Multiple sequence alignment - TraesCS3B01G149200

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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 TraesCS3B01G149200 chr3B 100.000 3865 0 0 964 4828 140686218 140690082 0.000000e+00 7138.0
1 TraesCS3B01G149200 chr3B 100.000 569 0 0 1 569 140685255 140685823 0.000000e+00 1051.0
2 TraesCS3B01G149200 chr3A 92.792 2955 142 37 964 3891 107316693 107319603 0.000000e+00 4211.0
3 TraesCS3B01G149200 chr3A 94.248 226 11 1 344 569 107316410 107316633 1.290000e-90 344.0
4 TraesCS3B01G149200 chr3A 81.678 453 34 20 3880 4301 107319679 107320113 1.000000e-86 331.0
5 TraesCS3B01G149200 chr3A 81.845 336 37 16 6 339 107315699 107316012 1.330000e-65 261.0
6 TraesCS3B01G149200 chr3D 91.979 3017 147 44 964 3947 91030225 91033179 0.000000e+00 4143.0
7 TraesCS3B01G149200 chr3D 89.531 640 37 13 4191 4828 91038332 91038943 0.000000e+00 784.0
8 TraesCS3B01G149200 chr3D 87.762 572 46 15 1 569 91029605 91030155 0.000000e+00 647.0
9 TraesCS3B01G149200 chr7B 80.597 134 20 5 4590 4718 56479063 56479195 1.110000e-16 99.0
10 TraesCS3B01G149200 chr4A 81.416 113 15 5 4355 4464 137521965 137522074 2.390000e-13 87.9
11 TraesCS3B01G149200 chr7D 76.596 141 23 8 4584 4721 503749193 503749060 8.670000e-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 TraesCS3B01G149200 chr3B 140685255 140690082 4827 False 4094.50 7138 100.00000 1 4828 2 chr3B.!!$F1 4827
1 TraesCS3B01G149200 chr3A 107315699 107320113 4414 False 1286.75 4211 87.64075 6 4301 4 chr3A.!!$F1 4295
2 TraesCS3B01G149200 chr3D 91029605 91033179 3574 False 2395.00 4143 89.87050 1 3947 2 chr3D.!!$F2 3946
3 TraesCS3B01G149200 chr3D 91038332 91038943 611 False 784.00 784 89.53100 4191 4828 1 chr3D.!!$F1 637

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
333 336 1.004745 GAGTCTGGATGGCAAAAGGGA 59.995 52.381 0.0 0.0 0.00 4.20 F
550 948 1.428448 TCCGTGCAATCTTCGTCAAG 58.572 50.000 0.0 0.0 0.00 3.02 F
1289 1694 1.891919 GCGTCAACTTGCTGTCCCA 60.892 57.895 0.0 0.0 0.00 4.37 F
2326 2745 0.313672 GAATTCGTGCTGGCAAACCA 59.686 50.000 0.0 0.0 46.51 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1412 1817 0.538584 CAGGCAGACACATGAGGCTA 59.461 55.000 0.00 0.00 34.91 3.93 R
1787 2193 0.663153 AAAACACTCCTGTTGAGCGC 59.337 50.000 0.00 0.00 45.61 5.92 R
3118 3549 1.336125 GCAAGAGCAAGCATCCCATAC 59.664 52.381 0.00 0.00 41.58 2.39 R
4246 4797 0.106708 TTGCACACAGAGGTCCTCAC 59.893 55.000 21.26 3.76 32.06 3.51 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
37 38 4.705110 TGGAAACATCTTCTTCCACTGA 57.295 40.909 0.00 0.00 44.87 3.41
68 69 8.519526 TCATCGTTGGAAGTGCTAAAATAAATT 58.480 29.630 0.00 0.00 0.00 1.82
97 99 1.202758 TGAGACGACCAATGCCAAGTT 60.203 47.619 0.00 0.00 0.00 2.66
101 103 2.159382 ACGACCAATGCCAAGTTTAGG 58.841 47.619 0.00 0.00 0.00 2.69
141 143 3.181484 CCACCAATGCGATCACAATGAAT 60.181 43.478 0.22 0.00 0.00 2.57
150 152 5.007921 TGCGATCACAATGAATCTAACCATG 59.992 40.000 0.00 0.00 0.00 3.66
158 160 8.393366 CACAATGAATCTAACCATGTGAGTTAG 58.607 37.037 11.88 11.88 45.28 2.34
159 161 8.103305 ACAATGAATCTAACCATGTGAGTTAGT 58.897 33.333 15.60 3.13 44.57 2.24
160 162 9.599866 CAATGAATCTAACCATGTGAGTTAGTA 57.400 33.333 15.60 7.24 44.57 1.82
161 163 9.601217 AATGAATCTAACCATGTGAGTTAGTAC 57.399 33.333 15.60 10.76 44.57 2.73
163 165 8.758829 TGAATCTAACCATGTGAGTTAGTACAT 58.241 33.333 15.60 4.68 44.57 2.29
164 166 9.601217 GAATCTAACCATGTGAGTTAGTACATT 57.399 33.333 15.60 10.53 44.57 2.71
165 167 9.601217 AATCTAACCATGTGAGTTAGTACATTC 57.399 33.333 15.60 0.00 44.57 2.67
166 168 8.129496 TCTAACCATGTGAGTTAGTACATTCA 57.871 34.615 15.60 0.00 44.57 2.57
167 169 8.590204 TCTAACCATGTGAGTTAGTACATTCAA 58.410 33.333 15.60 0.00 44.57 2.69
168 170 9.383519 CTAACCATGTGAGTTAGTACATTCAAT 57.616 33.333 10.53 0.00 41.08 2.57
169 171 8.635765 AACCATGTGAGTTAGTACATTCAATT 57.364 30.769 0.00 0.00 35.46 2.32
170 172 8.268850 ACCATGTGAGTTAGTACATTCAATTC 57.731 34.615 0.00 0.00 35.46 2.17
171 173 7.064609 ACCATGTGAGTTAGTACATTCAATTCG 59.935 37.037 0.00 0.00 35.46 3.34
