Multiple sequence alignment - TraesCS6D01G291800

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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 TraesCS6D01G291800 chr6D 100.000 5014 0 0 1 5014 402354411 402349398 0.000000e+00 9260
1 TraesCS6D01G291800 chr6D 85.912 362 47 3 1125 1485 78752726 78753084 2.830000e-102 383
2 TraesCS6D01G291800 chr6B 92.096 2657 104 52 2415 5014 603146528 603143921 0.000000e+00 3646
3 TraesCS6D01G291800 chr6B 89.556 1350 70 27 217 1548 603148770 603147474 0.000000e+00 1646
4 TraesCS6D01G291800 chr6B 88.270 844 35 31 1571 2398 603147313 603146518 0.000000e+00 952
5 TraesCS6D01G291800 chr6B 85.912 362 47 3 1125 1485 151372525 151372883 2.830000e-102 383
6 TraesCS6D01G291800 chr6B 88.152 211 22 2 2013 2220 151373017 151373227 1.080000e-61 248
7 TraesCS6D01G291800 chr6B 97.260 73 2 0 2 74 603149175 603149103 1.900000e-24 124
8 TraesCS6D01G291800 chr6A 92.188 1869 82 28 2412 4252 549044282 549042450 0.000000e+00 2584
9 TraesCS6D01G291800 chr6A 86.978 1797 82 68 157 1921 549046435 549044759 0.000000e+00 1882
10 TraesCS6D01G291800 chr6A 92.727 495 16 12 1907 2398 549044746 549044269 0.000000e+00 697
11 TraesCS6D01G291800 chr6A 95.122 287 13 1 4729 5014 549042049 549041763 7.650000e-123 451
12 TraesCS6D01G291800 chr6A 87.861 346 40 2 1141 1485 94226999 94227343 6.040000e-109 405
13 TraesCS6D01G291800 chr6A 88.152 211 22 2 2013 2220 94227468 94227678 1.080000e-61 248
14 TraesCS6D01G291800 chr6A 95.789 95 1 2 2 96 549046522 549046431 3.130000e-32 150
15 TraesCS6D01G291800 chr7D 84.194 620 73 15 3358 3963 159738424 159739032 3.370000e-161 579
16 TraesCS6D01G291800 chr7D 84.840 343 46 6 1146 1485 93033803 93033464 1.730000e-89 340
17 TraesCS6D01G291800 chr7D 89.020 255 28 0 2963 3217 159738124 159738378 2.910000e-82 316
18 TraesCS6D01G291800 chr7D 92.233 206 16 0 2014 2219 159737274 159737479 4.910000e-75 292
19 TraesCS6D01G291800 chr7A 82.727 660 83 19 3318 3960 158396998 158397643 4.380000e-155 558
20 TraesCS6D01G291800 chr7A 88.031 259 30 1 2959 3217 158396735 158396992 6.310000e-79 305
21 TraesCS6D01G291800 chr7A 91.748 206 17 0 2014 2219 158395916 158396121 2.280000e-73 287
22 TraesCS6D01G291800 chr7A 74.843 636 125 30 3311 3935 96050703 96050092 6.440000e-64 255
23 TraesCS6D01G291800 chr7A 74.688 640 119 35 3311 3935 95236684 95236073 1.390000e-60 244
24 TraesCS6D01G291800 chr7A 74.531 640 120 35 3311 3935 95229509 95228898 6.490000e-59 239
25 TraesCS6D01G291800 chr7B 83.717 608 77 16 3358 3954 120588782 120589378 5.670000e-154 555
26 TraesCS6D01G291800 chr7B 89.804 255 26 0 2963 3217 120588482 120588736 1.350000e-85 327
27 TraesCS6D01G291800 chr7B 90.777 206 19 0 2014 2219 120587634 120587839 4.940000e-70 276
28 TraesCS6D01G291800 chr5A 86.236 356 43 6 1146 1498 410203609 410203257 1.020000e-101 381
29 TraesCS6D01G291800 chr5A 76.290 620 107 28 3360 3966 410196270 410195678 1.370000e-75 294
30 TraesCS6D01G291800 chr5A 85.874 269 36 2 2959 3226 410202817 410202550 8.220000e-73 285
31 TraesCS6D01G291800 chr5D 85.593 354 45 6 1146 1496 315485497 315485147 2.850000e-97 366
32 TraesCS6D01G291800 chr5D 85.130 269 38 2 2959 3226 315484703 315484436 1.780000e-69 274
33 TraesCS6D01G291800 chr5D 86.957 207 27 0 2014 2220 315484973 315484767 3.020000e-57 233
34 TraesCS6D01G291800 chr5B 85.429 350 44 7 1150 1496 363669765 363669420 1.720000e-94 357
35 TraesCS6D01G291800 chr5B 86.957 207 27 0 2014 2220 363669246 363669040 3.020000e-57 233
36 TraesCS6D01G291800 chrUn 74.688 640 119 35 3311 3935 82677692 82678303 1.390000e-60 244


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 TraesCS6D01G291800 chr6D 402349398 402354411 5013 True 9260.000000 9260 100.000000 1 5014 1 chr6D.!!$R1 5013
1 TraesCS6D01G291800 chr6B 603143921 603149175 5254 True 1592.000000 3646 91.795500 2 5014 4 chr6B.!!$R1 5012
2 TraesCS6D01G291800 chr6B 151372525 151373227 702 False 315.500000 383 87.032000 1125 2220 2 chr6B.!!$F1 1095
3 TraesCS6D01G291800 chr6A 549041763 549046522 4759 True 1152.800000 2584 92.560800 2 5014 5 chr6A.!!$R1 5012
4 TraesCS6D01G291800 chr6A 94226999 94227678 679 False 326.500000 405 88.006500 1141 2220 2 chr6A.!!$F1 1079
5 TraesCS6D01G291800 chr7D 159737274 159739032 1758 False 395.666667 579 88.482333 2014 3963 3 chr7D.!!$F1 1949
