Multiple sequence alignment - TraesCS7A01G376300

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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 TraesCS7A01G376300 chr7A 100.000 3186 0 0 1 3186 549359182 549355997 0.000000e+00 5884.0
1 TraesCS7A01G376300 chr7A 84.884 86 8 2 2985 3065 514724022 514724107 7.320000e-12 82.4
2 TraesCS7A01G376300 chr7A 100.000 32 0 0 3029 3060 129872554 129872585 3.430000e-05 60.2
3 TraesCS7A01G376300 chr7D 91.990 3071 110 58 1 2987 482135424 482132406 0.000000e+00 4183.0
4 TraesCS7A01G376300 chr7D 91.935 62 5 0 1090 1151 93949361 93949300 1.570000e-13 87.9
5 TraesCS7A01G376300 chr7D 91.935 62 5 0 1090 1151 94005574 94005635 1.570000e-13 87.9
6 TraesCS7A01G376300 chr7D 97.297 37 1 0 3024 3060 506723942 506723906 2.650000e-06 63.9
7 TraesCS7A01G376300 chr7B 90.470 3064 122 67 1 2987 508196701 508193731 0.000000e+00 3884.0
8 TraesCS7A01G376300 chr6B 82.507 383 45 19 1360 1741 277624375 277624014 1.840000e-82 316.0
9 TraesCS7A01G376300 chr6B 86.364 110 14 1 1054 1162 277624600 277624491 5.580000e-23 119.0
10 TraesCS7A01G376300 chr6B 93.443 61 4 0 1090 1150 668029995 668029935 1.220000e-14 91.6
11 TraesCS7A01G376300 chr6D 82.245 383 46 19 1360 1741 153865439 153865078 8.580000e-81 311.0
12 TraesCS7A01G376300 chr6D 89.691 97 10 0 1066 1162 153865652 153865556 1.200000e-24 124.0
13 TraesCS7A01G376300 chr6D 87.805 82 10 0 1838 1919 153865009 153864928 2.620000e-16 97.1
14 TraesCS7A01G376300 chr6A 81.579 380 48 18 1363 1741 206352287 206351929 8.640000e-76 294.0
15 TraesCS7A01G376300 chr6A 89.691 97 10 0 1066 1162 206352502 206352406 1.200000e-24 124.0
16 TraesCS7A01G376300 chr6A 87.805 82 10 0 1838 1919 206351860 206351779 2.620000e-16 97.1
17 TraesCS7A01G376300 chr6A 93.443 61 4 0 1090 1150 591381175 591381115 1.220000e-14 91.6
18 TraesCS7A01G376300 chr6A 100.000 36 0 0 3025 3060 40610917 40610882 2.050000e-07 67.6
19 TraesCS7A01G376300 chr4B 87.778 90 10 1 2985 3073 492207656 492207567 1.560000e-18 104.0
20 TraesCS7A01G376300 chr4B 89.362 47 5 0 3027 3073 492207536 492207490 3.430000e-05 60.2
21 TraesCS7A01G376300 chr1A 84.615 91 9 2 2990 3075 171466809 171466719 5.660000e-13 86.1
22 TraesCS7A01G376300 chr3D 100.000 37 0 0 3024 3060 477885426 477885462 5.700000e-08 69.4
23 TraesCS7A01G376300 chr3D 100.000 29 0 0 3023 3051 568816549 568816577 2.000000e-03 54.7


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 TraesCS7A01G376300 chr7A 549355997 549359182 3185 True 5884.0 5884 100.0000 1 3186 1 chr7A.!!$R1 3185
1 TraesCS7A01G376300 chr7D 482132406 482135424 3018 True 4183.0 4183 91.9900 1 2987 1 chr7D.!!$R2 2986
2 TraesCS7A01G376300 chr7B 508193731 508196701 2970 True 3884.0 3884 90.4700 1 2987 1 chr7B.!!$R1 2986
3 TraesCS7A01G376300 chr6B 277624014 277624600 586 True 217.5 316 84.4355 1054 1741 2 chr6B.!!$R2 687

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
542 580 0.250684 TACAGTGGGTGCACACATGG 60.251 55.0 27.25 21.88 43.72 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2505 2657 0.09715 GTTACGACGACTACGGGACC 59.903 60.0 0.0 0.0 44.46 4.46 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
143 145 2.461637 CCCCTCTTCCCTTCCCCT 59.538 66.667 0.00 0.00 0.00 4.79
195 212 3.034635 TCTATGTCTTTCCCTCTGGCTC 58.965 50.000 0.00 0.00 0.00 4.70
232 255 2.022764 TGCTACACGCATGCTGTTAT 57.977 45.000 22.11 12.32 45.47 1.89
270 293 1.214305 CCCAACCTCCCTCCATGGAA 61.214 60.000 17.00 0.00 38.35 3.53
327 361 3.815401 CCTTTAGGCACCACTACATATGC 59.185 47.826 1.58 0.00 37.35 3.14
333 367 4.838423 AGGCACCACTACATATGCTGTATA 59.162 41.667 1.58 0.00 39.58 1.47
341 375 9.574458 CCACTACATATGCTGTATACTTGTATC 57.426 37.037 1.58 0.00 39.58 2.24
344 378 9.574458 CTACATATGCTGTATACTTGTATCCAC 57.426 37.037 1.58 0.00 39.58 4.02
345 379 7.962441 ACATATGCTGTATACTTGTATCCACA 58.038 34.615 1.58 0.00 35.91 4.17
351 385 8.793592 TGCTGTATACTTGTATCCACATAGTAG 58.206 37.037 4.17 0.00 34.61 2.57
352 386 8.794553 GCTGTATACTTGTATCCACATAGTAGT 58.205 37.037 4.17 0.00 34.61 2.73
357 391 7.584122 ACTTGTATCCACATAGTAGTACCTG 57.416 40.000 0.00 0.00 33.76 4.00
401 436 3.593442 AGGGAGTGGTGAATTTCAACA 57.407 42.857 13.07 13.07 42.67 3.33
473 511 4.841246 GTCCTGGTAAGATGATGGGTAGAT 59.159 45.833 0.00 0.00 0.00 1.98
542 580 0.250684 TACAGTGGGTGCACACATGG 60.251 55.000 27.25 21.88 43.72 3.66
543 581 2.598394 AGTGGGTGCACACATGGC 60.598 61.111 27.25 12.94 43.72 4.40
544 582 2.911509 GTGGGTGCACACATGGCA 60.912 61.111 27.25 0.00 40.99 4.92
545 583 2.598099 TGGGTGCACACATGGCAG 60.598 61.111 20.21 0.00 42.85 4.85
578 616 0.382515 GTCCTAGCGGAGTAGCAGTG 59.617 60.000 0.00 0.00 40.84 3.66
598 636 0.508641 CAAGTGAACAAGGACGAGCG 59.491 55.000 0.00 0.00 0.00 5.03
619 657 1.607178 CATGGAAGCAGCCCAACCA 60.607 57.895 0.00 0.00 37.22 3.67
734 773 0.884704 CCCCCTCTTTCACACACACG 60.885 60.000 0.00 0.00 0.00 4.49
736 775 0.532862 CCCTCTTTCACACACACGCT 60.533 55.000 0.00 0.00 0.00 5.07
761 809 6.378848 TCATACGCAATGTAGGCCTATGTATA 59.621 38.462 17.38 7.57 36.25 1.47
1019 1095 2.685380 CCTCTGCCCGTCCTCCTT 60.685 66.667 0.00 0.00 0.00 3.36
