Multiple sequence alignment - TraesCS3B01G258600

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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 TraesCS3B01G258600 chr3B 100.000 3073 0 0 3033 6105 416277911 416280983 0.000000e+00 5675
1 TraesCS3B01G258600 chr3B 100.000 2681 0 0 1 2681 416274879 416277559 0.000000e+00 4951
2 TraesCS3B01G258600 chr3D 94.695 2413 85 17 266 2670 305457390 305455013 0.000000e+00 3707
3 TraesCS3B01G258600 chr3D 96.144 1141 24 5 4245 5375 305453547 305452417 0.000000e+00 1845
4 TraesCS3B01G258600 chr3D 97.146 876 20 3 3290 4164 305454417 305453546 0.000000e+00 1474
5 TraesCS3B01G258600 chr3D 91.854 712 44 6 5404 6105 305452347 305451640 0.000000e+00 981
6 TraesCS3B01G258600 chr3D 96.000 150 6 0 3161 3310 305454678 305454529 1.700000e-60 244
7 TraesCS3B01G258600 chr3D 100.000 81 0 0 3048 3128 305454745 305454665 3.810000e-32 150
8 TraesCS3B01G258600 chr3D 89.583 96 8 2 4152 4246 398703869 398703775 2.990000e-23 121
9 TraesCS3B01G258600 chr3D 87.619 105 11 2 4144 4246 517884838 517884734 2.990000e-23 121
10 TraesCS3B01G258600 chr3A 94.563 1876 60 11 4245 6103 423488393 423486543 0.000000e+00 2861
11 TraesCS3B01G258600 chr3A 90.230 1607 98 14 1 1576 423492208 423490630 0.000000e+00 2043
12 TraesCS3B01G258600 chr3A 97.096 861 20 4 3308 4164 423489251 423488392 0.000000e+00 1447
13 TraesCS3B01G258600 chr3A 87.469 407 31 13 2034 2430 423490347 423489951 9.330000e-123 451
14 TraesCS3B01G258600 chr3A 96.175 183 7 0 2499 2681 423489931 423489749 3.580000e-77 300
15 TraesCS3B01G258600 chr3A 91.071 56 4 1 3041 3096 423489753 423489699 2.360000e-09 75
16 TraesCS3B01G258600 chr4D 93.939 99 6 0 4066 4164 246080529 246080431 3.810000e-32 150
17 TraesCS3B01G258600 chr7A 95.506 89 2 2 4161 4248 50004311 50004224 2.290000e-29 141
18 TraesCS3B01G258600 chr6A 93.617 94 5 1 4163 4255 457397430 457397523 8.250000e-29 139
19 TraesCS3B01G258600 chr5A 94.186 86 4 1 4162 4246 549199813 549199728 4.970000e-26 130
20 TraesCS3B01G258600 chr2D 92.941 85 5 1 4163 4246 188966993 188966909 8.310000e-24 122
21 TraesCS3B01G258600 chr6D 91.111 90 7 1 4163 4251 29740997 29741086 2.990000e-23 121
22 TraesCS3B01G258600 chr6B 90.217 92 7 2 4156 4246 576199780 576199690 1.070000e-22 119
23 TraesCS3B01G258600 chr1D 90.217 92 8 1 4163 4253 231076939 231077030 1.070000e-22 119


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 TraesCS3B01G258600 chr3B 416274879 416280983 6104 False 5313.000000 5675 100.000000 1 6105 2 chr3B.!!$F1 6104
1 TraesCS3B01G258600 chr3D 305451640 305457390 5750 True 1400.166667 3707 95.973167 266 6105 6 chr3D.!!$R3 5839
2 TraesCS3B01G258600 chr3A 423486543 423492208 5665 True 1196.166667 2861 92.767333 1 6103 6 chr3A.!!$R1 6102

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
786 792 0.308684 CTTGCATGCACGTGAGTTGT 59.691 50.000 22.58 0.0 46.40 3.32 F
1248 1258 0.036765 GACACCAGACGCCATACCAA 60.037 55.000 0.00 0.0 0.00 3.67 F
1811 1843 1.469703 CTCGCATGATTTCCAGTGCAA 59.530 47.619 0.00 0.0 37.44 4.08 F
2651 2731 2.355716 CCAATCTCGTTTTCTGGGCCTA 60.356 50.000 4.53 0.0 0.00 3.93 F
3159 3288 0.106469 TTACAACACCTGCAAGCCCA 60.106 50.000 0.00 0.0 0.00 5.36 F
4178 4726 0.113776 AACTACTCCCTCCGTCCACA 59.886 55.000 0.00 0.0 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1811 1843 0.598065 GTGACAATTTCCTGCGGCTT 59.402 50.000 0.0 0.0 0.00 4.35 R
3140 3269 0.106469 TGGGCTTGCAGGTGTTGTAA 60.106 50.000 0.0 0.0 0.00 2.41 R
3146 3275 0.323725 ATAAGGTGGGCTTGCAGGTG 60.324 55.000 0.0 0.0 0.00 4.00 R
4307 4855 0.830444 TGTAGTCTGGAACTGCCCGT 60.830 55.000 0.0 0.0 39.66 5.28 R
4826 5384 1.219124 CTGATACCGCCACTGCTGT 59.781 57.895 0.0 0.0 38.56 4.40 R
5606 6223 1.003580 TGCCCAAGTGCCAAAACAAAA 59.996 42.857 0.0 0.0 0.00 2.44 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
36 37 5.766222 ACTGACTAAATTCTGCAAAGCAAG 58.234 37.500 0.00 0.00 38.41 4.01
49 50 2.880890 CAAAGCAAGTGAGCTGTTAGGT 59.119 45.455 0.00 0.00 45.89 3.08
65 66 4.530553 TGTTAGGTTTGCCTGAGATGACTA 59.469 41.667 0.00 0.00 46.47 2.59
110 112 7.567771 CGTTGTTTCTTAGAGCTGTAAACAGAG 60.568 40.741 14.21 2.26 46.59 3.35
