Multiple sequence alignment - TraesCS3D01G002600

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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 TraesCS3D01G002600 chr3D 100.000 3275 0 0 1 3275 1197983 1194709 0.000000e+00 6048
1 TraesCS3D01G002600 chr3D 84.792 480 43 9 2585 3048 1209466 1209001 3.850000e-124 455
2 TraesCS3D01G002600 chr3D 94.372 231 13 0 3045 3275 501269163 501269393 4.020000e-94 355
3 TraesCS3D01G002600 chrUn 95.790 2114 48 10 959 3053 34465425 34463334 0.000000e+00 3373
4 TraesCS3D01G002600 chrUn 95.109 2106 57 10 805 2885 34009437 34011521 0.000000e+00 3277
5 TraesCS3D01G002600 chrUn 90.340 559 20 7 1 545 34008573 34009111 0.000000e+00 702
6 TraesCS3D01G002600 chrUn 95.694 209 1 3 601 809 34009108 34009308 2.440000e-86 329
7 TraesCS3D01G002600 chrUn 93.043 230 5 2 1 230 34008199 34008417 3.150000e-85 326
8 TraesCS3D01G002600 chr2B 80.984 1362 197 32 978 2285 163977222 163978575 0.000000e+00 1024
9 TraesCS3D01G002600 chr2B 79.912 1364 206 39 978 2285 163741756 163743107 0.000000e+00 939
10 TraesCS3D01G002600 chr2A 80.784 1327 186 37 1012 2275 115094759 115096079 0.000000e+00 974
11 TraesCS3D01G002600 chr2A 80.160 1003 158 24 1310 2284 114498414 114497425 0.000000e+00 712
12 TraesCS3D01G002600 chr2D 80.219 1370 202 37 978 2285 113480468 113481830 0.000000e+00 965
13 TraesCS3D01G002600 chr2D 79.970 1328 200 35 1012 2285 113091364 113092679 0.000000e+00 918
14 TraesCS3D01G002600 chr2D 94.737 228 12 0 3048 3275 557687335 557687108 4.020000e-94 355
15 TraesCS3D01G002600 chr2D 94.714 227 12 0 3049 3275 573915920 573915694 1.450000e-93 353
16 TraesCS3D01G002600 chr2D 94.298 228 13 0 3048 3275 390402908 390402681 1.870000e-92 350
17 TraesCS3D01G002600 chr3A 79.350 1230 207 30 1073 2275 100847869 100849078 0.000000e+00 821
18 TraesCS3D01G002600 chr3B 78.973 1227 217 23 1073 2275 132910076 132911285 0.000000e+00 798
19 TraesCS3D01G002600 chr6D 94.118 238 13 1 3039 3275 445691741 445691504 8.640000e-96 361
20 TraesCS3D01G002600 chr6D 94.690 226 12 0 3050 3275 421551820 421552045 5.200000e-93 351
21 TraesCS3D01G002600 chr6D 79.511 327 33 10 2608 2917 388126917 388126608 5.540000e-48 202
22 TraesCS3D01G002600 chr7D 95.089 224 11 0 3052 3275 385710557 385710780 1.450000e-93 353
23 TraesCS3D01G002600 chr4D 94.298 228 13 0 3048 3275 175781827 175782054 1.870000e-92 350
24 TraesCS3D01G002600 chr4D 93.220 236 16 0 3040 3275 35601650 35601885 6.730000e-92 348
25 TraesCS3D01G002600 chr6A 79.205 327 34 10 2608 2917 533407072 533406763 2.580000e-46 196
26 TraesCS3D01G002600 chr6B 83.249 197 18 1 2604 2785 579539248 579539052 2.020000e-37 167


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 TraesCS3D01G002600 chr3D 1194709 1197983 3274 True 6048.0 6048 100.0000 1 3275 1 chr3D.!!$R1 3274
1 TraesCS3D01G002600 chrUn 34463334 34465425 2091 True 3373.0 3373 95.7900 959 3053 1 chrUn.!!$R1 2094
2 TraesCS3D01G002600 chrUn 34008199 34011521 3322 False 1158.5 3277 93.5465 1 2885 4 chrUn.!!$F1 2884
3 TraesCS3D01G002600 chr2B 163977222 163978575 1353 False 1024.0 1024 80.9840 978 2285 1 chr2B.!!$F2 1307
4 TraesCS3D01G002600 chr2B 163741756 163743107 1351 False 939.0 939 79.9120 978 2285 1 chr2B.!!$F1 1307
5 TraesCS3D01G002600 chr2A 115094759 115096079 1320 False 974.0 974 80.7840 1012 2275 1 chr2A.!!$F1 1263
6 TraesCS3D01G002600 chr2A 114497425 114498414 989 True 712.0 712 80.1600 1310 2284 1 chr2A.!!$R1 974
7 TraesCS3D01G002600 chr2D 113480468 113481830 1362 False 965.0 965 80.2190 978 2285 1 chr2D.!!$F2 1307
8 TraesCS3D01G002600 chr2D 113091364 113092679 1315 False 918.0 918 79.9700 1012 2285 1 chr2D.!!$F1 1273
9 TraesCS3D01G002600 chr3A 100847869 100849078 1209 False 821.0 821 79.3500 1073 2275 1 chr3A.!!$F1 1202
10 TraesCS3D01G002600 chr3B 132910076 132911285 1209 False 798.0 798 78.9730 1073 2275 1 chr3B.!!$F1 1202

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
436 825 0.858583 CATTTGCGACGTCTGTGTCA 59.141 50.0 14.7 0.89 38.84 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2321 2913 0.325933 TCACATGGGCCAGAAGTCAG 59.674 55.0 13.78 0.17 0.0 3.51 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
