Multiple sequence alignment - TraesCS3A01G391000

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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 TraesCS3A01G391000 chr3A 100.000 6618 0 0 1 6618 639019449 639026066 0.000000e+00 12222.0
1 TraesCS3A01G391000 chr3D 92.325 4573 206 77 2117 6616 499028767 499033267 0.000000e+00 6366.0
2 TraesCS3A01G391000 chr3D 93.053 1900 103 15 185 2073 499026884 499028765 0.000000e+00 2750.0
3 TraesCS3A01G391000 chr3D 88.489 556 38 8 1 535 499026291 499026841 0.000000e+00 649.0
4 TraesCS3A01G391000 chr3B 92.402 2619 141 35 3550 6140 659785964 659788552 0.000000e+00 3681.0
5 TraesCS3A01G391000 chr3B 93.535 1454 62 13 2117 3552 659784412 659785851 0.000000e+00 2135.0
6 TraesCS3A01G391000 chr3B 86.792 1590 154 30 11 1594 659782298 659783837 0.000000e+00 1722.0
7 TraesCS3A01G391000 chr3B 95.622 434 15 3 1624 2054 659783834 659784266 0.000000e+00 693.0
8 TraesCS3A01G391000 chr3B 82.556 493 37 16 6139 6615 659800365 659800824 8.050000e-104 388.0
9 TraesCS3A01G391000 chr5D 92.593 54 3 1 2059 2112 410399103 410399155 7.120000e-10 76.8
10 TraesCS3A01G391000 chr5A 92.593 54 3 1 2059 2112 521937810 521937862 7.120000e-10 76.8
11 TraesCS3A01G391000 chr5A 92.000 50 4 0 2063 2112 382114850 382114899 3.310000e-08 71.3
12 TraesCS3A01G391000 chr2B 95.556 45 2 0 2071 2115 775170286 775170242 9.210000e-09 73.1
13 TraesCS3A01G391000 chr7D 93.750 48 2 1 2068 2114 190083216 190083263 3.310000e-08 71.3
14 TraesCS3A01G391000 chr4B 90.385 52 5 0 2063 2114 47623486 47623435 1.190000e-07 69.4
15 TraesCS3A01G391000 chr4B 90.566 53 3 2 2071 2122 83310533 83310584 1.190000e-07 69.4
16 TraesCS3A01G391000 chr4A 90.385 52 5 0 2063 2114 569867879 569867930 1.190000e-07 69.4
17 TraesCS3A01G391000 chr6B 88.889 54 6 0 2064 2117 130941242 130941295 4.280000e-07 67.6


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 TraesCS3A01G391000 chr3A 639019449 639026066 6617 False 12222.00 12222 100.00000 1 6618 1 chr3A.!!$F1 6617
1 TraesCS3A01G391000 chr3D 499026291 499033267 6976 False 3255.00 6366 91.28900 1 6616 3 chr3D.!!$F1 6615
2 TraesCS3A01G391000 chr3B 659782298 659788552 6254 False 2057.75 3681 92.08775 11 6140 4 chr3B.!!$F2 6129

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
632 1048 0.249996 GGTTCAAAACGGACGGAGGA 60.250 55.0 0.0 0.00 0.00 3.71 F
672 1088 0.329261 CAGAAGCAATGTGGGGAGGA 59.671 55.0 0.0 0.00 0.00 3.71 F
673 1089 0.622665 AGAAGCAATGTGGGGAGGAG 59.377 55.0 0.0 0.00 0.00 3.69 F
1363 1793 0.794605 GCTTTGGAAGCGACGCAATC 60.795 55.0 23.7 18.69 45.74 2.67 F
2626 3194 0.193069 ATAGAGGGCTCAGGGCTCAT 59.807 55.0 0.0 0.00 45.61 2.90 F
2627 3195 0.762082 TAGAGGGCTCAGGGCTCATG 60.762 60.0 0.0 0.00 45.61 3.07 F
3891 4587 0.827507 TCCCTTTTGCTCACCTTGCC 60.828 55.0 0.0 0.00 0.00 4.52 F
4810 5540 0.326264 ATCTTGTGGTCAGTGCCCTC 59.674 55.0 0.0 0.00 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1722 2152 1.202687 CCTGACCAGTGAAGCAACAGA 60.203 52.381 0.00 0.00 0.00 3.41 R
1886 2319 1.514087 CAGATGCCATTTTGCGCCT 59.486 52.632 4.18 0.00 0.00 5.52 R
2002 2435 3.853355 TGCAAATTGTGTTCCCCAAAT 57.147 38.095 0.00 0.00 0.00 2.32 R
3135 3712 1.821136 TGCAGTCTGACATCATCGTCT 59.179 47.619 10.88 0.00 36.82 4.18 R
3986 4682 0.541863 ATGGTAGGCTACAGCACACC 59.458 55.000 24.96 10.06 44.36 4.16 R
4178 4880 2.857186 TGCTCAGAACATTACCAGCA 57.143 45.000 0.00 0.00 34.54 4.41 R
5458 6189 0.388778 TTTCAATCTGCGGACGCGTA 60.389 50.000 13.97 0.00 45.51 4.42 R
5987 6728 0.179000 CAGATTCGCCCAGGCTAAGT 59.821 55.000 7.17 0.00 39.32 2.24 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
31 32 4.816925 CGCTAAGATTTTAGGAAGAAGGGG 59.183 45.833 5.26 0.00 37.37 4.79
38 39 5.871324 TTTTAGGAAGAAGGGGGTACAAT 57.129 39.130 0.00 0.00 0.00 2.71
89 90 8.978874 TCAACATGGTTCTTGCTTATGTATAT 57.021 30.769 0.00 0.00 32.18 0.86
94 95 9.836076 CATGGTTCTTGCTTATGTATATGAATG 57.164 33.333 0.00 0.00 0.00 2.67
219 222 5.122396 CCTATTGCATTTATTACCCTCTCGC 59.878 44.000 0.00 0.00 0.00 5.03
292 295 5.809464 TCATTGATGTTTCGAAATCCATCG 58.191 37.500 24.72 16.30 44.04 3.84
323 326 4.388773 CACTGTCACATTTGTAGTATGCGT 59.611 41.667 0.00 0.00 0.00 5.24
