Multiple sequence alignment - TraesCS4A01G148400

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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 TraesCS4A01G148400 chr4A 100.000 3773 0 0 1 3773 279468002 279471774 0.000000e+00 6968.0
1 TraesCS4A01G148400 chr4A 90.000 100 9 1 272 371 556768052 556767954 1.100000e-25 128.0
2 TraesCS4A01G148400 chr4A 95.833 48 2 0 3376 3423 279471330 279471377 1.120000e-10 78.7
3 TraesCS4A01G148400 chr4A 95.833 48 2 0 3329 3376 279471377 279471424 1.120000e-10 78.7
4 TraesCS4A01G148400 chr4D 96.376 2235 50 11 166 2390 266786614 266784401 0.000000e+00 3650.0
5 TraesCS4A01G148400 chr4D 98.551 552 8 0 2386 2937 266784263 266783712 0.000000e+00 976.0
6 TraesCS4A01G148400 chr4D 91.560 391 16 7 2935 3325 266783687 266783314 1.200000e-144 523.0
7 TraesCS4A01G148400 chr4D 90.959 365 13 8 3412 3756 266783284 266782920 1.230000e-129 473.0
8 TraesCS4A01G148400 chr4D 94.286 105 6 0 90 194 498045970 498045866 1.080000e-35 161.0
9 TraesCS4A01G148400 chr4D 89.256 121 8 1 1 116 266786814 266786694 3.040000e-31 147.0
10 TraesCS4A01G148400 chr6B 97.959 98 2 0 90 187 276668917 276668820 1.800000e-38 171.0
11 TraesCS4A01G148400 chr4B 95.283 106 5 0 90 195 260038696 260038591 6.480000e-38 169.0
12 TraesCS4A01G148400 chrUn 95.238 105 4 1 86 189 362465798 362465902 8.380000e-37 165.0
13 TraesCS4A01G148400 chr3B 95.192 104 4 1 87 189 822536380 822536277 3.020000e-36 163.0
14 TraesCS4A01G148400 chr3B 95.402 87 4 0 284 370 409607303 409607217 5.080000e-29 139.0
15 TraesCS4A01G148400 chr7B 94.286 105 6 0 89 193 562993065 562993169 1.080000e-35 161.0
16 TraesCS4A01G148400 chr7B 92.793 111 7 1 79 189 425252179 425252070 3.900000e-35 159.0
17 TraesCS4A01G148400 chr7A 90.598 117 7 4 78 193 249279424 249279311 6.530000e-33 152.0
18 TraesCS4A01G148400 chr5B 89.916 119 11 1 79 196 671343393 671343275 6.530000e-33 152.0
19 TraesCS4A01G148400 chr5D 95.402 87 4 0 286 372 62715158 62715244 5.080000e-29 139.0
20 TraesCS4A01G148400 chr7D 94.382 89 5 0 282 370 141292084 141292172 1.830000e-28 137.0
21 TraesCS4A01G148400 chr7D 91.489 47 2 2 3325 3370 34219547 34219502 3.150000e-06 63.9
22 TraesCS4A01G148400 chr7D 100.000 30 0 0 3338 3367 440044939 440044968 5.260000e-04 56.5
23 TraesCS4A01G148400 chr5A 93.478 92 6 0 284 375 390156985 390157076 1.830000e-28 137.0
24 TraesCS4A01G148400 chr2D 94.382 89 5 0 286 374 619321093 619321005 1.830000e-28 137.0
25 TraesCS4A01G148400 chr2A 94.382 89 5 0 283 371 16861357 16861445 1.830000e-28 137.0
26 TraesCS4A01G148400 chr1D 91.579 95 8 0 283 377 124334424 124334330 8.500000e-27 132.0
27 TraesCS4A01G148400 chr1D 93.478 46 3 0 3322 3367 19408024 19408069 6.760000e-08 69.4
28 TraesCS4A01G148400 chr1A 97.561 41 1 0 3325 3365 31162217 31162177 1.880000e-08 71.3
29 TraesCS4A01G148400 chr1A 95.122 41 1 1 3325 3365 557156606 557156567 3.150000e-06 63.9
30 TraesCS4A01G148400 chr3A 97.500 40 1 0 3325 3364 442290652 442290691 6.760000e-08 69.4
31 TraesCS4A01G148400 chr6D 100.000 28 0 0 3338 3365 366703398 366703425 7.000000e-03 52.8
32 TraesCS4A01G148400 chr6A 100.000 28 0 0 3338 3365 507148684 507148711 7.000000e-03 52.8


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 TraesCS4A01G148400 chr4A 279468002 279471774 3772 False 2375.133333 6968 97.2220 1 3773 3 chr4A.!!$F1 3772
1 TraesCS4A01G148400 chr4D 266782920 266786814 3894 True 1153.800000 3650 93.3404 1 3756 5 chr4D.!!$R2 3755

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
508 544 0.243636 GACCATGCTTCCCAAAACGG 59.756 55.0 0.0 0.0 0.00 4.44 F
1219 1257 0.388134 GTGCATTTGTGCTGCTCCAG 60.388 55.0 0.0 0.0 40.34 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1456 1496 0.320421 GCCTACAAGTTGGACAGCGA 60.32 55.0 7.96 0.0 0.0 4.93 R
3173 3388 0.110056 GCGTCAGAACAGTTGGCATG 60.11 55.0 0.00 0.0 0.0 4.06 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
82 88 8.169977 TCATGATTTGCTCAAGAGTAAAGTTT 57.830 30.769 16.32 3.04 44.07 2.66
97 103 9.761504 AGAGTAAAGTTTTGTTACTACTTCCTC 57.238 33.333 0.00 0.00 40.93 3.71
98 104 8.585189 AGTAAAGTTTTGTTACTACTTCCTCG 57.415 34.615 0.00 0.00 39.47 4.63
103 109 2.450476 TGTTACTACTTCCTCGGTCCC 58.550 52.381 0.00 0.00 0.00 4.46
110 116 4.533311 ACTACTTCCTCGGTCCCAAAATAA 59.467 41.667 0.00 0.00 0.00 1.40
111 117 3.951663 ACTTCCTCGGTCCCAAAATAAG 58.048 45.455 0.00 0.00 0.00 1.73
116 122 3.307480 CCTCGGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
118 124 5.484715 CTCGGTCCCAAAATAAGTGTCTTA 58.515 41.667 0.00 0.00 0.00 2.10
