Multiple sequence alignment - TraesCS3D01G380300

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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 TraesCS3D01G380300 chr3D 100.000 4848 0 0 1 4848 496747677 496742830 0.000000e+00 8953
1 TraesCS3D01G380300 chr3D 89.474 209 20 2 4641 4848 544444256 544444049 3.720000e-66 263
2 TraesCS3D01G380300 chr3D 88.995 209 17 6 4641 4846 536440561 536440356 2.240000e-63 254
3 TraesCS3D01G380300 chr3D 89.048 210 16 7 4641 4846 536441804 536441598 2.240000e-63 254
4 TraesCS3D01G380300 chr3B 92.627 3133 164 30 1 3099 655862196 655859097 0.000000e+00 4444
5 TraesCS3D01G380300 chr3B 90.267 1048 67 24 3341 4373 655858474 655857447 0.000000e+00 1338
6 TraesCS3D01G380300 chr3B 87.755 343 19 8 4507 4848 655857321 655857001 3.540000e-101 379
7 TraesCS3D01G380300 chr3B 90.000 210 18 3 4641 4848 720265210 720265002 8.000000e-68 268
8 TraesCS3D01G380300 chr3B 90.722 194 16 1 3149 3342 655859019 655858828 1.730000e-64 257
9 TraesCS3D01G380300 chr3A 92.215 3147 172 37 1 3103 638059524 638062641 0.000000e+00 4386
10 TraesCS3D01G380300 chr3A 90.383 1539 78 25 3341 4846 638063126 638064627 0.000000e+00 1958
11 TraesCS3D01G380300 chrUn 89.048 210 16 7 4641 4846 359852775 359852569 2.240000e-63 254
12 TraesCS3D01G380300 chrUn 89.048 210 16 7 4641 4846 404926739 404926945 2.240000e-63 254
13 TraesCS3D01G380300 chrUn 89.048 210 16 7 4641 4846 466164471 466164265 2.240000e-63 254


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 TraesCS3D01G380300 chr3D 496742830 496747677 4847 True 8953.0 8953 100.00000 1 4848 1 chr3D.!!$R1 4847
1 TraesCS3D01G380300 chr3D 536440356 536441804 1448 True 254.0 254 89.02150 4641 4846 2 chr3D.!!$R3 205
2 TraesCS3D01G380300 chr3B 655857001 655862196 5195 True 1604.5 4444 90.34275 1 4848 4 chr3B.!!$R2 4847
3 TraesCS3D01G380300 chr3A 638059524 638064627 5103 False 3172.0 4386 91.29900 1 4846 2 chr3A.!!$F1 4845

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
948 970 0.111253 CTGTTTGCTGACCTTCCCCT 59.889 55.0 0.0 0.0 0.00 4.79 F
2433 2475 0.464036 TGAGCAGTACCATTAGCCGG 59.536 55.0 0.0 0.0 0.00 6.13 F
3110 3159 0.108615 AGTGCCGAATGAGGACTTCG 60.109 55.0 0.0 0.0 43.82 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2472 2514 0.250338 GGAGGTGAAAGAGTTGCCGT 60.250 55.0 0.00 0.0 0.00 5.68 R
3447 3888 0.032615 AAGGCAGGGTGTGAAAACCA 60.033 50.0 0.00 0.0 42.47 3.67 R
4564 5071 0.108019 CCTCCGGGTTAGGCCAATAC 59.892 60.0 5.01 0.0 39.65 1.89 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
194 195 4.248058 CAAAGTTTTTCCATGGCCTCATC 58.752 43.478 6.96 0.00 0.00 2.92
244 245 5.005094 TGATCATGCTCTTGACATGTTCAA 58.995 37.500 12.63 5.24 44.87 2.69
262 263 8.918658 CATGTTCAAAATTATGAAGAGTTGTGG 58.081 33.333 0.00 0.00 39.84 4.17
320 321 5.780793 AGAAAAGCTTTCTAGGAGTGGTAGA 59.219 40.000 13.10 0.00 0.00 2.59
475 476 4.081420 TCAGAACTGTAAGAGCTTGATCCC 60.081 45.833 1.73 0.00 37.43 3.85
563 564 4.600983 GGGAGTCTAGGTACTATGGGACTA 59.399 50.000 0.00 0.00 41.82 2.59
635 644 7.402054 ACTATGTGATGATGACCCTTGTTTTA 58.598 34.615 0.00 0.00 0.00 1.52
647 656 8.441312 TGACCCTTGTTTTAGTTGTTACTTAG 57.559 34.615 0.00 0.00 35.78 2.18
673 682 9.434559 GTAAACTCAAGTAATCAGTTGTCAAAC 57.565 33.333 0.00 0.00 36.60 2.93
682 691 3.287222 TCAGTTGTCAAACCTTTCCTGG 58.713 45.455 0.00 0.00 36.94 4.45
686 695 2.661718 TGTCAAACCTTTCCTGGAACC 58.338 47.619 9.04 0.00 0.00 3.62
693 702 2.290960 ACCTTTCCTGGAACCTACATGC 60.291 50.000 9.04 0.00 0.00 4.06
716 725 8.006298 TGCAATTACCCTATTTTTATGTGGAG 57.994 34.615 0.00 0.00 0.00 3.86
717 726 7.617723 TGCAATTACCCTATTTTTATGTGGAGT 59.382 33.333 0.00 0.00 0.00 3.85
718 727 8.135529 GCAATTACCCTATTTTTATGTGGAGTC 58.864 37.037 0.00 0.00 0.00 3.36
719 728 8.630037 CAATTACCCTATTTTTATGTGGAGTCC 58.370 37.037 0.73 0.73 0.00 3.85
720 729 4.777463 ACCCTATTTTTATGTGGAGTCCG 58.223 43.478 4.30 0.00 0.00 4.79
787 800 6.942532 ATTCAGTGAAGCTGTTACTTTTGA 57.057 33.333 11.91 0.00 45.23 2.69
811 824 9.748708 TGATTTTAGTATTTTATTGCCATCTGC 57.251 29.630 0.00 0.00 41.77 4.26
823 837 4.286297 TGCCATCTGCCCATTATAGTAC 57.714 45.455 0.00 0.00 40.16 2.73