325 328 6.090223 CACTGTCACATTTGTAGTATGCGTTA 59.910 38.462 0.00 0.00 0.00 3.18
396 399 1.231963 ATTTACCCATCCTCCCACCC 58.768 55.000 0.00 0.00 0.00 4.61
399 402 2.126375 TACCCATCCTCCCACCCACA 62.126 60.000 0.00 0.00 0.00 4.17
412 828 2.513753 CACCCACAGGCTACATTTTGA 58.486 47.619 0.00 0.00 36.11 2.69
443 859 9.725019 ACATATTTGATCCGATATACATTGTGT 57.275 29.630 0.00 0.00 0.00 3.72
451 867 7.234661 TCCGATATACATTGTGTAAGCCATA 57.765 36.000 0.00 0.00 36.31 2.74
462 878 5.189180 TGTGTAAGCCATATATTGCACACA 58.811 37.500 21.51 21.51 43.85 3.72
464 880 5.296780 GTGTAAGCCATATATTGCACACACT 59.703 40.000 24.01 1.29 40.43 3.55
465 881 5.885352 TGTAAGCCATATATTGCACACACTT 59.115 36.000 11.08 0.00 0.00 3.16
472 888 1.436748 TTGCACACACTTGCGCAAT 59.563 47.368 25.26 11.22 44.07 3.56
535 951 4.520846 GTGGCGCGCCGATTTCAG 62.521 66.667 41.73 0.00 39.42 3.02
561 977 1.226831 CTCTCTTCTTCCCTCGCGC 60.227 63.158 0.00 0.00 0.00 6.86
607 1023 1.942712 GTGTGCCCGTAGTATCGCG 60.943 63.158 0.00 0.00 0.00 5.87
629 1045 4.030821 CGGTTCAAAACGGACGGA 57.969 55.556 0.00 0.00 34.00 4.69
630 1046 1.857364 CGGTTCAAAACGGACGGAG 59.143 57.895 0.00 0.00 34.00 4.63
631 1047 1.562575 CGGTTCAAAACGGACGGAGG 61.563 60.000 0.00 0.00 34.00 4.30
632 1048 0.249996 GGTTCAAAACGGACGGAGGA 60.250 55.000 0.00 0.00 0.00 3.71
662 1078 2.361771 CCAGGGGGCAGAAGCAAT 59.638 61.111 0.00 0.00 44.61 3.56
664 1080 1.304713 CAGGGGGCAGAAGCAATGT 60.305 57.895 0.00 0.00 44.61 2.71
665 1081 1.304713 AGGGGGCAGAAGCAATGTG 60.305 57.895 0.00 0.00 44.61 3.21
666 1082 2.353610 GGGGGCAGAAGCAATGTGG 61.354 63.158 0.00 0.00 44.61 4.17
667 1083 2.353610 GGGGCAGAAGCAATGTGGG 61.354 63.158 0.00 0.00 44.61 4.61
668 1084 2.353610 GGGCAGAAGCAATGTGGGG 61.354 63.158 0.00 0.00 44.61 4.96
669 1085 1.304381 GGCAGAAGCAATGTGGGGA 60.304 57.895 0.00 0.00 44.61 4.81
670 1086 1.318158 GGCAGAAGCAATGTGGGGAG 61.318 60.000 0.00 0.00 44.61 4.30
671 1087 1.318158 GCAGAAGCAATGTGGGGAGG 61.318 60.000 0.00 0.00 41.58 4.30
672 1088 0.329261 CAGAAGCAATGTGGGGAGGA 59.671 55.000 0.00 0.00 0.00 3.71
673 1089 0.622665 AGAAGCAATGTGGGGAGGAG 59.377 55.000 0.00 0.00 0.00 3.69
715 1131 1.379527 GAGCCCAGATTGGTTAACCG 58.620 55.000 19.65 4.89 39.43 4.44
762 1182 1.016130 AGCACACGCACAGCAGTATC 61.016 55.000 0.00 0.00 42.27 2.24
862 1290 1.275573 GTTTCTTACCGCTCTCCAGGT 59.724 52.381 0.00 0.00 44.08 4.00
1274 1704 2.030862 TCGGCACCGGTTGTAACC 59.969 61.111 2.97 3.67 45.76 2.85
1295 1725 1.745489 CCGTGGGGAAGTTGCTAGC 60.745 63.158 8.10 8.10 34.06 3.42
1296 1726 1.296715 CGTGGGGAAGTTGCTAGCT 59.703 57.895 17.23 0.00 0.00 3.32
1335 1765 5.818857 TGGTAAACCGCAAGTTAATATCTCC 59.181 40.000 0.00 0.00 37.88 3.71
1363 1793 0.794605 GCTTTGGAAGCGACGCAATC 60.795 55.000 23.70 18.69 45.74 2.67
1421 1851 5.499047 GGCAAATCTACACGTACTTAATGC 58.501 41.667 0.00 0.00 0.00 3.56
1569 1999 7.444183 TGAGAACATGACTGGTTAAAGTTTAGG 59.556 37.037 0.00 0.00 0.00 2.69
1581 2011 7.128331 GGTTAAAGTTTAGGTTTTCGTCTGAC 58.872 38.462 0.00 0.00 0.00 3.51
1676 2106 4.846779 TTTCTAATGCAGTTTCCCACAC 57.153 40.909 0.00 0.00 0.00 3.82
1722 2152 4.037565 GCTTACTACTTGCTTTTGGTTGGT 59.962 41.667 0.00 0.00 0.00 3.67
1769 2199 3.003793 GTGGACCTTCAGAAAAGCACTTC 59.996 47.826 0.00 0.00 0.00 3.01
1807 2237 2.161855 TGGCTATGTTTTGAGTGCCAG 58.838 47.619 0.00 0.00 44.35 4.85
1824 2254 1.201647 CCAGAAATCCAGCAGCAACTG 59.798 52.381 0.00 0.00 37.42 3.16
1839 2270 4.445385 CAGCAACTGGACTTATTTTGCAAC 59.555 41.667 0.00 0.00 44.06 4.17
2026 2459 3.274288 TGGGGAACACAATTTGCAAAAC 58.726 40.909 17.19 2.34 0.00 2.43
2035 2468 4.270808 CACAATTTGCAAAACTGGAGAACC 59.729 41.667 17.19 0.00 0.00 3.62
2097 2655 9.813446 ACTACCTTTGTTCCTAAATATAAGACG 57.187 33.333 0.00 0.00 0.00 4.18
2098 2656 9.813446 CTACCTTTGTTCCTAAATATAAGACGT 57.187 33.333 0.00 0.00 0.00 4.34
2100 2658 9.511272 ACCTTTGTTCCTAAATATAAGACGTTT 57.489 29.630 0.00 0.00 0.00 3.60
2104 2662 9.615295 TTGTTCCTAAATATAAGACGTTTTTGC 57.385 29.630 0.00 0.00 0.00 3.68
2105 2663 8.784994 TGTTCCTAAATATAAGACGTTTTTGCA 58.215 29.630 0.00 0.00 0.00 4.08
2106 2664 9.274065 GTTCCTAAATATAAGACGTTTTTGCAG 57.726 33.333 0.00 0.00 0.00 4.41
2107 2665 8.556213 TCCTAAATATAAGACGTTTTTGCAGT 57.444 30.769 0.00 0.00 0.00 4.40
