Multiple sequence alignment - TraesCS2A01G388600

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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 TraesCS2A01G388600 chr2A 100.000 3810 0 0 1 3810 635929456 635933265 0.000000e+00 7036.0
1 TraesCS2A01G388600 chr2A 78.903 474 80 12 2357 2817 608922638 608922172 1.720000e-78 303.0
2 TraesCS2A01G388600 chr2A 80.282 213 26 8 2244 2456 608593414 608593610 3.070000e-31 147.0
3 TraesCS2A01G388600 chr2A 86.916 107 12 2 1381 1487 608898955 608899059 6.690000e-23 119.0
4 TraesCS2A01G388600 chr2D 93.631 3454 162 32 266 3680 491498293 491501727 0.000000e+00 5107.0
5 TraesCS2A01G388600 chr2D 82.151 465 77 6 1381 1844 468978060 468978519 9.920000e-106 394.0
6 TraesCS2A01G388600 chr2D 80.822 511 77 11 2559 3062 548267030 548266534 7.720000e-102 381.0
7 TraesCS2A01G388600 chr2D 79.237 472 79 11 2359 2817 469103332 469102867 1.030000e-80 311.0
8 TraesCS2A01G388600 chr2D 81.081 333 51 9 1773 2097 548267640 548267312 4.880000e-64 255.0
9 TraesCS2A01G388600 chr2D 91.892 111 9 0 3696 3806 491501964 491502074 5.100000e-34 156.0
10 TraesCS2A01G388600 chr2B 95.719 1635 61 4 1524 3152 575935283 575936914 0.000000e+00 2623.0
11 TraesCS2A01G388600 chr2B 89.495 1228 53 41 309 1492 575934088 575935283 0.000000e+00 1483.0
12 TraesCS2A01G388600 chr2B 91.536 319 19 3 3168 3479 575937203 575937520 2.100000e-117 433.0
13 TraesCS2A01G388600 chr2B 79.225 568 102 12 1372 1930 546817634 546818194 7.720000e-102 381.0
14 TraesCS2A01G388600 chr2B 79.630 486 93 5 1331 1815 547350714 547350234 1.010000e-90 344.0
15 TraesCS2A01G388600 chr2B 90.404 198 19 0 3613 3810 575948262 575948459 1.050000e-65 261.0
16 TraesCS2A01G388600 chr2B 91.558 154 11 2 3469 3620 575946568 575946721 1.070000e-50 211.0
17 TraesCS2A01G388600 chr2B 78.972 214 27 8 2244 2456 546833987 546834183 3.090000e-26 130.0
18 TraesCS2A01G388600 chr2B 87.342 79 10 0 186 264 601432970 601433048 1.460000e-14 91.6
19 TraesCS2A01G388600 chr2B 94.286 35 1 1 212 246 49688979 49688946 7.000000e-03 52.8
20 TraesCS2A01G388600 chr2B 94.286 35 1 1 212 246 49720967 49720934 7.000000e-03 52.8
21 TraesCS2A01G388600 chr3D 81.379 580 92 14 3207 3776 438263986 438263413 3.470000e-125 459.0
22 TraesCS2A01G388600 chr7D 81.282 577 95 9 3207 3773 83375319 83375892 4.490000e-124 455.0
23 TraesCS2A01G388600 chr7D 82.427 478 73 5 1372 1843 32998002 32998474 1.270000e-109 407.0
24 TraesCS2A01G388600 chr7D 93.976 166 10 0 1 166 548476415 548476580 6.320000e-63 252.0
25 TraesCS2A01G388600 chr7D 95.000 160 8 0 1 160 562059821 562059662 6.320000e-63 252.0
26 TraesCS2A01G388600 chr7D 89.474 133 13 1 2482 2614 32998720 32998851 2.350000e-37 167.0
27 TraesCS2A01G388600 chr7D 88.608 79 9 0 185 263 479293137 479293059 3.130000e-16 97.1
28 TraesCS2A01G388600 chr5D 81.010 574 99 8 3207 3773 331210731 331211301 7.510000e-122 448.0
29 TraesCS2A01G388600 chr5D 81.274 518 84 11 3265 3773 381781863 381782376 1.270000e-109 407.0
30 TraesCS2A01G388600 chr5D 95.597 159 7 0 1 159 425853695 425853853 4.880000e-64 255.0
31 TraesCS2A01G388600 chr5A 80.277 578 98 14 3207 3776 377929509 377928940 4.550000e-114 422.0
32 TraesCS2A01G388600 chr5A 96.226 159 6 0 1 159 120079337 120079495 1.050000e-65 261.0
33 TraesCS2A01G388600 chr5A 92.442 172 12 1 1 171 566553189 566553018 1.060000e-60 244.0
34 TraesCS2A01G388600 chr1A 81.008 516 88 9 3265 3776 93392150 93391641 5.930000e-108 401.0
35 TraesCS2A01G388600 chr1A 94.969 159 8 0 1 159 574816837 574816995 2.270000e-62 250.0
36 TraesCS2A01G388600 chr1A 92.442 172 12 1 1 171 54297769 54297940 1.060000e-60 244.0
37 TraesCS2A01G388600 chr6B 80.741 540 79 17 2482 3020 46692719 46693234 7.670000e-107 398.0
38 TraesCS2A01G388600 chr5B 80.594 438 77 6 3256 3688 480245032 480245466 7.890000e-87 331.0
39 TraesCS2A01G388600 chr4A 96.226 159 6 0 1 159 682027790 682027632 1.050000e-65 261.0
40 TraesCS2A01G388600 chr4A 94.643 56 3 0 205 260 454815164 454815109 1.890000e-13 87.9
41 TraesCS2A01G388600 chr4D 93.902 164 10 0 1 164 44833866 44834029 8.170000e-62 248.0
42 TraesCS2A01G388600 chr7B 90.244 82 6 2 183 264 719859579 719859658 5.210000e-19 106.0
43 TraesCS2A01G388600 chr7A 91.837 49 4 0 212 260 9995774 9995726 6.830000e-08 69.4
44 TraesCS2A01G388600 chrUn 96.875 32 0 1 212 243 321237805 321237835 7.000000e-03 52.8


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 TraesCS2A01G388600 chr2A 635929456 635933265 3809 False 7036.0 7036 100.0000 1 3810 1 chr2A.!!$F3 3809
1 TraesCS2A01G388600 chr2D 491498293 491502074 3781 False 2631.5 5107 92.7615 266 3806 2 chr2D.!!$F2 3540
2 TraesCS2A01G388600 chr2D 548266534 548267640 1106 True 318.0 381 80.9515 1773 3062 2 chr2D.!!$R2 1289
3 TraesCS2A01G388600 chr2B 575934088 575937520 3432 False 1513.0 2623 92.2500 309 3479 3 chr2B.!!$F4 3170
4 TraesCS2A01G388600 chr2B 546817634 546818194 560 False 381.0 381 79.2250 1372 1930 1 chr2B.!!$F1 558
5 TraesCS2A01G388600 chr2B 575946568 575948459 1891 False 236.0 261 90.9810 3469 3810 2 chr2B.!!$F5 341
