Multiple sequence alignment - TraesCS4B01G098200

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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 TraesCS4B01G098200 chr4B 100.000 2565 0 0 941 3505 103056465 103053901 0.000000e+00 4737.0
1 TraesCS4B01G098200 chr4B 100.000 509 0 0 1 509 103057405 103056897 0.000000e+00 941.0
2 TraesCS4B01G098200 chr4B 100.000 114 0 0 3050 3163 103054238 103054125 9.860000e-51 211.0
3 TraesCS4B01G098200 chr4B 100.000 114 0 0 3168 3281 103054356 103054243 9.860000e-51 211.0
4 TraesCS4B01G098200 chr4A 92.397 2236 102 26 947 3163 521919955 521917769 0.000000e+00 3125.0
5 TraesCS4B01G098200 chr4A 89.808 520 23 11 20 509 521920605 521920086 1.060000e-179 640.0
6 TraesCS4B01G098200 chr4A 91.500 200 13 3 3168 3364 521917884 521917686 4.460000e-69 272.0
7 TraesCS4B01G098200 chr4D 91.878 1699 67 27 1511 3163 69679680 69678007 0.000000e+00 2307.0
8 TraesCS4B01G098200 chr4D 94.805 539 16 3 946 1479 69680212 69679681 0.000000e+00 830.0
9 TraesCS4B01G098200 chr4D 92.969 512 22 7 1 509 69680833 69680333 0.000000e+00 734.0
10 TraesCS4B01G098200 chr4D 92.670 191 12 1 3171 3359 69678119 69677929 1.240000e-69 274.0
11 TraesCS4B01G098200 chr4D 91.304 69 5 1 3364 3431 499845374 499845442 3.730000e-15 93.5
12 TraesCS4B01G098200 chr2B 95.152 1052 24 14 2122 3163 214818215 214819249 0.000000e+00 1635.0
13 TraesCS4B01G098200 chr2B 96.465 198 6 1 3168 3364 214819136 214819333 3.370000e-85 326.0
14 TraesCS4B01G098200 chr2B 87.838 74 6 3 1034 1106 799029270 799029341 2.240000e-12 84.2
15 TraesCS4B01G098200 chr2B 92.453 53 4 0 1034 1086 799107558 799107506 3.750000e-10 76.8
16 TraesCS4B01G098200 chr1D 91.915 235 17 2 1202 1435 359665806 359665573 9.380000e-86 327.0
17 TraesCS4B01G098200 chr1A 91.064 235 19 2 1202 1435 459188125 459187892 2.030000e-82 316.0
18 TraesCS4B01G098200 chr3D 90.638 235 20 2 1202 1435 515776705 515776938 9.450000e-81 311.0
19 TraesCS4B01G098200 chr3A 90.638 235 20 2 1202 1435 650056443 650056676 9.450000e-81 311.0
20 TraesCS4B01G098200 chr1B 90.638 235 20 2 1202 1435 481542083 481541850 9.450000e-81 311.0
21 TraesCS4B01G098200 chr3B 90.213 235 21 2 1202 1435 678548566 678548799 4.400000e-79 305.0
22 TraesCS4B01G098200 chr6D 79.177 413 70 14 1031 1438 27820272 27819871 4.460000e-69 272.0
23 TraesCS4B01G098200 chr7D 97.500 40 1 0 1032 1071 412761583 412761622 6.280000e-08 69.4
24 TraesCS4B01G098200 chr7B 97.500 40 1 0 1032 1071 426972987 426973026 6.280000e-08 69.4
25 TraesCS4B01G098200 chr7B 85.294 68 7 3 3372 3437 667472042 667472108 2.260000e-07 67.6
26 TraesCS4B01G098200 chr7A 97.500 40 1 0 1032 1071 473921377 473921416 6.280000e-08 69.4


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 TraesCS4B01G098200 chr4B 103053901 103057405 3504 True 1525.000000 4737 100.0000 1 3505 4 chr4B.!!$R1 3504
1 TraesCS4B01G098200 chr4A 521917686 521920605 2919 True 1345.666667 3125 91.2350 20 3364 3 chr4A.!!$R1 3344
2 TraesCS4B01G098200 chr4D 69677929 69680833 2904 True 1036.250000 2307 93.0805 1 3359 4 chr4D.!!$R1 3358
3 TraesCS4B01G098200 chr2B 214818215 214819333 1118 False 980.500000 1635 95.8085 2122 3364 2 chr2B.!!$F2 1242

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
244 256 0.046397 ATGCCTCCCTTCCTAACCCT 59.954 55.0 0.00 0.0 0.00 4.34 F
435 462 0.098200 GTCCGATGATCGACACGTGA 59.902 55.0 25.01 0.0 43.74 4.35 F
1461 1499 0.663153 GCAAGAAGTCCAACAACGCT 59.337 50.0 0.00 0.0 0.00 5.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1499 1537 0.322997 AGACTGACAGAGAGGGGACG 60.323 60.0 10.08 0.0 0.0 4.79 R
1501 1539 0.613292 GCAGACTGACAGAGAGGGGA 60.613 60.0 10.08 0.0 0.0 4.81 R
3095 3183 0.033504 GAGACCACCACTGAAAGCGA 59.966 55.0 0.00 0.0 37.6 4.93 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
144 150 3.579534 TTACCCTACGAGCTGAGAGAT 57.420 47.619 0.00 0.00 0.00 2.75
145 151 1.975660 ACCCTACGAGCTGAGAGATC 58.024 55.000 0.00 0.00 0.00 2.75
196 203 2.488347 CCCGTACAATTATCCCAAGGGG 60.488 54.545 5.08 0.00 46.11 4.79
244 256 0.046397 ATGCCTCCCTTCCTAACCCT 59.954 55.000 0.00 0.00 0.00 4.34
255 267 4.619419 TAACCCTGGGCCCCACCA 62.619 66.667 22.27 0.00 42.05 4.17
266 278 3.569210 CCCACCACACAGGCAGGA 61.569 66.667 0.00 0.00 43.14 3.86
269 287 1.480212 CCACCACACAGGCAGGAGTA 61.480 60.000 0.00 0.00 43.14 2.59
371 398 1.064166 CATGACAATTGAGCTCCCCCT 60.064 52.381 13.59 0.00 0.00 4.79
435 462 0.098200 GTCCGATGATCGACACGTGA 59.902 55.000 25.01 0.00 43.74 4.35
436 463 0.098200 TCCGATGATCGACACGTGAC 59.902 55.000 25.01 16.07 43.74 3.67
437 464 0.866061 CCGATGATCGACACGTGACC 60.866 60.000 25.01 12.41 43.74 4.02
439 466 1.329599 CGATGATCGACACGTGACCTA 59.670 52.381 25.01 6.36 43.74 3.08
