Multiple sequence alignment - TraesCS3D01G443100

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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 TraesCS3D01G443100 chr3D 100.000 2597 0 0 1 2597 552732540 552735136 0.000000e+00 4796.0
1 TraesCS3D01G443100 chr3D 86.014 715 62 24 904 1603 552576362 552575671 0.000000e+00 732.0
2 TraesCS3D01G443100 chr3D 87.664 608 70 4 999 1605 552727801 552728404 0.000000e+00 702.0
3 TraesCS3D01G443100 chr3D 93.258 89 6 0 1702 1790 427225831 427225743 5.830000e-27 132.0
4 TraesCS3D01G443100 chr3D 81.560 141 18 6 1826 1960 942069 942207 2.730000e-20 110.0
5 TraesCS3D01G443100 chr3D 80.576 139 18 5 1826 1957 549742768 549742632 5.910000e-17 99.0
6 TraesCS3D01G443100 chr3A 87.512 1073 90 18 565 1603 689002385 689003447 0.000000e+00 1199.0
7 TraesCS3D01G443100 chr3A 86.261 706 78 15 904 1603 688978122 688977430 0.000000e+00 749.0
8 TraesCS3D01G443100 chr3A 87.728 603 65 8 999 1597 688898994 688898397 0.000000e+00 695.0
9 TraesCS3D01G443100 chr3A 86.919 581 50 10 1971 2525 710256802 710257382 1.700000e-176 628.0
10 TraesCS3D01G443100 chr3A 88.591 149 11 2 1826 1968 710256597 710256745 2.660000e-40 176.0
11 TraesCS3D01G443100 chr3A 92.453 106 7 1 1596 1701 689003496 689003600 1.610000e-32 150.0
12 TraesCS3D01G443100 chr3B 88.518 958 88 13 665 1609 733356121 733357069 0.000000e+00 1140.0
13 TraesCS3D01G443100 chr3B 88.962 607 62 4 999 1601 732841631 732841026 0.000000e+00 745.0
14 TraesCS3D01G443100 chr3B 85.897 702 83 14 904 1603 733257755 733257068 0.000000e+00 734.0
15 TraesCS3D01G443100 chr3B 87.087 635 69 6 975 1603 733270866 733271493 0.000000e+00 706.0
16 TraesCS3D01G443100 chr3B 90.188 479 43 3 1 476 733354877 733355354 2.840000e-174 621.0
17 TraesCS3D01G443100 chr3B 85.985 264 35 2 1 264 733276520 733276781 5.470000e-72 281.0
18 TraesCS3D01G443100 chr3B 88.889 189 17 2 488 674 733355898 733356084 2.010000e-56 230.0
19 TraesCS3D01G443100 chr3B 89.773 88 9 0 1615 1702 733357132 733357219 2.110000e-21 113.0
20 TraesCS3D01G443100 chr3B 94.366 71 4 0 497 567 814498685 814498755 2.730000e-20 110.0
21 TraesCS3D01G443100 chr1D 92.819 557 38 2 1969 2525 30853887 30853333 0.000000e+00 806.0
22 TraesCS3D01G443100 chr1D 92.460 557 40 2 1969 2525 30728745 30728191 0.000000e+00 795.0
23 TraesCS3D01G443100 chr1D 88.591 149 11 2 1826 1968 30728949 30728801 2.660000e-40 176.0
24 TraesCS3D01G443100 chr1D 87.919 149 12 2 1826 1968 30854091 30853943 1.240000e-38 171.0
25 TraesCS3D01G443100 chr7B 93.679 443 27 1 1969 2411 201459401 201459842 0.000000e+00 662.0
26 TraesCS3D01G443100 chr7B 93.023 129 8 1 2397 2525 201461136 201461263 1.230000e-43 187.0
27 TraesCS3D01G443100 chr2B 86.621 583 51 10 1969 2525 675388702 675388121 1.020000e-173 619.0
28 TraesCS3D01G443100 chr2B 87.220 313 39 1 1969 2281 675437144 675436833 3.180000e-94 355.0
29 TraesCS3D01G443100 chr2B 82.909 275 20 4 2277 2525 675430771 675430498 3.360000e-54 222.0
30 TraesCS3D01G443100 chr2B 89.116 147 12 4 1826 1968 675388904 675388758 2.050000e-41 180.0
31 TraesCS3D01G443100 chr2B 93.506 77 3 2 500 574 51079519 51079443 2.110000e-21 113.0
32 TraesCS3D01G443100 chr2B 95.588 68 3 0 500 567 317234187 317234120 2.730000e-20 110.0
33 TraesCS3D01G443100 chr7A 85.349 587 45 8 1969 2525 48439134 48438559 1.040000e-158 569.0
34 TraesCS3D01G443100 chr2D 87.872 437 49 2 1969 2401 556405699 556405263 6.410000e-141 510.0
35 TraesCS3D01G443100 chr2D 94.253 87 5 0 1702 1788 54674325 54674239 1.620000e-27 134.0
36 TraesCS3D01G443100 chr2D 94.253 87 5 0 1702 1788 436111423 436111337 1.620000e-27 134.0
37 TraesCS3D01G443100 chr6A 83.445 447 51 10 1969 2402 602134156 602134592 6.740000e-106 394.0
38 TraesCS3D01G443100 chr6A 93.333 90 6 0 1702 1791 610509393 610509304 1.620000e-27 134.0
39 TraesCS3D01G443100 chr6A 93.333 90 5 1 1701 1789 557970047 557970136 5.830000e-27 132.0
40 TraesCS3D01G443100 chr6A 85.075 67 8 2 2532 2597 190658496 190658431 1.670000e-07 67.6
41 TraesCS3D01G443100 chr6A 85.714 63 7 2 2532 2593 190736856 190736795 6.000000e-07 65.8
42 TraesCS3D01G443100 chrUn 92.576 229 15 2 2297 2525 479245624 479245398 6.930000e-86 327.0
43 TraesCS3D01G443100 chr2A 93.023 172 12 0 1969 2140 101900857 101901028 4.290000e-63 252.0
44 TraesCS3D01G443100 chr2A 94.558 147 7 1 2379 2525 101901029 101901174 2.600000e-55 226.0
45 TraesCS3D01G443100 chr5B 90.351 114 10 1 2401 2514 36873686 36873798 5.790000e-32 148.0
46 TraesCS3D01G443100 chr5B 93.243 74 4 1 494 566 532767946 532768019 9.830000e-20 108.0
47 TraesCS3D01G443100 chr5B 93.333 45 3 0 2532 2576 661220028 661220072 1.670000e-07 67.6
48 TraesCS3D01G443100 chr7D 94.186 86 5 0 1701 1786 141292087 141292172 5.830000e-27 132.0
49 TraesCS3D01G443100 chr7D 81.699 153 17 7 1826 1968 105481155 105481306 1.630000e-22 117.0
50 TraesCS3D01G443100 chr5D 93.258 89 6 0 1702 1790 111788728 111788640 5.830000e-27 132.0
51 TraesCS3D01G443100 chr5D 94.186 86 5 0 1702 1787 240428042 240428127 5.830000e-27 132.0
