Multiple sequence alignment - TraesCS2B01G201400

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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 TraesCS2B01G201400 chr2B 100.000 3713 0 0 1 3713 180557461 180561173 0.000000e+00 6857.0
1 TraesCS2B01G201400 chr2B 96.226 53 2 0 12 64 361567079 361567027 1.840000e-13 87.9
2 TraesCS2B01G201400 chr2D 90.930 2668 100 69 139 2747 126967228 126969812 0.000000e+00 3456.0
3 TraesCS2B01G201400 chr2D 93.750 64 2 2 2 64 615708456 615708518 1.100000e-15 95.3
4 TraesCS2B01G201400 chr2D 91.071 56 5 0 3 58 643290124 643290069 3.980000e-10 76.8
5 TraesCS2B01G201400 chr2A 88.983 2723 121 70 139 2747 133669848 133672505 0.000000e+00 3201.0
6 TraesCS2B01G201400 chr2A 93.750 64 3 1 1 64 262307876 262307814 1.100000e-15 95.3
7 TraesCS2B01G201400 chr2A 87.273 55 7 0 1 55 693885929 693885983 3.100000e-06 63.9
8 TraesCS2B01G201400 chr3B 98.803 919 9 2 2797 3713 434310999 434310081 0.000000e+00 1635.0
9 TraesCS2B01G201400 chr3B 73.950 476 76 30 2793 3243 775564575 775565027 8.310000e-32 148.0
10 TraesCS2B01G201400 chr3B 98.039 51 1 0 2747 2797 548570206 548570156 5.110000e-14 89.8
11 TraesCS2B01G201400 chr5B 97.005 935 14 7 2793 3713 448803147 448802213 0.000000e+00 1559.0
12 TraesCS2B01G201400 chr5B 90.015 661 49 10 3068 3713 429833101 429833759 0.000000e+00 839.0
13 TraesCS2B01G201400 chr5B 84.889 450 68 0 1327 1776 134448512 134448063 4.370000e-124 455.0
14 TraesCS2B01G201400 chr5B 81.366 483 51 30 1867 2331 134448068 134447607 1.270000e-94 357.0
15 TraesCS2B01G201400 chr3A 96.667 930 18 5 2797 3713 623817265 623816336 0.000000e+00 1533.0
16 TraesCS2B01G201400 chr4B 96.659 928 19 6 2798 3713 33815854 33816781 0.000000e+00 1531.0
17 TraesCS2B01G201400 chr4B 85.938 320 34 7 3405 3713 54324287 54324606 7.690000e-87 331.0
18 TraesCS2B01G201400 chr7A 94.352 903 33 9 2797 3688 493458746 493457851 0.000000e+00 1369.0
19 TraesCS2B01G201400 chr7A 73.718 468 78 31 2798 3243 538797611 538798055 1.390000e-29 141.0
20 TraesCS2B01G201400 chr4A 93.600 750 34 7 2972 3713 695742462 695741719 0.000000e+00 1107.0
21 TraesCS2B01G201400 chr1A 87.915 662 53 14 3068 3713 518956234 518956884 0.000000e+00 754.0
22 TraesCS2B01G201400 chr5D 84.222 450 71 0 1327 1776 121174283 121173834 4.400000e-119 438.0
23 TraesCS2B01G201400 chr5D 89.815 324 26 7 3068 3389 58144716 58145034 3.450000e-110 409.0
24 TraesCS2B01G201400 chr5D 80.962 478 62 24 1867 2331 121173839 121173378 5.900000e-93 351.0
25 TraesCS2B01G201400 chr5A 84.222 450 71 0 1327 1776 132596319 132595870 4.400000e-119 438.0
26 TraesCS2B01G201400 chr5A 81.328 482 53 30 1867 2331 132595875 132595414 1.270000e-94 357.0
27 TraesCS2B01G201400 chr3D 78.099 484 81 21 1867 2339 17792518 17792987 2.180000e-72 283.0
28 TraesCS2B01G201400 chr3D 81.560 282 49 3 1493 1773 17792241 17792520 2.880000e-56 230.0
29 TraesCS2B01G201400 chr3D 85.714 210 28 2 2432 2640 17807823 17808031 1.740000e-53 220.0
30 TraesCS2B01G201400 chr3D 79.870 308 38 10 2797 3102 491175439 491175154 1.750000e-48 204.0
31 TraesCS2B01G201400 chr3D 82.488 217 36 2 2432 2647 17792990 17793205 4.900000e-44 189.0
32 TraesCS2B01G201400 chr3D 96.078 51 2 0 14 64 486727202 486727252 2.380000e-12 84.2
33 TraesCS2B01G201400 chrUn 97.183 142 4 0 2797 2938 475790836 475790977 1.330000e-59 241.0


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 TraesCS2B01G201400 chr2B 180557461 180561173 3712 False 6857.0 6857 100.000000 1 3713 1 chr2B.!!$F1 3712
1 TraesCS2B01G201400 chr2D 126967228 126969812 2584 False 3456.0 3456 90.930000 139 2747 1 chr2D.!!$F1 2608
2 TraesCS2B01G201400 chr2A 133669848 133672505 2657 False 3201.0 3201 88.983000 139 2747 1 chr2A.!!$F1 2608
3 TraesCS2B01G201400 chr3B 434310081 434310999 918 True 1635.0 1635 98.803000 2797 3713 1 chr3B.!!$R1 916
4 TraesCS2B01G201400 chr5B 448802213 448803147 934 True 1559.0 1559 97.005000 2793 3713 1 chr5B.!!$R1 920
5 TraesCS2B01G201400 chr5B 429833101 429833759 658 False 839.0 839 90.015000 3068 3713 1 chr5B.!!$F1 645
6 TraesCS2B01G201400 chr5B 134447607 134448512 905 True 406.0 455 83.127500 1327 2331 2 chr5B.!!$R2 1004
7 TraesCS2B01G201400 chr3A 623816336 623817265 929 True 1533.0 1533 96.667000 2797 3713 1 chr3A.!!$R1 916
8 TraesCS2B01G201400 chr4B 33815854 33816781 927 False 1531.0 1531 96.659000 2798 3713 1 chr4B.!!$F1 915