120 126 5.702209 TCGGTCCCAAAATAAGTGTCTTAAC 59.298 40.000 0.00 0.00 0.00 2.01
121 127 5.106436 CGGTCCCAAAATAAGTGTCTTAACC 60.106 44.000 0.00 0.00 0.00 2.85
122 128 6.008331 GGTCCCAAAATAAGTGTCTTAACCT 58.992 40.000 0.00 0.00 0.00 3.50
124 130 7.666804 GGTCCCAAAATAAGTGTCTTAACCTTA 59.333 37.037 0.00 0.00 0.00 2.69
126 132 8.442374 TCCCAAAATAAGTGTCTTAACCTTAGT 58.558 33.333 0.00 0.00 0.00 2.24
127 133 9.729281 CCCAAAATAAGTGTCTTAACCTTAGTA 57.271 33.333 0.00 0.00 0.00 1.82
136 142 8.262933 AGTGTCTTAACCTTAGTACAACTTTGT 58.737 33.333 0.00 0.00 44.86 2.83
137 143 9.533253 GTGTCTTAACCTTAGTACAACTTTGTA 57.467 33.333 0.00 0.00 42.35 2.41
163 199 8.351461 ACTAGAGTTAGTACAAAGTTGAGACAC 58.649 37.037 0.00 0.00 38.35 3.67
164 200 7.349412 AGAGTTAGTACAAAGTTGAGACACT 57.651 36.000 0.00 0.00 0.00 3.55
175 211 7.287696 ACAAAGTTGAGACACTTATTTTGGGAT 59.712 33.333 0.00 0.00 35.87 3.85
227 263 2.111384 GCAGTGTCAGATTCTCCCCTA 58.889 52.381 0.00 0.00 0.00 3.53
237 273 0.830648 TTCTCCCCTATCAACCTGCG 59.169 55.000 0.00 0.00 0.00 5.18
244 280 0.796312 CTATCAACCTGCGCGTGTTT 59.204 50.000 8.43 2.16 0.00 2.83
257 293 3.915569 GCGCGTGTTTGTTTATTATTGGT 59.084 39.130 8.43 0.00 0.00 3.67
280 316 1.668751 ACCATTTGCGCCTATGTTACG 59.331 47.619 4.18 0.00 0.00 3.18
308 344 4.611367 ACTCCCTCCGTCCCATAATATAG 58.389 47.826 0.00 0.00 0.00 1.31
508 544 0.243636 GACCATGCTTCCCAAAACGG 59.756 55.000 0.00 0.00 0.00 4.44
582 618 4.081406 TGCACTCCAAATAGCACTCATTT 58.919 39.130 0.00 0.00 31.05 2.32
640 676 5.827797 ACCTAACATCAGCAAGTTCTTTGAA 59.172 36.000 0.00 0.00 39.21 2.69
662 698 1.001048 CTTGTGATGTGTTGGTGCAGG 60.001 52.381 0.00 0.00 0.00 4.85
685 721 5.879223 GGTCTAGTAAGAACTAAAAAGGCCC 59.121 44.000 0.00 0.00 37.75 5.80
751 787 6.587273 ACTCTTATAATTTCTGCTCCACTCC 58.413 40.000 0.00 0.00 0.00 3.85
814 850 7.770801 TTCCAATCATGTAACGAGACTAATG 57.229 36.000 0.00 0.00 0.00 1.90
860 896 2.178580 GAAAGATGGTTTGATGGGGCA 58.821 47.619 0.00 0.00 0.00 5.36
861 897 2.323999 AAGATGGTTTGATGGGGCAA 57.676 45.000 0.00 0.00 0.00 4.52
862 898 2.555732 AGATGGTTTGATGGGGCAAT 57.444 45.000 0.00 0.00 0.00 3.56
863 899 2.112998 AGATGGTTTGATGGGGCAATG 58.887 47.619 0.00 0.00 0.00 2.82
938 975 5.195553 TCATTTCCCCCTTGATAATCCTCAA 59.804 40.000 0.00 0.00 34.14 3.02
1017 1055 1.228063 CATGGCCTCGGCTGCTTAT 60.228 57.895 3.32 0.00 41.60 1.73
1097 1135 3.384668 CTGAACTTGTCGGCGATCATAT 58.615 45.455 14.79 0.00 0.00 1.78
1098 1136 3.381045 TGAACTTGTCGGCGATCATATC 58.619 45.455 14.79 10.25 0.00 1.63
1125 1163 7.651304 CAGCTTACACAAAAATCAAATGTGGTA 59.349 33.333 9.61 0.00 46.67 3.25
1161 1199 0.603065 GCGAACTTTTGGAATGCCCT 59.397 50.000 0.00 0.00 35.38 5.19
1219 1257 0.388134 GTGCATTTGTGCTGCTCCAG 60.388 55.000 0.00 0.00 40.34 3.86
1456 1496 0.681175 GCAAGCCAAGGGTTCACAAT 59.319 50.000 0.00 0.00 33.16 2.71
1462 1502 1.238439 CAAGGGTTCACAATCGCTGT 58.762 50.000 0.00 0.00 39.56 4.40
1483 1523 3.189287 GTCCAACTTGTAGGCATGAACTG 59.811 47.826 0.00 0.00 0.00 3.16
1612 1652 0.109153 AGCATGAGTCACAGTGCCAA 59.891 50.000 12.50 0.00 35.35 4.52
1711 1751 8.697067 CATTTGAAAGATGATCACAAAGTTGAC 58.303 33.333 12.31 0.00 34.73 3.18
1717 1757 5.417894 AGATGATCACAAAGTTGACATGCAT 59.582 36.000 0.00 0.00 0.00 3.96
1720 1760 4.424061 TCACAAAGTTGACATGCATAGC 57.576 40.909 0.00 0.00 0.00 2.97
1802 1842 5.071250 ACCTGGATGCTTACGGTATTAATCA 59.929 40.000 0.00 0.00 0.00 2.57
1803 1843 6.173339 CCTGGATGCTTACGGTATTAATCAT 58.827 40.000 0.00 0.00 0.00 2.45
1818 1858 7.701924 GGTATTAATCATCAACACCAACATGTG 59.298 37.037 0.00 0.00 42.05 3.21
1846 1886 8.897752 ACTAAGAATTTCCATGTAGCATCTTTC 58.102 33.333 5.86 0.00 0.00 2.62
1849 1889 8.443953 AGAATTTCCATGTAGCATCTTTCTAC 57.556 34.615 0.00 0.00 37.50 2.59
2016 2057 6.248433 TGATTAGTTCCCTTTCTGCAAAGAT 58.752 36.000 0.00 0.00 41.60 2.40
2154 2196 7.665690 TGTCATGCAGTATAAAACAAAATGGT 58.334 30.769 0.00 0.00 0.00 3.55
2196 2238 4.631131 TGGACCATAATAGTTGCTCATCG 58.369 43.478 0.00 0.00 0.00 3.84
2197 2239 4.100963 TGGACCATAATAGTTGCTCATCGT 59.899 41.667 0.00 0.00 0.00 3.73
2198 2240 5.303333 TGGACCATAATAGTTGCTCATCGTA 59.697 40.000 0.00 0.00 0.00 3.43
2199 2241 6.014584 TGGACCATAATAGTTGCTCATCGTAT 60.015 38.462 0.00 0.00 0.00 3.06
2200 2242 6.874134 GGACCATAATAGTTGCTCATCGTATT 59.126 38.462 0.00 0.00 0.00 1.89
2201 2243 7.063544 GGACCATAATAGTTGCTCATCGTATTC 59.936 40.741 0.00 0.00 0.00 1.75
2202 2244 7.671302 ACCATAATAGTTGCTCATCGTATTCT 58.329 34.615 0.00 0.00 0.00 2.40
