Multiple sequence alignment - TraesCS1A01G380000

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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 TraesCS1A01G380000 chr1A 100.000 4211 0 0 1 4211 551635927 551631717 0.000000e+00 7777.0
1 TraesCS1A01G380000 chr1D 88.790 3140 282 27 942 4035 460149971 460146856 0.000000e+00 3784.0
2 TraesCS1A01G380000 chr1D 90.177 906 61 8 89 975 460150864 460149968 0.000000e+00 1155.0
3 TraesCS1A01G380000 chr1D 94.231 52 3 0 20 71 460150985 460150934 3.490000e-11 80.5
4 TraesCS1A01G380000 chr1B 88.762 3141 281 29 942 4035 632016810 632013695 0.000000e+00 3779.0
5 TraesCS1A01G380000 chr1B 90.287 906 60 8 89 975 632017703 632016807 0.000000e+00 1160.0
6 TraesCS1A01G380000 chr1B 94.231 52 3 0 20 71 632017824 632017773 3.490000e-11 80.5
7 TraesCS1A01G380000 chr2D 84.991 3338 402 45 809 4074 528322628 528325938 0.000000e+00 3297.0
8 TraesCS1A01G380000 chr2D 84.024 169 26 1 89 257 528321607 528321774 1.210000e-35 161.0
9 TraesCS1A01G380000 chr2D 88.776 98 11 0 311 408 528321793 528321890 2.060000e-23 121.0
10 TraesCS1A01G380000 chr3D 83.299 3425 419 65 826 4146 545033064 545036439 0.000000e+00 3014.0
11 TraesCS1A01G380000 chr3D 82.836 3385 428 76 844 4128 544823818 544827149 0.000000e+00 2891.0
12 TraesCS1A01G380000 chr3D 82.286 3421 464 71 826 4152 545060628 545064000 0.000000e+00 2830.0
13 TraesCS1A01G380000 chr3D 82.311 3262 429 85 826 3993 545155388 545158595 0.000000e+00 2691.0
14 TraesCS1A01G380000 chr3D 83.464 2806 370 49 833 3584 545073600 545076365 0.000000e+00 2525.0
15 TraesCS1A01G380000 chr3D 93.029 373 26 0 3317 3689 263277031 263277403 2.860000e-151 545.0
16 TraesCS1A01G380000 chr3D 79.541 523 58 29 309 811 545032237 545032730 1.130000e-85 327.0
17 TraesCS1A01G380000 chr3D 78.957 537 63 22 305 820 544822795 544823302 1.890000e-83 320.0
18 TraesCS1A01G380000 chr3D 77.170 530 65 22 311 811 545072779 545073281 1.500000e-64 257.0
19 TraesCS1A01G380000 chr3D 76.505 515 61 30 309 811 545154744 545155210 4.240000e-55 226.0
20 TraesCS1A01G380000 chr3D 76.800 375 49 17 304 653 545055094 545055455 4.330000e-40 176.0
21 TraesCS1A01G380000 chr3B 82.784 3398 458 70 826 4140 721039053 721042406 0.000000e+00 2916.0
22 TraesCS1A01G380000 chr3B 83.496 2872 383 48 818 3636 721046193 721049026 0.000000e+00 2593.0
23 TraesCS1A01G380000 chr3B 77.944 535 64 23 309 820 721038088 721038591 6.890000e-73 285.0
24 TraesCS1A01G380000 chr3B 77.213 531 58 30 311 811 721044844 721045341 6.990000e-63 252.0
25 TraesCS1A01G380000 chr3A 82.648 3406 436 73 834 4136 681561996 681565349 0.000000e+00 2872.0
26 TraesCS1A01G380000 chr3A 82.499 3417 462 65 826 4152 681652790 681656160 0.000000e+00 2872.0
27 TraesCS1A01G380000 chr3A 82.403 3404 469 68 826 4152 681523405 681526755 0.000000e+00 2848.0
28 TraesCS1A01G380000 chr3A 82.092 3317 447 80 828 4043 681662998 681666268 0.000000e+00 2699.0
29 TraesCS1A01G380000 chr3A 83.817 2651 345 45 878 3477 681465848 681468465 0.000000e+00 2442.0
30 TraesCS1A01G380000 chr3A 84.344 2012 270 16 1287 3258 681633201 681635207 0.000000e+00 1929.0
31 TraesCS1A01G380000 chr3A 80.749 935 118 29 3255 4139 681640369 681641291 0.000000e+00 673.0
32 TraesCS1A01G380000 chr3A 80.155 645 72 26 3467 4068 681468507 681469138 8.360000e-117 431.0
33 TraesCS1A01G380000 chr3A 78.049 533 70 20 309 820 681465103 681465609 4.120000e-75 292.0
34 TraesCS1A01G380000 chr3A 77.674 533 69 24 309 820 681651475 681651978 3.210000e-71 279.0
35 TraesCS1A01G380000 chr3A 79.769 173 31 2 88 257 681662080 681662251 5.720000e-24 122.0


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 TraesCS1A01G380000 chr1A 551631717 551635927 4210 True 7777.000000 7777 100.000000 1 4211 1 chr1A.!!$R1 4210
1 TraesCS1A01G380000 chr1D 460146856 460150985 4129 True 1673.166667 3784 91.066000 20 4035 3 chr1D.!!$R1 4015
2 TraesCS1A01G380000 chr1B 632013695 632017824 4129 True 1673.166667 3779 91.093333 20 4035 3 chr1B.!!$R1 4015
3 TraesCS1A01G380000 chr2D 528321607 528325938 4331 False 1193.000000 3297 85.930333 89 4074 3 chr2D.!!$F1 3985
4 TraesCS1A01G380000 chr3D 545060628 545064000 3372 False 2830.000000 2830 82.286000 826 4152 1 chr3D.!!$F3 3326