824 838 3.909995 TGCCATCTGCCCATTATAGTACT 59.090 43.478 0.00 0.00 40.16 2.73
825 839 4.020218 TGCCATCTGCCCATTATAGTACTC 60.020 45.833 0.00 0.00 40.16 2.59
826 840 4.223923 GCCATCTGCCCATTATAGTACTCT 59.776 45.833 0.00 0.00 0.00 3.24
827 841 5.422331 GCCATCTGCCCATTATAGTACTCTA 59.578 44.000 0.00 0.00 0.00 2.43
863 877 0.745845 GGCACTCTGGCAGTATGGTG 60.746 60.000 15.27 18.02 43.14 4.17
872 886 2.280628 GGCAGTATGGTGTAGCAACTC 58.719 52.381 0.00 0.00 35.86 3.01
873 887 2.093447 GGCAGTATGGTGTAGCAACTCT 60.093 50.000 0.00 0.00 35.86 3.24
883 904 4.202172 GGTGTAGCAACTCTCCTCCTTATC 60.202 50.000 0.00 0.00 0.00 1.75
948 970 0.111253 CTGTTTGCTGACCTTCCCCT 59.889 55.000 0.00 0.00 0.00 4.79
965 987 6.413783 TTCCCCTTTTTCTTTATTGTCACC 57.586 37.500 0.00 0.00 0.00 4.02
982 1004 4.093703 TGTCACCGTTACAGTTCTGTTTTG 59.906 41.667 10.74 1.81 0.00 2.44
985 1007 4.331717 CACCGTTACAGTTCTGTTTTGAGT 59.668 41.667 10.74 1.23 0.00 3.41
992 1014 4.158394 ACAGTTCTGTTTTGAGTGCACATT 59.842 37.500 21.04 0.00 0.00 2.71
1012 1034 7.859377 GCACATTGAACTTTATGGACATATCTG 59.141 37.037 0.00 0.00 0.00 2.90
1094 1116 8.429641 TCAAAACTCCAGACTTGTATAGTTTCT 58.570 33.333 0.00 0.00 36.45 2.52
1095 1117 9.706691 CAAAACTCCAGACTTGTATAGTTTCTA 57.293 33.333 0.00 0.00 36.45 2.10
1154 1176 4.226761 GTTTGCAGAGGGTATTTGTTTCG 58.773 43.478 0.00 0.00 0.00 3.46
1190 1212 4.403453 GAAAATGCGTAATCAAAGAGCGT 58.597 39.130 0.00 0.00 0.00 5.07
1215 1237 4.188247 TCAAAGAAGTATCGACACCCAG 57.812 45.455 0.00 0.00 0.00 4.45
1303 1325 9.822727 TTTTCTTTTGAGATAATCTACCCCTTT 57.177 29.630 0.00 0.00 0.00 3.11
1304 1326 9.822727 TTTCTTTTGAGATAATCTACCCCTTTT 57.177 29.630 0.00 0.00 0.00 2.27
1367 1389 8.365399 TCTTTCAAAGATGTATAGTATTGCCG 57.635 34.615 0.00 0.00 31.20 5.69
1368 1390 7.985184 TCTTTCAAAGATGTATAGTATTGCCGT 59.015 33.333 0.00 0.00 31.20 5.68
1369 1391 9.256477 CTTTCAAAGATGTATAGTATTGCCGTA 57.744 33.333 0.00 0.00 0.00 4.02
1370 1392 9.772973 TTTCAAAGATGTATAGTATTGCCGTAT 57.227 29.630 0.00 0.00 0.00 3.06
1371 1393 9.772973 TTCAAAGATGTATAGTATTGCCGTATT 57.227 29.630 0.00 0.00 0.00 1.89
1372 1394 9.203421 TCAAAGATGTATAGTATTGCCGTATTG 57.797 33.333 0.00 0.00 0.00 1.90
1373 1395 8.443160 CAAAGATGTATAGTATTGCCGTATTGG 58.557 37.037 0.00 0.00 42.50 3.16
1414 1436 6.790285 ATTTTGTTTATCAAGCAGCAAAGG 57.210 33.333 0.00 0.00 37.35 3.11
1469 1491 8.641498 AACTCTTGTCCAGTTTCATATTGAAT 57.359 30.769 0.00 0.00 36.11 2.57
1472 1494 8.634335 TCTTGTCCAGTTTCATATTGAATGAA 57.366 30.769 0.00 0.00 36.11 2.57
1473 1495 8.733458 TCTTGTCCAGTTTCATATTGAATGAAG 58.267 33.333 1.18 0.00 38.98 3.02
1475 1497 8.634335 TGTCCAGTTTCATATTGAATGAAGAA 57.366 30.769 1.18 0.00 38.98 2.52
1499 1521 9.290988 GAAGATAGAACCATAGAGTGATCTGTA 57.709 37.037 0.00 0.00 0.00 2.74
1500 1522 8.862325 AGATAGAACCATAGAGTGATCTGTAG 57.138 38.462 0.00 0.00 0.00 2.74
1556 1578 6.290294 AGTATTAAAACTCGGCTTACCTCA 57.710 37.500 0.00 0.00 0.00 3.86
1602 1624 4.142534 GCTAGATGCATGACAAAAGCAAGA 60.143 41.667 2.46 0.00 42.15 3.02
1746 1768 9.057089 GGGATAAATGAAGAACGTCTTAATGAT 57.943 33.333 0.00 0.00 36.73 2.45
1881 1903 4.625311 CGCACAATATTCTTTGTTTTCCCC 59.375 41.667 0.00 0.00 37.73 4.81
1900 1922 8.533569 TTTCCCCCTGTTTTAATTCATCTATC 57.466 34.615 0.00 0.00 0.00 2.08
1903 1926 6.017109 CCCCCTGTTTTAATTCATCTATCACG 60.017 42.308 0.00 0.00 0.00 4.35
1938 1968 7.961326 AAAAGTCTGGCTATCAATTTACCAT 57.039 32.000 0.00 0.00 0.00 3.55
2000 2030 6.818644 GTCTGAGCTTTACATCAACTATTCCA 59.181 38.462 0.00 0.00 0.00 3.53
2021 2051 1.003233 GGACAAGGCAGTGGACCTC 60.003 63.158 0.00 0.00 36.14 3.85
2027 2057 1.490574 AGGCAGTGGACCTCTATGTC 58.509 55.000 0.00 0.00 28.76 3.06
2039 2069 3.052944 ACCTCTATGTCCTTGAGAGAGCT 60.053 47.826 0.00 0.00 39.29 4.09
2042 2072 5.596361 CCTCTATGTCCTTGAGAGAGCTTTA 59.404 44.000 0.00 0.00 39.29 1.85
2102 2134 7.979537 AGCGAATTGTGTAAATCATGTACTAGA 59.020 33.333 0.00 0.00 0.00 2.43
2174 2209 8.642935 TGATATCCTAAATGTGTCCAAAAACA 57.357 30.769 0.00 0.00 0.00 2.83
2222 2258 6.806959 AAGGTATATAGGGGGCCATTTTTA 57.193 37.500 4.39 0.00 0.00 1.52
2264 2300 2.051334 TTGTATATGGTGCAGCCCAC 57.949 50.000 14.36 6.40 43.90 4.61
2327 2367 4.543590 TCAAAGAGTTCAGGGATCTCAC 57.456 45.455 0.00 0.00 32.59 3.51