441 468 3.185797 CGATGATCGACACGTGACCTATA 59.814 47.826 25.01 4.63 43.74 1.31
446 473 3.548770 TCGACACGTGACCTATAATCCT 58.451 45.455 25.01 0.00 0.00 3.24
449 476 4.274214 CGACACGTGACCTATAATCCTACA 59.726 45.833 25.01 0.00 0.00 2.74
469 502 2.612115 CAACCAGCCCCCTCCTCT 60.612 66.667 0.00 0.00 0.00 3.69
494 527 1.560004 CTTGCACGTGCGTCACATCT 61.560 55.000 33.22 0.00 45.83 2.90
495 528 1.157257 TTGCACGTGCGTCACATCTT 61.157 50.000 33.22 0.00 45.83 2.40
964 997 1.327690 TAACCAATCTCCCGAGCGCT 61.328 55.000 11.27 11.27 0.00 5.92
1006 1044 3.379445 ACCGGACGCGAATGGACT 61.379 61.111 15.93 0.00 0.00 3.85
1227 1265 1.872679 GTACTTCTTCTCGCCGCGG 60.873 63.158 24.05 24.05 0.00 6.46
1461 1499 0.663153 GCAAGAAGTCCAACAACGCT 59.337 50.000 0.00 0.00 0.00 5.07
1484 1522 3.681473 GGTAACCACCTTGCCTGC 58.319 61.111 0.00 0.00 42.11 4.85
1485 1523 1.977009 GGTAACCACCTTGCCTGCC 60.977 63.158 0.00 0.00 42.11 4.85
1486 1524 1.074951 GTAACCACCTTGCCTGCCT 59.925 57.895 0.00 0.00 0.00 4.75
1487 1525 1.074775 TAACCACCTTGCCTGCCTG 59.925 57.895 0.00 0.00 0.00 4.85
1488 1526 4.982701 ACCACCTTGCCTGCCTGC 62.983 66.667 0.00 0.00 0.00 4.85
1515 1553 2.055042 CCCGTCCCCTCTCTGTCAG 61.055 68.421 0.00 0.00 0.00 3.51
1555 1593 4.142004 GCTGTCTCGTTTAATCCCTTCCTA 60.142 45.833 0.00 0.00 0.00 2.94
1593 1631 6.641314 CGAGAGATTTACCGTGCATTTAGTAT 59.359 38.462 0.00 0.00 0.00 2.12
1601 1639 9.602568 TTTACCGTGCATTTAGTATAGAAATCA 57.397 29.630 0.00 0.00 0.00 2.57
1603 1641 8.142994 ACCGTGCATTTAGTATAGAAATCAAG 57.857 34.615 0.00 0.00 0.00 3.02
1606 1644 7.306574 CGTGCATTTAGTATAGAAATCAAGCGA 60.307 37.037 0.00 0.00 0.00 4.93
1630 1668 7.319142 AGAGATCTTTCTTGAAATAGCAAGC 57.681 36.000 0.00 0.00 43.78 4.01
1631 1669 7.111466 AGAGATCTTTCTTGAAATAGCAAGCT 58.889 34.615 0.00 0.00 43.78 3.74
1709 1747 3.680777 AAGAACAAGGGAAAAGGGTCA 57.319 42.857 0.00 0.00 0.00 4.02
1814 1859 2.358615 GTCATGGCTCACGCACCA 60.359 61.111 0.00 0.00 41.06 4.17
1894 1939 6.534059 CGTACACGTACACTAGCTTTAGTTA 58.466 40.000 8.02 0.00 35.87 2.24
2114 2159 4.015406 CAGTACCACGCTGGGCCA 62.015 66.667 5.85 5.85 43.37 5.36
2420 2468 1.589993 CATCGACGGCTCGCTGATT 60.590 57.895 4.48 0.00 38.11 2.57
2513 2561 2.270352 AACCGTTCTGAATGAAGGCA 57.730 45.000 11.11 0.00 38.73 4.75
2527 2575 1.548357 AAGGCAGCATCCGTCAGACT 61.548 55.000 0.00 0.00 0.00 3.24
2537 2585 0.750182 CCGTCAGACTCCTCCTCCTC 60.750 65.000 0.00 0.00 0.00 3.71
2543 2591 1.675720 GACTCCTCCTCCTCAGCAGC 61.676 65.000 0.00 0.00 0.00 5.25
2595 2664 0.603065 ATTCGGTTTGCAAGCTTCCC 59.397 50.000 13.27 2.66 0.00 3.97
2663 2732 6.019748 ACAAATCTGATACCCCTAGATCGAT 58.980 40.000 0.00 0.00 31.16 3.59
2758 2829 2.573340 GGCATTTGGGCGACTTGG 59.427 61.111 0.00 0.00 33.57 3.61
2854 2926 1.897423 CATGGTCAGGTAGCCGTCA 59.103 57.895 0.00 0.00 0.00 4.35
2866 2938 3.985925 GGTAGCCGTCAGGTAATATTTCG 59.014 47.826 0.00 0.00 40.50 3.46
2920 3005 6.579865 AGAAGTAGAGGTCGAACAAGAAAAA 58.420 36.000 1.87 0.00 0.00 1.94
2924 3009 5.993106 AGAGGTCGAACAAGAAAAAGAAG 57.007 39.130 1.87 0.00 0.00 2.85
3031 3119 1.227556 GGTTCAGTGTCGTGGCAGT 60.228 57.895 0.00 0.00 0.00 4.40
3065 3153 6.975772 GCTTTTAGGTTTTGTTGTGTCATGTA 59.024 34.615 0.00 0.00 0.00 2.29
3066 3154 7.489757 GCTTTTAGGTTTTGTTGTGTCATGTAA 59.510 33.333 0.00 0.00 0.00 2.41
3067 3155 9.528018 CTTTTAGGTTTTGTTGTGTCATGTAAT 57.472 29.630 0.00 0.00 0.00 1.89
3068 3156 9.877178 TTTTAGGTTTTGTTGTGTCATGTAATT 57.123 25.926 0.00 0.00 0.00 1.40
3069 3157 8.864069 TTAGGTTTTGTTGTGTCATGTAATTG 57.136 30.769 0.00 0.00 0.00 2.32
3070 3158 6.872920 AGGTTTTGTTGTGTCATGTAATTGT 58.127 32.000 0.00 0.00 0.00 2.71
3071 3159 8.001881 AGGTTTTGTTGTGTCATGTAATTGTA 57.998 30.769 0.00 0.00 0.00 2.41
3072 3160 8.470805 AGGTTTTGTTGTGTCATGTAATTGTAA 58.529 29.630 0.00 0.00 0.00 2.41
3073 3161 9.255304 GGTTTTGTTGTGTCATGTAATTGTAAT 57.745 29.630 0.00 0.00 0.00 1.89
3076 3164 7.865875 TGTTGTGTCATGTAATTGTAATTGC 57.134 32.000 0.27 0.00 0.00 3.56
3077 3165 6.580416 TGTTGTGTCATGTAATTGTAATTGCG 59.420 34.615 0.27 0.00 34.29 4.85
3078 3166 6.487689 TGTGTCATGTAATTGTAATTGCGA 57.512 33.333 0.27 0.00 34.29 5.10
3079 3167 6.903419 TGTGTCATGTAATTGTAATTGCGAA 58.097 32.000 0.27 0.00 34.29 4.70
3080 3168 7.020602 TGTGTCATGTAATTGTAATTGCGAAG 58.979 34.615 0.27 0.00 34.29 3.79
3081 3169 7.095017 TGTGTCATGTAATTGTAATTGCGAAGA 60.095 33.333 0.27 0.00 34.29 2.87
3082 3170 7.910162 GTGTCATGTAATTGTAATTGCGAAGAT 59.090 33.333 0.27 0.00 34.29 2.40
3083 3171 7.909641 TGTCATGTAATTGTAATTGCGAAGATG 59.090 33.333 0.27 0.31 34.29 2.90
3084 3172 8.122330 GTCATGTAATTGTAATTGCGAAGATGA 58.878 33.333 0.27 2.33 34.29 2.92
3085 3173 8.839343 TCATGTAATTGTAATTGCGAAGATGAT 58.161 29.630 0.27 0.00 34.29 2.45
3086 3174 8.898792 CATGTAATTGTAATTGCGAAGATGATG 58.101 33.333 0.27 0.00 34.29 3.07
