Multiple sequence alignment - TraesCS7D01G086200

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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 TraesCS7D01G086200 chr7D 100.000 5254 0 0 1 5254 52854071 52848818 0.000000e+00 9703.0
1 TraesCS7D01G086200 chr7A 97.047 2743 52 11 2402 5123 55344321 55347055 0.000000e+00 4590.0
2 TraesCS7D01G086200 chr7A 91.852 540 15 7 1844 2369 55343489 55344013 0.000000e+00 726.0
3 TraesCS7D01G086200 chr7A 87.269 542 29 12 918 1429 55342240 55342771 2.730000e-162 582.0
4 TraesCS7D01G086200 chr7A 90.941 287 21 4 1557 1841 55342858 55343141 1.070000e-101 381.0
5 TraesCS7D01G086200 chr7A 98.529 68 0 1 5187 5254 55347069 55347135 9.240000e-23 119.0
6 TraesCS7D01G086200 chr7A 100.000 27 0 0 2509 2535 55344309 55344335 3.400000e-02 51.0
7 TraesCS7D01G086200 chr4A 93.957 1059 44 7 3335 4384 667844604 667845651 0.000000e+00 1583.0
8 TraesCS7D01G086200 chr4A 91.221 934 55 9 2418 3337 667843402 667844322 0.000000e+00 1245.0
9 TraesCS7D01G086200 chr4A 86.770 839 65 28 1284 2098 667842419 667843235 0.000000e+00 893.0
10 TraesCS7D01G086200 chr4A 93.671 474 17 7 691 1162 667841745 667842207 0.000000e+00 697.0
11 TraesCS7D01G086200 chr4A 86.833 600 67 6 2 592 667839615 667840211 0.000000e+00 660.0
12 TraesCS7D01G086200 chr5A 81.022 137 24 2 4679 4814 403708273 403708138 2.000000e-19 108.0
13 TraesCS7D01G086200 chr5A 97.222 36 1 0 249 284 84130004 84129969 1.580000e-05 62.1
14 TraesCS7D01G086200 chr2B 83.146 89 15 0 1070 1158 729627580 729627668 1.210000e-11 82.4
15 TraesCS7D01G086200 chr5D 89.286 56 4 1 238 291 90332793 90332738 9.440000e-08 69.4


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 TraesCS7D01G086200 chr7D 52848818 52854071 5253 True 9703.000000 9703 100.0000 1 5254 1 chr7D.!!$R1 5253
1 TraesCS7D01G086200 chr7A 55342240 55347135 4895 False 1074.833333 4590 94.2730 918 5254 6 chr7A.!!$F1 4336
2 TraesCS7D01G086200 chr4A 667839615 667845651 6036 False 1015.600000 1583 90.4904 2 4384 5 chr4A.!!$F1 4382

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
416 426 0.043485 TATACTGCCACCCTCCACCA 59.957 55.000 0.0 0.0 0.0 4.17 F
895 2385 0.250513 ATGGTGGAGAAGAAGCCGTC 59.749 55.000 0.0 0.0 0.0 4.79 F
1571 3225 0.528470 CACACACCCACAAAAACGGT 59.472 50.000 0.0 0.0 0.0 4.83 F
2455 4811 0.668096 TCCGCCGTTGATGTGTGTAC 60.668 55.000 0.0 0.0 0.0 2.90 F
2716 5072 1.344438 CTGCGAATCATGGCCCTAGTA 59.656 52.381 0.0 0.0 0.0 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1847 3852 0.179174 GGCTACCAACAAAATCGCCG 60.179 55.000 0.00 0.0 0.00 6.46 R
2369 4388 2.098280 CCACCGACACACATTGTTTTCA 59.902 45.455 0.00 0.0 39.17 2.69 R
3474 6126 1.267334 CGGCATTGTATTTGTCGTCGG 60.267 52.381 0.00 0.0 37.42 4.79 R
4147 6812 0.530650 AGCACATATGAAGGCGACGG 60.531 55.000 10.38 0.0 0.00 4.79 R
4335 7009 1.211949 GGCACTGCATAAACCTCCCTA 59.788 52.381 2.82 0.0 0.00 3.53 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
34 35 0.464036 TGACAAGGACACAAGAGCGT 59.536 50.000 0.00 0.00 0.00 5.07
44 45 3.311110 AAGAGCGTCGAGGCCCAA 61.311 61.111 25.27 0.00 0.00 4.12
47 48 1.745489 GAGCGTCGAGGCCCAAAAT 60.745 57.895 25.27 6.73 0.00 1.82
52 53 1.376683 TCGAGGCCCAAAATCACCG 60.377 57.895 0.00 0.00 0.00 4.94
58 59 2.478746 CCAAAATCACCGGACGCG 59.521 61.111 9.46 3.53 0.00 6.01
59 60 2.478746 CAAAATCACCGGACGCGG 59.521 61.111 9.46 0.00 0.00 6.46
90 91 1.251251 CAAAAAGAGGCCTCCACCAG 58.749 55.000 29.54 13.11 0.00 4.00
98 99 1.980772 GCCTCCACCAGCTTTGCAT 60.981 57.895 0.00 0.00 0.00 3.96
102 103 1.214589 CCACCAGCTTTGCATGAGC 59.785 57.895 13.16 13.16 40.43 4.26
112 113 2.034104 TTGCATGAGCTCTCATCCAC 57.966 50.000 16.19 3.89 46.57 4.02
113 114 0.906775 TGCATGAGCTCTCATCCACA 59.093 50.000 16.19 6.15 46.57 4.17
119 120 0.969149 AGCTCTCATCCACAACACGA 59.031 50.000 0.00 0.00 0.00 4.35
126 127 1.841663 ATCCACAACACGACTTGCGC 61.842 55.000 0.00 0.00 46.04 6.09
129 130 4.368808 CAACACGACTTGCGCCCG 62.369 66.667 4.18 5.96 46.04 6.13
160 161 5.458779 CGTTGAAGAAAGAACCATGGAAAAC 59.541 40.000 21.47 6.44 0.00 2.43
161 162 6.337356 GTTGAAGAAAGAACCATGGAAAACA 58.663 36.000 21.47 3.12 0.00 2.83
