Multiple sequence alignment - TraesCS3B01G349900

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 TraesCS3B01G349900 chr3B 100.000 4810 0 0 1 4810 559897666 559892857 0.000000e+00 8883.0
1 TraesCS3B01G349900 chr3B 91.153 373 30 3 3663 4033 559886073 559885702 2.000000e-138 503.0
2 TraesCS3B01G349900 chr3B 82.353 272 36 9 395 665 5608753 5608493 4.840000e-55 226.0
3 TraesCS3B01G349900 chr3B 75.911 494 85 21 200 688 3751412 3750948 6.270000e-54 222.0
4 TraesCS3B01G349900 chr3B 92.357 157 11 1 1 157 559915558 559915403 6.270000e-54 222.0
5 TraesCS3B01G349900 chr3D 93.251 2593 109 29 1460 4033 428259213 428256668 0.000000e+00 3759.0
6 TraesCS3B01G349900 chr3D 86.107 1346 117 34 157 1461 428260696 428259380 0.000000e+00 1386.0
7 TraesCS3B01G349900 chr3D 97.847 511 10 1 4301 4810 428256155 428255645 0.000000e+00 881.0
8 TraesCS3B01G349900 chr3D 87.965 457 41 9 3588 4033 428250676 428250223 1.190000e-145 527.0
9 TraesCS3B01G349900 chr3D 94.828 232 9 3 4075 4305 428256430 428256201 4.580000e-95 359.0
10 TraesCS3B01G349900 chr3D 91.139 158 12 2 1 158 409946753 409946598 3.770000e-51 213.0
11 TraesCS3B01G349900 chr3D 94.595 37 2 0 4042 4078 428256435 428256471 1.870000e-04 58.4
12 TraesCS3B01G349900 chr3A 92.441 2130 115 18 2190 4305 557406526 557408623 0.000000e+00 3000.0
13 TraesCS3B01G349900 chr3A 89.283 1409 88 26 698 2077 557387697 557389071 0.000000e+00 1707.0
14 TraesCS3B01G349900 chr3A 92.661 1199 54 14 1025 2199 557405301 557406489 0.000000e+00 1696.0
15 TraesCS3B01G349900 chr3A 95.070 284 12 2 4298 4579 557408666 557408949 3.420000e-121 446.0
16 TraesCS3B01G349900 chr3A 81.174 409 48 17 3643 4028 557414122 557414524 7.820000e-78 302.0
17 TraesCS3B01G349900 chr3A 95.161 186 3 1 4631 4810 557408942 557409127 6.090000e-74 289.0
18 TraesCS3B01G349900 chr3A 90.798 163 11 4 1 162 479152847 479152688 1.050000e-51 215.0
19 TraesCS3B01G349900 chr3A 82.042 284 18 13 698 973 557404525 557404783 1.360000e-50 211.0
20 TraesCS3B01G349900 chr3A 74.378 402 74 18 297 684 581243962 581244348 1.400000e-30 145.0
21 TraesCS3B01G349900 chr3A 75.000 324 64 12 296 616 587557690 587557381 3.020000e-27 134.0
22 TraesCS3B01G349900 chr3A 92.857 42 3 0 4037 4078 649547136 649547177 1.450000e-05 62.1
23 TraesCS3B01G349900 chr4D 78.493 544 87 19 158 690 385985274 385984750 3.590000e-86 329.0
24 TraesCS3B01G349900 chr6D 76.723 537 91 18 172 689 334239000 334238479 7.940000e-68 268.0
25 TraesCS3B01G349900 chr6D 91.139 158 13 1 1 158 384551502 384551346 3.770000e-51 213.0
26 TraesCS3B01G349900 chr6D 91.558 154 11 2 1 154 337000116 337000267 1.360000e-50 211.0
27 TraesCS3B01G349900 chr5D 95.455 154 6 1 1 154 384059385 384059233 1.340000e-60 244.0
28 TraesCS3B01G349900 chr6B 76.016 492 90 18 204 690 549710755 549710287 3.740000e-56 230.0
29 TraesCS3B01G349900 chr6B 76.016 492 90 17 204 690 578685060 578684592 3.740000e-56 230.0
30 TraesCS3B01G349900 chr6B 80.534 262 47 4 292 553 487122522 487122779 1.060000e-46 198.0
31 TraesCS3B01G349900 chr1A 75.681 477 100 13 184 659 239907488 239907027 1.740000e-54 224.0
32 TraesCS3B01G349900 chr1A 92.357 157 10 2 1 157 304180206 304180360 6.270000e-54 222.0
33 TraesCS3B01G349900 chr1A 81.696 224 33 5 437 659 121569368 121569152 3.820000e-41 180.0
34 TraesCS3B01G349900 chr2A 92.258 155 10 2 1 154 673085631 673085784 8.110000e-53 219.0
35 TraesCS3B01G349900 chr2A 76.683 416 71 21 288 689 451014739 451014336 1.750000e-49 207.0
36 TraesCS3B01G349900 chr2A 76.515 396 73 14 297 682 17894423 17894038 1.060000e-46 198.0
37 TraesCS3B01G349900 chr5B 91.720 157 12 1 1 157 38402930 38402775 2.920000e-52 217.0
38 TraesCS3B01G349900 chr7B 79.021 286 41 14 409 690 496337318 496337588 1.380000e-40 178.0
39 TraesCS3B01G349900 chr7B 93.182 44 3 0 4037 4080 327273013 327273056 1.120000e-06 65.8
40 TraesCS3B01G349900 chr7D 75.806 310 61 8 295 604 385433595 385433300 1.400000e-30 145.0
41 TraesCS3B01G349900 chr2D 91.489 47 4 0 4037 4083 592625050 592625004 1.120000e-06 65.8


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 TraesCS3B01G349900 chr3B 559892857 559897666 4809 True 8883.00 8883 100.00000 1 4810 1 chr3B.!!$R4 4809
1 TraesCS3B01G349900 chr3D 428255645 428260696 5051 True 1596.25 3759 93.00825 157 4810 4 chr3D.!!$R3 4653
2 TraesCS3B01G349900 chr3A 557387697 557389071 1374 False 1707.00 1707 89.28300 698 2077 1 chr3A.!!$F1 1379
3 TraesCS3B01G349900 chr3A 557404525 557409127 4602 False 1128.40 3000 91.47500 698 4810 5 chr3A.!!$F5 4112
4 TraesCS3B01G349900 chr4D 385984750 385985274 524 True 329.00 329 78.49300 158 690 1 chr4D.!!$R1 532
