Multiple sequence alignment - TraesCS7A01G421300

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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 TraesCS7A01G421300 chr7A 100.000 3125 0 0 1 3125 612380364 612377240 0.000000e+00 5771.0
1 TraesCS7A01G421300 chr7A 91.176 102 9 0 2829 2930 279180090 279180191 4.200000e-29 139.0
2 TraesCS7A01G421300 chr7D 96.430 2521 85 5 609 3125 531835795 531833276 0.000000e+00 4152.0
3 TraesCS7A01G421300 chr7D 79.573 656 83 31 1948 2573 531832089 531831455 3.730000e-114 422.0
4 TraesCS7A01G421300 chr7D 91.760 267 22 0 145 411 531836058 531835792 3.810000e-99 372.0
5 TraesCS7A01G421300 chr7D 91.176 102 9 0 2829 2930 258222765 258222866 4.200000e-29 139.0
6 TraesCS7A01G421300 chr7B 94.945 2532 88 12 609 3125 572403039 572400533 0.000000e+00 3930.0
7 TraesCS7A01G421300 chr7B 84.404 218 30 4 408 622 388845440 388845656 8.780000e-51 211.0
8 TraesCS7A01G421300 chr7B 83.590 195 22 6 2256 2445 572398868 572398679 1.150000e-39 174.0
9 TraesCS7A01G421300 chr7B 86.585 82 9 2 2830 2910 418753000 418752920 4.290000e-14 89.8
10 TraesCS7A01G421300 chr6A 85.427 199 28 1 414 611 556682718 556682520 4.090000e-49 206.0
11 TraesCS7A01G421300 chr3B 86.667 165 19 3 446 608 450836622 450836785 2.480000e-41 180.0
12 TraesCS7A01G421300 chr3B 82.178 202 30 6 414 610 409870762 409870562 5.360000e-38 169.0
13 TraesCS7A01G421300 chr5B 87.500 152 17 2 460 610 83795694 83795544 1.150000e-39 174.0
14 TraesCS7A01G421300 chr5A 82.524 206 28 8 414 615 338237568 338237769 1.150000e-39 174.0
15 TraesCS7A01G421300 chr5A 89.024 82 7 2 2830 2910 230068499 230068419 1.980000e-17 100.0
16 TraesCS7A01G421300 chr1D 84.768 151 18 5 1 148 234745311 234745459 2.510000e-31 147.0
17 TraesCS7A01G421300 chr5D 84.932 146 18 4 1 144 28645500 28645357 9.030000e-31 145.0
18 TraesCS7A01G421300 chr5D 78.082 146 16 7 1 144 227774374 227774243 9.290000e-11 78.7
19 TraesCS7A01G421300 chr4B 86.869 99 13 0 512 610 516973656 516973754 9.160000e-21 111.0
20 TraesCS7A01G421300 chr1B 86.538 104 11 3 2828 2930 429281735 429281836 9.160000e-21 111.0
21 TraesCS7A01G421300 chr6D 87.654 81 10 0 2830 2910 110873577 110873497 9.230000e-16 95.3
22 TraesCS7A01G421300 chr6D 88.406 69 7 1 148 216 115791439 115791506 7.180000e-12 82.4
23 TraesCS7A01G421300 chr4D 89.189 74 8 0 148 221 121808814 121808741 3.320000e-15 93.5
24 TraesCS7A01G421300 chr1A 86.047 86 10 1 2825 2910 365069861 365069944 1.190000e-14 91.6
25 TraesCS7A01G421300 chr2D 94.444 54 3 0 557 610 110932507 110932454 2.000000e-12 84.2


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 TraesCS7A01G421300 chr7A 612377240 612380364 3124 True 5771.000000 5771 100.000000 1 3125 1 chr7A.!!$R1 3124
1 TraesCS7A01G421300 chr7D 531831455 531836058 4603 True 1648.666667 4152 89.254333 145 3125 3 chr7D.!!$R1 2980
2 TraesCS7A01G421300 chr7B 572398679 572403039 4360 True 2052.000000 3930 89.267500 609 3125 2 chr7B.!!$R2 2516

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
79 80 0.106619 TTAACGGTTGGTTGTGGCCT 60.107 50.0 3.32 0.0 39.75 5.19 F
81 82 0.106619 AACGGTTGGTTGTGGCCTAA 60.107 50.0 3.32 0.0 37.50 2.69 F
82 83 0.111639 ACGGTTGGTTGTGGCCTAAT 59.888 50.0 3.32 0.0 0.00 1.73 F
580 581 0.323451 GGTGGGGAGGTGGTCAATTC 60.323 60.0 0.00 0.0 0.00 2.17 F
1937 1947 0.531532 GTGATCGACATGGAGCCTGG 60.532 60.0 0.00 0.0 0.00 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1614 1624 0.984230 CAGGCCAGAACCCTTGTCTA 59.016 55.000 5.01 0.00 0.00 2.59 R
1700 1710 1.535462 CGACCATGGACTTGAACAACC 59.465 52.381 21.47 0.00 0.00 3.77 R
1937 1947 1.615392 GCACATAATTCCCCTCATGGC 59.385 52.381 0.00 0.00 0.00 4.40 R
1980 1990 2.253610 ACACGTCCCCAGTTCTCATTA 58.746 47.619 0.00 0.00 0.00 1.90 R
3013 3027 4.146058 TGCTCCAGTGCACTTGTG 57.854 55.556 18.94 15.94 38.12 3.33 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
19 20 1.176527 ATGGGAATTGCTGGTCAACG 58.823 50.000 0.00 0.00 37.53 4.10
20 21 1.212751 GGGAATTGCTGGTCAACGC 59.787 57.895 0.00 0.00 37.53 4.84
21 22 1.523154 GGGAATTGCTGGTCAACGCA 61.523 55.000 0.00 0.00 37.53 5.24
22 23 0.109597 GGAATTGCTGGTCAACGCAG 60.110 55.000 0.00 0.00 37.53 5.18
23 24 0.874390 GAATTGCTGGTCAACGCAGA 59.126 50.000 0.00 0.00 37.53 4.26
24 25 0.877071 AATTGCTGGTCAACGCAGAG 59.123 50.000 0.00 0.00 37.53 3.35
25 26 1.580845 ATTGCTGGTCAACGCAGAGC 61.581 55.000 0.00 0.44 37.53 4.09
26 27 3.426568 GCTGGTCAACGCAGAGCC 61.427 66.667 4.71 0.00 35.23 4.70
27 28 2.031012 CTGGTCAACGCAGAGCCA 59.969 61.111 4.71 2.81 35.23 4.75
28 29 2.031012 TGGTCAACGCAGAGCCAG 59.969 61.111 4.71 0.00 35.23 4.85
29 30 2.343758 GGTCAACGCAGAGCCAGA 59.656 61.111 0.00 0.00 0.00 3.86
30 31 1.078848 GGTCAACGCAGAGCCAGAT 60.079 57.895 0.00 0.00 0.00 2.90
31 32 1.364626 GGTCAACGCAGAGCCAGATG 61.365 60.000 0.00 0.00 0.00 2.90
32 33 1.742880 TCAACGCAGAGCCAGATGC 60.743 57.895 0.00 0.00 39.09 3.91
41 42 4.941609 GCCAGATGCGAAAGGAGA 57.058 55.556 0.00 0.00 32.19 3.71
42 43 2.687842 GCCAGATGCGAAAGGAGAG 58.312 57.895 0.00 0.00 32.19 3.20
43 44 0.813210 GCCAGATGCGAAAGGAGAGG 60.813 60.000 0.00 0.00 32.19 3.69
44 45 0.813210 CCAGATGCGAAAGGAGAGGC 60.813 60.000 0.00 0.00 32.19 4.70