52 TraesCS3D01G443100 chr1B 93.258 89 5 1 1702 1790 161298706 161298793 2.100000e-26 130.0
53 TraesCS3D01G443100 chr6B 95.775 71 3 0 497 567 44245772 44245842 5.870000e-22 115.0
54 TraesCS3D01G443100 chr6B 95.714 70 3 0 500 569 382980112 382980043 2.110000e-21 113.0
55 TraesCS3D01G443100 chr6B 94.366 71 4 0 497 567 320542747 320542817 2.730000e-20 110.0
56 TraesCS3D01G443100 chr6B 92.683 41 3 0 2532 2572 199923893 199923853 2.790000e-05 60.2
57 TraesCS3D01G443100 chr6B 90.244 41 4 0 2529 2569 14352154 14352194 1.000000e-03 54.7
58 TraesCS3D01G443100 chr6B 86.957 46 6 0 2532 2577 514682736 514682691 5.000000e-03 52.8
59 TraesCS3D01G443100 chr4A 94.366 71 4 0 497 567 714427014 714427084 2.730000e-20 110.0
60 TraesCS3D01G443100 chr5A 87.302 63 7 1 2532 2593 78918301 78918363 1.290000e-08 71.3
61 TraesCS3D01G443100 chr6D 86.885 61 7 1 2532 2591 59429322 59429382 1.670000e-07 67.6
62 TraesCS3D01G443100 chr1A 92.683 41 3 0 2532 2572 432933000 432932960 2.790000e-05 60.2


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 TraesCS3D01G443100 chr3D 552732540 552735136 2596 False 4796.0 4796 100.0000 1 2597 1 chr3D.!!$F3 2596
1 TraesCS3D01G443100 chr3D 552575671 552576362 691 True 732.0 732 86.0140 904 1603 1 chr3D.!!$R3 699
2 TraesCS3D01G443100 chr3D 552727801 552728404 603 False 702.0 702 87.6640 999 1605 1 chr3D.!!$F2 606
3 TraesCS3D01G443100 chr3A 688977430 688978122 692 True 749.0 749 86.2610 904 1603 1 chr3A.!!$R2 699
4 TraesCS3D01G443100 chr3A 688898397 688898994 597 True 695.0 695 87.7280 999 1597 1 chr3A.!!$R1 598
5 TraesCS3D01G443100 chr3A 689002385 689003600 1215 False 674.5 1199 89.9825 565 1701 2 chr3A.!!$F1 1136
6 TraesCS3D01G443100 chr3A 710256597 710257382 785 False 402.0 628 87.7550 1826 2525 2 chr3A.!!$F2 699
7 TraesCS3D01G443100 chr3B 732841026 732841631 605 True 745.0 745 88.9620 999 1601 1 chr3B.!!$R1 602
8 TraesCS3D01G443100 chr3B 733257068 733257755 687 True 734.0 734 85.8970 904 1603 1 chr3B.!!$R2 699
9 TraesCS3D01G443100 chr3B 733270866 733271493 627 False 706.0 706 87.0870 975 1603 1 chr3B.!!$F1 628
10 TraesCS3D01G443100 chr3B 733354877 733357219 2342 False 526.0 1140 89.3420 1 1702 4 chr3B.!!$F4 1701
11 TraesCS3D01G443100 chr1D 30853333 30854091 758 True 488.5 806 90.3690 1826 2525 2 chr1D.!!$R2 699
12 TraesCS3D01G443100 chr1D 30728191 30728949 758 True 485.5 795 90.5255 1826 2525 2 chr1D.!!$R1 699
13 TraesCS3D01G443100 chr7B 201459401 201461263 1862 False 424.5 662 93.3510 1969 2525 2 chr7B.!!$F1 556
14 TraesCS3D01G443100 chr2B 675388121 675388904 783 True 399.5 619 87.8685 1826 2525 2 chr2B.!!$R5 699
15 TraesCS3D01G443100 chr7A 48438559 48439134 575 True 569.0 569 85.3490 1969 2525 1 chr7A.!!$R1 556

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
896 1498 0.035739 TCCCAGGGTAACGAACAAGC 59.964 55.0 5.01 0.0 37.6 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1775 2514 0.106894 GCTCCCAAATACTCCCTCCG 59.893 60.0 0.0 0.0 0.0 4.63 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
29 30 4.041198 TCATAGGTAGGGGCGGAAAATTAG 59.959 45.833 0.00 0.00 0.00 1.73
33 34 2.420058 AGGGGCGGAAAATTAGTCAG 57.580 50.000 0.00 0.00 0.00 3.51
35 36 2.014857 GGGGCGGAAAATTAGTCAGAC 58.985 52.381 0.00 0.00 0.00 3.51
41 42 4.181578 CGGAAAATTAGTCAGACCGTGAT 58.818 43.478 0.00 0.00 37.56 3.06
42 43 4.630069 CGGAAAATTAGTCAGACCGTGATT 59.370 41.667 0.00 0.00 37.56 2.57
122 126 1.225691 GACGACGACGAGACTTCCG 60.226 63.158 15.32 0.00 42.66 4.30
126 130 2.097918 CGACGAGACTTCCGGACG 59.902 66.667 1.83 4.48 0.00 4.79
149 153 2.053116 CGTGCCGATGCGTAATGC 60.053 61.111 0.00 0.00 46.70 3.56
171 175 3.554934 GGCATTGGACACCTCAATATCA 58.445 45.455 0.00 0.00 33.94 2.15
179 183 8.021983 ATTGGACACCTCAATATCATGGAAACA 61.022 37.037 0.00 0.00 37.66 2.83
204 208 3.025599 ATGGCCTCACCCCATGCT 61.026 61.111 3.32 0.00 41.40 3.79
206 210 4.828296 GGCCTCACCCCATGCTGG 62.828 72.222 0.00 0.00 37.25 4.85
230 234 1.266718 TGTGCGCAGGAAGACATTTTC 59.733 47.619 12.22 0.00 0.00 2.29
243 247 3.119495 AGACATTTTCGGGTTGCAATAGC 60.119 43.478 0.59 0.00 42.57 2.97
262 266 2.166254 AGCGAATAAATGGGCCAGTTTG 59.834 45.455 25.53 14.19 0.00 2.93
285 289 0.243365 TCATTGCACGCCAACCATTC 59.757 50.000 0.00 0.00 35.99 2.67
331 335 4.160635 GCGCACGGTCCCAAATCG 62.161 66.667 0.30 0.00 0.00 3.34
358 362 1.288439 CTCTCGGCATCCATCCTCG 59.712 63.158 0.00 0.00 0.00 4.63
359 363 2.152297 CTCTCGGCATCCATCCTCGG 62.152 65.000 0.00 0.00 0.00 4.63
369 373 1.672854 CCATCCTCGGACTAACGCCA 61.673 60.000 0.00 0.00 0.00 5.69
387 391 1.476085 CCAAAGGCATTATCAACGGCA 59.524 47.619 0.00 0.00 0.00 5.69
388 392 2.529151 CAAAGGCATTATCAACGGCAC 58.471 47.619 0.00 0.00 0.00 5.01
402 406 2.504519 GCACCCCGGTAGACATCC 59.495 66.667 0.00 0.00 0.00 3.51
404 408 1.906105 GCACCCCGGTAGACATCCAA 61.906 60.000 0.00 0.00 0.00 3.53
408 412 1.227263 CCGGTAGACATCCAAGCCG 60.227 63.158 0.00 0.00 38.99 5.52
424 428 2.762875 CGTACACCTCCCCCTCCC 60.763 72.222 0.00 0.00 0.00 4.30
