Multiple sequence alignment - TraesCS3D01G112600

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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 TraesCS3D01G112600 chr3D 100.000 2577 0 0 1 2577 66560650 66563226 0.000000e+00 4759
1 TraesCS3D01G112600 chr3D 88.655 1569 108 30 767 2280 66553119 66554672 0.000000e+00 1847
2 TraesCS3D01G112600 chr3A 88.327 1542 117 32 767 2268 77594673 77596191 0.000000e+00 1792
3 TraesCS3D01G112600 chr3A 88.031 1529 124 33 767 2280 77708227 77709711 0.000000e+00 1755
4 TraesCS3D01G112600 chr3A 87.758 1552 118 31 767 2274 77548142 77549665 0.000000e+00 1748
5 TraesCS3D01G112600 chr3A 91.082 527 40 6 1833 2358 77720470 77720990 0.000000e+00 706
6 TraesCS3D01G112600 chr3A 95.238 63 3 0 1773 1835 77714801 77714863 1.630000e-17 100
7 TraesCS3D01G112600 chr3B 89.433 1164 95 13 769 1915 110735711 110736863 0.000000e+00 1443
8 TraesCS3D01G112600 chr3B 87.969 906 68 13 767 1667 110741543 110742412 0.000000e+00 1031
9 TraesCS3D01G112600 chr3B 91.460 644 36 9 1726 2358 110742413 110743048 0.000000e+00 867
10 TraesCS3D01G112600 chr7D 99.099 666 4 2 1 665 608449137 608449801 0.000000e+00 1195
11 TraesCS3D01G112600 chr7D 81.325 830 107 35 975 1777 30984584 30983776 4.680000e-177 630
12 TraesCS3D01G112600 chr7D 99.273 275 2 0 386 660 608446139 608446413 4.950000e-137 497
13 TraesCS3D01G112600 chr4D 98.338 662 10 1 1 661 245834943 245834282 0.000000e+00 1160
14 TraesCS3D01G112600 chr4D 99.270 274 2 0 387 660 245837940 245837667 1.780000e-136 496
15 TraesCS3D01G112600 chr4D 98.561 278 4 0 387 664 14514628 14514351 2.300000e-135 492
16 TraesCS3D01G112600 chr4D 90.308 227 13 5 2357 2577 434530890 434531113 3.240000e-74 289
17 TraesCS3D01G112600 chr4D 88.839 224 19 6 2358 2577 449822883 449823104 1.180000e-68 270
18 TraesCS3D01G112600 chr6D 94.619 669 31 3 1 665 294094349 294093682 0.000000e+00 1031
19 TraesCS3D01G112600 chr6D 99.273 275 2 0 387 661 414540522 414540248 4.950000e-137 497
20 TraesCS3D01G112600 chr6D 89.236 288 27 2 376 660 294097359 294097073 8.770000e-95 357
21 TraesCS3D01G112600 chr1B 93.383 665 40 2 1 662 280692893 280692230 0.000000e+00 981
22 TraesCS3D01G112600 chr1B 88.739 222 22 3 2358 2577 657343492 657343272 4.230000e-68 268
23 TraesCS3D01G112600 chr1B 88.060 134 14 2 638 770 91533131 91532999 9.550000e-35 158
24 TraesCS3D01G112600 chr1B 88.060 134 14 2 638 770 98565387 98565519 9.550000e-35 158
25 TraesCS3D01G112600 chr1B 86.567 134 16 2 638 770 21800435 21800303 2.070000e-31 147
26 TraesCS3D01G112600 chr4A 83.147 807 101 24 1043 1817 697439333 697440136 0.000000e+00 704
27 TraesCS3D01G112600 chr4A 83.639 764 95 22 1037 1777 697432888 697433644 0.000000e+00 691
28 TraesCS3D01G112600 chr4A 88.341 223 23 3 2357 2577 710292984 710292763 5.470000e-67 265
29 TraesCS3D01G112600 chr7A 82.705 769 95 29 1037 1777 31511965 31511207 0.000000e+00 649
30 TraesCS3D01G112600 chr7A 82.660 767 99 23 1037 1777 31529767 31529009 0.000000e+00 649
31 TraesCS3D01G112600 chr7A 82.660 767 99 23 1037 1777 31548207 31547449 0.000000e+00 649
32 TraesCS3D01G112600 chr7A 88.739 222 19 5 2358 2577 543445174 543445391 1.520000e-67 267
33 TraesCS3D01G112600 chrUn 92.444 225 11 5 2355 2577 305305812 305306032 1.490000e-82 316
34 TraesCS3D01G112600 chr4B 91.480 223 14 5 2357 2577 299555978 299556197 4.170000e-78 302
35 TraesCS3D01G112600 chr2B 90.222 225 15 7 2357 2577 16197764 16197543 1.170000e-73 287
36 TraesCS3D01G112600 chr2B 91.803 122 9 1 650 770 518517787 518517908 4.410000e-38 169
37 TraesCS3D01G112600 chr2B 88.806 134 13 2 638 770 764550635 764550767 2.050000e-36 163
38 TraesCS3D01G112600 chr2B 88.060 134 14 2 638 770 120603268 120603400 9.550000e-35 158
39 TraesCS3D01G112600 chr2B 88.889 126 11 2 645 769 11451730 11451607 4.440000e-33 152
40 TraesCS3D01G112600 chr2B 86.567 134 16 2 637 769 779185955 779185823 2.070000e-31 147
41 TraesCS3D01G112600 chr2B 86.364 132 16 2 638 768 635761004 635761134 2.670000e-30 143
42 TraesCS3D01G112600 chr7B 89.189 222 20 3 2357 2577 418044753 418044971 9.080000e-70 274
43 TraesCS3D01G112600 chr7B 93.805 113 7 0 663 775 695049395 695049283 1.230000e-38 171
44 TraesCS3D01G112600 chr5D 95.370 108 5 0 663 770 243401383 243401276 3.410000e-39 172
45 TraesCS3D01G112600 chr5B 92.500 120 7 2 655 773 622630491 622630609 1.230000e-38 171