33 34 3.316501 AGAAAGAGGATAGCTCTGCCAT 58.683 45.455 0.00 0.00 0.00 4.40
34 35 4.487804 AGAAAGAGGATAGCTCTGCCATA 58.512 43.478 0.00 0.00 0.00 2.74
35 36 4.527816 AGAAAGAGGATAGCTCTGCCATAG 59.472 45.833 0.00 0.00 0.00 2.23
36 37 3.541242 AGAGGATAGCTCTGCCATAGT 57.459 47.619 0.00 0.00 0.00 2.12
37 38 3.164268 AGAGGATAGCTCTGCCATAGTG 58.836 50.000 0.00 0.00 0.00 2.74
38 39 1.622811 AGGATAGCTCTGCCATAGTGC 59.377 52.381 0.00 0.00 44.28 4.40
39 40 1.338579 GGATAGCTCTGCCATAGTGCC 60.339 57.143 0.00 0.00 44.87 5.01
40 41 1.345741 GATAGCTCTGCCATAGTGCCA 59.654 52.381 0.00 0.00 44.87 4.92
182 183 1.897560 GCTCACTTGTAAGCCACCTT 58.102 50.000 0.00 0.00 32.22 3.50
186 187 3.476552 TCACTTGTAAGCCACCTTTCTG 58.523 45.455 0.00 0.00 32.47 3.02
195 196 3.308401 AGCCACCTTTCTGACCAAAAAT 58.692 40.909 0.00 0.00 0.00 1.82
206 207 7.411486 TTCTGACCAAAAATTTGTGGAAGTA 57.589 32.000 30.43 18.14 38.36 2.24
260 645 8.738645 AAGGAAGAATCAATTCTACCATGTAC 57.261 34.615 5.71 0.00 45.83 2.90
311 700 5.707764 ACTAAGCTAAAAAGGCTCCTCAAAG 59.292 40.000 0.00 0.00 39.30 2.77
348 737 6.194508 CACATTTCCATAAATCGCAAACTACG 59.805 38.462 0.00 0.00 32.87 3.51
349 738 5.866335 TTTCCATAAATCGCAAACTACGT 57.134 34.783 0.00 0.00 0.00 3.57
350 739 6.964741 TTTCCATAAATCGCAAACTACGTA 57.035 33.333 0.00 0.00 0.00 3.57
351 740 5.954434 TCCATAAATCGCAAACTACGTAC 57.046 39.130 0.00 0.00 0.00 3.67
365 754 2.951458 GTACAAGCCAACGCACCC 59.049 61.111 0.00 0.00 37.52 4.61
384 773 6.127451 CGCACCCATATAGGTAGATTATGTCA 60.127 42.308 0.00 0.00 38.39 3.58
416 805 5.465056 CCTTCAATGTTGGCGTTTGTTTTAT 59.535 36.000 0.00 0.00 0.00 1.40
428 817 4.377445 CGTTTGTTTTATCATTTGCGACGT 59.623 37.500 0.00 0.00 0.00 4.34
436 825 0.858583 CATTTGCGACGTCTGTGTCA 59.141 50.000 14.70 0.89 38.84 3.58
445 834 3.978855 CGACGTCTGTGTCATTGAGTTAA 59.021 43.478 14.70 0.00 38.84 2.01
446 835 4.143597 CGACGTCTGTGTCATTGAGTTAAC 60.144 45.833 14.70 0.00 38.84 2.01
447 836 4.689071 ACGTCTGTGTCATTGAGTTAACA 58.311 39.130 8.61 0.00 0.00 2.41
448 837 4.506654 ACGTCTGTGTCATTGAGTTAACAC 59.493 41.667 8.61 1.71 41.80 3.32
458 847 3.535280 TGAGTTAACACAGACAGCACA 57.465 42.857 8.61 0.00 0.00 4.57
475 864 2.863137 GCACAATGAAGAAACGCCAAAA 59.137 40.909 0.00 0.00 0.00 2.44
519 908 4.083643 CGCAGTCACTGATTCTGTTTCATT 60.084 41.667 9.70 0.00 32.44 2.57
520 909 5.561532 CGCAGTCACTGATTCTGTTTCATTT 60.562 40.000 9.70 0.00 32.44 2.32
544 933 4.689612 TTTTCCAGTCTTGTAGTCTGCT 57.310 40.909 0.00 0.00 31.46 4.24
545 934 3.667497 TTCCAGTCTTGTAGTCTGCTG 57.333 47.619 0.00 0.00 31.46 4.41
546 935 2.598565 TCCAGTCTTGTAGTCTGCTGT 58.401 47.619 0.00 0.00 31.46 4.40
547 936 2.558795 TCCAGTCTTGTAGTCTGCTGTC 59.441 50.000 0.00 0.00 31.46 3.51
548 937 2.297315 CCAGTCTTGTAGTCTGCTGTCA 59.703 50.000 0.00 0.00 31.46 3.58
549 938 3.573598 CAGTCTTGTAGTCTGCTGTCAG 58.426 50.000 0.00 0.00 41.67 3.51
550 939 3.005261 CAGTCTTGTAGTCTGCTGTCAGT 59.995 47.826 0.93 0.00 41.10 3.41
551 940 3.639094 AGTCTTGTAGTCTGCTGTCAGTT 59.361 43.478 0.93 0.00 41.10 3.16
552 941 3.984633 GTCTTGTAGTCTGCTGTCAGTTC 59.015 47.826 0.93 0.00 41.10 3.01
553 942 3.636764 TCTTGTAGTCTGCTGTCAGTTCA 59.363 43.478 0.93 0.00 41.10 3.18
554 943 3.371102 TGTAGTCTGCTGTCAGTTCAC 57.629 47.619 0.93 0.00 41.10 3.18
555 944 2.035961 TGTAGTCTGCTGTCAGTTCACC 59.964 50.000 0.93 0.00 41.10 4.02
556 945 1.123077 AGTCTGCTGTCAGTTCACCA 58.877 50.000 0.93 0.00 41.10 4.17
557 946 1.202580 AGTCTGCTGTCAGTTCACCAC 60.203 52.381 0.93 0.00 41.10 4.16
558 947 1.123077 TCTGCTGTCAGTTCACCACT 58.877 50.000 0.93 0.00 41.10 4.00
559 948 2.035961 GTCTGCTGTCAGTTCACCACTA 59.964 50.000 0.93 0.00 41.10 2.74
560 949 2.698274 TCTGCTGTCAGTTCACCACTAA 59.302 45.455 0.93 0.00 41.10 2.24
561 950 3.133901 TCTGCTGTCAGTTCACCACTAAA 59.866 43.478 0.93 0.00 41.10 1.85
562 951 3.202906 TGCTGTCAGTTCACCACTAAAC 58.797 45.455 0.93 0.00 32.76 2.01
563 952 2.548480 GCTGTCAGTTCACCACTAAACC 59.452 50.000 0.93 0.00 32.76 3.27
564 953 3.139077 CTGTCAGTTCACCACTAAACCC 58.861 50.000 0.00 0.00 32.76 4.11
565 954 2.158726 TGTCAGTTCACCACTAAACCCC 60.159 50.000 0.00 0.00 32.76 4.95
566 955 1.422402 TCAGTTCACCACTAAACCCCC 59.578 52.381 0.00 0.00 32.76 5.40
