Multiple sequence alignment - TraesCS4A01G359900

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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 TraesCS4A01G359900 chr4A 100.000 3611 0 0 1 3611 632988683 632992293 0.000000e+00 6669.0
1 TraesCS4A01G359900 chr4A 97.037 1890 31 9 848 2720 633000038 632998157 0.000000e+00 3157.0
2 TraesCS4A01G359900 chr4A 85.456 1547 202 19 1024 2557 685834814 685836350 0.000000e+00 1589.0
3 TraesCS4A01G359900 chr4A 90.308 227 22 0 172 398 435907155 435906929 7.580000e-77 298.0
4 TraesCS4A01G359900 chr4A 93.909 197 12 0 506 702 633000239 633000043 7.580000e-77 298.0
5 TraesCS4A01G359900 chr5D 92.495 2798 108 35 879 3610 537163025 537160264 0.000000e+00 3910.0
6 TraesCS4A01G359900 chr5D 96.763 1699 44 4 990 2681 537088043 537089737 0.000000e+00 2822.0
7 TraesCS4A01G359900 chr5D 86.347 271 31 4 3340 3609 537150243 537149978 1.270000e-74 291.0
8 TraesCS4A01G359900 chr5D 78.549 317 38 19 395 701 537163367 537163071 7.960000e-42 182.0
9 TraesCS4A01G359900 chr5D 94.118 51 3 0 11 61 537163414 537163364 1.070000e-10 78.7
10 TraesCS4A01G359900 chr5B 94.442 1943 67 19 830 2748 677537259 677539184 0.000000e+00 2952.0
11 TraesCS4A01G359900 chr5B 95.358 1788 48 10 879 2641 677545202 677543425 0.000000e+00 2809.0
12 TraesCS4A01G359900 chr5B 86.130 721 39 28 2902 3609 677539308 677539980 0.000000e+00 721.0
13 TraesCS4A01G359900 chr5B 91.436 362 30 1 182 542 677535411 677535772 2.500000e-136 496.0
14 TraesCS4A01G359900 chr5B 89.316 234 25 0 163 396 399955558 399955791 9.800000e-76 294.0
15 TraesCS4A01G359900 chr5B 89.427 227 23 1 172 398 401658473 401658248 5.900000e-73 285.0
16 TraesCS4A01G359900 chr4D 85.456 1547 206 15 1024 2559 479540668 479542206 0.000000e+00 1592.0
17 TraesCS4A01G359900 chr4D 92.754 138 10 0 694 831 10249966 10250103 2.200000e-47 200.0
18 TraesCS4A01G359900 chr4B 85.133 1547 207 18 1024 2557 606764722 606766258 0.000000e+00 1561.0
19 TraesCS4A01G359900 chr2A 82.527 1551 230 28 1029 2554 18358280 18359814 0.000000e+00 1325.0
20 TraesCS4A01G359900 chr2A 88.793 232 26 0 172 403 214842469 214842238 5.900000e-73 285.0
21 TraesCS4A01G359900 chr2A 93.478 138 9 0 694 831 470645641 470645778 4.730000e-49 206.0
22 TraesCS4A01G359900 chr2A 92.754 138 8 2 694 831 778800749 778800614 7.910000e-47 198.0
23 TraesCS4A01G359900 chr5A 81.584 1553 243 37 1040 2560 670104836 670103295 0.000000e+00 1243.0
24 TraesCS4A01G359900 chr5A 95.385 130 6 0 702 831 25118728 25118857 1.310000e-49 207.0
25 TraesCS4A01G359900 chr3B 89.744 234 23 1 163 396 795224304 795224536 7.580000e-77 298.0
26 TraesCS4A01G359900 chrUn 90.222 225 22 0 172 396 87719828 87719604 9.800000e-76 294.0
27 TraesCS4A01G359900 chr7B 90.222 225 22 0 172 396 713698687 713698463 9.800000e-76 294.0
28 TraesCS4A01G359900 chr7B 88.430 242 27 1 159 400 349758259 349758499 1.270000e-74 291.0
29 TraesCS4A01G359900 chr7A 93.525 139 8 1 694 831 127916441 127916303 4.730000e-49 206.0
30 TraesCS4A01G359900 chr7A 94.615 130 7 0 702 831 610448573 610448702 6.110000e-48 202.0
31 TraesCS4A01G359900 chr7A 93.284 134 9 0 698 831 3635044 3634911 7.910000e-47 198.0
32 TraesCS4A01G359900 chr6A 94.697 132 7 0 700 831 446526733 446526602 4.730000e-49 206.0
33 TraesCS4A01G359900 chr3D 91.489 141 11 1 691 831 468376851 468376990 3.680000e-45 193.0
34 TraesCS4A01G359900 chr3D 93.182 44 2 1 120 163 48257676 48257718 3.010000e-06 63.9


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 TraesCS4A01G359900 chr4A 632988683 632992293 3610 False 6669.000000 6669 100.000000 1 3611 1 chr4A.!!$F1 3610
1 TraesCS4A01G359900 chr4A 632998157 633000239 2082 True 1727.500000 3157 95.473000 506 2720 2 chr4A.!!$R2 2214
2 TraesCS4A01G359900 chr4A 685834814 685836350 1536 False 1589.000000 1589 85.456000 1024 2557 1 chr4A.!!$F2 1533
3 TraesCS4A01G359900 chr5D 537088043 537089737 1694 False 2822.000000 2822 96.763000 990 2681 1 chr5D.!!$F1 1691
4 TraesCS4A01G359900 chr5D 537160264 537163414 3150 True 1390.233333 3910 88.387333 11 3610 3 chr5D.!!$R2 3599
5 TraesCS4A01G359900 chr5B 677543425 677545202 1777 True 2809.000000 2809 95.358000 879 2641 1 chr5B.!!$R2 1762
6 TraesCS4A01G359900 chr5B 677535411 677539980 4569 False 1389.666667 2952 90.669333 182 3609 3 chr5B.!!$F2 3427
7 TraesCS4A01G359900 chr4D 479540668 479542206 1538 False 1592.000000 1592 85.456000 1024 2559 1 chr4D.!!$F2 1535
8 TraesCS4A01G359900 chr4B 606764722 606766258 1536 False 1561.000000 1561 85.133000 1024 2557 1 chr4B.!!$F1 1533
