Multiple sequence alignment - TraesCS7D01G053000

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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 TraesCS7D01G053000 chr7D 100.000 5469 0 0 1 5469 27837053 27842521 0.000000e+00 10100.0
1 TraesCS7D01G053000 chr7D 99.855 690 0 1 4780 5469 27847656 27848344 0.000000e+00 1267.0
2 TraesCS7D01G053000 chr7D 98.116 690 2 2 4780 5469 27859307 27859985 0.000000e+00 1192.0
3 TraesCS7D01G053000 chr7D 97.971 690 3 2 4780 5469 27853485 27854163 0.000000e+00 1186.0
4 TraesCS7D01G053000 chr7D 93.197 147 10 0 2324 2470 27839229 27839375 3.320000e-52 217.0
5 TraesCS7D01G053000 chr7D 93.197 147 10 0 2177 2323 27839376 27839522 3.320000e-52 217.0
6 TraesCS7D01G053000 chr7A 90.502 3264 221 32 108 3333 28038054 28041266 0.000000e+00 4228.0
7 TraesCS7D01G053000 chr7A 88.444 2146 155 39 3358 5469 28041339 28043425 0.000000e+00 2503.0
8 TraesCS7D01G053000 chr7A 94.118 527 24 2 4780 5300 28120174 28120699 0.000000e+00 795.0
9 TraesCS7D01G053000 chr7A 93.169 527 29 2 4780 5300 28106295 28106820 0.000000e+00 767.0
10 TraesCS7D01G053000 chr7A 83.807 704 73 16 1219 1899 28185593 28186278 1.000000e-176 630.0
11 TraesCS7D01G053000 chr7A 94.402 393 21 1 1939 2331 28186280 28186671 2.180000e-168 603.0
12 TraesCS7D01G053000 chr7A 95.238 147 7 0 2324 2470 28040111 28040257 3.290000e-57 233.0
13 TraesCS7D01G053000 chr7A 90.411 146 14 0 2177 2322 28040258 28040403 5.590000e-45 193.0
14 TraesCS7D01G053000 chr4A 95.728 1498 57 6 1820 3316 703337609 703339100 0.000000e+00 2405.0
15 TraesCS7D01G053000 chr4A 94.995 1079 48 2 3867 4940 703340130 703341207 0.000000e+00 1688.0
16 TraesCS7D01G053000 chr4A 85.192 1121 87 35 4342 5440 703359534 703360597 0.000000e+00 1077.0
17 TraesCS7D01G053000 chr4A 86.015 1044 58 46 811 1821 703336577 703337565 0.000000e+00 1038.0
18 TraesCS7D01G053000 chr4A 89.981 529 35 10 3359 3878 703339202 703339721 0.000000e+00 667.0
19 TraesCS7D01G053000 chr4A 85.586 555 64 11 192 736 703333280 703333828 7.950000e-158 568.0
20 TraesCS7D01G053000 chr4A 84.588 279 33 6 5123 5395 703341302 703341576 9.030000e-68 268.0
21 TraesCS7D01G053000 chr4A 93.197 147 10 0 2324 2470 703337962 703338108 3.320000e-52 217.0
22 TraesCS7D01G053000 chr4A 91.837 147 12 0 2177 2323 703338109 703338255 7.180000e-49 206.0
23 TraesCS7D01G053000 chr4A 95.833 72 3 0 108 179 703333165 703333236 3.460000e-22 117.0
24 TraesCS7D01G053000 chrUn 100.000 257 0 0 5213 5469 442720989 442721245 4.960000e-130 475.0
25 TraesCS7D01G053000 chr3B 80.392 306 59 1 1904 2208 817765248 817765553 1.180000e-56 231.0
26 TraesCS7D01G053000 chr2D 95.283 106 5 0 3 108 627666146 627666041 9.420000e-38 169.0
27 TraesCS7D01G053000 chr5D 94.286 105 6 0 3 107 333347546 333347650 1.580000e-35 161.0
28 TraesCS7D01G053000 chr4D 94.286 105 6 0 3 107 121471274 121471378 1.580000e-35 161.0
29 TraesCS7D01G053000 chr3D 90.984 122 8 2 1 120 106944207 106944327 1.580000e-35 161.0
30 TraesCS7D01G053000 chr3D 92.035 113 9 0 1 113 9345655 9345543 5.670000e-35 159.0
31 TraesCS7D01G053000 chr3D 92.035 113 9 0 1 113 9360341 9360229 5.670000e-35 159.0
32 TraesCS7D01G053000 chr6D 93.519 108 6 1 1 107 13622508 13622401 5.670000e-35 159.0
33 TraesCS7D01G053000 chr1D 93.519 108 6 1 2 108 462259927 462260034 5.670000e-35 159.0
34 TraesCS7D01G053000 chr2B 89.431 123 10 3 1 121 768328166 768328287 9.490000e-33 152.0
35 TraesCS7D01G053000 chr5B 76.786 112 24 2 2098 2208 415765961 415765851 1.640000e-05 62.1
36 TraesCS7D01G053000 chr1B 96.970 33 1 0 2325 2357 61955732 61955700 7.650000e-04 56.5
37 TraesCS7D01G053000 chr1B 96.970 33 1 0 2178 2210 61955732 61955700 7.650000e-04 56.5


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 TraesCS7D01G053000 chr7D 27837053 27842521 5468 False 3511.333333 10100 95.464667 1 5469 3 chr7D.!!$F4 5468
1 TraesCS7D01G053000 chr7D 27847656 27848344 688 False 1267.000000 1267 99.855000 4780 5469 1 chr7D.!!$F1 689
2 TraesCS7D01G053000 chr7D 27859307 27859985 678 False 1192.000000 1192 98.116000 4780 5469 1 chr7D.!!$F3 689
3 TraesCS7D01G053000 chr7D 27853485 27854163 678 False 1186.000000 1186 97.971000 4780 5469 1 chr7D.!!$F2 689
4 TraesCS7D01G053000 chr7A 28038054 28043425 5371 False 1789.250000 4228 91.148750 108 5469 4 chr7A.!!$F3 5361
5 TraesCS7D01G053000 chr7A 28120174 28120699 525 False 795.000000 795 94.118000 4780 5300 1 chr7A.!!$F2 520
6 TraesCS7D01G053000 chr7A 28106295 28106820 525 False 767.000000 767 93.169000 4780 5300 1 chr7A.!!$F1 520
7 TraesCS7D01G053000 chr7A 28185593 28186671 1078 False 616.500000 630 89.104500 1219 2331 2 chr7A.!!$F4 1112
