Multiple sequence alignment - TraesCS2A01G128700

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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 TraesCS2A01G128700 chr2A 100.000 6802 0 0 1 6802 77171545 77164744 0.000000e+00 12562.0
1 TraesCS2A01G128700 chr2A 91.667 72 6 0 634 705 77170840 77170769 4.340000e-17 100.0
2 TraesCS2A01G128700 chr2A 91.667 72 6 0 706 777 77170912 77170841 4.340000e-17 100.0
3 TraesCS2A01G128700 chr2A 92.105 38 3 0 624 661 100834633 100834670 3.000000e-03 54.7
4 TraesCS2A01G128700 chr2B 94.510 3133 124 18 2859 5976 117887654 117884555 0.000000e+00 4789.0
5 TraesCS2A01G128700 chr2B 90.904 1836 105 31 772 2589 117890193 117888402 0.000000e+00 2409.0
6 TraesCS2A01G128700 chr2B 87.562 804 54 23 6007 6794 117884555 117883782 0.000000e+00 889.0
7 TraesCS2A01G128700 chr2B 78.170 481 63 27 4668 5122 117693838 117694302 1.120000e-67 268.0
8 TraesCS2A01G128700 chr2B 91.892 185 9 3 2680 2860 117888097 117887915 3.150000e-63 254.0
9 TraesCS2A01G128700 chr2B 96.552 87 3 0 2588 2674 117888243 117888157 1.980000e-30 145.0
10 TraesCS2A01G128700 chr2B 77.778 108 20 3 522 626 24241892 24241998 5.700000e-06 63.9
11 TraesCS2A01G128700 chr2D 94.828 2243 75 19 2680 4909 76642960 76640746 0.000000e+00 3461.0
12 TraesCS2A01G128700 chr2D 94.046 1898 80 19 4910 6790 76640437 76638556 0.000000e+00 2848.0
13 TraesCS2A01G128700 chr2D 91.341 1998 126 31 706 2675 76644985 76643007 0.000000e+00 2687.0
14 TraesCS2A01G128700 chr2D 82.609 644 66 18 1 626 76645766 76645151 1.680000e-145 527.0
15 TraesCS2A01G128700 chr2D 89.286 84 6 2 625 705 76644995 76644912 1.210000e-17 102.0
16 TraesCS2A01G128700 chr6A 84.832 1312 157 24 3097 4379 84925679 84924381 0.000000e+00 1282.0
17 TraesCS2A01G128700 chr6A 79.592 1764 219 70 4614 6345 84924059 84922405 0.000000e+00 1133.0
18 TraesCS2A01G128700 chr6A 81.854 755 109 16 994 1726 84927840 84927092 1.620000e-170 610.0
19 TraesCS2A01G128700 chr6A 87.013 385 41 6 2716 3097 84926100 84925722 6.310000e-115 425.0
20 TraesCS2A01G128700 chr6A 87.055 309 29 8 1937 2238 84926884 84926580 8.450000e-89 339.0
21 TraesCS2A01G128700 chr6A 86.897 145 10 7 4485 4629 84924326 84924191 3.290000e-33 154.0
22 TraesCS2A01G128700 chr6A 78.873 142 17 5 1805 1933 84927066 84926925 4.370000e-12 84.2
23 TraesCS2A01G128700 chr6B 85.162 1139 140 18 3266 4379 142232436 142231302 0.000000e+00 1140.0
24 TraesCS2A01G128700 chr6B 83.278 1202 133 33 4614 5807 142230990 142229849 0.000000e+00 1044.0
25 TraesCS2A01G128700 chr6B 81.950 759 99 23 995 1726 142234825 142234078 5.830000e-170 608.0
26 TraesCS2A01G128700 chr6B 79.315 788 90 34 1937 2672 142233869 142233103 1.030000e-132 484.0
27 TraesCS2A01G128700 chr6B 83.000 400 41 12 2699 3097 142233104 142232731 3.040000e-88 337.0
28 TraesCS2A01G128700 chr6B 89.655 145 6 7 4485 4629 142231247 142231112 7.010000e-40 176.0
29 TraesCS2A01G128700 chr6B 86.466 133 11 2 3099 3224 142232684 142232552 9.200000e-29 139.0
30 TraesCS2A01G128700 chr6B 83.444 151 22 3 4590 4739 213549302 213549450 3.310000e-28 137.0
31 TraesCS2A01G128700 chr6B 86.667 90 12 0 1844 1933 142233999 142233910 4.340000e-17 100.0
32 TraesCS2A01G128700 chr6D 83.761 1207 128 34 4612 5807 67378796 67377647 0.000000e+00 1081.0
33 TraesCS2A01G128700 chr6D 86.137 642 56 20 3099 3720 67380126 67379498 0.000000e+00 662.0
34 TraesCS2A01G128700 chr6D 81.698 754 102 23 995 1726 67382327 67381588 4.540000e-166 595.0
35 TraesCS2A01G128700 chr6D 89.068 311 22 6 1937 2236 67381385 67381076 6.440000e-100 375.0
36 TraesCS2A01G128700 chr6D 83.791 401 52 7 3986 4379 67379495 67379101 1.080000e-97 368.0
37 TraesCS2A01G128700 chr6D 87.814 279 29 3 2826 3101 67380444 67380168 8.510000e-84 322.0
38 TraesCS2A01G128700 chr6D 88.571 140 7 7 4485 4624 67379046 67378916 1.960000e-35 161.0
39 TraesCS2A01G128700 chr6D 81.295 139 18 2 1803 1933 67381564 67381426 9.330000e-19 106.0
40 TraesCS2A01G128700 chr7B 77.358 106 23 1 522 626 157803073 157803178 2.050000e-05 62.1
41 TraesCS2A01G128700 chrUn 97.059 34 1 0 629 662 16908385 16908352 2.650000e-04 58.4
42 TraesCS2A01G128700 chr3B 100.000 31 0 0 2589 2619 760308598 760308568 2.650000e-04 58.4
43 TraesCS2A01G128700 chr3A 97.059 34 1 0 629 662 741673409 741673442 2.650000e-04 58.4
44 TraesCS2A01G128700 chr3A 100.000 28 0 0 2592 2619 547993288 547993315 1.200000e-02 52.8
45 TraesCS2A01G128700 chr5A 96.970 33 1 0 630 662 434795898 434795866 1.000000e-03 56.5
46 TraesCS2A01G128700 chr5A 100.000 28 0 0 707 734 23178911 23178884 1.200000e-02 52.8
47 TraesCS2A01G128700 chr4A 100.000 30 0 0 2594 2623 625265981 625266010 1.000000e-03 56.5
48 TraesCS2A01G128700 chr1B 96.970 33 1 0 630 662 434994102 434994070 1.000000e-03 56.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G128700 chr2A 77164744 77171545 6801 True 4254.000000 12562 94.444667 1 6802 3 chr2A.!!$R1 6801