172 174 7.064609 CCATGTGAGTTAGTACATTCAATTCGT 59.935 37.037 0.00 0.00 35.46 3.85
173 175 7.576750 TGTGAGTTAGTACATTCAATTCGTC 57.423 36.000 0.00 0.00 0.00 4.20
193 196 9.774742 ATTCGTCTTTGTAAAGCAGATTTATTC 57.225 29.630 0.00 0.00 35.83 1.75
227 230 9.745323 GCTTTGCATCACTTTTTATAAAATCAC 57.255 29.630 11.33 0.00 0.00 3.06
321 324 3.956744 TCTCTTGAATCTCGAGTCTGGA 58.043 45.455 13.13 5.56 0.00 3.86
330 333 2.005451 CTCGAGTCTGGATGGCAAAAG 58.995 52.381 3.62 0.00 0.00 2.27
333 336 1.004745 GAGTCTGGATGGCAAAAGGGA 59.995 52.381 0.00 0.00 0.00 4.20
336 339 3.269381 AGTCTGGATGGCAAAAGGGATTA 59.731 43.478 0.00 0.00 0.00 1.75
337 340 4.078980 AGTCTGGATGGCAAAAGGGATTAT 60.079 41.667 0.00 0.00 0.00 1.28
338 341 4.279420 GTCTGGATGGCAAAAGGGATTATC 59.721 45.833 0.00 0.00 0.00 1.75
339 342 3.221771 TGGATGGCAAAAGGGATTATCG 58.778 45.455 0.00 0.00 0.00 2.92
340 343 2.029918 GGATGGCAAAAGGGATTATCGC 60.030 50.000 0.68 0.68 0.00 4.58
341 344 2.435372 TGGCAAAAGGGATTATCGCT 57.565 45.000 5.94 5.94 41.77 4.93
342 345 2.023673 TGGCAAAAGGGATTATCGCTG 58.976 47.619 12.50 2.94 39.75 5.18
495 893 2.605580 GCGAAGAGGCAAAACTCCAAAG 60.606 50.000 0.00 0.00 38.26 2.77
550 948 1.428448 TCCGTGCAATCTTCGTCAAG 58.572 50.000 0.00 0.00 0.00 3.02
1263 1664 2.472695 TTCTTGCCTGCTGATACGTT 57.527 45.000 0.00 0.00 0.00 3.99
1277 1678 2.712539 CGTTGTTGCCAGCGTCAA 59.287 55.556 0.00 0.00 40.01 3.18
1289 1694 1.891919 GCGTCAACTTGCTGTCCCA 60.892 57.895 0.00 0.00 0.00 4.37
1295 1700 3.568007 GTCAACTTGCTGTCCCAATTACA 59.432 43.478 0.00 0.00 0.00 2.41
1298 1703 3.832527 ACTTGCTGTCCCAATTACACTT 58.167 40.909 0.00 0.00 0.00 3.16
1424 1829 7.394359 ACTTGTCAAAATTATAGCCTCATGTGT 59.606 33.333 0.00 0.00 0.00 3.72
1466 1871 2.167487 TCTTGCTGTGTGTCAGTGTGTA 59.833 45.455 0.00 0.00 45.23 2.90
1799 2206 1.655484 CATATGTGCGCTCAACAGGA 58.345 50.000 16.95 1.39 0.00 3.86
1832 2239 4.260907 CCACATCTACGCATTTTCCAGATG 60.261 45.833 8.03 8.03 45.21 2.90
1855 2262 4.260334 GCCTTTGCAAACATCAAACTTGAC 60.260 41.667 8.05 0.00 37.46 3.18
1878 2285 2.184533 TGGCCGAATCTCCTGTCTTTA 58.815 47.619 0.00 0.00 0.00 1.85
1879 2286 2.168521 TGGCCGAATCTCCTGTCTTTAG 59.831 50.000 0.00 0.00 0.00 1.85
1943 2352 7.811713 ACCTACGTTTTGTTCAGTCTATCTTAC 59.188 37.037 0.00 0.00 0.00 2.34
1946 2355 8.018677 ACGTTTTGTTCAGTCTATCTTACATG 57.981 34.615 0.00 0.00 0.00 3.21
1953 2362 9.367160 TGTTCAGTCTATCTTACATGATCCATA 57.633 33.333 0.00 0.00 0.00 2.74
1964 2373 9.764363 TCTTACATGATCCATAATGTTGAGTAC 57.236 33.333 0.00 0.00 38.05 2.73
1965 2374 9.546428 CTTACATGATCCATAATGTTGAGTACA 57.454 33.333 0.00 0.00 41.97 2.90
1995 2404 4.446051 GCTTGATAGCACGGTAGAAAGATC 59.554 45.833 0.00 0.00 46.95 2.75
1998 2407 2.969628 AGCACGGTAGAAAGATCCAG 57.030 50.000 0.00 0.00 0.00 3.86
1999 2408 2.180276 AGCACGGTAGAAAGATCCAGT 58.820 47.619 0.00 0.00 0.00 4.00
2000 2409 3.362706 AGCACGGTAGAAAGATCCAGTA 58.637 45.455 0.00 0.00 0.00 2.74
2001 2410 3.130693 AGCACGGTAGAAAGATCCAGTAC 59.869 47.826 0.00 0.00 0.00 2.73
2078 2489 6.990341 AGTCGGTTACCAATGGTATTTTAC 57.010 37.500 13.55 8.13 38.05 2.01
2092 2503 5.897377 GTATTTTACCAAGACCAGTGCAT 57.103 39.130 0.00 0.00 0.00 3.96
2108 2519 5.239087 CCAGTGCATTTGCTTTACCATTTTT 59.761 36.000 3.94 0.00 42.66 1.94
2228 2640 2.163412 CGAGCTAGAGTTTCAGCAGAGT 59.837 50.000 0.00 0.00 40.36 3.24
2237 2649 9.424319 CTAGAGTTTCAGCAGAGTATTTGTTTA 57.576 33.333 0.00 0.00 0.00 2.01
2268 2687 9.559958 CTTCGAGTTCATACTTTATTTTGCATT 57.440 29.630 0.00 0.00 33.84 3.56
2270 2689 9.982291 TCGAGTTCATACTTTATTTTGCATTAC 57.018 29.630 0.00 0.00 33.84 1.89
2288 2707 6.601613 TGCATTACGTCTTCCATATTTTCCTT 59.398 34.615 0.00 0.00 0.00 3.36
2310 2729 9.238368 TCCTTCTAAATTTGGATTGTAACGAAT 57.762 29.630 4.96 0.00 0.00 3.34
2326 2745 0.313672 GAATTCGTGCTGGCAAACCA 59.686 50.000 0.00 0.00 46.51 3.67
2357 2778 2.623418 TTCCTGAGCAGTAAGGGAGA 57.377 50.000 0.00 0.00 34.08 3.71
2392 2813 3.627395 TGCCATTCTTGTCTAACGGAT 57.373 42.857 0.00 0.00 0.00 4.18
2430 2851 4.067896 CACATGTCTGCCTGTTAAGAGTT 58.932 43.478 0.00 0.00 0.00 3.01