8 TraesCS7D01G053000 chr4A 703359534 703360597 1063 False 1077.000000 1077 85.192000 4342 5440 1 chr4A.!!$F1 1098
9 TraesCS7D01G053000 chr4A 703333165 703341576 8411 False 797.111111 2405 90.862222 108 5395 9 chr4A.!!$F2 5287

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
62 63 0.178955 TGGTGACAGAACCGGGACTA 60.179 55.000 6.32 0.00 43.73 2.59 F
1191 3917 0.341609 CCCTCTTCCTTCCCCTCTCT 59.658 60.000 0.00 0.00 0.00 3.10 F
1559 4295 0.806102 GATTCACGCGCTAAGCCTCA 60.806 55.000 5.73 0.00 44.76 3.86 F
2931 5750 0.620556 TTGAAGGCATCCCTCCTGAC 59.379 55.000 0.00 0.00 41.90 3.51 F
3723 6627 1.133407 CGTGGACTTGAGACTAGGCTC 59.867 57.143 19.48 19.48 35.46 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1696 4459 0.590195 CACAGAACAGCTTGCTGTCC 59.410 55.000 25.63 15.74 40.63 4.02 R
2627 5445 0.091344 CAGTACGCAGAAAACGCTCG 59.909 55.000 0.00 0.00 0.00 5.03 R
3503 6402 1.134753 CACAAACTGACAGCTTTGGCA 59.865 47.619 22.87 0.00 41.70 4.92 R
4267 7601 0.318022 CGCAAAGTGACAATGCTGCA 60.318 50.000 4.13 4.13 37.92 4.41 R
4711 8051 0.721718 GGAAATCACCTTGCGAGACG 59.278 55.000 1.22 0.00 0.00 4.18 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
19 20 2.124109 TGGGCGCACAAACCAGAA 60.124 55.556 11.60 0.00 0.00 3.02
20 21 2.335011 GGGCGCACAAACCAGAAC 59.665 61.111 10.83 0.00 0.00 3.01
21 22 2.051345 GGCGCACAAACCAGAACG 60.051 61.111 10.83 0.00 0.00 3.95
22 23 2.713154 GCGCACAAACCAGAACGT 59.287 55.556 0.30 0.00 0.00 3.99
23 24 1.500512 GGCGCACAAACCAGAACGTA 61.501 55.000 10.83 0.00 0.00 3.57
24 25 0.515564 GCGCACAAACCAGAACGTAT 59.484 50.000 0.30 0.00 0.00 3.06
25 26 1.724654 GCGCACAAACCAGAACGTATG 60.725 52.381 0.30 0.00 0.00 2.39
26 27 1.724654 CGCACAAACCAGAACGTATGC 60.725 52.381 0.00 0.00 0.00 3.14
27 28 1.401018 GCACAAACCAGAACGTATGCC 60.401 52.381 0.00 0.00 0.00 4.40
28 29 1.199097 CACAAACCAGAACGTATGCCC 59.801 52.381 0.00 0.00 0.00 5.36
29 30 0.808755 CAAACCAGAACGTATGCCCC 59.191 55.000 0.00 0.00 0.00 5.80
30 31 0.323087 AAACCAGAACGTATGCCCCC 60.323 55.000 0.00 0.00 0.00 5.40
31 32 1.493854 AACCAGAACGTATGCCCCCA 61.494 55.000 0.00 0.00 0.00 4.96
32 33 1.279025 ACCAGAACGTATGCCCCCAT 61.279 55.000 0.00 0.00 35.44 4.00
33 34 0.819259 CCAGAACGTATGCCCCCATG 60.819 60.000 0.00 0.00 32.85 3.66
34 35 0.819259 CAGAACGTATGCCCCCATGG 60.819 60.000 4.14 4.14 32.85 3.66
44 45 2.360191 CCCCATGGGTCCCAGTTG 59.640 66.667 29.33 10.67 38.25 3.16
45 46 2.360191 CCCATGGGTCCCAGTTGG 59.640 66.667 23.93 20.23 36.75 3.77
46 47 2.547595 CCCATGGGTCCCAGTTGGT 61.548 63.158 23.93 2.61 36.75 3.67
47 48 1.304381 CCATGGGTCCCAGTTGGTG 60.304 63.158 19.24 11.17 36.75 4.17
48 49 1.767036 CATGGGTCCCAGTTGGTGA 59.233 57.895 17.70 0.00 36.75 4.02
49 50 0.609131 CATGGGTCCCAGTTGGTGAC 60.609 60.000 17.70 9.82 36.75 3.67
50 51 1.065410 ATGGGTCCCAGTTGGTGACA 61.065 55.000 17.70 0.00 36.75 3.58
51 52 1.073199 GGGTCCCAGTTGGTGACAG 59.927 63.158 1.78 0.00 44.54 3.51
52 53 1.415672 GGGTCCCAGTTGGTGACAGA 61.416 60.000 1.78 0.00 44.54 3.41
53 54 0.472471 GGTCCCAGTTGGTGACAGAA 59.528 55.000 16.42 0.00 44.54 3.02
54 55 1.594331 GTCCCAGTTGGTGACAGAAC 58.406 55.000 12.19 0.00 44.54 3.01
55 56 0.472471 TCCCAGTTGGTGACAGAACC 59.528 55.000 0.00 0.00 44.54 3.62
56 57 0.884704 CCCAGTTGGTGACAGAACCG 60.885 60.000 0.00 0.00 43.73 4.44
57 58 0.884704 CCAGTTGGTGACAGAACCGG 60.885 60.000 0.00 0.00 43.73 5.28
58 59 0.884704 CAGTTGGTGACAGAACCGGG 60.885 60.000 6.32 0.00 43.73 5.73
59 60 1.052124 AGTTGGTGACAGAACCGGGA 61.052 55.000 6.32 0.00 43.73 5.14
60 61 0.883370 GTTGGTGACAGAACCGGGAC 60.883 60.000 6.32 0.00 43.73 4.46
61 62 1.052124 TTGGTGACAGAACCGGGACT 61.052 55.000 6.32 0.73 43.73 3.85
62 63 0.178955 TGGTGACAGAACCGGGACTA 60.179 55.000 6.32 0.00 43.73 2.59
63 64 0.971386 GGTGACAGAACCGGGACTAA 59.029 55.000 6.32 0.00 0.00 2.24
64 65 1.553704 GGTGACAGAACCGGGACTAAT 59.446 52.381 6.32 0.00 0.00 1.73
65 66 2.618053 GTGACAGAACCGGGACTAATG 58.382 52.381 6.32 0.00 0.00 1.90
66 67 1.553248 TGACAGAACCGGGACTAATGG 59.447 52.381 6.32 0.00 0.00 3.16
67 68 0.909623 ACAGAACCGGGACTAATGGG 59.090 55.000 6.32 0.00 0.00 4.00
68 69 0.463833 CAGAACCGGGACTAATGGGC 60.464 60.000 6.32 0.00 0.00 5.36
69 70 0.620700 AGAACCGGGACTAATGGGCT 60.621 55.000 6.32 0.00 0.00 5.19
70 71 0.463833 GAACCGGGACTAATGGGCTG 60.464 60.000 6.32 0.00 0.00 4.85
71 72 0.912487 AACCGGGACTAATGGGCTGA 60.912 55.000 6.32 0.00 0.00 4.26
72 73 1.146263 CCGGGACTAATGGGCTGAC 59.854 63.158 0.00 0.00 0.00 3.51
73 74 1.146263 CGGGACTAATGGGCTGACC 59.854 63.158 0.00 0.00 40.81 4.02
85 86 3.579302 CTGACCAGGCCCCAACCA 61.579 66.667 0.00 0.00 0.00 3.67
86 87 3.106609 TGACCAGGCCCCAACCAA 61.107 61.111 0.00 0.00 0.00 3.67
87 88 2.200092 GACCAGGCCCCAACCAAA 59.800 61.111 0.00 0.00 0.00 3.28