5 TraesCS1A01G380000 chr3D 545032237 545036439 4202 False 1670.500000 3014 81.420000 309 4146 2 chr3D.!!$F5 3837
6 TraesCS1A01G380000 chr3D 544822795 544827149 4354 False 1605.500000 2891 80.896500 305 4128 2 chr3D.!!$F4 3823
7 TraesCS1A01G380000 chr3D 545154744 545158595 3851 False 1458.500000 2691 79.408000 309 3993 2 chr3D.!!$F7 3684
8 TraesCS1A01G380000 chr3D 545072779 545076365 3586 False 1391.000000 2525 80.317000 311 3584 2 chr3D.!!$F6 3273
9 TraesCS1A01G380000 chr3B 721038088 721049026 10938 False 1511.500000 2916 80.359250 309 4140 4 chr3B.!!$F1 3831
10 TraesCS1A01G380000 chr3A 681561996 681565349 3353 False 2872.000000 2872 82.648000 834 4136 1 chr3A.!!$F2 3302
11 TraesCS1A01G380000 chr3A 681523405 681526755 3350 False 2848.000000 2848 82.403000 826 4152 1 chr3A.!!$F1 3326
12 TraesCS1A01G380000 chr3A 681633201 681635207 2006 False 1929.000000 1929 84.344000 1287 3258 1 chr3A.!!$F3 1971
13 TraesCS1A01G380000 chr3A 681651475 681656160 4685 False 1575.500000 2872 80.086500 309 4152 2 chr3A.!!$F6 3843
14 TraesCS1A01G380000 chr3A 681662080 681666268 4188 False 1410.500000 2699 80.930500 88 4043 2 chr3A.!!$F7 3955
15 TraesCS1A01G380000 chr3A 681465103 681469138 4035 False 1055.000000 2442 80.673667 309 4068 3 chr3A.!!$F5 3759
16 TraesCS1A01G380000 chr3A 681640369 681641291 922 False 673.000000 673 80.749000 3255 4139 1 chr3A.!!$F4 884

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
899 2253 0.037882 TGGAAGCTCTTCTGCACGAG 60.038 55.0 9.23 0.0 39.45 4.18 F
2029 3478 0.105039 CCTCCAACTCCGTGGCTATC 59.895 60.0 0.00 0.0 38.68 2.08 F
2900 4385 0.034896 GTTGAGGGCTCGGACTTGAA 59.965 55.0 0.00 0.0 0.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2343 3804 0.030908 GAATCCGACCACTAGAGCCG 59.969 60.0 0.00 0.0 0.00 5.52 R
2915 4403 0.183492 AAGCTCACAGGCTGTTCCAA 59.817 50.0 19.43 3.0 42.24 3.53 R
4171 5869 0.105964 TTAAACACCTTGCAGGGCCA 60.106 50.0 16.02 0.0 40.58 5.36 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
57 58 2.281070 CTGCTGTGCGAGGTGGTT 60.281 61.111 0.00 0.00 0.00 3.67
66 67 0.179084 GCGAGGTGGTTATGCTGCTA 60.179 55.000 0.00 0.00 0.00 3.49
71 72 1.421646 GGTGGTTATGCTGCTAGGGAT 59.578 52.381 0.00 0.00 0.00 3.85
72 73 2.551071 GGTGGTTATGCTGCTAGGGATC 60.551 54.545 0.00 0.00 0.00 3.36
74 75 2.369860 TGGTTATGCTGCTAGGGATCAG 59.630 50.000 0.00 0.00 0.00 2.90
84 137 2.392662 CTAGGGATCAGCCTGTTCTGA 58.607 52.381 2.98 0.00 45.97 3.27
145 198 1.132640 CGTCAAGGCAAAGCTACGC 59.867 57.895 0.00 0.00 0.00 4.42
172 225 5.970289 TGGATAGATGGAACTCCTACAGAT 58.030 41.667 0.00 0.00 36.82 2.90
175 228 3.652055 AGATGGAACTCCTACAGATGCT 58.348 45.455 0.00 0.00 36.82 3.79
193 246 1.006571 TGGCGAGACTTTGTCCGTC 60.007 57.895 0.00 6.35 33.78 4.79
209 265 4.308458 TCGTCCTTGTGGCACCGG 62.308 66.667 16.26 15.42 0.00 5.28
228 284 1.763545 GGACACTTATCAGGACCTCCC 59.236 57.143 0.00 0.00 36.42 4.30
280 336 1.370587 CGGACTCAGACCTCGACTCC 61.371 65.000 0.00 0.00 0.00 3.85
284 340 1.272760 ACTCAGACCTCGACTCCCATT 60.273 52.381 0.00 0.00 0.00 3.16
297 353 0.958382 TCCCATTCCTCGGTTTTGCG 60.958 55.000 0.00 0.00 0.00 4.85
298 354 1.506262 CCATTCCTCGGTTTTGCGG 59.494 57.895 0.00 0.00 0.00 5.69
306 362 2.325082 CGGTTTTGCGGGTGGAGAG 61.325 63.158 0.00 0.00 0.00 3.20
307 363 1.228154 GGTTTTGCGGGTGGAGAGT 60.228 57.895 0.00 0.00 0.00 3.24
431 520 2.057137 AAGCACAAAAGGCAGAGTGA 57.943 45.000 0.00 0.00 33.99 3.41
438 527 3.072944 CAAAAGGCAGAGTGAGGAAGAG 58.927 50.000 0.00 0.00 0.00 2.85
471 560 4.577283 CCCTTTGGAAGTTCACGTAAGAAA 59.423 41.667 5.01 0.00 43.62 2.52
541 630 7.440523 TGCTCTTCTTAAAATCAAGGAGAAC 57.559 36.000 0.00 0.00 39.23 3.01
544 633 7.967303 GCTCTTCTTAAAATCAAGGAGAACATG 59.033 37.037 0.00 0.00 39.23 3.21
627 716 2.828549 GGGCGACGGGCAATCAAT 60.829 61.111 0.00 0.00 46.16 2.57
635 742 1.153588 GGGCAATCAATGGGCAACG 60.154 57.895 0.00 0.00 37.60 4.10
815 928 3.936564 CTTAAGGAGCATATGGAGGAGC 58.063 50.000 4.56 0.00 0.00 4.70
820 2053 0.394565 AGCATATGGAGGAGCGGAAC 59.605 55.000 4.56 0.00 0.00 3.62
831 2064 0.733223 GAGCGGAACTCGGAAGTCAC 60.733 60.000 0.00 0.00 39.69 3.67
893 2247 2.027377 ACATCCTGTGGAAGCTCTTCTG 60.027 50.000 9.23 1.53 39.45 3.02
