Multiple sequence alignment - TraesCS2A01G401400

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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 TraesCS2A01G401400 chr2A 100.000 4805 0 0 1 4805 655029339 655034143 0.000000e+00 8874.0
1 TraesCS2A01G401400 chr2D 92.345 3318 148 41 1 3269 511915272 511918532 0.000000e+00 4623.0
2 TraesCS2A01G401400 chr2D 93.818 1100 40 13 3545 4632 511919775 511920858 0.000000e+00 1629.0
3 TraesCS2A01G401400 chr2D 87.940 199 18 2 3275 3473 511919578 511919770 3.740000e-56 230.0
4 TraesCS2A01G401400 chr2B 90.803 1196 72 14 2091 3278 601176229 601177394 0.000000e+00 1565.0
5 TraesCS2A01G401400 chr2B 96.216 925 29 3 786 1710 601175272 601176190 0.000000e+00 1509.0
6 TraesCS2A01G401400 chr2B 91.254 686 41 9 3545 4217 601178815 601179494 0.000000e+00 917.0
7 TraesCS2A01G401400 chr2B 86.500 200 18 4 3275 3473 601178619 601178810 1.350000e-50 211.0
8 TraesCS2A01G401400 chr2B 87.013 154 17 3 4653 4805 601181491 601181642 2.300000e-38 171.0
9 TraesCS2A01G401400 chr2B 93.333 60 4 0 1726 1785 601176175 601176234 6.620000e-14 89.8
10 TraesCS2A01G401400 chr6D 88.000 175 19 2 2860 3033 334344627 334344454 6.300000e-49 206.0
11 TraesCS2A01G401400 chr6D 83.938 193 30 1 3616 3807 334342988 334342796 2.950000e-42 183.0
12 TraesCS2A01G401400 chr6B 87.571 177 18 3 2860 3034 485871978 485872152 8.150000e-48 202.0
13 TraesCS2A01G401400 chr6B 84.974 193 28 1 3616 3807 485873584 485873776 1.360000e-45 195.0
14 TraesCS2A01G401400 chr6A 85.492 193 27 1 3616 3807 473743313 473743121 2.930000e-47 200.0
15 TraesCS2A01G401400 chr6A 86.857 175 21 2 2860 3033 473744906 473744733 1.360000e-45 195.0


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 TraesCS2A01G401400 chr2A 655029339 655034143 4804 False 8874.000000 8874 100.000000 1 4805 1 chr2A.!!$F1 4804
1 TraesCS2A01G401400 chr2D 511915272 511920858 5586 False 2160.666667 4623 91.367667 1 4632 3 chr2D.!!$F1 4631
2 TraesCS2A01G401400 chr2B 601175272 601181642 6370 False 743.800000 1565 90.853167 786 4805 6 chr2B.!!$F1 4019

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
189 190 0.181114 TGAGGGGGATGCGATGAAAG 59.819 55.0 0.00 0.00 0.00 2.62 F
201 214 0.459585 GATGAAAGGTGTCGCGCCTA 60.460 55.0 0.00 0.00 44.35 3.93 F
402 415 0.537188 TCCGAGTTTCCAGATCCAGC 59.463 55.0 0.00 0.00 0.00 4.85 F
1683 1723 0.597637 CGTCAAGTAGCCCATAGCCG 60.598 60.0 0.00 0.00 45.47 5.52 F
1928 1971 0.111253 AAGCAAGGAAGGTGGAGTGG 59.889 55.0 0.00 0.00 0.00 4.00 F
2823 2878 0.608130 ACTCGTATGCCAGTCTTGCA 59.392 50.0 0.37 0.37 43.97 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1611 1651 0.110823 CCGGTTTCGCTGAACTTTCG 60.111 55.000 0.00 0.00 34.56 3.46 R
1905 1948 0.250901 TCCACCTTCCTTGCTTCAGC 60.251 55.000 0.00 0.00 42.50 4.26 R
1906 1949 1.072965 ACTCCACCTTCCTTGCTTCAG 59.927 52.381 0.00 0.00 0.00 3.02 R
3085 3140 0.535780 CAGGTTCAGAGGTGCAGCAA 60.536 55.000 19.63 0.00 0.00 3.91 R
3087 3142 0.536006 AACAGGTTCAGAGGTGCAGC 60.536 55.000 8.11 8.11 0.00 5.25 R
4668 7578 0.036732 TGCGGCAGTTCCTCTCAAAT 59.963 50.000 0.00 0.00 0.00 2.32 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
67 68 0.732880 CACTAGCTGGAACGACCACG 60.733 60.000 3.17 0.00 44.64 4.94
87 88 2.113139 CACACCACCACCACCCTC 59.887 66.667 0.00 0.00 0.00 4.30
90 91 3.556306 ACCACCACCACCCTCGTG 61.556 66.667 0.00 0.00 39.91 4.35
113 114 4.436998 GAGACCCGCACGACCCAG 62.437 72.222 0.00 0.00 0.00 4.45
184 185 1.528824 CTTGTGAGGGGGATGCGAT 59.471 57.895 0.00 0.00 0.00 4.58
186 187 1.271127 TTGTGAGGGGGATGCGATGA 61.271 55.000 0.00 0.00 0.00 2.92
187 188 1.271127 TGTGAGGGGGATGCGATGAA 61.271 55.000 0.00 0.00 0.00 2.57
189 190 0.181114 TGAGGGGGATGCGATGAAAG 59.819 55.000 0.00 0.00 0.00 2.62
201 214 0.459585 GATGAAAGGTGTCGCGCCTA 60.460 55.000 0.00 0.00 44.35 3.93
230 243 1.079503 GCCGACAAAGAATCGAGCTT 58.920 50.000 0.00 0.00 42.25 3.74
245 258 2.978010 CTTCCACCCCACACGTGC 60.978 66.667 17.22 0.00 0.00 5.34
280 293 2.278596 CGTATCGTCGCCACCCAG 60.279 66.667 0.00 0.00 0.00 4.45
303 316 4.029809 GGCCAACCACGTAGCCCT 62.030 66.667 0.00 0.00 39.60 5.19
325 338 4.988598 CCACCTTGCGCCACGACT 62.989 66.667 4.18 0.00 0.00 4.18
329 342 2.661537 CTTGCGCCACGACTGACA 60.662 61.111 4.18 0.00 0.00 3.58
356 369 1.745489 GCCACCTCCACGCTAAAGG 60.745 63.158 0.00 0.00 36.21 3.11
367 380 3.202706 CTAAAGGGAAGCCGCCGC 61.203 66.667 0.00 0.00 0.00 6.53
368 381 4.789123 TAAAGGGAAGCCGCCGCC 62.789 66.667 0.00 0.00 34.57 6.13
402 415 0.537188 TCCGAGTTTCCAGATCCAGC 59.463 55.000 0.00 0.00 0.00 4.85
423 436 3.883744 AACGCGTTGCCCTCCTCTG 62.884 63.158 26.00 0.00 0.00 3.35