2203 2245 8.150945 ACCATAATAGTTGCTCATCGTATTCTT 58.849 33.333 0.00 0.00 0.00 2.52
2204 2246 9.639601 CCATAATAGTTGCTCATCGTATTCTTA 57.360 33.333 0.00 0.00 0.00 2.10
2250 2292 0.179026 CCCAGATCCACCTGCATCTG 60.179 60.000 5.87 5.87 43.94 2.90
2454 2642 2.421424 CCAGTACTTCTGCCTGCATTTC 59.579 50.000 0.00 0.00 42.38 2.17
2601 2789 4.191015 GGGGTTCCCCGGAGCATC 62.191 72.222 11.50 0.00 46.66 3.91
2757 2945 2.486472 ATGATCCAGCCGATTCATCC 57.514 50.000 0.00 0.00 0.00 3.51
2779 2967 3.297134 TTTCCCTGGTATGAATGAGCC 57.703 47.619 0.00 0.00 0.00 4.70
2810 2998 5.647658 TCGCATCATGAAAACTGTATTTCCT 59.352 36.000 0.00 2.35 38.30 3.36
2870 3058 1.398390 GCCTGTTTTAGCCATCGTCTG 59.602 52.381 0.00 0.00 0.00 3.51
3009 3224 6.323266 TCTATGTAGCTTTCGTTCTCTGTTC 58.677 40.000 0.00 0.00 0.00 3.18
3027 3242 2.882137 GTTCCAAACTCCGTTTCCATGA 59.118 45.455 0.00 0.00 33.10 3.07
3075 3290 6.431234 AGCTTGAGAATTAGAACGTGGATTTT 59.569 34.615 0.00 0.00 0.00 1.82
3134 3349 6.129115 CGTTGCAAACTAATTTCAGGAATGTG 60.129 38.462 0.00 0.00 46.99 3.21
3160 3375 0.528466 TGAGCGTGAATCGAGATGGC 60.528 55.000 0.00 0.00 42.86 4.40
3165 3380 1.857217 CGTGAATCGAGATGGCTCTTG 59.143 52.381 0.00 0.00 42.86 3.02
3166 3381 2.736719 CGTGAATCGAGATGGCTCTTGT 60.737 50.000 0.00 0.00 42.86 3.16
3167 3382 2.863137 GTGAATCGAGATGGCTCTTGTC 59.137 50.000 0.00 0.00 39.06 3.18
3168 3383 2.497273 TGAATCGAGATGGCTCTTGTCA 59.503 45.455 0.00 0.00 39.06 3.58
3169 3384 3.055891 TGAATCGAGATGGCTCTTGTCAA 60.056 43.478 0.00 0.00 39.06 3.18
3170 3385 2.370281 TCGAGATGGCTCTTGTCAAC 57.630 50.000 0.00 0.00 39.06 3.18
3171 3386 0.994995 CGAGATGGCTCTTGTCAACG 59.005 55.000 0.00 0.00 39.06 4.10
3172 3387 0.723981 GAGATGGCTCTTGTCAACGC 59.276 55.000 0.00 0.00 38.16 4.84
3173 3388 0.674895 AGATGGCTCTTGTCAACGCC 60.675 55.000 12.26 12.26 42.78 5.68
3175 3390 1.073025 TGGCTCTTGTCAACGCCAT 59.927 52.632 16.23 0.00 46.75 4.40
3176 3391 1.236616 TGGCTCTTGTCAACGCCATG 61.237 55.000 16.23 0.00 46.75 3.66
3177 3392 1.154150 GCTCTTGTCAACGCCATGC 60.154 57.895 0.00 0.00 0.00 4.06
3178 3393 1.503542 CTCTTGTCAACGCCATGCC 59.496 57.895 0.00 0.00 0.00 4.40
3179 3394 1.228094 TCTTGTCAACGCCATGCCA 60.228 52.632 0.00 0.00 0.00 4.92
3189 3404 1.236616 CGCCATGCCAACTGTTCTGA 61.237 55.000 0.00 0.00 0.00 3.27
3190 3405 0.242017 GCCATGCCAACTGTTCTGAC 59.758 55.000 0.00 0.00 0.00 3.51
3208 3423 2.286833 TGACGCTAATAAAATGGCTCGC 59.713 45.455 0.00 0.00 0.00 5.03
3209 3424 2.544267 GACGCTAATAAAATGGCTCGCT 59.456 45.455 0.00 0.00 0.00 4.93
3254 3469 1.806623 GCTCCTACCCACACATTAGCG 60.807 57.143 0.00 0.00 0.00 4.26
3255 3470 0.177141 TCCTACCCACACATTAGCGC 59.823 55.000 0.00 0.00 0.00 5.92
3265 3480 0.238289 ACATTAGCGCACACAGCAAC 59.762 50.000 11.47 0.00 46.13 4.17
3325 3540 9.802039 GAGAAGAGAAAGATAATACTCCCTCTA 57.198 37.037 0.00 0.00 32.53 2.43
3326 3541 9.807921 AGAAGAGAAAGATAATACTCCCTCTAG 57.192 37.037 0.00 0.00 32.53 2.43
3327 3542 9.582648 GAAGAGAAAGATAATACTCCCTCTAGT 57.417 37.037 0.00 0.00 32.53 2.57
3328 3543 8.934023 AGAGAAAGATAATACTCCCTCTAGTG 57.066 38.462 0.00 0.00 31.74 2.74
3330 3545 9.528489 GAGAAAGATAATACTCCCTCTAGTGAT 57.472 37.037 0.00 0.00 0.00 3.06
3331 3546 9.528489 AGAAAGATAATACTCCCTCTAGTGATC 57.472 37.037 0.00 0.00 0.00 2.92
3332 3547 8.658840 AAAGATAATACTCCCTCTAGTGATCC 57.341 38.462 0.00 0.00 0.00 3.36
3334 3549 7.770662 AGATAATACTCCCTCTAGTGATCCAA 58.229 38.462 0.00 0.00 0.00 3.53
3337 3552 2.761208 ACTCCCTCTAGTGATCCAAACG 59.239 50.000 0.00 0.00 0.00 3.60
3338 3553 1.480954 TCCCTCTAGTGATCCAAACGC 59.519 52.381 0.00 0.00 0.00 4.84
3339 3554 1.482593 CCCTCTAGTGATCCAAACGCT 59.517 52.381 0.00 0.00 0.00 5.07
3340 3555 2.482142 CCCTCTAGTGATCCAAACGCTC 60.482 54.545 0.00 0.00 0.00 5.03
3341 3556 2.428890 CCTCTAGTGATCCAAACGCTCT 59.571 50.000 0.00 0.00 0.00 4.09
3342 3557 3.118956 CCTCTAGTGATCCAAACGCTCTT 60.119 47.826 0.00 0.00 0.00 2.85
3343 3558 4.109050 CTCTAGTGATCCAAACGCTCTTC 58.891 47.826 0.00 0.00 0.00 2.87
3345 3560 4.948004 TCTAGTGATCCAAACGCTCTTCTA 59.052 41.667 0.00 0.00 0.00 2.10
3347 3562 5.091261 AGTGATCCAAACGCTCTTCTATT 57.909 39.130 0.00 0.00 0.00 1.73
3349 3564 5.582665 AGTGATCCAAACGCTCTTCTATTTC 59.417 40.000 0.00 0.00 0.00 2.17
3350 3565 5.582665 GTGATCCAAACGCTCTTCTATTTCT 59.417 40.000 0.00 0.00 0.00 2.52
3351 3566 6.092807 GTGATCCAAACGCTCTTCTATTTCTT 59.907 38.462 0.00 0.00 0.00 2.52
3353 3568 7.822334 TGATCCAAACGCTCTTCTATTTCTTTA 59.178 33.333 0.00 0.00 0.00 1.85
3354 3569 7.360575 TCCAAACGCTCTTCTATTTCTTTAC 57.639 36.000 0.00 0.00 0.00 2.01
