Multiple sequence alignment - TraesCS5B01G497100

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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 TraesCS5B01G497100 chr5B 100.000 7059 0 0 1 7059 664028258 664021200 0.000000e+00 13036
1 TraesCS5B01G497100 chr5B 91.715 857 63 7 43 895 657200176 657201028 0.000000e+00 1182
2 TraesCS5B01G497100 chr5D 94.014 2957 114 20 843 3769 527503831 527500908 0.000000e+00 4421
3 TraesCS5B01G497100 chr5D 91.594 1713 75 31 5384 7057 527499259 527497577 0.000000e+00 2302
4 TraesCS5B01G497100 chr5D 95.099 1367 45 6 4024 5385 527500640 527499291 0.000000e+00 2134
5 TraesCS5B01G497100 chr5D 94.932 809 38 2 43 850 527506017 527505211 0.000000e+00 1264
6 TraesCS5B01G497100 chr5D 97.740 177 4 0 3766 3942 527500815 527500639 8.900000e-79 305
7 TraesCS5B01G497100 chr5A 94.267 2250 67 14 1707 3942 654622289 654620088 0.000000e+00 3384
8 TraesCS5B01G497100 chr5A 95.780 1019 36 5 5384 6401 654618423 654617411 0.000000e+00 1637
9 TraesCS5B01G497100 chr5A 95.186 644 24 4 4674 5313 654619385 654618745 0.000000e+00 1011
10 TraesCS5B01G497100 chr5A 94.817 656 14 5 4024 4675 654620089 654619450 0.000000e+00 1005
11 TraesCS5B01G497100 chr5A 90.507 769 44 15 956 1712 654623118 654622367 0.000000e+00 989
12 TraesCS5B01G497100 chr5A 91.085 673 27 7 6406 7050 654617433 654616766 0.000000e+00 880
13 TraesCS5B01G497100 chr5A 94.000 100 3 3 3929 4025 505609581 505609680 1.590000e-31 148
14 TraesCS5B01G497100 chr1D 92.532 857 58 6 43 895 403063127 403062273 0.000000e+00 1223
15 TraesCS5B01G497100 chr1D 94.845 97 4 1 3931 4027 295954309 295954214 4.410000e-32 150
16 TraesCS5B01G497100 chr3D 92.065 857 62 6 43 895 591110643 591109789 0.000000e+00 1201
17 TraesCS5B01G497100 chr3A 92.155 854 60 7 46 895 634079254 634078404 0.000000e+00 1199
18 TraesCS5B01G497100 chr3A 92.467 531 38 2 43 572 595775692 595776221 0.000000e+00 758
19 TraesCS5B01G497100 chr1A 92.047 855 60 6 43 895 585642345 585641497 0.000000e+00 1195
20 TraesCS5B01G497100 chr1A 91.365 857 68 6 43 895 590117973 590117119 0.000000e+00 1168
21 TraesCS5B01G497100 chr1A 90.946 497 42 3 43 537 543489844 543490339 0.000000e+00 665
22 TraesCS5B01G497100 chr2D 84.802 454 63 6 447 895 137558123 137558575 1.080000e-122 451
23 TraesCS5B01G497100 chr2D 94.000 100 4 2 3927 4025 53145713 53145811 4.410000e-32 150
24 TraesCS5B01G497100 chr7B 75.910 797 165 27 57 839 544130854 544130071 4.000000e-102 383
25 TraesCS5B01G497100 chr7B 93.750 112 6 1 2864 2974 357651486 357651597 4.380000e-37 167
26 TraesCS5B01G497100 chr3B 93.578 109 6 1 2860 2968 672778077 672778184 2.040000e-35 161
27 TraesCS5B01G497100 chr6D 90.678 118 9 2 2854 2970 391925993 391925877 9.480000e-34 156
28 TraesCS5B01G497100 chr6D 89.916 119 7 5 2852 2968 317078777 317078892 1.590000e-31 148
29 TraesCS5B01G497100 chr6D 92.233 103 6 2 3933 4033 17316617 17316719 2.050000e-30 145
30 TraesCS5B01G497100 chr6B 90.678 118 7 4 2852 2968 507471663 507471549 3.410000e-33 154
31 TraesCS5B01G497100 chr6B 89.831 118 10 2 2854 2970 585524848 585524732 4.410000e-32 150
32 TraesCS5B01G497100 chr6B 93.814 97 6 0 3936 4032 471227574 471227670 5.710000e-31 147
33 TraesCS5B01G497100 chr6A 90.678 118 7 4 2852 2968 454677961 454678075 3.410000e-33 154
34 TraesCS5B01G497100 chr4A 93.333 105 6 1 3928 4032 556768051 556767948 3.410000e-33 154
35 TraesCS5B01G497100 chr4A 94.792 96 4 1 3930 4025 489039934 489039840 1.590000e-31 148
36 TraesCS5B01G497100 chr4A 92.381 105 6 2 3936 4038 597739877 597739981 1.590000e-31 148
37 TraesCS5B01G497100 chr7D 91.346 104 7 2 3926 4029 4643979 4644080 2.650000e-29 141


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 TraesCS5B01G497100 chr5B 664021200 664028258 7058 True 13036.000000 13036 100.0000 1 7059 1 chr5B.!!$R1 7058
1 TraesCS5B01G497100 chr5B 657200176 657201028 852 False 1182.000000 1182 91.7150 43 895 1 chr5B.!!$F1 852
2 TraesCS5B01G497100 chr5D 527497577 527506017 8440 True 2085.200000 4421 94.6758 43 7057 5 chr5D.!!$R1 7014
3 TraesCS5B01G497100 chr5A 654616766 654623118 6352 True 1484.333333 3384 93.6070 956 7050 6 chr5A.!!$R1 6094
4 TraesCS5B01G497100 chr1D 403062273 403063127 854 True 1223.000000 1223 92.5320 43 895 1 chr1D.!!$R2 852
5 TraesCS5B01G497100 chr3D 591109789 591110643 854 True 1201.000000 1201 92.0650 43 895 1 chr3D.!!$R1 852
6 TraesCS5B01G497100 chr3A 634078404 634079254 850 True 1199.000000 1199 92.1550 46 895 1 chr3A.!!$R1 849
7 TraesCS5B01G497100 chr3A 595775692 595776221 529 False 758.000000 758 92.4670 43 572 1 chr3A.!!$F1 529
8 TraesCS5B01G497100 chr1A 585641497 585642345 848 True 1195.000000 1195 92.0470 43 895 1 chr1A.!!$R1 852
9 TraesCS5B01G497100 chr1A 590117119 590117973 854 True 1168.000000 1168 91.3650 43 895 1 chr1A.!!$R2 852
10 TraesCS5B01G497100 chr7B 544130071 544130854 783 True 383.000000 383 75.9100 57 839 1 chr7B.!!$R1 782

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
