Multiple sequence alignment - TraesCS6A01G154700

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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 TraesCS6A01G154700 chr6A 100.000 3343 0 0 1 3343 143454050 143450708 0.000000e+00 6174
1 TraesCS6A01G154700 chr6B 92.803 2098 92 15 992 3057 204477563 204475493 0.000000e+00 2983
2 TraesCS6A01G154700 chr6B 90.654 214 15 2 511 719 195381674 195381887 2.540000e-71 279
3 TraesCS6A01G154700 chr6B 95.455 176 6 1 3168 3343 204475371 204475198 2.540000e-71 279
4 TraesCS6A01G154700 chr6B 93.258 89 6 0 5 93 204479536 204479448 7.530000e-27 132
5 TraesCS6A01G154700 chr6D 92.852 1301 55 12 1748 3022 115050784 115049496 0.000000e+00 1853
6 TraesCS6A01G154700 chr6D 96.126 955 29 4 800 1751 115051860 115050911 0.000000e+00 1552
7 TraesCS6A01G154700 chr6D 92.381 420 23 7 3 418 115052668 115052254 1.030000e-164 590
8 TraesCS6A01G154700 chr6D 81.285 529 74 16 2035 2561 7275540 7276045 4.020000e-109 405
9 TraesCS6A01G154700 chr6D 97.159 176 5 0 3168 3343 115049476 115049301 7.010000e-77 298
10 TraesCS6A01G154700 chr6D 90.141 213 16 2 511 718 108897933 108897721 4.250000e-69 272
11 TraesCS6A01G154700 chr2D 79.198 524 87 10 2043 2563 399963032 399962528 8.880000e-91 344
12 TraesCS6A01G154700 chr1A 79.206 529 81 16 2035 2561 79272207 79271706 1.150000e-89 340
13 TraesCS6A01G154700 chr7A 78.519 540 86 16 2040 2576 671293437 671293949 8.940000e-86 327
14 TraesCS6A01G154700 chr7A 78.333 540 87 15 2040 2576 729968131 729968643 4.160000e-84 322
15 TraesCS6A01G154700 chr1B 78.679 530 84 14 2035 2561 16063286 16062783 3.220000e-85 326
16 TraesCS6A01G154700 chr5A 78.333 540 88 15 2040 2576 647910466 647910979 4.160000e-84 322
17 TraesCS6A01G154700 chr5A 90.187 214 16 2 511 719 367958164 367958377 1.180000e-69 274
18 TraesCS6A01G154700 chr1D 90.654 214 15 2 511 719 106577777 106577564 2.540000e-71 279
19 TraesCS6A01G154700 chr1D 90.187 214 16 2 511 719 220163135 220162922 1.180000e-69 274
20 TraesCS6A01G154700 chr4B 90.187 214 16 2 511 719 109740549 109740336 1.180000e-69 274
21 TraesCS6A01G154700 chr3D 90.187 214 15 3 511 719 272661539 272661327 1.180000e-69 274
22 TraesCS6A01G154700 chr3B 90.187 214 16 2 511 719 508598837 508599050 1.180000e-69 274
23 TraesCS6A01G154700 chr5D 90.141 213 16 2 511 718 301731024 301730812 4.250000e-69 272


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 TraesCS6A01G154700 chr6A 143450708 143454050 3342 True 6174.000000 6174 100.000000 1 3343 1 chr6A.!!$R1 3342
1 TraesCS6A01G154700 chr6B 204475198 204479536 4338 True 1131.333333 2983 93.838667 5 3343 3 chr6B.!!$R1 3338
2 TraesCS6A01G154700 chr6D 115049301 115052668 3367 True 1073.250000 1853 94.629500 3 3343 4 chr6D.!!$R2 3340
3 TraesCS6A01G154700 chr6D 7275540 7276045 505 False 405.000000 405 81.285000 2035 2561 1 chr6D.!!$F1 526
4 TraesCS6A01G154700 chr2D 399962528 399963032 504 True 344.000000 344 79.198000 2043 2563 1 chr2D.!!$R1 520
5 TraesCS6A01G154700 chr1A 79271706 79272207 501 True 340.000000 340 79.206000 2035 2561 1 chr1A.!!$R1 526
6 TraesCS6A01G154700 chr7A 671293437 671293949 512 False 327.000000 327 78.519000 2040 2576 1 chr7A.!!$F1 536
7 TraesCS6A01G154700 chr7A 729968131 729968643 512 False 322.000000 322 78.333000 2040 2576 1 chr7A.!!$F2 536
8 TraesCS6A01G154700 chr1B 16062783 16063286 503 True 326.000000 326 78.679000 2035 2561 1 chr1B.!!$R1 526
9 TraesCS6A01G154700 chr5A 647910466 647910979 513 False 322.000000 322 78.333000 2040 2576 1 chr5A.!!$F2 536

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
595 2011 0.031111 TCTGTGGAGAGGGGTATGGG 60.031 60.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2505 4200 0.096976 CATTTCGCGGTGGACATGAC 59.903 55.0 6.13 0.0 0.0 3.06 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
70 71 1.000955 TCAGAAAGTTCACGAGCCTCC 59.999 52.381 0.00 0.00 0.00 4.30
112 113 4.572985 TGAAAACAAAGGCATGTGAGAG 57.427 40.909 0.00 0.00 32.81 3.20
113 114 3.243501 TGAAAACAAAGGCATGTGAGAGC 60.244 43.478 0.00 0.00 32.81 4.09
114 115 2.283145 AACAAAGGCATGTGAGAGCT 57.717 45.000 0.00 0.00 32.81 4.09
237 239 0.676466 CAACATGGACAGCCGGCTAA 60.676 55.000 32.30 15.85 36.79 3.09
239 241 0.037590 ACATGGACAGCCGGCTAAAA 59.962 50.000 32.30 15.84 36.79 1.52
268 270 6.398935 GCAAAAAGCTGAATAAACAAGCTACG 60.399 38.462 0.00 0.00 41.15 3.51
292 295 5.642491 GGGTACACATGAAACTTTCCTACTC 59.358 44.000 0.00 0.00 0.00 2.59
309 312 3.928005 ACTCATGCATCCAGAGACAAT 57.072 42.857 16.97 0.00 33.69 2.71
318 321 7.792374 TGCATCCAGAGACAATTAATTCTAC 57.208 36.000 0.00 0.00 0.00 2.59
357 360 0.036388 TGGGGAAGCTAAAGTGCTCG 60.036 55.000 0.00 0.00 43.24 5.03
464 1880 6.587608 GCAGATGAAAAAGGACAAGTTATTGG 59.412 38.462 0.00 0.00 40.97 3.16
519 1935 9.006839 TCATGGAATATTCTACAATCAAGATGC 57.993 33.333 14.95 0.00 0.00 3.91
520 1936 8.789762 CATGGAATATTCTACAATCAAGATGCA 58.210 33.333 14.95 0.00 0.00 3.96
521 1937 8.929260 TGGAATATTCTACAATCAAGATGCAT 57.071 30.769 14.95 0.00 0.00 3.96