9 TraesCS4A01G359900 chr2A 18358280 18359814 1534 False 1325.000000 1325 82.527000 1029 2554 1 chr2A.!!$F1 1525
10 TraesCS4A01G359900 chr5A 670103295 670104836 1541 True 1243.000000 1243 81.584000 1040 2560 1 chr5A.!!$R1 1520

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
804 2157 0.098025 GTGTGTGTTGACGTGGGTTG 59.902 55.0 0.0 0.0 0.0 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2657 4094 0.183492 AACTCAACAGCCTGCCTGAA 59.817 50.0 0.0 0.0 44.64 3.02 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
49 50 6.447162 TCGGATATGAGTAATGCTACAACTG 58.553 40.000 0.00 0.00 0.00 3.16
51 52 5.991606 GGATATGAGTAATGCTACAACTGCA 59.008 40.000 0.00 0.00 44.95 4.41
55 56 3.866651 AGTAATGCTACAACTGCAGAGG 58.133 45.455 23.35 14.17 44.04 3.69
56 57 2.119801 AATGCTACAACTGCAGAGGG 57.880 50.000 23.35 11.48 44.04 4.30
57 58 0.393537 ATGCTACAACTGCAGAGGGC 60.394 55.000 23.35 18.91 44.04 5.19
58 59 1.298014 GCTACAACTGCAGAGGGCT 59.702 57.895 23.35 0.00 45.15 5.19
59 60 0.322008 GCTACAACTGCAGAGGGCTT 60.322 55.000 23.35 0.00 45.15 4.35
60 61 1.066143 GCTACAACTGCAGAGGGCTTA 60.066 52.381 23.35 1.67 45.15 3.09
61 62 2.898705 CTACAACTGCAGAGGGCTTAG 58.101 52.381 23.35 7.79 45.15 2.18
62 63 1.352083 ACAACTGCAGAGGGCTTAGA 58.648 50.000 23.35 0.00 45.15 2.10
63 64 1.002544 ACAACTGCAGAGGGCTTAGAC 59.997 52.381 23.35 0.00 45.15 2.59
64 65 1.277557 CAACTGCAGAGGGCTTAGACT 59.722 52.381 23.35 0.00 45.15 3.24
65 66 0.901124 ACTGCAGAGGGCTTAGACTG 59.099 55.000 23.35 0.00 45.15 3.51
66 67 0.177604 CTGCAGAGGGCTTAGACTGG 59.822 60.000 8.42 0.00 45.15 4.00
67 68 0.545309 TGCAGAGGGCTTAGACTGGT 60.545 55.000 0.00 0.00 45.15 4.00
68 69 0.615850 GCAGAGGGCTTAGACTGGTT 59.384 55.000 0.00 0.00 40.25 3.67
69 70 1.677217 GCAGAGGGCTTAGACTGGTTG 60.677 57.143 0.00 0.00 40.25 3.77
70 71 1.625818 CAGAGGGCTTAGACTGGTTGT 59.374 52.381 0.00 0.00 0.00 3.32
71 72 2.832129 CAGAGGGCTTAGACTGGTTGTA 59.168 50.000 0.00 0.00 0.00 2.41
72 73 3.260884 CAGAGGGCTTAGACTGGTTGTAA 59.739 47.826 0.00 0.00 0.00 2.41
73 74 4.080863 CAGAGGGCTTAGACTGGTTGTAAT 60.081 45.833 0.00 0.00 0.00 1.89
74 75 4.080863 AGAGGGCTTAGACTGGTTGTAATG 60.081 45.833 0.00 0.00 0.00 1.90
75 76 3.844211 AGGGCTTAGACTGGTTGTAATGA 59.156 43.478 0.00 0.00 0.00 2.57
76 77 4.080863 AGGGCTTAGACTGGTTGTAATGAG 60.081 45.833 0.00 0.00 0.00 2.90
77 78 4.192317 GGCTTAGACTGGTTGTAATGAGG 58.808 47.826 0.00 0.00 0.00 3.86
78 79 4.081087 GGCTTAGACTGGTTGTAATGAGGA 60.081 45.833 0.00 0.00 0.00 3.71
79 80 5.112686 GCTTAGACTGGTTGTAATGAGGAG 58.887 45.833 0.00 0.00 0.00 3.69
80 81 5.337652 GCTTAGACTGGTTGTAATGAGGAGT 60.338 44.000 0.00 0.00 0.00 3.85
81 82 4.543590 AGACTGGTTGTAATGAGGAGTG 57.456 45.455 0.00 0.00 0.00 3.51
82 83 3.904339 AGACTGGTTGTAATGAGGAGTGT 59.096 43.478 0.00 0.00 0.00 3.55
83 84 4.021016 AGACTGGTTGTAATGAGGAGTGTC 60.021 45.833 0.00 0.00 0.00 3.67
84 85 3.646162 ACTGGTTGTAATGAGGAGTGTCA 59.354 43.478 0.00 0.00 0.00 3.58
85 86 4.287067 ACTGGTTGTAATGAGGAGTGTCAT 59.713 41.667 0.00 0.00 38.91 3.06
86 87 5.483937 ACTGGTTGTAATGAGGAGTGTCATA 59.516 40.000 0.00 0.00 36.07 2.15
87 88 6.156949 ACTGGTTGTAATGAGGAGTGTCATAT 59.843 38.462 0.00 0.00 36.07 1.78
88 89 7.344612 ACTGGTTGTAATGAGGAGTGTCATATA 59.655 37.037 0.00 0.00 36.07 0.86
89 90 8.084985 TGGTTGTAATGAGGAGTGTCATATAA 57.915 34.615 0.00 0.00 36.07 0.98
90 91 8.713971 TGGTTGTAATGAGGAGTGTCATATAAT 58.286 33.333 0.00 0.00 36.07 1.28
123 124 9.914834 ATAGTGTATCTTTTTAGGGTAATTGCA 57.085 29.630 0.00 0.00 0.00 4.08
124 125 8.644374 AGTGTATCTTTTTAGGGTAATTGCAA 57.356 30.769 0.00 0.00 0.00 4.08
125 126 9.255029 AGTGTATCTTTTTAGGGTAATTGCAAT 57.745 29.630 5.99 5.99 0.00 3.56
152 153 8.911918 TTTTAGTTGATAGTTTACCAAGCTGA 57.088 30.769 0.00 0.00 0.00 4.26
153 154 7.900782 TTAGTTGATAGTTTACCAAGCTGAC 57.099 36.000 0.00 0.00 0.00 3.51
154 155 5.246307 AGTTGATAGTTTACCAAGCTGACC 58.754 41.667 0.00 0.00 0.00 4.02
155 156 4.901197 TGATAGTTTACCAAGCTGACCA 57.099 40.909 0.00 0.00 0.00 4.02
156 157 4.575885 TGATAGTTTACCAAGCTGACCAC 58.424 43.478 0.00 0.00 0.00 4.16
157 158 4.286032 TGATAGTTTACCAAGCTGACCACT 59.714 41.667 0.00 0.00 0.00 4.00
158 159 3.577805 AGTTTACCAAGCTGACCACTT 57.422 42.857 0.00 0.00 0.00 3.16
159 160 3.214328 AGTTTACCAAGCTGACCACTTG 58.786 45.455 0.00 0.00 43.36 3.16
200 201 7.880713 TGTATGGTATTACATCCGTAATGCATT 59.119 33.333 17.56 17.56 46.61 3.56
223 224 7.728847 TTGTATCACATGTTGGTATCATAGC 57.271 36.000 0.00 0.00 0.00 2.97
229 230 4.587262 ACATGTTGGTATCATAGCGGACTA 59.413 41.667 0.00 0.00 0.00 2.59
