Multiple sequence alignment - TraesCS3A01G346300

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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 TraesCS3A01G346300 chr3A 100.000 2739 0 0 424 3162 595643540 595646278 0.000000e+00 5059.0
1 TraesCS3A01G346300 chr3A 100.000 160 0 0 1 160 595643117 595643276 2.380000e-76 296.0
2 TraesCS3A01G346300 chr3D 95.087 2585 71 30 605 3161 453628990 453631546 0.000000e+00 4019.0
3 TraesCS3A01G346300 chr3B 93.461 1774 54 21 644 2401 596047267 596048994 0.000000e+00 2577.0
4 TraesCS3A01G346300 chr3B 93.526 726 35 7 2442 3161 596049347 596050066 0.000000e+00 1070.0
5 TraesCS3A01G346300 chr3B 100.000 29 0 0 525 553 536050367 536050339 2.000000e-03 54.7
6 TraesCS3A01G346300 chr6D 90.446 157 14 1 2 158 144100367 144100212 4.130000e-49 206.0
7 TraesCS3A01G346300 chr6D 85.185 162 20 3 1 160 137487465 137487306 2.520000e-36 163.0
8 TraesCS3A01G346300 chr6D 84.906 159 21 3 2 158 370871231 370871074 1.170000e-34 158.0
9 TraesCS3A01G346300 chr6B 88.679 159 17 1 2 160 694260605 694260448 3.220000e-45 193.0
10 TraesCS3A01G346300 chr6B 96.970 33 1 0 525 557 707161230 707161198 4.410000e-04 56.5
11 TraesCS3A01G346300 chr1D 85.876 177 20 5 1754 1928 109477204 109477031 1.940000e-42 183.0
12 TraesCS3A01G346300 chr1D 87.162 148 19 0 1480 1627 109478071 109477924 5.420000e-38 169.0
13 TraesCS3A01G346300 chr1D 84.932 146 20 2 1484 1628 311750431 311750287 2.540000e-31 147.0
14 TraesCS3A01G346300 chr1B 84.324 185 23 6 1728 1909 165076540 165076359 3.240000e-40 176.0
15 TraesCS3A01G346300 chr1B 87.838 148 18 0 1480 1627 165077397 165077250 1.170000e-39 174.0
16 TraesCS3A01G346300 chr1B 84.932 146 20 2 1484 1628 422346955 422346811 2.540000e-31 147.0
17 TraesCS3A01G346300 chr1A 84.324 185 23 6 1728 1909 112943081 112942900 3.240000e-40 176.0
18 TraesCS3A01G346300 chr4B 85.987 157 21 1 5 160 447360033 447359877 1.950000e-37 167.0
19 TraesCS3A01G346300 chr7D 85.625 160 18 3 2 160 488807009 488806854 2.520000e-36 163.0
20 TraesCS3A01G346300 chr7D 86.567 134 18 0 2 135 203168162 203168295 7.070000e-32 148.0
21 TraesCS3A01G346300 chr7D 100.000 29 0 0 525 553 4736891 4736919 2.000000e-03 54.7
22 TraesCS3A01G346300 chr7A 86.232 138 17 2 2 138 362735482 362735618 7.070000e-32 148.0
23 TraesCS3A01G346300 chr7A 96.970 33 1 0 525 557 253808175 253808143 4.410000e-04 56.5
24 TraesCS3A01G346300 chr7B 83.125 160 25 2 2 160 3542392 3542234 9.140000e-31 145.0
25 TraesCS3A01G346300 chrUn 94.444 54 3 0 502 555 108393945 108393892 2.020000e-12 84.2
26 TraesCS3A01G346300 chr6A 100.000 33 0 0 525 557 52472819 52472787 9.470000e-06 62.1
27 TraesCS3A01G346300 chr6A 89.362 47 5 0 507 553 553181417 553181371 3.410000e-05 60.2
28 TraesCS3A01G346300 chr5D 88.889 45 3 1 510 552 402948677 402948721 2.000000e-03 54.7
29 TraesCS3A01G346300 chr4A 100.000 29 0 0 525 553 64953505 64953533 2.000000e-03 54.7


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 TraesCS3A01G346300 chr3A 595643117 595646278 3161 False 2677.5 5059 100.0000 1 3162 2 chr3A.!!$F1 3161
1 TraesCS3A01G346300 chr3D 453628990 453631546 2556 False 4019.0 4019 95.0870 605 3161 1 chr3D.!!$F1 2556
2 TraesCS3A01G346300 chr3B 596047267 596050066 2799 False 1823.5 2577 93.4935 644 3161 2 chr3B.!!$F1 2517

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
97 98 0.036164 AAACAGTGCGGGATGCTACA 59.964 50.0 0.00 0.0 46.63 2.74 F
468 469 0.037326 ACATGTCTGAATCACGCCGT 60.037 50.0 0.00 0.0 0.00 5.68 F
482 483 0.248743 CGCCGTAAGCCGATACAGAA 60.249 55.0 0.00 0.0 39.56 3.02 F
492 493 0.457166 CGATACAGAACCGCGTTGGA 60.457 55.0 4.92 0.0 42.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1659 1670 0.036105 ACGGACGGTGGAATTAACCC 60.036 55.000 4.58 0.00 33.88 4.11 R
1937 1954 0.109919 TCGTCGTCGACAATGAGGTG 60.110 55.000 24.13 6.28 41.35 4.00 R
2035 2052 3.249189 ACTTCTTGGCCGGCCTCA 61.249 61.111 43.34 29.40 36.94 3.86 R
2176 2193 3.256383 CCATCAATCACCAGAACAGCAAA 59.744 43.478 0.00 0.00 0.00 3.68 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
18 19 2.556286 GGAGGGTGGAAGAAAAGCG 58.444 57.895 0.00 0.00 0.00 4.68
19 20 0.250770 GGAGGGTGGAAGAAAAGCGT 60.251 55.000 0.00 0.00 0.00 5.07
20 21 0.875059 GAGGGTGGAAGAAAAGCGTG 59.125 55.000 0.00 0.00 0.00 5.34
21 22 0.537371 AGGGTGGAAGAAAAGCGTGG 60.537 55.000 0.00 0.00 0.00 4.94
22 23 1.524008 GGGTGGAAGAAAAGCGTGGG 61.524 60.000 0.00 0.00 0.00 4.61
23 24 0.536460 GGTGGAAGAAAAGCGTGGGA 60.536 55.000 0.00 0.00 0.00 4.37
24 25 1.314730 GTGGAAGAAAAGCGTGGGAA 58.685 50.000 0.00 0.00 0.00 3.97
25 26 1.886542 GTGGAAGAAAAGCGTGGGAAT 59.113 47.619 0.00 0.00 0.00 3.01
26 27 2.296190 GTGGAAGAAAAGCGTGGGAATT 59.704 45.455 0.00 0.00 0.00 2.17
27 28 2.295909 TGGAAGAAAAGCGTGGGAATTG 59.704 45.455 0.00 0.00 0.00 2.32
28 29 2.352715 GGAAGAAAAGCGTGGGAATTGG 60.353 50.000 0.00 0.00 0.00 3.16
29 30 1.256812 AGAAAAGCGTGGGAATTGGG 58.743 50.000 0.00 0.00 0.00 4.12
30 31 0.389817 GAAAAGCGTGGGAATTGGGC 60.390 55.000 0.00 0.00 0.00 5.36
31 32 2.153547 AAAAGCGTGGGAATTGGGCG 62.154 55.000 0.00 0.00 0.00 6.13
