Multiple sequence alignment - TraesCS4A01G000400

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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 TraesCS4A01G000400 chr4A 100.000 3194 0 0 1 3194 198072 194879 0.000000e+00 5899
1 TraesCS4A01G000400 chr5B 99.232 781 5 1 2299 3078 48315498 48316278 0.000000e+00 1408
2 TraesCS4A01G000400 chr7A 99.105 782 6 1 2299 3079 136189914 136189133 0.000000e+00 1404
3 TraesCS4A01G000400 chr7A 98.022 809 11 5 2299 3102 496918658 496919466 0.000000e+00 1400
4 TraesCS4A01G000400 chr2A 99.105 782 6 1 2299 3079 676078864 676079645 0.000000e+00 1404
5 TraesCS4A01G000400 chr2A 98.020 808 11 5 2299 3104 438397731 438396927 0.000000e+00 1399
6 TraesCS4A01G000400 chr6B 99.229 778 5 1 2299 3075 410234469 410235246 0.000000e+00 1402
7 TraesCS4A01G000400 chr6B 99.104 781 6 1 2299 3078 504593694 504594474 0.000000e+00 1402
8 TraesCS4A01G000400 chr1B 98.980 784 6 2 2299 3080 451911235 451910452 0.000000e+00 1402
9 TraesCS4A01G000400 chr1A 98.854 785 8 1 2299 3082 492997730 492998514 0.000000e+00 1399
10 TraesCS4A01G000400 chr4B 88.538 855 35 33 1479 2301 236433 235610 0.000000e+00 977
11 TraesCS4A01G000400 chr4B 92.977 655 41 5 142 792 20751531 20752184 0.000000e+00 950
12 TraesCS4A01G000400 chr4B 89.545 220 9 7 1140 1350 236976 236762 1.890000e-67 267
13 TraesCS4A01G000400 chr4B 86.441 118 7 6 3080 3194 235625 235514 1.560000e-23 121
14 TraesCS4A01G000400 chr1D 93.282 655 38 6 142 792 393530003 393529351 0.000000e+00 961
15 TraesCS4A01G000400 chr1D 93.721 637 36 4 155 789 387955734 387956368 0.000000e+00 952
16 TraesCS4A01G000400 chr1D 92.530 656 44 5 142 794 460872382 460871729 0.000000e+00 935
17 TraesCS4A01G000400 chr6D 93.109 653 39 6 142 789 58443563 58444214 0.000000e+00 952
18 TraesCS4A01G000400 chr6D 93.098 652 39 6 142 789 61756152 61755503 0.000000e+00 950
19 TraesCS4A01G000400 chr6D 93.088 651 38 6 142 789 455132109 455132755 0.000000e+00 946
20 TraesCS4A01G000400 chr4D 90.897 725 34 9 1606 2305 466671 465954 0.000000e+00 944
21 TraesCS4A01G000400 chr4D 84.431 501 30 20 876 1337 467552 467061 1.750000e-122 449
22 TraesCS4A01G000400 chr4D 87.603 121 2 2 3080 3192 465973 465858 9.300000e-26 128
23 TraesCS4A01G000400 chr3D 92.694 657 42 6 142 794 608916774 608917428 0.000000e+00 942
24 TraesCS4A01G000400 chr7D 92.683 656 39 9 142 792 536432270 536431619 0.000000e+00 937


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 TraesCS4A01G000400 chr4A 194879 198072 3193 True 5899 5899 100.000000 1 3194 1 chr4A.!!$R1 3193
1 TraesCS4A01G000400 chr5B 48315498 48316278 780 False 1408 1408 99.232000 2299 3078 1 chr5B.!!$F1 779
2 TraesCS4A01G000400 chr7A 136189133 136189914 781 True 1404 1404 99.105000 2299 3079 1 chr7A.!!$R1 780
3 TraesCS4A01G000400 chr7A 496918658 496919466 808 False 1400 1400 98.022000 2299 3102 1 chr7A.!!$F1 803
4 TraesCS4A01G000400 chr2A 676078864 676079645 781 False 1404 1404 99.105000 2299 3079 1 chr2A.!!$F1 780
5 TraesCS4A01G000400 chr2A 438396927 438397731 804 True 1399 1399 98.020000 2299 3104 1 chr2A.!!$R1 805
6 TraesCS4A01G000400 chr6B 410234469 410235246 777 False 1402 1402 99.229000 2299 3075 1 chr6B.!!$F1 776
7 TraesCS4A01G000400 chr6B 504593694 504594474 780 False 1402 1402 99.104000 2299 3078 1 chr6B.!!$F2 779
8 TraesCS4A01G000400 chr1B 451910452 451911235 783 True 1402 1402 98.980000 2299 3080 1 chr1B.!!$R1 781
9 TraesCS4A01G000400 chr1A 492997730 492998514 784 False 1399 1399 98.854000 2299 3082 1 chr1A.!!$F1 783
10 TraesCS4A01G000400 chr4B 20751531 20752184 653 False 950 950 92.977000 142 792 1 chr4B.!!$F1 650
11 TraesCS4A01G000400 chr4B 235514 236976 1462 True 455 977 88.174667 1140 3194 3 chr4B.!!$R1 2054
12 TraesCS4A01G000400 chr1D 393529351 393530003 652 True 961 961 93.282000 142 792 1 chr1D.!!$R1 650
13 TraesCS4A01G000400 chr1D 387955734 387956368 634 False 952 952 93.721000 155 789 1 chr1D.!!$F1 634
14 TraesCS4A01G000400 chr1D 460871729 460872382 653 True 935 935 92.530000 142 794 1 chr1D.!!$R2 652
15 TraesCS4A01G000400 chr6D 58443563 58444214 651 False 952 952 93.109000 142 789 1 chr6D.!!$F1 647
16 TraesCS4A01G000400 chr6D 61755503 61756152 649 True 950 950 93.098000 142 789 1 chr6D.!!$R1 647
17 TraesCS4A01G000400 chr6D 455132109 455132755 646 False 946 946 93.088000 142 789 1 chr6D.!!$F2 647
18 TraesCS4A01G000400 chr4D 465858 467552 1694 True 507 944 87.643667 876 3192 3 chr4D.!!$R1 2316
19 TraesCS4A01G000400 chr3D 608916774 608917428 654 False 942 942 92.694000 142 794 1 chr3D.!!$F1 652
20 TraesCS4A01G000400 chr7D 536431619 536432270 651 True 937 937 92.683000 142 792 1 chr7D.!!$R1 650

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
804 812 0.023103 GAGACTACGACGACGACGAC 59.977 60.0 25.15 7.02 42.66 4.34 F
