Multiple sequence alignment - TraesCS2B01G115400

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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 TraesCS2B01G115400 chr2B 100.000 5909 0 0 1 5909 78824274 78830182 0.000000e+00 10912
1 TraesCS2B01G115400 chr2D 93.058 4595 224 34 819 5362 50468079 50472629 0.000000e+00 6630
2 TraesCS2B01G115400 chr2D 86.588 507 29 18 5429 5909 50472754 50473247 1.890000e-144 523
3 TraesCS2B01G115400 chr2D 79.266 463 40 23 320 752 50467541 50467977 7.550000e-69 272
4 TraesCS2B01G115400 chr2D 89.560 182 16 3 143 324 50467321 50467499 1.660000e-55 228
5 TraesCS2B01G115400 chr2D 83.806 247 30 5 3957 4199 50470944 50471184 5.960000e-55 226
6 TraesCS2B01G115400 chr2A 91.495 4668 274 60 320 4909 52126952 52131574 0.000000e+00 6307
7 TraesCS2B01G115400 chr2A 84.632 475 49 11 5441 5909 52132175 52132631 9.030000e-123 451
8 TraesCS2B01G115400 chr2A 89.097 321 25 5 5016 5330 52131663 52131979 2.000000e-104 390
9 TraesCS2B01G115400 chr2A 86.813 182 19 3 141 322 52126734 52126910 1.300000e-46 198


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 TraesCS2B01G115400 chr2B 78824274 78830182 5908 False 10912.0 10912 100.00000 1 5909 1 chr2B.!!$F1 5908
1 TraesCS2B01G115400 chr2D 50467321 50473247 5926 False 1575.8 6630 86.45560 143 5909 5 chr2D.!!$F1 5766
2 TraesCS2B01G115400 chr2A 52126734 52132631 5897 False 1836.5 6307 88.00925 141 5909 4 chr2A.!!$F1 5768

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
748 831 0.460459 GCCGTTAGAGACCTCTTGCC 60.460 60.000 4.73 0.0 40.93 4.52 F
780 867 0.688487 TGTCCGTTTCCGAAATCCCT 59.312 50.000 0.00 0.0 35.63 4.20 F
977 1102 0.958091 TGGCGGGACACTGAATTTTG 59.042 50.000 0.00 0.0 0.00 2.44 F
1999 2128 1.005097 TCATGCTCAACAGGCCATTCT 59.995 47.619 5.01 0.0 0.00 2.40 F
2021 2150 0.413832 TCCTACCTCTCCTGTTGCCT 59.586 55.000 0.00 0.0 0.00 4.75 F
3220 3349 0.674895 AATCTGTTCGGTCCAGCAGC 60.675 55.000 0.00 0.0 0.00 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1683 1812 1.021390 GGAGTGGTGAACGATGCCTG 61.021 60.000 0.00 0.0 0.00 4.85 R
1999 2128 1.619977 GCAACAGGAGAGGTAGGAGGA 60.620 57.143 0.00 0.0 0.00 3.71 R
2021 2150 1.674441 CCTCGTAGACCTGCATCGTAA 59.326 52.381 0.00 0.0 0.00 3.18 R
3694 3823 0.175073 GCTTCCGTACCTCATCCGTT 59.825 55.000 0.00 0.0 0.00 4.44 R
3746 3877 0.944386 GAGAAAGAAACACGGCAGCA 59.056 50.000 0.00 0.0 0.00 4.41 R
5013 5201 0.183492 AGGCATATGAACACGGCCAT 59.817 50.000 6.97 0.0 46.96 4.40 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
17 18 2.503375 GACTACGCACACCCGACG 60.503 66.667 0.00 0.00 0.00 5.12
18 19 3.958822 GACTACGCACACCCGACGG 62.959 68.421 6.99 6.99 0.00 4.79
55 56 3.854669 CACAGGAGCGCCCCCTAG 61.855 72.222 17.29 13.89 34.66 3.02
56 57 4.075793 ACAGGAGCGCCCCCTAGA 62.076 66.667 17.29 0.00 34.66 2.43
57 58 3.230245 CAGGAGCGCCCCCTAGAG 61.230 72.222 17.29 3.68 34.66 2.43
58 59 4.548513 AGGAGCGCCCCCTAGAGG 62.549 72.222 16.36 0.00 34.66 3.69
59 60 4.541648 GGAGCGCCCCCTAGAGGA 62.542 72.222 2.29 0.00 38.24 3.71
60 61 2.915137 GAGCGCCCCCTAGAGGAG 60.915 72.222 2.29 0.00 38.24 3.69
61 62 3.742248 GAGCGCCCCCTAGAGGAGT 62.742 68.421 2.29 0.00 38.24 3.85
62 63 3.228017 GCGCCCCCTAGAGGAGTC 61.228 72.222 0.00 0.00 38.24 3.36
63 64 2.279073 CGCCCCCTAGAGGAGTCA 59.721 66.667 0.00 0.00 38.24 3.41
64 65 2.128507 CGCCCCCTAGAGGAGTCAC 61.129 68.421 0.00 0.00 38.24 3.67
65 66 1.311747 GCCCCCTAGAGGAGTCACT 59.688 63.158 0.00 0.00 38.24 3.41
66 67 0.757561 GCCCCCTAGAGGAGTCACTC 60.758 65.000 0.00 0.00 38.24 3.51
68 69 1.133606 CCCCCTAGAGGAGTCACTCTC 60.134 61.905 4.40 0.52 44.23 3.20
69 70 1.850345 CCCCTAGAGGAGTCACTCTCT 59.150 57.143 4.40 8.21 44.23 3.10
70 71 2.158667 CCCCTAGAGGAGTCACTCTCTC 60.159 59.091 4.40 9.68 44.23 3.20
71 72 2.507886 CCCTAGAGGAGTCACTCTCTCA 59.492 54.545 19.59 9.20 44.23 3.27
72 73 3.138283 CCCTAGAGGAGTCACTCTCTCAT 59.862 52.174 19.59 10.81 44.23 2.90
73 74 4.386312 CCCTAGAGGAGTCACTCTCTCATT 60.386 50.000 19.59 7.69 44.23 2.57
74 75 5.200483 CCTAGAGGAGTCACTCTCTCATTT 58.800 45.833 19.59 7.17 44.23 2.32
75 76 5.656416 CCTAGAGGAGTCACTCTCTCATTTT 59.344 44.000 19.59 6.91 44.23 1.82
76 77 6.154363 CCTAGAGGAGTCACTCTCTCATTTTT 59.846 42.308 19.59 6.64 44.23 1.94
77 78 7.340743 CCTAGAGGAGTCACTCTCTCATTTTTA 59.659 40.741 19.59 7.23 44.23 1.52
78 79 7.732222 AGAGGAGTCACTCTCTCATTTTTAT 57.268 36.000 19.59 1.54 44.23 1.40
79 80 8.144862 AGAGGAGTCACTCTCTCATTTTTATT 57.855 34.615 19.59 1.00 44.23 1.40
80 81 8.601546 AGAGGAGTCACTCTCTCATTTTTATTT 58.398 33.333 19.59 0.46 44.23 1.40
81 82 9.225436 GAGGAGTCACTCTCTCATTTTTATTTT 57.775 33.333 14.96 0.00 42.40 1.82
82 83 9.579932 AGGAGTCACTCTCTCATTTTTATTTTT 57.420 29.630 4.40 0.00 42.40 1.94
109 110 7.546250 TTTTTGAGAATAGGAGTCACTCTCT 57.454 36.000 4.40 0.00 42.40 3.10
