Multiple sequence alignment - TraesCS3D01G299900

Loading Multiple Alignment...

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 TraesCS3D01G299900 chr3D 100.000 4481 0 0 1 4481 414770141 414765661 0.000000e+00 8275.0
1 TraesCS3D01G299900 chr3D 85.000 480 62 9 3001 3477 414640313 414639841 3.140000e-131 479.0
2 TraesCS3D01G299900 chr3D 92.308 156 12 0 1001 1156 414641866 414641711 5.830000e-54 222.0
3 TraesCS3D01G299900 chr3A 93.186 2216 117 17 2283 4481 535325497 535327695 0.000000e+00 3225.0
4 TraesCS3D01G299900 chr3A 92.426 779 31 12 736 1490 535323513 535324287 0.000000e+00 1086.0
5 TraesCS3D01G299900 chr3A 93.498 323 19 2 75 395 535322840 535323162 3.140000e-131 479.0
6 TraesCS3D01G299900 chr3A 84.472 483 64 9 2998 3477 535719205 535719679 2.440000e-127 466.0
7 TraesCS3D01G299900 chr3A 89.961 259 15 7 395 646 535323189 535323443 1.550000e-84 324.0
8 TraesCS3D01G299900 chr3A 90.446 157 14 1 2100 2255 535325209 535325365 5.880000e-49 206.0
9 TraesCS3D01G299900 chr3A 93.651 63 3 1 1475 1537 535325148 535325209 4.770000e-15 93.5
10 TraesCS3D01G299900 chr3B 90.505 1485 72 26 2283 3747 540659182 540657747 0.000000e+00 1897.0
11 TraesCS3D01G299900 chr3B 90.307 1238 53 24 733 1924 540660879 540659663 0.000000e+00 1559.0
12 TraesCS3D01G299900 chr3B 84.807 441 65 2 3038 3477 540482533 540482094 4.110000e-120 442.0
13 TraesCS3D01G299900 chr3B 93.722 223 14 0 3871 4093 540657397 540657175 7.180000e-88 335.0
14 TraesCS3D01G299900 chr3B 88.341 223 22 2 1918 2139 540659612 540659393 9.560000e-67 265.0
15 TraesCS3D01G299900 chr3B 80.886 361 37 18 296 628 540661266 540660910 5.750000e-64 255.0
16 TraesCS3D01G299900 chr3B 83.658 257 30 9 4219 4466 375984125 375983872 9.690000e-57 231.0
17 TraesCS3D01G299900 chr3B 91.720 157 13 0 1000 1156 540484021 540483865 7.550000e-53 219.0
18 TraesCS3D01G299900 chr3B 87.313 134 16 1 98 230 540661394 540661261 7.760000e-33 152.0
19 TraesCS3D01G299900 chr3B 95.161 62 3 0 397 458 540680086 540680025 1.030000e-16 99.0
20 TraesCS3D01G299900 chr7B 82.670 352 51 8 4128 4471 446699712 446699363 2.030000e-78 303.0
21 TraesCS3D01G299900 chr7B 100.000 30 0 0 4098 4127 70866008 70866037 6.260000e-04 56.5
22 TraesCS3D01G299900 chr5D 78.788 363 55 16 4125 4471 57817448 57817804 1.620000e-54 224.0
23 TraesCS3D01G299900 chr5D 87.349 166 18 3 4308 4471 503436567 503436403 2.130000e-43 187.0
24 TraesCS3D01G299900 chr2B 87.425 167 17 4 4308 4471 380245816 380245651 5.920000e-44 189.0
25 TraesCS3D01G299900 chrUn 80.827 266 27 12 4217 4471 358274370 358274118 2.130000e-43 187.0
26 TraesCS3D01G299900 chr2A 86.826 167 18 4 4308 4471 424447170 424447335 2.750000e-42 183.0
27 TraesCS3D01G299900 chr6B 85.632 174 19 5 4299 4469 640917721 640917551 1.280000e-40 178.0
28 TraesCS3D01G299900 chr1B 100.000 38 0 0 1064 1101 133075744 133075781 2.240000e-08 71.3
29 TraesCS3D01G299900 chr1D 97.368 38 1 0 1064 1101 80537156 80537193 1.040000e-06 65.8
30 TraesCS3D01G299900 chr1D 100.000 32 0 0 1064 1095 80448391 80448422 4.840000e-05 60.2
31 TraesCS3D01G299900 chr4A 100.000 29 0 0 4097 4125 610457951 610457923 2.000000e-03 54.7
32 TraesCS3D01G299900 chr2D 100.000 29 0 0 4097 4125 128486509 128486537 2.000000e-03 54.7


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 TraesCS3D01G299900 chr3D 414765661 414770141 4480 True 8275.000000 8275 100.000000 1 4481 1 chr3D.!!$R1 4480
1 TraesCS3D01G299900 chr3D 414639841 414641866 2025 True 350.500000 479 88.654000 1001 3477 2 chr3D.!!$R2 2476
2 TraesCS3D01G299900 chr3A 535322840 535327695 4855 False 902.250000 3225 92.194667 75 4481 6 chr3A.!!$F2 4406
3 TraesCS3D01G299900 chr3B 540657175 540661394 4219 True 743.833333 1897 88.512333 98 4093 6 chr3B.!!$R4 3995
4 TraesCS3D01G299900 chr3B 540482094 540484021 1927 True 330.500000 442 88.263500 1000 3477 2 chr3B.!!$R3 2477


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
31 32 0.029300 CGCCATGGTTTTATGAGCCG 59.971 55.0 14.67 0.0 0.00 5.52 F
68 69 0.039165 CAGCTCGGGCCAAACTTTTC 60.039 55.0 2.00 0.0 39.73 2.29 F
71 72 0.040425 CTCGGGCCAAACTTTTCACG 60.040 55.0 4.39 0.0 0.00 4.35 F
1191 1292 0.257616 CCGCCCTCCCCTTGAATTTA 59.742 55.0 0.00 0.0 0.00 1.40 F
2216 3332 0.038744 CCCAAGAGTCCCAAGCACAT 59.961 55.0 0.00 0.0 0.00 3.21 F
3273 4872 0.035317 AGATCAAGAACGTGCTGGCA 59.965 50.0 0.00 0.0 0.00 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1191 1292 0.173481 CATCGACAGTCACGGATGGT 59.827 55.0 0.41 0.0 0.00 3.55 R
