Multiple sequence alignment - TraesCS5A01G302500

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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 TraesCS5A01G302500 chr5A 100.000 3899 0 0 1 3899 512053104 512049206 0.000000e+00 7201.0
1 TraesCS5A01G302500 chr5D 94.470 2640 82 27 673 3274 406395560 406392947 0.000000e+00 4008.0
2 TraesCS5A01G302500 chr5D 82.353 714 78 23 1 677 406401721 406401019 9.390000e-161 577.0
3 TraesCS5A01G302500 chr5D 85.714 413 15 21 3308 3678 406392945 406392535 2.820000e-106 396.0
4 TraesCS5A01G302500 chr5D 87.705 122 12 3 2962 3081 410378301 410378181 5.250000e-29 139.0
5 TraesCS5A01G302500 chr5B 93.021 2794 110 39 673 3442 487346542 487343810 0.000000e+00 4000.0
6 TraesCS5A01G302500 chr5B 85.714 413 41 10 3438 3844 487342980 487342580 1.680000e-113 420.0
7 TraesCS5A01G302500 chr5B 80.745 483 47 17 198 680 487347137 487346701 6.240000e-88 335.0
8 TraesCS5A01G302500 chr5B 86.885 122 15 1 2961 3081 524558882 524558761 6.800000e-28 135.0
9 TraesCS5A01G302500 chr3D 86.224 1960 209 36 988 2899 613056905 613058851 0.000000e+00 2067.0
10 TraesCS5A01G302500 chr3D 88.235 119 13 1 2955 3072 66248262 66248380 1.460000e-29 141.0
11 TraesCS5A01G302500 chr3D 100.000 28 0 0 3714 3741 248217097 248217070 7.000000e-03 52.8
12 TraesCS5A01G302500 chr3B 88.159 1706 170 16 1226 2900 825994053 825992349 0.000000e+00 2002.0
13 TraesCS5A01G302500 chr3B 87.402 127 13 3 2951 3075 773147652 773147777 4.060000e-30 143.0
14 TraesCS5A01G302500 chr3A 88.007 1701 181 16 1224 2904 747723739 747725436 0.000000e+00 1989.0
15 TraesCS5A01G302500 chr1D 85.573 707 72 14 1409 2100 104593966 104594657 0.000000e+00 713.0
16 TraesCS5A01G302500 chr1D 82.540 315 44 9 1233 1543 440718648 440718955 2.310000e-67 267.0
17 TraesCS5A01G302500 chr1D 84.932 146 22 0 2478 2623 265986820 265986675 8.730000e-32 148.0
18 TraesCS5A01G302500 chr7D 84.411 526 76 6 2377 2899 555233265 555232743 2.690000e-141 512.0
19 TraesCS5A01G302500 chr7D 77.231 549 112 12 1723 2263 509631640 509631097 3.780000e-80 309.0
20 TraesCS5A01G302500 chr7D 82.258 310 48 6 1233 1540 599798852 599798548 1.070000e-65 261.0
21 TraesCS5A01G302500 chr7D 86.885 122 14 2 2961 3081 351664459 351664339 6.800000e-28 135.0
22 TraesCS5A01G302500 chr1A 76.050 714 140 29 1723 2419 537346917 537346218 3.730000e-90 342.0
23 TraesCS5A01G302500 chr1B 90.558 233 22 0 1179 1411 616824823 616825055 3.780000e-80 309.0
24 TraesCS5A01G302500 chr1B 91.011 178 16 0 2280 2457 616824819 616824642 1.400000e-59 241.0
25 TraesCS5A01G302500 chr1B 93.151 146 10 0 2313 2458 616963177 616963032 8.480000e-52 215.0
26 TraesCS5A01G302500 chr1B 88.535 157 15 2 2313 2468 616958867 616959021 1.850000e-43 187.0
27 TraesCS5A01G302500 chr7B 76.895 554 114 13 1719 2263 538052963 538052415 6.330000e-78 302.0
28 TraesCS5A01G302500 chr2A 89.381 113 11 1 2961 3072 326257918 326258030 1.460000e-29 141.0
29 TraesCS5A01G302500 chr2D 86.066 122 16 1 2961 3081 582558796 582558675 3.160000e-26 130.0


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 TraesCS5A01G302500 chr5A 512049206 512053104 3898 True 7201 7201 100.000000 1 3899 1 chr5A.!!$R1 3898
1 TraesCS5A01G302500 chr5D 406392535 406395560 3025 True 2202 4008 90.092000 673 3678 2 chr5D.!!$R3 3005
2 TraesCS5A01G302500 chr5D 406401019 406401721 702 True 577 577 82.353000 1 677 1 chr5D.!!$R1 676
3 TraesCS5A01G302500 chr5B 487342580 487347137 4557 True 1585 4000 86.493333 198 3844 3 chr5B.!!$R2 3646
4 TraesCS5A01G302500 chr3D 613056905 613058851 1946 False 2067 2067 86.224000 988 2899 1 chr3D.!!$F2 1911
5 TraesCS5A01G302500 chr3B 825992349 825994053 1704 True 2002 2002 88.159000 1226 2900 1 chr3B.!!$R1 1674
6 TraesCS5A01G302500 chr3A 747723739 747725436 1697 False 1989 1989 88.007000 1224 2904 1 chr3A.!!$F1 1680
7 TraesCS5A01G302500 chr1D 104593966 104594657 691 False 713 713 85.573000 1409 2100 1 chr1D.!!$F1 691
8 TraesCS5A01G302500 chr7D 555232743 555233265 522 True 512 512 84.411000 2377 2899 1 chr7D.!!$R3 522
9 TraesCS5A01G302500 chr7D 509631097 509631640 543 True 309 309 77.231000 1723 2263 1 chr7D.!!$R2 540
