Multiple sequence alignment - TraesCS1A01G343800

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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 TraesCS1A01G343800 chr1A 100.000 3400 0 0 2105 5504 532103528 532106927 0.000000e+00 6279
1 TraesCS1A01G343800 chr1A 100.000 1762 0 0 1 1762 532101424 532103185 0.000000e+00 3254
2 TraesCS1A01G343800 chr1A 87.856 2001 202 25 2142 4115 547255383 547257369 0.000000e+00 2311
3 TraesCS1A01G343800 chr1A 82.421 347 49 5 4282 4617 547257734 547258079 5.390000e-75 292
4 TraesCS1A01G343800 chr1A 97.945 146 3 0 1617 1762 99154866 99155011 2.540000e-63 254
5 TraesCS1A01G343800 chr1A 98.601 143 2 0 1620 1762 259053003 259052861 2.540000e-63 254
6 TraesCS1A01G343800 chr1A 87.591 137 17 0 1010 1146 547254555 547254691 5.710000e-35 159
7 TraesCS1A01G343800 chr1B 94.954 2616 98 18 2113 4708 585882570 585885171 0.000000e+00 4069
8 TraesCS1A01G343800 chr1B 88.018 2003 204 24 2142 4115 622186833 622184838 0.000000e+00 2337
9 TraesCS1A01G343800 chr1B 92.839 796 45 4 836 1620 585881783 585882577 0.000000e+00 1144
10 TraesCS1A01G343800 chr1B 88.360 756 34 17 112 836 585880710 585881442 0.000000e+00 859
11 TraesCS1A01G343800 chr1B 85.507 276 32 6 5191 5463 585885697 585885967 1.170000e-71 281
12 TraesCS1A01G343800 chr1B 87.591 137 17 0 1010 1146 622187490 622187354 5.710000e-35 159
13 TraesCS1A01G343800 chr1D 95.760 2052 57 14 2110 4138 433516821 433518865 0.000000e+00 3280
14 TraesCS1A01G343800 chr1D 87.824 2004 206 24 2142 4115 452342344 452344339 0.000000e+00 2314
15 TraesCS1A01G343800 chr1D 92.717 865 32 6 389 1224 433515691 433516553 0.000000e+00 1219
16 TraesCS1A01G343800 chr1D 95.329 471 12 7 4149 4613 433519063 433519529 0.000000e+00 739
17 TraesCS1A01G343800 chr1D 94.949 297 12 1 31 327 433515149 433515442 3.880000e-126 462
18 TraesCS1A01G343800 chr1D 92.606 284 19 2 1338 1620 433516549 433516831 1.850000e-109 407
19 TraesCS1A01G343800 chr1D 84.319 389 39 10 5083 5469 433519663 433520031 1.460000e-95 361
20 TraesCS1A01G343800 chr1D 83.188 345 44 5 4286 4617 452344870 452345213 2.490000e-78 303
21 TraesCS1A01G343800 chr1D 91.538 130 7 3 4943 5068 433519549 433519678 5.670000e-40 176
22 TraesCS1A01G343800 chr3D 87.882 1964 203 19 2142 4082 178535440 178533489 0.000000e+00 2276
23 TraesCS1A01G343800 chr3D 85.517 290 32 5 4285 4573 178533078 178532798 1.500000e-75 294
24 TraesCS1A01G343800 chr3D 80.155 388 49 16 270 641 522947053 522946678 1.180000e-66 265
25 TraesCS1A01G343800 chr3D 88.356 146 17 0 1010 1155 178537058 178536913 5.670000e-40 176
26 TraesCS1A01G343800 chr3A 86.900 2000 209 32 2142 4096 219800541 219798550 0.000000e+00 2193
27 TraesCS1A01G343800 chr3A 78.456 557 75 23 130 670 456508014 456508541 6.880000e-84 322
28 TraesCS1A01G343800 chr3A 84.828 290 34 5 4285 4573 219798057 219797777 3.250000e-72 283
29 TraesCS1A01G343800 chr3A 97.297 148 4 0 1615 1762 290423939 290424086 9.150000e-63 252
30 TraesCS1A01G343800 chr3A 78.169 284 48 13 869 1144 219801301 219801024 9.480000e-38 169
31 TraesCS1A01G343800 chr3A 88.060 134 9 5 712 843 686842306 686842434 9.550000e-33 152
32 TraesCS1A01G343800 chr3B 86.790 2006 215 33 2142 4105 256786579 256784582 0.000000e+00 2191
33 TraesCS1A01G343800 chr3B 83.533 334 41 9 4285 4617 256784134 256783814 3.220000e-77 300
34 TraesCS1A01G343800 chr3B 81.132 371 52 13 313 670 436704098 436704463 1.170000e-71 281
35 TraesCS1A01G343800 chr3B 89.051 137 15 0 1010 1146 256787196 256787060 2.640000e-38 171
36 TraesCS1A01G343800 chr3B 85.821 134 12 6 712 843 436705077 436705205 9.620000e-28 135
37 TraesCS1A01G343800 chr7B 91.511 801 54 5 834 1620 637024260 637025060 0.000000e+00 1090
38 TraesCS1A01G343800 chr7B 93.204 412 26 1 2110 2519 637025050 637025461 6.100000e-169 604
39 TraesCS1A01G343800 chr7B 97.351 151 4 0 1612 1762 672656379 672656229 1.970000e-64 257
40 TraesCS1A01G343800 chr5B 93.038 632 42 2 990 1620 517328140 517328770 0.000000e+00 922
41 TraesCS1A01G343800 chr5B 88.350 412 21 11 2110 2519 517328760 517329146 2.320000e-128 470
