Multiple sequence alignment - TraesCS3A01G326400

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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 TraesCS3A01G326400 chr3A 100.000 3695 0 0 1 3695 571789351 571793045 0.000000e+00 6824.0
1 TraesCS3A01G326400 chr3A 98.361 61 1 0 862 922 571790155 571790215 1.400000e-19 108.0
2 TraesCS3A01G326400 chr3A 98.361 61 1 0 805 865 571790212 571790272 1.400000e-19 108.0
3 TraesCS3A01G326400 chr3B 93.814 2845 137 25 862 3695 566161141 566163957 0.000000e+00 4242.0
4 TraesCS3A01G326400 chr3B 91.538 520 25 5 363 865 566160684 566161201 0.000000e+00 699.0
5 TraesCS3A01G326400 chr3D 95.444 2568 70 22 862 3416 433414173 433416706 0.000000e+00 4050.0
6 TraesCS3A01G326400 chr3D 90.797 728 50 7 150 865 433413511 433414233 0.000000e+00 957.0
7 TraesCS3A01G326400 chr3D 90.650 246 20 3 3450 3694 433416702 433416945 1.280000e-84 324.0
8 TraesCS3A01G326400 chr3D 95.413 109 5 0 1 109 17693653 17693761 1.360000e-39 174.0
9 TraesCS3A01G326400 chr3D 91.743 109 9 0 1 109 523341798 523341690 6.390000e-33 152.0
10 TraesCS3A01G326400 chr4A 82.500 280 47 2 2004 2282 193732 193454 1.030000e-60 244.0
11 TraesCS3A01G326400 chr4D 82.143 280 48 2 2004 2282 464286 464008 4.770000e-59 239.0
12 TraesCS3A01G326400 chr4B 82.143 280 48 2 2004 2282 234393 234115 4.770000e-59 239.0
13 TraesCS3A01G326400 chr4B 84.496 129 20 0 2131 2259 178071960 178072088 1.080000e-25 128.0
14 TraesCS3A01G326400 chr2D 87.500 144 18 0 1 144 38625035 38625178 2.280000e-37 167.0
15 TraesCS3A01G326400 chr2D 91.743 109 9 0 1 109 7717900 7718008 6.390000e-33 152.0
16 TraesCS3A01G326400 chr2D 89.908 109 11 0 1 109 81058316 81058424 1.380000e-29 141.0
17 TraesCS3A01G326400 chr2D 82.716 81 14 0 1724 1804 121704762 121704682 5.120000e-09 73.1
18 TraesCS3A01G326400 chr5A 92.727 110 8 0 1 110 338298620 338298511 3.820000e-35 159.0
19 TraesCS3A01G326400 chr5A 83.871 155 22 2 1 155 516127282 516127131 1.070000e-30 145.0
20 TraesCS3A01G326400 chr5A 86.250 80 7 2 74 152 557350679 557350603 2.360000e-12 84.2
21 TraesCS3A01G326400 chr5A 95.745 47 2 0 2199 2245 67471168 67471122 3.960000e-10 76.8
22 TraesCS3A01G326400 chr5A 82.090 67 12 0 1685 1751 697735620 697735554 1.430000e-04 58.4
23 TraesCS3A01G326400 chr1A 91.743 109 9 0 1 109 84915635 84915743 6.390000e-33 152.0
24 TraesCS3A01G326400 chr1A 100.000 32 0 0 1778 1809 453074401 453074432 3.990000e-05 60.2
25 TraesCS3A01G326400 chr1A 100.000 28 0 0 1685 1712 448344226 448344199 7.000000e-03 52.8
26 TraesCS3A01G326400 chr6D 89.908 109 11 0 1 109 93607247 93607355 1.380000e-29 141.0
27 TraesCS3A01G326400 chr7A 85.897 78 8 1 72 149 326094848 326094922 3.060000e-11 80.5
28 TraesCS3A01G326400 chr7A 84.615 78 9 1 72 149 321661047 321661121 1.420000e-09 75.0
29 TraesCS3A01G326400 chr7A 82.090 67 12 0 1685 1751 32963639 32963573 1.430000e-04 58.4
30 TraesCS3A01G326400 chr7A 80.597 67 13 0 1685 1751 115783003 115782937 7.000000e-03 52.8
31 TraesCS3A01G326400 chr7D 83.333 90 9 4 74 162 545388771 545388855 1.100000e-10 78.7
32 TraesCS3A01G326400 chr7D 82.895 76 10 3 74 149 29110697 29110625 8.570000e-07 65.8
33 TraesCS3A01G326400 chr7D 96.875 32 1 0 1784 1815 618488597 618488628 2.000000e-03 54.7
34 TraesCS3A01G326400 chr5D 93.617 47 3 0 2199 2245 72902355 72902309 1.840000e-08 71.3
35 TraesCS3A01G326400 chr2B 81.481 81 15 0 1724 1804 174829932 174829852 2.380000e-07 67.6
36 TraesCS3A01G326400 chr6B 94.595 37 2 0 1778 1814 216356328 216356364 1.430000e-04 58.4
37 TraesCS3A01G326400 chr6A 94.595 37 2 0 1778 1814 160475787 160475823 1.430000e-04 58.4
38 TraesCS3A01G326400 chr1D 82.090 67 12 0 1685 1751 211986031 211986097 1.430000e-04 58.4
39 TraesCS3A01G326400 chr1B 96.875 32 1 0 1781 1812 474835275 474835244 2.000000e-03 54.7


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G326400 chr3A 571789351 571793045 3694 False 2346.666667 6824 98.907333 1 3695 3 chr3A.!!$F1 3694
1 TraesCS3A01G326400 chr3B 566160684 566163957 3273 False 2470.500000 4242 92.676000 363 3695 2 chr3B.!!$F1 3332
2 TraesCS3A01G326400 chr3D 433413511 433416945 3434 False 1777.000000 4050 92.297000 150 3694 3 chr3D.!!$F2 3544

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
134 135 0.035439 CAAACCGGTGATACTGCCCT 60.035 55.0 8.52 0.00 0.0 5.19 F
135 136 0.035439 AAACCGGTGATACTGCCCTG 60.035 55.0 8.52 0.00 0.0 4.45 F
1471 1491 0.040958 GCGACCAACAACTTCAGCTG 60.041 55.0 7.63 7.63 0.0 4.24 F
1473 1493 0.040958 GACCAACAACTTCAGCTGCG 60.041 55.0 9.47 4.98 0.0 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1294 1314 0.326595 TCAAACCAATCGGCAGCCTA 59.673 50.0 10.54 0.0 34.57 3.93 R
1473 1493 0.463833 CCCTCGCCCACAAGGTTATC 60.464 60.0 0.00 0.0 38.26 1.75 R
2364 2394 0.328592 TACAGAGGTGGTCTCGAGCT 59.671 55.0 7.81 0.0 46.82 4.09 R
