Multiple sequence alignment - TraesCS4A01G276200

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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 TraesCS4A01G276200 chr4A 100.000 4545 0 0 1 4545 584796507 584801051 0.000000e+00 8394
1 TraesCS4A01G276200 chr4A 82.051 156 22 5 379 534 362112299 362112150 1.330000e-25 128
2 TraesCS4A01G276200 chr4D 91.419 1480 67 22 2173 3614 15801024 15799567 0.000000e+00 1975
3 TraesCS4A01G276200 chr4D 88.774 1256 95 21 933 2174 15802371 15801148 0.000000e+00 1496
4 TraesCS4A01G276200 chr4D 86.710 775 66 24 89 855 15803169 15802424 0.000000e+00 826
5 TraesCS4A01G276200 chr4D 83.824 340 35 10 3041 3367 15791195 15790863 5.710000e-79 305
6 TraesCS4A01G276200 chr4D 84.566 311 34 10 3100 3405 15793480 15793179 3.440000e-76 296
7 TraesCS4A01G276200 chr4D 79.747 158 27 5 379 534 437964015 437963861 4.810000e-20 110
8 TraesCS4A01G276200 chr4D 80.690 145 17 6 2970 3105 15793700 15793558 8.040000e-18 102
9 TraesCS4A01G276200 chr2A 100.000 927 0 0 3619 4545 614101479 614100553 0.000000e+00 1712
10 TraesCS4A01G276200 chr2B 99.249 932 6 1 3615 4545 234642926 234643857 0.000000e+00 1681
11 TraesCS4A01G276200 chr7B 99.353 927 6 0 3619 4545 261114158 261115084 0.000000e+00 1679
12 TraesCS4A01G276200 chr7A 99.353 927 6 0 3619 4545 285478238 285479164 0.000000e+00 1679
13 TraesCS4A01G276200 chr7A 98.930 935 9 1 3612 4545 175820944 175821878 0.000000e+00 1670
14 TraesCS4A01G276200 chr5B 99.353 927 6 0 3619 4545 216227381 216226455 0.000000e+00 1679
15 TraesCS4A01G276200 chr5A 99.353 927 6 0 3619 4545 522622580 522623506 0.000000e+00 1679
16 TraesCS4A01G276200 chr5A 99.353 927 6 0 3619 4545 522629552 522630478 0.000000e+00 1679
17 TraesCS4A01G276200 chr5A 79.874 159 29 3 379 537 645267349 645267194 3.720000e-21 113
18 TraesCS4A01G276200 chr6B 99.245 927 7 0 3619 4545 227138354 227137428 0.000000e+00 1674
19 TraesCS4A01G276200 chr4B 85.610 1376 112 40 2267 3603 27177015 27175687 0.000000e+00 1365
20 TraesCS4A01G276200 chr4B 90.695 892 60 11 990 1872 27178624 27177747 0.000000e+00 1166
21 TraesCS4A01G276200 chr4B 91.809 293 20 2 1863 2155 27177727 27177439 5.470000e-109 405
22 TraesCS4A01G276200 chr4B 78.842 449 57 19 3016 3439 27114076 27113641 7.490000e-68 268
23 TraesCS4A01G276200 chr4B 78.230 418 47 19 2977 3387 27116105 27115725 1.270000e-55 228
24 TraesCS4A01G276200 chr4B 77.679 224 32 12 311 534 242748650 242748445 2.220000e-23 121
25 TraesCS4A01G276200 chr5D 82.051 156 25 3 379 534 517846876 517846724 3.690000e-26 130
26 TraesCS4A01G276200 chr5D 80.769 156 23 6 379 532 538354144 538354294 1.030000e-21 115
27 TraesCS4A01G276200 chr2D 80.128 156 26 4 379 534 172409475 172409625 1.340000e-20 111
28 TraesCS4A01G276200 chr1D 79.487 156 29 3 379 534 365802896 365802744 1.730000e-19 108


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 TraesCS4A01G276200 chr4A 584796507 584801051 4544 False 8394.000000 8394 100.000000 1 4545 1 chr4A.!!$F1 4544
1 TraesCS4A01G276200 chr4D 15799567 15803169 3602 True 1432.333333 1975 88.967667 89 3614 3 chr4D.!!$R3 3525
2 TraesCS4A01G276200 chr4D 15790863 15793700 2837 True 234.333333 305 83.026667 2970 3405 3 chr4D.!!$R2 435
3 TraesCS4A01G276200 chr2A 614100553 614101479 926 True 1712.000000 1712 100.000000 3619 4545 1 chr2A.!!$R1 926
4 TraesCS4A01G276200 chr2B 234642926 234643857 931 False 1681.000000 1681 99.249000 3615 4545 1 chr2B.!!$F1 930
5 TraesCS4A01G276200 chr7B 261114158 261115084 926 False 1679.000000 1679 99.353000 3619 4545 1 chr7B.!!$F1 926
6 TraesCS4A01G276200 chr7A 285478238 285479164 926 False 1679.000000 1679 99.353000 3619 4545 1 chr7A.!!$F2 926
7 TraesCS4A01G276200 chr7A 175820944 175821878 934 False 1670.000000 1670 98.930000 3612 4545 1 chr7A.!!$F1 933
8 TraesCS4A01G276200 chr5B 216226455 216227381 926 True 1679.000000 1679 99.353000 3619 4545 1 chr5B.!!$R1 926
9 TraesCS4A01G276200 chr5A 522622580 522623506 926 False 1679.000000 1679 99.353000 3619 4545 1 chr5A.!!$F1 926
10 TraesCS4A01G276200 chr5A 522629552 522630478 926 False 1679.000000 1679 99.353000 3619 4545 1 chr5A.!!$F2 926
11 TraesCS4A01G276200 chr6B 227137428 227138354 926 True 1674.000000 1674 99.245000 3619 4545 1 chr6B.!!$R1 926
12 TraesCS4A01G276200 chr4B 27175687 27178624 2937 True 978.666667 1365 89.371333 990 3603 3 chr4B.!!$R3 2613