1021 1097 3.068691 TCTGCCCGTCCTCCTTCG 61.069 66.667 0.00 0.00 0.00 3.79
1045 1124 1.068921 GAGAATCTCCCCGCTCTGC 59.931 63.158 0.00 0.00 0.00 4.26
1177 1259 0.250727 CCCCCTAGCTCTCTCTCTCG 60.251 65.000 0.00 0.00 0.00 4.04
1181 1263 1.139989 CTAGCTCTCTCTCTCGCTCG 58.860 60.000 0.00 0.00 34.14 5.03
1187 1271 1.841663 CTCTCTCTCGCTCGCTAGCC 61.842 65.000 9.66 0.00 46.68 3.93
1198 1282 2.910345 CGCTAGCCGCTCTACTCCC 61.910 68.421 9.66 0.00 36.13 4.30
1222 1314 2.412112 CGGCCTACTCGTGTAGCC 59.588 66.667 17.23 18.54 43.51 3.93
1230 1322 1.144057 CTCGTGTAGCCATCCCACC 59.856 63.158 0.00 0.00 0.00 4.61
1241 1333 1.990060 ATCCCACCGTGTCCTGAGG 60.990 63.158 0.00 0.00 0.00 3.86
1260 1352 8.401894 TCCTGAGGGATAGATACATTGATTCTA 58.598 37.037 0.00 0.00 36.57 2.10
1261 1353 9.211410 CCTGAGGGATAGATACATTGATTCTAT 57.789 37.037 10.72 10.72 35.83 1.98
1275 1367 9.507280 ACATTGATTCTATTTTGAATTGCTACG 57.493 29.630 0.00 0.00 36.86 3.51
1276 1368 9.507280 CATTGATTCTATTTTGAATTGCTACGT 57.493 29.630 0.00 0.00 36.86 3.57
1795 1932 2.432628 GGTGTCGGCGACTCCTTG 60.433 66.667 39.18 0.00 41.36 3.61
1960 2097 2.538437 CAGCCTCGTCATCTGAAGAAG 58.462 52.381 0.00 0.00 32.49 2.85
1961 2098 2.165234 CAGCCTCGTCATCTGAAGAAGA 59.835 50.000 0.00 0.00 39.94 2.87
1962 2099 2.828520 AGCCTCGTCATCTGAAGAAGAA 59.171 45.455 0.69 0.00 38.79 2.52
1963 2100 3.259374 AGCCTCGTCATCTGAAGAAGAAA 59.741 43.478 0.69 0.00 38.79 2.52
2054 2191 2.031314 CGCACAGGCAGTTAAGATCATG 59.969 50.000 0.00 0.00 41.24 3.07
2055 2192 2.223433 GCACAGGCAGTTAAGATCATGC 60.223 50.000 0.00 0.00 40.72 4.06
2056 2193 3.011818 CACAGGCAGTTAAGATCATGCA 58.988 45.455 0.00 0.00 40.46 3.96
2066 2203 1.306148 AGATCATGCATTGCTCCACG 58.694 50.000 10.49 0.00 0.00 4.94
2209 2359 9.419297 CTTGTATGTAACTATGTATATGCCGTT 57.581 33.333 0.00 0.00 0.00 4.44
2385 2537 8.510243 TGTTAGACTATACCGATGAAGTGTTA 57.490 34.615 0.00 0.00 0.00 2.41
2411 2563 0.445043 GTCGGGCGAATTTAAGCGTT 59.555 50.000 0.00 0.00 0.00 4.84
2431 2583 6.092807 AGCGTTTCTCTTCATCAAAAGGATAC 59.907 38.462 0.00 0.00 33.95 2.24
2505 2657 4.143242 CGTCTGTAAGCACTGTTCATTCTG 60.143 45.833 0.00 0.00 0.00 3.02
2514 2666 2.233922 ACTGTTCATTCTGGTCCCGTAG 59.766 50.000 0.00 0.00 0.00 3.51
2515 2667 2.233922 CTGTTCATTCTGGTCCCGTAGT 59.766 50.000 0.00 0.00 0.00 2.73
2516 2668 2.232941 TGTTCATTCTGGTCCCGTAGTC 59.767 50.000 0.00 0.00 0.00 2.59
2618 2778 7.270047 ACATGTATGCGGTATGTTAGTACTTT 58.730 34.615 0.00 0.00 31.38 2.66
2677 2837 1.674322 ATGCACCCCGAGTTTTCCG 60.674 57.895 0.00 0.00 0.00 4.30
2799 2959 0.591659 GCCCAACCAAGACGAAGAAC 59.408 55.000 0.00 0.00 0.00 3.01
2802 2962 2.285083 CCAACCAAGACGAAGAACACA 58.715 47.619 0.00 0.00 0.00 3.72
2835 2995 8.229811 CGAAAACATCTGTCAATCAATTACTCA 58.770 33.333 0.00 0.00 0.00 3.41
2874 3034 1.358787 TGCAATTCCTGGATGTTCCCT 59.641 47.619 0.00 0.00 35.03 4.20
2883 3043 3.497763 CCTGGATGTTCCCTTGTGTAACA 60.498 47.826 0.00 0.00 40.15 2.41
2910 3072 2.134789 AATGCAAGGGATCAGTCACC 57.865 50.000 0.00 0.00 0.00 4.02
2911 3073 0.994247 ATGCAAGGGATCAGTCACCA 59.006 50.000 0.00 0.00 0.00 4.17
2912 3074 0.994247 TGCAAGGGATCAGTCACCAT 59.006 50.000 0.00 0.00 0.00 3.55
2913 3075 1.355381 TGCAAGGGATCAGTCACCATT 59.645 47.619 0.00 0.00 0.00 3.16
2914 3076 2.575735 TGCAAGGGATCAGTCACCATTA 59.424 45.455 0.00 0.00 0.00 1.90
2915 3077 3.209410 GCAAGGGATCAGTCACCATTAG 58.791 50.000 0.00 0.00 0.00 1.73
2916 3078 3.118261 GCAAGGGATCAGTCACCATTAGA 60.118 47.826 0.00 0.00 0.00 2.10
2971 3138 3.776969 TGGAAACATCATCCTCAGCTAGT 59.223 43.478 0.00 0.00 37.85 2.57
2987 3154 3.522553 GCTAGTGGCGAACTCAAATACT 58.477 45.455 0.00 0.00 40.56 2.12
2988 3155 3.552294 GCTAGTGGCGAACTCAAATACTC 59.448 47.826 0.00 0.00 40.56 2.59
2989 3156 2.973945 AGTGGCGAACTCAAATACTCC 58.026 47.619 0.00 0.00 31.64 3.85
2990 3157 2.007608 GTGGCGAACTCAAATACTCCC 58.992 52.381 0.00 0.00 0.00 4.30
2991 3158 1.906574 TGGCGAACTCAAATACTCCCT 59.093 47.619 0.00 0.00 0.00 4.20
2992 3159 2.093658 TGGCGAACTCAAATACTCCCTC 60.094 50.000 0.00 0.00 0.00 4.30
2993 3160 2.552031 GCGAACTCAAATACTCCCTCC 58.448 52.381 0.00 0.00 0.00 4.30
2994 3161 2.742204 GCGAACTCAAATACTCCCTCCC 60.742 54.545 0.00 0.00 0.00 4.30
2995 3162 2.766828 CGAACTCAAATACTCCCTCCCT 59.233 50.000 0.00 0.00 0.00 4.20
2996 3163 3.197983 CGAACTCAAATACTCCCTCCCTT 59.802 47.826 0.00 0.00 0.00 3.95
2997 3164 4.680975 CGAACTCAAATACTCCCTCCCTTC 60.681 50.000 0.00 0.00 0.00 3.46
2998 3165 2.766828 ACTCAAATACTCCCTCCCTTCG 59.233 50.000 0.00 0.00 0.00 3.79
2999 3166 2.103263 CTCAAATACTCCCTCCCTTCGG 59.897 54.545 0.00 0.00 0.00 4.30
3000 3167 2.116238 CAAATACTCCCTCCCTTCGGA 58.884 52.381 0.00 0.00 36.45 4.55
3001 3168 2.504175 CAAATACTCCCTCCCTTCGGAA 59.496 50.000 0.00 0.00 37.86 4.30
3002 3169 2.563039 ATACTCCCTCCCTTCGGAAA 57.437 50.000 0.00 0.00 37.86 3.13
3003 3170 2.563039 TACTCCCTCCCTTCGGAAAT 57.437 50.000 0.00 0.00 37.86 2.17
3004 3171 2.563039 ACTCCCTCCCTTCGGAAATA 57.437 50.000 0.00 0.00 37.86 1.40
3005 3172 2.841795 ACTCCCTCCCTTCGGAAATAA 58.158 47.619 0.00 0.00 37.86 1.40
3006 3173 2.772515 ACTCCCTCCCTTCGGAAATAAG 59.227 50.000 0.00 0.00 37.86 1.73