2108 2666 9.005777 TCCTAAATATAAGACGTTTTTGCAGTT 57.994 29.630 0.00 0.00 0.00 3.16
2109 2667 9.274065 CCTAAATATAAGACGTTTTTGCAGTTC 57.726 33.333 0.00 0.00 0.00 3.01
2110 2668 9.820229 CTAAATATAAGACGTTTTTGCAGTTCA 57.180 29.630 0.00 0.00 0.00 3.18
2112 2670 9.691362 AAATATAAGACGTTTTTGCAGTTCAAT 57.309 25.926 0.00 0.00 34.12 2.57
2113 2671 9.691362 AATATAAGACGTTTTTGCAGTTCAATT 57.309 25.926 0.00 0.00 34.12 2.32
2141 2699 8.588290 ATTAAATATTTTGCTACTGACACCCA 57.412 30.769 5.91 0.00 0.00 4.51
2161 2719 7.121611 ACACCCATATACACATTCATGCATATG 59.878 37.037 0.00 3.04 32.84 1.78
2318 2879 2.287977 ACAAGGTAAGTGAAAGCCCC 57.712 50.000 0.00 0.00 0.00 5.80
2376 2937 8.774546 TTTCATCTCATCTGTCTATACCTCTT 57.225 34.615 0.00 0.00 0.00 2.85
2377 2938 7.994425 TCATCTCATCTGTCTATACCTCTTC 57.006 40.000 0.00 0.00 0.00 2.87
2378 2939 7.521669 TCATCTCATCTGTCTATACCTCTTCA 58.478 38.462 0.00 0.00 0.00 3.02
2379 2940 8.169393 TCATCTCATCTGTCTATACCTCTTCAT 58.831 37.037 0.00 0.00 0.00 2.57
2380 2941 7.994425 TCTCATCTGTCTATACCTCTTCATC 57.006 40.000 0.00 0.00 0.00 2.92
2381 2942 7.521669 TCTCATCTGTCTATACCTCTTCATCA 58.478 38.462 0.00 0.00 0.00 3.07
2382 2943 8.001292 TCTCATCTGTCTATACCTCTTCATCAA 58.999 37.037 0.00 0.00 0.00 2.57
2510 3078 5.479124 ACGTAAATTACTTCACTCCCACT 57.521 39.130 1.42 0.00 0.00 4.00
2587 3155 7.178712 AGTTTATTACACTCGCAATGCTATC 57.821 36.000 2.94 0.00 0.00 2.08
2626 3194 0.193069 ATAGAGGGCTCAGGGCTCAT 59.807 55.000 0.00 0.00 45.61 2.90
2627 3195 0.762082 TAGAGGGCTCAGGGCTCATG 60.762 60.000 0.00 0.00 45.61 3.07
2754 3323 2.769095 GCTCTAGATTGGTCCCTCTGTT 59.231 50.000 0.00 0.00 0.00 3.16
2831 3400 7.584987 TCGAGAAGAAACCTTGATGAAATTTC 58.415 34.615 11.41 11.41 0.00 2.17
2992 3568 9.408648 AGGAAAGACATTCGTAATTTTATGGAT 57.591 29.630 0.00 0.00 39.05 3.41
2998 3574 5.893512 TTCGTAATTTTATGGATCCGTCG 57.106 39.130 10.55 6.18 0.00 5.12
3016 3592 3.670091 CGTCGTAGGACTTTCTTCTGACC 60.670 52.174 13.31 0.00 41.16 4.02
3135 3712 9.905713 AAGGACAGCAAATATGTTCTATTTCTA 57.094 29.630 0.00 0.00 35.36 2.10
3230 3807 1.978473 TGCTCTGGCACTCTCCTTC 59.022 57.895 0.00 0.00 44.28 3.46
3261 3838 4.689062 TCATCCTTCTCACCTTCCTAACT 58.311 43.478 0.00 0.00 0.00 2.24
3267 3844 0.834687 TCACCTTCCTAACTGGGCGT 60.835 55.000 0.00 0.00 36.20 5.68
3473 4050 3.279434 GCTGTAGATAAGGGGTTTGGTG 58.721 50.000 0.00 0.00 0.00 4.17
3481 4058 7.460214 AGATAAGGGGTTTGGTGTATGAATA 57.540 36.000 0.00 0.00 0.00 1.75
3486 4063 5.489637 AGGGGTTTGGTGTATGAATAGTACA 59.510 40.000 0.00 0.00 0.00 2.90
3493 4070 5.114081 GGTGTATGAATAGTACAAACGCCT 58.886 41.667 0.00 0.00 34.15 5.52
3568 4260 3.570926 TGTATGATCGTTATCCGCCTC 57.429 47.619 0.00 0.00 36.19 4.70
3569 4261 2.230508 TGTATGATCGTTATCCGCCTCC 59.769 50.000 0.00 0.00 36.19 4.30
3707 4403 2.461695 TCTTTGTTGTTGCCCCTTTGA 58.538 42.857 0.00 0.00 0.00 2.69
3721 4417 3.897505 CCCCTTTGATAATTGGTGGGATC 59.102 47.826 0.00 0.00 35.40 3.36
3740 4436 8.251721 GTGGGATCGCTTATGTACTTAGATTAT 58.748 37.037 11.46 0.00 0.00 1.28
3782 4478 7.168637 GGTTGCTCATATTGTCTGCATTAATTG 59.831 37.037 0.00 0.00 33.50 2.32
3854 4550 8.642020 AGTTAGCTCGTTATTTAACTTTGTACG 58.358 33.333 0.00 0.00 33.76 3.67
3891 4587 0.827507 TCCCTTTTGCTCACCTTGCC 60.828 55.000 0.00 0.00 0.00 4.52
3986 4682 2.487265 GGGTGGCTGTATGATGGTAAGG 60.487 54.545 0.00 0.00 0.00 2.69
4001 4697 1.829222 GTAAGGGTGTGCTGTAGCCTA 59.171 52.381 0.80 0.00 44.78 3.93
4010 4706 1.062886 TGCTGTAGCCTACCATCTCCT 60.063 52.381 0.00 0.00 41.18 3.69
4178 4880 2.091720 TGATATGACCCTGGCTGCAATT 60.092 45.455 0.50 0.00 0.00 2.32
4268 4973 9.450807 GCATGGAAATTAGTGTTGATAATGTAC 57.549 33.333 0.00 0.00 0.00 2.90
4283 4992 7.984391 TGATAATGTACACAATGTTAGCCTTG 58.016 34.615 0.00 0.00 0.00 3.61
4338 5050 8.797438 ACCATTTATCCTTTTTCTCTTTGAGAC 58.203 33.333 0.00 0.00 38.51 3.36
4453 5183 1.066143 AGGCTCATAACTTCACCACCG 60.066 52.381 0.00 0.00 0.00 4.94
4632 5362 6.534793 GGAAGCAAACTTTTGTTCTTGAATCA 59.465 34.615 3.74 0.00 42.67 2.57
4765 5495 3.099905 ACTCTTAGAGCACCATACAGCA 58.900 45.455 9.44 0.00 32.04 4.41
4810 5540 0.326264 ATCTTGTGGTCAGTGCCCTC 59.674 55.000 0.00 0.00 0.00 4.30
4819 5549 0.998928 TCAGTGCCCTCTCTCTCTCT 59.001 55.000 0.00 0.00 0.00 3.10
