Multiple sequence alignment - TraesCS1B01G007200

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 TraesCS1B01G007200 chr1B 100.000 3674 0 0 1 3674 4109289 4112962 0.000000e+00 6785.0
1 TraesCS1B01G007200 chr1B 90.655 3039 215 35 133 3149 4519749 4516758 0.000000e+00 3975.0
2 TraesCS1B01G007200 chr1B 88.980 2686 227 33 76 2746 4143956 4146587 0.000000e+00 3256.0
3 TraesCS1B01G007200 chr1B 85.675 726 64 20 133 844 538505174 538505873 0.000000e+00 728.0
4 TraesCS1B01G007200 chr1B 80.075 532 55 18 2692 3207 4933205 4932709 7.550000e-92 348.0
5 TraesCS1B01G007200 chr1B 88.514 296 18 9 3320 3612 46827827 46827545 9.770000e-91 344.0
6 TraesCS1B01G007200 chr1B 94.500 200 7 4 3326 3524 4595068 4594872 4.610000e-79 305.0
7 TraesCS1B01G007200 chr1B 90.217 184 14 2 128 311 46691329 46691508 1.710000e-58 237.0
8 TraesCS1B01G007200 chr1B 87.912 182 11 4 133 314 4955086 4954916 1.730000e-48 204.0
9 TraesCS1B01G007200 chr1B 92.857 140 7 1 128 267 46830541 46830405 2.240000e-47 200.0
10 TraesCS1B01G007200 chr1B 82.239 259 17 16 3417 3670 46694578 46694812 2.890000e-46 196.0
11 TraesCS1B01G007200 chr1B 84.577 201 17 7 3433 3628 4951755 4951564 1.740000e-43 187.0
12 TraesCS1B01G007200 chr1B 83.654 208 23 4 277 476 4954559 4954355 6.270000e-43 185.0
13 TraesCS1B01G007200 chr1B 87.975 158 11 3 128 285 4597750 4597601 2.910000e-41 180.0
14 TraesCS1B01G007200 chr1B 82.775 209 15 9 99 307 4543354 4543167 2.270000e-37 167.0
15 TraesCS1B01G007200 chr1B 92.784 97 5 2 3217 3313 46827976 46827882 4.950000e-29 139.0
16 TraesCS1B01G007200 chr1B 94.186 86 5 0 3229 3314 46694290 46694375 8.280000e-27 132.0
17 TraesCS1B01G007200 chr1B 77.381 252 18 24 574 804 4143927 4144160 3.000000e-21 113.0
18 TraesCS1B01G007200 chr1B 93.651 63 3 1 1 63 4519966 4519905 3.910000e-15 93.5
19 TraesCS1B01G007200 chr3D 91.339 2725 205 15 499 3207 560025276 560022567 0.000000e+00 3696.0
20 TraesCS1B01G007200 chr3D 83.807 352 26 20 133 476 560025661 560025333 4.610000e-79 305.0
21 TraesCS1B01G007200 chr3D 83.500 200 22 6 277 476 560024964 560024776 3.770000e-40 176.0
22 TraesCS1B01G007200 chr6A 90.280 2428 175 28 805 3199 613493534 613495933 0.000000e+00 3120.0
23 TraesCS1B01G007200 chr6A 86.833 2400 215 45 534 2905 64168192 64165866 0.000000e+00 2588.0
24 TraesCS1B01G007200 chr6A 88.562 306 17 9 3351 3653 613496142 613496432 4.510000e-94 355.0
25 TraesCS1B01G007200 chr6A 86.842 190 17 3 277 462 613493540 613493725 4.810000e-49 206.0
26 TraesCS1B01G007200 chr5B 88.925 2456 201 37 785 3197 60826101 60823674 0.000000e+00 2963.0
27 TraesCS1B01G007200 chr5B 85.784 204 19 4 277 476 60826075 60825878 1.340000e-49 207.0
28 TraesCS1B01G007200 chr5B 91.667 96 5 2 3221 3315 617173099 617173192 2.980000e-26 130.0
29 TraesCS1B01G007200 chr5D 88.875 2355 192 35 785 3096 57819423 57821750 0.000000e+00 2833.0
30 TraesCS1B01G007200 chr5D 84.804 204 20 4 277 476 57819449 57819645 1.040000e-45 195.0
31 TraesCS1B01G007200 chr6B 87.326 2438 245 39 793 3207 120132997 120130601 0.000000e+00 2732.0
32 TraesCS1B01G007200 chr6D 87.037 2430 220 39 499 2905 53176378 53174021 0.000000e+00 2654.0
33 TraesCS1B01G007200 chr6D 85.927 2480 262 53 768 3207 53144956 53142524 0.000000e+00 2566.0
34 TraesCS1B01G007200 chr1A 87.908 2266 210 37 945 3170 2943274 2945515 0.000000e+00 2608.0
35 TraesCS1B01G007200 chr1A 84.817 382 39 15 3227 3599 3520772 3520401 2.080000e-97 366.0
36 TraesCS1B01G007200 chr1A 85.000 300 33 8 2909 3204 3015085 3015376 9.980000e-76 294.0
37 TraesCS1B01G007200 chr1A 81.513 357 36 12 128 476 32545358 32545692 2.180000e-67 267.0
38 TraesCS1B01G007200 chr1A 86.631 187 13 9 3455 3636 32548113 32548292 2.890000e-46 196.0
39 TraesCS1B01G007200 chr2B 85.537 726 53 19 133 844 741895713 741896400 0.000000e+00 712.0
40 TraesCS1B01G007200 chr1D 86.895 496 37 11 2722 3207 387236 387713 6.990000e-147 531.0
41 TraesCS1B01G007200 chr1D 83.836 365 28 14 3320 3670 387910 388257 5.920000e-83 318.0
42 TraesCS1B01G007200 chr1D 81.408 355 38 12 130 476 33984114 33984448 7.820000e-67 265.0
43 TraesCS1B01G007200 chr1D 92.754 69 4 1 3216 3284 387763 387830 8.400000e-17 99.0
44 TraesCS1B01G007200 chr1D 92.537 67 1 4 3216 3279 665831 665896 3.910000e-15 93.5
45 TraesCS1B01G007200 chrUn 83.846 260 18 12 3427 3670 318171549 318171800 3.690000e-55 226.0


