Multiple sequence alignment - TraesCS4A01G308400

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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 TraesCS4A01G308400 chr4A 100.000 5675 0 0 1 5675 602119639 602113965 0.000000e+00 10480.0
1 TraesCS4A01G308400 chr4A 91.829 820 59 6 1062 1877 629599146 629598331 0.000000e+00 1136.0
2 TraesCS4A01G308400 chr4A 92.021 188 15 0 2020 2207 629598266 629598079 1.210000e-66 265.0
3 TraesCS4A01G308400 chr4A 80.645 248 23 7 1892 2123 602117690 602117452 9.780000e-38 169.0
4 TraesCS4A01G308400 chr4A 80.645 248 23 7 1950 2188 602117748 602117517 9.780000e-38 169.0
5 TraesCS4A01G308400 chr4D 88.006 5436 391 106 392 5673 3332334 3337662 0.000000e+00 6185.0
6 TraesCS4A01G308400 chr4D 81.205 415 43 14 3 410 3329566 3329952 9.240000e-78 302.0
7 TraesCS4A01G308400 chr4B 88.277 3122 206 85 490 3552 3907187 3904167 0.000000e+00 3591.0
8 TraesCS4A01G308400 chr4B 90.252 1549 89 34 3977 5484 3903820 3902293 0.000000e+00 1967.0
9 TraesCS4A01G308400 chr4B 94.944 356 15 3 3594 3948 3904170 3903817 6.420000e-154 555.0
10 TraesCS4A01G308400 chr4B 77.143 665 106 28 2815 3448 20222321 20221672 1.510000e-90 344.0
11 TraesCS4A01G308400 chrUn 90.188 958 55 21 1099 2028 362463995 362464941 0.000000e+00 1212.0
12 TraesCS4A01G308400 chrUn 91.544 816 61 6 1062 1873 271827097 271827908 0.000000e+00 1118.0
13 TraesCS4A01G308400 chrUn 87.608 807 55 17 2024 2819 362465034 362465806 0.000000e+00 894.0
14 TraesCS4A01G308400 chr3A 92.166 817 56 6 1062 1874 144009452 144010264 0.000000e+00 1147.0
15 TraesCS4A01G308400 chr5A 91.422 816 62 6 1062 1873 618023140 618022329 0.000000e+00 1112.0
16 TraesCS4A01G308400 chr7A 91.299 816 63 6 1062 1873 616253740 616254551 0.000000e+00 1107.0
17 TraesCS4A01G308400 chr7A 89.621 819 66 7 1062 1877 94867284 94866482 0.000000e+00 1024.0
18 TraesCS4A01G308400 chr7D 93.237 621 34 6 1261 1877 45848963 45848347 0.000000e+00 907.0
19 TraesCS4A01G308400 chr7D 92.553 188 14 0 2020 2207 45848282 45848095 2.610000e-68 270.0
20 TraesCS4A01G308400 chr7D 91.667 84 7 0 2236 2319 589558964 589559047 3.590000e-22 117.0
21 TraesCS4A01G308400 chr3B 85.057 348 28 11 1979 2306 758007799 758008142 3.280000e-87 333.0
22 TraesCS4A01G308400 chr3B 92.553 188 14 0 2020 2207 821885106 821885293 2.610000e-68 270.0
23 TraesCS4A01G308400 chr3B 77.707 157 15 11 1892 2028 758007821 758007977 1.700000e-10 78.7
24 TraesCS4A01G308400 chr6B 87.900 281 24 5 2033 2306 71979444 71979167 7.090000e-84 322.0
25 TraesCS4A01G308400 chr6B 92.553 188 14 0 2020 2207 105312559 105312746 2.610000e-68 270.0
26 TraesCS4A01G308400 chr6D 81.250 336 49 10 3512 3837 471020624 471020293 5.640000e-65 259.0
27 TraesCS4A01G308400 chr5B 90.798 163 10 2 2148 2306 381220390 381220551 4.450000e-51 213.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G308400 chr4A 602113965 602119639 5674 True 3606.000000 10480 87.096667 1 5675 3 chr4A.!!$R1 5674
1 TraesCS4A01G308400 chr4A 629598079 629599146 1067 True 700.500000 1136 91.925000 1062 2207 2 chr4A.!!$R2 1145
2 TraesCS4A01G308400 chr4D 3329566 3337662 8096 False 3243.500000 6185 84.605500 3 5673 2 chr4D.!!$F1 5670
3 TraesCS4A01G308400 chr4B 3902293 3907187 4894 True 2037.666667 3591 91.157667 490 5484 3 chr4B.!!$R2 4994
4 TraesCS4A01G308400 chr4B 20221672 20222321 649 True 344.000000 344 77.143000 2815 3448 1 chr4B.!!$R1 633
5 TraesCS4A01G308400 chrUn 271827097 271827908 811 False 1118.000000 1118 91.544000 1062 1873 1 chrUn.!!$F1 811