42 TraesCS1A01G343800 chr5B 99.296 142 1 0 1621 1762 294561023 294560882 1.970000e-64 257
43 TraesCS1A01G343800 chr5B 85.490 255 26 7 2142 2386 239395565 239395312 7.080000e-64 255
44 TraesCS1A01G343800 chr4D 84.239 368 28 13 228 579 331630573 331630926 1.140000e-86 331
45 TraesCS1A01G343800 chr7A 98.621 145 2 0 1618 1762 605175711 605175567 1.970000e-64 257
46 TraesCS1A01G343800 chr7A 90.446 157 15 0 126 282 42598126 42597970 2.010000e-49 207
47 TraesCS1A01G343800 chr6A 98.611 144 2 0 1619 1762 168007030 168007173 7.080000e-64 255
48 TraesCS1A01G343800 chr6A 96.129 155 4 2 1610 1762 540617408 540617254 9.150000e-63 252
49 TraesCS1A01G343800 chr2B 98.611 144 1 1 1620 1762 309492658 309492801 2.540000e-63 254
50 TraesCS1A01G343800 chr5D 88.889 135 6 6 712 843 558017431 558017303 2.050000e-34 158
51 TraesCS1A01G343800 chr2D 86.567 134 11 5 712 843 204490273 204490401 2.070000e-29 141
52 TraesCS1A01G343800 chr7D 85.821 134 13 4 712 843 138178478 138178349 2.670000e-28 137


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 TraesCS1A01G343800 chr1A 532101424 532106927 5503 False 4766.500000 6279 100.000000 1 5504 2 chr1A.!!$F2 5503
1 TraesCS1A01G343800 chr1A 547254555 547258079 3524 False 920.666667 2311 85.956000 1010 4617 3 chr1A.!!$F3 3607
2 TraesCS1A01G343800 chr1B 585880710 585885967 5257 False 1588.250000 4069 90.415000 112 5463 4 chr1B.!!$F1 5351
3 TraesCS1A01G343800 chr1B 622184838 622187490 2652 True 1248.000000 2337 87.804500 1010 4115 2 chr1B.!!$R1 3105
4 TraesCS1A01G343800 chr1D 452342344 452345213 2869 False 1308.500000 2314 85.506000 2142 4617 2 chr1D.!!$F2 2475
5 TraesCS1A01G343800 chr1D 433515149 433520031 4882 False 949.142857 3280 92.459714 31 5469 7 chr1D.!!$F1 5438
6 TraesCS1A01G343800 chr3D 178532798 178537058 4260 True 915.333333 2276 87.251667 1010 4573 3 chr3D.!!$R2 3563
7 TraesCS1A01G343800 chr3A 219797777 219801301 3524 True 881.666667 2193 83.299000 869 4573 3 chr3A.!!$R1 3704
8 TraesCS1A01G343800 chr3A 456508014 456508541 527 False 322.000000 322 78.456000 130 670 1 chr3A.!!$F2 540
9 TraesCS1A01G343800 chr3B 256783814 256787196 3382 True 887.333333 2191 86.458000 1010 4617 3 chr3B.!!$R1 3607
10 TraesCS1A01G343800 chr3B 436704098 436705205 1107 False 208.000000 281 83.476500 313 843 2 chr3B.!!$F1 530
11 TraesCS1A01G343800 chr7B 637024260 637025461 1201 False 847.000000 1090 92.357500 834 2519 2 chr7B.!!$F1 1685
12 TraesCS1A01G343800 chr5B 517328140 517329146 1006 False 696.000000 922 90.694000 990 2519 2 chr5B.!!$F1 1529

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
29 30 0.178973 GCCCCCTCTACTCCTCTCTC 60.179 65.0 0.0 0.0 0.00 3.20 F
1648 4048 0.174162 TAAAGCGTCCCTAAGGCGAC 59.826 55.0 0.0 0.0 43.57 5.19 F
1700 4100 0.170339 GGAAAATCGACCGCTTTGGG 59.830 55.0 0.0 0.0 44.64 4.12 F
1701 4101 0.456142 GAAAATCGACCGCTTTGGGC 60.456 55.0 0.0 0.0 45.45 5.36 F
3114 5587 0.753111 GCAACCCTGATCCCCATCAC 60.753 60.0 0.0 0.0 33.80 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1681 4081 0.170339 CCCAAAGCGGTCGATTTTCC 59.830 55.000 3.79 0.00 30.80 3.13 R
3312 5785 0.529992 GCGCTTGCTAAGGACGGTAT 60.530 55.000 0.00 0.00 35.07 2.73 R
3313 5786 1.153706 GCGCTTGCTAAGGACGGTA 60.154 57.895 0.00 0.00 35.07 4.02 R
3367 5840 2.801162 CGTGCGTCAGTCCAGTCG 60.801 66.667 0.00 0.00 0.00 4.18 R
4697 7885 0.036952 AGAACGGCTCACAGATGTGG 60.037 55.000 12.77 5.32 45.65 4.17 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
24 25 4.862823 GCCGCCCCCTCTACTCCT 62.863 72.222 0.00 0.00 0.00 3.69
25 26 2.522193 CCGCCCCCTCTACTCCTC 60.522 72.222 0.00 0.00 0.00 3.71
26 27 2.604152 CGCCCCCTCTACTCCTCT 59.396 66.667 0.00 0.00 0.00 3.69
27 28 1.529713 CGCCCCCTCTACTCCTCTC 60.530 68.421 0.00 0.00 0.00 3.20
28 29 1.935191 GCCCCCTCTACTCCTCTCT 59.065 63.158 0.00 0.00 0.00 3.10
29 30 0.178973 GCCCCCTCTACTCCTCTCTC 60.179 65.000 0.00 0.00 0.00 3.20
447 658 4.156556 GTCATTGCCTGTGATTGCTAGAAA 59.843 41.667 0.00 0.00 0.00 2.52