1344 1409 0.099082 GCTTCTGCATCTGCTTCTGC 59.901 55.0 3.53 0.23 42.66 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2171 2709 0.405585 ACTGATTTCCCCACCACCAG 59.594 55.000 0.0 0.0 0.00 4.00 R
3108 3662 3.397482 AGTGAGTGAAGTGATGCTCAAC 58.603 45.455 0.0 0.0 39.33 3.18 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
17 18 3.544772 TGTGAGAGGGTGACGCAA 58.455 55.556 1.61 0.00 0.00 4.85
18 19 1.826709 TGTGAGAGGGTGACGCAAA 59.173 52.632 1.61 0.00 0.00 3.68
19 20 0.179234 TGTGAGAGGGTGACGCAAAA 59.821 50.000 1.61 0.00 0.00 2.44
20 21 1.305201 GTGAGAGGGTGACGCAAAAA 58.695 50.000 1.61 0.00 0.00 1.94
21 22 1.880027 GTGAGAGGGTGACGCAAAAAT 59.120 47.619 1.61 0.00 0.00 1.82
22 23 3.071479 GTGAGAGGGTGACGCAAAAATA 58.929 45.455 1.61 0.00 0.00 1.40
23 24 3.500680 GTGAGAGGGTGACGCAAAAATAA 59.499 43.478 1.61 0.00 0.00 1.40
24 25 3.500680 TGAGAGGGTGACGCAAAAATAAC 59.499 43.478 1.61 0.00 0.00 1.89
25 26 2.817844 AGAGGGTGACGCAAAAATAACC 59.182 45.455 1.61 0.00 0.00 2.85
26 27 1.890489 AGGGTGACGCAAAAATAACCC 59.110 47.619 1.61 0.20 46.38 4.11
27 28 1.401800 GGGTGACGCAAAAATAACCCG 60.402 52.381 0.00 0.00 38.05 5.28
28 29 1.536331 GGTGACGCAAAAATAACCCGA 59.464 47.619 0.00 0.00 0.00 5.14
29 30 2.162809 GGTGACGCAAAAATAACCCGAT 59.837 45.455 0.00 0.00 0.00 4.18
30 31 3.168193 GTGACGCAAAAATAACCCGATG 58.832 45.455 0.00 0.00 0.00 3.84
31 32 3.075148 TGACGCAAAAATAACCCGATGA 58.925 40.909 0.00 0.00 0.00 2.92
32 33 3.502595 TGACGCAAAAATAACCCGATGAA 59.497 39.130 0.00 0.00 0.00 2.57
33 34 4.156922 TGACGCAAAAATAACCCGATGAAT 59.843 37.500 0.00 0.00 0.00 2.57
34 35 5.066968 ACGCAAAAATAACCCGATGAATT 57.933 34.783 0.00 0.00 0.00 2.17
35 36 4.862018 ACGCAAAAATAACCCGATGAATTG 59.138 37.500 0.00 0.00 0.00 2.32
36 37 4.267452 CGCAAAAATAACCCGATGAATTGG 59.733 41.667 0.00 0.00 0.00 3.16
43 44 3.713902 CCGATGAATTGGGAGGAGG 57.286 57.895 0.00 0.00 0.00 4.30
44 45 0.109342 CCGATGAATTGGGAGGAGGG 59.891 60.000 0.00 0.00 0.00 4.30
45 46 0.109342 CGATGAATTGGGAGGAGGGG 59.891 60.000 0.00 0.00 0.00 4.79
46 47 1.522900 GATGAATTGGGAGGAGGGGA 58.477 55.000 0.00 0.00 0.00 4.81
47 48 2.068977 GATGAATTGGGAGGAGGGGAT 58.931 52.381 0.00 0.00 0.00 3.85
48 49 1.225373 TGAATTGGGAGGAGGGGATG 58.775 55.000 0.00 0.00 0.00 3.51
49 50 1.274943 TGAATTGGGAGGAGGGGATGA 60.275 52.381 0.00 0.00 0.00 2.92
50 51 1.852965 GAATTGGGAGGAGGGGATGAA 59.147 52.381 0.00 0.00 0.00 2.57
51 52 2.000290 ATTGGGAGGAGGGGATGAAA 58.000 50.000 0.00 0.00 0.00 2.69
52 53 1.766951 TTGGGAGGAGGGGATGAAAA 58.233 50.000 0.00 0.00 0.00 2.29
53 54 1.766951 TGGGAGGAGGGGATGAAAAA 58.233 50.000 0.00 0.00 0.00 1.94
89 90 2.685380 AGCGAAGGTGGGAGGAGG 60.685 66.667 0.00 0.00 36.17 4.30
90 91 3.003763 GCGAAGGTGGGAGGAGGT 61.004 66.667 0.00 0.00 0.00 3.85
91 92 1.684734 GCGAAGGTGGGAGGAGGTA 60.685 63.158 0.00 0.00 0.00 3.08
92 93 1.957765 GCGAAGGTGGGAGGAGGTAC 61.958 65.000 0.00 0.00 0.00 3.34
93 94 1.328430 CGAAGGTGGGAGGAGGTACC 61.328 65.000 2.73 2.73 39.35 3.34
94 95 0.252558 GAAGGTGGGAGGAGGTACCA 60.253 60.000 15.94 0.00 42.04 3.25
95 96 0.195096 AAGGTGGGAGGAGGTACCAA 59.805 55.000 15.94 0.00 42.04 3.67
96 97 0.195096 AGGTGGGAGGAGGTACCAAA 59.805 55.000 15.94 0.00 42.04 3.28
97 98 1.069775 GGTGGGAGGAGGTACCAAAA 58.930 55.000 15.94 0.00 42.04 2.44
98 99 1.426215 GGTGGGAGGAGGTACCAAAAA 59.574 52.381 15.94 0.00 42.04 1.94
114 115 3.474083 AAAAACCATGGGAGGTGGG 57.526 52.632 18.09 0.00 42.25 4.61
115 116 0.863956 AAAAACCATGGGAGGTGGGA 59.136 50.000 18.09 0.00 42.25 4.37
116 117 0.114364 AAAACCATGGGAGGTGGGAC 59.886 55.000 18.09 0.00 42.25 4.46
117 118 2.137177 AAACCATGGGAGGTGGGACG 62.137 60.000 18.09 0.00 42.25 4.79
118 119 2.687200 CCATGGGAGGTGGGACGA 60.687 66.667 2.85 0.00 32.98 4.20
119 120 2.297895 CCATGGGAGGTGGGACGAA 61.298 63.158 2.85 0.00 32.98 3.85
120 121 1.682849 CATGGGAGGTGGGACGAAA 59.317 57.895 0.00 0.00 0.00 3.46
121 122 0.037590 CATGGGAGGTGGGACGAAAA 59.962 55.000 0.00 0.00 0.00 2.29
122 123 0.774908 ATGGGAGGTGGGACGAAAAA 59.225 50.000 0.00 0.00 0.00 1.94
140 141 2.640316 AAAAACCTGGAAGCGAGACT 57.360 45.000 0.00 0.00 0.00 3.24
141 142 3.764237 AAAAACCTGGAAGCGAGACTA 57.236 42.857 0.00 0.00 0.00 2.59
142 143 2.745515 AAACCTGGAAGCGAGACTAC 57.254 50.000 0.00 0.00 0.00 2.73
143 144 0.896226 AACCTGGAAGCGAGACTACC 59.104 55.000 0.00 0.00 0.00 3.18
144 145 0.251653 ACCTGGAAGCGAGACTACCA 60.252 55.000 0.00 0.00 0.00 3.25
145 146 0.895530 CCTGGAAGCGAGACTACCAA 59.104 55.000 0.00 0.00 0.00 3.67
146 147 1.404315 CCTGGAAGCGAGACTACCAAC 60.404 57.143 0.00 0.00 0.00 3.77
147 148 1.546476 CTGGAAGCGAGACTACCAACT 59.454 52.381 0.00 0.00 0.00 3.16
148 149 2.753452 CTGGAAGCGAGACTACCAACTA 59.247 50.000 0.00 0.00 0.00 2.24
149 150 2.490903 TGGAAGCGAGACTACCAACTAC 59.509 50.000 0.00 0.00 0.00 2.73
150 151 2.754002 GGAAGCGAGACTACCAACTACT 59.246 50.000 0.00 0.00 0.00 2.57
160 161 2.747686 CAACTACTGGGCCACGGT 59.252 61.111 0.00 8.07 42.62 4.83