6 TraesCS2A01G388600 chr3D 438263413 438263986 573 True 459.0 459 81.3790 3207 3776 1 chr3D.!!$R1 569
7 TraesCS2A01G388600 chr7D 83375319 83375892 573 False 455.0 455 81.2820 3207 3773 1 chr7D.!!$F1 566
8 TraesCS2A01G388600 chr7D 32998002 32998851 849 False 287.0 407 85.9505 1372 2614 2 chr7D.!!$F3 1242
9 TraesCS2A01G388600 chr5D 331210731 331211301 570 False 448.0 448 81.0100 3207 3773 1 chr5D.!!$F1 566
10 TraesCS2A01G388600 chr5D 381781863 381782376 513 False 407.0 407 81.2740 3265 3773 1 chr5D.!!$F2 508
11 TraesCS2A01G388600 chr5A 377928940 377929509 569 True 422.0 422 80.2770 3207 3776 1 chr5A.!!$R1 569
12 TraesCS2A01G388600 chr1A 93391641 93392150 509 True 401.0 401 81.0080 3265 3776 1 chr1A.!!$R1 511
13 TraesCS2A01G388600 chr6B 46692719 46693234 515 False 398.0 398 80.7410 2482 3020 1 chr6B.!!$F1 538

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
536 554 0.032952 TGTACGGCAAGGTGACAGAC 59.967 55.0 0.00 0.0 0.0 3.51 F
916 941 0.106519 GTCCCCTACCTACCTACGCA 60.107 60.0 0.00 0.0 0.0 5.24 F
1290 1351 0.169672 CCTGAAACGCAATGCTCCTG 59.830 55.0 2.94 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2341 2457 0.039437 AGTCGGTGTAGTTGCTGACG 60.039 55.000 0.0 0.0 43.61 4.35 R
2511 2788 0.523072 CCCCGTGTCATCTGCAAAAG 59.477 55.000 0.0 0.0 0.00 2.27 R
3111 3431 4.155826 CCGACCAATTGCTTGACTGAATTA 59.844 41.667 0.0 0.0 34.04 1.40 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
26 27 7.602265 AGTCAAAACATGTTTATAACCAATGGC 59.398 33.333 23.53 16.19 31.63 4.40
27 28 6.587990 TCAAAACATGTTTATAACCAATGGCG 59.412 34.615 23.53 0.00 31.63 5.69
28 29 4.647424 ACATGTTTATAACCAATGGCGG 57.353 40.909 0.00 0.00 0.00 6.13
29 30 4.020543 ACATGTTTATAACCAATGGCGGT 58.979 39.130 0.00 0.00 42.71 5.68
30 31 4.142271 ACATGTTTATAACCAATGGCGGTG 60.142 41.667 0.00 0.00 39.95 4.94
31 32 2.755655 TGTTTATAACCAATGGCGGTGG 59.244 45.455 0.00 4.81 39.95 4.61
36 37 4.676951 CCAATGGCGGTGGTGGGT 62.677 66.667 0.00 0.00 0.00 4.51
37 38 2.353189 CAATGGCGGTGGTGGGTA 59.647 61.111 0.00 0.00 0.00 3.69
38 39 1.303724 CAATGGCGGTGGTGGGTAA 60.304 57.895 0.00 0.00 0.00 2.85
39 40 0.682855 CAATGGCGGTGGTGGGTAAT 60.683 55.000 0.00 0.00 0.00 1.89
40 41 0.040499 AATGGCGGTGGTGGGTAATT 59.960 50.000 0.00 0.00 0.00 1.40
41 42 0.920438 ATGGCGGTGGTGGGTAATTA 59.080 50.000 0.00 0.00 0.00 1.40
42 43 0.253610 TGGCGGTGGTGGGTAATTAG 59.746 55.000 0.00 0.00 0.00 1.73
43 44 0.542805 GGCGGTGGTGGGTAATTAGA 59.457 55.000 0.00 0.00 0.00 2.10
44 45 1.474498 GGCGGTGGTGGGTAATTAGAG 60.474 57.143 0.00 0.00 0.00 2.43
45 46 1.949465 CGGTGGTGGGTAATTAGAGC 58.051 55.000 0.00 0.00 0.00 4.09
46 47 1.805120 CGGTGGTGGGTAATTAGAGCG 60.805 57.143 0.00 0.00 0.00 5.03
47 48 1.208776 GGTGGTGGGTAATTAGAGCGT 59.791 52.381 0.00 0.00 0.00 5.07
48 49 2.355412 GGTGGTGGGTAATTAGAGCGTT 60.355 50.000 0.00 0.00 0.00 4.84
49 50 2.676342 GTGGTGGGTAATTAGAGCGTTG 59.324 50.000 0.00 0.00 0.00 4.10
50 51 2.568062 TGGTGGGTAATTAGAGCGTTGA 59.432 45.455 0.00 0.00 0.00 3.18
51 52 3.008157 TGGTGGGTAATTAGAGCGTTGAA 59.992 43.478 0.00 0.00 0.00 2.69
52 53 3.373130 GGTGGGTAATTAGAGCGTTGAAC 59.627 47.826 0.00 0.00 0.00 3.18
53 54 3.061697 GTGGGTAATTAGAGCGTTGAACG 59.938 47.826 14.16 14.16 45.88 3.95
54 55 3.256558 GGGTAATTAGAGCGTTGAACGT 58.743 45.455 19.53 6.06 44.73 3.99
55 56 3.061697 GGGTAATTAGAGCGTTGAACGTG 59.938 47.826 19.53 0.00 44.73 4.49
56 57 3.676646 GGTAATTAGAGCGTTGAACGTGT 59.323 43.478 19.53 7.01 44.73 4.49
57 58 4.151157 GGTAATTAGAGCGTTGAACGTGTT 59.849 41.667 19.53 5.45 44.73 3.32
58 59 4.806342 AATTAGAGCGTTGAACGTGTTT 57.194 36.364 19.53 5.18 44.73 2.83
59 60 3.579147 TTAGAGCGTTGAACGTGTTTG 57.421 42.857 19.53 0.00 44.73 2.93
60 61 0.655733 AGAGCGTTGAACGTGTTTGG 59.344 50.000 19.53 0.00 44.73 3.28
61 62 0.375803 GAGCGTTGAACGTGTTTGGT 59.624 50.000 19.53 0.00 44.73 3.67
62 63 0.098025 AGCGTTGAACGTGTTTGGTG 59.902 50.000 19.53 0.00 44.73 4.17
63 64 1.468340 GCGTTGAACGTGTTTGGTGC 61.468 55.000 19.53 0.00 44.73 5.01
64 65 0.098025 CGTTGAACGTGTTTGGTGCT 59.902 50.000 9.94 0.00 36.74 4.40
65 66 1.822581 GTTGAACGTGTTTGGTGCTC 58.177 50.000 0.00 0.00 0.00 4.26
66 67 1.131504 GTTGAACGTGTTTGGTGCTCA 59.868 47.619 0.00 0.00 0.00 4.26
67 68 1.454201 TGAACGTGTTTGGTGCTCAA 58.546 45.000 0.00 0.00 0.00 3.02
68 69 1.131504 TGAACGTGTTTGGTGCTCAAC 59.868 47.619 0.00 0.00 34.67 3.18
69 70 1.131504 GAACGTGTTTGGTGCTCAACA 59.868 47.619 0.00 0.00 34.67 3.33
70 71 1.169577 ACGTGTTTGGTGCTCAACAA 58.830 45.000 0.00 0.00 36.00 2.83
71 72 1.748493 ACGTGTTTGGTGCTCAACAAT 59.252 42.857 0.76 0.00 37.91 2.71
72 73 2.118683 CGTGTTTGGTGCTCAACAATG 58.881 47.619 0.76 0.00 37.91 2.82
73 74 2.472816 GTGTTTGGTGCTCAACAATGG 58.527 47.619 0.76 0.00 37.91 3.16
74 75 2.100584 GTGTTTGGTGCTCAACAATGGA 59.899 45.455 0.76 0.00 37.91 3.41
75 76 2.361757 TGTTTGGTGCTCAACAATGGAG 59.638 45.455 0.76 0.00 37.91 3.86
82 83 2.888513 CTCAACAATGGAGCGACTTG 57.111 50.000 0.00 0.00 0.00 3.16
83 84 2.416747 CTCAACAATGGAGCGACTTGA 58.583 47.619 0.00 0.00 0.00 3.02
84 85 2.807967 CTCAACAATGGAGCGACTTGAA 59.192 45.455 0.00 0.00 0.00 2.69
