Multiple sequence alignment - TraesCS4A01G017400

Loading Multiple Alignment...

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 TraesCS4A01G017400 chr4A 100.000 3601 0 0 1 3601 11679425 11675825 0.000000e+00 6650.0
1 TraesCS4A01G017400 chr4A 79.029 453 71 22 1049 1494 715912636 715913071 4.550000e-74 289.0
2 TraesCS4A01G017400 chr4A 79.233 443 65 22 1058 1494 715641656 715641235 2.120000e-72 283.0
3 TraesCS4A01G017400 chr4A 81.675 382 30 19 418 762 16831357 16831735 7.610000e-72 281.0
4 TraesCS4A01G017400 chr4A 80.488 164 10 8 172 313 16831142 16831305 4.920000e-19 106.0
5 TraesCS4A01G017400 chr4B 88.657 2733 161 76 418 3037 570137799 570140495 0.000000e+00 3192.0
6 TraesCS4A01G017400 chr4B 86.857 525 33 12 3108 3601 570141065 570141584 4.060000e-154 555.0
7 TraesCS4A01G017400 chr4B 80.488 164 10 8 172 313 570137584 570137747 4.920000e-19 106.0
8 TraesCS4A01G017400 chr4D 94.054 1850 79 15 1000 2831 456047003 456048839 0.000000e+00 2778.0
9 TraesCS4A01G017400 chr4D 79.864 884 60 47 111 899 456046007 456046867 4.090000e-149 538.0
10 TraesCS4A01G017400 chr4D 84.199 462 21 13 3168 3601 456049431 456049868 5.600000e-108 401.0
11 TraesCS4A01G017400 chr4D 77.239 268 28 16 2835 3102 456049007 456049241 3.770000e-25 126.0
12 TraesCS4A01G017400 chr6D 83.378 373 58 4 1317 1687 97914626 97914256 3.440000e-90 342.0
13 TraesCS4A01G017400 chr6B 83.422 374 56 6 1317 1687 182585983 182585613 3.440000e-90 342.0
14 TraesCS4A01G017400 chr7B 79.750 400 56 19 1123 1502 679930886 679930492 2.130000e-67 267.0
15 TraesCS4A01G017400 chr7D 78.555 429 67 15 1075 1494 17762575 17762163 3.570000e-65 259.0
16 TraesCS4A01G017400 chr7D 79.032 372 57 15 1124 1475 600748578 600748948 6.010000e-58 235.0
17 TraesCS4A01G017400 chr3D 87.500 176 22 0 1319 1494 12300251 12300076 1.700000e-48 204.0
18 TraesCS4A01G017400 chr3D 87.151 179 23 0 1316 1494 12374581 12374759 1.700000e-48 204.0
19 TraesCS4A01G017400 chr3D 88.000 75 8 1 2999 3073 91781788 91781715 1.780000e-13 87.9
20 TraesCS4A01G017400 chr3B 89.744 156 16 0 1776 1931 17688509 17688354 2.190000e-47 200.0
21 TraesCS4A01G017400 chr3B 87.006 177 21 2 1319 1494 17783914 17783739 7.890000e-47 198.0
22 TraesCS4A01G017400 chr3B 84.270 178 28 0 1317 1494 17988607 17988784 1.330000e-39 174.0
23 TraesCS4A01G017400 chr3B 92.562 121 8 1 1114 1233 17988382 17988502 4.780000e-39 172.0
24 TraesCS4A01G017400 chr7A 90.400 125 10 2 1123 1245 692523287 692523163 2.880000e-36 163.0
25 TraesCS4A01G017400 chr2A 90.667 75 6 1 2999 3073 47790493 47790420 8.230000e-17 99.0
26 TraesCS4A01G017400 chr1B 86.667 75 9 1 2999 3073 113020841 113020768 8.290000e-12 82.4


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 TraesCS4A01G017400 chr4A 11675825 11679425 3600 True 6650.000000 6650 100.000 1 3601 1 chr4A.!!$R1 3600
1 TraesCS4A01G017400 chr4B 570137584 570141584 4000 False 1284.333333 3192 85.334 172 3601 3 chr4B.!!$F1 3429
2 TraesCS4A01G017400 chr4D 456046007 456049868 3861 False 960.750000 2778 83.839 111 3601 4 chr4D.!!$F1 3490

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
206 207 0.039256 TCCTTACGACGGTTTCCACG 60.039 55.0 0.0 0.0 37.36 4.94 F
1875 2062 0.038744 ACCAAGGACAAGGATGGCAG 59.961 55.0 0.0 0.0 35.69 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2138 2331 0.467384 CGAGGGAGAGCACCATGAAT 59.533 55.0 0.0 0.0 0.00 2.57 R
2866 3244 0.036010 CTGGGTTTCAGATGACGCCT 60.036 55.0 0.0 0.0 46.18 5.52 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
37 38 9.522804 TCATTTATCAATTTTAATAACCGTGGC 57.477 29.630 0.00 0.00 0.00 5.01
38 39 9.307121 CATTTATCAATTTTAATAACCGTGGCA 57.693 29.630 0.00 0.00 0.00 4.92
39 40 8.918961 TTTATCAATTTTAATAACCGTGGCAG 57.081 30.769 0.00 0.00 0.00 4.85
40 41 5.968528 TCAATTTTAATAACCGTGGCAGT 57.031 34.783 0.00 0.00 0.00 4.40
41 42 6.334102 TCAATTTTAATAACCGTGGCAGTT 57.666 33.333 0.00 0.00 0.00 3.16
42 43 6.750148 TCAATTTTAATAACCGTGGCAGTTT 58.250 32.000 0.00 0.00 0.00 2.66
43 44 6.642950 TCAATTTTAATAACCGTGGCAGTTTG 59.357 34.615 0.00 0.00 0.00 2.93
44 45 5.769484 TTTTAATAACCGTGGCAGTTTGA 57.231 34.783 0.00 0.00 0.00 2.69
45 46 5.968528 TTTAATAACCGTGGCAGTTTGAT 57.031 34.783 0.00 0.00 0.00 2.57
46 47 5.968528 TTAATAACCGTGGCAGTTTGATT 57.031 34.783 0.00 0.00 0.00 2.57
47 48 4.864704 AATAACCGTGGCAGTTTGATTT 57.135 36.364 0.00 0.00 0.00 2.17
48 49 4.864704 ATAACCGTGGCAGTTTGATTTT 57.135 36.364 0.00 0.00 0.00 1.82
49 50 3.535280 AACCGTGGCAGTTTGATTTTT 57.465 38.095 0.00 0.00 0.00 1.94
