Multiple sequence alignment - TraesCS5D01G442000

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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 TraesCS5D01G442000 chr5D 100.000 5223 0 0 1 5223 494220679 494215457 0.000000e+00 9646
1 TraesCS5D01G442000 chr5D 89.808 677 45 9 3431 4107 510553684 510554336 0.000000e+00 846
2 TraesCS5D01G442000 chr5B 93.259 3130 141 33 1850 4942 610502689 610499593 0.000000e+00 4547
3 TraesCS5D01G442000 chr5B 91.089 909 51 11 4344 5223 610306149 610305242 0.000000e+00 1203
4 TraesCS5D01G442000 chr5B 86.220 1045 59 30 361 1370 610504169 610503175 0.000000e+00 1053
5 TraesCS5D01G442000 chr5B 96.654 269 7 2 4082 4349 610311504 610311237 3.710000e-121 446
6 TraesCS5D01G442000 chr5B 94.681 94 5 0 266 359 187861666 187861759 4.210000e-31 147
7 TraesCS5D01G442000 chr5B 92.929 99 7 0 258 356 331307503 331307405 1.520000e-30 145
8 TraesCS5D01G442000 chr5B 84.000 150 18 5 119 267 276909224 276909080 7.050000e-29 139
9 TraesCS5D01G442000 chr5B 83.125 160 15 8 115 267 577371200 577371046 9.120000e-28 135
10 TraesCS5D01G442000 chr5A 94.619 2360 81 19 2897 5223 617208922 617206576 0.000000e+00 3613
11 TraesCS5D01G442000 chr5A 89.058 2632 141 64 321 2861 617211495 617208920 0.000000e+00 3129
12 TraesCS5D01G442000 chr5A 87.766 752 67 12 3281 4032 470929929 470930655 0.000000e+00 856
13 TraesCS5D01G442000 chr5A 87.500 280 22 6 1 267 617211753 617211474 1.410000e-80 311
14 TraesCS5D01G442000 chr5A 94.737 95 5 0 265 359 16500227 16500321 1.170000e-31 148
15 TraesCS5D01G442000 chr7B 89.614 828 67 11 3281 4107 228802385 228803194 0.000000e+00 1035
16 TraesCS5D01G442000 chr7B 87.367 752 70 12 3281 4032 593349525 593348799 0.000000e+00 839
17 TraesCS5D01G442000 chr7B 93.000 100 4 2 271 367 616099848 616099749 5.450000e-30 143
18 TraesCS5D01G442000 chr6D 89.117 827 65 12 3281 4107 450188604 450187803 0.000000e+00 1005
19 TraesCS5D01G442000 chr4A 88.165 752 62 13 3281 4032 742009662 742008938 0.000000e+00 870
20 TraesCS5D01G442000 chr4A 76.346 520 82 22 4604 5105 508274030 508274526 1.880000e-59 241
21 TraesCS5D01G442000 chr4A 77.644 331 63 8 4604 4925 508494130 508494458 1.920000e-44 191
22 TraesCS5D01G442000 chr4A 83.444 151 21 3 119 267 137099100 137099248 2.540000e-28 137
23 TraesCS5D01G442000 chr3A 87.302 756 70 15 3281 4035 662598914 662598184 0.000000e+00 841
24 TraesCS5D01G442000 chr7D 89.481 675 46 10 3434 4107 574099720 574099070 0.000000e+00 830
25 TraesCS5D01G442000 chr3B 88.802 384 24 6 1850 2214 235457921 235457538 2.220000e-123 453
26 TraesCS5D01G442000 chr3B 89.420 293 24 6 1084 1370 235458654 235458363 3.840000e-96 363
27 TraesCS5D01G442000 chr3B 95.455 132 5 1 2314 2445 235444695 235444565 5.300000e-50 209
28 TraesCS5D01G442000 chr4B 77.551 490 79 16 4604 5079 109222879 109222407 3.100000e-67 267
29 TraesCS5D01G442000 chr4B 96.629 89 3 0 271 359 29271923 29271835 1.170000e-31 148
30 TraesCS5D01G442000 chr4B 83.893 149 20 3 119 265 223381041 223381187 7.050000e-29 139
31 TraesCS5D01G442000 chr6A 86.000 150 18 2 119 267 113538128 113537981 1.950000e-34 158
32 TraesCS5D01G442000 chr6B 94.737 95 3 2 265 358 65452495 65452588 4.210000e-31 147
33 TraesCS5D01G442000 chr6B 92.929 99 7 0 259 357 531739466 531739564 1.520000e-30 145
34 TraesCS5D01G442000 chr2A 91.509 106 5 4 256 358 675835699 675835803 5.450000e-30 143
35 TraesCS5D01G442000 chr2A 90.090 111 7 4 251 360 695156874 695156767 1.960000e-29 141
36 TraesCS5D01G442000 chr2A 84.545 110 17 0 1252 1361 638688747 638688638 5.530000e-20 110
37 TraesCS5D01G442000 chr7A 83.333 156 23 2 112 266 36554625 36554778 1.960000e-29 141
38 TraesCS5D01G442000 chr7A 83.893 149 20 3 119 265 246561422 246561568 7.050000e-29 139
39 TraesCS5D01G442000 chr1A 83.226 155 19 7 116 267 585838349 585838499 9.120000e-28 135
40 TraesCS5D01G442000 chr2D 85.455 110 16 0 1252 1361 495095137 495095246 1.190000e-21 115
41 TraesCS5D01G442000 chr2B 85.455 110 16 0 1252 1361 582803074 582803183 1.190000e-21 115


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 TraesCS5D01G442000 chr5D 494215457 494220679 5222 True 9646 9646 100.000000 1 5223 1 chr5D.!!$R1 5222