449 660 3.423539 TGCCTGTGATTGCTAGAAAGT 57.576 42.857 0.00 0.00 0.00 2.66
455 669 6.043411 CCTGTGATTGCTAGAAAGTAGTACC 58.957 44.000 0.00 0.00 0.00 3.34
626 870 2.026915 TGACCAATGTCCATCAGTCCAG 60.027 50.000 7.00 0.00 41.01 3.86
644 896 4.424566 GCCACATTGCCACTGCCG 62.425 66.667 0.00 0.00 36.33 5.69
654 906 1.798735 CCACTGCCGCTGATTTCTG 59.201 57.895 4.02 0.00 0.00 3.02
922 2090 9.709495 TTGAAAAGGAAAAAGATGAATATGTGG 57.291 29.630 0.00 0.00 0.00 4.17
1077 2266 3.754965 TGCTAAGATTGCAGTTGTTCCT 58.245 40.909 0.00 0.00 35.31 3.36
1344 2597 4.578928 GCGACCATTAGAACATTATGGGTT 59.421 41.667 0.00 0.00 42.49 4.11
1399 3797 1.985159 TCCACTACTCATTGCCCTTGT 59.015 47.619 0.00 0.00 0.00 3.16
1491 3889 2.368980 GTGTCAACACAGTTCTTCGC 57.631 50.000 8.37 0.00 45.75 4.70
1514 3913 5.800941 GCTATATTGCCGTACTACATCTGTC 59.199 44.000 0.00 0.00 0.00 3.51
1533 3932 1.035923 CTCCAGCTTCTATGGCGAGA 58.964 55.000 0.00 0.00 37.76 4.04
1602 4001 6.583427 TGCTTGTCAATGATTTTCAAGAATCG 59.417 34.615 17.42 0.00 38.57 3.34
1620 4020 9.123709 CAAGAATCGTCTCAGTATATTCTAAGC 57.876 37.037 0.00 0.00 36.21 3.09
1621 4021 8.630054 AGAATCGTCTCAGTATATTCTAAGCT 57.370 34.615 0.00 0.00 35.64 3.74
1622 4022 9.727859 AGAATCGTCTCAGTATATTCTAAGCTA 57.272 33.333 0.00 0.00 35.64 3.32
1625 4025 8.850007 TCGTCTCAGTATATTCTAAGCTATGT 57.150 34.615 0.00 0.00 0.00 2.29
1626 4026 9.286170 TCGTCTCAGTATATTCTAAGCTATGTT 57.714 33.333 0.00 0.00 0.00 2.71
1627 4027 9.900710 CGTCTCAGTATATTCTAAGCTATGTTT 57.099 33.333 0.00 0.00 0.00 2.83
1638 4038 7.068692 TCTAAGCTATGTTTTTAAAGCGTCC 57.931 36.000 0.00 0.00 39.94 4.79
1639 4039 4.696899 AGCTATGTTTTTAAAGCGTCCC 57.303 40.909 0.00 0.00 39.94 4.46
1640 4040 4.332828 AGCTATGTTTTTAAAGCGTCCCT 58.667 39.130 0.00 0.00 39.94 4.20
1641 4041 5.493809 AGCTATGTTTTTAAAGCGTCCCTA 58.506 37.500 0.00 0.00 39.94 3.53
1642 4042 5.941647 AGCTATGTTTTTAAAGCGTCCCTAA 59.058 36.000 0.00 0.00 39.94 2.69
1643 4043 6.093633 AGCTATGTTTTTAAAGCGTCCCTAAG 59.906 38.462 0.00 0.00 39.94 2.18
1644 4044 5.638596 ATGTTTTTAAAGCGTCCCTAAGG 57.361 39.130 0.00 0.00 0.00 2.69
1645 4045 3.253921 TGTTTTTAAAGCGTCCCTAAGGC 59.746 43.478 0.00 0.00 39.09 4.35
1646 4046 1.729284 TTTAAAGCGTCCCTAAGGCG 58.271 50.000 0.00 0.00 43.57 5.52
1647 4047 0.896923 TTAAAGCGTCCCTAAGGCGA 59.103 50.000 0.00 0.00 43.57 5.54
1648 4048 0.174162 TAAAGCGTCCCTAAGGCGAC 59.826 55.000 0.00 0.00 43.57 5.19
1674 4074 4.516195 GTCGAAGCGCTCCCCCTC 62.516 72.222 12.06 2.47 0.00 4.30
1682 4082 4.803908 GCTCCCCCTCCGCTTTGG 62.804 72.222 0.00 0.00 40.09 3.28
1692 4092 1.161843 TCCGCTTTGGAAAATCGACC 58.838 50.000 0.00 0.00 46.38 4.79
1693 4093 0.179200 CCGCTTTGGAAAATCGACCG 60.179 55.000 0.00 0.00 42.00 4.79
1694 4094 0.793104 CGCTTTGGAAAATCGACCGC 60.793 55.000 0.00 0.00 0.00 5.68
1695 4095 0.521735 GCTTTGGAAAATCGACCGCT 59.478 50.000 0.00 0.00 0.00 5.52
1696 4096 1.068541 GCTTTGGAAAATCGACCGCTT 60.069 47.619 0.00 0.00 0.00 4.68
1697 4097 2.607038 GCTTTGGAAAATCGACCGCTTT 60.607 45.455 0.00 0.00 0.00 3.51
1698 4098 2.697431 TTGGAAAATCGACCGCTTTG 57.303 45.000 0.00 0.00 0.00 2.77
1699 4099 0.878416 TGGAAAATCGACCGCTTTGG 59.122 50.000 0.00 0.00 46.41 3.28
1700 4100 0.170339 GGAAAATCGACCGCTTTGGG 59.830 55.000 0.00 0.00 44.64 4.12
1701 4101 0.456142 GAAAATCGACCGCTTTGGGC 60.456 55.000 0.00 0.00 45.45 5.36
1719 4119 2.049063 GCCTAGGCGTCCATAGCG 60.049 66.667 20.16 0.00 35.00 4.26
1727 4127 3.612681 GTCCATAGCGCCCGCCTA 61.613 66.667 2.29 2.05 43.17 3.93
1728 4128 3.303135 TCCATAGCGCCCGCCTAG 61.303 66.667 2.29 0.00 43.17 3.02
1729 4129 4.379243 CCATAGCGCCCGCCTAGG 62.379 72.222 2.29 3.67 43.17 3.02
2383 4830 4.201920 GGAGGTCACAACTGTTTTCTTCAC 60.202 45.833 0.00 0.00 0.00 3.18
2478 4931 5.107259 CGTAGCTGTAGACTATGCACTAGAG 60.107 48.000 0.00 6.15 34.52 2.43
2492 4962 4.772624 TGCACTAGAGGAAGTTACATCTGT 59.227 41.667 0.00 0.00 33.10 3.41
2560 5033 2.592102 AGAAAAGATGCCTGGCTTGA 57.408 45.000 21.03 0.00 0.00 3.02
2715 5188 7.147143 TGCAGATAGATATAAAGGACGTCTC 57.853 40.000 16.46 5.70 0.00 3.36
2799 5272 4.370776 TGAAGGATATTGAGACCCTTGGA 58.629 43.478 0.00 0.00 38.97 3.53