46 TraesCS3D01G112600 chr5B 88.806 134 13 2 638 770 419085721 419085589 2.050000e-36 163
47 TraesCS3D01G112600 chr6B 75.773 388 53 29 265 634 145209551 145209187 9.550000e-35 158


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 TraesCS3D01G112600 chr3D 66560650 66563226 2576 False 4759 4759 100.0000 1 2577 1 chr3D.!!$F2 2576
1 TraesCS3D01G112600 chr3D 66553119 66554672 1553 False 1847 1847 88.6550 767 2280 1 chr3D.!!$F1 1513
2 TraesCS3D01G112600 chr3A 77594673 77596191 1518 False 1792 1792 88.3270 767 2268 1 chr3A.!!$F2 1501
3 TraesCS3D01G112600 chr3A 77708227 77709711 1484 False 1755 1755 88.0310 767 2280 1 chr3A.!!$F3 1513
4 TraesCS3D01G112600 chr3A 77548142 77549665 1523 False 1748 1748 87.7580 767 2274 1 chr3A.!!$F1 1507
5 TraesCS3D01G112600 chr3A 77720470 77720990 520 False 706 706 91.0820 1833 2358 1 chr3A.!!$F5 525
6 TraesCS3D01G112600 chr3B 110735711 110736863 1152 False 1443 1443 89.4330 769 1915 1 chr3B.!!$F1 1146
7 TraesCS3D01G112600 chr3B 110741543 110743048 1505 False 949 1031 89.7145 767 2358 2 chr3B.!!$F2 1591
8 TraesCS3D01G112600 chr7D 608446139 608449801 3662 False 846 1195 99.1860 1 665 2 chr7D.!!$F1 664
9 TraesCS3D01G112600 chr7D 30983776 30984584 808 True 630 630 81.3250 975 1777 1 chr7D.!!$R1 802
10 TraesCS3D01G112600 chr4D 245834282 245837940 3658 True 828 1160 98.8040 1 661 2 chr4D.!!$R2 660
11 TraesCS3D01G112600 chr6D 294093682 294097359 3677 True 694 1031 91.9275 1 665 2 chr6D.!!$R2 664
12 TraesCS3D01G112600 chr1B 280692230 280692893 663 True 981 981 93.3830 1 662 1 chr1B.!!$R3 661
13 TraesCS3D01G112600 chr4A 697439333 697440136 803 False 704 704 83.1470 1043 1817 1 chr4A.!!$F2 774
14 TraesCS3D01G112600 chr4A 697432888 697433644 756 False 691 691 83.6390 1037 1777 1 chr4A.!!$F1 740
15 TraesCS3D01G112600 chr7A 31511207 31511965 758 True 649 649 82.7050 1037 1777 1 chr7A.!!$R1 740
16 TraesCS3D01G112600 chr7A 31529009 31529767 758 True 649 649 82.6600 1037 1777 1 chr7A.!!$R2 740
17 TraesCS3D01G112600 chr7A 31547449 31548207 758 True 649 649 82.6600 1037 1777 1 chr7A.!!$R3 740

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
678 3694 0.037303 ACGTACTCCCTCCGTTCAGA 59.963 55.0 0.0 0.0 0.0 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1641 4750 0.033011 ATGACTCGCTAGGGGTCACT 60.033 55.0 23.61 14.74 41.75 3.41 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
112 3124 5.658634 TGGAGCACTCTACTATTGACAAGAT 59.341 40.000 0.00 0.00 0.00 2.40
662 3678 3.181479 TGAGAAGAGTGCTGTTAACACGT 60.181 43.478 3.59 0.00 42.94 4.49
665 3681 4.037684 AGAAGAGTGCTGTTAACACGTACT 59.962 41.667 20.22 20.22 42.94 2.73
666 3682 3.898529 AGAGTGCTGTTAACACGTACTC 58.101 45.455 28.13 28.13 42.94 2.59
667 3683 2.985139 GAGTGCTGTTAACACGTACTCC 59.015 50.000 26.72 17.42 42.94 3.85
668 3684 2.064014 GTGCTGTTAACACGTACTCCC 58.936 52.381 3.59 0.00 0.00 4.30
669 3685 1.965643 TGCTGTTAACACGTACTCCCT 59.034 47.619 3.59 0.00 0.00 4.20
670 3686 2.029649 TGCTGTTAACACGTACTCCCTC 60.030 50.000 3.59 0.00 0.00 4.30
671 3687 2.673326 GCTGTTAACACGTACTCCCTCC 60.673 54.545 3.59 0.00 0.00 4.30
672 3688 1.541147 TGTTAACACGTACTCCCTCCG 59.459 52.381 3.59 0.00 0.00 4.63
673 3689 1.541588 GTTAACACGTACTCCCTCCGT 59.458 52.381 0.00 0.00 34.71 4.69
674 3690 1.909700 TAACACGTACTCCCTCCGTT 58.090 50.000 0.00 0.00 31.46 4.44
675 3691 0.600057 AACACGTACTCCCTCCGTTC 59.400 55.000 0.00 0.00 31.46 3.95
676 3692 0.538057 ACACGTACTCCCTCCGTTCA 60.538 55.000 0.00 0.00 31.46 3.18
677 3693 0.170561 CACGTACTCCCTCCGTTCAG 59.829 60.000 0.00 0.00 31.46 3.02
678 3694 0.037303 ACGTACTCCCTCCGTTCAGA 59.963 55.000 0.00 0.00 0.00 3.27
679 3695 1.171308 CGTACTCCCTCCGTTCAGAA 58.829 55.000 0.00 0.00 0.00 3.02
680 3696 1.749634 CGTACTCCCTCCGTTCAGAAT 59.250 52.381 0.00 0.00 0.00 2.40
681 3697 2.165845 CGTACTCCCTCCGTTCAGAATT 59.834 50.000 0.00 0.00 0.00 2.17
682 3698 3.379372 CGTACTCCCTCCGTTCAGAATTA 59.621 47.826 0.00 0.00 0.00 1.40
683 3699 3.889520 ACTCCCTCCGTTCAGAATTAC 57.110 47.619 0.00 0.00 0.00 1.89
684 3700 3.442076 ACTCCCTCCGTTCAGAATTACT 58.558 45.455 0.00 0.00 0.00 2.24
685 3701 3.447944 ACTCCCTCCGTTCAGAATTACTC 59.552 47.826 0.00 0.00 0.00 2.59
686 3702 3.437213 TCCCTCCGTTCAGAATTACTCA 58.563 45.455 0.00 0.00 0.00 3.41
687 3703 4.030913 TCCCTCCGTTCAGAATTACTCAT 58.969 43.478 0.00 0.00 0.00 2.90