235 236 5.538118 TGGTATCATAGCGGACTACATTTG 58.462 41.667 0.00 0.00 0.00 2.32
239 240 3.621268 TCATAGCGGACTACATTTGTTGC 59.379 43.478 0.00 0.00 0.00 4.17
258 259 5.047448 TGTTGCCATGCATAACACAAAGTAT 60.047 36.000 9.03 0.00 38.76 2.12
261 262 5.036737 GCCATGCATAACACAAAGTATCAC 58.963 41.667 0.00 0.00 0.00 3.06
345 347 8.851541 ATTTTATGCCAACTCATCAAAATTGT 57.148 26.923 0.00 0.00 0.00 2.71
349 351 9.770097 TTATGCCAACTCATCAAAATTGTTTAA 57.230 25.926 0.00 0.00 0.00 1.52
353 355 8.772705 GCCAACTCATCAAAATTGTTTAATTGA 58.227 29.630 0.00 0.00 36.65 2.57
401 403 1.399744 ATCACGGGCAGCCTTATCGA 61.400 55.000 12.43 1.68 0.00 3.59
417 419 3.587797 ATCGAAGTTTTACAGCCTCGA 57.412 42.857 0.00 0.00 0.00 4.04
454 456 6.561519 TTTTGGTTGGTAATTTGGAGGAAA 57.438 33.333 0.00 0.00 0.00 3.13
484 495 3.551846 ACCCTAAAGCGGTGATTATTGG 58.448 45.455 0.00 0.00 30.39 3.16
486 497 3.434453 CCCTAAAGCGGTGATTATTGGGA 60.434 47.826 0.50 0.00 33.14 4.37
544 555 6.042143 CACCTTGCAAGTCTTAACATTTTGT 58.958 36.000 24.35 7.89 0.00 2.83
547 558 6.980397 CCTTGCAAGTCTTAACATTTTGTCTT 59.020 34.615 24.35 0.00 0.00 3.01
560 1906 8.408043 AACATTTTGTCTTGGATGTTGATAGA 57.592 30.769 0.00 0.00 40.21 1.98
585 1931 9.798994 GATTGCATTCAGATGATATTATTTCCC 57.201 33.333 3.73 0.00 35.16 3.97
586 1932 8.709272 TTGCATTCAGATGATATTATTTCCCA 57.291 30.769 0.00 0.00 35.16 4.37
587 1933 8.888836 TGCATTCAGATGATATTATTTCCCAT 57.111 30.769 0.00 0.00 35.16 4.00
588 1934 8.745590 TGCATTCAGATGATATTATTTCCCATG 58.254 33.333 0.00 0.00 35.16 3.66
589 1935 7.705325 GCATTCAGATGATATTATTTCCCATGC 59.295 37.037 0.00 0.00 35.16 4.06
590 1936 7.707624 TTCAGATGATATTATTTCCCATGCC 57.292 36.000 0.00 0.00 0.00 4.40
591 1937 5.882000 TCAGATGATATTATTTCCCATGCCG 59.118 40.000 0.00 0.00 0.00 5.69
614 1967 4.751600 GCATGATATCCTTGTCAACGATGA 59.248 41.667 0.00 0.00 0.00 2.92
699 2052 6.823689 GGAGCCAAGACAAGAGAACATAATAA 59.176 38.462 0.00 0.00 0.00 1.40
702 2055 8.049117 AGCCAAGACAAGAGAACATAATAATCA 58.951 33.333 0.00 0.00 0.00 2.57
703 2056 8.341173 GCCAAGACAAGAGAACATAATAATCAG 58.659 37.037 0.00 0.00 0.00 2.90
704 2057 9.388506 CCAAGACAAGAGAACATAATAATCAGT 57.611 33.333 0.00 0.00 0.00 3.41
726 2079 9.645059 TCAGTTTTGTTAGAACTCATCTAGATG 57.355 33.333 24.32 24.32 41.59 2.90
727 2080 9.645059 CAGTTTTGTTAGAACTCATCTAGATGA 57.355 33.333 29.17 29.17 44.83 2.92
774 2127 6.588719 TTTTATAGCCATTGGATATGGTGC 57.411 37.500 21.07 0.00 41.17 5.01
775 2128 5.519183 TTATAGCCATTGGATATGGTGCT 57.481 39.130 21.07 4.64 41.17 4.40
776 2129 6.634889 TTATAGCCATTGGATATGGTGCTA 57.365 37.500 21.07 6.59 41.17 3.49
777 2130 5.722172 ATAGCCATTGGATATGGTGCTAT 57.278 39.130 12.58 3.75 41.17 2.97
778 2131 6.829985 ATAGCCATTGGATATGGTGCTATA 57.170 37.500 12.58 0.00 41.17 1.31
779 2132 5.519183 AGCCATTGGATATGGTGCTATAA 57.481 39.130 6.95 0.00 41.17 0.98
780 2133 5.503927 AGCCATTGGATATGGTGCTATAAG 58.496 41.667 6.95 0.00 41.17 1.73
781 2134 5.251468 AGCCATTGGATATGGTGCTATAAGA 59.749 40.000 6.95 0.00 41.17 2.10
782 2135 6.069206 AGCCATTGGATATGGTGCTATAAGAT 60.069 38.462 6.95 0.00 41.17 2.40
783 2136 6.039047 GCCATTGGATATGGTGCTATAAGATG 59.961 42.308 6.95 0.00 41.17 2.90
784 2137 6.039047 CCATTGGATATGGTGCTATAAGATGC 59.961 42.308 0.00 0.00 34.56 3.91
785 2138 4.758688 TGGATATGGTGCTATAAGATGCG 58.241 43.478 0.00 0.00 0.00 4.73
786 2139 4.222810 TGGATATGGTGCTATAAGATGCGT 59.777 41.667 0.00 0.00 0.00 5.24
787 2140 4.568359 GGATATGGTGCTATAAGATGCGTG 59.432 45.833 0.00 0.00 0.00 5.34
788 2141 2.979814 TGGTGCTATAAGATGCGTGT 57.020 45.000 0.00 0.00 0.00 4.49
789 2142 2.549926 TGGTGCTATAAGATGCGTGTG 58.450 47.619 0.00 0.00 0.00 3.82
790 2143 2.093711 TGGTGCTATAAGATGCGTGTGT 60.094 45.455 0.00 0.00 0.00 3.72
791 2144 2.285220 GGTGCTATAAGATGCGTGTGTG 59.715 50.000 0.00 0.00 0.00 3.82
792 2145 2.930040 GTGCTATAAGATGCGTGTGTGT 59.070 45.455 0.00 0.00 0.00 3.72
793 2146 3.370978 GTGCTATAAGATGCGTGTGTGTT 59.629 43.478 0.00 0.00 0.00 3.32
794 2147 3.370672 TGCTATAAGATGCGTGTGTGTTG 59.629 43.478 0.00 0.00 0.00 3.33
795 2148 3.616821 GCTATAAGATGCGTGTGTGTTGA 59.383 43.478 0.00 0.00 0.00 3.18
796 2149 4.492570 GCTATAAGATGCGTGTGTGTTGAC 60.493 45.833 0.00 0.00 0.00 3.18
797 2150 0.581529 AAGATGCGTGTGTGTTGACG 59.418 50.000 0.00 0.00 38.63 4.35
798 2151 0.529773 AGATGCGTGTGTGTTGACGT 60.530 50.000 0.00 0.00 37.89 4.34
799 2152 0.383002 GATGCGTGTGTGTTGACGTG 60.383 55.000 0.00 0.00 37.89 4.49
800 2153 1.771073 ATGCGTGTGTGTTGACGTGG 61.771 55.000 0.00 0.00 37.89 4.94
