.038837 GTTTAGGTGCGGGCCTGAC 61.039 63.158 18.31 10.68 39.60 3.51
3839 6642 2.349755 GTTTAGGTGCGGGCCTGA 59.650 61.111 18.31 0.00 39.60 3.86
3840 6643 2.869503 ATCGTTTAGGTGCGGGCCTG 62.870 60.000 7.41 7.41 39.60 4.85
3843 6646 2.178235 GGATCGTTTAGGTGCGGGC 61.178 63.158 0.00 0.00 0.00 6.13
3844 6647 1.881252 CGGATCGTTTAGGTGCGGG 60.881 63.158 0.00 0.00 41.32 6.13
3845 6648 3.700961 CGGATCGTTTAGGTGCGG 58.299 61.111 0.00 0.00 41.32 5.69
3847 6650 2.857592 TAGACGGATCGTTTAGGTGC 57.142 50.000 0.00 0.00 41.37 5.01
3848 6651 5.231568 GTCAAATAGACGGATCGTTTAGGTG 59.768 44.000 0.00 0.00 41.37 4.00
3849 6652 5.346522 GTCAAATAGACGGATCGTTTAGGT 58.653 41.667 0.00 0.00 41.37 3.08
3862 6665 5.640357 TGGTCAAATACACGGTCAAATAGAC 59.360 40.000 0.00 0.00 46.83 2.59
3863 6666 5.795972 TGGTCAAATACACGGTCAAATAGA 58.204 37.500 0.00 0.00 0.00 1.98
3864 6667 6.677781 ATGGTCAAATACACGGTCAAATAG 57.322 37.500 0.00 0.00 0.00 1.73
3865 6668 8.452534 GTTAATGGTCAAATACACGGTCAAATA 58.547 33.333 0.00 0.00 0.00 1.40
3866 6669 5.975693 AATGGTCAAATACACGGTCAAAT 57.024 34.783 0.00 0.00 0.00 2.32
3868 6671 5.998981 AGTTAATGGTCAAATACACGGTCAA 59.001 36.000 0.00 0.00 0.00 3.18
3869 6672 5.410132 CAGTTAATGGTCAAATACACGGTCA 59.590 40.000 0.00 0.00 0.00 4.02
3870 6673 5.640357 TCAGTTAATGGTCAAATACACGGTC 59.360 40.000 0.00 0.00 0.00 4.79
3871 6674 5.410439 GTCAGTTAATGGTCAAATACACGGT 59.590 40.000 0.00 0.00 0.00 4.83
3872 6675 5.410132 TGTCAGTTAATGGTCAAATACACGG 59.590 40.000 0.00 0.00 0.00 4.94
3873 6676 6.474819 TGTCAGTTAATGGTCAAATACACG 57.525 37.500 0.00 0.00 0.00 4.49
3875 6678 7.094420 CCACATGTCAGTTAATGGTCAAATACA 60.094 37.037 0.00 0.00 0.00 2.29
3878 6681 5.185635 CCCACATGTCAGTTAATGGTCAAAT 59.814 40.000 0.00 0.00 0.00 2.32
3879 6682 4.522405 CCCACATGTCAGTTAATGGTCAAA 59.478 41.667 0.00 0.00 0.00 2.69
3880 6683 4.078537 CCCACATGTCAGTTAATGGTCAA 58.921 43.478 0.00 0.00 0.00 3.18
3881 6684 3.073798 ACCCACATGTCAGTTAATGGTCA 59.926 43.478 0.00 0.00 0.00 4.02
3883 6686 3.561313 GGACCCACATGTCAGTTAATGGT 60.561 47.826 0.00 0.00 36.97 3.55
3884 6687 3.016736 GGACCCACATGTCAGTTAATGG 58.983 50.000 0.00 0.00 36.97 3.16
3885 6688 3.016736 GGGACCCACATGTCAGTTAATG 58.983 50.000 5.33 0.00 36.97 1.90
3886 6689 2.647299 TGGGACCCACATGTCAGTTAAT 59.353 45.455 9.95 0.00 36.97 1.40
3887 6690 2.058705 TGGGACCCACATGTCAGTTAA 58.941 47.619 9.95 0.00 36.97 2.01
3888 6691 1.735926 TGGGACCCACATGTCAGTTA 58.264 50.000 9.95 0.00 36.97 2.24
3889 6692 2.550787 TGGGACCCACATGTCAGTT 58.449 52.632 9.95 0.00 36.97 3.16
3890 6693 4.330056 TGGGACCCACATGTCAGT 57.670 55.556 9.95 0.00 36.97 3.41
3899 6702 2.858476 ACTGCCATGTGGGACCCA 60.858 61.111 9.95 9.95 40.01 4.51
3900 6703 2.361610 CACTGCCATGTGGGACCC 60.362 66.667 2.45 2.45 40.01 4.46
3902 6705 0.957395 CAGACACTGCCATGTGGGAC 60.957 60.000 0.54 0.00 41.84 4.46
3906 6709 3.141398 AGTTTACAGACACTGCCATGTG 58.859 45.455 0.00 0.00 43.07 3.21