2533 2954 5.705905 ACTGAGAATACAAGGTTAAGGCAAC 59.294 40.000 0.00 0.00 36.32 4.17
2583 3004 4.158394 CCAGTGTTGAGGTATGAAAATGGG 59.842 45.833 0.00 0.00 0.00 4.00
2594 3015 2.930950 TGAAAATGGGATGTCCGATCC 58.069 47.619 0.00 0.00 38.76 3.36
2696 3117 5.518848 TGATCAACAGTTTGTTTGCATCT 57.481 34.783 0.00 0.00 38.77 2.90
2703 3124 7.434897 TCAACAGTTTGTTTGCATCTTTCATAC 59.565 33.333 0.00 0.00 38.77 2.39
2710 3131 5.695816 TGTTTGCATCTTTCATACTTTTGCC 59.304 36.000 0.00 0.00 0.00 4.52
2718 3139 8.956426 CATCTTTCATACTTTTGCCCTTAGTTA 58.044 33.333 0.00 0.00 0.00 2.24
2744 3165 3.771577 ATTCACACCCTTTCTTCGACT 57.228 42.857 0.00 0.00 0.00 4.18
2847 3268 3.348647 TTGCTCTTAATGGTGCTAGCA 57.651 42.857 14.93 14.93 38.14 3.49
2952 3381 6.866480 TGTTGATCTCTGAATTTAATTGGCC 58.134 36.000 0.00 0.00 0.00 5.36
2961 3390 8.827177 TCTGAATTTAATTGGCCGTATAGTAG 57.173 34.615 0.00 0.00 0.00 2.57
2962 3391 8.426489 TCTGAATTTAATTGGCCGTATAGTAGT 58.574 33.333 0.00 0.00 0.00 2.73
2963 3392 9.701098 CTGAATTTAATTGGCCGTATAGTAGTA 57.299 33.333 0.00 0.00 0.00 1.82
2964 3393 9.701098 TGAATTTAATTGGCCGTATAGTAGTAG 57.299 33.333 0.00 0.00 0.00 2.57
3001 3430 6.706270 TGGTAGAGAAGCTTAGTTTTTCTGTG 59.294 38.462 11.08 0.00 31.67 3.66
3053 3484 6.862209 ACAAGCAACAAACAAAGTATCTTGA 58.138 32.000 0.00 0.00 34.92 3.02
3095 3526 7.630924 AGAGACGTTTGAAAACAAGTTAGATG 58.369 34.615 6.72 0.00 38.81 2.90
3099 3530 6.691388 ACGTTTGAAAACAAGTTAGATGCTTC 59.309 34.615 6.72 0.00 38.81 3.86
3101 3532 6.371809 TTGAAAACAAGTTAGATGCTTCGT 57.628 33.333 0.00 0.00 0.00 3.85
3111 3542 3.559238 AGATGCTTCGTCGCAAAAATT 57.441 38.095 5.57 0.00 44.06 1.82
3112 3543 3.236816 AGATGCTTCGTCGCAAAAATTG 58.763 40.909 5.57 0.00 44.06 2.32
3113 3544 2.483583 TGCTTCGTCGCAAAAATTGT 57.516 40.000 0.00 0.00 36.89 2.71
3118 3549 5.052040 TGCTTCGTCGCAAAAATTGTAAAAG 60.052 36.000 0.00 0.00 36.89 2.27
3168 3599 6.573664 TTTTCTTGATCAAATCGACACCAT 57.426 33.333 9.88 0.00 0.00 3.55
3364 3795 6.602410 TGCTTGGATCAAATAAACCATTCA 57.398 33.333 0.00 0.00 32.31 2.57
3365 3796 7.185318 TGCTTGGATCAAATAAACCATTCAT 57.815 32.000 0.00 0.00 32.31 2.57
3366 3797 7.042950 TGCTTGGATCAAATAAACCATTCATG 58.957 34.615 0.00 0.00 32.31 3.07
3429 3860 9.985318 CAGTTGATCTGAAAAAGATGATCTAAC 57.015 33.333 0.00 0.00 46.12 2.34
3434 3865 7.840342 TCTGAAAAAGATGATCTAACTCAGC 57.160 36.000 16.62 0.00 31.12 4.26
3449 3880 7.380536 TCTAACTCAGCTTATTTTACCGTTCA 58.619 34.615 0.00 0.00 0.00 3.18
3450 3881 6.870971 AACTCAGCTTATTTTACCGTTCAA 57.129 33.333 0.00 0.00 0.00 2.69
3451 3882 6.870971 ACTCAGCTTATTTTACCGTTCAAA 57.129 33.333 0.00 0.00 0.00 2.69
3475 3906 5.822204 TGTAAGGCATGTGGTTAAACCTAT 58.178 37.500 0.00 0.00 39.58 2.57
3477 3908 7.051623 TGTAAGGCATGTGGTTAAACCTATAG 58.948 38.462 0.00 0.00 39.58 1.31
3478 3909 5.968676 AGGCATGTGGTTAAACCTATAGA 57.031 39.130 0.00 0.00 39.58 1.98
3479 3910 5.681639 AGGCATGTGGTTAAACCTATAGAC 58.318 41.667 0.00 0.00 39.58 2.59
3480 3911 4.510340 GGCATGTGGTTAAACCTATAGACG 59.490 45.833 0.00 0.00 39.58 4.18
3481 3912 5.353938 GCATGTGGTTAAACCTATAGACGA 58.646 41.667 0.00 0.00 39.58 4.20
3482 3913 5.989777 GCATGTGGTTAAACCTATAGACGAT 59.010 40.000 0.00 0.00 39.58 3.73
3483 3914 6.073765 GCATGTGGTTAAACCTATAGACGATG 60.074 42.308 0.00 0.00 39.58 3.84
3484 3915 5.909477 TGTGGTTAAACCTATAGACGATGG 58.091 41.667 0.00 0.00 39.58 3.51
3485 3916 5.422970 TGTGGTTAAACCTATAGACGATGGT 59.577 40.000 0.00 0.00 39.58 3.55
3486 3917 6.070653 TGTGGTTAAACCTATAGACGATGGTT 60.071 38.462 0.00 0.00 43.73 3.67
3487 3918 6.257193 GTGGTTAAACCTATAGACGATGGTTG 59.743 42.308 0.00 0.00 41.36 3.77
3585 4016 4.320275 CCGCGAGAATAACATAGCTGTAGA 60.320 45.833 8.23 0.00 33.36 2.59
3599 4030 5.528043 AGCTGTAGATCTGATGTGGTAAG 57.472 43.478 5.18 0.00 0.00 2.34
3607 4038 2.187958 CTGATGTGGTAAGGAGGGTGA 58.812 52.381 0.00 0.00 0.00 4.02
3645 4077 0.895100 TTTGTGCATGGAGGCCTGTC 60.895 55.000 12.00 2.06 0.00 3.51
3653 4085 3.426568 GAGGCCTGTCGTGCTTGC 61.427 66.667 12.00 0.00 0.00 4.01
3747 4179 2.057137 TGTCAAAGAAAGCAGCTGGT 57.943 45.000 13.85 13.85 0.00 4.00