13 TraesCS4A01G276200 chr4B 27113641 27116105 2464 True 248.000000 268 78.536000 2977 3439 2 chr4B.!!$R2 462

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
671 684 0.105039 GTCGTCCCTGGCTTATGGAG 59.895 60.0 0.0 0.0 0.00 3.86 F
1299 1346 0.320771 TCTCTCGCTCCCTTTGTTGC 60.321 55.0 0.0 0.0 0.00 4.17 F
2428 2961 0.037605 AGTAGTAACTGTGCCGTGGC 60.038 55.0 3.3 3.3 36.68 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1706 1765 0.037512 CACCACTGAGAGGCACAGAG 60.038 60.0 11.91 5.44 38.55 3.35 R
2947 3498 0.659427 TGCTATGATGCAAGCTTCGC 59.341 50.0 9.40 12.25 40.29 4.70 R
3615 6307 0.175073 GAGGTCGGGTCGCTACAATT 59.825 55.0 0.00 0.00 0.00 2.32 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
28 29 2.525422 CATCTCATGCGATGGACGG 58.475 57.895 16.40 0.00 42.83 4.79
29 30 1.301244 ATCTCATGCGATGGACGGC 60.301 57.895 0.00 0.00 42.83 5.68
30 31 2.031674 ATCTCATGCGATGGACGGCA 62.032 55.000 0.00 0.00 42.83 5.69
31 32 1.596203 CTCATGCGATGGACGGCAT 60.596 57.895 0.00 0.00 42.83 4.40
32 33 1.838568 CTCATGCGATGGACGGCATG 61.839 60.000 17.34 17.34 46.64 4.06
33 34 2.505494 ATGCGATGGACGGCATGA 59.495 55.556 0.00 0.00 42.83 3.07
34 35 1.596203 ATGCGATGGACGGCATGAG 60.596 57.895 0.00 0.00 42.83 2.90
35 36 2.969238 GCGATGGACGGCATGAGG 60.969 66.667 0.00 0.00 42.83 3.86
36 37 2.280389 CGATGGACGGCATGAGGG 60.280 66.667 0.00 0.00 38.46 4.30
37 38 2.796193 CGATGGACGGCATGAGGGA 61.796 63.158 0.00 0.00 38.46 4.20
38 39 1.070445 GATGGACGGCATGAGGGAG 59.930 63.158 0.00 0.00 0.00 4.30
39 40 3.112205 ATGGACGGCATGAGGGAGC 62.112 63.158 0.00 0.00 0.00 4.70
44 45 4.891037 GGCATGAGGGAGCCCAGC 62.891 72.222 8.53 6.09 45.18 4.85
45 46 4.891037 GCATGAGGGAGCCCAGCC 62.891 72.222 8.53 0.00 38.92 4.85
46 47 4.201122 CATGAGGGAGCCCAGCCC 62.201 72.222 8.53 0.00 46.40 5.19
55 56 3.161450 GCCCAGCCCCACTCGATA 61.161 66.667 0.00 0.00 0.00 2.92
56 57 2.742116 GCCCAGCCCCACTCGATAA 61.742 63.158 0.00 0.00 0.00 1.75
57 58 1.447643 CCCAGCCCCACTCGATAAG 59.552 63.158 0.00 0.00 0.00 1.73
58 59 1.227674 CCAGCCCCACTCGATAAGC 60.228 63.158 0.00 0.00 0.00 3.09
59 60 1.227674 CAGCCCCACTCGATAAGCC 60.228 63.158 0.00 0.00 0.00 4.35
60 61 1.689233 AGCCCCACTCGATAAGCCA 60.689 57.895 0.00 0.00 0.00 4.75
61 62 1.523938 GCCCCACTCGATAAGCCAC 60.524 63.158 0.00 0.00 0.00 5.01
62 63 1.146263 CCCCACTCGATAAGCCACC 59.854 63.158 0.00 0.00 0.00 4.61
63 64 1.146263 CCCACTCGATAAGCCACCC 59.854 63.158 0.00 0.00 0.00 4.61
64 65 1.146263 CCACTCGATAAGCCACCCC 59.854 63.158 0.00 0.00 0.00 4.95
65 66 1.146263 CACTCGATAAGCCACCCCC 59.854 63.158 0.00 0.00 0.00 5.40
66 67 1.306654 ACTCGATAAGCCACCCCCA 60.307 57.895 0.00 0.00 0.00 4.96
67 68 1.146263 CTCGATAAGCCACCCCCAC 59.854 63.158 0.00 0.00 0.00 4.61
68 69 2.192175 CGATAAGCCACCCCCACC 59.808 66.667 0.00 0.00 0.00 4.61
69 70 2.601299 GATAAGCCACCCCCACCC 59.399 66.667 0.00 0.00 0.00 4.61
70 71 3.027472 ATAAGCCACCCCCACCCC 61.027 66.667 0.00 0.00 0.00 4.95
93 94 2.434884 CCCTCGTGCGTTGATGCT 60.435 61.111 0.00 0.00 35.36 3.79
107 108 4.848000 TGCTGACAATGCATGGGT 57.152 50.000 5.94 4.92 35.31 4.51
139 140 8.424133 GGGATGCATATGAACTTTCCTATTTTT 58.576 33.333 6.97 0.00 0.00 1.94
144 145 9.101655 GCATATGAACTTTCCTATTTTTGCATT 57.898 29.630 6.97 0.00 0.00 3.56
150 151 6.825610 ACTTTCCTATTTTTGCATTTGTCCA 58.174 32.000 0.00 0.00 0.00 4.02
158 159 2.064434 TGCATTTGTCCACACTCCAA 57.936 45.000 0.00 0.00 0.00 3.53
161 162 2.863704 GCATTTGTCCACACTCCAAAGC 60.864 50.000 0.00 0.00 32.17 3.51
190 191 0.874175 CGTCGACAAGTCTTGCACCA 60.874 55.000 17.16 0.00 0.00 4.17
195 196 0.882042 ACAAGTCTTGCACCAGCTCG 60.882 55.000 12.66 0.00 42.74 5.03
204 205 3.699894 ACCAGCTCGTCCTGCCTG 61.700 66.667 0.00 0.00 0.00 4.85
267 268 1.816835 TGCCAGTACTAAGTGACCGAG 59.183 52.381 0.00 0.00 0.00 4.63
299 300 8.288689 TCTTTTTGCCCTTATATAAGTGAACC 57.711 34.615 18.91 5.36 0.00 3.62
326 327 6.379386 TCGTTCTAGAATATAAGGTGCATCG 58.621 40.000 8.75 2.89 0.00 3.84
336 337 1.209127 GGTGCATCGGTTTTCGTGG 59.791 57.895 0.00 0.00 40.32 4.94
471 475 9.831737 GATCTAATGATACAAATGTGGTATTGC 57.168 33.333 0.00 0.00 31.84 3.56
472 476 8.744568 TCTAATGATACAAATGTGGTATTGCA 57.255 30.769 0.00 0.00 31.84 4.08
473 477 8.839343 TCTAATGATACAAATGTGGTATTGCAG 58.161 33.333 0.00 0.00 31.84 4.41
476 480 8.922931 ATGATACAAATGTGGTATTGCAGATA 57.077 30.769 0.00 0.00 31.84 1.98
477 481 8.744568 TGATACAAATGTGGTATTGCAGATAA 57.255 30.769 0.00 0.00 31.84 1.75