3057 5530 3.568007 GTGGTAAACTTGACATGCAGGAA 59.432 43.478 4.84 0.00 0.00 3.36
3114 5587 0.753111 GCAACCCTGATCCCCATCAC 60.753 60.000 0.00 0.00 33.80 3.06
3117 5590 1.766059 CCCTGATCCCCATCACCGA 60.766 63.158 0.00 0.00 33.80 4.69
3367 5840 5.570234 TTGTACAAAACAAGAAGGTGGAC 57.430 39.130 5.64 0.00 43.22 4.02
3465 5938 7.040617 CCAGTTTATACTCGAGCAGGTAATCTA 60.041 40.741 13.61 0.00 30.26 1.98
3478 5951 9.849166 GAGCAGGTAATCTACTAATGAGTTATC 57.151 37.037 0.00 0.00 37.10 1.75
3479 5952 9.594936 AGCAGGTAATCTACTAATGAGTTATCT 57.405 33.333 0.00 0.00 37.10 1.98
3710 6196 2.358195 GGCCCAGAGGTACCATTCATTT 60.358 50.000 15.94 0.00 34.57 2.32
4015 6503 8.398665 GTGGATTTTGACTACCTAATCATCAAC 58.601 37.037 0.00 0.00 0.00 3.18
4017 6505 8.616076 GGATTTTGACTACCTAATCATCAACAG 58.384 37.037 0.00 0.00 0.00 3.16
4049 6537 5.587844 AGGCATCATGTTCTATGTTCAAGTC 59.412 40.000 0.00 0.00 0.00 3.01
4140 6901 9.162764 ACTTATTAATCTGTTCAACTATGCGTT 57.837 29.630 0.00 0.00 35.88 4.84
4194 7364 6.611236 TGTCCATATTGTCTCAGTCAATCCTA 59.389 38.462 0.00 0.00 36.92 2.94
4378 7552 2.693069 ACATCAAGCGAGGAGAAGTTG 58.307 47.619 0.00 0.00 0.00 3.16
4434 7608 2.224646 TGTTCCATTTGTCGGGTCATCA 60.225 45.455 0.00 0.00 0.00 3.07
4534 7709 8.117813 ACAAGTTATGTTGGGTAAATAGTTGG 57.882 34.615 0.00 0.00 40.06 3.77
4535 7710 7.726738 ACAAGTTATGTTGGGTAAATAGTTGGT 59.273 33.333 0.00 0.00 40.06 3.67
4536 7711 9.233649 CAAGTTATGTTGGGTAAATAGTTGGTA 57.766 33.333 0.00 0.00 0.00 3.25
4621 7809 0.597637 CGGTTCTTCAGTGTCGCTGT 60.598 55.000 13.00 0.00 45.23 4.40
4642 7830 5.971763 TGTGTAGTTCCTTTTGCATGTTTT 58.028 33.333 0.00 0.00 0.00 2.43
4643 7831 5.809562 TGTGTAGTTCCTTTTGCATGTTTTG 59.190 36.000 0.00 0.00 0.00 2.44
4644 7832 6.039616 GTGTAGTTCCTTTTGCATGTTTTGA 58.960 36.000 0.00 0.00 0.00 2.69
4646 7834 4.696455 AGTTCCTTTTGCATGTTTTGAGG 58.304 39.130 0.00 0.00 0.00 3.86
4647 7835 4.405358 AGTTCCTTTTGCATGTTTTGAGGA 59.595 37.500 0.00 0.00 0.00 3.71
4649 7837 3.069443 TCCTTTTGCATGTTTTGAGGACC 59.931 43.478 0.00 0.00 0.00 4.46
4650 7838 3.070015 CCTTTTGCATGTTTTGAGGACCT 59.930 43.478 0.00 0.00 0.00 3.85
4651 7839 3.731652 TTTGCATGTTTTGAGGACCTG 57.268 42.857 0.00 0.00 0.00 4.00
4652 7840 2.363306 TGCATGTTTTGAGGACCTGT 57.637 45.000 0.00 0.00 0.00 4.00
4653 7841 3.500448 TGCATGTTTTGAGGACCTGTA 57.500 42.857 0.00 0.00 0.00 2.74
4654 7842 3.411446 TGCATGTTTTGAGGACCTGTAG 58.589 45.455 0.00 0.00 0.00 2.74
4655 7843 3.072330 TGCATGTTTTGAGGACCTGTAGA 59.928 43.478 0.00 0.00 0.00 2.59
4656 7844 4.263462 TGCATGTTTTGAGGACCTGTAGAT 60.263 41.667 0.00 0.00 0.00 1.98
4662 7850 1.207089 TGAGGACCTGTAGATTTGCGG 59.793 52.381 0.00 0.00 0.00 5.69
4726 8011 2.355946 AGCCGTTCTGCTCTCTTCA 58.644 52.632 0.00 0.00 36.75 3.02
4727 8012 0.246086 AGCCGTTCTGCTCTCTTCAG 59.754 55.000 0.00 0.00 36.75 3.02
4754 8042 5.229921 TGCTGTGTTGTTTAAGTTCTCAC 57.770 39.130 0.00 0.00 0.00 3.51
4755 8043 4.201773 TGCTGTGTTGTTTAAGTTCTCACG 60.202 41.667 0.00 0.00 0.00 4.35
4760 8048 7.140048 TGTGTTGTTTAAGTTCTCACGTTTTT 58.860 30.769 0.00 0.00 0.00 1.94
4843 8131 6.259346 TGGTGTGATTCCCATATATGTTGA 57.741 37.500 11.73 5.20 0.00 3.18
4845 8133 5.473504 GGTGTGATTCCCATATATGTTGACC 59.526 44.000 11.73 2.99 0.00 4.02
4855 8143 5.008514 CCATATATGTTGACCGTTTCATGCA 59.991 40.000 11.73 0.00 32.84 3.96
4884 8173 5.918608 TGCTTTACTTTTAAATTGCACCCA 58.081 33.333 0.00 0.00 28.47 4.51
4892 8181 7.109501 ACTTTTAAATTGCACCCAAAACTTCT 58.890 30.769 0.00 0.00 34.05 2.85
4900 8189 3.565063 GCACCCAAAACTTCTACGGTTAA 59.435 43.478 0.00 0.00 0.00 2.01
4924 8213 3.845781 TGGCAGTTTTTCTCTCTCTGT 57.154 42.857 0.00 0.00 0.00 3.41
4926 8215 4.632153 TGGCAGTTTTTCTCTCTCTGTAC 58.368 43.478 0.00 0.00 0.00 2.90
4929 8218 5.241662 GCAGTTTTTCTCTCTCTGTACCAT 58.758 41.667 0.00 0.00 0.00 3.55
4941 8230 2.151202 CTGTACCATTCGCACCTTGTT 58.849 47.619 0.00 0.00 0.00 2.83
5009 8302 7.332182 GGTATAAACTATGCCTGCAATCTCTAC 59.668 40.741 0.00 0.00 37.86 2.59
5010 8303 4.760530 AACTATGCCTGCAATCTCTACA 57.239 40.909 0.00 0.00 0.00 2.74