6 TraesCS6D01G291800 chr7A 158395916 158397643 1727 False 383.333333 558 87.502000 2014 3960 3 chr7A.!!$F1 1946
7 TraesCS6D01G291800 chr7A 96050092 96050703 611 True 255.000000 255 74.843000 3311 3935 1 chr7A.!!$R3 624
8 TraesCS6D01G291800 chr7A 95236073 95236684 611 True 244.000000 244 74.688000 3311 3935 1 chr7A.!!$R2 624
9 TraesCS6D01G291800 chr7A 95228898 95229509 611 True 239.000000 239 74.531000 3311 3935 1 chr7A.!!$R1 624
10 TraesCS6D01G291800 chr7B 120587634 120589378 1744 False 386.000000 555 88.099333 2014 3954 3 chr7B.!!$F1 1940
11 TraesCS6D01G291800 chr5A 410202550 410203609 1059 True 333.000000 381 86.055000 1146 3226 2 chr5A.!!$R2 2080
12 TraesCS6D01G291800 chr5A 410195678 410196270 592 True 294.000000 294 76.290000 3360 3966 1 chr5A.!!$R1 606
13 TraesCS6D01G291800 chr5D 315484436 315485497 1061 True 291.000000 366 85.893333 1146 3226 3 chr5D.!!$R1 2080
14 TraesCS6D01G291800 chr5B 363669040 363669765 725 True 295.000000 357 86.193000 1150 2220 2 chr5B.!!$R1 1070
15 TraesCS6D01G291800 chrUn 82677692 82678303 611 False 244.000000 244 74.688000 3311 3935 1 chrUn.!!$F1 624

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
410 713 0.031043 CCAACCGACTCACGTGTACA 59.969 55.0 16.51 0.00 40.78 2.90 F
532 848 0.034574 CCCAACCATCCCAATCACGA 60.035 55.0 0.00 0.00 0.00 4.35 F
1567 1914 0.839853 GATCCATCCCCTGGCTAGCT 60.840 60.0 15.72 0.00 45.52 3.32 F
2373 2995 0.095762 GCGTACCGGATTTTGGAACG 59.904 55.0 9.46 5.77 0.00 3.95 F
3234 4187 0.605319 CCGCAAGAGTAAGCCCAACA 60.605 55.0 0.00 0.00 43.02 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1602 2103 0.103755 TCGGTCTCATCTCATGCTGC 59.896 55.0 0.00 0.00 0.00 5.25 R
2227 2783 0.379669 GTGTATGCACATGAGGCAGC 59.620 55.0 18.59 14.65 45.68 5.25 R
3238 4191 0.031314 CCGATCATAGTGCGCTCTGT 59.969 55.0 21.59 12.64 0.00 3.41 R
4000 5014 0.179056 ATCCATTTACACCTCGGCCG 60.179 55.0 22.12 22.12 0.00 6.13 R
4320 5355 0.512518 CGTGCTTTGCTGTTGATCGA 59.487 50.0 0.00 0.00 0.00 3.59 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
72 73 3.514645 CAACCACTTATAACTACCGCGT 58.485 45.455 4.92 0.00 0.00 6.01
73 74 4.439974 CCAACCACTTATAACTACCGCGTA 60.440 45.833 4.92 0.00 0.00 4.42
74 75 4.981806 ACCACTTATAACTACCGCGTAA 57.018 40.909 4.92 0.00 0.00 3.18
75 76 4.672409 ACCACTTATAACTACCGCGTAAC 58.328 43.478 4.92 0.00 0.00 2.50
76 77 3.725740 CCACTTATAACTACCGCGTAACG 59.274 47.826 4.92 0.00 43.15 3.18
77 78 4.342772 CACTTATAACTACCGCGTAACGT 58.657 43.478 4.92 0.00 41.42 3.99
78 79 4.202959 CACTTATAACTACCGCGTAACGTG 59.797 45.833 4.92 0.00 41.42 4.49
79 80 2.919666 ATAACTACCGCGTAACGTGT 57.080 45.000 4.92 0.00 41.42 4.49
80 81 5.064198 ACTTATAACTACCGCGTAACGTGTA 59.936 40.000 4.92 0.00 41.42 2.90
81 82 1.963747 AACTACCGCGTAACGTGTAC 58.036 50.000 4.92 0.00 41.42 2.90
82 83 0.168128 ACTACCGCGTAACGTGTACC 59.832 55.000 4.92 0.00 41.42 3.34
83 84 0.857311 CTACCGCGTAACGTGTACCG 60.857 60.000 4.92 2.71 41.42 4.02
84 85 2.842588 TACCGCGTAACGTGTACCGC 62.843 60.000 4.92 10.25 41.42 5.68
85 86 2.800331 CGCGTAACGTGTACCGCA 60.800 61.111 17.46 0.00 46.02 5.69
86 87 2.153945 CGCGTAACGTGTACCGCAT 61.154 57.895 17.46 1.73 46.02 4.73
87 88 1.676438 CGCGTAACGTGTACCGCATT 61.676 55.000 17.46 0.53 46.02 3.56
88 89 1.267365 GCGTAACGTGTACCGCATTA 58.733 50.000 14.03 0.00 45.12 1.90
89 90 1.854126 GCGTAACGTGTACCGCATTAT 59.146 47.619 14.03 0.00 45.12 1.28
90 91 2.097733 GCGTAACGTGTACCGCATTATC 60.098 50.000 14.03 0.00 45.12 1.75
91 92 3.107407 CGTAACGTGTACCGCATTATCA 58.893 45.455 0.00 0.00 41.42 2.15
92 93 3.061666 CGTAACGTGTACCGCATTATCAC 60.062 47.826 0.00 0.00 41.42 3.06
93 94 2.953466 ACGTGTACCGCATTATCACT 57.047 45.000 0.00 0.00 41.42 3.41
94 95 4.374843 AACGTGTACCGCATTATCACTA 57.625 40.909 0.00 0.00 41.42 2.74
95 96 4.374843 ACGTGTACCGCATTATCACTAA 57.625 40.909 0.00 0.00 41.42 2.24
96 97 4.940463 ACGTGTACCGCATTATCACTAAT 58.060 39.130 0.00 0.00 41.42 1.73
97 98 6.075762 ACGTGTACCGCATTATCACTAATA 57.924 37.500 0.00 0.00 41.42 0.98
98 99 6.147581 ACGTGTACCGCATTATCACTAATAG 58.852 40.000 0.00 0.00 41.42 1.73
99 100 6.147581 CGTGTACCGCATTATCACTAATAGT 58.852 40.000 0.00 0.00 0.00 2.12
100 101 7.041167 ACGTGTACCGCATTATCACTAATAGTA 60.041 37.037 0.00 0.00 41.42 1.82
101 102 7.966753 CGTGTACCGCATTATCACTAATAGTAT 59.033 37.037 0.00 0.00 0.00 2.12
102 103 9.073368 GTGTACCGCATTATCACTAATAGTATG 57.927 37.037 0.00 0.00 0.00 2.39