162 163 6.537453 TGAAGAAAGAACCATGGAAAACAA 57.463 33.333 21.47 0.00 0.00 2.83
164 165 7.563906 TGAAGAAAGAACCATGGAAAACAAAT 58.436 30.769 21.47 0.00 0.00 2.32
166 167 9.196552 GAAGAAAGAACCATGGAAAACAAATAG 57.803 33.333 21.47 0.00 0.00 1.73
171 177 8.887036 AGAACCATGGAAAACAAATAGAAAAC 57.113 30.769 21.47 0.00 0.00 2.43
172 178 7.931407 AGAACCATGGAAAACAAATAGAAAACC 59.069 33.333 21.47 0.00 0.00 3.27
178 184 7.717568 TGGAAAACAAATAGAAAACCGAATGA 58.282 30.769 0.00 0.00 0.00 2.57
180 186 9.036671 GGAAAACAAATAGAAAACCGAATGAAA 57.963 29.630 0.00 0.00 0.00 2.69
190 196 7.272244 AGAAAACCGAATGAAAGTTTCCAAAT 58.728 30.769 13.01 0.00 32.73 2.32
196 202 7.550906 ACCGAATGAAAGTTTCCAAATCAAAAA 59.449 29.630 13.01 0.00 0.00 1.94
234 240 9.368674 GTTCTCTAGTGTATTTCTTTTAGGACC 57.631 37.037 0.00 0.00 0.00 4.46
235 241 8.075761 TCTCTAGTGTATTTCTTTTAGGACCC 57.924 38.462 0.00 0.00 0.00 4.46
236 242 7.676893 TCTCTAGTGTATTTCTTTTAGGACCCA 59.323 37.037 0.00 0.00 0.00 4.51
247 253 6.472887 TCTTTTAGGACCCACAATTGTAGAG 58.527 40.000 11.53 5.49 0.00 2.43
266 272 0.456995 GACTTCAGGCGAGACCGAAG 60.457 60.000 0.63 0.63 46.08 3.79
303 309 1.678627 CGATATATAGCCTCTGCGCCT 59.321 52.381 4.18 0.00 44.33 5.52
309 315 1.103987 TAGCCTCTGCGCCTAGTCAG 61.104 60.000 4.18 0.00 44.33 3.51
310 316 2.716017 GCCTCTGCGCCTAGTCAGT 61.716 63.158 4.18 0.00 0.00 3.41
311 317 1.140589 CCTCTGCGCCTAGTCAGTG 59.859 63.158 4.18 0.00 0.00 3.66
318 328 0.737715 CGCCTAGTCAGTGACCTTGC 60.738 60.000 19.71 16.97 32.18 4.01
320 330 1.065854 GCCTAGTCAGTGACCTTGCAT 60.066 52.381 19.71 2.66 32.18 3.96
325 335 0.320683 TCAGTGACCTTGCATCCACG 60.321 55.000 0.00 0.00 34.93 4.94
349 359 1.077716 GGCCGAGCACCCAGTTATT 60.078 57.895 0.00 0.00 0.00 1.40
352 362 0.463833 CCGAGCACCCAGTTATTCCC 60.464 60.000 0.00 0.00 0.00 3.97
386 396 2.712944 CGCAATGCATGGCCCAAGA 61.713 57.895 20.50 0.00 0.00 3.02
393 403 1.252904 GCATGGCCCAAGACATGTGT 61.253 55.000 1.15 0.00 44.74 3.72
416 426 0.043485 TATACTGCCACCCTCCACCA 59.957 55.000 0.00 0.00 0.00 4.17
417 427 1.562672 ATACTGCCACCCTCCACCAC 61.563 60.000 0.00 0.00 0.00 4.16
418 428 2.974435 TACTGCCACCCTCCACCACA 62.974 60.000 0.00 0.00 0.00 4.17
419 429 3.557903 CTGCCACCCTCCACCACAG 62.558 68.421 0.00 0.00 0.00 3.66
420 430 3.570212 GCCACCCTCCACCACAGT 61.570 66.667 0.00 0.00 0.00 3.55
438 448 2.807045 CGCACACGAGTCTGAGCC 60.807 66.667 0.00 0.00 43.93 4.70
446 456 3.655810 GAGTCTGAGCCCGGCACAG 62.656 68.421 26.11 26.11 45.83 3.66
497 507 1.134175 CCACCATTTTGCCGTATCCAC 59.866 52.381 0.00 0.00 0.00 4.02
526 536 2.069165 GAAGCCCTCCACACCAACCT 62.069 60.000 0.00 0.00 0.00 3.50
562 572 2.202797 CCGCACCATCGTCCTCTG 60.203 66.667 0.00 0.00 0.00 3.35
566 576 1.883732 CACCATCGTCCTCTGTCGT 59.116 57.895 0.00 0.00 0.00 4.34
568 578 1.471287 CACCATCGTCCTCTGTCGTTA 59.529 52.381 0.00 0.00 0.00 3.18
587 597 2.892425 GGTGCTCCCAATCGCTCG 60.892 66.667 0.00 0.00 0.00 5.03
592 602 2.759973 TCCCAATCGCTCGCTCCT 60.760 61.111 0.00 0.00 0.00 3.69
593 603 2.587194 CCCAATCGCTCGCTCCTG 60.587 66.667 0.00 0.00 0.00 3.86
595 605 1.153568 CCAATCGCTCGCTCCTGAA 60.154 57.895 0.00 0.00 0.00 3.02
659 2147 8.800231 TTTTTAGTCGCAAACCCTTTTAATAC 57.200 30.769 0.00 0.00 0.00 1.89
660 2148 6.499234 TTAGTCGCAAACCCTTTTAATACC 57.501 37.500 0.00 0.00 0.00 2.73
661 2149 4.659115 AGTCGCAAACCCTTTTAATACCT 58.341 39.130 0.00 0.00 0.00 3.08
662 2150 4.457949 AGTCGCAAACCCTTTTAATACCTG 59.542 41.667 0.00 0.00 0.00 4.00
663 2151 4.456566 GTCGCAAACCCTTTTAATACCTGA 59.543 41.667 0.00 0.00 0.00 3.86
664 2152 5.048573 GTCGCAAACCCTTTTAATACCTGAA 60.049 40.000 0.00 0.00 0.00 3.02
665 2153 5.182380 TCGCAAACCCTTTTAATACCTGAAG 59.818 40.000 0.00 0.00 0.00 3.02
666 2154 5.182380 CGCAAACCCTTTTAATACCTGAAGA 59.818 40.000 0.00 0.00 0.00 2.87
667 2155 6.127730 CGCAAACCCTTTTAATACCTGAAGAT 60.128 38.462 0.00 0.00 0.00 2.40
668 2156 7.576856 CGCAAACCCTTTTAATACCTGAAGATT 60.577 37.037 0.00 0.00 0.00 2.40
669 2157 8.094548 GCAAACCCTTTTAATACCTGAAGATTT 58.905 33.333 0.00 0.00 0.00 2.17
670 2158 9.996554 CAAACCCTTTTAATACCTGAAGATTTT 57.003 29.630 0.00 0.00 0.00 1.82