34 35 2.824041 CGTGGGAATTGGGCGGAG 60.824 66.667 0.00 0.00 0.00 4.63
35 36 2.674754 GTGGGAATTGGGCGGAGA 59.325 61.111 0.00 0.00 0.00 3.71
36 37 1.452108 GTGGGAATTGGGCGGAGAG 60.452 63.158 0.00 0.00 0.00 3.20
48 49 4.918201 GGAGAGCGGCGGGGAATG 62.918 72.222 9.78 0.00 0.00 2.67
49 50 4.918201 GAGAGCGGCGGGGAATGG 62.918 72.222 9.78 0.00 0.00 3.16
51 52 3.857038 GAGCGGCGGGGAATGGTA 61.857 66.667 9.78 0.00 0.00 3.25
52 53 3.809374 GAGCGGCGGGGAATGGTAG 62.809 68.421 9.78 0.00 0.00 3.18
53 54 3.857038 GCGGCGGGGAATGGTAGA 61.857 66.667 9.78 0.00 0.00 2.59
54 55 2.904905 CGGCGGGGAATGGTAGAA 59.095 61.111 0.00 0.00 0.00 2.10
55 56 1.227556 CGGCGGGGAATGGTAGAAG 60.228 63.158 0.00 0.00 0.00 2.85
56 57 1.148498 GGCGGGGAATGGTAGAAGG 59.852 63.158 0.00 0.00 0.00 3.46
57 58 1.148498 GCGGGGAATGGTAGAAGGG 59.852 63.158 0.00 0.00 0.00 3.95
58 59 1.342672 GCGGGGAATGGTAGAAGGGA 61.343 60.000 0.00 0.00 0.00 4.20
59 60 0.468648 CGGGGAATGGTAGAAGGGAC 59.531 60.000 0.00 0.00 0.00 4.46
61 62 2.691850 CGGGGAATGGTAGAAGGGACTA 60.692 54.545 0.00 0.00 38.49 2.59
62 63 2.973406 GGGGAATGGTAGAAGGGACTAG 59.027 54.545 0.00 0.00 38.49 2.57
63 64 2.973406 GGGAATGGTAGAAGGGACTAGG 59.027 54.545 0.00 0.00 38.49 3.02
64 65 2.973406 GGAATGGTAGAAGGGACTAGGG 59.027 54.545 0.00 0.00 38.49 3.53
65 66 2.797285 ATGGTAGAAGGGACTAGGGG 57.203 55.000 0.00 0.00 38.49 4.79
66 67 1.400941 TGGTAGAAGGGACTAGGGGT 58.599 55.000 0.00 0.00 38.49 4.95
67 68 1.726352 TGGTAGAAGGGACTAGGGGTT 59.274 52.381 0.00 0.00 38.49 4.11
68 69 2.114871 TGGTAGAAGGGACTAGGGGTTT 59.885 50.000 0.00 0.00 38.49 3.27
69 70 3.187942 GGTAGAAGGGACTAGGGGTTTT 58.812 50.000 0.00 0.00 38.49 2.43
70 71 3.590630 GGTAGAAGGGACTAGGGGTTTTT 59.409 47.826 0.00 0.00 38.49 1.94
71 72 3.808834 AGAAGGGACTAGGGGTTTTTG 57.191 47.619 0.00 0.00 38.49 2.44
72 73 2.378886 AGAAGGGACTAGGGGTTTTTGG 59.621 50.000 0.00 0.00 38.49 3.28
73 74 0.408309 AGGGACTAGGGGTTTTTGGC 59.592 55.000 0.00 0.00 36.02 4.52
74 75 0.963856 GGGACTAGGGGTTTTTGGCG 60.964 60.000 0.00 0.00 0.00 5.69
75 76 1.592400 GGACTAGGGGTTTTTGGCGC 61.592 60.000 0.00 0.00 0.00 6.53
76 77 1.918868 GACTAGGGGTTTTTGGCGCG 61.919 60.000 0.00 0.00 0.00 6.86
77 78 1.673009 CTAGGGGTTTTTGGCGCGA 60.673 57.895 12.10 0.00 0.00 5.87
78 79 1.228184 TAGGGGTTTTTGGCGCGAA 60.228 52.632 12.10 0.00 0.00 4.70
79 80 0.822532 TAGGGGTTTTTGGCGCGAAA 60.823 50.000 13.91 13.91 0.00 3.46
80 81 1.227292 GGGGTTTTTGGCGCGAAAA 60.227 52.632 23.88 23.88 0.00 2.29
81 82 1.492319 GGGGTTTTTGGCGCGAAAAC 61.492 55.000 26.79 27.68 43.26 2.43
82 83 0.806492 GGGTTTTTGGCGCGAAAACA 60.806 50.000 32.70 21.60 44.80 2.83
83 84 0.574922 GGTTTTTGGCGCGAAAACAG 59.425 50.000 32.70 0.00 44.80 3.16
84 85 1.273688 GTTTTTGGCGCGAAAACAGT 58.726 45.000 29.86 0.00 43.39 3.55
85 86 1.006494 GTTTTTGGCGCGAAAACAGTG 60.006 47.619 29.86 0.00 43.39 3.66
86 87 1.142778 TTTTGGCGCGAAAACAGTGC 61.143 50.000 23.88 0.00 43.68 4.40
91 92 3.263941 GCGAAAACAGTGCGGGAT 58.736 55.556 0.00 0.00 0.00 3.85
92 93 1.154225 GCGAAAACAGTGCGGGATG 60.154 57.895 0.00 0.00 0.00 3.51
93 94 1.154225 CGAAAACAGTGCGGGATGC 60.154 57.895 0.00 0.00 46.70 3.91
94 95 1.577328 CGAAAACAGTGCGGGATGCT 61.577 55.000 0.00 0.00 46.63 3.79
95 96 1.448985 GAAAACAGTGCGGGATGCTA 58.551 50.000 0.00 0.00 46.63 3.49
96 97 1.130561 GAAAACAGTGCGGGATGCTAC 59.869 52.381 0.00 0.00 46.63 3.58
97 98 0.036164 AAACAGTGCGGGATGCTACA 59.964 50.000 0.00 0.00 46.63 2.74
98 99 0.036164 AACAGTGCGGGATGCTACAA 59.964 50.000 0.00 0.00 46.63 2.41
99 100 0.036164 ACAGTGCGGGATGCTACAAA 59.964 50.000 0.00 0.00 46.63 2.83
100 101 1.164411 CAGTGCGGGATGCTACAAAA 58.836 50.000 0.00 0.00 46.63 2.44
101 102 1.131126 CAGTGCGGGATGCTACAAAAG 59.869 52.381 0.00 0.00 46.63 2.27
124 125 1.586541 GGCTCCGCCTTCTTTTTGG 59.413 57.895 0.00 0.00 46.69 3.28
125 126 1.586541 GCTCCGCCTTCTTTTTGGG 59.413 57.895 0.00 0.00 0.00 4.12
126 127 1.179174 GCTCCGCCTTCTTTTTGGGT 61.179 55.000 0.00 0.00 0.00 4.51
127 128 0.598065 CTCCGCCTTCTTTTTGGGTG 59.402 55.000 0.00 0.00 0.00 4.61
128 129 1.665442 CCGCCTTCTTTTTGGGTGG 59.335 57.895 0.00 0.00 43.13 4.61
129 130 1.665442 CGCCTTCTTTTTGGGTGGG 59.335 57.895 0.00 0.00 0.00 4.61
130 131 1.371183 GCCTTCTTTTTGGGTGGGC 59.629 57.895 0.00 0.00 0.00 5.36
131 132 2.057830 CCTTCTTTTTGGGTGGGCC 58.942 57.895 0.00 0.00 0.00 5.80
132 133 1.665442 CTTCTTTTTGGGTGGGCCG 59.335 57.895 0.00 0.00 34.97 6.13
133 134 1.815817 CTTCTTTTTGGGTGGGCCGG 61.816 60.000 0.00 0.00 34.97 6.13
134 135 3.310307 CTTTTTGGGTGGGCCGGG 61.310 66.667 2.18 0.00 34.97 5.73
135 136 4.944069 TTTTTGGGTGGGCCGGGG 62.944 66.667 2.18 0.00 34.97 5.73
150 151 4.575180 GGGGGTAGAGATCGACGT 57.425 61.111 0.00 0.00 0.00 4.34
151 152 2.804549 GGGGGTAGAGATCGACGTT 58.195 57.895 0.00 0.00 0.00 3.99
152 153 1.109609 GGGGGTAGAGATCGACGTTT 58.890 55.000 0.00 0.00 0.00 3.60
153 154 1.066757 GGGGGTAGAGATCGACGTTTC 59.933 57.143 0.00 0.00 0.00 2.78
155 156 1.464821 GGTAGAGATCGACGTTTCGC 58.535 55.000 0.00 0.00 45.46 4.70
156 157 1.103015 GTAGAGATCGACGTTTCGCG 58.897 55.000 0.00 0.00 45.46 5.87