3007 3174 2.772515 CTCCCTCCCTTCGGAAATAAGT 59.227 50.000 0.00 0.00 37.86 2.24
3008 3175 2.504175 TCCCTCCCTTCGGAAATAAGTG 59.496 50.000 0.00 0.00 37.86 3.16
3009 3176 2.504175 CCCTCCCTTCGGAAATAAGTGA 59.496 50.000 0.00 0.00 37.86 3.41
3010 3177 3.136626 CCCTCCCTTCGGAAATAAGTGAT 59.863 47.826 0.00 0.00 37.86 3.06
3011 3178 4.130118 CCTCCCTTCGGAAATAAGTGATG 58.870 47.826 0.00 0.00 37.86 3.07
3012 3179 3.541632 TCCCTTCGGAAATAAGTGATGC 58.458 45.455 0.00 0.00 34.19 3.91
3013 3180 3.199946 TCCCTTCGGAAATAAGTGATGCT 59.800 43.478 0.00 0.00 34.19 3.79
3014 3181 3.313526 CCCTTCGGAAATAAGTGATGCTG 59.686 47.826 0.00 0.00 0.00 4.41
3015 3182 3.941483 CCTTCGGAAATAAGTGATGCTGT 59.059 43.478 0.00 0.00 0.00 4.40
3016 3183 4.396166 CCTTCGGAAATAAGTGATGCTGTT 59.604 41.667 0.00 0.00 0.00 3.16
3017 3184 5.106157 CCTTCGGAAATAAGTGATGCTGTTT 60.106 40.000 0.00 0.00 0.00 2.83
3018 3185 5.957842 TCGGAAATAAGTGATGCTGTTTT 57.042 34.783 0.00 0.00 0.00 2.43
3019 3186 7.361713 CCTTCGGAAATAAGTGATGCTGTTTTA 60.362 37.037 0.00 0.00 0.00 1.52
3020 3187 7.441890 TCGGAAATAAGTGATGCTGTTTTAA 57.558 32.000 0.00 0.00 0.00 1.52
3021 3188 7.302524 TCGGAAATAAGTGATGCTGTTTTAAC 58.697 34.615 0.00 0.00 0.00 2.01
3022 3189 7.041030 TCGGAAATAAGTGATGCTGTTTTAACA 60.041 33.333 0.00 0.00 37.37 2.41
3023 3190 7.754924 CGGAAATAAGTGATGCTGTTTTAACAT 59.245 33.333 0.00 0.00 38.41 2.71
3024 3191 9.423061 GGAAATAAGTGATGCTGTTTTAACATT 57.577 29.630 0.00 0.00 38.41 2.71
3026 3193 9.979578 AAATAAGTGATGCTGTTTTAACATTGA 57.020 25.926 0.00 0.00 38.41 2.57
3027 3194 9.979578 AATAAGTGATGCTGTTTTAACATTGAA 57.020 25.926 0.00 0.00 38.41 2.69
3028 3195 7.698836 AAGTGATGCTGTTTTAACATTGAAC 57.301 32.000 0.00 0.00 38.41 3.18
3029 3196 7.042797 AGTGATGCTGTTTTAACATTGAACT 57.957 32.000 0.00 0.00 38.41 3.01
3030 3197 8.165239 AGTGATGCTGTTTTAACATTGAACTA 57.835 30.769 0.00 0.00 38.41 2.24
3031 3198 8.629158 AGTGATGCTGTTTTAACATTGAACTAA 58.371 29.630 0.00 0.00 38.41 2.24
3032 3199 9.243637 GTGATGCTGTTTTAACATTGAACTAAA 57.756 29.630 0.00 0.00 38.41 1.85
3033 3200 9.809096 TGATGCTGTTTTAACATTGAACTAAAA 57.191 25.926 0.00 0.00 38.41 1.52
3035 3202 8.988064 TGCTGTTTTAACATTGAACTAAAACA 57.012 26.923 21.14 21.14 45.92 2.83
3038 3205 8.109843 TGTTTTAACATTGAACTAAAACAGCG 57.890 30.769 19.92 0.00 44.49 5.18
3039 3206 7.755822 TGTTTTAACATTGAACTAAAACAGCGT 59.244 29.630 19.92 0.00 44.49 5.07
3040 3207 7.901874 TTTAACATTGAACTAAAACAGCGTC 57.098 32.000 0.00 0.00 0.00 5.19
3041 3208 5.493133 AACATTGAACTAAAACAGCGTCA 57.507 34.783 0.00 0.00 0.00 4.35
3042 3209 4.844267 ACATTGAACTAAAACAGCGTCAC 58.156 39.130 0.00 0.00 0.00 3.67
3043 3210 4.574828 ACATTGAACTAAAACAGCGTCACT 59.425 37.500 0.00 0.00 0.00 3.41
3044 3211 5.065988 ACATTGAACTAAAACAGCGTCACTT 59.934 36.000 0.00 0.00 0.00 3.16
3045 3212 6.259167 ACATTGAACTAAAACAGCGTCACTTA 59.741 34.615 0.00 0.00 0.00 2.24
3046 3213 6.854496 TTGAACTAAAACAGCGTCACTTAT 57.146 33.333 0.00 0.00 0.00 1.73
3047 3214 6.854496 TGAACTAAAACAGCGTCACTTATT 57.146 33.333 0.00 0.00 0.00 1.40
3048 3215 7.254227 TGAACTAAAACAGCGTCACTTATTT 57.746 32.000 0.00 0.00 0.00 1.40
3049 3216 7.349711 TGAACTAAAACAGCGTCACTTATTTC 58.650 34.615 0.00 0.00 0.00 2.17
3050 3217 6.237313 ACTAAAACAGCGTCACTTATTTCC 57.763 37.500 0.00 0.00 0.00 3.13
3051 3218 3.806316 AAACAGCGTCACTTATTTCCG 57.194 42.857 0.00 0.00 0.00 4.30
3052 3219 2.736144 ACAGCGTCACTTATTTCCGA 57.264 45.000 0.00 0.00 0.00 4.55
3053 3220 3.034721 ACAGCGTCACTTATTTCCGAA 57.965 42.857 0.00 0.00 0.00 4.30
3054 3221 2.735134 ACAGCGTCACTTATTTCCGAAC 59.265 45.455 0.00 0.00 0.00 3.95
3055 3222 1.990563 AGCGTCACTTATTTCCGAACG 59.009 47.619 0.00 0.00 0.00 3.95
3056 3223 1.060122 GCGTCACTTATTTCCGAACGG 59.940 52.381 6.94 6.94 0.00 4.44
3057 3224 2.598589 CGTCACTTATTTCCGAACGGA 58.401 47.619 12.04 12.04 43.52 4.69
3058 3225 2.597305 CGTCACTTATTTCCGAACGGAG 59.403 50.000 15.34 6.93 46.06 4.63
3059 3226 2.928116 GTCACTTATTTCCGAACGGAGG 59.072 50.000 15.34 7.95 46.06 4.30
3060 3227 2.564062 TCACTTATTTCCGAACGGAGGT 59.436 45.455 15.34 10.86 46.06 3.85
3061 3228 3.763360 TCACTTATTTCCGAACGGAGGTA 59.237 43.478 15.34 9.98 46.06 3.08
3062 3229 4.220382 TCACTTATTTCCGAACGGAGGTAA 59.780 41.667 15.34 15.58 46.06 2.85
3063 3230 5.105228 TCACTTATTTCCGAACGGAGGTAAT 60.105 40.000 15.34 14.30 46.06 1.89
3064 3231 6.096705 TCACTTATTTCCGAACGGAGGTAATA 59.903 38.462 15.34 13.43 46.06 0.98
3065 3232 6.199719 CACTTATTTCCGAACGGAGGTAATAC 59.800 42.308 15.34 0.00 46.06 1.89
3066 3233 6.097412 ACTTATTTCCGAACGGAGGTAATACT 59.903 38.462 15.34 3.84 46.06 2.12
3067 3234 4.806640 TTTCCGAACGGAGGTAATACTT 57.193 40.909 15.34 0.00 46.06 2.24
3068 3235 3.788333 TCCGAACGGAGGTAATACTTG 57.212 47.619 12.04 0.00 39.76 3.16
3069 3236 3.091545 TCCGAACGGAGGTAATACTTGT 58.908 45.455 12.04 0.00 39.76 3.16
3070 3237 3.129287 TCCGAACGGAGGTAATACTTGTC 59.871 47.826 12.04 0.00 39.76 3.18
3071 3238 3.119388 CCGAACGGAGGTAATACTTGTCA 60.119 47.826 7.53 0.00 37.50 3.58
3072 3239 4.487948 CGAACGGAGGTAATACTTGTCAA 58.512 43.478 0.00 0.00 0.00 3.18
3073 3240 4.325472 CGAACGGAGGTAATACTTGTCAAC 59.675 45.833 0.00 0.00 0.00 3.18