703 2191 9.528018 GTGAGAAAAATTTAAATTCCACAGACA 57.472 29.630 13.68 6.52 30.95 3.41
717 2205 9.480053 AATTCCACAGACATATTTTTGAACTTG 57.520 29.630 0.00 0.00 0.00 3.16
722 2210 8.961092 CACAGACATATTTTTGAACTTGTGAAG 58.039 33.333 0.00 0.00 0.00 3.02
753 2241 5.888412 AATGCACGAACATTTTTGAACTC 57.112 34.783 0.00 0.00 36.91 3.01
846 2336 2.025699 GTGGTAGAAAAGGCCCACCATA 60.026 50.000 0.00 0.00 41.12 2.74
863 2353 2.614259 CATACCATACCAGAGGGCTCT 58.386 52.381 0.00 0.00 41.37 4.09
895 2385 0.250513 ATGGTGGAGAAGAAGCCGTC 59.749 55.000 0.00 0.00 0.00 4.79
896 2386 0.832135 TGGTGGAGAAGAAGCCGTCT 60.832 55.000 0.00 0.00 38.69 4.18
897 2387 1.183549 GGTGGAGAAGAAGCCGTCTA 58.816 55.000 0.00 0.00 34.56 2.59
898 2388 1.135333 GGTGGAGAAGAAGCCGTCTAG 59.865 57.143 0.00 0.00 34.56 2.43
899 2389 1.819903 GTGGAGAAGAAGCCGTCTAGT 59.180 52.381 0.00 0.00 34.56 2.57
900 2390 1.819288 TGGAGAAGAAGCCGTCTAGTG 59.181 52.381 0.00 0.00 34.56 2.74
901 2391 1.819903 GGAGAAGAAGCCGTCTAGTGT 59.180 52.381 0.00 0.00 34.56 3.55
902 2392 2.416162 GGAGAAGAAGCCGTCTAGTGTG 60.416 54.545 0.00 0.00 34.56 3.82
1068 2561 3.588891 GAAAAACCTGACGGCCGCG 62.589 63.158 28.58 14.22 0.00 6.46
1197 2696 1.336440 CCGACTGCTACCTCTCATCTG 59.664 57.143 0.00 0.00 0.00 2.90
1207 2706 7.290813 TGCTACCTCTCATCTGTTCTAATCTA 58.709 38.462 0.00 0.00 0.00 1.98
1208 2707 7.229707 TGCTACCTCTCATCTGTTCTAATCTAC 59.770 40.741 0.00 0.00 0.00 2.59
1209 2708 6.627395 ACCTCTCATCTGTTCTAATCTACG 57.373 41.667 0.00 0.00 0.00 3.51
1210 2709 5.533154 ACCTCTCATCTGTTCTAATCTACGG 59.467 44.000 0.00 0.00 0.00 4.02
1211 2710 5.765677 CCTCTCATCTGTTCTAATCTACGGA 59.234 44.000 0.00 0.00 34.40 4.69
1212 2711 6.072728 CCTCTCATCTGTTCTAATCTACGGAG 60.073 46.154 0.00 0.00 33.47 4.63
1219 2718 8.830201 TCTGTTCTAATCTACGGAGTATCTAC 57.170 38.462 0.00 0.00 44.56 2.59
1241 2740 5.961272 ACAAACGGACAAAGTCAAATTTCT 58.039 33.333 0.00 0.00 33.68 2.52
1244 2743 7.700656 ACAAACGGACAAAGTCAAATTTCTTAG 59.299 33.333 0.00 0.00 33.68 2.18
1249 2748 8.009974 CGGACAAAGTCAAATTTCTTAGTACTG 58.990 37.037 5.39 0.00 33.68 2.74
1288 2910 6.112734 TGTTATATTCACGATGGCTCTGTTT 58.887 36.000 0.00 0.00 0.00 2.83
1334 2956 1.280710 TGGGATTCCGCACAAGTATGT 59.719 47.619 0.00 0.00 36.51 2.29
1342 2964 2.518949 CGCACAAGTATGTTTCCATGC 58.481 47.619 0.00 0.00 37.82 4.06
1385 3007 2.151202 TGGATTTCTGGTGAGCGTTTC 58.849 47.619 0.00 0.00 0.00 2.78
1419 3041 6.509199 CGATCTCATCTTGTCTTCAATTTCCG 60.509 42.308 0.00 0.00 32.82 4.30
1436 3090 0.599558 CCGTCGTCTTGTAACCAGGA 59.400 55.000 0.00 0.00 0.00 3.86
1476 3130 2.535984 CTGTCAAGCTTATCTAACGCCG 59.464 50.000 0.00 0.00 0.00 6.46
1481 3135 1.496403 GCTTATCTAACGCCGGTGCC 61.496 60.000 16.69 0.00 0.00 5.01
1501 3155 5.824904 GCCTGAGCAAAATCATCTCTTTA 57.175 39.130 0.00 0.00 39.53 1.85
1505 3159 7.470900 CCTGAGCAAAATCATCTCTTTAAGAC 58.529 38.462 0.00 0.00 36.65 3.01
1508 3162 8.725148 TGAGCAAAATCATCTCTTTAAGACTTC 58.275 33.333 0.00 0.00 36.65 3.01
1510 3164 8.728833 AGCAAAATCATCTCTTTAAGACTTCTG 58.271 33.333 0.00 0.00 36.65 3.02
1513 3167 5.745312 TCATCTCTTTAAGACTTCTGCCA 57.255 39.130 0.00 0.00 36.65 4.92
1546 3200 8.247562 AGTCTTAACTAATCTCAACTAGCACAG 58.752 37.037 0.00 0.00 32.59 3.66
1547 3201 8.244802 GTCTTAACTAATCTCAACTAGCACAGA 58.755 37.037 0.00 0.00 0.00 3.41
1548 3202 8.244802 TCTTAACTAATCTCAACTAGCACAGAC 58.755 37.037 0.00 0.00 0.00 3.51
1550 3204 5.715070 ACTAATCTCAACTAGCACAGACAC 58.285 41.667 0.00 0.00 0.00 3.67
1551 3205 4.607293 AATCTCAACTAGCACAGACACA 57.393 40.909 0.00 0.00 0.00 3.72
1552 3206 3.371102 TCTCAACTAGCACAGACACAC 57.629 47.619 0.00 0.00 0.00 3.82
1553 3207 2.693074 TCTCAACTAGCACAGACACACA 59.307 45.455 0.00 0.00 0.00 3.72
1554 3208 2.797156 CTCAACTAGCACAGACACACAC 59.203 50.000 0.00 0.00 0.00 3.82
1555 3209 2.167487 TCAACTAGCACAGACACACACA 59.833 45.455 0.00 0.00 0.00 3.72
1568 3222 2.288518 ACACACACACACCCACAAAAAC 60.289 45.455 0.00 0.00 0.00 2.43
1571 3225 0.528470 CACACACCCACAAAAACGGT 59.472 50.000 0.00 0.00 0.00 4.83
1581 3235 3.865745 CCACAAAAACGGTGCAACATTTA 59.134 39.130 0.98 0.00 39.98 1.40
