Multiple sequence alignment - TraesCS4A01G015700

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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 TraesCS4A01G015700 chr4A 100.000 2666 0 0 1 2666 9909077 9906412 0.000000e+00 4924.0
1 TraesCS4A01G015700 chr4A 90.976 820 39 8 1851 2660 630904102 630904896 0.000000e+00 1072.0
2 TraesCS4A01G015700 chr4A 84.504 413 35 11 1249 1653 9629193 9628802 5.390000e-102 381.0
3 TraesCS4A01G015700 chr4A 83.135 421 32 10 1076 1493 9626503 9626119 5.460000e-92 348.0
4 TraesCS4A01G015700 chr4A 79.452 292 27 9 1076 1364 9623470 9623209 2.730000e-40 176.0
5 TraesCS4A01G015700 chr4A 92.424 66 2 1 1799 1864 630904022 630904084 1.020000e-14 91.6
6 TraesCS4A01G015700 chr4D 92.004 963 42 11 720 1647 459059931 459060893 0.000000e+00 1319.0
7 TraesCS4A01G015700 chr4D 86.998 523 35 16 162 664 459059418 459059927 2.320000e-155 558.0
8 TraesCS4A01G015700 chr4D 83.705 583 48 16 1076 1644 459066149 459066698 8.520000e-140 507.0
9 TraesCS4A01G015700 chr4D 80.702 285 22 13 1076 1357 459068477 459068731 9.740000e-45 191.0
10 TraesCS4A01G015700 chr4B 91.327 957 52 19 702 1644 573295969 573296908 0.000000e+00 1279.0
11 TraesCS4A01G015700 chr4B 90.939 309 21 6 257 560 573295530 573295836 2.470000e-110 409.0
12 TraesCS4A01G015700 chr6D 93.973 813 38 8 1857 2660 3832232 3833042 0.000000e+00 1219.0
13 TraesCS4A01G015700 chr6D 92.330 704 26 3 1851 2550 430311300 430310621 0.000000e+00 976.0
14 TraesCS4A01G015700 chr6D 96.825 63 2 0 1802 1864 430311380 430311318 3.630000e-19 106.0
15 TraesCS4A01G015700 chr6D 92.188 64 5 0 1715 1778 3826252 3826315 1.020000e-14 91.6
16 TraesCS4A01G015700 chr3D 91.697 819 33 7 1851 2660 144777834 144778626 0.000000e+00 1103.0
17 TraesCS4A01G015700 chr3D 95.455 66 3 0 1799 1864 144777751 144777816 3.630000e-19 106.0
18 TraesCS4A01G015700 chr3D 94.118 68 4 0 1714 1781 144779377 144779310 1.310000e-18 104.0
19 TraesCS4A01G015700 chr5B 91.575 819 37 11 1851 2660 426623277 426624072 0.000000e+00 1101.0
20 TraesCS4A01G015700 chr5B 95.455 66 3 0 1799 1864 426623194 426623259 3.630000e-19 106.0
21 TraesCS4A01G015700 chr1B 91.453 819 35 8 1851 2660 435185790 435184998 0.000000e+00 1092.0
22 TraesCS4A01G015700 chr6B 90.319 816 46 8 1853 2660 704702272 704701482 0.000000e+00 1038.0
23 TraesCS4A01G015700 chr6B 92.424 66 5 0 1716 1781 704700736 704700801 7.860000e-16 95.3
24 TraesCS4A01G015700 chr6B 92.424 66 5 0 1716 1781 704704386 704704321 7.860000e-16 95.3
25 TraesCS4A01G015700 chr1A 90.763 747 37 5 1856 2594 531692568 531691846 0.000000e+00 968.0
26 TraesCS4A01G015700 chr1A 92.537 67 5 0 1715 1781 531706456 531706390 2.180000e-16 97.1
27 TraesCS4A01G015700 chr1A 92.424 66 5 0 1716 1781 531691144 531691209 7.860000e-16 95.3
28 TraesCS4A01G015700 chrUn 93.581 592 32 4 2074 2660 342225984 342225394 0.000000e+00 878.0
29 TraesCS4A01G015700 chrUn 92.424 66 5 0 1716 1781 342224649 342224714 7.860000e-16 95.3
30 TraesCS4A01G015700 chr3B 89.716 457 39 5 1853 2304 42486563 42487016 6.400000e-161 577.0
31 TraesCS4A01G015700 chr3B 86.093 302 14 8 1851 2148 262185445 262185168 1.550000e-77 300.0
32 TraesCS4A01G015700 chr2B 89.634 164 11 3 2503 2661 765787072 765786910 1.250000e-48 204.0
33 TraesCS4A01G015700 chr7B 93.548 62 4 0 1803 1864 552036367 552036428 2.830000e-15 93.5


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 TraesCS4A01G015700 chr4A 9906412 9909077 2665 True 4924.000000 4924 100.000000 1 2666 1 chr4A.!!$R1 2665
1 TraesCS4A01G015700 chr4A 630904022 630904896 874 False 581.800000 1072 91.700000 1799 2660 2 chr4A.!!$F1 861
2 TraesCS4A01G015700 chr4A 9623209 9629193 5984 True 301.666667 381 82.363667 1076 1653 3 chr4A.!!$R2 577
3 TraesCS4A01G015700 chr4D 459059418 459060893 1475 False 938.500000 1319 89.501000 162 1647 2 chr4D.!!$F1 1485
4 TraesCS4A01G015700 chr4D 459066149 459068731 2582 False 349.000000 507 82.203500 1076 1644 2 chr4D.!!$F2 568
5 TraesCS4A01G015700 chr4B 573295530 573296908 1378 False 844.000000 1279 91.133000 257 1644 2 chr4B.!!$F1 1387
6 TraesCS4A01G015700 chr6D 3832232 3833042 810 False 1219.000000 1219 93.973000 1857 2660 1 chr6D.!!$F2 803
7 TraesCS4A01G015700 chr6D 430310621 430311380 759 True 541.000000 976 94.577500 1802 2550 2 chr6D.!!$R1 748
8 TraesCS4A01G015700 chr3D 144777751 144778626 875 False 604.500000 1103 93.576000 1799 2660 2 chr3D.!!$F1 861
9 TraesCS4A01G015700 chr5B 426623194 426624072 878 False 603.500000 1101 93.515000 1799 2660 2 chr5B.!!$F1 861
10 TraesCS4A01G015700 chr1B 435184998 435185790 792 True 1092.000000 1092 91.453000 1851 2660 1 chr1B.!!$R1 809