50 51 3.092334 ACCGTGGCAGTTTGATTTTTC 57.908 42.857 0.00 0.00 0.00 2.29
51 52 2.693074 ACCGTGGCAGTTTGATTTTTCT 59.307 40.909 0.00 0.00 0.00 2.52
52 53 3.052036 CCGTGGCAGTTTGATTTTTCTG 58.948 45.455 0.00 0.00 0.00 3.02
53 54 3.490761 CCGTGGCAGTTTGATTTTTCTGT 60.491 43.478 0.00 0.00 0.00 3.41
54 55 3.730715 CGTGGCAGTTTGATTTTTCTGTC 59.269 43.478 0.00 0.00 33.79 3.51
55 56 4.498009 CGTGGCAGTTTGATTTTTCTGTCT 60.498 41.667 0.00 0.00 34.23 3.41
56 57 4.741676 GTGGCAGTTTGATTTTTCTGTCTG 59.258 41.667 0.00 0.00 34.23 3.51
57 58 3.737774 GGCAGTTTGATTTTTCTGTCTGC 59.262 43.478 0.00 0.00 43.88 4.26
58 59 4.362279 GCAGTTTGATTTTTCTGTCTGCA 58.638 39.130 0.00 0.00 43.99 4.41
59 60 4.443394 GCAGTTTGATTTTTCTGTCTGCAG 59.557 41.667 7.63 7.63 43.99 4.41
67 68 2.854522 TCTGTCTGCAGACGATCGA 58.145 52.632 35.00 25.86 45.94 3.59
68 69 0.729690 TCTGTCTGCAGACGATCGAG 59.270 55.000 35.00 27.15 45.94 4.04
69 70 2.609723 TCTGTCTGCAGACGATCGAGG 61.610 57.143 35.00 20.32 45.94 4.63
70 71 2.099143 GTCTGCAGACGATCGAGGA 58.901 57.895 29.84 11.25 35.12 3.71
71 72 0.248296 GTCTGCAGACGATCGAGGAC 60.248 60.000 29.84 14.69 35.12 3.85
72 73 1.297967 CTGCAGACGATCGAGGACG 60.298 63.158 24.34 6.28 41.26 4.79
73 74 1.983196 CTGCAGACGATCGAGGACGT 61.983 60.000 24.34 13.23 45.32 4.34
77 78 3.873883 ACGATCGAGGACGTCCGC 61.874 66.667 28.26 27.39 42.08 5.54
78 79 3.574445 CGATCGAGGACGTCCGCT 61.574 66.667 31.48 17.32 42.08 5.52
79 80 2.799371 GATCGAGGACGTCCGCTT 59.201 61.111 31.48 20.74 42.08 4.68
80 81 1.586564 GATCGAGGACGTCCGCTTG 60.587 63.158 31.48 19.43 42.08 4.01
81 82 3.701604 ATCGAGGACGTCCGCTTGC 62.702 63.158 31.48 17.53 42.08 4.01
82 83 4.717629 CGAGGACGTCCGCTTGCA 62.718 66.667 31.48 0.00 42.08 4.08
83 84 2.125512 GAGGACGTCCGCTTGCAT 60.126 61.111 28.62 10.57 42.08 3.96
84 85 2.125512 AGGACGTCCGCTTGCATC 60.126 61.111 28.26 1.55 42.08 3.91
85 86 3.195698 GGACGTCCGCTTGCATCC 61.196 66.667 20.85 0.00 0.00 3.51
86 87 3.195698 GACGTCCGCTTGCATCCC 61.196 66.667 3.51 0.00 0.00 3.85
87 88 4.778143 ACGTCCGCTTGCATCCCC 62.778 66.667 0.00 0.00 0.00 4.81
88 89 4.776322 CGTCCGCTTGCATCCCCA 62.776 66.667 0.00 0.00 0.00 4.96
89 90 2.825836 GTCCGCTTGCATCCCCAG 60.826 66.667 0.00 0.00 0.00 4.45
90 91 3.329889 TCCGCTTGCATCCCCAGT 61.330 61.111 0.00 0.00 0.00 4.00
91 92 2.361610 CCGCTTGCATCCCCAGTT 60.362 61.111 0.00 0.00 0.00 3.16
92 93 1.978617 CCGCTTGCATCCCCAGTTT 60.979 57.895 0.00 0.00 0.00 2.66
93 94 1.508088 CGCTTGCATCCCCAGTTTC 59.492 57.895 0.00 0.00 0.00 2.78
94 95 1.508088 GCTTGCATCCCCAGTTTCG 59.492 57.895 0.00 0.00 0.00 3.46
95 96 1.937546 GCTTGCATCCCCAGTTTCGG 61.938 60.000 0.00 0.00 0.00 4.30
96 97 0.609131 CTTGCATCCCCAGTTTCGGT 60.609 55.000 0.00 0.00 0.00 4.69
97 98 0.608035 TTGCATCCCCAGTTTCGGTC 60.608 55.000 0.00 0.00 0.00 4.79
98 99 1.749258 GCATCCCCAGTTTCGGTCC 60.749 63.158 0.00 0.00 0.00 4.46
99 100 1.682849 CATCCCCAGTTTCGGTCCA 59.317 57.895 0.00 0.00 0.00 4.02
100 101 0.255890 CATCCCCAGTTTCGGTCCAT 59.744 55.000 0.00 0.00 0.00 3.41
101 102 1.488812 CATCCCCAGTTTCGGTCCATA 59.511 52.381 0.00 0.00 0.00 2.74
102 103 1.887797 TCCCCAGTTTCGGTCCATAT 58.112 50.000 0.00 0.00 0.00 1.78
103 104 3.049108 TCCCCAGTTTCGGTCCATATA 57.951 47.619 0.00 0.00 0.00 0.86
104 105 2.701951 TCCCCAGTTTCGGTCCATATAC 59.298 50.000 0.00 0.00 0.00 1.47
105 106 2.436542 CCCCAGTTTCGGTCCATATACA 59.563 50.000 0.00 0.00 0.00 2.29
106 107 3.072476 CCCCAGTTTCGGTCCATATACAT 59.928 47.826 0.00 0.00 0.00 2.29
107 108 4.285003 CCCCAGTTTCGGTCCATATACATA 59.715 45.833 0.00 0.00 0.00 2.29
108 109 5.045869 CCCCAGTTTCGGTCCATATACATAT 60.046 44.000 0.00 0.00 0.00 1.78
109 110 5.874810 CCCAGTTTCGGTCCATATACATATG 59.125 44.000 0.00 0.00 39.80 1.78
168 169 2.915463 CCTTGTAAACTGTAGCTCGTCG 59.085 50.000 0.00 0.00 0.00 5.12
206 207 0.039256 TCCTTACGACGGTTTCCACG 60.039 55.000 0.00 0.00 37.36 4.94
214 229 0.591170 ACGGTTTCCACGCATTTCTG 59.409 50.000 0.00 0.00 34.00 3.02
273 304 2.109126 GTTCCATCCACAGCCGCTC 61.109 63.158 0.00 0.00 0.00 5.03
334 370 2.277084 GTCGTATCCGGCTGAACAAAT 58.723 47.619 0.00 0.00 35.32 2.32
336 372 1.330521 CGTATCCGGCTGAACAAATGG 59.669 52.381 0.00 0.00 0.00 3.16
340 376 1.508088 CGGCTGAACAAATGGAGCC 59.492 57.895 0.00 0.00 46.44 4.70
345 381 2.611224 GCTGAACAAATGGAGCCAAAGG 60.611 50.000 0.00 0.00 0.00 3.11
391 427 2.530297 CGATCGATCACTGGTTTACACG 59.470 50.000 24.40 3.19 0.00 4.49
392 428 1.705256 TCGATCACTGGTTTACACGC 58.295 50.000 0.00 0.00 0.00 5.34
393 429 0.365523 CGATCACTGGTTTACACGCG 59.634 55.000 3.53 3.53 0.00 6.01