103 104 8.799367 TGTACCGCATTATCACTAATAGTATGT 58.201 33.333 0.00 0.00 0.00 2.29
104 105 9.635520 GTACCGCATTATCACTAATAGTATGTT 57.364 33.333 0.00 0.00 0.00 2.71
106 107 9.555727 ACCGCATTATCACTAATAGTATGTTTT 57.444 29.630 0.00 0.00 0.00 2.43
121 122 6.799512 AGTATGTTTTTCATATTGCAGAGGC 58.200 36.000 0.00 0.00 40.54 4.70
122 123 4.454728 TGTTTTTCATATTGCAGAGGCC 57.545 40.909 0.00 0.00 40.13 5.19
123 124 3.195396 TGTTTTTCATATTGCAGAGGCCC 59.805 43.478 0.00 0.00 40.13 5.80
124 125 1.679139 TTTCATATTGCAGAGGCCCG 58.321 50.000 0.00 0.00 40.13 6.13
125 126 0.179020 TTCATATTGCAGAGGCCCGG 60.179 55.000 0.00 0.00 40.13 5.73
126 127 1.601759 CATATTGCAGAGGCCCGGG 60.602 63.158 19.09 19.09 40.13 5.73
127 128 2.833913 ATATTGCAGAGGCCCGGGG 61.834 63.158 25.28 9.31 40.13 5.73
132 133 3.012722 CAGAGGCCCGGGGGTTTA 61.013 66.667 25.28 0.00 37.65 2.01
133 134 2.204182 AGAGGCCCGGGGGTTTAA 60.204 61.111 25.28 0.00 37.65 1.52
134 135 1.621514 AGAGGCCCGGGGGTTTAAT 60.622 57.895 25.28 0.00 37.65 1.40
135 136 1.152819 GAGGCCCGGGGGTTTAATC 60.153 63.158 25.28 1.53 37.65 1.75
136 137 1.621514 AGGCCCGGGGGTTTAATCT 60.622 57.895 25.28 0.00 37.65 2.40
137 138 1.152819 GGCCCGGGGGTTTAATCTC 60.153 63.158 25.28 0.00 37.65 2.75
138 139 1.152819 GCCCGGGGGTTTAATCTCC 60.153 63.158 25.28 0.00 37.65 3.71
139 140 1.642513 GCCCGGGGGTTTAATCTCCT 61.643 60.000 25.28 0.00 37.65 3.69
140 141 0.924090 CCCGGGGGTTTAATCTCCTT 59.076 55.000 14.71 0.00 0.00 3.36
141 142 1.286849 CCCGGGGGTTTAATCTCCTTT 59.713 52.381 14.71 0.00 0.00 3.11
142 143 2.291996 CCCGGGGGTTTAATCTCCTTTT 60.292 50.000 14.71 0.00 0.00 2.27
143 144 3.021695 CCGGGGGTTTAATCTCCTTTTC 58.978 50.000 2.45 0.00 0.00 2.29
144 145 3.562609 CCGGGGGTTTAATCTCCTTTTCA 60.563 47.826 2.45 0.00 0.00 2.69
145 146 4.083565 CGGGGGTTTAATCTCCTTTTCAA 58.916 43.478 2.45 0.00 0.00 2.69
146 147 4.525100 CGGGGGTTTAATCTCCTTTTCAAA 59.475 41.667 2.45 0.00 0.00 2.69
147 148 5.011227 CGGGGGTTTAATCTCCTTTTCAAAA 59.989 40.000 2.45 0.00 0.00 2.44
148 149 6.228258 GGGGGTTTAATCTCCTTTTCAAAAC 58.772 40.000 2.45 0.00 0.00 2.43
149 150 6.183361 GGGGGTTTAATCTCCTTTTCAAAACA 60.183 38.462 2.45 0.00 0.00 2.83
150 151 7.276658 GGGGTTTAATCTCCTTTTCAAAACAA 58.723 34.615 0.00 0.00 0.00 2.83
151 152 7.771361 GGGGTTTAATCTCCTTTTCAAAACAAA 59.229 33.333 0.00 0.00 0.00 2.83
152 153 9.168451 GGGTTTAATCTCCTTTTCAAAACAAAA 57.832 29.630 0.00 0.00 0.00 2.44
181 203 1.616159 ATGTTTTTCCACGGGAGGTG 58.384 50.000 0.00 0.00 46.57 4.00
230 531 0.174845 TATTTGACCGACCGCCTGAG 59.825 55.000 0.00 0.00 0.00 3.35
286 589 0.517316 GAAAGCTGTTACAGGCCACG 59.483 55.000 14.63 0.00 31.21 4.94
410 713 0.031043 CCAACCGACTCACGTGTACA 59.969 55.000 16.51 0.00 40.78 2.90
470 782 1.001641 AAAATCTGCTCCGCTGCCT 60.002 52.632 0.00 0.00 0.00 4.75
471 783 1.028868 AAAATCTGCTCCGCTGCCTC 61.029 55.000 0.00 0.00 0.00 4.70
472 784 2.883267 AAATCTGCTCCGCTGCCTCC 62.883 60.000 0.00 0.00 0.00 4.30
523 839 0.114364 AGAACCCAACCCAACCATCC 59.886 55.000 0.00 0.00 0.00 3.51
529 845 1.552023 CCAACCCAACCATCCCAATCA 60.552 52.381 0.00 0.00 0.00 2.57
531 847 0.323360 ACCCAACCATCCCAATCACG 60.323 55.000 0.00 0.00 0.00 4.35
532 848 0.034574 CCCAACCATCCCAATCACGA 60.035 55.000 0.00 0.00 0.00 4.35
548 867 1.064952 CACGACCTCACCAAACAAACC 59.935 52.381 0.00 0.00 0.00 3.27
651 970 3.580604 CTTTCCTGCCTGCCTGCCT 62.581 63.158 0.00 0.00 0.00 4.75
652 971 3.873679 TTTCCTGCCTGCCTGCCTG 62.874 63.158 0.00 0.00 0.00 4.85
661 980 3.082701 GCCTGCCTGCTCCTCTCT 61.083 66.667 0.00 0.00 0.00 3.10
674 996 5.067273 TGCTCCTCTCTTGCTATCTACTAC 58.933 45.833 0.00 0.00 0.00 2.73
679 1001 5.938125 CCTCTCTTGCTATCTACTACCTCTC 59.062 48.000 0.00 0.00 0.00 3.20
844 1178 4.962122 CACAGCACACAACGGCGC 62.962 66.667 6.90 0.00 34.54 6.53
983 1324 0.889186 GGCACACCAACAATCCGAGT 60.889 55.000 0.00 0.00 35.26 4.18
1018 1359 2.374830 AATGAGATCAGGGAGCGCCG 62.375 60.000 2.29 0.00 33.83 6.46
1019 1360 4.959596 GAGATCAGGGAGCGCCGC 62.960 72.222 2.29 0.00 33.83 6.53
1053 1394 2.670592 TTGTCTCGACGGCTCGGA 60.671 61.111 0.00 1.66 40.58 4.55
1068 1409 3.730761 GGAGCCGTGTTGCTGCTG 61.731 66.667 0.00 0.00 45.22 4.41
1089 1436 2.510012 CTGCTTCTGATCGCGGCA 60.510 61.111 6.13 4.84 0.00 5.69
1090 1437 2.047370 TGCTTCTGATCGCGGCAA 60.047 55.556 6.13 0.00 0.00 4.52
1091 1438 2.301902 CTGCTTCTGATCGCGGCAAC 62.302 60.000 6.13 0.00 32.43 4.17
