Multiple sequence alignment - TraesCS1D01G390400

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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 TraesCS1D01G390400 chr1D 100.000 2499 0 0 1 2499 461823919 461821421 0.000000e+00 4615
1 TraesCS1D01G390400 chr1D 89.697 1223 92 10 788 1985 461787875 461786662 0.000000e+00 1530
2 TraesCS1D01G390400 chr1D 88.706 425 31 8 1993 2408 461786043 461785627 1.030000e-138 503
3 TraesCS1D01G390400 chr1D 85.253 434 40 18 368 789 461823131 461823552 2.300000e-115 425
4 TraesCS1D01G390400 chr1D 87.556 225 28 0 1744 1968 461751765 461751541 6.860000e-66 261
5 TraesCS1D01G390400 chr1B 94.748 1371 58 5 788 2147 634866516 634865149 0.000000e+00 2121
6 TraesCS1D01G390400 chr1B 94.675 1371 59 5 788 2147 634935070 634933703 0.000000e+00 2115
7 TraesCS1D01G390400 chr1B 90.268 1233 84 11 787 1985 634785192 634783962 0.000000e+00 1580
8 TraesCS1D01G390400 chr1B 90.202 1235 82 11 788 1985 635000679 634999447 0.000000e+00 1574
9 TraesCS1D01G390400 chr1B 90.196 1224 85 13 788 1985 635140459 635139245 0.000000e+00 1563
10 TraesCS1D01G390400 chr1B 87.529 425 40 4 1993 2408 635127215 635126795 1.740000e-131 479
11 TraesCS1D01G390400 chr1B 89.560 364 22 7 2147 2499 634863667 634863309 4.900000e-122 448
12 TraesCS1D01G390400 chr1B 89.560 364 22 7 2147 2499 634932221 634931863 4.900000e-122 448
13 TraesCS1D01G390400 chr1B 93.382 272 16 2 258 528 634867522 634867252 3.870000e-108 401
14 TraesCS1D01G390400 chr1B 93.382 272 16 2 258 528 634936076 634935806 3.870000e-108 401
15 TraesCS1D01G390400 chr1B 92.647 272 17 3 258 528 635141444 635141175 3.010000e-104 388
16 TraesCS1D01G390400 chr1B 92.373 236 17 1 554 789 634867177 634867411 3.980000e-88 335
17 TraesCS1D01G390400 chr1B 92.704 233 16 1 554 786 634935179 634935410 3.980000e-88 335
18 TraesCS1D01G390400 chr1B 92.373 236 17 1 554 789 634935731 634935965 3.980000e-88 335
19 TraesCS1D01G390400 chr1B 92.373 236 15 3 554 789 635140568 635140800 1.430000e-87 333
20 TraesCS1D01G390400 chr1B 94.064 219 12 1 556 774 635141102 635141319 5.150000e-87 331
21 TraesCS1D01G390400 chr1B 92.275 233 17 1 554 786 634866625 634866856 1.850000e-86 329
22 TraesCS1D01G390400 chr1B 91.875 160 10 3 367 526 635140801 635140645 1.160000e-53 220
23 TraesCS1D01G390400 chr1B 90.741 162 14 1 367 528 634935414 634935254 5.410000e-52 215
24 TraesCS1D01G390400 chrUn 95.092 1141 44 3 788 1917 350030111 350031250 0.000000e+00 1786
25 TraesCS1D01G390400 chrUn 93.382 272 16 2 258 528 350029105 350029375 3.870000e-108 401
26 TraesCS1D01G390400 chrUn 92.373 236 17 1 554 789 350029450 350029216 3.980000e-88 335
27 TraesCS1D01G390400 chrUn 92.373 236 17 1 554 789 350030002 350029768 3.980000e-88 335
28 TraesCS1D01G390400 chrUn 90.303 165 15 1 364 528 350029764 350029927 5.410000e-52 215
29 TraesCS1D01G390400 chr1A 94.980 976 49 0 697 1672 553466153 553465178 0.000000e+00 1531
30 TraesCS1D01G390400 chr1A 94.034 771 28 8 1666 2419 553464877 553464108 0.000000e+00 1153
31 TraesCS1D01G390400 chr1A 87.699 691 52 5 788 1452 553135346 553136029 0.000000e+00 774
32 TraesCS1D01G390400 chr1A 90.753 292 23 3 1875 2166 553067502 553067215 1.080000e-103 387
33 TraesCS1D01G390400 chr1A 90.943 265 22 2 265 528 553466520 553466257 3.060000e-94 355
34 TraesCS1D01G390400 chr1A 86.822 258 34 0 4 261 28642860 28642603 3.140000e-74 289
35 TraesCS1D01G390400 chr1A 93.506 77 3 1 2419 2495 553464027 553463953 2.030000e-21 113
36 TraesCS1D01G390400 chr6B 89.816 1139 74 15 874 1985 661863203 661862080 0.000000e+00 1423
37 TraesCS1D01G390400 chr6B 89.802 353 22 4 1993 2334 661861476 661861127 8.200000e-120 440
38 TraesCS1D01G390400 chr2D 89.147 258 27 1 4 261 449558996 449558740 1.120000e-83 320
39 TraesCS1D01G390400 chr4A 88.372 258 30 0 4 261 157232172 157231915 6.710000e-81 311
40 TraesCS1D01G390400 chr7A 87.500 264 29 4 4 265 135085362 135085101 4.040000e-78 302
41 TraesCS1D01G390400 chr7A 87.597 258 32 0 4 261 80836846 80836589 1.450000e-77 300
42 TraesCS1D01G390400 chr7A 87.259 259 33 0 4 262 204085093 204085351 1.880000e-76 296
43 TraesCS1D01G390400 chr5A 87.452 263 32 1 4 265 389607249 389606987 4.040000e-78 302
44 TraesCS1D01G390400 chr2A 87.597 258 32 0 4 261 38983786 38984043 1.450000e-77 300
45 TraesCS1D01G390400 chr3B 87.209 258 33 0 4 261 777634115 777633858 6.760000e-76 294
46 TraesCS1D01G390400 chr5D 84.255 235 35 2 555 789 302777948 302778180 6.950000e-56 228
47 TraesCS1D01G390400 chr6D 93.805 113 6 1 258 369 171922955 171923067 4.270000e-38 169
48 TraesCS1D01G390400 chr7B 92.035 113 8 1 258 369 270494754 270494866 9.250000e-35 158
49 TraesCS1D01G390400 chr4D 86.667 105 14 0 259 363 503608230 503608334 1.570000e-22 117
50 TraesCS1D01G390400 chr4B 85.981 107 11 4 265 369 360214136 360214032 7.310000e-21 111


