Multiple sequence alignment - TraesCS4B01G193200

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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 TraesCS4B01G193200 chr4B 100.000 4599 0 0 1 4599 416302829 416307427 0.000000e+00 8493
1 TraesCS4B01G193200 chr4B 87.121 132 16 1 4436 4567 416436542 416436412 1.030000e-31 148
2 TraesCS4B01G193200 chr4D 92.839 3910 167 47 70 3919 337149804 337153660 0.000000e+00 5565
3 TraesCS4B01G193200 chr4D 87.862 725 58 22 3880 4599 337153656 337154355 0.000000e+00 824
4 TraesCS4B01G193200 chr4D 85.242 454 42 7 2950 3403 439783654 439783226 1.170000e-120 444
5 TraesCS4B01G193200 chr4D 82.353 289 26 17 3576 3853 439782530 439782256 1.290000e-55 228
6 TraesCS4B01G193200 chr4A 91.489 2479 104 55 1974 4395 135615838 135613410 0.000000e+00 3310
7 TraesCS4B01G193200 chr4A 93.314 1346 67 13 604 1933 135617180 135615842 0.000000e+00 1965
8 TraesCS4B01G193200 chr4A 90.354 311 13 2 141 451 135617933 135617640 4.310000e-105 392
9 TraesCS4B01G193200 chr4A 89.205 176 7 4 433 606 135617618 135617453 4.660000e-50 209
10 TraesCS4B01G193200 chr4A 87.417 151 16 3 4450 4599 135612100 135611952 2.200000e-38 171
11 TraesCS4B01G193200 chr2A 83.257 657 108 2 2166 2821 41756832 41756177 1.830000e-168 603
12 TraesCS4B01G193200 chr2A 88.620 413 46 1 1116 1527 758449604 758449192 6.870000e-138 501
13 TraesCS4B01G193200 chr2A 87.374 396 50 0 1131 1526 41992682 41993077 5.420000e-124 455
14 TraesCS4B01G193200 chr2A 90.592 287 21 3 3117 3403 644310944 644310664 4.340000e-100 375
15 TraesCS4B01G193200 chr2A 88.688 221 13 7 3631 3840 644309316 644309097 4.560000e-65 259
16 TraesCS4B01G193200 chr2A 87.113 194 25 0 3141 3334 41755980 41755787 2.150000e-53 220
17 TraesCS4B01G193200 chr2B 82.470 656 115 0 2166 2821 64777820 64777165 3.990000e-160 575
18 TraesCS4B01G193200 chr2B 88.862 413 45 1 1116 1527 770767412 770767000 1.480000e-139 507
19 TraesCS4B01G193200 chr2B 86.849 403 53 0 1124 1526 64778504 64778102 7.020000e-123 451
20 TraesCS4B01G193200 chr2B 86.239 218 18 7 3634 3840 746115040 746115256 4.630000e-55 226
21 TraesCS4B01G193200 chr2B 86.598 194 26 0 3141 3334 64857739 64857932 1.000000e-51 215
22 TraesCS4B01G193200 chr2B 84.459 148 18 3 3000 3146 707174343 707174200 1.730000e-29 141
23 TraesCS4B01G193200 chr2D 82.317 656 116 0 2166 2821 37055066 37054411 1.860000e-158 569
24 TraesCS4B01G193200 chr2D 82.317 656 116 0 2166 2821 37073687 37073032 1.860000e-158 569
25 TraesCS4B01G193200 chr2D 86.849 403 53 0 1124 1526 37055749 37055347 7.020000e-123 451
26 TraesCS4B01G193200 chr2D 86.600 403 54 0 1124 1526 37074381 37073979 3.260000e-121 446
27 TraesCS4B01G193200 chr2D 88.660 194 22 0 3141 3334 37072918 37072725 2.140000e-58 237
28 TraesCS4B01G193200 chr2D 87.629 194 24 0 3141 3334 37054297 37054104 4.630000e-55 226
29 TraesCS4B01G193200 chr2D 87.629 194 24 0 3141 3334 37209720 37209913 4.630000e-55 226
30 TraesCS4B01G193200 chrUn 88.264 409 48 0 1119 1527 17299756 17299348 1.490000e-134 490
31 TraesCS4B01G193200 chrUn 88.500 200 23 0 3141 3340 17298413 17298214 4.600000e-60 243
32 TraesCS4B01G193200 chr3B 85.408 233 19 7 3619 3840 333940456 333940228 1.290000e-55 228
33 TraesCS4B01G193200 chr3B 82.979 188 31 1 4412 4599 12597785 12597971 7.910000e-38 169
34 TraesCS4B01G193200 chr6A 82.703 185 31 1 4415 4599 553934359 553934542 3.680000e-36 163
35 TraesCS4B01G193200 chr6A 83.030 165 26 2 4436 4599 569685419 569685256 1.030000e-31 148


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 TraesCS4B01G193200 chr4B 416302829 416307427 4598 False 8493.000000 8493 100.000000 1 4599 1 chr4B.!!$F1 4598
1 TraesCS4B01G193200 chr4D 337149804 337154355 4551 False 3194.500000 5565 90.350500 70 4599 2 chr4D.!!$F1 4529
2 TraesCS4B01G193200 chr4D 439782256 439783654 1398 True 336.000000 444 83.797500 2950 3853 2 chr4D.!!$R1 903
3 TraesCS4B01G193200 chr4A 135611952 135617933 5981 True 1209.400000 3310 90.355800 141 4599 5 chr4A.!!$R1 4458