85 86 2.548057 TCAACAATGGAGCGACTTGAAC 59.452 45.455 0.00 0.00 0.00 3.18
86 87 1.523758 ACAATGGAGCGACTTGAACC 58.476 50.000 0.00 0.00 0.00 3.62
87 88 0.443869 CAATGGAGCGACTTGAACCG 59.556 55.000 0.00 0.00 0.00 4.44
92 93 4.883026 GCGACTTGAACCGCTAGA 57.117 55.556 0.00 0.00 46.96 2.43
93 94 3.347411 GCGACTTGAACCGCTAGAT 57.653 52.632 0.00 0.00 46.96 1.98
94 95 2.486951 GCGACTTGAACCGCTAGATA 57.513 50.000 0.00 0.00 46.96 1.98
95 96 2.805845 GCGACTTGAACCGCTAGATAA 58.194 47.619 0.00 0.00 46.96 1.75
96 97 2.534757 GCGACTTGAACCGCTAGATAAC 59.465 50.000 0.00 0.00 46.96 1.89
97 98 3.766151 CGACTTGAACCGCTAGATAACA 58.234 45.455 0.00 0.00 0.00 2.41
98 99 4.360563 CGACTTGAACCGCTAGATAACAT 58.639 43.478 0.00 0.00 0.00 2.71
99 100 4.207224 CGACTTGAACCGCTAGATAACATG 59.793 45.833 0.00 0.00 0.00 3.21
100 101 5.339008 ACTTGAACCGCTAGATAACATGA 57.661 39.130 0.00 0.00 0.00 3.07
101 102 5.918608 ACTTGAACCGCTAGATAACATGAT 58.081 37.500 0.00 0.00 0.00 2.45
102 103 6.349300 ACTTGAACCGCTAGATAACATGATT 58.651 36.000 0.00 0.00 0.00 2.57
103 104 6.823689 ACTTGAACCGCTAGATAACATGATTT 59.176 34.615 0.00 0.00 0.00 2.17
104 105 6.603237 TGAACCGCTAGATAACATGATTTG 57.397 37.500 0.00 0.00 0.00 2.32
105 106 6.345298 TGAACCGCTAGATAACATGATTTGA 58.655 36.000 0.00 0.00 0.00 2.69
106 107 6.257849 TGAACCGCTAGATAACATGATTTGAC 59.742 38.462 0.00 0.00 0.00 3.18
107 108 4.745125 ACCGCTAGATAACATGATTTGACG 59.255 41.667 0.00 0.00 0.00 4.35
108 109 4.150627 CCGCTAGATAACATGATTTGACGG 59.849 45.833 0.00 0.00 0.00 4.79
109 110 4.745125 CGCTAGATAACATGATTTGACGGT 59.255 41.667 0.00 0.00 0.00 4.83
110 111 5.332581 CGCTAGATAACATGATTTGACGGTG 60.333 44.000 0.00 0.00 0.00 4.94
111 112 5.050091 GCTAGATAACATGATTTGACGGTGG 60.050 44.000 0.00 0.00 0.00 4.61
112 113 5.097742 AGATAACATGATTTGACGGTGGA 57.902 39.130 0.00 0.00 0.00 4.02
113 114 5.118990 AGATAACATGATTTGACGGTGGAG 58.881 41.667 0.00 0.00 0.00 3.86
114 115 3.417069 AACATGATTTGACGGTGGAGA 57.583 42.857 0.00 0.00 0.00 3.71
115 116 3.634397 ACATGATTTGACGGTGGAGAT 57.366 42.857 0.00 0.00 0.00 2.75
116 117 3.273434 ACATGATTTGACGGTGGAGATG 58.727 45.455 0.00 0.00 0.00 2.90
117 118 2.401583 TGATTTGACGGTGGAGATGG 57.598 50.000 0.00 0.00 0.00 3.51
118 119 1.628340 TGATTTGACGGTGGAGATGGT 59.372 47.619 0.00 0.00 0.00 3.55
119 120 2.039746 TGATTTGACGGTGGAGATGGTT 59.960 45.455 0.00 0.00 0.00 3.67
120 121 2.649531 TTTGACGGTGGAGATGGTTT 57.350 45.000 0.00 0.00 0.00 3.27
121 122 1.890876 TTGACGGTGGAGATGGTTTG 58.109 50.000 0.00 0.00 0.00 2.93
122 123 0.036164 TGACGGTGGAGATGGTTTGG 59.964 55.000 0.00 0.00 0.00 3.28
123 124 0.323629 GACGGTGGAGATGGTTTGGA 59.676 55.000 0.00 0.00 0.00 3.53
124 125 0.991920 ACGGTGGAGATGGTTTGGAT 59.008 50.000 0.00 0.00 0.00 3.41
125 126 1.065418 ACGGTGGAGATGGTTTGGATC 60.065 52.381 0.00 0.00 0.00 3.36
126 127 1.210478 CGGTGGAGATGGTTTGGATCT 59.790 52.381 0.00 0.00 32.63 2.75
127 128 2.648059 GGTGGAGATGGTTTGGATCTG 58.352 52.381 0.00 0.00 29.97 2.90
128 129 2.019984 GTGGAGATGGTTTGGATCTGC 58.980 52.381 0.00 0.00 38.43 4.26
129 130 1.064463 TGGAGATGGTTTGGATCTGCC 60.064 52.381 0.00 0.00 37.46 4.85
130 131 1.213926 GGAGATGGTTTGGATCTGCCT 59.786 52.381 0.00 0.00 33.40 4.75
131 132 2.439507 GGAGATGGTTTGGATCTGCCTA 59.560 50.000 0.00 0.00 33.40 3.93
132 133 3.073650 GGAGATGGTTTGGATCTGCCTAT 59.926 47.826 0.00 0.00 33.40 2.57
133 134 4.446889 GGAGATGGTTTGGATCTGCCTATT 60.447 45.833 0.00 0.00 33.40 1.73
134 135 5.134725 AGATGGTTTGGATCTGCCTATTT 57.865 39.130 0.00 0.00 37.63 1.40
135 136 4.891756 AGATGGTTTGGATCTGCCTATTTG 59.108 41.667 0.00 0.00 37.63 2.32
136 137 3.364549 TGGTTTGGATCTGCCTATTTGG 58.635 45.455 0.00 0.00 37.63 3.28
137 138 2.695147 GGTTTGGATCTGCCTATTTGGG 59.305 50.000 0.00 0.00 37.63 4.12
138 139 3.365472 GTTTGGATCTGCCTATTTGGGT 58.635 45.455 0.00 0.00 37.63 4.51
139 140 3.297134 TTGGATCTGCCTATTTGGGTC 57.703 47.619 0.00 0.00 37.63 4.46
140 141 2.492025 TGGATCTGCCTATTTGGGTCT 58.508 47.619 0.00 0.00 37.63 3.85
141 142 2.852449 TGGATCTGCCTATTTGGGTCTT 59.148 45.455 0.00 0.00 37.63 3.01
142 143 3.269381 TGGATCTGCCTATTTGGGTCTTT 59.731 43.478 0.00 0.00 37.63 2.52
143 144 4.264352 TGGATCTGCCTATTTGGGTCTTTT 60.264 41.667 0.00 0.00 37.63 2.27
144 145 4.711846 GGATCTGCCTATTTGGGTCTTTTT 59.288 41.667 0.00 0.00 36.00 1.94
145 146 5.891551 GGATCTGCCTATTTGGGTCTTTTTA 59.108 40.000 0.00 0.00 36.00 1.52
146 147 6.551227 GGATCTGCCTATTTGGGTCTTTTTAT 59.449 38.462 0.00 0.00 36.00 1.40
147 148 7.724061 GGATCTGCCTATTTGGGTCTTTTTATA 59.276 37.037 0.00 0.00 36.00 0.98
148 149 9.301897 GATCTGCCTATTTGGGTCTTTTTATAT 57.698 33.333 0.00 0.00 36.00 0.86
149 150 9.660544 ATCTGCCTATTTGGGTCTTTTTATATT 57.339 29.630 0.00 0.00 36.00 1.28
150 151 8.912988 TCTGCCTATTTGGGTCTTTTTATATTG 58.087 33.333 0.00 0.00 36.00 1.90
151 152 8.017418 TGCCTATTTGGGTCTTTTTATATTGG 57.983 34.615 0.00 0.00 36.00 3.16
152 153 7.621683 TGCCTATTTGGGTCTTTTTATATTGGT 59.378 33.333 0.00 0.00 36.00 3.67
153 154 9.138596 GCCTATTTGGGTCTTTTTATATTGGTA 57.861 33.333 0.00 0.00 36.00 3.25
229 230 7.961325 TGAATGTTTCAAAATAAAGGGCTTC 57.039 32.000 0.00 0.00 36.59 3.86