3087 3175 7.984391 TGTAATTGTAATTGCGAAGATGATGT 58.016 30.769 0.27 0.00 34.29 3.06
3088 3176 7.909641 TGTAATTGTAATTGCGAAGATGATGTG 59.090 33.333 0.27 0.00 34.29 3.21
3089 3177 6.682423 ATTGTAATTGCGAAGATGATGTGA 57.318 33.333 0.00 0.00 0.00 3.58
3090 3178 6.682423 TTGTAATTGCGAAGATGATGTGAT 57.318 33.333 0.00 0.00 0.00 3.06
3091 3179 7.784633 TTGTAATTGCGAAGATGATGTGATA 57.215 32.000 0.00 0.00 0.00 2.15
3092 3180 7.412137 TGTAATTGCGAAGATGATGTGATAG 57.588 36.000 0.00 0.00 0.00 2.08
3093 3181 7.209475 TGTAATTGCGAAGATGATGTGATAGA 58.791 34.615 0.00 0.00 0.00 1.98
3094 3182 6.782298 AATTGCGAAGATGATGTGATAGAG 57.218 37.500 0.00 0.00 0.00 2.43
3095 3183 4.926140 TGCGAAGATGATGTGATAGAGT 57.074 40.909 0.00 0.00 0.00 3.24
3096 3184 4.864633 TGCGAAGATGATGTGATAGAGTC 58.135 43.478 0.00 0.00 0.00 3.36
3097 3185 3.911365 GCGAAGATGATGTGATAGAGTCG 59.089 47.826 0.00 0.00 0.00 4.18
3098 3186 3.911365 CGAAGATGATGTGATAGAGTCGC 59.089 47.826 0.00 0.00 37.86 5.19
3099 3187 4.320129 CGAAGATGATGTGATAGAGTCGCT 60.320 45.833 0.00 0.00 38.20 4.93
3100 3188 5.527951 GAAGATGATGTGATAGAGTCGCTT 58.472 41.667 0.00 0.00 38.20 4.68
3101 3189 5.528043 AGATGATGTGATAGAGTCGCTTT 57.472 39.130 0.00 0.00 38.20 3.51
3102 3190 5.527951 AGATGATGTGATAGAGTCGCTTTC 58.472 41.667 0.00 0.00 38.20 2.62
3103 3191 4.718940 TGATGTGATAGAGTCGCTTTCA 57.281 40.909 0.00 0.00 38.20 2.69
3104 3192 4.676546 TGATGTGATAGAGTCGCTTTCAG 58.323 43.478 0.00 0.00 35.64 3.02
3105 3193 4.158579 TGATGTGATAGAGTCGCTTTCAGT 59.841 41.667 0.00 0.00 35.64 3.41
3106 3194 3.838120 TGTGATAGAGTCGCTTTCAGTG 58.162 45.455 0.00 0.00 35.64 3.66
3107 3195 3.182967 GTGATAGAGTCGCTTTCAGTGG 58.817 50.000 0.00 0.00 35.64 4.00
3108 3196 2.826128 TGATAGAGTCGCTTTCAGTGGT 59.174 45.455 0.00 0.00 31.99 4.16
3109 3197 2.724977 TAGAGTCGCTTTCAGTGGTG 57.275 50.000 0.00 0.00 0.00 4.17
3110 3198 0.034059 AGAGTCGCTTTCAGTGGTGG 59.966 55.000 0.00 0.00 0.00 4.61
3111 3199 0.249911 GAGTCGCTTTCAGTGGTGGT 60.250 55.000 0.00 0.00 0.00 4.16
3112 3200 0.249911 AGTCGCTTTCAGTGGTGGTC 60.250 55.000 0.00 0.00 0.00 4.02
3113 3201 0.249911 GTCGCTTTCAGTGGTGGTCT 60.250 55.000 0.00 0.00 0.00 3.85
3114 3202 0.033504 TCGCTTTCAGTGGTGGTCTC 59.966 55.000 0.00 0.00 0.00 3.36
3115 3203 0.034059 CGCTTTCAGTGGTGGTCTCT 59.966 55.000 0.00 0.00 0.00 3.10
3116 3204 1.802069 GCTTTCAGTGGTGGTCTCTC 58.198 55.000 0.00 0.00 0.00 3.20
3117 3205 1.937108 GCTTTCAGTGGTGGTCTCTCG 60.937 57.143 0.00 0.00 0.00 4.04
3118 3206 0.679505 TTTCAGTGGTGGTCTCTCGG 59.320 55.000 0.00 0.00 0.00 4.63
3119 3207 1.185618 TTCAGTGGTGGTCTCTCGGG 61.186 60.000 0.00 0.00 0.00 5.14
3120 3208 1.908793 CAGTGGTGGTCTCTCGGGT 60.909 63.158 0.00 0.00 0.00 5.28
3121 3209 1.908793 AGTGGTGGTCTCTCGGGTG 60.909 63.158 0.00 0.00 0.00 4.61
3122 3210 1.906824 GTGGTGGTCTCTCGGGTGA 60.907 63.158 0.00 0.00 0.00 4.02
3123 3211 1.906824 TGGTGGTCTCTCGGGTGAC 60.907 63.158 9.01 9.01 35.83 3.67
3135 3223 2.112297 GGTGACCTGGAACGCCAA 59.888 61.111 17.82 0.00 45.41 4.52
3136 3224 1.303317 GGTGACCTGGAACGCCAAT 60.303 57.895 17.82 0.00 45.41 3.16
3137 3225 0.893727 GGTGACCTGGAACGCCAATT 60.894 55.000 17.82 0.00 45.41 2.32
3138 3226 0.958822 GTGACCTGGAACGCCAATTT 59.041 50.000 0.00 0.00 45.41 1.82
3139 3227 1.339929 GTGACCTGGAACGCCAATTTT 59.660 47.619 0.00 0.00 45.41 1.82
3140 3228 1.339610 TGACCTGGAACGCCAATTTTG 59.660 47.619 0.00 0.00 45.41 2.44
3141 3229 1.339929 GACCTGGAACGCCAATTTTGT 59.660 47.619 0.00 0.00 45.41 2.83
3142 3230 2.554893 GACCTGGAACGCCAATTTTGTA 59.445 45.455 0.00 0.00 45.41 2.41
3143 3231 2.959707 ACCTGGAACGCCAATTTTGTAA 59.040 40.909 0.00 0.00 45.41 2.41
3144 3232 3.576550 ACCTGGAACGCCAATTTTGTAAT 59.423 39.130 0.00 0.00 45.41 1.89
3145 3233 3.925913 CCTGGAACGCCAATTTTGTAATG 59.074 43.478 0.00 0.00 45.41 1.90
3146 3234 3.321497 TGGAACGCCAATTTTGTAATGC 58.679 40.909 0.00 0.00 42.49 3.56
3147 3235 3.243873 TGGAACGCCAATTTTGTAATGCA 60.244 39.130 0.00 0.00 42.49 3.96
3148 3236 3.743396 GGAACGCCAATTTTGTAATGCAA 59.257 39.130 0.00 0.00 34.87 4.08
3149 3237 4.391523 GGAACGCCAATTTTGTAATGCAAT 59.608 37.500 0.00 0.00 36.89 3.56
3150 3238 5.106752 GGAACGCCAATTTTGTAATGCAATT 60.107 36.000 0.00 0.00 41.28 2.32
3151 3239 5.280328 ACGCCAATTTTGTAATGCAATTG 57.720 34.783 0.00 0.00 36.99 2.32
3152 3240 4.754114 ACGCCAATTTTGTAATGCAATTGT 59.246 33.333 7.40 0.00 36.99 2.71
3153 3241 5.107143 ACGCCAATTTTGTAATGCAATTGTC 60.107 36.000 7.40 0.07 36.99 3.18
3154 3242 5.315195 GCCAATTTTGTAATGCAATTGTCG 58.685 37.500 7.40 0.00 36.99 4.35
3155 3243 5.107143 GCCAATTTTGTAATGCAATTGTCGT 60.107 36.000 7.40 0.00 36.99 4.34
3156 3244 6.090088 GCCAATTTTGTAATGCAATTGTCGTA 59.910 34.615 7.40 0.00 36.99 3.43
3157 3245 7.359598 GCCAATTTTGTAATGCAATTGTCGTAA 60.360 33.333 7.40 0.00 36.99 3.18
