Multiple sequence alignment - TraesCS1A01G134200

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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 TraesCS1A01G134200 chr1A 100.000 2827 0 0 1 2827 200580212 200577386 0.000000e+00 5221.0
1 TraesCS1A01G134200 chr1A 97.087 206 4 2 1 204 154646410 154646615 2.080000e-91 346.0
2 TraesCS1A01G134200 chr1A 94.907 216 7 4 1 213 499641267 499641053 4.510000e-88 335.0
3 TraesCS1A01G134200 chr1A 79.832 119 15 9 195 309 327385568 327385455 8.400000e-11 78.7
4 TraesCS1A01G134200 chr1A 92.157 51 2 2 197 246 335855857 335855906 1.410000e-08 71.3
5 TraesCS1A01G134200 chr1A 78.632 117 16 9 197 309 335889722 335889833 5.050000e-08 69.4
6 TraesCS1A01G134200 chr7A 95.363 2631 115 6 197 2827 558249021 558251644 0.000000e+00 4176.0
7 TraesCS1A01G134200 chr7A 97.087 206 4 2 1 204 262311404 262311609 2.080000e-91 346.0
8 TraesCS1A01G134200 chr2B 92.619 1680 115 7 1151 2827 268008753 268007080 0.000000e+00 2407.0
9 TraesCS1A01G134200 chr2B 92.455 1047 71 6 1707 2751 262504496 262505536 0.000000e+00 1489.0
10 TraesCS1A01G134200 chr2B 89.307 1169 99 15 546 1712 262482393 262483537 0.000000e+00 1443.0
11 TraesCS1A01G134200 chr2B 87.348 577 49 13 546 1121 268009303 268008750 8.540000e-180 640.0
12 TraesCS1A01G134200 chr2B 91.525 118 9 1 384 500 268013496 268013379 8.100000e-36 161.0
13 TraesCS1A01G134200 chr2B 73.591 337 56 29 186 512 409250045 409250358 6.450000e-17 99.0
14 TraesCS1A01G134200 chr5A 94.244 1355 78 0 196 1550 220458260 220456906 0.000000e+00 2071.0
15 TraesCS1A01G134200 chr5A 95.611 1276 54 1 1552 2827 220456671 220455398 0.000000e+00 2045.0
16 TraesCS1A01G134200 chr5A 88.732 284 24 7 1 280 294708052 294708331 9.700000e-90 340.0
17 TraesCS1A01G134200 chr4B 95.538 1255 53 2 931 2184 300057889 300056637 0.000000e+00 2004.0
18 TraesCS1A01G134200 chr4B 89.782 734 55 4 934 1647 375826968 375827701 0.000000e+00 922.0
19 TraesCS1A01G134200 chr2A 95.828 719 25 4 1466 2184 761151984 761152697 0.000000e+00 1157.0
20 TraesCS1A01G134200 chr2A 80.922 1085 112 24 1425 2500 49298643 49299641 0.000000e+00 769.0
21 TraesCS1A01G134200 chr2A 96.618 207 5 2 1 205 417234706 417234500 2.700000e-90 342.0
22 TraesCS1A01G134200 chr2A 96.602 206 5 2 1 204 270336863 270337068 9.700000e-90 340.0
23 TraesCS1A01G134200 chr2A 91.463 246 20 1 1 246 361483597 361483841 1.250000e-88 337.0
24 TraesCS1A01G134200 chr6B 89.145 737 57 11 934 1648 162102448 162101713 0.000000e+00 896.0
25 TraesCS1A01G134200 chr6B 81.052 1103 146 29 1409 2500 438300188 438301238 0.000000e+00 821.0
26 TraesCS1A01G134200 chr6B 87.870 676 56 8 934 1587 516270453 516271124 0.000000e+00 771.0
27 TraesCS1A01G134200 chr6B 88.146 329 27 8 547 871 516270132 516270452 5.710000e-102 381.0
28 TraesCS1A01G134200 chr6B 87.500 328 31 6 547 871 162102769 162102449 1.240000e-98 370.0
29 TraesCS1A01G134200 chr6B 87.671 292 24 12 543 830 576574255 576573972 2.100000e-86 329.0
30 TraesCS1A01G134200 chr6D 82.521 1047 124 27 1417 2455 431253970 431254965 0.000000e+00 865.0
31 TraesCS1A01G134200 chr5B 82.025 484 75 11 1417 1894 647943015 647942538 4.390000e-108 401.0
32 TraesCS1A01G134200 chr6A 96.602 206 5 2 1 204 184696670 184696875 9.700000e-90 340.0
33 TraesCS1A01G134200 chr6A 94.907 216 7 4 1 213 499982650 499982436 4.510000e-88 335.0
34 TraesCS1A01G134200 chr6A 92.157 51 2 2 197 246 200746565 200746516 1.410000e-08 71.3
35 TraesCS1A01G134200 chr5D 87.676 284 24 7 550 830 172591382 172591657 1.260000e-83 320.0
36 TraesCS1A01G134200 chr3B 86.806 288 27 7 546 830 422524864 422524585 7.600000e-81 311.0
37 TraesCS1A01G134200 chr3B 84.429 289 23 11 546 830 589967218 589966948 6.000000e-67 265.0
38 TraesCS1A01G134200 chr3A 86.667 285 25 10 550 830 276941110 276941385 1.270000e-78 303.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G134200 chr1A 200577386 200580212 2826 True 5221.0 5221 100.0000 1 2827 1 chr1A.!!$R1 2826
1 TraesCS1A01G134200 chr7A 558249021 558251644 2623 False 4176.0 4176 95.3630 197 2827 1 chr7A.!!$F2 2630
2 TraesCS1A01G134200 chr2B 268007080 268009303 2223 True 1523.5 2407 89.9835 546 2827 2 chr2B.!!$R2 2281
3 TraesCS1A01G134200 chr2B 262504496 262505536 1040 False 1489.0 1489 92.4550 1707 2751 1 chr2B.!!$F2 1044