394 430 1.425412 GATCACTGGTTTACACGCGT 58.575 50.000 5.58 5.58 0.00 6.01
395 431 1.796459 GATCACTGGTTTACACGCGTT 59.204 47.619 10.22 3.81 0.00 4.84
396 432 1.210870 TCACTGGTTTACACGCGTTC 58.789 50.000 10.22 0.00 0.00 3.95
397 433 0.111442 CACTGGTTTACACGCGTTCG 60.111 55.000 10.22 0.71 42.43 3.95
398 434 1.154727 CTGGTTTACACGCGTTCGC 60.155 57.895 10.22 7.14 39.84 4.70
399 435 1.554042 CTGGTTTACACGCGTTCGCT 61.554 55.000 10.22 0.00 39.84 4.93
400 436 1.129209 GGTTTACACGCGTTCGCTC 59.871 57.895 10.22 0.00 39.84 5.03
426 472 2.334295 GCCCTACGCCTACGCTAC 59.666 66.667 0.00 0.00 45.53 3.58
427 473 2.635899 CCCTACGCCTACGCTACG 59.364 66.667 0.00 0.00 45.53 3.51
473 522 3.793144 GCGAGAGGCAGCAAACCG 61.793 66.667 0.00 0.00 42.87 4.44
474 523 2.357517 CGAGAGGCAGCAAACCGT 60.358 61.111 0.00 0.00 0.00 4.83
475 524 2.671177 CGAGAGGCAGCAAACCGTG 61.671 63.158 0.00 0.00 0.00 4.94
476 525 1.301716 GAGAGGCAGCAAACCGTGA 60.302 57.895 0.00 0.00 0.00 4.35
477 526 1.294659 GAGAGGCAGCAAACCGTGAG 61.295 60.000 0.00 0.00 0.00 3.51
508 557 0.231279 CACAGTTTCACGGCGTACAC 59.769 55.000 14.22 9.85 0.00 2.90
541 613 8.999431 TGACCTGACAGAGTAAAAATATTGTTC 58.001 33.333 3.32 0.00 0.00 3.18
545 617 8.621532 TGACAGAGTAAAAATATTGTTCTGCT 57.378 30.769 5.93 0.00 35.24 4.24
553 625 9.787532 GTAAAAATATTGTTCTGCTCATTGCTA 57.212 29.630 0.00 0.00 43.37 3.49
636 731 3.716195 CAGGTCCGTCATGCCCCA 61.716 66.667 0.00 0.00 0.00 4.96
637 732 2.933287 AGGTCCGTCATGCCCCAA 60.933 61.111 0.00 0.00 0.00 4.12
641 736 2.751436 CCGTCATGCCCCAACCTG 60.751 66.667 0.00 0.00 0.00 4.00
642 737 2.751436 CGTCATGCCCCAACCTGG 60.751 66.667 0.00 0.00 37.25 4.45
692 787 0.163788 GTGCGGATCACTTCAACGTG 59.836 55.000 0.00 0.00 42.38 4.49
795 909 2.505557 CGTACCAGACCGCCGTTC 60.506 66.667 0.00 0.00 0.00 3.95
801 915 1.087771 CCAGACCGCCGTTCCATTAC 61.088 60.000 0.00 0.00 0.00 1.89
845 959 2.509336 CACGCCGGTCAGCCTAAG 60.509 66.667 1.90 0.00 0.00 2.18
879 993 1.906757 CGCAACACAACACAACACAT 58.093 45.000 0.00 0.00 0.00 3.21
899 1018 0.979665 AGCCACAGAAGAGCAGCTAA 59.020 50.000 0.00 0.00 0.00 3.09
900 1019 1.066286 AGCCACAGAAGAGCAGCTAAG 60.066 52.381 0.00 0.00 0.00 2.18
901 1020 2.011046 GCCACAGAAGAGCAGCTAAGG 61.011 57.143 0.00 0.00 0.00 2.69
906 1083 0.746204 GAAGAGCAGCTAAGGCACCC 60.746 60.000 0.00 0.00 41.70 4.61
915 1092 1.742750 GCTAAGGCACCCGTAAAGAGG 60.743 57.143 0.00 0.00 38.54 3.69
942 1123 2.903784 TGGTTTAGCAGCTCTCCTGTAA 59.096 45.455 0.00 0.00 43.71 2.41
945 1126 4.563786 GGTTTAGCAGCTCTCCTGTAAGTT 60.564 45.833 0.00 0.00 43.71 2.66
947 1128 1.203523 AGCAGCTCTCCTGTAAGTTCG 59.796 52.381 0.00 0.00 43.71 3.95
950 1131 3.760537 CAGCTCTCCTGTAAGTTCGTAC 58.239 50.000 0.00 0.00 36.79 3.67
951 1132 3.440872 CAGCTCTCCTGTAAGTTCGTACT 59.559 47.826 0.00 0.00 36.79 2.73
952 1133 4.634883 CAGCTCTCCTGTAAGTTCGTACTA 59.365 45.833 0.00 0.00 36.79 1.82
953 1134 4.635324 AGCTCTCCTGTAAGTTCGTACTAC 59.365 45.833 0.00 0.00 33.17 2.73
954 1135 4.201901 GCTCTCCTGTAAGTTCGTACTACC 60.202 50.000 0.00 0.00 33.17 3.18
955 1136 5.171339 TCTCCTGTAAGTTCGTACTACCT 57.829 43.478 0.00 0.00 33.17 3.08
956 1137 6.299805 TCTCCTGTAAGTTCGTACTACCTA 57.700 41.667 0.00 0.00 33.17 3.08
957 1138 6.344500 TCTCCTGTAAGTTCGTACTACCTAG 58.656 44.000 0.00 0.00 33.17 3.02
958 1139 4.878397 TCCTGTAAGTTCGTACTACCTAGC 59.122 45.833 0.00 0.00 33.17 3.42
959 1140 4.880696 CCTGTAAGTTCGTACTACCTAGCT 59.119 45.833 0.00 0.00 33.17 3.32
960 1141 5.220815 CCTGTAAGTTCGTACTACCTAGCTG 60.221 48.000 0.00 0.00 33.17 4.24
961 1142 5.491070 TGTAAGTTCGTACTACCTAGCTGA 58.509 41.667 0.00 0.00 33.17 4.26
962 1143 5.939883 TGTAAGTTCGTACTACCTAGCTGAA 59.060 40.000 0.00 0.00 33.17 3.02
1236 1417 1.899142 GAAGAGAAGCTCCAGGTGAGT 59.101 52.381 0.00 0.00 43.48 3.41
1237 1418 2.909504 AGAGAAGCTCCAGGTGAGTA 57.090 50.000 0.00 0.00 43.48 2.59
1238 1419 2.733956 AGAGAAGCTCCAGGTGAGTAG 58.266 52.381 0.00 0.00 43.48 2.57
1239 1420 2.042433 AGAGAAGCTCCAGGTGAGTAGT 59.958 50.000 0.00 0.00 43.48 2.73
1307 1488 3.127030 CACCGGTTCTAATGGCTTTCTTC 59.873 47.826 2.97 0.00 0.00 2.87
1318 1499 8.462016 TCTAATGGCTTTCTTCTTATTTTCTGC 58.538 33.333 0.00 0.00 0.00 4.26
1377 1558 4.124351 GACGTGATCGCCGGGACA 62.124 66.667 2.18 0.00 41.18 4.02
1482 1663 3.376935 CTACCTGGAGCACTGCCCG 62.377 68.421 0.00 0.00 0.00 6.13
1494 1675 1.147153 CTGCCCGAAGATCTTCCCC 59.853 63.158 26.08 15.99 36.27 4.81
1499 1680 2.109181 GAAGATCTTCCCCGCCGG 59.891 66.667 22.68 0.00 33.64 6.13
1672 1853 0.394899 CCAGCCAACCATCTTCTCCC 60.395 60.000 0.00 0.00 0.00 4.30