2738 2769 0.540923 GTTCTGCTGCATCTCCTCCT 59.459 55.0 1.31 0.0 0.00 3.69 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.503851 GTACCGGTTTGTGTTACGAAC 57.496 47.619 15.04 0.00 40.84 3.95
26 27 3.503851 GTTTGTGTTACGAACCGGTAC 57.496 47.619 8.00 1.54 36.68 3.34
27 28 3.123050 GTTTGTGTTACGAACCGGTACT 58.877 45.455 8.00 0.00 36.68 2.73
28 29 4.295051 GTTTGTGTTACGAACCGGTACTA 58.705 43.478 8.00 0.00 36.68 1.82
29 30 4.576216 TTGTGTTACGAACCGGTACTAA 57.424 40.909 8.00 0.45 0.00 2.24
30 31 4.576216 TGTGTTACGAACCGGTACTAAA 57.424 40.909 8.00 0.00 0.00 1.85
31 32 4.545610 TGTGTTACGAACCGGTACTAAAG 58.454 43.478 8.00 0.00 0.00 1.85
32 33 3.920412 GTGTTACGAACCGGTACTAAAGG 59.080 47.826 8.00 0.00 0.00 3.11
33 34 3.572255 TGTTACGAACCGGTACTAAAGGT 59.428 43.478 8.00 0.75 40.50 3.50
34 35 4.166523 GTTACGAACCGGTACTAAAGGTC 58.833 47.826 8.00 0.00 37.26 3.85
35 36 2.519013 ACGAACCGGTACTAAAGGTCT 58.481 47.619 8.00 0.00 37.26 3.85
36 37 2.489722 ACGAACCGGTACTAAAGGTCTC 59.510 50.000 8.00 0.00 37.26 3.36
37 38 2.159324 CGAACCGGTACTAAAGGTCTCC 60.159 54.545 8.00 0.00 37.26 3.71
38 39 1.857965 ACCGGTACTAAAGGTCTCCC 58.142 55.000 4.49 0.00 31.69 4.30
39 40 1.117994 CCGGTACTAAAGGTCTCCCC 58.882 60.000 0.00 0.00 0.00 4.81
40 41 0.743097 CGGTACTAAAGGTCTCCCCG 59.257 60.000 0.00 0.00 38.74 5.73
41 42 0.463204 GGTACTAAAGGTCTCCCCGC 59.537 60.000 0.00 0.00 38.74 6.13
42 43 0.463204 GTACTAAAGGTCTCCCCGCC 59.537 60.000 0.00 0.00 38.74 6.13
43 44 0.688749 TACTAAAGGTCTCCCCGCCC 60.689 60.000 0.00 0.00 38.74 6.13
44 45 1.993391 CTAAAGGTCTCCCCGCCCA 60.993 63.158 0.00 0.00 38.74 5.36
45 46 2.253403 CTAAAGGTCTCCCCGCCCAC 62.253 65.000 0.00 0.00 38.74 4.61
58 59 4.011517 CCCACGGCCCTAACACGT 62.012 66.667 0.00 0.00 42.17 4.49
61 62 4.692475 ACGGCCCTAACACGTGCC 62.692 66.667 17.22 9.04 39.64 5.01
62 63 4.690719 CGGCCCTAACACGTGCCA 62.691 66.667 17.22 2.00 44.22 4.92
63 64 3.053896 GGCCCTAACACGTGCCAC 61.054 66.667 17.22 0.00 43.46 5.01
78 79 3.981308 CACGTGGTGGCCCTTTAG 58.019 61.111 7.95 0.00 0.00 1.85
79 80 1.072505 CACGTGGTGGCCCTTTAGT 59.927 57.895 7.95 0.00 0.00 2.24
80 81 1.072505 ACGTGGTGGCCCTTTAGTG 59.927 57.895 0.00 0.00 0.00 2.74
81 82 1.373435 CGTGGTGGCCCTTTAGTGA 59.627 57.895 0.00 0.00 0.00 3.41
82 83 0.953960 CGTGGTGGCCCTTTAGTGAC 60.954 60.000 0.00 0.00 0.00 3.67
83 84 0.953960 GTGGTGGCCCTTTAGTGACG 60.954 60.000 0.00 0.00 0.00 4.35
84 85 1.376812 GGTGGCCCTTTAGTGACGG 60.377 63.158 0.00 0.00 0.00 4.79
85 86 1.373812 GTGGCCCTTTAGTGACGGT 59.626 57.895 0.00 0.00 0.00 4.83
86 87 0.250597 GTGGCCCTTTAGTGACGGTT 60.251 55.000 0.00 0.00 0.00 4.44
87 88 0.035739 TGGCCCTTTAGTGACGGTTC 59.964 55.000 0.00 0.00 0.00 3.62
88 89 1.017701 GGCCCTTTAGTGACGGTTCG 61.018 60.000 0.00 0.00 0.00 3.95
89 90 0.320160 GCCCTTTAGTGACGGTTCGT 60.320 55.000 0.00 0.00 45.10 3.85
90 91 1.425412 CCCTTTAGTGACGGTTCGTG 58.575 55.000 0.00 0.00 41.37 4.35
91 92 0.788391 CCTTTAGTGACGGTTCGTGC 59.212 55.000 0.00 0.00 41.37 5.34
92 93 1.493772 CTTTAGTGACGGTTCGTGCA 58.506 50.000 0.00 0.00 41.37 4.57
93 94 1.455786 CTTTAGTGACGGTTCGTGCAG 59.544 52.381 0.00 0.00 41.37 4.41
94 95 0.669619 TTAGTGACGGTTCGTGCAGA 59.330 50.000 0.00 0.00 41.37 4.26
95 96 0.669619 TAGTGACGGTTCGTGCAGAA 59.330 50.000 0.00 0.00 41.37 3.02
102 103 4.659480 TTCGTGCAGAACCGGTAC 57.341 55.556 8.00 0.00 33.14 3.34
103 104 2.043625 TTCGTGCAGAACCGGTACT 58.956 52.632 8.00 0.00 33.14 2.73
104 105 1.246649 TTCGTGCAGAACCGGTACTA 58.753 50.000 8.00 0.00 33.14 1.82
105 106 1.246649 TCGTGCAGAACCGGTACTAA 58.753 50.000 8.00 0.00 0.00 2.24
106 107 1.612950 TCGTGCAGAACCGGTACTAAA 59.387 47.619 8.00 0.00 0.00 1.85
107 108 1.990563 CGTGCAGAACCGGTACTAAAG 59.009 52.381 8.00 0.00 0.00 1.85
108 109 2.344025 GTGCAGAACCGGTACTAAAGG 58.656 52.381 8.00 0.00 0.00 3.11
109 110 1.338389 TGCAGAACCGGTACTAAAGGC 60.338 52.381 8.00 5.92 0.00 4.35
110 111 2.010544 GCAGAACCGGTACTAAAGGCC 61.011 57.143 8.00 0.00 0.00 5.19
111 112 0.907486 AGAACCGGTACTAAAGGCCC 59.093 55.000 8.00 0.00 0.00 5.80
112 113 0.907486 GAACCGGTACTAAAGGCCCT 59.093 55.000 8.00 0.00 0.00 5.19
113 114 1.280133 GAACCGGTACTAAAGGCCCTT 59.720 52.381 8.00 0.00 0.00 3.95
114 115 2.252535 ACCGGTACTAAAGGCCCTTA 57.747 50.000 4.49 0.00 0.00 2.69
115 116 1.833630 ACCGGTACTAAAGGCCCTTAC 59.166 52.381 4.49 0.00 0.00 2.34
116 117 1.832998 CCGGTACTAAAGGCCCTTACA 59.167 52.381 0.00 0.00 0.00 2.41
117 118 2.236893 CCGGTACTAAAGGCCCTTACAA 59.763 50.000 0.00 0.00 0.00 2.41
118 119 3.307621 CCGGTACTAAAGGCCCTTACAAA 60.308 47.826 0.00 0.00 0.00 2.83
119 120 3.686241 CGGTACTAAAGGCCCTTACAAAC 59.314 47.826 0.00 0.00 0.00 2.93
120 121 4.012374 GGTACTAAAGGCCCTTACAAACC 58.988 47.826 0.00 0.00 0.00 3.27
121 122 2.786777 ACTAAAGGCCCTTACAAACCG 58.213 47.619 0.00 0.00 0.00 4.44
122 123 2.089201 CTAAAGGCCCTTACAAACCGG 58.911 52.381 0.00 0.00 0.00 5.28
123 124 0.186630 AAAGGCCCTTACAAACCGGT 59.813 50.000 0.00 0.00 0.00 5.28