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 TraesCS1D01G390400 chr1D 461821421 461823919 2498 True 4615.000000 4615 100.000000 1 2499 1 chr1D.!!$R2 2498
1 TraesCS1D01G390400 chr1D 461785627 461787875 2248 True 1016.500000 1530 89.201500 788 2408 2 chr1D.!!$R3 1620
2 TraesCS1D01G390400 chr1B 634783962 634785192 1230 True 1580.000000 1580 90.268000 787 1985 1 chr1B.!!$R1 1198
3 TraesCS1D01G390400 chr1B 634999447 635000679 1232 True 1574.000000 1574 90.202000 788 1985 1 chr1B.!!$R2 1197
4 TraesCS1D01G390400 chr1B 634863309 634867522 4213 True 990.000000 2121 92.563333 258 2499 3 chr1B.!!$R4 2241
5 TraesCS1D01G390400 chr1B 634931863 634936076 4213 True 794.750000 2115 92.089500 258 2499 4 chr1B.!!$R5 2241
6 TraesCS1D01G390400 chr1B 635139245 635141444 2199 True 723.666667 1563 91.572667 258 1985 3 chr1B.!!$R6 1727
7 TraesCS1D01G390400 chr1B 634935179 634935965 786 False 335.000000 335 92.538500 554 789 2 chr1B.!!$F2 235
8 TraesCS1D01G390400 chr1B 634866625 634867411 786 False 332.000000 335 92.324000 554 789 2 chr1B.!!$F1 235
9 TraesCS1D01G390400 chr1B 635140568 635141319 751 False 332.000000 333 93.218500 554 789 2 chr1B.!!$F3 235
10 TraesCS1D01G390400 chrUn 350029105 350031250 2145 False 800.666667 1786 92.925667 258 1917 3 chrUn.!!$F1 1659
11 TraesCS1D01G390400 chrUn 350029216 350030002 786 True 335.000000 335 92.373000 554 789 2 chrUn.!!$R1 235
12 TraesCS1D01G390400 chr1A 553463953 553466520 2567 True 788.000000 1531 93.365750 265 2495 4 chr1A.!!$R3 2230
13 TraesCS1D01G390400 chr1A 553135346 553136029 683 False 774.000000 774 87.699000 788 1452 1 chr1A.!!$F1 664
14 TraesCS1D01G390400 chr6B 661861127 661863203 2076 True 931.500000 1423 89.809000 874 2334 2 chr6B.!!$R1 1460

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
103 104 0.03759 ACTCGTTAATGGGCCAGCAA 59.962 50.0 13.78 5.32 0.0 3.91 F
172 173 0.17920 GGGCTTGACATGTTAACGCG 60.179 55.0 3.53 3.53 0.0 6.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1003 1884 0.173708 GCAACCGCTCTAGCACTAGT 59.826 55.0 2.44 0.0 42.21 2.57 R
1954 3185 1.018148 CAACCAGTGGCGTGTAAACA 58.982 50.0 9.78 0.0 0.00 2.83 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
33 34 8.968969 ACTATTAATCCTAGGTATTAAGGAGCG 58.031 37.037 21.02 13.81 44.92 5.03
34 35 6.600882 TTAATCCTAGGTATTAAGGAGCGG 57.399 41.667 9.08 0.00 44.92 5.52
35 36 2.245582 TCCTAGGTATTAAGGAGCGGC 58.754 52.381 9.08 0.00 36.97 6.53
36 37 1.968493 CCTAGGTATTAAGGAGCGGCA 59.032 52.381 1.45 0.00 34.58 5.69
37 38 2.567615 CCTAGGTATTAAGGAGCGGCAT 59.432 50.000 1.45 0.00 34.58 4.40
38 39 2.550830 AGGTATTAAGGAGCGGCATG 57.449 50.000 1.45 0.00 0.00 4.06
39 40 1.072331 AGGTATTAAGGAGCGGCATGG 59.928 52.381 1.45 0.00 0.00 3.66
40 41 1.523758 GTATTAAGGAGCGGCATGGG 58.476 55.000 1.45 0.00 0.00 4.00
41 42 0.400213 TATTAAGGAGCGGCATGGGG 59.600 55.000 1.45 0.00 0.00 4.96
42 43 2.983725 ATTAAGGAGCGGCATGGGGC 62.984 60.000 1.45 0.00 43.74 5.80
45 46 4.632974 GGAGCGGCATGGGGCTAG 62.633 72.222 1.45 0.00 44.01 3.42
46 47 3.550431 GAGCGGCATGGGGCTAGA 61.550 66.667 1.45 0.00 44.01 2.43
47 48 3.089874 AGCGGCATGGGGCTAGAA 61.090 61.111 1.45 0.00 44.01 2.10
48 49 2.592861 GCGGCATGGGGCTAGAAG 60.593 66.667 0.00 0.00 44.01 2.85
49 50 2.111878 CGGCATGGGGCTAGAAGG 59.888 66.667 0.00 0.00 44.01 3.46
50 51 2.517919 GGCATGGGGCTAGAAGGG 59.482 66.667 0.00 0.00 44.01 3.95
51 52 2.517919 GCATGGGGCTAGAAGGGG 59.482 66.667 0.00 0.00 40.25 4.79
52 53 2.386935 GCATGGGGCTAGAAGGGGT 61.387 63.158 0.00 0.00 40.25 4.95
53 54 1.839894 CATGGGGCTAGAAGGGGTC 59.160 63.158 0.00 0.00 0.00 4.46
54 55 0.988145 CATGGGGCTAGAAGGGGTCA 60.988 60.000 0.00 0.00 0.00 4.02
55 56 0.988678 ATGGGGCTAGAAGGGGTCAC 60.989 60.000 0.00 0.00 0.00 3.67
56 57 2.732619 GGGGCTAGAAGGGGTCACG 61.733 68.421 0.00 0.00 0.00 4.35
57 58 1.684734 GGGCTAGAAGGGGTCACGA 60.685 63.158 0.00 0.00 0.00 4.35
58 59 1.677637 GGGCTAGAAGGGGTCACGAG 61.678 65.000 0.00 0.00 0.00 4.18
59 60 1.142097 GCTAGAAGGGGTCACGAGC 59.858 63.158 0.00 0.00 0.00 5.03
83 84 5.347342 CAAAAATTTGGGCTTTGTTTTCCC 58.653 37.500 0.00 0.00 40.47 3.97
86 87 3.625314 TGGGCTTTGTTTTCCCACT 57.375 47.368 0.00 0.00 44.62 4.00
87 88 1.408969 TGGGCTTTGTTTTCCCACTC 58.591 50.000 0.00 0.00 44.62 3.51
88 89 0.313987 GGGCTTTGTTTTCCCACTCG 59.686 55.000 0.00 0.00 39.82 4.18
89 90 1.029681 GGCTTTGTTTTCCCACTCGT 58.970 50.000 0.00 0.00 0.00 4.18
90 91 1.407618 GGCTTTGTTTTCCCACTCGTT 59.592 47.619 0.00 0.00 0.00 3.85
91 92 2.619646 GGCTTTGTTTTCCCACTCGTTA 59.380 45.455 0.00 0.00 0.00 3.18
92 93 3.067040 GGCTTTGTTTTCCCACTCGTTAA 59.933 43.478 0.00 0.00 0.00 2.01
93 94 4.261867 GGCTTTGTTTTCCCACTCGTTAAT 60.262 41.667 0.00 0.00 0.00 1.40
94 95 4.679654 GCTTTGTTTTCCCACTCGTTAATG 59.320 41.667 0.00 0.00 0.00 1.90
95 96 4.839668 TTGTTTTCCCACTCGTTAATGG 57.160 40.909 0.00 0.00 35.59 3.16
100 101 2.780595 CCACTCGTTAATGGGCCAG 58.219 57.895 13.78 0.00 31.83 4.85
101 102 1.376609 CCACTCGTTAATGGGCCAGC 61.377 60.000 13.78 1.01 31.83 4.85