11 TraesCS4A01G015700 chr6B 704701482 704704386 2904 True 566.650000 1038 91.371500 1716 2660 2 chr6B.!!$R1 944
12 TraesCS4A01G015700 chr1A 531691846 531692568 722 True 968.000000 968 90.763000 1856 2594 1 chr1A.!!$R1 738
13 TraesCS4A01G015700 chrUn 342225394 342225984 590 True 878.000000 878 93.581000 2074 2660 1 chrUn.!!$R1 586

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
151 152 0.034059 GTATCATCTGGTCGGGGCTG 59.966 60.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1693 4010 0.10104 ATTTCCACGCGCAATCCATG 59.899 50.0 5.73 0.0 0.0 3.66 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
17 18 2.359850 TGCCGCACCCATTCAGTC 60.360 61.111 0.00 0.00 0.00 3.51
18 19 2.359850 GCCGCACCCATTCAGTCA 60.360 61.111 0.00 0.00 0.00 3.41
19 20 1.750399 GCCGCACCCATTCAGTCAT 60.750 57.895 0.00 0.00 0.00 3.06
24 25 1.406069 GCACCCATTCAGTCATCGTCT 60.406 52.381 0.00 0.00 0.00 4.18
25 26 2.936993 GCACCCATTCAGTCATCGTCTT 60.937 50.000 0.00 0.00 0.00 3.01
26 27 3.338249 CACCCATTCAGTCATCGTCTTT 58.662 45.455 0.00 0.00 0.00 2.52
27 28 3.753272 CACCCATTCAGTCATCGTCTTTT 59.247 43.478 0.00 0.00 0.00 2.27
50 51 7.901874 TTTTGTTATTGTTACGAAGAACAGC 57.098 32.000 0.00 0.00 38.07 4.40
51 52 6.606234 TTGTTATTGTTACGAAGAACAGCA 57.394 33.333 0.00 0.00 38.07 4.41
52 53 6.795098 TGTTATTGTTACGAAGAACAGCAT 57.205 33.333 0.00 0.00 40.31 3.79
55 56 1.724623 TGTTACGAAGAACAGCATCGC 59.275 47.619 0.00 0.00 41.10 4.58
56 57 1.724623 GTTACGAAGAACAGCATCGCA 59.275 47.619 0.00 0.00 41.10 5.10
57 58 2.293677 TACGAAGAACAGCATCGCAT 57.706 45.000 0.00 0.00 41.10 4.73
58 59 0.723414 ACGAAGAACAGCATCGCATG 59.277 50.000 0.00 0.00 41.10 4.06
59 60 0.723414 CGAAGAACAGCATCGCATGT 59.277 50.000 0.00 0.00 30.53 3.21
61 62 2.285256 CGAAGAACAGCATCGCATGTAC 60.285 50.000 0.00 0.00 30.53 2.90
62 63 2.680312 AGAACAGCATCGCATGTACT 57.320 45.000 0.00 0.00 0.00 2.73
63 64 2.544685 AGAACAGCATCGCATGTACTC 58.455 47.619 0.00 0.00 0.00 2.59
64 65 1.256376 GAACAGCATCGCATGTACTCG 59.744 52.381 0.00 0.00 0.00 4.18
65 66 0.173481 ACAGCATCGCATGTACTCGT 59.827 50.000 0.00 0.00 0.00 4.18
66 67 1.404035 ACAGCATCGCATGTACTCGTA 59.596 47.619 0.00 0.00 0.00 3.43
67 68 2.047040 CAGCATCGCATGTACTCGTAG 58.953 52.381 0.00 0.00 0.00 3.51
69 70 1.269102 GCATCGCATGTACTCGTAGGT 60.269 52.381 0.00 0.00 0.00 3.08
71 72 3.444916 CATCGCATGTACTCGTAGGTTT 58.555 45.455 0.00 0.00 0.00 3.27
73 74 2.488937 TCGCATGTACTCGTAGGTTTGA 59.511 45.455 0.00 0.00 0.00 2.69
74 75 3.057386 TCGCATGTACTCGTAGGTTTGAA 60.057 43.478 0.00 0.00 0.00 2.69
75 76 3.676172 CGCATGTACTCGTAGGTTTGAAA 59.324 43.478 0.00 0.00 0.00 2.69
76 77 4.201589 CGCATGTACTCGTAGGTTTGAAAG 60.202 45.833 0.00 0.00 0.00 2.62
78 79 4.942761 TGTACTCGTAGGTTTGAAAGGT 57.057 40.909 0.00 0.00 0.00 3.50
79 80 4.624015 TGTACTCGTAGGTTTGAAAGGTG 58.376 43.478 0.00 0.00 0.00 4.00
80 81 3.121738 ACTCGTAGGTTTGAAAGGTGG 57.878 47.619 0.00 0.00 0.00 4.61
81 82 2.701951 ACTCGTAGGTTTGAAAGGTGGA 59.298 45.455 0.00 0.00 0.00 4.02
82 83 3.326880 ACTCGTAGGTTTGAAAGGTGGAT 59.673 43.478 0.00 0.00 0.00 3.41
83 84 3.670625 TCGTAGGTTTGAAAGGTGGATG 58.329 45.455 0.00 0.00 0.00 3.51
85 86 3.435671 CGTAGGTTTGAAAGGTGGATGTC 59.564 47.826 0.00 0.00 0.00 3.06
86 87 3.593442 AGGTTTGAAAGGTGGATGTCA 57.407 42.857 0.00 0.00 0.00 3.58
88 89 3.117512 AGGTTTGAAAGGTGGATGTCAGT 60.118 43.478 0.00 0.00 0.00 3.41
89 90 3.004734 GGTTTGAAAGGTGGATGTCAGTG 59.995 47.826 0.00 0.00 0.00 3.66
90 91 3.576078 TTGAAAGGTGGATGTCAGTGT 57.424 42.857 0.00 0.00 0.00 3.55
91 92 2.849942 TGAAAGGTGGATGTCAGTGTG 58.150 47.619 0.00 0.00 0.00 3.82
92 93 2.172505 TGAAAGGTGGATGTCAGTGTGT 59.827 45.455 0.00 0.00 0.00 3.72
93 94 2.260844 AAGGTGGATGTCAGTGTGTG 57.739 50.000 0.00 0.00 0.00 3.82
94 95 0.397941 AGGTGGATGTCAGTGTGTGG 59.602 55.000 0.00 0.00 0.00 4.17
95 96 0.396435 GGTGGATGTCAGTGTGTGGA 59.604 55.000 0.00 0.00 0.00 4.02
98 99 2.485426 GTGGATGTCAGTGTGTGGATTG 59.515 50.000 0.00 0.00 0.00 2.67
99 100 2.371510 TGGATGTCAGTGTGTGGATTGA 59.628 45.455 0.00 0.00 0.00 2.57
100 101 3.181446 TGGATGTCAGTGTGTGGATTGAA 60.181 43.478 0.00 0.00 0.00 2.69
101 102 3.820467 GGATGTCAGTGTGTGGATTGAAA 59.180 43.478 0.00 0.00 0.00 2.69
103 104 3.884895 TGTCAGTGTGTGGATTGAAAGT 58.115 40.909 0.00 0.00 0.00 2.66
105 106 4.335315 TGTCAGTGTGTGGATTGAAAGTTC 59.665 41.667 0.00 0.00 0.00 3.01
106 107 4.335315 GTCAGTGTGTGGATTGAAAGTTCA 59.665 41.667 0.00 0.00 34.92 3.18
121 122 7.915293 TGAAAGTTCAAAGAGTTGTTGTAGA 57.085 32.000 0.00 0.00 36.07 2.59
123 124 8.612619 TGAAAGTTCAAAGAGTTGTTGTAGATC 58.387 33.333 0.00 0.00 36.07 2.75
124 125 8.738645 AAAGTTCAAAGAGTTGTTGTAGATCT 57.261 30.769 0.00 0.00 36.07 2.75
125 126 9.832445 AAAGTTCAAAGAGTTGTTGTAGATCTA 57.168 29.630 0.00 0.00 36.07 1.98
