Multiple sequence alignment - TraesCS2A01G421100

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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 TraesCS2A01G421100 chr2A 100.000 9175 0 0 1 9175 676723501 676714327 0.000000e+00 16944.0
1 TraesCS2A01G421100 chr2A 80.870 115 18 3 8939 9052 699167880 699167991 4.560000e-13 87.9
2 TraesCS2A01G421100 chr2A 80.172 116 22 1 8938 9052 640703541 640703656 1.640000e-12 86.1
3 TraesCS2A01G421100 chr2B 94.736 8359 344 48 568 8872 632173276 632164960 0.000000e+00 12911.0
4 TraesCS2A01G421100 chr2B 91.859 2039 125 22 6653 8668 632012099 632010079 0.000000e+00 2808.0
5 TraesCS2A01G421100 chr2B 90.227 573 33 14 4 571 632173871 632173317 0.000000e+00 726.0
6 TraesCS2A01G421100 chr2B 89.714 175 16 2 8952 9126 632159681 632159509 1.200000e-53 222.0
7 TraesCS2A01G421100 chr2B 94.690 113 6 0 6536 6648 632018584 632018472 9.470000e-40 176.0
8 TraesCS2A01G421100 chr2B 90.217 92 2 4 8869 8960 632164922 632164838 7.530000e-21 113.0
9 TraesCS2A01G421100 chr2B 83.621 116 18 1 8938 9052 667092673 667092788 3.500000e-19 108.0
10 TraesCS2A01G421100 chr2B 81.982 111 19 1 8943 9052 579694323 579694213 9.810000e-15 93.5
11 TraesCS2A01G421100 chr2B 100.000 32 0 0 8869 8900 632021538 632021507 9.950000e-05 60.2
12 TraesCS2A01G421100 chr2D 94.126 8239 375 49 568 8759 532184889 532176713 0.000000e+00 12432.0
13 TraesCS2A01G421100 chr2D 88.947 570 34 14 4 571 532185472 532184930 0.000000e+00 676.0
14 TraesCS2A01G421100 chr2D 92.664 259 12 3 8869 9127 532176418 532176167 5.230000e-97 366.0
15 TraesCS2A01G421100 chr2D 92.784 97 2 1 8781 8872 532176550 532176454 1.610000e-27 135.0
16 TraesCS2A01G421100 chr5B 89.646 792 57 10 5367 6147 530694598 530693821 0.000000e+00 985.0
17 TraesCS2A01G421100 chr5B 90.476 189 15 2 6255 6441 530693825 530693638 7.120000e-61 246.0
18 TraesCS2A01G421100 chr5B 79.851 134 23 4 8938 9068 527947794 527947662 2.730000e-15 95.3
19 TraesCS2A01G421100 chr3B 84.685 111 16 1 8943 9052 13497384 13497274 9.740000e-20 110.0


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 TraesCS2A01G421100 chr2A 676714327 676723501 9174 True 16944.000000 16944 100.000000 1 9175 1 chr2A.!!$R1 9174
1 TraesCS2A01G421100 chr2B 632164838 632173871 9033 True 4583.333333 12911 91.726667 4 8960 3 chr2B.!!$R5 8956
2 TraesCS2A01G421100 chr2B 632010079 632012099 2020 True 2808.000000 2808 91.859000 6653 8668 1 chr2B.!!$R2 2015
3 TraesCS2A01G421100 chr2D 532176167 532185472 9305 True 3402.250000 12432 92.130250 4 9127 4 chr2D.!!$R1 9123
4 TraesCS2A01G421100 chr5B 530693638 530694598 960 True 615.500000 985 90.061000 5367 6441 2 chr5B.!!$R2 1074

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
588 639 0.172578 TCGGATCCTTGTGCGTGTAG 59.827 55.000 10.75 0.0 34.37 2.74 F
847 909 0.467290 TTTGGGAGACTGTTGCACCC 60.467 55.000 0.00 0.0 40.79 4.61 F
852 914 2.031870 GGAGACTGTTGCACCCTTTTT 58.968 47.619 0.00 0.0 0.00 1.94 F
2088 2168 1.902508 TCCCTACAAGAAGCACAGAGG 59.097 52.381 0.00 0.0 0.00 3.69 F
2725 2805 3.077359 GCTACATTGGAGAAGCAACAGT 58.923 45.455 0.00 0.0 35.05 3.55 F
3483 3563 0.381801 AACTTGAAGCCACACAAGCG 59.618 50.000 0.00 0.0 44.75 4.68 F
4869 4949 1.676635 GGCATTGGCTGAGAGCACA 60.677 57.895 2.42 0.0 44.75 4.57 F
6071 6162 0.038310 GTAGCAGAAAAGCAGGGGGT 59.962 55.000 0.00 0.0 36.85 4.95 F
6927 7036 0.035056 AGTTGCCTCTGTGTATGGCC 60.035 55.000 0.00 0.0 45.56 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1982 2062 1.237533 TTCAAGCTCTTCAATGCGCA 58.762 45.000 14.96 14.96 0.00 6.09 R
2070 2150 2.564947 AGACCTCTGTGCTTCTTGTAGG 59.435 50.000 0.00 0.00 0.00 3.18 R
2664 2744 3.571401 CCTTCACATGCTCTTCCAGTTTT 59.429 43.478 0.00 0.00 0.00 2.43 R
2991 3071 2.157738 GCCTGAATCTGTGCTTCAAGT 58.842 47.619 0.00 0.00 32.53 3.16 R
4637 4717 2.231478 TGACAATCCGTCTCCTTCTGAC 59.769 50.000 0.00 0.00 45.60 3.51 R
5151 5231 1.348696 TGAACTGCAATCAGCCTCTCA 59.651 47.619 0.00 0.00 44.10 3.27 R
6181 6272 0.037326 TGAAGACGGGTAAGCAGCAG 60.037 55.000 0.00 0.00 0.00 4.24 R
7253 7363 0.676782 ACCCTTCGCATGTAACAGGC 60.677 55.000 0.00 0.00 37.83 4.85 R
8342 8459 0.179070 GAAGCTTCCGGATCCCTGAC 60.179 60.000 15.97 0.00 0.00 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
58 60 3.589654 TTCCGGCGCCTGAACTGAG 62.590 63.158 27.02 7.95 0.00 3.35
183 186 2.746277 GGCTCCCGCACACGATTT 60.746 61.111 0.00 0.00 43.93 2.17
185 188 3.081133 CTCCCGCACACGATTTCG 58.919 61.111 0.00 0.00 43.93 3.46
186 189 3.083600 CTCCCGCACACGATTTCGC 62.084 63.158 0.00 0.00 43.93 4.70
187 190 3.118454 CCCGCACACGATTTCGCT 61.118 61.111 0.00 0.00 43.93 4.93
188 191 2.395690 CCGCACACGATTTCGCTC 59.604 61.111 0.00 0.00 43.93 5.03
189 192 2.018670 CGCACACGATTTCGCTCG 59.981 61.111 0.00 1.18 43.93 5.03
190 193 2.395690 GCACACGATTTCGCTCGG 59.604 61.111 0.00 0.00 42.88 4.63
191 194 2.092291 GCACACGATTTCGCTCGGA 61.092 57.895 0.00 0.00 42.88 4.55
192 195 1.991430 CACACGATTTCGCTCGGAG 59.009 57.895 0.00 0.00 42.88 4.63
193 196 1.805945 ACACGATTTCGCTCGGAGC 60.806 57.895 19.92 19.92 42.88 4.70
194 197 2.202756 ACGATTTCGCTCGGAGCC 60.203 61.111 23.36 8.61 42.88 4.70
198 201 4.760047 TTTCGCTCGGAGCCAGCC 62.760 66.667 23.36 0.00 38.18 4.85
245 248 0.179113 GTGGTGGGTTTGTTGCTGTG 60.179 55.000 0.00 0.00 0.00 3.66
248 251 1.039856 GTGGGTTTGTTGCTGTGGAT 58.960 50.000 0.00 0.00 0.00 3.41
425 432 5.929415 TCGTTTTTGTCTTTTGCCTTTTTCT 59.071 32.000 0.00 0.00 0.00 2.52
