Multiple sequence alignment - TraesCS4A01G378000

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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 TraesCS4A01G378000 chr4A 100.000 4335 0 0 1 4335 655258746 655254412 0.000000e+00 8006.0
1 TraesCS4A01G378000 chr4A 89.583 384 18 8 2017 2380 15147936 15147555 6.560000e-128 468.0
2 TraesCS4A01G378000 chr7A 89.924 1975 129 40 2386 4335 46715175 46713246 0.000000e+00 2481.0
3 TraesCS4A01G378000 chr7A 90.476 546 29 8 1856 2381 622859346 622858804 0.000000e+00 699.0
4 TraesCS4A01G378000 chr7A 92.143 420 29 3 1263 1681 622859755 622859339 1.340000e-164 590.0
5 TraesCS4A01G378000 chr7A 78.816 963 115 45 315 1257 46716071 46715178 2.260000e-157 566.0
6 TraesCS4A01G378000 chr7A 91.176 102 9 0 85 186 46720399 46720298 5.850000e-29 139.0
7 TraesCS4A01G378000 chr2B 98.752 1122 12 2 1259 2380 94264671 94263552 0.000000e+00 1993.0
8 TraesCS4A01G378000 chr2B 90.659 546 26 10 1856 2380 773869062 773869603 0.000000e+00 702.0
9 TraesCS4A01G378000 chr2B 92.417 422 28 3 1262 1681 773868650 773869069 2.230000e-167 599.0
10 TraesCS4A01G378000 chr2B 88.542 384 20 8 2017 2381 437815793 437816171 1.110000e-120 444.0
11 TraesCS4A01G378000 chr2B 92.553 188 12 2 1678 1864 801141531 801141345 7.150000e-68 268.0
12 TraesCS4A01G378000 chr7D 92.781 845 38 8 3505 4335 44295967 44295132 0.000000e+00 1201.0
13 TraesCS4A01G378000 chr7D 85.891 1134 92 29 2388 3495 44297120 44296029 0.000000e+00 1146.0
14 TraesCS4A01G378000 chr7D 79.968 1233 140 59 85 1256 44298312 44297126 0.000000e+00 809.0
15 TraesCS4A01G378000 chr7D 87.931 406 39 5 1262 1661 628012468 628012869 1.830000e-128 470.0
16 TraesCS4A01G378000 chr7D 87.438 406 41 7 1262 1661 627738702 627739103 3.950000e-125 459.0
17 TraesCS4A01G378000 chr7D 87.105 411 43 7 1262 1666 628092093 628092499 1.420000e-124 457.0
18 TraesCS4A01G378000 chr4D 91.026 546 27 11 1856 2381 154548983 154549526 0.000000e+00 717.0
19 TraesCS4A01G378000 chr1A 90.859 547 26 8 1856 2381 582698956 582698413 0.000000e+00 712.0
20 TraesCS4A01G378000 chr1A 91.489 423 26 4 1261 1681 582699363 582698949 1.350000e-159 573.0
21 TraesCS4A01G378000 chr1A 80.060 331 44 15 3908 4219 545891277 545890950 4.360000e-55 226.0
22 TraesCS4A01G378000 chr5D 90.996 522 25 9 1856 2358 48673706 48673188 0.000000e+00 684.0
23 TraesCS4A01G378000 chr5D 100.000 28 0 0 373 400 333078311 333078338 8.000000e-03 52.8
24 TraesCS4A01G378000 chr7B 89.852 542 36 11 1856 2380 662425301 662424762 0.000000e+00 678.0
25 TraesCS4A01G378000 chr7B 93.079 419 28 1 1263 1681 662425711 662425294 2.870000e-171 612.0
26 TraesCS4A01G378000 chr7B 99.419 172 1 0 1686 1857 599805912 599805741 3.250000e-81 313.0
27 TraesCS4A01G378000 chr7B 94.915 177 9 0 1680 1856 505370403 505370227 1.190000e-70 278.0
28 TraesCS4A01G378000 chr5B 84.771 545 53 12 1856 2380 246217705 246217171 1.790000e-143 520.0
29 TraesCS4A01G378000 chr5B 88.372 430 39 4 1263 1681 246218127 246217698 1.390000e-139 507.0
30 TraesCS4A01G378000 chr5B 94.444 180 10 0 1680 1859 363665476 363665297 1.190000e-70 278.0
31 TraesCS4A01G378000 chr5B 92.473 186 14 0 1680 1865 641216163 641215978 2.570000e-67 267.0
32 TraesCS4A01G378000 chr2A 85.242 454 47 12 1901 2337 525418926 525419376 2.380000e-122 449.0
33 TraesCS4A01G378000 chr1B 81.050 438 60 15 3802 4219 619420247 619419813 1.160000e-85 327.0
34 TraesCS4A01G378000 chr1B 94.413 179 10 0 1678 1856 567720197 567720375 4.270000e-70 276.0
35 TraesCS4A01G378000 chr1D 77.221 619 97 33 3640 4219 451132400 451131787 5.410000e-84 322.0
36 TraesCS4A01G378000 chr3B 95.455 176 8 0 1680 1855 819814909 819815084 9.180000e-72 281.0
37 TraesCS4A01G378000 chr4B 94.915 177 9 0 1682 1858 123497919 123497743 1.190000e-70 278.0
38 TraesCS4A01G378000 chr4B 100.000 28 0 0 373 400 88841085 88841058 8.000000e-03 52.8
39 TraesCS4A01G378000 chr6B 100.000 28 0 0 373 400 535624724 535624697 8.000000e-03 52.8


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 TraesCS4A01G378000 chr4A 655254412 655258746 4334 True 8006.0 8006 100.000000 1 4335 1 chr4A.!!$R2 4334
1 TraesCS4A01G378000 chr7A 46713246 46716071 2825 True 1523.5 2481 84.370000 315 4335 2 chr7A.!!$R2 4020
2 TraesCS4A01G378000 chr7A 622858804 622859755 951 True 644.5 699 91.309500 1263 2381 2 chr7A.!!$R3 1118
3 TraesCS4A01G378000 chr2B 94263552 94264671 1119 True 1993.0 1993 98.752000 1259 2380 1 chr2B.!!$R1 1121
4 TraesCS4A01G378000 chr2B 773868650 773869603 953 False 650.5 702 91.538000 1262 2380 2 chr2B.!!$F2 1118
5 TraesCS4A01G378000 chr7D 44295132 44298312 3180 True 1052.0 1201 86.213333 85 4335 3 chr7D.!!$R1 4250
6 TraesCS4A01G378000 chr4D 154548983 154549526 543 False 717.0 717 91.026000 1856 2381 1 chr4D.!!$F1 525
7 TraesCS4A01G378000 chr1A 582698413 582699363 950 True 642.5 712 91.174000 1261 2381 2 chr1A.!!$R2 1120
8 TraesCS4A01G378000 chr5D 48673188 48673706 518 True 684.0 684 90.996000 1856 2358 1 chr5D.!!$R1 502
9 TraesCS4A01G378000 chr7B 662424762 662425711 949 True 645.0 678 91.465500 1263 2380 2 chr7B.!!$R3 1117
10 TraesCS4A01G378000 chr5B 246217171 246218127 956 True 513.5 520 86.571500 1263 2380 2 chr5B.!!$R3 1117
11 TraesCS4A01G378000 chr1D 451131787 451132400 613 True 322.0 322 77.221000 3640 4219 1 chr1D.!!$R1 579

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
948 998 0.313357 GTACTAGGGTTCGGCGATCC 59.687 60.0 25.14 25.14 0.00 3.36 F