5011 8304 4.970860 ACTATGCCTGCAATCTCTACAT 57.029 40.909 0.00 0.00 0.00 2.29
5053 8350 9.881529 CAAATTTTTGTACATTTGGGAATCAAG 57.118 29.630 10.51 0.00 36.93 3.02
5054 8351 8.620116 AATTTTTGTACATTTGGGAATCAAGG 57.380 30.769 0.00 0.00 36.62 3.61
5055 8352 6.985653 TTTTGTACATTTGGGAATCAAGGA 57.014 33.333 0.00 0.00 36.62 3.36
5056 8353 6.985653 TTTGTACATTTGGGAATCAAGGAA 57.014 33.333 0.00 0.00 36.62 3.36
5057 8354 5.975693 TGTACATTTGGGAATCAAGGAAC 57.024 39.130 0.00 0.00 36.62 3.62
5059 8356 6.785076 TGTACATTTGGGAATCAAGGAACTA 58.215 36.000 0.00 0.00 38.49 2.24
5060 8357 7.235079 TGTACATTTGGGAATCAAGGAACTAA 58.765 34.615 0.00 0.00 38.49 2.24
5061 8358 6.590234 ACATTTGGGAATCAAGGAACTAAC 57.410 37.500 0.00 0.00 38.49 2.34
5062 8359 6.314917 ACATTTGGGAATCAAGGAACTAACT 58.685 36.000 0.00 0.00 38.49 2.24
5063 8360 6.209391 ACATTTGGGAATCAAGGAACTAACTG 59.791 38.462 0.00 0.00 38.49 3.16
5064 8361 4.301072 TGGGAATCAAGGAACTAACTGG 57.699 45.455 0.00 0.00 38.49 4.00
5065 8362 3.913799 TGGGAATCAAGGAACTAACTGGA 59.086 43.478 0.00 0.00 38.49 3.86
5066 8363 4.352595 TGGGAATCAAGGAACTAACTGGAA 59.647 41.667 0.00 0.00 38.49 3.53
5067 8364 4.700692 GGGAATCAAGGAACTAACTGGAAC 59.299 45.833 0.00 0.00 38.49 3.62
5068 8365 4.700692 GGAATCAAGGAACTAACTGGAACC 59.299 45.833 0.00 0.00 38.49 3.62
5069 8366 5.515008 GGAATCAAGGAACTAACTGGAACCT 60.515 44.000 0.00 0.00 38.49 3.50
5070 8367 5.584551 ATCAAGGAACTAACTGGAACCTT 57.415 39.130 0.00 0.00 38.49 3.50
5071 8368 5.382664 TCAAGGAACTAACTGGAACCTTT 57.617 39.130 0.00 0.00 38.49 3.11
5072 8369 5.762279 TCAAGGAACTAACTGGAACCTTTT 58.238 37.500 0.00 0.00 38.49 2.27
5073 8370 6.192044 TCAAGGAACTAACTGGAACCTTTTT 58.808 36.000 0.00 0.00 38.49 1.94
5141 8438 8.169977 TGCTTAGGCATGAAAATAAGAATAGG 57.830 34.615 0.00 0.00 44.28 2.57
5154 8451 0.480252 GAATAGGGGAAGGGCAGCAT 59.520 55.000 0.00 0.00 0.00 3.79
5155 8452 0.480252 AATAGGGGAAGGGCAGCATC 59.520 55.000 0.00 0.00 0.00 3.91
5248 8557 2.672651 CAAGGGCACATGTCCGCA 60.673 61.111 6.60 0.00 46.49 5.69
5295 8605 5.919707 GCGTTTTTATTCCCCGAACTTTTAA 59.080 36.000 0.00 0.00 0.00 1.52
5431 8742 8.752005 ATAGGATACAAACACAAATAGCACAT 57.248 30.769 0.00 0.00 41.41 3.21
5435 8746 5.385509 ACAAACACAAATAGCACATACCC 57.614 39.130 0.00 0.00 0.00 3.69
5452 8763 1.493022 ACCCGGCCTCTGCATAATTAA 59.507 47.619 0.00 0.00 40.13 1.40
5453 8764 2.108250 ACCCGGCCTCTGCATAATTAAT 59.892 45.455 0.00 0.00 40.13 1.40
5470 8781 9.786105 CATAATTAATATGCACACAGACAACAA 57.214 29.630 0.00 0.00 35.31 2.83
5472 8783 6.875948 TTAATATGCACACAGACAACAAGT 57.124 33.333 0.00 0.00 0.00 3.16
5473 8784 7.971183 TTAATATGCACACAGACAACAAGTA 57.029 32.000 0.00 0.00 0.00 2.24
5474 8785 8.560355 TTAATATGCACACAGACAACAAGTAT 57.440 30.769 0.00 0.00 0.00 2.12
5475 8786 6.668541 ATATGCACACAGACAACAAGTATC 57.331 37.500 0.00 0.00 0.00 2.24
5476 8787 3.802866 TGCACACAGACAACAAGTATCA 58.197 40.909 0.00 0.00 0.00 2.15
5477 8788 4.195416 TGCACACAGACAACAAGTATCAA 58.805 39.130 0.00 0.00 0.00 2.57
5478 8789 4.637977 TGCACACAGACAACAAGTATCAAA 59.362 37.500 0.00 0.00 0.00 2.69
5479 8790 5.207768 GCACACAGACAACAAGTATCAAAG 58.792 41.667 0.00 0.00 0.00 2.77
5480 8791 5.220854 GCACACAGACAACAAGTATCAAAGT 60.221 40.000 0.00 0.00 0.00 2.66
5481 8792 6.422223 CACACAGACAACAAGTATCAAAGTC 58.578 40.000 0.00 0.00 0.00 3.01
5482 8793 6.037062 CACACAGACAACAAGTATCAAAGTCA 59.963 38.462 0.00 0.00 0.00 3.41
5483 8794 6.767902 ACACAGACAACAAGTATCAAAGTCAT 59.232 34.615 0.00 0.00 0.00 3.06
5484 8795 7.931407 ACACAGACAACAAGTATCAAAGTCATA 59.069 33.333 0.00 0.00 0.00 2.15
5485 8796 8.939929 CACAGACAACAAGTATCAAAGTCATAT 58.060 33.333 0.00 0.00 0.00 1.78
5503 8814 8.429237 AGTCATATAAGACTAAAGCTATGCCT 57.571 34.615 8.83 0.00 46.52 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.862823 AGGAGTAGAGGGGGCGGC 62.863 72.222 0.00 0.00 0.00 6.53
11 12 0.481128 GGAGAGAGGAGTAGAGGGGG 59.519 65.000 0.00 0.00 0.00 5.40
12 13 0.481128 GGGAGAGAGGAGTAGAGGGG 59.519 65.000 0.00 0.00 0.00 4.79
13 14 0.109723 CGGGAGAGAGGAGTAGAGGG 59.890 65.000 0.00 0.00 0.00 4.30
15 16 0.536460 GGCGGGAGAGAGGAGTAGAG 60.536 65.000 0.00 0.00 0.00 2.43