462 469 5.277828 GGACTATTTGGTGGATATTGCGTTC 60.278 44.000 0.00 0.00 0.00 3.95
487 494 2.032528 TGGGAGCCGCTTGTTCTG 59.967 61.111 0.00 0.00 0.00 3.02
514 521 0.813821 CAGTGTGAGCTCGGATCAGA 59.186 55.000 9.64 0.00 0.00 3.27
515 522 1.102154 AGTGTGAGCTCGGATCAGAG 58.898 55.000 17.49 17.49 41.03 3.35
520 527 2.670414 GTGAGCTCGGATCAGAGTTTTG 59.330 50.000 21.66 0.19 40.26 2.44
566 573 0.652592 GGCCACTTGTTGATCGATCG 59.347 55.000 20.03 9.36 0.00 3.69
586 637 0.460284 GATCGGATCCTTGTGCGTGT 60.460 55.000 10.75 0.00 34.37 4.49
588 639 0.172578 TCGGATCCTTGTGCGTGTAG 59.827 55.000 10.75 0.00 34.37 2.74
673 735 6.909550 AGGCTATGTATACAGGAAGAAGAG 57.090 41.667 11.91 0.00 0.00 2.85
688 750 8.958506 CAGGAAGAAGAGATCATGAAATTCTTT 58.041 33.333 19.89 5.90 37.18 2.52
707 769 8.841444 ATTCTTTACGATATCATTGTGTTTGC 57.159 30.769 3.12 0.00 0.00 3.68
761 823 1.294659 GCTGTCGCCTTTCCTCTGTG 61.295 60.000 0.00 0.00 0.00 3.66
780 842 4.466827 TGTGTCCAGTCTGTAGTGAAGTA 58.533 43.478 0.00 0.00 0.00 2.24
828 890 0.770557 TACCCCCACTCAGCCTGTTT 60.771 55.000 0.00 0.00 0.00 2.83
830 892 0.469892 CCCCCACTCAGCCTGTTTTT 60.470 55.000 0.00 0.00 0.00 1.94
833 895 0.675633 CCACTCAGCCTGTTTTTGGG 59.324 55.000 0.00 0.00 0.00 4.12
843 905 2.223805 CCTGTTTTTGGGAGACTGTTGC 60.224 50.000 0.00 0.00 0.00 4.17
844 906 2.426738 CTGTTTTTGGGAGACTGTTGCA 59.573 45.455 0.00 0.00 0.00 4.08
847 909 0.467290 TTTGGGAGACTGTTGCACCC 60.467 55.000 0.00 0.00 40.79 4.61
852 914 2.031870 GGAGACTGTTGCACCCTTTTT 58.968 47.619 0.00 0.00 0.00 1.94
860 922 2.255252 CACCCTTTTTGGCTCGCG 59.745 61.111 0.00 0.00 0.00 5.87
926 988 8.837788 TTATCTTGATGCCTGTATACTCATTG 57.162 34.615 4.17 0.00 0.00 2.82
947 1009 6.381481 TTGATGATGTGAGTATTTGATGCC 57.619 37.500 0.00 0.00 0.00 4.40
948 1010 5.438833 TGATGATGTGAGTATTTGATGCCA 58.561 37.500 0.00 0.00 0.00 4.92
949 1011 5.529800 TGATGATGTGAGTATTTGATGCCAG 59.470 40.000 0.00 0.00 0.00 4.85
950 1012 4.847198 TGATGTGAGTATTTGATGCCAGT 58.153 39.130 0.00 0.00 0.00 4.00
951 1013 5.988287 TGATGTGAGTATTTGATGCCAGTA 58.012 37.500 0.00 0.00 0.00 2.74
952 1014 6.594744 TGATGTGAGTATTTGATGCCAGTAT 58.405 36.000 0.00 0.00 0.00 2.12
968 1031 6.215121 TGCCAGTATTTTCTTGTTGTGAATG 58.785 36.000 0.00 0.00 0.00 2.67
1091 1154 4.782691 TCTGGTAAGGAGAACATTCATCCA 59.217 41.667 10.70 0.00 35.45 3.41
1093 1156 5.439721 TGGTAAGGAGAACATTCATCCATG 58.560 41.667 10.70 0.00 35.45 3.66
1168 1231 9.278978 TGTGTGCATATCTTGTTACTTTCTTAA 57.721 29.630 0.00 0.00 0.00 1.85
1264 1327 3.375782 AGTTTCTGAGCATGTTTTGGC 57.624 42.857 0.00 0.00 0.00 4.52
1289 1352 7.624360 TGGGTGACTGAAATATATTGTTGTC 57.376 36.000 0.00 8.05 0.00 3.18
1328 1393 8.028354 GTCATTTGTCAATTCATACATTGGTCA 58.972 33.333 0.00 0.00 35.22 4.02
1454 1523 3.118445 TCTGTGGTCGATGATAATTGGCA 60.118 43.478 0.00 0.00 0.00 4.92
1515 1588 9.897744 CACATTTAGTATTGAGAATTGTTGTGT 57.102 29.630 0.00 0.00 0.00 3.72
1522 1595 3.615155 TGAGAATTGTTGTGTGGTGTCA 58.385 40.909 0.00 0.00 0.00 3.58
1551 1624 5.769662 TCAGCATAACTTTCAGACCAATGTT 59.230 36.000 0.00 0.00 0.00 2.71
1776 1856 4.700213 ACAATGCCAATGTCTTAGGTACAC 59.300 41.667 0.00 0.00 0.00 2.90
1791 1871 7.711772 TCTTAGGTACACGATGACAAAGAAAAA 59.288 33.333 0.00 0.00 0.00 1.94
1947 2027 3.064900 ACTTCAGAATCTGCCACCTTC 57.935 47.619 5.18 0.00 0.00 3.46
2056 2136 5.180868 ACAGAAGCAGAAAATAAGCAGACAG 59.819 40.000 0.00 0.00 0.00 3.51
2088 2168 1.902508 TCCCTACAAGAAGCACAGAGG 59.097 52.381 0.00 0.00 0.00 3.69
2250 2330 3.947868 TGAAGAGCTGAAGGATGAAAGG 58.052 45.455 0.00 0.00 0.00 3.11
2286 2366 3.804193 GAGGCGAAAAGGGCTGCG 61.804 66.667 0.00 0.00 43.66 5.18
2348 2428 8.742777 CATGAAAGAGATGGAAAACCAGATTAA 58.257 33.333 0.00 0.00 0.00 1.40
2664 2744 6.475504 TCTGAGTTTGCAAGAAATGGAGATA 58.524 36.000 0.00 0.00 0.00 1.98
2725 2805 3.077359 GCTACATTGGAGAAGCAACAGT 58.923 45.455 0.00 0.00 35.05 3.55
2991 3071 3.218453 TGCAAACGGGAAGATTCTTGAA 58.782 40.909 3.03 0.00 0.00 2.69
3070 3150 3.432749 GGAAGAGGCTAGCATGAATGTGA 60.433 47.826 18.24 0.00 0.00 3.58
3078 3158 2.937591 AGCATGAATGTGAAAGTTGCG 58.062 42.857 0.00 0.00 33.99 4.85
3214 3294 4.989279 TCAGCAGAAAAAGAAAAGCAGT 57.011 36.364 0.00 0.00 0.00 4.40
3302 3382 4.443598 GGATTCCTCGGCATCTAAAACTCT 60.444 45.833 0.00 0.00 0.00 3.24
3303 3383 4.553330 TTCCTCGGCATCTAAAACTCTT 57.447 40.909 0.00 0.00 0.00 2.85
3395 3475 4.451096 TCACGAAAGAAGTATTGAACTGGC 59.549 41.667 0.00 0.00 38.88 4.85
3483 3563 0.381801 AACTTGAAGCCACACAAGCG 59.618 50.000 0.00 0.00 44.75 4.68
3550 3630 3.445096 GGTTTCCCACCTTTCTGATGATG 59.555 47.826 0.00 0.00 43.29 3.07
3621 3701 4.077822 CTGCAAGTGGAAAGGAGAAAGAT 58.922 43.478 0.00 0.00 0.00 2.40
4081 4161 4.699257 AGGAATTAAGTGCTGCTGAAGAAG 59.301 41.667 0.00 0.00 0.00 2.85
4092 4172 3.470709 TGCTGAAGAAGGTCTGAAGTTG 58.529 45.455 0.00 0.00 0.00 3.16
4218 4298 4.022849 GTGAAGGTTGATGAACTTTCTGGG 60.023 45.833 18.05 0.00 44.56 4.45
4223 4303 3.439857 TGATGAACTTTCTGGGGAAGG 57.560 47.619 0.00 0.00 35.12 3.46
4227 4307 2.512056 TGAACTTTCTGGGGAAGGTGAA 59.488 45.455 0.00 0.00 40.18 3.18
4461 4541 2.092753 GGTGGAGAATGATCTTCAGGCA 60.093 50.000 0.00 0.00 41.99 4.75
4869 4949 1.676635 GGCATTGGCTGAGAGCACA 60.677 57.895 2.42 0.00 44.75 4.57
4902 4982 3.695060 CAGCAAATCAGGCTCTGAAAGAT 59.305 43.478 8.66 0.00 45.62 2.40
5031 5111 6.525578 ACGATAGAACATTTGACTGAGGTA 57.474 37.500 0.00 0.00 41.38 3.08
