Multiple sequence alignment - TraesCS5A01G337500

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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 TraesCS5A01G337500 chr5A 100.000 3661 0 0 1 3661 545869553 545873213 0.000000e+00 6761.0
1 TraesCS5A01G337500 chr5A 90.574 1464 128 5 1117 2573 546146219 546147679 0.000000e+00 1930.0
2 TraesCS5A01G337500 chr5A 90.978 1441 116 7 1116 2547 545984616 545986051 0.000000e+00 1929.0
3 TraesCS5A01G337500 chr5A 82.407 108 13 6 2609 2711 473648451 473648557 5.040000e-14 89.8
4 TraesCS5A01G337500 chr5B 93.545 2107 89 26 658 2747 519450881 519452957 0.000000e+00 3094.0
5 TraesCS5A01G337500 chr5B 91.763 1469 112 4 1116 2576 519661043 519662510 0.000000e+00 2034.0
6 TraesCS5A01G337500 chr5B 90.574 1464 128 6 1116 2572 520036805 520038265 0.000000e+00 1930.0
7 TraesCS5A01G337500 chr5B 91.673 1321 110 0 1116 2436 520046519 520047839 0.000000e+00 1831.0
8 TraesCS5A01G337500 chr5B 92.473 372 16 7 3 373 519449911 519450271 4.190000e-144 521.0
9 TraesCS5A01G337500 chr5B 86.444 450 52 3 3216 3661 519453024 519453468 5.500000e-133 484.0
10 TraesCS5A01G337500 chr5B 91.139 79 5 2 566 643 519450819 519450896 5.000000e-19 106.0
11 TraesCS5A01G337500 chr5D 93.491 2074 89 16 667 2718 430163617 430165666 0.000000e+00 3040.0
12 TraesCS5A01G337500 chr5D 92.022 1454 107 6 1116 2561 430445541 430446993 0.000000e+00 2034.0
13 TraesCS5A01G337500 chr5D 91.597 1321 111 0 1116 2436 430511644 430512964 0.000000e+00 1825.0
14 TraesCS5A01G337500 chr5D 83.448 725 97 15 2952 3660 45057971 45057254 0.000000e+00 652.0
15 TraesCS5A01G337500 chr5D 88.222 450 44 3 3216 3661 430165757 430166201 2.500000e-146 529.0
16 TraesCS5A01G337500 chr5D 87.903 372 21 8 1 360 430161975 430162334 2.030000e-112 416.0
17 TraesCS5A01G337500 chr5D 88.479 217 21 2 3379 3595 2283813 2283601 3.630000e-65 259.0
18 TraesCS5A01G337500 chr5D 89.655 58 6 0 2649 2706 524330695 524330638 1.410000e-09 75.0
19 TraesCS5A01G337500 chr2A 82.735 724 101 12 2952 3661 1553504 1554217 1.120000e-174 623.0
20 TraesCS5A01G337500 chrUn 80.610 820 122 17 2802 3595 300168860 300168052 1.880000e-167 599.0
21 TraesCS5A01G337500 chr7A 89.474 152 16 0 3510 3661 540870018 540869867 3.730000e-45 193.0
22 TraesCS5A01G337500 chr7A 81.818 110 16 4 2607 2712 730877269 730877378 5.040000e-14 89.8
23 TraesCS5A01G337500 chr2D 82.828 99 15 2 2609 2706 27802127 27802030 1.810000e-13 87.9
24 TraesCS5A01G337500 chr6B 88.571 70 7 1 2638 2706 77149784 77149853 2.340000e-12 84.2
25 TraesCS5A01G337500 chr3D 91.228 57 5 0 2649 2705 56231533 56231589 1.090000e-10 78.7
26 TraesCS5A01G337500 chr3B 78.899 109 21 1 2606 2712 118789677 118789569 5.070000e-09 73.1


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 TraesCS5A01G337500 chr5A 545869553 545873213 3660 False 6761.000000 6761 100.00000 1 3661 1 chr5A.!!$F2 3660
1 TraesCS5A01G337500 chr5A 546146219 546147679 1460 False 1930.000000 1930 90.57400 1117 2573 1 chr5A.!!$F4 1456
2 TraesCS5A01G337500 chr5A 545984616 545986051 1435 False 1929.000000 1929 90.97800 1116 2547 1 chr5A.!!$F3 1431
3 TraesCS5A01G337500 chr5B 519661043 519662510 1467 False 2034.000000 2034 91.76300 1116 2576 1 chr5B.!!$F1 1460
4 TraesCS5A01G337500 chr5B 520036805 520038265 1460 False 1930.000000 1930 90.57400 1116 2572 1 chr5B.!!$F2 1456
5 TraesCS5A01G337500 chr5B 520046519 520047839 1320 False 1831.000000 1831 91.67300 1116 2436 1 chr5B.!!$F3 1320
6 TraesCS5A01G337500 chr5B 519449911 519453468 3557 False 1051.250000 3094 90.90025 3 3661 4 chr5B.!!$F4 3658
7 TraesCS5A01G337500 chr5D 430445541 430446993 1452 False 2034.000000 2034 92.02200 1116 2561 1 chr5D.!!$F1 1445
8 TraesCS5A01G337500 chr5D 430511644 430512964 1320 False 1825.000000 1825 91.59700 1116 2436 1 chr5D.!!$F2 1320
9 TraesCS5A01G337500 chr5D 430161975 430166201 4226 False 1328.333333 3040 89.87200 1 3661 3 chr5D.!!$F3 3660
10 TraesCS5A01G337500 chr5D 45057254 45057971 717 True 652.000000 652 83.44800 2952 3660 1 chr5D.!!$R2 708
11 TraesCS5A01G337500 chr2A 1553504 1554217 713 False 623.000000 623 82.73500 2952 3661 1 chr2A.!!$F1 709
12 TraesCS5A01G337500 chrUn 300168052 300168860 808 True 599.000000 599 80.61000 2802 3595 1 chrUn.!!$R1 793

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