1659 1747 0.028770 CGTTCGTTGGTGCATTGTGT 59.971 50.0 0.00 0.00 0.00 3.72 F
2384 2498 0.384669 GTAGCTCCGCCGTTGAGTAT 59.615 55.0 0.00 0.00 32.31 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2749 2881 0.108138 GCCATGAGCGACAACCTAGT 60.108 55.0 0.00 0.0 0.0 2.57 R
2760 2892 0.169009 GAACGAACAAGGCCATGAGC 59.831 55.0 16.33 4.9 42.6 4.26 R
4169 4424 0.603975 AGAGAAAACTCGGTGCAGGC 60.604 55.0 0.00 0.0 0.0 4.85 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 5.358298 AGAAGCGTTCTTATTCACAAACC 57.642 39.130 0.00 0.00 36.36 3.27
24 25 4.819630 AGAAGCGTTCTTATTCACAAACCA 59.180 37.500 0.00 0.00 36.36 3.67
25 26 5.473504 AGAAGCGTTCTTATTCACAAACCAT 59.526 36.000 0.00 0.00 36.36 3.55
26 27 5.705609 AGCGTTCTTATTCACAAACCATT 57.294 34.783 0.00 0.00 0.00 3.16
27 28 6.084326 AGCGTTCTTATTCACAAACCATTT 57.916 33.333 0.00 0.00 0.00 2.32
28 29 6.512297 AGCGTTCTTATTCACAAACCATTTT 58.488 32.000 0.00 0.00 0.00 1.82
29 30 7.653647 AGCGTTCTTATTCACAAACCATTTTA 58.346 30.769 0.00 0.00 0.00 1.52
30 31 8.303876 AGCGTTCTTATTCACAAACCATTTTAT 58.696 29.630 0.00 0.00 0.00 1.40
31 32 8.921670 GCGTTCTTATTCACAAACCATTTTATT 58.078 29.630 0.00 0.00 0.00 1.40
39 40 9.775854 ATTCACAAACCATTTTATTCACAATCA 57.224 25.926 0.00 0.00 0.00 2.57
40 41 9.775854 TTCACAAACCATTTTATTCACAATCAT 57.224 25.926 0.00 0.00 0.00 2.45
41 42 9.205719 TCACAAACCATTTTATTCACAATCATG 57.794 29.630 0.00 0.00 0.00 3.07
42 43 8.991026 CACAAACCATTTTATTCACAATCATGT 58.009 29.630 0.00 0.00 41.61 3.21
58 59 8.687292 ACAATCATGTGTATAGAAGCATCAAT 57.313 30.769 0.00 0.00 38.69 2.57
59 60 9.128404 ACAATCATGTGTATAGAAGCATCAATT 57.872 29.630 0.00 0.00 38.69 2.32
60 61 9.608617 CAATCATGTGTATAGAAGCATCAATTC 57.391 33.333 0.00 0.00 0.00 2.17
61 62 8.913487 ATCATGTGTATAGAAGCATCAATTCA 57.087 30.769 0.00 0.00 0.00 2.57
62 63 8.913487 TCATGTGTATAGAAGCATCAATTCAT 57.087 30.769 0.00 0.00 0.00 2.57
63 64 8.996271 TCATGTGTATAGAAGCATCAATTCATC 58.004 33.333 0.00 0.00 0.00 2.92
64 65 8.780249 CATGTGTATAGAAGCATCAATTCATCA 58.220 33.333 0.00 0.00 0.00 3.07
65 66 8.374327 TGTGTATAGAAGCATCAATTCATCAG 57.626 34.615 0.00 0.00 0.00 2.90
66 67 7.989170 TGTGTATAGAAGCATCAATTCATCAGT 59.011 33.333 0.00 0.00 0.00 3.41
67 68 8.834465 GTGTATAGAAGCATCAATTCATCAGTT 58.166 33.333 0.00 0.00 0.00 3.16
68 69 9.049523 TGTATAGAAGCATCAATTCATCAGTTC 57.950 33.333 0.00 0.00 0.00 3.01
69 70 9.049523 GTATAGAAGCATCAATTCATCAGTTCA 57.950 33.333 0.00 0.00 0.00 3.18
70 71 8.693120 ATAGAAGCATCAATTCATCAGTTCAT 57.307 30.769 0.00 0.00 0.00 2.57
71 72 7.028926 AGAAGCATCAATTCATCAGTTCATC 57.971 36.000 0.00 0.00 0.00 2.92
72 73 6.602009 AGAAGCATCAATTCATCAGTTCATCA 59.398 34.615 0.00 0.00 0.00 3.07
73 74 6.769134 AGCATCAATTCATCAGTTCATCAA 57.231 33.333 0.00 0.00 0.00 2.57
74 75 7.348080 AGCATCAATTCATCAGTTCATCAAT 57.652 32.000 0.00 0.00 0.00 2.57
75 76 7.426410 AGCATCAATTCATCAGTTCATCAATC 58.574 34.615 0.00 0.00 0.00 2.67
76 77 7.068226 AGCATCAATTCATCAGTTCATCAATCA 59.932 33.333 0.00 0.00 0.00 2.57
77 78 7.867909 GCATCAATTCATCAGTTCATCAATCAT 59.132 33.333 0.00 0.00 0.00 2.45
78 79 9.399403 CATCAATTCATCAGTTCATCAATCATC 57.601 33.333 0.00 0.00 0.00 2.92
79 80 8.747538 TCAATTCATCAGTTCATCAATCATCT 57.252 30.769 0.00 0.00 0.00 2.90
80 81 8.621286 TCAATTCATCAGTTCATCAATCATCTG 58.379 33.333 0.00 0.00 0.00 2.90
81 82 8.406297 CAATTCATCAGTTCATCAATCATCTGT 58.594 33.333 0.00 0.00 0.00 3.41
82 83 7.933215 TTCATCAGTTCATCAATCATCTGTT 57.067 32.000 0.00 0.00 0.00 3.16
83 84 9.623000 ATTCATCAGTTCATCAATCATCTGTTA 57.377 29.630 0.00 0.00 0.00 2.41
153 154 3.031736 GGAGATAACACTACTGCTCCCA 58.968 50.000 0.00 0.00 36.73 4.37
165 166 1.136695 CTGCTCCCAACAAAGTTGCAA 59.863 47.619 0.00 0.00 0.00 4.08
170 171 4.448732 GCTCCCAACAAAGTTGCAATAAAG 59.551 41.667 0.59 0.00 0.00 1.85
174 175 4.810491 CCAACAAAGTTGCAATAAAGCAGT 59.190 37.500 0.59 0.00 46.54 4.40
181 182 8.928733 CAAAGTTGCAATAAAGCAGTATCAATT 58.071 29.630 0.59 0.00 46.54 2.32
225 246 6.991531 TGCATAATAATTCTCATTTTTGCCCC 59.008 34.615 0.00 0.00 0.00 5.80
238 259 3.386932 TTTGCCCCTGCTGATTATTCT 57.613 42.857 0.00 0.00 38.71 2.40
239 260 2.353357 TGCCCCTGCTGATTATTCTG 57.647 50.000 0.00 0.00 38.71 3.02
264 286 9.508642 TGTTGAGGTTCCTTTTGTTTTAAAAAT 57.491 25.926 1.31 0.00 0.00 1.82
285 307 2.296073 TAAACGGCATCCCTGGTTTT 57.704 45.000 0.00 0.00 0.00 2.43
286 308 0.678950 AAACGGCATCCCTGGTTTTG 59.321 50.000 0.00 0.00 0.00 2.44
287 309 1.815817 AACGGCATCCCTGGTTTTGC 61.816 55.000 4.66 4.66 0.00 3.68
307 330 1.746787 CGCTACCCCCACAAATAAACC 59.253 52.381 0.00 0.00 0.00 3.27
312 335 2.249139 CCCCCACAAATAAACCCGAAA 58.751 47.619 0.00 0.00 0.00 3.46
313 336 2.633481 CCCCCACAAATAAACCCGAAAA 59.367 45.455 0.00 0.00 0.00 2.29
325 348 8.821147 AATAAACCCGAAAAGGAACAAAATAC 57.179 30.769 0.00 0.00 45.00 1.89
332 355 5.912955 CGAAAAGGAACAAAATACTGGTGTC 59.087 40.000 0.00 0.00 0.00 3.67
362 385 2.629017 AATGGCCAAAGGAGTCCATT 57.371 45.000 10.96 2.08 42.61 3.16
369 392 3.259123 GCCAAAGGAGTCCATTTCACAAT 59.741 43.478 12.86 0.00 0.00 2.71
373 396 7.147915 GCCAAAGGAGTCCATTTCACAATAATA 60.148 37.037 12.86 0.00 0.00 0.98
384 407 9.144747 CCATTTCACAATAATATACTCTCTCCG 57.855 37.037 0.00 0.00 0.00 4.63
385 408 8.651588 CATTTCACAATAATATACTCTCTCCGC 58.348 37.037 0.00 0.00 0.00 5.54
389 412 2.696526 AATATACTCTCTCCGCCCCA 57.303 50.000 0.00 0.00 0.00 4.96
390 413 2.696526 ATATACTCTCTCCGCCCCAA 57.303 50.000 0.00 0.00 0.00 4.12
401 424 2.560981 CTCCGCCCCAAAAATAAGTGTT 59.439 45.455 0.00 0.00 0.00 3.32