10 TraesCS5A01G302500 chr1A 537346218 537346917 699 True 342 342 76.050000 1723 2419 1 chr1A.!!$R1 696
11 TraesCS5A01G302500 chr7B 538052415 538052963 548 True 302 302 76.895000 1719 2263 1 chr7B.!!$R1 544

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
655 689 0.033781 AGGTTGGCGTTACGTTAGCA 59.966 50.0 6.63 0.0 0.0 3.49 F
808 1010 0.179081 GAGTCGGTTCCCCTGCATAC 60.179 60.0 0.00 0.0 0.0 2.39 F
912 1114 0.254299 AACCTCCCAATCCCATCCCT 60.254 55.0 0.00 0.0 0.0 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2652 2934 0.036732 ACTTCTTCTTGATGGCCGCA 59.963 50.000 0.0 0.0 0.0 5.69 R
2654 2936 1.394917 CGAACTTCTTCTTGATGGCCG 59.605 52.381 0.0 0.0 0.0 6.13 R
2926 3232 6.281405 ACCCTATCTGAGCAAACTAATAACG 58.719 40.000 0.0 0.0 0.0 3.18 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 8.463607 CCCAAAACAAGAAAGTTTACAGTAGAA 58.536 33.333 0.00 0.00 40.60 2.10
43 44 6.821616 ACAGTAGAATCCTTGGAGATCAAT 57.178 37.500 0.00 0.00 34.45 2.57
47 48 4.205587 AGAATCCTTGGAGATCAATGTGC 58.794 43.478 0.00 0.00 34.45 4.57
48 49 3.657398 ATCCTTGGAGATCAATGTGCA 57.343 42.857 0.00 0.00 34.45 4.57
49 50 3.657398 TCCTTGGAGATCAATGTGCAT 57.343 42.857 0.00 0.00 34.45 3.96
53 54 2.730382 TGGAGATCAATGTGCATTGCT 58.270 42.857 17.36 9.92 45.77 3.91
55 56 3.512329 TGGAGATCAATGTGCATTGCTTT 59.488 39.130 17.36 5.90 45.77 3.51
58 59 5.163581 GGAGATCAATGTGCATTGCTTTACT 60.164 40.000 17.36 11.86 45.77 2.24
59 60 5.647589 AGATCAATGTGCATTGCTTTACTG 58.352 37.500 17.36 1.64 45.77 2.74
61 62 4.797471 TCAATGTGCATTGCTTTACTGTC 58.203 39.130 17.36 0.00 45.77 3.51
72 73 3.008157 TGCTTTACTGTCGTCCCCAAATA 59.992 43.478 0.00 0.00 0.00 1.40
78 79 2.761208 CTGTCGTCCCCAAATAGACTCT 59.239 50.000 0.00 0.00 33.40 3.24
82 83 1.559682 GTCCCCAAATAGACTCTGCCA 59.440 52.381 0.00 0.00 0.00 4.92
84 85 1.561542 CCCCAAATAGACTCTGCCACT 59.438 52.381 0.00 0.00 0.00 4.00
85 86 2.771943 CCCCAAATAGACTCTGCCACTA 59.228 50.000 0.00 0.00 0.00 2.74
95 104 0.607217 TCTGCCACTAACGTCGGAGA 60.607 55.000 0.00 0.00 0.00 3.71
106 115 1.340211 ACGTCGGAGAGAGATGGAAGT 60.340 52.381 0.00 0.00 36.95 3.01
108 117 2.943690 CGTCGGAGAGAGATGGAAGTTA 59.056 50.000 0.00 0.00 36.95 2.24
112 121 2.362717 GGAGAGAGATGGAAGTTACCGG 59.637 54.545 0.00 0.00 0.00 5.28
125 134 1.755380 GTTACCGGCACACCTAGATCT 59.245 52.381 0.00 0.00 0.00 2.75
127 136 0.324368 ACCGGCACACCTAGATCTGA 60.324 55.000 5.18 0.00 0.00 3.27
129 138 1.207089 CCGGCACACCTAGATCTGAAA 59.793 52.381 5.18 0.00 0.00 2.69
146 155 4.705023 TCTGAAAGATCACCATCGTAGACA 59.295 41.667 0.00 0.00 37.47 3.41
149 158 6.227522 TGAAAGATCACCATCGTAGACAAAA 58.772 36.000 0.00 0.00 42.51 2.44
150 159 6.878923 TGAAAGATCACCATCGTAGACAAAAT 59.121 34.615 0.00 0.00 42.51 1.82
151 160 6.910536 AAGATCACCATCGTAGACAAAATC 57.089 37.500 0.00 0.00 42.51 2.17
152 161 5.360591 AGATCACCATCGTAGACAAAATCC 58.639 41.667 0.00 0.00 42.51 3.01
153 162 3.517602 TCACCATCGTAGACAAAATCCG 58.482 45.455 0.00 0.00 42.51 4.18
155 164 1.597663 CCATCGTAGACAAAATCCGCC 59.402 52.381 0.00 0.00 42.51 6.13
160 169 3.816523 TCGTAGACAAAATCCGCCTTTTT 59.183 39.130 0.00 0.00 0.00 1.94
190 199 0.167470 ACGGTCTATCACACACGACG 59.833 55.000 0.00 0.00 0.00 5.12
196 205 1.245376 TATCACACACGACGGAGCCA 61.245 55.000 0.00 0.00 0.00 4.75
204 238 1.143838 CGACGGAGCCAATCATCCA 59.856 57.895 0.00 0.00 35.14 3.41
223 257 1.206610 CATATCTCCGCCTGATCCCAG 59.793 57.143 0.00 0.00 40.09 4.45
227 261 4.473520 CCGCCTGATCCCAGCGTT 62.474 66.667 16.66 0.00 39.07 4.84
268 302 2.655685 GAGAAGATCGGCGTCGCC 60.656 66.667 26.69 26.69 46.75 5.54
316 350 2.037121 TCAAATCCTTCGCACACTCTGA 59.963 45.455 0.00 0.00 0.00 3.27
323 357 1.375140 CGCACACTCTGACATGGCT 60.375 57.895 0.00 0.00 0.00 4.75
327 361 0.109153 ACACTCTGACATGGCTGCAA 59.891 50.000 0.00 0.00 0.00 4.08
357 391 4.706842 ACTCAGGGTGACACTAAACATT 57.293 40.909 5.39 0.00 0.00 2.71
367 401 5.238650 GTGACACTAAACATTAGCCAACACT 59.761 40.000 0.00 0.00 0.00 3.55
381 415 3.151554 CCAACACTACCTAAAACCACCC 58.848 50.000 0.00 0.00 0.00 4.61
384 418 2.037641 ACACTACCTAAAACCACCCGAC 59.962 50.000 0.00 0.00 0.00 4.79
385 419 2.037511 CACTACCTAAAACCACCCGACA 59.962 50.000 0.00 0.00 0.00 4.35
413 447 0.534412 CATGAGACGAAGAGGCCACT 59.466 55.000 5.01 0.00 0.00 4.00