102 103 0.676466 CACTCGTTAATGGGCCAGCA 60.676 55.000 13.78 0.00 0.00 4.41
103 104 0.037590 ACTCGTTAATGGGCCAGCAA 59.962 50.000 13.78 5.32 0.00 3.91
104 105 0.734889 CTCGTTAATGGGCCAGCAAG 59.265 55.000 13.78 2.22 0.00 4.01
105 106 0.679640 TCGTTAATGGGCCAGCAAGG 60.680 55.000 13.78 13.63 41.84 3.61
106 107 0.679640 CGTTAATGGGCCAGCAAGGA 60.680 55.000 13.78 0.00 41.22 3.36
107 108 1.780503 GTTAATGGGCCAGCAAGGAT 58.219 50.000 13.78 0.00 41.22 3.24
108 109 2.110578 GTTAATGGGCCAGCAAGGATT 58.889 47.619 13.78 1.38 41.22 3.01
109 110 3.295973 GTTAATGGGCCAGCAAGGATTA 58.704 45.455 13.78 0.25 41.22 1.75
110 111 2.548464 AATGGGCCAGCAAGGATTAA 57.452 45.000 13.78 0.00 41.22 1.40
111 112 2.781403 ATGGGCCAGCAAGGATTAAT 57.219 45.000 13.78 0.00 41.22 1.40
112 113 2.071778 TGGGCCAGCAAGGATTAATC 57.928 50.000 0.00 6.93 41.22 1.75
113 114 0.954452 GGGCCAGCAAGGATTAATCG 59.046 55.000 4.39 0.00 41.22 3.34
114 115 0.954452 GGCCAGCAAGGATTAATCGG 59.046 55.000 9.32 5.10 41.22 4.18
115 116 1.680338 GCCAGCAAGGATTAATCGGT 58.320 50.000 9.32 0.00 41.22 4.69
116 117 2.486548 GGCCAGCAAGGATTAATCGGTA 60.487 50.000 9.32 0.00 41.22 4.02
117 118 3.412386 GCCAGCAAGGATTAATCGGTAT 58.588 45.455 9.32 0.00 41.22 2.73
118 119 3.189287 GCCAGCAAGGATTAATCGGTATG 59.811 47.826 9.32 6.69 41.22 2.39
119 120 4.641396 CCAGCAAGGATTAATCGGTATGA 58.359 43.478 9.32 0.00 41.22 2.15
120 121 4.452455 CCAGCAAGGATTAATCGGTATGAC 59.548 45.833 9.32 0.00 41.22 3.06
121 122 5.056480 CAGCAAGGATTAATCGGTATGACA 58.944 41.667 9.32 0.00 0.00 3.58
122 123 5.527214 CAGCAAGGATTAATCGGTATGACAA 59.473 40.000 9.32 0.00 0.00 3.18
123 124 5.527582 AGCAAGGATTAATCGGTATGACAAC 59.472 40.000 9.32 0.00 0.00 3.32
124 125 5.527582 GCAAGGATTAATCGGTATGACAACT 59.472 40.000 9.32 0.00 0.00 3.16
125 126 6.511767 GCAAGGATTAATCGGTATGACAACTG 60.512 42.308 9.32 0.00 0.00 3.16
126 127 6.479972 AGGATTAATCGGTATGACAACTGA 57.520 37.500 9.32 2.96 39.05 3.41
127 128 7.067496 AGGATTAATCGGTATGACAACTGAT 57.933 36.000 9.32 6.37 45.40 2.90
134 135 5.286438 TCGGTATGACAACTGATTAATCGG 58.714 41.667 20.59 20.59 39.11 4.18
136 137 5.175126 CGGTATGACAACTGATTAATCGGTC 59.825 44.000 26.34 20.53 45.23 4.79
137 138 6.281405 GGTATGACAACTGATTAATCGGTCT 58.719 40.000 26.34 16.27 45.23 3.85
138 139 7.431249 GGTATGACAACTGATTAATCGGTCTA 58.569 38.462 26.34 14.92 45.23 2.59
139 140 7.924412 GGTATGACAACTGATTAATCGGTCTAA 59.076 37.037 26.34 14.75 45.23 2.10
140 141 7.772332 ATGACAACTGATTAATCGGTCTAAC 57.228 36.000 26.34 18.29 45.23 2.34
141 142 6.931838 TGACAACTGATTAATCGGTCTAACT 58.068 36.000 26.34 10.86 45.23 2.24
142 143 6.811665 TGACAACTGATTAATCGGTCTAACTG 59.188 38.462 26.34 21.87 45.23 3.16
143 144 6.106673 ACAACTGATTAATCGGTCTAACTGG 58.893 40.000 26.34 13.89 45.23 4.00
144 145 5.934402 ACTGATTAATCGGTCTAACTGGT 57.066 39.130 21.88 0.00 42.52 4.00
145 146 5.903810 ACTGATTAATCGGTCTAACTGGTC 58.096 41.667 21.88 0.00 42.52 4.02
146 147 5.421056 ACTGATTAATCGGTCTAACTGGTCA 59.579 40.000 21.88 0.00 42.52 4.02
147 148 6.070995 ACTGATTAATCGGTCTAACTGGTCAA 60.071 38.462 21.88 0.00 42.52 3.18
148 149 6.884832 TGATTAATCGGTCTAACTGGTCAAT 58.115 36.000 10.80 0.00 0.00 2.57
149 150 7.335627 TGATTAATCGGTCTAACTGGTCAATT 58.664 34.615 10.80 0.00 0.00 2.32
150 151 8.479689 TGATTAATCGGTCTAACTGGTCAATTA 58.520 33.333 10.80 0.00 0.00 1.40
151 152 9.321562 GATTAATCGGTCTAACTGGTCAATTAA 57.678 33.333 0.00 0.00 0.00 1.40
152 153 9.847224 ATTAATCGGTCTAACTGGTCAATTAAT 57.153 29.630 0.00 0.00 0.00 1.40
153 154 7.553881 AATCGGTCTAACTGGTCAATTAATG 57.446 36.000 0.00 0.00 0.00 1.90
154 155 5.424757 TCGGTCTAACTGGTCAATTAATGG 58.575 41.667 0.00 0.00 0.00 3.16
155 156 4.574828 CGGTCTAACTGGTCAATTAATGGG 59.425 45.833 0.00 0.00 0.00 4.00
156 157 4.338400 GGTCTAACTGGTCAATTAATGGGC 59.662 45.833 0.00 0.00 0.00 5.36
157 158 5.193679 GTCTAACTGGTCAATTAATGGGCT 58.806 41.667 0.00 0.00 0.00 5.19
158 159 5.652452 GTCTAACTGGTCAATTAATGGGCTT 59.348 40.000 0.00 0.00 0.00 4.35
159 160 4.806640 AACTGGTCAATTAATGGGCTTG 57.193 40.909 0.00 0.00 0.00 4.01
160 161 4.046286 ACTGGTCAATTAATGGGCTTGA 57.954 40.909 0.00 0.00 0.00 3.02
161 162 3.763897 ACTGGTCAATTAATGGGCTTGAC 59.236 43.478 9.44 9.44 45.04 3.18
162 163 3.763360 CTGGTCAATTAATGGGCTTGACA 59.237 43.478 16.64 6.23 46.69 3.58
163 164 4.352009 TGGTCAATTAATGGGCTTGACAT 58.648 39.130 16.64 0.00 46.69 3.06
164 165 4.160065 TGGTCAATTAATGGGCTTGACATG 59.840 41.667 16.64 0.00 46.69 3.21
165 166 4.160252 GGTCAATTAATGGGCTTGACATGT 59.840 41.667 16.64 0.00 46.69 3.21
166 167 5.337491 GGTCAATTAATGGGCTTGACATGTT 60.337 40.000 16.64 0.00 46.69 2.71
167 168 6.127479 GGTCAATTAATGGGCTTGACATGTTA 60.127 38.462 16.64 0.00 46.69 2.41
168 169 7.319646 GTCAATTAATGGGCTTGACATGTTAA 58.680 34.615 12.04 0.25 45.09 2.01
169 170 7.275560 GTCAATTAATGGGCTTGACATGTTAAC 59.724 37.037 12.04 0.00 45.09 2.01
170 171 3.848272 AATGGGCTTGACATGTTAACG 57.152 42.857 0.00 0.00 0.00 3.18