438 442 1.639635 CCTCCCCCTTGATGAGTGGG 61.640 65.000 0.00 0.00 40.59 4.61
476 480 3.260475 TGCTGGCTTTATCTCGCTTAA 57.740 42.857 0.00 0.00 0.00 1.85
477 481 3.808728 TGCTGGCTTTATCTCGCTTAAT 58.191 40.909 0.00 0.00 0.00 1.40
478 482 3.561310 TGCTGGCTTTATCTCGCTTAATG 59.439 43.478 0.00 0.00 0.00 1.90
479 483 3.608008 GCTGGCTTTATCTCGCTTAATGC 60.608 47.826 0.00 0.00 38.57 3.56
480 484 3.808728 TGGCTTTATCTCGCTTAATGCT 58.191 40.909 0.00 0.00 40.11 3.79
481 485 3.561310 TGGCTTTATCTCGCTTAATGCTG 59.439 43.478 0.00 0.00 40.11 4.41
482 486 3.561725 GGCTTTATCTCGCTTAATGCTGT 59.438 43.478 0.00 0.00 40.11 4.40
483 487 4.521943 GCTTTATCTCGCTTAATGCTGTG 58.478 43.478 0.00 0.00 40.11 3.66
484 488 4.034510 GCTTTATCTCGCTTAATGCTGTGT 59.965 41.667 0.00 0.00 40.11 3.72
486 490 6.238103 GCTTTATCTCGCTTAATGCTGTGTAA 60.238 38.462 0.00 0.00 40.11 2.41
548 1084 0.964700 CATCTCAGGCTCGGCTGATA 59.035 55.000 21.25 15.59 0.00 2.15
589 1125 8.978874 AAACACCATATGAGCTGTTATTATGA 57.021 30.769 3.65 0.00 0.00 2.15
606 1142 2.284263 TGATGATCCGAGCGATATGC 57.716 50.000 0.00 0.00 46.98 3.14
647 1183 3.007635 TCTCATTGTGCTGCTTCAGATG 58.992 45.455 0.00 7.43 32.44 2.90
664 1200 3.022406 AGATGAATTTGCTCTTCTGGCC 58.978 45.455 0.00 0.00 30.77 5.36
666 1202 2.811410 TGAATTTGCTCTTCTGGCCAT 58.189 42.857 5.51 0.00 0.00 4.40
772 1357 1.003580 CCAAGTCCACATACAGGCACT 59.996 52.381 0.00 0.00 43.88 4.40
855 1447 8.521176 AGAACTATTCTGTACTTACGTGTGATT 58.479 33.333 0.00 0.00 38.91 2.57
874 1466 0.248336 TTGTACAGCGCCGATAGACG 60.248 55.000 2.29 0.00 42.18 4.18
896 1498 0.035739 TCCCAGGGTAACGAACAAGC 59.964 55.000 5.01 0.00 37.60 4.01
917 1519 3.502920 CTGCGAGTATAAATAGGCGGAG 58.497 50.000 0.00 0.00 0.00 4.63
945 1552 0.182537 TAAGCCCACCATCCCAATCG 59.817 55.000 0.00 0.00 0.00 3.34
968 1575 2.592194 TCATCTACTTCGTCGCAACAC 58.408 47.619 0.00 0.00 0.00 3.32
972 1579 0.669619 TACTTCGTCGCAACACCAGA 59.330 50.000 0.00 0.00 0.00 3.86
992 1607 4.330620 CAGAAGAGCAGAGCAATCTTTCTC 59.669 45.833 0.00 0.00 33.53 2.87
993 1608 2.891112 AGAGCAGAGCAATCTTTCTCG 58.109 47.619 0.00 0.00 34.66 4.04
994 1609 2.495270 AGAGCAGAGCAATCTTTCTCGA 59.505 45.455 0.00 0.00 34.66 4.04
1035 1650 0.977395 CCCTTTCTTCGTCTCCCTGT 59.023 55.000 0.00 0.00 0.00 4.00
1040 1655 1.257743 TCTTCGTCTCCCTGTTCCAG 58.742 55.000 0.00 0.00 0.00 3.86
1061 1676 2.034878 CTCTTCCTCCGATGATCACCA 58.965 52.381 0.00 0.00 0.00 4.17
1074 1698 4.753662 CACCAGCAGGGCAGGCAT 62.754 66.667 0.00 0.00 38.85 4.40
1225 1849 2.932234 CGTCAGGGGAACGCACTCT 61.932 63.158 0.00 0.00 46.88 3.24
1235 1859 2.263077 GAACGCACTCTTCACGATCAT 58.737 47.619 0.00 0.00 0.00 2.45
1252 1876 1.097547 CATACGCAAGGGCTTCTGGG 61.098 60.000 0.00 0.00 46.39 4.45
1398 2022 2.093106 GGGACGTGCTATAGGATCGAT 58.907 52.381 17.97 0.00 0.00 3.59
1406 2030 2.417924 GCTATAGGATCGATGGGTGCTG 60.418 54.545 0.54 0.00 0.00 4.41
1581 2208 2.183300 GTCGTGCGTGGCCTCATA 59.817 61.111 3.32 0.00 0.00 2.15
1583 2210 1.447140 TCGTGCGTGGCCTCATAAC 60.447 57.895 3.32 0.00 0.00 1.89
1612 2294 1.094785 GTGATGGATGAAACGGGGTG 58.905 55.000 0.00 0.00 0.00 4.61
1682 2421 5.620011 GCTAGTTTAAGAGTTTGTTTCACGC 59.380 40.000 0.00 0.00 0.00 5.34
1702 2441 6.421501 TCACGCGAAACATTTAGAAACTCTTA 59.578 34.615 15.93 0.00 0.00 2.10
1703 2442 6.515340 CACGCGAAACATTTAGAAACTCTTAC 59.485 38.462 15.93 0.00 0.00 2.34
1704 2443 6.423001 ACGCGAAACATTTAGAAACTCTTACT 59.577 34.615 15.93 0.00 0.00 2.24
1705 2444 6.948777 CGCGAAACATTTAGAAACTCTTACTC 59.051 38.462 0.00 0.00 0.00 2.59
1706 2445 7.235080 GCGAAACATTTAGAAACTCTTACTCC 58.765 38.462 0.00 0.00 0.00 3.85
1707 2446 7.623715 GCGAAACATTTAGAAACTCTTACTCCC 60.624 40.741 0.00 0.00 0.00 4.30
1708 2447 7.603024 CGAAACATTTAGAAACTCTTACTCCCT 59.397 37.037 0.00 0.00 0.00 4.20
1709 2448 8.850007 AAACATTTAGAAACTCTTACTCCCTC 57.150 34.615 0.00 0.00 0.00 4.30
1710 2449 6.948589 ACATTTAGAAACTCTTACTCCCTCC 58.051 40.000 0.00 0.00 0.00 4.30
1711 2450 5.656213 TTTAGAAACTCTTACTCCCTCCG 57.344 43.478 0.00 0.00 0.00 4.63
1712 2451 3.172471 AGAAACTCTTACTCCCTCCGT 57.828 47.619 0.00 0.00 0.00 4.69
1713 2452 3.090790 AGAAACTCTTACTCCCTCCGTC 58.909 50.000 0.00 0.00 0.00 4.79
1714 2453 1.849977 AACTCTTACTCCCTCCGTCC 58.150 55.000 0.00 0.00 0.00 4.79
1715 2454 0.033306 ACTCTTACTCCCTCCGTCCC 60.033 60.000 0.00 0.00 0.00 4.46
1716 2455 0.033405 CTCTTACTCCCTCCGTCCCA 60.033 60.000 0.00 0.00 0.00 4.37
1717 2456 0.635009 TCTTACTCCCTCCGTCCCAT 59.365 55.000 0.00 0.00 0.00 4.00
1718 2457 1.854939 TCTTACTCCCTCCGTCCCATA 59.145 52.381 0.00 0.00 0.00 2.74
1719 2458 2.245546 TCTTACTCCCTCCGTCCCATAA 59.754 50.000 0.00 0.00 0.00 1.90
1720 2459 3.116862 TCTTACTCCCTCCGTCCCATAAT 60.117 47.826 0.00 0.00 0.00 1.28
1721 2460 4.106825 TCTTACTCCCTCCGTCCCATAATA 59.893 45.833 0.00 0.00 0.00 0.98
1722 2461 2.606378 ACTCCCTCCGTCCCATAATAC 58.394 52.381 0.00 0.00 0.00 1.89
1723 2462 2.090943 ACTCCCTCCGTCCCATAATACA 60.091 50.000 0.00 0.00 0.00 2.29
1724 2463 2.969950 CTCCCTCCGTCCCATAATACAA 59.030 50.000 0.00 0.00 0.00 2.41
1725 2464 2.969950 TCCCTCCGTCCCATAATACAAG 59.030 50.000 0.00 0.00 0.00 3.16