369 382 0.164217 CGATCGACGACCTAGCTAGC 59.836 60.0 15.74 6.62 45.77 3.42 F
643 1765 0.250640 CAGTGCAGTTCAGGCTCCTT 60.251 55.0 0.00 0.00 0.00 3.36 F
877 2179 0.250727 CCCGCTCTTTCCAAGTTCCA 60.251 55.0 0.00 0.00 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1877 3181 2.038813 TGGGCGAGGATGGTCTCA 59.961 61.111 0.00 0.00 33.59 3.27 R
2444 3751 0.534412 ATGCCTCACTGTCTCTTCGG 59.466 55.000 0.00 0.00 0.00 4.30 R
2818 4145 0.320374 TGTAACCGACTCTGGCCAAG 59.680 55.000 7.01 10.13 0.00 3.61 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
52 53 2.157738 ACTTCCATGAAACTCAGCTGC 58.842 47.619 9.47 0.00 0.00 5.25
66 67 3.997681 CTCAGCTGCAGATAAGATCCATG 59.002 47.826 20.43 0.00 0.00 3.66
71 72 3.321039 TGCAGATAAGATCCATGGTCCT 58.679 45.455 12.58 7.23 0.00 3.85
72 73 3.326006 TGCAGATAAGATCCATGGTCCTC 59.674 47.826 12.58 7.57 0.00 3.71
73 74 3.582208 GCAGATAAGATCCATGGTCCTCT 59.418 47.826 12.58 9.79 0.00 3.69
77 83 7.555087 CAGATAAGATCCATGGTCCTCTAATC 58.445 42.308 12.58 5.42 0.00 1.75
120 126 5.460419 GTCCTGATATGATGTCTCAACGTTC 59.540 44.000 0.00 0.00 34.37 3.95
329 342 1.136147 GCATGCGTGAGGCTTTCTG 59.864 57.895 10.93 0.00 44.05 3.02
332 345 0.322975 ATGCGTGAGGCTTTCTGTCT 59.677 50.000 0.00 0.00 44.05 3.41
365 378 0.940126 TAACCGATCGACGACCTAGC 59.060 55.000 18.66 0.00 45.77 3.42
369 382 0.164217 CGATCGACGACCTAGCTAGC 59.836 60.000 15.74 6.62 45.77 3.42
398 453 0.802607 TTTTGTTGCGTTTCCGTGCC 60.803 50.000 0.00 0.00 36.15 5.01
406 461 0.871722 CGTTTCCGTGCCTGAATTGA 59.128 50.000 0.00 0.00 0.00 2.57
407 462 1.399727 CGTTTCCGTGCCTGAATTGAC 60.400 52.381 0.00 0.00 0.00 3.18
409 464 1.808411 TTCCGTGCCTGAATTGACTC 58.192 50.000 0.00 0.00 0.00 3.36
422 1194 7.548075 GCCTGAATTGACTCATCATTTTGAAAT 59.452 33.333 0.00 0.00 33.85 2.17
428 1200 5.858049 TGACTCATCATTTTGAAATTCACGC 59.142 36.000 0.00 0.00 0.00 5.34
447 1219 3.491581 GTACCAGACGGACACACAG 57.508 57.895 0.00 0.00 35.59 3.66
448 1220 0.956633 GTACCAGACGGACACACAGA 59.043 55.000 0.00 0.00 35.59 3.41
449 1221 0.956633 TACCAGACGGACACACAGAC 59.043 55.000 0.00 0.00 35.59 3.51
451 1223 0.318441 CCAGACGGACACACAGACAT 59.682 55.000 0.00 0.00 0.00 3.06
452 1224 1.422388 CAGACGGACACACAGACATG 58.578 55.000 0.00 0.00 0.00 3.21
453 1225 0.318441 AGACGGACACACAGACATGG 59.682 55.000 0.00 0.00 0.00 3.66
454 1226 0.317160 GACGGACACACAGACATGGA 59.683 55.000 0.00 0.00 0.00 3.41
457 1229 1.544246 CGGACACACAGACATGGAGTA 59.456 52.381 0.00 0.00 0.00 2.59
458 1230 2.671351 CGGACACACAGACATGGAGTAC 60.671 54.545 0.00 0.00 0.00 2.73
460 1232 3.006967 GGACACACAGACATGGAGTACTT 59.993 47.826 0.00 0.00 0.00 2.24
461 1233 3.990469 GACACACAGACATGGAGTACTTG 59.010 47.826 0.00 0.00 0.00 3.16
463 1235 3.742882 CACACAGACATGGAGTACTTGTG 59.257 47.826 16.39 16.39 37.56 3.33
464 1236 3.388024 ACACAGACATGGAGTACTTGTGT 59.612 43.478 17.44 17.44 37.56 3.72
466 1238 5.164233 CACAGACATGGAGTACTTGTGTAG 58.836 45.833 11.70 8.85 37.56 2.74
467 1239 4.220821 ACAGACATGGAGTACTTGTGTAGG 59.779 45.833 3.42 4.86 37.56 3.18
468 1240 4.220821 CAGACATGGAGTACTTGTGTAGGT 59.779 45.833 3.42 0.00 37.56 3.08
469 1241 4.838986 AGACATGGAGTACTTGTGTAGGTT 59.161 41.667 3.42 0.00 37.56 3.50
470 1242 4.894784 ACATGGAGTACTTGTGTAGGTTG 58.105 43.478 0.00 0.00 36.25 3.77
471 1243 3.396260 TGGAGTACTTGTGTAGGTTGC 57.604 47.619 0.00 0.00 0.00 4.17
473 1245 3.134985 TGGAGTACTTGTGTAGGTTGCAA 59.865 43.478 0.00 0.00 0.00 4.08
474 1246 4.131596 GGAGTACTTGTGTAGGTTGCAAA 58.868 43.478 0.00 0.00 0.00 3.68
476 1248 5.066764 GGAGTACTTGTGTAGGTTGCAAAAA 59.933 40.000 0.00 0.00 0.00 1.94
509 1299 4.635765 CGTATTATATTACGGACCGAGGGA 59.364 45.833 23.38 3.16 40.90 4.20
511 1301 6.183360 CGTATTATATTACGGACCGAGGGAAT 60.183 42.308 23.38 15.44 40.90 3.01
512 1302 7.012327 CGTATTATATTACGGACCGAGGGAATA 59.988 40.741 23.38 16.95 40.90 1.75
514 1304 7.722949 TTATATTACGGACCGAGGGAATAAT 57.277 36.000 23.38 14.69 0.00 1.28
515 1305 3.738830 TTACGGACCGAGGGAATAATG 57.261 47.619 23.38 0.00 0.00 1.90
519 1309 4.410099 ACGGACCGAGGGAATAATGTATA 58.590 43.478 23.38 0.00 0.00 1.47
521 1311 5.482878 ACGGACCGAGGGAATAATGTATATT 59.517 40.000 23.38 0.00 0.00 1.28
522 1312 6.664816 ACGGACCGAGGGAATAATGTATATTA 59.335 38.462 23.38 0.00 33.54 0.98
523 1313 7.343833 ACGGACCGAGGGAATAATGTATATTAT 59.656 37.037 23.38 0.00 40.37 1.28