445 458 1.402456 CGAGGAAACGAACACGAGGAT 60.402 52.381 0.00 0.00 35.09 3.24
534 547 1.893786 CGAGACAGGAGGGAAGGTG 59.106 63.158 0.00 0.00 0.00 4.00
581 594 3.782443 GGATTCCGGCGTGTCCCT 61.782 66.667 6.01 0.00 0.00 4.20
583 596 1.067582 GATTCCGGCGTGTCCCTAG 59.932 63.158 6.01 0.00 0.00 3.02
595 608 1.621377 TCCCTAGAGGAGAGGTGGC 59.379 63.158 0.00 0.00 40.93 5.01
737 752 5.278858 CGCTCTTATATTTCCTTACGGAGGT 60.279 44.000 6.95 0.00 46.39 3.85
865 896 1.002134 CTGGTCCAACCCGCATTCT 60.002 57.895 0.00 0.00 37.50 2.40
900 931 1.132657 GGGGAGGAAAAGGGGGAAAAA 60.133 52.381 0.00 0.00 0.00 1.94
943 974 1.689258 CCAACCCATCCCAATTCCCTC 60.689 57.143 0.00 0.00 0.00 4.30
1555 1595 4.301072 TTGGAGGGATTTGACAAGTAGG 57.699 45.455 0.00 0.00 0.00 3.18
1611 1651 3.568430 CCCTGGTTGTTTCAAGTTACCTC 59.432 47.826 0.00 0.00 0.00 3.85
1647 1687 7.201291 GCGAAACCGGTTTATGAAAGTTTAATC 60.201 37.037 31.70 13.49 32.11 1.75
1651 1691 7.404481 ACCGGTTTATGAAAGTTTAATCCCTA 58.596 34.615 0.00 0.00 0.00 3.53
1652 1692 7.889600 ACCGGTTTATGAAAGTTTAATCCCTAA 59.110 33.333 0.00 0.00 0.00 2.69
1677 1717 3.745799 TGATTTTTCGTCAAGTAGCCCA 58.254 40.909 0.00 0.00 0.00 5.36
1683 1723 0.597637 CGTCAAGTAGCCCATAGCCG 60.598 60.000 0.00 0.00 45.47 5.52
1707 1747 6.419710 CGCGGTAGTGATAACTTTGATTGATA 59.580 38.462 0.00 0.00 0.00 2.15
1747 1788 8.218338 AGAAACTTTGATTGATATAGTGCCTG 57.782 34.615 0.00 0.00 0.00 4.85
1785 1826 5.324409 AGGAAAGACAGACCATTGCATAAA 58.676 37.500 0.00 0.00 0.00 1.40
1786 1827 5.774690 AGGAAAGACAGACCATTGCATAAAA 59.225 36.000 0.00 0.00 0.00 1.52
1823 1864 3.790089 ACAGTTCTCTACCCCCAAAAG 57.210 47.619 0.00 0.00 0.00 2.27
1877 1920 5.192327 CCATGGATGGTTTCTTAATCTGC 57.808 43.478 5.56 0.00 43.05 4.26
1878 1921 4.646040 CCATGGATGGTTTCTTAATCTGCA 59.354 41.667 5.56 0.00 43.05 4.41
1887 1930 6.265196 TGGTTTCTTAATCTGCAATGTTCAGT 59.735 34.615 0.00 0.00 33.48 3.41
1889 1932 5.300969 TCTTAATCTGCAATGTTCAGTGC 57.699 39.130 16.51 16.51 41.29 4.40
1890 1933 5.005740 TCTTAATCTGCAATGTTCAGTGCT 58.994 37.500 22.06 8.01 41.48 4.40
1891 1934 3.570926 AATCTGCAATGTTCAGTGCTG 57.429 42.857 22.06 21.01 41.48 4.41
1892 1935 2.259266 TCTGCAATGTTCAGTGCTGA 57.741 45.000 23.00 23.00 43.68 4.26
1893 1936 2.574450 TCTGCAATGTTCAGTGCTGAA 58.426 42.857 24.00 10.26 46.27 3.02
1923 1966 1.246737 GGCTGAAGCAAGGAAGGTGG 61.247 60.000 4.43 0.00 44.36 4.61
1928 1971 0.111253 AAGCAAGGAAGGTGGAGTGG 59.889 55.000 0.00 0.00 0.00 4.00
1939 1984 2.505819 AGGTGGAGTGGATTCATGGTAC 59.494 50.000 0.00 0.00 0.00 3.34
1983 2028 7.554835 TGTGAAGTTTAGTTTGGTCTGTTATGT 59.445 33.333 0.00 0.00 0.00 2.29
1986 2031 6.002082 AGTTTAGTTTGGTCTGTTATGTCCC 58.998 40.000 0.00 0.00 0.00 4.46
2114 2162 7.147742 TGGCATAAGTTTCTCTTCCTTGTTTTT 60.148 33.333 0.00 0.00 37.56 1.94
2129 2177 7.759465 TCCTTGTTTTTATGACACGTTTTGTA 58.241 30.769 0.00 0.00 39.17 2.41
2139 2187 3.660865 ACACGTTTTGTATGTCTCCCTC 58.339 45.455 0.00 0.00 36.32 4.30
2153 2201 1.548269 CTCCCTCTTTCTTCTGCTCGT 59.452 52.381 0.00 0.00 0.00 4.18
2184 2233 7.337689 ACATGCAGTGATTATTAGTGTCACATT 59.662 33.333 5.62 0.00 43.51 2.71
2206 2255 4.661222 TGGTTGGTGTATTCATGATGTGT 58.339 39.130 0.00 0.00 0.00 3.72
2422 2476 1.591768 GGGGGTGAAGAGGTTATCCA 58.408 55.000 0.00 0.00 35.89 3.41
2514 2568 8.786826 TTTCTTCTGTTCGGTATCATAAACAT 57.213 30.769 0.00 0.00 31.73 2.71
2521 2575 8.735303 TGTTCGGTATCATAAACATGTTTTTG 57.265 30.769 27.66 27.00 34.34 2.44
2522 2576 8.353684 TGTTCGGTATCATAAACATGTTTTTGT 58.646 29.630 29.09 21.78 34.56 2.83
2692 2746 6.553953 TCAGGTATGGCTTTCAAGTATGTA 57.446 37.500 0.00 0.00 0.00 2.29
2701 2755 6.655848 TGGCTTTCAAGTATGTAAAATACGGT 59.344 34.615 0.00 0.00 0.00 4.83
2725 2780 8.660373 GGTGATACAATTATAGATGCTTGCTAC 58.340 37.037 0.00 0.00 0.00 3.58
2726 2781 8.376203 GTGATACAATTATAGATGCTTGCTACG 58.624 37.037 0.00 0.00 0.00 3.51
2727 2782 8.088365 TGATACAATTATAGATGCTTGCTACGT 58.912 33.333 0.00 0.00 0.00 3.57
2728 2783 9.569167 GATACAATTATAGATGCTTGCTACGTA 57.431 33.333 0.00 0.00 0.00 3.57
2739 2794 9.397280 AGATGCTTGCTACGTATATAATCTAGA 57.603 33.333 0.00 0.00 0.00 2.43
2741 2796 9.790389 ATGCTTGCTACGTATATAATCTAGAAC 57.210 33.333 0.00 0.00 0.00 3.01
2742 2797 8.789762 TGCTTGCTACGTATATAATCTAGAACA 58.210 33.333 0.00 0.00 0.00 3.18
2743 2798 9.622004 GCTTGCTACGTATATAATCTAGAACAA 57.378 33.333 0.00 0.00 0.00 2.83
2784 2839 6.975772 GTCATACTGTTGATTCTCCTACAGAC 59.024 42.308 11.22 0.00 40.24 3.51
2816 2871 2.348666 GCAGTTAACACTCGTATGCCAG 59.651 50.000 8.61 0.00 0.00 4.85
2823 2878 0.608130 ACTCGTATGCCAGTCTTGCA 59.392 50.000 0.37 0.37 43.97 4.08
3044 3099 4.713553 TGCAGTAAGTTTTCATGTCCTCA 58.286 39.130 0.00 0.00 0.00 3.86
