Multiple sequence alignment - TraesCS2B01G225700

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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 TraesCS2B01G225700 chr2B 100.000 2367 0 0 929 3295 216445668 216443302 0.000000e+00 4372
1 TraesCS2B01G225700 chr2B 94.226 2061 118 1 929 2988 359186503 359188563 0.000000e+00 3145
2 TraesCS2B01G225700 chr2B 94.115 2056 117 3 933 2988 381088996 381091047 0.000000e+00 3123
3 TraesCS2B01G225700 chr2B 94.063 2055 120 2 932 2986 163954012 163951960 0.000000e+00 3118
4 TraesCS2B01G225700 chr2B 93.832 2059 126 1 929 2987 464348357 464346300 0.000000e+00 3097
5 TraesCS2B01G225700 chr2B 100.000 747 0 0 1 747 216446596 216445850 0.000000e+00 1380
6 TraesCS2B01G225700 chr2B 94.489 744 41 0 1 744 550581195 550581938 0.000000e+00 1147
7 TraesCS2B01G225700 chr2B 94.102 746 43 1 1 745 164591445 164590700 0.000000e+00 1133
8 TraesCS2B01G225700 chr2B 93.976 747 45 0 1 747 283104390 283105136 0.000000e+00 1131
9 TraesCS2B01G225700 chr2B 93.574 747 48 0 1 747 524554204 524553458 0.000000e+00 1114
10 TraesCS2B01G225700 chr2B 99.016 305 3 0 2991 3295 214683765 214683461 6.220000e-152 547
11 TraesCS2B01G225700 chr2B 99.016 305 3 0 2991 3295 590608418 590608722 6.220000e-152 547
12 TraesCS2B01G225700 chr2B 98.697 307 4 0 2989 3295 3140216 3139910 2.240000e-151 545
13 TraesCS2B01G225700 chr2B 98.361 305 5 0 2991 3295 214690671 214690367 1.350000e-148 536
14 TraesCS2B01G225700 chr2B 97.452 314 8 0 2982 3295 623584041 623583728 1.350000e-148 536
15 TraesCS2B01G225700 chr1B 94.175 2060 115 5 929 2988 303747880 303745826 0.000000e+00 3134
16 TraesCS2B01G225700 chr1B 94.110 747 43 1 1 747 303748662 303747917 0.000000e+00 1134
17 TraesCS2B01G225700 chr1B 94.110 747 43 1 1 747 525543189 525542444 0.000000e+00 1134
18 TraesCS2B01G225700 chr1B 98.689 305 4 0 2991 3295 478927095 478926791 2.890000e-150 542
19 TraesCS2B01G225700 chr1B 98.058 309 6 0 2987 3295 169504010 169504318 3.740000e-149 538
20 TraesCS2B01G225700 chr5B 93.984 2061 119 4 932 2988 324884046 324881987 0.000000e+00 3114
21 TraesCS2B01G225700 chr5B 93.641 2060 131 0 929 2988 464749653 464751712 0.000000e+00 3079
22 TraesCS2B01G225700 chr5B 98.697 307 4 0 2989 3295 96700701 96701007 2.240000e-151 545
23 TraesCS2B01G225700 chr5B 98.382 309 5 0 2987 3295 327041550 327041242 8.040000e-151 544
24 TraesCS2B01G225700 chr5B 98.689 305 4 0 2991 3295 88815620 88815316 2.890000e-150 542
25 TraesCS2B01G225700 chr5B 98.689 305 4 0 2991 3295 346833356 346833052 2.890000e-150 542
26 TraesCS2B01G225700 chr5B 97.484 318 5 2 2978 3295 280914931 280914617 1.040000e-149 540
27 TraesCS2B01G225700 chr5B 98.371 307 5 0 2989 3295 705835873 705836179 1.040000e-149 540
28 TraesCS2B01G225700 chr6B 93.826 2057 126 1 932 2988 530815539 530813484 0.000000e+00 3094
29 TraesCS2B01G225700 chr6B 93.732 2058 123 6 932 2988 373831219 373829167 0.000000e+00 3081
30 TraesCS2B01G225700 chr6B 94.779 747 38 1 1 747 373832003 373831258 0.000000e+00 1162
31 TraesCS2B01G225700 chr6B 94.378 747 41 1 1 747 50272448 50271703 0.000000e+00 1146
32 TraesCS2B01G225700 chr6B 98.697 307 4 0 2989 3295 591552619 591552313 2.240000e-151 545
33 TraesCS2B01G225700 chr6B 98.371 307 5 0 2989 3295 427247256 427247562 1.040000e-149 540
34 TraesCS2B01G225700 chr4B 93.583 748 46 2 1 747 434147071 434147817 0.000000e+00 1114
35 TraesCS2B01G225700 chr4B 98.361 305 5 0 2991 3295 445184915 445185219 1.350000e-148 536
36 TraesCS2B01G225700 chr4B 98.361 305 5 0 2991 3295 505521389 505521693 1.350000e-148 536
37 TraesCS2B01G225700 chr4B 97.742 310 7 0 2986 3295 30766135 30766444 4.840000e-148 534
38 TraesCS2B01G225700 chr4B 98.046 307 6 0 2989 3295 147846883 147846577 4.840000e-148 534
39 TraesCS2B01G225700 chr4B 97.143 315 7 1 2981 3295 660615603 660615915 6.260000e-147 531
40 TraesCS2B01G225700 chr4B 96.835 316 10 0 2980 3295 615329513 615329828 2.250000e-146 529
41 TraesCS2B01G225700 chr4B 96.835 316 8 2 2980 3295 402908822 402908509 8.100000e-146 527
42 TraesCS2B01G225700 chr4B 96.262 321 11 1 2975 3295 520492502 520492183 2.910000e-145 525
43 TraesCS2B01G225700 chr3B 98.697 307 4 0 2989 3295 42635413 42635107 2.240000e-151 545
44 TraesCS2B01G225700 chr3B 98.697 307 4 0 2989 3295 42674843 42674537 2.240000e-151 545
45 TraesCS2B01G225700 chr3B 95.575 339 12 2 2958 3295 77074835 77074499 1.040000e-149 540
46 TraesCS2B01G225700 chrUn 98.361 305 5 0 2991 3295 42279723 42279419 1.350000e-148 536
47 TraesCS2B01G225700 chrUn 98.361 305 5 0 2991 3295 178217200 178216896 1.350000e-148 536
48 TraesCS2B01G225700 chrUn 97.143 315 8 1 2981 3295 42286630 42286317 6.260000e-147 531
49 TraesCS2B01G225700 chrUn 98.033 305 6 0 2991 3295 215463377 215463681 6.260000e-147 531
50 TraesCS2B01G225700 chrUn 97.720 307 7 0 2989 3295 59612722 59613028 2.250000e-146 529
51 TraesCS2B01G225700 chrUn 97.125 313 7 2 2984 3295 129216666 129216355 8.100000e-146 527
52 TraesCS2B01G225700 chrUn 97.411 309 8 0 2987 3295 274627592 274627284 8.100000e-146 527
53 TraesCS2B01G225700 chrUn 97.419 310 7 1 2987 3295 292007158 292006849 8.100000e-146 527