688 3704 4.099573 TCCCTCCGTTCAGAATTACTCATC 59.900 45.833 0.00 0.00 0.00 2.92
689 3705 4.100189 CCCTCCGTTCAGAATTACTCATCT 59.900 45.833 0.00 0.00 0.00 2.90
690 3706 5.302059 CCCTCCGTTCAGAATTACTCATCTA 59.698 44.000 0.00 0.00 0.00 1.98
691 3707 6.183360 CCCTCCGTTCAGAATTACTCATCTAA 60.183 42.308 0.00 0.00 0.00 2.10
692 3708 6.920758 CCTCCGTTCAGAATTACTCATCTAAG 59.079 42.308 0.00 0.00 0.00 2.18
693 3709 7.201830 CCTCCGTTCAGAATTACTCATCTAAGA 60.202 40.741 0.00 0.00 0.00 2.10
694 3710 8.063200 TCCGTTCAGAATTACTCATCTAAGAA 57.937 34.615 0.00 0.00 0.00 2.52
695 3711 8.528643 TCCGTTCAGAATTACTCATCTAAGAAA 58.471 33.333 0.00 0.00 0.00 2.52
696 3712 9.319143 CCGTTCAGAATTACTCATCTAAGAAAT 57.681 33.333 0.00 0.00 0.00 2.17
754 3770 9.260002 ACATTCATTTTTGTGACAAGTAATTCC 57.740 29.630 0.00 0.00 0.00 3.01
755 3771 7.922505 TTCATTTTTGTGACAAGTAATTCCG 57.077 32.000 0.00 0.00 0.00 4.30
756 3772 6.442952 TCATTTTTGTGACAAGTAATTCCGG 58.557 36.000 0.00 0.00 0.00 5.14
757 3773 6.263392 TCATTTTTGTGACAAGTAATTCCGGA 59.737 34.615 0.00 0.00 0.00 5.14
758 3774 5.427036 TTTTGTGACAAGTAATTCCGGAC 57.573 39.130 1.83 0.00 0.00 4.79
759 3775 2.679450 TGTGACAAGTAATTCCGGACG 58.321 47.619 1.83 0.00 0.00 4.79
760 3776 2.296752 TGTGACAAGTAATTCCGGACGA 59.703 45.455 1.83 0.00 0.00 4.20
761 3777 3.243805 TGTGACAAGTAATTCCGGACGAA 60.244 43.478 1.83 0.00 34.14 3.85
762 3778 3.367025 GTGACAAGTAATTCCGGACGAAG 59.633 47.826 1.83 0.00 32.78 3.79
763 3779 2.928116 GACAAGTAATTCCGGACGAAGG 59.072 50.000 1.83 0.00 32.78 3.46
764 3780 2.277084 CAAGTAATTCCGGACGAAGGG 58.723 52.381 1.83 0.00 32.78 3.95
765 3781 1.856629 AGTAATTCCGGACGAAGGGA 58.143 50.000 1.83 0.00 32.78 4.20
842 3861 1.746727 CGAGCTTCTTCCGTGATGCG 61.747 60.000 0.00 0.00 40.58 4.73
859 3878 2.604174 CGTCCACACGCCTCAAACC 61.604 63.158 0.00 0.00 39.69 3.27
867 3890 2.750237 GCCTCAAACCGGCCGATT 60.750 61.111 30.73 15.33 41.73 3.34
878 3901 2.158871 ACCGGCCGATTGCTATTTAAGA 60.159 45.455 30.73 0.00 40.92 2.10
880 3903 3.120199 CCGGCCGATTGCTATTTAAGATG 60.120 47.826 30.73 0.00 40.92 2.90
881 3904 3.745975 CGGCCGATTGCTATTTAAGATGA 59.254 43.478 24.07 0.00 40.92 2.92
946 3988 7.776030 ACTAGCTAGCTAGAGATCAGTTAACAA 59.224 37.037 43.93 14.05 46.56 2.83
984 4026 2.352651 GCTACGTACGTACACATCCTCA 59.647 50.000 23.60 1.97 0.00 3.86
1125 4173 2.169789 CCAGAAGGTGCATCTCGCG 61.170 63.158 0.00 0.00 46.97 5.87
1239 4310 0.180406 ACGACAAGCCCTTCAACACT 59.820 50.000 0.00 0.00 0.00 3.55
1257 4328 2.441164 GCCACACACACCAACCCA 60.441 61.111 0.00 0.00 0.00 4.51
1292 4371 1.335689 GCTCCGGGTAAGTACATAGCG 60.336 57.143 0.00 0.00 0.00 4.26
1338 4426 2.510906 GGCCATGGCGTCACCTAT 59.489 61.111 29.90 0.00 43.06 2.57
1339 4427 1.752198 GGCCATGGCGTCACCTATA 59.248 57.895 29.90 0.00 43.06 1.31
1340 4428 0.320771 GGCCATGGCGTCACCTATAG 60.321 60.000 29.90 0.00 43.06 1.31
1358 4460 8.682710 CACCTATAGTATGAGCTATCTTCTTCC 58.317 40.741 0.00 0.00 34.00 3.46
1359 4461 8.394822 ACCTATAGTATGAGCTATCTTCTTCCA 58.605 37.037 0.00 0.00 34.00 3.53
1360 4462 8.902806 CCTATAGTATGAGCTATCTTCTTCCAG 58.097 40.741 0.00 0.00 34.00 3.86
1387 4489 2.873288 GACTACTCGTCGGGCGTT 59.127 61.111 0.49 0.00 42.13 4.84
1494 4603 0.320334 TCGACGGTGTTGATGTGCAT 60.320 50.000 0.00 0.00 0.00 3.96
1641 4750 0.181114 AGCACAAGTTCAGCACCAGA 59.819 50.000 0.00 0.00 0.00 3.86
1700 4809 3.792047 CATGCAGCACCACGACCG 61.792 66.667 0.00 0.00 0.00 4.79
1745 4854 3.827876 TGGACCAACGTCACACTCTATAA 59.172 43.478 0.00 0.00 41.13 0.98
1749 4858 6.696148 GGACCAACGTCACACTCTATAATAAG 59.304 42.308 0.00 0.00 41.13 1.73
1923 5058 4.499019 GCCCGTGACTTCTTTTTCAAATGA 60.499 41.667 0.00 0.00 0.00 2.57
1924 5059 5.772521 CCCGTGACTTCTTTTTCAAATGAT 58.227 37.500 0.00 0.00 0.00 2.45
1927 5062 7.306749 CCCGTGACTTCTTTTTCAAATGATTTG 60.307 37.037 11.54 11.54 41.96 2.32
2055 5221 5.912149 AAAGGGTGATCTATATGAGCCAA 57.088 39.130 0.00 0.00 39.13 4.52
2058 5224 5.096521 AGGGTGATCTATATGAGCCAATCA 58.903 41.667 0.00 0.00 39.13 2.57
2068 5234 8.884323 TCTATATGAGCCAATCATCCTTTACTT 58.116 33.333 0.00 0.00 46.01 2.24
2069 5235 7.756395 ATATGAGCCAATCATCCTTTACTTG 57.244 36.000 0.00 0.00 46.01 3.16
2070 5236 3.696051 TGAGCCAATCATCCTTTACTTGC 59.304 43.478 0.00 0.00 31.12 4.01
2071 5237 3.026694 AGCCAATCATCCTTTACTTGCC 58.973 45.455 0.00 0.00 0.00 4.52
