Multiple sequence alignment - TraesCS1D01G416300

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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 TraesCS1D01G416300 chr1D 100.000 3551 0 0 1 3551 475198204 475194654 0.000000e+00 6558.0
1 TraesCS1D01G416300 chr1D 83.234 1503 222 20 2058 3551 475178440 475176959 0.000000e+00 1352.0
2 TraesCS1D01G416300 chr1D 81.572 1183 188 21 2090 3267 473406702 473407859 0.000000e+00 950.0
3 TraesCS1D01G416300 chr1B 94.007 2386 125 8 1167 3551 660998173 660995805 0.000000e+00 3598.0
4 TraesCS1D01G416300 chr1B 87.926 1615 155 15 1939 3545 660950573 660948991 0.000000e+00 1866.0
5 TraesCS1D01G416300 chr1B 88.005 1509 159 16 2049 3551 661055239 661053747 0.000000e+00 1764.0
6 TraesCS1D01G416300 chr1B 86.855 1377 159 9 2077 3446 660880797 660879436 0.000000e+00 1520.0
7 TraesCS1D01G416300 chr1B 86.514 1394 169 10 2058 3446 661122557 661121178 0.000000e+00 1515.0
8 TraesCS1D01G416300 chr1B 84.298 1503 206 21 2058 3551 660684229 660682748 0.000000e+00 1441.0
9 TraesCS1D01G416300 chr1B 83.668 1494 208 21 2064 3545 660964157 660962688 0.000000e+00 1375.0
10 TraesCS1D01G416300 chr1B 89.006 946 86 8 2610 3551 660640412 660639481 0.000000e+00 1155.0
11 TraesCS1D01G416300 chr1B 85.468 1101 142 10 668 1762 660882201 660881113 0.000000e+00 1131.0
12 TraesCS1D01G416300 chr1B 86.828 949 101 11 2607 3551 660914435 660913507 0.000000e+00 1038.0
13 TraesCS1D01G416300 chr1B 81.311 1220 192 24 2058 3269 658354318 658355509 0.000000e+00 957.0
14 TraesCS1D01G416300 chr1B 84.731 930 128 11 770 1689 661124577 661123652 0.000000e+00 918.0
15 TraesCS1D01G416300 chr1B 84.690 934 124 11 668 1590 660726172 660725247 0.000000e+00 915.0
16 TraesCS1D01G416300 chr1B 83.140 1032 129 31 668 1671 660653052 660652038 0.000000e+00 900.0
17 TraesCS1D01G416300 chr1B 84.699 830 118 7 765 1590 660966155 660965331 0.000000e+00 821.0
18 TraesCS1D01G416300 chr1B 81.732 1051 130 40 668 1670 661061920 661060884 0.000000e+00 821.0
19 TraesCS1D01G416300 chr1B 83.241 901 130 10 702 1590 660749561 660748670 0.000000e+00 808.0
20 TraesCS1D01G416300 chr1B 88.800 625 45 16 1267 1888 660951116 660950514 0.000000e+00 743.0
21 TraesCS1D01G416300 chr1B 85.103 678 82 10 1220 1887 660916281 660915613 0.000000e+00 675.0
22 TraesCS1D01G416300 chr1B 83.287 718 75 25 495 1172 661019662 661018950 1.400000e-173 619.0
23 TraesCS1D01G416300 chr1B 88.378 413 46 2 766 1177 660916775 660916364 2.460000e-136 496.0
24 TraesCS1D01G416300 chr1B 82.828 198 18 9 196 383 661019972 661019781 2.840000e-36 163.0
25 TraesCS1D01G416300 chr1B 94.030 67 4 0 332 398 660882427 660882361 6.270000e-18 102.0
26 TraesCS1D01G416300 chr1A 83.884 1483 209 20 2079 3551 570862191 570860729 0.000000e+00 1387.0
27 TraesCS1D01G416300 chr1A 86.231 995 104 10 2058 3051 570878555 570877593 0.000000e+00 1048.0
28 TraesCS1D01G416300 chr1A 85.541 823 108 7 770 1590 570864952 570864139 0.000000e+00 850.0
29 TraesCS1D01G416300 chr1A 85.855 608 70 9 2949 3551 570877590 570876994 1.800000e-177 632.0
30 TraesCS1D01G416300 chr5B 83.212 137 15 5 42 171 20128657 20128522 6.230000e-23 119.0
31 TraesCS1D01G416300 chr5B 79.200 125 17 8 37 152 13180895 13180771 1.060000e-10 78.7
32 TraesCS1D01G416300 chr6B 79.012 162 26 5 18 172 689517735 689517575 1.740000e-18 104.0
33 TraesCS1D01G416300 chr4B 77.297 185 30 10 3 178 571904401 571904582 8.110000e-17 99.0
34 TraesCS1D01G416300 chr3B 82.243 107 16 3 1 106 712774574 712774470 4.880000e-14 89.8
35 TraesCS1D01G416300 chr3A 92.308 52 3 1 57 108 515848725 515848675 4.920000e-09 73.1


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G416300 chr1D 475194654 475198204 3550 True 6558.000000 6558 100.000000 1 3551 1 chr1D.!!$R2 3550
1 TraesCS1D01G416300 chr1D 475176959 475178440 1481 True 1352.000000 1352 83.234000 2058 3551 1 chr1D.!!$R1 1493
2 TraesCS1D01G416300 chr1D 473406702 473407859 1157 False 950.000000 950 81.572000 2090 3267 1 chr1D.!!$F1 1177
3 TraesCS1D01G416300 chr1B 660995805 660998173 2368 True 3598.000000 3598 94.007000 1167 3551 1 chr1B.!!$R6 2384
4 TraesCS1D01G416300 chr1B 661053747 661055239 1492 True 1764.000000 1764 88.005000 2049 3551 1 chr1B.!!$R7 1502
5 TraesCS1D01G416300 chr1B 660682748 660684229 1481 True 1441.000000 1441 84.298000 2058 3551 1 chr1B.!!$R3 1493