3355 3570 6.932400 TCCAAACGCTCTTCTATTTCTTTACA 59.068 34.615 0.00 0.00 0.00 2.41
3356 3571 7.117812 TCCAAACGCTCTTCTATTTCTTTACAG 59.882 37.037 0.00 0.00 0.00 2.74
3358 3573 7.820044 AACGCTCTTCTATTTCTTTACAGAG 57.180 36.000 0.00 0.00 0.00 3.35
3359 3574 6.334202 ACGCTCTTCTATTTCTTTACAGAGG 58.666 40.000 0.00 0.00 0.00 3.69
3360 3575 5.751028 CGCTCTTCTATTTCTTTACAGAGGG 59.249 44.000 0.00 0.00 34.68 4.30
3361 3576 6.405953 CGCTCTTCTATTTCTTTACAGAGGGA 60.406 42.308 4.76 0.00 40.49 4.20
3362 3577 6.983890 GCTCTTCTATTTCTTTACAGAGGGAG 59.016 42.308 0.00 0.00 0.00 4.30
3363 3578 7.364320 GCTCTTCTATTTCTTTACAGAGGGAGT 60.364 40.741 0.00 0.00 0.00 3.85
3364 3579 9.191479 CTCTTCTATTTCTTTACAGAGGGAGTA 57.809 37.037 0.00 0.00 0.00 2.59
3365 3580 8.968969 TCTTCTATTTCTTTACAGAGGGAGTAC 58.031 37.037 0.00 0.00 0.00 2.73
3366 3581 8.896722 TTCTATTTCTTTACAGAGGGAGTACT 57.103 34.615 0.00 0.00 0.00 2.73
3367 3582 8.294954 TCTATTTCTTTACAGAGGGAGTACTG 57.705 38.462 0.00 0.00 39.65 2.74
3368 3583 8.114102 TCTATTTCTTTACAGAGGGAGTACTGA 58.886 37.037 0.00 0.00 37.54 3.41
3369 3584 6.591750 TTTCTTTACAGAGGGAGTACTGAG 57.408 41.667 0.00 0.00 37.54 3.35
3370 3585 5.516059 TCTTTACAGAGGGAGTACTGAGA 57.484 43.478 0.00 0.00 37.54 3.27
3371 3586 6.080969 TCTTTACAGAGGGAGTACTGAGAT 57.919 41.667 0.00 0.00 37.54 2.75
3372 3587 5.888724 TCTTTACAGAGGGAGTACTGAGATG 59.111 44.000 0.00 0.00 37.54 2.90
3373 3588 5.452341 TTACAGAGGGAGTACTGAGATGA 57.548 43.478 0.00 0.00 37.54 2.92
3374 3589 3.897239 ACAGAGGGAGTACTGAGATGAG 58.103 50.000 0.00 0.00 37.54 2.90
3375 3590 3.221771 CAGAGGGAGTACTGAGATGAGG 58.778 54.545 0.00 0.00 36.38 3.86
3376 3591 3.117701 CAGAGGGAGTACTGAGATGAGGA 60.118 52.174 0.00 0.00 36.38 3.71
3377 3592 3.726859 AGAGGGAGTACTGAGATGAGGAT 59.273 47.826 0.00 0.00 0.00 3.24
3378 3593 4.079253 GAGGGAGTACTGAGATGAGGATC 58.921 52.174 0.00 0.00 0.00 3.36
3379 3594 3.726859 AGGGAGTACTGAGATGAGGATCT 59.273 47.826 0.00 0.00 42.02 2.75
3380 3595 4.917040 AGGGAGTACTGAGATGAGGATCTA 59.083 45.833 0.00 0.00 39.19 1.98
3381 3596 5.374154 AGGGAGTACTGAGATGAGGATCTAA 59.626 44.000 0.00 0.00 39.19 2.10
3382 3597 6.071984 GGGAGTACTGAGATGAGGATCTAAA 58.928 44.000 0.00 0.00 39.19 1.85
3383 3598 6.015772 GGGAGTACTGAGATGAGGATCTAAAC 60.016 46.154 0.00 0.00 39.19 2.01
3384 3599 6.293735 GGAGTACTGAGATGAGGATCTAAACG 60.294 46.154 0.00 0.00 39.19 3.60
3385 3600 4.314740 ACTGAGATGAGGATCTAAACGC 57.685 45.455 0.00 0.00 39.19 4.84
3386 3601 3.957497 ACTGAGATGAGGATCTAAACGCT 59.043 43.478 0.00 0.00 39.19 5.07
3387 3602 4.037446 ACTGAGATGAGGATCTAAACGCTC 59.963 45.833 0.00 0.00 39.19 5.03
3388 3603 4.211125 TGAGATGAGGATCTAAACGCTCT 58.789 43.478 0.00 0.00 39.19 4.09
3389 3604 4.646945 TGAGATGAGGATCTAAACGCTCTT 59.353 41.667 0.00 0.00 39.19 2.85
3390 3605 5.195001 AGATGAGGATCTAAACGCTCTTC 57.805 43.478 0.00 0.00 37.15 2.87
3391 3606 4.892934 AGATGAGGATCTAAACGCTCTTCT 59.107 41.667 0.00 0.00 37.15 2.85
3392 3607 6.065374 AGATGAGGATCTAAACGCTCTTCTA 58.935 40.000 9.56 0.00 37.15 2.10
3393 3608 6.719370 AGATGAGGATCTAAACGCTCTTCTAT 59.281 38.462 9.56 0.00 37.15 1.98
3394 3609 7.885922 AGATGAGGATCTAAACGCTCTTCTATA 59.114 37.037 9.56 0.00 37.15 1.31
3395 3610 8.588290 ATGAGGATCTAAACGCTCTTCTATAT 57.412 34.615 0.00 0.00 34.92 0.86
3396 3611 8.046294 TGAGGATCTAAACGCTCTTCTATATC 57.954 38.462 0.00 0.00 34.92 1.63
3397 3612 7.885922 TGAGGATCTAAACGCTCTTCTATATCT 59.114 37.037 0.00 0.00 34.92 1.98
3398 3613 8.644374 AGGATCTAAACGCTCTTCTATATCTT 57.356 34.615 0.00 0.00 0.00 2.40
3399 3614 9.084533 AGGATCTAAACGCTCTTCTATATCTTT 57.915 33.333 0.00 0.00 0.00 2.52
3406 3621 7.209471 ACGCTCTTCTATATCTTTACAGAGG 57.791 40.000 0.00 0.00 30.36 3.69
3407 3622 6.207810 ACGCTCTTCTATATCTTTACAGAGGG 59.792 42.308 8.36 8.36 42.53 4.30
3408 3623 6.431543 CGCTCTTCTATATCTTTACAGAGGGA 59.568 42.308 4.76 0.00 40.49 4.20
3409 3624 7.361713 CGCTCTTCTATATCTTTACAGAGGGAG 60.362 44.444 4.76 0.00 40.49 4.30
3410 3625 7.450323 GCTCTTCTATATCTTTACAGAGGGAGT 59.550 40.741 0.00 0.00 30.36 3.85
3412 3627 9.796180 TCTTCTATATCTTTACAGAGGGAGTAC 57.204 37.037 0.00 0.00 30.36 2.73
3413 3628 9.802039 CTTCTATATCTTTACAGAGGGAGTACT 57.198 37.037 0.00 0.00 30.36 2.73
3414 3629 9.575868 TTCTATATCTTTACAGAGGGAGTACTG 57.424 37.037 0.00 0.00 39.65 2.74
3460 3675 9.642327 TTCTTGATGGTGTTAAATGAAATCATG 57.358 29.630 0.00 0.00 36.56 3.07
3489 3704 7.252708 TGTTTCAAAGCAGCAACATATCTATG 58.747 34.615 0.00 0.00 39.55 2.23
3547 3763 5.649395 CCATTGTGCTAAAGATGGAGAGAAA 59.351 40.000 0.00 0.00 41.20 2.52