5044 5124 2.729194 CTGAGGTACACAGTAGAGGCT 58.271 52.381 10.01 0.00 42.04 4.58
5072 5152 4.521639 ACTTCAATCTGCAGCTGAATCAAA 59.478 37.500 23.28 8.41 0.00 2.69
5133 5213 5.578336 TGAGACAATAGCACAGAAAGATTCG 59.422 40.000 0.00 0.00 34.02 3.34
5167 5247 2.640184 TGAATGAGAGGCTGATTGCAG 58.360 47.619 0.00 0.00 45.15 4.41
5348 5428 7.945134 ACAATAAAACATTTGACAGAAGAGCT 58.055 30.769 0.00 0.00 0.00 4.09
5415 5495 3.364366 CGGAAATTGAGAGTCAACTGCAC 60.364 47.826 0.00 0.00 39.45 4.57
5725 5812 7.530426 AAGATTGGTGAAACTGAAGCTAAAT 57.470 32.000 0.00 0.00 36.74 1.40
5751 5838 2.093658 TGAAGCCCTCGAGACAATAACC 60.094 50.000 15.71 0.00 0.00 2.85
5895 5982 4.717233 TGATGAAGTTGTGCACAAACTT 57.283 36.364 32.61 31.21 37.63 2.66
5909 5996 4.998033 GCACAAACTTAAGAGCCTAGAAGT 59.002 41.667 10.09 0.00 33.60 3.01
6014 6105 6.373005 TGAGGAATTGGAAGTACATCAGAA 57.627 37.500 0.00 0.00 0.00 3.02
6034 6125 6.936335 TCAGAACAAGCTGAATGAATTACAGA 59.064 34.615 0.00 0.00 41.65 3.41
6070 6161 0.329596 AGTAGCAGAAAAGCAGGGGG 59.670 55.000 0.00 0.00 36.85 5.40
6071 6162 0.038310 GTAGCAGAAAAGCAGGGGGT 59.962 55.000 0.00 0.00 36.85 4.95
6106 6197 5.180367 TCATTCATTGCGAAAAACACTCA 57.820 34.783 0.00 0.00 37.12 3.41
6132 6223 3.730061 GCATGATTCAACGCAAGGAAGAG 60.730 47.826 0.00 0.00 46.39 2.85
6135 6226 1.512926 TTCAACGCAAGGAAGAGCTC 58.487 50.000 5.27 5.27 46.39 4.09
6150 6241 2.859992 GCTCGAAAGCCAGGTGATT 58.140 52.632 0.00 0.00 43.10 2.57
6166 6257 7.970614 GCCAGGTGATTAAGAGTTCTATTTTTG 59.029 37.037 0.00 0.00 0.00 2.44
6181 6272 6.894828 TCTATTTTTGTTGTTCTCGGCTTAC 58.105 36.000 0.00 0.00 0.00 2.34
6193 6284 1.090052 CGGCTTACTGCTGCTTACCC 61.090 60.000 0.00 0.00 41.61 3.69
6196 6287 1.641577 CTTACTGCTGCTTACCCGTC 58.358 55.000 0.00 0.00 0.00 4.79
6199 6290 0.037232 ACTGCTGCTTACCCGTCTTC 60.037 55.000 0.00 0.00 0.00 2.87
6200 6291 0.037326 CTGCTGCTTACCCGTCTTCA 60.037 55.000 0.00 0.00 0.00 3.02
6205 6296 1.001633 TGCTTACCCGTCTTCACTTCC 59.998 52.381 0.00 0.00 0.00 3.46
6207 6298 2.354805 GCTTACCCGTCTTCACTTCCAT 60.355 50.000 0.00 0.00 0.00 3.41
6216 6307 6.992715 CCCGTCTTCACTTCCATATATTTCTT 59.007 38.462 0.00 0.00 0.00 2.52
6245 6336 7.071196 ACCATTACATAGCTCTTACCAAGATGA 59.929 37.037 0.00 0.00 36.82 2.92
6249 6340 6.711277 ACATAGCTCTTACCAAGATGAAACA 58.289 36.000 0.00 0.00 36.82 2.83
6290 6383 1.349026 TGGAAGAGCAGGAAGAACTGG 59.651 52.381 0.00 0.00 38.90 4.00
6357 6452 8.673626 AATGACAAATATGAAACTGTAAAGCG 57.326 30.769 0.00 0.00 0.00 4.68
6445 6540 9.630098 GAATTGCATATTTCAAAACTTGAGAGA 57.370 29.630 0.00 0.00 41.38 3.10
6518 6613 8.747538 TTTATCTCCCTCTAAACTATTTTGGC 57.252 34.615 0.00 0.00 0.00 4.52
6520 6615 7.691993 ATCTCCCTCTAAACTATTTTGGCTA 57.308 36.000 0.00 0.00 0.00 3.93
6522 6617 6.442564 TCTCCCTCTAAACTATTTTGGCTACA 59.557 38.462 0.00 0.00 0.00 2.74
6523 6618 7.127339 TCTCCCTCTAAACTATTTTGGCTACAT 59.873 37.037 0.00 0.00 0.00 2.29
6524 6619 7.639378 TCCCTCTAAACTATTTTGGCTACATT 58.361 34.615 0.00 0.00 0.00 2.71
6525 6620 8.113462 TCCCTCTAAACTATTTTGGCTACATTT 58.887 33.333 0.00 0.00 0.00 2.32
6526 6621 8.749354 CCCTCTAAACTATTTTGGCTACATTTT 58.251 33.333 0.00 0.00 0.00 1.82
6533 6628 9.869757 AACTATTTTGGCTACATTTTATTGACC 57.130 29.630 0.00 0.00 0.00 4.02
6534 6629 9.030452 ACTATTTTGGCTACATTTTATTGACCA 57.970 29.630 0.00 0.00 0.00 4.02
6539 6640 5.480073 TGGCTACATTTTATTGACCAAGCTT 59.520 36.000 0.00 0.00 0.00 3.74
6774 6875 2.096980 GCTAACCAGGTAAATTGGCGTC 59.903 50.000 0.00 0.00 39.39 5.19
6775 6876 2.279935 AACCAGGTAAATTGGCGTCA 57.720 45.000 0.00 0.00 39.39 4.35
6786 6887 8.403236 AGGTAAATTGGCGTCATAACTATTTTC 58.597 33.333 2.28 0.00 0.00 2.29
6830 6939 5.709631 TGTCAAGCATGCTAAATACAAAGGA 59.290 36.000 23.00 3.37 0.00 3.36
6833 6942 7.761249 GTCAAGCATGCTAAATACAAAGGAATT 59.239 33.333 23.00 0.00 0.00 2.17
6873 6982 4.402793 TCTTACTGTCAACCCTATCTGCTC 59.597 45.833 0.00 0.00 0.00 4.26
6892 7001 4.263462 TGCTCAACTGGTACCATCAGAAAT 60.263 41.667 16.75 0.00 36.22 2.17
6907 7016 4.139786 TCAGAAATTGATGGCAGATAGGC 58.860 43.478 0.00 0.00 44.50 3.93
6927 7036 0.035056 AGTTGCCTCTGTGTATGGCC 60.035 55.000 0.00 0.00 45.56 5.36
7015 7125 6.998968 TCAAAATTTGGTTGTTGCTTGAAT 57.001 29.167 5.83 0.00 0.00 2.57
7016 7126 7.014092 TCAAAATTTGGTTGTTGCTTGAATC 57.986 32.000 5.83 0.00 0.00 2.52
7017 7127 6.596888 TCAAAATTTGGTTGTTGCTTGAATCA 59.403 30.769 5.83 0.00 0.00 2.57
7132 7242 5.067674 TCAACTAGAAGCTGCACAAAAACAT 59.932 36.000 1.02 0.00 0.00 2.71
7171 7281 9.587772 GAAGTACAAGTATCAGCTCTTAATCAA 57.412 33.333 0.00 0.00 0.00 2.57
7204 7314 4.314740 AGCTGAGATCCATTACGAGAAC 57.685 45.455 0.00 0.00 0.00 3.01
7211 7321 5.805728 AGATCCATTACGAGAACAAGGTTT 58.194 37.500 0.00 0.00 0.00 3.27
7216 7326 6.488683 TCCATTACGAGAACAAGGTTTGATTT 59.511 34.615 0.00 0.00 0.00 2.17
7217 7327 6.582295 CCATTACGAGAACAAGGTTTGATTTG 59.418 38.462 0.00 0.00 0.00 2.32
7221 7331 5.765182 ACGAGAACAAGGTTTGATTTGATCT 59.235 36.000 0.00 0.00 38.59 2.75
7228 7338 8.048534 ACAAGGTTTGATTTGATCTGAGTATG 57.951 34.615 0.00 0.00 0.00 2.39
7235 7345 7.034685 TGATTTGATCTGAGTATGCATTTGG 57.965 36.000 3.54 0.00 0.00 3.28
7236 7346 6.604396 TGATTTGATCTGAGTATGCATTTGGT 59.396 34.615 3.54 0.00 0.00 3.67
7264 7374 9.343103 CTATAATACTAGTTCGCCTGTTACATG 57.657 37.037 0.00 0.00 0.00 3.21
7265 7375 2.618053 ACTAGTTCGCCTGTTACATGC 58.382 47.619 2.53 2.53 0.00 4.06
7289 7399 4.713792 AGGGTGTTATGGATCCAAGATC 57.286 45.455 20.67 9.58 0.00 2.75