162 164 4.414852 TGTGAGCGTTAGTAATTCCGTAC 58.585 43.478 0.00 0.00 0.00 3.67
163 165 4.156556 TGTGAGCGTTAGTAATTCCGTACT 59.843 41.667 0.00 0.00 37.98 2.73
184 187 5.968254 ACTTTAGTAAGAGCAACTCTAGCC 58.032 41.667 0.00 0.00 40.28 3.93
207 210 1.625818 GTCCTCATATTGGGCCGATCT 59.374 52.381 10.27 0.00 0.00 2.75
215 218 3.719268 ATTGGGCCGATCTGCATAATA 57.281 42.857 11.45 0.00 0.00 0.98
218 221 2.084546 GGGCCGATCTGCATAATAACC 58.915 52.381 11.45 0.00 0.00 2.85
219 222 2.290323 GGGCCGATCTGCATAATAACCT 60.290 50.000 11.45 0.00 0.00 3.50
221 224 3.437049 GGCCGATCTGCATAATAACCTTC 59.563 47.826 11.45 0.00 0.00 3.46
228 231 7.702348 CGATCTGCATAATAACCTTCGATATGA 59.298 37.037 4.52 0.00 0.00 2.15
237 240 8.433421 AATAACCTTCGATATGACGATTTTGT 57.567 30.769 0.00 0.00 41.82 2.83
238 241 5.968387 ACCTTCGATATGACGATTTTGTC 57.032 39.130 0.00 0.00 41.82 3.18
245 248 8.024146 TCGATATGACGATTTTGTCTGAAAAA 57.976 30.769 0.00 0.00 39.64 1.94
287 290 1.205655 GAGCTTGGGGGAAAAAGATGC 59.794 52.381 0.00 0.00 0.00 3.91
313 316 0.381089 GACGAGTAGGTCCCACGATG 59.619 60.000 0.00 0.00 0.00 3.84
471 476 7.822822 GGGAAGCATATATATAAAGGACAACGT 59.177 37.037 0.00 0.00 0.00 3.99
533 538 2.943033 CTCCCCGCTCGTGAATAAATTT 59.057 45.455 0.00 0.00 0.00 1.82
597 602 3.364889 CGGAGCAAACGGTATAGATGA 57.635 47.619 0.00 0.00 0.00 2.92
658 664 2.613390 GGTTCACCACCGACAAGTC 58.387 57.895 0.00 0.00 35.12 3.01
686 692 4.972201 TGAATAACCGCCGTAAACAAATC 58.028 39.130 0.00 0.00 0.00 2.17
743 749 4.083271 GCAACAAGAAGACATCACTTACCC 60.083 45.833 0.00 0.00 0.00 3.69
786 792 0.308684 CTTGCATGCACGTGAGTTGT 59.691 50.000 22.58 0.00 46.40 3.32
822 828 7.068593 TCCCGCATTCATTTTCATCTAATCTTT 59.931 33.333 0.00 0.00 0.00 2.52
823 829 7.707893 CCCGCATTCATTTTCATCTAATCTTTT 59.292 33.333 0.00 0.00 0.00 2.27
865 871 0.890996 CGCCCTGAACCTGAAGCTTT 60.891 55.000 0.00 0.00 0.00 3.51
935 942 5.423015 CACCTCTTGTGTATGCTGTCTATT 58.577 41.667 0.00 0.00 40.26 1.73
1056 1066 1.805345 CTCCTTGTCTTGCTTGCTCTG 59.195 52.381 0.00 0.00 0.00 3.35
1116 1126 1.847506 TTGGAGGCCAAGGAGCTCA 60.848 57.895 17.19 0.00 38.75 4.26
1161 1171 0.115152 AAGGGAAGGCAAAGAAGGGG 59.885 55.000 0.00 0.00 0.00 4.79
1248 1258 0.036765 GACACCAGACGCCATACCAA 60.037 55.000 0.00 0.00 0.00 3.67
1483 1499 1.831106 AGGTCGGTCAATATCACTGCA 59.169 47.619 0.00 0.00 0.00 4.41
1594 1626 8.917088 ACATTTCCTTTTGTAATCCATATCAGG 58.083 33.333 0.00 0.00 0.00 3.86
1677 1709 8.906867 CATGGGCTTTCTAAGATTAGAATTTCA 58.093 33.333 14.16 11.06 45.99 2.69
1699 1731 7.801716 TCAGTATTTGTATATTTGGAGTGGC 57.198 36.000 0.00 0.00 0.00 5.01
1731 1763 6.366061 GGTAGTGTGAAGATTTGGATTTTTGC 59.634 38.462 0.00 0.00 0.00 3.68
1733 1765 4.150451 GTGTGAAGATTTGGATTTTTGCCG 59.850 41.667 0.00 0.00 0.00 5.69
1762 1794 8.938906 CATATGATCCGATGTACATTTCATTGA 58.061 33.333 20.17 10.63 0.00 2.57
1768 1800 5.007039 CCGATGTACATTTCATTGAGTCCTG 59.993 44.000 10.30 0.00 0.00 3.86
1794 1826 2.095008 CCATCATCATCGACTACCCTCG 60.095 54.545 0.00 0.00 34.83 4.63
1811 1843 1.469703 CTCGCATGATTTCCAGTGCAA 59.530 47.619 0.00 0.00 37.44 4.08
1928 1960 6.295249 TGGATTGTTCTGTTCTTCACATGTA 58.705 36.000 0.00 0.00 33.76 2.29
1989 2021 4.401925 CTTTTTGAGGAATCCACTCAGGT 58.598 43.478 0.61 0.00 44.91 4.00
1990 2022 5.560724 CTTTTTGAGGAATCCACTCAGGTA 58.439 41.667 0.61 0.00 44.91 3.08
1991 2023 4.553330 TTTGAGGAATCCACTCAGGTAC 57.447 45.455 0.61 0.00 44.91 3.34
1992 2024 3.474798 TGAGGAATCCACTCAGGTACT 57.525 47.619 0.61 0.00 39.87 2.73
2227 2300 6.916360 AGAGGCATACTTGAAATCCAAAAA 57.084 33.333 0.00 0.00 33.76 1.94
2228 2301 7.486407 AGAGGCATACTTGAAATCCAAAAAT 57.514 32.000 0.00 0.00 33.76 1.82
2229 2302 7.325694 AGAGGCATACTTGAAATCCAAAAATG 58.674 34.615 0.00 0.00 33.76 2.32
2282 2356 4.868172 ACTCATGGAAATTGGGAGATGA 57.132 40.909 0.00 0.00 0.00 2.92
2367 2441 6.829849 TCAGCCAAAAGAAATCCTCATTTTT 58.170 32.000 0.00 0.00 31.94 1.94
2466 2546 3.446873 AGGATCTGAGCTCTACAAGTGTG 59.553 47.826 16.19 0.00 0.00 3.82
2472 2552 4.513442 TGAGCTCTACAAGTGTGTTTTGT 58.487 39.130 16.19 0.00 41.36 2.83
2495 2575 3.192422 CGCTGGGTTCATTTTATGGAACA 59.808 43.478 6.82 0.00 43.96 3.18
2520 2600 9.050601 CAAGAGTCTAGTCTTTTGAGAACAAAT 57.949 33.333 12.84 0.00 43.99 2.32