3569 3789 9.865321 AGAAAATATGGATAATATGCATGCAAC 57.135 29.630 26.68 11.45 41.64 4.17
3666 3886 9.561069 ACAAACATATAATCTAATCACAGACCC 57.439 33.333 0.00 0.00 0.00 4.46
3667 3887 8.712363 CAAACATATAATCTAATCACAGACCCG 58.288 37.037 0.00 0.00 0.00 5.28
3668 3888 6.398918 ACATATAATCTAATCACAGACCCGC 58.601 40.000 0.00 0.00 0.00 6.13
3669 3889 2.225068 AATCTAATCACAGACCCGCG 57.775 50.000 0.00 0.00 0.00 6.46
3672 3892 1.546923 TCTAATCACAGACCCGCGAAA 59.453 47.619 8.23 0.00 0.00 3.46
3674 3894 0.673644 AATCACAGACCCGCGAAAGG 60.674 55.000 8.23 2.08 0.00 3.11
3675 3895 3.423154 CACAGACCCGCGAAAGGC 61.423 66.667 8.23 0.00 38.69 4.35
3676 3896 4.699522 ACAGACCCGCGAAAGGCC 62.700 66.667 8.23 0.00 38.94 5.19
3678 3898 3.717294 AGACCCGCGAAAGGCCAT 61.717 61.111 8.23 0.00 38.94 4.40
3679 3899 2.750237 GACCCGCGAAAGGCCATT 60.750 61.111 8.23 0.00 38.94 3.16
3680 3900 2.750237 ACCCGCGAAAGGCCATTC 60.750 61.111 8.23 10.76 38.94 2.67
3756 3991 1.005394 GCCAAGCACAAGCAGCAAT 60.005 52.632 0.00 0.00 45.49 3.56
3757 3992 0.601841 GCCAAGCACAAGCAGCAATT 60.602 50.000 0.00 0.00 45.49 2.32
3758 3993 1.144969 CCAAGCACAAGCAGCAATTG 58.855 50.000 0.00 0.00 45.49 2.32
3759 3994 1.269883 CCAAGCACAAGCAGCAATTGA 60.270 47.619 10.34 0.00 45.49 2.57
3760 3995 2.058798 CAAGCACAAGCAGCAATTGAG 58.941 47.619 10.34 1.47 45.49 3.02
3761 3996 1.325355 AGCACAAGCAGCAATTGAGT 58.675 45.000 10.34 0.00 45.49 3.41
3762 3997 1.000607 AGCACAAGCAGCAATTGAGTG 60.001 47.619 10.34 6.75 45.49 3.51
3763 3998 1.269413 GCACAAGCAGCAATTGAGTGT 60.269 47.619 10.34 2.06 41.58 3.55
3764 3999 2.658285 CACAAGCAGCAATTGAGTGTC 58.342 47.619 10.34 2.66 0.00 3.67
3765 4000 1.610522 ACAAGCAGCAATTGAGTGTCC 59.389 47.619 10.34 0.00 0.00 4.02
3766 4001 1.610038 CAAGCAGCAATTGAGTGTCCA 59.390 47.619 10.34 0.00 0.00 4.02
3767 4002 2.211250 AGCAGCAATTGAGTGTCCAT 57.789 45.000 10.34 0.00 0.00 3.41
3768 4003 1.816835 AGCAGCAATTGAGTGTCCATG 59.183 47.619 10.34 0.00 0.00 3.66
3769 4004 1.814394 GCAGCAATTGAGTGTCCATGA 59.186 47.619 10.34 0.00 0.00 3.07
3770 4005 2.415090 GCAGCAATTGAGTGTCCATGAC 60.415 50.000 10.34 0.00 0.00 3.06
3771 4006 2.163010 CAGCAATTGAGTGTCCATGACC 59.837 50.000 10.34 0.00 0.00 4.02
3772 4007 2.161855 GCAATTGAGTGTCCATGACCA 58.838 47.619 10.34 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 8.308207 GGAATCCATATCTCTACTGAAACCTAC 58.692 40.741 0.00 0.00 0.00 3.18
82 88 2.827921 GGGACCGAGGAAGTAGTAACAA 59.172 50.000 0.00 0.00 0.00 2.83
93 99 2.640826 ACACTTATTTTGGGACCGAGGA 59.359 45.455 0.00 0.00 0.00 3.71
97 103 5.106436 GGTTAAGACACTTATTTTGGGACCG 60.106 44.000 0.00 0.00 0.00 4.79
98 104 6.008331 AGGTTAAGACACTTATTTTGGGACC 58.992 40.000 0.00 0.00 0.00 4.46
110 116 8.262933 ACAAAGTTGTACTAAGGTTAAGACACT 58.737 33.333 0.00 0.00 40.16 3.55
111 117 8.429493 ACAAAGTTGTACTAAGGTTAAGACAC 57.571 34.615 0.00 0.00 40.16 3.67
136 142 9.565090 TGTCTCAACTTTGTACTAACTCTAGTA 57.435 33.333 0.00 0.00 39.23 1.82
137 143 8.351461 GTGTCTCAACTTTGTACTAACTCTAGT 58.649 37.037 0.00 0.00 41.43 2.57
138 144 8.569641 AGTGTCTCAACTTTGTACTAACTCTAG 58.430 37.037 0.00 0.00 0.00 2.43
141 147 9.694137 ATAAGTGTCTCAACTTTGTACTAACTC 57.306 33.333 0.00 0.00 40.77 3.01
147 153 7.860872 CCCAAAATAAGTGTCTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
148 154 7.776030 TCCCAAAATAAGTGTCTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
149 155 6.605594 TCCCAAAATAAGTGTCTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
150 156 7.038154 TCCCAAAATAAGTGTCTCAACTTTG 57.962 36.000 0.00 0.00 40.77 2.77
154 160 5.710099 TCCATCCCAAAATAAGTGTCTCAAC 59.290 40.000 0.00 0.00 0.00 3.18
155 161 5.886609 TCCATCCCAAAATAAGTGTCTCAA 58.113 37.500 0.00 0.00 0.00 3.02
156 162 5.500234 CTCCATCCCAAAATAAGTGTCTCA 58.500 41.667 0.00 0.00 0.00 3.27
157 163 4.884164 CCTCCATCCCAAAATAAGTGTCTC 59.116 45.833 0.00 0.00 0.00 3.36
158 164 4.325344 CCCTCCATCCCAAAATAAGTGTCT 60.325 45.833 0.00 0.00 0.00 3.41
163 199 4.526438 ACTCCCTCCATCCCAAAATAAG 57.474 45.455 0.00 0.00 0.00 1.73
164 200 5.043762 AGTACTCCCTCCATCCCAAAATAA 58.956 41.667 0.00 0.00 0.00 1.40
170 206 4.295905 AAATAGTACTCCCTCCATCCCA 57.704 45.455 0.00 0.00 0.00 4.37
171 207 5.404395 ACTAAATAGTACTCCCTCCATCCC 58.596 45.833 0.00 0.00 34.13 3.85
227 263 1.282570 CAAACACGCGCAGGTTGAT 59.717 52.632 21.24 1.24 0.00 2.57
237 273 6.129035 GGTTCACCAATAATAAACAAACACGC 60.129 38.462 0.00 0.00 35.64 5.34
257 293 1.832883 ACATAGGCGCAAATGGTTCA 58.167 45.000 20.96 0.00 0.00 3.18
280 316 0.179054 GGGACGGAGGGAGTAATTGC 60.179 60.000 0.00 0.00 0.00 3.56