6 TraesCS1D01G416300 chr1B 660948991 660951116 2125 True 1304.500000 1866 88.363000 1267 3545 2 chr1B.!!$R11 2278
7 TraesCS1D01G416300 chr1B 661121178 661124577 3399 True 1216.500000 1515 85.622500 770 3446 2 chr1B.!!$R14 2676
8 TraesCS1D01G416300 chr1B 660639481 660640412 931 True 1155.000000 1155 89.006000 2610 3551 1 chr1B.!!$R1 941
9 TraesCS1D01G416300 chr1B 660962688 660966155 3467 True 1098.000000 1375 84.183500 765 3545 2 chr1B.!!$R12 2780
10 TraesCS1D01G416300 chr1B 658354318 658355509 1191 False 957.000000 957 81.311000 2058 3269 1 chr1B.!!$F1 1211
11 TraesCS1D01G416300 chr1B 660879436 660882427 2991 True 917.666667 1520 88.784333 332 3446 3 chr1B.!!$R9 3114
12 TraesCS1D01G416300 chr1B 660725247 660726172 925 True 915.000000 915 84.690000 668 1590 1 chr1B.!!$R4 922
13 TraesCS1D01G416300 chr1B 660652038 660653052 1014 True 900.000000 900 83.140000 668 1671 1 chr1B.!!$R2 1003
14 TraesCS1D01G416300 chr1B 661060884 661061920 1036 True 821.000000 821 81.732000 668 1670 1 chr1B.!!$R8 1002
15 TraesCS1D01G416300 chr1B 660748670 660749561 891 True 808.000000 808 83.241000 702 1590 1 chr1B.!!$R5 888
16 TraesCS1D01G416300 chr1B 660913507 660916775 3268 True 736.333333 1038 86.769667 766 3551 3 chr1B.!!$R10 2785
17 TraesCS1D01G416300 chr1B 661018950 661019972 1022 True 391.000000 619 83.057500 196 1172 2 chr1B.!!$R13 976
18 TraesCS1D01G416300 chr1A 570860729 570864952 4223 True 1118.500000 1387 84.712500 770 3551 2 chr1A.!!$R1 2781
19 TraesCS1D01G416300 chr1A 570876994 570878555 1561 True 840.000000 1048 86.043000 2058 3551 2 chr1A.!!$R2 1493

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
56 57 0.173708 GAGTGAGGGGTGATGACGAC 59.826 60.0 0.00 0.00 0.0 4.34 F
259 260 0.249120 ACGGGTCTGCATCGAAATCA 59.751 50.0 0.00 0.00 0.0 2.57 F
941 1050 0.321653 AAACTGACCGACATGGAGGC 60.322 55.0 8.42 3.29 42.0 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1079 1188 0.683973 CCACAGAGTCTTGAGCTGGT 59.316 55.000 0.0 0.0 34.05 4.00 R
1164 1273 1.270147 GGAAGCTTGTACCTGTCACGT 60.270 52.381 2.1 0.0 0.00 4.49 R
2678 5591 0.695924 ACATCATCCAAACGTCCCCA 59.304 50.000 0.0 0.0 0.00 4.96 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
30 31 9.169592 TGTGTAGTATAATAAGTTTTTCCTGGC 57.830 33.333 0.00 0.00 0.00 4.85
31 32 9.392259 GTGTAGTATAATAAGTTTTTCCTGGCT 57.608 33.333 0.00 0.00 0.00 4.75
32 33 9.609346 TGTAGTATAATAAGTTTTTCCTGGCTC 57.391 33.333 0.00 0.00 0.00 4.70
33 34 9.833917 GTAGTATAATAAGTTTTTCCTGGCTCT 57.166 33.333 0.00 0.00 0.00 4.09
35 36 9.833917 AGTATAATAAGTTTTTCCTGGCTCTAC 57.166 33.333 0.00 0.00 0.00 2.59
36 37 9.833917 GTATAATAAGTTTTTCCTGGCTCTACT 57.166 33.333 0.00 0.00 0.00 2.57
37 38 8.738645 ATAATAAGTTTTTCCTGGCTCTACTG 57.261 34.615 0.00 0.00 0.00 2.74
38 39 4.706842 AAGTTTTTCCTGGCTCTACTGA 57.293 40.909 0.00 0.00 0.00 3.41
39 40 4.278975 AGTTTTTCCTGGCTCTACTGAG 57.721 45.455 0.00 0.00 42.96 3.35
40 41 3.648545 AGTTTTTCCTGGCTCTACTGAGT 59.351 43.478 0.00 0.00 42.13 3.41
41 42 3.685139 TTTTCCTGGCTCTACTGAGTG 57.315 47.619 0.00 0.00 42.13 3.51
42 43 2.604912 TTCCTGGCTCTACTGAGTGA 57.395 50.000 0.00 0.00 42.13 3.41
43 44 2.136298 TCCTGGCTCTACTGAGTGAG 57.864 55.000 0.00 1.53 42.13 3.51
44 45 1.110442 CCTGGCTCTACTGAGTGAGG 58.890 60.000 11.92 0.00 42.13 3.86
45 46 1.110442 CTGGCTCTACTGAGTGAGGG 58.890 60.000 11.92 0.91 42.13 4.30
46 47 0.324738 TGGCTCTACTGAGTGAGGGG 60.325 60.000 11.92 0.00 42.13 4.79
47 48 0.324830 GGCTCTACTGAGTGAGGGGT 60.325 60.000 11.92 0.00 42.13 4.95
48 49 0.820871 GCTCTACTGAGTGAGGGGTG 59.179 60.000 11.92 0.00 42.13 4.61
49 50 1.617263 GCTCTACTGAGTGAGGGGTGA 60.617 57.143 11.92 0.00 42.13 4.02
50 51 2.952702 GCTCTACTGAGTGAGGGGTGAT 60.953 54.545 11.92 0.00 42.13 3.06
51 52 2.692557 CTCTACTGAGTGAGGGGTGATG 59.307 54.545 0.00 0.00 35.67 3.07
52 53 2.311841 TCTACTGAGTGAGGGGTGATGA 59.688 50.000 0.00 0.00 0.00 2.92
53 54 1.270907 ACTGAGTGAGGGGTGATGAC 58.729 55.000 0.00 0.00 0.00 3.06
54 55 0.174389 CTGAGTGAGGGGTGATGACG 59.826 60.000 0.00 0.00 0.00 4.35
55 56 0.251608 TGAGTGAGGGGTGATGACGA 60.252 55.000 0.00 0.00 0.00 4.20
56 57 0.173708 GAGTGAGGGGTGATGACGAC 59.826 60.000 0.00 0.00 0.00 4.34
57 58 1.153823 GTGAGGGGTGATGACGACG 60.154 63.158 0.00 0.00 0.00 5.12
58 59 2.348104 TGAGGGGTGATGACGACGG 61.348 63.158 0.00 0.00 0.00 4.79