41 42 0.331278 CCAAGGAGCACCCCACATTA 59.669 55.000 0.00 0.0 36.73 1.90 F
1258 2649 0.251787 GTGTGCCCCCTTCCAATTCT 60.252 55.000 0.00 0.0 0.00 2.40 F
1886 3371 0.246360 TCACTGTCCGCGTCATTGAT 59.754 50.000 4.92 0.0 0.00 2.57 F
2291 3779 1.126948 TGGCACAGTGTGATCAGGGA 61.127 55.000 27.37 0.0 35.23 4.20 F
4001 5608 2.034305 ACACTAGTGTCGAAAACGCTCT 59.966 45.455 22.95 0.0 45.69 4.09 F
4023 5630 0.042131 TATTGTGGGACGGAGGGAGT 59.958 55.000 0.00 0.0 0.00 3.85 F
5242 6923 1.188863 GTCTTGGGCTTGCCATGAAT 58.811 50.000 14.04 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1318 2709 0.250513 GAACTGCCTCCCACTGTAGG 59.749 60.000 0.00 0.0 35.86 3.18 R
2578 4068 0.537188 AGGACATCAAGTGCCTACCG 59.463 55.000 0.00 0.0 39.79 4.02 R
2955 4451 1.553248 CCATGTTGTACTCCCTCCGAA 59.447 52.381 0.00 0.0 0.00 4.30 R
4004 5611 0.042131 ACTCCCTCCGTCCCACAATA 59.958 55.000 0.00 0.0 0.00 1.90 R
5176 6857 0.179020 TGACCACCTCCTGCAAAGTG 60.179 55.000 0.00 0.0 0.00 3.16 R
5810 7753 1.286570 CAGCGCCTGCATTTTGTCA 59.713 52.632 2.29 0.0 46.23 3.58 R
6891 8876 1.112916 TGCACTGTTCTCTGGACCGA 61.113 55.000 0.00 0.0 0.00 4.69 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
21 22 2.450476 AGACATGGGATCTTTGGTTGC 58.550 47.619 0.00 0.00 0.00 4.17
22 23 1.478105 GACATGGGATCTTTGGTTGCC 59.522 52.381 0.00 0.00 0.00 4.52
23 24 0.826062 CATGGGATCTTTGGTTGCCC 59.174 55.000 0.00 0.00 39.29 5.36
24 25 1.857049 TGGGATCTTTGGTTGCCCA 59.143 52.632 0.00 0.00 46.10 5.36
31 32 2.605873 TTGGTTGCCCAAGGAGCA 59.394 55.556 0.00 0.00 45.93 4.26
32 33 1.832167 TTGGTTGCCCAAGGAGCAC 60.832 57.895 2.37 0.00 45.93 4.40
33 34 2.991540 GGTTGCCCAAGGAGCACC 60.992 66.667 0.00 0.00 40.69 5.01
34 35 2.991540 GTTGCCCAAGGAGCACCC 60.992 66.667 0.00 0.00 40.69 4.61
35 36 4.299796 TTGCCCAAGGAGCACCCC 62.300 66.667 0.00 0.00 40.69 4.95
38 39 3.579302 CCCAAGGAGCACCCCACA 61.579 66.667 0.00 0.00 36.73 4.17
39 40 2.765969 CCAAGGAGCACCCCACAT 59.234 61.111 0.00 0.00 36.73 3.21
40 41 1.077265 CCAAGGAGCACCCCACATT 59.923 57.895 0.00 0.00 36.73 2.71
41 42 0.331278 CCAAGGAGCACCCCACATTA 59.669 55.000 0.00 0.00 36.73 1.90
154 156 7.843490 AATTTTCAATGGCATCTTCATTCTG 57.157 32.000 0.00 0.00 33.08 3.02
177 179 6.364701 TGCACAGCAACTTATAAGGGAATAT 58.635 36.000 16.73 0.00 34.76 1.28
226 228 6.981559 GGTACAGAGATTTAATCGAGAAGCTT 59.018 38.462 0.00 0.00 0.00 3.74
227 229 8.136165 GGTACAGAGATTTAATCGAGAAGCTTA 58.864 37.037 0.00 0.00 0.00 3.09
230 232 8.035394 ACAGAGATTTAATCGAGAAGCTTACAA 58.965 33.333 0.00 0.00 0.00 2.41
233 235 8.779354 AGATTTAATCGAGAAGCTTACAAAGT 57.221 30.769 0.00 0.00 0.00 2.66
258 260 9.223099 GTAGGTAAGAAGCCATTTAACTTTGTA 57.777 33.333 0.00 0.00 30.02 2.41
279 281 1.697432 TGGTTCCTCCGACAAAGTCAT 59.303 47.619 0.00 0.00 39.52 3.06
281 283 2.347731 GTTCCTCCGACAAAGTCATCC 58.652 52.381 0.00 0.00 32.09 3.51
383 386 1.812571 CTGGCTAAACACCTTCGCAAT 59.187 47.619 0.00 0.00 0.00 3.56
472 475 2.906568 ACCAAGCATCCTCCCAAAATT 58.093 42.857 0.00 0.00 0.00 1.82
503 506 3.945921 CGACTATCACCCACAACTCTCTA 59.054 47.826 0.00 0.00 0.00 2.43
518 521 8.812329 CACAACTCTCTAACAGCATCTATAAAC 58.188 37.037 0.00 0.00 0.00 2.01
684 687 8.096414 AGCCATTTGCACAAAAGACTTATATTT 58.904 29.630 0.00 0.00 44.83 1.40
740 743 1.072266 TCCCTAGGTTGGCACACATT 58.928 50.000 8.29 0.00 39.29 2.71
747 750 3.505386 AGGTTGGCACACATTAATCCAA 58.495 40.909 2.27 2.27 39.29 3.53
755 758 6.014242 TGGCACACATTAATCCAATTTACCAA 60.014 34.615 0.00 0.00 0.00 3.67
777 780 6.017192 CCAAATGATATTTACGCACATCCTCA 60.017 38.462 0.00 0.00 0.00 3.86
788 791 2.733227 GCACATCCTCATTTTCTTGCCG 60.733 50.000 0.00 0.00 0.00 5.69
948 2339 1.270625 CCCGTAACTTTCCTCTGCACA 60.271 52.381 0.00 0.00 0.00 4.57
1153 2544 2.040043 AGCCCCATCTCCCCTCTG 60.040 66.667 0.00 0.00 0.00 3.35
1161 2552 0.693767 ATCTCCCCTCTGCCCTTCTG 60.694 60.000 0.00 0.00 0.00 3.02
1177 2568 1.458777 CTGCCCGTATACCCCAGGA 60.459 63.158 0.00 0.00 0.00 3.86
1198 2589 1.880340 GCAACGGCCATCTCTCTCG 60.880 63.158 2.24 0.00 0.00 4.04
1258 2649 0.251787 GTGTGCCCCCTTCCAATTCT 60.252 55.000 0.00 0.00 0.00 2.40
1261 2652 0.323360 TGCCCCCTTCCAATTCTTCG 60.323 55.000 0.00 0.00 0.00 3.79
1318 2709 1.389555 CCTAACCAATTTCGGCTCCC 58.610 55.000 0.00 0.00 0.00 4.30
1460 2861 3.130516 GCTGGGTTTTAATTAGGAGTGCC 59.869 47.826 0.00 0.00 0.00 5.01
1516 2917 8.767085 ACGACTAACTTCGAATATTTTGTCAAA 58.233 29.630 19.11 0.00 41.78 2.69
1517 2918 9.037417 CGACTAACTTCGAATATTTTGTCAAAC 57.963 33.333 19.11 0.00 41.78 2.93
1518 2919 9.872757 GACTAACTTCGAATATTTTGTCAAACA 57.127 29.630 16.57 0.00 0.00 2.83
1550 2951 9.935241 CTGACCAGCTATGTGATATATAAACTT 57.065 33.333 0.00 0.00 0.00 2.66
1551 2952 9.929180 TGACCAGCTATGTGATATATAAACTTC 57.071 33.333 0.00 0.00 0.00 3.01
1552 2953 9.372369 GACCAGCTATGTGATATATAAACTTCC 57.628 37.037 0.00 0.00 0.00 3.46
1553 2954 9.105844 ACCAGCTATGTGATATATAAACTTCCT 57.894 33.333 0.00 0.00 0.00 3.36
1611 3012 3.469008 TCGACCTCGATAAATGGCATT 57.531 42.857 6.96 6.96 44.22 3.56