6 TraesCS4A01G308400 chrUn 362463995 362465806 1811 False 1053.000000 1212 88.898000 1099 2819 2 chrUn.!!$F2 1720
7 TraesCS4A01G308400 chr3A 144009452 144010264 812 False 1147.000000 1147 92.166000 1062 1874 1 chr3A.!!$F1 812
8 TraesCS4A01G308400 chr5A 618022329 618023140 811 True 1112.000000 1112 91.422000 1062 1873 1 chr5A.!!$R1 811
9 TraesCS4A01G308400 chr7A 616253740 616254551 811 False 1107.000000 1107 91.299000 1062 1873 1 chr7A.!!$F1 811
10 TraesCS4A01G308400 chr7A 94866482 94867284 802 True 1024.000000 1024 89.621000 1062 1877 1 chr7A.!!$R1 815
11 TraesCS4A01G308400 chr7D 45848095 45848963 868 True 588.500000 907 92.895000 1261 2207 2 chr7D.!!$R1 946

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
86 88 0.040246 TTGCACACACATCACGCATG 60.040 50.0 0.00 0.00 38.64 4.06 F
728 3166 0.251698 TTGGCATGCCTTGTCATCCA 60.252 50.0 35.53 11.01 40.31 3.41 F
758 3199 0.251832 TCAGTCCCTGTCTCTCACCC 60.252 60.0 0.00 0.00 32.61 4.61 F
759 3200 0.252012 CAGTCCCTGTCTCTCACCCT 60.252 60.0 0.00 0.00 0.00 4.34 F
761 3202 0.543174 GTCCCTGTCTCTCACCCTGT 60.543 60.0 0.00 0.00 0.00 4.00 F
1879 4334 0.806868 AGACATTGCATTGCTGACCG 59.193 50.0 10.49 0.00 0.00 4.79 F
2732 5343 0.252197 GAGCACGAGTTTACCCCCAT 59.748 55.0 0.00 0.00 0.00 4.00 F
3126 5764 0.037590 TGTAGCCGGGCTGTTTGATT 59.962 50.0 31.26 4.99 40.10 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1493 3941 0.039437 CGTGAAGGTGAGCGTGTACT 60.039 55.000 0.00 0.0 0.00 2.73 R
2168 4765 0.393820 AGCACCCAACAAAATGCAGG 59.606 50.000 0.00 0.0 40.63 4.85 R
2459 5064 1.377333 GGAAGTACTGGCTGGCCAC 60.377 63.158 10.55 0.0 41.89 5.01 R
2509 5114 2.480759 GCTATGGCTTGTCATTGGCTTG 60.481 50.000 0.00 0.0 35.22 4.01 R
2706 5316 4.113354 GGGTAAACTCGTGCTCAGATAAG 58.887 47.826 0.00 0.0 0.00 1.73 R
2827 5439 0.106669 GGGGAAGGGCATCAAGGTAC 60.107 60.000 0.00 0.0 0.00 3.34 R
4629 7272 0.103208 GCACTATCTGTCCACCCTCG 59.897 60.000 0.00 0.0 0.00 4.63 R
4926 7586 1.774254 ACAACCCACTCTCACCATTCA 59.226 47.619 0.00 0.0 0.00 2.57 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
61 62 6.915300 GGACAAATTTTGTTTTTATTGCCACC 59.085 34.615 15.54 4.70 45.52 4.61
73 74 2.203337 GCCACCACCTCTTGCACA 60.203 61.111 0.00 0.00 0.00 4.57
86 88 0.040246 TTGCACACACATCACGCATG 60.040 50.000 0.00 0.00 38.64 4.06
100 102 1.354506 GCATGCGAGCATCTTGGAC 59.645 57.895 7.70 0.00 33.90 4.02
105 107 1.522355 CGAGCATCTTGGACGCCAT 60.522 57.895 0.00 0.00 31.53 4.40
113 115 5.359576 AGCATCTTGGACGCCATTTTATTTA 59.640 36.000 0.00 0.00 31.53 1.40
115 117 6.701400 GCATCTTGGACGCCATTTTATTTATT 59.299 34.615 0.00 0.00 31.53 1.40
116 118 7.224557 GCATCTTGGACGCCATTTTATTTATTT 59.775 33.333 0.00 0.00 31.53 1.40
118 120 9.965824 ATCTTGGACGCCATTTTATTTATTTAG 57.034 29.630 0.00 0.00 31.53 1.85
121 123 9.575783 TTGGACGCCATTTTATTTATTTAGTTC 57.424 29.630 0.00 0.00 31.53 3.01
122 124 8.962679 TGGACGCCATTTTATTTATTTAGTTCT 58.037 29.630 0.00 0.00 0.00 3.01
123 125 9.797556 GGACGCCATTTTATTTATTTAGTTCTT 57.202 29.630 0.00 0.00 0.00 2.52
197 200 3.679980 GCATATGTACCTAGCACCGAATG 59.320 47.826 4.29 0.00 0.00 2.67
199 202 1.855295 TGTACCTAGCACCGAATGGA 58.145 50.000 0.00 0.00 39.21 3.41
201 204 2.102420 TGTACCTAGCACCGAATGGATG 59.898 50.000 0.00 0.00 39.21 3.51
320 325 4.069304 TCCACGAAATCAAAACCGATTCT 58.931 39.130 0.00 0.00 34.49 2.40
321 326 4.083537 TCCACGAAATCAAAACCGATTCTG 60.084 41.667 0.00 0.00 34.49 3.02
333 338 7.925483 TCAAAACCGATTCTGAAATTCAAACAT 59.075 29.630 0.00 0.00 0.00 2.71
335 340 9.927668 AAAACCGATTCTGAAATTCAAACATAT 57.072 25.926 0.00 0.00 0.00 1.78