522 1938 9.358406 TGGAATATTCTACAATCAAGATGCATT 57.642 29.630 14.95 0.00 0.00 3.56
528 1944 9.961265 ATTCTACAATCAAGATGCATTTGTATG 57.039 29.630 17.10 17.03 33.65 2.39
529 1945 8.735692 TCTACAATCAAGATGCATTTGTATGA 57.264 30.769 17.10 14.13 33.65 2.15
530 1946 8.833493 TCTACAATCAAGATGCATTTGTATGAG 58.167 33.333 17.10 10.52 33.65 2.90
531 1947 7.400599 ACAATCAAGATGCATTTGTATGAGT 57.599 32.000 11.13 4.21 33.37 3.41
532 1948 8.510243 ACAATCAAGATGCATTTGTATGAGTA 57.490 30.769 11.13 0.00 33.37 2.59
533 1949 8.618677 ACAATCAAGATGCATTTGTATGAGTAG 58.381 33.333 11.13 4.70 33.37 2.57
534 1950 8.618677 CAATCAAGATGCATTTGTATGAGTAGT 58.381 33.333 0.00 0.00 33.37 2.73
535 1951 8.743085 ATCAAGATGCATTTGTATGAGTAGTT 57.257 30.769 0.00 0.00 33.37 2.24
536 1952 8.565896 TCAAGATGCATTTGTATGAGTAGTTT 57.434 30.769 0.00 0.00 33.37 2.66
537 1953 9.665719 TCAAGATGCATTTGTATGAGTAGTTTA 57.334 29.630 0.00 0.00 33.37 2.01
561 1977 9.982651 TTATCTTATAGGAGAAAAGGATGAACG 57.017 33.333 0.00 0.00 0.00 3.95
562 1978 7.655521 TCTTATAGGAGAAAAGGATGAACGA 57.344 36.000 0.00 0.00 0.00 3.85
563 1979 7.717568 TCTTATAGGAGAAAAGGATGAACGAG 58.282 38.462 0.00 0.00 0.00 4.18
564 1980 3.618690 AGGAGAAAAGGATGAACGAGG 57.381 47.619 0.00 0.00 0.00 4.63
565 1981 2.237392 AGGAGAAAAGGATGAACGAGGG 59.763 50.000 0.00 0.00 0.00 4.30
566 1982 2.236395 GGAGAAAAGGATGAACGAGGGA 59.764 50.000 0.00 0.00 0.00 4.20
567 1983 3.307480 GGAGAAAAGGATGAACGAGGGAA 60.307 47.826 0.00 0.00 0.00 3.97
568 1984 4.324267 GAGAAAAGGATGAACGAGGGAAA 58.676 43.478 0.00 0.00 0.00 3.13
569 1985 4.725490 AGAAAAGGATGAACGAGGGAAAA 58.275 39.130 0.00 0.00 0.00 2.29
570 1986 4.519350 AGAAAAGGATGAACGAGGGAAAAC 59.481 41.667 0.00 0.00 0.00 2.43
571 1987 2.491675 AGGATGAACGAGGGAAAACC 57.508 50.000 0.00 0.00 40.67 3.27
585 2001 4.918588 GGGAAAACCTTATTCTGTGGAGA 58.081 43.478 0.00 0.00 35.85 3.71
586 2002 4.944317 GGGAAAACCTTATTCTGTGGAGAG 59.056 45.833 0.00 0.00 35.85 3.20
587 2003 4.944317 GGAAAACCTTATTCTGTGGAGAGG 59.056 45.833 0.00 0.00 0.00 3.69
588 2004 4.576330 AAACCTTATTCTGTGGAGAGGG 57.424 45.455 0.00 0.00 0.00 4.30
589 2005 2.482494 ACCTTATTCTGTGGAGAGGGG 58.518 52.381 0.00 0.00 0.00 4.79
590 2006 2.225908 ACCTTATTCTGTGGAGAGGGGT 60.226 50.000 0.00 0.00 0.00 4.95
591 2007 3.013648 ACCTTATTCTGTGGAGAGGGGTA 59.986 47.826 0.00 0.00 0.00 3.69
592 2008 4.235372 CCTTATTCTGTGGAGAGGGGTAT 58.765 47.826 0.00 0.00 0.00 2.73
593 2009 4.040952 CCTTATTCTGTGGAGAGGGGTATG 59.959 50.000 0.00 0.00 0.00 2.39
594 2010 1.879575 TTCTGTGGAGAGGGGTATGG 58.120 55.000 0.00 0.00 0.00 2.74
595 2011 0.031111 TCTGTGGAGAGGGGTATGGG 60.031 60.000 0.00 0.00 0.00 4.00
596 2012 0.326618 CTGTGGAGAGGGGTATGGGT 60.327 60.000 0.00 0.00 0.00 4.51
597 2013 1.020462 TGTGGAGAGGGGTATGGGTA 58.980 55.000 0.00 0.00 0.00 3.69
598 2014 1.583611 TGTGGAGAGGGGTATGGGTAT 59.416 52.381 0.00 0.00 0.00 2.73
599 2015 2.258109 GTGGAGAGGGGTATGGGTATC 58.742 57.143 0.00 0.00 0.00 2.24
600 2016 2.158143 GTGGAGAGGGGTATGGGTATCT 60.158 54.545 0.00 0.00 0.00 1.98
601 2017 2.527057 TGGAGAGGGGTATGGGTATCTT 59.473 50.000 0.00 0.00 0.00 2.40
602 2018 3.050564 TGGAGAGGGGTATGGGTATCTTT 60.051 47.826 0.00 0.00 0.00 2.52
603 2019 3.981375 GGAGAGGGGTATGGGTATCTTTT 59.019 47.826 0.00 0.00 0.00 2.27
604 2020 4.415846 GGAGAGGGGTATGGGTATCTTTTT 59.584 45.833 0.00 0.00 0.00 1.94
605 2021 5.609708 GGAGAGGGGTATGGGTATCTTTTTA 59.390 44.000 0.00 0.00 0.00 1.52
606 2022 6.465464 GGAGAGGGGTATGGGTATCTTTTTAC 60.465 46.154 0.00 0.00 0.00 2.01
607 2023 5.974370 AGAGGGGTATGGGTATCTTTTTACA 59.026 40.000 0.00 0.00 0.00 2.41
608 2024 6.449041 AGAGGGGTATGGGTATCTTTTTACAA 59.551 38.462 0.00 0.00 0.00 2.41
609 2025 7.036425 AGAGGGGTATGGGTATCTTTTTACAAA 60.036 37.037 0.00 0.00 0.00 2.83
610 2026 7.480437 AGGGGTATGGGTATCTTTTTACAAAA 58.520 34.615 0.00 0.00 0.00 2.44
611 2027 8.126385 AGGGGTATGGGTATCTTTTTACAAAAT 58.874 33.333 0.00 0.00 0.00 1.82
612 2028 8.764558 GGGGTATGGGTATCTTTTTACAAAATT 58.235 33.333 0.00 0.00 0.00 1.82
638 2054 8.904099 ATAATAGTTTCCTTTCTATCCGTTGG 57.096 34.615 0.00 0.00 0.00 3.77
639 2055 4.903045 AGTTTCCTTTCTATCCGTTGGA 57.097 40.909 0.00 0.00 35.55 3.53
640 2056 5.437191 AGTTTCCTTTCTATCCGTTGGAT 57.563 39.130 3.49 3.49 45.40 3.41
641 2057 6.555463 AGTTTCCTTTCTATCCGTTGGATA 57.445 37.500 5.49 5.49 41.16 2.59
642 2058 7.138054 AGTTTCCTTTCTATCCGTTGGATAT 57.862 36.000 6.03 0.00 42.88 1.63
643 2059 8.258850 AGTTTCCTTTCTATCCGTTGGATATA 57.741 34.615 6.03 0.00 42.88 0.86
644 2060 8.711170 AGTTTCCTTTCTATCCGTTGGATATAA 58.289 33.333 6.03 3.26 42.88 0.98
645 2061 9.333724 GTTTCCTTTCTATCCGTTGGATATAAA 57.666 33.333 12.86 12.86 42.88 1.40
647 2063 9.720769 TTCCTTTCTATCCGTTGGATATAAATC 57.279 33.333 13.52 0.00 42.88 2.17
648 2064 8.033038 TCCTTTCTATCCGTTGGATATAAATCG 58.967 37.037 13.52 9.14 42.88 3.34
649 2065 7.277981 CCTTTCTATCCGTTGGATATAAATCGG 59.722 40.741 13.52 10.15 42.88 4.18
653 2069 5.731957 TCCGTTGGATATAAATCGGATCA 57.268 39.130 0.00 0.00 41.45 2.92