88 89 1.908299 GACCAGGCCCCAACCAAAG 60.908 63.158 0.00 0.00 0.00 2.77
89 90 3.313524 CCAGGCCCCAACCAAAGC 61.314 66.667 0.00 0.00 0.00 3.51
90 91 3.313524 CAGGCCCCAACCAAAGCC 61.314 66.667 0.00 0.00 46.13 4.35
92 93 4.638895 GGCCCCAACCAAAGCCCT 62.639 66.667 0.00 0.00 39.60 5.19
93 94 3.313524 GCCCCAACCAAAGCCCTG 61.314 66.667 0.00 0.00 0.00 4.45
94 95 2.201210 CCCCAACCAAAGCCCTGT 59.799 61.111 0.00 0.00 0.00 4.00
95 96 1.459348 CCCCAACCAAAGCCCTGTT 60.459 57.895 0.00 0.00 0.00 3.16
96 97 1.053835 CCCCAACCAAAGCCCTGTTT 61.054 55.000 0.00 0.00 0.00 2.83
97 98 0.836606 CCCAACCAAAGCCCTGTTTT 59.163 50.000 0.00 0.00 0.00 2.43
98 99 1.202639 CCCAACCAAAGCCCTGTTTTC 60.203 52.381 0.00 0.00 0.00 2.29
99 100 1.762370 CCAACCAAAGCCCTGTTTTCT 59.238 47.619 0.00 0.00 0.00 2.52
100 101 2.962421 CCAACCAAAGCCCTGTTTTCTA 59.038 45.455 0.00 0.00 0.00 2.10
101 102 3.243737 CCAACCAAAGCCCTGTTTTCTAC 60.244 47.826 0.00 0.00 0.00 2.59
102 103 3.595190 ACCAAAGCCCTGTTTTCTACT 57.405 42.857 0.00 0.00 0.00 2.57
103 104 4.717279 ACCAAAGCCCTGTTTTCTACTA 57.283 40.909 0.00 0.00 0.00 1.82
104 105 4.652822 ACCAAAGCCCTGTTTTCTACTAG 58.347 43.478 0.00 0.00 0.00 2.57
105 106 4.104261 ACCAAAGCCCTGTTTTCTACTAGT 59.896 41.667 0.00 0.00 0.00 2.57
106 107 4.455877 CCAAAGCCCTGTTTTCTACTAGTG 59.544 45.833 5.39 0.00 0.00 2.74
138 139 5.552178 ACATCTTGTCTTCTTTGGTACTCC 58.448 41.667 0.00 0.00 0.00 3.85
142 143 1.982958 GTCTTCTTTGGTACTCCCCCA 59.017 52.381 0.00 0.00 0.00 4.96
179 180 4.564782 ACAAAGCTCTCATCTTCCATGA 57.435 40.909 0.00 0.00 0.00 3.07
180 181 4.515361 ACAAAGCTCTCATCTTCCATGAG 58.485 43.478 5.39 5.39 45.08 2.90
189 190 6.788684 CTCATCTTCCATGAGAATGTGATC 57.211 41.667 5.80 0.00 46.25 2.92
190 191 6.496144 TCATCTTCCATGAGAATGTGATCT 57.504 37.500 0.00 0.00 32.82 2.75
211 243 6.688637 TCTTCTTATGATGCACATTCTTGG 57.311 37.500 7.02 0.00 40.07 3.61
217 249 2.025131 TGATGCACATTCTTGGGATGGA 60.025 45.455 0.00 0.00 0.00 3.41
230 262 6.730447 TCTTGGGATGGAAAATCTTGTGATA 58.270 36.000 0.00 0.00 31.70 2.15
236 268 9.354673 GGGATGGAAAATCTTGTGATAGAAATA 57.645 33.333 0.00 0.00 31.70 1.40
241 273 6.619801 AAATCTTGTGATAGAAATACCGGC 57.380 37.500 0.00 0.00 31.70 6.13
249 281 1.722011 AGAAATACCGGCTCAACACG 58.278 50.000 0.00 0.00 0.00 4.49
261 293 2.355756 GCTCAACACGGATGTATTGCAT 59.644 45.455 0.00 0.00 38.45 3.96
281 315 6.085573 TGCATAAAAGTTTCATCATCACACG 58.914 36.000 0.00 0.00 0.00 4.49
305 339 7.077605 CGACATACATCAAGTGTGAACAAAAT 58.922 34.615 0.00 0.00 41.41 1.82
410 446 4.475944 GTCATTTGATCGAACAAGTTGGG 58.524 43.478 8.19 0.00 0.00 4.12
413 449 0.608035 TGATCGAACAAGTTGGGGGC 60.608 55.000 7.96 0.00 0.00 5.80
414 450 1.644786 GATCGAACAAGTTGGGGGCG 61.645 60.000 7.96 5.34 0.00 6.13
415 451 2.119484 ATCGAACAAGTTGGGGGCGA 62.119 55.000 7.96 10.36 0.00 5.54
417 453 1.883021 GAACAAGTTGGGGGCGATG 59.117 57.895 7.96 0.00 0.00 3.84
419 455 2.035626 CAAGTTGGGGGCGATGGT 59.964 61.111 0.00 0.00 0.00 3.55
423 459 4.041762 TTGGGGGCGATGGTGGTC 62.042 66.667 0.00 0.00 0.00 4.02
431 467 3.799755 GATGGTGGTCGCGGCAAC 61.800 66.667 14.93 12.69 0.00 4.17
462 498 0.389948 GCTCGACCTTGGACGACAAT 60.390 55.000 9.84 0.00 38.65 2.71
470 506 1.278127 CTTGGACGACAATGGTAGGGT 59.722 52.381 0.00 0.00 38.65 4.34
480 516 6.325545 ACGACAATGGTAGGGTATCAGAATAA 59.674 38.462 0.00 0.00 0.00 1.40
559 595 2.372690 GCGTCTTCTTTCTCGCGCA 61.373 57.895 8.75 0.00 43.62 6.09
586 622 2.431454 CCACGACCGATGGATCCCA 61.431 63.158 9.90 0.00 39.87 4.37
599 635 0.391263 GATCCCACGGTGACCACTTC 60.391 60.000 10.28 0.00 0.00 3.01
604 640 1.911766 ACGGTGACCACTTCCCGAT 60.912 57.895 1.11 0.00 39.27 4.18
646 683 1.430632 CTTGGCGCGATGCTCATTT 59.569 52.632 12.10 0.00 45.43 2.32
647 684 0.864377 CTTGGCGCGATGCTCATTTG 60.864 55.000 12.10 0.00 45.43 2.32
652 689 1.720852 GCGCGATGCTCATTTGTTTTT 59.279 42.857 12.10 0.00 41.73 1.94
693 730 9.571810 TTTATTGTTCATCATTGTTGTGATAGC 57.428 29.630 0.00 0.00 36.72 2.97
740 2630 2.232208 AGCTCATCACTCATGTCGAACA 59.768 45.455 0.00 0.00 33.66 3.18
750 2640 4.062293 CTCATGTCGAACAGTACCCAAAA 58.938 43.478 0.00 0.00 0.00 2.44
842 3556 3.352338 GATCCGGACCGTTCACGCT 62.352 63.158 6.12 0.00 38.18 5.07
955 3669 2.041405 CCCTCCCCCACTCTCTCC 60.041 72.222 0.00 0.00 0.00 3.71
956 3670 2.780693 CCTCCCCCACTCTCTCCA 59.219 66.667 0.00 0.00 0.00 3.86
1166 3892 4.867599 CTACTCCGCCGGTTCGCC 62.868 72.222 1.63 0.00 0.00 5.54
1185 3911 1.694525 CCCCTCCCTCTTCCTTCCC 60.695 68.421 0.00 0.00 0.00 3.97
1187 3913 1.398234 CCTCCCTCTTCCTTCCCCT 59.602 63.158 0.00 0.00 0.00 4.79
1191 3917 0.341609 CCCTCTTCCTTCCCCTCTCT 59.658 60.000 0.00 0.00 0.00 3.10
1358 4090 2.185350 CTCGCTGCCCTGTTCGAT 59.815 61.111 0.00 0.00 0.00 3.59
1359 4091 1.880340 CTCGCTGCCCTGTTCGATC 60.880 63.158 0.00 0.00 0.00 3.69