129 130 7.827701 TCAAAGAGTTGTTGTAGATCTATCGT 58.172 34.615 5.57 0.00 36.07 3.73
130 131 8.304596 TCAAAGAGTTGTTGTAGATCTATCGTT 58.695 33.333 5.57 0.00 36.07 3.85
133 134 6.153000 AGAGTTGTTGTAGATCTATCGTTGGT 59.847 38.462 5.57 0.00 0.00 3.67
134 135 7.338703 AGAGTTGTTGTAGATCTATCGTTGGTA 59.661 37.037 5.57 0.00 0.00 3.25
136 137 8.136165 AGTTGTTGTAGATCTATCGTTGGTATC 58.864 37.037 5.57 0.00 0.00 2.24
137 138 7.576861 TGTTGTAGATCTATCGTTGGTATCA 57.423 36.000 5.57 0.00 0.00 2.15
138 139 8.178313 TGTTGTAGATCTATCGTTGGTATCAT 57.822 34.615 5.57 0.00 0.00 2.45
140 141 8.516234 GTTGTAGATCTATCGTTGGTATCATCT 58.484 37.037 5.57 0.00 0.00 2.90
142 143 6.522625 AGATCTATCGTTGGTATCATCTGG 57.477 41.667 0.00 0.00 0.00 3.86
143 144 6.013379 AGATCTATCGTTGGTATCATCTGGT 58.987 40.000 0.00 0.00 0.00 4.00
144 145 5.707242 TCTATCGTTGGTATCATCTGGTC 57.293 43.478 0.00 0.00 0.00 4.02
147 148 1.538204 CGTTGGTATCATCTGGTCGGG 60.538 57.143 0.00 0.00 0.00 5.14
149 150 1.371558 GGTATCATCTGGTCGGGGC 59.628 63.158 0.00 0.00 0.00 5.80
150 151 1.122019 GGTATCATCTGGTCGGGGCT 61.122 60.000 0.00 0.00 0.00 5.19
151 152 0.034059 GTATCATCTGGTCGGGGCTG 59.966 60.000 0.00 0.00 0.00 4.85
152 153 0.398522 TATCATCTGGTCGGGGCTGT 60.399 55.000 0.00 0.00 0.00 4.40
153 154 1.976132 ATCATCTGGTCGGGGCTGTG 61.976 60.000 0.00 0.00 0.00 3.66
159 160 3.845259 GTCGGGGCTGTGCGGATA 61.845 66.667 0.00 0.00 0.00 2.59
161 162 4.910585 CGGGGCTGTGCGGATACC 62.911 72.222 0.00 0.00 0.00 2.73
179 180 0.240945 CCGCTTTTTCGCAGAACCAT 59.759 50.000 0.00 0.00 45.90 3.55
184 185 3.612479 GCTTTTTCGCAGAACCATGTGAT 60.612 43.478 0.00 0.00 45.90 3.06
194 197 2.485677 CCATGTGATGGCTGTGGTC 58.514 57.895 0.00 0.00 44.70 4.02
198 201 0.035317 TGTGATGGCTGTGGTCTGTC 59.965 55.000 0.00 0.00 0.00 3.51
207 210 3.256960 TGGTCTGTCCAAGGGGCC 61.257 66.667 0.00 0.00 44.12 5.80
209 212 4.410400 GTCTGTCCAAGGGGCCCG 62.410 72.222 18.95 3.17 0.00 6.13
251 254 0.040958 GCGGGCGACATGAATGAATC 60.041 55.000 0.00 0.00 0.00 2.52
259 262 5.628193 GGCGACATGAATGAATCAATCAATC 59.372 40.000 5.00 5.65 42.54 2.67
295 300 3.334691 CTCACATGCCGGTTTCTTTCTA 58.665 45.455 1.90 0.00 0.00 2.10
307 312 5.276536 CGGTTTCTTTCTAGTTTTCGTTCGT 60.277 40.000 0.00 0.00 0.00 3.85
494 505 5.723492 TGACTCGAGAATTCGTCGTTATA 57.277 39.130 21.68 6.69 46.72 0.98
530 551 1.411493 GGATTTCGTCGTCGGTGCTC 61.411 60.000 1.55 0.00 37.69 4.26
542 563 2.202570 GTGCTCGCCGTCGTGTAT 60.203 61.111 0.00 0.00 36.96 2.29
562 586 1.967319 TCCAAGTCTCCAACAACTGC 58.033 50.000 0.00 0.00 0.00 4.40
580 632 7.147976 ACAACTGCAAGATAAACAAGATTTCC 58.852 34.615 0.00 0.00 37.43 3.13
618 670 5.022787 AGGAGCCTGGAAGATACATATCTC 58.977 45.833 0.00 0.00 41.96 2.75
680 732 3.768922 GCTCTGGCTGGCGAGTCT 61.769 66.667 18.51 0.00 35.22 3.24
682 734 1.153667 CTCTGGCTGGCGAGTCTTC 60.154 63.158 0.97 0.00 0.00 2.87
683 735 2.125350 CTGGCTGGCGAGTCTTCC 60.125 66.667 0.97 0.00 0.00 3.46
685 737 3.394836 GGCTGGCGAGTCTTCCCT 61.395 66.667 0.00 0.00 0.00 4.20
686 738 2.185608 GCTGGCGAGTCTTCCCTC 59.814 66.667 0.00 0.00 0.00 4.30
687 739 2.650116 GCTGGCGAGTCTTCCCTCA 61.650 63.158 0.00 0.00 0.00 3.86
688 740 1.975327 CTGGCGAGTCTTCCCTCAA 59.025 57.895 0.00 0.00 0.00 3.02
689 741 0.321671 CTGGCGAGTCTTCCCTCAAA 59.678 55.000 0.00 0.00 0.00 2.69
690 742 0.762418 TGGCGAGTCTTCCCTCAAAA 59.238 50.000 0.00 0.00 0.00 2.44
691 743 1.142060 TGGCGAGTCTTCCCTCAAAAA 59.858 47.619 0.00 0.00 0.00 1.94
715 767 2.041153 AAAAAGGTTCTGGCTGGCG 58.959 52.632 0.00 0.00 0.00 5.69
716 768 0.467290 AAAAAGGTTCTGGCTGGCGA 60.467 50.000 0.00 0.00 0.00 5.54
717 769 0.890996 AAAAGGTTCTGGCTGGCGAG 60.891 55.000 0.00 0.00 0.00 5.03
758 811 2.563013 GATCCACCCAGCACCAGCAT 62.563 60.000 0.00 0.00 45.49 3.79
852 910 1.423845 GCGTGGCGGAAACATACAG 59.576 57.895 0.00 0.00 0.00 2.74
890 948 3.614630 GCACCCGGTAATAAACAAAACCC 60.615 47.826 0.00 0.00 0.00 4.11
1033 1109 2.098770 GCAAAGAGCATCCAGATTCCAC 59.901 50.000 0.00 0.00 44.79 4.02
1047 1123 1.131638 TTCCACACTCCAGAGCAACT 58.868 50.000 0.00 0.00 0.00 3.16
1423 3042 1.529309 CTCTCCCCCTTAAGCCAGC 59.471 63.158 0.00 0.00 0.00 4.85
1429 3048 0.468226 CCCCTTAAGCCAGCGTCATA 59.532 55.000 0.00 0.00 0.00 2.15
1474 3097 2.116366 GTGCTTTACTGGTTTGCAACG 58.884 47.619 0.00 0.00 35.34 4.10
1493 3116 5.558463 GCAACGAGGAAGAAGTGTACTTTTC 60.558 44.000 0.00 5.31 36.11 2.29
1506 3132 4.088213 GTGTACTTTTCGTACTGCTCTTCG 59.912 45.833 0.00 0.00 46.89 3.79
1512 3138 1.078759 CGTACTGCTCTTCGCTTGGG 61.079 60.000 0.00 0.00 40.11 4.12
1545 3832 6.761731 TGCGTTTTGACATTTTATCTTTGG 57.238 33.333 0.00 0.00 0.00 3.28
1547 3834 6.640499 TGCGTTTTGACATTTTATCTTTGGAG 59.360 34.615 0.00 0.00 0.00 3.86
