Multiple sequence alignment - TraesCS4A01G104100

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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 TraesCS4A01G104100 chr4A 100.000 7187 0 0 1 7187 117699577 117692391 0.000000e+00 13272.0
1 TraesCS4A01G104100 chr4A 91.176 68 4 2 6606 6672 666015239 666015305 2.760000e-14 91.6
2 TraesCS4A01G104100 chr4B 94.607 4135 153 26 560 4660 428198844 428202942 0.000000e+00 6336.0
3 TraesCS4A01G104100 chr4B 96.692 1602 50 2 4699 6298 428203034 428204634 0.000000e+00 2662.0
4 TraesCS4A01G104100 chr4B 92.885 520 30 4 6674 7186 428204919 428205438 0.000000e+00 749.0
5 TraesCS4A01G104100 chr4B 93.548 310 15 3 6309 6613 428204617 428204926 2.360000e-124 457.0
6 TraesCS4A01G104100 chr4B 82.573 482 57 14 1 456 428198324 428198804 4.040000e-107 399.0
7 TraesCS4A01G104100 chr4B 94.393 107 6 0 1 107 449518499 449518393 1.600000e-36 165.0
8 TraesCS4A01G104100 chr4B 93.103 58 3 1 4642 4699 428202995 428203051 4.620000e-12 84.2
9 TraesCS4A01G104100 chr4D 94.524 3780 131 28 908 4660 348042475 348046205 0.000000e+00 5764.0
10 TraesCS4A01G104100 chr4D 97.391 2491 62 2 4699 7187 348046297 348048786 0.000000e+00 4237.0
11 TraesCS4A01G104100 chr4D 83.465 508 53 16 1 482 348041402 348041904 1.840000e-120 444.0
12 TraesCS4A01G104100 chr4D 91.379 58 4 1 4642 4699 348046258 348046314 2.150000e-10 78.7
13 TraesCS4A01G104100 chr5D 97.196 107 3 0 1 107 538686905 538686799 1.590000e-41 182.0
14 TraesCS4A01G104100 chr5D 90.667 75 5 2 6600 6672 66982613 66982687 1.650000e-16 99.0
15 TraesCS4A01G104100 chr1D 97.196 107 3 0 1 107 80674444 80674338 1.590000e-41 182.0
16 TraesCS4A01G104100 chr1D 83.871 93 8 5 6606 6695 74410468 74410556 1.660000e-11 82.4
17 TraesCS4A01G104100 chr6B 96.262 107 4 0 1 107 672729531 672729425 7.410000e-40 176.0
18 TraesCS4A01G104100 chr5A 96.262 107 4 0 1 107 78449185 78449079 7.410000e-40 176.0
19 TraesCS4A01G104100 chr7A 95.327 107 5 0 1 107 62735961 62735855 3.450000e-38 171.0
20 TraesCS4A01G104100 chr1A 94.393 107 6 0 1 107 80284050 80284156 1.600000e-36 165.0
21 TraesCS4A01G104100 chr6D 95.385 65 2 1 6609 6672 259292219 259292283 1.280000e-17 102.0
22 TraesCS4A01G104100 chr2B 92.424 66 5 0 6607 6672 99270065 99270000 2.130000e-15 95.3
23 TraesCS4A01G104100 chr5B 92.308 65 5 0 6608 6672 597288184 597288120 7.680000e-15 93.5
24 TraesCS4A01G104100 chr3B 93.651 63 3 1 6605 6667 446451006 446450945 7.680000e-15 93.5
25 TraesCS4A01G104100 chr2D 92.424 66 4 1 6608 6672 441760444 441760379 7.680000e-15 93.5


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 TraesCS4A01G104100 chr4A 117692391 117699577 7186 True 13272.000 13272 100.000000 1 7187 1 chr4A.!!$R1 7186
1 TraesCS4A01G104100 chr4B 428198324 428205438 7114 False 1781.200 6336 92.234667 1 7186 6 chr4B.!!$F1 7185
2 TraesCS4A01G104100 chr4D 348041402 348048786 7384 False 2630.925 5764 91.689750 1 7187 4 chr4D.!!$F1 7186

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
556 809 0.036010 ATGCTTTCACACGGGAGGAG 60.036 55.000 0.00 0.0 0.00 3.69 F
1728 2034 0.037590 GGTGTGTGATTGGTAGGCCA 59.962 55.000 5.01 0.0 44.38 5.36 F
2070 2383 0.322997 TTTTACATGGGGCCTGACCG 60.323 55.000 0.84 0.0 40.62 4.79 F
2863 3184 1.136891 TGAGCCACCGTCATCTATGTG 59.863 52.381 0.00 0.0 0.00 3.21 F
4190 4518 0.095935 CAGTTCTTGCAATCCTCGCG 59.904 55.000 0.00 0.0 0.00 5.87 F
5257 5657 1.024579 GCATTGGTGTACAGGGACCG 61.025 60.000 0.00 0.0 34.69 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2101 2414 0.391927 TTCTCCGTTGCCAATACCGG 60.392 55.000 0.00 0.0 41.75 5.28 R
3430 3756 1.192146 ACGCCCAGGTAAAGCAGAGA 61.192 55.000 0.00 0.0 0.00 3.10 R
3846 4172 1.072331 TCCTTTGAGTGAAGTGAGCCC 59.928 52.381 0.00 0.0 0.00 5.19 R
4697 5095 1.020437 GCCAGCTGCAGAAATAGACC 58.980 55.000 20.43 0.0 40.77 3.85 R
6011 6411 1.271856 TCCCTGGCGTTCAGTAATCA 58.728 50.000 7.05 0.0 41.83 2.57 R
6662 7068 0.937441 AGAGCTCCTACTCCATCCCA 59.063 55.000 10.93 0.0 37.39 4.37 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
31 32 1.743772 CGGATGGTCCATGTCACTTCC 60.744 57.143 9.76 1.92 35.91 3.46
114 115 7.661437 AGCTATAACAATGTCAACTCAAGAACA 59.339 33.333 0.00 0.00 0.00 3.18
121 122 5.084818 TGTCAACTCAAGAACAAGAGTCA 57.915 39.130 0.00 0.00 43.88 3.41
133 134 6.522054 AGAACAAGAGTCAACCGAATAAGAA 58.478 36.000 0.00 0.00 0.00 2.52
145 146 7.659799 TCAACCGAATAAGAATTTGTGAAGAGA 59.340 33.333 0.00 0.00 0.00 3.10
152 153 9.877178 AATAAGAATTTGTGAAGAGATAGTCGT 57.123 29.630 0.00 0.00 0.00 4.34
153 154 9.877178 ATAAGAATTTGTGAAGAGATAGTCGTT 57.123 29.630 0.00 0.00 0.00 3.85
190 191 4.208632 GGTGCTTGATGACCGGAG 57.791 61.111 9.46 0.00 0.00 4.63
210 211 1.700186 GGTGAAGGAGGACAAGGACTT 59.300 52.381 0.00 0.00 0.00 3.01
217 218 0.182775 AGGACAAGGACTTTTGCGGT 59.817 50.000 0.00 0.00 0.00 5.68
218 219 1.418637 AGGACAAGGACTTTTGCGGTA 59.581 47.619 0.00 0.00 0.00 4.02
238 264 0.668096 ATTCTGCGCGACGTGGTAAA 60.668 50.000 12.10 0.00 0.00 2.01
250 276 1.196127 CGTGGTAAAAGGTCGGCTTTC 59.804 52.381 0.00 0.00 0.00 2.62
255 281 2.561478 AAAAGGTCGGCTTTCAGCTA 57.439 45.000 0.00 0.00 41.99 3.32
266 292 0.902984 TTTCAGCTAGACGGGCCAGA 60.903 55.000 10.86 0.00 0.00 3.86
268 294 2.443016 AGCTAGACGGGCCAGAGG 60.443 66.667 10.86 0.00 0.00 3.69
274 300 1.218316 GACGGGCCAGAGGTACAAG 59.782 63.158 10.86 0.00 0.00 3.16