1698 1879 3.234386 CGACGTACGTGCATCATGATAT 58.766 45.455 28.16 0.00 37.22 1.63
1713 1894 8.383619 GCATCATGATATATTTCCTACGTGAAC 58.616 37.037 8.15 0.00 0.00 3.18
1755 1941 1.021390 GTGCTTACGTGAGGCATGCT 61.021 55.000 18.92 3.20 38.27 3.79
1875 2062 0.038744 ACCAAGGACAAGGATGGCAG 59.961 55.000 0.00 0.00 35.69 4.85
1937 2124 5.416083 CAAACAATCCGGTGAGTGATAGTA 58.584 41.667 0.00 0.00 38.86 1.82
1938 2125 4.920640 ACAATCCGGTGAGTGATAGTAG 57.079 45.455 0.00 0.00 38.86 2.57
1941 2128 3.639672 TCCGGTGAGTGATAGTAGACA 57.360 47.619 0.00 0.00 0.00 3.41
1942 2129 3.542648 TCCGGTGAGTGATAGTAGACAG 58.457 50.000 0.00 0.00 0.00 3.51
1943 2130 3.054582 TCCGGTGAGTGATAGTAGACAGT 60.055 47.826 0.00 0.00 0.00 3.55
1948 2135 5.403246 GTGAGTGATAGTAGACAGTTGGTG 58.597 45.833 0.00 0.00 0.00 4.17
1960 2147 2.367567 ACAGTTGGTGTATGTCTCCGTT 59.632 45.455 0.00 0.00 37.75 4.44
1970 2157 6.128363 GGTGTATGTCTCCGTTCCTTAAAAAG 60.128 42.308 0.00 0.00 0.00 2.27
1997 2185 9.669353 CACTCCAAAGAATATAATGGAATTTCG 57.331 33.333 0.00 0.00 41.20 3.46
2049 2242 6.345298 TGATATGTTGACATTGGATACGTGT 58.655 36.000 0.00 0.00 40.26 4.49
2123 2316 0.253327 ACTTCTTCCCGATCAAGCCC 59.747 55.000 0.00 0.00 0.00 5.19
2198 2391 2.430244 GAGAAGTTCGACGCCGCA 60.430 61.111 0.00 0.00 35.37 5.69
2366 2559 1.513158 CATCCAGGACGACGAGCTT 59.487 57.895 0.00 0.00 0.00 3.74
2369 2562 1.250328 TCCAGGACGACGAGCTTAAA 58.750 50.000 0.00 0.00 0.00 1.52
2411 2604 2.920912 TCCACGCCGGAGAACCTT 60.921 61.111 13.83 0.00 39.64 3.50
2477 2670 1.080705 CAGGGTGAACGTCGAGACC 60.081 63.158 0.00 1.26 0.00 3.85
2529 2722 1.269309 CCAACGAGGAGGAGCTAATCG 60.269 57.143 0.00 0.00 41.22 3.34
2539 2732 1.355971 GAGCTAATCGGTTTCGCACA 58.644 50.000 5.38 0.00 36.13 4.57
2540 2733 1.933853 GAGCTAATCGGTTTCGCACAT 59.066 47.619 5.38 0.00 36.13 3.21
2589 2782 0.687354 GCAGAAGAAGGGAGTCACCA 59.313 55.000 0.00 0.00 41.20 4.17
2592 2785 2.568956 CAGAAGAAGGGAGTCACCATCA 59.431 50.000 0.00 0.00 41.20 3.07
2602 2795 3.746492 GGAGTCACCATCACACAGTAAAC 59.254 47.826 0.00 0.00 38.79 2.01
2604 2797 4.973168 AGTCACCATCACACAGTAAACAT 58.027 39.130 0.00 0.00 0.00 2.71
2605 2798 4.756642 AGTCACCATCACACAGTAAACATG 59.243 41.667 0.00 0.00 0.00 3.21
2606 2799 4.515191 GTCACCATCACACAGTAAACATGT 59.485 41.667 0.00 0.00 0.00 3.21
2666 2879 9.726438 GTGTAAGGCAAATATAGGATAAGTCAT 57.274 33.333 0.00 0.00 0.00 3.06
2716 2929 4.708726 ATATTGAACTGCCAAAGCTCAC 57.291 40.909 0.00 0.00 40.80 3.51
2726 2939 2.159462 GCCAAAGCTCACAGACTTATGC 60.159 50.000 0.00 0.00 35.50 3.14
2727 2940 3.076621 CCAAAGCTCACAGACTTATGCA 58.923 45.455 0.00 0.00 0.00 3.96
2729 2942 4.379186 CCAAAGCTCACAGACTTATGCAAG 60.379 45.833 0.00 0.00 37.81 4.01
2785 2999 6.044682 GGAGAATGAAATAAATGGCCAACTG 58.955 40.000 10.96 0.00 0.00 3.16
2787 3001 7.147915 GGAGAATGAAATAAATGGCCAACTGTA 60.148 37.037 10.96 0.00 0.00 2.74
2800 3014 2.354510 CCAACTGTATATTGTGGGCACG 59.645 50.000 0.00 0.00 0.00 5.34
2831 3045 8.829373 AAATTTATCAGCCTATATTGGATCCC 57.171 34.615 9.90 0.00 0.00 3.85
2853 3231 2.183679 GAAAATACACATTGGCCCCCA 58.816 47.619 0.00 0.00 0.00 4.96
2894 3272 0.035458 CTGAAACCCAGACGCTCCTT 59.965 55.000 0.00 0.00 45.78 3.36
2907 3285 3.976701 CTCCTTGCCACCGCCGAAT 62.977 63.158 0.00 0.00 0.00 3.34
2911 3289 0.532862 CTTGCCACCGCCGAATAGAT 60.533 55.000 0.00 0.00 0.00 1.98
2912 3290 0.813610 TTGCCACCGCCGAATAGATG 60.814 55.000 0.00 0.00 0.00 2.90
2913 3291 1.069090 GCCACCGCCGAATAGATGA 59.931 57.895 0.00 0.00 0.00 2.92
2914 3292 1.222115 GCCACCGCCGAATAGATGAC 61.222 60.000 0.00 0.00 0.00 3.06
2915 3293 0.939577 CCACCGCCGAATAGATGACG 60.940 60.000 0.00 0.00 0.00 4.35
2917 3295 1.372997 CCGCCGAATAGATGACGGG 60.373 63.158 0.00 0.00 45.66 5.28
2918 3296 2.022129 CGCCGAATAGATGACGGGC 61.022 63.158 0.00 0.00 45.66 6.13
2919 3297 1.069090 GCCGAATAGATGACGGGCA 59.931 57.895 0.00 0.00 45.66 5.36
2920 3298 0.320771 GCCGAATAGATGACGGGCAT 60.321 55.000 0.00 0.00 45.66 4.40
2930 3310 0.464036 TGACGGGCATCCACTATGAC 59.536 55.000 0.00 0.00 43.67 3.06
2962 3342 5.713792 TTTGGCATTCGTCATTTTAGGAA 57.286 34.783 0.00 0.00 0.00 3.36
2963 3343 5.913137 TTGGCATTCGTCATTTTAGGAAT 57.087 34.783 0.00 0.00 35.04 3.01
3004 3386 5.221521 ACGAACATGCATAGGTAGTCATCAT 60.222 40.000 0.00 0.00 0.00 2.45
3005 3387 5.347093 CGAACATGCATAGGTAGTCATCATC 59.653 44.000 0.00 0.00 0.00 2.92
3023 3405 5.515797 TCATCGTAGGAGTAATCCTTGTG 57.484 43.478 18.34 11.02 41.12 3.33
3030 3412 7.776969 TCGTAGGAGTAATCCTTGTGTATAAGT 59.223 37.037 18.34 0.00 41.12 2.24
3033 3415 8.247666 AGGAGTAATCCTTGTGTATAAGTACC 57.752 38.462 5.74 0.00 36.56 3.34
