Multiple sequence alignment - TraesCS6A01G013200

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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 TraesCS6A01G013200 chr6A 100.000 4870 0 0 1 4870 6189121 6193990 0.000000e+00 8994.0
1 TraesCS6A01G013200 chr6D 90.218 4181 226 73 7 4121 6575390 6571327 0.000000e+00 5286.0
2 TraesCS6A01G013200 chr6D 95.883 753 28 1 4118 4870 388409337 388408588 0.000000e+00 1216.0
3 TraesCS6A01G013200 chr6B 91.172 1903 81 38 2241 4101 12117618 12115761 0.000000e+00 2503.0
4 TraesCS6A01G013200 chr6B 86.555 2142 143 70 108 2189 12119681 12117625 0.000000e+00 2226.0
5 TraesCS6A01G013200 chr2A 98.535 751 11 0 4120 4870 710091046 710090296 0.000000e+00 1327.0
6 TraesCS6A01G013200 chr7A 98.011 754 15 0 4117 4870 576888864 576888111 0.000000e+00 1310.0
7 TraesCS6A01G013200 chr3A 96.804 751 24 0 4120 4870 12834521 12833771 0.000000e+00 1254.0
8 TraesCS6A01G013200 chr3D 96.414 753 26 1 4118 4870 407386740 407385989 0.000000e+00 1240.0
9 TraesCS6A01G013200 chr5A 96.405 751 27 0 4120 4870 644019665 644020415 0.000000e+00 1238.0
10 TraesCS6A01G013200 chr5A 95.883 753 31 0 4118 4870 698066026 698065274 0.000000e+00 1219.0
11 TraesCS6A01G013200 chr5B 95.872 751 31 0 4120 4870 558340694 558339944 0.000000e+00 1216.0
12 TraesCS6A01G013200 chr1B 95.623 754 33 0 4117 4870 200901543 200902296 0.000000e+00 1210.0
13 TraesCS6A01G013200 chr1B 83.295 437 52 12 3320 3738 457954775 457954342 2.750000e-102 383.0
14 TraesCS6A01G013200 chr1B 79.348 276 48 7 3280 3552 365021480 365021749 8.320000e-43 185.0
15 TraesCS6A01G013200 chr1B 94.340 53 0 3 2367 2419 458005518 458005469 1.450000e-10 78.7
16 TraesCS6A01G013200 chr1D 83.472 599 53 24 3317 3871 342121197 342120601 2.600000e-142 516.0
17 TraesCS6A01G013200 chr1D 77.673 318 59 10 3280 3594 231465068 231464760 2.990000e-42 183.0
18 TraesCS6A01G013200 chr1D 94.340 53 0 3 2367 2419 342121718 342121669 1.450000e-10 78.7
19 TraesCS6A01G013200 chr1A 83.473 357 41 12 3373 3711 441794158 441793802 2.830000e-82 316.0
20 TraesCS6A01G013200 chr1A 77.287 317 62 8 3280 3594 317813383 317813691 1.390000e-40 178.0
21 TraesCS6A01G013200 chr1A 92.453 53 1 3 2367 2419 441797332 441797283 6.760000e-09 73.1
22 TraesCS6A01G013200 chr2D 77.778 279 53 8 3277 3552 492509718 492509446 3.900000e-36 163.0


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 TraesCS6A01G013200 chr6A 6189121 6193990 4869 False 8994.00 8994 100.0000 1 4870 1 chr6A.!!$F1 4869
1 TraesCS6A01G013200 chr6D 6571327 6575390 4063 True 5286.00 5286 90.2180 7 4121 1 chr6D.!!$R1 4114
2 TraesCS6A01G013200 chr6D 388408588 388409337 749 True 1216.00 1216 95.8830 4118 4870 1 chr6D.!!$R2 752
3 TraesCS6A01G013200 chr6B 12115761 12119681 3920 True 2364.50 2503 88.8635 108 4101 2 chr6B.!!$R1 3993
4 TraesCS6A01G013200 chr2A 710090296 710091046 750 True 1327.00 1327 98.5350 4120 4870 1 chr2A.!!$R1 750
5 TraesCS6A01G013200 chr7A 576888111 576888864 753 True 1310.00 1310 98.0110 4117 4870 1 chr7A.!!$R1 753
6 TraesCS6A01G013200 chr3A 12833771 12834521 750 True 1254.00 1254 96.8040 4120 4870 1 chr3A.!!$R1 750
7 TraesCS6A01G013200 chr3D 407385989 407386740 751 True 1240.00 1240 96.4140 4118 4870 1 chr3D.!!$R1 752
8 TraesCS6A01G013200 chr5A 644019665 644020415 750 False 1238.00 1238 96.4050 4120 4870 1 chr5A.!!$F1 750
9 TraesCS6A01G013200 chr5A 698065274 698066026 752 True 1219.00 1219 95.8830 4118 4870 1 chr5A.!!$R1 752
10 TraesCS6A01G013200 chr5B 558339944 558340694 750 True 1216.00 1216 95.8720 4120 4870 1 chr5B.!!$R1 750
11 TraesCS6A01G013200 chr1B 200901543 200902296 753 False 1210.00 1210 95.6230 4117 4870 1 chr1B.!!$F1 753
12 TraesCS6A01G013200 chr1D 342120601 342121718 1117 True 297.35 516 88.9060 2367 3871 2 chr1D.!!$R2 1504

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
137 140 0.169672 TGACTGCTAACTACCGCGAC 59.830 55.0 8.23 0.0 0.00 5.19 F
1869 1980 0.099436 GCACATGTCAATTCCTCCGC 59.901 55.0 0.00 0.0 0.00 5.54 F