441 442 3.729004 GGTTTGTCTTCAGTTCGCG 57.271 52.632 0.00 0.00 0.00 5.87
442 443 0.234884 GGTTTGTCTTCAGTTCGCGG 59.765 55.000 6.13 0.00 0.00 6.46
443 444 0.234884 GTTTGTCTTCAGTTCGCGGG 59.765 55.000 6.13 0.00 0.00 6.13
444 445 0.105224 TTTGTCTTCAGTTCGCGGGA 59.895 50.000 6.13 0.00 0.00 5.14
445 446 0.319555 TTGTCTTCAGTTCGCGGGAG 60.320 55.000 6.13 0.00 0.00 4.30
446 447 1.176619 TGTCTTCAGTTCGCGGGAGA 61.177 55.000 6.13 0.00 0.00 3.71
447 448 0.038526 GTCTTCAGTTCGCGGGAGAA 60.039 55.000 6.13 5.17 0.00 2.87
448 449 0.677288 TCTTCAGTTCGCGGGAGAAA 59.323 50.000 6.13 0.00 0.00 2.52
449 450 1.069513 TCTTCAGTTCGCGGGAGAAAA 59.930 47.619 6.13 0.00 0.00 2.29
450 451 1.194772 CTTCAGTTCGCGGGAGAAAAC 59.805 52.381 6.13 1.47 0.00 2.43
451 452 0.105224 TCAGTTCGCGGGAGAAAACA 59.895 50.000 6.13 0.00 0.00 2.83
452 453 1.156736 CAGTTCGCGGGAGAAAACAT 58.843 50.000 6.13 0.00 0.00 2.71
453 454 1.135972 CAGTTCGCGGGAGAAAACATG 60.136 52.381 6.13 0.00 0.00 3.21
454 455 0.872388 GTTCGCGGGAGAAAACATGT 59.128 50.000 6.13 0.00 0.00 3.21
455 456 1.136057 GTTCGCGGGAGAAAACATGTC 60.136 52.381 6.13 0.00 0.00 3.06
456 457 0.320374 TCGCGGGAGAAAACATGTCT 59.680 50.000 6.13 0.00 0.00 3.41
457 458 0.443869 CGCGGGAGAAAACATGTCTG 59.556 55.000 0.00 0.00 0.00 3.51
458 459 1.808411 GCGGGAGAAAACATGTCTGA 58.192 50.000 0.00 0.00 0.00 3.27
459 460 2.151202 GCGGGAGAAAACATGTCTGAA 58.849 47.619 0.00 0.00 0.00 3.02
460 461 2.749621 GCGGGAGAAAACATGTCTGAAT 59.250 45.455 0.00 0.00 0.00 2.57
461 462 3.181506 GCGGGAGAAAACATGTCTGAATC 60.182 47.826 0.00 0.00 0.00 2.52
462 463 4.002982 CGGGAGAAAACATGTCTGAATCA 58.997 43.478 0.00 0.00 0.00 2.57
463 464 4.142816 CGGGAGAAAACATGTCTGAATCAC 60.143 45.833 0.00 0.00 0.00 3.06
464 465 4.142816 GGGAGAAAACATGTCTGAATCACG 60.143 45.833 0.00 0.00 0.00 4.35
465 466 4.398247 GAGAAAACATGTCTGAATCACGC 58.602 43.478 0.00 0.00 0.00 5.34
466 467 3.189287 AGAAAACATGTCTGAATCACGCC 59.811 43.478 0.00 0.00 0.00 5.68
467 468 1.078709 AACATGTCTGAATCACGCCG 58.921 50.000 0.00 0.00 0.00 6.46
468 469 0.037326 ACATGTCTGAATCACGCCGT 60.037 50.000 0.00 0.00 0.00 5.68
469 470 1.203758 ACATGTCTGAATCACGCCGTA 59.796 47.619 0.00 0.00 0.00 4.02
470 471 2.267426 CATGTCTGAATCACGCCGTAA 58.733 47.619 0.00 0.00 0.00 3.18
471 472 1.990799 TGTCTGAATCACGCCGTAAG 58.009 50.000 0.00 0.00 0.00 2.34
472 473 0.645868 GTCTGAATCACGCCGTAAGC 59.354 55.000 0.00 0.00 38.52 3.09
473 474 0.459585 TCTGAATCACGCCGTAAGCC 60.460 55.000 0.00 0.00 38.78 4.35
474 475 1.752501 CTGAATCACGCCGTAAGCCG 61.753 60.000 0.00 0.00 38.78 5.52
475 476 1.517694 GAATCACGCCGTAAGCCGA 60.518 57.895 0.00 0.00 39.56 5.54
476 477 0.874607 GAATCACGCCGTAAGCCGAT 60.875 55.000 0.00 0.00 39.56 4.18
477 478 0.386476 AATCACGCCGTAAGCCGATA 59.614 50.000 0.00 0.00 39.56 2.92
478 479 0.318445 ATCACGCCGTAAGCCGATAC 60.318 55.000 0.00 0.00 39.56 2.24
479 480 1.226745 CACGCCGTAAGCCGATACA 60.227 57.895 0.00 0.00 39.56 2.29
480 481 1.065273 ACGCCGTAAGCCGATACAG 59.935 57.895 0.00 0.00 39.56 2.74
481 482 1.357690 CGCCGTAAGCCGATACAGA 59.642 57.895 0.00 0.00 39.56 3.41
482 483 0.248743 CGCCGTAAGCCGATACAGAA 60.249 55.000 0.00 0.00 39.56 3.02
483 484 1.206523 GCCGTAAGCCGATACAGAAC 58.793 55.000 0.00 0.00 39.56 3.01
484 485 1.849097 CCGTAAGCCGATACAGAACC 58.151 55.000 0.00 0.00 39.56 3.62
485 486 1.474017 CGTAAGCCGATACAGAACCG 58.526 55.000 0.00 0.00 39.56 4.44
486 487 1.206523 GTAAGCCGATACAGAACCGC 58.793 55.000 0.00 0.00 0.00 5.68
487 488 0.248743 TAAGCCGATACAGAACCGCG 60.249 55.000 0.00 0.00 0.00 6.46
488 489 2.202703 GCCGATACAGAACCGCGT 60.203 61.111 4.92 0.00 0.00 6.01
489 490 1.808390 GCCGATACAGAACCGCGTT 60.808 57.895 4.92 0.00 0.00 4.84
490 491 1.995991 CCGATACAGAACCGCGTTG 59.004 57.895 4.92 0.09 0.00 4.10
491 492 1.418342 CCGATACAGAACCGCGTTGG 61.418 60.000 4.92 0.00 46.41 3.77
492 493 0.457166 CGATACAGAACCGCGTTGGA 60.457 55.000 4.92 0.00 42.00 3.53
493 494 0.997196 GATACAGAACCGCGTTGGAC 59.003 55.000 4.92 0.00 42.00 4.02
494 495 0.734942 ATACAGAACCGCGTTGGACG 60.735 55.000 4.92 0.00 45.88 4.79
522 523 4.838152 CCCGGACGCATGTGGGAG 62.838 72.222 11.65 0.82 44.88 4.30
523 524 4.838152 CCGGACGCATGTGGGAGG 62.838 72.222 11.65 6.50 0.00 4.30
524 525 4.082523 CGGACGCATGTGGGAGGT 62.083 66.667 11.65 0.00 0.00 3.85
525 526 2.351276 GGACGCATGTGGGAGGTT 59.649 61.111 11.65 0.00 0.00 3.50
526 527 1.303317 GGACGCATGTGGGAGGTTT 60.303 57.895 11.65 0.00 0.00 3.27
527 528 1.586154 GGACGCATGTGGGAGGTTTG 61.586 60.000 11.65 0.00 0.00 2.93
528 529 2.200170 GACGCATGTGGGAGGTTTGC 62.200 60.000 11.65 0.00 0.00 3.68
529 530 2.568090 GCATGTGGGAGGTTTGCG 59.432 61.111 0.00 0.00 0.00 4.85
530 531 2.993471 GCATGTGGGAGGTTTGCGG 61.993 63.158 0.00 0.00 0.00 5.69
531 532 2.035626 ATGTGGGAGGTTTGCGGG 59.964 61.111 0.00 0.00 0.00 6.13
532 533 2.840753 ATGTGGGAGGTTTGCGGGT 61.841 57.895 0.00 0.00 0.00 5.28
533 534 2.671963 GTGGGAGGTTTGCGGGTC 60.672 66.667 0.00 0.00 0.00 4.46
534 535 4.323477 TGGGAGGTTTGCGGGTCG 62.323 66.667 0.00 0.00 0.00 4.79
545 546 2.125673 CGGGTCGCCGTTGAAGAT 60.126 61.111 0.00 0.00 0.00 2.40