1351 1458 0.180878 CTCCGGCCCCCGTTAAAATA 59.819 55.0 0.00 0.0 46.80 1.40 R
1882 2889 0.400594 AAGAGTAACAGGGTGGGTGC 59.599 55.0 0.00 0.0 0.00 5.01 R
2485 3725 0.527113 TGCAAAAGCATCATGACCCG 59.473 50.0 0.00 0.0 0.00 5.28 R
3384 4983 0.098376 GGTACGCGTCGAACAGAGAT 59.902 55.0 18.63 0.0 0.00 2.75 R
4363 6189 0.034337 TGTGCTCCACGGACTAAACC 59.966 55.0 0.00 0.0 37.14 3.27 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
23 24 2.953821 CGCAGACGCCATGGTTTT 59.046 55.556 14.67 0.00 33.11 2.43
24 25 2.167161 CGCAGACGCCATGGTTTTA 58.833 52.632 14.67 0.00 33.11 1.52
25 26 0.732571 CGCAGACGCCATGGTTTTAT 59.267 50.000 14.67 0.00 33.11 1.40
26 27 1.531677 CGCAGACGCCATGGTTTTATG 60.532 52.381 14.67 6.62 33.11 1.90
27 28 1.742831 GCAGACGCCATGGTTTTATGA 59.257 47.619 14.67 0.00 0.00 2.15
28 29 2.223340 GCAGACGCCATGGTTTTATGAG 60.223 50.000 14.67 0.00 0.00 2.90
29 30 2.017049 AGACGCCATGGTTTTATGAGC 58.983 47.619 14.67 0.00 0.00 4.26
30 31 1.065551 GACGCCATGGTTTTATGAGCC 59.934 52.381 14.67 0.00 0.00 4.70
31 32 0.029300 CGCCATGGTTTTATGAGCCG 59.971 55.000 14.67 0.00 0.00 5.52
32 33 0.385390 GCCATGGTTTTATGAGCCGG 59.615 55.000 14.67 0.00 0.00 6.13
33 34 1.032014 CCATGGTTTTATGAGCCGGG 58.968 55.000 2.18 0.00 0.00 5.73
34 35 0.385390 CATGGTTTTATGAGCCGGGC 59.615 55.000 12.11 12.11 0.00 6.13
35 36 0.755327 ATGGTTTTATGAGCCGGGCC 60.755 55.000 17.02 8.02 0.00 5.80
36 37 1.076995 GGTTTTATGAGCCGGGCCT 60.077 57.895 17.02 2.62 0.00 5.19
37 38 0.683179 GGTTTTATGAGCCGGGCCTT 60.683 55.000 17.02 8.14 0.00 4.35
38 39 1.182667 GTTTTATGAGCCGGGCCTTT 58.817 50.000 17.02 2.68 0.00 3.11
39 40 1.548719 GTTTTATGAGCCGGGCCTTTT 59.451 47.619 17.02 0.00 0.00 2.27
40 41 1.931635 TTTATGAGCCGGGCCTTTTT 58.068 45.000 17.02 0.00 0.00 1.94
58 59 3.402628 TTTTATAGGATCAGCTCGGGC 57.597 47.619 0.00 0.00 39.06 6.13
59 60 1.267121 TTATAGGATCAGCTCGGGCC 58.733 55.000 2.00 0.00 39.73 5.80
60 61 0.114364 TATAGGATCAGCTCGGGCCA 59.886 55.000 2.00 0.00 39.73 5.36
61 62 0.764369 ATAGGATCAGCTCGGGCCAA 60.764 55.000 2.00 0.00 39.73 4.52
62 63 0.980754 TAGGATCAGCTCGGGCCAAA 60.981 55.000 2.00 0.00 39.73 3.28
63 64 2.115291 GGATCAGCTCGGGCCAAAC 61.115 63.158 2.00 0.00 39.73 2.93
64 65 1.078143 GATCAGCTCGGGCCAAACT 60.078 57.895 2.00 0.00 39.73 2.66
65 66 0.678048 GATCAGCTCGGGCCAAACTT 60.678 55.000 2.00 0.00 39.73 2.66
66 67 0.251341 ATCAGCTCGGGCCAAACTTT 60.251 50.000 2.00 0.00 39.73 2.66
67 68 0.467290 TCAGCTCGGGCCAAACTTTT 60.467 50.000 2.00 0.00 39.73 2.27
68 69 0.039165 CAGCTCGGGCCAAACTTTTC 60.039 55.000 2.00 0.00 39.73 2.29
69 70 0.467290 AGCTCGGGCCAAACTTTTCA 60.467 50.000 2.00 0.00 39.73 2.69
70 71 0.318699 GCTCGGGCCAAACTTTTCAC 60.319 55.000 4.39 0.00 0.00 3.18
71 72 0.040425 CTCGGGCCAAACTTTTCACG 60.040 55.000 4.39 0.00 0.00 4.35
72 73 1.007849 CGGGCCAAACTTTTCACGG 60.008 57.895 4.39 0.00 0.00 4.94
73 74 1.365999 GGGCCAAACTTTTCACGGG 59.634 57.895 4.39 0.00 0.00 5.28
86 87 3.495434 TTCACGGGTCATGTAAAAGGT 57.505 42.857 0.00 0.00 0.00 3.50
225 226 6.771188 AGAAGACGTTTTTGTCACTATGAG 57.229 37.500 0.00 0.00 41.41 2.90
233 234 4.829064 TTTGTCACTATGAGGTGTTTGC 57.171 40.909 0.00 0.00 38.28 3.68
259 260 7.435488 CGATAACTTCGTCCATCTTAAGATTGT 59.565 37.037 15.49 3.92 43.01 2.71
260 261 6.727824 AACTTCGTCCATCTTAAGATTGTG 57.272 37.500 15.49 6.42 31.21 3.33
303 305 1.559065 GCTTAGGGGTAGGGTGTGCA 61.559 60.000 0.00 0.00 0.00 4.57
330 332 1.133407 TGTTCGTGCGTGTGTACATC 58.867 50.000 0.00 0.00 0.00 3.06
464 494 3.291809 AACAAACTTAATTTCCGGCCG 57.708 42.857 21.04 21.04 0.00 6.13
465 495 2.506444 ACAAACTTAATTTCCGGCCGA 58.494 42.857 30.73 7.23 0.00 5.54
466 496 2.885894 ACAAACTTAATTTCCGGCCGAA 59.114 40.909 30.73 15.30 0.00 4.30
468 498 2.484742 ACTTAATTTCCGGCCGAACT 57.515 45.000 30.73 6.18 0.00 3.01
469 499 3.615224 ACTTAATTTCCGGCCGAACTA 57.385 42.857 30.73 4.95 0.00 2.24
470 500 3.941573 ACTTAATTTCCGGCCGAACTAA 58.058 40.909 30.73 13.44 0.00 2.24
472 502 4.761227 ACTTAATTTCCGGCCGAACTAAAA 59.239 37.500 30.73 17.94 0.00 1.52
473 503 3.842732 AATTTCCGGCCGAACTAAAAG 57.157 42.857 30.73 7.15 0.00 2.27
474 504 2.259266 TTTCCGGCCGAACTAAAAGT 57.741 45.000 30.73 0.00 0.00 2.66
545 591 5.966742 AACTAAAAGTGATGGAGAAAGGC 57.033 39.130 0.00 0.00 0.00 4.35
628 678 3.546271 GTCGCTGAAAAGTGAAAACCAAC 59.454 43.478 0.00 0.00 0.00 3.77
637 705 8.617809 TGAAAAGTGAAAACCAACTATACAGAC 58.382 33.333 0.00 0.00 0.00 3.51
649 717 7.616150 ACCAACTATACAGACACAGAATAGAGT 59.384 37.037 0.00 0.00 0.00 3.24
652 720 7.347252 ACTATACAGACACAGAATAGAGTGGA 58.653 38.462 0.00 0.00 39.99 4.02