3907 6710 3.492102 AGTTTACAGACACTGCCATGT 57.508 42.857 0.00 0.00 34.37 3.21
3908 6711 4.836125 AAAGTTTACAGACACTGCCATG 57.164 40.909 0.00 0.00 34.37 3.66
3910 6713 4.265893 TGAAAAGTTTACAGACACTGCCA 58.734 39.130 0.00 0.00 34.37 4.92
3913 6716 8.110002 GCATTTTTGAAAAGTTTACAGACACTG 58.890 33.333 0.00 0.00 37.52 3.66
3914 6717 7.277760 GGCATTTTTGAAAAGTTTACAGACACT 59.722 33.333 0.00 0.00 0.00 3.55
3915 6718 7.064016 TGGCATTTTTGAAAAGTTTACAGACAC 59.936 33.333 0.00 0.00 0.00 3.67
3916 6719 7.099764 TGGCATTTTTGAAAAGTTTACAGACA 58.900 30.769 0.00 0.00 0.00 3.41
3918 6721 7.984050 TGATGGCATTTTTGAAAAGTTTACAGA 59.016 29.630 0.00 0.00 0.00 3.41
3919 6722 8.140677 TGATGGCATTTTTGAAAAGTTTACAG 57.859 30.769 0.00 0.00 0.00 2.74
3922 6725 7.278875 ACCTGATGGCATTTTTGAAAAGTTTA 58.721 30.769 0.00 0.00 36.63 2.01
3923 6726 6.121590 ACCTGATGGCATTTTTGAAAAGTTT 58.878 32.000 0.00 0.00 36.63 2.66
3924 6727 5.683681 ACCTGATGGCATTTTTGAAAAGTT 58.316 33.333 0.00 0.00 36.63 2.66
3925 6728 5.294734 ACCTGATGGCATTTTTGAAAAGT 57.705 34.783 0.00 0.00 36.63 2.66
3926 6729 4.692155 GGACCTGATGGCATTTTTGAAAAG 59.308 41.667 0.00 0.00 36.63 2.27
3927 6730 4.504689 GGGACCTGATGGCATTTTTGAAAA 60.505 41.667 0.00 0.00 36.63 2.29
3932 6735 2.181975 CAGGGACCTGATGGCATTTTT 58.818 47.619 13.06 0.00 46.30 1.94
3933 6736 1.856629 CAGGGACCTGATGGCATTTT 58.143 50.000 13.06 0.00 46.30 1.82
3934 6737 0.685458 GCAGGGACCTGATGGCATTT 60.685 55.000 22.03 0.00 46.30 2.32
3935 6738 1.076485 GCAGGGACCTGATGGCATT 60.076 57.895 22.03 0.00 46.30 3.56
3936 6739 1.866483 TTGCAGGGACCTGATGGCAT 61.866 55.000 22.03 0.00 46.30 4.40
3937 6740 2.079088 TTTGCAGGGACCTGATGGCA 62.079 55.000 22.03 9.61 46.30 4.92
3938 6741 1.304381 TTTGCAGGGACCTGATGGC 60.304 57.895 22.03 6.98 46.30 4.40
3939 6742 0.038744 AGTTTGCAGGGACCTGATGG 59.961 55.000 22.03 0.00 46.30 3.51
3940 6743 1.915141 AAGTTTGCAGGGACCTGATG 58.085 50.000 22.03 5.28 46.30 3.07
3941 6744 2.683211 AAAGTTTGCAGGGACCTGAT 57.317 45.000 22.03 0.00 46.30 2.90
3942 6745 2.306847 GAAAAGTTTGCAGGGACCTGA 58.693 47.619 22.03 4.63 46.30 3.86
3943 6746 2.031120 TGAAAAGTTTGCAGGGACCTG 58.969 47.619 13.99 13.99 46.15 4.00
3944 6747 2.452600 TGAAAAGTTTGCAGGGACCT 57.547 45.000 0.00 0.00 0.00 3.85
3945 6748 3.535280 TTTGAAAAGTTTGCAGGGACC 57.465 42.857 0.00 0.00 0.00 4.46
3946 6749 3.305897 CGTTTTGAAAAGTTTGCAGGGAC 59.694 43.478 0.00 0.00 0.00 4.46
3947 6750 3.516615 CGTTTTGAAAAGTTTGCAGGGA 58.483 40.909 0.00 0.00 0.00 4.20
3948 6751 2.030335 GCGTTTTGAAAAGTTTGCAGGG 59.970 45.455 0.00 0.00 0.00 4.45
3949 6752 2.670414 TGCGTTTTGAAAAGTTTGCAGG 59.330 40.909 0.00 0.00 0.00 4.85
3950 6753 3.987807 TGCGTTTTGAAAAGTTTGCAG 57.012 38.095 0.00 0.00 0.00 4.41
3951 6754 4.491602 CGATTGCGTTTTGAAAAGTTTGCA 60.492 37.500 0.00 0.00 0.00 4.08
3952 6755 3.953242 CGATTGCGTTTTGAAAAGTTTGC 59.047 39.130 0.00 0.00 0.00 3.68