896 2250 1.155042 CTGTGGAAGCTCTTCTGCAC 58.845 55.000 9.23 9.80 39.45 4.57
899 2253 0.037882 TGGAAGCTCTTCTGCACGAG 60.038 55.000 9.23 0.00 39.45 4.18
937 2300 1.079266 CTGCAGGCTCAGGACAGAC 60.079 63.158 5.57 0.00 0.00 3.51
960 2323 1.871039 TCGGACAAGCAAGCTACAAAC 59.129 47.619 0.00 0.00 0.00 2.93
1073 2481 2.398588 TGACAAGAGTGAAGGGACAGT 58.601 47.619 0.00 0.00 0.00 3.55
1081 2489 5.087323 AGAGTGAAGGGACAGTTGAATCTA 58.913 41.667 0.00 0.00 0.00 1.98
1084 2492 4.932200 GTGAAGGGACAGTTGAATCTAGTG 59.068 45.833 0.00 0.00 0.00 2.74
1183 2606 1.353694 AGCAGCTCAAGATCAAAGGGT 59.646 47.619 0.00 0.00 0.00 4.34
1225 2654 9.965902 AACATAACTTGAATTATCTTCCAGAGT 57.034 29.630 0.00 0.00 0.00 3.24
1255 2690 6.055588 AGTTATGAATGTCCCCTGTTTATCG 58.944 40.000 0.00 0.00 0.00 2.92
1317 2755 3.655276 ACCAGAAATGCTTTGAGCTTG 57.345 42.857 1.29 0.00 42.97 4.01
1371 2809 3.335356 AAGGGACATCCAGCTGGCG 62.335 63.158 28.91 22.55 38.24 5.69
1405 2849 4.158764 GCTATCCACAGCGAGAACCTATAT 59.841 45.833 0.00 0.00 0.00 0.86
1436 2880 1.973515 TGCTGGCCTCTACCATGATAG 59.026 52.381 3.32 0.00 39.54 2.08
1446 2890 4.745351 TCTACCATGATAGAGTGCTCCAT 58.255 43.478 0.00 0.00 0.00 3.41
1449 2893 3.324268 ACCATGATAGAGTGCTCCATCTG 59.676 47.826 8.58 5.28 30.66 2.90
1468 2912 3.131933 TCTGACTAGCCAGCAGAAGAATC 59.868 47.826 0.35 0.00 34.27 2.52
1518 2962 7.277174 TCATGATATCTTGTACGAGTGTGAT 57.723 36.000 15.93 0.00 0.00 3.06
1522 2966 6.265422 TGATATCTTGTACGAGTGTGATCCAT 59.735 38.462 10.00 0.00 0.00 3.41
1571 3015 2.126882 TGCTCTGTATGCTAACCCCAT 58.873 47.619 0.00 0.00 0.00 4.00
1634 3081 2.056094 GCTTTGCCACAATCACTCAC 57.944 50.000 0.00 0.00 0.00 3.51
1645 3092 2.398252 ATCACTCACCAGCATCACTG 57.602 50.000 0.00 0.00 46.77 3.66
1681 3128 3.510388 TCTCTTACAACGATCTGCCTG 57.490 47.619 0.00 0.00 0.00 4.85
1684 3131 4.021456 TCTCTTACAACGATCTGCCTGAAA 60.021 41.667 0.00 0.00 0.00 2.69
1770 3217 2.107950 TGATTGGACGGTGGATTGTC 57.892 50.000 0.00 0.00 0.00 3.18
1786 3233 1.153349 GTCGAAGGGCTGACATCCC 60.153 63.158 6.22 6.22 44.25 3.85
1811 3258 3.505790 ATTGGGCCCGTTCTGTGCA 62.506 57.895 19.37 0.00 0.00 4.57
1822 3269 0.178995 TTCTGTGCATCAGGCCAACA 60.179 50.000 5.01 0.00 43.76 3.33
1823 3270 0.890542 TCTGTGCATCAGGCCAACAC 60.891 55.000 5.01 6.09 43.76 3.32
1834 3281 2.101249 CAGGCCAACACATGTTTTGACT 59.899 45.455 23.16 17.50 35.83 3.41
1845 3293 6.263842 ACACATGTTTTGACTCACTCATTGAT 59.736 34.615 0.00 0.00 32.17 2.57
1851 3299 2.562738 TGACTCACTCATTGATCGGTGT 59.437 45.455 4.92 0.00 32.17 4.16
1880 3328 1.284491 TCCTGCTGATATTGGTGCCAA 59.716 47.619 6.08 6.08 40.47 4.52
1885 3333 2.579873 CTGATATTGGTGCCAAGGGAG 58.420 52.381 9.65 0.00 39.47 4.30
1895 3343 3.010420 GTGCCAAGGGAGATGTAAAGAC 58.990 50.000 0.00 0.00 0.00 3.01
1912 3360 7.791029 TGTAAAGACCTGCATTGTAGATGATA 58.209 34.615 3.03 0.00 0.00 2.15
1945 3394 3.003394 TCATTACCACCATTGCCAGAG 57.997 47.619 0.00 0.00 0.00 3.35
1988 3437 0.179048 CTGTCACACCACTTGGCTCA 60.179 55.000 0.00 0.00 39.32 4.26
1999 3448 3.483587 TGGCTCACCACTTCTCCC 58.516 61.111 0.00 0.00 42.67 4.30
2010 3459 2.548480 CCACTTCTCCCTTTTCAACGAC 59.452 50.000 0.00 0.00 0.00 4.34
2029 3478 0.105039 CCTCCAACTCCGTGGCTATC 59.895 60.000 0.00 0.00 38.68 2.08
2043 3492 7.851228 TCCGTGGCTATCATAGAATTGATAAT 58.149 34.615 0.00 0.00 37.95 1.28
2111 3572 3.498774 AGAAGGATGTCAGTGCTTTGT 57.501 42.857 0.00 0.00 29.32 2.83
2112 3573 3.825328 AGAAGGATGTCAGTGCTTTGTT 58.175 40.909 0.00 0.00 29.32 2.83
2113 3574 3.567164 AGAAGGATGTCAGTGCTTTGTTG 59.433 43.478 0.00 0.00 29.32 3.33
2114 3575 2.233271 AGGATGTCAGTGCTTTGTTGG 58.767 47.619 0.00 0.00 0.00 3.77
2131 3592 2.582978 GGAACCGGCAGTACCTCC 59.417 66.667 0.00 0.00 35.61 4.30
2132 3593 2.183555 GAACCGGCAGTACCTCCG 59.816 66.667 14.45 14.45 44.89 4.63
2139 3600 1.623542 GGCAGTACCTCCGGGACATT 61.624 60.000 0.00 0.00 36.25 2.71
2152 3613 1.820519 GGGACATTTGCAGCAAGATGA 59.179 47.619 24.91 8.14 0.00 2.92
2157 3618 6.016024 GGGACATTTGCAGCAAGATGATATTA 60.016 38.462 24.91 5.38 0.00 0.98
2178 3639 9.815306 ATATTACTCAAGTATCTGAGCCTAAGA 57.185 33.333 0.56 0.00 45.72 2.10
2179 3640 5.845391 ACTCAAGTATCTGAGCCTAAGAC 57.155 43.478 0.56 0.00 45.72 3.01
2205 3666 7.338703 CGAACAGATATTACCCAGCTACCTATA 59.661 40.741 0.00 0.00 0.00 1.31