54 TraesCS2B01G225700 chrUn 97.419 310 7 1 2987 3295 312415247 312414938 8.100000e-146 527
55 TraesCS2B01G225700 chr1A 98.361 305 5 0 2991 3295 287889200 287888896 1.350000e-148 536
56 TraesCS2B01G225700 chr1A 98.361 305 5 0 2991 3295 575374095 575373791 1.350000e-148 536


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 TraesCS2B01G225700 chr2B 216443302 216446596 3294 True 2876.0 4372 100.0000 1 3295 2 chr2B.!!$R9 3294
1 TraesCS2B01G225700 chr2B 359186503 359188563 2060 False 3145.0 3145 94.2260 929 2988 1 chr2B.!!$F2 2059
2 TraesCS2B01G225700 chr2B 381088996 381091047 2051 False 3123.0 3123 94.1150 933 2988 1 chr2B.!!$F3 2055
3 TraesCS2B01G225700 chr2B 163951960 163954012 2052 True 3118.0 3118 94.0630 932 2986 1 chr2B.!!$R2 2054
4 TraesCS2B01G225700 chr2B 464346300 464348357 2057 True 3097.0 3097 93.8320 929 2987 1 chr2B.!!$R6 2058
5 TraesCS2B01G225700 chr2B 550581195 550581938 743 False 1147.0 1147 94.4890 1 744 1 chr2B.!!$F4 743
6 TraesCS2B01G225700 chr2B 164590700 164591445 745 True 1133.0 1133 94.1020 1 745 1 chr2B.!!$R3 744
7 TraesCS2B01G225700 chr2B 283104390 283105136 746 False 1131.0 1131 93.9760 1 747 1 chr2B.!!$F1 746
8 TraesCS2B01G225700 chr2B 524553458 524554204 746 True 1114.0 1114 93.5740 1 747 1 chr2B.!!$R7 746
9 TraesCS2B01G225700 chr1B 303745826 303748662 2836 True 2134.0 3134 94.1425 1 2988 2 chr1B.!!$R3 2987
10 TraesCS2B01G225700 chr1B 525542444 525543189 745 True 1134.0 1134 94.1100 1 747 1 chr1B.!!$R2 746
11 TraesCS2B01G225700 chr5B 324881987 324884046 2059 True 3114.0 3114 93.9840 932 2988 1 chr5B.!!$R3 2056
12 TraesCS2B01G225700 chr5B 464749653 464751712 2059 False 3079.0 3079 93.6410 929 2988 1 chr5B.!!$F2 2059
13 TraesCS2B01G225700 chr6B 530813484 530815539 2055 True 3094.0 3094 93.8260 932 2988 1 chr6B.!!$R2 2056
14 TraesCS2B01G225700 chr6B 373829167 373832003 2836 True 2121.5 3081 94.2555 1 2988 2 chr6B.!!$R4 2987
15 TraesCS2B01G225700 chr6B 50271703 50272448 745 True 1146.0 1146 94.3780 1 747 1 chr6B.!!$R1 746
16 TraesCS2B01G225700 chr4B 434147071 434147817 746 False 1114.0 1114 93.5830 1 747 1 chr4B.!!$F2 746

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
152 156 0.250513 GGCGGAGAGAATCAGGTGTT 59.749 55.000 0.00 0.00 37.82 3.32 F
1082 1086 1.002868 TGCTCAGAGGCTTTGAGGC 60.003 57.895 29.61 22.73 41.82 4.70 F
1490 1497 1.151668 CCAAGGAACAAGCTCGAGTG 58.848 55.000 15.13 7.93 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2106 2113 0.454600 CGTGCACCCTCTATACACGT 59.545 55.000 12.15 0.00 46.56 4.49 R
2159 2166 1.145738 ACAATGGTGGCCTCCATATCC 59.854 52.381 33.91 12.05 46.14 2.59 R
3248 3258 0.033109 GGCTTAGGATTGGGCCTTGT 60.033 55.000 4.53 0.00 41.20 3.16 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
152 156 0.250513 GGCGGAGAGAATCAGGTGTT 59.749 55.000 0.00 0.00 37.82 3.32
456 460 2.351276 GGGCGTCCTCACCATGTT 59.649 61.111 0.00 0.00 0.00 2.71
533 537 2.416972 GGTACTGCGTTTCTCCGAGATT 60.417 50.000 0.00 0.00 0.00 2.40
626 630 2.317973 CTCTGGAGATGATGGAGAGCA 58.682 52.381 0.00 0.00 0.00 4.26
723 727 1.736032 GCCAGAAGCGAATACGTCAGT 60.736 52.381 0.00 0.00 41.98 3.41
946 950 1.375396 TTTGATGTCCGGCCAGACG 60.375 57.895 14.38 0.00 39.77 4.18
984 988 4.862092 CGAGCTGCGCTGTCGGAT 62.862 66.667 21.99 4.08 39.88 4.18
990 994 2.587194 GCGCTGTCGGATGAGCAT 60.587 61.111 0.00 0.00 34.69 3.79
1082 1086 1.002868 TGCTCAGAGGCTTTGAGGC 60.003 57.895 29.61 22.73 41.82 4.70
1156 1163 4.366267 CTCCATATGGATAGTAGCCCCTT 58.634 47.826 24.73 0.00 44.46 3.95
1333 1340 1.959226 GGTGAACGAGCGGCTGAAA 60.959 57.895 7.50 0.00 0.00 2.69
1375 1382 9.595823 TGCTCTACTTTCCTTATTATGTTGTAC 57.404 33.333 0.00 0.00 0.00 2.90
1465 1472 2.750350 CCTGAGGGCGGAACTTGT 59.250 61.111 0.00 0.00 0.00 3.16
1487 1494 1.302511 GGCCAAGGAACAAGCTCGA 60.303 57.895 0.00 0.00 0.00 4.04
1490 1497 1.151668 CCAAGGAACAAGCTCGAGTG 58.848 55.000 15.13 7.93 0.00 3.51
1566 1573 3.178539 GCCGAAGCGAGGAAAAGG 58.821 61.111 0.00 0.00 0.00 3.11
1572 1579 2.159282 CGAAGCGAGGAAAAGGTAGCTA 60.159 50.000 0.00 0.00 34.24 3.32
1574 1581 3.528597 AGCGAGGAAAAGGTAGCTAAG 57.471 47.619 0.00 0.00 32.73 2.18
1581 1588 4.969359 AGGAAAAGGTAGCTAAGATGGCTA 59.031 41.667 0.00 0.00 40.74 3.93
1721 1728 1.302511 GCGGGAGGAGCTTCAACAA 60.303 57.895 0.00 0.00 0.00 2.83
1954 1961 2.301870 TGCCGTTAAGTGAGAAGATGGT 59.698 45.455 0.00 0.00 0.00 3.55
2106 2113 1.511305 GACGCCATGAGAAGGTCGA 59.489 57.895 0.00 0.00 32.57 4.20
2159 2166 2.220133 CCGCGTTAAATCCTATTGGACG 59.780 50.000 4.92 0.00 46.51 4.79
2312 2319 5.536554 AGTGACAAAGCGAATCATTGTAG 57.463 39.130 0.00 0.00 36.81 2.74
2314 2321 5.349817 AGTGACAAAGCGAATCATTGTAGAG 59.650 40.000 0.00 0.00 36.81 2.43
2409 2416 6.253013 GGCCGTTTTTATGTCTATGTGTAAC 58.747 40.000 0.00 0.00 37.35 2.50
2516 2523 2.747446 CAACGTCTTGGTCCATTAAGGG 59.253 50.000 0.00 0.00 38.24 3.95
2527 2534 1.202927 CCATTAAGGGGGTGATCGCAT 60.203 52.381 8.82 0.00 0.00 4.73
2637 2644 1.443802 TTTGCGTGCATCCGAATACA 58.556 45.000 0.24 0.00 0.00 2.29
2745 2752 1.338020 TCTCGCGCTGTATCATGACAT 59.662 47.619 5.56 0.00 0.00 3.06
2780 2787 3.660970 TCTCTACTGAGGTGCTCATCT 57.339 47.619 1.88 0.00 39.92 2.90