7294 7404 4.823989 GTGTTATGGATCCAAGATCAAGGG 59.176 45.833 20.67 0.00 0.00 3.95
7300 7410 0.627451 TCCAAGATCAAGGGCAGCAT 59.373 50.000 0.00 0.00 0.00 3.79
7313 7423 4.228824 AGGGCAGCATGATAAAATCCATT 58.771 39.130 0.00 0.00 39.69 3.16
7340 7450 9.434420 TGTTATTTGCCTTCAAATCCTTAAATG 57.566 29.630 6.53 0.00 46.79 2.32
7361 7471 1.321474 TGAAGCCTGCTTTGTTCTGG 58.679 50.000 5.76 0.00 36.26 3.86
7415 7525 6.602009 TCATTGAGAACAGAAGCATCATGATT 59.398 34.615 5.16 0.00 0.00 2.57
7470 7580 4.923893 TGAATAGAAAATGCATTGCCTCG 58.076 39.130 13.82 0.00 0.00 4.63
7485 7596 1.736032 GCCTCGCACGATTACAGAACT 60.736 52.381 0.00 0.00 0.00 3.01
7488 7599 1.724623 TCGCACGATTACAGAACTTGC 59.275 47.619 0.00 0.00 0.00 4.01
7531 7643 7.719633 AGCCTTTTCAATCTTTGTAGTAGTCAA 59.280 33.333 0.00 0.00 0.00 3.18
7548 7660 6.939163 AGTAGTCAAACTTGCAGATTCTTGAT 59.061 34.615 0.00 0.00 0.00 2.57
7600 7712 6.741724 ACCCCCATACTTCACATTAGAAAAT 58.258 36.000 0.00 0.00 0.00 1.82
7617 7729 2.368655 AATTTGCTTCGCCATTGGAC 57.631 45.000 6.95 0.00 0.00 4.02
7643 7756 0.473755 TCCTCCTGCTGCTTTGACAA 59.526 50.000 0.00 0.00 0.00 3.18
7705 7820 6.558771 TTCTCATGTATTGATTTATGCGGG 57.441 37.500 0.00 0.00 32.72 6.13
7872 7989 2.358898 TCTGAAGAACAGGCAAGCAAAC 59.641 45.455 0.00 0.00 45.76 2.93
7874 7991 2.099592 TGAAGAACAGGCAAGCAAACAG 59.900 45.455 0.00 0.00 0.00 3.16
7937 8054 9.278978 TCAGTAGTTATCAGCAATTAACAACAA 57.721 29.630 5.76 0.00 0.00 2.83
8001 8118 0.250234 CCGAGAATTCAGCCTGGACA 59.750 55.000 8.44 0.00 0.00 4.02
8006 8123 1.197721 GAATTCAGCCTGGACACGTTG 59.802 52.381 0.00 0.00 0.00 4.10
8057 8174 3.151022 GCTCCTAGCACGGCCTCT 61.151 66.667 0.00 0.00 41.89 3.69
8058 8175 2.811101 CTCCTAGCACGGCCTCTG 59.189 66.667 0.00 0.00 0.00 3.35
8151 8268 3.295304 CTGTCCGTGGTCATCGGCA 62.295 63.158 0.00 0.00 46.49 5.69
8166 8283 2.115291 GGCATGTTCCTCGGAAGGC 61.115 63.158 0.00 3.84 43.02 4.35
8258 8375 1.542915 CTGTTGCTTCCCATGAACCTG 59.457 52.381 0.00 0.00 0.00 4.00
8341 8458 2.376518 ACTGATGGCTTTCAGGGAGAAA 59.623 45.455 18.07 0.00 46.04 2.52
8384 8501 5.836898 TCTTATTGGCGAGTTCTCCCTATAA 59.163 40.000 15.30 15.30 0.00 0.98
8495 8612 1.380403 TTGGTGTTTGCTGTCGGTGG 61.380 55.000 0.00 0.00 0.00 4.61
8511 8628 2.365617 CGGTGGGCTTGTATCTACATCT 59.634 50.000 0.00 0.00 35.89 2.90
8512 8629 3.553096 CGGTGGGCTTGTATCTACATCTC 60.553 52.174 0.00 0.00 35.89 2.75
8513 8630 3.244249 GGTGGGCTTGTATCTACATCTCC 60.244 52.174 0.00 0.00 35.89 3.71
8514 8631 2.972713 TGGGCTTGTATCTACATCTCCC 59.027 50.000 11.87 11.87 38.61 4.30
8536 8653 4.775253 CCTCCCTCTCTCTCTGTAAAAAGT 59.225 45.833 0.00 0.00 0.00 2.66
8537 8654 5.247337 CCTCCCTCTCTCTCTGTAAAAAGTT 59.753 44.000 0.00 0.00 0.00 2.66
8598 8715 7.318893 AGTATATGCTGTGTCATATGCTGTAG 58.681 38.462 11.63 0.00 44.79 2.74
8603 8720 4.149571 GCTGTGTCATATGCTGTAGAATCG 59.850 45.833 0.00 0.00 0.00 3.34
8695 8822 7.893302 TGTATTTTCAGATGGGTTTATCCACTT 59.107 33.333 0.00 0.00 39.97 3.16
8723 8850 1.278985 TGCTCGTTTGATCAGATGGGT 59.721 47.619 7.15 0.00 0.00 4.51
8759 8893 7.719483 ACCATTCATTACTTTCTTGCCATATG 58.281 34.615 0.00 0.00 0.00 1.78
8760 8894 7.560991 ACCATTCATTACTTTCTTGCCATATGA 59.439 33.333 3.65 0.00 0.00 2.15
8764 8898 8.310406 TCATTACTTTCTTGCCATATGATACG 57.690 34.615 3.65 0.00 0.00 3.06
8765 8899 7.387673 TCATTACTTTCTTGCCATATGATACGG 59.612 37.037 3.65 0.00 0.00 4.02
8766 8900 4.389374 ACTTTCTTGCCATATGATACGGG 58.611 43.478 3.65 0.00 0.00 5.28
8768 8902 1.003118 TCTTGCCATATGATACGGGCC 59.997 52.381 12.71 0.00 45.83 5.80
8769 8903 0.767998 TTGCCATATGATACGGGCCA 59.232 50.000 4.39 1.57 45.83 5.36
8770 8904 0.036164 TGCCATATGATACGGGCCAC 59.964 55.000 4.39 0.00 45.83 5.01
8771 8905 0.324943 GCCATATGATACGGGCCACT 59.675 55.000 4.39 0.00 40.55 4.00
8773 8907 1.404181 CCATATGATACGGGCCACTCG 60.404 57.143 4.39 0.56 0.00 4.18
8774 8908 1.272490 CATATGATACGGGCCACTCGT 59.728 52.381 4.39 8.08 43.64 4.18
8775 8909 1.405872 TATGATACGGGCCACTCGTT 58.594 50.000 10.83 0.00 41.38 3.85
8776 8910 0.539986 ATGATACGGGCCACTCGTTT 59.460 50.000 10.83 3.34 41.38 3.60
8777 8911 1.184431 TGATACGGGCCACTCGTTTA 58.816 50.000 10.83 0.00 41.38 2.01
8778 8912 1.758280 TGATACGGGCCACTCGTTTAT 59.242 47.619 10.83 0.00 41.38 1.40
8783 9058 1.667212 CGGGCCACTCGTTTATTTACC 59.333 52.381 4.39 0.00 0.00 2.85
8902 9224 2.032528 CCAGGCCACAAGCGAGAA 59.967 61.111 5.01 0.00 45.17 2.87
8903 9225 2.037136 CCAGGCCACAAGCGAGAAG 61.037 63.158 5.01 0.00 45.17 2.85
8904 9226 2.359230 AGGCCACAAGCGAGAAGC 60.359 61.111 5.01 0.00 45.17 3.86
8965 9287 9.419297 GAGAAAGTCCAAAACAAAGTTAAACTT 57.581 29.630 0.00 0.00 40.80 2.66
8983 9305 9.526286 GTTAAACTTGTAGACGAAAGCTAAATC 57.474 33.333 0.00 0.00 0.00 2.17
8984 9306 6.390987 AACTTGTAGACGAAAGCTAAATCG 57.609 37.500 13.11 13.11 44.33 3.34
8987 9309 6.812160 ACTTGTAGACGAAAGCTAAATCGAAT 59.188 34.615 19.45 11.33 41.43 3.34
9004 9326 6.884280 ATCGAATCCTGAATTTGTAATCCC 57.116 37.500 0.00 0.00 31.52 3.85
9016 9338 5.913137 TTTGTAATCCCGAAAATCAGCAT 57.087 34.783 0.00 0.00 0.00 3.79
9035 9357 3.882888 GCATACCGAATTTTCTGATCCCA 59.117 43.478 0.00 0.00 0.00 4.37
9050 9372 7.510675 TCTGATCCCACTCTATTTTTAACCT 57.489 36.000 0.00 0.00 0.00 3.50
9127 9449 2.182842 GGCTGGCTGGACATTAGCG 61.183 63.158 0.00 0.00 42.03 4.26
9128 9450 2.828128 GCTGGCTGGACATTAGCGC 61.828 63.158 0.00 0.00 42.03 5.92
9129 9451 1.450134 CTGGCTGGACATTAGCGCA 60.450 57.895 11.47 0.00 42.03 6.09