110 111 6.767524 TTTGAGAATAGGAGTCACTCTCTC 57.232 41.667 12.78 12.78 42.40 3.20
111 112 5.443230 TGAGAATAGGAGTCACTCTCTCA 57.557 43.478 16.75 16.75 42.40 3.27
112 113 6.012337 TGAGAATAGGAGTCACTCTCTCAT 57.988 41.667 16.75 1.89 42.40 2.90
113 114 6.430864 TGAGAATAGGAGTCACTCTCTCATT 58.569 40.000 16.75 6.84 42.40 2.57
114 115 7.578203 TGAGAATAGGAGTCACTCTCTCATTA 58.422 38.462 16.75 0.10 42.40 1.90
115 116 8.224025 TGAGAATAGGAGTCACTCTCTCATTAT 58.776 37.037 16.75 4.82 42.40 1.28
116 117 8.635765 AGAATAGGAGTCACTCTCTCATTATC 57.364 38.462 4.40 0.00 42.40 1.75
117 118 8.448008 AGAATAGGAGTCACTCTCTCATTATCT 58.552 37.037 4.40 0.00 42.40 1.98
118 119 9.077885 GAATAGGAGTCACTCTCTCATTATCTT 57.922 37.037 4.40 0.00 42.40 2.40
119 120 9.432982 AATAGGAGTCACTCTCTCATTATCTTT 57.567 33.333 4.40 0.00 42.40 2.52
120 121 7.732222 AGGAGTCACTCTCTCATTATCTTTT 57.268 36.000 4.40 0.00 42.40 2.27
121 122 8.144862 AGGAGTCACTCTCTCATTATCTTTTT 57.855 34.615 4.40 0.00 42.40 1.94
204 205 3.050275 GCACACCGAGAAGCCCAC 61.050 66.667 0.00 0.00 0.00 4.61
229 230 3.316573 GAGAGAACCACGGCCCAGG 62.317 68.421 6.57 6.57 0.00 4.45
240 241 2.437895 GCCCAGGTAAACCCGCTC 60.438 66.667 0.00 0.00 38.74 5.03
388 436 3.124921 CGCGCCCACCGAGATTTT 61.125 61.111 0.00 0.00 39.21 1.82
545 616 1.657751 GCTGTTCCTGAATTCCGGGC 61.658 60.000 15.12 7.45 41.29 6.13
554 625 2.225791 GAATTCCGGGCTGGGTTTGC 62.226 60.000 13.58 0.00 38.76 3.68
600 683 2.452600 TCTGGGTTCTTGCCTTGTTT 57.547 45.000 0.00 0.00 0.00 2.83
602 685 1.756538 CTGGGTTCTTGCCTTGTTTGT 59.243 47.619 0.00 0.00 0.00 2.83
612 695 1.802508 GCCTTGTTTGTTCCTGTGTGC 60.803 52.381 0.00 0.00 0.00 4.57
643 726 1.000896 CGACCAATTTCCTGGCCCT 60.001 57.895 0.00 0.00 40.45 5.19
644 727 1.315257 CGACCAATTTCCTGGCCCTG 61.315 60.000 0.00 0.00 40.45 4.45
655 738 4.468689 GGCCCTGCCTCGGTACAC 62.469 72.222 0.00 0.00 46.69 2.90
699 782 0.955905 GCCGGTTAGGTTTCTTGCAA 59.044 50.000 1.90 0.00 43.70 4.08
702 785 2.607038 CCGGTTAGGTTTCTTGCAAAGC 60.607 50.000 0.00 0.00 38.53 3.51
709 792 1.985684 GTTTCTTGCAAAGCGTATGCC 59.014 47.619 2.51 0.00 45.70 4.40
717 800 2.627945 CAAAGCGTATGCCTAGTTCCA 58.372 47.619 2.51 0.00 44.31 3.53
724 807 6.717986 GCGTATGCCTAGTTCCAGGAACTT 62.718 50.000 35.06 21.31 41.68 2.66
731 814 2.509052 GTTCCAGGAACTTTGTTGCC 57.491 50.000 23.40 0.00 39.23 4.52
740 823 3.059120 GGAACTTTGTTGCCGTTAGAGAC 60.059 47.826 0.00 0.00 0.00 3.36
745 828 1.968493 TGTTGCCGTTAGAGACCTCTT 59.032 47.619 4.73 0.00 40.93 2.85
748 831 0.460459 GCCGTTAGAGACCTCTTGCC 60.460 60.000 4.73 0.00 40.93 4.52
752 835 2.796383 CGTTAGAGACCTCTTGCCGATG 60.796 54.545 4.73 0.00 40.93 3.84
753 836 0.747255 TAGAGACCTCTTGCCGATGC 59.253 55.000 4.73 0.00 40.93 3.91
758 845 2.203126 CTCTTGCCGATGCCCTCC 60.203 66.667 0.00 0.00 36.33 4.30
765 852 4.530857 CGATGCCCTCCCGTGTCC 62.531 72.222 0.00 0.00 0.00 4.02
775 862 1.594836 CCCGTGTCCGTTTCCGAAA 60.595 57.895 0.00 0.00 35.63 3.46
780 867 0.688487 TGTCCGTTTCCGAAATCCCT 59.312 50.000 0.00 0.00 35.63 4.20
785 899 2.095415 CCGTTTCCGAAATCCCTTGTTC 60.095 50.000 0.00 0.00 35.63 3.18
788 902 4.671766 CGTTTCCGAAATCCCTTGTTCATC 60.672 45.833 0.00 0.00 35.63 2.92
799 913 4.103153 TCCCTTGTTCATCTGTTCTTGTCT 59.897 41.667 0.00 0.00 0.00 3.41
803 917 6.367422 CCTTGTTCATCTGTTCTTGTCTACTC 59.633 42.308 0.00 0.00 0.00 2.59
814 928 3.899360 TCTTGTCTACTCCCCGAAGAAAA 59.101 43.478 0.00 0.00 0.00 2.29
815 929 3.672767 TGTCTACTCCCCGAAGAAAAC 57.327 47.619 0.00 0.00 0.00 2.43
816 930 2.967201 TGTCTACTCCCCGAAGAAAACA 59.033 45.455 0.00 0.00 0.00 2.83
907 1030 3.567164 AGGTCAACTTGCTGTCAGATTTG 59.433 43.478 3.32 0.86 0.00 2.32
916 1039 4.873817 TGCTGTCAGATTTGTTTTCATGG 58.126 39.130 3.32 0.00 0.00 3.66
917 1040 4.341806 TGCTGTCAGATTTGTTTTCATGGT 59.658 37.500 3.32 0.00 0.00 3.55
919 1042 5.754890 GCTGTCAGATTTGTTTTCATGGTTT 59.245 36.000 3.32 0.00 0.00 3.27
920 1043 6.258507 GCTGTCAGATTTGTTTTCATGGTTTT 59.741 34.615 3.32 0.00 0.00 2.43
921 1044 7.517259 GCTGTCAGATTTGTTTTCATGGTTTTC 60.517 37.037 3.32 0.00 0.00 2.29
923 1046 8.690884 TGTCAGATTTGTTTTCATGGTTTTCTA 58.309 29.630 0.00 0.00 0.00 2.10
924 1047 9.528018 GTCAGATTTGTTTTCATGGTTTTCTAA 57.472 29.630 0.00 0.00 0.00 2.10
977 1102 0.958091 TGGCGGGACACTGAATTTTG 59.042 50.000 0.00 0.00 0.00 2.44
996 1121 2.925724 TGAAATCACAACAGTCCCGTT 58.074 42.857 0.00 0.00 0.00 4.44
1170 1298 1.683385 CATGGCACGAGGATGTCTAGA 59.317 52.381 0.00 0.00 0.00 2.43
1185 1313 3.195591 TAGATCGAGAAGCCGCCGC 62.196 63.158 0.00 0.00 0.00 6.53
1215 1343 2.032681 AACGAGGAGCCAGCCAAC 59.967 61.111 0.00 0.00 0.00 3.77
1254 1382 1.920051 CATGTCGTTCTCATCCGCG 59.080 57.895 0.00 0.00 0.00 6.46
1257 1385 3.449227 TCGTTCTCATCCGCGGCT 61.449 61.111 23.51 8.48 0.00 5.52