2377 2418 0.610232 GAGCATGAGCCCACACCTTT 60.610 55.000 0.00 0.00 43.56 3.11
2433 2475 0.464036 TGAGCAGTACCATTAGCCGG 59.536 55.000 0.00 0.00 0.00 6.13
2458 2500 2.225727 CCGAACCCAGCTAACTTTGAAC 59.774 50.000 0.00 0.00 0.00 3.18
2496 2538 2.550180 GCAACTCTTTCACCTCCTGAAC 59.450 50.000 0.00 0.00 38.70 3.18
2508 2550 1.002134 CCTGAACGATTGGCCCAGT 60.002 57.895 0.00 0.00 0.00 4.00
2525 2567 2.564771 CAGTGGCTGACAAGTTCTTCA 58.435 47.619 0.00 0.00 32.44 3.02
2544 2586 9.494271 GTTCTTCATAGGATCATTTAGCATACA 57.506 33.333 0.00 0.00 0.00 2.29
2563 2605 2.093890 CATACCACAGCCTTGCAATCA 58.906 47.619 0.00 0.00 0.00 2.57
2566 2608 1.274167 ACCACAGCCTTGCAATCAATG 59.726 47.619 0.00 0.00 0.00 2.82
2570 2612 0.813184 AGCCTTGCAATCAATGTCGG 59.187 50.000 0.00 0.00 0.00 4.79
2598 2640 6.205464 TGAAGTTTCAGAATGTTCATCTCCAC 59.795 38.462 4.31 0.00 37.40 4.02
2686 2733 1.542375 AGGCACCCCCTCTGAATGT 60.542 57.895 0.00 0.00 41.21 2.71
2692 2739 1.002134 CCCCTCTGAATGTGCCGTT 60.002 57.895 0.00 0.00 0.00 4.44
2698 2745 2.485426 CTCTGAATGTGCCGTTGTGATT 59.515 45.455 0.00 0.00 0.00 2.57
2715 2762 2.242965 TGATTCCTGAAGACCATGCCAT 59.757 45.455 0.00 0.00 0.00 4.40
2717 2764 1.588239 TCCTGAAGACCATGCCATCT 58.412 50.000 0.00 0.00 0.00 2.90
2741 2788 1.341209 CCTTTGTCCCCAGCTTTTGAC 59.659 52.381 0.00 0.00 0.00 3.18
2759 2806 2.093890 GACATTGCACCATCCACATCA 58.906 47.619 0.00 0.00 0.00 3.07
2766 2813 1.399440 CACCATCCACATCAGCTTTCG 59.601 52.381 0.00 0.00 0.00 3.46
2825 2872 2.652590 GCCTGATGCATTTTCCTCTCT 58.347 47.619 0.00 0.00 40.77 3.10
2856 2903 1.935327 GACCGACTTCCAGTCCTCCG 61.935 65.000 0.00 0.00 42.12 4.63
2860 2907 2.569059 CGACTTCCAGTCCTCCGTATA 58.431 52.381 0.00 0.00 42.12 1.47
2871 2918 0.243907 CTCCGTATAGGCCATCACCG 59.756 60.000 5.01 0.00 40.77 4.94
2916 2963 1.442769 GATCTTCTTGCCTTCACGCA 58.557 50.000 0.00 0.00 36.85 5.24
2934 2981 3.244353 ACGCATATCATTCCTTGCTAGCT 60.244 43.478 17.23 0.00 32.97 3.32
2949 2996 5.282055 TGCTAGCTAGAGTGCATAAACAT 57.718 39.130 25.15 0.00 34.99 2.71
2950 2997 5.674525 TGCTAGCTAGAGTGCATAAACATT 58.325 37.500 25.15 0.00 34.99 2.71
2985 3032 2.611722 GCTCTTTCCTCTTCTGAAGCGT 60.612 50.000 12.54 0.00 0.00 5.07
3000 3047 2.451693 GCGTCAGCAAACCACGATA 58.548 52.632 0.00 0.00 44.35 2.92
3018 3065 5.586643 CACGATAGCAGCCATCTAGATAGTA 59.413 44.000 4.54 0.00 42.67 1.82
3019 3066 6.262049 CACGATAGCAGCCATCTAGATAGTAT 59.738 42.308 4.54 0.00 42.67 2.12
3020 3067 6.262049 ACGATAGCAGCCATCTAGATAGTATG 59.738 42.308 4.54 3.34 42.67 2.39
3081 3130 0.672401 TCCCAATTCCGAGCACGAAC 60.672 55.000 4.70 0.00 42.66 3.95
3096 3145 0.868406 CGAACTTCCAGAACAGTGCC 59.132 55.000 0.00 0.00 0.00 5.01
3099 3148 0.468226 ACTTCCAGAACAGTGCCGAA 59.532 50.000 0.00 0.00 0.00 4.30
3100 3149 1.072331 ACTTCCAGAACAGTGCCGAAT 59.928 47.619 0.00 0.00 0.00 3.34
3101 3150 1.466167 CTTCCAGAACAGTGCCGAATG 59.534 52.381 0.00 0.00 0.00 2.67
3102 3151 0.684535 TCCAGAACAGTGCCGAATGA 59.315 50.000 0.00 0.00 0.00 2.57
3103 3152 1.081892 CCAGAACAGTGCCGAATGAG 58.918 55.000 0.00 0.00 0.00 2.90
3104 3153 1.081892 CAGAACAGTGCCGAATGAGG 58.918 55.000 0.00 0.00 0.00 3.86
3105 3154 0.976641 AGAACAGTGCCGAATGAGGA 59.023 50.000 0.00 0.00 0.00 3.71
3107 3156 0.687354 AACAGTGCCGAATGAGGACT 59.313 50.000 0.00 0.00 0.00 3.85
3108 3157 0.687354 ACAGTGCCGAATGAGGACTT 59.313 50.000 0.00 0.00 0.00 3.01
3109 3158 1.338200 ACAGTGCCGAATGAGGACTTC 60.338 52.381 0.00 0.00 0.00 3.01
3110 3159 0.108615 AGTGCCGAATGAGGACTTCG 60.109 55.000 0.00 0.00 43.82 3.79
3115 3164 0.867753 CGAATGAGGACTTCGGAGCG 60.868 60.000 0.00 0.00 41.27 5.03
3116 3165 1.148759 GAATGAGGACTTCGGAGCGC 61.149 60.000 0.00 0.00 0.00 5.92
3118 3167 1.680522 ATGAGGACTTCGGAGCGCAT 61.681 55.000 11.47 0.00 0.00 4.73
3119 3168 1.880340 GAGGACTTCGGAGCGCATG 60.880 63.158 11.47 0.00 0.00 4.06
3120 3169 2.184322 GGACTTCGGAGCGCATGA 59.816 61.111 11.47 0.07 0.00 3.07
3121 3170 1.447838 GGACTTCGGAGCGCATGAA 60.448 57.895 11.47 9.54 0.00 2.57
3122 3171 1.696832 GGACTTCGGAGCGCATGAAC 61.697 60.000 11.47 0.00 0.00 3.18
3123 3172 0.737715 GACTTCGGAGCGCATGAACT 60.738 55.000 11.47 0.00 0.00 3.01