171 172 0.878416 TGGGCTTGACATGTTAACGC 59.122 50.000 0.00 7.90 0.00 4.84
172 173 0.179200 GGGCTTGACATGTTAACGCG 60.179 55.000 3.53 3.53 0.00 6.01
173 174 0.793861 GGCTTGACATGTTAACGCGA 59.206 50.000 15.93 0.00 0.00 5.87
174 175 1.463528 GGCTTGACATGTTAACGCGAC 60.464 52.381 15.93 0.00 0.00 5.19
175 176 1.782023 GCTTGACATGTTAACGCGACG 60.782 52.381 15.93 0.00 0.00 5.12
176 177 1.717113 CTTGACATGTTAACGCGACGA 59.283 47.619 15.93 0.00 0.00 4.20
177 178 1.768510 TGACATGTTAACGCGACGAA 58.231 45.000 15.93 0.00 0.00 3.85
178 179 2.330286 TGACATGTTAACGCGACGAAT 58.670 42.857 15.93 0.00 0.00 3.34
179 180 3.500014 TGACATGTTAACGCGACGAATA 58.500 40.909 15.93 1.88 0.00 1.75
180 181 4.106909 TGACATGTTAACGCGACGAATAT 58.893 39.130 15.93 4.44 0.00 1.28
181 182 4.027214 TGACATGTTAACGCGACGAATATG 60.027 41.667 15.93 18.17 0.00 1.78
182 183 3.861113 ACATGTTAACGCGACGAATATGT 59.139 39.130 15.93 18.79 0.00 2.29
183 184 3.892527 TGTTAACGCGACGAATATGTG 57.107 42.857 15.93 0.00 0.00 3.21
184 185 3.244156 TGTTAACGCGACGAATATGTGT 58.756 40.909 15.93 0.00 0.00 3.72
185 186 3.674281 TGTTAACGCGACGAATATGTGTT 59.326 39.130 15.93 0.00 39.43 3.32
186 187 4.855937 TGTTAACGCGACGAATATGTGTTA 59.144 37.500 15.93 0.00 37.49 2.41
187 188 5.515982 TGTTAACGCGACGAATATGTGTTAT 59.484 36.000 15.93 0.00 38.10 1.89
188 189 6.034790 TGTTAACGCGACGAATATGTGTTATT 59.965 34.615 15.93 0.00 38.10 1.40
189 190 4.687458 ACGCGACGAATATGTGTTATTC 57.313 40.909 15.93 0.00 41.87 1.75
197 198 5.978934 GAATATGTGTTATTCGGTTCGGT 57.021 39.130 0.00 0.00 37.51 4.69
198 199 5.970879 GAATATGTGTTATTCGGTTCGGTC 58.029 41.667 0.00 0.00 37.51 4.79
199 200 2.816204 TGTGTTATTCGGTTCGGTCA 57.184 45.000 0.00 0.00 0.00 4.02
200 201 3.322211 TGTGTTATTCGGTTCGGTCAT 57.678 42.857 0.00 0.00 0.00 3.06
201 202 2.997303 TGTGTTATTCGGTTCGGTCATG 59.003 45.455 0.00 0.00 0.00 3.07
202 203 2.004017 TGTTATTCGGTTCGGTCATGC 58.996 47.619 0.00 0.00 0.00 4.06
203 204 2.277084 GTTATTCGGTTCGGTCATGCT 58.723 47.619 0.00 0.00 0.00 3.79
204 205 3.119065 TGTTATTCGGTTCGGTCATGCTA 60.119 43.478 0.00 0.00 0.00 3.49
205 206 2.910688 ATTCGGTTCGGTCATGCTAT 57.089 45.000 0.00 0.00 0.00 2.97
206 207 1.934589 TTCGGTTCGGTCATGCTATG 58.065 50.000 0.00 0.00 0.00 2.23
207 208 1.107945 TCGGTTCGGTCATGCTATGA 58.892 50.000 0.00 0.00 36.84 2.15
208 209 1.067060 TCGGTTCGGTCATGCTATGAG 59.933 52.381 0.00 0.00 40.53 2.90
209 210 1.202417 CGGTTCGGTCATGCTATGAGT 60.202 52.381 0.00 0.00 40.53 3.41
210 211 2.034179 CGGTTCGGTCATGCTATGAGTA 59.966 50.000 0.00 0.00 40.53 2.59
211 212 3.643763 GGTTCGGTCATGCTATGAGTAG 58.356 50.000 0.00 0.00 40.53 2.57
226 227 7.881643 CTATGAGTAGCAATTAACTAGCCTG 57.118 40.000 0.00 0.00 0.00 4.85
227 228 5.677319 TGAGTAGCAATTAACTAGCCTGT 57.323 39.130 0.00 0.00 0.00 4.00
228 229 6.049955 TGAGTAGCAATTAACTAGCCTGTT 57.950 37.500 0.00 0.00 0.00 3.16
229 230 7.177832 TGAGTAGCAATTAACTAGCCTGTTA 57.822 36.000 0.00 0.00 0.00 2.41
230 231 7.617225 TGAGTAGCAATTAACTAGCCTGTTAA 58.383 34.615 12.31 12.31 43.63 2.01
231 232 7.548075 TGAGTAGCAATTAACTAGCCTGTTAAC 59.452 37.037 12.21 0.00 42.72 2.01
232 233 7.621796 AGTAGCAATTAACTAGCCTGTTAACT 58.378 34.615 7.22 8.89 42.72 2.24
233 234 6.743575 AGCAATTAACTAGCCTGTTAACTG 57.256 37.500 7.22 13.01 42.72 3.16
234 235 6.472887 AGCAATTAACTAGCCTGTTAACTGA 58.527 36.000 18.41 0.13 40.11 3.41
235 236 7.112779 AGCAATTAACTAGCCTGTTAACTGAT 58.887 34.615 18.41 12.51 40.11 2.90
236 237 7.611855 AGCAATTAACTAGCCTGTTAACTGATT 59.388 33.333 18.41 7.12 40.11 2.57
237 238 8.889717 GCAATTAACTAGCCTGTTAACTGATTA 58.110 33.333 18.41 5.26 40.11 1.75
260 261 6.659361 AATCAGATGAATTCTCGAACAGTG 57.341 37.500 7.05 0.00 29.93 3.66
277 278 8.455682 TCGAACAGTGTTATTTTCACTTCTTTT 58.544 29.630 8.88 0.00 43.14 2.27
282 283 7.973388 CAGTGTTATTTTCACTTCTTTTCACCA 59.027 33.333 0.00 0.00 43.14 4.17
355 356 1.000385 ACCAACAAATGCATGTGACCG 60.000 47.619 23.90 11.32 32.81 4.79
391 393 1.226746 CCTCCGTCCGGATTTATTGC 58.773 55.000 7.81 0.00 44.24 3.56
412 414 2.325082 CCGAGAGCCAAAACACGGG 61.325 63.158 0.00 0.00 36.82 5.28
448 450 9.988815 ATACACTCTTCTAGGCACAATTAATAG 57.011 33.333 0.00 0.00 0.00 1.73
528 530 2.588027 TGCATGTAATTGGCTGCATG 57.412 45.000 0.50 0.00 39.54 4.06
545 566 3.438434 TGCATGCGCAGTAATTTAAGTGA 59.562 39.130 18.32 0.00 45.36 3.41
546 567 3.786048 GCATGCGCAGTAATTTAAGTGAC 59.214 43.478 18.32 0.00 38.36 3.67
548 569 5.220586 GCATGCGCAGTAATTTAAGTGACTA 60.221 40.000 18.32 0.00 38.36 2.59
549 570 5.773239 TGCGCAGTAATTTAAGTGACTAC 57.227 39.130 5.66 0.00 0.00 2.73
550 571 4.628333 TGCGCAGTAATTTAAGTGACTACC 59.372 41.667 5.66 0.00 0.00 3.18
551 572 4.033702 GCGCAGTAATTTAAGTGACTACCC 59.966 45.833 0.30 0.00 0.00 3.69
552 573 4.569564 CGCAGTAATTTAAGTGACTACCCC 59.430 45.833 0.00 0.00 0.00 4.95
553 574 5.493809 GCAGTAATTTAAGTGACTACCCCA 58.506 41.667 0.00 0.00 0.00 4.96
554 575 5.585047 GCAGTAATTTAAGTGACTACCCCAG 59.415 44.000 0.00 0.00 0.00 4.45
555 576 6.708285 CAGTAATTTAAGTGACTACCCCAGT 58.292 40.000 0.00 0.00 41.47 4.00