1326 1673 2.032681 GTCAAGTTCGGCCTGCCT 59.967 61.111 6.60 0.00 0.00 4.75
1376 1723 3.323136 CATGCTCGAGTACGGCGC 61.323 66.667 15.13 0.00 38.08 6.53
1492 1839 3.134127 GGGCCGAGGTACGTACGT 61.134 66.667 25.98 25.98 40.78 3.57
1548 1895 1.091771 GTGCGTCACCTCCATCCATG 61.092 60.000 0.00 0.00 0.00 3.66
1556 1903 1.991070 ACCTCCATCCATGATCCATCC 59.009 52.381 0.00 0.00 0.00 3.51
1559 1906 1.131970 TCCATCCATGATCCATCCCCT 60.132 52.381 0.00 0.00 0.00 4.79
1562 1909 1.076192 CCATGATCCATCCCCTGGC 59.924 63.158 0.00 0.00 45.52 4.85
1563 1910 1.432852 CCATGATCCATCCCCTGGCT 61.433 60.000 0.00 0.00 45.52 4.75
1564 1911 1.365293 CATGATCCATCCCCTGGCTA 58.635 55.000 0.00 0.00 45.52 3.93
1567 1914 0.839853 GATCCATCCCCTGGCTAGCT 60.840 60.000 15.72 0.00 45.52 3.32
1568 1915 0.839853 ATCCATCCCCTGGCTAGCTC 60.840 60.000 15.72 5.44 45.52 4.09
1569 1916 1.767672 CCATCCCCTGGCTAGCTCA 60.768 63.158 15.72 10.05 38.47 4.26
1602 2103 5.634896 TCAGATACGATCGATCATGACATG 58.365 41.667 24.34 9.28 0.00 3.21
1603 2104 4.264849 CAGATACGATCGATCATGACATGC 59.735 45.833 24.34 5.76 0.00 4.06
1604 2105 2.514205 ACGATCGATCATGACATGCA 57.486 45.000 24.34 0.00 0.00 3.96
1675 2176 2.346847 CAGCGATCGTTCCAAGAAAGAG 59.653 50.000 17.81 0.00 0.00 2.85
1681 2186 4.506886 TCGTTCCAAGAAAGAGAGAGAC 57.493 45.455 0.00 0.00 0.00 3.36
1702 2216 5.481473 AGACCAATTCAATTATGCACACCTT 59.519 36.000 0.00 0.00 0.00 3.50
1958 2508 3.501828 TGCATATGTTTCACAGCTTCGTT 59.498 39.130 4.29 0.00 0.00 3.85
1995 2548 1.409412 CAGAGCCGTCGGATTAATCG 58.591 55.000 17.49 5.35 0.00 3.34
2221 2777 2.746277 CCACGCCCAGCAGGTAAC 60.746 66.667 0.00 0.00 38.26 2.50
2225 2781 2.434331 GCCCAGCAGGTAACACCA 59.566 61.111 0.00 0.00 41.95 4.17
2227 2783 1.671054 CCCAGCAGGTAACACCACG 60.671 63.158 0.00 0.00 41.95 4.94
2228 2784 2.325082 CCAGCAGGTAACACCACGC 61.325 63.158 0.00 0.16 41.95 5.34
2229 2785 1.301716 CAGCAGGTAACACCACGCT 60.302 57.895 6.49 6.49 46.19 5.07
2230 2786 1.301716 AGCAGGTAACACCACGCTG 60.302 57.895 10.45 0.00 44.39 5.18
2234 2790 2.033194 GGTAACACCACGCTGCCTC 61.033 63.158 0.00 0.00 38.42 4.70
2235 2791 1.301401 GTAACACCACGCTGCCTCA 60.301 57.895 0.00 0.00 0.00 3.86
2236 2792 0.673644 GTAACACCACGCTGCCTCAT 60.674 55.000 0.00 0.00 0.00 2.90
2237 2793 0.673333 TAACACCACGCTGCCTCATG 60.673 55.000 0.00 0.00 0.00 3.07
2239 2795 2.359107 ACCACGCTGCCTCATGTG 60.359 61.111 0.00 0.00 0.00 3.21
2317 2923 5.409643 AATGAGAGAAAAATATCGGTGCG 57.590 39.130 0.00 0.00 0.00 5.34
2336 2958 1.852895 CGAGTTTGGAGCATAGCGTAC 59.147 52.381 0.00 0.00 0.00 3.67
2373 2995 0.095762 GCGTACCGGATTTTGGAACG 59.904 55.000 9.46 5.77 0.00 3.95
2397 3019 4.690122 AGCGTACGAATATTGGTAGCTTT 58.310 39.130 21.65 7.66 29.25 3.51
2456 3078 0.881118 CCGGTCTTTTCATGGGTGTG 59.119 55.000 0.00 0.00 0.00 3.82
2457 3079 1.544537 CCGGTCTTTTCATGGGTGTGA 60.545 52.381 0.00 0.00 0.00 3.58
2458 3080 2.436417 CGGTCTTTTCATGGGTGTGAT 58.564 47.619 0.00 0.00 0.00 3.06
2460 3082 3.374058 CGGTCTTTTCATGGGTGTGATAC 59.626 47.826 0.00 0.00 0.00 2.24
2461 3083 4.589908 GGTCTTTTCATGGGTGTGATACT 58.410 43.478 0.00 0.00 0.00 2.12
2462 3084 4.396166 GGTCTTTTCATGGGTGTGATACTG 59.604 45.833 0.00 0.00 0.00 2.74
2463 3085 5.003804 GTCTTTTCATGGGTGTGATACTGT 58.996 41.667 0.00 0.00 0.00 3.55
2464 3086 5.003160 TCTTTTCATGGGTGTGATACTGTG 58.997 41.667 0.00 0.00 0.00 3.66
2465 3087 4.632327 TTTCATGGGTGTGATACTGTGA 57.368 40.909 0.00 0.00 0.00 3.58
2466 3088 4.842531 TTCATGGGTGTGATACTGTGAT 57.157 40.909 0.00 0.00 0.00 3.06
2467 3089 5.948742 TTCATGGGTGTGATACTGTGATA 57.051 39.130 0.00 0.00 0.00 2.15
2890 3554 9.443323 GGGCTTTTTCTTAATTATTTTTGGCTA 57.557 29.630 0.00 0.00 0.00 3.93
3230 4183 3.195698 CGCCGCAAGAGTAAGCCC 61.196 66.667 0.00 0.00 43.02 5.19
3231 4184 2.046314 GCCGCAAGAGTAAGCCCA 60.046 61.111 0.00 0.00 43.02 5.36
3232 4185 1.674322 GCCGCAAGAGTAAGCCCAA 60.674 57.895 0.00 0.00 43.02 4.12
3233 4186 1.923227 GCCGCAAGAGTAAGCCCAAC 61.923 60.000 0.00 0.00 43.02 3.77
3234 4187 0.605319 CCGCAAGAGTAAGCCCAACA 60.605 55.000 0.00 0.00 43.02 3.33
3235 4188 1.453155 CGCAAGAGTAAGCCCAACAT 58.547 50.000 0.00 0.00 43.02 2.71
3237 4190 1.745653 GCAAGAGTAAGCCCAACATCC 59.254 52.381 0.00 0.00 0.00 3.51
3238 4191 2.879756 GCAAGAGTAAGCCCAACATCCA 60.880 50.000 0.00 0.00 0.00 3.41
3239 4192 2.749621 CAAGAGTAAGCCCAACATCCAC 59.250 50.000 0.00 0.00 0.00 4.02