600 1720 2.038952 AGCTGAATGCACTGGAGTACAA 59.961 45.455 0.00 0.00 45.94 2.41
605 1725 3.610040 ATGCACTGGAGTACAATTCGA 57.390 42.857 0.00 0.00 0.00 3.71
609 1729 3.659786 CACTGGAGTACAATTCGAACCA 58.340 45.455 0.00 0.00 0.00 3.67
610 1730 4.253685 CACTGGAGTACAATTCGAACCAT 58.746 43.478 0.00 0.00 0.00 3.55
611 1731 4.093408 CACTGGAGTACAATTCGAACCATG 59.907 45.833 0.00 2.75 0.00 3.66
618 1740 4.685169 ACAATTCGAACCATGTGACATC 57.315 40.909 0.00 0.00 0.00 3.06
624 1746 2.012673 GAACCATGTGACATCAGCTCC 58.987 52.381 0.00 0.00 0.00 4.70
634 1756 1.085091 CATCAGCTCCAGTGCAGTTC 58.915 55.000 0.00 0.00 34.99 3.01
638 1760 2.331132 GCTCCAGTGCAGTTCAGGC 61.331 63.158 0.00 0.00 0.00 4.85
640 1762 0.673022 CTCCAGTGCAGTTCAGGCTC 60.673 60.000 0.00 0.00 0.00 4.70
643 1765 0.250640 CAGTGCAGTTCAGGCTCCTT 60.251 55.000 0.00 0.00 0.00 3.36
645 1767 1.133668 AGTGCAGTTCAGGCTCCTTTT 60.134 47.619 0.00 0.00 0.00 2.27
648 1770 3.507622 GTGCAGTTCAGGCTCCTTTTATT 59.492 43.478 0.00 0.00 0.00 1.40
649 1771 4.021981 GTGCAGTTCAGGCTCCTTTTATTT 60.022 41.667 0.00 0.00 0.00 1.40
650 1772 4.022068 TGCAGTTCAGGCTCCTTTTATTTG 60.022 41.667 0.00 0.00 0.00 2.32
651 1773 4.218417 GCAGTTCAGGCTCCTTTTATTTGA 59.782 41.667 0.00 0.00 0.00 2.69
652 1774 5.620879 GCAGTTCAGGCTCCTTTTATTTGAG 60.621 44.000 0.00 0.00 0.00 3.02
653 1775 5.012893 AGTTCAGGCTCCTTTTATTTGAGG 58.987 41.667 0.00 0.00 0.00 3.86
654 1776 3.968265 TCAGGCTCCTTTTATTTGAGGG 58.032 45.455 0.00 0.00 33.73 4.30
655 1777 3.026694 CAGGCTCCTTTTATTTGAGGGG 58.973 50.000 0.00 0.00 36.56 4.79
656 1778 2.654896 AGGCTCCTTTTATTTGAGGGGT 59.345 45.455 0.00 0.00 35.86 4.95
677 1952 4.564821 GGTTGCAGTTCAGGTTCCTATACA 60.565 45.833 0.00 0.00 0.00 2.29
678 1953 4.202245 TGCAGTTCAGGTTCCTATACAC 57.798 45.455 0.00 0.00 0.00 2.90
679 1954 3.055385 TGCAGTTCAGGTTCCTATACACC 60.055 47.826 0.00 0.00 0.00 4.16
680 1955 3.782046 CAGTTCAGGTTCCTATACACCG 58.218 50.000 0.00 0.00 38.21 4.94
682 1957 1.784358 TCAGGTTCCTATACACCGGG 58.216 55.000 6.32 0.00 38.21 5.73
683 1958 1.288633 TCAGGTTCCTATACACCGGGA 59.711 52.381 6.32 0.00 38.21 5.14
684 1959 2.112998 CAGGTTCCTATACACCGGGAA 58.887 52.381 6.32 0.00 38.21 3.97
685 1960 2.704065 CAGGTTCCTATACACCGGGAAT 59.296 50.000 6.32 0.00 40.58 3.01
686 1961 3.135895 CAGGTTCCTATACACCGGGAATT 59.864 47.826 6.32 0.00 40.58 2.17
762 2040 1.129326 CGACCGTGTCAAAGTCTCAC 58.871 55.000 5.15 0.00 32.09 3.51
763 2041 1.535226 CGACCGTGTCAAAGTCTCACA 60.535 52.381 5.15 0.00 32.09 3.58
764 2042 2.546778 GACCGTGTCAAAGTCTCACAA 58.453 47.619 0.00 0.00 32.09 3.33
766 2044 2.093658 ACCGTGTCAAAGTCTCACAACT 60.094 45.455 0.00 0.00 33.04 3.16
768 2046 2.216488 CGTGTCAAAGTCTCACAACTCG 59.784 50.000 0.00 0.00 33.04 4.18
769 2047 2.033662 GTGTCAAAGTCTCACAACTCGC 60.034 50.000 0.00 0.00 33.04 5.03
771 2049 1.138069 TCAAAGTCTCACAACTCGCCA 59.862 47.619 0.00 0.00 0.00 5.69
789 2069 4.446385 TCGCCAATATGTGCTCGTAATTAC 59.554 41.667 5.47 5.47 0.00 1.89
793 2073 6.459024 GCCAATATGTGCTCGTAATTACCAAA 60.459 38.462 10.01 0.00 0.00 3.28
795 2075 7.201696 CCAATATGTGCTCGTAATTACCAAAGT 60.202 37.037 10.01 0.00 0.00 2.66
814 2094 9.975218 ACCAAAGTTAGATTATTTGACCATACT 57.025 29.630 0.00 0.00 36.28 2.12
828 2108 6.554334 TGACCATACTAACAAAAGCAGTTC 57.446 37.500 0.00 0.00 0.00 3.01
837 2125 7.147976 ACTAACAAAAGCAGTTCCATGATTTC 58.852 34.615 0.00 0.00 37.79 2.17
840 2128 6.917533 ACAAAAGCAGTTCCATGATTTCTAG 58.082 36.000 0.00 0.00 37.79 2.43
870 2172 1.378762 CTTTCCCCCGCTCTTTCCA 59.621 57.895 0.00 0.00 0.00 3.53
871 2173 0.251165 CTTTCCCCCGCTCTTTCCAA 60.251 55.000 0.00 0.00 0.00 3.53
872 2174 0.251165 TTTCCCCCGCTCTTTCCAAG 60.251 55.000 0.00 0.00 0.00 3.61
873 2175 1.423794 TTCCCCCGCTCTTTCCAAGT 61.424 55.000 0.00 0.00 0.00 3.16
874 2176 1.074951 CCCCCGCTCTTTCCAAGTT 59.925 57.895 0.00 0.00 0.00 2.66
875 2177 0.960861 CCCCCGCTCTTTCCAAGTTC 60.961 60.000 0.00 0.00 0.00 3.01
876 2178 0.960861 CCCCGCTCTTTCCAAGTTCC 60.961 60.000 0.00 0.00 0.00 3.62
877 2179 0.250727 CCCGCTCTTTCCAAGTTCCA 60.251 55.000 0.00 0.00 0.00 3.53
878 2180 1.604604 CCGCTCTTTCCAAGTTCCAA 58.395 50.000 0.00 0.00 0.00 3.53
879 2181 1.266989 CCGCTCTTTCCAAGTTCCAAC 59.733 52.381 0.00 0.00 0.00 3.77
880 2182 1.069906 CGCTCTTTCCAAGTTCCAACG 60.070 52.381 0.00 0.00 0.00 4.10
881 2183 1.266989 GCTCTTTCCAAGTTCCAACGG 59.733 52.381 0.00 0.00 0.00 4.44