4 TraesCS1A01G134200 chr2B 262482393 262483537 1144 False 1443.0 1443 89.3070 546 1712 1 chr2B.!!$F1 1166
5 TraesCS1A01G134200 chr5A 220455398 220458260 2862 True 2058.0 2071 94.9275 196 2827 2 chr5A.!!$R1 2631
6 TraesCS1A01G134200 chr4B 300056637 300057889 1252 True 2004.0 2004 95.5380 931 2184 1 chr4B.!!$R1 1253
7 TraesCS1A01G134200 chr4B 375826968 375827701 733 False 922.0 922 89.7820 934 1647 1 chr4B.!!$F1 713
8 TraesCS1A01G134200 chr2A 761151984 761152697 713 False 1157.0 1157 95.8280 1466 2184 1 chr2A.!!$F4 718
9 TraesCS1A01G134200 chr2A 49298643 49299641 998 False 769.0 769 80.9220 1425 2500 1 chr2A.!!$F1 1075
10 TraesCS1A01G134200 chr6B 438300188 438301238 1050 False 821.0 821 81.0520 1409 2500 1 chr6B.!!$F1 1091
11 TraesCS1A01G134200 chr6B 162101713 162102769 1056 True 633.0 896 88.3225 547 1648 2 chr6B.!!$R2 1101
12 TraesCS1A01G134200 chr6B 516270132 516271124 992 False 576.0 771 88.0080 547 1587 2 chr6B.!!$F2 1040
13 TraesCS1A01G134200 chr6D 431253970 431254965 995 False 865.0 865 82.5210 1417 2455 1 chr6D.!!$F1 1038

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
900 904 0.392336 GCCATTCGCATCTCTCCTCT 59.608 55.0 0.0 0.0 37.47 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2127 2402 0.586319 GCTTGTCGTGTAGCTTGCAA 59.414 50.0 0.0 0.0 34.57 4.08 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
21 22 4.078639 CTTGGGGGAGTTGATACATCTC 57.921 50.000 0.00 0.00 31.58 2.75
22 23 2.408565 TGGGGGAGTTGATACATCTCC 58.591 52.381 16.12 16.12 44.93 3.71
23 24 1.344763 GGGGGAGTTGATACATCTCCG 59.655 57.143 17.18 0.00 45.96 4.63
24 25 2.040178 GGGGAGTTGATACATCTCCGT 58.960 52.381 17.18 0.00 45.96 4.69
25 26 2.036089 GGGGAGTTGATACATCTCCGTC 59.964 54.545 17.18 11.19 45.96 4.79
26 27 2.287668 GGGAGTTGATACATCTCCGTCG 60.288 54.545 17.18 0.00 45.96 5.12
27 28 2.358267 GGAGTTGATACATCTCCGTCGT 59.642 50.000 11.43 0.00 39.54 4.34
28 29 3.562973 GGAGTTGATACATCTCCGTCGTA 59.437 47.826 11.43 0.00 39.54 3.43
29 30 4.215827 GGAGTTGATACATCTCCGTCGTAT 59.784 45.833 11.43 0.00 39.54 3.06
30 31 5.359716 AGTTGATACATCTCCGTCGTATC 57.640 43.478 0.00 0.00 41.14 2.24
31 32 4.215827 AGTTGATACATCTCCGTCGTATCC 59.784 45.833 0.00 0.00 40.41 2.59
32 33 3.746940 TGATACATCTCCGTCGTATCCA 58.253 45.455 0.00 0.00 40.41 3.41
33 34 3.501062 TGATACATCTCCGTCGTATCCAC 59.499 47.826 0.00 0.00 40.41 4.02
34 35 2.054232 ACATCTCCGTCGTATCCACT 57.946 50.000 0.00 0.00 0.00 4.00
35 36 2.376109 ACATCTCCGTCGTATCCACTT 58.624 47.619 0.00 0.00 0.00 3.16
36 37 2.758979 ACATCTCCGTCGTATCCACTTT 59.241 45.455 0.00 0.00 0.00 2.66
37 38 3.194968 ACATCTCCGTCGTATCCACTTTT 59.805 43.478 0.00 0.00 0.00 2.27
38 39 3.498927 TCTCCGTCGTATCCACTTTTC 57.501 47.619 0.00 0.00 0.00 2.29
39 40 2.165030 TCTCCGTCGTATCCACTTTTCC 59.835 50.000 0.00 0.00 0.00 3.13
40 41 1.894466 TCCGTCGTATCCACTTTTCCA 59.106 47.619 0.00 0.00 0.00 3.53
41 42 2.299582 TCCGTCGTATCCACTTTTCCAA 59.700 45.455 0.00 0.00 0.00 3.53
42 43 3.068560 CCGTCGTATCCACTTTTCCAAA 58.931 45.455 0.00 0.00 0.00 3.28
43 44 3.120442 CCGTCGTATCCACTTTTCCAAAC 60.120 47.826 0.00 0.00 0.00 2.93
44 45 3.495377 CGTCGTATCCACTTTTCCAAACA 59.505 43.478 0.00 0.00 0.00 2.83
45 46 4.609783 CGTCGTATCCACTTTTCCAAACAC 60.610 45.833 0.00 0.00 0.00 3.32
46 47 4.514066 GTCGTATCCACTTTTCCAAACACT 59.486 41.667 0.00 0.00 0.00 3.55
47 48 5.008316 GTCGTATCCACTTTTCCAAACACTT 59.992 40.000 0.00 0.00 0.00 3.16
48 49 5.591067 TCGTATCCACTTTTCCAAACACTTT 59.409 36.000 0.00 0.00 0.00 2.66
49 50 6.095720 TCGTATCCACTTTTCCAAACACTTTT 59.904 34.615 0.00 0.00 0.00 2.27
50 51 6.198216 CGTATCCACTTTTCCAAACACTTTTG 59.802 38.462 0.00 0.00 41.71 2.44
51 52 4.249661 TCCACTTTTCCAAACACTTTTGC 58.750 39.130 0.00 0.00 40.84 3.68
52 53 3.373748 CCACTTTTCCAAACACTTTTGCC 59.626 43.478 0.00 0.00 40.84 4.52
53 54 3.373748 CACTTTTCCAAACACTTTTGCCC 59.626 43.478 0.00 0.00 40.84 5.36
54 55 3.263170 ACTTTTCCAAACACTTTTGCCCT 59.737 39.130 0.00 0.00 40.84 5.19
55 56 3.990959 TTTCCAAACACTTTTGCCCTT 57.009 38.095 0.00 0.00 40.84 3.95
56 57 2.977772 TCCAAACACTTTTGCCCTTG 57.022 45.000 0.00 0.00 40.84 3.61
57 58 2.183679 TCCAAACACTTTTGCCCTTGT 58.816 42.857 0.00 0.00 40.84 3.16
58 59 2.569404 TCCAAACACTTTTGCCCTTGTT 59.431 40.909 0.00 0.00 40.84 2.83
59 60 3.008485 TCCAAACACTTTTGCCCTTGTTT 59.992 39.130 0.00 0.00 41.69 2.83
60 61 3.755905 CCAAACACTTTTGCCCTTGTTTT 59.244 39.130 0.00 0.00 39.56 2.43