124 125 0.538746 AAGGCCCTTACAAACCGGTG 60.539 55.000 8.52 0.00 0.00 4.94
125 126 1.073548 GGCCCTTACAAACCGGTGA 59.926 57.895 8.52 0.00 0.00 4.02
126 127 0.323087 GGCCCTTACAAACCGGTGAT 60.323 55.000 8.52 0.00 0.00 3.06
127 128 1.065272 GGCCCTTACAAACCGGTGATA 60.065 52.381 8.52 0.00 0.00 2.15
128 129 2.011947 GCCCTTACAAACCGGTGATAC 58.988 52.381 8.52 0.00 0.00 2.24
129 130 2.355412 GCCCTTACAAACCGGTGATACT 60.355 50.000 8.52 0.00 0.00 2.12
130 131 3.267483 CCCTTACAAACCGGTGATACTG 58.733 50.000 8.52 3.45 0.00 2.74
131 132 2.676342 CCTTACAAACCGGTGATACTGC 59.324 50.000 8.52 0.00 0.00 4.40
132 133 2.389962 TACAAACCGGTGATACTGCC 57.610 50.000 8.52 0.00 0.00 4.85
133 134 0.322187 ACAAACCGGTGATACTGCCC 60.322 55.000 8.52 0.00 0.00 5.36
134 135 0.035439 CAAACCGGTGATACTGCCCT 60.035 55.000 8.52 0.00 0.00 5.19
135 136 0.035439 AAACCGGTGATACTGCCCTG 60.035 55.000 8.52 0.00 0.00 4.45
136 137 1.198759 AACCGGTGATACTGCCCTGT 61.199 55.000 8.52 0.00 0.00 4.00
137 138 1.198759 ACCGGTGATACTGCCCTGTT 61.199 55.000 6.12 0.00 0.00 3.16
138 139 0.462047 CCGGTGATACTGCCCTGTTC 60.462 60.000 0.00 0.00 0.00 3.18
139 140 0.806102 CGGTGATACTGCCCTGTTCG 60.806 60.000 0.00 0.00 0.00 3.95
140 141 0.462047 GGTGATACTGCCCTGTTCGG 60.462 60.000 0.00 0.00 0.00 4.30
156 157 4.693283 TGTTCGGCATTAGTGAATCTAGG 58.307 43.478 0.00 0.00 0.00 3.02
191 192 9.985730 ATTAAATTCATGTGTGTTCAACAAGAT 57.014 25.926 0.00 0.00 41.57 2.40
203 204 9.554395 TGTGTTCAACAAGATTCTAGTGAAATA 57.446 29.630 0.00 1.01 35.24 1.40
222 223 8.715998 GTGAAATATGCATATTTGTCTCGAGAT 58.284 33.333 37.23 17.80 41.59 2.75
223 224 9.927668 TGAAATATGCATATTTGTCTCGAGATA 57.072 29.630 37.23 13.87 41.59 1.98
240 241 4.024556 CGAGATACCCTTGATTGCACAATC 60.025 45.833 14.99 14.99 45.55 2.67
242 243 4.885907 AGATACCCTTGATTGCACAATCTG 59.114 41.667 20.72 14.23 45.55 2.90
250 251 2.857186 TTGCACAATCTGAGGCACTA 57.143 45.000 0.00 0.00 41.55 2.74
265 266 5.303078 TGAGGCACTAGTTTTAAATGGCAAA 59.697 36.000 12.96 0.78 41.55 3.68
272 273 8.213812 CACTAGTTTTAAATGGCAAAACAATCG 58.786 33.333 13.31 3.39 44.58 3.34
322 323 1.228552 TCCAAACCAGCTCCTTGGC 60.229 57.895 11.55 0.00 42.18 4.52
329 330 1.651240 CCAGCTCCTTGGCGTCATTG 61.651 60.000 0.00 0.00 37.29 2.82
331 332 2.787249 CTCCTTGGCGTCATTGCG 59.213 61.111 0.00 0.00 35.06 4.85
346 347 1.588824 TTGCGCATTTGCTCCTCAGG 61.589 55.000 12.75 0.00 39.32 3.86
359 360 0.546598 CCTCAGGGTGGGATTGGTAC 59.453 60.000 0.00 0.00 0.00 3.34
365 366 1.073284 GGGTGGGATTGGTACGCATAT 59.927 52.381 0.00 0.00 33.24 1.78
393 394 4.446311 CCGGATATTCTTGTGAGGGGATTT 60.446 45.833 0.00 0.00 0.00 2.17
398 399 7.998964 GGATATTCTTGTGAGGGGATTTAAGAA 59.001 37.037 0.00 0.00 38.18 2.52
399 400 8.753497 ATATTCTTGTGAGGGGATTTAAGAAC 57.247 34.615 0.00 0.00 37.09 3.01
403 404 7.695055 TCTTGTGAGGGGATTTAAGAACATAA 58.305 34.615 0.00 0.00 0.00 1.90
507 508 2.829120 ACCATTTAATTGGAACACGGGG 59.171 45.455 20.56 0.00 39.29 5.73
588 589 3.075884 GGCAAATGGAAATGCAACATGT 58.924 40.909 0.00 0.00 44.32 3.21
642 643 5.722021 TTGTTGGCCTTAGAATTTCCTTC 57.278 39.130 3.32 0.00 0.00 3.46
644 645 4.766891 TGTTGGCCTTAGAATTTCCTTCTG 59.233 41.667 3.32 0.00 44.12 3.02
715 727 1.898154 GTAGGTCACCATGCGTCCT 59.102 57.895 0.00 4.93 0.00 3.85
738 750 2.172717 TCCCTATTCCTGGTGCTAAAGC 59.827 50.000 0.00 0.00 42.50 3.51
803 821 3.864983 TTTGGGTCCTCGCCTCCCT 62.865 63.158 0.00 0.00 41.58 4.20
840 858 0.179000 AGCATTCCCGTCCACAGATC 59.821 55.000 0.00 0.00 0.00 2.75
841 859 0.815615 GCATTCCCGTCCACAGATCC 60.816 60.000 0.00 0.00 0.00 3.36
842 860 0.833287 CATTCCCGTCCACAGATCCT 59.167 55.000 0.00 0.00 0.00 3.24
843 861 1.210478 CATTCCCGTCCACAGATCCTT 59.790 52.381 0.00 0.00 0.00 3.36
844 862 0.613260 TTCCCGTCCACAGATCCTTG 59.387 55.000 0.00 0.00 0.00 3.61
845 863 0.544357 TCCCGTCCACAGATCCTTGT 60.544 55.000 0.00 0.00 0.00 3.16
846 864 0.391661 CCCGTCCACAGATCCTTGTG 60.392 60.000 7.88 7.88 46.24 3.33
847 865 1.021390 CCGTCCACAGATCCTTGTGC 61.021 60.000 9.11 0.00 45.52 4.57
848 866 1.354337 CGTCCACAGATCCTTGTGCG 61.354 60.000 9.11 5.48 45.52 5.34
849 867 1.375908 TCCACAGATCCTTGTGCGC 60.376 57.895 0.00 0.00 45.52 6.09
850 868 1.672030 CCACAGATCCTTGTGCGCA 60.672 57.895 5.66 5.66 45.52 6.09
851 869 1.028330 CCACAGATCCTTGTGCGCAT 61.028 55.000 15.91 0.00 45.52 4.73
852 870 0.098200 CACAGATCCTTGTGCGCATG 59.902 55.000 15.91 7.72 41.65 4.06
853 871 1.028330 ACAGATCCTTGTGCGCATGG 61.028 55.000 22.80 22.80 40.24 3.66
854 872 2.117156 AGATCCTTGTGCGCATGGC 61.117 57.895 23.71 12.99 39.14 4.40
855 873 2.044650 ATCCTTGTGCGCATGGCT 60.045 55.556 23.71 14.04 44.05 4.75
856 874 2.332362 GATCCTTGTGCGCATGGCTG 62.332 60.000 23.71 1.51 44.05 4.85
857 875 3.367743 CCTTGTGCGCATGGCTGT 61.368 61.111 15.91 0.00 44.05 4.40
858 876 2.646719 CTTGTGCGCATGGCTGTT 59.353 55.556 15.91 0.00 44.05 3.16
859 877 1.443194 CTTGTGCGCATGGCTGTTC 60.443 57.895 15.91 0.00 44.05 3.18