2898 2906 4.984161 CCAACATTTGACCAAAGACATGAC 59.016 41.667 0.00 0.00 33.32 3.06
2911 2921 1.135915 GACATGACTCGGAGCTGATGT 59.864 52.381 13.82 13.82 0.00 3.06
2934 2944 2.851263 TAAGGCCAAACTCATGACGT 57.149 45.000 5.01 0.00 0.00 4.34
2988 2998 4.154942 ACAGAAAATGGGCTGAAGAATGT 58.845 39.130 0.00 0.00 36.07 2.71
2989 2999 5.324409 ACAGAAAATGGGCTGAAGAATGTA 58.676 37.500 0.00 0.00 36.07 2.29
2990 3000 5.954150 ACAGAAAATGGGCTGAAGAATGTAT 59.046 36.000 0.00 0.00 36.07 2.29
2991 3001 6.438425 ACAGAAAATGGGCTGAAGAATGTATT 59.562 34.615 0.00 0.00 36.07 1.89
2992 3002 6.755141 CAGAAAATGGGCTGAAGAATGTATTG 59.245 38.462 0.00 0.00 34.06 1.90
2993 3003 5.603170 AAATGGGCTGAAGAATGTATTGG 57.397 39.130 0.00 0.00 0.00 3.16
2994 3004 4.524802 ATGGGCTGAAGAATGTATTGGA 57.475 40.909 0.00 0.00 0.00 3.53
2995 3005 4.314522 TGGGCTGAAGAATGTATTGGAA 57.685 40.909 0.00 0.00 0.00 3.53
2996 3006 4.671831 TGGGCTGAAGAATGTATTGGAAA 58.328 39.130 0.00 0.00 0.00 3.13
2997 3007 5.271598 TGGGCTGAAGAATGTATTGGAAAT 58.728 37.500 0.00 0.00 0.00 2.17
2998 3008 6.430864 TGGGCTGAAGAATGTATTGGAAATA 58.569 36.000 0.00 0.00 0.00 1.40
2999 3009 7.068702 TGGGCTGAAGAATGTATTGGAAATAT 58.931 34.615 0.00 0.00 0.00 1.28
3000 3010 7.014518 TGGGCTGAAGAATGTATTGGAAATATG 59.985 37.037 0.00 0.00 0.00 1.78
3001 3011 6.865205 GGCTGAAGAATGTATTGGAAATATGC 59.135 38.462 0.00 0.00 0.00 3.14
3002 3012 6.865205 GCTGAAGAATGTATTGGAAATATGCC 59.135 38.462 0.00 0.00 0.00 4.40
3003 3013 7.288810 TGAAGAATGTATTGGAAATATGCCC 57.711 36.000 0.00 0.00 0.00 5.36
3004 3014 7.068702 TGAAGAATGTATTGGAAATATGCCCT 58.931 34.615 0.00 0.00 0.00 5.19
3005 3015 8.224025 TGAAGAATGTATTGGAAATATGCCCTA 58.776 33.333 0.00 0.00 0.00 3.53
3006 3016 8.641498 AAGAATGTATTGGAAATATGCCCTAG 57.359 34.615 0.00 0.00 0.00 3.02
3007 3017 7.988937 AGAATGTATTGGAAATATGCCCTAGA 58.011 34.615 0.00 0.00 0.00 2.43
3008 3018 8.105829 AGAATGTATTGGAAATATGCCCTAGAG 58.894 37.037 0.00 0.00 0.00 2.43
3009 3019 6.126863 TGTATTGGAAATATGCCCTAGAGG 57.873 41.667 0.00 0.00 39.47 3.69
3059 3069 9.621629 TTATATTTCCTTGTTCATGATAACCGT 57.378 29.630 0.00 0.00 0.00 4.83
3060 3070 6.834168 ATTTCCTTGTTCATGATAACCGTT 57.166 33.333 0.00 0.00 0.00 4.44
3061 3071 6.642707 TTTCCTTGTTCATGATAACCGTTT 57.357 33.333 0.00 0.00 0.00 3.60
3062 3072 7.747155 TTTCCTTGTTCATGATAACCGTTTA 57.253 32.000 0.00 0.00 0.00 2.01
3063 3073 7.931578 TTCCTTGTTCATGATAACCGTTTAT 57.068 32.000 0.00 0.00 0.00 1.40
3064 3074 7.931578 TCCTTGTTCATGATAACCGTTTATT 57.068 32.000 0.00 0.00 0.00 1.40
3065 3075 9.451002 TTCCTTGTTCATGATAACCGTTTATTA 57.549 29.630 0.00 0.00 0.00 0.98
3066 3076 9.621629 TCCTTGTTCATGATAACCGTTTATTAT 57.378 29.630 0.00 0.00 0.00 1.28
3067 3077 9.878599 CCTTGTTCATGATAACCGTTTATTATC 57.121 33.333 0.00 0.00 38.83 1.75
3068 3078 9.878599 CTTGTTCATGATAACCGTTTATTATCC 57.121 33.333 0.00 0.00 37.97 2.59
3069 3079 8.966069 TGTTCATGATAACCGTTTATTATCCA 57.034 30.769 0.00 0.00 37.97 3.41
3070 3080 9.567776 TGTTCATGATAACCGTTTATTATCCAT 57.432 29.630 0.00 0.00 37.97 3.41
3071 3081 9.825972 GTTCATGATAACCGTTTATTATCCATG 57.174 33.333 0.00 6.03 37.97 3.66
3072 3082 8.039603 TCATGATAACCGTTTATTATCCATGC 57.960 34.615 7.04 0.00 37.97 4.06
3073 3083 7.882791 TCATGATAACCGTTTATTATCCATGCT 59.117 33.333 7.04 0.00 37.97 3.79
3074 3084 9.161629 CATGATAACCGTTTATTATCCATGCTA 57.838 33.333 0.00 0.00 37.97 3.49
3075 3085 9.905713 ATGATAACCGTTTATTATCCATGCTAT 57.094 29.630 0.00 0.00 37.97 2.97
3081 3091 9.515226 ACCGTTTATTATCCATGCTATAATTGT 57.485 29.630 13.58 0.00 32.93 2.71
3105 3115 9.987272 TGTATTGATAGGAAACTCAGATACATG 57.013 33.333 0.00 0.00 43.67 3.21
3106 3116 9.988815 GTATTGATAGGAAACTCAGATACATGT 57.011 33.333 2.69 2.69 43.67 3.21
3107 3117 8.899427 ATTGATAGGAAACTCAGATACATGTG 57.101 34.615 9.11 0.00 43.67 3.21
3108 3118 7.423844 TGATAGGAAACTCAGATACATGTGT 57.576 36.000 9.11 0.10 43.67 3.72
3109 3119 7.267857 TGATAGGAAACTCAGATACATGTGTG 58.732 38.462 9.11 3.44 43.67 3.82
3110 3120 4.836825 AGGAAACTCAGATACATGTGTGG 58.163 43.478 9.11 0.00 32.90 4.17
3111 3121 4.532126 AGGAAACTCAGATACATGTGTGGA 59.468 41.667 9.11 1.00 32.90 4.02
3112 3122 5.190528 AGGAAACTCAGATACATGTGTGGAT 59.809 40.000 9.11 0.00 32.90 3.41
3113 3123 6.384015 AGGAAACTCAGATACATGTGTGGATA 59.616 38.462 9.11 0.00 32.90 2.59
3114 3124 6.480320 GGAAACTCAGATACATGTGTGGATAC 59.520 42.308 9.11 0.00 0.00 2.24
3130 3140 5.692115 TGGATACATAGACAACACCATGT 57.308 39.130 0.00 0.00 46.17 3.21
3131 3141 5.670485 TGGATACATAGACAACACCATGTC 58.330 41.667 0.00 0.00 45.97 3.06
3132 3142 5.396324 TGGATACATAGACAACACCATGTCC 60.396 44.000 3.95 0.00 46.44 4.02
3133 3143 8.319752 TGGATACATAGACAACACCATGTCCC 62.320 46.154 3.95 0.00 46.44 4.46
3139 3149 4.546829 GACAACACCATGTCCCTAGTAA 57.453 45.455 0.00 0.00 43.11 2.24
3140 3150 4.504858 GACAACACCATGTCCCTAGTAAG 58.495 47.826 0.00 0.00 43.11 2.34
3141 3151 3.270877 CAACACCATGTCCCTAGTAAGC 58.729 50.000 0.00 0.00 0.00 3.09
3142 3152 1.838077 ACACCATGTCCCTAGTAAGCC 59.162 52.381 0.00 0.00 0.00 4.35
3143 3153 2.119495 CACCATGTCCCTAGTAAGCCT 58.881 52.381 0.00 0.00 0.00 4.58
3144 3154 2.103263 CACCATGTCCCTAGTAAGCCTC 59.897 54.545 0.00 0.00 0.00 4.70
3145 3155 2.022918 ACCATGTCCCTAGTAAGCCTCT 60.023 50.000 0.00 0.00 0.00 3.69