654 2070 5.475719 TCCGTTGGATATAAATCGGATCAC 58.524 41.667 0.00 0.00 41.45 3.06
655 2071 4.630069 CCGTTGGATATAAATCGGATCACC 59.370 45.833 0.00 0.00 40.29 4.02
656 2072 5.479306 CGTTGGATATAAATCGGATCACCT 58.521 41.667 0.00 0.00 32.44 4.00
657 2073 6.350696 CCGTTGGATATAAATCGGATCACCTA 60.351 42.308 0.00 0.00 40.29 3.08
658 2074 7.265673 CGTTGGATATAAATCGGATCACCTAT 58.734 38.462 0.00 0.00 32.44 2.57
659 2075 8.410912 CGTTGGATATAAATCGGATCACCTATA 58.589 37.037 0.00 0.00 32.44 1.31
663 2079 9.209175 GGATATAAATCGGATCACCTATATTGC 57.791 37.037 0.00 0.00 32.44 3.56
664 2080 9.764363 GATATAAATCGGATCACCTATATTGCA 57.236 33.333 0.00 0.00 0.00 4.08
665 2081 9.770097 ATATAAATCGGATCACCTATATTGCAG 57.230 33.333 0.00 0.00 0.00 4.41
666 2082 3.961480 TCGGATCACCTATATTGCAGG 57.039 47.619 0.00 0.00 39.25 4.85
667 2083 3.506398 TCGGATCACCTATATTGCAGGA 58.494 45.455 0.00 0.00 36.61 3.86
668 2084 4.096681 TCGGATCACCTATATTGCAGGAT 58.903 43.478 0.00 0.00 36.61 3.24
669 2085 4.081476 TCGGATCACCTATATTGCAGGATG 60.081 45.833 0.00 0.00 36.61 3.51
670 2086 4.521146 GGATCACCTATATTGCAGGATGG 58.479 47.826 0.00 0.00 36.61 3.51
671 2087 3.423539 TCACCTATATTGCAGGATGGC 57.576 47.619 0.00 0.00 36.61 4.40
672 2088 2.710471 TCACCTATATTGCAGGATGGCA 59.290 45.455 0.00 0.00 43.19 4.92
678 2094 2.115695 TGCAGGATGGCAAGCACA 59.884 55.556 0.00 0.00 41.65 4.57
679 2095 2.270257 TGCAGGATGGCAAGCACAC 61.270 57.895 0.00 0.00 41.65 3.82
680 2096 2.998279 GCAGGATGGCAAGCACACC 61.998 63.158 0.00 0.00 35.86 4.16
681 2097 1.604308 CAGGATGGCAAGCACACCA 60.604 57.895 0.00 0.00 41.06 4.17
684 2100 4.848000 ATGGCAAGCACACCATCA 57.152 50.000 0.00 0.00 43.26 3.07
685 2101 3.293199 ATGGCAAGCACACCATCAT 57.707 47.368 0.00 0.00 43.26 2.45
686 2102 1.108776 ATGGCAAGCACACCATCATC 58.891 50.000 0.00 0.00 43.26 2.92
687 2103 0.251253 TGGCAAGCACACCATCATCA 60.251 50.000 0.00 0.00 0.00 3.07
688 2104 1.108776 GGCAAGCACACCATCATCAT 58.891 50.000 0.00 0.00 0.00 2.45
689 2105 1.066605 GGCAAGCACACCATCATCATC 59.933 52.381 0.00 0.00 0.00 2.92
690 2106 1.746787 GCAAGCACACCATCATCATCA 59.253 47.619 0.00 0.00 0.00 3.07
691 2107 2.164827 GCAAGCACACCATCATCATCAA 59.835 45.455 0.00 0.00 0.00 2.57
692 2108 3.766151 CAAGCACACCATCATCATCAAC 58.234 45.455 0.00 0.00 0.00 3.18
693 2109 3.361281 AGCACACCATCATCATCAACT 57.639 42.857 0.00 0.00 0.00 3.16
694 2110 3.276857 AGCACACCATCATCATCAACTC 58.723 45.455 0.00 0.00 0.00 3.01
695 2111 3.054582 AGCACACCATCATCATCAACTCT 60.055 43.478 0.00 0.00 0.00 3.24
696 2112 3.064958 GCACACCATCATCATCAACTCTG 59.935 47.826 0.00 0.00 0.00 3.35
697 2113 4.259356 CACACCATCATCATCAACTCTGT 58.741 43.478 0.00 0.00 0.00 3.41
698 2114 4.698780 CACACCATCATCATCAACTCTGTT 59.301 41.667 0.00 0.00 0.00 3.16
699 2115 5.182570 CACACCATCATCATCAACTCTGTTT 59.817 40.000 0.00 0.00 0.00 2.83
700 2116 5.771666 ACACCATCATCATCAACTCTGTTTT 59.228 36.000 0.00 0.00 0.00 2.43
701 2117 6.266103 ACACCATCATCATCAACTCTGTTTTT 59.734 34.615 0.00 0.00 0.00 1.94
878 2403 1.061346 CCTCCCTTCCCTCCTCCATTA 60.061 57.143 0.00 0.00 0.00 1.90
879 2404 2.334023 CTCCCTTCCCTCCTCCATTAG 58.666 57.143 0.00 0.00 0.00 1.73
880 2405 1.657162 TCCCTTCCCTCCTCCATTAGT 59.343 52.381 0.00 0.00 0.00 2.24
881 2406 2.869689 TCCCTTCCCTCCTCCATTAGTA 59.130 50.000 0.00 0.00 0.00 1.82
883 2408 4.077387 TCCCTTCCCTCCTCCATTAGTATT 60.077 45.833 0.00 0.00 0.00 1.89
884 2409 4.287326 CCCTTCCCTCCTCCATTAGTATTC 59.713 50.000 0.00 0.00 0.00 1.75
886 2411 5.608860 CCTTCCCTCCTCCATTAGTATTCTT 59.391 44.000 0.00 0.00 0.00 2.52
893 2418 4.932200 CCTCCATTAGTATTCTTCATCGGC 59.068 45.833 0.00 0.00 0.00 5.54
913 2438 1.616187 CGAGACAGGTGGTTAGGAGGA 60.616 57.143 0.00 0.00 0.00 3.71
927 2455 1.439143 AGGAGGAAAGAGAAGAGGGGT 59.561 52.381 0.00 0.00 0.00 4.95
965 2493 1.111277 ACAAAACTGAAGCCCACACC 58.889 50.000 0.00 0.00 0.00 4.16
966 2494 1.341976 ACAAAACTGAAGCCCACACCT 60.342 47.619 0.00 0.00 0.00 4.00
983 2511 2.507886 CACCTCTCTCTCTCTCCCACTA 59.492 54.545 0.00 0.00 0.00 2.74
1353 2883 1.374758 GGACAGCTGGTTCGTGGAG 60.375 63.158 19.93 0.00 0.00 3.86
1398 2928 2.095252 GGACGACTTCTTGAGCCGC 61.095 63.158 0.00 0.00 0.00 6.53
1480 3010 1.065709 ACCAACCAACAACTGACGAGT 60.066 47.619 0.00 0.00 0.00 4.18
1552 3082 9.740239 AAACAAATAAGCTACAAGATGCATATG 57.260 29.630 0.00 4.65 0.00 1.78
1946 3629 3.777522 ACAGCCTAGTTCAGCTATCCTTT 59.222 43.478 0.00 0.00 37.18 3.11
1981 3664 5.665459 AGACAGATAAGTTGTGATAGGTGC 58.335 41.667 0.00 0.00 0.00 5.01
1994 3677 8.462016 GTTGTGATAGGTGCAGAATTTTATCTT 58.538 33.333 0.00 0.00 0.00 2.40
1995 3678 9.679661 TTGTGATAGGTGCAGAATTTTATCTTA 57.320 29.630 0.00 0.00 0.00 2.10
1996 3679 9.679661 TGTGATAGGTGCAGAATTTTATCTTAA 57.320 29.630 0.00 0.00 0.00 1.85
2146 3830 5.104652 ACAAGGAACAGTACACTAACCACTT 60.105 40.000 0.00 0.00 0.00 3.16
2162 3846 6.441088 AACCACTTGATTACCTCTCTTCTT 57.559 37.500 0.00 0.00 0.00 2.52
2179 3863 3.393089 TCTTCTCTTGACCTGCAACTC 57.607 47.619 0.00 0.00 31.96 3.01