860 878 2.132517 CTTGTGCGCATGGCTGTTCA 62.133 55.000 15.91 0.00 44.05 3.18
861 879 1.732417 TTGTGCGCATGGCTGTTCAA 61.732 50.000 15.91 7.63 44.05 2.69
862 880 1.443194 GTGCGCATGGCTGTTCAAG 60.443 57.895 15.91 0.00 44.05 3.02
863 881 1.898094 TGCGCATGGCTGTTCAAGT 60.898 52.632 5.66 0.00 44.05 3.16
864 882 0.605050 TGCGCATGGCTGTTCAAGTA 60.605 50.000 5.66 0.00 44.05 2.24
865 883 0.179189 GCGCATGGCTGTTCAAGTAC 60.179 55.000 0.30 0.00 39.11 2.73
866 884 1.155889 CGCATGGCTGTTCAAGTACA 58.844 50.000 0.00 0.00 0.00 2.90
867 885 1.535028 CGCATGGCTGTTCAAGTACAA 59.465 47.619 0.00 0.00 0.00 2.41
868 886 2.031245 CGCATGGCTGTTCAAGTACAAA 60.031 45.455 0.00 0.00 0.00 2.83
869 887 3.549827 CGCATGGCTGTTCAAGTACAAAA 60.550 43.478 0.00 0.00 0.00 2.44
870 888 4.559153 GCATGGCTGTTCAAGTACAAAAT 58.441 39.130 0.00 0.00 0.00 1.82
871 889 5.618863 CGCATGGCTGTTCAAGTACAAAATA 60.619 40.000 0.00 0.00 0.00 1.40
872 890 6.155827 GCATGGCTGTTCAAGTACAAAATAA 58.844 36.000 0.00 0.00 0.00 1.40
873 891 6.308766 GCATGGCTGTTCAAGTACAAAATAAG 59.691 38.462 0.00 0.00 0.00 1.73
874 892 5.768317 TGGCTGTTCAAGTACAAAATAAGC 58.232 37.500 0.00 0.00 0.00 3.09
875 893 5.534654 TGGCTGTTCAAGTACAAAATAAGCT 59.465 36.000 0.00 0.00 0.00 3.74
876 894 6.040391 TGGCTGTTCAAGTACAAAATAAGCTT 59.960 34.615 3.48 3.48 0.00 3.74
877 895 6.923508 GGCTGTTCAAGTACAAAATAAGCTTT 59.076 34.615 3.20 0.00 0.00 3.51
878 896 8.079809 GGCTGTTCAAGTACAAAATAAGCTTTA 58.920 33.333 3.20 0.00 0.00 1.85
879 897 9.118236 GCTGTTCAAGTACAAAATAAGCTTTAG 57.882 33.333 3.20 0.00 0.00 1.85
880 898 9.118236 CTGTTCAAGTACAAAATAAGCTTTAGC 57.882 33.333 3.20 0.00 42.49 3.09
881 899 8.625651 TGTTCAAGTACAAAATAAGCTTTAGCA 58.374 29.630 3.20 0.00 45.16 3.49
882 900 9.626045 GTTCAAGTACAAAATAAGCTTTAGCAT 57.374 29.630 3.20 0.00 45.16 3.79
884 902 9.840427 TCAAGTACAAAATAAGCTTTAGCATTC 57.160 29.630 3.20 0.00 45.16 2.67
885 903 9.076596 CAAGTACAAAATAAGCTTTAGCATTCC 57.923 33.333 3.20 0.00 45.16 3.01
886 904 7.772166 AGTACAAAATAAGCTTTAGCATTCCC 58.228 34.615 3.20 0.00 45.16 3.97
887 905 5.650543 ACAAAATAAGCTTTAGCATTCCCG 58.349 37.500 3.20 0.00 45.16 5.14
888 906 5.185056 ACAAAATAAGCTTTAGCATTCCCGT 59.815 36.000 3.20 0.00 45.16 5.28
889 907 5.500645 AAATAAGCTTTAGCATTCCCGTC 57.499 39.130 3.20 0.00 45.16 4.79
890 908 1.751437 AAGCTTTAGCATTCCCGTCC 58.249 50.000 4.33 0.00 45.16 4.79
891 909 0.618458 AGCTTTAGCATTCCCGTCCA 59.382 50.000 4.33 0.00 45.16 4.02
892 910 0.733150 GCTTTAGCATTCCCGTCCAC 59.267 55.000 0.00 0.00 41.59 4.02
893 911 1.948611 GCTTTAGCATTCCCGTCCACA 60.949 52.381 0.00 0.00 41.59 4.17
894 912 2.009774 CTTTAGCATTCCCGTCCACAG 58.990 52.381 0.00 0.00 0.00 3.66
895 913 1.271856 TTAGCATTCCCGTCCACAGA 58.728 50.000 0.00 0.00 0.00 3.41
896 914 1.496060 TAGCATTCCCGTCCACAGAT 58.504 50.000 0.00 0.00 0.00 2.90
904 922 1.021390 CCGTCCACAGATCCTTGTGC 61.021 60.000 9.11 0.00 45.52 4.57
1108 1128 1.175983 GGAACAACCATTGACGCCCA 61.176 55.000 0.00 0.00 38.79 5.36
1171 1191 2.760374 AGAAGTCCAGCAAGAAGTTCG 58.240 47.619 0.00 0.00 0.00 3.95
1293 1313 7.882179 ACCAAAATGACACTAGGATTTTACAC 58.118 34.615 0.00 0.00 30.07 2.90
1294 1314 7.724061 ACCAAAATGACACTAGGATTTTACACT 59.276 33.333 0.00 0.00 30.07 3.55
1367 1387 3.169198 GCTGCAGACGTTACCAGC 58.831 61.111 20.43 15.94 43.10 4.85
1409 1429 1.077501 CCTGCGGATCACCAACCAT 60.078 57.895 0.00 0.00 35.59 3.55
1421 1441 2.000048 ACCAACCATAACATCCCCAGT 59.000 47.619 0.00 0.00 0.00 4.00
1424 1444 3.458118 CCAACCATAACATCCCCAGTAGA 59.542 47.826 0.00 0.00 0.00 2.59
1470 1490 1.166531 GGCGACCAACAACTTCAGCT 61.167 55.000 0.00 0.00 0.00 4.24
1471 1491 0.040958 GCGACCAACAACTTCAGCTG 60.041 55.000 7.63 7.63 0.00 4.24
1473 1493 0.040958 GACCAACAACTTCAGCTGCG 60.041 55.000 9.47 4.98 0.00 5.18
1475 1495 0.877071 CCAACAACTTCAGCTGCGAT 59.123 50.000 9.47 0.00 0.00 4.58
1566 1586 2.679837 ACTGCAACAAGCCGATCAATAG 59.320 45.455 0.00 0.00 44.83 1.73
1589 1609 4.755629 GTCTGCAGCAGATTGTATCATCAT 59.244 41.667 27.86 0.00 42.73 2.45
1590 1610 5.238868 GTCTGCAGCAGATTGTATCATCATT 59.761 40.000 27.86 0.00 42.73 2.57
1608 1634 7.405292 TCATCATTTTCCCTTCTCATGTAACT 58.595 34.615 0.00 0.00 0.00 2.24
1618 1644 6.127054 CCCTTCTCATGTAACTTGGATGAGTA 60.127 42.308 0.00 0.00 42.48 2.59
2351 2381 6.843208 TCGAACGTTTAATCCAATGCAAATA 58.157 32.000 0.46 0.00 0.00 1.40
2352 2382 7.476667 TCGAACGTTTAATCCAATGCAAATAT 58.523 30.769 0.46 0.00 0.00 1.28
2353 2383 7.971168 TCGAACGTTTAATCCAATGCAAATATT 59.029 29.630 0.46 0.00 0.00 1.28
2354 2384 9.227490 CGAACGTTTAATCCAATGCAAATATTA 57.773 29.630 0.46 0.00 0.00 0.98
2381 2411 0.108898 CAAGCTCGAGACCACCTCTG 60.109 60.000 18.75 1.42 39.78 3.35
2385 2415 1.751924 GCTCGAGACCACCTCTGTATT 59.248 52.381 18.75 0.00 39.78 1.89
2568 2598 4.443266 GCGCTCACCTTCCTCGCT 62.443 66.667 0.00 0.00 42.19 4.93
2577 2607 1.001406 ACCTTCCTCGCTGAACAGAAG 59.999 52.381 5.97 2.46 34.94 2.85