1610 3927 2.273912 GGTGACCCTCGGAGTCGTT 61.274 63.158 4.02 0.00 37.04 3.85
1640 3957 1.551430 TCCCATGTACGGTCACGATTT 59.449 47.619 0.00 0.00 44.60 2.17
1644 3961 4.116961 CCATGTACGGTCACGATTTGTAT 58.883 43.478 0.00 0.00 44.60 2.29
1647 3964 4.417506 TGTACGGTCACGATTTGTATGAG 58.582 43.478 0.00 0.00 44.60 2.90
1650 3967 2.530297 CGGTCACGATTTGTATGAGTCG 59.470 50.000 0.00 0.00 44.60 4.18
1653 3970 3.303495 GTCACGATTTGTATGAGTCGGTG 59.697 47.826 0.00 0.00 38.33 4.94
1655 3972 3.547868 CACGATTTGTATGAGTCGGTGAG 59.452 47.826 0.00 0.00 38.33 3.51
1656 3973 2.535984 CGATTTGTATGAGTCGGTGAGC 59.464 50.000 0.00 0.00 0.00 4.26
1657 3974 1.990799 TTTGTATGAGTCGGTGAGCG 58.009 50.000 0.00 0.00 0.00 5.03
1658 3975 1.170442 TTGTATGAGTCGGTGAGCGA 58.830 50.000 1.26 1.26 0.00 4.93
1659 3976 0.733150 TGTATGAGTCGGTGAGCGAG 59.267 55.000 7.11 0.00 0.00 5.03
1660 3977 1.015109 GTATGAGTCGGTGAGCGAGA 58.985 55.000 7.11 0.00 0.00 4.04
1661 3978 1.400846 GTATGAGTCGGTGAGCGAGAA 59.599 52.381 7.11 0.00 0.00 2.87
1662 3979 0.888619 ATGAGTCGGTGAGCGAGAAA 59.111 50.000 7.11 0.00 0.00 2.52
1663 3980 0.671796 TGAGTCGGTGAGCGAGAAAA 59.328 50.000 7.11 0.00 0.00 2.29
1664 3981 1.067974 TGAGTCGGTGAGCGAGAAAAA 59.932 47.619 7.11 0.00 0.00 1.94
1683 4000 2.629017 AAAAATCCTCCCATGTGCCT 57.371 45.000 0.00 0.00 0.00 4.75
1684 4001 2.629017 AAAATCCTCCCATGTGCCTT 57.371 45.000 0.00 0.00 0.00 4.35
1685 4002 2.149973 AAATCCTCCCATGTGCCTTC 57.850 50.000 0.00 0.00 0.00 3.46
1686 4003 0.107017 AATCCTCCCATGTGCCTTCG 60.107 55.000 0.00 0.00 0.00 3.79
1687 4004 2.615227 ATCCTCCCATGTGCCTTCGC 62.615 60.000 0.00 0.00 0.00 4.70
1688 4005 2.270205 CTCCCATGTGCCTTCGCT 59.730 61.111 0.00 0.00 35.36 4.93
1689 4006 1.377725 CTCCCATGTGCCTTCGCTT 60.378 57.895 0.00 0.00 35.36 4.68
1690 4007 0.962356 CTCCCATGTGCCTTCGCTTT 60.962 55.000 0.00 0.00 35.36 3.51
1691 4008 0.960364 TCCCATGTGCCTTCGCTTTC 60.960 55.000 0.00 0.00 35.36 2.62
1692 4009 1.508088 CCATGTGCCTTCGCTTTCC 59.492 57.895 0.00 0.00 35.36 3.13
1693 4010 1.508088 CATGTGCCTTCGCTTTCCC 59.492 57.895 0.00 0.00 35.36 3.97
1694 4011 1.074775 ATGTGCCTTCGCTTTCCCA 59.925 52.632 0.00 0.00 35.36 4.37
1695 4012 0.323725 ATGTGCCTTCGCTTTCCCAT 60.324 50.000 0.00 0.00 35.36 4.00
1696 4013 1.243342 TGTGCCTTCGCTTTCCCATG 61.243 55.000 0.00 0.00 35.36 3.66
1697 4014 1.678635 TGCCTTCGCTTTCCCATGG 60.679 57.895 4.14 4.14 35.36 3.66
1698 4015 1.378514 GCCTTCGCTTTCCCATGGA 60.379 57.895 15.22 0.00 0.00 3.41
1699 4016 0.753111 GCCTTCGCTTTCCCATGGAT 60.753 55.000 15.22 0.00 0.00 3.41
1700 4017 1.767759 CCTTCGCTTTCCCATGGATT 58.232 50.000 15.22 0.00 0.00 3.01
1701 4018 1.406539 CCTTCGCTTTCCCATGGATTG 59.593 52.381 15.22 0.00 0.00 2.67
1702 4019 0.817013 TTCGCTTTCCCATGGATTGC 59.183 50.000 15.22 10.84 0.00 3.56
1703 4020 1.064621 CGCTTTCCCATGGATTGCG 59.935 57.895 15.22 18.56 43.02 4.85
1704 4021 1.227060 GCTTTCCCATGGATTGCGC 60.227 57.895 15.22 0.00 0.00 6.09
1705 4022 1.064621 CTTTCCCATGGATTGCGCG 59.935 57.895 15.22 0.00 0.00 6.86
1706 4023 1.656818 CTTTCCCATGGATTGCGCGT 61.657 55.000 15.22 0.00 0.00 6.01
1707 4024 1.932011 TTTCCCATGGATTGCGCGTG 61.932 55.000 15.22 0.00 0.00 5.34
1708 4025 3.891400 CCCATGGATTGCGCGTGG 61.891 66.667 15.22 5.18 0.00 4.94
1709 4026 2.823593 CCATGGATTGCGCGTGGA 60.824 61.111 5.56 0.00 31.59 4.02
1710 4027 2.405805 CCATGGATTGCGCGTGGAA 61.406 57.895 5.56 5.09 31.59 3.53
1711 4028 1.505807 CATGGATTGCGCGTGGAAA 59.494 52.632 7.09 0.00 0.00 3.13
1712 4029 0.101040 CATGGATTGCGCGTGGAAAT 59.899 50.000 7.09 2.93 0.00 2.17
1713 4030 1.333308 CATGGATTGCGCGTGGAAATA 59.667 47.619 7.09 0.00 0.00 1.40
1714 4031 1.013596 TGGATTGCGCGTGGAAATAG 58.986 50.000 7.09 0.00 0.00 1.73
1726 4043 3.381949 GTGGAAATAGGGAACGAGATCG 58.618 50.000 0.00 0.00 46.33 3.69
1757 4074 0.818445 TCGATCTACTGCCGAGGGAC 60.818 60.000 0.00 0.00 0.00 4.46
1761 4078 0.035152 TCTACTGCCGAGGGACGTAA 60.035 55.000 0.00 0.00 40.78 3.18
1788 4105 3.829044 CGCCGTCCGTGGACCATA 61.829 66.667 13.24 0.00 41.76 2.74
1790 4107 1.798234 CGCCGTCCGTGGACCATATA 61.798 60.000 13.24 0.00 41.76 0.86
1791 4108 0.606604 GCCGTCCGTGGACCATATAT 59.393 55.000 13.24 0.00 41.76 0.86
1792 4109 1.820519 GCCGTCCGTGGACCATATATA 59.179 52.381 13.24 0.00 41.76 0.86
1793 4110 2.429610 GCCGTCCGTGGACCATATATAT 59.570 50.000 13.24 0.00 41.76 0.86
1794 4111 3.737047 GCCGTCCGTGGACCATATATATG 60.737 52.174 14.78 14.78 41.76 1.78
1795 4112 3.446161 CCGTCCGTGGACCATATATATGT 59.554 47.826 19.11 9.12 41.76 2.29
1796 4113 4.641541 CCGTCCGTGGACCATATATATGTA 59.358 45.833 19.11 2.93 41.76 2.29
1800 6062 7.228108 CGTCCGTGGACCATATATATGTACTAT 59.772 40.741 19.11 2.18 41.76 2.12
1832 6094 0.676466 TGCTAGCCCACCAAATGACG 60.676 55.000 13.29 0.00 0.00 4.35