351 356 8.112016 TCAAACATATACAAATTCCAAACCGA 57.888 30.769 0.00 0.00 0.00 4.69
354 359 5.885912 ACATATACAAATTCCAAACCGAGCT 59.114 36.000 0.00 0.00 0.00 4.09
374 379 2.380084 TTGAATCTTCCGTTCCTCCG 57.620 50.000 0.00 0.00 0.00 4.63
377 382 1.550130 AATCTTCCGTTCCTCCGCCA 61.550 55.000 0.00 0.00 0.00 5.69
380 388 1.574702 CTTCCGTTCCTCCGCCAAAC 61.575 60.000 0.00 0.00 0.00 2.93
387 395 2.485122 CTCCGCCAAACAATCGCC 59.515 61.111 0.00 0.00 0.00 5.54
390 398 2.392181 CCGCCAAACAATCGCCGTA 61.392 57.895 0.00 0.00 0.00 4.02
400 408 7.411274 CCAAACAATCGCCGTATAATCTAAAA 58.589 34.615 0.00 0.00 0.00 1.52
422 430 3.469008 AGTGGACACTTTGATTCGACA 57.531 42.857 0.00 0.00 38.83 4.35
425 433 3.184581 GTGGACACTTTGATTCGACACTC 59.815 47.826 0.00 0.00 0.00 3.51
426 434 2.737252 GGACACTTTGATTCGACACTCC 59.263 50.000 0.00 0.00 0.00 3.85
428 436 3.393800 ACACTTTGATTCGACACTCCTG 58.606 45.455 0.00 0.00 0.00 3.86
429 437 2.738846 CACTTTGATTCGACACTCCTGG 59.261 50.000 0.00 0.00 0.00 4.45
432 440 3.526931 TTGATTCGACACTCCTGGATC 57.473 47.619 0.00 0.00 0.00 3.36
433 441 1.757118 TGATTCGACACTCCTGGATCC 59.243 52.381 4.20 4.20 0.00 3.36
434 442 1.757118 GATTCGACACTCCTGGATCCA 59.243 52.381 15.27 15.27 0.00 3.41
435 443 1.639722 TTCGACACTCCTGGATCCAA 58.360 50.000 17.00 0.10 0.00 3.53
437 445 2.187958 TCGACACTCCTGGATCCAAAT 58.812 47.619 17.00 0.00 0.00 2.32
438 446 2.571653 TCGACACTCCTGGATCCAAATT 59.428 45.455 17.00 0.00 0.00 1.82
439 447 2.939103 CGACACTCCTGGATCCAAATTC 59.061 50.000 17.00 5.74 0.00 2.17
441 449 4.335416 GACACTCCTGGATCCAAATTCAA 58.665 43.478 17.00 0.00 0.00 2.69
442 450 4.739793 ACACTCCTGGATCCAAATTCAAA 58.260 39.130 17.00 0.00 0.00 2.69
443 451 4.768968 ACACTCCTGGATCCAAATTCAAAG 59.231 41.667 17.00 7.80 0.00 2.77
444 452 3.766051 ACTCCTGGATCCAAATTCAAAGC 59.234 43.478 17.00 0.00 0.00 3.51
446 454 2.159198 CCTGGATCCAAATTCAAAGCCG 60.159 50.000 17.00 0.00 0.00 5.52
447 455 2.493278 CTGGATCCAAATTCAAAGCCGT 59.507 45.455 17.00 0.00 0.00 5.68
448 456 2.896685 TGGATCCAAATTCAAAGCCGTT 59.103 40.909 13.46 0.00 0.00 4.44
449 457 3.056891 TGGATCCAAATTCAAAGCCGTTC 60.057 43.478 13.46 0.00 0.00 3.95
450 458 3.193479 GGATCCAAATTCAAAGCCGTTCT 59.807 43.478 6.95 0.00 0.00 3.01
451 459 3.915437 TCCAAATTCAAAGCCGTTCTC 57.085 42.857 0.00 0.00 0.00 2.87
453 461 3.634448 TCCAAATTCAAAGCCGTTCTCAA 59.366 39.130 0.00 0.00 0.00 3.02
454 462 4.098654 TCCAAATTCAAAGCCGTTCTCAAA 59.901 37.500 0.00 0.00 0.00 2.69
455 463 4.209080 CCAAATTCAAAGCCGTTCTCAAAC 59.791 41.667 0.00 0.00 0.00 2.93
456 464 3.643159 ATTCAAAGCCGTTCTCAAACC 57.357 42.857 0.00 0.00 31.27 3.27
457 465 1.314730 TCAAAGCCGTTCTCAAACCC 58.685 50.000 0.00 0.00 31.27 4.11
459 467 1.613437 CAAAGCCGTTCTCAAACCCAT 59.387 47.619 0.00 0.00 31.27 4.00
460 468 2.817258 CAAAGCCGTTCTCAAACCCATA 59.183 45.455 0.00 0.00 31.27 2.74
461 469 2.109425 AGCCGTTCTCAAACCCATAC 57.891 50.000 0.00 0.00 31.27 2.39
462 470 1.349688 AGCCGTTCTCAAACCCATACA 59.650 47.619 0.00 0.00 31.27 2.29
463 471 1.467342 GCCGTTCTCAAACCCATACAC 59.533 52.381 0.00 0.00 31.27 2.90
464 472 1.730064 CCGTTCTCAAACCCATACACG 59.270 52.381 0.00 0.00 31.27 4.49
466 474 3.259064 CGTTCTCAAACCCATACACGAT 58.741 45.455 0.00 0.00 31.27 3.73
467 475 3.682858 CGTTCTCAAACCCATACACGATT 59.317 43.478 0.00 0.00 31.27 3.34
468 476 4.201685 CGTTCTCAAACCCATACACGATTC 60.202 45.833 0.00 0.00 31.27 2.52
469 477 4.545208 TCTCAAACCCATACACGATTCA 57.455 40.909 0.00 0.00 0.00 2.57
471 479 5.496556 TCTCAAACCCATACACGATTCAAT 58.503 37.500 0.00 0.00 0.00 2.57