61 62 4.379290 CCAAACACTTTTGCCCTTGTTTTG 60.379 41.667 0.00 0.00 39.56 2.44
62 63 2.984562 ACACTTTTGCCCTTGTTTTGG 58.015 42.857 0.00 0.00 0.00 3.28
63 64 2.569404 ACACTTTTGCCCTTGTTTTGGA 59.431 40.909 0.00 0.00 0.00 3.53
64 65 2.935849 CACTTTTGCCCTTGTTTTGGAC 59.064 45.455 0.00 0.00 0.00 4.02
65 66 2.837591 ACTTTTGCCCTTGTTTTGGACT 59.162 40.909 0.00 0.00 0.00 3.85
66 67 3.118775 ACTTTTGCCCTTGTTTTGGACTC 60.119 43.478 0.00 0.00 0.00 3.36
67 68 2.452600 TTGCCCTTGTTTTGGACTCT 57.547 45.000 0.00 0.00 0.00 3.24
68 69 3.586470 TTGCCCTTGTTTTGGACTCTA 57.414 42.857 0.00 0.00 0.00 2.43
69 70 3.586470 TGCCCTTGTTTTGGACTCTAA 57.414 42.857 0.00 0.00 0.00 2.10
70 71 3.219281 TGCCCTTGTTTTGGACTCTAAC 58.781 45.455 0.00 0.00 0.00 2.34
71 72 3.117663 TGCCCTTGTTTTGGACTCTAACT 60.118 43.478 0.00 0.00 0.00 2.24
72 73 3.889538 GCCCTTGTTTTGGACTCTAACTT 59.110 43.478 0.00 0.00 0.00 2.66
73 74 4.261614 GCCCTTGTTTTGGACTCTAACTTG 60.262 45.833 0.00 0.00 0.00 3.16
74 75 4.261614 CCCTTGTTTTGGACTCTAACTTGC 60.262 45.833 0.00 0.00 0.00 4.01
75 76 4.338118 CCTTGTTTTGGACTCTAACTTGCA 59.662 41.667 0.00 0.00 0.00 4.08
76 77 5.010012 CCTTGTTTTGGACTCTAACTTGCAT 59.990 40.000 0.00 0.00 0.00 3.96
77 78 5.437289 TGTTTTGGACTCTAACTTGCATG 57.563 39.130 0.00 0.00 0.00 4.06
78 79 5.129634 TGTTTTGGACTCTAACTTGCATGA 58.870 37.500 6.60 0.00 0.00 3.07
79 80 5.769662 TGTTTTGGACTCTAACTTGCATGAT 59.230 36.000 6.60 0.00 0.00 2.45
80 81 6.265196 TGTTTTGGACTCTAACTTGCATGATT 59.735 34.615 6.60 0.30 0.00 2.57
81 82 6.899393 TTTGGACTCTAACTTGCATGATTT 57.101 33.333 6.60 0.00 0.00 2.17
82 83 5.885230 TGGACTCTAACTTGCATGATTTG 57.115 39.130 6.60 0.00 0.00 2.32
83 84 5.559770 TGGACTCTAACTTGCATGATTTGA 58.440 37.500 6.60 3.51 0.00 2.69
84 85 6.003326 TGGACTCTAACTTGCATGATTTGAA 58.997 36.000 6.60 0.00 0.00 2.69
85 86 6.660521 TGGACTCTAACTTGCATGATTTGAAT 59.339 34.615 6.60 0.00 0.00 2.57
86 87 6.971184 GGACTCTAACTTGCATGATTTGAATG 59.029 38.462 6.60 0.00 0.00 2.67
87 88 6.860080 ACTCTAACTTGCATGATTTGAATGG 58.140 36.000 6.60 0.00 0.00 3.16
88 89 6.660521 ACTCTAACTTGCATGATTTGAATGGA 59.339 34.615 6.60 0.00 0.00 3.41
89 90 7.177216 ACTCTAACTTGCATGATTTGAATGGAA 59.823 33.333 6.60 0.00 34.65 3.53
90 91 7.315142 TCTAACTTGCATGATTTGAATGGAAC 58.685 34.615 6.60 0.00 32.71 3.62
91 92 5.733620 ACTTGCATGATTTGAATGGAACT 57.266 34.783 6.60 0.00 32.71 3.01
92 93 6.839124 ACTTGCATGATTTGAATGGAACTA 57.161 33.333 6.60 0.00 32.71 2.24
93 94 7.230849 ACTTGCATGATTTGAATGGAACTAA 57.769 32.000 6.60 0.00 32.71 2.24
94 95 7.092716 ACTTGCATGATTTGAATGGAACTAAC 58.907 34.615 6.60 0.00 32.71 2.34
95 96 5.964758 TGCATGATTTGAATGGAACTAACC 58.035 37.500 0.00 0.00 0.00 2.85
96 97 5.716228 TGCATGATTTGAATGGAACTAACCT 59.284 36.000 0.00 0.00 0.00 3.50
97 98 6.038356 GCATGATTTGAATGGAACTAACCTG 58.962 40.000 0.00 0.00 0.00 4.00
98 99 6.567050 CATGATTTGAATGGAACTAACCTGG 58.433 40.000 0.00 0.00 0.00 4.45
99 100 5.886609 TGATTTGAATGGAACTAACCTGGA 58.113 37.500 0.00 0.00 0.00 3.86
100 101 5.710099 TGATTTGAATGGAACTAACCTGGAC 59.290 40.000 0.00 0.00 0.00 4.02
101 102 4.993705 TTGAATGGAACTAACCTGGACT 57.006 40.909 0.00 0.00 0.00 3.85
102 103 4.286297 TGAATGGAACTAACCTGGACTG 57.714 45.455 0.00 0.00 0.00 3.51
103 104 3.907474 TGAATGGAACTAACCTGGACTGA 59.093 43.478 0.00 0.00 0.00 3.41
104 105 3.983044 ATGGAACTAACCTGGACTGAC 57.017 47.619 0.00 0.00 0.00 3.51
105 106 1.616865 TGGAACTAACCTGGACTGACG 59.383 52.381 0.00 0.00 0.00 4.35
106 107 1.617357 GGAACTAACCTGGACTGACGT 59.383 52.381 0.00 0.00 0.00 4.34
107 108 2.036862 GGAACTAACCTGGACTGACGTT 59.963 50.000 0.00 0.00 0.00 3.99
108 109 2.814280 ACTAACCTGGACTGACGTTG 57.186 50.000 0.00 0.00 0.00 4.10
109 110 2.037144 ACTAACCTGGACTGACGTTGT 58.963 47.619 0.00 0.00 0.00 3.32
110 111 2.433239 ACTAACCTGGACTGACGTTGTT 59.567 45.455 0.00 0.00 0.00 2.83
111 112 2.413310 AACCTGGACTGACGTTGTTT 57.587 45.000 0.00 0.00 0.00 2.83
112 113 2.413310 ACCTGGACTGACGTTGTTTT 57.587 45.000 0.00 0.00 0.00 2.43
113 114 2.285977 ACCTGGACTGACGTTGTTTTC 58.714 47.619 0.00 0.00 0.00 2.29
114 115 2.285083 CCTGGACTGACGTTGTTTTCA 58.715 47.619 0.00 0.00 0.00 2.69
115 116 2.287915 CCTGGACTGACGTTGTTTTCAG 59.712 50.000 0.00 0.00 44.19 3.02
116 117 1.668751 TGGACTGACGTTGTTTTCAGC 59.331 47.619 0.00 0.00 42.67 4.26
117 118 1.668751 GGACTGACGTTGTTTTCAGCA 59.331 47.619 0.00 0.00 42.67 4.41