2214 3675 8.506196 TTACCCAGCTACCTATAGAAATCAAT 57.494 34.615 0.00 0.00 0.00 2.57
2223 3684 9.930693 CTACCTATAGAAATCAATAACCTCCAC 57.069 37.037 0.00 0.00 0.00 4.02
2264 3725 1.841663 CGACAAACCAAGGTGCCTCG 61.842 60.000 0.00 0.00 0.00 4.63
2274 3735 2.476051 GTGCCTCGACATGCAACG 59.524 61.111 0.00 0.00 39.57 4.10
2343 3804 4.282950 TGATCTGAATGCGAGCAATTTC 57.717 40.909 0.57 3.22 0.00 2.17
2395 3856 5.309638 TCGACAAAATGGTAAACATGGAGA 58.690 37.500 0.00 0.00 40.44 3.71
2437 3898 6.476706 GGCCAAGCATAGTCATGATTTAAAAC 59.523 38.462 0.00 0.00 38.70 2.43
2517 3978 2.494870 GCACCTCAGGAATTTGCTTCAT 59.505 45.455 0.00 0.00 35.41 2.57
2528 3989 6.038356 GGAATTTGCTTCATACAATCAGTGG 58.962 40.000 0.00 0.00 35.41 4.00
2559 4020 3.906846 AGTCCCTCTGTTCTCTGACAATT 59.093 43.478 0.00 0.00 0.00 2.32
2573 4034 6.209589 TCTCTGACAATTACTGCTAGTGTTCT 59.790 38.462 0.00 0.00 0.00 3.01
2586 4071 1.977854 AGTGTTCTGGTAGCCACATCA 59.022 47.619 2.62 0.00 0.00 3.07
2589 4074 1.740025 GTTCTGGTAGCCACATCAAGC 59.260 52.381 0.00 0.00 0.00 4.01
2591 4076 0.108186 CTGGTAGCCACATCAAGCGA 60.108 55.000 0.00 0.00 0.00 4.93
2650 4135 3.618351 CATCCCAAGATGCTTGAGAGTT 58.382 45.455 8.64 0.00 43.35 3.01
2699 4184 3.186613 GGACGTCTTCTTCCATTGTTCAC 59.813 47.826 16.46 0.00 32.98 3.18
2747 4232 3.412237 GGTAACTCTAAGTTGCACCCA 57.588 47.619 9.58 0.00 41.68 4.51
2751 4236 2.257207 ACTCTAAGTTGCACCCAGCTA 58.743 47.619 0.00 0.00 45.94 3.32
2771 4256 2.345124 AGCCAAGATGATCTGGAAGC 57.655 50.000 12.96 6.62 0.00 3.86
2796 4281 0.605319 CCAAGCTGCCCAAGTTACGA 60.605 55.000 0.00 0.00 0.00 3.43
2827 4312 2.819019 CTCCAACACATTACATGCACCA 59.181 45.455 0.00 0.00 0.00 4.17
2828 4313 2.819019 TCCAACACATTACATGCACCAG 59.181 45.455 0.00 0.00 0.00 4.00
2830 4315 2.819019 CAACACATTACATGCACCAGGA 59.181 45.455 0.00 0.00 0.00 3.86
2853 4338 0.250901 TGCTCAACTTCAAGGAGGGC 60.251 55.000 0.00 0.00 0.00 5.19
2873 4358 2.223203 GCGAATTCAGATGCCTCAAGTG 60.223 50.000 6.22 0.00 0.00 3.16
2900 4385 0.034896 GTTGAGGGCTCGGACTTGAA 59.965 55.000 0.00 0.00 0.00 2.69
2915 4403 6.884295 TCGGACTTGAATATCATTTTTGAGGT 59.116 34.615 0.00 0.00 0.00 3.85
2920 4408 8.869109 ACTTGAATATCATTTTTGAGGTTGGAA 58.131 29.630 0.00 0.00 0.00 3.53
2934 4422 0.183492 TTGGAACAGCCTGTGAGCTT 59.817 50.000 0.00 0.00 42.61 3.74
2959 4447 5.449553 AGAAGATGGTTTTGTCTTTCACCT 58.550 37.500 0.00 0.00 34.97 4.00
2966 4454 4.278419 GGTTTTGTCTTTCACCTGCATAGT 59.722 41.667 0.00 0.00 0.00 2.12
3006 4494 4.023291 ACTGCCTTCCAAAACTGAAAGAA 58.977 39.130 0.00 0.00 37.43 2.52
3028 4516 4.009675 ACTTGAGTTGAACAACAGCTTCA 58.990 39.130 17.85 10.63 43.47 3.02
3054 4542 4.280174 GGCAGGTTGCTATCATCATTTGAT 59.720 41.667 0.67 0.00 44.28 2.57
3129 4617 3.259064 TGCTCTACAAATACTCGCCAAC 58.741 45.455 0.00 0.00 0.00 3.77
3133 4621 5.671329 GCTCTACAAATACTCGCCAACAAAG 60.671 44.000 0.00 0.00 0.00 2.77
3148 4636 4.290155 CAACAAAGCAAATCTACGCTGTT 58.710 39.130 0.00 0.00 38.82 3.16
3180 4668 3.636300 TGGACAAGTCTTTTGGTGGAATG 59.364 43.478 0.00 0.00 0.00 2.67
3200 4688 7.335673 TGGAATGCAGAACGAGATTACATTAAA 59.664 33.333 0.00 0.00 0.00 1.52
3322 4810 3.942829 TGTCTGGTCATCTTTCACATCC 58.057 45.455 0.00 0.00 0.00 3.51
3406 4918 1.422531 ATGAGGTGAGAGAGGGCATC 58.577 55.000 0.00 0.00 0.00 3.91
3437 4949 8.314021 AGCATAAAAACAAGCTTAGCCTTAAAT 58.686 29.630 0.00 0.00 32.52 1.40
3459 4971 5.993748 TTTATGGGCCAGAAACTTTAAGG 57.006 39.130 21.71 0.00 0.00 2.69
3465 4977 2.489722 GCCAGAAACTTTAAGGCTGAGG 59.510 50.000 11.40 3.04 42.01 3.86
3490 5056 3.370104 AGGAGATGAACAAGAGGACGAT 58.630 45.455 0.00 0.00 0.00 3.73
3504 5070 0.933097 GACGATGACGATGCTGCAAT 59.067 50.000 6.36 0.00 42.66 3.56
3616 5185 3.358707 TTGCAATCTGTTCTGCTTGTG 57.641 42.857 0.00 0.00 39.38 3.33
3629 5199 6.751425 TGTTCTGCTTGTGTGTTAATTTCTTG 59.249 34.615 0.00 0.00 0.00 3.02
3672 5278 4.819630 GTGTGTTTACTTTCTCCACATGGA 59.180 41.667 0.00 0.00 43.08 3.41
3698 5305 0.109226 GTGACTCTGACTGGGCGTAC 60.109 60.000 0.00 0.00 0.00 3.67
3849 5486 6.976934 AAGTATGTTTTGATTGGGTTCTGT 57.023 33.333 0.00 0.00 0.00 3.41
3870 5517 4.520111 TGTGACTCAAAGATGAATTGGTGG 59.480 41.667 0.00 0.00 34.49 4.61
3891 5556 6.183361 GGTGGGTGTCATGATATAGTTACCTT 60.183 42.308 0.00 0.00 0.00 3.50