9 TraesCS2B01G201400 chr7A 493457851 493458746 895 True 1369.0 1369 94.352000 2797 3688 1 chr7A.!!$R1 891
10 TraesCS2B01G201400 chr4A 695741719 695742462 743 True 1107.0 1107 93.600000 2972 3713 1 chr4A.!!$R1 741
11 TraesCS2B01G201400 chr1A 518956234 518956884 650 False 754.0 754 87.915000 3068 3713 1 chr1A.!!$F1 645
12 TraesCS2B01G201400 chr5D 121173378 121174283 905 True 394.5 438 82.592000 1327 2331 2 chr5D.!!$R1 1004
13 TraesCS2B01G201400 chr5A 132595414 132596319 905 True 397.5 438 82.775000 1327 2331 2 chr5A.!!$R1 1004
14 TraesCS2B01G201400 chr3D 17792241 17793205 964 False 234.0 283 80.715667 1493 2647 3 chr3D.!!$F3 1154

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
64 65 0.180171 TGGGTATGGCTTGGATCACG 59.820 55.0 0.0 0.0 0.00 4.35 F
446 449 0.246635 AATCCACGAGACAGGAACCG 59.753 55.0 0.0 0.0 37.48 4.44 F
1112 1171 0.033601 TTTGTTCAGTGGTGGTGGCT 60.034 50.0 0.0 0.0 0.00 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1087 1123 1.063469 CCACCACTGAACAAACACGAC 59.937 52.381 0.00 0.0 0.0 4.34 R
2348 2510 1.355971 TTGAACCGAGATAGCGTTGC 58.644 50.000 0.00 0.0 0.0 4.17 R
2718 2905 0.254178 AAAGCATCATGACCGCCTCT 59.746 50.000 13.87 0.0 0.0 3.69 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
39 40 8.736751 TTAGAAATTTTAAAGACCGACATTGC 57.263 30.769 0.00 0.00 0.00 3.56
40 41 6.744112 AGAAATTTTAAAGACCGACATTGCA 58.256 32.000 0.00 0.00 0.00 4.08
41 42 7.378181 AGAAATTTTAAAGACCGACATTGCAT 58.622 30.769 0.00 0.00 0.00 3.96
42 43 8.519526 AGAAATTTTAAAGACCGACATTGCATA 58.480 29.630 0.00 0.00 0.00 3.14
43 44 9.301153 GAAATTTTAAAGACCGACATTGCATAT 57.699 29.630 0.00 0.00 0.00 1.78
44 45 8.633075 AATTTTAAAGACCGACATTGCATATG 57.367 30.769 0.00 0.00 0.00 1.78
45 46 6.751514 TTTAAAGACCGACATTGCATATGT 57.248 33.333 12.41 12.41 34.52 2.29
46 47 4.621068 AAAGACCGACATTGCATATGTG 57.379 40.909 16.02 7.94 31.52 3.21
47 48 2.564771 AGACCGACATTGCATATGTGG 58.435 47.619 16.02 17.13 31.52 4.17
49 50 1.679139 CCGACATTGCATATGTGGGT 58.321 50.000 22.80 0.00 41.22 4.51
50 51 2.844946 CCGACATTGCATATGTGGGTA 58.155 47.619 22.80 0.00 41.22 3.69
51 52 3.411446 CCGACATTGCATATGTGGGTAT 58.589 45.455 22.80 0.00 41.22 2.73
52 53 3.189080 CCGACATTGCATATGTGGGTATG 59.811 47.826 22.80 10.01 41.22 2.39
53 54 3.189080 CGACATTGCATATGTGGGTATGG 59.811 47.826 16.02 0.00 33.61 2.74
54 55 2.892852 ACATTGCATATGTGGGTATGGC 59.107 45.455 11.96 0.00 33.61 4.40
55 56 3.159472 CATTGCATATGTGGGTATGGCT 58.841 45.455 4.29 0.00 33.61 4.75
56 57 3.311167 TTGCATATGTGGGTATGGCTT 57.689 42.857 4.29 0.00 33.61 4.35
57 58 2.585330 TGCATATGTGGGTATGGCTTG 58.415 47.619 4.29 0.00 33.61 4.01
58 59 1.888512 GCATATGTGGGTATGGCTTGG 59.111 52.381 4.29 0.00 33.61 3.61
59 60 2.488891 GCATATGTGGGTATGGCTTGGA 60.489 50.000 4.29 0.00 33.61 3.53
60 61 3.815396 GCATATGTGGGTATGGCTTGGAT 60.815 47.826 4.29 0.00 33.61 3.41
61 62 2.664402 ATGTGGGTATGGCTTGGATC 57.336 50.000 0.00 0.00 0.00 3.36
62 63 1.294041 TGTGGGTATGGCTTGGATCA 58.706 50.000 0.00 0.00 0.00 2.92
63 64 1.064758 TGTGGGTATGGCTTGGATCAC 60.065 52.381 0.00 0.00 0.00 3.06
64 65 0.180171 TGGGTATGGCTTGGATCACG 59.820 55.000 0.00 0.00 0.00 4.35
65 66 0.535102 GGGTATGGCTTGGATCACGG 60.535 60.000 0.00 0.00 0.00 4.94
66 67 0.468226 GGTATGGCTTGGATCACGGA 59.532 55.000 0.00 0.00 0.00 4.69
67 68 1.134220 GGTATGGCTTGGATCACGGAA 60.134 52.381 0.00 0.00 0.00 4.30
68 69 1.940613 GTATGGCTTGGATCACGGAAC 59.059 52.381 0.00 0.00 0.00 3.62
69 70 0.394352 ATGGCTTGGATCACGGAACC 60.394 55.000 0.00 0.00 0.00 3.62
70 71 2.106683 GGCTTGGATCACGGAACCG 61.107 63.158 11.83 11.83 46.03 4.44
71 72 2.750888 GCTTGGATCACGGAACCGC 61.751 63.158 13.32 0.00 44.19 5.68
72 73 2.433491 TTGGATCACGGAACCGCG 60.433 61.111 13.32 0.00 44.19 6.46
73 74 3.943479 TTGGATCACGGAACCGCGG 62.943 63.158 26.86 26.86 44.19 6.46
74 75 4.446413 GGATCACGGAACCGCGGT 62.446 66.667 28.70 28.70 44.19 5.68
75 76 3.186047 GATCACGGAACCGCGGTG 61.186 66.667 34.95 22.48 45.99 4.94
81 82 3.423154 GGAACCGCGGTGAAGCTG 61.423 66.667 34.95 1.49 34.40 4.24
82 83 3.423154 GAACCGCGGTGAAGCTGG 61.423 66.667 34.95 0.60 37.04 4.85
85 86 4.451150 CCGCGGTGAAGCTGGCTA 62.451 66.667 19.50 0.00 34.40 3.93
86 87 2.887568 CGCGGTGAAGCTGGCTAG 60.888 66.667 0.00 0.00 34.40 3.42
104 105 3.932009 CCATTGGCCGGCATTGTA 58.068 55.556 30.85 8.28 0.00 2.41
105 106 2.197250 CCATTGGCCGGCATTGTAA 58.803 52.632 30.85 14.76 0.00 2.41
106 107 0.752054 CCATTGGCCGGCATTGTAAT 59.248 50.000 30.85 16.36 0.00 1.89