176 177 4.295119 GTCACGGCCACGACCAGT 62.295 66.667 2.24 0.00 44.60 4.00
231 232 4.444024 CAACGCGGTGCCACGATG 62.444 66.667 13.03 0.13 35.47 3.84
312 313 1.404181 CGGCCTCGAGAATCAAGAACA 60.404 52.381 15.71 0.00 39.00 3.18
373 375 8.603898 TGTCATAAGAAAGGGAGTTATCTACA 57.396 34.615 0.00 0.00 0.00 2.74
421 423 5.825532 TGTTTGGAGATTGATTACCATCCA 58.174 37.500 0.00 0.00 35.10 3.41
655 658 4.093703 TGACGCGAAAATAAACCGATGAAT 59.906 37.500 15.93 0.00 0.00 2.57
660 663 5.677598 GCGAAAATAAACCGATGAATTGGGA 60.678 40.000 1.63 0.00 35.53 4.37
794 802 5.883685 TCCATTAGGAGTAGAGACTACGA 57.116 43.478 0.00 0.00 42.02 3.43
795 803 5.609423 TCCATTAGGAGTAGAGACTACGAC 58.391 45.833 0.00 0.00 42.02 4.34
796 804 4.448395 CCATTAGGAGTAGAGACTACGACG 59.552 50.000 0.00 0.00 42.02 5.12
797 805 4.991153 TTAGGAGTAGAGACTACGACGA 57.009 45.455 0.00 0.00 42.02 4.20
798 806 3.163630 AGGAGTAGAGACTACGACGAC 57.836 52.381 0.00 0.00 42.02 4.34
799 807 1.851666 GGAGTAGAGACTACGACGACG 59.148 57.143 5.58 5.58 39.92 5.12
800 808 2.478709 GGAGTAGAGACTACGACGACGA 60.479 54.545 15.32 0.00 38.37 4.20
801 809 2.525055 AGTAGAGACTACGACGACGAC 58.475 52.381 15.32 0.00 43.06 4.34
802 810 1.251508 GTAGAGACTACGACGACGACG 59.748 57.143 17.60 17.60 42.66 5.12
803 811 0.109551 AGAGACTACGACGACGACGA 60.110 55.000 25.15 8.82 42.66 4.20
804 812 0.023103 GAGACTACGACGACGACGAC 59.977 60.000 25.15 7.02 42.66 4.34
810 818 2.864248 GACGACGACGACGACTGC 60.864 66.667 25.15 8.43 42.66 4.40
811 819 3.292518 GACGACGACGACGACTGCT 62.293 63.158 25.15 3.08 42.66 4.24
812 820 1.949015 GACGACGACGACGACTGCTA 61.949 60.000 25.15 0.00 42.66 3.49
813 821 1.577117 CGACGACGACGACTGCTAC 60.577 63.158 15.32 0.00 42.66 3.58
814 822 1.786582 GACGACGACGACTGCTACT 59.213 57.895 15.32 0.00 42.66 2.57
815 823 0.994995 GACGACGACGACTGCTACTA 59.005 55.000 15.32 0.00 42.66 1.82
816 824 0.718343 ACGACGACGACTGCTACTAC 59.282 55.000 15.32 0.00 42.66 2.73
817 825 0.997932 CGACGACGACTGCTACTACT 59.002 55.000 0.00 0.00 42.66 2.57
818 826 2.188524 CGACGACGACTGCTACTACTA 58.811 52.381 0.00 0.00 42.66 1.82
819 827 2.035009 CGACGACGACTGCTACTACTAC 60.035 54.545 0.00 0.00 42.66 2.73
820 828 3.186119 GACGACGACTGCTACTACTACT 58.814 50.000 0.00 0.00 0.00 2.57
821 829 4.355437 GACGACGACTGCTACTACTACTA 58.645 47.826 0.00 0.00 0.00 1.82
822 830 4.109050 ACGACGACTGCTACTACTACTAC 58.891 47.826 0.00 0.00 0.00 2.73
823 831 4.142271 ACGACGACTGCTACTACTACTACT 60.142 45.833 0.00 0.00 0.00 2.57
824 832 4.440758 CGACGACTGCTACTACTACTACTC 59.559 50.000 0.00 0.00 0.00 2.59
825 833 4.358851 ACGACTGCTACTACTACTACTCG 58.641 47.826 0.00 0.00 0.00 4.18
826 834 4.097135 ACGACTGCTACTACTACTACTCGA 59.903 45.833 0.00 0.00 0.00 4.04
827 835 4.676471 CGACTGCTACTACTACTACTCGAG 59.324 50.000 11.84 11.84 0.00 4.04
828 836 5.505489 CGACTGCTACTACTACTACTCGAGA 60.505 48.000 21.68 1.61 0.00 4.04
829 837 6.219417 ACTGCTACTACTACTACTCGAGAA 57.781 41.667 21.68 0.27 0.00 2.87
830 838 6.275335 ACTGCTACTACTACTACTCGAGAAG 58.725 44.000 21.68 12.66 0.00 2.85
831 839 5.599732 TGCTACTACTACTACTCGAGAAGG 58.400 45.833 21.68 10.68 0.00 3.46
832 840 5.362143 TGCTACTACTACTACTCGAGAAGGA 59.638 44.000 21.68 6.52 0.00 3.36
833 841 6.127225 TGCTACTACTACTACTCGAGAAGGAA 60.127 42.308 21.68 0.00 0.00 3.36
834 842 6.930722 GCTACTACTACTACTCGAGAAGGAAT 59.069 42.308 21.68 2.82 0.00 3.01
835 843 8.087750 GCTACTACTACTACTCGAGAAGGAATA 58.912 40.741 21.68 3.90 0.00 1.75
838 846 9.850198 ACTACTACTACTCGAGAAGGAATATTT 57.150 33.333 21.68 0.00 0.00 1.40
840 848 8.522542 ACTACTACTCGAGAAGGAATATTTGT 57.477 34.615 21.68 2.90 0.00 2.83
841 849 8.968969 ACTACTACTCGAGAAGGAATATTTGTT 58.031 33.333 21.68 0.00 0.00 2.83
842 850 9.804758 CTACTACTCGAGAAGGAATATTTGTTT 57.195 33.333 21.68 0.00 0.00 2.83
844 852 9.503399 ACTACTCGAGAAGGAATATTTGTTTTT 57.497 29.630 21.68 0.00 0.00 1.94
867 875 7.944729 TTTTATGAGGAAAGGATTGGAGAAG 57.055 36.000 0.00 0.00 0.00 2.85
868 876 4.516652 ATGAGGAAAGGATTGGAGAAGG 57.483 45.455 0.00 0.00 0.00 3.46
869 877 3.531059 TGAGGAAAGGATTGGAGAAGGA 58.469 45.455 0.00 0.00 0.00 3.36
870 878 3.916349 TGAGGAAAGGATTGGAGAAGGAA 59.084 43.478 0.00 0.00 0.00 3.36
871 879 4.018960 TGAGGAAAGGATTGGAGAAGGAAG 60.019 45.833 0.00 0.00 0.00 3.46
872 880 4.179133 AGGAAAGGATTGGAGAAGGAAGA 58.821 43.478 0.00 0.00 0.00 2.87
873 881 4.792972 AGGAAAGGATTGGAGAAGGAAGAT 59.207 41.667 0.00 0.00 0.00 2.40
874 882 5.254972 AGGAAAGGATTGGAGAAGGAAGATT 59.745 40.000 0.00 0.00 0.00 2.40
937 945 2.677228 CCCACCGAATGAAGGCCT 59.323 61.111 0.00 0.00 0.00 5.19
961 969 5.471116 TGACCTGATCATTTCAGTTCAGTTG 59.529 40.000 0.00 0.00 45.71 3.16
976 984 1.600916 GTTGAGCCCACACCCACTC 60.601 63.158 0.00 0.00 0.00 3.51
986 994 2.122954 ACCCACTCACCCTCCTCC 59.877 66.667 0.00 0.00 0.00 4.30
999 1007 0.465460 CTCCTCCTCCTCAGTCCTCG 60.465 65.000 0.00 0.00 0.00 4.63
1164 1208 2.835156 GTTTCAGCTCCTCCTCCTACTT 59.165 50.000 0.00 0.00 0.00 2.24