59 60 3.718210 GAGGGGTGATGACGACGGC 62.718 68.421 0.00 0.00 0.00 5.68
82 83 3.066369 GCCTTCGGCTTATTTTAGTGC 57.934 47.619 0.00 0.00 46.69 4.40
83 84 2.683362 GCCTTCGGCTTATTTTAGTGCT 59.317 45.455 0.00 0.00 46.69 4.40
84 85 3.128764 GCCTTCGGCTTATTTTAGTGCTT 59.871 43.478 0.00 0.00 46.69 3.91
85 86 4.662145 CCTTCGGCTTATTTTAGTGCTTG 58.338 43.478 0.00 0.00 0.00 4.01
86 87 4.156008 CCTTCGGCTTATTTTAGTGCTTGT 59.844 41.667 0.00 0.00 0.00 3.16
87 88 5.353123 CCTTCGGCTTATTTTAGTGCTTGTA 59.647 40.000 0.00 0.00 0.00 2.41
88 89 6.417191 TTCGGCTTATTTTAGTGCTTGTAG 57.583 37.500 0.00 0.00 0.00 2.74
89 90 5.484715 TCGGCTTATTTTAGTGCTTGTAGT 58.515 37.500 0.00 0.00 0.00 2.73
90 91 5.579511 TCGGCTTATTTTAGTGCTTGTAGTC 59.420 40.000 0.00 0.00 0.00 2.59
91 92 5.500290 CGGCTTATTTTAGTGCTTGTAGTCG 60.500 44.000 0.00 0.00 0.00 4.18
92 93 5.350640 GGCTTATTTTAGTGCTTGTAGTCGT 59.649 40.000 0.00 0.00 0.00 4.34
93 94 6.455246 GGCTTATTTTAGTGCTTGTAGTCGTC 60.455 42.308 0.00 0.00 0.00 4.20
94 95 6.090358 GCTTATTTTAGTGCTTGTAGTCGTCA 59.910 38.462 0.00 0.00 0.00 4.35
95 96 5.840940 ATTTTAGTGCTTGTAGTCGTCAC 57.159 39.130 0.00 0.00 0.00 3.67
96 97 4.579454 TTTAGTGCTTGTAGTCGTCACT 57.421 40.909 0.00 0.00 40.60 3.41
97 98 5.694231 TTTAGTGCTTGTAGTCGTCACTA 57.306 39.130 0.00 0.00 38.71 2.74
98 99 3.833545 AGTGCTTGTAGTCGTCACTAG 57.166 47.619 0.00 0.00 35.67 2.57
99 100 3.409570 AGTGCTTGTAGTCGTCACTAGA 58.590 45.455 0.00 0.00 35.67 2.43
100 101 4.011023 AGTGCTTGTAGTCGTCACTAGAT 58.989 43.478 0.00 0.00 35.67 1.98
101 102 4.099120 GTGCTTGTAGTCGTCACTAGATG 58.901 47.826 0.00 0.00 35.67 2.90
102 103 3.128764 TGCTTGTAGTCGTCACTAGATGG 59.871 47.826 0.00 0.00 35.67 3.51
103 104 3.377485 GCTTGTAGTCGTCACTAGATGGA 59.623 47.826 0.00 0.00 35.67 3.41
104 105 4.036971 GCTTGTAGTCGTCACTAGATGGAT 59.963 45.833 0.00 0.00 35.67 3.41
105 106 5.752892 TTGTAGTCGTCACTAGATGGATC 57.247 43.478 0.00 0.00 35.67 3.36
106 107 5.037383 TGTAGTCGTCACTAGATGGATCT 57.963 43.478 0.00 0.00 35.67 2.75
107 108 6.170846 TGTAGTCGTCACTAGATGGATCTA 57.829 41.667 0.00 0.00 35.67 1.98
108 109 6.589135 TGTAGTCGTCACTAGATGGATCTAA 58.411 40.000 0.00 0.00 38.80 2.10
109 110 7.052248 TGTAGTCGTCACTAGATGGATCTAAA 58.948 38.462 0.00 0.00 38.80 1.85
110 111 7.720074 TGTAGTCGTCACTAGATGGATCTAAAT 59.280 37.037 0.00 0.00 38.80 1.40
111 112 6.976088 AGTCGTCACTAGATGGATCTAAATG 58.024 40.000 0.00 0.96 38.80 2.32
112 113 6.547880 AGTCGTCACTAGATGGATCTAAATGT 59.452 38.462 0.00 0.00 38.80 2.71
113 114 7.720074 AGTCGTCACTAGATGGATCTAAATGTA 59.280 37.037 0.00 0.00 38.80 2.29
114 115 8.516234 GTCGTCACTAGATGGATCTAAATGTAT 58.484 37.037 0.00 0.00 38.80 2.29
115 116 9.078990 TCGTCACTAGATGGATCTAAATGTATT 57.921 33.333 0.00 0.00 38.80 1.89
116 117 9.698309 CGTCACTAGATGGATCTAAATGTATTT 57.302 33.333 0.00 0.00 38.80 1.40
152 153 9.887629 TTTTTATGTTCATTGTAATGCCATGAT 57.112 25.926 14.45 0.00 36.36 2.45
153 154 9.887629 TTTTATGTTCATTGTAATGCCATGATT 57.112 25.926 14.45 0.00 36.36 2.57
157 158 8.929827 TGTTCATTGTAATGCCATGATTAAAG 57.070 30.769 0.00 0.00 36.36 1.85
158 159 8.747471 TGTTCATTGTAATGCCATGATTAAAGA 58.253 29.630 0.00 0.00 36.36 2.52
159 160 9.754382 GTTCATTGTAATGCCATGATTAAAGAT 57.246 29.630 0.00 0.00 36.36 2.40
160 161 9.752961 TTCATTGTAATGCCATGATTAAAGATG 57.247 29.630 0.00 0.00 36.36 2.90
161 162 9.134055 TCATTGTAATGCCATGATTAAAGATGA 57.866 29.630 0.00 0.51 36.36 2.92
162 163 9.752961 CATTGTAATGCCATGATTAAAGATGAA 57.247 29.630 0.00 0.00 0.00 2.57
170 171 9.577222 TGCCATGATTAAAGATGAATAGATTGA 57.423 29.630 0.00 0.00 0.00 2.57
243 244 1.278127 AGTTGAATAGTCCACCCACGG 59.722 52.381 0.00 0.00 0.00 4.94
254 255 3.770040 CCCACGGGTCTGCATCGA 61.770 66.667 0.00 0.00 0.00 3.59
255 256 2.264480 CCACGGGTCTGCATCGAA 59.736 61.111 0.00 0.00 0.00 3.71
256 257 1.375396 CCACGGGTCTGCATCGAAA 60.375 57.895 0.00 0.00 0.00 3.46
257 258 0.744414 CCACGGGTCTGCATCGAAAT 60.744 55.000 0.00 0.00 0.00 2.17
258 259 0.652592 CACGGGTCTGCATCGAAATC 59.347 55.000 0.00 0.00 0.00 2.17
259 260 0.249120 ACGGGTCTGCATCGAAATCA 59.751 50.000 0.00 0.00 0.00 2.57
260 261 0.933097 CGGGTCTGCATCGAAATCAG 59.067 55.000 0.00 0.00 0.00 2.90
261 262 1.740380 CGGGTCTGCATCGAAATCAGT 60.740 52.381 10.40 0.00 0.00 3.41
262 263 1.667724 GGGTCTGCATCGAAATCAGTG 59.332 52.381 10.40 0.00 0.00 3.66
263 264 2.621338 GGTCTGCATCGAAATCAGTGA 58.379 47.619 0.00 0.00 0.00 3.41
