Multiple sequence alignment - TraesCS3B01G248300

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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 TraesCS3B01G248300 chr3B 100.000 4540 0 0 1 4540 395851873 395847334 0.000000e+00 8384.0
1 TraesCS3B01G248300 chr3B 94.397 232 11 2 338 569 395846868 395847097 5.590000e-94 355.0
2 TraesCS3B01G248300 chr3B 98.438 64 1 0 209 272 395838340 395838277 3.710000e-21 113.0
3 TraesCS3B01G248300 chr3B 91.935 62 4 1 280 341 822713864 822713804 8.090000e-13 86.1
4 TraesCS3B01G248300 chr3B 97.674 43 1 0 1421 1463 395850348 395850306 1.750000e-09 75.0
5 TraesCS3B01G248300 chr6B 98.716 4207 34 5 338 4540 646581663 646585853 0.000000e+00 7452.0
6 TraesCS3B01G248300 chr6B 98.443 1349 20 1 3193 4540 705773195 705771847 0.000000e+00 2374.0
7 TraesCS3B01G248300 chr6B 97.584 1283 22 3 359 1633 705774468 705773187 0.000000e+00 2189.0
8 TraesCS3B01G248300 chr6B 93.590 234 13 2 337 569 646586322 646586090 9.350000e-92 348.0
9 TraesCS3B01G248300 chr6B 97.196 107 3 0 1 107 172239654 172239760 1.000000e-41 182.0
10 TraesCS3B01G248300 chr6B 94.118 51 3 0 1518 1568 646582726 646582776 1.350000e-10 78.7
11 TraesCS3B01G248300 chr6B 97.674 43 1 0 1421 1463 705773294 705773252 1.750000e-09 75.0
12 TraesCS3B01G248300 chr1B 98.644 4204 47 2 340 4540 474829595 474833791 0.000000e+00 7439.0
13 TraesCS3B01G248300 chr1B 97.868 4222 68 4 340 4540 132053779 132049559 0.000000e+00 7278.0
14 TraesCS3B01G248300 chr1B 96.983 232 5 2 338 569 132049111 132049340 5.510000e-104 388.0
15 TraesCS3B01G248300 chr1B 97.196 107 3 0 1 107 623687603 623687709 1.000000e-41 182.0
16 TraesCS3B01G248300 chr1B 96.078 51 2 0 1518 1568 132052703 132052653 2.910000e-12 84.2
17 TraesCS3B01G248300 chr1B 96.078 51 2 0 1518 1568 474830671 474830721 2.910000e-12 84.2
18 TraesCS3B01G248300 chr1B 97.674 43 1 0 1421 1463 474830784 474830826 1.750000e-09 75.0
19 TraesCS3B01G248300 chr1A 98.478 4206 60 2 338 4540 183928067 183932271 0.000000e+00 7409.0
20 TraesCS3B01G248300 chr1A 91.603 131 8 3 1 129 415644552 415644681 1.300000e-40 178.0
21 TraesCS3B01G248300 chr1A 97.143 105 2 1 1 105 496854501 496854604 4.670000e-40 176.0
22 TraesCS3B01G248300 chr1A 97.778 45 1 0 1518 1562 183929144 183929188 1.350000e-10 78.7
23 TraesCS3B01G248300 chr1A 97.674 43 1 0 1421 1463 183929257 183929299 1.750000e-09 75.0
24 TraesCS3B01G248300 chr1A 80.000 95 19 0 169 263 493630429 493630335 2.270000e-08 71.3
25 TraesCS3B01G248300 chr2D 93.718 589 22 5 338 912 593134022 593133435 0.000000e+00 869.0
26 TraesCS3B01G248300 chr2D 82.736 753 80 22 574 1298 414960967 414961697 3.860000e-175 625.0
27 TraesCS3B01G248300 chr2D 96.700 303 8 1 2156 2456 593133436 593133134 1.890000e-138 503.0
28 TraesCS3B01G248300 chr5D 75.279 716 153 22 3020 3723 396167572 396166869 2.040000e-83 320.0
29 TraesCS3B01G248300 chr7D 75.140 716 153 23 3020 3723 22667941 22668643 3.410000e-81 313.0
30 TraesCS3B01G248300 chr2A 85.443 316 29 9 991 1298 581962195 581962501 3.410000e-81 313.0
31 TraesCS3B01G248300 chr3A 95.376 173 7 1 101 272 399573312 399573140 1.610000e-69 274.0
32 TraesCS3B01G248300 chr3D 94.767 172 8 1 101 272 323334506 323334676 2.690000e-67 267.0
33 TraesCS3B01G248300 chr3D 90.698 129 7 4 1 128 7921094 7920970 2.810000e-37 167.0
34 TraesCS3B01G248300 chr3D 93.333 60 3 1 269 327 565648607 565648548 2.250000e-13 87.9
35 TraesCS3B01G248300 chr3D 87.302 63 6 2 270 332 591622149 591622089 2.270000e-08 71.3
36 TraesCS3B01G248300 chr2B 98.113 106 2 0 3 108 783653886 783653991 7.760000e-43 185.0
37 TraesCS3B01G248300 chrUn 94.783 115 6 0 1 115 322720513 322720399 3.610000e-41 180.0
38 TraesCS3B01G248300 chr5B 95.495 111 5 0 3 113 563340533 563340643 1.300000e-40 178.0
39 TraesCS3B01G248300 chr5B 85.417 96 14 0 168 263 137108603 137108508 2.890000e-17 100.0
40 TraesCS3B01G248300 chr5A 95.536 112 4 1 1 112 658989118 658989008 1.300000e-40 178.0
41 TraesCS3B01G248300 chr5A 88.298 94 11 0 170 263 680523536 680523443 3.710000e-21 113.0
42 TraesCS3B01G248300 chr5A 90.698 43 3 1 281 323 475834212 475834253 6.340000e-04 56.5
43 TraesCS3B01G248300 chr7B 86.022 93 13 0 168 260 612635064 612634972 2.890000e-17 100.0
44 TraesCS3B01G248300 chr4B 96.721 61 1 1 281 341 104746182 104746123 2.890000e-17 100.0
45 TraesCS3B01G248300 chr4B 94.643 56 3 0 280 335 496426791 496426846 2.250000e-13 87.9
46 TraesCS3B01G248300 chr7A 94.545 55 3 0 281 335 520797407 520797353 8.090000e-13 86.1


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 TraesCS3B01G248300 chr3B 395847334 395851873 4539 True 4229.500000 8384 98.837000 1 4540 2 chr3B.!!$R3 4539
1 TraesCS3B01G248300 chr6B 646581663 646585853 4190 False 3765.350000 7452 96.417000 338 4540 2 chr6B.!!$F2 4202
2 TraesCS3B01G248300 chr6B 705771847 705774468 2621 True 1546.000000 2374 97.900333 359 4540 3 chr6B.!!$R2 4181