1582 3236 4.330074 CCACAAAAACGGTGCAACATTTAA 59.670 37.500 0.98 0.00 39.98 1.52
1645 3299 5.106475 TGTGAACCCAACTGATTATAAACGC 60.106 40.000 0.00 0.00 0.00 4.84
1646 3300 5.004448 TGAACCCAACTGATTATAAACGCA 58.996 37.500 0.00 0.00 0.00 5.24
1668 3322 5.400485 GCACATTTCACAAGAAAGACATGAC 59.600 40.000 0.00 0.00 46.13 3.06
1670 3324 6.415867 CACATTTCACAAGAAAGACATGACAC 59.584 38.462 0.00 0.00 46.13 3.67
1697 3354 6.669278 TCGATAGATCATAACACTGTGCTAC 58.331 40.000 7.90 0.00 42.67 3.58
1750 3409 0.966179 ATAGCGACCGATGCACCATA 59.034 50.000 0.00 0.00 33.85 2.74
1765 3424 2.628178 CACCATAAGGATAGGACGCAGA 59.372 50.000 0.00 0.00 38.69 4.26
1833 3493 7.877612 TGTAAGCTCATCAAAACTCATGTTCTA 59.122 33.333 0.00 0.00 34.96 2.10
1847 3852 8.281212 ACTCATGTTCTAATTTCCATTGTACC 57.719 34.615 0.00 0.00 0.00 3.34
1851 3856 3.199677 TCTAATTTCCATTGTACCGGCG 58.800 45.455 0.00 0.00 0.00 6.46
1857 3862 1.740585 TCCATTGTACCGGCGATTTTG 59.259 47.619 9.30 0.00 0.00 2.44
1860 3865 2.690173 TTGTACCGGCGATTTTGTTG 57.310 45.000 9.30 0.00 0.00 3.33
2100 4119 8.618702 ATCATTAAGATATGGCACTCTGAAAG 57.381 34.615 2.46 0.00 34.43 2.62
2117 4136 4.647611 TGAAAGAAGCCGAAACCTAATGA 58.352 39.130 0.00 0.00 0.00 2.57
2118 4137 5.067273 TGAAAGAAGCCGAAACCTAATGAA 58.933 37.500 0.00 0.00 0.00 2.57
2119 4138 5.710099 TGAAAGAAGCCGAAACCTAATGAAT 59.290 36.000 0.00 0.00 0.00 2.57
2120 4139 6.882140 TGAAAGAAGCCGAAACCTAATGAATA 59.118 34.615 0.00 0.00 0.00 1.75
2152 4171 2.364972 ACACTCTTGAAACAAGGGGG 57.635 50.000 11.43 11.43 0.00 5.40
2297 4316 1.278337 GCATGCACACGAAACACGA 59.722 52.632 14.21 0.00 45.77 4.35
2341 4360 6.176183 ACTCATTTCTTAGCTTGCATGTAGT 58.824 36.000 0.00 0.00 0.00 2.73
2342 4361 6.314896 ACTCATTTCTTAGCTTGCATGTAGTC 59.685 38.462 0.00 0.00 0.00 2.59
2343 4362 5.291858 TCATTTCTTAGCTTGCATGTAGTCG 59.708 40.000 0.00 0.00 0.00 4.18
2344 4363 4.450082 TTCTTAGCTTGCATGTAGTCGA 57.550 40.909 0.00 0.00 0.00 4.20
2345 4364 3.770666 TCTTAGCTTGCATGTAGTCGAC 58.229 45.455 7.70 7.70 0.00 4.20
2346 4365 3.444034 TCTTAGCTTGCATGTAGTCGACT 59.556 43.478 23.66 23.66 0.00 4.18
2347 4366 2.751166 AGCTTGCATGTAGTCGACTT 57.249 45.000 25.44 2.19 0.00 3.01
2348 4367 2.341257 AGCTTGCATGTAGTCGACTTG 58.659 47.619 25.44 17.12 36.51 3.16
2367 4386 2.115427 TGCGTCCCCTTTATCTGATGA 58.885 47.619 0.00 0.00 0.00 2.92
2368 4387 2.503765 TGCGTCCCCTTTATCTGATGAA 59.496 45.455 0.00 0.00 0.00 2.57
2369 4388 3.136443 TGCGTCCCCTTTATCTGATGAAT 59.864 43.478 0.00 0.00 0.00 2.57
2386 4405 5.914074 TGATGAATGAAAACAATGTGTGTCG 59.086 36.000 0.00 0.00 40.60 4.35
2455 4811 0.668096 TCCGCCGTTGATGTGTGTAC 60.668 55.000 0.00 0.00 0.00 2.90
2461 4817 3.390135 CCGTTGATGTGTGTACTGTTCT 58.610 45.455 0.00 0.00 0.00 3.01
2462 4818 3.807622 CCGTTGATGTGTGTACTGTTCTT 59.192 43.478 0.00 0.00 0.00 2.52
2463 4819 4.084537 CCGTTGATGTGTGTACTGTTCTTC 60.085 45.833 0.00 0.00 0.00 2.87
2716 5072 1.344438 CTGCGAATCATGGCCCTAGTA 59.656 52.381 0.00 0.00 0.00 1.82
2774 5130 3.272334 CATCCTTGGCTACGCGGC 61.272 66.667 12.47 4.60 38.97 6.53
3470 6122 4.308458 CGAACGGGGTGGCTGACA 62.308 66.667 0.00 0.00 0.00 3.58
3471 6123 2.351276 GAACGGGGTGGCTGACAT 59.649 61.111 0.00 0.00 0.00 3.06
3472 6124 2.034066 AACGGGGTGGCTGACATG 59.966 61.111 0.00 0.00 0.00 3.21
3473 6125 3.567579 AACGGGGTGGCTGACATGG 62.568 63.158 0.00 0.00 0.00 3.66
3678 6339 1.402456 CGTCTCGACAAAGGGGTACAG 60.402 57.143 0.00 0.00 0.00 2.74
3992 6657 5.183331 TCATATCCCTATCGCAAGTGAGTAC 59.817 44.000 0.00 0.00 39.48 2.73
4085 6750 2.496817 CTGCTAGTCGGCCTCACC 59.503 66.667 0.00 0.00 0.00 4.02
4147 6812 1.654023 GCCTTTGGTATCGGTGGTGC 61.654 60.000 0.00 0.00 0.00 5.01
4335 7009 7.945134 ACTGTGATGCTGAAACTTTTTATCTT 58.055 30.769 0.00 0.00 0.00 2.40
4398 7072 6.761242 GTGTTACTGATATTGATACACTGCCA 59.239 38.462 0.00 0.00 33.50 4.92
4416 7090 3.197766 TGCCATCTTTCATAGTCCTCGTT 59.802 43.478 0.00 0.00 0.00 3.85
4469 7143 3.308832 CCCACAGCCCTTCCACTTTATTA 60.309 47.826 0.00 0.00 0.00 0.98
4619 7294 3.420893 CAGCCCTTTTGTAGTCCATTGA 58.579 45.455 0.00 0.00 0.00 2.57
4635 7310 8.463930 AGTCCATTGAACTGTCAAAATCTTTA 57.536 30.769 0.00 0.00 46.66 1.85