4820 5550 1.064758 TCAGTGCCCTCTCTCTCTCTC 60.065 57.143 0.00 0.00 0.00 3.20
4821 5551 1.064463 CAGTGCCCTCTCTCTCTCTCT 60.064 57.143 0.00 0.00 0.00 3.10
4822 5552 1.212935 AGTGCCCTCTCTCTCTCTCTC 59.787 57.143 0.00 0.00 0.00 3.20
4930 5660 2.863132 AACAAATACACCTACGCCCA 57.137 45.000 0.00 0.00 0.00 5.36
5361 6092 4.024048 ACACAACATCGTCTGAACATTTCC 60.024 41.667 0.00 0.00 0.00 3.13
5362 6093 3.186409 ACAACATCGTCTGAACATTTCCG 59.814 43.478 0.00 0.00 0.00 4.30
5366 6097 2.066262 TCGTCTGAACATTTCCGCTTC 58.934 47.619 0.00 0.00 0.00 3.86
5367 6098 1.798223 CGTCTGAACATTTCCGCTTCA 59.202 47.619 0.00 0.00 0.00 3.02
5373 6104 3.243367 TGAACATTTCCGCTTCAACCTTG 60.243 43.478 0.00 0.00 0.00 3.61
5376 6107 3.383185 ACATTTCCGCTTCAACCTTGAAA 59.617 39.130 2.25 0.00 45.61 2.69
5384 6115 4.438744 CGCTTCAACCTTGAAACTGTTTCT 60.439 41.667 27.75 10.17 45.61 2.52
5390 6121 3.035942 CCTTGAAACTGTTTCTTTCGCG 58.964 45.455 27.75 0.00 40.32 5.87
5426 6157 5.237779 TCTTTCGAACTTGCTCCGTAAAATT 59.762 36.000 0.00 0.00 0.00 1.82
5458 6189 4.721776 TCCTCTATGCCTCACTTGGTTATT 59.278 41.667 0.00 0.00 0.00 1.40
5460 6191 5.992217 CCTCTATGCCTCACTTGGTTATTAC 59.008 44.000 0.00 0.00 0.00 1.89
5462 6193 2.352388 TGCCTCACTTGGTTATTACGC 58.648 47.619 0.00 0.00 0.00 4.42
5463 6194 1.326548 GCCTCACTTGGTTATTACGCG 59.673 52.381 3.53 3.53 0.00 6.01
5490 6225 4.279420 GCAGATTGAAAGGGAGAACAGTTT 59.721 41.667 0.00 0.00 0.00 2.66
5500 6235 4.409247 AGGGAGAACAGTTTGAAGTACACT 59.591 41.667 0.00 0.00 0.00 3.55
5623 6358 7.549488 CCCAAGAAGTACGATGTCTAAGAAATT 59.451 37.037 0.00 0.00 0.00 1.82
5637 6372 7.154656 GTCTAAGAAATTTGCCAAGTGGAATT 58.845 34.615 0.18 0.00 37.39 2.17
5707 6442 6.867519 TCTTCTTCCTTTTCCTTTGGTTTT 57.132 33.333 0.00 0.00 0.00 2.43
5834 6572 0.464373 ATGTGTAGCGGGCAGATTGG 60.464 55.000 0.00 0.00 0.00 3.16
5859 6597 7.809806 GGTTGAAGAAGTGAAAATGTTCCATAG 59.190 37.037 0.00 0.00 32.28 2.23
5869 6607 2.489938 TGTTCCATAGTGGCCTGTTC 57.510 50.000 3.32 0.00 37.47 3.18
5870 6608 1.985159 TGTTCCATAGTGGCCTGTTCT 59.015 47.619 3.32 0.00 37.47 3.01
5919 6657 7.901889 CACATCGTGAAAATTGATCTTCTAGTG 59.098 37.037 0.00 0.00 35.23 2.74
5920 6658 6.408858 TCGTGAAAATTGATCTTCTAGTGC 57.591 37.500 0.00 0.00 0.00 4.40
5928 6666 7.992754 AATTGATCTTCTAGTGCTCTTTGTT 57.007 32.000 0.00 0.00 0.00 2.83
5963 6701 9.831737 AAAGTCGATGAATAGATCAAAAAGTTG 57.168 29.630 0.00 0.00 42.54 3.16
5964 6702 8.553459 AGTCGATGAATAGATCAAAAAGTTGT 57.447 30.769 0.00 0.00 42.54 3.32
5965 6703 8.660373 AGTCGATGAATAGATCAAAAAGTTGTC 58.340 33.333 0.00 0.00 42.54 3.18
5966 6704 7.632515 GTCGATGAATAGATCAAAAAGTTGTCG 59.367 37.037 0.00 0.00 42.54 4.35
6019 6760 5.105106 TGGGCGAATCTGATTCTACTTTGTA 60.105 40.000 23.67 4.20 37.13 2.41
6020 6761 5.815740 GGGCGAATCTGATTCTACTTTGTAA 59.184 40.000 23.67 0.00 37.13 2.41
6032 6773 6.300354 TCTACTTTGTAAAGCTTTGCAGTC 57.700 37.500 25.63 10.43 39.63 3.51
6067 6808 1.659794 GTCAATGCCTGGCAAACGT 59.340 52.632 27.24 5.99 43.62 3.99
6078 6819 1.587613 GCAAACGTTCGCTGCCAAA 60.588 52.632 11.53 0.00 0.00 3.28
6090 6831 1.774639 CTGCCAAACATGACAGTTGC 58.225 50.000 0.00 0.00 0.00 4.17
6096 6837 4.050553 CCAAACATGACAGTTGCGAATTT 58.949 39.130 0.00 0.00 0.00 1.82
6097 6838 4.507388 CCAAACATGACAGTTGCGAATTTT 59.493 37.500 0.00 0.00 0.00 1.82
6107 6868 6.329496 ACAGTTGCGAATTTTCAAAAGAAGA 58.671 32.000 0.00 0.00 0.00 2.87
6144 6905 8.865590 TTAATTTTAGTGCAAGTTTTCTGACC 57.134 30.769 0.00 0.00 0.00 4.02
6145 6906 5.906113 TTTTAGTGCAAGTTTTCTGACCA 57.094 34.783 0.00 0.00 0.00 4.02
6146 6907 5.499139 TTTAGTGCAAGTTTTCTGACCAG 57.501 39.130 0.00 0.00 0.00 4.00
6147 6908 3.281727 AGTGCAAGTTTTCTGACCAGA 57.718 42.857 0.00 0.00 35.27 3.86
6148 6909 3.825328 AGTGCAAGTTTTCTGACCAGAT 58.175 40.909 0.01 0.00 37.29 2.90
6150 6911 2.886523 TGCAAGTTTTCTGACCAGATGG 59.113 45.455 0.01 0.00 37.29 3.51
6151 6912 2.352127 GCAAGTTTTCTGACCAGATGGC 60.352 50.000 0.00 0.00 37.29 4.40
6152 6913 3.152341 CAAGTTTTCTGACCAGATGGCT 58.848 45.455 0.00 0.00 37.29 4.75
6153 6914 3.064900 AGTTTTCTGACCAGATGGCTC 57.935 47.619 0.00 0.00 37.29 4.70
6154 6915 2.087646 GTTTTCTGACCAGATGGCTCC 58.912 52.381 0.00 0.00 37.29 4.70
6155 6916 0.620556 TTTCTGACCAGATGGCTCCC 59.379 55.000 0.00 0.00 37.29 4.30