882 2184 1.266989 CTCTTTCCAAGTTCCAACGGC 59.733 52.381 0.00 0.00 0.00 5.68
883 2185 0.313987 CTTTCCAAGTTCCAACGGCC 59.686 55.000 0.00 0.00 0.00 6.13
905 2207 4.330250 CCTGCATGCTGCCTATAAATAGT 58.670 43.478 20.33 0.00 44.23 2.12
907 2209 5.335426 CCTGCATGCTGCCTATAAATAGTTG 60.335 44.000 20.33 0.00 44.23 3.16
908 2210 4.022935 TGCATGCTGCCTATAAATAGTTGC 60.023 41.667 20.33 0.00 44.23 4.17
972 2274 2.244651 GCACGCAACAAGGACTCGT 61.245 57.895 0.00 0.00 0.00 4.18
1005 2307 0.669318 TCGAGCTAACCTTGGCAACG 60.669 55.000 0.00 0.00 37.10 4.10
1033 2335 6.764308 ACAATCTCTCTCTTTCTCTCTCTG 57.236 41.667 0.00 0.00 0.00 3.35
1036 2338 4.503910 TCTCTCTCTTTCTCTCTCTGTCG 58.496 47.826 0.00 0.00 0.00 4.35
1037 2339 3.605634 TCTCTCTTTCTCTCTCTGTCGG 58.394 50.000 0.00 0.00 0.00 4.79
1038 2340 3.008594 TCTCTCTTTCTCTCTCTGTCGGT 59.991 47.826 0.00 0.00 0.00 4.69
1129 2433 3.617263 CGACAGTTAGCAATGGAGGTTAC 59.383 47.826 0.00 0.00 0.00 2.50
2333 3637 1.959226 GCTTTTCCTCGTGCCGTCA 60.959 57.895 0.00 0.00 0.00 4.35
2438 3745 2.305052 GGAGTAGGTGGCCTAACTGTTT 59.695 50.000 3.32 0.00 37.91 2.83
2444 3751 3.509967 AGGTGGCCTAACTGTTTATTTGC 59.490 43.478 3.32 0.00 28.47 3.68
2451 3758 5.673818 GCCTAACTGTTTATTTGCCGAAGAG 60.674 44.000 0.00 0.00 0.00 2.85
2494 3815 0.329261 TTCATTGAGAGGGTGGCAGG 59.671 55.000 0.00 0.00 0.00 4.85
2598 3919 8.025445 AGTACGTAACACGAGTTTTCAGATAAT 58.975 33.333 2.93 0.00 46.05 1.28
2599 3920 7.647907 ACGTAACACGAGTTTTCAGATAATT 57.352 32.000 2.93 0.00 46.05 1.40
2601 3922 8.553696 ACGTAACACGAGTTTTCAGATAATTTT 58.446 29.630 2.93 0.00 46.05 1.82
2602 3923 9.377383 CGTAACACGAGTTTTCAGATAATTTTT 57.623 29.630 2.93 0.00 46.05 1.94
2625 3947 0.605589 ACTAGCAAAAGGGTCCGTGC 60.606 55.000 0.00 5.59 37.26 5.34
2626 3948 1.302993 TAGCAAAAGGGTCCGTGCC 60.303 57.895 8.87 0.00 37.73 5.01
2633 3955 0.696501 AAGGGTCCGTGCCTTGTAAT 59.303 50.000 0.00 0.00 0.00 1.89
2634 3956 1.575419 AGGGTCCGTGCCTTGTAATA 58.425 50.000 0.00 0.00 0.00 0.98
2635 3957 2.124411 AGGGTCCGTGCCTTGTAATAT 58.876 47.619 0.00 0.00 0.00 1.28
2643 3965 7.012989 GGTCCGTGCCTTGTAATATAAGAAAAT 59.987 37.037 0.00 0.00 0.00 1.82
2697 4024 2.893489 TGCTGCATCACCGAGATATACT 59.107 45.455 0.00 0.00 34.43 2.12
2702 4029 6.460814 GCTGCATCACCGAGATATACTATCAT 60.461 42.308 0.00 0.00 34.43 2.45
2773 4100 9.956720 ACATACATTTCACAAAGAAGAAAGAAG 57.043 29.630 0.00 0.00 37.19 2.85
2777 4104 8.960591 ACATTTCACAAAGAAGAAAGAAGAAGA 58.039 29.630 0.00 0.00 37.19 2.87
2778 4105 9.793252 CATTTCACAAAGAAGAAAGAAGAAGAA 57.207 29.630 0.00 0.00 37.19 2.52
2780 4107 8.792830 TTCACAAAGAAGAAAGAAGAAGAAGA 57.207 30.769 0.00 0.00 0.00 2.87
2781 4108 8.792830 TCACAAAGAAGAAAGAAGAAGAAGAA 57.207 30.769 0.00 0.00 0.00 2.52
2782 4109 8.887717 TCACAAAGAAGAAAGAAGAAGAAGAAG 58.112 33.333 0.00 0.00 0.00 2.85
2783 4110 8.887717 CACAAAGAAGAAAGAAGAAGAAGAAGA 58.112 33.333 0.00 0.00 0.00 2.87
2784 4111 9.454859 ACAAAGAAGAAAGAAGAAGAAGAAGAA 57.545 29.630 0.00 0.00 0.00 2.52
2785 4112 9.934190 CAAAGAAGAAAGAAGAAGAAGAAGAAG 57.066 33.333 0.00 0.00 0.00 2.85
2786 4113 9.898152 AAAGAAGAAAGAAGAAGAAGAAGAAGA 57.102 29.630 0.00 0.00 0.00 2.87
2787 4114 9.898152 AAGAAGAAAGAAGAAGAAGAAGAAGAA 57.102 29.630 0.00 0.00 0.00 2.52
2788 4115 9.546428 AGAAGAAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
2789 4116 9.541143 GAAGAAAGAAGAAGAAGAAGAAGAAGA 57.459 33.333 0.00 0.00 0.00 2.87
2790 4117 9.898152 AAGAAAGAAGAAGAAGAAGAAGAAGAA 57.102 29.630 0.00 0.00 0.00 2.52
2791 4118 9.546428 AGAAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
2792 4119 9.541143 GAAAGAAGAAGAAGAAGAAGAAGAAGA 57.459 33.333 0.00 0.00 0.00 2.87
2793 4120 9.898152 AAAGAAGAAGAAGAAGAAGAAGAAGAA 57.102 29.630 0.00 0.00 0.00 2.52
2794 4121 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
2795 4122 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
2796 4123 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
2797 4124 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
2798 4125 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
2799 4126 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
2800 4127 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
2825 4152 8.890472 AGAAGATAATTGTATATACCTTGGCCA 58.110 33.333 0.00 0.00 0.00 5.36
2826 4153 9.167311 GAAGATAATTGTATATACCTTGGCCAG 57.833 37.037 5.11 0.00 0.00 4.85