2074 5240 4.019174 CCAATCATCCTTTACTTGCCTGT 58.981 43.478 0.00 0.00 0.00 4.00
2163 5337 4.021456 TCCTCTTGTCTCGCAAAACTATGA 60.021 41.667 0.00 0.00 36.53 2.15
2254 5428 1.022735 GGAGAAGGCGTCGAGATGTA 58.977 55.000 0.00 0.00 0.00 2.29
2317 5491 3.627395 TCTCACATACCGCCTTGATTT 57.373 42.857 0.00 0.00 0.00 2.17
2347 5521 0.908180 CCTCCCACGGGTAGACCTTT 60.908 60.000 1.07 0.00 36.97 3.11
2349 5523 0.178926 TCCCACGGGTAGACCTTTGA 60.179 55.000 1.07 0.00 36.97 2.69
2358 5532 5.359292 ACGGGTAGACCTTTGATAGTTCTAC 59.641 44.000 0.00 0.25 36.97 2.59
2359 5533 5.593502 CGGGTAGACCTTTGATAGTTCTACT 59.406 44.000 7.35 0.00 36.97 2.57
2360 5534 6.769822 CGGGTAGACCTTTGATAGTTCTACTA 59.230 42.308 7.35 0.00 36.97 1.82
2361 5535 7.041235 CGGGTAGACCTTTGATAGTTCTACTAG 60.041 44.444 7.35 0.00 33.43 2.57
2362 5536 7.779326 GGGTAGACCTTTGATAGTTCTACTAGT 59.221 40.741 0.00 0.00 33.05 2.57
2363 5537 8.623030 GGTAGACCTTTGATAGTTCTACTAGTG 58.377 40.741 5.39 0.00 33.66 2.74
2364 5538 7.648039 AGACCTTTGATAGTTCTACTAGTGG 57.352 40.000 5.39 1.87 33.66 4.00
2365 5539 7.183460 AGACCTTTGATAGTTCTACTAGTGGT 58.817 38.462 5.39 0.00 33.66 4.16
2366 5540 7.674772 AGACCTTTGATAGTTCTACTAGTGGTT 59.325 37.037 5.39 0.00 33.66 3.67
2367 5541 7.612677 ACCTTTGATAGTTCTACTAGTGGTTG 58.387 38.462 5.39 0.00 33.66 3.77
2368 5542 7.042335 CCTTTGATAGTTCTACTAGTGGTTGG 58.958 42.308 5.39 0.00 33.66 3.77
2369 5543 6.540438 TTGATAGTTCTACTAGTGGTTGGG 57.460 41.667 5.39 0.00 33.66 4.12
2370 5544 4.960469 TGATAGTTCTACTAGTGGTTGGGG 59.040 45.833 5.39 0.00 33.66 4.96
2371 5545 1.907255 AGTTCTACTAGTGGTTGGGGC 59.093 52.381 5.39 0.00 0.00 5.80
2372 5546 1.065636 GTTCTACTAGTGGTTGGGGCC 60.066 57.143 5.39 0.00 0.00 5.80
2373 5547 0.619543 TCTACTAGTGGTTGGGGCCC 60.620 60.000 18.17 18.17 0.00 5.80
2374 5548 1.968050 CTACTAGTGGTTGGGGCCCG 61.968 65.000 19.83 2.78 0.00 6.13
2375 5549 2.752036 TACTAGTGGTTGGGGCCCGT 62.752 60.000 19.83 9.47 0.00 5.28
2376 5550 3.324108 TAGTGGTTGGGGCCCGTC 61.324 66.667 19.83 13.23 0.00 4.79
2378 5552 4.360405 GTGGTTGGGGCCCGTCAT 62.360 66.667 19.83 0.00 0.00 3.06
2379 5553 3.585428 TGGTTGGGGCCCGTCATT 61.585 61.111 19.83 0.00 0.00 2.57
2380 5554 3.068064 GGTTGGGGCCCGTCATTG 61.068 66.667 19.83 0.00 0.00 2.82
2381 5555 3.758931 GTTGGGGCCCGTCATTGC 61.759 66.667 19.83 0.00 0.00 3.56
2382 5556 4.292145 TTGGGGCCCGTCATTGCA 62.292 61.111 19.83 2.48 0.00 4.08
2383 5557 4.738998 TGGGGCCCGTCATTGCAG 62.739 66.667 19.83 0.00 0.00 4.41
2390 5564 3.434319 CGTCATTGCAGGCCGCTT 61.434 61.111 18.14 5.69 43.06 4.68
2391 5565 2.180017 GTCATTGCAGGCCGCTTG 59.820 61.111 18.14 15.22 43.06 4.01
2392 5566 2.033911 TCATTGCAGGCCGCTTGA 59.966 55.556 18.14 16.79 43.06 3.02
2393 5567 2.042259 TCATTGCAGGCCGCTTGAG 61.042 57.895 18.14 7.87 43.06 3.02
2394 5568 2.042259 CATTGCAGGCCGCTTGAGA 61.042 57.895 18.14 0.00 43.06 3.27
2395 5569 1.748122 ATTGCAGGCCGCTTGAGAG 60.748 57.895 18.14 0.00 43.06 3.20
2396 5570 3.907260 TTGCAGGCCGCTTGAGAGG 62.907 63.158 18.14 0.00 43.06 3.69
2397 5571 4.087892 GCAGGCCGCTTGAGAGGA 62.088 66.667 6.68 0.00 37.14 3.71
2398 5572 2.665000 CAGGCCGCTTGAGAGGAA 59.335 61.111 4.87 0.00 37.14 3.36
2399 5573 1.449246 CAGGCCGCTTGAGAGGAAG 60.449 63.158 4.87 0.00 37.14 3.46
2400 5574 2.821810 GGCCGCTTGAGAGGAAGC 60.822 66.667 4.87 0.00 44.21 3.86
2401 5575 2.267324 GCCGCTTGAGAGGAAGCT 59.733 61.111 4.87 0.00 45.26 3.74
2402 5576 1.517832 GCCGCTTGAGAGGAAGCTA 59.482 57.895 4.87 0.00 45.26 3.32
2403 5577 0.105778 GCCGCTTGAGAGGAAGCTAT 59.894 55.000 4.87 0.00 45.26 2.97
2404 5578 1.863267 CCGCTTGAGAGGAAGCTATG 58.137 55.000 0.00 0.00 45.26 2.23
2405 5579 1.216122 CGCTTGAGAGGAAGCTATGC 58.784 55.000 0.00 0.00 45.26 3.14
2406 5580 1.216122 GCTTGAGAGGAAGCTATGCG 58.784 55.000 0.00 0.00 44.26 4.73
2407 5581 1.216122 CTTGAGAGGAAGCTATGCGC 58.784 55.000 0.00 0.00 39.57 6.09
2408 5582 0.536724 TTGAGAGGAAGCTATGCGCA 59.463 50.000 14.96 14.96 42.61 6.09
2409 5583 0.179100 TGAGAGGAAGCTATGCGCAC 60.179 55.000 14.90 0.00 42.61 5.34
2410 5584 0.878086 GAGAGGAAGCTATGCGCACC 60.878 60.000 14.90 8.62 42.61 5.01
2411 5585 1.144936 GAGGAAGCTATGCGCACCT 59.855 57.895 14.90 14.49 45.53 4.00
2412 5586 1.144936 AGGAAGCTATGCGCACCTC 59.855 57.895 14.90 4.04 41.47 3.85
2413 5587 1.153369 GGAAGCTATGCGCACCTCA 60.153 57.895 14.90 0.00 42.61 3.86
2414 5588 1.432270 GGAAGCTATGCGCACCTCAC 61.432 60.000 14.90 7.57 42.61 3.51