276 302 0.617820 ACGGGCCAGAGGTACAAGAT 60.618 55.000 10.86 0.00 0.00 2.40
290 316 1.956477 ACAAGATGGTGCACTTTGGAC 59.044 47.619 17.98 0.00 38.03 4.02
308 334 0.532573 ACGATGAGTGTCGGCTTGAT 59.467 50.000 0.00 0.00 45.49 2.57
336 362 1.202371 CGCCGCCTTCTACATCTTGTA 60.202 52.381 0.00 0.00 0.00 2.41
337 363 2.545952 CGCCGCCTTCTACATCTTGTAT 60.546 50.000 0.00 0.00 31.66 2.29
339 365 2.802816 CCGCCTTCTACATCTTGTATGC 59.197 50.000 0.00 0.00 31.66 3.14
349 375 5.184892 ACATCTTGTATGCCTTCTCCTTT 57.815 39.130 0.00 0.00 0.00 3.11
353 379 1.635487 TGTATGCCTTCTCCTTTGCCT 59.365 47.619 0.00 0.00 0.00 4.75
375 402 4.506255 GCCCCGGCCTTGCATAGT 62.506 66.667 0.00 0.00 34.56 2.12
406 433 2.244436 CTTGCAGGCGAACACATCCG 62.244 60.000 0.00 0.00 0.00 4.18
409 436 4.778143 AGGCGAACACATCCGGGC 62.778 66.667 0.00 0.00 0.00 6.13
411 438 4.778143 GCGAACACATCCGGGCCT 62.778 66.667 0.84 0.00 0.00 5.19
431 458 1.339097 GGGTCCTACATATGCGACCT 58.661 55.000 25.09 3.33 43.61 3.85
456 483 1.421410 GCGAACATCGTCATCGGCTT 61.421 55.000 1.45 0.00 42.81 4.35
458 485 0.931005 GAACATCGTCATCGGCTTCC 59.069 55.000 0.00 0.00 37.69 3.46
469 496 3.069318 GGCTTCCCCGACGACTCT 61.069 66.667 0.00 0.00 0.00 3.24
482 509 3.802377 GACTCTATCGTGTCGACGG 57.198 57.895 11.62 5.54 46.11 4.79
484 511 1.005137 GACTCTATCGTGTCGACGGAC 60.005 57.143 11.62 3.35 46.11 4.79
485 512 0.043224 CTCTATCGTGTCGACGGACG 60.043 60.000 19.15 19.15 46.49 4.79
502 529 4.816984 GACGGAGCGGAGGGAGGA 62.817 72.222 0.00 0.00 0.00 3.71
503 530 4.824515 ACGGAGCGGAGGGAGGAG 62.825 72.222 0.00 0.00 0.00 3.69
504 531 4.507916 CGGAGCGGAGGGAGGAGA 62.508 72.222 0.00 0.00 0.00 3.71
505 532 2.200092 GGAGCGGAGGGAGGAGAT 59.800 66.667 0.00 0.00 0.00 2.75
506 533 2.206536 GGAGCGGAGGGAGGAGATG 61.207 68.421 0.00 0.00 0.00 2.90
507 534 1.152652 GAGCGGAGGGAGGAGATGA 60.153 63.158 0.00 0.00 0.00 2.92
543 796 3.566130 GCAGGAGAGGACATGCTTT 57.434 52.632 0.00 0.00 42.93 3.51
544 797 1.377536 GCAGGAGAGGACATGCTTTC 58.622 55.000 0.00 0.00 42.93 2.62
545 798 1.339438 GCAGGAGAGGACATGCTTTCA 60.339 52.381 0.00 0.00 42.93 2.69
546 799 2.354259 CAGGAGAGGACATGCTTTCAC 58.646 52.381 0.00 0.00 0.00 3.18
547 800 1.980765 AGGAGAGGACATGCTTTCACA 59.019 47.619 0.00 0.00 0.00 3.58
548 801 2.079925 GGAGAGGACATGCTTTCACAC 58.920 52.381 0.00 0.00 0.00 3.82
549 802 1.728971 GAGAGGACATGCTTTCACACG 59.271 52.381 0.00 0.00 0.00 4.49
550 803 0.798776 GAGGACATGCTTTCACACGG 59.201 55.000 0.00 0.00 0.00 4.94
551 804 0.606401 AGGACATGCTTTCACACGGG 60.606 55.000 0.00 0.00 0.00 5.28
552 805 0.605319 GGACATGCTTTCACACGGGA 60.605 55.000 0.00 0.00 0.00 5.14
553 806 0.798776 GACATGCTTTCACACGGGAG 59.201 55.000 0.00 0.00 0.00 4.30
554 807 0.606401 ACATGCTTTCACACGGGAGG 60.606 55.000 0.00 0.00 0.00 4.30
555 808 0.321564 CATGCTTTCACACGGGAGGA 60.322 55.000 0.00 0.00 0.00 3.71
556 809 0.036010 ATGCTTTCACACGGGAGGAG 60.036 55.000 0.00 0.00 0.00 3.69
557 810 1.376037 GCTTTCACACGGGAGGAGG 60.376 63.158 0.00 0.00 0.00 4.30
558 811 1.296715 CTTTCACACGGGAGGAGGG 59.703 63.158 0.00 0.00 0.00 4.30
559 812 2.185310 CTTTCACACGGGAGGAGGGG 62.185 65.000 0.00 0.00 0.00 4.79
576 829 1.353609 GGGCGTGATTGTGCAAATGC 61.354 55.000 0.00 0.00 42.50 3.56
577 830 1.676438 GGCGTGATTGTGCAAATGCG 61.676 55.000 0.35 0.14 45.83 4.73
588 841 1.580845 GCAAATGCGCAGACTCCACT 61.581 55.000 18.32 0.00 0.00 4.00
589 842 1.725641 CAAATGCGCAGACTCCACTA 58.274 50.000 18.32 0.00 0.00 2.74
613 866 2.619332 CGATTTGGGTGGGTCCATGTTA 60.619 50.000 0.00 0.00 36.58 2.41
617 870 0.834612 GGGTGGGTCCATGTTATCGA 59.165 55.000 0.00 0.00 38.11 3.59
621 874 3.951680 GGTGGGTCCATGTTATCGAAATT 59.048 43.478 0.00 0.00 35.97 1.82
622 875 4.401202 GGTGGGTCCATGTTATCGAAATTT 59.599 41.667 0.00 0.00 35.97 1.82
637 890 3.389221 GAAATTTGTTGTGGCGGATGTT 58.611 40.909 0.00 0.00 0.00 2.71
646 899 0.953471 TGGCGGATGTTGAAACTCCG 60.953 55.000 20.33 20.33 44.75 4.63
647 900 0.953960 GGCGGATGTTGAAACTCCGT 60.954 55.000 22.96 0.63 44.29 4.69
658 911 5.221561 TGTTGAAACTCCGTGAAATCTCCTA 60.222 40.000 0.00 0.00 0.00 2.94
660 913 5.419542 TGAAACTCCGTGAAATCTCCTATG 58.580 41.667 0.00 0.00 0.00 2.23
662 915 4.927978 ACTCCGTGAAATCTCCTATGAG 57.072 45.455 0.00 0.00 40.17 2.90
668 921 6.051717 CCGTGAAATCTCCTATGAGTTGATT 58.948 40.000 0.00 0.00 39.75 2.57
677 930 7.453393 TCTCCTATGAGTTGATTTCAGTTTGT 58.547 34.615 0.00 0.00 39.75 2.83
685 938 6.515832 AGTTGATTTCAGTTTGTGGGATTTC 58.484 36.000 0.00 0.00 0.00 2.17
686 939 6.324770 AGTTGATTTCAGTTTGTGGGATTTCT 59.675 34.615 0.00 0.00 0.00 2.52
690 943 4.387026 TCAGTTTGTGGGATTTCTGGAT 57.613 40.909 0.00 0.00 0.00 3.41
694 947 4.082125 GTTTGTGGGATTTCTGGATCAGT 58.918 43.478 0.00 0.00 32.61 3.41
697 950 3.330405 TGTGGGATTTCTGGATCAGTTCA 59.670 43.478 0.00 0.00 32.61 3.18
730 983 5.496556 TGTGACCAACATTAGATGGGTAAG 58.503 41.667 0.00 0.00 41.68 2.34
732 985 6.177610 GTGACCAACATTAGATGGGTAAGAA 58.822 40.000 0.00 0.00 41.68 2.52
763 1016 2.159430 CGTTCAATCCAGACATTTGCGA 59.841 45.455 0.00 0.00 0.00 5.10
772 1025 2.549754 CAGACATTTGCGAGAGGTTTGT 59.450 45.455 0.00 0.00 0.00 2.83
773 1026 2.808543 AGACATTTGCGAGAGGTTTGTC 59.191 45.455 0.00 0.00 33.84 3.18
779 1032 2.027625 CGAGAGGTTTGTCCCGCAC 61.028 63.158 0.00 0.00 36.75 5.34
781 1034 0.606604 GAGAGGTTTGTCCCGCACTA 59.393 55.000 0.00 0.00 36.75 2.74
791 1044 2.125106 CCGCACTAGAGTTGCCCC 60.125 66.667 0.00 0.00 0.00 5.80