3146 3156 3.206866 ACCATGTCCCTAGTAAGCCTCTA 59.793 47.826 0.00 0.00 0.00 2.43
3147 3157 3.829601 CCATGTCCCTAGTAAGCCTCTAG 59.170 52.174 0.00 0.00 35.86 2.43
3148 3158 4.475345 CATGTCCCTAGTAAGCCTCTAGT 58.525 47.826 0.00 0.00 34.72 2.57
3149 3159 5.457778 CCATGTCCCTAGTAAGCCTCTAGTA 60.458 48.000 0.00 0.00 34.72 1.82
3150 3160 5.307544 TGTCCCTAGTAAGCCTCTAGTAG 57.692 47.826 0.00 0.00 34.72 2.57
3151 3161 4.973856 TGTCCCTAGTAAGCCTCTAGTAGA 59.026 45.833 0.00 0.00 34.72 2.59
3152 3162 5.163216 TGTCCCTAGTAAGCCTCTAGTAGAC 60.163 48.000 0.00 14.07 37.38 2.59
3153 3163 5.072193 GTCCCTAGTAAGCCTCTAGTAGACT 59.928 48.000 0.00 0.00 35.88 3.24
3154 3164 6.269769 GTCCCTAGTAAGCCTCTAGTAGACTA 59.730 46.154 0.00 0.00 35.88 2.59
3155 3165 6.497954 TCCCTAGTAAGCCTCTAGTAGACTAG 59.502 46.154 10.00 10.00 45.57 2.57
3156 3166 6.168389 CCTAGTAAGCCTCTAGTAGACTAGC 58.832 48.000 11.22 8.98 44.24 3.42
3157 3167 5.899631 AGTAAGCCTCTAGTAGACTAGCT 57.100 43.478 11.22 8.23 44.24 3.32
3158 3168 5.861727 AGTAAGCCTCTAGTAGACTAGCTC 58.138 45.833 11.22 3.98 44.24 4.09
3159 3169 3.396260 AGCCTCTAGTAGACTAGCTCG 57.604 52.381 11.22 0.00 44.24 5.03
3160 3170 2.701951 AGCCTCTAGTAGACTAGCTCGT 59.298 50.000 11.22 0.00 44.24 4.18
3161 3171 3.135167 AGCCTCTAGTAGACTAGCTCGTT 59.865 47.826 11.22 0.00 44.24 3.85
3162 3172 3.249080 GCCTCTAGTAGACTAGCTCGTTG 59.751 52.174 11.22 0.00 44.24 4.10
3163 3173 4.695396 CCTCTAGTAGACTAGCTCGTTGA 58.305 47.826 11.22 0.00 44.24 3.18
3164 3174 5.302360 CCTCTAGTAGACTAGCTCGTTGAT 58.698 45.833 11.22 0.00 44.24 2.57
3165 3175 5.407387 CCTCTAGTAGACTAGCTCGTTGATC 59.593 48.000 11.22 0.00 44.24 2.92
3166 3176 5.915175 TCTAGTAGACTAGCTCGTTGATCA 58.085 41.667 11.22 0.00 44.24 2.92
3167 3177 6.346896 TCTAGTAGACTAGCTCGTTGATCAA 58.653 40.000 3.38 3.38 44.24 2.57
3168 3178 6.993308 TCTAGTAGACTAGCTCGTTGATCAAT 59.007 38.462 12.12 0.00 44.24 2.57
3169 3179 8.148999 TCTAGTAGACTAGCTCGTTGATCAATA 58.851 37.037 12.12 2.38 44.24 1.90
3170 3180 7.197071 AGTAGACTAGCTCGTTGATCAATAG 57.803 40.000 12.12 13.07 0.00 1.73
3171 3181 6.993308 AGTAGACTAGCTCGTTGATCAATAGA 59.007 38.462 19.51 16.55 0.00 1.98
3172 3182 6.892658 AGACTAGCTCGTTGATCAATAGAT 57.107 37.500 19.51 16.66 37.13 1.98
3173 3183 6.676950 AGACTAGCTCGTTGATCAATAGATG 58.323 40.000 19.51 12.48 33.72 2.90
3174 3184 5.777802 ACTAGCTCGTTGATCAATAGATGG 58.222 41.667 19.51 17.62 33.72 3.51
3175 3185 4.679373 AGCTCGTTGATCAATAGATGGT 57.321 40.909 19.51 14.02 33.72 3.55
3176 3186 5.028549 AGCTCGTTGATCAATAGATGGTT 57.971 39.130 19.51 6.05 33.72 3.67
3177 3187 6.161855 AGCTCGTTGATCAATAGATGGTTA 57.838 37.500 19.51 0.00 33.72 2.85
3178 3188 5.986135 AGCTCGTTGATCAATAGATGGTTAC 59.014 40.000 19.51 1.79 33.72 2.50
3179 3189 5.107837 GCTCGTTGATCAATAGATGGTTACG 60.108 44.000 19.51 12.22 33.72 3.18
3180 3190 5.286438 TCGTTGATCAATAGATGGTTACGG 58.714 41.667 12.12 0.00 33.72 4.02
3181 3191 5.047847 CGTTGATCAATAGATGGTTACGGT 58.952 41.667 12.12 0.00 33.72 4.83
3182 3192 5.522460 CGTTGATCAATAGATGGTTACGGTT 59.478 40.000 12.12 0.00 33.72 4.44
3183 3193 6.036735 CGTTGATCAATAGATGGTTACGGTTT 59.963 38.462 12.12 0.00 33.72 3.27
3184 3194 7.407337 GTTGATCAATAGATGGTTACGGTTTC 58.593 38.462 12.12 0.00 33.72 2.78
3185 3195 6.053005 TGATCAATAGATGGTTACGGTTTCC 58.947 40.000 0.00 0.00 33.72 3.13
3186 3196 5.687166 TCAATAGATGGTTACGGTTTCCT 57.313 39.130 0.00 0.00 0.00 3.36
3187 3197 5.424757 TCAATAGATGGTTACGGTTTCCTG 58.575 41.667 0.00 0.00 0.00 3.86
3188 3198 5.188163 TCAATAGATGGTTACGGTTTCCTGA 59.812 40.000 0.00 0.00 0.00 3.86
3189 3199 3.329929 AGATGGTTACGGTTTCCTGAC 57.670 47.619 0.00 0.00 0.00 3.51
3190 3200 2.027469 AGATGGTTACGGTTTCCTGACC 60.027 50.000 0.00 0.00 36.31 4.02
3191 3201 1.129917 TGGTTACGGTTTCCTGACCA 58.870 50.000 0.00 0.00 39.78 4.02
3192 3202 1.700739 TGGTTACGGTTTCCTGACCAT 59.299 47.619 0.00 0.00 39.78 3.55
3193 3203 2.081462 GGTTACGGTTTCCTGACCATG 58.919 52.381 0.00 0.00 39.78 3.66
3194 3204 2.081462 GTTACGGTTTCCTGACCATGG 58.919 52.381 11.19 11.19 39.78 3.66
3195 3205 1.646912 TACGGTTTCCTGACCATGGA 58.353 50.000 21.47 0.00 39.78 3.41
3196 3206 0.036306 ACGGTTTCCTGACCATGGAC 59.964 55.000 21.47 13.94 39.78 4.02
3197 3207 0.036164 CGGTTTCCTGACCATGGACA 59.964 55.000 21.47 18.47 39.78 4.02
3198 3208 1.340017 CGGTTTCCTGACCATGGACAT 60.340 52.381 21.47 0.00 39.78 3.06
3199 3209 2.807676 GGTTTCCTGACCATGGACATT 58.192 47.619 21.47 0.00 39.57 2.71
3200 3210 2.493278 GGTTTCCTGACCATGGACATTG 59.507 50.000 21.47 12.72 39.57 2.82
3201 3211 2.493278 GTTTCCTGACCATGGACATTGG 59.507 50.000 21.47 16.85 32.65 3.16
3202 3212 1.667595 TCCTGACCATGGACATTGGA 58.332 50.000 21.47 18.93 0.00 3.53
3203 3213 2.207988 TCCTGACCATGGACATTGGAT 58.792 47.619 21.47 0.00 0.00 3.41
3204 3214 2.092267 TCCTGACCATGGACATTGGATG 60.092 50.000 21.47 5.31 0.00 3.51
3232 3242 8.012151 GTTGATAACGAGATCACATCATTAGG 57.988 38.462 0.00 0.00 35.56 2.69
3233 3243 7.524717 TGATAACGAGATCACATCATTAGGA 57.475 36.000 0.00 0.00 30.75 2.94
3234 3244 7.597386 TGATAACGAGATCACATCATTAGGAG 58.403 38.462 0.00 0.00 30.75 3.69
3235 3245 7.448469 TGATAACGAGATCACATCATTAGGAGA 59.552 37.037 0.00 0.00 30.75 3.71