1726 2465 2.969950 CCCTCCGTCCCATAATACAAGA 59.030 50.000 0.00 0.00 0.00 3.02
1727 2466 3.006967 CCCTCCGTCCCATAATACAAGAG 59.993 52.174 0.00 0.00 0.00 2.85
1728 2467 3.895656 CCTCCGTCCCATAATACAAGAGA 59.104 47.826 0.00 0.00 0.00 3.10
1729 2468 4.021894 CCTCCGTCCCATAATACAAGAGAG 60.022 50.000 0.00 0.00 0.00 3.20
1730 2469 4.543689 TCCGTCCCATAATACAAGAGAGT 58.456 43.478 0.00 0.00 0.00 3.24
1731 2470 4.960469 TCCGTCCCATAATACAAGAGAGTT 59.040 41.667 0.00 0.00 0.00 3.01
1732 2471 5.424252 TCCGTCCCATAATACAAGAGAGTTT 59.576 40.000 0.00 0.00 0.00 2.66
1733 2472 6.070424 TCCGTCCCATAATACAAGAGAGTTTT 60.070 38.462 0.00 0.00 0.00 2.43
1734 2473 6.598064 CCGTCCCATAATACAAGAGAGTTTTT 59.402 38.462 0.00 0.00 0.00 1.94
1735 2474 7.414098 CCGTCCCATAATACAAGAGAGTTTTTG 60.414 40.741 0.00 0.00 0.00 2.44
1736 2475 7.333423 CGTCCCATAATACAAGAGAGTTTTTGA 59.667 37.037 0.00 0.00 0.00 2.69
1737 2476 8.451748 GTCCCATAATACAAGAGAGTTTTTGAC 58.548 37.037 0.00 0.00 0.00 3.18
1738 2477 8.160765 TCCCATAATACAAGAGAGTTTTTGACA 58.839 33.333 0.00 0.00 0.00 3.58
1739 2478 8.960591 CCCATAATACAAGAGAGTTTTTGACAT 58.039 33.333 0.00 0.00 0.00 3.06
1745 2484 7.865706 ACAAGAGAGTTTTTGACATAAGTGT 57.134 32.000 0.00 0.00 42.49 3.55
1746 2485 8.958119 ACAAGAGAGTTTTTGACATAAGTGTA 57.042 30.769 0.00 0.00 39.09 2.90
1747 2486 9.046296 ACAAGAGAGTTTTTGACATAAGTGTAG 57.954 33.333 0.00 0.00 39.09 2.74
1748 2487 9.046296 CAAGAGAGTTTTTGACATAAGTGTAGT 57.954 33.333 0.00 0.00 39.09 2.73
1749 2488 8.594881 AGAGAGTTTTTGACATAAGTGTAGTG 57.405 34.615 0.00 0.00 39.09 2.74
1750 2489 8.204836 AGAGAGTTTTTGACATAAGTGTAGTGT 58.795 33.333 0.00 0.00 39.09 3.55
1751 2490 8.366671 AGAGTTTTTGACATAAGTGTAGTGTC 57.633 34.615 0.00 0.00 39.09 3.67
1758 2497 6.939627 TGACATAAGTGTAGTGTCAAAAACG 58.060 36.000 5.07 0.00 46.45 3.60
1759 2498 5.744490 ACATAAGTGTAGTGTCAAAAACGC 58.256 37.500 0.00 0.00 36.63 4.84
1760 2499 8.585726 TGACATAAGTGTAGTGTCAAAAACGCT 61.586 37.037 5.07 0.00 46.45 5.07
1761 2500 4.531659 AAGTGTAGTGTCAAAAACGCTC 57.468 40.909 0.00 0.00 45.69 5.03
1762 2501 3.793559 AGTGTAGTGTCAAAAACGCTCT 58.206 40.909 0.00 0.00 45.69 4.09
1763 2502 4.189231 AGTGTAGTGTCAAAAACGCTCTT 58.811 39.130 0.00 0.00 45.69 2.85
1764 2503 5.353938 AGTGTAGTGTCAAAAACGCTCTTA 58.646 37.500 0.00 0.00 45.69 2.10
1765 2504 5.989777 AGTGTAGTGTCAAAAACGCTCTTAT 59.010 36.000 0.00 0.00 45.69 1.73
1766 2505 7.149973 AGTGTAGTGTCAAAAACGCTCTTATA 58.850 34.615 0.00 0.00 45.69 0.98
1767 2506 7.817962 AGTGTAGTGTCAAAAACGCTCTTATAT 59.182 33.333 0.00 0.00 45.69 0.86
1768 2507 8.440833 GTGTAGTGTCAAAAACGCTCTTATATT 58.559 33.333 0.00 0.00 45.69 1.28
1769 2508 9.642327 TGTAGTGTCAAAAACGCTCTTATATTA 57.358 29.630 0.00 0.00 45.69 0.98
1772 2511 9.378551 AGTGTCAAAAACGCTCTTATATTATGA 57.621 29.630 0.00 0.00 45.69 2.15
1773 2512 9.638300 GTGTCAAAAACGCTCTTATATTATGAG 57.362 33.333 0.00 0.00 35.42 2.90
1774 2513 9.594478 TGTCAAAAACGCTCTTATATTATGAGA 57.406 29.630 0.00 0.00 33.20 3.27
1775 2514 9.851043 GTCAAAAACGCTCTTATATTATGAGAC 57.149 33.333 0.00 0.00 33.20 3.36
1776 2515 8.752254 TCAAAAACGCTCTTATATTATGAGACG 58.248 33.333 13.57 13.57 36.53 4.18
1777 2516 7.639162 AAAACGCTCTTATATTATGAGACGG 57.361 36.000 16.71 7.11 35.72 4.79
1778 2517 6.570672 AACGCTCTTATATTATGAGACGGA 57.429 37.500 16.71 0.00 35.72 4.69
1779 2518 6.184580 ACGCTCTTATATTATGAGACGGAG 57.815 41.667 16.71 6.33 35.72 4.63
1780 2519 5.124138 ACGCTCTTATATTATGAGACGGAGG 59.876 44.000 16.71 3.20 35.72 4.30
1781 2520 5.449314 CGCTCTTATATTATGAGACGGAGGG 60.449 48.000 0.00 0.00 33.20 4.30
1782 2521 5.652891 GCTCTTATATTATGAGACGGAGGGA 59.347 44.000 0.00 0.00 33.20 4.20
1783 2522 6.183360 GCTCTTATATTATGAGACGGAGGGAG 60.183 46.154 0.00 0.00 33.20 4.30
1784 2523 6.791371 TCTTATATTATGAGACGGAGGGAGT 58.209 40.000 0.00 0.00 0.00 3.85
1785 2524 7.925622 TCTTATATTATGAGACGGAGGGAGTA 58.074 38.462 0.00 0.00 0.00 2.59
1786 2525 8.558312 TCTTATATTATGAGACGGAGGGAGTAT 58.442 37.037 0.00 0.00 0.00 2.12
1787 2526 9.191479 CTTATATTATGAGACGGAGGGAGTATT 57.809 37.037 0.00 0.00 0.00 1.89
1788 2527 9.543231 TTATATTATGAGACGGAGGGAGTATTT 57.457 33.333 0.00 0.00 0.00 1.40
1789 2528 5.531122 TTATGAGACGGAGGGAGTATTTG 57.469 43.478 0.00 0.00 0.00 2.32
1790 2529 2.108168 TGAGACGGAGGGAGTATTTGG 58.892 52.381 0.00 0.00 0.00 3.28
1791 2530 1.413077 GAGACGGAGGGAGTATTTGGG 59.587 57.143 0.00 0.00 0.00 4.12
1792 2531 1.007963 AGACGGAGGGAGTATTTGGGA 59.992 52.381 0.00 0.00 0.00 4.37
1793 2532 1.413077 GACGGAGGGAGTATTTGGGAG 59.587 57.143 0.00 0.00 0.00 4.30
1794 2533 0.106894 CGGAGGGAGTATTTGGGAGC 59.893 60.000 0.00 0.00 0.00 4.70
1795 2534 0.474614 GGAGGGAGTATTTGGGAGCC 59.525 60.000 0.00 0.00 0.00 4.70
1796 2535 1.512735 GAGGGAGTATTTGGGAGCCT 58.487 55.000 0.00 0.00 0.00 4.58
1797 2536 1.847088 GAGGGAGTATTTGGGAGCCTT 59.153 52.381 0.00 0.00 0.00 4.35
1798 2537 2.242452 GAGGGAGTATTTGGGAGCCTTT 59.758 50.000 0.00 0.00 0.00 3.11
1799 2538 2.654896 AGGGAGTATTTGGGAGCCTTTT 59.345 45.455 0.00 0.00 0.00 2.27
1800 2539 3.077543 AGGGAGTATTTGGGAGCCTTTTT 59.922 43.478 0.00 0.00 0.00 1.94