3054 3109 5.964958 TTTCATGTCCTCATCTTTTGGTC 57.035 39.130 0.00 0.00 31.15 4.02
3066 3121 4.508461 TCTTTTGGTCATGCATGTCTTG 57.492 40.909 25.43 10.92 0.00 3.02
3085 3140 1.005805 TGGCCCTAACAATGCATGAGT 59.994 47.619 0.00 0.00 0.00 3.41
3087 3142 2.159198 GGCCCTAACAATGCATGAGTTG 60.159 50.000 21.58 11.16 0.00 3.16
3104 3159 0.535780 TTGCTGCACCTCTGAACCTG 60.536 55.000 0.00 0.00 0.00 4.00
3130 3185 7.303182 TCGATTATACTTTGGACCATCTCAT 57.697 36.000 0.00 0.00 0.00 2.90
3138 3193 6.586344 ACTTTGGACCATCTCATGTAGTATG 58.414 40.000 0.00 0.00 0.00 2.39
3139 3194 6.156949 ACTTTGGACCATCTCATGTAGTATGT 59.843 38.462 0.00 0.00 0.00 2.29
3142 3197 6.582636 TGGACCATCTCATGTAGTATGTTTC 58.417 40.000 0.00 0.00 0.00 2.78
3153 3208 8.817100 TCATGTAGTATGTTTCGTTCATCATTC 58.183 33.333 0.00 0.00 0.00 2.67
3199 3254 6.673537 AGTCAATGGGATGGAATAAAACCATT 59.326 34.615 0.00 0.00 46.48 3.16
3234 3290 8.023021 TGGTCAGCTCATACTAATGAAATACT 57.977 34.615 0.00 0.00 41.57 2.12
3269 3325 6.098409 TGCACTTAGTTATTGGTTTGGGAAAA 59.902 34.615 0.00 0.00 0.00 2.29
3278 3334 9.093970 GTTATTGGTTTGGGAAAATATGTTAGC 57.906 33.333 0.00 0.00 0.00 3.09
3292 4575 3.643199 TGTTAGCCCATGCATGACTTA 57.357 42.857 28.31 15.05 41.13 2.24
3298 4581 4.599041 AGCCCATGCATGACTTAAGTTTA 58.401 39.130 28.31 2.75 41.13 2.01
3299 4582 4.641989 AGCCCATGCATGACTTAAGTTTAG 59.358 41.667 28.31 6.24 41.13 1.85
3300 4583 4.399303 GCCCATGCATGACTTAAGTTTAGT 59.601 41.667 28.31 0.00 37.47 2.24
3301 4584 5.449177 GCCCATGCATGACTTAAGTTTAGTC 60.449 44.000 28.31 13.82 38.97 2.59
3302 4585 5.882557 CCCATGCATGACTTAAGTTTAGTCT 59.117 40.000 28.31 6.04 41.99 3.24
3308 4591 7.063426 TGCATGACTTAAGTTTAGTCTTCATCG 59.937 37.037 19.64 6.24 41.99 3.84
3396 4679 2.618709 GCTTCTGTAAAACCTGTGCACT 59.381 45.455 19.41 0.00 0.00 4.40
3411 4694 5.371526 CTGTGCACTCCAGGATATAACATT 58.628 41.667 19.41 0.00 0.00 2.71
3412 4695 5.125356 TGTGCACTCCAGGATATAACATTG 58.875 41.667 19.41 0.00 0.00 2.82
3435 4718 5.585445 TGTTTTCCGCACTACTTTTCTGTTA 59.415 36.000 0.00 0.00 0.00 2.41
3439 4722 4.153475 TCCGCACTACTTTTCTGTTATTGC 59.847 41.667 0.00 0.00 0.00 3.56
3452 4736 3.936453 CTGTTATTGCGCTACCTGGTTTA 59.064 43.478 9.73 0.00 0.00 2.01
3463 4747 4.876679 GCTACCTGGTTTATCTTCCAACTC 59.123 45.833 3.84 0.00 33.06 3.01
3464 4748 4.302559 ACCTGGTTTATCTTCCAACTCC 57.697 45.455 0.00 0.00 33.06 3.85
3467 4751 2.026636 TGGTTTATCTTCCAACTCCCGG 60.027 50.000 0.00 0.00 0.00 5.73
3473 4757 2.124507 CTTCCAACTCCCGGCAGGAA 62.125 60.000 3.68 4.35 46.94 3.36
3474 4758 2.359975 CCAACTCCCGGCAGGAAC 60.360 66.667 3.68 0.00 46.94 3.62
3475 4759 2.429930 CAACTCCCGGCAGGAACA 59.570 61.111 3.68 0.00 46.94 3.18
3476 4760 1.002134 CAACTCCCGGCAGGAACAT 60.002 57.895 3.68 0.00 46.94 2.71
3477 4761 0.609131 CAACTCCCGGCAGGAACATT 60.609 55.000 3.68 0.00 46.94 2.71
3478 4762 0.112412 AACTCCCGGCAGGAACATTT 59.888 50.000 3.68 0.00 46.94 2.32
3479 4763 0.988832 ACTCCCGGCAGGAACATTTA 59.011 50.000 3.68 0.00 46.94 1.40
3480 4764 1.564348 ACTCCCGGCAGGAACATTTAT 59.436 47.619 3.68 0.00 46.94 1.40
3481 4765 2.025321 ACTCCCGGCAGGAACATTTATT 60.025 45.455 3.68 0.00 46.94 1.40
3482 4766 2.358898 CTCCCGGCAGGAACATTTATTG 59.641 50.000 3.68 0.00 46.94 1.90
3483 4767 1.202405 CCCGGCAGGAACATTTATTGC 60.202 52.381 3.68 0.00 41.02 3.56
3484 4768 1.476085 CCGGCAGGAACATTTATTGCA 59.524 47.619 0.00 0.00 41.02 4.08
3485 4769 2.480073 CCGGCAGGAACATTTATTGCAG 60.480 50.000 0.00 0.00 41.02 4.41
3486 4770 2.543641 GGCAGGAACATTTATTGCAGC 58.456 47.619 0.00 0.00 36.53 5.25
3487 4771 2.543641 GCAGGAACATTTATTGCAGCC 58.456 47.619 0.00 0.00 34.99 4.85
3488 4772 2.094078 GCAGGAACATTTATTGCAGCCA 60.094 45.455 0.00 0.00 34.99 4.75
3489 4773 3.617045 GCAGGAACATTTATTGCAGCCAA 60.617 43.478 0.00 0.00 34.99 4.52
3490 4774 4.761975 CAGGAACATTTATTGCAGCCAAT 58.238 39.130 0.00 0.00 43.74 3.16
3491 4775 4.569162 CAGGAACATTTATTGCAGCCAATG 59.431 41.667 10.63 10.63 41.58 2.82
3502 4786 4.016838 GCCAATGCTGCCAACCTA 57.983 55.556 0.00 0.00 33.53 3.08
3503 4787 2.508361 GCCAATGCTGCCAACCTAT 58.492 52.632 0.00 0.00 33.53 2.57
3504 4788 1.691196 GCCAATGCTGCCAACCTATA 58.309 50.000 0.00 0.00 33.53 1.31
3505 4789 2.242043 GCCAATGCTGCCAACCTATAT 58.758 47.619 0.00 0.00 33.53 0.86
3506 4790 3.420893 GCCAATGCTGCCAACCTATATA 58.579 45.455 0.00 0.00 33.53 0.86
3507 4791 3.826157 GCCAATGCTGCCAACCTATATAA 59.174 43.478 0.00 0.00 33.53 0.98
3508 4792 4.082571 GCCAATGCTGCCAACCTATATAAG 60.083 45.833 0.00 0.00 33.53 1.73
3509 4793 4.082571 CCAATGCTGCCAACCTATATAAGC 60.083 45.833 0.00 0.00 0.00 3.09
3510 4794 3.140325 TGCTGCCAACCTATATAAGCC 57.860 47.619 0.00 0.00 0.00 4.35
3511 4795 2.441375 TGCTGCCAACCTATATAAGCCA 59.559 45.455 0.00 0.00 0.00 4.75