3074 3241 4.877378 ACGGAGGTAATACTTGTCAACA 57.123 40.909 0.00 0.00 0.00 3.33
3075 3242 5.416271 ACGGAGGTAATACTTGTCAACAT 57.584 39.130 0.00 0.00 0.00 2.71
3076 3243 5.801380 ACGGAGGTAATACTTGTCAACATT 58.199 37.500 0.00 0.00 0.00 2.71
3077 3244 6.938507 ACGGAGGTAATACTTGTCAACATTA 58.061 36.000 0.00 0.00 0.00 1.90
3078 3245 7.388437 ACGGAGGTAATACTTGTCAACATTAA 58.612 34.615 0.00 0.00 0.00 1.40
3079 3246 7.879160 ACGGAGGTAATACTTGTCAACATTAAA 59.121 33.333 0.00 0.00 0.00 1.52
3080 3247 8.173130 CGGAGGTAATACTTGTCAACATTAAAC 58.827 37.037 0.00 0.00 0.00 2.01
3081 3248 9.005777 GGAGGTAATACTTGTCAACATTAAACA 57.994 33.333 0.00 0.00 0.00 2.83
3089 3256 8.578308 ACTTGTCAACATTAAACATCAACATG 57.422 30.769 0.00 0.00 35.92 3.21
3090 3257 8.196771 ACTTGTCAACATTAAACATCAACATGT 58.803 29.630 0.00 0.00 45.89 3.21
3091 3258 7.927305 TGTCAACATTAAACATCAACATGTG 57.073 32.000 0.00 0.00 42.89 3.21
3092 3259 7.487484 TGTCAACATTAAACATCAACATGTGT 58.513 30.769 0.00 0.00 42.89 3.72
3093 3260 7.978414 TGTCAACATTAAACATCAACATGTGTT 59.022 29.630 0.00 0.00 42.89 3.32
3094 3261 9.457110 GTCAACATTAAACATCAACATGTGTTA 57.543 29.630 0.00 0.00 42.89 2.41
3095 3262 9.676195 TCAACATTAAACATCAACATGTGTTAG 57.324 29.630 0.00 0.00 42.89 2.34
3096 3263 9.462174 CAACATTAAACATCAACATGTGTTAGT 57.538 29.630 0.00 0.00 42.89 2.24
3097 3264 9.462174 AACATTAAACATCAACATGTGTTAGTG 57.538 29.630 0.00 0.00 42.89 2.74
3098 3265 7.594758 ACATTAAACATCAACATGTGTTAGTGC 59.405 33.333 0.00 0.00 42.89 4.40
3099 3266 5.512753 AAACATCAACATGTGTTAGTGCA 57.487 34.783 0.00 0.00 42.89 4.57
3100 3267 5.710513 AACATCAACATGTGTTAGTGCAT 57.289 34.783 0.00 0.00 42.89 3.96
3101 3268 5.300969 ACATCAACATGTGTTAGTGCATC 57.699 39.130 0.00 0.00 42.05 3.91
3102 3269 4.142838 ACATCAACATGTGTTAGTGCATCG 60.143 41.667 0.00 0.00 42.05 3.84
3103 3270 3.658709 TCAACATGTGTTAGTGCATCGA 58.341 40.909 0.00 0.00 36.32 3.59
3104 3271 4.061596 TCAACATGTGTTAGTGCATCGAA 58.938 39.130 0.00 0.00 36.32 3.71
3105 3272 4.694982 TCAACATGTGTTAGTGCATCGAAT 59.305 37.500 0.00 0.00 36.32 3.34
3106 3273 5.181056 TCAACATGTGTTAGTGCATCGAATT 59.819 36.000 0.00 0.00 36.32 2.17
3107 3274 5.627499 ACATGTGTTAGTGCATCGAATTT 57.373 34.783 0.00 0.00 0.00 1.82
3108 3275 5.631026 ACATGTGTTAGTGCATCGAATTTC 58.369 37.500 0.00 0.00 0.00 2.17
3109 3276 5.181056 ACATGTGTTAGTGCATCGAATTTCA 59.819 36.000 0.00 0.00 0.00 2.69
3110 3277 5.681337 TGTGTTAGTGCATCGAATTTCAA 57.319 34.783 0.00 0.00 0.00 2.69
3111 3278 6.066054 TGTGTTAGTGCATCGAATTTCAAA 57.934 33.333 0.00 0.00 0.00 2.69
3112 3279 6.142139 TGTGTTAGTGCATCGAATTTCAAAG 58.858 36.000 0.00 0.00 0.00 2.77
3113 3280 6.017523 TGTGTTAGTGCATCGAATTTCAAAGA 60.018 34.615 0.00 0.00 0.00 2.52
3114 3281 6.855914 GTGTTAGTGCATCGAATTTCAAAGAA 59.144 34.615 0.00 0.00 0.00 2.52
3115 3282 7.378461 GTGTTAGTGCATCGAATTTCAAAGAAA 59.622 33.333 0.00 0.00 0.00 2.52
3116 3283 8.081633 TGTTAGTGCATCGAATTTCAAAGAAAT 58.918 29.630 0.00 0.00 0.00 2.17
3117 3284 8.578769 GTTAGTGCATCGAATTTCAAAGAAATC 58.421 33.333 5.54 0.45 0.00 2.17
3118 3285 6.680810 AGTGCATCGAATTTCAAAGAAATCA 58.319 32.000 5.54 0.00 0.00 2.57
3119 3286 6.805271 AGTGCATCGAATTTCAAAGAAATCAG 59.195 34.615 5.54 3.90 0.00 2.90
3120 3287 6.803320 GTGCATCGAATTTCAAAGAAATCAGA 59.197 34.615 5.54 8.30 0.00 3.27
3121 3288 7.487189 GTGCATCGAATTTCAAAGAAATCAGAT 59.513 33.333 5.54 9.85 0.00 2.90
3122 3289 8.030692 TGCATCGAATTTCAAAGAAATCAGATT 58.969 29.630 14.39 0.00 0.00 2.40
3123 3290 8.529911 GCATCGAATTTCAAAGAAATCAGATTC 58.470 33.333 14.39 9.74 0.00 2.52
3124 3291 9.563898 CATCGAATTTCAAAGAAATCAGATTCA 57.436 29.630 14.39 1.78 0.00 2.57
3125 3292 8.955061 TCGAATTTCAAAGAAATCAGATTCAC 57.045 30.769 5.54 0.00 0.00 3.18
3126 3293 8.567104 TCGAATTTCAAAGAAATCAGATTCACA 58.433 29.630 5.54 0.00 0.00 3.58
3127 3294 9.350357 CGAATTTCAAAGAAATCAGATTCACAT 57.650 29.630 5.54 0.00 0.00 3.21
3132 3299 9.903682 TTCAAAGAAATCAGATTCACATTTCTC 57.096 29.630 16.95 0.00 43.14 2.87
3133 3300 8.517878 TCAAAGAAATCAGATTCACATTTCTCC 58.482 33.333 16.95 0.00 43.14 3.71
3134 3301 6.674694 AGAAATCAGATTCACATTTCTCCG 57.325 37.500 13.31 0.00 41.11 4.63
3135 3302 4.889832 AATCAGATTCACATTTCTCCGC 57.110 40.909 0.00 0.00 0.00 5.54
3136 3303 3.333029 TCAGATTCACATTTCTCCGCA 57.667 42.857 0.00 0.00 0.00 5.69
3137 3304 3.877559 TCAGATTCACATTTCTCCGCAT 58.122 40.909 0.00 0.00 0.00 4.73
3138 3305 4.264253 TCAGATTCACATTTCTCCGCATT 58.736 39.130 0.00 0.00 0.00 3.56
3139 3306 5.427378 TCAGATTCACATTTCTCCGCATTA 58.573 37.500 0.00 0.00 0.00 1.90
3140 3307 5.879777 TCAGATTCACATTTCTCCGCATTAA 59.120 36.000 0.00 0.00 0.00 1.40
3141 3308 6.374053 TCAGATTCACATTTCTCCGCATTAAA 59.626 34.615 0.00 0.00 0.00 1.52
3142 3309 7.028962 CAGATTCACATTTCTCCGCATTAAAA 58.971 34.615 0.00 0.00 0.00 1.52
3143 3310 7.703621 CAGATTCACATTTCTCCGCATTAAAAT 59.296 33.333 0.00 0.00 0.00 1.82
3144 3311 8.902806 AGATTCACATTTCTCCGCATTAAAATA 58.097 29.630 0.00 0.00 0.00 1.40
3145 3312 9.173939 GATTCACATTTCTCCGCATTAAAATAG 57.826 33.333 0.00 0.00 0.00 1.73
3146 3313 7.026631 TCACATTTCTCCGCATTAAAATAGG 57.973 36.000 0.00 0.00 0.00 2.57