1615 3016 5.408299 TCGACCTCGATAAATGGCATTTATG 59.592 40.000 37.13 28.94 43.46 1.90
1646 3047 6.016360 CCTTTTGACACAGACAACAATATCCA 60.016 38.462 0.00 0.00 0.00 3.41
1648 3049 6.741992 TTGACACAGACAACAATATCCATC 57.258 37.500 0.00 0.00 0.00 3.51
1681 3082 8.220434 GTGATTTAGCGTTAAACATTTGCAAAT 58.780 29.630 18.99 18.99 31.90 2.32
1694 3095 6.804770 CATTTGCAAATGGGAATTTTCTCA 57.195 33.333 34.70 1.63 42.82 3.27
1865 3350 3.842923 CGCTCCTCCGTGCCTGAT 61.843 66.667 0.00 0.00 0.00 2.90
1886 3371 0.246360 TCACTGTCCGCGTCATTGAT 59.754 50.000 4.92 0.00 0.00 2.57
1953 3438 5.917541 TGTCGGTTTTTAGTCTTCATGTC 57.082 39.130 0.00 0.00 0.00 3.06
1968 3453 6.917477 GTCTTCATGTCTTCTCTATGCTACTG 59.083 42.308 0.00 0.00 0.00 2.74
2032 3517 2.220824 GCCAACCGATTTTGTGCTTTTC 59.779 45.455 0.00 0.00 0.00 2.29
2165 3650 2.596452 GTGATGACAGTACTGTGTCCG 58.404 52.381 32.51 3.46 45.42 4.79
2201 3686 3.365364 GCAACTTGCAATCACTACTCCAC 60.365 47.826 8.97 0.00 44.26 4.02
2209 3694 4.808364 GCAATCACTACTCCACTCTCAATC 59.192 45.833 0.00 0.00 0.00 2.67
2224 3709 9.906660 CCACTCTCAATCAGTAATAGAAGATAC 57.093 37.037 0.00 0.00 0.00 2.24
2291 3779 1.126948 TGGCACAGTGTGATCAGGGA 61.127 55.000 27.37 0.00 35.23 4.20
2335 3823 2.557452 CCCTCCCTGTGCTATGGTTTTT 60.557 50.000 0.00 0.00 0.00 1.94
2336 3824 2.493278 CCTCCCTGTGCTATGGTTTTTG 59.507 50.000 0.00 0.00 0.00 2.44
2352 3840 5.480772 TGGTTTTTGGAACCACTCAAGTTTA 59.519 36.000 6.54 0.00 44.74 2.01
2353 3841 6.014499 TGGTTTTTGGAACCACTCAAGTTTAA 60.014 34.615 6.54 0.00 44.74 1.52
2441 3931 7.282224 TGTTGTTGTTTCTTGAGCAGTTACTAT 59.718 33.333 0.00 0.00 0.00 2.12
2578 4068 4.515191 TGCTTCGGGAATAAGATATTGTGC 59.485 41.667 0.00 0.00 0.00 4.57
2611 4101 6.772716 ACTTGATGTCCTGTTTATTGACTGTT 59.227 34.615 0.00 0.00 0.00 3.16
2612 4102 6.558771 TGATGTCCTGTTTATTGACTGTTG 57.441 37.500 0.00 0.00 0.00 3.33
2667 4157 9.556030 CTAATATGAGCATAGCACAATGAAATG 57.444 33.333 0.00 0.00 32.39 2.32
2742 4232 6.981559 GCAATAGAAGTCAGGTAGTAAAGAGG 59.018 42.308 0.00 0.00 0.00 3.69
2955 4451 8.731275 TCCATTTGAACGACAAGTAATATGAT 57.269 30.769 0.00 0.00 39.77 2.45
2997 4493 3.500471 GGAAATTGGAGGGACAGACCTTT 60.500 47.826 0.00 0.00 42.10 3.11
3010 4506 9.004231 AGGGACAGACCTTTATAAATAAGATGT 57.996 33.333 0.00 1.36 37.69 3.06
3089 4592 7.928706 CCTACACAAAGTATCCTATTGAAGAGG 59.071 40.741 0.00 0.00 35.17 3.69
3676 5187 7.804843 TCTAGAGGTAGTCAAATACAGTAGC 57.195 40.000 0.00 0.00 0.00 3.58
3737 5248 8.360390 TGCGTGATCTGAATCAGTACTAATATT 58.640 33.333 10.36 0.00 42.53 1.28
3800 5407 7.582667 TGTCTAGTAGCTTATGCATTACTCA 57.417 36.000 3.54 0.00 42.74 3.41
3952 5559 9.822185 TTATTTTAGTTAATTACTCCCTCCGTC 57.178 33.333 0.00 0.00 38.33 4.79
3953 5560 5.859205 TTAGTTAATTACTCCCTCCGTCC 57.141 43.478 0.00 0.00 38.33 4.79
3954 5561 3.036819 AGTTAATTACTCCCTCCGTCCC 58.963 50.000 0.00 0.00 28.23 4.46
3955 5562 2.767960 GTTAATTACTCCCTCCGTCCCA 59.232 50.000 0.00 0.00 0.00 4.37
3956 5563 2.191981 AATTACTCCCTCCGTCCCAT 57.808 50.000 0.00 0.00 0.00 4.00
3957 5564 3.339713 AATTACTCCCTCCGTCCCATA 57.660 47.619 0.00 0.00 0.00 2.74
3958 5565 2.852714 TTACTCCCTCCGTCCCATAA 57.147 50.000 0.00 0.00 0.00 1.90
3959 5566 3.339713 TTACTCCCTCCGTCCCATAAT 57.660 47.619 0.00 0.00 0.00 1.28
3960 5567 4.474303 TTACTCCCTCCGTCCCATAATA 57.526 45.455 0.00 0.00 0.00 0.98
3961 5568 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
3962 5569 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
3963 5570 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
3964 5571 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
3965 5572 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
3966 5573 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
3967 5574 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
3968 5575 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
3969 5576 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
3970 5577 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
3971 5578 4.863131 CCGTCCCATAATATAAGAGCGTTC 59.137 45.833 0.00 0.00 0.00 3.95
3972 5579 5.336531 CCGTCCCATAATATAAGAGCGTTCT 60.337 44.000 0.00 0.00 34.29 3.01
3973 5580 6.157211 CGTCCCATAATATAAGAGCGTTCTT 58.843 40.000 18.78 18.78 45.45 2.52
3974 5581 6.645415 CGTCCCATAATATAAGAGCGTTCTTT 59.355 38.462 19.95 10.21 40.79 2.52
3975 5582 7.811236 CGTCCCATAATATAAGAGCGTTCTTTA 59.189 37.037 19.95 11.90 40.79 1.85
3976 5583 8.923683 GTCCCATAATATAAGAGCGTTCTTTAC 58.076 37.037 19.95 0.00 40.79 2.01
3977 5584 8.644216 TCCCATAATATAAGAGCGTTCTTTACA 58.356 33.333 19.95 2.51 40.79 2.41
3978 5585 8.709646 CCCATAATATAAGAGCGTTCTTTACAC 58.290 37.037 19.95 0.00 40.79 2.90
3979 5586 9.477484 CCATAATATAAGAGCGTTCTTTACACT 57.523 33.333 19.95 4.53 40.79 3.55
3983 5590 8.853469 ATATAAGAGCGTTCTTTACACTACAC 57.147 34.615 19.95 0.00 40.79 2.90
3984 5591 4.850347 AGAGCGTTCTTTACACTACACT 57.150 40.909 0.00 0.00 0.00 3.55
3985 5592 5.954296 AGAGCGTTCTTTACACTACACTA 57.046 39.130 0.00 0.00 0.00 2.74