1204 1269 3.352648 CGGAGAGAAGAAGAAGAGGTCT 58.647 50.000 0.00 0.00 38.69 3.85
1309 1374 2.665000 CACGGATGCACCAGGTCT 59.335 61.111 0.00 0.00 38.90 3.85
1310 1375 1.448540 CACGGATGCACCAGGTCTC 60.449 63.158 0.00 0.00 38.90 3.36
1311 1376 1.610673 ACGGATGCACCAGGTCTCT 60.611 57.895 0.00 0.00 38.90 3.10
1312 1377 0.324368 ACGGATGCACCAGGTCTCTA 60.324 55.000 0.00 0.00 38.90 2.43
1313 1378 0.387202 CGGATGCACCAGGTCTCTAG 59.613 60.000 0.00 0.00 38.90 2.43
1314 1379 0.755686 GGATGCACCAGGTCTCTAGG 59.244 60.000 0.00 0.00 38.79 3.02
1315 1380 1.689575 GGATGCACCAGGTCTCTAGGA 60.690 57.143 0.00 0.00 38.79 2.94
1316 1381 2.324541 GATGCACCAGGTCTCTAGGAT 58.675 52.381 0.00 0.00 0.00 3.24
1317 1382 1.489481 TGCACCAGGTCTCTAGGATG 58.511 55.000 0.00 0.00 0.00 3.51
1327 1392 2.364970 GTCTCTAGGATGTGCATCTGCT 59.635 50.000 11.39 4.62 42.66 4.24
1343 1408 1.450025 TGCTTCTGCATCTGCTTCTG 58.550 50.000 3.53 0.00 45.31 3.02
1344 1409 0.099082 GCTTCTGCATCTGCTTCTGC 59.901 55.000 3.53 0.23 42.66 4.26
1345 1410 1.740297 CTTCTGCATCTGCTTCTGCT 58.260 50.000 3.53 0.00 42.66 4.24
1346 1411 2.085320 CTTCTGCATCTGCTTCTGCTT 58.915 47.619 3.53 0.00 42.66 3.91
1347 1412 1.735386 TCTGCATCTGCTTCTGCTTC 58.265 50.000 3.53 0.00 42.66 3.86
1348 1413 1.278413 TCTGCATCTGCTTCTGCTTCT 59.722 47.619 3.53 0.00 42.66 2.85
1349 1414 1.398739 CTGCATCTGCTTCTGCTTCTG 59.601 52.381 3.53 0.00 42.66 3.02
1350 1415 0.099082 GCATCTGCTTCTGCTTCTGC 59.901 55.000 0.00 0.00 40.48 4.26
1351 1416 1.740297 CATCTGCTTCTGCTTCTGCT 58.260 50.000 0.00 0.00 40.48 4.24
1352 1417 1.666700 CATCTGCTTCTGCTTCTGCTC 59.333 52.381 0.00 0.00 40.48 4.26
1353 1418 0.975135 TCTGCTTCTGCTTCTGCTCT 59.025 50.000 0.00 0.00 40.48 4.09
1354 1419 1.080298 CTGCTTCTGCTTCTGCTCTG 58.920 55.000 0.00 0.00 40.48 3.35
1355 1420 0.954449 TGCTTCTGCTTCTGCTCTGC 60.954 55.000 0.00 0.00 40.48 4.26
1356 1421 0.674269 GCTTCTGCTTCTGCTCTGCT 60.674 55.000 0.00 0.00 40.48 4.24
1357 1422 1.361793 CTTCTGCTTCTGCTCTGCTC 58.638 55.000 0.00 0.00 40.48 4.26
1358 1423 0.975135 TTCTGCTTCTGCTCTGCTCT 59.025 50.000 0.00 0.00 40.48 4.09
1359 1424 0.246910 TCTGCTTCTGCTCTGCTCTG 59.753 55.000 0.00 0.00 40.48 3.35
1360 1425 1.363145 CTGCTTCTGCTCTGCTCTGC 61.363 60.000 0.00 0.00 40.48 4.26
1361 1426 1.078988 GCTTCTGCTCTGCTCTGCT 60.079 57.895 0.00 0.00 36.03 4.24
1362 1427 1.085501 GCTTCTGCTCTGCTCTGCTC 61.086 60.000 0.00 0.00 36.03 4.26
1363 1428 0.533491 CTTCTGCTCTGCTCTGCTCT 59.467 55.000 0.00 0.00 0.00 4.09
1364 1429 0.246910 TTCTGCTCTGCTCTGCTCTG 59.753 55.000 0.00 0.00 0.00 3.35
1365 1430 1.812093 CTGCTCTGCTCTGCTCTGC 60.812 63.158 0.00 0.00 0.00 4.26
1366 1431 2.233605 CTGCTCTGCTCTGCTCTGCT 62.234 60.000 0.00 0.00 0.00 4.24
1367 1432 1.519898 GCTCTGCTCTGCTCTGCTC 60.520 63.158 0.00 0.00 0.00 4.26
1368 1433 1.952102 GCTCTGCTCTGCTCTGCTCT 61.952 60.000 0.00 0.00 0.00 4.09
1431 1707 6.590068 ACATGATATAACTGCTCTGCTTTCT 58.410 36.000 0.00 0.00 0.00 2.52
1434 1710 5.819379 TGATATAACTGCTCTGCTTTCTTGG 59.181 40.000 0.00 0.00 0.00 3.61
1435 1711 2.645838 AACTGCTCTGCTTTCTTGGA 57.354 45.000 0.00 0.00 0.00 3.53
1440 1716 4.235360 CTGCTCTGCTTTCTTGGAATTTG 58.765 43.478 0.00 0.00 0.00 2.32
1457 1751 6.712998 TGGAATTTGTCACCTTTCTTCGAATA 59.287 34.615 0.00 0.00 0.00 1.75
1458 1752 7.229707 TGGAATTTGTCACCTTTCTTCGAATAA 59.770 33.333 0.00 0.00 0.00 1.40
1526 2031 5.801531 GGTTTGGACCCTTTTTCAGTTAT 57.198 39.130 0.00 0.00 40.25 1.89
1527 2032 6.169557 GGTTTGGACCCTTTTTCAGTTATT 57.830 37.500 0.00 0.00 40.25 1.40
1528 2033 7.292713 GGTTTGGACCCTTTTTCAGTTATTA 57.707 36.000 0.00 0.00 40.25 0.98
1529 2034 7.903145 GGTTTGGACCCTTTTTCAGTTATTAT 58.097 34.615 0.00 0.00 40.25 1.28
1530 2035 8.372459 GGTTTGGACCCTTTTTCAGTTATTATT 58.628 33.333 0.00 0.00 40.25 1.40
1533 2038 8.817092 TGGACCCTTTTTCAGTTATTATTAGG 57.183 34.615 0.00 0.00 0.00 2.69
1534 2039 8.616598 TGGACCCTTTTTCAGTTATTATTAGGA 58.383 33.333 0.00 0.00 0.00 2.94
1535 2040 9.470399 GGACCCTTTTTCAGTTATTATTAGGAA 57.530 33.333 0.00 0.00 0.00 3.36
1571 2076 2.995466 ATGCACCAACGAAGAACATG 57.005 45.000 0.00 0.00 0.00 3.21
1907 2435 9.372369 TGACACTCATACATAGATAGATACTCG 57.628 37.037 0.00 0.00 0.00 4.18
1925 2453 3.056035 ACTCGTGGATTTCCTTCAGTACC 60.056 47.826 0.00 0.00 36.82 3.34
1995 2524 1.813513 AAGAGGATGGTGTGCTTTCG 58.186 50.000 0.00 0.00 0.00 3.46
2055 2584 2.230994 CTCGCCTGGAACTGCAGCTA 62.231 60.000 15.27 0.00 0.00 3.32
2080 2615 2.420547 GCACTACCTTCAGATGATGGCA 60.421 50.000 13.21 0.00 41.56 4.92
2131 2666 2.283145 AAACCTGATGAGCAGCACTT 57.717 45.000 0.00 0.00 43.50 3.16
2151 2689 1.202348 TCTGCTGATGACGACGACAAT 59.798 47.619 0.00 0.00 0.00 2.71
2165 2703 6.384224 ACGACGACAATTGTAAGATTAGTGA 58.616 36.000 11.95 0.00 0.00 3.41
2171 2709 8.269424 CGACAATTGTAAGATTAGTGATACTGC 58.731 37.037 11.95 0.00 0.00 4.40