2639 2669 2.125753 GGACTGCAGCACTCCTCG 60.126 66.667 15.27 0.00 0.00 4.63
2689 2720 1.263484 CCGATGATGACATGAAGCAGC 59.737 52.381 0.00 0.00 36.82 5.25
2720 2751 9.642343 AGCCAGACGACCATAGAATATAATATA 57.358 33.333 0.00 0.00 0.00 0.86
2933 2965 0.890996 CTGTTCCAAGGACTGCCACC 60.891 60.000 0.00 0.00 36.29 4.61
3008 3044 9.851686 ATTCTGGTCTGCATGTAATCTAAAATA 57.148 29.630 0.00 0.00 0.00 1.40
3051 3087 8.188799 TGTGGAATTGATAACTCTAGTAGAACG 58.811 37.037 0.64 0.00 0.00 3.95
3052 3088 8.189460 GTGGAATTGATAACTCTAGTAGAACGT 58.811 37.037 0.64 0.00 0.00 3.99
3095 3132 7.920151 TGATCGAAGTTGCAAATAATTATTGGG 59.080 33.333 11.42 8.29 0.00 4.12
3119 3156 4.574421 TGCGATGAACCGTGATTGAATAAT 59.426 37.500 0.00 0.00 0.00 1.28
3143 3181 8.785329 ATGAAAAGACTTCCAATTCTAGTCTC 57.215 34.615 11.86 4.22 45.81 3.36
3144 3182 7.967908 TGAAAAGACTTCCAATTCTAGTCTCT 58.032 34.615 11.86 5.37 45.81 3.10
3145 3183 8.091449 TGAAAAGACTTCCAATTCTAGTCTCTC 58.909 37.037 11.86 11.71 45.81 3.20
3147 3185 5.258051 AGACTTCCAATTCTAGTCTCTCGT 58.742 41.667 7.49 0.00 43.81 4.18
3191 3229 4.502259 GGTCTCAAGAGAGTCAAGCTTCAA 60.502 45.833 0.00 0.00 42.66 2.69
3202 3240 5.410924 AGTCAAGCTTCAAAAACTTTGACC 58.589 37.500 0.00 0.00 0.00 4.02
3216 3254 4.377897 ACTTTGACCAAGTTTACGGAGAG 58.622 43.478 0.00 0.00 43.89 3.20
3356 3394 7.772332 ATCTCCGTCAAAGTTTACATATGTC 57.228 36.000 12.68 0.00 0.00 3.06
3397 3436 5.562635 ACACACTATTTTGGGACGGAATAA 58.437 37.500 0.00 0.00 0.00 1.40
3430 3469 4.493618 TCATTTTTGTTGGGTGGGGATAA 58.506 39.130 0.00 0.00 0.00 1.75
3438 3477 4.017037 TGTTGGGTGGGGATAATGTATTGT 60.017 41.667 0.00 0.00 0.00 2.71
3470 3509 8.006298 TGTCTTTTCTTTCCTATTTGAAAGCA 57.994 30.769 8.31 0.00 46.94 3.91
3510 3550 4.141135 TCCCTCACTTCCAAAATAACCACA 60.141 41.667 0.00 0.00 0.00 4.17
3531 3571 6.459024 CCACAACACTTATTTTGAAACGGAGA 60.459 38.462 0.00 0.00 0.00 3.71
3580 3620 1.620819 ACAACTCTGAAGACCATCGCT 59.379 47.619 0.00 0.00 0.00 4.93
3608 3648 2.099756 TGACAGACGGCTCATCACTATG 59.900 50.000 0.00 0.00 0.00 2.23
3611 3651 1.335182 AGACGGCTCATCACTATGACG 59.665 52.381 0.00 0.00 37.20 4.35
3620 3660 0.319986 TCACTATGACGTTTGCCGCA 60.320 50.000 0.00 0.00 41.42 5.69
3678 3718 5.410439 CCATCAAGATCACATCAATCGCATA 59.590 40.000 0.00 0.00 0.00 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.220824 GGTTCGTAACACAAACCGGTAC 59.779 50.000 8.00 0.00 33.68 3.34
1 2 2.478831 GGTTCGTAACACAAACCGGTA 58.521 47.619 8.00 0.00 33.68 4.02
2 3 1.298602 GGTTCGTAACACAAACCGGT 58.701 50.000 0.00 0.00 33.68 5.28
5 6 1.298602 ACCGGTTCGTAACACAAACC 58.701 50.000 0.00 0.00 39.25 3.27
6 7 3.123050 AGTACCGGTTCGTAACACAAAC 58.877 45.455 15.04 0.00 0.00 2.93
7 8 3.451141 AGTACCGGTTCGTAACACAAA 57.549 42.857 15.04 0.00 0.00 2.83
8 9 4.576216 TTAGTACCGGTTCGTAACACAA 57.424 40.909 15.04 0.00 0.00 3.33
9 10 4.545610 CTTTAGTACCGGTTCGTAACACA 58.454 43.478 15.04 0.00 0.00 3.72
10 11 3.920412 CCTTTAGTACCGGTTCGTAACAC 59.080 47.826 15.04 1.99 0.00 3.32
11 12 3.572255 ACCTTTAGTACCGGTTCGTAACA 59.428 43.478 15.04 0.00 0.00 2.41
12 13 4.082733 AGACCTTTAGTACCGGTTCGTAAC 60.083 45.833 15.04 3.84 0.00 2.50
13 14 4.079253 AGACCTTTAGTACCGGTTCGTAA 58.921 43.478 15.04 5.59 0.00 3.18
14 15 3.686016 AGACCTTTAGTACCGGTTCGTA 58.314 45.455 15.04 0.00 0.00 3.43
15 16 2.489722 GAGACCTTTAGTACCGGTTCGT 59.510 50.000 15.04 0.00 0.00 3.85
16 17 2.159324 GGAGACCTTTAGTACCGGTTCG 60.159 54.545 15.04 0.00 0.00 3.95
17 18 3.516981 GGAGACCTTTAGTACCGGTTC 57.483 52.381 15.04 8.12 0.00 3.62
41 42 4.011517 ACGTGTTAGGGCCGTGGG 62.012 66.667 8.57 0.00 32.86 4.61
42 43 2.740826 CACGTGTTAGGGCCGTGG 60.741 66.667 8.57 0.00 45.97 4.94
47 48 3.419759 CGTGGCACGTGTTAGGGC 61.420 66.667 30.56 3.15 40.45 5.19
61 62 1.072505 ACTAAAGGGCCACCACGTG 59.927 57.895 9.08 9.08 40.13 4.49
62 63 1.072505 CACTAAAGGGCCACCACGT 59.927 57.895 6.18 0.00 40.13 4.49
63 64 0.953960 GTCACTAAAGGGCCACCACG 60.954 60.000 6.18 0.00 40.13 4.94
64 65 0.953960 CGTCACTAAAGGGCCACCAC 60.954 60.000 6.18 0.00 40.13 4.16
65 66 1.373435 CGTCACTAAAGGGCCACCA 59.627 57.895 6.18 0.00 40.13 4.17
66 67 1.376812 CCGTCACTAAAGGGCCACC 60.377 63.158 6.18 0.00 0.00 4.61
67 68 0.250597 AACCGTCACTAAAGGGCCAC 60.251 55.000 6.18 0.00 0.00 5.01
68 69 0.035739 GAACCGTCACTAAAGGGCCA 59.964 55.000 6.18 0.00 0.00 5.36
69 70 1.017701 CGAACCGTCACTAAAGGGCC 61.018 60.000 0.00 0.00 0.00 5.80
70 71 0.320160 ACGAACCGTCACTAAAGGGC 60.320 55.000 0.00 0.00 33.69 5.19
71 72 1.425412 CACGAACCGTCACTAAAGGG 58.575 55.000 0.00 0.00 38.32 3.95
72 73 0.788391 GCACGAACCGTCACTAAAGG 59.212 55.000 0.00 0.00 38.32 3.11
73 74 1.455786 CTGCACGAACCGTCACTAAAG 59.544 52.381 0.00 0.00 38.32 1.85
74 75 1.067364 TCTGCACGAACCGTCACTAAA 59.933 47.619 0.00 0.00 38.32 1.85
75 76 0.669619 TCTGCACGAACCGTCACTAA 59.330 50.000 0.00 0.00 38.32 2.24
76 77 0.669619 TTCTGCACGAACCGTCACTA 59.330 50.000 0.00 0.00 38.32 2.74
77 78 0.874607 GTTCTGCACGAACCGTCACT 60.875 55.000 14.47 0.00 45.00 3.41