1269 1397 3.420943 GCGGCTGCGAATAATGGT 58.579 55.556 0.00 0.00 0.00 3.55
1325 1453 2.500098 TCCCTGGTTCTTTCTATGACGG 59.500 50.000 0.00 0.00 0.00 4.79
1326 1454 2.236395 CCCTGGTTCTTTCTATGACGGT 59.764 50.000 0.00 0.00 0.00 4.83
1334 1462 4.433615 TCTTTCTATGACGGTTCTGATGC 58.566 43.478 0.00 0.00 0.00 3.91
1416 1544 7.498900 AGGAACGTTATGAATCTGATTGCATAA 59.501 33.333 19.67 19.67 32.54 1.90
1444 1572 5.605069 TCCCATATAGCTAGGCTGTTTTACA 59.395 40.000 0.00 0.00 40.10 2.41
1511 1639 7.048629 TGATCCATGCTAGTAAAGAGAAGAG 57.951 40.000 0.00 0.00 0.00 2.85
1512 1640 6.836007 TGATCCATGCTAGTAAAGAGAAGAGA 59.164 38.462 0.00 0.00 0.00 3.10
1513 1641 7.343057 TGATCCATGCTAGTAAAGAGAAGAGAA 59.657 37.037 0.00 0.00 0.00 2.87
1514 1642 7.106439 TCCATGCTAGTAAAGAGAAGAGAAG 57.894 40.000 0.00 0.00 0.00 2.85
1515 1643 6.892456 TCCATGCTAGTAAAGAGAAGAGAAGA 59.108 38.462 0.00 0.00 0.00 2.87
1526 1654 8.904099 AAAGAGAAGAGAAGAAACGGAAAATA 57.096 30.769 0.00 0.00 0.00 1.40
1527 1655 8.904099 AAGAGAAGAGAAGAAACGGAAAATAA 57.096 30.769 0.00 0.00 0.00 1.40
1616 1745 9.007901 GCTCATGAGGTATTTCTATAAATGCTT 57.992 33.333 23.89 0.00 37.70 3.91
1669 1798 4.717233 AAATGTTCAGTTTCAGTGCACA 57.283 36.364 21.04 0.00 29.87 4.57
1732 1861 7.605691 GCTTGTACTTGATATAATCTCATGCCT 59.394 37.037 0.00 0.00 0.00 4.75
1733 1862 9.499479 CTTGTACTTGATATAATCTCATGCCTT 57.501 33.333 0.00 0.00 0.00 4.35
1830 1959 8.678199 CAGTTCTACTGTATCAGTTGTCTGATA 58.322 37.037 19.87 12.14 46.81 2.15
1900 2029 1.026718 GGTCACCAGAAAGGCATCCG 61.027 60.000 0.00 0.00 43.14 4.18
1919 2048 4.350245 TCCGGTCTTAAGAGAATCCTCAA 58.650 43.478 5.12 0.00 41.87 3.02
1924 2053 7.934120 CCGGTCTTAAGAGAATCCTCAATAAAT 59.066 37.037 5.12 0.00 41.87 1.40
1930 2059 7.888250 AAGAGAATCCTCAATAAATGTTCCC 57.112 36.000 0.00 0.00 41.87 3.97
1993 2122 2.019249 TGCTATTCATGCTCAACAGGC 58.981 47.619 0.00 0.00 0.00 4.85
1996 2125 2.154567 ATTCATGCTCAACAGGCCAT 57.845 45.000 5.01 0.00 0.00 4.40
1999 2128 1.005097 TCATGCTCAACAGGCCATTCT 59.995 47.619 5.01 0.00 0.00 2.40
2021 2150 0.413832 TCCTACCTCTCCTGTTGCCT 59.586 55.000 0.00 0.00 0.00 4.75
2176 2305 1.693083 CGAATTCAAGACGTCCGCCC 61.693 60.000 13.01 0.00 0.00 6.13
2347 2476 9.213799 GATTACAGATCAGAAAGTATTCCATCC 57.786 37.037 0.00 0.00 36.12 3.51
2403 2532 6.222389 TGCAACCTTCAAAAGTTATTCATGG 58.778 36.000 0.00 0.00 0.00 3.66
2407 2536 5.539955 ACCTTCAAAAGTTATTCATGGTGCT 59.460 36.000 0.00 0.00 0.00 4.40
2492 2621 3.457610 TGCTTCAAAGGGCAAAAGAAG 57.542 42.857 0.00 0.00 38.88 2.85
2723 2852 4.082845 ACTTGAGATCAGAACTCGAAGGA 58.917 43.478 16.82 0.00 37.22 3.36
2978 3107 8.940768 AAAACTATCTGATGAGCTAGAGAAAC 57.059 34.615 0.00 0.00 0.00 2.78
3043 3172 3.510753 TGCATGCTCAATTTTCTAAGGCA 59.489 39.130 20.33 0.00 0.00 4.75
3220 3349 0.674895 AATCTGTTCGGTCCAGCAGC 60.675 55.000 0.00 0.00 0.00 5.25
3265 3394 2.616510 GGAACTCATCAGGTTGTCAGGG 60.617 54.545 0.00 0.00 0.00 4.45
3360 3489 6.462073 TGCACTCTTAAATCGTCTACAAAC 57.538 37.500 0.00 0.00 0.00 2.93
3437 3566 2.418368 AGTGGACAACTTGCAGAACA 57.582 45.000 0.00 0.00 34.57 3.18
3627 3756 1.889105 CAACCAGTGCTGTGCTCGT 60.889 57.895 0.00 0.00 0.00 4.18
3628 3757 1.153168 AACCAGTGCTGTGCTCGTT 60.153 52.632 0.00 0.00 0.00 3.85
3694 3823 2.912956 AGGTAGTCCTTTCATGGAGCAA 59.087 45.455 0.00 0.00 42.12 3.91
3723 3852 1.406887 GGTACGGAAGCACACATCCAT 60.407 52.381 0.00 0.00 33.01 3.41
3767 3898 1.604278 GCTGCCGTGTTTCTTTCTCTT 59.396 47.619 0.00 0.00 0.00 2.85
3798 3929 5.567138 AGAACCATGGATTTGATTTCGAC 57.433 39.130 21.47 0.00 0.00 4.20
3810 3941 2.288518 TGATTTCGACGGTCACATGTCA 60.289 45.455 9.10 2.99 34.78 3.58
3827 3958 8.081633 TCACATGTCATTGTAATGTTTTTCTCC 58.918 33.333 0.00 0.00 37.65 3.71
3869 4000 1.658994 TATAAGGAAACCGCGGCTTG 58.341 50.000 28.58 0.59 0.00 4.01
3870 4001 0.322187 ATAAGGAAACCGCGGCTTGT 60.322 50.000 28.58 15.70 0.00 3.16
3873 4004 2.251371 GAAACCGCGGCTTGTGAC 59.749 61.111 28.58 3.08 0.00 3.67
3878 4010 1.082104 CCGCGGCTTGTGACTTTTC 60.082 57.895 14.67 0.00 0.00 2.29
3939 4071 9.034544 AGCTGCTTAAACTTTTATGAAAACTTG 57.965 29.630 0.00 0.00 0.00 3.16
3982 4115 1.376543 AAGCACGCATTCCATGAGAG 58.623 50.000 0.00 0.00 34.01 3.20
4017 4151 1.949525 TGCTGCTGTGTTTCTTTCTCC 59.050 47.619 0.00 0.00 0.00 3.71
4048 4182 7.922811 GGATAAAACAAGAACCATGGATTGATC 59.077 37.037 21.47 16.03 0.00 2.92
4050 4184 6.521151 AAACAAGAACCATGGATTGATCTC 57.479 37.500 21.47 3.03 0.00 2.75
4182 4346 6.703165 CCAAATCAGAAGCTGCTTAAACTTTT 59.297 34.615 15.95 9.00 0.00 2.27
4183 4347 7.867403 CCAAATCAGAAGCTGCTTAAACTTTTA 59.133 33.333 15.95 0.00 0.00 1.52
4184 4348 9.248291 CAAATCAGAAGCTGCTTAAACTTTTAA 57.752 29.630 15.95 0.00 0.00 1.52
4185 4349 9.987272 AAATCAGAAGCTGCTTAAACTTTTAAT 57.013 25.926 15.95 0.00 32.69 1.40