556 577 7.166167 CAGTAATTTAAGTGACTACCCCAGTT 58.834 38.462 0.00 0.00 37.72 3.16
557 578 7.119262 CAGTAATTTAAGTGACTACCCCAGTTG 59.881 40.741 0.00 0.00 37.72 3.16
573 594 3.848272 AGTTGTTCACTGTGTTGGTTG 57.152 42.857 7.79 0.00 32.83 3.77
676 697 4.273235 CGCATGCATCCACTTAAATCACTA 59.727 41.667 19.57 0.00 0.00 2.74
731 752 4.695455 TGTTAATTGTGCCTAGAAGAGTGC 59.305 41.667 0.00 0.00 0.00 4.40
812 1665 9.202273 GTACTAAATGAATCAAATGCAACCAAA 57.798 29.630 0.00 0.00 0.00 3.28
843 1696 3.154710 AGCAAGATATCACCCATGCATG 58.845 45.455 20.19 20.19 36.30 4.06
862 1715 7.019774 TGCATGACTTAAGCATGAAGATAAC 57.980 36.000 28.70 16.81 44.49 1.89
883 1736 3.018856 CTGAGCATTTCCCATAGCACAA 58.981 45.455 0.00 0.00 0.00 3.33
1003 1884 7.911727 CGCATCTTTCAAAGTTGATTGATATGA 59.088 33.333 11.72 0.00 38.98 2.15
1036 1917 1.751437 GGTTGCCATGTTCTACCTCC 58.249 55.000 8.02 0.00 0.00 4.30
1522 2412 3.052082 CACTCCGTGCAAGGCCAG 61.052 66.667 14.54 9.73 0.00 4.85
1584 2492 5.741425 CATCCGCATAGTGTGTTCTATTTG 58.259 41.667 0.00 0.00 0.00 2.32
1892 3122 5.860941 ATCTCCGATGCGATCCTTATATT 57.139 39.130 0.00 0.00 0.00 1.28
1954 3185 0.673644 GCACCGTGATTGCCTACTGT 60.674 55.000 1.65 0.00 33.58 3.55
1959 3190 3.244284 ACCGTGATTGCCTACTGTGTTTA 60.244 43.478 0.00 0.00 0.00 2.01
2179 5501 7.054124 TGTCTATTCAATGGTTATGGACTTCC 58.946 38.462 0.00 0.00 32.81 3.46
2347 5681 7.401080 CACCACTTGCTTTATTTTCTGTTTTG 58.599 34.615 0.00 0.00 0.00 2.44
2354 5688 8.666580 TGCTTTATTTTCTGTTTTGTTTTTGC 57.333 26.923 0.00 0.00 0.00 3.68
2360 5694 1.663135 CTGTTTTGTTTTTGCCGTGGG 59.337 47.619 0.00 0.00 0.00 4.61
2386 5720 0.673644 GCGATGGTGTGGCAACTAGT 60.674 55.000 0.00 0.00 37.61 2.57
2419 5753 4.341520 CCTTGCCGTTTCTATACTACTCCT 59.658 45.833 0.00 0.00 0.00 3.69
2426 5841 9.623350 GCCGTTTCTATACTACTCCTATAAAAG 57.377 37.037 0.00 0.00 0.00 2.27
2467 5883 5.833131 CCATAAAGCCATACCCATAAAGTGT 59.167 40.000 0.00 0.00 0.00 3.55
2468 5884 7.001674 CCATAAAGCCATACCCATAAAGTGTA 58.998 38.462 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 8.968969 CGCTCCTTAATACCTAGGATTAATAGT 58.031 37.037 17.98 0.00 39.72 2.12
8 9 8.414778 CCGCTCCTTAATACCTAGGATTAATAG 58.585 40.741 17.98 18.08 39.72 1.73
9 10 7.147776 GCCGCTCCTTAATACCTAGGATTAATA 60.148 40.741 17.98 10.71 39.72 0.98
10 11 6.351966 GCCGCTCCTTAATACCTAGGATTAAT 60.352 42.308 17.98 0.12 39.72 1.40
11 12 5.046807 GCCGCTCCTTAATACCTAGGATTAA 60.047 44.000 17.98 17.94 39.72 1.40
12 13 4.465305 GCCGCTCCTTAATACCTAGGATTA 59.535 45.833 17.98 12.03 39.72 1.75
13 14 3.261137 GCCGCTCCTTAATACCTAGGATT 59.739 47.826 17.98 13.02 39.72 3.01
14 15 2.832733 GCCGCTCCTTAATACCTAGGAT 59.167 50.000 17.98 3.64 39.72 3.24
15 16 2.245582 GCCGCTCCTTAATACCTAGGA 58.754 52.381 17.98 0.00 38.22 2.94
16 17 1.968493 TGCCGCTCCTTAATACCTAGG 59.032 52.381 7.41 7.41 0.00 3.02
17 18 3.589988 CATGCCGCTCCTTAATACCTAG 58.410 50.000 0.00 0.00 0.00 3.02
18 19 2.301870 CCATGCCGCTCCTTAATACCTA 59.698 50.000 0.00 0.00 0.00 3.08
19 20 1.072331 CCATGCCGCTCCTTAATACCT 59.928 52.381 0.00 0.00 0.00 3.08
20 21 1.523758 CCATGCCGCTCCTTAATACC 58.476 55.000 0.00 0.00 0.00 2.73
21 22 1.523758 CCCATGCCGCTCCTTAATAC 58.476 55.000 0.00 0.00 0.00 1.89
22 23 0.400213 CCCCATGCCGCTCCTTAATA 59.600 55.000 0.00 0.00 0.00 0.98
23 24 1.151450 CCCCATGCCGCTCCTTAAT 59.849 57.895 0.00 0.00 0.00 1.40
24 25 2.595095 CCCCATGCCGCTCCTTAA 59.405 61.111 0.00 0.00 0.00 1.85
25 26 4.189580 GCCCCATGCCGCTCCTTA 62.190 66.667 0.00 0.00 0.00 2.69
28 29 4.632974 CTAGCCCCATGCCGCTCC 62.633 72.222 7.92 0.00 42.71 4.70
29 30 3.106986 TTCTAGCCCCATGCCGCTC 62.107 63.158 7.92 0.00 42.71 5.03
30 31 3.089874 TTCTAGCCCCATGCCGCT 61.090 61.111 9.41 9.41 42.71 5.52
31 32 2.592861 CTTCTAGCCCCATGCCGC 60.593 66.667 0.00 0.00 42.71 6.53
32 33 2.111878 CCTTCTAGCCCCATGCCG 59.888 66.667 0.00 0.00 42.71 5.69
33 34 2.517919 CCCTTCTAGCCCCATGCC 59.482 66.667 0.00 0.00 42.71 4.40
34 35 2.344878 GACCCCTTCTAGCCCCATGC 62.345 65.000 0.00 0.00 41.71 4.06
35 36 0.988145 TGACCCCTTCTAGCCCCATG 60.988 60.000 0.00 0.00 0.00 3.66
36 37 0.988678 GTGACCCCTTCTAGCCCCAT 60.989 60.000 0.00 0.00 0.00 4.00
37 38 1.615424 GTGACCCCTTCTAGCCCCA 60.615 63.158 0.00 0.00 0.00 4.96
38 39 2.732619 CGTGACCCCTTCTAGCCCC 61.733 68.421 0.00 0.00 0.00 5.80
39 40 1.677637 CTCGTGACCCCTTCTAGCCC 61.678 65.000 0.00 0.00 0.00 5.19
40 41 1.817209 CTCGTGACCCCTTCTAGCC 59.183 63.158 0.00 0.00 0.00 3.93
41 42 1.142097 GCTCGTGACCCCTTCTAGC 59.858 63.158 0.00 0.00 0.00 3.42
42 43 0.970937 TGGCTCGTGACCCCTTCTAG 60.971 60.000 0.00 0.00 0.00 2.43
43 44 0.543410 TTGGCTCGTGACCCCTTCTA 60.543 55.000 0.00 0.00 0.00 2.10
44 45 1.415672 TTTGGCTCGTGACCCCTTCT 61.416 55.000 0.00 0.00 0.00 2.85
45 46 0.536460 TTTTGGCTCGTGACCCCTTC 60.536 55.000 0.00 0.00 0.00 3.46
46 47 0.106419 TTTTTGGCTCGTGACCCCTT 60.106 50.000 0.00 0.00 0.00 3.95
47 48 0.112412 ATTTTTGGCTCGTGACCCCT 59.888 50.000 0.00 0.00 0.00 4.79