654 722 4.411927 ACAGACACAGAATAGAGTGGAGT 58.588 43.478 0.00 0.00 39.99 3.85
655 723 5.571285 ACAGACACAGAATAGAGTGGAGTA 58.429 41.667 0.00 0.00 39.99 2.59
656 724 5.416326 ACAGACACAGAATAGAGTGGAGTAC 59.584 44.000 0.00 0.00 39.99 2.73
657 725 5.650266 CAGACACAGAATAGAGTGGAGTACT 59.350 44.000 0.00 0.00 44.02 2.73
658 726 6.824196 CAGACACAGAATAGAGTGGAGTACTA 59.176 42.308 0.00 0.00 40.53 1.82
659 727 7.011950 CAGACACAGAATAGAGTGGAGTACTAG 59.988 44.444 0.00 0.00 40.53 2.57
691 763 9.810231 AGCTCGTGCAAAAATAAAATAAAATTG 57.190 25.926 12.58 0.00 42.74 2.32
692 764 9.804547 GCTCGTGCAAAAATAAAATAAAATTGA 57.195 25.926 4.26 0.00 39.41 2.57
710 782 8.870075 AAAATTGAGGAGTACTGCTATTTCTT 57.130 30.769 17.74 5.87 0.00 2.52
711 783 8.870075 AAATTGAGGAGTACTGCTATTTCTTT 57.130 30.769 17.74 9.78 0.00 2.52
712 784 8.870075 AATTGAGGAGTACTGCTATTTCTTTT 57.130 30.769 17.74 2.22 0.00 2.27
713 785 8.870075 ATTGAGGAGTACTGCTATTTCTTTTT 57.130 30.769 17.74 0.00 0.00 1.94
800 872 2.606519 AGCCGCACCTTCCACCTA 60.607 61.111 0.00 0.00 0.00 3.08
809 881 1.358152 CCTTCCACCTAACCTCACCA 58.642 55.000 0.00 0.00 0.00 4.17
985 1074 2.468532 AAAAAGGTTCGAGTGCGTTG 57.531 45.000 0.00 0.00 38.98 4.10
1170 1266 1.268992 TACGTGCCCATGCCCTAACT 61.269 55.000 0.00 0.00 36.33 2.24
1191 1292 0.257616 CCGCCCTCCCCTTGAATTTA 59.742 55.000 0.00 0.00 0.00 1.40
1213 1314 0.456221 ATCCGTGACTGTCGATGGTC 59.544 55.000 11.97 11.97 0.00 4.02
1341 1448 1.069204 GTCGCTTCCATGCCTCTATCA 59.931 52.381 0.00 0.00 0.00 2.15
1349 1456 5.894298 TCCATGCCTCTATCACTGTTTAT 57.106 39.130 0.00 0.00 0.00 1.40
1350 1457 6.252599 TCCATGCCTCTATCACTGTTTATT 57.747 37.500 0.00 0.00 0.00 1.40
1351 1458 6.662755 TCCATGCCTCTATCACTGTTTATTT 58.337 36.000 0.00 0.00 0.00 1.40
1352 1459 7.801104 TCCATGCCTCTATCACTGTTTATTTA 58.199 34.615 0.00 0.00 0.00 1.40
1384 1491 1.064946 CGGAGAGATGTCGCTGTCC 59.935 63.158 0.00 0.00 43.07 4.02
1405 1514 8.148437 TGTCCCTCTCGTATAATCTAGTATCT 57.852 38.462 0.00 0.00 0.00 1.98
1466 1576 5.671493 AGACTGGGGTTCGATATTTACAAG 58.329 41.667 0.00 0.00 0.00 3.16
1483 2474 3.703420 ACAAGTCATTCGAGTATACGGC 58.297 45.455 0.00 0.00 0.00 5.68
1512 2503 1.140589 CCGCAGCTCGTCTCAGATT 59.859 57.895 5.15 0.00 36.19 2.40
1556 2547 3.429272 CCGCGTGGTGACCTTAATTAGTA 60.429 47.826 6.91 0.00 0.00 1.82
1585 2577 4.700213 GCTGCTACCCAATCTTTTAGTCAA 59.300 41.667 0.00 0.00 0.00 3.18
1620 2612 5.375417 CACTTGCAGTGTGGATAAAATCA 57.625 39.130 12.37 0.00 41.19 2.57
1621 2613 5.957798 CACTTGCAGTGTGGATAAAATCAT 58.042 37.500 12.37 0.00 41.19 2.45
1623 2615 6.968904 CACTTGCAGTGTGGATAAAATCATAC 59.031 38.462 12.37 0.00 41.19 2.39
1624 2616 6.658816 ACTTGCAGTGTGGATAAAATCATACA 59.341 34.615 0.00 0.00 0.00 2.29
1625 2617 6.682423 TGCAGTGTGGATAAAATCATACAG 57.318 37.500 0.00 0.00 31.54 2.74
1626 2618 6.179756 TGCAGTGTGGATAAAATCATACAGT 58.820 36.000 0.00 0.00 34.19 3.55
1627 2619 7.334858 TGCAGTGTGGATAAAATCATACAGTA 58.665 34.615 0.00 0.00 33.27 2.74
1649 2641 3.550820 TCATATTTTCCCCACATCCACG 58.449 45.455 0.00 0.00 0.00 4.94
1690 2682 4.627467 CACCTACTTCACTGTATCAAGTGC 59.373 45.833 8.47 0.00 45.93 4.40
1695 2687 5.479306 ACTTCACTGTATCAAGTGCGTTAT 58.521 37.500 0.00 0.00 45.93 1.89
1707 2699 4.916099 AGTGCGTTATTTTACGTCTTCC 57.084 40.909 0.00 0.00 43.22 3.46
1744 2737 5.818136 ATACAAGATTTGGATTCGGTGTG 57.182 39.130 0.00 0.00 26.62 3.82
1746 2739 3.081061 CAAGATTTGGATTCGGTGTGGA 58.919 45.455 0.00 0.00 0.00 4.02
1758 2751 5.682943 TTCGGTGTGGAAATTTGTTCTAG 57.317 39.130 0.00 0.00 0.00 2.43
1772 2779 7.602517 ATTTGTTCTAGATGTGTTAGTGCTC 57.397 36.000 0.00 0.00 0.00 4.26
1797 2804 4.082571 GCTAGTTCGTAGGTACCTTGACAA 60.083 45.833 22.11 7.54 0.00 3.18
1821 2828 5.680594 TTAATCTTGCAGCAAATCCCAAT 57.319 34.783 9.65 0.00 0.00 3.16
1850 2857 4.034510 GCAGTATACAGTGTGAGCAAATCC 59.965 45.833 5.88 0.00 0.00 3.01
1897 2904 1.303317 CCAGCACCCACCCTGTTAC 60.303 63.158 0.00 0.00 0.00 2.50
1898 2905 1.761174 CAGCACCCACCCTGTTACT 59.239 57.895 0.00 0.00 0.00 2.24
1899 2906 0.321653 CAGCACCCACCCTGTTACTC 60.322 60.000 0.00 0.00 0.00 2.59
1919 2932 5.250200 ACTCTTGTGTCACTTTGTACCAAA 58.750 37.500 4.27 0.00 0.00 3.28
2018 3134 5.365021 AGTCATCCCTATCCTTTGACTTG 57.635 43.478 0.00 0.00 43.24 3.16
2035 3151 9.612620 CTTTGACTTGTTTCTTATCAATACACC 57.387 33.333 0.00 0.00 0.00 4.16
2036 3152 8.684386 TTGACTTGTTTCTTATCAATACACCA 57.316 30.769 0.00 0.00 0.00 4.17
2060 3176 7.443272 CCACATACATCTATCAGATTTGCTTGA 59.557 37.037 0.00 0.00 31.32 3.02