3512 4796 3.077359 GCTGCCAACCTATATAAGCCAG 58.923 50.000 0.00 0.00 0.00 4.85
3513 4797 3.496870 GCTGCCAACCTATATAAGCCAGT 60.497 47.826 0.00 0.00 0.00 4.00
3514 4798 4.718961 CTGCCAACCTATATAAGCCAGTT 58.281 43.478 0.00 0.00 0.00 3.16
3515 4799 4.460263 TGCCAACCTATATAAGCCAGTTG 58.540 43.478 0.00 0.00 35.51 3.16
3516 4800 4.080015 TGCCAACCTATATAAGCCAGTTGT 60.080 41.667 0.00 0.00 34.26 3.32
3517 4801 4.887655 GCCAACCTATATAAGCCAGTTGTT 59.112 41.667 0.00 0.00 34.26 2.83
3518 4802 5.221048 GCCAACCTATATAAGCCAGTTGTTG 60.221 44.000 0.00 0.00 34.26 3.33
3519 4803 5.221048 CCAACCTATATAAGCCAGTTGTTGC 60.221 44.000 0.00 0.00 34.26 4.17
3520 4804 5.110814 ACCTATATAAGCCAGTTGTTGCA 57.889 39.130 0.00 0.00 0.00 4.08
3521 4805 5.694995 ACCTATATAAGCCAGTTGTTGCAT 58.305 37.500 0.00 0.00 0.00 3.96
3522 4806 6.837312 ACCTATATAAGCCAGTTGTTGCATA 58.163 36.000 0.00 0.00 0.00 3.14
3523 4807 7.287061 ACCTATATAAGCCAGTTGTTGCATAA 58.713 34.615 0.00 0.00 0.00 1.90
3524 4808 7.445402 ACCTATATAAGCCAGTTGTTGCATAAG 59.555 37.037 0.00 0.00 0.00 1.73
3525 4809 7.661437 CCTATATAAGCCAGTTGTTGCATAAGA 59.339 37.037 0.00 0.00 0.00 2.10
3526 4810 7.880160 ATATAAGCCAGTTGTTGCATAAGAA 57.120 32.000 0.00 0.00 0.00 2.52
3527 4811 6.780457 ATAAGCCAGTTGTTGCATAAGAAT 57.220 33.333 0.00 0.00 0.00 2.40
3528 4812 5.473066 AAGCCAGTTGTTGCATAAGAATT 57.527 34.783 0.00 0.00 0.00 2.17
3529 4813 5.473066 AGCCAGTTGTTGCATAAGAATTT 57.527 34.783 0.00 0.00 0.00 1.82
3530 4814 5.857268 AGCCAGTTGTTGCATAAGAATTTT 58.143 33.333 0.00 0.00 0.00 1.82
3531 4815 6.991938 AGCCAGTTGTTGCATAAGAATTTTA 58.008 32.000 0.00 0.00 0.00 1.52
3532 4816 7.614494 AGCCAGTTGTTGCATAAGAATTTTAT 58.386 30.769 0.00 0.00 0.00 1.40
3533 4817 7.546667 AGCCAGTTGTTGCATAAGAATTTTATG 59.453 33.333 12.35 12.35 35.92 1.90
3534 4818 7.545265 GCCAGTTGTTGCATAAGAATTTTATGA 59.455 33.333 17.35 6.54 35.06 2.15
3535 4819 9.421806 CCAGTTGTTGCATAAGAATTTTATGAA 57.578 29.630 17.35 9.30 35.06 2.57
3560 4844 2.682155 TGCACCATGCTGTATCGTTA 57.318 45.000 2.02 0.00 45.31 3.18
3570 4854 3.243737 TGCTGTATCGTTAGCATAGGTGG 60.244 47.826 0.00 0.00 44.36 4.61
3586 4870 6.456988 GCATAGGTGGCGCTTTATGATATTAC 60.457 42.308 19.78 4.82 0.00 1.89
3589 4873 5.012148 AGGTGGCGCTTTATGATATTACTCT 59.988 40.000 7.64 0.00 0.00 3.24
3590 4874 5.120830 GGTGGCGCTTTATGATATTACTCTG 59.879 44.000 7.64 0.00 0.00 3.35
3592 4876 6.591834 GTGGCGCTTTATGATATTACTCTGAT 59.408 38.462 7.64 0.00 0.00 2.90
3714 4999 1.135199 CATTTCCACTGTGCCTGCATC 60.135 52.381 1.29 0.00 0.00 3.91
3813 5098 6.665992 AGCGAGGAAGTATAAATGTATCCA 57.334 37.500 0.00 0.00 0.00 3.41
3836 5121 0.617935 TGAGAATGCCATCGGTTCCA 59.382 50.000 0.00 0.00 0.00 3.53
3839 5124 0.455815 GAATGCCATCGGTTCCAACC 59.544 55.000 0.00 0.00 45.76 3.77
4044 5329 4.649674 TGAGCGATTCATACTATATCCCCC 59.350 45.833 0.00 0.00 0.00 5.40
4081 5366 2.437200 TCGGGCTTGCAAAATTCTTG 57.563 45.000 0.00 0.00 0.00 3.02
4121 5415 4.913355 TGATGAAAGAGGCCAGGGATATAA 59.087 41.667 5.01 0.00 0.00 0.98
4136 5430 5.253096 AGGGATATAATTCCGGGCTGTAAAT 59.747 40.000 0.00 0.00 36.58 1.40
4217 5511 4.084328 CGCTTTTCTTGACTGGTACTCTTG 60.084 45.833 0.00 0.00 0.00 3.02
4270 6910 1.380380 GGTTGCCATGGAAGGGAGG 60.380 63.158 18.40 0.00 43.46 4.30
4333 6973 0.109132 CATCGGGAAAAAGCAGTGGC 60.109 55.000 0.00 0.00 41.61 5.01
4362 7008 3.497262 GGTCGAGTGTTCAGTAAAAAGGG 59.503 47.826 0.00 0.00 0.00 3.95
4437 7089 0.459237 GTCTGCTGGTCTGTGATCCG 60.459 60.000 0.00 0.00 0.00 4.18
4442 7094 1.892819 CTGGTCTGTGATCCGGCAGT 61.893 60.000 0.00 0.00 34.57 4.40
4453 7105 6.946340 TGTGATCCGGCAGTATTGAATATAT 58.054 36.000 0.00 0.00 0.00 0.86
4454 7106 7.041721 TGTGATCCGGCAGTATTGAATATATC 58.958 38.462 0.00 0.00 0.00 1.63
4455 7107 6.480320 GTGATCCGGCAGTATTGAATATATCC 59.520 42.308 0.00 0.00 0.00 2.59
4456 7108 6.156083 TGATCCGGCAGTATTGAATATATCCA 59.844 38.462 0.00 0.00 0.00 3.41
4462 7114 5.882557 GCAGTATTGAATATATCCACCCAGG 59.117 44.000 0.00 0.00 39.47 4.45
4503 7155 0.111446 TCAAATCACCTCCCCGCAAA 59.889 50.000 0.00 0.00 0.00 3.68
4545 7197 0.393077 ACCTCCTTTGTGGACAGACG 59.607 55.000 0.00 0.00 40.56 4.18
4546 7198 0.679505 CCTCCTTTGTGGACAGACGA 59.320 55.000 0.00 0.00 40.56 4.20
4547 7199 1.605712 CCTCCTTTGTGGACAGACGAC 60.606 57.143 0.00 0.00 40.56 4.34
4548 7200 1.068588 CTCCTTTGTGGACAGACGACA 59.931 52.381 0.00 0.00 40.56 4.35
4549 7201 1.202486 TCCTTTGTGGACAGACGACAC 60.202 52.381 0.00 0.00 40.56 3.67
4604 7257 0.177604 CACCAGATGAGCAGGAGACC 59.822 60.000 0.00 0.00 0.00 3.85
4632 7542 7.984050 ACCATCGATGACCAGATATATGAATTC 59.016 37.037 26.86 0.00 0.00 2.17
4633 7543 7.983484 CCATCGATGACCAGATATATGAATTCA 59.017 37.037 26.86 11.26 0.00 2.57