230 231 7.504403 TGAATGTTTCAAAATAAAGGGCTTCA 58.496 30.769 0.00 0.00 36.59 3.02
231 232 8.156165 TGAATGTTTCAAAATAAAGGGCTTCAT 58.844 29.630 0.00 0.00 36.59 2.57
232 233 7.910441 ATGTTTCAAAATAAAGGGCTTCATG 57.090 32.000 0.00 0.00 0.00 3.07
233 234 6.229733 TGTTTCAAAATAAAGGGCTTCATGG 58.770 36.000 0.00 0.00 0.00 3.66
234 235 6.042552 TGTTTCAAAATAAAGGGCTTCATGGA 59.957 34.615 0.00 0.00 0.00 3.41
235 236 5.920193 TCAAAATAAAGGGCTTCATGGAG 57.080 39.130 0.00 0.00 0.00 3.86
236 237 4.160252 TCAAAATAAAGGGCTTCATGGAGC 59.840 41.667 18.45 18.45 41.96 4.70
237 238 3.677156 AATAAAGGGCTTCATGGAGCT 57.323 42.857 25.16 8.32 42.32 4.09
238 239 2.717639 TAAAGGGCTTCATGGAGCTC 57.282 50.000 25.16 22.36 43.65 4.09
239 240 0.700564 AAAGGGCTTCATGGAGCTCA 59.299 50.000 27.94 1.87 45.78 4.26
240 241 0.255318 AAGGGCTTCATGGAGCTCAG 59.745 55.000 27.94 4.75 45.78 3.35
241 242 0.913451 AGGGCTTCATGGAGCTCAGT 60.913 55.000 27.94 5.07 45.78 3.41
242 243 0.463474 GGGCTTCATGGAGCTCAGTC 60.463 60.000 25.16 8.25 42.81 3.51
243 244 0.540923 GGCTTCATGGAGCTCAGTCT 59.459 55.000 25.16 0.00 42.32 3.24
244 245 1.065564 GGCTTCATGGAGCTCAGTCTT 60.066 52.381 25.16 0.00 42.32 3.01
245 246 2.278854 GCTTCATGGAGCTCAGTCTTC 58.721 52.381 19.38 0.00 39.57 2.87
246 247 2.354503 GCTTCATGGAGCTCAGTCTTCA 60.355 50.000 19.38 3.06 39.57 3.02
247 248 3.867600 GCTTCATGGAGCTCAGTCTTCAA 60.868 47.826 19.38 0.00 39.57 2.69
248 249 4.321718 CTTCATGGAGCTCAGTCTTCAAA 58.678 43.478 17.19 0.00 0.00 2.69
249 250 4.356405 TCATGGAGCTCAGTCTTCAAAA 57.644 40.909 17.19 0.00 0.00 2.44
250 251 4.914983 TCATGGAGCTCAGTCTTCAAAAT 58.085 39.130 17.19 0.00 0.00 1.82
251 252 4.698780 TCATGGAGCTCAGTCTTCAAAATG 59.301 41.667 17.19 0.00 0.00 2.32
252 253 3.415212 TGGAGCTCAGTCTTCAAAATGG 58.585 45.455 17.19 0.00 0.00 3.16
253 254 2.163211 GGAGCTCAGTCTTCAAAATGGC 59.837 50.000 17.19 0.00 0.00 4.40
254 255 2.163211 GAGCTCAGTCTTCAAAATGGCC 59.837 50.000 9.40 0.00 0.00 5.36
255 256 2.165998 GCTCAGTCTTCAAAATGGCCT 58.834 47.619 3.32 0.00 0.00 5.19
256 257 3.009473 AGCTCAGTCTTCAAAATGGCCTA 59.991 43.478 3.32 0.00 0.00 3.93
257 258 3.127721 GCTCAGTCTTCAAAATGGCCTAC 59.872 47.826 3.32 0.00 0.00 3.18
258 259 4.583871 CTCAGTCTTCAAAATGGCCTACT 58.416 43.478 3.32 0.00 0.00 2.57
259 260 4.579869 TCAGTCTTCAAAATGGCCTACTC 58.420 43.478 3.32 0.00 0.00 2.59
260 261 4.287067 TCAGTCTTCAAAATGGCCTACTCT 59.713 41.667 3.32 0.00 0.00 3.24
261 262 5.483937 TCAGTCTTCAAAATGGCCTACTCTA 59.516 40.000 3.32 0.00 0.00 2.43
262 263 6.156949 TCAGTCTTCAAAATGGCCTACTCTAT 59.843 38.462 3.32 0.00 0.00 1.98
263 264 6.825721 CAGTCTTCAAAATGGCCTACTCTATT 59.174 38.462 3.32 0.00 0.00 1.73
264 265 6.825721 AGTCTTCAAAATGGCCTACTCTATTG 59.174 38.462 3.32 0.05 0.00 1.90
275 276 1.221840 CTCTATTGCCGCCACCTGT 59.778 57.895 0.00 0.00 0.00 4.00
284 285 2.434359 GCCACCTGTGTAGCCGTC 60.434 66.667 0.00 0.00 0.00 4.79
287 288 2.282674 ACCTGTGTAGCCGTCGGA 60.283 61.111 17.49 0.00 0.00 4.55
314 315 1.446099 GATCGAGCGCTCACCACAA 60.446 57.895 34.69 14.03 0.00 3.33
316 317 1.291877 ATCGAGCGCTCACCACAAAC 61.292 55.000 34.69 7.57 0.00 2.93
382 391 5.047802 CCAACCAAGAGCATCAATTACAACT 60.048 40.000 0.00 0.00 37.82 3.16
420 429 3.052036 CCAAGTTTTGGTCATTTCGCTG 58.948 45.455 0.00 0.00 45.93 5.18
430 439 0.523968 CATTTCGCTGAATGGCACCG 60.524 55.000 0.00 0.00 34.20 4.94
459 468 3.811083 TGAACAAGTATCACCACCGTTT 58.189 40.909 0.00 0.00 0.00 3.60
460 469 3.562141 TGAACAAGTATCACCACCGTTTG 59.438 43.478 0.00 0.00 0.00 2.93
461 470 1.877443 ACAAGTATCACCACCGTTTGC 59.123 47.619 0.00 0.00 0.00 3.68
462 471 1.876799 CAAGTATCACCACCGTTTGCA 59.123 47.619 0.00 0.00 0.00 4.08
463 472 2.487762 CAAGTATCACCACCGTTTGCAT 59.512 45.455 0.00 0.00 0.00 3.96
465 474 1.132262 GTATCACCACCGTTTGCATGG 59.868 52.381 1.63 1.63 39.57 3.66
467 476 2.203480 ACCACCGTTTGCATGGCT 60.203 55.556 3.12 0.00 36.96 4.75
536 554 0.032952 TGTACGGCAAGGTGACAGAC 59.967 55.000 0.00 0.00 0.00 3.51
538 556 2.758770 TACGGCAAGGTGACAGACGC 62.759 60.000 0.00 0.00 42.09 5.19
655 673 2.566529 CACTGTCGACTAGGCGCA 59.433 61.111 14.83 13.88 0.00 6.09
878 903 0.618458 TACCCACAGTCTTGCCATCC 59.382 55.000 0.00 0.00 0.00 3.51
879 904 1.379044 CCCACAGTCTTGCCATCCC 60.379 63.158 0.00 0.00 0.00 3.85
880 905 1.379044 CCACAGTCTTGCCATCCCC 60.379 63.158 0.00 0.00 0.00 4.81
881 906 1.379044 CACAGTCTTGCCATCCCCC 60.379 63.158 0.00 0.00 0.00 5.40
910 935 0.817229 CGTCTCGTCCCCTACCTACC 60.817 65.000 0.00 0.00 0.00 3.18
911 936 0.550432 GTCTCGTCCCCTACCTACCT 59.450 60.000 0.00 0.00 0.00 3.08
913 938 1.771255 TCTCGTCCCCTACCTACCTAC 59.229 57.143 0.00 0.00 0.00 3.18
914 939 0.469917 TCGTCCCCTACCTACCTACG 59.530 60.000 0.00 0.00 0.00 3.51
916 941 0.106519 GTCCCCTACCTACCTACGCA 60.107 60.000 0.00 0.00 0.00 5.24
917 942 0.184451 TCCCCTACCTACCTACGCAG 59.816 60.000 0.00 0.00 0.00 5.18
918 943 0.184451 CCCCTACCTACCTACGCAGA 59.816 60.000 0.00 0.00 0.00 4.26
919 944 1.316651 CCCTACCTACCTACGCAGAC 58.683 60.000 0.00 0.00 0.00 3.51
921 946 0.942962 CTACCTACCTACGCAGACCG 59.057 60.000 0.00 0.00 44.21 4.79
925 950 1.445716 CTACCTACGCAGACCGAGGG 61.446 65.000 0.00 0.00 41.02 4.30