45 46 0.107993 CAGATGCGAAAGGAGAGGCA 60.108 55.000 0.00 0.00 40.06 4.75
46 47 0.615331 AGATGCGAAAGGAGAGGCAA 59.385 50.000 0.00 0.00 39.09 4.52
47 48 1.211457 AGATGCGAAAGGAGAGGCAAT 59.789 47.619 0.00 0.00 39.09 3.56
48 49 1.332997 GATGCGAAAGGAGAGGCAATG 59.667 52.381 0.00 0.00 39.09 2.82
49 50 0.324614 TGCGAAAGGAGAGGCAATGA 59.675 50.000 0.00 0.00 31.50 2.57
50 51 1.065199 TGCGAAAGGAGAGGCAATGAT 60.065 47.619 0.00 0.00 31.50 2.45
51 52 1.332997 GCGAAAGGAGAGGCAATGATG 59.667 52.381 0.00 0.00 0.00 3.07
52 53 2.636830 CGAAAGGAGAGGCAATGATGT 58.363 47.619 0.00 0.00 0.00 3.06
53 54 2.353889 CGAAAGGAGAGGCAATGATGTG 59.646 50.000 0.00 0.00 0.00 3.21
54 55 2.431954 AAGGAGAGGCAATGATGTGG 57.568 50.000 0.00 0.00 0.00 4.17
55 56 1.588239 AGGAGAGGCAATGATGTGGA 58.412 50.000 0.00 0.00 0.00 4.02
56 57 1.918262 AGGAGAGGCAATGATGTGGAA 59.082 47.619 0.00 0.00 0.00 3.53
57 58 2.309755 AGGAGAGGCAATGATGTGGAAA 59.690 45.455 0.00 0.00 0.00 3.13
58 59 3.091545 GGAGAGGCAATGATGTGGAAAA 58.908 45.455 0.00 0.00 0.00 2.29
59 60 3.511146 GGAGAGGCAATGATGTGGAAAAA 59.489 43.478 0.00 0.00 0.00 1.94
60 61 4.161001 GGAGAGGCAATGATGTGGAAAAAT 59.839 41.667 0.00 0.00 0.00 1.82
61 62 5.337813 GGAGAGGCAATGATGTGGAAAAATT 60.338 40.000 0.00 0.00 0.00 1.82
62 63 6.127366 GGAGAGGCAATGATGTGGAAAAATTA 60.127 38.462 0.00 0.00 0.00 1.40
63 64 7.243604 AGAGGCAATGATGTGGAAAAATTAA 57.756 32.000 0.00 0.00 0.00 1.40
64 65 7.099120 AGAGGCAATGATGTGGAAAAATTAAC 58.901 34.615 0.00 0.00 0.00 2.01
65 66 5.868801 AGGCAATGATGTGGAAAAATTAACG 59.131 36.000 0.00 0.00 0.00 3.18
66 67 5.063312 GGCAATGATGTGGAAAAATTAACGG 59.937 40.000 0.00 0.00 0.00 4.44
67 68 5.637387 GCAATGATGTGGAAAAATTAACGGT 59.363 36.000 0.00 0.00 0.00 4.83
68 69 6.147000 GCAATGATGTGGAAAAATTAACGGTT 59.853 34.615 0.00 0.00 0.00 4.44
69 70 7.508965 CAATGATGTGGAAAAATTAACGGTTG 58.491 34.615 3.07 0.00 0.00 3.77
70 71 5.533482 TGATGTGGAAAAATTAACGGTTGG 58.467 37.500 3.07 0.00 0.00 3.77
71 72 5.069251 TGATGTGGAAAAATTAACGGTTGGT 59.931 36.000 3.07 0.00 0.00 3.67
72 73 5.340439 TGTGGAAAAATTAACGGTTGGTT 57.660 34.783 3.07 0.00 42.75 3.67
73 74 5.109903 TGTGGAAAAATTAACGGTTGGTTG 58.890 37.500 3.07 0.00 39.75 3.77
74 75 5.110598 GTGGAAAAATTAACGGTTGGTTGT 58.889 37.500 3.07 0.00 39.75 3.32
75 76 5.005875 GTGGAAAAATTAACGGTTGGTTGTG 59.994 40.000 3.07 0.00 39.75 3.33
76 77 4.508492 GGAAAAATTAACGGTTGGTTGTGG 59.492 41.667 3.07 0.00 39.75 4.17
77 78 2.804697 AATTAACGGTTGGTTGTGGC 57.195 45.000 3.07 0.00 39.75 5.01
78 79 0.963225 ATTAACGGTTGGTTGTGGCC 59.037 50.000 3.07 0.00 39.75 5.36
79 80 0.106619 TTAACGGTTGGTTGTGGCCT 60.107 50.000 3.32 0.00 39.75 5.19
80 81 0.763652 TAACGGTTGGTTGTGGCCTA 59.236 50.000 3.32 0.00 39.75 3.93
81 82 0.106619 AACGGTTGGTTGTGGCCTAA 60.107 50.000 3.32 0.00 37.50 2.69
82 83 0.111639 ACGGTTGGTTGTGGCCTAAT 59.888 50.000 3.32 0.00 0.00 1.73
83 84 0.808755 CGGTTGGTTGTGGCCTAATC 59.191 55.000 3.32 0.00 0.00 1.75
84 85 1.182667 GGTTGGTTGTGGCCTAATCC 58.817 55.000 3.32 2.29 0.00 3.01
85 86 1.272480 GGTTGGTTGTGGCCTAATCCT 60.272 52.381 3.32 0.00 0.00 3.24
86 87 2.025699 GGTTGGTTGTGGCCTAATCCTA 60.026 50.000 3.32 0.00 0.00 2.94
87 88 3.014623 GTTGGTTGTGGCCTAATCCTAC 58.985 50.000 3.32 5.45 0.00 3.18
88 89 1.208535 TGGTTGTGGCCTAATCCTACG 59.791 52.381 3.32 0.00 0.00 3.51
89 90 1.483415 GGTTGTGGCCTAATCCTACGA 59.517 52.381 3.32 0.00 0.00 3.43
90 91 2.547826 GTTGTGGCCTAATCCTACGAC 58.452 52.381 3.32 0.00 0.00 4.34
91 92 2.154567 TGTGGCCTAATCCTACGACT 57.845 50.000 3.32 0.00 0.00 4.18
92 93 1.754803 TGTGGCCTAATCCTACGACTG 59.245 52.381 3.32 0.00 0.00 3.51
93 94 1.068741 GTGGCCTAATCCTACGACTGG 59.931 57.143 3.32 0.00 0.00 4.00
94 95 0.680061 GGCCTAATCCTACGACTGGG 59.320 60.000 0.00 0.00 0.00 4.45
95 96 0.680061 GCCTAATCCTACGACTGGGG 59.320 60.000 0.00 0.00 0.00 4.96
96 97 1.339097 CCTAATCCTACGACTGGGGG 58.661 60.000 0.00 0.00 0.00 5.40
97 98 0.680061 CTAATCCTACGACTGGGGGC 59.320 60.000 0.00 0.00 0.00 5.80
98 99 1.111116 TAATCCTACGACTGGGGGCG 61.111 60.000 0.00 0.00 0.00 6.13
101 102 3.834799 CTACGACTGGGGGCGGAC 61.835 72.222 0.00 0.00 0.00 4.79
113 114 3.274067 GCGGACCGGCTGAAATTT 58.726 55.556 17.22 0.00 0.00 1.82
114 115 1.136774 GCGGACCGGCTGAAATTTC 59.863 57.895 17.22 11.41 0.00 2.17
115 116 1.423845 CGGACCGGCTGAAATTTCG 59.576 57.895 13.34 9.21 0.00 3.46
116 117 1.800681 GGACCGGCTGAAATTTCGG 59.199 57.895 20.69 20.69 46.95 4.30
123 124 1.154035 CTGAAATTTCGGCCGGTGC 60.154 57.895 27.83 7.72 0.00 5.01
124 125 2.202427 GAAATTTCGGCCGGTGCG 60.202 61.111 27.83 0.00 38.85 5.34
125 126 4.413800 AAATTTCGGCCGGTGCGC 62.414 61.111 27.83 0.00 38.85 6.09
140 141 4.796231 CGCCGACGCCTAGCAGTT 62.796 66.667 0.00 0.00 0.00 3.16
141 142 3.188786 GCCGACGCCTAGCAGTTG 61.189 66.667 0.00 0.00 0.00 3.16
142 143 3.188786 CCGACGCCTAGCAGTTGC 61.189 66.667 0.00 0.00 42.49 4.17
143 144 3.188786 CGACGCCTAGCAGTTGCC 61.189 66.667 0.00 0.00 43.38 4.52
166 167 7.656948 TGCCAAAAGAGAAACCATAAGAAAATG 59.343 33.333 0.00 0.00 0.00 2.32
317 318 9.456797 CAAATTACGTGACGAGTTTAAGATAAC 57.543 33.333 13.70 0.00 0.00 1.89
319 320 8.922058 ATTACGTGACGAGTTTAAGATAACAT 57.078 30.769 13.70 0.00 0.00 2.71
320 321 8.746922 TTACGTGACGAGTTTAAGATAACATT 57.253 30.769 13.70 0.00 0.00 2.71