2415 5589 1.432270 GAAGCTATGCGCACCTCACC 61.432 60.000 14.90 0.00 42.61 4.02
2416 5590 2.125147 GCTATGCGCACCTCACCA 60.125 61.111 14.90 0.00 38.92 4.17
2417 5591 1.524621 GCTATGCGCACCTCACCAT 60.525 57.895 14.90 0.00 38.92 3.55
2418 5592 1.502163 GCTATGCGCACCTCACCATC 61.502 60.000 14.90 0.00 38.92 3.51
2419 5593 0.179076 CTATGCGCACCTCACCATCA 60.179 55.000 14.90 0.00 0.00 3.07
2420 5594 0.469494 TATGCGCACCTCACCATCAT 59.531 50.000 14.90 0.00 0.00 2.45
2421 5595 1.099295 ATGCGCACCTCACCATCATG 61.099 55.000 14.90 0.00 0.00 3.07
2422 5596 1.746615 GCGCACCTCACCATCATGT 60.747 57.895 0.30 0.00 0.00 3.21
2423 5597 1.709147 GCGCACCTCACCATCATGTC 61.709 60.000 0.30 0.00 0.00 3.06
2424 5598 0.391528 CGCACCTCACCATCATGTCA 60.392 55.000 0.00 0.00 0.00 3.58
2425 5599 1.825090 GCACCTCACCATCATGTCAA 58.175 50.000 0.00 0.00 0.00 3.18
2426 5600 2.161855 GCACCTCACCATCATGTCAAA 58.838 47.619 0.00 0.00 0.00 2.69
2427 5601 2.557924 GCACCTCACCATCATGTCAAAA 59.442 45.455 0.00 0.00 0.00 2.44
2428 5602 3.194116 GCACCTCACCATCATGTCAAAAT 59.806 43.478 0.00 0.00 0.00 1.82
2429 5603 4.676196 GCACCTCACCATCATGTCAAAATC 60.676 45.833 0.00 0.00 0.00 2.17
2430 5604 4.460034 CACCTCACCATCATGTCAAAATCA 59.540 41.667 0.00 0.00 0.00 2.57
2431 5605 5.126545 CACCTCACCATCATGTCAAAATCAT 59.873 40.000 0.00 0.00 0.00 2.45
2432 5606 6.319405 CACCTCACCATCATGTCAAAATCATA 59.681 38.462 0.00 0.00 0.00 2.15
2433 5607 6.891361 ACCTCACCATCATGTCAAAATCATAA 59.109 34.615 0.00 0.00 0.00 1.90
2434 5608 7.396907 ACCTCACCATCATGTCAAAATCATAAA 59.603 33.333 0.00 0.00 0.00 1.40
2435 5609 8.252417 CCTCACCATCATGTCAAAATCATAAAA 58.748 33.333 0.00 0.00 0.00 1.52
2436 5610 9.642327 CTCACCATCATGTCAAAATCATAAAAA 57.358 29.630 0.00 0.00 0.00 1.94
2454 5628 3.729526 AAAAGAATCTCGCATCACGTG 57.270 42.857 9.94 9.94 44.19 4.49
2455 5629 1.645034 AAGAATCTCGCATCACGTGG 58.355 50.000 17.00 0.92 44.19 4.94
2456 5630 0.817654 AGAATCTCGCATCACGTGGA 59.182 50.000 17.00 3.87 44.19 4.02
2457 5631 0.924090 GAATCTCGCATCACGTGGAC 59.076 55.000 17.00 4.49 44.19 4.02
2458 5632 0.246360 AATCTCGCATCACGTGGACA 59.754 50.000 17.00 0.00 44.19 4.02
2459 5633 0.461548 ATCTCGCATCACGTGGACAT 59.538 50.000 17.00 0.00 44.19 3.06
2460 5634 0.179137 TCTCGCATCACGTGGACATC 60.179 55.000 17.00 0.14 44.19 3.06
2461 5635 0.458370 CTCGCATCACGTGGACATCA 60.458 55.000 17.00 0.00 44.19 3.07
2462 5636 0.735978 TCGCATCACGTGGACATCAC 60.736 55.000 17.00 0.00 44.19 3.06
2463 5637 1.013524 CGCATCACGTGGACATCACA 61.014 55.000 17.00 0.00 46.36 3.58
2464 5638 1.155889 GCATCACGTGGACATCACAA 58.844 50.000 17.00 0.00 46.36 3.33
2465 5639 1.135972 GCATCACGTGGACATCACAAC 60.136 52.381 17.00 0.00 46.36 3.32
2466 5640 1.464608 CATCACGTGGACATCACAACC 59.535 52.381 17.00 0.00 46.36 3.77
2467 5641 0.466124 TCACGTGGACATCACAACCA 59.534 50.000 17.00 0.00 46.36 3.67
2468 5642 1.071542 TCACGTGGACATCACAACCAT 59.928 47.619 17.00 0.00 46.36 3.55
2469 5643 1.464608 CACGTGGACATCACAACCATC 59.535 52.381 7.95 0.00 46.36 3.51
2470 5644 1.347707 ACGTGGACATCACAACCATCT 59.652 47.619 0.00 0.00 46.36 2.90
2471 5645 2.224523 ACGTGGACATCACAACCATCTT 60.225 45.455 0.00 0.00 46.36 2.40
2472 5646 3.007506 ACGTGGACATCACAACCATCTTA 59.992 43.478 0.00 0.00 46.36 2.10
2473 5647 4.000325 CGTGGACATCACAACCATCTTAA 59.000 43.478 0.00 0.00 46.36 1.85
2474 5648 4.454161 CGTGGACATCACAACCATCTTAAA 59.546 41.667 0.00 0.00 46.36 1.52
2475 5649 5.049060 CGTGGACATCACAACCATCTTAAAA 60.049 40.000 0.00 0.00 46.36 1.52
2476 5650 6.381801 GTGGACATCACAACCATCTTAAAAG 58.618 40.000 0.00 0.00 45.39 2.27
2477 5651 6.206634 GTGGACATCACAACCATCTTAAAAGA 59.793 38.462 0.00 0.00 45.39 2.52
2478 5652 6.775142 TGGACATCACAACCATCTTAAAAGAA 59.225 34.615 0.00 0.00 38.77 2.52
2479 5653 7.286546 TGGACATCACAACCATCTTAAAAGAAA 59.713 33.333 0.00 0.00 38.77 2.52
2480 5654 8.141268 GGACATCACAACCATCTTAAAAGAAAA 58.859 33.333 0.00 0.00 38.77 2.29
2481 5655 9.528018 GACATCACAACCATCTTAAAAGAAAAA 57.472 29.630 0.00 0.00 38.77 1.94
2507 5681 9.794685 AAGAAAAAGCTTAGAAAAACTTCTCTG 57.205 29.630 0.00 0.00 32.72 3.35
2508 5682 8.409371 AGAAAAAGCTTAGAAAAACTTCTCTGG 58.591 33.333 0.00 0.00 32.72 3.86
2509 5683 7.881775 AAAAGCTTAGAAAAACTTCTCTGGA 57.118 32.000 0.00 0.00 32.72 3.86
2510 5684 7.881775 AAAGCTTAGAAAAACTTCTCTGGAA 57.118 32.000 0.00 0.00 32.72 3.53