4 TraesCS4B01G193200 chr2A 41755787 41756832 1045 True 411.500000 603 85.185000 2166 3334 2 chr2A.!!$R2 1168
5 TraesCS4B01G193200 chr2A 644309097 644310944 1847 True 317.000000 375 89.640000 3117 3840 2 chr2A.!!$R3 723
6 TraesCS4B01G193200 chr2B 64777165 64778504 1339 True 513.000000 575 84.659500 1124 2821 2 chr2B.!!$R3 1697
7 TraesCS4B01G193200 chr2D 37072725 37074381 1656 True 417.333333 569 85.859000 1124 3334 3 chr2D.!!$R2 2210
8 TraesCS4B01G193200 chr2D 37054104 37055749 1645 True 415.333333 569 85.598333 1124 3334 3 chr2D.!!$R1 2210
9 TraesCS4B01G193200 chrUn 17298214 17299756 1542 True 366.500000 490 88.382000 1119 3340 2 chrUn.!!$R1 2221

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
506 547 0.099791 ACAAACCAAAACCGCTGTCG 59.900 50.000 0.00 0.00 0.00 4.35 F
800 1131 0.411848 ACGAAACCCCAATCCCCATT 59.588 50.000 0.00 0.00 0.00 3.16 F
898 1234 1.190763 CGTCAACGGAACAGGTTAACG 59.809 52.381 0.00 7.05 33.28 3.18 F
2306 2679 0.246635 CCTTCGTCGACCTTGTGGAT 59.753 55.000 10.58 0.00 37.04 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1540 1889 1.518774 GGGCAATGCATGTTGAGGG 59.481 57.895 7.79 0.0 0.00 4.30 R
1612 1961 1.721489 CGCCTGAATCGACAAACAACG 60.721 52.381 0.00 0.0 0.00 4.10 R
2894 3282 0.591236 CGTGCGAACAAACAACCCTG 60.591 55.000 0.00 0.0 0.00 4.45 R
4051 5748 0.307760 CTTTGCCGAGAACAAAGCGT 59.692 50.000 3.56 0.0 45.23 5.07 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
17 18 2.190578 CCACCTTCATCGGAGGCC 59.809 66.667 0.00 0.00 0.00 5.19
27 28 3.726517 CGGAGGCCGCACAACAAG 61.727 66.667 9.31 0.00 41.17 3.16
28 29 3.365265 GGAGGCCGCACAACAAGG 61.365 66.667 9.31 0.00 0.00 3.61
35 36 4.347453 GCACAACAAGGCCGGCAG 62.347 66.667 30.85 19.78 0.00 4.85
36 37 2.594303 CACAACAAGGCCGGCAGA 60.594 61.111 30.85 0.00 0.00 4.26
37 38 1.973281 CACAACAAGGCCGGCAGAT 60.973 57.895 30.85 10.95 0.00 2.90
38 39 1.228552 ACAACAAGGCCGGCAGATT 60.229 52.632 30.85 16.95 0.00 2.40
39 40 0.827507 ACAACAAGGCCGGCAGATTT 60.828 50.000 30.85 13.74 0.00 2.17
40 41 0.109132 CAACAAGGCCGGCAGATTTC 60.109 55.000 30.85 9.73 0.00 2.17
41 42 0.251341 AACAAGGCCGGCAGATTTCT 60.251 50.000 30.85 12.30 0.00 2.52
42 43 0.678048 ACAAGGCCGGCAGATTTCTC 60.678 55.000 30.85 8.01 0.00 2.87
43 44 0.677731 CAAGGCCGGCAGATTTCTCA 60.678 55.000 30.85 0.00 0.00 3.27
44 45 0.257039 AAGGCCGGCAGATTTCTCAT 59.743 50.000 30.85 0.00 0.00 2.90
45 46 1.131638 AGGCCGGCAGATTTCTCATA 58.868 50.000 30.85 0.00 0.00 2.15
46 47 1.490490 AGGCCGGCAGATTTCTCATAA 59.510 47.619 30.85 0.00 0.00 1.90
47 48 2.092429 AGGCCGGCAGATTTCTCATAAA 60.092 45.455 30.85 0.00 0.00 1.40
48 49 2.887152 GGCCGGCAGATTTCTCATAAAT 59.113 45.455 30.85 0.00 0.00 1.40
49 50 4.072131 GGCCGGCAGATTTCTCATAAATA 58.928 43.478 30.85 0.00 0.00 1.40
50 51 4.518970 GGCCGGCAGATTTCTCATAAATAA 59.481 41.667 30.85 0.00 0.00 1.40
51 52 5.183904 GGCCGGCAGATTTCTCATAAATAAT 59.816 40.000 30.85 0.00 0.00 1.28
52 53 6.088824 GCCGGCAGATTTCTCATAAATAATG 58.911 40.000 24.80 0.00 36.88 1.90
53 54 6.294176 GCCGGCAGATTTCTCATAAATAATGT 60.294 38.462 24.80 0.00 36.89 2.71
54 55 7.301054 CCGGCAGATTTCTCATAAATAATGTC 58.699 38.462 0.00 0.00 36.89 3.06
55 56 7.011773 CGGCAGATTTCTCATAAATAATGTCG 58.988 38.462 7.37 7.37 36.89 4.35
56 57 7.307396 CGGCAGATTTCTCATAAATAATGTCGT 60.307 37.037 11.15 0.00 36.89 4.34
57 58 7.800380 GGCAGATTTCTCATAAATAATGTCGTG 59.200 37.037 0.00 0.00 36.89 4.35
58 59 8.551205 GCAGATTTCTCATAAATAATGTCGTGA 58.449 33.333 0.00 0.00 36.89 4.35
65 66 9.468532 TCTCATAAATAATGTCGTGATTCTCTG 57.531 33.333 0.00 0.00 36.89 3.35
66 67 8.593492 TCATAAATAATGTCGTGATTCTCTGG 57.407 34.615 0.00 0.00 36.89 3.86
67 68 8.421002 TCATAAATAATGTCGTGATTCTCTGGA 58.579 33.333 0.00 0.00 36.89 3.86
68 69 9.212641 CATAAATAATGTCGTGATTCTCTGGAT 57.787 33.333 0.00 0.00 0.00 3.41
69 70 7.488187 AAATAATGTCGTGATTCTCTGGATG 57.512 36.000 0.00 0.00 0.00 3.51
70 71 2.299993 TGTCGTGATTCTCTGGATGC 57.700 50.000 0.00 0.00 0.00 3.91