4636 7546 9.948964 TCGATGACCAGATATATGAATTCATTT 57.051 29.630 25.26 19.48 37.76 2.32
4663 7573 9.357161 AGATCATTATACTTTAGGAGAGAACGT 57.643 33.333 0.00 0.00 0.00 3.99
4679 7589 6.055588 AGAGAACGTCAAAATTTGAGAGGAA 58.944 36.000 8.88 0.00 41.01 3.36
4684 7594 4.550422 GTCAAAATTTGAGAGGAACTGCC 58.450 43.478 8.88 0.00 41.01 4.85
4688 7598 0.603707 TTTGAGAGGAACTGCCGCAG 60.604 55.000 19.08 19.08 41.55 5.18
4708 7619 5.111989 GCAGGGAAAATATTCAAAAGGAGC 58.888 41.667 0.00 0.00 37.29 4.70
4709 7620 5.664457 CAGGGAAAATATTCAAAAGGAGCC 58.336 41.667 0.00 0.00 37.29 4.70
4710 7621 4.402474 AGGGAAAATATTCAAAAGGAGCCG 59.598 41.667 0.00 0.00 37.29 5.52
4712 7623 4.441495 GGAAAATATTCAAAAGGAGCCGGG 60.441 45.833 2.18 0.00 37.29 5.73
4713 7624 3.382083 AATATTCAAAAGGAGCCGGGT 57.618 42.857 5.45 5.45 0.00 5.28
4744 7655 4.883300 GTACGCCGGTCGCTCTCG 62.883 72.222 16.48 6.05 43.23 4.04
4762 7673 2.540931 CTCGCTACTAGTCTTCCGTCTC 59.459 54.545 0.00 0.00 0.00 3.36
4763 7674 1.258458 CGCTACTAGTCTTCCGTCTCG 59.742 57.143 0.00 0.00 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 2.044848 TGTGGTGTTGGGCGTTGT 60.045 55.556 0.00 0.00 0.00 3.32
28 29 1.752310 TGGCAGTGGTGTGGTGTTG 60.752 57.895 0.00 0.00 0.00 3.33
67 68 2.203294 GGTGGTGGTGGTGTGACC 60.203 66.667 0.00 0.00 39.22 4.02
113 114 3.329542 TTGCTCCGGTGCCCAGATC 62.330 63.158 24.73 0.00 0.00 2.75
120 121 4.947147 TGGTGGTTGCTCCGGTGC 62.947 66.667 21.41 21.41 39.52 5.01
125 126 0.250166 ACTACGTTGGTGGTTGCTCC 60.250 55.000 0.00 0.00 33.63 4.70
128 129 1.281656 GCACTACGTTGGTGGTTGC 59.718 57.895 18.39 8.21 35.45 4.17
161 162 1.930656 ATCCCCCTCACAAGGTGGG 60.931 63.158 10.27 10.27 46.81 4.61
168 169 1.271127 TTCATCGCATCCCCCTCACA 61.271 55.000 0.00 0.00 0.00 3.58
174 175 0.394352 ACACCTTTCATCGCATCCCC 60.394 55.000 0.00 0.00 0.00 4.81
184 185 1.080093 CTAGGCGCGACACCTTTCA 60.080 57.895 17.71 0.00 38.81 2.69
186 187 2.264794 CCTAGGCGCGACACCTTT 59.735 61.111 17.71 0.00 38.81 3.11
187 188 4.452733 GCCTAGGCGCGACACCTT 62.453 66.667 20.16 0.00 38.81 3.50
189 190 4.530857 ATGCCTAGGCGCGACACC 62.531 66.667 28.28 3.27 45.51 4.16
212 225 1.661112 GGAAGCTCGATTCTTTGTCGG 59.339 52.381 0.00 0.00 39.45 4.79
215 228 2.427506 GGTGGAAGCTCGATTCTTTGT 58.572 47.619 0.00 0.00 0.00 2.83
230 243 4.248842 CAGCACGTGTGGGGTGGA 62.249 66.667 18.38 0.00 35.94 4.02
265 278 3.845259 GGCTGGGTGGCGACGATA 61.845 66.667 0.00 0.00 0.00 2.92
269 282 2.125106 CTAAGGCTGGGTGGCGAC 60.125 66.667 0.00 0.00 46.88 5.19
284 297 2.662070 GGGCTACGTGGTTGGCCTA 61.662 63.158 13.80 0.00 46.47 3.93
303 316 3.318384 TGGCGCAAGGTGGAGCTA 61.318 61.111 10.83 0.00 33.80 3.32
325 338 4.314440 GTGGCAGCTCGGGTGTCA 62.314 66.667 6.33 6.33 43.40 3.58
402 415 4.025401 GGAGGGCAACGCGTTGTG 62.025 66.667 41.95 26.81 42.31 3.33
423 436 1.615107 CTCGTGTTCGTTTCCTCGCC 61.615 60.000 0.00 0.00 38.33 5.54
428 441 1.337447 TGGATCCTCGTGTTCGTTTCC 60.337 52.381 14.23 0.00 38.33 3.13
525 538 2.287194 CCCCATCCCACCTTCCCT 60.287 66.667 0.00 0.00 0.00 4.20
581 594 1.754621 CTGCGCCACCTCTCCTCTA 60.755 63.158 4.18 0.00 0.00 2.43
583 596 4.154347 CCTGCGCCACCTCTCCTC 62.154 72.222 4.18 0.00 0.00 3.71
594 607 2.825836 CATTGACTCCCCCTGCGC 60.826 66.667 0.00 0.00 0.00 6.09
595 608 1.746615 CACATTGACTCCCCCTGCG 60.747 63.158 0.00 0.00 0.00 5.18
684 699 3.834813 TCTATGCGCTCCTCTCCATAAAT 59.165 43.478 9.73 0.00 0.00 1.40
727 742 5.595952 ACCTGGTTATTACTACCTCCGTAAG 59.404 44.000 0.00 0.00 36.60 2.34
730 745 3.703052 CACCTGGTTATTACTACCTCCGT 59.297 47.826 0.00 0.00 36.60 4.69
865 896 0.266453 TCCCCCGGTTCTATGATGGA 59.734 55.000 0.00 0.00 0.00 3.41
900 931 2.559231 GACTGGAAGAGTCCTTTCTCGT 59.441 50.000 0.00 0.00 44.95 4.18
995 1026 4.864334 GGCTGCTGGACATCGGGG 62.864 72.222 0.00 0.00 0.00 5.73
1023 1054 3.760035 GGCGCCGAGTCAAGGAGA 61.760 66.667 12.58 0.00 0.00 3.71
1473 1513 2.584418 CTGGCATCCTCGTCGCTG 60.584 66.667 0.00 0.00 0.00 5.18
1555 1595 5.725362 ACAGCTTAGAAATGTCCACTACTC 58.275 41.667 0.00 0.00 0.00 2.59
1605 1645 3.374220 TTCGCTGAACTTTCGAGGTAA 57.626 42.857 0.00 0.00 33.56 2.85
1611 1651 0.110823 CCGGTTTCGCTGAACTTTCG 60.111 55.000 0.00 0.00 34.56 3.46
1647 1687 9.341899 CTACTTGACGAAAAATCAATTTTAGGG 57.658 33.333 1.36 0.00 41.27 3.53
1651 1691 6.645003 GGGCTACTTGACGAAAAATCAATTTT 59.355 34.615 0.00 0.00 43.85 1.82
1652 1692 6.156519 GGGCTACTTGACGAAAAATCAATTT 58.843 36.000 0.00 0.00 35.57 1.82
1677 1717 2.236766 AGTTATCACTACCGCGGCTAT 58.763 47.619 28.58 13.95 0.00 2.97
1683 1723 6.604735 ATCAATCAAAGTTATCACTACCGC 57.395 37.500 0.00 0.00 30.68 5.68
1723 1763 7.912250 CACAGGCACTATATCAATCAAAGTTTC 59.088 37.037 0.00 0.00 36.02 2.78