48 49 0.966179 AATTTTTGGCTCGTGACCCC 59.034 50.000 0.00 0.00 0.00 4.95
49 50 2.403259 CAAATTTTTGGCTCGTGACCC 58.597 47.619 0.00 0.00 34.59 4.46
60 61 5.347342 GGGAAAACAAAGCCCAAATTTTTG 58.653 37.500 0.00 0.00 41.64 2.44
61 62 5.590530 GGGAAAACAAAGCCCAAATTTTT 57.409 34.783 0.00 0.00 41.64 1.94
69 70 0.313987 CGAGTGGGAAAACAAAGCCC 59.686 55.000 0.00 0.00 42.38 5.19
70 71 1.029681 ACGAGTGGGAAAACAAAGCC 58.970 50.000 0.00 0.00 0.00 4.35
71 72 2.863401 AACGAGTGGGAAAACAAAGC 57.137 45.000 0.00 0.00 0.00 3.51
72 73 5.219633 CCATTAACGAGTGGGAAAACAAAG 58.780 41.667 0.00 0.00 0.00 2.77
73 74 5.189659 CCATTAACGAGTGGGAAAACAAA 57.810 39.130 0.00 0.00 0.00 2.83
74 75 4.839668 CCATTAACGAGTGGGAAAACAA 57.160 40.909 0.00 0.00 0.00 2.83
82 83 1.376609 GCTGGCCCATTAACGAGTGG 61.377 60.000 0.00 0.00 35.22 4.00
83 84 0.676466 TGCTGGCCCATTAACGAGTG 60.676 55.000 0.00 0.00 0.00 3.51
84 85 0.037590 TTGCTGGCCCATTAACGAGT 59.962 50.000 0.00 0.00 0.00 4.18
85 86 0.734889 CTTGCTGGCCCATTAACGAG 59.265 55.000 0.00 0.00 0.00 4.18
86 87 0.679640 CCTTGCTGGCCCATTAACGA 60.680 55.000 0.00 0.00 0.00 3.85
87 88 0.679640 TCCTTGCTGGCCCATTAACG 60.680 55.000 0.00 0.00 35.26 3.18
88 89 1.780503 ATCCTTGCTGGCCCATTAAC 58.219 50.000 0.00 0.00 35.26 2.01
89 90 2.548464 AATCCTTGCTGGCCCATTAA 57.452 45.000 0.00 0.00 35.26 1.40
90 91 3.678965 TTAATCCTTGCTGGCCCATTA 57.321 42.857 0.00 0.00 35.26 1.90
91 92 2.548464 TTAATCCTTGCTGGCCCATT 57.452 45.000 0.00 0.00 35.26 3.16
92 93 2.601905 GATTAATCCTTGCTGGCCCAT 58.398 47.619 0.00 0.00 35.26 4.00
93 94 1.750332 CGATTAATCCTTGCTGGCCCA 60.750 52.381 9.87 0.00 35.26 5.36
94 95 0.954452 CGATTAATCCTTGCTGGCCC 59.046 55.000 9.87 0.00 35.26 5.80
95 96 0.954452 CCGATTAATCCTTGCTGGCC 59.046 55.000 9.87 0.00 35.26 5.36
96 97 1.680338 ACCGATTAATCCTTGCTGGC 58.320 50.000 9.87 0.00 35.26 4.85
97 98 4.452455 GTCATACCGATTAATCCTTGCTGG 59.548 45.833 9.87 6.57 37.10 4.85
98 99 5.056480 TGTCATACCGATTAATCCTTGCTG 58.944 41.667 9.87 2.39 0.00 4.41
99 100 5.290493 TGTCATACCGATTAATCCTTGCT 57.710 39.130 9.87 0.00 0.00 3.91
100 101 5.527582 AGTTGTCATACCGATTAATCCTTGC 59.472 40.000 9.87 1.35 0.00 4.01
101 102 6.761242 TCAGTTGTCATACCGATTAATCCTTG 59.239 38.462 9.87 1.82 0.00 3.61
102 103 6.884832 TCAGTTGTCATACCGATTAATCCTT 58.115 36.000 9.87 0.00 0.00 3.36
103 104 6.479972 TCAGTTGTCATACCGATTAATCCT 57.520 37.500 9.87 0.00 0.00 3.24
104 105 7.730364 AATCAGTTGTCATACCGATTAATCC 57.270 36.000 9.87 0.00 0.00 3.01
107 108 8.974408 CGATTAATCAGTTGTCATACCGATTAA 58.026 33.333 15.57 13.22 39.67 1.40
108 109 7.597369 CCGATTAATCAGTTGTCATACCGATTA 59.403 37.037 15.57 0.00 30.16 1.75
109 110 6.423905 CCGATTAATCAGTTGTCATACCGATT 59.576 38.462 15.57 0.00 31.82 3.34
110 111 5.926542 CCGATTAATCAGTTGTCATACCGAT 59.073 40.000 15.57 0.00 0.00 4.18
111 112 5.163488 ACCGATTAATCAGTTGTCATACCGA 60.163 40.000 15.57 0.00 0.00 4.69
112 113 5.047847 ACCGATTAATCAGTTGTCATACCG 58.952 41.667 15.57 0.00 0.00 4.02
113 114 6.281405 AGACCGATTAATCAGTTGTCATACC 58.719 40.000 15.57 0.00 0.00 2.73
114 115 8.753175 GTTAGACCGATTAATCAGTTGTCATAC 58.247 37.037 15.57 11.97 0.00 2.39
115 116 8.692710 AGTTAGACCGATTAATCAGTTGTCATA 58.307 33.333 15.57 7.46 0.00 2.15
116 117 7.492669 CAGTTAGACCGATTAATCAGTTGTCAT 59.507 37.037 15.57 8.18 0.00 3.06
117 118 6.811665 CAGTTAGACCGATTAATCAGTTGTCA 59.188 38.462 15.57 5.01 0.00 3.58
118 119 6.255887 CCAGTTAGACCGATTAATCAGTTGTC 59.744 42.308 15.57 13.93 0.00 3.18
119 120 6.106673 CCAGTTAGACCGATTAATCAGTTGT 58.893 40.000 15.57 6.47 0.00 3.32
120 121 6.106673 ACCAGTTAGACCGATTAATCAGTTG 58.893 40.000 15.57 5.14 0.00 3.16
121 122 6.070995 TGACCAGTTAGACCGATTAATCAGTT 60.071 38.462 15.57 4.53 0.00 3.16
122 123 5.421056 TGACCAGTTAGACCGATTAATCAGT 59.579 40.000 15.57 10.07 0.00 3.41
123 124 5.902681 TGACCAGTTAGACCGATTAATCAG 58.097 41.667 15.57 6.70 0.00 2.90
124 125 5.925506 TGACCAGTTAGACCGATTAATCA 57.074 39.130 15.57 0.00 0.00 2.57
125 126 7.787725 AATTGACCAGTTAGACCGATTAATC 57.212 36.000 5.30 5.30 0.00 1.75
126 127 9.847224 ATTAATTGACCAGTTAGACCGATTAAT 57.153 29.630 0.00 0.00 32.85 1.40
127 128 9.104965 CATTAATTGACCAGTTAGACCGATTAA 57.895 33.333 0.00 0.00 31.53 1.40
128 129 7.713507 CCATTAATTGACCAGTTAGACCGATTA 59.286 37.037 0.00 0.00 0.00 1.75
129 130 6.542370 CCATTAATTGACCAGTTAGACCGATT 59.458 38.462 0.00 0.00 0.00 3.34
130 131 6.055588 CCATTAATTGACCAGTTAGACCGAT 58.944 40.000 0.00 0.00 0.00 4.18
131 132 5.424757 CCATTAATTGACCAGTTAGACCGA 58.575 41.667 0.00 0.00 0.00 4.69
132 133 4.574828 CCCATTAATTGACCAGTTAGACCG 59.425 45.833 0.00 0.00 0.00 4.79
133 134 4.338400 GCCCATTAATTGACCAGTTAGACC 59.662 45.833 0.00 0.00 0.00 3.85
134 135 5.193679 AGCCCATTAATTGACCAGTTAGAC 58.806 41.667 0.00 0.00 0.00 2.59
135 136 5.450818 AGCCCATTAATTGACCAGTTAGA 57.549 39.130 0.00 0.00 0.00 2.10
136 137 5.652014 TCAAGCCCATTAATTGACCAGTTAG 59.348 40.000 0.00 0.00 0.00 2.34
137 138 5.417580 GTCAAGCCCATTAATTGACCAGTTA 59.582 40.000 7.39 0.00 44.45 2.24