6179 6940 1.439353 CGTTCGCTGGGATCCCATTG 61.439 60.000 33.89 26.65 46.15 2.82
6214 6976 6.687081 TTGCCGATATCTAAACCGAAATTT 57.313 33.333 0.34 0.00 0.00 1.82
6240 7002 1.180029 CCTCAACATTTGGAGGCTGG 58.820 55.000 0.00 0.00 43.80 4.85
6343 7105 1.460504 CCAGCTGACATGCTTGACAT 58.539 50.000 17.39 0.00 41.98 3.06
6351 7113 3.656457 ATGCTTGACATGACAGCCA 57.344 47.368 0.00 0.86 37.70 4.75
6352 7114 2.139323 ATGCTTGACATGACAGCCAT 57.861 45.000 0.00 3.36 37.70 4.40
6388 7151 5.680619 AGAAAATGTATTGACGGCCATCTA 58.319 37.500 2.24 0.00 0.00 1.98
6398 7161 9.601217 GTATTGACGGCCATCTATTTTCTATAT 57.399 33.333 2.24 0.00 0.00 0.86
6429 7192 4.826274 ATTGGAGACTTGGAATTCGAGA 57.174 40.909 12.75 0.00 0.00 4.04
6454 7217 4.637387 TTTTACGTTGGTTCCCCATCTA 57.363 40.909 0.00 0.00 41.49 1.98
6458 7221 2.170607 ACGTTGGTTCCCCATCTAGATG 59.829 50.000 23.53 23.53 41.49 2.90
6459 7222 2.576615 GTTGGTTCCCCATCTAGATGC 58.423 52.381 24.81 12.04 41.49 3.91
6460 7223 2.173569 GTTGGTTCCCCATCTAGATGCT 59.826 50.000 24.81 0.00 41.49 3.79
6461 7224 1.770658 TGGTTCCCCATCTAGATGCTG 59.229 52.381 24.81 17.51 35.17 4.41
6508 7271 7.797123 CGGTTTCTATTTAAATCGATTGGTAGC 59.203 37.037 12.25 0.00 43.90 3.58
6514 7277 3.764885 AAATCGATTGGTAGCAGCAAC 57.235 42.857 12.25 0.00 38.51 4.17
6524 7287 0.889994 TAGCAGCAACAGCAAATGGG 59.110 50.000 0.00 0.00 0.00 4.00
6525 7288 2.030958 GCAGCAACAGCAAATGGGC 61.031 57.895 0.00 0.00 34.55 5.36
6529 7292 0.800012 GCAACAGCAAATGGGCAATG 59.200 50.000 0.00 0.00 34.50 2.82
6537 7300 3.778360 AATGGGCAATGCATCGCGC 62.778 57.895 18.97 18.97 41.14 6.86
6559 7322 1.183030 TCCTCCCGAGTCGCTTTCAA 61.183 55.000 7.12 0.00 0.00 2.69
6562 7325 1.661112 CTCCCGAGTCGCTTTCAATTC 59.339 52.381 7.12 0.00 0.00 2.17
6564 7327 2.076863 CCCGAGTCGCTTTCAATTCTT 58.923 47.619 7.12 0.00 0.00 2.52
6565 7328 2.094417 CCCGAGTCGCTTTCAATTCTTC 59.906 50.000 7.12 0.00 0.00 2.87
6567 7330 3.061429 CCGAGTCGCTTTCAATTCTTCTC 59.939 47.826 7.12 0.00 0.00 2.87
6568 7331 3.923461 CGAGTCGCTTTCAATTCTTCTCT 59.077 43.478 0.00 0.00 0.00 3.10
6569 7332 5.096169 CGAGTCGCTTTCAATTCTTCTCTA 58.904 41.667 0.00 0.00 0.00 2.43
6579 7342 9.837525 CTTTCAATTCTTCTCTATTTGAACAGG 57.162 33.333 0.00 0.00 36.38 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
200 203 3.118408 ACTGCGAGAGGGTAATAAATGCA 60.118 43.478 0.00 0.00 0.00 3.96
219 222 5.469373 TTTGCGAGAGTATTTATGCACTG 57.531 39.130 0.00 0.00 31.16 3.66
266 269 4.701651 TGGATTTCGAAACATCAATGAGCT 59.298 37.500 13.81 0.00 0.00 4.09
292 295 3.682858 ACAAATGTGACAGTGCGGTATAC 59.317 43.478 0.00 0.00 0.00 1.47
323 326 2.185867 GAGCACCGTGGGCGATAA 59.814 61.111 0.00 0.00 41.33 1.75
372 375 4.292306 GGTGGGAGGATGGGTAAATATCAT 59.708 45.833 0.00 0.00 0.00 2.45
373 376 3.655777 GGTGGGAGGATGGGTAAATATCA 59.344 47.826 0.00 0.00 0.00 2.15
374 377 3.010250 GGGTGGGAGGATGGGTAAATATC 59.990 52.174 0.00 0.00 0.00 1.63
379 382 0.917333 GTGGGTGGGAGGATGGGTAA 60.917 60.000 0.00 0.00 0.00 2.85
396 399 6.682423 TGTATCATCAAAATGTAGCCTGTG 57.318 37.500 0.00 0.00 34.32 3.66
428 844 9.764363 ATATATGGCTTACACAATGTATATCGG 57.236 33.333 0.00 0.00 32.20 4.18
436 852 6.638063 GTGTGCAATATATGGCTTACACAATG 59.362 38.462 22.12 1.00 38.40 2.82
439 855 5.065859 GTGTGTGCAATATATGGCTTACACA 59.934 40.000 28.50 26.61 41.59 3.72
443 859 5.221028 GCAAGTGTGTGCAATATATGGCTTA 60.221 40.000 13.31 0.00 44.29 3.09
462 878 2.350772 GCTTACTGACAATTGCGCAAGT 60.351 45.455 28.62 23.97 41.68 3.16
464 880 1.068610 GGCTTACTGACAATTGCGCAA 60.069 47.619 27.24 27.24 0.00 4.85
465 881 0.521291 GGCTTACTGACAATTGCGCA 59.479 50.000 5.66 5.66 0.00 6.09
472 888 9.109393 GAGAATTATGTTATGGCTTACTGACAA 57.891 33.333 0.00 0.00 37.17 3.18
540 956 1.681486 GCGAGGGAAGAAGAGAGGGG 61.681 65.000 0.00 0.00 0.00 4.79
544 960 2.711922 GGCGCGAGGGAAGAAGAGA 61.712 63.158 12.10 0.00 0.00 3.10
545 961 2.202810 GGCGCGAGGGAAGAAGAG 60.203 66.667 12.10 0.00 0.00 2.85
546 962 2.994995 TGGCGCGAGGGAAGAAGA 60.995 61.111 12.10 0.00 0.00 2.87
547 963 2.815647 GTGGCGCGAGGGAAGAAG 60.816 66.667 12.10 0.00 0.00 2.85
548 964 3.621805 TGTGGCGCGAGGGAAGAA 61.622 61.111 12.10 0.00 0.00 2.52
607 1023 3.676605 CCGTTTTGAACCGGGGCC 61.677 66.667 6.32 0.00 40.54 5.80