3158 3246 8.655092 CCAATTTTGTAATGCAATTGTCGTAAT 58.345 29.630 7.40 0.00 36.99 1.89
3164 3252 8.760703 TGTAATGCAATTGTCGTAATAATTCG 57.239 30.769 7.40 0.00 36.99 3.34
3165 3253 8.604890 TGTAATGCAATTGTCGTAATAATTCGA 58.395 29.630 7.40 0.00 36.99 3.71
3177 3265 7.853524 TCGTAATAATTCGACTTTTGTTGTGT 58.146 30.769 0.00 0.00 35.36 3.72
3178 3266 8.005466 TCGTAATAATTCGACTTTTGTTGTGTC 58.995 33.333 0.00 0.00 35.36 3.67
3179 3267 7.794810 CGTAATAATTCGACTTTTGTTGTGTCA 59.205 33.333 0.00 0.00 35.36 3.58
3269 3358 5.280328 ACGCCAATTTTGTAATGCAATTG 57.720 34.783 0.00 0.00 36.99 2.32
3287 3376 8.903570 TGCAATTGTCGTAATAATTAAACAGG 57.096 30.769 7.40 0.00 0.00 4.00
3325 3414 6.608808 AGTTATCTATGGCCTCATTTTGCTTT 59.391 34.615 3.32 0.00 34.96 3.51
3337 3426 2.676016 TTTGCTTTTGTCCTGCGCCG 62.676 55.000 4.18 0.00 0.00 6.46
3364 3454 1.308783 TTTGCTTGCACGGTCACACA 61.309 50.000 0.00 0.00 0.00 3.72
3365 3455 1.308783 TTGCTTGCACGGTCACACAA 61.309 50.000 0.00 0.00 0.00 3.33
3366 3456 1.009675 GCTTGCACGGTCACACAAG 60.010 57.895 0.00 0.00 41.89 3.16
3367 3457 1.714899 GCTTGCACGGTCACACAAGT 61.715 55.000 0.00 0.00 41.22 3.16
3368 3458 0.732571 CTTGCACGGTCACACAAGTT 59.267 50.000 0.00 0.00 35.81 2.66
3369 3459 1.132262 CTTGCACGGTCACACAAGTTT 59.868 47.619 0.00 0.00 35.81 2.66
3370 3460 1.169577 TGCACGGTCACACAAGTTTT 58.830 45.000 0.00 0.00 0.00 2.43
3371 3461 1.542030 TGCACGGTCACACAAGTTTTT 59.458 42.857 0.00 0.00 0.00 1.94
3372 3462 2.182014 GCACGGTCACACAAGTTTTTC 58.818 47.619 0.00 0.00 0.00 2.29
3373 3463 2.414824 GCACGGTCACACAAGTTTTTCA 60.415 45.455 0.00 0.00 0.00 2.69
3374 3464 3.827625 CACGGTCACACAAGTTTTTCAA 58.172 40.909 0.00 0.00 0.00 2.69
3375 3465 4.420168 CACGGTCACACAAGTTTTTCAAT 58.580 39.130 0.00 0.00 0.00 2.57
3376 3466 4.862018 CACGGTCACACAAGTTTTTCAATT 59.138 37.500 0.00 0.00 0.00 2.32
3377 3467 5.347364 CACGGTCACACAAGTTTTTCAATTT 59.653 36.000 0.00 0.00 0.00 1.82
3378 3468 5.575218 ACGGTCACACAAGTTTTTCAATTTC 59.425 36.000 0.00 0.00 0.00 2.17
3379 3469 5.574830 CGGTCACACAAGTTTTTCAATTTCA 59.425 36.000 0.00 0.00 0.00 2.69
3380 3470 6.237542 CGGTCACACAAGTTTTTCAATTTCAG 60.238 38.462 0.00 0.00 0.00 3.02
3381 3471 6.589907 GGTCACACAAGTTTTTCAATTTCAGT 59.410 34.615 0.00 0.00 0.00 3.41
3382 3472 7.117667 GGTCACACAAGTTTTTCAATTTCAGTT 59.882 33.333 0.00 0.00 0.00 3.16
3383 3473 8.495148 GTCACACAAGTTTTTCAATTTCAGTTT 58.505 29.630 0.00 0.00 0.00 2.66
3384 3474 8.707839 TCACACAAGTTTTTCAATTTCAGTTTC 58.292 29.630 0.00 0.00 0.00 2.78
3385 3475 8.494347 CACACAAGTTTTTCAATTTCAGTTTCA 58.506 29.630 0.00 0.00 0.00 2.69
3386 3476 8.711457 ACACAAGTTTTTCAATTTCAGTTTCAG 58.289 29.630 0.00 0.00 0.00 3.02
3387 3477 8.924691 CACAAGTTTTTCAATTTCAGTTTCAGA 58.075 29.630 0.00 0.00 0.00 3.27
3388 3478 9.487790 ACAAGTTTTTCAATTTCAGTTTCAGAA 57.512 25.926 0.00 0.00 0.00 3.02
3401 3491 8.419076 TTCAGTTTCAGAAAATTTTTAGCACC 57.581 30.769 4.63 0.00 0.00 5.01
3402 3492 7.551585 TCAGTTTCAGAAAATTTTTAGCACCA 58.448 30.769 4.63 0.00 0.00 4.17
3403 3493 8.037758 TCAGTTTCAGAAAATTTTTAGCACCAA 58.962 29.630 4.63 0.00 0.00 3.67
3404 3494 8.116136 CAGTTTCAGAAAATTTTTAGCACCAAC 58.884 33.333 4.63 3.27 0.00 3.77
3405 3495 7.279981 AGTTTCAGAAAATTTTTAGCACCAACC 59.720 33.333 4.63 0.00 0.00 3.77
3406 3496 5.285651 TCAGAAAATTTTTAGCACCAACCG 58.714 37.500 4.63 0.00 0.00 4.44
3407 3497 5.067936 TCAGAAAATTTTTAGCACCAACCGA 59.932 36.000 4.63 0.00 0.00 4.69
3408 3498 5.751028 CAGAAAATTTTTAGCACCAACCGAA 59.249 36.000 4.63 0.00 0.00 4.30
3409 3499 6.256757 CAGAAAATTTTTAGCACCAACCGAAA 59.743 34.615 4.63 0.00 0.00 3.46
3410 3500 6.989759 AGAAAATTTTTAGCACCAACCGAAAT 59.010 30.769 4.63 0.00 0.00 2.17
3411 3501 6.779115 AAATTTTTAGCACCAACCGAAATC 57.221 33.333 0.00 0.00 0.00 2.17
3412 3502 4.920640 TTTTTAGCACCAACCGAAATCA 57.079 36.364 0.00 0.00 0.00 2.57
3413 3503 5.461032 TTTTTAGCACCAACCGAAATCAT 57.539 34.783 0.00 0.00 0.00 2.45
3414 3504 4.695217 TTTAGCACCAACCGAAATCATC 57.305 40.909 0.00 0.00 0.00 2.92
3437 3527 5.500740 GAAATTCAGTGATTTCGGTTTGC 57.499 39.130 0.00 0.00 36.59 3.68
3438 3528 4.582701 AATTCAGTGATTTCGGTTTGCA 57.417 36.364 0.00 0.00 0.00 4.08
3439 3529 3.347958 TTCAGTGATTTCGGTTTGCAC 57.652 42.857 0.00 0.00 0.00 4.57
3440 3530 2.571212 TCAGTGATTTCGGTTTGCACT 58.429 42.857 0.00 0.00 40.17 4.40
3441 3531 2.948979 TCAGTGATTTCGGTTTGCACTT 59.051 40.909 0.00 0.00 37.69 3.16
3442 3532 3.003275 TCAGTGATTTCGGTTTGCACTTC 59.997 43.478 0.00 0.00 37.69 3.01
3443 3533 2.948979 AGTGATTTCGGTTTGCACTTCA 59.051 40.909 0.00 0.00 36.49 3.02
3444 3534 3.003689 AGTGATTTCGGTTTGCACTTCAG 59.996 43.478 0.00 0.00 36.49 3.02
3445 3535 2.287547 TGATTTCGGTTTGCACTTCAGC 60.288 45.455 0.00 0.00 0.00 4.26
3446 3536 0.383949 TTTCGGTTTGCACTTCAGCC 59.616 50.000 0.00 0.00 0.00 4.85
