Multiple sequence alignment - TraesCS4B01G284600

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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 TraesCS4B01G284600 chr4B 100.000 3641 0 0 1 3641 568420075 568416435 0.000000e+00 6724.0
1 TraesCS4B01G284600 chr4B 86.139 101 11 1 1 101 657827623 657827720 4.970000e-19 106.0
2 TraesCS4B01G284600 chr4B 95.833 48 0 1 2627 2672 568417407 568417360 3.900000e-10 76.8
3 TraesCS4B01G284600 chr4B 95.833 48 0 1 2669 2716 568417449 568417404 3.900000e-10 76.8
4 TraesCS4B01G284600 chr4A 96.510 2665 73 12 882 3531 12622616 12625275 0.000000e+00 4388.0
5 TraesCS4B01G284600 chr4A 95.833 48 0 1 2669 2716 12624369 12624414 3.900000e-10 76.8
6 TraesCS4B01G284600 chr4A 93.750 48 1 1 2627 2672 12624411 12624458 1.810000e-08 71.3
7 TraesCS4B01G284600 chr4D 92.951 1901 106 16 785 2672 455329604 455327719 0.000000e+00 2743.0
8 TraesCS4B01G284600 chr4D 94.340 212 11 1 2964 3174 455327134 455326923 1.260000e-84 324.0
9 TraesCS4B01G284600 chr4D 93.421 152 8 1 3382 3531 455326900 455326749 1.320000e-54 224.0
10 TraesCS4B01G284600 chr4D 83.333 90 13 2 3527 3616 78864654 78864741 8.380000e-12 82.4
11 TraesCS4B01G284600 chr6D 85.642 592 67 7 116 691 460404403 460403814 1.120000e-169 606.0
12 TraesCS4B01G284600 chr6D 85.513 497 58 7 179 663 202967104 202966610 1.170000e-139 507.0
13 TraesCS4B01G284600 chr6A 85.640 578 68 8 99 663 290265377 290265952 8.700000e-166 593.0
14 TraesCS4B01G284600 chr6A 83.871 93 14 1 3529 3621 586352888 586352979 1.800000e-13 87.9
15 TraesCS4B01G284600 chr1D 85.442 577 69 7 99 663 363506546 363507119 1.460000e-163 586.0
16 TraesCS4B01G284600 chr1D 90.789 76 7 0 1 76 338746096 338746171 6.430000e-18 102.0
17 TraesCS4B01G284600 chr1D 85.897 78 9 1 1 76 141897360 141897437 8.380000e-12 82.4
18 TraesCS4B01G284600 chr6B 86.074 517 50 9 113 617 640697082 640697588 1.490000e-148 536.0
19 TraesCS4B01G284600 chr6B 95.000 40 2 0 2605 2644 236574943 236574904 3.040000e-06 63.9
20 TraesCS4B01G284600 chr7B 83.420 579 79 7 101 663 113638265 113638842 4.170000e-144 521.0
21 TraesCS4B01G284600 chr7B 85.000 420 52 5 99 509 172567951 172568368 2.020000e-112 416.0
22 TraesCS4B01G284600 chr2D 84.035 570 59 14 99 663 648257509 648258051 1.500000e-143 520.0
23 TraesCS4B01G284600 chr2D 83.275 574 84 8 101 663 4662024 4662596 5.390000e-143 518.0
24 TraesCS4B01G284600 chr2D 86.223 421 44 12 99 514 342463181 342463592 9.280000e-121 444.0
25 TraesCS4B01G284600 chr2D 82.209 163 26 2 501 661 447249774 447249935 1.760000e-28 137.0
26 TraesCS4B01G284600 chr2B 85.106 235 28 1 99 326 618970859 618971093 2.190000e-57 233.0
27 TraesCS4B01G284600 chr2B 91.089 101 9 0 1 101 513269849 513269749 1.760000e-28 137.0
28 TraesCS4B01G284600 chr2B 90.099 101 9 1 1 101 657863689 657863590 2.950000e-26 130.0
29 TraesCS4B01G284600 chr2B 79.058 191 27 7 501 691 526885485 526885662 6.390000e-23 119.0
30 TraesCS4B01G284600 chr3B 83.951 243 31 2 114 349 805778928 805779169 3.660000e-55 226.0
31 TraesCS4B01G284600 chr3B 86.316 95 12 1 3521 3615 41084353 41084446 6.430000e-18 102.0
32 TraesCS4B01G284600 chr3B 92.424 66 5 0 3529 3594 20747277 20747212 1.080000e-15 95.3
33 TraesCS4B01G284600 chr2A 76.577 444 77 17 95 514 513643309 513643749 6.120000e-53 219.0
34 TraesCS4B01G284600 chr1A 91.089 101 9 0 1 101 480575459 480575559 1.760000e-28 137.0
35 TraesCS4B01G284600 chr7A 89.109 101 11 0 1 101 531109211 531109111 3.820000e-25 126.0
36 TraesCS4B01G284600 chr5D 89.796 98 10 0 3 100 300127883 300127786 3.820000e-25 126.0
37 TraesCS4B01G284600 chr3A 87.500 88 11 0 3527 3614 671733600 671733687 6.430000e-18 102.0
38 TraesCS4B01G284600 chr3A 87.500 88 10 1 3529 3616 32829540 32829626 2.310000e-17 100.0
39 TraesCS4B01G284600 chr3D 85.057 87 13 0 3529 3615 114081769 114081855 5.010000e-14 89.8
40 TraesCS4B01G284600 chrUn 83.505 97 13 3 3528 3623 357027323 357027229 1.800000e-13 87.9
41 TraesCS4B01G284600 chr1B 83.505 97 13 3 3528 3623 73363930 73363836 1.800000e-13 87.9
42 TraesCS4B01G284600 chr1B 82.895 76 13 0 1 76 196059326 196059401 6.520000e-08 69.4


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 TraesCS4B01G284600 chr4B 568416435 568420075 3640 True 2292.533333 6724 97.222000 1 3641 3 chr4B.!!$R1 3640
1 TraesCS4B01G284600 chr4A 12622616 12625275 2659 False 1512.033333 4388 95.364333 882 3531 3 chr4A.!!$F1 2649
2 TraesCS4B01G284600 chr4D 455326749 455329604 2855 True 1097.000000 2743 93.570667 785 3531 3 chr4D.!!$R1 2746
3 TraesCS4B01G284600 chr6D 460403814 460404403 589 True 606.000000 606 85.642000 116 691 1 chr6D.!!$R2 575
4 TraesCS4B01G284600 chr6A 290265377 290265952 575 False 593.000000 593 85.640000 99 663 1 chr6A.!!$F1 564