5 TraesCS3B01G349900 chr6D 334238479 334239000 521 True 268.00 268 76.72300 172 689 1 chr6D.!!$R1 517

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
38 39 0.029834 GCTTGCCTTCCACGCATATG 59.970 55.000 0.00 0.0 38.48 1.78 F
905 966 0.033228 CGATCCACATCTCCCTCTGC 59.967 60.000 0.00 0.0 0.00 4.26 F
1996 2720 1.153628 GACAGGGGTCGAATCCACG 60.154 63.158 8.14 0.0 35.77 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1864 2585 0.385723 GATCCCGTCGTATCTCGCAC 60.386 60.0 0.0 0.0 39.67 5.34 R
2308 3099 0.103937 GCTTCCTCCCAGTCTGATCG 59.896 60.0 0.0 0.0 0.00 3.69 R
3978 4789 0.830023 CGGTTTGGGTTGGTTGGGAT 60.830 55.0 0.0 0.0 0.00 3.85 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
20 21 1.668419 AACATATCCAGACGCCAAGC 58.332 50.000 0.00 0.00 0.00 4.01
21 22 0.833287 ACATATCCAGACGCCAAGCT 59.167 50.000 0.00 0.00 0.00 3.74
22 23 1.210478 ACATATCCAGACGCCAAGCTT 59.790 47.619 0.00 0.00 0.00 3.74
23 24 1.600957 CATATCCAGACGCCAAGCTTG 59.399 52.381 19.93 19.93 0.00 4.01
24 25 0.744414 TATCCAGACGCCAAGCTTGC 60.744 55.000 21.43 14.85 0.00 4.01
25 26 3.741476 CCAGACGCCAAGCTTGCC 61.741 66.667 21.43 9.45 0.00 4.52
26 27 2.670934 CAGACGCCAAGCTTGCCT 60.671 61.111 21.43 11.30 0.00 4.75
27 28 2.113986 AGACGCCAAGCTTGCCTT 59.886 55.556 21.43 2.97 0.00 4.35
28 29 1.968540 AGACGCCAAGCTTGCCTTC 60.969 57.895 21.43 13.32 0.00 3.46
29 30 2.982744 GACGCCAAGCTTGCCTTCC 61.983 63.158 21.43 4.80 0.00 3.46
30 31 2.985282 CGCCAAGCTTGCCTTCCA 60.985 61.111 21.43 0.00 0.00 3.53
31 32 2.653115 GCCAAGCTTGCCTTCCAC 59.347 61.111 21.43 0.12 0.00 4.02
32 33 2.956987 CCAAGCTTGCCTTCCACG 59.043 61.111 21.43 0.62 0.00 4.94
33 34 2.256461 CAAGCTTGCCTTCCACGC 59.744 61.111 14.65 0.00 38.87 5.34
34 35 2.203337 AAGCTTGCCTTCCACGCA 60.203 55.556 0.00 0.00 40.87 5.24
35 36 1.604593 AAGCTTGCCTTCCACGCAT 60.605 52.632 0.00 0.00 40.87 4.73
36 37 0.322456 AAGCTTGCCTTCCACGCATA 60.322 50.000 0.00 0.00 40.87 3.14
37 38 0.107017 AGCTTGCCTTCCACGCATAT 60.107 50.000 0.00 0.00 40.87 1.78
38 39 0.029834 GCTTGCCTTCCACGCATATG 59.970 55.000 0.00 0.00 38.48 1.78
39 40 0.664761 CTTGCCTTCCACGCATATGG 59.335 55.000 4.56 0.00 41.57 2.74
40 41 0.751277 TTGCCTTCCACGCATATGGG 60.751 55.000 17.56 17.56 40.49 4.00
41 42 1.148273 GCCTTCCACGCATATGGGA 59.852 57.895 25.04 10.65 40.49 4.37
42 43 0.886490 GCCTTCCACGCATATGGGAG 60.886 60.000 25.04 17.22 44.27 4.30
43 44 0.469917 CCTTCCACGCATATGGGAGT 59.530 55.000 25.04 1.87 43.24 3.85
44 45 1.541233 CCTTCCACGCATATGGGAGTC 60.541 57.143 25.04 0.00 43.24 3.36
45 46 0.468226 TTCCACGCATATGGGAGTCC 59.532 55.000 25.04 0.00 40.49 3.85
46 47 0.398522 TCCACGCATATGGGAGTCCT 60.399 55.000 25.04 0.36 40.49 3.85
47 48 1.133294 TCCACGCATATGGGAGTCCTA 60.133 52.381 25.04 2.54 40.49 2.94
48 49 1.000955 CCACGCATATGGGAGTCCTAC 59.999 57.143 25.04 0.00 35.95 3.18
49 50 1.000955 CACGCATATGGGAGTCCTACC 59.999 57.143 25.04 0.00 0.00 3.18
50 51 0.608640 CGCATATGGGAGTCCTACCC 59.391 60.000 14.32 0.00 46.87 3.69
60 61 2.044650 TCCTACCCGGACACGAGG 60.045 66.667 0.73 1.47 44.60 4.63
65 66 3.315949 CCCGGACACGAGGGGAAA 61.316 66.667 0.73 0.00 44.10 3.13
66 67 2.745037 CCGGACACGAGGGGAAAA 59.255 61.111 0.00 0.00 44.60 2.29
67 68 1.375523 CCGGACACGAGGGGAAAAG 60.376 63.158 0.00 0.00 44.60 2.27
68 69 1.370064 CGGACACGAGGGGAAAAGT 59.630 57.895 0.00 0.00 44.60 2.66
69 70 0.669625 CGGACACGAGGGGAAAAGTC 60.670 60.000 0.00 0.00 44.60 3.01
70 71 0.685660 GGACACGAGGGGAAAAGTCT 59.314 55.000 0.00 0.00 0.00 3.24
71 72 1.071857 GGACACGAGGGGAAAAGTCTT 59.928 52.381 0.00 0.00 0.00 3.01
72 73 2.414806 GACACGAGGGGAAAAGTCTTC 58.585 52.381 0.00 0.00 0.00 2.87
73 74 2.037381 GACACGAGGGGAAAAGTCTTCT 59.963 50.000 0.00 0.00 0.00 2.85
74 75 2.224305 ACACGAGGGGAAAAGTCTTCTG 60.224 50.000 0.00 0.00 0.00 3.02
75 76 1.270893 ACGAGGGGAAAAGTCTTCTGC 60.271 52.381 0.00 0.00 0.00 4.26
76 77 1.002544 CGAGGGGAAAAGTCTTCTGCT 59.997 52.381 0.00 0.00 0.00 4.24
77 78 2.551071 CGAGGGGAAAAGTCTTCTGCTT 60.551 50.000 0.00 0.00 0.00 3.91
78 79 3.491342 GAGGGGAAAAGTCTTCTGCTTT 58.509 45.455 0.00 0.00 37.73 3.51
79 80 3.891977 GAGGGGAAAAGTCTTCTGCTTTT 59.108 43.478 3.12 3.12 45.45 2.27
80 81 5.061721 AGGGGAAAAGTCTTCTGCTTTTA 57.938 39.130 3.44 0.00 43.60 1.52
81 82 5.645201 AGGGGAAAAGTCTTCTGCTTTTAT 58.355 37.500 3.44 0.00 43.60 1.40
82 83 5.712446 AGGGGAAAAGTCTTCTGCTTTTATC 59.288 40.000 3.44 0.82 43.60 1.75
83 84 5.712446 GGGGAAAAGTCTTCTGCTTTTATCT 59.288 40.000 3.44 0.00 43.60 1.98
84 85 6.209589 GGGGAAAAGTCTTCTGCTTTTATCTT 59.790 38.462 3.44 0.00 43.60 2.40
85 86 7.309177 GGGAAAAGTCTTCTGCTTTTATCTTC 58.691 38.462 3.44 0.00 43.60 2.87
86 87 7.040409 GGGAAAAGTCTTCTGCTTTTATCTTCA 60.040 37.037 3.44 0.00 43.60 3.02