795 1048 1.153823 CACTAGAGTTGCCCCGACG 60.154 63.158 0.00 0.00 0.00 5.12
812 1065 2.797278 CGGCTCTAAGATGGGGCGT 61.797 63.158 2.18 0.00 41.57 5.68
818 1071 1.077787 TAAGATGGGGCGTTGCTGG 60.078 57.895 0.00 0.00 0.00 4.85
830 1083 0.590195 GTTGCTGGAGTTGCTCACAG 59.410 55.000 8.99 8.99 34.37 3.66
841 1094 6.661613 GGAGTTGCTCACAGGTAACTTTGTT 61.662 44.000 0.00 0.00 44.86 2.83
854 1107 5.106038 GGTAACTTTGTTTAATTCTCCCCCG 60.106 44.000 0.00 0.00 0.00 5.73
855 1108 2.823747 ACTTTGTTTAATTCTCCCCCGC 59.176 45.455 0.00 0.00 0.00 6.13
858 1111 2.877866 TGTTTAATTCTCCCCCGCAAA 58.122 42.857 0.00 0.00 0.00 3.68
859 1112 3.231818 TGTTTAATTCTCCCCCGCAAAA 58.768 40.909 0.00 0.00 0.00 2.44
860 1113 3.641906 TGTTTAATTCTCCCCCGCAAAAA 59.358 39.130 0.00 0.00 0.00 1.94
921 1213 4.986054 AGTAGATTTGTGGTTGTGGGTA 57.014 40.909 0.00 0.00 0.00 3.69
1002 1294 2.032550 CCAAAACCGATCAGCAGCTATG 59.967 50.000 0.00 0.00 0.00 2.23
1018 1310 7.484007 CAGCAGCTATGACAATAAACAAAGAAG 59.516 37.037 0.00 0.00 0.00 2.85
1359 1654 2.115911 CACCTCGACCTCCTCCTCG 61.116 68.421 0.00 0.00 0.00 4.63
1460 1755 1.067582 CGTCATCTAAGGCCGGGAC 59.932 63.158 2.18 0.00 0.00 4.46
1620 1915 9.448438 GAAATGTGGCTTCCCTTTATTTATTTT 57.552 29.630 0.00 0.00 0.00 1.82
1632 1927 8.807581 CCCTTTATTTATTTTCGATTGCTTGTC 58.192 33.333 0.00 0.00 0.00 3.18
1692 1987 4.927978 ATTAGATCTCTCGTCTGGGTTG 57.072 45.455 0.00 0.00 0.00 3.77
1705 2011 0.109723 TGGGTTGGTGTTAGCCTGTC 59.890 55.000 0.00 0.00 34.29 3.51
1728 2034 0.037590 GGTGTGTGATTGGTAGGCCA 59.962 55.000 5.01 0.00 44.38 5.36
1785 2091 7.388776 TGTCTAAGTTTGGTGATCTTGAGATTG 59.611 37.037 0.00 0.00 34.37 2.67
1817 2123 8.752005 TCATATGGAATTTACTTTCCTTGAGG 57.248 34.615 2.13 0.00 44.63 3.86
1818 2124 8.336235 TCATATGGAATTTACTTTCCTTGAGGT 58.664 33.333 2.13 0.00 44.63 3.85
1819 2125 9.627123 CATATGGAATTTACTTTCCTTGAGGTA 57.373 33.333 4.96 0.00 44.63 3.08
1906 2219 2.863809 AGTGGAAAGGAATTTGCTCGT 58.136 42.857 0.00 0.00 0.00 4.18
1907 2220 3.222603 AGTGGAAAGGAATTTGCTCGTT 58.777 40.909 0.00 0.00 0.00 3.85
2068 2381 0.817654 GCTTTTACATGGGGCCTGAC 59.182 55.000 0.84 0.00 0.00 3.51
2069 2382 1.474330 CTTTTACATGGGGCCTGACC 58.526 55.000 0.84 0.00 37.93 4.02
2070 2383 0.322997 TTTTACATGGGGCCTGACCG 60.323 55.000 0.84 0.00 40.62 4.79
2084 2397 3.226429 GACCGCCTGAGTGCAGACA 62.226 63.158 0.00 0.00 45.17 3.41
2101 2414 4.453819 GCAGACATAGGCTCCAATTATGAC 59.546 45.833 0.00 0.00 0.00 3.06
2105 2418 1.213296 AGGCTCCAATTATGACCGGT 58.787 50.000 6.92 6.92 0.00 5.28
2159 2473 3.748048 CCTGGTATTCGGTTCTGCATATG 59.252 47.826 0.00 0.00 0.00 1.78
2319 2635 5.524646 GCGGTGTTTAGCAGTTATGGTATAA 59.475 40.000 0.00 0.00 39.08 0.98
2436 2752 7.770433 TCAATACTTCAGTCATTCCATGTAAGG 59.230 37.037 0.00 0.00 0.00 2.69
2647 2963 8.690203 TCTTATTTTGTTCTGATTTCAGGTCA 57.310 30.769 7.68 5.00 43.91 4.02
2746 3067 8.773404 TTTTCAAGATAGAGCTAAGTTGGTAC 57.227 34.615 0.00 0.00 0.00 3.34
2791 3112 2.072298 GTCAAGCTCTAACACTGGCAG 58.928 52.381 14.16 14.16 0.00 4.85
2806 3127 5.882557 ACACTGGCAGTCATTCTATTTTAGG 59.117 40.000 19.13 3.67 0.00 2.69
2852 3173 3.247006 ACTTGTATAGTTGAGCCACCG 57.753 47.619 0.00 0.00 31.29 4.94
2856 3177 2.764010 TGTATAGTTGAGCCACCGTCAT 59.236 45.455 0.00 0.00 0.00 3.06
2862 3183 1.485124 TGAGCCACCGTCATCTATGT 58.515 50.000 0.00 0.00 0.00 2.29
2863 3184 1.136891 TGAGCCACCGTCATCTATGTG 59.863 52.381 0.00 0.00 0.00 3.21
2916 3242 8.783093 TCTCTGTCATGTACAAAAATAGTTTGG 58.217 33.333 0.00 0.00 37.74 3.28
3183 3509 7.985184 AGCATATGATAAGTCACTTAAAACCGA 59.015 33.333 6.97 0.00 37.14 4.69
3213 3539 3.995199 TGGAATCGATGCAGGAACTATC 58.005 45.455 5.57 0.00 36.02 2.08
3255 3581 1.654997 TGGTAGGTCCCTAGGTGGAAT 59.345 52.381 8.29 0.00 35.80 3.01
3335 3661 4.584325 TGTTGGTAGAAGCTTGCTTTGATT 59.416 37.500 2.10 0.00 0.00 2.57
3344 3670 5.464030 AGCTTGCTTTGATTGTGAGAATT 57.536 34.783 0.00 0.00 0.00 2.17
3430 3756 6.131264 TGGGATTAATCAGATGCTTCACAAT 58.869 36.000 17.07 0.00 0.00 2.71
3465 3791 1.260297 GGCGTTGTTCAACCATTTTGC 59.740 47.619 9.62 6.34 0.00 3.68
3472 3798 3.133542 TGTTCAACCATTTTGCCACATCA 59.866 39.130 0.00 0.00 0.00 3.07
3487 3813 4.993584 GCCACATCAGACCAAGTAGATATG 59.006 45.833 0.00 0.00 0.00 1.78
3505 3831 2.928801 TGGAGTTACTTTCTGCTGCA 57.071 45.000 0.88 0.88 0.00 4.41
3514 3840 3.748083 ACTTTCTGCTGCAGAGAATCAA 58.252 40.909 28.91 19.80 41.75 2.57
3519 3845 6.432607 TTCTGCTGCAGAGAATCAATTAAG 57.567 37.500 28.91 1.07 41.75 1.85
3543 3869 8.628882 AGTGTAGTTGTAAAAGATGCAAAAAC 57.371 30.769 0.00 0.00 35.30 2.43
3545 3871 7.489757 GTGTAGTTGTAAAAGATGCAAAAACCA 59.510 33.333 0.00 0.00 35.30 3.67
3569 3895 5.481824 ACAGAAGATCCAGATTACTGTGACA 59.518 40.000 0.00 0.00 42.05 3.58
3652 3978 6.103997 CCATGAAACTTTCAATGCTAGCAAT 58.896 36.000 23.54 11.27 43.95 3.56
3677 4003 3.124466 TGTTTCGATGCAAGGTATTGTCG 59.876 43.478 0.00 0.00 38.76 4.35
3846 4172 6.974622 AGTTTAAACTGTGAATTGTTCTGCTG 59.025 34.615 19.94 0.00 37.98 4.41
4004 4330 4.026228 CACTGTCAGCAATACTAATCTGCG 60.026 45.833 0.00 0.00 41.05 5.18
4057 4385 6.585695 ATGCTTGATCTTAATATTGGCCTG 57.414 37.500 3.32 0.00 0.00 4.85
4078 4406 2.218953 TGACACTCGTTCTGGTGTTC 57.781 50.000 0.00 0.00 45.17 3.18
4119 4447 5.478407 TGATTCTGACGCTCTGTTGATTTA 58.522 37.500 0.00 0.00 0.00 1.40
4190 4518 0.095935 CAGTTCTTGCAATCCTCGCG 59.904 55.000 0.00 0.00 0.00 5.87
4436 4764 6.634805 TGAAGACTTTCTGGATAGTGATGAC 58.365 40.000 0.00 0.00 34.31 3.06