3 TraesCS3B01G248300 chr1B 132049559 132053779 4220 True 3681.100000 7278 96.973000 340 4540 2 chr1B.!!$R1 4200
4 TraesCS3B01G248300 chr1B 474829595 474833791 4196 False 2532.733333 7439 97.465333 340 4540 3 chr1B.!!$F3 4200
5 TraesCS3B01G248300 chr1A 183928067 183932271 4204 False 2520.900000 7409 97.976667 338 4540 3 chr1A.!!$F3 4202
6 TraesCS3B01G248300 chr2D 593133134 593134022 888 True 686.000000 869 95.209000 338 2456 2 chr2D.!!$R1 2118
7 TraesCS3B01G248300 chr2D 414960967 414961697 730 False 625.000000 625 82.736000 574 1298 1 chr2D.!!$F1 724
8 TraesCS3B01G248300 chr5D 396166869 396167572 703 True 320.000000 320 75.279000 3020 3723 1 chr5D.!!$R1 703
9 TraesCS3B01G248300 chr7D 22667941 22668643 702 False 313.000000 313 75.140000 3020 3723 1 chr7D.!!$F1 703

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
216 217 0.031178 CACCTGGCTTCTGCAACAAC 59.969 55.000 0.00 0.00 41.91 3.32 F
319 320 0.036306 GAAGAAAGGGCGGAGAACCA 59.964 55.000 0.00 0.00 35.59 3.67 F
324 325 0.404040 AAGGGCGGAGAACCAAATCA 59.596 50.000 0.00 0.00 35.59 2.57 F
325 326 0.625849 AGGGCGGAGAACCAAATCAT 59.374 50.000 0.00 0.00 35.59 2.45 F
326 327 1.025041 GGGCGGAGAACCAAATCATC 58.975 55.000 0.00 0.00 35.59 2.92 F
327 328 1.681780 GGGCGGAGAACCAAATCATCA 60.682 52.381 0.00 0.00 35.59 3.07 F
328 329 2.301346 GGCGGAGAACCAAATCATCAT 58.699 47.619 0.00 0.00 35.59 2.45 F
2919 2973 3.181475 GGCTCTTTATGGTCGACTCATCA 60.181 47.826 16.46 5.01 0.00 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2045 2099 3.194116 GTCAGTGAATGCCATTCCAACAT 59.806 43.478 14.58 0.0 38.50 2.71 R
2389 2443 6.395426 TTTGCACTTTGAGAGATTCACATT 57.605 33.333 0.00 0.0 34.94 2.71 R
2896 2950 2.457598 TGAGTCGACCATAAAGAGCCT 58.542 47.619 13.01 0.0 0.00 4.58 R
2919 2973 0.826715 ATGCATGTACAGTCGAGGCT 59.173 50.000 0.00 0.0 0.00 4.58 R
3205 3259 3.626930 TCTCTAGCTCCTTCTGGACTTC 58.373 50.000 0.00 0.0 37.46 3.01 R
3246 3300 5.246203 TGAAGTATGCTCTACTCCAGTGTTT 59.754 40.000 0.85 0.0 0.00 2.83 R
3537 3592 5.834460 TGTGTACCTCCTATGTTCTCCTTA 58.166 41.667 0.00 0.0 0.00 2.69 R
4160 4215 1.377536 GCTGAGAAGATGTTGCTCCC 58.622 55.000 0.00 0.0 0.00 4.30 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
24 25 7.789202 TGTCATCAAAATGAATAAAAGGGGA 57.211 32.000 0.00 0.00 43.42 4.81
25 26 8.378115 TGTCATCAAAATGAATAAAAGGGGAT 57.622 30.769 0.00 0.00 43.42 3.85
26 27 8.259411 TGTCATCAAAATGAATAAAAGGGGATG 58.741 33.333 0.00 0.00 43.42 3.51
27 28 8.260114 GTCATCAAAATGAATAAAAGGGGATGT 58.740 33.333 0.00 0.00 43.42 3.06
28 29 9.486123 TCATCAAAATGAATAAAAGGGGATGTA 57.514 29.630 0.00 0.00 38.97 2.29
31 32 9.713684 TCAAAATGAATAAAAGGGGATGTATCT 57.286 29.630 0.00 0.00 0.00 1.98
37 38 9.170890 TGAATAAAAGGGGATGTATCTAGATGT 57.829 33.333 15.79 1.25 0.00 3.06
45 46 9.845214 AGGGGATGTATCTAGATGTATTTTAGT 57.155 33.333 15.79 0.00 0.00 2.24
68 69 8.265165 AGTTCTAAATACATCCTTTTTCGTCC 57.735 34.615 0.00 0.00 0.00 4.79
69 70 7.881232 AGTTCTAAATACATCCTTTTTCGTCCA 59.119 33.333 0.00 0.00 0.00 4.02
70 71 8.674607 GTTCTAAATACATCCTTTTTCGTCCAT 58.325 33.333 0.00 0.00 0.00 3.41
71 72 8.801882 TCTAAATACATCCTTTTTCGTCCATT 57.198 30.769 0.00 0.00 0.00 3.16
72 73 9.238368 TCTAAATACATCCTTTTTCGTCCATTT 57.762 29.630 0.00 0.00 0.00 2.32
73 74 9.855021 CTAAATACATCCTTTTTCGTCCATTTT 57.145 29.630 0.00 0.00 0.00 1.82
74 75 8.532977 AAATACATCCTTTTTCGTCCATTTTG 57.467 30.769 0.00 0.00 0.00 2.44
75 76 5.782893 ACATCCTTTTTCGTCCATTTTGA 57.217 34.783 0.00 0.00 0.00 2.69
76 77 6.345096 ACATCCTTTTTCGTCCATTTTGAT 57.655 33.333 0.00 0.00 0.00 2.57
77 78 6.158598 ACATCCTTTTTCGTCCATTTTGATG 58.841 36.000 0.00 0.00 33.80 3.07
78 79 6.015519 ACATCCTTTTTCGTCCATTTTGATGA 60.016 34.615 0.00 0.00 32.39 2.92
79 80 5.768317 TCCTTTTTCGTCCATTTTGATGAC 58.232 37.500 0.00 0.00 30.19 3.06
80 81 5.300539 TCCTTTTTCGTCCATTTTGATGACA 59.699 36.000 0.00 0.00 30.19 3.58
81 82 5.982516 CCTTTTTCGTCCATTTTGATGACAA 59.017 36.000 0.00 0.00 30.19 3.18
82 83 6.144402 CCTTTTTCGTCCATTTTGATGACAAG 59.856 38.462 0.00 0.00 37.32 3.16
83 84 5.766150 TTTCGTCCATTTTGATGACAAGT 57.234 34.783 0.00 0.00 37.32 3.16
84 85 6.869315 TTTCGTCCATTTTGATGACAAGTA 57.131 33.333 0.00 0.00 37.32 2.24
85 86 7.447374 TTTCGTCCATTTTGATGACAAGTAT 57.553 32.000 0.00 0.00 37.32 2.12
86 87 7.447374 TTCGTCCATTTTGATGACAAGTATT 57.553 32.000 0.00 0.00 37.32 1.89
87 88 7.447374 TCGTCCATTTTGATGACAAGTATTT 57.553 32.000 0.00 0.00 37.32 1.40
88 89 7.881142 TCGTCCATTTTGATGACAAGTATTTT 58.119 30.769 0.00 0.00 37.32 1.82
89 90 8.020819 TCGTCCATTTTGATGACAAGTATTTTC 58.979 33.333 0.00 0.00 37.32 2.29
90 91 7.007367 CGTCCATTTTGATGACAAGTATTTTCG 59.993 37.037 0.00 0.00 37.32 3.46
91 92 7.273381 GTCCATTTTGATGACAAGTATTTTCGG 59.727 37.037 0.00 0.00 37.32 4.30
92 93 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
93 94 7.273381 CCATTTTGATGACAAGTATTTTCGGAC 59.727 37.037 0.00 0.00 37.32 4.79
94 95 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