2180 2718 0.615331 AGTGATACTGCTGGTGGTGG 59.385 55.000 0.00 0.00 0.00 4.61
2207 2745 3.733337 TCAGTTGAGAGTTGAGCCTTTC 58.267 45.455 0.00 0.00 0.00 2.62
2246 2799 1.205893 GTTGCGACAAGAGGAGGAGAT 59.794 52.381 0.00 0.00 0.00 2.75
3024 3578 3.130734 TGGGTTTCACCTCTAGCCTAT 57.869 47.619 0.00 0.00 38.64 2.57
3083 3637 4.747108 TGTTGTTGTTGTTGTTGTTTGGAG 59.253 37.500 0.00 0.00 0.00 3.86
3084 3638 4.855715 TGTTGTTGTTGTTGTTTGGAGA 57.144 36.364 0.00 0.00 0.00 3.71
3085 3639 5.398603 TGTTGTTGTTGTTGTTTGGAGAT 57.601 34.783 0.00 0.00 0.00 2.75
3086 3640 5.167121 TGTTGTTGTTGTTGTTTGGAGATG 58.833 37.500 0.00 0.00 0.00 2.90
3087 3641 4.383850 TGTTGTTGTTGTTTGGAGATGG 57.616 40.909 0.00 0.00 0.00 3.51
3088 3642 3.123050 GTTGTTGTTGTTTGGAGATGGC 58.877 45.455 0.00 0.00 0.00 4.40
3090 3644 2.762887 TGTTGTTGTTTGGAGATGGCAA 59.237 40.909 0.00 0.00 0.00 4.52
3091 3645 3.387374 TGTTGTTGTTTGGAGATGGCAAT 59.613 39.130 0.00 0.00 0.00 3.56
3093 3647 5.069648 TGTTGTTGTTTGGAGATGGCAATAA 59.930 36.000 0.00 0.00 0.00 1.40
3094 3648 5.999205 TGTTGTTTGGAGATGGCAATAAT 57.001 34.783 0.00 0.00 0.00 1.28
3095 3649 6.357579 TGTTGTTTGGAGATGGCAATAATT 57.642 33.333 0.00 0.00 0.00 1.40
3096 3650 6.164876 TGTTGTTTGGAGATGGCAATAATTG 58.835 36.000 0.00 0.00 0.00 2.32
3097 3651 6.014755 TGTTGTTTGGAGATGGCAATAATTGA 60.015 34.615 0.00 0.00 0.00 2.57
3098 3652 6.602410 TGTTTGGAGATGGCAATAATTGAA 57.398 33.333 0.00 0.00 0.00 2.69
3099 3653 7.185318 TGTTTGGAGATGGCAATAATTGAAT 57.815 32.000 0.00 0.00 0.00 2.57
3100 3654 7.622713 TGTTTGGAGATGGCAATAATTGAATT 58.377 30.769 0.00 0.00 0.00 2.17
3101 3655 7.549842 TGTTTGGAGATGGCAATAATTGAATTG 59.450 33.333 0.00 0.00 39.41 2.32
3108 3662 9.542462 AGATGGCAATAATTGAATTGAATTGAG 57.458 29.630 12.47 4.25 38.84 3.02
3141 3695 4.274459 ACTTCACTCACTTGCTTTGATGTC 59.726 41.667 0.00 0.00 0.00 3.06
3160 3714 7.944176 TGATGTCTGAATCCTATCCTATCCTA 58.056 38.462 0.00 0.00 0.00 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.179234 TTTTGCGTCACCCTCTCACA 59.821 50.000 0.00 0.00 0.00 3.58
1 2 1.305201 TTTTTGCGTCACCCTCTCAC 58.695 50.000 0.00 0.00 0.00 3.51
2 3 2.270352 ATTTTTGCGTCACCCTCTCA 57.730 45.000 0.00 0.00 0.00 3.27
3 4 3.119955 GGTTATTTTTGCGTCACCCTCTC 60.120 47.826 0.00 0.00 0.00 3.20
5 6 2.094906 GGGTTATTTTTGCGTCACCCTC 60.095 50.000 0.00 0.00 40.78 4.30
6 7 1.890489 GGGTTATTTTTGCGTCACCCT 59.110 47.619 0.00 0.00 40.78 4.34
7 8 1.401800 CGGGTTATTTTTGCGTCACCC 60.402 52.381 0.00 0.00 40.59 4.61
8 9 1.536331 TCGGGTTATTTTTGCGTCACC 59.464 47.619 0.00 0.00 0.00 4.02
9 10 2.973419 TCGGGTTATTTTTGCGTCAC 57.027 45.000 0.00 0.00 0.00 3.67
10 11 3.075148 TCATCGGGTTATTTTTGCGTCA 58.925 40.909 0.00 0.00 0.00 4.35
11 12 3.750639 TCATCGGGTTATTTTTGCGTC 57.249 42.857 0.00 0.00 0.00 5.19
12 13 4.712122 ATTCATCGGGTTATTTTTGCGT 57.288 36.364 0.00 0.00 0.00 5.24
13 14 4.267452 CCAATTCATCGGGTTATTTTTGCG 59.733 41.667 0.00 0.00 0.00 4.85
14 15 4.570369 CCCAATTCATCGGGTTATTTTTGC 59.430 41.667 0.00 0.00 37.70 3.68
15 16 5.971763 TCCCAATTCATCGGGTTATTTTTG 58.028 37.500 0.00 0.00 43.57 2.44
16 17 5.128663 CCTCCCAATTCATCGGGTTATTTTT 59.871 40.000 0.00 0.00 43.57 1.94
17 18 4.649218 CCTCCCAATTCATCGGGTTATTTT 59.351 41.667 0.00 0.00 43.57 1.82
18 19 4.079443 TCCTCCCAATTCATCGGGTTATTT 60.079 41.667 0.00 0.00 43.57 1.40
19 20 3.461831 TCCTCCCAATTCATCGGGTTATT 59.538 43.478 0.00 0.00 43.57 1.40
20 21 3.053077 TCCTCCCAATTCATCGGGTTAT 58.947 45.455 0.00 0.00 43.57 1.89
21 22 2.438021 CTCCTCCCAATTCATCGGGTTA 59.562 50.000 0.00 0.00 43.57 2.85
22 23 1.212935 CTCCTCCCAATTCATCGGGTT 59.787 52.381 0.00 0.00 43.57 4.11
23 24 0.839946 CTCCTCCCAATTCATCGGGT 59.160 55.000 0.00 0.00 43.57 5.28
24 25 0.109342 CCTCCTCCCAATTCATCGGG 59.891 60.000 0.00 0.00 44.60 5.14
25 26 0.109342 CCCTCCTCCCAATTCATCGG 59.891 60.000 0.00 0.00 0.00 4.18
26 27 0.109342 CCCCTCCTCCCAATTCATCG 59.891 60.000 0.00 0.00 0.00 3.84
27 28 1.522900 TCCCCTCCTCCCAATTCATC 58.477 55.000 0.00 0.00 0.00 2.92
28 29 1.785208 CATCCCCTCCTCCCAATTCAT 59.215 52.381 0.00 0.00 0.00 2.57
29 30 1.225373 CATCCCCTCCTCCCAATTCA 58.775 55.000 0.00 0.00 0.00 2.57
30 31 1.522900 TCATCCCCTCCTCCCAATTC 58.477 55.000 0.00 0.00 0.00 2.17
31 32 2.000290 TTCATCCCCTCCTCCCAATT 58.000 50.000 0.00 0.00 0.00 2.32
32 33 2.000290 TTTCATCCCCTCCTCCCAAT 58.000 50.000 0.00 0.00 0.00 3.16
33 34 1.766951 TTTTCATCCCCTCCTCCCAA 58.233 50.000 0.00 0.00 0.00 4.12
34 35 1.766951 TTTTTCATCCCCTCCTCCCA 58.233 50.000 0.00 0.00 0.00 4.37
65 66 0.106419 TCCCACCTTCGCTGGTTTTT 60.106 50.000 0.00 0.00 38.45 1.94
66 67 0.537371 CTCCCACCTTCGCTGGTTTT 60.537 55.000 0.00 0.00 38.45 2.43
67 68 1.073199 CTCCCACCTTCGCTGGTTT 59.927 57.895 0.00 0.00 38.45 3.27
68 69 2.750350 CTCCCACCTTCGCTGGTT 59.250 61.111 0.00 0.00 38.45 3.67
69 70 3.322466 CCTCCCACCTTCGCTGGT 61.322 66.667 0.00 0.00 41.77 4.00
70 71 3.003173 TCCTCCCACCTTCGCTGG 61.003 66.667 0.00 0.00 0.00 4.85