3034 3416 8.066247 AGGAGTAATCCTTGTGTATAAGTACCT 58.934 37.037 5.74 0.00 36.56 3.08
3035 3417 8.358895 GGAGTAATCCTTGTGTATAAGTACCTC 58.641 40.741 0.88 0.00 0.00 3.85
3040 3789 7.636150 TCCTTGTGTATAAGTACCTCACTAC 57.364 40.000 0.00 0.00 36.04 2.73
3044 3793 5.291858 TGTGTATAAGTACCTCACTACGTCG 59.708 44.000 0.00 0.00 36.04 5.12
3057 3806 3.060339 CACTACGTCGGTTGTACCAAAAC 60.060 47.826 0.00 0.00 38.47 2.43
3065 3814 3.545822 CGGTTGTACCAAAACGTACCAAC 60.546 47.826 0.00 0.00 38.47 3.77
3073 3822 5.823353 ACCAAAACGTACCAACAACAATAG 58.177 37.500 0.00 0.00 0.00 1.73
3075 3824 5.008811 CCAAAACGTACCAACAACAATAGGA 59.991 40.000 0.00 0.00 0.00 2.94
3079 3828 3.625764 CGTACCAACAACAATAGGATGGG 59.374 47.826 0.00 0.00 32.21 4.00
3080 3829 4.624364 CGTACCAACAACAATAGGATGGGA 60.624 45.833 0.00 0.00 32.21 4.37
3083 3832 4.202441 CCAACAACAATAGGATGGGAGAG 58.798 47.826 0.00 0.00 0.00 3.20
3087 3836 1.366319 CAATAGGATGGGAGAGGGGG 58.634 60.000 0.00 0.00 0.00 5.40
3105 3854 3.998672 GAGGGGTTGGCACGACGA 61.999 66.667 0.00 0.00 0.00 4.20
3106 3855 3.524648 GAGGGGTTGGCACGACGAA 62.525 63.158 0.00 0.00 0.00 3.85
3108 3857 2.635338 GGGTTGGCACGACGAAAC 59.365 61.111 0.00 0.51 0.00 2.78
3109 3858 2.181521 GGGTTGGCACGACGAAACA 61.182 57.895 0.00 0.00 0.00 2.83
3110 3859 1.512156 GGGTTGGCACGACGAAACAT 61.512 55.000 0.00 0.00 0.00 2.71
3111 3860 1.149987 GGTTGGCACGACGAAACATA 58.850 50.000 0.00 0.00 0.00 2.29
3112 3861 1.735571 GGTTGGCACGACGAAACATAT 59.264 47.619 0.00 0.00 0.00 1.78
3113 3862 2.475519 GGTTGGCACGACGAAACATATG 60.476 50.000 0.00 0.00 0.00 1.78
3114 3863 2.087501 TGGCACGACGAAACATATGT 57.912 45.000 1.41 1.41 0.00 2.29
3115 3864 1.729517 TGGCACGACGAAACATATGTG 59.270 47.619 9.63 0.00 0.00 3.21
3116 3865 1.062002 GGCACGACGAAACATATGTGG 59.938 52.381 9.63 4.76 0.00 4.17
3119 3868 2.997303 CACGACGAAACATATGTGGGAA 59.003 45.455 9.63 0.00 0.00 3.97
3122 3871 3.306166 CGACGAAACATATGTGGGAAGAC 59.694 47.826 9.63 0.19 0.00 3.01
3123 3872 4.250464 GACGAAACATATGTGGGAAGACA 58.750 43.478 9.63 0.00 0.00 3.41
3125 3874 4.020573 ACGAAACATATGTGGGAAGACAGA 60.021 41.667 9.63 0.00 0.00 3.41
3136 4024 5.047021 TGTGGGAAGACAGACAAAGAGATAG 60.047 44.000 0.00 0.00 0.00 2.08
3140 4028 5.396213 GGAAGACAGACAAAGAGATAGGCAT 60.396 44.000 0.00 0.00 0.00 4.40
3176 4085 0.598562 GACAGACGAAGAGACAGGCA 59.401 55.000 0.00 0.00 0.00 4.75
3197 4106 6.716628 AGGCAGAAGAAAATTGACACAAGATA 59.283 34.615 0.00 0.00 0.00 1.98
3257 4186 8.707796 TCTATTTCCTTATAACGAGGATGAGT 57.292 34.615 0.00 0.00 42.63 3.41
3322 4251 8.821686 AATATGAACCAGGTCATTTCATACAA 57.178 30.769 12.22 0.00 42.27 2.41
3473 4408 1.271379 CCTGTCTGCATTTGTGCACAT 59.729 47.619 22.39 3.15 40.23 3.21
3517 4452 5.189180 ACTCTTCATAGGAGTGCAAAATCC 58.811 41.667 5.86 5.86 41.76 3.01
3529 4464 4.813161 AGTGCAAAATCCGTGATATCTCTG 59.187 41.667 3.98 0.00 0.00 3.35
3552 4487 7.658575 TCTGAAAGCAATCATCATGATTCGATA 59.341 33.333 10.13 0.00 43.03 2.92
3572 4509 8.897457 TCGATAGATTGACGAGAAAATATAGC 57.103 34.615 0.00 0.00 42.67 2.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 9.522804 GCCACGGTTATTAAAATTGATAAATGA 57.477 29.630 0.00 0.00 0.00 2.57
12 13 9.307121 TGCCACGGTTATTAAAATTGATAAATG 57.693 29.630 0.00 0.00 0.00 2.32
13 14 9.528018 CTGCCACGGTTATTAAAATTGATAAAT 57.472 29.630 0.00 0.00 0.00 1.40
14 15 8.524487 ACTGCCACGGTTATTAAAATTGATAAA 58.476 29.630 0.00 0.00 0.00 1.40
15 16 8.057536 ACTGCCACGGTTATTAAAATTGATAA 57.942 30.769 0.00 0.00 0.00 1.75
16 17 7.633193 ACTGCCACGGTTATTAAAATTGATA 57.367 32.000 0.00 0.00 0.00 2.15
17 18 6.524101 ACTGCCACGGTTATTAAAATTGAT 57.476 33.333 0.00 0.00 0.00 2.57
18 19 5.968528 ACTGCCACGGTTATTAAAATTGA 57.031 34.783 0.00 0.00 0.00 2.57
19 20 6.642950 TCAAACTGCCACGGTTATTAAAATTG 59.357 34.615 0.00 0.00 32.14 2.32
20 21 6.750148 TCAAACTGCCACGGTTATTAAAATT 58.250 32.000 0.00 0.00 32.14 1.82
21 22 6.334102 TCAAACTGCCACGGTTATTAAAAT 57.666 33.333 0.00 0.00 32.14 1.82
22 23 5.769484 TCAAACTGCCACGGTTATTAAAA 57.231 34.783 0.00 0.00 32.14 1.52
23 24 5.968528 ATCAAACTGCCACGGTTATTAAA 57.031 34.783 0.00 0.00 32.14 1.52
24 25 5.968528 AATCAAACTGCCACGGTTATTAA 57.031 34.783 0.00 0.00 32.14 1.40
25 26 5.968528 AAATCAAACTGCCACGGTTATTA 57.031 34.783 0.00 0.00 32.14 0.98
26 27 4.864704 AAATCAAACTGCCACGGTTATT 57.135 36.364 0.00 0.00 32.14 1.40
27 28 4.864704 AAAATCAAACTGCCACGGTTAT 57.135 36.364 0.00 0.00 32.14 1.89
28 29 4.339814 AGAAAAATCAAACTGCCACGGTTA 59.660 37.500 0.00 0.00 32.14 2.85
29 30 3.132111 AGAAAAATCAAACTGCCACGGTT 59.868 39.130 0.00 0.00 34.04 4.44
