Multiple sequence alignment - TraesCS5D01G497600

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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 TraesCS5D01G497600 chr5D 100.000 3608 0 0 1 3608 527843937 527840330 0.000000e+00 6663.0
1 TraesCS5D01G497600 chr5D 93.036 359 22 1 3252 3607 16595107 16595465 4.130000e-144 521.0
2 TraesCS5D01G497600 chr5B 95.466 772 20 10 2065 2834 664503416 664502658 0.000000e+00 1218.0
3 TraesCS5D01G497600 chr5B 92.619 691 23 16 1397 2086 664504151 664503488 0.000000e+00 968.0
4 TraesCS5D01G497600 chr5B 91.692 662 35 11 2078 2719 664475107 664474446 0.000000e+00 900.0
5 TraesCS5D01G497600 chr5B 90.732 669 35 12 2078 2719 664416688 664416020 0.000000e+00 867.0
6 TraesCS5D01G497600 chr5B 89.281 709 33 16 1 708 664507008 664506342 0.000000e+00 848.0
7 TraesCS5D01G497600 chr5B 93.974 531 31 1 788 1318 664504740 664504211 0.000000e+00 802.0
8 TraesCS5D01G497600 chr5B 90.347 404 28 5 2826 3227 664501950 664501556 1.480000e-143 520.0
9 TraesCS5D01G497600 chr5B 91.867 332 22 5 1770 2097 664417090 664416760 3.280000e-125 459.0
10 TraesCS5D01G497600 chr5B 92.453 318 21 3 1770 2085 664475509 664475193 5.490000e-123 451.0
11 TraesCS5D01G497600 chr5B 84.069 408 58 5 896 1296 664476028 664475621 1.570000e-103 387.0
12 TraesCS5D01G497600 chr5B 83.824 408 59 5 896 1296 664417609 664417202 7.310000e-102 381.0
13 TraesCS5D01G497600 chr5B 81.481 189 19 9 493 680 664417935 664417762 1.350000e-29 141.0
14 TraesCS5D01G497600 chr5B 79.085 153 23 9 2964 3111 129361564 129361416 2.970000e-16 97.1
15 TraesCS5D01G497600 chr3D 89.597 769 59 13 2065 2816 2968294 2967530 0.000000e+00 957.0
16 TraesCS5D01G497600 chr3D 88.138 607 40 14 1507 2085 2968969 2968367 0.000000e+00 693.0
17 TraesCS5D01G497600 chr3D 92.222 360 25 1 3252 3608 45344331 45344690 1.160000e-139 507.0
18 TraesCS5D01G497600 chr3D 87.814 279 22 5 1022 1290 2969418 2969142 2.090000e-82 316.0
19 TraesCS5D01G497600 chr3D 92.453 53 4 0 2964 3016 32340997 32340945 3.860000e-10 76.8
20 TraesCS5D01G497600 chr5A 92.284 648 38 8 2065 2704 655188969 655188326 0.000000e+00 909.0
21 TraesCS5D01G497600 chr5A 92.284 648 38 8 2065 2704 655225131 655224488 0.000000e+00 909.0
22 TraesCS5D01G497600 chr5A 90.647 556 34 10 1 551 655192784 655192242 0.000000e+00 723.0
23 TraesCS5D01G497600 chr5A 90.647 556 34 10 1 551 655227286 655226744 0.000000e+00 723.0
24 TraesCS5D01G497600 chr5A 87.346 648 48 25 2089 2725 654851372 654850748 0.000000e+00 712.0
25 TraesCS5D01G497600 chr5A 83.730 799 80 26 612 1390 655226738 655225970 0.000000e+00 710.0
26 TraesCS5D01G497600 chr5A 93.808 323 14 3 1768 2085 654851791 654851470 7.010000e-132 481.0
27 TraesCS5D01G497600 chr5A 92.749 331 20 3 1755 2083 655189372 655189044 3.260000e-130 475.0
28 TraesCS5D01G497600 chr5A 92.447 331 21 3 1755 2083 655225534 655225206 1.520000e-128 470.0
29 TraesCS5D01G497600 chr5A 84.504 413 34 11 1357 1752 655189808 655189409 7.310000e-102 381.0
30 TraesCS5D01G497600 chr5A 84.504 413 34 11 1357 1752 655225970 655225571 7.310000e-102 381.0
31 TraesCS5D01G497600 chr5A 90.411 219 20 1 1173 1390 655190026 655189808 1.640000e-73 287.0
32 TraesCS5D01G497600 chr5A 83.594 256 32 7 2966 3220 216991447 216991201 7.790000e-57 231.0
33 TraesCS5D01G497600 chr5A 80.738 244 35 9 2972 3212 698891534 698891768 2.860000e-41 180.0
34 TraesCS5D01G497600 chr5A 91.176 102 6 3 2718 2819 655188270 655188172 6.280000e-28 135.0
35 TraesCS5D01G497600 chr5A 91.176 102 6 3 2718 2819 655224432 655224334 6.280000e-28 135.0
36 TraesCS5D01G497600 chr5A 89.873 79 5 3 2741 2819 654849939 654849864 8.240000e-17 99.0
37 TraesCS5D01G497600 chr3B 88.114 774 62 20 2065 2816 2879248 2880013 0.000000e+00 893.0
38 TraesCS5D01G497600 chr3B 86.634 606 45 17 1507 2085 2878579 2879175 3.930000e-179 638.0
39 TraesCS5D01G497600 chr3B 83.776 339 39 10 1038 1370 2878147 2878475 1.260000e-79 307.0
40 TraesCS5D01G497600 chr7D 88.026 618 55 15 2086 2695 401550545 401549939 0.000000e+00 713.0
41 TraesCS5D01G497600 chr7D 93.315 359 21 2 3252 3607 209584752 209584394 8.870000e-146 527.0
42 TraesCS5D01G497600 chr7D 92.758 359 23 2 3252 3607 110218558 110218200 1.920000e-142 516.0
43 TraesCS5D01G497600 chr7D 92.440 291 22 0 1795 2085 401550930 401550640 2.000000e-112 416.0
44 TraesCS5D01G497600 chr7D 86.486 74 7 3 2978 3049 524866034 524866106 1.070000e-10 78.7
45 TraesCS5D01G497600 chr7A 86.230 610 54 19 2083 2669 459209773 459209171 5.080000e-178 634.0