2228 2341 0.166814 GTTTCCTGCTGCTAGTTGCG 59.833 55.0 0.00 0.0 46.63 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2080 2191 0.396556 AAAGTTGGGCGGTCTTTGGT 60.397 50.0 0.0 0.0 31.47 3.67 R
2762 3046 0.388649 CCGAAGTCTCCGAGGTGTTG 60.389 60.0 0.0 0.0 0.00 3.33 R
3904 4276 0.521735 CGCCGATCGATCATGTCCTA 59.478 55.0 24.4 0.0 41.67 2.94 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
25 26 1.945394 CTTTCCCATCATGGAGAAGCG 59.055 52.381 4.75 0.00 40.96 4.68
60 63 4.212214 GGAGCTCGTCCTTTTGCATTATAG 59.788 45.833 7.83 0.00 42.99 1.31
68 71 6.293626 CGTCCTTTTGCATTATAGGAAGATGG 60.294 42.308 11.63 0.00 38.17 3.51
88 91 5.682943 TGGGACATTCTTTGTAAAGTTCG 57.317 39.130 4.45 0.00 39.18 3.95
102 105 7.925703 TGTAAAGTTCGAAAAACAAAACACA 57.074 28.000 0.00 0.00 0.00 3.72
106 109 7.644986 AAGTTCGAAAAACAAAACACATGAA 57.355 28.000 0.00 0.00 0.00 2.57
122 125 8.677148 AACACATGAAAACTACATTAGTGACT 57.323 30.769 0.00 0.00 39.39 3.41
123 126 8.087982 ACACATGAAAACTACATTAGTGACTG 57.912 34.615 0.00 0.00 39.39 3.51
124 127 7.017645 CACATGAAAACTACATTAGTGACTGC 58.982 38.462 0.00 0.00 39.39 4.40
133 136 4.995124 ACATTAGTGACTGCTAACTACCG 58.005 43.478 0.00 0.00 34.25 4.02
135 138 0.170561 AGTGACTGCTAACTACCGCG 59.829 55.000 0.00 0.00 0.00 6.46
137 140 0.169672 TGACTGCTAACTACCGCGAC 59.830 55.000 8.23 0.00 0.00 5.19
169 175 0.537143 AAGGTTGCACAGAATCGCCA 60.537 50.000 0.00 0.00 0.00 5.69
174 180 1.349627 GCACAGAATCGCCATCACG 59.650 57.895 0.00 0.00 0.00 4.35
198 204 0.909623 ACGCCCAATACCTAGCAACT 59.090 50.000 0.00 0.00 0.00 3.16
209 215 1.927174 CCTAGCAACTCCGATTTCACG 59.073 52.381 0.00 0.00 0.00 4.35
223 229 6.087522 CCGATTTCACGGCAATTAAAAGTTA 58.912 36.000 0.00 0.00 46.20 2.24
224 230 6.250527 CCGATTTCACGGCAATTAAAAGTTAG 59.749 38.462 0.00 0.00 46.20 2.34
225 231 6.799925 CGATTTCACGGCAATTAAAAGTTAGT 59.200 34.615 0.00 0.00 0.00 2.24
227 233 6.621316 TTCACGGCAATTAAAAGTTAGTGA 57.379 33.333 0.00 0.00 34.78 3.41
228 234 6.621316 TCACGGCAATTAAAAGTTAGTGAA 57.379 33.333 0.00 0.00 33.85 3.18
229 235 6.664515 TCACGGCAATTAAAAGTTAGTGAAG 58.335 36.000 0.00 0.00 33.85 3.02
230 236 6.483974 TCACGGCAATTAAAAGTTAGTGAAGA 59.516 34.615 0.00 0.00 33.85 2.87
231 237 7.012515 TCACGGCAATTAAAAGTTAGTGAAGAA 59.987 33.333 0.00 0.00 33.85 2.52
232 238 7.807907 CACGGCAATTAAAAGTTAGTGAAGAAT 59.192 33.333 0.00 0.00 0.00 2.40
233 239 9.005777 ACGGCAATTAAAAGTTAGTGAAGAATA 57.994 29.630 0.00 0.00 0.00 1.75
234 240 9.834628 CGGCAATTAAAAGTTAGTGAAGAATAA 57.165 29.630 0.00 0.00 0.00 1.40
243 249 9.569122 AAAGTTAGTGAAGAATAAGTAAAGCCA 57.431 29.630 0.00 0.00 0.00 4.75
249 255 7.015877 GTGAAGAATAAGTAAAGCCAAGTTCG 58.984 38.462 0.00 0.00 0.00 3.95
254 260 3.102052 AGTAAAGCCAAGTTCGAACGA 57.898 42.857 21.87 0.00 0.00 3.85
256 262 2.969443 AAAGCCAAGTTCGAACGATG 57.031 45.000 21.87 22.24 0.00 3.84
261 267 2.668279 GCCAAGTTCGAACGATGCAAAT 60.668 45.455 21.87 0.00 0.00 2.32
265 271 3.009723 AGTTCGAACGATGCAAATCCAT 58.990 40.909 21.87 0.00 0.00 3.41
269 275 2.347939 CGAACGATGCAAATCCATCTCG 60.348 50.000 0.00 0.00 39.51 4.04
271 277 2.477825 ACGATGCAAATCCATCTCGAG 58.522 47.619 5.93 5.93 39.51 4.04
293 299 1.452145 GGTTTCACCGCTCAAGGCAA 61.452 55.000 0.00 0.00 41.91 4.52
311 317 4.392940 GGCAACTATGATATCAGCAAGGT 58.607 43.478 11.78 4.55 0.00 3.50
354 360 2.046604 GCCGGTAGACCCACAACC 60.047 66.667 1.90 0.00 0.00 3.77
364 370 2.049248 CCACAACCACATTGCGCC 60.049 61.111 4.18 0.00 42.62 6.53
409 415 3.047877 GCCGGAAACCGTCACCAG 61.048 66.667 5.05 0.00 46.80 4.00
413 419 1.338389 CCGGAAACCGTCACCAGTTAT 60.338 52.381 0.00 0.00 46.80 1.89
415 421 2.610976 CGGAAACCGTCACCAGTTATGA 60.611 50.000 1.80 0.00 42.73 2.15
421 427 2.607635 CCGTCACCAGTTATGATTTCCG 59.392 50.000 0.00 0.00 0.00 4.30
422 428 2.030457 CGTCACCAGTTATGATTTCCGC 59.970 50.000 0.00 0.00 0.00 5.54
425 431 3.009723 CACCAGTTATGATTTCCGCAGT 58.990 45.455 0.00 0.00 0.00 4.40
428 434 5.296780 CACCAGTTATGATTTCCGCAGTAAT 59.703 40.000 0.00 0.00 0.00 1.89