118 119 2.286418 GGACTGACGTTGTTTTCAGCAG 60.286 50.000 0.00 0.00 42.67 4.24
119 120 2.607635 GACTGACGTTGTTTTCAGCAGA 59.392 45.455 0.00 0.00 42.67 4.26
120 121 3.006940 ACTGACGTTGTTTTCAGCAGAA 58.993 40.909 0.00 0.00 42.67 3.02
121 122 3.627577 ACTGACGTTGTTTTCAGCAGAAT 59.372 39.130 0.00 0.00 42.67 2.40
122 123 4.096382 ACTGACGTTGTTTTCAGCAGAATT 59.904 37.500 0.00 0.00 42.67 2.17
123 124 4.350346 TGACGTTGTTTTCAGCAGAATTG 58.650 39.130 0.00 0.00 32.89 2.32
135 136 3.806625 GCAGAATTGCCATGGTGTTAT 57.193 42.857 14.67 0.41 44.74 1.89
136 137 4.127566 GCAGAATTGCCATGGTGTTATT 57.872 40.909 14.67 7.92 44.74 1.40
137 138 4.506758 GCAGAATTGCCATGGTGTTATTT 58.493 39.130 14.67 0.00 44.74 1.40
138 139 4.567959 GCAGAATTGCCATGGTGTTATTTC 59.432 41.667 14.67 8.44 44.74 2.17
139 140 5.625197 GCAGAATTGCCATGGTGTTATTTCT 60.625 40.000 14.67 10.43 44.74 2.52
140 141 5.808540 CAGAATTGCCATGGTGTTATTTCTG 59.191 40.000 14.67 17.25 0.00 3.02
141 142 5.481473 AGAATTGCCATGGTGTTATTTCTGT 59.519 36.000 14.67 0.00 0.00 3.41
142 143 4.517952 TTGCCATGGTGTTATTTCTGTG 57.482 40.909 14.67 0.00 0.00 3.66
143 144 2.230992 TGCCATGGTGTTATTTCTGTGC 59.769 45.455 14.67 0.00 0.00 4.57
144 145 2.230992 GCCATGGTGTTATTTCTGTGCA 59.769 45.455 14.67 0.00 0.00 4.57
145 146 3.674138 GCCATGGTGTTATTTCTGTGCAG 60.674 47.826 14.67 0.00 0.00 4.41
146 147 3.758023 CCATGGTGTTATTTCTGTGCAGA 59.242 43.478 2.57 0.00 35.27 4.26
147 148 4.218200 CCATGGTGTTATTTCTGTGCAGAA 59.782 41.667 10.26 10.26 44.94 3.02
160 161 6.228273 TCTGTGCAGAAATAAAAGTTCTCG 57.772 37.500 0.00 0.00 32.96 4.04
161 162 5.179368 TCTGTGCAGAAATAAAAGTTCTCGG 59.821 40.000 0.00 0.00 32.96 4.63
162 163 5.060506 TGTGCAGAAATAAAAGTTCTCGGA 58.939 37.500 0.00 0.00 32.96 4.55
163 164 5.529430 TGTGCAGAAATAAAAGTTCTCGGAA 59.471 36.000 0.00 0.00 32.96 4.30
164 165 6.206634 TGTGCAGAAATAAAAGTTCTCGGAAT 59.793 34.615 0.00 0.00 32.96 3.01
165 166 6.524586 GTGCAGAAATAAAAGTTCTCGGAATG 59.475 38.462 0.00 0.00 32.96 2.67
166 167 6.429692 TGCAGAAATAAAAGTTCTCGGAATGA 59.570 34.615 0.00 0.00 32.96 2.57
167 168 6.743172 GCAGAAATAAAAGTTCTCGGAATGAC 59.257 38.462 0.00 0.00 32.96 3.06
168 169 7.244192 CAGAAATAAAAGTTCTCGGAATGACC 58.756 38.462 0.00 0.00 32.96 4.02
169 170 7.119846 CAGAAATAAAAGTTCTCGGAATGACCT 59.880 37.037 0.00 0.00 32.96 3.85
170 171 8.319146 AGAAATAAAAGTTCTCGGAATGACCTA 58.681 33.333 0.00 0.00 36.31 3.08
171 172 8.857694 AAATAAAAGTTCTCGGAATGACCTAA 57.142 30.769 0.00 0.00 36.31 2.69
172 173 8.857694 AATAAAAGTTCTCGGAATGACCTAAA 57.142 30.769 0.00 0.00 36.31 1.85
173 174 8.857694 ATAAAAGTTCTCGGAATGACCTAAAA 57.142 30.769 0.00 0.00 36.31 1.52
174 175 7.576861 AAAAGTTCTCGGAATGACCTAAAAA 57.423 32.000 0.00 0.00 36.31 1.94
175 176 7.761038 AAAGTTCTCGGAATGACCTAAAAAT 57.239 32.000 0.00 0.00 36.31 1.82
176 177 6.986904 AGTTCTCGGAATGACCTAAAAATC 57.013 37.500 0.00 0.00 36.31 2.17
177 178 6.472887 AGTTCTCGGAATGACCTAAAAATCA 58.527 36.000 0.00 0.00 36.31 2.57
178 179 6.940298 AGTTCTCGGAATGACCTAAAAATCAA 59.060 34.615 0.00 0.00 36.31 2.57
179 180 6.737254 TCTCGGAATGACCTAAAAATCAAC 57.263 37.500 0.00 0.00 36.31 3.18
180 181 5.350365 TCTCGGAATGACCTAAAAATCAACG 59.650 40.000 0.00 0.00 36.31 4.10
181 182 4.393680 TCGGAATGACCTAAAAATCAACGG 59.606 41.667 0.00 0.00 36.31 4.44
182 183 4.393680 CGGAATGACCTAAAAATCAACGGA 59.606 41.667 0.00 0.00 36.31 4.69
183 184 5.447279 CGGAATGACCTAAAAATCAACGGAG 60.447 44.000 0.00 0.00 36.31 4.63
184 185 5.646360 GGAATGACCTAAAAATCAACGGAGA 59.354 40.000 0.00 0.00 35.41 3.71
185 186 6.150474 GGAATGACCTAAAAATCAACGGAGAA 59.850 38.462 0.00 0.00 35.41 2.87
186 187 7.148069 GGAATGACCTAAAAATCAACGGAGAAT 60.148 37.037 0.00 0.00 35.41 2.40
187 188 7.703058 ATGACCTAAAAATCAACGGAGAATT 57.297 32.000 0.00 0.00 0.00 2.17
188 189 8.801882 ATGACCTAAAAATCAACGGAGAATTA 57.198 30.769 0.00 0.00 0.00 1.40
189 190 8.801882 TGACCTAAAAATCAACGGAGAATTAT 57.198 30.769 0.00 0.00 0.00 1.28
190 191 9.238368 TGACCTAAAAATCAACGGAGAATTATT 57.762 29.630 0.00 0.00 0.00 1.40
233 234 1.826024 CTAGCCAACTCGCTCCCAT 59.174 57.895 0.00 0.00 40.39 4.00
237 238 2.825836 CAACTCGCTCCCATGGCC 60.826 66.667 6.09 0.00 0.00 5.36
357 358 3.376859 CGTAGTGCTTTGAATGCCCAATA 59.623 43.478 0.39 0.00 0.00 1.90
359 360 5.450412 CGTAGTGCTTTGAATGCCCAATAAT 60.450 40.000 0.39 0.00 0.00 1.28
523 524 1.862138 TCCCTCCTCCTCACTCCCA 60.862 63.158 0.00 0.00 0.00 4.37