46 TraesCS5D01G497600 chr6D 93.333 360 21 1 3252 3608 465425665 465425306 2.470000e-146 529.0
47 TraesCS5D01G497600 chr6D 86.000 450 36 14 54 496 418300059 418300488 1.180000e-124 457.0
48 TraesCS5D01G497600 chr6D 91.667 48 2 2 564 610 300940726 300940772 8.360000e-07 65.8
49 TraesCS5D01G497600 chr4D 93.333 360 20 2 3252 3608 297111471 297111113 2.470000e-146 529.0
50 TraesCS5D01G497600 chr6B 92.737 358 23 1 3254 3608 673360597 673360240 6.910000e-142 514.0
51 TraesCS5D01G497600 chr6B 84.328 134 13 3 3088 3220 695011087 695011213 1.360000e-24 124.0
52 TraesCS5D01G497600 chr6B 85.567 97 6 6 2964 3056 684786560 684786652 1.070000e-15 95.3
53 TraesCS5D01G497600 chrUn 92.033 364 25 2 3248 3608 214075073 214074711 3.210000e-140 508.0
54 TraesCS5D01G497600 chrUn 91.489 47 3 1 564 610 372396295 372396250 3.010000e-06 63.9
55 TraesCS5D01G497600 chrUn 91.489 47 3 1 564 610 470897580 470897625 3.010000e-06 63.9
56 TraesCS5D01G497600 chrUn 100.000 30 0 0 2963 2992 283527878 283527907 5.030000e-04 56.5
57 TraesCS5D01G497600 chr1D 91.803 366 26 2 3246 3608 472353300 472353664 1.160000e-139 507.0
58 TraesCS5D01G497600 chr2B 89.412 85 8 1 2965 3048 17109475 17109391 4.930000e-19 106.0
59 TraesCS5D01G497600 chr2B 78.676 136 28 1 2963 3097 159851528 159851393 4.960000e-14 89.8
60 TraesCS5D01G497600 chr2B 91.667 48 2 2 564 610 108073417 108073371 8.360000e-07 65.8
61 TraesCS5D01G497600 chr2B 90.000 50 3 2 564 613 801173729 801173682 3.010000e-06 63.9
62 TraesCS5D01G497600 chr4A 97.436 39 1 0 563 601 602090803 602090841 2.320000e-07 67.6
63 TraesCS5D01G497600 chr6A 90.196 51 3 2 563 611 55729372 55729322 8.360000e-07 65.8
64 TraesCS5D01G497600 chr1B 91.667 48 2 2 564 610 619497398 619497444 8.360000e-07 65.8
65 TraesCS5D01G497600 chr1B 90.000 50 4 1 564 613 297337123 297337075 3.010000e-06 63.9


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 TraesCS5D01G497600 chr5D 527840330 527843937 3607 True 6663.000000 6663 100.000000 1 3608 1 chr5D.!!$R1 3607
1 TraesCS5D01G497600 chr5B 664501556 664507008 5452 True 871.200000 1218 92.337400 1 3227 5 chr5B.!!$R4 3226
2 TraesCS5D01G497600 chr5B 664474446 664476028 1582 True 579.333333 900 89.404667 896 2719 3 chr5B.!!$R3 1823
3 TraesCS5D01G497600 chr5B 664416020 664417935 1915 True 462.000000 867 86.976000 493 2719 4 chr5B.!!$R2 2226
4 TraesCS5D01G497600 chr3D 2967530 2969418 1888 True 655.333333 957 88.516333 1022 2816 3 chr3D.!!$R2 1794
5 TraesCS5D01G497600 chr5A 655224334 655227286 2952 True 554.666667 909 89.131333 1 2819 6 chr5A.!!$R4 2818
6 TraesCS5D01G497600 chr5A 655188172 655192784 4612 True 485.000000 909 90.295167 1 2819 6 chr5A.!!$R3 2818
7 TraesCS5D01G497600 chr5A 654849864 654851791 1927 True 430.666667 712 90.342333 1768 2819 3 chr5A.!!$R2 1051
8 TraesCS5D01G497600 chr3B 2878147 2880013 1866 False 612.666667 893 86.174667 1038 2816 3 chr3B.!!$F1 1778
9 TraesCS5D01G497600 chr7D 401549939 401550930 991 True 564.500000 713 90.233000 1795 2695 2 chr7D.!!$R3 900
10 TraesCS5D01G497600 chr7A 459209171 459209773 602 True 634.000000 634 86.230000 2083 2669 1 chr7A.!!$R1 586

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
715 748 0.321671 CCTTCAGGAACCTCTCGCAA 59.678 55.0 0.0 0.0 37.39 4.85 F
1338 3046 0.436913 CACGCGCGTTAGATTGTTGA 59.563 50.0 35.9 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2494 4443 0.239347 GCGTTTGAGAACTGCAGCAT 59.761 50.0 15.27 2.22 36.23 3.79 R
2787 5548 0.031585 TCTTCCGAACACACGTCCAG 59.968 55.0 0.00 0.00 0.00 3.86 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 22 2.711542 CCCGATCTACCAGCTTTTGTT 58.288 47.619 0.00 0.00 0.00 2.83
21 23 3.869065 CCCGATCTACCAGCTTTTGTTA 58.131 45.455 0.00 0.00 0.00 2.41
118 120 2.485122 GCCCCGTCGCTTCAATTG 59.515 61.111 0.00 0.00 0.00 2.32
134 136 2.593468 ATTGGGCCGTCGATGGTCTG 62.593 60.000 26.63 1.12 32.87 3.51
146 148 4.344865 GGTCTGGGAAGCCGCCAA 62.345 66.667 0.00 0.00 0.00 4.52
170 181 4.840005 CGCTCCTTCCCGGCCTTC 62.840 72.222 0.00 0.00 0.00 3.46
171 182 4.491409 GCTCCTTCCCGGCCTTCC 62.491 72.222 0.00 0.00 0.00 3.46
172 183 2.689034 CTCCTTCCCGGCCTTCCT 60.689 66.667 0.00 0.00 0.00 3.36
173 184 2.687566 TCCTTCCCGGCCTTCCTC 60.688 66.667 0.00 0.00 0.00 3.71
174 185 3.798511 CCTTCCCGGCCTTCCTCC 61.799 72.222 0.00 0.00 0.00 4.30
175 186 4.162690 CTTCCCGGCCTTCCTCCG 62.163 72.222 0.00 0.00 46.05 4.63
187 198 3.839432 CCTCCGCCTCCTTCCGTC 61.839 72.222 0.00 0.00 0.00 4.79
275 288 4.457496 CGCTGCTGGTCCGGTCAT 62.457 66.667 0.00 0.00 0.00 3.06
367 381 1.048601 ACTCGTGCCCTATATGGTGG 58.951 55.000 0.00 0.00 0.00 4.61