3236 3246 6.471233 AACGAGATCACATCATTAGGAGAA 57.529 37.500 0.00 0.00 0.00 2.87
3237 3247 6.662865 ACGAGATCACATCATTAGGAGAAT 57.337 37.500 0.00 0.00 0.00 2.40
3238 3248 6.453943 ACGAGATCACATCATTAGGAGAATG 58.546 40.000 0.00 0.00 0.00 2.67
3239 3249 6.266330 ACGAGATCACATCATTAGGAGAATGA 59.734 38.462 2.66 2.66 40.50 2.57
3240 3250 7.039152 ACGAGATCACATCATTAGGAGAATGAT 60.039 37.037 6.90 6.90 45.40 2.45
3248 3258 6.752285 TCATTAGGAGAATGATGTGATGGA 57.248 37.500 0.00 0.00 32.21 3.41
3249 3259 6.528321 TCATTAGGAGAATGATGTGATGGAC 58.472 40.000 0.00 0.00 32.21 4.02
3250 3260 5.955961 TTAGGAGAATGATGTGATGGACA 57.044 39.130 0.00 0.00 39.53 4.02
3251 3261 4.849813 AGGAGAATGATGTGATGGACAA 57.150 40.909 0.00 0.00 38.36 3.18
3252 3262 4.778579 AGGAGAATGATGTGATGGACAAG 58.221 43.478 0.00 0.00 38.36 3.16
3253 3263 3.881688 GGAGAATGATGTGATGGACAAGG 59.118 47.826 0.00 0.00 38.36 3.61
3254 3264 3.285484 AGAATGATGTGATGGACAAGGC 58.715 45.455 0.00 0.00 38.36 4.35
3255 3265 2.062971 ATGATGTGATGGACAAGGCC 57.937 50.000 0.00 0.00 38.36 5.19
3256 3266 0.034186 TGATGTGATGGACAAGGCCC 60.034 55.000 0.00 0.00 38.36 5.80
3257 3267 0.034186 GATGTGATGGACAAGGCCCA 60.034 55.000 0.00 0.00 38.36 5.36
3258 3268 0.409092 ATGTGATGGACAAGGCCCAA 59.591 50.000 0.00 0.00 38.36 4.12
3259 3269 0.409092 TGTGATGGACAAGGCCCAAT 59.591 50.000 0.00 0.00 37.22 3.16
3260 3270 1.106285 GTGATGGACAAGGCCCAATC 58.894 55.000 0.00 0.00 37.22 2.67
3261 3271 0.033208 TGATGGACAAGGCCCAATCC 60.033 55.000 0.00 4.18 37.22 3.01
3262 3272 0.259938 GATGGACAAGGCCCAATCCT 59.740 55.000 15.77 4.09 37.22 3.24
3263 3273 1.494721 GATGGACAAGGCCCAATCCTA 59.505 52.381 15.77 5.27 37.22 2.94
3264 3274 1.377690 TGGACAAGGCCCAATCCTAA 58.622 50.000 15.77 0.00 34.82 2.69
3265 3275 1.284785 TGGACAAGGCCCAATCCTAAG 59.715 52.381 15.77 0.00 34.82 2.18
3266 3276 1.393603 GACAAGGCCCAATCCTAAGC 58.606 55.000 0.00 0.00 34.82 3.09
3267 3277 0.033109 ACAAGGCCCAATCCTAAGCC 60.033 55.000 0.00 0.00 46.13 4.35
3271 3281 0.250945 GGCCCAATCCTAAGCCTAGC 60.251 60.000 0.00 0.00 42.34 3.42
3272 3282 0.474184 GCCCAATCCTAAGCCTAGCA 59.526 55.000 0.00 0.00 0.00 3.49
3273 3283 1.815795 GCCCAATCCTAAGCCTAGCAC 60.816 57.143 0.00 0.00 0.00 4.40
3274 3284 1.490490 CCCAATCCTAAGCCTAGCACA 59.510 52.381 0.00 0.00 0.00 4.57
3275 3285 2.092429 CCCAATCCTAAGCCTAGCACAA 60.092 50.000 0.00 0.00 0.00 3.33
3276 3286 3.620488 CCAATCCTAAGCCTAGCACAAA 58.380 45.455 0.00 0.00 0.00 2.83
3277 3287 3.629398 CCAATCCTAAGCCTAGCACAAAG 59.371 47.826 0.00 0.00 0.00 2.77
3278 3288 4.517285 CAATCCTAAGCCTAGCACAAAGA 58.483 43.478 0.00 0.00 0.00 2.52
3279 3289 5.128919 CAATCCTAAGCCTAGCACAAAGAT 58.871 41.667 0.00 0.00 0.00 2.40
3280 3290 4.408182 TCCTAAGCCTAGCACAAAGATC 57.592 45.455 0.00 0.00 0.00 2.75
3281 3291 3.126831 CCTAAGCCTAGCACAAAGATCG 58.873 50.000 0.00 0.00 0.00 3.69
3282 3292 2.770164 AAGCCTAGCACAAAGATCGT 57.230 45.000 0.00 0.00 0.00 3.73
3283 3293 2.015736 AGCCTAGCACAAAGATCGTG 57.984 50.000 0.00 0.00 37.43 4.35
3284 3294 1.276421 AGCCTAGCACAAAGATCGTGT 59.724 47.619 0.00 0.00 36.71 4.49
3285 3295 2.496070 AGCCTAGCACAAAGATCGTGTA 59.504 45.455 4.96 0.00 36.71 2.90
3286 3296 2.860735 GCCTAGCACAAAGATCGTGTAG 59.139 50.000 4.96 0.78 36.71 2.74
3287 3297 3.676324 GCCTAGCACAAAGATCGTGTAGT 60.676 47.826 4.96 0.00 36.71 2.73
3288 3298 4.495422 CCTAGCACAAAGATCGTGTAGTT 58.505 43.478 4.96 2.32 36.71 2.24
3289 3299 4.563184 CCTAGCACAAAGATCGTGTAGTTC 59.437 45.833 4.96 0.00 36.71 3.01
3290 3300 2.987149 AGCACAAAGATCGTGTAGTTCG 59.013 45.455 4.96 0.00 36.71 3.95
3291 3301 2.729882 GCACAAAGATCGTGTAGTTCGT 59.270 45.455 4.96 0.00 36.71 3.85
3292 3302 3.916172 GCACAAAGATCGTGTAGTTCGTA 59.084 43.478 4.96 0.00 36.71 3.43
3293 3303 4.561606 GCACAAAGATCGTGTAGTTCGTAT 59.438 41.667 4.96 0.00 36.71 3.06
3294 3304 5.498700 GCACAAAGATCGTGTAGTTCGTATG 60.499 44.000 4.96 0.00 36.71 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
308 312 1.228925 CTCCCCGACTATCCTCCCC 60.229 68.421 0.00 0.00 0.00 4.81
486 490 6.417191 TGAATTAACGATTAACTCACAGCC 57.583 37.500 0.00 0.00 27.62 4.85
533 537 5.941058 TGCAAAAGACGAATCCTGGTTATTA 59.059 36.000 0.00 0.00 0.00 0.98
626 630 1.539124 GAGAGGTGGGTGGGGTCTT 60.539 63.158 0.00 0.00 0.00 3.01
942 946 0.889306 GAAGGCCTGTCAGTACGTCT 59.111 55.000 5.69 0.00 0.00 4.18
946 950 1.205893 CTCCAGAAGGCCTGTCAGTAC 59.794 57.143 5.69 0.00 41.33 2.73
1156 1163 1.553690 GGGCAGGCAACCAGAGTCTA 61.554 60.000 0.00 0.00 37.17 2.59
1375 1382 3.582998 TGCCCCTCTCATATTTTCCTG 57.417 47.619 0.00 0.00 0.00 3.86
1465 1472 1.228552 GCTTGTTCCTTGGCCTGGA 60.229 57.895 12.98 12.98 0.00 3.86
1487 1494 3.437795 GCAGCCGCATTGCTCACT 61.438 61.111 7.12 0.00 40.32 3.41
1566 1573 5.011125 TCAACTCCATAGCCATCTTAGCTAC 59.989 44.000 0.00 0.00 45.16 3.58
1572 1579 6.628844 GCATTTTTCAACTCCATAGCCATCTT 60.629 38.462 0.00 0.00 0.00 2.40
1574 1581 5.045872 GCATTTTTCAACTCCATAGCCATC 58.954 41.667 0.00 0.00 0.00 3.51
1581 1588 1.066929 GGCGGCATTTTTCAACTCCAT 60.067 47.619 3.07 0.00 0.00 3.41
1613 1620 6.784031 AGCCTTATTCTTCTTTTCAAGGAGA 58.216 36.000 2.43 0.00 41.42 3.71
1931 1938 3.368427 CCATCTTCTCACTTAACGGCAGA 60.368 47.826 0.00 0.00 0.00 4.26
1954 1961 2.472695 ATGAAGCTCCGCTACAACAA 57.527 45.000 0.00 0.00 38.25 2.83