5 TraesCS4B01G284600 chr1D 363506546 363507119 573 False 586.000000 586 85.442000 99 663 1 chr1D.!!$F3 564
6 TraesCS4B01G284600 chr6B 640697082 640697588 506 False 536.000000 536 86.074000 113 617 1 chr6B.!!$F1 504
7 TraesCS4B01G284600 chr7B 113638265 113638842 577 False 521.000000 521 83.420000 101 663 1 chr7B.!!$F1 562
8 TraesCS4B01G284600 chr2D 648257509 648258051 542 False 520.000000 520 84.035000 99 663 1 chr2D.!!$F4 564
9 TraesCS4B01G284600 chr2D 4662024 4662596 572 False 518.000000 518 83.275000 101 663 1 chr2D.!!$F1 562

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
688 711 0.037975 CCTACGGCTACCAAACACGT 60.038 55.0 0.0 0.0 41.1 4.49 F
859 887 0.464036 TGTGGATGCATAGGTCGGAC 59.536 55.0 0.0 0.0 0.0 4.79 F
860 888 0.597637 GTGGATGCATAGGTCGGACG 60.598 60.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1597 1638 1.004277 GGACACTCGTCGAACAGCTG 61.004 60.000 13.48 13.48 43.61 4.24 R
2599 2640 1.134818 TCCAGGATGTGATTTCGACCG 60.135 52.381 0.00 0.00 0.00 4.79 R
2717 2759 4.569943 TCAGTGCTAGATGTTCAGTTTCC 58.430 43.478 0.00 0.00 0.00 3.13 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
20 21 4.424711 GGTGCCGCCCATGGAGAA 62.425 66.667 15.22 0.00 0.00 2.87
21 22 2.825836 GTGCCGCCCATGGAGAAG 60.826 66.667 15.22 0.00 0.00 2.85
22 23 4.113815 TGCCGCCCATGGAGAAGG 62.114 66.667 15.22 11.60 0.00 3.46
27 28 4.672251 CCCATGGAGAAGGGCAAG 57.328 61.111 15.22 0.00 38.44 4.01
28 29 1.076485 CCCATGGAGAAGGGCAAGG 60.076 63.158 15.22 0.00 38.44 3.61
29 30 1.574526 CCCATGGAGAAGGGCAAGGA 61.575 60.000 15.22 0.00 38.44 3.36
30 31 0.106819 CCATGGAGAAGGGCAAGGAG 60.107 60.000 5.56 0.00 0.00 3.69
31 32 0.106819 CATGGAGAAGGGCAAGGAGG 60.107 60.000 0.00 0.00 0.00 4.30
32 33 0.551131 ATGGAGAAGGGCAAGGAGGT 60.551 55.000 0.00 0.00 0.00 3.85
33 34 1.301293 GGAGAAGGGCAAGGAGGTG 59.699 63.158 0.00 0.00 0.00 4.00
34 35 1.301293 GAGAAGGGCAAGGAGGTGG 59.699 63.158 0.00 0.00 0.00 4.61
35 36 1.464198 AGAAGGGCAAGGAGGTGGT 60.464 57.895 0.00 0.00 0.00 4.16
36 37 1.303643 GAAGGGCAAGGAGGTGGTG 60.304 63.158 0.00 0.00 0.00 4.17
37 38 2.771328 GAAGGGCAAGGAGGTGGTGG 62.771 65.000 0.00 0.00 0.00 4.61
51 52 4.740822 GTGGCGCCCATGGAGGTT 62.741 66.667 26.77 0.00 35.28 3.50
52 53 4.738998 TGGCGCCCATGGAGGTTG 62.739 66.667 26.77 0.00 34.66 3.77
53 54 4.740822 GGCGCCCATGGAGGTTGT 62.741 66.667 18.11 0.00 34.66 3.32
54 55 3.443045 GCGCCCATGGAGGTTGTG 61.443 66.667 15.22 3.47 34.66 3.33
55 56 3.443045 CGCCCATGGAGGTTGTGC 61.443 66.667 15.22 4.93 34.66 4.57
56 57 3.070576 GCCCATGGAGGTTGTGCC 61.071 66.667 15.22 0.00 34.66 5.01
57 58 2.751436 CCCATGGAGGTTGTGCCG 60.751 66.667 15.22 0.00 43.70 5.69
58 59 2.350895 CCATGGAGGTTGTGCCGA 59.649 61.111 5.56 0.00 43.70 5.54
59 60 2.040544 CCATGGAGGTTGTGCCGAC 61.041 63.158 5.56 0.00 43.70 4.79
60 61 1.003355 CATGGAGGTTGTGCCGACT 60.003 57.895 0.00 0.00 43.70 4.18
61 62 0.249120 CATGGAGGTTGTGCCGACTA 59.751 55.000 0.00 0.00 43.70 2.59
62 63 0.249398 ATGGAGGTTGTGCCGACTAC 59.751 55.000 0.00 0.00 43.70 2.73
63 64 1.445582 GGAGGTTGTGCCGACTACG 60.446 63.158 0.00 0.00 43.70 3.51
64 65 2.048503 AGGTTGTGCCGACTACGC 60.049 61.111 0.00 0.00 43.70 4.42
65 66 3.116531 GGTTGTGCCGACTACGCC 61.117 66.667 0.00 0.00 38.29 5.68
66 67 2.048503 GTTGTGCCGACTACGCCT 60.049 61.111 0.00 0.00 38.29 5.52
67 68 1.213537 GTTGTGCCGACTACGCCTA 59.786 57.895 0.00 0.00 38.29 3.93
68 69 0.388907 GTTGTGCCGACTACGCCTAA 60.389 55.000 0.00 0.00 38.29 2.69
69 70 0.108992 TTGTGCCGACTACGCCTAAG 60.109 55.000 0.00 0.00 38.29 2.18
70 71 1.226888 GTGCCGACTACGCCTAAGG 60.227 63.158 0.00 0.00 38.29 2.69
71 72 1.378911 TGCCGACTACGCCTAAGGA 60.379 57.895 0.00 0.00 38.29 3.36
72 73 1.359475 GCCGACTACGCCTAAGGAG 59.641 63.158 0.00 0.00 38.29 3.69
73 74 2.031360 CCGACTACGCCTAAGGAGG 58.969 63.158 0.00 0.00 46.93 4.30
74 75 0.750911 CCGACTACGCCTAAGGAGGT 60.751 60.000 0.00 0.00 45.78 3.85
81 82 1.218316 GCCTAAGGAGGTGACCACG 59.782 63.158 3.63 0.00 45.78 4.94
82 83 1.898154 CCTAAGGAGGTGACCACGG 59.102 63.158 3.63 0.00 38.16 4.94
83 84 0.613853 CCTAAGGAGGTGACCACGGA 60.614 60.000 3.63 0.00 38.16 4.69
84 85 1.486211 CTAAGGAGGTGACCACGGAT 58.514 55.000 3.63 0.00 0.00 4.18
85 86 1.137086 CTAAGGAGGTGACCACGGATG 59.863 57.143 3.63 0.00 0.00 3.51
86 87 0.544357 AAGGAGGTGACCACGGATGA 60.544 55.000 3.63 0.00 0.00 2.92
87 88 0.972983 AGGAGGTGACCACGGATGAG 60.973 60.000 3.63 0.00 0.00 2.90
88 89 1.517832 GAGGTGACCACGGATGAGG 59.482 63.158 3.63 0.00 0.00 3.86
89 90 0.970937 GAGGTGACCACGGATGAGGA 60.971 60.000 3.63 0.00 0.00 3.71
90 91 1.218316 GGTGACCACGGATGAGGAC 59.782 63.158 0.00 0.00 0.00 3.85
91 92 1.153823 GTGACCACGGATGAGGACG 60.154 63.158 0.00 0.00 0.00 4.79