3883 4316 2.497138 TGAACCATGCTGTGAGTCTTG 58.503 47.619 0.00 0.00 0.00 3.02
3942 4462 5.538433 TGGCTTCTACAAGGTTTTTATGCTT 59.462 36.000 0.00 0.00 0.00 3.91
3943 4463 5.863935 GGCTTCTACAAGGTTTTTATGCTTG 59.136 40.000 0.00 0.00 0.00 4.01
3944 4464 5.346011 GCTTCTACAAGGTTTTTATGCTTGC 59.654 40.000 0.00 0.00 0.00 4.01
3945 4465 6.398234 TTCTACAAGGTTTTTATGCTTGCA 57.602 33.333 0.00 0.00 0.00 4.08
3946 4466 5.768317 TCTACAAGGTTTTTATGCTTGCAC 58.232 37.500 0.00 0.00 0.00 4.57
3947 4467 4.399004 ACAAGGTTTTTATGCTTGCACA 57.601 36.364 0.00 0.00 0.00 4.57
3948 4468 4.370917 ACAAGGTTTTTATGCTTGCACAG 58.629 39.130 0.00 0.00 0.00 3.66
3949 4469 4.141959 ACAAGGTTTTTATGCTTGCACAGT 60.142 37.500 0.00 0.00 0.00 3.55
3995 4517 6.500910 TGATATTGCAAATCATCAGTGCTTC 58.499 36.000 1.71 0.00 39.09 3.86
4006 4528 2.220953 AGTGCTTCACCACTGTGGA 58.779 52.632 32.30 9.09 44.00 4.02
4007 4529 0.767375 AGTGCTTCACCACTGTGGAT 59.233 50.000 32.30 14.25 44.00 3.41
4015 4537 2.028476 TCACCACTGTGGATAAACTCGG 60.028 50.000 32.30 9.99 40.96 4.63
4026 4548 4.454161 TGGATAAACTCGGTCACACAAATG 59.546 41.667 0.00 0.00 0.00 2.32
4028 4550 1.604604 AACTCGGTCACACAAATGGG 58.395 50.000 0.00 0.00 0.00 4.00
4035 4557 4.457603 TCGGTCACACAAATGGGAAAATAG 59.542 41.667 0.00 0.00 40.97 1.73
4046 4568 7.290714 ACAAATGGGAAAATAGGATATGCATGT 59.709 33.333 10.16 1.23 0.00 3.21
4047 4569 7.860649 AATGGGAAAATAGGATATGCATGTT 57.139 32.000 10.16 0.00 0.00 2.71
4051 4573 6.660949 GGGAAAATAGGATATGCATGTTAGCT 59.339 38.462 10.16 0.00 34.99 3.32
4062 4584 5.011090 TGCATGTTAGCTAGAGACGAAAT 57.989 39.130 0.00 0.00 34.99 2.17
4071 4593 3.666334 GCTAGAGACGAAATAGATGTGCG 59.334 47.826 0.00 0.00 0.00 5.34
4074 4596 3.128764 AGAGACGAAATAGATGTGCGACA 59.871 43.478 0.00 0.00 0.00 4.35
4081 4603 3.680642 ATAGATGTGCGACATGTTTGC 57.319 42.857 14.98 14.98 39.27 3.68
4101 4623 7.651304 TGTTTGCAACGAATTAAATCATGAAGT 59.349 29.630 0.00 0.00 0.00 3.01
4102 4624 7.565450 TTGCAACGAATTAAATCATGAAGTG 57.435 32.000 0.00 0.00 0.00 3.16
4103 4625 6.676950 TGCAACGAATTAAATCATGAAGTGT 58.323 32.000 0.00 0.00 0.00 3.55
4104 4626 7.811653 TGCAACGAATTAAATCATGAAGTGTA 58.188 30.769 0.00 0.00 0.00 2.90
4105 4627 8.293157 TGCAACGAATTAAATCATGAAGTGTAA 58.707 29.630 0.00 0.00 0.00 2.41
4106 4628 9.289303 GCAACGAATTAAATCATGAAGTGTAAT 57.711 29.630 0.00 0.00 0.00 1.89
4113 4635 6.446781 AAATCATGAAGTGTAATCAGCTGG 57.553 37.500 15.13 0.00 0.00 4.85
4116 4638 3.334583 TGAAGTGTAATCAGCTGGTCC 57.665 47.619 15.13 1.37 0.00 4.46
4133 4655 2.549349 GGTCCGGTGCTTTTCTACAAGA 60.549 50.000 0.00 0.00 0.00 3.02
4147 4669 9.467258 CTTTTCTACAAGAAATTCATTCAGCAA 57.533 29.630 3.12 0.00 43.06 3.91
4148 4670 8.801715 TTTCTACAAGAAATTCATTCAGCAAC 57.198 30.769 0.00 0.00 39.13 4.17
4185 4707 6.590068 CCAGAAGGTGATGATTTAGTCTGAT 58.410 40.000 0.00 0.00 34.50 2.90
4246 4797 3.207669 GGCAGCGGCTCCAATCTG 61.208 66.667 9.17 0.00 40.87 2.90
4254 4805 0.107459 GGCTCCAATCTGTGAGGACC 60.107 60.000 0.00 0.00 0.00 4.46
4309 4860 5.682659 TGTCTACTCTCACTGTCCTATACC 58.317 45.833 0.00 0.00 0.00 2.73
4355 4906 6.317789 ACACTGGTGAATGATTGTAAGTTG 57.682 37.500 7.78 0.00 0.00 3.16
4373 4924 5.319043 AGTTGAAGAGTTCCATTTGGGTA 57.681 39.130 0.00 0.00 38.11 3.69
4458 5009 1.911357 AGGAGCCATGATGACAGTTCA 59.089 47.619 0.00 0.00 35.73 3.18
4529 5080 7.610305 AGTTTGTCCTTTCTAGTTTCAAAGACA 59.390 33.333 3.78 0.00 32.20 3.41
4569 5120 0.538057 TGGCTTGAAGGAACCTGCAG 60.538 55.000 6.78 6.78 32.39 4.41
4581 5132 3.595691 CCTGCAGGGTTCTATAGCG 57.404 57.895 26.14 0.00 0.00 4.26
4582 5133 0.034059 CCTGCAGGGTTCTATAGCGG 59.966 60.000 26.14 0.00 0.00 5.52
4583 5134 1.040646 CTGCAGGGTTCTATAGCGGA 58.959 55.000 5.57 0.00 33.54 5.54
4584 5135 1.412710 CTGCAGGGTTCTATAGCGGAA 59.587 52.381 5.57 0.00 33.54 4.30
4585 5136 1.834896 TGCAGGGTTCTATAGCGGAAA 59.165 47.619 0.00 0.00 0.00 3.13
4586 5137 2.438021 TGCAGGGTTCTATAGCGGAAAT 59.562 45.455 0.00 0.00 0.00 2.17
4587 5138 2.808543 GCAGGGTTCTATAGCGGAAATG 59.191 50.000 0.00 0.00 0.00 2.32
4588 5139 2.808543 CAGGGTTCTATAGCGGAAATGC 59.191 50.000 0.00 0.00 0.00 3.56