634 1023 1.423541 ACCTATGTCCTTGCCACAACA 59.576 47.619 0.00 0.00 0.00 3.33
635 1024 1.812571 CCTATGTCCTTGCCACAACAC 59.187 52.381 0.00 0.00 0.00 3.32
636 1025 2.503331 CTATGTCCTTGCCACAACACA 58.497 47.619 0.00 0.00 0.00 3.72
637 1026 1.999648 ATGTCCTTGCCACAACACAT 58.000 45.000 0.00 0.00 0.00 3.21
638 1027 2.647683 TGTCCTTGCCACAACACATA 57.352 45.000 0.00 0.00 0.00 2.29
639 1028 2.503331 TGTCCTTGCCACAACACATAG 58.497 47.619 0.00 0.00 0.00 2.23
640 1029 1.812571 GTCCTTGCCACAACACATAGG 59.187 52.381 0.00 0.00 0.00 2.57
641 1030 1.702401 TCCTTGCCACAACACATAGGA 59.298 47.619 0.00 0.00 0.00 2.94
693 1082 6.384224 TGACCTACTCAAATACGTGTAGTTG 58.616 40.000 12.58 12.58 41.05 3.16
703 1092 1.275291 ACGTGTAGTTGCTGGCTGTAT 59.725 47.619 0.00 0.00 0.00 2.29
809 1198 4.021925 GCAGGTTCAGAGGCCGGT 62.022 66.667 1.90 0.00 0.00 5.28
856 1378 6.240894 TCTTCTTCCTGTTCACATGCTTTAT 58.759 36.000 0.00 0.00 0.00 1.40
895 1417 9.755064 CGTTGTCAAAACCTTGTATAAATAGAG 57.245 33.333 0.00 0.00 33.94 2.43
972 1494 9.462174 CTGAATTAGAAGTTAGACATCTAGCTG 57.538 37.037 6.10 0.00 39.46 4.24
1430 1996 0.107456 ATATGGAGCCGGAACTGCAG 59.893 55.000 13.48 13.48 41.60 4.41
1431 1997 1.264749 TATGGAGCCGGAACTGCAGT 61.265 55.000 15.25 15.25 41.60 4.40
1432 1998 1.264749 ATGGAGCCGGAACTGCAGTA 61.265 55.000 22.01 0.34 41.60 2.74
1446 2012 1.296715 CAGTACCCCAAGCTCGCTT 59.703 57.895 0.00 0.00 36.60 4.68
1540 2118 3.449227 CCTCTAGCGCACCCGTCA 61.449 66.667 11.47 0.00 36.67 4.35
1671 2249 0.179108 GCGTCGGCAAGTTCTCCTAT 60.179 55.000 0.00 0.00 39.62 2.57
1674 2252 2.674177 CGTCGGCAAGTTCTCCTATTGT 60.674 50.000 0.00 0.00 0.00 2.71
1796 2377 4.699522 GAGCCCGCAGAACCCGTT 62.700 66.667 0.00 0.00 0.00 4.44
2287 2877 5.642919 AGTAAGCTCTGAAGATTGAAGCAAG 59.357 40.000 0.00 0.00 32.32 4.01
2317 2909 3.873952 GCTGAACAGTGGATATCCTTCAC 59.126 47.826 22.35 12.41 36.82 3.18
2321 2913 2.101582 ACAGTGGATATCCTTCACGCTC 59.898 50.000 22.35 3.69 36.60 5.03
2384 2976 5.124457 CGATCCTTCAGATTTGGTCAATGTT 59.876 40.000 0.00 0.00 34.42 2.71
2385 2977 5.964958 TCCTTCAGATTTGGTCAATGTTC 57.035 39.130 0.00 0.00 0.00 3.18
2386 2978 5.384336 TCCTTCAGATTTGGTCAATGTTCA 58.616 37.500 0.00 0.00 0.00 3.18
2397 2991 3.256631 GGTCAATGTTCATGCAAAGTCCT 59.743 43.478 0.00 0.00 0.00 3.85
2419 3013 5.474876 CCTGTTGAAGAATACTCTTTTGGCT 59.525 40.000 0.00 0.00 42.19 4.75
2527 3121 8.889000 GTTAATGTGTAACTTCGTCAACAATTC 58.111 33.333 0.00 0.00 38.04 2.17
2647 3241 8.896722 ATAGTCTACCTGTTATATAACCAGGG 57.103 38.462 28.61 24.20 38.07 4.45
2653 3247 5.493250 ACCTGTTATATAACCAGGGTCCAAA 59.507 40.000 28.61 10.07 38.07 3.28
2655 3249 7.066781 CCTGTTATATAACCAGGGTCCAAATT 58.933 38.462 23.20 0.00 35.37 1.82
2658 3252 3.845109 ATAACCAGGGTCCAAATTGGT 57.155 42.857 12.28 0.00 45.47 3.67
2677 3271 2.159517 GGTAATTGCAGAAAGACCGCTG 60.160 50.000 0.00 0.00 35.28 5.18
2704 3298 3.087031 CCTTGACTTGCATTCTGGATGT 58.913 45.455 0.00 0.00 38.07 3.06
2775 3384 6.071447 AGCTGCACCATGTTAAACATATCAAA 60.071 34.615 1.02 0.00 36.53 2.69
2917 3526 9.956797 CACTTTTCTTTTGAACATGTTAAACAG 57.043 29.630 11.95 12.99 38.30 3.16
3053 3662 3.563223 ACTGCGGTATAGCCTTCTTAGA 58.437 45.455 0.00 0.00 36.02 2.10
3054 3663 3.570550 ACTGCGGTATAGCCTTCTTAGAG 59.429 47.826 0.00 0.00 36.02 2.43
3055 3664 2.296471 TGCGGTATAGCCTTCTTAGAGC 59.704 50.000 0.00 0.00 36.02 4.09
3056 3665 2.296471 GCGGTATAGCCTTCTTAGAGCA 59.704 50.000 0.00 0.00 34.25 4.26
3057 3666 3.243771 GCGGTATAGCCTTCTTAGAGCAA 60.244 47.826 0.00 0.00 34.25 3.91
3058 3667 4.299978 CGGTATAGCCTTCTTAGAGCAAC 58.700 47.826 0.00 0.00 34.25 4.17
3059 3668 4.038162 CGGTATAGCCTTCTTAGAGCAACT 59.962 45.833 0.00 0.00 34.25 3.16
3060 3669 5.534407 GGTATAGCCTTCTTAGAGCAACTC 58.466 45.833 0.00 0.00 0.00 3.01
3061 3670 5.303333 GGTATAGCCTTCTTAGAGCAACTCT 59.697 44.000 2.23 2.23 43.83 3.24
3062 3671 6.490721 GGTATAGCCTTCTTAGAGCAACTCTA 59.509 42.308 0.16 0.16 41.50 2.43
3063 3672 6.648879 ATAGCCTTCTTAGAGCAACTCTAG 57.351 41.667 4.64 1.08 42.92 2.43
3064 3673 3.132111 AGCCTTCTTAGAGCAACTCTAGC 59.868 47.826 4.64 4.96 42.92 3.42
3065 3674 3.118956 GCCTTCTTAGAGCAACTCTAGCA 60.119 47.826 4.64 0.00 42.92 3.49