3986 5593 5.940595 AGAGCGTTCTTTACACTACACTAG 58.059 41.667 0.00 0.00 0.00 2.57
3987 5594 5.472820 AGAGCGTTCTTTACACTACACTAGT 59.527 40.000 0.00 0.00 40.28 2.57
3998 5605 3.303406 ACTACACTAGTGTCGAAAACGC 58.697 45.455 31.11 0.00 43.74 4.84
4000 5607 2.391879 ACACTAGTGTCGAAAACGCTC 58.608 47.619 22.95 0.00 45.69 5.03
4001 5608 2.034305 ACACTAGTGTCGAAAACGCTCT 59.966 45.455 22.95 0.00 45.69 4.09
4002 5609 3.050619 CACTAGTGTCGAAAACGCTCTT 58.949 45.455 15.06 0.00 45.69 2.85
4003 5610 4.224433 CACTAGTGTCGAAAACGCTCTTA 58.776 43.478 15.06 0.00 45.69 2.10
4004 5611 4.857588 CACTAGTGTCGAAAACGCTCTTAT 59.142 41.667 15.06 0.00 45.69 1.73
4005 5612 6.025896 CACTAGTGTCGAAAACGCTCTTATA 58.974 40.000 15.06 0.00 45.69 0.98
4006 5613 6.691818 CACTAGTGTCGAAAACGCTCTTATAT 59.308 38.462 15.06 0.00 45.69 0.86
4007 5614 7.220300 CACTAGTGTCGAAAACGCTCTTATATT 59.780 37.037 15.06 0.00 45.69 1.28
4008 5615 6.332504 AGTGTCGAAAACGCTCTTATATTG 57.667 37.500 0.00 0.00 45.69 1.90
4009 5616 5.867716 AGTGTCGAAAACGCTCTTATATTGT 59.132 36.000 0.00 0.00 45.69 2.71
4010 5617 5.952064 GTGTCGAAAACGCTCTTATATTGTG 59.048 40.000 0.00 0.00 35.42 3.33
4011 5618 5.062934 TGTCGAAAACGCTCTTATATTGTGG 59.937 40.000 0.00 0.00 0.00 4.17
4012 5619 4.569162 TCGAAAACGCTCTTATATTGTGGG 59.431 41.667 0.00 0.00 0.00 4.61
4013 5620 4.569162 CGAAAACGCTCTTATATTGTGGGA 59.431 41.667 0.00 0.00 0.00 4.37
4014 5621 5.501897 CGAAAACGCTCTTATATTGTGGGAC 60.502 44.000 0.00 0.00 0.00 4.46
4015 5622 3.093717 ACGCTCTTATATTGTGGGACG 57.906 47.619 0.00 0.00 0.00 4.79
4016 5623 2.223971 ACGCTCTTATATTGTGGGACGG 60.224 50.000 0.00 0.00 0.00 4.79
4017 5624 2.035449 CGCTCTTATATTGTGGGACGGA 59.965 50.000 0.00 0.00 0.00 4.69
4018 5625 3.654414 GCTCTTATATTGTGGGACGGAG 58.346 50.000 0.00 0.00 0.00 4.63
4019 5626 3.555168 GCTCTTATATTGTGGGACGGAGG 60.555 52.174 0.00 0.00 0.00 4.30
4020 5627 2.969950 TCTTATATTGTGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
4021 5628 2.779429 TATATTGTGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
4022 5629 1.424638 ATATTGTGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
4023 5630 0.042131 TATTGTGGGACGGAGGGAGT 59.958 55.000 0.00 0.00 0.00 3.85
4024 5631 0.042131 ATTGTGGGACGGAGGGAGTA 59.958 55.000 0.00 0.00 0.00 2.59
4078 5685 8.884124 TTCTTTTCACAATCCTTTCTATCCAT 57.116 30.769 0.00 0.00 0.00 3.41
4202 5809 8.972458 TTATCCCATTTGATCGATCTGTTTTA 57.028 30.769 25.02 1.75 0.00 1.52
4402 6009 5.124297 TCATTGATTGACTACAACTGCATGG 59.876 40.000 0.00 0.00 38.90 3.66
4678 6356 6.631016 TCCTAGACAAGCACTAAACTATGTG 58.369 40.000 0.00 0.00 37.26 3.21
4688 6366 7.904205 AGCACTAAACTATGTGGTAAGTAGTT 58.096 34.615 0.00 0.00 42.13 2.24
4876 6557 5.359756 TCCAGATGAACCATATCTCAAACG 58.640 41.667 0.00 0.00 32.75 3.60
4880 6561 7.307632 CCAGATGAACCATATCTCAAACGAATC 60.308 40.741 0.00 0.00 32.75 2.52
4889 6570 5.613358 ATCTCAAACGAATCCTGTCAAAC 57.387 39.130 0.00 0.00 0.00 2.93
4937 6618 8.865590 TGCAAAAACAATTAAAGTCTTCCTAC 57.134 30.769 0.00 0.00 0.00 3.18
4994 6675 6.703607 CAGTACTGTTCCATTCATACTGGATC 59.296 42.308 15.06 0.00 42.26 3.36
5176 6857 3.191162 TGCAAACCTGTGATATGAACTGC 59.809 43.478 0.00 0.00 0.00 4.40
5242 6923 1.188863 GTCTTGGGCTTGCCATGAAT 58.811 50.000 14.04 0.00 0.00 2.57
5257 6938 6.425735 TGCCATGAATAAGATTTCTCTTGGA 58.574 36.000 0.00 0.00 41.83 3.53
5258 6939 6.544931 TGCCATGAATAAGATTTCTCTTGGAG 59.455 38.462 0.00 0.00 41.83 3.86
5290 6971 7.398829 TGCCAACTATATCCTTTACTGTTTGA 58.601 34.615 0.00 0.00 0.00 2.69
5291 6972 7.552687 TGCCAACTATATCCTTTACTGTTTGAG 59.447 37.037 0.00 0.00 0.00 3.02
5489 7432 4.732672 TCTGTCTCATGGTCTCAATCTG 57.267 45.455 0.00 0.00 0.00 2.90
5502 7445 5.832060 GGTCTCAATCTGGAATTGGATTCAT 59.168 40.000 3.39 0.00 41.03 2.57
5631 7574 2.543067 GAAGATCGGTTGGCCTGCCT 62.543 60.000 9.97 0.00 36.94 4.75
5757 7700 5.694910 TGTTGACTACTTGAACCGAGAAATC 59.305 40.000 0.00 0.00 0.00 2.17
5801 7744 6.242396 AGTAGTCCTGCCTATGATGTACTAG 58.758 44.000 0.00 0.00 0.00 2.57
5810 7753 5.148502 CCTATGATGTACTAGTTCCCAGGT 58.851 45.833 0.00 0.00 0.00 4.00
5875 7818 1.566298 ATCTGGCTTCTTTCGGGGCT 61.566 55.000 0.00 0.00 0.00 5.19
5995 7938 0.814457 TCGCTGGTGTTTGCAACTTT 59.186 45.000 0.00 0.00 32.44 2.66
6000 7943 4.259770 CGCTGGTGTTTGCAACTTTTAAAG 60.260 41.667 0.00 2.81 32.44 1.85
6163 8106 1.312884 AATGGGAGGCCCTTCAGATT 58.687 50.000 0.00 0.00 45.70 2.40
6164 8107 1.312884 ATGGGAGGCCCTTCAGATTT 58.687 50.000 0.00 0.00 45.70 2.17
6168 8111 3.076785 TGGGAGGCCCTTCAGATTTAAAA 59.923 43.478 0.00 0.00 45.70 1.52
6169 8112 4.093743 GGGAGGCCCTTCAGATTTAAAAA 58.906 43.478 0.00 0.00 41.34 1.94
6170 8113 4.160439 GGGAGGCCCTTCAGATTTAAAAAG 59.840 45.833 0.00 0.00 41.34 2.27
6205 8148 6.066054 TGTTGATTATGTCGTGCAGAAAAA 57.934 33.333 0.00 0.00 31.56 1.94
6297 8240 2.341257 CATGACCGGACAAAGACAGAG 58.659 52.381 9.46 0.00 0.00 3.35
6337 8281 9.219603 CTCTAAATACCTCAATCACAAAGACAA 57.780 33.333 0.00 0.00 0.00 3.18