472 480 5.584649 TCTCAAACCCATACACGATTCAATC 59.415 40.000 0.00 0.00 0.00 2.67
473 481 5.249420 TCAAACCCATACACGATTCAATCA 58.751 37.500 0.00 0.00 0.00 2.57
475 483 6.376864 TCAAACCCATACACGATTCAATCAAT 59.623 34.615 0.00 0.00 0.00 2.57
476 484 6.773976 AACCCATACACGATTCAATCAATT 57.226 33.333 0.00 0.00 0.00 2.32
477 485 6.135290 ACCCATACACGATTCAATCAATTG 57.865 37.500 0.00 0.00 39.10 2.32
478 486 5.067674 ACCCATACACGATTCAATCAATTGG 59.932 40.000 5.42 0.00 38.30 3.16
482 490 3.257873 ACACGATTCAATCAATTGGGCAA 59.742 39.130 5.42 0.00 32.81 4.52
483 491 4.244066 CACGATTCAATCAATTGGGCAAA 58.756 39.130 5.42 0.00 38.30 3.68
518 2949 5.464965 TCTCTTCAAACACAAAAGTCGAC 57.535 39.130 7.70 7.70 0.00 4.20
520 2951 5.584649 TCTCTTCAAACACAAAAGTCGACAT 59.415 36.000 19.50 1.86 0.00 3.06
529 2960 5.763204 ACACAAAAGTCGACATAGAACCAAT 59.237 36.000 19.50 0.00 0.00 3.16
531 2962 5.995282 ACAAAAGTCGACATAGAACCAATCA 59.005 36.000 19.50 0.00 0.00 2.57
534 2965 8.664798 CAAAAGTCGACATAGAACCAATCATAA 58.335 33.333 19.50 0.00 0.00 1.90
537 2968 5.177696 GTCGACATAGAACCAATCATAAGCC 59.822 44.000 11.55 0.00 0.00 4.35
538 2969 5.056480 CGACATAGAACCAATCATAAGCCA 58.944 41.667 0.00 0.00 0.00 4.75
540 2971 6.347969 CGACATAGAACCAATCATAAGCCATG 60.348 42.308 0.00 0.00 35.81 3.66
569 3000 1.608283 GCGACACTTTGTAGCCCTCTT 60.608 52.381 0.36 0.00 42.06 2.85
589 3020 3.702048 CCGCCCTCCAGAACCGAA 61.702 66.667 0.00 0.00 0.00 4.30
592 3023 1.153147 GCCCTCCAGAACCGAATCC 60.153 63.158 0.00 0.00 0.00 3.01
596 3027 1.475751 CCTCCAGAACCGAATCCCATG 60.476 57.143 0.00 0.00 0.00 3.66
616 3053 2.220824 TGTTTCACATGAAAGCGACGAG 59.779 45.455 7.30 0.00 43.82 4.18
623 3060 3.186909 CATGAAAGCGACGAGTTATCCA 58.813 45.455 0.00 0.00 0.00 3.41
654 3091 2.125431 CGCCCGTATCACCGGTTT 60.125 61.111 2.97 0.00 46.66 3.27
669 3106 3.342627 TTTGACAACGAGGCGCCG 61.343 61.111 23.20 13.22 0.00 6.46
671 3108 3.583276 TTGACAACGAGGCGCCGAT 62.583 57.895 23.20 3.63 0.00 4.18
680 3118 0.811616 GAGGCGCCGATGATGACTTT 60.812 55.000 23.20 0.00 0.00 2.66
681 3119 0.811616 AGGCGCCGATGATGACTTTC 60.812 55.000 23.20 0.00 0.00 2.62
682 3120 1.273887 GCGCCGATGATGACTTTCG 59.726 57.895 0.00 0.00 0.00 3.46
691 3129 1.883926 TGATGACTTTCGTCGACCTCA 59.116 47.619 10.58 3.68 43.21 3.86
695 3133 0.318445 ACTTTCGTCGACCTCAACGG 60.318 55.000 10.58 0.00 39.31 4.44
715 3153 2.431782 GGTCCACTGCAATATTTGGCAT 59.568 45.455 1.31 0.00 39.65 4.40
716 3154 3.450578 GTCCACTGCAATATTTGGCATG 58.549 45.455 1.31 0.00 39.65 4.06
717 3155 2.159071 TCCACTGCAATATTTGGCATGC 60.159 45.455 9.90 9.90 39.65 4.06
718 3156 2.206750 CACTGCAATATTTGGCATGCC 58.793 47.619 30.54 30.54 39.65 4.40
719 3157 2.112998 ACTGCAATATTTGGCATGCCT 58.887 42.857 35.53 19.66 39.65 4.75
720 3158 2.502538 ACTGCAATATTTGGCATGCCTT 59.497 40.909 35.53 22.48 39.65 4.35
721 3159 2.869801 CTGCAATATTTGGCATGCCTTG 59.130 45.455 35.53 29.20 39.65 3.61
722 3160 2.236644 TGCAATATTTGGCATGCCTTGT 59.763 40.909 35.53 22.66 38.00 3.16
723 3161 2.867975 GCAATATTTGGCATGCCTTGTC 59.132 45.455 35.53 21.21 36.94 3.18
726 3164 2.973694 ATTTGGCATGCCTTGTCATC 57.026 45.000 35.53 8.82 40.31 2.92
728 3166 0.251698 TTGGCATGCCTTGTCATCCA 60.252 50.000 35.53 11.01 40.31 3.41
745 3186 2.582052 TCCACATTGTTTGGTCAGTCC 58.418 47.619 0.00 0.00 35.42 3.85
746 3187 1.613437 CCACATTGTTTGGTCAGTCCC 59.387 52.381 0.00 0.00 34.77 4.46
752 3193 1.416401 TGTTTGGTCAGTCCCTGTCTC 59.584 52.381 0.00 0.00 34.77 3.36
758 3199 0.251832 TCAGTCCCTGTCTCTCACCC 60.252 60.000 0.00 0.00 32.61 4.61
759 3200 0.252012 CAGTCCCTGTCTCTCACCCT 60.252 60.000 0.00 0.00 0.00 4.34