3124 3173 0.320771 ACTTCGGAGCGCATGAACTT 60.321 50.000 11.47 0.00 0.00 2.66
3125 3174 0.371645 CTTCGGAGCGCATGAACTTC 59.628 55.000 11.47 0.00 0.00 3.01
3126 3175 1.019278 TTCGGAGCGCATGAACTTCC 61.019 55.000 11.47 4.61 0.00 3.46
3127 3176 1.741401 CGGAGCGCATGAACTTCCA 60.741 57.895 11.47 0.00 0.00 3.53
3131 3180 2.555199 GAGCGCATGAACTTCCAGTAT 58.445 47.619 11.47 0.00 0.00 2.12
3132 3181 2.283298 AGCGCATGAACTTCCAGTATG 58.717 47.619 11.47 0.00 0.00 2.39
3145 3194 1.656652 CAGTATGGCGTTTCCTCTGG 58.343 55.000 0.00 0.00 35.26 3.86
3154 3240 2.872038 GCGTTTCCTCTGGACATGAAGT 60.872 50.000 0.00 0.00 0.00 3.01
3171 3257 0.900647 AGTAGCTCGGCTCCAACAGT 60.901 55.000 1.46 0.00 40.44 3.55
3210 3296 5.705609 AGTCGCCAAGTATGAATTTTTGT 57.294 34.783 0.00 0.00 0.00 2.83
3217 3303 9.739786 CGCCAAGTATGAATTTTTGTTTTATTC 57.260 29.630 0.00 0.00 0.00 1.75
3226 3312 5.456548 TTTTTGTTTTATTCGGAGTCCCC 57.543 39.130 2.80 0.00 0.00 4.81
3295 3381 1.480954 GATTCCGGCTGTCCAGTCTTA 59.519 52.381 0.00 0.00 0.00 2.10
3315 3401 0.796312 ACACGGTTCTTTGCTATGCG 59.204 50.000 0.00 0.00 0.00 4.73
3324 3410 3.304251 TGCTATGCGCAGGTGGTA 58.696 55.556 18.32 1.17 45.47 3.25
3325 3411 1.143838 TGCTATGCGCAGGTGGTAG 59.856 57.895 18.32 13.44 45.47 3.18
3385 3826 9.935682 ATAATTGTTATTCTGCGATTGTTAGTG 57.064 29.630 0.00 0.00 0.00 2.74
3388 3829 5.353956 TGTTATTCTGCGATTGTTAGTGCAT 59.646 36.000 0.00 0.00 36.64 3.96
3394 3835 4.503910 TGCGATTGTTAGTGCATCTACTT 58.496 39.130 0.00 0.00 31.31 2.24
3403 3844 8.662781 TGTTAGTGCATCTACTTCATTTATCC 57.337 34.615 0.00 0.00 32.19 2.59
3405 3846 8.983724 GTTAGTGCATCTACTTCATTTATCCTC 58.016 37.037 0.00 0.00 32.19 3.71
3406 3847 6.219473 AGTGCATCTACTTCATTTATCCTCG 58.781 40.000 0.00 0.00 0.00 4.63
3410 3851 6.393990 CATCTACTTCATTTATCCTCGGGAG 58.606 44.000 0.00 0.00 34.05 4.30
3416 3857 7.978925 ACTTCATTTATCCTCGGGAGATATTT 58.021 34.615 0.00 0.00 38.80 1.40
3421 3862 9.102757 CATTTATCCTCGGGAGATATTTATGTG 57.897 37.037 0.00 0.00 38.80 3.21
3422 3863 5.683876 ATCCTCGGGAGATATTTATGTGG 57.316 43.478 0.00 0.00 38.80 4.17
3423 3864 4.489737 TCCTCGGGAGATATTTATGTGGT 58.510 43.478 0.00 0.00 38.80 4.16
3424 3865 4.283467 TCCTCGGGAGATATTTATGTGGTG 59.717 45.833 0.00 0.00 38.80 4.17
3425 3866 4.040461 CCTCGGGAGATATTTATGTGGTGT 59.960 45.833 0.00 0.00 38.80 4.16
3426 3867 4.956085 TCGGGAGATATTTATGTGGTGTG 58.044 43.478 0.00 0.00 0.00 3.82
3427 3868 4.407621 TCGGGAGATATTTATGTGGTGTGT 59.592 41.667 0.00 0.00 0.00 3.72
3428 3869 4.750098 CGGGAGATATTTATGTGGTGTGTC 59.250 45.833 0.00 0.00 0.00 3.67
3447 3888 2.297597 GTCTGTGTGTGACTTCCTAGCT 59.702 50.000 0.00 0.00 0.00 3.32
3478 3919 3.199946 CACCCTGCCTTAGAAGAATGGTA 59.800 47.826 0.00 0.00 0.00 3.25
3542 3983 2.171448 AGTTAGTCTGATGCCATGGGAC 59.829 50.000 15.13 11.77 0.00 4.46
3547 3988 1.019673 CTGATGCCATGGGACTTTCG 58.980 55.000 15.13 0.00 0.00 3.46
3565 4006 1.591703 GGTGCTCGACATGGACTGA 59.408 57.895 0.00 0.00 0.00 3.41
3608 4049 5.197451 TGTTCCAGTTTTGTGGATAACAGT 58.803 37.500 0.00 0.00 46.31 3.55
3664 4105 2.663478 CGCTGCGTACCGAAAAGCA 61.663 57.895 14.93 0.00 38.03 3.91
3786 4231 4.668138 ACCTAATCCCTTGGCTTGTTTA 57.332 40.909 0.00 0.00 0.00 2.01
3829 4274 4.729918 AGGCAGCGGGGCAGAAAG 62.730 66.667 7.65 0.00 46.44 2.62
3873 4318 2.338015 CCCGCAGTTGCTGAATGCT 61.338 57.895 10.41 0.00 43.37 3.79
3885 4330 4.002982 TGCTGAATGCTACGAATTGAACT 58.997 39.130 0.00 0.00 43.37 3.01
3891 4336 4.340894 TGCTACGAATTGAACTTGCATC 57.659 40.909 0.00 0.00 0.00 3.91
4022 4496 8.953665 AGGAATCATATATCTCCCAACTCTTTT 58.046 33.333 2.64 0.00 0.00 2.27
4064 4538 6.920817 TGATCGTTGTGTATCTTAGTGAACT 58.079 36.000 0.00 0.00 0.00 3.01
4070 4544 7.753580 CGTTGTGTATCTTAGTGAACTGATACA 59.246 37.037 14.81 14.81 44.82 2.29
4151 4626 1.135603 CCATGTGTGTTCTCCGCATTG 60.136 52.381 0.00 0.00 35.67 2.82
4171 4646 2.750166 TGGCAGAAGTTTGAACGAAACA 59.250 40.909 0.00 0.00 45.69 2.83
4172 4647 3.380004 TGGCAGAAGTTTGAACGAAACAT 59.620 39.130 0.00 0.00 45.69 2.71
4191 4666 2.433868 TAAACTCTGTCGCACCAGTC 57.566 50.000 0.08 0.00 34.02 3.51
4295 4770 0.307760 CCGCACCACTTCAACTGTTC 59.692 55.000 0.00 0.00 0.00 3.18
4297 4772 2.479837 CGCACCACTTCAACTGTTCTA 58.520 47.619 0.00 0.00 0.00 2.10