4186 4350 8.976986 ATCAGAAGCTGCTTAAACTTTTAATG 57.023 30.769 15.95 2.40 32.69 1.90
4187 4351 8.165239 TCAGAAGCTGCTTAAACTTTTAATGA 57.835 30.769 15.95 4.51 32.69 2.57
4188 4352 8.292448 TCAGAAGCTGCTTAAACTTTTAATGAG 58.708 33.333 15.95 0.00 32.69 2.90
4227 4391 8.138928 TCAGTATCATCGATCCAATATTCCTT 57.861 34.615 0.00 0.00 0.00 3.36
4230 4394 9.442047 AGTATCATCGATCCAATATTCCTTTTC 57.558 33.333 0.00 0.00 0.00 2.29
4233 4397 8.383318 TCATCGATCCAATATTCCTTTTCTTC 57.617 34.615 0.00 0.00 0.00 2.87
4234 4398 8.213679 TCATCGATCCAATATTCCTTTTCTTCT 58.786 33.333 0.00 0.00 0.00 2.85
4237 4401 9.243105 TCGATCCAATATTCCTTTTCTTCTTTT 57.757 29.630 0.00 0.00 0.00 2.27
4238 4402 9.508567 CGATCCAATATTCCTTTTCTTCTTTTC 57.491 33.333 0.00 0.00 0.00 2.29
4295 4459 5.485353 TGAAAGAGGAGGCTCTTCTGAATAA 59.515 40.000 27.32 9.56 42.26 1.40
4462 4626 5.392057 GCTAAACATTTGGAGCTTCAGGTAC 60.392 44.000 0.00 0.00 32.04 3.34
4463 4627 4.373156 AACATTTGGAGCTTCAGGTACT 57.627 40.909 0.00 0.00 43.88 2.73
4464 4628 4.373156 ACATTTGGAGCTTCAGGTACTT 57.627 40.909 0.00 0.00 34.60 2.24
4465 4629 5.499004 ACATTTGGAGCTTCAGGTACTTA 57.501 39.130 0.00 0.00 34.60 2.24
4466 4630 5.876357 ACATTTGGAGCTTCAGGTACTTAA 58.124 37.500 0.00 0.00 34.60 1.85
4467 4631 6.485171 ACATTTGGAGCTTCAGGTACTTAAT 58.515 36.000 0.00 0.00 34.60 1.40
4469 4633 7.121315 ACATTTGGAGCTTCAGGTACTTAATTC 59.879 37.037 0.00 0.00 34.60 2.17
4471 4635 6.374417 TGGAGCTTCAGGTACTTAATTCTT 57.626 37.500 0.00 0.00 34.60 2.52
4472 4636 6.779860 TGGAGCTTCAGGTACTTAATTCTTT 58.220 36.000 0.00 0.00 34.60 2.52
4473 4637 7.231467 TGGAGCTTCAGGTACTTAATTCTTTT 58.769 34.615 0.00 0.00 34.60 2.27
4496 4681 2.026262 GCCTGGTAGAAGGTGGATTTGA 60.026 50.000 0.00 0.00 39.75 2.69
4503 4688 8.348285 TGGTAGAAGGTGGATTTGAAAAATAG 57.652 34.615 0.00 0.00 0.00 1.73
4567 4752 5.666462 TCTGCAGCCTGTATATTTTTCGTA 58.334 37.500 9.47 0.00 0.00 3.43
4614 4800 3.936372 TCGAAGAAAGACGAGTCCATT 57.064 42.857 0.00 0.00 34.49 3.16
4776 4962 2.717809 GGTCGCGTCGCTGAAGAAC 61.718 63.158 16.36 3.77 0.00 3.01
4905 5091 0.250684 TGAAGCAGTTCGGCATGGAA 60.251 50.000 0.00 0.00 35.17 3.53
4943 5130 3.565482 TGCACAGAGGAAAGTAAGCAAAG 59.435 43.478 0.00 0.00 0.00 2.77
4944 5131 3.057946 GCACAGAGGAAAGTAAGCAAAGG 60.058 47.826 0.00 0.00 0.00 3.11
4945 5132 3.503748 CACAGAGGAAAGTAAGCAAAGGG 59.496 47.826 0.00 0.00 0.00 3.95
4946 5133 2.489722 CAGAGGAAAGTAAGCAAAGGGC 59.510 50.000 0.00 0.00 45.30 5.19
5013 5201 9.492730 TTTCACCTGCATGGATAGATATATAGA 57.507 33.333 8.91 0.00 39.71 1.98
5049 5252 5.931441 ATGCCTTTATCGCAGTATCTTTC 57.069 39.130 0.00 0.00 40.15 2.62
5056 5259 7.306283 CCTTTATCGCAGTATCTTTCTTTCGAG 60.306 40.741 0.00 0.00 0.00 4.04
5139 5347 7.323656 CGAAGTTTGCTGTATCTTTTGTAAAGG 59.676 37.037 0.00 0.00 0.00 3.11
5182 5390 2.820037 GCCTTGCCGTGCCTACTC 60.820 66.667 0.00 0.00 0.00 2.59
5195 5403 3.995048 GTGCCTACTCAAGTTTCTGTACC 59.005 47.826 0.00 0.00 0.00 3.34
5196 5404 3.251571 GCCTACTCAAGTTTCTGTACCG 58.748 50.000 0.00 0.00 0.00 4.02
5362 5573 2.515854 AGTACATCTGTCACCGACTGT 58.484 47.619 0.00 0.00 34.05 3.55
5367 5578 3.701542 ACATCTGTCACCGACTGTATGAT 59.298 43.478 14.25 0.00 34.05 2.45
5368 5579 3.782889 TCTGTCACCGACTGTATGATG 57.217 47.619 0.00 0.00 34.05 3.07
5370 5581 3.761752 TCTGTCACCGACTGTATGATGAA 59.238 43.478 0.00 0.00 34.05 2.57
5424 5649 9.836864 AATATGTAGATGATAATGTGTGTGTGT 57.163 29.630 0.00 0.00 0.00 3.72
5426 5651 6.463360 TGTAGATGATAATGTGTGTGTGTGT 58.537 36.000 0.00 0.00 0.00 3.72
5427 5652 5.868043 AGATGATAATGTGTGTGTGTGTG 57.132 39.130 0.00 0.00 0.00 3.82
5431 5700 4.272261 TGATAATGTGTGTGTGTGTGTGTC 59.728 41.667 0.00 0.00 0.00 3.67
5497 5767 4.464951 CCTGGTTACTGTACACATGGACTA 59.535 45.833 0.00 0.00 0.00 2.59
5501 5771 1.831736 ACTGTACACATGGACTAGGCC 59.168 52.381 8.06 8.06 0.00 5.19
5542 5924 8.006741 ACTTTTCATTTGTCACGATTTATTGC 57.993 30.769 0.00 0.00 0.00 3.56
5543 5925 6.942886 TTTCATTTGTCACGATTTATTGCC 57.057 33.333 0.00 0.00 0.00 4.52
5544 5926 5.895636 TCATTTGTCACGATTTATTGCCT 57.104 34.783 0.00 0.00 0.00 4.75
5545 5927 5.879237 TCATTTGTCACGATTTATTGCCTC 58.121 37.500 0.00 0.00 0.00 4.70
5571 5953 3.891366 AGTGGAGGTTGATGTTTCTTTGG 59.109 43.478 0.00 0.00 0.00 3.28
5630 6012 2.808543 GTTTGCAAGTGAGAGGTACCAG 59.191 50.000 15.94 0.00 0.00 4.00
5698 6083 7.423199 TGTTCTGGATAATACGATCTGTGTAC 58.577 38.462 0.00 0.00 0.00 2.90
5700 6085 6.066032 TCTGGATAATACGATCTGTGTACCA 58.934 40.000 0.00 0.00 0.00 3.25
5719 6112 3.245730 ACCAATCCATCACCACAAGGAAT 60.246 43.478 0.00 0.00 38.69 3.01
5720 6113 3.770933 CCAATCCATCACCACAAGGAATT 59.229 43.478 0.00 0.00 38.69 2.17
5721 6114 4.223477 CCAATCCATCACCACAAGGAATTT 59.777 41.667 0.00 0.00 38.69 1.82
5835 6248 3.402691 ATCACGCGAGCTCTGACCG 62.403 63.158 15.93 11.20 0.00 4.79