383 397 2.230025 TGGTGGCCAATTTTACATCACG 59.770 45.455 7.24 0.00 0.00 4.35
476 492 3.756082 TTGAGTCCTATTTTGGGGCAT 57.244 42.857 0.00 0.00 0.00 4.40
566 582 7.222611 ACATAAAAATGTTGTGCTCAAGAACAC 59.777 33.333 0.50 0.00 32.21 3.32
568 584 4.924305 AATGTTGTGCTCAAGAACACAT 57.076 36.364 7.08 0.00 45.59 3.21
569 585 3.696281 TGTTGTGCTCAAGAACACATG 57.304 42.857 7.08 0.00 45.59 3.21
570 586 3.016031 TGTTGTGCTCAAGAACACATGT 58.984 40.909 7.08 0.00 45.59 3.21
572 588 1.948834 TGTGCTCAAGAACACATGTGG 59.051 47.619 28.64 11.40 41.67 4.17
573 589 1.949525 GTGCTCAAGAACACATGTGGT 59.050 47.619 28.64 24.25 36.77 4.16
574 590 3.138304 GTGCTCAAGAACACATGTGGTA 58.862 45.455 28.64 7.36 36.77 3.25
577 593 3.365364 GCTCAAGAACACATGTGGTAAGC 60.365 47.826 28.64 22.78 34.19 3.09
578 594 3.814625 TCAAGAACACATGTGGTAAGCA 58.185 40.909 28.64 5.91 34.19 3.91
579 595 4.203226 TCAAGAACACATGTGGTAAGCAA 58.797 39.130 28.64 6.11 34.19 3.91
580 596 4.826733 TCAAGAACACATGTGGTAAGCAAT 59.173 37.500 28.64 3.06 34.19 3.56
581 597 5.048782 TCAAGAACACATGTGGTAAGCAATC 60.049 40.000 28.64 9.46 34.19 2.67
582 598 3.758554 AGAACACATGTGGTAAGCAATCC 59.241 43.478 28.64 8.72 34.19 3.01
583 599 3.153369 ACACATGTGGTAAGCAATCCA 57.847 42.857 28.64 0.00 34.19 3.41
584 600 3.495331 ACACATGTGGTAAGCAATCCAA 58.505 40.909 28.64 0.00 35.38 3.53
585 601 3.894427 ACACATGTGGTAAGCAATCCAAA 59.106 39.130 28.64 0.00 35.38 3.28
586 602 4.236935 CACATGTGGTAAGCAATCCAAAC 58.763 43.478 18.51 0.00 35.38 2.93
587 603 3.894427 ACATGTGGTAAGCAATCCAAACA 59.106 39.130 0.00 0.00 35.38 2.83
588 604 4.343526 ACATGTGGTAAGCAATCCAAACAA 59.656 37.500 0.00 0.00 35.38 2.83
589 605 5.011943 ACATGTGGTAAGCAATCCAAACAAT 59.988 36.000 0.00 0.00 35.38 2.71
590 606 5.543507 TGTGGTAAGCAATCCAAACAATT 57.456 34.783 0.00 0.00 35.38 2.32
591 607 6.656632 TGTGGTAAGCAATCCAAACAATTA 57.343 33.333 0.00 0.00 35.38 1.40
592 608 7.055667 TGTGGTAAGCAATCCAAACAATTAA 57.944 32.000 0.00 0.00 35.38 1.40
593 609 7.500992 TGTGGTAAGCAATCCAAACAATTAAA 58.499 30.769 0.00 0.00 35.38 1.52
594 610 7.987458 TGTGGTAAGCAATCCAAACAATTAAAA 59.013 29.630 0.00 0.00 35.38 1.52
595 611 8.831550 GTGGTAAGCAATCCAAACAATTAAAAA 58.168 29.630 0.00 0.00 35.38 1.94
661 686 0.831307 GGTCGGCCAGTCTAAAGGAT 59.169 55.000 0.00 0.00 34.09 3.24
703 736 7.814264 ATATAGTCAAGCAAAATCCTTCAGG 57.186 36.000 0.00 0.00 0.00 3.86
713 746 2.277858 TCCTTCAGGAACCTCTCGC 58.722 57.895 0.00 0.00 42.18 5.03
714 747 0.541998 TCCTTCAGGAACCTCTCGCA 60.542 55.000 0.00 0.00 42.18 5.10
715 748 0.321671 CCTTCAGGAACCTCTCGCAA 59.678 55.000 0.00 0.00 37.39 4.85
716 749 1.270839 CCTTCAGGAACCTCTCGCAAA 60.271 52.381 0.00 0.00 37.39 3.68
717 750 2.494059 CTTCAGGAACCTCTCGCAAAA 58.506 47.619 0.00 0.00 0.00 2.44
718 751 2.631160 TCAGGAACCTCTCGCAAAAA 57.369 45.000 0.00 0.00 0.00 1.94
837 2422 6.764877 ATTGAATACTAGCGGATTGTAACG 57.235 37.500 0.00 0.00 0.00 3.18
926 2511 2.282462 CGCCAAGCCAAACCTCCT 60.282 61.111 0.00 0.00 0.00 3.69
978 2569 4.033709 TCCCAACTTCCAATCCAACAAAA 58.966 39.130 0.00 0.00 0.00 2.44
1114 2730 2.736719 CGGTGAGATGCTGATCGACTTT 60.737 50.000 0.00 0.00 33.34 2.66
1204 2879 2.970324 AACGTCGCATGTGCCGTT 60.970 55.556 21.02 21.02 41.55 4.44
1255 2940 0.940126 GCAAGGTACGCATGGATCAG 59.060 55.000 0.00 0.00 0.00 2.90
1265 2950 2.058001 ATGGATCAGTCGCCGTCCA 61.058 57.895 0.00 0.00 44.22 4.02
1277 2962 1.151668 GCCGTCCATGATAGCACATC 58.848 55.000 0.00 0.00 0.00 3.06
1338 3046 0.436913 CACGCGCGTTAGATTGTTGA 59.563 50.000 35.90 0.00 0.00 3.18
1346 3054 4.565166 CGCGTTAGATTGTTGATTGGTAGA 59.435 41.667 0.00 0.00 0.00 2.59
1458 3203 5.784750 TGACTTACGATTGCTGATTCTTG 57.215 39.130 0.00 0.00 0.00 3.02
1464 3209 8.391106 ACTTACGATTGCTGATTCTTGTTTATC 58.609 33.333 0.00 0.00 0.00 1.75
1485 3240 2.993899 CAGTAGTGTCACGATTTGGTCC 59.006 50.000 0.00 0.00 0.00 4.46
1488 3243 1.420138 AGTGTCACGATTTGGTCCCTT 59.580 47.619 0.00 0.00 0.00 3.95
1601 3372 8.051535 AGTCATTGATCAGTCCAAATCTAACAT 58.948 33.333 0.00 0.00 0.00 2.71
1766 3575 4.880120 TCGTCTAGACTATACACACCCTTG 59.120 45.833 20.34 0.25 0.00 3.61
1785 3594 6.151985 ACCCTTGTCGCATATGAAATTGTAAA 59.848 34.615 6.97 0.00 0.00 2.01
2018 3834 1.186200 CTCAACCTCGACCTCATCCA 58.814 55.000 0.00 0.00 0.00 3.41
2435 4377 6.441093 TCAATTCCATTATGACTTGTGAGC 57.559 37.500 0.00 0.00 0.00 4.26
2494 4443 1.992277 GAGGCCAAGCTGAGGGAGA 60.992 63.158 5.01 0.00 0.00 3.71
2677 4636 9.520515 TTAGCTCCATTTTTATTAGGGATGATC 57.479 33.333 0.00 0.00 0.00 2.92
2787 5548 8.445493 CAAAAATTTATCAGAACCTTGAATGCC 58.555 33.333 0.00 0.00 0.00 4.40
