Multiple sequence alignment - TraesCS2B01G205800

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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 TraesCS2B01G205800 chr2B 100.000 2873 0 0 1 2873 184799227 184802099 0.000000e+00 5306.0
1 TraesCS2B01G205800 chr2B 92.010 776 39 12 641 1410 184899485 184900243 0.000000e+00 1068.0
2 TraesCS2B01G205800 chr2B 79.100 1000 134 39 1262 2242 184899948 184900891 1.130000e-173 619.0
3 TraesCS2B01G205800 chr2B 80.271 811 102 33 788 1548 184909431 184910233 2.500000e-155 558.0
4 TraesCS2B01G205800 chr2B 88.667 450 41 5 2424 2873 503354750 503355189 9.060000e-150 540.0
5 TraesCS2B01G205800 chr2B 84.735 452 35 22 808 1236 184876821 184877261 3.420000e-114 422.0
6 TraesCS2B01G205800 chr2B 80.551 581 75 15 1401 1977 184877351 184877897 2.060000e-111 412.0
7 TraesCS2B01G205800 chr2B 78.094 703 104 23 1459 2129 184910015 184910699 1.600000e-107 399.0
8 TraesCS2B01G205800 chr2B 84.029 407 35 4 998 1398 184930645 184931027 5.850000e-97 364.0
9 TraesCS2B01G205800 chr2B 91.964 224 18 0 1017 1240 184789387 184789610 5.980000e-82 315.0
10 TraesCS2B01G205800 chr2B 77.881 538 62 27 1721 2253 184789877 184790362 6.060000e-72 281.0
11 TraesCS2B01G205800 chr2B 87.013 154 11 4 707 851 184928202 184928355 6.370000e-37 165.0
12 TraesCS2B01G205800 chr2B 78.571 182 27 5 2 172 219499515 219499695 3.030000e-20 110.0
13 TraesCS2B01G205800 chr2B 75.962 208 38 6 2 198 49851932 49852138 2.360000e-16 97.1
14 TraesCS2B01G205800 chr2A 92.390 749 40 8 641 1374 137941975 137942721 0.000000e+00 1051.0
15 TraesCS2B01G205800 chr2A 83.291 784 89 21 641 1401 138084020 138084784 0.000000e+00 684.0
16 TraesCS2B01G205800 chr2A 83.203 768 70 31 709 1421 137950936 137951699 0.000000e+00 649.0
17 TraesCS2B01G205800 chr2A 78.084 981 134 52 1459 2392 137951621 137952567 1.950000e-151 545.0
18 TraesCS2B01G205800 chr2A 81.369 628 71 21 1 617 55869929 55869337 1.210000e-128 470.0
19 TraesCS2B01G205800 chr2A 82.909 550 49 17 1412 1947 137942720 137943238 1.210000e-123 453.0
20 TraesCS2B01G205800 chr2A 80.882 544 65 18 1401 1940 137936400 137936908 2.680000e-105 392.0
21 TraesCS2B01G205800 chr2A 92.727 220 16 0 1017 1236 137936091 137936310 4.620000e-83 318.0
22 TraesCS2B01G205800 chr2A 78.778 311 47 12 1262 1570 137942462 137942755 1.050000e-44 191.0
23 TraesCS2B01G205800 chr2A 75.598 209 40 5 1397 1598 137951643 137951847 3.050000e-15 93.5
24 TraesCS2B01G205800 chr2D 81.665 1009 123 35 641 1603 131359837 131360829 0.000000e+00 782.0
25 TraesCS2B01G205800 chr2D 92.152 446 17 9 674 1102 131294951 131295395 5.260000e-172 614.0
26 TraesCS2B01G205800 chr2D 79.055 974 122 42 1459 2392 131317137 131318068 6.850000e-166 593.0
27 TraesCS2B01G205800 chr2D 88.589 482 36 6 1445 1908 131303382 131303862 4.150000e-158 568.0
28 TraesCS2B01G205800 chr2D 85.130 538 51 16 912 1421 131316679 131317215 9.120000e-145 523.0
29 TraesCS2B01G205800 chr2D 78.064 661 100 27 1610 2253 131284818 131285450 2.700000e-100 375.0
30 TraesCS2B01G205800 chr2D 81.250 336 48 9 1274 1606 131316922 131317245 1.020000e-64 257.0
31 TraesCS2B01G205800 chr2D 88.542 192 22 0 1210 1401 131360469 131360660 1.720000e-57 233.0
32 TraesCS2B01G205800 chr2D 83.168 202 29 5 1210 1410 131284643 131284840 2.270000e-41 180.0
33 TraesCS2B01G205800 chr2D 84.211 171 27 0 1400 1570 131360503 131360673 1.770000e-37 167.0
34 TraesCS2B01G205800 chr2D 82.716 162 9 2 709 851 131316494 131316655 3.010000e-25 126.0
35 TraesCS2B01G205800 chr3B 86.551 632 65 13 1 619 459250000 459250624 0.000000e+00 678.0
36 TraesCS2B01G205800 chr1B 91.781 438 32 3 2424 2861 121833091 121832658 8.800000e-170 606.0
37 TraesCS2B01G205800 chr4A 83.882 608 68 22 18 620 376723538 376722956 1.160000e-153 553.0
38 TraesCS2B01G205800 chr6D 83.415 609 74 15 1 608 464668296 464667714 9.060000e-150 540.0
39 TraesCS2B01G205800 chr6D 83.266 496 56 17 1 495 386409856 386409387 5.690000e-117 431.0
40 TraesCS2B01G205800 chr6D 79.968 624 83 24 1 620 295111720 295111135 3.420000e-114 422.0
41 TraesCS2B01G205800 chrUn 82.862 636 71 25 1 620 55810627 55810014 1.170000e-148 536.0
42 TraesCS2B01G205800 chr5D 82.927 615 70 17 1 604 484158288 484157698 3.280000e-144 521.0
43 TraesCS2B01G205800 chr6A 82.400 625 81 15 1 620 531468044 531467444 4.240000e-143 518.0
44 TraesCS2B01G205800 chr6B 87.075 441 54 3 2433 2873 260139476 260139039 1.990000e-136 496.0
45 TraesCS2B01G205800 chr6B 85.232 237 35 0 2637 2873 644929311 644929547 7.950000e-61 244.0
46 TraesCS2B01G205800 chr6B 77.348 181 31 3 2 172 239373766 239373946 6.550000e-17 99.0
47 TraesCS2B01G205800 chr3D 90.514 253 23 1 92 343 593206017 593206269 1.650000e-87 333.0
48 TraesCS2B01G205800 chr4B 78.286 175 28 3 8 172 6078476 6078650 1.410000e-18 104.0
49 TraesCS2B01G205800 chr5B 76.555 209 29 9 2 198 17848873 17849073 2.360000e-16 97.1
50 TraesCS2B01G205800 chr7D 93.878 49 3 0 2706 2754 548336738 548336690 1.100000e-09 75.0