3895 5560 9.841295 GGGTGTCATGATATAGTTACCTTTAAA 57.159 33.333 0.00 0.00 0.00 1.52
3974 5648 3.680196 GCCTTAGGTACTTGAAGCAGAGG 60.680 52.174 0.00 0.00 41.75 3.69
4061 5754 2.014068 GCACCCCAGGAAGAATCGAAG 61.014 57.143 0.00 0.00 0.00 3.79
4074 5767 6.073222 GGAAGAATCGAAGTTGTTTTCAGCTA 60.073 38.462 0.00 0.00 40.37 3.32
4099 5796 0.893270 TGGCGTGCATTTGGTAGCTT 60.893 50.000 0.00 0.00 0.00 3.74
4101 5798 0.240945 GCGTGCATTTGGTAGCTTGT 59.759 50.000 0.00 0.00 0.00 3.16
4104 5801 2.664916 GTGCATTTGGTAGCTTGTGTG 58.335 47.619 0.00 0.00 0.00 3.82
4111 5808 4.425180 TTGGTAGCTTGTGTGGTTTCTA 57.575 40.909 0.00 0.00 0.00 2.10
4146 5844 5.245531 TGGTGAAAAGCCAGTATAGTTCAG 58.754 41.667 0.00 0.00 0.00 3.02
4148 5846 5.938125 GGTGAAAAGCCAGTATAGTTCAGAA 59.062 40.000 0.00 0.00 0.00 3.02
4149 5847 6.092807 GGTGAAAAGCCAGTATAGTTCAGAAG 59.907 42.308 0.00 0.00 0.00 2.85
4151 5849 7.173390 GTGAAAAGCCAGTATAGTTCAGAAGTT 59.827 37.037 0.00 0.00 0.00 2.66
4152 5850 8.372459 TGAAAAGCCAGTATAGTTCAGAAGTTA 58.628 33.333 0.00 0.00 0.00 2.24
4153 5851 9.216117 GAAAAGCCAGTATAGTTCAGAAGTTAA 57.784 33.333 0.00 0.00 0.00 2.01
4154 5852 9.740710 AAAAGCCAGTATAGTTCAGAAGTTAAT 57.259 29.630 0.00 0.00 0.00 1.40
4155 5853 8.723942 AAGCCAGTATAGTTCAGAAGTTAATG 57.276 34.615 0.00 0.00 0.00 1.90
4156 5854 8.079211 AGCCAGTATAGTTCAGAAGTTAATGA 57.921 34.615 0.00 0.00 0.00 2.57
4157 5855 8.709308 AGCCAGTATAGTTCAGAAGTTAATGAT 58.291 33.333 0.00 0.00 0.00 2.45
4158 5856 8.768955 GCCAGTATAGTTCAGAAGTTAATGATG 58.231 37.037 0.00 0.00 0.00 3.07
4166 5864 7.721399 AGTTCAGAAGTTAATGATGAAGTTGGT 59.279 33.333 0.00 0.00 31.21 3.67
4168 5866 7.223584 TCAGAAGTTAATGATGAAGTTGGTGA 58.776 34.615 0.00 0.00 0.00 4.02
4169 5867 7.884877 TCAGAAGTTAATGATGAAGTTGGTGAT 59.115 33.333 0.00 0.00 0.00 3.06
4171 5869 9.082313 AGAAGTTAATGATGAAGTTGGTGATTT 57.918 29.630 0.00 0.00 0.00 2.17
4172 5870 9.132521 GAAGTTAATGATGAAGTTGGTGATTTG 57.867 33.333 0.00 0.00 0.00 2.32
4174 5872 3.940209 TGATGAAGTTGGTGATTTGGC 57.060 42.857 0.00 0.00 0.00 4.52
4177 5875 1.133199 TGAAGTTGGTGATTTGGCCCT 60.133 47.619 0.00 0.00 0.00 5.19
4178 5876 1.273327 GAAGTTGGTGATTTGGCCCTG 59.727 52.381 0.00 0.00 0.00 4.45
4180 5878 1.152376 TTGGTGATTTGGCCCTGCA 60.152 52.632 0.00 0.00 0.00 4.41
4181 5879 0.762082 TTGGTGATTTGGCCCTGCAA 60.762 50.000 0.00 0.00 0.00 4.08
4182 5880 1.186917 TGGTGATTTGGCCCTGCAAG 61.187 55.000 0.00 0.00 0.00 4.01
4196 5894 2.863809 CTGCAAGGTGTTTAAGGAGGT 58.136 47.619 0.00 0.00 0.00 3.85
4198 5896 4.003648 CTGCAAGGTGTTTAAGGAGGTAG 58.996 47.826 0.00 0.00 0.00 3.18
4201 5899 4.695928 GCAAGGTGTTTAAGGAGGTAGAAG 59.304 45.833 0.00 0.00 0.00 2.85
4202 5900 5.745181 GCAAGGTGTTTAAGGAGGTAGAAGT 60.745 44.000 0.00 0.00 0.00 3.01
4203 5901 6.296803 CAAGGTGTTTAAGGAGGTAGAAGTT 58.703 40.000 0.00 0.00 0.00 2.66
4205 5903 5.012871 AGGTGTTTAAGGAGGTAGAAGTTCC 59.987 44.000 0.00 0.00 0.00 3.62
4207 5905 6.164876 GTGTTTAAGGAGGTAGAAGTTCCTC 58.835 44.000 0.00 0.00 46.62 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 2.031012 TCCGTGCTGAAGGTGCAG 59.969 61.111 0.00 0.00 41.41 4.41
23 24 2.280797 GTCCGTGCTGAAGGTGCA 60.281 61.111 0.00 0.00 38.19 4.57
66 67 3.406442 TCAGAACAGGCTGATCCCT 57.594 52.632 23.66 9.02 39.84 4.20
72 73 0.820226 TCGAGGATCAGAACAGGCTG 59.180 55.000 14.16 14.16 37.24 4.85
74 75 1.478510 TCTTCGAGGATCAGAACAGGC 59.521 52.381 0.00 0.00 33.17 4.85
75 76 2.481104 GCTCTTCGAGGATCAGAACAGG 60.481 54.545 0.00 0.00 33.17 4.00
76 77 2.481104 GGCTCTTCGAGGATCAGAACAG 60.481 54.545 0.00 0.00 33.17 3.16
77 78 1.478510 GGCTCTTCGAGGATCAGAACA 59.521 52.381 0.00 0.00 33.17 3.18
84 137 2.768527 TCAATGAAGGCTCTTCGAGGAT 59.231 45.455 0.00 0.00 0.00 3.24
86 139 2.548875 CTCAATGAAGGCTCTTCGAGG 58.451 52.381 9.47 0.00 0.00 4.63
145 198 4.881019 AGGAGTTCCATCTATCCAATCG 57.119 45.455 0.28 0.00 38.89 3.34
172 225 1.301716 GGACAAAGTCTCGCCAGCA 60.302 57.895 0.00 0.00 32.47 4.41
175 228 1.006571 GACGGACAAAGTCTCGCCA 60.007 57.895 7.57 0.00 35.84 5.69
193 246 4.308458 TCCGGTGCCACAAGGACG 62.308 66.667 0.00 0.00 36.89 4.79
209 265 1.409427 CGGGAGGTCCTGATAAGTGTC 59.591 57.143 0.00 0.00 45.36 3.67
228 284 7.730364 ACCAAATATTCTTGTATAAGAGCCG 57.270 36.000 1.97 0.00 43.41 5.52