4597 4925 4.527038 CCTACTCAATGTCCCATACCGTAT 59.473 45.833 0.00 0.00 0.00 3.06
4598 4926 4.602340 ACTCAATGTCCCATACCGTATC 57.398 45.455 0.00 0.00 0.00 2.24
4599 4927 4.223953 ACTCAATGTCCCATACCGTATCT 58.776 43.478 0.00 0.00 0.00 1.98
4600 4928 5.391256 ACTCAATGTCCCATACCGTATCTA 58.609 41.667 0.00 0.00 0.00 1.98
4601 4929 6.017192 ACTCAATGTCCCATACCGTATCTAT 58.983 40.000 0.00 0.00 0.00 1.98
4602 4930 7.179966 ACTCAATGTCCCATACCGTATCTATA 58.820 38.462 0.00 0.00 0.00 1.31
4603 4931 7.122353 ACTCAATGTCCCATACCGTATCTATAC 59.878 40.741 0.00 0.00 0.00 1.47
4604 4932 7.179966 TCAATGTCCCATACCGTATCTATACT 58.820 38.462 0.00 0.00 0.00 2.12
4696 5094 6.477053 TCAGATTAGTCTATTTCTGCAGCT 57.523 37.500 9.47 0.44 36.41 4.24
4697 5095 6.279123 TCAGATTAGTCTATTTCTGCAGCTG 58.721 40.000 10.11 10.11 36.41 4.24
4698 5096 5.466058 CAGATTAGTCTATTTCTGCAGCTGG 59.534 44.000 17.12 0.00 32.09 4.85
4699 5097 4.826274 TTAGTCTATTTCTGCAGCTGGT 57.174 40.909 17.12 0.00 0.00 4.00
4700 5098 3.258971 AGTCTATTTCTGCAGCTGGTC 57.741 47.619 17.12 0.00 0.00 4.02
4701 5099 2.836981 AGTCTATTTCTGCAGCTGGTCT 59.163 45.455 17.12 0.00 0.00 3.85
4742 5140 7.541162 TGATGCACGTTATAAACTACTAGTGT 58.459 34.615 5.39 0.00 0.00 3.55
4779 5177 5.833131 TGGATAATAGAAGGTGCATTTTCCC 59.167 40.000 8.90 0.00 32.14 3.97
4925 5323 6.879276 TGCTGTATAGTCTGGTATCACTAC 57.121 41.667 0.00 0.00 0.00 2.73
4945 5343 6.916387 CACTACAGAATAACCGTACCACTATG 59.084 42.308 0.00 0.00 0.00 2.23
5101 5499 6.057533 CCCATATCAATGCACTCTACTTTGA 58.942 40.000 0.00 0.00 36.15 2.69
5247 5647 4.160252 GGTGGATTCATTTAGCATTGGTGT 59.840 41.667 0.00 0.00 0.00 4.16
5257 5657 1.024579 GCATTGGTGTACAGGGACCG 61.025 60.000 0.00 0.00 34.69 4.79
5397 5797 1.978580 ACTGGAAAGTCGGAAGGATGT 59.021 47.619 0.00 0.00 0.00 3.06
5445 5845 9.624697 CAAATAAATACATTCCATTACATCCGG 57.375 33.333 0.00 0.00 0.00 5.14
5529 5929 3.642938 TGGTATTGGCACCACTGAC 57.357 52.632 0.00 0.00 43.76 3.51
5700 6100 2.487265 GGTGGAGCCTTTGTTGAGAGAA 60.487 50.000 0.00 0.00 0.00 2.87
5829 6229 1.404479 TTGCTGGTGGACCTACACGT 61.404 55.000 0.00 0.00 42.23 4.49
6011 6411 1.267806 CATCCAGCGTTTCAAGCAAGT 59.732 47.619 0.00 0.00 37.01 3.16
6129 6529 2.613691 CGAGTTTTGTGCTACCGGTAT 58.386 47.619 16.25 0.00 0.00 2.73
6309 6711 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
6326 6728 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
6415 6817 7.066163 TGCGGATATCTTGGAATAAAGCATATG 59.934 37.037 2.05 0.00 0.00 1.78
6441 6843 7.201723 GGTGAATAAGCACAATATGATCACACA 60.202 37.037 0.00 0.00 40.52 3.72
6470 6872 5.925509 TGGGCATAAACTGTATAGAGGAAC 58.074 41.667 1.49 0.00 0.00 3.62
6528 6934 5.806502 TCTGAGTTGTTTGAAATTGTTGCTG 59.193 36.000 0.00 0.00 0.00 4.41
6546 6952 4.858935 TGCTGCTTGTGTGTTCTTTTATC 58.141 39.130 0.00 0.00 0.00 1.75
6591 6997 7.878127 TGAGTTACTTTTTGACTCCTATGAAGG 59.122 37.037 0.00 0.00 45.21 3.46
6609 7015 5.630121 TGAAGGAAGGCATTCTGAAAAGTA 58.370 37.500 11.37 0.00 35.90 2.24
6610 7016 5.473504 TGAAGGAAGGCATTCTGAAAAGTAC 59.526 40.000 11.37 0.00 35.90 2.73
6611 7017 5.248380 AGGAAGGCATTCTGAAAAGTACT 57.752 39.130 11.37 0.00 35.63 2.73
6612 7018 5.249420 AGGAAGGCATTCTGAAAAGTACTC 58.751 41.667 11.37 0.00 35.63 2.59
6613 7019 4.396478 GGAAGGCATTCTGAAAAGTACTCC 59.604 45.833 11.37 0.00 35.63 3.85
6614 7020 3.956744 AGGCATTCTGAAAAGTACTCCC 58.043 45.455 0.00 0.00 0.00 4.30
6615 7021 3.589288 AGGCATTCTGAAAAGTACTCCCT 59.411 43.478 0.00 0.00 0.00 4.20
6616 7022 3.942115 GGCATTCTGAAAAGTACTCCCTC 59.058 47.826 0.00 0.00 0.00 4.30
6617 7023 3.942115 GCATTCTGAAAAGTACTCCCTCC 59.058 47.826 0.00 0.00 0.00 4.30
6618 7024 3.955650 TTCTGAAAAGTACTCCCTCCG 57.044 47.619 0.00 0.00 0.00 4.63
6619 7025 2.885616 TCTGAAAAGTACTCCCTCCGT 58.114 47.619 0.00 0.00 0.00 4.69
6620 7026 2.824341 TCTGAAAAGTACTCCCTCCGTC 59.176 50.000 0.00 0.00 0.00 4.79
6621 7027 1.897802 TGAAAAGTACTCCCTCCGTCC 59.102 52.381 0.00 0.00 0.00 4.79
6622 7028 1.206610 GAAAAGTACTCCCTCCGTCCC 59.793 57.143 0.00 0.00 0.00 4.46
6623 7029 0.115745 AAAGTACTCCCTCCGTCCCA 59.884 55.000 0.00 0.00 0.00 4.37
6624 7030 0.338814 AAGTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
6625 7031 1.229131 AGTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
6626 7032 1.572415 AGTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
6627 7033 2.179424 AGTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
6628 7034 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
6629 7035 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
6630 7036 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
6631 7037 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
6632 7038 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
6633 7039 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
6634 7040 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
6635 7041 3.386726 CCTCCGTCCCATAATGTAAGACA 59.613 47.826 0.00 0.00 0.00 3.41
6636 7042 4.040461 CCTCCGTCCCATAATGTAAGACAT 59.960 45.833 0.00 0.00 41.31 3.06
6638 7044 5.996644 TCCGTCCCATAATGTAAGACATTT 58.003 37.500 9.92 0.00 45.80 2.32
6639 7045 6.419791 TCCGTCCCATAATGTAAGACATTTT 58.580 36.000 9.92 0.33 45.80 1.82
6640 7046 6.887545 TCCGTCCCATAATGTAAGACATTTTT 59.112 34.615 9.92 0.00 45.80 1.94
6668 7074 8.908786 ACACTAACATCTTACATTATGGGATG 57.091 34.615 16.81 16.81 39.45 3.51