760 3201 0.252012 AGTCCCTGTCTCTCACCCTG 60.252 60.000 0.00 0.00 0.00 4.45
761 3202 0.543174 GTCCCTGTCTCTCACCCTGT 60.543 60.000 0.00 0.00 0.00 4.00
771 3214 3.205282 TCTCTCACCCTGTATCCATCTGA 59.795 47.826 0.00 0.00 0.00 3.27
773 3216 3.052566 TCTCACCCTGTATCCATCTGACT 60.053 47.826 0.00 0.00 0.00 3.41
795 3238 7.440856 TGACTCCCAATCTTAATTTTGTTTTGC 59.559 33.333 0.00 0.00 0.00 3.68
904 3350 2.043248 TCTCCGTCCCCAGCTACC 60.043 66.667 0.00 0.00 0.00 3.18
938 3384 2.032071 CCACCGCCGGAATATCCC 59.968 66.667 11.71 0.00 31.13 3.85
939 3385 2.813726 CCACCGCCGGAATATCCCA 61.814 63.158 11.71 0.00 31.13 4.37
940 3386 1.597027 CACCGCCGGAATATCCCAC 60.597 63.158 11.71 0.00 31.13 4.61
941 3387 2.032071 CCGCCGGAATATCCCACC 59.968 66.667 5.05 0.00 31.13 4.61
942 3388 2.032071 CGCCGGAATATCCCACCC 59.968 66.667 5.05 0.00 31.13 4.61
1491 3939 2.274760 CTCCTCGACCGGTACCCT 59.725 66.667 7.34 0.00 0.00 4.34
1493 3941 2.044650 CCTCGACCGGTACCCTGA 60.045 66.667 7.34 0.00 0.00 3.86
1494 3942 2.119655 CCTCGACCGGTACCCTGAG 61.120 68.421 7.34 10.07 0.00 3.35
1711 4159 2.997315 TGAGCCAGTGAGGACCCG 60.997 66.667 0.00 0.00 41.22 5.28
1733 4181 1.868469 TGATTTGGTTGCTTGCTTGC 58.132 45.000 0.00 0.00 0.00 4.01
1764 4213 3.811497 GGTGGTTACAGGTTCAGTTGTAC 59.189 47.826 0.00 0.00 30.03 2.90
1780 4233 5.567534 CAGTTGTACGAATTTGGTTACATGC 59.432 40.000 0.00 0.00 0.00 4.06
1803 4256 8.032952 TGCAGTATGTCTGAATTTTGTTAGAG 57.967 34.615 4.31 0.00 46.27 2.43
1807 4262 5.342806 TGTCTGAATTTTGTTAGAGTGCG 57.657 39.130 0.00 0.00 0.00 5.34
1829 4284 4.024556 CGACTGCTGTCAGACTGAATTTTT 60.025 41.667 21.72 0.00 42.95 1.94
1861 4316 4.946445 TGCTCTGCTTCTGAATGAGATAG 58.054 43.478 14.87 1.79 0.00 2.08
1879 4334 0.806868 AGACATTGCATTGCTGACCG 59.193 50.000 10.49 0.00 0.00 4.79
1892 4347 2.095110 TGCTGACCGATTGATTTGCTTG 60.095 45.455 0.00 0.00 0.00 4.01
1909 4364 2.746269 CTTGCTTGCTTGCTGCTAAAA 58.254 42.857 0.00 0.00 43.37 1.52
1921 4376 3.250762 TGCTGCTAAAAGTACAGTTGCAG 59.749 43.478 16.67 16.67 46.11 4.41
1943 4430 6.510536 CAGAAGTTTGCCTCTCTGAATTTTT 58.489 36.000 0.00 0.00 0.00 1.94
1962 4450 1.105457 TTTGAGTGCTTGCTTGCTGT 58.895 45.000 3.47 0.00 0.00 4.40
1970 4458 5.118286 AGTGCTTGCTTGCTGTTAAAAATT 58.882 33.333 3.47 0.00 0.00 1.82
1971 4459 5.006941 AGTGCTTGCTTGCTGTTAAAAATTG 59.993 36.000 3.47 0.00 0.00 2.32
1999 4500 5.047164 TGCATGCCTATCTGAATTTTGTTGT 60.047 36.000 16.68 0.00 0.00 3.32
2023 4537 4.149396 GTGCTTGCTTGCTGTTAGAAATTG 59.851 41.667 3.47 0.00 0.00 2.32
2036 4633 7.144722 TGTTAGAAATTGAGTTACATGCCTG 57.855 36.000 0.00 0.00 0.00 4.85
2065 4662 1.387539 TGTTGTGTGCTTGCTTGCTA 58.612 45.000 3.47 0.00 0.00 3.49
2101 4698 8.610035 GTTATTACAGAAGTTAGTTACATGCCC 58.390 37.037 0.00 0.00 0.00 5.36
2117 4714 1.339610 TGCCCGTCTGAATTTTGTTGG 59.660 47.619 0.00 0.00 0.00 3.77
2152 4749 4.920376 TGCTAAAAGTTCAGTTGCAGAAC 58.080 39.130 8.81 8.81 44.32 3.01
2168 4765 7.599245 AGTTGCAGAACTTAGTTACATGTCTAC 59.401 37.037 0.00 1.83 39.56 2.59
2404 5009 7.403421 TGCGGTTTATTCTATGTTCGTATTTG 58.597 34.615 0.00 0.00 0.00 2.32
2479 5084 2.125106 GCCAGCCAGTACTTCCGG 60.125 66.667 0.00 0.00 0.00 5.14
2509 5114 7.120138 TCCCTTTTACTCCAATCGAACATTAAC 59.880 37.037 0.00 0.00 0.00 2.01
2569 5174 8.458573 AACTAAGTGTTGGAATGTGATAAACA 57.541 30.769 0.00 0.00 39.39 2.83
2703 5313 3.822735 CACTGTGATATAGGGGCATTTGG 59.177 47.826 0.32 0.00 0.00 3.28
2704 5314 3.463329 ACTGTGATATAGGGGCATTTGGT 59.537 43.478 0.00 0.00 0.00 3.67
2706 5316 4.469657 TGTGATATAGGGGCATTTGGTTC 58.530 43.478 0.00 0.00 0.00 3.62