2651 2731 2.355716 CCAATCTCGTTTTCTGGGCCTA 60.356 50.000 4.53 0.00 0.00 3.93
2679 2759 5.427378 CAAACCAAACATTCTTTTCCAGGT 58.573 37.500 0.00 0.00 0.00 4.00
2680 2760 6.578023 CAAACCAAACATTCTTTTCCAGGTA 58.422 36.000 0.00 0.00 0.00 3.08
3127 3256 4.576873 CAGCACGACTCCTTATTCTAGAGA 59.423 45.833 0.00 0.00 0.00 3.10
3128 3257 5.066634 CAGCACGACTCCTTATTCTAGAGAA 59.933 44.000 0.00 0.00 38.56 2.87
3129 3258 5.298276 AGCACGACTCCTTATTCTAGAGAAG 59.702 44.000 8.75 8.75 37.48 2.85
3130 3259 5.516090 CACGACTCCTTATTCTAGAGAAGC 58.484 45.833 9.83 0.00 37.48 3.86
3131 3260 5.066634 CACGACTCCTTATTCTAGAGAAGCA 59.933 44.000 9.83 0.00 37.48 3.91
3132 3261 5.066764 ACGACTCCTTATTCTAGAGAAGCAC 59.933 44.000 9.83 2.78 37.48 4.40
3133 3262 5.298276 CGACTCCTTATTCTAGAGAAGCACT 59.702 44.000 9.83 0.00 37.48 4.40
3134 3263 6.483974 CGACTCCTTATTCTAGAGAAGCACTA 59.516 42.308 9.83 0.00 37.48 2.74
3135 3264 7.307751 CGACTCCTTATTCTAGAGAAGCACTAG 60.308 44.444 9.83 0.00 37.48 2.57
3136 3265 7.579105 ACTCCTTATTCTAGAGAAGCACTAGA 58.421 38.462 0.00 0.00 42.72 2.43
3137 3266 8.224720 ACTCCTTATTCTAGAGAAGCACTAGAT 58.775 37.037 0.00 0.00 43.48 1.98
3138 3267 9.077885 CTCCTTATTCTAGAGAAGCACTAGATT 57.922 37.037 0.00 0.00 43.48 2.40
3139 3268 9.427821 TCCTTATTCTAGAGAAGCACTAGATTT 57.572 33.333 0.00 0.00 43.48 2.17
3146 3275 9.640963 TCTAGAGAAGCACTAGATTTTTACAAC 57.359 33.333 0.00 0.00 40.57 3.32
3147 3276 9.424319 CTAGAGAAGCACTAGATTTTTACAACA 57.576 33.333 0.00 0.00 39.48 3.33
3148 3277 8.089115 AGAGAAGCACTAGATTTTTACAACAC 57.911 34.615 0.00 0.00 0.00 3.32
3149 3278 7.173390 AGAGAAGCACTAGATTTTTACAACACC 59.827 37.037 0.00 0.00 0.00 4.16
3150 3279 6.998673 AGAAGCACTAGATTTTTACAACACCT 59.001 34.615 0.00 0.00 0.00 4.00
3151 3280 6.560253 AGCACTAGATTTTTACAACACCTG 57.440 37.500 0.00 0.00 0.00 4.00
3152 3281 5.048713 AGCACTAGATTTTTACAACACCTGC 60.049 40.000 0.00 0.00 0.00 4.85
3153 3282 5.278266 GCACTAGATTTTTACAACACCTGCA 60.278 40.000 0.00 0.00 0.00 4.41
3154 3283 6.734137 CACTAGATTTTTACAACACCTGCAA 58.266 36.000 0.00 0.00 0.00 4.08
3155 3284 6.857964 CACTAGATTTTTACAACACCTGCAAG 59.142 38.462 0.00 0.00 0.00 4.01
3156 3285 4.620982 AGATTTTTACAACACCTGCAAGC 58.379 39.130 0.00 0.00 0.00 4.01
3157 3286 2.880963 TTTTACAACACCTGCAAGCC 57.119 45.000 0.00 0.00 0.00 4.35
3158 3287 1.036707 TTTACAACACCTGCAAGCCC 58.963 50.000 0.00 0.00 0.00 5.19
3159 3288 0.106469 TTACAACACCTGCAAGCCCA 60.106 50.000 0.00 0.00 0.00 5.36
3160 3289 0.821711 TACAACACCTGCAAGCCCAC 60.822 55.000 0.00 0.00 0.00 4.61
3161 3290 2.521708 AACACCTGCAAGCCCACC 60.522 61.111 0.00 0.00 0.00 4.61
3162 3291 3.073599 AACACCTGCAAGCCCACCT 62.074 57.895 0.00 0.00 0.00 4.00
3163 3292 2.203538 CACCTGCAAGCCCACCTT 60.204 61.111 0.00 0.00 0.00 3.50
3164 3293 1.074775 CACCTGCAAGCCCACCTTA 59.925 57.895 0.00 0.00 31.00 2.69
3165 3294 0.323725 CACCTGCAAGCCCACCTTAT 60.324 55.000 0.00 0.00 31.00 1.73
3166 3295 0.409484 ACCTGCAAGCCCACCTTATT 59.591 50.000 0.00 0.00 31.00 1.40
3167 3296 1.106285 CCTGCAAGCCCACCTTATTC 58.894 55.000 0.00 0.00 31.00 1.75
3168 3297 1.341383 CCTGCAAGCCCACCTTATTCT 60.341 52.381 0.00 0.00 31.00 2.40
3169 3298 2.092429 CCTGCAAGCCCACCTTATTCTA 60.092 50.000 0.00 0.00 31.00 2.10
3170 3299 3.209410 CTGCAAGCCCACCTTATTCTAG 58.791 50.000 0.00 0.00 31.00 2.43
3171 3300 2.843730 TGCAAGCCCACCTTATTCTAGA 59.156 45.455 0.00 0.00 31.00 2.43
3172 3301 3.118261 TGCAAGCCCACCTTATTCTAGAG 60.118 47.826 0.00 0.00 31.00 2.43
3238 3367 8.540507 AGTATGTACTCTTATATATGCAGGGG 57.459 38.462 0.00 0.00 0.00 4.79
3246 3375 8.618385 ACTCTTATATATGCAGGGGAAATGATT 58.382 33.333 0.00 0.00 0.00 2.57
3284 3413 7.286087 TGAGCATGTAAAAGATTCCAATGCTAT 59.714 33.333 7.19 0.00 42.09 2.97
3801 4349 0.750546 TCTGATGCAGGCATTGAGGC 60.751 55.000 8.34 0.00 44.61 4.70
4171 4719 3.782656 TTCCAACAAACTACTCCCTCC 57.217 47.619 0.00 0.00 0.00 4.30
4172 4720 1.621814 TCCAACAAACTACTCCCTCCG 59.378 52.381 0.00 0.00 0.00 4.63
4173 4721 1.346722 CCAACAAACTACTCCCTCCGT 59.653 52.381 0.00 0.00 0.00 4.69
4174 4722 2.612221 CCAACAAACTACTCCCTCCGTC 60.612 54.545 0.00 0.00 0.00 4.79
4175 4723 1.264295 ACAAACTACTCCCTCCGTCC 58.736 55.000 0.00 0.00 0.00 4.79
4176 4724 1.263356 CAAACTACTCCCTCCGTCCA 58.737 55.000 0.00 0.00 0.00 4.02