3447 3537 0.749818 TTCGGTTTGCACTTCAGCCA 60.750 50.000 0.00 0.00 0.00 4.75
3448 3538 0.749818 TCGGTTTGCACTTCAGCCAA 60.750 50.000 0.00 0.00 0.00 4.52
3449 3539 0.102120 CGGTTTGCACTTCAGCCAAA 59.898 50.000 0.00 0.00 0.00 3.28
3450 3540 1.269726 CGGTTTGCACTTCAGCCAAAT 60.270 47.619 0.00 0.00 0.00 2.32
3451 3541 2.407090 GGTTTGCACTTCAGCCAAATC 58.593 47.619 0.00 0.00 0.00 2.17
3452 3542 2.224018 GGTTTGCACTTCAGCCAAATCA 60.224 45.455 0.00 0.00 0.00 2.57
3453 3543 2.796593 GTTTGCACTTCAGCCAAATCAC 59.203 45.455 0.00 0.00 0.00 3.06
3454 3544 0.961019 TGCACTTCAGCCAAATCACC 59.039 50.000 0.00 0.00 0.00 4.02
3455 3545 0.961019 GCACTTCAGCCAAATCACCA 59.039 50.000 0.00 0.00 0.00 4.17
3456 3546 1.340889 GCACTTCAGCCAAATCACCAA 59.659 47.619 0.00 0.00 0.00 3.67
3457 3547 2.224018 GCACTTCAGCCAAATCACCAAA 60.224 45.455 0.00 0.00 0.00 3.28
3458 3548 3.740764 GCACTTCAGCCAAATCACCAAAA 60.741 43.478 0.00 0.00 0.00 2.44
3459 3549 4.634199 CACTTCAGCCAAATCACCAAAAT 58.366 39.130 0.00 0.00 0.00 1.82
3460 3550 5.782047 CACTTCAGCCAAATCACCAAAATA 58.218 37.500 0.00 0.00 0.00 1.40
3461 3551 6.400568 CACTTCAGCCAAATCACCAAAATAT 58.599 36.000 0.00 0.00 0.00 1.28
3462 3552 6.875195 CACTTCAGCCAAATCACCAAAATATT 59.125 34.615 0.00 0.00 0.00 1.28
3463 3553 7.063780 CACTTCAGCCAAATCACCAAAATATTC 59.936 37.037 0.00 0.00 0.00 1.75
3464 3554 6.855763 TCAGCCAAATCACCAAAATATTCT 57.144 33.333 0.00 0.00 0.00 2.40
3465 3555 7.243604 TCAGCCAAATCACCAAAATATTCTT 57.756 32.000 0.00 0.00 0.00 2.52
3466 3556 7.678837 TCAGCCAAATCACCAAAATATTCTTT 58.321 30.769 0.00 0.00 0.00 2.52
3467 3557 8.156165 TCAGCCAAATCACCAAAATATTCTTTT 58.844 29.630 0.00 0.00 0.00 2.27
3468 3558 8.231837 CAGCCAAATCACCAAAATATTCTTTTG 58.768 33.333 3.95 3.95 38.68 2.44
3469 3559 8.156165 AGCCAAATCACCAAAATATTCTTTTGA 58.844 29.630 11.03 0.00 40.73 2.69
3470 3560 8.782144 GCCAAATCACCAAAATATTCTTTTGAA 58.218 29.630 11.03 0.00 40.73 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
145 151 1.447838 CCCATCGTCCACTTGGTCG 60.448 63.158 8.41 8.41 45.66 4.79
255 267 1.174783 CGTAGTACTCCTGCCTGTGT 58.825 55.000 0.00 0.00 0.00 3.72
266 278 1.452833 GAGGGCGGTCCGTAGTACT 60.453 63.158 13.94 0.00 41.52 2.73
269 287 4.729918 ACGAGGGCGGTCCGTAGT 62.730 66.667 13.94 3.45 43.17 2.73
435 462 5.070580 GCTGGTTGACTGTAGGATTATAGGT 59.929 44.000 0.00 0.00 0.00 3.08
436 463 5.511545 GGCTGGTTGACTGTAGGATTATAGG 60.512 48.000 0.00 0.00 0.00 2.57
437 464 5.511545 GGGCTGGTTGACTGTAGGATTATAG 60.512 48.000 0.00 0.00 0.00 1.31
439 466 3.136626 GGGCTGGTTGACTGTAGGATTAT 59.863 47.826 0.00 0.00 0.00 1.28
441 468 1.282157 GGGCTGGTTGACTGTAGGATT 59.718 52.381 0.00 0.00 0.00 3.01
446 473 1.151899 AGGGGGCTGGTTGACTGTA 60.152 57.895 0.00 0.00 0.00 2.74
449 476 2.936032 GGAGGGGGCTGGTTGACT 60.936 66.667 0.00 0.00 0.00 3.41
469 502 3.276091 CGCACGTGCAAGTTGGGA 61.276 61.111 37.03 0.00 42.21 4.37
940 973 2.103263 GCTCGGGAGATTGGTTATCAGT 59.897 50.000 0.00 0.00 38.80 3.41
941 974 2.760374 GCTCGGGAGATTGGTTATCAG 58.240 52.381 0.00 0.00 38.80 2.90
942 975 1.068588 CGCTCGGGAGATTGGTTATCA 59.931 52.381 0.00 0.00 38.80 2.15
943 976 1.784525 CGCTCGGGAGATTGGTTATC 58.215 55.000 0.00 0.00 38.80 1.75
944 977 0.249911 GCGCTCGGGAGATTGGTTAT 60.250 55.000 0.00 0.00 38.80 1.89
964 997 2.683933 GGGTTGAGCTCGGAGGGA 60.684 66.667 9.64 0.00 0.00 4.20
989 1027 2.048023 TAGTCCATTCGCGTCCGGT 61.048 57.895 5.77 0.00 34.56 5.28
990 1028 1.588139 GTAGTCCATTCGCGTCCGG 60.588 63.158 5.77 4.94 34.56 5.14
991 1029 1.937846 CGTAGTCCATTCGCGTCCG 60.938 63.158 5.77 0.00 0.00 4.79
992 1030 1.588139 CCGTAGTCCATTCGCGTCC 60.588 63.158 5.77 0.00 0.00 4.79
993 1031 2.228914 GCCGTAGTCCATTCGCGTC 61.229 63.158 5.77 0.00 0.00 5.19
994 1032 2.202703 GCCGTAGTCCATTCGCGT 60.203 61.111 5.77 0.00 0.00 6.01
995 1033 1.480219 GAAGCCGTAGTCCATTCGCG 61.480 60.000 0.00 0.00 0.00 5.87
996 1034 1.480219 CGAAGCCGTAGTCCATTCGC 61.480 60.000 0.00 0.00 36.69 4.70
997 1035 0.099968 TCGAAGCCGTAGTCCATTCG 59.900 55.000 0.00 0.00 42.98 3.34
1227 1265 1.673337 GTTGGGGTACTTGCGGTCC 60.673 63.158 0.00 0.00 0.00 4.46
1495 1533 4.400251 ACAGAGAGGGGACGGGGG 62.400 72.222 0.00 0.00 0.00 5.40
1496 1534 2.760385 GACAGAGAGGGGACGGGG 60.760 72.222 0.00 0.00 0.00 5.73
1497 1535 2.037367 TGACAGAGAGGGGACGGG 59.963 66.667 0.00 0.00 0.00 5.28
1498 1536 1.304547 ACTGACAGAGAGGGGACGG 60.305 63.158 10.08 0.00 0.00 4.79
1499 1537 0.322997 AGACTGACAGAGAGGGGACG 60.323 60.000 10.08 0.00 0.00 4.79
1500 1538 1.181786 CAGACTGACAGAGAGGGGAC 58.818 60.000 10.08 0.00 0.00 4.46
1501 1539 0.613292 GCAGACTGACAGAGAGGGGA 60.613 60.000 10.08 0.00 0.00 4.81
1502 1540 1.896694 GCAGACTGACAGAGAGGGG 59.103 63.158 10.08 0.00 0.00 4.79
1503 1541 1.510383 CGCAGACTGACAGAGAGGG 59.490 63.158 10.08 2.74 0.00 4.30