6363 8318 8.535335 AGAAACTATCTCAAGCACTGAAAGATA 58.465 33.333 0.00 0.00 32.22 1.98
6398 8353 1.605710 CCACAGAACAAGAAGCACCTG 59.394 52.381 0.00 0.00 0.00 4.00
6399 8354 2.292267 CACAGAACAAGAAGCACCTGT 58.708 47.619 0.00 0.00 35.51 4.00
6400 8355 3.466836 CACAGAACAAGAAGCACCTGTA 58.533 45.455 0.00 0.00 34.01 2.74
6401 8356 3.248602 CACAGAACAAGAAGCACCTGTAC 59.751 47.826 0.00 0.00 34.01 2.90
6402 8357 3.134804 ACAGAACAAGAAGCACCTGTACT 59.865 43.478 0.00 0.00 33.65 2.73
6403 8358 4.130118 CAGAACAAGAAGCACCTGTACTT 58.870 43.478 0.00 0.00 0.00 2.24
6404 8359 4.576463 CAGAACAAGAAGCACCTGTACTTT 59.424 41.667 0.00 0.00 0.00 2.66
6405 8360 4.816925 AGAACAAGAAGCACCTGTACTTTC 59.183 41.667 0.00 0.00 0.00 2.62
6406 8361 3.477530 ACAAGAAGCACCTGTACTTTCC 58.522 45.455 0.00 0.00 0.00 3.13
6407 8362 3.118038 ACAAGAAGCACCTGTACTTTCCA 60.118 43.478 0.00 0.00 0.00 3.53
6408 8363 3.127425 AGAAGCACCTGTACTTTCCAC 57.873 47.619 0.00 0.00 0.00 4.02
6409 8364 2.438021 AGAAGCACCTGTACTTTCCACA 59.562 45.455 0.00 0.00 0.00 4.17
6410 8365 2.550830 AGCACCTGTACTTTCCACAG 57.449 50.000 0.00 0.00 42.52 3.66
6411 8366 2.047061 AGCACCTGTACTTTCCACAGA 58.953 47.619 4.11 0.00 45.10 3.41
6412 8367 2.639839 AGCACCTGTACTTTCCACAGAT 59.360 45.455 4.11 0.00 45.10 2.90
6413 8368 3.003480 GCACCTGTACTTTCCACAGATC 58.997 50.000 4.11 0.00 45.10 2.75
6414 8369 3.557054 GCACCTGTACTTTCCACAGATCA 60.557 47.826 4.11 0.00 45.10 2.92
6415 8370 4.641396 CACCTGTACTTTCCACAGATCAA 58.359 43.478 4.11 0.00 45.10 2.57
6416 8371 4.692625 CACCTGTACTTTCCACAGATCAAG 59.307 45.833 4.11 0.00 45.10 3.02
6417 8372 4.593206 ACCTGTACTTTCCACAGATCAAGA 59.407 41.667 4.11 0.00 45.10 3.02
6418 8373 5.071788 ACCTGTACTTTCCACAGATCAAGAA 59.928 40.000 4.11 0.00 45.10 2.52
6419 8374 5.641209 CCTGTACTTTCCACAGATCAAGAAG 59.359 44.000 4.11 0.00 45.10 2.85
6420 8375 4.997395 TGTACTTTCCACAGATCAAGAAGC 59.003 41.667 0.00 0.00 0.00 3.86
6421 8376 4.090761 ACTTTCCACAGATCAAGAAGCA 57.909 40.909 0.00 0.00 0.00 3.91
6422 8377 3.817647 ACTTTCCACAGATCAAGAAGCAC 59.182 43.478 0.00 0.00 0.00 4.40
6423 8378 2.479566 TCCACAGATCAAGAAGCACC 57.520 50.000 0.00 0.00 0.00 5.01
6424 8379 1.980765 TCCACAGATCAAGAAGCACCT 59.019 47.619 0.00 0.00 0.00 4.00
6425 8380 2.027745 TCCACAGATCAAGAAGCACCTC 60.028 50.000 0.00 0.00 0.00 3.85
6653 8637 5.336150 TCCAAGTTAGAGCTCTCTTCATG 57.664 43.478 22.17 13.63 40.93 3.07
6739 8724 3.210227 TCATCGACTCCTGCAAACAAAA 58.790 40.909 0.00 0.00 0.00 2.44
6741 8726 3.896648 TCGACTCCTGCAAACAAAATC 57.103 42.857 0.00 0.00 0.00 2.17
6891 8876 2.129555 ATCCAGTTTGGCTGCTCCGT 62.130 55.000 0.00 0.00 43.71 4.69
6973 8958 3.003394 ACCGAGATTGGATCAAATGCA 57.997 42.857 0.00 0.00 0.00 3.96
7004 8992 7.120579 CCTTGTATTGTTGCCTATGAACAGTTA 59.879 37.037 0.00 0.00 34.85 2.24
7007 8995 9.104965 TGTATTGTTGCCTATGAACAGTTATAC 57.895 33.333 0.00 0.00 34.85 1.47
7009 8997 8.752005 ATTGTTGCCTATGAACAGTTATACAT 57.248 30.769 0.00 0.00 34.85 2.29
7010 8998 9.845740 ATTGTTGCCTATGAACAGTTATACATA 57.154 29.630 0.00 0.00 34.85 2.29
7011 8999 8.887036 TGTTGCCTATGAACAGTTATACATAG 57.113 34.615 11.24 11.24 40.70 2.23
7052 9040 6.855836 CATCCATGCTTTGCTAGTTTTTCTA 58.144 36.000 0.00 0.00 0.00 2.10
7053 9041 7.486647 CATCCATGCTTTGCTAGTTTTTCTAT 58.513 34.615 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.827921 GCAACCAAAGATCCCATGTCTT 59.172 45.455 0.00 0.00 37.52 3.01
2 3 1.478105 GGCAACCAAAGATCCCATGTC 59.522 52.381 0.00 0.00 0.00 3.06
3 4 1.560505 GGCAACCAAAGATCCCATGT 58.439 50.000 0.00 0.00 0.00 3.21
17 18 2.991540 GGGTGCTCCTTGGGCAAC 60.992 66.667 4.53 0.00 45.58 4.17
18 19 4.299796 GGGGTGCTCCTTGGGCAA 62.300 66.667 4.53 0.00 41.54 4.52
21 22 2.445492 AATGTGGGGTGCTCCTTGGG 62.445 60.000 4.53 0.00 35.33 4.12
22 23 0.331278 TAATGTGGGGTGCTCCTTGG 59.669 55.000 4.53 0.00 35.33 3.61
23 24 1.271871 TGTAATGTGGGGTGCTCCTTG 60.272 52.381 4.53 0.00 35.33 3.61
24 25 1.072266 TGTAATGTGGGGTGCTCCTT 58.928 50.000 4.53 0.00 35.33 3.36
25 26 0.328258 GTGTAATGTGGGGTGCTCCT 59.672 55.000 4.53 0.00 35.33 3.69
26 27 0.037590 TGTGTAATGTGGGGTGCTCC 59.962 55.000 0.00 0.00 0.00 4.70
27 28 1.904287 TTGTGTAATGTGGGGTGCTC 58.096 50.000 0.00 0.00 0.00 4.26
28 29 2.170166 CATTGTGTAATGTGGGGTGCT 58.830 47.619 0.00 0.00 39.05 4.40
29 30 1.404047 GCATTGTGTAATGTGGGGTGC 60.404 52.381 0.00 0.00 44.41 5.01
30 31 2.170166 AGCATTGTGTAATGTGGGGTG 58.830 47.619 0.00 0.00 44.41 4.61
31 32 2.603075 AGCATTGTGTAATGTGGGGT 57.397 45.000 0.00 0.00 44.41 4.95
32 33 3.181487 GCTAAGCATTGTGTAATGTGGGG 60.181 47.826 0.00 0.00 44.41 4.96
33 34 3.443329 TGCTAAGCATTGTGTAATGTGGG 59.557 43.478 0.00 0.00 44.41 4.61
34 35 4.414852 GTGCTAAGCATTGTGTAATGTGG 58.585 43.478 0.00 0.00 44.41 4.17
35 36 4.156556 AGGTGCTAAGCATTGTGTAATGTG 59.843 41.667 0.00 0.00 44.41 3.21
36 37 4.335416 AGGTGCTAAGCATTGTGTAATGT 58.665 39.130 0.00 0.00 44.41 2.71
37 38 4.970662 AGGTGCTAAGCATTGTGTAATG 57.029 40.909 0.00 0.00 45.17 1.90
38 39 5.105756 GGAAAGGTGCTAAGCATTGTGTAAT 60.106 40.000 0.00 0.00 41.91 1.89