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 TraesCS1B01G007200 chr1B 4109289 4112962 3673 False 6785.000000 6785 100.000000 1 3674 1 chr1B.!!$F1 3673
1 TraesCS1B01G007200 chr1B 4516758 4519966 3208 True 2034.250000 3975 92.153000 1 3149 2 chr1B.!!$R3 3148
2 TraesCS1B01G007200 chr1B 4143927 4146587 2660 False 1684.500000 3256 83.180500 76 2746 2 chr1B.!!$F3 2670
3 TraesCS1B01G007200 chr1B 538505174 538505873 699 False 728.000000 728 85.675000 133 844 1 chr1B.!!$F2 711
4 TraesCS1B01G007200 chr1B 4594872 4597750 2878 True 242.500000 305 91.237500 128 3524 2 chr1B.!!$R4 3396
5 TraesCS1B01G007200 chr1B 46827545 46830541 2996 True 227.666667 344 91.385000 128 3612 3 chr1B.!!$R6 3484
6 TraesCS1B01G007200 chr3D 560022567 560025661 3094 True 1392.333333 3696 86.215333 133 3207 3 chr3D.!!$R1 3074
7 TraesCS1B01G007200 chr6A 64165866 64168192 2326 True 2588.000000 2588 86.833000 534 2905 1 chr6A.!!$R1 2371
8 TraesCS1B01G007200 chr6A 613493534 613496432 2898 False 1227.000000 3120 88.561333 277 3653 3 chr6A.!!$F1 3376
9 TraesCS1B01G007200 chr5B 60823674 60826101 2427 True 1585.000000 2963 87.354500 277 3197 2 chr5B.!!$R1 2920
10 TraesCS1B01G007200 chr5D 57819423 57821750 2327 False 1514.000000 2833 86.839500 277 3096 2 chr5D.!!$F1 2819
11 TraesCS1B01G007200 chr6B 120130601 120132997 2396 True 2732.000000 2732 87.326000 793 3207 1 chr6B.!!$R1 2414
12 TraesCS1B01G007200 chr6D 53174021 53176378 2357 True 2654.000000 2654 87.037000 499 2905 1 chr6D.!!$R2 2406
13 TraesCS1B01G007200 chr6D 53142524 53144956 2432 True 2566.000000 2566 85.927000 768 3207 1 chr6D.!!$R1 2439
14 TraesCS1B01G007200 chr1A 2943274 2945515 2241 False 2608.000000 2608 87.908000 945 3170 1 chr1A.!!$F1 2225
15 TraesCS1B01G007200 chr1A 32545358 32548292 2934 False 231.500000 267 84.072000 128 3636 2 chr1A.!!$F3 3508
16 TraesCS1B01G007200 chr2B 741895713 741896400 687 False 712.000000 712 85.537000 133 844 1 chr2B.!!$F1 711
17 TraesCS1B01G007200 chr1D 387236 388257 1021 False 316.000000 531 87.828333 2722 3670 3 chr1D.!!$F3 948

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
675 1858 0.036765 TATGAACTCGCCGGCTTTGT 60.037 50.000 26.68 17.0 0.00 2.83 F
2090 3945 1.071228 TGCATTATCTCGGAGCTGCAT 59.929 47.619 5.91 0.0 34.92 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2191 4046 0.824759 CGGCAGTTTAGGGCTAGAGT 59.175 55.0 0.0 0.0 0.0 3.24 R
3344 5431 0.035056 AGATGCGACCCCCTCAAAAG 60.035 55.0 0.0 0.0 0.0 2.27 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
29 30 2.754552 CCCCAACTTCACATGTACATGG 59.245 50.000 33.32 23.51 42.91 3.66
59 60 3.806316 TTCGATTCGCTTTCTTGTTCC 57.194 42.857 0.00 0.00 0.00 3.62
61 62 3.399330 TCGATTCGCTTTCTTGTTCCTT 58.601 40.909 0.00 0.00 0.00 3.36
62 63 3.186409 TCGATTCGCTTTCTTGTTCCTTG 59.814 43.478 0.00 0.00 0.00 3.61
63 64 3.058914 CGATTCGCTTTCTTGTTCCTTGT 60.059 43.478 0.00 0.00 0.00 3.16
64 65 3.963383 TTCGCTTTCTTGTTCCTTGTC 57.037 42.857 0.00 0.00 0.00 3.18
65 66 1.864711 TCGCTTTCTTGTTCCTTGTCG 59.135 47.619 0.00 0.00 0.00 4.35
66 67 1.069906 CGCTTTCTTGTTCCTTGTCGG 60.070 52.381 0.00 0.00 0.00 4.79
67 68 1.266989 GCTTTCTTGTTCCTTGTCGGG 59.733 52.381 0.00 0.00 0.00 5.14
68 69 1.880027 CTTTCTTGTTCCTTGTCGGGG 59.120 52.381 0.00 0.00 0.00 5.73
94 201 7.159372 GGAACCAGTATTTCTAGTTGAACAGA 58.841 38.462 0.00 0.00 33.88 3.41
95 202 7.117956 GGAACCAGTATTTCTAGTTGAACAGAC 59.882 40.741 0.00 0.00 33.88 3.51
96 203 7.062749 ACCAGTATTTCTAGTTGAACAGACA 57.937 36.000 0.00 0.00 33.88 3.41
97 204 7.680730 ACCAGTATTTCTAGTTGAACAGACAT 58.319 34.615 0.00 0.69 33.88 3.06
121 228 3.806949 TTAGATTGGCCCTGTGAACTT 57.193 42.857 0.00 0.00 0.00 2.66
122 229 4.919774 TTAGATTGGCCCTGTGAACTTA 57.080 40.909 0.00 0.00 0.00 2.24
123 230 3.806949 AGATTGGCCCTGTGAACTTAA 57.193 42.857 0.00 0.00 0.00 1.85
124 231 3.421844 AGATTGGCCCTGTGAACTTAAC 58.578 45.455 0.00 0.00 0.00 2.01
125 232 3.074538 AGATTGGCCCTGTGAACTTAACT 59.925 43.478 0.00 0.00 0.00 2.24
126 233 2.561478 TGGCCCTGTGAACTTAACTC 57.439 50.000 0.00 0.00 0.00 3.01
166 277 3.372822 GTGGCTGGCAAAATGATTGATTG 59.627 43.478 5.14 0.00 0.00 2.67
167 278 3.261137 TGGCTGGCAAAATGATTGATTGA 59.739 39.130 0.00 0.00 0.00 2.57
168 279 4.080807 TGGCTGGCAAAATGATTGATTGAT 60.081 37.500 0.00 0.00 0.00 2.57