87 88 7.805542 GGAAAAGTCTTCTGCTTTTATCTTCAC 59.194 37.037 3.44 0.00 43.60 3.18
88 89 6.473397 AAGTCTTCTGCTTTTATCTTCACG 57.527 37.500 0.00 0.00 0.00 4.35
89 90 4.932200 AGTCTTCTGCTTTTATCTTCACGG 59.068 41.667 0.00 0.00 0.00 4.94
90 91 3.684788 TCTTCTGCTTTTATCTTCACGGC 59.315 43.478 0.00 0.00 0.00 5.68
91 92 2.356135 TCTGCTTTTATCTTCACGGCC 58.644 47.619 0.00 0.00 0.00 6.13
92 93 1.401905 CTGCTTTTATCTTCACGGCCC 59.598 52.381 0.00 0.00 0.00 5.80
93 94 1.271652 TGCTTTTATCTTCACGGCCCA 60.272 47.619 0.00 0.00 0.00 5.36
94 95 2.024414 GCTTTTATCTTCACGGCCCAT 58.976 47.619 0.00 0.00 0.00 4.00
95 96 2.033424 GCTTTTATCTTCACGGCCCATC 59.967 50.000 0.00 0.00 0.00 3.51
96 97 3.278574 CTTTTATCTTCACGGCCCATCA 58.721 45.455 0.00 0.00 0.00 3.07
97 98 2.620251 TTATCTTCACGGCCCATCAG 57.380 50.000 0.00 0.00 0.00 2.90
98 99 1.496060 TATCTTCACGGCCCATCAGT 58.504 50.000 0.00 0.00 0.00 3.41
99 100 0.620556 ATCTTCACGGCCCATCAGTT 59.379 50.000 0.00 0.00 0.00 3.16
100 101 0.036388 TCTTCACGGCCCATCAGTTC 60.036 55.000 0.00 0.00 0.00 3.01
101 102 0.036010 CTTCACGGCCCATCAGTTCT 60.036 55.000 0.00 0.00 0.00 3.01
102 103 0.321564 TTCACGGCCCATCAGTTCTG 60.322 55.000 0.00 0.00 0.00 3.02
103 104 2.045926 ACGGCCCATCAGTTCTGC 60.046 61.111 0.00 0.00 0.00 4.26
104 105 2.825836 CGGCCCATCAGTTCTGCC 60.826 66.667 0.00 0.00 38.74 4.85
105 106 2.440980 GGCCCATCAGTTCTGCCC 60.441 66.667 0.00 0.00 36.07 5.36
106 107 2.356278 GCCCATCAGTTCTGCCCA 59.644 61.111 0.00 0.00 0.00 5.36
107 108 1.076485 GCCCATCAGTTCTGCCCAT 60.076 57.895 0.00 0.00 0.00 4.00
108 109 0.183492 GCCCATCAGTTCTGCCCATA 59.817 55.000 0.00 0.00 0.00 2.74
109 110 1.202976 GCCCATCAGTTCTGCCCATAT 60.203 52.381 0.00 0.00 0.00 1.78
110 111 2.754186 GCCCATCAGTTCTGCCCATATT 60.754 50.000 0.00 0.00 0.00 1.28
111 112 3.498481 GCCCATCAGTTCTGCCCATATTA 60.498 47.826 0.00 0.00 0.00 0.98
112 113 4.728772 CCCATCAGTTCTGCCCATATTAA 58.271 43.478 0.00 0.00 0.00 1.40
113 114 5.139727 CCCATCAGTTCTGCCCATATTAAA 58.860 41.667 0.00 0.00 0.00 1.52
114 115 5.010012 CCCATCAGTTCTGCCCATATTAAAC 59.990 44.000 0.00 0.00 0.00 2.01
115 116 5.277974 CCATCAGTTCTGCCCATATTAAACG 60.278 44.000 0.00 0.00 0.00 3.60
116 117 4.196193 TCAGTTCTGCCCATATTAAACGG 58.804 43.478 0.00 0.00 0.00 4.44
117 118 3.945285 CAGTTCTGCCCATATTAAACGGT 59.055 43.478 0.00 0.00 0.00 4.83
118 119 4.035208 CAGTTCTGCCCATATTAAACGGTC 59.965 45.833 0.00 0.00 0.00 4.79
119 120 3.202829 TCTGCCCATATTAAACGGTCC 57.797 47.619 0.00 0.00 0.00 4.46
120 121 1.871039 CTGCCCATATTAAACGGTCCG 59.129 52.381 10.48 10.48 0.00 4.79
121 122 1.232119 GCCCATATTAAACGGTCCGG 58.768 55.000 17.28 0.00 0.00 5.14
122 123 1.202675 GCCCATATTAAACGGTCCGGA 60.203 52.381 17.28 0.00 0.00 5.14
123 124 2.486918 CCCATATTAAACGGTCCGGAC 58.513 52.381 27.04 27.04 0.00 4.79
124 125 2.158928 CCCATATTAAACGGTCCGGACA 60.159 50.000 34.40 14.72 0.00 4.02
125 126 2.867975 CCATATTAAACGGTCCGGACAC 59.132 50.000 34.40 22.34 0.00 3.67
126 127 2.671130 TATTAAACGGTCCGGACACC 57.329 50.000 34.40 19.23 0.00 4.16
127 128 0.036105 ATTAAACGGTCCGGACACCC 60.036 55.000 34.40 17.88 31.99 4.61
137 138 3.162154 GGACACCCGAGGATCCCC 61.162 72.222 8.55 0.00 0.00 4.81
139 140 1.232216 GACACCCGAGGATCCCCTA 59.768 63.158 8.55 0.00 44.53 3.53
140 141 0.398098 GACACCCGAGGATCCCCTAA 60.398 60.000 8.55 0.00 44.53 2.69
141 142 0.267960 ACACCCGAGGATCCCCTAAT 59.732 55.000 8.55 0.00 44.53 1.73
142 143 0.977395 CACCCGAGGATCCCCTAATC 59.023 60.000 8.55 0.00 44.53 1.75
143 144 0.178900 ACCCGAGGATCCCCTAATCC 60.179 60.000 8.55 0.00 44.53 3.01
144 145 0.178903 CCCGAGGATCCCCTAATCCA 60.179 60.000 8.55 0.00 46.56 3.41
145 146 1.270907 CCGAGGATCCCCTAATCCAG 58.729 60.000 8.55 0.00 46.56 3.86
146 147 1.270907 CGAGGATCCCCTAATCCAGG 58.729 60.000 8.55 0.00 46.56 4.45
175 176 2.046217 GGAGGGGTCTTGTTCCGC 60.046 66.667 0.00 0.00 38.04 5.54
187 188 3.562557 TCTTGTTCCGCTTTTAGGTGTTC 59.437 43.478 0.00 0.00 0.00 3.18
190 191 3.314080 TGTTCCGCTTTTAGGTGTTCTTG 59.686 43.478 0.00 0.00 0.00 3.02
202 204 8.918202 TTTAGGTGTTCTTGTGAGTTCATTAT 57.082 30.769 0.00 0.00 0.00 1.28
221 223 2.636647 TGGTTTGTGTCATGCTCAGA 57.363 45.000 0.00 0.00 0.00 3.27
226 228 4.036734 GGTTTGTGTCATGCTCAGAAAGAA 59.963 41.667 11.18 0.00 30.82 2.52
252 254 0.756903 GTGGCGGCTCCCTAAAGATA 59.243 55.000 11.43 0.00 0.00 1.98
278 280 2.284331 TTCACTCCGCCTAGCCCA 60.284 61.111 0.00 0.00 0.00 5.36
290 292 1.818674 CCTAGCCCACATTTTGGTGAC 59.181 52.381 0.00 0.00 45.25 3.67
312 314 2.823147 CTAGCGTCGTCGGAGGGT 60.823 66.667 3.90 0.00 41.24 4.34
319 321 3.612681 CGTCGGAGGGTGTGTGGT 61.613 66.667 0.00 0.00 0.00 4.16
321 323 2.123208 TCGGAGGGTGTGTGGTGA 60.123 61.111 0.00 0.00 0.00 4.02