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 TraesCS2B01G205800 chr2B 184799227 184802099 2872 False 5306.000000 5306 100.000000 1 2873 1 chr2B.!!$F2 2872
1 TraesCS2B01G205800 chr2B 184899485 184900891 1406 False 843.500000 1068 85.555000 641 2242 2 chr2B.!!$F7 1601
2 TraesCS2B01G205800 chr2B 184909431 184910699 1268 False 478.500000 558 79.182500 788 2129 2 chr2B.!!$F8 1341
3 TraesCS2B01G205800 chr2B 184876821 184877897 1076 False 417.000000 422 82.643000 808 1977 2 chr2B.!!$F6 1169
4 TraesCS2B01G205800 chr2B 184789387 184790362 975 False 298.000000 315 84.922500 1017 2253 2 chr2B.!!$F5 1236
5 TraesCS2B01G205800 chr2B 184928202 184931027 2825 False 264.500000 364 85.521000 707 1398 2 chr2B.!!$F9 691
6 TraesCS2B01G205800 chr2A 138084020 138084784 764 False 684.000000 684 83.291000 641 1401 1 chr2A.!!$F1 760
7 TraesCS2B01G205800 chr2A 137941975 137943238 1263 False 565.000000 1051 84.692333 641 1947 3 chr2A.!!$F3 1306
8 TraesCS2B01G205800 chr2A 55869337 55869929 592 True 470.000000 470 81.369000 1 617 1 chr2A.!!$R1 616
9 TraesCS2B01G205800 chr2A 137950936 137952567 1631 False 429.166667 649 78.961667 709 2392 3 chr2A.!!$F4 1683
10 TraesCS2B01G205800 chr2A 137936091 137936908 817 False 355.000000 392 86.804500 1017 1940 2 chr2A.!!$F2 923
11 TraesCS2B01G205800 chr2D 131359837 131360829 992 False 394.000000 782 84.806000 641 1603 3 chr2D.!!$F5 962
12 TraesCS2B01G205800 chr2D 131316494 131318068 1574 False 374.750000 593 82.037750 709 2392 4 chr2D.!!$F4 1683
13 TraesCS2B01G205800 chr2D 131284643 131285450 807 False 277.500000 375 80.616000 1210 2253 2 chr2D.!!$F3 1043
14 TraesCS2B01G205800 chr3B 459250000 459250624 624 False 678.000000 678 86.551000 1 619 1 chr3B.!!$F1 618
15 TraesCS2B01G205800 chr4A 376722956 376723538 582 True 553.000000 553 83.882000 18 620 1 chr4A.!!$R1 602
16 TraesCS2B01G205800 chr6D 464667714 464668296 582 True 540.000000 540 83.415000 1 608 1 chr6D.!!$R3 607
17 TraesCS2B01G205800 chr6D 295111135 295111720 585 True 422.000000 422 79.968000 1 620 1 chr6D.!!$R1 619
18 TraesCS2B01G205800 chrUn 55810014 55810627 613 True 536.000000 536 82.862000 1 620 1 chrUn.!!$R1 619
19 TraesCS2B01G205800 chr5D 484157698 484158288 590 True 521.000000 521 82.927000 1 604 1 chr5D.!!$R1 603
20 TraesCS2B01G205800 chr6A 531467444 531468044 600 True 518.000000 518 82.400000 1 620 1 chr6A.!!$R1 619

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
624 672 0.041386 AGGAGGGTTAGGAGCTTCGT 59.959 55.0 0.0 0.0 30.83 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2418 5071 0.179089 CCAGAGACGCCCATCAGAAG 60.179 60.0 0.0 0.0 0.0 2.85 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
85 107 3.274067 GCCATCGGCTCGGTTTTT 58.726 55.556 0.00 0.00 46.69 1.94
88 110 1.734163 CCATCGGCTCGGTTTTTACT 58.266 50.000 0.00 0.00 0.00 2.24
153 175 1.203300 TCTGGAGATCAGACCACCCAA 60.203 52.381 0.00 0.00 46.71 4.12
175 199 2.039624 AGGCTGACCATCTCCGGT 59.960 61.111 0.00 0.00 43.91 5.28
232 256 1.228644 TCCCCGAAGTCCTCGTGAA 60.229 57.895 0.00 0.00 46.65 3.18
272 298 1.375396 CATGCCGTTGAAGGGACGA 60.375 57.895 8.30 0.00 42.82 4.20
277 303 1.472728 GCCGTTGAAGGGACGATACAT 60.473 52.381 8.30 0.00 42.82 2.29
422 464 1.138859 CTGTTGTAGATCCGGCCATCA 59.861 52.381 2.24 0.00 0.00 3.07
423 465 1.768275 TGTTGTAGATCCGGCCATCAT 59.232 47.619 2.24 0.00 0.00 2.45
620 668 0.689412 GAGCAGGAGGGTTAGGAGCT 60.689 60.000 0.00 0.00 0.00 4.09
621 669 0.252927 AGCAGGAGGGTTAGGAGCTT 60.253 55.000 0.00 0.00 0.00 3.74
622 670 0.179234 GCAGGAGGGTTAGGAGCTTC 59.821 60.000 0.00 0.00 0.00 3.86
623 671 0.461961 CAGGAGGGTTAGGAGCTTCG 59.538 60.000 0.00 0.00 30.83 3.79
624 672 0.041386 AGGAGGGTTAGGAGCTTCGT 59.959 55.000 0.00 0.00 30.83 3.85
625 673 0.175989 GGAGGGTTAGGAGCTTCGTG 59.824 60.000 0.00 0.00 30.83 4.35
626 674 1.183549 GAGGGTTAGGAGCTTCGTGA 58.816 55.000 0.00 0.00 0.00 4.35
627 675 1.135333 GAGGGTTAGGAGCTTCGTGAG 59.865 57.143 0.00 0.00 0.00 3.51
628 676 1.183549 GGGTTAGGAGCTTCGTGAGA 58.816 55.000 0.00 0.00 39.20 3.27
629 677 1.757699 GGGTTAGGAGCTTCGTGAGAT 59.242 52.381 0.00 0.00 41.60 2.75
630 678 2.482142 GGGTTAGGAGCTTCGTGAGATG 60.482 54.545 0.00 0.00 41.60 2.90
638 686 1.485397 CTTCGTGAGATGCGATCTGG 58.515 55.000 3.76 0.00 40.38 3.86
639 687 1.066152 CTTCGTGAGATGCGATCTGGA 59.934 52.381 3.76 0.00 40.38 3.86
700 748 8.947055 AACAAACAATTAGAGCTTGAAATGTT 57.053 26.923 8.44 8.44 0.00 2.71
744 792 7.289549 TCATCACTCATGTCTCCTCAATATTCT 59.710 37.037 0.00 0.00 33.66 2.40
1003 3255 1.079405 CGTACGGCCTCAACCATGT 60.079 57.895 7.57 0.00 0.00 3.21
1074 3332 2.435410 TCCATGAGCAGTGCAGCG 60.435 61.111 19.20 2.27 40.15 5.18
1108 3366 1.376466 GCTGTGCCCAAGAAGGAGA 59.624 57.895 0.00 0.00 41.22 3.71
1129 3387 0.968393 TCCACCACATCCGATCGTCA 60.968 55.000 15.09 0.00 0.00 4.35
1157 3415 3.580319 AAAGCCCCAACTCCCGCT 61.580 61.111 0.00 0.00 0.00 5.52
1392 3851 4.643387 ACTGAAGCGCCACACCCC 62.643 66.667 2.29 0.00 0.00 4.95
1416 3926 1.064003 TGCCAAAGGAGCCTGAAGTA 58.936 50.000 0.00 0.00 0.00 2.24