107 108 1.959985 CCATTGGCCGGCATTGTAATA 59.040 47.619 30.85 3.55 0.00 0.98
108 109 2.562298 CCATTGGCCGGCATTGTAATAT 59.438 45.455 30.85 5.91 0.00 1.28
109 110 3.577667 CATTGGCCGGCATTGTAATATG 58.422 45.455 30.85 14.15 0.00 1.78
110 111 2.356665 TGGCCGGCATTGTAATATGT 57.643 45.000 30.85 0.00 0.00 2.29
111 112 2.226330 TGGCCGGCATTGTAATATGTC 58.774 47.619 30.85 6.12 0.00 3.06
112 113 2.226330 GGCCGGCATTGTAATATGTCA 58.774 47.619 30.85 0.00 30.53 3.58
113 114 2.819608 GGCCGGCATTGTAATATGTCAT 59.180 45.455 30.85 0.00 30.53 3.06
114 115 4.006989 GGCCGGCATTGTAATATGTCATA 58.993 43.478 30.85 0.00 30.53 2.15
115 116 4.457603 GGCCGGCATTGTAATATGTCATAA 59.542 41.667 30.85 0.00 30.53 1.90
116 117 5.390613 GCCGGCATTGTAATATGTCATAAC 58.609 41.667 24.80 0.00 30.53 1.89
117 118 5.181245 GCCGGCATTGTAATATGTCATAACT 59.819 40.000 24.80 0.00 30.53 2.24
118 119 6.620733 GCCGGCATTGTAATATGTCATAACTC 60.621 42.308 24.80 0.00 30.53 3.01
119 120 6.650807 CCGGCATTGTAATATGTCATAACTCT 59.349 38.462 0.00 0.00 30.53 3.24
120 121 7.173218 CCGGCATTGTAATATGTCATAACTCTT 59.827 37.037 0.00 0.00 30.53 2.85
121 122 8.223769 CGGCATTGTAATATGTCATAACTCTTC 58.776 37.037 0.00 0.00 30.53 2.87
122 123 9.277783 GGCATTGTAATATGTCATAACTCTTCT 57.722 33.333 0.00 0.00 30.53 2.85
150 151 0.792640 GATATGATGCGCGTTCCAGG 59.207 55.000 8.43 0.00 0.00 4.45
162 163 3.596214 GCGTTCCAGGAAAGAGATACAA 58.404 45.455 18.52 0.00 0.00 2.41
204 205 7.113658 TCTAAAGGCTCTCATTAAATCGACT 57.886 36.000 0.00 0.00 0.00 4.18
220 221 4.903638 TCGACTGAAACATGAATCGTTC 57.096 40.909 0.00 0.00 0.00 3.95
226 227 3.431912 TGAAACATGAATCGTTCTCCGTG 59.568 43.478 0.00 0.00 37.94 4.94
253 254 4.979204 CGTACTTGGGACGCAAGA 57.021 55.556 32.00 16.59 43.62 3.02
254 255 3.204505 CGTACTTGGGACGCAAGAA 57.795 52.632 32.00 0.85 43.62 2.52
260 261 3.482436 ACTTGGGACGCAAGAAACATAA 58.518 40.909 32.00 0.00 43.62 1.90
373 376 1.425428 GCCGCTACACTGCATCAAC 59.575 57.895 0.00 0.00 0.00 3.18
374 377 1.982073 GCCGCTACACTGCATCAACC 61.982 60.000 0.00 0.00 0.00 3.77
375 378 0.673333 CCGCTACACTGCATCAACCA 60.673 55.000 0.00 0.00 0.00 3.67
376 379 0.723414 CGCTACACTGCATCAACCAG 59.277 55.000 0.00 0.00 36.41 4.00
377 380 1.813513 GCTACACTGCATCAACCAGT 58.186 50.000 0.00 0.00 43.92 4.00
378 381 2.673893 CGCTACACTGCATCAACCAGTA 60.674 50.000 0.00 0.00 41.34 2.74
379 382 2.673368 GCTACACTGCATCAACCAGTAC 59.327 50.000 0.00 0.00 41.34 2.73
380 383 3.617531 GCTACACTGCATCAACCAGTACT 60.618 47.826 0.00 0.00 41.34 2.73
381 384 4.381612 GCTACACTGCATCAACCAGTACTA 60.382 45.833 0.00 0.00 41.34 1.82
382 385 3.926616 ACACTGCATCAACCAGTACTAC 58.073 45.455 0.00 0.00 41.34 2.73
406 409 8.110860 ACTACCAGTTTCTACAAAATTCCATG 57.889 34.615 0.00 0.00 0.00 3.66
421 424 2.311463 TCCATGTCCCGCAAAAGAAAA 58.689 42.857 0.00 0.00 0.00 2.29
422 425 2.295909 TCCATGTCCCGCAAAAGAAAAG 59.704 45.455 0.00 0.00 0.00 2.27
423 426 2.295909 CCATGTCCCGCAAAAGAAAAGA 59.704 45.455 0.00 0.00 0.00 2.52
424 427 3.568538 CATGTCCCGCAAAAGAAAAGAG 58.431 45.455 0.00 0.00 0.00 2.85
425 428 2.925724 TGTCCCGCAAAAGAAAAGAGA 58.074 42.857 0.00 0.00 0.00 3.10
446 449 0.246635 AATCCACGAGACAGGAACCG 59.753 55.000 0.00 0.00 37.48 4.44
447 450 1.605058 ATCCACGAGACAGGAACCGG 61.605 60.000 0.00 0.00 37.48 5.28
530 533 1.326951 ACCAAACCGCAAGCAAACCT 61.327 50.000 0.00 0.00 0.00 3.50
652 663 4.101448 ACTCAGGGACGGCATGGC 62.101 66.667 9.69 9.69 0.00 4.40
681 692 0.389817 TCGAGTCACCAATCGCCAAG 60.390 55.000 0.00 0.00 38.79 3.61
721 732 1.364626 GACCATCAGTTCAGCAGCGG 61.365 60.000 0.00 0.00 0.00 5.52
817 832 4.715523 GGTGGCTGGCACGCCTTA 62.716 66.667 25.26 6.69 45.44 2.69
941 973 1.351707 CACGCGCACCACAATATCC 59.648 57.895 5.73 0.00 0.00 2.59
944 976 2.468670 GCGCACCACAATATCCGCA 61.469 57.895 0.30 0.00 40.94 5.69
950 982 1.308998 CCACAATATCCGCACCTTCC 58.691 55.000 0.00 0.00 0.00 3.46
967 1003 2.874780 CGGTGAGAGTACGTGCGC 60.875 66.667 0.00 0.00 0.00 6.09
1069 1105 3.358076 CTCTCCGTCGCAGGTTCCC 62.358 68.421 0.00 0.00 0.00 3.97
1070 1106 3.691342 CTCCGTCGCAGGTTCCCA 61.691 66.667 0.00 0.00 0.00 4.37
1087 1123 0.600557 CCATCTAGCTCCCTACGCTG 59.399 60.000 0.00 0.00 38.38 5.18
1088 1124 1.323412 CATCTAGCTCCCTACGCTGT 58.677 55.000 0.00 0.00 38.38 4.40
1089 1125 1.268352 CATCTAGCTCCCTACGCTGTC 59.732 57.143 0.00 0.00 38.38 3.51
1109 1168 1.202132 CGTGTTTGTTCAGTGGTGGTG 60.202 52.381 0.00 0.00 0.00 4.17
1110 1169 1.134175 GTGTTTGTTCAGTGGTGGTGG 59.866 52.381 0.00 0.00 0.00 4.61