411 434 8.947115 CCCCAAAAATAAGTGTTGTTGTTTTAA 58.053 29.630 0.00 0.00 31.71 1.52
449 476 8.699283 ATAACTAGAACAACGACACTTATTCC 57.301 34.615 0.00 0.00 0.00 3.01
451 478 4.247267 AGAACAACGACACTTATTCCGA 57.753 40.909 0.00 0.00 0.00 4.55
475 510 6.268566 AGACGGACGGACTACATATTTAAAC 58.731 40.000 0.00 0.00 0.00 2.01
480 515 6.764560 GGACGGACTACATATTTAAACACCAT 59.235 38.462 0.00 0.00 0.00 3.55
498 533 9.877178 AAACACCATATTTCTACAACACAAAAA 57.123 25.926 0.00 0.00 0.00 1.94
591 626 9.964303 TCATAACAATATATTTTCACACATGGC 57.036 29.630 0.00 0.00 0.00 4.40
592 627 8.904712 CATAACAATATATTTTCACACATGGCG 58.095 33.333 0.00 0.00 0.00 5.69
593 628 6.449635 ACAATATATTTTCACACATGGCGT 57.550 33.333 0.00 0.00 0.00 5.68
595 630 7.414436 ACAATATATTTTCACACATGGCGTAC 58.586 34.615 0.00 0.00 0.00 3.67
596 631 7.066404 ACAATATATTTTCACACATGGCGTACA 59.934 33.333 0.00 0.00 0.00 2.90
597 632 5.888691 ATATTTTCACACATGGCGTACAA 57.111 34.783 0.00 0.00 0.00 2.41
598 633 4.782019 ATTTTCACACATGGCGTACAAT 57.218 36.364 0.00 0.00 0.00 2.71
599 634 5.888691 ATTTTCACACATGGCGTACAATA 57.111 34.783 0.00 0.00 0.00 1.90
600 635 5.690997 TTTTCACACATGGCGTACAATAA 57.309 34.783 0.00 0.00 0.00 1.40
601 636 4.671880 TTCACACATGGCGTACAATAAC 57.328 40.909 0.00 0.00 0.00 1.89
602 637 3.665190 TCACACATGGCGTACAATAACA 58.335 40.909 0.00 0.00 0.00 2.41
607 642 5.688176 ACACATGGCGTACAATAACAAAAAC 59.312 36.000 0.00 0.00 0.00 2.43
608 643 5.687730 CACATGGCGTACAATAACAAAAACA 59.312 36.000 0.00 0.00 0.00 2.83
662 699 3.250762 GGCCAGGATTTTGTTTTCTTTGC 59.749 43.478 0.00 0.00 0.00 3.68
709 746 4.965062 TGAACGAAAATTTACAGATCCGC 58.035 39.130 0.00 0.00 0.00 5.54
730 767 4.436852 CGCCGTGAACATGTATAAGCTTTT 60.437 41.667 3.20 0.00 0.00 2.27
731 768 5.399013 GCCGTGAACATGTATAAGCTTTTT 58.601 37.500 3.20 0.00 0.00 1.94
732 769 6.548171 GCCGTGAACATGTATAAGCTTTTTA 58.452 36.000 3.20 0.00 0.00 1.52
733 770 6.468000 GCCGTGAACATGTATAAGCTTTTTAC 59.532 38.462 3.20 8.23 0.00 2.01
734 771 6.964934 CCGTGAACATGTATAAGCTTTTTACC 59.035 38.462 3.20 0.00 0.00 2.85
735 772 6.964934 CGTGAACATGTATAAGCTTTTTACCC 59.035 38.462 3.20 0.00 0.00 3.69
736 773 6.964934 GTGAACATGTATAAGCTTTTTACCCG 59.035 38.462 3.20 4.25 0.00 5.28
737 774 5.494632 ACATGTATAAGCTTTTTACCCGC 57.505 39.130 3.20 0.00 0.00 6.13
738 775 4.944930 ACATGTATAAGCTTTTTACCCGCA 59.055 37.500 3.20 0.00 0.00 5.69
739 776 5.416326 ACATGTATAAGCTTTTTACCCGCAA 59.584 36.000 3.20 0.00 0.00 4.85
740 777 5.961396 TGTATAAGCTTTTTACCCGCAAA 57.039 34.783 3.20 0.00 0.00 3.68
741 778 6.328641 TGTATAAGCTTTTTACCCGCAAAA 57.671 33.333 3.20 0.00 0.00 2.44
742 779 6.746120 TGTATAAGCTTTTTACCCGCAAAAA 58.254 32.000 3.20 0.00 36.31 1.94
771 808 6.893958 AGAGAACATGTATAAGCTTTCGTG 57.106 37.500 3.20 10.05 0.00 4.35
772 809 5.812642 AGAGAACATGTATAAGCTTTCGTGG 59.187 40.000 3.20 0.00 0.00 4.94
773 810 5.730550 AGAACATGTATAAGCTTTCGTGGA 58.269 37.500 3.20 0.00 0.00 4.02
839 889 4.787280 AGGTCTCCCTGGAGCCCG 62.787 72.222 17.62 0.00 44.25 6.13
854 904 2.747686 CCGGCCCGGCACTATAAT 59.252 61.111 10.42 0.00 41.17 1.28
855 905 1.546589 CCCGGCCCGGCACTATAATA 61.547 60.000 19.21 0.00 46.86 0.98
856 906 0.322322 CCGGCCCGGCACTATAATAA 59.678 55.000 10.42 0.00 41.17 1.40
857 907 1.435577 CGGCCCGGCACTATAATAAC 58.564 55.000 12.58 0.00 0.00 1.89
858 908 1.001633 CGGCCCGGCACTATAATAACT 59.998 52.381 12.58 0.00 0.00 2.24
859 909 2.549349 CGGCCCGGCACTATAATAACTT 60.549 50.000 12.58 0.00 0.00 2.66
860 910 2.812011 GGCCCGGCACTATAATAACTTG 59.188 50.000 12.58 0.00 0.00 3.16
861 911 2.812011 GCCCGGCACTATAATAACTTGG 59.188 50.000 3.91 0.00 0.00 3.61
862 912 2.812011 CCCGGCACTATAATAACTTGGC 59.188 50.000 0.00 0.00 0.00 4.52
863 913 3.472652 CCGGCACTATAATAACTTGGCA 58.527 45.455 0.00 0.00 33.17 4.92
864 914 3.250040 CCGGCACTATAATAACTTGGCAC 59.750 47.826 0.00 0.00 33.17 5.01
865 915 4.127171 CGGCACTATAATAACTTGGCACT 58.873 43.478 0.00 0.00 33.17 4.40
866 916 4.211374 CGGCACTATAATAACTTGGCACTC 59.789 45.833 0.00 0.00 33.17 3.51
867 917 5.123227 GGCACTATAATAACTTGGCACTCA 58.877 41.667 0.00 0.00 33.17 3.41
868 918 5.237344 GGCACTATAATAACTTGGCACTCAG 59.763 44.000 0.00 0.00 33.17 3.35
869 919 5.277538 GCACTATAATAACTTGGCACTCAGC 60.278 44.000 0.00 0.00 44.65 4.26
891 941 1.685224 ACCTCCGGGTGTACTACGA 59.315 57.895 0.00 0.00 45.43 3.43
892 942 0.393537 ACCTCCGGGTGTACTACGAG 60.394 60.000 0.00 0.00 45.43 4.18
893 943 1.099879 CCTCCGGGTGTACTACGAGG 61.100 65.000 0.00 0.00 0.00 4.63
894 944 1.077501 TCCGGGTGTACTACGAGGG 60.078 63.158 0.00 0.91 0.00 4.30
895 945 1.379044 CCGGGTGTACTACGAGGGT 60.379 63.158 0.00 0.00 0.00 4.34
942 992 4.532314 AAAAGAGTGTACTAGGGTTCGG 57.468 45.455 0.00 0.00 0.00 4.30
943 993 1.472188 AGAGTGTACTAGGGTTCGGC 58.528 55.000 0.00 0.00 0.00 5.54
945 995 0.322816 AGTGTACTAGGGTTCGGCGA 60.323 55.000 4.99 4.99 0.00 5.54
947 997 1.027357 TGTACTAGGGTTCGGCGATC 58.973 55.000 11.76 10.41 0.00 3.69
948 998 0.313357 GTACTAGGGTTCGGCGATCC 59.687 60.000 25.14 25.14 0.00 3.36
969 1019 2.016704 CGTGTCGCTGACCACTCAC 61.017 63.158 6.30 0.00 0.00 3.51
976 1026 1.139734 CTGACCACTCACCGATCGG 59.860 63.158 32.20 32.20 42.03 4.18
1017 1067 0.179045 CGATGCCCGGGAAGAAGAAT 60.179 55.000 29.31 0.00 33.91 2.40
1098 1164 4.162690 CCCCGGCCTCCTCGAAAG 62.163 72.222 0.00 0.00 0.00 2.62
1099 1165 3.391382 CCCGGCCTCCTCGAAAGT 61.391 66.667 0.00 0.00 0.00 2.66
1100 1166 2.184579 CCGGCCTCCTCGAAAGTC 59.815 66.667 0.00 0.00 0.00 3.01
1103 1169 2.184579 GCCTCCTCGAAAGTCCGG 59.815 66.667 0.00 0.00 0.00 5.14