4177 4725 1.067071 CAAACTACTCCCTCCGTCCAC 60.067 57.143 0.00 0.00 0.00 4.02
4178 4726 0.113776 AACTACTCCCTCCGTCCACA 59.886 55.000 0.00 0.00 0.00 4.17
4179 4727 0.113776 ACTACTCCCTCCGTCCACAA 59.886 55.000 0.00 0.00 0.00 3.33
4180 4728 1.273098 ACTACTCCCTCCGTCCACAAT 60.273 52.381 0.00 0.00 0.00 2.71
4181 4729 1.137086 CTACTCCCTCCGTCCACAATG 59.863 57.143 0.00 0.00 0.00 2.82
4182 4730 0.836400 ACTCCCTCCGTCCACAATGT 60.836 55.000 0.00 0.00 0.00 2.71
4183 4731 1.191535 CTCCCTCCGTCCACAATGTA 58.808 55.000 0.00 0.00 0.00 2.29
4184 4732 1.553248 CTCCCTCCGTCCACAATGTAA 59.447 52.381 0.00 0.00 0.00 2.41
4185 4733 1.553248 TCCCTCCGTCCACAATGTAAG 59.447 52.381 0.00 0.00 0.00 2.34
4186 4734 1.553248 CCCTCCGTCCACAATGTAAGA 59.447 52.381 0.00 0.00 0.00 2.10
4187 4735 2.618053 CCTCCGTCCACAATGTAAGAC 58.382 52.381 5.85 5.85 0.00 3.01
4192 4740 4.461992 CGTCCACAATGTAAGACGTTTT 57.538 40.909 22.21 0.00 45.25 2.43
4193 4741 4.839796 CGTCCACAATGTAAGACGTTTTT 58.160 39.130 22.21 0.00 45.25 1.94
4194 4742 4.668837 CGTCCACAATGTAAGACGTTTTTG 59.331 41.667 22.21 0.00 45.25 2.44
4195 4743 4.439776 GTCCACAATGTAAGACGTTTTTGC 59.560 41.667 0.00 0.00 0.00 3.68
4196 4744 4.096532 TCCACAATGTAAGACGTTTTTGCA 59.903 37.500 0.00 1.87 0.00 4.08
4197 4745 4.800993 CCACAATGTAAGACGTTTTTGCAA 59.199 37.500 0.00 0.00 0.00 4.08
4198 4746 5.051774 CCACAATGTAAGACGTTTTTGCAAG 60.052 40.000 0.00 2.28 0.00 4.01
4199 4747 4.502645 ACAATGTAAGACGTTTTTGCAAGC 59.497 37.500 0.00 0.00 0.00 4.01
4200 4748 4.568152 ATGTAAGACGTTTTTGCAAGCT 57.432 36.364 0.00 0.00 0.00 3.74
4201 4749 5.682943 ATGTAAGACGTTTTTGCAAGCTA 57.317 34.783 0.00 0.00 0.00 3.32
4202 4750 5.682943 TGTAAGACGTTTTTGCAAGCTAT 57.317 34.783 0.00 0.00 0.00 2.97
4203 4751 6.788684 TGTAAGACGTTTTTGCAAGCTATA 57.211 33.333 0.00 0.00 0.00 1.31
4204 4752 7.372451 TGTAAGACGTTTTTGCAAGCTATAT 57.628 32.000 0.00 0.00 0.00 0.86
4205 4753 7.812648 TGTAAGACGTTTTTGCAAGCTATATT 58.187 30.769 0.00 0.00 0.00 1.28
4206 4754 8.937884 TGTAAGACGTTTTTGCAAGCTATATTA 58.062 29.630 0.00 0.00 0.00 0.98
4207 4755 9.422196 GTAAGACGTTTTTGCAAGCTATATTAG 57.578 33.333 0.00 0.00 0.00 1.73
4238 4786 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
4239 4787 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
4240 4788 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
4241 4789 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
4242 4790 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
4243 4791 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
4311 4859 3.730761 GCTCTGCAGTGCAACGGG 61.731 66.667 30.45 9.67 45.86 5.28
4340 4897 1.001633 GACTACACTGGAAAAGGGCGA 59.998 52.381 0.00 0.00 29.26 5.54
4642 5200 6.566197 CCTGGCAGGTAAGATCAATAATTC 57.434 41.667 25.74 0.00 0.00 2.17
4711 5269 1.549203 TTGAATTCTCCTTGCAGGGC 58.451 50.000 10.65 0.00 35.59 5.19
4826 5384 4.734398 AGAACCTGCACAAATCAAACAA 57.266 36.364 0.00 0.00 0.00 2.83
4939 5497 4.504864 CCTTGTTCAGGGATCACACTTACA 60.505 45.833 0.00 0.00 39.39 2.41
4957 5515 7.147602 ACACTTACAGGAGTACAACTTAAACCT 60.148 37.037 0.00 0.00 0.00 3.50
5263 5821 2.799207 GCAAGTGTGTCATGTTTGTGGG 60.799 50.000 0.00 0.00 0.00 4.61
5279 5837 5.389859 TTGTGGGAAAGCAAACATAGATG 57.610 39.130 0.00 0.00 0.00 2.90
5401 6012 9.573133 AAAAATAATATTACAGCACTTCTGCAC 57.427 29.630 0.00 0.00 46.97 4.57
5402 6013 7.864108 AATAATATTACAGCACTTCTGCACA 57.136 32.000 0.00 0.00 46.97 4.57
5403 6014 7.864108 ATAATATTACAGCACTTCTGCACAA 57.136 32.000 0.00 0.00 46.97 3.33
5404 6015 3.904136 ATTACAGCACTTCTGCACAAC 57.096 42.857 0.00 0.00 46.97 3.32
5405 6016 2.620251 TACAGCACTTCTGCACAACT 57.380 45.000 0.00 0.00 46.97 3.16
5406 6017 1.755179 ACAGCACTTCTGCACAACTT 58.245 45.000 0.00 0.00 46.97 2.66
5452 6064 9.638239 ACTATTAATAAAAACAGTGCCAACATG 57.362 29.630 0.00 0.00 0.00 3.21
5549 6161 7.158697 TCGGTTAAGATTCAGAAACAGATTGA 58.841 34.615 0.00 0.00 0.00 2.57
5590 6207 9.599866 TGTTTAGATGACAAGTATACTGATTGG 57.400 33.333 6.06 0.00 0.00 3.16
5635 6252 1.856265 GCACTTGGGCAGAAGGAACG 61.856 60.000 0.00 0.00 0.00 3.95
5649 6266 6.473455 GCAGAAGGAACGGAAAAATGATATTG 59.527 38.462 0.00 0.00 0.00 1.90