2252 3939 0.462225 TGGACGACCACGCAGAAAAA 60.462 50.000 1.37 0.00 41.77 1.94
2294 3981 3.151022 AGCAGCTACTCGGCCTCC 61.151 66.667 0.00 0.00 36.50 4.30
2501 4196 9.952188 CGAATAAAAGAGAGGAAGAAAGTTTTT 57.048 29.630 0.00 0.00 0.00 1.94
2505 4200 4.474394 AGAGAGGAAGAAAGTTTTTGGGG 58.526 43.478 0.00 0.00 0.00 4.96
2521 4216 2.047655 GGTCATGTCCACCGCGAA 60.048 61.111 8.23 0.00 0.00 4.70
2588 4284 7.615403 CAGGGATAATTATGCTAGCACTTAGA 58.385 38.462 22.07 6.22 0.00 2.10
2599 4295 7.611213 TGCTAGCACTTAGAAAAGAAATACC 57.389 36.000 14.93 0.00 36.50 2.73
2623 4319 1.134367 TCGCGTCCTATCCTGAAGTTG 59.866 52.381 5.77 0.00 0.00 3.16
2625 4321 1.405526 GCGTCCTATCCTGAAGTTGCA 60.406 52.381 0.00 0.00 0.00 4.08
2626 4322 2.743183 GCGTCCTATCCTGAAGTTGCAT 60.743 50.000 0.00 0.00 0.00 3.96
2655 4351 2.049077 TGCTGCATGTTAAACGCTTG 57.951 45.000 0.00 0.00 0.00 4.01
2676 4373 6.406849 GCTTGATTGGCCTGGTAAAAATATCA 60.407 38.462 3.32 0.00 0.00 2.15
2701 4398 7.693969 ATTAACAAACTTCTTCTGAGGGATG 57.306 36.000 0.00 0.00 0.00 3.51
2702 4399 4.982241 ACAAACTTCTTCTGAGGGATGA 57.018 40.909 0.00 0.00 0.00 2.92
2708 4405 4.782156 ACTTCTTCTGAGGGATGACAGAAT 59.218 41.667 0.00 0.00 46.95 2.40
2709 4406 5.250313 ACTTCTTCTGAGGGATGACAGAATT 59.750 40.000 0.00 0.00 46.95 2.17
2710 4407 5.768980 TCTTCTGAGGGATGACAGAATTT 57.231 39.130 0.00 0.00 46.95 1.82
2711 4408 5.494724 TCTTCTGAGGGATGACAGAATTTG 58.505 41.667 0.00 0.00 46.95 2.32
2742 4443 3.256383 TGGCATTTCACATTCCAGTTCTG 59.744 43.478 0.00 0.00 0.00 3.02
2754 4455 5.623956 TTCCAGTTCTGAACTCAGGTAAA 57.376 39.130 19.65 8.15 43.91 2.01
2755 4456 5.623956 TCCAGTTCTGAACTCAGGTAAAA 57.376 39.130 19.65 1.72 43.91 1.52
2796 4497 5.003804 GTCTCCTGAGGCAAAATCAAACTA 58.996 41.667 0.00 0.00 32.23 2.24
2816 4517 0.466543 TGGTGGTACATCCGTATGGC 59.533 55.000 0.00 0.00 39.87 4.40
3018 4721 5.163652 ACACACTGGAAGCTTAAAACTCAAC 60.164 40.000 0.00 0.00 37.60 3.18
3057 4763 8.607441 TCTTGGCACTATTCATTCATATACAC 57.393 34.615 0.00 0.00 0.00 2.90
3058 4764 8.210265 TCTTGGCACTATTCATTCATATACACA 58.790 33.333 0.00 0.00 0.00 3.72
3059 4765 7.967890 TGGCACTATTCATTCATATACACAG 57.032 36.000 0.00 0.00 0.00 3.66
3060 4766 6.427853 TGGCACTATTCATTCATATACACAGC 59.572 38.462 0.00 0.00 0.00 4.40
3061 4767 6.427853 GGCACTATTCATTCATATACACAGCA 59.572 38.462 0.00 0.00 0.00 4.41
3062 4768 7.041167 GGCACTATTCATTCATATACACAGCAA 60.041 37.037 0.00 0.00 0.00 3.91
3063 4769 7.800380 GCACTATTCATTCATATACACAGCAAC 59.200 37.037 0.00 0.00 0.00 4.17
3064 4770 8.285394 CACTATTCATTCATATACACAGCAACC 58.715 37.037 0.00 0.00 0.00 3.77
3065 4771 8.213679 ACTATTCATTCATATACACAGCAACCT 58.786 33.333 0.00 0.00 0.00 3.50
3066 4772 7.886629 ATTCATTCATATACACAGCAACCTT 57.113 32.000 0.00 0.00 0.00 3.50
3067 4773 6.682423 TCATTCATATACACAGCAACCTTG 57.318 37.500 0.00 0.00 0.00 3.61
3068 4774 5.589855 TCATTCATATACACAGCAACCTTGG 59.410 40.000 0.00 0.00 0.00 3.61
3069 4775 3.278574 TCATATACACAGCAACCTTGGC 58.721 45.455 0.00 0.00 0.00 4.52
3070 4776 1.732941 TATACACAGCAACCTTGGCG 58.267 50.000 0.00 0.00 36.08 5.69
3071 4777 0.036164 ATACACAGCAACCTTGGCGA 59.964 50.000 0.00 0.00 36.08 5.54
3072 4778 0.179043 TACACAGCAACCTTGGCGAA 60.179 50.000 0.00 0.00 36.08 4.70
3073 4779 1.034838 ACACAGCAACCTTGGCGAAA 61.035 50.000 0.00 0.00 36.08 3.46
3074 4780 0.314935 CACAGCAACCTTGGCGAAAT 59.685 50.000 0.00 0.00 36.08 2.17
3075 4781 1.039856 ACAGCAACCTTGGCGAAATT 58.960 45.000 0.00 0.00 36.08 1.82
3076 4782 1.000274 ACAGCAACCTTGGCGAAATTC 60.000 47.619 0.00 0.00 36.08 2.17
3077 4783 0.240945 AGCAACCTTGGCGAAATTCG 59.759 50.000 11.47 11.47 43.89 3.34
3094 4800 8.612791 CGAAATTCGCAAAAAGAAAAATACTG 57.387 30.769 1.35 0.00 31.14 2.74
3095 4801 8.476142 CGAAATTCGCAAAAAGAAAAATACTGA 58.524 29.630 1.35 0.00 31.14 3.41
3096 4802 9.567917 GAAATTCGCAAAAAGAAAAATACTGAC 57.432 29.630 0.00 0.00 0.00 3.51
3097 4803 7.637709 ATTCGCAAAAAGAAAAATACTGACC 57.362 32.000 0.00 0.00 0.00 4.02
3098 4804 6.385649 TCGCAAAAAGAAAAATACTGACCT 57.614 33.333 0.00 0.00 0.00 3.85
3099 4805 6.205784 TCGCAAAAAGAAAAATACTGACCTG 58.794 36.000 0.00 0.00 0.00 4.00
3100 4806 5.402270 CGCAAAAAGAAAAATACTGACCTGG 59.598 40.000 0.00 0.00 0.00 4.45
3101 4807 5.696270 GCAAAAAGAAAAATACTGACCTGGG 59.304 40.000 0.00 0.00 0.00 4.45
3102 4808 6.462347 GCAAAAAGAAAAATACTGACCTGGGA 60.462 38.462 0.00 0.00 0.00 4.37
3103 4809 6.901081 AAAAGAAAAATACTGACCTGGGAG 57.099 37.500 0.00 0.00 0.00 4.30
3104 4810 5.843019 AAGAAAAATACTGACCTGGGAGA 57.157 39.130 0.00 0.00 0.00 3.71
3105 4811 5.843019 AGAAAAATACTGACCTGGGAGAA 57.157 39.130 0.00 0.00 0.00 2.87
3106 4812 6.200878 AGAAAAATACTGACCTGGGAGAAA 57.799 37.500 0.00 0.00 0.00 2.52
3107 4813 6.610830 AGAAAAATACTGACCTGGGAGAAAA 58.389 36.000 0.00 0.00 0.00 2.29
3108 4814 6.490381 AGAAAAATACTGACCTGGGAGAAAAC 59.510 38.462 0.00 0.00 0.00 2.43
3109 4815 3.611766 ATACTGACCTGGGAGAAAACG 57.388 47.619 0.00 0.00 0.00 3.60
3110 4816 1.420430 ACTGACCTGGGAGAAAACGA 58.580 50.000 0.00 0.00 0.00 3.85