1111 1170 0.102300 GTTTGTTCAGTGGTGGTGGC 59.898 55.000 0.00 0.00 0.00 5.01
1112 1171 0.033601 TTTGTTCAGTGGTGGTGGCT 60.034 50.000 0.00 0.00 0.00 4.75
1113 1172 0.751277 TTGTTCAGTGGTGGTGGCTG 60.751 55.000 0.00 0.00 0.00 4.85
1114 1173 1.148273 GTTCAGTGGTGGTGGCTGA 59.852 57.895 0.00 0.00 37.47 4.26
1246 1305 0.675837 CGTCGTGAGTACCCTCTCCA 60.676 60.000 0.00 0.00 38.61 3.86
1284 1361 1.877637 TCGTGTCAGGAACAATGTGG 58.122 50.000 0.00 0.00 40.31 4.17
1311 1388 2.404789 CCGATCGGTTGCATGCAC 59.595 61.111 26.35 15.35 0.00 4.57
1788 1869 2.772691 GGCCCTCAGTACGTCCTCG 61.773 68.421 0.00 0.00 43.34 4.63
1838 1943 8.951787 ATGCATGCATGAAATAGTTTTGTAAT 57.048 26.923 31.74 1.84 35.03 1.89
2344 2506 2.092049 TCCTACGGCTCCATCAGTAAGA 60.092 50.000 0.00 0.00 0.00 2.10
2348 2510 3.600388 ACGGCTCCATCAGTAAGAAAAG 58.400 45.455 0.00 0.00 0.00 2.27
2352 2514 4.379918 GGCTCCATCAGTAAGAAAAGCAAC 60.380 45.833 0.00 0.00 33.33 4.17
2353 2515 4.670221 GCTCCATCAGTAAGAAAAGCAACG 60.670 45.833 0.00 0.00 32.50 4.10
2355 2517 3.189287 CCATCAGTAAGAAAAGCAACGCT 59.811 43.478 0.00 0.00 42.56 5.07
2356 2518 4.391830 CCATCAGTAAGAAAAGCAACGCTA 59.608 41.667 0.00 0.00 38.25 4.26
2357 2519 5.065218 CCATCAGTAAGAAAAGCAACGCTAT 59.935 40.000 0.00 0.00 38.25 2.97
2358 2520 5.779806 TCAGTAAGAAAAGCAACGCTATC 57.220 39.130 0.00 0.00 38.25 2.08
2359 2521 5.479306 TCAGTAAGAAAAGCAACGCTATCT 58.521 37.500 0.00 0.00 38.25 1.98
2360 2522 5.577164 TCAGTAAGAAAAGCAACGCTATCTC 59.423 40.000 5.10 0.00 38.25 2.75
2361 2523 3.999229 AAGAAAAGCAACGCTATCTCG 57.001 42.857 5.10 0.00 38.25 4.04
2362 2524 2.271800 AGAAAAGCAACGCTATCTCGG 58.728 47.619 0.00 0.00 38.25 4.63
2363 2525 2.000447 GAAAAGCAACGCTATCTCGGT 59.000 47.619 0.00 0.00 38.25 4.69
2364 2526 2.094762 AAAGCAACGCTATCTCGGTT 57.905 45.000 0.00 0.00 38.25 4.44
2365 2527 1.641577 AAGCAACGCTATCTCGGTTC 58.358 50.000 0.00 0.00 38.25 3.62
2366 2528 0.530744 AGCAACGCTATCTCGGTTCA 59.469 50.000 0.00 0.00 36.99 3.18
2367 2529 1.067142 AGCAACGCTATCTCGGTTCAA 60.067 47.619 0.00 0.00 36.99 2.69
2368 2530 1.933853 GCAACGCTATCTCGGTTCAAT 59.066 47.619 0.00 0.00 0.00 2.57
2369 2531 2.033662 GCAACGCTATCTCGGTTCAATC 60.034 50.000 0.00 0.00 0.00 2.67
2370 2532 3.186909 CAACGCTATCTCGGTTCAATCA 58.813 45.455 0.00 0.00 0.00 2.57
2371 2533 3.735237 ACGCTATCTCGGTTCAATCAT 57.265 42.857 0.00 0.00 0.00 2.45
2372 2534 3.643763 ACGCTATCTCGGTTCAATCATC 58.356 45.455 0.00 0.00 0.00 2.92
2373 2535 3.068165 ACGCTATCTCGGTTCAATCATCA 59.932 43.478 0.00 0.00 0.00 3.07
2381 2543 4.301628 TCGGTTCAATCATCATCGATCAG 58.698 43.478 0.00 0.00 0.00 2.90
2384 2546 5.557703 CGGTTCAATCATCATCGATCAGTTG 60.558 44.000 0.00 0.00 0.00 3.16
2389 2551 3.877559 TCATCATCGATCAGTTGCCTTT 58.122 40.909 0.00 0.00 0.00 3.11
2390 2552 3.873361 TCATCATCGATCAGTTGCCTTTC 59.127 43.478 0.00 0.00 0.00 2.62
2393 2555 3.935203 TCATCGATCAGTTGCCTTTCTTC 59.065 43.478 0.00 0.00 0.00 2.87
2394 2556 3.685139 TCGATCAGTTGCCTTTCTTCT 57.315 42.857 0.00 0.00 0.00 2.85
2395 2557 3.589988 TCGATCAGTTGCCTTTCTTCTC 58.410 45.455 0.00 0.00 0.00 2.87
2396 2558 3.006859 TCGATCAGTTGCCTTTCTTCTCA 59.993 43.478 0.00 0.00 0.00 3.27
2397 2559 3.937706 CGATCAGTTGCCTTTCTTCTCAT 59.062 43.478 0.00 0.00 0.00 2.90
2398 2560 4.033817 CGATCAGTTGCCTTTCTTCTCATC 59.966 45.833 0.00 0.00 0.00 2.92
2399 2561 4.356405 TCAGTTGCCTTTCTTCTCATCA 57.644 40.909 0.00 0.00 0.00 3.07
2402 2567 4.153835 CAGTTGCCTTTCTTCTCATCAGAC 59.846 45.833 0.00 0.00 0.00 3.51
2411 2576 7.278424 CCTTTCTTCTCATCAGACTTTGATCTC 59.722 40.741 0.00 0.00 44.76 2.75
2420 2585 7.333672 TCATCAGACTTTGATCTCAATCTGTTG 59.666 37.037 18.19 18.19 44.76 3.33
2421 2586 5.410746 TCAGACTTTGATCTCAATCTGTTGC 59.589 40.000 17.03 0.00 35.98 4.17
2640 2827 0.475828 ACCCTTACCTGCCCAACTCT 60.476 55.000 0.00 0.00 0.00 3.24
2726 2913 3.071206 ATGAGCGTCAGAGGCGGT 61.071 61.111 9.42 1.18 42.96 5.68
2734 2921 1.144716 TCAGAGGCGGTCATGATGC 59.855 57.895 12.95 12.95 0.00 3.91
2747 2934 3.064545 GTCATGATGCTTTGCCTGTAGAC 59.935 47.826 0.00 0.00 0.00 2.59
2748 2935 3.054875 TCATGATGCTTTGCCTGTAGACT 60.055 43.478 0.00 0.00 0.00 3.24
2749 2936 4.162131 TCATGATGCTTTGCCTGTAGACTA 59.838 41.667 0.00 0.00 0.00 2.59
2750 2937 4.128925 TGATGCTTTGCCTGTAGACTAG 57.871 45.455 0.00 0.00 0.00 2.57
2751 2938 3.769300 TGATGCTTTGCCTGTAGACTAGA 59.231 43.478 0.00 0.00 0.00 2.43
2752 2939 4.222810 TGATGCTTTGCCTGTAGACTAGAA 59.777 41.667 0.00 0.00 0.00 2.10