577 578 2.997315 ACCAGCCGCAGCACTAGA 60.997 61.111 0.00 0.00 43.56 2.43
628 631 3.292481 AAGGTCCTCGGGTCGGCTA 62.292 63.158 0.00 0.00 0.00 3.93
633 636 3.288290 CTCGGGTCGGCTATCGCT 61.288 66.667 0.00 0.00 39.05 4.93
637 640 3.224324 GGTCGGCTATCGCTCCCA 61.224 66.667 0.00 0.00 39.05 4.37
649 652 3.760035 CTCCCACCACTCCGTCGG 61.760 72.222 4.39 4.39 0.00 4.79
712 716 2.513204 CCTCTGCTCCACCATGCG 60.513 66.667 0.00 0.00 0.00 4.73
744 748 2.833913 GGATGACGGGGCCATGGAT 61.834 63.158 18.40 0.00 0.00 3.41
900 904 0.392336 GCCATTCGCATCTCTCCTCT 59.608 55.000 0.00 0.00 37.47 3.69
925 929 1.375908 GCTCTCGACCACCAATGCA 60.376 57.895 0.00 0.00 0.00 3.96
936 940 2.311854 CCAATGCACCCCCTCCTCT 61.312 63.158 0.00 0.00 0.00 3.69
1156 1183 4.566004 AGTTTCTGTACTATGCGCTTGAA 58.434 39.130 9.73 0.00 0.00 2.69
1198 1225 3.379372 GCAGAGCATAAAATGAAGCCAGA 59.621 43.478 0.00 0.00 0.00 3.86
1210 1237 2.108075 TGAAGCCAGAAACAGGGATGAA 59.892 45.455 0.00 0.00 0.00 2.57
1242 1269 0.465460 GGTGGCTGAACAGTGGACAA 60.465 55.000 3.77 0.00 0.00 3.18
1289 1316 2.922503 TGCGTGGCAGAAGAGGGA 60.923 61.111 0.00 0.00 33.32 4.20
1440 1468 3.265791 GAAGTCTTCTATGTGCAGGTGG 58.734 50.000 5.27 0.00 0.00 4.61
1501 1530 5.440610 CTCCCAGAGGTATTAAAGCACAAT 58.559 41.667 0.00 0.00 0.00 2.71
1772 2034 2.292569 AGACTTTGTTCGACAGACGCTA 59.707 45.455 0.00 0.00 42.26 4.26
1822 2085 0.040336 ACACACGTACTCAGTGAGCG 60.040 55.000 20.31 17.76 41.83 5.03
1959 2233 6.602803 TGAGCAATGGATAATTAACTTGCAGA 59.397 34.615 16.68 5.26 40.98 4.26
2018 2292 3.404224 TGTGGCATTGTTGATTGCATT 57.596 38.095 0.00 0.00 40.66 3.56
2033 2307 9.056005 GTTGATTGCATTAGTAGAACATCCATA 57.944 33.333 0.00 0.00 0.00 2.74
2127 2402 4.724074 AACATGCGTCATCAAATCCAAT 57.276 36.364 0.00 0.00 0.00 3.16
2219 2494 9.712305 CAAATAAAGGATACAAGACGGAGATAT 57.288 33.333 0.00 0.00 41.41 1.63
2246 2521 1.086067 ACGCATGGAGCATGAACTCG 61.086 55.000 0.00 0.00 43.81 4.18
2248 2523 1.089920 GCATGGAGCATGAACTCGTT 58.910 50.000 0.00 0.00 43.81 3.85
2435 2711 3.814842 CACTGAATTGTAGACCACTTGCA 59.185 43.478 0.00 0.00 0.00 4.08
2487 2763 6.500684 TCTACCTCAAATTTGCAGATCAAC 57.499 37.500 13.54 0.00 33.73 3.18
2514 2790 2.246067 TGCCTAAATATTTCCCTGGGCA 59.754 45.455 8.22 18.75 44.75 5.36
2547 2823 7.990886 ACTTCTTATCCCAAAGCGATAAACATA 59.009 33.333 0.00 0.00 33.06 2.29
2617 2893 5.587388 TGAAATCCTGGAAGCATTTCATC 57.413 39.130 15.67 0.00 40.15 2.92
2624 2900 4.703575 CCTGGAAGCATTTCATCTTCTCAA 59.296 41.667 0.00 0.00 38.86 3.02
2696 2972 8.787818 TCCTTAATTAATCCAAACCTACATCCT 58.212 33.333 0.00 0.00 0.00 3.24
2802 3081 4.203226 TGTCTGTAAGTCACCAAATGCAA 58.797 39.130 0.00 0.00 33.76 4.08
2814 3093 9.193806 AGTCACCAAATGCAAAAGATAGATATT 57.806 29.630 0.00 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.181450 GGAGATGTATCAACTCCCCCAAG 60.181 52.174 12.88 0.00 44.34 3.61
2 3 2.408565 GGAGATGTATCAACTCCCCCA 58.591 52.381 12.88 0.00 44.34 4.96
3 4 1.344763 CGGAGATGTATCAACTCCCCC 59.655 57.143 16.47 0.00 46.37 5.40
4 5 2.036089 GACGGAGATGTATCAACTCCCC 59.964 54.545 16.47 8.19 46.37 4.81
5 6 2.287668 CGACGGAGATGTATCAACTCCC 60.288 54.545 16.47 6.44 46.37 4.30
6 7 2.358267 ACGACGGAGATGTATCAACTCC 59.642 50.000 13.59 13.59 45.87 3.85
7 8 3.694535 ACGACGGAGATGTATCAACTC 57.305 47.619 0.00 0.00 33.44 3.01
8 9 4.215827 GGATACGACGGAGATGTATCAACT 59.784 45.833 12.15 0.00 43.89 3.16
9 10 4.023450 TGGATACGACGGAGATGTATCAAC 60.023 45.833 12.15 0.00 43.89 3.18
10 11 4.023450 GTGGATACGACGGAGATGTATCAA 60.023 45.833 12.15 0.26 43.89 2.57
11 12 3.501062 GTGGATACGACGGAGATGTATCA 59.499 47.826 12.15 0.00 43.89 2.15
12 13 3.752222 AGTGGATACGACGGAGATGTATC 59.248 47.826 0.00 3.60 42.59 2.24
13 14 3.752665 AGTGGATACGACGGAGATGTAT 58.247 45.455 0.00 0.00 42.51 2.29
14 15 3.204306 AGTGGATACGACGGAGATGTA 57.796 47.619 0.00 0.00 42.51 2.29
15 16 2.054232 AGTGGATACGACGGAGATGT 57.946 50.000 0.00 0.00 42.51 3.06
16 17 3.438297 AAAGTGGATACGACGGAGATG 57.562 47.619 0.00 0.00 42.51 2.90
17 18 3.181478 GGAAAAGTGGATACGACGGAGAT 60.181 47.826 0.00 0.00 42.51 2.75
18 19 2.165030 GGAAAAGTGGATACGACGGAGA 59.835 50.000 0.00 0.00 42.51 3.71
19 20 2.094390 TGGAAAAGTGGATACGACGGAG 60.094 50.000 0.00 0.00 42.51 4.63
20 21 1.894466 TGGAAAAGTGGATACGACGGA 59.106 47.619 0.00 0.00 42.51 4.69
21 22 2.373540 TGGAAAAGTGGATACGACGG 57.626 50.000 0.00 0.00 42.51 4.79