5902 6316 2.446848 CCATGAGAGGTGCCCGGAT 61.447 63.158 0.73 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.503375 CGTCGGGTGTGCGTAGTC 60.503 66.667 0.00 0.00 0.00 2.59
1 2 4.047059 CCGTCGGGTGTGCGTAGT 62.047 66.667 2.34 0.00 0.00 2.73
2 3 4.789075 CCCGTCGGGTGTGCGTAG 62.789 72.222 23.02 0.00 38.25 3.51
38 39 3.854669 CTAGGGGGCGCTCCTGTG 61.855 72.222 28.78 12.48 35.92 3.66
39 40 4.075793 TCTAGGGGGCGCTCCTGT 62.076 66.667 28.78 16.91 35.92 4.00
40 41 3.230245 CTCTAGGGGGCGCTCCTG 61.230 72.222 28.78 16.87 35.92 3.86
41 42 4.548513 CCTCTAGGGGGCGCTCCT 62.549 72.222 28.78 24.83 38.36 3.69
42 43 4.541648 TCCTCTAGGGGGCGCTCC 62.542 72.222 21.29 21.29 35.41 4.70
43 44 2.915137 CTCCTCTAGGGGGCGCTC 60.915 72.222 9.36 1.18 35.41 5.03
44 45 3.742248 GACTCCTCTAGGGGGCGCT 62.742 68.421 9.36 0.00 41.02 5.92
45 46 3.228017 GACTCCTCTAGGGGGCGC 61.228 72.222 9.36 0.00 41.02 6.53
47 48 0.757561 GAGTGACTCCTCTAGGGGGC 60.758 65.000 9.36 0.00 46.86 5.80
48 49 0.930726 AGAGTGACTCCTCTAGGGGG 59.069 60.000 9.36 1.82 41.02 5.40
49 50 1.850345 AGAGAGTGACTCCTCTAGGGG 59.150 57.143 9.33 0.52 45.96 4.79
50 51 2.507886 TGAGAGAGTGACTCCTCTAGGG 59.492 54.545 22.61 0.00 45.96 3.53
51 52 3.924114 TGAGAGAGTGACTCCTCTAGG 57.076 52.381 22.61 0.00 45.96 3.02
52 53 6.773976 AAAATGAGAGAGTGACTCCTCTAG 57.226 41.667 22.61 0.00 45.96 2.43
53 54 8.830915 ATAAAAATGAGAGAGTGACTCCTCTA 57.169 34.615 22.61 14.17 45.96 2.43
54 55 7.732222 ATAAAAATGAGAGAGTGACTCCTCT 57.268 36.000 22.61 17.94 45.96 3.69
55 56 8.785329 AAATAAAAATGAGAGAGTGACTCCTC 57.215 34.615 18.30 18.30 45.96 3.71
56 57 9.579932 AAAAATAAAAATGAGAGAGTGACTCCT 57.420 29.630 9.33 6.14 45.96 3.69
85 86 7.233553 TGAGAGAGTGACTCCTATTCTCAAAAA 59.766 37.037 22.32 6.55 45.96 1.94
86 87 6.721668 TGAGAGAGTGACTCCTATTCTCAAAA 59.278 38.462 22.32 6.82 45.96 2.44
87 88 6.249192 TGAGAGAGTGACTCCTATTCTCAAA 58.751 40.000 22.32 7.37 45.96 2.69
88 89 5.821097 TGAGAGAGTGACTCCTATTCTCAA 58.179 41.667 22.32 11.27 45.96 3.02
89 90 5.443230 TGAGAGAGTGACTCCTATTCTCA 57.557 43.478 21.31 21.31 45.96 3.27
90 91 6.959639 AATGAGAGAGTGACTCCTATTCTC 57.040 41.667 17.70 17.70 45.96 2.87
91 92 8.448008 AGATAATGAGAGAGTGACTCCTATTCT 58.552 37.037 9.33 5.36 45.96 2.40
92 93 8.635765 AGATAATGAGAGAGTGACTCCTATTC 57.364 38.462 9.33 0.00 45.96 1.75
93 94 9.432982 AAAGATAATGAGAGAGTGACTCCTATT 57.567 33.333 9.33 7.55 45.96 1.73
94 95 9.432982 AAAAGATAATGAGAGAGTGACTCCTAT 57.567 33.333 9.33 0.00 45.96 2.57
95 96 8.830915 AAAAGATAATGAGAGAGTGACTCCTA 57.169 34.615 9.33 0.00 45.96 2.94
96 97 7.732222 AAAAGATAATGAGAGAGTGACTCCT 57.268 36.000 9.33 6.14 45.96 3.69
119 120 4.695455 CGAGATTGACTCCTTGCCTAAAAA 59.305 41.667 0.00 0.00 42.18 1.94
120 121 4.020573 TCGAGATTGACTCCTTGCCTAAAA 60.021 41.667 0.00 0.00 42.18 1.52
121 122 3.513912 TCGAGATTGACTCCTTGCCTAAA 59.486 43.478 0.00 0.00 42.18 1.85
122 123 3.096852 TCGAGATTGACTCCTTGCCTAA 58.903 45.455 0.00 0.00 42.18 2.69
123 124 2.735151 TCGAGATTGACTCCTTGCCTA 58.265 47.619 0.00 0.00 42.18 3.93
124 125 1.561643 TCGAGATTGACTCCTTGCCT 58.438 50.000 0.00 0.00 42.18 4.75
125 126 2.386661 TTCGAGATTGACTCCTTGCC 57.613 50.000 0.00 0.00 42.18 4.52
126 127 2.869192 GGATTCGAGATTGACTCCTTGC 59.131 50.000 0.31 0.00 42.18 4.01
127 128 4.367450 GAGGATTCGAGATTGACTCCTTG 58.633 47.826 9.66 0.00 45.14 3.61
128 129 3.386402 GGAGGATTCGAGATTGACTCCTT 59.614 47.826 9.66 0.00 45.14 3.36
130 131 2.695666 TGGAGGATTCGAGATTGACTCC 59.304 50.000 0.00 0.00 42.18 3.85
131 132 3.798548 GCTGGAGGATTCGAGATTGACTC 60.799 52.174 0.00 0.00 41.79 3.36
132 133 2.102252 GCTGGAGGATTCGAGATTGACT 59.898 50.000 0.00 0.00 31.39 3.41
133 134 2.478831 GCTGGAGGATTCGAGATTGAC 58.521 52.381 0.00 0.00 31.39 3.18
134 135 1.067669 CGCTGGAGGATTCGAGATTGA 59.932 52.381 0.00 0.00 31.39 2.57
135 136 1.495878 CGCTGGAGGATTCGAGATTG 58.504 55.000 0.00 0.00 31.39 2.67
136 137 0.249657 GCGCTGGAGGATTCGAGATT 60.250 55.000 0.00 0.00 31.39 2.40
137 138 1.365633 GCGCTGGAGGATTCGAGAT 59.634 57.895 0.00 0.00 31.39 2.75
138 139 2.808315 GCGCTGGAGGATTCGAGA 59.192 61.111 0.00 0.00 31.39 4.04
139 140 2.656651 CGCGCTGGAGGATTCGAG 60.657 66.667 5.56 0.00 32.80 4.04
158 159 0.240945 GGCTGCGTGTGCTTAAATGT 59.759 50.000 0.00 0.00 43.34 2.71
186 187 4.680237 TGGGCTTCTCGGTGTGCG 62.680 66.667 0.00 0.00 0.00 5.34
190 191 4.410400 GGGGTGGGCTTCTCGGTG 62.410 72.222 0.00 0.00 0.00 4.94
192 193 4.410400 GTGGGGTGGGCTTCTCGG 62.410 72.222 0.00 0.00 0.00 4.63
204 205 2.663196 GTGGTTCTCTCGGTGGGG 59.337 66.667 0.00 0.00 0.00 4.96
229 230 1.673337 GTGTGGGGAGCGGGTTTAC 60.673 63.158 0.00 0.00 0.00 2.01
240 241 2.352032 GGAGGAGACGAGTGTGGGG 61.352 68.421 0.00 0.00 0.00 4.96
318 319 3.508840 CAGCGGATTTGCGGGGAC 61.509 66.667 0.00 0.00 40.67 4.46
545 616 1.228675 AGGGAAGCAGCAAACCCAG 60.229 57.895 19.22 0.00 44.25 4.45