323 324 7.148853 ACGTGACGAGTTTAAGATAACATTGTC 60.149 37.037 13.70 0.00 0.00 3.18
327 328 8.603242 ACGAGTTTAAGATAACATTGTCAACT 57.397 30.769 0.00 0.00 0.00 3.16
366 367 8.047413 TCTCGAAAACACACACACTATAGATA 57.953 34.615 6.78 0.00 0.00 1.98
368 369 7.823665 TCGAAAACACACACACTATAGATACT 58.176 34.615 6.78 0.00 0.00 2.12
397 398 6.610830 AGAATGGCAATTAATAACACCCATGA 59.389 34.615 0.00 0.00 32.35 3.07
411 412 3.811497 CACCCATGACATGTGCTACTATG 59.189 47.826 14.26 0.00 0.00 2.23
412 413 3.711190 ACCCATGACATGTGCTACTATGA 59.289 43.478 14.26 0.00 0.00 2.15
413 414 4.202295 ACCCATGACATGTGCTACTATGAG 60.202 45.833 14.26 0.00 0.00 2.90
414 415 3.744942 CCATGACATGTGCTACTATGAGC 59.255 47.826 14.26 0.00 43.16 4.26
415 416 3.459232 TGACATGTGCTACTATGAGCC 57.541 47.619 1.15 0.00 42.11 4.70
416 417 2.765699 TGACATGTGCTACTATGAGCCA 59.234 45.455 1.15 0.00 42.11 4.75
417 418 3.181472 TGACATGTGCTACTATGAGCCAG 60.181 47.826 1.15 0.00 42.11 4.85
418 419 2.768527 ACATGTGCTACTATGAGCCAGT 59.231 45.455 0.00 0.00 42.11 4.00
419 420 3.198635 ACATGTGCTACTATGAGCCAGTT 59.801 43.478 0.00 0.00 42.11 3.16
420 421 3.526931 TGTGCTACTATGAGCCAGTTC 57.473 47.619 0.00 0.00 42.11 3.01
421 422 3.099905 TGTGCTACTATGAGCCAGTTCT 58.900 45.455 0.00 0.00 42.11 3.01
422 423 3.515502 TGTGCTACTATGAGCCAGTTCTT 59.484 43.478 0.00 0.00 42.11 2.52
423 424 4.020218 TGTGCTACTATGAGCCAGTTCTTT 60.020 41.667 0.00 0.00 42.11 2.52
424 425 4.938226 GTGCTACTATGAGCCAGTTCTTTT 59.062 41.667 0.00 0.00 42.11 2.27
425 426 6.106673 GTGCTACTATGAGCCAGTTCTTTTA 58.893 40.000 0.00 0.00 42.11 1.52
426 427 6.256757 GTGCTACTATGAGCCAGTTCTTTTAG 59.743 42.308 0.00 0.00 42.11 1.85
427 428 5.755861 GCTACTATGAGCCAGTTCTTTTAGG 59.244 44.000 0.00 0.00 36.38 2.69
434 435 4.790765 GCCAGTTCTTTTAGGCAATTCT 57.209 40.909 0.00 0.00 46.26 2.40
435 436 5.139435 GCCAGTTCTTTTAGGCAATTCTT 57.861 39.130 0.00 0.00 46.26 2.52
436 437 5.164233 GCCAGTTCTTTTAGGCAATTCTTC 58.836 41.667 0.00 0.00 46.26 2.87
437 438 5.047731 GCCAGTTCTTTTAGGCAATTCTTCT 60.048 40.000 0.00 0.00 46.26 2.85
438 439 6.151144 GCCAGTTCTTTTAGGCAATTCTTCTA 59.849 38.462 0.00 0.00 46.26 2.10
439 440 7.627300 GCCAGTTCTTTTAGGCAATTCTTCTAG 60.627 40.741 0.00 0.00 46.26 2.43
440 441 7.607991 CCAGTTCTTTTAGGCAATTCTTCTAGA 59.392 37.037 0.00 0.00 0.00 2.43
441 442 9.003658 CAGTTCTTTTAGGCAATTCTTCTAGAA 57.996 33.333 4.81 4.81 38.78 2.10
442 443 9.746457 AGTTCTTTTAGGCAATTCTTCTAGAAT 57.254 29.630 5.44 0.00 46.22 2.40
454 455 6.809976 TTCTTCTAGAATTAACCCCCTCTC 57.190 41.667 5.44 0.00 0.00 3.20
455 456 5.217400 TCTTCTAGAATTAACCCCCTCTCC 58.783 45.833 5.44 0.00 0.00 3.71
456 457 4.637288 TCTAGAATTAACCCCCTCTCCA 57.363 45.455 0.00 0.00 0.00 3.86
457 458 4.557705 TCTAGAATTAACCCCCTCTCCAG 58.442 47.826 0.00 0.00 0.00 3.86
458 459 1.847088 AGAATTAACCCCCTCTCCAGC 59.153 52.381 0.00 0.00 0.00 4.85
459 460 1.847088 GAATTAACCCCCTCTCCAGCT 59.153 52.381 0.00 0.00 0.00 4.24
460 461 1.987080 ATTAACCCCCTCTCCAGCTT 58.013 50.000 0.00 0.00 0.00 3.74
461 462 1.286248 TTAACCCCCTCTCCAGCTTC 58.714 55.000 0.00 0.00 0.00 3.86
462 463 0.417841 TAACCCCCTCTCCAGCTTCT 59.582 55.000 0.00 0.00 0.00 2.85
463 464 0.417841 AACCCCCTCTCCAGCTTCTA 59.582 55.000 0.00 0.00 0.00 2.10
464 465 0.325765 ACCCCCTCTCCAGCTTCTAC 60.326 60.000 0.00 0.00 0.00 2.59
465 466 1.051556 CCCCCTCTCCAGCTTCTACC 61.052 65.000 0.00 0.00 0.00 3.18
466 467 0.325671 CCCCTCTCCAGCTTCTACCA 60.326 60.000 0.00 0.00 0.00 3.25
467 468 1.118838 CCCTCTCCAGCTTCTACCAG 58.881 60.000 0.00 0.00 0.00 4.00
468 469 1.342474 CCCTCTCCAGCTTCTACCAGA 60.342 57.143 0.00 0.00 0.00 3.86
469 470 2.461695 CCTCTCCAGCTTCTACCAGAA 58.538 52.381 0.00 0.00 32.50 3.02
470 471 3.037549 CCTCTCCAGCTTCTACCAGAAT 58.962 50.000 0.00 0.00 33.13 2.40
471 472 3.454082 CCTCTCCAGCTTCTACCAGAATT 59.546 47.826 0.00 0.00 33.13 2.17
472 473 4.440880 CTCTCCAGCTTCTACCAGAATTG 58.559 47.826 0.00 0.00 33.13 2.32
473 474 3.840666 TCTCCAGCTTCTACCAGAATTGT 59.159 43.478 0.00 0.00 33.13 2.71
474 475 4.081420 TCTCCAGCTTCTACCAGAATTGTC 60.081 45.833 0.00 0.00 33.13 3.18
475 476 3.582647 TCCAGCTTCTACCAGAATTGTCA 59.417 43.478 0.00 0.00 33.13 3.58
476 477 4.225942 TCCAGCTTCTACCAGAATTGTCAT 59.774 41.667 0.00 0.00 33.13 3.06
477 478 4.946157 CCAGCTTCTACCAGAATTGTCATT 59.054 41.667 0.00 0.00 33.13 2.57
478 479 5.065731 CCAGCTTCTACCAGAATTGTCATTC 59.934 44.000 0.00 0.00 39.45 2.67
479 480 5.065731 CAGCTTCTACCAGAATTGTCATTCC 59.934 44.000 0.00 0.00 39.95 3.01
480 481 4.943705 GCTTCTACCAGAATTGTCATTCCA 59.056 41.667 0.00 0.00 39.95 3.53
481 482 5.591877 GCTTCTACCAGAATTGTCATTCCAT 59.408 40.000 0.00 0.00 39.95 3.41
482 483 6.096001 GCTTCTACCAGAATTGTCATTCCATT 59.904 38.462 0.00 0.00 39.95 3.16
483 484 7.363268 GCTTCTACCAGAATTGTCATTCCATTT 60.363 37.037 0.00 0.00 39.95 2.32
484 485 8.421249 TTCTACCAGAATTGTCATTCCATTTT 57.579 30.769 0.00 0.00 39.95 1.82
485 486 8.421249 TCTACCAGAATTGTCATTCCATTTTT 57.579 30.769 0.00 0.00 39.95 1.94
555 556 5.362556 AAACGATGAAGTGACAATTCTGG 57.637 39.130 15.91 8.03 0.00 3.86
556 557 4.271696 ACGATGAAGTGACAATTCTGGA 57.728 40.909 15.91 0.00 0.00 3.86
557 558 4.641396 ACGATGAAGTGACAATTCTGGAA 58.359 39.130 15.91 0.00 0.00 3.53