71 72 1.134699 TGTCGTGATTCTCTGGATGCC 60.135 52.381 0.00 0.00 0.00 4.40
72 73 0.103026 TCGTGATTCTCTGGATGCCG 59.897 55.000 0.00 0.00 0.00 5.69
73 74 0.179100 CGTGATTCTCTGGATGCCGT 60.179 55.000 0.00 0.00 0.00 5.68
74 75 1.293924 GTGATTCTCTGGATGCCGTG 58.706 55.000 0.00 0.00 0.00 4.94
75 76 0.462581 TGATTCTCTGGATGCCGTGC 60.463 55.000 0.00 0.00 0.00 5.34
76 77 0.179062 GATTCTCTGGATGCCGTGCT 60.179 55.000 0.00 0.00 0.00 4.40
77 78 0.179062 ATTCTCTGGATGCCGTGCTC 60.179 55.000 0.00 0.00 0.00 4.26
78 79 2.202987 CTCTGGATGCCGTGCTCC 60.203 66.667 0.00 3.40 0.00 4.70
95 96 2.303311 GCTCCTCTCCTTAAGTGGTGTT 59.697 50.000 0.97 0.00 39.30 3.32
98 99 4.748701 TCCTCTCCTTAAGTGGTGTTAGT 58.251 43.478 0.97 0.00 39.30 2.24
112 113 1.068264 TGTTAGTCTCTGCGCTGACAG 60.068 52.381 22.92 12.53 39.12 3.51
113 114 0.109086 TTAGTCTCTGCGCTGACAGC 60.109 55.000 17.84 17.84 37.59 4.40
123 124 4.641645 CTGACAGCGGTGGCCCAA 62.642 66.667 19.55 0.00 41.24 4.12
125 126 2.270850 GACAGCGGTGGCCCAATA 59.729 61.111 20.20 0.00 41.24 1.90
132 133 2.676265 GGTGGCCCAATACGGTCCT 61.676 63.158 0.00 0.00 0.00 3.85
133 134 1.301954 GTGGCCCAATACGGTCCTT 59.698 57.895 0.00 0.00 0.00 3.36
134 135 1.029947 GTGGCCCAATACGGTCCTTG 61.030 60.000 0.00 0.00 0.00 3.61
135 136 1.453197 GGCCCAATACGGTCCTTGG 60.453 63.158 12.97 12.97 41.34 3.61
136 137 1.301954 GCCCAATACGGTCCTTGGT 59.698 57.895 16.66 0.00 40.28 3.67
137 138 0.323087 GCCCAATACGGTCCTTGGTT 60.323 55.000 16.66 0.00 40.28 3.67
138 139 1.889262 GCCCAATACGGTCCTTGGTTT 60.889 52.381 16.66 0.00 40.28 3.27
139 140 2.521126 CCCAATACGGTCCTTGGTTTT 58.479 47.619 16.66 0.00 40.28 2.43
148 149 2.158579 GGTCCTTGGTTTTGGTACCTCA 60.159 50.000 14.36 0.00 39.04 3.86
166 167 4.643385 CGTTGACGTGGCGTGCAC 62.643 66.667 6.82 6.82 41.37 4.57
185 186 1.101049 CGGTTGGCTGGTGACTTGTT 61.101 55.000 0.00 0.00 0.00 2.83
186 187 0.668535 GGTTGGCTGGTGACTTGTTC 59.331 55.000 0.00 0.00 0.00 3.18
217 218 2.433970 TCCAGAATGTCAGTGACACACA 59.566 45.455 27.70 6.47 45.65 3.72
218 219 3.071457 TCCAGAATGTCAGTGACACACAT 59.929 43.478 27.70 14.27 45.65 3.21
286 287 2.701780 CGACCGGACTCCACCTCTG 61.702 68.421 9.46 0.00 0.00 3.35
314 315 3.792047 CATGACAGTGCGGTGCGG 61.792 66.667 0.00 0.00 0.00 5.69
506 547 0.099791 ACAAACCAAAACCGCTGTCG 59.900 50.000 0.00 0.00 0.00 4.35
667 989 0.469917 CATAATGCTCCGACCCCACT 59.530 55.000 0.00 0.00 0.00 4.00
736 1065 1.663739 GCCCGTGGTTTTCCTTTCC 59.336 57.895 0.00 0.00 41.38 3.13
765 1095 1.082756 CAGGCGAGTTTTGCACGAC 60.083 57.895 0.00 0.00 39.55 4.34
791 1122 1.452801 GTCTTCCCACGAAACCCCA 59.547 57.895 0.00 0.00 0.00 4.96
797 1128 1.680989 CCACGAAACCCCAATCCCC 60.681 63.158 0.00 0.00 0.00 4.81
800 1131 0.411848 ACGAAACCCCAATCCCCATT 59.588 50.000 0.00 0.00 0.00 3.16
812 1143 2.515901 CCCATTCCCATCCCGTCC 59.484 66.667 0.00 0.00 0.00 4.79
846 1182 1.697982 AGGTATAAATGGAGGACGGCC 59.302 52.381 0.00 0.00 0.00 6.13
847 1183 1.607251 GGTATAAATGGAGGACGGCCG 60.607 57.143 26.86 26.86 39.96 6.13
892 1228 1.931551 CACACGTCAACGGAACAGG 59.068 57.895 7.53 0.00 44.95 4.00
896 1232 2.203401 CACGTCAACGGAACAGGTTAA 58.797 47.619 7.53 0.00 44.95 2.01
898 1234 1.190763 CGTCAACGGAACAGGTTAACG 59.809 52.381 0.00 7.05 33.28 3.18
909 1245 1.735571 CAGGTTAACGAAATCCCCACG 59.264 52.381 0.00 0.00 0.00 4.94
1569 1918 1.287442 TGCATTGCCCCTTCCTCATTA 59.713 47.619 6.12 0.00 0.00 1.90
1612 1961 1.546476 ACTCGATCTGGTTGGTCTGTC 59.454 52.381 0.00 0.00 0.00 3.51
1716 2066 1.003718 GAGCAAGCCGGTGTACCTT 60.004 57.895 1.90 0.00 0.00 3.50
1844 2203 2.322161 CGAGTTGTCGTTTCCGTGTAT 58.678 47.619 0.00 0.00 41.57 2.29
1848 2207 4.813027 AGTTGTCGTTTCCGTGTATGTAT 58.187 39.130 0.00 0.00 35.01 2.29
1849 2208 5.953183 AGTTGTCGTTTCCGTGTATGTATA 58.047 37.500 0.00 0.00 35.01 1.47
1851 2210 5.565592 TGTCGTTTCCGTGTATGTATAGT 57.434 39.130 0.00 0.00 35.01 2.12
1852 2211 5.334319 TGTCGTTTCCGTGTATGTATAGTG 58.666 41.667 0.00 0.00 35.01 2.74