2932 6408 3.495193 CTGTGAATGCTGTCAAAATCCG 58.505 45.455 0.00 0.00 0.00 4.18
2983 6460 1.870402 GGGGCCAATTTTCGTGTTTTG 59.130 47.619 4.39 0.00 0.00 2.44
3006 6483 5.702209 TGACCCTTTTACTAAAGTTTAGCCG 59.298 40.000 20.31 6.45 39.29 5.52
3010 6487 6.037940 CCCTTTTACTAAAGTTTAGCCGGATC 59.962 42.308 20.31 0.00 39.29 3.36
3016 6493 1.867363 AGTTTAGCCGGATCTGACCT 58.133 50.000 5.05 1.53 0.00 3.85
3017 6494 1.757699 AGTTTAGCCGGATCTGACCTC 59.242 52.381 5.05 0.00 0.00 3.85
3018 6495 1.480954 GTTTAGCCGGATCTGACCTCA 59.519 52.381 5.05 0.00 0.00 3.86
3019 6496 2.088104 TTAGCCGGATCTGACCTCAT 57.912 50.000 5.05 0.00 0.00 2.90
3021 6498 1.118356 AGCCGGATCTGACCTCATCC 61.118 60.000 5.05 0.00 36.01 3.51
3025 6502 2.105477 CCGGATCTGACCTCATCCAAAT 59.895 50.000 2.08 0.00 38.92 2.32
3026 6503 3.434167 CCGGATCTGACCTCATCCAAATT 60.434 47.826 2.08 0.00 38.92 1.82
3027 6504 4.202441 CGGATCTGACCTCATCCAAATTT 58.798 43.478 0.00 0.00 38.92 1.82
3028 6505 4.641989 CGGATCTGACCTCATCCAAATTTT 59.358 41.667 0.00 0.00 38.92 1.82
3029 6506 5.126061 CGGATCTGACCTCATCCAAATTTTT 59.874 40.000 0.00 0.00 38.92 1.94
3054 6531 3.718956 CAGGATCTGACCCTTTTCCCTAT 59.281 47.826 0.00 0.00 32.44 2.57
3057 6534 4.352298 GGATCTGACCCTTTTCCCTATCAT 59.648 45.833 0.00 0.00 0.00 2.45
3058 6535 5.163045 GGATCTGACCCTTTTCCCTATCATT 60.163 44.000 0.00 0.00 0.00 2.57
3111 6588 1.995484 CGCCATGATCAATAGCGGTAG 59.005 52.381 22.47 5.91 42.93 3.18
3121 6598 5.592104 TCAATAGCGGTAGAAGTTGATCA 57.408 39.130 0.00 0.00 0.00 2.92
3134 6611 5.945155 GAAGTTGATCAACGTCTAGAGTCT 58.055 41.667 33.62 13.60 45.50 3.24
3198 6675 3.396260 GCGGTAGCCTTCAATACCATA 57.604 47.619 2.61 0.00 41.35 2.74
3202 6679 2.256117 AGCCTTCAATACCATACCGC 57.744 50.000 0.00 0.00 0.00 5.68
3213 6690 0.957395 CCATACCGCCATGGCATCTC 60.957 60.000 34.93 6.90 43.94 2.75
3215 6692 1.471829 ATACCGCCATGGCATCTCGA 61.472 55.000 34.93 14.57 43.94 4.04
3220 6697 0.322975 GCCATGGCATCTCGAGGTAT 59.677 55.000 32.08 0.00 41.49 2.73
3222 6699 1.066573 CCATGGCATCTCGAGGTATCC 60.067 57.143 13.56 10.74 0.00 2.59
3234 6711 3.974871 GAGGTATCCTCTTGACTCGTC 57.025 52.381 8.38 0.00 46.41 4.20
3235 6712 2.619646 GAGGTATCCTCTTGACTCGTCC 59.380 54.545 8.38 0.00 46.41 4.79
3236 6713 1.682323 GGTATCCTCTTGACTCGTCCC 59.318 57.143 0.00 0.00 0.00 4.46
3237 6714 1.334243 GTATCCTCTTGACTCGTCCCG 59.666 57.143 0.00 0.00 0.00 5.14
3238 6715 0.323542 ATCCTCTTGACTCGTCCCGT 60.324 55.000 0.00 0.00 0.00 5.28
3239 6716 0.325933 TCCTCTTGACTCGTCCCGTA 59.674 55.000 0.00 0.00 0.00 4.02
3240 6717 1.064906 TCCTCTTGACTCGTCCCGTAT 60.065 52.381 0.00 0.00 0.00 3.06
3241 6718 1.334243 CCTCTTGACTCGTCCCGTATC 59.666 57.143 0.00 0.00 0.00 2.24
3242 6719 1.334243 CTCTTGACTCGTCCCGTATCC 59.666 57.143 0.00 0.00 0.00 2.59
3243 6720 1.064906 TCTTGACTCGTCCCGTATCCT 60.065 52.381 0.00 0.00 0.00 3.24
3244 6721 1.334243 CTTGACTCGTCCCGTATCCTC 59.666 57.143 0.00 0.00 0.00 3.71
3245 6722 0.465097 TGACTCGTCCCGTATCCTCC 60.465 60.000 0.00 0.00 0.00 4.30
3246 6723 0.179023 GACTCGTCCCGTATCCTCCT 60.179 60.000 0.00 0.00 0.00 3.69
3247 6724 0.465824 ACTCGTCCCGTATCCTCCTG 60.466 60.000 0.00 0.00 0.00 3.86
3248 6725 0.465824 CTCGTCCCGTATCCTCCTGT 60.466 60.000 0.00 0.00 0.00 4.00
3249 6726 0.750546 TCGTCCCGTATCCTCCTGTG 60.751 60.000 0.00 0.00 0.00 3.66
3250 6727 1.035932 CGTCCCGTATCCTCCTGTGT 61.036 60.000 0.00 0.00 0.00 3.72
3251 6728 0.460311 GTCCCGTATCCTCCTGTGTG 59.540 60.000 0.00 0.00 0.00 3.82
3252 6729 0.686441 TCCCGTATCCTCCTGTGTGG 60.686 60.000 0.00 0.00 37.10 4.17
3253 6730 0.686441 CCCGTATCCTCCTGTGTGGA 60.686 60.000 0.00 0.00 43.86 4.02
3254 6731 1.191535 CCGTATCCTCCTGTGTGGAA 58.808 55.000 0.00 0.00 45.63 3.53
3255 6732 1.134788 CCGTATCCTCCTGTGTGGAAC 60.135 57.143 0.00 0.00 45.63 3.62
3256 6733 1.134788 CGTATCCTCCTGTGTGGAACC 60.135 57.143 0.00 0.00 45.63 3.62
3257 6734 1.209747 GTATCCTCCTGTGTGGAACCC 59.790 57.143 0.00 0.00 45.63 4.11
3258 6735 0.178861 ATCCTCCTGTGTGGAACCCT 60.179 55.000 0.00 0.00 45.63 4.34
3259 6736 0.490017 TCCTCCTGTGTGGAACCCTA 59.510 55.000 0.00 0.00 45.63 3.53
3260 6737 0.905357 CCTCCTGTGTGGAACCCTAG 59.095 60.000 0.00 0.00 45.63 3.02
3261 6738 0.250513 CTCCTGTGTGGAACCCTAGC 59.749 60.000 0.00 0.00 45.63 3.42
3262 6739 1.079127 CCTGTGTGGAACCCTAGCG 60.079 63.158 0.00 0.00 38.35 4.26
3263 6740 1.741770 CTGTGTGGAACCCTAGCGC 60.742 63.158 0.00 0.00 34.36 5.92
3264 6741 2.436115 GTGTGGAACCCTAGCGCC 60.436 66.667 2.29 0.00 34.36 6.53
3265 6742 4.077184 TGTGGAACCCTAGCGCCG 62.077 66.667 2.29 0.00 34.36 6.46
3286 6763 4.444081 CGTCCTCGTCCCTCCCCT 62.444 72.222 0.00 0.00 0.00 4.79