3241 4194 2.026822 AGAGTAAGCCCAACATCCACAG 60.027 50.000 0.00 0.00 0.00 3.66
3242 4195 1.985159 AGTAAGCCCAACATCCACAGA 59.015 47.619 0.00 0.00 0.00 3.41
3243 4196 2.026822 AGTAAGCCCAACATCCACAGAG 60.027 50.000 0.00 0.00 0.00 3.35
3253 4206 1.114627 ATCCACAGAGCGCACTATGA 58.885 50.000 14.96 8.44 37.30 2.15
3255 4208 1.067669 TCCACAGAGCGCACTATGATC 59.932 52.381 14.96 0.00 37.30 2.92
3260 4213 1.280886 GAGCGCACTATGATCGGCAG 61.281 60.000 11.47 0.00 0.00 4.85
3261 4214 1.300156 GCGCACTATGATCGGCAGA 60.300 57.895 0.30 0.00 0.00 4.26
3262 4215 1.552348 GCGCACTATGATCGGCAGAC 61.552 60.000 0.30 0.00 0.00 3.51
3270 4232 2.413351 ATCGGCAGACGGTCATCG 59.587 61.111 11.27 10.59 44.45 3.84
3298 4260 1.126846 GATCACTGACGAAAACGGCTG 59.873 52.381 0.00 0.00 0.00 4.85
3299 4261 1.082756 CACTGACGAAAACGGCTGC 60.083 57.895 0.00 0.00 0.00 5.25
3303 4265 1.668151 GACGAAAACGGCTGCCTCT 60.668 57.895 17.92 0.00 0.00 3.69
3304 4266 1.227853 ACGAAAACGGCTGCCTCTT 60.228 52.632 17.92 6.71 0.00 2.85
3306 4268 1.581447 GAAAACGGCTGCCTCTTGG 59.419 57.895 17.92 2.80 0.00 3.61
3307 4269 1.152756 AAAACGGCTGCCTCTTGGT 60.153 52.632 17.92 3.51 35.27 3.67
3308 4270 0.755327 AAAACGGCTGCCTCTTGGTT 60.755 50.000 17.92 10.00 35.27 3.67
3530 4502 3.414700 GCGTTCCTGCTGTCCACG 61.415 66.667 0.00 0.00 0.00 4.94
3779 4769 3.621805 TGCTCGCAGGGGTTCGAA 61.622 61.111 0.00 0.00 34.07 3.71
3970 4960 2.520741 GAGGGAGGAGAGGGAGCG 60.521 72.222 0.00 0.00 0.00 5.03
3990 5004 4.742201 GAGCTGCCACGGCGAGAA 62.742 66.667 16.62 0.00 45.51 2.87
3991 5005 4.749310 AGCTGCCACGGCGAGAAG 62.749 66.667 16.62 9.81 45.51 2.85
4019 5033 0.179056 CGGCCGAGGTGTAAATGGAT 60.179 55.000 24.07 0.00 0.00 3.41
4137 5152 5.334421 AGGATGGAGATGGGTGTAGTATAC 58.666 45.833 0.00 0.00 43.42 1.47
4141 5156 4.103627 TGGAGATGGGTGTAGTATACGAGA 59.896 45.833 0.00 0.00 46.99 4.04
4142 5157 5.068636 GGAGATGGGTGTAGTATACGAGAA 58.931 45.833 0.00 0.00 46.99 2.87
4145 5160 7.040473 AGATGGGTGTAGTATACGAGAAAAG 57.960 40.000 0.00 0.00 46.99 2.27
4260 5295 8.758633 TGATTCTAGTTTGCTTAGTTGTCTAC 57.241 34.615 0.00 0.00 0.00 2.59
4267 5302 2.000447 GCTTAGTTGTCTACGCTTGGG 59.000 52.381 0.00 0.00 38.07 4.12
4272 5307 2.565834 AGTTGTCTACGCTTGGGTATGT 59.434 45.455 0.00 0.00 0.00 2.29
4275 5310 2.764010 TGTCTACGCTTGGGTATGTGAT 59.236 45.455 0.00 0.00 0.00 3.06
4276 5311 3.181479 TGTCTACGCTTGGGTATGTGATC 60.181 47.826 0.00 0.00 0.00 2.92
4277 5312 2.034179 TCTACGCTTGGGTATGTGATCG 59.966 50.000 0.00 0.00 0.00 3.69
4287 5322 1.513178 GTATGTGATCGCTCGTCAACG 59.487 52.381 7.94 0.00 41.45 4.10
4303 5338 2.093447 TCAACGGGTGTTTGCCAATTTT 60.093 40.909 0.00 0.00 35.72 1.82
4305 5340 3.378911 ACGGGTGTTTGCCAATTTTAG 57.621 42.857 0.00 0.00 0.00 1.85
4320 5355 5.422012 CCAATTTTAGTGGCAAAGGGTAGAT 59.578 40.000 0.00 0.00 0.00 1.98
4352 5387 0.890996 AAGCACGAAAGAAGGCCCAG 60.891 55.000 0.00 0.00 0.00 4.45
4359 5394 1.719063 AAAGAAGGCCCAGAGCACCA 61.719 55.000 0.00 0.00 46.50 4.17
4364 5399 2.821366 GCCCAGAGCACCACGATG 60.821 66.667 0.00 0.00 42.97 3.84
4366 5401 1.003355 CCCAGAGCACCACGATGTT 60.003 57.895 0.00 0.00 0.00 2.71
4371 5406 3.525537 CAGAGCACCACGATGTTATTCT 58.474 45.455 0.00 0.00 0.00 2.40
4372 5407 3.935203 CAGAGCACCACGATGTTATTCTT 59.065 43.478 0.00 0.00 0.00 2.52
4373 5408 4.033358 CAGAGCACCACGATGTTATTCTTC 59.967 45.833 0.00 0.00 0.00 2.87
4377 5414 5.122396 AGCACCACGATGTTATTCTTCTTTC 59.878 40.000 0.00 0.00 0.00 2.62
4416 5453 6.154534 ACATGTAGGTAGAGCACTCAAACATA 59.845 38.462 0.00 0.00 0.00 2.29
4418 5455 5.715279 TGTAGGTAGAGCACTCAAACATAGT 59.285 40.000 0.00 0.00 0.00 2.12
4419 5456 5.746990 AGGTAGAGCACTCAAACATAGTT 57.253 39.130 0.00 0.00 0.00 2.24
4667 5704 4.156739 CCATAGGACAGCAAGAGAAAAACC 59.843 45.833 0.00 0.00 0.00 3.27
4672 5709 3.823304 GACAGCAAGAGAAAAACCAGGAT 59.177 43.478 0.00 0.00 0.00 3.24
4724 5765 0.668535 GGTGGCCAGAAGAACACAAC 59.331 55.000 5.11 0.00 35.62 3.32
4784 5887 5.343307 TCAAAGAATCACGATCCAGATCA 57.657 39.130 8.31 0.00 37.69 2.92
4793 5896 3.739810 CACGATCCAGATCACTTGCATAG 59.260 47.826 8.31 0.00 37.69 2.23
4814 5917 2.315925 ACACCAAGCATATCACCTCG 57.684 50.000 0.00 0.00 0.00 4.63
4911 6014 2.886523 TGCCAGTTTGATGGAAGACTTG 59.113 45.455 0.00 0.00 43.57 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 4.374843 AGTGATAATGCGGTACACGTTA 57.625 40.909 0.00 0.00 46.52 3.18
73 74 3.241067 AGTGATAATGCGGTACACGTT 57.759 42.857 0.00 0.00 46.52 3.99