308 344 7.190920 ACTACAGTAGTGTCAAAAATGCTTC 57.809 36.000 12.75 0.00 37.69 3.86
326 362 4.795970 AAGAGCGTTTTTGACACTACAG 57.204 40.909 0.00 0.00 0.00 2.74
341 377 4.713824 TCCGTCCCATAATATAAGAGCG 57.286 45.455 0.00 0.00 0.00 5.03
467 503 3.379452 TCTTTTGGGGAAGAAAAAGGCA 58.621 40.909 7.75 0.00 41.58 4.75
478 514 1.075601 AGCATGGTCTCTTTTGGGGA 58.924 50.000 0.00 0.00 0.00 4.81
582 618 8.940768 AAGCTTTTAAGTTGCAACATTCTAAA 57.059 26.923 30.11 21.62 0.00 1.85
640 676 2.098614 TGCACCAACACATCACAAGTT 58.901 42.857 0.00 0.00 0.00 2.66
662 698 5.579904 CGGGCCTTTTTAGTTCTTACTAGAC 59.420 44.000 0.84 0.00 38.09 2.59
685 721 4.392921 AGATCCAATCAAGTGTAGACCG 57.607 45.455 0.00 0.00 0.00 4.79
727 763 6.408662 GGGAGTGGAGCAGAAATTATAAGAGT 60.409 42.308 0.00 0.00 0.00 3.24
763 799 5.619625 CCTAAAGGCTTTGAAAGAGACAG 57.380 43.478 22.32 8.04 0.00 3.51
1017 1055 3.384789 CCTCGGAACCAGAATCATCAGTA 59.615 47.826 0.00 0.00 0.00 2.74
1097 1135 6.700960 CACATTTGATTTTTGTGTAAGCTGGA 59.299 34.615 0.00 0.00 36.77 3.86
1098 1136 6.073657 CCACATTTGATTTTTGTGTAAGCTGG 60.074 38.462 0.00 0.00 39.23 4.85
1125 1163 1.807573 GCGAACGCTGCTAGAAGCT 60.808 57.895 20.73 2.25 42.97 3.74
1161 1199 0.109153 ACATGGCACTCAAGCAGACA 59.891 50.000 0.00 0.00 35.83 3.41
1219 1257 6.747280 ACAGAACATAAACTAAATGAATGCGC 59.253 34.615 0.00 0.00 0.00 6.09
1347 1387 2.058593 TGTGTGGGTTGCACAATGTA 57.941 45.000 0.00 0.00 42.96 2.29
1353 1393 2.888834 AAAGAATGTGTGGGTTGCAC 57.111 45.000 0.00 0.00 37.37 4.57
1456 1496 0.320421 GCCTACAAGTTGGACAGCGA 60.320 55.000 7.96 0.00 0.00 4.93
1462 1502 3.411446 CAGTTCATGCCTACAAGTTGGA 58.589 45.455 7.96 0.00 0.00 3.53
1483 1523 3.555966 AGCAAGGCATCTTATGTTACCC 58.444 45.455 0.00 0.00 0.00 3.69
1612 1652 7.417570 GCGTATGGACAACTATAAGGCCTATAT 60.418 40.741 5.16 9.12 0.00 0.86
1711 1751 1.019673 AAGTGCTTCCGCTATGCATG 58.980 50.000 10.16 0.26 40.08 4.06
1717 1757 1.202710 TGGTTGAAAGTGCTTCCGCTA 60.203 47.619 0.00 0.00 36.97 4.26
1720 1760 1.135972 CGATGGTTGAAAGTGCTTCCG 60.136 52.381 0.00 0.00 32.53 4.30
1802 1842 3.228188 AGTCCACATGTTGGTGTTGAT 57.772 42.857 0.00 0.00 46.97 2.57
1803 1843 2.727123 AGTCCACATGTTGGTGTTGA 57.273 45.000 0.00 0.00 46.97 3.18
1818 1858 6.995091 AGATGCTACATGGAAATTCTTAGTCC 59.005 38.462 0.00 0.00 0.00 3.85
1846 1886 6.166279 TCTTCACAAGATGTAAAGGCAGTAG 58.834 40.000 0.00 0.00 31.20 2.57
2154 2196 5.008980 TCCAACAAGTATGCAACATGATCA 58.991 37.500 0.00 0.00 31.22 2.92
2204 2246 9.577110 CATGTGCAGTGTCTTCATTAAATATTT 57.423 29.630 5.89 5.89 0.00 1.40
2205 2247 7.703621 GCATGTGCAGTGTCTTCATTAAATATT 59.296 33.333 0.00 0.00 41.59 1.28
2206 2248 7.198390 GCATGTGCAGTGTCTTCATTAAATAT 58.802 34.615 0.00 0.00 41.59 1.28
2207 2249 6.404623 GGCATGTGCAGTGTCTTCATTAAATA 60.405 38.462 7.36 0.00 44.36 1.40
2208 2250 5.404946 GCATGTGCAGTGTCTTCATTAAAT 58.595 37.500 0.00 0.00 41.59 1.40
2209 2251 4.321156 GGCATGTGCAGTGTCTTCATTAAA 60.321 41.667 7.36 0.00 44.36 1.52
2210 2252 3.191162 GGCATGTGCAGTGTCTTCATTAA 59.809 43.478 7.36 0.00 44.36 1.40
2211 2253 2.749076 GGCATGTGCAGTGTCTTCATTA 59.251 45.455 7.36 0.00 44.36 1.90
2212 2254 1.542915 GGCATGTGCAGTGTCTTCATT 59.457 47.619 7.36 0.00 44.36 2.57
2250 2292 3.985279 GGCAGACCGTTAAAATTGGAAAC 59.015 43.478 0.00 0.00 0.00 2.78
2400 2588 5.106515 GCTGAAAACCTACATGGAGAAACTC 60.107 44.000 6.48 0.00 39.71 3.01
2402 2590 4.762251 AGCTGAAAACCTACATGGAGAAAC 59.238 41.667 6.48 0.00 39.71 2.78
2454 2642 1.243342 TGCCCAACTGAAATGCCTCG 61.243 55.000 0.00 0.00 0.00 4.63
2757 2945 3.571401 GGCTCATTCATACCAGGGAAATG 59.429 47.826 0.00 0.00 0.00 2.32
2779 2967 1.391577 TTTCATGATGCGACCCATGG 58.608 50.000 4.14 4.14 40.26 3.66
2810 2998 0.465705 CGCTTCAGAATCAGCCCCTA 59.534 55.000 0.00 0.00 31.82 3.53
2870 3058 0.390340 TGAGCAGACACCAATCGAGC 60.390 55.000 0.00 0.00 0.00 5.03
2968 3183 7.928706 GCTACATAGAACCTTTACATCTCATGT 59.071 37.037 0.00 0.00 46.92 3.21
3027 3242 7.831193 AGCTGTTACACATCCTCTTAAATGAAT 59.169 33.333 0.00 0.00 0.00 2.57
3075 3290 9.308318 CAATGTTTCTTGCATTTCATCATGATA 57.692 29.630 8.15 0.00 34.68 2.15
3134 3349 2.066262 TCGATTCACGCTCAAAAGGAC 58.934 47.619 0.00 0.00 42.26 3.85
3137 3352 3.242220 CCATCTCGATTCACGCTCAAAAG 60.242 47.826 0.00 0.00 42.26 2.27
3141 3356 0.528466 GCCATCTCGATTCACGCTCA 60.528 55.000 0.00 0.00 42.26 4.26
3160 3375 1.236616 TGGCATGGCGTTGACAAGAG 61.237 55.000 15.27 0.00 29.64 2.85
3165 3380 1.081242 CAGTTGGCATGGCGTTGAC 60.081 57.895 15.27 10.30 0.00 3.18
3166 3381 1.106351 AACAGTTGGCATGGCGTTGA 61.106 50.000 15.27 0.00 0.00 3.18