3066 3675 4.681744 CCTTCTTAGAGCAACTCTAGCAG 58.318 47.826 4.64 1.69 42.92 4.24
3067 3676 4.400884 CCTTCTTAGAGCAACTCTAGCAGA 59.599 45.833 4.64 3.80 42.92 4.26
3068 3677 4.974368 TCTTAGAGCAACTCTAGCAGAC 57.026 45.455 4.64 0.00 42.92 3.51
3069 3678 3.697045 TCTTAGAGCAACTCTAGCAGACC 59.303 47.826 4.64 0.00 42.92 3.85
3070 3679 1.190643 AGAGCAACTCTAGCAGACCC 58.809 55.000 0.00 0.00 39.28 4.46
3071 3680 0.176910 GAGCAACTCTAGCAGACCCC 59.823 60.000 0.00 0.00 0.00 4.95
3072 3681 1.153549 GCAACTCTAGCAGACCCCG 60.154 63.158 0.00 0.00 0.00 5.73
3073 3682 1.153549 CAACTCTAGCAGACCCCGC 60.154 63.158 0.00 0.00 0.00 6.13
3074 3683 1.609501 AACTCTAGCAGACCCCGCA 60.610 57.895 0.00 0.00 0.00 5.69
3075 3684 0.978146 AACTCTAGCAGACCCCGCAT 60.978 55.000 0.00 0.00 0.00 4.73
3076 3685 1.365633 CTCTAGCAGACCCCGCATC 59.634 63.158 0.00 0.00 0.00 3.91
3077 3686 2.093537 CTCTAGCAGACCCCGCATCC 62.094 65.000 0.00 0.00 0.00 3.51
3078 3687 3.506059 CTAGCAGACCCCGCATCCG 62.506 68.421 0.00 0.00 0.00 4.18
3089 3698 4.481112 GCATCCGGCGCAAACCAG 62.481 66.667 10.83 0.00 0.00 4.00
3090 3699 4.481112 CATCCGGCGCAAACCAGC 62.481 66.667 10.83 0.00 0.00 4.85
3093 3702 2.884997 ATCCGGCGCAAACCAGCATA 62.885 55.000 10.83 0.00 34.54 3.14
3094 3703 2.695759 CCGGCGCAAACCAGCATAA 61.696 57.895 10.83 0.00 34.54 1.90
3095 3704 1.433064 CGGCGCAAACCAGCATAAT 59.567 52.632 10.83 0.00 34.54 1.28
3096 3705 0.179140 CGGCGCAAACCAGCATAATT 60.179 50.000 10.83 0.00 34.54 1.40
3097 3706 1.559831 GGCGCAAACCAGCATAATTC 58.440 50.000 10.83 0.00 34.54 2.17
3098 3707 1.559831 GCGCAAACCAGCATAATTCC 58.440 50.000 0.30 0.00 0.00 3.01
3099 3708 1.826327 CGCAAACCAGCATAATTCCG 58.174 50.000 0.00 0.00 0.00 4.30
3100 3709 1.533756 CGCAAACCAGCATAATTCCGG 60.534 52.381 0.00 0.00 0.00 5.14
3101 3710 1.802508 GCAAACCAGCATAATTCCGGC 60.803 52.381 0.00 0.00 0.00 6.13
3102 3711 0.738389 AAACCAGCATAATTCCGGCG 59.262 50.000 0.00 0.00 0.00 6.46
3103 3712 0.107410 AACCAGCATAATTCCGGCGA 60.107 50.000 9.30 0.00 0.00 5.54
3104 3713 0.108585 ACCAGCATAATTCCGGCGAT 59.891 50.000 9.30 0.00 0.00 4.58
3105 3714 1.238439 CCAGCATAATTCCGGCGATT 58.762 50.000 9.30 3.36 0.00 3.34
3106 3715 2.224426 ACCAGCATAATTCCGGCGATTA 60.224 45.455 9.30 5.92 0.00 1.75
3107 3716 3.009723 CCAGCATAATTCCGGCGATTAT 58.990 45.455 9.30 8.29 31.57 1.28
3108 3717 4.188462 CCAGCATAATTCCGGCGATTATA 58.812 43.478 9.30 0.00 30.59 0.98
3109 3718 4.034048 CCAGCATAATTCCGGCGATTATAC 59.966 45.833 9.30 13.76 30.59 1.47
3110 3719 3.863424 AGCATAATTCCGGCGATTATACG 59.137 43.478 9.30 10.65 30.59 3.06
3115 3724 2.818350 CCGGCGATTATACGGGTTC 58.182 57.895 9.30 0.00 43.69 3.62
3116 3725 1.005294 CCGGCGATTATACGGGTTCG 61.005 60.000 9.30 0.00 43.69 3.95
3117 3726 1.005294 CGGCGATTATACGGGTTCGG 61.005 60.000 0.00 0.00 41.39 4.30
3118 3727 2.147820 GCGATTATACGGGTTCGGC 58.852 57.895 0.00 0.00 41.39 5.54
3119 3728 1.287041 GCGATTATACGGGTTCGGCC 61.287 60.000 0.00 0.00 41.39 6.13
3129 3738 3.812577 GGTTCGGCCCATTTTTCTG 57.187 52.632 0.00 0.00 0.00 3.02
3130 3739 0.246360 GGTTCGGCCCATTTTTCTGG 59.754 55.000 0.00 0.00 35.95 3.86
3131 3740 0.389817 GTTCGGCCCATTTTTCTGGC 60.390 55.000 0.00 0.00 44.59 4.85
3135 3744 2.669878 GCCCATTTTTCTGGCCAGA 58.330 52.632 32.00 32.00 39.30 3.86
3136 3745 0.247460 GCCCATTTTTCTGGCCAGAC 59.753 55.000 35.26 17.07 39.30 3.51
3137 3746 0.897621 CCCATTTTTCTGGCCAGACC 59.102 55.000 35.26 0.00 37.14 3.85
3146 3755 3.680786 GGCCAGACCAAAACCCGC 61.681 66.667 0.00 0.00 38.86 6.13
3147 3756 2.909965 GCCAGACCAAAACCCGCA 60.910 61.111 0.00 0.00 0.00 5.69
3148 3757 2.275380 GCCAGACCAAAACCCGCAT 61.275 57.895 0.00 0.00 0.00 4.73
3149 3758 1.883021 CCAGACCAAAACCCGCATC 59.117 57.895 0.00 0.00 0.00 3.91
3150 3759 1.501741 CAGACCAAAACCCGCATCG 59.498 57.895 0.00 0.00 0.00 3.84
3152 3761 1.969589 GACCAAAACCCGCATCGGT 60.970 57.895 4.47 0.00 46.80 4.69
3153 3762 2.195123 GACCAAAACCCGCATCGGTG 62.195 60.000 4.47 0.00 46.80 4.94
3154 3763 2.265182 CCAAAACCCGCATCGGTGT 61.265 57.895 0.00 0.00 46.80 4.16
3155 3764 1.209127 CAAAACCCGCATCGGTGTC 59.791 57.895 0.00 0.00 46.80 3.67
3156 3765 1.969589 AAAACCCGCATCGGTGTCC 60.970 57.895 0.00 0.00 46.80 4.02
3157 3766 4.752879 AACCCGCATCGGTGTCCG 62.753 66.667 0.00 1.45 46.80 4.79