9130 9452 1.434622 CTGGCTGGACATTAGCGCAG 61.435 60.000 11.47 0.00 42.03 5.18
9131 9453 1.450312 GGCTGGACATTAGCGCAGT 60.450 57.895 11.47 1.63 42.03 4.40
9132 9454 1.432270 GGCTGGACATTAGCGCAGTC 61.432 60.000 11.47 11.86 42.03 3.51
9133 9455 1.756375 GCTGGACATTAGCGCAGTCG 61.756 60.000 11.47 0.00 39.07 4.18
9150 9472 3.628193 GCTCGCGCTGCTCTGATG 61.628 66.667 5.56 0.00 0.00 3.07
9151 9473 2.202716 CTCGCGCTGCTCTGATGT 60.203 61.111 5.56 0.00 0.00 3.06
9152 9474 1.808799 CTCGCGCTGCTCTGATGTT 60.809 57.895 5.56 0.00 0.00 2.71
9153 9475 1.357258 CTCGCGCTGCTCTGATGTTT 61.357 55.000 5.56 0.00 0.00 2.83
9154 9476 1.059994 CGCGCTGCTCTGATGTTTC 59.940 57.895 5.56 0.00 0.00 2.78
9155 9477 1.427020 GCGCTGCTCTGATGTTTCC 59.573 57.895 0.00 0.00 0.00 3.13
9156 9478 1.023513 GCGCTGCTCTGATGTTTCCT 61.024 55.000 0.00 0.00 0.00 3.36
9157 9479 1.446907 CGCTGCTCTGATGTTTCCTT 58.553 50.000 0.00 0.00 0.00 3.36
9158 9480 1.808945 CGCTGCTCTGATGTTTCCTTT 59.191 47.619 0.00 0.00 0.00 3.11
9159 9481 2.227388 CGCTGCTCTGATGTTTCCTTTT 59.773 45.455 0.00 0.00 0.00 2.27
9160 9482 3.304928 CGCTGCTCTGATGTTTCCTTTTT 60.305 43.478 0.00 0.00 0.00 1.94
9161 9483 4.233005 GCTGCTCTGATGTTTCCTTTTTC 58.767 43.478 0.00 0.00 0.00 2.29
9162 9484 4.022503 GCTGCTCTGATGTTTCCTTTTTCT 60.023 41.667 0.00 0.00 0.00 2.52
9163 9485 5.508657 GCTGCTCTGATGTTTCCTTTTTCTT 60.509 40.000 0.00 0.00 0.00 2.52
9164 9486 6.469782 TGCTCTGATGTTTCCTTTTTCTTT 57.530 33.333 0.00 0.00 0.00 2.52
9165 9487 6.877236 TGCTCTGATGTTTCCTTTTTCTTTT 58.123 32.000 0.00 0.00 0.00 2.27
9166 9488 7.330262 TGCTCTGATGTTTCCTTTTTCTTTTT 58.670 30.769 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.208535 AGGTCGGATCAAATGGCGTAA 59.791 47.619 0.00 0.00 0.00 3.18
1 2 0.828022 AGGTCGGATCAAATGGCGTA 59.172 50.000 0.00 0.00 0.00 4.42
2 3 0.462047 GAGGTCGGATCAAATGGCGT 60.462 55.000 0.00 0.00 0.00 5.68
11 12 2.119886 CAGAGGTGGAGGTCGGATC 58.880 63.158 0.00 0.00 0.00 3.36
99 102 2.417719 GGCAGAATCGGAGCGATAATT 58.582 47.619 0.00 0.00 46.30 1.40
177 180 2.202756 GGCTCCGAGCGAAATCGT 60.203 61.111 14.21 0.00 43.62 3.73
178 181 2.202743 TGGCTCCGAGCGAAATCG 60.203 61.111 14.21 0.00 43.62 3.34
179 182 2.529619 GCTGGCTCCGAGCGAAATC 61.530 63.158 14.21 0.63 43.62 2.17
180 183 2.512515 GCTGGCTCCGAGCGAAAT 60.513 61.111 14.21 0.00 43.62 2.17
245 248 0.321653 AAACAGCACGGTCCTCATCC 60.322 55.000 0.00 0.00 0.00 3.51
248 251 1.300620 CGAAACAGCACGGTCCTCA 60.301 57.895 0.00 0.00 0.00 3.86
395 402 5.063312 AGGCAAAAGACAAAAACGACAATTG 59.937 36.000 3.24 3.24 0.00 2.32
425 432 1.264749 ATAGTCCAGCAACCGAGCCA 61.265 55.000 0.00 0.00 34.23 4.75
487 494 2.578495 CGAGCTCACACTGAATTTTGC 58.422 47.619 15.40 0.00 0.00 3.68
534 541 6.321945 TCAACAAGTGGCCGTCTAAGTATATA 59.678 38.462 0.00 0.00 0.00 0.86
535 542 5.128171 TCAACAAGTGGCCGTCTAAGTATAT 59.872 40.000 0.00 0.00 0.00 0.86
536 543 4.463539 TCAACAAGTGGCCGTCTAAGTATA 59.536 41.667 0.00 0.00 0.00 1.47
542 549 1.403647 CGATCAACAAGTGGCCGTCTA 60.404 52.381 0.00 0.00 0.00 2.59
544 551 0.669318 TCGATCAACAAGTGGCCGTC 60.669 55.000 0.00 0.00 0.00 4.79
545 552 0.036388 ATCGATCAACAAGTGGCCGT 60.036 50.000 0.00 0.00 0.00 5.68
548 555 0.652592 CCGATCGATCAACAAGTGGC 59.347 55.000 24.40 0.00 0.00 5.01
586 637 5.624159 CCAATCAGGACCAGAATTATGCTA 58.376 41.667 0.00 0.00 41.22 3.49
588 639 3.005155 GCCAATCAGGACCAGAATTATGC 59.995 47.826 0.00 0.00 41.22 3.14
688 750 6.526325 GCAAAAGCAAACACAATGATATCGTA 59.474 34.615 0.00 0.00 0.00 3.43
690 752 5.220265 GGCAAAAGCAAACACAATGATATCG 60.220 40.000 0.00 0.00 0.00 2.92
706 768 5.396750 TTCGTTGTTATTTTGGCAAAAGC 57.603 34.783 27.21 19.84 33.22 3.51
707 769 8.293114 ACTATTCGTTGTTATTTTGGCAAAAG 57.707 30.769 27.21 13.91 33.22 2.27
761 823 5.005094 AGACTACTTCACTACAGACTGGAC 58.995 45.833 7.51 0.00 0.00 4.02
780 842 9.730420 GTAAACAATTGATTTTGTGTACAGACT 57.270 29.630 13.59 0.00 44.44 3.24
828 890 0.467290 GGGTGCAACAGTCTCCCAAA 60.467 55.000 3.06 0.00 39.98 3.28
830 892 1.352622 AAGGGTGCAACAGTCTCCCA 61.353 55.000 3.06 0.00 39.98 4.37
833 895 2.223805 CCAAAAAGGGTGCAACAGTCTC 60.224 50.000 3.06 0.00 39.98 3.36
847 909 1.715519 CAATCAACGCGAGCCAAAAAG 59.284 47.619 15.93 0.00 0.00 2.27
852 914 1.078497 ATCCAATCAACGCGAGCCA 60.078 52.632 15.93 0.00 0.00 4.75
860 922 4.127566 CCACAAATGGGATCCAATCAAC 57.872 45.455 15.23 0.00 43.04 3.18
926 988 5.530171 ACTGGCATCAAATACTCACATCATC 59.470 40.000 0.00 0.00 0.00 2.92
941 1003 5.534278 TCACAACAAGAAAATACTGGCATCA 59.466 36.000 0.00 0.00 0.00 3.07
942 1004 6.012658 TCACAACAAGAAAATACTGGCATC 57.987 37.500 0.00 0.00 0.00 3.91
943 1005 6.403866 TTCACAACAAGAAAATACTGGCAT 57.596 33.333 0.00 0.00 0.00 4.40
944 1006 5.843673 TTCACAACAAGAAAATACTGGCA 57.156 34.783 0.00 0.00 0.00 4.92
945 1007 5.634859 CCATTCACAACAAGAAAATACTGGC 59.365 40.000 0.00 0.00 0.00 4.85
947 1009 6.215121 TGCCATTCACAACAAGAAAATACTG 58.785 36.000 0.00 0.00 0.00 2.74
948 1010 6.265196 TCTGCCATTCACAACAAGAAAATACT 59.735 34.615 0.00 0.00 0.00 2.12
949 1011 6.446318 TCTGCCATTCACAACAAGAAAATAC 58.554 36.000 0.00 0.00 0.00 1.89
950 1012 6.647334 TCTGCCATTCACAACAAGAAAATA 57.353 33.333 0.00 0.00 0.00 1.40
951 1013 5.534207 TCTGCCATTCACAACAAGAAAAT 57.466 34.783 0.00 0.00 0.00 1.82
952 1014 4.998671 TCTGCCATTCACAACAAGAAAA 57.001 36.364 0.00 0.00 0.00 2.29
968 1031 5.232414 CACTAGCTTAGTATTCGTTTCTGCC 59.768 44.000 0.00 0.00 37.23 4.85
1021 1084 1.134965 CGTCTCCCCAGAGCTTACTTG 60.135 57.143 0.00 0.00 40.22 3.16