2753 2940 3.926616 TGCTTTGCCTGTAGACTAGAAC 58.073 45.455 0.00 0.00 0.00 3.01
2754 2941 3.323691 TGCTTTGCCTGTAGACTAGAACA 59.676 43.478 0.00 0.00 0.00 3.18
2755 2942 4.020218 TGCTTTGCCTGTAGACTAGAACAT 60.020 41.667 0.00 0.00 0.00 2.71
2756 2943 4.568760 GCTTTGCCTGTAGACTAGAACATC 59.431 45.833 0.00 0.00 0.00 3.06
2757 2944 5.724328 CTTTGCCTGTAGACTAGAACATCA 58.276 41.667 0.00 0.00 0.00 3.07
2758 2945 5.738619 TTGCCTGTAGACTAGAACATCAA 57.261 39.130 0.00 3.30 0.00 2.57
2759 2946 5.738619 TGCCTGTAGACTAGAACATCAAA 57.261 39.130 0.00 0.00 0.00 2.69
2760 2947 5.724328 TGCCTGTAGACTAGAACATCAAAG 58.276 41.667 0.00 0.00 0.00 2.77
2761 2948 4.568760 GCCTGTAGACTAGAACATCAAAGC 59.431 45.833 0.00 0.00 0.00 3.51
2762 2949 4.800993 CCTGTAGACTAGAACATCAAAGCG 59.199 45.833 0.00 0.00 0.00 4.68
2763 2950 4.174009 TGTAGACTAGAACATCAAAGCGC 58.826 43.478 0.00 0.00 0.00 5.92
2764 2951 2.263077 AGACTAGAACATCAAAGCGCG 58.737 47.619 0.00 0.00 0.00 6.86
2765 2952 0.721718 ACTAGAACATCAAAGCGCGC 59.278 50.000 26.66 26.66 0.00 6.86
2766 2953 0.314578 CTAGAACATCAAAGCGCGCG 60.315 55.000 28.44 28.44 0.00 6.86
2767 2954 1.011968 TAGAACATCAAAGCGCGCGT 61.012 50.000 32.35 21.73 0.00 6.01
2768 2955 1.440353 GAACATCAAAGCGCGCGTT 60.440 52.632 32.35 26.36 0.00 4.84
2769 2956 1.655697 GAACATCAAAGCGCGCGTTG 61.656 55.000 41.20 41.20 36.89 4.10
2770 2957 3.526536 CATCAAAGCGCGCGTTGC 61.527 61.111 41.71 15.23 35.84 4.17
2771 2958 4.759096 ATCAAAGCGCGCGTTGCC 62.759 61.111 41.71 14.78 42.08 4.52
2789 2976 4.849310 GCGCCCGCCCATGTCTAA 62.849 66.667 0.00 0.00 34.56 2.10
2790 2977 2.124901 CGCCCGCCCATGTCTAAA 60.125 61.111 0.00 0.00 0.00 1.85
2791 2978 2.180204 CGCCCGCCCATGTCTAAAG 61.180 63.158 0.00 0.00 0.00 1.85
2792 2979 1.223487 GCCCGCCCATGTCTAAAGA 59.777 57.895 0.00 0.00 0.00 2.52
2793 2980 0.393808 GCCCGCCCATGTCTAAAGAA 60.394 55.000 0.00 0.00 0.00 2.52
2794 2981 1.750682 GCCCGCCCATGTCTAAAGAAT 60.751 52.381 0.00 0.00 0.00 2.40
2795 2982 2.486548 GCCCGCCCATGTCTAAAGAATA 60.487 50.000 0.00 0.00 0.00 1.75
2827 3014 8.746052 TGTCTATTTTACATCCGGATGAAATT 57.254 30.769 43.42 31.31 41.20 1.82
3020 3215 3.717707 GATACAGCGATACAGCCAAAGA 58.282 45.455 0.00 0.00 38.01 2.52
3368 3568 7.947890 TCCACTAAAAAGACCTTGTAAATCCAT 59.052 33.333 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 9.187455 GCAATGTCGGTCTTTAAAATTTCTAAA 57.813 29.630 0.00 0.00 0.00 1.85
14 15 8.353684 TGCAATGTCGGTCTTTAAAATTTCTAA 58.646 29.630 0.00 0.00 0.00 2.10
15 16 7.877003 TGCAATGTCGGTCTTTAAAATTTCTA 58.123 30.769 0.00 0.00 0.00 2.10
16 17 6.744112 TGCAATGTCGGTCTTTAAAATTTCT 58.256 32.000 0.00 0.00 0.00 2.52
17 18 7.581011 ATGCAATGTCGGTCTTTAAAATTTC 57.419 32.000 0.00 0.00 0.00 2.17
18 19 9.086336 CATATGCAATGTCGGTCTTTAAAATTT 57.914 29.630 0.00 0.00 0.00 1.82
19 20 8.250332 ACATATGCAATGTCGGTCTTTAAAATT 58.750 29.630 1.58 0.00 0.00 1.82
20 21 7.701924 CACATATGCAATGTCGGTCTTTAAAAT 59.298 33.333 1.58 0.00 0.00 1.82
21 22 7.026562 CACATATGCAATGTCGGTCTTTAAAA 58.973 34.615 1.58 0.00 0.00 1.52
22 23 6.404184 CCACATATGCAATGTCGGTCTTTAAA 60.404 38.462 1.58 0.00 0.00 1.52
23 24 5.065859 CCACATATGCAATGTCGGTCTTTAA 59.934 40.000 1.58 0.00 0.00 1.52
24 25 4.574421 CCACATATGCAATGTCGGTCTTTA 59.426 41.667 1.58 0.00 0.00 1.85
25 26 3.378112 CCACATATGCAATGTCGGTCTTT 59.622 43.478 1.58 0.00 0.00 2.52
26 27 2.945008 CCACATATGCAATGTCGGTCTT 59.055 45.455 1.58 0.00 0.00 3.01
27 28 2.564771 CCACATATGCAATGTCGGTCT 58.435 47.619 1.58 0.00 0.00 3.85
28 29 1.603802 CCCACATATGCAATGTCGGTC 59.396 52.381 13.55 0.00 0.00 4.79
29 30 1.064758 ACCCACATATGCAATGTCGGT 60.065 47.619 18.44 18.44 38.41 4.69
30 31 1.679139 ACCCACATATGCAATGTCGG 58.321 50.000 17.53 17.53 36.54 4.79
31 32 3.189080 CCATACCCACATATGCAATGTCG 59.811 47.826 1.58 5.86 32.12 4.35
32 33 3.057315 GCCATACCCACATATGCAATGTC 60.057 47.826 1.58 0.00 32.12 3.06
33 34 2.892852 GCCATACCCACATATGCAATGT 59.107 45.455 1.58 8.21 32.12 2.71
34 35 3.159472 AGCCATACCCACATATGCAATG 58.841 45.455 1.58 0.00 32.12 2.82
35 36 3.530928 AGCCATACCCACATATGCAAT 57.469 42.857 1.58 0.00 32.12 3.56
36 37 2.957680 CAAGCCATACCCACATATGCAA 59.042 45.455 1.58 0.00 32.12 4.08
37 38 2.585330 CAAGCCATACCCACATATGCA 58.415 47.619 1.58 0.00 32.12 3.96
38 39 1.888512 CCAAGCCATACCCACATATGC 59.111 52.381 1.58 0.00 32.12 3.14
39 40 3.507162 TCCAAGCCATACCCACATATG 57.493 47.619 0.00 0.00 33.10 1.78
40 41 3.657239 TGATCCAAGCCATACCCACATAT 59.343 43.478 0.00 0.00 0.00 1.78