1862 6266 0.239879 TGCGCGCCTAAAGAAAAAGG 59.760 50.000 30.77 0.00 35.86 3.11
1864 6268 1.728179 GCGCGCCTAAAGAAAAAGGAC 60.728 52.381 23.24 0.00 34.58 3.85
1876 6280 4.536765 AGAAAAAGGACTTGGCTTGAGAA 58.463 39.130 0.00 0.00 0.00 2.87
1930 6334 6.106673 ACAAAACTACATCATAGTTCGAGGG 58.893 40.000 0.05 0.00 36.82 4.30
2031 6438 7.568199 TTCTTTAGAAGAAACAAGAGGTTGG 57.432 36.000 0.88 0.00 44.10 3.77
2033 6440 3.229697 AGAAGAAACAAGAGGTTGGGG 57.770 47.619 0.00 0.00 40.35 4.96
2034 6441 2.783510 AGAAGAAACAAGAGGTTGGGGA 59.216 45.455 0.00 0.00 40.35 4.81
2036 6443 3.229697 AGAAACAAGAGGTTGGGGAAG 57.770 47.619 0.00 0.00 40.35 3.46
2038 6445 2.959465 AACAAGAGGTTGGGGAAGAG 57.041 50.000 0.00 0.00 38.60 2.85
2041 6448 0.772124 AAGAGGTTGGGGAAGAGGCA 60.772 55.000 0.00 0.00 0.00 4.75
2042 6449 0.551131 AGAGGTTGGGGAAGAGGCAT 60.551 55.000 0.00 0.00 0.00 4.40
2044 6451 1.142688 AGGTTGGGGAAGAGGCATGT 61.143 55.000 0.00 0.00 0.00 3.21
2045 6452 0.623723 GGTTGGGGAAGAGGCATGTA 59.376 55.000 0.00 0.00 0.00 2.29
2047 6454 1.282157 GTTGGGGAAGAGGCATGTAGT 59.718 52.381 0.00 0.00 0.00 2.73
2048 6455 0.911769 TGGGGAAGAGGCATGTAGTG 59.088 55.000 0.00 0.00 0.00 2.74
2050 6457 0.912486 GGGAAGAGGCATGTAGTGGT 59.088 55.000 0.00 0.00 0.00 4.16
2124 7249 9.436957 GTCTCAAGATTACAAGGACAATCTTAA 57.563 33.333 8.73 0.00 45.33 1.85
2153 7278 7.823745 ACTCAACTTTTGATGGTAATCTTGT 57.176 32.000 0.00 0.00 39.30 3.16
2241 7384 5.588845 TCAATTTCCAGGGACCAATTACAT 58.411 37.500 0.00 0.00 0.00 2.29
2242 7385 5.421693 TCAATTTCCAGGGACCAATTACATG 59.578 40.000 0.00 0.00 0.00 3.21
2275 7418 0.249398 GGGTCGTGGTGAAGTGCTAT 59.751 55.000 0.00 0.00 0.00 2.97
2277 7420 2.000447 GGTCGTGGTGAAGTGCTATTC 59.000 52.381 0.00 0.00 0.00 1.75
2335 7478 2.935201 GCACAAACAAGCATGGTTTTGA 59.065 40.909 22.47 0.00 36.27 2.69
2345 7488 5.549742 AGCATGGTTTTGAGAAATTTGGA 57.450 34.783 0.00 0.00 0.00 3.53
2355 7498 8.882736 GTTTTGAGAAATTTGGACATTCAGTTT 58.117 29.630 0.00 0.00 0.00 2.66
2385 7529 7.913674 AGGTTCTAGTTGATCAATCACTTTC 57.086 36.000 12.12 0.00 36.36 2.62
2550 8194 3.855950 GCTCACAAATTGTCAATAGCAGC 59.144 43.478 10.94 8.59 0.00 5.25
2551 8195 4.616604 GCTCACAAATTGTCAATAGCAGCA 60.617 41.667 10.94 0.00 0.00 4.41
2660 8309 1.064803 GTCCGATTTTGCACACACACA 59.935 47.619 0.00 0.00 0.00 3.72
2662 8311 1.202234 CCGATTTTGCACACACACACA 60.202 47.619 0.00 0.00 0.00 3.72
2665 8314 2.627863 TTTTGCACACACACACAGAC 57.372 45.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.359850 GACTGAATGGGTGCGGCA 60.360 61.111 0.00 0.00 0.00 5.69
3 4 0.740868 ACGATGACTGAATGGGTGCG 60.741 55.000 0.00 0.00 0.00 5.34
4 5 1.009829 GACGATGACTGAATGGGTGC 58.990 55.000 0.00 0.00 0.00 5.01
5 6 2.680312 AGACGATGACTGAATGGGTG 57.320 50.000 0.00 0.00 0.00 4.61
6 7 3.703001 AAAGACGATGACTGAATGGGT 57.297 42.857 0.00 0.00 0.00 4.51
25 26 7.968956 TGCTGTTCTTCGTAACAATAACAAAAA 59.031 29.630 0.00 0.00 38.81 1.94
26 27 7.473366 TGCTGTTCTTCGTAACAATAACAAAA 58.527 30.769 0.00 0.00 38.81 2.44
27 28 7.017498 TGCTGTTCTTCGTAACAATAACAAA 57.983 32.000 0.00 0.00 38.81 2.83
29 30 6.400621 CGATGCTGTTCTTCGTAACAATAACA 60.401 38.462 0.00 0.00 38.81 2.41
30 31 5.952064 CGATGCTGTTCTTCGTAACAATAAC 59.048 40.000 0.00 0.00 38.81 1.89
32 33 4.032445 GCGATGCTGTTCTTCGTAACAATA 59.968 41.667 0.00 0.00 42.32 1.90
33 34 3.181520 GCGATGCTGTTCTTCGTAACAAT 60.182 43.478 0.00 0.00 42.32 2.71
35 36 1.724623 GCGATGCTGTTCTTCGTAACA 59.275 47.619 0.00 0.00 42.32 2.41
36 37 1.724623 TGCGATGCTGTTCTTCGTAAC 59.275 47.619 0.00 0.00 42.32 2.50
37 38 2.073117 TGCGATGCTGTTCTTCGTAA 57.927 45.000 0.00 0.00 42.32 3.18
38 39 1.926510 CATGCGATGCTGTTCTTCGTA 59.073 47.619 0.00 0.00 42.32 3.43
39 40 0.723414 CATGCGATGCTGTTCTTCGT 59.277 50.000 0.00 0.00 42.32 3.85
41 42 2.932614 AGTACATGCGATGCTGTTCTTC 59.067 45.455 0.00 0.00 0.00 2.87
42 43 2.932614 GAGTACATGCGATGCTGTTCTT 59.067 45.455 0.00 0.00 0.00 2.52
44 45 1.256376 CGAGTACATGCGATGCTGTTC 59.744 52.381 0.00 0.00 0.00 3.18
46 47 0.173481 ACGAGTACATGCGATGCTGT 59.827 50.000 9.30 0.00 0.00 4.40
47 48 2.047040 CTACGAGTACATGCGATGCTG 58.953 52.381 9.30 0.00 0.00 4.41
48 49 1.001268 CCTACGAGTACATGCGATGCT 60.001 52.381 9.30 0.00 0.00 3.79
49 50 1.269102 ACCTACGAGTACATGCGATGC 60.269 52.381 9.30 0.00 0.00 3.91
50 51 2.776312 ACCTACGAGTACATGCGATG 57.224 50.000 9.30 0.00 0.00 3.84
51 52 3.129813 TCAAACCTACGAGTACATGCGAT 59.870 43.478 9.30 0.00 0.00 4.58
52 53 2.488937 TCAAACCTACGAGTACATGCGA 59.511 45.455 9.30 0.00 0.00 5.10
55 56 5.120208 CACCTTTCAAACCTACGAGTACATG 59.880 44.000 0.00 0.00 0.00 3.21
56 57 5.235516 CACCTTTCAAACCTACGAGTACAT 58.764 41.667 0.00 0.00 0.00 2.29
57 58 4.501915 CCACCTTTCAAACCTACGAGTACA 60.502 45.833 0.00 0.00 0.00 2.90