1820 2559 2.879103 TTTGGAGTGGATTCTGGTCC 57.121 50.000 0.00 0.00 38.81 4.46
1821 2560 0.991920 TTGGAGTGGATTCTGGTCCC 59.008 55.000 0.00 0.00 37.48 4.46
1822 2561 0.914417 TGGAGTGGATTCTGGTCCCC 60.914 60.000 0.00 0.00 37.48 4.81
1823 2562 1.636769 GGAGTGGATTCTGGTCCCCC 61.637 65.000 0.00 0.00 37.48 5.40
1875 2614 5.182169 TCATCCGTTTTACCCCATTTAGT 57.818 39.130 0.00 0.00 0.00 2.24
1894 2633 9.755064 CATTTAGTAAAAGTTCTACCACGATTG 57.245 33.333 0.00 0.00 0.00 2.67
1995 2795 3.701604 GATGGAGGTCGCTCGCGTT 62.702 63.158 5.77 0.00 40.74 4.84
2040 2840 0.530744 GACCACGCTCCATACTCACA 59.469 55.000 0.00 0.00 0.00 3.58
2065 2865 2.203070 GATTGCATCGCCCGTCCT 60.203 61.111 0.00 0.00 0.00 3.85
2127 2927 1.215423 GGGTTAGGGATTGTCAGGCAT 59.785 52.381 0.00 0.00 0.00 4.40
2144 2944 3.399105 ATCGGCAATGGCTACGGCA 62.399 57.895 5.02 0.00 43.52 5.69
2196 3000 1.351707 GTTGTATGGCCGCGACATG 59.648 57.895 21.33 1.34 31.56 3.21
2229 3033 3.470888 CCCGTGGAATCCGGCTCT 61.471 66.667 0.00 0.00 44.13 4.09
2261 3065 4.498520 CGTCTGGCCGCGACATCT 62.499 66.667 20.78 0.00 0.00 2.90
2363 3167 1.891919 GGTTGTGCTCAGTTGCGGA 60.892 57.895 0.00 0.00 35.36 5.54
2429 4542 5.648178 TTCCACATGATTTTGACCATCTG 57.352 39.130 0.00 0.00 0.00 2.90
2509 4622 0.721718 GGCGTTTGATTCGGACAGAG 59.278 55.000 0.00 0.00 0.00 3.35
2525 4638 7.748847 TCGGACAGAGTTAAAAATGCTTATTC 58.251 34.615 0.00 0.00 0.00 1.75
2526 4639 6.682863 CGGACAGAGTTAAAAATGCTTATTCG 59.317 38.462 0.00 0.00 0.00 3.34
2527 4640 6.967199 GGACAGAGTTAAAAATGCTTATTCGG 59.033 38.462 0.00 0.00 0.00 4.30
2528 4641 7.148306 GGACAGAGTTAAAAATGCTTATTCGGA 60.148 37.037 0.00 0.00 0.00 4.55
2529 4642 7.527457 ACAGAGTTAAAAATGCTTATTCGGAC 58.473 34.615 0.00 0.00 0.00 4.79
2530 4643 7.174253 ACAGAGTTAAAAATGCTTATTCGGACA 59.826 33.333 0.00 0.00 0.00 4.02
2531 4644 8.184192 CAGAGTTAAAAATGCTTATTCGGACAT 58.816 33.333 0.00 0.00 0.00 3.06
2532 4645 9.391006 AGAGTTAAAAATGCTTATTCGGACATA 57.609 29.630 0.00 0.00 0.00 2.29
2538 4651 9.965824 AAAAATGCTTATTCGGACATATTAAGG 57.034 29.630 0.00 0.00 0.00 2.69
2539 4652 8.918202 AAATGCTTATTCGGACATATTAAGGA 57.082 30.769 0.00 0.00 0.00 3.36
2540 4653 7.907214 ATGCTTATTCGGACATATTAAGGAC 57.093 36.000 0.00 0.00 0.00 3.85
2541 4654 6.822442 TGCTTATTCGGACATATTAAGGACA 58.178 36.000 0.00 0.00 0.00 4.02
2542 4655 6.929049 TGCTTATTCGGACATATTAAGGACAG 59.071 38.462 0.00 0.00 0.00 3.51
2543 4656 6.929606 GCTTATTCGGACATATTAAGGACAGT 59.070 38.462 0.00 0.00 0.00 3.55
2544 4657 8.086522 GCTTATTCGGACATATTAAGGACAGTA 58.913 37.037 0.00 0.00 0.00 2.74
2545 4658 9.976511 CTTATTCGGACATATTAAGGACAGTAA 57.023 33.333 0.00 0.00 0.00 2.24
2548 4661 8.483307 TTCGGACATATTAAGGACAGTAAAAC 57.517 34.615 0.00 0.00 0.00 2.43
2549 4662 7.844009 TCGGACATATTAAGGACAGTAAAACT 58.156 34.615 0.00 0.00 0.00 2.66
2564 4677 6.502136 AGTAAAACTGAGCCTAAAATGAGC 57.498 37.500 0.00 0.00 0.00 4.26
2565 4678 6.003950 AGTAAAACTGAGCCTAAAATGAGCA 58.996 36.000 0.00 0.00 0.00 4.26
2566 4679 4.773323 AAACTGAGCCTAAAATGAGCAC 57.227 40.909 0.00 0.00 0.00 4.40
2567 4680 3.710209 ACTGAGCCTAAAATGAGCACT 57.290 42.857 0.00 0.00 0.00 4.40
2568 4681 3.604582 ACTGAGCCTAAAATGAGCACTC 58.395 45.455 0.00 0.00 0.00 3.51
2569 4682 3.262915 ACTGAGCCTAAAATGAGCACTCT 59.737 43.478 0.00 0.00 0.00 3.24
2570 4683 3.866651 TGAGCCTAAAATGAGCACTCTC 58.133 45.455 0.00 0.00 39.78 3.20
2577 4690 2.965783 TGAGCACTCTCACGCCTC 59.034 61.111 0.00 0.00 43.95 4.70
2578 4691 1.903404 TGAGCACTCTCACGCCTCA 60.903 57.895 0.00 0.00 43.95 3.86
2579 4692 1.290324 GAGCACTCTCACGCCTCAA 59.710 57.895 0.00 0.00 39.16 3.02
2580 4693 1.005630 AGCACTCTCACGCCTCAAC 60.006 57.895 0.00 0.00 0.00 3.18
2581 4694 1.300931 GCACTCTCACGCCTCAACA 60.301 57.895 0.00 0.00 0.00 3.33
2582 4695 0.671781 GCACTCTCACGCCTCAACAT 60.672 55.000 0.00 0.00 0.00 2.71
2583 4696 1.800805 CACTCTCACGCCTCAACATT 58.199 50.000 0.00 0.00 0.00 2.71
2584 4697 2.146342 CACTCTCACGCCTCAACATTT 58.854 47.619 0.00 0.00 0.00 2.32
2585 4698 2.549754 CACTCTCACGCCTCAACATTTT 59.450 45.455 0.00 0.00 0.00 1.82
2586 4699 3.003689 CACTCTCACGCCTCAACATTTTT 59.996 43.478 0.00 0.00 0.00 1.94
2587 4700 3.003689 ACTCTCACGCCTCAACATTTTTG 59.996 43.478 0.00 0.00 0.00 2.44
2588 4701 3.210227 TCTCACGCCTCAACATTTTTGA 58.790 40.909 0.00 0.00 0.00 2.69
2589 4702 3.003275 TCTCACGCCTCAACATTTTTGAC 59.997 43.478 0.00 0.00 0.00 3.18
2590 4703 2.034053 TCACGCCTCAACATTTTTGACC 59.966 45.455 0.00 0.00 0.00 4.02
2591 4704 1.001815 ACGCCTCAACATTTTTGACCG 60.002 47.619 0.00 0.00 0.00 4.79
2592 4705 1.001815 CGCCTCAACATTTTTGACCGT 60.002 47.619 0.00 0.00 0.00 4.83
2593 4706 2.542824 CGCCTCAACATTTTTGACCGTT 60.543 45.455 0.00 0.00 0.00 4.44
2594 4707 3.049912 GCCTCAACATTTTTGACCGTTC 58.950 45.455 0.00 0.00 0.00 3.95
2595 4708 3.296628 CCTCAACATTTTTGACCGTTCG 58.703 45.455 0.00 0.00 0.00 3.95
2596 4709 3.002862 CCTCAACATTTTTGACCGTTCGA 59.997 43.478 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 8.420374 TTTATGAATCTAAATCACGGTCTGAC 57.580 34.615 0.00 0.00 0.00 3.51