558 559 4.692625 ACGATGAAGTGACAATTCTGGAAG 59.307 41.667 15.91 6.45 0.00 3.46
559 560 4.931601 CGATGAAGTGACAATTCTGGAAGA 59.068 41.667 15.91 0.00 44.68 2.87
569 570 3.088923 TCTGGAAGAAGGTGGGGAG 57.911 57.895 0.00 0.00 42.31 4.30
570 571 0.547712 TCTGGAAGAAGGTGGGGAGG 60.548 60.000 0.00 0.00 42.31 4.30
571 572 0.842467 CTGGAAGAAGGTGGGGAGGT 60.842 60.000 0.00 0.00 34.07 3.85
572 573 1.133809 TGGAAGAAGGTGGGGAGGTG 61.134 60.000 0.00 0.00 0.00 4.00
573 574 1.685820 GAAGAAGGTGGGGAGGTGG 59.314 63.158 0.00 0.00 0.00 4.61
574 575 1.072930 AAGAAGGTGGGGAGGTGGT 60.073 57.895 0.00 0.00 0.00 4.16
575 576 1.134438 AAGAAGGTGGGGAGGTGGTC 61.134 60.000 0.00 0.00 0.00 4.02
576 577 1.846124 GAAGGTGGGGAGGTGGTCA 60.846 63.158 0.00 0.00 0.00 4.02
577 578 1.386772 AAGGTGGGGAGGTGGTCAA 60.387 57.895 0.00 0.00 0.00 3.18
578 579 0.776080 AAGGTGGGGAGGTGGTCAAT 60.776 55.000 0.00 0.00 0.00 2.57
579 580 0.776080 AGGTGGGGAGGTGGTCAATT 60.776 55.000 0.00 0.00 0.00 2.32
580 581 0.323451 GGTGGGGAGGTGGTCAATTC 60.323 60.000 0.00 0.00 0.00 2.17
581 582 0.698818 GTGGGGAGGTGGTCAATTCT 59.301 55.000 0.00 0.00 0.00 2.40
582 583 0.698238 TGGGGAGGTGGTCAATTCTG 59.302 55.000 0.00 0.00 0.00 3.02
583 584 0.991920 GGGGAGGTGGTCAATTCTGA 59.008 55.000 0.00 0.00 0.00 3.27
584 585 1.065126 GGGGAGGTGGTCAATTCTGAG 60.065 57.143 0.00 0.00 30.14 3.35
585 586 1.909302 GGGAGGTGGTCAATTCTGAGA 59.091 52.381 0.00 0.00 30.14 3.27
586 587 2.093235 GGGAGGTGGTCAATTCTGAGAG 60.093 54.545 0.00 0.00 30.14 3.20
587 588 2.834549 GGAGGTGGTCAATTCTGAGAGA 59.165 50.000 0.00 0.00 30.14 3.10
588 589 3.261897 GGAGGTGGTCAATTCTGAGAGAA 59.738 47.826 0.00 0.00 38.78 2.87
589 590 4.080638 GGAGGTGGTCAATTCTGAGAGAAT 60.081 45.833 0.00 0.00 46.22 2.40
599 600 5.656213 ATTCTGAGAGAATTGCCCAAAAG 57.344 39.130 0.00 0.00 41.90 2.27
600 601 4.371624 TCTGAGAGAATTGCCCAAAAGA 57.628 40.909 0.00 0.00 0.00 2.52
601 602 4.728772 TCTGAGAGAATTGCCCAAAAGAA 58.271 39.130 0.00 0.00 0.00 2.52
602 603 4.520492 TCTGAGAGAATTGCCCAAAAGAAC 59.480 41.667 0.00 0.00 0.00 3.01
603 604 4.473444 TGAGAGAATTGCCCAAAAGAACT 58.527 39.130 0.00 0.00 0.00 3.01
604 605 4.279169 TGAGAGAATTGCCCAAAAGAACTG 59.721 41.667 0.00 0.00 0.00 3.16
605 606 4.473444 AGAGAATTGCCCAAAAGAACTGA 58.527 39.130 0.00 0.00 0.00 3.41
606 607 4.279420 AGAGAATTGCCCAAAAGAACTGAC 59.721 41.667 0.00 0.00 0.00 3.51
607 608 3.321968 AGAATTGCCCAAAAGAACTGACC 59.678 43.478 0.00 0.00 0.00 4.02
608 609 1.408969 TTGCCCAAAAGAACTGACCC 58.591 50.000 0.00 0.00 0.00 4.46
609 610 0.555769 TGCCCAAAAGAACTGACCCT 59.444 50.000 0.00 0.00 0.00 4.34
610 611 1.777878 TGCCCAAAAGAACTGACCCTA 59.222 47.619 0.00 0.00 0.00 3.53
611 612 2.378547 TGCCCAAAAGAACTGACCCTAT 59.621 45.455 0.00 0.00 0.00 2.57
612 613 3.589735 TGCCCAAAAGAACTGACCCTATA 59.410 43.478 0.00 0.00 0.00 1.31
857 867 0.892063 GCTCGTCCTTCCTCAAGTCT 59.108 55.000 0.00 0.00 0.00 3.24
863 873 2.029290 GTCCTTCCTCAAGTCTTACGCA 60.029 50.000 0.00 0.00 0.00 5.24
907 917 1.282875 GCCAGCTGTTCGACCAAAC 59.717 57.895 13.81 0.00 0.00 2.93
1048 1058 2.750637 TCTCCGTCACGAGCCTCC 60.751 66.667 0.00 0.00 0.00 4.30
1182 1192 4.796495 GGGAGATGCGGGCGGTTT 62.796 66.667 0.00 0.00 0.00 3.27
1267 1277 1.302752 AATGCCTGCTGCGAGAACA 60.303 52.632 0.00 0.00 45.60 3.18
1269 1279 2.358003 GCCTGCTGCGAGAACAGT 60.358 61.111 0.00 0.00 39.96 3.55
1344 1354 0.904865 TCGATGAGGTCACCCTGCTT 60.905 55.000 0.00 0.00 42.86 3.91
1356 1366 1.088340 CCCTGCTTGCAGTCATCTCG 61.088 60.000 19.49 4.26 0.00 4.04
1444 1454 1.001633 GCTTCTTGGAGAACACCCGTA 59.998 52.381 0.00 0.00 29.89 4.02
1449 1459 0.968901 TGGAGAACACCCGTATCGCT 60.969 55.000 0.00 0.00 0.00 4.93
1455 1465 2.129823 ACACCCGTATCGCTAATTCG 57.870 50.000 0.00 0.00 0.00 3.34
1614 1624 1.069227 GTTCGGTTTTCGCAGATGCTT 60.069 47.619 2.95 0.00 39.32 3.91
1700 1710 2.890847 CTAGTGAGTGAAGGGCGCCG 62.891 65.000 22.54 0.00 0.00 6.46
1721 1731 2.218603 GTTGTTCAAGTCCATGGTCGT 58.781 47.619 12.58 0.77 0.00 4.34
1842 1852 1.203441 TGCCTGTGAAGCCTGATCCT 61.203 55.000 0.00 0.00 0.00 3.24
1885 1895 0.534427 AGCATGCCGTGATCATGGAG 60.534 55.000 33.81 22.84 41.08 3.86
1937 1947 0.531532 GTGATCGACATGGAGCCTGG 60.532 60.000 0.00 0.00 0.00 4.45
1980 1990 3.270027 TGCGTCAAACTTATATGCTGCT 58.730 40.909 0.00 0.00 0.00 4.24
2042 2052 1.070289 GGGTGTGAGGAAAGAGACGTT 59.930 52.381 0.00 0.00 0.00 3.99
2075 2085 2.421424 CTGCCCTGTCTTACATTGAAGC 59.579 50.000 0.00 0.00 0.00 3.86
2159 2169 6.577103 TCCACTACTATGAGATTTGCTTGAG 58.423 40.000 0.00 0.00 0.00 3.02
2276 2287 4.871933 CAAAAGATGCAAAAGGGTAGGT 57.128 40.909 0.00 0.00 0.00 3.08
2360 2371 2.032860 AACTGTCAGCACGCCTGTCT 62.033 55.000 0.00 0.00 42.38 3.41
2364 2375 0.880278 GTCAGCACGCCTGTCTTTCA 60.880 55.000 3.92 0.00 42.38 2.69
2366 2377 0.040958 CAGCACGCCTGTCTTTCAAC 60.041 55.000 0.00 0.00 36.79 3.18
2367 2378 0.463654 AGCACGCCTGTCTTTCAACA 60.464 50.000 0.00 0.00 0.00 3.33
2368 2379 0.593128 GCACGCCTGTCTTTCAACAT 59.407 50.000 0.00 0.00 0.00 2.71
2369 2380 1.400242 GCACGCCTGTCTTTCAACATC 60.400 52.381 0.00 0.00 0.00 3.06
2370 2381 2.146342 CACGCCTGTCTTTCAACATCT 58.854 47.619 0.00 0.00 0.00 2.90
2485 2499 0.250234 CTCACATCGAAAGGGCCAGA 59.750 55.000 6.18 0.00 0.00 3.86