1747 1788 1.448985 TTCCTTGTAGAATGGCGCAC 58.551 50.000 10.83 0.00 0.00 5.34
1785 1826 5.593679 ACTGTATAATACTGACACGGCTT 57.406 39.130 0.00 0.00 0.00 4.35
1786 1827 5.360144 AGAACTGTATAATACTGACACGGCT 59.640 40.000 0.00 0.00 0.00 5.52
1823 1864 7.119262 ACAAACATACTGTTGCAGGACTATAAC 59.881 37.037 1.08 0.00 40.14 1.89
1896 1939 2.699846 TCCTTGCTTCAGCCACATTTTT 59.300 40.909 0.00 0.00 41.18 1.94
1897 1940 2.318908 TCCTTGCTTCAGCCACATTTT 58.681 42.857 0.00 0.00 41.18 1.82
1898 1941 1.999648 TCCTTGCTTCAGCCACATTT 58.000 45.000 0.00 0.00 41.18 2.32
1899 1942 1.891150 CTTCCTTGCTTCAGCCACATT 59.109 47.619 0.00 0.00 41.18 2.71
1900 1943 1.542492 CTTCCTTGCTTCAGCCACAT 58.458 50.000 0.00 0.00 41.18 3.21
1901 1944 0.538057 CCTTCCTTGCTTCAGCCACA 60.538 55.000 0.00 0.00 41.18 4.17
1902 1945 0.538287 ACCTTCCTTGCTTCAGCCAC 60.538 55.000 0.00 0.00 41.18 5.01
1903 1946 0.538057 CACCTTCCTTGCTTCAGCCA 60.538 55.000 0.00 0.00 41.18 4.75
1904 1947 1.246737 CCACCTTCCTTGCTTCAGCC 61.247 60.000 0.00 0.00 41.18 4.85
1905 1948 0.250901 TCCACCTTCCTTGCTTCAGC 60.251 55.000 0.00 0.00 42.50 4.26
1906 1949 1.072965 ACTCCACCTTCCTTGCTTCAG 59.927 52.381 0.00 0.00 0.00 3.02
1923 1966 4.744795 ACTCTGTACCATGAATCCACTC 57.255 45.455 0.00 0.00 0.00 3.51
1928 1971 9.817809 TGTATTTAGAACTCTGTACCATGAATC 57.182 33.333 0.00 0.00 0.00 2.52
1939 1984 8.594881 ACTTCACAACTGTATTTAGAACTCTG 57.405 34.615 0.00 0.00 0.00 3.35
1983 2028 3.071892 ACACCTAAACAAGATGAACGGGA 59.928 43.478 0.00 0.00 0.00 5.14
1986 2031 6.645415 AGAAGTACACCTAAACAAGATGAACG 59.355 38.462 0.00 0.00 0.00 3.95
2114 2162 5.046878 AGGGAGACATACAAAACGTGTCATA 60.047 40.000 7.39 0.00 43.51 2.15
2129 2177 3.180507 AGCAGAAGAAAGAGGGAGACAT 58.819 45.455 0.00 0.00 0.00 3.06
2139 2187 5.340667 GCATGTTTTAACGAGCAGAAGAAAG 59.659 40.000 0.00 0.00 33.33 2.62
2184 2233 4.661222 ACACATCATGAATACACCAACCA 58.339 39.130 0.00 0.00 0.00 3.67
2218 2267 7.062722 CACTCGTATATGGAATCACATGATGAC 59.937 40.741 0.00 0.00 41.24 3.06
2422 2476 4.410228 ACCAGTATAGTTGAGGTGCATCAT 59.590 41.667 0.00 0.00 0.00 2.45
2482 2536 7.617225 TGATACCGAACAGAAGAAATAAGGAA 58.383 34.615 0.00 0.00 0.00 3.36
2514 2568 5.871524 TGCAAAGCAAGACATAACAAAAACA 59.128 32.000 0.00 0.00 34.76 2.83
2521 2575 2.229784 AGCCTGCAAAGCAAGACATAAC 59.770 45.455 10.73 0.00 38.41 1.89
2522 2576 2.517959 AGCCTGCAAAGCAAGACATAA 58.482 42.857 10.73 0.00 38.41 1.90
2555 2609 2.254546 AGAACACATCAAACGCCAGA 57.745 45.000 0.00 0.00 0.00 3.86
2701 2755 8.088365 ACGTAGCAAGCATCTATAATTGTATCA 58.912 33.333 0.00 0.00 0.00 2.15
2725 2780 8.456471 TGGATCCGTTGTTCTAGATTATATACG 58.544 37.037 7.39 0.00 0.00 3.06
2726 2781 9.790389 CTGGATCCGTTGTTCTAGATTATATAC 57.210 37.037 7.39 0.00 0.00 1.47
2727 2782 9.529823 ACTGGATCCGTTGTTCTAGATTATATA 57.470 33.333 7.39 0.00 0.00 0.86
2728 2783 8.423906 ACTGGATCCGTTGTTCTAGATTATAT 57.576 34.615 7.39 0.00 0.00 0.86
2729 2784 7.834881 ACTGGATCCGTTGTTCTAGATTATA 57.165 36.000 7.39 0.00 0.00 0.98
2730 2785 6.732896 ACTGGATCCGTTGTTCTAGATTAT 57.267 37.500 7.39 0.00 0.00 1.28
2731 2786 6.380274 AGAACTGGATCCGTTGTTCTAGATTA 59.620 38.462 29.82 2.97 44.70 1.75
2732 2787 5.187967 AGAACTGGATCCGTTGTTCTAGATT 59.812 40.000 29.82 16.09 44.70 2.40
2733 2788 4.712337 AGAACTGGATCCGTTGTTCTAGAT 59.288 41.667 29.82 16.34 44.70 1.98
2734 2789 4.082190 CAGAACTGGATCCGTTGTTCTAGA 60.082 45.833 30.09 4.59 44.73 2.43
2735 2790 4.177026 CAGAACTGGATCCGTTGTTCTAG 58.823 47.826 30.09 23.60 44.73 2.43
2736 2791 3.576982 ACAGAACTGGATCCGTTGTTCTA 59.423 43.478 30.09 5.82 44.73 2.10
2737 2792 2.368875 ACAGAACTGGATCCGTTGTTCT 59.631 45.455 27.52 27.52 46.63 3.01
2738 2793 2.480419 CACAGAACTGGATCCGTTGTTC 59.520 50.000 25.11 25.11 39.06 3.18
2739 2794 2.158813 ACACAGAACTGGATCCGTTGTT 60.159 45.455 21.44 18.13 34.19 2.83
2740 2795 1.416401 ACACAGAACTGGATCCGTTGT 59.584 47.619 21.44 16.45 34.19 3.32
2741 2796 2.069273 GACACAGAACTGGATCCGTTG 58.931 52.381 21.44 13.77 34.19 4.10
2742 2797 1.691976 TGACACAGAACTGGATCCGTT 59.308 47.619 17.99 17.99 34.19 4.44
2743 2798 1.338107 TGACACAGAACTGGATCCGT 58.662 50.000 7.39 5.31 34.19 4.69
2744 2799 2.680312 ATGACACAGAACTGGATCCG 57.320 50.000 7.39 4.62 34.19 4.18
2808 2863 5.567138 AACTAATTGCAAGACTGGCATAC 57.433 39.130 5.07 0.00 41.58 2.39
2816 2871 8.968242 CAAAGAAAGGTTAACTAATTGCAAGAC 58.032 33.333 4.94 0.00 0.00 3.01
2823 2878 9.309224 AGTATGGCAAAGAAAGGTTAACTAATT 57.691 29.630 5.42 0.00 0.00 1.40
2887 2942 5.575218 ACGGAATTTGTATTTCGGAATTTGC 59.425 36.000 0.00 0.00 45.22 3.68
2915 2970 5.012893 AGAATCCTTTTCAGGTTCATCCAC 58.987 41.667 0.00 0.00 41.69 4.02
3033 3088 4.984295 TGACCAAAAGATGAGGACATGAA 58.016 39.130 0.00 0.00 36.82 2.57