478 482 9.353431 TGATACAAATGTGGTATTGCAGATAAT 57.647 29.630 0.00 0.00 31.84 1.28
479 483 9.616634 GATACAAATGTGGTATTGCAGATAATG 57.383 33.333 0.00 0.00 31.84 1.90
562 566 8.336806 CGAGTATTTGTGTTTGGTGTTAAACTA 58.663 33.333 0.00 0.00 40.36 2.24
608 621 3.254060 TGTCAGATAGAAGCGCAGAAAC 58.746 45.455 11.47 0.00 0.00 2.78
611 624 3.928992 TCAGATAGAAGCGCAGAAACTTG 59.071 43.478 11.47 0.12 0.00 3.16
632 645 9.790389 AACTTGACACAAAATAAATAACAACGA 57.210 25.926 0.00 0.00 0.00 3.85
633 646 9.228636 ACTTGACACAAAATAAATAACAACGAC 57.771 29.630 0.00 0.00 0.00 4.34
634 647 7.824100 TGACACAAAATAAATAACAACGACG 57.176 32.000 0.00 0.00 0.00 5.12
635 648 7.408123 TGACACAAAATAAATAACAACGACGT 58.592 30.769 0.00 0.00 0.00 4.34
636 649 7.583401 TGACACAAAATAAATAACAACGACGTC 59.417 33.333 5.18 5.18 0.00 4.34
637 650 6.852345 ACACAAAATAAATAACAACGACGTCC 59.148 34.615 10.58 0.00 0.00 4.79
638 651 7.073265 CACAAAATAAATAACAACGACGTCCT 58.927 34.615 10.58 0.00 0.00 3.85
639 652 8.222433 CACAAAATAAATAACAACGACGTCCTA 58.778 33.333 10.58 0.00 0.00 2.94
640 653 8.772705 ACAAAATAAATAACAACGACGTCCTAA 58.227 29.630 10.58 0.00 0.00 2.69
641 654 9.763465 CAAAATAAATAACAACGACGTCCTAAT 57.237 29.630 10.58 0.00 0.00 1.73
645 658 7.887996 AAATAACAACGACGTCCTAATTACA 57.112 32.000 10.58 0.00 0.00 2.41
646 659 8.483307 AAATAACAACGACGTCCTAATTACAT 57.517 30.769 10.58 0.00 0.00 2.29
647 660 5.773239 AACAACGACGTCCTAATTACATG 57.227 39.130 10.58 0.00 0.00 3.21
648 661 5.063180 ACAACGACGTCCTAATTACATGA 57.937 39.130 10.58 0.00 0.00 3.07
649 662 5.100259 ACAACGACGTCCTAATTACATGAG 58.900 41.667 10.58 0.00 0.00 2.90
650 663 3.703420 ACGACGTCCTAATTACATGAGC 58.297 45.455 10.58 0.00 0.00 4.26
653 666 2.429610 ACGTCCTAATTACATGAGCCGT 59.570 45.455 0.00 0.00 0.00 5.68
655 668 3.050619 GTCCTAATTACATGAGCCGTCG 58.949 50.000 0.00 0.00 0.00 5.12
667 680 3.090219 GCCGTCGTCCCTGGCTTAT 62.090 63.158 0.00 0.00 45.40 1.73
668 681 1.227263 CCGTCGTCCCTGGCTTATG 60.227 63.158 0.00 0.00 0.00 1.90
669 682 1.227263 CGTCGTCCCTGGCTTATGG 60.227 63.158 0.00 0.00 0.00 2.74
670 683 1.672854 CGTCGTCCCTGGCTTATGGA 61.673 60.000 0.00 0.00 0.00 3.41
671 684 0.105039 GTCGTCCCTGGCTTATGGAG 59.895 60.000 0.00 0.00 0.00 3.86
672 685 0.325296 TCGTCCCTGGCTTATGGAGT 60.325 55.000 0.00 0.00 0.00 3.85
673 686 1.063492 TCGTCCCTGGCTTATGGAGTA 60.063 52.381 0.00 0.00 0.00 2.59
677 690 2.771943 TCCCTGGCTTATGGAGTAAGTG 59.228 50.000 0.00 0.00 41.55 3.16
696 709 4.148838 AGTGTATGCCAACTAGCCAAAAA 58.851 39.130 0.00 0.00 0.00 1.94
704 717 4.610945 CCAACTAGCCAAAAACAGACTTG 58.389 43.478 0.00 0.00 0.00 3.16
723 736 4.142227 ACTTGTGACCGTGGTAGATATGAC 60.142 45.833 0.00 0.00 0.00 3.06
727 740 3.383505 TGACCGTGGTAGATATGACTTGG 59.616 47.826 0.00 0.00 0.00 3.61
731 744 5.046159 ACCGTGGTAGATATGACTTGGAAAA 60.046 40.000 0.00 0.00 0.00 2.29
744 757 7.323049 TGACTTGGAAAACAATCGAAACTAA 57.677 32.000 0.00 0.00 38.65 2.24
745 758 7.190871 TGACTTGGAAAACAATCGAAACTAAC 58.809 34.615 0.00 0.00 38.65 2.34
749 762 5.009210 TGGAAAACAATCGAAACTAACCAGG 59.991 40.000 0.00 0.00 0.00 4.45
774 787 6.607600 GCCCAAATCCTCTAAAATAAGGAACT 59.392 38.462 0.00 0.00 44.61 3.01
775 788 7.778382 GCCCAAATCCTCTAAAATAAGGAACTA 59.222 37.037 0.00 0.00 44.61 2.24
776 789 9.121658 CCCAAATCCTCTAAAATAAGGAACTAC 57.878 37.037 0.00 0.00 44.61 2.73
777 790 8.827677 CCAAATCCTCTAAAATAAGGAACTACG 58.172 37.037 0.00 0.00 44.61 3.51
802 815 2.667969 TCATGCGATGAGTTTCGAGTTG 59.332 45.455 0.00 0.00 41.62 3.16
832 845 3.941704 ATGAGAGATGTTTCCCCCTTC 57.058 47.619 0.00 0.00 0.00 3.46
833 846 2.921221 TGAGAGATGTTTCCCCCTTCT 58.079 47.619 0.00 0.00 0.00 2.85
836 849 5.039645 TGAGAGATGTTTCCCCCTTCTTAT 58.960 41.667 0.00 0.00 0.00 1.73
837 850 6.209774 TGAGAGATGTTTCCCCCTTCTTATA 58.790 40.000 0.00 0.00 0.00 0.98
841 854 8.661345 AGAGATGTTTCCCCCTTCTTATAATAC 58.339 37.037 0.00 0.00 0.00 1.89
842 855 8.344939 AGATGTTTCCCCCTTCTTATAATACA 57.655 34.615 0.00 0.00 0.00 2.29
844 857 8.996651 ATGTTTCCCCCTTCTTATAATACAAG 57.003 34.615 0.00 0.00 0.00 3.16
847 860 8.900781 GTTTCCCCCTTCTTATAATACAAGAAC 58.099 37.037 0.00 0.00 37.15 3.01
848 861 6.823497 TCCCCCTTCTTATAATACAAGAACG 58.177 40.000 0.00 0.00 37.15 3.95
849 862 5.469084 CCCCCTTCTTATAATACAAGAACGC 59.531 44.000 0.00 0.00 37.15 4.84
850 863 6.289064 CCCCTTCTTATAATACAAGAACGCT 58.711 40.000 0.00 0.00 37.15 5.07
863 902 6.044512 ACAAGAACGCTTTTTACAGTAGTG 57.955 37.500 0.00 0.00 30.14 2.74