95 96 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
96 97 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
97 98 3.992643 TGACAAGTATTTTCGGACGGAA 58.007 40.909 0.00 0.00 0.00 4.30
98 99 3.991773 TGACAAGTATTTTCGGACGGAAG 59.008 43.478 0.00 0.00 35.70 3.46
99 100 3.332034 ACAAGTATTTTCGGACGGAAGG 58.668 45.455 0.00 0.00 35.70 3.46
100 101 3.007182 ACAAGTATTTTCGGACGGAAGGA 59.993 43.478 0.00 0.00 35.70 3.36
101 102 3.521947 AGTATTTTCGGACGGAAGGAG 57.478 47.619 0.00 0.00 35.70 3.69
102 103 2.830321 AGTATTTTCGGACGGAAGGAGT 59.170 45.455 0.00 0.00 35.70 3.85
103 104 4.019174 AGTATTTTCGGACGGAAGGAGTA 58.981 43.478 0.00 0.00 35.70 2.59
104 105 2.730550 TTTTCGGACGGAAGGAGTAC 57.269 50.000 0.00 0.00 35.70 2.73
105 106 1.619654 TTTCGGACGGAAGGAGTACA 58.380 50.000 0.00 0.00 35.70 2.90
106 107 1.843368 TTCGGACGGAAGGAGTACAT 58.157 50.000 0.00 0.00 0.00 2.29
107 108 1.386533 TCGGACGGAAGGAGTACATC 58.613 55.000 0.00 0.00 0.00 3.06
108 109 1.100510 CGGACGGAAGGAGTACATCA 58.899 55.000 0.00 0.00 0.00 3.07
109 110 1.681793 CGGACGGAAGGAGTACATCAT 59.318 52.381 0.00 0.00 0.00 2.45
110 111 2.882761 CGGACGGAAGGAGTACATCATA 59.117 50.000 0.00 0.00 0.00 2.15
111 112 3.058155 CGGACGGAAGGAGTACATCATAG 60.058 52.174 0.00 0.00 0.00 2.23
112 113 4.142790 GGACGGAAGGAGTACATCATAGA 58.857 47.826 0.00 0.00 0.00 1.98
113 114 4.216687 GGACGGAAGGAGTACATCATAGAG 59.783 50.000 0.00 0.00 0.00 2.43
114 115 4.145807 ACGGAAGGAGTACATCATAGAGG 58.854 47.826 0.00 0.00 0.00 3.69
115 116 4.145807 CGGAAGGAGTACATCATAGAGGT 58.854 47.826 0.00 0.00 0.00 3.85
116 117 4.216687 CGGAAGGAGTACATCATAGAGGTC 59.783 50.000 0.00 0.00 0.00 3.85
117 118 5.390387 GGAAGGAGTACATCATAGAGGTCT 58.610 45.833 0.00 0.00 0.00 3.85
118 119 6.544650 GGAAGGAGTACATCATAGAGGTCTA 58.455 44.000 0.00 0.00 0.00 2.59
119 120 7.179269 GGAAGGAGTACATCATAGAGGTCTAT 58.821 42.308 0.00 0.00 39.61 1.98
120 121 7.338449 GGAAGGAGTACATCATAGAGGTCTATC 59.662 44.444 0.00 0.00 37.07 2.08
121 122 7.582909 AGGAGTACATCATAGAGGTCTATCT 57.417 40.000 0.00 0.00 37.07 1.98
122 123 7.995663 AGGAGTACATCATAGAGGTCTATCTT 58.004 38.462 0.00 0.00 37.07 2.40
123 124 8.452868 AGGAGTACATCATAGAGGTCTATCTTT 58.547 37.037 0.00 0.00 37.07 2.52
124 125 9.084533 GGAGTACATCATAGAGGTCTATCTTTT 57.915 37.037 0.00 0.00 37.07 2.27
125 126 9.906660 GAGTACATCATAGAGGTCTATCTTTTG 57.093 37.037 0.00 0.00 37.07 2.44
126 127 8.865090 AGTACATCATAGAGGTCTATCTTTTGG 58.135 37.037 0.00 0.00 37.07 3.28
127 128 7.921041 ACATCATAGAGGTCTATCTTTTGGA 57.079 36.000 0.00 0.00 37.07 3.53
128 129 8.324191 ACATCATAGAGGTCTATCTTTTGGAA 57.676 34.615 0.00 0.00 37.07 3.53
129 130 8.772250 ACATCATAGAGGTCTATCTTTTGGAAA 58.228 33.333 0.00 0.00 37.07 3.13
130 131 9.050601 CATCATAGAGGTCTATCTTTTGGAAAC 57.949 37.037 0.00 0.00 37.07 2.78
131 132 8.146053 TCATAGAGGTCTATCTTTTGGAAACA 57.854 34.615 0.00 0.00 37.07 2.83
132 133 8.772250 TCATAGAGGTCTATCTTTTGGAAACAT 58.228 33.333 0.00 0.00 37.33 2.71
133 134 9.401058 CATAGAGGTCTATCTTTTGGAAACATT 57.599 33.333 0.00 0.00 37.33 2.71
134 135 9.981460 ATAGAGGTCTATCTTTTGGAAACATTT 57.019 29.630 0.00 0.00 35.63 2.32
135 136 8.712228 AGAGGTCTATCTTTTGGAAACATTTT 57.288 30.769 0.00 0.00 42.32 1.82
136 137 8.579863 AGAGGTCTATCTTTTGGAAACATTTTG 58.420 33.333 0.00 0.00 42.32 2.44
137 138 7.154656 AGGTCTATCTTTTGGAAACATTTTGC 58.845 34.615 0.00 0.00 42.32 3.68
138 139 6.928492 GGTCTATCTTTTGGAAACATTTTGCA 59.072 34.615 0.00 0.00 42.32 4.08
139 140 7.095649 GGTCTATCTTTTGGAAACATTTTGCAC 60.096 37.037 0.00 0.00 42.32 4.57
140 141 6.928492 TCTATCTTTTGGAAACATTTTGCACC 59.072 34.615 0.00 0.00 42.32 5.01
141 142 3.868077 TCTTTTGGAAACATTTTGCACCG 59.132 39.130 0.00 0.00 42.32 4.94
142 143 1.576356 TTGGAAACATTTTGCACCGC 58.424 45.000 0.00 0.00 42.32 5.68
143 144 0.461548 TGGAAACATTTTGCACCGCA 59.538 45.000 0.00 0.00 32.94 5.69
144 145 0.858583 GGAAACATTTTGCACCGCAC 59.141 50.000 0.00 0.00 38.71 5.34
145 146 0.502275 GAAACATTTTGCACCGCACG 59.498 50.000 0.00 0.00 38.71 5.34
146 147 0.101399 AAACATTTTGCACCGCACGA 59.899 45.000 0.00 0.00 38.71 4.35
147 148 0.101399 AACATTTTGCACCGCACGAA 59.899 45.000 0.00 0.00 38.71 3.85
148 149 0.313672 ACATTTTGCACCGCACGAAT 59.686 45.000 0.00 0.00 38.71 3.34
149 150 0.709467 CATTTTGCACCGCACGAATG 59.291 50.000 8.82 8.82 38.71 2.67
166 167 6.129457 GCACGAATGCTTGTTTTAGTAAACAG 60.129 38.462 0.00 0.00 46.50 3.16
167 168 8.199777 GCACGAATGCTTGTTTTAGTAAACAGA 61.200 37.037 0.00 0.00 46.50 3.41
201 202 6.716934 ATCAAGACGATATCAAGTACACCT 57.283 37.500 3.12 0.00 30.32 4.00
202 203 5.891451 TCAAGACGATATCAAGTACACCTG 58.109 41.667 3.12 0.00 0.00 4.00
203 204 4.920640 AGACGATATCAAGTACACCTGG 57.079 45.455 3.12 0.00 0.00 4.45
204 205 3.068307 AGACGATATCAAGTACACCTGGC 59.932 47.826 3.12 0.00 0.00 4.85
205 206 3.031736 ACGATATCAAGTACACCTGGCT 58.968 45.455 3.12 0.00 0.00 4.75
206 207 3.451178 ACGATATCAAGTACACCTGGCTT 59.549 43.478 3.12 0.00 0.00 4.35
207 208 4.051922 CGATATCAAGTACACCTGGCTTC 58.948 47.826 3.12 0.00 0.00 3.86