17 18 1.894756 CGGCGGGAGAGAGGAGTAG 60.895 68.421 0.00 0.00 0.00 2.57
18 19 2.192443 CGGCGGGAGAGAGGAGTA 59.808 66.667 0.00 0.00 0.00 2.59
98 99 3.844741 GGCGGAGACTAGAGGACC 58.155 66.667 0.00 0.00 0.00 4.46
420 631 3.119245 AGCAATCACAGGCAATGACATTC 60.119 43.478 0.00 0.00 0.00 2.67
516 757 7.293073 AGGTTCATTATGTCTATCTGGCAATT 58.707 34.615 0.00 0.00 32.16 2.32
644 896 6.151691 TCAAATACACAAAGCAGAAATCAGC 58.848 36.000 0.00 0.00 0.00 4.26
654 906 7.972277 ACATCTTCATCATCAAATACACAAAGC 59.028 33.333 0.00 0.00 0.00 3.51
796 1622 7.481275 CAACCAAGCAGTTGTTCAAATATTT 57.519 32.000 0.00 0.00 41.80 1.40
922 2090 4.096833 TGAGCCAATGCATATGTTTCACTC 59.903 41.667 0.00 5.85 41.13 3.51
985 2174 1.147824 CCATCGCCTCCATCAAGCT 59.852 57.895 0.00 0.00 0.00 3.74
1070 2259 5.036916 AGGGATCAGTGGTTATAGGAACAA 58.963 41.667 0.00 0.00 0.00 2.83
1077 2266 2.972713 GAGGCAGGGATCAGTGGTTATA 59.027 50.000 0.00 0.00 0.00 0.98
1288 2541 9.741168 CGTTAACATAATTTCTTACAGTCACAG 57.259 33.333 6.39 0.00 0.00 3.66
1321 2574 4.134563 ACCCATAATGTTCTAATGGTCGC 58.865 43.478 0.00 0.00 38.83 5.19
1446 3844 7.442364 CCATGTATAAAGTCCCTGTACAGAATG 59.558 40.741 24.68 11.94 46.00 2.67
1491 3889 7.147143 AGACAGATGTAGTACGGCAATATAG 57.853 40.000 0.00 0.00 0.00 1.31
1514 3913 1.035923 TCTCGCCATAGAAGCTGGAG 58.964 55.000 0.00 0.00 35.70 3.86
1533 3932 1.337823 ACGTGCTTCCTGAATAGCGTT 60.338 47.619 0.00 0.00 40.26 4.84
1614 4014 6.093082 GGGACGCTTTAAAAACATAGCTTAGA 59.907 38.462 0.00 0.00 0.00 2.10
1620 4020 6.677187 GCCTTAGGGACGCTTTAAAAACATAG 60.677 42.308 0.00 0.00 33.58 2.23
1621 4021 5.124297 GCCTTAGGGACGCTTTAAAAACATA 59.876 40.000 0.00 0.00 33.58 2.29
1622 4022 4.082408 GCCTTAGGGACGCTTTAAAAACAT 60.082 41.667 0.00 0.00 33.58 2.71
1623 4023 3.253921 GCCTTAGGGACGCTTTAAAAACA 59.746 43.478 0.00 0.00 33.58 2.83
1624 4024 3.668757 CGCCTTAGGGACGCTTTAAAAAC 60.669 47.826 0.00 0.00 33.58 2.43
1625 4025 2.485038 CGCCTTAGGGACGCTTTAAAAA 59.515 45.455 0.00 0.00 33.58 1.94
1626 4026 2.078392 CGCCTTAGGGACGCTTTAAAA 58.922 47.619 0.00 0.00 33.58 1.52
1627 4027 1.275856 TCGCCTTAGGGACGCTTTAAA 59.724 47.619 0.00 0.00 34.09 1.52
1628 4028 0.896923 TCGCCTTAGGGACGCTTTAA 59.103 50.000 0.00 0.00 34.09 1.52
1629 4029 0.174162 GTCGCCTTAGGGACGCTTTA 59.826 55.000 0.00 0.00 44.82 1.85
1630 4030 1.079336 GTCGCCTTAGGGACGCTTT 60.079 57.895 0.00 0.00 44.82 3.51
1631 4031 2.577593 GTCGCCTTAGGGACGCTT 59.422 61.111 0.00 0.00 44.82 4.68
1657 4057 4.516195 GAGGGGGAGCGCTTCGAC 62.516 72.222 13.26 5.82 0.00 4.20
1665 4065 4.803908 CCAAAGCGGAGGGGGAGC 62.804 72.222 0.00 0.00 36.56 4.70
1666 4066 3.009115 TCCAAAGCGGAGGGGGAG 61.009 66.667 0.00 0.00 39.64 4.30
1673 4073 1.161843 GGTCGATTTTCCAAAGCGGA 58.838 50.000 7.00 0.00 44.40 5.54
1674 4074 0.179200 CGGTCGATTTTCCAAAGCGG 60.179 55.000 7.00 0.00 0.00 5.52
1675 4075 0.793104 GCGGTCGATTTTCCAAAGCG 60.793 55.000 0.54 0.54 0.00 4.68
1676 4076 0.521735 AGCGGTCGATTTTCCAAAGC 59.478 50.000 0.00 0.00 0.00 3.51
1677 4077 2.979813 CAAAGCGGTCGATTTTCCAAAG 59.020 45.455 3.79 0.00 30.80 2.77
1678 4078 2.287909 CCAAAGCGGTCGATTTTCCAAA 60.288 45.455 3.79 0.00 30.80 3.28
1679 4079 1.268352 CCAAAGCGGTCGATTTTCCAA 59.732 47.619 3.79 0.00 30.80 3.53
1680 4080 0.878416 CCAAAGCGGTCGATTTTCCA 59.122 50.000 3.79 0.00 30.80 3.53
1681 4081 0.170339 CCCAAAGCGGTCGATTTTCC 59.830 55.000 3.79 0.00 30.80 3.13
1682 4082 0.456142 GCCCAAAGCGGTCGATTTTC 60.456 55.000 3.79 0.00 30.80 2.29
1683 4083 1.584495 GCCCAAAGCGGTCGATTTT 59.416 52.632 3.79 0.00 30.80 1.82
1684 4084 3.274067 GCCCAAAGCGGTCGATTT 58.726 55.556 0.55 0.55 33.72 2.17
1702 4102 2.049063 CGCTATGGACGCCTAGGC 60.049 66.667 24.75 24.75 37.85 3.93
1710 4110 3.575351 CTAGGCGGGCGCTATGGAC 62.575 68.421 7.64 0.00 41.60 4.02
1711 4111 3.303135 CTAGGCGGGCGCTATGGA 61.303 66.667 7.64 0.00 41.60 3.41
1712 4112 4.379243 CCTAGGCGGGCGCTATGG 62.379 72.222 7.64 0.00 41.60 2.74
2104 4504 6.942576 ACAGTGGCAACTTAGAATCTATGTTT 59.057 34.615 15.99 2.70 32.98 2.83
2105 4505 6.476378 ACAGTGGCAACTTAGAATCTATGTT 58.524 36.000 13.67 13.67 32.98 2.71