4663 7338 3.067320 GTCTATCCATTGCTCAAAAGGCC 59.933 47.826 0.00 0.00 0.00 5.19
4686 7361 1.367471 GCAGGGGCTGTTTTTGACC 59.633 57.895 0.00 0.00 36.96 4.02
4746 7421 6.407202 AGTTTTGAGCACTGTAATAGGGTAG 58.593 40.000 0.00 0.00 30.24 3.18
4831 7506 4.279169 TGAGGAGCTTTTGAGTGAAATTGG 59.721 41.667 0.00 0.00 0.00 3.16
4957 7632 2.241281 TGGATGAAGAACCGACCCTA 57.759 50.000 0.00 0.00 0.00 3.53
5105 7792 2.284258 AGGGCTTCGAGCTCCTGT 60.284 61.111 8.47 0.00 44.67 4.00
5109 7796 1.375268 GCTTCGAGCTCCTGTGCTT 60.375 57.895 8.47 0.00 44.17 3.91
5156 7850 4.416738 GAGGGGCAGCCACTGGAC 62.417 72.222 25.22 2.09 37.42 4.02
5165 7859 4.363990 CCACTGGACGCAGCGAGT 62.364 66.667 24.65 12.20 0.00 4.18
5166 7860 2.356313 CACTGGACGCAGCGAGTT 60.356 61.111 24.65 0.00 0.00 3.01
5167 7861 1.956170 CACTGGACGCAGCGAGTTT 60.956 57.895 24.65 0.00 0.00 2.66
5168 7862 1.664965 ACTGGACGCAGCGAGTTTC 60.665 57.895 24.65 8.35 0.00 2.78
5169 7863 2.357034 TGGACGCAGCGAGTTTCC 60.357 61.111 24.65 18.36 0.00 3.13
5170 7864 2.048127 GGACGCAGCGAGTTTCCT 60.048 61.111 24.65 0.00 0.00 3.36
5171 7865 2.383527 GGACGCAGCGAGTTTCCTG 61.384 63.158 24.65 0.00 0.00 3.86
5172 7866 2.357517 ACGCAGCGAGTTTCCTGG 60.358 61.111 24.65 0.00 0.00 4.45
5173 7867 3.121030 CGCAGCGAGTTTCCTGGG 61.121 66.667 9.98 0.00 36.02 4.45
5174 7868 3.435186 GCAGCGAGTTTCCTGGGC 61.435 66.667 0.00 0.00 0.00 5.36
5175 7869 3.121030 CAGCGAGTTTCCTGGGCG 61.121 66.667 0.00 0.00 0.00 6.13
5176 7870 4.394712 AGCGAGTTTCCTGGGCGG 62.395 66.667 0.00 0.00 0.00 6.13
5179 7873 4.388499 GAGTTTCCTGGGCGGCGA 62.388 66.667 12.98 0.00 0.00 5.54
5180 7874 4.394712 AGTTTCCTGGGCGGCGAG 62.395 66.667 12.98 14.30 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.828273 TGTCCTTGTCAAACTATATTCCATGG 59.172 38.462 4.97 4.97 0.00 3.66
12 13 2.286418 CGCTCTTGTGTCCTTGTCAAAC 60.286 50.000 0.00 0.00 0.00 2.93
22 23 2.089349 GCCTCGACGCTCTTGTGTC 61.089 63.158 0.00 0.00 46.82 3.67
34 35 1.376683 CGGTGATTTTGGGCCTCGA 60.377 57.895 4.53 0.00 0.00 4.04
52 53 1.883084 CTGGACTTATGCCGCGTCC 60.883 63.158 4.92 3.74 45.76 4.79
58 59 3.119352 CCTCTTTTTGCTGGACTTATGCC 60.119 47.826 0.00 0.00 0.00 4.40
59 60 3.674410 GCCTCTTTTTGCTGGACTTATGC 60.674 47.826 0.00 0.00 0.00 3.14
98 99 1.337167 CGTGTTGTGGATGAGAGCTCA 60.337 52.381 17.77 2.23 44.59 4.26
102 103 2.732412 AGTCGTGTTGTGGATGAGAG 57.268 50.000 0.00 0.00 0.00 3.20
119 120 2.511600 GCATAGACGGGCGCAAGT 60.512 61.111 10.83 8.48 41.68 3.16
125 126 0.459585 TCTTCAACGCATAGACGGGC 60.460 55.000 0.00 0.00 37.37 6.13
126 127 2.004583 TTCTTCAACGCATAGACGGG 57.995 50.000 0.00 0.00 37.37 5.28
129 130 4.451096 TGGTTCTTTCTTCAACGCATAGAC 59.549 41.667 0.00 0.00 0.00 2.59
137 138 6.337356 TGTTTTCCATGGTTCTTTCTTCAAC 58.663 36.000 12.58 2.30 0.00 3.18
160 161 8.699749 GGAAACTTTCATTCGGTTTTCTATTTG 58.300 33.333 3.93 0.00 34.00 2.32
161 162 8.417884 TGGAAACTTTCATTCGGTTTTCTATTT 58.582 29.630 3.93 0.00 34.00 1.40
162 163 7.947282 TGGAAACTTTCATTCGGTTTTCTATT 58.053 30.769 3.93 0.00 34.00 1.73
164 165 6.945938 TGGAAACTTTCATTCGGTTTTCTA 57.054 33.333 3.93 0.00 34.00 2.10
166 167 6.895607 TTTGGAAACTTTCATTCGGTTTTC 57.104 33.333 3.93 0.00 34.00 2.29
171 177 7.475771 TTTTGATTTGGAAACTTTCATTCGG 57.524 32.000 3.93 0.00 0.00 4.30
200 206 8.526667 AGAAATACACTAGAGAACTGCATCTA 57.473 34.615 0.00 0.00 0.00 1.98
202 208 8.485976 AAAGAAATACACTAGAGAACTGCATC 57.514 34.615 0.00 0.00 0.00 3.91
211 217 7.764901 GTGGGTCCTAAAAGAAATACACTAGAG 59.235 40.741 0.00 0.00 0.00 2.43
234 240 3.686726 GCCTGAAGTCTCTACAATTGTGG 59.313 47.826 21.42 18.31 0.00 4.17
235 241 3.369147 CGCCTGAAGTCTCTACAATTGTG 59.631 47.826 21.42 10.97 0.00 3.33
236 242 3.258372 TCGCCTGAAGTCTCTACAATTGT 59.742 43.478 16.68 16.68 0.00 2.71
247 253 0.456995 CTTCGGTCTCGCCTGAAGTC 60.457 60.000 8.93 0.00 40.09 3.01
279 285 3.111838 CGCAGAGGCTATATATCGCTTG 58.888 50.000 8.92 6.81 38.10 4.01
303 309 2.028112 GTGGATGCAAGGTCACTGACTA 60.028 50.000 9.08 0.00 32.47 2.59
309 315 0.238289 CAACGTGGATGCAAGGTCAC 59.762 55.000 5.02 0.00 0.00 3.67
310 316 0.888736 CCAACGTGGATGCAAGGTCA 60.889 55.000 5.02 0.00 40.96 4.02
311 317 0.605319 TCCAACGTGGATGCAAGGTC 60.605 55.000 5.02 0.00 42.67 3.85