3044 3099 4.081862 CCAAGACATGCATGACCAAAAGAT 60.082 41.667 32.75 7.05 0.00 2.40
3054 3109 1.406539 GTTAGGGCCAAGACATGCATG 59.593 52.381 25.09 25.09 0.00 4.06
3066 3121 1.767759 ACTCATGCATTGTTAGGGCC 58.232 50.000 0.00 0.00 0.00 5.80
3085 3140 0.535780 CAGGTTCAGAGGTGCAGCAA 60.536 55.000 19.63 0.00 0.00 3.91
3087 3142 0.536006 AACAGGTTCAGAGGTGCAGC 60.536 55.000 8.11 8.11 0.00 5.25
3093 3148 6.150396 AGTATAATCGAACAGGTTCAGAGG 57.850 41.667 12.22 0.00 39.46 3.69
3104 3159 6.984474 TGAGATGGTCCAAAGTATAATCGAAC 59.016 38.462 0.00 0.00 0.00 3.95
3130 3185 8.716646 ATGAATGATGAACGAAACATACTACA 57.283 30.769 0.00 0.00 0.00 2.74
3138 3193 6.685828 CAGTCATGATGAATGATGAACGAAAC 59.314 38.462 17.08 0.00 44.38 2.78
3139 3194 6.594937 TCAGTCATGATGAATGATGAACGAAA 59.405 34.615 20.16 0.00 45.10 3.46
3142 3197 5.978934 TCAGTCATGATGAATGATGAACG 57.021 39.130 20.16 0.00 45.10 3.95
3175 3230 5.930837 TGGTTTTATTCCATCCCATTGAC 57.069 39.130 0.00 0.00 0.00 3.18
3181 3236 8.250143 ACAGAATAATGGTTTTATTCCATCCC 57.750 34.615 12.24 0.00 43.85 3.85
3199 3254 6.711277 AGTATGAGCTGACCAAAACAGAATA 58.289 36.000 0.00 0.00 37.54 1.75
3209 3264 8.023021 AGTATTTCATTAGTATGAGCTGACCA 57.977 34.615 0.00 0.00 41.60 4.02
3210 3265 8.768955 CAAGTATTTCATTAGTATGAGCTGACC 58.231 37.037 0.00 0.00 41.60 4.02
3234 3290 2.065899 ACTAAGTGCACCAAAGCCAA 57.934 45.000 14.63 0.00 0.00 4.52
3269 3325 4.377762 AGTCATGCATGGGCTAACATAT 57.622 40.909 25.97 0.00 41.91 1.78
3278 3334 5.882557 AGACTAAACTTAAGTCATGCATGGG 59.117 40.000 25.97 11.69 44.77 4.00
3298 4581 6.446781 TCGTAATTCTTACCGATGAAGACT 57.553 37.500 0.00 0.00 32.68 3.24
3299 4582 5.173492 GCTCGTAATTCTTACCGATGAAGAC 59.827 44.000 0.00 0.00 32.68 3.01
3300 4583 5.163591 TGCTCGTAATTCTTACCGATGAAGA 60.164 40.000 0.00 0.00 32.49 2.87
3301 4584 5.041287 TGCTCGTAATTCTTACCGATGAAG 58.959 41.667 0.00 0.00 32.49 3.02
3302 4585 5.001237 TGCTCGTAATTCTTACCGATGAA 57.999 39.130 0.00 0.00 32.49 2.57
3308 4591 7.311364 TGGTTTAATGCTCGTAATTCTTACC 57.689 36.000 0.00 0.00 32.49 2.85
3316 4599 5.637006 AGCAAATGGTTTAATGCTCGTAA 57.363 34.783 0.00 0.00 45.49 3.18
3326 4609 5.011533 AGCCATACAACAAGCAAATGGTTTA 59.988 36.000 0.00 0.00 39.45 2.01
3396 4679 5.298276 GCGGAAAACAATGTTATATCCTGGA 59.702 40.000 17.53 0.00 0.00 3.86
3405 4688 6.380095 AAAGTAGTGCGGAAAACAATGTTA 57.620 33.333 0.00 0.00 0.00 2.41
3411 4694 3.942748 ACAGAAAAGTAGTGCGGAAAACA 59.057 39.130 0.00 0.00 0.00 2.83
3412 4695 4.547406 ACAGAAAAGTAGTGCGGAAAAC 57.453 40.909 0.00 0.00 0.00 2.43
3435 4718 3.560636 AGATAAACCAGGTAGCGCAAT 57.439 42.857 11.47 0.00 0.00 3.56
3439 4722 3.536956 TGGAAGATAAACCAGGTAGCG 57.463 47.619 0.00 0.00 0.00 4.26
3452 4736 1.604378 CTGCCGGGAGTTGGAAGAT 59.396 57.895 16.00 0.00 33.51 2.40
3463 4747 1.202405 GCAATAAATGTTCCTGCCGGG 60.202 52.381 2.18 0.00 0.00 5.73
3464 4748 1.476085 TGCAATAAATGTTCCTGCCGG 59.524 47.619 0.00 0.00 31.92 6.13
3467 4751 2.094078 TGGCTGCAATAAATGTTCCTGC 60.094 45.455 0.50 0.00 0.00 4.85
3486 4770 4.082571 GCTTATATAGGTTGGCAGCATTGG 60.083 45.833 3.14 0.00 0.00 3.16
3487 4771 4.082571 GGCTTATATAGGTTGGCAGCATTG 60.083 45.833 3.14 0.00 0.00 2.82
3488 4772 4.082125 GGCTTATATAGGTTGGCAGCATT 58.918 43.478 3.14 0.00 0.00 3.56
3489 4773 3.074390 TGGCTTATATAGGTTGGCAGCAT 59.926 43.478 3.14 0.00 0.00 3.79
3490 4774 2.441375 TGGCTTATATAGGTTGGCAGCA 59.559 45.455 3.14 0.00 0.00 4.41
3491 4775 3.077359 CTGGCTTATATAGGTTGGCAGC 58.923 50.000 13.37 0.00 42.58 5.25
3493 4777 4.080015 ACAACTGGCTTATATAGGTTGGCA 60.080 41.667 0.00 0.00 38.49 4.92
3494 4778 4.461198 ACAACTGGCTTATATAGGTTGGC 58.539 43.478 0.00 0.00 38.49 4.52
3495 4779 5.221048 GCAACAACTGGCTTATATAGGTTGG 60.221 44.000 0.00 0.00 38.49 3.77
3496 4780 5.356751 TGCAACAACTGGCTTATATAGGTTG 59.643 40.000 0.00 0.00 39.58 3.77
3497 4781 5.505780 TGCAACAACTGGCTTATATAGGTT 58.494 37.500 0.00 0.00 0.00 3.50
3498 4782 5.110814 TGCAACAACTGGCTTATATAGGT 57.889 39.130 0.00 0.00 0.00 3.08
3499 4783 7.661437 TCTTATGCAACAACTGGCTTATATAGG 59.339 37.037 0.00 0.00 0.00 2.57
3500 4784 8.607441 TCTTATGCAACAACTGGCTTATATAG 57.393 34.615 0.00 0.00 0.00 1.31
3501 4785 8.972458 TTCTTATGCAACAACTGGCTTATATA 57.028 30.769 0.00 0.00 0.00 0.86
3502 4786 7.880160 TTCTTATGCAACAACTGGCTTATAT 57.120 32.000 0.00 0.00 0.00 0.86
3503 4787 7.880160 ATTCTTATGCAACAACTGGCTTATA 57.120 32.000 0.00 0.00 0.00 0.98
3504 4788 6.780457 ATTCTTATGCAACAACTGGCTTAT 57.220 33.333 0.00 0.00 0.00 1.73
3505 4789 6.588719 AATTCTTATGCAACAACTGGCTTA 57.411 33.333 0.00 0.00 0.00 3.09
3506 4790 5.473066 AATTCTTATGCAACAACTGGCTT 57.527 34.783 0.00 0.00 0.00 4.35
3507 4791 5.473066 AAATTCTTATGCAACAACTGGCT 57.527 34.783 0.00 0.00 0.00 4.75