41 42 3.052329 TGATCCAAGCCATACCCACATA 58.948 45.455 0.00 0.00 0.00 2.29
42 43 1.852309 TGATCCAAGCCATACCCACAT 59.148 47.619 0.00 0.00 0.00 3.21
43 44 1.064758 GTGATCCAAGCCATACCCACA 60.065 52.381 0.00 0.00 0.00 4.17
44 45 1.680338 GTGATCCAAGCCATACCCAC 58.320 55.000 0.00 0.00 0.00 4.61
45 46 0.180171 CGTGATCCAAGCCATACCCA 59.820 55.000 0.00 0.00 0.00 4.51
46 47 0.535102 CCGTGATCCAAGCCATACCC 60.535 60.000 0.00 0.00 0.00 3.69
47 48 0.468226 TCCGTGATCCAAGCCATACC 59.532 55.000 0.00 0.00 0.00 2.73
48 49 1.940613 GTTCCGTGATCCAAGCCATAC 59.059 52.381 0.00 0.00 0.00 2.39
49 50 1.134220 GGTTCCGTGATCCAAGCCATA 60.134 52.381 0.00 0.00 0.00 2.74
50 51 0.394352 GGTTCCGTGATCCAAGCCAT 60.394 55.000 0.00 0.00 0.00 4.40
51 52 1.002624 GGTTCCGTGATCCAAGCCA 60.003 57.895 0.00 0.00 0.00 4.75
52 53 2.106683 CGGTTCCGTGATCCAAGCC 61.107 63.158 2.82 0.00 0.00 4.35
53 54 2.750888 GCGGTTCCGTGATCCAAGC 61.751 63.158 12.81 0.00 0.00 4.01
54 55 2.452813 CGCGGTTCCGTGATCCAAG 61.453 63.158 18.24 0.00 41.75 3.61
55 56 2.433491 CGCGGTTCCGTGATCCAA 60.433 61.111 18.24 0.00 41.75 3.53
56 57 4.444838 CCGCGGTTCCGTGATCCA 62.445 66.667 23.53 0.00 41.75 3.41
57 58 4.446413 ACCGCGGTTCCGTGATCC 62.446 66.667 28.70 1.52 41.75 3.36
58 59 3.186047 CACCGCGGTTCCGTGATC 61.186 66.667 32.11 1.87 41.75 2.92
59 60 3.229156 TTCACCGCGGTTCCGTGAT 62.229 57.895 32.11 0.00 41.75 3.06
60 61 3.851845 CTTCACCGCGGTTCCGTGA 62.852 63.158 32.11 20.32 41.75 4.35
61 62 3.411351 CTTCACCGCGGTTCCGTG 61.411 66.667 32.11 17.99 39.33 4.94
64 65 3.423154 CAGCTTCACCGCGGTTCC 61.423 66.667 32.11 16.80 34.40 3.62
65 66 3.423154 CCAGCTTCACCGCGGTTC 61.423 66.667 32.11 17.83 34.40 3.62
68 69 4.451150 TAGCCAGCTTCACCGCGG 62.451 66.667 26.86 26.86 34.40 6.46
69 70 2.887568 CTAGCCAGCTTCACCGCG 60.888 66.667 0.00 0.00 34.40 6.46
70 71 3.198489 GCTAGCCAGCTTCACCGC 61.198 66.667 2.29 0.00 44.93 5.68
87 88 0.752054 ATTACAATGCCGGCCAATGG 59.248 50.000 26.77 12.19 0.00 3.16
88 89 3.005684 ACATATTACAATGCCGGCCAATG 59.994 43.478 26.77 21.74 0.00 2.82
89 90 3.230134 ACATATTACAATGCCGGCCAAT 58.770 40.909 26.77 16.73 0.00 3.16
90 91 2.621055 GACATATTACAATGCCGGCCAA 59.379 45.455 26.77 6.41 0.00 4.52
91 92 2.226330 GACATATTACAATGCCGGCCA 58.774 47.619 26.77 12.96 0.00 5.36
92 93 2.226330 TGACATATTACAATGCCGGCC 58.774 47.619 26.77 6.44 0.00 6.13
93 94 5.181245 AGTTATGACATATTACAATGCCGGC 59.819 40.000 22.73 22.73 0.00 6.13
94 95 6.650807 AGAGTTATGACATATTACAATGCCGG 59.349 38.462 0.00 0.00 0.00 6.13
95 96 7.658179 AGAGTTATGACATATTACAATGCCG 57.342 36.000 0.00 0.00 0.00 5.69
96 97 9.277783 AGAAGAGTTATGACATATTACAATGCC 57.722 33.333 0.00 0.00 0.00 4.40
115 116 8.986847 CGCATCATATCATTAAGAAAGAAGAGT 58.013 33.333 0.00 0.00 0.00 3.24
116 117 7.956403 GCGCATCATATCATTAAGAAAGAAGAG 59.044 37.037 0.30 0.00 0.00 2.85
117 118 7.359514 CGCGCATCATATCATTAAGAAAGAAGA 60.360 37.037 8.75 0.00 0.00 2.87
118 119 6.735510 CGCGCATCATATCATTAAGAAAGAAG 59.264 38.462 8.75 0.00 0.00 2.85
119 120 6.202762 ACGCGCATCATATCATTAAGAAAGAA 59.797 34.615 5.73 0.00 0.00 2.52
120 121 5.696270 ACGCGCATCATATCATTAAGAAAGA 59.304 36.000 5.73 0.00 0.00 2.52
121 122 5.920312 ACGCGCATCATATCATTAAGAAAG 58.080 37.500 5.73 0.00 0.00 2.62
122 123 5.922739 ACGCGCATCATATCATTAAGAAA 57.077 34.783 5.73 0.00 0.00 2.52
123 124 5.107104 GGAACGCGCATCATATCATTAAGAA 60.107 40.000 5.73 0.00 0.00 2.52
124 125 4.388773 GGAACGCGCATCATATCATTAAGA 59.611 41.667 5.73 0.00 0.00 2.10
125 126 4.152223 TGGAACGCGCATCATATCATTAAG 59.848 41.667 5.73 0.00 0.00 1.85
126 127 4.061596 TGGAACGCGCATCATATCATTAA 58.938 39.130 5.73 0.00 0.00 1.40
127 128 3.658709 TGGAACGCGCATCATATCATTA 58.341 40.909 5.73 0.00 0.00 1.90
128 129 2.481568 CTGGAACGCGCATCATATCATT 59.518 45.455 5.73 0.00 0.00 2.57
129 130 2.071540 CTGGAACGCGCATCATATCAT 58.928 47.619 5.73 0.00 0.00 2.45
130 131 1.501169 CTGGAACGCGCATCATATCA 58.499 50.000 5.73 0.00 0.00 2.15
131 132 0.792640 CCTGGAACGCGCATCATATC 59.207 55.000 5.73 0.00 0.00 1.63
132 133 0.392706 TCCTGGAACGCGCATCATAT 59.607 50.000 5.73 0.00 0.00 1.78
133 134 0.176910 TTCCTGGAACGCGCATCATA 59.823 50.000 5.73 0.00 0.00 2.15
134 135 0.676466 TTTCCTGGAACGCGCATCAT 60.676 50.000 9.04 0.00 0.00 2.45
135 136 1.298157 CTTTCCTGGAACGCGCATCA 61.298 55.000 9.04 0.06 0.00 3.07
136 137 1.019278 TCTTTCCTGGAACGCGCATC 61.019 55.000 9.04 4.70 0.00 3.91
137 138 1.003839 TCTTTCCTGGAACGCGCAT 60.004 52.632 9.04 0.00 0.00 4.73
162 163 7.064728 GCCTTTAGATTCTAATTCAACGACTGT 59.935 37.037 6.95 0.00 0.00 3.55