1 TraesCS2A01G128700 chr2B 117883782 117890193 6411 True 1697.200000 4789 92.284000 772 6794 5 chr2B.!!$R1 6022
2 TraesCS2A01G128700 chr2D 76638556 76645766 7210 True 1925.000000 3461 90.422000 1 6790 5 chr2D.!!$R1 6789
3 TraesCS2A01G128700 chr6A 84922405 84927840 5435 True 575.314286 1282 83.730857 994 6345 7 chr6A.!!$R1 5351
4 TraesCS2A01G128700 chr6B 142229849 142234825 4976 True 503.500000 1140 84.436625 995 5807 8 chr6B.!!$R1 4812
5 TraesCS2A01G128700 chr6D 67377647 67382327 4680 True 458.750000 1081 85.266875 995 5807 8 chr6D.!!$R1 4812

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
709 895 0.037326 CCGCTCCAAGTGACTGCTAA 60.037 55.0 0.00 0.0 0.00 3.09 F
1569 1798 0.250295 TGCTCAGTGGTAAGTGGTGC 60.250 55.0 0.00 0.0 0.00 5.01 F
1825 2061 0.099436 GTGAAGCCAAAGCATAGCGG 59.901 55.0 0.00 0.0 43.56 5.52 F
3715 4805 0.035820 GTTGGTGGGTATTCAGGCGA 60.036 55.0 0.00 0.0 0.00 5.54 F
4095 5201 1.160329 ACTGCAACGTGCTTGTCTCC 61.160 55.0 10.54 0.0 45.31 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1757 1993 0.178068 ATTCTAACAGCGCCACCGAT 59.822 50.000 2.29 0.0 36.29 4.18 R
3446 4536 2.787994 AGTTGACAATGAAGGCTCCAG 58.212 47.619 0.00 0.0 0.00 3.86 R
3724 4814 1.522668 TGGCTCACTGAATGAAACCG 58.477 50.000 0.00 0.0 36.70 4.44 R
5421 7003 0.933097 CCAGCTATGTGTGCGATGAC 59.067 55.000 0.00 0.0 35.28 3.06 R
5867 7461 1.090052 AATAGCTTTCGCGAGGTGGC 61.090 55.000 9.59 12.3 42.32 5.01 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
74 75 4.027437 TGCACCAAAACCTAAGGAAAACT 58.973 39.130 0.00 0.00 0.00 2.66
77 78 6.183360 TGCACCAAAACCTAAGGAAAACTAAG 60.183 38.462 0.00 0.00 0.00 2.18
78 79 6.213677 CACCAAAACCTAAGGAAAACTAAGC 58.786 40.000 0.00 0.00 0.00 3.09
82 101 7.766738 CCAAAACCTAAGGAAAACTAAGCAAAA 59.233 33.333 0.00 0.00 0.00 2.44
139 158 3.629142 ACACCTAAATCCCGAAGAAGG 57.371 47.619 0.00 0.00 0.00 3.46
140 159 3.178865 ACACCTAAATCCCGAAGAAGGA 58.821 45.455 0.00 0.00 37.93 3.36
141 160 3.585732 ACACCTAAATCCCGAAGAAGGAA 59.414 43.478 0.00 0.00 36.85 3.36
143 162 3.200165 ACCTAAATCCCGAAGAAGGAAGG 59.800 47.826 0.00 0.00 36.85 3.46
146 165 1.972660 ATCCCGAAGAAGGAAGGGCG 61.973 60.000 0.00 0.00 43.46 6.13
147 166 2.125106 CCGAAGAAGGAAGGGCGG 60.125 66.667 0.00 0.00 0.00 6.13
161 180 4.000557 GCGGGCGTGCGACATATG 62.001 66.667 0.00 0.00 0.00 1.78
162 181 3.337889 CGGGCGTGCGACATATGG 61.338 66.667 7.80 0.00 0.00 2.74
163 182 3.649986 GGGCGTGCGACATATGGC 61.650 66.667 7.80 2.25 0.00 4.40
164 183 2.894879 GGCGTGCGACATATGGCA 60.895 61.111 9.77 5.95 37.19 4.92
165 184 2.468670 GGCGTGCGACATATGGCAA 61.469 57.895 9.77 0.00 41.66 4.52
166 185 1.648720 GCGTGCGACATATGGCAAT 59.351 52.632 9.77 0.00 41.66 3.56
167 186 0.658244 GCGTGCGACATATGGCAATG 60.658 55.000 9.77 2.74 41.66 2.82
168 187 0.657312 CGTGCGACATATGGCAATGT 59.343 50.000 9.77 12.87 41.66 2.71
181 200 3.149899 CAATGTCTGCTCGCTTCCT 57.850 52.632 0.00 0.00 0.00 3.36
195 214 2.817258 CGCTTCCTGTCCACCAAAAATA 59.183 45.455 0.00 0.00 0.00 1.40
199 218 4.463050 TCCTGTCCACCAAAAATAACCT 57.537 40.909 0.00 0.00 0.00 3.50
217 236 1.063867 CCTCTAGGTTCCCCGAGAAGA 60.064 57.143 6.58 0.00 41.33 2.87
223 242 0.757512 GTTCCCCGAGAAGATACCCC 59.242 60.000 0.00 0.00 34.29 4.95
224 243 0.399519 TTCCCCGAGAAGATACCCCC 60.400 60.000 0.00 0.00 0.00 5.40
249 268 5.297776 CCAATTGGTTGCTCTCGAAGAATAT 59.702 40.000 16.90 0.00 32.09 1.28
259 278 5.697473 TCTCGAAGAATATGAGCACCTAG 57.303 43.478 0.00 0.00 34.09 3.02
272 291 4.216708 GAGCACCTAGGTGTAATACTCCT 58.783 47.826 36.31 24.31 46.90 3.69
292 311 7.229308 ACTCCTTCCGTTTTTATTTACTTCCT 58.771 34.615 0.00 0.00 0.00 3.36
368 395 6.671614 AACAATCTAAACAGTGACGAACAA 57.328 33.333 0.00 0.00 0.00 2.83
436 464 4.458951 CAAGTTTGCTCACTGTCTGTAC 57.541 45.455 0.00 0.00 0.00 2.90
445 473 4.082190 GCTCACTGTCTGTACCAGATACAA 60.082 45.833 4.82 0.00 43.35 2.41
451 479 7.275779 CACTGTCTGTACCAGATACAATGTTAC 59.724 40.741 4.82 0.00 43.35 2.50
454 482 7.817478 TGTCTGTACCAGATACAATGTTACAAG 59.183 37.037 0.00 0.00 43.35 3.16
460 488 7.648142 ACCAGATACAATGTTACAAGTTTGTG 58.352 34.615 11.63 7.24 42.31 3.33
481 509 6.418946 TGTGCTGTTCCATATTGTACCATTA 58.581 36.000 0.00 0.00 0.00 1.90
497 525 2.241176 CCATTAAGGTTGGCCTAGGACA 59.759 50.000 15.37 15.37 46.33 4.02
501 529 0.912486 AGGTTGGCCTAGGACATGAC 59.088 55.000 20.86 15.03 44.90 3.06
526 554 1.666311 GGCTGGCTACGCGACTAATAG 60.666 57.143 15.93 4.44 0.00 1.73
527 555 1.001597 GCTGGCTACGCGACTAATAGT 60.002 52.381 15.93 0.00 0.00 2.12
643 829 6.489127 AAGTTTGTACAACGCTAATATGCA 57.511 33.333 8.07 0.00 0.00 3.96
666 852 9.050601 TGCAAAGTAAATAAAAATGGAGTTTGG 57.949 29.630 0.00 0.00 31.10 3.28
667 853 9.267084 GCAAAGTAAATAAAAATGGAGTTTGGA 57.733 29.630 0.00 0.00 31.10 3.53
670 856 9.981114 AAGTAAATAAAAATGGAGTTTGGAGTG 57.019 29.630 0.00 0.00 0.00 3.51
671 857 8.585018 AGTAAATAAAAATGGAGTTTGGAGTGG 58.415 33.333 0.00 0.00 0.00 4.00
672 858 6.358974 AATAAAAATGGAGTTTGGAGTGGG 57.641 37.500 0.00 0.00 0.00 4.61