6669 7075 7.939039 ACACTAACATCTTACATTATGGGATGG 59.061 37.037 19.96 10.91 38.33 3.51
6670 7076 8.156820 CACTAACATCTTACATTATGGGATGGA 58.843 37.037 19.96 11.83 38.33 3.41
6671 7077 8.378565 ACTAACATCTTACATTATGGGATGGAG 58.621 37.037 19.96 18.22 38.33 3.86
6672 7078 6.770286 ACATCTTACATTATGGGATGGAGT 57.230 37.500 19.96 5.89 38.33 3.85
6673 7079 7.872061 ACATCTTACATTATGGGATGGAGTA 57.128 36.000 19.96 0.00 38.33 2.59
6674 7080 7.911651 ACATCTTACATTATGGGATGGAGTAG 58.088 38.462 19.96 4.49 38.33 2.57
6675 7081 6.935240 TCTTACATTATGGGATGGAGTAGG 57.065 41.667 0.00 0.00 0.00 3.18
6820 7296 3.122480 TGGAATTCTTATCTCCTGGCCA 58.878 45.455 4.71 4.71 0.00 5.36
6828 7304 0.706433 ATCTCCTGGCCATGTGGTTT 59.294 50.000 5.51 0.00 37.57 3.27
6858 7334 2.300433 TCTGCAAGCAAACATCACAGT 58.700 42.857 0.00 0.00 0.00 3.55
6904 7380 2.672874 TCATCACGCTGTTCTTGTATGC 59.327 45.455 0.00 0.00 0.00 3.14
6907 7383 3.858040 CGCTGTTCTTGTATGCGTC 57.142 52.632 0.00 0.00 41.45 5.19
7001 7480 1.305297 AGATGCCGACTCCACCTGA 60.305 57.895 0.00 0.00 0.00 3.86
7008 7488 0.962489 CGACTCCACCTGAAGACAGT 59.038 55.000 0.00 0.00 42.05 3.55
7025 7505 8.247562 TGAAGACAGTAGATTTAAGAGCTTCTC 58.752 37.037 0.00 0.00 31.80 2.87
7080 7560 1.425066 TGGTTGCAGTGAGAGGGAAAT 59.575 47.619 0.00 0.00 0.00 2.17
7171 7651 0.679640 CGCCCTAGCCAATTGACCAA 60.680 55.000 7.12 0.00 34.57 3.67
7172 7652 1.780503 GCCCTAGCCAATTGACCAAT 58.219 50.000 7.12 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.656652 GAAGTGACATGGACCATCCG 58.343 55.000 3.21 0.00 40.17 4.18
14 15 0.253044 CCGGAAGTGACATGGACCAT 59.747 55.000 0.00 0.00 0.00 3.55
15 16 1.125093 ACCGGAAGTGACATGGACCA 61.125 55.000 9.46 0.00 0.00 4.02
31 32 8.721478 CAAGGGATTGATGACTTTATTATACCG 58.279 37.037 0.00 0.00 0.00 4.02
114 115 7.444183 TCACAAATTCTTATTCGGTTGACTCTT 59.556 33.333 0.00 0.00 0.00 2.85
121 122 7.979444 TCTCTTCACAAATTCTTATTCGGTT 57.021 32.000 0.00 0.00 0.00 4.44
133 134 6.929049 TCAACAACGACTATCTCTTCACAAAT 59.071 34.615 0.00 0.00 0.00 2.32
145 146 0.892755 TCGGCCTCAACAACGACTAT 59.107 50.000 0.00 0.00 0.00 2.12
152 153 1.303236 CCACCATCGGCCTCAACAA 60.303 57.895 0.00 0.00 0.00 2.83
153 154 2.220586 TCCACCATCGGCCTCAACA 61.221 57.895 0.00 0.00 0.00 3.33
174 175 1.021390 CACCTCCGGTCATCAAGCAC 61.021 60.000 0.00 0.00 31.02 4.40
175 176 1.191489 TCACCTCCGGTCATCAAGCA 61.191 55.000 0.00 0.00 31.02 3.91
190 191 1.353091 AGTCCTTGTCCTCCTTCACC 58.647 55.000 0.00 0.00 0.00 4.02
217 218 0.170784 TACCACGTCGCGCAGAATTA 59.829 50.000 8.75 0.00 0.00 1.40
218 219 0.668096 TTACCACGTCGCGCAGAATT 60.668 50.000 8.75 0.00 0.00 2.17
225 251 1.777199 GACCTTTTACCACGTCGCG 59.223 57.895 0.00 0.00 0.00 5.87
227 253 1.620413 GCCGACCTTTTACCACGTCG 61.620 60.000 0.00 0.00 45.79 5.12
250 276 2.790791 CCTCTGGCCCGTCTAGCTG 61.791 68.421 0.00 0.00 0.00 4.24
255 281 1.229082 TTGTACCTCTGGCCCGTCT 60.229 57.895 0.00 0.00 0.00 4.18
266 292 3.149196 CAAAGTGCACCATCTTGTACCT 58.851 45.455 14.63 0.00 32.90 3.08
268 294 3.058224 GTCCAAAGTGCACCATCTTGTAC 60.058 47.826 14.63 5.94 32.66 2.90
274 300 1.131126 CATCGTCCAAAGTGCACCATC 59.869 52.381 14.63 0.00 0.00 3.51
276 302 0.107643 TCATCGTCCAAAGTGCACCA 59.892 50.000 14.63 0.00 0.00 4.17
290 316 1.203928 GATCAAGCCGACACTCATCG 58.796 55.000 0.00 0.00 41.89 3.84
317 343 2.596904 TACAAGATGTAGAAGGCGGC 57.403 50.000 0.00 0.00 0.00 6.53
328 354 4.201990 GCAAAGGAGAAGGCATACAAGATG 60.202 45.833 0.00 0.00 0.00 2.90
329 355 3.950395 GCAAAGGAGAAGGCATACAAGAT 59.050 43.478 0.00 0.00 0.00 2.40
336 362 1.553706 CAAGGCAAAGGAGAAGGCAT 58.446 50.000 0.00 0.00 0.00 4.40
337 363 0.540365 CCAAGGCAAAGGAGAAGGCA 60.540 55.000 0.00 0.00 0.00 4.75
339 365 0.613012 CCCCAAGGCAAAGGAGAAGG 60.613 60.000 0.00 0.00 0.00 3.46
360 386 3.211963 GCACTATGCAAGGCCGGG 61.212 66.667 2.18 0.00 44.26 5.73
370 396 2.285220 GCAAGGTCGTGTATGCACTATG 59.715 50.000 12.30 4.99 43.16 2.23
371 397 2.093711 TGCAAGGTCGTGTATGCACTAT 60.094 45.455 12.30 0.00 43.32 2.12
375 402 2.839629 CTGCAAGGTCGTGTATGCA 58.160 52.632 0.00 0.00 45.75 3.96
406 433 0.693049 CATATGTAGGACCCAGGCCC 59.307 60.000 0.00 0.00 0.00 5.80
409 436 1.000955 GTCGCATATGTAGGACCCAGG 59.999 57.143 4.29 0.00 0.00 4.45
411 438 1.045407 GGTCGCATATGTAGGACCCA 58.955 55.000 22.05 0.00 42.45 4.51
431 458 0.673333 ATGACGATGTTCGCCTGCAA 60.673 50.000 0.00 0.00 45.12 4.08
435 462 1.226974 CCGATGACGATGTTCGCCT 60.227 57.895 0.00 0.00 45.12 5.52
456 483 4.451241 CGATAGAGTCGTCGGGGA 57.549 61.111 11.62 0.00 45.19 4.81
485 512 4.816984 TCCTCCCTCCGCTCCGTC 62.817 72.222 0.00 0.00 0.00 4.79
487 514 3.801068 ATCTCCTCCCTCCGCTCCG 62.801 68.421 0.00 0.00 0.00 4.63
488 515 2.200092 ATCTCCTCCCTCCGCTCC 59.800 66.667 0.00 0.00 0.00 4.70
489 516 0.541764 ATCATCTCCTCCCTCCGCTC 60.542 60.000 0.00 0.00 0.00 5.03
490 517 0.831288 CATCATCTCCTCCCTCCGCT 60.831 60.000 0.00 0.00 0.00 5.52
491 518 0.829602 TCATCATCTCCTCCCTCCGC 60.830 60.000 0.00 0.00 0.00 5.54
492 519 1.824230 GATCATCATCTCCTCCCTCCG 59.176 57.143 0.00 0.00 0.00 4.63
493 520 1.824230 CGATCATCATCTCCTCCCTCC 59.176 57.143 0.00 0.00 0.00 4.30
494 521 1.824230 CCGATCATCATCTCCTCCCTC 59.176 57.143 0.00 0.00 0.00 4.30
495 522 1.552023 CCCGATCATCATCTCCTCCCT 60.552 57.143 0.00 0.00 0.00 4.20
496 523 0.901124 CCCGATCATCATCTCCTCCC 59.099 60.000 0.00 0.00 0.00 4.30
497 524 1.548269 GTCCCGATCATCATCTCCTCC 59.452 57.143 0.00 0.00 0.00 4.30