1104 1170 2.348888 GCCTCCTCGAAAGTCCGGA 61.349 63.158 0.00 0.00 0.00 5.14
1107 1173 2.184579 CCTCGAAAGTCCGGAGCC 59.815 66.667 3.06 0.00 0.00 4.70
1108 1174 2.352032 CCTCGAAAGTCCGGAGCCT 61.352 63.158 3.06 0.00 0.00 4.58
1110 1176 2.202623 CGAAAGTCCGGAGCCTCG 60.203 66.667 3.06 9.67 0.00 4.63
1111 1177 2.509561 GAAAGTCCGGAGCCTCGC 60.510 66.667 3.06 0.00 0.00 5.03
1112 1178 4.083862 AAAGTCCGGAGCCTCGCC 62.084 66.667 3.06 0.00 0.00 5.54
1148 1214 1.393603 GCCCTCTGGTTTTATGCTCC 58.606 55.000 0.00 0.00 0.00 4.70
1155 1221 1.436983 GGTTTTATGCTCCCGGCTCG 61.437 60.000 0.00 0.00 42.39 5.03
1195 1264 1.137872 AGCCGATTTCGCTCAAGAGAT 59.862 47.619 0.32 0.00 38.18 2.75
1200 1269 3.974401 CGATTTCGCTCAAGAGATCTCTC 59.026 47.826 25.29 11.92 39.39 3.20
1211 1280 6.502652 TCAAGAGATCTCTCATCTTTTAGCG 58.497 40.000 25.29 0.00 45.21 4.26
1253 1322 2.424956 CTGTGCTTGGGAGGAATTAAGC 59.575 50.000 0.00 0.00 44.26 3.09
1258 1327 4.464947 GCTTGGGAGGAATTAAGCAGTAT 58.535 43.478 0.00 0.00 43.65 2.12
1259 1328 4.889995 GCTTGGGAGGAATTAAGCAGTATT 59.110 41.667 0.00 0.00 43.65 1.89
1416 1496 6.496565 TCCAATTCAATCAACCACTAACCAAT 59.503 34.615 0.00 0.00 0.00 3.16
1420 1500 5.309638 TCAATCAACCACTAACCAATCGAA 58.690 37.500 0.00 0.00 0.00 3.71
1481 1568 2.963548 TTATAATGTCGTCGCCACCA 57.036 45.000 0.00 0.00 0.00 4.17
1493 1580 1.365633 GCCACCATTCCAAACGCAA 59.634 52.632 0.00 0.00 0.00 4.85
1659 1747 0.028770 CGTTCGTTGGTGCATTGTGT 59.971 50.000 0.00 0.00 0.00 3.72
1769 1857 2.985282 AACCCATGCCAGCACACG 60.985 61.111 0.00 0.00 0.00 4.49
1790 1878 3.241900 CGCGCATCTTATAGCATCACATC 60.242 47.826 8.75 0.00 0.00 3.06
2381 2495 2.579787 CGTAGCTCCGCCGTTGAG 60.580 66.667 0.00 0.00 0.00 3.02
2382 2496 2.572284 GTAGCTCCGCCGTTGAGT 59.428 61.111 0.00 0.00 32.31 3.41
2383 2497 1.805254 GTAGCTCCGCCGTTGAGTA 59.195 57.895 0.00 0.00 32.31 2.59
2384 2498 0.384669 GTAGCTCCGCCGTTGAGTAT 59.615 55.000 0.00 0.00 32.31 2.12
2418 2532 7.138692 TGTACATCTCTGATGATCGTATCTG 57.861 40.000 13.63 0.00 0.00 2.90
2420 2534 5.076182 ACATCTCTGATGATCGTATCTGGT 58.924 41.667 13.63 0.00 0.00 4.00
2421 2535 5.048154 ACATCTCTGATGATCGTATCTGGTG 60.048 44.000 13.63 0.00 0.00 4.17
2422 2536 4.718961 TCTCTGATGATCGTATCTGGTGA 58.281 43.478 0.00 0.00 0.00 4.02
2424 2538 5.772169 TCTCTGATGATCGTATCTGGTGAAT 59.228 40.000 0.00 0.00 0.00 2.57
2425 2539 6.266330 TCTCTGATGATCGTATCTGGTGAATT 59.734 38.462 0.00 0.00 0.00 2.17
2426 2540 6.218746 TCTGATGATCGTATCTGGTGAATTG 58.781 40.000 0.00 0.00 0.00 2.32
2427 2541 6.040842 TCTGATGATCGTATCTGGTGAATTGA 59.959 38.462 0.00 0.00 0.00 2.57
2428 2542 6.762333 TGATGATCGTATCTGGTGAATTGAT 58.238 36.000 0.00 0.00 0.00 2.57
2429 2543 6.647895 TGATGATCGTATCTGGTGAATTGATG 59.352 38.462 0.00 0.00 0.00 3.07
2430 2544 6.160576 TGATCGTATCTGGTGAATTGATGA 57.839 37.500 0.00 0.00 0.00 2.92
2431 2545 6.581712 TGATCGTATCTGGTGAATTGATGAA 58.418 36.000 0.00 0.00 0.00 2.57
2432 2546 6.479990 TGATCGTATCTGGTGAATTGATGAAC 59.520 38.462 0.00 0.00 0.00 3.18
2433 2547 5.729510 TCGTATCTGGTGAATTGATGAACA 58.270 37.500 0.00 0.00 0.00 3.18
2434 2548 5.580691 TCGTATCTGGTGAATTGATGAACAC 59.419 40.000 0.00 0.00 0.00 3.32
2435 2549 4.952262 ATCTGGTGAATTGATGAACACG 57.048 40.909 0.00 0.00 34.59 4.49
2436 2550 3.738982 TCTGGTGAATTGATGAACACGT 58.261 40.909 0.00 0.00 34.59 4.49
2437 2551 3.498018 TCTGGTGAATTGATGAACACGTG 59.502 43.478 15.48 15.48 34.59 4.49
2438 2552 3.471680 TGGTGAATTGATGAACACGTGA 58.528 40.909 25.01 0.00 34.59 4.35
2439 2553 4.071423 TGGTGAATTGATGAACACGTGAT 58.929 39.130 25.01 11.26 34.59 3.06
2440 2554 4.083377 TGGTGAATTGATGAACACGTGATG 60.083 41.667 25.01 0.00 34.59 3.07
2441 2555 4.154015 GGTGAATTGATGAACACGTGATGA 59.846 41.667 25.01 4.57 34.59 2.92
2442 2556 5.082059 GTGAATTGATGAACACGTGATGAC 58.918 41.667 25.01 10.45 0.00 3.06
2447 2561 3.928375 TGATGAACACGTGATGACATGAG 59.072 43.478 25.01 0.00 36.88 2.90
2448 2562 3.658757 TGAACACGTGATGACATGAGA 57.341 42.857 25.01 0.00 36.88 3.27
2450 2564 3.928375 TGAACACGTGATGACATGAGATG 59.072 43.478 25.01 0.00 36.88 2.90
2466 2580 3.315191 TGAGATGATGAGACGCACGATTA 59.685 43.478 0.00 0.00 0.00 1.75
2478 2592 2.285256 CGCACGATTACTGATGAACTGC 60.285 50.000 0.00 0.00 0.00 4.40
2479 2593 2.672874 GCACGATTACTGATGAACTGCA 59.327 45.455 0.00 0.00 0.00 4.41
2487 2610 7.306457 CGATTACTGATGAACTGCAGAGTAATG 60.306 40.741 27.68 19.59 41.51 1.90
2491 2614 4.154737 TGATGAACTGCAGAGTAATGTTGC 59.845 41.667 23.35 0.00 38.30 4.17
2514 2637 3.311966 GAAAAATCTTGTGCAGCCTGTC 58.688 45.455 0.00 0.00 0.00 3.51
2516 2639 2.211250 AATCTTGTGCAGCCTGTCAT 57.789 45.000 0.00 0.00 0.00 3.06
2523 2646 0.467844 TGCAGCCTGTCATGGTGTTT 60.468 50.000 8.76 0.00 0.00 2.83
2544 2667 1.669760 GTTGAACGATGGCGGTGGA 60.670 57.895 0.00 0.00 37.73 4.02
2556 2679 1.745320 GCGGTGGATGGGACGACTAT 61.745 60.000 0.00 0.00 0.00 2.12
2559 2682 0.393077 GTGGATGGGACGACTATGGG 59.607 60.000 0.00 0.00 0.00 4.00
2619 2750 1.081892 CGCCTGTTCACCAGAGATTG 58.918 55.000 0.00 0.00 44.49 2.67
2631 2762 0.392193 AGAGATTGGCAGTGCTTCCG 60.392 55.000 16.11 0.00 0.00 4.30
2632 2763 1.372087 GAGATTGGCAGTGCTTCCGG 61.372 60.000 16.11 0.00 0.00 5.14
2633 2764 3.056313 GATTGGCAGTGCTTCCGGC 62.056 63.158 16.11 0.00 42.22 6.13
2645 2776 1.852067 CTTCCGGCCTTTCCAACACG 61.852 60.000 0.00 0.00 34.01 4.49
2653 2784 4.196971 GGCCTTTCCAACACGATATAAGT 58.803 43.478 0.00 0.00 34.01 2.24
2695 2826 2.681778 ACGGAGGGAGTGGCAGAG 60.682 66.667 0.00 0.00 0.00 3.35