74 75 2.953466 AGTGATAATGCGGTACACGT 57.047 45.000 0.00 0.00 46.52 4.49
76 77 9.073368 CATACTATTAGTGATAATGCGGTACAC 57.927 37.037 6.60 0.00 0.00 2.90
77 78 8.799367 ACATACTATTAGTGATAATGCGGTACA 58.201 33.333 6.60 0.00 0.00 2.90
78 79 9.635520 AACATACTATTAGTGATAATGCGGTAC 57.364 33.333 6.60 0.00 0.00 3.34
80 81 9.555727 AAAACATACTATTAGTGATAATGCGGT 57.444 29.630 6.60 0.00 0.00 5.68
95 96 8.571336 GCCTCTGCAATATGAAAAACATACTAT 58.429 33.333 0.00 0.00 39.61 2.12
96 97 7.013274 GGCCTCTGCAATATGAAAAACATACTA 59.987 37.037 0.00 0.00 40.66 1.82
97 98 6.183360 GGCCTCTGCAATATGAAAAACATACT 60.183 38.462 0.00 0.00 40.66 2.12
98 99 5.979517 GGCCTCTGCAATATGAAAAACATAC 59.020 40.000 0.00 0.00 40.66 2.39
99 100 5.068987 GGGCCTCTGCAATATGAAAAACATA 59.931 40.000 0.84 0.00 41.41 2.29
100 101 4.141869 GGGCCTCTGCAATATGAAAAACAT 60.142 41.667 0.84 0.00 40.09 2.71
101 102 3.195396 GGGCCTCTGCAATATGAAAAACA 59.805 43.478 0.84 0.00 40.13 2.83
102 103 3.734902 CGGGCCTCTGCAATATGAAAAAC 60.735 47.826 0.84 0.00 40.13 2.43
103 104 2.426738 CGGGCCTCTGCAATATGAAAAA 59.573 45.455 0.84 0.00 40.13 1.94
104 105 2.023673 CGGGCCTCTGCAATATGAAAA 58.976 47.619 0.84 0.00 40.13 2.29
105 106 1.679139 CGGGCCTCTGCAATATGAAA 58.321 50.000 0.84 0.00 40.13 2.69
106 107 0.179020 CCGGGCCTCTGCAATATGAA 60.179 55.000 0.84 0.00 40.13 2.57
107 108 1.451504 CCGGGCCTCTGCAATATGA 59.548 57.895 0.84 0.00 40.13 2.15
108 109 1.601759 CCCGGGCCTCTGCAATATG 60.602 63.158 8.08 0.00 40.13 1.78
109 110 2.833913 CCCCGGGCCTCTGCAATAT 61.834 63.158 17.73 0.00 40.13 1.28
110 111 3.488569 CCCCGGGCCTCTGCAATA 61.489 66.667 17.73 0.00 40.13 1.90
115 116 1.933307 ATTAAACCCCCGGGCCTCTG 61.933 60.000 17.73 0.00 39.32 3.35
116 117 1.621514 ATTAAACCCCCGGGCCTCT 60.622 57.895 17.73 1.16 39.32 3.69
117 118 1.152819 GATTAAACCCCCGGGCCTC 60.153 63.158 17.73 0.00 39.32 4.70
118 119 1.621514 AGATTAAACCCCCGGGCCT 60.622 57.895 17.73 0.00 39.32 5.19
119 120 1.152819 GAGATTAAACCCCCGGGCC 60.153 63.158 17.73 0.00 39.32 5.80
120 121 1.152819 GGAGATTAAACCCCCGGGC 60.153 63.158 17.73 0.00 39.32 6.13
121 122 0.924090 AAGGAGATTAAACCCCCGGG 59.076 55.000 15.80 15.80 42.03 5.73
122 123 2.820728 AAAGGAGATTAAACCCCCGG 57.179 50.000 0.00 0.00 0.00 5.73
123 124 3.692690 TGAAAAGGAGATTAAACCCCCG 58.307 45.455 0.00 0.00 0.00 5.73
124 125 6.183361 TGTTTTGAAAAGGAGATTAAACCCCC 60.183 38.462 0.00 0.00 0.00 5.40
125 126 6.822442 TGTTTTGAAAAGGAGATTAAACCCC 58.178 36.000 0.00 0.00 0.00 4.95
126 127 8.725405 TTTGTTTTGAAAAGGAGATTAAACCC 57.275 30.769 0.00 0.00 0.00 4.11
154 155 6.152154 CCTCCCGTGGAAAAACATATTAGTTT 59.848 38.462 0.00 0.00 43.13 2.66
155 156 5.650703 CCTCCCGTGGAAAAACATATTAGTT 59.349 40.000 0.00 0.00 0.00 2.24
156 157 5.190677 CCTCCCGTGGAAAAACATATTAGT 58.809 41.667 0.00 0.00 0.00 2.24
157 158 5.065988 CACCTCCCGTGGAAAAACATATTAG 59.934 44.000 0.00 0.00 38.96 1.73
158 159 4.944930 CACCTCCCGTGGAAAAACATATTA 59.055 41.667 0.00 0.00 38.96 0.98
159 160 3.761752 CACCTCCCGTGGAAAAACATATT 59.238 43.478 0.00 0.00 38.96 1.28
160 161 3.352648 CACCTCCCGTGGAAAAACATAT 58.647 45.455 0.00 0.00 38.96 1.78
204 226 3.485633 GCGGTCGGTCAAATAAAAAGAC 58.514 45.455 0.00 0.00 0.00 3.01
205 227 2.485038 GGCGGTCGGTCAAATAAAAAGA 59.515 45.455 0.00 0.00 0.00 2.52
206 228 2.486592 AGGCGGTCGGTCAAATAAAAAG 59.513 45.455 0.00 0.00 0.00 2.27
214 515 4.373116 GCTCAGGCGGTCGGTCAA 62.373 66.667 0.00 0.00 0.00 3.18
215 516 3.931190 TAGCTCAGGCGGTCGGTCA 62.931 63.158 0.00 0.00 44.37 4.02
221 522 2.346597 GCTATCTAGCTCAGGCGGT 58.653 57.895 0.00 0.00 45.62 5.68
230 531 3.006323 TCTTAGCAGGCAAGCTATCTAGC 59.994 47.826 11.63 0.81 45.72 3.42
470 782 4.332543 ACGCAAGGGAGGGAGGGA 62.333 66.667 0.00 0.00 46.39 4.20
523 839 1.535462 GTTTGGTGAGGTCGTGATTGG 59.465 52.381 0.00 0.00 0.00 3.16
529 845 1.340211 TGGTTTGTTTGGTGAGGTCGT 60.340 47.619 0.00 0.00 0.00 4.34
531 847 3.886505 TGTATGGTTTGTTTGGTGAGGTC 59.113 43.478 0.00 0.00 0.00 3.85
532 848 3.904717 TGTATGGTTTGTTTGGTGAGGT 58.095 40.909 0.00 0.00 0.00 3.85
548 867 2.414138 GGACTCGTTCGGGTTTTGTATG 59.586 50.000 0.00 0.00 0.00 2.39
651 970 4.177537 AGTAGATAGCAAGAGAGGAGCA 57.822 45.455 0.00 0.00 0.00 4.26
652 971 4.457949 GGTAGTAGATAGCAAGAGAGGAGC 59.542 50.000 0.00 0.00 0.00 4.70
661 980 5.293319 ACTCGAGAGGTAGTAGATAGCAA 57.707 43.478 21.68 0.00 34.15 3.91