3147 3314 6.601613 TCACATTTCTCCGCATTAAAATAGGT 59.398 34.615 0.00 0.00 0.00 3.08
3148 3315 6.912591 CACATTTCTCCGCATTAAAATAGGTC 59.087 38.462 0.00 0.00 0.00 3.85
3149 3316 6.039382 ACATTTCTCCGCATTAAAATAGGTCC 59.961 38.462 0.00 0.00 0.00 4.46
3150 3317 3.724374 TCTCCGCATTAAAATAGGTCCG 58.276 45.455 0.00 0.00 0.00 4.79
3151 3318 2.806244 CTCCGCATTAAAATAGGTCCGG 59.194 50.000 0.00 0.00 36.05 5.14
3152 3319 2.171027 TCCGCATTAAAATAGGTCCGGT 59.829 45.455 0.00 0.00 36.15 5.28
3153 3320 2.946990 CCGCATTAAAATAGGTCCGGTT 59.053 45.455 0.00 0.00 0.00 4.44
3154 3321 3.242936 CCGCATTAAAATAGGTCCGGTTG 60.243 47.826 0.00 0.00 0.00 3.77
3155 3322 3.242936 CGCATTAAAATAGGTCCGGTTGG 60.243 47.826 0.00 0.00 0.00 3.77
3156 3323 3.067601 GCATTAAAATAGGTCCGGTTGGG 59.932 47.826 0.00 0.00 35.24 4.12
3157 3324 4.528920 CATTAAAATAGGTCCGGTTGGGA 58.471 43.478 0.00 0.00 44.68 4.37
3169 3336 5.897851 TCCGGTTGGGAGATCATTAATAA 57.102 39.130 0.00 0.00 40.94 1.40
3170 3337 6.448369 TCCGGTTGGGAGATCATTAATAAT 57.552 37.500 0.00 0.00 40.94 1.28
3171 3338 6.472887 TCCGGTTGGGAGATCATTAATAATC 58.527 40.000 0.00 0.00 40.94 1.75
3172 3339 6.043822 TCCGGTTGGGAGATCATTAATAATCA 59.956 38.462 0.00 0.00 40.94 2.57
3173 3340 6.372659 CCGGTTGGGAGATCATTAATAATCAG 59.627 42.308 1.39 0.00 38.47 2.90
3174 3341 6.936900 CGGTTGGGAGATCATTAATAATCAGT 59.063 38.462 1.39 0.00 0.00 3.41
3175 3342 8.094548 CGGTTGGGAGATCATTAATAATCAGTA 58.905 37.037 1.39 0.00 0.00 2.74
3176 3343 9.793259 GGTTGGGAGATCATTAATAATCAGTAA 57.207 33.333 1.39 0.00 0.00 2.24
3178 3345 9.793259 TTGGGAGATCATTAATAATCAGTAACC 57.207 33.333 1.39 0.00 0.00 2.85
3179 3346 8.944138 TGGGAGATCATTAATAATCAGTAACCA 58.056 33.333 1.39 0.00 0.00 3.67
3180 3347 9.965902 GGGAGATCATTAATAATCAGTAACCAT 57.034 33.333 1.39 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 1.224069 CTGTCGGTGAACTGTGGCTG 61.224 60.000 0.00 0.00 0.00 4.85
81 82 1.069765 CTGTCGGTGAACTGTGGCT 59.930 57.895 0.00 0.00 0.00 4.75
82 83 2.607892 GCTGTCGGTGAACTGTGGC 61.608 63.158 0.00 0.00 0.00 5.01
123 125 3.421386 GGAAGGGAAGAGGGGGCC 61.421 72.222 0.00 0.00 0.00 5.80
173 185 2.769095 AGCCAGAGGGAAAGACATAGAC 59.231 50.000 0.00 0.00 35.59 2.59
177 194 0.539051 CGAGCCAGAGGGAAAGACAT 59.461 55.000 0.00 0.00 35.59 3.06
195 212 2.939103 AGCAAGTGATAAAGCTTAGCCG 59.061 45.455 0.00 0.00 32.52 5.52
232 255 3.074281 CCGTGGGGTTGGAAGCTA 58.926 61.111 0.00 0.00 0.00 3.32
251 274 1.214305 TTCCATGGAGGGAGGTTGGG 61.214 60.000 15.53 0.00 38.42 4.12
270 293 6.726299 TCAGCTAGCAATTATCTACCCTGTAT 59.274 38.462 18.83 0.00 0.00 2.29
333 367 6.550108 CCAGGTACTACTATGTGGATACAAGT 59.450 42.308 0.00 0.00 46.31 3.16
341 375 4.279145 AGTGACCAGGTACTACTATGTGG 58.721 47.826 0.00 0.00 36.02 4.17
344 378 7.284716 TGACATTAGTGACCAGGTACTACTATG 59.715 40.741 10.24 11.96 36.02 2.23
345 379 7.284944 GTGACATTAGTGACCAGGTACTACTAT 59.715 40.741 10.24 1.85 36.02 2.12
351 385 4.530710 TGTGACATTAGTGACCAGGTAC 57.469 45.455 0.00 0.00 30.11 3.34
352 386 4.591498 AGTTGTGACATTAGTGACCAGGTA 59.409 41.667 0.00 0.00 30.11 3.08
353 387 3.391296 AGTTGTGACATTAGTGACCAGGT 59.609 43.478 0.00 0.00 30.11 4.00
354 388 4.008074 AGTTGTGACATTAGTGACCAGG 57.992 45.455 0.00 0.00 30.11 4.45
355 389 4.452455 GGAAGTTGTGACATTAGTGACCAG 59.548 45.833 0.00 0.00 30.11 4.00
356 390 4.141597 TGGAAGTTGTGACATTAGTGACCA 60.142 41.667 0.00 0.00 30.11 4.02
357 391 4.385825 TGGAAGTTGTGACATTAGTGACC 58.614 43.478 0.00 0.00 30.11 4.02
418 456 5.656213 TCCAGGAGCTAAGTACAAGTTAC 57.344 43.478 0.00 0.00 0.00 2.50
419 457 5.778750 ACTTCCAGGAGCTAAGTACAAGTTA 59.221 40.000 0.00 0.00 31.84 2.24
420 458 4.593634 ACTTCCAGGAGCTAAGTACAAGTT 59.406 41.667 0.00 0.00 31.84 2.66
421 459 4.161102 ACTTCCAGGAGCTAAGTACAAGT 58.839 43.478 0.00 0.00 31.84 3.16
422 460 4.810191 ACTTCCAGGAGCTAAGTACAAG 57.190 45.455 0.00 0.00 31.84 3.16
424 462 5.331069 AGTTACTTCCAGGAGCTAAGTACA 58.669 41.667 5.69 0.00 35.90 2.90
425 463 5.918426 AGTTACTTCCAGGAGCTAAGTAC 57.082 43.478 5.69 3.03 35.90 2.73
426 464 6.269307 ACAAAGTTACTTCCAGGAGCTAAGTA 59.731 38.462 0.00 2.54 35.23 2.24
427 465 5.071923 ACAAAGTTACTTCCAGGAGCTAAGT 59.928 40.000 0.00 4.35 37.27 2.24
428 466 5.552178 ACAAAGTTACTTCCAGGAGCTAAG 58.448 41.667 0.00 0.00 0.00 2.18
429 467 5.512576 GGACAAAGTTACTTCCAGGAGCTAA 60.513 44.000 0.00 0.00 0.00 3.09
473 511 1.005512 ATGCAGTACACGCACCGAA 60.006 52.632 11.67 0.00 43.35 4.30
542 580 2.234908 AGGACATTGGAGTACTGTCTGC 59.765 50.000 0.00 0.00 39.36 4.26
543 581 4.440802 GCTAGGACATTGGAGTACTGTCTG 60.441 50.000 0.00 0.00 39.36 3.51
544 582 3.702045 GCTAGGACATTGGAGTACTGTCT 59.298 47.826 0.00 0.00 39.36 3.41
545 583 3.489398 CGCTAGGACATTGGAGTACTGTC 60.489 52.174 0.00 1.41 38.82 3.51
578 616 0.235926 GCTCGTCCTTGTTCACTTGC 59.764 55.000 0.00 0.00 0.00 4.01
598 636 2.277591 TTGGGCTGCTTCCATGCAC 61.278 57.895 0.00 0.00 38.12 4.57
619 657 2.268298 GCGTTCCACGTATCTGTTGAT 58.732 47.619 0.00 0.00 44.73 2.57
653 692 1.946768 TGGCAGTAACTTCAAGTGTGC 59.053 47.619 10.16 10.16 32.52 4.57
734 773 0.868406 GGCCTACATTGCGTATGAGC 59.132 55.000 0.00 5.45 37.69 4.26
761 809 1.217882 GTACGCTTCCGCTTGCATAT 58.782 50.000 0.00 0.00 38.22 1.78