58 59 3.992427 CCACCTTTCAAACCTACGAGTAC 59.008 47.826 0.00 0.00 0.00 2.73
59 60 3.896888 TCCACCTTTCAAACCTACGAGTA 59.103 43.478 0.00 0.00 0.00 2.59
61 62 3.396260 TCCACCTTTCAAACCTACGAG 57.604 47.619 0.00 0.00 0.00 4.18
62 63 3.071892 ACATCCACCTTTCAAACCTACGA 59.928 43.478 0.00 0.00 0.00 3.43
63 64 3.408634 ACATCCACCTTTCAAACCTACG 58.591 45.455 0.00 0.00 0.00 3.51
64 65 4.394729 TGACATCCACCTTTCAAACCTAC 58.605 43.478 0.00 0.00 0.00 3.18
65 66 4.104102 ACTGACATCCACCTTTCAAACCTA 59.896 41.667 0.00 0.00 0.00 3.08
66 67 3.117512 ACTGACATCCACCTTTCAAACCT 60.118 43.478 0.00 0.00 0.00 3.50
67 68 3.004734 CACTGACATCCACCTTTCAAACC 59.995 47.826 0.00 0.00 0.00 3.27
69 70 3.631686 CACACTGACATCCACCTTTCAAA 59.368 43.478 0.00 0.00 0.00 2.69
71 72 2.172505 ACACACTGACATCCACCTTTCA 59.827 45.455 0.00 0.00 0.00 2.69
73 74 2.575532 CACACACTGACATCCACCTTT 58.424 47.619 0.00 0.00 0.00 3.11
74 75 1.202806 CCACACACTGACATCCACCTT 60.203 52.381 0.00 0.00 0.00 3.50
75 76 0.397941 CCACACACTGACATCCACCT 59.602 55.000 0.00 0.00 0.00 4.00
76 77 0.396435 TCCACACACTGACATCCACC 59.604 55.000 0.00 0.00 0.00 4.61
78 79 2.371510 TCAATCCACACACTGACATCCA 59.628 45.455 0.00 0.00 0.00 3.41
79 80 3.057969 TCAATCCACACACTGACATCC 57.942 47.619 0.00 0.00 0.00 3.51
80 81 4.516698 ACTTTCAATCCACACACTGACATC 59.483 41.667 0.00 0.00 0.00 3.06
81 82 4.464008 ACTTTCAATCCACACACTGACAT 58.536 39.130 0.00 0.00 0.00 3.06
82 83 3.884895 ACTTTCAATCCACACACTGACA 58.115 40.909 0.00 0.00 0.00 3.58
83 84 4.335315 TGAACTTTCAATCCACACACTGAC 59.665 41.667 0.00 0.00 33.55 3.51
85 86 4.898829 TGAACTTTCAATCCACACACTG 57.101 40.909 0.00 0.00 33.55 3.66
86 87 5.652014 TCTTTGAACTTTCAATCCACACACT 59.348 36.000 5.26 0.00 45.65 3.55
88 89 5.652014 ACTCTTTGAACTTTCAATCCACACA 59.348 36.000 5.26 0.00 45.65 3.72
89 90 6.136541 ACTCTTTGAACTTTCAATCCACAC 57.863 37.500 5.26 0.00 45.65 3.82
90 91 6.152661 ACAACTCTTTGAACTTTCAATCCACA 59.847 34.615 5.26 0.00 45.65 4.17
91 92 6.564328 ACAACTCTTTGAACTTTCAATCCAC 58.436 36.000 5.26 0.00 45.65 4.02
92 93 6.773976 ACAACTCTTTGAACTTTCAATCCA 57.226 33.333 5.26 0.00 45.65 3.41
93 94 7.035612 ACAACAACTCTTTGAACTTTCAATCC 58.964 34.615 5.26 0.00 45.65 3.01
94 95 9.226345 CTACAACAACTCTTTGAACTTTCAATC 57.774 33.333 5.26 0.00 45.65 2.67
95 96 8.956426 TCTACAACAACTCTTTGAACTTTCAAT 58.044 29.630 5.26 0.00 45.65 2.57
98 99 8.831550 AGATCTACAACAACTCTTTGAACTTTC 58.168 33.333 0.00 0.00 36.48 2.62
99 100 8.738645 AGATCTACAACAACTCTTTGAACTTT 57.261 30.769 0.00 0.00 36.48 2.66
101 102 9.646427 GATAGATCTACAACAACTCTTTGAACT 57.354 33.333 4.10 0.00 36.48 3.01
103 104 8.304596 ACGATAGATCTACAACAACTCTTTGAA 58.695 33.333 4.10 0.00 36.75 2.69
105 106 8.376203 CAACGATAGATCTACAACAACTCTTTG 58.624 37.037 4.10 3.72 38.18 2.77
106 107 7.545965 CCAACGATAGATCTACAACAACTCTTT 59.454 37.037 4.10 0.00 41.38 2.52
108 109 6.153000 ACCAACGATAGATCTACAACAACTCT 59.847 38.462 4.10 0.00 41.38 3.24
113 114 7.576861 TGATACCAACGATAGATCTACAACA 57.423 36.000 4.10 0.00 41.38 3.33
114 115 8.516234 AGATGATACCAACGATAGATCTACAAC 58.484 37.037 4.10 0.00 41.38 3.32
115 116 8.515414 CAGATGATACCAACGATAGATCTACAA 58.485 37.037 4.10 0.00 41.38 2.41
116 117 7.121315 CCAGATGATACCAACGATAGATCTACA 59.879 40.741 4.10 0.00 41.38 2.74
117 118 7.121463 ACCAGATGATACCAACGATAGATCTAC 59.879 40.741 4.10 0.00 41.38 2.59
119 120 6.013379 ACCAGATGATACCAACGATAGATCT 58.987 40.000 0.00 0.00 41.38 2.75
120 121 6.274157 ACCAGATGATACCAACGATAGATC 57.726 41.667 0.00 0.00 41.38 2.75
121 122 5.106118 CGACCAGATGATACCAACGATAGAT 60.106 44.000 0.00 0.00 41.38 1.98
123 124 4.476862 CGACCAGATGATACCAACGATAG 58.523 47.826 0.00 0.00 46.19 2.08
124 125 3.254903 CCGACCAGATGATACCAACGATA 59.745 47.826 0.00 0.00 0.00 2.92
125 126 2.035961 CCGACCAGATGATACCAACGAT 59.964 50.000 0.00 0.00 0.00 3.73
129 130 1.128200 CCCCGACCAGATGATACCAA 58.872 55.000 0.00 0.00 0.00 3.67
130 131 1.407656 GCCCCGACCAGATGATACCA 61.408 60.000 0.00 0.00 0.00 3.25
133 134 0.398522 ACAGCCCCGACCAGATGATA 60.399 55.000 0.00 0.00 0.00 2.15
134 135 1.690633 ACAGCCCCGACCAGATGAT 60.691 57.895 0.00 0.00 0.00 2.45
136 137 2.124983 CACAGCCCCGACCAGATG 60.125 66.667 0.00 0.00 0.00 2.90
137 138 4.101448 GCACAGCCCCGACCAGAT 62.101 66.667 0.00 0.00 0.00 2.90
142 143 3.845259 TATCCGCACAGCCCCGAC 61.845 66.667 0.00 0.00 0.00 4.79
143 144 3.845259 GTATCCGCACAGCCCCGA 61.845 66.667 0.00 0.00 0.00 5.14
144 145 4.910585 GGTATCCGCACAGCCCCG 62.911 72.222 0.00 0.00 0.00 5.73
155 156 1.365699 TCTGCGAAAAAGCGGTATCC 58.634 50.000 0.00 0.00 43.62 2.59
156 157 2.475685 GGTTCTGCGAAAAAGCGGTATC 60.476 50.000 0.00 0.00 43.62 2.24
157 158 1.467342 GGTTCTGCGAAAAAGCGGTAT 59.533 47.619 0.00 0.00 43.62 2.73