1417 3927 1.423541 TGCCAAAGGAGCCTGAAGTAA 59.576 47.619 0.00 0.00 0.00 2.24
1427 3937 1.477923 GCCTGAAGTAACACACCCCAA 60.478 52.381 0.00 0.00 0.00 4.12
1480 3990 2.041922 ACCCTGCTATGCCCGAGA 60.042 61.111 0.00 0.00 0.00 4.04
1531 4041 2.069776 CCTGAGGTGCCAAAGGAGA 58.930 57.895 0.00 0.00 30.92 3.71
1534 4044 0.687354 TGAGGTGCCAAAGGAGACTC 59.313 55.000 0.00 0.00 42.68 3.36
1538 4048 1.528129 GTGCCAAAGGAGACTCAAGG 58.472 55.000 4.53 1.39 42.68 3.61
1574 4084 2.759795 GGAGGTGCCAAAGGAGCT 59.240 61.111 0.00 0.00 36.34 4.09
1578 4088 1.078143 GGTGCCAAAGGAGCTCGAT 60.078 57.895 7.83 0.00 0.00 3.59
1579 4089 1.092345 GGTGCCAAAGGAGCTCGATC 61.092 60.000 7.83 0.00 0.00 3.69
1580 4090 0.107945 GTGCCAAAGGAGCTCGATCT 60.108 55.000 7.83 0.00 0.00 2.75
1581 4091 0.107993 TGCCAAAGGAGCTCGATCTG 60.108 55.000 7.83 2.32 0.00 2.90
1582 4092 1.435408 GCCAAAGGAGCTCGATCTGC 61.435 60.000 7.83 0.00 0.00 4.26
1583 4093 0.813210 CCAAAGGAGCTCGATCTGCC 60.813 60.000 7.83 0.94 0.00 4.85
1584 4094 0.107993 CAAAGGAGCTCGATCTGCCA 60.108 55.000 7.83 0.00 0.00 4.92
1585 4095 0.107945 AAAGGAGCTCGATCTGCCAC 60.108 55.000 7.83 0.00 0.00 5.01
1586 4096 2.279120 GGAGCTCGATCTGCCACG 60.279 66.667 7.83 0.00 0.00 4.94
1587 4097 2.959071 GAGCTCGATCTGCCACGC 60.959 66.667 0.00 0.00 0.00 5.34
1588 4098 4.521062 AGCTCGATCTGCCACGCC 62.521 66.667 4.31 0.00 0.00 5.68
1590 4100 3.842923 CTCGATCTGCCACGCCCT 61.843 66.667 0.00 0.00 0.00 5.19
1591 4101 4.147449 TCGATCTGCCACGCCCTG 62.147 66.667 0.00 0.00 0.00 4.45
1592 4102 4.457496 CGATCTGCCACGCCCTGT 62.457 66.667 0.00 0.00 0.00 4.00
1593 4103 2.512515 GATCTGCCACGCCCTGTC 60.513 66.667 0.00 0.00 0.00 3.51
1594 4104 3.315142 GATCTGCCACGCCCTGTCA 62.315 63.158 0.00 0.00 0.00 3.58
1595 4105 2.599645 GATCTGCCACGCCCTGTCAT 62.600 60.000 0.00 0.00 0.00 3.06
1596 4106 2.881539 ATCTGCCACGCCCTGTCATG 62.882 60.000 0.00 0.00 0.00 3.07
1641 4151 1.265454 CGGAGGTACCAAAGGAGCCT 61.265 60.000 15.94 3.62 38.90 4.58
1667 4177 2.125391 GCACTCTGCGATGCCAGA 60.125 61.111 0.00 0.00 39.42 3.86
1671 4181 4.604114 TCTGCGATGCCAGAGTTG 57.396 55.556 0.00 0.00 36.96 3.16
1672 4182 1.742880 TCTGCGATGCCAGAGTTGC 60.743 57.895 0.00 0.00 36.96 4.17
1673 4183 2.747460 TGCGATGCCAGAGTTGCC 60.747 61.111 0.00 0.00 0.00 4.52
1674 4184 3.869272 GCGATGCCAGAGTTGCCG 61.869 66.667 0.00 0.00 0.00 5.69
1675 4185 2.125552 CGATGCCAGAGTTGCCGA 60.126 61.111 0.00 0.00 0.00 5.54
1676 4186 1.741401 CGATGCCAGAGTTGCCGAA 60.741 57.895 0.00 0.00 0.00 4.30
1677 4187 1.699656 CGATGCCAGAGTTGCCGAAG 61.700 60.000 0.00 0.00 0.00 3.79
1678 4188 1.986575 GATGCCAGAGTTGCCGAAGC 61.987 60.000 0.00 0.00 40.48 3.86
1679 4189 3.435186 GCCAGAGTTGCCGAAGCC 61.435 66.667 0.00 0.00 38.69 4.35
1680 4190 2.348998 CCAGAGTTGCCGAAGCCT 59.651 61.111 0.00 0.00 38.69 4.58
1681 4191 2.037136 CCAGAGTTGCCGAAGCCTG 61.037 63.158 0.00 0.00 38.69 4.85
1682 4192 1.004560 CAGAGTTGCCGAAGCCTGA 60.005 57.895 0.00 0.00 38.69 3.86
1683 4193 0.603707 CAGAGTTGCCGAAGCCTGAA 60.604 55.000 0.00 0.00 38.69 3.02
1684 4194 0.321122 AGAGTTGCCGAAGCCTGAAG 60.321 55.000 0.00 0.00 38.69 3.02
1685 4195 0.603975 GAGTTGCCGAAGCCTGAAGT 60.604 55.000 0.00 0.00 38.69 3.01
1686 4196 0.886490 AGTTGCCGAAGCCTGAAGTG 60.886 55.000 0.00 0.00 38.69 3.16
1687 4197 2.260869 TTGCCGAAGCCTGAAGTGC 61.261 57.895 0.00 0.00 38.69 4.40
1688 4198 3.435186 GCCGAAGCCTGAAGTGCC 61.435 66.667 0.00 0.00 0.00 5.01
1689 4199 2.032528 CCGAAGCCTGAAGTGCCA 59.967 61.111 0.00 0.00 0.00 4.92
1690 4200 2.328099 CCGAAGCCTGAAGTGCCAC 61.328 63.158 0.00 0.00 0.00 5.01
1691 4201 1.597854 CGAAGCCTGAAGTGCCACA 60.598 57.895 0.00 0.00 0.00 4.17
1692 4202 1.845809 CGAAGCCTGAAGTGCCACAC 61.846 60.000 0.00 0.00 34.10 3.82
1693 4203 1.518903 GAAGCCTGAAGTGCCACACC 61.519 60.000 0.00 0.00 34.49 4.16
1694 4204 2.203337 GCCTGAAGTGCCACACCA 60.203 61.111 0.00 0.00 34.49 4.17
1695 4205 1.604593 GCCTGAAGTGCCACACCAT 60.605 57.895 0.00 0.00 34.49 3.55
1696 4206 1.870055 GCCTGAAGTGCCACACCATG 61.870 60.000 0.00 0.00 34.49 3.66
1890 4448 3.223674 TGATCGGACTAGCTACATCCA 57.776 47.619 16.25 6.88 32.35 3.41
1895 4453 2.032204 CGGACTAGCTACATCCACGTAC 60.032 54.545 16.25 0.73 32.35 3.67
1899 4457 1.182667 AGCTACATCCACGTACTGCA 58.817 50.000 0.00 0.00 0.00 4.41
1900 4458 1.757118 AGCTACATCCACGTACTGCAT 59.243 47.619 0.00 0.00 0.00 3.96
1951 4565 4.944962 ATACATGTGTATGTGTGTGTGC 57.055 40.909 9.11 0.00 46.63 4.57
1953 4567 0.516877 ATGTGTATGTGTGTGTGCGC 59.483 50.000 0.00 0.00 0.00 6.09
1955 4569 2.202171 GTATGTGTGTGTGCGCGC 60.202 61.111 27.26 27.26 36.27 6.86
1976 4607 1.910020 GCGCGCGTGTGATTGTTATAC 60.910 52.381 32.35 4.98 0.00 1.47
1979 4610 3.121795 CGCGCGTGTGATTGTTATACTAG 60.122 47.826 24.19 0.00 0.00 2.57
1984 4615 7.201215 GCGCGTGTGATTGTTATACTAGTATAC 60.201 40.741 20.01 15.41 0.00 1.47
1985 4616 7.799914 CGCGTGTGATTGTTATACTAGTATACA 59.200 37.037 20.01 17.31 0.00 2.29
1986 4617 8.899776 GCGTGTGATTGTTATACTAGTATACAC 58.100 37.037 20.01 21.23 0.00 2.90
2001 4632 2.168621 CACTATATGTGCGCGCGC 59.831 61.111 45.02 45.02 40.06 6.86