1 TraesCS5D01G442000 chr5D 510553684 510554336 652 False 846 846 89.808000 3431 4107 1 chr5D.!!$F1 676
2 TraesCS5D01G442000 chr5B 610499593 610504169 4576 True 2800 4547 89.739500 361 4942 2 chr5B.!!$R6 4581
3 TraesCS5D01G442000 chr5B 610305242 610306149 907 True 1203 1203 91.089000 4344 5223 1 chr5B.!!$R4 879
4 TraesCS5D01G442000 chr5A 617206576 617211753 5177 True 2351 3613 90.392333 1 5223 3 chr5A.!!$R1 5222
5 TraesCS5D01G442000 chr5A 470929929 470930655 726 False 856 856 87.766000 3281 4032 1 chr5A.!!$F2 751
6 TraesCS5D01G442000 chr7B 228802385 228803194 809 False 1035 1035 89.614000 3281 4107 1 chr7B.!!$F1 826
7 TraesCS5D01G442000 chr7B 593348799 593349525 726 True 839 839 87.367000 3281 4032 1 chr7B.!!$R1 751
8 TraesCS5D01G442000 chr6D 450187803 450188604 801 True 1005 1005 89.117000 3281 4107 1 chr6D.!!$R1 826
9 TraesCS5D01G442000 chr4A 742008938 742009662 724 True 870 870 88.165000 3281 4032 1 chr4A.!!$R1 751
10 TraesCS5D01G442000 chr3A 662598184 662598914 730 True 841 841 87.302000 3281 4035 1 chr3A.!!$R1 754
11 TraesCS5D01G442000 chr7D 574099070 574099720 650 True 830 830 89.481000 3434 4107 1 chr7D.!!$R1 673
12 TraesCS5D01G442000 chr3B 235457538 235458654 1116 True 408 453 89.111000 1084 2214 2 chr3B.!!$R2 1130

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
997 1080 0.036294 GAGGGGTTCAGTGTGCCTAC 60.036 60.0 5.88 0.0 0.00 3.18 F
1090 1174 0.388649 AACACTTCGCCGCTACTCTG 60.389 55.0 0.00 0.0 0.00 3.35 F
1665 1827 0.390472 ACTCTCTTGCTTGCCGTAGC 60.390 55.0 0.00 0.0 41.59 3.58 F
2319 2524 0.729116 GACACTGGCAACCATGATCG 59.271 55.0 0.00 0.0 30.82 3.69 F
2849 3066 0.776810 TGGGAGCACCAGGATTTGAA 59.223 50.0 1.58 0.0 46.80 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1846 2014 0.031178 CTCAACCTGCAACCACAAGC 59.969 55.0 0.00 0.0 0.00 4.01 R
2913 3130 0.107459 GTGATCCTCCAAGGTCCTGC 60.107 60.0 0.00 0.0 36.53 4.85 R
3608 3835 0.174617 GAGCTGGGACGAGGAGAAAG 59.825 60.0 0.00 0.0 0.00 2.62 R
4006 4251 0.456312 CGAAGTAGCTCACCGTCACC 60.456 60.0 0.00 0.0 0.00 4.02 R
4507 4766 0.249699 TCATGACGTCGTTGGCTTGT 60.250 50.0 7.76 0.0 0.00 3.16 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 1.522092 CATCTCTTACAGGCGGCCA 59.478 57.895 23.09 0.00 0.00 5.36
33 34 0.321653 CTCTTACAGGCGGCCAAAGT 60.322 55.000 23.09 18.11 0.00 2.66
41 42 0.887387 GGCGGCCAAAGTACAGACAA 60.887 55.000 15.62 0.00 0.00 3.18
43 44 1.878953 CGGCCAAAGTACAGACAACT 58.121 50.000 2.24 0.00 0.00 3.16
58 62 7.291411 ACAGACAACTGATTTCTACAGTAGT 57.709 36.000 7.50 0.00 46.01 2.73
97 101 4.689612 AGACCAAGTTGTTGAGCTCTAA 57.310 40.909 16.19 4.90 35.46 2.10
128 132 6.323225 GCTGTAATTAAGTACTACTCCCTCCA 59.677 42.308 13.68 0.00 0.00 3.86
130 134 8.849543 TGTAATTAAGTACTACTCCCTCCATT 57.150 34.615 13.68 0.00 0.00 3.16
134 138 9.725206 AATTAAGTACTACTCCCTCCATTTCTA 57.275 33.333 0.00 0.00 0.00 2.10
167 172 7.939588 AGCTTTTTAGAGATTTTGGTACAGACT 59.060 33.333 0.00 0.00 42.39 3.24
168 173 9.216117 GCTTTTTAGAGATTTTGGTACAGACTA 57.784 33.333 0.00 0.00 42.39 2.59
174 186 8.596781 AGAGATTTTGGTACAGACTACATACT 57.403 34.615 0.00 0.00 42.39 2.12
220 232 9.547753 ACACTCCAAAACATGTCTATATACATC 57.452 33.333 0.00 0.00 38.01 3.06
222 234 9.770097 ACTCCAAAACATGTCTATATACATCTG 57.230 33.333 0.00 0.00 38.01 2.90
276 290 8.791675 AGAAGCCTTATATTTAGTACGTACTCC 58.208 37.037 30.53 2.17 37.73 3.85
277 291 8.703378 AAGCCTTATATTTAGTACGTACTCCT 57.297 34.615 30.53 18.15 37.73 3.69
278 292 8.703378 AGCCTTATATTTAGTACGTACTCCTT 57.297 34.615 30.53 17.97 37.73 3.36
280 294 8.791675 GCCTTATATTTAGTACGTACTCCTTCT 58.208 37.037 30.53 16.21 37.73 2.85
287 301 7.986085 TTAGTACGTACTCCTTCTGTAAACT 57.014 36.000 30.53 7.28 37.73 2.66
288 302 9.502091 TTTAGTACGTACTCCTTCTGTAAACTA 57.498 33.333 30.53 6.25 37.73 2.24
289 303 7.986085 AGTACGTACTCCTTCTGTAAACTAA 57.014 36.000 22.45 0.00 0.00 2.24
290 304 8.572855 AGTACGTACTCCTTCTGTAAACTAAT 57.427 34.615 22.45 0.00 0.00 1.73
291 305 9.672673 AGTACGTACTCCTTCTGTAAACTAATA 57.327 33.333 22.45 0.00 0.00 0.98
299 313 9.400638 CTCCTTCTGTAAACTAATATAAGAGCG 57.599 37.037 0.00 0.00 0.00 5.03
300 314 8.910944 TCCTTCTGTAAACTAATATAAGAGCGT 58.089 33.333 0.00 0.00 0.00 5.07