430 436 5.296780 CCAGTTATGATTTCCGCAGTAATGT 59.703 40.000 0.00 0.00 0.00 2.71
432 438 5.527582 AGTTATGATTTCCGCAGTAATGTCC 59.472 40.000 0.00 0.00 0.00 4.02
433 439 2.276201 TGATTTCCGCAGTAATGTCCG 58.724 47.619 0.00 0.00 0.00 4.79
437 446 3.530265 TTCCGCAGTAATGTCCGTAAT 57.470 42.857 0.00 0.00 0.00 1.89
438 447 2.816689 TCCGCAGTAATGTCCGTAATG 58.183 47.619 0.00 0.00 0.00 1.90
471 481 3.390639 ACTTGATCAAGCCCTCTATCCTG 59.609 47.826 30.95 7.98 41.99 3.86
474 484 1.794714 TCAAGCCCTCTATCCTGACC 58.205 55.000 0.00 0.00 0.00 4.02
477 487 2.507471 CAAGCCCTCTATCCTGACCTTT 59.493 50.000 0.00 0.00 0.00 3.11
478 488 3.708236 AGCCCTCTATCCTGACCTTTA 57.292 47.619 0.00 0.00 0.00 1.85
482 492 4.262678 GCCCTCTATCCTGACCTTTATGTC 60.263 50.000 0.00 0.00 35.77 3.06
493 506 6.863126 CCTGACCTTTATGTCACAATTGAAAC 59.137 38.462 13.59 9.96 40.22 2.78
503 516 5.579904 TGTCACAATTGAAACCAAACACATG 59.420 36.000 13.59 0.00 31.90 3.21
504 517 5.580297 GTCACAATTGAAACCAAACACATGT 59.420 36.000 13.59 0.00 31.90 3.21
507 520 2.200792 TGAAACCAAACACATGTGCG 57.799 45.000 25.68 13.92 0.00 5.34
534 547 8.572855 AGATAGATAAGCTCCAAATAAATGCC 57.427 34.615 0.00 0.00 0.00 4.40
535 548 8.166061 AGATAGATAAGCTCCAAATAAATGCCA 58.834 33.333 0.00 0.00 0.00 4.92
551 567 9.941325 AATAAATGCCATCACATAAACAAAAGA 57.059 25.926 0.00 0.00 0.00 2.52
570 589 8.040132 ACAAAAGAGGAGATGTTAATGAGAGAG 58.960 37.037 0.00 0.00 0.00 3.20
571 590 6.729690 AAGAGGAGATGTTAATGAGAGAGG 57.270 41.667 0.00 0.00 0.00 3.69
572 591 5.147032 AGAGGAGATGTTAATGAGAGAGGG 58.853 45.833 0.00 0.00 0.00 4.30
573 592 3.645687 AGGAGATGTTAATGAGAGAGGGC 59.354 47.826 0.00 0.00 0.00 5.19
574 593 3.389329 GGAGATGTTAATGAGAGAGGGCA 59.611 47.826 0.00 0.00 0.00 5.36
575 594 4.041444 GGAGATGTTAATGAGAGAGGGCAT 59.959 45.833 0.00 0.00 0.00 4.40
576 595 5.455899 GGAGATGTTAATGAGAGAGGGCATT 60.456 44.000 0.00 0.00 38.24 3.56
577 596 5.619220 AGATGTTAATGAGAGAGGGCATTC 58.381 41.667 0.00 0.00 36.27 2.67
578 597 4.156455 TGTTAATGAGAGAGGGCATTCC 57.844 45.455 0.00 0.00 36.27 3.01
611 632 1.453155 CTCCATTCAAACCGGGACAG 58.547 55.000 6.32 0.00 0.00 3.51
625 646 0.689080 GGACAGGGAGCAGGAGATGA 60.689 60.000 0.00 0.00 0.00 2.92
626 647 0.752054 GACAGGGAGCAGGAGATGAG 59.248 60.000 0.00 0.00 0.00 2.90
627 648 0.690411 ACAGGGAGCAGGAGATGAGG 60.690 60.000 0.00 0.00 0.00 3.86
628 649 1.074623 AGGGAGCAGGAGATGAGGG 60.075 63.158 0.00 0.00 0.00 4.30
629 650 1.074926 GGGAGCAGGAGATGAGGGA 60.075 63.158 0.00 0.00 0.00 4.20
630 651 0.473501 GGGAGCAGGAGATGAGGGAT 60.474 60.000 0.00 0.00 0.00 3.85
631 652 0.686224 GGAGCAGGAGATGAGGGATG 59.314 60.000 0.00 0.00 0.00 3.51
731 761 0.390209 CGGCCAAGAAGCAAAATGGG 60.390 55.000 2.24 0.00 33.45 4.00
747 777 4.432741 GGAACCTGCCCTGCCTCC 62.433 72.222 0.00 0.00 0.00 4.30
771 801 1.152963 CTGCCCTTAACCCCATCCG 60.153 63.158 0.00 0.00 0.00 4.18
781 811 3.958860 CCCATCCGCATCCCCTCC 61.959 72.222 0.00 0.00 0.00 4.30
782 812 3.170672 CCATCCGCATCCCCTCCA 61.171 66.667 0.00 0.00 0.00 3.86
783 813 2.532532 CCATCCGCATCCCCTCCAT 61.533 63.158 0.00 0.00 0.00 3.41
813 847 2.488545 CGGGTAGTCCATATCCTCTTCG 59.511 54.545 0.00 0.00 31.67 3.79
818 852 3.492337 AGTCCATATCCTCTTCGACCTC 58.508 50.000 0.00 0.00 0.00 3.85
839 873 2.406616 CCTCGCCCACCAAATTCCG 61.407 63.158 0.00 0.00 0.00 4.30
878 912 3.052082 CCGGAGCTGCCACTGTTG 61.052 66.667 0.00 0.00 35.94 3.33
916 950 1.472728 CGGAGTAATTTCAGGTCGGGG 60.473 57.143 0.00 0.00 0.00 5.73
927 975 4.083862 GTCGGGGGTGAGTGAGCC 62.084 72.222 0.00 0.00 42.09 4.70
943 991 2.325082 GCCGTGCTGGTGGTAGTTG 61.325 63.158 0.00 0.00 41.21 3.16
978 1040 2.204151 AGTGGAGTTGGGAGGGGG 60.204 66.667 0.00 0.00 0.00 5.40
1014 1076 1.464376 CCGAGATGCAGTCCGGGTAT 61.464 60.000 13.59 0.00 37.16 2.73
1017 1079 0.398522 AGATGCAGTCCGGGTATGGA 60.399 55.000 0.00 0.00 35.04 3.41
1187 1273 3.945434 CGCGATGCAGCACCATCC 61.945 66.667 0.00 4.07 38.68 3.51
1341 1430 3.289834 CACCACCACCAGCAGCAC 61.290 66.667 0.00 0.00 0.00 4.40