2702 2833 0.747283 GGGAGTGGCAGAGCAGATTG 60.747 60.000 0.00 0.00 0.00 2.67
2748 2880 1.550072 CATTGGGGGTTTCGCTGATTT 59.450 47.619 0.00 0.00 0.00 2.17
2749 2881 2.588464 TTGGGGGTTTCGCTGATTTA 57.412 45.000 0.00 0.00 0.00 1.40
2760 2892 3.766151 TCGCTGATTTACTAGGTTGTCG 58.234 45.455 0.00 0.00 0.00 4.35
2772 2904 1.503542 GTTGTCGCTCATGGCCTTG 59.496 57.895 12.41 12.41 37.74 3.61
2798 2930 0.179235 CCCGTATGTTTGTTGTCGCG 60.179 55.000 0.00 0.00 0.00 5.87
2806 2938 3.943479 TTGTTGTCGCGGGGATCGG 62.943 63.158 6.13 0.00 39.69 4.18
2825 2957 0.665972 GCATCGGAGAAGGAGATCGC 60.666 60.000 0.00 0.00 43.58 4.58
2850 2982 1.269309 GCTGTCATAGACGCGGAGAAT 60.269 52.381 12.47 0.00 34.95 2.40
2865 2997 3.610585 CGGAGAATAAGGAGACGATGCTC 60.611 52.174 0.00 0.00 34.25 4.26
2896 3028 0.741927 CACCCCGGACGACATTTACC 60.742 60.000 0.73 0.00 0.00 2.85
2947 3079 1.776969 CTTCCCCTGCTTTCCCCTT 59.223 57.895 0.00 0.00 0.00 3.95
2950 3082 1.071314 TCCCCTGCTTTCCCCTTTCA 61.071 55.000 0.00 0.00 0.00 2.69
2951 3083 0.613012 CCCCTGCTTTCCCCTTTCAG 60.613 60.000 0.00 0.00 0.00 3.02
2952 3084 0.113190 CCCTGCTTTCCCCTTTCAGT 59.887 55.000 0.00 0.00 0.00 3.41
2966 3099 4.212214 CCCTTTCAGTTTTCTGTTCTCTCG 59.788 45.833 0.00 0.00 46.98 4.04
2970 3103 5.006153 TCAGTTTTCTGTTCTCTCGACAA 57.994 39.130 0.00 0.00 46.98 3.18
2972 3105 6.049149 TCAGTTTTCTGTTCTCTCGACAATT 58.951 36.000 0.00 0.00 46.98 2.32
2973 3106 6.018751 TCAGTTTTCTGTTCTCTCGACAATTG 60.019 38.462 3.24 3.24 46.98 2.32
3038 3171 6.616774 AAGTTAATTTGTTTGCAATGGTGG 57.383 33.333 0.00 0.00 34.18 4.61
3039 3172 5.679601 AGTTAATTTGTTTGCAATGGTGGT 58.320 33.333 0.00 0.00 34.18 4.16
3052 3185 2.829741 TGGTGGTGCCTTTATTTTGC 57.170 45.000 0.00 0.00 38.35 3.68
3072 3205 3.073798 TGCTTGTTCCCCTCTGTTCAATA 59.926 43.478 0.00 0.00 0.00 1.90
3078 3211 1.656652 CCCTCTGTTCAATAGCACCG 58.343 55.000 0.00 0.00 0.00 4.94
3295 3430 0.618458 TGGTATCTTGCAGGGACACC 59.382 55.000 10.93 10.93 0.00 4.16
3333 3468 3.330701 AGAAAACTGAGGCCTGATGGTTA 59.669 43.478 12.00 0.00 35.27 2.85
3450 3598 2.346766 TTGTGCAGCTCCTCAAGAAA 57.653 45.000 0.00 0.00 0.00 2.52
3457 3605 3.549625 GCAGCTCCTCAAGAAACAGTTTG 60.550 47.826 2.34 0.00 0.00 2.93
3475 3623 4.019321 AGTTTGCCCTATGAAGTGAAGCTA 60.019 41.667 0.00 0.00 0.00 3.32
3548 3751 6.723052 CAGGATTTATTGAATTAGGATGCCCT 59.277 38.462 0.00 0.00 46.62 5.19
3573 3776 4.175489 CAGCGCCATGTGCAGAGC 62.175 66.667 2.29 0.00 42.00 4.09
3583 3786 2.280119 TGCAGAGCACACACCGTC 60.280 61.111 0.00 0.00 31.71 4.79
3593 3796 3.568007 AGCACACACCGTCAATTTTATGT 59.432 39.130 0.00 0.00 0.00 2.29
3594 3797 4.757657 AGCACACACCGTCAATTTTATGTA 59.242 37.500 0.00 0.00 0.00 2.29
3595 3798 5.239744 AGCACACACCGTCAATTTTATGTAA 59.760 36.000 0.00 0.00 0.00 2.41
3661 3864 6.473455 GCATCAACATTGCTCTGTATTTTACC 59.527 38.462 0.00 0.00 37.14 2.85
3704 3908 1.279271 ACATTAGACCAGGTCAGGTGC 59.721 52.381 22.31 0.00 43.38 5.01
3705 3909 0.912486 ATTAGACCAGGTCAGGTGCC 59.088 55.000 22.31 0.00 43.38 5.01
3709 3913 2.348998 CCAGGTCAGGTGCCACTC 59.651 66.667 0.00 0.00 0.00 3.51
3748 3954 5.047188 TGTTCATATATACACTGCCACACG 58.953 41.667 0.00 0.00 0.00 4.49
3773 3992 2.875933 GAGAAAATTGTCCCGTGTGACA 59.124 45.455 0.00 0.00 43.26 3.58
3971 4214 2.258591 GGTCGTCTCGCTCTGCAA 59.741 61.111 0.00 0.00 0.00 4.08
4046 4293 5.019785 AGTGCGGTTAGGGTTTAGAATAG 57.980 43.478 0.00 0.00 0.00 1.73
4169 4424 2.283173 GGGGTCAGGTGGCAAAGG 60.283 66.667 0.00 0.00 0.00 3.11
4208 4463 4.703897 TCTTCTCGTCTGTGGTCATTTTT 58.296 39.130 0.00 0.00 0.00 1.94
4219 4474 6.655003 TCTGTGGTCATTTTTCTACAAGATCC 59.345 38.462 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.819630 TGGTTTGTGAATAAGAACGCTTCT 59.180 37.500 0.00 0.00 43.15 2.85
2 3 5.103290 TGGTTTGTGAATAAGAACGCTTC 57.897 39.130 0.00 0.00 35.56 3.86
3 4 5.705609 ATGGTTTGTGAATAAGAACGCTT 57.294 34.783 0.00 0.00 38.15 4.68
4 5 5.705609 AATGGTTTGTGAATAAGAACGCT 57.294 34.783 0.00 0.00 0.00 5.07
5 6 6.763303 AAAATGGTTTGTGAATAAGAACGC 57.237 33.333 0.00 0.00 0.00 4.84
13 14 9.775854 TGATTGTGAATAAAATGGTTTGTGAAT 57.224 25.926 0.00 0.00 0.00 2.57
14 15 9.775854 ATGATTGTGAATAAAATGGTTTGTGAA 57.224 25.926 0.00 0.00 0.00 3.18
15 16 9.205719 CATGATTGTGAATAAAATGGTTTGTGA 57.794 29.630 0.00 0.00 0.00 3.58
16 17 8.991026 ACATGATTGTGAATAAAATGGTTTGTG 58.009 29.630 0.00 0.00 33.85 3.33
33 34 8.687292 ATTGATGCTTCTATACACATGATTGT 57.313 30.769 0.00 0.00 36.15 2.71
34 35 9.608617 GAATTGATGCTTCTATACACATGATTG 57.391 33.333 0.00 0.00 0.00 2.67
35 36 9.346005 TGAATTGATGCTTCTATACACATGATT 57.654 29.630 0.00 0.00 0.00 2.57
36 37 8.913487 TGAATTGATGCTTCTATACACATGAT 57.087 30.769 0.00 0.00 0.00 2.45
37 38 8.913487 ATGAATTGATGCTTCTATACACATGA 57.087 30.769 0.00 0.00 0.00 3.07
38 39 8.780249 TGATGAATTGATGCTTCTATACACATG 58.220 33.333 0.88 0.00 0.00 3.21
39 40 8.913487 TGATGAATTGATGCTTCTATACACAT 57.087 30.769 0.88 6.21 0.00 3.21
40 41 7.989170 ACTGATGAATTGATGCTTCTATACACA 59.011 33.333 0.88 2.27 0.00 3.72
41 42 8.375608 ACTGATGAATTGATGCTTCTATACAC 57.624 34.615 0.88 0.00 0.00 2.90
42 43 8.969260 AACTGATGAATTGATGCTTCTATACA 57.031 30.769 0.88 0.00 0.00 2.29
43 44 9.049523 TGAACTGATGAATTGATGCTTCTATAC 57.950 33.333 0.88 0.00 0.00 1.47
44 45 9.788889 ATGAACTGATGAATTGATGCTTCTATA 57.211 29.630 0.88 0.00 0.00 1.31
45 46 8.693120 ATGAACTGATGAATTGATGCTTCTAT 57.307 30.769 0.88 0.00 0.00 1.98
46 47 7.771826 TGATGAACTGATGAATTGATGCTTCTA 59.228 33.333 0.88 0.00 0.00 2.10
47 48 6.602009 TGATGAACTGATGAATTGATGCTTCT 59.398 34.615 0.88 0.00 0.00 2.85