301 315 9.530633 CCTTCTGTAAACTAATATAAGAGCGTT 57.469 33.333 0.00 0.00 0.00 4.84
353 367 8.773033 ACTCTTATATTAGTTTACGGAGGGAA 57.227 34.615 0.00 0.00 0.00 3.97
489 503 1.234615 ACAAGCCCGTACATGCACAC 61.235 55.000 6.41 0.00 0.00 3.82
512 526 5.186992 ACCTCAGTACAGTGCATACATACAA 59.813 40.000 0.00 0.00 0.00 2.41
513 527 5.520288 CCTCAGTACAGTGCATACATACAAC 59.480 44.000 0.00 0.00 0.00 3.32
515 529 4.267690 CAGTACAGTGCATACATACAACCG 59.732 45.833 0.00 0.00 0.00 4.44
516 530 3.603158 ACAGTGCATACATACAACCGA 57.397 42.857 0.00 0.00 0.00 4.69
517 531 4.137116 ACAGTGCATACATACAACCGAT 57.863 40.909 0.00 0.00 0.00 4.18
518 532 4.513442 ACAGTGCATACATACAACCGATT 58.487 39.130 0.00 0.00 0.00 3.34
519 533 4.941263 ACAGTGCATACATACAACCGATTT 59.059 37.500 0.00 0.00 0.00 2.17
520 534 5.163764 ACAGTGCATACATACAACCGATTTG 60.164 40.000 0.00 0.00 41.49 2.32
523 563 4.035091 TGCATACATACAACCGATTTGAGC 59.965 41.667 3.99 0.00 38.73 4.26
532 572 4.278170 ACAACCGATTTGAGCAATCTGAAA 59.722 37.500 3.99 0.00 39.50 2.69
562 608 1.528129 CAGAGGCTTCCTTGAACACC 58.472 55.000 0.00 0.00 31.76 4.16
573 620 0.184933 TTGAACACCCCTTCCACTGG 59.815 55.000 0.00 0.00 0.00 4.00
578 625 2.677875 CCCCTTCCACTGGCTTGC 60.678 66.667 0.00 0.00 0.00 4.01
666 713 1.136828 TGTTGGCCCTAGAACAGTGT 58.863 50.000 0.00 0.00 0.00 3.55
668 715 2.706723 TGTTGGCCCTAGAACAGTGTTA 59.293 45.455 8.88 0.00 0.00 2.41
675 722 5.243060 GGCCCTAGAACAGTGTTATTTTTGT 59.757 40.000 8.88 0.00 0.00 2.83
676 723 6.431852 GGCCCTAGAACAGTGTTATTTTTGTA 59.568 38.462 8.88 0.00 0.00 2.41
677 724 7.303261 GCCCTAGAACAGTGTTATTTTTGTAC 58.697 38.462 8.88 0.00 0.00 2.90
678 725 7.174426 GCCCTAGAACAGTGTTATTTTTGTACT 59.826 37.037 8.88 0.98 0.00 2.73
700 749 7.571080 ACTGTAGATGTTAGTAAGCTCCTAC 57.429 40.000 0.00 0.00 0.00 3.18
701 750 7.348033 ACTGTAGATGTTAGTAAGCTCCTACT 58.652 38.462 3.65 3.65 36.16 2.57
702 751 8.492782 ACTGTAGATGTTAGTAAGCTCCTACTA 58.507 37.037 1.82 1.82 34.03 1.82
703 752 8.905660 TGTAGATGTTAGTAAGCTCCTACTAG 57.094 38.462 5.64 0.00 36.11 2.57
704 753 6.887626 AGATGTTAGTAAGCTCCTACTAGC 57.112 41.667 10.80 10.80 43.11 3.42
705 754 6.366340 AGATGTTAGTAAGCTCCTACTAGCA 58.634 40.000 18.66 18.66 44.54 3.49
706 755 5.831702 TGTTAGTAAGCTCCTACTAGCAC 57.168 43.478 14.62 8.44 45.30 4.40
707 756 4.334759 TGTTAGTAAGCTCCTACTAGCACG 59.665 45.833 14.62 0.00 45.30 5.34
708 757 3.002038 AGTAAGCTCCTACTAGCACGT 57.998 47.619 0.00 0.00 45.30 4.49
709 758 4.148128 AGTAAGCTCCTACTAGCACGTA 57.852 45.455 0.00 0.00 45.30 3.57
710 759 4.716794 AGTAAGCTCCTACTAGCACGTAT 58.283 43.478 0.00 0.00 45.30 3.06
711 760 5.862845 AGTAAGCTCCTACTAGCACGTATA 58.137 41.667 0.00 0.00 45.30 1.47
712 761 5.933463 AGTAAGCTCCTACTAGCACGTATAG 59.067 44.000 0.00 5.63 45.30 1.31
713 762 4.620589 AGCTCCTACTAGCACGTATAGA 57.379 45.455 12.56 0.00 45.30 1.98
714 763 5.168647 AGCTCCTACTAGCACGTATAGAT 57.831 43.478 12.56 0.00 45.30 1.98
715 764 6.297080 AGCTCCTACTAGCACGTATAGATA 57.703 41.667 12.56 0.00 45.30 1.98
716 765 6.342906 AGCTCCTACTAGCACGTATAGATAG 58.657 44.000 12.56 4.83 45.30 2.08
717 766 5.006941 GCTCCTACTAGCACGTATAGATAGC 59.993 48.000 12.56 10.70 42.30 2.97
718 767 6.046290 TCCTACTAGCACGTATAGATAGCA 57.954 41.667 12.56 0.00 0.00 3.49
720 769 5.064962 CCTACTAGCACGTATAGATAGCACC 59.935 48.000 12.56 0.00 0.00 5.01
740 811 8.919777 AGCACCTCTAAACTAAATAAAAGTGT 57.080 30.769 0.00 0.00 0.00 3.55
755 826 4.819105 AAAGTGTAGATGGTCGATTCCA 57.181 40.909 0.00 0.00 42.01 3.53
769 840 4.153117 GTCGATTCCATGGCATAGATTGAC 59.847 45.833 10.12 15.57 0.00 3.18
788 859 4.014406 TGACGCTCTTCAATCTGGTACTA 58.986 43.478 0.00 0.00 0.00 1.82
800 871 5.926580 ATCTGGTACTAGTAGGCTAGGAA 57.073 43.478 1.87 0.00 46.81 3.36
839 916 0.834687 TTACAGACAGGGCTCGGGTT 60.835 55.000 0.00 0.00 0.00 4.11
842 919 2.046217 GACAGGGCTCGGGTTTCC 60.046 66.667 0.00 0.00 0.00 3.13
865 942 2.554142 GGAAATTAATTGCAGGCAGGC 58.446 47.619 8.47 0.00 0.00 4.85
872 949 4.704833 TGCAGGCAGGCCGAGAAC 62.705 66.667 4.37 0.00 41.95 3.01
997 1080 0.036294 GAGGGGTTCAGTGTGCCTAC 60.036 60.000 5.88 0.00 0.00 3.18
1069 1153 2.359169 CCCCTGCTCTCGCCACTAA 61.359 63.158 0.00 0.00 34.43 2.24