264 265 3.201290 GGTCTGCATCGAAATCAGTGAT 58.799 45.455 0.00 0.00 0.00 3.06
265 266 3.002042 GGTCTGCATCGAAATCAGTGATG 59.998 47.826 6.34 0.00 41.84 3.07
271 272 3.401033 TCGAAATCAGTGATGTGTGGT 57.599 42.857 6.34 0.00 0.00 4.16
274 275 3.686241 CGAAATCAGTGATGTGTGGTCAT 59.314 43.478 6.34 0.00 0.00 3.06
280 281 3.686241 CAGTGATGTGTGGTCATCGATTT 59.314 43.478 0.00 0.00 44.82 2.17
284 285 6.040247 GTGATGTGTGGTCATCGATTTAGTA 58.960 40.000 0.00 0.00 44.82 1.82
285 286 6.701841 GTGATGTGTGGTCATCGATTTAGTAT 59.298 38.462 0.00 0.00 44.82 2.12
286 287 7.865889 GTGATGTGTGGTCATCGATTTAGTATA 59.134 37.037 0.00 0.00 44.82 1.47
287 288 8.585018 TGATGTGTGGTCATCGATTTAGTATAT 58.415 33.333 0.00 0.00 44.82 0.86
405 460 5.009510 CCAGTCTACATCGAGATTGAGTCAT 59.990 44.000 0.00 0.00 35.72 3.06
406 461 6.142139 CAGTCTACATCGAGATTGAGTCATC 58.858 44.000 0.00 0.00 35.72 2.92
410 465 6.992715 TCTACATCGAGATTGAGTCATCAGTA 59.007 38.462 0.00 0.00 36.61 2.74
413 468 8.171164 ACATCGAGATTGAGTCATCAGTATTA 57.829 34.615 0.00 0.00 36.61 0.98
414 469 8.296000 ACATCGAGATTGAGTCATCAGTATTAG 58.704 37.037 0.00 0.00 36.61 1.73
450 505 8.842358 TTTTATTTAGGATCGGCCATTAGTAG 57.158 34.615 2.24 0.00 40.02 2.57
451 506 7.549147 TTATTTAGGATCGGCCATTAGTAGT 57.451 36.000 2.24 0.00 40.02 2.73
452 507 4.866508 TTAGGATCGGCCATTAGTAGTG 57.133 45.455 2.24 0.00 40.02 2.74
453 508 2.679082 AGGATCGGCCATTAGTAGTGT 58.321 47.619 2.24 0.00 40.02 3.55
454 509 3.840991 AGGATCGGCCATTAGTAGTGTA 58.159 45.455 2.24 0.00 40.02 2.90
455 510 4.417437 AGGATCGGCCATTAGTAGTGTAT 58.583 43.478 2.24 0.00 40.02 2.29
456 511 4.838986 AGGATCGGCCATTAGTAGTGTATT 59.161 41.667 2.24 0.00 40.02 1.89
457 512 5.307196 AGGATCGGCCATTAGTAGTGTATTT 59.693 40.000 2.24 0.00 40.02 1.40
459 514 6.485648 GGATCGGCCATTAGTAGTGTATTTTT 59.514 38.462 2.24 0.00 36.34 1.94
496 551 2.780595 GGCAACTCTGTGTGTGTGT 58.219 52.632 0.00 0.00 0.00 3.72
497 552 0.378257 GGCAACTCTGTGTGTGTGTG 59.622 55.000 0.00 0.00 0.00 3.82
561 616 3.390521 CGGCAGCCTCCACTACCA 61.391 66.667 10.54 0.00 0.00 3.25
622 681 0.523125 CCACACCAATAATGCACGCG 60.523 55.000 3.53 3.53 0.00 6.01
623 682 0.523125 CACACCAATAATGCACGCGG 60.523 55.000 12.47 0.00 0.00 6.46
649 713 4.120755 GCCAGGGCCAAGGAGGAG 62.121 72.222 18.11 0.00 41.22 3.69
674 762 2.671070 GGTAGAGCAAGCCCAGCA 59.329 61.111 0.00 0.00 0.00 4.41
694 782 1.688197 ACCATTGCTTCACCACCAAAG 59.312 47.619 0.00 0.00 0.00 2.77
700 788 1.691196 CTTCACCACCAAAGAAGGCA 58.309 50.000 0.00 0.00 36.11 4.75
734 830 3.136763 TGTTCAGCAGCTTCTTCTCTTG 58.863 45.455 0.00 0.00 0.00 3.02
755 861 3.075148 GCTAAGAACTTGTCCACCTTCC 58.925 50.000 0.00 0.00 0.00 3.46
760 866 2.640316 ACTTGTCCACCTTCCTTCAC 57.360 50.000 0.00 0.00 0.00 3.18
762 868 0.476771 TTGTCCACCTTCCTTCACCC 59.523 55.000 0.00 0.00 0.00 4.61
807 913 2.610859 ACGGGGGCCATGAACTCT 60.611 61.111 4.39 0.00 0.00 3.24
847 953 1.607713 CTTGCTCAGTGACGAGTACG 58.392 55.000 0.00 0.00 45.75 3.67
940 1049 1.276421 AGAAACTGACCGACATGGAGG 59.724 52.381 7.12 7.12 42.00 4.30
941 1050 0.321653 AAACTGACCGACATGGAGGC 60.322 55.000 8.42 3.29 42.00 4.70
968 1077 2.268920 CGGCCTTGGCAAGAGCTA 59.731 61.111 28.18 0.00 41.70 3.32
1039 1148 1.002624 TTCATGGACCGGCTTGGAC 60.003 57.895 0.00 0.00 42.00 4.02
1069 1178 2.802247 GCCAAACCAAAGTTCATGAAGC 59.198 45.455 8.80 4.22 34.19 3.86
1164 1273 1.153568 CATGGAGGAAAGCGAGCGA 60.154 57.895 0.00 0.00 0.00 4.93
1213 1367 4.719773 ACTCTTGGGGTTGTATGTGCTATA 59.280 41.667 0.00 0.00 0.00 1.31
1218 1372 4.904853 TGGGGTTGTATGTGCTATATCTCA 59.095 41.667 0.00 0.00 0.00 3.27
1525 1685 0.246635 GACTTCCAGTGCCGAGCTTA 59.753 55.000 0.00 0.00 0.00 3.09
1787 1973 9.205513 ACTATTTTTAAATGGCCAGATCAGATT 57.794 29.630 13.05 0.00 30.88 2.40
1886 4050 7.106439 TGATGCAAAAGAAGTTACCTGAAAA 57.894 32.000 0.00 0.00 0.00 2.29
1962 4126 4.273148 AGCCCTAATCTATTTGTAGCCG 57.727 45.455 0.00 0.00 0.00 5.52
1972 4287 7.592885 ATCTATTTGTAGCCGGAGTAGTTTA 57.407 36.000 5.05 0.00 0.00 2.01
2047 4369 6.844097 TGTGGGGAATACAAATTAGTTTCC 57.156 37.500 0.00 0.00 36.04 3.13
2048 4370 6.315714 TGTGGGGAATACAAATTAGTTTCCA 58.684 36.000 10.00 0.00 38.05 3.53
2049 4371 6.957020 TGTGGGGAATACAAATTAGTTTCCAT 59.043 34.615 10.00 0.00 38.05 3.41
2050 4372 7.456269 TGTGGGGAATACAAATTAGTTTCCATT 59.544 33.333 10.00 0.00 38.05 3.16