169 280 4.879545 GGCTGGCAAAATGATTGATTGATT 59.120 37.500 0.00 0.00 0.00 2.57
182 297 8.884124 TGATTGATTGATTTCCCTACTTTCTT 57.116 30.769 0.00 0.00 0.00 2.52
183 298 9.312904 TGATTGATTGATTTCCCTACTTTCTTT 57.687 29.630 0.00 0.00 0.00 2.52
184 299 9.794685 GATTGATTGATTTCCCTACTTTCTTTC 57.205 33.333 0.00 0.00 0.00 2.62
209 328 1.202879 TGCCCAACCAAGACCTACAAG 60.203 52.381 0.00 0.00 0.00 3.16
268 392 6.441093 TTCATGTCCAGATTCAGCAATTAC 57.559 37.500 0.00 0.00 0.00 1.89
269 393 5.499313 TCATGTCCAGATTCAGCAATTACA 58.501 37.500 0.00 0.00 0.00 2.41
277 401 8.677300 TCCAGATTCAGCAATTACAAGTAATTC 58.323 33.333 13.67 9.75 42.11 2.17
367 1026 3.944015 AGGCTCTGCTTGCTACTTAATTG 59.056 43.478 0.00 0.00 0.00 2.32
373 1032 4.393834 TGCTTGCTACTTAATTGTGGTGA 58.606 39.130 0.00 0.00 0.00 4.02
394 1571 8.846211 TGGTGATAGCTAGTTTAATTTAATGGC 58.154 33.333 0.00 0.00 0.00 4.40
400 1580 4.792521 AGTTTAATTTAATGGCGTGGCA 57.207 36.364 0.00 0.00 0.00 4.92
416 1596 1.097547 GGCACGCCTGTAGCATCATT 61.098 55.000 0.00 0.00 44.04 2.57
417 1597 0.734889 GCACGCCTGTAGCATCATTT 59.265 50.000 0.00 0.00 44.04 2.32
458 1638 8.267894 ACAATTTAGACACAGATAAGGTGCTAT 58.732 33.333 0.00 0.00 39.87 2.97
459 1639 8.768955 CAATTTAGACACAGATAAGGTGCTATC 58.231 37.037 0.00 0.00 39.87 2.08
460 1640 7.661536 TTTAGACACAGATAAGGTGCTATCT 57.338 36.000 0.00 0.00 38.86 1.98
461 1641 8.762481 TTTAGACACAGATAAGGTGCTATCTA 57.238 34.615 0.00 0.00 36.66 1.98
462 1642 8.762481 TTAGACACAGATAAGGTGCTATCTAA 57.238 34.615 0.00 0.00 36.66 2.10
463 1643 7.847711 AGACACAGATAAGGTGCTATCTAAT 57.152 36.000 0.00 0.00 36.66 1.73
464 1644 8.256356 AGACACAGATAAGGTGCTATCTAATT 57.744 34.615 0.00 0.00 36.66 1.40
465 1645 8.709308 AGACACAGATAAGGTGCTATCTAATTT 58.291 33.333 0.00 0.00 36.66 1.82
466 1646 9.982651 GACACAGATAAGGTGCTATCTAATTTA 57.017 33.333 0.00 0.00 36.66 1.40
484 1664 8.765219 TCTAATTTAATAAATCTCTCTGCGTGC 58.235 33.333 0.00 0.00 0.00 5.34
485 1665 5.734855 TTTAATAAATCTCTCTGCGTGCC 57.265 39.130 0.00 0.00 0.00 5.01
486 1666 3.550437 AATAAATCTCTCTGCGTGCCT 57.450 42.857 0.00 0.00 0.00 4.75
487 1667 2.299993 TAAATCTCTCTGCGTGCCTG 57.700 50.000 0.00 0.00 0.00 4.85
488 1668 0.392193 AAATCTCTCTGCGTGCCTGG 60.392 55.000 0.00 0.00 0.00 4.45
489 1669 1.548357 AATCTCTCTGCGTGCCTGGT 61.548 55.000 0.00 0.00 0.00 4.00
490 1670 1.548357 ATCTCTCTGCGTGCCTGGTT 61.548 55.000 0.00 0.00 0.00 3.67
491 1671 2.031012 TCTCTGCGTGCCTGGTTG 59.969 61.111 0.00 0.00 0.00 3.77
492 1672 3.052082 CTCTGCGTGCCTGGTTGG 61.052 66.667 0.00 0.00 39.35 3.77
493 1673 3.535629 CTCTGCGTGCCTGGTTGGA 62.536 63.158 0.00 0.00 38.35 3.53
494 1674 3.357079 CTGCGTGCCTGGTTGGAC 61.357 66.667 0.00 0.00 38.35 4.02
495 1675 4.947147 TGCGTGCCTGGTTGGACC 62.947 66.667 0.00 0.00 39.22 4.46
496 1676 4.643387 GCGTGCCTGGTTGGACCT 62.643 66.667 0.00 0.00 39.58 3.85
497 1677 2.669569 CGTGCCTGGTTGGACCTG 60.670 66.667 0.00 0.00 39.58 4.00
503 1683 1.897560 CCTGGTTGGACCTGAAGTTC 58.102 55.000 5.67 0.00 39.29 3.01
514 1694 4.514066 GGACCTGAAGTTCGTTAATGTTGT 59.486 41.667 0.00 0.00 0.00 3.32
518 1698 7.636326 ACCTGAAGTTCGTTAATGTTGTAAAG 58.364 34.615 0.00 0.00 0.00 1.85
525 1705 6.561737 TCGTTAATGTTGTAAAGCCATTCA 57.438 33.333 0.00 0.00 31.63 2.57
526 1706 6.971602 TCGTTAATGTTGTAAAGCCATTCAA 58.028 32.000 0.00 0.00 31.63 2.69
527 1707 7.598278 TCGTTAATGTTGTAAAGCCATTCAAT 58.402 30.769 0.00 0.00 31.63 2.57
528 1708 8.085296 TCGTTAATGTTGTAAAGCCATTCAATT 58.915 29.630 0.00 0.00 31.63 2.32
529 1709 8.372521 CGTTAATGTTGTAAAGCCATTCAATTC 58.627 33.333 0.00 0.00 31.63 2.17
539 1719 5.297569 AGCCATTCAATTCTCCTAGGTAC 57.702 43.478 9.08 0.00 0.00 3.34
564 1747 6.207691 AGAAAGTAAGCTTTTTGCAACTGA 57.792 33.333 3.20 0.00 44.25 3.41
565 1748 6.809869 AGAAAGTAAGCTTTTTGCAACTGAT 58.190 32.000 3.20 0.00 44.25 2.90
566 1749 6.920210 AGAAAGTAAGCTTTTTGCAACTGATC 59.080 34.615 3.20 3.80 44.25 2.92
567 1750 5.772825 AGTAAGCTTTTTGCAACTGATCA 57.227 34.783 3.20 0.00 45.94 2.92
574 1757 5.979517 GCTTTTTGCAACTGATCAAGTACTT 59.020 36.000 1.12 1.12 38.56 2.24
607 1790 9.057089 GGTTGCAGCAAATACTAGTATTTCTAT 57.943 33.333 29.71 18.88 42.11 1.98
631 1814 8.970691 ATTTTGAACATATATTAGATTGGCGC 57.029 30.769 0.00 0.00 0.00 6.53
665 1848 2.386661 AACTGCACCCTATGAACTCG 57.613 50.000 0.00 0.00 0.00 4.18
666 1849 0.108138 ACTGCACCCTATGAACTCGC 60.108 55.000 0.00 0.00 0.00 5.03