4302 4777 6.273071 GCACCACTTCAACTGTTCTATTTTT 58.727 36.000 0.00 0.00 0.00 1.94
4303 4778 6.417930 GCACCACTTCAACTGTTCTATTTTTC 59.582 38.462 0.00 0.00 0.00 2.29
4304 4779 7.682021 GCACCACTTCAACTGTTCTATTTTTCT 60.682 37.037 0.00 0.00 0.00 2.52
4305 4780 7.645340 CACCACTTCAACTGTTCTATTTTTCTG 59.355 37.037 0.00 0.00 0.00 3.02
4306 4781 6.638468 CCACTTCAACTGTTCTATTTTTCTGC 59.362 38.462 0.00 0.00 0.00 4.26
4347 4822 4.656100 TTGAGGGACAGGAAATCATCAA 57.344 40.909 0.00 0.00 0.00 2.57
4436 4943 5.816258 GCCTATAAAGTTACTCCAACCTGAC 59.184 44.000 0.00 0.00 37.93 3.51
4524 5031 5.065474 CGAAACTCTAGACTAGAAGAGGTGG 59.935 48.000 13.18 2.89 38.85 4.61
4528 5035 1.142097 GACTAGAAGAGGTGGCCGC 59.858 63.158 8.12 8.12 0.00 6.53
4530 5037 1.192146 ACTAGAAGAGGTGGCCGCAA 61.192 55.000 19.98 0.00 0.00 4.85
4531 5038 0.741221 CTAGAAGAGGTGGCCGCAAC 60.741 60.000 19.98 11.18 0.00 4.17
4532 5039 1.192146 TAGAAGAGGTGGCCGCAACT 61.192 55.000 19.98 13.42 0.00 3.16
4564 5071 0.906282 AAAGGCCCAATTCAGCAGGG 60.906 55.000 0.00 0.00 45.68 4.45
4629 5145 2.835431 ACCATCCTCGCCTCTCGG 60.835 66.667 0.00 0.00 39.05 4.63
4808 6567 1.845791 TCTGATATGTGGGCCATGTGT 59.154 47.619 10.70 0.00 34.86 3.72
4809 6568 2.241941 TCTGATATGTGGGCCATGTGTT 59.758 45.455 10.70 0.00 34.86 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 8.169977 TCATCAAATAGAGGATTTTGTATGCC 57.830 34.615 0.00 0.00 35.45 4.40
209 210 5.558818 AGAGCATGATCAACTTTCTCTGTT 58.441 37.500 14.38 0.00 0.00 3.16
244 245 7.176690 CCACTAACCCACAACTCTTCATAATTT 59.823 37.037 0.00 0.00 0.00 1.82
262 263 7.050970 TCATATGTATGAGTGTCCACTAACC 57.949 40.000 1.90 0.00 42.66 2.85
313 314 2.380084 TGCAACCTCGAATCTACCAC 57.620 50.000 0.00 0.00 0.00 4.16
314 315 3.334691 CTTTGCAACCTCGAATCTACCA 58.665 45.455 0.00 0.00 0.00 3.25
320 321 2.568623 ACTCCTTTGCAACCTCGAAT 57.431 45.000 0.00 0.00 0.00 3.34
475 476 3.003480 GCAGCAGTACCCTTCTTAGTTG 58.997 50.000 0.00 0.00 0.00 3.16
563 564 7.251704 CAAATATGCTCGGATAAGTTGACTT 57.748 36.000 1.60 1.60 39.85 3.01
595 596 4.586841 TCACATAGTTCCAAACCAAAAGGG 59.413 41.667 0.00 0.00 44.81 3.95
598 599 6.968263 TCATCACATAGTTCCAAACCAAAA 57.032 33.333 0.00 0.00 0.00 2.44
647 656 9.434559 GTTTGACAACTGATTACTTGAGTTTAC 57.565 33.333 0.00 0.00 0.00 2.01
657 666 6.438763 CAGGAAAGGTTTGACAACTGATTAC 58.561 40.000 0.00 0.00 32.90 1.89
673 682 2.290896 TGCATGTAGGTTCCAGGAAAGG 60.291 50.000 2.45 0.00 0.00 3.11
682 691 7.582667 AAATAGGGTAATTGCATGTAGGTTC 57.417 36.000 0.00 0.00 0.00 3.62
693 702 8.630037 GGACTCCACATAAAAATAGGGTAATTG 58.370 37.037 0.00 0.00 0.00 2.32
716 725 3.314541 AACAGTAGTCATGGAACGGAC 57.685 47.619 0.00 0.00 35.85 4.79
717 726 4.345859 AAAACAGTAGTCATGGAACGGA 57.654 40.909 0.00 0.00 0.00 4.69
718 727 6.737254 ATTAAAACAGTAGTCATGGAACGG 57.263 37.500 0.00 0.00 0.00 4.44
719 728 9.755064 CTTTATTAAAACAGTAGTCATGGAACG 57.245 33.333 0.00 0.00 0.00 3.95
806 819 8.589338 CAAACTAGAGTACTATAATGGGCAGAT 58.411 37.037 0.00 0.00 0.00 2.90
808 821 6.647067 GCAAACTAGAGTACTATAATGGGCAG 59.353 42.308 0.00 0.00 0.00 4.85
809 822 6.099125 TGCAAACTAGAGTACTATAATGGGCA 59.901 38.462 0.00 2.61 0.00 5.36
810 823 6.522054 TGCAAACTAGAGTACTATAATGGGC 58.478 40.000 0.00 0.00 0.00 5.36
811 824 8.958119 TTTGCAAACTAGAGTACTATAATGGG 57.042 34.615 8.05 0.00 0.00 4.00
823 837 4.919754 GCCAGTCATTTTTGCAAACTAGAG 59.080 41.667 12.39 0.79 0.00 2.43
824 838 4.340666 TGCCAGTCATTTTTGCAAACTAGA 59.659 37.500 12.39 6.94 0.00 2.43
825 839 4.445385 GTGCCAGTCATTTTTGCAAACTAG 59.555 41.667 12.39 4.50 33.11 2.57
826 840 4.099266 AGTGCCAGTCATTTTTGCAAACTA 59.901 37.500 12.39 3.33 33.11 2.24
827 841 3.118665 AGTGCCAGTCATTTTTGCAAACT 60.119 39.130 12.39 2.75 33.11 2.66
860 874 1.562783 AGGAGGAGAGTTGCTACACC 58.437 55.000 0.13 1.45 38.40 4.16
863 877 4.023536 CGAGATAAGGAGGAGAGTTGCTAC 60.024 50.000 0.00 0.00 0.00 3.58
872 886 5.130350 AGAGAACTTCGAGATAAGGAGGAG 58.870 45.833 0.00 0.00 0.00 3.69
873 887 5.118729 AGAGAACTTCGAGATAAGGAGGA 57.881 43.478 0.00 0.00 0.00 3.71
917 938 7.649057 AGGTCAGCAAACAGATAAAAACTAAC 58.351 34.615 0.00 0.00 0.00 2.34
927 948 1.272147 GGGGAAGGTCAGCAAACAGAT 60.272 52.381 0.00 0.00 0.00 2.90