138 139 4.220602 GTCAAGCCCATTAATTGACCAGTT 59.779 41.667 7.39 0.00 44.45 3.16
139 140 3.763897 GTCAAGCCCATTAATTGACCAGT 59.236 43.478 7.39 0.00 44.45 4.00
140 141 4.376340 GTCAAGCCCATTAATTGACCAG 57.624 45.455 7.39 0.00 44.45 4.00
144 145 5.999205 AACATGTCAAGCCCATTAATTGA 57.001 34.783 0.00 0.00 0.00 2.57
145 146 6.253298 CGTTAACATGTCAAGCCCATTAATTG 59.747 38.462 6.39 0.00 0.00 2.32
146 147 6.329496 CGTTAACATGTCAAGCCCATTAATT 58.671 36.000 6.39 0.00 0.00 1.40
147 148 5.678616 GCGTTAACATGTCAAGCCCATTAAT 60.679 40.000 6.39 0.00 0.00 1.40
148 149 4.380023 GCGTTAACATGTCAAGCCCATTAA 60.380 41.667 6.39 0.00 0.00 1.40
149 150 3.127895 GCGTTAACATGTCAAGCCCATTA 59.872 43.478 6.39 0.00 0.00 1.90
150 151 2.094752 GCGTTAACATGTCAAGCCCATT 60.095 45.455 6.39 0.00 0.00 3.16
151 152 1.472480 GCGTTAACATGTCAAGCCCAT 59.528 47.619 6.39 0.00 0.00 4.00
152 153 0.878416 GCGTTAACATGTCAAGCCCA 59.122 50.000 6.39 0.00 0.00 5.36
153 154 0.179200 CGCGTTAACATGTCAAGCCC 60.179 55.000 6.39 0.00 0.00 5.19
154 155 0.793861 TCGCGTTAACATGTCAAGCC 59.206 50.000 5.77 0.00 0.00 4.35
155 156 1.782023 CGTCGCGTTAACATGTCAAGC 60.782 52.381 5.77 2.20 0.00 4.01
156 157 1.717113 TCGTCGCGTTAACATGTCAAG 59.283 47.619 5.77 0.00 0.00 3.02
157 158 1.768510 TCGTCGCGTTAACATGTCAA 58.231 45.000 5.77 0.00 0.00 3.18
158 159 1.768510 TTCGTCGCGTTAACATGTCA 58.231 45.000 5.77 0.00 0.00 3.58
159 160 4.027132 ACATATTCGTCGCGTTAACATGTC 60.027 41.667 5.77 0.00 0.00 3.06
160 161 3.861113 ACATATTCGTCGCGTTAACATGT 59.139 39.130 5.77 7.41 0.00 3.21
161 162 4.193380 CACATATTCGTCGCGTTAACATG 58.807 43.478 5.77 6.77 0.00 3.21
162 163 3.861113 ACACATATTCGTCGCGTTAACAT 59.139 39.130 5.77 0.00 0.00 2.71
163 164 3.244156 ACACATATTCGTCGCGTTAACA 58.756 40.909 5.77 0.00 0.00 2.41
164 165 3.894351 ACACATATTCGTCGCGTTAAC 57.106 42.857 5.77 0.00 0.00 2.01
165 166 6.572153 AATAACACATATTCGTCGCGTTAA 57.428 33.333 5.77 0.00 27.47 2.01
166 167 6.189041 GAATAACACATATTCGTCGCGTTA 57.811 37.500 5.77 0.00 40.28 3.18
167 168 5.062109 GAATAACACATATTCGTCGCGTT 57.938 39.130 5.77 0.00 40.28 4.84
168 169 4.687458 GAATAACACATATTCGTCGCGT 57.313 40.909 5.77 0.00 40.28 6.01
175 176 5.521010 TGACCGAACCGAATAACACATATTC 59.479 40.000 0.00 0.00 44.32 1.75
176 177 5.421277 TGACCGAACCGAATAACACATATT 58.579 37.500 0.00 0.00 36.91 1.28
177 178 5.013568 TGACCGAACCGAATAACACATAT 57.986 39.130 0.00 0.00 0.00 1.78
178 179 4.453177 TGACCGAACCGAATAACACATA 57.547 40.909 0.00 0.00 0.00 2.29
179 180 3.322211 TGACCGAACCGAATAACACAT 57.678 42.857 0.00 0.00 0.00 3.21
180 181 2.816204 TGACCGAACCGAATAACACA 57.184 45.000 0.00 0.00 0.00 3.72
181 182 2.222953 GCATGACCGAACCGAATAACAC 60.223 50.000 0.00 0.00 0.00 3.32
182 183 2.004017 GCATGACCGAACCGAATAACA 58.996 47.619 0.00 0.00 0.00 2.41
183 184 2.277084 AGCATGACCGAACCGAATAAC 58.723 47.619 0.00 0.00 0.00 1.89
184 185 2.684001 AGCATGACCGAACCGAATAA 57.316 45.000 0.00 0.00 0.00 1.40
185 186 3.319689 TCATAGCATGACCGAACCGAATA 59.680 43.478 0.00 0.00 33.59 1.75
186 187 2.102420 TCATAGCATGACCGAACCGAAT 59.898 45.455 0.00 0.00 33.59 3.34
187 188 1.478916 TCATAGCATGACCGAACCGAA 59.521 47.619 0.00 0.00 33.59 4.30
188 189 1.067060 CTCATAGCATGACCGAACCGA 59.933 52.381 0.00 0.00 35.06 4.69
189 190 1.202417 ACTCATAGCATGACCGAACCG 60.202 52.381 0.00 0.00 35.06 4.44
190 191 2.604046 ACTCATAGCATGACCGAACC 57.396 50.000 0.00 0.00 35.06 3.62
202 203 7.437748 ACAGGCTAGTTAATTGCTACTCATAG 58.562 38.462 0.00 0.00 0.00 2.23
203 204 7.361457 ACAGGCTAGTTAATTGCTACTCATA 57.639 36.000 0.00 0.00 0.00 2.15
204 205 6.240549 ACAGGCTAGTTAATTGCTACTCAT 57.759 37.500 0.00 0.00 0.00 2.90
205 206 5.677319 ACAGGCTAGTTAATTGCTACTCA 57.323 39.130 0.00 0.00 0.00 3.41
206 207 7.764901 AGTTAACAGGCTAGTTAATTGCTACTC 59.235 37.037 18.49 8.66 43.49 2.59
207 208 7.549488 CAGTTAACAGGCTAGTTAATTGCTACT 59.451 37.037 20.48 13.05 43.49 2.57
208 209 7.548075 TCAGTTAACAGGCTAGTTAATTGCTAC 59.452 37.037 23.80 13.83 44.52 3.58
209 210 7.617225 TCAGTTAACAGGCTAGTTAATTGCTA 58.383 34.615 23.80 14.41 44.52 3.49
210 211 6.472887 TCAGTTAACAGGCTAGTTAATTGCT 58.527 36.000 23.80 15.39 44.52 3.91
211 212 6.737254 TCAGTTAACAGGCTAGTTAATTGC 57.263 37.500 23.80 14.17 44.52 3.56
232 233 8.947055 TGTTCGAGAATTCATCTGATTAATCA 57.053 30.769 17.07 17.07 38.96 2.57
233 234 9.039870 ACTGTTCGAGAATTCATCTGATTAATC 57.960 33.333 8.44 8.60 38.96 1.75
234 235 8.824781 CACTGTTCGAGAATTCATCTGATTAAT 58.175 33.333 8.44 0.00 38.96 1.40
235 236 7.819415 ACACTGTTCGAGAATTCATCTGATTAA 59.181 33.333 8.44 0.00 38.96 1.40
236 237 7.323420 ACACTGTTCGAGAATTCATCTGATTA 58.677 34.615 8.44 0.00 38.96 1.75
237 238 6.169094 ACACTGTTCGAGAATTCATCTGATT 58.831 36.000 8.44 0.00 38.96 2.57
238 239 5.728471 ACACTGTTCGAGAATTCATCTGAT 58.272 37.500 8.44 0.00 38.96 2.90
239 240 5.139435 ACACTGTTCGAGAATTCATCTGA 57.861 39.130 8.44 0.00 38.96 3.27
240 241 5.852738 AACACTGTTCGAGAATTCATCTG 57.147 39.130 8.44 0.00 38.96 2.90