1070 1154 1.153549 CCCTGCTCTCGCCACTAAC 60.154 63.158 0.00 0.00 34.43 2.34
1090 1174 0.388649 AACACTTCGCCGCTACTCTG 60.389 55.000 0.00 0.00 0.00 3.35
1121 1211 9.871238 TCGGTAATATAAAAGCAGATTATCCTC 57.129 33.333 0.00 0.00 0.00 3.71
1172 1262 3.807622 TGTCTCGTGTGATTTGGTTTCTC 59.192 43.478 0.00 0.00 0.00 2.87
1183 1276 6.801862 GTGATTTGGTTTCTCGGATTTTACTG 59.198 38.462 0.00 0.00 0.00 2.74
1204 1298 3.452264 TGATGATGTTGGGTTCTCGATCT 59.548 43.478 0.00 0.00 0.00 2.75
1205 1299 3.526931 TGATGTTGGGTTCTCGATCTC 57.473 47.619 0.00 0.00 0.00 2.75
1383 1477 6.472887 GTGATTATTCCTTGATCCCGGATTA 58.527 40.000 0.73 0.00 0.00 1.75
1385 1479 8.265055 GTGATTATTCCTTGATCCCGGATTATA 58.735 37.037 0.73 0.00 0.00 0.98
1386 1480 8.265055 TGATTATTCCTTGATCCCGGATTATAC 58.735 37.037 0.73 0.00 0.00 1.47
1389 1487 7.749377 ATTCCTTGATCCCGGATTATACATA 57.251 36.000 0.73 0.00 0.00 2.29
1423 1521 4.944619 TGAGTGAATCTGGATAGCGATT 57.055 40.909 0.00 0.00 32.86 3.34
1464 1599 5.071788 TGGAGTTCAGTGGTTATTGAGAAGT 59.928 40.000 0.00 0.00 0.00 3.01
1465 1600 6.269077 TGGAGTTCAGTGGTTATTGAGAAGTA 59.731 38.462 0.00 0.00 0.00 2.24
1466 1601 6.814146 GGAGTTCAGTGGTTATTGAGAAGTAG 59.186 42.308 0.00 0.00 0.00 2.57
1606 1767 7.514721 TCCAACCTACTACTTCACTTGATTTT 58.485 34.615 0.00 0.00 0.00 1.82
1644 1806 7.042456 CGAGAGACTTCACTTGATTTTCTTTCA 60.042 37.037 0.00 0.00 0.00 2.69
1648 1810 7.337942 AGACTTCACTTGATTTTCTTTCACACT 59.662 33.333 0.00 0.00 0.00 3.55
1653 1815 7.554118 TCACTTGATTTTCTTTCACACTCTCTT 59.446 33.333 0.00 0.00 0.00 2.85
1654 1816 7.642978 CACTTGATTTTCTTTCACACTCTCTTG 59.357 37.037 0.00 0.00 0.00 3.02
1656 1818 5.824624 TGATTTTCTTTCACACTCTCTTGCT 59.175 36.000 0.00 0.00 0.00 3.91
1657 1819 6.319658 TGATTTTCTTTCACACTCTCTTGCTT 59.680 34.615 0.00 0.00 0.00 3.91
1658 1820 5.490139 TTTCTTTCACACTCTCTTGCTTG 57.510 39.130 0.00 0.00 0.00 4.01
1659 1821 2.874701 TCTTTCACACTCTCTTGCTTGC 59.125 45.455 0.00 0.00 0.00 4.01
1660 1822 1.597742 TTCACACTCTCTTGCTTGCC 58.402 50.000 0.00 0.00 0.00 4.52
1661 1823 0.601046 TCACACTCTCTTGCTTGCCG 60.601 55.000 0.00 0.00 0.00 5.69
1662 1824 0.882042 CACACTCTCTTGCTTGCCGT 60.882 55.000 0.00 0.00 0.00 5.68
1663 1825 0.679505 ACACTCTCTTGCTTGCCGTA 59.320 50.000 0.00 0.00 0.00 4.02
1664 1826 1.337260 ACACTCTCTTGCTTGCCGTAG 60.337 52.381 0.00 0.00 0.00 3.51
1665 1827 0.390472 ACTCTCTTGCTTGCCGTAGC 60.390 55.000 0.00 0.00 41.59 3.58
1666 1828 1.079127 TCTCTTGCTTGCCGTAGCC 60.079 57.895 0.00 0.00 40.49 3.93
1667 1829 2.046314 TCTTGCTTGCCGTAGCCC 60.046 61.111 0.00 0.00 40.49 5.19
1690 1856 7.040686 GCCCGTATCCATGTTAATTTATTCTGT 60.041 37.037 0.00 0.00 0.00 3.41
1735 1903 2.301346 AGTTGTTGAACTGGCCTCTTG 58.699 47.619 3.32 0.00 41.12 3.02
1765 1933 7.924947 ACTTACTCTGTAAGGTTAAACTGTGTC 59.075 37.037 18.05 0.00 0.00 3.67
1773 1941 2.501261 GTTAAACTGTGTCCAGGACCC 58.499 52.381 17.59 6.07 43.36 4.46
1783 1951 4.847512 TGTGTCCAGGACCCTTCTAATTTA 59.152 41.667 17.59 0.00 0.00 1.40
1793 1961 6.016777 GGACCCTTCTAATTTATGAGCATGTG 60.017 42.308 0.00 0.00 0.00 3.21
1795 1963 6.543831 ACCCTTCTAATTTATGAGCATGTGTC 59.456 38.462 0.00 0.00 0.00 3.67
1806 1974 3.193263 GAGCATGTGTCCTGTCTATGTG 58.807 50.000 0.00 0.00 0.00 3.21
1809 1977 3.790091 CATGTGTCCTGTCTATGTGAGG 58.210 50.000 0.00 0.00 0.00 3.86
1811 1979 2.562738 TGTGTCCTGTCTATGTGAGGTG 59.437 50.000 0.00 0.00 0.00 4.00
1848 2016 9.851686 TCCATTATTCAGTATAACAATGAAGCT 57.148 29.630 0.00 0.00 36.47 3.74
1985 2153 3.942351 CCATGAGGTGAGCAACTGA 57.058 52.632 0.00 0.00 0.00 3.41
1995 2163 3.124578 TGAGCAACTGAGCACACATAA 57.875 42.857 0.00 0.00 36.85 1.90
2031 2217 4.326826 TGGGTTCTTCTGTTCATCATGAC 58.673 43.478 0.00 0.00 0.00 3.06
2039 2225 4.067192 TCTGTTCATCATGACACAACCAG 58.933 43.478 0.00 0.14 0.00 4.00
2118 2305 6.293135 GCATAAATTCGATCTCCTTCAGGAAC 60.293 42.308 0.00 0.00 44.91 3.62
2161 2348 2.710096 TTGTTCAGCCCATACCTAGC 57.290 50.000 0.00 0.00 0.00 3.42
2241 2428 7.090953 AGTCACATCTCACTAAAGCTACTAC 57.909 40.000 0.00 0.00 0.00 2.73
2275 2470 8.090214 CACATTCTGACTTGGTTTCCATAAAAT 58.910 33.333 0.00 0.00 31.53 1.82
2276 2471 8.650490 ACATTCTGACTTGGTTTCCATAAAATT 58.350 29.630 0.00 0.00 31.53 1.82