2068 3184 4.574674 TCAGATTTGCTTGATGGTAGGT 57.425 40.909 0.00 0.00 0.00 3.08
2092 3208 4.637600 AGGTGTGGTAATAATAGGGTGGA 58.362 43.478 0.00 0.00 0.00 4.02
2093 3209 5.232347 AGGTGTGGTAATAATAGGGTGGAT 58.768 41.667 0.00 0.00 0.00 3.41
2110 3226 4.321230 GGTGGATGTTAAGGTTTGCAAGAG 60.321 45.833 0.00 0.00 0.00 2.85
2135 3251 5.486526 CATATTCTCTTCCAGTATGAGGCC 58.513 45.833 0.00 0.00 39.69 5.19
2190 3306 6.348540 CCTTGGTTCAGCAAACTATCTTACAC 60.349 42.308 2.53 0.00 38.02 2.90
2195 3311 7.309194 GGTTCAGCAAACTATCTTACACCATTT 60.309 37.037 2.53 0.00 38.02 2.32
2201 3317 7.094118 GCAAACTATCTTACACCATTTACCCAA 60.094 37.037 0.00 0.00 0.00 4.12
2214 3330 0.690762 TACCCAAGAGTCCCAAGCAC 59.309 55.000 0.00 0.00 0.00 4.40
2215 3331 1.352622 ACCCAAGAGTCCCAAGCACA 61.353 55.000 0.00 0.00 0.00 4.57
2216 3332 0.038744 CCCAAGAGTCCCAAGCACAT 59.961 55.000 0.00 0.00 0.00 3.21
2217 3333 1.171308 CCAAGAGTCCCAAGCACATG 58.829 55.000 0.00 0.00 0.00 3.21
2218 3334 1.546323 CCAAGAGTCCCAAGCACATGT 60.546 52.381 0.00 0.00 0.00 3.21
2219 3335 1.538512 CAAGAGTCCCAAGCACATGTG 59.461 52.381 21.83 21.83 0.00 3.21
2251 3368 8.031864 TCAGAAAGTTGACAGCAAAACATAAAA 58.968 29.630 0.00 0.00 35.42 1.52
2255 3436 6.630071 AGTTGACAGCAAAACATAAAACAGT 58.370 32.000 0.00 0.00 35.42 3.55
2275 3456 3.956848 AGTCACTACAGCAGCATCTCATA 59.043 43.478 0.00 0.00 0.00 2.15
2280 3461 4.520111 ACTACAGCAGCATCTCATAGAGAG 59.480 45.833 2.94 0.00 42.26 3.20
2447 3686 4.557695 CGGTATGATGCTACCTCTTGAGAC 60.558 50.000 0.00 0.00 39.26 3.36
2485 3725 8.921205 TCTACCCCTCATAAACAGAACTATAAC 58.079 37.037 0.00 0.00 0.00 1.89
2572 3829 7.307455 GCCTTGTAGTATAACAAAGCTAGCATC 60.307 40.741 18.83 0.00 41.50 3.91
2590 3852 3.448660 GCATCTCCACTTGGGCTTAAATT 59.551 43.478 0.00 0.00 36.21 1.82
2618 3880 6.183361 ACCTGAGCCTTTACTAGAAACAAAGA 60.183 38.462 0.00 0.00 32.20 2.52
2712 3989 3.328382 TGTCTAATTGTTAGCTGCCGT 57.672 42.857 0.00 0.00 33.23 5.68
2733 4010 5.047306 CCGTCTGGCATTATATTAGGAGTCA 60.047 44.000 0.00 0.00 0.00 3.41
2734 4011 6.455647 CGTCTGGCATTATATTAGGAGTCAA 58.544 40.000 0.00 0.00 0.00 3.18
2788 4385 3.515630 CTCGTATGCTTGAAGCTTGAGA 58.484 45.455 18.94 13.60 42.97 3.27
2801 4398 8.975663 TTGAAGCTTGAGATTAGAATGATGAT 57.024 30.769 2.10 0.00 0.00 2.45
2834 4431 8.726870 TTATATAGTTACCAACCACAAGCTTC 57.273 34.615 0.00 0.00 0.00 3.86
2993 4592 9.722184 GGAATAAAATAGTACCATACTCCCTTC 57.278 37.037 0.00 0.00 40.14 3.46
3035 4634 7.360361 TGGTTCTATTTTCTTTTTCTCTTCGC 58.640 34.615 0.00 0.00 0.00 4.70
3273 4872 0.035317 AGATCAAGAACGTGCTGGCA 59.965 50.000 0.00 0.00 0.00 4.92
3320 4919 1.205893 CAAGTACCTGGCTGGAGACTC 59.794 57.143 18.12 0.00 39.71 3.36
3433 5032 2.520536 GCCTGGTGGACTGACCTGT 61.521 63.158 0.00 0.00 39.86 4.00
3527 5126 1.659098 CGAAATAAGCCGAGGTGTGTC 59.341 52.381 0.00 0.00 0.00 3.67
3583 5182 2.562738 TGTGATGTCTCCTCGTGTTGAT 59.437 45.455 0.00 0.00 0.00 2.57
3639 5239 5.645067 TCTTGTACTGAAATGAGCATTCCTG 59.355 40.000 0.00 0.00 0.00 3.86
3670 5270 7.560368 TGGTTTAATAATAAATTGTGCCCAGG 58.440 34.615 0.00 0.00 33.76 4.45
3682 5282 4.853468 TGTGCCCAGGTATTTATCTCAA 57.147 40.909 0.00 0.00 0.00 3.02
3686 5286 5.652452 GTGCCCAGGTATTTATCTCAACTTT 59.348 40.000 0.00 0.00 0.00 2.66
3719 5319 2.897436 TCTGTTGCTTCGATGATCTGG 58.103 47.619 1.89 0.00 0.00 3.86
3728 5328 1.973515 TCGATGATCTGGCCATTAGCT 59.026 47.619 5.51 0.00 43.05 3.32
3729 5329 2.028658 TCGATGATCTGGCCATTAGCTC 60.029 50.000 5.51 0.00 43.05 4.09
3787 5387 0.387929 AGTCTGTTTCGGAAGACGCA 59.612 50.000 3.39 0.00 46.05 5.24
3789 5389 0.944311 TCTGTTTCGGAAGACGCAGC 60.944 55.000 0.00 0.00 43.86 5.25
3846 5446 2.827921 GTTTGTGCCATTTGATCCTCCT 59.172 45.455 0.00 0.00 0.00 3.69
3861 5461 9.449719 TTTGATCCTCCTAAGTTGAATAGTTTC 57.550 33.333 0.00 0.00 0.00 2.78
3863 5463 8.260818 TGATCCTCCTAAGTTGAATAGTTTCAG 58.739 37.037 0.00 0.00 42.60 3.02
3889 5715 4.340381 GCCAAAGAGCACCATATGATTCTT 59.660 41.667 3.65 4.95 36.10 2.52
3946 5772 7.926018 CACACCTAGCATGTGTAGTGATATTTA 59.074 37.037 14.28 0.00 44.77 1.40
3963 5789 7.800380 GTGATATTTATCCAATGCTTCTTCACG 59.200 37.037 0.00 0.00 31.71 4.35
4103 5929 1.303561 GGGCCTCTGACATGCACAA 60.304 57.895 0.84 0.00 0.00 3.33
4124 5950 4.399004 AGTGCTTAGATGAGGTGCTAAG 57.601 45.455 0.00 0.00 43.95 2.18
4159 5985 3.508426 GACTAGGGGTCCTAACCTATGG 58.492 54.545 0.00 0.00 45.66 2.74
4187 6013 4.184629 GTTATCTATGGGCCGAGCTAATG 58.815 47.826 0.00 0.00 0.00 1.90
4197 6023 0.753262 CGAGCTAATGGCCCACTAGT 59.247 55.000 0.00 0.00 43.05 2.57
4198 6024 1.139058 CGAGCTAATGGCCCACTAGTT 59.861 52.381 0.00 0.00 43.05 2.24