1412 1504 4.487412 GCATCACAAGCCGCAGCC 62.487 66.667 0.00 0.00 41.25 4.85
1608 1709 1.165907 TGAACTTCAAGCTGGCCGTG 61.166 55.000 0.00 0.00 0.00 4.94
1704 1805 3.469970 ATGATGCTCCACGGCGGA 61.470 61.111 13.24 0.00 43.61 5.54
1869 1980 0.099436 GCACATGTCAATTCCTCCGC 59.901 55.000 0.00 0.00 0.00 5.54
1875 1986 4.489771 CAATTCCTCCGCCCGCCT 62.490 66.667 0.00 0.00 0.00 5.52
1896 2007 2.796193 CGGATCCACTCATGGCGGA 61.796 63.158 13.41 0.00 46.80 5.54
2080 2191 1.071228 CTGATGCCGATGATTCCTCCA 59.929 52.381 0.00 0.00 0.00 3.86
2083 2194 1.271127 TGCCGATGATTCCTCCACCA 61.271 55.000 0.00 0.00 0.00 4.17
2086 2197 2.292267 CCGATGATTCCTCCACCAAAG 58.708 52.381 0.00 0.00 0.00 2.77
2087 2198 2.092968 CCGATGATTCCTCCACCAAAGA 60.093 50.000 0.00 0.00 0.00 2.52
2088 2199 2.939103 CGATGATTCCTCCACCAAAGAC 59.061 50.000 0.00 0.00 0.00 3.01
2089 2200 2.879103 TGATTCCTCCACCAAAGACC 57.121 50.000 0.00 0.00 0.00 3.85
2090 2201 1.003118 TGATTCCTCCACCAAAGACCG 59.997 52.381 0.00 0.00 0.00 4.79
2091 2202 0.322546 ATTCCTCCACCAAAGACCGC 60.323 55.000 0.00 0.00 0.00 5.68
2092 2203 2.359975 CCTCCACCAAAGACCGCC 60.360 66.667 0.00 0.00 0.00 6.13
2093 2204 2.359975 CTCCACCAAAGACCGCCC 60.360 66.667 0.00 0.00 0.00 6.13
2094 2205 3.172106 TCCACCAAAGACCGCCCA 61.172 61.111 0.00 0.00 0.00 5.36
2095 2206 2.203422 CCACCAAAGACCGCCCAA 60.203 61.111 0.00 0.00 0.00 4.12
2096 2207 2.561037 CCACCAAAGACCGCCCAAC 61.561 63.158 0.00 0.00 0.00 3.77
2100 2211 0.750249 CCAAAGACCGCCCAACTTTT 59.250 50.000 0.00 0.00 32.59 2.27
2101 2212 1.957877 CCAAAGACCGCCCAACTTTTA 59.042 47.619 0.00 0.00 32.59 1.52
2113 2224 4.221924 GCCCAACTTTTATCCCTTTTAGCA 59.778 41.667 0.00 0.00 0.00 3.49
2114 2225 5.104941 GCCCAACTTTTATCCCTTTTAGCAT 60.105 40.000 0.00 0.00 0.00 3.79
2118 2229 7.416777 CCAACTTTTATCCCTTTTAGCATCCTC 60.417 40.741 0.00 0.00 0.00 3.71
2134 2245 1.067060 TCCTCCTCATTACATCACGCG 59.933 52.381 3.53 3.53 0.00 6.01
2162 2274 6.705863 AGAAACTCTTCTCTTGCACAATTT 57.294 33.333 0.00 0.00 37.31 1.82
2163 2275 6.501781 AGAAACTCTTCTCTTGCACAATTTG 58.498 36.000 0.00 0.00 37.31 2.32
2164 2276 6.954073 AGAAACTCTTCTCTTGCACAATTTGC 60.954 38.462 0.00 5.87 44.31 3.68
2172 2285 3.220447 GCACAATTTGCCATGCACT 57.780 47.368 5.80 0.00 46.63 4.40
2178 2291 4.093703 CACAATTTGCCATGCACTATTTGG 59.906 41.667 0.00 0.00 38.71 3.28
2208 2321 3.093717 GCAGATGGGATGCAATTCTTG 57.906 47.619 0.00 0.00 43.31 3.02
2213 2326 3.959535 TGGGATGCAATTCTTGGTTTC 57.040 42.857 0.00 0.00 0.00 2.78
2219 2332 2.036217 TGCAATTCTTGGTTTCCTGCTG 59.964 45.455 0.00 0.00 0.00 4.41
2228 2341 0.166814 GTTTCCTGCTGCTAGTTGCG 59.833 55.000 0.00 0.00 46.63 4.85
2239 2352 1.529826 GCTAGTTGCGAAATTGCTCCG 60.530 52.381 0.00 0.00 35.36 4.63
2242 2355 1.812571 AGTTGCGAAATTGCTCCGAAT 59.187 42.857 0.00 0.00 35.36 3.34
2244 2357 2.542766 TGCGAAATTGCTCCGAATTC 57.457 45.000 0.00 0.00 35.36 2.17
2270 2383 2.925578 TGGCAGATGAAATTCTTGCG 57.074 45.000 9.99 0.00 0.00 4.85
2271 2384 2.435422 TGGCAGATGAAATTCTTGCGA 58.565 42.857 9.99 5.44 0.00 5.10
2272 2385 2.819019 TGGCAGATGAAATTCTTGCGAA 59.181 40.909 9.99 0.00 0.00 4.70
2274 2387 4.082081 TGGCAGATGAAATTCTTGCGAAAT 60.082 37.500 9.99 0.00 31.91 2.17
2276 2389 5.220340 GGCAGATGAAATTCTTGCGAAATTG 60.220 40.000 9.99 0.00 31.91 2.32
2277 2390 5.346822 GCAGATGAAATTCTTGCGAAATTGT 59.653 36.000 0.00 0.00 31.91 2.71
2279 2392 7.442657 CAGATGAAATTCTTGCGAAATTGTTC 58.557 34.615 0.00 0.00 31.91 3.18
2281 2394 4.679197 TGAAATTCTTGCGAAATTGTTCCG 59.321 37.500 0.00 0.00 31.91 4.30
2283 2396 4.701956 ATTCTTGCGAAATTGTTCCGAT 57.298 36.364 0.00 0.00 31.91 4.18
2295 2408 3.363341 TGTTCCGATTTTCTTGTTGCC 57.637 42.857 0.00 0.00 0.00 4.52
2344 2457 7.987458 TGGTTTGGTTTGTTTATCATTGCTTAA 59.013 29.630 0.00 0.00 0.00 1.85
2451 2565 3.441290 GCAGCAGCAGCAAGAGGG 61.441 66.667 4.63 0.00 45.49 4.30
2452 2566 3.441290 CAGCAGCAGCAAGAGGGC 61.441 66.667 3.17 0.00 45.49 5.19
2780 3064 0.388649 CCAACACCTCGGAGACTTCG 60.389 60.000 6.58 0.00 0.00 3.79