546 547 2.452813 CGGGTCGCCGTTGAAGATG 61.453 63.158 0.00 0.00 0.00 2.90
547 548 2.750888 GGGTCGCCGTTGAAGATGC 61.751 63.158 0.00 0.00 0.00 3.91
548 549 2.750888 GGTCGCCGTTGAAGATGCC 61.751 63.158 0.00 0.00 0.00 4.40
549 550 2.435938 TCGCCGTTGAAGATGCCC 60.436 61.111 0.00 0.00 0.00 5.36
550 551 2.436646 CGCCGTTGAAGATGCCCT 60.437 61.111 0.00 0.00 0.00 5.19
551 552 1.153449 CGCCGTTGAAGATGCCCTA 60.153 57.895 0.00 0.00 0.00 3.53
552 553 0.742990 CGCCGTTGAAGATGCCCTAA 60.743 55.000 0.00 0.00 0.00 2.69
553 554 0.733150 GCCGTTGAAGATGCCCTAAC 59.267 55.000 0.00 0.00 0.00 2.34
554 555 1.948611 GCCGTTGAAGATGCCCTAACA 60.949 52.381 0.00 0.00 0.00 2.41
555 556 2.432444 CCGTTGAAGATGCCCTAACAA 58.568 47.619 0.00 0.00 0.00 2.83
556 557 2.161609 CCGTTGAAGATGCCCTAACAAC 59.838 50.000 0.00 0.00 38.12 3.32
557 558 3.074412 CGTTGAAGATGCCCTAACAACT 58.926 45.455 0.00 0.00 38.70 3.16
558 559 3.502211 CGTTGAAGATGCCCTAACAACTT 59.498 43.478 0.00 0.00 38.70 2.66
559 560 4.613622 CGTTGAAGATGCCCTAACAACTTG 60.614 45.833 0.00 0.00 38.70 3.16
560 561 3.420893 TGAAGATGCCCTAACAACTTGG 58.579 45.455 0.00 0.00 33.35 3.61
561 562 3.073798 TGAAGATGCCCTAACAACTTGGA 59.926 43.478 0.00 0.00 33.35 3.53
562 563 3.356529 AGATGCCCTAACAACTTGGAG 57.643 47.619 0.00 0.00 0.00 3.86
563 564 2.644798 AGATGCCCTAACAACTTGGAGT 59.355 45.455 0.00 0.00 0.00 3.85
564 565 3.074538 AGATGCCCTAACAACTTGGAGTT 59.925 43.478 0.00 0.00 39.39 3.01
577 578 6.524101 AACTTGGAGTTGCTAGAAAACAAA 57.476 33.333 10.34 0.00 37.00 2.83
578 579 6.715347 ACTTGGAGTTGCTAGAAAACAAAT 57.285 33.333 10.34 0.00 0.00 2.32
579 580 7.817418 ACTTGGAGTTGCTAGAAAACAAATA 57.183 32.000 10.34 0.00 0.00 1.40
580 581 7.649057 ACTTGGAGTTGCTAGAAAACAAATAC 58.351 34.615 10.34 0.00 0.00 1.89
581 582 7.284489 ACTTGGAGTTGCTAGAAAACAAATACA 59.716 33.333 10.34 1.37 33.20 2.29
582 583 6.966021 TGGAGTTGCTAGAAAACAAATACAC 58.034 36.000 10.34 0.00 30.28 2.90
583 584 6.544197 TGGAGTTGCTAGAAAACAAATACACA 59.456 34.615 10.34 0.00 30.28 3.72
584 585 7.067615 TGGAGTTGCTAGAAAACAAATACACAA 59.932 33.333 10.34 0.00 30.28 3.33
585 586 7.591426 GGAGTTGCTAGAAAACAAATACACAAG 59.409 37.037 10.34 0.00 0.00 3.16
586 587 8.220755 AGTTGCTAGAAAACAAATACACAAGA 57.779 30.769 10.34 0.00 0.00 3.02
587 588 8.345565 AGTTGCTAGAAAACAAATACACAAGAG 58.654 33.333 10.34 0.00 0.00 2.85
588 589 8.342634 GTTGCTAGAAAACAAATACACAAGAGA 58.657 33.333 0.00 0.00 0.00 3.10
589 590 8.445275 TGCTAGAAAACAAATACACAAGAGAA 57.555 30.769 0.00 0.00 0.00 2.87
590 591 8.559536 TGCTAGAAAACAAATACACAAGAGAAG 58.440 33.333 0.00 0.00 0.00 2.85
591 592 8.560374 GCTAGAAAACAAATACACAAGAGAAGT 58.440 33.333 0.00 0.00 0.00 3.01
594 595 8.548721 AGAAAACAAATACACAAGAGAAGTACG 58.451 33.333 0.00 0.00 0.00 3.67
595 596 8.428186 AAAACAAATACACAAGAGAAGTACGA 57.572 30.769 0.00 0.00 0.00 3.43
596 597 8.428186 AAACAAATACACAAGAGAAGTACGAA 57.572 30.769 0.00 0.00 0.00 3.85
597 598 8.603242 AACAAATACACAAGAGAAGTACGAAT 57.397 30.769 0.00 0.00 0.00 3.34
598 599 8.603242 ACAAATACACAAGAGAAGTACGAATT 57.397 30.769 0.00 0.00 0.00 2.17
599 600 8.495949 ACAAATACACAAGAGAAGTACGAATTG 58.504 33.333 0.00 0.00 0.00 2.32
600 601 8.495949 CAAATACACAAGAGAAGTACGAATTGT 58.504 33.333 0.00 0.00 0.00 2.71
601 602 9.701098 AAATACACAAGAGAAGTACGAATTGTA 57.299 29.630 0.00 0.00 30.23 2.41
602 603 9.701098 AATACACAAGAGAAGTACGAATTGTAA 57.299 29.630 0.00 0.09 34.07 2.41
603 604 9.871238 ATACACAAGAGAAGTACGAATTGTAAT 57.129 29.630 0.00 0.00 34.07 1.89
630 631 3.671716 ACCGAGGTAAAATGGTCAAGTC 58.328 45.455 0.00 0.00 0.00 3.01
631 632 3.071892 ACCGAGGTAAAATGGTCAAGTCA 59.928 43.478 0.00 0.00 0.00 3.41
632 633 4.069304 CCGAGGTAAAATGGTCAAGTCAA 58.931 43.478 0.00 0.00 0.00 3.18
633 634 4.154195 CCGAGGTAAAATGGTCAAGTCAAG 59.846 45.833 0.00 0.00 0.00 3.02
635 636 5.334105 CGAGGTAAAATGGTCAAGTCAAGTG 60.334 44.000 0.00 0.00 0.00 3.16
636 637 4.827284 AGGTAAAATGGTCAAGTCAAGTGG 59.173 41.667 0.00 0.00 0.00 4.00
637 638 4.825085 GGTAAAATGGTCAAGTCAAGTGGA 59.175 41.667 0.00 0.00 0.00 4.02
638 639 5.476945 GGTAAAATGGTCAAGTCAAGTGGAT 59.523 40.000 0.00 0.00 0.00 3.41
639 640 5.712152 AAAATGGTCAAGTCAAGTGGATC 57.288 39.130 0.00 0.00 0.00 3.36
640 641 2.859165 TGGTCAAGTCAAGTGGATCC 57.141 50.000 4.20 4.20 0.00 3.36
815 816 3.493873 CCTCGCCCATTTACTTACTACCC 60.494 52.174 0.00 0.00 0.00 3.69
957 958 2.158449 GCTCTCAATTGTTCCTGTGTCG 59.842 50.000 5.13 0.00 0.00 4.35
981 982 1.248785 CCGTCTCTCCGTCTCCCAAA 61.249 60.000 0.00 0.00 0.00 3.28
1065 1073 6.402118 GCTTCGATGCTTGTACTTGATTTGTA 60.402 38.462 15.51 0.00 0.00 2.41
1097 1105 3.103742 AGGCTCCCTTTGTTTGTTTTGA 58.896 40.909 0.00 0.00 0.00 2.69
1098 1106 3.711190 AGGCTCCCTTTGTTTGTTTTGAT 59.289 39.130 0.00 0.00 0.00 2.57
1099 1107 4.164030 AGGCTCCCTTTGTTTGTTTTGATT 59.836 37.500 0.00 0.00 0.00 2.57
1100 1108 4.881273 GGCTCCCTTTGTTTGTTTTGATTT 59.119 37.500 0.00 0.00 0.00 2.17
1101 1109 5.007626 GGCTCCCTTTGTTTGTTTTGATTTC 59.992 40.000 0.00 0.00 0.00 2.17
1238 1246 2.327568 CGGCCACAATTTTAGCACTTG 58.672 47.619 2.24 0.00 0.00 3.16
1251 1259 2.045926 ACTTGGGTCTGCATCGCC 60.046 61.111 0.00 0.00 0.00 5.54