2051 4373 7.763985 GTGGGGAATACAAATTAGTTTCCATTG 59.236 37.037 10.00 0.00 38.05 2.82
2052 4374 6.761242 GGGGAATACAAATTAGTTTCCATTGC 59.239 38.462 10.00 0.00 38.05 3.56
2053 4375 7.327214 GGGAATACAAATTAGTTTCCATTGCA 58.673 34.615 10.00 0.00 38.05 4.08
2054 4376 7.821846 GGGAATACAAATTAGTTTCCATTGCAA 59.178 33.333 0.00 0.00 38.05 4.08
2055 4377 9.382275 GGAATACAAATTAGTTTCCATTGCAAT 57.618 29.630 5.99 5.99 36.64 3.56
2274 4985 1.676006 GGTGAACCCTATCAAATGGCG 59.324 52.381 0.00 0.00 0.00 5.69
2308 5019 4.877282 TGTTGATTCCCGAAAATTGTTCC 58.123 39.130 0.00 0.00 0.00 3.62
2341 5052 3.391506 TCCGCATAGATGATCCTTGTG 57.608 47.619 0.00 0.00 0.00 3.33
2472 5186 2.027745 TGAATGGGAGAGACTGCAAGAC 60.028 50.000 0.00 0.00 37.43 3.01
2501 5215 4.192317 GGTACTGGTCCTTTGCTTGATAG 58.808 47.826 0.00 0.00 0.00 2.08
2676 5589 2.767644 TCCTTGATAGACGATGGGGA 57.232 50.000 0.00 0.00 0.00 4.81
2677 5590 2.598565 TCCTTGATAGACGATGGGGAG 58.401 52.381 0.00 0.00 0.00 4.30
2678 5591 2.091278 TCCTTGATAGACGATGGGGAGT 60.091 50.000 0.00 0.00 0.00 3.85
2679 5592 2.036475 CCTTGATAGACGATGGGGAGTG 59.964 54.545 0.00 0.00 0.00 3.51
2680 5593 1.704641 TGATAGACGATGGGGAGTGG 58.295 55.000 0.00 0.00 0.00 4.00
2681 5594 0.969894 GATAGACGATGGGGAGTGGG 59.030 60.000 0.00 0.00 0.00 4.61
2682 5595 0.471971 ATAGACGATGGGGAGTGGGG 60.472 60.000 0.00 0.00 0.00 4.96
2704 5617 3.932710 GACGTTTGGATGATGTAGCAGAA 59.067 43.478 0.00 0.00 0.00 3.02
2719 5632 8.743085 ATGTAGCAGAAAACTGTATCAATGAT 57.257 30.769 0.00 0.00 0.00 2.45
2908 5821 2.425668 TCGACGTCTCTCCATGCAATTA 59.574 45.455 14.70 0.00 0.00 1.40
2933 5846 2.094078 GGCAAAGAGCATAATGGCACAA 60.094 45.455 0.00 0.00 45.66 3.33
2934 5847 3.587923 GCAAAGAGCATAATGGCACAAA 58.412 40.909 0.00 0.00 43.65 2.83
2957 5966 2.724839 CGTGCGATTACAGAAACCAAGC 60.725 50.000 0.00 0.00 0.00 4.01
2963 5972 5.502544 GCGATTACAGAAACCAAGCTACATC 60.503 44.000 0.00 0.00 0.00 3.06
3006 6021 0.322546 CAAGTTCAGCAGGTACCCCC 60.323 60.000 8.74 0.00 0.00 5.40
3179 6194 0.166814 CGGAAAGCTGCAGCACTTAC 59.833 55.000 38.24 28.43 45.16 2.34
3181 6196 1.608590 GGAAAGCTGCAGCACTTACAA 59.391 47.619 38.24 0.00 45.16 2.41
3212 6227 7.439356 TCGATTTGAGAGGCTGTTATTATCTTG 59.561 37.037 0.00 0.00 0.00 3.02
3334 6349 1.946984 TGGGGGAGTTACGATTCAGT 58.053 50.000 0.00 0.00 0.00 3.41
3408 6426 2.534757 GCAACCTTCGCTATCTTCGTAC 59.465 50.000 0.00 0.00 0.00 3.67
3442 6463 0.038526 AGCGTCTGTTCTGTAACCCG 60.039 55.000 0.00 0.00 34.49 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.169592 GCCAGGAAAAACTTATTATACTACACA 57.830 33.333 0.00 0.00 0.00 3.72
5 6 9.392259 AGCCAGGAAAAACTTATTATACTACAC 57.608 33.333 0.00 0.00 0.00 2.90
6 7 9.609346 GAGCCAGGAAAAACTTATTATACTACA 57.391 33.333 0.00 0.00 0.00 2.74
7 8 9.833917 AGAGCCAGGAAAAACTTATTATACTAC 57.166 33.333 0.00 0.00 0.00 2.73
9 10 9.833917 GTAGAGCCAGGAAAAACTTATTATACT 57.166 33.333 0.00 0.00 0.00 2.12
10 11 9.833917 AGTAGAGCCAGGAAAAACTTATTATAC 57.166 33.333 0.00 0.00 0.00 1.47
11 12 9.832445 CAGTAGAGCCAGGAAAAACTTATTATA 57.168 33.333 0.00 0.00 0.00 0.98
12 13 8.548877 TCAGTAGAGCCAGGAAAAACTTATTAT 58.451 33.333 0.00 0.00 0.00 1.28
13 14 7.913789 TCAGTAGAGCCAGGAAAAACTTATTA 58.086 34.615 0.00 0.00 0.00 0.98
14 15 6.779860 TCAGTAGAGCCAGGAAAAACTTATT 58.220 36.000 0.00 0.00 0.00 1.40
15 16 6.013293 ACTCAGTAGAGCCAGGAAAAACTTAT 60.013 38.462 0.00 0.00 46.09 1.73
16 17 5.307196 ACTCAGTAGAGCCAGGAAAAACTTA 59.693 40.000 0.00 0.00 46.09 2.24
17 18 4.103311 ACTCAGTAGAGCCAGGAAAAACTT 59.897 41.667 0.00 0.00 46.09 2.66
18 19 3.648545 ACTCAGTAGAGCCAGGAAAAACT 59.351 43.478 0.00 0.00 46.09 2.66
19 20 3.748568 CACTCAGTAGAGCCAGGAAAAAC 59.251 47.826 0.00 0.00 46.09 2.43
20 21 3.646162 TCACTCAGTAGAGCCAGGAAAAA 59.354 43.478 0.00 0.00 46.09 1.94
21 22 3.239449 TCACTCAGTAGAGCCAGGAAAA 58.761 45.455 0.00 0.00 46.09 2.29
22 23 2.828520 CTCACTCAGTAGAGCCAGGAAA 59.171 50.000 0.00 0.00 46.09 3.13
23 24 2.451490 CTCACTCAGTAGAGCCAGGAA 58.549 52.381 0.00 0.00 46.09 3.36
24 25 1.341482 CCTCACTCAGTAGAGCCAGGA 60.341 57.143 0.00 0.00 46.09 3.86
25 26 1.110442 CCTCACTCAGTAGAGCCAGG 58.890 60.000 0.00 0.00 46.09 4.45
26 27 1.110442 CCCTCACTCAGTAGAGCCAG 58.890 60.000 0.00 0.00 46.09 4.85
27 28 0.324738 CCCCTCACTCAGTAGAGCCA 60.325 60.000 0.00 0.00 46.09 4.75
28 29 0.324830 ACCCCTCACTCAGTAGAGCC 60.325 60.000 0.00 0.00 46.09 4.70