2106 2113 0.454600 CGTGCACCCTCTATACACGT 59.545 55.000 12.15 0.00 46.56 4.49
2159 2166 1.145738 ACAATGGTGGCCTCCATATCC 59.854 52.381 33.91 12.05 46.14 2.59
2312 2319 9.455847 GCCTCATAATCAAAATAACATTGTCTC 57.544 33.333 0.00 0.00 0.00 3.36
2409 2416 3.430218 CCAACGACTGCTAACTTTCAGAG 59.570 47.826 0.00 0.00 34.57 3.35
2527 2534 1.180456 TCCGGTTGCCTAGTTCGACA 61.180 55.000 0.00 0.00 0.00 4.35
2637 2644 1.594293 GCCATGTACATACGCGCCT 60.594 57.895 8.32 0.00 0.00 5.52
2745 2752 4.750098 CAGTAGAGAAAGCCGAAAACTGAA 59.250 41.667 0.00 0.00 36.13 3.02
2780 2787 2.733956 GATTGTGCCCTGGTTATTCCA 58.266 47.619 0.00 0.00 45.01 3.53
2898 2906 4.440802 GGCCTTATATACATCAGCTCCGAG 60.441 50.000 0.00 0.00 0.00 4.63
2911 2921 6.169557 ACGTCATGAGTTTGGCCTTATATA 57.830 37.500 3.32 0.00 0.00 0.86
2934 2944 1.843368 ATACCTTCGGGAGTGTTCGA 58.157 50.000 0.00 0.00 38.77 3.71
3033 3043 9.621629 ACGGTTATCATGAACAAGGAAATATAA 57.378 29.630 0.00 0.00 0.00 0.98
3034 3044 9.621629 AACGGTTATCATGAACAAGGAAATATA 57.378 29.630 0.00 0.00 0.00 0.86
3035 3045 8.519799 AACGGTTATCATGAACAAGGAAATAT 57.480 30.769 0.00 0.00 0.00 1.28
3036 3046 7.931578 AACGGTTATCATGAACAAGGAAATA 57.068 32.000 0.00 0.00 0.00 1.40
3037 3047 6.834168 AACGGTTATCATGAACAAGGAAAT 57.166 33.333 0.00 0.00 0.00 2.17
3038 3048 6.642707 AAACGGTTATCATGAACAAGGAAA 57.357 33.333 0.00 0.00 0.00 3.13
3039 3049 7.931578 ATAAACGGTTATCATGAACAAGGAA 57.068 32.000 0.00 0.00 0.00 3.36
3040 3050 7.931578 AATAAACGGTTATCATGAACAAGGA 57.068 32.000 6.10 0.00 0.00 3.36
3041 3051 9.878599 GATAATAAACGGTTATCATGAACAAGG 57.121 33.333 6.10 0.00 38.08 3.61
3042 3052 9.878599 GGATAATAAACGGTTATCATGAACAAG 57.121 33.333 6.10 0.00 39.29 3.16
3043 3053 9.397280 TGGATAATAAACGGTTATCATGAACAA 57.603 29.630 6.10 0.00 39.29 2.83
3044 3054 8.966069 TGGATAATAAACGGTTATCATGAACA 57.034 30.769 6.10 0.00 39.29 3.18
3045 3055 9.825972 CATGGATAATAAACGGTTATCATGAAC 57.174 33.333 20.10 6.31 39.29 3.18
3046 3056 8.511321 GCATGGATAATAAACGGTTATCATGAA 58.489 33.333 25.33 8.04 39.29 2.57
3047 3057 7.882791 AGCATGGATAATAAACGGTTATCATGA 59.117 33.333 25.33 0.00 39.29 3.07
3048 3058 8.044060 AGCATGGATAATAAACGGTTATCATG 57.956 34.615 20.31 20.31 39.29 3.07
3049 3059 9.905713 ATAGCATGGATAATAAACGGTTATCAT 57.094 29.630 6.10 0.00 39.29 2.45
3055 3065 9.515226 ACAATTATAGCATGGATAATAAACGGT 57.485 29.630 0.00 0.00 30.86 4.83
3079 3089 9.987272 CATGTATCTGAGTTTCCTATCAATACA 57.013 33.333 0.00 0.00 35.88 2.29
3080 3090 9.988815 ACATGTATCTGAGTTTCCTATCAATAC 57.011 33.333 0.00 0.00 0.00 1.89
3081 3091 9.987272 CACATGTATCTGAGTTTCCTATCAATA 57.013 33.333 0.00 0.00 0.00 1.90
3082 3092 8.489489 ACACATGTATCTGAGTTTCCTATCAAT 58.511 33.333 0.00 0.00 0.00 2.57
3083 3093 7.765819 CACACATGTATCTGAGTTTCCTATCAA 59.234 37.037 0.00 0.00 0.00 2.57
3084 3094 7.267857 CACACATGTATCTGAGTTTCCTATCA 58.732 38.462 0.00 0.00 0.00 2.15
3085 3095 6.703607 CCACACATGTATCTGAGTTTCCTATC 59.296 42.308 0.00 0.00 0.00 2.08
3086 3096 6.384015 TCCACACATGTATCTGAGTTTCCTAT 59.616 38.462 0.00 0.00 0.00 2.57
3087 3097 5.719563 TCCACACATGTATCTGAGTTTCCTA 59.280 40.000 0.00 0.00 0.00 2.94
3088 3098 4.532126 TCCACACATGTATCTGAGTTTCCT 59.468 41.667 0.00 0.00 0.00 3.36
3089 3099 4.832248 TCCACACATGTATCTGAGTTTCC 58.168 43.478 0.00 0.00 0.00 3.13
3090 3100 7.041721 TGTATCCACACATGTATCTGAGTTTC 58.958 38.462 0.00 0.00 0.00 2.78
3091 3101 6.946340 TGTATCCACACATGTATCTGAGTTT 58.054 36.000 0.00 0.00 0.00 2.66
3092 3102 6.544928 TGTATCCACACATGTATCTGAGTT 57.455 37.500 0.00 0.00 0.00 3.01
3093 3103 6.737720 ATGTATCCACACATGTATCTGAGT 57.262 37.500 0.00 0.00 37.74 3.41
3094 3104 8.026026 GTCTATGTATCCACACATGTATCTGAG 58.974 40.741 0.00 0.00 39.46 3.35
3095 3105 7.505585 TGTCTATGTATCCACACATGTATCTGA 59.494 37.037 0.00 0.00 39.46 3.27
3096 3106 7.661040 TGTCTATGTATCCACACATGTATCTG 58.339 38.462 0.00 0.00 39.46 2.90
3097 3107 7.839680 TGTCTATGTATCCACACATGTATCT 57.160 36.000 0.00 0.00 39.46 1.98
3098 3108 7.926018 TGTTGTCTATGTATCCACACATGTATC 59.074 37.037 0.00 0.00 39.46 2.24
3099 3109 7.710907 GTGTTGTCTATGTATCCACACATGTAT 59.289 37.037 0.00 0.00 39.46 2.29
3100 3110 7.039270 GTGTTGTCTATGTATCCACACATGTA 58.961 38.462 0.00 0.00 39.46 2.29
3101 3111 5.874810 GTGTTGTCTATGTATCCACACATGT 59.125 40.000 0.00 0.00 39.46 3.21
3102 3112 5.294306 GGTGTTGTCTATGTATCCACACATG 59.706 44.000 0.00 0.00 39.46 3.21
3103 3113 5.045942 TGGTGTTGTCTATGTATCCACACAT 60.046 40.000 0.00 0.00 41.88 3.21
3104 3114 4.284746 TGGTGTTGTCTATGTATCCACACA 59.715 41.667 0.00 0.00 37.54 3.72
3105 3115 4.827692 TGGTGTTGTCTATGTATCCACAC 58.172 43.478 0.00 0.00 37.54 3.82
3106 3116 5.045942 ACATGGTGTTGTCTATGTATCCACA 60.046 40.000 0.00 0.00 39.52 4.17
3107 3117 5.428253 ACATGGTGTTGTCTATGTATCCAC 58.572 41.667 0.00 0.00 32.41 4.02
3108 3118 5.396324 GGACATGGTGTTGTCTATGTATCCA 60.396 44.000 0.00 0.00 44.39 3.41
3109 3119 5.057149 GGACATGGTGTTGTCTATGTATCC 58.943 45.833 0.00 0.00 44.39 2.59
3110 3120 5.057149 GGGACATGGTGTTGTCTATGTATC 58.943 45.833 0.00 0.00 44.39 2.24
3111 3121 4.721776 AGGGACATGGTGTTGTCTATGTAT 59.278 41.667 0.00 0.00 44.39 2.29
3112 3122 4.101114 AGGGACATGGTGTTGTCTATGTA 58.899 43.478 0.00 0.00 44.39 2.29