71 72 2.581354 CTCCTCCCACCTTCGCTG 59.419 66.667 0.00 0.00 0.00 5.18
72 73 2.164332 TACCTCCTCCCACCTTCGCT 62.164 60.000 0.00 0.00 0.00 4.93
73 74 1.684734 TACCTCCTCCCACCTTCGC 60.685 63.158 0.00 0.00 0.00 4.70
74 75 1.328430 GGTACCTCCTCCCACCTTCG 61.328 65.000 4.06 0.00 0.00 3.79
75 76 0.252558 TGGTACCTCCTCCCACCTTC 60.253 60.000 14.36 0.00 37.07 3.46
76 77 0.195096 TTGGTACCTCCTCCCACCTT 59.805 55.000 14.36 0.00 37.07 3.50
77 78 0.195096 TTTGGTACCTCCTCCCACCT 59.805 55.000 14.36 0.00 37.07 4.00
78 79 1.069775 TTTTGGTACCTCCTCCCACC 58.930 55.000 14.36 0.00 37.07 4.61
79 80 2.963599 TTTTTGGTACCTCCTCCCAC 57.036 50.000 14.36 0.00 37.07 4.61
96 97 0.863956 TCCCACCTCCCATGGTTTTT 59.136 50.000 11.73 0.00 38.45 1.94
97 98 0.114364 GTCCCACCTCCCATGGTTTT 59.886 55.000 11.73 0.00 38.45 2.43
98 99 1.774300 GTCCCACCTCCCATGGTTT 59.226 57.895 11.73 0.00 38.45 3.27
99 100 2.602676 CGTCCCACCTCCCATGGTT 61.603 63.158 11.73 0.00 38.45 3.67
100 101 3.009115 CGTCCCACCTCCCATGGT 61.009 66.667 11.73 0.00 41.77 3.55
101 102 1.847798 TTTCGTCCCACCTCCCATGG 61.848 60.000 4.14 4.14 36.94 3.66
102 103 0.037590 TTTTCGTCCCACCTCCCATG 59.962 55.000 0.00 0.00 0.00 3.66
103 104 0.774908 TTTTTCGTCCCACCTCCCAT 59.225 50.000 0.00 0.00 0.00 4.00
104 105 2.232622 TTTTTCGTCCCACCTCCCA 58.767 52.632 0.00 0.00 0.00 4.37
121 122 2.640316 AGTCTCGCTTCCAGGTTTTT 57.360 45.000 0.00 0.00 0.00 1.94
122 123 2.289506 GGTAGTCTCGCTTCCAGGTTTT 60.290 50.000 0.00 0.00 35.06 2.43
123 124 1.275573 GGTAGTCTCGCTTCCAGGTTT 59.724 52.381 0.00 0.00 35.06 3.27
124 125 0.896226 GGTAGTCTCGCTTCCAGGTT 59.104 55.000 0.00 0.00 35.06 3.50
125 126 0.251653 TGGTAGTCTCGCTTCCAGGT 60.252 55.000 0.00 0.00 39.34 4.00
126 127 0.895530 TTGGTAGTCTCGCTTCCAGG 59.104 55.000 0.00 0.00 43.94 4.45
127 128 1.546476 AGTTGGTAGTCTCGCTTCCAG 59.454 52.381 0.00 0.00 43.94 3.86
128 129 1.629043 AGTTGGTAGTCTCGCTTCCA 58.371 50.000 0.00 0.00 41.97 3.53
129 130 2.754002 AGTAGTTGGTAGTCTCGCTTCC 59.246 50.000 0.00 0.00 35.47 3.46
130 131 3.427773 CCAGTAGTTGGTAGTCTCGCTTC 60.428 52.174 0.00 0.00 42.41 3.86
131 132 2.492484 CCAGTAGTTGGTAGTCTCGCTT 59.508 50.000 0.00 0.00 42.41 4.68
132 133 2.093106 CCAGTAGTTGGTAGTCTCGCT 58.907 52.381 0.00 0.00 42.41 4.93
133 134 1.134560 CCCAGTAGTTGGTAGTCTCGC 59.865 57.143 0.00 0.00 46.25 5.03
134 135 1.134560 GCCCAGTAGTTGGTAGTCTCG 59.865 57.143 0.00 0.00 46.25 4.04
135 136 1.481363 GGCCCAGTAGTTGGTAGTCTC 59.519 57.143 0.00 0.00 46.25 3.36
136 137 1.203262 TGGCCCAGTAGTTGGTAGTCT 60.203 52.381 0.00 0.00 46.25 3.24
137 138 1.066358 GTGGCCCAGTAGTTGGTAGTC 60.066 57.143 0.00 0.00 46.25 2.59
138 139 0.981943 GTGGCCCAGTAGTTGGTAGT 59.018 55.000 0.00 0.00 46.25 2.73
139 140 0.108329 CGTGGCCCAGTAGTTGGTAG 60.108 60.000 0.00 0.00 46.25 3.18
140 141 1.546589 CCGTGGCCCAGTAGTTGGTA 61.547 60.000 0.00 0.00 46.25 3.25
141 142 2.747686 CGTGGCCCAGTAGTTGGT 59.252 61.111 0.00 0.00 46.25 3.67
143 144 1.375523 GACCGTGGCCCAGTAGTTG 60.376 63.158 0.00 0.00 0.00 3.16
144 145 1.839747 TGACCGTGGCCCAGTAGTT 60.840 57.895 0.00 0.00 0.00 2.24
145 146 2.203728 TGACCGTGGCCCAGTAGT 60.204 61.111 0.00 0.00 0.00 2.73
146 147 2.264794 GTGACCGTGGCCCAGTAG 59.735 66.667 0.00 0.00 0.00 2.57
147 148 3.687102 CGTGACCGTGGCCCAGTA 61.687 66.667 0.00 0.00 0.00 2.74
160 161 4.293648 CACTGGTCGTGGCCGTGA 62.294 66.667 0.00 0.00 40.02 4.35
176 177 2.268076 GCAAAGAAGGGCGGCTTCA 61.268 57.895 9.56 0.00 33.57 3.02
266 267 2.046892 GCTGCATCACTGGGTCGT 60.047 61.111 0.00 0.00 0.00 4.34
312 313 0.538977 TTCCCTCTCCGTTGTCGAGT 60.539 55.000 0.00 0.00 39.71 4.18
367 368 2.373335 ACATCGAGGGAGCTGTAGAT 57.627 50.000 0.69 0.00 0.00 1.98
368 369 3.510531 ATACATCGAGGGAGCTGTAGA 57.489 47.619 0.69 0.00 0.00 2.59
369 370 3.319405 ACAATACATCGAGGGAGCTGTAG 59.681 47.826 0.69 0.00 0.00 2.74
373 375 3.432326 GGAAACAATACATCGAGGGAGCT 60.432 47.826 0.69 0.00 0.00 4.09
442 444 8.403606 GATTTTCAGAAAAATCGCTCAATCAT 57.596 30.769 12.38 0.00 46.40 2.45
579 582 5.879223 CAGATCAGAACTTTTCATACTGGCT 59.121 40.000 0.00 0.00 0.00 4.75
655 658 0.768997 TTTTCGTCCCCTCCTCCCAA 60.769 55.000 0.00 0.00 0.00 4.12
792 800 2.567522 CAGTCGTCGTCGTCGTCG 60.568 66.667 14.18 14.18 46.06 5.12
793 801 1.949015 TAGCAGTCGTCGTCGTCGTC 61.949 60.000 11.41 6.41 38.33 4.20
794 802 2.023771 TAGCAGTCGTCGTCGTCGT 61.024 57.895 11.41 0.00 38.33 4.34
795 803 1.577117 GTAGCAGTCGTCGTCGTCG 60.577 63.158 5.50 5.50 38.33 5.12
796 804 0.994995 TAGTAGCAGTCGTCGTCGTC 59.005 55.000 1.33 0.00 38.33 4.20
797 805 0.718343 GTAGTAGCAGTCGTCGTCGT 59.282 55.000 1.33 0.00 38.33 4.34
798 806 0.997932 AGTAGTAGCAGTCGTCGTCG 59.002 55.000 0.00 0.00 38.55 5.12
799 807 3.186119 AGTAGTAGTAGCAGTCGTCGTC 58.814 50.000 0.00 0.00 0.00 4.20
800 808 3.244033 AGTAGTAGTAGCAGTCGTCGT 57.756 47.619 0.00 0.00 0.00 4.34
801 809 4.358851 AGTAGTAGTAGTAGCAGTCGTCG 58.641 47.826 0.00 0.00 0.00 5.12