158 159 0.869730 GGTTCTGCGAAAAAGCGGTA 59.130 50.000 0.00 0.00 43.62 4.02
159 160 1.098712 TGGTTCTGCGAAAAAGCGGT 61.099 50.000 0.00 0.00 43.62 5.68
161 162 1.330306 CATGGTTCTGCGAAAAAGCG 58.670 50.000 0.00 0.00 40.67 4.68
162 163 2.053627 CACATGGTTCTGCGAAAAAGC 58.946 47.619 0.00 0.00 37.71 3.51
163 164 3.624326 TCACATGGTTCTGCGAAAAAG 57.376 42.857 0.00 0.00 0.00 2.27
164 165 3.305267 CCATCACATGGTTCTGCGAAAAA 60.305 43.478 0.00 0.00 45.54 1.94
165 166 2.228582 CCATCACATGGTTCTGCGAAAA 59.771 45.455 0.00 0.00 45.54 2.29
179 180 0.035317 GACAGACCACAGCCATCACA 59.965 55.000 0.00 0.00 0.00 3.58
229 232 4.467084 ATTCATGTCGCCCGCCGT 62.467 61.111 0.00 0.00 38.35 5.68
251 254 4.221342 CCGTGTTGAGTGTTGATTGATTG 58.779 43.478 0.00 0.00 0.00 2.67
259 262 0.304705 GTGAGCCGTGTTGAGTGTTG 59.695 55.000 0.00 0.00 0.00 3.33
260 263 0.107897 TGTGAGCCGTGTTGAGTGTT 60.108 50.000 0.00 0.00 0.00 3.32
261 264 0.106708 ATGTGAGCCGTGTTGAGTGT 59.893 50.000 0.00 0.00 0.00 3.55
262 265 0.514255 CATGTGAGCCGTGTTGAGTG 59.486 55.000 0.00 0.00 0.00 3.51
263 266 1.230635 GCATGTGAGCCGTGTTGAGT 61.231 55.000 0.00 0.00 32.30 3.41
264 267 1.499056 GCATGTGAGCCGTGTTGAG 59.501 57.895 0.00 0.00 32.30 3.02
283 286 5.128468 CGAACGAAAACTAGAAAGAAACCG 58.872 41.667 0.00 0.00 0.00 4.44
295 300 2.056577 CCTAGCGAACGAACGAAAACT 58.943 47.619 9.67 0.00 35.09 2.66
329 334 4.203764 CCGACGAGAAATAACACGATACAC 59.796 45.833 0.00 0.00 0.00 2.90
458 469 2.553602 TCGAGTCAGCCGTACTTGTTAA 59.446 45.455 0.00 0.00 31.38 2.01
494 505 8.122472 ACGAAATCCCTTTGTTTTAGATGATT 57.878 30.769 0.00 0.00 0.00 2.57
530 551 0.734942 ACTTGGAATACACGACGGCG 60.735 55.000 10.39 10.39 44.79 6.46
542 563 2.297701 GCAGTTGTTGGAGACTTGGAA 58.702 47.619 0.00 0.00 0.00 3.53
562 586 4.788100 CGCGTGGAAATCTTGTTTATCTTG 59.212 41.667 0.00 0.00 0.00 3.02
580 632 3.705638 CCTGCACAGTCACGCGTG 61.706 66.667 32.76 32.76 36.18 5.34
697 749 0.467290 TCGCCAGCCAGAACCTTTTT 60.467 50.000 0.00 0.00 0.00 1.94
698 750 0.890996 CTCGCCAGCCAGAACCTTTT 60.891 55.000 0.00 0.00 0.00 2.27
699 751 1.302832 CTCGCCAGCCAGAACCTTT 60.303 57.895 0.00 0.00 0.00 3.11
700 752 2.348998 CTCGCCAGCCAGAACCTT 59.651 61.111 0.00 0.00 0.00 3.50
701 753 2.925170 ACTCGCCAGCCAGAACCT 60.925 61.111 0.00 0.00 0.00 3.50
702 754 2.435059 GACTCGCCAGCCAGAACC 60.435 66.667 0.00 0.00 0.00 3.62
703 755 2.435059 GGACTCGCCAGCCAGAAC 60.435 66.667 0.00 0.00 36.34 3.01
706 758 4.803426 GACGGACTCGCCAGCCAG 62.803 72.222 0.00 0.00 40.63 4.85
726 778 2.125106 GGATCAGTGGGTGCGTCC 60.125 66.667 0.00 0.00 0.00 4.79
758 811 1.906990 TTTAAAATCCCGTTGGCCGA 58.093 45.000 0.00 0.00 39.56 5.54
852 910 2.251371 GCCGTTCGCCTGTTTGTC 59.749 61.111 0.00 0.00 0.00 3.18
1047 1123 3.281727 AACTCAACTCAGCCTGAAACA 57.718 42.857 0.00 0.00 0.00 2.83
1423 3042 5.342433 TGTACAAACCGGAGTTATATGACG 58.658 41.667 9.46 0.00 34.19 4.35
1506 3132 2.800736 CATAGTTGCCGCCCAAGC 59.199 61.111 0.00 0.00 33.21 4.01
1512 3138 0.109964 TCAAAACGCATAGTTGCCGC 60.110 50.000 0.00 0.00 46.57 6.53
1606 3916 1.000843 CATGGGACTGTGACTGAACGA 59.999 52.381 0.00 0.00 0.00 3.85
1610 3927 1.544246 CGTACATGGGACTGTGACTGA 59.456 52.381 0.00 0.00 0.00 3.41
1640 3957 0.733150 CTCGCTCACCGACTCATACA 59.267 55.000 0.00 0.00 41.89 2.29
1644 3961 0.671796 TTTTCTCGCTCACCGACTCA 59.328 50.000 0.00 0.00 41.89 3.41
1664 3981 2.629017 AGGCACATGGGAGGATTTTT 57.371 45.000 0.00 0.00 0.00 1.94
1665 3982 2.460669 GAAGGCACATGGGAGGATTTT 58.539 47.619 0.00 0.00 0.00 1.82
1666 3983 1.683011 CGAAGGCACATGGGAGGATTT 60.683 52.381 0.00 0.00 0.00 2.17
1667 3984 0.107017 CGAAGGCACATGGGAGGATT 60.107 55.000 0.00 0.00 0.00 3.01
1668 3985 1.528824 CGAAGGCACATGGGAGGAT 59.471 57.895 0.00 0.00 0.00 3.24
1669 3986 2.989639 CGAAGGCACATGGGAGGA 59.010 61.111 0.00 0.00 0.00 3.71
1670 3987 2.825836 GCGAAGGCACATGGGAGG 60.826 66.667 0.00 0.00 39.62 4.30
1671 3988 0.962356 AAAGCGAAGGCACATGGGAG 60.962 55.000 0.00 0.00 43.41 4.30
1672 3989 0.960364 GAAAGCGAAGGCACATGGGA 60.960 55.000 0.00 0.00 43.41 4.37
1673 3990 1.508088 GAAAGCGAAGGCACATGGG 59.492 57.895 0.00 0.00 43.41 4.00
1674 3991 1.508088 GGAAAGCGAAGGCACATGG 59.492 57.895 0.00 0.00 43.41 3.66
1675 3992 1.243342 TGGGAAAGCGAAGGCACATG 61.243 55.000 0.00 0.00 43.41 3.21
1676 3993 0.323725 ATGGGAAAGCGAAGGCACAT 60.324 50.000 0.00 0.00 43.41 3.21
1677 3994 1.074775 ATGGGAAAGCGAAGGCACA 59.925 52.632 0.00 0.00 43.41 4.57
1678 3995 1.508088 CATGGGAAAGCGAAGGCAC 59.492 57.895 0.00 0.00 43.41 5.01
1679 3996 1.678635 CCATGGGAAAGCGAAGGCA 60.679 57.895 2.85 0.00 43.41 4.75
1680 3997 0.753111 ATCCATGGGAAAGCGAAGGC 60.753 55.000 13.02 0.00 34.34 4.35
1681 3998 1.406539 CAATCCATGGGAAAGCGAAGG 59.593 52.381 13.02 0.00 34.34 3.46