320 330 3.691342 CTCGGCCTCCAACGTGGA 61.691 66.667 0.00 0.00 45.98 4.02
341 351 2.214376 TTGGCACTGGGAATAACTGG 57.786 50.000 0.00 0.00 0.00 4.00
375 385 2.019249 CTACACATGTCTTGGGCCATG 58.981 52.381 7.26 10.70 43.21 3.66
376 386 1.635487 ACTACACATGTCTTGGGCCAT 59.365 47.619 7.26 0.00 28.72 4.40
386 396 4.383770 GGGTGGCAGTATAACTACACATGT 60.384 45.833 12.94 0.00 37.15 3.21
393 403 3.036091 GTGGAGGGTGGCAGTATAACTA 58.964 50.000 0.00 0.00 0.00 2.24
416 426 1.008424 CAGACTCGTGTGCGACTGT 60.008 57.895 0.00 0.00 42.81 3.55
417 427 0.727457 CTCAGACTCGTGTGCGACTG 60.727 60.000 0.00 0.00 42.81 3.51
418 428 1.576920 CTCAGACTCGTGTGCGACT 59.423 57.895 0.00 0.00 42.81 4.18
419 429 2.083522 GCTCAGACTCGTGTGCGAC 61.084 63.158 0.00 0.00 42.81 5.19
420 430 2.255554 GCTCAGACTCGTGTGCGA 59.744 61.111 0.00 0.00 45.79 5.10
448 458 0.744414 TGCAAATGGCCGAGCTACTC 60.744 55.000 0.00 0.00 43.89 2.59
452 462 1.811860 GATTGCAAATGGCCGAGCT 59.188 52.632 1.71 0.00 43.89 4.09
500 510 1.817099 GTGGAGGGCTTCGCATCAG 60.817 63.158 0.00 0.00 0.00 2.90
504 514 4.329545 GGTGTGGAGGGCTTCGCA 62.330 66.667 0.00 0.00 0.00 5.10
520 530 1.272425 TGATGGGTTTGGCTAGGTTGG 60.272 52.381 0.00 0.00 0.00 3.77
526 536 0.680921 GCTGCTGATGGGTTTGGCTA 60.681 55.000 0.00 0.00 0.00 3.93
580 590 0.749649 AATCTTCAGGAGCGAGCGAT 59.250 50.000 0.00 0.00 0.00 4.58
606 2094 3.489416 GTGAATTCAAAAGGGTTTGCGAC 59.511 43.478 10.35 0.00 43.30 5.19
639 2127 4.457949 CAGGTATTAAAAGGGTTTGCGACT 59.542 41.667 0.00 0.00 0.00 4.18
640 2128 4.456566 TCAGGTATTAAAAGGGTTTGCGAC 59.543 41.667 0.00 0.00 0.00 5.19
642 2130 5.182380 TCTTCAGGTATTAAAAGGGTTTGCG 59.818 40.000 0.00 0.00 0.00 4.85
643 2131 6.584185 TCTTCAGGTATTAAAAGGGTTTGC 57.416 37.500 0.00 0.00 0.00 3.68
644 2132 9.996554 AAAATCTTCAGGTATTAAAAGGGTTTG 57.003 29.630 0.00 0.00 0.00 2.93
676 2164 9.528018 GTCTGTGGAATTTAAATTTTTCTCACA 57.472 29.630 14.45 18.36 33.55 3.58
677 2165 9.528018 TGTCTGTGGAATTTAAATTTTTCTCAC 57.472 29.630 14.45 15.70 0.00 3.51
734 2222 3.975035 GGAGAGTTCAAAAATGTTCGTGC 59.025 43.478 0.00 0.00 0.00 5.34
737 2225 4.787598 CCAGGAGAGTTCAAAAATGTTCG 58.212 43.478 0.00 0.00 0.00 3.95
802 2292 6.265196 CACCCATTAGCTAATCCATTGCTTTA 59.735 38.462 16.21 0.00 38.15 1.85
846 2336 1.972588 AAAGAGCCCTCTGGTATGGT 58.027 50.000 0.00 0.00 40.36 3.55
873 2363 2.093447 ACGGCTTCTTCTCCACCATAAG 60.093 50.000 0.00 0.00 0.00 1.73
874 2364 1.906574 ACGGCTTCTTCTCCACCATAA 59.093 47.619 0.00 0.00 0.00 1.90
875 2365 1.480954 GACGGCTTCTTCTCCACCATA 59.519 52.381 0.00 0.00 0.00 2.74
876 2366 0.250513 GACGGCTTCTTCTCCACCAT 59.749 55.000 0.00 0.00 0.00 3.55
878 2368 1.135333 CTAGACGGCTTCTTCTCCACC 59.865 57.143 0.00 0.00 35.55 4.61
890 2380 1.732259 CCAAATGTCACACTAGACGGC 59.268 52.381 0.00 0.00 41.41 5.68
895 2385 2.086869 CTGGGCCAAATGTCACACTAG 58.913 52.381 8.04 0.00 0.00 2.57
896 2386 1.271871 CCTGGGCCAAATGTCACACTA 60.272 52.381 8.04 0.00 0.00 2.74
897 2387 0.540365 CCTGGGCCAAATGTCACACT 60.540 55.000 8.04 0.00 0.00 3.55
898 2388 0.539438 TCCTGGGCCAAATGTCACAC 60.539 55.000 8.04 0.00 0.00 3.82
899 2389 0.187117 TTCCTGGGCCAAATGTCACA 59.813 50.000 8.04 0.00 0.00 3.58
900 2390 1.337118 TTTCCTGGGCCAAATGTCAC 58.663 50.000 8.04 0.00 0.00 3.67
901 2391 2.323999 ATTTCCTGGGCCAAATGTCA 57.676 45.000 8.04 0.00 0.00 3.58
902 2392 4.817318 TTTATTTCCTGGGCCAAATGTC 57.183 40.909 8.04 0.00 0.00 3.06
1176 2669 0.031449 GATGAGAGGTAGCAGTCGGC 59.969 60.000 0.00 0.00 45.30 5.54
1177 2670 1.336440 CAGATGAGAGGTAGCAGTCGG 59.664 57.143 0.00 0.00 0.00 4.79
1178 2671 2.020720 ACAGATGAGAGGTAGCAGTCG 58.979 52.381 0.00 0.00 0.00 4.18
1179 2672 3.699038 AGAACAGATGAGAGGTAGCAGTC 59.301 47.826 0.00 0.00 0.00 3.51
1180 2673 3.707316 AGAACAGATGAGAGGTAGCAGT 58.293 45.455 0.00 0.00 0.00 4.40
1181 2674 5.843673 TTAGAACAGATGAGAGGTAGCAG 57.156 43.478 0.00 0.00 0.00 4.24
1182 2675 6.132658 AGATTAGAACAGATGAGAGGTAGCA 58.867 40.000 0.00 0.00 0.00 3.49
1183 2676 6.648879 AGATTAGAACAGATGAGAGGTAGC 57.351 41.667 0.00 0.00 0.00 3.58
1184 2677 7.094975 CCGTAGATTAGAACAGATGAGAGGTAG 60.095 44.444 0.00 0.00 0.00 3.18