33 34 7.484035 AGCTTTATGAATCTAAATCACGGTC 57.516 36.000 0.00 0.00 0.00 4.79
35 36 8.594881 AGTAGCTTTATGAATCTAAATCACGG 57.405 34.615 0.00 0.00 0.00 4.94
110 114 1.154263 CACGTCCGGAAGTCTCGTC 60.154 63.158 20.79 0.00 32.47 4.20
112 116 2.178521 CCACGTCCGGAAGTCTCG 59.821 66.667 20.79 14.84 0.00 4.04
140 144 1.746991 TCCAATGCCGCATTACGCA 60.747 52.632 18.10 0.39 42.60 5.24
144 148 0.034574 AGGTGTCCAATGCCGCATTA 60.035 50.000 18.10 1.24 32.35 1.90
149 153 2.036958 TATTGAGGTGTCCAATGCCG 57.963 50.000 0.00 0.00 35.94 5.69
157 161 6.599244 TCTTGTTTCCATGATATTGAGGTGTC 59.401 38.462 0.00 0.00 0.00 3.67
171 175 2.357569 GGCCATCCTCTCTTGTTTCCAT 60.358 50.000 0.00 0.00 0.00 3.41
230 234 3.684103 TTTATTCGCTATTGCAACCCG 57.316 42.857 0.00 5.00 39.64 5.28
243 247 3.163630 CCAAACTGGCCCATTTATTCG 57.836 47.619 0.00 0.00 0.00 3.34
262 266 3.372730 TTGGCGTGCAATGAGGCC 61.373 61.111 0.00 0.00 45.42 5.19
288 292 3.255379 GCTTCGACGCCGACCATC 61.255 66.667 1.75 0.00 45.50 3.51
369 373 1.476488 GGTGCCGTTGATAATGCCTTT 59.524 47.619 0.00 0.00 0.00 3.11
384 388 2.504519 GATGTCTACCGGGGTGCC 59.495 66.667 6.32 0.00 0.00 5.01
387 391 1.623542 GCTTGGATGTCTACCGGGGT 61.624 60.000 6.32 0.00 0.00 4.95
388 392 1.146263 GCTTGGATGTCTACCGGGG 59.854 63.158 6.32 0.00 0.00 5.73
402 406 2.267961 GGGGAGGTGTACGGCTTG 59.732 66.667 0.00 0.00 0.00 4.01
404 408 3.978410 GAGGGGGAGGTGTACGGCT 62.978 68.421 0.00 0.00 0.00 5.52
408 412 2.366569 GGGGAGGGGGAGGTGTAC 60.367 72.222 0.00 0.00 0.00 2.90
424 428 3.890527 CCTTCCCACTCATCAAGGG 57.109 57.895 0.00 0.00 44.22 3.95
438 442 3.156511 GCATTAAGCAAGCTTCCCTTC 57.843 47.619 11.05 0.00 44.79 3.46
494 1030 2.492088 GCCCGGCTTTGAATTAAGAAGT 59.508 45.455 0.71 0.00 0.00 3.01
495 1031 2.755103 AGCCCGGCTTTGAATTAAGAAG 59.245 45.455 5.94 0.00 33.89 2.85
498 1034 2.618709 CCTAGCCCGGCTTTGAATTAAG 59.381 50.000 19.35 5.89 40.44 1.85
503 1039 2.045340 GCCTAGCCCGGCTTTGAA 60.045 61.111 19.35 0.00 46.63 2.69
535 1071 0.912486 AAAAGGTATCAGCCGAGCCT 59.088 50.000 0.00 0.00 33.37 4.58
578 1114 5.402398 TCGCTCGGATCATCATAATAACAG 58.598 41.667 0.00 0.00 0.00 3.16
587 1123 1.134995 GGCATATCGCTCGGATCATCA 60.135 52.381 0.00 0.00 41.91 3.07
589 1125 0.179127 CGGCATATCGCTCGGATCAT 60.179 55.000 0.00 0.00 41.91 2.45
606 1142 5.727646 GAGAACAAACTCTAGCAGATGCGG 61.728 50.000 0.00 0.00 38.71 5.69
647 1183 3.881937 AATGGCCAGAAGAGCAAATTC 57.118 42.857 13.05 0.00 0.00 2.17
664 1200 9.976255 CATAGTGGTTAATGAAATTTGCAAATG 57.024 29.630 24.74 4.40 37.87 2.32
666 1202 7.118971 GGCATAGTGGTTAATGAAATTTGCAAA 59.881 33.333 15.44 15.44 37.87 3.68
772 1357 2.924926 CAGTTAGCGCCACGTTTACATA 59.075 45.455 2.29 0.00 0.00 2.29
845 1437 1.722464 GCGCTGTACAAATCACACGTA 59.278 47.619 0.00 0.00 0.00 3.57
849 1441 0.319986 TCGGCGCTGTACAAATCACA 60.320 50.000 17.37 0.00 0.00 3.58
855 1447 0.248336 CGTCTATCGGCGCTGTACAA 60.248 55.000 17.37 0.00 35.71 2.41
874 1466 0.906775 TGTTCGTTACCCTGGGATCC 59.093 55.000 22.23 1.92 0.00 3.36
875 1467 2.629051 CTTGTTCGTTACCCTGGGATC 58.371 52.381 22.23 8.05 0.00 3.36
878 1470 0.036306 AGCTTGTTCGTTACCCTGGG 59.964 55.000 12.28 12.28 0.00 4.45
880 1472 0.517316 GCAGCTTGTTCGTTACCCTG 59.483 55.000 0.00 0.00 0.00 4.45
882 1474 0.947180 TCGCAGCTTGTTCGTTACCC 60.947 55.000 0.00 0.00 0.00 3.69
883 1475 0.438830 CTCGCAGCTTGTTCGTTACC 59.561 55.000 0.00 0.00 0.00 2.85
896 1498 3.502920 CTCCGCCTATTTATACTCGCAG 58.497 50.000 0.00 0.00 0.00 5.18
917 1519 2.426406 GGTGGGCTTAATGGCTGGC 61.426 63.158 0.00 0.00 41.48 4.85
927 1529 1.076777 CGATTGGGATGGTGGGCTT 60.077 57.895 0.00 0.00 0.00 4.35
968 1575 2.695127 AGATTGCTCTGCTCTTCTGG 57.305 50.000 0.00 0.00 0.00 3.86
972 1579 3.056250 TCGAGAAAGATTGCTCTGCTCTT 60.056 43.478 0.00 0.00 34.20 2.85
992 1607 0.652592 GATCTTGGCCATTGTCGTCG 59.347 55.000 6.09 0.00 0.00 5.12
993 1608 1.017387 GGATCTTGGCCATTGTCGTC 58.983 55.000 6.09 0.00 0.00 4.20
994 1609 0.327924 TGGATCTTGGCCATTGTCGT 59.672 50.000 6.09 0.00 0.00 4.34
1035 1650 0.826715 CATCGGAGGAAGAGCTGGAA 59.173 55.000 0.00 0.00 0.00 3.53
1040 1655 1.270041 GGTGATCATCGGAGGAAGAGC 60.270 57.143 0.00 0.00 0.00 4.09
1074 1698 1.373622 CATCCACACCGTGTACGCA 60.374 57.895 3.25 0.00 38.18 5.24
1164 1788 3.026431 GCCCCTGCAGCCGTAGTTA 62.026 63.158 8.66 0.00 37.47 2.24
1225 1849 1.934589 CCCTTGCGTATGATCGTGAA 58.065 50.000 0.00 0.00 0.00 3.18
1235 1859 2.668632 CCCAGAAGCCCTTGCGTA 59.331 61.111 0.00 0.00 44.33 4.42
1252 1876 2.743928 CTCCCACCTGCTGAACGC 60.744 66.667 0.00 0.00 39.77 4.84
1260 1884 4.087892 CGGCAGACCTCCCACCTG 62.088 72.222 0.00 0.00 0.00 4.00
1389 2013 0.752658 CACAGCACCCATCGATCCTA 59.247 55.000 0.00 0.00 0.00 2.94
1581 2208 1.002134 CCATCACAAGGAGCGGGTT 60.002 57.895 0.00 0.00 0.00 4.11
1583 2210 0.816825 CATCCATCACAAGGAGCGGG 60.817 60.000 0.00 0.00 38.83 6.13
1612 2294 4.682050 GCCAAAATCTCTAGGAGAGTCACC 60.682 50.000 0.00 0.00 42.26 4.02
1666 2405 3.750639 TTTCGCGTGAAACAAACTCTT 57.249 38.095 19.69 0.00 39.13 2.85
1682 2421 7.603024 AGGGAGTAAGAGTTTCTAAATGTTTCG 59.397 37.037 0.00 0.00 0.00 3.46