1853 2212 5.106197 TGTCGTTTCCGTGTATGTATAGTGT 60.106 40.000 0.00 0.00 35.01 3.55
1863 2222 8.540492 CCGTGTATGTATAGTGTTTTGAATCTC 58.460 37.037 0.00 0.00 0.00 2.75
1871 2230 9.593134 GTATAGTGTTTTGAATCTCATCAGAGT 57.407 33.333 0.00 0.00 42.66 3.24
1945 2305 4.910458 CCCCCAATTATGTAGGAGTAGG 57.090 50.000 0.00 0.00 0.00 3.18
1964 2324 6.769512 AGTAGGTCTTAACTCTTGATTTGCA 58.230 36.000 0.00 0.00 0.00 4.08
1965 2325 7.398024 AGTAGGTCTTAACTCTTGATTTGCAT 58.602 34.615 0.00 0.00 0.00 3.96
1966 2326 6.506500 AGGTCTTAACTCTTGATTTGCATG 57.493 37.500 0.00 0.00 0.00 4.06
1967 2327 6.006449 AGGTCTTAACTCTTGATTTGCATGT 58.994 36.000 0.00 0.00 0.00 3.21
1968 2328 7.168219 AGGTCTTAACTCTTGATTTGCATGTA 58.832 34.615 0.00 0.00 0.00 2.29
1969 2329 7.119846 AGGTCTTAACTCTTGATTTGCATGTAC 59.880 37.037 0.00 0.00 0.00 2.90
1970 2330 7.119846 GGTCTTAACTCTTGATTTGCATGTACT 59.880 37.037 0.00 0.00 0.00 2.73
1971 2331 9.151471 GTCTTAACTCTTGATTTGCATGTACTA 57.849 33.333 0.00 0.00 0.00 1.82
1978 2338 9.239002 CTCTTGATTTGCATGTACTAGTACTAC 57.761 37.037 28.56 19.32 37.00 2.73
1986 2346 3.285484 TGTACTAGTACTACCTGCTGGC 58.715 50.000 28.56 3.63 37.00 4.85
2088 2456 4.640789 ATCTGTATCTGAAGTGACCGAC 57.359 45.455 0.00 0.00 0.00 4.79
2306 2679 0.246635 CCTTCGTCGACCTTGTGGAT 59.753 55.000 10.58 0.00 37.04 3.41
2546 2919 1.738099 GCCTGAGCGTGTCATCGTT 60.738 57.895 0.00 0.00 33.51 3.85
2798 3177 0.595095 GGTTCAACTGCCAGAAGCTG 59.405 55.000 0.00 0.00 44.23 4.24
2836 3215 1.756430 GGGTGAGCTTTCCTGATTCC 58.244 55.000 7.81 0.00 0.00 3.01
2890 3278 4.022416 TGTTTGTCTTTGTCTTGTTGTGCT 60.022 37.500 0.00 0.00 0.00 4.40
2892 3280 5.888691 TTGTCTTTGTCTTGTTGTGCTAA 57.111 34.783 0.00 0.00 0.00 3.09
2893 3281 5.484173 TGTCTTTGTCTTGTTGTGCTAAG 57.516 39.130 0.00 0.00 0.00 2.18
2894 3282 4.201910 TGTCTTTGTCTTGTTGTGCTAAGC 60.202 41.667 0.00 0.00 0.00 3.09
2895 3283 3.944650 TCTTTGTCTTGTTGTGCTAAGCA 59.055 39.130 0.00 0.00 35.60 3.91
2896 3284 3.969117 TTGTCTTGTTGTGCTAAGCAG 57.031 42.857 0.00 0.00 40.08 4.24
2908 3302 2.360801 TGCTAAGCAGGGTTGTTTGTTC 59.639 45.455 0.00 0.00 33.32 3.18
3085 3479 3.577229 CTGCCGTGTGCTGCAATA 58.423 55.556 2.77 0.00 42.00 1.90
3087 3481 1.298602 CTGCCGTGTGCTGCAATATA 58.701 50.000 2.77 0.00 42.00 0.86
3089 3483 3.066380 CTGCCGTGTGCTGCAATATATA 58.934 45.455 2.77 0.00 42.00 0.86
3091 3485 4.071423 TGCCGTGTGCTGCAATATATATT 58.929 39.130 2.77 1.91 42.00 1.28
3092 3486 4.083377 TGCCGTGTGCTGCAATATATATTG 60.083 41.667 25.10 25.10 42.29 1.90
3126 3531 1.128200 TCTAATGTGATGTCCGGGGG 58.872 55.000 0.00 0.00 0.00 5.40
3359 3765 1.689959 GCACTCTTTTGTCCATTGCG 58.310 50.000 0.00 0.00 0.00 4.85
3465 4911 4.329697 GACGGCGGCGATCGAGAT 62.330 66.667 38.93 14.02 42.43 2.75
3589 5035 1.077265 CAACTCCAGGCCACCCAAT 59.923 57.895 5.01 0.00 0.00 3.16
3601 5227 1.285280 CACCCAATCCCCAGTAGACA 58.715 55.000 0.00 0.00 0.00 3.41
3602 5228 1.210478 CACCCAATCCCCAGTAGACAG 59.790 57.143 0.00 0.00 0.00 3.51
3604 5230 1.486726 CCCAATCCCCAGTAGACAGAC 59.513 57.143 0.00 0.00 0.00 3.51
3605 5231 1.486726 CCAATCCCCAGTAGACAGACC 59.513 57.143 0.00 0.00 0.00 3.85
3606 5232 1.137086 CAATCCCCAGTAGACAGACCG 59.863 57.143 0.00 0.00 0.00 4.79
3607 5233 0.629596 ATCCCCAGTAGACAGACCGA 59.370 55.000 0.00 0.00 0.00 4.69
3608 5234 0.323178 TCCCCAGTAGACAGACCGAC 60.323 60.000 0.00 0.00 0.00 4.79
3609 5235 1.321074 CCCCAGTAGACAGACCGACC 61.321 65.000 0.00 0.00 0.00 4.79
3610 5236 0.611062 CCCAGTAGACAGACCGACCA 60.611 60.000 0.00 0.00 0.00 4.02
3611 5237 1.254026 CCAGTAGACAGACCGACCAA 58.746 55.000 0.00 0.00 0.00 3.67
3612 5238 1.616865 CCAGTAGACAGACCGACCAAA 59.383 52.381 0.00 0.00 0.00 3.28
3613 5239 2.352814 CCAGTAGACAGACCGACCAAAG 60.353 54.545 0.00 0.00 0.00 2.77
3614 5240 1.272769 AGTAGACAGACCGACCAAAGC 59.727 52.381 0.00 0.00 0.00 3.51
3632 5264 1.219124 CCACGCCTGCATCAGTAGT 59.781 57.895 0.00 0.00 0.00 2.73
3633 5265 0.459899 CCACGCCTGCATCAGTAGTA 59.540 55.000 0.00 0.00 0.00 1.82
3634 5266 1.536922 CCACGCCTGCATCAGTAGTAG 60.537 57.143 0.00 0.00 0.00 2.57