2319 2524 0.729116 GACACTGGCAACCATGATCG 59.271 55.000 0.00 0.00 30.82 3.69
2354 2568 6.816134 TGCACTGACAAGCTATGATAAAAA 57.184 33.333 0.00 0.00 0.00 1.94
2560 2774 1.450312 CACCGATGTTCCAGCTCCC 60.450 63.158 0.00 0.00 0.00 4.30
2595 2810 3.945346 ACGCACAGGTATTTATTGTCCA 58.055 40.909 0.00 0.00 0.00 4.02
2683 2898 4.751098 TCTTTTGCTTGTTTCATTCATGGC 59.249 37.500 0.00 0.00 0.00 4.40
2684 2899 4.339872 TTTGCTTGTTTCATTCATGGCT 57.660 36.364 0.00 0.00 0.00 4.75
2773 2988 4.929146 AGGAAAGCCTGTGGTAAGTATT 57.071 40.909 0.00 0.00 44.90 1.89
2833 3050 3.731652 TGTTTGCAGATGAAAAGTGGG 57.268 42.857 0.00 0.00 0.00 4.61
2836 3053 1.538047 TGCAGATGAAAAGTGGGAGC 58.462 50.000 0.00 0.00 0.00 4.70
2837 3054 1.202915 TGCAGATGAAAAGTGGGAGCA 60.203 47.619 0.00 0.00 0.00 4.26
2838 3055 1.200948 GCAGATGAAAAGTGGGAGCAC 59.799 52.381 0.00 0.00 0.00 4.40
2849 3066 0.776810 TGGGAGCACCAGGATTTGAA 59.223 50.000 1.58 0.00 46.80 2.69
2854 3071 2.424956 GAGCACCAGGATTTGAATGTCC 59.575 50.000 0.00 0.00 34.64 4.02
2885 3102 6.793505 TCTGGTTTCTAGTTATCCCTCTTC 57.206 41.667 0.00 0.00 0.00 2.87
2886 3103 5.360144 TCTGGTTTCTAGTTATCCCTCTTCG 59.640 44.000 0.00 0.00 0.00 3.79
3219 3436 1.600013 TCGCACAATACGCACTTTTGT 59.400 42.857 0.00 0.00 34.03 2.83
3330 3555 4.279169 TGCAGAGATAAGCAATTATTGGCC 59.721 41.667 7.08 0.00 37.90 5.36
3348 3574 1.290009 CGCTTGCCTTTTTCAGGGG 59.710 57.895 0.00 0.00 44.16 4.79
3396 3622 2.634453 TCAACTGATCACTGAAGCTGGA 59.366 45.455 0.00 0.00 0.00 3.86
3432 3658 4.101448 AGCGATGTCACAGGGGCC 62.101 66.667 0.00 0.00 0.00 5.80
3576 3803 3.785859 GTCCTCATCCCGGCAGCA 61.786 66.667 0.00 0.00 0.00 4.41
3607 3834 9.308318 GAGGAGTCATAAACAAGTAATCTTCTC 57.692 37.037 0.00 0.00 0.00 2.87
3608 3835 8.261522 AGGAGTCATAAACAAGTAATCTTCTCC 58.738 37.037 0.00 0.00 34.88 3.71
3609 3836 8.261522 GGAGTCATAAACAAGTAATCTTCTCCT 58.738 37.037 0.00 0.00 33.38 3.69
3610 3837 9.660180 GAGTCATAAACAAGTAATCTTCTCCTT 57.340 33.333 0.00 0.00 0.00 3.36
3656 3888 8.871629 TCATCCTACCTTCTATCAGATTACTC 57.128 38.462 0.00 0.00 0.00 2.59
3660 3892 6.661805 CCTACCTTCTATCAGATTACTCCTCC 59.338 46.154 0.00 0.00 0.00 4.30
3902 4142 5.228635 GCTCGCATTTGTTGACATAATTCAG 59.771 40.000 0.00 0.00 0.00 3.02
4292 4537 2.412112 GGGATCCCGTCGAAGTCG 59.588 66.667 17.02 0.00 39.05 4.18
4302 4547 1.205657 GTCGAAGTCGCAACTCAACA 58.794 50.000 0.00 0.00 39.60 3.33
4366 4611 2.808906 TCCGATCTCTTGGAGACTGA 57.191 50.000 0.00 0.00 41.76 3.41
4479 4736 2.068519 GTGTTGATGATGCGTGAGTCA 58.931 47.619 0.00 0.00 0.00 3.41
4503 4762 3.902261 TTATTAGCATCGCATGGCAAG 57.098 42.857 0.00 0.00 0.00 4.01
4504 4763 0.956633 ATTAGCATCGCATGGCAAGG 59.043 50.000 0.00 0.00 0.00 3.61
4505 4764 1.727511 TTAGCATCGCATGGCAAGGC 61.728 55.000 4.59 4.59 0.00 4.35
4506 4765 2.890201 TAGCATCGCATGGCAAGGCA 62.890 55.000 13.78 0.00 30.73 4.75
4507 4766 2.886610 CATCGCATGGCAAGGCAA 59.113 55.556 13.78 0.00 30.73 4.52
4509 4768 1.978080 ATCGCATGGCAAGGCAACA 60.978 52.632 13.78 0.00 41.41 3.33
4557 4820 2.181584 GATGAGTGGGTCGTCGTCT 58.818 57.895 0.00 0.00 31.39 4.18
5134 5409 4.680237 TGGACGCACGAGGCCAAG 62.680 66.667 5.01 0.00 40.31 3.61
5152 5429 1.185618 AGGCGAGTGAGTGGCTTACA 61.186 55.000 0.00 0.00 37.82 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 8.204836 ACTGTAGAAATCAGTTGTCTGTACTTT 58.795 33.333 0.00 0.00 42.50 2.66
33 34 8.405418 ACTACTGTAGAAATCAGTTGTCTGTA 57.595 34.615 21.01 0.00 43.89 2.74
41 42 9.908747 AGTGATACTACTACTGTAGAAATCAGT 57.091 33.333 21.01 18.80 46.76 3.41
43 44 9.901172 TGAGTGATACTACTACTGTAGAAATCA 57.099 33.333 21.01 17.43 46.76 2.57
58 62 5.506708 TGGTCTAGCAGTTGAGTGATACTA 58.493 41.667 0.00 0.00 0.00 1.82
97 101 8.901793 GGAGTAGTACTTAATTACAGCTACAGT 58.098 37.037 0.00 4.57 32.31 3.55
108 112 8.625467 AGAAATGGAGGGAGTAGTACTTAATT 57.375 34.615 0.00 0.00 0.00 1.40
161 166 9.026121 ACTCATTTTACTCAGTATGTAGTCTGT 57.974 33.333 0.00 0.00 37.40 3.41
162 167 9.295214 CACTCATTTTACTCAGTATGTAGTCTG 57.705 37.037 0.00 0.00 37.40 3.51
164 169 9.856488 TTCACTCATTTTACTCAGTATGTAGTC 57.144 33.333 0.00 0.00 37.40 2.59
196 208 9.770097 CAGATGTATATAGACATGTTTTGGAGT 57.230 33.333 17.40 0.00 40.18 3.85