265 321 1.407258 GAATGGGAGTCGAGGTCTGAG 59.593 57.143 0.00 0.00 0.00 3.35
280 336 1.506262 CCGCAAAACCGAGGAATGG 59.494 57.895 0.00 0.00 0.00 3.16
284 340 2.281208 CACCCGCAAAACCGAGGA 60.281 61.111 0.00 0.00 0.00 3.71
297 353 0.912486 ATTGTAGCCACTCTCCACCC 59.088 55.000 0.00 0.00 0.00 4.61
298 354 1.471676 CGATTGTAGCCACTCTCCACC 60.472 57.143 0.00 0.00 0.00 4.61
431 520 3.786213 AGGGTCAAGATACCTCTTCCT 57.214 47.619 0.00 0.00 39.78 3.36
438 527 4.302559 ACTTCCAAAGGGTCAAGATACC 57.697 45.455 0.00 0.00 38.94 2.73
544 633 8.901793 AGCTTTTCATAAATCTTCATCTCTTCC 58.098 33.333 0.00 0.00 0.00 3.46
621 710 0.813184 CAGCTCGTTGCCCATTGATT 59.187 50.000 0.00 0.00 44.23 2.57
635 742 0.250467 TCAAACTCACCCTGCAGCTC 60.250 55.000 8.66 0.00 0.00 4.09
777 890 5.124457 TCCTTAAGCTTCTTGACAATGATGC 59.876 40.000 0.00 13.07 34.77 3.91
815 928 0.388649 CTGGTGACTTCCGAGTTCCG 60.389 60.000 0.00 0.00 35.88 4.30
820 2053 1.068588 TGTTGTCTGGTGACTTCCGAG 59.931 52.381 0.00 0.00 43.29 4.63
831 2064 3.125829 CGAGGTGAATCAATGTTGTCTGG 59.874 47.826 0.00 0.00 0.00 3.86
837 2191 3.254060 CTCGTCGAGGTGAATCAATGTT 58.746 45.455 14.68 0.00 0.00 2.71
906 2260 3.633609 CTGCAGGGGCTTGCTGCTA 62.634 63.158 5.57 0.00 44.38 3.49
937 2300 1.071605 GTAGCTTGCTTGTCCGACAG 58.928 55.000 0.00 0.00 0.00 3.51
960 2323 1.468520 CCTAATTCAGCCGTTGTGGTG 59.531 52.381 0.00 0.00 41.21 4.17
999 2395 3.342377 TCCTTTGCGTTGTGGATCATA 57.658 42.857 0.00 0.00 0.00 2.15
1073 2481 6.303054 TGATTTGGAACACCACTAGATTCAA 58.697 36.000 0.00 0.00 39.29 2.69
1081 2489 2.365293 GGCTTTGATTTGGAACACCACT 59.635 45.455 0.00 0.00 39.29 4.00
1084 2492 1.691434 TGGGCTTTGATTTGGAACACC 59.309 47.619 0.00 0.00 39.29 4.16
1125 2533 7.828717 TGCTTTATTTTGTCTATCATCTGACCA 59.171 33.333 0.00 0.00 32.67 4.02
1221 2650 7.127955 AGGGGACATTCATAACTATTGAACTCT 59.872 37.037 0.00 0.00 36.02 3.24
1224 2653 6.828785 ACAGGGGACATTCATAACTATTGAAC 59.171 38.462 0.00 0.00 36.02 3.18
1225 2654 6.969043 ACAGGGGACATTCATAACTATTGAA 58.031 36.000 0.00 0.00 37.49 2.69
1227 2656 7.645058 AAACAGGGGACATTCATAACTATTG 57.355 36.000 0.00 0.00 0.00 1.90
1255 2690 2.165030 CCATGGGCTCATCAACTTTGAC 59.835 50.000 2.85 0.00 40.49 3.18
1317 2755 0.446222 TTAAATCGGCGCTGCAGTTC 59.554 50.000 16.64 7.19 0.00 3.01
1355 2793 2.819984 TTTCGCCAGCTGGATGTCCC 62.820 60.000 37.21 16.18 37.39 4.46
1371 2809 5.466728 TCGCTGTGGATAGCAATATTCTTTC 59.533 40.000 0.00 0.00 43.87 2.62
1405 2849 3.647636 AGAGGCCAGCAAGAGAATAGTA 58.352 45.455 5.01 0.00 0.00 1.82
1436 2880 1.068434 GGCTAGTCAGATGGAGCACTC 59.932 57.143 0.00 0.00 36.63 3.51
1446 2890 2.222227 TCTTCTGCTGGCTAGTCAGA 57.778 50.000 28.34 16.30 36.93 3.27
1449 2893 3.533606 TGATTCTTCTGCTGGCTAGTC 57.466 47.619 0.00 0.00 0.00 2.59
1468 2912 0.400213 TGGGGGTTGTAGCTGTCTTG 59.600 55.000 0.00 0.00 0.00 3.02
1518 2962 7.459234 AGATCTTCATGCAGAATTCATATGGA 58.541 34.615 8.44 0.00 35.25 3.41
1571 3015 5.023452 TGAGTAACTCCTCATTGCTCCTTA 58.977 41.667 0.00 0.00 37.83 2.69
1624 3071 2.418976 CAGTGATGCTGGTGAGTGATTG 59.581 50.000 0.00 0.00 41.42 2.67
1630 3077 0.743701 GCCTCAGTGATGCTGGTGAG 60.744 60.000 12.62 0.00 45.08 3.51
1634 3081 0.738975 CATTGCCTCAGTGATGCTGG 59.261 55.000 19.34 6.84 45.08 4.85
1645 3092 5.470098 TGTAAGAGAACTTGAACATTGCCTC 59.530 40.000 0.00 0.00 37.53 4.70
1649 3096 6.943981 TCGTTGTAAGAGAACTTGAACATTG 58.056 36.000 0.00 0.00 37.53 2.82
1650 3097 7.657761 AGATCGTTGTAAGAGAACTTGAACATT 59.342 33.333 0.00 0.00 37.53 2.71
1770 3217 0.816825 CATGGGATGTCAGCCCTTCG 60.817 60.000 26.24 11.17 46.19 3.79
1786 3233 0.740737 GAACGGGCCCAATCTTCATG 59.259 55.000 24.92 3.98 0.00 3.07
1811 3258 2.964464 TCAAAACATGTGTTGGCCTGAT 59.036 40.909 25.17 0.00 38.44 2.90
1822 3269 6.347969 CGATCAATGAGTGAGTCAAAACATGT 60.348 38.462 0.00 0.00 40.43 3.21
1823 3270 6.019762 CGATCAATGAGTGAGTCAAAACATG 58.980 40.000 0.00 0.00 40.43 3.21
1834 3281 2.159379 CGAGACACCGATCAATGAGTGA 60.159 50.000 7.91 0.00 41.67 3.41
1845 3293 1.135199 GCAGGATAAACGAGACACCGA 60.135 52.381 0.00 0.00 0.00 4.69
1851 3299 5.070446 ACCAATATCAGCAGGATAAACGAGA 59.930 40.000 0.00 0.00 41.66 4.04
1880 3328 2.551270 TGCAGGTCTTTACATCTCCCT 58.449 47.619 0.00 0.00 0.00 4.20
1885 3333 6.763135 TCATCTACAATGCAGGTCTTTACATC 59.237 38.462 0.00 0.00 0.00 3.06