3113 3123 2.912956 AGGGACATGGTGTTGTCTATGT 59.087 45.455 0.00 0.00 44.39 2.29
3114 3124 3.634397 AGGGACATGGTGTTGTCTATG 57.366 47.619 0.00 0.00 44.39 2.23
3115 3125 4.362677 ACTAGGGACATGGTGTTGTCTAT 58.637 43.478 0.00 0.00 44.39 1.98
3116 3126 3.786553 ACTAGGGACATGGTGTTGTCTA 58.213 45.455 0.00 0.00 44.39 2.59
3117 3127 2.621070 ACTAGGGACATGGTGTTGTCT 58.379 47.619 0.00 0.00 44.39 3.41
3118 3128 4.504858 CTTACTAGGGACATGGTGTTGTC 58.495 47.826 0.00 0.00 44.27 3.18
3119 3129 3.307480 GCTTACTAGGGACATGGTGTTGT 60.307 47.826 0.00 0.00 0.00 3.32
3120 3130 3.270877 GCTTACTAGGGACATGGTGTTG 58.729 50.000 0.00 0.00 0.00 3.33
3121 3131 2.238898 GGCTTACTAGGGACATGGTGTT 59.761 50.000 0.00 0.00 0.00 3.32
3122 3132 1.838077 GGCTTACTAGGGACATGGTGT 59.162 52.381 0.00 0.00 0.00 4.16
3123 3133 2.103263 GAGGCTTACTAGGGACATGGTG 59.897 54.545 0.00 0.00 0.00 4.17
3124 3134 2.022918 AGAGGCTTACTAGGGACATGGT 60.023 50.000 0.00 0.00 0.00 3.55
3125 3135 2.683768 AGAGGCTTACTAGGGACATGG 58.316 52.381 0.00 0.00 0.00 3.66
3126 3136 4.475345 ACTAGAGGCTTACTAGGGACATG 58.525 47.826 13.13 0.00 40.86 3.21
3127 3137 4.817874 ACTAGAGGCTTACTAGGGACAT 57.182 45.455 13.13 0.00 40.86 3.06
3128 3138 4.973856 TCTACTAGAGGCTTACTAGGGACA 59.026 45.833 13.13 0.00 40.86 4.02
3129 3139 5.072193 AGTCTACTAGAGGCTTACTAGGGAC 59.928 48.000 19.14 19.14 36.38 4.46
3130 3140 5.226015 AGTCTACTAGAGGCTTACTAGGGA 58.774 45.833 13.13 8.71 36.38 4.20
3131 3141 5.571791 AGTCTACTAGAGGCTTACTAGGG 57.428 47.826 13.13 7.01 36.38 3.53
3132 3142 6.013984 AGCTAGTCTACTAGAGGCTTACTAGG 60.014 46.154 19.06 0.00 46.80 3.02
3133 3143 7.001099 AGCTAGTCTACTAGAGGCTTACTAG 57.999 44.000 19.06 8.32 46.80 2.57
3134 3144 6.294675 CGAGCTAGTCTACTAGAGGCTTACTA 60.295 46.154 19.06 0.00 46.80 1.82
3135 3145 5.510179 CGAGCTAGTCTACTAGAGGCTTACT 60.510 48.000 19.06 6.21 46.80 2.24
3136 3146 4.687483 CGAGCTAGTCTACTAGAGGCTTAC 59.313 50.000 19.06 1.91 46.80 2.34
3137 3147 4.344679 ACGAGCTAGTCTACTAGAGGCTTA 59.655 45.833 19.06 0.00 46.80 3.09
3138 3148 3.135167 ACGAGCTAGTCTACTAGAGGCTT 59.865 47.826 19.06 0.91 46.80 4.35
3139 3149 2.701951 ACGAGCTAGTCTACTAGAGGCT 59.298 50.000 19.06 10.83 46.80 4.58
3140 3150 3.116079 ACGAGCTAGTCTACTAGAGGC 57.884 52.381 19.06 6.55 46.80 4.70
3141 3151 4.695396 TCAACGAGCTAGTCTACTAGAGG 58.305 47.826 19.06 10.03 46.80 3.69
3142 3152 5.986741 TGATCAACGAGCTAGTCTACTAGAG 59.013 44.000 19.06 11.89 46.80 2.43
3143 3153 5.915175 TGATCAACGAGCTAGTCTACTAGA 58.085 41.667 19.06 0.00 46.80 2.43
3144 3154 6.606234 TTGATCAACGAGCTAGTCTACTAG 57.394 41.667 3.38 11.98 46.63 2.57
3145 3155 8.148999 TCTATTGATCAACGAGCTAGTCTACTA 58.851 37.037 11.07 0.00 0.00 1.82
3146 3156 6.993308 TCTATTGATCAACGAGCTAGTCTACT 59.007 38.462 11.07 0.00 0.00 2.57
3147 3157 7.192148 TCTATTGATCAACGAGCTAGTCTAC 57.808 40.000 11.07 0.00 0.00 2.59
3148 3158 7.094592 CCATCTATTGATCAACGAGCTAGTCTA 60.095 40.741 11.07 0.00 0.00 2.59
3149 3159 6.294453 CCATCTATTGATCAACGAGCTAGTCT 60.294 42.308 11.07 0.00 0.00 3.24
3150 3160 5.861251 CCATCTATTGATCAACGAGCTAGTC 59.139 44.000 11.07 0.00 0.00 2.59
3151 3161 5.303078 ACCATCTATTGATCAACGAGCTAGT 59.697 40.000 11.07 6.23 0.00 2.57
3152 3162 5.777802 ACCATCTATTGATCAACGAGCTAG 58.222 41.667 11.07 8.38 0.00 3.42
3153 3163 5.791336 ACCATCTATTGATCAACGAGCTA 57.209 39.130 11.07 0.00 0.00 3.32
3154 3164 4.679373 ACCATCTATTGATCAACGAGCT 57.321 40.909 11.07 0.00 0.00 4.09
3155 3165 5.107837 CGTAACCATCTATTGATCAACGAGC 60.108 44.000 11.07 0.00 0.00 5.03
3156 3166 5.402568 CCGTAACCATCTATTGATCAACGAG 59.597 44.000 11.07 11.28 0.00 4.18
3157 3167 5.163488 ACCGTAACCATCTATTGATCAACGA 60.163 40.000 11.07 10.80 0.00 3.85
3158 3168 5.047847 ACCGTAACCATCTATTGATCAACG 58.952 41.667 11.07 6.28 0.00 4.10
3159 3169 6.920569 AACCGTAACCATCTATTGATCAAC 57.079 37.500 11.07 0.00 0.00 3.18
3160 3170 6.540914 GGAAACCGTAACCATCTATTGATCAA 59.459 38.462 11.26 11.26 0.00 2.57
3161 3171 6.053005 GGAAACCGTAACCATCTATTGATCA 58.947 40.000 0.00 0.00 0.00 2.92
3162 3172 6.202954 CAGGAAACCGTAACCATCTATTGATC 59.797 42.308 0.00 0.00 0.00 2.92
3163 3173 6.055588 CAGGAAACCGTAACCATCTATTGAT 58.944 40.000 0.00 0.00 0.00 2.57
3164 3174 5.188163 TCAGGAAACCGTAACCATCTATTGA 59.812 40.000 0.00 0.00 0.00 2.57
3165 3175 5.293569 GTCAGGAAACCGTAACCATCTATTG 59.706 44.000 0.00 0.00 0.00 1.90
3166 3176 5.425630 GTCAGGAAACCGTAACCATCTATT 58.574 41.667 0.00 0.00 0.00 1.73
3167 3177 4.141779 GGTCAGGAAACCGTAACCATCTAT 60.142 45.833 0.00 0.00 0.00 1.98
3168 3178 3.196254 GGTCAGGAAACCGTAACCATCTA 59.804 47.826 0.00 0.00 0.00 1.98
3169 3179 2.027469 GGTCAGGAAACCGTAACCATCT 60.027 50.000 0.00 0.00 0.00 2.90
3170 3180 2.289819 TGGTCAGGAAACCGTAACCATC 60.290 50.000 0.00 0.00 42.62 3.51
3171 3181 1.700739 TGGTCAGGAAACCGTAACCAT 59.299 47.619 0.00 0.00 42.62 3.55
3172 3182 1.129917 TGGTCAGGAAACCGTAACCA 58.870 50.000 0.00 0.00 42.62 3.67
3173 3183 2.081462 CATGGTCAGGAAACCGTAACC 58.919 52.381 0.00 0.00 42.62 2.85
3174 3184 2.081462 CCATGGTCAGGAAACCGTAAC 58.919 52.381 2.57 0.00 42.62 2.50
3175 3185 1.979308 TCCATGGTCAGGAAACCGTAA 59.021 47.619 12.58 0.00 42.62 3.18
3176 3186 1.276989 GTCCATGGTCAGGAAACCGTA 59.723 52.381 12.58 0.00 42.62 4.02