2732 5343 0.252197 GAGCACGAGTTTACCCCCAT 59.748 55.000 0.00 0.00 0.00 4.00
2881 5494 7.446013 TCTTGTCTCCATAAACGTTGGTTAATT 59.554 33.333 0.00 0.00 34.62 1.40
2885 5498 8.505625 GTCTCCATAAACGTTGGTTAATTAACA 58.494 33.333 25.59 12.03 37.92 2.41
2889 5502 8.077386 CCATAAACGTTGGTTAATTAACACTGT 58.923 33.333 25.59 16.25 37.92 3.55
2968 5581 6.349944 CCTCAATCATGGATAAATAGCAAGGC 60.350 42.308 0.00 0.00 0.00 4.35
2998 5611 2.161609 GCCGAAACCAGAACCAATACAG 59.838 50.000 0.00 0.00 0.00 2.74
3005 5618 2.092212 CCAGAACCAATACAGAGGCCAT 60.092 50.000 5.01 0.00 0.00 4.40
3113 5751 8.632679 TCAATAGGAATGAATTCAAATGTAGCC 58.367 33.333 13.09 6.37 38.53 3.93
3117 5755 1.748493 TGAATTCAAATGTAGCCGGGC 59.252 47.619 12.11 12.11 0.00 6.13
3126 5764 0.037590 TGTAGCCGGGCTGTTTGATT 59.962 50.000 31.26 4.99 40.10 2.57
3127 5765 0.733150 GTAGCCGGGCTGTTTGATTC 59.267 55.000 31.26 7.50 40.10 2.52
3130 5768 1.982073 GCCGGGCTGTTTGATTCGAG 61.982 60.000 12.87 0.00 0.00 4.04
3306 5945 6.055231 TGTTTGAGATGTTTAAAGGACACG 57.945 37.500 0.00 0.00 0.00 4.49
3404 6043 6.465439 AAGGAAAAGTTTCAGGTACCTTTG 57.535 37.500 13.15 2.73 38.92 2.77
3410 6052 5.847111 AGTTTCAGGTACCTTTGTTTTCC 57.153 39.130 13.15 0.00 0.00 3.13
3416 6058 5.829391 TCAGGTACCTTTGTTTTCCCTTTAC 59.171 40.000 13.15 0.00 0.00 2.01
3502 6144 9.530129 GTATCTTTCTTTACGAAACACTTCATG 57.470 33.333 0.00 0.00 36.72 3.07
3510 6152 5.940192 ACGAAACACTTCATGAGCAATAA 57.060 34.783 0.00 0.00 0.00 1.40
3622 6264 7.450074 AGAACCTTCATGTTGTCAGTATGTAA 58.550 34.615 0.00 0.00 37.40 2.41
3658 6300 4.261801 ACACTATTTATGACACAGCCCAC 58.738 43.478 0.00 0.00 0.00 4.61
3868 6511 5.105513 TGGTAGATTTGAGCATGTCGTTCTA 60.106 40.000 0.00 0.00 0.00 2.10
4044 6687 4.670896 AGTTTGCATGTTTGGTAGCTTT 57.329 36.364 0.00 0.00 0.00 3.51
4069 6712 1.032014 ACGCAATCCAGCACTTGTTT 58.968 45.000 0.00 0.00 0.00 2.83
4077 6720 2.951642 TCCAGCACTTGTTTTCTCAAGG 59.048 45.455 10.44 2.36 46.11 3.61
4120 6763 2.186826 AGGCCGTGTTGTGAAGCAC 61.187 57.895 0.00 0.00 34.56 4.40
4155 6798 5.468540 AGTTGTGCACAATCTAGAGTACA 57.531 39.130 33.16 5.40 38.24 2.90
4157 6800 5.928839 AGTTGTGCACAATCTAGAGTACAAG 59.071 40.000 33.16 0.00 36.00 3.16
4222 6865 2.457366 AAAGCGTCTAGGAAGGTGTG 57.543 50.000 0.00 0.00 0.00 3.82
4242 6885 6.370166 GGTGTGGAAATTTTGTTCAACTTCAA 59.630 34.615 0.00 0.00 33.29 2.69
4299 6942 5.239306 CAGCAATTTCCAGACTGAAACAGTA 59.761 40.000 3.32 0.00 45.44 2.74
4629 7272 1.604278 GAGCAGGTGTTTGACAAGGAC 59.396 52.381 0.00 0.00 0.00 3.85
4634 7277 1.226746 GTGTTTGACAAGGACGAGGG 58.773 55.000 0.00 0.00 0.00 4.30
4635 7278 0.834612 TGTTTGACAAGGACGAGGGT 59.165 50.000 0.00 0.00 0.00 4.34
4638 7281 0.761323 TTGACAAGGACGAGGGTGGA 60.761 55.000 0.00 0.00 0.00 4.02
4671 7314 1.557269 GCAGCCCCTCTCCTTCTTCA 61.557 60.000 0.00 0.00 0.00 3.02
4803 7463 0.516877 TGTGCTAGAAATGTGCGTGC 59.483 50.000 0.00 0.00 0.00 5.34
4870 7530 5.881923 TGTAATTAGTCCTATCCCACCAC 57.118 43.478 0.00 0.00 0.00 4.16
4937 7597 7.764141 TGAATCAAAATTCTGAATGGTGAGA 57.236 32.000 16.62 7.60 41.63 3.27
5043 7711 1.826720 AGGATTGGCAATTTGCGATGT 59.173 42.857 14.93 3.73 46.21 3.06
5176 7844 5.023533 TGTATGGCAATCCTCTGTACTTC 57.976 43.478 0.00 0.00 0.00 3.01
5178 7846 5.897250 TGTATGGCAATCCTCTGTACTTCTA 59.103 40.000 0.00 0.00 0.00 2.10
5180 7848 7.728532 TGTATGGCAATCCTCTGTACTTCTATA 59.271 37.037 0.00 0.00 0.00 1.31
5182 7850 7.618019 TGGCAATCCTCTGTACTTCTATATT 57.382 36.000 0.00 0.00 0.00 1.28
5184 7852 9.154632 TGGCAATCCTCTGTACTTCTATATTTA 57.845 33.333 0.00 0.00 0.00 1.40