208 209 4.202161 CGATATCAAGTACACCTGGCTTCT 60.202 45.833 3.12 0.00 0.00 2.85
209 210 2.839486 TCAAGTACACCTGGCTTCTG 57.161 50.000 0.00 0.00 0.00 3.02
210 211 1.160137 CAAGTACACCTGGCTTCTGC 58.840 55.000 0.00 0.00 38.76 4.26
211 212 0.764890 AAGTACACCTGGCTTCTGCA 59.235 50.000 0.00 0.00 41.91 4.41
212 213 0.764890 AGTACACCTGGCTTCTGCAA 59.235 50.000 0.00 0.00 41.91 4.08
213 214 0.875059 GTACACCTGGCTTCTGCAAC 59.125 55.000 0.00 0.00 41.91 4.17
214 215 0.472044 TACACCTGGCTTCTGCAACA 59.528 50.000 0.00 0.00 41.91 3.33
215 216 0.395586 ACACCTGGCTTCTGCAACAA 60.396 50.000 0.00 0.00 41.91 2.83
216 217 0.031178 CACCTGGCTTCTGCAACAAC 59.969 55.000 0.00 0.00 41.91 3.32
217 218 0.106519 ACCTGGCTTCTGCAACAACT 60.107 50.000 0.00 0.00 41.91 3.16
218 219 0.595095 CCTGGCTTCTGCAACAACTC 59.405 55.000 0.00 0.00 41.91 3.01
219 220 1.311859 CTGGCTTCTGCAACAACTCA 58.688 50.000 0.00 0.00 41.91 3.41
220 221 1.677576 CTGGCTTCTGCAACAACTCAA 59.322 47.619 0.00 0.00 41.91 3.02
221 222 2.295349 CTGGCTTCTGCAACAACTCAAT 59.705 45.455 0.00 0.00 41.91 2.57
222 223 3.485394 TGGCTTCTGCAACAACTCAATA 58.515 40.909 0.00 0.00 41.91 1.90
223 224 3.253188 TGGCTTCTGCAACAACTCAATAC 59.747 43.478 0.00 0.00 41.91 1.89
224 225 3.366374 GGCTTCTGCAACAACTCAATACC 60.366 47.826 0.00 0.00 41.91 2.73
225 226 3.253188 GCTTCTGCAACAACTCAATACCA 59.747 43.478 0.00 0.00 39.41 3.25
226 227 4.787598 CTTCTGCAACAACTCAATACCAC 58.212 43.478 0.00 0.00 0.00 4.16
227 228 2.805671 TCTGCAACAACTCAATACCACG 59.194 45.455 0.00 0.00 0.00 4.94
228 229 2.805671 CTGCAACAACTCAATACCACGA 59.194 45.455 0.00 0.00 0.00 4.35
229 230 2.805671 TGCAACAACTCAATACCACGAG 59.194 45.455 0.00 0.00 35.30 4.18
230 231 2.412847 GCAACAACTCAATACCACGAGC 60.413 50.000 0.00 0.00 32.21 5.03
231 232 2.805671 CAACAACTCAATACCACGAGCA 59.194 45.455 0.00 0.00 32.21 4.26
232 233 3.120321 ACAACTCAATACCACGAGCAA 57.880 42.857 0.00 0.00 32.21 3.91
233 234 2.806244 ACAACTCAATACCACGAGCAAC 59.194 45.455 0.00 0.00 32.21 4.17
234 235 3.067106 CAACTCAATACCACGAGCAACT 58.933 45.455 0.00 0.00 32.21 3.16
235 236 3.402628 ACTCAATACCACGAGCAACTT 57.597 42.857 0.00 0.00 32.21 2.66
236 237 3.067106 ACTCAATACCACGAGCAACTTG 58.933 45.455 0.00 0.00 32.21 3.16
237 238 3.244078 ACTCAATACCACGAGCAACTTGA 60.244 43.478 0.00 0.00 32.21 3.02
238 239 3.325870 TCAATACCACGAGCAACTTGAG 58.674 45.455 0.00 0.00 0.00 3.02
239 240 3.006430 TCAATACCACGAGCAACTTGAGA 59.994 43.478 0.00 0.00 0.00 3.27
240 241 2.433868 TACCACGAGCAACTTGAGAC 57.566 50.000 0.00 0.00 0.00 3.36
241 242 0.464036 ACCACGAGCAACTTGAGACA 59.536 50.000 0.00 0.00 0.00 3.41
242 243 1.070758 ACCACGAGCAACTTGAGACAT 59.929 47.619 0.00 0.00 0.00 3.06
243 244 2.146342 CCACGAGCAACTTGAGACATT 58.854 47.619 0.00 0.00 0.00 2.71
244 245 2.096069 CCACGAGCAACTTGAGACATTG 60.096 50.000 0.00 0.00 0.00 2.82
245 246 2.802247 CACGAGCAACTTGAGACATTGA 59.198 45.455 0.00 0.00 0.00 2.57
246 247 3.434641 CACGAGCAACTTGAGACATTGAT 59.565 43.478 0.00 0.00 0.00 2.57
247 248 3.434641 ACGAGCAACTTGAGACATTGATG 59.565 43.478 0.00 0.00 0.00 3.07
248 249 3.681417 CGAGCAACTTGAGACATTGATGA 59.319 43.478 0.00 0.00 0.00 2.92
249 250 4.331992 CGAGCAACTTGAGACATTGATGAT 59.668 41.667 0.00 0.00 0.00 2.45
250 251 5.562506 AGCAACTTGAGACATTGATGATG 57.437 39.130 0.00 0.00 41.71 3.07
251 252 4.103357 GCAACTTGAGACATTGATGATGC 58.897 43.478 0.00 0.00 39.47 3.91
252 253 4.380128 GCAACTTGAGACATTGATGATGCA 60.380 41.667 0.00 0.00 39.47 3.96
253 254 4.959596 ACTTGAGACATTGATGATGCAC 57.040 40.909 0.00 0.00 39.47 4.57
254 255 4.329392 ACTTGAGACATTGATGATGCACA 58.671 39.130 0.00 0.00 39.47 4.57
255 256 4.155462 ACTTGAGACATTGATGATGCACAC 59.845 41.667 0.00 0.00 39.47 3.82
256 257 3.677190 TGAGACATTGATGATGCACACA 58.323 40.909 0.00 0.00 39.47 3.72
257 258 4.266714 TGAGACATTGATGATGCACACAT 58.733 39.130 7.77 7.77 39.47 3.21
273 274 8.752005 ATGCACACATCCAAATTATTACTACT 57.248 30.769 0.00 0.00 0.00 2.57
274 275 8.208718 TGCACACATCCAAATTATTACTACTC 57.791 34.615 0.00 0.00 0.00 2.59
275 276 8.046708 TGCACACATCCAAATTATTACTACTCT 58.953 33.333 0.00 0.00 0.00 3.24
276 277 9.542462 GCACACATCCAAATTATTACTACTCTA 57.458 33.333 0.00 0.00 0.00 2.43
313 314 3.732048 ATAAAAGGAAGAAAGGGCGGA 57.268 42.857 0.00 0.00 0.00 5.54
314 315 1.911057 AAAAGGAAGAAAGGGCGGAG 58.089 50.000 0.00 0.00 0.00 4.63
315 316 1.064825 AAAGGAAGAAAGGGCGGAGA 58.935 50.000 0.00 0.00 0.00 3.71
316 317 1.064825 AAGGAAGAAAGGGCGGAGAA 58.935 50.000 0.00 0.00 0.00 2.87
317 318 0.325272 AGGAAGAAAGGGCGGAGAAC 59.675 55.000 0.00 0.00 0.00 3.01
318 319 0.677098 GGAAGAAAGGGCGGAGAACC 60.677 60.000 0.00 0.00 0.00 3.62
319 320 0.036306 GAAGAAAGGGCGGAGAACCA 59.964 55.000 0.00 0.00 35.59 3.67
320 321 0.476771 AAGAAAGGGCGGAGAACCAA 59.523 50.000 0.00 0.00 35.59 3.67
321 322 0.476771 AGAAAGGGCGGAGAACCAAA 59.523 50.000 0.00 0.00 35.59 3.28
322 323 1.075536 AGAAAGGGCGGAGAACCAAAT 59.924 47.619 0.00 0.00 35.59 2.32