801 2154 3.010767 CGTGTGTGTTGACGTGGG 58.989 61.111 0.00 0.00 0.00 4.61
802 2155 1.812093 CGTGTGTGTTGACGTGGGT 60.812 57.895 0.00 0.00 0.00 4.51
803 2156 1.363145 CGTGTGTGTTGACGTGGGTT 61.363 55.000 0.00 0.00 0.00 4.11
804 2157 0.098025 GTGTGTGTTGACGTGGGTTG 59.902 55.000 0.00 0.00 0.00 3.77
805 2158 0.321741 TGTGTGTTGACGTGGGTTGT 60.322 50.000 0.00 0.00 0.00 3.32
806 2159 1.066358 TGTGTGTTGACGTGGGTTGTA 60.066 47.619 0.00 0.00 0.00 2.41
807 2160 2.215196 GTGTGTTGACGTGGGTTGTAT 58.785 47.619 0.00 0.00 0.00 2.29
808 2161 2.222445 GTGTGTTGACGTGGGTTGTATC 59.778 50.000 0.00 0.00 0.00 2.24
809 2162 2.103432 TGTGTTGACGTGGGTTGTATCT 59.897 45.455 0.00 0.00 0.00 1.98
810 2163 2.478894 GTGTTGACGTGGGTTGTATCTG 59.521 50.000 0.00 0.00 0.00 2.90
811 2164 2.103432 TGTTGACGTGGGTTGTATCTGT 59.897 45.455 0.00 0.00 0.00 3.41
812 2165 3.135994 GTTGACGTGGGTTGTATCTGTT 58.864 45.455 0.00 0.00 0.00 3.16
813 2166 3.034721 TGACGTGGGTTGTATCTGTTC 57.965 47.619 0.00 0.00 0.00 3.18
814 2167 2.631062 TGACGTGGGTTGTATCTGTTCT 59.369 45.455 0.00 0.00 0.00 3.01
815 2168 3.070446 TGACGTGGGTTGTATCTGTTCTT 59.930 43.478 0.00 0.00 0.00 2.52
816 2169 3.399330 ACGTGGGTTGTATCTGTTCTTG 58.601 45.455 0.00 0.00 0.00 3.02
817 2170 3.181458 ACGTGGGTTGTATCTGTTCTTGT 60.181 43.478 0.00 0.00 0.00 3.16
818 2171 3.813166 CGTGGGTTGTATCTGTTCTTGTT 59.187 43.478 0.00 0.00 0.00 2.83
819 2172 4.274950 CGTGGGTTGTATCTGTTCTTGTTT 59.725 41.667 0.00 0.00 0.00 2.83
820 2173 5.220970 CGTGGGTTGTATCTGTTCTTGTTTT 60.221 40.000 0.00 0.00 0.00 2.43
821 2174 6.206498 GTGGGTTGTATCTGTTCTTGTTTTC 58.794 40.000 0.00 0.00 0.00 2.29
822 2175 5.300792 TGGGTTGTATCTGTTCTTGTTTTCC 59.699 40.000 0.00 0.00 0.00 3.13
823 2176 5.278808 GGGTTGTATCTGTTCTTGTTTTCCC 60.279 44.000 0.00 0.00 0.00 3.97
824 2177 5.449304 GTTGTATCTGTTCTTGTTTTCCCG 58.551 41.667 0.00 0.00 0.00 5.14
825 2178 4.069304 TGTATCTGTTCTTGTTTTCCCGG 58.931 43.478 0.00 0.00 0.00 5.73
826 2179 2.721425 TCTGTTCTTGTTTTCCCGGT 57.279 45.000 0.00 0.00 0.00 5.28
827 2180 2.294074 TCTGTTCTTGTTTTCCCGGTG 58.706 47.619 0.00 0.00 0.00 4.94
845 2198 9.675464 TTCCCGGTGAATAATAATATATCAACC 57.325 33.333 0.00 0.00 0.00 3.77
874 2239 2.262915 GTGACACCCAGCTCTCCG 59.737 66.667 0.00 0.00 0.00 4.63
875 2240 3.695606 TGACACCCAGCTCTCCGC 61.696 66.667 0.00 0.00 39.57 5.54
876 2241 4.803426 GACACCCAGCTCTCCGCG 62.803 72.222 0.00 0.00 45.59 6.46
912 2279 2.359900 CAGATAGCCGGCCCATAATTC 58.640 52.381 26.15 9.65 0.00 2.17
913 2280 1.066143 AGATAGCCGGCCCATAATTCG 60.066 52.381 26.15 0.00 0.00 3.34
966 2341 2.102553 GCACCGTCGTCTAGCTCC 59.897 66.667 0.00 0.00 0.00 4.70
970 2345 2.403987 CGTCGTCTAGCTCCCACG 59.596 66.667 0.00 0.00 34.78 4.94
2100 3511 1.597797 CCGGCTACTGGTTCACCGTA 61.598 60.000 0.00 0.00 42.29 4.02
2472 3889 4.116328 TCCCTCTTCGTGCTCGCG 62.116 66.667 0.00 0.00 36.96 5.87
2641 4078 2.354763 TTTCACAACTCGTGCGTGCG 62.355 55.000 3.47 0.00 45.92 5.34
2642 4079 3.626244 CACAACTCGTGCGTGCGT 61.626 61.111 1.25 0.00 39.19 5.24
2644 4081 4.993945 CAACTCGTGCGTGCGTGC 62.994 66.667 1.25 0.00 0.00 5.34
2651 4088 3.997397 TGCGTGCGTGCTAGGGAA 61.997 61.111 1.52 0.00 35.36 3.97
2652 4089 3.188786 GCGTGCGTGCTAGGGAAG 61.189 66.667 0.00 0.00 0.00 3.46
2675 4112 0.250640 CTTCAGGCAGGCTGTTGAGT 60.251 55.000 22.68 0.00 0.00 3.41
2738 4192 8.676761 CGTACACGCTTAAAATACTACTGTATC 58.323 37.037 0.00 0.00 38.33 2.24
2741 4195 9.298774 ACACGCTTAAAATACTACTGTATCTTC 57.701 33.333 0.00 0.00 38.33 2.87
2750 4204 1.153449 CTGTATCTTCGCGGGCCAA 60.153 57.895 6.13 0.00 0.00 4.52
2776 4230 4.559063 CAGGGCCGGCTCCTCATG 62.559 72.222 27.68 15.42 31.06 3.07
2778 4232 3.161450 GGGCCGGCTCCTCATGTA 61.161 66.667 28.56 0.00 0.00 2.29
2779 4233 2.109181 GGCCGGCTCCTCATGTAC 59.891 66.667 28.56 0.41 0.00 2.90
2780 4234 2.731571 GGCCGGCTCCTCATGTACA 61.732 63.158 28.56 0.00 0.00 2.90
2826 4281 7.218228 ACATCAATCAATCAACTTGCAGTTA 57.782 32.000 1.95 0.00 36.03 2.24
2859 4314 5.924475 TTGCACTCAAAGTTTAGAGCTAC 57.076 39.130 12.27 0.00 35.28 3.58
3002 4499 5.211174 AGTTCCTGTCACTGGTTACTTAC 57.789 43.478 0.00 0.00 0.00 2.34
3004 4501 6.073314 AGTTCCTGTCACTGGTTACTTACTA 58.927 40.000 0.00 0.00 0.00 1.82
3010 4507 7.760340 CCTGTCACTGGTTACTTACTAGATTTC 59.240 40.741 0.00 0.00 37.53 2.17
3055 4557 3.012934 AGGCTAGTCAAGAGTCTCCTC 57.987 52.381 0.00 0.00 38.04 3.71
3061 4563 4.550076 AGTCAAGAGTCTCCTCCATTTG 57.450 45.455 0.00 0.00 38.58 2.32
3062 4564 3.906846 AGTCAAGAGTCTCCTCCATTTGT 59.093 43.478 0.00 0.00 38.58 2.83
3063 4565 5.087323 AGTCAAGAGTCTCCTCCATTTGTA 58.913 41.667 0.00 0.00 38.58 2.41