5241 7909 9.382244 CGTGTTTTAGGAAAAAGAAGAATACAG 57.618 33.333 0.00 0.00 35.29 2.74
5336 8020 9.495754 TTTGTTTTTATTTTGCGAAAAGATTGG 57.504 25.926 2.54 0.00 33.22 3.16
5337 8021 7.634522 TGTTTTTATTTTGCGAAAAGATTGGG 58.365 30.769 2.54 0.00 33.22 4.12
5438 8126 9.294030 GCTCTACAAACCAATTCTGAAAATATG 57.706 33.333 0.00 0.00 0.00 1.78
5536 8224 0.875059 CCTGGAAAGTCTGAAACGCC 59.125 55.000 0.00 0.00 0.00 5.68
5539 8227 0.591659 GGAAAGTCTGAAACGCCCAC 59.408 55.000 0.00 0.00 0.00 4.61
5545 8233 1.000506 GTCTGAAACGCCCACTAGTGA 59.999 52.381 24.68 0.26 0.00 3.41
5560 8248 5.295292 CCACTAGTGATTTCATGACATGGTC 59.705 44.000 24.68 11.32 0.00 4.02
5561 8249 5.006068 CACTAGTGATTTCATGACATGGTCG 59.994 44.000 18.45 2.74 34.95 4.79
5592 8296 0.837272 CTATCCCGGGTGTGGACAAT 59.163 55.000 22.86 6.31 33.94 2.71
5603 8307 6.472887 CGGGTGTGGACAATATATAAGGAAT 58.527 40.000 0.00 0.00 0.00 3.01
5622 8326 6.688073 GGAATTCTCCTCCACATCCTATTA 57.312 41.667 5.23 0.00 38.88 0.98
5628 8332 4.155709 TCCTCCACATCCTATTAGAGCAG 58.844 47.826 0.00 0.00 0.00 4.24
5638 8342 4.417183 TCCTATTAGAGCAGGAGAAGAGGA 59.583 45.833 0.00 0.00 37.05 3.71
5646 8350 3.027412 GCAGGAGAAGAGGAGTGATACA 58.973 50.000 0.00 0.00 0.00 2.29
5658 8362 0.818296 GTGATACACACGCTCCTCCT 59.182 55.000 0.00 0.00 39.78 3.69
5661 8365 1.384989 ATACACACGCTCCTCCTCCG 61.385 60.000 0.00 0.00 0.00 4.63
5662 8366 4.803426 CACACGCTCCTCCTCCGC 62.803 72.222 0.00 0.00 0.00 5.54
5668 8372 3.080121 CTCCTCCTCCGCCTGCTT 61.080 66.667 0.00 0.00 0.00 3.91
5669 8373 2.607750 TCCTCCTCCGCCTGCTTT 60.608 61.111 0.00 0.00 0.00 3.51
5670 8374 2.437359 CCTCCTCCGCCTGCTTTG 60.437 66.667 0.00 0.00 0.00 2.77
5671 8375 3.130160 CTCCTCCGCCTGCTTTGC 61.130 66.667 0.00 0.00 0.00 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.206829 ACTTTGAAATAGTACACTCTTTGGGC 59.793 38.462 0.00 0.00 0.00 5.36
1 2 7.745620 ACTTTGAAATAGTACACTCTTTGGG 57.254 36.000 0.00 0.00 0.00 4.12
14 15 9.748708 TGTCCATGAAAAGAAACTTTGAAATAG 57.251 29.630 0.00 0.00 0.00 1.73
16 17 9.447157 TTTGTCCATGAAAAGAAACTTTGAAAT 57.553 25.926 0.00 0.00 0.00 2.17
61 62 1.265095 GTGATGTGTGTGCAAGAGGTG 59.735 52.381 0.00 0.00 0.00 4.00
73 74 2.743752 GCTCGCATGCGTGATGTGT 61.744 57.895 37.76 0.00 42.37 3.72
86 88 3.567797 GGCGTCCAAGATGCTCGC 61.568 66.667 8.57 0.00 43.35 5.03
152 154 7.053498 TGCACCTGAGCATGAATAGTAAAATA 58.947 34.615 0.00 0.00 40.11 1.40
178 180 3.568443 TCCATTCGGTGCTAGGTACATA 58.432 45.455 0.00 0.00 0.00 2.29
182 184 1.070134 GCATCCATTCGGTGCTAGGTA 59.930 52.381 0.00 0.00 36.77 3.08
187 189 0.745845 GAGTGCATCCATTCGGTGCT 60.746 55.000 0.00 0.00 39.01 4.40
241 244 9.631257 TCATTTAATCTTGATAGGCATTTGAGA 57.369 29.630 0.00 0.00 0.00 3.27
248 251 9.187996 TGTGAAATCATTTAATCTTGATAGGCA 57.812 29.630 0.00 0.00 32.40 4.75
297 302 4.517453 AGAATCGGTTTTGATTTCGTGGAA 59.483 37.500 0.00 0.00 38.65 3.53
299 304 4.083537 TCAGAATCGGTTTTGATTTCGTGG 60.084 41.667 0.00 0.00 38.65 4.94
333 338 6.431543 TCAAAGCTCGGTTTGGAATTTGTATA 59.568 34.615 18.14 0.00 37.89 1.47
335 340 4.580995 TCAAAGCTCGGTTTGGAATTTGTA 59.419 37.500 18.14 0.00 37.89 2.41
336 341 3.383185 TCAAAGCTCGGTTTGGAATTTGT 59.617 39.130 18.14 0.00 37.89 2.83
337 342 3.976169 TCAAAGCTCGGTTTGGAATTTG 58.024 40.909 18.14 1.97 37.89 2.32
351 356 3.339141 GAGGAACGGAAGATTCAAAGCT 58.661 45.455 0.00 0.00 0.00 3.74
354 359 2.695359 CGGAGGAACGGAAGATTCAAA 58.305 47.619 0.00 0.00 0.00 2.69
374 379 3.250040 AGATTATACGGCGATTGTTTGGC 59.750 43.478 16.62 0.00 0.00 4.52
403 411 3.131396 AGTGTCGAATCAAAGTGTCCAC 58.869 45.455 0.00 0.00 0.00 4.02