672 1855 1.144057 CCTATGAACTCGCCGGCTT 59.856 57.895 26.68 12.68 0.00 4.35
675 1858 0.036765 TATGAACTCGCCGGCTTTGT 60.037 50.000 26.68 17.00 0.00 2.83
685 1868 2.687370 GCCGGCTTTGTCAAAATGATT 58.313 42.857 22.15 0.00 0.00 2.57
686 1869 2.412770 GCCGGCTTTGTCAAAATGATTG 59.587 45.455 22.15 0.00 0.00 2.67
687 1870 3.860378 GCCGGCTTTGTCAAAATGATTGA 60.860 43.478 22.15 0.00 0.00 2.57
688 1871 4.497300 CCGGCTTTGTCAAAATGATTGAT 58.503 39.130 0.00 0.00 0.00 2.57
689 1872 4.931002 CCGGCTTTGTCAAAATGATTGATT 59.069 37.500 0.00 0.00 0.00 2.57
690 1873 5.409214 CCGGCTTTGTCAAAATGATTGATTT 59.591 36.000 0.00 0.00 35.65 2.17
691 1874 6.073112 CCGGCTTTGTCAAAATGATTGATTTT 60.073 34.615 0.00 0.00 43.77 1.82
712 1895 3.751518 TCCTACTTTCTTTCTTGCCCAC 58.248 45.455 0.00 0.00 0.00 4.61
730 1913 1.993370 CACGCAAGAGCTACAAGTACC 59.007 52.381 0.00 0.00 43.62 3.34
731 1914 1.616865 ACGCAAGAGCTACAAGTACCA 59.383 47.619 0.00 0.00 43.62 3.25
732 1915 2.036733 ACGCAAGAGCTACAAGTACCAA 59.963 45.455 0.00 0.00 43.62 3.67
733 1916 3.262420 CGCAAGAGCTACAAGTACCAAT 58.738 45.455 0.00 0.00 43.02 3.16
734 1917 3.684788 CGCAAGAGCTACAAGTACCAATT 59.315 43.478 0.00 0.00 43.02 2.32
735 1918 4.154195 CGCAAGAGCTACAAGTACCAATTT 59.846 41.667 0.00 0.00 43.02 1.82
736 1919 5.631992 GCAAGAGCTACAAGTACCAATTTC 58.368 41.667 0.00 0.00 37.91 2.17
764 1947 4.168760 GCATGCTCTGGTTTTCATGTTAC 58.831 43.478 11.37 0.00 38.72 2.50
836 2031 1.769733 GCAGAATTGCTTGCGTCAAA 58.230 45.000 0.00 0.00 46.95 2.69
850 2052 2.029365 GCGTCAAATCTAGCTCGTTTCC 59.971 50.000 0.00 0.00 0.00 3.13
870 2077 9.074443 CGTTTCCTTGTATTCTCTTAGTTAGTC 57.926 37.037 0.00 0.00 0.00 2.59
893 2102 5.104360 TCCATTATTCAGGCTCTGCTACTTT 60.104 40.000 0.00 0.00 0.00 2.66
894 2103 6.099701 TCCATTATTCAGGCTCTGCTACTTTA 59.900 38.462 0.00 0.00 0.00 1.85
895 2104 6.939163 CCATTATTCAGGCTCTGCTACTTTAT 59.061 38.462 0.00 0.00 0.00 1.40
896 2105 7.094890 CCATTATTCAGGCTCTGCTACTTTATG 60.095 40.741 0.00 0.00 0.00 1.90
897 2106 3.827008 TCAGGCTCTGCTACTTTATGG 57.173 47.619 0.00 0.00 0.00 2.74
903 2112 4.202367 GGCTCTGCTACTTTATGGTGGTAT 60.202 45.833 0.00 0.00 0.00 2.73
942 2155 2.391389 GGCCTGCTTGTAGCGTCAC 61.391 63.158 0.00 0.00 46.26 3.67
943 2156 2.391389 GCCTGCTTGTAGCGTCACC 61.391 63.158 0.00 0.00 46.26 4.02
955 2171 4.986659 TGTAGCGTCACCTTTTCTTTCTAC 59.013 41.667 0.00 0.00 0.00 2.59
999 2231 9.209175 AGGTGCTAGCTATTTTAATAAATCTCG 57.791 33.333 17.23 0.00 35.61 4.04
1038 2837 3.408634 ACAAGTTTTGGACGGATACAGG 58.591 45.455 0.00 0.00 34.12 4.00
1068 2872 6.201517 CCCAAACTTCGTCAGCAATATATTG 58.798 40.000 19.29 19.29 40.66 1.90
1284 3128 3.539604 CAGGACAGGTGATCTGAATTCC 58.460 50.000 0.00 0.00 46.18 3.01
1362 3208 1.385528 GTGTTGGTTCCGGTCTTTGT 58.614 50.000 0.00 0.00 0.00 2.83
1365 3211 2.093075 TGTTGGTTCCGGTCTTTGTACA 60.093 45.455 0.00 0.00 0.00 2.90
1444 3290 6.990349 GGAAATCGATTACTCTGGTTGGATAA 59.010 38.462 11.83 0.00 0.00 1.75
1677 3524 2.944129 AGTCTATCTGCTCTCCACCTC 58.056 52.381 0.00 0.00 0.00 3.85
1769 3616 6.572519 AGCTTGTAGTGAAGAATTGCAAAAA 58.427 32.000 1.71 0.00 0.00 1.94
2067 3922 9.013229 GTTCATGCCCTAAATGATAATGACATA 57.987 33.333 0.00 0.00 34.14 2.29
2090 3945 1.071228 TGCATTATCTCGGAGCTGCAT 59.929 47.619 5.91 0.00 34.92 3.96
2148 4003 4.872691 CAGCTTTACTCTAGTGATGTTGGG 59.127 45.833 0.00 0.00 0.00 4.12
2180 4035 5.263968 ACCAGGACGTCATTTACTGATAG 57.736 43.478 18.91 5.15 35.97 2.08
2191 4046 6.538742 GTCATTTACTGATAGCAGCCTTTACA 59.461 38.462 8.16 0.00 46.26 2.41
2312 4167 2.820178 TCTGGTGCTCATTCAGTCCTA 58.180 47.619 0.00 0.00 0.00 2.94
2377 4232 1.694169 GAGGGGATGAAGGCCCTCA 60.694 63.158 6.49 6.49 45.70 3.86
2531 4386 0.329596 GGAGTGGCTGAACTGGGATT 59.670 55.000 0.00 0.00 0.00 3.01
2583 4439 5.194432 GAGTATTGTGGTGAGGTCTCTCTA 58.806 45.833 0.00 0.00 40.58 2.43
2595 4451 1.066908 GTCTCTCTAGAAGCTGCGCAT 59.933 52.381 12.24 0.00 32.16 4.73
2668 4527 2.573340 CAATTGGTCTTGGCGCCC 59.427 61.111 26.77 8.13 0.00 6.13
2670 4529 1.532794 AATTGGTCTTGGCGCCCAA 60.533 52.632 26.77 20.49 41.69 4.12
2792 4683 5.534654 CCCAGATTCACCTCACTTTTTGTTA 59.465 40.000 0.00 0.00 0.00 2.41
2800 4697 7.340256 TCACCTCACTTTTTGTTACCTTCTTA 58.660 34.615 0.00 0.00 0.00 2.10
2802 4699 6.544931 ACCTCACTTTTTGTTACCTTCTTACC 59.455 38.462 0.00 0.00 0.00 2.85
2805 4702 8.217131 TCACTTTTTGTTACCTTCTTACCTTC 57.783 34.615 0.00 0.00 0.00 3.46