3111 4817 1.344763 ACTGACCTGGGAGAAAACGAG 59.655 52.381 0.00 0.00 0.00 4.18
3112 4818 0.034896 TGACCTGGGAGAAAACGAGC 59.965 55.000 0.00 0.00 0.00 5.03
3113 4819 0.673956 GACCTGGGAGAAAACGAGCC 60.674 60.000 0.00 0.00 0.00 4.70
3114 4820 1.377333 CCTGGGAGAAAACGAGCCC 60.377 63.158 0.00 0.00 41.08 5.19
3116 4822 0.955919 CTGGGAGAAAACGAGCCCAC 60.956 60.000 0.00 0.00 45.31 4.61
3117 4823 1.072505 GGGAGAAAACGAGCCCACA 59.927 57.895 0.00 0.00 40.39 4.17
3118 4824 0.955919 GGGAGAAAACGAGCCCACAG 60.956 60.000 0.00 0.00 40.39 3.66
3119 4825 1.578206 GGAGAAAACGAGCCCACAGC 61.578 60.000 0.00 0.00 44.25 4.40
3120 4826 1.578206 GAGAAAACGAGCCCACAGCC 61.578 60.000 0.00 0.00 45.47 4.85
3121 4827 1.896660 GAAAACGAGCCCACAGCCA 60.897 57.895 0.00 0.00 45.47 4.75
3122 4828 2.130073 GAAAACGAGCCCACAGCCAC 62.130 60.000 0.00 0.00 45.47 5.01
3142 4848 3.945921 CACGAGTAGTCTACTGAATGGGA 59.054 47.826 17.41 0.00 39.59 4.37
3145 4851 3.892588 GAGTAGTCTACTGAATGGGAGGG 59.107 52.174 17.41 0.00 39.59 4.30
3149 4855 1.143813 CTACTGAATGGGAGGGGCAT 58.856 55.000 0.00 0.00 0.00 4.40
3151 4857 1.607225 ACTGAATGGGAGGGGCATAA 58.393 50.000 0.00 0.00 0.00 1.90
3152 4858 1.929494 ACTGAATGGGAGGGGCATAAA 59.071 47.619 0.00 0.00 0.00 1.40
3153 4859 2.310538 CTGAATGGGAGGGGCATAAAC 58.689 52.381 0.00 0.00 0.00 2.01
3190 4967 1.890041 CCACTCCGCGTTTCAACCA 60.890 57.895 4.92 0.00 0.00 3.67
3238 5015 1.066143 AGCAGAACCCCAGTATTCACG 60.066 52.381 0.00 0.00 0.00 4.35
3276 5053 0.737715 GACCTGCTTCAGCTGTACCG 60.738 60.000 14.67 1.92 42.66 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.329379 GAAAGATATCCTCGCGCGATT 58.671 47.619 34.86 21.73 0.00 3.34
130 131 6.490534 GGAATGCAATTAGTTCTTCAGCTAC 58.509 40.000 0.00 0.00 36.07 3.58
230 232 2.159430 GCTTTTTGCCATTTTTAGCCGG 59.841 45.455 0.00 0.00 35.15 6.13
237 239 7.565323 TGTTTATTCAGCTTTTTGCCATTTT 57.435 28.000 0.00 0.00 44.23 1.82
239 241 6.293571 GCTTGTTTATTCAGCTTTTTGCCATT 60.294 34.615 0.00 0.00 44.23 3.16
268 270 5.557866 AGTAGGAAAGTTTCATGTGTACCC 58.442 41.667 17.16 0.00 0.00 3.69
292 295 7.273320 AGAATTAATTGTCTCTGGATGCATG 57.727 36.000 2.46 0.00 0.00 4.06
325 328 4.740902 AGCTTCCCCACTATGTTTTCTTT 58.259 39.130 0.00 0.00 0.00 2.52
332 335 3.622455 GCACTTTAGCTTCCCCACTATGT 60.622 47.826 0.00 0.00 0.00 2.29
338 341 0.036388 CGAGCACTTTAGCTTCCCCA 60.036 55.000 0.00 0.00 46.75 4.96
340 343 1.369839 GCCGAGCACTTTAGCTTCCC 61.370 60.000 0.00 0.00 46.75 3.97
357 360 0.877743 GCTTGTCCTCTTGTGAAGCC 59.122 55.000 0.00 0.00 34.26 4.35
493 1909 9.006839 GCATCTTGATTGTAGAATATTCCATGA 57.993 33.333 11.92 9.28 0.00 3.07
494 1910 8.789762 TGCATCTTGATTGTAGAATATTCCATG 58.210 33.333 11.92 4.69 0.00 3.66
507 1923 7.400599 ACTCATACAAATGCATCTTGATTGT 57.599 32.000 20.96 18.57 37.86 2.71
535 1951 9.982651 CGTTCATCCTTTTCTCCTATAAGATAA 57.017 33.333 0.00 0.00 0.00 1.75
536 1952 9.363401 TCGTTCATCCTTTTCTCCTATAAGATA 57.637 33.333 0.00 0.00 0.00 1.98
537 1953 8.251383 TCGTTCATCCTTTTCTCCTATAAGAT 57.749 34.615 0.00 0.00 0.00 2.40
538 1954 7.201920 CCTCGTTCATCCTTTTCTCCTATAAGA 60.202 40.741 0.00 0.00 0.00 2.10
539 1955 6.926272 CCTCGTTCATCCTTTTCTCCTATAAG 59.074 42.308 0.00 0.00 0.00 1.73
540 1956 6.183360 CCCTCGTTCATCCTTTTCTCCTATAA 60.183 42.308 0.00 0.00 0.00 0.98
541 1957 5.304614 CCCTCGTTCATCCTTTTCTCCTATA 59.695 44.000 0.00 0.00 0.00 1.31
542 1958 4.101741 CCCTCGTTCATCCTTTTCTCCTAT 59.898 45.833 0.00 0.00 0.00 2.57
543 1959 3.451178 CCCTCGTTCATCCTTTTCTCCTA 59.549 47.826 0.00 0.00 0.00 2.94
544 1960 2.237392 CCCTCGTTCATCCTTTTCTCCT 59.763 50.000 0.00 0.00 0.00 3.69
545 1961 2.236395 TCCCTCGTTCATCCTTTTCTCC 59.764 50.000 0.00 0.00 0.00 3.71
546 1962 3.611766 TCCCTCGTTCATCCTTTTCTC 57.388 47.619 0.00 0.00 0.00 2.87
547 1963 4.367039 TTTCCCTCGTTCATCCTTTTCT 57.633 40.909 0.00 0.00 0.00 2.52
548 1964 4.321008 GGTTTTCCCTCGTTCATCCTTTTC 60.321 45.833 0.00 0.00 0.00 2.29
549 1965 3.572682 GGTTTTCCCTCGTTCATCCTTTT 59.427 43.478 0.00 0.00 0.00 2.27
550 1966 3.154710 GGTTTTCCCTCGTTCATCCTTT 58.845 45.455 0.00 0.00 0.00 3.11
551 1967 2.375509 AGGTTTTCCCTCGTTCATCCTT 59.624 45.455 0.00 0.00 40.71 3.36
552 1968 1.985895 AGGTTTTCCCTCGTTCATCCT 59.014 47.619 0.00 0.00 40.71 3.24
553 1969 2.491675 AGGTTTTCCCTCGTTCATCC 57.508 50.000 0.00 0.00 40.71 3.51
554 1970 5.880887 AGAATAAGGTTTTCCCTCGTTCATC 59.119 40.000 0.00 0.00 45.47 2.92
555 1971 5.648092 CAGAATAAGGTTTTCCCTCGTTCAT 59.352 40.000 0.00 0.00 45.47 2.57
556 1972 5.001232 CAGAATAAGGTTTTCCCTCGTTCA 58.999 41.667 0.00 0.00 45.47 3.18
557 1973 5.001874 ACAGAATAAGGTTTTCCCTCGTTC 58.998 41.667 0.00 0.00 45.47 3.95
558 1974 4.760204 CACAGAATAAGGTTTTCCCTCGTT 59.240 41.667 0.00 0.00 45.47 3.85
559 1975 4.324267 CACAGAATAAGGTTTTCCCTCGT 58.676 43.478 0.00 0.00 45.47 4.18
560 1976 3.689649 CCACAGAATAAGGTTTTCCCTCG 59.310 47.826 0.00 0.00 45.47 4.63
561 1977 4.918588 TCCACAGAATAAGGTTTTCCCTC 58.081 43.478 0.00 0.00 45.47 4.30
563 1979 4.918588 TCTCCACAGAATAAGGTTTTCCC 58.081 43.478 0.00 0.00 41.86 3.97