5652 6269 8.462016 AGAAGGAACGGAAAAATGATATTGAAG 58.538 33.333 0.00 0.00 0.00 3.02
5681 6298 9.783256 AACTGTAAGAAAAATGAACAAGTACAC 57.217 29.630 0.00 0.00 37.43 2.90
5775 6395 1.801512 GCGCGGAAAGGAAATGTGC 60.802 57.895 8.83 0.00 0.00 4.57
5810 6431 9.216117 GGTTTAGTAGCTAGAAAGATTTTGACA 57.784 33.333 0.00 0.00 0.00 3.58
5911 6533 7.409697 CGAATTAACCATTAGAACATGACAGG 58.590 38.462 0.00 0.00 0.00 4.00
5914 6536 4.494091 ACCATTAGAACATGACAGGGAG 57.506 45.455 0.00 0.00 0.00 4.30
5925 6547 2.626785 TGACAGGGAGGTGACCATTTA 58.373 47.619 3.63 0.00 0.00 1.40
5987 6609 5.653255 AGTAACGGAGGGAGTAGGTTATA 57.347 43.478 0.00 0.00 0.00 0.98
6024 6646 6.456795 AGCATTTTTACCATCTTTCTAGCC 57.543 37.500 0.00 0.00 0.00 3.93
6034 6656 7.676683 ACCATCTTTCTAGCCTTATAACTCA 57.323 36.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 7.362662 TGCTTTGCAGAATTTAGTCAGTTTAG 58.637 34.615 0.00 0.00 33.32 1.85
77 79 4.062991 GCTCTAAGAAACAACGAGGGAAA 58.937 43.478 0.00 0.00 0.00 3.13
85 87 7.478520 TCTGTTTACAGCTCTAAGAAACAAC 57.521 36.000 5.00 0.00 43.46 3.32
125 127 0.108472 TCACAGGCATCTCGCTGAAG 60.108 55.000 0.00 0.00 41.91 3.02
139 141 3.508762 ACGGAATTACTAACGCTCACAG 58.491 45.455 0.00 0.00 0.00 3.66
162 164 5.038033 CGGCTAGAGTTGCTCTTACTAAAG 58.962 45.833 3.87 0.00 41.50 1.85
163 165 4.703575 TCGGCTAGAGTTGCTCTTACTAAA 59.296 41.667 3.87 0.00 41.50 1.85
184 187 0.319900 CGGCCCAATATGAGGACTCG 60.320 60.000 0.00 0.00 0.00 4.18
207 210 6.683715 TCGTCATATCGAAGGTTATTATGCA 58.316 36.000 0.00 0.00 36.89 3.96
215 218 6.036083 CAGACAAAATCGTCATATCGAAGGTT 59.964 38.462 0.00 0.00 42.99 3.50
218 221 6.812481 TCAGACAAAATCGTCATATCGAAG 57.188 37.500 0.00 0.00 42.99 3.79
219 222 7.589574 TTTCAGACAAAATCGTCATATCGAA 57.410 32.000 0.00 0.00 42.99 3.71
245 248 6.128063 GCTCTCAATTGACTGCTAAAGTGATT 60.128 38.462 16.35 0.00 40.07 2.57
246 249 5.353678 GCTCTCAATTGACTGCTAAAGTGAT 59.646 40.000 16.35 0.00 40.07 3.06
247 250 4.692625 GCTCTCAATTGACTGCTAAAGTGA 59.307 41.667 16.35 4.30 40.07 3.41
250 253 5.391736 CCAAGCTCTCAATTGACTGCTAAAG 60.392 44.000 22.84 17.19 30.72 1.85
259 262 1.371467 TCCCCCAAGCTCTCAATTGA 58.629 50.000 8.12 8.12 0.00 2.57
260 263 2.220653 TTCCCCCAAGCTCTCAATTG 57.779 50.000 0.00 0.00 0.00 2.32
261 264 2.999185 TTTCCCCCAAGCTCTCAATT 57.001 45.000 0.00 0.00 0.00 2.32
262 265 2.999185 TTTTCCCCCAAGCTCTCAAT 57.001 45.000 0.00 0.00 0.00 2.57
263 266 2.176798 TCTTTTTCCCCCAAGCTCTCAA 59.823 45.455 0.00 0.00 0.00 3.02
264 267 1.780309 TCTTTTTCCCCCAAGCTCTCA 59.220 47.619 0.00 0.00 0.00 3.27
287 290 1.962100 GGGACCTACTCGTCAATAGGG 59.038 57.143 2.55 0.00 42.11 3.53
471 476 1.848652 TTGTGGGGAAACAAAACGGA 58.151 45.000 0.00 0.00 37.12 4.69
533 538 7.994425 TTACTGAAACAGGAATGAAGCATAA 57.006 32.000 0.00 0.00 35.51 1.90
597 602 9.806448 TTCAGTAATCTCTCTCTGCTATAATCT 57.194 33.333 0.00 0.00 0.00 2.40
658 664 0.108329 ACGGCGGTTATTCAGTGAGG 60.108 55.000 13.24 0.00 0.00 3.86
686 692 2.095415 CCATGATCATGTATGCTTGGCG 60.095 50.000 29.23 10.18 37.11 5.69
743 749 1.741706 CTTGTAGCTGCACAGGGAATG 59.258 52.381 3.11 0.00 0.00 2.67
786 792 3.615480 AATGCGGGAAATGGGGCCA 62.615 57.895 4.39 0.00 0.00 5.36
822 828 1.302511 GTTTGCGCCTCCCTCTCAA 60.303 57.895 4.18 0.00 0.00 3.02
823 829 1.841302 ATGTTTGCGCCTCCCTCTCA 61.841 55.000 4.18 0.00 0.00 3.27
865 871 9.574516 AAAGACAGAGGCTTCTCTTTAAATAAA 57.425 29.630 10.25 0.00 44.95 1.40
935 942 2.463752 ACGTGCTTGGGGAGTAGATAA 58.536 47.619 0.00 0.00 0.00 1.75
1056 1066 1.741706 CAGACATCAATGGTGGAGCAC 59.258 52.381 0.00 0.00 0.00 4.40
1248 1258 0.039618 CAGGTACATTGGGGCTTGGT 59.960 55.000 0.00 0.00 0.00 3.67
1301 1317 3.642848 ACTTGAATGTCCATTGCCTTTGT 59.357 39.130 0.00 0.00 0.00 2.83
1404 1420 0.377554 CAACCACGTTAAACACCGCA 59.622 50.000 0.00 0.00 0.00 5.69
1528 1560 2.485814 GGCAGTGAGAATTTCTGTGTCC 59.514 50.000 3.03 1.92 0.00 4.02
1610 1642 1.078759 GGACTGATCAACACGGAGCG 61.079 60.000 0.00 0.00 0.00 5.03
1677 1709 7.346471 AGTGCCACTCCAAATATACAAATACT 58.654 34.615 0.00 0.00 0.00 2.12
1733 1765 6.873605 TGAAATGTACATCGGATCATATGTCC 59.126 38.462 9.23 8.22 37.50 4.02
1762 1794 3.006644 CGATGATGATGGATCACAGGACT 59.993 47.826 0.00 0.00 44.12 3.85
1768 1800 4.489810 GGTAGTCGATGATGATGGATCAC 58.510 47.826 0.00 0.00 44.12 3.06