3166 3775 4.376176 CGGTGTCCGGCCCGTAAA 62.376 66.667 16.10 0.00 44.15 2.01
3167 3776 2.269883 GGTGTCCGGCCCGTAAAT 59.730 61.111 0.85 0.00 0.00 1.40
3168 3777 1.521616 GGTGTCCGGCCCGTAAATA 59.478 57.895 0.85 0.00 0.00 1.40
3169 3778 0.107268 GGTGTCCGGCCCGTAAATAT 59.893 55.000 0.85 0.00 0.00 1.28
3170 3779 1.475571 GGTGTCCGGCCCGTAAATATT 60.476 52.381 0.85 0.00 0.00 1.28
3171 3780 2.291365 GTGTCCGGCCCGTAAATATTT 58.709 47.619 0.85 5.89 0.00 1.40
3172 3781 2.684374 GTGTCCGGCCCGTAAATATTTT 59.316 45.455 5.91 0.00 0.00 1.82
3173 3782 3.129113 GTGTCCGGCCCGTAAATATTTTT 59.871 43.478 5.91 0.00 0.00 1.94
3174 3783 3.128938 TGTCCGGCCCGTAAATATTTTTG 59.871 43.478 5.91 0.00 0.00 2.44
3175 3784 2.099427 TCCGGCCCGTAAATATTTTTGC 59.901 45.455 5.91 4.50 0.00 3.68
3176 3785 2.465855 CGGCCCGTAAATATTTTTGCC 58.534 47.619 5.91 11.75 30.58 4.52
3177 3786 2.465855 GGCCCGTAAATATTTTTGCCG 58.534 47.619 5.91 4.48 0.00 5.69
3178 3787 1.855978 GCCCGTAAATATTTTTGCCGC 59.144 47.619 5.91 0.00 0.00 6.53
3179 3788 2.735762 GCCCGTAAATATTTTTGCCGCA 60.736 45.455 5.91 0.00 0.00 5.69
3180 3789 3.112580 CCCGTAAATATTTTTGCCGCAG 58.887 45.455 5.91 0.00 0.00 5.18
3181 3790 2.533942 CCGTAAATATTTTTGCCGCAGC 59.466 45.455 5.91 0.00 40.48 5.25
3182 3791 2.533942 CGTAAATATTTTTGCCGCAGCC 59.466 45.455 5.91 0.00 38.69 4.85
3183 3792 2.022764 AAATATTTTTGCCGCAGCCC 57.977 45.000 0.00 0.00 38.69 5.19
3184 3793 0.179113 AATATTTTTGCCGCAGCCCG 60.179 50.000 0.00 0.00 38.69 6.13
3185 3794 2.627510 ATATTTTTGCCGCAGCCCGC 62.628 55.000 0.00 0.00 38.69 6.13
3195 3804 4.999939 CAGCCCGCAAACGCAACC 63.000 66.667 0.00 0.00 38.22 3.77
3208 3817 3.416880 CAACCCCCGGGCCAGTAT 61.417 66.667 17.73 0.48 39.32 2.12
3209 3818 2.073716 CAACCCCCGGGCCAGTATA 61.074 63.158 17.73 0.00 39.32 1.47
3210 3819 1.308041 AACCCCCGGGCCAGTATAA 60.308 57.895 17.73 0.00 39.32 0.98
3211 3820 1.638679 AACCCCCGGGCCAGTATAAC 61.639 60.000 17.73 0.00 39.32 1.89
3212 3821 1.768888 CCCCCGGGCCAGTATAACT 60.769 63.158 17.73 0.00 0.00 2.24
3213 3822 1.450211 CCCCGGGCCAGTATAACTG 59.550 63.158 17.73 0.00 45.53 3.16
3214 3823 1.227853 CCCGGGCCAGTATAACTGC 60.228 63.158 8.08 0.00 44.63 4.40
3215 3824 1.594293 CCGGGCCAGTATAACTGCG 60.594 63.158 4.39 0.00 44.63 5.18
3216 3825 1.594293 CGGGCCAGTATAACTGCGG 60.594 63.158 4.39 0.00 44.63 5.69
3217 3826 1.227853 GGGCCAGTATAACTGCGGG 60.228 63.158 4.39 0.00 44.63 6.13
3218 3827 1.525442 GGCCAGTATAACTGCGGGT 59.475 57.895 0.00 0.00 44.63 5.28
3219 3828 0.107361 GGCCAGTATAACTGCGGGTT 60.107 55.000 0.00 0.00 44.63 4.11
3220 3829 1.680860 GGCCAGTATAACTGCGGGTTT 60.681 52.381 0.00 0.00 44.63 3.27
3221 3830 1.400494 GCCAGTATAACTGCGGGTTTG 59.600 52.381 0.00 0.00 44.63 2.93
3222 3831 1.400494 CCAGTATAACTGCGGGTTTGC 59.600 52.381 0.00 0.00 44.63 3.68
3223 3832 1.062002 CAGTATAACTGCGGGTTTGCG 59.938 52.381 0.00 0.00 39.62 4.85
3224 3833 0.375803 GTATAACTGCGGGTTTGCGG 59.624 55.000 0.00 0.00 46.83 5.69
3225 3834 0.745128 TATAACTGCGGGTTTGCGGG 60.745 55.000 0.00 0.00 45.70 6.13
3232 3841 3.451894 GGGTTTGCGGGGCAGATG 61.452 66.667 0.00 0.00 40.61 2.90
3233 3842 4.133796 GGTTTGCGGGGCAGATGC 62.134 66.667 0.00 0.00 40.61 3.91
3234 3843 4.481112 GTTTGCGGGGCAGATGCG 62.481 66.667 0.00 0.00 40.61 4.73
3243 3852 4.179579 GCAGATGCGGGCCGAAAC 62.180 66.667 33.44 20.03 0.00 2.78
3244 3853 3.508840 CAGATGCGGGCCGAAACC 61.509 66.667 33.44 16.22 0.00 3.27
3252 3861 2.514395 GGCCGAAACCCTATCCCC 59.486 66.667 0.00 0.00 0.00 4.81
3253 3862 2.514395 GCCGAAACCCTATCCCCC 59.486 66.667 0.00 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 1.268899 GCTAACTGATGATGCCATGGC 59.731 52.381 30.54 30.54 42.35 4.40
38 39 1.534163 CGCTAACTGATGATGCCATGG 59.466 52.381 7.63 7.63 32.09 3.66
39 40 1.534163 CCGCTAACTGATGATGCCATG 59.466 52.381 0.00 0.00 32.09 3.66
40 41 1.141657 ACCGCTAACTGATGATGCCAT 59.858 47.619 0.00 0.00 35.29 4.40
81 82 9.159254 TGTATCAACAGTTATATCAGGAGGATT 57.841 33.333 0.00 0.00 37.44 3.01
82 83 8.727100 TGTATCAACAGTTATATCAGGAGGAT 57.273 34.615 0.00 0.00 40.14 3.24
83 84 8.547481 TTGTATCAACAGTTATATCAGGAGGA 57.453 34.615 0.00 0.00 36.83 3.71