1091 1154 4.158579 TCTCGAACATGCACTAGACTTCAT 59.841 41.667 0.00 0.00 0.00 2.57
1093 1156 4.098055 TCTCGAACATGCACTAGACTTC 57.902 45.455 0.00 0.00 0.00 3.01
1099 1162 3.785486 CTGGAATCTCGAACATGCACTA 58.215 45.455 0.00 0.00 0.00 2.74
1184 1247 4.226761 GGACGCCAAATAACAAAACTGAG 58.773 43.478 0.00 0.00 0.00 3.35
1231 1294 8.559536 CATGCTCAGAAACTACACTTTTTCTTA 58.440 33.333 0.00 0.00 39.54 2.10
1238 1301 6.460123 CCAAAACATGCTCAGAAACTACACTT 60.460 38.462 0.00 0.00 0.00 3.16
1244 1307 2.961062 AGCCAAAACATGCTCAGAAACT 59.039 40.909 0.00 0.00 30.33 2.66
1253 1316 0.319813 GTCACCCAGCCAAAACATGC 60.320 55.000 0.00 0.00 0.00 4.06
1264 1327 7.554118 AGACAACAATATATTTCAGTCACCCAG 59.446 37.037 16.87 0.00 0.00 4.45
1435 1504 2.549754 CCTGCCAATTATCATCGACCAC 59.450 50.000 0.00 0.00 0.00 4.16
1436 1505 2.849942 CCTGCCAATTATCATCGACCA 58.150 47.619 0.00 0.00 0.00 4.02
1511 1584 2.153645 GCTGATCATTGACACCACACA 58.846 47.619 0.00 0.00 0.00 3.72
1515 1588 4.847198 AGTTATGCTGATCATTGACACCA 58.153 39.130 0.00 0.00 36.63 4.17
1522 1595 6.182627 TGGTCTGAAAGTTATGCTGATCATT 58.817 36.000 0.00 0.00 33.99 2.57
1582 1655 2.766263 TCTATTCTCCACACTCCGCATT 59.234 45.455 0.00 0.00 0.00 3.56
1593 1669 9.448438 TTTTCATCGAGATTTTTCTATTCTCCA 57.552 29.630 0.00 0.00 33.81 3.86
1660 1737 8.730680 TCCTCATTGAAAGAAAAGTACTATTGC 58.269 33.333 0.00 0.00 0.00 3.56
1724 1804 9.545105 GAATACATTGGCATATTTGGAATTTCA 57.455 29.630 0.00 0.00 0.00 2.69
1776 1856 8.837059 CCGTTTACTAATTTTTCTTTGTCATCG 58.163 33.333 0.00 0.00 0.00 3.84
1791 1871 6.018180 GCAGATTCGAATTCCCGTTTACTAAT 60.018 38.462 12.81 0.00 0.00 1.73
1800 1880 1.942657 ACATGCAGATTCGAATTCCCG 59.057 47.619 12.81 2.67 0.00 5.14
1947 2027 5.818136 TCAGTCTTTCTGTTTCTTGGTTG 57.182 39.130 0.00 0.00 43.97 3.77
1982 2062 1.237533 TTCAAGCTCTTCAATGCGCA 58.762 45.000 14.96 14.96 0.00 6.09
2056 2136 6.509418 TTCTTGTAGGGAATTGTATTGCAC 57.491 37.500 0.00 0.00 0.00 4.57
2062 2142 5.012664 TCTGTGCTTCTTGTAGGGAATTGTA 59.987 40.000 0.00 0.00 0.00 2.41
2070 2150 2.564947 AGACCTCTGTGCTTCTTGTAGG 59.435 50.000 0.00 0.00 0.00 3.18
2286 2366 6.460676 CCATTTCCAGCATCTTATCAAGTTCC 60.461 42.308 0.00 0.00 0.00 3.62
2348 2428 6.445139 TCCCTTTATCTCTTCCTGAAGATTGT 59.555 38.462 9.87 2.95 45.40 2.71
2664 2744 3.571401 CCTTCACATGCTCTTCCAGTTTT 59.429 43.478 0.00 0.00 0.00 2.43
2725 2805 3.741029 GCAGGTTGAGTATCTGCGA 57.259 52.632 0.00 0.00 43.28 5.10
2991 3071 2.157738 GCCTGAATCTGTGCTTCAAGT 58.842 47.619 0.00 0.00 32.53 3.16
3070 3150 2.887152 AGCATTTCTTCTCCGCAACTTT 59.113 40.909 0.00 0.00 0.00 2.66
3078 3158 5.426504 TCAAGATCAGAGCATTTCTTCTCC 58.573 41.667 0.00 0.00 32.41 3.71
3214 3294 4.142204 TGCATTGTTCACTGCTTCTTCAAA 60.142 37.500 14.26 0.00 39.16 2.69
3302 3382 7.361457 TCCTTGACTTCTTCTTCAAGTAGAA 57.639 36.000 6.34 6.34 44.93 2.10
3303 3383 6.978674 TCCTTGACTTCTTCTTCAAGTAGA 57.021 37.500 9.77 0.00 44.93 2.59
3395 3475 5.931532 ACTTTGATGTATGAAGCAAACTCG 58.068 37.500 0.00 0.00 0.00 4.18
3483 3563 3.214328 TGCTTCAACCTCCTTGAACTTC 58.786 45.455 0.00 0.00 42.85 3.01
3543 3623 5.422012 TGTCTGGTAAGCTTCTACATCATCA 59.578 40.000 0.00 0.00 0.00 3.07
3550 3630 6.402658 GCTGATTTTGTCTGGTAAGCTTCTAC 60.403 42.308 0.00 0.00 0.00 2.59
3621 3701 7.550551 GTGATTTGAATCAGTGAGTCCATAAGA 59.449 37.037 17.37 0.00 45.38 2.10
3708 3788 3.914364 CGATAACTTGCTTTTCCTGCAAC 59.086 43.478 0.00 0.00 44.24 4.17
4081 4161 2.481952 CAGTAAGCTGCAACTTCAGACC 59.518 50.000 5.45 0.00 36.19 3.85
4092 4172 3.393800 TGACTCAAACTCAGTAAGCTGC 58.606 45.455 0.00 0.00 42.29 5.25
4167 4247 2.421073 ACCATTGCATTCATCTGTCACG 59.579 45.455 0.00 0.00 0.00 4.35
4218 4298 3.055094 TCTCCTTGTATGCTTCACCTTCC 60.055 47.826 0.00 0.00 0.00 3.46
4223 4303 5.448360 GCTGATTTCTCCTTGTATGCTTCAC 60.448 44.000 0.00 0.00 0.00 3.18
4227 4307 4.226427 TGCTGATTTCTCCTTGTATGCT 57.774 40.909 0.00 0.00 0.00 3.79
4323 4403 7.334858 ACAATTCTTCATACTTCTCCTTCTCC 58.665 38.462 0.00 0.00 0.00 3.71
4461 4541 2.972713 TGAGCTTTCTCTAACACCCAGT 59.027 45.455 0.00 0.00 40.03 4.00
4637 4717 2.231478 TGACAATCCGTCTCCTTCTGAC 59.769 50.000 0.00 0.00 45.60 3.51
4869 4949 1.610554 GATTTGCTGCACCCATGGCT 61.611 55.000 6.09 0.00 0.00 4.75
5031 5111 4.833380 TGAAGTTCTAAGCCTCTACTGTGT 59.167 41.667 4.17 0.00 0.00 3.72
5044 5124 4.898320 TCAGCTGCAGATTGAAGTTCTAA 58.102 39.130 20.43 0.00 0.00 2.10
5072 5152 3.748083 TGAGCTTCAACTTCTGCATTCT 58.252 40.909 0.00 0.00 0.00 2.40
5133 5213 8.473219 AGCCTCTCATTCAAATCTTTAATTTCC 58.527 33.333 0.00 0.00 0.00 3.13
5151 5231 1.348696 TGAACTGCAATCAGCCTCTCA 59.651 47.619 0.00 0.00 44.10 3.27
5348 5428 1.620822 GAGCTCCAAGCCCTTTGAAA 58.379 50.000 0.87 0.00 43.77 2.69
5415 5495 2.481568 TGCAATTGTCTCAAGAGCTTCG 59.518 45.455 7.40 0.00 0.00 3.79
5725 5812 0.391661 GTCTCGAGGGCTTCATGCAA 60.392 55.000 13.56 0.00 45.15 4.08
5751 5838 6.484977 AGTCTTTAACTTCAGCTTCTTTCTGG 59.515 38.462 0.00 0.00 33.03 3.86
5895 5982 5.245301 TGCAAGTTGTACTTCTAGGCTCTTA 59.755 40.000 4.48 0.00 36.03 2.10
5909 5996 5.773575 TGTTTTGTGTTTCTGCAAGTTGTA 58.226 33.333 4.48 0.00 33.76 2.41
6014 6105 6.656270 TGTCATCTGTAATTCATTCAGCTTGT 59.344 34.615 0.00 0.00 0.00 3.16
6070 6161 5.728898 GCAATGAATGAATCTCTTCCGACAC 60.729 44.000 0.00 0.00 0.00 3.67
6071 6162 4.333649 GCAATGAATGAATCTCTTCCGACA 59.666 41.667 0.00 0.00 0.00 4.35
6106 6197 2.417651 CCTTGCGTTGAATCATGCCATT 60.418 45.455 5.70 0.00 0.00 3.16