673 859 1.632589 AAATGGAGTTTGGAGTGGGC 58.367 50.000 0.00 0.00 0.00 5.36
674 860 0.779997 AATGGAGTTTGGAGTGGGCT 59.220 50.000 0.00 0.00 0.00 5.19
675 861 0.329596 ATGGAGTTTGGAGTGGGCTC 59.670 55.000 0.00 0.00 40.93 4.70
676 862 0.768221 TGGAGTTTGGAGTGGGCTCT 60.768 55.000 0.00 0.00 41.38 4.09
677 863 0.402121 GGAGTTTGGAGTGGGCTCTT 59.598 55.000 0.00 0.00 41.38 2.85
678 864 1.611936 GGAGTTTGGAGTGGGCTCTTC 60.612 57.143 0.00 0.00 41.38 2.87
679 865 0.402121 AGTTTGGAGTGGGCTCTTCC 59.598 55.000 1.15 1.15 41.38 3.46
688 874 3.839432 GGCTCTTCCCGGACCGAG 61.839 72.222 17.49 0.69 0.00 4.63
689 875 3.839432 GCTCTTCCCGGACCGAGG 61.839 72.222 17.49 15.11 0.00 4.63
690 876 3.839432 CTCTTCCCGGACCGAGGC 61.839 72.222 17.49 0.00 0.00 4.70
699 885 4.821589 GACCGAGGCCGCTCCAAG 62.822 72.222 4.53 0.00 37.29 3.61
702 888 4.069232 CGAGGCCGCTCCAAGTGA 62.069 66.667 4.53 0.00 37.29 3.41
703 889 2.435059 GAGGCCGCTCCAAGTGAC 60.435 66.667 0.00 0.00 37.29 3.67
704 890 2.925170 AGGCCGCTCCAAGTGACT 60.925 61.111 0.00 0.00 37.29 3.41
705 891 2.743928 GGCCGCTCCAAGTGACTG 60.744 66.667 0.00 0.00 34.01 3.51
706 892 3.426568 GCCGCTCCAAGTGACTGC 61.427 66.667 0.00 0.00 0.00 4.40
707 893 2.345244 CCGCTCCAAGTGACTGCT 59.655 61.111 0.00 0.00 0.00 4.24
708 894 1.591703 CCGCTCCAAGTGACTGCTA 59.408 57.895 0.00 0.00 0.00 3.49
709 895 0.037326 CCGCTCCAAGTGACTGCTAA 60.037 55.000 0.00 0.00 0.00 3.09
710 896 1.406069 CCGCTCCAAGTGACTGCTAAT 60.406 52.381 0.00 0.00 0.00 1.73
711 897 2.159099 CCGCTCCAAGTGACTGCTAATA 60.159 50.000 0.00 0.00 0.00 0.98
712 898 3.493350 CCGCTCCAAGTGACTGCTAATAT 60.493 47.826 0.00 0.00 0.00 1.28
713 899 3.492383 CGCTCCAAGTGACTGCTAATATG 59.508 47.826 0.00 0.00 0.00 1.78
714 900 3.249559 GCTCCAAGTGACTGCTAATATGC 59.750 47.826 0.00 0.00 0.00 3.14
715 901 3.457234 TCCAAGTGACTGCTAATATGCG 58.543 45.455 0.00 0.00 35.36 4.73
716 902 3.132111 TCCAAGTGACTGCTAATATGCGA 59.868 43.478 0.00 0.00 35.36 5.10
717 903 3.871006 CCAAGTGACTGCTAATATGCGAA 59.129 43.478 0.00 0.00 35.36 4.70
718 904 4.025396 CCAAGTGACTGCTAATATGCGAAG 60.025 45.833 0.00 0.00 35.36 3.79
719 905 4.392921 AGTGACTGCTAATATGCGAAGT 57.607 40.909 0.00 0.00 35.36 3.01
720 906 5.515797 AGTGACTGCTAATATGCGAAGTA 57.484 39.130 0.00 0.00 35.36 2.24
721 907 5.902681 AGTGACTGCTAATATGCGAAGTAA 58.097 37.500 0.00 0.00 35.36 2.24
722 908 6.338146 AGTGACTGCTAATATGCGAAGTAAA 58.662 36.000 0.00 0.00 35.36 2.01
723 909 6.986817 AGTGACTGCTAATATGCGAAGTAAAT 59.013 34.615 0.00 0.00 35.36 1.40
724 910 7.042456 AGTGACTGCTAATATGCGAAGTAAATG 60.042 37.037 0.00 0.00 35.36 2.32
725 911 6.983890 TGACTGCTAATATGCGAAGTAAATGA 59.016 34.615 0.00 0.00 35.36 2.57
726 912 7.494298 TGACTGCTAATATGCGAAGTAAATGAA 59.506 33.333 0.00 0.00 35.36 2.57
727 913 8.208718 ACTGCTAATATGCGAAGTAAATGAAA 57.791 30.769 0.00 0.00 35.36 2.69
728 914 8.673711 ACTGCTAATATGCGAAGTAAATGAAAA 58.326 29.630 0.00 0.00 35.36 2.29
729 915 8.835467 TGCTAATATGCGAAGTAAATGAAAAC 57.165 30.769 0.00 0.00 35.36 2.43
730 916 8.454894 TGCTAATATGCGAAGTAAATGAAAACA 58.545 29.630 0.00 0.00 35.36 2.83
731 917 8.947940 GCTAATATGCGAAGTAAATGAAAACAG 58.052 33.333 0.00 0.00 0.00 3.16
740 926 8.947940 CGAAGTAAATGAAAACAGAGTTTGAAG 58.052 33.333 0.00 0.00 0.00 3.02
814 1001 0.462047 CACGAGATTTTCCCCTCCGG 60.462 60.000 0.00 0.00 0.00 5.14
818 1005 0.252197 AGATTTTCCCCTCCGGTTCG 59.748 55.000 0.00 0.00 0.00 3.95
834 1021 2.199236 GTTCGTCCGCTAGGGTTTATG 58.801 52.381 6.02 0.00 38.33 1.90
977 1182 2.476199 CACAGAAGATTCCCCTCCTCT 58.524 52.381 0.00 0.00 0.00 3.69
978 1183 2.433970 CACAGAAGATTCCCCTCCTCTC 59.566 54.545 0.00 0.00 0.00 3.20
983 1190 0.472925 GATTCCCCTCCTCTCCTCCC 60.473 65.000 0.00 0.00 0.00 4.30
987 1194 2.612251 CCTCCTCTCCTCCCCTCC 59.388 72.222 0.00 0.00 0.00 4.30
992 1199 3.036959 TCTCCTCCCCTCCCCTCC 61.037 72.222 0.00 0.00 0.00 4.30
1242 1455 2.831685 TGTGCAGTTTATGACGGTCT 57.168 45.000 9.88 0.00 0.00 3.85
1255 1468 0.526662 ACGGTCTCAGGTCGTTGATC 59.473 55.000 0.00 0.00 32.95 2.92
1489 1718 1.525077 GCGGTTGTGGTGGTTCAGA 60.525 57.895 0.00 0.00 0.00 3.27
1498 1727 1.676384 GTGGTTCAGAGAGCTGGCT 59.324 57.895 0.00 0.00 42.53 4.75
1507 1736 3.573538 TCAGAGAGCTGGCTATTCAGATC 59.426 47.826 0.00 2.35 46.89 2.75
1534 1763 1.515736 GTTCGAGGCGTTAGGGTCG 60.516 63.158 0.00 0.00 0.00 4.79
1569 1798 0.250295 TGCTCAGTGGTAAGTGGTGC 60.250 55.000 0.00 0.00 0.00 5.01
1638 1870 2.205074 CCGACTGGATGTTCATACTGC 58.795 52.381 2.54 0.00 37.49 4.40
1662 1894 2.502510 CATTGTGTCCTTGCGCGC 60.503 61.111 27.26 27.26 0.00 6.86
1679 1911 3.422343 GCGCGCATCATAGTTCTGATTAC 60.422 47.826 29.10 0.00 33.59 1.89
1681 1913 4.310769 GCGCATCATAGTTCTGATTACCT 58.689 43.478 0.30 0.00 33.59 3.08
1686 1919 8.297426 CGCATCATAGTTCTGATTACCTAGTTA 58.703 37.037 0.00 0.00 33.59 2.24
1757 1993 5.221382 GGGCATAACACGAAGAGGAGTAATA 60.221 44.000 0.00 0.00 0.00 0.98
1762 1998 4.205587 ACACGAAGAGGAGTAATATCGGT 58.794 43.478 0.00 0.00 34.81 4.69
1784 2020 5.122711 GGTGGCGCTGTTAGAATTTTTAGTA 59.877 40.000 7.64 0.00 0.00 1.82