145 146 5.530171 AGTGAGCCTTTATCAGTTGCATATG 59.470 40.000 0.00 0.00 0.00 1.78
182 183 6.293004 ACTTCCACAAATTTTTGGTCAGAA 57.707 33.333 20.17 8.62 42.34 3.02
186 187 5.908341 TGGTACTTCCACAAATTTTTGGTC 58.092 37.500 20.17 8.97 41.93 4.02
260 645 0.457166 CATGCGTGCAAGGTGGATTG 60.457 55.000 0.79 0.00 0.00 2.67
297 686 3.508845 TGCTAACTTTGAGGAGCCTTT 57.491 42.857 0.00 0.00 33.87 3.11
311 700 8.755696 TTTATGGAAATGTGATTGTTGCTAAC 57.244 30.769 0.00 0.00 0.00 2.34
348 737 1.241315 ATGGGTGCGTTGGCTTGTAC 61.241 55.000 0.00 0.00 40.82 2.90
349 738 0.325272 TATGGGTGCGTTGGCTTGTA 59.675 50.000 0.00 0.00 40.82 2.41
350 739 0.323360 ATATGGGTGCGTTGGCTTGT 60.323 50.000 0.00 0.00 40.82 3.16
351 740 1.603802 CTATATGGGTGCGTTGGCTTG 59.396 52.381 0.00 0.00 40.82 4.01
384 773 5.606505 ACGCCAACATTGAAGGTAATTTTT 58.393 33.333 0.00 0.00 0.00 1.94
400 789 5.136711 GCAAATGATAAAACAAACGCCAAC 58.863 37.500 0.00 0.00 0.00 3.77
403 792 3.670991 TCGCAAATGATAAAACAAACGCC 59.329 39.130 0.00 0.00 0.00 5.68
416 805 1.136690 GACACAGACGTCGCAAATGA 58.863 50.000 10.46 0.00 0.00 2.57
436 825 4.450976 TGTGCTGTCTGTGTTAACTCAAT 58.549 39.130 11.22 0.00 0.00 2.57
445 834 3.198409 TCTTCATTGTGCTGTCTGTGT 57.802 42.857 0.00 0.00 0.00 3.72
446 835 4.285292 GTTTCTTCATTGTGCTGTCTGTG 58.715 43.478 0.00 0.00 0.00 3.66
447 836 3.002656 CGTTTCTTCATTGTGCTGTCTGT 59.997 43.478 0.00 0.00 0.00 3.41
448 837 3.548587 CGTTTCTTCATTGTGCTGTCTG 58.451 45.455 0.00 0.00 0.00 3.51
458 847 4.035278 TCGTTTTTGGCGTTTCTTCATT 57.965 36.364 0.00 0.00 0.00 2.57
475 864 5.983118 TGCGTCATTGAGTATATCATTCGTT 59.017 36.000 0.00 0.00 37.89 3.85
541 930 3.202906 GTTTAGTGGTGAACTGACAGCA 58.797 45.455 1.25 0.00 44.20 4.41
542 931 2.548480 GGTTTAGTGGTGAACTGACAGC 59.452 50.000 1.25 0.00 40.26 4.40
543 932 3.139077 GGGTTTAGTGGTGAACTGACAG 58.861 50.000 0.00 0.00 40.26 3.51
544 933 2.158726 GGGGTTTAGTGGTGAACTGACA 60.159 50.000 0.00 0.00 40.26 3.58
545 934 2.501261 GGGGTTTAGTGGTGAACTGAC 58.499 52.381 0.00 0.00 40.26 3.51
546 935 1.422402 GGGGGTTTAGTGGTGAACTGA 59.578 52.381 0.00 0.00 40.26 3.41
547 936 1.905637 GGGGGTTTAGTGGTGAACTG 58.094 55.000 0.00 0.00 40.26 3.16
598 987 9.474313 AGGACATAGGTTTTTCAAATAAGCATA 57.526 29.630 0.00 0.00 0.00 3.14
599 988 8.366359 AGGACATAGGTTTTTCAAATAAGCAT 57.634 30.769 0.00 0.00 0.00 3.79
634 1023 4.377897 GTTTTAGCCGCTATGTCCTATGT 58.622 43.478 0.00 0.00 0.00 2.29
635 1024 3.428870 CGTTTTAGCCGCTATGTCCTATG 59.571 47.826 0.00 0.00 0.00 2.23
636 1025 3.650139 CGTTTTAGCCGCTATGTCCTAT 58.350 45.455 0.00 0.00 0.00 2.57
637 1026 3.088194 CGTTTTAGCCGCTATGTCCTA 57.912 47.619 0.00 0.00 0.00 2.94
638 1027 1.935933 CGTTTTAGCCGCTATGTCCT 58.064 50.000 0.00 0.00 0.00 3.85
693 1082 3.059665 GCAAACAACAAAATACAGCCAGC 60.060 43.478 0.00 0.00 0.00 4.85
703 1092 3.993081 CCACAAGACTGCAAACAACAAAA 59.007 39.130 0.00 0.00 0.00 2.44
809 1198 2.691011 GGTTAAAAGTTGTGGACAGCCA 59.309 45.455 0.00 0.00 43.47 4.75
856 1378 1.338655 TGACAACGTCAAGATCACCGA 59.661 47.619 0.00 0.00 39.78 4.69
895 1417 8.692110 TGAAGAATCATGTTAAACATTGCATC 57.308 30.769 0.00 0.00 36.53 3.91
935 1457 4.161189 ACTTCTAATTCAGAGCTGCTAGCA 59.839 41.667 18.22 18.22 45.56 3.49
972 1494 2.826428 TGATCGATGCAAAGCTCTACC 58.174 47.619 0.54 0.00 0.00 3.18
1430 1996 1.923227 GCAAAGCGAGCTTGGGGTAC 61.923 60.000 11.38 0.00 36.26 3.34
1431 1997 1.674322 GCAAAGCGAGCTTGGGGTA 60.674 57.895 11.38 0.00 36.26 3.69
1432 1998 2.985847 GCAAAGCGAGCTTGGGGT 60.986 61.111 11.38 0.00 36.26 4.95
1446 2012 2.202960 GCATAGCGGTACCGGCAA 60.203 61.111 33.98 0.00 40.19 4.52
1674 2252 3.223435 AGAGTTGAAGAAGTCGGTGAGA 58.777 45.455 0.00 0.00 36.72 3.27
1798 2379 4.611825 CCTGGAGGGAGACGAAGTACCT 62.612 59.091 0.00 0.00 40.99 3.08
1914 2495 1.519455 CGCGAGGATGGTGAAGGTC 60.519 63.158 0.00 0.00 0.00 3.85
2287 2877 6.259608 GGATATCCACTGTTCAGCATATATGC 59.740 42.308 27.02 27.02 44.26 3.14
2317 2909 2.125350 GGGCCAGAAGTCAGAGCG 60.125 66.667 4.39 0.00 0.00 5.03
2321 2913 0.325933 TCACATGGGCCAGAAGTCAG 59.674 55.000 13.78 0.17 0.00 3.51
2384 2976 3.819368 TCTTCAACAGGACTTTGCATGA 58.181 40.909 0.00 0.00 0.00 3.07
2385 2977 4.572985 TTCTTCAACAGGACTTTGCATG 57.427 40.909 0.00 0.00 0.00 4.06