251 265 8.791675 AGGAGTACGTACTAAATATAAGGCTTC 58.208 37.037 27.44 10.26 36.50 3.86
273 287 9.400638 CGCTCTTATATTAGTTTACAGAAGGAG 57.599 37.037 0.00 0.00 0.00 3.69
274 288 8.910944 ACGCTCTTATATTAGTTTACAGAAGGA 58.089 33.333 0.00 0.00 0.00 3.36
275 289 9.530633 AACGCTCTTATATTAGTTTACAGAAGG 57.469 33.333 0.00 0.00 0.00 3.46
327 341 9.866655 TTCCCTCCGTAAACTAATATAAGAGTA 57.133 33.333 0.00 0.00 0.00 2.59
328 342 8.773033 TTCCCTCCGTAAACTAATATAAGAGT 57.227 34.615 0.00 0.00 0.00 3.24
334 348 9.151177 TCAAGTATTCCCTCCGTAAACTAATAT 57.849 33.333 0.00 0.00 0.00 1.28
335 349 8.416329 GTCAAGTATTCCCTCCGTAAACTAATA 58.584 37.037 0.00 0.00 0.00 0.98
336 350 7.125356 AGTCAAGTATTCCCTCCGTAAACTAAT 59.875 37.037 0.00 0.00 0.00 1.73
337 351 6.438425 AGTCAAGTATTCCCTCCGTAAACTAA 59.562 38.462 0.00 0.00 0.00 2.24
338 352 5.954150 AGTCAAGTATTCCCTCCGTAAACTA 59.046 40.000 0.00 0.00 0.00 2.24
339 353 4.776308 AGTCAAGTATTCCCTCCGTAAACT 59.224 41.667 0.00 0.00 0.00 2.66
340 354 4.868734 CAGTCAAGTATTCCCTCCGTAAAC 59.131 45.833 0.00 0.00 0.00 2.01
341 355 4.529377 ACAGTCAAGTATTCCCTCCGTAAA 59.471 41.667 0.00 0.00 0.00 2.01
342 356 4.091549 ACAGTCAAGTATTCCCTCCGTAA 58.908 43.478 0.00 0.00 0.00 3.18
343 357 3.705051 ACAGTCAAGTATTCCCTCCGTA 58.295 45.455 0.00 0.00 0.00 4.02
344 358 2.537143 ACAGTCAAGTATTCCCTCCGT 58.463 47.619 0.00 0.00 0.00 4.69
345 359 3.611766 AACAGTCAAGTATTCCCTCCG 57.388 47.619 0.00 0.00 0.00 4.63
346 360 4.695928 GTCAAACAGTCAAGTATTCCCTCC 59.304 45.833 0.00 0.00 0.00 4.30
347 361 5.305585 TGTCAAACAGTCAAGTATTCCCTC 58.694 41.667 0.00 0.00 0.00 4.30
348 362 5.071788 TCTGTCAAACAGTCAAGTATTCCCT 59.928 40.000 6.96 0.00 46.03 4.20
349 363 5.179555 GTCTGTCAAACAGTCAAGTATTCCC 59.820 44.000 6.96 0.00 46.03 3.97
350 364 5.758296 TGTCTGTCAAACAGTCAAGTATTCC 59.242 40.000 6.96 0.00 46.03 3.01
351 365 6.844696 TGTCTGTCAAACAGTCAAGTATTC 57.155 37.500 6.96 0.00 46.03 1.75
352 366 6.767902 ACATGTCTGTCAAACAGTCAAGTATT 59.232 34.615 11.50 0.00 44.69 1.89
353 367 6.291377 ACATGTCTGTCAAACAGTCAAGTAT 58.709 36.000 11.50 0.00 44.69 2.12
383 397 2.306805 TGATCCCTGACACTTCATGCTT 59.693 45.455 0.00 0.00 0.00 3.91
430 444 2.517450 GCTGATACGCTGACGGTGC 61.517 63.158 0.00 0.00 46.04 5.01
474 488 2.046314 AGGTGTGCATGTACGGGC 60.046 61.111 9.48 1.89 0.00 6.13
489 503 5.262588 TGTATGTATGCACTGTACTGAGG 57.737 43.478 6.77 0.00 0.00 3.86
562 608 3.058160 CGCAAGCCAGTGGAAGGG 61.058 66.667 15.20 5.97 0.00 3.95
573 620 0.457337 CCAGAATTTGAGCCGCAAGC 60.457 55.000 0.00 0.00 44.25 4.01
578 625 0.819582 AATGCCCAGAATTTGAGCCG 59.180 50.000 0.00 0.00 27.63 5.52
675 722 8.492782 AGTAGGAGCTTACTAACATCTACAGTA 58.507 37.037 0.00 0.00 32.25 2.74
676 723 7.348033 AGTAGGAGCTTACTAACATCTACAGT 58.652 38.462 0.00 0.00 32.25 3.55
677 724 7.811117 AGTAGGAGCTTACTAACATCTACAG 57.189 40.000 0.00 0.00 32.25 2.74
678 725 7.444792 GCTAGTAGGAGCTTACTAACATCTACA 59.555 40.741 6.73 0.00 39.50 2.74
700 749 4.938832 AGAGGTGCTATCTATACGTGCTAG 59.061 45.833 0.00 0.00 0.00 3.42
701 750 4.907809 AGAGGTGCTATCTATACGTGCTA 58.092 43.478 0.00 0.00 0.00 3.49
702 751 3.757270 AGAGGTGCTATCTATACGTGCT 58.243 45.455 0.00 0.00 0.00 4.40
703 752 5.624344 TTAGAGGTGCTATCTATACGTGC 57.376 43.478 0.00 0.00 0.00 5.34
704 753 7.204496 AGTTTAGAGGTGCTATCTATACGTG 57.796 40.000 0.00 0.00 36.74 4.49
705 754 8.915057 TTAGTTTAGAGGTGCTATCTATACGT 57.085 34.615 0.00 0.00 36.74 3.57
715 764 8.919777 ACACTTTTATTTAGTTTAGAGGTGCT 57.080 30.769 0.00 0.00 0.00 4.40
732 803 6.288941 TGGAATCGACCATCTACACTTTTA 57.711 37.500 0.00 0.00 34.77 1.52
738 809 2.224281 GCCATGGAATCGACCATCTACA 60.224 50.000 18.40 0.00 46.24 2.74
740 811 2.046292 TGCCATGGAATCGACCATCTA 58.954 47.619 18.40 0.00 46.24 1.98
755 826 3.181462 TGAAGAGCGTCAATCTATGCCAT 60.181 43.478 0.00 0.00 31.41 4.40
769 840 4.640789 ACTAGTACCAGATTGAAGAGCG 57.359 45.455 0.00 0.00 0.00 5.03
788 859 7.727634 ACCGTAATTAACTATTCCTAGCCTACT 59.272 37.037 0.00 0.00 0.00 2.57
839 916 3.197549 GCCTGCAATTAATTTCCCTGGAA 59.802 43.478 14.91 0.00 0.00 3.53
842 919 3.431207 CCTGCCTGCAATTAATTTCCCTG 60.431 47.826 0.00 0.00 0.00 4.45
872 949 5.365021 ACCAGGATAAGAACAAGATCTGG 57.635 43.478 0.00 0.00 0.00 3.86
997 1080 2.233676 TCAGGTAGGCCGTATGCATATG 59.766 50.000 17.55 17.55 43.89 1.78