1383 4115 2.164865 CTCGGTTGCCTGAGCTCTGT 62.165 60.000 16.19 0.00 40.80 3.41
1394 4126 2.745492 GCTCTGTGCTGGCTGTCC 60.745 66.667 0.00 0.00 38.95 4.02
1396 4128 3.618780 CTCTGTGCTGGCTGTCCCC 62.619 68.421 0.00 0.00 0.00 4.81
1469 4205 1.616628 AGGCCTTCGACCCCTGAAT 60.617 57.895 0.00 0.00 0.00 2.57
1495 4231 1.830477 GCCTCCCATGGTAAATTTGCA 59.170 47.619 11.73 0.00 0.00 4.08
1497 4233 2.830923 CCTCCCATGGTAAATTTGCACA 59.169 45.455 11.73 4.54 0.00 4.57
1559 4295 0.806102 GATTCACGCGCTAAGCCTCA 60.806 55.000 5.73 0.00 44.76 3.86
1637 4400 6.150474 GGGTTTCGATTTAGGATGAAAAGTGA 59.850 38.462 0.00 0.00 32.65 3.41
1679 4442 5.314923 TGATTTGATTGCTTGGTTCTAGC 57.685 39.130 0.00 0.00 39.10 3.42
1696 4459 1.722011 AGCCGTCGTTTATGAGTTGG 58.278 50.000 0.00 0.00 0.00 3.77
1700 4466 2.610976 CCGTCGTTTATGAGTTGGGACA 60.611 50.000 0.00 0.00 0.00 4.02
1779 4545 4.985409 GGTTTCAGTATATCTTCTCAGCCG 59.015 45.833 0.00 0.00 0.00 5.52
1802 4568 1.021202 TCACTGTTTTGACCTTGCCG 58.979 50.000 0.00 0.00 0.00 5.69
1826 4637 5.444877 GGAAAACTTTAACACAAAACGCCAC 60.445 40.000 0.00 0.00 0.00 5.01
1922 4733 3.181450 GCCAGTAGCATTTCACCTCCTAT 60.181 47.826 0.00 0.00 42.97 2.57
1998 4816 2.278330 GGTTGCTGCCCCAAGAAGG 61.278 63.158 0.00 0.00 37.03 3.46
2228 5046 5.013599 GGCCTATCTTCTCAACCAATATCCT 59.986 44.000 0.00 0.00 0.00 3.24
2252 5070 2.562298 TCCAGTACATTAAACGGACGGT 59.438 45.455 0.00 0.00 0.00 4.83
2393 5211 3.680490 TCCGAATCCAGCACATTAAACA 58.320 40.909 0.00 0.00 0.00 2.83
2593 5411 1.849039 AGAAAGGCCAGGATATGCTGT 59.151 47.619 21.19 3.86 0.00 4.40
2627 5445 2.093235 ACAGGCTCTCAATGCTTCCTAC 60.093 50.000 0.00 0.00 0.00 3.18
2655 5473 2.440517 TCTGCGTACTGGGGTATACA 57.559 50.000 5.01 0.00 0.00 2.29
2931 5750 0.620556 TTGAAGGCATCCCTCCTGAC 59.379 55.000 0.00 0.00 41.90 3.51
3010 5829 4.515191 TCTGCACTTGTTGTCCTTCATAAC 59.485 41.667 0.00 0.00 0.00 1.89
3012 5831 4.826733 TGCACTTGTTGTCCTTCATAACAT 59.173 37.500 0.00 0.00 34.63 2.71
3287 6106 2.159114 TGGAAGCTTTGCAAGGTGAAAC 60.159 45.455 10.54 0.00 39.57 2.78
3308 6127 3.627577 ACCGATGAACTTGGCATGAATAC 59.372 43.478 7.45 0.00 0.00 1.89
3316 6135 6.763135 TGAACTTGGCATGAATACATACTCTC 59.237 38.462 7.45 0.00 35.09 3.20
3324 6143 8.263640 GGCATGAATACATACTCTCCAATCTAT 58.736 37.037 0.00 0.00 35.09 1.98
3337 6156 9.606631 ACTCTCCAATCTATATTCTGTTGAAAC 57.393 33.333 0.00 0.00 35.63 2.78
3338 6157 9.829507 CTCTCCAATCTATATTCTGTTGAAACT 57.170 33.333 0.00 0.00 35.63 2.66
3370 6189 8.974060 TTTGTTCTCAACTAGTATGGTTTCTT 57.026 30.769 0.00 0.00 37.88 2.52
3372 6191 8.603242 TGTTCTCAACTAGTATGGTTTCTTTC 57.397 34.615 0.00 0.00 37.88 2.62
3373 6192 8.429641 TGTTCTCAACTAGTATGGTTTCTTTCT 58.570 33.333 0.00 0.00 37.88 2.52
3374 6193 9.274206 GTTCTCAACTAGTATGGTTTCTTTCTT 57.726 33.333 0.00 0.00 37.88 2.52
3375 6194 9.847224 TTCTCAACTAGTATGGTTTCTTTCTTT 57.153 29.630 0.00 0.00 37.88 2.52
3376 6195 9.847224 TCTCAACTAGTATGGTTTCTTTCTTTT 57.153 29.630 0.00 0.00 37.88 2.27
3394 6290 2.276732 TTTTCCTTGGAGAGTGCCAG 57.723 50.000 0.00 0.00 39.52 4.85
3414 6310 6.183360 TGCCAGTTATCTCATAGTTCTACCAC 60.183 42.308 0.00 0.00 0.00 4.16
3416 6312 7.472100 GCCAGTTATCTCATAGTTCTACCACAT 60.472 40.741 0.00 0.00 0.00 3.21
3476 6375 7.001674 AGGTGTTTGTAACATTGTGAGGAATA 58.998 34.615 0.00 0.00 44.35 1.75
3477 6376 7.669722 AGGTGTTTGTAACATTGTGAGGAATAT 59.330 33.333 0.00 0.00 44.35 1.28
3490 6389 5.411361 TGTGAGGAATATTGGTCGTTTGAAG 59.589 40.000 0.00 0.00 0.00 3.02
3503 6402 3.572255 TCGTTTGAAGCCTTTAGCCAAAT 59.428 39.130 0.00 0.00 45.47 2.32
3509 6408 1.977129 AGCCTTTAGCCAAATGCCAAA 59.023 42.857 1.61 0.00 45.47 3.28
3510 6409 2.027837 AGCCTTTAGCCAAATGCCAAAG 60.028 45.455 1.61 0.00 44.99 2.77
3511 6410 2.349590 CCTTTAGCCAAATGCCAAAGC 58.650 47.619 0.47 0.00 44.33 3.51
3518 6417 1.342174 CCAAATGCCAAAGCTGTCAGT 59.658 47.619 0.93 0.00 40.80 3.41
3528 6427 3.971032 AAGCTGTCAGTTTGTGTTAGC 57.029 42.857 0.54 0.00 36.83 3.09
3579 6482 7.393234 TCACTATCCTTTATTTTGGTGTGAAGG 59.607 37.037 0.00 0.00 35.98 3.46
3585 6488 7.288852 TCCTTTATTTTGGTGTGAAGGAATTGA 59.711 33.333 0.00 0.00 39.57 2.57
3593 6496 4.764823 GGTGTGAAGGAATTGACCAACATA 59.235 41.667 0.00 0.00 0.00 2.29
3620 6523 2.430465 AGTCATCGCACTTTGCTTCAT 58.570 42.857 0.00 0.00 42.25 2.57
3624 6527 5.994054 AGTCATCGCACTTTGCTTCATATAT 59.006 36.000 0.00 0.00 42.25 0.86
3627 6530 5.912360 TCGCACTTTGCTTCATATATCAG 57.088 39.130 0.00 0.00 42.25 2.90
3635 6538 6.425210 TTGCTTCATATATCAGCCTACTGT 57.575 37.500 9.89 0.00 44.77 3.55
3642 6545 6.875726 TCATATATCAGCCTACTGTTCATTGC 59.124 38.462 0.00 0.00 44.77 3.56
3649 6552 4.878397 AGCCTACTGTTCATTGCTGATTAC 59.122 41.667 0.00 0.00 0.00 1.89