626 1042 3.717294 CCCCACCCTGTTCCTCCG 61.717 72.222 0.00 0.00 0.00 4.63
660 1076 3.023735 GGCCCTCCTCCCCACATT 61.024 66.667 0.00 0.00 0.00 2.71
665 1081 4.523282 ATCAGGGCCCTCCTCCCC 62.523 72.222 25.77 0.00 46.12 4.81
666 1082 2.851588 GATCAGGGCCCTCCTCCC 60.852 72.222 25.77 5.82 46.12 4.30
667 1083 2.851588 GGATCAGGGCCCTCCTCC 60.852 72.222 25.77 26.19 46.12 4.30
668 1084 2.851588 GGGATCAGGGCCCTCCTC 60.852 72.222 25.77 21.17 46.12 3.71
670 1086 2.290021 CTTTGGGATCAGGGCCCTCC 62.290 65.000 25.77 21.46 46.19 4.30
671 1087 1.228510 CTTTGGGATCAGGGCCCTC 59.771 63.158 25.77 11.89 46.19 4.30
672 1088 1.230281 TCTTTGGGATCAGGGCCCT 60.230 57.895 22.28 22.28 46.19 5.19
673 1089 1.076705 GTCTTTGGGATCAGGGCCC 60.077 63.158 16.46 16.46 46.22 5.80
715 1131 1.613925 GTGGGGTTTTCTTCTCTTGCC 59.386 52.381 0.00 0.00 0.00 4.52
862 1290 1.674359 GTCTCTCGCTGGATCTCTGA 58.326 55.000 0.00 0.00 0.00 3.27
1274 1704 0.899720 TAGCAACTTCCCCACGGTAG 59.100 55.000 0.00 0.00 32.88 3.18
1295 1725 0.600255 ACCACCGTGAGAGCGAAAAG 60.600 55.000 0.00 0.00 0.00 2.27
1296 1726 0.675083 TACCACCGTGAGAGCGAAAA 59.325 50.000 0.00 0.00 0.00 2.29
1497 1927 2.602217 GCCACGCAGACAAAACAAGTAG 60.602 50.000 0.00 0.00 0.00 2.57
1569 1999 3.673809 AGTATTCAGCGTCAGACGAAAAC 59.326 43.478 27.29 13.67 46.05 2.43
1616 2046 7.842525 CAGTGTAAACTGTGAAAGCAAATAG 57.157 36.000 4.74 0.00 33.32 1.73
1676 2106 5.300752 CAGATACAGCACCCCTACATAAAG 58.699 45.833 0.00 0.00 0.00 1.85
1722 2152 1.202687 CCTGACCAGTGAAGCAACAGA 60.203 52.381 0.00 0.00 0.00 3.41
1839 2270 8.055335 TTCTGGTAAGAAAGCATGAATTGCATG 61.055 37.037 0.00 0.00 46.25 4.06
1886 2319 1.514087 CAGATGCCATTTTGCGCCT 59.486 52.632 4.18 0.00 0.00 5.52
2002 2435 3.853355 TGCAAATTGTGTTCCCCAAAT 57.147 38.095 0.00 0.00 0.00 2.32
2074 2632 9.511272 AAACGTCTTATATTTAGGAACAAAGGT 57.489 29.630 0.00 0.00 0.00 3.50
2078 2636 9.615295 GCAAAAACGTCTTATATTTAGGAACAA 57.385 29.630 0.00 0.00 0.00 2.83
2079 2637 8.784994 TGCAAAAACGTCTTATATTTAGGAACA 58.215 29.630 0.00 0.00 0.00 3.18
2080 2638 9.274065 CTGCAAAAACGTCTTATATTTAGGAAC 57.726 33.333 0.00 0.00 0.00 3.62
2081 2639 9.005777 ACTGCAAAAACGTCTTATATTTAGGAA 57.994 29.630 0.00 0.00 0.00 3.36
2082 2640 8.556213 ACTGCAAAAACGTCTTATATTTAGGA 57.444 30.769 0.00 0.00 0.00 2.94
2083 2641 9.274065 GAACTGCAAAAACGTCTTATATTTAGG 57.726 33.333 0.00 0.00 0.00 2.69
2084 2642 9.820229 TGAACTGCAAAAACGTCTTATATTTAG 57.180 29.630 0.00 0.00 0.00 1.85
2086 2644 9.691362 ATTGAACTGCAAAAACGTCTTATATTT 57.309 25.926 0.00 0.00 40.48 1.40
2087 2645 9.691362 AATTGAACTGCAAAAACGTCTTATATT 57.309 25.926 0.00 0.00 40.48 1.28
2092 2650 9.691362 AATATAATTGAACTGCAAAAACGTCTT 57.309 25.926 0.00 0.00 40.48 3.01
2115 2673 9.688091 TGGGTGTCAGTAGCAAAATATTTAATA 57.312 29.630 0.01 0.00 0.00 0.98
2121 2679 8.436778 TGTATATGGGTGTCAGTAGCAAAATAT 58.563 33.333 0.00 0.00 0.00 1.28
2318 2879 9.130312 GTAGAATAAGATCATTAACTGCTACCG 57.870 37.037 0.00 0.00 0.00 4.02
2351 2912 8.774546 AAGAGGTATAGACAGATGAGATGAAA 57.225 34.615 0.00 0.00 0.00 2.69
2373 2934 7.831691 TCCAAAAGGTTACAATTGATGAAGA 57.168 32.000 13.59 0.00 0.00 2.87
2831 3400 2.294791 CGCATACTAAGACCCCAGAGAG 59.705 54.545 0.00 0.00 0.00 3.20
2919 3495 3.704061 TCATGGATCAATGTACGACTCCA 59.296 43.478 9.96 5.33 37.21 3.86
2992 3568 2.486982 CAGAAGAAAGTCCTACGACGGA 59.513 50.000 0.00 0.00 44.28 4.69
2998 3574 3.938289 ACGGTCAGAAGAAAGTCCTAC 57.062 47.619 0.00 0.00 0.00 3.18
3135 3712 1.821136 TGCAGTCTGACATCATCGTCT 59.179 47.619 10.88 0.00 36.82 4.18
3230 3807 2.939103 GTGAGAAGGATGAAACGGGATG 59.061 50.000 0.00 0.00 0.00 3.51
3406 3983 6.480320 GCACTACATAGACCTCCTGTTTTATG 59.520 42.308 0.00 0.00 33.99 1.90
3448 4025 3.864789 AACCCCTTATCTACAGCATGG 57.135 47.619 0.00 0.00 43.62 3.66
3473 4050 5.114081 ACCAGGCGTTTGTACTATTCATAC 58.886 41.667 0.00 0.00 0.00 2.39
3481 4058 1.542547 CCTCAACCAGGCGTTTGTACT 60.543 52.381 0.00 0.00 34.56 2.73
3486 4063 2.224670 TGTTATCCTCAACCAGGCGTTT 60.225 45.455 0.00 0.00 43.08 3.60
3493 4070 7.148086 GCAATAAAGATGTGTTATCCTCAACCA 60.148 37.037 0.00 0.00 0.00 3.67
3562 4254 1.256812 AATTTTCAACAGGGAGGCGG 58.743 50.000 0.00 0.00 0.00 6.13
3568 4260 9.709495 TCAAATATCTCAAAATTTTCAACAGGG 57.291 29.630 0.00 0.00 0.00 4.45