3953 6756 4.504385 CCGATTGCGTTTTGAAAAGTTTG 58.496 39.130 0.00 0.00 35.23 2.93
3954 6757 3.553917 CCCGATTGCGTTTTGAAAAGTTT 59.446 39.130 0.00 0.00 35.23 2.66
3955 6758 3.120041 CCCGATTGCGTTTTGAAAAGTT 58.880 40.909 0.00 0.00 35.23 2.66
3956 6759 2.100087 ACCCGATTGCGTTTTGAAAAGT 59.900 40.909 0.00 0.00 35.23 2.66
3957 6760 2.724174 GACCCGATTGCGTTTTGAAAAG 59.276 45.455 0.00 0.00 35.23 2.27
3958 6761 2.544069 GGACCCGATTGCGTTTTGAAAA 60.544 45.455 0.00 0.00 35.23 2.29
3959 6762 1.001158 GGACCCGATTGCGTTTTGAAA 60.001 47.619 0.00 0.00 35.23 2.69
3960 6763 0.594110 GGACCCGATTGCGTTTTGAA 59.406 50.000 0.00 0.00 35.23 2.69
3961 6764 1.238625 GGGACCCGATTGCGTTTTGA 61.239 55.000 0.00 0.00 35.23 2.69
3962 6765 1.211709 GGGACCCGATTGCGTTTTG 59.788 57.895 0.00 0.00 35.23 2.44
3963 6766 1.074248 AGGGACCCGATTGCGTTTT 59.926 52.632 4.40 0.00 35.23 2.43
3964 6767 1.674322 CAGGGACCCGATTGCGTTT 60.674 57.895 4.40 0.00 35.23 3.60
3965 6768 2.046314 CAGGGACCCGATTGCGTT 60.046 61.111 4.40 0.00 35.23 4.84
3966 6769 4.778143 GCAGGGACCCGATTGCGT 62.778 66.667 4.40 0.00 35.23 5.24
3967 6770 4.776322 TGCAGGGACCCGATTGCG 62.776 66.667 16.25 0.00 39.34 4.85
3968 6771 1.976474 TTTGCAGGGACCCGATTGC 60.976 57.895 14.88 14.88 37.09 3.56
3969 6772 0.609131 AGTTTGCAGGGACCCGATTG 60.609 55.000 4.40 0.00 0.00 2.67
3970 6773 0.112412 AAGTTTGCAGGGACCCGATT 59.888 50.000 4.40 0.00 0.00 3.34
3971 6774 0.112412 AAAGTTTGCAGGGACCCGAT 59.888 50.000 4.40 0.00 0.00 4.18
3972 6775 0.106419 AAAAGTTTGCAGGGACCCGA 60.106 50.000 4.40 0.00 0.00 5.14
3973 6776 0.031994 CAAAAGTTTGCAGGGACCCG 59.968 55.000 4.40 1.05 0.00 5.28
3974 6777 1.408969 TCAAAAGTTTGCAGGGACCC 58.591 50.000 0.59 0.59 38.05 4.46
3975 6778 3.535280 TTTCAAAAGTTTGCAGGGACC 57.465 42.857 0.00 0.00 38.05 4.46
3994 6797 1.545841 GAGGGACCCGATTGCTTTTT 58.454 50.000 4.40 0.00 0.00 1.94
3995 6798 0.323451 GGAGGGACCCGATTGCTTTT 60.323 55.000 4.40 0.00 0.00 2.27
3996 6799 1.303282 GGAGGGACCCGATTGCTTT 59.697 57.895 4.40 0.00 0.00 3.51
3997 6800 2.998949 GGAGGGACCCGATTGCTT 59.001 61.111 4.40 0.00 0.00 3.91
4070 6873 4.821589 GAAGGGAGCTCCACGGCG 62.822 72.222 33.29 4.80 38.24 6.46
4073 6876 3.358076 GACGGAAGGGAGCTCCACG 62.358 68.421 33.29 29.18 38.24 4.94
4075 6878 2.683933 GGACGGAAGGGAGCTCCA 60.684 66.667 33.29 0.00 38.24 3.86
4101 6904 2.203126 CGGAAGGGAGCTCCATGC 60.203 66.667 33.29 26.06 43.29 4.06
4102 6905 1.144936 GACGGAAGGGAGCTCCATG 59.855 63.158 33.29 17.70 38.24 3.66
4103 6906 2.427245 CGACGGAAGGGAGCTCCAT 61.427 63.158 33.29 25.66 38.24 3.41
4104 6907 3.068691 CGACGGAAGGGAGCTCCA 61.069 66.667 33.29 0.00 38.24 3.86
4105 6908 4.516195 GCGACGGAAGGGAGCTCC 62.516 72.222 25.59 25.59 0.00 4.70
4117 9441 2.243957 TGCTGTTCCTGTTGCGACG 61.244 57.895 0.00 0.00 0.00 5.12
4118 9442 3.731136 TGCTGTTCCTGTTGCGAC 58.269 55.556 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.