2495 2509 3.313526 CGAAAGGGCCAGATAATTCAGTG 59.686 47.826 6.18 0.00 0.00 3.66
2558 2572 6.484540 CACAAAAGCATTGCACATGTTTTTA 58.515 32.000 22.68 0.00 39.33 1.52
2620 2634 1.559682 GACCCTCTCCACTTGCCAATA 59.440 52.381 0.00 0.00 0.00 1.90
2734 2748 3.099267 AGACCAAGAACAACACGAGAG 57.901 47.619 0.00 0.00 0.00 3.20
2750 2764 4.333649 CACGAGAGCCATACAATTTGTGAT 59.666 41.667 12.30 0.00 0.00 3.06
2823 2837 4.159244 ACAACCAGTGTAGTTGCCTTTA 57.841 40.909 10.97 0.00 46.85 1.85
2855 2869 7.415086 ACTCCCTCCGTCTCATAATATAAGAT 58.585 38.462 0.00 0.00 0.00 2.40
3013 3027 5.416271 TCACTGGGTTGATAAAGTCCTAC 57.584 43.478 0.00 0.00 0.00 3.18
3069 3084 3.068732 TCCATAGATGCTCCACGAAGAAG 59.931 47.826 0.00 0.00 0.00 2.85
3110 3125 6.973642 TGATTTCTTGGGATTTAGAGATGGT 58.026 36.000 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.176527 CGTTGACCAGCAATTCCCAT 58.823 50.000 0.00 0.00 39.03 4.00
2 3 1.212751 GCGTTGACCAGCAATTCCC 59.787 57.895 0.00 0.00 39.03 3.97
4 5 0.874390 TCTGCGTTGACCAGCAATTC 59.126 50.000 0.00 0.00 43.31 2.17
5 6 0.877071 CTCTGCGTTGACCAGCAATT 59.123 50.000 0.00 0.00 43.31 2.32
6 7 1.580845 GCTCTGCGTTGACCAGCAAT 61.581 55.000 0.00 0.00 43.31 3.56
7 8 2.253758 GCTCTGCGTTGACCAGCAA 61.254 57.895 0.00 0.00 43.31 3.91
8 9 2.666190 GCTCTGCGTTGACCAGCA 60.666 61.111 0.00 0.00 41.55 4.41
9 10 3.426568 GGCTCTGCGTTGACCAGC 61.427 66.667 0.00 0.00 0.00 4.85
10 11 2.031012 TGGCTCTGCGTTGACCAG 59.969 61.111 0.00 0.00 0.00 4.00
11 12 1.830587 ATCTGGCTCTGCGTTGACCA 61.831 55.000 0.00 0.00 0.00 4.02
12 13 1.078848 ATCTGGCTCTGCGTTGACC 60.079 57.895 0.00 0.00 0.00 4.02
13 14 1.975363 GCATCTGGCTCTGCGTTGAC 61.975 60.000 0.00 0.00 40.25 3.18
14 15 1.742880 GCATCTGGCTCTGCGTTGA 60.743 57.895 0.00 0.00 40.25 3.18
15 16 2.789917 GCATCTGGCTCTGCGTTG 59.210 61.111 0.00 0.00 40.25 4.10
19 20 1.712977 CCTTTCGCATCTGGCTCTGC 61.713 60.000 0.00 0.00 41.67 4.26
20 21 0.107993 TCCTTTCGCATCTGGCTCTG 60.108 55.000 0.00 0.00 41.67 3.35
21 22 0.177604 CTCCTTTCGCATCTGGCTCT 59.822 55.000 0.00 0.00 41.67 4.09
22 23 0.176680 TCTCCTTTCGCATCTGGCTC 59.823 55.000 0.00 0.00 41.67 4.70
23 24 0.177604 CTCTCCTTTCGCATCTGGCT 59.822 55.000 0.00 0.00 41.67 4.75
24 25 0.813210 CCTCTCCTTTCGCATCTGGC 60.813 60.000 0.00 0.00 39.90 4.85
25 26 0.813210 GCCTCTCCTTTCGCATCTGG 60.813 60.000 0.00 0.00 0.00 3.86
26 27 0.107993 TGCCTCTCCTTTCGCATCTG 60.108 55.000 0.00 0.00 0.00 2.90
27 28 0.615331 TTGCCTCTCCTTTCGCATCT 59.385 50.000 0.00 0.00 0.00 2.90
28 29 1.332997 CATTGCCTCTCCTTTCGCATC 59.667 52.381 0.00 0.00 0.00 3.91
29 30 1.065199 TCATTGCCTCTCCTTTCGCAT 60.065 47.619 0.00 0.00 0.00 4.73
30 31 0.324614 TCATTGCCTCTCCTTTCGCA 59.675 50.000 0.00 0.00 0.00 5.10
31 32 1.332997 CATCATTGCCTCTCCTTTCGC 59.667 52.381 0.00 0.00 0.00 4.70
32 33 2.353889 CACATCATTGCCTCTCCTTTCG 59.646 50.000 0.00 0.00 0.00 3.46
33 34 2.686915 CCACATCATTGCCTCTCCTTTC 59.313 50.000 0.00 0.00 0.00 2.62
34 35 2.309755 TCCACATCATTGCCTCTCCTTT 59.690 45.455 0.00 0.00 0.00 3.11
35 36 1.918262 TCCACATCATTGCCTCTCCTT 59.082 47.619 0.00 0.00 0.00 3.36
36 37 1.588239 TCCACATCATTGCCTCTCCT 58.412 50.000 0.00 0.00 0.00 3.69
37 38 2.425143 TTCCACATCATTGCCTCTCC 57.575 50.000 0.00 0.00 0.00 3.71
38 39 4.789012 TTTTTCCACATCATTGCCTCTC 57.211 40.909 0.00 0.00 0.00 3.20
39 40 5.750352 AATTTTTCCACATCATTGCCTCT 57.250 34.783 0.00 0.00 0.00 3.69
40 41 6.034898 CGTTAATTTTTCCACATCATTGCCTC 59.965 38.462 0.00 0.00 0.00 4.70
41 42 5.868801 CGTTAATTTTTCCACATCATTGCCT 59.131 36.000 0.00 0.00 0.00 4.75
42 43 5.063312 CCGTTAATTTTTCCACATCATTGCC 59.937 40.000 0.00 0.00 0.00 4.52
43 44 5.637387 ACCGTTAATTTTTCCACATCATTGC 59.363 36.000 0.00 0.00 0.00 3.56
44 45 7.359933 CCAACCGTTAATTTTTCCACATCATTG 60.360 37.037 0.00 0.00 0.00 2.82
45 46 6.648725 CCAACCGTTAATTTTTCCACATCATT 59.351 34.615 0.00 0.00 0.00 2.57
46 47 6.162777 CCAACCGTTAATTTTTCCACATCAT 58.837 36.000 0.00 0.00 0.00 2.45
47 48 5.069251 ACCAACCGTTAATTTTTCCACATCA 59.931 36.000 0.00 0.00 0.00 3.07
48 49 5.534407 ACCAACCGTTAATTTTTCCACATC 58.466 37.500 0.00 0.00 0.00 3.06
49 50 5.538849 ACCAACCGTTAATTTTTCCACAT 57.461 34.783 0.00 0.00 0.00 3.21
50 51 5.109903 CAACCAACCGTTAATTTTTCCACA 58.890 37.500 0.00 0.00 31.77 4.17
51 52 5.005875 CACAACCAACCGTTAATTTTTCCAC 59.994 40.000 0.00 0.00 31.77 4.02
52 53 5.109903 CACAACCAACCGTTAATTTTTCCA 58.890 37.500 0.00 0.00 31.77 3.53
53 54 4.508492 CCACAACCAACCGTTAATTTTTCC 59.492 41.667 0.00 0.00 31.77 3.13
54 55 4.025563 GCCACAACCAACCGTTAATTTTTC 60.026 41.667 0.00 0.00 31.77 2.29
55 56 3.872182 GCCACAACCAACCGTTAATTTTT 59.128 39.130 0.00 0.00 31.77 1.94
56 57 3.459145 GCCACAACCAACCGTTAATTTT 58.541 40.909 0.00 0.00 31.77 1.82
57 58 2.224090 GGCCACAACCAACCGTTAATTT 60.224 45.455 0.00 0.00 31.77 1.82
58 59 1.341852 GGCCACAACCAACCGTTAATT 59.658 47.619 0.00 0.00 31.77 1.40
59 60 0.963225 GGCCACAACCAACCGTTAAT 59.037 50.000 0.00 0.00 31.77 1.40
60 61 0.106619 AGGCCACAACCAACCGTTAA 60.107 50.000 5.01 0.00 31.77 2.01
61 62 0.763652 TAGGCCACAACCAACCGTTA 59.236 50.000 5.01 0.00 31.77 3.18
62 63 0.106619 TTAGGCCACAACCAACCGTT 60.107 50.000 5.01 0.00 33.90 4.44
63 64 0.111639 ATTAGGCCACAACCAACCGT 59.888 50.000 5.01 0.00 0.00 4.83