1785 2021 6.183360 GGTGGCGCTGTTAGAATTTTTAGTAT 60.183 38.462 7.64 0.00 0.00 2.12
1825 2061 0.099436 GTGAAGCCAAAGCATAGCGG 59.901 55.000 0.00 0.00 43.56 5.52
1841 2077 5.063944 GCATAGCGGAACATGGTTATATCTG 59.936 44.000 0.00 0.00 0.00 2.90
1847 2097 6.292919 GCGGAACATGGTTATATCTGAAGTTC 60.293 42.308 0.00 0.00 33.89 3.01
1929 2183 7.111247 TCAATGTTTGTTGATGACCTTTCTT 57.889 32.000 0.00 0.00 33.41 2.52
1964 2255 9.624373 ACTTCTGCTCAGTATAATTTGATGAAT 57.376 29.630 0.00 0.00 0.00 2.57
2010 2303 2.028112 GTCTCTTGGTGACCATGCTACA 60.028 50.000 4.56 0.00 31.53 2.74
2016 2309 2.843730 TGGTGACCATGCTACAACCTAT 59.156 45.455 0.00 0.00 0.00 2.57
2045 2338 8.948631 AATCAAGTATTCGTCATCAGTTATGT 57.051 30.769 0.00 0.00 36.89 2.29
2175 2472 7.901029 CACATATTGTGGTGAGTATCCTCTAT 58.099 38.462 0.00 0.00 44.27 1.98
2225 2526 4.525912 ATGGATCCTTTGTGCTTTGAAC 57.474 40.909 14.23 0.00 0.00 3.18
2255 2585 5.359009 AGTGAGGCATGTGATTAAAATCCAG 59.641 40.000 0.00 0.00 34.50 3.86
2260 2590 5.504665 GGCATGTGATTAAAATCCAGACTCG 60.505 44.000 0.00 0.00 34.50 4.18
2277 2607 0.684535 TCGACCATCAACAAGGCTCA 59.315 50.000 0.00 0.00 0.00 4.26
2303 2633 1.604604 TCCCAAAGTGGAAAAGCTCG 58.395 50.000 0.00 0.00 40.96 5.03
2675 3197 3.384789 TGACAAGCGCATCCTTATACTCT 59.615 43.478 11.47 0.00 0.00 3.24
2676 3198 3.722147 ACAAGCGCATCCTTATACTCTG 58.278 45.455 11.47 0.00 0.00 3.35
2677 3199 3.133003 ACAAGCGCATCCTTATACTCTGT 59.867 43.478 11.47 0.00 0.00 3.41
2678 3200 4.341235 ACAAGCGCATCCTTATACTCTGTA 59.659 41.667 11.47 0.00 0.00 2.74
2888 3783 8.429641 TGAAAACTGTCTTTATCAGGACTTAGT 58.570 33.333 0.00 0.00 37.25 2.24
3006 3901 3.000925 GTGAAATACCTGGTACGCATTCG 59.999 47.826 9.09 0.00 42.43 3.34
3058 3955 8.070034 ACATCATCCTGCTTTTTCATTTATGA 57.930 30.769 0.00 0.00 34.44 2.15
3078 3975 9.739276 TTTATGACTAGACCATTCTGATTGTTT 57.261 29.630 0.00 0.00 32.75 2.83
3140 4142 7.121168 CCTGCATTAAAGAAAGGAGTAATGTGA 59.879 37.037 0.00 0.00 36.66 3.58
3373 4452 1.331214 ACCATTGCTTGACTGGTTGG 58.669 50.000 0.00 0.00 40.34 3.77
3715 4805 0.035820 GTTGGTGGGTATTCAGGCGA 60.036 55.000 0.00 0.00 0.00 5.54
3724 4814 4.396790 TGGGTATTCAGGCGATTTTGTTAC 59.603 41.667 0.00 0.00 0.00 2.50
3725 4815 4.495184 GGGTATTCAGGCGATTTTGTTACG 60.495 45.833 0.00 0.00 0.00 3.18
3728 4825 2.496111 TCAGGCGATTTTGTTACGGTT 58.504 42.857 0.00 0.00 0.00 4.44
3730 4827 3.058777 TCAGGCGATTTTGTTACGGTTTC 60.059 43.478 0.00 0.00 0.00 2.78
3789 4888 3.181488 TGCCATTGTTGTGTTTGTCAGAG 60.181 43.478 0.00 0.00 0.00 3.35
4095 5201 1.160329 ACTGCAACGTGCTTGTCTCC 61.160 55.000 10.54 0.00 45.31 3.71
4117 5223 3.816523 CGAAACCCTGTTAAGGTAAAGCA 59.183 43.478 0.00 0.00 42.74 3.91
4154 5267 2.619013 ATAAGCAGCAAAGCGTCAAC 57.381 45.000 0.00 0.00 40.15 3.18
4159 5272 1.746760 CAGCAAAGCGTCAACAGAAC 58.253 50.000 0.00 0.00 0.00 3.01
4183 5296 1.290009 CTTTTGGGCCGCCTTCTTG 59.710 57.895 9.86 0.00 0.00 3.02
4195 5308 3.557595 CCGCCTTCTTGCTCTTACTAATG 59.442 47.826 0.00 0.00 0.00 1.90
4250 5363 9.699703 GAAGTATCCTCCAAATATTCTACAGTC 57.300 37.037 0.00 0.00 0.00 3.51
4357 5470 2.754946 AGTGCCGAAATCCGTTTCTA 57.245 45.000 0.00 0.00 41.24 2.10
4434 5547 4.825546 CAGGCCTGCATTATCTTGTTAG 57.174 45.455 22.33 0.00 0.00 2.34
4437 5550 5.126061 CAGGCCTGCATTATCTTGTTAGTTT 59.874 40.000 22.33 0.00 0.00 2.66
4515 5631 7.039504 ACTGATTAAAGCCTGTGTTGATGAAAT 60.040 33.333 0.00 0.00 0.00 2.17
4665 5931 6.546403 TCTCTATTTAGTAACAGTGGCTCGAT 59.454 38.462 0.00 0.00 0.00 3.59
4699 5966 6.036470 CCCTTTATTCTTCTTTCGCCATTTC 58.964 40.000 0.00 0.00 0.00 2.17
4747 6014 1.200948 GTTCTGAATGAGTTGCCAGGC 59.799 52.381 3.66 3.66 0.00 4.85
4872 6139 6.746120 TGAGTCAGGTTTACTTCTGTAACTC 58.254 40.000 0.00 0.00 38.26 3.01
4895 6162 8.301002 ACTCTTCTATCAGACAGACAAAAGTAC 58.699 37.037 0.00 0.00 0.00 2.73
4920 6499 4.402155 TGATTTCCCCATTCAGTTATGCAC 59.598 41.667 0.00 0.00 0.00 4.57
5218 6800 5.238432 TGCCGATCATCGTATATTGCTTTTT 59.762 36.000 6.25 0.00 38.40 1.94
5275 6857 6.874664 CACTGATCTTAGATCTTATGCTGCAT 59.125 38.462 20.18 20.18 0.00 3.96
5421 7003 4.749245 ATAGTTTTCCTCGTTGCTTGTG 57.251 40.909 0.00 0.00 0.00 3.33
5424 7006 2.031258 TTTCCTCGTTGCTTGTGTCA 57.969 45.000 0.00 0.00 0.00 3.58
5442 7025 1.206849 TCATCGCACACATAGCTGGAA 59.793 47.619 0.00 0.00 0.00 3.53
5471 7054 4.608170 TCTGAAGCCATCCCCTATTTTT 57.392 40.909 0.00 0.00 0.00 1.94
5619 7202 8.877864 AAGTGTCCATAATTGTCTTCCATAAA 57.122 30.769 0.00 0.00 0.00 1.40
5747 7331 2.547642 CGATGATGAAGAAGAGGAGGCC 60.548 54.545 0.00 0.00 0.00 5.19
5769 7353 2.289694 CCAAGAGGTCACCGACAGAAAT 60.290 50.000 0.00 0.00 33.68 2.17
5864 7458 5.195185 TGACCAGTAGAATCCGTACATACA 58.805 41.667 0.00 0.00 0.00 2.29
5867 7461 4.219802 CAGTAGAATCCGTACATACAGCG 58.780 47.826 0.00 0.00 0.00 5.18
5902 7496 8.122952 CGAAAGCTATTTATCGGAATTTTGTCT 58.877 33.333 0.00 0.00 0.00 3.41
5910 7504 8.842358 TTTATCGGAATTTTGTCTGTAGTTCT 57.158 30.769 0.00 0.00 0.00 3.01
5935 7529 4.754618 CCGATGCACCAGCTATATTGTTAA 59.245 41.667 0.00 0.00 42.74 2.01