414 448 0.534412 ATGAGACGAAGAGGCCACTG 59.466 55.000 5.01 0.00 0.00 3.66
415 449 1.216710 GAGACGAAGAGGCCACTGG 59.783 63.158 5.01 2.36 0.00 4.00
441 475 6.161855 TCCTAGCATCGTTGATTAGAACAT 57.838 37.500 0.00 0.00 0.00 2.71
446 480 2.546778 TCGTTGATTAGAACATCGCCC 58.453 47.619 0.00 0.00 32.73 6.13
452 486 1.179152 TTAGAACATCGCCCGAGTGA 58.821 50.000 0.00 0.00 36.82 3.41
463 497 1.801178 GCCCGAGTGAGAAAGAAACAG 59.199 52.381 0.00 0.00 0.00 3.16
503 537 2.513666 GTCGATCCCGCCAATGCA 60.514 61.111 0.00 0.00 37.32 3.96
508 542 2.597117 GATCCCGCCAATGCAACACG 62.597 60.000 0.00 0.00 37.32 4.49
538 572 0.596082 CAAACCCCAACCTAGCAACG 59.404 55.000 0.00 0.00 0.00 4.10
606 640 3.001406 GGTAGACCCACGGCCACT 61.001 66.667 2.24 0.00 0.00 4.00
655 689 0.033781 AGGTTGGCGTTACGTTAGCA 59.966 50.000 6.63 0.00 0.00 3.49
670 704 4.023193 ACGTTAGCACCATCAAAAGAAAGG 60.023 41.667 0.00 0.00 0.00 3.11
690 890 1.944430 GCCTCCAGTTTCCCTGTAACG 60.944 57.143 0.00 0.00 39.74 3.18
777 979 9.111702 GAAGTACAACTTCGTAGTACTACAAAG 57.888 37.037 25.46 25.46 45.49 2.77
778 980 8.159344 AGTACAACTTCGTAGTACTACAAAGT 57.841 34.615 26.59 26.59 43.01 2.66
808 1010 0.179081 GAGTCGGTTCCCCTGCATAC 60.179 60.000 0.00 0.00 0.00 2.39
840 1042 1.964933 GGATCCCGGACTCTCTTAAGG 59.035 57.143 0.73 0.00 0.00 2.69
912 1114 0.254299 AACCTCCCAATCCCATCCCT 60.254 55.000 0.00 0.00 0.00 4.20
922 1124 2.525381 CCATCCCTCCCTCCTCCG 60.525 72.222 0.00 0.00 0.00 4.63
1063 1268 4.429212 TCGACACCGACATGCCCG 62.429 66.667 0.00 0.00 40.30 6.13
1064 1269 4.429212 CGACACCGACATGCCCGA 62.429 66.667 9.34 0.00 38.22 5.14
1065 1270 2.813908 GACACCGACATGCCCGAC 60.814 66.667 9.34 0.00 0.00 4.79
1788 2062 2.282958 TCCGACCTCGAGCACCTT 60.283 61.111 6.99 0.00 43.02 3.50
2277 2556 2.997897 GTGTCCTCCCTGGCGTCT 60.998 66.667 0.00 0.00 35.26 4.18
2337 2619 2.604686 AGCTCGGTGGAGAAGCCA 60.605 61.111 0.00 0.00 46.96 4.75
2652 2934 4.760047 GCGTGGGTGTCGGAGCAT 62.760 66.667 0.00 0.00 0.00 3.79
2654 2936 3.127533 GTGGGTGTCGGAGCATGC 61.128 66.667 10.51 10.51 0.00 4.06
2912 3218 3.444916 TCGACTGATAACCGATTTGCTC 58.555 45.455 0.00 0.00 0.00 4.26
2922 3228 1.466360 CCGATTTGCTCTGCCTTTTCG 60.466 52.381 0.00 0.00 0.00 3.46
2926 3232 0.951558 TTGCTCTGCCTTTTCGTTCC 59.048 50.000 0.00 0.00 0.00 3.62
2930 3236 2.409975 CTCTGCCTTTTCGTTCCGTTA 58.590 47.619 0.00 0.00 0.00 3.18
2931 3237 3.000727 CTCTGCCTTTTCGTTCCGTTAT 58.999 45.455 0.00 0.00 0.00 1.89
2933 3239 4.567971 TCTGCCTTTTCGTTCCGTTATTA 58.432 39.130 0.00 0.00 0.00 0.98
2934 3240 4.628333 TCTGCCTTTTCGTTCCGTTATTAG 59.372 41.667 0.00 0.00 0.00 1.73
2935 3241 4.317488 TGCCTTTTCGTTCCGTTATTAGT 58.683 39.130 0.00 0.00 0.00 2.24
2936 3242 4.756135 TGCCTTTTCGTTCCGTTATTAGTT 59.244 37.500 0.00 0.00 0.00 2.24
2938 3244 5.566395 GCCTTTTCGTTCCGTTATTAGTTTG 59.434 40.000 0.00 0.00 0.00 2.93
2941 3247 5.520022 TTCGTTCCGTTATTAGTTTGCTC 57.480 39.130 0.00 0.00 0.00 4.26
2942 3248 4.558178 TCGTTCCGTTATTAGTTTGCTCA 58.442 39.130 0.00 0.00 0.00 4.26
2943 3249 4.624024 TCGTTCCGTTATTAGTTTGCTCAG 59.376 41.667 0.00 0.00 0.00 3.35
2944 3250 4.624024 CGTTCCGTTATTAGTTTGCTCAGA 59.376 41.667 0.00 0.00 0.00 3.27
2945 3251 5.291128 CGTTCCGTTATTAGTTTGCTCAGAT 59.709 40.000 0.00 0.00 0.00 2.90
2946 3252 6.474427 CGTTCCGTTATTAGTTTGCTCAGATA 59.526 38.462 0.00 0.00 0.00 1.98
2948 3254 6.513180 TCCGTTATTAGTTTGCTCAGATAGG 58.487 40.000 0.00 0.00 0.00 2.57
2949 3255 5.696724 CCGTTATTAGTTTGCTCAGATAGGG 59.303 44.000 0.00 0.00 0.00 3.53
2950 3256 6.281405 CGTTATTAGTTTGCTCAGATAGGGT 58.719 40.000 0.00 0.00 0.00 4.34
2951 3257 7.431249 CGTTATTAGTTTGCTCAGATAGGGTA 58.569 38.462 0.00 0.00 0.00 3.69
2952 3258 8.088981 CGTTATTAGTTTGCTCAGATAGGGTAT 58.911 37.037 0.00 0.00 0.00 2.73
2955 3261 8.728596 ATTAGTTTGCTCAGATAGGGTATACT 57.271 34.615 2.25 0.00 0.00 2.12
2956 3262 9.824216 ATTAGTTTGCTCAGATAGGGTATACTA 57.176 33.333 2.25 0.00 0.00 1.82
2957 3263 7.768807 AGTTTGCTCAGATAGGGTATACTAG 57.231 40.000 2.25 0.00 0.00 2.57
2958 3264 6.722129 AGTTTGCTCAGATAGGGTATACTAGG 59.278 42.308 2.25 0.00 0.00 3.02
2959 3265 5.194473 TGCTCAGATAGGGTATACTAGGG 57.806 47.826 2.25 0.00 0.00 3.53
3005 3311 1.865865 ACGCGTGTGTTCTGAATCTT 58.134 45.000 12.93 0.00 0.00 2.40