323 324 1.472878 GAAAGGGCGGAGAACCAAATC 59.527 52.381 0.00 0.00 35.59 2.17
324 325 0.404040 AAGGGCGGAGAACCAAATCA 59.596 50.000 0.00 0.00 35.59 2.57
325 326 0.625849 AGGGCGGAGAACCAAATCAT 59.374 50.000 0.00 0.00 35.59 2.45
326 327 1.025041 GGGCGGAGAACCAAATCATC 58.975 55.000 0.00 0.00 35.59 2.92
327 328 1.681780 GGGCGGAGAACCAAATCATCA 60.682 52.381 0.00 0.00 35.59 3.07
328 329 2.301346 GGCGGAGAACCAAATCATCAT 58.699 47.619 0.00 0.00 35.59 2.45
329 330 3.476552 GGCGGAGAACCAAATCATCATA 58.523 45.455 0.00 0.00 35.59 2.15
330 331 4.074970 GGCGGAGAACCAAATCATCATAT 58.925 43.478 0.00 0.00 35.59 1.78
331 332 4.154918 GGCGGAGAACCAAATCATCATATC 59.845 45.833 0.00 0.00 35.59 1.63
332 333 4.154918 GCGGAGAACCAAATCATCATATCC 59.845 45.833 0.00 0.00 35.59 2.59
333 334 5.308014 CGGAGAACCAAATCATCATATCCA 58.692 41.667 0.00 0.00 35.59 3.41
334 335 5.942236 CGGAGAACCAAATCATCATATCCAT 59.058 40.000 0.00 0.00 35.59 3.41
335 336 6.432162 CGGAGAACCAAATCATCATATCCATT 59.568 38.462 0.00 0.00 35.59 3.16
336 337 7.361542 CGGAGAACCAAATCATCATATCCATTC 60.362 40.741 0.00 0.00 35.59 2.67
1385 1436 4.166725 TGAATGGGAGGAAGAATATGCAGT 59.833 41.667 0.00 0.00 0.00 4.40
1403 1454 5.580998 TGCAGTAGATATAGGGGAAGGTAG 58.419 45.833 0.00 0.00 0.00 3.18
1640 1694 9.195411 CAGTAATCGTAAGTTACCAGTTAACAA 57.805 33.333 8.61 0.00 42.45 2.83
1882 1936 3.193267 GCCTGATGATTTTGTTGTGCCTA 59.807 43.478 0.00 0.00 0.00 3.93
1970 2024 3.649502 TCATATGATGAGGGCAGTGATGT 59.350 43.478 0.00 0.00 33.59 3.06
2045 2099 5.470098 GCACTAGTGAGAAACCTGAATTTGA 59.530 40.000 27.08 0.00 0.00 2.69
2389 2443 5.682471 GCAGTACTTGAGGATTTGCTAGCTA 60.682 44.000 17.23 5.31 0.00 3.32
2896 2950 6.009908 TGGTAGGTAGAGTCATGTTAGCTA 57.990 41.667 0.00 0.00 0.00 3.32
2919 2973 3.181475 GGCTCTTTATGGTCGACTCATCA 60.181 47.826 16.46 5.01 0.00 3.07
3205 3259 4.510038 ACAAAGCCAAATTAGCACAGAG 57.490 40.909 3.48 0.00 0.00 3.35
3246 3300 6.653020 AGAGATATTATGAACACTGCACCAA 58.347 36.000 0.00 0.00 0.00 3.67
3537 3592 8.073467 TGGAAAAGAAGGTTTTGAAGTACAAT 57.927 30.769 0.00 0.00 38.36 2.71
3561 3616 4.884961 AGGAGAACATAGGAGGTACACAT 58.115 43.478 0.00 0.00 0.00 3.21
3847 3902 4.720046 AGAAAAGAGGAGGGTGAAGAAAC 58.280 43.478 0.00 0.00 0.00 2.78
4249 4304 5.552178 AGTTCGCAAAGGAAAGAAGAGTAT 58.448 37.500 0.00 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.789202 TCCCCTTTTATTCATTTTGATGACA 57.211 32.000 0.00 0.00 0.00 3.58
1 2 8.260114 ACATCCCCTTTTATTCATTTTGATGAC 58.740 33.333 0.00 0.00 32.39 3.06
2 3 8.378115 ACATCCCCTTTTATTCATTTTGATGA 57.622 30.769 0.00 0.00 32.39 2.92
5 6 9.713684 AGATACATCCCCTTTTATTCATTTTGA 57.286 29.630 0.00 0.00 0.00 2.69
11 12 9.170890 ACATCTAGATACATCCCCTTTTATTCA 57.829 33.333 4.54 0.00 0.00 2.57
19 20 9.845214 ACTAAAATACATCTAGATACATCCCCT 57.155 33.333 4.54 0.00 0.00 4.79
42 43 9.374838 GGACGAAAAAGGATGTATTTAGAACTA 57.625 33.333 0.00 0.00 0.00 2.24
43 44 7.881232 TGGACGAAAAAGGATGTATTTAGAACT 59.119 33.333 0.00 0.00 0.00 3.01
44 45 8.036273 TGGACGAAAAAGGATGTATTTAGAAC 57.964 34.615 0.00 0.00 0.00 3.01
45 46 8.801882 ATGGACGAAAAAGGATGTATTTAGAA 57.198 30.769 0.00 0.00 0.00 2.10
46 47 8.801882 AATGGACGAAAAAGGATGTATTTAGA 57.198 30.769 0.00 0.00 0.00 2.10
47 48 9.855021 AAAATGGACGAAAAAGGATGTATTTAG 57.145 29.630 0.00 0.00 0.00 1.85
48 49 9.632807 CAAAATGGACGAAAAAGGATGTATTTA 57.367 29.630 0.00 0.00 0.00 1.40
49 50 8.364142 TCAAAATGGACGAAAAAGGATGTATTT 58.636 29.630 0.00 0.00 0.00 1.40
50 51 7.891561 TCAAAATGGACGAAAAAGGATGTATT 58.108 30.769 0.00 0.00 0.00 1.89
51 52 7.461182 TCAAAATGGACGAAAAAGGATGTAT 57.539 32.000 0.00 0.00 0.00 2.29
52 53 6.885952 TCAAAATGGACGAAAAAGGATGTA 57.114 33.333 0.00 0.00 0.00 2.29
53 54 5.782893 TCAAAATGGACGAAAAAGGATGT 57.217 34.783 0.00 0.00 0.00 3.06
54 55 6.308766 GTCATCAAAATGGACGAAAAAGGATG 59.691 38.462 0.00 0.00 33.42 3.51
55 56 6.015519 TGTCATCAAAATGGACGAAAAAGGAT 60.016 34.615 0.00 0.00 33.42 3.24
56 57 5.300539 TGTCATCAAAATGGACGAAAAAGGA 59.699 36.000 0.00 0.00 33.42 3.36
57 58 5.527951 TGTCATCAAAATGGACGAAAAAGG 58.472 37.500 0.00 0.00 33.42 3.11
58 59 6.697019 ACTTGTCATCAAAATGGACGAAAAAG 59.303 34.615 0.00 0.00 33.42 2.27
59 60 6.568869 ACTTGTCATCAAAATGGACGAAAAA 58.431 32.000 0.00 0.00 33.42 1.94
60 61 6.142818 ACTTGTCATCAAAATGGACGAAAA 57.857 33.333 0.00 0.00 33.42 2.29
61 62 5.766150 ACTTGTCATCAAAATGGACGAAA 57.234 34.783 0.00 0.00 33.42 3.46
62 63 7.447374 AATACTTGTCATCAAAATGGACGAA 57.553 32.000 0.00 0.00 33.42 3.85
63 64 7.447374 AAATACTTGTCATCAAAATGGACGA 57.553 32.000 0.00 0.00 33.42 4.20
64 65 7.007367 CGAAAATACTTGTCATCAAAATGGACG 59.993 37.037 0.00 0.00 33.42 4.79
65 66 7.273381 CCGAAAATACTTGTCATCAAAATGGAC 59.727 37.037 0.00 0.00 33.42 4.02
66 67 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
67 68 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
68 69 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
69 70 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