92 93 1.605451 TGACCACGGATGAGGACGT 60.605 57.895 0.00 0.00 45.25 4.34
96 97 2.970639 ACGGATGAGGACGTGGTG 59.029 61.111 0.00 0.00 42.39 4.17
97 98 1.605451 ACGGATGAGGACGTGGTGA 60.605 57.895 0.00 0.00 42.39 4.02
107 108 4.590487 CGTGGTGACGGCTAATGT 57.410 55.556 0.00 0.00 42.18 2.71
139 140 2.370445 CCTCGATCAGGGTTGGGCT 61.370 63.158 0.00 0.00 38.91 5.19
160 161 1.741401 CTTCGCCGCTGTCCATCAA 60.741 57.895 0.00 0.00 0.00 2.57
171 172 3.873361 GCTGTCCATCAAATCAGAATCGA 59.127 43.478 0.00 0.00 0.00 3.59
190 191 3.054166 CGACTACATGGTGACGTTCAAA 58.946 45.455 0.00 0.00 0.00 2.69
195 196 0.951558 ATGGTGACGTTCAAACTGCC 59.048 50.000 0.00 0.00 0.00 4.85
304 312 3.498121 CGTCTAGGACTGCCCTTCCTATA 60.498 52.174 5.73 0.00 44.85 1.31
336 344 6.694447 TGGTTTAGTTTCTTATCGTACTGCT 58.306 36.000 0.00 0.00 0.00 4.24
422 434 5.793817 ACTATCTTCTGTTGTGTGTGCATA 58.206 37.500 0.00 0.00 0.00 3.14
481 499 1.439679 CTCGCCAAAGAGGTTACCAC 58.560 55.000 3.51 0.00 40.61 4.16
499 517 3.888323 ACCACACAACAACTATTGCATGA 59.112 39.130 0.00 0.00 32.47 3.07
504 522 4.685628 CACAACAACTATTGCATGAAACCC 59.314 41.667 0.00 0.00 32.47 4.11
540 558 0.675837 GTGAGCTGAGCCAATGCAGA 60.676 55.000 0.00 0.00 41.13 4.26
557 575 2.165030 GCAGACAACCAAATGCTATGCT 59.835 45.455 0.00 0.00 35.78 3.79
579 597 4.989279 AAAATTGCTCACCTAATGCGAT 57.011 36.364 0.00 0.00 32.72 4.58
603 621 2.381911 CCTAGATGCAGGCAACCAAAT 58.618 47.619 0.00 0.00 37.17 2.32
684 707 0.461516 GGCTCCTACGGCTACCAAAC 60.462 60.000 0.00 0.00 0.00 2.93
688 711 0.037975 CCTACGGCTACCAAACACGT 60.038 55.000 0.00 0.00 41.10 4.49
691 714 1.301087 CGGCTACCAAACACGTCCA 60.301 57.895 0.00 0.00 0.00 4.02
692 715 0.672401 CGGCTACCAAACACGTCCAT 60.672 55.000 0.00 0.00 0.00 3.41
693 716 1.530323 GGCTACCAAACACGTCCATT 58.470 50.000 0.00 0.00 0.00 3.16
694 717 1.199097 GGCTACCAAACACGTCCATTG 59.801 52.381 0.00 0.00 0.00 2.82
695 718 1.877443 GCTACCAAACACGTCCATTGT 59.123 47.619 0.00 0.00 0.00 2.71
696 719 2.350388 GCTACCAAACACGTCCATTGTG 60.350 50.000 0.00 0.00 42.99 3.33
702 725 3.934521 CACGTCCATTGTGTTTGCA 57.065 47.368 0.00 0.00 32.68 4.08
703 726 2.420628 CACGTCCATTGTGTTTGCAT 57.579 45.000 0.00 0.00 32.68 3.96
704 727 2.318578 CACGTCCATTGTGTTTGCATC 58.681 47.619 0.00 0.00 32.68 3.91
705 728 1.952990 ACGTCCATTGTGTTTGCATCA 59.047 42.857 0.00 0.00 0.00 3.07
706 729 2.360483 ACGTCCATTGTGTTTGCATCAA 59.640 40.909 0.00 0.00 0.00 2.57
707 730 2.981805 CGTCCATTGTGTTTGCATCAAG 59.018 45.455 0.00 0.00 0.00 3.02
708 731 3.304592 CGTCCATTGTGTTTGCATCAAGA 60.305 43.478 0.00 0.00 0.00 3.02
709 732 4.232221 GTCCATTGTGTTTGCATCAAGAG 58.768 43.478 0.00 0.00 0.00 2.85
710 733 3.890756 TCCATTGTGTTTGCATCAAGAGT 59.109 39.130 0.00 0.00 0.00 3.24
711 734 4.341806 TCCATTGTGTTTGCATCAAGAGTT 59.658 37.500 0.00 0.00 0.00 3.01
712 735 5.534278 TCCATTGTGTTTGCATCAAGAGTTA 59.466 36.000 0.00 0.00 0.00 2.24
713 736 5.860182 CCATTGTGTTTGCATCAAGAGTTAG 59.140 40.000 0.00 0.00 0.00 2.34
714 737 6.294120 CCATTGTGTTTGCATCAAGAGTTAGA 60.294 38.462 0.00 0.00 0.00 2.10
715 738 5.673337 TGTGTTTGCATCAAGAGTTAGAC 57.327 39.130 0.00 0.00 0.00 2.59
716 739 5.368145 TGTGTTTGCATCAAGAGTTAGACT 58.632 37.500 0.00 0.00 0.00 3.24
717 740 5.237127 TGTGTTTGCATCAAGAGTTAGACTG 59.763 40.000 0.00 0.00 0.00 3.51
718 741 4.214119 TGTTTGCATCAAGAGTTAGACTGC 59.786 41.667 0.00 0.00 0.00 4.40
719 742 3.683365 TGCATCAAGAGTTAGACTGCA 57.317 42.857 0.00 0.00 35.93 4.41
720 743 4.212143 TGCATCAAGAGTTAGACTGCAT 57.788 40.909 0.00 0.00 33.59 3.96
721 744 4.186926 TGCATCAAGAGTTAGACTGCATC 58.813 43.478 0.00 0.00 33.59 3.91
722 745 4.186926 GCATCAAGAGTTAGACTGCATCA 58.813 43.478 0.00 0.00 0.00 3.07
723 746 4.815308 GCATCAAGAGTTAGACTGCATCAT 59.185 41.667 0.00 0.00 0.00 2.45
724 747 5.987953 GCATCAAGAGTTAGACTGCATCATA 59.012 40.000 0.00 0.00 0.00 2.15
725 748 6.649973 GCATCAAGAGTTAGACTGCATCATAT 59.350 38.462 0.00 0.00 0.00 1.78
726 749 7.172875 GCATCAAGAGTTAGACTGCATCATATT 59.827 37.037 0.00 0.00 0.00 1.28
727 750 9.053840 CATCAAGAGTTAGACTGCATCATATTT 57.946 33.333 0.00 0.00 0.00 1.40
728 751 9.624373 ATCAAGAGTTAGACTGCATCATATTTT 57.376 29.630 0.00 0.00 0.00 1.82
729 752 9.102757 TCAAGAGTTAGACTGCATCATATTTTC 57.897 33.333 0.00 0.00 0.00 2.29
730 753 9.107177 CAAGAGTTAGACTGCATCATATTTTCT 57.893 33.333 0.00 0.00 0.00 2.52
731 754 8.885494 AGAGTTAGACTGCATCATATTTTCTC 57.115 34.615 0.00 0.00 0.00 2.87
732 755 7.930865 AGAGTTAGACTGCATCATATTTTCTCC 59.069 37.037 0.00 0.00 0.00 3.71
733 756 6.703607 AGTTAGACTGCATCATATTTTCTCCG 59.296 38.462 0.00 0.00 0.00 4.63
734 757 4.384056 AGACTGCATCATATTTTCTCCGG 58.616 43.478 0.00 0.00 0.00 5.14
735 758 4.101585 AGACTGCATCATATTTTCTCCGGA 59.898 41.667 2.93 2.93 0.00 5.14
736 759 4.780815 ACTGCATCATATTTTCTCCGGAA 58.219 39.130 5.23 0.00 0.00 4.30