3654 6557 5.118990 ACTGTTCATTGCTGATTACGCTAT 58.881 37.500 0.00 0.00 0.00 2.97
3723 6627 1.133407 CGTGGACTTGAGACTAGGCTC 59.867 57.143 19.48 19.48 35.46 4.70
3817 6728 1.474143 GCCTTGCTCATACTCCTGGAC 60.474 57.143 0.00 0.00 0.00 4.02
3845 6756 1.133513 TGTCTGTCATTTTGCCACCCT 60.134 47.619 0.00 0.00 0.00 4.34
3862 6773 6.838612 TGCCACCCTTTTTAGCAAGATATATT 59.161 34.615 0.00 0.00 0.00 1.28
3863 6774 8.001875 TGCCACCCTTTTTAGCAAGATATATTA 58.998 33.333 0.00 0.00 0.00 0.98
3864 6775 8.856103 GCCACCCTTTTTAGCAAGATATATTAA 58.144 33.333 0.00 0.00 0.00 1.40
4158 7492 1.291877 GGTGTTGTCTGCTAGGCACG 61.292 60.000 0.00 0.00 33.79 5.34
4170 7504 2.536365 CTAGGCACGTGCTTCGAATTA 58.464 47.619 36.84 14.92 42.86 1.40
4198 7532 9.890629 TTAGGCATATCATGAATGGAGTATTAC 57.109 33.333 0.00 0.00 0.00 1.89
4210 7544 7.766738 TGAATGGAGTATTACGCATTTGTTAGA 59.233 33.333 0.00 0.00 0.00 2.10
4267 7601 2.433604 TCTAGCTGCTTAGCTCTTGCAT 59.566 45.455 7.79 0.00 45.00 3.96
4379 7713 1.005748 CGCAGTTCACCTCAGCTGA 60.006 57.895 17.19 17.19 0.00 4.26
4570 7910 3.545633 GCGCCAGCTAATTTATTTCTCG 58.454 45.455 0.00 0.00 41.01 4.04
4608 7948 0.102663 TAACGTGTGGAAGTGCGACA 59.897 50.000 0.00 0.00 32.45 4.35
4707 8047 7.013464 CCTCTACCGTTCTGAAGTCATTACTAT 59.987 40.741 0.00 0.00 33.75 2.12
4711 8051 7.259161 ACCGTTCTGAAGTCATTACTATCTTC 58.741 38.462 0.00 0.00 33.75 2.87
4730 8070 0.721718 CGTCTCGCAAGGTGATTTCC 59.278 55.000 0.00 0.00 38.47 3.13
4740 8080 2.779506 AGGTGATTTCCTGGACGAAAC 58.220 47.619 0.00 0.00 34.68 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.673484 CTGGTTTGTGCGCCCAGG 61.673 66.667 18.68 3.92 41.69 4.45
1 2 2.192861 TTCTGGTTTGTGCGCCCAG 61.193 57.895 19.95 19.95 45.81 4.45
2 3 2.124109 TTCTGGTTTGTGCGCCCA 60.124 55.556 4.18 3.04 0.00 5.36
3 4 2.335011 GTTCTGGTTTGTGCGCCC 59.665 61.111 4.18 0.00 0.00 6.13
4 5 1.500512 TACGTTCTGGTTTGTGCGCC 61.501 55.000 4.18 0.00 0.00 6.53
5 6 0.515564 ATACGTTCTGGTTTGTGCGC 59.484 50.000 0.00 0.00 0.00 6.09
6 7 1.724654 GCATACGTTCTGGTTTGTGCG 60.725 52.381 0.00 0.00 0.00 5.34
7 8 1.401018 GGCATACGTTCTGGTTTGTGC 60.401 52.381 0.00 0.00 0.00 4.57
8 9 1.199097 GGGCATACGTTCTGGTTTGTG 59.801 52.381 0.00 0.00 0.00 3.33
9 10 1.530323 GGGCATACGTTCTGGTTTGT 58.470 50.000 0.00 0.00 0.00 2.83
10 11 0.808755 GGGGCATACGTTCTGGTTTG 59.191 55.000 0.00 0.00 0.00 2.93
11 12 0.323087 GGGGGCATACGTTCTGGTTT 60.323 55.000 0.00 0.00 0.00 3.27
12 13 1.301954 GGGGGCATACGTTCTGGTT 59.698 57.895 0.00 0.00 0.00 3.67
13 14 1.279025 ATGGGGGCATACGTTCTGGT 61.279 55.000 0.00 0.00 0.00 4.00
14 15 0.819259 CATGGGGGCATACGTTCTGG 60.819 60.000 0.00 0.00 0.00 3.86
15 16 0.819259 CCATGGGGGCATACGTTCTG 60.819 60.000 2.85 0.00 0.00 3.02
16 17 1.531748 CCATGGGGGCATACGTTCT 59.468 57.895 2.85 0.00 0.00 3.01
17 18 4.157607 CCATGGGGGCATACGTTC 57.842 61.111 2.85 0.00 0.00 3.95
28 29 2.360191 CCAACTGGGACCCATGGG 59.640 66.667 30.23 30.23 40.01 4.00
29 30 1.304381 CACCAACTGGGACCCATGG 60.304 63.158 25.92 25.92 39.04 3.66
30 31 0.609131 GTCACCAACTGGGACCCATG 60.609 60.000 15.39 10.64 41.15 3.66
31 32 1.065410 TGTCACCAACTGGGACCCAT 61.065 55.000 15.39 0.00 41.15 4.00
32 33 1.694525 TGTCACCAACTGGGACCCA 60.695 57.895 14.08 14.08 41.15 4.51
33 34 1.073199 CTGTCACCAACTGGGACCC 59.927 63.158 2.45 2.45 41.15 4.46
34 35 0.472471 TTCTGTCACCAACTGGGACC 59.528 55.000 12.19 0.00 41.15 4.46
35 36 1.594331 GTTCTGTCACCAACTGGGAC 58.406 55.000 0.00 5.69 41.15 4.46
36 37 0.472471 GGTTCTGTCACCAACTGGGA 59.528 55.000 0.00 0.00 41.15 4.37
37 38 0.884704 CGGTTCTGTCACCAACTGGG 60.885 60.000 0.00 0.00 44.81 4.45
38 39 0.884704 CCGGTTCTGTCACCAACTGG 60.885 60.000 0.00 1.04 41.58 4.00
39 40 0.884704 CCCGGTTCTGTCACCAACTG 60.885 60.000 0.00 0.00 36.49 3.16
40 41 1.052124 TCCCGGTTCTGTCACCAACT 61.052 55.000 0.00 0.00 36.49 3.16
41 42 0.883370 GTCCCGGTTCTGTCACCAAC 60.883 60.000 0.00 0.00 36.49 3.77
42 43 1.052124 AGTCCCGGTTCTGTCACCAA 61.052 55.000 0.00 0.00 36.49 3.67
43 44 0.178955 TAGTCCCGGTTCTGTCACCA 60.179 55.000 0.00 0.00 36.49 4.17
44 45 0.971386 TTAGTCCCGGTTCTGTCACC 59.029 55.000 0.00 0.00 0.00 4.02
45 46 2.618053 CATTAGTCCCGGTTCTGTCAC 58.382 52.381 0.00 0.00 0.00 3.67
46 47 1.553248 CCATTAGTCCCGGTTCTGTCA 59.447 52.381 0.00 0.00 0.00 3.58
47 48 1.134491 CCCATTAGTCCCGGTTCTGTC 60.134 57.143 0.00 0.00 0.00 3.51
48 49 0.909623 CCCATTAGTCCCGGTTCTGT 59.090 55.000 0.00 0.00 0.00 3.41
49 50 0.463833 GCCCATTAGTCCCGGTTCTG 60.464 60.000 0.00 0.00 0.00 3.02
50 51 0.620700 AGCCCATTAGTCCCGGTTCT 60.621 55.000 0.00 0.15 0.00 3.01
51 52 0.463833 CAGCCCATTAGTCCCGGTTC 60.464 60.000 0.00 0.00 0.00 3.62
52 53 0.912487 TCAGCCCATTAGTCCCGGTT 60.912 55.000 0.00 0.00 0.00 4.44
53 54 1.306654 TCAGCCCATTAGTCCCGGT 60.307 57.895 0.00 0.00 0.00 5.28