3052 3358 6.039270 TCGTTTTGTCCTTCTGAATGAATTGT 59.961 34.615 0.00 0.00 33.71 2.71
3053 3359 6.142798 CGTTTTGTCCTTCTGAATGAATTGTG 59.857 38.462 0.00 0.00 33.71 3.33
3186 3510 7.570691 CGTTACAAGAATCTACTTCCACCAAAC 60.571 40.741 0.00 0.00 34.11 2.93
3191 3515 7.277174 AGAATCTACTTCCACCAAACAAAAG 57.723 36.000 0.00 0.00 34.11 2.27
3194 3518 3.245518 ACTTCCACCAAACAAAAGTGC 57.754 42.857 0.00 0.00 0.00 4.40
3270 3613 0.031721 GGCTGGCTGAAATGCATAGC 59.968 55.000 10.88 10.88 41.04 2.97
3272 3615 1.407979 GCTGGCTGAAATGCATAGCTT 59.592 47.619 17.25 0.94 39.71 3.74
3273 3616 2.543238 GCTGGCTGAAATGCATAGCTTC 60.543 50.000 17.25 10.52 39.71 3.86
3274 3617 2.686405 CTGGCTGAAATGCATAGCTTCA 59.314 45.455 17.25 14.07 37.58 3.02
3275 3618 2.424601 TGGCTGAAATGCATAGCTTCAC 59.575 45.455 17.25 10.21 37.58 3.18
3276 3619 2.223665 GGCTGAAATGCATAGCTTCACC 60.224 50.000 17.25 14.12 37.58 4.02
3277 3620 2.424601 GCTGAAATGCATAGCTTCACCA 59.575 45.455 11.87 0.00 34.70 4.17
3278 3621 3.119388 GCTGAAATGCATAGCTTCACCAA 60.119 43.478 11.87 0.00 34.70 3.67
3279 3622 4.618927 GCTGAAATGCATAGCTTCACCAAA 60.619 41.667 11.87 0.00 34.70 3.28
3280 3623 5.063180 TGAAATGCATAGCTTCACCAAAG 57.937 39.130 7.98 0.00 38.08 2.77
3281 3624 4.523943 TGAAATGCATAGCTTCACCAAAGT 59.476 37.500 7.98 0.00 37.31 2.66
3282 3625 4.445452 AATGCATAGCTTCACCAAAGTG 57.555 40.909 0.00 0.00 46.00 3.16
3283 3626 1.541147 TGCATAGCTTCACCAAAGTGC 59.459 47.619 0.00 0.00 44.16 4.40
3284 3627 1.541147 GCATAGCTTCACCAAAGTGCA 59.459 47.619 0.00 0.00 44.16 4.57
3285 3628 2.165030 GCATAGCTTCACCAAAGTGCAT 59.835 45.455 0.00 0.00 44.16 3.96
3286 3629 3.766151 CATAGCTTCACCAAAGTGCATG 58.234 45.455 0.00 0.00 44.16 4.06
3287 3630 1.696063 AGCTTCACCAAAGTGCATGT 58.304 45.000 0.00 0.00 44.16 3.21
3288 3631 2.862541 AGCTTCACCAAAGTGCATGTA 58.137 42.857 0.00 0.00 44.16 2.29
3289 3632 2.816087 AGCTTCACCAAAGTGCATGTAG 59.184 45.455 0.00 0.00 44.16 2.74
3290 3633 2.669391 GCTTCACCAAAGTGCATGTAGC 60.669 50.000 0.00 0.00 44.16 3.58
3291 3634 2.566833 TCACCAAAGTGCATGTAGCT 57.433 45.000 0.00 0.00 44.16 3.32
3292 3635 2.153645 TCACCAAAGTGCATGTAGCTG 58.846 47.619 0.00 0.00 44.16 4.24
3293 3636 1.881973 CACCAAAGTGCATGTAGCTGT 59.118 47.619 0.00 0.00 45.94 4.40
3294 3637 2.294233 CACCAAAGTGCATGTAGCTGTT 59.706 45.455 0.00 0.00 45.94 3.16
3295 3638 2.554032 ACCAAAGTGCATGTAGCTGTTC 59.446 45.455 0.00 0.00 45.94 3.18
3296 3639 2.095059 CCAAAGTGCATGTAGCTGTTCC 60.095 50.000 0.00 0.00 45.94 3.62
3297 3640 2.816087 CAAAGTGCATGTAGCTGTTCCT 59.184 45.455 0.00 0.00 45.94 3.36
3298 3641 3.981071 AAGTGCATGTAGCTGTTCCTA 57.019 42.857 0.00 0.00 45.94 2.94
3299 3642 4.494091 AAGTGCATGTAGCTGTTCCTAT 57.506 40.909 0.00 0.00 45.94 2.57
3300 3643 4.494091 AGTGCATGTAGCTGTTCCTATT 57.506 40.909 0.00 0.00 45.94 1.73
3301 3644 4.848357 AGTGCATGTAGCTGTTCCTATTT 58.152 39.130 0.00 0.00 45.94 1.40
3302 3645 4.637534 AGTGCATGTAGCTGTTCCTATTTG 59.362 41.667 0.00 0.00 45.94 2.32
3303 3646 4.396166 GTGCATGTAGCTGTTCCTATTTGT 59.604 41.667 0.00 0.00 45.94 2.83
3304 3647 5.584649 GTGCATGTAGCTGTTCCTATTTGTA 59.415 40.000 0.00 0.00 45.94 2.41
3305 3648 5.817296 TGCATGTAGCTGTTCCTATTTGTAG 59.183 40.000 0.00 0.00 45.94 2.74
3306 3649 5.277538 GCATGTAGCTGTTCCTATTTGTAGC 60.278 44.000 0.00 0.00 41.15 3.58
3314 3657 8.705594 AGCTGTTCCTATTTGTAGCTTCTATAA 58.294 33.333 0.00 0.00 38.24 0.98
3339 3682 4.809193 TCTCCTGAGGTATGAATGTAGCT 58.191 43.478 0.00 0.00 35.27 3.32
3355 3698 2.175878 AGCTGTTCACCACTCATGAC 57.824 50.000 0.00 0.00 0.00 3.06
3360 3703 0.475632 TTCACCACTCATGACCCCCT 60.476 55.000 0.00 0.00 0.00 4.79
3382 3725 2.553602 TCACCAAAGTGCAGCATTACAG 59.446 45.455 0.00 0.00 44.16 2.74
3384 3727 2.294233 ACCAAAGTGCAGCATTACAGTG 59.706 45.455 0.00 0.00 0.00 3.66
3653 4891 6.205658 ACTTGTTGCCTACATTCTTCTTCTTC 59.794 38.462 0.00 0.00 36.44 2.87
3658 4896 7.823745 TGCCTACATTCTTCTTCTTCTTTTT 57.176 32.000 0.00 0.00 0.00 1.94
3700 4938 6.991485 ATTTGTAGCTTGTTTGTTCATTCG 57.009 33.333 0.00 0.00 0.00 3.34
3707 4945 5.408604 AGCTTGTTTGTTCATTCGGTACTAG 59.591 40.000 0.00 0.00 0.00 2.57
3728 4966 6.949463 ACTAGCAAGGAATATACTACTCCCTC 59.051 42.308 0.00 0.00 0.00 4.30