981 1039 2.974698 GGGAATGATCAGCGGGCG 60.975 66.667 0.09 0.00 0.00 6.13
982 1040 1.599240 GAGGGAATGATCAGCGGGC 60.599 63.158 0.09 0.00 0.00 6.13
983 1041 1.072159 GGAGGGAATGATCAGCGGG 59.928 63.158 0.09 0.00 0.00 6.13
984 1042 1.072159 GGGAGGGAATGATCAGCGG 59.928 63.158 0.09 0.00 0.00 5.52
985 1043 1.072159 GGGGAGGGAATGATCAGCG 59.928 63.158 0.09 0.00 0.00 5.18
1017 1093 1.472376 GGGAGATTCTCTGGCACGAAG 60.472 57.143 13.22 0.00 0.00 3.79
1019 1095 1.330655 GGGGAGATTCTCTGGCACGA 61.331 60.000 13.22 0.00 0.00 4.35
1021 1097 1.144936 CGGGGAGATTCTCTGGCAC 59.855 63.158 13.22 0.00 0.00 5.01
1043 1122 0.250684 TGTTTCTCTGCGGAATGGCA 60.251 50.000 0.00 0.00 41.45 4.92
1044 1123 1.064654 GATGTTTCTCTGCGGAATGGC 59.935 52.381 0.00 0.00 0.00 4.40
1045 1124 2.358957 TGATGTTTCTCTGCGGAATGG 58.641 47.619 0.00 0.00 0.00 3.16
1187 1271 1.440938 CGGAGAGTGGGAGTAGAGCG 61.441 65.000 0.00 0.00 0.00 5.03
1198 1282 1.749638 ACGAGTAGGCCGGAGAGTG 60.750 63.158 5.05 0.00 0.00 3.51
1222 1314 1.219124 CTCAGGACACGGTGGGATG 59.781 63.158 13.48 7.63 0.00 3.51
1275 1367 6.399354 CGACGAAAGCAACCTTAAAGTACTAC 60.399 42.308 0.00 0.00 0.00 2.73
1276 1368 5.630680 CGACGAAAGCAACCTTAAAGTACTA 59.369 40.000 0.00 0.00 0.00 1.82
1277 1369 4.446719 CGACGAAAGCAACCTTAAAGTACT 59.553 41.667 0.00 0.00 0.00 2.73
1836 1973 0.103937 CTCTCCTCGTCCTCCATTGC 59.896 60.000 0.00 0.00 0.00 3.56
1962 2099 7.923878 ACACTTTCTTAACCGTGCAATATTTTT 59.076 29.630 0.00 0.00 0.00 1.94
1963 2100 7.381139 CACACTTTCTTAACCGTGCAATATTTT 59.619 33.333 0.00 0.00 0.00 1.82
2054 2191 1.421410 CCTACGACGTGGAGCAATGC 61.421 60.000 13.45 0.00 0.00 3.56
2055 2192 0.108804 ACCTACGACGTGGAGCAATG 60.109 55.000 13.45 0.00 0.00 2.82
2056 2193 1.133790 GTACCTACGACGTGGAGCAAT 59.866 52.381 13.45 0.00 0.00 3.56
2066 2203 0.100861 GCTCAGCTGGTACCTACGAC 59.899 60.000 15.13 0.00 0.00 4.34
2209 2359 5.826208 ACATAGTGTGACTATCATGACGGTA 59.174 40.000 0.00 0.00 39.26 4.02
2385 2537 4.674362 GCTTAAATTCGCCCGACTGAAAAT 60.674 41.667 0.00 0.00 0.00 1.82
2411 2563 6.215431 TCCTGGTATCCTTTTGATGAAGAGAA 59.785 38.462 0.00 0.00 34.76 2.87
2431 2583 5.768980 ATATCACCTCACCATATTCCTGG 57.231 43.478 0.00 0.00 42.35 4.45
2505 2657 0.097150 GTTACGACGACTACGGGACC 59.903 60.000 0.00 0.00 44.46 4.46
2514 2666 6.092748 TGTTCTTAATTAGGGTTACGACGAC 58.907 40.000 0.00 0.00 0.00 4.34
2515 2667 6.266168 TGTTCTTAATTAGGGTTACGACGA 57.734 37.500 0.00 0.00 0.00 4.20
2516 2668 6.035327 CCTTGTTCTTAATTAGGGTTACGACG 59.965 42.308 0.00 0.00 0.00 5.12
2618 2778 2.961062 GGTTACTCCTTCCGGCTATACA 59.039 50.000 0.00 0.00 0.00 2.29
2638 2798 2.690497 TGCTCTCTCTTATCTTCGGTGG 59.310 50.000 0.00 0.00 0.00 4.61
2677 2837 6.703607 CACTAATGGAGTTGAGATGATGTACC 59.296 42.308 0.00 0.00 35.64 3.34
2757 2917 6.093633 GGCTTACCAAATGATCTCGTAAGTTT 59.906 38.462 14.00 0.00 38.62 2.66
2786 2946 5.449304 GGTAAATTGTGTTCTTCGTCTTGG 58.551 41.667 0.00 0.00 0.00 3.61
2788 2948 5.051816 TCGGTAAATTGTGTTCTTCGTCTT 58.948 37.500 0.00 0.00 0.00 3.01
2799 2959 6.434596 TGACAGATGTTTTCGGTAAATTGTG 58.565 36.000 0.00 0.00 32.52 3.33
2802 2962 7.881142 TGATTGACAGATGTTTTCGGTAAATT 58.119 30.769 0.00 0.00 34.73 1.82
2835 2995 0.109913 ATGGATGGTCTCATGCGCAT 59.890 50.000 19.28 19.28 43.51 4.73
2874 3034 6.685527 TTGCATTACAAGAGTGTTACACAA 57.314 33.333 18.19 2.27 39.30 3.33
2894 3054 2.134789 AATGGTGACTGATCCCTTGC 57.865 50.000 0.00 0.00 0.00 4.01
2939 3101 3.239587 TGATGTTTCCATGCAGCAATG 57.760 42.857 0.00 0.00 0.00 2.82
2963 3125 0.966179 TTGAGTTCGCCACTAGCTGA 59.034 50.000 0.00 0.00 40.39 4.26
2964 3126 1.795768 TTTGAGTTCGCCACTAGCTG 58.204 50.000 0.00 0.00 40.39 4.24
2971 3138 1.906574 AGGGAGTATTTGAGTTCGCCA 59.093 47.619 0.00 0.00 0.00 5.69
2994 3161 5.551760 AACAGCATCACTTATTTCCGAAG 57.448 39.130 0.00 0.00 0.00 3.79
2995 3162 5.957842 AAACAGCATCACTTATTTCCGAA 57.042 34.783 0.00 0.00 0.00 4.30
2996 3163 5.957842 AAAACAGCATCACTTATTTCCGA 57.042 34.783 0.00 0.00 0.00 4.55
2997 3164 7.081349 TGTTAAAACAGCATCACTTATTTCCG 58.919 34.615 0.00 0.00 34.30 4.30
2998 3165 8.986477 ATGTTAAAACAGCATCACTTATTTCC 57.014 30.769 1.62 0.00 43.04 3.13
3000 3167 9.979578 TCAATGTTAAAACAGCATCACTTATTT 57.020 25.926 1.62 0.00 43.04 1.40
3001 3168 9.979578 TTCAATGTTAAAACAGCATCACTTATT 57.020 25.926 1.62 0.00 43.04 1.40
3002 3169 9.410556 GTTCAATGTTAAAACAGCATCACTTAT 57.589 29.630 1.62 0.00 43.04 1.73
3003 3170 8.629158 AGTTCAATGTTAAAACAGCATCACTTA 58.371 29.630 1.62 0.00 43.04 2.24
3004 3171 7.491682 AGTTCAATGTTAAAACAGCATCACTT 58.508 30.769 1.62 0.00 43.04 3.16
3005 3172 7.042797 AGTTCAATGTTAAAACAGCATCACT 57.957 32.000 1.62 0.00 43.04 3.41
3006 3173 8.795786 TTAGTTCAATGTTAAAACAGCATCAC 57.204 30.769 1.62 0.00 43.04 3.06
3007 3174 9.809096 TTTTAGTTCAATGTTAAAACAGCATCA 57.191 25.926 1.62 0.00 43.04 3.07
3009 3176 9.593134 TGTTTTAGTTCAATGTTAAAACAGCAT 57.407 25.926 18.85 0.00 45.19 3.79
3010 3177 8.988064 TGTTTTAGTTCAATGTTAAAACAGCA 57.012 26.923 18.85 6.89 45.19 4.41
3013 3180 7.755822 ACGCTGTTTTAGTTCAATGTTAAAACA 59.244 29.630 20.17 20.17 46.58 2.83
3014 3181 8.110970 ACGCTGTTTTAGTTCAATGTTAAAAC 57.889 30.769 15.95 15.95 42.93 2.43