498 525 1.201181 CGTCCCGATCATCATCTCCTC 59.799 57.143 0.00 0.00 0.00 3.71
499 526 1.252175 CGTCCCGATCATCATCTCCT 58.748 55.000 0.00 0.00 0.00 3.69
500 527 0.962489 ACGTCCCGATCATCATCTCC 59.038 55.000 0.00 0.00 0.00 3.71
501 528 3.366476 CCTTACGTCCCGATCATCATCTC 60.366 52.174 0.00 0.00 0.00 2.75
502 529 2.558795 CCTTACGTCCCGATCATCATCT 59.441 50.000 0.00 0.00 0.00 2.90
503 530 2.557056 TCCTTACGTCCCGATCATCATC 59.443 50.000 0.00 0.00 0.00 2.92
504 531 2.558795 CTCCTTACGTCCCGATCATCAT 59.441 50.000 0.00 0.00 0.00 2.45
505 532 1.954382 CTCCTTACGTCCCGATCATCA 59.046 52.381 0.00 0.00 0.00 3.07
506 533 1.336056 GCTCCTTACGTCCCGATCATC 60.336 57.143 0.00 0.00 0.00 2.92
507 534 0.674534 GCTCCTTACGTCCCGATCAT 59.325 55.000 0.00 0.00 0.00 2.45
527 780 1.980765 TGTGAAAGCATGTCCTCTCCT 59.019 47.619 0.00 0.00 0.00 3.69
541 794 2.221299 CCCCTCCTCCCGTGTGAAA 61.221 63.158 0.00 0.00 0.00 2.69
542 795 2.606519 CCCCTCCTCCCGTGTGAA 60.607 66.667 0.00 0.00 0.00 3.18
549 802 3.090532 AATCACGCCCCTCCTCCC 61.091 66.667 0.00 0.00 0.00 4.30
550 803 2.190578 CAATCACGCCCCTCCTCC 59.809 66.667 0.00 0.00 0.00 4.30
551 804 1.450312 CACAATCACGCCCCTCCTC 60.450 63.158 0.00 0.00 0.00 3.71
552 805 2.671070 CACAATCACGCCCCTCCT 59.329 61.111 0.00 0.00 0.00 3.69
553 806 3.134127 GCACAATCACGCCCCTCC 61.134 66.667 0.00 0.00 0.00 4.30
554 807 1.523154 TTTGCACAATCACGCCCCTC 61.523 55.000 0.00 0.00 0.00 4.30
555 808 0.899717 ATTTGCACAATCACGCCCCT 60.900 50.000 0.00 0.00 0.00 4.79
556 809 0.737019 CATTTGCACAATCACGCCCC 60.737 55.000 0.00 0.00 0.00 5.80
557 810 1.353609 GCATTTGCACAATCACGCCC 61.354 55.000 0.00 0.00 41.59 6.13
558 811 1.676438 CGCATTTGCACAATCACGCC 61.676 55.000 3.13 0.00 42.21 5.68
559 812 1.697770 CGCATTTGCACAATCACGC 59.302 52.632 3.13 0.00 42.21 5.34
560 813 1.002756 TGCGCATTTGCACAATCACG 61.003 50.000 5.66 0.00 40.62 4.35
564 817 0.599558 AGTCTGCGCATTTGCACAAT 59.400 45.000 12.24 0.00 40.62 2.71
581 834 2.233922 CACCCAAATCGACTAGTGGAGT 59.766 50.000 13.30 7.88 42.90 3.85
588 841 0.906775 GGACCCACCCAAATCGACTA 59.093 55.000 0.00 0.00 0.00 2.59
589 842 1.131303 TGGACCCACCCAAATCGACT 61.131 55.000 0.00 0.00 38.00 4.18
613 866 1.883275 TCCGCCACAACAAATTTCGAT 59.117 42.857 0.00 0.00 0.00 3.59
617 870 3.129871 CAACATCCGCCACAACAAATTT 58.870 40.909 0.00 0.00 0.00 1.82
621 874 1.393603 TTCAACATCCGCCACAACAA 58.606 45.000 0.00 0.00 0.00 2.83
622 875 1.066303 GTTTCAACATCCGCCACAACA 59.934 47.619 0.00 0.00 0.00 3.33
637 890 5.186992 TCATAGGAGATTTCACGGAGTTTCA 59.813 40.000 0.00 0.00 41.61 2.69
646 899 8.498054 TGAAATCAACTCATAGGAGATTTCAC 57.502 34.615 20.43 6.06 41.75 3.18
647 900 8.324306 ACTGAAATCAACTCATAGGAGATTTCA 58.676 33.333 21.80 21.80 42.95 2.69
658 911 5.139727 TCCCACAAACTGAAATCAACTCAT 58.860 37.500 0.00 0.00 0.00 2.90
660 913 5.712152 ATCCCACAAACTGAAATCAACTC 57.288 39.130 0.00 0.00 0.00 3.01
662 915 6.421801 CAGAAATCCCACAAACTGAAATCAAC 59.578 38.462 0.00 0.00 0.00 3.18
668 921 4.177537 TCCAGAAATCCCACAAACTGAA 57.822 40.909 0.00 0.00 0.00 3.02
671 924 4.202609 ACTGATCCAGAAATCCCACAAACT 60.203 41.667 0.45 0.00 35.18 2.66
677 930 4.868172 ATGAACTGATCCAGAAATCCCA 57.132 40.909 0.45 0.00 35.18 4.37
714 967 5.296780 CACGCATTCTTACCCATCTAATGTT 59.703 40.000 0.00 0.00 31.65 2.71
763 1016 0.608640 CTAGTGCGGGACAAACCTCT 59.391 55.000 1.61 0.00 38.98 3.69
772 1025 2.656069 GGGCAACTCTAGTGCGGGA 61.656 63.158 0.00 0.00 0.00 5.14
773 1026 2.125106 GGGCAACTCTAGTGCGGG 60.125 66.667 0.00 0.00 0.00 6.13
779 1032 2.494918 CCGTCGGGGCAACTCTAG 59.505 66.667 2.34 0.00 31.17 2.43
791 1044 1.364171 CCCCATCTTAGAGCCGTCG 59.636 63.158 0.00 0.00 0.00 5.12
795 1048 0.815615 CAACGCCCCATCTTAGAGCC 60.816 60.000 0.00 0.00 0.00 4.70
803 1056 2.825836 CTCCAGCAACGCCCCATC 60.826 66.667 0.00 0.00 0.00 3.51
812 1065 0.535780 CCTGTGAGCAACTCCAGCAA 60.536 55.000 7.27 0.00 31.89 3.91
818 1071 3.877508 ACAAAGTTACCTGTGAGCAACTC 59.122 43.478 0.00 0.00 31.06 3.01
830 1083 5.106038 CGGGGGAGAATTAAACAAAGTTACC 60.106 44.000 0.00 0.00 0.00 2.85
866 1119 9.862149 TCCCTTAGAATTAGACAAAGTTTCTTT 57.138 29.630 0.00 0.00 0.00 2.52
867 1120 9.862149 TTCCCTTAGAATTAGACAAAGTTTCTT 57.138 29.630 0.00 0.00 0.00 2.52
868 1121 9.862149 TTTCCCTTAGAATTAGACAAAGTTTCT 57.138 29.630 0.00 0.00 33.44 2.52
898 1152 4.542697 ACCCACAACCACAAATCTACTTT 58.457 39.130 0.00 0.00 0.00 2.66
921 1213 3.449632 GTTTGCAACAAACCACCGTATT 58.550 40.909 11.26 0.00 0.00 1.89
1142 1434 3.316573 GAGGAGGAGGTTGCGGTGG 62.317 68.421 0.00 0.00 0.00 4.61
1620 1915 0.737367 CCAGCGAGACAAGCAATCGA 60.737 55.000 0.00 0.00 38.72 3.59
1632 1927 1.280746 CACTGCAACAACCAGCGAG 59.719 57.895 0.00 0.00 33.65 5.03
1692 1987 1.812571 CACCAATGACAGGCTAACACC 59.187 52.381 0.00 0.00 0.00 4.16
1705 2011 2.164219 GCCTACCAATCACACACCAATG 59.836 50.000 0.00 0.00 0.00 2.82
1764 2070 4.768968 CCCAATCTCAAGATCACCAAACTT 59.231 41.667 0.00 0.00 32.75 2.66
1785 2091 8.797438 GGAAAGTAAATTCCATATGATCTTCCC 58.203 37.037 3.65 0.00 46.70 3.97
1818 2124 9.990360 TCAGTTGCGATCTTAACCAATATAATA 57.010 29.630 5.61 0.00 0.00 0.98
1819 2125 8.902540 TCAGTTGCGATCTTAACCAATATAAT 57.097 30.769 5.61 0.00 0.00 1.28
1820 2126 8.902540 ATCAGTTGCGATCTTAACCAATATAA 57.097 30.769 5.61 0.00 0.00 0.98
1822 2128 8.939929 CATATCAGTTGCGATCTTAACCAATAT 58.060 33.333 5.61 6.60 0.00 1.28
2070 2383 0.813210 GCCTATGTCTGCACTCAGGC 60.813 60.000 4.78 4.78 44.94 4.85