2106 4506 6.054860 ACAGTGGCAACTTAGAATCTATGT 57.945 37.500 0.00 3.31 32.98 2.29
2107 4507 6.992063 AACAGTGGCAACTTAGAATCTATG 57.008 37.500 0.00 2.10 32.98 2.23
2110 4510 9.113838 CATAATAACAGTGGCAACTTAGAATCT 57.886 33.333 0.00 0.00 32.98 2.40
2111 4511 7.857885 GCATAATAACAGTGGCAACTTAGAATC 59.142 37.037 0.00 0.00 32.98 2.52
2112 4512 7.201821 GGCATAATAACAGTGGCAACTTAGAAT 60.202 37.037 0.00 0.00 38.21 2.40
2113 4513 6.094881 GGCATAATAACAGTGGCAACTTAGAA 59.905 38.462 0.00 0.00 38.21 2.10
2114 4514 5.588648 GGCATAATAACAGTGGCAACTTAGA 59.411 40.000 0.00 0.00 38.21 2.10
2115 4515 5.590259 AGGCATAATAACAGTGGCAACTTAG 59.410 40.000 0.00 0.00 40.49 2.18
2116 4516 5.505780 AGGCATAATAACAGTGGCAACTTA 58.494 37.500 0.00 0.00 40.49 2.24
2117 4517 4.344104 AGGCATAATAACAGTGGCAACTT 58.656 39.130 0.00 0.00 40.49 2.66
2118 4518 3.968265 AGGCATAATAACAGTGGCAACT 58.032 40.909 0.00 0.00 40.49 3.16
2119 4519 5.299279 ACATAGGCATAATAACAGTGGCAAC 59.701 40.000 0.00 0.00 40.49 4.17
2383 4830 1.811266 CCCATCGTTGACCAGCTCG 60.811 63.158 0.00 0.00 0.00 5.03
2478 4931 7.681939 TCCAACATAAACAGATGTAACTTCC 57.318 36.000 0.00 0.00 39.16 3.46
2492 4962 4.782019 ATTGCTCGCTTTCCAACATAAA 57.218 36.364 0.00 0.00 0.00 1.40
2560 5033 3.692257 CTCATGACCTGAGGTGTTCTT 57.308 47.619 9.89 0.00 46.52 2.52
2643 5116 4.719026 AGCATGACCAATGTGGAGATAT 57.281 40.909 0.00 0.00 40.96 1.63
2745 5218 4.503734 TCAACAAATTCGCTGCTTTCTTTG 59.496 37.500 0.00 5.37 0.00 2.77
2799 5272 8.814235 GTGTATGTAACTGCATCGTATTTAACT 58.186 33.333 0.00 0.00 0.00 2.24
3057 5530 3.485463 TCTCGAAGTGATTTGTTGGGT 57.515 42.857 0.00 0.00 0.00 4.51
3114 5587 3.119849 CCTTGTATTTTGAGCCAACTCGG 60.120 47.826 0.00 0.00 46.69 4.63
3117 5590 4.729868 AGACCTTGTATTTTGAGCCAACT 58.270 39.130 0.00 0.00 0.00 3.16
3310 5783 2.800629 GCGCTTGCTAAGGACGGTATAA 60.801 50.000 0.00 0.00 35.07 0.98
3311 5784 1.269413 GCGCTTGCTAAGGACGGTATA 60.269 52.381 0.00 0.00 35.07 1.47
3312 5785 0.529992 GCGCTTGCTAAGGACGGTAT 60.530 55.000 0.00 0.00 35.07 2.73
3313 5786 1.153706 GCGCTTGCTAAGGACGGTA 60.154 57.895 0.00 0.00 35.07 4.02
3367 5840 2.801162 CGTGCGTCAGTCCAGTCG 60.801 66.667 0.00 0.00 0.00 4.18
3710 6196 7.232534 ACATTTCTTGTGCCTAGGTAAAATTCA 59.767 33.333 11.31 0.00 37.11 2.57
3949 6435 6.357579 AGGTCTTCAATATCTGATAGCCAG 57.642 41.667 3.48 0.00 44.27 4.85
4015 6503 2.719739 ACATGATGCCTCACCTTTCTG 58.280 47.619 0.00 0.00 33.22 3.02
4017 6505 3.350833 AGAACATGATGCCTCACCTTTC 58.649 45.455 0.00 0.00 33.22 2.62
4049 6537 0.320771 AAGTGACTGCAAGCCTACCG 60.321 55.000 0.00 0.00 37.60 4.02
4140 6901 2.418746 GGAAGAGATAAGTCGCCAAGCA 60.419 50.000 0.00 0.00 0.00 3.91
4142 6903 3.526931 TGGAAGAGATAAGTCGCCAAG 57.473 47.619 0.00 0.00 0.00 3.61
4194 7364 8.090788 ACATGTAGATGTACCACTTAGGAATT 57.909 34.615 3.19 0.00 41.27 2.17
4378 7552 1.732809 GCCTTTCCTTTCGAGCTGTAC 59.267 52.381 0.00 0.00 0.00 2.90
4621 7809 6.214191 TCAAAACATGCAAAAGGAACTACA 57.786 33.333 0.00 0.00 38.49 2.74
4642 7830 1.207089 CCGCAAATCTACAGGTCCTCA 59.793 52.381 0.00 0.00 0.00 3.86
4643 7831 1.480954 TCCGCAAATCTACAGGTCCTC 59.519 52.381 0.00 0.00 0.00 3.71
4644 7832 1.568504 TCCGCAAATCTACAGGTCCT 58.431 50.000 0.00 0.00 0.00 3.85
4646 7834 2.695359 TGTTCCGCAAATCTACAGGTC 58.305 47.619 0.00 0.00 0.00 3.85
4647 7835 2.851263 TGTTCCGCAAATCTACAGGT 57.149 45.000 0.00 0.00 0.00 4.00
4656 7844 7.099266 ATCATCTTGATATTTGTTCCGCAAA 57.901 32.000 0.00 0.00 39.28 3.68
4697 7885 0.036952 AGAACGGCTCACAGATGTGG 60.037 55.000 12.77 5.32 45.65 4.17
4727 8012 6.381801 AGAACTTAAACAACACAGCATATGC 58.618 36.000 20.36 20.36 42.49 3.14
4730 8015 6.292649 CGTGAGAACTTAAACAACACAGCATA 60.293 38.462 0.00 0.00 0.00 3.14
4731 8016 5.504010 CGTGAGAACTTAAACAACACAGCAT 60.504 40.000 0.00 0.00 0.00 3.79
4732 8017 4.201773 CGTGAGAACTTAAACAACACAGCA 60.202 41.667 0.00 0.00 0.00 4.41
4733 8018 4.201783 ACGTGAGAACTTAAACAACACAGC 60.202 41.667 0.00 0.00 0.00 4.40
4735 8020 5.866335 AACGTGAGAACTTAAACAACACA 57.134 34.783 0.00 0.00 0.00 3.72