241 242 8.553459 AAATAACACTGTTCGAGAATTCATCT 57.447 30.769 8.44 0.00 42.61 2.90
242 243 9.267096 GAAAATAACACTGTTCGAGAATTCATC 57.733 33.333 8.44 1.82 0.00 2.92
243 244 8.783093 TGAAAATAACACTGTTCGAGAATTCAT 58.217 29.630 8.44 0.00 0.00 2.57
244 245 8.067784 GTGAAAATAACACTGTTCGAGAATTCA 58.932 33.333 8.44 0.73 35.66 2.57
245 246 8.283291 AGTGAAAATAACACTGTTCGAGAATTC 58.717 33.333 0.00 0.00 45.19 2.17
246 247 8.154649 AGTGAAAATAACACTGTTCGAGAATT 57.845 30.769 0.00 0.00 45.19 2.17
247 248 7.730364 AGTGAAAATAACACTGTTCGAGAAT 57.270 32.000 0.00 0.00 45.19 2.40
248 249 7.494625 AGAAGTGAAAATAACACTGTTCGAGAA 59.505 33.333 0.00 0.00 46.01 2.87
249 250 6.984474 AGAAGTGAAAATAACACTGTTCGAGA 59.016 34.615 0.00 0.00 46.01 4.04
250 251 7.178712 AGAAGTGAAAATAACACTGTTCGAG 57.821 36.000 0.00 0.00 46.01 4.04
251 252 7.548196 AAGAAGTGAAAATAACACTGTTCGA 57.452 32.000 0.00 0.00 46.01 3.71
252 253 8.614994 AAAAGAAGTGAAAATAACACTGTTCG 57.385 30.769 0.00 0.00 46.01 3.95
253 254 9.567848 TGAAAAGAAGTGAAAATAACACTGTTC 57.432 29.630 0.00 0.00 46.01 3.18
254 255 9.353999 GTGAAAAGAAGTGAAAATAACACTGTT 57.646 29.630 0.00 0.00 46.01 3.16
255 256 7.973944 GGTGAAAAGAAGTGAAAATAACACTGT 59.026 33.333 0.00 0.00 46.01 3.55
256 257 7.973388 TGGTGAAAAGAAGTGAAAATAACACTG 59.027 33.333 0.00 0.00 46.01 3.66
260 261 8.755018 CATGTGGTGAAAAGAAGTGAAAATAAC 58.245 33.333 0.00 0.00 0.00 1.89
277 278 3.220674 TGGAATGTGAACATGTGGTGA 57.779 42.857 0.00 0.00 36.56 4.02
282 283 4.724399 TGTACCTTGGAATGTGAACATGT 58.276 39.130 0.00 0.00 36.56 3.21
355 356 4.892345 ACGGAGGGAGTAAATAGTAGGAAC 59.108 45.833 0.00 0.00 0.00 3.62
391 393 2.668212 TGTTTTGGCTCTCGGGCG 60.668 61.111 0.00 0.00 44.11 6.13
412 414 4.810191 AGAAGAGTGTATGACTTGGTCC 57.190 45.455 0.00 0.00 33.83 4.46
448 450 3.378112 TGCCTCTAAATTACTGTGCATGC 59.622 43.478 11.82 11.82 0.00 4.06
479 481 4.273235 CGCATGCATCCACTTAAATCACTA 59.727 41.667 19.57 0.00 0.00 2.74
528 530 4.033702 GGGTAGTCACTTAAATTACTGCGC 59.966 45.833 0.00 0.00 32.33 6.09
534 555 7.081857 ACAACTGGGGTAGTCACTTAAATTA 57.918 36.000 0.00 0.00 39.18 1.40
535 556 5.948842 ACAACTGGGGTAGTCACTTAAATT 58.051 37.500 0.00 0.00 39.18 1.82
553 574 2.094752 GCAACCAACACAGTGAACAACT 60.095 45.455 7.81 0.00 40.93 3.16
554 575 2.258755 GCAACCAACACAGTGAACAAC 58.741 47.619 7.81 0.00 0.00 3.32
555 576 1.889170 TGCAACCAACACAGTGAACAA 59.111 42.857 7.81 0.00 0.00 2.83
556 577 1.539157 TGCAACCAACACAGTGAACA 58.461 45.000 7.81 0.00 0.00 3.18
557 578 2.645730 TTGCAACCAACACAGTGAAC 57.354 45.000 7.81 0.00 0.00 3.18
564 585 1.257675 GCGTTTCATTGCAACCAACAC 59.742 47.619 0.00 0.00 32.95 3.32
573 594 0.439600 GGTTGCATGCGTTTCATTGC 59.560 50.000 14.09 0.00 31.79 3.56
661 682 5.235850 TGGTTGCTAGTGATTTAAGTGGA 57.764 39.130 0.00 0.00 0.00 4.02
731 752 2.169832 AACACGGAGACCAAGTCATG 57.830 50.000 0.00 0.00 34.60 3.07
766 1612 0.906282 TCCCTCCGTCTGGGTTTACC 60.906 60.000 0.00 0.00 44.84 2.85
767 1613 0.535797 CTCCCTCCGTCTGGGTTTAC 59.464 60.000 0.00 0.00 44.84 2.01
775 1621 4.246712 TCATTTAGTACTCCCTCCGTCT 57.753 45.455 0.00 0.00 0.00 4.18
812 1665 8.593945 TGGGTGATATCTTGCTAGAAATTTTT 57.406 30.769 0.99 0.00 33.20 1.94
816 1669 5.709164 GCATGGGTGATATCTTGCTAGAAAT 59.291 40.000 0.99 0.00 33.20 2.17
843 1696 6.536582 TGCTCAGTTATCTTCATGCTTAAGTC 59.463 38.462 4.02 0.00 0.00 3.01
862 1715 2.646930 TGTGCTATGGGAAATGCTCAG 58.353 47.619 0.00 0.00 0.00 3.35
883 1736 9.722317 ACCTAGGCTCTCTATTTATATAAGCAT 57.278 33.333 9.30 0.00 0.00 3.79
951 1806 0.970640 TACTTACGCAGGCAGGTGAA 59.029 50.000 0.00 0.00 0.00 3.18
1003 1884 0.173708 GCAACCGCTCTAGCACTAGT 59.826 55.000 2.44 0.00 42.21 2.57
1036 1917 5.986004 AAAGAGACCGTCACAAAAACTAG 57.014 39.130 0.40 0.00 0.00 2.57
1521 2411 4.023980 TCTATTTGTCCATCGACCAGACT 58.976 43.478 11.32 0.00 38.32 3.24
1522 2412 4.386867 TCTATTTGTCCATCGACCAGAC 57.613 45.455 0.00 0.00 38.32 3.51
1584 2492 6.281848 TCGATTTTATTAGTTGCATCGGAC 57.718 37.500 0.00 0.00 35.37 4.79
1793 3022 7.498900 TCGTATGATACAAGCTTTTCATTCCAT 59.501 33.333 17.03 8.70 31.59 3.41
1892 3122 1.354101 ACCATTCCGTGTAACTGGGA 58.646 50.000 0.00 0.00 32.58 4.37
1954 3185 1.018148 CAACCAGTGGCGTGTAAACA 58.982 50.000 9.78 0.00 0.00 2.83
2347 5681 1.227118 CCACACCCACGGCAAAAAC 60.227 57.895 0.00 0.00 0.00 2.43
2354 5688 4.697756 ATCGCACCACACCCACGG 62.698 66.667 0.00 0.00 0.00 4.94
2360 5694 2.616330 CCACACCATCGCACCACAC 61.616 63.158 0.00 0.00 0.00 3.82
2419 5753 9.261035 TGGGAATTTATGTTTGCTCCTTTTATA 57.739 29.630 0.00 0.00 0.00 0.98
2426 5841 6.479990 GCTTTATGGGAATTTATGTTTGCTCC 59.520 38.462 0.00 0.00 0.00 4.70
2427 5842 6.479990 GGCTTTATGGGAATTTATGTTTGCTC 59.520 38.462 0.00 0.00 0.00 4.26
2467 5883 6.070995 GGATGATTCAGGTTATCCCGTGTATA 60.071 42.308 0.00 0.00 38.74 1.47
2468 5884 5.280011 GGATGATTCAGGTTATCCCGTGTAT 60.280 44.000 0.00 0.00 38.74 2.29


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

AutoCloner maintained by Alex Coulton.