78 79 1.563173 GTTCTGCACGAACCGTCAC 59.437 57.895 14.47 0.00 45.00 3.67
79 80 4.021650 GTTCTGCACGAACCGTCA 57.978 55.556 14.47 0.00 45.00 4.35
85 86 1.246649 TAGTACCGGTTCTGCACGAA 58.753 50.000 22.71 0.00 0.00 3.85
86 87 1.246649 TTAGTACCGGTTCTGCACGA 58.753 50.000 22.71 3.53 0.00 4.35
87 88 1.990563 CTTTAGTACCGGTTCTGCACG 59.009 52.381 22.71 4.46 0.00 5.34
88 89 2.344025 CCTTTAGTACCGGTTCTGCAC 58.656 52.381 22.71 10.16 0.00 4.57
89 90 1.338389 GCCTTTAGTACCGGTTCTGCA 60.338 52.381 22.71 7.36 0.00 4.41
90 91 1.366679 GCCTTTAGTACCGGTTCTGC 58.633 55.000 22.71 13.80 0.00 4.26
91 92 1.406477 GGGCCTTTAGTACCGGTTCTG 60.406 57.143 22.71 7.85 0.00 3.02
92 93 0.907486 GGGCCTTTAGTACCGGTTCT 59.093 55.000 15.04 17.06 0.00 3.01
93 94 0.907486 AGGGCCTTTAGTACCGGTTC 59.093 55.000 15.04 8.12 0.00 3.62
94 95 1.365293 AAGGGCCTTTAGTACCGGTT 58.635 50.000 15.04 0.00 0.00 4.44
95 96 1.833630 GTAAGGGCCTTTAGTACCGGT 59.166 52.381 26.29 13.98 0.00 5.28
96 97 1.832998 TGTAAGGGCCTTTAGTACCGG 59.167 52.381 26.29 0.00 0.00 5.28
97 98 3.615224 TTGTAAGGGCCTTTAGTACCG 57.385 47.619 26.29 0.00 0.00 4.02
98 99 4.012374 GGTTTGTAAGGGCCTTTAGTACC 58.988 47.826 26.29 21.31 0.00 3.34
99 100 3.686241 CGGTTTGTAAGGGCCTTTAGTAC 59.314 47.826 26.29 16.82 0.00 2.73
100 101 3.307621 CCGGTTTGTAAGGGCCTTTAGTA 60.308 47.826 26.29 2.58 0.00 1.82
101 102 2.553685 CCGGTTTGTAAGGGCCTTTAGT 60.554 50.000 26.29 1.50 0.00 2.24
102 103 2.089201 CCGGTTTGTAAGGGCCTTTAG 58.911 52.381 26.29 8.03 0.00 1.85
103 104 1.424684 ACCGGTTTGTAAGGGCCTTTA 59.575 47.619 26.29 11.56 0.00 1.85
104 105 0.186630 ACCGGTTTGTAAGGGCCTTT 59.813 50.000 26.29 5.08 0.00 3.11
105 106 0.538746 CACCGGTTTGTAAGGGCCTT 60.539 55.000 24.44 24.44 0.00 4.35
106 107 1.074248 CACCGGTTTGTAAGGGCCT 59.926 57.895 2.97 0.00 0.00 5.19
107 108 0.323087 ATCACCGGTTTGTAAGGGCC 60.323 55.000 2.97 0.00 0.00 5.80
108 109 2.011947 GTATCACCGGTTTGTAAGGGC 58.988 52.381 2.97 0.00 0.00 5.19
109 110 3.267483 CAGTATCACCGGTTTGTAAGGG 58.733 50.000 2.97 0.00 0.00 3.95
110 111 2.676342 GCAGTATCACCGGTTTGTAAGG 59.324 50.000 2.97 0.00 0.00 2.69
111 112 2.676342 GGCAGTATCACCGGTTTGTAAG 59.324 50.000 2.97 0.00 0.00 2.34
112 113 2.616001 GGGCAGTATCACCGGTTTGTAA 60.616 50.000 2.97 0.00 0.00 2.41
113 114 1.065998 GGGCAGTATCACCGGTTTGTA 60.066 52.381 2.97 0.00 0.00 2.41
114 115 0.322187 GGGCAGTATCACCGGTTTGT 60.322 55.000 2.97 0.00 0.00 2.83
115 116 0.035439 AGGGCAGTATCACCGGTTTG 60.035 55.000 2.97 0.00 0.00 2.93
116 117 0.035439 CAGGGCAGTATCACCGGTTT 60.035 55.000 2.97 0.00 0.00 3.27
117 118 1.198759 ACAGGGCAGTATCACCGGTT 61.199 55.000 2.97 0.00 28.03 4.44
118 119 1.198759 AACAGGGCAGTATCACCGGT 61.199 55.000 0.00 0.00 34.11 5.28
119 120 0.462047 GAACAGGGCAGTATCACCGG 60.462 60.000 0.00 0.00 0.00 5.28
120 121 0.806102 CGAACAGGGCAGTATCACCG 60.806 60.000 0.00 0.00 0.00 4.94
121 122 0.462047 CCGAACAGGGCAGTATCACC 60.462 60.000 0.00 0.00 35.97 4.02
122 123 3.065575 CCGAACAGGGCAGTATCAC 57.934 57.895 0.00 0.00 35.97 3.06
131 132 2.107950 TTCACTAATGCCGAACAGGG 57.892 50.000 0.00 0.00 41.48 4.45
132 133 3.535561 AGATTCACTAATGCCGAACAGG 58.464 45.455 0.00 0.00 44.97 4.00
133 134 4.747108 CCTAGATTCACTAATGCCGAACAG 59.253 45.833 0.00 0.00 0.00 3.16
134 135 4.161565 ACCTAGATTCACTAATGCCGAACA 59.838 41.667 0.00 0.00 0.00 3.18
135 136 4.694339 ACCTAGATTCACTAATGCCGAAC 58.306 43.478 0.00 0.00 0.00 3.95
136 137 5.128827 AGAACCTAGATTCACTAATGCCGAA 59.871 40.000 0.00 0.00 0.00 4.30
137 138 4.649674 AGAACCTAGATTCACTAATGCCGA 59.350 41.667 0.00 0.00 0.00 5.54
138 139 4.950050 AGAACCTAGATTCACTAATGCCG 58.050 43.478 0.00 0.00 0.00 5.69
139 140 7.272978 TGTAAGAACCTAGATTCACTAATGCC 58.727 38.462 0.00 0.00 0.00 4.40
140 141 8.718102 TTGTAAGAACCTAGATTCACTAATGC 57.282 34.615 0.00 0.00 0.00 3.56
203 204 5.247110 AGGGTATCTCGAGACAAATATGCAT 59.753 40.000 19.30 3.79 0.00 3.96
205 206 5.140747 AGGGTATCTCGAGACAAATATGC 57.859 43.478 19.30 4.02 0.00 3.14
240 241 4.458989 TGCCATTTAAAACTAGTGCCTCAG 59.541 41.667 0.00 0.00 0.00 3.35
242 243 5.385509 TTGCCATTTAAAACTAGTGCCTC 57.614 39.130 0.00 0.00 0.00 4.70
250 251 7.278868 TGTTCGATTGTTTTGCCATTTAAAACT 59.721 29.630 12.69 0.00 44.34 2.66
272 273 0.857311 CGACATGCGCCGAAATGTTC 60.857 55.000 11.82 5.58 37.15 3.18
286 287 2.884012 TGGACAACAAAAGCATCGACAT 59.116 40.909 0.00 0.00 0.00 3.06
331 332 1.318158 CCACCCTGAGGAGCAAATGC 61.318 60.000 0.00 0.00 37.78 3.56
346 347 2.151202 CATATGCGTACCAATCCCACC 58.849 52.381 0.00 0.00 0.00 4.61
359 360 2.159043 AGAATATCCGGCCTCATATGCG 60.159 50.000 0.00 0.00 0.00 4.73
365 366 2.103094 CTCACAAGAATATCCGGCCTCA 59.897 50.000 0.00 0.00 0.00 3.86
423 424 6.600822 CCTTGTCTTGTGATCTTTATCCACAT 59.399 38.462 0.00 0.00 0.00 3.21
433 434 2.289945 GGCACTCCTTGTCTTGTGATCT 60.290 50.000 0.00 0.00 32.72 2.75
486 487 2.829120 CCCCGTGTTCCAATTAAATGGT 59.171 45.455 9.41 0.00 41.46 3.55