564 1980 4.944317 CCTCTCCACAGAATAAGGTTTTCC 59.056 45.833 0.00 0.00 41.05 3.13
565 1981 4.944317 CCCTCTCCACAGAATAAGGTTTTC 59.056 45.833 0.00 0.00 0.00 2.29
566 1982 4.263949 CCCCTCTCCACAGAATAAGGTTTT 60.264 45.833 0.00 0.00 0.00 2.43
567 1983 3.267031 CCCCTCTCCACAGAATAAGGTTT 59.733 47.826 0.00 0.00 0.00 3.27
568 1984 2.846827 CCCCTCTCCACAGAATAAGGTT 59.153 50.000 0.00 0.00 0.00 3.50
569 1985 2.225908 ACCCCTCTCCACAGAATAAGGT 60.226 50.000 0.00 0.00 0.00 3.50
570 1986 2.482494 ACCCCTCTCCACAGAATAAGG 58.518 52.381 0.00 0.00 0.00 2.69
571 1987 4.040952 CCATACCCCTCTCCACAGAATAAG 59.959 50.000 0.00 0.00 0.00 1.73
572 1988 3.973973 CCATACCCCTCTCCACAGAATAA 59.026 47.826 0.00 0.00 0.00 1.40
573 1989 3.587498 CCATACCCCTCTCCACAGAATA 58.413 50.000 0.00 0.00 0.00 1.75
574 1990 2.412591 CCATACCCCTCTCCACAGAAT 58.587 52.381 0.00 0.00 0.00 2.40
575 1991 1.625228 CCCATACCCCTCTCCACAGAA 60.625 57.143 0.00 0.00 0.00 3.02
576 1992 0.031111 CCCATACCCCTCTCCACAGA 60.031 60.000 0.00 0.00 0.00 3.41
577 1993 0.326618 ACCCATACCCCTCTCCACAG 60.327 60.000 0.00 0.00 0.00 3.66
578 1994 1.020462 TACCCATACCCCTCTCCACA 58.980 55.000 0.00 0.00 0.00 4.17
579 1995 2.158143 AGATACCCATACCCCTCTCCAC 60.158 54.545 0.00 0.00 0.00 4.02
580 1996 2.161624 AGATACCCATACCCCTCTCCA 58.838 52.381 0.00 0.00 0.00 3.86
581 1997 3.277416 AAGATACCCATACCCCTCTCC 57.723 52.381 0.00 0.00 0.00 3.71
582 1998 5.648330 AAAAAGATACCCATACCCCTCTC 57.352 43.478 0.00 0.00 0.00 3.20
583 1999 5.974370 TGTAAAAAGATACCCATACCCCTCT 59.026 40.000 0.00 0.00 0.00 3.69
584 2000 6.256643 TGTAAAAAGATACCCATACCCCTC 57.743 41.667 0.00 0.00 0.00 4.30
585 2001 6.661740 TTGTAAAAAGATACCCATACCCCT 57.338 37.500 0.00 0.00 0.00 4.79
586 2002 7.721409 TTTTGTAAAAAGATACCCATACCCC 57.279 36.000 0.00 0.00 0.00 4.95
612 2028 9.991906 CCAACGGATAGAAAGGAAACTATTATA 57.008 33.333 0.00 0.00 42.68 0.98
613 2029 8.711170 TCCAACGGATAGAAAGGAAACTATTAT 58.289 33.333 0.00 0.00 42.68 1.28
614 2030 8.081517 TCCAACGGATAGAAAGGAAACTATTA 57.918 34.615 0.00 0.00 42.68 0.98
615 2031 6.954232 TCCAACGGATAGAAAGGAAACTATT 58.046 36.000 0.00 0.00 42.68 1.73
616 2032 6.555463 TCCAACGGATAGAAAGGAAACTAT 57.445 37.500 0.00 0.00 42.68 2.12
617 2033 6.555463 ATCCAACGGATAGAAAGGAAACTA 57.445 37.500 0.00 0.00 41.16 2.24
618 2034 5.437191 ATCCAACGGATAGAAAGGAAACT 57.563 39.130 0.00 0.00 41.16 2.66
619 2035 8.897872 TTATATCCAACGGATAGAAAGGAAAC 57.102 34.615 7.47 0.00 46.25 2.78
626 2042 7.470935 TCCGATTTATATCCAACGGATAGAA 57.529 36.000 8.60 7.33 46.25 2.10
632 2048 4.630069 GGTGATCCGATTTATATCCAACGG 59.370 45.833 0.00 0.00 41.39 4.44
633 2049 5.479306 AGGTGATCCGATTTATATCCAACG 58.521 41.667 0.00 0.00 39.05 4.10
637 2053 9.209175 GCAATATAGGTGATCCGATTTATATCC 57.791 37.037 0.00 0.00 39.05 2.59
638 2054 9.764363 TGCAATATAGGTGATCCGATTTATATC 57.236 33.333 0.00 0.00 39.05 1.63
639 2055 9.770097 CTGCAATATAGGTGATCCGATTTATAT 57.230 33.333 0.00 0.00 39.05 0.86
640 2056 8.204160 CCTGCAATATAGGTGATCCGATTTATA 58.796 37.037 0.00 0.00 39.05 0.98
641 2057 7.050377 CCTGCAATATAGGTGATCCGATTTAT 58.950 38.462 0.00 0.00 39.05 1.40
642 2058 6.212589 TCCTGCAATATAGGTGATCCGATTTA 59.787 38.462 0.00 0.00 39.05 1.40
643 2059 5.013079 TCCTGCAATATAGGTGATCCGATTT 59.987 40.000 0.00 0.00 39.05 2.17
644 2060 4.532126 TCCTGCAATATAGGTGATCCGATT 59.468 41.667 0.00 0.00 39.05 3.34
645 2061 4.096681 TCCTGCAATATAGGTGATCCGAT 58.903 43.478 0.00 0.00 39.05 4.18
646 2062 3.506398 TCCTGCAATATAGGTGATCCGA 58.494 45.455 0.00 0.00 39.05 4.55
647 2063 3.961480 TCCTGCAATATAGGTGATCCG 57.039 47.619 0.00 0.00 39.05 4.18
648 2064 4.521146 CCATCCTGCAATATAGGTGATCC 58.479 47.826 0.00 0.00 36.67 3.36
649 2065 3.944015 GCCATCCTGCAATATAGGTGATC 59.056 47.826 0.00 0.00 36.67 2.92
650 2066 3.331591 TGCCATCCTGCAATATAGGTGAT 59.668 43.478 0.00 0.00 38.56 3.06
651 2067 2.710471 TGCCATCCTGCAATATAGGTGA 59.290 45.455 0.00 0.00 38.56 4.02
652 2068 3.144657 TGCCATCCTGCAATATAGGTG 57.855 47.619 0.00 0.00 38.56 4.00
653 2069 3.882102 TTGCCATCCTGCAATATAGGT 57.118 42.857 0.00 0.00 45.77 3.08
661 2077 2.115695 TGTGCTTGCCATCCTGCA 59.884 55.556 0.00 0.00 40.07 4.41
662 2078 2.570181 GTGTGCTTGCCATCCTGC 59.430 61.111 0.00 0.00 0.00 4.85
663 2079 0.968901 ATGGTGTGCTTGCCATCCTG 60.969 55.000 0.00 0.00 41.24 3.86
664 2080 1.385368 ATGGTGTGCTTGCCATCCT 59.615 52.632 0.00 0.00 41.24 3.24
665 2081 4.023137 ATGGTGTGCTTGCCATCC 57.977 55.556 0.00 0.00 41.24 3.51
668 2084 0.251253 TGATGATGGTGTGCTTGCCA 60.251 50.000 0.00 0.00 39.33 4.92
669 2085 1.066605 GATGATGATGGTGTGCTTGCC 59.933 52.381 0.00 0.00 0.00 4.52
670 2086 1.746787 TGATGATGATGGTGTGCTTGC 59.253 47.619 0.00 0.00 0.00 4.01
671 2087 3.442625 AGTTGATGATGATGGTGTGCTTG 59.557 43.478 0.00 0.00 0.00 4.01
672 2088 3.693085 GAGTTGATGATGATGGTGTGCTT 59.307 43.478 0.00 0.00 0.00 3.91
673 2089 3.054582 AGAGTTGATGATGATGGTGTGCT 60.055 43.478 0.00 0.00 0.00 4.40
674 2090 3.064958 CAGAGTTGATGATGATGGTGTGC 59.935 47.826 0.00 0.00 0.00 4.57
675 2091 4.259356 ACAGAGTTGATGATGATGGTGTG 58.741 43.478 0.00 0.00 0.00 3.82