1060 1143 1.493772 CGAAGTGTTGTTAGTGGCGA 58.506 50.000 0.00 0.00 0.00 5.54
1062 1145 0.237498 GGCGAAGTGTTGTTAGTGGC 59.763 55.000 0.00 0.00 0.00 5.01
1067 1151 1.000060 AGTAGCGGCGAAGTGTTGTTA 60.000 47.619 12.98 0.00 0.00 2.41
1069 1153 0.666577 GAGTAGCGGCGAAGTGTTGT 60.667 55.000 12.98 0.00 0.00 3.32
1070 1154 0.388649 AGAGTAGCGGCGAAGTGTTG 60.389 55.000 12.98 0.00 0.00 3.33
1090 1174 4.980434 TCTGCTTTTATATTACCGACGAGC 59.020 41.667 0.00 0.00 0.00 5.03
1121 1211 2.507992 CTCTGCGCGAGGAACCAG 60.508 66.667 12.10 6.55 36.06 4.00
1172 1262 4.640201 ACCCAACATCATCAGTAAAATCCG 59.360 41.667 0.00 0.00 0.00 4.18
1183 1276 4.054671 GAGATCGAGAACCCAACATCATC 58.945 47.826 0.00 0.00 0.00 2.92
1204 1298 3.722295 CGCCGCGCCTGAAAAAGA 61.722 61.111 0.00 0.00 0.00 2.52
1205 1299 4.759096 CCGCCGCGCCTGAAAAAG 62.759 66.667 7.42 0.00 0.00 2.27
1383 1477 8.510243 TCACTCATTCACAGCAAAATATGTAT 57.490 30.769 0.00 0.00 0.00 2.29
1385 1479 6.822667 TCACTCATTCACAGCAAAATATGT 57.177 33.333 0.00 0.00 0.00 2.29
1386 1480 8.188799 AGATTCACTCATTCACAGCAAAATATG 58.811 33.333 0.00 0.00 0.00 1.78
1389 1487 6.387465 CAGATTCACTCATTCACAGCAAAAT 58.613 36.000 0.00 0.00 0.00 1.82
1423 1521 5.401531 ACTCCATAGAACAAAGAGCGTAA 57.598 39.130 0.00 0.00 0.00 3.18
1464 1599 3.112263 CCCAAGGACCAAGGTGATACTA 58.888 50.000 0.00 0.00 0.00 1.82
1465 1600 1.916181 CCCAAGGACCAAGGTGATACT 59.084 52.381 0.00 0.00 0.00 2.12
1466 1601 1.064685 CCCCAAGGACCAAGGTGATAC 60.065 57.143 0.00 0.00 33.47 2.24
1620 1782 7.554118 TGTGAAAGAAAATCAAGTGAAGTCTCT 59.446 33.333 0.00 0.00 0.00 3.10
1644 1806 0.679505 TACGGCAAGCAAGAGAGTGT 59.320 50.000 0.00 0.00 0.00 3.55
1648 1810 1.079127 GGCTACGGCAAGCAAGAGA 60.079 57.895 10.58 0.00 44.64 3.10
1661 1823 7.916914 ATAAATTAACATGGATACGGGCTAC 57.083 36.000 0.00 0.00 42.51 3.58
1662 1824 8.380099 AGAATAAATTAACATGGATACGGGCTA 58.620 33.333 0.00 0.00 42.51 3.93
1663 1825 7.174946 CAGAATAAATTAACATGGATACGGGCT 59.825 37.037 0.00 0.00 42.51 5.19
1664 1826 7.040686 ACAGAATAAATTAACATGGATACGGGC 60.041 37.037 0.00 0.00 42.51 6.13
1665 1827 8.391075 ACAGAATAAATTAACATGGATACGGG 57.609 34.615 0.00 0.00 42.51 5.28
1690 1856 5.480642 TTTGCCATATTCAGCAGGAAAAA 57.519 34.783 0.00 0.00 40.73 1.94
1716 1882 1.338020 CCAAGAGGCCAGTTCAACAAC 59.662 52.381 5.01 0.00 0.00 3.32
1717 1883 1.691196 CCAAGAGGCCAGTTCAACAA 58.309 50.000 5.01 0.00 0.00 2.83
1735 1903 3.697619 AACCTTACAGAGTAAGTGGCC 57.302 47.619 13.92 0.00 0.00 5.36
1765 1933 5.066593 GCTCATAAATTAGAAGGGTCCTGG 58.933 45.833 0.00 0.00 0.00 4.45
1773 1941 7.281774 ACAGGACACATGCTCATAAATTAGAAG 59.718 37.037 0.00 0.00 0.00 2.85
1783 1951 3.453717 ACATAGACAGGACACATGCTCAT 59.546 43.478 0.00 0.00 0.00 2.90
1793 1961 3.511934 AGTTCACCTCACATAGACAGGAC 59.488 47.826 0.00 0.00 0.00 3.85
1795 1963 3.259374 ACAGTTCACCTCACATAGACAGG 59.741 47.826 0.00 0.00 0.00 4.00
1836 2004 3.382865 TGCAACCACAAGCTTCATTGTTA 59.617 39.130 0.00 0.00 41.41 2.41
1837 2005 2.168106 TGCAACCACAAGCTTCATTGTT 59.832 40.909 0.00 0.00 41.41 2.83
1839 2007 2.400399 CTGCAACCACAAGCTTCATTG 58.600 47.619 0.00 0.00 36.22 2.82
1840 2008 1.342174 CCTGCAACCACAAGCTTCATT 59.658 47.619 0.00 0.00 0.00 2.57
1841 2009 0.963962 CCTGCAACCACAAGCTTCAT 59.036 50.000 0.00 0.00 0.00 2.57
1844 2012 0.461135 CAACCTGCAACCACAAGCTT 59.539 50.000 0.00 0.00 0.00 3.74
1845 2013 0.395586 TCAACCTGCAACCACAAGCT 60.396 50.000 0.00 0.00 0.00 3.74
1846 2014 0.031178 CTCAACCTGCAACCACAAGC 59.969 55.000 0.00 0.00 0.00 4.01
1847 2015 1.066002 CACTCAACCTGCAACCACAAG 59.934 52.381 0.00 0.00 0.00 3.16
1848 2016 1.102154 CACTCAACCTGCAACCACAA 58.898 50.000 0.00 0.00 0.00 3.33
1995 2163 9.845214 ACAGAAGAACCCAGGAATATATATACT 57.155 33.333 0.00 0.00 0.00 2.12
2031 2217 1.888512 AGTGCTTAATGGCTGGTTGTG 59.111 47.619 0.00 0.00 0.00 3.33
2039 2225 3.861689 GCAAGAATCAAGTGCTTAATGGC 59.138 43.478 0.00 0.00 35.36 4.40
2118 2305 8.824781 CAATAAGTCATTCAACTATCTGACAGG 58.175 37.037 1.81 0.00 40.32 4.00
2241 2428 3.688185 CCAAGTCAGAATGTGATCCAGTG 59.312 47.826 0.00 0.00 37.56 3.66
2275 2470 2.086094 ACTTGCATGCACATGATCGAA 58.914 42.857 22.58 0.59 41.20 3.71