554 625 2.186384 CTCCGAGCAGGGAAGCAG 59.814 66.667 0.00 0.00 41.52 4.24
600 683 2.158682 AGGTTACATGCACACAGGAACA 60.159 45.455 0.00 0.00 0.00 3.18
602 685 2.158682 ACAGGTTACATGCACACAGGAA 60.159 45.455 0.00 0.00 0.00 3.36
612 695 5.371115 AAATTGGTCGAACAGGTTACATG 57.629 39.130 2.09 0.00 0.00 3.21
671 754 4.832608 CTAACCGGCGTGCCCTCC 62.833 72.222 6.01 0.00 0.00 4.30
672 755 4.832608 CCTAACCGGCGTGCCCTC 62.833 72.222 6.01 0.00 0.00 4.30
674 757 4.710167 AACCTAACCGGCGTGCCC 62.710 66.667 6.01 0.00 35.61 5.36
699 782 1.139058 CCTGGAACTAGGCATACGCTT 59.861 52.381 0.00 0.00 38.60 4.68
702 785 2.822764 GTTCCTGGAACTAGGCATACG 58.177 52.381 28.07 0.00 39.23 3.06
717 800 3.139077 CTCTAACGGCAACAAAGTTCCT 58.861 45.455 0.00 0.00 0.00 3.36
724 807 1.968493 AGAGGTCTCTAACGGCAACAA 59.032 47.619 0.00 0.00 38.35 2.83
731 814 0.809385 TCGGCAAGAGGTCTCTAACG 59.191 55.000 0.43 6.72 39.39 3.18
740 823 2.203126 GAGGGCATCGGCAAGAGG 60.203 66.667 0.00 0.00 43.71 3.69
748 831 4.530857 GGACACGGGAGGGCATCG 62.531 72.222 0.00 0.00 35.95 3.84
752 835 4.324991 AAACGGACACGGGAGGGC 62.325 66.667 0.00 0.00 46.48 5.19
753 836 2.047560 GAAACGGACACGGGAGGG 60.048 66.667 0.00 0.00 46.48 4.30
767 854 4.458989 CAGATGAACAAGGGATTTCGGAAA 59.541 41.667 5.52 5.52 0.00 3.13
775 862 4.990526 ACAAGAACAGATGAACAAGGGAT 58.009 39.130 0.00 0.00 0.00 3.85
780 867 6.223852 GGAGTAGACAAGAACAGATGAACAA 58.776 40.000 0.00 0.00 0.00 2.83
785 899 3.429547 CGGGGAGTAGACAAGAACAGATG 60.430 52.174 0.00 0.00 0.00 2.90
788 902 2.168496 TCGGGGAGTAGACAAGAACAG 58.832 52.381 0.00 0.00 0.00 3.16
799 913 4.975631 TCAATTGTTTTCTTCGGGGAGTA 58.024 39.130 5.13 0.00 0.00 2.59
803 917 4.690280 CCAAATCAATTGTTTTCTTCGGGG 59.310 41.667 10.82 5.72 37.32 5.73
814 928 3.259876 AGATGCTGCACCAAATCAATTGT 59.740 39.130 3.57 0.00 37.32 2.71
815 929 3.616821 CAGATGCTGCACCAAATCAATTG 59.383 43.478 3.57 0.00 38.84 2.32
816 930 3.369052 CCAGATGCTGCACCAAATCAATT 60.369 43.478 3.57 0.00 0.00 2.32
847 968 1.202405 GGTTGGCCCGCAAATAGATTG 60.202 52.381 0.00 0.00 42.21 2.67
861 982 4.211164 GCTGAAATAAAAACACTGGTTGGC 59.789 41.667 0.00 0.00 37.30 4.52
862 983 5.355596 TGCTGAAATAAAAACACTGGTTGG 58.644 37.500 0.00 0.00 37.30 3.77
907 1030 6.922957 TGCACAGATTAGAAAACCATGAAAAC 59.077 34.615 0.00 0.00 0.00 2.43
916 1039 5.351465 TCGGATCTTGCACAGATTAGAAAAC 59.649 40.000 11.18 0.48 42.92 2.43
917 1040 5.487433 TCGGATCTTGCACAGATTAGAAAA 58.513 37.500 11.18 0.00 42.92 2.29
919 1042 4.736126 TCGGATCTTGCACAGATTAGAA 57.264 40.909 11.18 0.00 42.92 2.10
920 1043 4.262207 GGATCGGATCTTGCACAGATTAGA 60.262 45.833 16.96 12.61 42.92 2.10
921 1044 3.993081 GGATCGGATCTTGCACAGATTAG 59.007 47.826 16.96 9.12 42.92 1.73
923 1046 2.171237 TGGATCGGATCTTGCACAGATT 59.829 45.455 16.96 0.00 42.92 2.40
924 1047 1.764723 TGGATCGGATCTTGCACAGAT 59.235 47.619 16.96 10.07 45.86 2.90
929 1054 0.180878 TGCATGGATCGGATCTTGCA 59.819 50.000 28.70 28.70 42.04 4.08
977 1102 4.753107 TCTTAACGGGACTGTTGTGATTTC 59.247 41.667 6.78 0.00 33.32 2.17
996 1121 9.155975 CCGAAGAAAAAGAATCTTCTCATCTTA 57.844 33.333 12.78 0.00 46.81 2.10
1067 1195 0.179179 GTTCTTGCTCTTGCCATCGC 60.179 55.000 0.00 0.00 38.71 4.58
1152 1280 1.957177 GATCTAGACATCCTCGTGCCA 59.043 52.381 0.00 0.00 0.00 4.92
1156 1284 3.755112 TCTCGATCTAGACATCCTCGT 57.245 47.619 11.35 0.00 0.00 4.18
1158 1286 3.190535 GGCTTCTCGATCTAGACATCCTC 59.809 52.174 0.00 0.00 0.00 3.71
1185 1313 2.048222 TCGTTGCTCAGCCTTCCG 60.048 61.111 0.00 0.00 0.00 4.30
1215 1343 2.186384 CTCCTGAGCTGCTTCGGG 59.814 66.667 16.26 16.26 43.72 5.14
1254 1382 1.953559 TCAGACCATTATTCGCAGCC 58.046 50.000 0.00 0.00 0.00 4.85
1257 1385 3.904800 TCCTTCAGACCATTATTCGCA 57.095 42.857 0.00 0.00 0.00 5.10
1260 1388 4.766375 TCCGTTCCTTCAGACCATTATTC 58.234 43.478 0.00 0.00 0.00 1.75
1263 1391 2.093658 GCTCCGTTCCTTCAGACCATTA 60.094 50.000 0.00 0.00 0.00 1.90
1265 1393 0.250513 GCTCCGTTCCTTCAGACCAT 59.749 55.000 0.00 0.00 0.00 3.55
1269 1397 2.353803 GCTAAAGCTCCGTTCCTTCAGA 60.354 50.000 0.00 0.00 38.21 3.27
1344 1472 2.607187 ACTTACTTGACATCTTCGGCG 58.393 47.619 0.00 0.00 0.00 6.46
1395 1523 9.964253 GAGTATTATGCAATCAGATTCATAACG 57.036 33.333 19.60 2.44 35.17 3.18
1416 1544 5.213868 ACAGCCTAGCTATATGGGAGTAT 57.786 43.478 0.00 0.00 36.40 2.12
1419 1547 4.899352 AAACAGCCTAGCTATATGGGAG 57.101 45.455 0.00 0.00 36.40 4.30
1444 1572 9.295825 TCAATAACAAATACTGGTTTGATCACT 57.704 29.630 12.65 0.00 40.64 3.41
1669 1798 1.624336 TGCCTGAAAGAAAGCTGCAT 58.376 45.000 1.02 0.00 34.07 3.96
1683 1812 1.021390 GGAGTGGTGAACGATGCCTG 61.021 60.000 0.00 0.00 0.00 4.85
1769 1898 7.472334 AATGGAGCTCAAACACAAGATAATT 57.528 32.000 17.19 0.00 0.00 1.40
1770 1899 7.472334 AAATGGAGCTCAAACACAAGATAAT 57.528 32.000 17.19 0.00 0.00 1.28