3759 4997 1.016130 AGTTGACGCTCAAGCCGATG 61.016 55.000 0.00 0.00 37.00 3.84
3760 4998 1.005037 TTGACGCTCAAGCCGATGT 60.005 52.632 0.00 0.00 37.91 3.06
3769 5007 1.409064 TCAAGCCGATGTACCTAGCAG 59.591 52.381 0.00 0.00 0.00 4.24
3792 5030 8.374327 CAGTGAATCAATGCTAGATACATTCA 57.626 34.615 0.00 0.00 35.58 2.57
3818 5059 5.034797 TGAATCTATAGAGTCAAACGCACG 58.965 41.667 26.17 0.00 44.75 5.34
3825 5066 1.436606 GTCAAACGCACGCTTCGTC 60.437 57.895 0.00 0.00 38.32 4.20
3840 5081 3.730715 GCTTCGTCATTTTTCACTTGTGG 59.269 43.478 0.64 0.00 0.00 4.17
3844 5085 6.142818 TCGTCATTTTTCACTTGTGGAAAT 57.857 33.333 7.90 8.47 34.50 2.17
3845 5086 7.265647 TCGTCATTTTTCACTTGTGGAAATA 57.734 32.000 7.90 1.36 34.50 1.40
3846 5087 7.708051 TCGTCATTTTTCACTTGTGGAAATAA 58.292 30.769 7.90 0.00 34.50 1.40
3847 5088 7.646130 TCGTCATTTTTCACTTGTGGAAATAAC 59.354 33.333 7.90 7.16 34.50 1.89
3848 5089 7.357206 CGTCATTTTTCACTTGTGGAAATAACG 60.357 37.037 16.45 16.45 34.50 3.18
3849 5090 7.646130 GTCATTTTTCACTTGTGGAAATAACGA 59.354 33.333 7.90 1.41 34.50 3.85
3850 5091 8.191446 TCATTTTTCACTTGTGGAAATAACGAA 58.809 29.630 7.90 0.00 34.50 3.85
3851 5092 8.812329 CATTTTTCACTTGTGGAAATAACGAAA 58.188 29.630 7.90 0.00 34.50 3.46
3852 5093 8.758633 TTTTTCACTTGTGGAAATAACGAAAA 57.241 26.923 7.90 0.00 34.50 2.29
3853 5094 8.758633 TTTTCACTTGTGGAAATAACGAAAAA 57.241 26.923 3.31 0.00 34.50 1.94
3876 5117 8.560576 AAAAACATTTATCGTGTTGACTTGAG 57.439 30.769 0.00 0.00 39.57 3.02
3877 5118 6.861065 AACATTTATCGTGTTGACTTGAGT 57.139 33.333 0.00 0.00 38.31 3.41
3878 5119 6.861065 ACATTTATCGTGTTGACTTGAGTT 57.139 33.333 0.00 0.00 0.00 3.01
3879 5120 7.259290 ACATTTATCGTGTTGACTTGAGTTT 57.741 32.000 0.00 0.00 0.00 2.66
3880 5121 7.703328 ACATTTATCGTGTTGACTTGAGTTTT 58.297 30.769 0.00 0.00 0.00 2.43
3881 5122 8.832521 ACATTTATCGTGTTGACTTGAGTTTTA 58.167 29.630 0.00 0.00 0.00 1.52
3882 5123 9.658475 CATTTATCGTGTTGACTTGAGTTTTAA 57.342 29.630 0.00 0.00 0.00 1.52
3883 5124 9.659830 ATTTATCGTGTTGACTTGAGTTTTAAC 57.340 29.630 0.00 0.00 0.00 2.01
3884 5125 6.920569 ATCGTGTTGACTTGAGTTTTAACT 57.079 33.333 0.00 0.00 43.16 2.24
3885 5126 6.730960 TCGTGTTGACTTGAGTTTTAACTT 57.269 33.333 0.00 0.00 39.88 2.66
3886 5127 7.136289 TCGTGTTGACTTGAGTTTTAACTTT 57.864 32.000 0.00 0.00 39.88 2.66
3887 5128 7.586747 TCGTGTTGACTTGAGTTTTAACTTTT 58.413 30.769 0.00 0.00 39.88 2.27
3888 5129 8.719648 TCGTGTTGACTTGAGTTTTAACTTTTA 58.280 29.630 0.00 0.00 39.88 1.52
3889 5130 9.332301 CGTGTTGACTTGAGTTTTAACTTTTAA 57.668 29.630 0.00 0.00 39.88 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 7.556844 TGATCTCCAAGGATTCTACTGTAAAC 58.443 38.462 0.00 0.00 0.00 2.01
21 22 6.482641 CACATTGATCTCCAAGGATTCTACTG 59.517 42.308 0.00 0.00 38.74 2.74
28 29 3.657398 TGCACATTGATCTCCAAGGAT 57.343 42.857 0.00 0.00 38.74 3.24
43 44 2.217750 ACGACAGTAAAGCAATGCACA 58.782 42.857 8.35 0.00 0.00 4.57
47 48 1.737793 GGGGACGACAGTAAAGCAATG 59.262 52.381 0.00 0.00 0.00 2.82
48 49 1.349688 TGGGGACGACAGTAAAGCAAT 59.650 47.619 0.00 0.00 0.00 3.56
49 50 0.759959 TGGGGACGACAGTAAAGCAA 59.240 50.000 0.00 0.00 0.00 3.91
53 54 4.529377 AGTCTATTTGGGGACGACAGTAAA 59.471 41.667 0.00 0.00 37.52 2.01
55 56 3.698040 GAGTCTATTTGGGGACGACAGTA 59.302 47.826 0.00 0.00 37.52 2.74
58 59 2.496070 CAGAGTCTATTTGGGGACGACA 59.504 50.000 0.00 0.00 37.52 4.35
59 60 2.738964 GCAGAGTCTATTTGGGGACGAC 60.739 54.545 0.00 0.00 37.52 4.34
61 62 1.473434 GGCAGAGTCTATTTGGGGACG 60.473 57.143 0.00 0.00 37.52 4.79
72 73 0.522180 CGACGTTAGTGGCAGAGTCT 59.478 55.000 0.00 0.00 0.00 3.24
78 79 0.607217 TCTCTCCGACGTTAGTGGCA 60.607 55.000 0.00 0.00 0.00 4.92
82 83 2.093075 TCCATCTCTCTCCGACGTTAGT 60.093 50.000 0.00 0.00 0.00 2.24
84 85 2.704464 TCCATCTCTCTCCGACGTTA 57.296 50.000 0.00 0.00 0.00 3.18
85 86 1.746220 CTTCCATCTCTCTCCGACGTT 59.254 52.381 0.00 0.00 0.00 3.99
95 104 1.207329 GTGCCGGTAACTTCCATCTCT 59.793 52.381 1.90 0.00 0.00 3.10
106 115 1.754803 CAGATCTAGGTGTGCCGGTAA 59.245 52.381 1.90 0.00 40.50 2.85
108 117 0.324368 TCAGATCTAGGTGTGCCGGT 60.324 55.000 1.90 0.00 40.50 5.28
125 134 5.400066 TTGTCTACGATGGTGATCTTTCA 57.600 39.130 0.00 0.00 0.00 2.69
127 136 6.316390 GGATTTTGTCTACGATGGTGATCTTT 59.684 38.462 0.00 0.00 0.00 2.52