3177 3187 0.036306 GTCCATGGTCAGGAAACCGT 59.964 55.000 12.58 0.00 42.62 4.83
3178 3188 0.036164 TGTCCATGGTCAGGAAACCG 59.964 55.000 12.58 0.00 42.62 4.44
3179 3189 2.493278 CAATGTCCATGGTCAGGAAACC 59.507 50.000 16.79 0.00 36.80 3.27
3180 3190 2.493278 CCAATGTCCATGGTCAGGAAAC 59.507 50.000 16.79 4.30 36.80 2.78
3181 3191 2.378208 TCCAATGTCCATGGTCAGGAAA 59.622 45.455 16.79 1.08 39.09 3.13
3182 3192 1.991813 TCCAATGTCCATGGTCAGGAA 59.008 47.619 16.79 0.75 39.09 3.36
3183 3193 1.667595 TCCAATGTCCATGGTCAGGA 58.332 50.000 16.79 15.06 39.09 3.86
3184 3194 2.304092 CATCCAATGTCCATGGTCAGG 58.696 52.381 16.79 13.14 39.09 3.86
3185 3195 3.008835 ACATCCAATGTCCATGGTCAG 57.991 47.619 16.79 4.75 39.92 3.51
3207 3217 7.867909 TCCTAATGATGTGATCTCGTTATCAAC 59.132 37.037 4.42 1.68 37.61 3.18
3208 3218 7.951591 TCCTAATGATGTGATCTCGTTATCAA 58.048 34.615 4.42 0.00 37.61 2.57
3209 3219 7.448469 TCTCCTAATGATGTGATCTCGTTATCA 59.552 37.037 0.00 0.00 33.48 2.15
3210 3220 7.821652 TCTCCTAATGATGTGATCTCGTTATC 58.178 38.462 0.00 0.00 0.00 1.75
3211 3221 7.767250 TCTCCTAATGATGTGATCTCGTTAT 57.233 36.000 0.00 0.00 0.00 1.89
3212 3222 7.582667 TTCTCCTAATGATGTGATCTCGTTA 57.417 36.000 0.00 0.00 0.00 3.18
3213 3223 6.471233 TTCTCCTAATGATGTGATCTCGTT 57.529 37.500 0.00 0.00 0.00 3.85
3214 3224 6.266330 TCATTCTCCTAATGATGTGATCTCGT 59.734 38.462 0.00 0.00 32.21 4.18
3215 3225 6.685657 TCATTCTCCTAATGATGTGATCTCG 58.314 40.000 0.00 0.00 32.21 4.04
3224 3234 7.166851 GTCCATCACATCATTCTCCTAATGAT 58.833 38.462 7.28 7.28 45.40 2.45
3225 3235 6.100134 TGTCCATCACATCATTCTCCTAATGA 59.900 38.462 3.13 3.13 40.50 2.57
3226 3236 6.293698 TGTCCATCACATCATTCTCCTAATG 58.706 40.000 0.00 0.00 0.00 1.90
3227 3237 6.505048 TGTCCATCACATCATTCTCCTAAT 57.495 37.500 0.00 0.00 0.00 1.73
3228 3238 5.955961 TGTCCATCACATCATTCTCCTAA 57.044 39.130 0.00 0.00 0.00 2.69
3229 3239 5.163269 CCTTGTCCATCACATCATTCTCCTA 60.163 44.000 0.00 0.00 33.90 2.94
3230 3240 4.384978 CCTTGTCCATCACATCATTCTCCT 60.385 45.833 0.00 0.00 33.90 3.69
3231 3241 3.881688 CCTTGTCCATCACATCATTCTCC 59.118 47.826 0.00 0.00 33.90 3.71
3232 3242 3.314635 GCCTTGTCCATCACATCATTCTC 59.685 47.826 0.00 0.00 33.90 2.87
3233 3243 3.285484 GCCTTGTCCATCACATCATTCT 58.715 45.455 0.00 0.00 33.90 2.40
3234 3244 2.360165 GGCCTTGTCCATCACATCATTC 59.640 50.000 0.00 0.00 33.90 2.67
3235 3245 2.381911 GGCCTTGTCCATCACATCATT 58.618 47.619 0.00 0.00 33.90 2.57
3236 3246 1.410648 GGGCCTTGTCCATCACATCAT 60.411 52.381 0.84 0.00 33.90 2.45
3237 3247 0.034186 GGGCCTTGTCCATCACATCA 60.034 55.000 0.84 0.00 33.90 3.07
3238 3248 0.034186 TGGGCCTTGTCCATCACATC 60.034 55.000 4.53 0.00 29.54 3.06
3239 3249 0.409092 TTGGGCCTTGTCCATCACAT 59.591 50.000 4.53 0.00 37.08 3.21
3240 3250 0.409092 ATTGGGCCTTGTCCATCACA 59.591 50.000 4.53 0.00 37.08 3.58
3241 3251 1.106285 GATTGGGCCTTGTCCATCAC 58.894 55.000 4.53 0.00 37.08 3.06
3242 3252 0.033208 GGATTGGGCCTTGTCCATCA 60.033 55.000 4.53 0.00 37.08 3.07
3243 3253 0.259938 AGGATTGGGCCTTGTCCATC 59.740 55.000 19.63 3.63 37.08 3.51
3244 3254 1.607225 TAGGATTGGGCCTTGTCCAT 58.393 50.000 19.63 10.43 37.08 3.41
3245 3255 1.284785 CTTAGGATTGGGCCTTGTCCA 59.715 52.381 19.63 0.00 39.50 4.02
3246 3256 2.024306 GCTTAGGATTGGGCCTTGTCC 61.024 57.143 4.53 9.67 39.50 4.02
3247 3257 1.393603 GCTTAGGATTGGGCCTTGTC 58.606 55.000 4.53 0.00 39.50 3.18
3248 3258 0.033109 GGCTTAGGATTGGGCCTTGT 60.033 55.000 4.53 0.00 41.20 3.16
3249 3259 2.812664 GGCTTAGGATTGGGCCTTG 58.187 57.895 4.53 0.00 41.20 3.61
3252 3262 0.250945 GCTAGGCTTAGGATTGGGCC 60.251 60.000 4.88 0.00 44.38 5.80
3253 3263 0.474184 TGCTAGGCTTAGGATTGGGC 59.526 55.000 4.88 0.00 0.00 5.36
3254 3264 1.490490 TGTGCTAGGCTTAGGATTGGG 59.510 52.381 4.88 0.00 29.47 4.12
3255 3265 3.281727 TTGTGCTAGGCTTAGGATTGG 57.718 47.619 4.88 0.00 29.47 3.16
3256 3266 4.517285 TCTTTGTGCTAGGCTTAGGATTG 58.483 43.478 4.88 0.00 29.47 2.67
3257 3267 4.844349 TCTTTGTGCTAGGCTTAGGATT 57.156 40.909 4.88 0.00 29.47 3.01
3258 3268 4.502259 CGATCTTTGTGCTAGGCTTAGGAT 60.502 45.833 4.88 0.00 29.47 3.24
3259 3269 3.181475 CGATCTTTGTGCTAGGCTTAGGA 60.181 47.826 4.88 0.00 0.00 2.94
3260 3270 3.126831 CGATCTTTGTGCTAGGCTTAGG 58.873 50.000 4.88 0.00 0.00 2.69
3261 3271 3.553511 CACGATCTTTGTGCTAGGCTTAG 59.446 47.826 0.00 0.00 0.00 2.18
3262 3272 3.056107 ACACGATCTTTGTGCTAGGCTTA 60.056 43.478 0.00 0.00 41.03 3.09
3263 3273 2.289694 ACACGATCTTTGTGCTAGGCTT 60.290 45.455 0.00 0.00 41.03 4.35
3264 3274 1.276421 ACACGATCTTTGTGCTAGGCT 59.724 47.619 0.00 0.00 41.03 4.58
3265 3275 1.726853 ACACGATCTTTGTGCTAGGC 58.273 50.000 0.00 0.00 41.03 3.93
3266 3276 4.111375 ACTACACGATCTTTGTGCTAGG 57.889 45.455 7.01 0.00 41.03 3.02
3267 3277 4.263209 CGAACTACACGATCTTTGTGCTAG 59.737 45.833 7.01 7.00 41.03 3.42
3268 3278 4.163552 CGAACTACACGATCTTTGTGCTA 58.836 43.478 7.01 0.00 41.03 3.49
3269 3279 2.987149 CGAACTACACGATCTTTGTGCT 59.013 45.455 7.01 0.00 41.03 4.40
3270 3280 2.729882 ACGAACTACACGATCTTTGTGC 59.270 45.455 7.01 0.00 41.03 4.57
3271 3281 6.009512 CATACGAACTACACGATCTTTGTG 57.990 41.667 7.01 2.92 42.99 3.33


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

AutoCloner maintained by Alex Coulton.