6021 7617 7.201767 GCAATAGCCAGTATTTCTCTGTTTGAT 60.202 37.037 0.00 0.00 33.58 2.57
6097 7699 4.092279 TCTCTCATGGATGAACTCACTGT 58.908 43.478 0.00 0.00 36.18 3.55
6134 7736 6.325919 TGTAAATCAATTTTCTTCCTGCGT 57.674 33.333 0.00 0.00 0.00 5.24
6136 7738 4.853924 AATCAATTTTCTTCCTGCGTGT 57.146 36.364 0.00 0.00 0.00 4.49
6170 7772 1.070134 ACTTTGTAGGCGCAGAGTTGA 59.930 47.619 10.83 0.00 30.91 3.18
6171 7773 2.143122 CTTTGTAGGCGCAGAGTTGAA 58.857 47.619 10.83 0.00 0.00 2.69
6172 7774 2.248280 TTGTAGGCGCAGAGTTGAAA 57.752 45.000 10.83 0.00 0.00 2.69
6173 7775 2.248280 TGTAGGCGCAGAGTTGAAAA 57.752 45.000 10.83 0.00 0.00 2.29
6174 7776 2.143122 TGTAGGCGCAGAGTTGAAAAG 58.857 47.619 10.83 0.00 0.00 2.27
6189 7791 4.722700 AAGGCAGCCGGCGATGTT 62.723 61.111 23.20 11.15 46.16 2.71
6303 7905 3.386237 GCTGCCCTCACCGTCTCT 61.386 66.667 0.00 0.00 0.00 3.10
6375 7977 4.508662 CACTCCCTCACTGAATAAAGACC 58.491 47.826 0.00 0.00 0.00 3.85
6376 7978 4.223923 CACTCCCTCACTGAATAAAGACCT 59.776 45.833 0.00 0.00 0.00 3.85
6378 7980 6.098982 CACTCCCTCACTGAATAAAGACCTAT 59.901 42.308 0.00 0.00 0.00 2.57
6385 7997 6.897966 TCACTGAATAAAGACCTATGGAGAGT 59.102 38.462 0.00 0.00 0.00 3.24
6418 8031 5.002516 AGAGTTGAAGAAGCAGAAATCCAG 58.997 41.667 0.00 0.00 0.00 3.86
6419 8032 4.978099 AGTTGAAGAAGCAGAAATCCAGA 58.022 39.130 0.00 0.00 0.00 3.86
6420 8033 4.759183 AGTTGAAGAAGCAGAAATCCAGAC 59.241 41.667 0.00 0.00 0.00 3.51
6434 8047 0.912486 CCAGACGGGGAAAAGAGGAT 59.088 55.000 0.00 0.00 0.00 3.24
6443 8056 4.081087 CGGGGAAAAGAGGATGAAGAGTTA 60.081 45.833 0.00 0.00 0.00 2.24
6447 8060 7.168905 GGGAAAAGAGGATGAAGAGTTAAAGA 58.831 38.462 0.00 0.00 0.00 2.52
6514 8128 1.202031 GCTTTAACGGGCACGAATCTG 60.202 52.381 19.19 2.85 44.60 2.90
6550 8164 3.292492 TGGAGTAGGAGAGCGTCATAA 57.708 47.619 0.00 0.00 0.00 1.90
6642 8256 4.885426 GGTGATGATGCCGATGGT 57.115 55.556 0.00 0.00 0.00 3.55
6644 8258 1.800805 GGTGATGATGCCGATGGTAG 58.199 55.000 0.00 0.00 0.00 3.18
6645 8259 1.151668 GTGATGATGCCGATGGTAGC 58.848 55.000 0.00 0.00 0.00 3.58
6646 8260 0.035317 TGATGATGCCGATGGTAGCC 59.965 55.000 0.00 0.00 0.00 3.93
6647 8261 0.035317 GATGATGCCGATGGTAGCCA 59.965 55.000 0.00 0.00 38.19 4.75
6693 8310 4.422073 TCCATGGCAACGAATATCTCTT 57.578 40.909 6.96 0.00 42.51 2.85
6695 8312 3.879295 CCATGGCAACGAATATCTCTTGT 59.121 43.478 0.00 0.00 42.51 3.16
6698 8315 5.545658 TGGCAACGAATATCTCTTGTTTC 57.454 39.130 0.00 0.00 42.51 2.78
6791 8408 1.737735 CGCAAGTGTCCGAGATGCA 60.738 57.895 0.00 0.00 36.84 3.96
6794 8411 2.487934 GCAAGTGTCCGAGATGCATAT 58.512 47.619 0.00 0.00 37.00 1.78
6795 8412 2.478134 GCAAGTGTCCGAGATGCATATC 59.522 50.000 11.38 11.38 37.00 1.63
6796 8413 3.062763 CAAGTGTCCGAGATGCATATCC 58.937 50.000 15.42 2.66 33.64 2.59
6797 8414 2.319844 AGTGTCCGAGATGCATATCCA 58.680 47.619 15.42 5.29 33.64 3.41
6798 8415 2.036475 AGTGTCCGAGATGCATATCCAC 59.964 50.000 15.42 16.14 33.64 4.02
6799 8416 2.038659 TGTCCGAGATGCATATCCACA 58.961 47.619 15.42 14.60 33.64 4.17
6800 8417 2.036346 TGTCCGAGATGCATATCCACAG 59.964 50.000 15.42 1.63 33.64 3.66
6801 8418 1.620323 TCCGAGATGCATATCCACAGG 59.380 52.381 15.42 10.65 33.64 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 5.422214 TTCCTTAGGTTTTGGTGCAAAAA 57.578 34.783 0.00 0.00 43.50 1.94
49 50 5.422214 TTTCCTTAGGTTTTGGTGCAAAA 57.578 34.783 0.00 0.00 40.41 2.44
50 51 5.046231 AGTTTTCCTTAGGTTTTGGTGCAAA 60.046 36.000 0.00 0.00 0.00 3.68
51 52 4.468153 AGTTTTCCTTAGGTTTTGGTGCAA 59.532 37.500 0.00 0.00 0.00 4.08
52 53 4.027437 AGTTTTCCTTAGGTTTTGGTGCA 58.973 39.130 0.00 0.00 0.00 4.57
53 54 4.665833 AGTTTTCCTTAGGTTTTGGTGC 57.334 40.909 0.00 0.00 0.00 5.01
54 55 6.183360 TGCTTAGTTTTCCTTAGGTTTTGGTG 60.183 38.462 0.00 0.00 0.00 4.17
55 56 5.894964 TGCTTAGTTTTCCTTAGGTTTTGGT 59.105 36.000 0.00 0.00 0.00 3.67
56 57 6.399639 TGCTTAGTTTTCCTTAGGTTTTGG 57.600 37.500 0.00 0.00 0.00 3.28
57 58 8.710835 TTTTGCTTAGTTTTCCTTAGGTTTTG 57.289 30.769 0.00 0.00 0.00 2.44
118 137 3.585732 TCCTTCTTCGGGATTTAGGTGTT 59.414 43.478 0.00 0.00 0.00 3.32
124 143 2.092592 GCCCTTCCTTCTTCGGGATTTA 60.093 50.000 0.00 0.00 39.08 1.40
146 165 3.649986 GCCATATGTCGCACGCCC 61.650 66.667 1.24 0.00 0.00 6.13
147 166 1.785041 ATTGCCATATGTCGCACGCC 61.785 55.000 6.19 0.00 33.97 5.68
163 182 0.725686 CAGGAAGCGAGCAGACATTG 59.274 55.000 0.00 0.00 0.00 2.82
164 183 0.322975 ACAGGAAGCGAGCAGACATT 59.677 50.000 0.00 0.00 0.00 2.71
165 184 0.108424 GACAGGAAGCGAGCAGACAT 60.108 55.000 0.00 0.00 0.00 3.06
166 185 1.290324 GACAGGAAGCGAGCAGACA 59.710 57.895 0.00 0.00 0.00 3.41
167 186 1.446966 GGACAGGAAGCGAGCAGAC 60.447 63.158 0.00 0.00 0.00 3.51
168 187 1.908299 TGGACAGGAAGCGAGCAGA 60.908 57.895 0.00 0.00 0.00 4.26
169 188 1.739562 GTGGACAGGAAGCGAGCAG 60.740 63.158 0.00 0.00 0.00 4.24
170 189 2.343758 GTGGACAGGAAGCGAGCA 59.656 61.111 0.00 0.00 0.00 4.26
171 190 2.435059 GGTGGACAGGAAGCGAGC 60.435 66.667 0.00 0.00 0.00 5.03
