Multiple sequence alignment - TraesCS3A01G214100

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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 TraesCS3A01G214100 chr3A 100.000 3467 0 0 1 3467 388801050 388804516 0.000000e+00 6403.0
1 TraesCS3A01G214100 chr3A 93.989 183 7 4 1240 1420 647803438 647803618 1.230000e-69 274.0
2 TraesCS3A01G214100 chr3A 74.419 473 98 21 1366 1827 30544407 30544867 7.640000e-42 182.0
3 TraesCS3A01G214100 chr3A 97.802 91 2 0 68 158 498772610 498772520 1.290000e-34 158.0
4 TraesCS3A01G214100 chr3D 92.207 2823 77 51 711 3467 294048113 294050858 0.000000e+00 3862.0
5 TraesCS3A01G214100 chr3D 94.585 277 10 5 1258 1532 31092519 31092792 1.150000e-114 424.0
6 TraesCS3A01G214100 chr3D 89.340 197 12 3 414 602 294047312 294047507 4.470000e-59 239.0
7 TraesCS3A01G214100 chr3D 96.000 125 2 1 152 276 294046985 294047106 2.110000e-47 200.0
8 TraesCS3A01G214100 chr3D 83.824 136 14 4 645 773 294041580 294041714 4.700000e-24 122.0
9 TraesCS3A01G214100 chr3B 93.199 2029 66 29 639 2631 387886520 387888512 0.000000e+00 2916.0
10 TraesCS3A01G214100 chr3B 88.178 516 27 15 2968 3467 387889518 387890015 4.990000e-163 584.0
11 TraesCS3A01G214100 chr3B 81.505 319 19 12 2629 2937 387888902 387889190 3.480000e-55 226.0
12 TraesCS3A01G214100 chr3B 74.105 475 105 18 1366 1832 36543826 36543362 2.750000e-41 180.0
13 TraesCS3A01G214100 chr3B 100.000 86 0 0 70 155 607220383 607220468 3.580000e-35 159.0
14 TraesCS3A01G214100 chr3B 94.118 102 3 2 71 169 20744579 20744680 5.990000e-33 152.0
15 TraesCS3A01G214100 chr3B 97.778 45 1 0 204 248 387885436 387885480 1.030000e-10 78.7
16 TraesCS3A01G214100 chr1D 91.973 299 20 4 1249 1545 390266504 390266800 1.920000e-112 416.0
17 TraesCS3A01G214100 chr2A 95.028 181 9 0 1240 1420 211481983 211481803 5.660000e-73 285.0
18 TraesCS3A01G214100 chr2A 95.789 95 4 0 64 158 207651970 207651876 1.670000e-33 154.0
19 TraesCS3A01G214100 chr5A 92.818 181 13 0 1240 1420 328711518 328711698 2.650000e-66 263.0
20 TraesCS3A01G214100 chr2B 92.667 150 7 4 1273 1420 153890281 153890134 2.710000e-51 213.0
21 TraesCS3A01G214100 chr7B 97.849 93 2 0 63 155 616099755 616099847 9.960000e-36 161.0
22 TraesCS3A01G214100 chr7D 98.876 89 1 0 67 155 343752016 343751928 3.580000e-35 159.0
23 TraesCS3A01G214100 chr4A 86.395 147 11 5 939 1084 541017662 541017800 5.990000e-33 152.0
24 TraesCS3A01G214100 chr4A 94.000 100 5 1 67 166 713028227 713028129 2.160000e-32 150.0
25 TraesCS3A01G214100 chr4A 83.226 155 7 2 939 1087 602718830 602718971 1.310000e-24 124.0
26 TraesCS3A01G214100 chr4A 90.909 88 8 0 1241 1328 541017812 541017899 6.080000e-23 119.0
27 TraesCS3A01G214100 chrUn 93.939 99 3 3 66 161 8111540 8111442 2.790000e-31 147.0
28 TraesCS3A01G214100 chr4B 91.589 107 8 1 68 173 317037325 317037431 2.790000e-31 147.0
29 TraesCS3A01G214100 chr6A 94.444 72 4 0 1 72 126642249 126642320 1.020000e-20 111.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G214100 chr3A 388801050 388804516 3466 False 6403.000000 6403 100.000000 1 3467 1 chr3A.!!$F2 3466
1 TraesCS3A01G214100 chr3D 294046985 294050858 3873 False 1433.666667 3862 92.515667 152 3467 3 chr3D.!!$F3 3315
2 TraesCS3A01G214100 chr3B 387885436 387890015 4579 False 951.175000 2916 90.165000 204 3467 4 chr3B.!!$F3 3263

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
918 2405 0.038251 TGATGACTCGCGCACTCTTT 60.038 50.0 8.75 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2611 4130 0.18135 CTTATCCTCACACCCTGCCC 59.819 60.0 0.0 0.0 0.0 5.36 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
20 21 3.598019 GCTTCCTGCAATGAAAATCCA 57.402 42.857 0.00 0.00 42.31 3.41
21 22 4.133013 GCTTCCTGCAATGAAAATCCAT 57.867 40.909 0.00 0.00 42.31 3.41
22 23 5.266733 GCTTCCTGCAATGAAAATCCATA 57.733 39.130 0.00 0.00 42.31 2.74
23 24 5.045872 GCTTCCTGCAATGAAAATCCATAC 58.954 41.667 0.00 0.00 42.31 2.39
24 25 5.594926 CTTCCTGCAATGAAAATCCATACC 58.405 41.667 0.00 0.00 0.00 2.73
25 26 3.631686 TCCTGCAATGAAAATCCATACCG 59.368 43.478 0.00 0.00 0.00 4.02
26 27 3.381272 CCTGCAATGAAAATCCATACCGT 59.619 43.478 0.00 0.00 0.00 4.83
27 28 4.498009 CCTGCAATGAAAATCCATACCGTC 60.498 45.833 0.00 0.00 0.00 4.79