941 972 3.677648 GGTGCCAAGTGCCTGCAG 61.678 66.667 6.78 6.78 40.16 4.41
985 1042 3.423154 GGTGCGTGAAGAAGCCCG 61.423 66.667 0.00 0.00 0.00 6.13
986 1043 2.357034 GTGCGTGAAGAAGCCCGA 60.357 61.111 0.00 0.00 0.00 5.14
1007 1064 2.797278 GGACGAGACCCATGGCGAT 61.797 63.158 15.23 0.00 0.00 4.58
1035 1092 4.092529 CAGTTCGTCCTGTTCATCTTCATG 59.907 45.833 0.00 0.00 0.00 3.07
1038 1095 3.006859 TCGTCCTGTTCATCTTCATGTGT 59.993 43.478 0.00 0.00 0.00 3.72
1053 1110 1.668151 GTGTTGTCTGTCCTCCCGC 60.668 63.158 0.00 0.00 0.00 6.13
1064 1121 2.577059 CTCCCGCTTCGCTGGTAA 59.423 61.111 0.00 0.00 34.54 2.85
1065 1122 1.144057 CTCCCGCTTCGCTGGTAAT 59.856 57.895 0.00 0.00 34.54 1.89
1066 1123 0.462047 CTCCCGCTTCGCTGGTAATT 60.462 55.000 0.00 0.00 34.54 1.40
1067 1124 0.461339 TCCCGCTTCGCTGGTAATTC 60.461 55.000 0.00 0.00 34.54 2.17
1068 1125 0.742990 CCCGCTTCGCTGGTAATTCA 60.743 55.000 0.00 0.00 0.00 2.57
1078 1135 4.082463 TCGCTGGTAATTCATTGGTTTTCC 60.082 41.667 0.00 0.00 41.14 3.13
1110 1170 3.935203 TCATGATTCTTCCTTTCTGCGTC 59.065 43.478 0.00 0.00 0.00 5.19
1140 1200 4.359971 TTCTGCGATTGATGATTGTTGG 57.640 40.909 0.00 0.00 0.00 3.77
1230 1290 0.463833 ATTTTCCGTCCATCGAGCCC 60.464 55.000 0.00 0.00 42.86 5.19
1267 1327 4.021544 TGCGCATAGTTGGGATTTTTCTTT 60.022 37.500 5.66 0.00 38.00 2.52
1271 1332 6.528072 CGCATAGTTGGGATTTTTCTTTTCTC 59.472 38.462 0.00 0.00 38.00 2.87
1290 1351 0.169672 CCTGAAACGCAATGCTCCTG 59.830 55.000 2.94 0.00 0.00 3.86
1291 1352 1.159285 CTGAAACGCAATGCTCCTGA 58.841 50.000 2.94 0.00 0.00 3.86
1293 1354 0.179215 GAAACGCAATGCTCCTGACG 60.179 55.000 2.94 0.00 0.00 4.35
1550 1645 0.389817 CGAGAAGCAACCGGTCATGA 60.390 55.000 8.04 0.00 0.00 3.07
1671 1771 4.784329 TCGCAGTTCGAGATGTATATCAC 58.216 43.478 2.04 0.00 43.16 3.06
1852 1962 2.238521 TCTTTCTTGCCAACATCCACC 58.761 47.619 0.00 0.00 0.00 4.61
2007 2123 3.427098 CCTTCTACAACAGCACGATCGTA 60.427 47.826 22.26 1.20 0.00 3.43
2139 2255 1.337728 TGCCGTCATTCTGATTCGTGT 60.338 47.619 0.00 0.00 0.00 4.49
2144 2260 2.028523 GTCATTCTGATTCGTGTCTGCG 59.971 50.000 0.00 0.00 0.00 5.18
2318 2434 1.272554 GGGGTACTGGAGGGTGAAGG 61.273 65.000 0.00 0.00 0.00 3.46
2319 2435 0.546988 GGGTACTGGAGGGTGAAGGT 60.547 60.000 0.00 0.00 0.00 3.50
2321 2437 0.613777 GTACTGGAGGGTGAAGGTGG 59.386 60.000 0.00 0.00 0.00 4.61
2404 2520 4.069232 CTCCGGAGCCTGACGCAA 62.069 66.667 20.67 0.00 41.38 4.85
2407 2523 2.357517 CGGAGCCTGACGCAACTT 60.358 61.111 0.00 0.00 41.38 2.66
2467 2731 7.239166 CACGATCAGTAAGTGCATAATCTTT 57.761 36.000 0.00 0.00 0.00 2.52
2511 2788 5.622233 GCAAGAATGGGTAAGAAATGTGGTC 60.622 44.000 0.00 0.00 0.00 4.02
2908 3225 3.321497 CATATACCTCCTCTTTGAGCGC 58.679 50.000 0.00 0.00 0.00 5.92
3022 3342 7.546358 CAATTACATGGTCCTTTGATGCTTAA 58.454 34.615 0.00 0.00 0.00 1.85
3111 3431 6.365970 ACATGTTCTACTCACTCCAATCTT 57.634 37.500 0.00 0.00 0.00 2.40
3358 3962 1.984570 CGGCAGGGACTTCTCCTCA 60.985 63.158 0.00 0.00 34.60 3.86
3484 4097 1.106944 GCTTCTCTCCTCCTCCCTCG 61.107 65.000 0.00 0.00 0.00 4.63
3733 6116 2.280797 GTGCACTGCCAACTCCGA 60.281 61.111 10.32 0.00 0.00 4.55
3790 6173 0.320771 GGTGGTCTGCTCGTGATTGT 60.321 55.000 0.00 0.00 0.00 2.71
3800 6183 0.317160 TCGTGATTGTTGGAGCGACT 59.683 50.000 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.602265 GCCATTGGTTATAAACATGTTTTGACT 59.398 33.333 27.66 13.23 34.23 3.41
1 2 7.411372 CGCCATTGGTTATAAACATGTTTTGAC 60.411 37.037 27.66 21.04 34.23 3.18
2 3 6.587990 CGCCATTGGTTATAAACATGTTTTGA 59.412 34.615 27.66 12.43 34.23 2.69
4 5 5.872070 CCGCCATTGGTTATAAACATGTTTT 59.128 36.000 27.66 17.34 34.23 2.43
5 6 5.046950 ACCGCCATTGGTTATAAACATGTTT 60.047 36.000 25.99 25.99 39.99 2.83
7 8 4.020543 ACCGCCATTGGTTATAAACATGT 58.979 39.130 3.54 0.00 39.99 3.21
8 9 4.358851 CACCGCCATTGGTTATAAACATG 58.641 43.478 3.54 5.19 41.38 3.21
9 10 3.383185 CCACCGCCATTGGTTATAAACAT 59.617 43.478 3.54 0.00 41.38 2.71
10 11 2.755655 CCACCGCCATTGGTTATAAACA 59.244 45.455 0.00 0.00 41.38 2.83
11 12 2.756207 ACCACCGCCATTGGTTATAAAC 59.244 45.455 4.26 0.00 45.62 2.01
12 13 2.755655 CACCACCGCCATTGGTTATAAA 59.244 45.455 4.26 0.00 45.62 1.40
13 14 2.370349 CACCACCGCCATTGGTTATAA 58.630 47.619 4.26 0.00 45.62 0.98
14 15 1.408961 CCACCACCGCCATTGGTTATA 60.409 52.381 4.26 0.00 45.62 0.98
15 16 0.682855 CCACCACCGCCATTGGTTAT 60.683 55.000 4.26 0.00 45.62 1.89
16 17 1.303724 CCACCACCGCCATTGGTTA 60.304 57.895 4.26 0.00 45.62 2.85
17 18 2.600173 CCACCACCGCCATTGGTT 60.600 61.111 4.26 0.00 45.62 3.67
19 20 2.773007 TTACCCACCACCGCCATTGG 62.773 60.000 0.00 0.00 40.32 3.16
20 21 0.682855 ATTACCCACCACCGCCATTG 60.683 55.000 0.00 0.00 0.00 2.82
21 22 0.040499 AATTACCCACCACCGCCATT 59.960 50.000 0.00 0.00 0.00 3.16
22 23 0.920438 TAATTACCCACCACCGCCAT 59.080 50.000 0.00 0.00 0.00 4.40
23 24 0.253610 CTAATTACCCACCACCGCCA 59.746 55.000 0.00 0.00 0.00 5.69
24 25 0.542805 TCTAATTACCCACCACCGCC 59.457 55.000 0.00 0.00 0.00 6.13
25 26 1.949465 CTCTAATTACCCACCACCGC 58.051 55.000 0.00 0.00 0.00 5.68
26 27 1.805120 CGCTCTAATTACCCACCACCG 60.805 57.143 0.00 0.00 0.00 4.94