2018 4651 0.179250 CGCTCGTGTTGTGTACATGC 60.179 55.000 0.00 0.00 42.42 4.06
2031 4664 1.136305 GTACATGCCGTTAGAGCCTGA 59.864 52.381 0.00 0.00 31.26 3.86
2047 4680 0.741915 CTGAGCTCTAGTTCCCGACC 59.258 60.000 16.19 0.00 0.00 4.79
2048 4681 1.030488 TGAGCTCTAGTTCCCGACCG 61.030 60.000 16.19 0.00 0.00 4.79
2052 4685 0.394080 CTCTAGTTCCCGACCGGAGT 60.394 60.000 9.46 0.00 43.39 3.85
2056 4689 1.373873 GTTCCCGACCGGAGTGTTC 60.374 63.158 9.46 0.00 43.39 3.18
2063 4696 0.667792 GACCGGAGTGTTCTGTCTGC 60.668 60.000 9.46 0.00 0.00 4.26
2065 4698 1.285950 CGGAGTGTTCTGTCTGCGA 59.714 57.895 0.23 0.00 45.53 5.10
2094 4727 0.251033 TGGTGCAGCTGCTCAATCTT 60.251 50.000 36.61 0.00 42.66 2.40
2097 4730 2.288640 GGTGCAGCTGCTCAATCTTTTT 60.289 45.455 36.61 0.00 42.66 1.94
2100 4733 2.029649 GCAGCTGCTCAATCTTTTTCCA 60.030 45.455 31.33 0.00 38.21 3.53
2101 4734 3.368116 GCAGCTGCTCAATCTTTTTCCAT 60.368 43.478 31.33 0.00 38.21 3.41
2113 4748 7.728083 TCAATCTTTTTCCATCTTCCCTTTACA 59.272 33.333 0.00 0.00 0.00 2.41
2119 4754 9.983024 TTTTTCCATCTTCCCTTTACATGTATA 57.017 29.630 6.36 0.68 0.00 1.47
2203 4843 5.102313 GGATCGGATTTTGTGTTTGGATTC 58.898 41.667 0.00 0.00 0.00 2.52
2214 4857 4.097714 GTGTTTGGATTCACATATGTGCG 58.902 43.478 27.71 8.78 45.25 5.34
2223 4868 5.524511 TTCACATATGTGCGTCACTAAAC 57.475 39.130 27.71 0.00 45.25 2.01
2253 4898 4.140518 TGTTTTGGCTATATTATGCGCG 57.859 40.909 0.00 0.00 0.00 6.86
2256 4901 0.249120 TGGCTATATTATGCGCGCCT 59.751 50.000 30.77 22.56 38.33 5.52
2257 4902 1.478916 TGGCTATATTATGCGCGCCTA 59.521 47.619 30.77 21.29 38.33 3.93
2268 4913 0.170339 GCGCGCCTAGGACAAATTTT 59.830 50.000 23.24 0.00 0.00 1.82
2269 4914 1.399089 GCGCGCCTAGGACAAATTTTA 59.601 47.619 23.24 0.00 0.00 1.52
2272 4917 4.668289 CGCGCCTAGGACAAATTTTATTT 58.332 39.130 14.75 0.00 0.00 1.40
2274 4919 5.575218 CGCGCCTAGGACAAATTTTATTTTT 59.425 36.000 14.75 0.00 0.00 1.94
2276 4921 6.672118 GCGCCTAGGACAAATTTTATTTTTGC 60.672 38.462 14.75 0.00 37.54 3.68
2284 4929 6.418141 ACAAATTTTATTTTTGCGCAGACAC 58.582 32.000 11.31 0.00 37.54 3.67
2285 4930 6.036517 ACAAATTTTATTTTTGCGCAGACACA 59.963 30.769 11.31 0.00 37.54 3.72
2286 4931 6.783892 AATTTTATTTTTGCGCAGACACAT 57.216 29.167 11.31 0.78 0.00 3.21
2287 4932 6.783892 ATTTTATTTTTGCGCAGACACATT 57.216 29.167 11.31 0.00 0.00 2.71
2288 4933 6.595772 TTTTATTTTTGCGCAGACACATTT 57.404 29.167 11.31 0.00 0.00 2.32
2291 4936 4.513000 TTTTTGCGCAGACACATTTTTC 57.487 36.364 11.31 0.00 0.00 2.29
2297 4942 4.032672 TGCGCAGACACATTTTTCTTTTTG 59.967 37.500 5.66 0.00 0.00 2.44
2302 4947 6.313658 GCAGACACATTTTTCTTTTTGGTCTT 59.686 34.615 0.00 0.00 31.27 3.01
2353 5005 1.402968 CCAGGTTTCATCCGAAGCATG 59.597 52.381 0.00 0.00 34.26 4.06
2362 5014 7.173218 GGTTTCATCCGAAGCATGATAAGATAA 59.827 37.037 0.00 0.00 34.26 1.75
2363 5015 7.658179 TTCATCCGAAGCATGATAAGATAAC 57.342 36.000 0.00 0.00 0.00 1.89
2365 5017 7.216494 TCATCCGAAGCATGATAAGATAACAA 58.784 34.615 0.00 0.00 0.00 2.83
2366 5018 6.844696 TCCGAAGCATGATAAGATAACAAC 57.155 37.500 0.00 0.00 0.00 3.32
2367 5019 5.462068 TCCGAAGCATGATAAGATAACAACG 59.538 40.000 0.00 0.00 0.00 4.10
2368 5020 5.234329 CCGAAGCATGATAAGATAACAACGT 59.766 40.000 0.00 0.00 0.00 3.99
2381 5034 7.653767 AGATAACAACGTCTCTAACCAAAAG 57.346 36.000 0.00 0.00 0.00 2.27
2382 5035 4.547406 AACAACGTCTCTAACCAAAAGC 57.453 40.909 0.00 0.00 0.00 3.51
2383 5036 3.805207 ACAACGTCTCTAACCAAAAGCT 58.195 40.909 0.00 0.00 0.00 3.74
2384 5037 4.952460 ACAACGTCTCTAACCAAAAGCTA 58.048 39.130 0.00 0.00 0.00 3.32
2385 5038 4.989168 ACAACGTCTCTAACCAAAAGCTAG 59.011 41.667 0.00 0.00 0.00 3.42
2386 5039 3.586892 ACGTCTCTAACCAAAAGCTAGC 58.413 45.455 6.62 6.62 0.00 3.42
2387 5040 3.006537 ACGTCTCTAACCAAAAGCTAGCA 59.993 43.478 18.83 0.00 0.00 3.49
2388 5041 3.368236 CGTCTCTAACCAAAAGCTAGCAC 59.632 47.826 18.83 0.00 0.00 4.40
2390 5043 2.673368 CTCTAACCAAAAGCTAGCACCG 59.327 50.000 18.83 1.85 0.00 4.94
2393 5046 2.046285 CCAAAAGCTAGCACCGGGG 61.046 63.158 18.83 0.84 0.00 5.73
2394 5047 1.002624 CAAAAGCTAGCACCGGGGA 60.003 57.895 18.83 0.00 0.00 4.81
2395 5048 0.394352 CAAAAGCTAGCACCGGGGAT 60.394 55.000 18.83 2.04 0.00 3.85
2396 5049 0.331616 AAAAGCTAGCACCGGGGATT 59.668 50.000 18.83 0.00 0.00 3.01
2397 5050 0.394352 AAAGCTAGCACCGGGGATTG 60.394 55.000 18.83 2.09 0.00 2.67
2398 5051 2.893682 AAGCTAGCACCGGGGATTGC 62.894 60.000 20.99 20.99 39.16 3.56
2399 5052 2.589540 CTAGCACCGGGGATTGCA 59.410 61.111 8.67 0.00 41.48 4.08
2400 5053 1.077787 CTAGCACCGGGGATTGCAA 60.078 57.895 8.67 0.00 41.48 4.08
2401 5054 1.376609 CTAGCACCGGGGATTGCAAC 61.377 60.000 8.67 0.00 41.48 4.17
2402 5055 2.830186 TAGCACCGGGGATTGCAACC 62.830 60.000 8.67 5.33 41.48 3.77
2403 5056 2.282816 CACCGGGGATTGCAACCA 60.283 61.111 6.32 0.00 0.00 3.67
2404 5057 2.035626 ACCGGGGATTGCAACCAG 59.964 61.111 6.32 9.17 0.00 4.00
2405 5058 2.755469 CCGGGGATTGCAACCAGG 60.755 66.667 10.20 10.20 35.80 4.45
2406 5059 2.035626 CGGGGATTGCAACCAGGT 59.964 61.111 16.55 0.00 0.00 4.00
2407 5060 1.606313 CGGGGATTGCAACCAGGTT 60.606 57.895 16.55 0.00 0.00 3.50