2386 2978 6.006449 AGTATTCTTCAACAGGACTTTGCAT 58.994 36.000 0.00 0.00 0.00 3.96
2397 2991 6.061441 TGAGCCAAAAGAGTATTCTTCAACA 58.939 36.000 0.40 0.00 42.80 3.33
2419 3013 8.282592 CGTTGATAGAATGACTGAAAACTTTGA 58.717 33.333 0.00 0.00 0.00 2.69
2483 3077 2.765689 ACAAATGGACCTCAAACCCA 57.234 45.000 0.00 0.00 0.00 4.51
2527 3121 3.891324 TCTTTTTAATTTCCACGTGCCG 58.109 40.909 10.91 0.00 0.00 5.69
2647 3241 6.366061 GTCTTTCTGCAATTACCAATTTGGAC 59.634 38.462 22.19 0.76 40.96 4.02
2653 3247 3.119495 GCGGTCTTTCTGCAATTACCAAT 60.119 43.478 0.00 0.00 46.78 3.16
2655 3249 1.810151 GCGGTCTTTCTGCAATTACCA 59.190 47.619 0.00 0.00 46.78 3.25
2690 3284 3.754850 CAGACTGAACATCCAGAATGCAA 59.245 43.478 0.00 0.00 39.12 4.08
2704 3298 6.412214 GCTTAACCCTTATAACCAGACTGAA 58.588 40.000 3.32 0.00 0.00 3.02
2801 3410 5.402398 GTTGCTCCCAGATTGACATTTTAC 58.598 41.667 0.00 0.00 0.00 2.01
2917 3526 5.024785 ACTAGGCTAGGCTATTTCAACAC 57.975 43.478 24.81 0.00 0.00 3.32
3053 3662 1.608717 CGGGGTCTGCTAGAGTTGCT 61.609 60.000 0.00 0.00 0.00 3.91
3054 3663 1.153549 CGGGGTCTGCTAGAGTTGC 60.154 63.158 0.00 0.00 0.00 4.17
3055 3664 1.153549 GCGGGGTCTGCTAGAGTTG 60.154 63.158 0.00 0.00 0.00 3.16
3056 3665 0.978146 ATGCGGGGTCTGCTAGAGTT 60.978 55.000 0.00 0.00 0.00 3.01
3057 3666 1.381872 ATGCGGGGTCTGCTAGAGT 60.382 57.895 0.00 0.00 0.00 3.24
3058 3667 1.365633 GATGCGGGGTCTGCTAGAG 59.634 63.158 0.00 0.00 0.00 2.43
3059 3668 2.134287 GGATGCGGGGTCTGCTAGA 61.134 63.158 0.00 0.00 0.00 2.43
3060 3669 2.423446 GGATGCGGGGTCTGCTAG 59.577 66.667 0.30 0.00 0.00 3.42
3061 3670 3.536917 CGGATGCGGGGTCTGCTA 61.537 66.667 0.00 0.00 0.00 3.49
3072 3681 4.481112 CTGGTTTGCGCCGGATGC 62.481 66.667 5.05 9.32 37.06 3.91
3073 3682 4.481112 GCTGGTTTGCGCCGGATG 62.481 66.667 5.05 0.00 37.06 3.51
3074 3683 2.884997 TATGCTGGTTTGCGCCGGAT 62.885 55.000 5.05 0.00 37.06 4.18
3075 3684 3.613877 TATGCTGGTTTGCGCCGGA 62.614 57.895 5.05 0.00 37.06 5.14
3076 3685 2.003658 ATTATGCTGGTTTGCGCCGG 62.004 55.000 4.18 0.00 37.94 6.13
3077 3686 0.179140 AATTATGCTGGTTTGCGCCG 60.179 50.000 4.18 0.00 35.36 6.46
3078 3687 1.559831 GAATTATGCTGGTTTGCGCC 58.440 50.000 4.18 0.00 35.36 6.53
3079 3688 1.559831 GGAATTATGCTGGTTTGCGC 58.440 50.000 0.00 0.00 35.36 6.09
3080 3689 1.533756 CCGGAATTATGCTGGTTTGCG 60.534 52.381 0.00 0.00 35.36 4.85
3081 3690 1.802508 GCCGGAATTATGCTGGTTTGC 60.803 52.381 5.05 0.00 0.00 3.68
3082 3691 1.533756 CGCCGGAATTATGCTGGTTTG 60.534 52.381 5.05 0.00 0.00 2.93
3083 3692 0.738389 CGCCGGAATTATGCTGGTTT 59.262 50.000 5.05 0.00 0.00 3.27
3084 3693 0.107410 TCGCCGGAATTATGCTGGTT 60.107 50.000 5.05 0.00 0.00 3.67
3085 3694 0.108585 ATCGCCGGAATTATGCTGGT 59.891 50.000 5.05 0.00 0.00 4.00
3086 3695 1.238439 AATCGCCGGAATTATGCTGG 58.762 50.000 5.05 0.00 0.00 4.85
3087 3696 4.259810 CGTATAATCGCCGGAATTATGCTG 60.260 45.833 22.93 16.54 0.00 4.41
3088 3697 3.863424 CGTATAATCGCCGGAATTATGCT 59.137 43.478 22.93 8.76 0.00 3.79
3089 3698 3.000925 CCGTATAATCGCCGGAATTATGC 59.999 47.826 22.93 21.08 44.41 3.14
3090 3699 3.554324 CCCGTATAATCGCCGGAATTATG 59.446 47.826 22.93 12.84 44.41 1.90
3091 3700 3.196254 ACCCGTATAATCGCCGGAATTAT 59.804 43.478 20.06 20.06 44.41 1.28
3092 3701 2.562298 ACCCGTATAATCGCCGGAATTA 59.438 45.455 5.05 9.02 44.41 1.40
3093 3702 1.345415 ACCCGTATAATCGCCGGAATT 59.655 47.619 5.05 6.70 44.41 2.17
3094 3703 0.971386 ACCCGTATAATCGCCGGAAT 59.029 50.000 5.05 0.00 44.41 3.01
3095 3704 0.752054 AACCCGTATAATCGCCGGAA 59.248 50.000 5.05 0.00 44.41 4.30
3096 3705 0.314935 GAACCCGTATAATCGCCGGA 59.685 55.000 5.05 0.00 44.41 5.14
3097 3706 1.005294 CGAACCCGTATAATCGCCGG 61.005 60.000 0.00 0.00 41.37 6.13
3098 3707 1.005294 CCGAACCCGTATAATCGCCG 61.005 60.000 0.00 0.00 34.13 6.46
3099 3708 1.287041 GCCGAACCCGTATAATCGCC 61.287 60.000 0.00 0.00 34.13 5.54
3100 3709 1.287041 GGCCGAACCCGTATAATCGC 61.287 60.000 0.00 0.00 34.13 4.58
3101 3710 2.818350 GGCCGAACCCGTATAATCG 58.182 57.895 0.00 0.00 35.19 3.34
3111 3720 0.246360 CCAGAAAAATGGGCCGAACC 59.754 55.000 0.00 0.00 36.64 3.62
3112 3721 0.389817 GCCAGAAAAATGGGCCGAAC 60.390 55.000 0.00 0.00 41.90 3.95
3113 3722 1.971418 GCCAGAAAAATGGGCCGAA 59.029 52.632 0.00 0.00 41.90 4.30