870 909 6.044682 ACGCTTTTTACAGTAGTGTAGTGTT 58.955 36.000 10.25 0.00 42.12 3.32
903 942 9.698309 AATCTTATGTTATGTTATGAGACGGAG 57.302 33.333 0.00 0.00 0.00 4.63
904 943 7.658261 TCTTATGTTATGTTATGAGACGGAGG 58.342 38.462 0.00 0.00 0.00 4.30
905 944 7.504574 TCTTATGTTATGTTATGAGACGGAGGA 59.495 37.037 0.00 0.00 0.00 3.71
906 945 6.672266 ATGTTATGTTATGAGACGGAGGAT 57.328 37.500 0.00 0.00 0.00 3.24
907 946 6.479972 TGTTATGTTATGAGACGGAGGATT 57.520 37.500 0.00 0.00 0.00 3.01
908 947 6.884832 TGTTATGTTATGAGACGGAGGATTT 58.115 36.000 0.00 0.00 0.00 2.17
909 948 7.335627 TGTTATGTTATGAGACGGAGGATTTT 58.664 34.615 0.00 0.00 0.00 1.82
910 949 7.827236 TGTTATGTTATGAGACGGAGGATTTTT 59.173 33.333 0.00 0.00 0.00 1.94
952 991 3.695060 TCTGTTATGAGACGGAGGAAGTC 59.305 47.826 0.00 0.00 38.81 3.01
969 1008 6.060788 AGGAAGTCCTTATGAATCTGAATGC 58.939 40.000 0.00 0.00 46.09 3.56
973 1012 6.363065 AGTCCTTATGAATCTGAATGCACAT 58.637 36.000 0.00 0.00 0.00 3.21
977 1016 7.012989 TCCTTATGAATCTGAATGCACATCAAG 59.987 37.037 5.62 1.48 0.00 3.02
1030 1069 4.271816 CCCTCGTCGCAGATCCGG 62.272 72.222 0.00 0.00 40.67 5.14
1095 1142 1.131826 CGACCCGCACAAACGAATC 59.868 57.895 0.00 0.00 34.06 2.52
1278 1325 2.165357 AAGCCATCCCCAAAAGATCC 57.835 50.000 0.00 0.00 0.00 3.36
1285 1332 4.396522 CATCCCCAAAAGATCCATCTCTC 58.603 47.826 0.00 0.00 35.76 3.20
1288 1335 2.158842 CCCAAAAGATCCATCTCTCGCT 60.159 50.000 0.00 0.00 35.76 4.93
1293 1340 1.133199 AGATCCATCTCTCGCTCCCTT 60.133 52.381 0.00 0.00 29.30 3.95
1295 1342 0.826715 TCCATCTCTCGCTCCCTTTG 59.173 55.000 0.00 0.00 0.00 2.77
1296 1343 0.539051 CCATCTCTCGCTCCCTTTGT 59.461 55.000 0.00 0.00 0.00 2.83
1299 1346 0.320771 TCTCTCGCTCCCTTTGTTGC 60.321 55.000 0.00 0.00 0.00 4.17
1311 1358 3.253432 CCCTTTGTTGCTACTGTTTCTCC 59.747 47.826 0.00 0.00 0.00 3.71
1464 1516 2.069273 GCGTCATGGGATACAGTATGC 58.931 52.381 3.46 3.46 42.53 3.14
1561 1613 1.227380 CCCCCTCGATTTCGCTCTG 60.227 63.158 0.00 0.00 39.60 3.35
1572 1627 2.732412 TTCGCTCTGGAGAGTTGAAG 57.268 50.000 5.57 0.00 43.85 3.02
1608 1666 7.989947 TTAGGGATAGGTTTATCTGTCTGTT 57.010 36.000 0.00 0.00 36.67 3.16
1617 1676 7.305474 AGGTTTATCTGTCTGTTTAATTTGCG 58.695 34.615 0.00 0.00 0.00 4.85
1658 1717 5.302568 TGGAGGTGCATATTCATTTCAATCC 59.697 40.000 0.00 0.00 0.00 3.01
1659 1718 5.537674 GGAGGTGCATATTCATTTCAATCCT 59.462 40.000 0.00 0.00 0.00 3.24
1666 1725 8.139350 TGCATATTCATTTCAATCCTGTGAATC 58.861 33.333 2.54 0.00 39.47 2.52
1677 1736 6.013379 TCAATCCTGTGAATCTTGGTAGAGTT 60.013 38.462 0.00 0.00 32.92 3.01
1683 1742 7.278868 CCTGTGAATCTTGGTAGAGTTTATGAC 59.721 40.741 0.00 0.00 32.92 3.06
1706 1765 1.344114 TGTTCTCCAATTTGGCCTTGC 59.656 47.619 10.76 1.07 37.47 4.01
1730 1789 0.250467 TGCCTCTCAGTGGTGAAAGC 60.250 55.000 0.00 0.00 30.14 3.51
1738 1797 1.008538 GTGGTGAAAGCGGCACTTG 60.009 57.895 1.45 0.00 39.09 3.16
1760 1819 4.022935 TGTGATTGTGTGAGATTTGAAGGC 60.023 41.667 0.00 0.00 0.00 4.35
1762 1821 5.412594 GTGATTGTGTGAGATTTGAAGGCTA 59.587 40.000 0.00 0.00 0.00 3.93
1763 1822 6.094603 GTGATTGTGTGAGATTTGAAGGCTAT 59.905 38.462 0.00 0.00 0.00 2.97
1764 1823 6.660521 TGATTGTGTGAGATTTGAAGGCTATT 59.339 34.615 0.00 0.00 0.00 1.73
1765 1824 6.899393 TTGTGTGAGATTTGAAGGCTATTT 57.101 33.333 0.00 0.00 0.00 1.40
1766 1825 7.994425 TTGTGTGAGATTTGAAGGCTATTTA 57.006 32.000 0.00 0.00 0.00 1.40
1819 1878 6.775708 ACTGTAGTTAGCTTATGGGTTTGAA 58.224 36.000 0.00 0.00 0.00 2.69
1828 1887 5.774690 AGCTTATGGGTTTGAACTTGAATGA 59.225 36.000 0.00 0.00 0.00 2.57
1833 1892 5.669477 TGGGTTTGAACTTGAATGAAAAGG 58.331 37.500 0.00 0.00 0.00 3.11
1861 1920 9.636879 AATGAACATCATCATATTAGAGAGACG 57.363 33.333 0.00 0.00 39.08 4.18
1880 1969 1.336440 CGATGCCTTTTTGTGGTGTCA 59.664 47.619 0.00 0.00 0.00 3.58
1930 2019 7.067372 TGTTATATCTGTTCCATTTCTGCCTTG 59.933 37.037 0.00 0.00 0.00 3.61
1936 2025 1.425066 TCCATTTCTGCCTTGTCCACT 59.575 47.619 0.00 0.00 0.00 4.00
1937 2026 1.815003 CCATTTCTGCCTTGTCCACTC 59.185 52.381 0.00 0.00 0.00 3.51
1952 2041 5.827756 TGTCCACTCTCTCATAGTTTAGGA 58.172 41.667 0.00 0.00 0.00 2.94
1953 2042 5.888724 TGTCCACTCTCTCATAGTTTAGGAG 59.111 44.000 0.00 0.00 37.91 3.69
1954 2043 5.300792 GTCCACTCTCTCATAGTTTAGGAGG 59.699 48.000 0.00 0.00 37.22 4.30
1995 2084 0.396435 TATCGGCTGCAGTTATGGGG 59.604 55.000 16.64 0.00 0.00 4.96
2061 2150 1.880027 GTGTCCGTTGCCTCAGAATTT 59.120 47.619 0.00 0.00 0.00 1.82
2161 2252 7.345653 TCCTTCTGACTGAATCACCAGTATTAT 59.654 37.037 0.00 0.00 46.45 1.28