6132 6223 2.024176 TAATCACCTGGCTTTCGAGC 57.976 50.000 0.00 0.00 0.00 5.03
6135 6226 3.600388 ACTCTTAATCACCTGGCTTTCG 58.400 45.455 0.00 0.00 0.00 3.46
6150 6241 8.770828 CCGAGAACAACAAAAATAGAACTCTTA 58.229 33.333 0.00 0.00 0.00 2.10
6181 6272 0.037326 TGAAGACGGGTAAGCAGCAG 60.037 55.000 0.00 0.00 0.00 4.24
6190 6281 5.888982 AATATATGGAAGTGAAGACGGGT 57.111 39.130 0.00 0.00 0.00 5.28
6216 6307 9.596308 TCTTGGTAAGAGCTATGTAATGGTATA 57.404 33.333 0.00 0.00 32.71 1.47
6245 6336 9.442047 CAGAGTAGAAGATACCTGAAAATGTTT 57.558 33.333 0.00 0.00 0.00 2.83
6249 6340 7.979786 TCCAGAGTAGAAGATACCTGAAAAT 57.020 36.000 0.00 0.00 0.00 1.82
6280 6373 0.603975 ACTTGCTCGCCAGTTCTTCC 60.604 55.000 0.00 0.00 0.00 3.46
6290 6383 0.110192 GTGCTTTGGTACTTGCTCGC 60.110 55.000 0.00 0.00 0.00 5.03
6373 6468 1.354031 TGCTCCTCCAATTTGGCTACA 59.646 47.619 10.76 2.04 37.47 2.74
6374 6469 2.128771 TGCTCCTCCAATTTGGCTAC 57.871 50.000 10.76 0.00 37.47 3.58
6445 6540 7.801716 TTTTAGCTCAGACACTGTAATTTGT 57.198 32.000 0.00 0.00 32.61 2.83
6512 6607 6.648725 GCTTGGTCAATAAAATGTAGCCAAAA 59.351 34.615 0.00 0.00 34.82 2.44
6523 6618 8.527810 CCCTAATGTAAAGCTTGGTCAATAAAA 58.472 33.333 0.00 0.00 0.00 1.52
6524 6619 7.363443 GCCCTAATGTAAAGCTTGGTCAATAAA 60.363 37.037 0.00 0.00 0.00 1.40
6525 6620 6.096282 GCCCTAATGTAAAGCTTGGTCAATAA 59.904 38.462 0.00 0.00 0.00 1.40
6526 6621 5.592688 GCCCTAATGTAAAGCTTGGTCAATA 59.407 40.000 0.00 0.00 0.00 1.90
6527 6622 4.402474 GCCCTAATGTAAAGCTTGGTCAAT 59.598 41.667 0.00 0.00 0.00 2.57
6528 6623 3.761752 GCCCTAATGTAAAGCTTGGTCAA 59.238 43.478 0.00 0.00 0.00 3.18
6529 6624 3.245087 TGCCCTAATGTAAAGCTTGGTCA 60.245 43.478 0.00 0.00 0.00 4.02
6530 6625 3.352648 TGCCCTAATGTAAAGCTTGGTC 58.647 45.455 0.00 0.00 0.00 4.02
6531 6626 3.449746 TGCCCTAATGTAAAGCTTGGT 57.550 42.857 0.00 0.00 0.00 3.67
6532 6627 5.111293 CAATTGCCCTAATGTAAAGCTTGG 58.889 41.667 0.00 0.00 0.00 3.61
6533 6628 5.111293 CCAATTGCCCTAATGTAAAGCTTG 58.889 41.667 0.00 0.00 0.00 4.01
6534 6629 4.777366 ACCAATTGCCCTAATGTAAAGCTT 59.223 37.500 0.00 0.00 0.00 3.74
6539 6640 4.601406 AGGACCAATTGCCCTAATGTAA 57.399 40.909 13.86 0.00 0.00 2.41
6544 6645 4.595986 GAAAGTAGGACCAATTGCCCTAA 58.404 43.478 19.90 7.71 34.64 2.69
6588 6689 8.689061 CATGGTCTGGATCTGAAAATATTTGAA 58.311 33.333 0.39 0.00 0.00 2.69
6598 6699 2.306805 ACTTGCATGGTCTGGATCTGAA 59.693 45.455 4.44 0.00 0.00 3.02
6798 6902 5.991328 TTAGCATGCTTGACAGTAATAGC 57.009 39.130 28.02 0.00 0.00 2.97
6799 6903 9.045223 TGTATTTAGCATGCTTGACAGTAATAG 57.955 33.333 28.02 0.00 0.00 1.73
6801 6905 7.864108 TGTATTTAGCATGCTTGACAGTAAT 57.136 32.000 28.02 15.03 0.00 1.89
6830 6939 6.555463 AAGAAAATGATGGATCCAGCAATT 57.445 33.333 34.56 29.24 45.67 2.32
6833 6942 5.591472 CAGTAAGAAAATGATGGATCCAGCA 59.409 40.000 33.28 33.28 46.61 4.41
6873 6982 6.764308 ATCAATTTCTGATGGTACCAGTTG 57.236 37.500 21.41 14.44 43.49 3.16
6892 7001 2.646930 CAACTGCCTATCTGCCATCAA 58.353 47.619 0.00 0.00 0.00 2.57
6918 7027 2.556189 TGTCAACAACATGGCCATACAC 59.444 45.455 20.30 7.78 31.20 2.90
7009 7119 8.706035 GGTTTTTCATGTCAAGATTGATTCAAG 58.294 33.333 5.21 0.00 39.73 3.02
7015 7125 7.555087 ACAAAGGTTTTTCATGTCAAGATTGA 58.445 30.769 0.00 0.00 34.20 2.57
7016 7126 7.775397 ACAAAGGTTTTTCATGTCAAGATTG 57.225 32.000 0.00 0.00 0.00 2.67
7017 7127 8.791327 AAACAAAGGTTTTTCATGTCAAGATT 57.209 26.923 0.00 0.00 44.63 2.40
7103 7213 1.550524 TGCAGCTTCTAGTTGATCCGT 59.449 47.619 0.00 0.00 0.00 4.69
7204 7314 6.971184 GCATACTCAGATCAAATCAAACCTTG 59.029 38.462 0.00 0.00 0.00 3.61
7211 7321 6.604396 ACCAAATGCATACTCAGATCAAATCA 59.396 34.615 0.00 0.00 0.00 2.57
7235 7345 5.770417 ACAGGCGAACTAGTATTATAGCAC 58.230 41.667 0.00 0.00 0.00 4.40
7236 7346 6.401047 AACAGGCGAACTAGTATTATAGCA 57.599 37.500 0.00 0.00 0.00 3.49
7253 7363 0.676782 ACCCTTCGCATGTAACAGGC 60.677 55.000 0.00 0.00 37.83 4.85
7264 7374 1.134220 TGGATCCATAACACCCTTCGC 60.134 52.381 11.44 0.00 0.00 4.70
7265 7375 3.118408 TCTTGGATCCATAACACCCTTCG 60.118 47.826 17.06 0.00 0.00 3.79
7268 7378 4.047166 TGATCTTGGATCCATAACACCCT 58.953 43.478 17.06 0.00 0.00 4.34
7289 7399 3.385433 TGGATTTTATCATGCTGCCCTTG 59.615 43.478 0.00 0.00 0.00 3.61
7294 7404 6.913873 AACAAATGGATTTTATCATGCTGC 57.086 33.333 0.00 0.00 0.00 5.25
7300 7410 9.956640 AAGGCAAATAACAAATGGATTTTATCA 57.043 25.926 0.00 0.00 0.00 2.15
7340 7450 2.544486 CCAGAACAAAGCAGGCTTCAAC 60.544 50.000 7.03 0.51 34.84 3.18
7342 7452 1.321474 CCAGAACAAAGCAGGCTTCA 58.679 50.000 7.03 0.00 34.84 3.02
7415 7525 3.900971 TCCATTATCATGCAAGCCTTCA 58.099 40.909 0.00 0.00 0.00 3.02
7470 7580 3.813529 AAGCAAGTTCTGTAATCGTGC 57.186 42.857 0.00 0.00 36.98 5.34
7488 7599 9.638239 TGAAAAGGCTATTTGTGCTAATTTAAG 57.362 29.630 0.00 0.00 0.00 1.85
7531 7643 9.635520 CTTTTTATCATCAAGAATCTGCAAGTT 57.364 29.630 0.00 0.00 33.76 2.66
7548 7660 8.791327 TGTGTGAATCTATCAGCTTTTTATCA 57.209 30.769 0.00 0.00 39.19 2.15
7617 7729 1.484038 AGCAGCAGGAGGACTAGAAG 58.516 55.000 0.00 0.00 0.00 2.85
7722 7839 4.426879 AGAGCGAGTTTCTCACTCTCCTC 61.427 52.174 10.34 9.67 43.76 3.71
7745 7862 4.410492 CTTGTTGAGCTGTGTATTGACC 57.590 45.455 0.00 0.00 0.00 4.02
7888 8005 7.730084 TGATCAGGGTACTCAAGATATTTCAG 58.270 38.462 0.00 0.00 0.00 3.02
7898 8015 7.123383 TGATAACTACTGATCAGGGTACTCAA 58.877 38.462 26.08 4.15 0.00 3.02
7969 8086 2.871182 TTCTCGGGATCTCGTTGATG 57.129 50.000 15.95 1.95 35.14 3.07