928 949 0.110486 GGGGAAGGTCAGCAAACAGA 59.890 55.000 0.00 0.00 0.00 3.41
929 950 0.111253 AGGGGAAGGTCAGCAAACAG 59.889 55.000 0.00 0.00 0.00 3.16
948 970 7.987649 ACTGTAACGGTGACAATAAAGAAAAA 58.012 30.769 0.00 0.00 0.00 1.94
965 987 4.201773 TGCACTCAAAACAGAACTGTAACG 60.202 41.667 7.90 0.44 44.13 3.18
982 1004 5.048782 TGTCCATAAAGTTCAATGTGCACTC 60.049 40.000 19.41 0.00 0.00 3.51
985 1007 5.981088 ATGTCCATAAAGTTCAATGTGCA 57.019 34.783 0.00 0.00 0.00 4.57
992 1014 7.675161 TCCTCAGATATGTCCATAAAGTTCA 57.325 36.000 0.00 0.00 0.00 3.18
1012 1034 4.202151 ACCAAAATCTTGTTGTTGCTCCTC 60.202 41.667 0.00 0.00 0.00 3.71
1084 1106 9.984190 CAGGTAAGGGAGAAATAGAAACTATAC 57.016 37.037 0.00 0.00 0.00 1.47
1094 1116 9.681062 CTATTGAAAACAGGTAAGGGAGAAATA 57.319 33.333 0.00 0.00 0.00 1.40
1095 1117 8.170730 ACTATTGAAAACAGGTAAGGGAGAAAT 58.829 33.333 0.00 0.00 0.00 2.17
1154 1176 3.119463 CGCATTTTCGTCCAACAAATGTC 59.881 43.478 5.90 0.00 39.24 3.06
1190 1212 5.823570 TGGGTGTCGATACTTCTTTGAAAAA 59.176 36.000 12.29 0.00 0.00 1.94
1215 1237 2.545946 GAGTCAACTTTGAGTCCAGCAC 59.454 50.000 13.74 0.00 46.84 4.40
1230 1252 6.017440 ACAGCATTTAAGCGTTTTAGAGTCAA 60.017 34.615 0.00 0.00 40.15 3.18
1355 1377 6.914654 TGGTACCAATACGGCAATACTATA 57.085 37.500 13.60 0.00 39.03 1.31
1365 1387 7.153217 AGAAAGAAATTTGGTACCAATACGG 57.847 36.000 27.57 0.00 42.50 4.02
1469 1491 8.774546 ATCACTCTATGGTTCTATCTTCTTCA 57.225 34.615 0.00 0.00 0.00 3.02
1472 1494 8.004215 ACAGATCACTCTATGGTTCTATCTTCT 58.996 37.037 0.00 0.00 0.00 2.85
1473 1495 8.177119 ACAGATCACTCTATGGTTCTATCTTC 57.823 38.462 0.00 0.00 0.00 2.87
1475 1497 8.444783 ACTACAGATCACTCTATGGTTCTATCT 58.555 37.037 0.00 0.00 0.00 1.98
1483 1505 4.576873 ACGTGACTACAGATCACTCTATGG 59.423 45.833 0.00 0.00 43.60 2.74
1499 1521 4.389890 TGTTACAACCTAACACGTGACT 57.610 40.909 25.01 11.37 33.05 3.41
1500 1522 4.508861 ACATGTTACAACCTAACACGTGAC 59.491 41.667 25.01 6.14 39.83 3.67
1533 1555 6.070938 ACTGAGGTAAGCCGAGTTTTAATACT 60.071 38.462 0.00 0.00 40.50 2.12
1534 1556 6.104665 ACTGAGGTAAGCCGAGTTTTAATAC 58.895 40.000 0.00 0.00 40.50 1.89
1535 1557 6.154021 AGACTGAGGTAAGCCGAGTTTTAATA 59.846 38.462 0.00 0.00 40.50 0.98
1556 1578 2.587777 TCCTACAGATGGAAGGGAGACT 59.412 50.000 4.29 0.00 0.00 3.24
1602 1624 2.138595 TGTAGGAACACCAAGCCGT 58.861 52.632 0.00 0.00 0.00 5.68
1746 1768 4.717877 CATTCCCTATCTGTGTGGCAATA 58.282 43.478 0.00 0.00 0.00 1.90
1881 1903 7.065803 ACACCGTGATAGATGAATTAAAACAGG 59.934 37.037 5.28 0.00 0.00 4.00
1900 1922 5.744490 CCAGACTTTTAAGTTAACACCGTG 58.256 41.667 8.61 0.00 39.88 4.94
1903 1926 7.389607 TGATAGCCAGACTTTTAAGTTAACACC 59.610 37.037 8.61 0.00 39.88 4.16
1938 1968 9.995003 AAGAACCTGCAAAATGAAAATATAACA 57.005 25.926 0.00 0.00 0.00 2.41
2000 2030 1.484444 GGTCCACTGCCTTGTCCTCT 61.484 60.000 0.00 0.00 0.00 3.69
2021 2051 8.729805 AAATTAAAGCTCTCTCAAGGACATAG 57.270 34.615 0.00 0.00 0.00 2.23
2027 2057 6.679884 GCATGGAAATTAAAGCTCTCTCAAGG 60.680 42.308 0.00 0.00 0.00 3.61
2209 2244 2.167693 GCTACTTGTAAAAATGGCCCCC 59.832 50.000 0.00 0.00 0.00 5.40
2222 2258 7.239773 ACAATTATATATGGAGGGGCTACTTGT 59.760 37.037 0.00 0.00 0.00 3.16
2253 2289 2.736531 CAAAAGGTGGGCTGCACC 59.263 61.111 0.00 4.90 42.81 5.01
2254 2290 2.736531 CCAAAAGGTGGGCTGCAC 59.263 61.111 0.50 0.00 44.64 4.57
2258 2294 9.436043 TTCAAAAAGAAATCCAAAAGGTGGGCT 62.436 37.037 0.00 0.00 39.70 5.19
2261 2297 7.622893 TTTCAAAAAGAAATCCAAAAGGTGG 57.377 32.000 0.00 0.00 44.03 4.61
2273 2309 7.716123 AGCATGAATGGTGATTTCAAAAAGAAA 59.284 29.630 0.00 0.00 42.55 2.52
2274 2310 7.218614 AGCATGAATGGTGATTTCAAAAAGAA 58.781 30.769 0.00 0.00 36.72 2.52
2276 2312 8.712285 ATAGCATGAATGGTGATTTCAAAAAG 57.288 30.769 0.00 0.00 39.14 2.27
2309 2349 2.836981 CTGGTGAGATCCCTGAACTCTT 59.163 50.000 0.00 0.00 33.53 2.85
2327 2367 5.160607 TGTATTCTGGGTACTGTTTCTGG 57.839 43.478 0.00 0.00 0.00 3.86
2377 2418 6.962182 AGAGGGAGTGAATAATGATTTGTGA 58.038 36.000 0.00 0.00 0.00 3.58
2472 2514 0.250338 GGAGGTGAAAGAGTTGCCGT 60.250 55.000 0.00 0.00 0.00 5.68
2474 2516 1.072331 TCAGGAGGTGAAAGAGTTGCC 59.928 52.381 0.00 0.00 29.64 4.52