2511 5685 7.881775 AAGCTTAGAAAAACTTCTCTGGAAA 57.118 32.000 0.00 0.00 32.72 3.13
2512 5686 7.881775 AGCTTAGAAAAACTTCTCTGGAAAA 57.118 32.000 0.00 0.00 32.72 2.29
2513 5687 8.293699 AGCTTAGAAAAACTTCTCTGGAAAAA 57.706 30.769 0.00 0.00 32.72 1.94
2566 5740 5.828299 AAAAACTTTCTCACCGTGATCAA 57.172 34.783 0.62 0.00 0.00 2.57
2567 5741 4.813296 AAACTTTCTCACCGTGATCAAC 57.187 40.909 0.62 0.00 0.00 3.18
2568 5742 2.767505 ACTTTCTCACCGTGATCAACC 58.232 47.619 0.62 0.00 0.00 3.77
2569 5743 2.104111 ACTTTCTCACCGTGATCAACCA 59.896 45.455 0.62 0.00 0.00 3.67
2570 5744 2.455674 TTCTCACCGTGATCAACCAG 57.544 50.000 0.62 0.00 0.00 4.00
2571 5745 0.037326 TCTCACCGTGATCAACCAGC 60.037 55.000 0.62 0.00 0.00 4.85
2572 5746 0.320683 CTCACCGTGATCAACCAGCA 60.321 55.000 0.62 0.00 0.00 4.41
2573 5747 0.324614 TCACCGTGATCAACCAGCAT 59.675 50.000 0.00 0.00 0.00 3.79
2574 5748 0.448990 CACCGTGATCAACCAGCATG 59.551 55.000 0.00 0.00 0.00 4.06
2575 5749 1.308069 ACCGTGATCAACCAGCATGC 61.308 55.000 10.51 10.51 31.97 4.06
2576 5750 1.061411 CGTGATCAACCAGCATGCG 59.939 57.895 13.01 7.31 31.97 4.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
112 3124 7.093465 CCTCAGTGTTTCTACAGGAATTAGGTA 60.093 40.741 0.00 0.00 34.24 3.08
534 3547 3.295973 GAGGAGATACAGAAGCAGAGGT 58.704 50.000 0.00 0.00 0.00 3.85
662 3678 4.607239 AGTAATTCTGAACGGAGGGAGTA 58.393 43.478 0.00 0.00 0.00 2.59
665 3681 3.437213 TGAGTAATTCTGAACGGAGGGA 58.563 45.455 0.00 0.00 0.00 4.20
666 3682 3.887621 TGAGTAATTCTGAACGGAGGG 57.112 47.619 0.00 0.00 0.00 4.30
667 3683 5.269505 AGATGAGTAATTCTGAACGGAGG 57.730 43.478 0.00 0.00 0.00 4.30
668 3684 7.708051 TCTTAGATGAGTAATTCTGAACGGAG 58.292 38.462 0.00 0.00 0.00 4.63
669 3685 7.640597 TCTTAGATGAGTAATTCTGAACGGA 57.359 36.000 0.00 0.00 0.00 4.69
670 3686 8.703604 TTTCTTAGATGAGTAATTCTGAACGG 57.296 34.615 0.00 0.00 0.00 4.44
728 3744 9.260002 GGAATTACTTGTCACAAAAATGAATGT 57.740 29.630 0.00 0.00 0.00 2.71
729 3745 8.427012 CGGAATTACTTGTCACAAAAATGAATG 58.573 33.333 0.00 0.00 0.00 2.67
730 3746 7.598493 CCGGAATTACTTGTCACAAAAATGAAT 59.402 33.333 0.00 0.00 0.00 2.57
731 3747 6.920758 CCGGAATTACTTGTCACAAAAATGAA 59.079 34.615 0.00 0.00 0.00 2.57
732 3748 6.263392 TCCGGAATTACTTGTCACAAAAATGA 59.737 34.615 0.00 0.00 0.00 2.57
733 3749 6.362283 GTCCGGAATTACTTGTCACAAAAATG 59.638 38.462 5.23 0.00 0.00 2.32
734 3750 6.443792 GTCCGGAATTACTTGTCACAAAAAT 58.556 36.000 5.23 0.00 0.00 1.82
735 3751 5.504337 CGTCCGGAATTACTTGTCACAAAAA 60.504 40.000 5.23 0.00 0.00 1.94
736 3752 4.024725 CGTCCGGAATTACTTGTCACAAAA 60.025 41.667 5.23 0.00 0.00 2.44
737 3753 3.495377 CGTCCGGAATTACTTGTCACAAA 59.505 43.478 5.23 0.00 0.00 2.83
738 3754 3.061322 CGTCCGGAATTACTTGTCACAA 58.939 45.455 5.23 0.00 0.00 3.33
739 3755 2.296752 TCGTCCGGAATTACTTGTCACA 59.703 45.455 5.23 0.00 0.00 3.58
740 3756 2.950433 TCGTCCGGAATTACTTGTCAC 58.050 47.619 5.23 0.00 0.00 3.67
741 3757 3.581755 CTTCGTCCGGAATTACTTGTCA 58.418 45.455 5.23 0.00 33.26 3.58
742 3758 2.928116 CCTTCGTCCGGAATTACTTGTC 59.072 50.000 5.23 0.00 33.26 3.18
743 3759 2.354403 CCCTTCGTCCGGAATTACTTGT 60.354 50.000 5.23 0.00 33.26 3.16
744 3760 2.093869 TCCCTTCGTCCGGAATTACTTG 60.094 50.000 5.23 0.00 33.26 3.16
745 3761 2.167900 CTCCCTTCGTCCGGAATTACTT 59.832 50.000 5.23 0.00 33.26 2.24
746 3762 1.755380 CTCCCTTCGTCCGGAATTACT 59.245 52.381 5.23 0.00 33.26 2.24
747 3763 1.479730 ACTCCCTTCGTCCGGAATTAC 59.520 52.381 5.23 0.00 33.26 1.89
748 3764 1.856629 ACTCCCTTCGTCCGGAATTA 58.143 50.000 5.23 0.00 33.26 1.40
749 3765 1.479730 GTACTCCCTTCGTCCGGAATT 59.520 52.381 5.23 0.00 33.26 2.17
750 3766 1.109609 GTACTCCCTTCGTCCGGAAT 58.890 55.000 5.23 0.00 33.26 3.01
751 3767 1.308069 CGTACTCCCTTCGTCCGGAA 61.308 60.000 5.23 0.00 0.00 4.30
752 3768 1.746615 CGTACTCCCTTCGTCCGGA 60.747 63.158 0.00 0.00 0.00 5.14
753 3769 2.042831 ACGTACTCCCTTCGTCCGG 61.043 63.158 0.00 0.00 32.26 5.14
754 3770 1.136147 CACGTACTCCCTTCGTCCG 59.864 63.158 0.00 0.00 35.62 4.79
755 3771 1.153881 GCACGTACTCCCTTCGTCC 60.154 63.158 0.00 0.00 35.62 4.79
756 3772 0.243095 AAGCACGTACTCCCTTCGTC 59.757 55.000 0.00 0.00 35.62 4.20
757 3773 0.038526 CAAGCACGTACTCCCTTCGT 60.039 55.000 0.00 0.00 38.34 3.85
758 3774 0.736325 CCAAGCACGTACTCCCTTCG 60.736 60.000 0.00 0.00 0.00 3.79
759 3775 0.391263 CCCAAGCACGTACTCCCTTC 60.391 60.000 0.00 0.00 0.00 3.46