332 334 1.005037 TGTGGTGATGTGTCTCCGC 60.005 57.895 3.78 3.78 44.73 5.54
351 353 0.104855 CTGGATCTTGCGGGATTCGA 59.895 55.000 0.00 0.00 42.43 3.71
413 442 4.415881 TGTTCATGTGTCTACAGGTTGT 57.584 40.909 0.00 0.00 40.79 3.32
417 446 4.993905 TCATGTGTCTACAGGTTGTATCG 58.006 43.478 0.00 0.00 40.79 2.92
429 458 5.125097 ACAGGTTGTATCGTTTCGATCTACT 59.875 40.000 7.90 0.00 43.45 2.57
431 460 6.632035 CAGGTTGTATCGTTTCGATCTACTAC 59.368 42.308 7.90 8.80 43.45 2.73
475 504 0.865111 TTGTTCTGATGCGTTGGTCG 59.135 50.000 0.00 0.00 43.12 4.79
591 627 0.889638 TCTTCGACTCGCTCCAGTGT 60.890 55.000 0.00 0.00 0.00 3.55
594 630 0.387929 TCGACTCGCTCCAGTGTTTT 59.612 50.000 0.00 0.00 0.00 2.43
604 640 3.378339 CTCCAGTGTTTTTAGTCGTCGT 58.622 45.455 0.00 0.00 0.00 4.34
619 655 2.485426 TCGTCGTTAGGTGGTCTACAAG 59.515 50.000 0.00 0.00 0.00 3.16
623 663 5.294306 CGTCGTTAGGTGGTCTACAAGTATA 59.706 44.000 0.00 0.00 0.00 1.47
680 723 6.304624 ACTGTGATGGCATGATGAATAGATT 58.695 36.000 3.81 0.00 0.00 2.40
690 733 7.437267 GGCATGATGAATAGATTGAAGGTTTTG 59.563 37.037 0.00 0.00 0.00 2.44
692 735 9.297586 CATGATGAATAGATTGAAGGTTTTGTG 57.702 33.333 0.00 0.00 0.00 3.33
693 736 8.634335 TGATGAATAGATTGAAGGTTTTGTGA 57.366 30.769 0.00 0.00 0.00 3.58
694 737 9.246670 TGATGAATAGATTGAAGGTTTTGTGAT 57.753 29.630 0.00 0.00 0.00 3.06
792 842 2.033299 ACGTACGTTTTCTTCTCGTCCA 59.967 45.455 16.72 0.00 38.69 4.02
793 843 3.240069 CGTACGTTTTCTTCTCGTCCAT 58.760 45.455 7.22 0.00 38.69 3.41
794 844 3.300066 CGTACGTTTTCTTCTCGTCCATC 59.700 47.826 7.22 0.00 38.69 3.51
808 858 6.227522 TCTCGTCCATCAAAATACTCAAACA 58.772 36.000 0.00 0.00 0.00 2.83
835 885 1.220206 CAAGCCGATCACTGGAGCT 59.780 57.895 0.00 0.00 34.64 4.09
866 924 1.890510 GCAAGTCGGAAACCCACGT 60.891 57.895 0.00 0.00 0.00 4.49
871 932 1.003769 GTCGGAAACCCACGTCGTAC 61.004 60.000 0.00 0.00 0.00 3.67
872 933 1.172180 TCGGAAACCCACGTCGTACT 61.172 55.000 0.00 0.00 0.00 2.73
873 934 1.005294 CGGAAACCCACGTCGTACTG 61.005 60.000 0.00 0.00 0.00 2.74
875 936 0.314935 GAAACCCACGTCGTACTGGA 59.685 55.000 13.02 0.00 0.00 3.86
879 940 1.505353 CCACGTCGTACTGGAGTCC 59.495 63.158 0.73 0.73 0.00 3.85
880 941 1.239296 CCACGTCGTACTGGAGTCCA 61.239 60.000 12.40 12.40 0.00 4.02
885 946 1.063764 GTCGTACTGGAGTCCATCGAC 59.936 57.143 30.05 30.05 40.89 4.20
892 953 1.107538 GGAGTCCATCGACCGATCCA 61.108 60.000 3.60 0.00 40.12 3.41
900 961 1.107538 TCGACCGATCCACATCTCCC 61.108 60.000 0.00 0.00 0.00 4.30
902 963 0.676736 GACCGATCCACATCTCCCTC 59.323 60.000 0.00 0.00 0.00 4.30
904 965 0.678395 CCGATCCACATCTCCCTCTG 59.322 60.000 0.00 0.00 0.00 3.35
905 966 0.033228 CGATCCACATCTCCCTCTGC 59.967 60.000 0.00 0.00 0.00 4.26
928 1000 3.710722 CAACTCCTCCGCCCTGCT 61.711 66.667 0.00 0.00 0.00 4.24
1198 1738 2.637383 GGCAAGGAGGTCGTCGTCT 61.637 63.158 2.61 0.00 0.00 4.18
1200 1740 1.444553 CAAGGAGGTCGTCGTCTGC 60.445 63.158 2.61 0.00 0.00 4.26
1278 1818 3.003113 GCGCAGGAGGGAGTACGTT 62.003 63.158 0.30 0.00 0.00 3.99
1347 1887 4.785453 CGGGGCTGCTTGGACTCC 62.785 72.222 0.00 0.00 0.00 3.85
1477 2185 1.403323 TCTAGATGTGACGAGCTGCTG 59.597 52.381 7.01 1.88 0.00 4.41
1722 2443 2.403252 ATGCAAGGTAAGGTTCTCCG 57.597 50.000 0.00 0.00 39.05 4.63
1996 2720 1.153628 GACAGGGGTCGAATCCACG 60.154 63.158 8.14 0.00 35.77 4.94
2038 2768 1.300465 CCGATATGCAGCTGCGAGT 60.300 57.895 32.11 22.49 45.83 4.18
2073 2806 5.651612 AATGGTAATGGATGGATCTCACA 57.348 39.130 0.00 0.00 0.00 3.58
2111 2844 1.737793 AGGCTGGCGATAAACGAAAAG 59.262 47.619 0.00 0.00 45.77 2.27
2295 3086 2.426522 TCTGGCATGTAGCTTGTGAAC 58.573 47.619 0.00 0.00 44.79 3.18
2298 3089 1.438651 GCATGTAGCTTGTGAACGGA 58.561 50.000 0.00 0.00 41.15 4.69
2308 3099 3.300009 CTTGTGAACGGAATTCTGCAAC 58.700 45.455 14.40 10.28 38.25 4.17
2429 3224 4.150804 GTCAGACACTAGTAGCACAAAAGC 59.849 45.833 0.00 0.00 0.00 3.51
2536 3331 1.935065 GCGAGACGTGCTCAGTTTCG 61.935 60.000 14.43 14.43 45.23 3.46
2573 3368 6.498303 TGCCATTATCAGAGGTCATAGTATGT 59.502 38.462 9.94 0.00 0.00 2.29
2605 3400 5.705441 CACATAATATAAGTTCCCACGGCAT 59.295 40.000 0.00 0.00 0.00 4.40
2704 3499 0.031616 AGTGCAAGGGGGAAAAACCA 60.032 50.000 0.00 0.00 41.20 3.67
2893 3694 1.458064 CGCGGTTCGACTTTTATGTGT 59.542 47.619 0.00 0.00 41.67 3.72
2966 3768 3.829948 TCACATCGTAACGAGTTCTTCC 58.170 45.455 0.00 0.00 39.91 3.46
2976 3778 5.413309 AACGAGTTCTTCCTGATTGATCT 57.587 39.130 0.00 0.00 0.00 2.75
3036 3838 4.681978 AGCGTCCACTTCGTGCCC 62.682 66.667 0.00 0.00 31.34 5.36
3113 3915 0.796312 GAGCAAAACGGCGAATCTCA 59.204 50.000 16.62 0.00 39.27 3.27
3150 3952 0.175989 GTCCTAGGGCCGAGTTTCAG 59.824 60.000 12.90 0.00 0.00 3.02