129 138 5.360591 GGATTTTGTCTACGATGGTGATCT 58.639 41.667 0.00 0.00 0.00 2.75
139 148 3.824414 AAAAGGCGGATTTTGTCTACG 57.176 42.857 0.00 0.00 31.30 3.51
153 162 2.515912 CGTTTCATCGGCTAAAAAGGC 58.484 47.619 0.00 0.00 0.00 4.35
174 183 1.794437 GCTCCGTCGTGTGTGATAGAC 60.794 57.143 0.00 0.00 0.00 2.59
176 185 0.525668 GGCTCCGTCGTGTGTGATAG 60.526 60.000 0.00 0.00 0.00 2.08
178 187 2.094757 TTGGCTCCGTCGTGTGTGAT 62.095 55.000 0.00 0.00 0.00 3.06
180 189 1.626654 GATTGGCTCCGTCGTGTGTG 61.627 60.000 0.00 0.00 0.00 3.82
181 190 1.374252 GATTGGCTCCGTCGTGTGT 60.374 57.895 0.00 0.00 0.00 3.72
190 199 3.681034 CGGAGATATGGATGATTGGCTCC 60.681 52.174 0.00 0.00 37.81 4.70
196 205 3.176411 TCAGGCGGAGATATGGATGATT 58.824 45.455 0.00 0.00 0.00 2.57
204 238 1.566211 CTGGGATCAGGCGGAGATAT 58.434 55.000 0.00 0.00 37.36 1.63
223 257 0.653636 TTGGTTGAAGTCGACAACGC 59.346 50.000 19.50 8.28 45.56 4.84
227 261 1.960417 TGCATTGGTTGAAGTCGACA 58.040 45.000 19.50 0.00 31.82 4.35
268 302 4.340019 TGCAAATGGCCGTGTGCG 62.340 61.111 30.58 7.16 43.89 5.34
275 309 4.067913 CGGGGTGTGCAAATGGCC 62.068 66.667 0.00 0.00 43.89 5.36
316 350 3.367743 CAGCGGTTGCAGCCATGT 61.368 61.111 20.42 0.00 46.23 3.21
338 372 4.564821 GGCTAATGTTTAGTGTCACCCTGA 60.565 45.833 0.00 0.00 0.00 3.86
357 391 4.505390 GGTGGTTTTAGGTAGTGTTGGCTA 60.505 45.833 0.00 0.00 0.00 3.93
367 401 1.000731 CGTGTCGGGTGGTTTTAGGTA 59.999 52.381 0.00 0.00 0.00 3.08
381 415 1.884464 CTCATGGGGCATCGTGTCG 60.884 63.158 0.00 0.00 0.00 4.35
384 418 1.884464 CGTCTCATGGGGCATCGTG 60.884 63.158 0.00 0.00 0.00 4.35
385 419 1.613317 TTCGTCTCATGGGGCATCGT 61.613 55.000 0.00 0.00 0.00 3.73
393 427 0.460987 GTGGCCTCTTCGTCTCATGG 60.461 60.000 3.32 0.00 0.00 3.66
426 460 2.546778 GGGCGATGTTCTAATCAACGA 58.453 47.619 0.00 0.00 34.04 3.85
430 464 1.754803 ACTCGGGCGATGTTCTAATCA 59.245 47.619 0.00 0.00 0.00 2.57
441 475 0.677288 TTTCTTTCTCACTCGGGCGA 59.323 50.000 0.00 0.00 0.00 5.54
446 480 1.801178 GCCCTGTTTCTTTCTCACTCG 59.199 52.381 0.00 0.00 0.00 4.18
452 486 6.498303 AGAATAATTTGGCCCTGTTTCTTTCT 59.502 34.615 0.00 0.00 0.00 2.52
463 497 1.268539 CGCGTGAGAATAATTTGGCCC 60.269 52.381 0.00 0.00 0.00 5.80
503 537 4.037089 GGGGTTTGTTTTCATAGACGTGTT 59.963 41.667 0.00 0.00 0.00 3.32
508 542 4.587262 AGGTTGGGGTTTGTTTTCATAGAC 59.413 41.667 0.00 0.00 0.00 2.59
577 611 0.248565 GGTCTACCCTTCCGGTTGTC 59.751 60.000 0.00 0.00 45.36 3.18
606 640 0.535335 CTTTCCCCATCTTCGTCGGA 59.465 55.000 0.00 0.00 0.00 4.55
655 689 2.158325 TGGAGGCCTTTCTTTTGATGGT 60.158 45.455 6.77 0.00 0.00 3.55
690 890 0.721718 CGTTTAGCACTACAGGCTGC 59.278 55.000 15.89 0.00 42.62 5.25
771 973 8.385898 ACCGACTCAAATATTTCAACTTTGTA 57.614 30.769 0.00 0.00 32.89 2.41
773 975 7.326063 GGAACCGACTCAAATATTTCAACTTTG 59.674 37.037 0.00 0.00 0.00 2.77
774 976 7.368059 GGAACCGACTCAAATATTTCAACTTT 58.632 34.615 0.00 0.00 0.00 2.66
775 977 6.072119 GGGAACCGACTCAAATATTTCAACTT 60.072 38.462 0.00 0.00 40.86 2.66
776 978 5.414765 GGGAACCGACTCAAATATTTCAACT 59.585 40.000 0.00 0.00 40.86 3.16
777 979 5.637809 GGGAACCGACTCAAATATTTCAAC 58.362 41.667 0.00 0.00 40.86 3.18
778 980 5.890424 GGGAACCGACTCAAATATTTCAA 57.110 39.130 0.00 0.00 40.86 2.69
808 1010 2.409870 GGGATCCTTTGTGGCTGCG 61.410 63.158 12.58 0.00 35.26 5.18
857 1059 1.738099 GCTCATATAGGCGTGCCGG 60.738 63.158 5.02 0.00 41.95 6.13
912 1114 0.471971 GGATTGGATCGGAGGAGGGA 60.472 60.000 0.00 0.00 0.00 4.20
922 1124 1.002544 GATCGAGGTGGGGATTGGATC 59.997 57.143 0.00 0.00 0.00 3.36
1602 1846 2.172419 CGCTTGTTGTTACGGCCG 59.828 61.111 26.86 26.86 0.00 6.13
1603 1847 2.559330 CCGCTTGTTGTTACGGCC 59.441 61.111 0.00 0.00 39.08 6.13
1606 1850 2.498887 GCGCCGCTTGTTGTTACG 60.499 61.111 0.00 0.00 0.00 3.18
1607 1851 1.440353 CAGCGCCGCTTGTTGTTAC 60.440 57.895 9.89 0.00 36.40 2.50
2133 2412 1.443194 GCGCACCTCGTCGTAGAAA 60.443 57.895 0.30 0.00 39.69 2.52
2652 2934 0.036732 ACTTCTTCTTGATGGCCGCA 59.963 50.000 0.00 0.00 0.00 5.69
2654 2936 1.394917 CGAACTTCTTCTTGATGGCCG 59.605 52.381 0.00 0.00 0.00 6.13
2922 3228 6.663944 ATCTGAGCAAACTAATAACGGAAC 57.336 37.500 0.00 0.00 0.00 3.62
2926 3232 6.281405 ACCCTATCTGAGCAAACTAATAACG 58.719 40.000 0.00 0.00 0.00 3.18