27 28 1.208776 ACGCTCTAATTACCCACCACC 59.791 52.381 0.00 0.00 0.00 4.61
28 29 2.676342 CAACGCTCTAATTACCCACCAC 59.324 50.000 0.00 0.00 0.00 4.16
29 30 2.568062 TCAACGCTCTAATTACCCACCA 59.432 45.455 0.00 0.00 0.00 4.17
30 31 3.255969 TCAACGCTCTAATTACCCACC 57.744 47.619 0.00 0.00 0.00 4.61
31 32 3.061697 CGTTCAACGCTCTAATTACCCAC 59.938 47.826 0.00 0.00 33.65 4.61
32 33 3.255725 CGTTCAACGCTCTAATTACCCA 58.744 45.455 0.00 0.00 33.65 4.51
33 34 3.920112 CGTTCAACGCTCTAATTACCC 57.080 47.619 0.00 0.00 33.65 3.69
46 47 1.131504 TGAGCACCAAACACGTTCAAC 59.868 47.619 0.00 0.00 0.00 3.18
47 48 1.454201 TGAGCACCAAACACGTTCAA 58.546 45.000 0.00 0.00 0.00 2.69
48 49 1.131504 GTTGAGCACCAAACACGTTCA 59.868 47.619 0.00 0.00 36.36 3.18
49 50 1.131504 TGTTGAGCACCAAACACGTTC 59.868 47.619 0.00 0.00 36.36 3.95
50 51 1.169577 TGTTGAGCACCAAACACGTT 58.830 45.000 0.00 0.00 36.36 3.99
51 52 1.169577 TTGTTGAGCACCAAACACGT 58.830 45.000 0.00 0.00 36.36 4.49
52 53 2.118683 CATTGTTGAGCACCAAACACG 58.881 47.619 0.00 0.00 36.36 4.49
53 54 2.100584 TCCATTGTTGAGCACCAAACAC 59.899 45.455 0.00 0.00 36.36 3.32
54 55 2.361757 CTCCATTGTTGAGCACCAAACA 59.638 45.455 0.00 0.00 36.36 2.83
55 56 3.017265 CTCCATTGTTGAGCACCAAAC 57.983 47.619 0.00 0.00 36.36 2.93
63 64 2.416747 TCAAGTCGCTCCATTGTTGAG 58.583 47.619 0.00 0.00 0.00 3.02
64 65 2.542020 TCAAGTCGCTCCATTGTTGA 57.458 45.000 0.00 0.00 0.00 3.18
65 66 2.350772 GGTTCAAGTCGCTCCATTGTTG 60.351 50.000 0.00 0.00 0.00 3.33
66 67 1.880027 GGTTCAAGTCGCTCCATTGTT 59.120 47.619 0.00 0.00 0.00 2.83
67 68 1.523758 GGTTCAAGTCGCTCCATTGT 58.476 50.000 0.00 0.00 0.00 2.71
68 69 0.443869 CGGTTCAAGTCGCTCCATTG 59.556 55.000 0.00 0.00 0.00 2.82
69 70 2.840974 CGGTTCAAGTCGCTCCATT 58.159 52.632 0.00 0.00 0.00 3.16
70 71 4.598257 CGGTTCAAGTCGCTCCAT 57.402 55.556 0.00 0.00 0.00 3.41
76 77 3.766151 TGTTATCTAGCGGTTCAAGTCG 58.234 45.455 0.00 0.00 0.00 4.18
77 78 5.348986 TCATGTTATCTAGCGGTTCAAGTC 58.651 41.667 0.00 0.00 0.00 3.01
78 79 5.339008 TCATGTTATCTAGCGGTTCAAGT 57.661 39.130 0.00 0.00 0.00 3.16
79 80 6.851222 AATCATGTTATCTAGCGGTTCAAG 57.149 37.500 0.00 0.00 0.00 3.02
80 81 6.821160 TCAAATCATGTTATCTAGCGGTTCAA 59.179 34.615 0.00 0.00 0.00 2.69
81 82 6.257849 GTCAAATCATGTTATCTAGCGGTTCA 59.742 38.462 0.00 0.00 0.00 3.18
82 83 6.562270 CGTCAAATCATGTTATCTAGCGGTTC 60.562 42.308 0.00 0.00 0.00 3.62
83 84 5.234329 CGTCAAATCATGTTATCTAGCGGTT 59.766 40.000 0.00 0.00 0.00 4.44
84 85 4.745125 CGTCAAATCATGTTATCTAGCGGT 59.255 41.667 0.00 0.00 0.00 5.68
85 86 4.150627 CCGTCAAATCATGTTATCTAGCGG 59.849 45.833 0.00 0.00 0.00 5.52
86 87 4.745125 ACCGTCAAATCATGTTATCTAGCG 59.255 41.667 0.00 0.00 0.00 4.26
87 88 5.050091 CCACCGTCAAATCATGTTATCTAGC 60.050 44.000 0.00 0.00 0.00 3.42
88 89 6.280643 TCCACCGTCAAATCATGTTATCTAG 58.719 40.000 0.00 0.00 0.00 2.43
89 90 6.097696 TCTCCACCGTCAAATCATGTTATCTA 59.902 38.462 0.00 0.00 0.00 1.98
90 91 5.097742 TCCACCGTCAAATCATGTTATCT 57.902 39.130 0.00 0.00 0.00 1.98
91 92 5.116180 TCTCCACCGTCAAATCATGTTATC 58.884 41.667 0.00 0.00 0.00 1.75
92 93 5.097742 TCTCCACCGTCAAATCATGTTAT 57.902 39.130 0.00 0.00 0.00 1.89
93 94 4.545208 TCTCCACCGTCAAATCATGTTA 57.455 40.909 0.00 0.00 0.00 2.41
94 95 3.417069 TCTCCACCGTCAAATCATGTT 57.583 42.857 0.00 0.00 0.00 2.71
95 96 3.273434 CATCTCCACCGTCAAATCATGT 58.727 45.455 0.00 0.00 0.00 3.21
96 97 2.615447 CCATCTCCACCGTCAAATCATG 59.385 50.000 0.00 0.00 0.00 3.07
97 98 2.239654 ACCATCTCCACCGTCAAATCAT 59.760 45.455 0.00 0.00 0.00 2.45
98 99 1.628340 ACCATCTCCACCGTCAAATCA 59.372 47.619 0.00 0.00 0.00 2.57
99 100 2.403252 ACCATCTCCACCGTCAAATC 57.597 50.000 0.00 0.00 0.00 2.17
100 101 2.819608 CAAACCATCTCCACCGTCAAAT 59.180 45.455 0.00 0.00 0.00 2.32
101 102 2.226330 CAAACCATCTCCACCGTCAAA 58.774 47.619 0.00 0.00 0.00 2.69
102 103 1.544537 CCAAACCATCTCCACCGTCAA 60.545 52.381 0.00 0.00 0.00 3.18
103 104 0.036164 CCAAACCATCTCCACCGTCA 59.964 55.000 0.00 0.00 0.00 4.35
104 105 0.323629 TCCAAACCATCTCCACCGTC 59.676 55.000 0.00 0.00 0.00 4.79
105 106 0.991920 ATCCAAACCATCTCCACCGT 59.008 50.000 0.00 0.00 0.00 4.83
106 107 1.210478 AGATCCAAACCATCTCCACCG 59.790 52.381 0.00 0.00 0.00 4.94
107 108 2.648059 CAGATCCAAACCATCTCCACC 58.352 52.381 0.00 0.00 0.00 4.61
108 109 2.019984 GCAGATCCAAACCATCTCCAC 58.980 52.381 0.00 0.00 0.00 4.02
109 110 1.064463 GGCAGATCCAAACCATCTCCA 60.064 52.381 0.00 0.00 34.01 3.86
110 111 1.213926 AGGCAGATCCAAACCATCTCC 59.786 52.381 0.00 0.00 37.29 3.71
111 112 2.725221 AGGCAGATCCAAACCATCTC 57.275 50.000 0.00 0.00 37.29 2.75
112 113 4.803329 AATAGGCAGATCCAAACCATCT 57.197 40.909 0.00 0.00 37.29 2.90
113 114 4.038402 CCAAATAGGCAGATCCAAACCATC 59.962 45.833 0.00 0.00 37.29 3.51
114 115 3.962718 CCAAATAGGCAGATCCAAACCAT 59.037 43.478 0.00 0.00 37.29 3.55
115 116 3.364549 CCAAATAGGCAGATCCAAACCA 58.635 45.455 0.00 0.00 37.29 3.67
116 117 2.695147 CCCAAATAGGCAGATCCAAACC 59.305 50.000 0.00 0.00 37.29 3.27
117 118 3.365472 ACCCAAATAGGCAGATCCAAAC 58.635 45.455 0.00 0.00 37.29 2.93
118 119 3.269381 AGACCCAAATAGGCAGATCCAAA 59.731 43.478 0.00 0.00 37.29 3.28