3172 3974 3.196469 GTGTTCAGACTGGAGATCCATCA 59.804 47.826 1.15 0.00 46.46 3.07
3294 4097 5.064558 CCAATGCTAATCTGATCAAGCTCT 58.935 41.667 16.07 3.62 35.95 4.09
3300 4103 6.709397 TGCTAATCTGATCAAGCTCTATTTGG 59.291 38.462 16.07 0.00 35.95 3.28
3338 4141 3.004315 CCGTTGAGTGCTGGTGTAATTTT 59.996 43.478 0.00 0.00 0.00 1.82
3452 4256 0.738762 TGCTGCTGAAGATGAGCGAC 60.739 55.000 0.00 0.00 39.47 5.19
3470 4274 0.892755 ACGGGAGCTACGTGAAATCA 59.107 50.000 14.30 0.00 43.78 2.57
3620 4428 5.055812 GGTTTGAATTTGCAGGTGAAATCA 58.944 37.500 0.00 0.00 0.00 2.57
3672 4480 2.749839 CGAAAAGGGGCGGCATCA 60.750 61.111 12.47 0.00 0.00 3.07
3713 4521 1.072331 GTTGCCAGAGGAGAAGGAACA 59.928 52.381 0.00 0.00 0.00 3.18
3724 4532 3.495100 GGAGAAGGAACATACGGCATGAT 60.495 47.826 0.00 0.00 38.10 2.45
3767 4575 0.034670 ATGGCCCTTCTGTTCAGCTC 60.035 55.000 0.00 0.00 0.00 4.09
3814 4622 7.173907 CACTGTATATTGTCCCAAATGATCCTC 59.826 40.741 0.00 0.00 0.00 3.71
3816 4624 5.937492 ATATTGTCCCAAATGATCCTCCT 57.063 39.130 0.00 0.00 0.00 3.69
3821 4629 2.312741 TCCCAAATGATCCTCCTTTGCT 59.687 45.455 0.00 0.00 32.83 3.91
3823 4631 3.131755 CCCAAATGATCCTCCTTTGCTTC 59.868 47.826 0.00 0.00 32.83 3.86
3824 4632 4.021916 CCAAATGATCCTCCTTTGCTTCT 58.978 43.478 0.00 0.00 32.83 2.85
3825 4633 4.097589 CCAAATGATCCTCCTTTGCTTCTC 59.902 45.833 0.00 0.00 32.83 2.87
3829 4640 2.334006 TCCTCCTTTGCTTCTCCTCT 57.666 50.000 0.00 0.00 0.00 3.69
3852 4663 0.580104 GAGGTTGTCCGTTTGTGTCG 59.420 55.000 0.00 0.00 39.05 4.35
3978 4789 4.096382 GTCTTGCTTCAGTTTCAGTTCCAA 59.904 41.667 0.00 0.00 0.00 3.53
4028 4839 2.966708 CGTTGTGCTTTCGTTGAATCAG 59.033 45.455 0.00 0.00 0.00 2.90
4033 4844 3.494626 GTGCTTTCGTTGAATCAGACTGA 59.505 43.478 7.80 7.80 0.00 3.41
4034 4845 4.153117 GTGCTTTCGTTGAATCAGACTGAT 59.847 41.667 12.37 12.37 39.09 2.90
4035 4846 4.152938 TGCTTTCGTTGAATCAGACTGATG 59.847 41.667 18.63 6.09 37.15 3.07
4061 4872 9.562583 GCCGTATCTAGATAAATCTAAGACAAG 57.437 37.037 14.09 0.00 38.80 3.16
4070 4881 8.543774 AGATAAATCTAAGACAAGCTTCTTGGA 58.456 33.333 14.39 14.39 44.41 3.53
4080 5087 1.275573 AGCTTCTTGGAACCGAGGTAC 59.724 52.381 8.09 0.00 0.00 3.34
4254 5262 0.321653 GTGGTGGAGCCGTTCAGAAT 60.322 55.000 0.00 0.00 41.21 2.40
4263 5271 1.002366 CCGTTCAGAATGGAAGAGCG 58.998 55.000 15.69 0.00 40.11 5.03
4526 5585 4.332828 TCAGACTTCACGGTTCTCATCTA 58.667 43.478 0.00 0.00 0.00 1.98
4527 5586 4.765339 TCAGACTTCACGGTTCTCATCTAA 59.235 41.667 0.00 0.00 0.00 2.10
4530 5589 6.591834 CAGACTTCACGGTTCTCATCTAAAAT 59.408 38.462 0.00 0.00 0.00 1.82
4573 5632 2.546795 CGCTCAGTCTTGACAAAGAGGT 60.547 50.000 14.72 0.00 43.13 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.434336 AGCTTGGCGTCTGGATATGTTA 59.566 45.455 0.00 0.00 0.00 2.41
1 2 1.210478 AGCTTGGCGTCTGGATATGTT 59.790 47.619 0.00 0.00 0.00 2.71
2 3 0.833287 AGCTTGGCGTCTGGATATGT 59.167 50.000 0.00 0.00 0.00 2.29
3 4 1.600957 CAAGCTTGGCGTCTGGATATG 59.399 52.381 19.14 0.00 0.00 1.78
4 5 1.959042 CAAGCTTGGCGTCTGGATAT 58.041 50.000 19.14 0.00 0.00 1.63
5 6 0.744414 GCAAGCTTGGCGTCTGGATA 60.744 55.000 27.10 0.00 0.00 2.59
6 7 2.042831 GCAAGCTTGGCGTCTGGAT 61.043 57.895 27.10 0.00 0.00 3.41
7 8 2.669569 GCAAGCTTGGCGTCTGGA 60.670 61.111 27.10 0.00 0.00 3.86
8 9 3.741476 GGCAAGCTTGGCGTCTGG 61.741 66.667 33.68 4.49 43.97 3.86
15 16 2.956987 CGTGGAAGGCAAGCTTGG 59.043 61.111 27.10 9.80 0.00 3.61
24 25 0.469917 ACTCCCATATGCGTGGAAGG 59.530 55.000 0.00 0.00 42.02 3.46
25 26 1.541233 GGACTCCCATATGCGTGGAAG 60.541 57.143 0.00 0.00 42.02 3.46
26 27 0.468226 GGACTCCCATATGCGTGGAA 59.532 55.000 0.00 0.00 42.02 3.53
27 28 0.398522 AGGACTCCCATATGCGTGGA 60.399 55.000 0.00 0.00 42.02 4.02
28 29 1.000955 GTAGGACTCCCATATGCGTGG 59.999 57.143 0.00 0.00 39.05 4.94
29 30 1.000955 GGTAGGACTCCCATATGCGTG 59.999 57.143 0.00 0.00 33.88 5.34
30 31 1.339097 GGTAGGACTCCCATATGCGT 58.661 55.000 0.00 0.00 33.88 5.24
31 32 0.608640 GGGTAGGACTCCCATATGCG 59.391 60.000 0.00 0.00 44.05 4.73
32 33 0.608640 CGGGTAGGACTCCCATATGC 59.391 60.000 0.00 0.00 44.81 3.14
33 34 1.203137 TCCGGGTAGGACTCCCATATG 60.203 57.143 0.00 0.00 45.98 1.78
34 35 1.164313 TCCGGGTAGGACTCCCATAT 58.836 55.000 0.00 0.00 45.98 1.78
35 36 2.649472 TCCGGGTAGGACTCCCATA 58.351 57.895 0.00 0.00 45.98 2.74
36 37 3.447261 TCCGGGTAGGACTCCCAT 58.553 61.111 0.00 0.00 45.98 4.00
44 45 3.145551 CCCTCGTGTCCGGGTAGG 61.146 72.222 0.00 1.38 42.97 3.18
45 46 3.145551 CCCCTCGTGTCCGGGTAG 61.146 72.222 0.00 0.00 38.88 3.18
46 47 2.728460 TTTCCCCTCGTGTCCGGGTA 62.728 60.000 0.00 0.00 38.88 3.69
47 48 4.626402 TTCCCCTCGTGTCCGGGT 62.626 66.667 0.00 0.00 38.88 5.28
48 49 2.798148 CTTTTCCCCTCGTGTCCGGG 62.798 65.000 0.00 0.00 40.29 5.73