2163 2254 9.469807 CTTCTGACTGAATCACCAGTATTATAC 57.530 37.037 0.00 0.00 46.45 1.47
2220 2502 3.512724 CCCCATTGAAAGCTTTCATCACT 59.487 43.478 35.66 20.71 45.65 3.41
2232 2514 6.240894 AGCTTTCATCACTCTCCACAATTTA 58.759 36.000 0.00 0.00 0.00 1.40
2325 2637 1.204786 TGTGTGTCCTATGGGTGGGG 61.205 60.000 0.00 0.00 0.00 4.96
2408 2935 6.594788 ACACATCTTGGCAGAATTTTGTAT 57.405 33.333 0.00 0.00 30.76 2.29
2428 2961 0.037605 AGTAGTAACTGTGCCGTGGC 60.038 55.000 3.30 3.30 36.68 5.01
2468 3002 1.662686 AGCTCCCCTTACAGCTTCTT 58.337 50.000 0.00 0.00 43.80 2.52
2595 3130 2.797156 CTCTATTGATGCCGTACTGCAC 59.203 50.000 14.54 9.09 45.48 4.57
2612 3147 2.961741 TGCACTTCACTCTTCTCTCTGT 59.038 45.455 0.00 0.00 0.00 3.41
2617 3152 7.039714 TGCACTTCACTCTTCTCTCTGTTAATA 60.040 37.037 0.00 0.00 0.00 0.98
2684 3219 8.086522 TGTAATCTGTTGAACCTTGTACTAGAC 58.913 37.037 5.85 0.00 0.00 2.59
2759 3310 2.280628 GTGGATCTCTTTGTAAGGGCG 58.719 52.381 0.00 0.00 0.00 6.13
2797 3348 7.352739 GCAATAAGGATGTATGAAAAGGTACG 58.647 38.462 0.00 0.00 0.00 3.67
2813 3364 1.535462 GTACGCCTGCAAACTTCATGT 59.465 47.619 0.00 0.00 0.00 3.21
2822 3373 5.295292 CCTGCAAACTTCATGTTCGATATCT 59.705 40.000 0.34 0.00 38.03 1.98
2824 3375 7.144722 TGCAAACTTCATGTTCGATATCTTT 57.855 32.000 0.34 0.00 38.03 2.52
2838 3389 6.616017 TCGATATCTTTCTGCTGCTGTATAG 58.384 40.000 0.00 0.74 0.00 1.31
2847 3398 7.582667 TTCTGCTGCTGTATAGTACTGATAA 57.417 36.000 5.39 0.00 0.00 1.75
2911 3462 8.855110 TCTTATGCTTCCAGTGAACAAAAATTA 58.145 29.630 0.00 0.00 0.00 1.40
2942 3493 1.202200 TGGCAACGAAACCAAGAAACG 60.202 47.619 0.00 0.00 42.51 3.60
2943 3494 1.064357 GGCAACGAAACCAAGAAACGA 59.936 47.619 0.00 0.00 0.00 3.85
2947 3498 4.553429 GCAACGAAACCAAGAAACGATATG 59.447 41.667 0.00 0.00 0.00 1.78
2948 3499 4.336532 ACGAAACCAAGAAACGATATGC 57.663 40.909 0.00 0.00 0.00 3.14
3363 6022 6.649155 TCTATGGCAGCTCAACAAGTTATTA 58.351 36.000 0.00 0.00 0.00 0.98
3397 6057 7.014518 TGTTGTTGAATGAGTGATCCTGAATTT 59.985 33.333 0.00 0.00 0.00 1.82
3448 6137 0.109597 GCAGTTTTCATGGTGAGCCG 60.110 55.000 0.00 0.00 37.67 5.52
3590 6282 4.436050 CGAAATTCTAACATCTGCAGCGTT 60.436 41.667 20.57 20.57 0.00 4.84
3611 6303 3.427573 TGGTTGAGTACTAGCTGCAGTA 58.572 45.455 16.64 5.76 0.00 2.74
3614 6306 4.639310 GGTTGAGTACTAGCTGCAGTAGTA 59.361 45.833 21.94 21.94 35.30 1.82
3615 6307 5.125097 GGTTGAGTACTAGCTGCAGTAGTAA 59.875 44.000 24.94 15.53 35.30 2.24
3616 6308 6.349944 GGTTGAGTACTAGCTGCAGTAGTAAA 60.350 42.308 24.94 17.81 35.30 2.01
3617 6309 7.259161 GTTGAGTACTAGCTGCAGTAGTAAAT 58.741 38.462 24.94 19.72 35.30 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.563435 GCCGTCCATCGCATGAGATG 61.563 60.000 27.00 27.00 45.56 2.90
11 12 1.301244 GCCGTCCATCGCATGAGAT 60.301 57.895 6.07 6.07 38.35 2.75
12 13 2.031674 ATGCCGTCCATCGCATGAGA 62.032 55.000 0.28 0.28 35.94 3.27
13 14 1.596203 ATGCCGTCCATCGCATGAG 60.596 57.895 0.00 0.00 35.94 2.90
14 15 1.888638 CATGCCGTCCATCGCATGA 60.889 57.895 15.16 0.00 46.29 3.07
15 16 1.838568 CTCATGCCGTCCATCGCATG 61.839 60.000 14.31 14.31 45.59 4.06
16 17 1.596203 CTCATGCCGTCCATCGCAT 60.596 57.895 0.00 0.00 37.00 4.73
17 18 2.202919 CTCATGCCGTCCATCGCA 60.203 61.111 0.00 0.00 38.35 5.10
18 19 2.969238 CCTCATGCCGTCCATCGC 60.969 66.667 0.00 0.00 38.35 4.58
19 20 2.280389 CCCTCATGCCGTCCATCG 60.280 66.667 0.00 0.00 39.52 3.84
20 21 1.070445 CTCCCTCATGCCGTCCATC 59.930 63.158 0.00 0.00 29.71 3.51
21 22 3.112205 GCTCCCTCATGCCGTCCAT 62.112 63.158 0.00 0.00 33.39 3.41
22 23 3.785859 GCTCCCTCATGCCGTCCA 61.786 66.667 0.00 0.00 0.00 4.02
23 24 4.554036 GGCTCCCTCATGCCGTCC 62.554 72.222 0.00 0.00 39.71 4.79
28 29 4.891037 GGCTGGGCTCCCTCATGC 62.891 72.222 6.50 5.57 36.94 4.06
29 30 4.201122 GGGCTGGGCTCCCTCATG 62.201 72.222 6.50 0.00 40.66 3.07
37 38 3.696518 TATCGAGTGGGGCTGGGCT 62.697 63.158 0.00 0.00 0.00 5.19
38 39 2.666596 CTTATCGAGTGGGGCTGGGC 62.667 65.000 0.00 0.00 0.00 5.36
39 40 1.447643 CTTATCGAGTGGGGCTGGG 59.552 63.158 0.00 0.00 0.00 4.45
40 41 1.227674 GCTTATCGAGTGGGGCTGG 60.228 63.158 0.00 0.00 0.00 4.85
41 42 1.227674 GGCTTATCGAGTGGGGCTG 60.228 63.158 0.00 0.00 0.00 4.85
42 43 1.689233 TGGCTTATCGAGTGGGGCT 60.689 57.895 0.00 0.00 0.00 5.19
43 44 1.523938 GTGGCTTATCGAGTGGGGC 60.524 63.158 0.00 0.00 0.00 5.80
44 45 1.146263 GGTGGCTTATCGAGTGGGG 59.854 63.158 0.00 0.00 0.00 4.96