3119 3406 3.032609 GAGACGGCCATCATCGCG 61.033 66.667 0.00 0.00 0.00 5.87
3160 3447 2.286121 GACCATCACCCTCCCCCA 60.286 66.667 0.00 0.00 0.00 4.96
3161 3448 1.928567 GACCATCACCCTCCCCCAA 60.929 63.158 0.00 0.00 0.00 4.12
3163 3450 2.237965 CCATCACCCTCCCCCAACA 61.238 63.158 0.00 0.00 0.00 3.33
3165 3452 2.616458 ATCACCCTCCCCCAACAGC 61.616 63.158 0.00 0.00 0.00 4.40
3631 3966 2.723746 CGCCAATGCCATAGCCAC 59.276 61.111 0.00 0.00 38.69 5.01
3738 4082 2.592287 GGTTCCCAAACGACGGCA 60.592 61.111 0.00 0.00 36.16 5.69
3739 4083 2.188161 GGTTCCCAAACGACGGCAA 61.188 57.895 0.00 0.00 36.16 4.52
3740 4084 1.281656 GTTCCCAAACGACGGCAAG 59.718 57.895 0.00 0.00 0.00 4.01
3741 4085 1.894756 TTCCCAAACGACGGCAAGG 60.895 57.895 0.00 0.00 0.00 3.61
3742 4086 2.281208 CCCAAACGACGGCAAGGA 60.281 61.111 0.00 0.00 0.00 3.36
3743 4087 2.325082 CCCAAACGACGGCAAGGAG 61.325 63.158 0.00 0.00 0.00 3.69
3745 4089 1.301401 CAAACGACGGCAAGGAGGA 60.301 57.895 0.00 0.00 0.00 3.71
3821 4180 4.148825 GCAGGCGAGGACCACGAT 62.149 66.667 15.98 0.00 0.00 3.73
3888 4253 8.540507 TCATTAGAGCTTGATTAACTAGGACT 57.459 34.615 0.00 0.00 0.00 3.85
3946 4318 5.410924 GCCGGAGATAAATTTGCTTCTTTT 58.589 37.500 5.05 0.00 0.00 2.27
3958 4330 9.881649 AAATTTGCTTCTTTTCTTCTTCTTCTT 57.118 25.926 0.00 0.00 0.00 2.52
4036 4410 8.728833 ACTTACTTGTTAGTACTACTACTGCTG 58.271 37.037 0.91 0.00 36.61 4.41
4037 4411 5.952033 ACTTGTTAGTACTACTACTGCTGC 58.048 41.667 0.91 0.00 34.79 5.25
4038 4412 5.711036 ACTTGTTAGTACTACTACTGCTGCT 59.289 40.000 0.91 0.00 34.79 4.24
4039 4413 5.562506 TGTTAGTACTACTACTGCTGCTG 57.437 43.478 0.91 4.89 34.79 4.41
4040 4414 4.142447 TGTTAGTACTACTACTGCTGCTGC 60.142 45.833 8.89 8.89 34.79 5.25
4041 4415 2.729194 AGTACTACTACTGCTGCTGCT 58.271 47.619 17.00 0.00 40.48 4.24
4185 4559 9.696917 GCATATTAAATAGCTTAGCAACCAAAT 57.303 29.630 7.07 3.44 0.00 2.32
4222 4596 6.531021 AGGTGCTTAGCTTCTTGTAACTAAA 58.469 36.000 5.60 0.00 0.00 1.85
4549 4923 2.295602 ACCTGGGCGAATACCGGTT 61.296 57.895 15.04 0.00 39.04 4.44
4688 5062 3.801698 TGCAAGCTATCATGACCTTCTC 58.198 45.455 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.277921 GCTTCTCCATGATGGGAAAGAATC 59.722 45.833 22.54 12.66 38.32 2.52
4 5 2.420547 CGCTTCTCCATGATGGGAAAGA 60.421 50.000 22.54 12.42 38.32 2.52
6 7 1.408683 CCGCTTCTCCATGATGGGAAA 60.409 52.381 12.26 5.52 38.32 3.13
7 8 0.181114 CCGCTTCTCCATGATGGGAA 59.819 55.000 12.26 12.50 38.32 3.97
8 9 0.690744 TCCGCTTCTCCATGATGGGA 60.691 55.000 12.26 5.09 38.32 4.37
9 10 0.399454 ATCCGCTTCTCCATGATGGG 59.601 55.000 12.26 2.55 38.32 4.00
10 11 1.071228 TCATCCGCTTCTCCATGATGG 59.929 52.381 4.74 4.74 39.43 3.51
11 12 2.036862 TCTCATCCGCTTCTCCATGATG 59.963 50.000 0.00 0.00 35.32 3.07
12 13 2.323599 TCTCATCCGCTTCTCCATGAT 58.676 47.619 0.00 0.00 0.00 2.45
25 26 1.686052 ACGAGCTCCTTCATCTCATCC 59.314 52.381 8.47 0.00 0.00 3.51
60 63 6.434340 ACTTTACAAAGAATGTCCCATCTTCC 59.566 38.462 8.65 0.00 42.70 3.46
68 71 8.529102 GTTTTTCGAACTTTACAAAGAATGTCC 58.471 33.333 8.65 0.00 42.70 4.02
79 82 8.640291 TCATGTGTTTTGTTTTTCGAACTTTAC 58.360 29.630 0.00 0.00 0.00 2.01
87 90 8.428536 TGTAGTTTTCATGTGTTTTGTTTTTCG 58.571 29.630 0.00 0.00 0.00 3.46
102 105 8.936864 GTTAGCAGTCACTAATGTAGTTTTCAT 58.063 33.333 0.00 0.00 36.76 2.57
106 109 8.033626 GGTAGTTAGCAGTCACTAATGTAGTTT 58.966 37.037 0.00 0.00 36.76 2.66
122 125 2.486504 CCGTCGCGGTAGTTAGCA 59.513 61.111 6.13 0.00 42.73 3.49
140 143 1.001068 TGTGCAACCTTCATGGCATTG 59.999 47.619 0.00 0.00 38.68 2.82
143 146 0.178995 TCTGTGCAACCTTCATGGCA 60.179 50.000 0.00 0.00 40.22 4.92
169 175 2.547218 GGTATTGGGCGTGATACGTGAT 60.547 50.000 0.00 0.00 44.73 3.06
174 180 2.036733 TGCTAGGTATTGGGCGTGATAC 59.963 50.000 0.00 0.00 0.00 2.24
219 225 9.220767 CTTGGCTTTACTTATTCTTCACTAACT 57.779 33.333 0.00 0.00 0.00 2.24
220 226 9.000486 ACTTGGCTTTACTTATTCTTCACTAAC 58.000 33.333 0.00 0.00 0.00 2.34
223 229 7.095187 CGAACTTGGCTTTACTTATTCTTCACT 60.095 37.037 0.00 0.00 0.00 3.41