2806 4703 7.830201 TCACTTTTTGTTACCTTCTTACCTTCA 59.170 33.333 0.00 0.00 0.00 3.02
2807 4704 7.913821 CACTTTTTGTTACCTTCTTACCTTCAC 59.086 37.037 0.00 0.00 0.00 3.18
2808 4705 7.832685 ACTTTTTGTTACCTTCTTACCTTCACT 59.167 33.333 0.00 0.00 0.00 3.41
2809 4706 7.562454 TTTTGTTACCTTCTTACCTTCACTG 57.438 36.000 0.00 0.00 0.00 3.66
2810 4707 4.638304 TGTTACCTTCTTACCTTCACTGC 58.362 43.478 0.00 0.00 0.00 4.40
2811 4708 4.101898 TGTTACCTTCTTACCTTCACTGCA 59.898 41.667 0.00 0.00 0.00 4.41
2812 4709 3.857157 ACCTTCTTACCTTCACTGCAA 57.143 42.857 0.00 0.00 0.00 4.08
2813 4710 4.373156 ACCTTCTTACCTTCACTGCAAT 57.627 40.909 0.00 0.00 0.00 3.56
2814 4711 4.729868 ACCTTCTTACCTTCACTGCAATT 58.270 39.130 0.00 0.00 0.00 2.32
2815 4712 4.520492 ACCTTCTTACCTTCACTGCAATTG 59.480 41.667 0.00 0.00 0.00 2.32
2824 4722 5.929992 ACCTTCACTGCAATTGATGATTTTG 59.070 36.000 10.34 0.00 0.00 2.44
2834 4733 7.820386 TGCAATTGATGATTTTGCTTTATGACT 59.180 29.630 10.34 0.00 44.62 3.41
2877 4777 3.426695 CGGCATCTGGTGAATGAAACTTC 60.427 47.826 0.00 0.00 0.00 3.01
2962 4886 3.090037 TCTCTGTAGCCGCTTCTAAACT 58.910 45.455 0.00 0.00 0.00 2.66
2973 4897 4.873827 CCGCTTCTAAACTGGCATAAGTAA 59.126 41.667 0.00 0.00 0.00 2.24
2990 4914 0.926293 TAAGCCCCAAGATTCCCTGG 59.074 55.000 0.00 0.00 0.00 4.45
3024 4950 3.707611 AGGCACTATATGACCGTTTGGTA 59.292 43.478 0.00 0.00 45.00 3.25
3027 4960 7.184863 AGGCACTATATGACCGTTTGGTATTG 61.185 42.308 0.00 0.00 45.00 1.90
3057 4990 9.169468 GTATTATTTAAGCAAATGTCATGGACG 57.831 33.333 0.00 0.00 35.88 4.79
3129 5069 3.201290 TGTTCGCATGGCAATTTTTGTT 58.799 36.364 0.00 0.00 0.00 2.83
3185 5130 1.272369 TGATGGGCATGTACAAAGGCA 60.272 47.619 21.29 11.44 0.00 4.75
3209 5154 6.035650 CAGCATGCTTGTTTTCTTGATATTGG 59.964 38.462 19.98 0.00 0.00 3.16
3210 5155 6.071221 AGCATGCTTGTTTTCTTGATATTGGA 60.071 34.615 16.30 0.00 0.00 3.53
3211 5156 6.255020 GCATGCTTGTTTTCTTGATATTGGAG 59.745 38.462 11.37 0.00 0.00 3.86
3212 5157 6.271488 TGCTTGTTTTCTTGATATTGGAGG 57.729 37.500 0.00 0.00 0.00 4.30
3213 5158 6.009589 TGCTTGTTTTCTTGATATTGGAGGA 58.990 36.000 0.00 0.00 0.00 3.71
3214 5159 6.664816 TGCTTGTTTTCTTGATATTGGAGGAT 59.335 34.615 0.00 0.00 0.00 3.24
3215 5160 6.976925 GCTTGTTTTCTTGATATTGGAGGATG 59.023 38.462 0.00 0.00 0.00 3.51
3217 5162 8.421249 TTGTTTTCTTGATATTGGAGGATGTT 57.579 30.769 0.00 0.00 0.00 2.71
3218 5163 9.527157 TTGTTTTCTTGATATTGGAGGATGTTA 57.473 29.630 0.00 0.00 0.00 2.41
3219 5164 8.956426 TGTTTTCTTGATATTGGAGGATGTTAC 58.044 33.333 0.00 0.00 0.00 2.50
3220 5165 9.178758 GTTTTCTTGATATTGGAGGATGTTACT 57.821 33.333 0.00 0.00 0.00 2.24
3223 5168 8.195165 TCTTGATATTGGAGGATGTTACTAGG 57.805 38.462 0.00 0.00 0.00 3.02
3224 5169 8.010697 TCTTGATATTGGAGGATGTTACTAGGA 58.989 37.037 0.00 0.00 0.00 2.94
3315 5348 4.872664 ACTGAAGGCATATAACGTAGCTC 58.127 43.478 0.00 0.00 0.00 4.09
3317 5350 5.768662 ACTGAAGGCATATAACGTAGCTCTA 59.231 40.000 0.00 0.00 0.00 2.43
3318 5351 6.072397 ACTGAAGGCATATAACGTAGCTCTAG 60.072 42.308 0.00 0.00 0.00 2.43
3379 5471 6.483640 GGTCGCATCTCTTTTTACCTATCATT 59.516 38.462 0.00 0.00 0.00 2.57
3394 5486 5.772672 ACCTATCATTTGTTTGCTTGGTACA 59.227 36.000 0.00 0.00 0.00 2.90
3421 5513 6.318112 AGATTCATCTCTTTTTGAGGGGTTT 58.682 36.000 0.00 0.00 42.86 3.27
3425 5517 6.077322 TCATCTCTTTTTGAGGGGTTTTGAT 58.923 36.000 0.00 0.00 42.86 2.57
3441 5534 7.041167 GGGGTTTTGATTTTCTGAATCCTTTTG 60.041 37.037 0.00 0.00 0.00 2.44
3548 5647 3.441572 ACTTTGCTTTGCTGGCTATGTAG 59.558 43.478 0.00 0.00 0.00 2.74
3555 5654 2.710377 TGCTGGCTATGTAGTTTGTGG 58.290 47.619 0.00 0.00 0.00 4.17
3649 5753 2.317149 ATTAGCTCCTGCACGCCCTC 62.317 60.000 0.00 0.00 42.74 4.30
3653 5757 3.002583 TCCTGCACGCCCTCATCA 61.003 61.111 0.00 0.00 0.00 3.07
3670 5774 7.885399 GCCCTCATCATGGAATATTTACTAGTT 59.115 37.037 0.00 0.00 0.00 2.24
3671 5775 9.799106 CCCTCATCATGGAATATTTACTAGTTT 57.201 33.333 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.822758 CGGCGGCCATGTACATGTG 61.823 63.158 29.25 22.10 37.11 3.21
29 30 1.861715 CGAATCGAAAAACGGCGGC 60.862 57.895 13.24 0.00 42.82 6.53
66 67 4.226620 TCAACTAGAAATACTGGTTCCCCC 59.773 45.833 0.00 0.00 44.87 5.40
67 68 5.431179 TCAACTAGAAATACTGGTTCCCC 57.569 43.478 0.00 0.00 44.87 4.81
68 69 6.235664 TGTTCAACTAGAAATACTGGTTCCC 58.764 40.000 0.00 0.00 44.87 3.97