2930 3236 8.728596 AGTATACCCTATCTGAGCAAACTAAT 57.271 34.615 0.00 0.00 0.00 1.73
2931 3237 9.298250 CTAGTATACCCTATCTGAGCAAACTAA 57.702 37.037 0.00 0.00 0.00 2.24
2933 3239 6.722129 CCTAGTATACCCTATCTGAGCAAACT 59.278 42.308 0.00 0.00 0.00 2.66
2934 3240 6.071278 CCCTAGTATACCCTATCTGAGCAAAC 60.071 46.154 0.00 0.00 0.00 2.93
2935 3241 6.017192 CCCTAGTATACCCTATCTGAGCAAA 58.983 44.000 0.00 0.00 0.00 3.68
2936 3242 5.518546 CCCCTAGTATACCCTATCTGAGCAA 60.519 48.000 0.00 0.00 0.00 3.91
2938 3244 4.230041 TCCCCTAGTATACCCTATCTGAGC 59.770 50.000 0.00 0.00 0.00 4.26
2941 3247 7.423341 AGATTTCCCCTAGTATACCCTATCTG 58.577 42.308 0.00 0.00 0.00 2.90
2942 3248 7.469488 AGAGATTTCCCCTAGTATACCCTATCT 59.531 40.741 0.00 0.00 0.00 1.98
2943 3249 7.654452 AGAGATTTCCCCTAGTATACCCTATC 58.346 42.308 0.00 0.00 0.00 2.08
2944 3250 7.469488 AGAGAGATTTCCCCTAGTATACCCTAT 59.531 40.741 0.00 0.00 0.00 2.57
2945 3251 6.803691 AGAGAGATTTCCCCTAGTATACCCTA 59.196 42.308 0.00 0.00 0.00 3.53
2946 3252 5.622204 AGAGAGATTTCCCCTAGTATACCCT 59.378 44.000 0.00 0.00 0.00 4.34
2948 3254 6.553857 TCAGAGAGATTTCCCCTAGTATACC 58.446 44.000 0.00 0.00 0.00 2.73
2949 3255 7.309560 GCTTCAGAGAGATTTCCCCTAGTATAC 60.310 44.444 0.00 0.00 0.00 1.47
2950 3256 6.722129 GCTTCAGAGAGATTTCCCCTAGTATA 59.278 42.308 0.00 0.00 0.00 1.47
2951 3257 5.542251 GCTTCAGAGAGATTTCCCCTAGTAT 59.458 44.000 0.00 0.00 0.00 2.12
2952 3258 4.896482 GCTTCAGAGAGATTTCCCCTAGTA 59.104 45.833 0.00 0.00 0.00 1.82
2953 3259 3.709141 GCTTCAGAGAGATTTCCCCTAGT 59.291 47.826 0.00 0.00 0.00 2.57
2954 3260 3.966665 AGCTTCAGAGAGATTTCCCCTAG 59.033 47.826 0.00 0.00 0.00 3.02
2955 3261 3.708631 CAGCTTCAGAGAGATTTCCCCTA 59.291 47.826 0.00 0.00 0.00 3.53
2956 3262 2.504996 CAGCTTCAGAGAGATTTCCCCT 59.495 50.000 0.00 0.00 0.00 4.79
2957 3263 2.238395 ACAGCTTCAGAGAGATTTCCCC 59.762 50.000 0.00 0.00 0.00 4.81
2958 3264 3.055530 TCACAGCTTCAGAGAGATTTCCC 60.056 47.826 0.00 0.00 0.00 3.97
2959 3265 4.199432 TCACAGCTTCAGAGAGATTTCC 57.801 45.455 0.00 0.00 0.00 3.13
3005 3311 8.722480 ACGATATTTCATTCATTCAGTTCAGA 57.278 30.769 0.00 0.00 0.00 3.27
3025 3331 7.921786 ATTCATTCAGAAGGACAAAACGATA 57.078 32.000 0.00 0.00 40.15 2.92
3052 3358 3.081061 AGTTCAAACAGTCACAAGCACA 58.919 40.909 0.00 0.00 0.00 4.57
3053 3359 3.119849 ACAGTTCAAACAGTCACAAGCAC 60.120 43.478 0.00 0.00 0.00 4.40
3077 3387 8.800370 TGTAACTGAAGAATAACCATGCAATA 57.200 30.769 0.00 0.00 0.00 1.90
3156 3479 6.527372 GTGGAAGTAGATTCTTGTAACGTCTC 59.473 42.308 0.00 0.00 38.07 3.36
3160 3483 5.475719 TGGTGGAAGTAGATTCTTGTAACG 58.524 41.667 0.00 0.00 38.07 3.18
3186 3510 7.254084 GGTCTAAAATCAACAGTTGCACTTTTG 60.254 37.037 20.23 14.50 37.27 2.44
3191 3515 5.438761 AGGTCTAAAATCAACAGTTGCAC 57.561 39.130 8.58 0.00 0.00 4.57
3194 3518 6.633500 TTGGAGGTCTAAAATCAACAGTTG 57.367 37.500 6.99 6.99 0.00 3.16
3207 3531 9.308000 ACAAAACATAATCATTTTGGAGGTCTA 57.692 29.630 12.56 0.00 45.80 2.59
3239 3582 2.040278 TCAGCCAGCCAGAATACAAAGT 59.960 45.455 0.00 0.00 0.00 2.66
3240 3583 2.715046 TCAGCCAGCCAGAATACAAAG 58.285 47.619 0.00 0.00 0.00 2.77
3270 3613 2.816087 AGCTACATGCACTTTGGTGAAG 59.184 45.455 0.00 0.00 45.61 3.02
3272 3615 2.153645 CAGCTACATGCACTTTGGTGA 58.846 47.619 0.00 0.00 45.61 4.02
3273 3616 1.881973 ACAGCTACATGCACTTTGGTG 59.118 47.619 0.00 0.00 45.94 4.17
3274 3617 2.276732 ACAGCTACATGCACTTTGGT 57.723 45.000 0.00 0.00 45.94 3.67
3275 3618 2.095059 GGAACAGCTACATGCACTTTGG 60.095 50.000 0.00 0.00 45.94 3.28
3276 3619 2.816087 AGGAACAGCTACATGCACTTTG 59.184 45.455 0.00 0.00 45.94 2.77
3277 3620 3.146104 AGGAACAGCTACATGCACTTT 57.854 42.857 0.00 0.00 45.94 2.66
3278 3621 2.867109 AGGAACAGCTACATGCACTT 57.133 45.000 0.00 0.00 45.94 3.16
3279 3622 4.494091 AATAGGAACAGCTACATGCACT 57.506 40.909 0.00 0.00 45.94 4.40
3280 3623 4.396166 ACAAATAGGAACAGCTACATGCAC 59.604 41.667 0.00 0.00 45.94 4.57
3281 3624 4.588899 ACAAATAGGAACAGCTACATGCA 58.411 39.130 0.00 0.00 45.94 3.96
3282 3625 5.277538 GCTACAAATAGGAACAGCTACATGC 60.278 44.000 0.00 0.00 43.29 4.06
3283 3626 6.051717 AGCTACAAATAGGAACAGCTACATG 58.948 40.000 0.00 0.00 37.58 3.21
3284 3627 6.240549 AGCTACAAATAGGAACAGCTACAT 57.759 37.500 0.00 0.00 37.58 2.29