1702 2441 2.090943 TGTATTATGGGACGGAGGGAGT 60.091 50.000 0.00 0.00 0.00 3.85
1703 2442 2.605257 TGTATTATGGGACGGAGGGAG 58.395 52.381 0.00 0.00 0.00 4.30
1704 2443 2.779429 TGTATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
1705 2444 2.969950 TCTTGTATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
1706 2445 3.895656 TCTCTTGTATTATGGGACGGAGG 59.104 47.826 0.00 0.00 0.00 4.30
1707 2446 4.585162 ACTCTCTTGTATTATGGGACGGAG 59.415 45.833 0.00 0.00 0.00 4.63
1708 2447 4.543689 ACTCTCTTGTATTATGGGACGGA 58.456 43.478 0.00 0.00 0.00 4.69
1709 2448 4.939052 ACTCTCTTGTATTATGGGACGG 57.061 45.455 0.00 0.00 0.00 4.79
1710 2449 7.333423 TCAAAAACTCTCTTGTATTATGGGACG 59.667 37.037 0.00 0.00 0.00 4.79
1711 2450 8.451748 GTCAAAAACTCTCTTGTATTATGGGAC 58.548 37.037 0.00 0.00 0.00 4.46
1712 2451 8.160765 TGTCAAAAACTCTCTTGTATTATGGGA 58.839 33.333 0.00 0.00 0.00 4.37
1713 2452 8.335532 TGTCAAAAACTCTCTTGTATTATGGG 57.664 34.615 0.00 0.00 0.00 4.00
1719 2458 9.561069 ACACTTATGTCAAAAACTCTCTTGTAT 57.439 29.630 0.00 0.00 31.55 2.29
1720 2459 8.958119 ACACTTATGTCAAAAACTCTCTTGTA 57.042 30.769 0.00 0.00 31.55 2.41
1721 2460 7.865706 ACACTTATGTCAAAAACTCTCTTGT 57.134 32.000 0.00 0.00 31.55 3.16
1722 2461 9.046296 ACTACACTTATGTCAAAAACTCTCTTG 57.954 33.333 0.00 0.00 40.48 3.02
1723 2462 9.046296 CACTACACTTATGTCAAAAACTCTCTT 57.954 33.333 0.00 0.00 40.48 2.85
1724 2463 8.204836 ACACTACACTTATGTCAAAAACTCTCT 58.795 33.333 0.00 0.00 40.48 3.10
1725 2464 8.366671 ACACTACACTTATGTCAAAAACTCTC 57.633 34.615 0.00 0.00 40.48 3.20
1726 2465 8.366671 GACACTACACTTATGTCAAAAACTCT 57.633 34.615 0.00 0.00 41.94 3.24
1735 2474 5.844396 GCGTTTTTGACACTACACTTATGTC 59.156 40.000 0.00 0.00 42.54 3.06
1736 2475 5.526111 AGCGTTTTTGACACTACACTTATGT 59.474 36.000 0.00 0.00 43.30 2.29
1737 2476 5.985781 AGCGTTTTTGACACTACACTTATG 58.014 37.500 0.00 0.00 0.00 1.90
1738 2477 5.989777 AGAGCGTTTTTGACACTACACTTAT 59.010 36.000 0.00 0.00 0.00 1.73
1739 2478 5.353938 AGAGCGTTTTTGACACTACACTTA 58.646 37.500 0.00 0.00 0.00 2.24
1740 2479 4.189231 AGAGCGTTTTTGACACTACACTT 58.811 39.130 0.00 0.00 0.00 3.16
1741 2480 3.793559 AGAGCGTTTTTGACACTACACT 58.206 40.909 0.00 0.00 0.00 3.55
1742 2481 4.531659 AAGAGCGTTTTTGACACTACAC 57.468 40.909 0.00 0.00 0.00 2.90
1743 2482 8.542497 AATATAAGAGCGTTTTTGACACTACA 57.458 30.769 0.00 0.00 0.00 2.74
1746 2485 9.378551 TCATAATATAAGAGCGTTTTTGACACT 57.621 29.630 0.00 0.00 0.00 3.55
1747 2486 9.638300 CTCATAATATAAGAGCGTTTTTGACAC 57.362 33.333 0.00 0.00 0.00 3.67
1748 2487 9.594478 TCTCATAATATAAGAGCGTTTTTGACA 57.406 29.630 0.00 0.00 0.00 3.58
1749 2488 9.851043 GTCTCATAATATAAGAGCGTTTTTGAC 57.149 33.333 0.00 0.00 0.00 3.18
1750 2489 8.752254 CGTCTCATAATATAAGAGCGTTTTTGA 58.248 33.333 0.00 0.00 0.00 2.69
1751 2490 8.004344 CCGTCTCATAATATAAGAGCGTTTTTG 58.996 37.037 0.00 0.00 31.69 2.44
1752 2491 7.924412 TCCGTCTCATAATATAAGAGCGTTTTT 59.076 33.333 0.00 0.00 31.69 1.94
1753 2492 7.431249 TCCGTCTCATAATATAAGAGCGTTTT 58.569 34.615 0.00 0.00 31.69 2.43
1754 2493 6.978338 TCCGTCTCATAATATAAGAGCGTTT 58.022 36.000 0.00 0.00 31.69 3.60
1755 2494 6.349445 CCTCCGTCTCATAATATAAGAGCGTT 60.349 42.308 0.00 0.00 31.69 4.84
1756 2495 5.124138 CCTCCGTCTCATAATATAAGAGCGT 59.876 44.000 0.00 0.00 31.69 5.07
1757 2496 5.449314 CCCTCCGTCTCATAATATAAGAGCG 60.449 48.000 0.00 0.00 0.00 5.03
1758 2497 5.652891 TCCCTCCGTCTCATAATATAAGAGC 59.347 44.000 0.00 0.00 0.00 4.09
1759 2498 6.887545 ACTCCCTCCGTCTCATAATATAAGAG 59.112 42.308 0.00 0.00 0.00 2.85
1760 2499 6.791371 ACTCCCTCCGTCTCATAATATAAGA 58.209 40.000 0.00 0.00 0.00 2.10
1761 2500 8.754991 ATACTCCCTCCGTCTCATAATATAAG 57.245 38.462 0.00 0.00 0.00 1.73
1762 2501 9.543231 AAATACTCCCTCCGTCTCATAATATAA 57.457 33.333 0.00 0.00 0.00 0.98
1763 2502 8.967918 CAAATACTCCCTCCGTCTCATAATATA 58.032 37.037 0.00 0.00 0.00 0.86
1764 2503 7.093289 CCAAATACTCCCTCCGTCTCATAATAT 60.093 40.741 0.00 0.00 0.00 1.28
1765 2504 6.210784 CCAAATACTCCCTCCGTCTCATAATA 59.789 42.308 0.00 0.00 0.00 0.98
1766 2505 5.012148 CCAAATACTCCCTCCGTCTCATAAT 59.988 44.000 0.00 0.00 0.00 1.28
1767 2506 4.344102 CCAAATACTCCCTCCGTCTCATAA 59.656 45.833 0.00 0.00 0.00 1.90
1768 2507 3.895656 CCAAATACTCCCTCCGTCTCATA 59.104 47.826 0.00 0.00 0.00 2.15
1769 2508 2.700897 CCAAATACTCCCTCCGTCTCAT 59.299 50.000 0.00 0.00 0.00 2.90
1770 2509 2.108168 CCAAATACTCCCTCCGTCTCA 58.892 52.381 0.00 0.00 0.00 3.27
1771 2510 1.413077 CCCAAATACTCCCTCCGTCTC 59.587 57.143 0.00 0.00 0.00 3.36
1772 2511 1.007963 TCCCAAATACTCCCTCCGTCT 59.992 52.381 0.00 0.00 0.00 4.18
1773 2512 1.413077 CTCCCAAATACTCCCTCCGTC 59.587 57.143 0.00 0.00 0.00 4.79
1774 2513 1.497161 CTCCCAAATACTCCCTCCGT 58.503 55.000 0.00 0.00 0.00 4.69
1775 2514 0.106894 GCTCCCAAATACTCCCTCCG 59.893 60.000 0.00 0.00 0.00 4.63
1776 2515 0.474614 GGCTCCCAAATACTCCCTCC 59.525 60.000 0.00 0.00 0.00 4.30
1777 2516 1.512735 AGGCTCCCAAATACTCCCTC 58.487 55.000 0.00 0.00 0.00 4.30
1778 2517 1.987080 AAGGCTCCCAAATACTCCCT 58.013 50.000 0.00 0.00 0.00 4.20