2408 5061 1.876497 CGGGGATTGCAACCAGGTTG 61.876 60.000 26.09 26.09 45.24 3.77
2409 5062 0.541764 GGGGATTGCAACCAGGTTGA 60.542 55.000 33.10 15.71 45.28 3.18
2410 5063 1.337118 GGGATTGCAACCAGGTTGAA 58.663 50.000 33.10 22.71 45.28 2.69
2411 5064 1.691434 GGGATTGCAACCAGGTTGAAA 59.309 47.619 33.10 29.42 45.28 2.69
2416 5069 3.658757 TGCAACCAGGTTGAAATAAGC 57.341 42.857 33.10 17.50 45.28 3.09
2417 5070 2.961741 TGCAACCAGGTTGAAATAAGCA 59.038 40.909 33.10 19.80 45.28 3.91
2418 5071 3.243704 TGCAACCAGGTTGAAATAAGCAC 60.244 43.478 33.10 13.93 45.28 4.40
2419 5072 3.005791 GCAACCAGGTTGAAATAAGCACT 59.994 43.478 33.10 0.00 45.28 4.40
2420 5073 4.501400 GCAACCAGGTTGAAATAAGCACTT 60.501 41.667 33.10 0.00 45.28 3.16
2421 5074 5.222631 CAACCAGGTTGAAATAAGCACTTC 58.777 41.667 26.28 0.00 45.28 3.01
2422 5075 4.729868 ACCAGGTTGAAATAAGCACTTCT 58.270 39.130 0.00 0.00 0.00 2.85
2423 5076 4.520492 ACCAGGTTGAAATAAGCACTTCTG 59.480 41.667 0.00 0.00 0.00 3.02
2424 5077 4.761739 CCAGGTTGAAATAAGCACTTCTGA 59.238 41.667 0.00 0.00 0.00 3.27
2425 5078 5.416952 CCAGGTTGAAATAAGCACTTCTGAT 59.583 40.000 0.00 0.00 0.00 2.90
2426 5079 6.320171 CAGGTTGAAATAAGCACTTCTGATG 58.680 40.000 0.00 0.00 0.00 3.07
2427 5080 5.416952 AGGTTGAAATAAGCACTTCTGATGG 59.583 40.000 0.00 0.00 0.00 3.51
2428 5081 5.393461 GGTTGAAATAAGCACTTCTGATGGG 60.393 44.000 0.00 0.00 0.00 4.00
2429 5082 3.696051 TGAAATAAGCACTTCTGATGGGC 59.304 43.478 9.58 9.58 0.00 5.36
2430 5083 1.959042 ATAAGCACTTCTGATGGGCG 58.041 50.000 11.54 0.00 0.00 6.13
2431 5084 0.613260 TAAGCACTTCTGATGGGCGT 59.387 50.000 11.54 11.08 0.00 5.68
2432 5085 0.674895 AAGCACTTCTGATGGGCGTC 60.675 55.000 11.54 0.00 0.00 5.19
2433 5086 1.078848 GCACTTCTGATGGGCGTCT 60.079 57.895 1.78 0.00 0.00 4.18
2434 5087 1.086634 GCACTTCTGATGGGCGTCTC 61.087 60.000 1.78 0.00 0.00 3.36
2435 5088 0.534412 CACTTCTGATGGGCGTCTCT 59.466 55.000 0.00 0.00 0.00 3.10
2436 5089 0.534412 ACTTCTGATGGGCGTCTCTG 59.466 55.000 0.00 0.00 0.00 3.35
2437 5090 0.179089 CTTCTGATGGGCGTCTCTGG 60.179 60.000 0.00 0.00 0.00 3.86
2438 5091 2.202987 CTGATGGGCGTCTCTGGC 60.203 66.667 0.00 0.00 0.00 4.85
2439 5092 4.147449 TGATGGGCGTCTCTGGCG 62.147 66.667 0.00 0.00 34.76 5.69
2440 5093 3.838271 GATGGGCGTCTCTGGCGA 61.838 66.667 0.00 0.00 34.76 5.54
2441 5094 3.157217 GATGGGCGTCTCTGGCGAT 62.157 63.158 0.00 0.00 35.59 4.58
2442 5095 2.650813 GATGGGCGTCTCTGGCGATT 62.651 60.000 0.00 0.00 33.10 3.34
2443 5096 2.586357 GGGCGTCTCTGGCGATTC 60.586 66.667 0.00 0.00 34.76 2.52
2444 5097 2.956964 GGCGTCTCTGGCGATTCG 60.957 66.667 0.62 0.62 0.00 3.34
2445 5098 2.956964 GCGTCTCTGGCGATTCGG 60.957 66.667 8.34 0.00 0.00 4.30
2446 5099 2.798689 CGTCTCTGGCGATTCGGA 59.201 61.111 8.34 0.00 0.00 4.55
2447 5100 1.586564 CGTCTCTGGCGATTCGGAC 60.587 63.158 8.34 5.39 0.00 4.79
2448 5101 1.586564 GTCTCTGGCGATTCGGACG 60.587 63.158 8.34 0.00 0.00 4.79
2449 5102 2.278857 CTCTGGCGATTCGGACGG 60.279 66.667 8.34 0.00 0.00 4.79
2487 5140 4.888325 CCCTCCCCGATGCTCCCT 62.888 72.222 0.00 0.00 0.00 4.20
2488 5141 3.237741 CCTCCCCGATGCTCCCTC 61.238 72.222 0.00 0.00 0.00 4.30
2489 5142 3.237741 CTCCCCGATGCTCCCTCC 61.238 72.222 0.00 0.00 0.00 4.30
2494 5147 4.292178 CGATGCTCCCTCCGCCTC 62.292 72.222 0.00 0.00 0.00 4.70
2495 5148 3.934962 GATGCTCCCTCCGCCTCC 61.935 72.222 0.00 0.00 0.00 4.30
2503 5156 4.214327 CTCCGCCTCCGCTCCTTC 62.214 72.222 0.00 0.00 0.00 3.46
2507 5160 4.821589 GCCTCCGCTCCTTCCGTG 62.822 72.222 0.00 0.00 0.00 4.94
2508 5161 4.821589 CCTCCGCTCCTTCCGTGC 62.822 72.222 0.00 0.00 0.00 5.34
2509 5162 4.821589 CTCCGCTCCTTCCGTGCC 62.822 72.222 0.00 0.00 0.00 5.01
2615 5268 4.547367 CCCCGCTTCCGATGGTCC 62.547 72.222 0.00 0.00 36.29 4.46
2616 5269 4.891727 CCCGCTTCCGATGGTCCG 62.892 72.222 0.00 0.00 36.29 4.79
2617 5270 3.833645 CCGCTTCCGATGGTCCGA 61.834 66.667 0.00 0.00 36.29 4.55
2618 5271 2.582498 CGCTTCCGATGGTCCGAC 60.582 66.667 0.00 0.00 36.29 4.79
2619 5272 2.893398 GCTTCCGATGGTCCGACT 59.107 61.111 0.00 0.00 0.00 4.18
2620 5273 1.519455 GCTTCCGATGGTCCGACTG 60.519 63.158 0.00 0.00 0.00 3.51
2621 5274 1.519455 CTTCCGATGGTCCGACTGC 60.519 63.158 0.00 0.00 0.00 4.40
2622 5275 3.350909 TTCCGATGGTCCGACTGCG 62.351 63.158 0.00 0.48 37.24 5.18
2641 5294 2.506472 GGATGACGAGCCCTTCCC 59.494 66.667 0.00 0.00 0.00 3.97
2642 5295 2.107141 GATGACGAGCCCTTCCCG 59.893 66.667 0.00 0.00 0.00 5.14
2643 5296 4.162690 ATGACGAGCCCTTCCCGC 62.163 66.667 0.00 0.00 0.00 6.13
2739 5392 4.760047 CCCTCGTGCGGGGTTCTG 62.760 72.222 9.82 0.00 40.75 3.02
2864 5517 4.394712 GGTCTCACCTGGGGCGTG 62.395 72.222 0.00 0.00 34.73 5.34
2865 5518 4.394712 GTCTCACCTGGGGCGTGG 62.395 72.222 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 5.556355 TCATCGTGTAACTTATGTCGACT 57.444 39.130 17.92 4.95 31.97 4.18
48 49 0.598158 GGTGTCTTGCGTCGTTACCA 60.598 55.000 0.00 0.00 0.00 3.25
143 165 2.529744 GCCTGAGGTTGGGTGGTCT 61.530 63.158 0.00 0.00 0.00 3.85
153 175 0.980231 GGAGATGGTCAGCCTGAGGT 60.980 60.000 0.00 0.00 35.27 3.85
232 256 2.835431 CCCTGGGATCGACTCGCT 60.835 66.667 7.01 0.00 37.69 4.93