70 71 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
71 72 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
72 73 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
73 74 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
74 75 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
75 76 4.196626 TCCGTCCGAAAATACTTGTCAT 57.803 40.909 0.00 0.00 0.00 3.06
76 77 3.663995 TCCGTCCGAAAATACTTGTCA 57.336 42.857 0.00 0.00 0.00 3.58
77 78 3.370061 CCTTCCGTCCGAAAATACTTGTC 59.630 47.826 0.00 0.00 0.00 3.18
78 79 3.007182 TCCTTCCGTCCGAAAATACTTGT 59.993 43.478 0.00 0.00 0.00 3.16
79 80 3.592059 TCCTTCCGTCCGAAAATACTTG 58.408 45.455 0.00 0.00 0.00 3.16
80 81 3.260128 ACTCCTTCCGTCCGAAAATACTT 59.740 43.478 0.00 0.00 0.00 2.24
81 82 2.830321 ACTCCTTCCGTCCGAAAATACT 59.170 45.455 0.00 0.00 0.00 2.12
82 83 3.242549 ACTCCTTCCGTCCGAAAATAC 57.757 47.619 0.00 0.00 0.00 1.89
83 84 3.763360 TGTACTCCTTCCGTCCGAAAATA 59.237 43.478 0.00 0.00 0.00 1.40
84 85 2.564062 TGTACTCCTTCCGTCCGAAAAT 59.436 45.455 0.00 0.00 0.00 1.82
85 86 1.962807 TGTACTCCTTCCGTCCGAAAA 59.037 47.619 0.00 0.00 0.00 2.29
86 87 1.619654 TGTACTCCTTCCGTCCGAAA 58.380 50.000 0.00 0.00 0.00 3.46
87 88 1.747355 GATGTACTCCTTCCGTCCGAA 59.253 52.381 0.00 0.00 0.00 4.30
88 89 1.340308 TGATGTACTCCTTCCGTCCGA 60.340 52.381 0.00 0.00 0.00 4.55
89 90 1.100510 TGATGTACTCCTTCCGTCCG 58.899 55.000 0.00 0.00 0.00 4.79
90 91 4.142790 TCTATGATGTACTCCTTCCGTCC 58.857 47.826 0.00 0.00 0.00 4.79
91 92 4.216687 CCTCTATGATGTACTCCTTCCGTC 59.783 50.000 0.00 0.00 0.00 4.79
92 93 4.145807 CCTCTATGATGTACTCCTTCCGT 58.854 47.826 0.00 0.00 0.00 4.69
93 94 4.145807 ACCTCTATGATGTACTCCTTCCG 58.854 47.826 0.00 0.00 0.00 4.30
94 95 5.390387 AGACCTCTATGATGTACTCCTTCC 58.610 45.833 0.00 0.00 0.00 3.46
95 96 8.107095 AGATAGACCTCTATGATGTACTCCTTC 58.893 40.741 0.00 0.00 39.14 3.46
96 97 7.995663 AGATAGACCTCTATGATGTACTCCTT 58.004 38.462 0.00 0.00 39.14 3.36
97 98 7.582909 AGATAGACCTCTATGATGTACTCCT 57.417 40.000 0.00 0.00 39.14 3.69
98 99 8.644374 AAAGATAGACCTCTATGATGTACTCC 57.356 38.462 0.00 0.00 39.14 3.85
99 100 9.906660 CAAAAGATAGACCTCTATGATGTACTC 57.093 37.037 0.00 0.00 39.14 2.59
100 101 8.865090 CCAAAAGATAGACCTCTATGATGTACT 58.135 37.037 0.00 0.00 39.14 2.73
101 102 8.861086 TCCAAAAGATAGACCTCTATGATGTAC 58.139 37.037 0.00 0.00 39.14 2.90
102 103 9.434275 TTCCAAAAGATAGACCTCTATGATGTA 57.566 33.333 0.00 0.00 39.14 2.29
103 104 7.921041 TCCAAAAGATAGACCTCTATGATGT 57.079 36.000 0.00 0.00 39.14 3.06
104 105 9.050601 GTTTCCAAAAGATAGACCTCTATGATG 57.949 37.037 0.00 0.00 39.14 3.07
105 106 8.772250 TGTTTCCAAAAGATAGACCTCTATGAT 58.228 33.333 0.00 0.00 39.14 2.45
106 107 8.146053 TGTTTCCAAAAGATAGACCTCTATGA 57.854 34.615 0.00 0.00 39.14 2.15
107 108 8.970859 ATGTTTCCAAAAGATAGACCTCTATG 57.029 34.615 0.00 0.00 39.14 2.23
108 109 9.981460 AAATGTTTCCAAAAGATAGACCTCTAT 57.019 29.630 0.00 0.00 41.56 1.98
109 110 9.807921 AAAATGTTTCCAAAAGATAGACCTCTA 57.192 29.630 0.00 0.00 0.00 2.43
110 111 8.579863 CAAAATGTTTCCAAAAGATAGACCTCT 58.420 33.333 0.00 0.00 0.00 3.69
111 112 7.329471 GCAAAATGTTTCCAAAAGATAGACCTC 59.671 37.037 0.00 0.00 0.00 3.85
112 113 7.154656 GCAAAATGTTTCCAAAAGATAGACCT 58.845 34.615 0.00 0.00 0.00 3.85
113 114 6.928492 TGCAAAATGTTTCCAAAAGATAGACC 59.072 34.615 0.00 0.00 0.00 3.85
114 115 7.095649 GGTGCAAAATGTTTCCAAAAGATAGAC 60.096 37.037 0.00 0.00 0.00 2.59
115 116 6.928492 GGTGCAAAATGTTTCCAAAAGATAGA 59.072 34.615 0.00 0.00 0.00 1.98
116 117 6.128849 CGGTGCAAAATGTTTCCAAAAGATAG 60.129 38.462 0.00 0.00 0.00 2.08
117 118 5.694006 CGGTGCAAAATGTTTCCAAAAGATA 59.306 36.000 0.00 0.00 0.00 1.98
118 119 4.511082 CGGTGCAAAATGTTTCCAAAAGAT 59.489 37.500 0.00 0.00 0.00 2.40
119 120 3.868077 CGGTGCAAAATGTTTCCAAAAGA 59.132 39.130 0.00 0.00 0.00 2.52
120 121 3.545822 GCGGTGCAAAATGTTTCCAAAAG 60.546 43.478 0.00 0.00 0.00 2.27
121 122 2.352960 GCGGTGCAAAATGTTTCCAAAA 59.647 40.909 0.00 0.00 0.00 2.44
122 123 1.936547 GCGGTGCAAAATGTTTCCAAA 59.063 42.857 0.00 0.00 0.00 3.28
123 124 1.134699 TGCGGTGCAAAATGTTTCCAA 60.135 42.857 0.00 0.00 34.76 3.53
124 125 0.461548 TGCGGTGCAAAATGTTTCCA 59.538 45.000 0.00 0.00 34.76 3.53
125 126 0.858583 GTGCGGTGCAAAATGTTTCC 59.141 50.000 0.00 0.00 41.47 3.13
126 127 0.502275 CGTGCGGTGCAAAATGTTTC 59.498 50.000 0.00 0.00 41.47 2.78
127 128 0.101399 TCGTGCGGTGCAAAATGTTT 59.899 45.000 0.00 0.00 41.47 2.83
128 129 0.101399 TTCGTGCGGTGCAAAATGTT 59.899 45.000 0.00 0.00 41.47 2.71
129 130 0.313672 ATTCGTGCGGTGCAAAATGT 59.686 45.000 0.00 0.00 41.47 2.71
130 131 0.709467 CATTCGTGCGGTGCAAAATG 59.291 50.000 11.39 11.39 41.47 2.32
131 132 1.008361 GCATTCGTGCGGTGCAAAAT 61.008 50.000 14.37 0.00 41.47 1.82
132 133 1.659954 GCATTCGTGCGGTGCAAAA 60.660 52.632 14.37 0.00 41.47 2.44
133 134 2.050533 GCATTCGTGCGGTGCAAA 60.051 55.556 14.37 0.00 41.47 3.68
134 135 2.551006 AAGCATTCGTGCGGTGCAA 61.551 52.632 18.87 0.00 41.47 4.08