3064 4566 5.046950 AGTCAAGAGTCTCCTCCATTTGTAC 60.047 44.000 0.00 0.00 38.58 2.90
3077 4609 6.035758 CCTCCATTTGTACGTAGTTTTCTAGC 59.964 42.308 0.00 0.00 37.78 3.42
3115 4647 8.883731 CCTGAGTACTAACCAGTGAAAATAATG 58.116 37.037 0.00 0.00 36.14 1.90
3142 4674 4.249661 GGAGTGAAGTCATCTTCCAAGAC 58.750 47.826 5.68 0.00 46.66 3.01
3159 4691 4.141620 CCAAGACTATGACTAAGGCACCAT 60.142 45.833 0.00 0.00 0.00 3.55
3224 4756 4.220693 TGCATACATAAACCTGCTCAGT 57.779 40.909 0.00 0.00 35.66 3.41
3259 4791 4.343814 ACAAAAGGTGTCAATCGGGAAAAT 59.656 37.500 0.00 0.00 34.38 1.82
3265 4798 6.007703 AGGTGTCAATCGGGAAAATAAGAAA 58.992 36.000 0.00 0.00 0.00 2.52
3266 4799 6.663523 AGGTGTCAATCGGGAAAATAAGAAAT 59.336 34.615 0.00 0.00 0.00 2.17
3269 4802 8.889717 GTGTCAATCGGGAAAATAAGAAATAGA 58.110 33.333 0.00 0.00 0.00 1.98
3308 4841 3.244181 GGTTGTCTGCATCAAACCCAATT 60.244 43.478 11.62 0.00 0.00 2.32
3314 4847 5.015515 TCTGCATCAAACCCAATTCACATA 58.984 37.500 0.00 0.00 0.00 2.29
3350 4885 9.799106 AGCTTGATATTAGCACCTTATTTACAT 57.201 29.630 11.83 0.00 41.11 2.29
3363 4898 9.573133 CACCTTATTTACATGGAAAGAAATGTC 57.427 33.333 11.45 0.00 38.05 3.06
3369 4904 3.753272 ACATGGAAAGAAATGTCCAGACG 59.247 43.478 0.00 0.00 46.87 4.18
3373 4908 1.714794 AAGAAATGTCCAGACGAGCG 58.285 50.000 0.00 0.00 0.00 5.03
3374 4909 0.108615 AGAAATGTCCAGACGAGCGG 60.109 55.000 0.00 0.00 0.00 5.52
3403 4938 1.786937 ATTGCAACCCACCAACTCAA 58.213 45.000 0.00 0.00 0.00 3.02
3467 5002 1.686355 TTTTCCATGTGAGCACGGTT 58.314 45.000 0.00 0.00 0.00 4.44
3480 5015 5.810587 GTGAGCACGGTTAAGAAGATCATTA 59.189 40.000 0.00 0.00 0.00 1.90
3484 5019 5.502544 GCACGGTTAAGAAGATCATTAGCAC 60.503 44.000 0.00 0.00 0.00 4.40
3487 5022 6.823689 ACGGTTAAGAAGATCATTAGCACATT 59.176 34.615 0.00 0.00 0.00 2.71
3516 5054 0.477597 TGGGTCAAGGTCATTCCCCT 60.478 55.000 0.00 0.00 37.52 4.79
3544 5082 5.048504 GTCAACTCAAATCAGCCTCAAATCA 60.049 40.000 0.00 0.00 0.00 2.57
3593 5134 8.964476 AATCATTGATAGTAAACGAACTGGAT 57.036 30.769 0.00 0.00 0.00 3.41
3598 5139 9.661563 ATTGATAGTAAACGAACTGGATAAACA 57.338 29.630 0.00 0.00 0.00 2.83
3610 5151 1.664151 GGATAAACAGGAAACGAGGCG 59.336 52.381 0.00 0.00 0.00 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.555956 GCGGAGAATACCACTATGTTGTG 59.444 47.826 0.00 0.00 37.66 3.33
3 4 3.451178 AGTGCGGAGAATACCACTATGTT 59.549 43.478 0.00 0.00 36.82 2.71
4 5 3.031736 AGTGCGGAGAATACCACTATGT 58.968 45.455 0.00 0.00 36.82 2.29
5 6 3.643763 GAGTGCGGAGAATACCACTATG 58.356 50.000 0.00 0.00 38.55 2.23
6 7 2.293677 CGAGTGCGGAGAATACCACTAT 59.706 50.000 0.00 0.00 38.55 2.12
7 8 1.674441 CGAGTGCGGAGAATACCACTA 59.326 52.381 0.00 0.00 38.55 2.74
8 9 0.456221 CGAGTGCGGAGAATACCACT 59.544 55.000 0.00 0.00 40.92 4.00
9 10 2.959275 CGAGTGCGGAGAATACCAC 58.041 57.895 0.00 0.00 0.00 4.16
20 21 2.663602 GCATTACTCATATCCGAGTGCG 59.336 50.000 6.07 0.00 45.79 5.34
49 50 0.615850 AACCAGTCTAAGCCCTCTGC 59.384 55.000 0.00 0.00 41.71 4.26
51 52 2.031495 ACAACCAGTCTAAGCCCTCT 57.969 50.000 0.00 0.00 0.00 3.69
55 56 4.081087 TCCTCATTACAACCAGTCTAAGCC 60.081 45.833 0.00 0.00 0.00 4.35
56 57 5.086104 TCCTCATTACAACCAGTCTAAGC 57.914 43.478 0.00 0.00 0.00 3.09
57 58 6.102663 CACTCCTCATTACAACCAGTCTAAG 58.897 44.000 0.00 0.00 0.00 2.18
58 59 5.542635 ACACTCCTCATTACAACCAGTCTAA 59.457 40.000 0.00 0.00 0.00 2.10
59 60 5.084519 ACACTCCTCATTACAACCAGTCTA 58.915 41.667 0.00 0.00 0.00 2.59
60 61 3.904339 ACACTCCTCATTACAACCAGTCT 59.096 43.478 0.00 0.00 0.00 3.24
61 62 4.246458 GACACTCCTCATTACAACCAGTC 58.754 47.826 0.00 0.00 0.00 3.51
62 63 3.646162 TGACACTCCTCATTACAACCAGT 59.354 43.478 0.00 0.00 0.00 4.00
63 64 4.271696 TGACACTCCTCATTACAACCAG 57.728 45.455 0.00 0.00 0.00 4.00
64 65 4.908601 ATGACACTCCTCATTACAACCA 57.091 40.909 0.00 0.00 0.00 3.67
97 98 9.914834 TGCAATTACCCTAAAAAGATACACTAT 57.085 29.630 0.00 0.00 0.00 2.12
98 99 9.742144 TTGCAATTACCCTAAAAAGATACACTA 57.258 29.630 0.00 0.00 0.00 2.74
99 100 8.644374 TTGCAATTACCCTAAAAAGATACACT 57.356 30.769 0.00 0.00 0.00 3.55
126 127 9.515226 TCAGCTTGGTAAACTATCAACTAAAAT 57.485 29.630 0.00 0.00 0.00 1.82
127 128 8.780249 GTCAGCTTGGTAAACTATCAACTAAAA 58.220 33.333 0.00 0.00 0.00 1.52
128 129 7.389607 GGTCAGCTTGGTAAACTATCAACTAAA 59.610 37.037 0.00 0.00 0.00 1.85
129 130 6.877322 GGTCAGCTTGGTAAACTATCAACTAA 59.123 38.462 0.00 0.00 0.00 2.24
130 131 6.014070 TGGTCAGCTTGGTAAACTATCAACTA 60.014 38.462 0.00 0.00 0.00 2.24
131 132 5.221843 TGGTCAGCTTGGTAAACTATCAACT 60.222 40.000 0.00 0.00 0.00 3.16