2071 2384 0.829333 AGCCTATGTCTGCACTCAGG 59.171 55.000 0.00 0.00 40.69 3.86
2072 2385 1.202510 GGAGCCTATGTCTGCACTCAG 60.203 57.143 0.00 0.00 41.67 3.35
2073 2386 0.826715 GGAGCCTATGTCTGCACTCA 59.173 55.000 0.00 0.00 0.00 3.41
2074 2387 0.826715 TGGAGCCTATGTCTGCACTC 59.173 55.000 0.00 0.00 0.00 3.51
2075 2388 1.279496 TTGGAGCCTATGTCTGCACT 58.721 50.000 0.00 0.00 31.60 4.40
2084 2397 2.979678 ACCGGTCATAATTGGAGCCTAT 59.020 45.455 0.00 0.00 0.00 2.57
2101 2414 0.391927 TTCTCCGTTGCCAATACCGG 60.392 55.000 0.00 0.00 41.75 5.28
2105 2418 5.461032 ACAATTTTTCTCCGTTGCCAATA 57.539 34.783 0.00 0.00 0.00 1.90
2225 2541 0.820226 CTCAGAGCTTGACGGGATGA 59.180 55.000 0.00 0.00 0.00 2.92
2226 2542 0.534412 ACTCAGAGCTTGACGGGATG 59.466 55.000 0.00 0.00 0.00 3.51
2319 2635 8.976353 AGTTCACAGAGATTGTATCAGATAACT 58.024 33.333 0.00 0.00 38.16 2.24
2473 2789 7.531857 TCTATTCAGGTTATTGTTGCCAAAA 57.468 32.000 0.00 0.00 33.44 2.44
2474 2790 7.716799 ATCTATTCAGGTTATTGTTGCCAAA 57.283 32.000 0.00 0.00 33.44 3.28
2475 2791 7.716799 AATCTATTCAGGTTATTGTTGCCAA 57.283 32.000 0.00 0.00 34.45 4.52
2476 2792 7.013274 GCTAATCTATTCAGGTTATTGTTGCCA 59.987 37.037 0.00 0.00 26.94 4.92
2647 2963 7.148373 GCATTTCAGGTTTTGCATGTCAATAAT 60.148 33.333 0.00 0.00 34.12 1.28
2652 2968 3.181468 TGCATTTCAGGTTTTGCATGTCA 60.181 39.130 0.00 0.00 39.98 3.58
2735 3056 6.780706 AACAAGAATGTCGTACCAACTTAG 57.219 37.500 0.00 0.00 39.40 2.18
2736 3057 6.539464 ACAAACAAGAATGTCGTACCAACTTA 59.461 34.615 0.00 0.00 39.40 2.24
2746 3067 4.273480 AGTCCAGAACAAACAAGAATGTCG 59.727 41.667 0.00 0.00 39.40 4.35
2791 3112 9.508567 GCAATTCACTTCCTAAAATAGAATGAC 57.491 33.333 0.00 0.00 0.00 3.06
2916 3242 8.478066 AGAAAAGGTGGAATTAATCTTAATGGC 58.522 33.333 0.00 0.00 33.85 4.40
2932 3258 3.551659 GCTGCTTGAAGAAGAAAAGGTGG 60.552 47.826 3.86 0.00 0.00 4.61
3176 3502 4.213482 CGATTCCAAGTTCTTCTCGGTTTT 59.787 41.667 0.00 0.00 0.00 2.43
3180 3506 3.232213 TCGATTCCAAGTTCTTCTCGG 57.768 47.619 0.00 0.00 0.00 4.63
3183 3509 3.937706 CTGCATCGATTCCAAGTTCTTCT 59.062 43.478 0.00 0.00 0.00 2.85
3213 3539 2.358737 GGGACTTCACCGCACTGG 60.359 66.667 0.00 0.00 46.41 4.00
3255 3581 3.084039 GCCCAGTGACATTCATCAGAAA 58.916 45.455 0.00 0.00 37.29 2.52
3298 3624 9.494271 GCTTCTACCAACATTTGATAGATATGA 57.506 33.333 0.00 0.00 0.00 2.15
3335 3661 5.029807 TCAACCACAGTACAATTCTCACA 57.970 39.130 0.00 0.00 0.00 3.58
3344 3670 6.714356 TCATCAATTTCATCAACCACAGTACA 59.286 34.615 0.00 0.00 0.00 2.90
3430 3756 1.192146 ACGCCCAGGTAAAGCAGAGA 61.192 55.000 0.00 0.00 0.00 3.10
3465 3791 5.305386 TCCATATCTACTTGGTCTGATGTGG 59.695 44.000 15.64 15.64 44.30 4.17
3472 3798 8.611051 AAAGTAACTCCATATCTACTTGGTCT 57.389 34.615 0.00 0.00 35.35 3.85
3487 3813 2.999355 CTCTGCAGCAGAAAGTAACTCC 59.001 50.000 25.35 0.00 40.18 3.85
3519 3845 7.489757 TGGTTTTTGCATCTTTTACAACTACAC 59.510 33.333 0.00 0.00 0.00 2.90
3543 3869 5.105187 TCACAGTAATCTGGATCTTCTGTGG 60.105 44.000 24.03 15.11 46.02 4.17
3545 3871 5.481824 TGTCACAGTAATCTGGATCTTCTGT 59.518 40.000 0.00 0.00 45.14 3.41
3652 3978 6.456315 CGACAATACCTTGCATCGAAACAATA 60.456 38.462 4.19 0.00 34.52 1.90
3677 4003 1.580815 GCAGCTGAGACTCCTATTGC 58.419 55.000 20.43 1.67 0.00 3.56
3728 4054 6.321945 GTCTTTTGTTTCCTTTTACCAGGGTA 59.678 38.462 0.00 0.00 34.24 3.69
3846 4172 1.072331 TCCTTTGAGTGAAGTGAGCCC 59.928 52.381 0.00 0.00 0.00 5.19
3997 4323 9.490379 CTCCCTAAAACTATAAATACGCAGATT 57.510 33.333 0.00 0.00 0.00 2.40
4031 4357 7.929785 CAGGCCAATATTAAGATCAAGCATTTT 59.070 33.333 5.01 0.00 0.00 1.82
4057 4385 1.935933 ACACCAGAACGAGTGTCAAC 58.064 50.000 0.00 0.00 43.62 3.18
4078 4406 6.806739 CAGAATCAATGCATATTACTGGCATG 59.193 38.462 0.00 0.00 46.77 4.06
4119 4447 1.493446 TGCCTCATCCATTCTCTGCAT 59.507 47.619 0.00 0.00 0.00 3.96
4190 4518 5.463724 CGAAGCAAGGTCACTAATATCCTTC 59.536 44.000 0.00 0.00 38.09 3.46
4436 4764 3.557595 GTCTAATCAATGACTTGCCTCCG 59.442 47.826 0.00 0.00 32.11 4.63
4491 4819 1.202806 CCAACCTTTGACCAGAGCAGA 60.203 52.381 0.00 0.00 0.00 4.26
4685 5083 4.639310 CAGAAATAGACCAGCTGCAGAAAT 59.361 41.667 20.43 0.00 0.00 2.17
4686 5084 4.005650 CAGAAATAGACCAGCTGCAGAAA 58.994 43.478 20.43 0.00 0.00 2.52
4687 5085 3.603532 CAGAAATAGACCAGCTGCAGAA 58.396 45.455 20.43 0.00 0.00 3.02
4688 5086 3.257469 CAGAAATAGACCAGCTGCAGA 57.743 47.619 20.43 0.00 0.00 4.26
4692 5090 1.669779 GCTGCAGAAATAGACCAGCTG 59.330 52.381 20.43 6.78 44.00 4.24
4693 5091 2.035530 GCTGCAGAAATAGACCAGCT 57.964 50.000 20.43 0.00 44.00 4.24
4694 5092 1.669779 CAGCTGCAGAAATAGACCAGC 59.330 52.381 20.43 0.00 46.82 4.85
4695 5093 2.286872 CCAGCTGCAGAAATAGACCAG 58.713 52.381 20.43 0.00 0.00 4.00
4696 5094 1.679944 GCCAGCTGCAGAAATAGACCA 60.680 52.381 20.43 0.00 40.77 4.02
4697 5095 1.020437 GCCAGCTGCAGAAATAGACC 58.980 55.000 20.43 0.00 40.77 3.85
4698 5096 1.669779 CAGCCAGCTGCAGAAATAGAC 59.330 52.381 20.43 0.00 44.83 2.59
4699 5097 1.556451 TCAGCCAGCTGCAGAAATAGA 59.444 47.619 20.43 4.45 44.83 1.98
4700 5098 2.034104 TCAGCCAGCTGCAGAAATAG 57.966 50.000 20.43 1.81 44.83 1.73
4701 5099 2.294979 CATCAGCCAGCTGCAGAAATA 58.705 47.619 20.43 0.00 44.83 1.40
4821 5219 3.216800 GGTTGAGAATGGCTGCATATCA 58.783 45.455 0.50 0.00 0.00 2.15
4925 5323 4.056050 GGCATAGTGGTACGGTTATTCTG 58.944 47.826 0.00 0.00 0.00 3.02
4945 5343 9.508567 GATTCACAAAATTAGAAGAATACTGGC 57.491 33.333 0.00 0.00 0.00 4.85