30 31 2.693074 AGAAAAATCAAACTGCCACGGT 59.307 40.909 0.00 0.00 0.00 4.83
31 32 3.052036 CAGAAAAATCAAACTGCCACGG 58.948 45.455 0.00 0.00 0.00 4.94
32 33 3.705604 ACAGAAAAATCAAACTGCCACG 58.294 40.909 0.00 0.00 34.25 4.94
33 34 4.741676 CAGACAGAAAAATCAAACTGCCAC 59.258 41.667 0.00 0.00 34.25 5.01
34 35 4.737352 GCAGACAGAAAAATCAAACTGCCA 60.737 41.667 0.00 0.00 42.04 4.92
35 36 3.737774 GCAGACAGAAAAATCAAACTGCC 59.262 43.478 0.00 0.00 42.04 4.85
36 37 4.362279 TGCAGACAGAAAAATCAAACTGC 58.638 39.130 0.00 0.00 46.07 4.40
50 51 0.248417 CCTCGATCGTCTGCAGACAG 60.248 60.000 38.31 30.58 44.99 3.51
51 52 0.676782 TCCTCGATCGTCTGCAGACA 60.677 55.000 38.31 27.61 44.99 3.41
52 53 0.248296 GTCCTCGATCGTCTGCAGAC 60.248 60.000 32.73 32.73 41.47 3.51
53 54 1.706287 CGTCCTCGATCGTCTGCAGA 61.706 60.000 13.74 13.74 39.71 4.26
54 55 1.297967 CGTCCTCGATCGTCTGCAG 60.298 63.158 15.94 7.63 39.71 4.41
55 56 2.038837 ACGTCCTCGATCGTCTGCA 61.039 57.895 15.94 0.00 40.62 4.41
56 57 2.792599 ACGTCCTCGATCGTCTGC 59.207 61.111 15.94 3.92 40.62 4.26
60 61 3.873883 GCGGACGTCCTCGATCGT 61.874 66.667 30.92 9.49 43.00 3.73
61 62 3.109612 AAGCGGACGTCCTCGATCG 62.110 63.158 30.92 17.87 40.62 3.69
62 63 1.586564 CAAGCGGACGTCCTCGATC 60.587 63.158 30.92 14.70 40.62 3.69
63 64 2.490217 CAAGCGGACGTCCTCGAT 59.510 61.111 30.92 15.78 40.62 3.59
64 65 4.415332 GCAAGCGGACGTCCTCGA 62.415 66.667 30.92 0.00 40.62 4.04
65 66 3.989698 ATGCAAGCGGACGTCCTCG 62.990 63.158 30.92 20.02 43.34 4.63
66 67 2.125512 ATGCAAGCGGACGTCCTC 60.126 61.111 30.92 24.38 0.00 3.71
67 68 2.125512 GATGCAAGCGGACGTCCT 60.126 61.111 30.92 12.01 0.00 3.85
68 69 3.195698 GGATGCAAGCGGACGTCC 61.196 66.667 25.28 25.28 34.94 4.79
69 70 3.195698 GGGATGCAAGCGGACGTC 61.196 66.667 7.13 7.13 0.00 4.34
70 71 4.778143 GGGGATGCAAGCGGACGT 62.778 66.667 0.00 0.00 0.00 4.34
71 72 4.776322 TGGGGATGCAAGCGGACG 62.776 66.667 0.00 0.00 0.00 4.79
72 73 2.825836 CTGGGGATGCAAGCGGAC 60.826 66.667 0.00 0.00 0.00 4.79
73 74 2.424842 AAACTGGGGATGCAAGCGGA 62.425 55.000 0.00 0.00 0.00 5.54
74 75 1.937546 GAAACTGGGGATGCAAGCGG 61.938 60.000 0.00 0.00 0.00 5.52
75 76 1.508088 GAAACTGGGGATGCAAGCG 59.492 57.895 0.00 0.00 0.00 4.68
76 77 1.508088 CGAAACTGGGGATGCAAGC 59.492 57.895 0.00 0.00 0.00 4.01
77 78 0.609131 ACCGAAACTGGGGATGCAAG 60.609 55.000 0.00 0.00 0.00 4.01
78 79 0.608035 GACCGAAACTGGGGATGCAA 60.608 55.000 0.00 0.00 0.00 4.08
79 80 1.002624 GACCGAAACTGGGGATGCA 60.003 57.895 0.00 0.00 0.00 3.96
80 81 1.749258 GGACCGAAACTGGGGATGC 60.749 63.158 0.00 0.00 0.00 3.91
81 82 0.255890 ATGGACCGAAACTGGGGATG 59.744 55.000 0.00 0.00 0.00 3.51
82 83 1.887797 TATGGACCGAAACTGGGGAT 58.112 50.000 0.00 0.00 0.00 3.85
83 84 1.887797 ATATGGACCGAAACTGGGGA 58.112 50.000 0.00 0.00 0.00 4.81
84 85 2.436542 TGTATATGGACCGAAACTGGGG 59.563 50.000 0.00 0.00 0.00 4.96
85 86 3.830744 TGTATATGGACCGAAACTGGG 57.169 47.619 0.00 0.00 0.00 4.45
86 87 6.968131 CATATGTATATGGACCGAAACTGG 57.032 41.667 4.33 0.00 37.16 4.00
120 121 8.094798 TGTTTTTATCTGCAACCACTTAGTAG 57.905 34.615 0.00 0.00 0.00 2.57
121 122 8.347035 GTTGTTTTTATCTGCAACCACTTAGTA 58.653 33.333 0.00 0.00 36.25 1.82
122 123 6.952773 TGTTTTTATCTGCAACCACTTAGT 57.047 33.333 0.00 0.00 0.00 2.24
150 151 1.973138 GCGACGAGCTACAGTTTACA 58.027 50.000 0.00 0.00 44.04 2.41
168 169 1.531578 GAGTTCCTTTCACAGAACGGC 59.468 52.381 0.00 0.00 45.60 5.68
206 207 0.742281 TGAGGAGCGCTCAGAAATGC 60.742 55.000 36.27 18.46 0.00 3.56
214 229 1.731720 ATTTGACTTGAGGAGCGCTC 58.268 50.000 29.38 29.38 0.00 5.03
273 304 1.811266 CTCGCAACCCTCGGTCATG 60.811 63.158 0.00 0.00 33.12 3.07
340 376 0.170561 CTTGCTAGCTGCTGCCTTTG 59.829 55.000 17.23 1.52 43.37 2.77
345 381 3.048941 GCCACTTGCTAGCTGCTGC 62.049 63.158 17.23 14.04 43.37 5.25
350 386 1.903877 ATCGGTGCCACTTGCTAGCT 61.904 55.000 17.23 0.00 42.00 3.32
351 387 1.432270 GATCGGTGCCACTTGCTAGC 61.432 60.000 8.10 8.10 42.00 3.42
352 388 1.148157 CGATCGGTGCCACTTGCTAG 61.148 60.000 7.38 0.00 42.00 3.42
353 389 1.153647 CGATCGGTGCCACTTGCTA 60.154 57.895 7.38 0.00 42.00 3.49
398 434 4.537433 GTAGGGCCTGCCTGCGAG 62.537 72.222 18.53 0.00 36.10 5.03
472 521 2.279517 GATAGCCGCCACCTCACG 60.280 66.667 0.00 0.00 0.00 4.35
473 522 1.521681 GTGATAGCCGCCACCTCAC 60.522 63.158 0.00 0.00 0.00 3.51
474 523 1.960040 CTGTGATAGCCGCCACCTCA 61.960 60.000 0.00 0.00 32.61 3.86
475 524 1.227380 CTGTGATAGCCGCCACCTC 60.227 63.158 0.00 0.00 32.61 3.85
476 525 1.553690 AACTGTGATAGCCGCCACCT 61.554 55.000 0.00 0.00 32.61 4.00