49 50 1.375523 CTTTTCCCCTCGTGTCCGG 60.376 63.158 0.00 0.00 33.95 5.14
50 51 0.669625 GACTTTTCCCCTCGTGTCCG 60.670 60.000 0.00 0.00 0.00 4.79
51 52 0.685660 AGACTTTTCCCCTCGTGTCC 59.314 55.000 0.00 0.00 0.00 4.02
52 53 2.037381 AGAAGACTTTTCCCCTCGTGTC 59.963 50.000 0.00 0.00 0.00 3.67
53 54 2.047830 AGAAGACTTTTCCCCTCGTGT 58.952 47.619 0.00 0.00 0.00 4.49
54 55 2.417719 CAGAAGACTTTTCCCCTCGTG 58.582 52.381 0.00 0.00 0.00 4.35
55 56 1.270893 GCAGAAGACTTTTCCCCTCGT 60.271 52.381 0.00 0.00 0.00 4.18
56 57 1.002544 AGCAGAAGACTTTTCCCCTCG 59.997 52.381 0.00 0.00 0.00 4.63
57 58 2.869101 AGCAGAAGACTTTTCCCCTC 57.131 50.000 0.00 0.00 0.00 4.30
58 59 3.602205 AAAGCAGAAGACTTTTCCCCT 57.398 42.857 0.00 0.00 33.62 4.79
59 60 5.712446 AGATAAAAGCAGAAGACTTTTCCCC 59.288 40.000 4.87 0.00 44.16 4.81
60 61 6.825944 AGATAAAAGCAGAAGACTTTTCCC 57.174 37.500 4.87 0.20 44.16 3.97
61 62 7.805542 GTGAAGATAAAAGCAGAAGACTTTTCC 59.194 37.037 4.87 0.50 44.16 3.13
62 63 7.532209 CGTGAAGATAAAAGCAGAAGACTTTTC 59.468 37.037 4.87 0.00 44.16 2.29
63 64 7.355778 CGTGAAGATAAAAGCAGAAGACTTTT 58.644 34.615 6.70 6.70 46.30 2.27
64 65 6.073003 CCGTGAAGATAAAAGCAGAAGACTTT 60.073 38.462 0.00 0.00 38.98 2.66
65 66 5.409826 CCGTGAAGATAAAAGCAGAAGACTT 59.590 40.000 0.00 0.00 0.00 3.01
66 67 4.932200 CCGTGAAGATAAAAGCAGAAGACT 59.068 41.667 0.00 0.00 0.00 3.24
67 68 4.436183 GCCGTGAAGATAAAAGCAGAAGAC 60.436 45.833 0.00 0.00 0.00 3.01
68 69 3.684788 GCCGTGAAGATAAAAGCAGAAGA 59.315 43.478 0.00 0.00 0.00 2.87
69 70 3.181506 GGCCGTGAAGATAAAAGCAGAAG 60.182 47.826 0.00 0.00 0.00 2.85
70 71 2.747446 GGCCGTGAAGATAAAAGCAGAA 59.253 45.455 0.00 0.00 0.00 3.02
71 72 2.356135 GGCCGTGAAGATAAAAGCAGA 58.644 47.619 0.00 0.00 0.00 4.26
72 73 1.401905 GGGCCGTGAAGATAAAAGCAG 59.598 52.381 0.00 0.00 0.00 4.24
73 74 1.271652 TGGGCCGTGAAGATAAAAGCA 60.272 47.619 0.00 0.00 0.00 3.91
74 75 1.459450 TGGGCCGTGAAGATAAAAGC 58.541 50.000 0.00 0.00 0.00 3.51
75 76 3.278574 TGATGGGCCGTGAAGATAAAAG 58.721 45.455 1.02 0.00 0.00 2.27
76 77 3.278574 CTGATGGGCCGTGAAGATAAAA 58.721 45.455 1.02 0.00 0.00 1.52
77 78 2.238646 ACTGATGGGCCGTGAAGATAAA 59.761 45.455 1.02 0.00 0.00 1.40
78 79 1.837439 ACTGATGGGCCGTGAAGATAA 59.163 47.619 1.02 0.00 0.00 1.75
79 80 1.496060 ACTGATGGGCCGTGAAGATA 58.504 50.000 1.02 0.00 0.00 1.98
80 81 0.620556 AACTGATGGGCCGTGAAGAT 59.379 50.000 1.02 0.00 0.00 2.40
81 82 0.036388 GAACTGATGGGCCGTGAAGA 60.036 55.000 1.02 0.00 0.00 2.87
82 83 0.036010 AGAACTGATGGGCCGTGAAG 60.036 55.000 1.02 2.89 0.00 3.02
83 84 0.321564 CAGAACTGATGGGCCGTGAA 60.322 55.000 1.02 0.00 0.00 3.18
84 85 1.296392 CAGAACTGATGGGCCGTGA 59.704 57.895 1.02 0.00 0.00 4.35
85 86 2.401766 GCAGAACTGATGGGCCGTG 61.402 63.158 1.02 0.00 0.00 4.94
86 87 2.045926 GCAGAACTGATGGGCCGT 60.046 61.111 0.00 0.00 0.00 5.68
87 88 2.825836 GGCAGAACTGATGGGCCG 60.826 66.667 5.97 0.00 34.56 6.13
88 89 2.440980 GGGCAGAACTGATGGGCC 60.441 66.667 5.97 0.00 43.86 5.80
89 90 0.183492 TATGGGCAGAACTGATGGGC 59.817 55.000 5.97 0.00 0.00 5.36
90 91 2.965671 ATATGGGCAGAACTGATGGG 57.034 50.000 5.97 0.00 0.00 4.00
91 92 5.277974 CGTTTAATATGGGCAGAACTGATGG 60.278 44.000 5.97 0.00 0.00 3.51
92 93 5.277974 CCGTTTAATATGGGCAGAACTGATG 60.278 44.000 5.97 0.00 0.00 3.07
93 94 4.821805 CCGTTTAATATGGGCAGAACTGAT 59.178 41.667 5.97 0.00 0.00 2.90
94 95 4.196193 CCGTTTAATATGGGCAGAACTGA 58.804 43.478 5.97 0.00 0.00 3.41
95 96 3.945285 ACCGTTTAATATGGGCAGAACTG 59.055 43.478 0.00 0.00 37.22 3.16
96 97 4.196971 GACCGTTTAATATGGGCAGAACT 58.803 43.478 0.00 0.00 41.10 3.01
97 98 3.314357 GGACCGTTTAATATGGGCAGAAC 59.686 47.826 4.71 0.00 43.54 3.01
98 99 3.547746 GGACCGTTTAATATGGGCAGAA 58.452 45.455 4.71 0.00 43.54 3.02
99 100 2.484065 CGGACCGTTTAATATGGGCAGA 60.484 50.000 5.48 0.00 43.54 4.26
100 101 1.871039 CGGACCGTTTAATATGGGCAG 59.129 52.381 5.48 0.00 43.54 4.85
101 102 1.475392 CCGGACCGTTTAATATGGGCA 60.475 52.381 13.94 0.00 43.54 5.36
102 103 1.202675 TCCGGACCGTTTAATATGGGC 60.203 52.381 13.94 0.00 40.65 5.36
103 104 2.158928 TGTCCGGACCGTTTAATATGGG 60.159 50.000 31.19 0.00 37.22 4.00
104 105 2.867975 GTGTCCGGACCGTTTAATATGG 59.132 50.000 31.19 0.00 39.00 2.74
105 106 2.867975 GGTGTCCGGACCGTTTAATATG 59.132 50.000 31.19 0.00 0.00 1.78
106 107 2.158914 GGGTGTCCGGACCGTTTAATAT 60.159 50.000 31.19 0.00 36.80 1.28
107 108 1.206849 GGGTGTCCGGACCGTTTAATA 59.793 52.381 31.19 7.57 36.80 0.98
108 109 0.036105 GGGTGTCCGGACCGTTTAAT 60.036 55.000 31.19 0.00 36.80 1.40
109 110 1.370810 GGGTGTCCGGACCGTTTAA 59.629 57.895 31.19 9.20 36.80 1.52
110 111 3.059099 GGGTGTCCGGACCGTTTA 58.941 61.111 31.19 10.01 36.80 2.01