3114 3723 3.693411 GCCAGAAAAATGGGCCGA 58.307 55.556 0.00 0.00 41.90 5.54
3118 3727 0.897621 GGTCTGGCCAGAAAAATGGG 59.102 55.000 36.66 6.78 40.97 4.00
3119 3728 1.631405 TGGTCTGGCCAGAAAAATGG 58.369 50.000 36.66 7.62 43.61 3.16
3129 3738 3.680786 GCGGGTTTTGGTCTGGCC 61.681 66.667 0.00 0.00 37.90 5.36
3130 3739 2.212900 GATGCGGGTTTTGGTCTGGC 62.213 60.000 0.00 0.00 0.00 4.85
3131 3740 1.883021 GATGCGGGTTTTGGTCTGG 59.117 57.895 0.00 0.00 0.00 3.86
3132 3741 1.501741 CGATGCGGGTTTTGGTCTG 59.498 57.895 0.00 0.00 0.00 3.51
3133 3742 1.674322 CCGATGCGGGTTTTGGTCT 60.674 57.895 0.00 0.00 44.15 3.85
3134 3743 2.874751 CCGATGCGGGTTTTGGTC 59.125 61.111 0.00 0.00 44.15 4.02
3150 3759 0.107268 ATATTTACGGGCCGGACACC 59.893 55.000 31.78 4.67 0.00 4.16
3151 3760 1.957668 AATATTTACGGGCCGGACAC 58.042 50.000 31.78 0.00 0.00 3.67
3152 3761 2.713863 AAATATTTACGGGCCGGACA 57.286 45.000 31.78 16.89 0.00 4.02
3153 3762 3.697982 CAAAAATATTTACGGGCCGGAC 58.302 45.455 31.78 0.00 0.00 4.79
3154 3763 2.099427 GCAAAAATATTTACGGGCCGGA 59.901 45.455 31.78 21.84 0.00 5.14
3155 3764 2.465855 GCAAAAATATTTACGGGCCGG 58.534 47.619 31.78 12.53 0.00 6.13
3156 3765 2.465855 GGCAAAAATATTTACGGGCCG 58.534 47.619 27.06 27.06 28.11 6.13
3157 3766 2.465855 CGGCAAAAATATTTACGGGCC 58.534 47.619 16.39 16.39 33.01 5.80
3158 3767 1.855978 GCGGCAAAAATATTTACGGGC 59.144 47.619 0.01 5.76 32.18 6.13
3159 3768 3.112580 CTGCGGCAAAAATATTTACGGG 58.887 45.455 3.44 0.00 32.18 5.28
3160 3769 2.533942 GCTGCGGCAAAAATATTTACGG 59.466 45.455 14.08 0.87 38.54 4.02
3161 3770 2.533942 GGCTGCGGCAAAAATATTTACG 59.466 45.455 21.31 5.76 40.87 3.18
3162 3771 2.863740 GGGCTGCGGCAAAAATATTTAC 59.136 45.455 21.31 0.00 40.87 2.01
3163 3772 2.480416 CGGGCTGCGGCAAAAATATTTA 60.480 45.455 21.31 0.00 40.87 1.40
3164 3773 1.738700 CGGGCTGCGGCAAAAATATTT 60.739 47.619 21.31 0.00 40.87 1.40
3165 3774 0.179113 CGGGCTGCGGCAAAAATATT 60.179 50.000 21.31 0.00 40.87 1.28
3166 3775 1.437160 CGGGCTGCGGCAAAAATAT 59.563 52.632 21.31 0.00 40.87 1.28
3167 3776 2.881389 CGGGCTGCGGCAAAAATA 59.119 55.556 21.31 0.00 40.87 1.40
3168 3777 4.740431 GCGGGCTGCGGCAAAAAT 62.740 61.111 21.31 0.00 40.87 1.82
3191 3800 1.637724 TTATACTGGCCCGGGGGTTG 61.638 60.000 25.28 0.00 37.65 3.77
3192 3801 1.308041 TTATACTGGCCCGGGGGTT 60.308 57.895 25.28 0.00 37.65 4.11
3193 3802 2.074332 GTTATACTGGCCCGGGGGT 61.074 63.158 25.28 6.96 37.65 4.95
3194 3803 1.768888 AGTTATACTGGCCCGGGGG 60.769 63.158 25.28 2.24 38.57 5.40
3195 3804 1.450211 CAGTTATACTGGCCCGGGG 59.550 63.158 25.28 9.31 42.35 5.73
3196 3805 1.227853 GCAGTTATACTGGCCCGGG 60.228 63.158 19.09 19.09 46.01 5.73
3197 3806 1.594293 CGCAGTTATACTGGCCCGG 60.594 63.158 0.00 0.00 46.01 5.73
3198 3807 1.594293 CCGCAGTTATACTGGCCCG 60.594 63.158 0.00 0.00 46.01 6.13
3199 3808 1.227853 CCCGCAGTTATACTGGCCC 60.228 63.158 0.00 0.00 46.01 5.80
3200 3809 0.107361 AACCCGCAGTTATACTGGCC 60.107 55.000 8.73 0.00 46.01 5.36
3201 3810 1.400494 CAAACCCGCAGTTATACTGGC 59.600 52.381 8.73 1.21 46.01 4.85
3202 3811 1.400494 GCAAACCCGCAGTTATACTGG 59.600 52.381 8.73 0.00 46.01 4.00
3204 3813 1.365699 CGCAAACCCGCAGTTATACT 58.634 50.000 0.00 0.00 37.88 2.12
3205 3814 0.375803 CCGCAAACCCGCAGTTATAC 59.624 55.000 0.00 0.00 37.88 1.47
3206 3815 0.745128 CCCGCAAACCCGCAGTTATA 60.745 55.000 0.00 0.00 37.88 0.98
3207 3816 2.043980 CCCGCAAACCCGCAGTTAT 61.044 57.895 0.00 0.00 37.88 1.89
3208 3817 2.670251 CCCGCAAACCCGCAGTTA 60.670 61.111 0.00 0.00 37.88 2.24
3215 3824 3.451894 CATCTGCCCCGCAAACCC 61.452 66.667 0.00 0.00 38.41 4.11
3216 3825 4.133796 GCATCTGCCCCGCAAACC 62.134 66.667 0.00 0.00 38.41 3.27
3217 3826 4.481112 CGCATCTGCCCCGCAAAC 62.481 66.667 0.00 0.00 38.41 2.93
3226 3835 4.179579 GTTTCGGCCCGCATCTGC 62.180 66.667 0.00 0.00 37.78 4.26
3227 3836 3.508840 GGTTTCGGCCCGCATCTG 61.509 66.667 0.00 0.00 0.00 2.90
3228 3837 4.796495 GGGTTTCGGCCCGCATCT 62.796 66.667 0.00 0.00 39.17 2.90
3235 3844 2.514395 GGGGATAGGGTTTCGGCC 59.486 66.667 0.00 0.00 0.00 6.13
3236 3845 2.514395 GGGGGATAGGGTTTCGGC 59.486 66.667 0.00 0.00 0.00 5.54


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

AutoCloner maintained by Alex Coulton.