22 23 3.495377 TGTTTGGAAAAGTGGATACGACG 59.505 43.478 0.00 0.00 42.51 5.12
23 24 4.514066 AGTGTTTGGAAAAGTGGATACGAC 59.486 41.667 0.00 0.00 42.51 4.34
24 25 4.710324 AGTGTTTGGAAAAGTGGATACGA 58.290 39.130 0.00 0.00 42.51 3.43
25 26 5.432885 AAGTGTTTGGAAAAGTGGATACG 57.567 39.130 0.00 0.00 42.51 3.06
26 27 6.019075 GCAAAAGTGTTTGGAAAAGTGGATAC 60.019 38.462 1.72 0.00 43.73 2.24
27 28 6.045955 GCAAAAGTGTTTGGAAAAGTGGATA 58.954 36.000 1.72 0.00 43.73 2.59
28 29 4.875536 GCAAAAGTGTTTGGAAAAGTGGAT 59.124 37.500 1.72 0.00 43.73 3.41
29 30 4.249661 GCAAAAGTGTTTGGAAAAGTGGA 58.750 39.130 1.72 0.00 43.73 4.02
30 31 3.373748 GGCAAAAGTGTTTGGAAAAGTGG 59.626 43.478 1.72 0.00 43.73 4.00
31 32 3.373748 GGGCAAAAGTGTTTGGAAAAGTG 59.626 43.478 1.72 0.00 43.73 3.16
32 33 3.263170 AGGGCAAAAGTGTTTGGAAAAGT 59.737 39.130 1.72 0.00 43.73 2.66
33 34 3.872696 AGGGCAAAAGTGTTTGGAAAAG 58.127 40.909 1.72 0.00 43.73 2.27
34 35 3.990959 AGGGCAAAAGTGTTTGGAAAA 57.009 38.095 1.72 0.00 43.73 2.29
35 36 3.008485 ACAAGGGCAAAAGTGTTTGGAAA 59.992 39.130 1.72 0.00 43.73 3.13
36 37 2.569404 ACAAGGGCAAAAGTGTTTGGAA 59.431 40.909 1.72 0.00 43.73 3.53
37 38 2.183679 ACAAGGGCAAAAGTGTTTGGA 58.816 42.857 1.72 0.00 43.73 3.53
38 39 2.689553 ACAAGGGCAAAAGTGTTTGG 57.310 45.000 1.72 0.00 43.73 3.28
39 40 4.379290 CCAAAACAAGGGCAAAAGTGTTTG 60.379 41.667 1.73 0.00 41.94 2.93
40 41 3.755905 CCAAAACAAGGGCAAAAGTGTTT 59.244 39.130 0.00 0.00 44.01 2.83
41 42 3.008485 TCCAAAACAAGGGCAAAAGTGTT 59.992 39.130 0.00 0.00 35.77 3.32
42 43 2.569404 TCCAAAACAAGGGCAAAAGTGT 59.431 40.909 0.00 0.00 0.00 3.55
43 44 2.935849 GTCCAAAACAAGGGCAAAAGTG 59.064 45.455 0.00 0.00 0.00 3.16
44 45 2.837591 AGTCCAAAACAAGGGCAAAAGT 59.162 40.909 0.00 0.00 31.65 2.66
45 46 3.132824 AGAGTCCAAAACAAGGGCAAAAG 59.867 43.478 0.00 0.00 31.65 2.27
46 47 3.103742 AGAGTCCAAAACAAGGGCAAAA 58.896 40.909 0.00 0.00 31.65 2.44
47 48 2.745968 AGAGTCCAAAACAAGGGCAAA 58.254 42.857 0.00 0.00 31.65 3.68
48 49 2.452600 AGAGTCCAAAACAAGGGCAA 57.547 45.000 0.00 0.00 31.65 4.52
49 50 3.117663 AGTTAGAGTCCAAAACAAGGGCA 60.118 43.478 0.00 0.00 31.65 5.36
50 51 3.487372 AGTTAGAGTCCAAAACAAGGGC 58.513 45.455 4.12 0.00 0.00 5.19
51 52 4.261614 GCAAGTTAGAGTCCAAAACAAGGG 60.262 45.833 4.12 0.00 0.00 3.95
52 53 4.338118 TGCAAGTTAGAGTCCAAAACAAGG 59.662 41.667 0.00 0.00 0.00 3.61
53 54 5.499139 TGCAAGTTAGAGTCCAAAACAAG 57.501 39.130 0.00 0.00 0.00 3.16
54 55 5.592282 TCATGCAAGTTAGAGTCCAAAACAA 59.408 36.000 0.00 0.00 0.00 2.83
55 56 5.129634 TCATGCAAGTTAGAGTCCAAAACA 58.870 37.500 0.00 0.00 0.00 2.83
56 57 5.689383 TCATGCAAGTTAGAGTCCAAAAC 57.311 39.130 0.00 0.00 0.00 2.43
57 58 6.899393 AATCATGCAAGTTAGAGTCCAAAA 57.101 33.333 0.00 0.00 0.00 2.44
58 59 6.489700 TCAAATCATGCAAGTTAGAGTCCAAA 59.510 34.615 0.00 0.00 0.00 3.28
59 60 6.003326 TCAAATCATGCAAGTTAGAGTCCAA 58.997 36.000 0.00 0.00 0.00 3.53
60 61 5.559770 TCAAATCATGCAAGTTAGAGTCCA 58.440 37.500 0.00 0.00 0.00 4.02
61 62 6.500684 TTCAAATCATGCAAGTTAGAGTCC 57.499 37.500 0.00 0.00 0.00 3.85
62 63 6.971184 CCATTCAAATCATGCAAGTTAGAGTC 59.029 38.462 0.00 0.00 0.00 3.36
63 64 6.660521 TCCATTCAAATCATGCAAGTTAGAGT 59.339 34.615 0.00 0.00 0.00 3.24
64 65 7.092137 TCCATTCAAATCATGCAAGTTAGAG 57.908 36.000 0.00 0.00 0.00 2.43
65 66 7.177216 AGTTCCATTCAAATCATGCAAGTTAGA 59.823 33.333 0.00 0.00 0.00 2.10
66 67 7.318141 AGTTCCATTCAAATCATGCAAGTTAG 58.682 34.615 0.00 0.00 0.00 2.34
67 68 7.230849 AGTTCCATTCAAATCATGCAAGTTA 57.769 32.000 0.00 0.00 0.00 2.24
68 69 6.105397 AGTTCCATTCAAATCATGCAAGTT 57.895 33.333 0.00 0.00 0.00 2.66
69 70 5.733620 AGTTCCATTCAAATCATGCAAGT 57.266 34.783 0.00 0.00 0.00 3.16
70 71 6.532657 GGTTAGTTCCATTCAAATCATGCAAG 59.467 38.462 0.00 0.00 0.00 4.01
71 72 6.211184 AGGTTAGTTCCATTCAAATCATGCAA 59.789 34.615 0.00 0.00 0.00 4.08
72 73 5.716228 AGGTTAGTTCCATTCAAATCATGCA 59.284 36.000 0.00 0.00 0.00 3.96
73 74 6.038356 CAGGTTAGTTCCATTCAAATCATGC 58.962 40.000 0.00 0.00 0.00 4.06
74 75 6.377996 TCCAGGTTAGTTCCATTCAAATCATG 59.622 38.462 0.00 0.00 0.00 3.07
75 76 6.378280 GTCCAGGTTAGTTCCATTCAAATCAT 59.622 38.462 0.00 0.00 0.00 2.45
76 77 5.710099 GTCCAGGTTAGTTCCATTCAAATCA 59.290 40.000 0.00 0.00 0.00 2.57
77 78 5.946377 AGTCCAGGTTAGTTCCATTCAAATC 59.054 40.000 0.00 0.00 0.00 2.17
78 79 5.711976 CAGTCCAGGTTAGTTCCATTCAAAT 59.288 40.000 0.00 0.00 0.00 2.32