2508 2550 3.582647 TCCTATGAAGAACTTGTCAGCCA 59.417 43.478 0.00 0.00 0.00 4.75
2525 2567 8.825774 TGTGGTATGTATGCTAAATGATCCTAT 58.174 33.333 0.00 0.00 0.00 2.57
2544 2586 2.512692 TGATTGCAAGGCTGTGGTAT 57.487 45.000 4.94 0.00 0.00 2.73
2563 2605 3.411446 TCTGAAACTTCATGCCGACATT 58.589 40.909 0.00 0.00 36.46 2.71
2566 2608 3.189287 ACATTCTGAAACTTCATGCCGAC 59.811 43.478 0.00 0.00 36.46 4.79
2570 2612 6.618811 AGATGAACATTCTGAAACTTCATGC 58.381 36.000 21.39 15.41 36.46 4.06
2625 2667 1.070134 CAACCCCGAGTGAACTTCTCA 59.930 52.381 0.00 0.00 32.79 3.27
2686 2733 1.071542 TCTTCAGGAATCACAACGGCA 59.928 47.619 0.00 0.00 0.00 5.69
2692 2739 2.618816 GGCATGGTCTTCAGGAATCACA 60.619 50.000 0.00 0.00 0.00 3.58
2698 2745 1.211212 CAGATGGCATGGTCTTCAGGA 59.789 52.381 3.81 0.00 0.00 3.86
2715 2762 2.451493 TGGGGACAAAGGGGCAGA 60.451 61.111 0.00 0.00 37.44 4.26
2717 2764 4.299796 GCTGGGGACAAAGGGGCA 62.300 66.667 0.00 0.00 42.06 5.36
2741 2788 1.202371 GCTGATGTGGATGGTGCAATG 60.202 52.381 0.00 0.00 0.00 2.82
2759 2806 1.218316 GATCGGGTGGACGAAAGCT 59.782 57.895 0.00 0.00 46.92 3.74
2825 2872 6.751211 TGGAAGTCGGTCCATGGAAACAAA 62.751 45.833 18.20 0.93 42.97 2.83
2856 2903 1.692519 AGGTTCGGTGATGGCCTATAC 59.307 52.381 3.32 0.00 0.00 1.47
2860 2907 2.671070 CAGGTTCGGTGATGGCCT 59.329 61.111 3.32 0.00 0.00 5.19
2916 2963 6.574073 GCACTCTAGCTAGCAAGGAATGATAT 60.574 42.308 18.83 0.00 0.00 1.63
2949 2996 0.111061 AGAGCCACAATGGTGCAGAA 59.889 50.000 0.00 0.00 43.88 3.02
2950 2997 0.111061 AAGAGCCACAATGGTGCAGA 59.889 50.000 0.00 0.00 43.88 4.26
2985 3032 1.725641 CTGCTATCGTGGTTTGCTGA 58.274 50.000 0.00 0.00 0.00 4.26
3000 3047 4.352009 AGCATACTATCTAGATGGCTGCT 58.648 43.478 27.23 27.23 37.04 4.24
3045 3092 3.453070 GAGCTCTGGTGGCGATCCC 62.453 68.421 6.43 0.00 34.52 3.85
3076 3123 1.583054 GCACTGTTCTGGAAGTTCGT 58.417 50.000 0.00 0.00 33.76 3.85
3081 3130 1.466167 CATTCGGCACTGTTCTGGAAG 59.534 52.381 0.00 0.00 0.00 3.46
3096 3145 0.867753 CGCTCCGAAGTCCTCATTCG 60.868 60.000 1.29 1.29 46.94 3.34
3099 3148 1.680522 ATGCGCTCCGAAGTCCTCAT 61.681 55.000 9.73 0.00 0.00 2.90
3100 3149 2.351244 ATGCGCTCCGAAGTCCTCA 61.351 57.895 9.73 0.00 0.00 3.86
3101 3150 1.880340 CATGCGCTCCGAAGTCCTC 60.880 63.158 9.73 0.00 0.00 3.71
3102 3151 1.888436 TTCATGCGCTCCGAAGTCCT 61.888 55.000 9.73 0.00 0.00 3.85
3103 3152 1.447838 TTCATGCGCTCCGAAGTCC 60.448 57.895 9.73 0.00 0.00 3.85
3104 3153 0.737715 AGTTCATGCGCTCCGAAGTC 60.738 55.000 9.73 0.00 0.00 3.01
3105 3154 0.320771 AAGTTCATGCGCTCCGAAGT 60.321 50.000 9.73 8.67 0.00 3.01
3107 3156 1.019278 GGAAGTTCATGCGCTCCGAA 61.019 55.000 9.73 5.75 0.00 4.30
3108 3157 1.447838 GGAAGTTCATGCGCTCCGA 60.448 57.895 9.73 0.00 0.00 4.55
3109 3158 1.699656 CTGGAAGTTCATGCGCTCCG 61.700 60.000 9.73 0.00 0.00 4.63
3110 3159 2.093216 CTGGAAGTTCATGCGCTCC 58.907 57.895 9.73 5.71 0.00 4.70
3116 3165 7.380253 GGAAACGCCATACTGGAAGTTCATG 62.380 48.000 5.01 0.00 40.16 3.07
3118 3167 4.115703 GGAAACGCCATACTGGAAGTTCA 61.116 47.826 5.01 0.00 40.16 3.18
3119 3168 2.418976 GGAAACGCCATACTGGAAGTTC 59.581 50.000 0.00 0.00 40.16 3.01
3120 3169 2.039879 AGGAAACGCCATACTGGAAGTT 59.960 45.455 0.00 0.00 42.70 2.66
3121 3170 1.628846 AGGAAACGCCATACTGGAAGT 59.371 47.619 0.00 0.00 46.25 3.01
3122 3171 2.093447 AGAGGAAACGCCATACTGGAAG 60.093 50.000 0.00 0.00 40.96 3.46
3123 3172 1.906574 AGAGGAAACGCCATACTGGAA 59.093 47.619 0.00 0.00 40.96 3.53
3124 3173 1.207089 CAGAGGAAACGCCATACTGGA 59.793 52.381 0.00 0.00 40.96 3.86
3125 3174 1.656652 CAGAGGAAACGCCATACTGG 58.343 55.000 0.00 0.00 41.55 4.00
3126 3175 1.207089 TCCAGAGGAAACGCCATACTG 59.793 52.381 0.00 0.00 40.02 2.74
3127 3176 1.207329 GTCCAGAGGAAACGCCATACT 59.793 52.381 0.00 0.00 40.02 2.12
3131 3180 0.321564 CATGTCCAGAGGAAACGCCA 60.322 55.000 0.00 0.00 40.02 5.69
3132 3181 0.036388 TCATGTCCAGAGGAAACGCC 60.036 55.000 0.00 0.00 31.38 5.68
3143 3192 0.175760 GCCGAGCTACTTCATGTCCA 59.824 55.000 0.00 0.00 0.00 4.02
3144 3193 0.461961 AGCCGAGCTACTTCATGTCC 59.538 55.000 0.00 0.00 36.99 4.02
3145 3194 1.537135 GGAGCCGAGCTACTTCATGTC 60.537 57.143 1.26 0.00 39.88 3.06
3154 3240 0.898326 TCACTGTTGGAGCCGAGCTA 60.898 55.000 0.00 0.00 39.88 3.32