28 29 4.269183 TGCAATGAAAATCCATACCGTCT 58.731 39.130 0.00 0.00 0.00 4.18
29 30 4.335315 TGCAATGAAAATCCATACCGTCTC 59.665 41.667 0.00 0.00 0.00 3.36
30 31 4.576463 GCAATGAAAATCCATACCGTCTCT 59.424 41.667 0.00 0.00 0.00 3.10
31 32 5.758296 GCAATGAAAATCCATACCGTCTCTA 59.242 40.000 0.00 0.00 0.00 2.43
32 33 6.292919 GCAATGAAAATCCATACCGTCTCTAC 60.293 42.308 0.00 0.00 0.00 2.59
33 34 6.732896 ATGAAAATCCATACCGTCTCTACT 57.267 37.500 0.00 0.00 0.00 2.57
34 35 6.145338 TGAAAATCCATACCGTCTCTACTC 57.855 41.667 0.00 0.00 0.00 2.59
35 36 5.655090 TGAAAATCCATACCGTCTCTACTCA 59.345 40.000 0.00 0.00 0.00 3.41
36 37 6.323996 TGAAAATCCATACCGTCTCTACTCAT 59.676 38.462 0.00 0.00 0.00 2.90
37 38 7.504574 TGAAAATCCATACCGTCTCTACTCATA 59.495 37.037 0.00 0.00 0.00 2.15
38 39 7.455641 AAATCCATACCGTCTCTACTCATAG 57.544 40.000 0.00 0.00 0.00 2.23
39 40 4.325119 TCCATACCGTCTCTACTCATAGC 58.675 47.826 0.00 0.00 0.00 2.97
40 41 4.072839 CCATACCGTCTCTACTCATAGCA 58.927 47.826 0.00 0.00 0.00 3.49
41 42 4.083217 CCATACCGTCTCTACTCATAGCAC 60.083 50.000 0.00 0.00 0.00 4.40
42 43 3.000684 ACCGTCTCTACTCATAGCACA 57.999 47.619 0.00 0.00 0.00 4.57
43 44 3.353557 ACCGTCTCTACTCATAGCACAA 58.646 45.455 0.00 0.00 0.00 3.33
44 45 3.762288 ACCGTCTCTACTCATAGCACAAA 59.238 43.478 0.00 0.00 0.00 2.83
45 46 4.219944 ACCGTCTCTACTCATAGCACAAAA 59.780 41.667 0.00 0.00 0.00 2.44
46 47 4.800993 CCGTCTCTACTCATAGCACAAAAG 59.199 45.833 0.00 0.00 0.00 2.27
47 48 5.393135 CCGTCTCTACTCATAGCACAAAAGA 60.393 44.000 0.00 0.00 0.00 2.52
48 49 6.269315 CGTCTCTACTCATAGCACAAAAGAT 58.731 40.000 0.00 0.00 0.00 2.40
49 50 6.198029 CGTCTCTACTCATAGCACAAAAGATG 59.802 42.308 0.00 0.00 0.00 2.90
50 51 7.038659 GTCTCTACTCATAGCACAAAAGATGT 58.961 38.462 0.00 0.00 45.34 3.06
51 52 7.221838 GTCTCTACTCATAGCACAAAAGATGTC 59.778 40.741 0.00 0.00 41.46 3.06
52 53 7.123397 TCTCTACTCATAGCACAAAAGATGTCT 59.877 37.037 0.00 0.00 41.46 3.41
53 54 7.038048 TCTACTCATAGCACAAAAGATGTCTG 58.962 38.462 0.00 0.00 41.46 3.51
54 55 5.798132 ACTCATAGCACAAAAGATGTCTGA 58.202 37.500 0.00 0.00 41.46 3.27
55 56 5.873712 ACTCATAGCACAAAAGATGTCTGAG 59.126 40.000 0.00 0.00 41.46 3.35
56 57 6.041423 TCATAGCACAAAAGATGTCTGAGA 57.959 37.500 0.00 0.00 41.46 3.27
57 58 6.466812 TCATAGCACAAAAGATGTCTGAGAA 58.533 36.000 0.00 0.00 41.46 2.87
58 59 6.936335 TCATAGCACAAAAGATGTCTGAGAAA 59.064 34.615 0.00 0.00 41.46 2.52
59 60 7.445096 TCATAGCACAAAAGATGTCTGAGAAAA 59.555 33.333 0.00 0.00 41.46 2.29
60 61 5.825507 AGCACAAAAGATGTCTGAGAAAAC 58.174 37.500 0.00 0.00 41.46 2.43
61 62 5.591877 AGCACAAAAGATGTCTGAGAAAACT 59.408 36.000 0.00 0.00 41.46 2.66
62 63 5.684626 GCACAAAAGATGTCTGAGAAAACTG 59.315 40.000 0.00 0.00 41.46 3.16
63 64 6.678900 GCACAAAAGATGTCTGAGAAAACTGT 60.679 38.462 0.00 0.00 41.46 3.55
64 65 6.909357 CACAAAAGATGTCTGAGAAAACTGTC 59.091 38.462 0.00 0.00 41.46 3.51
65 66 6.599244 ACAAAAGATGTCTGAGAAAACTGTCA 59.401 34.615 0.00 0.00 37.96 3.58
66 67 7.284034 ACAAAAGATGTCTGAGAAAACTGTCAT 59.716 33.333 0.00 0.00 37.96 3.06
67 68 8.777413 CAAAAGATGTCTGAGAAAACTGTCATA 58.223 33.333 0.00 0.00 0.00 2.15
68 69 8.908786 AAAGATGTCTGAGAAAACTGTCATAA 57.091 30.769 0.00 0.00 0.00 1.90
69 70 8.545229 AAGATGTCTGAGAAAACTGTCATAAG 57.455 34.615 0.00 0.00 0.00 1.73
70 71 7.675062 AGATGTCTGAGAAAACTGTCATAAGT 58.325 34.615 0.00 0.00 0.00 2.24
71 72 8.807118 AGATGTCTGAGAAAACTGTCATAAGTA 58.193 33.333 0.00 0.00 0.00 2.24
72 73 8.764524 ATGTCTGAGAAAACTGTCATAAGTAC 57.235 34.615 0.00 0.00 0.00 2.73
73 74 7.952671 TGTCTGAGAAAACTGTCATAAGTACT 58.047 34.615 0.00 0.00 0.00 2.73
74 75 8.082852 TGTCTGAGAAAACTGTCATAAGTACTC 58.917 37.037 0.00 0.00 0.00 2.59
75 76 7.542824 GTCTGAGAAAACTGTCATAAGTACTCC 59.457 40.741 0.00 0.00 30.71 3.85
76 77 6.698380 TGAGAAAACTGTCATAAGTACTCCC 58.302 40.000 0.00 0.00 30.71 4.30
77 78 6.497259 TGAGAAAACTGTCATAAGTACTCCCT 59.503 38.462 0.00 0.00 30.71 4.20
78 79 6.937392 AGAAAACTGTCATAAGTACTCCCTC 58.063 40.000 0.00 0.00 0.00 4.30
79 80 5.678955 AAACTGTCATAAGTACTCCCTCC 57.321 43.478 0.00 0.00 0.00 4.30
80 81 3.288964 ACTGTCATAAGTACTCCCTCCG 58.711 50.000 0.00 0.00 0.00 4.63
81 82 3.288964 CTGTCATAAGTACTCCCTCCGT 58.711 50.000 0.00 0.00 0.00 4.69