3723 5355 7.284489 TCTGTTATGTTCTTAGTTTTGTGCCTT 59.716 33.333 0.00 0.00 0.00 4.35
3724 5356 7.199766 TGTTATGTTCTTAGTTTTGTGCCTTG 58.800 34.615 0.00 0.00 0.00 3.61
3733 5365 4.270008 AGTTTTGTGCCTTGTAGTGACTT 58.730 39.130 0.00 0.00 0.00 3.01
3734 5366 4.096382 AGTTTTGTGCCTTGTAGTGACTTG 59.904 41.667 0.00 0.00 0.00 3.16
3735 5367 3.275617 TTGTGCCTTGTAGTGACTTGT 57.724 42.857 0.00 0.00 0.00 3.16
3868 5526 3.701532 AATCACGAGCTACTACTGAGC 57.298 47.619 0.00 0.00 40.42 4.26
3897 5555 3.568430 TCGAGGAATCTAGAAGCGCAATA 59.432 43.478 11.47 0.00 0.00 1.90
3980 5677 6.459923 AGTGAGCTAATAATGGTAAGCTAGC 58.540 40.000 6.62 6.62 45.04 3.42
4015 5712 0.673985 GCAGTTCGGCCCTTTTTCTT 59.326 50.000 0.00 0.00 0.00 2.52
4059 5756 2.256117 AAGTAGGCTTGACGCTTTGT 57.744 45.000 0.00 0.00 39.13 2.83
4188 5888 0.032952 TAAAAGACGGACAGCGTGCT 59.967 50.000 0.00 0.00 0.00 4.40
4195 5895 1.522569 GGACAGCGTGCTAGGGATT 59.477 57.895 0.00 0.00 0.00 3.01
4198 5898 1.221840 CAGCGTGCTAGGGATTGGT 59.778 57.895 0.00 0.00 0.00 3.67
4338 6043 0.320683 TCCGCATGTGACAAGGACAG 60.321 55.000 8.11 0.00 0.00 3.51
4341 6046 0.250901 GCATGTGACAAGGACAGGGT 60.251 55.000 0.00 0.00 0.00 4.34
4343 6048 2.356125 GCATGTGACAAGGACAGGGTAT 60.356 50.000 0.00 0.00 0.00 2.73
4356 6069 2.717485 GGTATCGCCGCTACGTGA 59.283 61.111 0.00 0.00 0.00 4.35
4380 6093 1.810151 GGTTCATCTGCCGCTTGTTTA 59.190 47.619 0.00 0.00 0.00 2.01
4382 6095 1.448985 TCATCTGCCGCTTGTTTACC 58.551 50.000 0.00 0.00 0.00 2.85
4383 6096 1.003118 TCATCTGCCGCTTGTTTACCT 59.997 47.619 0.00 0.00 0.00 3.08
4384 6097 1.131126 CATCTGCCGCTTGTTTACCTG 59.869 52.381 0.00 0.00 0.00 4.00
4409 7321 3.901667 CGTCACGCTGGTTTAGATTAC 57.098 47.619 0.00 0.00 0.00 1.89
4425 7338 9.836076 GTTTAGATTACGGAAAGTTAAAAGCAT 57.164 29.630 0.00 0.00 0.00 3.79
4427 7340 7.681939 AGATTACGGAAAGTTAAAAGCATCA 57.318 32.000 0.00 0.00 0.00 3.07
4434 7347 6.128007 CGGAAAGTTAAAAGCATCACAGGTAT 60.128 38.462 0.00 0.00 0.00 2.73
4448 7361 2.308570 ACAGGTATCCCAACTTGCATGA 59.691 45.455 6.60 0.00 30.00 3.07
4507 7475 1.466856 CACCATACACCAGCTTGCAT 58.533 50.000 0.00 0.00 0.00 3.96
4553 7521 2.536928 GCCTATCACAACGCGACAATTC 60.537 50.000 15.93 0.00 0.00 2.17
4590 7558 2.654912 CGGTCGTCGCCAACACTTC 61.655 63.158 6.53 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.190578 GGCCTCCGATGAAGGTGG 59.809 66.667 0.00 0.14 45.26 4.61
11 12 3.365265 CCTTGTTGTGCGGCCTCC 61.365 66.667 0.00 0.00 0.00 4.30
12 13 4.043200 GCCTTGTTGTGCGGCCTC 62.043 66.667 0.00 0.00 37.86 4.70
18 19 4.347453 CTGCCGGCCTTGTTGTGC 62.347 66.667 26.77 0.00 0.00 4.57
19 20 1.526575 AATCTGCCGGCCTTGTTGTG 61.527 55.000 26.77 3.78 0.00 3.33
20 21 0.827507 AAATCTGCCGGCCTTGTTGT 60.828 50.000 26.77 1.41 0.00 3.32
21 22 0.109132 GAAATCTGCCGGCCTTGTTG 60.109 55.000 26.77 7.14 0.00 3.33
22 23 0.251341 AGAAATCTGCCGGCCTTGTT 60.251 50.000 26.77 13.33 0.00 2.83
23 24 0.678048 GAGAAATCTGCCGGCCTTGT 60.678 55.000 26.77 10.52 0.00 3.16
24 25 0.677731 TGAGAAATCTGCCGGCCTTG 60.678 55.000 26.77 14.54 0.00 3.61
25 26 0.257039 ATGAGAAATCTGCCGGCCTT 59.743 50.000 26.77 12.30 0.00 4.35
26 27 1.131638 TATGAGAAATCTGCCGGCCT 58.868 50.000 26.77 12.83 0.00 5.19
27 28 1.967319 TTATGAGAAATCTGCCGGCC 58.033 50.000 26.77 7.06 0.00 6.13
28 29 5.689383 TTATTTATGAGAAATCTGCCGGC 57.311 39.130 22.73 22.73 0.00 6.13
29 30 7.206981 ACATTATTTATGAGAAATCTGCCGG 57.793 36.000 0.00 0.00 37.69 6.13
30 31 7.011773 CGACATTATTTATGAGAAATCTGCCG 58.988 38.462 0.00 0.00 37.69 5.69
31 32 7.800380 CACGACATTATTTATGAGAAATCTGCC 59.200 37.037 0.00 0.00 37.69 4.85
32 33 8.551205 TCACGACATTATTTATGAGAAATCTGC 58.449 33.333 0.00 0.00 37.69 4.26
39 40 9.468532 CAGAGAATCACGACATTATTTATGAGA 57.531 33.333 0.00 0.00 37.82 3.27
40 41 8.706936 CCAGAGAATCACGACATTATTTATGAG 58.293 37.037 0.00 0.00 37.82 2.90
41 42 8.421002 TCCAGAGAATCACGACATTATTTATGA 58.579 33.333 0.00 0.00 37.82 2.15
42 43 8.593492 TCCAGAGAATCACGACATTATTTATG 57.407 34.615 0.00 0.00 37.82 1.90