3287 6764 2.760385 GTCCTCGTCCCTCCCCTG 60.760 72.222 0.00 0.00 0.00 4.45
3288 6765 2.944954 TCCTCGTCCCTCCCCTGA 60.945 66.667 0.00 0.00 0.00 3.86
3289 6766 2.760385 CCTCGTCCCTCCCCTGAC 60.760 72.222 0.00 0.00 0.00 3.51
3290 6767 2.037367 CTCGTCCCTCCCCTGACA 59.963 66.667 0.00 0.00 0.00 3.58
3291 6768 1.381872 CTCGTCCCTCCCCTGACAT 60.382 63.158 0.00 0.00 0.00 3.06
3292 6769 1.381327 TCGTCCCTCCCCTGACATC 60.381 63.158 0.00 0.00 0.00 3.06
3293 6770 1.381872 CGTCCCTCCCCTGACATCT 60.382 63.158 0.00 0.00 0.00 2.90
3294 6771 1.395826 CGTCCCTCCCCTGACATCTC 61.396 65.000 0.00 0.00 0.00 2.75
3295 6772 1.051556 GTCCCTCCCCTGACATCTCC 61.052 65.000 0.00 0.00 0.00 3.71
3296 6773 1.231751 TCCCTCCCCTGACATCTCCT 61.232 60.000 0.00 0.00 0.00 3.69
3297 6774 0.762461 CCCTCCCCTGACATCTCCTC 60.762 65.000 0.00 0.00 0.00 3.71
3298 6775 0.762461 CCTCCCCTGACATCTCCTCC 60.762 65.000 0.00 0.00 0.00 4.30
3299 6776 0.264359 CTCCCCTGACATCTCCTCCT 59.736 60.000 0.00 0.00 0.00 3.69
3300 6777 0.263172 TCCCCTGACATCTCCTCCTC 59.737 60.000 0.00 0.00 0.00 3.71
3301 6778 1.112315 CCCCTGACATCTCCTCCTCG 61.112 65.000 0.00 0.00 0.00 4.63
3302 6779 1.739049 CCTGACATCTCCTCCTCGC 59.261 63.158 0.00 0.00 0.00 5.03
3303 6780 1.739049 CTGACATCTCCTCCTCGCC 59.261 63.158 0.00 0.00 0.00 5.54
3304 6781 2.069465 CTGACATCTCCTCCTCGCCG 62.069 65.000 0.00 0.00 0.00 6.46
3305 6782 3.492311 GACATCTCCTCCTCGCCGC 62.492 68.421 0.00 0.00 0.00 6.53
3306 6783 4.292178 CATCTCCTCCTCGCCGCC 62.292 72.222 0.00 0.00 0.00 6.13
3360 6837 4.951963 CGGCGGCGGGATCTCTTC 62.952 72.222 25.36 0.00 0.00 2.87
3361 6838 3.541713 GGCGGCGGGATCTCTTCT 61.542 66.667 9.78 0.00 0.00 2.85
3362 6839 2.028337 GCGGCGGGATCTCTTCTC 59.972 66.667 9.78 0.00 0.00 2.87
3363 6840 2.731374 CGGCGGGATCTCTTCTCC 59.269 66.667 0.00 0.00 0.00 3.71
3370 6847 1.770294 GGATCTCTTCTCCCACGACT 58.230 55.000 0.00 0.00 0.00 4.18
3371 6848 1.679153 GGATCTCTTCTCCCACGACTC 59.321 57.143 0.00 0.00 0.00 3.36
3372 6849 1.332375 GATCTCTTCTCCCACGACTCG 59.668 57.143 0.00 0.00 0.00 4.18
3373 6850 1.137825 CTCTTCTCCCACGACTCGC 59.862 63.158 0.00 0.00 0.00 5.03
3374 6851 1.303398 TCTTCTCCCACGACTCGCT 60.303 57.895 0.00 0.00 0.00 4.93
3375 6852 1.153939 CTTCTCCCACGACTCGCTG 60.154 63.158 0.00 0.00 0.00 5.18
3376 6853 2.549611 CTTCTCCCACGACTCGCTGG 62.550 65.000 11.13 11.13 0.00 4.85
3377 6854 3.062466 CTCCCACGACTCGCTGGA 61.062 66.667 16.87 13.04 32.71 3.86
3378 6855 2.362503 TCCCACGACTCGCTGGAT 60.363 61.111 16.87 0.00 32.71 3.41
3379 6856 1.949847 CTCCCACGACTCGCTGGATT 61.950 60.000 16.87 0.00 32.71 3.01
3380 6857 1.079127 CCCACGACTCGCTGGATTT 60.079 57.895 16.87 0.00 32.71 2.17
3381 6858 1.361668 CCCACGACTCGCTGGATTTG 61.362 60.000 16.87 0.28 32.71 2.32
3382 6859 1.361668 CCACGACTCGCTGGATTTGG 61.362 60.000 12.21 1.91 32.71 3.28
3383 6860 1.741770 ACGACTCGCTGGATTTGGC 60.742 57.895 0.00 0.00 0.00 4.52
3405 6882 2.890474 GCGGATCGCGATGGTTGT 60.890 61.111 29.09 0.38 44.55 3.32
3406 6883 2.461110 GCGGATCGCGATGGTTGTT 61.461 57.895 29.09 0.00 44.55 2.83
3407 6884 1.348250 CGGATCGCGATGGTTGTTG 59.652 57.895 29.09 3.92 0.00 3.33
3408 6885 1.721487 GGATCGCGATGGTTGTTGG 59.279 57.895 29.09 0.00 0.00 3.77
3409 6886 1.062525 GATCGCGATGGTTGTTGGC 59.937 57.895 29.09 4.43 0.00 4.52
3411 6888 4.459331 CGCGATGGTTGTTGGCGG 62.459 66.667 0.00 0.00 42.86 6.13
3412 6889 4.776647 GCGATGGTTGTTGGCGGC 62.777 66.667 0.00 0.00 0.00 6.53
3413 6890 4.459331 CGATGGTTGTTGGCGGCG 62.459 66.667 0.51 0.51 0.00 6.46
3414 6891 4.776647 GATGGTTGTTGGCGGCGC 62.777 66.667 26.17 26.17 0.00 6.53
3477 6954 4.135493 GCTCACGCTCGCGGTTTC 62.135 66.667 16.18 0.00 44.69 2.78
3478 6955 3.479269 CTCACGCTCGCGGTTTCC 61.479 66.667 16.18 0.00 44.69 3.13
3484 6961 4.016706 CTCGCGGTTTCCCCTGGT 62.017 66.667 6.13 0.00 0.00 4.00
3485 6962 4.323477 TCGCGGTTTCCCCTGGTG 62.323 66.667 6.13 0.00 0.00 4.17
3486 6963 4.636435 CGCGGTTTCCCCTGGTGT 62.636 66.667 0.00 0.00 0.00 4.16
3487 6964 2.983592 GCGGTTTCCCCTGGTGTG 60.984 66.667 0.00 0.00 0.00 3.82
3488 6965 2.983592 CGGTTTCCCCTGGTGTGC 60.984 66.667 0.00 0.00 0.00 4.57
3489 6966 2.197324 GGTTTCCCCTGGTGTGCA 59.803 61.111 0.00 0.00 0.00 4.57
3490 6967 1.228862 GGTTTCCCCTGGTGTGCAT 60.229 57.895 0.00 0.00 0.00 3.96
3491 6968 1.535204 GGTTTCCCCTGGTGTGCATG 61.535 60.000 0.00 0.00 0.00 4.06
3492 6969 1.228831 TTTCCCCTGGTGTGCATGG 60.229 57.895 0.00 0.00 0.00 3.66
3493 6970 2.728460 TTTCCCCTGGTGTGCATGGG 62.728 60.000 0.00 0.00 39.37 4.00
3494 6971 3.660571 CCCCTGGTGTGCATGGGA 61.661 66.667 11.53 0.00 42.11 4.37