1771 1900 6.899393 AAATGGAGCTCAAACACAAGATAA 57.101 33.333 17.19 0.00 0.00 1.75
1772 1901 6.899393 AAAATGGAGCTCAAACACAAGATA 57.101 33.333 17.19 0.00 0.00 1.98
1773 1902 5.796424 AAAATGGAGCTCAAACACAAGAT 57.204 34.783 17.19 0.00 0.00 2.40
1900 2029 9.620259 ACATTTATTGAGGATTCTCTTAAGACC 57.380 33.333 0.00 1.19 40.58 3.85
1919 2048 6.269769 ACTGAACATGGTTTGGGAACATTTAT 59.730 34.615 0.00 0.00 42.32 1.40
1924 2053 2.955660 GACTGAACATGGTTTGGGAACA 59.044 45.455 0.00 0.00 37.51 3.18
1930 2059 2.862541 TCCAGGACTGAACATGGTTTG 58.137 47.619 0.00 0.00 41.63 2.93
1993 2122 2.178984 AGGAGAGGTAGGAGGAGAATGG 59.821 54.545 0.00 0.00 0.00 3.16
1996 2125 2.289467 ACAGGAGAGGTAGGAGGAGAA 58.711 52.381 0.00 0.00 0.00 2.87
1999 2128 1.619977 GCAACAGGAGAGGTAGGAGGA 60.620 57.143 0.00 0.00 0.00 3.71
2021 2150 1.674441 CCTCGTAGACCTGCATCGTAA 59.326 52.381 0.00 0.00 0.00 3.18
2105 2234 4.267536 CTCAGCTTCTCATTTTGGATGGA 58.732 43.478 0.00 0.00 0.00 3.41
2176 2305 2.159382 GGCATTGTATAATGGGGTCGG 58.841 52.381 13.35 0.00 43.12 4.79
2338 2467 9.255029 TCATAGATATCTTCAACGGATGGAATA 57.745 33.333 11.25 0.00 0.00 1.75
2347 2476 8.090831 TGGAAATCCTCATAGATATCTTCAACG 58.909 37.037 11.25 0.00 36.82 4.10
2403 2532 5.302568 TGATCATGAAAATATTGGGGAGCAC 59.697 40.000 0.00 0.00 0.00 4.40
2492 2621 8.315482 AGAAGGAGTTATAAACCTCTCTTCAAC 58.685 37.037 20.93 8.45 33.16 3.18
2723 2852 4.424842 ACTTCAGTCTTCTCCTTCTCCAT 58.575 43.478 0.00 0.00 0.00 3.41
3043 3172 4.293494 TGATATGTTCCTTCTCCTCTGCT 58.707 43.478 0.00 0.00 0.00 4.24
3220 3349 5.193663 TCTGCATCCTATTCTTTCTCTCG 57.806 43.478 0.00 0.00 0.00 4.04
3226 3355 6.011122 AGTTCCATCTGCATCCTATTCTTT 57.989 37.500 0.00 0.00 0.00 2.52
3256 3385 1.302832 CTGCTCCACCCCTGACAAC 60.303 63.158 0.00 0.00 0.00 3.32
3265 3394 1.338579 CCTCTCAACTTCTGCTCCACC 60.339 57.143 0.00 0.00 0.00 4.61
3360 3489 4.796038 AAGCTTGATCCATTTTCAGTGG 57.204 40.909 0.00 0.00 38.11 4.00
3436 3565 1.065401 TCAAGCAACGACAAGCCTTTG 59.935 47.619 0.00 0.00 40.24 2.77
3437 3566 1.388547 TCAAGCAACGACAAGCCTTT 58.611 45.000 0.00 0.00 0.00 3.11
3683 3812 2.358957 CTCATCCGTTTGCTCCATGAA 58.641 47.619 0.00 0.00 0.00 2.57
3694 3823 0.175073 GCTTCCGTACCTCATCCGTT 59.825 55.000 0.00 0.00 0.00 4.44
3745 3876 1.537202 GAGAAAGAAACACGGCAGCAT 59.463 47.619 0.00 0.00 0.00 3.79
3746 3877 0.944386 GAGAAAGAAACACGGCAGCA 59.056 50.000 0.00 0.00 0.00 4.41
3767 3898 6.259893 TCAAATCCATGGTTCTTATCCCAAA 58.740 36.000 12.58 0.00 33.66 3.28
3798 3929 4.944962 ACATTACAATGACATGTGACCG 57.055 40.909 1.15 0.00 39.67 4.79
3810 3941 5.957842 TGCTCGGAGAAAAACATTACAAT 57.042 34.783 9.69 0.00 34.09 2.71
3903 4035 6.884280 AAGTTTAAGCAGCTACTGATTTGT 57.116 33.333 3.17 0.00 36.68 2.83
3938 4070 7.851387 TCGTACCAAATAGCATAACATTTCA 57.149 32.000 0.00 0.00 0.00 2.69
3939 4071 9.221775 CTTTCGTACCAAATAGCATAACATTTC 57.778 33.333 0.00 0.00 0.00 2.17
3944 4076 5.963586 GTGCTTTCGTACCAAATAGCATAAC 59.036 40.000 3.41 0.00 40.32 1.89
3950 4082 2.413796 TGCGTGCTTTCGTACCAAATAG 59.586 45.455 0.00 0.00 0.00 1.73
3954 4086 1.195900 GAATGCGTGCTTTCGTACCAA 59.804 47.619 4.95 0.00 0.00 3.67
3982 4115 6.532657 ACACAGCAGCATAATGAAAAATAAGC 59.467 34.615 0.00 0.00 0.00 3.09
4017 4151 5.391950 CCATGGTTCTTGTTTTATCCAGACG 60.392 44.000 2.57 0.00 0.00 4.18
4048 4182 7.918033 ACATTATAAAGACATGTGACTCTCGAG 59.082 37.037 1.15 5.93 29.74 4.04
4050 4184 7.993821 ACATTATAAAGACATGTGACTCTCG 57.006 36.000 1.15 0.00 29.74 4.04
4108 4242 5.930837 AAAAACTGAAGTCATGGTTTCCA 57.069 34.783 0.00 0.00 38.19 3.53
4145 4279 5.733655 GCTTCTGATTTGGCTCATCTCATTG 60.734 44.000 0.00 0.00 0.00 2.82
4147 4281 3.884091 GCTTCTGATTTGGCTCATCTCAT 59.116 43.478 0.00 0.00 0.00 2.90
4184 4348 9.288576 TGATACTGAAACATTTTGAGTTCTCAT 57.711 29.630 3.28 0.00 0.00 2.90
4185 4349 8.675705 TGATACTGAAACATTTTGAGTTCTCA 57.324 30.769 0.00 0.00 0.00 3.27
4186 4350 9.766277 GATGATACTGAAACATTTTGAGTTCTC 57.234 33.333 0.00 0.00 0.00 2.87
4187 4351 8.446273 CGATGATACTGAAACATTTTGAGTTCT 58.554 33.333 0.00 0.00 0.00 3.01
4188 4352 8.443160 TCGATGATACTGAAACATTTTGAGTTC 58.557 33.333 0.00 0.00 0.00 3.01
4263 4427 3.481453 AGCCTCCTCTTTCAGTTTGAAC 58.519 45.455 0.00 0.00 35.89 3.18
4278 4442 6.045955 CAGTACTTTATTCAGAAGAGCCTCC 58.954 44.000 0.00 0.00 0.00 4.30
4295 4459 4.137543 CAAAAGTGCCTCCTTCAGTACTT 58.862 43.478 0.00 0.00 32.00 2.24
4462 4626 7.039714 ACCTTCTACCAGGCAAAAAGAATTAAG 60.040 37.037 0.00 0.00 37.47 1.85
4463 4627 6.780522 ACCTTCTACCAGGCAAAAAGAATTAA 59.219 34.615 0.00 0.00 37.47 1.40
4464 4628 6.208599 CACCTTCTACCAGGCAAAAAGAATTA 59.791 38.462 0.00 0.00 37.47 1.40
4465 4629 5.011023 CACCTTCTACCAGGCAAAAAGAATT 59.989 40.000 0.00 0.00 37.47 2.17
4466 4630 4.524328 CACCTTCTACCAGGCAAAAAGAAT 59.476 41.667 0.00 0.00 37.47 2.40