1303 1314 7.284489 TCCATCCAAAATAAACCCTAATCTTCG 59.716 37.037 0.00 0.00 0.00 3.79
1738 1749 2.328099 GCTGTTTCAGGAGGTGCCG 61.328 63.158 0.00 0.00 43.43 5.69
1903 1914 1.404717 GCCGAGATCTTCAAGCACAGA 60.405 52.381 0.00 0.00 0.00 3.41
2035 2052 4.338539 GACGTGGTGTCCGTCGCT 62.339 66.667 0.00 0.00 44.29 4.93
2176 2193 5.936187 TTGGTTGACATGCATGGATTTAT 57.064 34.783 29.41 8.33 0.00 1.40
2181 2198 5.601583 TGACATGCATGGATTTATTTGCT 57.398 34.783 29.41 4.67 36.10 3.91
2257 2274 8.934507 ACTTTATGTGCAAGTATAACTCTCTC 57.065 34.615 0.00 0.00 32.48 3.20
2258 2275 8.754080 ACTTTATGTGCAAGTATAACTCTCTCT 58.246 33.333 0.00 0.00 32.48 3.10
2304 2321 6.767524 ACTAGATATAGCTGCTGTGGATAC 57.232 41.667 13.43 0.00 0.00 2.24
2401 2420 4.446385 CAGTGTGATTGCTTGGTTGATTTG 59.554 41.667 0.00 0.00 0.00 2.32
2402 2421 4.099881 AGTGTGATTGCTTGGTTGATTTGT 59.900 37.500 0.00 0.00 0.00 2.83
2403 2422 5.301551 AGTGTGATTGCTTGGTTGATTTGTA 59.698 36.000 0.00 0.00 0.00 2.41
2407 2444 7.714377 TGTGATTGCTTGGTTGATTTGTAAAAT 59.286 29.630 0.00 0.00 0.00 1.82
2408 2445 9.202273 GTGATTGCTTGGTTGATTTGTAAAATA 57.798 29.630 0.00 0.00 0.00 1.40
2462 2796 6.436532 ACACTAGTTGCTAGGCTTAGAAGTTA 59.563 38.462 7.11 0.00 38.30 2.24
2677 3012 5.733226 ATGATTGATACGAATTTGCGTGA 57.267 34.783 2.68 0.00 45.23 4.35
2953 3295 4.815308 GCTCTGAAATGACACATATGAGCT 59.185 41.667 10.38 0.00 40.55 4.09
3010 3352 4.227538 GCATGCATGTCAATTCTGATAGC 58.772 43.478 26.79 4.38 33.05 2.97
3147 3489 9.571810 TGATATGACAAATTGAAATTAGTGCAC 57.428 29.630 9.40 9.40 0.00 4.57
3156 3498 7.759489 ATTGAAATTAGTGCACCTACAGAAA 57.241 32.000 14.63 1.75 0.00 2.52
3161 3503 2.862541 AGTGCACCTACAGAAATTGCA 58.137 42.857 14.63 0.00 40.81 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.250770 ACGCTTTTCTTCCACCCTCC 60.251 55.000 0.00 0.00 0.00 4.30
1 2 0.875059 CACGCTTTTCTTCCACCCTC 59.125 55.000 0.00 0.00 0.00 4.30
2 3 0.537371 CCACGCTTTTCTTCCACCCT 60.537 55.000 0.00 0.00 0.00 4.34
3 4 1.524008 CCCACGCTTTTCTTCCACCC 61.524 60.000 0.00 0.00 0.00 4.61
4 5 0.536460 TCCCACGCTTTTCTTCCACC 60.536 55.000 0.00 0.00 0.00 4.61
5 6 1.314730 TTCCCACGCTTTTCTTCCAC 58.685 50.000 0.00 0.00 0.00 4.02
6 7 2.286365 ATTCCCACGCTTTTCTTCCA 57.714 45.000 0.00 0.00 0.00 3.53
7 8 2.352715 CCAATTCCCACGCTTTTCTTCC 60.353 50.000 0.00 0.00 0.00 3.46
8 9 2.352715 CCCAATTCCCACGCTTTTCTTC 60.353 50.000 0.00 0.00 0.00 2.87
9 10 1.618343 CCCAATTCCCACGCTTTTCTT 59.382 47.619 0.00 0.00 0.00 2.52
10 11 1.256812 CCCAATTCCCACGCTTTTCT 58.743 50.000 0.00 0.00 0.00 2.52
11 12 0.389817 GCCCAATTCCCACGCTTTTC 60.390 55.000 0.00 0.00 0.00 2.29
12 13 1.671166 GCCCAATTCCCACGCTTTT 59.329 52.632 0.00 0.00 0.00 2.27
13 14 2.635443 CGCCCAATTCCCACGCTTT 61.635 57.895 0.00 0.00 0.00 3.51
14 15 3.061848 CGCCCAATTCCCACGCTT 61.062 61.111 0.00 0.00 0.00 4.68
17 18 2.824041 CTCCGCCCAATTCCCACG 60.824 66.667 0.00 0.00 0.00 4.94
18 19 1.452108 CTCTCCGCCCAATTCCCAC 60.452 63.158 0.00 0.00 0.00 4.61
19 20 2.998097 CTCTCCGCCCAATTCCCA 59.002 61.111 0.00 0.00 0.00 4.37
20 21 2.517166 GCTCTCCGCCCAATTCCC 60.517 66.667 0.00 0.00 0.00 3.97
21 22 2.897350 CGCTCTCCGCCCAATTCC 60.897 66.667 0.00 0.00 34.21 3.01
22 23 2.897350 CCGCTCTCCGCCCAATTC 60.897 66.667 0.00 0.00 35.03 2.17
31 32 4.918201 CATTCCCCGCCGCTCTCC 62.918 72.222 0.00 0.00 0.00 3.71
32 33 4.918201 CCATTCCCCGCCGCTCTC 62.918 72.222 0.00 0.00 0.00 3.20
34 35 3.809374 CTACCATTCCCCGCCGCTC 62.809 68.421 0.00 0.00 0.00 5.03
35 36 3.861797 CTACCATTCCCCGCCGCT 61.862 66.667 0.00 0.00 0.00 5.52
36 37 3.394635 TTCTACCATTCCCCGCCGC 62.395 63.158 0.00 0.00 0.00 6.53
37 38 1.227556 CTTCTACCATTCCCCGCCG 60.228 63.158 0.00 0.00 0.00 6.46
38 39 1.148498 CCTTCTACCATTCCCCGCC 59.852 63.158 0.00 0.00 0.00 6.13
39 40 1.148498 CCCTTCTACCATTCCCCGC 59.852 63.158 0.00 0.00 0.00 6.13
40 41 0.468648 GTCCCTTCTACCATTCCCCG 59.531 60.000 0.00 0.00 0.00 5.73
41 42 1.894699 AGTCCCTTCTACCATTCCCC 58.105 55.000 0.00 0.00 0.00 4.81
42 43 2.973406 CCTAGTCCCTTCTACCATTCCC 59.027 54.545 0.00 0.00 0.00 3.97
43 44 2.973406 CCCTAGTCCCTTCTACCATTCC 59.027 54.545 0.00 0.00 0.00 3.01
44 45 2.973406 CCCCTAGTCCCTTCTACCATTC 59.027 54.545 0.00 0.00 0.00 2.67
45 46 2.321296 ACCCCTAGTCCCTTCTACCATT 59.679 50.000 0.00 0.00 0.00 3.16
46 47 1.945317 ACCCCTAGTCCCTTCTACCAT 59.055 52.381 0.00 0.00 0.00 3.55
47 48 1.400941 ACCCCTAGTCCCTTCTACCA 58.599 55.000 0.00 0.00 0.00 3.25
48 49 2.564872 AACCCCTAGTCCCTTCTACC 57.435 55.000 0.00 0.00 0.00 3.18
49 50 4.567116 CCAAAAACCCCTAGTCCCTTCTAC 60.567 50.000 0.00 0.00 0.00 2.59
50 51 3.590182 CCAAAAACCCCTAGTCCCTTCTA 59.410 47.826 0.00 0.00 0.00 2.10
51 52 2.378886 CCAAAAACCCCTAGTCCCTTCT 59.621 50.000 0.00 0.00 0.00 2.85
52 53 2.803956 CCAAAAACCCCTAGTCCCTTC 58.196 52.381 0.00 0.00 0.00 3.46
53 54 1.203137 GCCAAAAACCCCTAGTCCCTT 60.203 52.381 0.00 0.00 0.00 3.95
54 55 0.408309 GCCAAAAACCCCTAGTCCCT 59.592 55.000 0.00 0.00 0.00 4.20
55 56 0.963856 CGCCAAAAACCCCTAGTCCC 60.964 60.000 0.00 0.00 0.00 4.46
56 57 1.592400 GCGCCAAAAACCCCTAGTCC 61.592 60.000 0.00 0.00 0.00 3.85