224 230 7.015877 CGAACTTGGCTTTACTTATTCTTCAC 58.984 38.462 0.00 0.00 0.00 3.18
225 231 6.932400 TCGAACTTGGCTTTACTTATTCTTCA 59.068 34.615 0.00 0.00 0.00 3.02
227 233 7.570691 CGTTCGAACTTGGCTTTACTTATTCTT 60.571 37.037 24.80 0.00 0.00 2.52
228 234 6.128634 CGTTCGAACTTGGCTTTACTTATTCT 60.129 38.462 24.80 0.00 0.00 2.40
229 235 6.013689 CGTTCGAACTTGGCTTTACTTATTC 58.986 40.000 24.80 0.00 0.00 1.75
230 236 5.697633 TCGTTCGAACTTGGCTTTACTTATT 59.302 36.000 24.80 0.00 0.00 1.40
231 237 5.232463 TCGTTCGAACTTGGCTTTACTTAT 58.768 37.500 24.80 0.00 0.00 1.73
232 238 4.619973 TCGTTCGAACTTGGCTTTACTTA 58.380 39.130 24.80 0.00 0.00 2.24
233 239 3.460103 TCGTTCGAACTTGGCTTTACTT 58.540 40.909 24.80 0.00 0.00 2.24
234 240 3.102052 TCGTTCGAACTTGGCTTTACT 57.898 42.857 24.80 0.00 0.00 2.24
235 241 3.732943 CATCGTTCGAACTTGGCTTTAC 58.267 45.455 24.80 0.00 0.00 2.01
236 242 2.158841 GCATCGTTCGAACTTGGCTTTA 59.841 45.455 24.80 2.07 0.00 1.85
237 243 1.069227 GCATCGTTCGAACTTGGCTTT 60.069 47.619 24.80 0.45 0.00 3.51
238 244 0.517316 GCATCGTTCGAACTTGGCTT 59.483 50.000 24.80 1.78 0.00 4.35
239 245 0.602638 TGCATCGTTCGAACTTGGCT 60.603 50.000 24.80 0.00 0.00 4.75
240 246 0.237235 TTGCATCGTTCGAACTTGGC 59.763 50.000 24.80 22.50 0.00 4.52
241 247 2.679355 TTTGCATCGTTCGAACTTGG 57.321 45.000 24.80 14.56 0.00 3.61
242 248 3.163594 GGATTTGCATCGTTCGAACTTG 58.836 45.455 24.80 21.23 0.00 3.16
243 249 2.811431 TGGATTTGCATCGTTCGAACTT 59.189 40.909 24.80 10.43 0.00 2.66
249 255 2.866156 TCGAGATGGATTTGCATCGTTC 59.134 45.455 6.44 0.18 33.37 3.95
254 260 2.569059 CCACTCGAGATGGATTTGCAT 58.431 47.619 21.68 0.00 39.87 3.96
256 262 1.303309 CCCACTCGAGATGGATTTGC 58.697 55.000 26.08 0.00 39.87 3.68
261 267 1.275291 GTGAAACCCACTCGAGATGGA 59.725 52.381 26.08 10.40 42.44 3.41
293 299 3.555795 CGCCACCTTGCTGATATCATAGT 60.556 47.826 5.72 0.00 0.00 2.12
301 307 1.745087 CAATAACGCCACCTTGCTGAT 59.255 47.619 0.00 0.00 0.00 2.90
333 339 4.468689 GTGGGTCTACCGGCAGGC 62.469 72.222 0.00 0.00 44.64 4.85
340 346 2.159382 CAATGTGGTTGTGGGTCTACC 58.841 52.381 0.00 0.00 41.19 3.18
341 347 1.539827 GCAATGTGGTTGTGGGTCTAC 59.460 52.381 0.00 0.00 40.07 2.59
354 360 3.098958 GTTGTGCGGCGCAATGTG 61.099 61.111 38.05 0.00 41.47 3.21
409 415 5.558273 CGGACATTACTGCGGAAATCATAAC 60.558 44.000 0.00 0.00 0.00 1.89
413 419 2.276201 CGGACATTACTGCGGAAATCA 58.724 47.619 0.00 0.00 0.00 2.57
415 421 2.396590 ACGGACATTACTGCGGAAAT 57.603 45.000 0.00 0.00 0.00 2.17
447 457 5.070981 CAGGATAGAGGGCTTGATCAAGTTA 59.929 44.000 30.88 17.91 40.45 2.24
455 465 1.292242 AGGTCAGGATAGAGGGCTTGA 59.708 52.381 0.00 0.00 0.00 3.02
458 468 2.577772 AAAGGTCAGGATAGAGGGCT 57.422 50.000 0.00 0.00 0.00 5.19
460 470 4.901849 TGACATAAAGGTCAGGATAGAGGG 59.098 45.833 0.00 0.00 42.56 4.30
471 481 6.744112 TGGTTTCAATTGTGACATAAAGGTC 58.256 36.000 5.13 0.00 38.29 3.85
474 484 8.327429 GTGTTTGGTTTCAATTGTGACATAAAG 58.673 33.333 5.13 0.00 31.90 1.85
477 487 6.867550 TGTGTTTGGTTTCAATTGTGACATA 58.132 32.000 5.13 0.00 31.90 2.29
478 488 5.728471 TGTGTTTGGTTTCAATTGTGACAT 58.272 33.333 5.13 0.00 31.90 3.06
482 492 5.727239 GCACATGTGTTTGGTTTCAATTGTG 60.727 40.000 26.01 0.00 32.28 3.33
493 506 2.995466 ATCTTCGCACATGTGTTTGG 57.005 45.000 26.01 14.37 0.00 3.28
503 516 4.244425 TGGAGCTTATCTATCTTCGCAC 57.756 45.455 0.00 0.00 0.00 5.34
504 517 4.937201 TTGGAGCTTATCTATCTTCGCA 57.063 40.909 0.00 0.00 0.00 5.10
533 546 7.121759 ACATCTCCTCTTTTGTTTATGTGATGG 59.878 37.037 0.00 0.00 33.11 3.51
534 547 8.048534 ACATCTCCTCTTTTGTTTATGTGATG 57.951 34.615 0.00 0.00 34.45 3.07
535 548 8.641498 AACATCTCCTCTTTTGTTTATGTGAT 57.359 30.769 0.00 0.00 0.00 3.06
551 567 3.645687 GCCCTCTCTCATTAACATCTCCT 59.354 47.826 0.00 0.00 0.00 3.69
571 590 2.234913 CTTGCTGCTTGGGGAATGCC 62.235 60.000 0.00 0.00 0.00 4.40
572 591 1.217244 CTTGCTGCTTGGGGAATGC 59.783 57.895 0.00 0.00 0.00 3.56
573 592 1.895238 CCTTGCTGCTTGGGGAATG 59.105 57.895 0.00 0.00 0.00 2.67