48 49 6.792326 TGATGAACTGATGAATTGATGCTTC 58.208 36.000 0.00 0.00 0.00 3.86
49 50 6.769134 TGATGAACTGATGAATTGATGCTT 57.231 33.333 0.00 0.00 0.00 3.91
50 51 6.769134 TTGATGAACTGATGAATTGATGCT 57.231 33.333 0.00 0.00 0.00 3.79
51 52 7.200455 TGATTGATGAACTGATGAATTGATGC 58.800 34.615 0.00 0.00 0.00 3.91
52 53 9.399403 GATGATTGATGAACTGATGAATTGATG 57.601 33.333 0.00 0.00 0.00 3.07
53 54 9.355916 AGATGATTGATGAACTGATGAATTGAT 57.644 29.630 0.00 0.00 0.00 2.57
54 55 8.621286 CAGATGATTGATGAACTGATGAATTGA 58.379 33.333 0.00 0.00 0.00 2.57
55 56 8.406297 ACAGATGATTGATGAACTGATGAATTG 58.594 33.333 0.00 0.00 0.00 2.32
56 57 8.521170 ACAGATGATTGATGAACTGATGAATT 57.479 30.769 0.00 0.00 0.00 2.17
57 58 8.521170 AACAGATGATTGATGAACTGATGAAT 57.479 30.769 0.00 0.00 0.00 2.57
58 59 7.933215 AACAGATGATTGATGAACTGATGAA 57.067 32.000 0.00 0.00 0.00 2.57
59 60 7.713942 CCTAACAGATGATTGATGAACTGATGA 59.286 37.037 0.00 0.00 0.00 2.92
60 61 7.041303 CCCTAACAGATGATTGATGAACTGATG 60.041 40.741 0.00 0.00 0.00 3.07
61 62 6.996879 CCCTAACAGATGATTGATGAACTGAT 59.003 38.462 0.00 0.00 0.00 2.90
62 63 6.156775 TCCCTAACAGATGATTGATGAACTGA 59.843 38.462 0.00 0.00 0.00 3.41
63 64 6.351711 TCCCTAACAGATGATTGATGAACTG 58.648 40.000 0.00 0.00 0.00 3.16
64 65 6.566079 TCCCTAACAGATGATTGATGAACT 57.434 37.500 0.00 0.00 0.00 3.01
65 66 7.814264 ATTCCCTAACAGATGATTGATGAAC 57.186 36.000 0.00 0.00 0.00 3.18
66 67 8.054572 TCAATTCCCTAACAGATGATTGATGAA 58.945 33.333 0.00 0.00 0.00 2.57
67 68 7.576403 TCAATTCCCTAACAGATGATTGATGA 58.424 34.615 0.00 0.00 0.00 2.92
68 69 7.812690 TCAATTCCCTAACAGATGATTGATG 57.187 36.000 0.00 0.00 0.00 3.07
69 70 8.857098 CATTCAATTCCCTAACAGATGATTGAT 58.143 33.333 0.00 0.00 0.00 2.57
70 71 7.286087 CCATTCAATTCCCTAACAGATGATTGA 59.714 37.037 0.00 0.00 0.00 2.57
71 72 7.286087 TCCATTCAATTCCCTAACAGATGATTG 59.714 37.037 0.00 0.00 0.00 2.67
72 73 7.356680 TCCATTCAATTCCCTAACAGATGATT 58.643 34.615 0.00 0.00 0.00 2.57
73 74 6.914665 TCCATTCAATTCCCTAACAGATGAT 58.085 36.000 0.00 0.00 0.00 2.45
74 75 6.325993 TCCATTCAATTCCCTAACAGATGA 57.674 37.500 0.00 0.00 0.00 2.92
75 76 7.592885 ATTCCATTCAATTCCCTAACAGATG 57.407 36.000 0.00 0.00 0.00 2.90
76 77 8.063770 AGAATTCCATTCAATTCCCTAACAGAT 58.936 33.333 0.65 0.00 41.82 2.90
77 78 7.413446 AGAATTCCATTCAATTCCCTAACAGA 58.587 34.615 0.65 0.00 41.82 3.41
78 79 7.651027 AGAATTCCATTCAATTCCCTAACAG 57.349 36.000 0.65 0.00 41.82 3.16
79 80 7.454380 ACAAGAATTCCATTCAATTCCCTAACA 59.546 33.333 0.65 0.00 41.82 2.41
80 81 7.840931 ACAAGAATTCCATTCAATTCCCTAAC 58.159 34.615 0.65 0.00 41.82 2.34
81 82 9.540538 TTACAAGAATTCCATTCAATTCCCTAA 57.459 29.630 0.65 0.00 41.82 2.69
82 83 9.540538 TTTACAAGAATTCCATTCAATTCCCTA 57.459 29.630 0.65 0.00 41.82 3.53
83 84 8.434589 TTTACAAGAATTCCATTCAATTCCCT 57.565 30.769 0.65 0.00 41.82 4.20
124 125 6.607600 AGCAGTAGTGTTATCTCCATCTGTAA 59.392 38.462 0.00 0.00 0.00 2.41
144 145 0.746659 GCAACTTTGTTGGGAGCAGT 59.253 50.000 11.64 0.00 0.00 4.40
147 148 2.531522 ATTGCAACTTTGTTGGGAGC 57.468 45.000 0.00 0.00 0.00 4.70
153 154 7.432869 TGATACTGCTTTATTGCAACTTTGTT 58.567 30.769 0.00 0.00 42.83 2.83
181 182 9.911138 ATTATGCATTGCAAACGATCAATATTA 57.089 25.926 16.46 0.00 43.62 0.98
187 188 8.136800 AGAATTATTATGCATTGCAAACGATCA 58.863 29.630 16.46 0.00 43.62 2.92
191 192 7.682593 TGAGAATTATTATGCATTGCAAACG 57.317 32.000 16.46 0.00 43.62 3.60
225 246 5.065731 GGAACCTCAACAGAATAATCAGCAG 59.934 44.000 0.00 0.00 0.00 4.24
238 259 8.904099 TTTTTAAAACAAAAGGAACCTCAACA 57.096 26.923 0.00 0.00 0.00 3.33
264 286 2.296073 AACCAGGGATGCCGTTTAAA 57.704 45.000 0.00 0.00 0.00 1.52
270 292 2.573340 GCAAAACCAGGGATGCCG 59.427 61.111 0.00 0.00 32.73 5.69
285 307 0.328592 TTATTTGTGGGGGTAGCGCA 59.671 50.000 11.47 0.00 0.00 6.09
286 308 1.133598 GTTTATTTGTGGGGGTAGCGC 59.866 52.381 0.00 0.00 0.00 5.92
287 309 1.746787 GGTTTATTTGTGGGGGTAGCG 59.253 52.381 0.00 0.00 0.00 4.26
307 330 5.219633 CACCAGTATTTTGTTCCTTTTCGG 58.780 41.667 0.00 0.00 0.00 4.30
312 335 5.531287 GTGAGACACCAGTATTTTGTTCCTT 59.469 40.000 0.00 0.00 0.00 3.36
313 336 5.063880 GTGAGACACCAGTATTTTGTTCCT 58.936 41.667 0.00 0.00 0.00 3.36
340 363 2.688477 TGGACTCCTTTGGCCATTTTT 58.312 42.857 6.09 0.00 0.00 1.94
341 364 2.397044 TGGACTCCTTTGGCCATTTT 57.603 45.000 6.09 0.00 0.00 1.82
362 385 6.295123 GGGCGGAGAGAGTATATTATTGTGAA 60.295 42.308 0.00 0.00 0.00 3.18
369 392 3.820195 TGGGGCGGAGAGAGTATATTA 57.180 47.619 0.00 0.00 0.00 0.98
373 396 1.580059 TTTTGGGGCGGAGAGAGTAT 58.420 50.000 0.00 0.00 0.00 2.12
375 398 0.698818 ATTTTTGGGGCGGAGAGAGT 59.301 50.000 0.00 0.00 0.00 3.24
376 399 2.710096 TATTTTTGGGGCGGAGAGAG 57.290 50.000 0.00 0.00 0.00 3.20
384 407 4.447290 ACAACAACACTTATTTTTGGGGC 58.553 39.130 0.00 0.00 0.00 5.80
385 408 6.993786 AAACAACAACACTTATTTTTGGGG 57.006 33.333 0.00 0.00 0.00 4.96
424 447 7.487189 CGGAATAAGTGTCGTTGTTCTAGTTAT 59.513 37.037 0.00 0.00 30.52 1.89
431 458 4.089636 GTCTCGGAATAAGTGTCGTTGTTC 59.910 45.833 0.00 0.00 0.00 3.18
449 476 1.575244 TATGTAGTCCGTCCGTCTCG 58.425 55.000 0.00 0.00 0.00 4.04
451 478 6.127647 TGTTTAAATATGTAGTCCGTCCGTCT 60.128 38.462 0.00 0.00 0.00 4.18
587 622 7.772332 TTTTGTTTTTGTTATTGTACGCCAT 57.228 28.000 0.00 0.00 0.00 4.40
588 623 7.772332 ATTTTGTTTTTGTTATTGTACGCCA 57.228 28.000 0.00 0.00 0.00 5.69
589 624 8.753175 TGTATTTTGTTTTTGTTATTGTACGCC 58.247 29.630 0.00 0.00 0.00 5.68
607 642 8.929827 TGGCTCATTTTCATGTATGTATTTTG 57.070 30.769 0.00 0.00 0.00 2.44