39 40 4.217550 GGAAAGGTGCTAAGCATTGTGTAA 59.782 41.667 0.00 0.00 41.91 2.41
40 41 3.756434 GGAAAGGTGCTAAGCATTGTGTA 59.244 43.478 0.00 0.00 41.91 2.90
41 42 2.558359 GGAAAGGTGCTAAGCATTGTGT 59.442 45.455 0.00 0.00 41.91 3.72
154 156 6.884280 ATATTCCCTTATAAGTTGCTGTGC 57.116 37.500 11.50 0.00 0.00 4.57
226 228 9.223099 GTTAAATGGCTTCTTACCTACTTTGTA 57.777 33.333 0.00 0.00 0.00 2.41
227 229 7.942894 AGTTAAATGGCTTCTTACCTACTTTGT 59.057 33.333 0.00 0.00 0.00 2.83
230 232 8.793592 CAAAGTTAAATGGCTTCTTACCTACTT 58.206 33.333 0.00 0.00 0.00 2.24
233 235 9.969001 ATACAAAGTTAAATGGCTTCTTACCTA 57.031 29.630 0.00 0.00 0.00 3.08
258 260 1.697432 TGACTTTGTCGGAGGAACCAT 59.303 47.619 0.00 0.00 38.90 3.55
279 281 8.255206 ACAAATTACTTGATATGTGTAGTCGGA 58.745 33.333 0.00 0.00 38.50 4.55
281 283 9.901724 GAACAAATTACTTGATATGTGTAGTCG 57.098 33.333 0.00 0.00 38.50 4.18
383 386 3.627395 CCTTTGGTAGGCATGTCACTA 57.373 47.619 0.00 0.00 37.17 2.74
472 475 3.998341 GTGGGTGATAGTCGCAAAACTAA 59.002 43.478 0.00 0.00 35.47 2.24
485 488 4.081642 GCTGTTAGAGAGTTGTGGGTGATA 60.082 45.833 0.00 0.00 0.00 2.15
518 521 8.292444 TGGTTTGATGGAGGTTAAAGATATTG 57.708 34.615 0.00 0.00 0.00 1.90
712 715 0.181350 CAACCTAGGGATCAGGGTGC 59.819 60.000 14.81 0.00 43.68 5.01
747 750 9.677567 GATGTGCGTAAATATCATTTGGTAAAT 57.322 29.630 0.00 0.00 0.00 1.40
755 758 7.750229 AATGAGGATGTGCGTAAATATCATT 57.250 32.000 9.46 9.46 31.79 2.57
777 780 0.966179 GGTTGGTCCGGCAAGAAAAT 59.034 50.000 0.00 0.00 0.00 1.82
808 811 3.119955 GGCGTGGGTAAAAGATTTGACTC 60.120 47.826 0.00 0.00 0.00 3.36
850 853 1.180029 GCATTCCCAGTCACATGCTT 58.820 50.000 0.00 0.00 39.20 3.91
923 2314 3.129502 GGAAAGTTACGGGCCGGC 61.130 66.667 31.78 21.18 0.00 6.13
1153 2544 1.070957 GGTATACGGGCAGAAGGGC 59.929 63.158 0.00 0.00 42.44 5.19
1161 2552 1.755393 CTGTCCTGGGGTATACGGGC 61.755 65.000 0.00 0.00 34.27 6.13
1177 2568 1.078848 GAGAGATGGCCGTTGCTGT 60.079 57.895 0.00 0.00 37.74 4.40
1318 2709 0.250513 GAACTGCCTCCCACTGTAGG 59.749 60.000 0.00 0.00 35.86 3.18
1334 2725 2.432628 CGAGGTGGTGGCGAGAAC 60.433 66.667 0.00 0.00 0.00 3.01
1549 2950 9.627123 ACGAGGAAATTGATGATTTATAAGGAA 57.373 29.630 0.00 0.00 38.06 3.36
1611 3012 2.243810 GTGTCAAAAGGGCCACCATAA 58.756 47.619 6.18 0.00 40.13 1.90
1615 3016 0.467290 TCTGTGTCAAAAGGGCCACC 60.467 55.000 6.18 0.00 0.00 4.61
1646 3047 3.895232 ACGCTAAATCACTCTGTGGAT 57.105 42.857 0.00 0.00 33.87 3.41
1648 3049 5.178623 TGTTTAACGCTAAATCACTCTGTGG 59.821 40.000 0.00 0.00 33.87 4.17
1681 3082 6.976934 AGCTAAAAGTTGAGAAAATTCCCA 57.023 33.333 0.00 0.00 0.00 4.37
1694 3095 9.077885 TCCATCTTCAAATACAAGCTAAAAGTT 57.922 29.630 0.00 0.00 0.00 2.66
1741 3225 8.251383 TGTAGAAACCTTAGGAGATGGATAAG 57.749 38.462 4.77 0.00 0.00 1.73
1865 3350 0.943835 CAATGACGCGGACAGTGACA 60.944 55.000 23.66 6.96 39.11 3.58
1886 3371 1.137675 CCAAGATGGAGCGATGACTCA 59.862 52.381 0.00 0.00 40.96 3.41
1953 3438 8.659925 ATGAATTGAACAGTAGCATAGAGAAG 57.340 34.615 0.00 0.00 0.00 2.85
2032 3517 8.792830 TTTCTCCACAACCATATCTAAGAAAG 57.207 34.615 0.00 0.00 0.00 2.62
2151 3636 6.770746 ATAGAATTACGGACACAGTACTGT 57.229 37.500 22.95 22.95 46.17 3.55
2165 3650 5.938883 GCAAGTTGCAGCAATAGAATTAC 57.061 39.130 22.90 0.00 44.26 1.89
2209 3694 7.591795 CGGTACTGCTTGTATCTTCTATTACTG 59.408 40.741 0.00 0.00 33.23 2.74
2261 3749 3.085533 ACACTGTGCCAAGTACAACAAA 58.914 40.909 7.90 0.00 0.00 2.83
2312 3800 1.384502 CCATAGCACAGGGAGGGGA 60.385 63.158 0.00 0.00 0.00 4.81
2335 3823 7.776030 TGTAATTCTTAAACTTGAGTGGTTCCA 59.224 33.333 0.00 0.00 0.00 3.53
2336 3824 8.161699 TGTAATTCTTAAACTTGAGTGGTTCC 57.838 34.615 0.00 0.00 0.00 3.62
2352 3840 5.352569 CGATGGACTTGAGCTTGTAATTCTT 59.647 40.000 0.00 0.00 0.00 2.52
2353 3841 4.872691 CGATGGACTTGAGCTTGTAATTCT 59.127 41.667 0.00 0.00 0.00 2.40
2478 3968 5.358725 TCATCACGCCTCTAACATAGTACAA 59.641 40.000 0.00 0.00 0.00 2.41
2485 3975 6.038271 GGTAAAAATCATCACGCCTCTAACAT 59.962 38.462 0.00 0.00 0.00 2.71
2540 4030 3.947841 GCACGCGCAAGACACCAA 61.948 61.111 5.73 0.00 43.02 3.67
2578 4068 0.537188 AGGACATCAAGTGCCTACCG 59.463 55.000 0.00 0.00 39.79 4.02
2611 4101 7.225784 ACCTGTTATGTGTAAAATGAATGCA 57.774 32.000 0.00 0.00 0.00 3.96
2612 4102 8.532977 AAACCTGTTATGTGTAAAATGAATGC 57.467 30.769 0.00 0.00 0.00 3.56
2742 4232 5.922544 GTGGCATTTATGATTATCTGGTTGC 59.077 40.000 0.00 0.00 0.00 4.17
2955 4451 1.553248 CCATGTTGTACTCCCTCCGAA 59.447 52.381 0.00 0.00 0.00 4.30
3089 4592 3.066760 GGCCAATAGTTTCTACATGCACC 59.933 47.826 0.00 0.00 0.00 5.01
3159 4662 8.447924 AGATGAAGTATGATGGAAATCACTTG 57.552 34.615 0.00 0.00 32.79 3.16
3785 5392 7.378966 TCTACTATGGTGAGTAATGCATAAGC 58.621 38.462 0.00 0.00 34.80 3.09
3800 5407 6.198639 AGAAGGACAGAACATCTACTATGGT 58.801 40.000 0.00 0.00 0.00 3.55
3942 5549 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
3943 5550 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
3944 5551 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