737 760 5.192927 ACTGCATCATATTTTCTCCGGAAA 58.807 37.500 5.23 0.00 39.38 3.13
738 761 5.829924 ACTGCATCATATTTTCTCCGGAAAT 59.170 36.000 5.23 5.24 40.57 2.17
739 762 6.016777 ACTGCATCATATTTTCTCCGGAAATC 60.017 38.462 5.23 0.00 40.57 2.17
740 763 5.827267 TGCATCATATTTTCTCCGGAAATCA 59.173 36.000 5.23 0.00 40.57 2.57
741 764 6.016860 TGCATCATATTTTCTCCGGAAATCAG 60.017 38.462 5.23 0.00 40.57 2.90
742 765 6.016777 GCATCATATTTTCTCCGGAAATCAGT 60.017 38.462 5.23 0.00 40.57 3.41
743 766 7.579726 CATCATATTTTCTCCGGAAATCAGTC 58.420 38.462 5.23 0.00 40.57 3.51
744 767 6.889198 TCATATTTTCTCCGGAAATCAGTCT 58.111 36.000 5.23 0.00 40.57 3.24
745 768 7.338710 TCATATTTTCTCCGGAAATCAGTCTT 58.661 34.615 5.23 0.00 40.57 3.01
746 769 8.482943 TCATATTTTCTCCGGAAATCAGTCTTA 58.517 33.333 5.23 0.00 40.57 2.10
747 770 9.109393 CATATTTTCTCCGGAAATCAGTCTTAA 57.891 33.333 5.23 0.00 40.57 1.85
748 771 7.617041 ATTTTCTCCGGAAATCAGTCTTAAG 57.383 36.000 5.23 0.00 40.57 1.85
749 772 5.995565 TTCTCCGGAAATCAGTCTTAAGA 57.004 39.130 5.23 0.00 0.00 2.10
750 773 5.995565 TCTCCGGAAATCAGTCTTAAGAA 57.004 39.130 5.23 0.00 0.00 2.52
751 774 6.354794 TCTCCGGAAATCAGTCTTAAGAAA 57.645 37.500 5.23 0.00 0.00 2.52
752 775 6.947464 TCTCCGGAAATCAGTCTTAAGAAAT 58.053 36.000 5.23 0.00 0.00 2.17
753 776 8.074613 TCTCCGGAAATCAGTCTTAAGAAATA 57.925 34.615 5.23 0.00 0.00 1.40
754 777 8.705594 TCTCCGGAAATCAGTCTTAAGAAATAT 58.294 33.333 5.23 0.00 0.00 1.28
755 778 9.331282 CTCCGGAAATCAGTCTTAAGAAATATT 57.669 33.333 5.23 4.39 0.00 1.28
756 779 9.681062 TCCGGAAATCAGTCTTAAGAAATATTT 57.319 29.630 6.78 12.20 0.00 1.40
836 864 9.368674 TCAAATTTGTATGTGCCAGAAATAATG 57.631 29.630 17.47 0.00 0.00 1.90
850 878 7.663827 CCAGAAATAATGTAATGTGGATGCAT 58.336 34.615 0.00 0.00 0.00 3.96
853 881 9.017509 AGAAATAATGTAATGTGGATGCATAGG 57.982 33.333 0.00 0.00 0.00 2.57
854 882 8.710749 AAATAATGTAATGTGGATGCATAGGT 57.289 30.769 0.00 0.00 0.00 3.08
855 883 7.928307 ATAATGTAATGTGGATGCATAGGTC 57.072 36.000 0.00 0.00 0.00 3.85
858 886 1.423584 ATGTGGATGCATAGGTCGGA 58.576 50.000 0.00 0.00 0.00 4.55
859 887 0.464036 TGTGGATGCATAGGTCGGAC 59.536 55.000 0.00 0.00 0.00 4.79
860 888 0.597637 GTGGATGCATAGGTCGGACG 60.598 60.000 0.00 0.00 0.00 4.79
862 890 0.956633 GGATGCATAGGTCGGACGTA 59.043 55.000 12.40 12.40 0.00 3.57
864 892 2.029290 GGATGCATAGGTCGGACGTAAT 60.029 50.000 13.81 4.31 0.00 1.89
865 893 3.554337 GGATGCATAGGTCGGACGTAATT 60.554 47.826 13.81 0.00 0.00 1.40
866 894 3.088194 TGCATAGGTCGGACGTAATTC 57.912 47.619 13.81 7.31 0.00 2.17
867 895 2.691526 TGCATAGGTCGGACGTAATTCT 59.308 45.455 13.81 1.63 0.00 2.40
868 896 3.131577 TGCATAGGTCGGACGTAATTCTT 59.868 43.478 13.81 0.00 0.00 2.52
869 897 3.734735 GCATAGGTCGGACGTAATTCTTC 59.265 47.826 13.81 0.00 0.00 2.87
870 898 4.499357 GCATAGGTCGGACGTAATTCTTCT 60.499 45.833 13.81 0.00 0.00 2.85
871 899 3.505464 AGGTCGGACGTAATTCTTCTG 57.495 47.619 0.75 0.00 0.00 3.02
872 900 2.824341 AGGTCGGACGTAATTCTTCTGT 59.176 45.455 0.75 0.00 0.00 3.41
873 901 3.257624 AGGTCGGACGTAATTCTTCTGTT 59.742 43.478 0.75 0.00 0.00 3.16
874 902 3.992427 GGTCGGACGTAATTCTTCTGTTT 59.008 43.478 1.43 0.00 0.00 2.83
875 903 4.450080 GGTCGGACGTAATTCTTCTGTTTT 59.550 41.667 1.43 0.00 0.00 2.43
876 904 5.389202 GGTCGGACGTAATTCTTCTGTTTTC 60.389 44.000 1.43 0.00 0.00 2.29
877 905 5.404667 GTCGGACGTAATTCTTCTGTTTTCT 59.595 40.000 0.00 0.00 0.00 2.52
878 906 5.987347 TCGGACGTAATTCTTCTGTTTTCTT 59.013 36.000 0.00 0.00 0.00 2.52
879 907 6.480981 TCGGACGTAATTCTTCTGTTTTCTTT 59.519 34.615 0.00 0.00 0.00 2.52
880 908 7.011669 TCGGACGTAATTCTTCTGTTTTCTTTT 59.988 33.333 0.00 0.00 0.00 2.27
985 1025 1.702299 CGCTCTGTCGCCTTTTACG 59.298 57.895 0.00 0.00 0.00 3.18
986 1026 1.420312 GCTCTGTCGCCTTTTACGC 59.580 57.895 0.00 0.00 0.00 4.42
1003 1044 2.938253 CGCACACAACGCAGATGT 59.062 55.556 0.00 0.00 46.93 3.06
1152 1193 3.816524 CTCCTCTTCGCGTCCGCT 61.817 66.667 5.77 0.00 39.32 5.52
1155 1196 2.483745 CTCTTCGCGTCCGCTGTA 59.516 61.111 5.77 0.00 39.32 2.74
1208 1249 2.030401 TGTTCGACCAAATCCCGCG 61.030 57.895 0.00 0.00 0.00 6.46
1464 1505 1.781555 CGTCAAGAACGCGCTCATT 59.218 52.632 12.67 0.00 45.76 2.57
1517 1558 0.819259 GCAGGTGCTCTGTTTGACCA 60.819 55.000 8.88 0.00 45.08 4.02
1597 1638 2.519302 ATATTGGTGCTGCCCGGC 60.519 61.111 1.04 1.04 36.04 6.13
1656 1697 1.631072 GAACGTGATGATCACCGCG 59.369 57.895 21.33 21.33 44.20 6.46
1671 1712 4.849310 GCGTATGCCAAGCGGGGA 62.849 66.667 0.00 0.00 43.39 4.81
1761 1802 3.323115 TGATCTCTGGGTATGTGAGATGC 59.677 47.826 9.10 3.27 44.58 3.91
1944 1985 3.832615 ACTGGTTTTACTGTCGTCCTT 57.167 42.857 0.00 0.00 0.00 3.36
2046 2087 3.906846 AGGATGTCTCAACTTGGAACTCT 59.093 43.478 0.00 0.00 0.00 3.24