132 133 5.001232 TGGTCAGCTTGGTAAACTATCAAC 58.999 41.667 0.00 0.00 0.00 3.18
133 134 5.001232 GTGGTCAGCTTGGTAAACTATCAA 58.999 41.667 0.00 0.00 0.00 2.57
134 135 4.286032 AGTGGTCAGCTTGGTAAACTATCA 59.714 41.667 0.00 0.00 0.00 2.15
135 136 4.833390 AGTGGTCAGCTTGGTAAACTATC 58.167 43.478 0.00 0.00 0.00 2.08
136 137 4.910458 AGTGGTCAGCTTGGTAAACTAT 57.090 40.909 0.00 0.00 0.00 2.12
137 138 4.385825 CAAGTGGTCAGCTTGGTAAACTA 58.614 43.478 0.00 0.00 39.53 2.24
138 139 3.214328 CAAGTGGTCAGCTTGGTAAACT 58.786 45.455 0.00 0.00 39.53 2.66
139 140 3.626028 CAAGTGGTCAGCTTGGTAAAC 57.374 47.619 0.00 0.00 39.53 2.01
171 172 8.030692 GCATTACGGATGTAATACCATACACTA 58.969 37.037 0.74 0.00 46.91 2.74
172 173 6.872020 GCATTACGGATGTAATACCATACACT 59.128 38.462 0.74 0.00 46.91 3.55
173 174 6.647481 TGCATTACGGATGTAATACCATACAC 59.353 38.462 0.74 0.00 46.91 2.90
174 175 6.760291 TGCATTACGGATGTAATACCATACA 58.240 36.000 0.74 0.00 46.91 2.29
175 176 7.843490 ATGCATTACGGATGTAATACCATAC 57.157 36.000 0.00 0.00 46.91 2.39
176 177 7.880713 ACAATGCATTACGGATGTAATACCATA 59.119 33.333 12.53 0.00 46.91 2.74
177 178 6.714810 ACAATGCATTACGGATGTAATACCAT 59.285 34.615 12.53 4.68 46.91 3.55
178 179 6.058833 ACAATGCATTACGGATGTAATACCA 58.941 36.000 12.53 2.85 46.91 3.25
179 180 6.554334 ACAATGCATTACGGATGTAATACC 57.446 37.500 12.53 0.00 46.91 2.73
180 181 8.931775 TGATACAATGCATTACGGATGTAATAC 58.068 33.333 12.53 6.85 46.91 1.89
181 182 8.931775 GTGATACAATGCATTACGGATGTAATA 58.068 33.333 12.53 1.24 46.91 0.98
183 184 6.763610 TGTGATACAATGCATTACGGATGTAA 59.236 34.615 12.53 0.00 44.27 2.41
200 201 5.925969 CGCTATGATACCAACATGTGATACA 59.074 40.000 0.00 0.00 0.00 2.29
235 236 3.652274 ACTTTGTGTTATGCATGGCAAC 58.348 40.909 10.16 6.67 43.62 4.17
239 240 6.193514 TGTGATACTTTGTGTTATGCATGG 57.806 37.500 10.16 0.00 0.00 3.66
320 322 8.851541 ACAATTTTGATGAGTTGGCATAAAAT 57.148 26.923 0.00 0.00 30.65 1.82
322 324 8.674263 AAACAATTTTGATGAGTTGGCATAAA 57.326 26.923 0.00 0.00 0.00 1.40
323 325 9.770097 TTAAACAATTTTGATGAGTTGGCATAA 57.230 25.926 0.00 0.00 0.00 1.90
361 363 7.339721 CGTGATGGGAGTATCATAGGTAGTATT 59.660 40.741 0.00 0.00 39.13 1.89
393 395 4.267928 CGAGGCTGTAAAACTTCGATAAGG 59.732 45.833 0.00 0.00 37.01 2.69
401 403 3.746045 TCAGTCGAGGCTGTAAAACTT 57.254 42.857 4.53 0.00 37.70 2.66
417 419 3.456380 ACCAAAATAGCCCACATCAGT 57.544 42.857 0.00 0.00 0.00 3.41
484 495 0.382515 CGGACTCATCCTTCTCGTCC 59.617 60.000 0.00 0.00 43.73 4.79
486 497 1.546961 AACGGACTCATCCTTCTCGT 58.453 50.000 0.00 0.00 43.73 4.18
544 555 6.829811 TGAATGCAATCTATCAACATCCAAGA 59.170 34.615 2.94 0.00 0.00 3.02
547 558 6.358991 TCTGAATGCAATCTATCAACATCCA 58.641 36.000 2.94 0.00 0.00 3.41
560 1906 9.316594 TGGGAAATAATATCATCTGAATGCAAT 57.683 29.630 0.00 0.00 32.58 3.56
585 1931 2.156917 ACAAGGATATCATGCGGCATG 58.843 47.619 31.85 31.85 42.60 4.06
586 1932 2.224597 TGACAAGGATATCATGCGGCAT 60.225 45.455 10.23 10.23 0.00 4.40
587 1933 1.140652 TGACAAGGATATCATGCGGCA 59.859 47.619 4.58 4.58 0.00 5.69
588 1934 1.882912 TGACAAGGATATCATGCGGC 58.117 50.000 4.83 0.00 0.00 6.53
589 1935 2.221749 CGTTGACAAGGATATCATGCGG 59.778 50.000 4.83 0.00 0.00 5.69
590 1936 3.123050 TCGTTGACAAGGATATCATGCG 58.877 45.455 6.48 2.83 0.00 4.73
591 1937 4.751600 TCATCGTTGACAAGGATATCATGC 59.248 41.667 19.93 1.22 34.50 4.06
614 1967 1.362237 TCCTGGGGAATTTCCATGCTT 59.638 47.619 17.08 0.00 38.64 3.91
672 2025 1.349357 GTTCTCTTGTCTTGGCTCCCT 59.651 52.381 0.00 0.00 0.00 4.20
750 2103 6.782000 AGCACCATATCCAATGGCTATAAAAA 59.218 34.615 3.93 0.00 42.82 1.94
751 2104 6.314120 AGCACCATATCCAATGGCTATAAAA 58.686 36.000 3.93 0.00 42.82 1.52
752 2105 5.891198 AGCACCATATCCAATGGCTATAAA 58.109 37.500 3.93 0.00 42.82 1.40
753 2106 5.519183 AGCACCATATCCAATGGCTATAA 57.481 39.130 3.93 0.00 42.82 0.98
754 2107 6.829985 ATAGCACCATATCCAATGGCTATA 57.170 37.500 3.93 0.00 42.82 1.31
755 2108 5.722172 ATAGCACCATATCCAATGGCTAT 57.278 39.130 3.93 0.00 42.82 2.97
756 2109 6.443527 TCTTATAGCACCATATCCAATGGCTA 59.556 38.462 3.93 0.00 42.82 3.93
757 2110 5.251468 TCTTATAGCACCATATCCAATGGCT 59.749 40.000 3.93 0.00 42.82 4.75
758 2111 5.500234 TCTTATAGCACCATATCCAATGGC 58.500 41.667 3.93 0.00 42.82 4.40
759 2112 6.039047 GCATCTTATAGCACCATATCCAATGG 59.961 42.308 2.46 2.46 44.54 3.16
760 2113 6.238293 CGCATCTTATAGCACCATATCCAATG 60.238 42.308 0.00 0.00 0.00 2.82
761 2114 5.819379 CGCATCTTATAGCACCATATCCAAT 59.181 40.000 0.00 0.00 0.00 3.16
762 2115 5.178061 CGCATCTTATAGCACCATATCCAA 58.822 41.667 0.00 0.00 0.00 3.53