3945 5552 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
3946 5553 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
3947 5554 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
3948 5555 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
3949 5556 5.710984 AGAACGCTCTTATATTATGGGACG 58.289 41.667 0.00 0.00 0.00 4.79
3950 5557 7.964604 AAAGAACGCTCTTATATTATGGGAC 57.035 36.000 0.67 0.00 41.23 4.46
3951 5558 8.644216 TGTAAAGAACGCTCTTATATTATGGGA 58.356 33.333 0.67 0.00 41.23 4.37
3952 5559 8.709646 GTGTAAAGAACGCTCTTATATTATGGG 58.290 37.037 0.67 0.00 41.23 4.00
3953 5560 9.477484 AGTGTAAAGAACGCTCTTATATTATGG 57.523 33.333 0.67 0.00 46.05 2.74
3957 5564 9.298774 GTGTAGTGTAAAGAACGCTCTTATATT 57.701 33.333 0.67 0.00 46.05 1.28
3958 5565 8.684520 AGTGTAGTGTAAAGAACGCTCTTATAT 58.315 33.333 0.67 0.00 46.05 0.86
3959 5566 8.048534 AGTGTAGTGTAAAGAACGCTCTTATA 57.951 34.615 0.67 0.00 46.05 0.98
3960 5567 6.921914 AGTGTAGTGTAAAGAACGCTCTTAT 58.078 36.000 0.67 0.00 46.05 1.73
3961 5568 6.323203 AGTGTAGTGTAAAGAACGCTCTTA 57.677 37.500 0.67 0.00 46.05 2.10
3962 5569 5.197682 AGTGTAGTGTAAAGAACGCTCTT 57.802 39.130 0.00 0.00 46.05 2.85
3963 5570 4.850347 AGTGTAGTGTAAAGAACGCTCT 57.150 40.909 0.00 0.00 46.05 4.09
3964 5571 5.568296 CACTAGTGTAGTGTAAAGAACGCTC 59.432 44.000 15.06 0.00 46.05 5.03
3977 5584 3.004106 AGCGTTTTCGACACTAGTGTAGT 59.996 43.478 27.98 6.32 45.05 2.73
3978 5585 3.562505 AGCGTTTTCGACACTAGTGTAG 58.437 45.455 27.98 26.46 45.05 2.74
3979 5586 3.251729 AGAGCGTTTTCGACACTAGTGTA 59.748 43.478 27.98 11.50 45.05 2.90
3991 5598 5.501897 CGTCCCACAATATAAGAGCGTTTTC 60.502 44.000 0.00 0.00 0.00 2.29
3992 5599 4.331717 CGTCCCACAATATAAGAGCGTTTT 59.668 41.667 0.00 0.00 0.00 2.43
3993 5600 3.869246 CGTCCCACAATATAAGAGCGTTT 59.131 43.478 0.00 0.00 0.00 3.60
3994 5601 3.454375 CGTCCCACAATATAAGAGCGTT 58.546 45.455 0.00 0.00 0.00 4.84
3995 5602 2.223971 CCGTCCCACAATATAAGAGCGT 60.224 50.000 0.00 0.00 0.00 5.07
3996 5603 2.035449 TCCGTCCCACAATATAAGAGCG 59.965 50.000 0.00 0.00 0.00 5.03
3997 5604 3.555168 CCTCCGTCCCACAATATAAGAGC 60.555 52.174 0.00 0.00 0.00 4.09
3998 5605 3.006967 CCCTCCGTCCCACAATATAAGAG 59.993 52.174 0.00 0.00 0.00 2.85
3999 5606 2.969950 CCCTCCGTCCCACAATATAAGA 59.030 50.000 0.00 0.00 0.00 2.10
4000 5607 2.969950 TCCCTCCGTCCCACAATATAAG 59.030 50.000 0.00 0.00 0.00 1.73
4001 5608 2.969950 CTCCCTCCGTCCCACAATATAA 59.030 50.000 0.00 0.00 0.00 0.98
4002 5609 2.090943 ACTCCCTCCGTCCCACAATATA 60.091 50.000 0.00 0.00 0.00 0.86
4003 5610 1.344087 ACTCCCTCCGTCCCACAATAT 60.344 52.381 0.00 0.00 0.00 1.28
4004 5611 0.042131 ACTCCCTCCGTCCCACAATA 59.958 55.000 0.00 0.00 0.00 1.90
4005 5612 0.042131 TACTCCCTCCGTCCCACAAT 59.958 55.000 0.00 0.00 0.00 2.71
4006 5613 0.613853 CTACTCCCTCCGTCCCACAA 60.614 60.000 0.00 0.00 0.00 3.33
4007 5614 1.000019 CTACTCCCTCCGTCCCACA 60.000 63.158 0.00 0.00 0.00 4.17
4008 5615 0.614134 AACTACTCCCTCCGTCCCAC 60.614 60.000 0.00 0.00 0.00 4.61
4009 5616 0.115745 AAACTACTCCCTCCGTCCCA 59.884 55.000 0.00 0.00 0.00 4.37
4010 5617 2.149973 TAAACTACTCCCTCCGTCCC 57.850 55.000 0.00 0.00 0.00 4.46
4011 5618 3.450096 ACAATAAACTACTCCCTCCGTCC 59.550 47.826 0.00 0.00 0.00 4.79
4012 5619 4.159135 TGACAATAAACTACTCCCTCCGTC 59.841 45.833 0.00 0.00 0.00 4.79
4013 5620 4.091549 TGACAATAAACTACTCCCTCCGT 58.908 43.478 0.00 0.00 0.00 4.69
4014 5621 4.401519 TCTGACAATAAACTACTCCCTCCG 59.598 45.833 0.00 0.00 0.00 4.63
4015 5622 5.187186 TGTCTGACAATAAACTACTCCCTCC 59.813 44.000 8.27 0.00 0.00 4.30
4016 5623 6.153000 TCTGTCTGACAATAAACTACTCCCTC 59.847 42.308 12.16 0.00 0.00 4.30
4017 5624 6.017192 TCTGTCTGACAATAAACTACTCCCT 58.983 40.000 12.16 0.00 0.00 4.20
4018 5625 6.282199 TCTGTCTGACAATAAACTACTCCC 57.718 41.667 12.16 0.00 0.00 4.30
4019 5626 8.603242 TTTTCTGTCTGACAATAAACTACTCC 57.397 34.615 12.16 0.00 0.00 3.85
4022 5629 9.827411 GGAATTTTCTGTCTGACAATAAACTAC 57.173 33.333 12.16 2.64 0.00 2.73
4023 5630 9.567776 TGGAATTTTCTGTCTGACAATAAACTA 57.432 29.630 12.16 2.82 0.00 2.24
4024 5631 8.463930 TGGAATTTTCTGTCTGACAATAAACT 57.536 30.769 12.16 5.14 0.00 2.66
4172 5779 7.101700 CAGATCGATCAAATGGGATAATGAGA 58.898 38.462 26.47 0.00 0.00 3.27
4385 5992 3.769739 AGACCATGCAGTTGTAGTCAA 57.230 42.857 0.00 0.00 0.00 3.18
4402 6009 9.921637 TTTGGAATTGTTTATGTATTGGAAGAC 57.078 29.630 0.00 0.00 0.00 3.01
4561 6173 1.846439 TGGATAGGCCAGCTTAGCTTT 59.154 47.619 3.00 0.00 43.33 3.51
4562 6174 1.511613 TGGATAGGCCAGCTTAGCTT 58.488 50.000 3.00 0.64 43.33 3.74
4563 6175 3.247424 TGGATAGGCCAGCTTAGCT 57.753 52.632 5.01 0.00 43.33 3.32
4678 6356 4.171754 CAGCACTTCCGTAACTACTTACC 58.828 47.826 0.00 0.00 30.00 2.85
4688 6366 2.036604 TCACATGAACAGCACTTCCGTA 59.963 45.455 0.00 0.00 0.00 4.02
4704 6382 2.198827 TTCGTGGGCAAGAATCACAT 57.801 45.000 0.00 0.00 0.00 3.21
4850 6531 7.012704 CGTTTGAGATATGGTTCATCTGGATTT 59.987 37.037 0.00 0.00 32.86 2.17
4876 6557 6.536941 GGAGTATTCAGAGTTTGACAGGATTC 59.463 42.308 0.00 0.00 34.94 2.52