135 136 2.977456 AAGCATTCGTGCGGTGCA 60.977 55.556 18.87 0.00 41.19 4.57
136 137 2.502510 CAAGCATTCGTGCGGTGC 60.503 61.111 12.39 12.39 40.27 5.01
137 138 0.317770 AAACAAGCATTCGTGCGGTG 60.318 50.000 5.85 5.85 40.27 4.94
138 139 0.383949 AAAACAAGCATTCGTGCGGT 59.616 45.000 0.00 0.00 40.27 5.68
139 140 2.241722 CTAAAACAAGCATTCGTGCGG 58.758 47.619 0.00 0.00 40.27 5.69
140 141 2.916111 ACTAAAACAAGCATTCGTGCG 58.084 42.857 0.00 0.00 40.27 5.34
141 142 6.123871 GTTTACTAAAACAAGCATTCGTGC 57.876 37.500 0.00 0.00 43.73 5.34
177 178 7.255486 CCAGGTGTACTTGATATCGTCTTGATA 60.255 40.741 0.00 0.00 43.54 2.15
178 179 6.461648 CCAGGTGTACTTGATATCGTCTTGAT 60.462 42.308 0.00 0.00 41.30 2.57
179 180 5.163550 CCAGGTGTACTTGATATCGTCTTGA 60.164 44.000 0.00 0.00 0.00 3.02
180 181 5.043903 CCAGGTGTACTTGATATCGTCTTG 58.956 45.833 0.00 0.00 0.00 3.02
181 182 4.441634 GCCAGGTGTACTTGATATCGTCTT 60.442 45.833 0.00 0.00 0.00 3.01
182 183 3.068307 GCCAGGTGTACTTGATATCGTCT 59.932 47.826 0.00 0.00 0.00 4.18
183 184 3.068307 AGCCAGGTGTACTTGATATCGTC 59.932 47.826 0.00 0.00 0.00 4.20
184 185 3.031736 AGCCAGGTGTACTTGATATCGT 58.968 45.455 0.00 0.00 0.00 3.73
185 186 3.735237 AGCCAGGTGTACTTGATATCG 57.265 47.619 0.00 0.00 0.00 2.92
186 187 5.053145 CAGAAGCCAGGTGTACTTGATATC 58.947 45.833 0.00 0.00 0.00 1.63
187 188 4.684485 GCAGAAGCCAGGTGTACTTGATAT 60.684 45.833 0.00 0.00 33.58 1.63
188 189 3.369471 GCAGAAGCCAGGTGTACTTGATA 60.369 47.826 0.00 0.00 33.58 2.15
189 190 2.616510 GCAGAAGCCAGGTGTACTTGAT 60.617 50.000 0.00 0.00 33.58 2.57
190 191 1.270839 GCAGAAGCCAGGTGTACTTGA 60.271 52.381 0.00 0.00 33.58 3.02
191 192 1.160137 GCAGAAGCCAGGTGTACTTG 58.840 55.000 0.00 0.00 33.58 3.16
192 193 0.764890 TGCAGAAGCCAGGTGTACTT 59.235 50.000 0.00 0.00 41.13 2.24
193 194 0.764890 TTGCAGAAGCCAGGTGTACT 59.235 50.000 0.00 0.00 41.13 2.73
194 195 0.875059 GTTGCAGAAGCCAGGTGTAC 59.125 55.000 0.00 0.00 41.13 2.90
195 196 0.472044 TGTTGCAGAAGCCAGGTGTA 59.528 50.000 0.00 0.00 41.13 2.90
196 197 0.395586 TTGTTGCAGAAGCCAGGTGT 60.396 50.000 0.00 0.00 41.13 4.16
197 198 0.031178 GTTGTTGCAGAAGCCAGGTG 59.969 55.000 0.00 0.00 41.13 4.00
198 199 0.106519 AGTTGTTGCAGAAGCCAGGT 60.107 50.000 0.00 0.00 41.13 4.00
199 200 0.595095 GAGTTGTTGCAGAAGCCAGG 59.405 55.000 0.00 0.00 41.13 4.45
200 201 1.311859 TGAGTTGTTGCAGAAGCCAG 58.688 50.000 0.00 0.00 41.13 4.85
201 202 1.761449 TTGAGTTGTTGCAGAAGCCA 58.239 45.000 0.00 0.00 41.13 4.75
202 203 3.366374 GGTATTGAGTTGTTGCAGAAGCC 60.366 47.826 0.00 0.00 41.13 4.35
203 204 3.253188 TGGTATTGAGTTGTTGCAGAAGC 59.747 43.478 0.00 0.00 42.57 3.86
204 205 4.611355 CGTGGTATTGAGTTGTTGCAGAAG 60.611 45.833 0.00 0.00 0.00 2.85
205 206 3.249799 CGTGGTATTGAGTTGTTGCAGAA 59.750 43.478 0.00 0.00 0.00 3.02
206 207 2.805671 CGTGGTATTGAGTTGTTGCAGA 59.194 45.455 0.00 0.00 0.00 4.26
207 208 2.805671 TCGTGGTATTGAGTTGTTGCAG 59.194 45.455 0.00 0.00 0.00 4.41
208 209 2.805671 CTCGTGGTATTGAGTTGTTGCA 59.194 45.455 0.00 0.00 0.00 4.08
209 210 2.412847 GCTCGTGGTATTGAGTTGTTGC 60.413 50.000 0.00 0.00 34.67 4.17
210 211 2.805671 TGCTCGTGGTATTGAGTTGTTG 59.194 45.455 0.00 0.00 34.67 3.33
211 212 3.120321 TGCTCGTGGTATTGAGTTGTT 57.880 42.857 0.00 0.00 34.67 2.83
212 213 2.806244 GTTGCTCGTGGTATTGAGTTGT 59.194 45.455 0.00 0.00 34.67 3.32
213 214 3.067106 AGTTGCTCGTGGTATTGAGTTG 58.933 45.455 0.00 0.00 34.67 3.16
214 215 3.402628 AGTTGCTCGTGGTATTGAGTT 57.597 42.857 0.00 0.00 34.67 3.01
215 216 3.067106 CAAGTTGCTCGTGGTATTGAGT 58.933 45.455 0.00 0.00 34.67 3.41
216 217 3.325870 TCAAGTTGCTCGTGGTATTGAG 58.674 45.455 0.00 0.00 35.30 3.02
217 218 3.006430 TCTCAAGTTGCTCGTGGTATTGA 59.994 43.478 0.00 0.00 0.00 2.57
218 219 3.123621 GTCTCAAGTTGCTCGTGGTATTG 59.876 47.826 0.00 0.00 0.00 1.90
219 220 3.244078 TGTCTCAAGTTGCTCGTGGTATT 60.244 43.478 0.00 0.00 0.00 1.89
220 221 2.299013 TGTCTCAAGTTGCTCGTGGTAT 59.701 45.455 0.00 0.00 0.00 2.73
221 222 1.684450 TGTCTCAAGTTGCTCGTGGTA 59.316 47.619 0.00 0.00 0.00 3.25
222 223 0.464036 TGTCTCAAGTTGCTCGTGGT 59.536 50.000 0.00 0.00 0.00 4.16
223 224 1.800805 ATGTCTCAAGTTGCTCGTGG 58.199 50.000 0.00 0.00 0.00 4.94
224 225 2.802247 TCAATGTCTCAAGTTGCTCGTG 59.198 45.455 0.00 0.00 0.00 4.35
225 226 3.111853 TCAATGTCTCAAGTTGCTCGT 57.888 42.857 0.00 0.00 0.00 4.18
226 227 3.681417 TCATCAATGTCTCAAGTTGCTCG 59.319 43.478 0.00 0.00 0.00 5.03
227 228 5.570344 CATCATCAATGTCTCAAGTTGCTC 58.430 41.667 0.00 0.00 0.00 4.26
228 229 4.142447 GCATCATCAATGTCTCAAGTTGCT 60.142 41.667 0.00 0.00 37.71 3.91
229 230 4.103357 GCATCATCAATGTCTCAAGTTGC 58.897 43.478 0.00 0.00 37.71 4.17
230 231 5.093457 GTGCATCATCAATGTCTCAAGTTG 58.907 41.667 0.00 0.00 37.71 3.16
231 232 4.763279 TGTGCATCATCAATGTCTCAAGTT 59.237 37.500 0.00 0.00 37.71 2.66
232 233 4.155462 GTGTGCATCATCAATGTCTCAAGT 59.845 41.667 0.00 0.00 37.71 3.16
233 234 4.155280 TGTGTGCATCATCAATGTCTCAAG 59.845 41.667 0.00 0.00 37.71 3.02