1504 1542 1.153862 GCGCAGACTGACAGAGAGG 60.154 63.158 10.08 0.00 0.00 3.69
1555 1593 7.095607 CGGTAAATCTCTCGCTAATGCTAAAAT 60.096 37.037 0.00 0.00 36.97 1.82
1593 1631 7.106439 AGAAAGATCTCTCGCTTGATTTCTA 57.894 36.000 0.00 0.00 0.00 2.10
1601 1639 6.257630 GCTATTTCAAGAAAGATCTCTCGCTT 59.742 38.462 0.00 0.00 33.77 4.68
1603 1641 5.521735 TGCTATTTCAAGAAAGATCTCTCGC 59.478 40.000 0.00 0.00 33.77 5.03
1606 1644 7.066043 CAGCTTGCTATTTCAAGAAAGATCTCT 59.934 37.037 7.60 0.00 44.61 3.10
1814 1859 2.978824 CCGTTGTCTCCATCCCGT 59.021 61.111 0.00 0.00 0.00 5.28
1927 1972 2.713770 GTCTCAGCGACGGCGATA 59.286 61.111 18.90 0.00 46.35 2.92
2092 2137 2.347490 CAGCGTGGTACTGGCCTT 59.653 61.111 3.32 0.00 0.00 4.35
2110 2155 2.892425 CGACCTTCATCGCTGGCC 60.892 66.667 0.00 0.00 34.90 5.36
2111 2156 1.880340 CTCGACCTTCATCGCTGGC 60.880 63.158 0.00 0.00 41.97 4.85
2112 2157 1.880340 GCTCGACCTTCATCGCTGG 60.880 63.158 0.00 0.00 41.97 4.85
2113 2158 1.140589 AGCTCGACCTTCATCGCTG 59.859 57.895 0.00 0.00 41.97 5.18
2114 2159 1.140589 CAGCTCGACCTTCATCGCT 59.859 57.895 0.00 0.00 41.97 4.93
2288 2336 4.493747 CTCGGGAAGTCGGGCGAC 62.494 72.222 0.00 0.00 44.86 5.19
2510 2558 1.520342 GAGTCTGACGGATGCTGCC 60.520 63.158 1.52 0.00 0.00 4.85
2513 2561 1.040339 GGAGGAGTCTGACGGATGCT 61.040 60.000 1.52 0.00 0.00 3.79
2527 2575 2.364842 GGCTGCTGAGGAGGAGGA 60.365 66.667 2.44 0.00 38.10 3.71
2595 2664 7.373493 AGTTTTCTCTAATCTGCATTGGTTTG 58.627 34.615 0.00 0.00 0.00 2.93
2677 2746 1.087501 GGGAAAACTCTGCATCCGAC 58.912 55.000 0.00 0.00 32.56 4.79
2756 2827 1.754803 CGATCCTAGCTTGTACCACCA 59.245 52.381 0.00 0.00 0.00 4.17
2757 2828 1.755380 ACGATCCTAGCTTGTACCACC 59.245 52.381 0.00 0.00 0.00 4.61
2758 2829 3.187700 CAACGATCCTAGCTTGTACCAC 58.812 50.000 0.00 0.00 0.00 4.16
2854 2926 7.229907 ACCACAACAAAAGTCGAAATATTACCT 59.770 33.333 0.00 0.00 0.00 3.08
2866 2938 6.261381 TGGAATGTACTACCACAACAAAAGTC 59.739 38.462 0.00 0.00 30.84 3.01
2920 3005 3.631250 TGAACCCAAAACTTCAGCTTCT 58.369 40.909 0.00 0.00 0.00 2.85
2924 3009 2.294512 CTCCTGAACCCAAAACTTCAGC 59.705 50.000 2.45 0.00 41.40 4.26
3031 3119 1.975660 AACCTAAAAGCGTCAGCCAA 58.024 45.000 0.00 0.00 46.67 4.52
3065 3153 7.087409 TCACATCATCTTCGCAATTACAATT 57.913 32.000 0.00 0.00 0.00 2.32
3066 3154 6.682423 TCACATCATCTTCGCAATTACAAT 57.318 33.333 0.00 0.00 0.00 2.71
3067 3155 6.682423 ATCACATCATCTTCGCAATTACAA 57.318 33.333 0.00 0.00 0.00 2.41
3068 3156 7.209475 TCTATCACATCATCTTCGCAATTACA 58.791 34.615 0.00 0.00 0.00 2.41
3069 3157 7.383572 ACTCTATCACATCATCTTCGCAATTAC 59.616 37.037 0.00 0.00 0.00 1.89
3070 3158 7.436933 ACTCTATCACATCATCTTCGCAATTA 58.563 34.615 0.00 0.00 0.00 1.40
3071 3159 6.286758 ACTCTATCACATCATCTTCGCAATT 58.713 36.000 0.00 0.00 0.00 2.32
3072 3160 5.851720 ACTCTATCACATCATCTTCGCAAT 58.148 37.500 0.00 0.00 0.00 3.56
3073 3161 5.268118 ACTCTATCACATCATCTTCGCAA 57.732 39.130 0.00 0.00 0.00 4.85
3074 3162 4.555511 CGACTCTATCACATCATCTTCGCA 60.556 45.833 0.00 0.00 0.00 5.10
3075 3163 3.911365 CGACTCTATCACATCATCTTCGC 59.089 47.826 0.00 0.00 0.00 4.70
3076 3164 3.911365 GCGACTCTATCACATCATCTTCG 59.089 47.826 0.00 0.00 0.00 3.79
3077 3165 5.119931 AGCGACTCTATCACATCATCTTC 57.880 43.478 0.00 0.00 0.00 2.87
3078 3166 5.528043 AAGCGACTCTATCACATCATCTT 57.472 39.130 0.00 0.00 0.00 2.40
3079 3167 5.068329 TGAAAGCGACTCTATCACATCATCT 59.932 40.000 0.00 0.00 0.00 2.90
3080 3168 5.284864 TGAAAGCGACTCTATCACATCATC 58.715 41.667 0.00 0.00 0.00 2.92
3081 3169 5.163468 ACTGAAAGCGACTCTATCACATCAT 60.163 40.000 0.00 0.00 37.60 2.45
3082 3170 4.158579 ACTGAAAGCGACTCTATCACATCA 59.841 41.667 0.00 0.00 37.60 3.07
3083 3171 4.502282 CACTGAAAGCGACTCTATCACATC 59.498 45.833 0.00 0.00 37.60 3.06
3084 3172 4.428209 CACTGAAAGCGACTCTATCACAT 58.572 43.478 0.00 0.00 37.60 3.21
3085 3173 3.367395 CCACTGAAAGCGACTCTATCACA 60.367 47.826 0.00 0.00 37.60 3.58
3086 3174 3.182967 CCACTGAAAGCGACTCTATCAC 58.817 50.000 0.00 0.00 37.60 3.06
3087 3175 2.826128 ACCACTGAAAGCGACTCTATCA 59.174 45.455 0.00 0.00 37.60 2.15
3088 3176 3.182967 CACCACTGAAAGCGACTCTATC 58.817 50.000 0.00 0.00 37.60 2.08
3089 3177 2.093973 CCACCACTGAAAGCGACTCTAT 60.094 50.000 0.00 0.00 37.60 1.98
3090 3178 1.272490 CCACCACTGAAAGCGACTCTA 59.728 52.381 0.00 0.00 37.60 2.43
3091 3179 0.034059 CCACCACTGAAAGCGACTCT 59.966 55.000 0.00 0.00 37.60 3.24
3092 3180 0.249911 ACCACCACTGAAAGCGACTC 60.250 55.000 0.00 0.00 37.60 3.36
3093 3181 0.249911 GACCACCACTGAAAGCGACT 60.250 55.000 0.00 0.00 37.60 4.18
3094 3182 0.249911 AGACCACCACTGAAAGCGAC 60.250 55.000 0.00 0.00 37.60 5.19
3095 3183 0.033504 GAGACCACCACTGAAAGCGA 59.966 55.000 0.00 0.00 37.60 4.93
3096 3184 0.034059 AGAGACCACCACTGAAAGCG 59.966 55.000 0.00 0.00 37.60 4.68