2831 4158 3.572682 TGTATATACCTTGGCCAGAGTCG 59.427 47.826 12.62 0.00 0.00 4.18
2848 4175 3.596214 AGTCGGTTACAAACATAGCCTG 58.404 45.455 0.00 0.00 0.00 4.85
2896 4223 0.109723 GCCTACAGGTGTCCCAACAA 59.890 55.000 0.00 0.00 37.08 2.83
2901 4228 3.817709 ACAGGTGTCCCAACAAAAATG 57.182 42.857 0.00 0.00 37.08 2.32
2912 4239 5.532779 TCCCAACAAAAATGCAAAAATACCC 59.467 36.000 0.00 0.00 0.00 3.69
2927 4254 7.255104 GCAAAAATACCCCCAAAGAAAAAGAAG 60.255 37.037 0.00 0.00 0.00 2.85
2936 4263 7.179160 CCCCCAAAGAAAAAGAAGATACAATCT 59.821 37.037 0.00 0.00 42.61 2.40
2938 4265 8.031277 CCCAAAGAAAAAGAAGATACAATCTGG 58.969 37.037 0.00 0.00 40.13 3.86
2939 4266 8.579863 CCAAAGAAAAAGAAGATACAATCTGGT 58.420 33.333 0.00 0.00 40.13 4.00
2940 4267 9.971922 CAAAGAAAAAGAAGATACAATCTGGTT 57.028 29.630 0.00 0.00 40.13 3.67
2944 4271 5.677319 AAGAAGATACAATCTGGTTCCGA 57.323 39.130 0.00 0.00 40.13 4.55
2945 4272 5.677319 AGAAGATACAATCTGGTTCCGAA 57.323 39.130 0.00 0.00 40.13 4.30
2969 4296 2.866065 GCTTAACGCAAACCAAGCCAAT 60.866 45.455 0.00 0.00 37.92 3.16
2974 4301 1.668628 CGCAAACCAAGCCAATACCAC 60.669 52.381 0.00 0.00 0.00 4.16
2984 4312 2.041081 AGCCAATACCACTTGCTAACCA 59.959 45.455 0.00 0.00 0.00 3.67
2987 4315 4.269183 CCAATACCACTTGCTAACCATCA 58.731 43.478 0.00 0.00 0.00 3.07
2992 4320 1.019278 ACTTGCTAACCATCACCGCG 61.019 55.000 0.00 0.00 0.00 6.46
3045 4375 2.778299 CCACCAAATCTTGAACCGAGA 58.222 47.619 0.00 0.00 0.00 4.04
3065 4395 0.739462 GCACACCATCGTCCGAATCA 60.739 55.000 0.00 0.00 0.00 2.57
3067 4397 0.895530 ACACCATCGTCCGAATCAGT 59.104 50.000 0.00 0.00 0.00 3.41
3093 4423 2.953648 TGAGTCGAATATGAAGCCCGTA 59.046 45.455 0.00 0.00 0.00 4.02
3107 4437 2.572290 GCCCGTAGCAAATGAATAGGT 58.428 47.619 0.00 0.00 42.97 3.08
3111 4441 4.035208 CCCGTAGCAAATGAATAGGTGTTC 59.965 45.833 0.00 0.00 0.00 3.18
3112 4442 4.876107 CCGTAGCAAATGAATAGGTGTTCT 59.124 41.667 0.00 0.00 0.00 3.01
3115 4445 3.445096 AGCAAATGAATAGGTGTTCTGGC 59.555 43.478 0.00 0.00 0.00 4.85
3116 4446 3.193267 GCAAATGAATAGGTGTTCTGGCA 59.807 43.478 0.00 0.00 0.00 4.92
3117 4447 4.142093 GCAAATGAATAGGTGTTCTGGCAT 60.142 41.667 0.00 0.00 0.00 4.40
3118 4448 5.345702 CAAATGAATAGGTGTTCTGGCATG 58.654 41.667 0.00 0.00 0.00 4.06
3119 4449 3.719268 TGAATAGGTGTTCTGGCATGT 57.281 42.857 0.00 0.00 0.00 3.21
3124 4465 1.133823 AGGTGTTCTGGCATGTTGACA 60.134 47.619 0.00 0.00 32.24 3.58
3149 4490 0.396435 TCAACACCGTGCATCTCCTT 59.604 50.000 0.00 0.00 0.00 3.36
3163 4504 1.845627 CTCCTTGGCTCCAGCTCCAA 61.846 60.000 4.67 4.67 39.81 3.53
3166 4507 1.228245 TTGGCTCCAGCTCCAACAC 60.228 57.895 0.56 0.00 37.43 3.32
3167 4508 2.360475 GGCTCCAGCTCCAACACC 60.360 66.667 0.00 0.00 41.70 4.16
3172 4513 2.046892 CAGCTCCAACACCCCTCG 60.047 66.667 0.00 0.00 0.00 4.63
3173 4514 3.322466 AGCTCCAACACCCCTCGG 61.322 66.667 0.00 0.00 0.00 4.63
3176 4517 1.913762 CTCCAACACCCCTCGGTCT 60.914 63.158 0.00 0.00 42.04 3.85
3179 4520 1.553690 CCAACACCCCTCGGTCTGAT 61.554 60.000 0.00 0.00 42.04 2.90
3180 4521 0.391661 CAACACCCCTCGGTCTGATG 60.392 60.000 0.00 0.00 42.04 3.07
3183 4524 0.613260 CACCCCTCGGTCTGATGAAA 59.387 55.000 0.00 0.00 42.04 2.69
3208 4549 6.881017 TCGAAGAAAAATCATCATATCTGCG 58.119 36.000 0.00 0.00 37.31 5.18
3258 4599 3.327404 AAATCTCCCACCGGCCGT 61.327 61.111 26.12 9.63 0.00 5.68
3309 4655 3.822594 TTTACGGACAATGTGCATGTC 57.177 42.857 9.93 9.93 45.08 3.06
3345 4695 5.920273 ACTTCAAACATAAAAGCATGGAACG 59.080 36.000 0.00 0.00 0.00 3.95
3354 4704 1.377202 GCATGGAACGGCTTCTCCA 60.377 57.895 0.00 4.09 45.65 3.86
3377 4739 3.118482 TGCATTGGATTTGTGTTGGTGTT 60.118 39.130 0.00 0.00 0.00 3.32
3409 4771 8.974060 AGACTAACAAAAGAAAAGGTGACATA 57.026 30.769 0.00 0.00 0.00 2.29
3475 4837 9.758651 AAATGACCTTTTGAGTTAATTAACCAC 57.241 29.630 21.92 16.95 36.88 4.16
3486 4848 9.226606 TGAGTTAATTAACCACATGTAAAGAGG 57.773 33.333 21.92 0.00 36.88 3.69
3544 4906 4.636206 GTGCCTAAAATCTTGAGGATCGTT 59.364 41.667 0.00 0.00 38.61 3.85
3637 4999 5.788450 TGCCCATTCGTGATTACAAAATTT 58.212 33.333 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 5.239306 CAGAATTCCAGTCACTACTTTGCAA 59.761 40.000 0.65 0.00 31.97 4.08
47 48 2.709934 ACCATGGATCTTATCTGCAGCT 59.290 45.455 21.47 0.82 0.00 4.24
52 53 6.924913 TTAGAGGACCATGGATCTTATCTG 57.075 41.667 21.47 0.00 0.00 2.90
66 67 1.396653 TCGAACGGGATTAGAGGACC 58.603 55.000 0.00 0.00 0.00 4.46