73 74 9.823647 ATATGTCTGTTCAACTAGAAATACTGG 57.176 33.333 0.00 0.00 38.13 4.00
94 201 6.702449 TCACAGGGCCAATCTAATATATGT 57.298 37.500 6.18 0.00 0.00 2.29
95 202 7.170965 AGTTCACAGGGCCAATCTAATATATG 58.829 38.462 6.18 0.00 0.00 1.78
96 203 7.335127 AGTTCACAGGGCCAATCTAATATAT 57.665 36.000 6.18 0.00 0.00 0.86
97 204 6.763715 AGTTCACAGGGCCAATCTAATATA 57.236 37.500 6.18 0.00 0.00 0.86
121 228 3.258372 AGCCGATGAGTTGAGTTGAGTTA 59.742 43.478 0.00 0.00 0.00 2.24
122 229 2.037772 AGCCGATGAGTTGAGTTGAGTT 59.962 45.455 0.00 0.00 0.00 3.01
123 230 1.620819 AGCCGATGAGTTGAGTTGAGT 59.379 47.619 0.00 0.00 0.00 3.41
124 231 1.998315 CAGCCGATGAGTTGAGTTGAG 59.002 52.381 0.00 0.00 0.00 3.02
125 232 1.344438 ACAGCCGATGAGTTGAGTTGA 59.656 47.619 0.00 0.00 0.00 3.18
126 233 1.462283 CACAGCCGATGAGTTGAGTTG 59.538 52.381 0.00 0.00 0.00 3.16
166 277 7.309177 GCAAGAAGAAAGAAAGTAGGGAAATC 58.691 38.462 0.00 0.00 0.00 2.17
167 278 6.209589 GGCAAGAAGAAAGAAAGTAGGGAAAT 59.790 38.462 0.00 0.00 0.00 2.17
168 279 5.535030 GGCAAGAAGAAAGAAAGTAGGGAAA 59.465 40.000 0.00 0.00 0.00 3.13
169 280 5.070685 GGCAAGAAGAAAGAAAGTAGGGAA 58.929 41.667 0.00 0.00 0.00 3.97
182 297 2.306847 GTCTTGGTTGGGCAAGAAGAA 58.693 47.619 0.00 0.00 38.90 2.52
183 298 1.478654 GGTCTTGGTTGGGCAAGAAGA 60.479 52.381 0.00 0.00 38.90 2.87
184 299 0.961753 GGTCTTGGTTGGGCAAGAAG 59.038 55.000 0.00 0.00 38.90 2.85
252 376 8.680903 AGAATTACTTGTAATTGCTGAATCTGG 58.319 33.333 19.53 0.00 30.51 3.86
268 392 5.258622 CAATTCCGCGAGAAGAATTACTTG 58.741 41.667 16.97 10.25 39.13 3.16
269 393 4.201822 GCAATTCCGCGAGAAGAATTACTT 60.202 41.667 16.97 3.54 42.03 2.24
277 401 0.522076 GCAAGCAATTCCGCGAGAAG 60.522 55.000 8.23 0.00 38.07 2.85
373 1032 7.521585 GCCACGCCATTAAATTAAACTAGCTAT 60.522 37.037 0.00 0.00 0.00 2.97
437 1617 8.762481 TTAGATAGCACCTTATCTGTGTCTAA 57.238 34.615 5.94 0.00 39.92 2.10
458 1638 8.765219 GCACGCAGAGAGATTTATTAAATTAGA 58.235 33.333 3.27 0.00 0.00 2.10
459 1639 8.012241 GGCACGCAGAGAGATTTATTAAATTAG 58.988 37.037 3.27 0.00 0.00 1.73
460 1640 7.715249 AGGCACGCAGAGAGATTTATTAAATTA 59.285 33.333 3.27 0.00 0.00 1.40
461 1641 6.543831 AGGCACGCAGAGAGATTTATTAAATT 59.456 34.615 3.27 0.00 0.00 1.82
462 1642 6.017605 CAGGCACGCAGAGAGATTTATTAAAT 60.018 38.462 1.25 1.25 0.00 1.40
463 1643 5.294306 CAGGCACGCAGAGAGATTTATTAAA 59.706 40.000 0.00 0.00 0.00 1.52
464 1644 4.811024 CAGGCACGCAGAGAGATTTATTAA 59.189 41.667 0.00 0.00 0.00 1.40
465 1645 4.371786 CAGGCACGCAGAGAGATTTATTA 58.628 43.478 0.00 0.00 0.00 0.98
466 1646 3.201290 CAGGCACGCAGAGAGATTTATT 58.799 45.455 0.00 0.00 0.00 1.40
467 1647 2.484417 CCAGGCACGCAGAGAGATTTAT 60.484 50.000 0.00 0.00 0.00 1.40
468 1648 1.134699 CCAGGCACGCAGAGAGATTTA 60.135 52.381 0.00 0.00 0.00 1.40
469 1649 0.392193 CCAGGCACGCAGAGAGATTT 60.392 55.000 0.00 0.00 0.00 2.17
470 1650 1.220206 CCAGGCACGCAGAGAGATT 59.780 57.895 0.00 0.00 0.00 2.40
471 1651 1.548357 AACCAGGCACGCAGAGAGAT 61.548 55.000 0.00 0.00 0.00 2.75
472 1652 2.210013 AACCAGGCACGCAGAGAGA 61.210 57.895 0.00 0.00 0.00 3.10
473 1653 2.031516 CAACCAGGCACGCAGAGAG 61.032 63.158 0.00 0.00 0.00 3.20
474 1654 2.031012 CAACCAGGCACGCAGAGA 59.969 61.111 0.00 0.00 0.00 3.10
475 1655 3.052082 CCAACCAGGCACGCAGAG 61.052 66.667 0.00 0.00 0.00 3.35
476 1656 3.555324 TCCAACCAGGCACGCAGA 61.555 61.111 0.00 0.00 37.29 4.26
477 1657 3.357079 GTCCAACCAGGCACGCAG 61.357 66.667 0.00 0.00 37.29 5.18
478 1658 4.947147 GGTCCAACCAGGCACGCA 62.947 66.667 0.00 0.00 38.42 5.24
479 1659 4.643387 AGGTCCAACCAGGCACGC 62.643 66.667 0.00 0.00 41.95 5.34
480 1660 2.669569 CAGGTCCAACCAGGCACG 60.670 66.667 0.00 0.00 41.95 5.34
481 1661 0.890996 CTTCAGGTCCAACCAGGCAC 60.891 60.000 0.00 0.00 41.95 5.01
482 1662 1.352622 ACTTCAGGTCCAACCAGGCA 61.353 55.000 0.00 0.00 41.95 4.75
483 1663 0.178990 AACTTCAGGTCCAACCAGGC 60.179 55.000 0.00 0.00 41.95 4.85
484 1664 1.878102 CGAACTTCAGGTCCAACCAGG 60.878 57.143 0.00 0.00 41.95 4.45
485 1665 1.202651 ACGAACTTCAGGTCCAACCAG 60.203 52.381 0.00 0.00 41.95 4.00
486 1666 0.834612 ACGAACTTCAGGTCCAACCA 59.165 50.000 0.00 0.00 41.95 3.67
487 1667 1.963172 AACGAACTTCAGGTCCAACC 58.037 50.000 0.00 0.00 38.99 3.77
488 1668 4.514066 ACATTAACGAACTTCAGGTCCAAC 59.486 41.667 0.00 0.00 0.00 3.77
489 1669 4.710324 ACATTAACGAACTTCAGGTCCAA 58.290 39.130 0.00 0.00 0.00 3.53