82 83 4.080129 ACTGTCATAAGTACTCCCTCCGTA 60.080 45.833 0.00 0.00 0.00 4.02
83 84 4.858850 TGTCATAAGTACTCCCTCCGTAA 58.141 43.478 0.00 0.00 0.00 3.18
84 85 5.263599 TGTCATAAGTACTCCCTCCGTAAA 58.736 41.667 0.00 0.00 0.00 2.01
85 86 5.126061 TGTCATAAGTACTCCCTCCGTAAAC 59.874 44.000 0.00 0.00 0.00 2.01
86 87 5.359292 GTCATAAGTACTCCCTCCGTAAACT 59.641 44.000 0.00 0.00 0.00 2.66
87 88 6.543831 GTCATAAGTACTCCCTCCGTAAACTA 59.456 42.308 0.00 0.00 0.00 2.24
88 89 7.067494 GTCATAAGTACTCCCTCCGTAAACTAA 59.933 40.741 0.00 0.00 0.00 2.24
89 90 7.781693 TCATAAGTACTCCCTCCGTAAACTAAT 59.218 37.037 0.00 0.00 0.00 1.73
90 91 9.071276 CATAAGTACTCCCTCCGTAAACTAATA 57.929 37.037 0.00 0.00 0.00 0.98
91 92 9.819754 ATAAGTACTCCCTCCGTAAACTAATAT 57.180 33.333 0.00 0.00 0.00 1.28
93 94 9.646522 AAGTACTCCCTCCGTAAACTAATATAA 57.353 33.333 0.00 0.00 0.00 0.98
94 95 9.294614 AGTACTCCCTCCGTAAACTAATATAAG 57.705 37.037 0.00 0.00 0.00 1.73
95 96 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
96 97 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
97 98 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
98 99 6.779049 TCCCTCCGTAAACTAATATAAGAGCA 59.221 38.462 0.00 0.00 0.00 4.26
99 100 7.453752 TCCCTCCGTAAACTAATATAAGAGCAT 59.546 37.037 0.00 0.00 0.00 3.79
100 101 8.095169 CCCTCCGTAAACTAATATAAGAGCATT 58.905 37.037 0.00 0.00 0.00 3.56
101 102 9.490379 CCTCCGTAAACTAATATAAGAGCATTT 57.510 33.333 0.00 0.00 0.00 2.32
150 151 9.490379 AACGCTCTTATATTAATTTACAGAGGG 57.510 33.333 21.96 21.96 42.53 4.30
276 961 7.035840 TGGGTAGTTCTATCGTTTCAGATAC 57.964 40.000 0.00 0.00 32.39 2.24
277 962 6.832384 TGGGTAGTTCTATCGTTTCAGATACT 59.168 38.462 0.00 0.00 32.39 2.12
278 963 7.013083 TGGGTAGTTCTATCGTTTCAGATACTC 59.987 40.741 0.00 0.00 32.39 2.59
279 964 7.361894 GGTAGTTCTATCGTTTCAGATACTCC 58.638 42.308 0.00 0.00 32.39 3.85
280 965 6.394025 AGTTCTATCGTTTCAGATACTCCC 57.606 41.667 0.00 0.00 32.39 4.30
282 967 5.769484 TCTATCGTTTCAGATACTCCCAC 57.231 43.478 0.00 0.00 32.39 4.61
283 968 3.821421 ATCGTTTCAGATACTCCCACC 57.179 47.619 0.00 0.00 0.00 4.61
284 969 2.531771 TCGTTTCAGATACTCCCACCA 58.468 47.619 0.00 0.00 0.00 4.17
289 974 5.334879 CGTTTCAGATACTCCCACCAAAAAG 60.335 44.000 0.00 0.00 0.00 2.27
291 976 3.073798 TCAGATACTCCCACCAAAAAGCA 59.926 43.478 0.00 0.00 0.00 3.91
293 978 2.286365 TACTCCCACCAAAAAGCAGG 57.714 50.000 0.00 0.00 0.00 4.85
295 980 1.075674 TCCCACCAAAAAGCAGGCA 60.076 52.632 0.00 0.00 0.00 4.75
323 1011 2.027460 GGCACAAAGGCCGTGTTG 59.973 61.111 11.99 12.75 45.40 3.33
326 1014 1.299316 CACAAAGGCCGTGTTGCTG 60.299 57.895 11.99 8.16 0.00 4.41
336 1024 0.247655 CGTGTTGCTGTGACACACAC 60.248 55.000 14.11 14.11 45.88 3.82
347 1035 3.141398 GTGACACACACCTGAATCACAT 58.859 45.455 0.00 0.00 43.05 3.21
375 1340 4.403585 AGATCACACTCATCACCATCAG 57.596 45.455 0.00 0.00 0.00 2.90
391 1356 6.317140 TCACCATCAGCTAAAGCATAGAAAAG 59.683 38.462 4.54 0.00 45.16 2.27
397 1362 6.037940 TCAGCTAAAGCATAGAAAAGCATCAG 59.962 38.462 4.54 0.00 45.16 2.90
404 1369 5.296283 AGCATAGAAAAGCATCAGCAACTAG 59.704 40.000 0.00 0.00 45.49 2.57
430 1395 0.107848 ACGCCTAGGGGAAAATCGTG 60.108 55.000 31.00 0.85 33.58 4.35
449 1414 3.181507 CGTGATGCCACTATGAAAACCAG 60.182 47.826 0.00 0.00 41.06 4.00
469 1434 4.083802 CCAGATTTCCCTATTCGATTTCGC 60.084 45.833 0.00 0.00 39.60 4.70
486 1451 1.140052 TCGCCATGTGATTACCGGATT 59.860 47.619 9.46 0.00 0.00 3.01
487 1452 2.365941 TCGCCATGTGATTACCGGATTA 59.634 45.455 9.46 0.00 0.00 1.75
488 1453 3.007506 TCGCCATGTGATTACCGGATTAT 59.992 43.478 9.46 0.00 0.00 1.28
489 1454 3.125146 CGCCATGTGATTACCGGATTATG 59.875 47.826 9.46 2.64 0.00 1.90
490 1455 4.323417 GCCATGTGATTACCGGATTATGA 58.677 43.478 9.46 0.00 0.00 2.15
491 1456 4.393062 GCCATGTGATTACCGGATTATGAG 59.607 45.833 9.46 0.00 0.00 2.90
492 1457 5.551233 CCATGTGATTACCGGATTATGAGT 58.449 41.667 9.46 0.00 0.00 3.41
494 1459 6.147821 CCATGTGATTACCGGATTATGAGTTC 59.852 42.308 9.46 0.00 0.00 3.01
501 1470 7.931578 TTACCGGATTATGAGTTCAAAACAT 57.068 32.000 9.46 0.00 0.00 2.71
567 1539 2.034221 GGCAGGGGAAAAGCTCGT 59.966 61.111 0.00 0.00 0.00 4.18
570 1542 1.679898 CAGGGGAAAAGCTCGTCCT 59.320 57.895 13.77 2.64 34.10 3.85
602 1574 1.959085 CAACAATGGCTTGCTCCGT 59.041 52.632 0.00 0.00 35.69 4.69