2250 2291 1.927487 TTGAGCCCAATGTCAAGCAT 58.073 45.000 0.00 0.00 40.03 3.79
2584 2625 0.895100 TGGCAGCACAAAGGATCCAC 60.895 55.000 15.82 0.00 0.00 4.02
2599 2640 2.533266 TCCACTGCAGTCTTTCAGAC 57.467 50.000 18.64 0.00 45.38 3.51
2683 2725 5.888105 CAGCTTCTGGATTTATTGGTTGAG 58.112 41.667 0.00 0.00 0.00 3.02
2855 2897 6.096141 TGTGAATCTCTCTCTGTTACTCATCC 59.904 42.308 0.00 0.00 0.00 3.51
2945 3310 3.899052 AGGTTAGTTATGCGGCACTAA 57.101 42.857 4.03 6.12 33.89 2.24
2956 3321 1.714794 CGGCACTAACCTTCTGACTG 58.285 55.000 0.00 0.00 0.00 3.51
3237 3617 8.540388 TCCATTAGAGATGTAAAGCACTAAACT 58.460 33.333 0.00 0.00 0.00 2.66
3264 3645 3.573538 TGCAGTACAGGCAATTCAACAAT 59.426 39.130 9.48 0.00 38.54 2.71
3317 3698 0.517316 GATGGTGCACGACAAGTTCC 59.483 55.000 11.45 0.00 0.00 3.62
3333 3714 1.133915 GTTCCGCCCATCCCAAAGATA 60.134 52.381 0.00 0.00 32.37 1.98
3344 3725 7.202084 GCCCATCCCAAAGATATTGGAAATTAA 60.202 37.037 8.75 0.00 42.06 1.40
3462 3845 6.479006 TGAGATTAATGGCCAGAGAATATGG 58.521 40.000 13.05 0.00 41.04 2.74
3481 3864 4.069312 TGGACTACCCATAAAGGACAGA 57.931 45.455 0.00 0.00 40.82 3.41
3532 3915 9.832445 TTGTCTAGTTCAAGTTCTGAAAATACT 57.168 29.630 0.00 0.00 45.67 2.12
3547 3930 8.648693 TCTGAAAATACTAAGAATACTAGGCCC 58.351 37.037 0.00 0.00 0.00 5.80
3548 3931 7.439381 TGAAAATACTAAGAATACTAGGCCCG 58.561 38.462 0.00 0.00 0.00 6.13
3549 3932 6.990908 AAATACTAAGAATACTAGGCCCGT 57.009 37.500 0.00 0.00 0.00 5.28
3550 3933 8.482852 AAAATACTAAGAATACTAGGCCCGTA 57.517 34.615 0.00 1.22 0.00 4.02
3551 3934 8.482852 AAATACTAAGAATACTAGGCCCGTAA 57.517 34.615 0.00 0.00 0.00 3.18
3552 3935 7.700022 ATACTAAGAATACTAGGCCCGTAAG 57.300 40.000 0.00 0.00 0.00 2.34
3568 3951 4.965119 CGTAAGGGATTCTTTTTCCTGG 57.035 45.455 0.00 0.00 36.93 4.45
3569 3952 4.332828 CGTAAGGGATTCTTTTTCCTGGT 58.667 43.478 0.00 0.00 36.93 4.00
3570 3953 4.765339 CGTAAGGGATTCTTTTTCCTGGTT 59.235 41.667 0.00 0.00 36.93 3.67
3571 3954 5.243060 CGTAAGGGATTCTTTTTCCTGGTTT 59.757 40.000 0.00 0.00 36.93 3.27
3572 3955 6.239204 CGTAAGGGATTCTTTTTCCTGGTTTT 60.239 38.462 0.00 0.00 36.93 2.43
3573 3956 6.575244 AAGGGATTCTTTTTCCTGGTTTTT 57.425 33.333 0.00 0.00 33.53 1.94
3603 3986 3.895232 TTTTTACTGCCCTTGTTTGCA 57.105 38.095 0.00 0.00 35.86 4.08
3604 3987 4.414337 TTTTTACTGCCCTTGTTTGCAT 57.586 36.364 0.00 0.00 36.79 3.96
3605 3988 3.383620 TTTACTGCCCTTGTTTGCATG 57.616 42.857 0.00 0.00 36.79 4.06
3606 3989 2.284754 TACTGCCCTTGTTTGCATGA 57.715 45.000 0.00 0.00 36.79 3.07
3607 3990 0.675633 ACTGCCCTTGTTTGCATGAC 59.324 50.000 0.00 0.00 36.79 3.06
3608 3991 0.387622 CTGCCCTTGTTTGCATGACG 60.388 55.000 0.00 0.00 36.79 4.35
3609 3992 1.734117 GCCCTTGTTTGCATGACGC 60.734 57.895 0.00 0.00 42.89 5.19
3610 3993 1.442520 CCCTTGTTTGCATGACGCG 60.443 57.895 3.53 3.53 46.97 6.01
3611 3994 1.282570 CCTTGTTTGCATGACGCGT 59.717 52.632 13.85 13.85 46.97 6.01
3612 3995 0.998226 CCTTGTTTGCATGACGCGTG 60.998 55.000 20.70 2.85 46.97 5.34
3613 3996 0.316937 CTTGTTTGCATGACGCGTGT 60.317 50.000 20.70 0.00 46.97 4.49
3614 3997 0.590984 TTGTTTGCATGACGCGTGTG 60.591 50.000 20.70 17.00 46.97 3.82
3615 3998 1.278337 GTTTGCATGACGCGTGTGA 59.722 52.632 20.70 0.00 46.97 3.58
3616 3999 0.110238 GTTTGCATGACGCGTGTGAT 60.110 50.000 20.70 0.00 46.97 3.06
3617 4000 1.127766 GTTTGCATGACGCGTGTGATA 59.872 47.619 20.70 5.52 46.97 2.15
3618 4001 0.998669 TTGCATGACGCGTGTGATAG 59.001 50.000 20.70 0.88 46.97 2.08
3619 4002 0.805711 TGCATGACGCGTGTGATAGG 60.806 55.000 20.70 0.00 46.97 2.57
3620 4003 0.527600 GCATGACGCGTGTGATAGGA 60.528 55.000 20.70 0.00 0.00 2.94
3621 4004 1.481240 CATGACGCGTGTGATAGGAG 58.519 55.000 20.70 0.00 0.00 3.69
3622 4005 0.249073 ATGACGCGTGTGATAGGAGC 60.249 55.000 20.70 0.00 0.00 4.70
3624 4007 2.102357 CGCGTGTGATAGGAGCGT 59.898 61.111 0.00 0.00 44.96 5.07
3625 4008 1.354155 CGCGTGTGATAGGAGCGTA 59.646 57.895 0.00 0.00 44.96 4.42
3626 4009 0.040336 CGCGTGTGATAGGAGCGTAT 60.040 55.000 0.00 0.00 44.96 3.06
3627 4010 1.687628 GCGTGTGATAGGAGCGTATC 58.312 55.000 3.84 3.84 0.00 2.24
3628 4011 1.267261 GCGTGTGATAGGAGCGTATCT 59.733 52.381 10.44 0.00 31.59 1.98
3629 4012 2.287668 GCGTGTGATAGGAGCGTATCTT 60.288 50.000 10.44 0.00 31.59 2.40
3630 4013 3.795826 GCGTGTGATAGGAGCGTATCTTT 60.796 47.826 10.44 0.00 31.59 2.52
3631 4014 4.360563 CGTGTGATAGGAGCGTATCTTTT 58.639 43.478 10.44 0.00 31.59 2.27
3632 4015 4.804139 CGTGTGATAGGAGCGTATCTTTTT 59.196 41.667 10.44 0.00 31.59 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.424711 TTCTCCATGGGCGGCACC 62.425 66.667 13.02 0.00 37.93 5.01
4 5 2.825836 CTTCTCCATGGGCGGCAC 60.826 66.667 13.02 0.00 0.00 5.01
5 6 4.113815 CCTTCTCCATGGGCGGCA 62.114 66.667 13.02 0.00 0.00 5.69