3171 3257 0.394216 ACTAATGCGCAATGGGCTCA 60.394 50.000 22.43 4.27 42.24 4.26
3258 3344 0.965866 ATCTTCCTCGACAGTCGCCA 60.966 55.000 18.62 0.76 40.21 5.69
3283 3369 2.814280 ACCGTGTTAAGACTGGACAG 57.186 50.000 16.54 0.00 0.00 3.51
3284 3370 2.696707 AGAACCGTGTTAAGACTGGACA 59.303 45.455 16.54 0.00 0.00 4.02
3295 3381 1.196808 CGCATAGCAAAGAACCGTGTT 59.803 47.619 0.00 0.00 0.00 3.32
3315 3401 0.674895 CAAGTCAGCCTACCACCTGC 60.675 60.000 0.00 0.00 0.00 4.85
3324 3410 2.330216 ACCTTACTGTCAAGTCAGCCT 58.670 47.619 0.00 0.00 38.84 4.58
3325 3411 2.841442 ACCTTACTGTCAAGTCAGCC 57.159 50.000 0.00 0.00 38.84 4.85
3360 3801 7.908082 GCACTAACAATCGCAGAATAACAATTA 59.092 33.333 0.00 0.00 43.58 1.40
3385 3826 4.932200 CCCGAGGATAAATGAAGTAGATGC 59.068 45.833 0.00 0.00 0.00 3.91
3388 3829 5.702266 TCTCCCGAGGATAAATGAAGTAGA 58.298 41.667 0.00 0.00 0.00 2.59
3394 3835 9.046846 ACATAAATATCTCCCGAGGATAAATGA 57.953 33.333 0.00 0.00 30.78 2.57
3403 3844 4.991056 CACACCACATAAATATCTCCCGAG 59.009 45.833 0.00 0.00 0.00 4.63
3405 3846 4.703897 ACACACCACATAAATATCTCCCG 58.296 43.478 0.00 0.00 0.00 5.14
3406 3847 5.760253 CAGACACACCACATAAATATCTCCC 59.240 44.000 0.00 0.00 0.00 4.30
3410 3851 6.371548 ACACACAGACACACCACATAAATATC 59.628 38.462 0.00 0.00 0.00 1.63
3416 3857 2.432510 TCACACACAGACACACCACATA 59.567 45.455 0.00 0.00 0.00 2.29
3421 3862 1.933853 GAAGTCACACACAGACACACC 59.066 52.381 0.00 0.00 38.46 4.16
3422 3863 1.933853 GGAAGTCACACACAGACACAC 59.066 52.381 0.00 0.00 38.46 3.82
3423 3864 1.831106 AGGAAGTCACACACAGACACA 59.169 47.619 0.00 0.00 38.46 3.72
3424 3865 2.604046 AGGAAGTCACACACAGACAC 57.396 50.000 0.00 0.00 38.46 3.67
3425 3866 2.035961 GCTAGGAAGTCACACACAGACA 59.964 50.000 0.00 0.00 38.46 3.41
3426 3867 2.297597 AGCTAGGAAGTCACACACAGAC 59.702 50.000 0.00 0.00 36.26 3.51
3427 3868 2.297315 CAGCTAGGAAGTCACACACAGA 59.703 50.000 0.00 0.00 0.00 3.41
3428 3869 2.611473 CCAGCTAGGAAGTCACACACAG 60.611 54.545 0.00 0.00 41.22 3.66
3447 3888 0.032615 AAGGCAGGGTGTGAAAACCA 60.033 50.000 0.00 0.00 42.47 3.67
3478 3919 7.512992 TGTCAAAACCCATGTTATTTTGGAAT 58.487 30.769 18.62 0.00 41.52 3.01
3529 3970 0.394216 CCGAAAGTCCCATGGCATCA 60.394 55.000 6.09 0.00 0.00 3.07
3547 3988 0.737715 GTCAGTCCATGTCGAGCACC 60.738 60.000 0.00 0.00 0.00 5.01
3608 4049 7.060383 TCTAATTCAAAGCAAAAATGGGTGA 57.940 32.000 0.00 0.00 0.00 4.02
3664 4105 4.085876 GCACACCACTGCCTTGAT 57.914 55.556 0.00 0.00 0.00 2.57
3786 4231 5.047802 ACTGAAAAATCCATGCGAAGAACAT 60.048 36.000 0.00 0.00 0.00 2.71
3829 4274 3.054166 GTTTTACCCAACCATTGTTCGC 58.946 45.455 0.00 0.00 30.42 4.70
3873 4318 4.068599 TGGTGATGCAAGTTCAATTCGTA 58.931 39.130 0.00 0.00 0.00 3.43
3885 4330 2.231721 CACACAATGGATGGTGATGCAA 59.768 45.455 0.95 0.00 38.38 4.08
3891 4336 5.449041 GCTATAACACACACAATGGATGGTG 60.449 44.000 0.00 0.00 40.78 4.17
4022 4496 5.995282 ACGATCATCCAAAACTCACAAGTTA 59.005 36.000 0.00 0.00 45.07 2.24
4064 4538 5.694816 CACCGCAACAAAGTAAATGTATCA 58.305 37.500 0.00 0.00 0.00 2.15
4070 4544 3.255642 AGATGCACCGCAACAAAGTAAAT 59.744 39.130 0.00 0.00 43.62 1.40
4151 4626 3.414549 TGTTTCGTTCAAACTTCTGCC 57.585 42.857 0.68 0.00 44.35 4.85
4171 4646 2.563179 AGACTGGTGCGACAGAGTTTAT 59.437 45.455 13.62 0.00 40.97 1.40
4172 4647 1.961394 AGACTGGTGCGACAGAGTTTA 59.039 47.619 13.62 0.00 40.97 2.01
4191 4666 5.030295 CGCAAAGTGATTTGGCAGTATAAG 58.970 41.667 3.17 0.00 32.78 1.73
4226 4701 6.828273 TCGTGGGAAAATCACTATGATTCAAT 59.172 34.615 4.59 0.00 45.57 2.57
4295 4770 6.909357 GTGATGATTTCCTCGCAGAAAAATAG 59.091 38.462 4.17 0.00 39.11 1.73
4297 4772 5.416952 AGTGATGATTTCCTCGCAGAAAAAT 59.583 36.000 4.17 2.39 39.11 1.82
4302 4777 3.616956 AAGTGATGATTTCCTCGCAGA 57.383 42.857 0.42 0.00 0.00 4.26
4303 4778 4.691860 AAAAGTGATGATTTCCTCGCAG 57.308 40.909 0.42 0.00 0.00 5.18
4524 5031 2.033194 GGACACCAGTAGTTGCGGC 61.033 63.158 0.00 0.00 0.00 6.53
4564 5071 0.108019 CCTCCGGGTTAGGCCAATAC 59.892 60.000 5.01 0.00 39.65 1.89
4629 5145 1.868251 CGAGTCGCGTAGAACCAGC 60.868 63.158 5.77 0.00 34.64 4.85
4721 6480 2.280628 GCCGAGAAAGGTATGAGTTGG 58.719 52.381 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.