604 1576 0.537143 AACAATGGCTTGCTCCGTCA 60.537 50.000 0.00 0.00 35.69 4.35
605 1577 1.237285 ACAATGGCTTGCTCCGTCAC 61.237 55.000 0.00 0.00 35.69 3.67
626 1638 2.050985 GCGCGTTTGCTCTTGCTT 60.051 55.556 8.43 0.00 40.48 3.91
700 1728 0.764890 CCAGGTCTTCCCACAGTCAA 59.235 55.000 0.00 0.00 34.66 3.18
701 1729 1.142870 CCAGGTCTTCCCACAGTCAAA 59.857 52.381 0.00 0.00 34.66 2.69
703 1731 3.490348 CAGGTCTTCCCACAGTCAAATT 58.510 45.455 0.00 0.00 34.66 1.82
705 1733 3.891366 AGGTCTTCCCACAGTCAAATTTG 59.109 43.478 12.15 12.15 34.66 2.32
706 1734 3.636764 GGTCTTCCCACAGTCAAATTTGT 59.363 43.478 17.47 0.00 0.00 2.83
708 1736 4.338118 GTCTTCCCACAGTCAAATTTGTCA 59.662 41.667 17.47 0.00 0.00 3.58
709 1737 5.010012 GTCTTCCCACAGTCAAATTTGTCAT 59.990 40.000 17.47 2.67 0.00 3.06
811 2298 3.119849 CCCAAACATCCGCAAAGAACTAG 60.120 47.826 0.00 0.00 0.00 2.57
812 2299 3.502211 CCAAACATCCGCAAAGAACTAGT 59.498 43.478 0.00 0.00 0.00 2.57
813 2300 4.693566 CCAAACATCCGCAAAGAACTAGTA 59.306 41.667 0.00 0.00 0.00 1.82
857 2344 2.194201 ATCGCCCAATAATTACCCCG 57.806 50.000 0.00 0.00 0.00 5.73
918 2405 0.038251 TGATGACTCGCGCACTCTTT 60.038 50.000 8.75 0.00 0.00 2.52
939 2426 1.818221 CTTCTTATACACGCCGCGCC 61.818 60.000 13.88 0.00 0.00 6.53
940 2427 3.688330 CTTATACACGCCGCGCCG 61.688 66.667 13.88 8.36 0.00 6.46
995 2488 1.293498 CCTCCAGTTCACACTCCCG 59.707 63.158 0.00 0.00 0.00 5.14
1305 2813 3.760035 GACGAGAAGAGGGCGGCA 61.760 66.667 12.47 0.00 32.27 5.69
1645 3153 2.646175 GCGTGCCTCTACCAGGTCA 61.646 63.158 0.00 0.00 45.61 4.02
2406 3914 0.962356 GCAACATACAGCAGCAGGGT 60.962 55.000 0.00 0.00 0.00 4.34
2525 4044 7.429340 CGGCTTTGTCAGTCATAATTTAATCAC 59.571 37.037 0.00 0.00 0.00 3.06
2532 4051 5.049405 CAGTCATAATTTAATCACGAGGGGC 60.049 44.000 0.00 0.00 0.00 5.80
2533 4052 5.063880 GTCATAATTTAATCACGAGGGGCT 58.936 41.667 0.00 0.00 0.00 5.19
2534 4053 5.179555 GTCATAATTTAATCACGAGGGGCTC 59.820 44.000 0.00 0.00 0.00 4.70
2535 4054 2.640316 ATTTAATCACGAGGGGCTCC 57.360 50.000 0.00 0.00 0.00 4.70
2536 4055 0.544697 TTTAATCACGAGGGGCTCCC 59.455 55.000 0.00 0.00 45.90 4.30
2609 4128 4.021925 AGAGTTGTCGGGCAGGGC 62.022 66.667 0.00 0.00 0.00 5.19
2611 4130 4.335647 AGTTGTCGGGCAGGGCAG 62.336 66.667 0.00 0.00 0.00 4.85
2649 4560 6.431852 GGATAAGGCTGTAAAAGTGTTGGTTA 59.568 38.462 0.00 0.00 0.00 2.85
2698 4616 8.442632 TCTAGCATTTCTCATCCATTTTACTG 57.557 34.615 0.00 0.00 0.00 2.74
2702 4620 7.395489 AGCATTTCTCATCCATTTTACTGAACT 59.605 33.333 0.00 0.00 0.00 3.01
2725 4643 0.663269 GTGGCCTTTTTACGTGCTGC 60.663 55.000 3.32 0.00 0.00 5.25
2726 4644 0.821711 TGGCCTTTTTACGTGCTGCT 60.822 50.000 3.32 0.00 0.00 4.24
2727 4645 0.387239 GGCCTTTTTACGTGCTGCTG 60.387 55.000 0.00 0.00 0.00 4.41
2728 4646 1.003769 GCCTTTTTACGTGCTGCTGC 61.004 55.000 8.89 8.89 40.20 5.25
2729 4647 0.593128 CCTTTTTACGTGCTGCTGCT 59.407 50.000 17.00 0.00 40.48 4.24
2730 4648 1.664016 CCTTTTTACGTGCTGCTGCTG 60.664 52.381 17.00 11.40 40.48 4.41
2731 4649 0.310543 TTTTTACGTGCTGCTGCTGG 59.689 50.000 17.00 10.52 40.48 4.85
2732 4650 0.533978 TTTTACGTGCTGCTGCTGGA 60.534 50.000 17.00 2.36 40.48 3.86
2744 4662 1.992170 CTGCTGGACTACCGTGTTAC 58.008 55.000 0.00 0.00 39.42 2.50
2745 4663 1.544691 CTGCTGGACTACCGTGTTACT 59.455 52.381 0.00 0.00 39.42 2.24
2746 4664 2.751259 CTGCTGGACTACCGTGTTACTA 59.249 50.000 0.00 0.00 39.42 1.82
2747 4665 2.489329 TGCTGGACTACCGTGTTACTAC 59.511 50.000 0.00 0.00 39.42 2.73
2748 4666 2.751806 GCTGGACTACCGTGTTACTACT 59.248 50.000 0.00 0.00 39.42 2.57
2749 4667 3.181502 GCTGGACTACCGTGTTACTACTC 60.182 52.174 0.00 0.00 39.42 2.59
2838 4756 2.278854 TCATCACACACACACACACAG 58.721 47.619 0.00 0.00 0.00 3.66
2840 4758 2.008752 TCACACACACACACACAGAG 57.991 50.000 0.00 0.00 0.00 3.35
2841 4759 1.548269 TCACACACACACACACAGAGA 59.452 47.619 0.00 0.00 0.00 3.10
2842 4760 1.660607 CACACACACACACACAGAGAC 59.339 52.381 0.00 0.00 0.00 3.36
2843 4761 1.275010 ACACACACACACACAGAGACA 59.725 47.619 0.00 0.00 0.00 3.41
2844 4762 1.660607 CACACACACACACAGAGACAC 59.339 52.381 0.00 0.00 0.00 3.67
2933 4854 5.112686 GTCGTCATTTGGAAGCTCTCTAAT 58.887 41.667 0.00 0.00 0.00 1.73
2990 5208 1.937191 AATTGTCCAGGGCCGAAAAT 58.063 45.000 0.00 0.00 0.00 1.82