120 121 2.308118 TAGGGGATCCTCGGGTGTCC 62.308 65.000 12.58 1.12 43.66 4.02
121 122 0.398098 TTAGGGGATCCTCGGGTGTC 60.398 60.000 12.58 0.00 43.66 3.67
122 123 0.267960 ATTAGGGGATCCTCGGGTGT 59.732 55.000 12.58 0.00 43.66 4.16
123 124 0.977395 GATTAGGGGATCCTCGGGTG 59.023 60.000 12.58 0.00 43.66 4.61
124 125 0.178900 GGATTAGGGGATCCTCGGGT 60.179 60.000 12.58 0.00 43.66 5.28
125 126 0.178903 TGGATTAGGGGATCCTCGGG 60.179 60.000 12.58 0.00 44.85 5.14
126 127 1.270907 CTGGATTAGGGGATCCTCGG 58.729 60.000 12.58 0.00 44.85 4.63
127 128 1.270907 CCTGGATTAGGGGATCCTCG 58.729 60.000 12.58 0.00 44.85 4.63
135 136 4.015073 CCTAAGGGAGTCCTGGATTAGGG 61.015 56.522 22.38 12.12 44.07 3.53
136 137 3.243724 CCTAAGGGAGTCCTGGATTAGG 58.756 54.545 19.46 19.46 44.07 2.69
151 152 0.253207 ACAAGACCCCTCCCCTAAGG 60.253 60.000 0.00 0.00 36.08 2.69
152 153 1.560146 GAACAAGACCCCTCCCCTAAG 59.440 57.143 0.00 0.00 0.00 2.18
153 154 1.665137 GAACAAGACCCCTCCCCTAA 58.335 55.000 0.00 0.00 0.00 2.69
154 155 0.253020 GGAACAAGACCCCTCCCCTA 60.253 60.000 0.00 0.00 0.00 3.53
155 156 1.541620 GGAACAAGACCCCTCCCCT 60.542 63.158 0.00 0.00 0.00 4.79
164 165 2.876550 ACACCTAAAAGCGGAACAAGAC 59.123 45.455 0.00 0.00 0.00 3.01
175 176 6.677781 TGAACTCACAAGAACACCTAAAAG 57.322 37.500 0.00 0.00 0.00 2.27
187 188 6.738114 ACACAAACCATAATGAACTCACAAG 58.262 36.000 0.00 0.00 0.00 3.16
190 191 6.312399 TGACACAAACCATAATGAACTCAC 57.688 37.500 0.00 0.00 0.00 3.51
202 204 2.636647 TCTGAGCATGACACAAACCA 57.363 45.000 0.00 0.00 0.00 3.67
221 223 2.358737 CGCCACCGCCTCTTCTTT 60.359 61.111 0.00 0.00 0.00 2.52
252 254 1.073923 AGGCGGAGTGAACCTCATTTT 59.926 47.619 0.00 0.00 42.40 1.82
278 280 2.699954 CTAGAGGCGTCACCAAAATGT 58.300 47.619 9.41 0.00 43.14 2.71
312 314 0.033366 CGGAGACACATCACCACACA 59.967 55.000 0.00 0.00 35.41 3.72
319 321 0.461548 GATCCAGCGGAGACACATCA 59.538 55.000 3.76 0.00 34.05 3.07
321 323 1.134580 CAAGATCCAGCGGAGACACAT 60.135 52.381 3.76 0.00 34.05 3.21
332 334 0.104855 TCGAATCCCGCAAGATCCAG 59.895 55.000 0.00 0.00 43.02 3.86
351 353 0.320421 CACCGAAGACCAACACCGAT 60.320 55.000 0.00 0.00 0.00 4.18
389 401 5.827797 ACAACCTGTAGACACATGAACAAAT 59.172 36.000 0.00 0.00 33.14 2.32
413 442 9.053840 AGAGAAATGTAGTAGATCGAAACGATA 57.946 33.333 6.63 0.00 47.00 2.92
417 446 8.912787 TGAAGAGAAATGTAGTAGATCGAAAC 57.087 34.615 0.00 0.00 0.00 2.78
429 458 4.340263 CGTCGTCGATGAAGAGAAATGTA 58.660 43.478 14.50 0.00 39.71 2.29
431 460 2.531912 CCGTCGTCGATGAAGAGAAATG 59.468 50.000 20.29 0.68 39.71 2.32
475 504 2.024414 CTTTGTGCTAAGGCCCCATAC 58.976 52.381 0.00 0.00 37.74 2.39
494 523 3.891977 TGCAGTAGACAGTTGAGAAGTCT 59.108 43.478 0.00 0.00 44.25 3.24
561 597 3.666253 TCGAAGACACGCTGCCGA 61.666 61.111 0.00 0.00 38.29 5.54
591 627 4.037923 AGACCACCTAACGACGACTAAAAA 59.962 41.667 0.00 0.00 0.00 1.94
594 630 2.783135 AGACCACCTAACGACGACTAA 58.217 47.619 0.00 0.00 0.00 2.24
604 640 9.925545 TTACATCTATACTTGTAGACCACCTAA 57.074 33.333 0.00 0.00 33.78 2.69
650 691 5.195185 TCATCATGCCATCACAGTACAAAT 58.805 37.500 0.00 0.00 0.00 2.32
659 700 6.812879 TCAATCTATTCATCATGCCATCAC 57.187 37.500 0.00 0.00 0.00 3.06
661 702 6.433404 ACCTTCAATCTATTCATCATGCCATC 59.567 38.462 0.00 0.00 0.00 3.51
762 811 9.731519 CGAGAAGAAAACGTACGTTATTTTATT 57.268 29.630 31.90 24.31 37.35 1.40
763 812 8.915654 ACGAGAAGAAAACGTACGTTATTTTAT 58.084 29.630 31.90 21.67 38.47 1.40
764 813 8.280909 ACGAGAAGAAAACGTACGTTATTTTA 57.719 30.769 31.90 0.00 38.47 1.52
767 816 5.343325 GGACGAGAAGAAAACGTACGTTATT 59.657 40.000 31.90 24.94 40.29 1.40
777 826 7.807680 AGTATTTTGATGGACGAGAAGAAAAC 58.192 34.615 0.00 0.00 0.00 2.43
792 842 4.277174 TGCCGTGTGTTTGAGTATTTTGAT 59.723 37.500 0.00 0.00 0.00 2.57
793 843 3.628032 TGCCGTGTGTTTGAGTATTTTGA 59.372 39.130 0.00 0.00 0.00 2.69
794 844 3.958704 TGCCGTGTGTTTGAGTATTTTG 58.041 40.909 0.00 0.00 0.00 2.44
845 903 0.600782 GTGGGTTTCCGACTTGCGTA 60.601 55.000 0.00 0.00 38.67 4.42
866 924 1.376543 GTCGATGGACTCCAGTACGA 58.623 55.000 15.91 15.91 40.15 3.43
871 932 0.312416 GATCGGTCGATGGACTCCAG 59.688 60.000 10.77 0.00 42.97 3.86
872 933 1.107538 GGATCGGTCGATGGACTCCA 61.108 60.000 10.77 0.00 42.97 3.86
873 934 1.107538 TGGATCGGTCGATGGACTCC 61.108 60.000 10.77 7.62 42.97 3.85
875 936 0.683179 TGTGGATCGGTCGATGGACT 60.683 55.000 10.77 0.00 42.97 3.85
879 940 1.336332 GGAGATGTGGATCGGTCGATG 60.336 57.143 10.77 0.00 34.60 3.84
880 941 0.962489 GGAGATGTGGATCGGTCGAT 59.038 55.000 5.49 5.49 37.59 3.59
885 946 0.678395 CAGAGGGAGATGTGGATCGG 59.322 60.000 0.00 0.00 33.34 4.18
892 953 1.343782 TGGAGATGCAGAGGGAGATGT 60.344 52.381 0.00 0.00 0.00 3.06