5101 5499 7.624549 TCTAGTCCAGCTGTTAAATCAGAAAT 58.375 34.615 13.81 0.00 37.61 2.17
5247 5647 1.681166 GCAGTACTCTCGGTCCCTGTA 60.681 57.143 0.00 0.00 32.77 2.74
5397 5797 6.405278 TGTACACAGAGTTCAGAAAGATCA 57.595 37.500 0.00 0.00 0.00 2.92
5445 5845 3.766591 TCTTCAGATTCTCCACCTCAGTC 59.233 47.826 0.00 0.00 0.00 3.51
5529 5929 4.083110 AGCTCAAACTTGATGTTCATTCCG 60.083 41.667 0.00 0.00 38.03 4.30
5658 6058 2.124529 TTTGACGCAGCACCACCA 60.125 55.556 0.00 0.00 0.00 4.17
5700 6100 1.657804 CCCCAAGGGTAGAGTGAAGT 58.342 55.000 4.11 0.00 38.25 3.01
5829 6229 1.593196 CGTCTTGAAGGGTGAAAGCA 58.407 50.000 0.00 0.00 34.77 3.91
6011 6411 1.271856 TCCCTGGCGTTCAGTAATCA 58.728 50.000 7.05 0.00 41.83 2.57
6129 6529 1.675310 CTTTGTGGCCGCCTCATCA 60.675 57.895 15.15 4.63 0.00 3.07
6309 6711 1.533299 GAACACACACACACACACACA 59.467 47.619 0.00 0.00 0.00 3.72
6326 6728 6.304882 GGCAAAACTAACTCGTCTTATGAAC 58.695 40.000 0.00 0.00 0.00 3.18
6415 6817 7.134815 GTGTGATCATATTGTGCTTATTCACC 58.865 38.462 0.00 0.00 36.17 4.02
6441 6843 6.717289 TCTATACAGTTTATGCCCAACACTT 58.283 36.000 0.00 0.00 0.00 3.16
6470 6872 3.365832 GCAGCACAAAACATATCATCCG 58.634 45.455 0.00 0.00 0.00 4.18
6528 6934 4.913924 CAGCAGATAAAAGAACACACAAGC 59.086 41.667 0.00 0.00 0.00 4.01
6546 6952 4.157289 ACTCATGTTAATTTCTGCCAGCAG 59.843 41.667 13.54 13.54 44.86 4.24
6558 6964 9.574516 AGGAGTCAAAAAGTAACTCATGTTAAT 57.425 29.630 4.35 0.00 40.94 1.40
6591 6997 4.396478 GGGAGTACTTTTCAGAATGCCTTC 59.604 45.833 0.00 0.00 34.76 3.46
6609 7015 1.344087 ACATTATGGGACGGAGGGAGT 60.344 52.381 0.00 0.00 0.00 3.85
6610 7016 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
6611 7017 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
6612 7018 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
6613 7019 3.386726 TGTCTTACATTATGGGACGGAGG 59.613 47.826 0.00 0.00 0.00 4.30
6614 7020 4.665833 TGTCTTACATTATGGGACGGAG 57.334 45.455 0.00 0.00 0.00 4.63
6615 7021 5.623956 AATGTCTTACATTATGGGACGGA 57.376 39.130 3.51 0.00 46.11 4.69
6642 7048 9.996554 CATCCCATAATGTAAGATGTTAGTGTA 57.003 33.333 0.00 0.00 31.71 2.90
6643 7049 7.939039 CCATCCCATAATGTAAGATGTTAGTGT 59.061 37.037 0.00 0.00 33.95 3.55
6644 7050 8.156820 TCCATCCCATAATGTAAGATGTTAGTG 58.843 37.037 0.00 0.00 33.95 2.74
6645 7051 8.275187 TCCATCCCATAATGTAAGATGTTAGT 57.725 34.615 0.00 0.00 33.95 2.24
6646 7052 8.378565 ACTCCATCCCATAATGTAAGATGTTAG 58.621 37.037 0.00 0.00 33.95 2.34
6647 7053 8.275187 ACTCCATCCCATAATGTAAGATGTTA 57.725 34.615 0.00 0.00 33.95 2.41
6648 7054 7.154191 ACTCCATCCCATAATGTAAGATGTT 57.846 36.000 0.00 0.00 33.95 2.71
6649 7055 6.770286 ACTCCATCCCATAATGTAAGATGT 57.230 37.500 0.00 0.00 33.95 3.06
6650 7056 7.180946 TCCTACTCCATCCCATAATGTAAGATG 59.819 40.741 0.00 0.00 35.24 2.90
6651 7057 7.256399 TCCTACTCCATCCCATAATGTAAGAT 58.744 38.462 0.00 0.00 0.00 2.40
6652 7058 6.630131 TCCTACTCCATCCCATAATGTAAGA 58.370 40.000 0.00 0.00 0.00 2.10
6653 7059 6.575254 GCTCCTACTCCATCCCATAATGTAAG 60.575 46.154 0.00 0.00 0.00 2.34
6654 7060 5.248477 GCTCCTACTCCATCCCATAATGTAA 59.752 44.000 0.00 0.00 0.00 2.41
6655 7061 4.777896 GCTCCTACTCCATCCCATAATGTA 59.222 45.833 0.00 0.00 0.00 2.29
6656 7062 3.584848 GCTCCTACTCCATCCCATAATGT 59.415 47.826 0.00 0.00 0.00 2.71
6657 7063 3.843027 AGCTCCTACTCCATCCCATAATG 59.157 47.826 0.00 0.00 0.00 1.90
6658 7064 4.100373 GAGCTCCTACTCCATCCCATAAT 58.900 47.826 0.87 0.00 0.00 1.28
6659 7065 3.142977 AGAGCTCCTACTCCATCCCATAA 59.857 47.826 10.93 0.00 37.39 1.90
6660 7066 2.724672 AGAGCTCCTACTCCATCCCATA 59.275 50.000 10.93 0.00 37.39 2.74
6661 7067 1.507300 AGAGCTCCTACTCCATCCCAT 59.493 52.381 10.93 0.00 37.39 4.00
6662 7068 0.937441 AGAGCTCCTACTCCATCCCA 59.063 55.000 10.93 0.00 37.39 4.37
6663 7069 2.982339 TAGAGCTCCTACTCCATCCC 57.018 55.000 10.93 0.00 37.39 3.85
6664 7070 4.219919 AGTTTAGAGCTCCTACTCCATCC 58.780 47.826 10.93 0.00 37.39 3.51
6665 7071 5.862678 AAGTTTAGAGCTCCTACTCCATC 57.137 43.478 10.93 0.00 37.39 3.51
6666 7072 5.599242 GGTAAGTTTAGAGCTCCTACTCCAT 59.401 44.000 10.93 0.00 37.39 3.41
6667 7073 4.954826 GGTAAGTTTAGAGCTCCTACTCCA 59.045 45.833 10.93 1.06 37.39 3.86
6668 7074 4.954826 TGGTAAGTTTAGAGCTCCTACTCC 59.045 45.833 10.93 9.98 37.39 3.85
6669 7075 5.887035 TCTGGTAAGTTTAGAGCTCCTACTC 59.113 44.000 10.93 0.97 36.91 2.59
6670 7076 5.828871 TCTGGTAAGTTTAGAGCTCCTACT 58.171 41.667 10.93 8.59 0.00 2.57
6671 7077 6.153170 ACTTCTGGTAAGTTTAGAGCTCCTAC 59.847 42.308 10.93 6.23 0.00 3.18
6672 7078 6.254522 ACTTCTGGTAAGTTTAGAGCTCCTA 58.745 40.000 10.93 0.00 0.00 2.94
6673 7079 5.088026 ACTTCTGGTAAGTTTAGAGCTCCT 58.912 41.667 10.93 0.00 0.00 3.69
6674 7080 5.047235 TGACTTCTGGTAAGTTTAGAGCTCC 60.047 44.000 10.93 0.00 0.00 4.70
6675 7081 6.026947 TGACTTCTGGTAAGTTTAGAGCTC 57.973 41.667 5.27 5.27 0.00 4.09
6820 7296 3.056607 GCAGATGCCAAGTTAAACCACAT 60.057 43.478 0.00 0.00 34.31 3.21
6828 7304 1.908344 TGCTTGCAGATGCCAAGTTA 58.092 45.000 1.72 0.00 41.18 2.24
6858 7334 4.009675 GTGCAGTTTCAGTGGATGGAATA 58.990 43.478 0.00 0.00 0.00 1.75
6904 7380 2.293677 ACTATCATGCGTAGGAAGGACG 59.706 50.000 0.00 0.00 43.19 4.79
6907 7383 2.802816 GCAACTATCATGCGTAGGAAGG 59.197 50.000 0.00 0.00 33.57 3.46
7001 7480 7.094118 ACGAGAAGCTCTTAAATCTACTGTCTT 60.094 37.037 0.00 0.00 0.00 3.01
7008 7488 7.069578 ACCCAATACGAGAAGCTCTTAAATCTA 59.930 37.037 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.