265 291 2.036475 GCTGATGTCATGTATCGTCCCT 59.964 50.000 0.00 0.00 0.00 4.20
272 298 2.610833 CGCACTTGCTGATGTCATGTAT 59.389 45.455 0.00 0.00 39.32 2.29
277 303 2.327343 GCCGCACTTGCTGATGTCA 61.327 57.895 0.00 0.00 39.32 3.58
541 586 1.134901 CCGTCTCTCGTTCACTCCG 59.865 63.158 0.00 0.00 37.94 4.63
598 644 2.073101 CCTAACCCTCCTGCTCCCC 61.073 68.421 0.00 0.00 0.00 4.81
620 668 1.066152 CTCCAGATCGCATCTCACGAA 59.934 52.381 0.00 0.00 43.71 3.85
621 669 0.665298 CTCCAGATCGCATCTCACGA 59.335 55.000 0.00 0.00 44.75 4.35
622 670 0.318529 CCTCCAGATCGCATCTCACG 60.319 60.000 0.00 0.00 37.58 4.35
623 671 0.749649 ACCTCCAGATCGCATCTCAC 59.250 55.000 0.00 0.00 37.58 3.51
624 672 1.957177 GTACCTCCAGATCGCATCTCA 59.043 52.381 0.00 0.00 37.58 3.27
625 673 1.957177 TGTACCTCCAGATCGCATCTC 59.043 52.381 0.00 0.00 37.58 2.75
626 674 2.073252 TGTACCTCCAGATCGCATCT 57.927 50.000 0.00 0.00 41.15 2.90
627 675 2.890808 TTGTACCTCCAGATCGCATC 57.109 50.000 0.00 0.00 0.00 3.91
628 676 2.968574 AGATTGTACCTCCAGATCGCAT 59.031 45.455 0.00 0.00 0.00 4.73
629 677 2.388735 AGATTGTACCTCCAGATCGCA 58.611 47.619 0.00 0.00 0.00 5.10
630 678 3.460857 AAGATTGTACCTCCAGATCGC 57.539 47.619 0.00 0.00 0.00 4.58
631 679 5.563867 GCTCTAAGATTGTACCTCCAGATCG 60.564 48.000 0.00 0.00 0.00 3.69
632 680 5.279256 GGCTCTAAGATTGTACCTCCAGATC 60.279 48.000 0.00 0.00 0.00 2.75
633 681 4.591072 GGCTCTAAGATTGTACCTCCAGAT 59.409 45.833 0.00 0.00 0.00 2.90
634 682 3.961408 GGCTCTAAGATTGTACCTCCAGA 59.039 47.826 0.00 0.00 0.00 3.86
635 683 3.964031 AGGCTCTAAGATTGTACCTCCAG 59.036 47.826 0.00 0.00 0.00 3.86
636 684 3.995636 AGGCTCTAAGATTGTACCTCCA 58.004 45.455 0.00 0.00 0.00 3.86
637 685 6.673839 AATAGGCTCTAAGATTGTACCTCC 57.326 41.667 0.00 0.00 0.00 4.30
638 686 8.966069 AAAAATAGGCTCTAAGATTGTACCTC 57.034 34.615 0.00 0.00 0.00 3.85
700 748 4.100808 TGATGACATGATATGGTCGGTGAA 59.899 41.667 0.00 0.00 36.83 3.18
768 816 3.627041 TCCTCTGCCTATCCATCTCTT 57.373 47.619 0.00 0.00 0.00 2.85
1003 3255 2.426738 CAAGGAAGGTGTTCTTGCACAA 59.573 45.455 0.00 0.00 44.91 3.33
1019 3277 0.250295 CGCCACAAGGAAGACAAGGA 60.250 55.000 0.00 0.00 36.89 3.36
1108 3366 0.830648 ACGATCGGATGTGGTGGATT 59.169 50.000 20.98 0.00 0.00 3.01
1182 3440 2.193536 GTGCGGTGGTTCAGGCTTT 61.194 57.895 0.00 0.00 0.00 3.51
1299 3641 1.990424 CATAGCAGGGTGTGGTGGA 59.010 57.895 0.00 0.00 37.49 4.02
1359 3818 0.890996 CAGTGTCCTTTGGCACCTCC 60.891 60.000 0.00 0.00 36.35 4.30
1374 3833 3.357079 GGGTGTGGCGCTTCAGTG 61.357 66.667 7.64 0.00 0.00 3.66
1392 3851 1.377725 AGGCTCCTTTGGCACGATG 60.378 57.895 0.00 0.00 34.73 3.84
1480 3990 0.613012 GGCAGTTCAGGCTTTGGGAT 60.613 55.000 0.00 0.00 0.00 3.85
1538 4048 1.747745 GGTACGATTGGGTGTGGCC 60.748 63.158 0.00 0.00 0.00 5.36
1574 4084 4.147449 CAGGGCGTGGCAGATCGA 62.147 66.667 0.00 0.00 0.00 3.59
1586 4096 4.864334 CCTCCGGCATGACAGGGC 62.864 72.222 3.18 3.18 33.79 5.19
1587 4097 3.402681 ACCTCCGGCATGACAGGG 61.403 66.667 9.66 5.03 33.79 4.45
1588 4098 2.124983 CACCTCCGGCATGACAGG 60.125 66.667 3.33 3.33 34.40 4.00
1589 4099 1.448540 GACACCTCCGGCATGACAG 60.449 63.158 0.00 0.00 0.00 3.51
1590 4100 2.213513 TGACACCTCCGGCATGACA 61.214 57.895 0.00 0.00 0.00 3.58
1591 4101 1.741770 GTGACACCTCCGGCATGAC 60.742 63.158 0.00 0.00 0.00 3.06
1592 4102 2.213513 TGTGACACCTCCGGCATGA 61.214 57.895 2.45 0.00 0.00 3.07
1593 4103 2.034879 GTGTGACACCTCCGGCATG 61.035 63.158 3.92 0.00 0.00 4.06
1594 4104 2.347490 GTGTGACACCTCCGGCAT 59.653 61.111 3.92 0.00 0.00 4.40
1621 4131 1.262640 GGCTCCTTTGGTACCTCCGA 61.263 60.000 14.36 2.61 39.52 4.55
1654 4164 1.742880 GCAACTCTGGCATCGCAGA 60.743 57.895 0.00 0.00 45.75 4.26
1662 4172 3.435186 GGCTTCGGCAACTCTGGC 61.435 66.667 0.00 0.00 43.96 4.85
1663 4173 2.037136 CAGGCTTCGGCAACTCTGG 61.037 63.158 0.00 0.00 43.96 3.86
1664 4174 0.603707 TTCAGGCTTCGGCAACTCTG 60.604 55.000 0.00 0.00 43.96 3.35
1665 4175 0.321122 CTTCAGGCTTCGGCAACTCT 60.321 55.000 0.00 0.00 43.96 3.24
1666 4176 0.603975 ACTTCAGGCTTCGGCAACTC 60.604 55.000 0.00 0.00 43.96 3.01
1667 4177 0.886490 CACTTCAGGCTTCGGCAACT 60.886 55.000 0.00 0.00 43.96 3.16
1668 4178 1.576421 CACTTCAGGCTTCGGCAAC 59.424 57.895 0.00 0.00 43.96 4.17
1669 4179 2.260869 GCACTTCAGGCTTCGGCAA 61.261 57.895 0.00 0.00 43.96 4.52
1670 4180 2.669569 GCACTTCAGGCTTCGGCA 60.670 61.111 0.00 0.00 43.96 5.69
1671 4181 3.435186 GGCACTTCAGGCTTCGGC 61.435 66.667 0.00 0.00 40.88 5.54
1672 4182 2.032528 TGGCACTTCAGGCTTCGG 59.967 61.111 0.00 0.00 34.73 4.30
1673 4183 1.597854 TGTGGCACTTCAGGCTTCG 60.598 57.895 19.83 0.00 34.73 3.79
1674 4184 1.518903 GGTGTGGCACTTCAGGCTTC 61.519 60.000 19.83 0.00 34.40 3.86
1675 4185 1.529244 GGTGTGGCACTTCAGGCTT 60.529 57.895 19.83 0.00 34.40 4.35
1676 4186 2.072874 ATGGTGTGGCACTTCAGGCT 62.073 55.000 19.83 0.00 34.40 4.58
1677 4187 1.604593 ATGGTGTGGCACTTCAGGC 60.605 57.895 19.83 2.21 34.40 4.85
1678 4188 1.246056 CCATGGTGTGGCACTTCAGG 61.246 60.000 19.83 16.83 42.12 3.86
1679 4189 2.260247 CCATGGTGTGGCACTTCAG 58.740 57.895 19.83 10.11 42.12 3.02