3495 6972 2.044650 CCCTGGTGTGCATGGGAG 60.045 66.667 0.00 0.00 42.11 4.30
3496 6973 2.759114 CCTGGTGTGCATGGGAGT 59.241 61.111 0.00 0.00 0.00 3.85
3497 6974 1.377725 CCTGGTGTGCATGGGAGTC 60.378 63.158 0.00 0.00 0.00 3.36
3498 6975 1.377725 CTGGTGTGCATGGGAGTCC 60.378 63.158 0.00 0.00 0.00 3.85
3499 6976 2.436646 GGTGTGCATGGGAGTCCG 60.437 66.667 2.26 0.00 35.24 4.79
3500 6977 3.127533 GTGTGCATGGGAGTCCGC 61.128 66.667 2.26 1.47 35.24 5.54
3501 6978 3.321648 TGTGCATGGGAGTCCGCT 61.322 61.111 2.26 0.00 35.24 5.52
3502 6979 2.512515 GTGCATGGGAGTCCGCTC 60.513 66.667 2.26 0.00 40.93 5.03
3503 6980 4.147449 TGCATGGGAGTCCGCTCG 62.147 66.667 2.26 0.00 42.53 5.03
3504 6981 4.899239 GCATGGGAGTCCGCTCGG 62.899 72.222 2.26 1.14 42.53 4.63
3505 6982 4.227134 CATGGGAGTCCGCTCGGG 62.227 72.222 8.59 0.00 42.53 5.14
3598 7075 4.626081 GTGGTCCCTGTGCGCAGT 62.626 66.667 24.85 0.00 41.02 4.40
3599 7076 3.872603 TGGTCCCTGTGCGCAGTT 61.873 61.111 24.85 0.00 41.02 3.16
3600 7077 3.357079 GGTCCCTGTGCGCAGTTG 61.357 66.667 24.85 15.77 41.02 3.16
3601 7078 3.357079 GTCCCTGTGCGCAGTTGG 61.357 66.667 24.85 19.35 41.02 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
118 120 4.530857 CCAGACCATCGACGGCCC 62.531 72.222 0.00 0.00 0.00 5.80
155 166 2.689034 AGGAAGGCCGGGAAGGAG 60.689 66.667 2.18 0.00 45.00 3.69
156 167 2.687566 GAGGAAGGCCGGGAAGGA 60.688 66.667 2.18 0.00 45.00 3.36
157 168 3.798511 GGAGGAAGGCCGGGAAGG 61.799 72.222 2.18 0.00 44.97 3.46
158 169 4.162690 CGGAGGAAGGCCGGGAAG 62.163 72.222 2.18 0.00 44.87 3.46
165 176 3.393149 GAAGGAGGCGGAGGAAGGC 62.393 68.421 0.00 0.00 0.00 4.35
166 177 2.736826 GGAAGGAGGCGGAGGAAGG 61.737 68.421 0.00 0.00 0.00 3.46
167 178 2.904131 GGAAGGAGGCGGAGGAAG 59.096 66.667 0.00 0.00 0.00 3.46
168 179 3.075005 CGGAAGGAGGCGGAGGAA 61.075 66.667 0.00 0.00 0.00 3.36
169 180 4.377760 ACGGAAGGAGGCGGAGGA 62.378 66.667 0.00 0.00 0.00 3.71
170 181 3.839432 GACGGAAGGAGGCGGAGG 61.839 72.222 0.00 0.00 0.00 4.30
171 182 3.839432 GGACGGAAGGAGGCGGAG 61.839 72.222 0.00 0.00 0.00 4.63
195 208 2.182842 GGCATGGTCGACCTGATGC 61.183 63.158 35.17 35.17 41.85 3.91
201 214 2.813908 GTGACGGCATGGTCGACC 60.814 66.667 28.17 28.17 39.83 4.79
261 274 1.561769 ATGGAATGACCGGACCAGCA 61.562 55.000 9.46 0.00 42.61 4.41
367 381 3.672867 CCAACACGTGATGTAAAATTGGC 59.327 43.478 25.01 0.00 42.31 4.52
383 397 3.550030 CCGAAAGTGTCCAATTCCAACAC 60.550 47.826 6.46 6.46 42.80 3.32
408 422 5.692613 TCACCAAATACGTGTTTTTAGGG 57.307 39.130 7.63 8.68 32.86 3.53
476 492 3.636679 AGCTTAGAGCATCACCAGTAGA 58.363 45.455 2.47 0.00 45.56 2.59
566 582 4.517952 TGTTTGGATTGCTTACCACATG 57.482 40.909 0.00 0.00 35.81 3.21
568 584 5.543507 AATTGTTTGGATTGCTTACCACA 57.456 34.783 0.00 0.00 35.81 4.17
569 585 7.954788 TTTAATTGTTTGGATTGCTTACCAC 57.045 32.000 0.00 0.00 35.81 4.16
570 586 8.964476 TTTTTAATTGTTTGGATTGCTTACCA 57.036 26.923 0.00 0.00 0.00 3.25
594 610 7.944554 TCTGATGGTTCTTTATGGAGTCTTTTT 59.055 33.333 0.00 0.00 0.00 1.94
595 611 7.461749 TCTGATGGTTCTTTATGGAGTCTTTT 58.538 34.615 0.00 0.00 0.00 2.27
596 612 7.020827 TCTGATGGTTCTTTATGGAGTCTTT 57.979 36.000 0.00 0.00 0.00 2.52
597 613 6.627087 TCTGATGGTTCTTTATGGAGTCTT 57.373 37.500 0.00 0.00 0.00 3.01
598 614 6.385176 TCATCTGATGGTTCTTTATGGAGTCT 59.615 38.462 17.06 0.00 0.00 3.24
725 758 3.502123 AATTGTTCGGTTCCTGAAGGA 57.498 42.857 0.00 0.00 43.73 3.36
726 759 3.439129 GGTAATTGTTCGGTTCCTGAAGG 59.561 47.826 0.00 0.00 0.00 3.46
727 760 3.439129 GGGTAATTGTTCGGTTCCTGAAG 59.561 47.826 0.00 0.00 0.00 3.02
728 761 3.181442 TGGGTAATTGTTCGGTTCCTGAA 60.181 43.478 0.00 0.00 0.00 3.02
729 762 2.372504 TGGGTAATTGTTCGGTTCCTGA 59.627 45.455 0.00 0.00 0.00 3.86
730 763 2.785562 TGGGTAATTGTTCGGTTCCTG 58.214 47.619 0.00 0.00 0.00 3.86
731 764 3.352648 CATGGGTAATTGTTCGGTTCCT 58.647 45.455 0.00 0.00 0.00 3.36
819 2404 2.298163 CCCCGTTACAATCCGCTAGTAT 59.702 50.000 0.00 0.00 0.00 2.12
837 2422 5.270794 AGTTATCGATCTTATCCTACCCCC 58.729 45.833 0.00 0.00 0.00 5.40
978 2569 2.056906 GCCGGGGATGATAGGTGCTT 62.057 60.000 2.18 0.00 0.00 3.91
1071 2687 4.612412 AAACGACGAAGCCGGGCA 62.612 61.111 23.09 0.00 40.78 5.36
1204 2879 4.760047 GAGCCGCCGAGCTTGGAA 62.760 66.667 25.25 0.00 45.15 3.53
1255 2940 1.067416 TGCTATCATGGACGGCGAC 59.933 57.895 16.62 7.58 0.00 5.19
1265 2950 5.251005 AGGGAGAATCATGATGTGCTATCAT 59.749 40.000 9.46 10.12 39.16 2.45
1277 2962 2.295885 GCAAGGACAGGGAGAATCATG 58.704 52.381 0.00 0.00 36.25 3.07
1320 3027 1.355971 ATCAACAATCTAACGCGCGT 58.644 45.000 32.73 32.73 0.00 6.01