760 3776 1.677552 CCCAAGCACGTACTCCCTT 59.322 57.895 0.00 0.00 0.00 3.95
761 3777 2.955881 GCCCAAGCACGTACTCCCT 61.956 63.158 0.00 0.00 39.53 4.20
762 3778 2.436115 GCCCAAGCACGTACTCCC 60.436 66.667 0.00 0.00 39.53 4.30
763 3779 2.436115 GGCCCAAGCACGTACTCC 60.436 66.667 0.00 0.00 42.56 3.85
764 3780 2.813908 CGGCCCAAGCACGTACTC 60.814 66.667 0.00 0.00 42.56 2.59
842 3861 2.604174 CGGTTTGAGGCGTGTGGAC 61.604 63.158 0.00 0.00 0.00 4.02
859 3878 3.745975 TCATCTTAAATAGCAATCGGCCG 59.254 43.478 22.12 22.12 46.50 6.13
867 3890 7.716998 GTGGGAGAAGATTCATCTTAAATAGCA 59.283 37.037 1.90 0.00 46.47 3.49
878 3901 4.592351 AGATCGATGTGGGAGAAGATTCAT 59.408 41.667 0.54 0.00 0.00 2.57
880 3903 4.305769 CAGATCGATGTGGGAGAAGATTC 58.694 47.826 14.53 0.00 0.00 2.52
881 3904 3.494048 GCAGATCGATGTGGGAGAAGATT 60.494 47.826 22.53 0.00 0.00 2.40
946 3988 0.767375 AGCAGGTGTCCACAATCAGT 59.233 50.000 0.00 0.00 0.00 3.41
962 4004 2.352651 GAGGATGTGTACGTACGTAGCA 59.647 50.000 27.48 26.04 0.00 3.49
984 4026 1.069049 GCCATTTTGCAACCTGTGAGT 59.931 47.619 0.00 0.00 0.00 3.41
1125 4173 2.106683 CACCTGGAAATCGCCGTCC 61.107 63.158 0.00 0.00 0.00 4.79
1239 4310 2.441164 GGGTTGGTGTGTGTGGCA 60.441 61.111 0.00 0.00 0.00 4.92
1257 4328 1.511768 GAGCCTAACTTCGGAGCGT 59.488 57.895 0.00 0.00 0.00 5.07
1292 4371 2.676076 ACGCAGGAATTTCAACAATGC 58.324 42.857 0.00 0.33 0.00 3.56
1335 4423 8.405531 GCTGGAAGAAGATAGCTCATACTATAG 58.594 40.741 0.00 0.00 34.07 1.31
1338 4426 6.071320 TGCTGGAAGAAGATAGCTCATACTA 58.929 40.000 0.00 0.00 37.10 1.82
1339 4427 4.898265 TGCTGGAAGAAGATAGCTCATACT 59.102 41.667 0.00 0.00 37.10 2.12
1340 4428 5.207110 TGCTGGAAGAAGATAGCTCATAC 57.793 43.478 0.00 0.00 37.10 2.39
1358 4460 2.125512 GTAGTCGTGGCCCTGCTG 60.126 66.667 0.00 0.00 0.00 4.41
1359 4461 2.283966 AGTAGTCGTGGCCCTGCT 60.284 61.111 0.00 0.00 0.00 4.24
1360 4462 2.184579 GAGTAGTCGTGGCCCTGC 59.815 66.667 0.00 0.00 0.00 4.85
1384 4486 2.966309 GCCCTCGAACTGCCAAACG 61.966 63.158 0.00 0.00 0.00 3.60
1387 4489 0.107703 CATAGCCCTCGAACTGCCAA 60.108 55.000 0.00 0.00 0.00 4.52
1444 4552 0.898320 CCTCCTCGTTGTGGATCTGT 59.102 55.000 0.00 0.00 32.56 3.41
1494 4603 1.807226 CAGGACGCCGTCATAGACA 59.193 57.895 20.08 0.00 33.68 3.41
1540 4649 1.092348 CACCGGTCGTAGATGTCAGA 58.908 55.000 2.59 0.00 40.67 3.27
1641 4750 0.033011 ATGACTCGCTAGGGGTCACT 60.033 55.000 23.61 14.74 41.75 3.41
1700 4809 1.451028 GACTCCATGCAGCTGGACC 60.451 63.158 17.12 0.00 40.43 4.46
1745 4854 4.701171 GCTATCTACCGTCTAGTGCCTTAT 59.299 45.833 0.00 0.00 0.00 1.73
1749 4858 1.540707 GGCTATCTACCGTCTAGTGCC 59.459 57.143 0.00 0.00 0.00 5.01
1958 5122 5.647589 GAATGGTCGTTACATGTCTACTCA 58.352 41.667 0.00 1.98 0.00 3.41
2055 5221 3.535561 CGACAGGCAAGTAAAGGATGAT 58.464 45.455 0.00 0.00 0.00 2.45
2058 5224 1.065418 CCCGACAGGCAAGTAAAGGAT 60.065 52.381 0.00 0.00 35.76 3.24
2070 5236 1.376037 GAGGAAAGTGCCCGACAGG 60.376 63.158 0.00 0.00 39.47 4.00
2071 5237 0.035458 AAGAGGAAAGTGCCCGACAG 59.965 55.000 0.00 0.00 0.00 3.51
2074 5240 0.608640 GAGAAGAGGAAAGTGCCCGA 59.391 55.000 0.00 0.00 0.00 5.14
2163 5337 3.572682 TCACGAGATAGGTCAACACACTT 59.427 43.478 0.00 0.00 0.00 3.16
2254 5428 0.179045 AAGACAAACTCGCTGCCACT 60.179 50.000 0.00 0.00 0.00 4.00
2297 5471 3.531538 GAAATCAAGGCGGTATGTGAGA 58.468 45.455 0.00 0.00 0.00 3.27
2298 5472 2.614057 GGAAATCAAGGCGGTATGTGAG 59.386 50.000 0.00 0.00 0.00 3.51
2304 5478 1.134907 GTCGAGGAAATCAAGGCGGTA 60.135 52.381 0.00 0.00 0.00 4.02
2317 5491 2.038813 TGGGAGGCATGTCGAGGA 59.961 61.111 0.00 0.00 0.00 3.71
2347 5521 4.960469 CCCCAACCACTAGTAGAACTATCA 59.040 45.833 3.59 0.00 29.08 2.15
2349 5523 3.710165 GCCCCAACCACTAGTAGAACTAT 59.290 47.826 3.59 0.00 29.08 2.12
2358 5532 3.325201 GACGGGCCCCAACCACTAG 62.325 68.421 18.66 0.08 0.00 2.57
2359 5533 3.324108 GACGGGCCCCAACCACTA 61.324 66.667 18.66 0.00 0.00 2.74
2361 5535 3.879180 AATGACGGGCCCCAACCAC 62.879 63.158 18.66 1.76 0.00 4.16
2362 5536 3.585428 AATGACGGGCCCCAACCA 61.585 61.111 18.66 9.45 0.00 3.67
2363 5537 3.068064 CAATGACGGGCCCCAACC 61.068 66.667 18.66 3.03 0.00 3.77
2364 5538 3.758931 GCAATGACGGGCCCCAAC 61.759 66.667 18.66 8.47 0.00 3.77
2365 5539 4.292145 TGCAATGACGGGCCCCAA 62.292 61.111 18.66 1.24 0.00 4.12
2366 5540 4.738998 CTGCAATGACGGGCCCCA 62.739 66.667 18.66 10.21 0.00 4.96
2380 5554 3.612247 TTCCTCTCAAGCGGCCTGC 62.612 63.158 11.02 11.02 46.98 4.85