477 526 0.676782 AAACTGTGATAGCCGCCACC 60.677 55.000 0.00 0.00 32.61 4.61
508 557 0.244994 CTCTGTCAGGTCAGGGTTCG 59.755 60.000 0.00 0.00 36.25 3.95
545 617 1.751536 CGCACGCACGATAGCAATGA 61.752 55.000 0.00 0.00 42.67 2.57
553 625 4.151297 CATGCACGCACGCACGAT 62.151 61.111 4.54 0.00 46.56 3.73
647 742 2.606378 GTACTACTACATGGGAGGGGG 58.394 57.143 0.00 0.00 0.00 5.40
648 743 2.236766 CGTACTACTACATGGGAGGGG 58.763 57.143 0.00 0.00 0.00 4.79
649 744 2.621998 CACGTACTACTACATGGGAGGG 59.378 54.545 0.00 0.00 0.00 4.30
656 751 1.202222 GCACCGCACGTACTACTACAT 60.202 52.381 0.00 0.00 0.00 2.29
664 759 3.252484 GATCCGCACCGCACGTAC 61.252 66.667 0.00 0.00 0.00 3.67
784 880 1.219935 GGTAATGGAACGGCGGTCT 59.780 57.895 25.63 7.74 0.00 3.85
786 882 2.269883 GGGTAATGGAACGGCGGT 59.730 61.111 13.24 3.35 0.00 5.68
838 952 2.638480 TTGTGAACTGTGCTTAGGCT 57.362 45.000 0.00 0.00 39.59 4.58
845 959 0.525242 TTGCGCTTTGTGAACTGTGC 60.525 50.000 9.73 0.00 36.59 4.57
879 993 1.852633 TAGCTGCTCTTCTGTGGCTA 58.147 50.000 4.91 0.00 0.00 3.93
899 1018 0.831307 GATCCTCTTTACGGGTGCCT 59.169 55.000 0.00 0.00 0.00 4.75
900 1019 0.831307 AGATCCTCTTTACGGGTGCC 59.169 55.000 0.00 0.00 0.00 5.01
901 1020 2.678336 CAAAGATCCTCTTTACGGGTGC 59.322 50.000 2.04 0.00 44.23 5.01
906 1083 5.642063 TGCTAAACCAAAGATCCTCTTTACG 59.358 40.000 2.04 0.00 44.23 3.18
915 1092 3.625313 GGAGAGCTGCTAAACCAAAGATC 59.375 47.826 0.15 0.00 0.00 2.75
926 1103 2.423892 CGAACTTACAGGAGAGCTGCTA 59.576 50.000 0.15 0.00 0.00 3.49
942 1123 4.841422 TCTTCAGCTAGGTAGTACGAACT 58.159 43.478 0.00 0.00 39.91 3.01
945 1126 3.626670 GCTTCTTCAGCTAGGTAGTACGA 59.373 47.826 0.00 0.00 46.27 3.43
958 1139 2.124942 GCCCCCGAGCTTCTTCAG 60.125 66.667 0.00 0.00 0.00 3.02
959 1140 2.927856 TGCCCCCGAGCTTCTTCA 60.928 61.111 0.00 0.00 0.00 3.02
960 1141 2.436824 GTGCCCCCGAGCTTCTTC 60.437 66.667 0.00 0.00 0.00 2.87
961 1142 4.035102 GGTGCCCCCGAGCTTCTT 62.035 66.667 0.00 0.00 0.00 2.52
986 1167 3.391665 GACATGCTGGGGTCCTCCG 62.392 68.421 0.00 0.00 36.01 4.63
1307 1488 3.525537 TCGAGCTCCTGCAGAAAATAAG 58.474 45.455 17.39 3.73 42.74 1.73
1318 1499 4.598894 CGGCCCATCGAGCTCCTG 62.599 72.222 8.47 6.05 0.00 3.86
1482 1663 2.109181 CCGGCGGGGAAGATCTTC 59.891 66.667 24.68 24.68 38.47 2.87
1698 1879 4.827692 ACATGCAGTTCACGTAGGAAATA 58.172 39.130 0.00 0.00 0.00 1.40
1713 1894 2.679837 ACGCAGAGGAAATAACATGCAG 59.320 45.455 0.00 0.00 33.33 4.41
1768 1955 0.776451 CGTTCTTGGAGACGTCGTTG 59.224 55.000 10.46 0.52 0.00 4.10
1885 2072 2.736978 CCTCCGTCGATGAGATTGAAG 58.263 52.381 14.49 0.00 31.26 3.02
1938 2125 2.029290 ACGGAGACATACACCAACTGTC 60.029 50.000 0.00 0.00 39.63 3.51
1941 2128 2.028385 GGAACGGAGACATACACCAACT 60.028 50.000 0.00 0.00 0.00 3.16
1942 2129 2.028385 AGGAACGGAGACATACACCAAC 60.028 50.000 0.00 0.00 0.00 3.77
1943 2130 2.253610 AGGAACGGAGACATACACCAA 58.746 47.619 0.00 0.00 0.00 3.67
1948 2135 5.410439 TGCTTTTTAAGGAACGGAGACATAC 59.590 40.000 0.00 0.00 0.00 2.39
1957 2144 4.561735 TTGGAGTGCTTTTTAAGGAACG 57.438 40.909 0.00 0.00 0.00 3.95
1960 2147 6.976934 ATTCTTTGGAGTGCTTTTTAAGGA 57.023 33.333 0.00 0.00 0.00 3.36
1970 2157 9.468532 GAAATTCCATTATATTCTTTGGAGTGC 57.531 33.333 0.00 0.00 39.33 4.40
2046 2239 3.081061 TCATGGCCAACATTGTCTACAC 58.919 45.455 10.96 0.00 37.84 2.90
2049 2242 2.355197 CGTCATGGCCAACATTGTCTA 58.645 47.619 10.96 0.00 37.84 2.59
2138 2331 0.467384 CGAGGGAGAGCACCATGAAT 59.533 55.000 0.00 0.00 0.00 2.57
2411 2604 1.642037 CGACCTCGACGAGCCTGTTA 61.642 60.000 19.55 0.00 43.02 2.41
2666 2879 3.057315 CCTACCAAAGTTCGACCGTCTAA 60.057 47.826 0.00 0.00 0.00 2.10
2680 2893 7.067008 GCAGTTCAATATTTCTAGCCTACCAAA 59.933 37.037 0.00 0.00 0.00 3.28
2681 2894 6.542370 GCAGTTCAATATTTCTAGCCTACCAA 59.458 38.462 0.00 0.00 0.00 3.67
2716 2929 6.092807 GGACCTCTAAAACTTGCATAAGTCTG 59.907 42.308 0.00 0.00 46.14 3.51
2726 2939 3.314080 TGTTTGCGGACCTCTAAAACTTG 59.686 43.478 0.00 0.00 33.07 3.16
2727 2940 3.547746 TGTTTGCGGACCTCTAAAACTT 58.452 40.909 0.00 0.00 33.07 2.66
2729 2942 3.314357 ACTTGTTTGCGGACCTCTAAAAC 59.686 43.478 0.00 0.00 0.00 2.43
2777 2991 1.681264 GCCCACAATATACAGTTGGCC 59.319 52.381 0.00 0.00 39.82 5.36
2785 2999 3.462982 TCATGTCGTGCCCACAATATAC 58.537 45.455 0.00 0.00 0.00 1.47
2787 3001 2.708216 TCATGTCGTGCCCACAATAT 57.292 45.000 0.00 0.00 0.00 1.28
2831 3045 2.168313 GGGGGCCAATGTGTATTTTCTG 59.832 50.000 4.39 0.00 0.00 3.02
2866 3244 0.036010 CTGGGTTTCAGATGACGCCT 60.036 55.000 0.00 0.00 46.18 5.52