64 65 0.808755 GATTAGGCCACAACCAACCG 59.191 55.000 5.01 0.00 0.00 4.44
65 66 1.182667 GGATTAGGCCACAACCAACC 58.817 55.000 5.01 0.00 0.00 3.77
66 67 2.215942 AGGATTAGGCCACAACCAAC 57.784 50.000 5.01 0.00 0.00 3.77
67 68 2.355310 CGTAGGATTAGGCCACAACCAA 60.355 50.000 5.01 0.00 0.00 3.67
68 69 1.208535 CGTAGGATTAGGCCACAACCA 59.791 52.381 5.01 0.00 0.00 3.67
69 70 1.483415 TCGTAGGATTAGGCCACAACC 59.517 52.381 5.01 2.89 0.00 3.77
70 71 2.167900 AGTCGTAGGATTAGGCCACAAC 59.832 50.000 5.01 0.00 0.00 3.32
71 72 2.167693 CAGTCGTAGGATTAGGCCACAA 59.832 50.000 5.01 0.00 0.00 3.33
72 73 1.754803 CAGTCGTAGGATTAGGCCACA 59.245 52.381 5.01 0.00 0.00 4.17
73 74 1.068741 CCAGTCGTAGGATTAGGCCAC 59.931 57.143 5.01 0.00 0.00 5.01
74 75 1.410004 CCAGTCGTAGGATTAGGCCA 58.590 55.000 5.01 0.00 0.00 5.36
75 76 0.680061 CCCAGTCGTAGGATTAGGCC 59.320 60.000 0.00 0.00 0.00 5.19
76 77 0.680061 CCCCAGTCGTAGGATTAGGC 59.320 60.000 0.00 0.00 0.00 3.93
77 78 1.339097 CCCCCAGTCGTAGGATTAGG 58.661 60.000 0.00 0.00 0.00 2.69
78 79 0.680061 GCCCCCAGTCGTAGGATTAG 59.320 60.000 0.00 0.00 0.00 1.73
79 80 1.111116 CGCCCCCAGTCGTAGGATTA 61.111 60.000 0.00 0.00 0.00 1.75
80 81 2.432300 CGCCCCCAGTCGTAGGATT 61.432 63.158 0.00 0.00 0.00 3.01
81 82 2.838225 CGCCCCCAGTCGTAGGAT 60.838 66.667 0.00 0.00 0.00 3.24
84 85 3.834799 GTCCGCCCCCAGTCGTAG 61.835 72.222 0.00 0.00 0.00 3.51
94 95 4.796495 ATTTCAGCCGGTCCGCCC 62.796 66.667 5.50 0.00 0.00 6.13
95 96 2.266376 GAAATTTCAGCCGGTCCGCC 62.266 60.000 13.40 0.00 0.00 6.13
96 97 1.136774 GAAATTTCAGCCGGTCCGC 59.863 57.895 13.40 1.24 0.00 5.54
97 98 1.423845 CGAAATTTCAGCCGGTCCG 59.576 57.895 17.99 3.60 0.00 4.79
98 99 1.800681 CCGAAATTTCAGCCGGTCC 59.199 57.895 17.99 0.00 37.40 4.46
99 100 1.136774 GCCGAAATTTCAGCCGGTC 59.863 57.895 17.99 6.81 43.51 4.79
100 101 2.340328 GGCCGAAATTTCAGCCGGT 61.340 57.895 25.61 0.00 40.58 5.28
101 102 2.489751 GGCCGAAATTTCAGCCGG 59.510 61.111 25.61 18.18 40.58 6.13
103 104 2.340328 ACCGGCCGAAATTTCAGCC 61.340 57.895 28.48 28.48 45.24 4.85
104 105 1.154035 CACCGGCCGAAATTTCAGC 60.154 57.895 30.73 16.54 0.00 4.26
105 106 1.154035 GCACCGGCCGAAATTTCAG 60.154 57.895 30.73 9.82 0.00 3.02
106 107 2.958576 GCACCGGCCGAAATTTCA 59.041 55.556 30.73 0.00 0.00 2.69
107 108 2.202427 CGCACCGGCCGAAATTTC 60.202 61.111 30.73 8.20 36.38 2.17
108 109 4.413800 GCGCACCGGCCGAAATTT 62.414 61.111 30.73 1.41 36.38 1.82
123 124 4.796231 AACTGCTAGGCGTCGGCG 62.796 66.667 13.61 4.29 41.24 6.46
124 125 3.188786 CAACTGCTAGGCGTCGGC 61.189 66.667 11.43 11.43 38.90 5.54
125 126 3.188786 GCAACTGCTAGGCGTCGG 61.189 66.667 0.00 0.00 38.21 4.79
126 127 3.188786 GGCAACTGCTAGGCGTCG 61.189 66.667 1.06 0.00 41.70 5.12
127 128 1.234615 TTTGGCAACTGCTAGGCGTC 61.235 55.000 0.00 0.00 41.70 5.19
128 129 0.821711 TTTTGGCAACTGCTAGGCGT 60.822 50.000 0.00 0.00 41.70 5.68
129 130 0.109597 CTTTTGGCAACTGCTAGGCG 60.110 55.000 0.00 0.00 41.70 5.52
130 131 1.200948 CTCTTTTGGCAACTGCTAGGC 59.799 52.381 0.00 0.00 41.70 3.93
131 132 2.783135 TCTCTTTTGGCAACTGCTAGG 58.217 47.619 0.00 0.00 41.70 3.02
132 133 4.540824 GTTTCTCTTTTGGCAACTGCTAG 58.459 43.478 0.00 0.00 41.70 3.42
133 134 3.317993 GGTTTCTCTTTTGGCAACTGCTA 59.682 43.478 0.00 0.00 41.70 3.49
134 135 2.101415 GGTTTCTCTTTTGGCAACTGCT 59.899 45.455 0.00 0.00 41.70 4.24
135 136 2.159114 TGGTTTCTCTTTTGGCAACTGC 60.159 45.455 0.00 0.00 41.14 4.40
136 137 3.799281 TGGTTTCTCTTTTGGCAACTG 57.201 42.857 0.00 0.00 37.61 3.16
137 138 5.833131 TCTTATGGTTTCTCTTTTGGCAACT 59.167 36.000 0.00 0.00 37.61 3.16
138 139 6.084326 TCTTATGGTTTCTCTTTTGGCAAC 57.916 37.500 0.00 0.00 0.00 4.17
139 140 6.723298 TTCTTATGGTTTCTCTTTTGGCAA 57.277 33.333 0.00 0.00 0.00 4.52
140 141 6.723298 TTTCTTATGGTTTCTCTTTTGGCA 57.277 33.333 0.00 0.00 0.00 4.92
141 142 7.657354 ACATTTTCTTATGGTTTCTCTTTTGGC 59.343 33.333 0.00 0.00 0.00 4.52
142 143 9.546428 AACATTTTCTTATGGTTTCTCTTTTGG 57.454 29.630 0.00 0.00 0.00 3.28
289 290 3.531262 AAACTCGTCACGTAATTTGGC 57.469 42.857 0.00 0.00 0.00 4.52
290 291 6.456447 TCTTAAACTCGTCACGTAATTTGG 57.544 37.500 0.00 0.00 0.00 3.28
291 292 9.456797 GTTATCTTAAACTCGTCACGTAATTTG 57.543 33.333 0.00 0.00 0.00 2.32
319 320 9.053840 CGAGAAGGTATCTATAGTAGTTGACAA 57.946 37.037 0.00 0.00 38.96 3.18
320 321 8.427276 TCGAGAAGGTATCTATAGTAGTTGACA 58.573 37.037 0.00 0.00 38.96 3.58
327 328 9.399797 TGTGTTTTCGAGAAGGTATCTATAGTA 57.600 33.333 0.00 0.00 38.96 1.82
331 332 6.812160 GTGTGTGTTTTCGAGAAGGTATCTAT 59.188 38.462 0.00 0.00 38.96 1.98
366 367 9.869757 GGTGTTATTAATTGCCATTCTAAAAGT 57.130 29.630 0.00 0.00 0.00 2.66
368 369 8.816894 TGGGTGTTATTAATTGCCATTCTAAAA 58.183 29.630 0.00 0.00 0.00 1.52
397 398 2.768527 ACTGGCTCATAGTAGCACATGT 59.231 45.455 0.00 0.00 44.64 3.21
411 412 4.460731 AGAATTGCCTAAAAGAACTGGCTC 59.539 41.667 0.00 0.00 45.11 4.70
412 413 4.411013 AGAATTGCCTAAAAGAACTGGCT 58.589 39.130 0.00 0.00 45.11 4.75
413 414 4.790765 AGAATTGCCTAAAAGAACTGGC 57.209 40.909 0.00 0.00 45.10 4.85
414 415 6.581171 AGAAGAATTGCCTAAAAGAACTGG 57.419 37.500 0.00 0.00 0.00 4.00
415 416 8.553459 TCTAGAAGAATTGCCTAAAAGAACTG 57.447 34.615 0.00 0.00 0.00 3.16
416 417 9.746457 ATTCTAGAAGAATTGCCTAAAAGAACT 57.254 29.630 11.53 0.00 41.90 3.01