574 593 1.986210 GCCTTGCTGCTTGGGGAAT 60.986 57.895 0.00 0.00 0.00 3.01
575 594 2.601367 GCCTTGCTGCTTGGGGAA 60.601 61.111 0.00 0.00 0.00 3.97
576 595 3.574074 GAGCCTTGCTGCTTGGGGA 62.574 63.158 0.00 0.00 42.95 4.81
577 596 3.066814 GAGCCTTGCTGCTTGGGG 61.067 66.667 0.00 0.00 42.95 4.96
578 597 3.066814 GGAGCCTTGCTGCTTGGG 61.067 66.667 0.00 1.51 43.58 4.12
581 600 0.251474 TGAATGGAGCCTTGCTGCTT 60.251 50.000 9.01 0.00 46.98 3.91
582 601 0.251474 TTGAATGGAGCCTTGCTGCT 60.251 50.000 9.01 0.00 46.98 4.24
584 603 1.067354 GGTTTGAATGGAGCCTTGCTG 60.067 52.381 0.00 0.00 39.88 4.41
611 632 0.473501 ATCCCTCATCTCCTGCTCCC 60.474 60.000 0.00 0.00 0.00 4.30
731 761 4.432741 GGGAGGCAGGGCAGGTTC 62.433 72.222 0.00 0.00 0.00 3.62
746 776 2.043953 GTTAAGGGCAGGGCAGGG 60.044 66.667 0.00 0.00 0.00 4.45
747 777 2.043953 GGTTAAGGGCAGGGCAGG 60.044 66.667 0.00 0.00 0.00 4.85
749 779 3.668142 GGGGTTAAGGGCAGGGCA 61.668 66.667 0.00 0.00 0.00 5.36
750 780 2.928988 GATGGGGTTAAGGGCAGGGC 62.929 65.000 0.00 0.00 0.00 5.19
751 781 1.230212 GATGGGGTTAAGGGCAGGG 59.770 63.158 0.00 0.00 0.00 4.45
771 801 1.227674 GTGACGATGGAGGGGATGC 60.228 63.158 0.00 0.00 0.00 3.91
781 811 0.381089 GACTACCCGGAGTGACGATG 59.619 60.000 0.73 0.00 35.47 3.84
782 812 0.750911 GGACTACCCGGAGTGACGAT 60.751 60.000 0.73 0.00 35.47 3.73
783 813 1.377725 GGACTACCCGGAGTGACGA 60.378 63.158 0.73 0.00 35.47 4.20
813 847 4.083862 GTGGGCGAGGGTGAGGTC 62.084 72.222 0.00 0.00 0.00 3.85
818 852 1.595093 GAATTTGGTGGGCGAGGGTG 61.595 60.000 0.00 0.00 0.00 4.61
839 873 3.705043 ATTGAAATGCGAGCAGGAATC 57.295 42.857 3.58 0.30 0.00 2.52
878 912 2.908940 CCTCCCGCATGATTGGGC 60.909 66.667 12.05 0.00 45.60 5.36
916 950 2.740055 CAGCACGGCTCACTCACC 60.740 66.667 0.00 0.00 36.40 4.02
927 975 1.301716 AGCAACTACCACCAGCACG 60.302 57.895 0.00 0.00 0.00 5.34
943 991 3.721706 CCACTCCCCACTCCCAGC 61.722 72.222 0.00 0.00 0.00 4.85
1014 1076 1.911766 GAACTCCGACACCCCTCCA 60.912 63.158 0.00 0.00 0.00 3.86
1017 1079 1.913762 CTGGAACTCCGACACCCCT 60.914 63.158 0.00 0.00 39.43 4.79
1341 1430 1.298014 GAAGAGCTGGAGGTGGTGG 59.702 63.158 0.00 0.00 0.00 4.61
1384 1473 1.862602 TTGTGATGCTGCTGCTGCTG 61.863 55.000 27.67 16.73 40.48 4.41
1385 1474 1.587043 CTTGTGATGCTGCTGCTGCT 61.587 55.000 27.67 15.76 40.48 4.24
1386 1475 1.154016 CTTGTGATGCTGCTGCTGC 60.154 57.895 22.51 22.51 40.48 5.25
1387 1476 1.154016 GCTTGTGATGCTGCTGCTG 60.154 57.895 17.00 0.77 40.48 4.41
1388 1477 2.341101 GGCTTGTGATGCTGCTGCT 61.341 57.895 17.00 2.26 40.48 4.24
1389 1478 2.181021 GGCTTGTGATGCTGCTGC 59.819 61.111 8.89 8.89 40.20 5.25
1390 1479 2.483745 CGGCTTGTGATGCTGCTG 59.516 61.111 0.00 0.00 0.00 4.41
1393 1482 2.483745 CTGCGGCTTGTGATGCTG 59.516 61.111 0.00 0.00 39.61 4.41
1755 1862 3.213402 GAGGTCTCCTCCTCGCCG 61.213 72.222 4.60 0.00 44.36 6.46
1807 1914 1.004918 GTGGGAGGAACAGTGACGG 60.005 63.158 0.00 0.00 0.00 4.79
1809 1916 2.427506 GATTGTGGGAGGAACAGTGAC 58.572 52.381 0.00 0.00 0.00 3.67
1810 1917 1.351017 GGATTGTGGGAGGAACAGTGA 59.649 52.381 0.00 0.00 0.00 3.41
1811 1918 1.073763 TGGATTGTGGGAGGAACAGTG 59.926 52.381 0.00 0.00 0.00 3.66
1812 1919 1.444933 TGGATTGTGGGAGGAACAGT 58.555 50.000 0.00 0.00 0.00 3.55
1896 2007 2.337532 CTTTCCGTGTCCGTCGGT 59.662 61.111 11.88 0.00 46.86 4.69
2080 2191 0.396556 AAAGTTGGGCGGTCTTTGGT 60.397 50.000 0.00 0.00 31.47 3.67
2083 2194 2.823747 GGATAAAAGTTGGGCGGTCTTT 59.176 45.455 0.00 0.00 33.61 2.52
2086 2197 1.100510 GGGATAAAAGTTGGGCGGTC 58.899 55.000 0.00 0.00 0.00 4.79
2087 2198 0.702316 AGGGATAAAAGTTGGGCGGT 59.298 50.000 0.00 0.00 0.00 5.68
2088 2199 1.847328 AAGGGATAAAAGTTGGGCGG 58.153 50.000 0.00 0.00 0.00 6.13
2089 2200 3.953712 AAAAGGGATAAAAGTTGGGCG 57.046 42.857 0.00 0.00 0.00 6.13
2090 2201 4.221924 TGCTAAAAGGGATAAAAGTTGGGC 59.778 41.667 0.00 0.00 0.00 5.36
2091 2202 5.993748 TGCTAAAAGGGATAAAAGTTGGG 57.006 39.130 0.00 0.00 0.00 4.12
2092 2203 6.381133 AGGATGCTAAAAGGGATAAAAGTTGG 59.619 38.462 0.00 0.00 0.00 3.77