29 30 0.820871 CACCCCTCACTCAGTAGAGC 59.179 60.000 0.00 0.00 46.09 4.09
31 32 2.311841 TCATCACCCCTCACTCAGTAGA 59.688 50.000 0.00 0.00 0.00 2.59
32 33 2.428890 GTCATCACCCCTCACTCAGTAG 59.571 54.545 0.00 0.00 0.00 2.57
33 34 2.457598 GTCATCACCCCTCACTCAGTA 58.542 52.381 0.00 0.00 0.00 2.74
34 35 1.270907 GTCATCACCCCTCACTCAGT 58.729 55.000 0.00 0.00 0.00 3.41
35 36 0.174389 CGTCATCACCCCTCACTCAG 59.826 60.000 0.00 0.00 0.00 3.35
36 37 0.251608 TCGTCATCACCCCTCACTCA 60.252 55.000 0.00 0.00 0.00 3.41
37 38 0.173708 GTCGTCATCACCCCTCACTC 59.826 60.000 0.00 0.00 0.00 3.51
38 39 1.595993 CGTCGTCATCACCCCTCACT 61.596 60.000 0.00 0.00 0.00 3.41
39 40 1.153823 CGTCGTCATCACCCCTCAC 60.154 63.158 0.00 0.00 0.00 3.51
40 41 2.348104 CCGTCGTCATCACCCCTCA 61.348 63.158 0.00 0.00 0.00 3.86
41 42 2.494918 CCGTCGTCATCACCCCTC 59.505 66.667 0.00 0.00 0.00 4.30
42 43 3.771160 GCCGTCGTCATCACCCCT 61.771 66.667 0.00 0.00 0.00 4.79
64 65 5.296813 ACAAGCACTAAAATAAGCCGAAG 57.703 39.130 0.00 0.00 0.00 3.79
65 66 5.935789 ACTACAAGCACTAAAATAAGCCGAA 59.064 36.000 0.00 0.00 0.00 4.30
66 67 5.484715 ACTACAAGCACTAAAATAAGCCGA 58.515 37.500 0.00 0.00 0.00 5.54
67 68 5.500290 CGACTACAAGCACTAAAATAAGCCG 60.500 44.000 0.00 0.00 0.00 5.52
68 69 5.350640 ACGACTACAAGCACTAAAATAAGCC 59.649 40.000 0.00 0.00 0.00 4.35
69 70 6.090358 TGACGACTACAAGCACTAAAATAAGC 59.910 38.462 0.00 0.00 0.00 3.09
70 71 7.328737 AGTGACGACTACAAGCACTAAAATAAG 59.671 37.037 0.00 0.00 37.98 1.73
71 72 7.149973 AGTGACGACTACAAGCACTAAAATAA 58.850 34.615 0.00 0.00 37.98 1.40
72 73 6.684686 AGTGACGACTACAAGCACTAAAATA 58.315 36.000 0.00 0.00 37.98 1.40
73 74 5.539048 AGTGACGACTACAAGCACTAAAAT 58.461 37.500 0.00 0.00 37.98 1.82
74 75 4.940463 AGTGACGACTACAAGCACTAAAA 58.060 39.130 0.00 0.00 37.98 1.52
75 76 4.579454 AGTGACGACTACAAGCACTAAA 57.421 40.909 0.00 0.00 37.98 1.85
76 77 4.999311 TCTAGTGACGACTACAAGCACTAA 59.001 41.667 0.00 0.00 40.36 2.24
77 78 4.572909 TCTAGTGACGACTACAAGCACTA 58.427 43.478 0.00 0.00 40.08 2.74
78 79 3.409570 TCTAGTGACGACTACAAGCACT 58.590 45.455 0.00 0.00 42.04 4.40
79 80 3.826236 TCTAGTGACGACTACAAGCAC 57.174 47.619 0.00 0.00 33.21 4.40
80 81 3.128764 CCATCTAGTGACGACTACAAGCA 59.871 47.826 0.00 0.00 33.21 3.91
81 82 3.377485 TCCATCTAGTGACGACTACAAGC 59.623 47.826 0.00 0.00 33.21 4.01
82 83 5.529430 AGATCCATCTAGTGACGACTACAAG 59.471 44.000 0.00 0.00 34.85 3.16
83 84 5.437946 AGATCCATCTAGTGACGACTACAA 58.562 41.667 0.00 0.00 34.85 2.41
84 85 5.037383 AGATCCATCTAGTGACGACTACA 57.963 43.478 0.00 0.00 34.85 2.74
85 86 7.493743 TTTAGATCCATCTAGTGACGACTAC 57.506 40.000 0.00 0.00 40.23 2.73
86 87 7.720074 ACATTTAGATCCATCTAGTGACGACTA 59.280 37.037 13.71 0.00 40.23 2.59
87 88 6.547880 ACATTTAGATCCATCTAGTGACGACT 59.452 38.462 13.71 0.00 40.23 4.18
88 89 6.740110 ACATTTAGATCCATCTAGTGACGAC 58.260 40.000 13.71 0.00 40.23 4.34
89 90 6.961360 ACATTTAGATCCATCTAGTGACGA 57.039 37.500 13.71 0.00 40.23 4.20
90 91 9.698309 AAATACATTTAGATCCATCTAGTGACG 57.302 33.333 13.71 0.00 40.23 4.35
126 127 9.887629 ATCATGGCATTACAATGAACATAAAAA 57.112 25.926 0.00 0.00 38.70 1.94
127 128 9.887629 AATCATGGCATTACAATGAACATAAAA 57.112 25.926 0.00 0.92 38.70 1.52
131 132 9.537192 CTTTAATCATGGCATTACAATGAACAT 57.463 29.630 0.00 6.47 38.70 2.71
132 133 8.747471 TCTTTAATCATGGCATTACAATGAACA 58.253 29.630 0.00 4.54 38.70 3.18
133 134 9.754382 ATCTTTAATCATGGCATTACAATGAAC 57.246 29.630 0.00 0.00 38.70 3.18
134 135 9.752961 CATCTTTAATCATGGCATTACAATGAA 57.247 29.630 0.00 0.00 38.70 2.57
135 136 9.134055 TCATCTTTAATCATGGCATTACAATGA 57.866 29.630 0.00 0.00 38.70 2.57
136 137 9.752961 TTCATCTTTAATCATGGCATTACAATG 57.247 29.630 0.00 0.00 39.40 2.82
144 145 9.577222 TCAATCTATTCATCTTTAATCATGGCA 57.423 29.630 0.00 0.00 0.00 4.92
185 186 8.275632 GCTTTCAGCGAATTTTCAATAGTTTTT 58.724 29.630 0.00 0.00 0.00 1.94
186 187 7.095649 GGCTTTCAGCGAATTTTCAATAGTTTT 60.096 33.333 0.00 0.00 43.62 2.43
187 188 6.366061 GGCTTTCAGCGAATTTTCAATAGTTT 59.634 34.615 0.00 0.00 43.62 2.66
188 189 5.863935 GGCTTTCAGCGAATTTTCAATAGTT 59.136 36.000 0.00 0.00 43.62 2.24
189 190 5.183904 AGGCTTTCAGCGAATTTTCAATAGT 59.816 36.000 0.00 0.00 43.62 2.12
190 191 5.644644 AGGCTTTCAGCGAATTTTCAATAG 58.355 37.500 0.00 0.00 43.62 1.73
191 192 5.182950 TGAGGCTTTCAGCGAATTTTCAATA 59.817 36.000 0.00 0.00 43.62 1.90