4760 8048 4.649674 AGATCGGCATCTAGGAGTACAAAA 59.350 41.667 0.00 0.00 37.63 2.44
4761 8049 4.215908 AGATCGGCATCTAGGAGTACAAA 58.784 43.478 0.00 0.00 37.63 2.83
4778 8066 4.818534 CCATTTGGGTCACAATAGATCG 57.181 45.455 0.00 0.00 39.21 3.69
4824 8112 5.305585 ACGGTCAACATATATGGGAATCAC 58.694 41.667 16.96 4.74 0.00 3.06
4877 8166 1.134037 ACCGTAGAAGTTTTGGGTGCA 60.134 47.619 0.00 0.00 0.00 4.57
4878 8167 1.601166 ACCGTAGAAGTTTTGGGTGC 58.399 50.000 0.00 0.00 0.00 5.01
4884 8173 6.807789 TGCCAAAATTAACCGTAGAAGTTTT 58.192 32.000 0.00 0.00 0.00 2.43
4892 8181 6.807789 AGAAAAACTGCCAAAATTAACCGTA 58.192 32.000 0.00 0.00 0.00 4.02
4900 8189 5.595952 ACAGAGAGAGAAAAACTGCCAAAAT 59.404 36.000 0.00 0.00 32.67 1.82
4924 8213 3.068560 GTGTAACAAGGTGCGAATGGTA 58.931 45.455 0.00 0.00 36.32 3.25
4926 8215 2.095768 CAGTGTAACAAGGTGCGAATGG 60.096 50.000 0.00 0.00 41.43 3.16
4929 8218 1.588674 CCAGTGTAACAAGGTGCGAA 58.411 50.000 0.00 0.00 41.43 4.70
4941 8230 0.840288 ACATGGTCCCAGCCAGTGTA 60.840 55.000 0.00 0.00 42.47 2.90
5030 8327 7.972301 TCCTTGATTCCCAAATGTACAAAAAT 58.028 30.769 0.00 0.00 33.76 1.82
5046 8343 5.561679 AGGTTCCAGTTAGTTCCTTGATTC 58.438 41.667 0.00 0.00 0.00 2.52
5049 8346 5.382664 AAAGGTTCCAGTTAGTTCCTTGA 57.617 39.130 0.00 0.00 35.78 3.02
5050 8347 6.465439 AAAAAGGTTCCAGTTAGTTCCTTG 57.535 37.500 0.00 0.00 35.78 3.61
5074 8371 8.802267 CCAGTTCCAGTTAATTCCTCAATTAAA 58.198 33.333 2.26 0.00 43.18 1.52
5075 8372 7.947890 ACCAGTTCCAGTTAATTCCTCAATTAA 59.052 33.333 0.00 0.00 40.63 1.40
5076 8373 7.466804 ACCAGTTCCAGTTAATTCCTCAATTA 58.533 34.615 0.00 0.00 33.95 1.40
5077 8374 6.314917 ACCAGTTCCAGTTAATTCCTCAATT 58.685 36.000 0.00 0.00 36.18 2.32
5078 8375 5.892348 ACCAGTTCCAGTTAATTCCTCAAT 58.108 37.500 0.00 0.00 0.00 2.57
5079 8376 5.319043 ACCAGTTCCAGTTAATTCCTCAA 57.681 39.130 0.00 0.00 0.00 3.02
5080 8377 4.993705 ACCAGTTCCAGTTAATTCCTCA 57.006 40.909 0.00 0.00 0.00 3.86
5081 8378 6.295719 TCTACCAGTTCCAGTTAATTCCTC 57.704 41.667 0.00 0.00 0.00 3.71
5132 8429 1.774856 GCTGCCCTTCCCCTATTCTTA 59.225 52.381 0.00 0.00 0.00 2.10
5141 8438 1.280421 CCTATAGATGCTGCCCTTCCC 59.720 57.143 0.00 0.00 0.00 3.97
5193 8490 5.675323 GCACGACAACCTTTCACTACTTTTT 60.675 40.000 0.00 0.00 0.00 1.94
5194 8491 4.201881 GCACGACAACCTTTCACTACTTTT 60.202 41.667 0.00 0.00 0.00 2.27
5195 8492 3.311596 GCACGACAACCTTTCACTACTTT 59.688 43.478 0.00 0.00 0.00 2.66
5196 8493 2.870411 GCACGACAACCTTTCACTACTT 59.130 45.455 0.00 0.00 0.00 2.24
5197 8494 2.480845 GCACGACAACCTTTCACTACT 58.519 47.619 0.00 0.00 0.00 2.57
5198 8495 1.529865 GGCACGACAACCTTTCACTAC 59.470 52.381 0.00 0.00 0.00 2.73
5199 8496 1.873698 GGCACGACAACCTTTCACTA 58.126 50.000 0.00 0.00 0.00 2.74
5200 8497 2.702847 GGCACGACAACCTTTCACT 58.297 52.632 0.00 0.00 0.00 3.41
5225 8522 2.045438 CATGTGCCCTTGCCGGTA 60.045 61.111 1.90 0.00 36.33 4.02
5248 8557 2.406559 CATCCTCCCTCTTGGTCTCAT 58.593 52.381 0.00 0.00 34.77 2.90
5250 8559 0.467804 GCATCCTCCCTCTTGGTCTC 59.532 60.000 0.00 0.00 34.77 3.36
5251 8560 1.333636 CGCATCCTCCCTCTTGGTCT 61.334 60.000 0.00 0.00 34.77 3.85
5254 8563 2.507944 CCGCATCCTCCCTCTTGG 59.492 66.667 0.00 0.00 0.00 3.61
5295 8605 8.582891 ACCCTAGGAGTATGGAATAAATCTTT 57.417 34.615 11.48 0.00 0.00 2.52
5314 8624 7.979444 TCTGTATCTTGTTTTTGAACCCTAG 57.021 36.000 0.00 0.00 0.00 3.02
5404 8715 8.673711 TGTGCTATTTGTGTTTGTATCCTATTC 58.326 33.333 0.00 0.00 0.00 1.75
5407 8718 9.104965 GTATGTGCTATTTGTGTTTGTATCCTA 57.895 33.333 0.00 0.00 0.00 2.94
5424 8735 1.075525 AGAGGCCGGGTATGTGCTA 60.076 57.895 2.18 0.00 0.00 3.49
5431 8742 1.136828 AATTATGCAGAGGCCGGGTA 58.863 50.000 2.18 0.00 40.13 3.69
5452 8763 6.172630 TGATACTTGTTGTCTGTGTGCATAT 58.827 36.000 0.00 0.00 0.00 1.78
5453 8764 5.546526 TGATACTTGTTGTCTGTGTGCATA 58.453 37.500 0.00 0.00 0.00 3.14
5476 8787 9.495572 GGCATAGCTTTAGTCTTATATGACTTT 57.504 33.333 22.23 6.26 44.01 2.66
5477 8788 8.875168 AGGCATAGCTTTAGTCTTATATGACTT 58.125 33.333 22.23 9.85 44.01 3.01


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

AutoCloner maintained by Alex Coulton.