3097 3185 1.802069 GAGAGACCACCACTGAAAGC 58.198 55.000 0.00 0.00 37.60 3.51
3098 3186 1.337260 CCGAGAGACCACCACTGAAAG 60.337 57.143 0.00 0.00 42.29 2.62
3099 3187 0.679505 CCGAGAGACCACCACTGAAA 59.320 55.000 0.00 0.00 0.00 2.69
3100 3188 1.185618 CCCGAGAGACCACCACTGAA 61.186 60.000 0.00 0.00 0.00 3.02
3101 3189 1.606601 CCCGAGAGACCACCACTGA 60.607 63.158 0.00 0.00 0.00 3.41
3102 3190 1.908793 ACCCGAGAGACCACCACTG 60.909 63.158 0.00 0.00 0.00 3.66
3103 3191 1.908793 CACCCGAGAGACCACCACT 60.909 63.158 0.00 0.00 0.00 4.00
3104 3192 1.906824 TCACCCGAGAGACCACCAC 60.907 63.158 0.00 0.00 0.00 4.16
3105 3193 1.906824 GTCACCCGAGAGACCACCA 60.907 63.158 0.00 0.00 0.00 4.17
3106 3194 2.971452 GTCACCCGAGAGACCACC 59.029 66.667 0.00 0.00 0.00 4.61
3110 3198 0.898789 TTCCAGGTCACCCGAGAGAC 60.899 60.000 0.00 0.00 35.12 3.36
3111 3199 0.898789 GTTCCAGGTCACCCGAGAGA 60.899 60.000 0.00 0.00 35.12 3.10
3112 3200 1.592223 GTTCCAGGTCACCCGAGAG 59.408 63.158 0.00 0.00 35.12 3.20
3113 3201 2.273179 CGTTCCAGGTCACCCGAGA 61.273 63.158 0.00 0.00 35.12 4.04
3114 3202 2.261671 CGTTCCAGGTCACCCGAG 59.738 66.667 0.00 0.00 35.12 4.63
3115 3203 3.998672 GCGTTCCAGGTCACCCGA 61.999 66.667 0.00 0.00 35.12 5.14
3117 3205 2.764637 ATTGGCGTTCCAGGTCACCC 62.765 60.000 0.00 0.00 44.53 4.61
3118 3206 0.893727 AATTGGCGTTCCAGGTCACC 60.894 55.000 0.00 0.00 44.53 4.02
3119 3207 0.958822 AAATTGGCGTTCCAGGTCAC 59.041 50.000 0.00 0.00 44.53 3.67
3120 3208 1.339610 CAAAATTGGCGTTCCAGGTCA 59.660 47.619 0.00 0.00 44.53 4.02
3121 3209 1.339929 ACAAAATTGGCGTTCCAGGTC 59.660 47.619 0.00 0.00 44.53 3.85
3122 3210 1.408969 ACAAAATTGGCGTTCCAGGT 58.591 45.000 0.00 0.00 44.53 4.00
3123 3211 3.651803 TTACAAAATTGGCGTTCCAGG 57.348 42.857 0.00 0.00 44.53 4.45
3124 3212 3.367630 GCATTACAAAATTGGCGTTCCAG 59.632 43.478 0.00 0.00 44.53 3.86
3125 3213 3.243873 TGCATTACAAAATTGGCGTTCCA 60.244 39.130 0.00 0.00 41.55 3.53
3126 3214 3.321497 TGCATTACAAAATTGGCGTTCC 58.679 40.909 0.00 0.00 0.00 3.62
3127 3215 4.981389 TTGCATTACAAAATTGGCGTTC 57.019 36.364 0.00 0.00 34.56 3.95
3128 3216 5.238214 ACAATTGCATTACAAAATTGGCGTT 59.762 32.000 5.05 0.00 42.78 4.84
3129 3217 4.754114 ACAATTGCATTACAAAATTGGCGT 59.246 33.333 5.05 0.00 42.78 5.68
3130 3218 5.280328 ACAATTGCATTACAAAATTGGCG 57.720 34.783 5.05 0.00 42.78 5.69
3131 3219 5.107143 ACGACAATTGCATTACAAAATTGGC 60.107 36.000 5.05 5.59 43.09 4.52
3132 3220 6.464895 ACGACAATTGCATTACAAAATTGG 57.535 33.333 5.05 0.00 42.78 3.16
3138 3226 9.216087 CGAATTATTACGACAATTGCATTACAA 57.784 29.630 5.05 0.00 44.01 2.41
3139 3227 8.604890 TCGAATTATTACGACAATTGCATTACA 58.395 29.630 5.05 0.00 33.62 2.41
3140 3228 8.981370 TCGAATTATTACGACAATTGCATTAC 57.019 30.769 5.05 0.00 33.62 1.89
3152 3240 7.853524 ACACAACAAAAGTCGAATTATTACGA 58.146 30.769 0.00 0.00 36.18 3.43
3153 3241 7.794810 TGACACAACAAAAGTCGAATTATTACG 59.205 33.333 0.00 0.00 35.09 3.18
3154 3242 8.996988 TGACACAACAAAAGTCGAATTATTAC 57.003 30.769 0.00 0.00 35.09 1.89
3155 3243 9.605955 CATGACACAACAAAAGTCGAATTATTA 57.394 29.630 0.00 0.00 35.09 0.98
3156 3244 8.134895 ACATGACACAACAAAAGTCGAATTATT 58.865 29.630 0.00 0.00 35.09 1.40
3157 3245 7.648142 ACATGACACAACAAAAGTCGAATTAT 58.352 30.769 0.00 0.00 35.09 1.28
3158 3246 7.022055 ACATGACACAACAAAAGTCGAATTA 57.978 32.000 0.00 0.00 35.09 1.40
3159 3247 5.890334 ACATGACACAACAAAAGTCGAATT 58.110 33.333 0.00 0.00 35.09 2.17
3160 3248 5.499139 ACATGACACAACAAAAGTCGAAT 57.501 34.783 0.00 0.00 35.09 3.34
3161 3249 4.955925 ACATGACACAACAAAAGTCGAA 57.044 36.364 0.00 0.00 35.09 3.71
3162 3250 6.612247 ATTACATGACACAACAAAAGTCGA 57.388 33.333 0.00 0.00 35.09 4.20
3163 3251 6.690957 ACAATTACATGACACAACAAAAGTCG 59.309 34.615 0.00 0.00 35.09 4.18
3164 3252 7.985634 ACAATTACATGACACAACAAAAGTC 57.014 32.000 0.00 0.00 0.00 3.01
3168 3256 8.759641 GCAATTACAATTACATGACACAACAAA 58.240 29.630 0.00 0.00 0.00 2.83
3169 3257 7.114106 CGCAATTACAATTACATGACACAACAA 59.886 33.333 0.00 0.00 0.00 2.83
3170 3258 6.580416 CGCAATTACAATTACATGACACAACA 59.420 34.615 0.00 0.00 0.00 3.33
3171 3259 6.799441 TCGCAATTACAATTACATGACACAAC 59.201 34.615 0.00 0.00 0.00 3.32
3172 3260 6.903419 TCGCAATTACAATTACATGACACAA 58.097 32.000 0.00 0.00 0.00 3.33
3173 3261 6.487689 TCGCAATTACAATTACATGACACA 57.512 33.333 0.00 0.00 0.00 3.72
3174 3262 7.240674 TCTTCGCAATTACAATTACATGACAC 58.759 34.615 0.00 0.00 0.00 3.67
3175 3263 7.371126 TCTTCGCAATTACAATTACATGACA 57.629 32.000 0.00 0.00 0.00 3.58
3176 3264 8.122330 TCATCTTCGCAATTACAATTACATGAC 58.878 33.333 0.00 0.00 0.00 3.06
3177 3265 8.207521 TCATCTTCGCAATTACAATTACATGA 57.792 30.769 0.00 0.00 0.00 3.07
3178 3266 8.898792 CATCATCTTCGCAATTACAATTACATG 58.101 33.333 0.00 0.00 0.00 3.21