3167 3382 0.664166 GAACAGTTGGCATGGCGTTG 60.664 55.000 15.27 14.22 0.00 4.10
3168 3383 0.823356 AGAACAGTTGGCATGGCGTT 60.823 50.000 15.27 12.05 0.00 4.84
3169 3384 1.228245 AGAACAGTTGGCATGGCGT 60.228 52.632 15.27 3.09 0.00 5.68
3170 3385 1.210931 CAGAACAGTTGGCATGGCG 59.789 57.895 15.27 2.39 0.00 5.69
3171 3386 0.242017 GTCAGAACAGTTGGCATGGC 59.758 55.000 13.29 13.29 0.00 4.40
3172 3387 0.518636 CGTCAGAACAGTTGGCATGG 59.481 55.000 0.00 0.00 0.00 3.66
3173 3388 0.110056 GCGTCAGAACAGTTGGCATG 60.110 55.000 0.00 0.00 0.00 4.06
3174 3389 0.250467 AGCGTCAGAACAGTTGGCAT 60.250 50.000 0.00 0.00 0.00 4.40
3175 3390 0.391228 TAGCGTCAGAACAGTTGGCA 59.609 50.000 0.00 0.00 0.00 4.92
3176 3391 1.508632 TTAGCGTCAGAACAGTTGGC 58.491 50.000 0.00 0.00 0.00 4.52
3177 3392 5.856126 TTTATTAGCGTCAGAACAGTTGG 57.144 39.130 0.00 0.00 0.00 3.77
3178 3393 6.742718 CCATTTTATTAGCGTCAGAACAGTTG 59.257 38.462 0.00 0.00 0.00 3.16
3179 3394 6.622896 GCCATTTTATTAGCGTCAGAACAGTT 60.623 38.462 0.00 0.00 0.00 3.16
3189 3404 2.544267 GAGCGAGCCATTTTATTAGCGT 59.456 45.455 0.00 0.00 0.00 5.07
3190 3405 2.096218 GGAGCGAGCCATTTTATTAGCG 60.096 50.000 0.00 0.00 0.00 4.26
3208 3423 3.679389 ACATTGGTTCTGTAAGCTGGAG 58.321 45.455 0.00 0.00 34.13 3.86
3209 3424 3.788227 ACATTGGTTCTGTAAGCTGGA 57.212 42.857 0.00 0.00 34.13 3.86
3246 3461 0.238289 GTTGCTGTGTGCGCTAATGT 59.762 50.000 9.73 0.00 46.63 2.71
3254 3469 2.026014 CCCAACGTTGCTGTGTGC 59.974 61.111 22.93 0.00 43.25 4.57
3255 3470 2.721231 CCCCAACGTTGCTGTGTG 59.279 61.111 22.93 7.83 0.00 3.82
3265 3480 7.428282 AAAATAAAAATAAACAGCCCCAACG 57.572 32.000 0.00 0.00 0.00 4.10
3307 3522 8.235230 TGGATCACTAGAGGGAGTATTATCTTT 58.765 37.037 0.00 0.00 0.00 2.52
3308 3523 7.770662 TGGATCACTAGAGGGAGTATTATCTT 58.229 38.462 0.00 0.00 0.00 2.40
3325 3540 4.744795 ATAGAAGAGCGTTTGGATCACT 57.255 40.909 0.00 0.00 32.03 3.41
3326 3541 5.582665 AGAAATAGAAGAGCGTTTGGATCAC 59.417 40.000 0.00 0.00 32.03 3.06
3327 3542 5.734720 AGAAATAGAAGAGCGTTTGGATCA 58.265 37.500 0.00 0.00 32.03 2.92
3328 3543 6.670077 AAGAAATAGAAGAGCGTTTGGATC 57.330 37.500 0.00 0.00 0.00 3.36
3330 3545 6.932400 TGTAAAGAAATAGAAGAGCGTTTGGA 59.068 34.615 0.00 0.00 0.00 3.53
3331 3546 7.117812 TCTGTAAAGAAATAGAAGAGCGTTTGG 59.882 37.037 0.00 0.00 0.00 3.28
3332 3547 8.018677 TCTGTAAAGAAATAGAAGAGCGTTTG 57.981 34.615 0.00 0.00 0.00 2.93
3334 3549 6.814146 CCTCTGTAAAGAAATAGAAGAGCGTT 59.186 38.462 0.00 0.00 0.00 4.84
3337 3552 6.879400 TCCCTCTGTAAAGAAATAGAAGAGC 58.121 40.000 0.00 0.00 0.00 4.09
3338 3553 8.073467 ACTCCCTCTGTAAAGAAATAGAAGAG 57.927 38.462 0.00 0.00 0.00 2.85
3339 3554 8.968969 GTACTCCCTCTGTAAAGAAATAGAAGA 58.031 37.037 0.00 0.00 0.00 2.87
3340 3555 8.973182 AGTACTCCCTCTGTAAAGAAATAGAAG 58.027 37.037 0.00 0.00 0.00 2.85
3341 3556 8.750298 CAGTACTCCCTCTGTAAAGAAATAGAA 58.250 37.037 0.00 0.00 0.00 2.10
3342 3557 8.114102 TCAGTACTCCCTCTGTAAAGAAATAGA 58.886 37.037 0.00 0.00 33.89 1.98
3343 3558 8.294954 TCAGTACTCCCTCTGTAAAGAAATAG 57.705 38.462 0.00 0.00 33.89 1.73
3345 3560 6.954684 TCTCAGTACTCCCTCTGTAAAGAAAT 59.045 38.462 0.00 0.00 33.89 2.17
3347 3562 5.888901 TCTCAGTACTCCCTCTGTAAAGAA 58.111 41.667 0.00 0.00 33.89 2.52
3349 3564 5.888724 TCATCTCAGTACTCCCTCTGTAAAG 59.111 44.000 0.00 0.00 33.89 1.85
3350 3565 5.827756 TCATCTCAGTACTCCCTCTGTAAA 58.172 41.667 0.00 0.00 33.89 2.01
3351 3566 5.441500 CTCATCTCAGTACTCCCTCTGTAA 58.558 45.833 0.00 0.00 33.89 2.41
3353 3568 3.372566 CCTCATCTCAGTACTCCCTCTGT 60.373 52.174 0.00 0.00 33.89 3.41
3354 3569 3.117701 TCCTCATCTCAGTACTCCCTCTG 60.118 52.174 0.00 0.00 0.00 3.35
3355 3570 3.127250 TCCTCATCTCAGTACTCCCTCT 58.873 50.000 0.00 0.00 0.00 3.69
3356 3571 3.586470 TCCTCATCTCAGTACTCCCTC 57.414 52.381 0.00 0.00 0.00 4.30
3358 3573 4.112634 AGATCCTCATCTCAGTACTCCC 57.887 50.000 0.00 0.00 33.71 4.30
3359 3574 6.293735 CGTTTAGATCCTCATCTCAGTACTCC 60.294 46.154 0.00 0.00 40.18 3.85
3360 3575 6.664515 CGTTTAGATCCTCATCTCAGTACTC 58.335 44.000 0.00 0.00 40.18 2.59
3361 3576 5.009210 GCGTTTAGATCCTCATCTCAGTACT 59.991 44.000 0.00 0.00 40.18 2.73
3362 3577 5.009210 AGCGTTTAGATCCTCATCTCAGTAC 59.991 44.000 0.00 0.00 40.18 2.73
3363 3578 5.133941 AGCGTTTAGATCCTCATCTCAGTA 58.866 41.667 0.00 0.00 40.18 2.74
3364 3579 3.957497 AGCGTTTAGATCCTCATCTCAGT 59.043 43.478 0.00 0.00 40.18 3.41
3365 3580 4.278170 AGAGCGTTTAGATCCTCATCTCAG 59.722 45.833 0.00 0.00 40.18 3.35
3366 3581 4.211125 AGAGCGTTTAGATCCTCATCTCA 58.789 43.478 0.00 0.00 40.18 3.27