43 44 9.212641 CATCCAGAGAATCACGACATTATTTAT 57.787 33.333 0.00 0.00 37.82 1.40
44 45 7.171508 GCATCCAGAGAATCACGACATTATTTA 59.828 37.037 0.00 0.00 37.82 1.40
45 46 6.017605 GCATCCAGAGAATCACGACATTATTT 60.018 38.462 0.00 0.00 37.82 1.40
46 47 5.468072 GCATCCAGAGAATCACGACATTATT 59.532 40.000 0.00 0.00 37.82 1.40
47 48 4.993584 GCATCCAGAGAATCACGACATTAT 59.006 41.667 0.00 0.00 37.82 1.28
48 49 4.371786 GCATCCAGAGAATCACGACATTA 58.628 43.478 0.00 0.00 37.82 1.90
49 50 3.201290 GCATCCAGAGAATCACGACATT 58.799 45.455 0.00 0.00 37.82 2.71
50 51 2.484417 GGCATCCAGAGAATCACGACAT 60.484 50.000 0.00 0.00 37.82 3.06
51 52 1.134699 GGCATCCAGAGAATCACGACA 60.135 52.381 0.00 0.00 37.82 4.35
52 53 1.576356 GGCATCCAGAGAATCACGAC 58.424 55.000 0.00 0.00 37.82 4.34
53 54 0.103026 CGGCATCCAGAGAATCACGA 59.897 55.000 0.00 0.00 37.82 4.35
54 55 0.179100 ACGGCATCCAGAGAATCACG 60.179 55.000 0.00 0.00 37.82 4.35
55 56 1.293924 CACGGCATCCAGAGAATCAC 58.706 55.000 0.00 0.00 37.82 3.06
56 57 0.462581 GCACGGCATCCAGAGAATCA 60.463 55.000 0.00 0.00 37.82 2.57
57 58 0.179062 AGCACGGCATCCAGAGAATC 60.179 55.000 0.00 0.00 0.00 2.52
58 59 0.179062 GAGCACGGCATCCAGAGAAT 60.179 55.000 0.00 0.00 0.00 2.40
59 60 1.219124 GAGCACGGCATCCAGAGAA 59.781 57.895 0.00 0.00 0.00 2.87
60 61 2.725312 GGAGCACGGCATCCAGAGA 61.725 63.158 0.00 0.00 35.54 3.10
61 62 2.202987 GGAGCACGGCATCCAGAG 60.203 66.667 0.00 0.00 35.54 3.35
62 63 2.685017 AGGAGCACGGCATCCAGA 60.685 61.111 12.89 0.00 38.12 3.86
63 64 2.202987 GAGGAGCACGGCATCCAG 60.203 66.667 12.89 0.00 38.12 3.86
64 65 2.685017 AGAGGAGCACGGCATCCA 60.685 61.111 12.89 0.00 38.12 3.41
65 66 2.107953 GAGAGGAGCACGGCATCC 59.892 66.667 0.00 3.36 35.71 3.51
66 67 1.965754 AAGGAGAGGAGCACGGCATC 61.966 60.000 0.00 0.00 0.00 3.91
67 68 0.687757 TAAGGAGAGGAGCACGGCAT 60.688 55.000 0.00 0.00 0.00 4.40
68 69 0.902984 TTAAGGAGAGGAGCACGGCA 60.903 55.000 0.00 0.00 0.00 5.69
69 70 0.179097 CTTAAGGAGAGGAGCACGGC 60.179 60.000 0.00 0.00 0.00 5.68
70 71 1.134965 CACTTAAGGAGAGGAGCACGG 60.135 57.143 7.53 0.00 0.00 4.94
71 72 1.134965 CCACTTAAGGAGAGGAGCACG 60.135 57.143 7.53 0.00 38.28 5.34
72 73 1.903183 ACCACTTAAGGAGAGGAGCAC 59.097 52.381 7.53 0.00 38.28 4.40
73 74 1.902508 CACCACTTAAGGAGAGGAGCA 59.097 52.381 7.53 0.00 38.28 4.26
74 75 1.903183 ACACCACTTAAGGAGAGGAGC 59.097 52.381 7.53 0.00 38.28 4.70
75 76 4.773149 ACTAACACCACTTAAGGAGAGGAG 59.227 45.833 7.53 4.71 38.28 3.69
76 77 4.748701 ACTAACACCACTTAAGGAGAGGA 58.251 43.478 7.53 0.00 38.28 3.71
77 78 4.773149 AGACTAACACCACTTAAGGAGAGG 59.227 45.833 7.53 5.78 41.45 3.69
78 79 5.712917 AGAGACTAACACCACTTAAGGAGAG 59.287 44.000 7.53 0.00 0.00 3.20
95 96 1.508545 GCTGTCAGCGCAGAGACTA 59.491 57.895 22.28 11.82 38.70 2.59
112 113 4.789123 ACCGTATTGGGCCACCGC 62.789 66.667 5.23 0.00 44.64 5.68
113 114 2.512974 GACCGTATTGGGCCACCG 60.513 66.667 5.23 9.26 41.58 4.94
123 124 2.963599 ACCAAAACCAAGGACCGTAT 57.036 45.000 0.00 0.00 0.00 3.06
125 126 1.477377 GGTACCAAAACCAAGGACCGT 60.477 52.381 7.15 0.00 39.50 4.83
132 133 2.683867 CAACGTGAGGTACCAAAACCAA 59.316 45.455 15.94 0.00 42.40 3.67
133 134 2.093075 TCAACGTGAGGTACCAAAACCA 60.093 45.455 15.94 0.80 42.40 3.67
134 135 2.288729 GTCAACGTGAGGTACCAAAACC 59.711 50.000 15.94 0.00 40.06 3.27
135 136 2.033492 CGTCAACGTGAGGTACCAAAAC 60.033 50.000 15.94 8.07 34.11 2.43
136 137 2.203401 CGTCAACGTGAGGTACCAAAA 58.797 47.619 15.94 0.00 34.11 2.44
137 138 1.855513 CGTCAACGTGAGGTACCAAA 58.144 50.000 15.94 0.00 34.11 3.28
138 139 3.573569 CGTCAACGTGAGGTACCAA 57.426 52.632 15.94 0.00 34.11 3.67
161 162 3.964875 CACCAGCCAACCGTGCAC 61.965 66.667 6.82 6.82 0.00 4.57
166 167 1.101049 AACAAGTCACCAGCCAACCG 61.101 55.000 0.00 0.00 0.00 4.44
185 186 2.237143 GACATTCTGGACCCAGTCATGA 59.763 50.000 24.57 0.00 43.96 3.07
186 187 2.026915 TGACATTCTGGACCCAGTCATG 60.027 50.000 19.93 19.93 43.96 3.07
217 218 1.953559 AAACGCAGACACAGACACAT 58.046 45.000 0.00 0.00 0.00 3.21