4203 6029 0.676782 AATGGCCCACTAGTTGTCGC 60.677 55.000 0.00 0.00 0.00 5.19
4252 6078 2.161609 CGTAAGCAAGATGGAAACCACC 59.838 50.000 0.00 0.00 35.80 4.61
4254 6080 0.400213 AGCAAGATGGAAACCACCGA 59.600 50.000 0.00 0.00 35.80 4.69
4281 6107 8.095169 AGACTTCGTATACTTCAAGGACAATTT 58.905 33.333 0.56 0.00 0.00 1.82
4317 6143 3.985019 TTATTCCTAGTTGCCAACCGA 57.015 42.857 3.45 0.00 0.00 4.69
4324 6150 3.070446 CCTAGTTGCCAACCGACCATATA 59.930 47.826 3.45 0.00 0.00 0.86
4358 6184 1.280998 ACCCCGGTGCATATATAAGCC 59.719 52.381 7.45 0.00 0.00 4.35
4363 6189 2.738643 CGGTGCATATATAAGCCGAGGG 60.739 54.545 7.45 0.00 41.45 4.30
4371 6197 4.886496 ATATAAGCCGAGGGGTTTAGTC 57.114 45.455 4.25 0.00 40.84 2.59
4373 6199 1.896122 AAGCCGAGGGGTTTAGTCCG 61.896 60.000 0.00 0.00 40.84 4.79
4375 6201 1.217244 CCGAGGGGTTTAGTCCGTG 59.783 63.158 0.00 0.00 0.00 4.94
4376 6202 1.217244 CGAGGGGTTTAGTCCGTGG 59.783 63.158 0.00 0.00 0.00 4.94
4388 6214 0.719465 GTCCGTGGAGCACAATTACG 59.281 55.000 0.00 0.00 33.40 3.18
4402 6228 5.180271 CACAATTACGAGCCTTAGGGTTTA 58.820 41.667 3.86 0.00 31.55 2.01
4412 6238 5.254115 AGCCTTAGGGTTTAGAACACAATC 58.746 41.667 0.00 0.00 37.23 2.67
4420 6246 8.682936 AGGGTTTAGAACACAATCATATGATC 57.317 34.615 18.44 6.18 37.23 2.92
4422 6248 8.778358 GGGTTTAGAACACAATCATATGATCTC 58.222 37.037 18.44 10.13 34.08 2.75
4458 6285 2.769663 TGTACCTGTACCCCATCACATC 59.230 50.000 5.07 0.00 35.26 3.06
4471 6298 6.612456 ACCCCATCACATCAATACAATCAAAT 59.388 34.615 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 0.732571 ATAAAACCATGGCGTCTGCG 59.267 50.000 13.04 0.00 44.10 5.18
7 8 1.742831 TCATAAAACCATGGCGTCTGC 59.257 47.619 13.04 0.00 41.71 4.26
8 9 2.223340 GCTCATAAAACCATGGCGTCTG 60.223 50.000 13.04 3.58 0.00 3.51
9 10 2.017049 GCTCATAAAACCATGGCGTCT 58.983 47.619 13.04 0.00 0.00 4.18
10 11 1.065551 GGCTCATAAAACCATGGCGTC 59.934 52.381 13.04 0.00 0.00 5.19
11 12 1.102978 GGCTCATAAAACCATGGCGT 58.897 50.000 13.04 0.00 0.00 5.68
12 13 0.029300 CGGCTCATAAAACCATGGCG 59.971 55.000 13.04 0.00 37.17 5.69
13 14 0.385390 CCGGCTCATAAAACCATGGC 59.615 55.000 13.04 0.00 0.00 4.40
14 15 1.032014 CCCGGCTCATAAAACCATGG 58.968 55.000 11.19 11.19 0.00 3.66
15 16 0.385390 GCCCGGCTCATAAAACCATG 59.615 55.000 0.71 0.00 0.00 3.66
16 17 0.755327 GGCCCGGCTCATAAAACCAT 60.755 55.000 9.86 0.00 0.00 3.55
17 18 1.379309 GGCCCGGCTCATAAAACCA 60.379 57.895 9.86 0.00 0.00 3.67
18 19 0.683179 AAGGCCCGGCTCATAAAACC 60.683 55.000 9.86 0.00 0.00 3.27
19 20 1.182667 AAAGGCCCGGCTCATAAAAC 58.817 50.000 9.86 0.00 0.00 2.43
20 21 1.931635 AAAAGGCCCGGCTCATAAAA 58.068 45.000 9.86 0.00 0.00 1.52
21 22 1.931635 AAAAAGGCCCGGCTCATAAA 58.068 45.000 9.86 0.00 0.00 1.40
22 23 3.681909 AAAAAGGCCCGGCTCATAA 57.318 47.368 9.86 0.00 0.00 1.90
37 38 3.496160 GGCCCGAGCTGATCCTATAAAAA 60.496 47.826 0.00 0.00 39.73 1.94
38 39 2.038557 GGCCCGAGCTGATCCTATAAAA 59.961 50.000 0.00 0.00 39.73 1.52
39 40 1.623811 GGCCCGAGCTGATCCTATAAA 59.376 52.381 0.00 0.00 39.73 1.40
40 41 1.267121 GGCCCGAGCTGATCCTATAA 58.733 55.000 0.00 0.00 39.73 0.98
41 42 0.114364 TGGCCCGAGCTGATCCTATA 59.886 55.000 0.00 0.00 39.73 1.31
42 43 0.764369 TTGGCCCGAGCTGATCCTAT 60.764 55.000 0.00 0.00 39.73 2.57
43 44 0.980754 TTTGGCCCGAGCTGATCCTA 60.981 55.000 0.00 0.00 39.73 2.94
44 45 2.300967 TTTGGCCCGAGCTGATCCT 61.301 57.895 0.00 0.00 39.73 3.24
45 46 2.115291 GTTTGGCCCGAGCTGATCC 61.115 63.158 0.00 0.00 39.73 3.36
46 47 0.678048 AAGTTTGGCCCGAGCTGATC 60.678 55.000 0.00 0.00 39.73 2.92
47 48 0.251341 AAAGTTTGGCCCGAGCTGAT 60.251 50.000 0.00 0.00 39.73 2.90
48 49 0.467290 AAAAGTTTGGCCCGAGCTGA 60.467 50.000 0.00 0.00 39.73 4.26
49 50 0.039165 GAAAAGTTTGGCCCGAGCTG 60.039 55.000 0.00 0.00 39.73 4.24
50 51 0.467290 TGAAAAGTTTGGCCCGAGCT 60.467 50.000 0.00 0.00 39.73 4.09
51 52 0.318699 GTGAAAAGTTTGGCCCGAGC 60.319 55.000 0.00 0.00 38.76 5.03
52 53 0.040425 CGTGAAAAGTTTGGCCCGAG 60.040 55.000 0.00 0.00 0.00 4.63
53 54 1.448922 CCGTGAAAAGTTTGGCCCGA 61.449 55.000 0.00 0.00 0.00 5.14
54 55 1.007849 CCGTGAAAAGTTTGGCCCG 60.008 57.895 0.00 0.00 0.00 6.13
55 56 1.365999 CCCGTGAAAAGTTTGGCCC 59.634 57.895 0.00 0.00 0.00 5.80
56 57 0.031585 GACCCGTGAAAAGTTTGGCC 59.968 55.000 0.00 0.00 0.00 5.36
57 58 0.741915 TGACCCGTGAAAAGTTTGGC 59.258 50.000 0.00 0.00 0.00 4.52
58 59 2.360801 ACATGACCCGTGAAAAGTTTGG 59.639 45.455 0.00 0.00 0.00 3.28
59 60 3.708563 ACATGACCCGTGAAAAGTTTG 57.291 42.857 0.00 0.00 0.00 2.93
60 61 5.838531 TTTACATGACCCGTGAAAAGTTT 57.161 34.783 0.00 0.00 0.00 2.66