185 186 5.344743 TTCAGTCGATTTAATGAGAGCCT 57.655 39.130 0.00 0.00 0.00 4.58
220 221 1.127951 GTACGCAATGTTTCCACGGAG 59.872 52.381 0.00 0.00 0.00 4.63
226 227 2.095415 GTCCCAAGTACGCAATGTTTCC 60.095 50.000 0.00 0.00 0.00 3.13
273 274 1.708680 GAACATTCTCAAAACGTGCGC 59.291 47.619 0.00 0.00 0.00 6.09
275 276 3.300009 CCTGAACATTCTCAAAACGTGC 58.700 45.455 0.00 0.00 0.00 5.34
373 376 7.458409 TTGTAGAAACTGGTAGTAGTACTGG 57.542 40.000 13.29 3.47 0.00 4.00
374 377 9.924650 ATTTTGTAGAAACTGGTAGTAGTACTG 57.075 33.333 13.29 0.00 0.00 2.74
377 380 9.933723 GGAATTTTGTAGAAACTGGTAGTAGTA 57.066 33.333 0.00 0.00 0.00 1.82
378 381 8.434392 TGGAATTTTGTAGAAACTGGTAGTAGT 58.566 33.333 0.00 0.00 0.00 2.73
379 382 8.842358 TGGAATTTTGTAGAAACTGGTAGTAG 57.158 34.615 0.00 0.00 0.00 2.57
380 383 9.226606 CATGGAATTTTGTAGAAACTGGTAGTA 57.773 33.333 0.00 0.00 0.00 1.82
381 384 7.724061 ACATGGAATTTTGTAGAAACTGGTAGT 59.276 33.333 0.00 0.00 0.00 2.73
382 385 8.110860 ACATGGAATTTTGTAGAAACTGGTAG 57.889 34.615 0.00 0.00 0.00 3.18
406 409 3.139077 TCTCTCTTTTCTTTTGCGGGAC 58.861 45.455 0.00 0.00 0.00 4.46
421 424 2.025793 TCCTGTCTCGTGGATTCTCTCT 60.026 50.000 0.00 0.00 0.00 3.10
422 425 2.370349 TCCTGTCTCGTGGATTCTCTC 58.630 52.381 0.00 0.00 0.00 3.20
423 426 2.494073 GTTCCTGTCTCGTGGATTCTCT 59.506 50.000 0.00 0.00 31.76 3.10
424 427 2.417515 GGTTCCTGTCTCGTGGATTCTC 60.418 54.545 0.00 0.00 31.76 2.87
425 428 1.550976 GGTTCCTGTCTCGTGGATTCT 59.449 52.381 0.00 0.00 31.76 2.40
446 449 1.826096 GAGTGGGAGTAGGAACAGTCC 59.174 57.143 0.00 0.00 45.35 3.85
447 450 1.826096 GGAGTGGGAGTAGGAACAGTC 59.174 57.143 0.00 0.00 33.61 3.51
530 533 1.078214 CTTTGGCTGGCTGGATCGA 60.078 57.895 2.00 0.00 0.00 3.59
635 646 4.101448 GCCATGCCGTCCCTGAGT 62.101 66.667 0.00 0.00 0.00 3.41
660 671 2.158959 GGCGATTGGTGACTCGACG 61.159 63.158 0.00 0.00 37.05 5.12
681 692 1.142465 ACATCACATGGGCTCTGATCC 59.858 52.381 0.00 0.00 33.60 3.36
737 752 3.939837 ATCGGTCTGGTGCTGCGTG 62.940 63.158 0.00 0.00 0.00 5.34
738 753 3.649277 GATCGGTCTGGTGCTGCGT 62.649 63.158 0.00 0.00 0.00 5.24
950 982 2.874780 GCGCACGTACTCTCACCG 60.875 66.667 0.30 0.00 0.00 4.94
967 1003 1.425412 GCAAATGCCTGCAAGAACAG 58.575 50.000 0.00 0.00 42.17 3.16
990 1026 1.376086 CAGCTCCATGGTCACCACA 59.624 57.895 12.58 0.00 35.80 4.17
1049 1085 3.282745 GAACCTGCGACGGAGAGCA 62.283 63.158 18.77 0.00 41.28 4.26
1069 1105 1.268352 GACAGCGTAGGGAGCTAGATG 59.732 57.143 0.00 0.00 44.06 2.90
1070 1106 1.611519 GACAGCGTAGGGAGCTAGAT 58.388 55.000 0.00 0.00 44.06 1.98
1087 1123 1.063469 CCACCACTGAACAAACACGAC 59.937 52.381 0.00 0.00 0.00 4.34
1088 1124 1.339247 ACCACCACTGAACAAACACGA 60.339 47.619 0.00 0.00 0.00 4.35
1089 1125 1.091537 ACCACCACTGAACAAACACG 58.908 50.000 0.00 0.00 0.00 4.49
1097 1156 1.451504 CTCAGCCACCACCACTGAA 59.548 57.895 0.00 0.00 39.79 3.02
1100 1159 2.851102 AGCTCAGCCACCACCACT 60.851 61.111 0.00 0.00 0.00 4.00
1238 1297 3.517100 TCAAGAGTTCAAGATGGAGAGGG 59.483 47.826 0.00 0.00 0.00 4.30
1246 1305 5.039984 CACGATCGATCAAGAGTTCAAGAT 58.960 41.667 24.34 0.00 0.00 2.40
1788 1869 2.039084 TGGACAGAAAAGGAGAGAAGGC 59.961 50.000 0.00 0.00 0.00 4.35
1838 1943 4.746535 TTCATCCATGGTAGCTCGTTAA 57.253 40.909 12.58 0.00 0.00 2.01
1843 1948 6.261826 GCCATTATATTCATCCATGGTAGCTC 59.738 42.308 12.58 0.00 37.34 4.09
1845 1950 5.008019 CGCCATTATATTCATCCATGGTAGC 59.992 44.000 12.58 0.00 37.34 3.58
1847 1952 4.881273 GCGCCATTATATTCATCCATGGTA 59.119 41.667 12.58 0.00 37.34 3.25
1849 1954 3.695556 TGCGCCATTATATTCATCCATGG 59.304 43.478 4.97 4.97 37.96 3.66
1850 1955 4.968812 TGCGCCATTATATTCATCCATG 57.031 40.909 4.18 0.00 0.00 3.66
2344 2506 2.094762 ACCGAGATAGCGTTGCTTTT 57.905 45.000 0.00 0.00 40.44 2.27
2348 2510 1.355971 TTGAACCGAGATAGCGTTGC 58.644 50.000 0.00 0.00 0.00 4.17
2352 2514 3.642705 TGATGATTGAACCGAGATAGCG 58.357 45.455 0.00 0.00 0.00 4.26
2353 2515 4.325741 CGATGATGATTGAACCGAGATAGC 59.674 45.833 0.00 0.00 0.00 2.97
2355 2517 5.705609 TCGATGATGATTGAACCGAGATA 57.294 39.130 0.00 0.00 0.00 1.98
2356 2518 4.590850 TCGATGATGATTGAACCGAGAT 57.409 40.909 0.00 0.00 0.00 2.75
2357 2519 4.037923 TGATCGATGATGATTGAACCGAGA 59.962 41.667 0.54 0.00 0.00 4.04
2358 2520 4.301628 TGATCGATGATGATTGAACCGAG 58.698 43.478 0.54 0.00 0.00 4.63
2359 2521 4.202151 ACTGATCGATGATGATTGAACCGA 60.202 41.667 0.54 0.00 0.00 4.69
2360 2522 4.053983 ACTGATCGATGATGATTGAACCG 58.946 43.478 0.54 0.00 0.00 4.44