218 219 2.159156 AGTAAACGCAGACACAGACACA 60.159 45.455 0.00 0.00 0.00 3.72
232 233 4.741342 ACCTCCGAAAGATACAGTAAACG 58.259 43.478 0.00 0.00 0.00 3.60
286 287 1.135199 CACTGTCATGCTTGAATGCCC 60.135 52.381 3.51 0.00 32.48 5.36
314 315 1.666553 TGCACGGACGATGGTGAAC 60.667 57.895 0.00 0.00 36.25 3.18
535 582 2.941025 TTCCTTCCCTGGGGCTGG 60.941 66.667 14.00 12.53 34.68 4.85
536 583 2.679716 CTTCCTTCCCTGGGGCTG 59.320 66.667 14.00 3.26 34.68 4.85
537 584 2.615288 CCTTCCTTCCCTGGGGCT 60.615 66.667 14.00 0.00 34.68 5.19
538 585 3.744155 CCCTTCCTTCCCTGGGGC 61.744 72.222 14.00 0.00 36.15 5.80
592 641 4.637977 TGTCTGTTCATTATATTTGCCGCA 59.362 37.500 0.00 0.00 0.00 5.69
602 651 7.341805 ACAAGGCTAGAATGTCTGTTCATTAT 58.658 34.615 0.00 0.00 38.03 1.28
736 1065 2.047274 TCGCCTGCTTTCTTCGGG 60.047 61.111 0.00 0.00 0.00 5.14
765 1095 4.029809 GTGGGAAGACGGGGGTGG 62.030 72.222 0.00 0.00 0.00 4.61
791 1122 0.998945 ACGGGATGGGAATGGGGATT 60.999 55.000 0.00 0.00 0.00 3.01
797 1128 2.591715 GCGGACGGGATGGGAATG 60.592 66.667 0.00 0.00 0.00 2.67
800 1131 3.781307 CTTGCGGACGGGATGGGA 61.781 66.667 0.00 0.00 0.00 4.37
812 1143 3.792588 TATACCTGGGCTTGGCTTGCG 62.793 57.143 0.00 0.00 0.00 4.85
846 1182 3.787001 GGTCTTCTGGGAGGGGCG 61.787 72.222 0.00 0.00 0.00 6.13
847 1183 2.610859 TGGTCTTCTGGGAGGGGC 60.611 66.667 0.00 0.00 0.00 5.80
892 1228 2.417586 CCTTCGTGGGGATTTCGTTAAC 59.582 50.000 0.00 0.00 0.00 2.01
896 1232 1.376812 GCCTTCGTGGGGATTTCGT 60.377 57.895 0.05 0.00 36.00 3.85
898 1234 0.544697 TAGGCCTTCGTGGGGATTTC 59.455 55.000 12.58 0.00 36.00 2.17
909 1245 4.724279 TTGGGGAATATTCTAGGCCTTC 57.276 45.455 12.58 0.00 0.00 3.46
1540 1889 1.518774 GGGCAATGCATGTTGAGGG 59.481 57.895 7.79 0.00 0.00 4.30
1569 1918 6.216456 AGTCAACAAATTAGAGGGAGGAATCT 59.784 38.462 0.00 0.00 0.00 2.40
1612 1961 1.721489 CGCCTGAATCGACAAACAACG 60.721 52.381 0.00 0.00 0.00 4.10
1844 2203 9.591792 CTCTGATGAGATTCAAAACACTATACA 57.408 33.333 0.00 0.00 42.73 2.29
1848 2207 7.901029 AGACTCTGATGAGATTCAAAACACTA 58.099 34.615 2.56 0.00 42.73 2.74
1849 2208 6.767456 AGACTCTGATGAGATTCAAAACACT 58.233 36.000 2.56 0.00 42.73 3.55
1851 2210 8.455903 AAAAGACTCTGATGAGATTCAAAACA 57.544 30.769 2.56 0.00 42.73 2.83
1935 2294 7.885009 ATCAAGAGTTAAGACCTACTCCTAC 57.115 40.000 0.00 0.00 41.31 3.18
1938 2297 6.314152 GCAAATCAAGAGTTAAGACCTACTCC 59.686 42.308 0.00 0.00 41.31 3.85
1939 2298 6.874134 TGCAAATCAAGAGTTAAGACCTACTC 59.126 38.462 0.00 0.00 40.82 2.59
1940 2299 6.769512 TGCAAATCAAGAGTTAAGACCTACT 58.230 36.000 0.00 0.00 0.00 2.57
1945 2305 8.034058 AGTACATGCAAATCAAGAGTTAAGAC 57.966 34.615 0.00 0.00 0.00 3.01
1964 2324 3.890147 GCCAGCAGGTAGTACTAGTACAT 59.110 47.826 29.87 18.81 36.49 2.29
1965 2325 3.285484 GCCAGCAGGTAGTACTAGTACA 58.715 50.000 29.87 15.95 36.49 2.90
1966 2326 3.285484 TGCCAGCAGGTAGTACTAGTAC 58.715 50.000 23.03 23.03 37.19 2.73
1967 2327 3.552875 CTGCCAGCAGGTAGTACTAGTA 58.447 50.000 11.91 0.00 42.15 1.82
1968 2328 2.379972 CTGCCAGCAGGTAGTACTAGT 58.620 52.381 11.91 0.00 42.15 2.57
1978 2338 1.760192 AATCTTAAGCTGCCAGCAGG 58.240 50.000 20.53 5.72 45.56 4.85
1986 2346 9.474920 TTTTTGTGGTGATAAAATCTTAAGCTG 57.525 29.630 0.00 0.00 0.00 4.24
2088 2456 3.494626 ACAACAATACTCTGTTCAGTGCG 59.505 43.478 0.00 0.00 37.43 5.34
2890 3278 1.335496 GCGAACAAACAACCCTGCTTA 59.665 47.619 0.00 0.00 0.00 3.09
2892 3280 1.034838 TGCGAACAAACAACCCTGCT 61.035 50.000 0.00 0.00 0.00 4.24
2893 3281 0.869880 GTGCGAACAAACAACCCTGC 60.870 55.000 0.00 0.00 0.00 4.85
2894 3282 0.591236 CGTGCGAACAAACAACCCTG 60.591 55.000 0.00 0.00 0.00 4.45
2895 3283 1.725066 CGTGCGAACAAACAACCCT 59.275 52.632 0.00 0.00 0.00 4.34
2896 3284 1.942223 GCGTGCGAACAAACAACCC 60.942 57.895 0.00 0.00 0.00 4.11
2998 3392 2.971660 TGCAGGCTATAACACGCTTA 57.028 45.000 0.00 0.00 0.00 3.09
3093 3487 6.726258 TCACATTAGAAACAGCACATAGTG 57.274 37.500 0.00 0.00 36.51 2.74
3094 3488 6.881065 ACATCACATTAGAAACAGCACATAGT 59.119 34.615 0.00 0.00 0.00 2.12