674 996 4.560919 CGGGGGAATATAAAACTCGAGAGG 60.561 50.000 21.68 0.00 0.00 3.69
679 1001 2.148768 GCCGGGGGAATATAAAACTCG 58.851 52.381 2.18 0.00 0.00 4.18
823 1150 1.817520 CCGTTGTGTGCTGTGTGGA 60.818 57.895 0.00 0.00 0.00 4.02
844 1178 2.997485 TGTGTGTGTGATCTCTCTCG 57.003 50.000 0.00 0.00 0.00 4.04
983 1324 2.610833 CTCATTGCGCAAGAAGATGCTA 59.389 45.455 28.62 5.53 44.21 3.49
1021 1362 3.937062 CAAGATTACGGCGGCGGC 61.937 66.667 35.05 24.75 38.90 6.53
1022 1363 2.510691 ACAAGATTACGGCGGCGG 60.511 61.111 35.05 17.60 0.00 6.13
1023 1364 1.480219 GAGACAAGATTACGGCGGCG 61.480 60.000 31.06 31.06 0.00 6.46
1024 1365 1.480219 CGAGACAAGATTACGGCGGC 61.480 60.000 13.24 0.00 0.00 6.53
1068 1409 2.806856 CGCGATCAGAAGCAGCACC 61.807 63.158 0.00 0.00 0.00 5.01
1326 1673 1.195442 TGGTGACGGTGAAGGCCATA 61.195 55.000 5.01 0.00 0.00 2.74
1492 1839 2.566529 CTCGTGGAGTGCTGCGTA 59.433 61.111 0.00 0.00 0.00 4.42
1567 1914 5.560953 CGATCGTATCTGAACACAGCTATGA 60.561 44.000 7.03 0.00 34.79 2.15
1568 1915 4.614702 CGATCGTATCTGAACACAGCTATG 59.385 45.833 7.03 0.00 0.00 2.23
1569 1916 4.515567 TCGATCGTATCTGAACACAGCTAT 59.484 41.667 15.94 0.00 0.00 2.97
1602 2103 0.103755 TCGGTCTCATCTCATGCTGC 59.896 55.000 0.00 0.00 0.00 5.25
1603 2104 1.537776 GGTCGGTCTCATCTCATGCTG 60.538 57.143 0.00 0.00 0.00 4.41
1604 2105 0.749649 GGTCGGTCTCATCTCATGCT 59.250 55.000 0.00 0.00 0.00 3.79
1675 2176 6.261118 GTGTGCATAATTGAATTGGTCTCTC 58.739 40.000 0.00 0.00 0.00 3.20
1702 2216 2.296792 TCAAAGTGCAACAAGCTAGCA 58.703 42.857 18.83 0.00 45.94 3.49
1707 2221 6.151691 TCTAATTGATCAAAGTGCAACAAGC 58.848 36.000 13.09 0.00 41.43 4.01
1832 2349 3.249799 CACGCTTGTTGTTATTCACCAGA 59.750 43.478 0.00 0.00 0.00 3.86
1995 2548 3.570125 ACCTGTTCAAGAAAAAGCTAGGC 59.430 43.478 0.00 0.00 0.00 3.93
2221 2777 2.359107 ACATGAGGCAGCGTGGTG 60.359 61.111 0.00 0.00 0.00 4.17
2225 2781 1.091771 GTATGCACATGAGGCAGCGT 61.092 55.000 18.59 9.70 45.68 5.07
2227 2783 0.379669 GTGTATGCACATGAGGCAGC 59.620 55.000 18.59 14.65 45.68 5.25
2273 2876 4.508461 TTTCCACATGAGACTTTGCATG 57.492 40.909 0.00 0.00 45.56 4.06
2286 2892 9.793252 CGATATTTTTCTCTCATTTTTCCACAT 57.207 29.630 0.00 0.00 0.00 3.21
2317 2923 1.852895 CGTACGCTATGCTCCAAACTC 59.147 52.381 0.52 0.00 0.00 3.01
2336 2958 0.734253 GCAGACAGACTGGTGCTACG 60.734 60.000 19.63 1.69 45.82 3.51
2373 2995 4.791974 AGCTACCAATATTCGTACGCTAC 58.208 43.478 11.24 0.00 0.00 3.58
2400 3022 8.474025 CCAAAGCTACCAATATCCATGTAAAAA 58.526 33.333 0.00 0.00 0.00 1.94
2402 3024 7.122715 ACCAAAGCTACCAATATCCATGTAAA 58.877 34.615 0.00 0.00 0.00 2.01
2403 3025 6.668645 ACCAAAGCTACCAATATCCATGTAA 58.331 36.000 0.00 0.00 0.00 2.41
2405 3027 5.129368 ACCAAAGCTACCAATATCCATGT 57.871 39.130 0.00 0.00 0.00 3.21
2406 3028 5.132502 TGACCAAAGCTACCAATATCCATG 58.867 41.667 0.00 0.00 0.00 3.66
2407 3029 5.387113 TGACCAAAGCTACCAATATCCAT 57.613 39.130 0.00 0.00 0.00 3.41
2410 3032 4.580580 CCCTTGACCAAAGCTACCAATATC 59.419 45.833 0.00 0.00 34.24 1.63
2456 3078 6.810911 AGAACACACCTCATATCACAGTATC 58.189 40.000 0.00 0.00 0.00 2.24
2457 3079 6.798427 AGAACACACCTCATATCACAGTAT 57.202 37.500 0.00 0.00 0.00 2.12
2458 3080 6.605471 AAGAACACACCTCATATCACAGTA 57.395 37.500 0.00 0.00 0.00 2.74
2460 3082 6.652481 AGAAAAGAACACACCTCATATCACAG 59.348 38.462 0.00 0.00 0.00 3.66
2461 3083 6.533730 AGAAAAGAACACACCTCATATCACA 58.466 36.000 0.00 0.00 0.00 3.58
2462 3084 7.041098 ACAAGAAAAGAACACACCTCATATCAC 60.041 37.037 0.00 0.00 0.00 3.06
2463 3085 6.998074 ACAAGAAAAGAACACACCTCATATCA 59.002 34.615 0.00 0.00 0.00 2.15
2464 3086 7.301054 CACAAGAAAAGAACACACCTCATATC 58.699 38.462 0.00 0.00 0.00 1.63
2465 3087 6.294176 GCACAAGAAAAGAACACACCTCATAT 60.294 38.462 0.00 0.00 0.00 1.78
2466 3088 5.008613 GCACAAGAAAAGAACACACCTCATA 59.991 40.000 0.00 0.00 0.00 2.15
2467 3089 4.202050 GCACAAGAAAAGAACACACCTCAT 60.202 41.667 0.00 0.00 0.00 2.90
2652 3304 2.301346 GAACTGGCCACCTAATCATGG 58.699 52.381 0.00 0.00 39.16 3.66
2886 3550 9.413048 CTAGTAAGATTGCATAAACTACTAGCC 57.587 37.037 13.25 0.00 31.62 3.93
2887 3551 9.968870 ACTAGTAAGATTGCATAAACTACTAGC 57.031 33.333 19.86 0.00 38.48 3.42
2896 3565 7.120579 CACCCAACAACTAGTAAGATTGCATAA 59.879 37.037 0.00 0.00 0.00 1.90
3106 4059 2.541120 CGTAGTCGAGGTAGCCGGG 61.541 68.421 2.18 0.00 39.71 5.73
3198 4151 4.593864 GCGAGGATCTGGACGCCC 62.594 72.222 0.00 0.00 44.27 6.13