1680 4190 4.498346 CCATGGTGTGGCACTTCA 57.502 55.556 19.83 16.37 42.12 3.02
1689 4199 3.907260 CTCTGGCACGCCATGGTGT 62.907 63.158 25.40 25.40 46.15 4.16
1690 4200 3.129502 CTCTGGCACGCCATGGTG 61.130 66.667 23.88 23.88 46.15 4.17
1691 4201 4.415150 CCTCTGGCACGCCATGGT 62.415 66.667 14.67 0.00 46.15 3.55
1692 4202 4.415150 ACCTCTGGCACGCCATGG 62.415 66.667 21.52 21.52 46.15 3.66
1693 4203 3.129502 CACCTCTGGCACGCCATG 61.130 66.667 11.97 7.65 46.15 3.66
1922 4483 7.973944 CACACACATACACATGTATAGTACTGT 59.026 37.037 5.39 0.39 43.73 3.55
1925 4486 7.253983 GCACACACACATACACATGTATAGTAC 60.254 40.741 0.00 0.00 43.73 2.73
1957 4571 1.586578 AGTATAACAATCACACGCGCG 59.413 47.619 30.96 30.96 0.00 6.86
1959 4573 7.799914 TGTATACTAGTATAACAATCACACGCG 59.200 37.037 21.51 3.53 30.60 6.01
1996 4627 3.399770 TACACAACACGAGCGCGC 61.400 61.111 26.66 26.66 42.48 6.86
1999 4630 0.179250 GCATGTACACAACACGAGCG 60.179 55.000 0.00 0.00 42.09 5.03
2001 4632 0.438445 CGGCATGTACACAACACGAG 59.562 55.000 0.00 0.00 42.09 4.18
2002 4633 0.249531 ACGGCATGTACACAACACGA 60.250 50.000 0.00 0.00 42.09 4.35
2003 4634 0.584396 AACGGCATGTACACAACACG 59.416 50.000 0.00 1.62 42.09 4.49
2008 4641 1.404986 GGCTCTAACGGCATGTACACA 60.405 52.381 0.00 0.00 0.00 3.72
2009 4642 1.134788 AGGCTCTAACGGCATGTACAC 60.135 52.381 0.00 0.00 0.00 2.90
2031 4664 1.753463 CCGGTCGGGAACTAGAGCT 60.753 63.158 0.00 0.00 38.47 4.09
2047 4680 0.730834 CTCGCAGACAGAACACTCCG 60.731 60.000 0.00 0.00 0.00 4.63
2048 4681 0.389166 CCTCGCAGACAGAACACTCC 60.389 60.000 0.00 0.00 0.00 3.85
2052 4685 0.464036 AACACCTCGCAGACAGAACA 59.536 50.000 0.00 0.00 0.00 3.18
2056 4689 0.952497 ATGCAACACCTCGCAGACAG 60.952 55.000 0.00 0.00 42.37 3.51
2063 4696 2.562912 GCACCATGCAACACCTCG 59.437 61.111 0.00 0.00 44.26 4.63
2094 4727 9.403583 GTATACATGTAAAGGGAAGATGGAAAA 57.596 33.333 10.14 0.00 0.00 2.29
2097 4730 7.506114 GTGTATACATGTAAAGGGAAGATGGA 58.494 38.462 10.14 0.00 0.00 3.41
2100 4733 7.356089 TCGTGTATACATGTAAAGGGAAGAT 57.644 36.000 21.61 0.00 34.59 2.40
2101 4734 6.778834 TCGTGTATACATGTAAAGGGAAGA 57.221 37.500 21.61 1.69 34.59 2.87
2172 4812 9.579768 CAAACACAAAATCCGATCCAATATAAA 57.420 29.630 0.00 0.00 0.00 1.40
2214 4857 7.378728 GCCAAAACATAAGAAGTGTTTAGTGAC 59.621 37.037 4.86 0.00 46.01 3.67
2253 4898 6.672118 GCGCAAAAATAAAATTTGTCCTAGGC 60.672 38.462 2.96 0.00 39.42 3.93
2256 4901 7.115663 GTCTGCGCAAAAATAAAATTTGTCCTA 59.884 33.333 13.05 0.00 39.42 2.94
2257 4902 5.988561 TCTGCGCAAAAATAAAATTTGTCCT 59.011 32.000 13.05 0.00 39.42 3.85
2268 4913 5.982516 AGAAAAATGTGTCTGCGCAAAAATA 59.017 32.000 13.05 0.00 38.73 1.40
2269 4914 4.810491 AGAAAAATGTGTCTGCGCAAAAAT 59.190 33.333 13.05 0.00 38.73 1.82
2272 4917 3.435105 AGAAAAATGTGTCTGCGCAAA 57.565 38.095 13.05 0.00 38.73 3.68
2274 4919 3.435105 AAAGAAAAATGTGTCTGCGCA 57.565 38.095 10.98 10.98 39.66 6.09
2276 4921 4.566360 ACCAAAAAGAAAAATGTGTCTGCG 59.434 37.500 0.00 0.00 0.00 5.18
2302 4947 9.970553 TCAGGTCTTCTCTACTACTAATACAAA 57.029 33.333 0.00 0.00 0.00 2.83
2308 4953 6.377712 GGCTTTCAGGTCTTCTCTACTACTAA 59.622 42.308 0.00 0.00 0.00 2.24
2311 4956 4.142116 GGGCTTTCAGGTCTTCTCTACTAC 60.142 50.000 0.00 0.00 0.00 2.73
2314 4959 2.567615 TGGGCTTTCAGGTCTTCTCTAC 59.432 50.000 0.00 0.00 0.00 2.59
2337 4989 5.991328 TCTTATCATGCTTCGGATGAAAC 57.009 39.130 2.25 0.00 33.59 2.78
2341 4993 7.293745 GTTGTTATCTTATCATGCTTCGGATG 58.706 38.462 0.00 0.00 0.00 3.51
2345 4997 6.199154 AGACGTTGTTATCTTATCATGCTTCG 59.801 38.462 0.00 0.00 0.00 3.79
2353 5005 8.922058 TTGGTTAGAGACGTTGTTATCTTATC 57.078 34.615 0.00 0.00 0.00 1.75
2362 5014 3.805207 AGCTTTTGGTTAGAGACGTTGT 58.195 40.909 0.00 0.00 0.00 3.32
2363 5015 4.143094 GCTAGCTTTTGGTTAGAGACGTTG 60.143 45.833 7.70 0.00 31.56 4.10
2365 5017 3.006537 TGCTAGCTTTTGGTTAGAGACGT 59.993 43.478 17.23 0.00 31.56 4.34
2366 5018 3.368236 GTGCTAGCTTTTGGTTAGAGACG 59.632 47.826 17.23 0.00 31.56 4.18
2367 5019 3.685272 GGTGCTAGCTTTTGGTTAGAGAC 59.315 47.826 17.23 0.15 31.56 3.36
2368 5020 3.616560 CGGTGCTAGCTTTTGGTTAGAGA 60.617 47.826 17.23 0.00 31.56 3.10
2381 5034 2.902343 GCAATCCCCGGTGCTAGC 60.902 66.667 8.10 8.10 37.78 3.42
2382 5035 1.077787 TTGCAATCCCCGGTGCTAG 60.078 57.895 15.00 0.00 41.48 3.42
2383 5036 1.377987 GTTGCAATCCCCGGTGCTA 60.378 57.895 15.00 5.65 41.48 3.49
2384 5037 2.676471 GTTGCAATCCCCGGTGCT 60.676 61.111 15.00 0.00 41.48 4.40
2385 5038 3.758931 GGTTGCAATCCCCGGTGC 61.759 66.667 0.59 7.78 41.29 5.01
2386 5039 2.282816 TGGTTGCAATCCCCGGTG 60.283 61.111 7.36 0.00 0.00 4.94
2387 5040 2.035626 CTGGTTGCAATCCCCGGT 59.964 61.111 7.36 0.00 0.00 5.28
2388 5041 2.755469 CCTGGTTGCAATCCCCGG 60.755 66.667 7.36 6.83 0.00 5.73
2390 5043 0.541764 TCAACCTGGTTGCAATCCCC 60.542 55.000 30.21 2.07 42.55 4.81
2393 5046 4.627035 GCTTATTTCAACCTGGTTGCAATC 59.373 41.667 31.21 18.61 42.55 2.67
2394 5047 4.040217 TGCTTATTTCAACCTGGTTGCAAT 59.960 37.500 30.45 30.45 42.55 3.56
2395 5048 3.386078 TGCTTATTTCAACCTGGTTGCAA 59.614 39.130 30.21 26.69 42.55 4.08