54 55 1.146263 GTCAGCCCATTAGTCCCGG 59.854 63.158 0.00 0.00 0.00 5.73
55 56 1.146263 GGTCAGCCCATTAGTCCCG 59.854 63.158 0.00 0.00 0.00 5.14
56 57 0.181350 CTGGTCAGCCCATTAGTCCC 59.819 60.000 0.00 0.00 44.15 4.46
57 58 0.181350 CCTGGTCAGCCCATTAGTCC 59.819 60.000 0.00 0.00 44.15 3.85
58 59 0.464554 GCCTGGTCAGCCCATTAGTC 60.465 60.000 0.00 0.00 44.15 2.59
59 60 1.609783 GCCTGGTCAGCCCATTAGT 59.390 57.895 0.00 0.00 44.15 2.24
60 61 1.152881 GGCCTGGTCAGCCCATTAG 60.153 63.158 0.00 0.00 44.15 1.73
61 62 3.006677 GGCCTGGTCAGCCCATTA 58.993 61.111 0.00 0.00 44.15 1.90
68 69 2.655077 TTTGGTTGGGGCCTGGTCAG 62.655 60.000 0.84 0.00 0.00 3.51
69 70 2.655077 CTTTGGTTGGGGCCTGGTCA 62.655 60.000 0.84 0.00 0.00 4.02
70 71 1.908299 CTTTGGTTGGGGCCTGGTC 60.908 63.158 0.84 0.00 0.00 4.02
71 72 2.201210 CTTTGGTTGGGGCCTGGT 59.799 61.111 0.84 0.00 0.00 4.00
72 73 3.313524 GCTTTGGTTGGGGCCTGG 61.314 66.667 0.84 0.00 0.00 4.45
73 74 3.313524 GGCTTTGGTTGGGGCCTG 61.314 66.667 0.84 0.00 41.20 4.85
74 75 4.638895 GGGCTTTGGTTGGGGCCT 62.639 66.667 0.84 0.00 43.62 5.19
75 76 4.638895 AGGGCTTTGGTTGGGGCC 62.639 66.667 0.00 0.00 44.57 5.80
76 77 3.313524 CAGGGCTTTGGTTGGGGC 61.314 66.667 0.00 0.00 0.00 5.80
77 78 1.053835 AAACAGGGCTTTGGTTGGGG 61.054 55.000 0.00 0.00 0.00 4.96
78 79 0.836606 AAAACAGGGCTTTGGTTGGG 59.163 50.000 0.00 0.00 0.00 4.12
79 80 1.762370 AGAAAACAGGGCTTTGGTTGG 59.238 47.619 0.00 0.00 0.00 3.77
80 81 3.636764 AGTAGAAAACAGGGCTTTGGTTG 59.363 43.478 0.00 0.00 0.00 3.77
81 82 3.910989 AGTAGAAAACAGGGCTTTGGTT 58.089 40.909 0.00 0.00 0.00 3.67
82 83 3.595190 AGTAGAAAACAGGGCTTTGGT 57.405 42.857 0.00 0.00 0.00 3.67
83 84 4.455877 CACTAGTAGAAAACAGGGCTTTGG 59.544 45.833 3.59 0.00 0.00 3.28
84 85 4.455877 CCACTAGTAGAAAACAGGGCTTTG 59.544 45.833 3.59 0.00 0.00 2.77
85 86 4.104261 ACCACTAGTAGAAAACAGGGCTTT 59.896 41.667 3.59 0.00 0.00 3.51
86 87 3.651423 ACCACTAGTAGAAAACAGGGCTT 59.349 43.478 3.59 0.00 0.00 4.35
87 88 3.248888 ACCACTAGTAGAAAACAGGGCT 58.751 45.455 3.59 0.00 0.00 5.19
88 89 3.007614 TGACCACTAGTAGAAAACAGGGC 59.992 47.826 3.59 0.00 0.00 5.19
89 90 4.039973 TGTGACCACTAGTAGAAAACAGGG 59.960 45.833 3.59 0.00 0.00 4.45
90 91 4.989168 GTGTGACCACTAGTAGAAAACAGG 59.011 45.833 3.59 0.00 38.61 4.00
91 92 5.597806 TGTGTGACCACTAGTAGAAAACAG 58.402 41.667 3.59 0.00 42.34 3.16
92 93 5.601583 TGTGTGACCACTAGTAGAAAACA 57.398 39.130 3.59 0.00 42.34 2.83
93 94 5.813672 TGTTGTGTGACCACTAGTAGAAAAC 59.186 40.000 3.59 0.00 42.34 2.43
94 95 5.979993 TGTTGTGTGACCACTAGTAGAAAA 58.020 37.500 3.59 0.00 42.34 2.29
95 96 5.601583 TGTTGTGTGACCACTAGTAGAAA 57.398 39.130 3.59 0.00 42.34 2.52
96 97 5.538813 AGATGTTGTGTGACCACTAGTAGAA 59.461 40.000 3.59 0.00 42.34 2.10
97 98 5.077564 AGATGTTGTGTGACCACTAGTAGA 58.922 41.667 3.59 0.00 42.34 2.59
98 99 5.392767 AGATGTTGTGTGACCACTAGTAG 57.607 43.478 0.00 0.00 42.34 2.57
99 100 5.069914 ACAAGATGTTGTGTGACCACTAGTA 59.930 40.000 7.55 0.00 45.58 1.82
100 101 4.141711 ACAAGATGTTGTGTGACCACTAGT 60.142 41.667 7.55 0.00 45.58 2.57
101 102 4.380531 ACAAGATGTTGTGTGACCACTAG 58.619 43.478 7.55 0.00 45.58 2.57
102 103 4.415881 ACAAGATGTTGTGTGACCACTA 57.584 40.909 7.55 0.00 45.58 2.74
103 104 3.281727 ACAAGATGTTGTGTGACCACT 57.718 42.857 7.55 0.00 45.58 4.00
138 139 4.085733 TGTTGTTCCAACTCAATATGGGG 58.914 43.478 8.41 0.00 37.31 4.96
142 143 6.491403 AGAGCTTTGTTGTTCCAACTCAATAT 59.509 34.615 8.41 0.00 0.00 1.28
179 180 7.052248 TGTGCATCATAAGAAGATCACATTCT 58.948 34.615 0.00 0.00 38.65 2.40
180 181 7.255491 TGTGCATCATAAGAAGATCACATTC 57.745 36.000 0.00 0.00 33.16 2.67
183 184 7.052248 AGAATGTGCATCATAAGAAGATCACA 58.948 34.615 0.00 0.00 37.63 3.58
184 185 7.493743 AGAATGTGCATCATAAGAAGATCAC 57.506 36.000 0.00 0.00 35.48 3.06
185 186 7.012989 CCAAGAATGTGCATCATAAGAAGATCA 59.987 37.037 0.00 0.00 35.48 2.92
186 187 7.361127 CCAAGAATGTGCATCATAAGAAGATC 58.639 38.462 0.00 0.00 35.48 2.75
187 188 6.264744 CCCAAGAATGTGCATCATAAGAAGAT 59.735 38.462 0.00 0.00 35.48 2.40
189 190 5.591472 TCCCAAGAATGTGCATCATAAGAAG 59.409 40.000 0.00 0.00 35.48 2.85
190 191 5.508567 TCCCAAGAATGTGCATCATAAGAA 58.491 37.500 0.00 0.00 35.48 2.52
217 249 6.828785 AGCCGGTATTTCTATCACAAGATTTT 59.171 34.615 1.90 0.00 35.67 1.82
230 262 1.674817 CCGTGTTGAGCCGGTATTTCT 60.675 52.381 1.90 0.00 39.38 2.52
236 268 1.537814 TACATCCGTGTTGAGCCGGT 61.538 55.000 1.90 0.00 44.51 5.28
241 273 5.733226 TTATGCAATACATCCGTGTTGAG 57.267 39.130 6.30 0.00 44.54 3.02
249 281 9.754382 ATGATGAAACTTTTATGCAATACATCC 57.246 29.630 0.00 0.00 40.38 3.51
261 293 6.852858 TGTCGTGTGATGATGAAACTTTTA 57.147 33.333 0.00 0.00 0.00 1.52
281 315 9.329913 GTATTTTGTTCACACTTGATGTATGTC 57.670 33.333 0.00 0.00 40.64 3.06