763 2116 4.222810 ACGCATCTTATAGCACCATATCCA 59.777 41.667 0.00 0.00 0.00 3.41
764 2117 4.568359 CACGCATCTTATAGCACCATATCC 59.432 45.833 0.00 0.00 0.00 2.59
765 2118 5.062683 CACACGCATCTTATAGCACCATATC 59.937 44.000 0.00 0.00 0.00 1.63
766 2119 4.931601 CACACGCATCTTATAGCACCATAT 59.068 41.667 0.00 0.00 0.00 1.78
767 2120 4.202212 ACACACGCATCTTATAGCACCATA 60.202 41.667 0.00 0.00 0.00 2.74
768 2121 3.133691 CACACGCATCTTATAGCACCAT 58.866 45.455 0.00 0.00 0.00 3.55
769 2122 2.093711 ACACACGCATCTTATAGCACCA 60.094 45.455 0.00 0.00 0.00 4.17
770 2123 2.285220 CACACACGCATCTTATAGCACC 59.715 50.000 0.00 0.00 0.00 5.01
771 2124 2.930040 ACACACACGCATCTTATAGCAC 59.070 45.455 0.00 0.00 0.00 4.40
772 2125 3.245518 ACACACACGCATCTTATAGCA 57.754 42.857 0.00 0.00 0.00 3.49
773 2126 3.616821 TCAACACACACGCATCTTATAGC 59.383 43.478 0.00 0.00 0.00 2.97
774 2127 4.259411 CGTCAACACACACGCATCTTATAG 60.259 45.833 0.00 0.00 0.00 1.31
775 2128 3.610677 CGTCAACACACACGCATCTTATA 59.389 43.478 0.00 0.00 0.00 0.98
776 2129 2.411748 CGTCAACACACACGCATCTTAT 59.588 45.455 0.00 0.00 0.00 1.73
777 2130 1.790043 CGTCAACACACACGCATCTTA 59.210 47.619 0.00 0.00 0.00 2.10
778 2131 0.581529 CGTCAACACACACGCATCTT 59.418 50.000 0.00 0.00 0.00 2.40
779 2132 0.529773 ACGTCAACACACACGCATCT 60.530 50.000 0.00 0.00 39.73 2.90
780 2133 0.383002 CACGTCAACACACACGCATC 60.383 55.000 0.00 0.00 39.73 3.91
781 2134 1.641140 CACGTCAACACACACGCAT 59.359 52.632 0.00 0.00 39.73 4.73
782 2135 2.456948 CCACGTCAACACACACGCA 61.457 57.895 0.00 0.00 39.73 5.24
783 2136 2.323105 CCACGTCAACACACACGC 59.677 61.111 0.00 0.00 39.73 5.34
784 2137 1.363145 AACCCACGTCAACACACACG 61.363 55.000 0.00 0.00 41.90 4.49
785 2138 0.098025 CAACCCACGTCAACACACAC 59.902 55.000 0.00 0.00 0.00 3.82
786 2139 0.321741 ACAACCCACGTCAACACACA 60.322 50.000 0.00 0.00 0.00 3.72
787 2140 1.654317 TACAACCCACGTCAACACAC 58.346 50.000 0.00 0.00 0.00 3.82
788 2141 2.103432 AGATACAACCCACGTCAACACA 59.897 45.455 0.00 0.00 0.00 3.72
789 2142 2.478894 CAGATACAACCCACGTCAACAC 59.521 50.000 0.00 0.00 0.00 3.32
790 2143 2.103432 ACAGATACAACCCACGTCAACA 59.897 45.455 0.00 0.00 0.00 3.33
791 2144 2.762745 ACAGATACAACCCACGTCAAC 58.237 47.619 0.00 0.00 0.00 3.18
792 2145 3.070446 AGAACAGATACAACCCACGTCAA 59.930 43.478 0.00 0.00 0.00 3.18
793 2146 2.631062 AGAACAGATACAACCCACGTCA 59.369 45.455 0.00 0.00 0.00 4.35
794 2147 3.314541 AGAACAGATACAACCCACGTC 57.685 47.619 0.00 0.00 0.00 4.34
795 2148 3.181458 ACAAGAACAGATACAACCCACGT 60.181 43.478 0.00 0.00 0.00 4.49
796 2149 3.399330 ACAAGAACAGATACAACCCACG 58.601 45.455 0.00 0.00 0.00 4.94
797 2150 5.767816 AAACAAGAACAGATACAACCCAC 57.232 39.130 0.00 0.00 0.00 4.61
798 2151 5.300792 GGAAAACAAGAACAGATACAACCCA 59.699 40.000 0.00 0.00 0.00 4.51
799 2152 5.278808 GGGAAAACAAGAACAGATACAACCC 60.279 44.000 0.00 0.00 0.00 4.11
800 2153 5.562113 CGGGAAAACAAGAACAGATACAACC 60.562 44.000 0.00 0.00 0.00 3.77
801 2154 5.449304 CGGGAAAACAAGAACAGATACAAC 58.551 41.667 0.00 0.00 0.00 3.32
802 2155 4.517453 CCGGGAAAACAAGAACAGATACAA 59.483 41.667 0.00 0.00 0.00 2.41
803 2156 4.069304 CCGGGAAAACAAGAACAGATACA 58.931 43.478 0.00 0.00 0.00 2.29
804 2157 4.070009 ACCGGGAAAACAAGAACAGATAC 58.930 43.478 6.32 0.00 0.00 2.24
805 2158 4.069304 CACCGGGAAAACAAGAACAGATA 58.931 43.478 6.32 0.00 0.00 1.98
806 2159 2.884639 CACCGGGAAAACAAGAACAGAT 59.115 45.455 6.32 0.00 0.00 2.90
807 2160 2.092861 TCACCGGGAAAACAAGAACAGA 60.093 45.455 6.32 0.00 0.00 3.41
808 2161 2.294074 TCACCGGGAAAACAAGAACAG 58.706 47.619 6.32 0.00 0.00 3.16
809 2162 2.421751 TCACCGGGAAAACAAGAACA 57.578 45.000 6.32 0.00 0.00 3.18
810 2163 5.441709 TTATTCACCGGGAAAACAAGAAC 57.558 39.130 6.32 0.00 39.39 3.01
811 2164 7.762588 TTATTATTCACCGGGAAAACAAGAA 57.237 32.000 6.32 4.22 39.39 2.52
812 2165 7.948034 ATTATTATTCACCGGGAAAACAAGA 57.052 32.000 6.32 0.00 39.39 3.02
819 2172 9.675464 GGTTGATATATTATTATTCACCGGGAA 57.325 33.333 6.32 7.16 40.46 3.97
820 2173 8.827758 TGGTTGATATATTATTATTCACCGGGA 58.172 33.333 6.32 0.00 0.00 5.14
821 2174 9.456147 TTGGTTGATATATTATTATTCACCGGG 57.544 33.333 6.32 0.00 0.00 5.73
839 2192 3.064820 GTCACCGCGAATATTTGGTTGAT 59.935 43.478 8.23 0.00 30.72 2.57
840 2193 2.417239 GTCACCGCGAATATTTGGTTGA 59.583 45.455 8.23 4.83 30.72 3.18
841 2194 2.160615 TGTCACCGCGAATATTTGGTTG 59.839 45.455 8.23 0.00 30.72 3.77
842 2195 2.160813 GTGTCACCGCGAATATTTGGTT 59.839 45.455 8.23 0.00 30.72 3.67
843 2196 1.735571 GTGTCACCGCGAATATTTGGT 59.264 47.619 8.23 3.82 34.29 3.67