6 7 4.883354 CCCTTCTCCATGGGCGGC 62.883 72.222 13.02 0.00 36.61 6.53
10 11 1.076485 CCTTGCCCTTCTCCATGGG 60.076 63.158 13.02 2.57 46.00 4.00
11 12 0.106819 CTCCTTGCCCTTCTCCATGG 60.107 60.000 4.97 4.97 0.00 3.66
12 13 0.106819 CCTCCTTGCCCTTCTCCATG 60.107 60.000 0.00 0.00 0.00 3.66
13 14 0.551131 ACCTCCTTGCCCTTCTCCAT 60.551 55.000 0.00 0.00 0.00 3.41
14 15 1.151810 ACCTCCTTGCCCTTCTCCA 60.152 57.895 0.00 0.00 0.00 3.86
15 16 1.301293 CACCTCCTTGCCCTTCTCC 59.699 63.158 0.00 0.00 0.00 3.71
16 17 1.301293 CCACCTCCTTGCCCTTCTC 59.699 63.158 0.00 0.00 0.00 2.87
17 18 1.464198 ACCACCTCCTTGCCCTTCT 60.464 57.895 0.00 0.00 0.00 2.85
18 19 1.303643 CACCACCTCCTTGCCCTTC 60.304 63.158 0.00 0.00 0.00 3.46
19 20 2.845345 CCACCACCTCCTTGCCCTT 61.845 63.158 0.00 0.00 0.00 3.95
20 21 3.260100 CCACCACCTCCTTGCCCT 61.260 66.667 0.00 0.00 0.00 5.19
34 35 4.740822 AACCTCCATGGGCGCCAC 62.741 66.667 30.85 18.39 41.11 5.01
35 36 4.738998 CAACCTCCATGGGCGCCA 62.739 66.667 30.85 15.30 41.11 5.69
36 37 4.740822 ACAACCTCCATGGGCGCC 62.741 66.667 21.18 21.18 41.11 6.53
37 38 3.443045 CACAACCTCCATGGGCGC 61.443 66.667 13.02 0.00 41.11 6.53
38 39 3.443045 GCACAACCTCCATGGGCG 61.443 66.667 13.02 4.56 37.48 6.13
39 40 3.070576 GGCACAACCTCCATGGGC 61.071 66.667 13.02 5.03 46.51 5.36
40 41 2.751436 CGGCACAACCTCCATGGG 60.751 66.667 13.02 2.26 41.11 4.00
41 42 2.040544 GTCGGCACAACCTCCATGG 61.041 63.158 4.97 4.97 42.93 3.66
42 43 0.249120 TAGTCGGCACAACCTCCATG 59.751 55.000 0.00 0.00 35.61 3.66
43 44 0.249398 GTAGTCGGCACAACCTCCAT 59.751 55.000 0.00 0.00 35.61 3.41
44 45 1.669440 GTAGTCGGCACAACCTCCA 59.331 57.895 0.00 0.00 35.61 3.86
45 46 1.445582 CGTAGTCGGCACAACCTCC 60.446 63.158 0.00 0.00 35.61 4.30
46 47 2.092882 GCGTAGTCGGCACAACCTC 61.093 63.158 0.00 0.00 37.56 3.85
47 48 2.048503 GCGTAGTCGGCACAACCT 60.049 61.111 0.00 0.00 37.56 3.50
55 56 2.031360 CCTCCTTAGGCGTAGTCGG 58.969 63.158 0.00 0.00 36.95 4.79
65 66 1.137086 CATCCGTGGTCACCTCCTTAG 59.863 57.143 0.00 0.00 0.00 2.18
66 67 1.191535 CATCCGTGGTCACCTCCTTA 58.808 55.000 0.00 0.00 0.00 2.69
67 68 0.544357 TCATCCGTGGTCACCTCCTT 60.544 55.000 0.00 0.00 0.00 3.36
68 69 0.972983 CTCATCCGTGGTCACCTCCT 60.973 60.000 0.00 0.00 0.00 3.69
69 70 1.517832 CTCATCCGTGGTCACCTCC 59.482 63.158 0.00 0.00 0.00 4.30
70 71 0.970937 TCCTCATCCGTGGTCACCTC 60.971 60.000 0.00 0.00 0.00 3.85
71 72 1.078528 TCCTCATCCGTGGTCACCT 59.921 57.895 0.00 0.00 0.00 4.00
72 73 1.218316 GTCCTCATCCGTGGTCACC 59.782 63.158 0.00 0.00 0.00 4.02
73 74 1.153823 CGTCCTCATCCGTGGTCAC 60.154 63.158 0.00 0.00 0.00 3.67
74 75 1.605451 ACGTCCTCATCCGTGGTCA 60.605 57.895 0.00 0.00 35.69 4.02
75 76 3.285371 ACGTCCTCATCCGTGGTC 58.715 61.111 0.00 0.00 35.69 4.02
79 80 1.605451 TCACCACGTCCTCATCCGT 60.605 57.895 0.00 0.00 37.90 4.69
80 81 1.153823 GTCACCACGTCCTCATCCG 60.154 63.158 0.00 0.00 0.00 4.18
81 82 1.153823 CGTCACCACGTCCTCATCC 60.154 63.158 0.00 0.00 41.42 3.51
82 83 1.153823 CCGTCACCACGTCCTCATC 60.154 63.158 0.00 0.00 45.17 2.92
83 84 2.970639 CCGTCACCACGTCCTCAT 59.029 61.111 0.00 0.00 45.17 2.90
84 85 3.986006 GCCGTCACCACGTCCTCA 61.986 66.667 0.00 0.00 45.17 3.86
85 86 1.870055 TTAGCCGTCACCACGTCCTC 61.870 60.000 0.00 0.00 45.17 3.71
86 87 1.255667 ATTAGCCGTCACCACGTCCT 61.256 55.000 0.00 0.00 45.17 3.85
87 88 1.082117 CATTAGCCGTCACCACGTCC 61.082 60.000 0.00 0.00 45.17 4.79
88 89 0.389426 ACATTAGCCGTCACCACGTC 60.389 55.000 0.00 0.00 45.17 4.34
89 90 0.889994 TACATTAGCCGTCACCACGT 59.110 50.000 0.00 0.00 45.17 4.49
90 91 1.274596 GTACATTAGCCGTCACCACG 58.725 55.000 0.00 0.00 46.29 4.94
91 92 1.135315 TCGTACATTAGCCGTCACCAC 60.135 52.381 0.00 0.00 0.00 4.16
92 93 1.135315 GTCGTACATTAGCCGTCACCA 60.135 52.381 0.00 0.00 0.00 4.17
93 94 1.135315 TGTCGTACATTAGCCGTCACC 60.135 52.381 0.00 0.00 0.00 4.02
94 95 2.182825 CTGTCGTACATTAGCCGTCAC 58.817 52.381 0.00 0.00 0.00 3.67
95 96 1.133598 CCTGTCGTACATTAGCCGTCA 59.866 52.381 0.00 0.00 0.00 4.35
96 97 1.535437 CCCTGTCGTACATTAGCCGTC 60.535 57.143 0.00 0.00 0.00 4.79
97 98 0.458669 CCCTGTCGTACATTAGCCGT 59.541 55.000 0.00 0.00 0.00 5.68
103 104 0.611714 GGGTCACCCTGTCGTACATT 59.388 55.000 5.22 0.00 41.34 2.71
160 161 5.352284 GTCACCATGTAGTCGATTCTGATT 58.648 41.667 0.00 0.00 0.00 2.57
171 172 3.807622 CAGTTTGAACGTCACCATGTAGT 59.192 43.478 0.00 0.00 0.00 2.73
190 191 3.626924 GTGTCGGGAGTGGGCAGT 61.627 66.667 0.00 0.00 0.00 4.40
195 196 0.319900 CTTGAGTGTGTCGGGAGTGG 60.320 60.000 0.00 0.00 0.00 4.00
304 312 6.649557 CGATAAGAAACTAAACCAACTGGAGT 59.350 38.462 1.86 0.00 38.94 3.85
336 344 8.858003 TTAAACATATCAGTTCAAACGCAAAA 57.142 26.923 0.00 0.00 0.00 2.44
481 499 4.685628 GGGTTTCATGCAATAGTTGTTGTG 59.314 41.667 0.00 0.00 0.00 3.33