61 62 5.221165 CCTTTTACATGACCCGTGAAAAGTT 60.221 40.000 0.00 0.00 32.46 2.66
62 63 4.277423 CCTTTTACATGACCCGTGAAAAGT 59.723 41.667 0.00 0.00 32.46 2.66
63 64 4.277423 ACCTTTTACATGACCCGTGAAAAG 59.723 41.667 0.00 3.86 33.17 2.27
64 65 4.208746 ACCTTTTACATGACCCGTGAAAA 58.791 39.130 0.00 0.00 0.00 2.29
65 66 3.816523 GACCTTTTACATGACCCGTGAAA 59.183 43.478 0.00 0.00 0.00 2.69
66 67 3.404899 GACCTTTTACATGACCCGTGAA 58.595 45.455 0.00 0.00 0.00 3.18
67 68 2.289819 GGACCTTTTACATGACCCGTGA 60.290 50.000 0.00 0.00 0.00 4.35
68 69 2.081462 GGACCTTTTACATGACCCGTG 58.919 52.381 0.00 0.00 0.00 4.94
69 70 1.338389 CGGACCTTTTACATGACCCGT 60.338 52.381 0.00 0.00 0.00 5.28
70 71 1.066716 TCGGACCTTTTACATGACCCG 60.067 52.381 0.00 0.00 37.29 5.28
71 72 2.353323 GTCGGACCTTTTACATGACCC 58.647 52.381 0.00 0.00 0.00 4.46
72 73 1.997606 CGTCGGACCTTTTACATGACC 59.002 52.381 0.00 0.00 0.00 4.02
73 74 2.921754 CTCGTCGGACCTTTTACATGAC 59.078 50.000 0.00 0.00 0.00 3.06
86 87 3.508793 GGATCCCATATAAACTCGTCGGA 59.491 47.826 0.00 0.00 0.00 4.55
200 201 7.173863 TCATAGTGACAAAAACGTCTTCTTC 57.826 36.000 0.00 0.00 36.82 2.87
233 234 7.435488 ACAATCTTAAGATGGACGAAGTTATCG 59.565 37.037 24.06 0.00 45.10 2.92
251 252 4.330944 ACTGAACCGACACACAATCTTA 57.669 40.909 0.00 0.00 0.00 2.10
254 255 4.495422 AGATACTGAACCGACACACAATC 58.505 43.478 0.00 0.00 0.00 2.67
259 260 4.219725 TCAATGAGATACTGAACCGACACA 59.780 41.667 0.00 0.00 0.00 3.72
260 261 4.744570 TCAATGAGATACTGAACCGACAC 58.255 43.478 0.00 0.00 0.00 3.67
303 305 1.540267 ACACGCACGAACACTCTAGAT 59.460 47.619 0.00 0.00 0.00 1.98
386 388 3.044305 GGACGCCTGTGCACACTC 61.044 66.667 17.42 9.46 36.29 3.51
405 435 7.361127 GCTTGGTTTACTTCCTTTTTCTCTAC 58.639 38.462 0.00 0.00 0.00 2.59
534 580 4.131376 CGCATCGCCTTTCTCCAT 57.869 55.556 0.00 0.00 0.00 3.41
545 591 2.126696 ATCGAGATCCGCGCATCG 60.127 61.111 8.75 9.05 38.37 3.84
628 678 7.500892 ACTCCACTCTATTCTGTGTCTGTATAG 59.499 40.741 0.00 0.00 32.76 1.31
637 705 7.867305 TTCTAGTACTCCACTCTATTCTGTG 57.133 40.000 0.00 0.00 38.80 3.66
666 738 9.804547 TCAATTTTATTTTATTTTTGCACGAGC 57.195 25.926 0.00 0.00 42.57 5.03
684 756 9.959721 AAGAAATAGCAGTACTCCTCAATTTTA 57.040 29.630 0.00 0.00 0.00 1.52
685 757 8.870075 AAGAAATAGCAGTACTCCTCAATTTT 57.130 30.769 0.00 0.00 0.00 1.82
686 758 8.870075 AAAGAAATAGCAGTACTCCTCAATTT 57.130 30.769 0.00 0.00 0.00 1.82
688 760 8.870075 AAAAAGAAATAGCAGTACTCCTCAAT 57.130 30.769 0.00 0.00 0.00 2.57
710 782 5.333798 CGATTAGTGCTCCTGTTTCGAAAAA 60.334 40.000 13.10 6.34 0.00 1.94
711 783 4.151689 CGATTAGTGCTCCTGTTTCGAAAA 59.848 41.667 13.10 2.56 0.00 2.29
712 784 3.678072 CGATTAGTGCTCCTGTTTCGAAA 59.322 43.478 6.47 6.47 0.00 3.46
713 785 3.057104 TCGATTAGTGCTCCTGTTTCGAA 60.057 43.478 0.00 0.00 30.95 3.71
714 786 2.490509 TCGATTAGTGCTCCTGTTTCGA 59.509 45.455 0.00 0.00 31.22 3.71
715 787 2.876091 TCGATTAGTGCTCCTGTTTCG 58.124 47.619 0.00 0.00 0.00 3.46
716 788 5.447818 CCATTTCGATTAGTGCTCCTGTTTC 60.448 44.000 0.00 0.00 0.00 2.78
717 789 4.396166 CCATTTCGATTAGTGCTCCTGTTT 59.604 41.667 0.00 0.00 0.00 2.83
718 790 3.941483 CCATTTCGATTAGTGCTCCTGTT 59.059 43.478 0.00 0.00 0.00 3.16
719 791 3.055094 ACCATTTCGATTAGTGCTCCTGT 60.055 43.478 0.00 0.00 0.00 4.00
720 792 3.535561 ACCATTTCGATTAGTGCTCCTG 58.464 45.455 0.00 0.00 0.00 3.86
721 793 3.914426 ACCATTTCGATTAGTGCTCCT 57.086 42.857 0.00 0.00 0.00 3.69
722 794 3.938963 TCAACCATTTCGATTAGTGCTCC 59.061 43.478 0.00 0.00 0.00 4.70
723 795 5.351465 TCTTCAACCATTTCGATTAGTGCTC 59.649 40.000 0.00 0.00 0.00 4.26
724 796 5.245531 TCTTCAACCATTTCGATTAGTGCT 58.754 37.500 0.00 0.00 0.00 4.40
725 797 5.545658 TCTTCAACCATTTCGATTAGTGC 57.454 39.130 0.00 0.00 0.00 4.40
726 798 6.519761 CGTTTCTTCAACCATTTCGATTAGTG 59.480 38.462 0.00 0.00 30.65 2.74
727 799 6.348213 CCGTTTCTTCAACCATTTCGATTAGT 60.348 38.462 0.00 0.00 30.65 2.24
728 800 6.021596 CCGTTTCTTCAACCATTTCGATTAG 58.978 40.000 0.00 0.00 30.65 1.73
729 801 5.701750 TCCGTTTCTTCAACCATTTCGATTA 59.298 36.000 0.00 0.00 30.65 1.75
730 802 4.517453 TCCGTTTCTTCAACCATTTCGATT 59.483 37.500 0.00 0.00 30.65 3.34
731 803 4.069304 TCCGTTTCTTCAACCATTTCGAT 58.931 39.130 0.00 0.00 30.65 3.59
800 872 2.430367 GAGCGGGTTGGTGAGGTT 59.570 61.111 0.00 0.00 0.00 3.50
809 881 3.986116 GAGGGAGAGGGAGCGGGTT 62.986 68.421 0.00 0.00 0.00 4.11
985 1074 1.481772 AGCCATCTCTTCTCACTCTGC 59.518 52.381 0.00 0.00 0.00 4.26
1191 1292 0.173481 CATCGACAGTCACGGATGGT 59.827 55.000 0.41 0.00 0.00 3.55