4880 6561 5.152623 TGGAGTATTCAGAGTTTGACAGG 57.847 43.478 0.00 0.00 34.94 4.00
4889 6570 6.669278 CATTTGCATCATGGAGTATTCAGAG 58.331 40.000 0.00 0.00 0.00 3.35
4937 6618 8.458052 TGGAAATACACAGTATTTGCACAATAG 58.542 33.333 23.72 0.00 39.28 1.73
5176 6857 0.179020 TGACCACCTCCTGCAAAGTG 60.179 55.000 0.00 0.00 0.00 3.16
5242 6923 3.769844 AGTCGGCTCCAAGAGAAATCTTA 59.230 43.478 0.00 0.00 0.00 2.10
5257 6938 2.224305 GGATATAGTTGGCAAGTCGGCT 60.224 50.000 11.55 1.41 41.89 5.52
5258 6939 2.143925 GGATATAGTTGGCAAGTCGGC 58.856 52.381 11.55 0.07 41.67 5.54
5298 6979 9.565213 CCTGCAATAATATAATTTGCTAAGAGC 57.435 33.333 14.54 0.00 44.62 4.09
5358 7267 5.163311 TGTGCATACAGAACATAGCCTACAT 60.163 40.000 0.00 0.00 27.92 2.29
5394 7336 8.496707 AGTCATTTGCAAGTTTGAAAAAGAAT 57.503 26.923 0.00 2.27 39.06 2.40
5517 7460 9.294030 CTTCACTTGATTATCTTATGGCAAAAC 57.706 33.333 0.00 0.00 0.00 2.43
5757 7700 1.482182 TCATCAGAGAATCACCCACCG 59.518 52.381 0.00 0.00 37.82 4.94
5801 7744 1.686052 TGCATTTTGTCACCTGGGAAC 59.314 47.619 0.00 0.00 0.00 3.62
5810 7753 1.286570 CAGCGCCTGCATTTTGTCA 59.713 52.632 2.29 0.00 46.23 3.58
5875 7818 4.640201 CGAGGCAAAATAATCTCCTTGGAA 59.360 41.667 0.00 0.00 0.00 3.53
6038 7981 0.030101 TTGTAACAAGTTGCAGCCGC 59.970 50.000 1.81 0.00 36.59 6.53
6071 8014 2.969628 AGAACACTAATCTGGAGCCG 57.030 50.000 0.00 0.00 0.00 5.52
6111 8054 5.581975 AGAAGGTAGTTGGACTAGTAGCTT 58.418 41.667 11.06 11.06 41.81 3.74
6205 8148 8.910666 GCAGCTTTGTTTTTGTTTTGTTTTATT 58.089 25.926 0.00 0.00 0.00 1.40
6218 8161 4.326504 AGTATGCAGCAGCTTTGTTTTT 57.673 36.364 0.00 0.00 42.74 1.94
6337 8281 6.763355 TCTTTCAGTGCTTGAGATAGTTTCT 58.237 36.000 0.00 0.00 37.07 2.52
6363 8318 8.514330 TTGTTCTGTGGTTTAGACTTTAATGT 57.486 30.769 0.00 0.00 0.00 2.71
6398 8353 4.997395 TGCTTCTTGATCTGTGGAAAGTAC 59.003 41.667 0.00 0.00 0.00 2.73
6399 8354 4.997395 GTGCTTCTTGATCTGTGGAAAGTA 59.003 41.667 0.00 0.00 0.00 2.24
6400 8355 3.817647 GTGCTTCTTGATCTGTGGAAAGT 59.182 43.478 0.00 0.00 0.00 2.66
6401 8356 3.190118 GGTGCTTCTTGATCTGTGGAAAG 59.810 47.826 0.00 0.00 0.00 2.62
6402 8357 3.149196 GGTGCTTCTTGATCTGTGGAAA 58.851 45.455 0.00 0.00 0.00 3.13
6403 8358 2.373169 AGGTGCTTCTTGATCTGTGGAA 59.627 45.455 0.00 0.00 0.00 3.53
6404 8359 1.980765 AGGTGCTTCTTGATCTGTGGA 59.019 47.619 0.00 0.00 0.00 4.02
6405 8360 2.027377 AGAGGTGCTTCTTGATCTGTGG 60.027 50.000 0.00 0.00 0.00 4.17
6406 8361 3.331478 AGAGGTGCTTCTTGATCTGTG 57.669 47.619 0.00 0.00 0.00 3.66
6407 8362 4.100808 GGATAGAGGTGCTTCTTGATCTGT 59.899 45.833 0.00 0.00 0.00 3.41
6408 8363 4.502950 GGGATAGAGGTGCTTCTTGATCTG 60.503 50.000 0.00 0.00 0.00 2.90
6409 8364 3.645687 GGGATAGAGGTGCTTCTTGATCT 59.354 47.826 0.00 0.00 0.00 2.75
6410 8365 3.645687 AGGGATAGAGGTGCTTCTTGATC 59.354 47.826 0.00 0.00 0.00 2.92
6411 8366 3.663198 AGGGATAGAGGTGCTTCTTGAT 58.337 45.455 0.00 0.00 0.00 2.57
6412 8367 3.121929 AGGGATAGAGGTGCTTCTTGA 57.878 47.619 0.00 0.00 0.00 3.02
6413 8368 3.054802 ACAAGGGATAGAGGTGCTTCTTG 60.055 47.826 0.00 0.00 0.00 3.02
6414 8369 3.185455 ACAAGGGATAGAGGTGCTTCTT 58.815 45.455 0.00 0.00 0.00 2.52
6415 8370 2.839228 ACAAGGGATAGAGGTGCTTCT 58.161 47.619 0.00 0.00 0.00 2.85
6416 8371 4.636249 CATACAAGGGATAGAGGTGCTTC 58.364 47.826 0.00 0.00 0.00 3.86
6417 8372 3.181450 GCATACAAGGGATAGAGGTGCTT 60.181 47.826 0.00 0.00 0.00 3.91
6418 8373 2.370189 GCATACAAGGGATAGAGGTGCT 59.630 50.000 0.00 0.00 0.00 4.40
6419 8374 2.370189 AGCATACAAGGGATAGAGGTGC 59.630 50.000 0.00 0.00 0.00 5.01
6420 8375 3.805108 GCAGCATACAAGGGATAGAGGTG 60.805 52.174 0.00 0.00 0.00 4.00
6421 8376 2.370189 GCAGCATACAAGGGATAGAGGT 59.630 50.000 0.00 0.00 0.00 3.85
6422 8377 2.636893 AGCAGCATACAAGGGATAGAGG 59.363 50.000 0.00 0.00 0.00 3.69
6423 8378 4.063689 CAAGCAGCATACAAGGGATAGAG 58.936 47.826 0.00 0.00 0.00 2.43
6424 8379 3.745480 GCAAGCAGCATACAAGGGATAGA 60.745 47.826 0.00 0.00 44.79 1.98
6425 8380 2.551459 GCAAGCAGCATACAAGGGATAG 59.449 50.000 0.00 0.00 44.79 2.08
6653 8637 5.801350 TGACGACAAAGATGATTCCAATC 57.199 39.130 0.00 0.00 35.97 2.67
6739 8724 7.781324 AATGTTGAGGGTTAAACATGAAGAT 57.219 32.000 0.00 0.00 44.24 2.40
6741 8726 7.312899 GGTAATGTTGAGGGTTAAACATGAAG 58.687 38.462 0.00 0.00 44.24 3.02
6781 8766 5.903010 TGAAGGTACATATCCTCCTTGCTTA 59.097 40.000 0.00 0.00 39.91 3.09
6891 8876 1.112916 TGCACTGTTCTCTGGACCGA 61.113 55.000 0.00 0.00 0.00 4.69
6973 8958 2.446435 AGGCAACAATACAAGGCGAAT 58.554 42.857 0.00 0.00 41.41 3.34
7004 8992 8.510243 TGCAACAAGTGATTTGATCTATGTAT 57.490 30.769 0.00 0.00 39.21 2.29
7007 8995 6.916387 GGATGCAACAAGTGATTTGATCTATG 59.084 38.462 0.00 0.00 39.21 2.23
7009 8997 5.945191 TGGATGCAACAAGTGATTTGATCTA 59.055 36.000 0.00 0.00 39.21 1.98
7010 8998 4.768448 TGGATGCAACAAGTGATTTGATCT 59.232 37.500 0.00 0.00 39.21 2.75
7011 8999 5.063180 TGGATGCAACAAGTGATTTGATC 57.937 39.130 0.00 0.00 39.21 2.92


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

AutoCloner maintained by Alex Coulton.