1338 3046 6.518706 GCATGATCAGATCAGAGTCTACCAAT 60.519 42.308 18.13 0.00 43.53 3.16
1346 3054 2.314246 TCGGCATGATCAGATCAGAGT 58.686 47.619 18.13 0.00 43.53 3.24
1401 3142 1.208776 TCGTCTAGTGAGGATCGGACA 59.791 52.381 0.00 0.00 38.61 4.02
1402 3143 1.950828 TCGTCTAGTGAGGATCGGAC 58.049 55.000 0.00 0.00 38.61 4.79
1404 3145 2.482336 CTCATCGTCTAGTGAGGATCGG 59.518 54.545 1.07 0.00 43.42 4.18
1405 3146 3.394719 TCTCATCGTCTAGTGAGGATCG 58.605 50.000 7.92 0.00 43.42 3.69
1458 3203 6.367969 ACCAAATCGTGACACTACTGATAAAC 59.632 38.462 3.68 0.00 0.00 2.01
1464 3209 2.993899 GGACCAAATCGTGACACTACTG 59.006 50.000 3.68 0.00 0.00 2.74
1601 3372 7.575414 TGCTTTTGTGTTAAGAGTGGATTAA 57.425 32.000 0.00 0.00 0.00 1.40
1682 3456 6.706295 TGATTGCACCGACCATATGAATATA 58.294 36.000 3.65 0.00 0.00 0.86
1683 3457 5.559770 TGATTGCACCGACCATATGAATAT 58.440 37.500 3.65 0.00 0.00 1.28
1728 3503 7.976826 AGTCTAGACGAGAAATAACTACTGTG 58.023 38.462 17.07 0.00 35.37 3.66
1766 3575 6.655062 TCCGATTTACAATTTCATATGCGAC 58.345 36.000 0.00 0.00 0.00 5.19
1974 3790 1.893062 CTCGGTGAGGAGCATGTCA 59.107 57.895 0.00 0.00 0.00 3.58
2435 4377 7.935338 AAGAAAACAACATCATTAGCAACTG 57.065 32.000 0.00 0.00 0.00 3.16
2494 4443 0.239347 GCGTTTGAGAACTGCAGCAT 59.761 50.000 15.27 2.22 36.23 3.79
2632 4585 4.093556 GCTAAACTCTCCCAAGATTCAACG 59.906 45.833 0.00 0.00 0.00 4.10
2677 4636 4.056050 ACTGGCACACGAACTAAACTTAG 58.944 43.478 0.00 0.00 36.82 2.18
2787 5548 0.031585 TCTTCCGAACACACGTCCAG 59.968 55.000 0.00 0.00 0.00 3.86
2975 6452 6.788243 ACTTTAGTAAAAGGGTCAAAACACG 58.212 36.000 0.00 0.00 45.39 4.49
2983 6460 5.122869 CCGGCTAAACTTTAGTAAAAGGGTC 59.877 44.000 9.77 0.00 45.39 4.46
3006 6483 6.535963 AAAAATTTGGATGAGGTCAGATCC 57.464 37.500 0.00 0.00 38.98 3.36
3027 6504 4.832823 GGAAAAGGGTCAGATCCTGAAAAA 59.167 41.667 1.77 0.00 42.46 1.94
3028 6505 4.407365 GGAAAAGGGTCAGATCCTGAAAA 58.593 43.478 1.77 0.00 42.46 2.29
3029 6506 3.245264 GGGAAAAGGGTCAGATCCTGAAA 60.245 47.826 1.77 0.00 42.46 2.69
3049 6526 4.991056 CCGTCACAGACAATAATGATAGGG 59.009 45.833 0.00 0.00 32.09 3.53
3054 6531 4.142026 CCCTACCGTCACAGACAATAATGA 60.142 45.833 0.00 0.00 32.09 2.57
3057 6534 3.167485 ACCCTACCGTCACAGACAATAA 58.833 45.455 0.00 0.00 32.09 1.40
3058 6535 2.811410 ACCCTACCGTCACAGACAATA 58.189 47.619 0.00 0.00 32.09 1.90
3111 6588 5.945155 AGACTCTAGACGTTGATCAACTTC 58.055 41.667 28.58 28.58 39.14 3.01
3128 6605 4.194640 TGTATAAACGCCGTCTAGACTCT 58.805 43.478 20.34 1.68 0.00 3.24
3129 6606 4.542662 TGTATAAACGCCGTCTAGACTC 57.457 45.455 20.34 10.93 0.00 3.36
3130 6607 4.261489 CCATGTATAAACGCCGTCTAGACT 60.261 45.833 20.34 3.41 0.00 3.24
3131 6608 3.979495 CCATGTATAAACGCCGTCTAGAC 59.021 47.826 13.18 13.18 0.00 2.59
3132 6609 3.884693 TCCATGTATAAACGCCGTCTAGA 59.115 43.478 0.00 0.00 0.00 2.43
3133 6610 4.023450 TCTCCATGTATAAACGCCGTCTAG 60.023 45.833 0.00 0.00 0.00 2.43
3134 6611 3.884693 TCTCCATGTATAAACGCCGTCTA 59.115 43.478 0.00 0.00 0.00 2.59
3142 6619 4.989168 CGGTAGGCTTCTCCATGTATAAAC 59.011 45.833 0.00 0.00 37.29 2.01
3179 6656 3.660865 GGTATGGTATTGAAGGCTACCG 58.339 50.000 0.00 0.00 40.28 4.02
3198 6675 3.451556 CTCGAGATGCCATGGCGGT 62.452 63.158 30.87 22.26 45.51 5.68
3202 6679 1.066573 GGATACCTCGAGATGCCATGG 60.067 57.143 15.71 7.63 0.00 3.66
3215 6692 2.657143 GGACGAGTCAAGAGGATACCT 58.343 52.381 5.55 0.00 36.03 3.08
3232 6709 0.460311 CACACAGGAGGATACGGGAC 59.540 60.000 0.00 0.00 46.39 4.46
3233 6710 0.686441 CCACACAGGAGGATACGGGA 60.686 60.000 0.00 0.00 46.39 5.14
3234 6711 0.686441 TCCACACAGGAGGATACGGG 60.686 60.000 0.00 0.00 43.07 5.28
3235 6712 2.896278 TCCACACAGGAGGATACGG 58.104 57.895 0.00 0.00 43.07 4.02
3244 6721 1.079127 CGCTAGGGTTCCACACAGG 60.079 63.158 0.00 0.00 39.47 4.00
3245 6722 1.741770 GCGCTAGGGTTCCACACAG 60.742 63.158 8.77 0.00 0.00 3.66
3246 6723 2.345991 GCGCTAGGGTTCCACACA 59.654 61.111 8.77 0.00 0.00 3.72
3247 6724 2.436115 GGCGCTAGGGTTCCACAC 60.436 66.667 7.64 0.00 0.00 3.82
3248 6725 4.077184 CGGCGCTAGGGTTCCACA 62.077 66.667 7.64 0.00 0.00 4.17
3269 6746 4.444081 AGGGGAGGGACGAGGACG 62.444 72.222 0.00 0.00 45.75 4.79
3270 6747 2.760385 CAGGGGAGGGACGAGGAC 60.760 72.222 0.00 0.00 0.00 3.85
3271 6748 2.944954 TCAGGGGAGGGACGAGGA 60.945 66.667 0.00 0.00 0.00 3.71
3272 6749 2.760385 GTCAGGGGAGGGACGAGG 60.760 72.222 0.00 0.00 0.00 4.63
3273 6750 1.381872 ATGTCAGGGGAGGGACGAG 60.382 63.158 0.00 0.00 36.83 4.18
3274 6751 1.381327 GATGTCAGGGGAGGGACGA 60.381 63.158 0.00 0.00 36.83 4.20
3275 6752 1.381872 AGATGTCAGGGGAGGGACG 60.382 63.158 0.00 0.00 36.83 4.79