57 58 1.880894 GCGCCAAAAACCCCTAGTC 59.119 57.895 0.00 0.00 0.00 2.59
58 59 1.969589 CGCGCCAAAAACCCCTAGT 60.970 57.895 0.00 0.00 0.00 2.57
59 60 1.238625 TTCGCGCCAAAAACCCCTAG 61.239 55.000 0.00 0.00 0.00 3.02
60 61 0.822532 TTTCGCGCCAAAAACCCCTA 60.823 50.000 0.00 0.00 0.00 3.53
61 62 1.677637 TTTTCGCGCCAAAAACCCCT 61.678 50.000 10.58 0.00 0.00 4.79
62 63 1.227292 TTTTCGCGCCAAAAACCCC 60.227 52.632 10.58 0.00 0.00 4.95
63 64 0.806492 TGTTTTCGCGCCAAAAACCC 60.806 50.000 28.63 14.54 42.98 4.11
64 65 0.574922 CTGTTTTCGCGCCAAAAACC 59.425 50.000 28.63 15.10 42.98 3.27
65 66 1.006494 CACTGTTTTCGCGCCAAAAAC 60.006 47.619 26.69 26.69 43.60 2.43
66 67 1.272781 CACTGTTTTCGCGCCAAAAA 58.727 45.000 14.53 12.23 0.00 1.94
67 68 1.142778 GCACTGTTTTCGCGCCAAAA 61.143 50.000 8.92 8.92 0.00 2.44
68 69 1.587613 GCACTGTTTTCGCGCCAAA 60.588 52.632 0.00 0.00 0.00 3.28
69 70 2.025441 GCACTGTTTTCGCGCCAA 59.975 55.556 0.00 0.00 0.00 4.52
70 71 4.306471 CGCACTGTTTTCGCGCCA 62.306 61.111 0.00 0.00 42.79 5.69
74 75 1.154225 CATCCCGCACTGTTTTCGC 60.154 57.895 0.00 0.00 0.00 4.70
75 76 1.154225 GCATCCCGCACTGTTTTCG 60.154 57.895 0.00 0.00 41.79 3.46
76 77 1.130561 GTAGCATCCCGCACTGTTTTC 59.869 52.381 0.00 0.00 46.13 2.29
77 78 1.165270 GTAGCATCCCGCACTGTTTT 58.835 50.000 0.00 0.00 46.13 2.43
78 79 0.036164 TGTAGCATCCCGCACTGTTT 59.964 50.000 0.00 0.00 46.13 2.83
79 80 0.036164 TTGTAGCATCCCGCACTGTT 59.964 50.000 0.00 0.00 46.13 3.16
80 81 0.036164 TTTGTAGCATCCCGCACTGT 59.964 50.000 0.00 0.00 46.13 3.55
81 82 1.131126 CTTTTGTAGCATCCCGCACTG 59.869 52.381 0.00 0.00 46.13 3.66
82 83 1.453155 CTTTTGTAGCATCCCGCACT 58.547 50.000 0.00 0.00 46.13 4.40
83 84 3.996825 CTTTTGTAGCATCCCGCAC 57.003 52.632 0.00 0.00 46.13 5.34
108 109 0.598065 CACCCAAAAAGAAGGCGGAG 59.402 55.000 0.00 0.00 0.00 4.63
109 110 0.825840 CCACCCAAAAAGAAGGCGGA 60.826 55.000 0.00 0.00 0.00 5.54
110 111 1.665442 CCACCCAAAAAGAAGGCGG 59.335 57.895 0.00 0.00 0.00 6.13
111 112 1.665442 CCCACCCAAAAAGAAGGCG 59.335 57.895 0.00 0.00 0.00 5.52
112 113 1.371183 GCCCACCCAAAAAGAAGGC 59.629 57.895 0.00 0.00 0.00 4.35
113 114 1.815817 CGGCCCACCCAAAAAGAAGG 61.816 60.000 0.00 0.00 0.00 3.46
114 115 1.665442 CGGCCCACCCAAAAAGAAG 59.335 57.895 0.00 0.00 0.00 2.85
115 116 1.834822 CCGGCCCACCCAAAAAGAA 60.835 57.895 0.00 0.00 0.00 2.52
116 117 2.203567 CCGGCCCACCCAAAAAGA 60.204 61.111 0.00 0.00 0.00 2.52
117 118 3.310307 CCCGGCCCACCCAAAAAG 61.310 66.667 0.00 0.00 0.00 2.27
118 119 4.944069 CCCCGGCCCACCCAAAAA 62.944 66.667 0.00 0.00 0.00 1.94
133 134 1.066757 GAAACGTCGATCTCTACCCCC 59.933 57.143 0.00 0.00 0.00 5.40
134 135 2.488639 GAAACGTCGATCTCTACCCC 57.511 55.000 0.00 0.00 0.00 4.95
423 424 0.234884 CCGCGAACTGAAGACAAACC 59.765 55.000 8.23 0.00 0.00 3.27
424 425 0.234884 CCCGCGAACTGAAGACAAAC 59.765 55.000 8.23 0.00 0.00 2.93
425 426 0.105224 TCCCGCGAACTGAAGACAAA 59.895 50.000 8.23 0.00 0.00 2.83
426 427 0.319555 CTCCCGCGAACTGAAGACAA 60.320 55.000 8.23 0.00 0.00 3.18
427 428 1.176619 TCTCCCGCGAACTGAAGACA 61.177 55.000 8.23 0.00 0.00 3.41
428 429 0.038526 TTCTCCCGCGAACTGAAGAC 60.039 55.000 8.23 0.00 0.00 3.01
429 430 0.677288 TTTCTCCCGCGAACTGAAGA 59.323 50.000 8.23 0.00 0.00 2.87
430 431 1.194772 GTTTTCTCCCGCGAACTGAAG 59.805 52.381 8.23 0.00 0.00 3.02
431 432 1.223187 GTTTTCTCCCGCGAACTGAA 58.777 50.000 8.23 3.55 0.00 3.02
432 433 0.105224 TGTTTTCTCCCGCGAACTGA 59.895 50.000 8.23 0.00 0.00 3.41
433 434 1.135972 CATGTTTTCTCCCGCGAACTG 60.136 52.381 8.23 0.00 0.00 3.16
434 435 1.156736 CATGTTTTCTCCCGCGAACT 58.843 50.000 8.23 0.00 0.00 3.01
435 436 0.872388 ACATGTTTTCTCCCGCGAAC 59.128 50.000 8.23 2.92 0.00 3.95
436 437 1.153353 GACATGTTTTCTCCCGCGAA 58.847 50.000 8.23 0.00 0.00 4.70
437 438 0.320374 AGACATGTTTTCTCCCGCGA 59.680 50.000 8.23 0.00 0.00 5.87
438 439 0.443869 CAGACATGTTTTCTCCCGCG 59.556 55.000 0.00 0.00 0.00 6.46
439 440 1.808411 TCAGACATGTTTTCTCCCGC 58.192 50.000 0.00 0.00 0.00 6.13
440 441 4.002982 TGATTCAGACATGTTTTCTCCCG 58.997 43.478 0.00 0.00 0.00 5.14
441 442 4.142816 CGTGATTCAGACATGTTTTCTCCC 60.143 45.833 0.00 0.00 0.00 4.30
442 443 4.670221 GCGTGATTCAGACATGTTTTCTCC 60.670 45.833 0.00 0.00 0.00 3.71
443 444 4.398247 GCGTGATTCAGACATGTTTTCTC 58.602 43.478 0.00 0.00 0.00 2.87
444 445 3.189287 GGCGTGATTCAGACATGTTTTCT 59.811 43.478 0.00 0.00 0.00 2.52
445 446 3.492313 GGCGTGATTCAGACATGTTTTC 58.508 45.455 0.00 0.00 0.00 2.29
446 447 2.095768 CGGCGTGATTCAGACATGTTTT 60.096 45.455 0.00 0.00 0.00 2.43
447 448 1.464608 CGGCGTGATTCAGACATGTTT 59.535 47.619 0.00 0.00 0.00 2.83
448 449 1.078709 CGGCGTGATTCAGACATGTT 58.921 50.000 0.00 0.00 0.00 2.71
449 450 0.037326 ACGGCGTGATTCAGACATGT 60.037 50.000 13.76 0.00 0.00 3.21
450 451 1.921243 TACGGCGTGATTCAGACATG 58.079 50.000 24.86 0.00 0.00 3.21
451 452 2.540515 CTTACGGCGTGATTCAGACAT 58.459 47.619 24.86 0.00 0.00 3.06
452 453 1.990799 CTTACGGCGTGATTCAGACA 58.009 50.000 24.86 0.00 0.00 3.41
453 454 0.645868 GCTTACGGCGTGATTCAGAC 59.354 55.000 24.86 0.00 0.00 3.51
454 455 0.459585 GGCTTACGGCGTGATTCAGA 60.460 55.000 24.86 0.00 42.94 3.27