1185 2678 6.711194 CCGTAGATTAGAACAGATGAGAGGTA 59.289 42.308 0.00 0.00 0.00 3.08
1186 2679 5.533154 CCGTAGATTAGAACAGATGAGAGGT 59.467 44.000 0.00 0.00 0.00 3.85
1187 2680 5.765677 TCCGTAGATTAGAACAGATGAGAGG 59.234 44.000 0.00 0.00 0.00 3.69
1190 2689 6.627395 ACTCCGTAGATTAGAACAGATGAG 57.373 41.667 0.00 0.00 0.00 2.90
1197 2696 9.662545 GTTTGTAGATACTCCGTAGATTAGAAC 57.337 37.037 0.00 0.00 0.00 3.01
1207 2706 3.084039 TGTCCGTTTGTAGATACTCCGT 58.916 45.455 0.00 0.00 0.00 4.69
1208 2707 3.770263 TGTCCGTTTGTAGATACTCCG 57.230 47.619 0.00 0.00 0.00 4.63
1209 2708 5.476614 ACTTTGTCCGTTTGTAGATACTCC 58.523 41.667 0.00 0.00 0.00 3.85
1210 2709 6.154445 TGACTTTGTCCGTTTGTAGATACTC 58.846 40.000 0.00 0.00 0.00 2.59
1211 2710 6.092955 TGACTTTGTCCGTTTGTAGATACT 57.907 37.500 0.00 0.00 0.00 2.12
1212 2711 6.774354 TTGACTTTGTCCGTTTGTAGATAC 57.226 37.500 0.00 0.00 0.00 2.24
1219 2718 6.885735 AAGAAATTTGACTTTGTCCGTTTG 57.114 33.333 0.00 0.00 0.00 2.93
1342 2964 1.987807 ATGGGTCCGCCAATCCAGAG 61.988 60.000 0.00 0.00 36.17 3.35
1385 3007 4.629092 ACAAGATGAGATCGATCACATGG 58.371 43.478 33.66 25.13 38.05 3.66
1419 3041 2.798847 GTGTTCCTGGTTACAAGACGAC 59.201 50.000 6.09 0.00 0.00 4.34
1436 3090 3.696051 ACAGCAATCACAAGTTCAGTGTT 59.304 39.130 0.00 0.00 38.16 3.32
1481 3135 8.266392 AGTCTTAAAGAGATGATTTTGCTCAG 57.734 34.615 0.00 0.00 36.61 3.35
1492 3146 7.930325 TGATATGGCAGAAGTCTTAAAGAGATG 59.070 37.037 0.00 0.00 36.61 2.90
1498 3152 8.928448 AGACTATGATATGGCAGAAGTCTTAAA 58.072 33.333 8.08 0.00 39.83 1.52
1501 3155 6.992664 AGACTATGATATGGCAGAAGTCTT 57.007 37.500 8.08 0.00 39.83 3.01
1546 3200 1.169577 TTTGTGGGTGTGTGTGTGTC 58.830 50.000 0.00 0.00 0.00 3.67
1547 3201 1.621992 TTTTGTGGGTGTGTGTGTGT 58.378 45.000 0.00 0.00 0.00 3.72
1548 3202 2.333014 GTTTTTGTGGGTGTGTGTGTG 58.667 47.619 0.00 0.00 0.00 3.82
1550 3204 1.623359 CGTTTTTGTGGGTGTGTGTG 58.377 50.000 0.00 0.00 0.00 3.82
1551 3205 0.528470 CCGTTTTTGTGGGTGTGTGT 59.472 50.000 0.00 0.00 0.00 3.72
1552 3206 0.528470 ACCGTTTTTGTGGGTGTGTG 59.472 50.000 0.00 0.00 31.52 3.82
1553 3207 0.528470 CACCGTTTTTGTGGGTGTGT 59.472 50.000 1.37 0.00 44.82 3.72
1554 3208 3.337398 CACCGTTTTTGTGGGTGTG 57.663 52.632 1.37 0.00 44.82 3.82
1568 3222 8.848948 TTATTGATATGTTAAATGTTGCACCG 57.151 30.769 0.00 0.00 0.00 4.94
1631 3285 7.139896 TGTGAAATGTGCGTTTATAATCAGT 57.860 32.000 0.00 0.00 0.00 3.41
1632 3286 7.962373 TCTTGTGAAATGTGCGTTTATAATCAG 59.038 33.333 0.00 0.00 0.00 2.90
1634 3288 8.667987 TTCTTGTGAAATGTGCGTTTATAATC 57.332 30.769 0.00 0.00 0.00 1.75
1645 3299 6.415867 GTGTCATGTCTTTCTTGTGAAATGTG 59.584 38.462 0.00 0.00 40.85 3.21
1646 3300 6.460123 GGTGTCATGTCTTTCTTGTGAAATGT 60.460 38.462 0.00 0.00 40.85 2.71
1668 3322 4.912187 CAGTGTTATGATCTATCGACGGTG 59.088 45.833 0.00 0.00 0.00 4.94
1670 3324 4.912187 CACAGTGTTATGATCTATCGACGG 59.088 45.833 0.00 0.00 0.00 4.79
1750 3409 0.466124 GCCTTCTGCGTCCTATCCTT 59.534 55.000 0.00 0.00 0.00 3.36
1765 3424 3.066208 TCTAGGATGATGAAGGGCCTT 57.934 47.619 21.09 21.09 0.00 4.35
1833 3493 2.116827 TCGCCGGTACAATGGAAATT 57.883 45.000 1.90 0.00 0.00 1.82
1847 3852 0.179174 GGCTACCAACAAAATCGCCG 60.179 55.000 0.00 0.00 0.00 6.46
2100 4119 6.848451 TGTTTATTCATTAGGTTTCGGCTTC 58.152 36.000 0.00 0.00 0.00 3.86
2117 4136 8.565896 TCAAGAGTGTATTCAGCATGTTTATT 57.434 30.769 0.00 0.00 37.40 1.40
2118 4137 8.565896 TTCAAGAGTGTATTCAGCATGTTTAT 57.434 30.769 0.00 0.00 37.40 1.40
2119 4138 7.977789 TTCAAGAGTGTATTCAGCATGTTTA 57.022 32.000 0.00 0.00 37.40 2.01
2120 4139 6.882610 TTCAAGAGTGTATTCAGCATGTTT 57.117 33.333 0.00 0.00 37.40 2.83
2194 4213 5.416639 TCTTGTTCCAATCTGCTAGTACGTA 59.583 40.000 0.00 0.00 0.00 3.57
2195 4214 4.219944 TCTTGTTCCAATCTGCTAGTACGT 59.780 41.667 0.00 0.00 0.00 3.57
2196 4215 4.563184 GTCTTGTTCCAATCTGCTAGTACG 59.437 45.833 0.00 0.00 0.00 3.67
2197 4216 5.479306 TGTCTTGTTCCAATCTGCTAGTAC 58.521 41.667 0.00 0.00 0.00 2.73
2346 4365 2.503765 TCATCAGATAAAGGGGACGCAA 59.496 45.455 0.00 0.00 0.00 4.85
2347 4366 2.115427 TCATCAGATAAAGGGGACGCA 58.885 47.619 0.00 0.00 0.00 5.24