1794 1826 1.997606 GCTTTGCACTGGAAATCATGC 59.002 47.619 0.00 0.00 38.59 4.06
1811 1843 0.598065 GTGACAATTTCCTGCGGCTT 59.402 50.000 0.00 0.00 0.00 4.35
1928 1960 1.540363 CCGTACCAGCTTGAAGTGTGT 60.540 52.381 0.00 0.00 0.00 3.72
1957 1989 8.154203 GTGGATTCCTCAAAAAGGGAAAAATAA 58.846 33.333 3.95 0.00 46.23 1.40
1981 2013 8.608844 AGAAATAAAAGAACAGTACCTGAGTG 57.391 34.615 0.00 0.00 35.18 3.51
1982 2014 8.652290 AGAGAAATAAAAGAACAGTACCTGAGT 58.348 33.333 0.00 0.00 35.18 3.41
1983 2015 9.495572 AAGAGAAATAAAAGAACAGTACCTGAG 57.504 33.333 0.00 0.00 35.18 3.35
1984 2016 9.273016 CAAGAGAAATAAAAGAACAGTACCTGA 57.727 33.333 0.00 0.00 35.18 3.86
1985 2017 8.507249 CCAAGAGAAATAAAAGAACAGTACCTG 58.493 37.037 0.00 0.00 37.52 4.00
1986 2018 8.218488 ACCAAGAGAAATAAAAGAACAGTACCT 58.782 33.333 0.00 0.00 0.00 3.08
1987 2019 8.290325 CACCAAGAGAAATAAAAGAACAGTACC 58.710 37.037 0.00 0.00 0.00 3.34
1988 2020 9.052759 TCACCAAGAGAAATAAAAGAACAGTAC 57.947 33.333 0.00 0.00 0.00 2.73
1989 2021 9.621629 TTCACCAAGAGAAATAAAAGAACAGTA 57.378 29.630 0.00 0.00 0.00 2.74
1990 2022 8.406297 GTTCACCAAGAGAAATAAAAGAACAGT 58.594 33.333 0.00 0.00 33.72 3.55
1991 2023 8.405531 TGTTCACCAAGAGAAATAAAAGAACAG 58.594 33.333 0.00 0.00 37.35 3.16
1992 2024 8.287439 TGTTCACCAAGAGAAATAAAAGAACA 57.713 30.769 0.00 0.00 39.19 3.18
1993 2025 9.581099 TTTGTTCACCAAGAGAAATAAAAGAAC 57.419 29.630 0.00 0.00 33.75 3.01
1994 2026 9.801873 CTTTGTTCACCAAGAGAAATAAAAGAA 57.198 29.630 0.00 0.00 33.75 2.52
1995 2027 8.966868 ACTTTGTTCACCAAGAGAAATAAAAGA 58.033 29.630 0.00 0.00 33.75 2.52
1996 2028 9.023967 CACTTTGTTCACCAAGAGAAATAAAAG 57.976 33.333 0.00 0.00 33.75 2.27
1997 2029 7.978975 CCACTTTGTTCACCAAGAGAAATAAAA 59.021 33.333 0.00 0.00 33.75 1.52
1998 2030 7.417342 CCCACTTTGTTCACCAAGAGAAATAAA 60.417 37.037 0.00 0.00 33.75 1.40
1999 2031 6.040391 CCCACTTTGTTCACCAAGAGAAATAA 59.960 38.462 0.00 0.00 33.75 1.40
2000 2032 5.534654 CCCACTTTGTTCACCAAGAGAAATA 59.465 40.000 0.00 0.00 33.75 1.40
2001 2033 4.342092 CCCACTTTGTTCACCAAGAGAAAT 59.658 41.667 0.00 0.00 33.75 2.17
2002 2034 3.699038 CCCACTTTGTTCACCAAGAGAAA 59.301 43.478 0.00 0.00 33.75 2.52
2065 2127 6.834959 TCTTGCGTGCAAAAATAATTTGAA 57.165 29.167 8.80 0.00 35.33 2.69
2066 2128 6.834959 TTCTTGCGTGCAAAAATAATTTGA 57.165 29.167 8.80 0.00 35.33 2.69
2067 2129 6.904011 TGTTTCTTGCGTGCAAAAATAATTTG 59.096 30.769 8.80 0.00 35.33 2.32
2070 2132 6.783892 ATGTTTCTTGCGTGCAAAAATAAT 57.216 29.167 8.80 7.66 35.33 1.28
2071 2133 7.201308 CGATATGTTTCTTGCGTGCAAAAATAA 60.201 33.333 8.80 6.09 35.33 1.40
2134 2197 6.884836 AGAACTGGTTTTTGAGAACTAACACT 59.115 34.615 0.00 0.00 0.00 3.55
2135 2198 7.085052 AGAACTGGTTTTTGAGAACTAACAC 57.915 36.000 0.00 0.00 0.00 3.32
2136 2199 7.696992 AAGAACTGGTTTTTGAGAACTAACA 57.303 32.000 0.00 0.00 0.00 2.41
2182 2254 8.585018 CCTCTACATAAAACATTTCCACCTTTT 58.415 33.333 0.00 0.00 0.00 2.27
2186 2258 5.417580 TGCCTCTACATAAAACATTTCCACC 59.582 40.000 0.00 0.00 0.00 4.61
2367 2441 4.370094 AACTATCCAAAACCGTACCCAA 57.630 40.909 0.00 0.00 0.00 4.12
2444 2524 3.446873 CACACTTGTAGAGCTCAGATCCT 59.553 47.826 17.77 0.00 0.00 3.24
2466 2546 2.793278 AATGAACCCAGCGACAAAAC 57.207 45.000 0.00 0.00 0.00 2.43
2472 2552 3.358111 TCCATAAAATGAACCCAGCGA 57.642 42.857 0.00 0.00 0.00 4.93
2495 2575 9.267084 GATTTGTTCTCAAAAGACTAGACTCTT 57.733 33.333 0.00 0.00 44.97 2.85
2520 2600 7.227314 CCTGCATGCACACTAATTTATTAGAGA 59.773 37.037 18.46 0.00 41.72 3.10
2571 2651 1.676635 GATGCTCCCAGCTTGCACA 60.677 57.895 3.11 0.00 42.97 4.57
2651 2731 5.353956 GGAAAAGAATGTTTGGTTTGCAGTT 59.646 36.000 0.00 0.00 0.00 3.16
3032 3112 6.731292 AGGTGCAGAATTACCTTTCTTTTT 57.269 33.333 0.00 0.00 44.72 1.94
3033 3113 7.833285 TTAGGTGCAGAATTACCTTTCTTTT 57.167 32.000 3.00 0.00 44.72 2.27
3034 3114 7.830739 CATTAGGTGCAGAATTACCTTTCTTT 58.169 34.615 3.00 0.00 44.72 2.52
3035 3115 7.396540 CATTAGGTGCAGAATTACCTTTCTT 57.603 36.000 3.00 0.00 44.72 2.52
3127 3256 6.515035 GCAGGTGTTGTAAAAATCTAGTGCTT 60.515 38.462 0.00 0.00 0.00 3.91
3128 3257 5.048713 GCAGGTGTTGTAAAAATCTAGTGCT 60.049 40.000 0.00 0.00 0.00 4.40
3129 3258 5.154222 GCAGGTGTTGTAAAAATCTAGTGC 58.846 41.667 0.00 0.00 0.00 4.40