844 2197 1.063469 GGTGTCACCGCGAATATTTGG 59.937 52.381 8.23 3.22 0.00 3.28
845 2198 1.063469 GGGTGTCACCGCGAATATTTG 59.937 52.381 15.93 0.00 39.83 2.32
874 2239 2.486982 TCTGGTATAAGTAGCCGATCGC 59.513 50.000 10.32 5.46 37.98 4.58
875 2240 4.966965 ATCTGGTATAAGTAGCCGATCG 57.033 45.455 8.51 8.51 29.77 3.69
876 2241 5.221087 GGCTATCTGGTATAAGTAGCCGATC 60.221 48.000 6.03 0.00 45.40 3.69
877 2242 4.645588 GGCTATCTGGTATAAGTAGCCGAT 59.354 45.833 6.03 0.00 45.40 4.18
912 2279 0.449786 TTCTTGTGTTGTGGTGCACG 59.550 50.000 11.45 0.00 37.14 5.34
913 2280 2.094752 ACTTTCTTGTGTTGTGGTGCAC 60.095 45.455 8.80 8.80 36.26 4.57
2100 3511 3.920144 GACGACGTCGATGAGGAAT 57.080 52.632 41.52 18.88 43.02 3.01
2472 3889 4.366684 CCCAGCAGGTTGACCCCC 62.367 72.222 0.00 0.00 36.42 5.40
2644 4081 0.463474 GCCTGAAGCTGCTTCCCTAG 60.463 60.000 32.70 24.39 39.51 3.02
2645 4082 1.200760 TGCCTGAAGCTGCTTCCCTA 61.201 55.000 32.70 17.78 44.23 3.53
2649 4086 2.698763 GCCTGCCTGAAGCTGCTTC 61.699 63.158 30.35 30.35 44.23 3.86
2651 4088 3.648830 AGCCTGCCTGAAGCTGCT 61.649 61.111 0.00 0.00 42.87 4.24
2652 4089 3.441290 CAGCCTGCCTGAAGCTGC 61.441 66.667 0.00 0.00 46.60 5.25
2654 4091 1.602888 CAACAGCCTGCCTGAAGCT 60.603 57.895 0.00 0.00 44.64 3.74
2655 4092 1.584380 CTCAACAGCCTGCCTGAAGC 61.584 60.000 0.00 0.00 44.64 3.86
2656 4093 0.250640 ACTCAACAGCCTGCCTGAAG 60.251 55.000 0.00 0.00 44.64 3.02
2657 4094 0.183492 AACTCAACAGCCTGCCTGAA 59.817 50.000 0.00 0.00 44.64 3.02
2658 4095 1.002430 CTAACTCAACAGCCTGCCTGA 59.998 52.381 0.00 0.00 44.64 3.86
2660 4097 1.002544 GACTAACTCAACAGCCTGCCT 59.997 52.381 0.00 0.00 0.00 4.75
2661 4098 1.443802 GACTAACTCAACAGCCTGCC 58.556 55.000 0.00 0.00 0.00 4.85
2774 4228 9.710900 CGTATATATCATGGGCATATTGTACAT 57.289 33.333 0.00 0.00 0.00 2.29
2775 4229 8.700973 ACGTATATATCATGGGCATATTGTACA 58.299 33.333 0.00 0.00 0.00 2.90
2778 4232 8.700973 TGTACGTATATATCATGGGCATATTGT 58.299 33.333 0.00 0.50 0.00 2.71
2779 4233 9.710900 ATGTACGTATATATCATGGGCATATTG 57.289 33.333 2.61 0.00 0.00 1.90
2780 4234 9.929180 GATGTACGTATATATCATGGGCATATT 57.071 33.333 4.66 0.00 31.08 1.28
2826 4281 4.588528 ACTTTGAGTGCAATACCCATTTGT 59.411 37.500 0.00 0.00 33.25 2.83
2859 4314 3.664930 GCGTTAGCTTTGCTCACTG 57.335 52.632 0.00 0.00 40.44 3.66
3029 4531 5.373222 GAGACTCTTGACTAGCCTAGATCA 58.627 45.833 5.58 3.07 0.00 2.92
3030 4532 4.760204 GGAGACTCTTGACTAGCCTAGATC 59.240 50.000 5.58 0.41 0.00 2.75
3031 4533 4.415512 AGGAGACTCTTGACTAGCCTAGAT 59.584 45.833 5.58 0.00 32.90 1.98
3055 4557 6.367969 AGTGCTAGAAAACTACGTACAAATGG 59.632 38.462 0.00 0.00 0.00 3.16
3061 4563 8.020244 ACTAAGAAGTGCTAGAAAACTACGTAC 58.980 37.037 0.00 0.00 33.57 3.67
3062 4564 8.103948 ACTAAGAAGTGCTAGAAAACTACGTA 57.896 34.615 0.00 0.00 33.57 3.57
3063 4565 6.979465 ACTAAGAAGTGCTAGAAAACTACGT 58.021 36.000 0.00 0.00 33.57 3.57
3064 4566 6.527372 GGACTAAGAAGTGCTAGAAAACTACG 59.473 42.308 0.00 0.00 40.68 3.51
3077 4609 6.127675 GGTTAGTACTCAGGGACTAAGAAGTG 60.128 46.154 0.00 0.00 38.50 3.16
3142 4674 3.572682 TCGGTATGGTGCCTTAGTCATAG 59.427 47.826 0.00 0.00 0.00 2.23
3159 4691 7.391620 ACCAAGAAAGTTTAGATGATTCGGTA 58.608 34.615 0.00 0.00 0.00 4.02
3224 4756 5.943416 TGACACCTTTTGTTCTCTTTGAGAA 59.057 36.000 5.97 5.97 45.01 2.87
3265 4798 8.055181 ACAACCAAACATGTCCTAATGATCTAT 58.945 33.333 0.00 0.00 0.00 1.98
3266 4799 7.402054 ACAACCAAACATGTCCTAATGATCTA 58.598 34.615 0.00 0.00 0.00 1.98
3269 4802 6.151648 CAGACAACCAAACATGTCCTAATGAT 59.848 38.462 0.00 0.00 45.55 2.45
3308 4841 8.978874 ATATCAAGCTAAACCAACATATGTGA 57.021 30.769 9.63 0.00 0.00 3.58
3314 4847 7.201821 GGTGCTAATATCAAGCTAAACCAACAT 60.202 37.037 10.42 0.00 40.73 2.71
3350 4885 3.664107 CTCGTCTGGACATTTCTTTCCA 58.336 45.455 1.63 0.00 39.72 3.53
3363 4898 1.433879 CTTACTCCCGCTCGTCTGG 59.566 63.158 0.00 0.00 0.00 3.86
3365 4900 0.254178 TACCTTACTCCCGCTCGTCT 59.746 55.000 0.00 0.00 0.00 4.18
3369 4904 1.138266 TGCAATACCTTACTCCCGCTC 59.862 52.381 0.00 0.00 0.00 5.03
3373 4908 2.025699 TGGGTTGCAATACCTTACTCCC 60.026 50.000 19.80 14.58 38.30 4.30
3374 4909 3.014623 GTGGGTTGCAATACCTTACTCC 58.985 50.000 19.80 6.55 38.30 3.85
3438 4973 1.727880 CACATGGAAAATTGCAAGGCG 59.272 47.619 4.94 0.00 30.51 5.52
3484 5019 4.340950 ACCTTGACCCAACACAAGTAAATG 59.659 41.667 0.00 0.00 40.98 2.32
3487 5022 3.054287 TGACCTTGACCCAACACAAGTAA 60.054 43.478 0.00 0.00 40.98 2.24
3544 5082 6.702716 TTGGTTGACTCGGTTAATTTCTTT 57.297 33.333 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.