1912 3360 8.961293 ATGGTGGTAATGAATCCATGAATTAT 57.039 30.769 0.00 0.00 37.48 1.28
1945 3394 2.221055 GTGTCTCCACGATGTGTTGTTC 59.779 50.000 0.00 0.00 0.00 3.18
1988 3437 2.171870 TCGTTGAAAAGGGAGAAGTGGT 59.828 45.455 0.00 0.00 31.46 4.16
1999 3448 2.548480 GGAGTTGGAGGTCGTTGAAAAG 59.452 50.000 0.00 0.00 0.00 2.27
2010 3459 0.105039 GATAGCCACGGAGTTGGAGG 59.895 60.000 0.00 0.00 41.61 4.30
2111 3572 1.833787 GAGGTACTGCCGGTTCCCAA 61.834 60.000 1.90 0.00 41.55 4.12
2112 3573 2.203877 AGGTACTGCCGGTTCCCA 60.204 61.111 1.90 0.00 43.70 4.37
2113 3574 2.582978 GAGGTACTGCCGGTTCCC 59.417 66.667 1.90 0.00 41.55 3.97
2114 3575 2.582978 GGAGGTACTGCCGGTTCC 59.417 66.667 1.90 0.00 42.57 3.62
2131 3592 0.813184 ATCTTGCTGCAAATGTCCCG 59.187 50.000 16.74 2.93 0.00 5.14
2132 3593 1.820519 TCATCTTGCTGCAAATGTCCC 59.179 47.619 23.72 0.00 0.00 4.46
2139 3600 6.825213 ACTTGAGTAATATCATCTTGCTGCAA 59.175 34.615 15.16 15.16 0.00 4.08
2152 3613 9.815306 TCTTAGGCTCAGATACTTGAGTAATAT 57.185 33.333 0.00 0.00 45.07 1.28
2157 3618 4.336993 CGTCTTAGGCTCAGATACTTGAGT 59.663 45.833 1.07 0.00 45.07 3.41
2178 3639 4.038883 GGTAGCTGGGTAATATCTGTTCGT 59.961 45.833 0.00 0.00 0.00 3.85
2179 3640 4.281182 AGGTAGCTGGGTAATATCTGTTCG 59.719 45.833 0.00 0.00 0.00 3.95
2205 3666 4.080863 AGCTCGTGGAGGTTATTGATTTCT 60.081 41.667 0.00 0.00 37.04 2.52
2214 3675 2.054232 CCTCTAGCTCGTGGAGGTTA 57.946 55.000 13.49 0.00 46.68 2.85
2223 3684 4.035792 CGGATATCCAATACCTCTAGCTCG 59.964 50.000 21.70 0.00 35.14 5.03
2274 3735 4.037858 CTTCAACAGCAGGATATTTGCC 57.962 45.455 8.92 0.00 42.48 4.52
2343 3804 0.030908 GAATCCGACCACTAGAGCCG 59.969 60.000 0.00 0.00 0.00 5.52
2395 3856 3.874316 TGGCCTGGACATTAGATAGGAT 58.126 45.455 3.32 0.00 0.00 3.24
2517 3978 3.774766 ACTCATGTAGGCCACTGATTGTA 59.225 43.478 5.01 0.00 0.00 2.41
2559 4020 2.758979 GGCTACCAGAACACTAGCAGTA 59.241 50.000 0.00 0.00 35.63 2.74
2573 4034 0.323302 TTCGCTTGATGTGGCTACCA 59.677 50.000 0.00 0.00 0.00 3.25
2586 4071 2.678190 GCCATCTGGTAACTCTTCGCTT 60.678 50.000 0.00 0.00 37.57 4.68
2589 4074 2.672961 TGCCATCTGGTAACTCTTCG 57.327 50.000 0.00 0.00 37.57 3.79
2591 4076 3.019564 GCAATGCCATCTGGTAACTCTT 58.980 45.455 0.00 0.00 37.57 2.85
2650 4135 1.707989 TGTGGTTCCCCTGATGCTTAA 59.292 47.619 0.00 0.00 0.00 1.85
2679 4164 3.804036 TGTGAACAATGGAAGAAGACGT 58.196 40.909 0.00 0.00 0.00 4.34
2699 4184 6.238076 GGCAAGTTTGTTGTTATCACCTTTTG 60.238 38.462 0.00 0.00 0.00 2.44
2740 4225 1.303561 CTTGGCTTAGCTGGGTGCA 60.304 57.895 3.59 0.00 45.94 4.57
2747 4232 3.044156 TCCAGATCATCTTGGCTTAGCT 58.956 45.455 3.59 0.00 0.00 3.32
2751 4236 2.652590 GCTTCCAGATCATCTTGGCTT 58.347 47.619 0.00 0.00 0.00 4.35
2796 4281 0.473755 TGTGTTGGAGCCTGACACAT 59.526 50.000 18.67 0.00 46.09 3.21
2827 4312 2.553904 CCTTGAAGTTGAGCATGGTCCT 60.554 50.000 21.58 9.91 0.00 3.85
2828 4313 1.815003 CCTTGAAGTTGAGCATGGTCC 59.185 52.381 21.58 7.69 0.00 4.46
2830 4315 2.553904 CCTCCTTGAAGTTGAGCATGGT 60.554 50.000 0.00 0.00 32.75 3.55
2853 4338 2.223203 GCACTTGAGGCATCTGAATTCG 60.223 50.000 0.00 0.00 0.00 3.34
2900 4385 6.351286 GGCTGTTCCAACCTCAAAAATGATAT 60.351 38.462 0.00 0.00 34.01 1.63
2915 4403 0.183492 AAGCTCACAGGCTGTTCCAA 59.817 50.000 19.43 3.00 42.24 3.53
2920 4408 0.761187 TTCTCAAGCTCACAGGCTGT 59.239 50.000 15.88 15.88 42.24 4.40
2934 4422 5.299279 GGTGAAAGACAAAACCATCTTCTCA 59.701 40.000 0.00 0.00 34.01 3.27
2959 4447 7.334421 GTCAACTCCAGAAATAGAAACTATGCA 59.666 37.037 0.00 0.00 0.00 3.96
2966 4454 5.003804 GGCAGTCAACTCCAGAAATAGAAA 58.996 41.667 0.00 0.00 0.00 2.52
3006 4494 4.009675 TGAAGCTGTTGTTCAACTCAAGT 58.990 39.130 15.18 0.00 30.89 3.16
3028 4516 0.533755 GATGATAGCAACCTGCCGCT 60.534 55.000 0.00 0.00 46.52 5.52
3054 4542 3.119173 GCTTGGCTATTTGTGTGGCATTA 60.119 43.478 0.00 0.00 36.21 1.90
3129 4617 3.670055 CCAAACAGCGTAGATTTGCTTTG 59.330 43.478 0.00 0.00 40.03 2.77
3133 4621 2.584791 CACCAAACAGCGTAGATTTGC 58.415 47.619 0.00 0.00 32.98 3.68
3148 4636 1.490490 AGACTTGTCCAAGAGCACCAA 59.510 47.619 13.69 0.00 40.79 3.67
3233 4721 0.322816 ATGGCCGAGCAGTCAACAAT 60.323 50.000 0.00 0.00 0.00 2.71
3322 4810 4.508662 GAAGTTTGTGGATACTGGAGAGG 58.491 47.826 0.00 0.00 37.61 3.69