172 191 0.250295 TTTGGTGGACAGGAAGCGAG 60.250 55.000 0.00 0.00 0.00 5.03
173 192 0.181587 TTTTGGTGGACAGGAAGCGA 59.818 50.000 0.00 0.00 0.00 4.93
174 193 1.028905 TTTTTGGTGGACAGGAAGCG 58.971 50.000 0.00 0.00 0.00 4.68
175 194 4.556233 GTTATTTTTGGTGGACAGGAAGC 58.444 43.478 0.00 0.00 0.00 3.86
176 195 4.832823 AGGTTATTTTTGGTGGACAGGAAG 59.167 41.667 0.00 0.00 0.00 3.46
177 196 4.810345 AGGTTATTTTTGGTGGACAGGAA 58.190 39.130 0.00 0.00 0.00 3.36
178 197 4.105697 AGAGGTTATTTTTGGTGGACAGGA 59.894 41.667 0.00 0.00 0.00 3.86
179 198 4.407365 AGAGGTTATTTTTGGTGGACAGG 58.593 43.478 0.00 0.00 0.00 4.00
180 199 5.648092 CCTAGAGGTTATTTTTGGTGGACAG 59.352 44.000 0.00 0.00 0.00 3.51
181 200 5.566469 CCTAGAGGTTATTTTTGGTGGACA 58.434 41.667 0.00 0.00 0.00 4.02
223 242 0.322456 TCGAGAGCAACCAATTGGGG 60.322 55.000 27.89 19.75 42.91 4.96
224 243 1.470098 CTTCGAGAGCAACCAATTGGG 59.530 52.381 27.89 12.58 44.81 4.12
259 278 7.854557 ATAAAAACGGAAGGAGTATTACACC 57.145 36.000 2.34 2.34 0.00 4.16
342 363 7.531716 TGTTCGTCACTGTTTAGATTGTTTTT 58.468 30.769 0.00 0.00 0.00 1.94
403 431 1.534717 AAACTTGCTGCCATGCCCT 60.535 52.632 0.00 0.00 0.00 5.19
434 462 8.779303 CACAAACTTGTAACATTGTATCTGGTA 58.221 33.333 0.00 0.00 39.91 3.25
436 464 6.582295 GCACAAACTTGTAACATTGTATCTGG 59.418 38.462 0.00 0.00 39.91 3.86
445 473 4.400884 TGGAACAGCACAAACTTGTAACAT 59.599 37.500 0.00 0.00 39.91 2.71
454 482 5.048364 TGGTACAATATGGAACAGCACAAAC 60.048 40.000 0.00 0.00 37.19 2.93
460 488 6.970484 CCTTAATGGTACAATATGGAACAGC 58.030 40.000 0.00 0.00 44.64 4.40
489 517 0.462047 GCCCAACGTCATGTCCTAGG 60.462 60.000 0.82 0.82 0.00 3.02
492 520 1.003355 CAGCCCAACGTCATGTCCT 60.003 57.895 0.00 0.00 0.00 3.85
497 525 1.078426 GTAGCCAGCCCAACGTCAT 60.078 57.895 0.00 0.00 0.00 3.06
612 640 3.064271 GCGTTGTACAAACTTTGACCAGA 59.936 43.478 10.51 0.00 0.00 3.86
613 641 3.064820 AGCGTTGTACAAACTTTGACCAG 59.935 43.478 10.51 0.00 0.00 4.00
616 644 7.007099 GCATATTAGCGTTGTACAAACTTTGAC 59.993 37.037 10.51 0.00 0.00 3.18
657 843 0.768221 AGAGCCCACTCCAAACTCCA 60.768 55.000 0.00 0.00 44.65 3.86
671 857 3.839432 CTCGGTCCGGGAAGAGCC 61.839 72.222 4.69 4.87 0.00 4.70
672 858 3.839432 CCTCGGTCCGGGAAGAGC 61.839 72.222 14.38 0.29 0.00 4.09
673 859 3.839432 GCCTCGGTCCGGGAAGAG 61.839 72.222 14.38 18.62 0.00 2.85
685 871 4.069232 TCACTTGGAGCGGCCTCG 62.069 66.667 0.00 0.00 39.06 4.63
686 872 2.435059 GTCACTTGGAGCGGCCTC 60.435 66.667 0.00 0.00 37.63 4.70
687 873 2.925170 AGTCACTTGGAGCGGCCT 60.925 61.111 0.00 0.00 37.63 5.19
688 874 2.743928 CAGTCACTTGGAGCGGCC 60.744 66.667 0.00 0.00 37.10 6.13
689 875 2.507110 TAGCAGTCACTTGGAGCGGC 62.507 60.000 0.00 0.00 0.00 6.53
690 876 0.037326 TTAGCAGTCACTTGGAGCGG 60.037 55.000 0.00 0.00 0.00 5.52
691 877 2.015736 ATTAGCAGTCACTTGGAGCG 57.984 50.000 0.00 0.00 0.00 5.03
692 878 3.249559 GCATATTAGCAGTCACTTGGAGC 59.750 47.826 0.00 0.00 0.00 4.70
693 879 3.492383 CGCATATTAGCAGTCACTTGGAG 59.508 47.826 0.00 0.00 0.00 3.86
694 880 3.132111 TCGCATATTAGCAGTCACTTGGA 59.868 43.478 0.00 0.00 0.00 3.53
695 881 3.457234 TCGCATATTAGCAGTCACTTGG 58.543 45.455 0.00 0.00 0.00 3.61
696 882 4.568359 ACTTCGCATATTAGCAGTCACTTG 59.432 41.667 0.00 0.00 0.00 3.16
697 883 4.759782 ACTTCGCATATTAGCAGTCACTT 58.240 39.130 0.00 0.00 0.00 3.16
698 884 4.392921 ACTTCGCATATTAGCAGTCACT 57.607 40.909 0.00 0.00 0.00 3.41
699 885 6.583912 TTTACTTCGCATATTAGCAGTCAC 57.416 37.500 0.00 0.00 0.00 3.67
700 886 6.983890 TCATTTACTTCGCATATTAGCAGTCA 59.016 34.615 0.00 0.00 0.00 3.41
701 887 7.408132 TCATTTACTTCGCATATTAGCAGTC 57.592 36.000 0.00 0.00 0.00 3.51
702 888 7.786178 TTCATTTACTTCGCATATTAGCAGT 57.214 32.000 0.00 0.00 0.00 4.40
703 889 8.947940 GTTTTCATTTACTTCGCATATTAGCAG 58.052 33.333 0.00 0.00 0.00 4.24
704 890 8.454894 TGTTTTCATTTACTTCGCATATTAGCA 58.545 29.630 0.00 0.00 0.00 3.49
705 891 8.835467 TGTTTTCATTTACTTCGCATATTAGC 57.165 30.769 0.00 0.00 0.00 3.09
708 894 8.730680 ACTCTGTTTTCATTTACTTCGCATATT 58.269 29.630 0.00 0.00 0.00 1.28
709 895 8.268850 ACTCTGTTTTCATTTACTTCGCATAT 57.731 30.769 0.00 0.00 0.00 1.78
710 896 7.667043 ACTCTGTTTTCATTTACTTCGCATA 57.333 32.000 0.00 0.00 0.00 3.14
711 897 6.560253 ACTCTGTTTTCATTTACTTCGCAT 57.440 33.333 0.00 0.00 0.00 4.73
712 898 6.371809 AACTCTGTTTTCATTTACTTCGCA 57.628 33.333 0.00 0.00 0.00 5.10
713 899 6.910433 TCAAACTCTGTTTTCATTTACTTCGC 59.090 34.615 0.00 0.00 0.00 4.70
714 900 8.835467 TTCAAACTCTGTTTTCATTTACTTCG 57.165 30.769 0.00 0.00 0.00 3.79
715 901 9.788960 ACTTCAAACTCTGTTTTCATTTACTTC 57.211 29.630 0.00 0.00 0.00 3.01
716 902 9.573133 CACTTCAAACTCTGTTTTCATTTACTT 57.427 29.630 0.00 0.00 0.00 2.24
717 903 8.190784 CCACTTCAAACTCTGTTTTCATTTACT 58.809 33.333 0.00 0.00 0.00 2.24
718 904 7.435192 CCCACTTCAAACTCTGTTTTCATTTAC 59.565 37.037 0.00 0.00 0.00 2.01
719 905 7.488322 CCCACTTCAAACTCTGTTTTCATTTA 58.512 34.615 0.00 0.00 0.00 1.40
720 906 6.340522 CCCACTTCAAACTCTGTTTTCATTT 58.659 36.000 0.00 0.00 0.00 2.32