430 431 6.330514 GGAGAGGGGGTTAATTCTAGAAGAAT 59.669 42.308 11.53 2.67 46.22 2.40
431 432 5.666265 GGAGAGGGGGTTAATTCTAGAAGAA 59.334 44.000 11.53 5.01 38.78 2.52
432 433 5.217400 GGAGAGGGGGTTAATTCTAGAAGA 58.783 45.833 11.53 0.00 0.00 2.87
433 434 4.969359 TGGAGAGGGGGTTAATTCTAGAAG 59.031 45.833 11.53 0.00 0.00 2.85
434 435 4.967871 TGGAGAGGGGGTTAATTCTAGAA 58.032 43.478 7.82 7.82 0.00 2.10
435 436 4.557705 CTGGAGAGGGGGTTAATTCTAGA 58.442 47.826 0.00 0.00 0.00 2.43
436 437 3.071747 GCTGGAGAGGGGGTTAATTCTAG 59.928 52.174 0.00 0.00 0.00 2.43
437 438 3.046374 GCTGGAGAGGGGGTTAATTCTA 58.954 50.000 0.00 0.00 0.00 2.10
438 439 1.847088 GCTGGAGAGGGGGTTAATTCT 59.153 52.381 0.00 0.00 0.00 2.40
439 440 1.847088 AGCTGGAGAGGGGGTTAATTC 59.153 52.381 0.00 0.00 0.00 2.17
440 441 1.987080 AGCTGGAGAGGGGGTTAATT 58.013 50.000 0.00 0.00 0.00 1.40
441 442 1.847088 GAAGCTGGAGAGGGGGTTAAT 59.153 52.381 0.00 0.00 0.00 1.40
442 443 1.203440 AGAAGCTGGAGAGGGGGTTAA 60.203 52.381 0.00 0.00 0.00 2.01
443 444 0.417841 AGAAGCTGGAGAGGGGGTTA 59.582 55.000 0.00 0.00 0.00 2.85
444 445 0.417841 TAGAAGCTGGAGAGGGGGTT 59.582 55.000 0.00 0.00 0.00 4.11
445 446 0.325765 GTAGAAGCTGGAGAGGGGGT 60.326 60.000 0.00 0.00 0.00 4.95
446 447 1.051556 GGTAGAAGCTGGAGAGGGGG 61.052 65.000 0.00 0.00 0.00 5.40
447 448 0.325671 TGGTAGAAGCTGGAGAGGGG 60.326 60.000 0.00 0.00 0.00 4.79
448 449 1.118838 CTGGTAGAAGCTGGAGAGGG 58.881 60.000 0.00 0.00 0.00 4.30
449 450 2.151502 TCTGGTAGAAGCTGGAGAGG 57.848 55.000 0.00 0.00 0.00 3.69
450 451 4.081198 ACAATTCTGGTAGAAGCTGGAGAG 60.081 45.833 0.00 0.00 37.69 3.20
451 452 3.840666 ACAATTCTGGTAGAAGCTGGAGA 59.159 43.478 0.00 0.00 37.69 3.71
452 453 4.187694 GACAATTCTGGTAGAAGCTGGAG 58.812 47.826 0.00 0.00 37.69 3.86
453 454 3.582647 TGACAATTCTGGTAGAAGCTGGA 59.417 43.478 0.00 0.00 37.69 3.86
454 455 3.942829 TGACAATTCTGGTAGAAGCTGG 58.057 45.455 0.00 0.00 37.69 4.85
455 456 5.065731 GGAATGACAATTCTGGTAGAAGCTG 59.934 44.000 0.00 0.00 41.74 4.24
456 457 5.189180 GGAATGACAATTCTGGTAGAAGCT 58.811 41.667 0.00 0.00 41.74 3.74
457 458 4.943705 TGGAATGACAATTCTGGTAGAAGC 59.056 41.667 0.00 0.00 41.74 3.86
458 459 7.636150 AATGGAATGACAATTCTGGTAGAAG 57.364 36.000 0.00 0.00 41.74 2.85
459 460 8.421249 AAAATGGAATGACAATTCTGGTAGAA 57.579 30.769 0.00 0.00 41.74 2.10
460 461 8.421249 AAAAATGGAATGACAATTCTGGTAGA 57.579 30.769 0.00 0.00 41.74 2.59
531 532 6.039270 TCCAGAATTGTCACTTCATCGTTTTT 59.961 34.615 5.79 0.00 0.00 1.94
532 533 5.530915 TCCAGAATTGTCACTTCATCGTTTT 59.469 36.000 5.79 0.00 0.00 2.43
533 534 5.063204 TCCAGAATTGTCACTTCATCGTTT 58.937 37.500 5.79 0.00 0.00 3.60
534 535 4.641396 TCCAGAATTGTCACTTCATCGTT 58.359 39.130 5.79 0.00 0.00 3.85
535 536 4.271696 TCCAGAATTGTCACTTCATCGT 57.728 40.909 5.79 0.00 0.00 3.73
536 537 4.931601 TCTTCCAGAATTGTCACTTCATCG 59.068 41.667 5.79 0.00 0.00 3.84
537 538 6.128063 CCTTCTTCCAGAATTGTCACTTCATC 60.128 42.308 5.79 0.00 33.13 2.92
538 539 5.709164 CCTTCTTCCAGAATTGTCACTTCAT 59.291 40.000 5.79 0.00 33.13 2.57
539 540 5.065914 CCTTCTTCCAGAATTGTCACTTCA 58.934 41.667 5.79 0.00 33.13 3.02
540 541 5.049129 CACCTTCTTCCAGAATTGTCACTTC 60.049 44.000 0.00 0.00 33.13 3.01
541 542 4.823989 CACCTTCTTCCAGAATTGTCACTT 59.176 41.667 0.00 0.00 33.13 3.16
542 543 4.392940 CACCTTCTTCCAGAATTGTCACT 58.607 43.478 0.00 0.00 33.13 3.41
543 544 3.503748 CCACCTTCTTCCAGAATTGTCAC 59.496 47.826 0.00 0.00 33.13 3.67
544 545 3.498481 CCCACCTTCTTCCAGAATTGTCA 60.498 47.826 0.00 0.00 33.13 3.58
545 546 3.084786 CCCACCTTCTTCCAGAATTGTC 58.915 50.000 0.00 0.00 33.13 3.18
546 547 2.225117 CCCCACCTTCTTCCAGAATTGT 60.225 50.000 0.00 0.00 33.13 2.71
547 548 2.041620 TCCCCACCTTCTTCCAGAATTG 59.958 50.000 0.00 0.00 33.13 2.32
548 549 2.310052 CTCCCCACCTTCTTCCAGAATT 59.690 50.000 0.00 0.00 33.13 2.17
549 550 1.918957 CTCCCCACCTTCTTCCAGAAT 59.081 52.381 0.00 0.00 33.13 2.40
550 551 1.362224 CTCCCCACCTTCTTCCAGAA 58.638 55.000 0.00 0.00 32.50 3.02
551 552 0.547712 CCTCCCCACCTTCTTCCAGA 60.548 60.000 0.00 0.00 0.00 3.86
552 553 0.842467 ACCTCCCCACCTTCTTCCAG 60.842 60.000 0.00 0.00 0.00 3.86
553 554 1.133809 CACCTCCCCACCTTCTTCCA 61.134 60.000 0.00 0.00 0.00 3.53
554 555 1.685820 CACCTCCCCACCTTCTTCC 59.314 63.158 0.00 0.00 0.00 3.46
555 556 1.134438 ACCACCTCCCCACCTTCTTC 61.134 60.000 0.00 0.00 0.00 2.87
556 557 1.072930 ACCACCTCCCCACCTTCTT 60.073 57.895 0.00 0.00 0.00 2.52
557 558 1.539124 GACCACCTCCCCACCTTCT 60.539 63.158 0.00 0.00 0.00 2.85
558 559 1.423794 TTGACCACCTCCCCACCTTC 61.424 60.000 0.00 0.00 0.00 3.46
559 560 0.776080 ATTGACCACCTCCCCACCTT 60.776 55.000 0.00 0.00 0.00 3.50
560 561 0.776080 AATTGACCACCTCCCCACCT 60.776 55.000 0.00 0.00 0.00 4.00
561 562 0.323451 GAATTGACCACCTCCCCACC 60.323 60.000 0.00 0.00 0.00 4.61
562 563 0.698818 AGAATTGACCACCTCCCCAC 59.301 55.000 0.00 0.00 0.00 4.61
563 564 0.698238 CAGAATTGACCACCTCCCCA 59.302 55.000 0.00 0.00 0.00 4.96
564 565 0.991920 TCAGAATTGACCACCTCCCC 59.008 55.000 0.00 0.00 0.00 4.81
565 566 1.909302 TCTCAGAATTGACCACCTCCC 59.091 52.381 0.00 0.00 0.00 4.30
566 567 2.834549 TCTCTCAGAATTGACCACCTCC 59.165 50.000 0.00 0.00 0.00 4.30
567 568 4.543590 TTCTCTCAGAATTGACCACCTC 57.456 45.455 0.00 0.00 0.00 3.85