499 517 2.364002 GCAACTACATGGTGTTGGGTTT 59.636 45.455 24.39 0.00 42.48 3.27
504 522 1.870402 TCACGCAACTACATGGTGTTG 59.130 47.619 21.21 21.21 44.33 3.33
540 558 6.092533 GCAATTTTAGCATAGCATTTGGTTGT 59.907 34.615 0.00 0.00 0.00 3.32
557 575 6.204688 CCTATCGCATTAGGTGAGCAATTTTA 59.795 38.462 1.54 0.00 39.86 1.52
603 621 5.688823 CAAAAAGTCGACATCTGCACATTA 58.311 37.500 19.50 0.00 0.00 1.90
677 700 2.920524 ACACAATGGACGTGTTTGGTA 58.079 42.857 0.00 0.00 45.12 3.25
684 707 2.287487 TGATGCAAACACAATGGACGTG 60.287 45.455 0.00 0.00 40.32 4.49
688 711 3.890756 ACTCTTGATGCAAACACAATGGA 59.109 39.130 0.00 0.00 0.00 3.41
691 714 6.488006 AGTCTAACTCTTGATGCAAACACAAT 59.512 34.615 0.00 0.00 0.00 2.71
692 715 5.822519 AGTCTAACTCTTGATGCAAACACAA 59.177 36.000 0.00 0.00 0.00 3.33
693 716 5.237127 CAGTCTAACTCTTGATGCAAACACA 59.763 40.000 0.00 0.00 0.00 3.72
694 717 5.683859 CAGTCTAACTCTTGATGCAAACAC 58.316 41.667 0.00 0.00 0.00 3.32
695 718 4.214119 GCAGTCTAACTCTTGATGCAAACA 59.786 41.667 0.00 0.00 32.58 2.83
696 719 4.214119 TGCAGTCTAACTCTTGATGCAAAC 59.786 41.667 0.00 0.00 39.08 2.93
697 720 4.388485 TGCAGTCTAACTCTTGATGCAAA 58.612 39.130 0.00 0.00 39.08 3.68
698 721 4.006780 TGCAGTCTAACTCTTGATGCAA 57.993 40.909 0.00 0.00 39.08 4.08
699 722 3.683365 TGCAGTCTAACTCTTGATGCA 57.317 42.857 0.00 0.00 39.67 3.96
700 723 4.186926 TGATGCAGTCTAACTCTTGATGC 58.813 43.478 0.00 0.00 0.00 3.91
701 724 8.604640 AATATGATGCAGTCTAACTCTTGATG 57.395 34.615 0.00 0.00 0.00 3.07
702 725 9.624373 AAAATATGATGCAGTCTAACTCTTGAT 57.376 29.630 0.00 0.00 0.00 2.57
703 726 9.102757 GAAAATATGATGCAGTCTAACTCTTGA 57.897 33.333 0.00 0.00 0.00 3.02
704 727 9.107177 AGAAAATATGATGCAGTCTAACTCTTG 57.893 33.333 0.00 0.00 0.00 3.02
705 728 9.323985 GAGAAAATATGATGCAGTCTAACTCTT 57.676 33.333 0.00 0.00 0.00 2.85
706 729 7.930865 GGAGAAAATATGATGCAGTCTAACTCT 59.069 37.037 0.00 0.00 0.00 3.24
707 730 7.095857 CGGAGAAAATATGATGCAGTCTAACTC 60.096 40.741 0.00 0.00 0.00 3.01
708 731 6.703607 CGGAGAAAATATGATGCAGTCTAACT 59.296 38.462 0.00 0.00 0.00 2.24
709 732 6.073548 CCGGAGAAAATATGATGCAGTCTAAC 60.074 42.308 0.00 0.00 0.00 2.34
710 733 5.991606 CCGGAGAAAATATGATGCAGTCTAA 59.008 40.000 0.00 0.00 0.00 2.10
711 734 5.304357 TCCGGAGAAAATATGATGCAGTCTA 59.696 40.000 0.00 0.00 0.00 2.59
712 735 4.101585 TCCGGAGAAAATATGATGCAGTCT 59.898 41.667 0.00 0.00 0.00 3.24
713 736 4.380531 TCCGGAGAAAATATGATGCAGTC 58.619 43.478 0.00 0.00 0.00 3.51
714 737 4.422073 TCCGGAGAAAATATGATGCAGT 57.578 40.909 0.00 0.00 0.00 4.40
715 738 5.756195 TTTCCGGAGAAAATATGATGCAG 57.244 39.130 3.34 0.00 39.05 4.41
716 739 5.827267 TGATTTCCGGAGAAAATATGATGCA 59.173 36.000 3.34 0.00 44.91 3.96
717 740 6.016777 ACTGATTTCCGGAGAAAATATGATGC 60.017 38.462 3.34 0.00 44.91 3.91
718 741 7.443575 AGACTGATTTCCGGAGAAAATATGATG 59.556 37.037 3.34 0.00 44.91 3.07
719 742 7.512992 AGACTGATTTCCGGAGAAAATATGAT 58.487 34.615 3.34 0.00 44.91 2.45
720 743 6.889198 AGACTGATTTCCGGAGAAAATATGA 58.111 36.000 3.34 0.00 44.91 2.15
721 744 7.559590 AAGACTGATTTCCGGAGAAAATATG 57.440 36.000 3.34 1.31 44.91 1.78
722 745 9.331282 CTTAAGACTGATTTCCGGAGAAAATAT 57.669 33.333 3.34 0.00 44.91 1.28
723 746 8.537016 TCTTAAGACTGATTTCCGGAGAAAATA 58.463 33.333 3.34 0.00 44.91 1.40
724 747 7.394816 TCTTAAGACTGATTTCCGGAGAAAAT 58.605 34.615 3.34 1.03 44.91 1.82
725 748 6.765403 TCTTAAGACTGATTTCCGGAGAAAA 58.235 36.000 3.34 0.00 44.91 2.29
726 749 6.354794 TCTTAAGACTGATTTCCGGAGAAA 57.645 37.500 3.34 0.00 45.78 2.52
727 750 5.995565 TCTTAAGACTGATTTCCGGAGAA 57.004 39.130 3.34 2.67 0.00 2.87
728 751 5.995565 TTCTTAAGACTGATTTCCGGAGA 57.004 39.130 3.34 0.00 0.00 3.71
729 752 8.894768 ATATTTCTTAAGACTGATTTCCGGAG 57.105 34.615 3.34 0.00 0.00 4.63
730 753 9.681062 AAATATTTCTTAAGACTGATTTCCGGA 57.319 29.630 4.18 0.00 0.00 5.14
777 800 9.554395 TGTGAATAGTTTGATTTGTAGAACTGA 57.446 29.630 0.00 0.00 34.46 3.41
816 839 8.965819 ACATTACATTATTTCTGGCACATACAA 58.034 29.630 0.00 0.00 38.20 2.41
817 840 8.404765 CACATTACATTATTTCTGGCACATACA 58.595 33.333 0.00 0.00 38.20 2.29
836 864 3.067106 CCGACCTATGCATCCACATTAC 58.933 50.000 0.19 0.00 0.00 1.89
840 868 0.464036 GTCCGACCTATGCATCCACA 59.536 55.000 0.19 0.00 0.00 4.17
850 878 4.012374 ACAGAAGAATTACGTCCGACCTA 58.988 43.478 0.00 0.00 0.00 3.08
853 881 5.404667 AGAAAACAGAAGAATTACGTCCGAC 59.595 40.000 0.00 0.00 0.00 4.79
854 882 5.535333 AGAAAACAGAAGAATTACGTCCGA 58.465 37.500 0.00 0.00 0.00 4.55
855 883 5.840940 AGAAAACAGAAGAATTACGTCCG 57.159 39.130 0.00 0.00 0.00 4.79
978 1018 1.584920 GCGTTGTGTGCGCGTAAAAG 61.585 55.000 8.43 0.00 45.36 2.27
979 1019 1.651730 GCGTTGTGTGCGCGTAAAA 60.652 52.632 8.43 0.00 45.36 1.52
986 1026 0.993251 CAACATCTGCGTTGTGTGCG 60.993 55.000 0.00 0.00 41.12 5.34