721 907 5.682212 GCCCACTTCAAACTCTGTTTTCATT 60.682 40.000 0.00 0.00 0.00 2.57
722 908 4.202151 GCCCACTTCAAACTCTGTTTTCAT 60.202 41.667 0.00 0.00 0.00 2.57
723 909 3.130340 GCCCACTTCAAACTCTGTTTTCA 59.870 43.478 0.00 0.00 0.00 2.69
724 910 3.381590 AGCCCACTTCAAACTCTGTTTTC 59.618 43.478 0.00 0.00 0.00 2.29
725 911 3.365472 AGCCCACTTCAAACTCTGTTTT 58.635 40.909 0.00 0.00 0.00 2.43
726 912 2.952310 GAGCCCACTTCAAACTCTGTTT 59.048 45.455 0.00 0.00 0.00 2.83
727 913 2.173569 AGAGCCCACTTCAAACTCTGTT 59.826 45.455 0.00 0.00 36.39 3.16
728 914 1.771255 AGAGCCCACTTCAAACTCTGT 59.229 47.619 0.00 0.00 36.39 3.41
729 915 2.557920 AGAGCCCACTTCAAACTCTG 57.442 50.000 0.00 0.00 36.39 3.35
730 916 2.224646 GGAAGAGCCCACTTCAAACTCT 60.225 50.000 14.63 0.00 45.39 3.24
731 917 2.155279 GGAAGAGCCCACTTCAAACTC 58.845 52.381 14.63 0.00 45.39 3.01
732 918 2.278332 GGAAGAGCCCACTTCAAACT 57.722 50.000 14.63 0.00 45.39 2.66
814 1001 2.199236 CATAAACCCTAGCGGACGAAC 58.801 52.381 4.45 0.00 34.64 3.95
818 1005 0.534427 GGCCATAAACCCTAGCGGAC 60.534 60.000 0.00 0.00 34.64 4.79
983 1190 3.776016 ATGGCTACGGGAGGGGAGG 62.776 68.421 0.00 0.00 0.00 4.30
987 1194 4.256180 GCCATGGCTACGGGAGGG 62.256 72.222 29.98 0.00 38.26 4.30
1222 1435 3.064207 GAGACCGTCATAAACTGCACAA 58.936 45.455 0.40 0.00 0.00 3.33
1255 1468 4.504916 CGCAGGACCGAGCTCAGG 62.505 72.222 15.40 17.55 0.00 3.86
1489 1718 1.000731 GCGATCTGAATAGCCAGCTCT 59.999 52.381 0.00 0.00 34.28 4.09
1498 1727 1.032794 ACTGCTCCGCGATCTGAATA 58.967 50.000 8.23 0.00 0.00 1.75
1534 1763 2.485122 CAAACCAAGCCGATCGCC 59.515 61.111 10.32 0.00 38.78 5.54
1620 1851 4.002982 TGTTGCAGTATGAACATCCAGTC 58.997 43.478 0.00 0.00 39.69 3.51
1622 1853 4.732647 GCATGTTGCAGTATGAACATCCAG 60.733 45.833 14.32 0.00 44.26 3.86
1638 1870 2.063266 GCAAGGACACAATGCATGTTG 58.937 47.619 0.00 2.76 41.46 3.33
1646 1878 2.257286 GATGCGCGCAAGGACACAAT 62.257 55.000 39.68 18.85 38.28 2.71
1679 1911 7.624360 TTCACAACCAGCAATTATAACTAGG 57.376 36.000 0.00 0.00 0.00 3.02
1681 1913 9.019656 ACAATTCACAACCAGCAATTATAACTA 57.980 29.630 0.00 0.00 0.00 2.24
1686 1919 5.933463 CCAACAATTCACAACCAGCAATTAT 59.067 36.000 0.00 0.00 0.00 1.28
1757 1993 0.178068 ATTCTAACAGCGCCACCGAT 59.822 50.000 2.29 0.00 36.29 4.18
1762 1998 6.995511 ATACTAAAAATTCTAACAGCGCCA 57.004 33.333 2.29 0.00 0.00 5.69
1784 2020 7.517320 TCACCACATTGAAATAGGCTACATAT 58.483 34.615 0.00 0.00 0.00 1.78
1785 2021 6.894682 TCACCACATTGAAATAGGCTACATA 58.105 36.000 0.00 0.00 0.00 2.29
1869 2119 5.014333 TGGGCTCCTATAACAACCAACTTAA 59.986 40.000 0.00 0.00 0.00 1.85
1876 2126 3.556423 CGGTATGGGCTCCTATAACAACC 60.556 52.174 7.87 1.19 0.00 3.77
1886 2136 1.947456 GAAATTGTCGGTATGGGCTCC 59.053 52.381 0.00 0.00 0.00 4.70
1929 2183 8.753497 TTATACTGAGCAGAAGTAATCAGAGA 57.247 34.615 4.21 0.00 41.35 3.10
2010 2303 8.786826 TGACGAATACTTGATTTGAATAGGTT 57.213 30.769 0.00 0.00 33.58 3.50
2016 2309 7.905604 ACTGATGACGAATACTTGATTTGAA 57.094 32.000 0.00 0.00 33.58 2.69
2090 2387 2.157738 CTCCTCCAACAAGCTGGAAAG 58.842 52.381 0.00 0.00 44.97 2.62
2175 2472 9.101325 CCTATATTGTCTTAGGTTAGGATTGGA 57.899 37.037 0.00 0.00 32.00 3.53
2225 2526 6.741992 TTAATCACATGCCTCACTTACAAG 57.258 37.500 0.00 0.00 0.00 3.16
2255 2585 1.079503 GCCTTGTTGATGGTCGAGTC 58.920 55.000 0.00 0.00 0.00 3.36
2260 2590 5.643379 TTAAATGAGCCTTGTTGATGGTC 57.357 39.130 0.00 0.00 0.00 4.02
2277 2607 7.078249 AGCTTTTCCACTTTGGGATTTAAAT 57.922 32.000 0.00 0.00 38.32 1.40
2346 2681 1.140652 CACATGTTGGCCAAAAGGGTT 59.859 47.619 23.62 1.22 39.65 4.11
2362 2697 0.250513 GAGAACCGGAGAAGCCACAT 59.749 55.000 9.46 0.00 35.94 3.21
2409 2744 3.832490 AGAAATGGAAGTTAAAGGGGCAC 59.168 43.478 0.00 0.00 0.00 5.01
2500 2842 9.995003 AATTCTAAATGCACTTTGTTTGGAATA 57.005 25.926 16.72 0.00 40.09 1.75
2537 2879 7.930865 TGAAAACTTGATAAAACTTTGATGGGG 59.069 33.333 0.00 0.00 0.00 4.96
2755 3385 8.480501 TGTATACCTAAGTCCCATGTCTTTTAC 58.519 37.037 0.00 0.00 0.00 2.01
2758 3388 7.402071 TCTTGTATACCTAAGTCCCATGTCTTT 59.598 37.037 0.00 0.00 0.00 2.52
2898 3793 7.141758 ACCTGCATTTTAGAGGAGATGATAA 57.858 36.000 0.00 0.00 0.00 1.75
3058 3955 7.170965 ACATCAAACAATCAGAATGGTCTAGT 58.829 34.615 0.00 0.00 36.16 2.57
3078 3975 5.539574 ACAACCAATCATTTTCCTGACATCA 59.460 36.000 0.00 0.00 0.00 3.07
3209 4211 2.943036 TAACACTTCAGGGGAACACC 57.057 50.000 0.00 0.00 39.11 4.16
3373 4452 8.850452 GCAATTGCAACTAAGAAACTATTACAC 58.150 33.333 25.36 0.00 41.59 2.90
3430 4520 5.367937 AGGCTCCAGACAGTATAATCAACAT 59.632 40.000 0.00 0.00 0.00 2.71
3446 4536 2.787994 AGTTGACAATGAAGGCTCCAG 58.212 47.619 0.00 0.00 0.00 3.86
3447 4537 2.957402 AGTTGACAATGAAGGCTCCA 57.043 45.000 0.00 0.00 0.00 3.86
3715 4805 7.033530 TCACTGAATGAAACCGTAACAAAAT 57.966 32.000 0.00 0.00 33.02 1.82
3724 4814 1.522668 TGGCTCACTGAATGAAACCG 58.477 50.000 0.00 0.00 36.70 4.44
3725 4815 4.301628 CTTTTGGCTCACTGAATGAAACC 58.698 43.478 0.00 0.00 36.69 3.27