577 578 5.327732 TCTTTTGGGCAATTCTCTCAGAAT 58.672 37.500 0.00 0.00 46.22 2.40
578 579 4.728772 TCTTTTGGGCAATTCTCTCAGAA 58.271 39.130 0.00 0.00 38.78 3.02
579 580 4.371624 TCTTTTGGGCAATTCTCTCAGA 57.628 40.909 0.00 0.00 0.00 3.27
580 581 4.522022 AGTTCTTTTGGGCAATTCTCTCAG 59.478 41.667 0.00 0.00 0.00 3.35
581 582 4.279169 CAGTTCTTTTGGGCAATTCTCTCA 59.721 41.667 0.00 0.00 0.00 3.27
582 583 4.520492 TCAGTTCTTTTGGGCAATTCTCTC 59.480 41.667 0.00 0.00 0.00 3.20
583 584 4.279420 GTCAGTTCTTTTGGGCAATTCTCT 59.721 41.667 0.00 0.00 0.00 3.10
584 585 4.550422 GTCAGTTCTTTTGGGCAATTCTC 58.450 43.478 0.00 0.00 0.00 2.87
585 586 3.321968 GGTCAGTTCTTTTGGGCAATTCT 59.678 43.478 0.00 0.00 0.00 2.40
586 587 3.554960 GGGTCAGTTCTTTTGGGCAATTC 60.555 47.826 0.00 0.00 0.00 2.17
587 588 2.368548 GGGTCAGTTCTTTTGGGCAATT 59.631 45.455 0.00 0.00 0.00 2.32
588 589 1.970640 GGGTCAGTTCTTTTGGGCAAT 59.029 47.619 0.00 0.00 0.00 3.56
589 590 1.063266 AGGGTCAGTTCTTTTGGGCAA 60.063 47.619 0.00 0.00 0.00 4.52
590 591 0.555769 AGGGTCAGTTCTTTTGGGCA 59.444 50.000 0.00 0.00 0.00 5.36
591 592 2.579410 TAGGGTCAGTTCTTTTGGGC 57.421 50.000 0.00 0.00 0.00 5.36
592 593 6.001449 TGATATAGGGTCAGTTCTTTTGGG 57.999 41.667 0.00 0.00 0.00 4.12
593 594 7.938140 TTTGATATAGGGTCAGTTCTTTTGG 57.062 36.000 0.00 0.00 0.00 3.28
594 595 9.793252 CAATTTGATATAGGGTCAGTTCTTTTG 57.207 33.333 0.00 0.00 0.00 2.44
595 596 9.533831 ACAATTTGATATAGGGTCAGTTCTTTT 57.466 29.630 2.79 0.00 0.00 2.27
596 597 8.960591 CACAATTTGATATAGGGTCAGTTCTTT 58.039 33.333 2.79 0.00 0.00 2.52
597 598 7.557719 CCACAATTTGATATAGGGTCAGTTCTT 59.442 37.037 2.79 0.00 0.00 2.52
598 599 7.056635 CCACAATTTGATATAGGGTCAGTTCT 58.943 38.462 2.79 0.00 0.00 3.01
599 600 7.054124 TCCACAATTTGATATAGGGTCAGTTC 58.946 38.462 2.79 0.00 0.00 3.01
600 601 6.969043 TCCACAATTTGATATAGGGTCAGTT 58.031 36.000 2.79 0.00 0.00 3.16
601 602 6.575244 TCCACAATTTGATATAGGGTCAGT 57.425 37.500 2.79 0.00 0.00 3.41
602 603 6.016777 GCTTCCACAATTTGATATAGGGTCAG 60.017 42.308 2.79 0.00 0.00 3.51
603 604 5.827797 GCTTCCACAATTTGATATAGGGTCA 59.172 40.000 2.79 0.00 0.00 4.02
604 605 5.049405 CGCTTCCACAATTTGATATAGGGTC 60.049 44.000 2.79 0.00 0.00 4.46
605 606 4.821805 CGCTTCCACAATTTGATATAGGGT 59.178 41.667 2.79 0.00 0.00 4.34
606 607 4.320494 GCGCTTCCACAATTTGATATAGGG 60.320 45.833 0.00 5.09 0.00 3.53
607 608 4.320494 GGCGCTTCCACAATTTGATATAGG 60.320 45.833 7.64 0.00 34.01 2.57
608 609 4.320494 GGGCGCTTCCACAATTTGATATAG 60.320 45.833 7.64 0.00 36.21 1.31
609 610 3.568007 GGGCGCTTCCACAATTTGATATA 59.432 43.478 7.64 0.00 36.21 0.86
610 611 2.362077 GGGCGCTTCCACAATTTGATAT 59.638 45.455 7.64 0.00 36.21 1.63
611 612 1.748493 GGGCGCTTCCACAATTTGATA 59.252 47.619 7.64 0.00 36.21 2.15
612 613 0.532115 GGGCGCTTCCACAATTTGAT 59.468 50.000 7.64 0.00 36.21 2.57
1101 1111 3.454858 AGGGATATTCCTGACGGCATAT 58.545 45.455 0.07 0.00 36.57 1.78
1254 1264 3.456798 CGACTGTTCTCGCAGCAG 58.543 61.111 0.00 0.00 39.96 4.24
1344 1354 2.125952 CACGCCGAGATGACTGCA 60.126 61.111 0.00 0.00 0.00 4.41
1356 1366 1.460359 CAATCCAATTTTGTGCACGCC 59.540 47.619 13.13 0.00 0.00 5.68
1444 1454 2.820059 TGGATGAGCGAATTAGCGAT 57.180 45.000 4.82 1.68 43.00 4.58
1449 1459 5.806366 CATGCATATGGATGAGCGAATTA 57.194 39.130 27.85 0.00 45.22 1.40
1614 1624 0.984230 CAGGCCAGAACCCTTGTCTA 59.016 55.000 5.01 0.00 0.00 2.59
1700 1710 1.535462 CGACCATGGACTTGAACAACC 59.465 52.381 21.47 0.00 0.00 3.77
1721 1731 5.208121 TCCATGGTGTGATGTGATAGTCTA 58.792 41.667 12.58 0.00 0.00 2.59
1842 1852 4.052608 CGGTCAATACACGCCATATTACA 58.947 43.478 0.00 0.00 0.00 2.41
1885 1895 6.223852 TCACCTTCCTCGCTAAATTCATATC 58.776 40.000 0.00 0.00 0.00 1.63
1937 1947 1.615392 GCACATAATTCCCCTCATGGC 59.385 52.381 0.00 0.00 0.00 4.40
1980 1990 2.253610 ACACGTCCCCAGTTCTCATTA 58.746 47.619 0.00 0.00 0.00 1.90
2075 2085 4.524316 TCTGCATTTTCTTCACCATTGG 57.476 40.909 0.00 0.00 0.00 3.16
2206 2217 8.579850 TCCTGAATTTGTATAGAAACTTGCAT 57.420 30.769 0.00 0.00 0.00 3.96
2229 2240 8.608317 GCAGAAGACTAAGAAGTATCAAATTCC 58.392 37.037 0.00 0.00 35.56 3.01
2269 2280 7.562088 TCCAATTTGACCAATAATAACCTACCC 59.438 37.037 0.00 0.00 0.00 3.69
2276 2287 7.148154 CCGACAGTCCAATTTGACCAATAATAA 60.148 37.037 6.07 0.00 35.83 1.40
2364 2375 9.953697 GTATACTAAGACGATCTTCAAGATGTT 57.046 33.333 4.06 0.00 37.89 2.71
2474 2488 3.633986 CCACTGAATTATCTGGCCCTTTC 59.366 47.826 0.00 0.00 0.00 2.62
2558 2572 9.458727 CCAAATGGCTGTATATCATCTTCTTAT 57.541 33.333 0.00 0.00 0.00 1.73
2592 2606 0.034896 GTGGAGAGGGTCGCTTTTCA 59.965 55.000 0.00 0.00 0.00 2.69
2620 2634 4.553330 TTTCTTAGCCAGGATCTCGTTT 57.447 40.909 0.00 0.00 0.00 3.60
2734 2748 3.953612 TCCAGGATCACAAATTGTATGGC 59.046 43.478 0.00 0.00 0.00 4.40
2750 2764 4.215908 AGAAATAGTCGCATACTCCAGGA 58.784 43.478 0.00 0.00 39.80 3.86
2823 2837 7.850935 TTATGAGACGGAGGGAGTAATAAAT 57.149 36.000 0.00 0.00 0.00 1.40
2892 2906 7.822334 TCCCATAAGCCATAATATAAGACGTTG 59.178 37.037 0.00 0.00 0.00 4.10
3013 3027 4.146058 TGCTCCAGTGCACTTGTG 57.854 55.556 18.94 15.94 38.12 3.33
3069 3084 4.569761 AATCATGATGCAAGATGTCAGC 57.430 40.909 9.46 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.