490 1670 4.345859 ACATTAACGAACTTCAGGTCCA 57.654 40.909 0.00 0.00 0.00 4.02
491 1671 4.514066 ACAACATTAACGAACTTCAGGTCC 59.486 41.667 0.00 0.00 0.00 4.46
492 1672 5.668558 ACAACATTAACGAACTTCAGGTC 57.331 39.130 0.00 0.00 0.00 3.85
493 1673 7.556733 TTTACAACATTAACGAACTTCAGGT 57.443 32.000 0.00 0.00 0.00 4.00
494 1674 6.577427 GCTTTACAACATTAACGAACTTCAGG 59.423 38.462 0.00 0.00 0.00 3.86
495 1675 6.577427 GGCTTTACAACATTAACGAACTTCAG 59.423 38.462 0.00 0.00 0.00 3.02
496 1676 6.038382 TGGCTTTACAACATTAACGAACTTCA 59.962 34.615 0.00 0.00 0.00 3.02
497 1677 6.432107 TGGCTTTACAACATTAACGAACTTC 58.568 36.000 0.00 0.00 0.00 3.01
503 1683 7.810766 ATTGAATGGCTTTACAACATTAACG 57.189 32.000 0.00 0.00 35.17 3.18
514 1694 6.327386 ACCTAGGAGAATTGAATGGCTTTA 57.673 37.500 17.98 0.00 0.00 1.85
518 1698 5.297569 AGTACCTAGGAGAATTGAATGGC 57.702 43.478 17.98 0.00 0.00 4.40
525 1705 8.916062 GCTTACTTTCTAGTACCTAGGAGAATT 58.084 37.037 17.98 6.77 36.61 2.17
526 1706 8.283708 AGCTTACTTTCTAGTACCTAGGAGAAT 58.716 37.037 17.98 4.63 36.61 2.40
527 1707 7.641249 AGCTTACTTTCTAGTACCTAGGAGAA 58.359 38.462 17.98 11.20 36.61 2.87
528 1708 7.210618 AGCTTACTTTCTAGTACCTAGGAGA 57.789 40.000 17.98 4.58 36.61 3.71
529 1709 7.885009 AAGCTTACTTTCTAGTACCTAGGAG 57.115 40.000 17.98 1.70 36.61 3.69
539 1719 7.417612 TCAGTTGCAAAAAGCTTACTTTCTAG 58.582 34.615 0.00 0.00 45.48 2.43
546 1729 5.979517 ACTTGATCAGTTGCAAAAAGCTTAC 59.020 36.000 0.00 0.00 45.94 2.34
564 1747 3.622455 GCAACCCTAGGCAAGTACTTGAT 60.622 47.826 34.43 24.20 42.93 2.57
565 1748 2.290071 GCAACCCTAGGCAAGTACTTGA 60.290 50.000 34.43 16.05 42.93 3.02
566 1749 2.084546 GCAACCCTAGGCAAGTACTTG 58.915 52.381 27.85 27.85 43.14 3.16
567 1750 1.702957 TGCAACCCTAGGCAAGTACTT 59.297 47.619 2.05 1.12 37.03 2.24
574 1757 0.251742 ATTTGCTGCAACCCTAGGCA 60.252 50.000 15.72 0.00 38.52 4.75
607 1790 8.165239 AGCGCCAATCTAATATATGTTCAAAA 57.835 30.769 2.29 0.00 0.00 2.44
610 1793 8.478066 AGATAGCGCCAATCTAATATATGTTCA 58.522 33.333 18.49 0.00 31.88 3.18
611 1794 8.879342 AGATAGCGCCAATCTAATATATGTTC 57.121 34.615 18.49 0.00 31.88 3.18
625 1808 8.879759 GCAGTTATTATTAATAGATAGCGCCAA 58.120 33.333 2.29 0.00 0.00 4.52
626 1809 8.038351 TGCAGTTATTATTAATAGATAGCGCCA 58.962 33.333 2.29 0.00 0.00 5.69
627 1810 8.328864 GTGCAGTTATTATTAATAGATAGCGCC 58.671 37.037 2.29 0.00 0.00 6.53
628 1811 8.328864 GGTGCAGTTATTATTAATAGATAGCGC 58.671 37.037 0.00 0.00 0.00 5.92
629 1812 8.818057 GGGTGCAGTTATTATTAATAGATAGCG 58.182 37.037 0.00 0.00 0.00 4.26
630 1813 9.892130 AGGGTGCAGTTATTATTAATAGATAGC 57.108 33.333 0.00 0.95 0.00 2.97
657 1840 1.298859 GACAAAGCCGGCGAGTTCAT 61.299 55.000 23.20 7.14 0.00 2.57
665 1848 2.368655 ATCATTTTGACAAAGCCGGC 57.631 45.000 21.89 21.89 0.00 6.13
666 1849 3.911868 TCAATCATTTTGACAAAGCCGG 58.088 40.909 0.00 0.00 0.00 6.13
685 1868 6.015434 GGGCAAGAAAGAAAGTAGGAAAATCA 60.015 38.462 0.00 0.00 0.00 2.57
686 1869 6.015434 TGGGCAAGAAAGAAAGTAGGAAAATC 60.015 38.462 0.00 0.00 0.00 2.17
687 1870 5.838521 TGGGCAAGAAAGAAAGTAGGAAAAT 59.161 36.000 0.00 0.00 0.00 1.82
688 1871 5.068591 GTGGGCAAGAAAGAAAGTAGGAAAA 59.931 40.000 0.00 0.00 0.00 2.29
689 1872 4.583073 GTGGGCAAGAAAGAAAGTAGGAAA 59.417 41.667 0.00 0.00 0.00 3.13
690 1873 4.142038 GTGGGCAAGAAAGAAAGTAGGAA 58.858 43.478 0.00 0.00 0.00 3.36
691 1874 3.751518 GTGGGCAAGAAAGAAAGTAGGA 58.248 45.455 0.00 0.00 0.00 2.94
712 1895 2.363788 TGGTACTTGTAGCTCTTGCG 57.636 50.000 10.65 0.00 45.42 4.85
730 1913 4.693566 ACCAGAGCATGCAAATTGAAATTG 59.306 37.500 21.98 2.69 0.00 2.32
731 1914 4.901868 ACCAGAGCATGCAAATTGAAATT 58.098 34.783 21.98 0.00 0.00 1.82
732 1915 4.546829 ACCAGAGCATGCAAATTGAAAT 57.453 36.364 21.98 0.00 0.00 2.17
733 1916 4.339872 AACCAGAGCATGCAAATTGAAA 57.660 36.364 21.98 0.00 0.00 2.69
734 1917 4.339872 AAACCAGAGCATGCAAATTGAA 57.660 36.364 21.98 0.00 0.00 2.69
735 1918 4.202233 TGAAAACCAGAGCATGCAAATTGA 60.202 37.500 21.98 0.00 0.00 2.57
736 1919 4.059511 TGAAAACCAGAGCATGCAAATTG 58.940 39.130 21.98 11.64 0.00 2.32
764 1947 7.707104 CAACTTATTTGGAGGCACCTAATTAG 58.293 38.462 14.67 16.15 42.31 1.73
836 2031 6.322712 AGAGAATACAAGGAAACGAGCTAGAT 59.677 38.462 0.00 0.00 0.00 1.98
870 2077 4.348863 AGTAGCAGAGCCTGAATAATGG 57.651 45.455 6.40 0.00 32.44 3.16
922 2133 1.671054 GACGCTACAAGCAGGCCAA 60.671 57.895 5.01 0.00 42.58 4.52