305 339 3.840124 TTGTGGTGTGGTATGTGTGTA 57.160 42.857 0.00 0.00 0.00 2.90
379 415 5.175859 GTTCGATCAAATGACCAGAGGTAA 58.824 41.667 0.00 0.00 35.25 2.85
382 418 3.599343 TGTTCGATCAAATGACCAGAGG 58.401 45.455 0.00 0.00 0.00 3.69
387 423 4.475944 CCAACTTGTTCGATCAAATGACC 58.524 43.478 17.08 0.00 0.00 4.02
395 431 1.644786 CGCCCCCAACTTGTTCGATC 61.645 60.000 0.00 0.00 0.00 3.69
397 433 2.119484 ATCGCCCCCAACTTGTTCGA 62.119 55.000 0.00 0.00 0.00 3.71
414 450 3.799755 GTTGCCGCGACCACCATC 61.800 66.667 8.23 0.00 0.00 3.51
425 461 2.738521 CAGTGTCTCCCGTTGCCG 60.739 66.667 0.00 0.00 0.00 5.69
429 465 2.932234 CGAGCCAGTGTCTCCCGTT 61.932 63.158 0.00 0.00 0.00 4.44
431 467 3.062466 TCGAGCCAGTGTCTCCCG 61.062 66.667 0.00 0.00 0.00 5.14
442 478 2.126031 GTCGTCCAAGGTCGAGCC 60.126 66.667 11.73 3.31 36.50 4.70
462 498 4.562767 TGGCTTATTCTGATACCCTACCA 58.437 43.478 0.00 0.00 0.00 3.25
537 573 0.667792 GCGAGAAAGAAGACGCTGGT 60.668 55.000 0.00 0.00 46.06 4.00
541 577 1.886861 TTGCGCGAGAAAGAAGACGC 61.887 55.000 12.10 0.00 46.05 5.19
586 622 1.911766 ATCGGGAAGTGGTCACCGT 60.912 57.895 0.00 0.00 46.06 4.83
622 658 4.845580 CATCGCGCCAAGGCTCCT 62.846 66.667 9.73 0.00 39.32 3.69
701 741 6.832520 TGAGCTATCACAAAAATTTGCCTA 57.167 33.333 5.82 0.00 41.79 3.93
740 2630 7.064229 TCAGAACTGGTAAAATTTTGGGTACT 58.936 34.615 13.76 2.25 0.00 2.73
842 3556 0.880278 GCTCCTCTGACACGCACAAA 60.880 55.000 0.00 0.00 0.00 2.83
927 3641 4.862823 GGGAGGGACGGGAGAGGG 62.863 77.778 0.00 0.00 0.00 4.30
928 3642 4.862823 GGGGAGGGACGGGAGAGG 62.863 77.778 0.00 0.00 0.00 3.69
929 3643 4.862823 GGGGGAGGGACGGGAGAG 62.863 77.778 0.00 0.00 0.00 3.20
955 3669 2.664185 CTGGATGCGCCGGAGATG 60.664 66.667 10.31 0.00 46.81 2.90
1005 3722 1.061570 GTACCTCCAGTACGCGTCG 59.938 63.158 18.63 5.50 41.94 5.12
1166 3892 1.694525 GGAAGGAAGAGGGAGGGGG 60.695 68.421 0.00 0.00 0.00 5.40
1181 3907 2.683933 GTGCGGGAGAGAGGGGAA 60.684 66.667 0.00 0.00 0.00 3.97
1185 3911 3.151022 GAGGGTGCGGGAGAGAGG 61.151 72.222 0.00 0.00 0.00 3.69
1187 3913 4.779733 GGGAGGGTGCGGGAGAGA 62.780 72.222 0.00 0.00 0.00 3.10
1272 4003 1.661821 GCGGATCGATTCGACCAGG 60.662 63.158 29.86 0.00 39.18 4.45
1383 4115 4.100084 CATCGGGGACAGCCAGCA 62.100 66.667 0.00 0.00 35.15 4.41
1388 4120 1.776034 GATTTCGCATCGGGGACAGC 61.776 60.000 0.00 0.00 35.48 4.40
1394 4126 1.010797 CGCTTGATTTCGCATCGGG 60.011 57.895 0.00 0.00 0.00 5.14
1396 4128 2.930230 ATACGCTTGATTTCGCATCG 57.070 45.000 0.00 0.00 0.00 3.84
1495 4231 3.861840 CACCATTACACCGAGAGATTGT 58.138 45.455 0.00 0.00 0.00 2.71
1497 4233 2.501723 AGCACCATTACACCGAGAGATT 59.498 45.455 0.00 0.00 0.00 2.40
1559 4295 0.798776 CAGCGCCTTCAAAAGTCGAT 59.201 50.000 2.29 0.00 0.00 3.59
1679 4442 1.997606 GTCCCAACTCATAAACGACGG 59.002 52.381 0.00 0.00 0.00 4.79
1696 4459 0.590195 CACAGAACAGCTTGCTGTCC 59.410 55.000 25.63 15.74 40.63 4.02
1700 4466 0.888285 GGCTCACAGAACAGCTTGCT 60.888 55.000 0.00 0.00 35.82 3.91
1710 4476 1.134521 ACGAAAGTGTTGGCTCACAGA 60.135 47.619 13.66 0.00 46.97 3.41
1737 4503 2.843730 ACCAGTGTGGCATGGATAACTA 59.156 45.455 12.41 0.00 42.67 2.24
1779 4545 4.051237 GGCAAGGTCAAAACAGTGATTTC 58.949 43.478 0.00 0.00 0.00 2.17
1802 4568 4.626172 TGGCGTTTTGTGTTAAAGTTTTCC 59.374 37.500 0.00 0.00 0.00 3.13
1900 4711 1.065126 AGGAGGTGAAATGCTACTGGC 60.065 52.381 0.00 0.00 42.22 4.85
1901 4712 4.141620 ACATAGGAGGTGAAATGCTACTGG 60.142 45.833 0.00 0.00 0.00 4.00
1902 4713 4.813161 CACATAGGAGGTGAAATGCTACTG 59.187 45.833 0.00 0.00 38.54 2.74
1922 4733 2.594303 CGTTTCTGCCCTGCCACA 60.594 61.111 0.00 0.00 0.00 4.17
1969 4787 3.593680 AGCAACCCCACAGGCCAT 61.594 61.111 5.01 0.00 40.58 4.40
1980 4798 2.278330 CCTTCTTGGGGCAGCAACC 61.278 63.158 0.00 0.00 0.00 3.77
1998 4816 0.664166 CGCCACAAGCAATGGTGTTC 60.664 55.000 6.35 0.00 44.04 3.18
2228 5046 5.105392 ACCGTCCGTTTAATGTACTGGATTA 60.105 40.000 0.00 0.00 0.00 1.75
2252 5070 1.051008 TGCTGACTGCCTCTCTCAAA 58.949 50.000 1.50 0.00 42.00 2.69
2393 5211 1.603236 CTGCCTCTCTCAAGCCGTCT 61.603 60.000 0.00 0.00 0.00 4.18
2479 5297 7.201530 GCAGTAAATACAGGTCACAAGACATAC 60.202 40.741 0.00 0.00 46.80 2.39
2593 5411 2.017782 GAGCCTGTGTATCTCTCACGA 58.982 52.381 0.00 0.00 38.48 4.35
2615 5433 1.359848 AACGCTCGTAGGAAGCATTG 58.640 50.000 0.00 0.00 0.00 2.82
2627 5445 0.091344 CAGTACGCAGAAAACGCTCG 59.909 55.000 0.00 0.00 0.00 5.03
2655 5473 9.484806 AAATGAGTAATCAGGAAAAAGGATGAT 57.515 29.630 0.00 0.00 33.91 2.45
2727 5546 2.109799 CCAGCGCCATAGGACTGG 59.890 66.667 2.29 10.06 40.43 4.00
2761 5580 4.853142 TCCCGCGGTAGGCCTGAT 62.853 66.667 26.12 0.00 38.94 2.90
2931 5750 1.192534 GAAACTTCTCGGCGTTCACAG 59.807 52.381 6.85 0.00 0.00 3.66
3010 5829 4.813027 ACAGCTAAAACATGAAGGCAATG 58.187 39.130 0.00 0.00 0.00 2.82