802 810 4.440758 CGAGTAGTAGTAGTAGCAGTCGTC 59.559 50.000 7.15 0.00 0.00 4.20
803 811 4.097135 TCGAGTAGTAGTAGTAGCAGTCGT 59.903 45.833 12.17 0.00 32.26 4.34
804 812 4.605968 TCGAGTAGTAGTAGTAGCAGTCG 58.394 47.826 8.39 8.39 0.00 4.18
805 813 5.830912 TCTCGAGTAGTAGTAGTAGCAGTC 58.169 45.833 13.13 0.00 0.00 3.51
806 814 5.850557 TCTCGAGTAGTAGTAGTAGCAGT 57.149 43.478 13.13 0.00 0.00 4.40
807 815 5.693104 CCTTCTCGAGTAGTAGTAGTAGCAG 59.307 48.000 16.67 0.00 0.00 4.24
808 816 5.362143 TCCTTCTCGAGTAGTAGTAGTAGCA 59.638 44.000 16.67 0.00 0.00 3.49
809 817 5.841810 TCCTTCTCGAGTAGTAGTAGTAGC 58.158 45.833 16.67 0.00 0.00 3.58
812 820 9.850198 AAATATTCCTTCTCGAGTAGTAGTAGT 57.150 33.333 16.67 0.53 0.00 2.73
814 822 9.624373 ACAAATATTCCTTCTCGAGTAGTAGTA 57.376 33.333 16.67 4.14 0.00 1.82
815 823 8.522542 ACAAATATTCCTTCTCGAGTAGTAGT 57.477 34.615 16.67 2.00 0.00 2.73
816 824 9.804758 AAACAAATATTCCTTCTCGAGTAGTAG 57.195 33.333 16.67 8.49 0.00 2.57
818 826 9.503399 AAAAACAAATATTCCTTCTCGAGTAGT 57.497 29.630 16.67 2.61 0.00 2.73
842 850 7.397192 CCTTCTCCAATCCTTTCCTCATAAAAA 59.603 37.037 0.00 0.00 0.00 1.94
843 851 6.891908 CCTTCTCCAATCCTTTCCTCATAAAA 59.108 38.462 0.00 0.00 0.00 1.52
844 852 6.217487 TCCTTCTCCAATCCTTTCCTCATAAA 59.783 38.462 0.00 0.00 0.00 1.40
845 853 5.731187 TCCTTCTCCAATCCTTTCCTCATAA 59.269 40.000 0.00 0.00 0.00 1.90
846 854 5.288687 TCCTTCTCCAATCCTTTCCTCATA 58.711 41.667 0.00 0.00 0.00 2.15
847 855 4.114597 TCCTTCTCCAATCCTTTCCTCAT 58.885 43.478 0.00 0.00 0.00 2.90
848 856 3.531059 TCCTTCTCCAATCCTTTCCTCA 58.469 45.455 0.00 0.00 0.00 3.86
849 857 4.226168 TCTTCCTTCTCCAATCCTTTCCTC 59.774 45.833 0.00 0.00 0.00 3.71
850 858 4.179133 TCTTCCTTCTCCAATCCTTTCCT 58.821 43.478 0.00 0.00 0.00 3.36
851 859 4.576330 TCTTCCTTCTCCAATCCTTTCC 57.424 45.455 0.00 0.00 0.00 3.13
852 860 7.569240 TCTAATCTTCCTTCTCCAATCCTTTC 58.431 38.462 0.00 0.00 0.00 2.62
853 861 7.516450 TCTAATCTTCCTTCTCCAATCCTTT 57.484 36.000 0.00 0.00 0.00 3.11
854 862 7.704359 ATCTAATCTTCCTTCTCCAATCCTT 57.296 36.000 0.00 0.00 0.00 3.36
855 863 7.038373 GCTATCTAATCTTCCTTCTCCAATCCT 60.038 40.741 0.00 0.00 0.00 3.24
856 864 7.038373 AGCTATCTAATCTTCCTTCTCCAATCC 60.038 40.741 0.00 0.00 0.00 3.01
857 865 7.906327 AGCTATCTAATCTTCCTTCTCCAATC 58.094 38.462 0.00 0.00 0.00 2.67
858 866 7.870426 AGCTATCTAATCTTCCTTCTCCAAT 57.130 36.000 0.00 0.00 0.00 3.16
859 867 7.682787 AAGCTATCTAATCTTCCTTCTCCAA 57.317 36.000 0.00 0.00 0.00 3.53
860 868 7.296628 GAAGCTATCTAATCTTCCTTCTCCA 57.703 40.000 0.00 0.00 32.31 3.86
868 876 4.019771 CCCAGGGGAAGCTATCTAATCTTC 60.020 50.000 0.00 0.00 37.50 2.87
869 877 3.913163 CCCAGGGGAAGCTATCTAATCTT 59.087 47.826 0.00 0.00 37.50 2.40
870 878 3.525862 CCCAGGGGAAGCTATCTAATCT 58.474 50.000 0.00 0.00 37.50 2.40
871 879 2.026729 GCCCAGGGGAAGCTATCTAATC 60.027 54.545 7.91 0.00 37.50 1.75
872 880 1.988846 GCCCAGGGGAAGCTATCTAAT 59.011 52.381 7.91 0.00 37.50 1.73
873 881 1.061346 AGCCCAGGGGAAGCTATCTAA 60.061 52.381 7.91 0.00 37.50 2.10
874 882 0.568192 AGCCCAGGGGAAGCTATCTA 59.432 55.000 7.91 0.00 37.50 1.98
907 915 4.394712 GTGGGCCGGACAGACAGG 62.395 72.222 11.00 0.00 36.93 4.00
908 916 4.394712 GGTGGGCCGGACAGACAG 62.395 72.222 11.00 0.00 0.00 3.51
947 955 2.887152 GTGGGCTCAACTGAACTGAAAT 59.113 45.455 0.00 0.00 0.00 2.17
961 969 2.032681 GTGAGTGGGTGTGGGCTC 59.967 66.667 0.00 0.00 0.00 4.70
976 984 0.686112 GACTGAGGAGGAGGAGGGTG 60.686 65.000 0.00 0.00 0.00 4.61
986 994 0.660488 CGACATCGAGGACTGAGGAG 59.340 60.000 3.06 0.00 43.02 3.69
1036 1044 2.677875 CAGGGGAAGGCCAAGCAC 60.678 66.667 5.01 0.00 35.15 4.40
1038 1046 4.372999 AGCAGGGGAAGGCCAAGC 62.373 66.667 5.01 0.00 35.15 4.01
1059 1067 3.267860 GATCTGCTGCTTCGGCCG 61.268 66.667 22.12 22.12 40.91 6.13
1062 1070 3.267860 GCGGATCTGCTGCTTCGG 61.268 66.667 19.63 1.59 45.70 4.30
1105 1119 4.466015 AGCTGGAAAGAAAACCAAACAAGA 59.534 37.500 0.00 0.00 35.67 3.02
1109 1123 4.385358 TGAGCTGGAAAGAAAACCAAAC 57.615 40.909 0.00 0.00 35.67 2.93
1111 1125 4.589216 CATGAGCTGGAAAGAAAACCAA 57.411 40.909 0.00 0.00 35.67 3.67
1226 1291 2.359230 GCTGATGGCCCCGATAGC 60.359 66.667 0.00 0.00 34.27 2.97
1309 1374 3.036819 AGAAGCAGATGCACATCCTAGA 58.963 45.455 7.68 0.00 45.16 2.43
1310 1375 3.132160 CAGAAGCAGATGCACATCCTAG 58.868 50.000 7.68 0.00 45.16 3.02
1311 1376 2.744166 GCAGAAGCAGATGCACATCCTA 60.744 50.000 7.68 0.00 45.16 2.94
1312 1377 2.017623 GCAGAAGCAGATGCACATCCT 61.018 52.381 7.68 0.00 45.16 3.24
1313 1378 0.381089 GCAGAAGCAGATGCACATCC 59.619 55.000 7.68 0.00 45.16 3.51
1314 1379 3.920144 GCAGAAGCAGATGCACATC 57.080 52.632 7.68 2.28 45.16 3.06
1327 1392 2.082231 GAAGCAGAAGCAGATGCAGAA 58.918 47.619 7.68 0.00 45.01 3.02
1339 1404 0.975135 AGAGCAGAGCAGAAGCAGAA 59.025 50.000 0.00 0.00 45.49 3.02
1343 1408 1.078988 AGCAGAGCAGAGCAGAAGC 60.079 57.895 0.00 0.00 42.56 3.86