3004 5222 2.614481 CCGAAAATTGGGACCGAAGAGA 60.614 50.000 0.00 0.00 0.00 3.10
3005 5223 2.673368 CGAAAATTGGGACCGAAGAGAG 59.327 50.000 0.00 0.00 0.00 3.20
3006 5224 3.616560 CGAAAATTGGGACCGAAGAGAGA 60.617 47.826 0.00 0.00 0.00 3.10
3007 5225 3.618690 AAATTGGGACCGAAGAGAGAG 57.381 47.619 0.00 0.00 0.00 3.20
3056 5287 3.041940 CGGTTTGTTCGCCTCGCT 61.042 61.111 0.00 0.00 0.00 4.93
3075 5306 0.033504 TGAGGAGAACGTTGGTGCTC 59.966 55.000 17.25 17.25 46.63 4.26
3077 5308 2.853914 GAGAACGTTGGTGCTCGC 59.146 61.111 5.00 0.00 39.04 5.03
3078 5309 1.664965 GAGAACGTTGGTGCTCGCT 60.665 57.895 5.00 0.00 39.04 4.93
3113 5350 3.329889 CTGTGGTGGGGCTGCCTA 61.330 66.667 19.68 5.30 0.00 3.93
3157 5394 1.835483 CTGTGTCTGTCGCTGTTGGC 61.835 60.000 0.00 0.00 37.64 4.52
3159 5396 1.595109 TGTCTGTCGCTGTTGGCTG 60.595 57.895 0.00 0.00 39.13 4.85
3218 5455 7.566709 TCCGAATTTCTTTAAAACACTCGTAC 58.433 34.615 0.00 0.00 0.00 3.67
3219 5456 6.793680 CCGAATTTCTTTAAAACACTCGTACC 59.206 38.462 0.00 0.00 0.00 3.34
3264 5504 2.437359 GCTGATGGCAACGCTCCT 60.437 61.111 0.00 0.00 41.35 3.69
3265 5505 2.467826 GCTGATGGCAACGCTCCTC 61.468 63.158 0.00 0.00 41.35 3.71
3266 5506 1.817099 CTGATGGCAACGCTCCTCC 60.817 63.158 0.00 0.00 42.51 4.30
3267 5507 2.892425 GATGGCAACGCTCCTCCG 60.892 66.667 0.00 0.00 42.51 4.63
3268 5508 4.473520 ATGGCAACGCTCCTCCGG 62.474 66.667 0.00 0.00 42.51 5.14
3375 5616 4.692041 TGGCACATGGGAGGGGGA 62.692 66.667 0.00 0.00 0.00 4.81
3376 5617 3.346734 GGCACATGGGAGGGGGAA 61.347 66.667 0.00 0.00 0.00 3.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.598019 TGGATTTTCATTGCAGGAAGC 57.402 42.857 3.54 0.00 45.96 3.86
1 2 5.594926 GGTATGGATTTTCATTGCAGGAAG 58.405 41.667 3.54 0.00 0.00 3.46
2 3 4.097741 CGGTATGGATTTTCATTGCAGGAA 59.902 41.667 0.00 0.00 0.00 3.36
3 4 3.631686 CGGTATGGATTTTCATTGCAGGA 59.368 43.478 0.00 0.00 0.00 3.86
4 5 3.381272 ACGGTATGGATTTTCATTGCAGG 59.619 43.478 0.00 0.00 0.00 4.85
5 6 4.336433 AGACGGTATGGATTTTCATTGCAG 59.664 41.667 0.00 0.00 0.00 4.41
6 7 4.269183 AGACGGTATGGATTTTCATTGCA 58.731 39.130 0.00 0.00 0.00 4.08
7 8 4.576463 AGAGACGGTATGGATTTTCATTGC 59.424 41.667 0.00 0.00 0.00 3.56
8 9 6.986817 AGTAGAGACGGTATGGATTTTCATTG 59.013 38.462 0.00 0.00 0.00 2.82
9 10 7.125792 AGTAGAGACGGTATGGATTTTCATT 57.874 36.000 0.00 0.00 0.00 2.57
10 11 6.323996 TGAGTAGAGACGGTATGGATTTTCAT 59.676 38.462 0.00 0.00 0.00 2.57
11 12 5.655090 TGAGTAGAGACGGTATGGATTTTCA 59.345 40.000 0.00 0.00 0.00 2.69
12 13 6.145338 TGAGTAGAGACGGTATGGATTTTC 57.855 41.667 0.00 0.00 0.00 2.29
13 14 6.732896 ATGAGTAGAGACGGTATGGATTTT 57.267 37.500 0.00 0.00 0.00 1.82
14 15 6.071840 GCTATGAGTAGAGACGGTATGGATTT 60.072 42.308 0.00 0.00 0.00 2.17
15 16 5.416326 GCTATGAGTAGAGACGGTATGGATT 59.584 44.000 0.00 0.00 0.00 3.01
16 17 4.944930 GCTATGAGTAGAGACGGTATGGAT 59.055 45.833 0.00 0.00 0.00 3.41
17 18 4.202430 TGCTATGAGTAGAGACGGTATGGA 60.202 45.833 0.00 0.00 0.00 3.41
18 19 4.072839 TGCTATGAGTAGAGACGGTATGG 58.927 47.826 0.00 0.00 0.00 2.74
19 20 4.515567 TGTGCTATGAGTAGAGACGGTATG 59.484 45.833 0.00 0.00 0.00 2.39
20 21 4.715713 TGTGCTATGAGTAGAGACGGTAT 58.284 43.478 0.00 0.00 0.00 2.73
21 22 4.146745 TGTGCTATGAGTAGAGACGGTA 57.853 45.455 0.00 0.00 0.00 4.02
22 23 3.000684 TGTGCTATGAGTAGAGACGGT 57.999 47.619 0.00 0.00 0.00 4.83
23 24 4.371855 TTTGTGCTATGAGTAGAGACGG 57.628 45.455 0.00 0.00 0.00 4.79
24 25 5.641709 TCTTTTGTGCTATGAGTAGAGACG 58.358 41.667 0.00 0.00 0.00 4.18
25 26 7.038659 ACATCTTTTGTGCTATGAGTAGAGAC 58.961 38.462 0.00 0.00 37.11 3.36
26 27 7.123397 AGACATCTTTTGTGCTATGAGTAGAGA 59.877 37.037 0.00 0.00 39.18 3.10
27 28 7.222417 CAGACATCTTTTGTGCTATGAGTAGAG 59.778 40.741 0.00 0.00 39.18 2.43
28 29 7.038048 CAGACATCTTTTGTGCTATGAGTAGA 58.962 38.462 0.00 0.00 39.18 2.59
29 30 7.038048 TCAGACATCTTTTGTGCTATGAGTAG 58.962 38.462 0.00 0.00 39.18 2.57
30 31 6.935167 TCAGACATCTTTTGTGCTATGAGTA 58.065 36.000 0.00 0.00 39.18 2.59
31 32 5.798132 TCAGACATCTTTTGTGCTATGAGT 58.202 37.500 0.00 0.00 39.18 3.41
32 33 6.104665 TCTCAGACATCTTTTGTGCTATGAG 58.895 40.000 0.00 0.00 39.18 2.90
33 34 6.041423 TCTCAGACATCTTTTGTGCTATGA 57.959 37.500 0.00 0.00 39.18 2.15
34 35 6.732531 TTCTCAGACATCTTTTGTGCTATG 57.267 37.500 0.00 0.00 39.18 2.23