2381 5555 1.449246 CTTCCTCTCAAGCGGCCTG 60.449 63.158 0.00 0.00 0.00 4.85
2382 5556 2.985456 CTTCCTCTCAAGCGGCCT 59.015 61.111 0.00 0.00 0.00 5.19
2383 5557 2.821810 GCTTCCTCTCAAGCGGCC 60.822 66.667 0.00 0.00 39.55 6.13
2388 5562 1.216122 GCGCATAGCTTCCTCTCAAG 58.784 55.000 0.30 0.00 44.04 3.02
2389 5563 3.369381 GCGCATAGCTTCCTCTCAA 57.631 52.632 0.30 0.00 44.04 3.02
2400 5574 0.179076 TGATGGTGAGGTGCGCATAG 60.179 55.000 15.91 0.00 0.00 2.23
2401 5575 0.469494 ATGATGGTGAGGTGCGCATA 59.531 50.000 15.91 0.00 0.00 3.14
2402 5576 1.099295 CATGATGGTGAGGTGCGCAT 61.099 55.000 15.91 0.00 0.00 4.73
2403 5577 1.746239 CATGATGGTGAGGTGCGCA 60.746 57.895 5.66 5.66 0.00 6.09
2404 5578 1.709147 GACATGATGGTGAGGTGCGC 61.709 60.000 0.00 0.00 0.00 6.09
2405 5579 0.391528 TGACATGATGGTGAGGTGCG 60.392 55.000 0.00 0.00 0.00 5.34
2406 5580 1.825090 TTGACATGATGGTGAGGTGC 58.175 50.000 0.00 0.00 0.00 5.01
2407 5581 4.460034 TGATTTTGACATGATGGTGAGGTG 59.540 41.667 0.00 0.00 0.00 4.00
2408 5582 4.665451 TGATTTTGACATGATGGTGAGGT 58.335 39.130 0.00 0.00 0.00 3.85
2409 5583 5.847111 ATGATTTTGACATGATGGTGAGG 57.153 39.130 0.00 0.00 0.00 3.86
2410 5584 9.642327 TTTTTATGATTTTGACATGATGGTGAG 57.358 29.630 0.00 0.00 0.00 3.51
2433 5607 3.120199 CCACGTGATGCGAGATTCTTTTT 60.120 43.478 19.30 0.00 44.77 1.94
2434 5608 2.416547 CCACGTGATGCGAGATTCTTTT 59.583 45.455 19.30 0.00 44.77 2.27
2435 5609 2.002586 CCACGTGATGCGAGATTCTTT 58.997 47.619 19.30 0.00 44.77 2.52
2436 5610 1.204704 TCCACGTGATGCGAGATTCTT 59.795 47.619 19.30 0.00 44.77 2.52
2437 5611 0.817654 TCCACGTGATGCGAGATTCT 59.182 50.000 19.30 0.00 44.77 2.40
2438 5612 0.924090 GTCCACGTGATGCGAGATTC 59.076 55.000 19.30 0.00 44.77 2.52
2439 5613 0.246360 TGTCCACGTGATGCGAGATT 59.754 50.000 19.30 0.00 44.77 2.40
2440 5614 0.461548 ATGTCCACGTGATGCGAGAT 59.538 50.000 19.30 6.74 44.77 2.75
2441 5615 0.179137 GATGTCCACGTGATGCGAGA 60.179 55.000 19.30 4.33 44.77 4.04
2442 5616 0.458370 TGATGTCCACGTGATGCGAG 60.458 55.000 19.30 0.00 44.77 5.03
2443 5617 0.735978 GTGATGTCCACGTGATGCGA 60.736 55.000 19.30 2.05 44.77 5.10
2452 5626 5.957842 TTTAAGATGGTTGTGATGTCCAC 57.042 39.130 0.00 0.00 45.88 4.02
2453 5627 6.303054 TCTTTTAAGATGGTTGTGATGTCCA 58.697 36.000 0.00 0.00 35.64 4.02
2454 5628 6.817765 TCTTTTAAGATGGTTGTGATGTCC 57.182 37.500 0.00 0.00 0.00 4.02
2455 5629 9.528018 TTTTTCTTTTAAGATGGTTGTGATGTC 57.472 29.630 0.00 0.00 34.49 3.06
2481 5655 9.794685 CAGAGAAGTTTTTCTAAGCTTTTTCTT 57.205 29.630 3.20 0.66 43.63 2.52
2482 5656 8.409371 CCAGAGAAGTTTTTCTAAGCTTTTTCT 58.591 33.333 3.20 2.06 43.63 2.52
2483 5657 8.406297 TCCAGAGAAGTTTTTCTAAGCTTTTTC 58.594 33.333 3.20 0.00 43.63 2.29
2484 5658 8.293699 TCCAGAGAAGTTTTTCTAAGCTTTTT 57.706 30.769 3.20 0.00 43.63 1.94
2485 5659 7.881775 TCCAGAGAAGTTTTTCTAAGCTTTT 57.118 32.000 3.20 0.00 43.63 2.27
2486 5660 7.881775 TTCCAGAGAAGTTTTTCTAAGCTTT 57.118 32.000 3.20 0.00 43.63 3.51
2487 5661 7.881775 TTTCCAGAGAAGTTTTTCTAAGCTT 57.118 32.000 3.48 3.48 43.63 3.74
2488 5662 7.881775 TTTTCCAGAGAAGTTTTTCTAAGCT 57.118 32.000 0.00 0.00 43.63 3.74
2544 5718 5.449999 GGTTGATCACGGTGAGAAAGTTTTT 60.450 40.000 16.84 0.00 0.00 1.94
2545 5719 4.036380 GGTTGATCACGGTGAGAAAGTTTT 59.964 41.667 16.84 0.00 0.00 2.43
2546 5720 3.564225 GGTTGATCACGGTGAGAAAGTTT 59.436 43.478 16.84 0.00 0.00 2.66
2547 5721 3.139077 GGTTGATCACGGTGAGAAAGTT 58.861 45.455 16.84 0.00 0.00 2.66
2548 5722 2.104111 TGGTTGATCACGGTGAGAAAGT 59.896 45.455 16.84 0.00 0.00 2.66
2549 5723 2.738846 CTGGTTGATCACGGTGAGAAAG 59.261 50.000 16.84 4.66 0.00 2.62
2550 5724 2.766313 CTGGTTGATCACGGTGAGAAA 58.234 47.619 16.84 10.14 0.00 2.52
2551 5725 1.608025 GCTGGTTGATCACGGTGAGAA 60.608 52.381 16.84 8.88 0.00 2.87
2552 5726 0.037326 GCTGGTTGATCACGGTGAGA 60.037 55.000 16.84 2.81 0.00 3.27
2553 5727 0.320683 TGCTGGTTGATCACGGTGAG 60.321 55.000 16.84 2.13 0.00 3.51
2554 5728 0.324614 ATGCTGGTTGATCACGGTGA 59.675 50.000 14.01 14.01 0.00 4.02
2555 5729 0.448990 CATGCTGGTTGATCACGGTG 59.551 55.000 0.56 0.56 0.00 4.94
2556 5730 1.308069 GCATGCTGGTTGATCACGGT 61.308 55.000 11.37 0.00 0.00 4.83
2557 5731 1.430632 GCATGCTGGTTGATCACGG 59.569 57.895 11.37 0.00 0.00 4.94
2558 5732 1.061411 CGCATGCTGGTTGATCACG 59.939 57.895 17.13 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.