1344 1409 0.533491 AGAGCAGAGCAGAGCAGAAG 59.467 55.000 0.00 0.00 0.00 2.85
1345 1410 0.246910 CAGAGCAGAGCAGAGCAGAA 59.753 55.000 0.00 0.00 0.00 3.02
1346 1411 1.891616 CAGAGCAGAGCAGAGCAGA 59.108 57.895 0.00 0.00 0.00 4.26
1347 1412 1.812093 GCAGAGCAGAGCAGAGCAG 60.812 63.158 0.00 0.00 0.00 4.24
1348 1413 2.228389 GAGCAGAGCAGAGCAGAGCA 62.228 60.000 0.00 0.00 0.00 4.26
1349 1414 1.519898 GAGCAGAGCAGAGCAGAGC 60.520 63.158 0.00 0.00 0.00 4.09
1350 1415 0.179121 CAGAGCAGAGCAGAGCAGAG 60.179 60.000 0.00 0.00 0.00 3.35
1351 1416 1.891616 CAGAGCAGAGCAGAGCAGA 59.108 57.895 0.00 0.00 0.00 4.26
1352 1417 1.812093 GCAGAGCAGAGCAGAGCAG 60.812 63.158 0.00 0.00 0.00 4.24
1353 1418 2.228389 GAGCAGAGCAGAGCAGAGCA 62.228 60.000 0.00 0.00 0.00 4.26
1354 1419 1.519898 GAGCAGAGCAGAGCAGAGC 60.520 63.158 0.00 0.00 0.00 4.09
1355 1420 0.179121 CAGAGCAGAGCAGAGCAGAG 60.179 60.000 0.00 0.00 0.00 3.35
1356 1421 1.891616 CAGAGCAGAGCAGAGCAGA 59.108 57.895 0.00 0.00 0.00 4.26
1357 1422 1.812093 GCAGAGCAGAGCAGAGCAG 60.812 63.158 0.00 0.00 0.00 4.24
1358 1423 2.228389 GAGCAGAGCAGAGCAGAGCA 62.228 60.000 0.00 0.00 0.00 4.26
1359 1424 1.519898 GAGCAGAGCAGAGCAGAGC 60.520 63.158 0.00 0.00 0.00 4.09
1360 1425 0.101759 GAGAGCAGAGCAGAGCAGAG 59.898 60.000 0.00 0.00 0.00 3.35
1361 1426 0.323633 AGAGAGCAGAGCAGAGCAGA 60.324 55.000 0.00 0.00 0.00 4.26
1362 1427 1.335810 CTAGAGAGCAGAGCAGAGCAG 59.664 57.143 0.00 0.00 0.00 4.24
1363 1428 1.064832 TCTAGAGAGCAGAGCAGAGCA 60.065 52.381 0.00 0.00 0.00 4.26
1364 1429 1.679139 TCTAGAGAGCAGAGCAGAGC 58.321 55.000 0.00 0.00 0.00 4.09
1365 1430 3.884693 TGATTCTAGAGAGCAGAGCAGAG 59.115 47.826 0.00 0.00 0.00 3.35
1366 1431 3.895998 TGATTCTAGAGAGCAGAGCAGA 58.104 45.455 0.00 0.00 0.00 4.26
1367 1432 4.652421 TTGATTCTAGAGAGCAGAGCAG 57.348 45.455 0.00 0.00 0.00 4.24
1368 1433 5.128335 TGAATTGATTCTAGAGAGCAGAGCA 59.872 40.000 5.42 0.00 37.67 4.26
1402 1467 8.183104 AGCAGAGCAGTTATATCATGTACTAA 57.817 34.615 0.00 0.00 0.00 2.24
1431 1707 4.884744 TCGAAGAAAGGTGACAAATTCCAA 59.115 37.500 0.00 0.00 0.00 3.53
1434 1710 9.278734 GATTATTCGAAGAAAGGTGACAAATTC 57.721 33.333 9.57 0.00 45.90 2.17
1435 1711 9.014297 AGATTATTCGAAGAAAGGTGACAAATT 57.986 29.630 9.57 0.00 45.90 1.82
1440 1716 7.835634 AGAAGATTATTCGAAGAAAGGTGAC 57.164 36.000 9.57 0.44 45.90 3.67
1458 1752 9.091220 GGTACAGGGTATACATAGAAAGAAGAT 57.909 37.037 5.01 0.00 0.00 2.40
1550 2055 3.365868 GCATGTTCTTCGTTGGTGCATAA 60.366 43.478 0.00 0.00 0.00 1.90
1560 2065 6.352016 AGATATATGGAGCATGTTCTTCGT 57.648 37.500 9.57 0.00 0.00 3.85
1562 2067 6.945218 AGGAGATATATGGAGCATGTTCTTC 58.055 40.000 9.57 0.00 0.00 2.87
1624 2129 9.733556 TCATCATCATCATCATCATACAAATCA 57.266 29.630 0.00 0.00 0.00 2.57
1907 2435 5.678955 ACTAGGTACTGAAGGAAATCCAC 57.321 43.478 1.67 0.00 41.52 4.02
1995 2524 2.970324 TCGTGGTGGCGCAGAAAC 60.970 61.111 10.83 0.92 0.00 2.78
2055 2584 4.141756 CCATCATCTGAAGGTAGTGCTTCT 60.142 45.833 0.00 0.00 0.00 2.85
2131 2666 0.596082 TTGTCGTCGTCATCAGCAGA 59.404 50.000 0.00 0.00 0.00 4.26
2151 2689 7.041721 CACCAGCAGTATCACTAATCTTACAA 58.958 38.462 0.00 0.00 0.00 2.41
2165 2703 0.844661 TTCCCCACCACCAGCAGTAT 60.845 55.000 0.00 0.00 0.00 2.12
2171 2709 0.405585 ACTGATTTCCCCACCACCAG 59.594 55.000 0.00 0.00 0.00 4.00
2180 2718 3.438434 GCTCAACTCTCAACTGATTTCCC 59.562 47.826 0.00 0.00 0.00 3.97
2207 2745 5.053025 CGCAACGACAAGAAAAGAAAAGAAG 60.053 40.000 0.00 0.00 0.00 2.85
3083 3637 9.321562 ACTCAATTCAATTCAATTATTGCCATC 57.678 29.630 0.00 0.00 35.86 3.51
3084 3638 9.675464 AACTCAATTCAATTCAATTATTGCCAT 57.325 25.926 0.00 0.00 35.86 4.40
3085 3639 8.937884 CAACTCAATTCAATTCAATTATTGCCA 58.062 29.630 0.00 0.00 35.86 4.92
3086 3640 9.153721 TCAACTCAATTCAATTCAATTATTGCC 57.846 29.630 0.00 0.00 35.86 4.52
3091 3645 9.577110 GATGCTCAACTCAATTCAATTCAATTA 57.423 29.630 0.00 0.00 0.00 1.40
3093 3647 7.544566 GTGATGCTCAACTCAATTCAATTCAAT 59.455 33.333 0.00 0.00 0.00 2.57
3094 3648 6.864685 GTGATGCTCAACTCAATTCAATTCAA 59.135 34.615 0.00 0.00 0.00 2.69
3095 3649 6.208007 AGTGATGCTCAACTCAATTCAATTCA 59.792 34.615 0.00 0.00 0.00 2.57
3096 3650 6.618811 AGTGATGCTCAACTCAATTCAATTC 58.381 36.000 0.00 0.00 0.00 2.17
3097 3651 6.585695 AGTGATGCTCAACTCAATTCAATT 57.414 33.333 0.00 0.00 0.00 2.32
3098 3652 6.208007 TGAAGTGATGCTCAACTCAATTCAAT 59.792 34.615 11.56 0.00 46.96 2.57
3099 3653 5.532032 TGAAGTGATGCTCAACTCAATTCAA 59.468 36.000 11.56 0.00 46.96 2.69
3100 3654 5.618056 GAAGTGATGCTCAACTCAATTCA 57.382 39.130 7.59 0.00 42.79 2.57
3101 3655 5.180868 AGTGAAGTGATGCTCAACTCAATTC 59.819 40.000 5.95 5.95 43.27 2.17
3108 3662 3.397482 AGTGAGTGAAGTGATGCTCAAC 58.603 45.455 0.00 0.00 39.33 3.18
3141 3695 9.532494 CATAGGATAGGATAGGATAGGATTCAG 57.468 40.741 0.00 0.00 0.00 3.02
3160 3714 4.574674 TCTTGTTTCAGGCACATAGGAT 57.425 40.909 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.