71 72 5.981315 GTGTTCAATATCGAACGGGATTAGA 59.019 40.000 2.22 0.00 46.77 2.10
72 73 5.107989 CGTGTTCAATATCGAACGGGATTAG 60.108 44.000 2.22 0.00 46.77 1.73
73 74 4.741185 CGTGTTCAATATCGAACGGGATTA 59.259 41.667 2.22 0.00 46.77 1.75
77 83 2.264813 ACGTGTTCAATATCGAACGGG 58.735 47.619 2.22 0.00 46.77 5.28
120 126 0.390603 TACGAGATGCCAACAACCCG 60.391 55.000 0.00 0.00 0.00 5.28
228 234 9.035607 CGACGACCTACTTAATCTACTTAACTA 57.964 37.037 0.00 0.00 0.00 2.24
229 235 7.766278 TCGACGACCTACTTAATCTACTTAACT 59.234 37.037 0.00 0.00 0.00 2.24
230 236 7.848539 GTCGACGACCTACTTAATCTACTTAAC 59.151 40.741 17.25 0.00 0.00 2.01
231 237 7.766278 AGTCGACGACCTACTTAATCTACTTAA 59.234 37.037 23.76 0.00 32.18 1.85
248 254 4.577687 TTGCATTTGATTAGTCGACGAC 57.422 40.909 20.25 20.25 0.00 4.34
332 345 9.984137 CGTCGATCGGTTAATTACGTACACGTA 62.984 44.444 16.41 10.39 43.45 3.57
365 378 4.210120 CGCAACAAAATCCTAGCTAGCTAG 59.790 45.833 35.39 35.39 44.07 3.42
369 382 4.946784 AACGCAACAAAATCCTAGCTAG 57.053 40.909 14.20 14.20 0.00 3.42
406 461 4.853196 CGCGTGAATTTCAAAATGATGAGT 59.147 37.500 0.00 0.00 0.00 3.41
407 462 4.853196 ACGCGTGAATTTCAAAATGATGAG 59.147 37.500 12.93 0.00 0.00 2.90
409 464 5.003402 GGTACGCGTGAATTTCAAAATGATG 59.997 40.000 24.59 0.00 0.00 3.07
438 1210 2.563179 AGTACTCCATGTCTGTGTGTCC 59.437 50.000 0.00 0.00 0.00 4.02
443 1215 3.995199 ACACAAGTACTCCATGTCTGTG 58.005 45.455 16.39 16.39 0.00 3.66
447 1219 4.803098 ACCTACACAAGTACTCCATGTC 57.197 45.455 9.25 0.00 0.00 3.06
448 1220 4.802918 GCAACCTACACAAGTACTCCATGT 60.803 45.833 0.00 3.88 0.00 3.21
449 1221 3.684788 GCAACCTACACAAGTACTCCATG 59.315 47.826 0.00 0.00 0.00 3.66
451 1223 2.701423 TGCAACCTACACAAGTACTCCA 59.299 45.455 0.00 0.00 0.00 3.86
452 1224 3.396260 TGCAACCTACACAAGTACTCC 57.604 47.619 0.00 0.00 0.00 3.85
453 1225 5.744666 TTTTGCAACCTACACAAGTACTC 57.255 39.130 0.00 0.00 0.00 2.59
484 1274 5.106157 CCCTCGGTCCGTAATATAATACGTT 60.106 44.000 16.89 0.00 45.43 3.99
485 1275 4.396166 CCCTCGGTCCGTAATATAATACGT 59.604 45.833 16.89 0.00 45.43 3.57
489 1279 7.722949 TTATTCCCTCGGTCCGTAATATAAT 57.277 36.000 11.88 7.66 0.00 1.28
497 1287 1.492764 ACATTATTCCCTCGGTCCGT 58.507 50.000 11.88 0.00 0.00 4.69
498 1288 3.955650 ATACATTATTCCCTCGGTCCG 57.044 47.619 4.39 4.39 0.00 4.79
559 1349 6.822676 TCAGCTAGAGTTAGTGAGTTAGTACC 59.177 42.308 0.00 0.00 0.00 3.34
569 1685 4.565962 CAGTGCATTCAGCTAGAGTTAGTG 59.434 45.833 0.00 0.00 45.94 2.74
600 1720 2.679837 GCTGATGTCACATGGTTCGAAT 59.320 45.455 0.00 0.00 0.00 3.34
605 1725 1.352017 TGGAGCTGATGTCACATGGTT 59.648 47.619 0.00 0.00 0.00 3.67
609 1729 1.678123 GCACTGGAGCTGATGTCACAT 60.678 52.381 0.00 0.00 0.00 3.21
610 1730 0.321034 GCACTGGAGCTGATGTCACA 60.321 55.000 0.00 0.00 0.00 3.58
611 1731 0.321034 TGCACTGGAGCTGATGTCAC 60.321 55.000 0.00 0.00 34.99 3.67
618 1740 0.954449 CCTGAACTGCACTGGAGCTG 60.954 60.000 0.00 0.00 39.11 4.24
624 1746 0.250640 AAGGAGCCTGAACTGCACTG 60.251 55.000 0.00 0.00 0.00 3.66
634 1756 3.026694 CCCCTCAAATAAAAGGAGCCTG 58.973 50.000 0.00 0.00 34.35 4.85
638 1760 3.831911 TGCAACCCCTCAAATAAAAGGAG 59.168 43.478 0.00 0.00 34.35 3.69
640 1762 3.578282 ACTGCAACCCCTCAAATAAAAGG 59.422 43.478 0.00 0.00 0.00 3.11
643 1765 4.219115 TGAACTGCAACCCCTCAAATAAA 58.781 39.130 0.00 0.00 0.00 1.40
645 1767 3.420893 CTGAACTGCAACCCCTCAAATA 58.579 45.455 0.00 0.00 0.00 1.40
648 1770 0.178992 CCTGAACTGCAACCCCTCAA 60.179 55.000 0.00 0.00 0.00 3.02
649 1771 1.352622 ACCTGAACTGCAACCCCTCA 61.353 55.000 0.00 0.00 0.00 3.86
650 1772 0.178990 AACCTGAACTGCAACCCCTC 60.179 55.000 0.00 0.00 0.00 4.30
651 1773 0.178990 GAACCTGAACTGCAACCCCT 60.179 55.000 0.00 0.00 0.00 4.79
652 1774 1.179174 GGAACCTGAACTGCAACCCC 61.179 60.000 0.00 0.00 0.00 4.95
653 1775 0.178990 AGGAACCTGAACTGCAACCC 60.179 55.000 0.00 0.00 0.00 4.11
654 1776 2.561478 TAGGAACCTGAACTGCAACC 57.439 50.000 3.36 0.00 0.00 3.77
655 1777 4.392138 GTGTATAGGAACCTGAACTGCAAC 59.608 45.833 3.36 0.00 0.00 4.17
656 1778 4.564821 GGTGTATAGGAACCTGAACTGCAA 60.565 45.833 3.36 0.00 33.40 4.08
682 1957 6.017026 GGCTGCTACCTACAGGAATTTAATTC 60.017 42.308 9.03 9.03 38.94 2.17
683 1958 5.828328 GGCTGCTACCTACAGGAATTTAATT 59.172 40.000 1.29 0.00 38.94 1.40
684 1959 5.377478 GGCTGCTACCTACAGGAATTTAAT 58.623 41.667 1.29 0.00 38.94 1.40