192 193 4.022068 TGAGGCTTTCAGCGAATTTTCAAT 60.022 37.500 0.00 0.00 43.62 2.57
193 194 3.317711 TGAGGCTTTCAGCGAATTTTCAA 59.682 39.130 0.00 0.00 43.62 2.69
194 195 2.884012 TGAGGCTTTCAGCGAATTTTCA 59.116 40.909 0.00 0.00 43.62 2.69
206 207 6.619801 TTCAACTTTTAGACTGAGGCTTTC 57.380 37.500 0.00 0.00 0.00 2.62
217 218 6.235664 GTGGGTGGACTATTCAACTTTTAGA 58.764 40.000 0.00 0.00 0.00 2.10
243 244 2.621338 TCACTGATTTCGATGCAGACC 58.379 47.619 14.24 0.00 33.94 3.85
254 255 3.686241 CGATGACCACACATCACTGATTT 59.314 43.478 0.00 0.00 44.57 2.17
255 256 3.055891 TCGATGACCACACATCACTGATT 60.056 43.478 0.00 0.00 44.57 2.57
256 257 2.497273 TCGATGACCACACATCACTGAT 59.503 45.455 0.00 0.00 44.57 2.90
257 258 1.892474 TCGATGACCACACATCACTGA 59.108 47.619 0.00 0.00 44.57 3.41
258 259 2.368655 TCGATGACCACACATCACTG 57.631 50.000 0.00 0.00 44.57 3.66
259 260 3.616956 AATCGATGACCACACATCACT 57.383 42.857 0.00 0.00 44.57 3.41
260 261 4.870426 ACTAAATCGATGACCACACATCAC 59.130 41.667 0.00 0.00 44.57 3.06
261 262 5.084818 ACTAAATCGATGACCACACATCA 57.915 39.130 0.00 0.00 44.57 3.07
262 263 8.988064 ATATACTAAATCGATGACCACACATC 57.012 34.615 0.00 0.00 41.98 3.06
263 264 9.778741 AAATATACTAAATCGATGACCACACAT 57.221 29.630 0.00 0.00 0.00 3.21
264 265 9.607988 AAAATATACTAAATCGATGACCACACA 57.392 29.630 0.00 0.00 0.00 3.72
302 313 8.687292 ACTACTCGTATTCATGGTTGATACTA 57.313 34.615 0.00 0.00 0.00 1.82
315 326 7.646922 ACCAACATTTCGATACTACTCGTATTC 59.353 37.037 0.00 0.00 38.90 1.75
350 368 1.225855 TCTTCATTGTGTGTCGGCAC 58.774 50.000 14.58 14.58 45.44 5.01
422 477 9.802039 ACTAATGGCCGATCCTAAATAAAATAA 57.198 29.630 0.00 0.00 35.26 1.40
424 479 9.449719 CTACTAATGGCCGATCCTAAATAAAAT 57.550 33.333 0.00 0.00 35.26 1.82
471 526 3.088532 ACACACAGAGTTGCCTCAAAAA 58.911 40.909 0.00 0.00 40.40 1.94
472 527 2.423185 CACACACAGAGTTGCCTCAAAA 59.577 45.455 0.00 0.00 40.40 2.44
473 528 2.016318 CACACACAGAGTTGCCTCAAA 58.984 47.619 0.00 0.00 40.40 2.69
474 529 1.065491 ACACACACAGAGTTGCCTCAA 60.065 47.619 0.00 0.00 40.40 3.02
475 530 0.541392 ACACACACAGAGTTGCCTCA 59.459 50.000 0.00 0.00 40.40 3.86
476 531 0.940126 CACACACACAGAGTTGCCTC 59.060 55.000 0.00 0.00 38.04 4.70
477 532 0.253044 ACACACACACAGAGTTGCCT 59.747 50.000 0.00 0.00 0.00 4.75
478 533 0.378257 CACACACACACAGAGTTGCC 59.622 55.000 0.00 0.00 0.00 4.52
479 534 1.086696 ACACACACACACAGAGTTGC 58.913 50.000 0.00 0.00 0.00 4.17
480 535 2.076100 ACACACACACACACAGAGTTG 58.924 47.619 0.00 0.00 0.00 3.16
481 536 2.076100 CACACACACACACACAGAGTT 58.924 47.619 0.00 0.00 0.00 3.01
482 537 1.001974 ACACACACACACACACAGAGT 59.998 47.619 0.00 0.00 0.00 3.24
483 538 1.394572 CACACACACACACACACAGAG 59.605 52.381 0.00 0.00 0.00 3.35
484 539 1.437625 CACACACACACACACACAGA 58.562 50.000 0.00 0.00 0.00 3.41
485 540 0.447406 CCACACACACACACACACAG 59.553 55.000 0.00 0.00 0.00 3.66
486 541 1.581727 GCCACACACACACACACACA 61.582 55.000 0.00 0.00 0.00 3.72
487 542 1.136565 GCCACACACACACACACAC 59.863 57.895 0.00 0.00 0.00 3.82
488 543 0.890996 TTGCCACACACACACACACA 60.891 50.000 0.00 0.00 0.00 3.72
489 544 0.455972 GTTGCCACACACACACACAC 60.456 55.000 0.00 0.00 0.00 3.82
490 545 1.590610 GGTTGCCACACACACACACA 61.591 55.000 0.00 0.00 0.00 3.72
491 546 1.138671 GGTTGCCACACACACACAC 59.861 57.895 0.00 0.00 0.00 3.82
492 547 2.402572 CGGTTGCCACACACACACA 61.403 57.895 0.00 0.00 0.00 3.72
493 548 1.928706 AACGGTTGCCACACACACAC 61.929 55.000 0.00 0.00 0.00 3.82
494 549 1.244697 AAACGGTTGCCACACACACA 61.245 50.000 0.00 0.00 0.00 3.72
495 550 0.524604 GAAACGGTTGCCACACACAC 60.525 55.000 0.00 0.00 0.00 3.82
496 551 1.803943 GAAACGGTTGCCACACACA 59.196 52.632 0.00 0.00 0.00 3.72
497 552 1.298041 CGAAACGGTTGCCACACAC 60.298 57.895 0.00 0.00 0.00 3.82
523 578 3.999001 CGACAGCAGCATGTGGATAATAT 59.001 43.478 0.00 0.00 39.31 1.28
549 604 1.804748 CGTTCTTTTGGTAGTGGAGGC 59.195 52.381 0.00 0.00 0.00 4.70
554 609 2.473984 GACGACCGTTCTTTTGGTAGTG 59.526 50.000 1.86 0.00 43.00 2.74
561 616 1.139455 TGGAAGGACGACCGTTCTTTT 59.861 47.619 16.18 0.00 43.44 2.27
636 698 1.002011 GTTGACTCCTCCTTGGCCC 60.002 63.158 0.00 0.00 35.26 5.80
649 713 0.790814 GCTTGCTCTACCGTGTTGAC 59.209 55.000 0.00 0.00 0.00 3.18
674 762 1.688197 CTTTGGTGGTGAAGCAATGGT 59.312 47.619 0.00 0.00 45.31 3.55
685 773 1.133199 TGGATTGCCTTCTTTGGTGGT 60.133 47.619 0.00 0.00 34.31 4.16