35 36 7.446625 AGTTTTCTCAGACATCTTTTGTGCTAT 59.553 33.333 0.00 0.00 39.18 2.97
36 37 6.767902 AGTTTTCTCAGACATCTTTTGTGCTA 59.232 34.615 0.00 0.00 39.18 3.49
37 38 5.591877 AGTTTTCTCAGACATCTTTTGTGCT 59.408 36.000 0.00 0.00 39.18 4.40
38 39 5.684626 CAGTTTTCTCAGACATCTTTTGTGC 59.315 40.000 0.00 0.00 39.18 4.57
39 40 6.789262 ACAGTTTTCTCAGACATCTTTTGTG 58.211 36.000 0.00 0.00 39.18 3.33
40 41 6.599244 TGACAGTTTTCTCAGACATCTTTTGT 59.401 34.615 0.00 0.00 42.79 2.83
41 42 7.019774 TGACAGTTTTCTCAGACATCTTTTG 57.980 36.000 0.00 0.00 0.00 2.44
42 43 7.814264 ATGACAGTTTTCTCAGACATCTTTT 57.186 32.000 0.00 0.00 0.00 2.27
43 44 8.908786 TTATGACAGTTTTCTCAGACATCTTT 57.091 30.769 0.00 0.00 0.00 2.52
44 45 8.153550 ACTTATGACAGTTTTCTCAGACATCTT 58.846 33.333 0.00 0.00 0.00 2.40
45 46 7.675062 ACTTATGACAGTTTTCTCAGACATCT 58.325 34.615 0.00 0.00 0.00 2.90
46 47 7.897575 ACTTATGACAGTTTTCTCAGACATC 57.102 36.000 0.00 0.00 0.00 3.06
47 48 8.589338 AGTACTTATGACAGTTTTCTCAGACAT 58.411 33.333 0.00 0.00 0.00 3.06
48 49 7.952671 AGTACTTATGACAGTTTTCTCAGACA 58.047 34.615 0.00 0.00 0.00 3.41
49 50 7.542824 GGAGTACTTATGACAGTTTTCTCAGAC 59.457 40.741 0.00 0.00 0.00 3.51
50 51 7.309867 GGGAGTACTTATGACAGTTTTCTCAGA 60.310 40.741 0.00 0.00 0.00 3.27
51 52 6.814146 GGGAGTACTTATGACAGTTTTCTCAG 59.186 42.308 0.00 0.00 0.00 3.35
52 53 6.497259 AGGGAGTACTTATGACAGTTTTCTCA 59.503 38.462 0.00 0.00 0.00 3.27
53 54 6.937392 AGGGAGTACTTATGACAGTTTTCTC 58.063 40.000 0.00 0.00 0.00 2.87
54 55 6.070710 GGAGGGAGTACTTATGACAGTTTTCT 60.071 42.308 0.00 0.00 0.00 2.52
55 56 6.107343 GGAGGGAGTACTTATGACAGTTTTC 58.893 44.000 0.00 0.00 0.00 2.29
56 57 5.337330 CGGAGGGAGTACTTATGACAGTTTT 60.337 44.000 0.00 0.00 0.00 2.43
57 58 4.159879 CGGAGGGAGTACTTATGACAGTTT 59.840 45.833 0.00 0.00 0.00 2.66
58 59 3.700038 CGGAGGGAGTACTTATGACAGTT 59.300 47.826 0.00 0.00 0.00 3.16
59 60 3.288964 CGGAGGGAGTACTTATGACAGT 58.711 50.000 0.00 0.00 0.00 3.55
60 61 3.288964 ACGGAGGGAGTACTTATGACAG 58.711 50.000 0.00 0.00 0.00 3.51
61 62 3.377253 ACGGAGGGAGTACTTATGACA 57.623 47.619 0.00 0.00 0.00 3.58
62 63 5.359292 AGTTTACGGAGGGAGTACTTATGAC 59.641 44.000 0.00 0.00 0.00 3.06
63 64 5.513233 AGTTTACGGAGGGAGTACTTATGA 58.487 41.667 0.00 0.00 0.00 2.15
64 65 5.848833 AGTTTACGGAGGGAGTACTTATG 57.151 43.478 0.00 0.00 0.00 1.90
65 66 9.819754 ATATTAGTTTACGGAGGGAGTACTTAT 57.180 33.333 0.00 0.00 0.00 1.73
67 68 9.646522 TTATATTAGTTTACGGAGGGAGTACTT 57.353 33.333 0.00 0.00 0.00 2.24
68 69 9.294614 CTTATATTAGTTTACGGAGGGAGTACT 57.705 37.037 0.00 0.00 0.00 2.73
69 70 9.289782 TCTTATATTAGTTTACGGAGGGAGTAC 57.710 37.037 0.00 0.00 0.00 2.73
70 71 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
71 72 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
72 73 7.039923 TGCTCTTATATTAGTTTACGGAGGGAG 60.040 40.741 0.00 0.00 0.00 4.30
73 74 6.779049 TGCTCTTATATTAGTTTACGGAGGGA 59.221 38.462 0.00 0.00 0.00 4.20
74 75 6.989659 TGCTCTTATATTAGTTTACGGAGGG 58.010 40.000 0.00 0.00 0.00 4.30
75 76 9.490379 AAATGCTCTTATATTAGTTTACGGAGG 57.510 33.333 0.00 0.00 0.00 4.30
124 125 9.490379 CCCTCTGTAAATTAATATAAGAGCGTT 57.510 33.333 9.98 0.00 0.00 4.84
125 126 8.867097 TCCCTCTGTAAATTAATATAAGAGCGT 58.133 33.333 9.98 0.00 0.00 5.07
126 127 9.360093 CTCCCTCTGTAAATTAATATAAGAGCG 57.640 37.037 9.98 4.77 0.00 5.03
149 150 9.827411 GCCGATGATTTTATTCTTTTATACTCC 57.173 33.333 0.00 0.00 0.00 3.85
167 168 1.417288 TGGATGAGACAGCCGATGAT 58.583 50.000 0.00 0.00 43.67 2.45
168 169 1.194218 TTGGATGAGACAGCCGATGA 58.806 50.000 0.00 0.00 43.67 2.92
169 170 2.028420 TTTGGATGAGACAGCCGATG 57.972 50.000 0.00 0.00 43.67 3.84
276 961 1.114722 TGCCTGCTTTTTGGTGGGAG 61.115 55.000 0.00 0.00 0.00 4.30
277 962 1.075674 TGCCTGCTTTTTGGTGGGA 60.076 52.632 0.00 0.00 0.00 4.37
278 963 1.069596 GTGCCTGCTTTTTGGTGGG 59.930 57.895 0.00 0.00 0.00 4.61
279 964 1.069596 GGTGCCTGCTTTTTGGTGG 59.930 57.895 0.00 0.00 0.00 4.61
280 965 0.177604 TTGGTGCCTGCTTTTTGGTG 59.822 50.000 0.00 0.00 0.00 4.17
282 967 2.035530 TTTTGGTGCCTGCTTTTTGG 57.964 45.000 0.00 0.00 0.00 3.28
326 1014 2.560504 TGTGATTCAGGTGTGTGTCAC 58.439 47.619 0.00 0.00 45.47 3.67
336 1024 8.554528 GTGTGATCTATGTTTATGTGATTCAGG 58.445 37.037 0.00 0.00 0.00 3.86