4610 5161 3.650942 CCCCTTGGCTCTTGGTGTATATA 59.349 47.826 0.00 0.00 0.00 0.86
4686 5237 3.287222 TGGAAACCAACTTGACCTTCTG 58.713 45.455 0.00 0.00 0.00 3.02
4692 5243 4.196971 ACCAACTTGACCTTCTGTTGTAC 58.803 43.478 0.00 0.00 38.35 2.90
4710 5261 9.577003 CTGTTGTACTTGTATAAAAAGTTCGAC 57.423 33.333 13.98 13.98 38.67 4.20
4721 5272 9.099820 GTATAAAAAGTTCGACGAAGGAAAAAG 57.900 33.333 11.25 0.00 0.00 2.27
4756 5307 9.773328 TCTTCAGTGCAAAGAAAATAAATATCG 57.227 29.630 0.00 0.00 30.00 2.92
4771 5322 9.840427 AAATAAATATCGAGGACAAAAAGTGTG 57.160 29.630 0.00 0.00 41.96 3.82
4772 5323 8.786826 ATAAATATCGAGGACAAAAAGTGTGA 57.213 30.769 0.00 0.00 41.96 3.58
4781 5332 7.148787 CGAGGACAAAAAGTGTGAGTAGTAATC 60.149 40.741 0.00 0.00 41.96 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 3.251004 GCGTTCAGTGGAAGAAGATGTTT 59.749 43.478 0.00 0.00 32.62 2.83
23 24 2.300152 TGAGCGTTCAGTGGAAGAAGAT 59.700 45.455 0.00 0.00 32.62 2.40
27 28 1.402852 CGATGAGCGTTCAGTGGAAGA 60.403 52.381 8.26 0.00 36.61 2.87
68 69 4.083324 GCATTGGTCGTCTCATTTTTCTGA 60.083 41.667 0.00 0.00 0.00 3.27
79 80 1.981256 AAACTTGGCATTGGTCGTCT 58.019 45.000 0.00 0.00 0.00 4.18
83 84 3.421844 AGTCCTAAACTTGGCATTGGTC 58.578 45.455 0.00 0.00 33.03 4.02
97 99 3.042682 TCCACCAGTGTTCAAGTCCTAA 58.957 45.455 0.00 0.00 0.00 2.69
101 103 1.134220 TGGTCCACCAGTGTTCAAGTC 60.134 52.381 0.00 0.00 42.01 3.01
114 116 0.676466 TGATCGCATTGGTGGTCCAC 60.676 55.000 14.13 14.13 44.22 4.02
131 133 6.475504 ACTCACATGGTTAGATTCATTGTGA 58.524 36.000 0.00 0.00 34.12 3.58
141 143 8.129496 TGAATGTACTAACTCACATGGTTAGA 57.871 34.615 20.52 5.50 45.06 2.10
150 152 7.813852 AGACGAATTGAATGTACTAACTCAC 57.186 36.000 0.00 0.00 0.00 3.51
158 160 7.801315 TGCTTTACAAAGACGAATTGAATGTAC 59.199 33.333 5.89 0.00 38.28 2.90
159 161 7.866729 TGCTTTACAAAGACGAATTGAATGTA 58.133 30.769 5.89 0.00 38.28 2.29
160 162 6.734137 TGCTTTACAAAGACGAATTGAATGT 58.266 32.000 5.89 0.00 38.28 2.71
161 163 7.077605 TCTGCTTTACAAAGACGAATTGAATG 58.922 34.615 5.89 0.00 38.28 2.67
163 165 6.612247 TCTGCTTTACAAAGACGAATTGAA 57.388 33.333 5.89 0.00 38.28 2.69
164 166 6.801539 ATCTGCTTTACAAAGACGAATTGA 57.198 33.333 5.89 0.00 38.28 2.57
165 167 7.858052 AAATCTGCTTTACAAAGACGAATTG 57.142 32.000 5.89 0.00 38.28 2.32
167 169 9.774742 GAATAAATCTGCTTTACAAAGACGAAT 57.225 29.630 5.89 0.00 38.28 3.34
168 170 7.955324 CGAATAAATCTGCTTTACAAAGACGAA 59.045 33.333 5.89 0.00 38.28 3.85
169 171 7.412563 CCGAATAAATCTGCTTTACAAAGACGA 60.413 37.037 5.89 1.70 38.28 4.20
170 172 6.682863 CCGAATAAATCTGCTTTACAAAGACG 59.317 38.462 5.89 0.00 38.28 4.18
171 173 7.527457 ACCGAATAAATCTGCTTTACAAAGAC 58.473 34.615 5.89 0.00 38.28 3.01
172 174 7.681939 ACCGAATAAATCTGCTTTACAAAGA 57.318 32.000 5.89 0.00 38.28 2.52
173 175 8.020819 TGAACCGAATAAATCTGCTTTACAAAG 58.979 33.333 0.00 0.00 39.03 2.77
211 214 9.349145 GCACATAACCGTGATTTTATAAAAAGT 57.651 29.630 14.35 0.00 39.34 2.66
222 225 4.142403 CCTCAAATGCACATAACCGTGATT 60.142 41.667 0.00 0.00 39.34 2.57
227 230 3.190327 TGAACCTCAAATGCACATAACCG 59.810 43.478 0.00 0.00 0.00 4.44
321 324 2.624838 CAGCGATAATCCCTTTTGCCAT 59.375 45.455 0.00 0.00 0.00 4.40
330 333 2.249139 AGAGGGTACAGCGATAATCCC 58.751 52.381 0.00 0.00 35.56 3.85
333 336 5.099042 ACAAAAGAGGGTACAGCGATAAT 57.901 39.130 0.00 0.00 0.00 1.28
336 339 3.008049 AGAACAAAAGAGGGTACAGCGAT 59.992 43.478 0.00 0.00 0.00 4.58
337 340 2.367567 AGAACAAAAGAGGGTACAGCGA 59.632 45.455 0.00 0.00 0.00 4.93
338 341 2.737252 GAGAACAAAAGAGGGTACAGCG 59.263 50.000 0.00 0.00 0.00 5.18
339 342 3.748568 CAGAGAACAAAAGAGGGTACAGC 59.251 47.826 0.00 0.00 0.00 4.40
340 343 3.748568 GCAGAGAACAAAAGAGGGTACAG 59.251 47.826 0.00 0.00 0.00 2.74
341 344 3.496160 GGCAGAGAACAAAAGAGGGTACA 60.496 47.826 0.00 0.00 0.00 2.90
342 345 3.075148 GGCAGAGAACAAAAGAGGGTAC 58.925 50.000 0.00 0.00 0.00 3.34
375 772 3.004839 ACCCTCGTCGTCATTATCATCAG 59.995 47.826 0.00 0.00 0.00 2.90
376 773 2.956333 ACCCTCGTCGTCATTATCATCA 59.044 45.455 0.00 0.00 0.00 3.07