3015 3182 7.968956 TGACGCTGTTTTAGTTCAATGTTAAAA 59.031 29.630 0.00 0.00 0.00 1.52
3016 3183 7.429920 GTGACGCTGTTTTAGTTCAATGTTAAA 59.570 33.333 0.00 0.00 0.00 1.52
3017 3184 6.908284 GTGACGCTGTTTTAGTTCAATGTTAA 59.092 34.615 0.00 0.00 0.00 2.01
3018 3185 6.259167 AGTGACGCTGTTTTAGTTCAATGTTA 59.741 34.615 0.00 0.00 0.00 2.41
3019 3186 5.065988 AGTGACGCTGTTTTAGTTCAATGTT 59.934 36.000 0.00 0.00 0.00 2.71
3020 3187 4.574828 AGTGACGCTGTTTTAGTTCAATGT 59.425 37.500 0.00 0.00 0.00 2.71
3021 3188 5.095691 AGTGACGCTGTTTTAGTTCAATG 57.904 39.130 0.00 0.00 0.00 2.82
3022 3189 5.751243 AAGTGACGCTGTTTTAGTTCAAT 57.249 34.783 0.00 0.00 0.00 2.57
3023 3190 6.854496 ATAAGTGACGCTGTTTTAGTTCAA 57.146 33.333 0.00 0.00 0.00 2.69
3024 3191 6.854496 AATAAGTGACGCTGTTTTAGTTCA 57.146 33.333 0.00 0.00 0.00 3.18
3025 3192 6.795593 GGAAATAAGTGACGCTGTTTTAGTTC 59.204 38.462 0.00 0.00 31.34 3.01
3026 3193 6.565247 CGGAAATAAGTGACGCTGTTTTAGTT 60.565 38.462 0.00 0.00 0.00 2.24
3027 3194 5.107220 CGGAAATAAGTGACGCTGTTTTAGT 60.107 40.000 0.00 0.00 0.00 2.24
3028 3195 5.119588 TCGGAAATAAGTGACGCTGTTTTAG 59.880 40.000 0.00 0.00 0.00 1.85
3029 3196 4.989797 TCGGAAATAAGTGACGCTGTTTTA 59.010 37.500 0.00 0.00 0.00 1.52
3030 3197 3.810941 TCGGAAATAAGTGACGCTGTTTT 59.189 39.130 0.00 0.00 0.00 2.43
3031 3198 3.395639 TCGGAAATAAGTGACGCTGTTT 58.604 40.909 0.00 0.00 0.00 2.83
3032 3199 3.034721 TCGGAAATAAGTGACGCTGTT 57.965 42.857 0.00 0.00 0.00 3.16
3033 3200 2.735134 GTTCGGAAATAAGTGACGCTGT 59.265 45.455 0.00 0.00 0.00 4.40
3034 3201 2.222508 CGTTCGGAAATAAGTGACGCTG 60.223 50.000 0.00 0.00 0.00 5.18
3035 3202 1.990563 CGTTCGGAAATAAGTGACGCT 59.009 47.619 0.00 0.00 0.00 5.07
3036 3203 1.060122 CCGTTCGGAAATAAGTGACGC 59.940 52.381 5.19 0.00 0.00 5.19
3037 3204 2.597305 CTCCGTTCGGAAATAAGTGACG 59.403 50.000 14.79 0.00 33.41 4.35
3038 3205 2.928116 CCTCCGTTCGGAAATAAGTGAC 59.072 50.000 14.79 0.00 33.41 3.67
3039 3206 2.564062 ACCTCCGTTCGGAAATAAGTGA 59.436 45.455 14.79 0.00 33.41 3.41
3040 3207 2.968675 ACCTCCGTTCGGAAATAAGTG 58.031 47.619 14.79 1.97 33.41 3.16
3041 3208 4.806640 TTACCTCCGTTCGGAAATAAGT 57.193 40.909 14.79 9.62 33.41 2.24
3042 3209 6.510536 AGTATTACCTCCGTTCGGAAATAAG 58.489 40.000 14.79 3.31 33.41 1.73
3043 3210 6.469782 AGTATTACCTCCGTTCGGAAATAA 57.530 37.500 14.79 14.75 33.41 1.40
3044 3211 6.127366 ACAAGTATTACCTCCGTTCGGAAATA 60.127 38.462 14.79 12.45 33.41 1.40
3045 3212 5.114081 CAAGTATTACCTCCGTTCGGAAAT 58.886 41.667 14.79 13.32 33.41 2.17
3046 3213 4.021192 ACAAGTATTACCTCCGTTCGGAAA 60.021 41.667 14.79 7.27 33.41 3.13
3047 3214 3.511146 ACAAGTATTACCTCCGTTCGGAA 59.489 43.478 14.79 0.81 33.41 4.30
3048 3215 3.091545 ACAAGTATTACCTCCGTTCGGA 58.908 45.455 13.34 13.34 0.00 4.55
3049 3216 3.119388 TGACAAGTATTACCTCCGTTCGG 60.119 47.826 4.74 4.74 0.00 4.30
3050 3217 4.100707 TGACAAGTATTACCTCCGTTCG 57.899 45.455 0.00 0.00 0.00 3.95
3051 3218 5.232463 TGTTGACAAGTATTACCTCCGTTC 58.768 41.667 0.00 0.00 0.00 3.95
3052 3219 5.217978 TGTTGACAAGTATTACCTCCGTT 57.782 39.130 0.00 0.00 0.00 4.44
3053 3220 4.877378 TGTTGACAAGTATTACCTCCGT 57.123 40.909 0.00 0.00 0.00 4.69
3054 3221 7.837202 TTAATGTTGACAAGTATTACCTCCG 57.163 36.000 0.00 0.00 0.00 4.63
3055 3222 9.005777 TGTTTAATGTTGACAAGTATTACCTCC 57.994 33.333 0.00 0.00 0.00 4.30
3063 3230 9.676195 CATGTTGATGTTTAATGTTGACAAGTA 57.324 29.630 0.00 0.00 0.00 2.24
3064 3231 8.196771 ACATGTTGATGTTTAATGTTGACAAGT 58.803 29.630 0.00 0.00 40.05 3.16
3065 3232 8.481641 CACATGTTGATGTTTAATGTTGACAAG 58.518 33.333 0.00 0.00 41.12 3.16
3066 3233 7.978414 ACACATGTTGATGTTTAATGTTGACAA 59.022 29.630 0.00 0.00 41.12 3.18
3067 3234 7.487484 ACACATGTTGATGTTTAATGTTGACA 58.513 30.769 0.00 0.00 41.12 3.58
3068 3235 7.928908 ACACATGTTGATGTTTAATGTTGAC 57.071 32.000 0.00 0.00 41.12 3.18
3069 3236 9.676195 CTAACACATGTTGATGTTTAATGTTGA 57.324 29.630 7.53 0.00 41.12 3.18
3070 3237 9.462174 ACTAACACATGTTGATGTTTAATGTTG 57.538 29.630 7.53 0.00 41.12 3.33
3071 3238 9.462174 CACTAACACATGTTGATGTTTAATGTT 57.538 29.630 7.53 0.00 41.12 2.71
3072 3239 7.594758 GCACTAACACATGTTGATGTTTAATGT 59.405 33.333 7.53 0.00 41.12 2.71
3073 3240 7.594386 TGCACTAACACATGTTGATGTTTAATG 59.406 33.333 7.53 0.00 41.12 1.90
3074 3241 7.656412 TGCACTAACACATGTTGATGTTTAAT 58.344 30.769 7.53 0.00 41.12 1.40
3075 3242 7.032377 TGCACTAACACATGTTGATGTTTAA 57.968 32.000 7.53 0.00 41.12 1.52
3076 3243 6.625873 TGCACTAACACATGTTGATGTTTA 57.374 33.333 7.53 0.00 41.12 2.01
3077 3244 5.512753 TGCACTAACACATGTTGATGTTT 57.487 34.783 7.53 0.00 41.12 2.83
3078 3245 5.617529 CGATGCACTAACACATGTTGATGTT 60.618 40.000 7.53 0.00 41.12 2.71
3079 3246 4.142838 CGATGCACTAACACATGTTGATGT 60.143 41.667 7.53 1.61 44.08 3.06
3080 3247 4.093261 TCGATGCACTAACACATGTTGATG 59.907 41.667 7.53 6.61 38.90 3.07
3081 3248 4.252878 TCGATGCACTAACACATGTTGAT 58.747 39.130 7.53 0.00 38.90 2.57
3082 3249 3.658709 TCGATGCACTAACACATGTTGA 58.341 40.909 7.53 0.00 38.90 3.18
3083 3250 4.403015 TTCGATGCACTAACACATGTTG 57.597 40.909 7.53 0.00 38.90 3.33
3084 3251 5.627499 AATTCGATGCACTAACACATGTT 57.373 34.783 0.00 2.32 41.73 2.71