3276 6753 1.051556 GGAGATGTCAGGGGAGGGAC 61.052 65.000 0.00 0.00 34.63 4.46
3277 6754 1.231751 AGGAGATGTCAGGGGAGGGA 61.232 60.000 0.00 0.00 0.00 4.20
3278 6755 0.762461 GAGGAGATGTCAGGGGAGGG 60.762 65.000 0.00 0.00 0.00 4.30
3279 6756 0.762461 GGAGGAGATGTCAGGGGAGG 60.762 65.000 0.00 0.00 0.00 4.30
3280 6757 0.264359 AGGAGGAGATGTCAGGGGAG 59.736 60.000 0.00 0.00 0.00 4.30
3281 6758 0.263172 GAGGAGGAGATGTCAGGGGA 59.737 60.000 0.00 0.00 0.00 4.81
3282 6759 1.112315 CGAGGAGGAGATGTCAGGGG 61.112 65.000 0.00 0.00 0.00 4.79
3283 6760 1.743321 GCGAGGAGGAGATGTCAGGG 61.743 65.000 0.00 0.00 0.00 4.45
3284 6761 1.739049 GCGAGGAGGAGATGTCAGG 59.261 63.158 0.00 0.00 0.00 3.86
3285 6762 1.739049 GGCGAGGAGGAGATGTCAG 59.261 63.158 0.00 0.00 0.00 3.51
3286 6763 2.121538 CGGCGAGGAGGAGATGTCA 61.122 63.158 0.00 0.00 0.00 3.58
3287 6764 2.725008 CGGCGAGGAGGAGATGTC 59.275 66.667 0.00 0.00 0.00 3.06
3288 6765 3.532155 GCGGCGAGGAGGAGATGT 61.532 66.667 12.98 0.00 0.00 3.06
3289 6766 4.292178 GGCGGCGAGGAGGAGATG 62.292 72.222 12.98 0.00 0.00 2.90
3343 6820 4.951963 GAAGAGATCCCGCCGCCG 62.952 72.222 0.00 0.00 0.00 6.46
3344 6821 3.507597 GAGAAGAGATCCCGCCGCC 62.508 68.421 0.00 0.00 0.00 6.13
3345 6822 2.028337 GAGAAGAGATCCCGCCGC 59.972 66.667 0.00 0.00 0.00 6.53
3346 6823 2.731374 GGAGAAGAGATCCCGCCG 59.269 66.667 0.00 0.00 0.00 6.46
3347 6824 3.143338 GGGAGAAGAGATCCCGCC 58.857 66.667 0.00 0.00 46.85 6.13
3351 6828 1.679153 GAGTCGTGGGAGAAGAGATCC 59.321 57.143 0.00 0.00 35.99 3.36
3352 6829 1.332375 CGAGTCGTGGGAGAAGAGATC 59.668 57.143 3.82 0.00 0.00 2.75
3353 6830 1.384525 CGAGTCGTGGGAGAAGAGAT 58.615 55.000 3.82 0.00 0.00 2.75
3354 6831 1.306642 GCGAGTCGTGGGAGAAGAGA 61.307 60.000 15.08 0.00 0.00 3.10
3355 6832 1.137825 GCGAGTCGTGGGAGAAGAG 59.862 63.158 15.08 0.00 0.00 2.85
3356 6833 1.303398 AGCGAGTCGTGGGAGAAGA 60.303 57.895 15.08 0.00 0.00 2.87
3357 6834 1.153939 CAGCGAGTCGTGGGAGAAG 60.154 63.158 15.08 0.00 0.00 2.85
3358 6835 2.636412 CCAGCGAGTCGTGGGAGAA 61.636 63.158 20.04 0.00 0.00 2.87
3359 6836 2.838748 ATCCAGCGAGTCGTGGGAGA 62.839 60.000 24.54 12.32 35.53 3.71
3360 6837 1.949847 AATCCAGCGAGTCGTGGGAG 61.950 60.000 24.54 8.17 35.53 4.30
3361 6838 1.541310 AAATCCAGCGAGTCGTGGGA 61.541 55.000 23.32 23.32 36.20 4.37
3362 6839 1.079127 AAATCCAGCGAGTCGTGGG 60.079 57.895 24.43 20.50 34.27 4.61
3363 6840 1.361668 CCAAATCCAGCGAGTCGTGG 61.362 60.000 21.13 21.13 34.87 4.94
3364 6841 1.970917 GCCAAATCCAGCGAGTCGTG 61.971 60.000 15.08 10.81 0.00 4.35
3365 6842 1.741770 GCCAAATCCAGCGAGTCGT 60.742 57.895 15.08 0.00 0.00 4.34
3366 6843 3.093278 GCCAAATCCAGCGAGTCG 58.907 61.111 8.54 8.54 0.00 4.18
3389 6866 1.348250 CAACAACCATCGCGATCCG 59.652 57.895 20.85 14.75 38.61 4.18
3390 6867 1.721487 CCAACAACCATCGCGATCC 59.279 57.895 20.85 0.00 0.00 3.36
3391 6868 1.062525 GCCAACAACCATCGCGATC 59.937 57.895 20.85 0.10 0.00 3.69
3392 6869 2.749865 CGCCAACAACCATCGCGAT 61.750 57.895 17.62 17.62 45.41 4.58
3393 6870 3.418913 CGCCAACAACCATCGCGA 61.419 61.111 13.09 13.09 45.41 5.87
3394 6871 4.459331 CCGCCAACAACCATCGCG 62.459 66.667 0.00 0.00 42.37 5.87
3395 6872 4.776647 GCCGCCAACAACCATCGC 62.777 66.667 0.00 0.00 0.00 4.58
3396 6873 4.459331 CGCCGCCAACAACCATCG 62.459 66.667 0.00 0.00 0.00 3.84
3397 6874 4.776647 GCGCCGCCAACAACCATC 62.777 66.667 0.00 0.00 0.00 3.51
3461 6938 3.479269 GGAAACCGCGAGCGTGAG 61.479 66.667 8.23 3.80 37.81 3.51
3473 6950 1.535204 CCATGCACACCAGGGGAAAC 61.535 60.000 0.00 0.00 41.66 2.78
3474 6951 1.228831 CCATGCACACCAGGGGAAA 60.229 57.895 0.00 0.00 41.66 3.13
3475 6952 2.440147 CCATGCACACCAGGGGAA 59.560 61.111 0.00 0.00 41.66 3.97
3478 6955 2.044650 CTCCCATGCACACCAGGG 60.045 66.667 0.00 0.00 44.92 4.45
3479 6956 1.377725 GACTCCCATGCACACCAGG 60.378 63.158 0.00 0.00 0.00 4.45
3480 6957 1.377725 GGACTCCCATGCACACCAG 60.378 63.158 0.00 0.00 0.00 4.00
3481 6958 2.756400 GGACTCCCATGCACACCA 59.244 61.111 0.00 0.00 0.00 4.17
3482 6959 2.436646 CGGACTCCCATGCACACC 60.437 66.667 0.00 0.00 0.00 4.16
3483 6960 3.127533 GCGGACTCCCATGCACAC 61.128 66.667 0.00 0.00 0.00 3.82
3484 6961 3.315142 GAGCGGACTCCCATGCACA 62.315 63.158 0.00 0.00 36.90 4.57
3485 6962 2.512515 GAGCGGACTCCCATGCAC 60.513 66.667 0.00 0.00 36.90 4.57
3486 6963 4.147449 CGAGCGGACTCCCATGCA 62.147 66.667 0.00 0.00 40.03 3.96
3487 6964 4.899239 CCGAGCGGACTCCCATGC 62.899 72.222 2.00 0.00 40.03 4.06
3488 6965 4.227134 CCCGAGCGGACTCCCATG 62.227 72.222 11.05 0.00 40.03 3.66


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

AutoCloner maintained by Alex Coulton.