377 774 3.644884 ACCCTCGTCGTCATTATCATC 57.355 47.619 0.00 0.00 0.00 2.92
383 780 0.731417 CGACTACCCTCGTCGTCATT 59.269 55.000 4.57 0.00 46.56 2.57
391 788 0.822164 AATTGGACCGACTACCCTCG 59.178 55.000 0.00 0.00 0.00 4.63
513 911 0.317854 GATGGATGACGATGACGCGA 60.318 55.000 15.93 0.00 43.96 5.87
1152 1553 4.087892 GCAGGCGGAGGAGAGCAA 62.088 66.667 0.00 0.00 34.54 3.91
1232 1633 3.734293 GCAGGCAAGAATCTGAATGAAGC 60.734 47.826 0.00 0.00 33.11 3.86
1248 1649 1.155889 CAACAACGTATCAGCAGGCA 58.844 50.000 0.00 0.00 0.00 4.75
1263 1664 1.726865 CAAGTTGACGCTGGCAACA 59.273 52.632 23.02 0.00 46.05 3.33
1277 1678 3.508845 AGTGTAATTGGGACAGCAAGT 57.491 42.857 0.00 0.00 42.39 3.16
1404 1809 6.204359 GCAGACACATGAGGCTATAATTTTG 58.796 40.000 0.00 0.00 0.00 2.44
1412 1817 0.538584 CAGGCAGACACATGAGGCTA 59.461 55.000 0.00 0.00 34.91 3.93
1419 1824 1.362224 AGTAACCCAGGCAGACACAT 58.638 50.000 0.00 0.00 0.00 3.21
1424 1829 2.979678 AGAAAGAAGTAACCCAGGCAGA 59.020 45.455 0.00 0.00 0.00 4.26
1466 1871 2.559668 CACTCACCAAATCAACAGGCAT 59.440 45.455 0.00 0.00 0.00 4.40
1665 2071 0.972983 ATGGTGCTCGTAGGTCTGCT 60.973 55.000 0.00 0.00 0.00 4.24
1787 2193 0.663153 AAAACACTCCTGTTGAGCGC 59.337 50.000 0.00 0.00 45.61 5.92
1788 2194 1.939934 TGAAAACACTCCTGTTGAGCG 59.060 47.619 0.00 0.00 45.61 5.03
1799 2206 2.806244 GCGTAGATGTGGTGAAAACACT 59.194 45.455 0.00 0.00 39.52 3.55
1832 2239 3.870419 TCAAGTTTGATGTTTGCAAAGGC 59.130 39.130 13.26 2.12 36.06 4.35
1855 2262 1.065854 AGACAGGAGATTCGGCCAAAG 60.066 52.381 2.24 0.00 0.00 2.77
1878 2285 4.226427 TGACTAAAGATGCTGAATGCCT 57.774 40.909 0.00 0.00 42.00 4.75
1879 2286 4.337555 ACATGACTAAAGATGCTGAATGCC 59.662 41.667 0.00 0.00 42.00 4.40
1892 2299 9.522804 GTGTTTTCCACAATTAACATGACTAAA 57.477 29.630 0.00 0.00 43.92 1.85
1893 2300 8.138712 GGTGTTTTCCACAATTAACATGACTAA 58.861 33.333 0.00 0.00 46.44 2.24
1955 2364 9.261180 GCTATCAAGCTAATATTGTACTCAACA 57.739 33.333 0.00 0.00 45.85 3.33
1995 2404 9.084164 GTGAACAGTGTTATTATGTAGTACTGG 57.916 37.037 8.88 0.00 38.60 4.00
1998 2407 8.679288 ACGTGAACAGTGTTATTATGTAGTAC 57.321 34.615 8.88 0.00 0.00 2.73
1999 2408 7.693536 CGACGTGAACAGTGTTATTATGTAGTA 59.306 37.037 8.88 0.00 0.00 1.82
2000 2409 6.525628 CGACGTGAACAGTGTTATTATGTAGT 59.474 38.462 8.88 1.25 0.00 2.73
2001 2410 6.744082 TCGACGTGAACAGTGTTATTATGTAG 59.256 38.462 8.88 10.13 0.00 2.74
2078 2489 0.963962 AGCAAATGCACTGGTCTTGG 59.036 50.000 8.28 0.00 45.16 3.61
2108 2519 5.502079 TCTTGGAACCACAACAACTAAGAA 58.498 37.500 0.00 0.00 0.00 2.52
2127 2538 7.568199 TTCCTAGAACAAACTTTCCTTCTTG 57.432 36.000 0.00 0.00 0.00 3.02
2138 2549 8.188139 TGTGAACTCAAATTTCCTAGAACAAAC 58.812 33.333 0.00 0.00 0.00 2.93
2355 2776 6.894103 AGAATGGCAATTGGACTTCTATTTCT 59.106 34.615 7.72 0.00 0.00 2.52
2357 2778 7.038799 ACAAGAATGGCAATTGGACTTCTATTT 60.039 33.333 7.72 0.00 0.00 1.40
2392 2813 6.313658 CAGACATGTGACGATTCCTTTAATCA 59.686 38.462 1.15 0.00 43.68 2.57
2430 2851 5.249622 TGGTCAGATTACCATGTCCACTAAA 59.750 40.000 0.00 0.00 44.68 1.85
2505 2926 6.653989 CCTTAACCTTGTATTCTCAGTCCAT 58.346 40.000 0.00 0.00 0.00 3.41
2533 2954 2.554032 GGATCTGTTTCACCACAGGTTG 59.446 50.000 1.14 0.00 43.92 3.77
2547 2968 1.734655 ACACTGGTTCCTGGATCTGT 58.265 50.000 0.00 0.92 0.00 3.41
2594 3015 4.080356 TGTCTTCCCCTTCTTCCACATATG 60.080 45.833 0.00 0.00 0.00 1.78
2696 3117 7.396055 AGCATAACTAAGGGCAAAAGTATGAAA 59.604 33.333 0.00 0.00 0.00 2.69
2703 3124 7.702348 GTGAATAAGCATAACTAAGGGCAAAAG 59.298 37.037 0.00 0.00 0.00 2.27
2710 3131 6.357367 AGGGTGTGAATAAGCATAACTAAGG 58.643 40.000 0.00 0.00 0.00 2.69
2718 3139 4.396166 CGAAGAAAGGGTGTGAATAAGCAT 59.604 41.667 0.00 0.00 0.00 3.79
2744 3165 8.349245 CACAATAACTCACATTTACCAACTTCA 58.651 33.333 0.00 0.00 0.00 3.02
2790 3211 2.230660 GGCAGTACTATCCAAATGGCC 58.769 52.381 0.00 0.00 34.44 5.36
2847 3268 6.069963 AGGGAAGTGACAAGCTTTATGATAGT 60.070 38.462 0.00 0.00 0.00 2.12
2946 3375 5.828871 AGATCCTACTACTATACGGCCAAT 58.171 41.667 2.24 0.00 0.00 3.16
2961 3390 8.463607 GCTTCTCTACCACATTATAGATCCTAC 58.536 40.741 0.00 0.00 0.00 3.18