3130 3259 6.312399 TGCAGGTGTTGTAAAAATCTAGTG 57.688 37.500 0.00 0.00 0.00 2.74
3131 3260 6.515035 GCTTGCAGGTGTTGTAAAAATCTAGT 60.515 38.462 0.00 0.00 30.72 2.57
3132 3261 5.858581 GCTTGCAGGTGTTGTAAAAATCTAG 59.141 40.000 0.00 0.00 30.72 2.43
3133 3262 5.278758 GGCTTGCAGGTGTTGTAAAAATCTA 60.279 40.000 0.00 0.00 30.72 1.98
3134 3263 4.501400 GGCTTGCAGGTGTTGTAAAAATCT 60.501 41.667 0.00 0.00 30.72 2.40
3135 3264 3.740832 GGCTTGCAGGTGTTGTAAAAATC 59.259 43.478 0.00 0.00 30.72 2.17
3136 3265 3.494223 GGGCTTGCAGGTGTTGTAAAAAT 60.494 43.478 0.00 0.00 30.72 1.82
3137 3266 2.159028 GGGCTTGCAGGTGTTGTAAAAA 60.159 45.455 0.00 0.00 30.72 1.94
3138 3267 1.410882 GGGCTTGCAGGTGTTGTAAAA 59.589 47.619 0.00 0.00 30.72 1.52
3139 3268 1.036707 GGGCTTGCAGGTGTTGTAAA 58.963 50.000 0.00 0.00 30.72 2.01
3140 3269 0.106469 TGGGCTTGCAGGTGTTGTAA 60.106 50.000 0.00 0.00 0.00 2.41
3141 3270 0.821711 GTGGGCTTGCAGGTGTTGTA 60.822 55.000 0.00 0.00 0.00 2.41
3142 3271 2.127232 GTGGGCTTGCAGGTGTTGT 61.127 57.895 0.00 0.00 0.00 3.32
3143 3272 2.730094 GTGGGCTTGCAGGTGTTG 59.270 61.111 0.00 0.00 0.00 3.33
3144 3273 2.521708 GGTGGGCTTGCAGGTGTT 60.522 61.111 0.00 0.00 0.00 3.32
3145 3274 1.715019 TAAGGTGGGCTTGCAGGTGT 61.715 55.000 0.00 0.00 0.00 4.16
3146 3275 0.323725 ATAAGGTGGGCTTGCAGGTG 60.324 55.000 0.00 0.00 0.00 4.00
3147 3276 0.409484 AATAAGGTGGGCTTGCAGGT 59.591 50.000 0.00 0.00 0.00 4.00
3148 3277 1.106285 GAATAAGGTGGGCTTGCAGG 58.894 55.000 0.00 0.00 0.00 4.85
3149 3278 2.134789 AGAATAAGGTGGGCTTGCAG 57.865 50.000 0.00 0.00 0.00 4.41
3150 3279 2.843730 TCTAGAATAAGGTGGGCTTGCA 59.156 45.455 0.00 0.00 0.00 4.08
3151 3280 3.134804 TCTCTAGAATAAGGTGGGCTTGC 59.865 47.826 0.00 0.00 0.00 4.01
3152 3281 5.559148 ATCTCTAGAATAAGGTGGGCTTG 57.441 43.478 0.00 0.00 0.00 4.01
3153 3282 7.691993 TTTATCTCTAGAATAAGGTGGGCTT 57.308 36.000 0.00 0.00 0.00 4.35
3154 3283 7.348537 ACTTTTATCTCTAGAATAAGGTGGGCT 59.651 37.037 0.00 0.00 0.00 5.19
3155 3284 7.510407 ACTTTTATCTCTAGAATAAGGTGGGC 58.490 38.462 0.00 0.00 0.00 5.36
3156 3285 9.907229 AAACTTTTATCTCTAGAATAAGGTGGG 57.093 33.333 0.00 0.00 0.00 4.61
3190 3319 7.575505 ACTACATAGGATGGCGTATCTATACT 58.424 38.462 0.00 0.00 36.03 2.12
3201 3330 7.469537 AAGAGTACATACTACATAGGATGGC 57.530 40.000 14.37 7.64 46.67 4.40
3238 3367 9.745880 ATGCTCATAACATCAAGAAATCATTTC 57.254 29.630 1.42 1.42 39.96 2.17
3246 3375 9.230122 TCTTTTACATGCTCATAACATCAAGAA 57.770 29.630 0.00 0.00 0.00 2.52
3318 3862 8.854979 TGTTTCTCTTTGTACACATGAAATTG 57.145 30.769 0.00 0.00 0.00 2.32
3320 3864 9.301153 GTTTGTTTCTCTTTGTACACATGAAAT 57.699 29.630 0.00 0.00 0.00 2.17
3801 4349 7.009631 CACTACGACATTTGAAGAACCATAGAG 59.990 40.741 0.00 0.00 0.00 2.43
4037 4585 7.350744 TGAATGCATGCTAGATTGGTAAAAT 57.649 32.000 20.33 0.00 0.00 1.82
4042 4590 8.683615 CATAATATGAATGCATGCTAGATTGGT 58.316 33.333 20.33 4.12 35.94 3.67
4162 4710 1.191535 CATTGTGGACGGAGGGAGTA 58.808 55.000 0.00 0.00 0.00 2.59
4163 4711 0.836400 ACATTGTGGACGGAGGGAGT 60.836 55.000 0.00 0.00 0.00 3.85
4164 4712 1.191535 TACATTGTGGACGGAGGGAG 58.808 55.000 0.00 0.00 0.00 4.30
4165 4713 1.553248 CTTACATTGTGGACGGAGGGA 59.447 52.381 0.00 0.00 0.00 4.20
4166 4714 1.553248 TCTTACATTGTGGACGGAGGG 59.447 52.381 0.00 0.00 0.00 4.30
4167 4715 2.618053 GTCTTACATTGTGGACGGAGG 58.382 52.381 0.00 0.00 0.00 4.30
4168 4716 2.259618 CGTCTTACATTGTGGACGGAG 58.740 52.381 25.43 9.63 44.92 4.63
4169 4717 2.357327 CGTCTTACATTGTGGACGGA 57.643 50.000 25.43 6.92 44.92 4.69
4172 4720 4.439776 GCAAAAACGTCTTACATTGTGGAC 59.560 41.667 0.00 7.05 0.00 4.02
4173 4721 4.096532 TGCAAAAACGTCTTACATTGTGGA 59.903 37.500 0.00 0.00 0.00 4.02
4174 4722 4.355437 TGCAAAAACGTCTTACATTGTGG 58.645 39.130 0.00 0.00 0.00 4.17
4175 4723 5.554324 GCTTGCAAAAACGTCTTACATTGTG 60.554 40.000 0.00 0.00 0.00 3.33
4176 4724 4.502645 GCTTGCAAAAACGTCTTACATTGT 59.497 37.500 0.00 0.00 0.00 2.71
4177 4725 4.739716 AGCTTGCAAAAACGTCTTACATTG 59.260 37.500 0.00 0.00 0.00 2.82
4178 4726 4.932146 AGCTTGCAAAAACGTCTTACATT 58.068 34.783 0.00 0.00 0.00 2.71
4179 4727 4.568152 AGCTTGCAAAAACGTCTTACAT 57.432 36.364 0.00 0.00 0.00 2.29