347 1035 7.181569 TGGTGATGAGTGTGATCTATGTTTA 57.818 36.000 0.00 0.00 0.00 2.01
375 1340 4.974888 GCTGATGCTTTTCTATGCTTTAGC 59.025 41.667 0.00 0.00 38.20 3.09
391 1356 3.242220 CGTGATTCACTAGTTGCTGATGC 60.242 47.826 14.54 0.00 34.19 3.91
397 1362 1.726853 AGGCGTGATTCACTAGTTGC 58.273 50.000 14.54 9.63 31.34 4.17
404 1369 0.539986 TTCCCCTAGGCGTGATTCAC 59.460 55.000 2.05 6.73 0.00 3.18
430 1395 5.841957 AATCTGGTTTTCATAGTGGCATC 57.158 39.130 0.00 0.00 0.00 3.91
449 1414 3.813166 TGGCGAAATCGAATAGGGAAATC 59.187 43.478 7.06 0.00 43.02 2.17
469 1434 5.551233 ACTCATAATCCGGTAATCACATGG 58.449 41.667 0.00 0.00 0.00 3.66
486 1451 7.418408 TGCGTGTTTAATGTTTTGAACTCATA 58.582 30.769 0.00 0.00 33.66 2.15
487 1452 6.269315 TGCGTGTTTAATGTTTTGAACTCAT 58.731 32.000 0.00 0.00 33.66 2.90
488 1453 5.641709 TGCGTGTTTAATGTTTTGAACTCA 58.358 33.333 0.00 0.00 33.66 3.41
489 1454 5.741982 ACTGCGTGTTTAATGTTTTGAACTC 59.258 36.000 0.00 0.00 33.66 3.01
490 1455 5.646606 ACTGCGTGTTTAATGTTTTGAACT 58.353 33.333 0.00 0.00 33.66 3.01
491 1456 5.942325 ACTGCGTGTTTAATGTTTTGAAC 57.058 34.783 0.00 0.00 33.25 3.18
492 1457 5.683743 GCTACTGCGTGTTTAATGTTTTGAA 59.316 36.000 0.00 0.00 0.00 2.69
494 1459 4.973051 TGCTACTGCGTGTTTAATGTTTTG 59.027 37.500 0.00 0.00 43.34 2.44
501 1470 5.487153 TTTTCTTGCTACTGCGTGTTTAA 57.513 34.783 0.00 0.00 43.34 1.52
602 1574 2.892334 GAGCAAACGCGCAAGGTGA 61.892 57.895 5.73 0.00 38.28 4.02
604 1576 2.186826 AAGAGCAAACGCGCAAGGT 61.187 52.632 5.73 0.18 38.28 3.50
605 1577 1.727022 CAAGAGCAAACGCGCAAGG 60.727 57.895 5.73 0.00 38.28 3.61
700 1728 2.939103 GCGCAGAGGAGTATGACAAATT 59.061 45.455 0.30 0.00 0.00 1.82
701 1729 2.093500 TGCGCAGAGGAGTATGACAAAT 60.093 45.455 5.66 0.00 0.00 2.32
703 1731 0.894835 TGCGCAGAGGAGTATGACAA 59.105 50.000 5.66 0.00 0.00 3.18
705 1733 1.929836 CTTTGCGCAGAGGAGTATGAC 59.070 52.381 19.69 0.00 0.00 3.06
706 1734 1.740380 GCTTTGCGCAGAGGAGTATGA 60.740 52.381 27.09 0.00 38.92 2.15
708 1736 0.250234 TGCTTTGCGCAGAGGAGTAT 59.750 50.000 27.09 0.00 45.47 2.12
709 1737 1.671166 TGCTTTGCGCAGAGGAGTA 59.329 52.632 27.09 13.16 45.47 2.59
811 2298 2.488153 GGCGGGGCAATTAATGAGATAC 59.512 50.000 0.00 0.00 0.00 2.24
812 2299 2.790433 GGCGGGGCAATTAATGAGATA 58.210 47.619 0.00 0.00 0.00 1.98
813 2300 1.620822 GGCGGGGCAATTAATGAGAT 58.379 50.000 0.00 0.00 0.00 2.75
857 2344 8.413229 TGCATTAAATTAAGATTAGAAGGGTGC 58.587 33.333 0.00 0.00 0.00 5.01
918 2405 0.248743 CGCGGCGTGTATAAGAAGGA 60.249 55.000 15.36 0.00 0.00 3.36
941 2428 4.803426 GAGTGGAGTGGAGCGGCG 62.803 72.222 0.51 0.51 0.00 6.46
942 2429 4.459089 GGAGTGGAGTGGAGCGGC 62.459 72.222 0.00 0.00 0.00 6.53
945 2432 0.533032 GTACTGGAGTGGAGTGGAGC 59.467 60.000 0.00 0.00 0.00 4.70
1645 3153 2.499685 GGAGCCATCGCCGTAAGT 59.500 61.111 0.00 0.00 34.57 2.24
1677 3185 2.920912 AGGGTCTCGGTGGCGAAA 60.921 61.111 0.00 0.00 0.00 3.46
2085 3593 2.579787 GAGTCCACGATGACGCCG 60.580 66.667 0.00 0.00 43.96 6.46
2406 3914 1.227615 GTCGAACACCACCCGGAAA 60.228 57.895 0.73 0.00 35.59 3.13
2536 4055 5.665459 CTCTCACCCATCACCTTAACTAAG 58.335 45.833 0.00 0.00 0.00 2.18
2609 4128 0.982852 TATCCTCACACCCTGCCCTG 60.983 60.000 0.00 0.00 0.00 4.45
2611 4130 0.181350 CTTATCCTCACACCCTGCCC 59.819 60.000 0.00 0.00 0.00 5.36
2612 4131 0.181350 CCTTATCCTCACACCCTGCC 59.819 60.000 0.00 0.00 0.00 4.85
2613 4132 0.464554 GCCTTATCCTCACACCCTGC 60.465 60.000 0.00 0.00 0.00 4.85
2614 4133 1.134280 CAGCCTTATCCTCACACCCTG 60.134 57.143 0.00 0.00 0.00 4.45
2615 4134 1.207791 CAGCCTTATCCTCACACCCT 58.792 55.000 0.00 0.00 0.00 4.34
2616 4135 0.912486 ACAGCCTTATCCTCACACCC 59.088 55.000 0.00 0.00 0.00 4.61
2698 4616 2.225727 CGTAAAAAGGCCACTGGAGTTC 59.774 50.000 5.01 0.00 0.00 3.01
2702 4620 1.600023 CACGTAAAAAGGCCACTGGA 58.400 50.000 5.01 0.00 0.00 3.86
2709 4627 1.003769 GCAGCAGCACGTAAAAAGGC 61.004 55.000 0.00 0.00 41.58 4.35
2710 4628 0.593128 AGCAGCAGCACGTAAAAAGG 59.407 50.000 3.17 0.00 45.49 3.11
2725 4643 1.544691 AGTAACACGGTAGTCCAGCAG 59.455 52.381 0.00 0.00 0.00 4.24
2726 4644 1.624336 AGTAACACGGTAGTCCAGCA 58.376 50.000 0.00 0.00 0.00 4.41
2727 4645 2.751806 AGTAGTAACACGGTAGTCCAGC 59.248 50.000 0.00 0.00 0.00 4.85
2728 4646 3.376546 GGAGTAGTAACACGGTAGTCCAG 59.623 52.174 0.00 0.00 36.59 3.86