3095 3489 7.312657 ACATCACATTAGAAACAGCACATAG 57.687 36.000 0.00 0.00 0.00 2.23
3096 3490 6.316140 GGACATCACATTAGAAACAGCACATA 59.684 38.462 0.00 0.00 0.00 2.29
3097 3491 5.124457 GGACATCACATTAGAAACAGCACAT 59.876 40.000 0.00 0.00 0.00 3.21
3098 3492 4.455533 GGACATCACATTAGAAACAGCACA 59.544 41.667 0.00 0.00 0.00 4.57
3126 3531 0.798776 CACCTGCAGACAACGGAATC 59.201 55.000 17.39 0.00 0.00 2.52
3359 3765 2.937799 CTCCTTCTTCTCTGATGCTTGC 59.062 50.000 0.00 0.00 0.00 4.01
3482 4928 2.033299 CGATGAAGCAGAGAGAGTCCTC 59.967 54.545 1.54 1.54 39.72 3.71
3589 5035 0.323178 GTCGGTCTGTCTACTGGGGA 60.323 60.000 0.00 0.00 0.00 4.81
3601 5227 2.030562 CGTGGCTTTGGTCGGTCT 59.969 61.111 0.00 0.00 0.00 3.85
3602 5228 3.723348 GCGTGGCTTTGGTCGGTC 61.723 66.667 0.00 0.00 0.00 4.79
3605 5231 3.726517 CAGGCGTGGCTTTGGTCG 61.727 66.667 0.00 0.00 0.00 4.79
3606 5232 4.043200 GCAGGCGTGGCTTTGGTC 62.043 66.667 8.72 0.00 0.00 4.02
3607 5233 4.892965 TGCAGGCGTGGCTTTGGT 62.893 61.111 8.72 0.00 0.00 3.67
3608 5234 3.346631 GATGCAGGCGTGGCTTTGG 62.347 63.158 8.72 0.00 0.00 3.28
3609 5235 2.180017 GATGCAGGCGTGGCTTTG 59.820 61.111 8.72 0.00 0.00 2.77
3610 5236 2.282391 TGATGCAGGCGTGGCTTT 60.282 55.556 8.72 0.00 0.00 3.51
3611 5237 2.184020 TACTGATGCAGGCGTGGCTT 62.184 55.000 8.72 0.00 35.51 4.35
3612 5238 2.584261 CTACTGATGCAGGCGTGGCT 62.584 60.000 8.72 0.00 35.51 4.75
3613 5239 2.125147 TACTGATGCAGGCGTGGC 60.125 61.111 8.72 1.33 35.51 5.01
3614 5240 0.459899 TACTACTGATGCAGGCGTGG 59.540 55.000 8.72 0.00 35.51 4.94
3734 5366 0.391130 TAGAACACAGGCGATGGCAC 60.391 55.000 1.01 0.00 42.47 5.01
3735 5367 0.541392 ATAGAACACAGGCGATGGCA 59.459 50.000 1.01 0.00 42.47 4.92
3807 5452 5.472137 CCGACCATTTTGAAAGAAGGTAGAA 59.528 40.000 7.01 0.00 0.00 2.10
3809 5460 4.379499 GCCGACCATTTTGAAAGAAGGTAG 60.379 45.833 0.00 0.00 0.00 3.18
3841 5499 7.097192 TCAGTAGTAGCTCGTGATTTTTCAAT 58.903 34.615 0.00 0.00 0.00 2.57
3845 5503 4.865365 GCTCAGTAGTAGCTCGTGATTTTT 59.135 41.667 0.00 0.00 37.01 1.94
3862 5520 3.137459 CTCGAGGAGCCGCTCAGT 61.137 66.667 21.76 8.41 31.08 3.41
3868 5526 0.878416 CTAGATTCCTCGAGGAGCCG 59.122 60.000 31.81 17.92 46.36 5.52
3897 5555 0.324614 TCCGAGTCCATGCATGTTGT 59.675 50.000 24.58 8.68 0.00 3.32
3939 5632 6.592870 AGCTCACTTTCTTACCAAAACTACT 58.407 36.000 0.00 0.00 0.00 2.57
3940 5633 6.862711 AGCTCACTTTCTTACCAAAACTAC 57.137 37.500 0.00 0.00 0.00 2.73
3942 5635 9.569122 TTATTAGCTCACTTTCTTACCAAAACT 57.431 29.630 0.00 0.00 0.00 2.66
3980 5677 0.309922 CTGCTCCACAAGTTGCAGTG 59.690 55.000 1.81 0.00 45.31 3.66
4051 5748 0.307760 CTTTGCCGAGAACAAAGCGT 59.692 50.000 3.56 0.00 45.23 5.07
4059 5756 2.641197 GGCTTTCCTTTGCCGAGAA 58.359 52.632 0.00 0.00 39.71 2.87
4213 5913 3.128852 TGCCTTTCGCTTTAGGTGTTA 57.871 42.857 0.00 0.00 38.78 2.41
4214 5914 1.975660 TGCCTTTCGCTTTAGGTGTT 58.024 45.000 0.00 0.00 38.78 3.32
4215 5915 1.812571 CATGCCTTTCGCTTTAGGTGT 59.187 47.619 0.00 0.00 38.78 4.16
4338 6043 2.138656 ATCACGTAGCGGCGATACCC 62.139 60.000 27.09 6.23 35.59 3.69
4341 6046 0.317519 CACATCACGTAGCGGCGATA 60.318 55.000 12.98 5.64 35.59 2.92
4343 6048 2.202557 CACATCACGTAGCGGCGA 60.203 61.111 12.98 0.00 35.59 5.54
4356 6069 0.322816 AAGCGGCAGATGAACCACAT 60.323 50.000 1.45 0.00 42.47 3.21
4372 6085 2.225491 TGACGCATTCAGGTAAACAAGC 59.775 45.455 0.00 0.00 0.00 4.01
4402 7314 8.662141 GTGATGCTTTTAACTTTCCGTAATCTA 58.338 33.333 0.00 0.00 0.00 1.98
4409 7321 4.023193 ACCTGTGATGCTTTTAACTTTCCG 60.023 41.667 0.00 0.00 0.00 4.30
4434 7347 3.229293 TCACATTTCATGCAAGTTGGGA 58.771 40.909 4.75 0.00 0.00 4.37
4470 7438 5.323371 TGGTGGAGTTGCATTTTATAAGC 57.677 39.130 0.00 0.00 0.00 3.09
4471 7439 7.915397 GTGTATGGTGGAGTTGCATTTTATAAG 59.085 37.037 0.00 0.00 0.00 1.73
4474 7442 5.127031 GGTGTATGGTGGAGTTGCATTTTAT 59.873 40.000 0.00 0.00 0.00 1.40
4507 7475 3.323403 GGGACCAAATCAAACACATCCAA 59.677 43.478 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.