694 782 3.019564 ACAAGTGCTATGGATTGCCTTC 58.980 45.455 0.00 0.00 34.31 3.46
700 788 3.689347 TGCTGAACAAGTGCTATGGATT 58.311 40.909 0.00 0.00 0.00 3.01
734 830 3.075148 GGAAGGTGGACAAGTTCTTAGC 58.925 50.000 0.00 0.00 0.00 3.09
755 861 1.597742 CGCCATATCCTTGGGTGAAG 58.402 55.000 0.00 0.00 37.24 3.02
760 866 2.436109 CCCCGCCATATCCTTGGG 59.564 66.667 0.00 0.00 37.24 4.12
762 868 1.228245 CACCCCCGCCATATCCTTG 60.228 63.158 0.00 0.00 0.00 3.61
788 894 4.096003 AGTTCATGGCCCCCGTCG 62.096 66.667 0.00 0.00 0.00 5.12
798 904 0.820226 TGCCGAGGAGAGAGTTCATG 59.180 55.000 0.00 0.00 0.00 3.07
807 913 2.650116 GGTGAGCTTGCCGAGGAGA 61.650 63.158 0.00 0.00 0.00 3.71
847 953 0.103937 CGGACCCTCTTGAGCAGATC 59.896 60.000 0.00 0.00 0.00 2.75
1077 1186 1.342496 CACAGAGTCTTGAGCTGGTGA 59.658 52.381 0.00 0.00 34.05 4.02
1079 1188 0.683973 CCACAGAGTCTTGAGCTGGT 59.316 55.000 0.00 0.00 34.05 4.00
1164 1273 1.270147 GGAAGCTTGTACCTGTCACGT 60.270 52.381 2.10 0.00 0.00 4.49
1213 1367 9.800433 CTATTAATCTCGATGTAGCATTGAGAT 57.200 33.333 25.07 25.07 46.13 2.75
1218 1372 9.632807 GAACTCTATTAATCTCGATGTAGCATT 57.367 33.333 0.00 0.00 0.00 3.56
1270 1430 8.409371 CACTATAGTAACTCTCATCAAGCTTGA 58.591 37.037 30.23 30.23 42.14 3.02
1525 1685 4.193826 AGAGTGCGTGAAACAGATACAT 57.806 40.909 0.00 0.00 35.74 2.29
1764 1948 8.081517 TCAATCTGATCTGGCCATTTAAAAAT 57.918 30.769 5.51 0.00 0.00 1.82
1787 1973 7.716799 AAATACAAATAGAGGCATTGGTTCA 57.283 32.000 0.00 0.00 0.00 3.18
1886 4050 6.127675 TGGCTGTTTAAACGTTTTAGTTCCTT 60.128 34.615 20.19 0.00 32.43 3.36
1962 4126 9.691362 TTTCTTTTGCATCAATTAAACTACTCC 57.309 29.630 0.00 0.00 0.00 3.85
2025 4342 6.844097 TGGAAACTAATTTGTATTCCCCAC 57.156 37.500 20.06 6.69 39.01 4.61
2029 4346 8.770438 TTGCAATGGAAACTAATTTGTATTCC 57.230 30.769 18.02 18.02 39.96 3.01
2051 4373 2.733026 GGTGTGATGACTTGCAAATTGC 59.267 45.455 11.58 11.58 45.29 3.56
2052 4374 4.247267 AGGTGTGATGACTTGCAAATTG 57.753 40.909 0.00 0.00 0.00 2.32
2053 4375 5.711506 TCATAGGTGTGATGACTTGCAAATT 59.288 36.000 0.00 0.00 0.00 1.82
2054 4376 5.255687 TCATAGGTGTGATGACTTGCAAAT 58.744 37.500 0.00 0.00 0.00 2.32
2055 4377 4.650734 TCATAGGTGTGATGACTTGCAAA 58.349 39.130 0.00 0.00 0.00 3.68
2274 4985 4.322567 GGGAATCAACATCATCTAGAGGC 58.677 47.826 0.00 0.00 0.00 4.70
2308 5019 6.925718 TCATCTATGCGGAATGTTCTCTTAAG 59.074 38.462 0.00 0.00 0.00 1.85
2341 5052 4.096382 TGAAACTTCTTCCAGTTCAACAGC 59.904 41.667 0.00 0.00 35.87 4.40
2472 5186 3.347216 CAAAGGACCAGTACCAATGGAG 58.653 50.000 6.16 0.00 40.51 3.86
2501 5215 5.261216 TCATCCCTTTTAAGTTCCCATCAC 58.739 41.667 0.00 0.00 0.00 3.06
2550 5264 5.006386 GTCTTCAAATGGTGTGGAAGATCT 58.994 41.667 6.26 0.00 45.13 2.75
2676 5589 0.991920 ATCATCCAAACGTCCCCACT 59.008 50.000 0.00 0.00 0.00 4.00
2677 5590 1.094785 CATCATCCAAACGTCCCCAC 58.905 55.000 0.00 0.00 0.00 4.61
2678 5591 0.695924 ACATCATCCAAACGTCCCCA 59.304 50.000 0.00 0.00 0.00 4.96
2679 5592 2.561569 CTACATCATCCAAACGTCCCC 58.438 52.381 0.00 0.00 0.00 4.81
2680 5593 1.940613 GCTACATCATCCAAACGTCCC 59.059 52.381 0.00 0.00 0.00 4.46
2681 5594 2.609459 CTGCTACATCATCCAAACGTCC 59.391 50.000 0.00 0.00 0.00 4.79
2682 5595 3.521560 TCTGCTACATCATCCAAACGTC 58.478 45.455 0.00 0.00 0.00 4.34
2719 5632 9.507329 GGCTGGATCATATTTCTATTAACAAGA 57.493 33.333 0.00 0.00 0.00 3.02
2908 5821 2.167075 GCCATTATGCTCTTTGCCACTT 59.833 45.455 0.00 0.00 42.00 3.16
2933 5846 1.802365 GGTTTCTGTAATCGCACGGTT 59.198 47.619 0.00 0.00 0.00 4.44
2934 5847 1.270412 TGGTTTCTGTAATCGCACGGT 60.270 47.619 0.00 0.00 0.00 4.83
2957 5966 3.773860 AGTCAGTGAGCGAAGATGTAG 57.226 47.619 0.00 0.00 0.00 2.74
2963 5972 3.305398 AAAGGTAGTCAGTGAGCGAAG 57.695 47.619 0.00 0.00 0.00 3.79
3207 6222 4.458295 CAGTTGATGGCAGTCTTTCAAGAT 59.542 41.667 0.92 0.00 37.39 2.40
3212 6227 2.227388 CCACAGTTGATGGCAGTCTTTC 59.773 50.000 0.00 0.00 0.00 2.62
3246 6261 1.472082 TGACAAATAGGCGCACCAATG 59.528 47.619 10.83 4.85 39.06 2.82
3334 6349 1.068588 CTCACTGGGTCGTCAGTTTCA 59.931 52.381 6.20 0.00 44.74 2.69
3408 6426 1.169661 ACGCTCGGCTATCTCTCCAG 61.170 60.000 0.00 0.00 0.00 3.86
3442 6463 2.335712 GCAAGGGTAGGTGCAGCAC 61.336 63.158 17.97 17.97 40.58 4.40
3512 6533 0.114954 TTTTGAAGGGAGGCCATGCT 59.885 50.000 5.01 0.00 0.00 3.79


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

AutoCloner maintained by Alex Coulton.