2729 4647 3.009473 AGGAGTAGTAACACGGTAGTCCA 59.991 47.826 5.48 0.00 38.34 4.02
2730 4648 3.615155 AGGAGTAGTAACACGGTAGTCC 58.385 50.000 0.00 0.00 36.77 3.85
2731 4649 4.673841 GCAAGGAGTAGTAACACGGTAGTC 60.674 50.000 0.00 0.00 0.00 2.59
2732 4650 3.192212 GCAAGGAGTAGTAACACGGTAGT 59.808 47.826 0.00 0.00 0.00 2.73
2744 4662 3.999663 CCAACAAAGAGAGCAAGGAGTAG 59.000 47.826 0.00 0.00 0.00 2.57
2745 4663 3.646162 TCCAACAAAGAGAGCAAGGAGTA 59.354 43.478 0.00 0.00 0.00 2.59
2746 4664 2.439507 TCCAACAAAGAGAGCAAGGAGT 59.560 45.455 0.00 0.00 0.00 3.85
2747 4665 3.131709 TCCAACAAAGAGAGCAAGGAG 57.868 47.619 0.00 0.00 0.00 3.69
2748 4666 3.072915 TGATCCAACAAAGAGAGCAAGGA 59.927 43.478 0.00 0.00 0.00 3.36
2749 4667 3.190118 GTGATCCAACAAAGAGAGCAAGG 59.810 47.826 0.00 0.00 0.00 3.61
2790 4708 8.298140 AGTGTGATCTTCAAAGTACAGTACTAC 58.702 37.037 13.87 5.72 38.26 2.73
2791 4709 8.405418 AGTGTGATCTTCAAAGTACAGTACTA 57.595 34.615 13.87 0.00 38.26 1.82
2792 4710 7.291411 AGTGTGATCTTCAAAGTACAGTACT 57.709 36.000 7.48 7.48 41.73 2.73
2793 4711 7.948278 AAGTGTGATCTTCAAAGTACAGTAC 57.052 36.000 2.05 2.05 0.00 2.73
2794 4712 8.201464 TGAAAGTGTGATCTTCAAAGTACAGTA 58.799 33.333 0.00 0.00 0.00 2.74
2795 4713 7.047891 TGAAAGTGTGATCTTCAAAGTACAGT 58.952 34.615 0.00 0.00 0.00 3.55
2801 4719 6.854892 GTGTGATGAAAGTGTGATCTTCAAAG 59.145 38.462 0.00 0.00 33.28 2.77
2806 4724 5.008019 GTGTGTGTGATGAAAGTGTGATCTT 59.992 40.000 0.00 0.00 0.00 2.40
2838 4756 0.940126 CCAAGCTGTGTGTGTGTCTC 59.060 55.000 0.00 0.00 0.00 3.36
2840 4758 1.356624 GCCAAGCTGTGTGTGTGTC 59.643 57.895 0.00 0.00 0.00 3.67
2841 4759 2.120909 GGCCAAGCTGTGTGTGTGT 61.121 57.895 0.00 0.00 0.00 3.72
2842 4760 2.723746 GGCCAAGCTGTGTGTGTG 59.276 61.111 0.00 0.00 0.00 3.82
2843 4761 2.901840 CGGCCAAGCTGTGTGTGT 60.902 61.111 2.24 0.00 0.00 3.72
2844 4762 3.663176 CCGGCCAAGCTGTGTGTG 61.663 66.667 2.24 0.00 32.22 3.82
2933 4854 1.373435 CTAACCCCACTGGCGACAA 59.627 57.895 0.00 0.00 42.06 3.18
2990 5208 1.258445 GCCTCTCTCTTCGGTCCCAA 61.258 60.000 0.00 0.00 0.00 4.12
3004 5222 1.110442 CAATCTCTCTCGTGGCCTCT 58.890 55.000 3.32 0.00 0.00 3.69
3005 5223 0.103937 CCAATCTCTCTCGTGGCCTC 59.896 60.000 3.32 0.00 0.00 4.70
3006 5224 2.206635 CCAATCTCTCTCGTGGCCT 58.793 57.895 3.32 0.00 0.00 5.19
3007 5225 4.844420 CCAATCTCTCTCGTGGCC 57.156 61.111 0.00 0.00 0.00 5.36
3056 5287 0.033504 GAGCACCAACGTTCTCCTCA 59.966 55.000 0.00 0.00 0.00 3.86
3075 5306 0.594796 AGAACGGCAAAGCAAAAGCG 60.595 50.000 0.00 0.00 0.00 4.68
3076 5307 1.522676 GAAGAACGGCAAAGCAAAAGC 59.477 47.619 0.00 0.00 0.00 3.51
3077 5308 2.791004 CAGAAGAACGGCAAAGCAAAAG 59.209 45.455 0.00 0.00 0.00 2.27
3078 5309 2.165437 ACAGAAGAACGGCAAAGCAAAA 59.835 40.909 0.00 0.00 0.00 2.44
3174 5411 2.969950 GGATGCATGGGGTAGTACAGTA 59.030 50.000 2.46 0.00 0.00 2.74
3175 5412 1.768870 GGATGCATGGGGTAGTACAGT 59.231 52.381 2.46 0.00 0.00 3.55
3176 5413 1.270305 CGGATGCATGGGGTAGTACAG 60.270 57.143 2.46 0.00 0.00 2.74
3177 5414 0.756294 CGGATGCATGGGGTAGTACA 59.244 55.000 2.46 0.00 0.00 2.90
3178 5415 1.045407 TCGGATGCATGGGGTAGTAC 58.955 55.000 2.46 0.00 0.00 2.73
3266 5506 2.183555 GTAGCCTCAACCGGACCG 59.816 66.667 9.46 6.99 0.00 4.79
3267 5507 1.218316 CAGTAGCCTCAACCGGACC 59.782 63.158 9.46 0.00 0.00 4.46
3268 5508 1.218316 CCAGTAGCCTCAACCGGAC 59.782 63.158 9.46 0.00 0.00 4.79
3296 5536 2.416162 CCTCTCTCTCGCTGTTTACACC 60.416 54.545 0.00 0.00 0.00 4.16
3309 5549 0.252012 CACCACCACCTCCTCTCTCT 60.252 60.000 0.00 0.00 0.00 3.10
3310 5550 1.261238 CCACCACCACCTCCTCTCTC 61.261 65.000 0.00 0.00 0.00 3.20
3311 5551 1.229336 CCACCACCACCTCCTCTCT 60.229 63.158 0.00 0.00 0.00 3.10
3312 5552 2.960688 GCCACCACCACCTCCTCTC 61.961 68.421 0.00 0.00 0.00 3.20
3370 5611 4.097361 GTGTCCTCCGCTTCCCCC 62.097 72.222 0.00 0.00 0.00 5.40
3372 5613 4.452733 CCGTGTCCTCCGCTTCCC 62.453 72.222 0.00 0.00 0.00 3.97
3374 5615 2.444700 TTTCCCGTGTCCTCCGCTTC 62.445 60.000 0.00 0.00 0.00 3.86
3375 5616 2.047213 TTTTCCCGTGTCCTCCGCTT 62.047 55.000 0.00 0.00 0.00 4.68
3376 5617 2.513259 TTTTCCCGTGTCCTCCGCT 61.513 57.895 0.00 0.00 0.00 5.52


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

AutoCloner maintained by Alex Coulton.