662 699 9.425893 CAAAAATGTTATGATCTGTAAGCTACG 57.574 33.333 0.00 0.00 0.00 3.51
682 719 8.911662 CGGATCTGTAAATTTTCGTTCAAAAAT 58.088 29.630 0.00 0.00 39.83 1.82
687 724 4.142773 GGCGGATCTGTAAATTTTCGTTCA 60.143 41.667 2.89 0.00 0.00 3.18
709 746 6.964934 GGTAAAAAGCTTATACATGTTCACGG 59.035 38.462 18.69 0.00 0.00 4.94
744 781 8.784043 ACGAAAGCTTATACATGTTCTCTTTTT 58.216 29.630 2.30 0.00 0.00 1.94
745 782 8.230486 CACGAAAGCTTATACATGTTCTCTTTT 58.770 33.333 2.30 0.00 0.00 2.27
746 783 7.148407 CCACGAAAGCTTATACATGTTCTCTTT 60.148 37.037 2.30 7.25 0.00 2.52
749 786 5.810587 TCCACGAAAGCTTATACATGTTCTC 59.189 40.000 2.30 0.00 0.00 2.87
751 788 6.604735 ATCCACGAAAGCTTATACATGTTC 57.395 37.500 2.30 0.00 0.00 3.18
753 790 7.391148 AAAATCCACGAAAGCTTATACATGT 57.609 32.000 2.69 2.69 0.00 3.21
839 889 2.812011 CAAGTTATTATAGTGCCGGGCC 59.188 50.000 17.97 8.02 0.00 5.80
847 897 5.989477 TGCTGAGTGCCAAGTTATTATAGT 58.011 37.500 0.00 0.00 42.00 2.12
854 904 2.426522 GTGATGCTGAGTGCCAAGTTA 58.573 47.619 0.00 0.00 42.00 2.24
855 905 1.242076 GTGATGCTGAGTGCCAAGTT 58.758 50.000 0.00 0.00 42.00 2.66
856 906 0.607489 GGTGATGCTGAGTGCCAAGT 60.607 55.000 0.00 0.00 42.00 3.16
857 907 0.322277 AGGTGATGCTGAGTGCCAAG 60.322 55.000 0.00 0.00 42.00 3.61
858 908 0.321919 GAGGTGATGCTGAGTGCCAA 60.322 55.000 0.00 0.00 42.00 4.52
859 909 1.297689 GAGGTGATGCTGAGTGCCA 59.702 57.895 0.00 0.00 42.00 4.92
860 910 1.451028 GGAGGTGATGCTGAGTGCC 60.451 63.158 0.00 0.00 42.00 5.01
861 911 1.812922 CGGAGGTGATGCTGAGTGC 60.813 63.158 0.00 0.00 43.25 4.40
862 912 4.509756 CGGAGGTGATGCTGAGTG 57.490 61.111 0.00 0.00 0.00 3.51
889 939 3.009612 TTTTTGACCCGAACCCTCG 57.990 52.632 0.00 0.00 45.02 4.63
923 973 1.823610 GCCGAACCCTAGTACACTCTT 59.176 52.381 0.00 0.00 0.00 2.85
925 975 0.100146 CGCCGAACCCTAGTACACTC 59.900 60.000 0.00 0.00 0.00 3.51
945 995 4.796231 GTCAGCGACACGGCGGAT 62.796 66.667 13.24 0.00 39.26 4.18
949 999 4.664677 AGTGGTCAGCGACACGGC 62.665 66.667 10.14 0.00 33.68 5.68
950 1000 2.430921 GAGTGGTCAGCGACACGG 60.431 66.667 10.14 0.00 33.68 4.94
951 1001 2.016704 GTGAGTGGTCAGCGACACG 61.017 63.158 10.14 0.00 33.68 4.49
952 1002 1.664965 GGTGAGTGGTCAGCGACAC 60.665 63.158 10.14 0.00 41.19 3.67
953 1003 2.734591 GGTGAGTGGTCAGCGACA 59.265 61.111 10.14 0.00 41.19 4.35
1086 1152 2.184579 CCGGACTTTCGAGGAGGC 59.815 66.667 0.00 0.00 0.00 4.70
1128 1194 1.017387 GAGCATAAAACCAGAGGGCG 58.983 55.000 0.00 0.00 37.90 6.13
1155 1221 3.818787 CTGTGCATCCAAGCCGCC 61.819 66.667 0.00 0.00 0.00 6.13
1161 1227 2.677524 GGCTGGCTGTGCATCCAA 60.678 61.111 6.73 0.00 30.98 3.53
1169 1238 3.127533 GCGAAATCGGCTGGCTGT 61.128 61.111 4.84 0.00 40.23 4.40
1195 1264 8.258007 TCTTAATTTCCGCTAAAAGATGAGAGA 58.742 33.333 0.00 0.00 0.00 3.10
1211 1280 8.703336 GCACAGACAAGAAAAATCTTAATTTCC 58.297 33.333 0.00 0.00 36.44 3.13
1227 1296 0.397941 TCCTCCCAAGCACAGACAAG 59.602 55.000 0.00 0.00 0.00 3.16
1253 1322 1.858091 CTCCGCCACTGCTAATACTG 58.142 55.000 0.00 0.00 34.43 2.74
1258 1327 0.683179 TCTAGCTCCGCCACTGCTAA 60.683 55.000 0.00 0.00 38.59 3.09
1259 1328 1.076995 TCTAGCTCCGCCACTGCTA 60.077 57.895 0.00 0.00 38.15 3.49
1416 1496 3.994392 AGCGCTACAATTTTCTCTTTCGA 59.006 39.130 8.99 0.00 0.00 3.71
1420 1500 5.874810 TGTGATAGCGCTACAATTTTCTCTT 59.125 36.000 21.49 0.00 0.00 2.85
1481 1568 2.029918 GGAAGAGCTTTGCGTTTGGAAT 60.030 45.455 0.00 0.00 0.00 3.01
1493 1580 2.093921 GCGAGGAAGTTAGGAAGAGCTT 60.094 50.000 0.00 0.00 0.00 3.74
1659 1747 2.515854 AGACTTAGGCTCGTCTTCACA 58.484 47.619 12.14 0.00 37.19 3.58
1769 1857 3.063180 GGATGTGATGCTATAAGATGCGC 59.937 47.826 0.00 0.00 0.00 6.09
1790 1878 8.190784 GTCTCATTCACATTTTATAACCCTTGG 58.809 37.037 0.00 0.00 0.00 3.61
2198 2294 3.032459 AGGTTAGGTGTAGCTAGGCTTC 58.968 50.000 0.00 0.00 40.44 3.86
2418 2532 4.154015 TCATCACGTGTTCATCAATTCACC 59.846 41.667 16.51 0.00 0.00 4.02
2420 2534 4.754114 TGTCATCACGTGTTCATCAATTCA 59.246 37.500 16.51 0.00 0.00 2.57
2421 2535 5.281693 TGTCATCACGTGTTCATCAATTC 57.718 39.130 16.51 0.00 0.00 2.17
2422 2536 5.412286 TCATGTCATCACGTGTTCATCAATT 59.588 36.000 16.51 0.00 40.10 2.32
2424 2538 4.314121 TCATGTCATCACGTGTTCATCAA 58.686 39.130 16.51 0.00 40.10 2.57
2425 2539 3.924144 TCATGTCATCACGTGTTCATCA 58.076 40.909 16.51 10.05 40.10 3.07
2426 2540 4.176271 TCTCATGTCATCACGTGTTCATC 58.824 43.478 16.51 4.70 40.10 2.92
2427 2541 4.192429 TCTCATGTCATCACGTGTTCAT 57.808 40.909 16.51 12.41 40.10 2.57
2428 2542 3.658757 TCTCATGTCATCACGTGTTCA 57.341 42.857 16.51 10.73 40.10 3.18
2429 2543 4.176271 TCATCTCATGTCATCACGTGTTC 58.824 43.478 16.51 5.39 40.10 3.18
2430 2544 4.192429 TCATCTCATGTCATCACGTGTT 57.808 40.909 16.51 3.97 40.10 3.32
2431 2545 3.874392 TCATCTCATGTCATCACGTGT 57.126 42.857 16.51 0.00 40.10 4.49
2432 2546 4.365723 TCATCATCTCATGTCATCACGTG 58.634 43.478 9.94 9.94 40.49 4.49
2433 2547 4.340381 TCTCATCATCTCATGTCATCACGT 59.660 41.667 0.00 0.00 0.00 4.49
2434 2548 4.680567 GTCTCATCATCTCATGTCATCACG 59.319 45.833 0.00 0.00 0.00 4.35
2435 2549 4.680567 CGTCTCATCATCTCATGTCATCAC 59.319 45.833 0.00 0.00 0.00 3.06
2436 2550 4.795308 GCGTCTCATCATCTCATGTCATCA 60.795 45.833 0.00 0.00 0.00 3.07
2437 2551 3.674281 GCGTCTCATCATCTCATGTCATC 59.326 47.826 0.00 0.00 0.00 2.92
2438 2552 3.069158 TGCGTCTCATCATCTCATGTCAT 59.931 43.478 0.00 0.00 0.00 3.06
2439 2553 2.428171 TGCGTCTCATCATCTCATGTCA 59.572 45.455 0.00 0.00 0.00 3.58
2440 2554 2.793790 GTGCGTCTCATCATCTCATGTC 59.206 50.000 0.00 0.00 0.00 3.06