1779 2518 2.828661 AAAGGCTCCCAAATACTCCC 57.171 50.000 0.00 0.00 0.00 4.30
1799 2538 3.496331 GGACCAGAATCCACTCCAAAAA 58.504 45.455 0.00 0.00 38.77 1.94
1800 2539 2.225017 GGGACCAGAATCCACTCCAAAA 60.225 50.000 0.00 0.00 40.96 2.44
1801 2540 1.354368 GGGACCAGAATCCACTCCAAA 59.646 52.381 0.00 0.00 40.96 3.28
1802 2541 0.991920 GGGACCAGAATCCACTCCAA 59.008 55.000 0.00 0.00 40.96 3.53
1803 2542 2.696864 GGGACCAGAATCCACTCCA 58.303 57.895 0.00 0.00 40.96 3.86
1820 2559 2.051692 TGGGATAATTAGTGTCGGGGG 58.948 52.381 0.00 0.00 0.00 5.40
1821 2560 4.367039 AATGGGATAATTAGTGTCGGGG 57.633 45.455 0.00 0.00 0.00 5.73
1822 2561 5.411669 GCTAAATGGGATAATTAGTGTCGGG 59.588 44.000 0.00 0.00 0.00 5.14
1823 2562 5.120208 CGCTAAATGGGATAATTAGTGTCGG 59.880 44.000 0.00 0.00 34.21 4.79
1824 2563 5.924254 TCGCTAAATGGGATAATTAGTGTCG 59.076 40.000 0.00 0.00 38.00 4.35
1875 2614 5.302360 ACAGCAATCGTGGTAGAACTTTTA 58.698 37.500 0.00 0.00 33.05 1.52
1885 2624 5.401079 CGAAATTTTAAACAGCAATCGTGGT 59.599 36.000 0.00 0.00 35.28 4.16
1894 2633 6.691388 AGAACACTCACGAAATTTTAAACAGC 59.309 34.615 0.00 0.00 0.00 4.40
1995 2795 0.455410 GGCATTATGCTTTGGACGCA 59.545 50.000 17.13 0.00 44.28 5.24
2004 2804 1.202580 GGTCGACTCAGGCATTATGCT 60.203 52.381 17.13 0.29 44.28 3.79
2127 2927 4.089239 TGCCGTAGCCATTGCCGA 62.089 61.111 0.00 0.00 38.69 5.54
2144 2944 0.461870 TATGAAATCGTGCCGCTGCT 60.462 50.000 0.70 0.00 38.71 4.24
2196 3000 1.574702 CGGGGTCGTTTCTTGCCTTC 61.575 60.000 0.00 0.00 0.00 3.46
2229 3033 1.154093 GACGTCGGCGAGATTGACA 60.154 57.895 20.03 0.00 42.00 3.58
2261 3065 0.988832 ATGGGGTCGTTTCTTGCCTA 59.011 50.000 0.00 0.00 0.00 3.93
2363 3167 1.074471 ACCAGCGGTCCCCATAGAT 60.074 57.895 0.00 0.00 0.00 1.98
2525 4638 7.762615 TCAGTTTTACTGTCCTTAATATGTCCG 59.237 37.037 6.71 0.00 46.03 4.79
2526 4639 9.099454 CTCAGTTTTACTGTCCTTAATATGTCC 57.901 37.037 6.71 0.00 46.03 4.02
2527 4640 8.604890 GCTCAGTTTTACTGTCCTTAATATGTC 58.395 37.037 6.71 0.00 46.03 3.06
2528 4641 7.553044 GGCTCAGTTTTACTGTCCTTAATATGT 59.447 37.037 6.71 0.00 46.03 2.29
2529 4642 7.770897 AGGCTCAGTTTTACTGTCCTTAATATG 59.229 37.037 13.52 0.00 46.03 1.78
2530 4643 7.862675 AGGCTCAGTTTTACTGTCCTTAATAT 58.137 34.615 13.52 0.00 46.03 1.28
2531 4644 7.253905 AGGCTCAGTTTTACTGTCCTTAATA 57.746 36.000 13.52 0.00 46.03 0.98
2532 4645 6.128138 AGGCTCAGTTTTACTGTCCTTAAT 57.872 37.500 13.52 0.00 46.03 1.40
2533 4646 5.562298 AGGCTCAGTTTTACTGTCCTTAA 57.438 39.130 13.52 0.00 46.03 1.85
2534 4647 6.675413 TTAGGCTCAGTTTTACTGTCCTTA 57.325 37.500 19.85 12.99 46.03 2.69
2535 4648 5.562298 TTAGGCTCAGTTTTACTGTCCTT 57.438 39.130 19.85 8.16 46.03 3.36
2536 4649 5.562298 TTTAGGCTCAGTTTTACTGTCCT 57.438 39.130 19.14 19.14 46.03 3.85
2537 4650 6.430000 TCATTTTAGGCTCAGTTTTACTGTCC 59.570 38.462 6.71 8.98 46.03 4.02
2538 4651 7.435068 TCATTTTAGGCTCAGTTTTACTGTC 57.565 36.000 6.71 1.28 46.03 3.51
2539 4652 6.072452 GCTCATTTTAGGCTCAGTTTTACTGT 60.072 38.462 6.71 0.00 46.03 3.55
2541 4654 6.003950 TGCTCATTTTAGGCTCAGTTTTACT 58.996 36.000 0.00 0.00 0.00 2.24
2542 4655 6.072452 AGTGCTCATTTTAGGCTCAGTTTTAC 60.072 38.462 0.00 0.00 0.00 2.01
2543 4656 6.003950 AGTGCTCATTTTAGGCTCAGTTTTA 58.996 36.000 0.00 0.00 0.00 1.52
2544 4657 4.829492 AGTGCTCATTTTAGGCTCAGTTTT 59.171 37.500 0.00 0.00 0.00 2.43
2545 4658 4.401925 AGTGCTCATTTTAGGCTCAGTTT 58.598 39.130 0.00 0.00 0.00 2.66
2546 4659 4.006319 GAGTGCTCATTTTAGGCTCAGTT 58.994 43.478 0.00 0.00 0.00 3.16
2547 4660 3.262915 AGAGTGCTCATTTTAGGCTCAGT 59.737 43.478 0.00 0.00 0.00 3.41
2548 4661 3.870419 GAGAGTGCTCATTTTAGGCTCAG 59.130 47.826 0.00 0.00 40.96 3.35
2549 4662 3.261643 TGAGAGTGCTCATTTTAGGCTCA 59.738 43.478 0.00 0.00 45.88 4.26
2550 4663 3.866651 TGAGAGTGCTCATTTTAGGCTC 58.133 45.455 0.00 0.00 45.88 4.70
2551 4664 3.988976 TGAGAGTGCTCATTTTAGGCT 57.011 42.857 1.82 0.00 45.88 4.58
2561 4674 1.011451 GTTGAGGCGTGAGAGTGCTC 61.011 60.000 0.00 0.00 41.67 4.26
2562 4675 1.005630 GTTGAGGCGTGAGAGTGCT 60.006 57.895 0.00 0.00 0.00 4.40
2563 4676 0.671781 ATGTTGAGGCGTGAGAGTGC 60.672 55.000 0.00 0.00 0.00 4.40
2564 4677 1.800805 AATGTTGAGGCGTGAGAGTG 58.199 50.000 0.00 0.00 0.00 3.51
2565 4678 2.550830 AAATGTTGAGGCGTGAGAGT 57.449 45.000 0.00 0.00 0.00 3.24
2566 4679 3.250762 TCAAAAATGTTGAGGCGTGAGAG 59.749 43.478 0.00 0.00 0.00 3.20
2567 4680 3.003275 GTCAAAAATGTTGAGGCGTGAGA 59.997 43.478 0.00 0.00 0.00 3.27
2568 4681 3.300009 GTCAAAAATGTTGAGGCGTGAG 58.700 45.455 0.00 0.00 0.00 3.51
2569 4682 2.034053 GGTCAAAAATGTTGAGGCGTGA 59.966 45.455 0.00 0.00 0.00 4.35
2570 4683 2.393764 GGTCAAAAATGTTGAGGCGTG 58.606 47.619 0.00 0.00 0.00 5.34
2571 4684 1.001815 CGGTCAAAAATGTTGAGGCGT 60.002 47.619 0.00 0.00 0.00 5.68
2572 4685 1.001815 ACGGTCAAAAATGTTGAGGCG 60.002 47.619 0.00 0.00 0.00 5.52
2573 4686 2.793278 ACGGTCAAAAATGTTGAGGC 57.207 45.000 0.00 0.00 0.00 4.70
2574 4687 3.002862 TCGAACGGTCAAAAATGTTGAGG 59.997 43.478 0.00 0.00 0.00 3.86
2575 4688 4.203950 TCGAACGGTCAAAAATGTTGAG 57.796 40.909 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.