45 46 1.146263 GGGTGGCTTATCGAGTGGG 59.854 63.158 0.00 0.00 0.00 4.61
46 47 1.146263 GGGGTGGCTTATCGAGTGG 59.854 63.158 0.00 0.00 0.00 4.00
47 48 1.146263 GGGGGTGGCTTATCGAGTG 59.854 63.158 0.00 0.00 0.00 3.51
48 49 1.306654 TGGGGGTGGCTTATCGAGT 60.307 57.895 0.00 0.00 0.00 4.18
49 50 1.146263 GTGGGGGTGGCTTATCGAG 59.854 63.158 0.00 0.00 0.00 4.04
50 51 2.372074 GGTGGGGGTGGCTTATCGA 61.372 63.158 0.00 0.00 0.00 3.59
51 52 2.192175 GGTGGGGGTGGCTTATCG 59.808 66.667 0.00 0.00 0.00 2.92
52 53 2.601299 GGGTGGGGGTGGCTTATC 59.399 66.667 0.00 0.00 0.00 1.75
53 54 3.027472 GGGGTGGGGGTGGCTTAT 61.027 66.667 0.00 0.00 0.00 1.73
74 75 2.819595 CATCAACGCACGAGGGGG 60.820 66.667 0.00 0.00 0.00 5.40
75 76 3.499737 GCATCAACGCACGAGGGG 61.500 66.667 0.00 0.00 0.00 4.79
76 77 2.434884 AGCATCAACGCACGAGGG 60.435 61.111 0.00 0.00 0.00 4.30
77 78 1.737735 TCAGCATCAACGCACGAGG 60.738 57.895 0.00 0.00 0.00 4.63
78 79 1.284297 TGTCAGCATCAACGCACGAG 61.284 55.000 0.00 0.00 0.00 4.18
79 80 0.878086 TTGTCAGCATCAACGCACGA 60.878 50.000 0.00 0.00 0.00 4.35
80 81 0.166597 ATTGTCAGCATCAACGCACG 59.833 50.000 0.00 0.00 0.00 5.34
81 82 1.609932 CATTGTCAGCATCAACGCAC 58.390 50.000 0.00 0.00 0.00 5.34
82 83 0.109643 GCATTGTCAGCATCAACGCA 60.110 50.000 2.76 0.00 34.75 5.24
83 84 0.109643 TGCATTGTCAGCATCAACGC 60.110 50.000 0.00 0.00 37.02 4.84
93 94 1.819903 CATGTCACCCATGCATTGTCA 59.180 47.619 0.00 0.00 44.21 3.58
107 108 4.442401 AGTTCATATGCATCCCATGTCA 57.558 40.909 0.19 0.00 35.34 3.58
139 140 2.064434 TTGGAGTGTGGACAAATGCA 57.936 45.000 0.00 0.00 0.00 3.96
144 145 0.817634 CGGCTTTGGAGTGTGGACAA 60.818 55.000 0.00 0.00 0.00 3.18
145 146 1.227823 CGGCTTTGGAGTGTGGACA 60.228 57.895 0.00 0.00 0.00 4.02
150 151 4.695560 GCTACGGCTTTGGAGTGT 57.304 55.556 0.00 0.00 35.22 3.55
161 162 1.674611 CTTGTCGACGCAAGCTACGG 61.675 60.000 11.62 0.00 39.26 4.02
172 173 0.861837 CTGGTGCAAGACTTGTCGAC 59.138 55.000 16.39 9.11 0.00 4.20
190 191 2.845638 TAGAGCAGGCAGGACGAGCT 62.846 60.000 0.00 0.00 38.43 4.09
195 196 1.403323 GCATTTTAGAGCAGGCAGGAC 59.597 52.381 0.00 0.00 0.00 3.85
204 205 7.685594 AGTCGTTTATTAGTGCATTTTAGAGC 58.314 34.615 0.00 0.00 0.00 4.09
249 250 1.202154 CGCTCGGTCACTTAGTACTGG 60.202 57.143 5.39 0.69 0.00 4.00
252 253 3.618774 CCGCTCGGTCACTTAGTAC 57.381 57.895 0.00 0.00 0.00 2.73
267 268 4.649088 ATAAGGGCAAAAAGATAACCGC 57.351 40.909 0.00 0.00 0.00 5.68
274 275 7.340999 GGGTTCACTTATATAAGGGCAAAAAGA 59.659 37.037 23.24 2.24 36.66 2.52
299 300 6.513180 TGCACCTTATATTCTAGAACGAAGG 58.487 40.000 26.07 26.07 38.34 3.46
308 309 6.422701 CGAAAACCGATGCACCTTATATTCTA 59.577 38.462 0.00 0.00 41.76 2.10
315 316 1.801771 CACGAAAACCGATGCACCTTA 59.198 47.619 0.00 0.00 41.76 2.69
326 327 3.768468 TGTTTGACTTCCACGAAAACC 57.232 42.857 0.00 0.00 31.28 3.27
500 504 5.732647 GTCAAACATGTACATGCGTTATCAC 59.267 40.000 31.19 18.48 42.39 3.06
506 510 4.829064 AAAGTCAAACATGTACATGCGT 57.171 36.364 31.19 19.01 42.39 5.24
507 511 5.211454 TCAAAAGTCAAACATGTACATGCG 58.789 37.500 31.19 21.01 42.39 4.73
508 512 7.462109 TTTCAAAAGTCAAACATGTACATGC 57.538 32.000 31.19 16.93 42.39 4.06
510 514 7.494298 GGGTTTTCAAAAGTCAAACATGTACAT 59.506 33.333 1.41 1.41 32.92 2.29
562 566 4.580580 AGATTTTCAAGCCAAACTTCGTCT 59.419 37.500 0.00 0.00 36.04 4.18
584 588 4.495911 TCTGCGCTTCTATCTGACATAG 57.504 45.455 9.73 0.00 0.00 2.23
608 621 8.406716 CGTCGTTGTTATTTATTTTGTGTCAAG 58.593 33.333 0.00 0.00 0.00 3.02
611 624 7.058693 GGACGTCGTTGTTATTTATTTTGTGTC 59.941 37.037 9.92 0.00 0.00 3.67
631 644 3.050619 CGGCTCATGTAATTAGGACGTC 58.949 50.000 7.13 7.13 0.00 4.34
632 645 2.429610 ACGGCTCATGTAATTAGGACGT 59.570 45.455 0.00 0.00 0.00 4.34
633 646 3.050619 GACGGCTCATGTAATTAGGACG 58.949 50.000 0.00 0.00 0.00 4.79
634 647 3.050619 CGACGGCTCATGTAATTAGGAC 58.949 50.000 0.00 0.00 0.00 3.85
635 648 2.691526 ACGACGGCTCATGTAATTAGGA 59.308 45.455 0.00 0.00 0.00 2.94
636 649 3.050619 GACGACGGCTCATGTAATTAGG 58.949 50.000 0.00 0.00 0.00 2.69
637 650 3.050619 GGACGACGGCTCATGTAATTAG 58.949 50.000 0.00 0.00 0.00 1.73
638 651 2.223876 GGGACGACGGCTCATGTAATTA 60.224 50.000 0.00 0.00 0.00 1.40
639 652 1.472728 GGGACGACGGCTCATGTAATT 60.473 52.381 0.00 0.00 0.00 1.40
640 653 0.104304 GGGACGACGGCTCATGTAAT 59.896 55.000 0.00 0.00 0.00 1.89
641 654 0.968901 AGGGACGACGGCTCATGTAA 60.969 55.000 1.92 0.00 0.00 2.41
642 655 1.379443 AGGGACGACGGCTCATGTA 60.379 57.895 1.92 0.00 0.00 2.29