2889 3267 2.587322 TATTCGGCGGTGGCAAGGAG 62.587 60.000 7.21 0.00 42.47 3.69
2894 3272 1.227527 CATCTATTCGGCGGTGGCA 60.228 57.895 7.21 0.00 42.47 4.92
2911 3289 0.464036 GTCATAGTGGATGCCCGTCA 59.536 55.000 0.00 0.00 35.29 4.35
2912 3290 0.464036 TGTCATAGTGGATGCCCGTC 59.536 55.000 0.00 0.00 35.29 4.79
2913 3291 0.178068 GTGTCATAGTGGATGCCCGT 59.822 55.000 0.00 0.00 35.29 5.28
2914 3292 0.465705 AGTGTCATAGTGGATGCCCG 59.534 55.000 0.00 0.00 35.29 6.13
2915 3293 1.959042 CAGTGTCATAGTGGATGCCC 58.041 55.000 0.00 0.00 35.29 5.36
2916 3294 1.303309 GCAGTGTCATAGTGGATGCC 58.697 55.000 0.00 0.00 35.29 4.40
2917 3295 2.028420 TGCAGTGTCATAGTGGATGC 57.972 50.000 0.00 0.00 35.29 3.91
2918 3296 5.571784 ATTTTGCAGTGTCATAGTGGATG 57.428 39.130 0.00 0.00 36.82 3.51
2919 3297 6.392354 CAAATTTTGCAGTGTCATAGTGGAT 58.608 36.000 0.00 0.00 29.58 3.41
2920 3298 5.278907 CCAAATTTTGCAGTGTCATAGTGGA 60.279 40.000 3.50 0.00 0.00 4.02
2921 3299 4.925054 CCAAATTTTGCAGTGTCATAGTGG 59.075 41.667 3.50 0.00 0.00 4.00
2926 3306 3.472283 TGCCAAATTTTGCAGTGTCAT 57.528 38.095 12.58 0.00 32.77 3.06
2927 3307 2.975732 TGCCAAATTTTGCAGTGTCA 57.024 40.000 12.58 0.00 32.77 3.58
2930 3310 2.801679 ACGAATGCCAAATTTTGCAGTG 59.198 40.909 20.14 14.34 41.46 3.66
2962 3342 6.403049 TGTTCGTCACACACAAGGATTATAT 58.597 36.000 0.00 0.00 0.00 0.86
2963 3343 5.785243 TGTTCGTCACACACAAGGATTATA 58.215 37.500 0.00 0.00 0.00 0.98
3030 3412 6.845923 TGGTACAACCGACGTAGTGAGGTA 62.846 50.000 0.00 0.00 45.29 3.08
3032 3414 3.707729 TGGTACAACCGACGTAGTGAGG 61.708 54.545 0.00 0.00 42.58 3.86
3033 3415 1.536766 TGGTACAACCGACGTAGTGAG 59.463 52.381 0.00 0.00 42.58 3.51
3034 3416 1.603456 TGGTACAACCGACGTAGTGA 58.397 50.000 0.00 0.00 42.58 3.41
3057 3806 3.625764 CCCATCCTATTGTTGTTGGTACG 59.374 47.826 0.00 0.00 0.00 3.67
3065 3814 2.107204 CCCCTCTCCCATCCTATTGTTG 59.893 54.545 0.00 0.00 0.00 3.33
3090 3839 2.592287 TTTCGTCGTGCCAACCCC 60.592 61.111 0.00 0.00 0.00 4.95
3094 3843 2.158645 CACATATGTTTCGTCGTGCCAA 59.841 45.455 5.37 0.00 0.00 4.52
3098 3847 2.612604 TCCCACATATGTTTCGTCGTG 58.387 47.619 5.37 0.00 0.00 4.35
3099 3848 3.056393 TCTTCCCACATATGTTTCGTCGT 60.056 43.478 5.37 0.00 0.00 4.34
3100 3849 3.306166 GTCTTCCCACATATGTTTCGTCG 59.694 47.826 5.37 0.00 0.00 5.12
3101 3850 4.250464 TGTCTTCCCACATATGTTTCGTC 58.750 43.478 5.37 0.00 0.00 4.20
3102 3851 4.020573 TCTGTCTTCCCACATATGTTTCGT 60.021 41.667 5.37 0.00 0.00 3.85
3104 3853 5.245531 TGTCTGTCTTCCCACATATGTTTC 58.754 41.667 5.37 0.00 0.00 2.78
3105 3854 5.241403 TGTCTGTCTTCCCACATATGTTT 57.759 39.130 5.37 0.00 0.00 2.83
3106 3855 4.908601 TGTCTGTCTTCCCACATATGTT 57.091 40.909 5.37 0.00 0.00 2.71
3108 3857 5.491070 TCTTTGTCTGTCTTCCCACATATG 58.509 41.667 0.00 0.00 0.00 1.78
3109 3858 5.485353 TCTCTTTGTCTGTCTTCCCACATAT 59.515 40.000 0.00 0.00 0.00 1.78
3110 3859 4.838423 TCTCTTTGTCTGTCTTCCCACATA 59.162 41.667 0.00 0.00 0.00 2.29
3111 3860 3.648067 TCTCTTTGTCTGTCTTCCCACAT 59.352 43.478 0.00 0.00 0.00 3.21
3112 3861 3.038280 TCTCTTTGTCTGTCTTCCCACA 58.962 45.455 0.00 0.00 0.00 4.17
3113 3862 3.753294 TCTCTTTGTCTGTCTTCCCAC 57.247 47.619 0.00 0.00 0.00 4.61
3114 3863 4.467795 CCTATCTCTTTGTCTGTCTTCCCA 59.532 45.833 0.00 0.00 0.00 4.37
3115 3864 4.682050 GCCTATCTCTTTGTCTGTCTTCCC 60.682 50.000 0.00 0.00 0.00 3.97
3116 3865 4.081420 TGCCTATCTCTTTGTCTGTCTTCC 60.081 45.833 0.00 0.00 0.00 3.46
3119 3868 6.798427 TTATGCCTATCTCTTTGTCTGTCT 57.202 37.500 0.00 0.00 0.00 3.41
3122 3871 9.330063 TGTTTATTATGCCTATCTCTTTGTCTG 57.670 33.333 0.00 0.00 0.00 3.51
3125 3874 9.632638 ACATGTTTATTATGCCTATCTCTTTGT 57.367 29.630 0.00 0.00 0.00 2.83
3136 4024 4.278419 GTCCTCCCACATGTTTATTATGCC 59.722 45.833 0.00 0.00 0.00 4.40
3140 4028 5.625886 CGTCTGTCCTCCCACATGTTTATTA 60.626 44.000 0.00 0.00 0.00 0.98
3281 4210 6.040166 GGTTCATATTCATGGCAAGACTTGAT 59.960 38.462 19.51 4.85 32.61 2.57
3292 4221 6.321945 TGAAATGACCTGGTTCATATTCATGG 59.678 38.462 0.00 0.00 35.02 3.66
3353 4282 7.672983 TCATCACTTTTAGAATGAGTTGGTC 57.327 36.000 0.00 0.00 0.00 4.02
3473 4408 6.028146 AGTTTATGCTTTCATGCACATTCA 57.972 33.333 0.00 0.00 46.33 2.57
3517 4452 6.423001 TGATGATTGCTTTCAGAGATATCACG 59.577 38.462 5.32 0.00 32.84 4.35
3529 4464 8.026341 TCTATCGAATCATGATGATTGCTTTC 57.974 34.615 24.04 10.06 46.20 2.62
3552 4487 8.363390 TGATCAGCTATATTTTCTCGTCAATCT 58.637 33.333 0.00 0.00 0.00 2.40
3572 4509 4.081254 TGTTTGTCTCCCATCTCTGATCAG 60.081 45.833 17.07 17.07 0.00 2.90


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

AutoCloner maintained by Alex Coulton.