2396 5049 2.961741 TGCTTATTTCAACCTGGTTGCA 59.038 40.909 30.21 20.16 42.55 4.08
2397 5050 3.005791 AGTGCTTATTTCAACCTGGTTGC 59.994 43.478 30.21 19.01 42.55 4.17
2398 5051 4.853924 AGTGCTTATTTCAACCTGGTTG 57.146 40.909 29.40 29.40 43.99 3.77
2399 5052 5.010012 CAGAAGTGCTTATTTCAACCTGGTT 59.990 40.000 6.18 6.18 0.00 3.67
2400 5053 4.520492 CAGAAGTGCTTATTTCAACCTGGT 59.480 41.667 0.00 0.00 0.00 4.00
2401 5054 4.761739 TCAGAAGTGCTTATTTCAACCTGG 59.238 41.667 0.00 0.00 0.00 4.45
2402 5055 5.947228 TCAGAAGTGCTTATTTCAACCTG 57.053 39.130 0.00 0.00 0.00 4.00
2403 5056 5.416952 CCATCAGAAGTGCTTATTTCAACCT 59.583 40.000 0.00 0.00 0.00 3.50
2404 5057 5.393461 CCCATCAGAAGTGCTTATTTCAACC 60.393 44.000 0.00 0.00 0.00 3.77
2405 5058 5.644644 CCCATCAGAAGTGCTTATTTCAAC 58.355 41.667 0.00 0.00 0.00 3.18
2406 5059 4.158394 GCCCATCAGAAGTGCTTATTTCAA 59.842 41.667 0.00 0.00 0.00 2.69
2407 5060 3.696051 GCCCATCAGAAGTGCTTATTTCA 59.304 43.478 0.00 0.00 0.00 2.69
2408 5061 3.242870 CGCCCATCAGAAGTGCTTATTTC 60.243 47.826 0.00 0.00 0.00 2.17
2409 5062 2.684881 CGCCCATCAGAAGTGCTTATTT 59.315 45.455 0.00 0.00 0.00 1.40
2410 5063 2.292267 CGCCCATCAGAAGTGCTTATT 58.708 47.619 0.00 0.00 0.00 1.40
2411 5064 1.210478 ACGCCCATCAGAAGTGCTTAT 59.790 47.619 0.00 0.00 0.00 1.73
2412 5065 0.613260 ACGCCCATCAGAAGTGCTTA 59.387 50.000 0.00 0.00 0.00 3.09
2413 5066 0.674895 GACGCCCATCAGAAGTGCTT 60.675 55.000 0.00 0.00 0.00 3.91
2414 5067 1.078848 GACGCCCATCAGAAGTGCT 60.079 57.895 0.00 0.00 0.00 4.40
2415 5068 1.078848 AGACGCCCATCAGAAGTGC 60.079 57.895 0.00 0.00 0.00 4.40
2416 5069 0.534412 AGAGACGCCCATCAGAAGTG 59.466 55.000 0.00 0.00 0.00 3.16
2417 5070 0.534412 CAGAGACGCCCATCAGAAGT 59.466 55.000 0.00 0.00 0.00 3.01
2418 5071 0.179089 CCAGAGACGCCCATCAGAAG 60.179 60.000 0.00 0.00 0.00 2.85
2419 5072 1.900351 CCAGAGACGCCCATCAGAA 59.100 57.895 0.00 0.00 0.00 3.02
2420 5073 2.725312 GCCAGAGACGCCCATCAGA 61.725 63.158 0.00 0.00 0.00 3.27
2421 5074 2.202987 GCCAGAGACGCCCATCAG 60.203 66.667 0.00 0.00 0.00 2.90
2422 5075 4.147449 CGCCAGAGACGCCCATCA 62.147 66.667 0.00 0.00 0.00 3.07
2423 5076 2.650813 AATCGCCAGAGACGCCCATC 62.651 60.000 0.00 0.00 0.00 3.51
2424 5077 2.650813 GAATCGCCAGAGACGCCCAT 62.651 60.000 0.00 0.00 0.00 4.00
2425 5078 3.371097 GAATCGCCAGAGACGCCCA 62.371 63.158 0.00 0.00 0.00 5.36
2426 5079 2.586357 GAATCGCCAGAGACGCCC 60.586 66.667 0.00 0.00 0.00 6.13
2427 5080 2.956964 CGAATCGCCAGAGACGCC 60.957 66.667 0.00 0.00 0.00 5.68
2428 5081 2.956964 CCGAATCGCCAGAGACGC 60.957 66.667 0.00 0.00 0.00 5.19
2429 5082 1.586564 GTCCGAATCGCCAGAGACG 60.587 63.158 0.00 0.00 0.00 4.18
2430 5083 1.586564 CGTCCGAATCGCCAGAGAC 60.587 63.158 0.00 0.00 0.00 3.36
2431 5084 2.771639 CCGTCCGAATCGCCAGAGA 61.772 63.158 0.00 0.00 0.00 3.10
2432 5085 2.278857 CCGTCCGAATCGCCAGAG 60.279 66.667 0.00 0.00 0.00 3.35
2433 5086 4.508128 GCCGTCCGAATCGCCAGA 62.508 66.667 0.00 0.00 0.00 3.86
2470 5123 4.888325 AGGGAGCATCGGGGAGGG 62.888 72.222 0.00 0.00 34.37 4.30
2471 5124 3.237741 GAGGGAGCATCGGGGAGG 61.238 72.222 0.00 0.00 34.37 4.30
2472 5125 3.237741 GGAGGGAGCATCGGGGAG 61.238 72.222 0.00 0.00 34.37 4.30
2477 5130 4.292178 GAGGCGGAGGGAGCATCG 62.292 72.222 0.00 0.00 35.71 3.84
2478 5131 3.934962 GGAGGCGGAGGGAGCATC 61.935 72.222 0.00 0.00 43.71 3.91
2486 5139 4.214327 GAAGGAGCGGAGGCGGAG 62.214 72.222 0.00 0.00 46.35 4.63
2490 5143 4.821589 CACGGAAGGAGCGGAGGC 62.822 72.222 0.00 0.00 40.37 4.70
2491 5144 4.821589 GCACGGAAGGAGCGGAGG 62.822 72.222 0.00 0.00 0.00 4.30
2492 5145 4.821589 GGCACGGAAGGAGCGGAG 62.822 72.222 0.00 0.00 37.16 4.63
2598 5251 4.547367 GGACCATCGGAAGCGGGG 62.547 72.222 0.00 0.00 0.00 5.73
2599 5252 4.891727 CGGACCATCGGAAGCGGG 62.892 72.222 0.00 0.00 0.00 6.13
2600 5253 3.833645 TCGGACCATCGGAAGCGG 61.834 66.667 0.00 0.00 0.00 5.52
2601 5254 2.582498 GTCGGACCATCGGAAGCG 60.582 66.667 0.00 0.00 0.00 4.68
2602 5255 1.519455 CAGTCGGACCATCGGAAGC 60.519 63.158 4.14 0.00 0.00 3.86
2603 5256 1.519455 GCAGTCGGACCATCGGAAG 60.519 63.158 4.14 0.00 0.00 3.46
2604 5257 2.577059 GCAGTCGGACCATCGGAA 59.423 61.111 4.14 0.00 0.00 4.30
2605 5258 3.822192 CGCAGTCGGACCATCGGA 61.822 66.667 4.14 0.00 0.00 4.55
2615 5268 4.829518 TCGTCATCCGCGCAGTCG 62.830 66.667 8.75 3.85 36.19 4.18
2616 5269 2.951745 CTCGTCATCCGCGCAGTC 60.952 66.667 8.75 0.00 36.19 3.51
2621 5274 4.514577 AAGGGCTCGTCATCCGCG 62.515 66.667 0.00 0.00 36.19 6.46
2622 5275 2.586357 GAAGGGCTCGTCATCCGC 60.586 66.667 0.00 0.00 36.19 5.54
2623 5276 2.107141 GGAAGGGCTCGTCATCCG 59.893 66.667 0.89 0.00 38.13 4.18
2624 5277 2.506472 GGGAAGGGCTCGTCATCC 59.494 66.667 0.89 0.00 0.00 3.51
2625 5278 2.107141 CGGGAAGGGCTCGTCATC 59.893 66.667 0.89 0.00 35.19 2.92
2626 5279 4.162690 GCGGGAAGGGCTCGTCAT 62.163 66.667 0.89 0.00 44.18 3.06
2847 5500 4.394712 CACGCCCCAGGTGAGACC 62.395 72.222 0.25 0.00 37.60 3.85
2848 5501 4.394712 CCACGCCCCAGGTGAGAC 62.395 72.222 0.25 0.00 37.60 3.36


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

AutoCloner maintained by Alex Coulton.