2962 3391 8.394822 AGCTTCTCTACCACATTATAGATCCTA 58.605 37.037 0.00 0.00 0.00 2.94
2963 3392 7.245292 AGCTTCTCTACCACATTATAGATCCT 58.755 38.462 0.00 0.00 0.00 3.24
2964 3393 7.475137 AGCTTCTCTACCACATTATAGATCC 57.525 40.000 0.00 0.00 0.00 3.36
3001 3430 8.789762 GGACTCCAGAATTATAGAACTCTAGAC 58.210 40.741 0.00 0.00 0.00 2.59
3053 3484 7.118496 ACGTCTCTTCTGGAAGATATGATTT 57.882 36.000 18.38 1.61 46.36 2.17
3095 3526 4.939948 TTTACAATTTTTGCGACGAAGC 57.060 36.364 0.00 0.00 37.71 3.86
3099 3530 6.183359 CCCATACTTTTACAATTTTTGCGACG 60.183 38.462 0.00 0.00 0.00 5.12
3101 3532 6.982852 TCCCATACTTTTACAATTTTTGCGA 58.017 32.000 0.00 0.00 0.00 5.10
3111 3542 4.599041 AGCAAGCATCCCATACTTTTACA 58.401 39.130 0.00 0.00 0.00 2.41
3112 3543 4.884164 AGAGCAAGCATCCCATACTTTTAC 59.116 41.667 0.00 0.00 0.00 2.01
3113 3544 5.116084 AGAGCAAGCATCCCATACTTTTA 57.884 39.130 0.00 0.00 0.00 1.52
3118 3549 1.336125 GCAAGAGCAAGCATCCCATAC 59.664 52.381 0.00 0.00 41.58 2.39
3153 3584 5.703978 TTCAAACATGGTGTCGATTTGAT 57.296 34.783 8.46 0.00 38.64 2.57
3168 3599 9.248291 GAATGTTCTTCAGCTAAAATTCAAACA 57.752 29.630 5.36 0.00 0.00 2.83
3238 3669 2.293399 GTCTCGAAACAAAAGGGCACAT 59.707 45.455 0.00 0.00 0.00 3.21
3364 3795 0.695462 TGTAGAGGGATGGGCTGCAT 60.695 55.000 0.50 0.00 0.00 3.96
3365 3796 0.695462 ATGTAGAGGGATGGGCTGCA 60.695 55.000 0.50 0.00 0.00 4.41
3366 3797 0.250640 CATGTAGAGGGATGGGCTGC 60.251 60.000 0.00 0.00 0.00 5.25
3429 3860 7.305474 ACATTTGAACGGTAAAATAAGCTGAG 58.695 34.615 0.00 0.00 0.00 3.35
3434 3865 8.024285 TGCCTTACATTTGAACGGTAAAATAAG 58.976 33.333 0.00 0.00 0.00 1.73
3443 3874 3.500982 CACATGCCTTACATTTGAACGG 58.499 45.455 0.00 0.00 38.50 4.44
3449 3880 5.542251 AGGTTTAACCACATGCCTTACATTT 59.458 36.000 17.10 0.00 41.95 2.32
3450 3881 5.083821 AGGTTTAACCACATGCCTTACATT 58.916 37.500 17.10 0.00 41.95 2.71
3451 3882 4.672899 AGGTTTAACCACATGCCTTACAT 58.327 39.130 17.10 0.00 41.95 2.29
3475 3906 3.055458 TCCTGCAAATCAACCATCGTCTA 60.055 43.478 0.00 0.00 0.00 2.59
3477 3908 2.083774 TCCTGCAAATCAACCATCGTC 58.916 47.619 0.00 0.00 0.00 4.20
3478 3909 2.086869 CTCCTGCAAATCAACCATCGT 58.913 47.619 0.00 0.00 0.00 3.73
3479 3910 2.358957 TCTCCTGCAAATCAACCATCG 58.641 47.619 0.00 0.00 0.00 3.84
3480 3911 3.067742 CCATCTCCTGCAAATCAACCATC 59.932 47.826 0.00 0.00 0.00 3.51
3481 3912 3.028850 CCATCTCCTGCAAATCAACCAT 58.971 45.455 0.00 0.00 0.00 3.55
3482 3913 2.225091 ACCATCTCCTGCAAATCAACCA 60.225 45.455 0.00 0.00 0.00 3.67
3483 3914 2.450476 ACCATCTCCTGCAAATCAACC 58.550 47.619 0.00 0.00 0.00 3.77
3484 3915 3.507233 TCAACCATCTCCTGCAAATCAAC 59.493 43.478 0.00 0.00 0.00 3.18
3485 3916 3.765381 TCAACCATCTCCTGCAAATCAA 58.235 40.909 0.00 0.00 0.00 2.57
3486 3917 3.438216 TCAACCATCTCCTGCAAATCA 57.562 42.857 0.00 0.00 0.00 2.57
3487 3918 4.996788 AATCAACCATCTCCTGCAAATC 57.003 40.909 0.00 0.00 0.00 2.17
3585 4016 2.774234 CACCCTCCTTACCACATCAGAT 59.226 50.000 0.00 0.00 0.00 2.90
3599 4030 0.691078 TATGACAGGCCTCACCCTCC 60.691 60.000 0.00 0.00 40.58 4.30
3645 4077 2.679837 AGGATTGTATTCAGCAAGCACG 59.320 45.455 0.00 0.00 34.33 5.34
3653 4085 2.947652 CAGCCCACAGGATTGTATTCAG 59.052 50.000 0.00 0.00 35.25 3.02
3747 4179 1.432514 GCTGTCACGCATCTTTCTCA 58.567 50.000 0.00 0.00 0.00 3.27
3827 4260 1.920574 CGTCATCAGACATCGGTGTTC 59.079 52.381 1.13 0.00 45.23 3.18
3876 4309 1.736681 GTCAGCAAGGCATCAAGACTC 59.263 52.381 0.00 0.00 30.53 3.36
3883 4316 4.274459 CAGGTTATAAGTCAGCAAGGCATC 59.726 45.833 0.00 0.00 0.00 3.91
3948 4468 6.072508 TCAGAAAGATATTTGTCCAGTGCAAC 60.073 38.462 0.00 0.00 0.00 4.17
3949 4469 6.003326 TCAGAAAGATATTTGTCCAGTGCAA 58.997 36.000 0.00 0.00 0.00 4.08
3979 4499 3.504906 AGTGGTGAAGCACTGATGATTTG 59.495 43.478 14.01 0.00 33.63 2.32
3981 4501 3.430042 AGTGGTGAAGCACTGATGATT 57.570 42.857 14.01 0.00 37.08 2.57
3995 4517 2.289444 ACCGAGTTTATCCACAGTGGTG 60.289 50.000 19.65 0.63 44.85 4.17
4003 4525 3.755112 TTGTGTGACCGAGTTTATCCA 57.245 42.857 0.00 0.00 0.00 3.41
4004 4526 4.142687 CCATTTGTGTGACCGAGTTTATCC 60.143 45.833 0.00 0.00 0.00 2.59