3012 5831 4.501229 CCAACAGCTAAAACATGAAGGCAA 60.501 41.667 0.00 0.00 0.00 4.52
3078 5897 3.760580 ACAAGTCTCACCTCCTGAAAG 57.239 47.619 0.00 0.00 0.00 2.62
3287 6106 3.627123 TGTATTCATGCCAAGTTCATCGG 59.373 43.478 0.00 0.00 0.00 4.18
3290 6109 7.285566 AGAGTATGTATTCATGCCAAGTTCAT 58.714 34.615 0.00 0.00 37.37 2.57
3343 6162 9.574516 AGAAACCATACTAGTTGAGAACAAATT 57.425 29.630 0.00 0.00 37.77 1.82
3344 6163 9.574516 AAGAAACCATACTAGTTGAGAACAAAT 57.425 29.630 0.00 0.00 37.77 2.32
3374 6193 2.091885 ACTGGCACTCTCCAAGGAAAAA 60.092 45.455 0.00 0.00 35.36 1.94
3375 6194 1.494721 ACTGGCACTCTCCAAGGAAAA 59.505 47.619 0.00 0.00 35.36 2.29
3376 6195 1.140312 ACTGGCACTCTCCAAGGAAA 58.860 50.000 0.00 0.00 35.36 3.13
3377 6196 1.140312 AACTGGCACTCTCCAAGGAA 58.860 50.000 0.00 0.00 35.36 3.36
3378 6197 2.024176 TAACTGGCACTCTCCAAGGA 57.976 50.000 0.00 0.00 35.36 3.36
3379 6198 2.503356 AGATAACTGGCACTCTCCAAGG 59.497 50.000 0.00 0.00 35.36 3.61
3382 6201 2.820178 TGAGATAACTGGCACTCTCCA 58.180 47.619 4.05 0.00 34.54 3.86
3383 6202 4.586841 ACTATGAGATAACTGGCACTCTCC 59.413 45.833 4.05 0.00 34.54 3.71
3394 6290 7.210174 TGCATGTGGTAGAACTATGAGATAAC 58.790 38.462 0.00 0.00 0.00 1.89
3445 6344 5.858049 CACAATGTTACAAACACCTATGCAG 59.142 40.000 0.00 0.00 45.50 4.41
3446 6345 5.532779 TCACAATGTTACAAACACCTATGCA 59.467 36.000 0.00 0.00 45.50 3.96
3476 6375 3.057526 GCTAAAGGCTTCAAACGACCAAT 60.058 43.478 0.00 0.00 38.06 3.16
3477 6376 2.292292 GCTAAAGGCTTCAAACGACCAA 59.708 45.455 0.00 0.00 38.06 3.67
3490 6389 2.470983 TTTGGCATTTGGCTAAAGGC 57.529 45.000 21.97 21.97 46.42 4.35
3503 6402 1.134753 CACAAACTGACAGCTTTGGCA 59.865 47.619 22.87 0.00 41.70 4.92
3509 6408 2.874701 CTGCTAACACAAACTGACAGCT 59.125 45.455 1.25 0.00 33.76 4.24
3510 6409 2.872245 TCTGCTAACACAAACTGACAGC 59.128 45.455 1.25 0.00 33.43 4.40
3511 6410 5.237127 TGATTCTGCTAACACAAACTGACAG 59.763 40.000 0.00 0.00 0.00 3.51
3518 6417 6.691754 TGAGTTTGATTCTGCTAACACAAA 57.308 33.333 0.00 0.00 0.00 2.83
3528 6427 9.604626 GACTTAAGTTGAATGAGTTTGATTCTG 57.395 33.333 10.02 0.00 32.04 3.02
3609 6512 6.933521 CAGTAGGCTGATATATGAAGCAAAGT 59.066 38.462 15.49 6.09 45.28 2.66
3611 6514 6.830912 ACAGTAGGCTGATATATGAAGCAAA 58.169 36.000 15.49 3.95 45.28 3.68
3620 6523 6.425210 AGCAATGAACAGTAGGCTGATATA 57.575 37.500 0.00 0.00 45.28 0.86
3627 6530 4.260375 CGTAATCAGCAATGAACAGTAGGC 60.260 45.833 0.00 0.00 0.00 3.93
3635 6538 5.356751 ACCAAATAGCGTAATCAGCAATGAA 59.643 36.000 0.00 0.00 37.01 2.57
3642 6545 5.597806 TCTACCACCAAATAGCGTAATCAG 58.402 41.667 0.00 0.00 0.00 2.90
3649 6552 4.380531 ACATCATCTACCACCAAATAGCG 58.619 43.478 0.00 0.00 0.00 4.26
3654 6557 4.042809 ACCTGAACATCATCTACCACCAAA 59.957 41.667 0.00 0.00 0.00 3.28
3723 6627 2.688507 ACTGTAGATTGTTCAGGCACG 58.311 47.619 0.00 0.00 34.02 5.34
3780 6686 4.085107 GCAAGGCACAATCTTGTTTTAACG 60.085 41.667 0.00 0.00 42.44 3.18
3817 6728 3.672511 GCAAAATGACAGACAGGATGCAG 60.673 47.826 0.00 0.00 42.53 4.41
3845 6756 9.860650 TCAGGGCTTAATATATCTTGCTAAAAA 57.139 29.630 0.00 0.00 0.00 1.94
3862 6773 4.483950 AGTAGTGCTCATATCAGGGCTTA 58.516 43.478 0.00 0.00 0.00 3.09
3863 6774 3.312890 AGTAGTGCTCATATCAGGGCTT 58.687 45.455 0.00 0.00 0.00 4.35
3864 6775 2.896685 GAGTAGTGCTCATATCAGGGCT 59.103 50.000 3.01 0.00 43.58 5.19
3865 6776 2.352225 CGAGTAGTGCTCATATCAGGGC 60.352 54.545 9.04 0.00 44.33 5.19
4058 7392 5.138125 TCATTGGAAATGCTTTCTGAACC 57.862 39.130 8.05 0.00 39.59 3.62
4074 7408 6.813152 CCCTAAATTAGTTTGCTGTTCATTGG 59.187 38.462 0.00 0.00 0.00 3.16
4111 7445 4.953667 TCAGAATGACCACTAGATCATGC 58.046 43.478 0.00 1.60 42.56 4.06
4158 7492 6.423905 TGATATGCCTAACTAATTCGAAGCAC 59.576 38.462 3.35 0.00 0.00 4.40
4170 7504 6.445451 ACTCCATTCATGATATGCCTAACT 57.555 37.500 0.00 0.00 0.00 2.24
4198 7532 5.398122 ACAAACGTTTCATCTAACAAATGCG 59.602 36.000 11.37 0.00 0.00 4.73
4210 7544 7.262048 ACCAAACAGATTAACAAACGTTTCAT 58.738 30.769 11.37 5.44 0.00 2.57
4251 7585 1.064208 CTGCATGCAAGAGCTAAGCAG 59.936 52.381 22.88 0.96 45.89 4.24
4267 7601 0.318022 CGCAAAGTGACAATGCTGCA 60.318 50.000 4.13 4.13 37.92 4.41
4570 7910 1.826921 TCGGGCCTACGAGGTGATC 60.827 63.158 0.84 0.00 37.80 2.92
4584 7924 1.355971 CACTTCCACACGTTATCGGG 58.644 55.000 0.00 0.00 46.92 5.14
4707 8047 0.888619 ATCACCTTGCGAGACGAAGA 59.111 50.000 1.22 0.00 0.00 2.87
4711 8051 0.721718 GGAAATCACCTTGCGAGACG 59.278 55.000 1.22 0.00 0.00 4.18
4730 8070 4.782252 TTAAACAGTTCGTTTCGTCCAG 57.218 40.909 0.00 0.00 44.78 3.86
4740 8080 5.009210 TCCCCTTCAACATTTAAACAGTTCG 59.991 40.000 5.21 3.20 0.00 3.95
4756 8096 1.598685 GCGGTCGTTTTCCCCTTCA 60.599 57.895 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.