1228 1329 1.590238 CGTGAAATTAGAGGCGAGCAG 59.410 52.381 0.00 0.00 0.00 4.24
1341 1448 6.351202 GGCCCCCGTTAAAATAAATAAACAGT 60.351 38.462 0.00 0.00 0.00 3.55
1349 1456 1.005215 TCCGGCCCCCGTTAAAATAAA 59.995 47.619 0.00 0.00 46.80 1.40
1350 1457 0.622665 TCCGGCCCCCGTTAAAATAA 59.377 50.000 0.00 0.00 46.80 1.40
1351 1458 0.180878 CTCCGGCCCCCGTTAAAATA 59.819 55.000 0.00 0.00 46.80 1.40
1352 1459 1.077285 CTCCGGCCCCCGTTAAAAT 60.077 57.895 0.00 0.00 46.80 1.82
1384 1491 9.537192 AATCGAGATACTAGATTATACGAGAGG 57.463 37.037 0.00 0.00 34.88 3.69
1466 1576 3.897325 TCATGCCGTATACTCGAATGAC 58.103 45.455 0.56 0.00 32.90 3.06
1483 2474 1.464687 CGAGCTGCGGAAAAACTCATG 60.465 52.381 0.00 0.00 36.03 3.07
1556 2547 1.972660 GATTGGGTAGCAGCGGAGGT 61.973 60.000 0.00 0.00 41.48 3.85
1585 2577 2.821969 CTGCAAGTGGCCTAAAGTCAAT 59.178 45.455 3.32 0.00 43.89 2.57
1617 2609 8.668653 TGTGGGGAAAATATGATACTGTATGAT 58.331 33.333 4.79 4.99 0.00 2.45
1618 2610 8.040002 TGTGGGGAAAATATGATACTGTATGA 57.960 34.615 4.79 0.00 0.00 2.15
1619 2611 8.868522 ATGTGGGGAAAATATGATACTGTATG 57.131 34.615 4.79 0.00 0.00 2.39
1620 2612 8.109634 GGATGTGGGGAAAATATGATACTGTAT 58.890 37.037 0.00 0.00 0.00 2.29
1621 2613 7.073088 TGGATGTGGGGAAAATATGATACTGTA 59.927 37.037 0.00 0.00 0.00 2.74
1623 2615 6.207417 GTGGATGTGGGGAAAATATGATACTG 59.793 42.308 0.00 0.00 0.00 2.74
1624 2616 6.306987 GTGGATGTGGGGAAAATATGATACT 58.693 40.000 0.00 0.00 0.00 2.12
1625 2617 5.181245 CGTGGATGTGGGGAAAATATGATAC 59.819 44.000 0.00 0.00 0.00 2.24
1626 2618 5.312895 CGTGGATGTGGGGAAAATATGATA 58.687 41.667 0.00 0.00 0.00 2.15
1627 2619 4.144297 CGTGGATGTGGGGAAAATATGAT 58.856 43.478 0.00 0.00 0.00 2.45
1695 2687 4.561326 CGAGGTTTAGGGGAAGACGTAAAA 60.561 45.833 0.00 0.00 33.93 1.52
1707 2699 8.395633 CAAATCTTGTATTTACGAGGTTTAGGG 58.604 37.037 13.41 2.21 44.95 3.53
1744 2737 7.750903 GCACTAACACATCTAGAACAAATTTCC 59.249 37.037 0.00 0.00 0.00 3.13
1746 2739 8.396272 AGCACTAACACATCTAGAACAAATTT 57.604 30.769 0.00 0.00 0.00 1.82
1758 2751 4.116747 ACTAGCAGAGCACTAACACATC 57.883 45.455 0.00 0.00 0.00 3.06
1772 2779 3.693085 TCAAGGTACCTACGAACTAGCAG 59.307 47.826 16.67 0.00 0.00 4.24
1797 2804 5.680594 TGGGATTTGCTGCAAGATTAATT 57.319 34.783 15.39 0.00 34.07 1.40
1821 2828 4.380973 GCTCACACTGTATACTGCTTGAGA 60.381 45.833 27.84 16.33 33.06 3.27
1882 2889 0.400594 AAGAGTAACAGGGTGGGTGC 59.599 55.000 0.00 0.00 0.00 5.01
1919 2932 2.423947 GGGCACATCCAGATCCAATCTT 60.424 50.000 0.00 0.00 37.58 2.40
2002 3073 7.829211 TGATAAGAAACAAGTCAAAGGATAGGG 59.171 37.037 0.00 0.00 0.00 3.53
2035 3151 8.374327 TCAAGCAAATCTGATAGATGTATGTG 57.626 34.615 0.00 0.00 34.65 3.21
2036 3152 9.000486 CATCAAGCAAATCTGATAGATGTATGT 58.000 33.333 0.00 0.00 34.65 2.29
2048 3164 5.297776 CCTTACCTACCATCAAGCAAATCTG 59.702 44.000 0.00 0.00 0.00 2.90
2060 3176 7.701257 ATTATTACCACACCTTACCTACCAT 57.299 36.000 0.00 0.00 0.00 3.55
2068 3184 6.211272 TCCACCCTATTATTACCACACCTTA 58.789 40.000 0.00 0.00 0.00 2.69
2092 3208 3.942130 GCCTCTTGCAAACCTTAACAT 57.058 42.857 0.00 0.00 40.77 2.71
2110 3226 5.486526 CCTCATACTGGAAGAGAATATGCC 58.513 45.833 0.00 0.00 37.43 4.40
2135 3251 1.171308 CCATGAGCAACACAGGGAAG 58.829 55.000 0.00 0.00 40.97 3.46
2190 3306 3.356290 CTTGGGACTCTTGGGTAAATGG 58.644 50.000 0.00 0.00 0.00 3.16
2195 3311 0.690762 GTGCTTGGGACTCTTGGGTA 59.309 55.000 0.00 0.00 0.00 3.69
2201 3317 1.059098 TCACATGTGCTTGGGACTCT 58.941 50.000 21.38 0.00 0.00 3.24
2214 3330 5.152097 GTCAACTTTCTGAGCATTCACATG 58.848 41.667 0.00 0.00 0.00 3.21
2215 3331 4.823442 TGTCAACTTTCTGAGCATTCACAT 59.177 37.500 0.00 0.00 0.00 3.21
2216 3332 4.198530 TGTCAACTTTCTGAGCATTCACA 58.801 39.130 0.00 0.00 0.00 3.58
2217 3333 4.781071 CTGTCAACTTTCTGAGCATTCAC 58.219 43.478 0.00 0.00 0.00 3.18
2218 3334 3.251729 GCTGTCAACTTTCTGAGCATTCA 59.748 43.478 0.00 0.00 0.00 2.57
2219 3335 3.251729 TGCTGTCAACTTTCTGAGCATTC 59.748 43.478 0.00 0.00 0.00 2.67
2251 3368 1.898472 AGATGCTGCTGTAGTGACTGT 59.102 47.619 0.00 0.00 0.00 3.55
2255 3436 4.210331 TCTATGAGATGCTGCTGTAGTGA 58.790 43.478 0.00 0.00 0.00 3.41
2447 3686 3.510360 TGAGGGGTAGAAAAGAGAGAACG 59.490 47.826 0.00 0.00 0.00 3.95
2485 3725 0.527113 TGCAAAAGCATCATGACCCG 59.473 50.000 0.00 0.00 0.00 5.28
2572 3829 4.157840 GGTACAATTTAAGCCCAAGTGGAG 59.842 45.833 0.00 0.00 37.39 3.86
2590 3852 5.541101 TGTTTCTAGTAAAGGCTCAGGTACA 59.459 40.000 0.00 0.00 0.00 2.90
2686 3959 5.801947 GGCAGCTAACAATTAGACAACATTG 59.198 40.000 0.00 0.00 35.20 2.82