942 2155 6.003950 TGTCCAGATTGGTAGAAAGAAAAGG 58.996 40.000 0.00 0.00 39.03 3.11
943 2156 6.486657 TGTGTCCAGATTGGTAGAAAGAAAAG 59.513 38.462 0.00 0.00 39.03 2.27
1068 2872 4.887763 GTGACAGACACTCATTACGAAC 57.112 45.455 0.00 0.00 45.13 3.95
1239 3083 5.486526 GTGATCCTGTTGAGAATCTCTGTT 58.513 41.667 11.92 0.00 34.92 3.16
1284 3128 0.875059 GCTTTGACACGAGGGAAAGG 59.125 55.000 0.00 0.00 0.00 3.11
1444 3290 3.074390 TCCAACTGATTTCCATGTCCAGT 59.926 43.478 0.00 0.00 39.49 4.00
1677 3524 4.297510 TGTCAATTTTCTCGCAACCAATG 58.702 39.130 0.00 0.00 0.00 2.82
1769 3616 9.471702 ACTTTAGGAAGTCATGATGATTGATTT 57.528 29.630 0.00 0.00 42.35 2.17
2067 3922 2.551459 GCAGCTCCGAGATAATGCAATT 59.449 45.455 0.00 0.00 41.28 2.32
2090 3945 6.239008 CCAAAGTGAGATGCTTTTAAGGTTGA 60.239 38.462 0.00 0.00 34.32 3.18
2148 4003 3.395639 TGACGTCCTGGTTTCACAATAC 58.604 45.455 14.12 0.00 0.00 1.89
2180 4035 1.657822 GGCTAGAGTGTAAAGGCTGC 58.342 55.000 0.00 0.00 33.32 5.25
2191 4046 0.824759 CGGCAGTTTAGGGCTAGAGT 59.175 55.000 0.00 0.00 0.00 3.24
2377 4232 2.023598 TCTCCAGATGAGGTGAGGATGT 60.024 50.000 0.00 0.00 41.76 3.06
2531 4386 8.644216 TGACCAAAGACTCTAACTTATGTACAA 58.356 33.333 0.00 0.00 0.00 2.41
2668 4527 8.556213 AAATTTTGGAGACCAATTCATCATTG 57.444 30.769 4.03 0.00 43.55 2.82
2670 4529 9.223099 GAAAAATTTTGGAGACCAATTCATCAT 57.777 29.630 3.73 0.00 43.55 2.45
2691 4550 8.939201 TTCAACAGCAAATTCATACTGAAAAA 57.061 26.923 0.00 0.00 40.12 1.94
2712 4571 5.359576 ACACTGAACAACTTAATGGCTTCAA 59.640 36.000 0.00 0.00 0.00 2.69
2792 4683 3.857157 TTGCAGTGAAGGTAAGAAGGT 57.143 42.857 0.00 0.00 0.00 3.50
2800 4697 5.733620 AAATCATCAATTGCAGTGAAGGT 57.266 34.783 0.00 0.00 0.00 3.50
2802 4699 5.854157 GCAAAATCATCAATTGCAGTGAAG 58.146 37.500 0.00 2.88 46.57 3.02
2810 4707 9.146984 ACAGTCATAAAGCAAAATCATCAATTG 57.853 29.630 0.00 0.00 0.00 2.32
2811 4708 9.362539 GACAGTCATAAAGCAAAATCATCAATT 57.637 29.630 0.00 0.00 0.00 2.32
2812 4709 8.746530 AGACAGTCATAAAGCAAAATCATCAAT 58.253 29.630 2.66 0.00 0.00 2.57
2813 4710 8.114331 AGACAGTCATAAAGCAAAATCATCAA 57.886 30.769 2.66 0.00 0.00 2.57
2814 4711 7.692460 AGACAGTCATAAAGCAAAATCATCA 57.308 32.000 2.66 0.00 0.00 3.07
2834 4733 5.758296 GCCGTCCAAAGATAATCATTAGACA 59.242 40.000 0.00 0.00 0.00 3.41
2845 4745 1.837439 ACCAGATGCCGTCCAAAGATA 59.163 47.619 0.00 0.00 0.00 1.98
2911 4828 7.675962 AATTAAGCAACCAGAATTACGTACA 57.324 32.000 0.00 0.00 0.00 2.90
2973 4897 1.149133 AACCAGGGAATCTTGGGGCT 61.149 55.000 8.66 0.00 0.00 5.19
2990 4914 1.604604 TAGTGCCTCCACAGCAAAAC 58.395 50.000 0.00 0.00 44.53 2.43
3102 5042 2.396700 TGCCATGCGAACATAGCAG 58.603 52.632 0.00 0.00 44.45 4.24
3103 5043 4.633769 TGCCATGCGAACATAGCA 57.366 50.000 0.00 0.00 46.63 3.49
3171 5115 1.917273 CATGCTGCCTTTGTACATGC 58.083 50.000 0.00 0.69 32.54 4.06
3185 5130 6.071221 TCCAATATCAAGAAAACAAGCATGCT 60.071 34.615 16.30 16.30 0.00 3.79
3199 5144 8.195165 TCCTAGTAACATCCTCCAATATCAAG 57.805 38.462 0.00 0.00 0.00 3.02
3209 5154 7.880195 ACATTTATGCATCCTAGTAACATCCTC 59.120 37.037 0.19 0.00 0.00 3.71
3210 5155 7.749666 ACATTTATGCATCCTAGTAACATCCT 58.250 34.615 0.19 0.00 0.00 3.24
3211 5156 7.986085 ACATTTATGCATCCTAGTAACATCC 57.014 36.000 0.19 0.00 0.00 3.51
3212 5157 9.929180 TCTACATTTATGCATCCTAGTAACATC 57.071 33.333 0.19 0.00 0.00 3.06
3214 5159 9.710900 CATCTACATTTATGCATCCTAGTAACA 57.289 33.333 0.19 0.00 0.00 2.41
3215 5160 9.712305 ACATCTACATTTATGCATCCTAGTAAC 57.288 33.333 0.19 0.00 0.00 2.50
3309 5342 3.254892 GTTGTTGAGTGCCTAGAGCTAC 58.745 50.000 0.00 0.00 44.23 3.58
3315 5348 5.186996 ACAAAATGTTGTTGAGTGCCTAG 57.813 39.130 0.00 0.00 46.01 3.02
3344 5431 0.035056 AGATGCGACCCCCTCAAAAG 60.035 55.000 0.00 0.00 0.00 2.27
3379 5471 6.634805 TGAATCTTTTGTACCAAGCAAACAA 58.365 32.000 0.00 0.00 35.82 2.83
3441 5534 6.283161 ACGAAGCTGTCTTGTTACTAAAAC 57.717 37.500 0.00 0.00 31.48 2.43
3567 5666 7.545265 GGTGCATGTTTCATTTTAGCTCAAATA 59.455 33.333 5.57 0.00 0.00 1.40
3568 5667 6.369615 GGTGCATGTTTCATTTTAGCTCAAAT 59.630 34.615 0.00 0.00 0.00 2.32
3569 5668 5.695816 GGTGCATGTTTCATTTTAGCTCAAA 59.304 36.000 0.00 0.00 0.00 2.69
3570 5669 5.010922 AGGTGCATGTTTCATTTTAGCTCAA 59.989 36.000 0.00 0.00 0.00 3.02
3624 5728 2.418628 GCGTGCAGGAGCTAATGTAAAA 59.581 45.455 11.29 0.00 42.74 1.52


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

AutoCloner maintained by Alex Coulton.