676 2092 4.564782 ACAGAGTTGATGATGATGGTGT 57.435 40.909 0.00 0.00 0.00 4.16
677 2093 5.892160 AAACAGAGTTGATGATGATGGTG 57.108 39.130 0.00 0.00 0.00 4.17
678 2094 6.906157 AAAAACAGAGTTGATGATGATGGT 57.094 33.333 0.00 0.00 0.00 3.55
766 2199 6.911993 TTCCTAATAATTAGTGGGGGTTGA 57.088 37.500 14.39 0.00 0.00 3.18
795 2228 9.541884 AAAGGGATAAATGGTTTGTTGTACTAT 57.458 29.630 0.00 0.00 0.00 2.12
796 2229 8.943594 AAAGGGATAAATGGTTTGTTGTACTA 57.056 30.769 0.00 0.00 0.00 1.82
797 2230 7.849322 AAAGGGATAAATGGTTTGTTGTACT 57.151 32.000 0.00 0.00 0.00 2.73
798 2231 9.984190 TTTAAAGGGATAAATGGTTTGTTGTAC 57.016 29.630 0.00 0.00 0.00 2.90
878 2403 2.688446 TGTCTCGCCGATGAAGAATACT 59.312 45.455 0.00 0.00 0.00 2.12
879 2404 3.046390 CTGTCTCGCCGATGAAGAATAC 58.954 50.000 0.00 0.00 0.00 1.89
880 2405 2.034685 CCTGTCTCGCCGATGAAGAATA 59.965 50.000 0.00 0.00 0.00 1.75
881 2406 1.202463 CCTGTCTCGCCGATGAAGAAT 60.202 52.381 0.00 0.00 0.00 2.40
883 2408 0.965866 ACCTGTCTCGCCGATGAAGA 60.966 55.000 0.00 0.00 0.00 2.87
884 2409 0.803768 CACCTGTCTCGCCGATGAAG 60.804 60.000 0.00 0.00 0.00 3.02
886 2411 2.710902 CCACCTGTCTCGCCGATGA 61.711 63.158 0.00 0.00 0.00 2.92
893 2418 0.818296 CCTCCTAACCACCTGTCTCG 59.182 60.000 0.00 0.00 0.00 4.04
913 2438 1.132365 ACTCCCACCCCTCTTCTCTTT 60.132 52.381 0.00 0.00 0.00 2.52
927 2455 0.114364 TACTGCTCTCCACACTCCCA 59.886 55.000 0.00 0.00 0.00 4.37
959 2487 1.684869 GGGAGAGAGAGAGAGGTGTGG 60.685 61.905 0.00 0.00 0.00 4.17
965 2493 4.398319 GGAATAGTGGGAGAGAGAGAGAG 58.602 52.174 0.00 0.00 0.00 3.20
966 2494 3.139397 GGGAATAGTGGGAGAGAGAGAGA 59.861 52.174 0.00 0.00 0.00 3.10
983 2511 2.614057 GTCATCATTTTCTCGCGGGAAT 59.386 45.455 24.20 5.45 0.00 3.01
1239 2769 1.863880 GACGCACGTGTAGCTCTCG 60.864 63.158 18.38 12.40 38.71 4.04
1339 2869 4.021925 GGCCTCCACGAACCAGCT 62.022 66.667 0.00 0.00 0.00 4.24
1480 3010 6.996879 ACTCCTTGCGATATGAAGTACTACTA 59.003 38.462 0.00 0.00 0.00 1.82
1552 3082 5.033589 ACATGTGAGATTCCTGAAGGATC 57.966 43.478 0.00 0.92 44.98 3.36
1679 3212 3.766591 TCACTGTCCACACAACCAAAATT 59.233 39.130 0.00 0.00 29.82 1.82
1777 3440 6.605119 TCTCTGAGAAAGGAAGGTGAAAAAT 58.395 36.000 4.57 0.00 0.00 1.82
1946 3629 8.150945 ACAACTTATCTGTCTTCTGCTTTCTTA 58.849 33.333 0.00 0.00 0.00 2.10
2030 3713 1.039856 TATGCGAGGTGCTATGCTGA 58.960 50.000 0.00 0.00 46.63 4.26
2146 3830 6.153680 GGTCAAGAGAAGAAGAGAGGTAATCA 59.846 42.308 0.00 0.00 0.00 2.57
2162 3846 2.828520 CCTAGAGTTGCAGGTCAAGAGA 59.171 50.000 0.00 0.00 34.91 3.10
2252 3939 1.489649 CTGAGGGCTTCTGATCCACAT 59.510 52.381 0.00 0.00 0.00 3.21
2501 4196 4.028490 GCGGTGGACATGACCCCA 62.028 66.667 11.80 6.92 0.00 4.96
2505 4200 0.096976 CATTTCGCGGTGGACATGAC 59.903 55.000 6.13 0.00 0.00 3.06
2519 4214 2.031682 ACGCTCAAGCACTGAACATTTC 60.032 45.455 2.50 0.00 42.21 2.17
2521 4216 1.265095 CACGCTCAAGCACTGAACATT 59.735 47.619 2.50 0.00 42.21 2.71
2588 4284 3.126343 GGACGCGACATGGTATTTCTTTT 59.874 43.478 15.93 0.00 0.00 2.27
2597 4293 0.755698 AGGATAGGACGCGACATGGT 60.756 55.000 15.93 0.00 0.00 3.55
2598 4294 0.319040 CAGGATAGGACGCGACATGG 60.319 60.000 15.93 0.00 0.00 3.66
2599 4295 0.668535 TCAGGATAGGACGCGACATG 59.331 55.000 15.93 4.89 0.00 3.21
2623 4319 2.933495 TGCAGCAAATCTCTTCATGC 57.067 45.000 0.00 0.00 39.06 4.06
2625 4321 6.519679 TTAACATGCAGCAAATCTCTTCAT 57.480 33.333 0.00 0.00 0.00 2.57
2626 4322 5.963176 TTAACATGCAGCAAATCTCTTCA 57.037 34.783 0.00 0.00 0.00 3.02
2676 4373 7.944554 TCATCCCTCAGAAGAAGTTTGTTAATT 59.055 33.333 0.00 0.00 0.00 1.40
2701 4398 6.509418 TGCCACCTATAAACAAATTCTGTC 57.491 37.500 0.00 0.00 37.23 3.51
2702 4399 7.480760 AATGCCACCTATAAACAAATTCTGT 57.519 32.000 0.00 0.00 41.27 3.41
2708 4405 6.656632 TGTGAAATGCCACCTATAAACAAA 57.343 33.333 0.00 0.00 36.26 2.83
2709 4406 6.849085 ATGTGAAATGCCACCTATAAACAA 57.151 33.333 0.00 0.00 36.26 2.83
2710 4407 6.127479 GGAATGTGAAATGCCACCTATAAACA 60.127 38.462 0.00 0.00 36.26 2.83
2711 4408 6.127479 TGGAATGTGAAATGCCACCTATAAAC 60.127 38.462 0.00 0.00 36.26 2.01
2742 4443 5.470098 TCTGCTGTGATTTTTACCTGAGTTC 59.530 40.000 0.00 0.00 0.00 3.01
2754 4455 4.147321 AGACCATGTTTCTGCTGTGATTT 58.853 39.130 0.00 0.00 0.00 2.17
2755 4456 3.755378 GAGACCATGTTTCTGCTGTGATT 59.245 43.478 0.00 0.00 0.00 2.57
2796 4497 1.071699 GCCATACGGATGTACCACCAT 59.928 52.381 6.92 0.00 38.90 3.55
3018 4721 2.295885 GCCAAGAGAATGTCATCAGGG 58.704 52.381 0.00 0.00 0.00 4.45
3057 4763 1.701704 GAATTTCGCCAAGGTTGCTG 58.298 50.000 0.00 0.00 0.00 4.41
3058 4764 0.240945 CGAATTTCGCCAAGGTTGCT 59.759 50.000 5.78 0.00 31.14 3.91
3059 4765 2.724403 CGAATTTCGCCAAGGTTGC 58.276 52.632 5.78 0.00 31.14 4.17
3069 4775 8.476142 TCAGTATTTTTCTTTTTGCGAATTTCG 58.524 29.630 14.33 14.33 43.89 3.46
3070 4776 9.567917 GTCAGTATTTTTCTTTTTGCGAATTTC 57.432 29.630 0.00 0.00 0.00 2.17
3071 4777 8.547894 GGTCAGTATTTTTCTTTTTGCGAATTT 58.452 29.630 0.00 0.00 0.00 1.82
3072 4778 7.926018 AGGTCAGTATTTTTCTTTTTGCGAATT 59.074 29.630 0.00 0.00 0.00 2.17