3230 4183 0.952497 AGTGCGCTCTGTGGATGTTG 60.952 55.000 11.84 0.00 0.00 3.33
3231 4184 0.608130 TAGTGCGCTCTGTGGATGTT 59.392 50.000 21.59 0.00 0.00 2.71
3232 4185 0.826715 ATAGTGCGCTCTGTGGATGT 59.173 50.000 21.59 0.00 0.00 3.06
3233 4186 1.202452 TCATAGTGCGCTCTGTGGATG 60.202 52.381 28.22 20.11 0.00 3.51
3234 4187 1.114627 TCATAGTGCGCTCTGTGGAT 58.885 50.000 28.22 10.74 0.00 3.41
3235 4188 1.067669 GATCATAGTGCGCTCTGTGGA 59.932 52.381 28.22 19.29 0.00 4.02
3237 4190 1.126890 CGATCATAGTGCGCTCTGTG 58.873 55.000 24.75 24.75 0.00 3.66
3238 4191 0.031314 CCGATCATAGTGCGCTCTGT 59.969 55.000 21.59 12.64 0.00 3.41
3239 4192 1.280886 GCCGATCATAGTGCGCTCTG 61.281 60.000 21.59 4.32 0.00 3.35
3241 4194 1.280886 CTGCCGATCATAGTGCGCTC 61.281 60.000 9.73 4.74 0.00 5.03
3242 4195 1.300465 CTGCCGATCATAGTGCGCT 60.300 57.895 9.73 4.58 0.00 5.92
3243 4196 1.300156 TCTGCCGATCATAGTGCGC 60.300 57.895 0.00 0.00 0.00 6.09
3253 4206 2.413351 CGATGACCGTCTGCCGAT 59.587 61.111 0.00 0.00 39.56 4.18
3255 4208 4.873129 CCCGATGACCGTCTGCCG 62.873 72.222 0.00 1.08 36.31 5.69
3260 4213 1.804326 CGTTCACCCGATGACCGTC 60.804 63.158 0.00 0.00 38.35 4.79
3261 4214 1.601419 ATCGTTCACCCGATGACCGT 61.601 55.000 6.51 0.00 45.28 4.83
3262 4215 0.870307 GATCGTTCACCCGATGACCG 60.870 60.000 0.23 1.10 46.85 4.79
3293 4255 1.463674 AATTAACCAAGAGGCAGCCG 58.536 50.000 5.55 0.00 39.06 5.52
3298 4260 4.488879 CAGCTGAAAATTAACCAAGAGGC 58.511 43.478 8.42 0.00 39.06 4.70
3299 4261 4.219288 AGCAGCTGAAAATTAACCAAGAGG 59.781 41.667 20.43 0.00 42.21 3.69
3303 4265 3.652274 GCAGCAGCTGAAAATTAACCAA 58.348 40.909 27.39 0.00 37.91 3.67
3304 4266 3.302365 GCAGCAGCTGAAAATTAACCA 57.698 42.857 27.39 0.00 37.91 3.67
3530 4502 2.103736 GCCAGGTAGTCGGCGTAC 59.896 66.667 6.85 2.56 38.82 3.67
3998 5012 2.124860 ATTTACACCTCGGCCGCC 60.125 61.111 23.51 0.00 0.00 6.13
3999 5013 2.469516 CCATTTACACCTCGGCCGC 61.470 63.158 23.51 0.00 0.00 6.53
4000 5014 0.179056 ATCCATTTACACCTCGGCCG 60.179 55.000 22.12 22.12 0.00 6.13
4001 5015 2.052782 AATCCATTTACACCTCGGCC 57.947 50.000 0.00 0.00 0.00 6.13
4019 5033 7.173722 CCCTCGAGACCTATAACCTATCTAAA 58.826 42.308 15.71 0.00 0.00 1.85
4137 5152 2.884639 TCCAGCCCTTTTTCTTTTCTCG 59.115 45.455 0.00 0.00 0.00 4.04
4141 5156 1.694150 GCCTCCAGCCCTTTTTCTTTT 59.306 47.619 0.00 0.00 34.35 2.27
4142 5157 1.342074 GCCTCCAGCCCTTTTTCTTT 58.658 50.000 0.00 0.00 34.35 2.52
4145 5160 1.066645 CAATGCCTCCAGCCCTTTTTC 60.067 52.381 0.00 0.00 42.71 2.29
4234 5249 9.372369 GTAGACAACTAAGCAAACTAGAATCAT 57.628 33.333 0.00 0.00 0.00 2.45
4252 5267 2.671396 CACATACCCAAGCGTAGACAAC 59.329 50.000 0.00 0.00 0.00 3.32
4260 5295 0.530650 AGCGATCACATACCCAAGCG 60.531 55.000 0.00 0.00 0.00 4.68
4267 5302 1.513178 CGTTGACGAGCGATCACATAC 59.487 52.381 0.00 1.81 43.02 2.39
4272 5307 2.180769 CCCGTTGACGAGCGATCA 59.819 61.111 0.00 0.00 43.02 2.92
4275 5310 2.632136 AAACACCCGTTGACGAGCGA 62.632 55.000 4.91 0.00 43.02 4.93
4276 5311 2.241880 AAACACCCGTTGACGAGCG 61.242 57.895 4.91 0.00 43.02 5.03
4277 5312 1.278637 CAAACACCCGTTGACGAGC 59.721 57.895 4.91 0.00 43.02 5.03
4287 5322 3.398406 CCACTAAAATTGGCAAACACCC 58.602 45.455 3.01 0.00 0.00 4.61
4303 5338 2.742348 TCGATCTACCCTTTGCCACTA 58.258 47.619 0.00 0.00 0.00 2.74
4305 5340 2.158957 TGATCGATCTACCCTTTGCCAC 60.159 50.000 25.02 0.00 0.00 5.01
4320 5355 0.512518 CGTGCTTTGCTGTTGATCGA 59.487 50.000 0.00 0.00 0.00 3.59
4352 5387 4.184629 AGAAGAATAACATCGTGGTGCTC 58.815 43.478 0.00 0.00 0.00 4.26
4359 5394 8.833231 TCAGAAAGAAAGAAGAATAACATCGT 57.167 30.769 0.00 0.00 0.00 3.73
4479 5516 2.163815 GCTCTTGAGCTCACATGCATTT 59.836 45.455 18.03 0.00 34.99 2.32
4557 5594 7.835822 AGAATCTCGAATGATTGTATAGGGAG 58.164 38.462 4.76 0.00 36.86 4.30
4667 5704 7.805071 GCTTCATCGTTGGATTTTAATATCCTG 59.195 37.037 21.18 13.03 43.75 3.86
4724 5765 5.525012 TCTTGAGCATTCTTGTTCATATCGG 59.475 40.000 0.00 0.00 41.87 4.18
4784 5887 2.862541 TGCTTGGTGTTCTATGCAAGT 58.137 42.857 0.00 0.00 33.74 3.16
4793 5896 2.609459 CGAGGTGATATGCTTGGTGTTC 59.391 50.000 0.00 0.00 0.00 3.18
4814 5917 7.095187 ACCTCACGAGACTCATGTTTTTATTTC 60.095 37.037 2.82 0.00 0.00 2.17
4911 6014 5.064707 TCTGAACTCTGTTGTTGTAACTTGC 59.935 40.000 0.00 0.00 0.00 4.01
4958 6061 3.007506 TCTCGGCCTGTGAGATTTTGTTA 59.992 43.478 0.00 0.00 37.55 2.41


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

AutoCloner maintained by Alex Coulton.