2361 2523 5.745514 CAACTGATCGATGATGATTGAACC 58.254 41.667 0.54 0.00 0.00 3.62
2362 2524 5.203370 GCAACTGATCGATGATGATTGAAC 58.797 41.667 0.54 0.00 0.00 3.18
2363 2525 4.274214 GGCAACTGATCGATGATGATTGAA 59.726 41.667 0.54 0.00 0.00 2.69
2364 2526 3.811497 GGCAACTGATCGATGATGATTGA 59.189 43.478 0.54 0.00 0.00 2.57
2365 2527 4.143194 GGCAACTGATCGATGATGATTG 57.857 45.455 0.54 0.91 0.00 2.67
2381 2543 4.322567 AGTCTGATGAGAAGAAAGGCAAC 58.677 43.478 0.00 0.00 0.00 4.17
2384 2546 4.999950 TCAAAGTCTGATGAGAAGAAAGGC 59.000 41.667 0.00 0.00 0.00 4.35
2389 2551 6.847421 TGAGATCAAAGTCTGATGAGAAGA 57.153 37.500 0.00 0.00 45.23 2.87
2390 2552 7.982919 AGATTGAGATCAAAGTCTGATGAGAAG 59.017 37.037 0.00 0.00 45.23 2.85
2393 2555 7.042950 ACAGATTGAGATCAAAGTCTGATGAG 58.957 38.462 23.37 6.23 45.23 2.90
2394 2556 6.944096 ACAGATTGAGATCAAAGTCTGATGA 58.056 36.000 23.37 0.00 45.23 2.92
2395 2557 7.465173 CAACAGATTGAGATCAAAGTCTGATG 58.535 38.462 23.37 19.47 41.77 3.07
2396 2558 6.093771 GCAACAGATTGAGATCAAAGTCTGAT 59.906 38.462 23.37 14.28 41.77 2.90
2397 2559 5.410746 GCAACAGATTGAGATCAAAGTCTGA 59.589 40.000 23.37 0.00 41.77 3.27
2398 2560 5.629097 GCAACAGATTGAGATCAAAGTCTG 58.371 41.667 18.22 18.22 43.41 3.51
2399 2561 4.391216 CGCAACAGATTGAGATCAAAGTCT 59.609 41.667 0.00 0.00 37.80 3.24
2402 2567 3.438087 ACCGCAACAGATTGAGATCAAAG 59.562 43.478 0.00 0.00 37.80 2.77
2411 2576 2.246841 TCTGCACCGCAACAGATTG 58.753 52.632 0.00 0.00 38.41 2.67
2420 2585 3.490759 CCGTGTCATCTGCACCGC 61.491 66.667 0.00 0.00 33.61 5.68
2421 2586 3.490759 GCCGTGTCATCTGCACCG 61.491 66.667 0.00 0.00 33.61 4.94
2681 2868 1.004918 AGAACCAAGAAGGCGACGG 60.005 57.895 0.00 0.00 43.14 4.79
2682 2869 1.014564 GGAGAACCAAGAAGGCGACG 61.015 60.000 0.00 0.00 43.14 5.12
2683 2870 0.321996 AGGAGAACCAAGAAGGCGAC 59.678 55.000 0.00 0.00 43.14 5.19
2718 2905 0.254178 AAAGCATCATGACCGCCTCT 59.746 50.000 13.87 0.00 0.00 3.69
2726 2913 3.054875 AGTCTACAGGCAAAGCATCATGA 60.055 43.478 0.00 0.00 0.00 3.07
2734 2921 5.724328 TGATGTTCTAGTCTACAGGCAAAG 58.276 41.667 0.00 0.00 0.00 2.77
2747 2934 0.314578 CGCGCGCTTTGATGTTCTAG 60.315 55.000 30.48 4.24 0.00 2.43
2748 2935 1.011968 ACGCGCGCTTTGATGTTCTA 61.012 50.000 32.58 0.00 0.00 2.10
2749 2936 1.841663 AACGCGCGCTTTGATGTTCT 61.842 50.000 32.58 1.63 0.00 3.01
2750 2937 1.440353 AACGCGCGCTTTGATGTTC 60.440 52.632 32.58 0.00 0.00 3.18
2751 2938 1.725625 CAACGCGCGCTTTGATGTT 60.726 52.632 37.84 25.64 0.00 2.71
2752 2939 2.127270 CAACGCGCGCTTTGATGT 60.127 55.556 37.84 21.49 0.00 3.06
2753 2940 3.526536 GCAACGCGCGCTTTGATG 61.527 61.111 42.59 26.91 0.00 3.07
2754 2941 4.759096 GGCAACGCGCGCTTTGAT 62.759 61.111 42.59 17.07 43.84 2.57
2772 2959 4.849310 TTAGACATGGGCGGGCGC 62.849 66.667 0.00 0.00 41.06 6.53
2773 2960 2.124901 TTTAGACATGGGCGGGCG 60.125 61.111 0.00 0.00 0.00 6.13
2774 2961 0.393808 TTCTTTAGACATGGGCGGGC 60.394 55.000 0.00 0.00 0.00 6.13
2775 2962 2.348411 ATTCTTTAGACATGGGCGGG 57.652 50.000 0.00 0.00 0.00 6.13
2776 2963 3.815401 CCTTATTCTTTAGACATGGGCGG 59.185 47.826 0.00 0.00 0.00 6.13
2777 2964 3.815401 CCCTTATTCTTTAGACATGGGCG 59.185 47.826 0.00 0.00 0.00 6.13
2778 2965 4.822350 GTCCCTTATTCTTTAGACATGGGC 59.178 45.833 0.00 0.00 32.62 5.36
2779 2966 6.058183 CAGTCCCTTATTCTTTAGACATGGG 58.942 44.000 0.00 0.00 0.00 4.00
2780 2967 6.653989 ACAGTCCCTTATTCTTTAGACATGG 58.346 40.000 0.00 0.00 0.00 3.66
2781 2968 7.560368 AGACAGTCCCTTATTCTTTAGACATG 58.440 38.462 0.00 0.00 0.00 3.21
2782 2969 7.741554 AGACAGTCCCTTATTCTTTAGACAT 57.258 36.000 0.00 0.00 0.00 3.06
2783 2970 8.840200 ATAGACAGTCCCTTATTCTTTAGACA 57.160 34.615 0.00 0.00 0.00 3.41
2791 2978 9.274206 GGATGTAAAATAGACAGTCCCTTATTC 57.726 37.037 0.00 0.00 0.00 1.75
2792 2979 7.931948 CGGATGTAAAATAGACAGTCCCTTATT 59.068 37.037 0.00 0.00 0.00 1.40
2793 2980 7.442656 CGGATGTAAAATAGACAGTCCCTTAT 58.557 38.462 0.00 0.00 0.00 1.73
2794 2981 6.183360 CCGGATGTAAAATAGACAGTCCCTTA 60.183 42.308 0.00 0.00 0.00 2.69
2795 2982 5.396436 CCGGATGTAAAATAGACAGTCCCTT 60.396 44.000 0.00 0.00 0.00 3.95
2810 2997 7.502226 AGCTAATTGAATTTCATCCGGATGTAA 59.498 33.333 36.95 33.85 39.72 2.41
3020 3215 9.515226 TTCTTTAGCTTAGTGTACATGGAAAAT 57.485 29.630 0.00 0.00 0.00 1.82
3368 3568 8.970020 ACTAGTGCAAATCATTTGGATTATTGA 58.030 29.630 12.14 0.00 45.46 2.57


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

AutoCloner maintained by Alex Coulton.