4006 4528 3.756434 CCCATTTGTGTGACCGAGTTTAT 59.244 43.478 0.00 0.00 0.00 1.40
4007 4529 3.142951 CCCATTTGTGTGACCGAGTTTA 58.857 45.455 0.00 0.00 0.00 2.01
4015 4537 5.975693 TCCTATTTTCCCATTTGTGTGAC 57.024 39.130 0.00 0.00 0.00 3.67
4026 4548 6.660949 AGCTAACATGCATATCCTATTTTCCC 59.339 38.462 0.00 0.00 34.99 3.97
4028 4550 9.658799 TCTAGCTAACATGCATATCCTATTTTC 57.341 33.333 0.00 0.00 34.99 2.29
4035 4557 5.098893 CGTCTCTAGCTAACATGCATATCC 58.901 45.833 0.00 0.00 34.99 2.59
4046 4568 6.439599 GCACATCTATTTCGTCTCTAGCTAA 58.560 40.000 0.00 0.00 0.00 3.09
4047 4569 5.334182 CGCACATCTATTTCGTCTCTAGCTA 60.334 44.000 0.00 0.00 0.00 3.32
4051 4573 4.334481 TGTCGCACATCTATTTCGTCTCTA 59.666 41.667 0.00 0.00 0.00 2.43
4062 4584 2.421619 TGCAAACATGTCGCACATCTA 58.578 42.857 16.59 0.00 36.53 1.98
4101 4623 0.249120 CACCGGACCAGCTGATTACA 59.751 55.000 17.39 0.00 0.00 2.41
4102 4624 1.090052 GCACCGGACCAGCTGATTAC 61.090 60.000 17.39 0.71 0.00 1.89
4103 4625 1.220749 GCACCGGACCAGCTGATTA 59.779 57.895 17.39 0.00 0.00 1.75
4104 4626 2.045926 GCACCGGACCAGCTGATT 60.046 61.111 17.39 0.32 0.00 2.57
4105 4627 2.129555 AAAGCACCGGACCAGCTGAT 62.130 55.000 17.39 0.00 38.86 2.90
4106 4628 2.337879 AAAAGCACCGGACCAGCTGA 62.338 55.000 17.39 0.00 38.86 4.26
4107 4629 1.856265 GAAAAGCACCGGACCAGCTG 61.856 60.000 9.46 6.78 38.86 4.24
4113 4635 2.762745 TCTTGTAGAAAAGCACCGGAC 58.237 47.619 9.46 0.00 0.00 4.79
4116 4638 5.757886 TGAATTTCTTGTAGAAAAGCACCG 58.242 37.500 6.01 0.00 46.08 4.94
4154 4676 0.256752 CATCACCTTCTGGCATCCCA 59.743 55.000 0.00 0.00 39.32 4.37
4246 4797 0.106708 TTGCACACAGAGGTCCTCAC 59.893 55.000 21.26 3.76 32.06 3.51
4254 4805 1.575576 GAGCTGGCTTGCACACAGAG 61.576 60.000 13.86 0.00 34.21 3.35
4309 4860 2.034939 TGAGCCACACAATTTGCTTCTG 59.965 45.455 0.00 0.00 33.41 3.02
4355 4906 5.745227 TCATCTACCCAAATGGAACTCTTC 58.255 41.667 0.00 0.00 37.39 2.87
4373 4924 8.117870 AGATTATAGAGCTAGGAGGATCATCT 57.882 38.462 7.39 0.00 36.25 2.90
4463 5014 4.615912 GCTTCGCACCAGAACAACATTTAT 60.616 41.667 0.00 0.00 0.00 1.40
4464 5015 3.304391 GCTTCGCACCAGAACAACATTTA 60.304 43.478 0.00 0.00 0.00 1.40
4536 5087 2.917227 GCCAGTTTGGGGTGGGTG 60.917 66.667 0.00 0.00 38.19 4.61
4537 5088 2.710826 AAGCCAGTTTGGGGTGGGT 61.711 57.895 0.00 0.00 46.62 4.51
4538 5089 2.201210 AAGCCAGTTTGGGGTGGG 59.799 61.111 0.00 0.00 38.98 4.61
4539 5090 0.758685 TTCAAGCCAGTTTGGGGTGG 60.759 55.000 0.00 0.00 38.98 4.61
4540 5091 0.675633 CTTCAAGCCAGTTTGGGGTG 59.324 55.000 0.00 0.00 38.98 4.61
4541 5092 0.469892 CCTTCAAGCCAGTTTGGGGT 60.470 55.000 0.00 0.00 38.19 4.95
4542 5093 0.178964 TCCTTCAAGCCAGTTTGGGG 60.179 55.000 0.00 0.00 38.19 4.96
4543 5094 1.341209 GTTCCTTCAAGCCAGTTTGGG 59.659 52.381 0.00 0.00 38.19 4.12
4544 5095 1.341209 GGTTCCTTCAAGCCAGTTTGG 59.659 52.381 0.00 0.00 41.55 3.28
4545 5096 2.035066 CAGGTTCCTTCAAGCCAGTTTG 59.965 50.000 0.00 0.00 32.37 2.93
4546 5097 2.310538 CAGGTTCCTTCAAGCCAGTTT 58.689 47.619 0.00 0.00 32.37 2.66
4547 5098 1.986882 CAGGTTCCTTCAAGCCAGTT 58.013 50.000 0.00 0.00 32.37 3.16
4569 5120 2.152016 GGCATTTCCGCTATAGAACCC 58.848 52.381 3.21 0.00 0.00 4.11
4588 5139 0.625849 ATACACCAAGAGCCAAGGGG 59.374 55.000 0.00 0.00 37.18 4.79
4667 5218 4.157840 ACAACAGAAGGTCAAGTTGGTTTC 59.842 41.667 2.34 5.14 44.10 2.78
4672 5223 5.354234 ACAAGTACAACAGAAGGTCAAGTTG 59.646 40.000 0.00 0.00 45.02 3.16
4686 5237 8.479280 TCGTCGAACTTTTTATACAAGTACAAC 58.521 33.333 0.00 0.00 33.12 3.32
4692 5243 7.342318 TCCTTCGTCGAACTTTTTATACAAG 57.658 36.000 2.90 0.00 0.00 3.16
4708 5259 3.626217 ACAACTGGACTTTTTCCTTCGTC 59.374 43.478 0.00 0.00 46.10 4.20
4710 5261 3.877508 AGACAACTGGACTTTTTCCTTCG 59.122 43.478 0.00 0.00 46.10 3.79
4721 5272 1.953559 TGCACTGAAGACAACTGGAC 58.046 50.000 0.00 0.00 0.00 4.02
4726 5277 7.985634 TTATTTTCTTTGCACTGAAGACAAC 57.014 32.000 0.00 0.00 33.15 3.32
4756 5307 7.873505 AGATTACTACTCACACTTTTTGTCCTC 59.126 37.037 0.00 0.00 35.67 3.71


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

AutoCloner maintained by Alex Coulton.