643 656 2.680352 AGGGACGACGGCTCATGT 60.680 61.111 1.92 0.00 0.00 3.21
644 657 2.202797 CAGGGACGACGGCTCATG 60.203 66.667 1.92 0.00 0.00 3.07
645 658 3.461773 CCAGGGACGACGGCTCAT 61.462 66.667 1.92 0.00 0.00 2.90
649 662 3.090219 ATAAGCCAGGGACGACGGC 62.090 63.158 0.00 0.00 46.62 5.68
650 663 1.227263 CATAAGCCAGGGACGACGG 60.227 63.158 0.00 0.00 0.00 4.79
653 666 0.325296 ACTCCATAAGCCAGGGACGA 60.325 55.000 0.00 0.00 32.44 4.20
655 668 2.772515 ACTTACTCCATAAGCCAGGGAC 59.227 50.000 0.00 0.00 43.76 4.46
667 680 4.382685 GCTAGTTGGCATACACTTACTCCA 60.383 45.833 0.00 0.00 0.00 3.86
668 681 4.120589 GCTAGTTGGCATACACTTACTCC 58.879 47.826 0.00 0.00 0.00 3.85
669 682 4.120589 GGCTAGTTGGCATACACTTACTC 58.879 47.826 0.00 0.00 41.37 2.59
670 683 3.517901 TGGCTAGTTGGCATACACTTACT 59.482 43.478 0.00 0.00 46.76 2.24
671 684 3.869065 TGGCTAGTTGGCATACACTTAC 58.131 45.455 0.00 0.00 46.76 2.34
696 709 1.340248 CTACCACGGTCACAAGTCTGT 59.660 52.381 0.00 0.00 35.63 3.41
704 717 4.360563 CAAGTCATATCTACCACGGTCAC 58.639 47.826 0.00 0.00 0.00 3.67
723 736 6.500041 TGGTTAGTTTCGATTGTTTTCCAAG 58.500 36.000 0.00 0.00 36.25 3.61
727 740 4.915667 GCCTGGTTAGTTTCGATTGTTTTC 59.084 41.667 0.00 0.00 0.00 2.29
731 744 2.433436 GGCCTGGTTAGTTTCGATTGT 58.567 47.619 0.00 0.00 0.00 2.71
744 757 1.681229 TTAGAGGATTTGGGCCTGGT 58.319 50.000 4.53 0.00 35.44 4.00
745 758 2.826674 TTTAGAGGATTTGGGCCTGG 57.173 50.000 4.53 0.00 35.44 4.45
749 762 6.607600 AGTTCCTTATTTTAGAGGATTTGGGC 59.392 38.462 0.00 0.00 41.48 5.36
813 826 2.921221 AGAAGGGGGAAACATCTCTCA 58.079 47.619 0.00 0.00 0.00 3.27
816 829 8.437575 TGTATTATAAGAAGGGGGAAACATCTC 58.562 37.037 0.00 0.00 0.00 2.75
826 839 6.289064 AGCGTTCTTGTATTATAAGAAGGGG 58.711 40.000 24.48 15.08 44.21 4.79
836 849 9.480053 ACTACTGTAAAAAGCGTTCTTGTATTA 57.520 29.630 0.00 0.00 31.78 0.98
837 850 8.280497 CACTACTGTAAAAAGCGTTCTTGTATT 58.720 33.333 0.00 0.00 31.78 1.89
841 854 6.044512 ACACTACTGTAAAAAGCGTTCTTG 57.955 37.500 0.00 0.00 31.78 3.02
842 855 6.982724 ACTACACTACTGTAAAAAGCGTTCTT 59.017 34.615 0.00 0.00 32.24 2.52
844 857 6.199719 ACACTACACTACTGTAAAAAGCGTTC 59.800 38.462 0.00 0.00 32.24 3.95
847 860 6.520792 AACACTACACTACTGTAAAAAGCG 57.479 37.500 0.00 0.00 32.24 4.68
922 961 5.849510 TCCGTCTCATAACAGACTCAAAAA 58.150 37.500 0.00 0.00 40.75 1.94
923 962 5.462530 TCCGTCTCATAACAGACTCAAAA 57.537 39.130 0.00 0.00 40.75 2.44
924 963 4.082190 CCTCCGTCTCATAACAGACTCAAA 60.082 45.833 0.00 0.00 40.75 2.69
925 964 3.444034 CCTCCGTCTCATAACAGACTCAA 59.556 47.826 0.00 0.00 40.75 3.02
926 965 3.017442 CCTCCGTCTCATAACAGACTCA 58.983 50.000 0.00 0.00 40.75 3.41
927 966 3.280295 TCCTCCGTCTCATAACAGACTC 58.720 50.000 0.00 0.00 40.75 3.36
928 967 3.367646 TCCTCCGTCTCATAACAGACT 57.632 47.619 0.00 0.00 40.75 3.24
929 968 3.444388 ACTTCCTCCGTCTCATAACAGAC 59.556 47.826 0.00 0.00 39.68 3.51
930 969 3.695060 GACTTCCTCCGTCTCATAACAGA 59.305 47.826 0.00 0.00 0.00 3.41
931 970 3.181485 GGACTTCCTCCGTCTCATAACAG 60.181 52.174 0.00 0.00 0.00 3.16
932 971 2.758979 GGACTTCCTCCGTCTCATAACA 59.241 50.000 0.00 0.00 0.00 2.41
933 972 3.025262 AGGACTTCCTCCGTCTCATAAC 58.975 50.000 0.00 0.00 44.77 1.89
934 973 3.383698 AGGACTTCCTCCGTCTCATAA 57.616 47.619 0.00 0.00 44.77 1.90
952 991 6.628919 TGATGTGCATTCAGATTCATAAGG 57.371 37.500 0.00 0.00 0.00 2.69
964 1003 0.179156 CGTGGGCTTGATGTGCATTC 60.179 55.000 0.00 0.00 0.00 2.67
988 1027 2.281761 CACTTGGAAGGCTGCCGT 60.282 61.111 13.96 10.59 0.00 5.68
1030 1069 1.068472 CGATGTACGGCTAGGATGGTC 60.068 57.143 0.00 0.00 38.46 4.02
1129 1176 4.508128 GCGGAATCTCGTGGCGGA 62.508 66.667 0.00 0.00 0.00 5.54
1278 1325 2.005451 CAACAAAGGGAGCGAGAGATG 58.995 52.381 0.00 0.00 0.00 2.90
1285 1332 0.798776 CAGTAGCAACAAAGGGAGCG 59.201 55.000 0.00 0.00 0.00 5.03
1288 1335 4.134563 GAGAAACAGTAGCAACAAAGGGA 58.865 43.478 0.00 0.00 0.00 4.20
1293 1340 2.869801 CGTGGAGAAACAGTAGCAACAA 59.130 45.455 0.00 0.00 0.00 2.83
1295 1342 2.475487 GTCGTGGAGAAACAGTAGCAAC 59.525 50.000 0.00 0.00 0.00 4.17
1296 1343 2.750948 GTCGTGGAGAAACAGTAGCAA 58.249 47.619 0.00 0.00 0.00 3.91
1299 1346 1.337821 GCGTCGTGGAGAAACAGTAG 58.662 55.000 0.00 0.00 0.00 2.57
1464 1516 1.143813 AATGGTATGAGGGCTGGAGG 58.856 55.000 0.00 0.00 0.00 4.30
1535 1587 1.003233 GAAATCGAGGGGGTTCACACT 59.997 52.381 0.00 0.00 0.00 3.55
1561 1613 4.846168 AATTCCTACCCTTCAACTCTCC 57.154 45.455 0.00 0.00 0.00 3.71