79 80 5.070001 CAGTCCAGGTTAGTTCCATTCAAA 58.930 41.667 0.00 0.00 0.00 2.69
80 81 4.349636 TCAGTCCAGGTTAGTTCCATTCAA 59.650 41.667 0.00 0.00 0.00 2.69
81 82 3.907474 TCAGTCCAGGTTAGTTCCATTCA 59.093 43.478 0.00 0.00 0.00 2.57
82 83 4.254492 GTCAGTCCAGGTTAGTTCCATTC 58.746 47.826 0.00 0.00 0.00 2.67
83 84 3.306780 CGTCAGTCCAGGTTAGTTCCATT 60.307 47.826 0.00 0.00 0.00 3.16
84 85 2.233922 CGTCAGTCCAGGTTAGTTCCAT 59.766 50.000 0.00 0.00 0.00 3.41
85 86 1.616865 CGTCAGTCCAGGTTAGTTCCA 59.383 52.381 0.00 0.00 0.00 3.53
86 87 1.617357 ACGTCAGTCCAGGTTAGTTCC 59.383 52.381 0.00 0.00 0.00 3.62
87 88 3.057734 CAACGTCAGTCCAGGTTAGTTC 58.942 50.000 0.00 0.00 0.00 3.01
88 89 2.433239 ACAACGTCAGTCCAGGTTAGTT 59.567 45.455 0.00 0.00 0.00 2.24
89 90 2.037144 ACAACGTCAGTCCAGGTTAGT 58.963 47.619 0.00 0.00 0.00 2.24
90 91 2.814280 ACAACGTCAGTCCAGGTTAG 57.186 50.000 0.00 0.00 0.00 2.34
91 92 3.547054 AAACAACGTCAGTCCAGGTTA 57.453 42.857 0.00 0.00 0.00 2.85
92 93 2.413310 AAACAACGTCAGTCCAGGTT 57.587 45.000 0.00 0.00 0.00 3.50
93 94 2.285977 GAAAACAACGTCAGTCCAGGT 58.714 47.619 0.00 0.00 0.00 4.00
94 95 2.285083 TGAAAACAACGTCAGTCCAGG 58.715 47.619 0.00 0.00 0.00 4.45
95 96 2.286418 GCTGAAAACAACGTCAGTCCAG 60.286 50.000 0.00 1.69 42.72 3.86
96 97 1.668751 GCTGAAAACAACGTCAGTCCA 59.331 47.619 0.00 0.00 42.72 4.02
97 98 1.668751 TGCTGAAAACAACGTCAGTCC 59.331 47.619 0.00 0.00 42.72 3.85
98 99 2.607635 TCTGCTGAAAACAACGTCAGTC 59.392 45.455 0.00 0.00 42.72 3.51
99 100 2.627945 TCTGCTGAAAACAACGTCAGT 58.372 42.857 0.00 0.00 42.72 3.41
100 101 3.673746 TTCTGCTGAAAACAACGTCAG 57.326 42.857 3.21 0.00 43.46 3.51
101 102 4.350346 CAATTCTGCTGAAAACAACGTCA 58.650 39.130 10.27 0.00 35.63 4.35
102 103 3.180387 GCAATTCTGCTGAAAACAACGTC 59.820 43.478 10.27 0.00 45.74 4.34
103 104 3.115554 GCAATTCTGCTGAAAACAACGT 58.884 40.909 10.27 0.00 45.74 3.99
104 105 3.758521 GCAATTCTGCTGAAAACAACG 57.241 42.857 10.27 0.00 45.74 4.10
116 117 5.808540 CAGAAATAACACCATGGCAATTCTG 59.191 40.000 13.04 17.62 36.44 3.02
117 118 5.481473 ACAGAAATAACACCATGGCAATTCT 59.519 36.000 13.04 10.40 0.00 2.40
118 119 5.577945 CACAGAAATAACACCATGGCAATTC 59.422 40.000 13.04 8.27 0.00 2.17
119 120 5.481105 CACAGAAATAACACCATGGCAATT 58.519 37.500 13.04 6.30 0.00 2.32
120 121 4.621274 GCACAGAAATAACACCATGGCAAT 60.621 41.667 13.04 0.00 0.00 3.56
121 122 3.305950 GCACAGAAATAACACCATGGCAA 60.306 43.478 13.04 0.00 0.00 4.52
122 123 2.230992 GCACAGAAATAACACCATGGCA 59.769 45.455 13.04 0.00 0.00 4.92
123 124 2.230992 TGCACAGAAATAACACCATGGC 59.769 45.455 13.04 0.00 0.00 4.40
124 125 3.758023 TCTGCACAGAAATAACACCATGG 59.242 43.478 11.19 11.19 33.91 3.66
125 126 5.375417 TTCTGCACAGAAATAACACCATG 57.625 39.130 10.58 0.00 43.79 3.66
136 137 6.293407 CCGAGAACTTTTATTTCTGCACAGAA 60.293 38.462 8.99 8.99 44.94 3.02
137 138 5.179368 CCGAGAACTTTTATTTCTGCACAGA 59.821 40.000 0.00 0.00 33.30 3.41
138 139 5.179368 TCCGAGAACTTTTATTTCTGCACAG 59.821 40.000 0.00 0.00 33.30 3.66
139 140 5.060506 TCCGAGAACTTTTATTTCTGCACA 58.939 37.500 0.00 0.00 33.30 4.57
140 141 5.607119 TCCGAGAACTTTTATTTCTGCAC 57.393 39.130 0.00 0.00 33.30 4.57
141 142 6.429692 TCATTCCGAGAACTTTTATTTCTGCA 59.570 34.615 0.00 0.00 33.30 4.41
142 143 6.743172 GTCATTCCGAGAACTTTTATTTCTGC 59.257 38.462 0.00 0.00 33.30 4.26
143 144 7.119846 AGGTCATTCCGAGAACTTTTATTTCTG 59.880 37.037 0.00 0.00 41.99 3.02
144 145 7.168905 AGGTCATTCCGAGAACTTTTATTTCT 58.831 34.615 0.00 0.00 41.99 2.52
145 146 7.379098 AGGTCATTCCGAGAACTTTTATTTC 57.621 36.000 0.00 0.00 41.99 2.17
146 147 8.857694 TTAGGTCATTCCGAGAACTTTTATTT 57.142 30.769 0.00 0.00 41.99 1.40
147 148 8.857694 TTTAGGTCATTCCGAGAACTTTTATT 57.142 30.769 0.00 0.00 41.99 1.40
148 149 8.857694 TTTTAGGTCATTCCGAGAACTTTTAT 57.142 30.769 0.00 0.00 41.99 1.40
149 150 8.680039 TTTTTAGGTCATTCCGAGAACTTTTA 57.320 30.769 0.00 0.00 41.99 1.52
150 151 7.576861 TTTTTAGGTCATTCCGAGAACTTTT 57.423 32.000 0.00 0.00 41.99 2.27
151 152 7.447238 TGATTTTTAGGTCATTCCGAGAACTTT 59.553 33.333 0.00 0.00 41.99 2.66
152 153 6.940298 TGATTTTTAGGTCATTCCGAGAACTT 59.060 34.615 0.00 0.00 41.99 2.66
153 154 6.472887 TGATTTTTAGGTCATTCCGAGAACT 58.527 36.000 0.00 0.00 41.99 3.01
154 155 6.737254 TGATTTTTAGGTCATTCCGAGAAC 57.263 37.500 0.00 0.00 41.99 3.01
155 156 6.128391 CGTTGATTTTTAGGTCATTCCGAGAA 60.128 38.462 0.00 0.00 41.99 2.87