3707 4403 4.985538 ACATAAGCGATCCCACCAATTAT 58.014 39.130 0.00 0.00 0.00 1.28
3740 4436 6.065374 TGAGCAACCTTGTTATGGAAACTTA 58.935 36.000 0.00 0.00 0.00 2.24
3749 4445 6.183360 GCAGACAATATGAGCAACCTTGTTAT 60.183 38.462 0.00 0.00 30.63 1.89
3758 4454 7.774134 ACAATTAATGCAGACAATATGAGCAA 58.226 30.769 0.00 0.00 38.85 3.91
3845 4541 9.485206 AAAATCAGTACAGATAACGTACAAAGT 57.515 29.630 0.65 0.00 41.40 2.66
3854 4550 9.626045 CAAAAGGGAAAAATCAGTACAGATAAC 57.374 33.333 0.65 0.00 0.00 1.89
3986 4682 0.541863 ATGGTAGGCTACAGCACACC 59.458 55.000 24.96 10.06 44.36 4.16
4178 4880 2.857186 TGCTCAGAACATTACCAGCA 57.143 45.000 0.00 0.00 34.54 4.41
4268 4973 5.058149 TGTAATGCAAGGCTAACATTGTG 57.942 39.130 19.62 1.09 35.68 3.33
4338 5050 7.671495 ATTTAATACAGGCAAAAGCCAAAAG 57.329 32.000 9.42 0.00 0.00 2.27
4407 5137 4.853468 TGTTGCCCTGTATAAAGGATGA 57.147 40.909 10.90 0.00 40.02 2.92
4527 5257 4.132336 GCTGAATGCAGATGAGGTGAATA 58.868 43.478 4.31 0.00 45.17 1.75
4765 5495 3.256631 CCAGCTGCTTCCTTTACAATTGT 59.743 43.478 16.68 16.68 0.00 2.71
4810 5540 7.449395 AGTGATGAATATTGGAGAGAGAGAGAG 59.551 40.741 0.00 0.00 0.00 3.20
4819 5549 7.071572 TGGATCTGAAGTGATGAATATTGGAGA 59.928 37.037 0.00 0.00 0.00 3.71
4820 5550 7.222161 TGGATCTGAAGTGATGAATATTGGAG 58.778 38.462 0.00 0.00 0.00 3.86
4821 5551 7.140522 TGGATCTGAAGTGATGAATATTGGA 57.859 36.000 0.00 0.00 0.00 3.53
4822 5552 7.812690 TTGGATCTGAAGTGATGAATATTGG 57.187 36.000 0.00 0.00 0.00 3.16
4930 5660 3.392616 ACAGAGAAATCTCAACCACAGGT 59.607 43.478 12.65 0.00 45.21 4.00
5050 5781 3.544684 AGACAACATGTTGCAGAGTTGA 58.455 40.909 33.23 0.00 42.87 3.18
5198 5929 4.196193 ACGAACACCTGAAATTGAAGTCA 58.804 39.130 0.00 0.00 0.00 3.41
5362 6093 4.998788 AGAAACAGTTTCAAGGTTGAAGC 58.001 39.130 24.85 10.39 46.68 3.86
5366 6097 4.265320 GCGAAAGAAACAGTTTCAAGGTTG 59.735 41.667 24.85 12.70 42.10 3.77
5367 6098 4.421058 GCGAAAGAAACAGTTTCAAGGTT 58.579 39.130 24.85 14.06 42.10 3.50
5373 6104 3.146250 CGATCGCGAAAGAAACAGTTTC 58.854 45.455 15.24 17.11 40.82 2.78
5376 6107 1.779569 ACGATCGCGAAAGAAACAGT 58.220 45.000 15.24 1.52 41.64 3.55
5402 6133 3.374220 TTACGGAGCAAGTTCGAAAGA 57.626 42.857 0.00 0.00 39.20 2.52
5403 6134 4.461992 TTTTACGGAGCAAGTTCGAAAG 57.538 40.909 0.00 0.00 0.00 2.62
5406 6137 4.512198 TGAAATTTTACGGAGCAAGTTCGA 59.488 37.500 0.00 0.00 0.00 3.71
5407 6138 4.778904 TGAAATTTTACGGAGCAAGTTCG 58.221 39.130 0.00 0.00 0.00 3.95
5408 6139 7.169140 ACAAATGAAATTTTACGGAGCAAGTTC 59.831 33.333 0.00 0.00 46.10 3.01
5409 6140 6.983890 ACAAATGAAATTTTACGGAGCAAGTT 59.016 30.769 0.00 0.00 46.10 2.66
5410 6141 6.512297 ACAAATGAAATTTTACGGAGCAAGT 58.488 32.000 0.00 0.00 46.10 3.16
5411 6142 7.359181 GGAACAAATGAAATTTTACGGAGCAAG 60.359 37.037 0.00 0.00 46.10 4.01
5412 6143 6.422400 GGAACAAATGAAATTTTACGGAGCAA 59.578 34.615 0.00 0.00 46.10 3.91
5413 6144 5.923684 GGAACAAATGAAATTTTACGGAGCA 59.076 36.000 0.00 0.00 46.10 4.26
5414 6145 6.156519 AGGAACAAATGAAATTTTACGGAGC 58.843 36.000 0.00 0.00 46.10 4.70
5415 6146 7.593825 AGAGGAACAAATGAAATTTTACGGAG 58.406 34.615 0.00 0.00 46.10 4.63
5416 6147 7.519032 AGAGGAACAAATGAAATTTTACGGA 57.481 32.000 0.00 0.00 46.10 4.69
5417 6148 9.289303 CATAGAGGAACAAATGAAATTTTACGG 57.711 33.333 0.00 0.00 46.10 4.02
5418 6149 8.798153 GCATAGAGGAACAAATGAAATTTTACG 58.202 33.333 0.00 0.00 46.10 3.18
5426 6157 4.943705 GTGAGGCATAGAGGAACAAATGAA 59.056 41.667 0.00 0.00 0.00 2.57
5458 6189 0.388778 TTTCAATCTGCGGACGCGTA 60.389 50.000 13.97 0.00 45.51 4.42
5460 6191 1.059369 CTTTCAATCTGCGGACGCG 59.941 57.895 3.53 3.53 45.51 6.01
5462 6193 0.391130 TCCCTTTCAATCTGCGGACG 60.391 55.000 0.00 0.00 0.00 4.79
5463 6194 1.066143 TCTCCCTTTCAATCTGCGGAC 60.066 52.381 0.00 0.00 0.00 4.79
5490 6225 1.132453 CGCCGAGATCAGTGTACTTCA 59.868 52.381 0.00 0.00 0.00 3.02
5500 6235 2.369257 GATGCTTCCCGCCGAGATCA 62.369 60.000 0.00 0.00 38.05 2.92
5623 6358 2.158475 AGGACAGAATTCCACTTGGCAA 60.158 45.455 0.65 0.00 38.25 4.52
5637 6372 2.875296 CCCCACAAAATTGAGGACAGA 58.125 47.619 10.68 0.00 40.79 3.41
5707 6442 6.678568 ACCATTACCAACCAATCAATCAAA 57.321 33.333 0.00 0.00 0.00 2.69
5859 6597 1.021968 AACAACGAAGAACAGGCCAC 58.978 50.000 5.01 0.00 0.00 5.01