3179 3267 8.623903 ACATCATCTTCGCAATTACAATTACAT 58.376 29.630 0.00 0.00 0.00 2.29
3269 3358 8.428186 TGACATCCCTGTTTAATTATTACGAC 57.572 34.615 0.00 0.00 35.14 4.34
3287 3376 7.119846 GGCCATAGATAACTACAATTGACATCC 59.880 40.741 13.59 0.00 0.00 3.51
3337 3426 0.455633 CGTGCAAGCAAAGATCAGCC 60.456 55.000 0.00 0.00 0.00 4.85
3375 3465 8.878769 GGTGCTAAAAATTTTCTGAAACTGAAA 58.121 29.630 3.41 0.00 31.39 2.69
3376 3466 8.037758 TGGTGCTAAAAATTTTCTGAAACTGAA 58.962 29.630 3.41 0.00 0.00 3.02
3377 3467 7.551585 TGGTGCTAAAAATTTTCTGAAACTGA 58.448 30.769 3.41 0.00 0.00 3.41
3378 3468 7.769272 TGGTGCTAAAAATTTTCTGAAACTG 57.231 32.000 3.41 0.00 0.00 3.16
3379 3469 7.279981 GGTTGGTGCTAAAAATTTTCTGAAACT 59.720 33.333 3.41 0.00 0.00 2.66
3380 3470 7.406553 GGTTGGTGCTAAAAATTTTCTGAAAC 58.593 34.615 3.41 0.00 0.00 2.78
3381 3471 6.256757 CGGTTGGTGCTAAAAATTTTCTGAAA 59.743 34.615 3.41 0.00 0.00 2.69
3382 3472 5.751028 CGGTTGGTGCTAAAAATTTTCTGAA 59.249 36.000 3.41 0.00 0.00 3.02
3383 3473 5.067936 TCGGTTGGTGCTAAAAATTTTCTGA 59.932 36.000 3.41 0.00 0.00 3.27
3384 3474 5.285651 TCGGTTGGTGCTAAAAATTTTCTG 58.714 37.500 3.41 1.62 0.00 3.02
3385 3475 5.523438 TCGGTTGGTGCTAAAAATTTTCT 57.477 34.783 3.41 0.00 0.00 2.52
3386 3476 6.591313 TTTCGGTTGGTGCTAAAAATTTTC 57.409 33.333 3.41 0.00 0.00 2.29
3387 3477 6.763610 TGATTTCGGTTGGTGCTAAAAATTTT 59.236 30.769 0.00 0.00 0.00 1.82
3388 3478 6.284459 TGATTTCGGTTGGTGCTAAAAATTT 58.716 32.000 0.00 0.00 0.00 1.82
3389 3479 5.848406 TGATTTCGGTTGGTGCTAAAAATT 58.152 33.333 0.00 0.00 0.00 1.82
3390 3480 5.461032 TGATTTCGGTTGGTGCTAAAAAT 57.539 34.783 0.00 0.00 0.00 1.82
3391 3481 4.920640 TGATTTCGGTTGGTGCTAAAAA 57.079 36.364 0.00 0.00 0.00 1.94
3392 3482 4.378978 CGATGATTTCGGTTGGTGCTAAAA 60.379 41.667 0.00 0.00 44.28 1.52
3393 3483 3.126171 CGATGATTTCGGTTGGTGCTAAA 59.874 43.478 0.00 0.00 44.28 1.85
3394 3484 2.675844 CGATGATTTCGGTTGGTGCTAA 59.324 45.455 0.00 0.00 44.28 3.09
3395 3485 2.276201 CGATGATTTCGGTTGGTGCTA 58.724 47.619 0.00 0.00 44.28 3.49
3396 3486 1.086696 CGATGATTTCGGTTGGTGCT 58.913 50.000 0.00 0.00 44.28 4.40
3397 3487 3.604130 CGATGATTTCGGTTGGTGC 57.396 52.632 0.00 0.00 44.28 5.01
3405 3495 7.959718 AAATCACTGAATTTCGATGATTTCG 57.040 32.000 22.56 0.00 43.21 3.46
3415 3505 4.981674 TGCAAACCGAAATCACTGAATTTC 59.018 37.500 8.96 8.96 40.63 2.17
3416 3506 4.744631 GTGCAAACCGAAATCACTGAATTT 59.255 37.500 0.00 0.00 0.00 1.82
3417 3507 4.037923 AGTGCAAACCGAAATCACTGAATT 59.962 37.500 0.00 0.00 36.72 2.17
3418 3508 3.569701 AGTGCAAACCGAAATCACTGAAT 59.430 39.130 0.00 0.00 36.72 2.57
3419 3509 2.948979 AGTGCAAACCGAAATCACTGAA 59.051 40.909 0.00 0.00 36.72 3.02
3420 3510 2.571212 AGTGCAAACCGAAATCACTGA 58.429 42.857 0.00 0.00 36.72 3.41
3421 3511 3.243035 TGAAGTGCAAACCGAAATCACTG 60.243 43.478 0.00 0.00 37.96 3.66
3422 3512 2.948979 TGAAGTGCAAACCGAAATCACT 59.051 40.909 0.00 0.00 39.42 3.41
3423 3513 3.300009 CTGAAGTGCAAACCGAAATCAC 58.700 45.455 0.00 0.00 0.00 3.06
3424 3514 2.287547 GCTGAAGTGCAAACCGAAATCA 60.288 45.455 0.00 0.00 0.00 2.57
3425 3515 2.319472 GCTGAAGTGCAAACCGAAATC 58.681 47.619 0.00 0.00 0.00 2.17
3426 3516 1.000274 GGCTGAAGTGCAAACCGAAAT 60.000 47.619 0.00 0.00 34.04 2.17
3427 3517 0.383949 GGCTGAAGTGCAAACCGAAA 59.616 50.000 0.00 0.00 34.04 3.46
3428 3518 0.749818 TGGCTGAAGTGCAAACCGAA 60.750 50.000 0.00 0.00 34.04 4.30
3429 3519 0.749818 TTGGCTGAAGTGCAAACCGA 60.750 50.000 0.00 0.00 34.04 4.69
3430 3520 0.102120 TTTGGCTGAAGTGCAAACCG 59.898 50.000 0.00 0.00 34.04 4.44
3431 3521 2.224018 TGATTTGGCTGAAGTGCAAACC 60.224 45.455 0.00 0.00 34.04 3.27
3432 3522 2.796593 GTGATTTGGCTGAAGTGCAAAC 59.203 45.455 0.00 0.00 34.04 2.93
3433 3523 2.224018 GGTGATTTGGCTGAAGTGCAAA 60.224 45.455 0.00 0.00 34.04 3.68
3434 3524 1.340889 GGTGATTTGGCTGAAGTGCAA 59.659 47.619 0.00 0.00 34.04 4.08
3435 3525 0.961019 GGTGATTTGGCTGAAGTGCA 59.039 50.000 0.00 0.00 34.04 4.57
3436 3526 0.961019 TGGTGATTTGGCTGAAGTGC 59.039 50.000 0.00 0.00 0.00 4.40
3437 3527 3.731652 TTTGGTGATTTGGCTGAAGTG 57.268 42.857 0.00 0.00 0.00 3.16
3438 3528 4.961438 ATTTTGGTGATTTGGCTGAAGT 57.039 36.364 0.00 0.00 0.00 3.01
3439 3529 7.325694 AGAATATTTTGGTGATTTGGCTGAAG 58.674 34.615 0.00 0.00 0.00 3.02
3440 3530 7.243604 AGAATATTTTGGTGATTTGGCTGAA 57.756 32.000 0.00 0.00 0.00 3.02
3441 3531 6.855763 AGAATATTTTGGTGATTTGGCTGA 57.144 33.333 0.00 0.00 0.00 4.26
3442 3532 7.910441 AAAGAATATTTTGGTGATTTGGCTG 57.090 32.000 0.00 0.00 0.00 4.85
3443 3533 8.156165 TCAAAAGAATATTTTGGTGATTTGGCT 58.844 29.630 12.37 0.00 39.25 4.75
3444 3534 8.321650 TCAAAAGAATATTTTGGTGATTTGGC 57.678 30.769 12.37 0.00 39.25 4.52


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

AutoCloner maintained by Alex Coulton.