2348 4367 2.910688 TCATCAGATAAAGGGGACGC 57.089 50.000 0.00 0.00 0.00 5.19
2349 4368 4.960938 TCATTCATCAGATAAAGGGGACG 58.039 43.478 0.00 0.00 0.00 4.79
2367 4386 4.358851 CACCGACACACATTGTTTTCATT 58.641 39.130 0.00 0.00 39.17 2.57
2368 4387 3.243367 CCACCGACACACATTGTTTTCAT 60.243 43.478 0.00 0.00 39.17 2.57
2369 4388 2.098280 CCACCGACACACATTGTTTTCA 59.902 45.455 0.00 0.00 39.17 2.69
2386 4405 4.208686 CCGTCTAGCTCCGCCACC 62.209 72.222 0.00 0.00 0.00 4.61
2455 4811 4.213059 GGTGCTGAAGAAGAAGAAGAACAG 59.787 45.833 0.00 0.00 0.00 3.16
2461 4817 4.345257 AGTGTAGGTGCTGAAGAAGAAGAA 59.655 41.667 0.00 0.00 0.00 2.52
2462 4818 3.898123 AGTGTAGGTGCTGAAGAAGAAGA 59.102 43.478 0.00 0.00 0.00 2.87
2463 4819 3.993081 CAGTGTAGGTGCTGAAGAAGAAG 59.007 47.826 0.00 0.00 34.87 2.85
3467 6119 1.326548 GTATTTGTCGTCGGCCATGTC 59.673 52.381 2.24 0.00 0.00 3.06
3468 6120 1.338294 TGTATTTGTCGTCGGCCATGT 60.338 47.619 2.24 0.00 0.00 3.21
3469 6121 1.364721 TGTATTTGTCGTCGGCCATG 58.635 50.000 2.24 0.00 0.00 3.66
3470 6122 2.102070 TTGTATTTGTCGTCGGCCAT 57.898 45.000 2.24 0.00 0.00 4.40
3471 6123 1.735018 CATTGTATTTGTCGTCGGCCA 59.265 47.619 2.24 0.00 0.00 5.36
3472 6124 1.531058 GCATTGTATTTGTCGTCGGCC 60.531 52.381 0.00 0.00 0.00 6.13
3473 6125 1.531058 GGCATTGTATTTGTCGTCGGC 60.531 52.381 0.00 0.00 0.00 5.54
3474 6126 1.267334 CGGCATTGTATTTGTCGTCGG 60.267 52.381 0.00 0.00 37.42 4.79
3475 6127 1.267334 CCGGCATTGTATTTGTCGTCG 60.267 52.381 0.00 0.00 40.43 5.12
3678 6339 3.655810 CTGGTGCTCAGAGACGGGC 62.656 68.421 0.00 0.00 46.18 6.13
3992 6657 1.881973 TGCAAAAACAGCTAGCAGGAG 59.118 47.619 18.83 6.22 0.00 3.69
4147 6812 0.530650 AGCACATATGAAGGCGACGG 60.531 55.000 10.38 0.00 0.00 4.79
4335 7009 1.211949 GGCACTGCATAAACCTCCCTA 59.788 52.381 2.82 0.00 0.00 3.53
4635 7310 7.718753 CCTTTTGAGCAATGGATAGACTATTCT 59.281 37.037 2.39 0.00 32.27 2.40
4663 7338 2.026945 AAAAACAGCCCCTGCAACCG 62.027 55.000 0.00 0.00 41.13 4.44
4686 7361 7.894376 AATCACAAGCCAAAAGATAACAATG 57.106 32.000 0.00 0.00 0.00 2.82
4746 7421 6.197842 GCAAGTTCATGAGCAACATTATTAGC 59.802 38.462 12.41 0.00 37.07 3.09
4831 7506 6.834168 TTCATTGAAATTAACAGAGGGGTC 57.166 37.500 0.00 0.00 0.00 4.46
4957 7632 7.335422 GCACTTAGCTGAATATATATGCACCTT 59.665 37.037 4.18 0.00 41.15 3.50
5021 7696 1.330655 CCCAAGAGCTCCTCGCCTTA 61.331 60.000 10.93 0.00 40.39 2.69
5085 7772 4.847444 GGAGCTCGAAGCCCTGGC 62.847 72.222 7.83 0.00 43.77 4.85
5139 7833 4.416738 GTCCAGTGGCTGCCCCTC 62.417 72.222 17.53 6.86 0.00 4.30
5148 7842 3.865929 AACTCGCTGCGTCCAGTGG 62.866 63.158 22.48 1.40 46.92 4.00
5150 7844 1.664965 GAAACTCGCTGCGTCCAGT 60.665 57.895 22.48 15.15 41.26 4.00
5151 7845 2.383527 GGAAACTCGCTGCGTCCAG 61.384 63.158 22.48 14.46 42.13 3.86
5152 7846 2.357034 GGAAACTCGCTGCGTCCA 60.357 61.111 22.48 1.35 0.00 4.02
5153 7847 2.048127 AGGAAACTCGCTGCGTCC 60.048 61.111 22.48 20.16 32.90 4.79
5154 7848 2.383527 CCAGGAAACTCGCTGCGTC 61.384 63.158 22.48 11.76 40.21 5.19
5155 7849 2.357517 CCAGGAAACTCGCTGCGT 60.358 61.111 22.48 1.55 40.21 5.24
5156 7850 3.121030 CCCAGGAAACTCGCTGCG 61.121 66.667 17.25 17.25 40.21 5.18
5157 7851 3.435186 GCCCAGGAAACTCGCTGC 61.435 66.667 0.00 0.00 40.21 5.25
5158 7852 3.121030 CGCCCAGGAAACTCGCTG 61.121 66.667 0.00 0.00 40.21 5.18
5159 7853 4.394712 CCGCCCAGGAAACTCGCT 62.395 66.667 0.00 0.00 45.00 4.93
5162 7856 4.388499 TCGCCGCCCAGGAAACTC 62.388 66.667 0.00 0.00 45.00 3.01
5163 7857 4.394712 CTCGCCGCCCAGGAAACT 62.395 66.667 0.00 0.00 45.00 2.66
5185 7879 4.845580 ATTCCTCGCTGCGCCCAG 62.846 66.667 18.65 9.77 42.13 4.45
5186 7880 3.918253 AAATTCCTCGCTGCGCCCA 62.918 57.895 18.65 0.00 0.00 5.36
5187 7881 3.134127 AAATTCCTCGCTGCGCCC 61.134 61.111 18.65 0.00 0.00 6.13
5188 7882 1.922135 TTCAAATTCCTCGCTGCGCC 61.922 55.000 18.65 0.00 0.00 6.53
5189 7883 0.099436 ATTCAAATTCCTCGCTGCGC 59.901 50.000 18.65 0.00 0.00 6.09
5190 7884 2.179589 CAATTCAAATTCCTCGCTGCG 58.820 47.619 17.25 17.25 0.00 5.18
5191 7885 1.922545 GCAATTCAAATTCCTCGCTGC 59.077 47.619 0.00 0.00 0.00 5.25


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

AutoCloner maintained by Alex Coulton.