3508 4792 7.545265 TCATAAAATTCTTATGCAACAACTGGC 59.455 33.333 0.00 0.00 33.57 4.85
3509 4793 8.984891 TCATAAAATTCTTATGCAACAACTGG 57.015 30.769 0.00 0.00 33.57 4.00
3521 4805 9.679661 TGGTGCATAGACTTCATAAAATTCTTA 57.320 29.630 0.00 0.00 0.00 2.10
3522 4806 8.579850 TGGTGCATAGACTTCATAAAATTCTT 57.420 30.769 0.00 0.00 0.00 2.52
3523 4807 8.627403 CATGGTGCATAGACTTCATAAAATTCT 58.373 33.333 0.00 0.00 0.00 2.40
3524 4808 7.380602 GCATGGTGCATAGACTTCATAAAATTC 59.619 37.037 0.00 0.00 44.26 2.17
3525 4809 7.205297 GCATGGTGCATAGACTTCATAAAATT 58.795 34.615 0.00 0.00 44.26 1.82
3526 4810 6.742109 GCATGGTGCATAGACTTCATAAAAT 58.258 36.000 0.00 0.00 44.26 1.82
3527 4811 6.135290 GCATGGTGCATAGACTTCATAAAA 57.865 37.500 0.00 0.00 44.26 1.52
3528 4812 5.756195 GCATGGTGCATAGACTTCATAAA 57.244 39.130 0.00 0.00 44.26 1.40
3542 4826 1.261619 GCTAACGATACAGCATGGTGC 59.738 52.381 24.31 7.81 43.62 5.01
3543 4827 2.549926 TGCTAACGATACAGCATGGTG 58.450 47.619 22.91 22.91 42.68 4.17
3560 4844 1.140852 TCATAAAGCGCCACCTATGCT 59.859 47.619 2.29 0.00 41.60 3.79
3566 4850 5.120830 CAGAGTAATATCATAAAGCGCCACC 59.879 44.000 2.29 0.00 0.00 4.61
3586 4870 9.894783 GAACAATGAATGGATGAATTATCAGAG 57.105 33.333 0.00 0.00 39.39 3.35
3589 4873 8.415553 GGTGAACAATGAATGGATGAATTATCA 58.584 33.333 0.00 0.00 40.57 2.15
3590 4874 8.636213 AGGTGAACAATGAATGGATGAATTATC 58.364 33.333 0.00 0.00 34.93 1.75
3592 4876 7.959658 AGGTGAACAATGAATGGATGAATTA 57.040 32.000 0.00 0.00 0.00 1.40
3714 4999 1.229975 TGATGTGCAGCCACTTGTCG 61.230 55.000 0.00 0.00 42.54 4.35
3813 5098 2.496899 ACCGATGGCATTCTCAAGTT 57.503 45.000 0.00 0.00 0.00 2.66
4044 5329 3.188460 CCCGATTTGACACAAACAGGTAG 59.812 47.826 14.03 2.73 0.00 3.18
4100 5385 6.474918 AATTATATCCCTGGCCTCTTTCAT 57.525 37.500 3.32 0.00 0.00 2.57
4106 5391 2.092914 CCGGAATTATATCCCTGGCCTC 60.093 54.545 3.32 0.00 36.00 4.70
4121 5415 2.525105 ACCAATTTACAGCCCGGAAT 57.475 45.000 0.73 0.00 0.00 3.01
4136 5430 3.512329 AGATGCATCATTGAGCAAACCAA 59.488 39.130 27.81 0.00 44.88 3.67
4270 6910 2.030540 TGCACCAGTACTACGAACAGTC 60.031 50.000 0.00 0.00 0.00 3.51
4362 7008 5.668558 ACGGCTACATTTCGAATATTTCC 57.331 39.130 0.00 0.00 0.00 3.13
4437 7089 5.815581 TGGGTGGATATATTCAATACTGCC 58.184 41.667 0.00 0.00 0.00 4.85
4442 7094 4.080582 CGGCCTGGGTGGATATATTCAATA 60.081 45.833 0.00 0.00 38.35 1.90
4462 7114 0.464373 TTCCTGAATCATCTGGCGGC 60.464 55.000 0.00 0.00 42.71 6.53
4545 7197 3.127533 GCCCGATGTGCAGGTGTC 61.128 66.667 0.00 0.00 0.00 3.67
4604 7257 7.573968 TCATATATCTGGTCATCGATGGTAG 57.426 40.000 24.61 18.60 0.00 3.18
4637 7547 9.357161 ACGTTCTCTCCTAAAGTATAATGATCT 57.643 33.333 0.00 0.00 0.00 2.75
4638 7548 9.615295 GACGTTCTCTCCTAAAGTATAATGATC 57.385 37.037 0.00 0.00 0.00 2.92
4639 7549 9.132923 TGACGTTCTCTCCTAAAGTATAATGAT 57.867 33.333 0.00 0.00 0.00 2.45
4640 7550 8.515695 TGACGTTCTCTCCTAAAGTATAATGA 57.484 34.615 0.00 0.00 0.00 2.57
4641 7551 9.582431 TTTGACGTTCTCTCCTAAAGTATAATG 57.418 33.333 0.00 0.00 0.00 1.90
4645 7555 9.503399 AAATTTTGACGTTCTCTCCTAAAGTAT 57.497 29.630 0.00 0.00 0.00 2.12
4646 7556 8.770828 CAAATTTTGACGTTCTCTCCTAAAGTA 58.229 33.333 2.88 0.00 0.00 2.24
4647 7557 7.497909 TCAAATTTTGACGTTCTCTCCTAAAGT 59.502 33.333 7.74 0.00 34.08 2.66
4648 7558 7.861630 TCAAATTTTGACGTTCTCTCCTAAAG 58.138 34.615 7.74 0.00 34.08 1.85
4649 7559 7.713507 TCTCAAATTTTGACGTTCTCTCCTAAA 59.286 33.333 7.74 0.00 35.46 1.85
4650 7560 7.214381 TCTCAAATTTTGACGTTCTCTCCTAA 58.786 34.615 7.74 0.00 35.46 2.69
4651 7561 6.755206 TCTCAAATTTTGACGTTCTCTCCTA 58.245 36.000 7.74 0.00 35.46 2.94
4662 7572 4.550422 GGCAGTTCCTCTCAAATTTTGAC 58.450 43.478 7.74 0.00 35.46 3.18
4663 7573 3.253188 CGGCAGTTCCTCTCAAATTTTGA 59.747 43.478 11.19 11.19 38.17 2.69
4668 7578 0.036732 TGCGGCAGTTCCTCTCAAAT 59.963 50.000 0.00 0.00 0.00 2.32
4669 7579 0.603707 CTGCGGCAGTTCCTCTCAAA 60.604 55.000 21.60 0.00 0.00 2.69
4679 7589 2.024414 GAATATTTTCCCTGCGGCAGT 58.976 47.619 26.79 11.10 0.00 4.40
4684 7594 5.323371 TCCTTTTGAATATTTTCCCTGCG 57.677 39.130 0.00 0.00 0.00 5.18
4688 7598 4.441495 CCGGCTCCTTTTGAATATTTTCCC 60.441 45.833 0.00 0.00 0.00 3.97
4690 7600 4.159693 ACCCGGCTCCTTTTGAATATTTTC 59.840 41.667 0.00 0.00 0.00 2.29
4693 7603 3.382083 ACCCGGCTCCTTTTGAATATT 57.618 42.857 0.00 0.00 0.00 1.28
4744 7655 2.540931 CTCGAGACGGAAGACTAGTAGC 59.459 54.545 6.58 0.00 35.94 3.58
4762 7673 1.739562 GCAGTGAAGGGAGCACTCG 60.740 63.158 0.00 0.00 44.28 4.18
4763 7674 1.376553 GGCAGTGAAGGGAGCACTC 60.377 63.158 0.00 0.00 44.28 3.51


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

AutoCloner maintained by Alex Coulton.