4467 4631 3.888930 CACCTTCTACCAGGCAAAAAGAA 59.111 43.478 0.00 0.00 37.47 2.52
4469 4633 2.558359 CCACCTTCTACCAGGCAAAAAG 59.442 50.000 0.00 0.00 37.47 2.27
4471 4635 1.777878 TCCACCTTCTACCAGGCAAAA 59.222 47.619 0.00 0.00 37.47 2.44
4472 4636 1.440618 TCCACCTTCTACCAGGCAAA 58.559 50.000 0.00 0.00 37.47 3.68
4473 4637 1.668826 ATCCACCTTCTACCAGGCAA 58.331 50.000 0.00 0.00 37.47 4.52
4503 4688 8.607441 TCAACATCCATCAGTAATACATAAGC 57.393 34.615 0.00 0.00 0.00 3.09
4567 4752 6.071391 CCCTGTTAGGTGCAAAAGAATATGTT 60.071 38.462 0.00 0.00 31.93 2.71
4614 4800 4.894719 TCCTGCTGGATCTGGTCA 57.105 55.556 8.48 0.00 37.46 4.02
4905 5091 2.490165 GCATGCAGCAACCTCTCAT 58.510 52.632 14.21 0.00 44.79 2.90
4917 5104 2.857186 TACTTTCCTCTGTGCATGCA 57.143 45.000 18.46 18.46 0.00 3.96
4943 5130 2.356069 GCTCTGCTGTATGTAAAAGCCC 59.644 50.000 0.00 0.00 36.05 5.19
4944 5131 3.274288 AGCTCTGCTGTATGTAAAAGCC 58.726 45.455 0.00 0.00 37.57 4.35
4945 5132 4.187694 AGAGCTCTGCTGTATGTAAAAGC 58.812 43.478 17.42 0.00 39.88 3.51
4946 5133 5.064452 CCAAGAGCTCTGCTGTATGTAAAAG 59.936 44.000 19.06 0.00 39.88 2.27
4947 5134 4.937620 CCAAGAGCTCTGCTGTATGTAAAA 59.062 41.667 19.06 0.00 39.88 1.52
4948 5135 4.507710 CCAAGAGCTCTGCTGTATGTAAA 58.492 43.478 19.06 0.00 39.88 2.01
4949 5136 3.118629 CCCAAGAGCTCTGCTGTATGTAA 60.119 47.826 19.06 0.00 39.88 2.41
4950 5137 2.432146 CCCAAGAGCTCTGCTGTATGTA 59.568 50.000 19.06 0.00 39.88 2.29
4989 5176 9.086758 CATCTATATATCTATCCATGCAGGTGA 57.913 37.037 0.00 0.00 39.02 4.02
5002 5190 7.898014 ATGAACACGGCCATCTATATATCTA 57.102 36.000 2.24 0.00 0.00 1.98
5010 5198 2.549992 GGCATATGAACACGGCCATCTA 60.550 50.000 6.97 0.00 44.01 1.98
5012 5200 0.593128 GGCATATGAACACGGCCATC 59.407 55.000 6.97 0.00 44.01 3.51
5013 5201 0.183492 AGGCATATGAACACGGCCAT 59.817 50.000 6.97 0.00 46.96 4.40
5049 5252 3.121030 CCTGCACGGGCTCGAAAG 61.121 66.667 15.95 6.67 41.91 2.62
5174 5382 3.305813 CGGTACAGAAACTTGAGTAGGCA 60.306 47.826 0.00 0.00 0.00 4.75
5182 5390 4.750098 ACAGATTCACGGTACAGAAACTTG 59.250 41.667 0.00 2.24 0.00 3.16
5195 5403 0.371301 CGCCACATCACAGATTCACG 59.629 55.000 0.00 0.00 0.00 4.35
5196 5404 1.725641 TCGCCACATCACAGATTCAC 58.274 50.000 0.00 0.00 0.00 3.18
5333 5544 5.402568 CGGTGACAGATGTACTATTATGCAC 59.597 44.000 0.00 0.00 0.00 4.57
5362 5573 7.759489 AACTGCTACCAAAGTTTTCATCATA 57.241 32.000 0.00 0.00 32.75 2.15
5370 5581 8.063200 AGAAACTAAAACTGCTACCAAAGTTT 57.937 30.769 0.00 0.00 46.03 2.66
5406 5631 5.049474 ACACACACACACACACATTATCATC 60.049 40.000 0.00 0.00 0.00 2.92
5407 5632 4.821260 ACACACACACACACACATTATCAT 59.179 37.500 0.00 0.00 0.00 2.45
5408 5633 4.195416 ACACACACACACACACATTATCA 58.805 39.130 0.00 0.00 0.00 2.15
5409 5634 4.511454 AGACACACACACACACACATTATC 59.489 41.667 0.00 0.00 0.00 1.75
5410 5635 4.273235 CAGACACACACACACACACATTAT 59.727 41.667 0.00 0.00 0.00 1.28
5412 5637 2.419673 CAGACACACACACACACACATT 59.580 45.455 0.00 0.00 0.00 2.71
5413 5638 2.009051 CAGACACACACACACACACAT 58.991 47.619 0.00 0.00 0.00 3.21
5414 5639 1.270571 ACAGACACACACACACACACA 60.271 47.619 0.00 0.00 0.00 3.72
5415 5640 1.438651 ACAGACACACACACACACAC 58.561 50.000 0.00 0.00 0.00 3.82
5416 5641 2.612604 GTACAGACACACACACACACA 58.387 47.619 0.00 0.00 0.00 3.72
5417 5642 1.931172 GGTACAGACACACACACACAC 59.069 52.381 0.00 0.00 0.00 3.82
5418 5643 1.828595 AGGTACAGACACACACACACA 59.171 47.619 0.00 0.00 0.00 3.72
5419 5644 2.596904 AGGTACAGACACACACACAC 57.403 50.000 0.00 0.00 0.00 3.82
5423 5648 4.441634 GGGATGATAGGTACAGACACACAC 60.442 50.000 0.00 0.00 0.00 3.82
5424 5649 3.704566 GGGATGATAGGTACAGACACACA 59.295 47.826 0.00 0.00 0.00 3.72
5426 5651 4.265856 AGGGATGATAGGTACAGACACA 57.734 45.455 0.00 0.00 0.00 3.72
5427 5652 6.919775 ATAAGGGATGATAGGTACAGACAC 57.080 41.667 0.00 0.00 0.00 3.67
5431 5700 7.016661 ACCAAGAATAAGGGATGATAGGTACAG 59.983 40.741 0.00 0.00 0.00 2.74
5501 5771 2.789409 AAGTTTACAGCCAGCCTAGG 57.211 50.000 3.67 3.67 0.00 3.02
5544 5926 0.475632 ACATCAACCTCCACTGGGGA 60.476 55.000 0.00 0.00 45.89 4.81
5545 5927 0.405585 AACATCAACCTCCACTGGGG 59.594 55.000 0.00 0.00 38.37 4.96
5571 5953 5.215160 CAGTCCAAGCATGTAACTTTCAAC 58.785 41.667 0.00 0.00 0.00 3.18
5617 5999 0.601558 TTGCGTCTGGTACCTCTCAC 59.398 55.000 14.36 3.43 0.00 3.51
5698 6083 2.512692 TCCTTGTGGTGATGGATTGG 57.487 50.000 0.00 0.00 34.23 3.16
5700 6085 6.438186 AAAAATTCCTTGTGGTGATGGATT 57.562 33.333 0.00 0.00 34.23 3.01
5756 6158 3.307059 CCCCACCTGTTCACAAAACAAAA 60.307 43.478 0.00 0.00 0.00 2.44
5757 6159 2.234908 CCCCACCTGTTCACAAAACAAA 59.765 45.455 0.00 0.00 0.00 2.83
5759 6161 1.479709 CCCCACCTGTTCACAAAACA 58.520 50.000 0.00 0.00 0.00 2.83
5762 6164 1.456705 GCCCCCACCTGTTCACAAA 60.457 57.895 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.