685 1960 4.682320 CGGCTGCTACCTACAGGAATTTAA 60.682 45.833 1.29 0.00 38.94 1.52
686 1961 3.181469 CGGCTGCTACCTACAGGAATTTA 60.181 47.826 1.29 0.00 38.94 1.40
745 2020 2.093658 AGTTGTGAGACTTTGACACGGT 60.094 45.455 0.00 0.00 37.35 4.83
747 2022 2.216488 CGAGTTGTGAGACTTTGACACG 59.784 50.000 0.00 0.00 37.35 4.49
749 2024 2.201732 GCGAGTTGTGAGACTTTGACA 58.798 47.619 0.00 0.00 0.00 3.58
762 2040 1.004610 CGAGCACATATTGGCGAGTTG 60.005 52.381 0.00 0.00 34.54 3.16
763 2041 1.290203 CGAGCACATATTGGCGAGTT 58.710 50.000 0.00 0.00 34.54 3.01
764 2042 0.175760 ACGAGCACATATTGGCGAGT 59.824 50.000 0.00 0.00 34.54 4.18
766 2044 2.588027 TTACGAGCACATATTGGCGA 57.412 45.000 0.00 0.00 34.54 5.54
768 2046 4.513692 TGGTAATTACGAGCACATATTGGC 59.486 41.667 9.46 0.00 0.00 4.52
769 2047 6.612247 TTGGTAATTACGAGCACATATTGG 57.388 37.500 9.46 0.00 0.00 3.16
771 2049 7.859325 ACTTTGGTAATTACGAGCACATATT 57.141 32.000 9.46 0.00 0.00 1.28
812 2092 6.655078 AATCATGGAACTGCTTTTGTTAGT 57.345 33.333 0.00 0.00 0.00 2.24
813 2093 7.373493 AGAAATCATGGAACTGCTTTTGTTAG 58.627 34.615 0.00 0.00 0.00 2.34
814 2094 7.288810 AGAAATCATGGAACTGCTTTTGTTA 57.711 32.000 0.00 0.00 0.00 2.41
823 2103 5.814705 GGTGAGACTAGAAATCATGGAACTG 59.185 44.000 0.00 0.00 0.00 3.16
828 2108 4.878397 GGTTGGTGAGACTAGAAATCATGG 59.122 45.833 0.00 0.00 0.00 3.66
837 2125 2.027100 GGGAAAGGGTTGGTGAGACTAG 60.027 54.545 0.00 0.00 0.00 2.57
840 2128 0.251209 GGGGAAAGGGTTGGTGAGAC 60.251 60.000 0.00 0.00 0.00 3.36
870 2172 2.597510 GCAGGGCCGTTGGAACTT 60.598 61.111 0.00 0.00 0.00 2.66
871 2173 3.210012 ATGCAGGGCCGTTGGAACT 62.210 57.895 0.00 0.00 0.00 3.01
872 2174 2.676471 ATGCAGGGCCGTTGGAAC 60.676 61.111 0.00 0.00 0.00 3.62
873 2175 2.676121 CATGCAGGGCCGTTGGAA 60.676 61.111 0.00 0.00 0.00 3.53
876 2178 4.124351 CAGCATGCAGGGCCGTTG 62.124 66.667 21.98 2.32 0.00 4.10
905 2207 4.243008 TTCGGACAGTGGCGGCAA 62.243 61.111 15.50 0.00 0.00 4.52
907 2209 4.980805 TGTTCGGACAGTGGCGGC 62.981 66.667 0.00 0.00 0.00 6.53
908 2210 1.234615 ATTTGTTCGGACAGTGGCGG 61.235 55.000 0.00 0.00 37.04 6.13
1005 2307 6.095440 AGAGAGAAAGAGAGAGATTGTAGCAC 59.905 42.308 0.00 0.00 0.00 4.40
1129 2433 3.365265 GCTTGGAGCCCAACACCG 61.365 66.667 2.84 0.00 38.75 4.94
1770 3074 2.749865 CGATGTTGTCGGCGGCATT 61.750 57.895 17.58 2.90 46.47 3.56
1877 3181 2.038813 TGGGCGAGGATGGTCTCA 59.961 61.111 0.00 0.00 33.59 3.27
2333 3637 3.041940 CTGCCGTCGCCGAAGTTT 61.042 61.111 0.00 0.00 35.63 2.66
2438 3745 3.368427 CCTCACTGTCTCTTCGGCAAATA 60.368 47.826 0.00 0.00 0.00 1.40
2444 3751 0.534412 ATGCCTCACTGTCTCTTCGG 59.466 55.000 0.00 0.00 0.00 4.30
2451 3758 5.419542 TGAACTAATGTATGCCTCACTGTC 58.580 41.667 0.00 0.00 0.00 3.51
2601 3922 2.882137 CGGACCCTTTTGCTAGTGAAAA 59.118 45.455 0.00 0.00 0.00 2.29
2602 3923 2.158726 ACGGACCCTTTTGCTAGTGAAA 60.159 45.455 0.00 0.00 0.00 2.69
2605 3927 1.156736 CACGGACCCTTTTGCTAGTG 58.843 55.000 0.00 0.00 0.00 2.74
2618 3940 6.913873 TTTCTTATATTACAAGGCACGGAC 57.086 37.500 0.00 0.00 0.00 4.79
2619 3941 9.616156 TTATTTTCTTATATTACAAGGCACGGA 57.384 29.630 0.00 0.00 0.00 4.69
2663 3990 1.598882 TGCAGCAAAACGTGGTCATA 58.401 45.000 0.00 0.00 35.13 2.15
2747 4074 9.956720 CTTCTTTCTTCTTTGTGAAATGTATGT 57.043 29.630 0.00 0.00 33.79 2.29
2751 4078 8.960591 TCTTCTTCTTTCTTCTTTGTGAAATGT 58.039 29.630 0.00 0.00 33.79 2.71
2752 4079 9.793252 TTCTTCTTCTTTCTTCTTTGTGAAATG 57.207 29.630 0.00 0.00 33.79 2.32
2758 4085 9.454859 TTCTTCTTCTTCTTCTTTCTTCTTTGT 57.545 29.630 0.00 0.00 0.00 2.83
2764 4091 9.898152 TTCTTCTTCTTCTTCTTCTTCTTTCTT 57.102 29.630 0.00 0.00 0.00 2.52
2765 4092 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTTCT 57.454 33.333 0.00 0.00 0.00 2.52
2766 4093 9.541143 TCTTCTTCTTCTTCTTCTTCTTCTTTC 57.459 33.333 0.00 0.00 0.00 2.62
2767 4094 9.898152 TTCTTCTTCTTCTTCTTCTTCTTCTTT 57.102 29.630 0.00 0.00 0.00 2.52
2768 4095 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
2769 4096 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
2770 4097 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
2771 4098 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
2772 4099 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
2773 4100 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
2774 4101 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