3073 4779 7.382218 CAGGTCAGTATTTTTCTTTTTGCGAAT 59.618 33.333 0.00 0.00 0.00 3.34
3074 4780 6.695278 CAGGTCAGTATTTTTCTTTTTGCGAA 59.305 34.615 0.00 0.00 0.00 4.70
3075 4781 6.205784 CAGGTCAGTATTTTTCTTTTTGCGA 58.794 36.000 0.00 0.00 0.00 5.10
3076 4782 5.402270 CCAGGTCAGTATTTTTCTTTTTGCG 59.598 40.000 0.00 0.00 0.00 4.85
3077 4783 5.696270 CCCAGGTCAGTATTTTTCTTTTTGC 59.304 40.000 0.00 0.00 0.00 3.68
3078 4784 7.014230 TCTCCCAGGTCAGTATTTTTCTTTTTG 59.986 37.037 0.00 0.00 0.00 2.44
3079 4785 7.066781 TCTCCCAGGTCAGTATTTTTCTTTTT 58.933 34.615 0.00 0.00 0.00 1.94
3080 4786 6.610830 TCTCCCAGGTCAGTATTTTTCTTTT 58.389 36.000 0.00 0.00 0.00 2.27
3081 4787 6.200878 TCTCCCAGGTCAGTATTTTTCTTT 57.799 37.500 0.00 0.00 0.00 2.52
3082 4788 5.843019 TCTCCCAGGTCAGTATTTTTCTT 57.157 39.130 0.00 0.00 0.00 2.52
3083 4789 5.843019 TTCTCCCAGGTCAGTATTTTTCT 57.157 39.130 0.00 0.00 0.00 2.52
3084 4790 6.567891 CGTTTTCTCCCAGGTCAGTATTTTTC 60.568 42.308 0.00 0.00 0.00 2.29
3085 4791 5.240844 CGTTTTCTCCCAGGTCAGTATTTTT 59.759 40.000 0.00 0.00 0.00 1.94
3086 4792 4.760204 CGTTTTCTCCCAGGTCAGTATTTT 59.240 41.667 0.00 0.00 0.00 1.82
3087 4793 4.041198 TCGTTTTCTCCCAGGTCAGTATTT 59.959 41.667 0.00 0.00 0.00 1.40
3088 4794 3.581332 TCGTTTTCTCCCAGGTCAGTATT 59.419 43.478 0.00 0.00 0.00 1.89
3089 4795 3.170717 TCGTTTTCTCCCAGGTCAGTAT 58.829 45.455 0.00 0.00 0.00 2.12
3090 4796 2.561419 CTCGTTTTCTCCCAGGTCAGTA 59.439 50.000 0.00 0.00 0.00 2.74
3091 4797 1.344763 CTCGTTTTCTCCCAGGTCAGT 59.655 52.381 0.00 0.00 0.00 3.41
3092 4798 1.941668 GCTCGTTTTCTCCCAGGTCAG 60.942 57.143 0.00 0.00 0.00 3.51
3093 4799 0.034896 GCTCGTTTTCTCCCAGGTCA 59.965 55.000 0.00 0.00 0.00 4.02
3094 4800 0.673956 GGCTCGTTTTCTCCCAGGTC 60.674 60.000 0.00 0.00 0.00 3.85
3095 4801 1.375326 GGCTCGTTTTCTCCCAGGT 59.625 57.895 0.00 0.00 0.00 4.00
3096 4802 1.377333 GGGCTCGTTTTCTCCCAGG 60.377 63.158 0.00 0.00 38.62 4.45
3097 4803 1.374947 TGGGCTCGTTTTCTCCCAG 59.625 57.895 0.00 0.00 43.40 4.45
3098 4804 1.072505 GTGGGCTCGTTTTCTCCCA 59.927 57.895 0.00 0.00 45.87 4.37
3099 4805 0.955919 CTGTGGGCTCGTTTTCTCCC 60.956 60.000 0.00 0.00 39.22 4.30
3100 4806 1.578206 GCTGTGGGCTCGTTTTCTCC 61.578 60.000 0.00 0.00 38.06 3.71
3101 4807 1.578206 GGCTGTGGGCTCGTTTTCTC 61.578 60.000 0.00 0.00 41.46 2.87
3102 4808 1.600916 GGCTGTGGGCTCGTTTTCT 60.601 57.895 0.00 0.00 41.46 2.52
3103 4809 1.896660 TGGCTGTGGGCTCGTTTTC 60.897 57.895 0.00 0.00 41.46 2.29
3104 4810 2.193536 GTGGCTGTGGGCTCGTTTT 61.194 57.895 0.00 0.00 41.46 2.43
3105 4811 2.594592 GTGGCTGTGGGCTCGTTT 60.595 61.111 0.00 0.00 41.46 3.60
3106 4812 4.988598 CGTGGCTGTGGGCTCGTT 62.989 66.667 6.01 0.00 45.41 3.85
3109 4815 2.564553 CTACTCGTGGCTGTGGGCTC 62.565 65.000 0.00 0.00 41.46 4.70
3110 4816 2.603473 TACTCGTGGCTGTGGGCT 60.603 61.111 0.00 0.00 41.46 5.19
3111 4817 2.125512 CTACTCGTGGCTGTGGGC 60.126 66.667 0.00 0.00 40.90 5.36
3112 4818 1.215647 GACTACTCGTGGCTGTGGG 59.784 63.158 0.00 0.00 0.00 4.61
3113 4819 1.132643 GTAGACTACTCGTGGCTGTGG 59.867 57.143 5.32 0.00 0.00 4.17
3114 4820 2.085320 AGTAGACTACTCGTGGCTGTG 58.915 52.381 9.45 0.00 32.47 3.66
3115 4821 2.085320 CAGTAGACTACTCGTGGCTGT 58.915 52.381 12.37 0.00 36.76 4.40
3116 4822 2.357075 TCAGTAGACTACTCGTGGCTG 58.643 52.381 12.37 1.16 36.76 4.85
3117 4823 2.783609 TCAGTAGACTACTCGTGGCT 57.216 50.000 12.37 0.00 36.76 4.75
3118 4824 3.489398 CCATTCAGTAGACTACTCGTGGC 60.489 52.174 12.37 0.00 36.76 5.01
3119 4825 3.066900 CCCATTCAGTAGACTACTCGTGG 59.933 52.174 20.62 20.62 36.76 4.94
3120 4826 3.945921 TCCCATTCAGTAGACTACTCGTG 59.054 47.826 12.37 10.78 36.76 4.35
3121 4827 4.200874 CTCCCATTCAGTAGACTACTCGT 58.799 47.826 12.37 0.00 36.76 4.18
3122 4828 3.566322 CCTCCCATTCAGTAGACTACTCG 59.434 52.174 12.37 8.58 36.76 4.18
3149 4855 4.937620 GTGGAGATGATGTTCAGCAGTTTA 59.062 41.667 0.00 0.00 34.77 2.01
3151 4857 3.341823 GTGGAGATGATGTTCAGCAGTT 58.658 45.455 0.00 0.00 34.77 3.16
3152 4858 2.355513 GGTGGAGATGATGTTCAGCAGT 60.356 50.000 0.00 0.00 34.77 4.40
3153 4859 2.286872 GGTGGAGATGATGTTCAGCAG 58.713 52.381 0.00 0.00 34.77 4.24
3156 4862 3.529533 GAGTGGTGGAGATGATGTTCAG 58.470 50.000 0.00 0.00 0.00 3.02
3157 4863 2.237143 GGAGTGGTGGAGATGATGTTCA 59.763 50.000 0.00 0.00 0.00 3.18
3158 4864 2.739932 CGGAGTGGTGGAGATGATGTTC 60.740 54.545 0.00 0.00 0.00 3.18
3159 4865 1.208052 CGGAGTGGTGGAGATGATGTT 59.792 52.381 0.00 0.00 0.00 2.71
3160 4866 0.826715 CGGAGTGGTGGAGATGATGT 59.173 55.000 0.00 0.00 0.00 3.06
3163 4869 2.710902 CGCGGAGTGGTGGAGATGA 61.711 63.158 0.00 0.00 0.00 2.92
3164 4870 2.202797 CGCGGAGTGGTGGAGATG 60.203 66.667 0.00 0.00 0.00 2.90
3166 4872 2.430382 GAAACGCGGAGTGGTGGAGA 62.430 60.000 12.47 0.00 36.15 3.71
3254 5031 1.185618 TACAGCTGAAGCAGGTCCGT 61.186 55.000 23.35 0.00 40.40 4.69
3276 5053 7.654568 TCCATTATTTGAATGATGATGCTCAC 58.345 34.615 9.33 0.00 35.17 3.51


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

AutoCloner maintained by Alex Coulton.