1208 1249 0.179081 GTACATGAAGAGGTCCGGGC 60.179 60.000 0.00 0.00 0.00 6.13
1597 1638 1.004277 GGACACTCGTCGAACAGCTG 61.004 60.000 13.48 13.48 43.61 4.24
1656 1697 1.227674 CTCTCCCCGCTTGGCATAC 60.228 63.158 0.00 0.00 0.00 2.39
1671 1712 1.617536 TCTTGCTGGGGCCATCTCT 60.618 57.895 4.39 0.00 37.74 3.10
1761 1802 4.824166 GCATGCTTGTGCGAGCCG 62.824 66.667 11.37 2.05 42.01 5.52
1875 1916 1.883021 CAACCTTCGGCCAACATCC 59.117 57.895 2.24 0.00 0.00 3.51
2046 2087 4.144297 GCAATGCCAAACCTCCTATGATA 58.856 43.478 0.00 0.00 0.00 2.15
2250 2291 1.968704 TGTCAACCATGCAACCGTAA 58.031 45.000 0.00 0.00 0.00 3.18
2427 2468 1.599047 CCCACTGTCATCGCTCCTT 59.401 57.895 0.00 0.00 0.00 3.36
2599 2640 1.134818 TCCAGGATGTGATTTCGACCG 60.135 52.381 0.00 0.00 0.00 4.79
2683 2725 5.524281 GCTGGGAGCTCAAAAGTACTTATAC 59.476 44.000 17.19 0.00 38.45 1.47
2717 2759 4.569943 TCAGTGCTAGATGTTCAGTTTCC 58.430 43.478 0.00 0.00 0.00 3.13
2772 2814 8.638565 GCATTATTGGCGATTTTATATTGTGAC 58.361 33.333 0.00 0.00 0.00 3.67
2855 2897 7.919313 TGTTTTATTCTATTACTCGCCGTAG 57.081 36.000 0.00 0.00 0.00 3.51
2885 2927 3.130633 GTTGGACATTTTGCCTTGGTTC 58.869 45.455 0.00 0.00 0.00 3.62
2945 3310 4.654262 TCCAGTCTAAAACAGTCAGAAGGT 59.346 41.667 0.00 0.00 0.00 3.50
2956 3321 5.104900 TGAGCCTAATCCTCCAGTCTAAAAC 60.105 44.000 0.00 0.00 0.00 2.43
3218 3598 7.522374 CAGGAAAGTTTAGTGCTTTACATCTC 58.478 38.462 3.30 0.00 38.80 2.75
3219 3599 6.072452 GCAGGAAAGTTTAGTGCTTTACATCT 60.072 38.462 12.40 0.00 38.80 2.90
3264 3645 8.453238 TTTGCTTTGGACTTAGTTGTATGTTA 57.547 30.769 0.00 0.00 0.00 2.41
3317 3698 1.888512 CCAATATCTTTGGGATGGGCG 59.111 52.381 0.00 0.00 35.96 6.13
3347 3728 3.515562 TGTGGGGGATATTGCTGTTTTT 58.484 40.909 0.00 0.00 0.00 1.94
3462 3845 6.166982 GCATATCTGTCCTTTATGGGTAGTC 58.833 44.000 0.00 0.00 36.20 2.59
3481 3864 5.410355 AAAGTTGATGTTGCTTGGCATAT 57.590 34.783 0.00 0.00 38.76 1.78
3531 3914 4.220163 CCCTTACGGGCCTAGTATTCTTAG 59.780 50.000 0.84 2.05 45.33 2.18
3532 3915 4.154942 CCCTTACGGGCCTAGTATTCTTA 58.845 47.826 0.84 0.00 45.33 2.10
3533 3916 2.970640 CCCTTACGGGCCTAGTATTCTT 59.029 50.000 0.84 0.00 45.33 2.52
3534 3917 2.606378 CCCTTACGGGCCTAGTATTCT 58.394 52.381 0.84 0.00 45.33 2.40
3546 3929 3.694566 CCAGGAAAAAGAATCCCTTACGG 59.305 47.826 0.00 0.00 37.71 4.02
3547 3930 4.332828 ACCAGGAAAAAGAATCCCTTACG 58.667 43.478 0.00 0.00 37.71 3.18
3548 3931 6.665992 AAACCAGGAAAAAGAATCCCTTAC 57.334 37.500 0.00 0.00 37.71 2.34
3549 3932 7.684317 AAAAACCAGGAAAAAGAATCCCTTA 57.316 32.000 0.00 0.00 37.71 2.69
3550 3933 6.575244 AAAAACCAGGAAAAAGAATCCCTT 57.425 33.333 0.00 0.00 37.71 3.95
3583 3966 3.895232 TGCAAACAAGGGCAGTAAAAA 57.105 38.095 0.00 0.00 34.58 1.94
3584 3967 3.386078 TCATGCAAACAAGGGCAGTAAAA 59.614 39.130 0.00 0.00 44.24 1.52
3585 3968 2.961741 TCATGCAAACAAGGGCAGTAAA 59.038 40.909 0.00 0.00 44.24 2.01
3586 3969 2.295909 GTCATGCAAACAAGGGCAGTAA 59.704 45.455 0.00 0.00 44.24 2.24
3587 3970 1.885887 GTCATGCAAACAAGGGCAGTA 59.114 47.619 0.00 0.00 44.24 2.74
3588 3971 0.675633 GTCATGCAAACAAGGGCAGT 59.324 50.000 0.00 0.00 44.24 4.40
3589 3972 0.387622 CGTCATGCAAACAAGGGCAG 60.388 55.000 0.00 0.00 44.24 4.85
3590 3973 1.659233 CGTCATGCAAACAAGGGCA 59.341 52.632 0.00 0.00 45.23 5.36
3591 3974 1.734117 GCGTCATGCAAACAAGGGC 60.734 57.895 0.00 0.00 45.45 5.19
3592 3975 1.442520 CGCGTCATGCAAACAAGGG 60.443 57.895 0.00 0.00 46.97 3.95
3593 3976 0.998226 CACGCGTCATGCAAACAAGG 60.998 55.000 9.86 0.00 46.97 3.61
3594 3977 0.316937 ACACGCGTCATGCAAACAAG 60.317 50.000 9.86 0.00 46.97 3.16
3595 3978 0.590984 CACACGCGTCATGCAAACAA 60.591 50.000 9.86 0.00 46.97 2.83
3596 3979 1.010238 CACACGCGTCATGCAAACA 60.010 52.632 9.86 0.00 46.97 2.83
3597 3980 0.110238 ATCACACGCGTCATGCAAAC 60.110 50.000 9.86 0.00 46.97 2.93
3598 3981 1.393196 CTATCACACGCGTCATGCAAA 59.607 47.619 9.86 0.00 46.97 3.68
3599 3982 0.998669 CTATCACACGCGTCATGCAA 59.001 50.000 9.86 1.50 46.97 4.08
3600 3983 0.805711 CCTATCACACGCGTCATGCA 60.806 55.000 9.86 1.79 46.97 3.96
3601 3984 0.527600 TCCTATCACACGCGTCATGC 60.528 55.000 9.86 0.00 41.47 4.06
3602 3985 1.481240 CTCCTATCACACGCGTCATG 58.519 55.000 9.86 11.70 0.00 3.07
3603 3986 0.249073 GCTCCTATCACACGCGTCAT 60.249 55.000 9.86 4.22 0.00 3.06
3604 3987 1.138883 GCTCCTATCACACGCGTCA 59.861 57.895 9.86 0.00 0.00 4.35
3605 3988 1.939785 CGCTCCTATCACACGCGTC 60.940 63.158 9.86 0.00 39.07 5.19
3606 3989 2.102357 CGCTCCTATCACACGCGT 59.898 61.111 5.58 5.58 39.07 6.01
3608 3991 1.267261 AGATACGCTCCTATCACACGC 59.733 52.381 0.00 0.00 0.00 5.34
3609 3992 3.627732 AAGATACGCTCCTATCACACG 57.372 47.619 0.00 0.00 0.00 4.49


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

AutoCloner maintained by Alex Coulton.