2276 2471 1.741528 ACTTGCATGCACATGATCGA 58.258 45.000 22.58 1.44 41.20 3.59
2319 2524 5.333416 GCTTGTCAGTGCAAGAACTTACTAC 60.333 44.000 23.11 6.03 46.34 2.73
2524 2738 2.097466 GGTGTGGATGCCAATTAAGTCG 59.903 50.000 0.00 0.00 34.18 4.18
2560 2774 1.817520 TGCGTTGGTGCCCATATCG 60.818 57.895 0.00 3.18 31.53 2.92
2683 2898 4.885907 AGTATCCATGCCATTGTCTGAAAG 59.114 41.667 0.00 0.00 0.00 2.62
2684 2899 4.641541 CAGTATCCATGCCATTGTCTGAAA 59.358 41.667 0.00 0.00 0.00 2.69
2818 3035 1.200948 GTGCTCCCACTTTTCATCTGC 59.799 52.381 0.00 0.00 38.93 4.26
2833 3050 2.424956 GGACATTCAAATCCTGGTGCTC 59.575 50.000 0.00 0.00 31.75 4.26
2836 3053 3.689347 TCTGGACATTCAAATCCTGGTG 58.311 45.455 0.00 0.00 35.86 4.17
2837 3054 3.588842 TCTCTGGACATTCAAATCCTGGT 59.411 43.478 0.00 0.00 35.86 4.00
2838 3055 4.226427 TCTCTGGACATTCAAATCCTGG 57.774 45.455 0.00 0.00 35.86 4.45
2870 3087 4.592485 ACATGCGAAGAGGGATAACTAG 57.408 45.455 0.00 0.00 0.00 2.57
2913 3130 0.107459 GTGATCCTCCAAGGTCCTGC 60.107 60.000 0.00 0.00 36.53 4.85
3169 3386 4.959723 ACGGCCACTTTTTAACTAGTACA 58.040 39.130 2.24 0.00 0.00 2.90
3170 3387 4.990426 TGACGGCCACTTTTTAACTAGTAC 59.010 41.667 2.24 0.00 0.00 2.73
3187 3404 3.188786 GTGCGATCCACTGACGGC 61.189 66.667 6.98 0.00 41.35 5.68
3219 3436 9.729281 CTTACTCCCTTTTGTAACCATAAAGTA 57.271 33.333 0.00 0.00 0.00 2.24
3330 3555 1.290009 CCCCTGAAAAAGGCAAGCG 59.710 57.895 0.00 0.00 45.89 4.68
3348 3574 2.231235 CCAGGAGCCAACATTACCAAAC 59.769 50.000 0.00 0.00 0.00 2.93
3432 3658 1.522668 TGCCATTGGAGTTCTTGACG 58.477 50.000 6.95 0.00 0.00 4.35
3531 3758 2.771763 CTTCCGTGAGCAGCGAGGTT 62.772 60.000 0.00 0.00 0.00 3.50
3576 3803 3.910627 ACTTGTTTATGACTCCTCCCAGT 59.089 43.478 0.00 0.00 0.00 4.00
3607 3834 1.219393 GCTGGGACGAGGAGAAAGG 59.781 63.158 0.00 0.00 0.00 3.11
3608 3835 0.174617 GAGCTGGGACGAGGAGAAAG 59.825 60.000 0.00 0.00 0.00 2.62
3609 3836 0.541998 TGAGCTGGGACGAGGAGAAA 60.542 55.000 0.00 0.00 0.00 2.52
3610 3837 1.076727 TGAGCTGGGACGAGGAGAA 59.923 57.895 0.00 0.00 0.00 2.87
3611 3838 1.679305 GTGAGCTGGGACGAGGAGA 60.679 63.158 0.00 0.00 0.00 3.71
3612 3839 1.254284 AAGTGAGCTGGGACGAGGAG 61.254 60.000 0.00 0.00 0.00 3.69
3656 3888 6.696441 ACTAGTATAACTGAACTTCGGAGG 57.304 41.667 4.52 0.00 0.00 4.30
3728 3965 3.799281 TGGTCAAGAACAGCCTTTTTG 57.201 42.857 0.00 0.00 0.00 2.44
4006 4251 0.456312 CGAAGTAGCTCACCGTCACC 60.456 60.000 0.00 0.00 0.00 4.02
4363 4608 2.064762 GTGCTGCTACTGTTCTGTCAG 58.935 52.381 0.00 0.00 40.80 3.51
4364 4609 1.270305 GGTGCTGCTACTGTTCTGTCA 60.270 52.381 0.00 0.00 0.00 3.58
4365 4610 1.270305 TGGTGCTGCTACTGTTCTGTC 60.270 52.381 0.00 0.00 0.00 3.51
4366 4611 0.758734 TGGTGCTGCTACTGTTCTGT 59.241 50.000 0.00 0.00 0.00 3.41
4479 4736 5.199024 TGCCATGCGATGCTAATAAAATT 57.801 34.783 0.00 0.00 0.00 1.82
4504 4763 1.368850 GACGTCGTTGGCTTGTTGC 60.369 57.895 0.00 0.00 41.94 4.17
4505 4764 0.586319 ATGACGTCGTTGGCTTGTTG 59.414 50.000 11.62 0.00 0.00 3.33
4506 4765 0.586319 CATGACGTCGTTGGCTTGTT 59.414 50.000 7.76 0.00 0.00 2.83
4507 4766 0.249699 TCATGACGTCGTTGGCTTGT 60.250 50.000 7.76 0.00 0.00 3.16
4509 4768 0.865769 GTTCATGACGTCGTTGGCTT 59.134 50.000 7.76 0.00 0.00 4.35
4517 4780 1.059264 GCTTACGCAGTTCATGACGTC 59.941 52.381 9.11 9.11 37.78 4.34
4537 4800 2.102357 CGACGACCCACTCATCGG 59.898 66.667 0.00 0.00 42.67 4.18
4557 4820 2.103373 GTCTACAGCCTCATCTCCACA 58.897 52.381 0.00 0.00 0.00 4.17
4863 5126 4.758251 CACACCTGGATCCGCGCA 62.758 66.667 8.75 0.00 0.00 6.09
5089 5364 1.272769 ACTCTGTCCAACGAACTAGGC 59.727 52.381 0.00 0.00 0.00 3.93
5094 5369 2.395654 GTCTCACTCTGTCCAACGAAC 58.604 52.381 0.00 0.00 0.00 3.95
5123 5398 4.379243 ACTCGCCTTGGCCTCGTG 62.379 66.667 3.32 6.09 0.00 4.35
5130 5405 2.738213 AAGCCACTCACTCGCCTTGG 62.738 60.000 0.00 0.00 0.00 3.61
5131 5406 0.037326 TAAGCCACTCACTCGCCTTG 60.037 55.000 0.00 0.00 0.00 3.61
5134 5409 0.108138 ATGTAAGCCACTCACTCGCC 60.108 55.000 0.00 0.00 0.00 5.54
5136 5411 2.427453 AGGTATGTAAGCCACTCACTCG 59.573 50.000 0.00 0.00 0.00 4.18
5152 5429 3.586174 CCCATCACATGAGGATGAGGTAT 59.414 47.826 24.11 0.00 43.80 2.73


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

AutoCloner maintained by Alex Coulton.