8001 8118 2.103340 GTTTTGCGGTGCCAACGT 59.897 55.556 3.21 0.00 0.00 3.99
8006 8123 1.761244 GCTGTTTGTTTTGCGGTGCC 61.761 55.000 0.00 0.00 0.00 5.01
8027 8144 3.161067 GCTAGGAGCCTGAGATATGTCA 58.839 50.000 2.15 2.15 34.48 3.58
8138 8255 1.705337 GGAACATGCCGATGACCACG 61.705 60.000 0.00 0.00 33.24 4.94
8151 8268 3.708210 TCGCCTTCCGAGGAACAT 58.292 55.556 0.00 0.00 46.74 2.71
8166 8283 1.065701 ACAAGAGCGGCACTAGTATCG 59.934 52.381 1.45 11.30 0.00 2.92
8180 8297 2.149578 CCAGCAGGAACTTCACAAGAG 58.850 52.381 0.00 0.00 34.60 2.85
8258 8375 5.575019 GCTGTTCAGCTAGAGTAGTAGTTC 58.425 45.833 16.29 0.00 0.00 3.01
8341 8458 0.618968 AAGCTTCCGGATCCCTGACT 60.619 55.000 4.15 0.00 0.00 3.41
8342 8459 0.179070 GAAGCTTCCGGATCCCTGAC 60.179 60.000 15.97 0.00 0.00 3.51
8343 8460 0.325671 AGAAGCTTCCGGATCCCTGA 60.326 55.000 22.81 0.00 0.00 3.86
8344 8461 0.543749 AAGAAGCTTCCGGATCCCTG 59.456 55.000 22.81 0.00 0.00 4.45
8345 8462 2.176247 TAAGAAGCTTCCGGATCCCT 57.824 50.000 22.81 0.00 0.00 4.20
8346 8463 3.142174 CAATAAGAAGCTTCCGGATCCC 58.858 50.000 22.81 0.00 0.00 3.85
8347 8464 3.142174 CCAATAAGAAGCTTCCGGATCC 58.858 50.000 22.81 0.00 0.00 3.36
8348 8465 2.550180 GCCAATAAGAAGCTTCCGGATC 59.450 50.000 22.81 0.00 0.00 3.36
8384 8501 5.576563 CCCCCTTAACCCAAAAGAAAAAT 57.423 39.130 0.00 0.00 0.00 1.82
8409 8526 7.984422 AGGAATGAACAAAAATCAAATTCCC 57.016 32.000 7.68 0.00 36.95 3.97
8495 8612 3.259625 GGAGGGAGATGTAGATACAAGCC 59.740 52.174 0.00 0.00 39.99 4.35
8511 8628 2.288598 TACAGAGAGAGAGGGAGGGA 57.711 55.000 0.00 0.00 0.00 4.20
8512 8629 3.390175 TTTACAGAGAGAGAGGGAGGG 57.610 52.381 0.00 0.00 0.00 4.30
8513 8630 4.775253 ACTTTTTACAGAGAGAGAGGGAGG 59.225 45.833 0.00 0.00 0.00 4.30
8514 8631 5.993748 ACTTTTTACAGAGAGAGAGGGAG 57.006 43.478 0.00 0.00 0.00 4.30
8576 8693 6.350629 TCTACAGCATATGACACAGCATAT 57.649 37.500 6.97 0.00 41.01 1.78
8579 8696 4.470334 TTCTACAGCATATGACACAGCA 57.530 40.909 6.97 0.00 0.00 4.41
8598 8715 3.896648 TCAAAAACACTGGAGCGATTC 57.103 42.857 0.00 0.00 0.00 2.52
8695 8822 6.552859 TCTGATCAAACGAGCAAATAAACA 57.447 33.333 0.00 0.00 0.00 2.83
8723 8850 3.756082 AATGAATGGTAGGGGCTGAAA 57.244 42.857 0.00 0.00 0.00 2.69
8759 8893 2.521105 ATAAACGAGTGGCCCGTATC 57.479 50.000 5.94 0.00 39.57 2.24
8760 8894 2.994186 AATAAACGAGTGGCCCGTAT 57.006 45.000 5.94 0.00 39.57 3.06
8762 8896 2.349590 GTAAATAAACGAGTGGCCCGT 58.650 47.619 0.00 0.00 42.61 5.28
8764 8898 1.667212 CGGTAAATAAACGAGTGGCCC 59.333 52.381 0.00 0.00 0.00 5.80
8765 8899 2.349590 ACGGTAAATAAACGAGTGGCC 58.650 47.619 0.00 0.00 0.00 5.36
8766 8900 5.045872 AGATACGGTAAATAAACGAGTGGC 58.954 41.667 0.00 0.00 0.00 5.01
8768 8902 8.526681 GTTACAGATACGGTAAATAAACGAGTG 58.473 37.037 0.00 0.00 32.94 3.51
8769 8903 7.702348 GGTTACAGATACGGTAAATAAACGAGT 59.298 37.037 0.00 0.00 32.94 4.18
8770 8904 7.096885 CGGTTACAGATACGGTAAATAAACGAG 60.097 40.741 12.35 2.27 32.94 4.18
8771 8905 6.690957 CGGTTACAGATACGGTAAATAAACGA 59.309 38.462 12.35 0.00 32.94 3.85
8773 8907 6.255453 TGCGGTTACAGATACGGTAAATAAAC 59.745 38.462 0.00 0.00 32.94 2.01
8774 8908 6.336566 TGCGGTTACAGATACGGTAAATAAA 58.663 36.000 0.00 0.00 32.94 1.40
8775 8909 5.900425 TGCGGTTACAGATACGGTAAATAA 58.100 37.500 0.00 0.00 32.94 1.40
8776 8910 5.512753 TGCGGTTACAGATACGGTAAATA 57.487 39.130 0.00 0.00 32.94 1.40
8777 8911 4.389890 TGCGGTTACAGATACGGTAAAT 57.610 40.909 0.00 0.00 32.94 1.40
8778 8912 3.865011 TGCGGTTACAGATACGGTAAA 57.135 42.857 0.00 0.00 32.94 2.01
8783 9058 0.502695 CGCATGCGGTTACAGATACG 59.497 55.000 31.99 0.00 35.56 3.06
8900 9222 2.117156 ATGCATGCTGGGTCGCTTC 61.117 57.895 20.33 0.00 0.00 3.86
8902 9224 2.827190 CATGCATGCTGGGTCGCT 60.827 61.111 20.33 0.00 0.00 4.93
8960 9282 6.643770 TCGATTTAGCTTTCGTCTACAAGTTT 59.356 34.615 11.56 0.00 36.74 2.66
8965 9287 5.747197 GGATTCGATTTAGCTTTCGTCTACA 59.253 40.000 11.56 0.00 36.74 2.74
8983 9305 4.814234 TCGGGATTACAAATTCAGGATTCG 59.186 41.667 0.00 0.00 0.00 3.34
8984 9306 6.693315 TTCGGGATTACAAATTCAGGATTC 57.307 37.500 0.00 0.00 0.00 2.52
8987 9309 6.661377 TGATTTTCGGGATTACAAATTCAGGA 59.339 34.615 0.00 0.00 0.00 3.86
9004 9326 6.195244 CAGAAAATTCGGTATGCTGATTTTCG 59.805 38.462 20.67 16.02 39.34 3.46
9016 9338 4.469945 AGAGTGGGATCAGAAAATTCGGTA 59.530 41.667 0.00 0.00 0.00 4.02
9035 9357 5.944007 ACGCCATGAAGGTTAAAAATAGAGT 59.056 36.000 0.00 0.00 40.61 3.24
9050 9372 2.772077 TACCAGCTAAACGCCATGAA 57.228 45.000 0.00 0.00 40.39 2.57
9073 9395 5.376854 AGTATTTGACTTGCCACATCAAC 57.623 39.130 0.00 0.00 33.13 3.18
9074 9396 5.647658 CCTAGTATTTGACTTGCCACATCAA 59.352 40.000 0.00 0.00 39.81 2.57
9134 9456 1.357258 AAACATCAGAGCAGCGCGAG 61.357 55.000 12.10 1.41 0.00 5.03
9135 9457 1.354337 GAAACATCAGAGCAGCGCGA 61.354 55.000 12.10 0.00 0.00 5.87
9136 9458 1.059994 GAAACATCAGAGCAGCGCG 59.940 57.895 0.00 0.00 0.00 6.86
9137 9459 1.023513 AGGAAACATCAGAGCAGCGC 61.024 55.000 0.00 0.00 0.00 5.92
9138 9460 1.446907 AAGGAAACATCAGAGCAGCG 58.553 50.000 0.00 0.00 0.00 5.18
9139 9461 3.930634 AAAAGGAAACATCAGAGCAGC 57.069 42.857 0.00 0.00 0.00 5.25
9140 9462 5.702349 AGAAAAAGGAAACATCAGAGCAG 57.298 39.130 0.00 0.00 0.00 4.24
9141 9463 6.469782 AAAGAAAAAGGAAACATCAGAGCA 57.530 33.333 0.00 0.00 0.00 4.26
9142 9464 7.776933 AAAAAGAAAAAGGAAACATCAGAGC 57.223 32.000 0.00 0.00 0.00 4.09


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

AutoCloner maintained by Alex Coulton.