455 456 2.006772 GGCTTACGGCGTGATTCAG 58.993 57.895 24.86 11.27 42.94 3.02
456 457 4.195308 GGCTTACGGCGTGATTCA 57.805 55.556 24.86 0.00 42.94 2.57
464 465 1.206523 GTTCTGTATCGGCTTACGGC 58.793 55.000 0.00 0.00 44.45 5.68
465 466 1.849097 GGTTCTGTATCGGCTTACGG 58.151 55.000 0.00 0.00 44.45 4.02
466 467 1.474017 CGGTTCTGTATCGGCTTACG 58.526 55.000 0.00 0.00 46.11 3.18
467 468 1.206523 GCGGTTCTGTATCGGCTTAC 58.793 55.000 0.00 0.00 0.00 2.34
468 469 0.248743 CGCGGTTCTGTATCGGCTTA 60.249 55.000 0.00 0.00 0.00 3.09
469 470 1.518572 CGCGGTTCTGTATCGGCTT 60.519 57.895 0.00 0.00 0.00 4.35
470 471 2.104331 CGCGGTTCTGTATCGGCT 59.896 61.111 0.00 0.00 0.00 5.52
471 472 1.808390 AACGCGGTTCTGTATCGGC 60.808 57.895 12.47 0.00 0.00 5.54
472 473 1.418342 CCAACGCGGTTCTGTATCGG 61.418 60.000 12.47 0.00 0.00 4.18
473 474 0.457166 TCCAACGCGGTTCTGTATCG 60.457 55.000 12.47 0.00 35.57 2.92
474 475 0.997196 GTCCAACGCGGTTCTGTATC 59.003 55.000 12.47 0.00 35.57 2.24
475 476 0.734942 CGTCCAACGCGGTTCTGTAT 60.735 55.000 12.47 0.00 33.65 2.29
476 477 1.372004 CGTCCAACGCGGTTCTGTA 60.372 57.895 12.47 0.00 33.65 2.74
477 478 2.660552 CGTCCAACGCGGTTCTGT 60.661 61.111 12.47 0.00 33.65 3.41
478 479 3.411351 CCGTCCAACGCGGTTCTG 61.411 66.667 12.47 1.55 43.84 3.02
505 506 4.838152 CTCCCACATGCGTCCGGG 62.838 72.222 0.00 3.07 40.32 5.73
506 507 4.838152 CCTCCCACATGCGTCCGG 62.838 72.222 0.00 0.00 0.00 5.14
507 508 3.605749 AACCTCCCACATGCGTCCG 62.606 63.158 0.00 0.00 0.00 4.79
508 509 1.303317 AAACCTCCCACATGCGTCC 60.303 57.895 0.00 0.00 0.00 4.79
509 510 1.875963 CAAACCTCCCACATGCGTC 59.124 57.895 0.00 0.00 0.00 5.19
510 511 2.268076 GCAAACCTCCCACATGCGT 61.268 57.895 0.00 0.00 0.00 5.24
511 512 2.568090 GCAAACCTCCCACATGCG 59.432 61.111 0.00 0.00 0.00 4.73
512 513 2.568090 CGCAAACCTCCCACATGC 59.432 61.111 0.00 0.00 0.00 4.06
513 514 2.342650 CCCGCAAACCTCCCACATG 61.343 63.158 0.00 0.00 0.00 3.21
514 515 2.035626 CCCGCAAACCTCCCACAT 59.964 61.111 0.00 0.00 0.00 3.21
515 516 3.485346 GACCCGCAAACCTCCCACA 62.485 63.158 0.00 0.00 0.00 4.17
516 517 2.671963 GACCCGCAAACCTCCCAC 60.672 66.667 0.00 0.00 0.00 4.61
517 518 4.323477 CGACCCGCAAACCTCCCA 62.323 66.667 0.00 0.00 0.00 4.37
529 530 2.750888 GCATCTTCAACGGCGACCC 61.751 63.158 16.62 0.00 0.00 4.46
530 531 2.750888 GGCATCTTCAACGGCGACC 61.751 63.158 16.62 0.00 0.00 4.79
531 532 2.750888 GGGCATCTTCAACGGCGAC 61.751 63.158 16.62 0.00 0.00 5.19
532 533 1.609635 TAGGGCATCTTCAACGGCGA 61.610 55.000 16.62 0.00 0.00 5.54
533 534 0.742990 TTAGGGCATCTTCAACGGCG 60.743 55.000 4.80 4.80 0.00 6.46
534 535 0.733150 GTTAGGGCATCTTCAACGGC 59.267 55.000 0.00 0.00 0.00 5.68
535 536 2.107950 TGTTAGGGCATCTTCAACGG 57.892 50.000 0.00 0.00 0.00 4.44
536 537 3.074412 AGTTGTTAGGGCATCTTCAACG 58.926 45.455 14.40 0.00 40.48 4.10
537 538 4.321230 CCAAGTTGTTAGGGCATCTTCAAC 60.321 45.833 1.45 13.42 38.31 3.18
538 539 3.826157 CCAAGTTGTTAGGGCATCTTCAA 59.174 43.478 1.45 0.00 0.00 2.69
539 540 3.073798 TCCAAGTTGTTAGGGCATCTTCA 59.926 43.478 1.45 0.00 0.00 3.02
540 541 3.686016 TCCAAGTTGTTAGGGCATCTTC 58.314 45.455 1.45 0.00 0.00 2.87
541 542 3.074538 ACTCCAAGTTGTTAGGGCATCTT 59.925 43.478 1.45 0.00 0.00 2.40
542 543 2.644798 ACTCCAAGTTGTTAGGGCATCT 59.355 45.455 1.45 0.00 0.00 2.90
543 544 3.073274 ACTCCAAGTTGTTAGGGCATC 57.927 47.619 1.45 0.00 0.00 3.91
544 545 3.525800 AACTCCAAGTTGTTAGGGCAT 57.474 42.857 1.45 0.00 37.00 4.40
554 555 6.524101 TTTGTTTTCTAGCAACTCCAAGTT 57.476 33.333 6.29 0.00 39.39 2.66
555 556 6.715347 ATTTGTTTTCTAGCAACTCCAAGT 57.285 33.333 6.29 0.00 0.00 3.16
556 557 7.591426 GTGTATTTGTTTTCTAGCAACTCCAAG 59.409 37.037 6.29 0.00 0.00 3.61
557 558 7.067615 TGTGTATTTGTTTTCTAGCAACTCCAA 59.932 33.333 6.29 0.00 0.00 3.53
558 559 6.544197 TGTGTATTTGTTTTCTAGCAACTCCA 59.456 34.615 6.29 0.00 0.00 3.86
559 560 6.966021 TGTGTATTTGTTTTCTAGCAACTCC 58.034 36.000 6.29 0.00 0.00 3.85
560 561 8.342634 TCTTGTGTATTTGTTTTCTAGCAACTC 58.657 33.333 6.29 0.00 0.00 3.01
561 562 8.220755 TCTTGTGTATTTGTTTTCTAGCAACT 57.779 30.769 6.29 0.00 0.00 3.16
562 563 8.342634 TCTCTTGTGTATTTGTTTTCTAGCAAC 58.657 33.333 0.00 0.00 0.00 4.17
563 564 8.445275 TCTCTTGTGTATTTGTTTTCTAGCAA 57.555 30.769 0.00 0.00 0.00 3.91
564 565 8.445275 TTCTCTTGTGTATTTGTTTTCTAGCA 57.555 30.769 0.00 0.00 0.00 3.49
565 566 8.560374 ACTTCTCTTGTGTATTTGTTTTCTAGC 58.440 33.333 0.00 0.00 0.00 3.42
568 569 8.548721 CGTACTTCTCTTGTGTATTTGTTTTCT 58.451 33.333 0.00 0.00 0.00 2.52
569 570 8.545420 TCGTACTTCTCTTGTGTATTTGTTTTC 58.455 33.333 0.00 0.00 0.00 2.29
570 571 8.428186 TCGTACTTCTCTTGTGTATTTGTTTT 57.572 30.769 0.00 0.00 0.00 2.43
571 572 8.428186 TTCGTACTTCTCTTGTGTATTTGTTT 57.572 30.769 0.00 0.00 0.00 2.83
572 573 8.603242 ATTCGTACTTCTCTTGTGTATTTGTT 57.397 30.769 0.00 0.00 0.00 2.83
573 574 8.495949 CAATTCGTACTTCTCTTGTGTATTTGT 58.504 33.333 0.00 0.00 0.00 2.83
574 575 8.495949 ACAATTCGTACTTCTCTTGTGTATTTG 58.504 33.333 0.00 0.00 0.00 2.32
575 576 8.603242 ACAATTCGTACTTCTCTTGTGTATTT 57.397 30.769 0.00 0.00 0.00 1.40