2441 2555 2.797439 CGTGCGTCTCATCATCTCATGT 60.797 50.000 0.00 0.00 0.00 3.21
2442 2556 1.785430 CGTGCGTCTCATCATCTCATG 59.215 52.381 0.00 0.00 0.00 3.07
2447 2561 3.423536 CAGTAATCGTGCGTCTCATCATC 59.576 47.826 0.00 0.00 0.00 2.92
2448 2562 3.066760 TCAGTAATCGTGCGTCTCATCAT 59.933 43.478 0.00 0.00 0.00 2.45
2450 2564 3.066369 TCAGTAATCGTGCGTCTCATC 57.934 47.619 0.00 0.00 0.00 2.92
2466 2580 5.157940 ACATTACTCTGCAGTTCATCAGT 57.842 39.130 14.67 11.02 33.62 3.41
2478 2592 5.942872 AGATTTTTCCGCAACATTACTCTG 58.057 37.500 0.00 0.00 0.00 3.35
2479 2593 6.016276 ACAAGATTTTTCCGCAACATTACTCT 60.016 34.615 0.00 0.00 0.00 3.24
2487 2610 2.468831 TGCACAAGATTTTTCCGCAAC 58.531 42.857 0.00 0.00 0.00 4.17
2491 2614 1.270550 AGGCTGCACAAGATTTTTCCG 59.729 47.619 0.50 0.00 0.00 4.30
2514 2637 4.379394 CCATCGTTCAACCTAAACACCATG 60.379 45.833 0.00 0.00 0.00 3.66
2516 2639 3.142951 CCATCGTTCAACCTAAACACCA 58.857 45.455 0.00 0.00 0.00 4.17
2523 2646 0.390603 CACCGCCATCGTTCAACCTA 60.391 55.000 0.00 0.00 0.00 3.08
2544 2667 2.147387 GGCCCCATAGTCGTCCCAT 61.147 63.158 0.00 0.00 0.00 4.00
2631 2762 4.196971 ACTTATATCGTGTTGGAAAGGCC 58.803 43.478 0.00 0.00 37.10 5.19
2632 2763 5.123344 ACAACTTATATCGTGTTGGAAAGGC 59.877 40.000 15.22 0.00 43.54 4.35
2633 2764 6.737254 ACAACTTATATCGTGTTGGAAAGG 57.263 37.500 15.22 0.00 43.54 3.11
2667 2798 1.825474 CTCCCTCCGTCGCCATATATT 59.175 52.381 0.00 0.00 0.00 1.28
2702 2833 5.009410 GCTATCTGGGGCATTATTATCATGC 59.991 44.000 2.98 2.98 45.47 4.06
2719 2851 2.442236 AACCCCCAATGTGCTATCTG 57.558 50.000 0.00 0.00 0.00 2.90
2720 2852 2.683742 CGAAACCCCCAATGTGCTATCT 60.684 50.000 0.00 0.00 0.00 1.98
2721 2853 1.676006 CGAAACCCCCAATGTGCTATC 59.324 52.381 0.00 0.00 0.00 2.08
2724 2856 2.275380 GCGAAACCCCCAATGTGCT 61.275 57.895 0.00 0.00 0.00 4.40
2748 2880 1.136305 GCCATGAGCGACAACCTAGTA 59.864 52.381 0.00 0.00 0.00 1.82
2749 2881 0.108138 GCCATGAGCGACAACCTAGT 60.108 55.000 0.00 0.00 0.00 2.57
2760 2892 0.169009 GAACGAACAAGGCCATGAGC 59.831 55.000 16.33 4.90 42.60 4.26
2798 2930 2.441822 CTTCTCCGATGCCGATCCCC 62.442 65.000 0.00 0.00 38.22 4.81
2806 2938 0.665972 GCGATCTCCTTCTCCGATGC 60.666 60.000 0.00 0.00 0.00 3.91
2825 2957 0.593518 CGCGTCTATGACAGCCAGAG 60.594 60.000 0.00 0.00 35.49 3.35
2850 2982 2.586258 GCAAGAGCATCGTCTCCTTA 57.414 50.000 0.00 0.00 42.67 2.69
2865 2997 0.816825 CCGGGGTGATGAGATGCAAG 60.817 60.000 0.00 0.00 0.00 4.01
2896 3028 4.697756 TTCACCTTGGCGCCTCCG 62.698 66.667 29.70 16.51 37.80 4.63
2947 3079 5.006153 TGTCGAGAGAACAGAAAACTGAA 57.994 39.130 0.00 0.00 45.01 3.02
2950 3082 6.049149 TCAATTGTCGAGAGAACAGAAAACT 58.951 36.000 5.13 0.00 45.01 2.66
2951 3083 6.287107 TCAATTGTCGAGAGAACAGAAAAC 57.713 37.500 5.13 0.00 45.01 2.43
2952 3084 6.918892 TTCAATTGTCGAGAGAACAGAAAA 57.081 33.333 5.13 0.00 45.01 2.29
2966 3099 6.438763 ACTTTTTGTCGGAGATTCAATTGTC 58.561 36.000 5.13 0.00 40.67 3.18
3029 3162 3.333029 AAATAAAGGCACCACCATTGC 57.667 42.857 0.00 0.00 43.14 3.56
3038 3171 3.745975 GGGAACAAGCAAAATAAAGGCAC 59.254 43.478 0.00 0.00 0.00 5.01
3039 3172 3.244387 GGGGAACAAGCAAAATAAAGGCA 60.244 43.478 0.00 0.00 0.00 4.75
3052 3185 3.691609 GCTATTGAACAGAGGGGAACAAG 59.308 47.826 0.00 0.00 0.00 3.16
3072 3205 1.141657 AGATGGCATAATCACGGTGCT 59.858 47.619 0.00 0.00 38.83 4.40
3078 3211 6.935771 AGAGAGATTGAAGATGGCATAATCAC 59.064 38.462 18.18 13.61 31.83 3.06
3200 3333 5.823209 TTAGCATTCTCATTGTGATGGTG 57.177 39.130 9.75 3.42 33.93 4.17
3214 3347 5.572511 TGAAACAACATTCGCATTAGCATTC 59.427 36.000 0.00 0.00 42.27 2.67
3333 3468 1.735376 CTACCATCGGCGCCACTACT 61.735 60.000 28.98 7.75 0.00 2.57
3424 3572 2.694628 TGAGGAGCTGCACAAAACAATT 59.305 40.909 8.35 0.00 0.00 2.32
3450 3598 3.788227 TCACTTCATAGGGCAAACTGT 57.212 42.857 0.00 0.00 0.00 3.55
3457 3605 4.708177 TCATTAGCTTCACTTCATAGGGC 58.292 43.478 0.00 0.00 0.00 5.19
3501 3704 7.559897 TCCTGAAGAAAACAACAGAGGTTAATT 59.440 33.333 0.00 0.00 34.87 1.40
3502 3705 7.060421 TCCTGAAGAAAACAACAGAGGTTAAT 58.940 34.615 0.00 0.00 34.87 1.40
3503 3706 6.419791 TCCTGAAGAAAACAACAGAGGTTAA 58.580 36.000 0.00 0.00 34.87 2.01
3573 3776 9.781834 ATTATTACATAAAATTGACGGTGTGTG 57.218 29.630 0.00 0.00 0.00 3.82
3593 3796 9.952030 TCACAACAGAGGTGATGTTTATTATTA 57.048 29.630 0.00 0.00 37.58 0.98
3594 3797 8.862325 TCACAACAGAGGTGATGTTTATTATT 57.138 30.769 0.00 0.00 37.58 1.40
3661 3864 4.821260 TGTAGCATGTTATTGCCACCTATG 59.179 41.667 0.00 0.00 43.83 2.23
3709 3913 7.741027 ATATGAACATGAATCTGCACTAAGG 57.259 36.000 0.00 0.00 0.00 2.69
3748 3954 2.084546 CACGGGACAATTTTCTCCCTC 58.915 52.381 9.86 0.00 43.86 4.30
3766 3985 4.768130 TCTGTAGAAGTAGCTGTCACAC 57.232 45.455 0.00 0.00 0.00 3.82
3767 3986 5.068591 TGTTTCTGTAGAAGTAGCTGTCACA 59.931 40.000 0.00 0.00 35.21 3.58
3768 3987 5.529791 TGTTTCTGTAGAAGTAGCTGTCAC 58.470 41.667 0.00 0.00 35.21 3.67
3773 3992 5.717178 TCAGGATGTTTCTGTAGAAGTAGCT 59.283 40.000 0.00 0.00 37.40 3.32
3904 4147 2.743928 GTTGGAGCGACAGGCCAG 60.744 66.667 5.01 0.00 45.17 4.85
3998 4245 5.741388 TGCGCCACATTGTTTTTAAAAAT 57.259 30.435 16.02 0.00 0.00 1.82
4022 4269 2.250031 TCTAAACCCTAACCGCACTCA 58.750 47.619 0.00 0.00 0.00 3.41
4046 4293 2.484594 GGATGCTCAGGTAAAGCTCCTC 60.485 54.545 0.00 0.00 40.50 3.71
4133 4388 1.134401 CCGGAAGATCTTAGCAAGGCA 60.134 52.381 8.25 0.00 0.00 4.75
4169 4424 0.603975 AGAGAAAACTCGGTGCAGGC 60.604 55.000 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.