156 157 5.350365 CGTTGATTTTTAGGTCATTCCGAGA 59.650 40.000 0.00 0.00 41.99 4.04
157 158 5.447279 CCGTTGATTTTTAGGTCATTCCGAG 60.447 44.000 0.00 0.00 41.99 4.63
158 159 4.393680 CCGTTGATTTTTAGGTCATTCCGA 59.606 41.667 0.00 0.00 41.99 4.55
159 160 4.393680 TCCGTTGATTTTTAGGTCATTCCG 59.606 41.667 0.00 0.00 41.99 4.30
160 161 5.646360 TCTCCGTTGATTTTTAGGTCATTCC 59.354 40.000 0.00 0.00 0.00 3.01
161 162 6.737254 TCTCCGTTGATTTTTAGGTCATTC 57.263 37.500 0.00 0.00 0.00 2.67
162 163 7.703058 ATTCTCCGTTGATTTTTAGGTCATT 57.297 32.000 0.00 0.00 0.00 2.57
163 164 7.703058 AATTCTCCGTTGATTTTTAGGTCAT 57.297 32.000 0.00 0.00 0.00 3.06
164 165 8.801882 ATAATTCTCCGTTGATTTTTAGGTCA 57.198 30.769 0.00 0.00 0.00 4.02
170 171 9.771534 TTCCAAAATAATTCTCCGTTGATTTTT 57.228 25.926 0.00 0.00 0.00 1.94
171 172 9.942850 ATTCCAAAATAATTCTCCGTTGATTTT 57.057 25.926 0.00 0.00 0.00 1.82
172 173 9.942850 AATTCCAAAATAATTCTCCGTTGATTT 57.057 25.926 0.00 0.00 0.00 2.17
173 174 9.942850 AAATTCCAAAATAATTCTCCGTTGATT 57.057 25.926 0.00 0.00 0.00 2.57
190 191 9.528489 AGCCTCTGTATAGTTTTAAATTCCAAA 57.472 29.630 0.00 0.00 0.00 3.28
192 193 9.832445 CTAGCCTCTGTATAGTTTTAAATTCCA 57.168 33.333 0.00 0.00 0.00 3.53
193 194 8.775527 GCTAGCCTCTGTATAGTTTTAAATTCC 58.224 37.037 2.29 0.00 0.00 3.01
194 195 8.775527 GGCTAGCCTCTGTATAGTTTTAAATTC 58.224 37.037 27.17 0.00 0.00 2.17
246 247 1.961277 GGCCACGAATAGCCCATCG 60.961 63.158 0.00 1.59 43.76 3.84
357 358 1.358787 TCTGAAATGAGCCCACCCATT 59.641 47.619 0.00 0.00 34.75 3.16
359 360 1.002069 ATCTGAAATGAGCCCACCCA 58.998 50.000 0.00 0.00 0.00 4.51
523 524 4.903010 GGTGTGACGGTGTGGCGT 62.903 66.667 0.00 0.00 0.00 5.68
536 537 1.003573 GGGAGGAGGGAGATGGTGT 59.996 63.158 0.00 0.00 0.00 4.16
577 578 0.320374 TCTCGTCGGTGGCAAATCTT 59.680 50.000 0.00 0.00 0.00 2.40
628 631 3.461773 CGGAGTGGTGGGAGCGAT 61.462 66.667 0.00 0.00 0.00 4.58
649 652 3.207669 CAAGGGCGCAGATCTGGC 61.208 66.667 23.89 22.41 0.00 4.85
712 716 0.468226 TCATCCATGAGGTAACCGCC 59.532 55.000 0.00 0.00 35.89 6.13
744 748 3.169099 CCTTCTCTCCTTCAAGGACAGA 58.831 50.000 7.32 7.32 40.06 3.41
900 904 1.251527 GGTGGTCGAGAGCAGGAGAA 61.252 60.000 5.13 0.00 39.74 2.87
925 929 0.550393 GAAGGGAAAGAGGAGGGGGT 60.550 60.000 0.00 0.00 0.00 4.95
936 940 4.171234 AGATGGTGAGAAGAGAAGGGAAA 58.829 43.478 0.00 0.00 0.00 3.13
1156 1183 0.749649 TGCACGGCCTTGTCATTTTT 59.250 45.000 11.38 0.00 0.00 1.94
1191 1218 2.556114 CCTTCATCCCTGTTTCTGGCTT 60.556 50.000 0.00 0.00 0.00 4.35
1198 1225 3.140144 TGTTTCTCCCTTCATCCCTGTTT 59.860 43.478 0.00 0.00 0.00 2.83
1210 1237 0.779997 AGCCACCATTGTTTCTCCCT 59.220 50.000 0.00 0.00 0.00 4.20
1242 1269 0.321122 CTTTCTCAGCCAGCTTCGGT 60.321 55.000 0.00 0.00 0.00 4.69
1289 1316 2.838202 AGAAACGGATACCACATGGACT 59.162 45.455 4.53 0.00 38.94 3.85
1423 1451 0.253044 GCCCACCTGCACATAGAAGA 59.747 55.000 0.00 0.00 0.00 2.87
1440 1468 4.577283 TGGCTACAATTTTAGTAATCCGCC 59.423 41.667 0.83 0.00 32.65 6.13
1501 1530 4.646040 CAGACATTGATTTCAGGGCCATAA 59.354 41.667 6.18 0.00 0.00 1.90
1550 1579 2.953020 TGTTTGCACACCACAAAGAAC 58.047 42.857 0.00 0.00 37.67 3.01
1591 1853 8.055181 ACAACATATATTCTGTCCAATCAAGGT 58.945 33.333 0.00 0.00 0.00 3.50
1772 2034 2.103771 CCGTGTGATTGGATCTGGATCT 59.896 50.000 9.96 0.00 37.92 2.75
1822 2085 6.433093 ACAATGGGAAAGGTAACATCACTAAC 59.567 38.462 0.00 0.00 41.41 2.34
1871 2134 5.659971 TGAATTCACCATCATGAGAGAGAGA 59.340 40.000 3.38 0.00 0.00 3.10
2059 2334 9.920946 ACACCACCTATTATATTGAGAAATGTT 57.079 29.630 0.00 0.00 0.00 2.71
2127 2402 0.586319 GCTTGTCGTGTAGCTTGCAA 59.414 50.000 0.00 0.00 34.57 4.08
2207 2482 2.361438 GTCCGTCCAATATCTCCGTCTT 59.639 50.000 0.00 0.00 0.00 3.01
2219 2494 2.264480 CTCCATGCGTCCGTCCAA 59.736 61.111 0.00 0.00 0.00 3.53
2312 2587 2.297033 TGGTTGAAATCAGCAAGGAAGC 59.703 45.455 0.00 0.00 0.00 3.86
2410 2685 5.560953 GCAAGTGGTCTACAATTCAGTGAAC 60.561 44.000 7.96 0.00 34.73 3.18
2487 2763 5.244626 CCAGGGAAATATTTAGGCAAGGATG 59.755 44.000 0.00 0.00 0.00 3.51
2514 2790 5.817816 CGCTTTGGGATAAGAAGTGTATTCT 59.182 40.000 0.00 0.00 0.00 2.40
2547 2823 2.105477 GGGTCATGATGCTCACATAGGT 59.895 50.000 0.00 0.00 36.35 3.08
2563 2839 1.567357 TGCTAGTGCTATGTGGGTCA 58.433 50.000 0.00 0.00 40.48 4.02
2713 2989 8.715191 AAAACTCACAAAATTATGCAAAGACA 57.285 26.923 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.