3728 4825 3.569701 GTCCTTTTGGCTCACTGAATGAA 59.430 43.478 0.00 0.00 40.12 2.57
3730 4827 3.152341 AGTCCTTTTGGCTCACTGAATG 58.848 45.455 0.00 0.00 40.12 2.67
3789 4888 2.235016 TGGTAAACAAGGCCACATCAC 58.765 47.619 5.01 0.00 0.00 3.06
3881 4980 7.828508 ATGATGCACAGTTCACCATAATAAT 57.171 32.000 0.00 0.00 0.00 1.28
3883 4982 7.643569 AAATGATGCACAGTTCACCATAATA 57.356 32.000 0.00 0.00 30.81 0.98
3887 4986 4.039488 ACAAAATGATGCACAGTTCACCAT 59.961 37.500 0.00 0.00 35.72 3.55
4095 5201 3.816523 TGCTTTACCTTAACAGGGTTTCG 59.183 43.478 0.00 0.00 46.01 3.46
4117 5223 8.302438 GCTGCTTATTGAATGCCTAAAATAGAT 58.698 33.333 0.00 0.00 0.00 1.98
4154 5267 0.961753 GCCCAAAAGGTCCTGTTCTG 59.038 55.000 0.00 0.00 38.26 3.02
4159 5272 3.373565 GCGGCCCAAAAGGTCCTG 61.374 66.667 0.00 0.00 36.62 3.86
4335 5448 0.879090 AAACGGATTTCGGCACTTCC 59.121 50.000 0.00 0.00 44.45 3.46
4357 5470 6.625267 ACTACAGGTCCTGATATTGAGGTAT 58.375 40.000 26.18 0.58 35.18 2.73
4515 5631 4.016105 AGAGGAGAATCTTAGTCCCAAGGA 60.016 45.833 0.00 0.00 33.73 3.36
4650 5916 4.106029 TCAGTAATCGAGCCACTGTTAC 57.894 45.455 18.08 8.60 40.44 2.50
4699 5966 6.683974 ACAAGATAACAATCCTGAAATCGG 57.316 37.500 0.00 0.00 0.00 4.18
4747 6014 3.364068 GCACGAAGATCATGATCATGCTG 60.364 47.826 31.99 22.26 40.22 4.41
4872 6139 8.920665 CAAGTACTTTTGTCTGTCTGATAGAAG 58.079 37.037 5.07 2.93 35.26 2.85
4895 6162 5.127519 TGCATAACTGAATGGGGAAATCAAG 59.872 40.000 0.00 0.00 0.00 3.02
4920 6499 2.943033 CACTTATACGGCCTCAAAAGGG 59.057 50.000 0.00 0.00 43.58 3.95
5167 6749 5.715753 AGGTACTGAAGTAAACAGGGTAGAG 59.284 44.000 0.00 0.00 37.18 2.43
5421 7003 0.933097 CCAGCTATGTGTGCGATGAC 59.067 55.000 0.00 0.00 35.28 3.06
5424 7006 2.401583 TTTCCAGCTATGTGTGCGAT 57.598 45.000 0.00 0.00 35.28 4.58
5436 7019 4.240888 GGCTTCAGAAAGAAATTTCCAGC 58.759 43.478 14.61 10.13 35.40 4.85
5442 7025 3.771479 GGGGATGGCTTCAGAAAGAAATT 59.229 43.478 2.60 0.00 35.40 1.82
5619 7202 1.208776 TCACTGCAGCAGTCATAGCAT 59.791 47.619 25.89 0.00 43.43 3.79
5747 7331 1.185618 TCTGTCGGTGACCTCTTGGG 61.186 60.000 0.00 0.00 41.89 4.12
5769 7353 5.793817 TGATGATTTCTTGAAAGACCTCGA 58.206 37.500 2.25 0.00 34.13 4.04
5867 7461 1.090052 AATAGCTTTCGCGAGGTGGC 61.090 55.000 9.59 12.30 42.32 5.01
5910 7504 3.181455 ACAATATAGCTGGTGCATCGGAA 60.181 43.478 10.85 0.00 42.74 4.30
5935 7529 1.737793 GCGCTGGTGCAACTTAGTAAT 59.262 47.619 2.04 0.00 39.64 1.89
6064 7661 6.111382 TCATCCATGAGAGAATGAGTTCAAC 58.889 40.000 0.00 0.00 33.13 3.18
6066 7663 5.945144 TCATCCATGAGAGAATGAGTTCA 57.055 39.130 0.00 0.00 33.13 3.18
6097 7699 5.222079 TGATTTACAGCAGTGTAACCAGA 57.778 39.130 0.00 0.00 46.63 3.86
6134 7736 2.361757 CAAAGTGGCAGTTCATTGGACA 59.638 45.455 8.24 0.00 0.00 4.02
6136 7738 2.665165 ACAAAGTGGCAGTTCATTGGA 58.335 42.857 8.24 0.00 0.00 3.53
6170 7772 3.443045 CATCGCCGGCTGCCTTTT 61.443 61.111 26.68 0.00 36.24 2.27
6171 7773 4.722700 ACATCGCCGGCTGCCTTT 62.723 61.111 26.68 0.00 36.24 3.11
6172 7774 4.722700 AACATCGCCGGCTGCCTT 62.723 61.111 26.68 7.69 36.24 4.35
6189 7791 3.599285 CTAAGGCCGGCCACGTTCA 62.599 63.158 45.13 22.07 38.78 3.18
6288 7890 3.695606 GCAGAGACGGTGAGGGCA 61.696 66.667 0.00 0.00 0.00 5.36
6339 7941 0.036858 GGAGTGCCTCTGAGTTGGAC 60.037 60.000 3.66 0.91 0.00 4.02
6375 7977 6.542821 ACTCTTCATCCTCTACTCTCCATAG 58.457 44.000 0.00 0.00 0.00 2.23
6376 7978 6.523035 ACTCTTCATCCTCTACTCTCCATA 57.477 41.667 0.00 0.00 0.00 2.74
6378 7980 4.871871 ACTCTTCATCCTCTACTCTCCA 57.128 45.455 0.00 0.00 0.00 3.86
6385 7997 5.481824 TGCTTCTTCAACTCTTCATCCTCTA 59.518 40.000 0.00 0.00 0.00 2.43
6418 8031 2.236395 TCTTCATCCTCTTTTCCCCGTC 59.764 50.000 0.00 0.00 0.00 4.79
6419 8032 2.237392 CTCTTCATCCTCTTTTCCCCGT 59.763 50.000 0.00 0.00 0.00 5.28
6420 8033 2.237392 ACTCTTCATCCTCTTTTCCCCG 59.763 50.000 0.00 0.00 0.00 5.73
6434 8047 7.768807 AAGCTCTACTCTCTTTAACTCTTCA 57.231 36.000 0.00 0.00 0.00 3.02
6443 8056 6.665680 TCATCAAGGTAAGCTCTACTCTCTTT 59.334 38.462 0.00 0.00 0.00 2.52
6447 8060 4.892934 CCTCATCAAGGTAAGCTCTACTCT 59.107 45.833 0.00 0.00 40.67 3.24
6514 8128 1.376037 CCAAGCAAGAGGTCGGTCC 60.376 63.158 0.00 0.00 0.00 4.46
6550 8164 0.890996 CAGCTTTCACTTTCGGCCCT 60.891 55.000 0.00 0.00 0.00 5.19
6639 8253 2.818169 GGATGGGCGATGGCTACCA 61.818 63.158 0.00 0.00 39.81 3.25
6640 8254 2.032681 GGATGGGCGATGGCTACC 59.967 66.667 0.00 0.00 39.81 3.18
6641 8255 2.032681 GGGATGGGCGATGGCTAC 59.967 66.667 0.00 0.00 39.81 3.58
6642 8256 1.352622 AAAGGGATGGGCGATGGCTA 61.353 55.000 0.00 0.00 39.81 3.93
6643 8257 2.631012 GAAAGGGATGGGCGATGGCT 62.631 60.000 0.00 0.00 39.81 4.75
6644 8258 2.123726 AAAGGGATGGGCGATGGC 60.124 61.111 0.00 0.00 38.90 4.40
6645 8259 1.103398 GTGAAAGGGATGGGCGATGG 61.103 60.000 0.00 0.00 0.00 3.51
6646 8260 1.103398 GGTGAAAGGGATGGGCGATG 61.103 60.000 0.00 0.00 0.00 3.84
6647 8261 1.227383 GGTGAAAGGGATGGGCGAT 59.773 57.895 0.00 0.00 0.00 4.58
6649 8263 2.824041 CGGTGAAAGGGATGGGCG 60.824 66.667 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.