1572 1627 6.526056 ACCTATCCCTAAAAATTCCTACCC 57.474 41.667 0.00 0.00 0.00 3.69
1608 1666 5.127693 ACCATTACTTGTGCGCAAATTAA 57.872 34.783 14.00 13.85 33.73 1.40
1617 1676 3.191371 CCTCCAGAAACCATTACTTGTGC 59.809 47.826 0.00 0.00 0.00 4.57
1658 1717 7.819415 TGTCATAAACTCTACCAAGATTCACAG 59.181 37.037 0.00 0.00 0.00 3.66
1659 1718 7.676004 TGTCATAAACTCTACCAAGATTCACA 58.324 34.615 0.00 0.00 0.00 3.58
1666 1725 8.553459 AGAACAATGTCATAAACTCTACCAAG 57.447 34.615 0.00 0.00 0.00 3.61
1669 1728 7.103641 TGGAGAACAATGTCATAAACTCTACC 58.896 38.462 0.00 0.00 0.00 3.18
1706 1765 0.037512 CACCACTGAGAGGCACAGAG 60.038 60.000 11.91 5.44 38.55 3.35
1730 1789 0.943673 TCACACAATCACAAGTGCCG 59.056 50.000 0.00 0.00 39.30 5.69
1738 1797 4.217118 AGCCTTCAAATCTCACACAATCAC 59.783 41.667 0.00 0.00 0.00 3.06
1772 1831 7.814107 CAGTTATACTGTCAATTGGCAACATTT 59.186 33.333 14.69 1.12 43.78 2.32
1819 1878 6.729690 TGTTCATTCCCTTTTCATTCAAGT 57.270 33.333 0.00 0.00 0.00 3.16
1860 1919 1.336440 TGACACCACAAAAAGGCATCG 59.664 47.619 0.00 0.00 0.00 3.84
1861 1920 3.451141 TTGACACCACAAAAAGGCATC 57.549 42.857 0.00 0.00 0.00 3.91
1880 1969 9.436957 ACATGAAAAGACTGTATTCGTCTAATT 57.563 29.630 0.00 0.00 40.65 1.40
1917 2006 1.815003 GAGTGGACAAGGCAGAAATGG 59.185 52.381 0.00 0.00 0.00 3.16
1930 2019 5.300792 CCTCCTAAACTATGAGAGAGTGGAC 59.699 48.000 0.00 0.00 0.00 4.02
1936 2025 9.357161 GTAAAGATCCTCCTAAACTATGAGAGA 57.643 37.037 0.00 0.00 0.00 3.10
1937 2026 9.362151 AGTAAAGATCCTCCTAAACTATGAGAG 57.638 37.037 0.00 0.00 0.00 3.20
1995 2084 3.208747 TCACCTTGTCCTTCAACCTTC 57.791 47.619 0.00 0.00 32.18 3.46
2061 2150 2.760634 TGGCTAATTTCTGTCTGCGA 57.239 45.000 0.00 0.00 0.00 5.10
2184 2400 4.882559 TCAATGGGGGATAAAGCAGAAAT 58.117 39.130 0.00 0.00 0.00 2.17
2191 2407 5.187576 TGAAAGCTTTCAATGGGGGATAAAG 59.812 40.000 34.01 0.00 43.62 1.85
2192 2408 5.090139 TGAAAGCTTTCAATGGGGGATAAA 58.910 37.500 34.01 10.65 43.62 1.40
2193 2409 4.682563 TGAAAGCTTTCAATGGGGGATAA 58.317 39.130 34.01 10.84 43.62 1.75
2232 2514 3.327757 TGCTGGAATCAGGAAGTACAACT 59.672 43.478 0.00 0.00 38.42 3.16
2325 2637 4.864334 CAGCCATCACGCCTCCCC 62.864 72.222 0.00 0.00 0.00 4.81
2408 2935 1.203052 GCCACGGCACAGTTACTACTA 59.797 52.381 2.36 0.00 41.49 1.82
2428 2961 5.213913 CTAGCAAGCACAGAACTGTAATG 57.786 43.478 7.15 7.93 42.83 1.90
2468 3002 4.835678 TGCTCTTGAGAATGCAACTGATA 58.164 39.130 1.30 0.00 32.12 2.15
2595 3130 9.959749 GGTATATTAACAGAGAGAAGAGTGAAG 57.040 37.037 0.00 0.00 0.00 3.02
2684 3219 6.746120 AGCCTTAGTGTAATATGGAGTAACG 58.254 40.000 0.00 0.00 0.00 3.18
2759 3310 0.814457 TTATTGCCGGCATGTTGGAC 59.186 50.000 33.25 0.00 0.00 4.02
2774 3325 6.485648 GGCGTACCTTTTCATACATCCTTATT 59.514 38.462 0.00 0.00 0.00 1.40
2797 3348 1.266718 TCGAACATGAAGTTTGCAGGC 59.733 47.619 0.00 0.00 41.51 4.85
2813 3364 4.128925 ACAGCAGCAGAAAGATATCGAA 57.871 40.909 0.00 0.00 0.00 3.71
2822 3373 5.914898 TCAGTACTATACAGCAGCAGAAA 57.085 39.130 0.00 0.00 0.00 2.52
2824 3375 6.773200 AGTTATCAGTACTATACAGCAGCAGA 59.227 38.462 0.00 0.00 0.00 4.26
2838 3389 7.873505 GGGGATTGACTAATCAGTTATCAGTAC 59.126 40.741 0.00 0.00 43.62 2.73
2847 3398 4.785376 AGAACTGGGGATTGACTAATCAGT 59.215 41.667 0.00 0.00 43.62 3.41
2857 3408 3.230134 TGGTTTCAAGAACTGGGGATTG 58.770 45.455 0.00 0.00 0.00 2.67
2911 3462 6.692486 TGGTTTCGTTGCCAAACATTATAAT 58.308 32.000 0.00 0.00 35.74 1.28
2947 3498 0.659427 TGCTATGATGCAAGCTTCGC 59.341 50.000 9.40 12.25 40.29 4.70
2948 3499 2.289820 ACATGCTATGATGCAAGCTTCG 59.710 45.455 9.40 0.00 46.61 3.79
3363 6022 6.997655 TCACTCATTCAACAACACTAGAGAT 58.002 36.000 0.00 0.00 0.00 2.75
3397 6057 6.876789 TCTTAACAGGAATGTGCGAATAGAAA 59.123 34.615 0.00 0.00 0.00 2.52
3405 6065 5.088739 GTCAAATCTTAACAGGAATGTGCG 58.911 41.667 0.00 0.00 0.00 5.34
3448 6137 0.520404 CACTTCAGCATGCACCAGTC 59.480 55.000 21.98 0.00 34.76 3.51
3528 6220 7.492669 TCAAACGAATTTTAACTTGCCAATTCA 59.507 29.630 8.16 0.00 36.01 2.57
3590 6282 2.248248 ACTGCAGCTAGTACTCAACCA 58.752 47.619 15.27 0.00 0.00 3.67
3611 6303 2.417787 GGTCGGGTCGCTACAATTTACT 60.418 50.000 0.00 0.00 0.00 2.24
3614 6306 0.611714 AGGTCGGGTCGCTACAATTT 59.388 50.000 0.00 0.00 0.00 1.82
3615 6307 0.175073 GAGGTCGGGTCGCTACAATT 59.825 55.000 0.00 0.00 0.00 2.32
3616 6308 0.968901 TGAGGTCGGGTCGCTACAAT 60.969 55.000 0.00 0.00 0.00 2.71
3617 6309 1.592400 CTGAGGTCGGGTCGCTACAA 61.592 60.000 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.