2775 4102 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
2776 4103 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
2777 4104 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
2778 4105 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
2779 4106 9.710900 ATCTTCTTCTTCTTCTTCTTCTTCTTC 57.289 33.333 0.00 0.00 0.00 2.87
2798 4125 9.740710 GGCCAAGGTATATACAATTATCTTCTT 57.259 33.333 14.70 2.92 0.00 2.52
2799 4126 8.890472 TGGCCAAGGTATATACAATTATCTTCT 58.110 33.333 14.70 0.00 0.00 2.85
2800 4127 9.167311 CTGGCCAAGGTATATACAATTATCTTC 57.833 37.037 7.01 0.00 0.00 2.87
2811 4138 3.162666 CCGACTCTGGCCAAGGTATATA 58.837 50.000 7.01 0.00 0.00 0.86
2818 4145 0.320374 TGTAACCGACTCTGGCCAAG 59.680 55.000 7.01 10.13 0.00 3.61
2822 4149 1.873698 TGTTTGTAACCGACTCTGGC 58.126 50.000 0.00 0.00 0.00 4.85
2825 4152 3.514309 AGGCTATGTTTGTAACCGACTCT 59.486 43.478 0.00 0.00 0.00 3.24
2826 4153 3.617263 CAGGCTATGTTTGTAACCGACTC 59.383 47.826 0.00 0.00 0.00 3.36
2831 4158 2.676342 CGTCCAGGCTATGTTTGTAACC 59.324 50.000 0.00 0.00 0.00 2.85
2848 4175 3.982058 GGTTTCTCGATGATGATACGTCC 59.018 47.826 0.00 0.00 0.00 4.79
2878 4205 2.649531 TTTGTTGGGACACCTGTAGG 57.350 50.000 0.00 0.00 39.29 3.18
2880 4207 3.068873 GCATTTTTGTTGGGACACCTGTA 59.931 43.478 0.00 0.00 39.29 2.74
2896 4223 5.946486 TCTTTGGGGGTATTTTTGCATTTT 58.054 33.333 0.00 0.00 0.00 1.82
2901 4228 6.058833 TCTTTTTCTTTGGGGGTATTTTTGC 58.941 36.000 0.00 0.00 0.00 3.68
2912 4239 8.031277 CCAGATTGTATCTTCTTTTTCTTTGGG 58.969 37.037 0.00 0.00 37.58 4.12
2927 4254 3.312697 GCCTTTCGGAACCAGATTGTATC 59.687 47.826 0.00 0.00 0.00 2.24
2936 4263 1.515081 CGTTAAGCCTTTCGGAACCA 58.485 50.000 0.00 0.00 0.00 3.67
2938 4265 3.670500 GCGTTAAGCCTTTCGGAAC 57.330 52.632 0.00 0.00 40.81 3.62
2969 4296 2.354303 CGGTGATGGTTAGCAAGTGGTA 60.354 50.000 0.00 0.00 0.00 3.25
2974 4301 1.705337 CCGCGGTGATGGTTAGCAAG 61.705 60.000 19.50 0.00 0.00 4.01
2984 4312 0.892755 TTAGTCTCAACCGCGGTGAT 59.107 50.000 34.95 15.54 0.00 3.06
2987 4315 0.390124 TTGTTAGTCTCAACCGCGGT 59.610 50.000 28.70 28.70 0.00 5.68
3045 4375 0.460284 GATTCGGACGATGGTGTGCT 60.460 55.000 0.00 0.00 0.00 4.40
3065 4395 5.582665 GGCTTCATATTCGACTCAGAAAACT 59.417 40.000 0.00 0.00 33.43 2.66
3067 4397 4.876107 GGGCTTCATATTCGACTCAGAAAA 59.124 41.667 0.00 0.00 33.43 2.29
3087 4417 2.290641 CACCTATTCATTTGCTACGGGC 59.709 50.000 0.00 0.00 42.22 6.13
3093 4423 3.445096 GCCAGAACACCTATTCATTTGCT 59.555 43.478 0.00 0.00 0.00 3.91
3096 4426 5.018809 ACATGCCAGAACACCTATTCATTT 58.981 37.500 0.00 0.00 0.00 2.32
3099 4429 3.719268 ACATGCCAGAACACCTATTCA 57.281 42.857 0.00 0.00 0.00 2.57
3103 4433 2.105649 TGTCAACATGCCAGAACACCTA 59.894 45.455 0.00 0.00 0.00 3.08
3107 4437 1.608055 CCTGTCAACATGCCAGAACA 58.392 50.000 0.00 0.00 0.00 3.18
3111 4441 0.033796 ATCCCCTGTCAACATGCCAG 60.034 55.000 0.00 0.00 0.00 4.85
3112 4442 0.034186 GATCCCCTGTCAACATGCCA 60.034 55.000 0.00 0.00 0.00 4.92
3119 4449 0.036164 CGGTGTTGATCCCCTGTCAA 59.964 55.000 0.00 0.00 33.46 3.18
3124 4465 1.852157 ATGCACGGTGTTGATCCCCT 61.852 55.000 10.24 0.00 0.00 4.79
3135 4476 2.045926 GCCAAGGAGATGCACGGT 60.046 61.111 0.00 0.00 0.00 4.83
3149 4490 2.431683 GTGTTGGAGCTGGAGCCA 59.568 61.111 0.00 0.00 43.38 4.75
3166 4507 1.539065 CGATTTCATCAGACCGAGGGG 60.539 57.143 0.00 0.00 40.11 4.79
3167 4508 1.409064 TCGATTTCATCAGACCGAGGG 59.591 52.381 0.00 0.00 0.00 4.30
3172 4513 7.530010 TGATTTTTCTTCGATTTCATCAGACC 58.470 34.615 0.00 0.00 0.00 3.85
3173 4514 9.219497 GATGATTTTTCTTCGATTTCATCAGAC 57.781 33.333 0.00 0.00 38.43 3.51
3183 4524 7.360691 CCGCAGATATGATGATTTTTCTTCGAT 60.361 37.037 0.00 0.00 0.00 3.59
3258 4599 1.540267 GTATCTCTTATGAGGCCGCGA 59.460 52.381 8.23 0.00 40.58 5.87
3294 4640 1.131126 CTTCGGACATGCACATTGTCC 59.869 52.381 22.77 22.77 46.24 4.02
3328 4678 2.446435 AGCCGTTCCATGCTTTTATGT 58.554 42.857 0.00 0.00 32.94 2.29
3354 4704 3.071312 ACACCAACACAAATCCAATGCAT 59.929 39.130 0.00 0.00 0.00 3.96
3409 4771 9.872684 AGTCAACTATTTATGATGGGAATGAAT 57.127 29.630 0.00 0.00 0.00 2.57
3453 4815 8.357402 ACATGTGGTTAATTAACTCAAAAGGTC 58.643 33.333 23.89 8.03 36.47 3.85
3522 4884 4.487714 ACGATCCTCAAGATTTTAGGCA 57.512 40.909 0.00 0.00 34.42 4.75
3637 4999 2.942804 TGTGAAAACAAGGCCAGATGA 58.057 42.857 5.01 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.