3406 4918 7.041848 AGGCTAAGCTTGTTTTTATGCTTTTTG 60.042 33.333 9.86 0.00 42.22 2.44
3437 4949 4.221924 GCCTTAAAGTTTCTGGCCCATAAA 59.778 41.667 16.56 0.00 37.81 1.40
3459 4971 3.679389 TGTTCATCTCCTTTTCCTCAGC 58.321 45.455 0.00 0.00 0.00 4.26
3465 4977 4.390297 CGTCCTCTTGTTCATCTCCTTTTC 59.610 45.833 0.00 0.00 0.00 2.29
3490 5056 4.063998 AGAGAATATTGCAGCATCGTCA 57.936 40.909 0.00 0.00 0.00 4.35
3616 5185 5.757886 TGTACAGCAGCAAGAAATTAACAC 58.242 37.500 0.00 0.00 0.00 3.32
3629 5199 4.929808 ACACATACTTAGTTGTACAGCAGC 59.070 41.667 12.54 0.00 0.00 5.25
3672 5278 1.002888 CCAGTCAGAGTCACAAGGCAT 59.997 52.381 0.00 0.00 0.00 4.40
3698 5305 6.889301 AATCCAAGCATAGATACAACCATG 57.111 37.500 0.00 0.00 0.00 3.66
3826 5458 6.549364 TCACAGAACCCAATCAAAACATACTT 59.451 34.615 0.00 0.00 0.00 2.24
3849 5486 4.081406 CCCACCAATTCATCTTTGAGTCA 58.919 43.478 0.00 0.00 32.27 3.41
3896 5561 1.093972 CAACGGATGCCTACATTGCA 58.906 50.000 0.00 0.00 43.97 4.08
3897 5562 3.924238 CAACGGATGCCTACATTGC 57.076 52.632 0.00 0.00 36.35 3.56
4004 5682 4.024725 GCAATCAGAAGATGCAGACAGATC 60.025 45.833 0.00 0.00 33.90 2.75
4061 5754 4.793216 CGCCAACATATAGCTGAAAACAAC 59.207 41.667 0.00 0.00 0.00 3.32
4074 5767 1.824230 ACCAAATGCACGCCAACATAT 59.176 42.857 0.00 0.00 0.00 1.78
4104 5801 3.913089 CCAGCAAACAATGGTAGAAACC 58.087 45.455 0.00 0.00 46.98 3.27
4146 5844 9.132521 CAAATCACCAACTTCATCATTAACTTC 57.867 33.333 0.00 0.00 0.00 3.01
4148 5846 7.605449 CCAAATCACCAACTTCATCATTAACT 58.395 34.615 0.00 0.00 0.00 2.24
4149 5847 6.311200 GCCAAATCACCAACTTCATCATTAAC 59.689 38.462 0.00 0.00 0.00 2.01
4151 5849 5.105392 GGCCAAATCACCAACTTCATCATTA 60.105 40.000 0.00 0.00 0.00 1.90
4152 5850 4.322953 GGCCAAATCACCAACTTCATCATT 60.323 41.667 0.00 0.00 0.00 2.57
4153 5851 3.196254 GGCCAAATCACCAACTTCATCAT 59.804 43.478 0.00 0.00 0.00 2.45
4154 5852 2.562298 GGCCAAATCACCAACTTCATCA 59.438 45.455 0.00 0.00 0.00 3.07
4155 5853 2.094026 GGGCCAAATCACCAACTTCATC 60.094 50.000 4.39 0.00 0.00 2.92
4156 5854 1.901833 GGGCCAAATCACCAACTTCAT 59.098 47.619 4.39 0.00 0.00 2.57
4157 5855 1.133199 AGGGCCAAATCACCAACTTCA 60.133 47.619 6.18 0.00 0.00 3.02
4158 5856 1.273327 CAGGGCCAAATCACCAACTTC 59.727 52.381 6.18 0.00 0.00 3.01
4159 5857 1.341080 CAGGGCCAAATCACCAACTT 58.659 50.000 6.18 0.00 0.00 2.66
4160 5858 1.187567 GCAGGGCCAAATCACCAACT 61.188 55.000 6.18 0.00 0.00 3.16
4161 5859 1.293179 GCAGGGCCAAATCACCAAC 59.707 57.895 6.18 0.00 0.00 3.77
4162 5860 0.762082 TTGCAGGGCCAAATCACCAA 60.762 50.000 6.18 0.00 0.00 3.67
4164 5862 1.593265 CTTGCAGGGCCAAATCACC 59.407 57.895 6.18 0.00 0.00 4.02
4166 5864 1.155859 ACCTTGCAGGGCCAAATCA 59.844 52.632 16.02 0.00 40.58 2.57
4168 5866 0.763986 AACACCTTGCAGGGCCAAAT 60.764 50.000 16.02 0.00 40.58 2.32
4169 5867 0.980231 AAACACCTTGCAGGGCCAAA 60.980 50.000 16.02 0.00 40.58 3.28
4171 5869 0.105964 TTAAACACCTTGCAGGGCCA 60.106 50.000 16.02 0.00 40.58 5.36
4172 5870 0.603065 CTTAAACACCTTGCAGGGCC 59.397 55.000 16.02 0.00 40.58 5.80
4174 5872 2.162681 CTCCTTAAACACCTTGCAGGG 58.837 52.381 14.35 14.35 40.58 4.45
4177 5875 3.649023 TCTACCTCCTTAAACACCTTGCA 59.351 43.478 0.00 0.00 0.00 4.08
4178 5876 4.281898 TCTACCTCCTTAAACACCTTGC 57.718 45.455 0.00 0.00 0.00 4.01
4180 5878 6.465464 GGAACTTCTACCTCCTTAAACACCTT 60.465 42.308 0.00 0.00 0.00 3.50
4181 5879 5.012871 GGAACTTCTACCTCCTTAAACACCT 59.987 44.000 0.00 0.00 0.00 4.00
4182 5880 5.012871 AGGAACTTCTACCTCCTTAAACACC 59.987 44.000 0.00 0.00 36.06 4.16
4183 5881 6.111669 AGGAACTTCTACCTCCTTAAACAC 57.888 41.667 0.00 0.00 36.06 3.32
4184 5882 5.047519 CGAGGAACTTCTACCTCCTTAAACA 60.048 44.000 0.00 0.00 46.87 2.83
4185 5883 5.409211 CGAGGAACTTCTACCTCCTTAAAC 58.591 45.833 0.00 0.00 46.87 2.01
4186 5884 4.465305 CCGAGGAACTTCTACCTCCTTAAA 59.535 45.833 0.00 0.00 46.87 1.52
4187 5885 4.021916 CCGAGGAACTTCTACCTCCTTAA 58.978 47.826 0.00 0.00 46.87 1.85
4189 5887 2.225318 ACCGAGGAACTTCTACCTCCTT 60.225 50.000 0.00 0.00 46.87 3.36
4190 5888 1.358445 ACCGAGGAACTTCTACCTCCT 59.642 52.381 0.00 0.00 46.87 3.69
4191 5889 1.849977 ACCGAGGAACTTCTACCTCC 58.150 55.000 0.00 0.00 46.87 4.30


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

AutoCloner maintained by Alex Coulton.