488 489 3.130340 CCTCCCCGTGTTCCAATTAAATG 59.870 47.826 0.00 0.00 0.00 2.32
629 630 7.015195 CCCCTCAAAAACAGAAGGAAATTCTAA 59.985 37.037 0.00 0.00 46.91 2.10
642 643 2.642807 TCTAGGGACCCCTCAAAAACAG 59.357 50.000 11.55 1.68 44.43 3.16
644 645 3.801307 TTCTAGGGACCCCTCAAAAAC 57.199 47.619 11.55 0.00 44.43 2.43
698 710 0.324368 AGAGGACGCATGGTGACCTA 60.324 55.000 2.11 0.00 38.20 3.08
715 727 3.414759 TTAGCACCAGGAATAGGGAGA 57.585 47.619 0.00 0.00 0.00 3.71
738 750 4.680237 TTCCTGCCACGGCGTCAG 62.680 66.667 18.63 18.63 45.51 3.51
803 821 7.068226 GGGAATGCTAAAGCTTATTTTGTCCTA 59.932 37.037 0.00 0.00 42.66 2.94
840 858 2.807631 GAACAGCCATGCGCACAAGG 62.808 60.000 14.90 17.03 41.38 3.61
841 859 1.443194 GAACAGCCATGCGCACAAG 60.443 57.895 14.90 5.33 41.38 3.16
842 860 1.732417 TTGAACAGCCATGCGCACAA 61.732 50.000 14.90 7.02 41.38 3.33
843 861 2.132517 CTTGAACAGCCATGCGCACA 62.133 55.000 14.90 0.00 41.38 4.57
844 862 1.443194 CTTGAACAGCCATGCGCAC 60.443 57.895 14.90 0.00 41.38 5.34
845 863 0.605050 TACTTGAACAGCCATGCGCA 60.605 50.000 14.96 14.96 41.38 6.09
846 864 0.179189 GTACTTGAACAGCCATGCGC 60.179 55.000 0.00 0.00 37.98 6.09
847 865 1.155889 TGTACTTGAACAGCCATGCG 58.844 50.000 0.00 0.00 0.00 4.73
848 866 3.641437 TTTGTACTTGAACAGCCATGC 57.359 42.857 0.00 0.00 0.00 4.06
849 867 6.308766 GCTTATTTTGTACTTGAACAGCCATG 59.691 38.462 0.00 0.00 0.00 3.66
850 868 6.209391 AGCTTATTTTGTACTTGAACAGCCAT 59.791 34.615 0.00 0.00 0.00 4.40
851 869 5.534654 AGCTTATTTTGTACTTGAACAGCCA 59.465 36.000 0.00 0.00 0.00 4.75
852 870 6.013842 AGCTTATTTTGTACTTGAACAGCC 57.986 37.500 0.00 0.00 0.00 4.85
853 871 7.930513 AAAGCTTATTTTGTACTTGAACAGC 57.069 32.000 0.00 0.00 0.00 4.40
854 872 9.118236 GCTAAAGCTTATTTTGTACTTGAACAG 57.882 33.333 0.00 0.00 38.21 3.16
855 873 8.625651 TGCTAAAGCTTATTTTGTACTTGAACA 58.374 29.630 0.00 0.00 42.66 3.18
856 874 9.626045 ATGCTAAAGCTTATTTTGTACTTGAAC 57.374 29.630 0.00 0.00 42.66 3.18
858 876 9.840427 GAATGCTAAAGCTTATTTTGTACTTGA 57.160 29.630 0.00 0.00 42.66 3.02
859 877 9.076596 GGAATGCTAAAGCTTATTTTGTACTTG 57.923 33.333 0.00 0.00 42.66 3.16
860 878 8.251026 GGGAATGCTAAAGCTTATTTTGTACTT 58.749 33.333 0.00 0.00 42.66 2.24
861 879 7.415206 CGGGAATGCTAAAGCTTATTTTGTACT 60.415 37.037 0.00 0.00 42.66 2.73
862 880 6.691388 CGGGAATGCTAAAGCTTATTTTGTAC 59.309 38.462 0.00 0.00 42.66 2.90
863 881 6.376018 ACGGGAATGCTAAAGCTTATTTTGTA 59.624 34.615 0.00 0.00 42.66 2.41
864 882 5.185056 ACGGGAATGCTAAAGCTTATTTTGT 59.815 36.000 0.00 0.00 42.66 2.83
865 883 5.650543 ACGGGAATGCTAAAGCTTATTTTG 58.349 37.500 0.00 0.00 42.66 2.44
866 884 5.163550 GGACGGGAATGCTAAAGCTTATTTT 60.164 40.000 0.00 0.00 42.66 1.82
867 885 4.338400 GGACGGGAATGCTAAAGCTTATTT 59.662 41.667 0.00 0.00 42.66 1.40
868 886 3.883489 GGACGGGAATGCTAAAGCTTATT 59.117 43.478 0.00 0.00 42.66 1.40
869 887 3.118038 TGGACGGGAATGCTAAAGCTTAT 60.118 43.478 0.00 0.00 42.66 1.73
870 888 2.237643 TGGACGGGAATGCTAAAGCTTA 59.762 45.455 0.00 0.00 42.66 3.09
871 889 1.004277 TGGACGGGAATGCTAAAGCTT 59.996 47.619 3.26 0.00 42.66 3.74
872 890 0.618458 TGGACGGGAATGCTAAAGCT 59.382 50.000 3.26 0.00 42.66 3.74
873 891 0.733150 GTGGACGGGAATGCTAAAGC 59.267 55.000 0.00 0.00 42.50 3.51
874 892 2.009774 CTGTGGACGGGAATGCTAAAG 58.990 52.381 0.00 0.00 0.00 1.85
875 893 1.626321 TCTGTGGACGGGAATGCTAAA 59.374 47.619 0.00 0.00 0.00 1.85
876 894 1.271856 TCTGTGGACGGGAATGCTAA 58.728 50.000 0.00 0.00 0.00 3.09
877 895 1.412710 GATCTGTGGACGGGAATGCTA 59.587 52.381 0.00 0.00 0.00 3.49
878 896 0.179000 GATCTGTGGACGGGAATGCT 59.821 55.000 0.00 0.00 0.00 3.79
879 897 0.815615 GGATCTGTGGACGGGAATGC 60.816 60.000 0.00 0.00 0.00 3.56
880 898 0.833287 AGGATCTGTGGACGGGAATG 59.167 55.000 0.00 0.00 0.00 2.67
881 899 1.210478 CAAGGATCTGTGGACGGGAAT 59.790 52.381 0.00 0.00 0.00 3.01
882 900 0.613260 CAAGGATCTGTGGACGGGAA 59.387 55.000 0.00 0.00 0.00 3.97
883 901 0.544357 ACAAGGATCTGTGGACGGGA 60.544 55.000 0.00 0.00 0.00 5.14
884 902 0.391661 CACAAGGATCTGTGGACGGG 60.392 60.000 7.11 0.00 42.52 5.28
885 903 1.021390 GCACAAGGATCTGTGGACGG 61.021 60.000 14.83 0.00 45.66 4.79
886 904 1.354337 CGCACAAGGATCTGTGGACG 61.354 60.000 14.83 8.37 45.66 4.79
887 905 1.639298 GCGCACAAGGATCTGTGGAC 61.639 60.000 14.83 1.39 45.66 4.02
888 906 1.375908 GCGCACAAGGATCTGTGGA 60.376 57.895 14.83 0.00 45.66 4.02
889 907 1.028330 ATGCGCACAAGGATCTGTGG 61.028 55.000 14.90 7.77 45.66 4.17
891 909 1.028330 CCATGCGCACAAGGATCTGT 61.028 55.000 14.90 0.00 36.75 3.41
892 910 1.725665 CCATGCGCACAAGGATCTG 59.274 57.895 14.90 3.89 36.75 2.90
893 911 2.117156 GCCATGCGCACAAGGATCT 61.117 57.895 24.60 0.00 36.75 2.75
894 912 2.117156 AGCCATGCGCACAAGGATC 61.117 57.895 24.60 10.97 36.75 3.36
895 913 2.044650 AGCCATGCGCACAAGGAT 60.045 55.556 24.60 17.83 36.75 3.24
896 914 3.057548 CAGCCATGCGCACAAGGA 61.058 61.111 24.60 0.00 36.75 3.36