234 235 4.073549 TGTGTGCATCATCAATGTCTCAA 58.926 39.130 0.00 0.00 37.71 3.02
235 236 3.677190 TGTGTGCATCATCAATGTCTCA 58.323 40.909 0.00 0.00 37.71 3.27
236 237 4.895224 ATGTGTGCATCATCAATGTCTC 57.105 40.909 0.00 0.00 37.71 3.36
248 249 8.752005 AGTAGTAATAATTTGGATGTGTGCAT 57.248 30.769 0.00 0.00 38.18 3.96
249 250 8.046708 AGAGTAGTAATAATTTGGATGTGTGCA 58.953 33.333 0.00 0.00 0.00 4.57
250 251 8.438676 AGAGTAGTAATAATTTGGATGTGTGC 57.561 34.615 0.00 0.00 0.00 4.57
280 281 9.739737 TTTCTTCCTTTTATAGGGGTAGTAGAT 57.260 33.333 0.00 0.00 44.86 1.98
281 282 9.210228 CTTTCTTCCTTTTATAGGGGTAGTAGA 57.790 37.037 0.00 0.00 44.86 2.59
282 283 8.430431 CCTTTCTTCCTTTTATAGGGGTAGTAG 58.570 40.741 0.00 0.00 44.86 2.57
283 284 7.349065 CCCTTTCTTCCTTTTATAGGGGTAGTA 59.651 40.741 0.00 0.00 44.86 1.82
284 285 6.159928 CCCTTTCTTCCTTTTATAGGGGTAGT 59.840 42.308 0.00 0.00 44.86 2.73
285 286 6.602278 CCCTTTCTTCCTTTTATAGGGGTAG 58.398 44.000 0.00 0.00 44.86 3.18
286 287 5.103813 GCCCTTTCTTCCTTTTATAGGGGTA 60.104 44.000 0.00 0.00 44.86 3.69
287 288 4.325895 GCCCTTTCTTCCTTTTATAGGGGT 60.326 45.833 0.00 0.00 44.86 4.95
288 289 4.215908 GCCCTTTCTTCCTTTTATAGGGG 58.784 47.826 0.00 0.00 44.86 4.79
289 290 3.883489 CGCCCTTTCTTCCTTTTATAGGG 59.117 47.826 0.00 0.00 44.86 3.53
290 291 3.883489 CCGCCCTTTCTTCCTTTTATAGG 59.117 47.826 0.00 0.00 46.27 2.57
291 292 4.777463 TCCGCCCTTTCTTCCTTTTATAG 58.223 43.478 0.00 0.00 0.00 1.31
292 293 4.472108 TCTCCGCCCTTTCTTCCTTTTATA 59.528 41.667 0.00 0.00 0.00 0.98
293 294 3.265995 TCTCCGCCCTTTCTTCCTTTTAT 59.734 43.478 0.00 0.00 0.00 1.40
294 295 2.640826 TCTCCGCCCTTTCTTCCTTTTA 59.359 45.455 0.00 0.00 0.00 1.52
295 296 1.423921 TCTCCGCCCTTTCTTCCTTTT 59.576 47.619 0.00 0.00 0.00 2.27
296 297 1.064825 TCTCCGCCCTTTCTTCCTTT 58.935 50.000 0.00 0.00 0.00 3.11
297 298 1.064825 TTCTCCGCCCTTTCTTCCTT 58.935 50.000 0.00 0.00 0.00 3.36
298 299 0.325272 GTTCTCCGCCCTTTCTTCCT 59.675 55.000 0.00 0.00 0.00 3.36
299 300 0.677098 GGTTCTCCGCCCTTTCTTCC 60.677 60.000 0.00 0.00 0.00 3.46
300 301 0.036306 TGGTTCTCCGCCCTTTCTTC 59.964 55.000 0.00 0.00 36.30 2.87
301 302 0.476771 TTGGTTCTCCGCCCTTTCTT 59.523 50.000 0.00 0.00 36.30 2.52
302 303 0.476771 TTTGGTTCTCCGCCCTTTCT 59.523 50.000 0.00 0.00 36.30 2.52
303 304 1.472878 GATTTGGTTCTCCGCCCTTTC 59.527 52.381 0.00 0.00 36.30 2.62
304 305 1.203001 TGATTTGGTTCTCCGCCCTTT 60.203 47.619 0.00 0.00 36.30 3.11
305 306 0.404040 TGATTTGGTTCTCCGCCCTT 59.596 50.000 0.00 0.00 36.30 3.95
306 307 0.625849 ATGATTTGGTTCTCCGCCCT 59.374 50.000 0.00 0.00 36.30 5.19
307 308 1.025041 GATGATTTGGTTCTCCGCCC 58.975 55.000 0.00 0.00 36.30 6.13
308 309 1.750193 TGATGATTTGGTTCTCCGCC 58.250 50.000 0.00 0.00 36.30 6.13
309 310 4.154918 GGATATGATGATTTGGTTCTCCGC 59.845 45.833 0.00 0.00 36.30 5.54
310 311 5.308014 TGGATATGATGATTTGGTTCTCCG 58.692 41.667 0.00 0.00 36.30 4.63
311 312 7.361542 CGAATGGATATGATGATTTGGTTCTCC 60.362 40.741 0.00 0.00 0.00 3.71
312 313 7.388776 TCGAATGGATATGATGATTTGGTTCTC 59.611 37.037 0.00 0.00 0.00 2.87
313 314 7.226441 TCGAATGGATATGATGATTTGGTTCT 58.774 34.615 0.00 0.00 0.00 3.01
314 315 7.439157 TCGAATGGATATGATGATTTGGTTC 57.561 36.000 0.00 0.00 0.00 3.62
315 316 7.822161 TTCGAATGGATATGATGATTTGGTT 57.178 32.000 0.00 0.00 0.00 3.67
316 317 7.822161 TTTCGAATGGATATGATGATTTGGT 57.178 32.000 0.00 0.00 0.00 3.67
418 428 5.384063 TTGACTTGTTTGTGAAAGCTCAA 57.616 34.783 0.00 0.00 31.88 3.02
1385 1436 7.170554 TCACAACTACCTTCCCCTATATCTA 57.829 40.000 0.00 0.00 0.00 1.98
1403 1454 4.394300 CCTCCTCTGAATCAACATCACAAC 59.606 45.833 0.00 0.00 0.00 3.32
1640 1694 5.579047 TGTCATGATTTTGTATGGGACCTT 58.421 37.500 0.00 0.00 0.00 3.50
1882 1936 7.624549 TCTGAATCATCTAGCTTACCTGTTTT 58.375 34.615 0.00 0.00 0.00 2.43
2045 2099 3.194116 GTCAGTGAATGCCATTCCAACAT 59.806 43.478 14.58 0.00 38.50 2.71
2389 2443 6.395426 TTTGCACTTTGAGAGATTCACATT 57.605 33.333 0.00 0.00 34.94 2.71
2896 2950 2.457598 TGAGTCGACCATAAAGAGCCT 58.542 47.619 13.01 0.00 0.00 4.58
2919 2973 0.826715 ATGCATGTACAGTCGAGGCT 59.173 50.000 0.00 0.00 0.00 4.58
3205 3259 3.626930 TCTCTAGCTCCTTCTGGACTTC 58.373 50.000 0.00 0.00 37.46 3.01
3246 3300 5.246203 TGAAGTATGCTCTACTCCAGTGTTT 59.754 40.000 0.85 0.00 0.00 2.83
3537 3592 5.834460 TGTGTACCTCCTATGTTCTCCTTA 58.166 41.667 0.00 0.00 0.00 2.69
3561 3616 3.096092 ACTGCCACTTTTCCAAGTTGAA 58.904 40.909 3.87 0.00 40.66 2.69
3847 3902 7.383300 CCTTCTTTGTCAGCTTTCCATTTTTAG 59.617 37.037 0.00 0.00 0.00 1.85
3958 4013 1.833630 CTCTGGTGTAGCTCCCATTGA 59.166 52.381 0.00 0.00 0.00 2.57
4160 4215 1.377536 GCTGAGAAGATGTTGCTCCC 58.622 55.000 0.00 0.00 0.00 4.30
4249 4304 6.605594 AGATGTTCCTGGTGTTGTTTTCTTTA 59.394 34.615 0.00 0.00 0.00 1.85
4333 4388 1.483827 CTCCTGGCTGAGATGTTGCTA 59.516 52.381 0.00 0.00 34.11 3.49
4405 4478 2.169352 GCTCCTGGCTGAGAAGATGTTA 59.831 50.000 8.50 0.00 38.06 2.41


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

AutoCloner maintained by Alex Coulton.