3367 3582 4.846779 AGAGCGTTTAGATCCTCATCTC 57.153 45.455 0.00 0.00 40.18 2.75
3368 3583 4.892934 AGAAGAGCGTTTAGATCCTCATCT 59.107 41.667 0.00 0.00 42.48 2.90
3369 3584 5.195001 AGAAGAGCGTTTAGATCCTCATC 57.805 43.478 0.00 0.00 35.47 2.92
3370 3585 6.909550 ATAGAAGAGCGTTTAGATCCTCAT 57.090 37.500 0.00 0.00 35.47 2.90
3371 3586 7.885922 AGATATAGAAGAGCGTTTAGATCCTCA 59.114 37.037 0.00 0.00 35.47 3.86
3372 3587 8.276252 AGATATAGAAGAGCGTTTAGATCCTC 57.724 38.462 0.00 0.00 35.47 3.71
3373 3588 8.644374 AAGATATAGAAGAGCGTTTAGATCCT 57.356 34.615 0.00 0.00 35.47 3.24
3380 3595 8.138712 CCTCTGTAAAGATATAGAAGAGCGTTT 58.861 37.037 0.00 0.00 30.03 3.60
3381 3596 7.255660 CCCTCTGTAAAGATATAGAAGAGCGTT 60.256 40.741 0.00 0.00 30.03 4.84
3382 3597 6.207810 CCCTCTGTAAAGATATAGAAGAGCGT 59.792 42.308 0.00 0.00 30.03 5.07
3383 3598 6.431543 TCCCTCTGTAAAGATATAGAAGAGCG 59.568 42.308 0.00 0.00 30.03 5.03
3384 3599 7.450323 ACTCCCTCTGTAAAGATATAGAAGAGC 59.550 40.741 0.00 0.00 35.42 4.09
3385 3600 8.934023 ACTCCCTCTGTAAAGATATAGAAGAG 57.066 38.462 0.00 0.00 36.64 2.85
3386 3601 9.796180 GTACTCCCTCTGTAAAGATATAGAAGA 57.204 37.037 0.00 0.00 30.03 2.87
3387 3602 9.802039 AGTACTCCCTCTGTAAAGATATAGAAG 57.198 37.037 0.00 0.00 30.03 2.85
3388 3603 9.575868 CAGTACTCCCTCTGTAAAGATATAGAA 57.424 37.037 0.00 0.00 30.03 2.10
3389 3604 8.946248 TCAGTACTCCCTCTGTAAAGATATAGA 58.054 37.037 0.00 0.00 33.89 1.98
3390 3605 9.226606 CTCAGTACTCCCTCTGTAAAGATATAG 57.773 40.741 0.00 0.00 33.89 1.31
3391 3606 8.946248 TCTCAGTACTCCCTCTGTAAAGATATA 58.054 37.037 0.00 0.00 33.89 0.86
3392 3607 7.817440 TCTCAGTACTCCCTCTGTAAAGATAT 58.183 38.462 0.00 0.00 33.89 1.63
3393 3608 7.209340 TCTCAGTACTCCCTCTGTAAAGATA 57.791 40.000 0.00 0.00 33.89 1.98
3394 3609 6.080969 TCTCAGTACTCCCTCTGTAAAGAT 57.919 41.667 0.00 0.00 33.89 2.40
3395 3610 5.516059 TCTCAGTACTCCCTCTGTAAAGA 57.484 43.478 0.00 0.00 33.89 2.52
3396 3611 5.888724 TCATCTCAGTACTCCCTCTGTAAAG 59.111 44.000 0.00 0.00 33.89 1.85
3397 3612 5.827756 TCATCTCAGTACTCCCTCTGTAAA 58.172 41.667 0.00 0.00 33.89 2.01
3398 3613 5.441500 CTCATCTCAGTACTCCCTCTGTAA 58.558 45.833 0.00 0.00 33.89 2.41
3399 3614 4.141367 CCTCATCTCAGTACTCCCTCTGTA 60.141 50.000 0.00 0.00 33.89 2.74
3400 3615 3.372566 CCTCATCTCAGTACTCCCTCTGT 60.373 52.174 0.00 0.00 33.89 3.41
3401 3616 3.221771 CCTCATCTCAGTACTCCCTCTG 58.778 54.545 0.00 0.00 0.00 3.35
3402 3617 2.176798 CCCTCATCTCAGTACTCCCTCT 59.823 54.545 0.00 0.00 0.00 3.69
3403 3618 2.175931 TCCCTCATCTCAGTACTCCCTC 59.824 54.545 0.00 0.00 0.00 4.30
3404 3619 2.091555 GTCCCTCATCTCAGTACTCCCT 60.092 54.545 0.00 0.00 0.00 4.20
3405 3620 2.312390 GTCCCTCATCTCAGTACTCCC 58.688 57.143 0.00 0.00 0.00 4.30
3406 3621 1.950909 CGTCCCTCATCTCAGTACTCC 59.049 57.143 0.00 0.00 0.00 3.85
3407 3622 2.356382 CACGTCCCTCATCTCAGTACTC 59.644 54.545 0.00 0.00 0.00 2.59
3408 3623 2.291024 ACACGTCCCTCATCTCAGTACT 60.291 50.000 0.00 0.00 0.00 2.73
3409 3624 2.093106 ACACGTCCCTCATCTCAGTAC 58.907 52.381 0.00 0.00 0.00 2.73
3410 3625 2.509166 ACACGTCCCTCATCTCAGTA 57.491 50.000 0.00 0.00 0.00 2.74
3411 3626 2.370349 CTACACGTCCCTCATCTCAGT 58.630 52.381 0.00 0.00 0.00 3.41
3412 3627 1.678627 CCTACACGTCCCTCATCTCAG 59.321 57.143 0.00 0.00 0.00 3.35
3413 3628 1.283905 TCCTACACGTCCCTCATCTCA 59.716 52.381 0.00 0.00 0.00 3.27
3414 3629 2.054232 TCCTACACGTCCCTCATCTC 57.946 55.000 0.00 0.00 0.00 2.75
3460 3675 7.756722 AGATATGTTGCTGCTTTGAAACATTAC 59.243 33.333 16.95 12.40 41.93 1.89
3466 3681 7.395190 ACATAGATATGTTGCTGCTTTGAAA 57.605 32.000 0.00 0.00 43.99 2.69
3547 3763 7.628769 TCGTTGCATGCATATTATCCATATT 57.371 32.000 23.37 0.00 0.00 1.28
3569 3789 3.001330 GGGTTTCTGCTAATCATCGTTCG 59.999 47.826 0.00 0.00 0.00 3.95
3654 3874 1.404986 CCTTTCGCGGGTCTGTGATTA 60.405 52.381 6.13 0.00 0.00 1.75
3664 3884 1.595093 AAAGAATGGCCTTTCGCGGG 61.595 55.000 21.91 0.00 38.94 6.13
3666 3886 1.339711 CAAAAGAATGGCCTTTCGCG 58.660 50.000 21.91 0.00 38.94 5.87
3667 3887 1.713597 CCAAAAGAATGGCCTTTCGC 58.286 50.000 21.91 4.14 35.50 4.70
3675 3895 4.326504 AGTTGTGAAGCCAAAAGAATGG 57.673 40.909 0.00 0.00 43.70 3.16
3676 3896 4.911610 CGTAGTTGTGAAGCCAAAAGAATG 59.088 41.667 0.00 0.00 0.00 2.67
3678 3898 3.942748 ACGTAGTTGTGAAGCCAAAAGAA 59.057 39.130 0.00 0.00 37.78 2.52
3679 3899 3.537580 ACGTAGTTGTGAAGCCAAAAGA 58.462 40.909 0.00 0.00 37.78 2.52
3680 3900 3.963383 ACGTAGTTGTGAAGCCAAAAG 57.037 42.857 0.00 0.00 37.78 2.27
3729 3960 4.043200 GTGCTTGGCTTGGCGGAC 62.043 66.667 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.