1682 3999 1.202336 GCAATCCATGGGAAAGCGAAG 60.202 52.381 13.02 0.00 34.34 3.79
1683 4000 0.817013 GCAATCCATGGGAAAGCGAA 59.183 50.000 13.02 0.00 34.34 4.70
1684 4001 2.492418 GCAATCCATGGGAAAGCGA 58.508 52.632 13.02 0.00 34.34 4.93
1685 4002 1.064621 CGCAATCCATGGGAAAGCG 59.935 57.895 20.92 20.92 46.29 4.68
1686 4003 1.227060 GCGCAATCCATGGGAAAGC 60.227 57.895 13.02 10.34 44.39 3.51
1687 4004 1.064621 CGCGCAATCCATGGGAAAG 59.935 57.895 13.02 0.82 44.39 2.62
1688 4005 1.677300 ACGCGCAATCCATGGGAAA 60.677 52.632 13.02 0.00 44.39 3.13
1689 4006 2.045438 ACGCGCAATCCATGGGAA 60.045 55.556 13.02 0.00 44.39 3.97
1690 4007 2.823593 CACGCGCAATCCATGGGA 60.824 61.111 13.02 0.00 44.39 4.37
1691 4008 3.891400 CCACGCGCAATCCATGGG 61.891 66.667 13.02 0.00 44.44 4.00
1692 4009 1.932011 TTTCCACGCGCAATCCATGG 61.932 55.000 5.73 4.97 0.00 3.66
1693 4010 0.101040 ATTTCCACGCGCAATCCATG 59.899 50.000 5.73 0.00 0.00 3.66
1694 4011 1.603802 CTATTTCCACGCGCAATCCAT 59.396 47.619 5.73 0.00 0.00 3.41
1695 4012 1.013596 CTATTTCCACGCGCAATCCA 58.986 50.000 5.73 0.00 0.00 3.41
1696 4013 0.307760 CCTATTTCCACGCGCAATCC 59.692 55.000 5.73 0.00 0.00 3.01
1697 4014 0.307760 CCCTATTTCCACGCGCAATC 59.692 55.000 5.73 0.00 0.00 2.67
1698 4015 0.107410 TCCCTATTTCCACGCGCAAT 60.107 50.000 5.73 1.06 0.00 3.56
1699 4016 0.321741 TTCCCTATTTCCACGCGCAA 60.322 50.000 5.73 0.00 0.00 4.85
1700 4017 1.022451 GTTCCCTATTTCCACGCGCA 61.022 55.000 5.73 0.00 0.00 6.09
1701 4018 1.719709 GTTCCCTATTTCCACGCGC 59.280 57.895 5.73 0.00 0.00 6.86
1702 4019 0.458889 TCGTTCCCTATTTCCACGCG 60.459 55.000 3.53 3.53 0.00 6.01
1703 4020 1.134907 TCTCGTTCCCTATTTCCACGC 60.135 52.381 0.00 0.00 0.00 5.34
1704 4021 2.953466 TCTCGTTCCCTATTTCCACG 57.047 50.000 0.00 0.00 0.00 4.94
1705 4022 3.381949 CGATCTCGTTCCCTATTTCCAC 58.618 50.000 0.00 0.00 34.11 4.02
1706 4023 3.728076 CGATCTCGTTCCCTATTTCCA 57.272 47.619 0.00 0.00 34.11 3.53
1726 4043 5.334569 GGCAGTAGATCGATCTAAGTCAGAC 60.335 48.000 31.49 21.51 40.77 3.51
1761 4078 2.812178 GGACGGCGCAACACGTAT 60.812 61.111 10.83 0.00 44.24 3.06
1772 4089 0.606604 ATATATGGTCCACGGACGGC 59.393 55.000 10.05 0.00 45.41 5.68
1792 4109 9.507329 CTAGCATTTGTGGGAATAATAGTACAT 57.493 33.333 0.00 0.00 0.00 2.29
1793 4110 7.444183 GCTAGCATTTGTGGGAATAATAGTACA 59.556 37.037 10.63 0.00 0.00 2.90
1794 4111 7.094762 GGCTAGCATTTGTGGGAATAATAGTAC 60.095 40.741 18.24 0.00 0.00 2.73
1795 4112 6.940298 GGCTAGCATTTGTGGGAATAATAGTA 59.060 38.462 18.24 0.00 0.00 1.82
1796 4113 5.770162 GGCTAGCATTTGTGGGAATAATAGT 59.230 40.000 18.24 0.00 0.00 2.12
1800 6062 3.295973 GGGCTAGCATTTGTGGGAATAA 58.704 45.455 18.24 0.00 0.00 1.40
1832 6094 2.576847 GCGCGCATTAGCCAACAC 60.577 61.111 29.10 0.00 37.52 3.32
2028 6435 1.281867 CACTACATGCCTCTTCCCCAA 59.718 52.381 0.00 0.00 0.00 4.12
2029 6436 0.911769 CACTACATGCCTCTTCCCCA 59.088 55.000 0.00 0.00 0.00 4.96
2030 6437 0.181350 CCACTACATGCCTCTTCCCC 59.819 60.000 0.00 0.00 0.00 4.81
2031 6438 0.912486 ACCACTACATGCCTCTTCCC 59.088 55.000 0.00 0.00 0.00 3.97
2033 6440 2.744202 CAACACCACTACATGCCTCTTC 59.256 50.000 0.00 0.00 0.00 2.87
2034 6441 2.553028 CCAACACCACTACATGCCTCTT 60.553 50.000 0.00 0.00 0.00 2.85
2036 6443 1.003118 TCCAACACCACTACATGCCTC 59.997 52.381 0.00 0.00 0.00 4.70
2038 6445 1.165270 GTCCAACACCACTACATGCC 58.835 55.000 0.00 0.00 0.00 4.40
2041 6448 3.857157 ACTTGTCCAACACCACTACAT 57.143 42.857 0.00 0.00 0.00 2.29
2042 6449 3.055021 TCAACTTGTCCAACACCACTACA 60.055 43.478 0.00 0.00 0.00 2.74
2044 6451 3.916359 TCAACTTGTCCAACACCACTA 57.084 42.857 0.00 0.00 0.00 2.74
2045 6452 2.799126 TCAACTTGTCCAACACCACT 57.201 45.000 0.00 0.00 0.00 4.00
2047 6454 3.358111 TCTTCAACTTGTCCAACACCA 57.642 42.857 0.00 0.00 0.00 4.17
2048 6455 3.632145 ACATCTTCAACTTGTCCAACACC 59.368 43.478 0.00 0.00 0.00 4.16
2050 6457 7.936847 ACTATAACATCTTCAACTTGTCCAACA 59.063 33.333 0.00 0.00 0.00 3.33
2124 7249 9.574516 AGATTACCATCAAAAGTTGAGTAAAGT 57.425 29.630 6.82 0.00 43.98 2.66
2241 7384 4.142026 CCACGACCCAGTAAATAGATCACA 60.142 45.833 0.00 0.00 0.00 3.58
2242 7385 4.142004 ACCACGACCCAGTAAATAGATCAC 60.142 45.833 0.00 0.00 0.00 3.06
2275 7418 2.744494 GCACATGGTTGCCCAAAAAGAA 60.744 45.455 0.00 0.00 46.04 2.52
2277 7420 1.202675 AGCACATGGTTGCCCAAAAAG 60.203 47.619 4.77 0.00 46.04 2.27
2355 7498 9.871238 GTGATTGATCAACTAGAACCTAAACTA 57.129 33.333 11.07 0.00 38.75 2.24
2385 7529 7.333921 GGGAGTATATCTCTGAAATGCATGAAG 59.666 40.741 0.00 0.00 42.40 3.02
2525 8169 6.678655 GCTGCTATTGACAATTTGTGAGCATA 60.679 38.462 18.33 2.72 37.98 3.14
2583 8232 9.559958 GTTGTGATATAAGGTTGTCAATTTGAG 57.440 33.333 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.