3285 3628 5.677319 AGCTACAAATAGGAACAGCTACA 57.323 39.130 0.00 0.00 37.58 2.74
3286 3629 6.342111 AGAAGCTACAAATAGGAACAGCTAC 58.658 40.000 0.00 0.00 38.36 3.58
3287 3630 6.546428 AGAAGCTACAAATAGGAACAGCTA 57.454 37.500 0.00 0.00 38.36 3.32
3288 3631 5.428184 AGAAGCTACAAATAGGAACAGCT 57.572 39.130 0.00 0.00 40.94 4.24
3289 3632 8.766151 GTTATAGAAGCTACAAATAGGAACAGC 58.234 37.037 0.00 0.00 0.00 4.40
3295 3638 9.699703 GGAGAAGTTATAGAAGCTACAAATAGG 57.300 37.037 0.00 0.00 0.00 2.57
3298 3641 8.982723 TCAGGAGAAGTTATAGAAGCTACAAAT 58.017 33.333 0.00 0.00 0.00 2.32
3299 3642 8.362464 TCAGGAGAAGTTATAGAAGCTACAAA 57.638 34.615 0.00 0.00 0.00 2.83
3300 3643 7.068839 CCTCAGGAGAAGTTATAGAAGCTACAA 59.931 40.741 0.00 0.00 0.00 2.41
3301 3644 6.547880 CCTCAGGAGAAGTTATAGAAGCTACA 59.452 42.308 0.00 0.00 0.00 2.74
3302 3645 6.548251 ACCTCAGGAGAAGTTATAGAAGCTAC 59.452 42.308 0.00 0.00 0.00 3.58
3303 3646 6.674573 ACCTCAGGAGAAGTTATAGAAGCTA 58.325 40.000 0.00 0.00 0.00 3.32
3304 3647 5.524535 ACCTCAGGAGAAGTTATAGAAGCT 58.475 41.667 0.00 0.00 0.00 3.74
3305 3648 5.862678 ACCTCAGGAGAAGTTATAGAAGC 57.137 43.478 0.00 0.00 0.00 3.86
3306 3649 8.698973 TCATACCTCAGGAGAAGTTATAGAAG 57.301 38.462 0.00 0.00 0.00 2.85
3314 3657 5.069781 GCTACATTCATACCTCAGGAGAAGT 59.930 44.000 0.00 2.43 0.00 3.01
3339 3682 0.400213 GGGGTCATGAGTGGTGAACA 59.600 55.000 0.00 0.00 34.99 3.18
3355 3698 1.152567 TGCACTTTGGTGAAGGGGG 60.153 57.895 0.00 0.00 45.61 5.40
3360 3703 2.954989 TGTAATGCTGCACTTTGGTGAA 59.045 40.909 3.57 0.00 45.61 3.18
3382 3725 9.599322 CATCTACATTTTTCTTGTTACAGACAC 57.401 33.333 0.00 0.00 38.18 3.67
3384 3727 8.999431 TCCATCTACATTTTTCTTGTTACAGAC 58.001 33.333 0.00 0.00 0.00 3.51
3463 4669 3.219281 GCAATTGTAACGGGGTGGATAT 58.781 45.455 7.40 0.00 0.00 1.63
3602 4815 5.995282 TCATGTTGAGTACGGAGAAAACAAT 59.005 36.000 0.00 0.00 31.90 2.71
3658 4896 3.627041 ATAGGATGGCCTGAGAGAGAA 57.373 47.619 3.32 0.00 46.45 2.87
3669 4907 5.105756 ACAAACAAGCTACAAATAGGATGGC 60.106 40.000 0.00 0.00 0.00 4.40
3700 4938 7.122501 GGGAGTAGTATATTCCTTGCTAGTACC 59.877 44.444 0.00 0.00 45.88 3.34
3707 4945 4.082136 CGGAGGGAGTAGTATATTCCTTGC 60.082 50.000 0.00 0.00 45.88 4.01
3728 4966 2.486951 CGTCAACTAGTATGGGACGG 57.513 55.000 21.70 10.41 45.36 4.79
3759 4997 4.446371 AGCATTGATTCACTGCTAGGTAC 58.554 43.478 24.92 0.00 45.91 3.34
3760 4998 4.760530 AGCATTGATTCACTGCTAGGTA 57.239 40.909 24.92 0.00 45.91 3.08
3769 5007 9.217278 AGATGAATGTATCTAGCATTGATTCAC 57.783 33.333 0.00 0.00 36.77 3.18
3790 5028 7.142021 GCGTTTGACTCTATAGATTCAGATGA 58.858 38.462 25.07 10.80 35.59 2.92
3792 5030 6.920758 GTGCGTTTGACTCTATAGATTCAGAT 59.079 38.462 18.81 0.00 35.59 2.90
3807 5048 1.436606 GACGAAGCGTGCGTTTGAC 60.437 57.895 0.00 0.00 41.37 3.18
3813 5054 0.967803 GAAAAATGACGAAGCGTGCG 59.032 50.000 0.00 0.00 41.37 5.34
3818 5059 3.730715 CCACAAGTGAAAAATGACGAAGC 59.269 43.478 0.94 0.00 0.00 3.86
3825 5066 7.922505 TCGTTATTTCCACAAGTGAAAAATG 57.077 32.000 16.72 10.87 32.26 2.32
3851 5092 8.188139 ACTCAAGTCAACACGATAAATGTTTTT 58.812 29.630 0.00 0.00 38.22 1.94
3852 5093 7.703328 ACTCAAGTCAACACGATAAATGTTTT 58.297 30.769 0.00 0.00 38.22 2.43
3853 5094 7.259290 ACTCAAGTCAACACGATAAATGTTT 57.741 32.000 0.00 0.00 38.22 2.83
3854 5095 6.861065 ACTCAAGTCAACACGATAAATGTT 57.139 33.333 0.00 0.00 40.95 2.71
3855 5096 6.861065 AACTCAAGTCAACACGATAAATGT 57.139 33.333 0.00 0.00 0.00 2.71
3856 5097 9.658475 TTAAAACTCAAGTCAACACGATAAATG 57.342 29.630 0.00 0.00 0.00 2.32
3857 5098 9.659830 GTTAAAACTCAAGTCAACACGATAAAT 57.340 29.630 0.00 0.00 0.00 1.40
3858 5099 8.885722 AGTTAAAACTCAAGTCAACACGATAAA 58.114 29.630 0.00 0.00 32.86 1.40
3859 5100 8.428186 AGTTAAAACTCAAGTCAACACGATAA 57.572 30.769 0.00 0.00 32.86 1.75
3860 5101 8.428186 AAGTTAAAACTCAAGTCAACACGATA 57.572 30.769 0.00 0.00 38.57 2.92
3861 5102 6.920569 AGTTAAAACTCAAGTCAACACGAT 57.079 33.333 0.00 0.00 32.86 3.73
3862 5103 6.730960 AAGTTAAAACTCAAGTCAACACGA 57.269 33.333 0.00 0.00 38.57 4.35
3863 5104 7.790861 AAAAGTTAAAACTCAAGTCAACACG 57.209 32.000 0.00 0.00 38.57 4.49


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

AutoCloner maintained by Alex Coulton.