4180 4728 5.682943 ATAGCTTGCAAAAACGTCTTACA 57.317 34.783 0.00 0.00 0.00 2.41
4181 4729 9.422196 CTAATATAGCTTGCAAAAACGTCTTAC 57.578 33.333 0.00 0.00 0.00 2.34
4213 4761 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
4214 4762 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
4215 4763 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
4216 4764 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
4217 4765 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
4219 4767 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
4220 4768 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
4221 4769 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
4222 4770 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
4223 4771 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
4224 4772 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
4225 4773 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
4226 4774 3.562108 ATACTCCCTCCGTCCCATAAT 57.438 47.619 0.00 0.00 0.00 1.28
4227 4775 4.474303 TTATACTCCCTCCGTCCCATAA 57.526 45.455 0.00 0.00 0.00 1.90
4228 4776 4.687262 ATTATACTCCCTCCGTCCCATA 57.313 45.455 0.00 0.00 0.00 2.74
4229 4777 3.562108 ATTATACTCCCTCCGTCCCAT 57.438 47.619 0.00 0.00 0.00 4.00
4230 4778 4.687262 ATATTATACTCCCTCCGTCCCA 57.313 45.455 0.00 0.00 0.00 4.37
4231 4779 5.597594 CCTTATATTATACTCCCTCCGTCCC 59.402 48.000 0.00 0.00 0.00 4.46
4232 4780 5.068855 GCCTTATATTATACTCCCTCCGTCC 59.931 48.000 0.00 0.00 0.00 4.79
4233 4781 5.655532 TGCCTTATATTATACTCCCTCCGTC 59.344 44.000 0.00 0.00 0.00 4.79
4234 4782 5.586877 TGCCTTATATTATACTCCCTCCGT 58.413 41.667 0.00 0.00 0.00 4.69
4235 4783 6.732896 ATGCCTTATATTATACTCCCTCCG 57.267 41.667 0.00 0.00 0.00 4.63
4236 4784 9.381038 TCATATGCCTTATATTATACTCCCTCC 57.619 37.037 0.00 0.00 29.37 4.30
4307 4855 0.830444 TGTAGTCTGGAACTGCCCGT 60.830 55.000 0.00 0.00 39.66 5.28
4340 4897 3.627732 AGATGCTTCGATACGATTCGT 57.372 42.857 16.86 16.86 44.35 3.85
4384 4942 9.433153 CATGTGATCTGTGCTATATACTCATTT 57.567 33.333 0.00 0.00 0.00 2.32
4642 5200 6.618811 AGTTTATTCTGCATGCTCTTTCTTG 58.381 36.000 20.33 0.00 0.00 3.02
4711 5269 3.446161 TGTCTTGAACCAGTCCTATACCG 59.554 47.826 0.00 0.00 0.00 4.02
4826 5384 1.219124 CTGATACCGCCACTGCTGT 59.781 57.895 0.00 0.00 38.56 4.40
4939 5497 4.141574 TGCACAGGTTTAAGTTGTACTCCT 60.142 41.667 0.00 0.00 0.00 3.69
5221 5779 9.723601 ACTTGCCATGATAACAAAACATAAATT 57.276 25.926 0.00 0.00 0.00 1.82
5222 5780 9.153721 CACTTGCCATGATAACAAAACATAAAT 57.846 29.630 0.00 0.00 0.00 1.40
5223 5781 8.147058 ACACTTGCCATGATAACAAAACATAAA 58.853 29.630 0.00 0.00 0.00 1.40
5224 5782 7.598118 CACACTTGCCATGATAACAAAACATAA 59.402 33.333 0.00 0.00 0.00 1.90
5279 5837 5.669477 TGCCTGCCCATTTTATATGAAAAC 58.331 37.500 0.00 0.00 0.00 2.43
5398 6009 2.372148 GCAATGTGCAAAAGTTGTGC 57.628 45.000 11.34 11.34 44.26 4.57
5452 6064 4.600692 AACATTTGCTTCACCTTTACCC 57.399 40.909 0.00 0.00 0.00 3.69
5516 6128 9.152595 GTTTCTGAATCTTAACCGAGTTATTCT 57.847 33.333 0.00 0.00 0.00 2.40
5597 6214 6.832520 AGTGCCAAAACAAAATTTTCCTTT 57.167 29.167 0.00 1.04 0.00 3.11
5606 6223 1.003580 TGCCCAAGTGCCAAAACAAAA 59.996 42.857 0.00 0.00 0.00 2.44
5649 6266 9.567848 TTGTTCATTTTTCTTACAGTTCACTTC 57.432 29.630 0.00 0.00 0.00 3.01
5652 6269 8.911247 ACTTGTTCATTTTTCTTACAGTTCAC 57.089 30.769 0.00 0.00 0.00 3.18
5788 6409 7.968956 CGTCTGTCAAAATCTTTCTAGCTACTA 59.031 37.037 0.00 0.00 0.00 1.82
5789 6410 6.809196 CGTCTGTCAAAATCTTTCTAGCTACT 59.191 38.462 0.00 0.00 0.00 2.57
5790 6411 6.035112 CCGTCTGTCAAAATCTTTCTAGCTAC 59.965 42.308 0.00 0.00 0.00 3.58
5911 6533 6.990939 GGAGTAGTTAATAAATGGTCACCTCC 59.009 42.308 0.00 0.00 0.00 4.30
5914 6536 6.896883 AGGGAGTAGTTAATAAATGGTCACC 58.103 40.000 0.00 0.00 0.00 4.02
5925 6547 7.961326 TTTAGTTACGGAGGGAGTAGTTAAT 57.039 36.000 0.00 0.00 0.00 1.40
5970 6592 5.715279 TGATCATTATAACCTACTCCCTCCG 59.285 44.000 0.00 0.00 0.00 4.63
5987 6609 8.970020 TGGTAAAAATGCTTATGAGTGATCATT 58.030 29.630 0.00 0.00 0.00 2.57
6024 6646 9.123709 GATAGCTGATTCTCGTTGAGTTATAAG 57.876 37.037 0.00 0.00 0.00 1.73
6034 6656 8.948631 TTATTCAAAGATAGCTGATTCTCGTT 57.051 30.769 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.