900 961 1.138661 GGAGGAGTTGGAGATGCAGAG 59.861 57.143 0.00 0.00 0.00 3.35
902 963 0.179089 CGGAGGAGTTGGAGATGCAG 60.179 60.000 0.00 0.00 0.00 4.41
904 965 1.522580 GCGGAGGAGTTGGAGATGC 60.523 63.158 0.00 0.00 0.00 3.91
905 966 1.144936 GGCGGAGGAGTTGGAGATG 59.855 63.158 0.00 0.00 0.00 2.90
1198 1738 4.680237 CTCCACCACGAAGGCGCA 62.680 66.667 10.83 0.00 43.14 6.09
1200 1740 3.691342 TCCTCCACCACGAAGGCG 61.691 66.667 0.00 0.00 43.14 5.52
1278 1818 2.183300 CCGTCGGCCATCTCGAAA 59.817 61.111 2.24 0.00 38.42 3.46
1347 1887 0.601841 ACCAAAGGCACGTACCGAAG 60.602 55.000 0.00 0.00 33.69 3.79
1423 1963 4.889995 ACTGTACATCATCAGAGGAATCGA 59.110 41.667 0.00 0.00 35.84 3.59
1864 2585 0.385723 GATCCCGTCGTATCTCGCAC 60.386 60.000 0.00 0.00 39.67 5.34
1961 2683 4.201679 CATGCCGTGCCATGCCAG 62.202 66.667 0.00 0.00 36.52 4.85
1996 2720 1.429463 CAACTACTGGAGTCAACGCC 58.571 55.000 0.00 0.00 37.44 5.68
2038 2768 8.685427 CATCCATTACCATTATGTGAAGTCAAA 58.315 33.333 0.00 0.00 0.00 2.69
2073 2806 3.458857 AGCCTTCCAGACAAGATGATCAT 59.541 43.478 8.25 8.25 0.00 2.45
2111 2844 9.323985 AGATGCTGTTAATATCTCTCAGTTTTC 57.676 33.333 0.00 0.00 0.00 2.29
2162 2898 7.569591 GCGAATGAGTATATTTGAAGGCACTAC 60.570 40.741 0.00 0.00 38.49 2.73
2295 3086 2.029728 GTCTGATCGTTGCAGAATTCCG 59.970 50.000 0.65 0.00 43.39 4.30
2298 3089 3.005554 CCAGTCTGATCGTTGCAGAATT 58.994 45.455 0.00 0.00 43.39 2.17
2308 3099 0.103937 GCTTCCTCCCAGTCTGATCG 59.896 60.000 0.00 0.00 0.00 3.69
2383 3175 8.397906 TGACCAAAGATCGATTGTTATTCATTC 58.602 33.333 0.00 0.00 0.00 2.67
2384 3176 8.279970 TGACCAAAGATCGATTGTTATTCATT 57.720 30.769 0.00 0.00 0.00 2.57
2385 3177 7.770433 TCTGACCAAAGATCGATTGTTATTCAT 59.230 33.333 0.00 0.00 0.00 2.57
2429 3224 4.974275 CACATGTTTGAGCACTTTCAGAAG 59.026 41.667 0.00 0.00 38.87 2.85
2536 3331 1.301423 TAATGGCAAATACGGCGTCC 58.699 50.000 19.21 12.35 0.00 4.79
2573 3368 7.836685 TGGGAACTTATATTATGTGCCTGAAAA 59.163 33.333 0.00 0.00 33.19 2.29
2704 3499 1.949525 AGTTGACAGCACGCTGAAAAT 59.050 42.857 25.09 14.45 46.30 1.82
2815 3616 1.603455 CATCCGCCACCAAACCTGT 60.603 57.895 0.00 0.00 0.00 4.00
2966 3768 2.435069 ACCAGAGCCTGAGATCAATCAG 59.565 50.000 5.23 5.23 45.24 2.90
2976 3778 0.901827 TTATGCGAACCAGAGCCTGA 59.098 50.000 4.00 0.00 32.44 3.86
3113 3915 2.237392 GGACCTTGATAAGAGCACACCT 59.763 50.000 0.00 0.00 0.00 4.00
3317 4120 3.896648 AAATTACACCAGCACTCAACG 57.103 42.857 0.00 0.00 0.00 4.10
3350 4153 2.669229 TGCATCACAGCCACACCG 60.669 61.111 0.00 0.00 0.00 4.94
3452 4256 1.278238 GTGATTTCACGTAGCTCCCG 58.722 55.000 0.00 0.00 37.10 5.14
3470 4274 6.313519 ACCTTGAGATATGTAACATGTGGT 57.686 37.500 0.00 0.00 0.00 4.16
3507 4311 4.630644 AGTTGATGATCAGGTTGACAGT 57.369 40.909 0.09 0.00 0.00 3.55
3519 4323 5.664457 TCTGAATCGCTGTAAGTTGATGAT 58.336 37.500 0.00 0.00 32.74 2.45
3520 4324 5.072040 TCTGAATCGCTGTAAGTTGATGA 57.928 39.130 0.00 0.00 32.74 2.92
3521 4325 5.120674 TGTTCTGAATCGCTGTAAGTTGATG 59.879 40.000 0.00 0.00 32.74 3.07
3593 4401 3.125316 CACCTGCAAATTCAAACCAGTG 58.875 45.455 0.00 0.00 0.00 3.66
3597 4405 5.055812 TGATTTCACCTGCAAATTCAAACC 58.944 37.500 0.00 0.00 0.00 3.27
3604 4412 4.021192 ACCGAAATGATTTCACCTGCAAAT 60.021 37.500 17.14 0.00 39.63 2.32
3672 4480 2.478890 CCTCGCCGTCCACGTCTAT 61.479 63.158 0.00 0.00 37.74 1.98
3713 4521 2.259917 TGATCCTGGATCATGCCGTAT 58.740 47.619 30.63 0.00 43.11 3.06
3814 4622 1.905215 TCTGGAGAGGAGAAGCAAAGG 59.095 52.381 0.00 0.00 0.00 3.11
3829 4640 0.834612 ACAAACGGACAACCTCTGGA 59.165 50.000 0.00 0.00 0.00 3.86
3836 4647 2.635444 CAATCGACACAAACGGACAAC 58.365 47.619 0.00 0.00 0.00 3.32
3978 4789 0.830023 CGGTTTGGGTTGGTTGGGAT 60.830 55.000 0.00 0.00 0.00 3.85
4028 4839 7.767261 AGATTTATCTAGATACGGCATCAGTC 58.233 38.462 12.12 2.93 35.96 3.51
4033 4844 9.244292 TGTCTTAGATTTATCTAGATACGGCAT 57.756 33.333 12.12 2.81 40.23 4.40
4034 4845 8.631480 TGTCTTAGATTTATCTAGATACGGCA 57.369 34.615 12.12 0.00 40.23 5.69
4035 4846 9.562583 CTTGTCTTAGATTTATCTAGATACGGC 57.437 37.037 12.12 4.67 40.23 5.68
4061 4872 1.275573 AGTACCTCGGTTCCAAGAAGC 59.724 52.381 0.00 0.00 0.00 3.86
4070 4881 9.675464 TCAATAATTTCATTTAGTACCTCGGTT 57.325 29.630 0.00 0.00 0.00 4.44
4217 5225 2.412870 CACCAGTGATGTAACGCTTGA 58.587 47.619 0.00 0.00 0.00 3.02
4254 5262 1.078285 TGCATGCATCGCTCTTCCA 60.078 52.632 18.46 0.00 0.00 3.53
4499 5558 4.142026 TGAGAACCGTGAAGTCTGAAGAAA 60.142 41.667 0.00 0.00 0.00 2.52
4530 5589 7.489160 AGCGAATAGTTGAATATACACTCACA 58.511 34.615 0.00 0.00 0.00 3.58
4573 5632 5.488919 AGTCTTGGATGAAGGTAATTGGAGA 59.511 40.000 0.00 0.00 31.85 3.71


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

AutoCloner maintained by Alex Coulton.