119 120 2.852449 AGACCCAAATAGGCAGATCCAA 59.148 45.455 0.00 0.00 37.29 3.53
120 121 2.492025 AGACCCAAATAGGCAGATCCA 58.508 47.619 0.00 0.00 37.29 3.41
121 122 3.584733 AAGACCCAAATAGGCAGATCC 57.415 47.619 0.00 0.00 35.39 3.36
122 123 5.921962 AAAAAGACCCAAATAGGCAGATC 57.078 39.130 0.00 0.00 35.39 2.75
123 124 9.660544 AATATAAAAAGACCCAAATAGGCAGAT 57.339 29.630 0.00 0.00 35.39 2.90
124 125 8.912988 CAATATAAAAAGACCCAAATAGGCAGA 58.087 33.333 0.00 0.00 35.39 4.26
125 126 8.143835 CCAATATAAAAAGACCCAAATAGGCAG 58.856 37.037 0.00 0.00 35.39 4.85
126 127 7.621683 ACCAATATAAAAAGACCCAAATAGGCA 59.378 33.333 0.00 0.00 35.39 4.75
127 128 8.018537 ACCAATATAAAAAGACCCAAATAGGC 57.981 34.615 0.00 0.00 35.39 3.93
205 206 7.504403 TGAAGCCCTTTATTTTGAAACATTCA 58.496 30.769 0.00 0.00 38.04 2.57
206 207 7.961325 TGAAGCCCTTTATTTTGAAACATTC 57.039 32.000 0.00 0.00 0.00 2.67
207 208 7.391275 CCATGAAGCCCTTTATTTTGAAACATT 59.609 33.333 0.00 0.00 0.00 2.71
208 209 6.880529 CCATGAAGCCCTTTATTTTGAAACAT 59.119 34.615 0.00 0.00 0.00 2.71
209 210 6.042552 TCCATGAAGCCCTTTATTTTGAAACA 59.957 34.615 0.00 0.00 0.00 2.83
210 211 6.463360 TCCATGAAGCCCTTTATTTTGAAAC 58.537 36.000 0.00 0.00 0.00 2.78
211 212 6.678568 TCCATGAAGCCCTTTATTTTGAAA 57.321 33.333 0.00 0.00 0.00 2.69
212 213 5.337491 GCTCCATGAAGCCCTTTATTTTGAA 60.337 40.000 0.00 0.00 36.22 2.69
213 214 4.160252 GCTCCATGAAGCCCTTTATTTTGA 59.840 41.667 0.00 0.00 36.22 2.69
214 215 4.161001 AGCTCCATGAAGCCCTTTATTTTG 59.839 41.667 0.00 0.00 43.56 2.44
215 216 4.356436 AGCTCCATGAAGCCCTTTATTTT 58.644 39.130 0.00 0.00 43.56 1.82
216 217 3.956848 GAGCTCCATGAAGCCCTTTATTT 59.043 43.478 0.00 0.00 43.56 1.40
217 218 3.053395 TGAGCTCCATGAAGCCCTTTATT 60.053 43.478 12.15 0.00 43.56 1.40
218 219 2.511218 TGAGCTCCATGAAGCCCTTTAT 59.489 45.455 12.15 0.00 43.56 1.40
219 220 1.915489 TGAGCTCCATGAAGCCCTTTA 59.085 47.619 12.15 0.00 43.56 1.85
220 221 0.700564 TGAGCTCCATGAAGCCCTTT 59.299 50.000 12.15 0.00 43.56 3.11
221 222 0.255318 CTGAGCTCCATGAAGCCCTT 59.745 55.000 12.15 0.00 43.56 3.95
222 223 0.913451 ACTGAGCTCCATGAAGCCCT 60.913 55.000 12.15 0.00 43.56 5.19
223 224 0.463474 GACTGAGCTCCATGAAGCCC 60.463 60.000 12.15 0.00 43.56 5.19
224 225 0.540923 AGACTGAGCTCCATGAAGCC 59.459 55.000 12.15 0.00 43.56 4.35
225 226 2.278854 GAAGACTGAGCTCCATGAAGC 58.721 52.381 12.15 0.00 42.82 3.86
226 227 3.606595 TGAAGACTGAGCTCCATGAAG 57.393 47.619 12.15 3.67 0.00 3.02
227 228 4.356405 TTTGAAGACTGAGCTCCATGAA 57.644 40.909 12.15 0.00 0.00 2.57
228 229 4.356405 TTTTGAAGACTGAGCTCCATGA 57.644 40.909 12.15 0.00 0.00 3.07
229 230 4.142447 CCATTTTGAAGACTGAGCTCCATG 60.142 45.833 12.15 4.07 0.00 3.66
230 231 4.015084 CCATTTTGAAGACTGAGCTCCAT 58.985 43.478 12.15 0.00 0.00 3.41
231 232 3.415212 CCATTTTGAAGACTGAGCTCCA 58.585 45.455 12.15 0.00 0.00 3.86
232 233 2.163211 GCCATTTTGAAGACTGAGCTCC 59.837 50.000 12.15 0.00 0.00 4.70
233 234 2.163211 GGCCATTTTGAAGACTGAGCTC 59.837 50.000 6.82 6.82 0.00 4.09
234 235 2.165998 GGCCATTTTGAAGACTGAGCT 58.834 47.619 0.00 0.00 0.00 4.09
235 236 2.165998 AGGCCATTTTGAAGACTGAGC 58.834 47.619 5.01 0.00 0.00 4.26
236 237 4.583871 AGTAGGCCATTTTGAAGACTGAG 58.416 43.478 5.01 0.00 0.00 3.35
237 238 4.287067 AGAGTAGGCCATTTTGAAGACTGA 59.713 41.667 5.01 0.00 0.00 3.41
238 239 4.583871 AGAGTAGGCCATTTTGAAGACTG 58.416 43.478 5.01 0.00 0.00 3.51
239 240 4.917906 AGAGTAGGCCATTTTGAAGACT 57.082 40.909 5.01 0.00 0.00 3.24
240 241 6.458888 GCAATAGAGTAGGCCATTTTGAAGAC 60.459 42.308 5.01 0.00 0.00 3.01
241 242 5.590259 GCAATAGAGTAGGCCATTTTGAAGA 59.410 40.000 5.01 0.00 0.00 2.87
242 243 5.221126 GGCAATAGAGTAGGCCATTTTGAAG 60.221 44.000 5.01 0.00 45.70 3.02
243 244 4.644685 GGCAATAGAGTAGGCCATTTTGAA 59.355 41.667 5.01 0.00 45.70 2.69
244 245 4.207165 GGCAATAGAGTAGGCCATTTTGA 58.793 43.478 5.01 0.00 45.70 2.69
245 246 3.003689 CGGCAATAGAGTAGGCCATTTTG 59.996 47.826 5.01 0.00 46.75 2.44
246 247 3.214328 CGGCAATAGAGTAGGCCATTTT 58.786 45.455 5.01 0.00 46.75 1.82
247 248 2.851195 CGGCAATAGAGTAGGCCATTT 58.149 47.619 5.01 0.00 46.75 2.32
248 249 1.543429 GCGGCAATAGAGTAGGCCATT 60.543 52.381 5.01 0.00 46.75 3.16
249 250 0.035458 GCGGCAATAGAGTAGGCCAT 59.965 55.000 5.01 0.00 46.75 4.40
250 251 1.445942 GCGGCAATAGAGTAGGCCA 59.554 57.895 5.01 0.00 46.75 5.36
251 252 1.301795 GGCGGCAATAGAGTAGGCC 60.302 63.158 3.07 0.00 42.98 5.19
252 253 0.880718 GTGGCGGCAATAGAGTAGGC 60.881 60.000 15.50 0.00 0.00 3.93
253 254 0.249911 GGTGGCGGCAATAGAGTAGG 60.250 60.000 15.50 0.00 0.00 3.18
254 255 0.753262 AGGTGGCGGCAATAGAGTAG 59.247 55.000 15.50 0.00 0.00 2.57
255 256 0.464036 CAGGTGGCGGCAATAGAGTA 59.536 55.000 15.50 0.00 0.00 2.59
256 257 1.221840 CAGGTGGCGGCAATAGAGT 59.778 57.895 15.50 0.00 0.00 3.24
257 258 1.091771 CACAGGTGGCGGCAATAGAG 61.092 60.000 15.50 4.87 0.00 2.43
258 259 1.078497 CACAGGTGGCGGCAATAGA 60.078 57.895 15.50 0.00 0.00 1.98
259 260 0.107897 TACACAGGTGGCGGCAATAG 60.108 55.000 15.50 8.84 34.19 1.73
260 261 0.107897 CTACACAGGTGGCGGCAATA 60.108 55.000 15.50 0.00 34.19 1.90
261 262 1.377202 CTACACAGGTGGCGGCAAT 60.377 57.895 15.50 1.83 34.19 3.56