904 922 5.063944 GGATATATACTTGAACAGCCATGCG 59.936 44.000 0.00 0.00 0.00 4.73
1108 1128 3.349006 CGACCGCTTGTGCTTGCT 61.349 61.111 0.00 0.00 36.97 3.91
1293 1313 0.734889 CAAACCAATCGGCAGCCTAG 59.265 55.000 10.54 0.00 34.57 3.02
1294 1314 0.326595 TCAAACCAATCGGCAGCCTA 59.673 50.000 10.54 0.00 34.57 3.93
1367 1387 4.805231 TCGGCCGCGTACATGTGG 62.805 66.667 23.51 1.56 42.55 4.17
1409 1429 3.031736 GAGCACTCTACTGGGGATGTTA 58.968 50.000 0.00 0.00 0.00 2.41
1421 1441 3.358554 ACGGAAGGTGAGCACTCTA 57.641 52.632 0.16 0.00 0.00 2.43
1470 1490 1.743623 CGCCCACAAGGTTATCGCA 60.744 57.895 0.00 0.00 38.26 5.10
1471 1491 1.429148 CTCGCCCACAAGGTTATCGC 61.429 60.000 0.00 0.00 38.26 4.58
1473 1493 0.463833 CCCTCGCCCACAAGGTTATC 60.464 60.000 0.00 0.00 38.26 1.75
1475 1495 3.074281 CCCTCGCCCACAAGGTTA 58.926 61.111 0.00 0.00 38.26 2.85
1566 1586 4.124970 TGATGATACAATCTGCTGCAGAC 58.875 43.478 32.54 19.45 43.63 3.51
1589 1609 5.947663 TCCAAGTTACATGAGAAGGGAAAA 58.052 37.500 0.00 0.00 0.00 2.29
1590 1610 5.576563 TCCAAGTTACATGAGAAGGGAAA 57.423 39.130 0.00 0.00 0.00 3.13
1608 1634 7.327975 ACGTGACAAAGATAATACTCATCCAA 58.672 34.615 0.00 0.00 0.00 3.53
1618 1644 6.807230 GCGATATCCTACGTGACAAAGATAAT 59.193 38.462 0.00 0.00 0.00 1.28
2351 2381 6.979238 GTGGTCTCGAGCTTGTAATTAGTAAT 59.021 38.462 7.81 0.00 0.00 1.89
2352 2382 6.327934 GTGGTCTCGAGCTTGTAATTAGTAA 58.672 40.000 7.81 0.00 0.00 2.24
2353 2383 5.163581 GGTGGTCTCGAGCTTGTAATTAGTA 60.164 44.000 7.81 0.00 0.00 1.82
2354 2384 4.381718 GGTGGTCTCGAGCTTGTAATTAGT 60.382 45.833 7.81 0.00 0.00 2.24
2355 2385 4.113354 GGTGGTCTCGAGCTTGTAATTAG 58.887 47.826 7.81 0.00 0.00 1.73
2356 2386 3.767673 AGGTGGTCTCGAGCTTGTAATTA 59.232 43.478 7.81 0.00 0.00 1.40
2357 2387 2.567615 AGGTGGTCTCGAGCTTGTAATT 59.432 45.455 7.81 0.00 0.00 1.40
2359 2389 1.544691 GAGGTGGTCTCGAGCTTGTAA 59.455 52.381 7.81 0.00 32.18 2.41
2360 2390 1.174783 GAGGTGGTCTCGAGCTTGTA 58.825 55.000 7.81 0.00 32.18 2.41
2363 2393 0.540830 ACAGAGGTGGTCTCGAGCTT 60.541 55.000 7.81 0.00 46.82 3.74
2364 2394 0.328592 TACAGAGGTGGTCTCGAGCT 59.671 55.000 7.81 0.00 46.82 4.09
2365 2395 1.394618 ATACAGAGGTGGTCTCGAGC 58.605 55.000 7.81 2.69 46.82 5.03
2366 2396 3.017442 TGAATACAGAGGTGGTCTCGAG 58.983 50.000 5.93 5.93 46.82 4.04
2367 2397 3.017442 CTGAATACAGAGGTGGTCTCGA 58.983 50.000 0.00 0.00 46.82 4.04
2568 2598 5.708697 TCGTTGAGGATAGTACTTCTGTTCA 59.291 40.000 0.00 0.00 0.00 3.18
2577 2607 2.290093 CCGGTCTCGTTGAGGATAGTAC 59.710 54.545 0.00 0.00 33.95 2.73
2639 2669 4.037923 TCTCAGAAACCATGTCCTTTTTGC 59.962 41.667 0.00 0.00 0.00 3.68
2689 2720 0.668535 TATGGTCGTCTGGCTCATCG 59.331 55.000 0.00 0.00 0.00 3.84
2720 2751 9.331466 TCTCCTCCTTTATGCATCTCTTATATT 57.669 33.333 0.19 0.00 0.00 1.28
2724 2755 6.519721 GCATCTCCTCCTTTATGCATCTCTTA 60.520 42.308 0.19 0.00 43.30 2.10
2725 2756 5.745476 GCATCTCCTCCTTTATGCATCTCTT 60.745 44.000 0.19 0.00 43.30 2.85
2738 2769 0.540923 GTTCTGCTGCATCTCCTCCT 59.459 55.000 1.31 0.00 0.00 3.69
3008 3044 2.586425 CACAAATCCTTGGCGGGATAT 58.414 47.619 11.34 1.75 44.50 1.63
3051 3087 6.721321 TCGATCACCTTTTGTTTTTGAGTAC 58.279 36.000 0.00 0.00 0.00 2.73
3052 3088 6.928979 TCGATCACCTTTTGTTTTTGAGTA 57.071 33.333 0.00 0.00 0.00 2.59
3095 3132 1.075542 TCAATCACGGTTCATCGCAC 58.924 50.000 0.00 0.00 0.00 5.34
3143 3181 7.430793 CCAATGCTCTCTATATTATTCGACGAG 59.569 40.741 0.00 0.00 0.00 4.18
3144 3182 7.094334 ACCAATGCTCTCTATATTATTCGACGA 60.094 37.037 0.00 0.00 0.00 4.20
3145 3183 7.030165 ACCAATGCTCTCTATATTATTCGACG 58.970 38.462 0.00 0.00 0.00 5.12
3147 3185 8.354711 AGACCAATGCTCTCTATATTATTCGA 57.645 34.615 0.00 0.00 0.00 3.71
3175 3213 6.375455 TCAAAGTTTTTGAAGCTTGACTCTCT 59.625 34.615 2.10 0.00 31.98 3.10
3176 3214 6.470556 GTCAAAGTTTTTGAAGCTTGACTCTC 59.529 38.462 2.10 0.00 31.98 3.20
3202 3240 6.934210 CGGATAATTTCTCTCCGTAAACTTG 58.066 40.000 2.18 0.00 45.30 3.16
3216 3254 5.587043 TGTGTATTGTGGGTCGGATAATTTC 59.413 40.000 0.00 0.00 0.00 2.17
3280 3318 7.565450 TGCAAAATCAACGAATCAAATACTG 57.435 32.000 0.00 0.00 0.00 2.74
3292 3330 9.888878 ATCAATATCTAGATTGCAAAATCAACG 57.111 29.630 11.25 0.00 36.85 4.10
3367 3405 5.584649 CGTCCCAAAATAGTGTGTATCACAT 59.415 40.000 5.88 0.00 46.32 3.21
3369 3407 4.331717 CCGTCCCAAAATAGTGTGTATCAC 59.668 45.833 0.00 0.00 46.46 3.06
3397 3436 9.487790 CACCCAACAAAAATGAACATTACTTAT 57.512 29.630 0.37 0.00 0.00 1.73
3464 3503 7.755373 GGGAGTATGTAAATTTCAGTTGCTTTC 59.245 37.037 0.00 0.00 0.00 2.62
3470 3509 7.690256 AGTGAGGGAGTATGTAAATTTCAGTT 58.310 34.615 0.00 0.00 0.00 3.16
3510 3550 7.768240 ACTTTCTCCGTTTCAAAATAAGTGTT 58.232 30.769 0.00 0.00 0.00 3.32
3580 3620 0.741326 GAGCCGTCTGTCATGAGCTA 59.259 55.000 4.99 0.00 0.00 3.32
3620 3660 4.166888 AGGCGCGGTCAGATGCAT 62.167 61.111 8.83 0.00 0.00 3.96


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

AutoCloner maintained by Alex Coulton.