2688 3961 4.094887 CGGCAGCTAACAATTAGACAACAT 59.905 41.667 0.00 0.00 35.20 2.71
2689 3962 3.435327 CGGCAGCTAACAATTAGACAACA 59.565 43.478 0.00 0.00 35.20 3.33
2690 3963 3.435671 ACGGCAGCTAACAATTAGACAAC 59.564 43.478 0.00 0.00 35.20 3.32
2691 3964 3.670625 ACGGCAGCTAACAATTAGACAA 58.329 40.909 0.00 0.00 35.20 3.18
2692 3965 3.056107 AGACGGCAGCTAACAATTAGACA 60.056 43.478 0.00 0.00 35.20 3.41
2693 3966 3.307242 CAGACGGCAGCTAACAATTAGAC 59.693 47.826 0.00 0.00 35.20 2.59
2694 3967 3.521560 CAGACGGCAGCTAACAATTAGA 58.478 45.455 0.00 0.00 35.20 2.10
2695 3968 2.609459 CCAGACGGCAGCTAACAATTAG 59.391 50.000 0.00 0.00 36.32 1.73
2712 3989 7.618019 ACTTGACTCCTAATATAATGCCAGA 57.382 36.000 0.00 0.00 0.00 3.86
2733 4010 8.229253 ACGAAAACTCCAAAAAGGTATAACTT 57.771 30.769 0.00 0.00 39.02 2.66
2734 4011 7.499895 TGACGAAAACTCCAAAAAGGTATAACT 59.500 33.333 0.00 0.00 39.02 2.24
2834 4431 3.247648 ACTCATGTTTTTGTCTTCCGACG 59.752 43.478 0.00 0.00 43.21 5.12
2976 4575 6.679542 TGATTCTGAAGGGAGTATGGTACTA 58.320 40.000 0.00 0.00 39.59 1.82
2993 4592 9.775854 AATAGAACCAGAGTTATGATGATTCTG 57.224 33.333 3.23 3.23 35.94 3.02
3273 4872 2.989824 AGGTGCGCCTCGTACACT 60.990 61.111 14.67 0.00 42.67 3.55
3320 4919 1.831652 AAGGTCCGCAAGACTGAGGG 61.832 60.000 4.07 0.00 45.54 4.30
3384 4983 0.098376 GGTACGCGTCGAACAGAGAT 59.902 55.000 18.63 0.00 0.00 2.75
3533 5132 0.966179 ACTCGTACAGGCACACATCA 59.034 50.000 0.00 0.00 0.00 3.07
3583 5182 0.102844 GCAAGCACAAGCCTGAACAA 59.897 50.000 0.00 0.00 43.56 2.83
3639 5239 8.807581 GCACAATTTATTATTAAACCAGAGCAC 58.192 33.333 0.00 0.00 30.33 4.40
3728 5328 3.647636 AGGATACAGAGGCAGCTAAAGA 58.352 45.455 0.00 0.00 41.41 2.52
3729 5329 4.414337 AAGGATACAGAGGCAGCTAAAG 57.586 45.455 0.00 0.00 41.41 1.85
3763 5363 2.037381 GTCTTCCGAAACAGACTCCCTT 59.963 50.000 0.00 0.00 37.12 3.95
3807 5407 5.243730 CACAAACAGGTTCCCAATCTTATGT 59.756 40.000 0.00 0.00 0.00 2.29
3829 5429 3.891049 ACTTAGGAGGATCAAATGGCAC 58.109 45.455 0.00 0.00 36.25 5.01
3846 5446 3.687698 GGCCGCTGAAACTATTCAACTTA 59.312 43.478 0.00 0.00 44.64 2.24
3861 5461 3.741476 GGTGCTCTTTGGCCGCTG 61.741 66.667 0.00 0.00 0.00 5.18
3863 5463 1.103398 ATATGGTGCTCTTTGGCCGC 61.103 55.000 0.00 0.00 0.00 6.53
3889 5715 6.183361 TGGCCGTTGAAACTATCCAATATAGA 60.183 38.462 0.00 0.00 0.00 1.98
3946 5772 2.947652 CCATCGTGAAGAAGCATTGGAT 59.052 45.455 0.00 0.00 0.00 3.41
3963 5789 3.942829 TCCTCTGAACAATGACACCATC 58.057 45.455 0.00 0.00 31.40 3.51
4084 5910 2.066700 TTGTGCATGTCAGAGGCCCA 62.067 55.000 0.00 0.00 0.00 5.36
4094 5920 3.678289 TCATCTAAGCACTTGTGCATGT 58.322 40.909 24.82 13.35 37.25 3.21
4103 5929 3.772025 ACTTAGCACCTCATCTAAGCACT 59.228 43.478 8.44 0.00 43.27 4.40
4118 5944 1.541310 CGGGACACCCTCACTTAGCA 61.541 60.000 5.27 0.00 42.67 3.49
4124 5950 1.304713 TAGTCCGGGACACCCTCAC 60.305 63.158 27.87 0.00 42.67 3.51
4159 5985 1.839424 GGCCCATAGATAACATGCCC 58.161 55.000 0.00 0.00 0.00 5.36
4187 6013 1.003718 AAGCGACAACTAGTGGGCC 60.004 57.895 1.45 0.00 32.77 5.80
4197 6023 0.178068 GGCTATCCTCCAAGCGACAA 59.822 55.000 0.00 0.00 39.71 3.18
4198 6024 1.823295 GGCTATCCTCCAAGCGACA 59.177 57.895 0.00 0.00 39.71 4.35
4203 6029 3.297391 GCTTCGGCTATCCTCCAAG 57.703 57.895 0.00 0.00 38.08 3.61
4254 6080 6.585695 TGTCCTTGAAGTATACGAAGTCTT 57.414 37.500 0.00 0.00 43.93 3.01
4270 6096 6.189677 TGCCGACTATTAAAATTGTCCTTG 57.810 37.500 10.35 3.25 37.71 3.61
4281 6107 8.426489 ACTAGGAATAAACATGCCGACTATTAA 58.574 33.333 0.00 0.00 0.00 1.40
4289 6115 3.243068 GGCAACTAGGAATAAACATGCCG 60.243 47.826 0.00 0.00 42.18 5.69
4317 6143 5.024118 GGTGCCTAGGTCTACATATATGGT 58.976 45.833 16.96 5.53 0.00 3.55
4324 6150 0.759436 CGGGGTGCCTAGGTCTACAT 60.759 60.000 11.31 0.00 0.00 2.29
4358 6184 1.217244 CCACGGACTAAACCCCTCG 59.783 63.158 0.00 0.00 0.00 4.63
4363 6189 0.034337 TGTGCTCCACGGACTAAACC 59.966 55.000 0.00 0.00 37.14 3.27
4371 6197 0.999406 CTCGTAATTGTGCTCCACGG 59.001 55.000 0.00 0.00 37.14 4.94
4373 6199 0.727398 GGCTCGTAATTGTGCTCCAC 59.273 55.000 0.00 0.00 34.56 4.02
4375 6201 1.739067 AAGGCTCGTAATTGTGCTCC 58.261 50.000 0.00 0.00 0.00 4.70
4376 6202 2.866762 CCTAAGGCTCGTAATTGTGCTC 59.133 50.000 0.00 0.00 0.00 4.26
4388 6214 4.281898 TGTGTTCTAAACCCTAAGGCTC 57.718 45.455 0.00 0.00 36.11 4.70
4402 6228 6.041409 ACCTCGAGATCATATGATTGTGTTCT 59.959 38.462 19.11 11.34 34.37 3.01
4422 6248 9.065734 GGTACAGGTACAAGAGAATCTACCTCG 62.066 48.148 11.35 0.00 46.13 4.63



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

AutoCloner maintained by Alex Coulton.