576 577 9.701098 TTACAATTCGTACTTCTCTTGTGTATT 57.299 29.630 0.00 0.00 0.00 1.89
577 578 9.871238 ATTACAATTCGTACTTCTCTTGTGTAT 57.129 29.630 0.00 0.00 0.00 2.29
578 579 9.701098 AATTACAATTCGTACTTCTCTTGTGTA 57.299 29.630 0.00 0.00 0.00 2.90
579 580 8.603242 AATTACAATTCGTACTTCTCTTGTGT 57.397 30.769 0.00 0.00 0.00 3.72
580 581 9.318041 CAAATTACAATTCGTACTTCTCTTGTG 57.682 33.333 0.00 0.00 0.00 3.33
581 582 9.052759 ACAAATTACAATTCGTACTTCTCTTGT 57.947 29.630 0.00 0.00 0.00 3.16
585 586 9.750882 GGTTACAAATTACAATTCGTACTTCTC 57.249 33.333 0.00 0.00 0.00 2.87
586 587 8.437742 CGGTTACAAATTACAATTCGTACTTCT 58.562 33.333 0.00 0.00 0.00 2.85
587 588 8.434661 TCGGTTACAAATTACAATTCGTACTTC 58.565 33.333 0.00 0.00 0.00 3.01
588 589 8.309163 TCGGTTACAAATTACAATTCGTACTT 57.691 30.769 0.00 0.00 0.00 2.24
589 590 7.063780 CCTCGGTTACAAATTACAATTCGTACT 59.936 37.037 0.00 0.00 0.00 2.73
590 591 7.148590 ACCTCGGTTACAAATTACAATTCGTAC 60.149 37.037 0.00 0.00 0.00 3.67
591 592 6.873076 ACCTCGGTTACAAATTACAATTCGTA 59.127 34.615 0.00 0.00 0.00 3.43
592 593 5.702209 ACCTCGGTTACAAATTACAATTCGT 59.298 36.000 0.00 0.00 0.00 3.85
593 594 6.173191 ACCTCGGTTACAAATTACAATTCG 57.827 37.500 0.00 0.00 0.00 3.34
594 595 9.896263 TTTTACCTCGGTTACAAATTACAATTC 57.104 29.630 0.00 0.00 0.00 2.17
596 597 9.849166 CATTTTACCTCGGTTACAAATTACAAT 57.151 29.630 0.00 0.00 0.00 2.71
597 598 8.298140 CCATTTTACCTCGGTTACAAATTACAA 58.702 33.333 0.00 0.00 0.00 2.41
598 599 7.447853 ACCATTTTACCTCGGTTACAAATTACA 59.552 33.333 0.00 0.00 0.00 2.41
599 600 7.819644 ACCATTTTACCTCGGTTACAAATTAC 58.180 34.615 0.00 0.00 0.00 1.89
600 601 7.664731 TGACCATTTTACCTCGGTTACAAATTA 59.335 33.333 0.00 0.00 0.00 1.40
601 602 6.490721 TGACCATTTTACCTCGGTTACAAATT 59.509 34.615 0.00 0.00 0.00 1.82
602 603 6.005198 TGACCATTTTACCTCGGTTACAAAT 58.995 36.000 0.00 0.00 0.00 2.32
603 604 5.374921 TGACCATTTTACCTCGGTTACAAA 58.625 37.500 0.00 0.00 0.00 2.83
630 631 1.077212 CTGCCTGGGGATCCACTTG 60.077 63.158 16.81 7.28 38.32 3.16
631 632 2.988839 GCTGCCTGGGGATCCACTT 61.989 63.158 16.81 0.00 38.32 3.16
632 633 3.415087 GCTGCCTGGGGATCCACT 61.415 66.667 16.81 0.00 38.32 4.00
633 634 2.900671 GAAGCTGCCTGGGGATCCAC 62.901 65.000 15.23 11.51 38.32 4.02
635 636 1.931007 AAGAAGCTGCCTGGGGATCC 61.931 60.000 1.92 1.92 0.00 3.36
636 637 0.750911 CAAGAAGCTGCCTGGGGATC 60.751 60.000 0.00 0.00 0.00 3.36
637 638 1.305623 CAAGAAGCTGCCTGGGGAT 59.694 57.895 0.00 0.00 0.00 3.85
638 639 1.719063 AACAAGAAGCTGCCTGGGGA 61.719 55.000 0.00 0.00 0.00 4.81
639 640 0.829182 AAACAAGAAGCTGCCTGGGG 60.829 55.000 0.00 0.00 0.00 4.96
640 641 1.000171 GAAAACAAGAAGCTGCCTGGG 60.000 52.381 0.00 0.00 0.00 4.45
815 816 3.957747 CGTAAAGCATGCACACAATTG 57.042 42.857 21.98 3.24 0.00 2.32
957 958 0.728542 GAGACGGAGAGACGGAGAAC 59.271 60.000 0.00 0.00 38.39 3.01
981 982 3.215245 GAGGCATGCTCTCCTCGT 58.785 61.111 18.92 0.00 39.43 4.18
1097 1105 8.331740 TCTTCTGACCAGAAAGGATAATGAAAT 58.668 33.333 12.82 0.00 45.75 2.17
1098 1106 7.689299 TCTTCTGACCAGAAAGGATAATGAAA 58.311 34.615 12.82 0.00 45.75 2.69
1099 1107 7.257790 TCTTCTGACCAGAAAGGATAATGAA 57.742 36.000 12.82 0.00 45.75 2.57
1100 1108 6.874278 TCTTCTGACCAGAAAGGATAATGA 57.126 37.500 12.82 2.85 45.75 2.57
1101 1109 7.992033 AGATTCTTCTGACCAGAAAGGATAATG 59.008 37.037 12.82 0.76 45.75 1.90
1251 1259 2.028125 TAGCGGGGATCTCAAAGCGG 62.028 60.000 0.00 0.00 0.00 5.52
1303 1314 3.732849 CTCCCTGGTGGAAGCCCC 61.733 72.222 0.00 0.00 44.57 5.80
1460 1471 4.215742 CTATGTTCGGGGCGCCGA 62.216 66.667 37.74 37.74 40.60 5.54
1468 1479 2.279252 CGGGGTCGCTATGTTCGG 60.279 66.667 0.00 0.00 0.00 4.30
1658 1669 0.745486 CGGACGGTGGAATTAACCCC 60.745 60.000 4.58 1.15 33.88 4.95
1659 1670 0.036105 ACGGACGGTGGAATTAACCC 60.036 55.000 4.58 0.00 33.88 4.11
1937 1954 0.109919 TCGTCGTCGACAATGAGGTG 60.110 55.000 24.13 6.28 41.35 4.00
2035 2052 3.249189 ACTTCTTGGCCGGCCTCA 61.249 61.111 43.34 29.40 36.94 3.86
2176 2193 3.256383 CCATCAATCACCAGAACAGCAAA 59.744 43.478 0.00 0.00 0.00 3.68
2181 2198 4.225717 TGATCTCCATCAATCACCAGAACA 59.774 41.667 0.00 0.00 35.99 3.18
2304 2321 4.021981 GGACAATCTTTTTCTCACCCAAGG 60.022 45.833 0.00 0.00 0.00 3.61
2414 2451 6.097839 TGTCAGTTAAAGTGTGAACTCTAGGT 59.902 38.462 0.00 0.00 33.60 3.08
2416 2453 7.203910 AGTGTCAGTTAAAGTGTGAACTCTAG 58.796 38.462 0.00 0.00 33.60 2.43
2422 2459 6.036735 GCAACTAGTGTCAGTTAAAGTGTGAA 59.963 38.462 0.00 0.00 36.61 3.18
2677 3012 5.142061 TCATGAACATGCTGAAAATGCTT 57.858 34.783 9.59 0.00 38.65 3.91
2868 3208 8.141268 TGATTGTAAACCCTTTTCAGCTTAAAG 58.859 33.333 9.98 9.98 33.42 1.85
2869 3209 8.012957 TGATTGTAAACCCTTTTCAGCTTAAA 57.987 30.769 0.00 0.00 0.00 1.52
2870 3210 7.589958 TGATTGTAAACCCTTTTCAGCTTAA 57.410 32.000 0.00 0.00 0.00 1.85
2925 3267 8.969260 TCATATGTGTCATTTCAGAGCTAATT 57.031 30.769 1.90 0.00 0.00 1.40
2934 3276 5.939296 TGTCAAGCTCATATGTGTCATTTCA 59.061 36.000 1.90 0.00 0.00 2.69
3103 3445 9.035607 GTCATATCAATGTACAGTTCTACTTGG 57.964 37.037 0.33 0.00 34.50 3.61


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

AutoCloner maintained by Alex Coulton.