262 263 2.031919 CTACACAGGTGGCGGCAA 59.968 61.111 15.50 0.00 34.19 4.52
263 264 4.697756 GCTACACAGGTGGCGGCA 62.698 66.667 7.97 7.97 41.80 5.69
275 276 1.512996 GGATCGATCCGACGGCTACA 61.513 60.000 27.93 0.00 39.18 2.74
343 344 3.469859 TGGTTGGAGGATGAATTCCCTA 58.530 45.455 2.27 0.00 46.81 3.53
356 365 4.701651 TGTAATTGATGCTCTTGGTTGGAG 59.298 41.667 0.00 0.00 0.00 3.86
382 391 0.106894 TGGCGTGTGTCCATGTGTAA 59.893 50.000 0.00 0.00 0.00 2.41
420 429 0.096976 CATCGTTCACGGTGCCATTC 59.903 55.000 2.51 0.00 43.89 2.67
430 439 4.688879 TGGTGATACTTGTTCATCGTTCAC 59.311 41.667 0.00 0.00 33.28 3.18
536 554 1.733041 TTCGTTTCCTCTCTGCGCG 60.733 57.895 0.00 0.00 0.00 6.86
538 556 1.945776 GCGTTCGTTTCCTCTCTGCG 61.946 60.000 0.00 0.00 0.00 5.18
611 629 1.371558 GGAAGTCCAGTTGGCGTCT 59.628 57.895 0.00 0.00 35.64 4.18
655 673 5.336849 CGGACACTGATTACTCTCCTTTTCT 60.337 44.000 0.00 0.00 0.00 2.52
878 903 1.758906 GAGACGAGGGGAAGAGGGG 60.759 68.421 0.00 0.00 0.00 4.79
879 904 2.122167 CGAGACGAGGGGAAGAGGG 61.122 68.421 0.00 0.00 0.00 4.30
880 905 1.378124 GACGAGACGAGGGGAAGAGG 61.378 65.000 0.00 0.00 0.00 3.69
881 906 1.378124 GGACGAGACGAGGGGAAGAG 61.378 65.000 0.00 0.00 0.00 2.85
910 935 2.490217 CACCCTCGGTCTGCGTAG 59.510 66.667 0.00 0.00 31.02 3.51
911 936 3.755628 GCACCCTCGGTCTGCGTA 61.756 66.667 0.00 0.00 31.02 4.42
914 939 4.329545 TTGGCACCCTCGGTCTGC 62.330 66.667 0.00 0.00 31.02 4.26
916 941 2.526873 ACTTGGCACCCTCGGTCT 60.527 61.111 0.00 0.00 31.02 3.85
917 942 2.358737 CACTTGGCACCCTCGGTC 60.359 66.667 0.00 0.00 31.02 4.79
918 943 4.643387 GCACTTGGCACCCTCGGT 62.643 66.667 0.00 0.00 43.97 4.69
941 972 1.203313 CCGACAAAACGACGCCTTC 59.797 57.895 0.00 0.00 35.09 3.46
985 1042 2.022240 GCCATGGGTCTCGTCCTCTC 62.022 65.000 15.13 0.00 0.00 3.20
986 1043 2.060980 GCCATGGGTCTCGTCCTCT 61.061 63.158 15.13 0.00 0.00 3.69
990 1047 1.592669 CATCGCCATGGGTCTCGTC 60.593 63.158 15.13 0.00 0.00 4.20
1007 1064 0.033504 GAACAGGACGAACTGCTCCA 59.966 55.000 10.25 0.00 42.21 3.86
1035 1092 1.668151 GCGGGAGGACAGACAACAC 60.668 63.158 0.00 0.00 0.00 3.32
1038 1095 1.671742 GAAGCGGGAGGACAGACAA 59.328 57.895 0.00 0.00 0.00 3.18
1053 1110 4.701956 AACCAATGAATTACCAGCGAAG 57.298 40.909 0.00 0.00 0.00 3.79
1064 1121 4.223477 CACATCAGGGGAAAACCAATGAAT 59.777 41.667 0.00 0.00 42.91 2.57
1065 1122 3.577848 CACATCAGGGGAAAACCAATGAA 59.422 43.478 0.00 0.00 42.91 2.57
1066 1123 3.164268 CACATCAGGGGAAAACCAATGA 58.836 45.455 0.00 0.00 42.91 2.57
1067 1124 2.899256 ACACATCAGGGGAAAACCAATG 59.101 45.455 0.00 0.00 42.91 2.82
1068 1125 3.165071 GACACATCAGGGGAAAACCAAT 58.835 45.455 0.00 0.00 42.91 3.16
1078 1135 3.881688 GGAAGAATCATGACACATCAGGG 59.118 47.826 0.00 0.00 38.57 4.45
1110 1170 4.573607 TCATCAATCGCAGAATCAAAGGAG 59.426 41.667 0.00 0.00 43.58 3.69
1140 1200 1.009389 CCAGAGAGACACGGCGAAAC 61.009 60.000 16.62 3.69 0.00 2.78
1267 1327 1.806542 GAGCATTGCGTTTCAGGAGAA 59.193 47.619 2.38 0.00 0.00 2.87
1271 1332 0.169672 CAGGAGCATTGCGTTTCAGG 59.830 55.000 2.38 0.00 0.00 3.86
1290 1351 2.694043 CAGAAAATCGCGATTTCCGTC 58.306 47.619 38.58 31.85 39.88 4.79
1291 1352 1.202031 GCAGAAAATCGCGATTTCCGT 60.202 47.619 38.58 27.22 39.88 4.69
1293 1354 1.132262 TGGCAGAAAATCGCGATTTCC 59.868 47.619 38.58 33.43 39.88 3.13
1880 1996 3.441572 CCACCAAGCCAAGAAATAGTCAG 59.558 47.826 0.00 0.00 0.00 3.51
1886 2002 0.190815 ACCCCACCAAGCCAAGAAAT 59.809 50.000 0.00 0.00 0.00 2.17
2028 2144 2.281484 GGAGAGTTTGCACCGCCA 60.281 61.111 0.00 0.00 0.00 5.69
2144 2260 1.503818 AACCGGACGAACATGCACAC 61.504 55.000 9.46 0.00 0.00 3.82
2318 2434 2.084681 CGTAGTTCGTCACCGCCAC 61.085 63.158 0.00 0.00 34.52 5.01
2319 2435 2.256158 CGTAGTTCGTCACCGCCA 59.744 61.111 0.00 0.00 34.52 5.69
2321 2437 2.142239 CGTCGTAGTTCGTCACCGC 61.142 63.158 0.00 0.00 40.80 5.68
2341 2457 0.039437 AGTCGGTGTAGTTGCTGACG 60.039 55.000 0.00 0.00 43.61 4.35
2404 2520 3.565902 GCTGGTAGTTGAAGCTGAAAAGT 59.434 43.478 0.00 0.00 34.05 2.66
2407 2523 2.504367 GGCTGGTAGTTGAAGCTGAAA 58.496 47.619 0.00 0.00 37.12 2.69
2446 2562 8.201554 TGTCAAAGATTATGCACTTACTGATC 57.798 34.615 0.00 0.00 0.00 2.92
2460 2576 9.869757 TTCGTATCATCTTCTTGTCAAAGATTA 57.130 29.630 0.00 0.00 42.04 1.75
2467 2731 5.072040 TGCTTCGTATCATCTTCTTGTCA 57.928 39.130 0.00 0.00 0.00 3.58
2511 2788 0.523072 CCCCGTGTCATCTGCAAAAG 59.477 55.000 0.00 0.00 0.00 2.27
3022 3342 5.661458 AGCTTGCACTTCGTACTATTGTAT 58.339 37.500 0.00 0.00 0.00 2.29
3111 3431 4.155826 CCGACCAATTGCTTGACTGAATTA 59.844 41.667 0.00 0.00 34.04 1.40
3249 3846 4.740822 GAATGGGGCGGCAGTGGT 62.741 66.667 12.47 0.00 0.00 4.16
3324 3928 2.456119 CCGCCGTCGTACGTCTAGT 61.456 63.158 16.05 0.00 40.58 2.57
3459 4069 0.543174 AGGAGGAGAGAAGCGGTGTT 60.543 55.000 0.00 0.00 0.00 3.32
3462 4072 1.380650 GGAGGAGGAGAGAAGCGGT 60.381 63.158 0.00 0.00 0.00 5.68
3516 4129 1.006805 GTGCTAGATCTGCGGCGAT 60.007 57.895 12.98 6.96 0.00 4.58
3757 6140 3.683937 CACCGCCAAAAGCCCTGG 61.684 66.667 0.00 0.00 38.78 4.45


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

AutoCloner maintained by Alex Coulton.