2093 2204 7.410120 AGGATGCTAAAAGGGATAAAAGTTG 57.590 36.000 0.00 0.00 0.00 3.16
2094 2205 6.607600 GGAGGATGCTAAAAGGGATAAAAGTT 59.392 38.462 0.00 0.00 0.00 2.66
2095 2206 6.068794 AGGAGGATGCTAAAAGGGATAAAAGT 60.069 38.462 0.00 0.00 31.62 2.66
2096 2207 6.368805 AGGAGGATGCTAAAAGGGATAAAAG 58.631 40.000 0.00 0.00 31.62 2.27
2100 2211 4.566837 TGAGGAGGATGCTAAAAGGGATA 58.433 43.478 0.00 0.00 36.27 2.59
2101 2212 3.397527 TGAGGAGGATGCTAAAAGGGAT 58.602 45.455 0.00 0.00 36.27 3.85
2113 2224 2.288457 CGCGTGATGTAATGAGGAGGAT 60.288 50.000 0.00 0.00 0.00 3.24
2114 2225 1.067060 CGCGTGATGTAATGAGGAGGA 59.933 52.381 0.00 0.00 0.00 3.71
2118 2229 3.186909 TCTTTCGCGTGATGTAATGAGG 58.813 45.455 5.77 0.00 0.00 3.86
2156 2268 4.255301 CCAAATAGTGCATGGCAAATTGT 58.745 39.130 0.00 0.00 41.47 2.71
2202 2315 2.299326 AGCAGCAGGAAACCAAGAAT 57.701 45.000 0.00 0.00 0.00 2.40
2204 2317 1.699634 ACTAGCAGCAGGAAACCAAGA 59.300 47.619 0.00 0.00 0.00 3.02
2205 2318 2.191128 ACTAGCAGCAGGAAACCAAG 57.809 50.000 0.00 0.00 0.00 3.61
2206 2319 2.229792 CAACTAGCAGCAGGAAACCAA 58.770 47.619 0.00 0.00 0.00 3.67
2207 2320 1.896220 CAACTAGCAGCAGGAAACCA 58.104 50.000 0.00 0.00 0.00 3.67
2208 2321 0.523519 GCAACTAGCAGCAGGAAACC 59.476 55.000 0.00 0.00 44.79 3.27
2213 2326 1.089920 ATTTCGCAACTAGCAGCAGG 58.910 50.000 7.64 0.00 46.13 4.85
2219 2332 1.529826 CGGAGCAATTTCGCAACTAGC 60.530 52.381 0.00 0.00 40.87 3.42
2228 2341 2.177173 GCACGAATTCGGAGCAATTTC 58.823 47.619 30.17 9.92 44.95 2.17
2270 2383 6.354858 GCAACAAGAAAATCGGAACAATTTC 58.645 36.000 0.00 0.00 33.13 2.17
2271 2384 5.236263 GGCAACAAGAAAATCGGAACAATTT 59.764 36.000 0.00 0.00 0.00 1.82
2272 2385 4.749598 GGCAACAAGAAAATCGGAACAATT 59.250 37.500 0.00 0.00 0.00 2.32
2274 2387 3.383185 AGGCAACAAGAAAATCGGAACAA 59.617 39.130 0.00 0.00 41.41 2.83
2276 2389 3.643159 AGGCAACAAGAAAATCGGAAC 57.357 42.857 0.00 0.00 41.41 3.62
2277 2390 4.664150 AAAGGCAACAAGAAAATCGGAA 57.336 36.364 0.00 0.00 41.41 4.30
2279 2392 3.059665 GCAAAAGGCAACAAGAAAATCGG 60.060 43.478 0.00 0.00 43.97 4.18
2365 2478 3.779759 TCATCACACAAAGCAACCAAAC 58.220 40.909 0.00 0.00 0.00 2.93
2454 2568 4.840005 CTTCTCCTTCCCGGCGCC 62.840 72.222 19.07 19.07 0.00 6.53
2455 2569 4.840005 CCTTCTCCTTCCCGGCGC 62.840 72.222 0.00 0.00 0.00 6.53
2456 2570 3.391382 ACCTTCTCCTTCCCGGCG 61.391 66.667 0.00 0.00 0.00 6.46
2457 2571 2.269241 CACCTTCTCCTTCCCGGC 59.731 66.667 0.00 0.00 0.00 6.13
2458 2572 2.990479 CCACCTTCTCCTTCCCGG 59.010 66.667 0.00 0.00 0.00 5.73
2459 2573 2.269241 GCCACCTTCTCCTTCCCG 59.731 66.667 0.00 0.00 0.00 5.14
2461 2575 1.002011 GTGGCCACCTTCTCCTTCC 60.002 63.158 26.31 0.00 0.00 3.46
2462 2576 1.376037 CGTGGCCACCTTCTCCTTC 60.376 63.158 29.95 0.98 0.00 3.46
2762 3046 0.388649 CCGAAGTCTCCGAGGTGTTG 60.389 60.000 0.00 0.00 0.00 3.33
3119 3406 0.658897 CGGAGAGCTTCTCGAGGTAC 59.341 60.000 13.56 1.84 44.28 3.34
3821 4180 3.385384 CTCTGGCCAGCCTCGTCA 61.385 66.667 28.91 7.95 36.94 4.35
3903 4275 1.466529 CGCCGATCGATCATGTCCTAG 60.467 57.143 24.40 6.01 41.67 3.02
3904 4276 0.521735 CGCCGATCGATCATGTCCTA 59.478 55.000 24.40 0.00 41.67 2.94
3905 4277 1.287191 CGCCGATCGATCATGTCCT 59.713 57.895 24.40 0.00 41.67 3.85
3906 4278 2.375766 GCGCCGATCGATCATGTCC 61.376 63.158 24.40 6.90 41.67 4.02
3907 4279 2.375766 GGCGCCGATCGATCATGTC 61.376 63.158 24.40 11.25 41.67 3.06
3908 4280 2.356313 GGCGCCGATCGATCATGT 60.356 61.111 24.40 0.00 41.67 3.21
3946 4318 2.551459 GCAGCAGCAAAGAAGAAGAAGA 59.449 45.455 0.00 0.00 41.58 2.87
4063 4437 9.135189 TGGGATTATGGAAGTGATTAATGAAAG 57.865 33.333 0.00 0.00 0.00 2.62
4067 4441 7.232127 AGCTTGGGATTATGGAAGTGATTAATG 59.768 37.037 0.00 0.00 0.00 1.90
4100 4474 3.827722 CCTAAGAGCTAGCTAGTGACCT 58.172 50.000 19.38 6.37 0.00 3.85
4549 4923 1.141645 GTATTCACACACGGCGACAA 58.858 50.000 16.62 0.00 0.00 3.18
4688 5062 1.890489 TGTATGACCGGGGTGATATCG 59.110 52.381 6.32 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.