3085 3252 5.181056 TGAAATTCGATGCACTAACACATGT 59.819 36.000 0.00 0.00 0.00 3.21
3086 3253 5.630061 TGAAATTCGATGCACTAACACATG 58.370 37.500 0.00 0.00 0.00 3.21
3087 3254 5.878332 TGAAATTCGATGCACTAACACAT 57.122 34.783 0.00 0.00 0.00 3.21
3088 3255 5.681337 TTGAAATTCGATGCACTAACACA 57.319 34.783 0.00 0.00 0.00 3.72
3089 3256 6.370593 TCTTTGAAATTCGATGCACTAACAC 58.629 36.000 0.00 0.00 0.00 3.32
3090 3257 6.552859 TCTTTGAAATTCGATGCACTAACA 57.447 33.333 0.00 0.00 0.00 2.41
3091 3258 7.851822 TTTCTTTGAAATTCGATGCACTAAC 57.148 32.000 0.00 0.00 0.00 2.34
3092 3259 8.296000 TGATTTCTTTGAAATTCGATGCACTAA 58.704 29.630 6.93 0.00 0.00 2.24
3093 3260 7.815641 TGATTTCTTTGAAATTCGATGCACTA 58.184 30.769 6.93 0.00 0.00 2.74
3094 3261 6.680810 TGATTTCTTTGAAATTCGATGCACT 58.319 32.000 6.93 0.00 0.00 4.40
3095 3262 6.803320 TCTGATTTCTTTGAAATTCGATGCAC 59.197 34.615 6.93 0.00 0.00 4.57
3096 3263 6.912082 TCTGATTTCTTTGAAATTCGATGCA 58.088 32.000 6.93 0.00 0.00 3.96
3097 3264 7.982371 ATCTGATTTCTTTGAAATTCGATGC 57.018 32.000 6.93 0.00 0.00 3.91
3098 3265 9.563898 TGAATCTGATTTCTTTGAAATTCGATG 57.436 29.630 4.11 0.00 0.00 3.84
3099 3266 9.565213 GTGAATCTGATTTCTTTGAAATTCGAT 57.435 29.630 4.11 8.66 0.00 3.59
3100 3267 8.567104 TGTGAATCTGATTTCTTTGAAATTCGA 58.433 29.630 4.11 7.12 0.00 3.71
3101 3268 8.732413 TGTGAATCTGATTTCTTTGAAATTCG 57.268 30.769 4.11 2.85 0.00 3.34
3106 3273 9.903682 GAGAAATGTGAATCTGATTTCTTTGAA 57.096 29.630 15.94 0.00 43.34 2.69
3107 3274 8.517878 GGAGAAATGTGAATCTGATTTCTTTGA 58.482 33.333 15.94 0.00 43.34 2.69
3108 3275 7.484007 CGGAGAAATGTGAATCTGATTTCTTTG 59.516 37.037 15.94 10.65 43.34 2.77
3109 3276 7.533426 CGGAGAAATGTGAATCTGATTTCTTT 58.467 34.615 15.94 2.97 43.34 2.52
3110 3277 6.404074 GCGGAGAAATGTGAATCTGATTTCTT 60.404 38.462 15.94 5.84 43.34 2.52
3111 3278 5.065731 GCGGAGAAATGTGAATCTGATTTCT 59.934 40.000 15.22 15.22 45.05 2.52
3112 3279 5.163723 TGCGGAGAAATGTGAATCTGATTTC 60.164 40.000 4.11 8.53 36.67 2.17
3113 3280 4.701651 TGCGGAGAAATGTGAATCTGATTT 59.298 37.500 4.11 0.00 0.00 2.17
3114 3281 4.264253 TGCGGAGAAATGTGAATCTGATT 58.736 39.130 1.81 1.81 0.00 2.57
3115 3282 3.877559 TGCGGAGAAATGTGAATCTGAT 58.122 40.909 0.00 0.00 0.00 2.90
3116 3283 3.333029 TGCGGAGAAATGTGAATCTGA 57.667 42.857 0.00 0.00 0.00 3.27
3117 3284 4.627611 AATGCGGAGAAATGTGAATCTG 57.372 40.909 0.00 0.00 0.00 2.90
3118 3285 6.757897 TTTAATGCGGAGAAATGTGAATCT 57.242 33.333 0.00 0.00 0.00 2.40
3119 3286 7.992180 ATTTTAATGCGGAGAAATGTGAATC 57.008 32.000 0.00 0.00 0.00 2.52
3120 3287 8.137437 CCTATTTTAATGCGGAGAAATGTGAAT 58.863 33.333 6.13 0.00 0.00 2.57
3121 3288 7.122055 ACCTATTTTAATGCGGAGAAATGTGAA 59.878 33.333 6.13 0.00 0.00 3.18
3122 3289 6.601613 ACCTATTTTAATGCGGAGAAATGTGA 59.398 34.615 6.13 0.00 0.00 3.58
3123 3290 6.795399 ACCTATTTTAATGCGGAGAAATGTG 58.205 36.000 6.13 1.59 0.00 3.21
3124 3291 6.039382 GGACCTATTTTAATGCGGAGAAATGT 59.961 38.462 6.13 0.00 0.00 2.71
3125 3292 6.438763 GGACCTATTTTAATGCGGAGAAATG 58.561 40.000 6.13 0.00 0.00 2.32
3126 3293 5.238650 CGGACCTATTTTAATGCGGAGAAAT 59.761 40.000 0.00 2.36 0.00 2.17
3127 3294 4.573201 CGGACCTATTTTAATGCGGAGAAA 59.427 41.667 0.00 0.00 0.00 2.52
3128 3295 4.124238 CGGACCTATTTTAATGCGGAGAA 58.876 43.478 0.00 0.00 0.00 2.87
3129 3296 3.724374 CGGACCTATTTTAATGCGGAGA 58.276 45.455 0.00 0.00 0.00 3.71
3133 3300 3.242936 CCAACCGGACCTATTTTAATGCG 60.243 47.826 9.46 0.00 0.00 4.73
3134 3301 3.067601 CCCAACCGGACCTATTTTAATGC 59.932 47.826 9.46 0.00 0.00 3.56
3135 3302 4.528920 TCCCAACCGGACCTATTTTAATG 58.471 43.478 9.46 0.00 34.86 1.90
3136 3303 4.475747 TCTCCCAACCGGACCTATTTTAAT 59.524 41.667 9.46 0.00 34.86 1.40
3137 3304 3.845398 TCTCCCAACCGGACCTATTTTAA 59.155 43.478 9.46 0.00 34.86 1.52
3138 3305 3.452878 TCTCCCAACCGGACCTATTTTA 58.547 45.455 9.46 0.00 34.86 1.52
3139 3306 2.271777 TCTCCCAACCGGACCTATTTT 58.728 47.619 9.46 0.00 34.86 1.82
3140 3307 1.961133 TCTCCCAACCGGACCTATTT 58.039 50.000 9.46 0.00 34.86 1.40
3141 3308 2.047830 GATCTCCCAACCGGACCTATT 58.952 52.381 9.46 0.00 34.86 1.73
3142 3309 1.062428 TGATCTCCCAACCGGACCTAT 60.062 52.381 9.46 0.00 34.86 2.57
3143 3310 0.337082 TGATCTCCCAACCGGACCTA 59.663 55.000 9.46 0.00 34.86 3.08
3144 3311 0.326618 ATGATCTCCCAACCGGACCT 60.327 55.000 9.46 0.00 34.86 3.85
3145 3312 0.546598 AATGATCTCCCAACCGGACC 59.453 55.000 9.46 0.00 34.86 4.46
3146 3313 3.553828 TTAATGATCTCCCAACCGGAC 57.446 47.619 9.46 0.00 34.86 4.79
3147 3314 5.897851 TTATTAATGATCTCCCAACCGGA 57.102 39.130 9.46 0.00 38.83 5.14
3148 3315 6.237901 TGATTATTAATGATCTCCCAACCGG 58.762 40.000 18.06 0.00 0.00 5.28
3149 3316 6.936900 ACTGATTATTAATGATCTCCCAACCG 59.063 38.462 18.06 3.37 0.00 4.44
3150 3317 9.793259 TTACTGATTATTAATGATCTCCCAACC 57.207 33.333 18.06 0.00 0.00 3.77
3152 3319 9.793259 GGTTACTGATTATTAATGATCTCCCAA 57.207 33.333 18.06 7.16 0.00 4.12
3153 3320 8.944138 TGGTTACTGATTATTAATGATCTCCCA 58.056 33.333 18.06 13.54 0.00 4.37
3154 3321 9.965902 ATGGTTACTGATTATTAATGATCTCCC 57.034 33.333 18.06 11.78 0.00 4.30


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

AutoCloner maintained by Alex Coulton.