5869 6607 6.970043 TGAATAAACAGGACAAAACAACGAAG 59.030 34.615 0.00 0.00 0.00 3.79
5870 6608 6.748198 GTGAATAAACAGGACAAAACAACGAA 59.252 34.615 0.00 0.00 0.00 3.85
5905 6643 7.333921 CAGAACAAAGAGCACTAGAAGATCAAT 59.666 37.037 0.00 0.00 0.00 2.57
5908 6646 5.063312 GCAGAACAAAGAGCACTAGAAGATC 59.937 44.000 0.00 0.00 0.00 2.75
5919 6657 3.067320 ACTTTCAAGGCAGAACAAAGAGC 59.933 43.478 0.00 0.00 0.00 4.09
5920 6658 4.553547 CGACTTTCAAGGCAGAACAAAGAG 60.554 45.833 0.00 0.00 31.90 2.85
5928 6666 3.401033 TTCATCGACTTTCAAGGCAGA 57.599 42.857 0.00 0.00 31.90 4.26
5973 6714 8.638873 GCCCAGGCTAAGTTAACATAAAATAAT 58.361 33.333 8.61 0.00 38.26 1.28
5985 6726 2.116238 AGATTCGCCCAGGCTAAGTTA 58.884 47.619 7.17 0.00 39.32 2.24
5986 6727 0.912486 AGATTCGCCCAGGCTAAGTT 59.088 50.000 7.17 0.00 39.32 2.66
5987 6728 0.179000 CAGATTCGCCCAGGCTAAGT 59.821 55.000 7.17 0.00 39.32 2.24
5988 6729 0.465705 TCAGATTCGCCCAGGCTAAG 59.534 55.000 7.17 0.00 39.32 2.18
5989 6730 1.131638 ATCAGATTCGCCCAGGCTAA 58.868 50.000 7.17 2.18 39.32 3.09
5992 6733 0.179034 AGAATCAGATTCGCCCAGGC 60.179 55.000 16.09 0.00 43.92 4.85
6005 6746 7.013274 ACTGCAAAGCTTTACAAAGTAGAATCA 59.987 33.333 12.25 0.00 38.28 2.57
6019 6760 6.396829 AAACTTATCAGACTGCAAAGCTTT 57.603 33.333 5.69 5.69 0.00 3.51
6020 6761 6.396829 AAAACTTATCAGACTGCAAAGCTT 57.603 33.333 13.50 0.00 0.00 3.74
6032 6773 6.456988 GGCATTGACGTCCTAAAACTTATCAG 60.457 42.308 14.12 0.00 0.00 2.90
6067 6808 2.712984 TGTCATGTTTGGCAGCGAA 58.287 47.368 0.00 0.00 30.95 4.70
6078 6819 4.566545 TGAAAATTCGCAACTGTCATGT 57.433 36.364 0.00 0.00 0.00 3.21
6090 6831 7.969387 TTGACAGTCTTCTTTTGAAAATTCG 57.031 32.000 1.31 0.00 38.07 3.34
6140 6901 3.083349 CCGGGAGCCATCTGGTCA 61.083 66.667 0.00 0.00 43.44 4.02
6141 6902 3.866582 CCCGGGAGCCATCTGGTC 61.867 72.222 18.48 0.00 40.86 4.02
6159 6920 4.467084 TGGGATCCCAGCGAACGC 62.467 66.667 30.62 11.31 41.89 4.84
6214 6976 4.513442 CCTCCAAATGTTGAGGACGATAA 58.487 43.478 0.00 0.00 36.99 1.75
6343 7105 1.077285 CTGCATCCCATGGCTGTCA 60.077 57.895 6.09 7.65 0.00 3.58
6344 7106 1.099879 GTCTGCATCCCATGGCTGTC 61.100 60.000 6.09 3.53 0.00 3.51
6345 7107 1.077212 GTCTGCATCCCATGGCTGT 60.077 57.895 6.09 0.00 0.00 4.40
6346 7108 0.471191 TAGTCTGCATCCCATGGCTG 59.529 55.000 6.09 7.22 0.00 4.85
6347 7109 0.763652 CTAGTCTGCATCCCATGGCT 59.236 55.000 6.09 0.00 0.00 4.75
6349 7111 3.565764 TTTCTAGTCTGCATCCCATGG 57.434 47.619 4.14 4.14 0.00 3.66
6350 7112 4.885907 ACATTTTCTAGTCTGCATCCCATG 59.114 41.667 0.00 0.00 0.00 3.66
6351 7113 5.121380 ACATTTTCTAGTCTGCATCCCAT 57.879 39.130 0.00 0.00 0.00 4.00
6352 7114 4.574674 ACATTTTCTAGTCTGCATCCCA 57.425 40.909 0.00 0.00 0.00 4.37
6388 7151 8.537728 TCCAATTGGCAACTGATATAGAAAAT 57.462 30.769 20.33 0.00 34.44 1.82
6398 7161 2.886523 CAAGTCTCCAATTGGCAACTGA 59.113 45.455 24.00 13.24 32.46 3.41
6454 7217 1.474077 GGAATTTCGCAACCAGCATCT 59.526 47.619 0.00 0.00 46.13 2.90
6458 7221 1.154035 CGGGAATTTCGCAACCAGC 60.154 57.895 13.16 0.00 40.87 4.85
6459 7222 0.447801 CTCGGGAATTTCGCAACCAG 59.552 55.000 13.16 0.72 0.00 4.00
6460 7223 1.582610 GCTCGGGAATTTCGCAACCA 61.583 55.000 13.16 0.00 0.00 3.67
6461 7224 1.136774 GCTCGGGAATTTCGCAACC 59.863 57.895 13.16 0.00 0.00 3.77
6485 7248 8.342634 GCTGCTACCAATCGATTTAAATAGAAA 58.657 33.333 13.94 0.00 0.00 2.52
6508 7271 0.249953 TTGCCCATTTGCTGTTGCTG 60.250 50.000 0.00 0.00 40.48 4.41
6514 7277 1.295792 GATGCATTGCCCATTTGCTG 58.704 50.000 6.12 0.00 37.28 4.41
6559 7322 6.109359 CGACCCTGTTCAAATAGAGAAGAAT 58.891 40.000 0.00 0.00 0.00 2.40
6562 7325 3.619038 GCGACCCTGTTCAAATAGAGAAG 59.381 47.826 0.00 0.00 0.00 2.85
6564 7327 2.832129 AGCGACCCTGTTCAAATAGAGA 59.168 45.455 0.00 0.00 0.00 3.10
6565 7328 3.252974 AGCGACCCTGTTCAAATAGAG 57.747 47.619 0.00 0.00 0.00 2.43
6567 7330 3.127030 GGAAAGCGACCCTGTTCAAATAG 59.873 47.826 0.00 0.00 0.00 1.73
6568 7331 3.078837 GGAAAGCGACCCTGTTCAAATA 58.921 45.455 0.00 0.00 0.00 1.40
6569 7332 1.886542 GGAAAGCGACCCTGTTCAAAT 59.113 47.619 0.00 0.00 0.00 2.32
6579 7342 4.636206 AGATGTTTCTAATGGAAAGCGACC 59.364 41.667 0.00 0.00 43.59 4.79


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

AutoCloner maintained by Alex Coulton.