404 412 3.390135 GAGTGTCGAATCAAAGTGTCCA 58.610 45.455 0.00 0.00 0.00 4.02
410 418 3.319137 TCCAGGAGTGTCGAATCAAAG 57.681 47.619 0.00 0.00 0.00 2.77
411 419 3.369471 GGATCCAGGAGTGTCGAATCAAA 60.369 47.826 6.95 0.00 0.00 2.69
413 421 1.757118 GGATCCAGGAGTGTCGAATCA 59.243 52.381 6.95 0.00 0.00 2.57
414 422 1.757118 TGGATCCAGGAGTGTCGAATC 59.243 52.381 11.44 0.00 0.00 2.52
415 423 1.866015 TGGATCCAGGAGTGTCGAAT 58.134 50.000 11.44 0.00 0.00 3.34
416 424 1.639722 TTGGATCCAGGAGTGTCGAA 58.360 50.000 15.53 0.00 0.00 3.71
418 426 2.698855 ATTTGGATCCAGGAGTGTCG 57.301 50.000 15.53 0.00 0.00 4.35
419 427 3.955471 TGAATTTGGATCCAGGAGTGTC 58.045 45.455 15.53 8.48 0.00 3.67
420 428 4.387026 TTGAATTTGGATCCAGGAGTGT 57.613 40.909 15.53 0.00 0.00 3.55
421 429 4.381292 GCTTTGAATTTGGATCCAGGAGTG 60.381 45.833 15.53 3.47 0.00 3.51
422 430 3.766051 GCTTTGAATTTGGATCCAGGAGT 59.234 43.478 15.53 7.21 0.00 3.85
425 433 2.159198 CGGCTTTGAATTTGGATCCAGG 60.159 50.000 15.53 0.00 0.00 4.45
426 434 2.493278 ACGGCTTTGAATTTGGATCCAG 59.507 45.455 15.53 1.50 0.00 3.86
428 436 3.193479 AGAACGGCTTTGAATTTGGATCC 59.807 43.478 4.20 4.20 0.00 3.36
429 437 4.082787 TGAGAACGGCTTTGAATTTGGATC 60.083 41.667 0.00 0.00 0.00 3.36
432 440 3.641437 TGAGAACGGCTTTGAATTTGG 57.359 42.857 0.00 0.00 0.00 3.28
433 441 4.209080 GGTTTGAGAACGGCTTTGAATTTG 59.791 41.667 0.00 0.00 36.61 2.32
434 442 4.368315 GGTTTGAGAACGGCTTTGAATTT 58.632 39.130 0.00 0.00 36.61 1.82
435 443 3.243737 GGGTTTGAGAACGGCTTTGAATT 60.244 43.478 0.00 0.00 36.61 2.17
437 445 1.679153 GGGTTTGAGAACGGCTTTGAA 59.321 47.619 0.00 0.00 36.61 2.69
438 446 1.314730 GGGTTTGAGAACGGCTTTGA 58.685 50.000 0.00 0.00 36.61 2.69
439 447 1.028905 TGGGTTTGAGAACGGCTTTG 58.971 50.000 0.00 0.00 36.61 2.77
441 449 2.224670 TGTATGGGTTTGAGAACGGCTT 60.225 45.455 0.00 0.00 36.61 4.35
442 450 1.349688 TGTATGGGTTTGAGAACGGCT 59.650 47.619 0.00 0.00 36.61 5.52
443 451 1.467342 GTGTATGGGTTTGAGAACGGC 59.533 52.381 0.00 0.00 36.61 5.68
444 452 1.730064 CGTGTATGGGTTTGAGAACGG 59.270 52.381 0.00 0.00 36.61 4.44
446 454 4.693566 TGAATCGTGTATGGGTTTGAGAAC 59.306 41.667 0.00 0.00 34.96 3.01
447 455 4.900684 TGAATCGTGTATGGGTTTGAGAA 58.099 39.130 0.00 0.00 0.00 2.87
448 456 4.545208 TGAATCGTGTATGGGTTTGAGA 57.455 40.909 0.00 0.00 0.00 3.27
449 457 5.353956 TGATTGAATCGTGTATGGGTTTGAG 59.646 40.000 0.18 0.00 0.00 3.02
450 458 5.249420 TGATTGAATCGTGTATGGGTTTGA 58.751 37.500 0.18 0.00 0.00 2.69
451 459 5.559427 TGATTGAATCGTGTATGGGTTTG 57.441 39.130 0.18 0.00 0.00 2.93
453 461 6.405731 CCAATTGATTGAATCGTGTATGGGTT 60.406 38.462 7.12 0.00 40.14 4.11
454 462 5.067674 CCAATTGATTGAATCGTGTATGGGT 59.932 40.000 7.12 0.00 40.14 4.51
455 463 5.507817 CCCAATTGATTGAATCGTGTATGGG 60.508 44.000 7.12 15.16 40.14 4.00
456 464 5.522456 CCCAATTGATTGAATCGTGTATGG 58.478 41.667 7.12 4.86 40.14 2.74
457 465 4.977963 GCCCAATTGATTGAATCGTGTATG 59.022 41.667 7.12 0.00 40.14 2.39
459 467 4.013050 TGCCCAATTGATTGAATCGTGTA 58.987 39.130 7.12 0.00 40.14 2.90
460 468 2.824936 TGCCCAATTGATTGAATCGTGT 59.175 40.909 7.12 0.00 40.14 4.49
461 469 3.507103 TGCCCAATTGATTGAATCGTG 57.493 42.857 7.12 0.00 40.14 4.35
462 470 4.533919 TTTGCCCAATTGATTGAATCGT 57.466 36.364 7.12 0.00 40.14 3.73
463 471 5.110598 TGATTTGCCCAATTGATTGAATCG 58.889 37.500 7.12 0.00 40.14 3.34
464 472 6.540914 ACATGATTTGCCCAATTGATTGAATC 59.459 34.615 7.12 11.22 40.14 2.52
466 474 5.806818 ACATGATTTGCCCAATTGATTGAA 58.193 33.333 7.12 0.00 40.14 2.69
467 475 5.423704 ACATGATTTGCCCAATTGATTGA 57.576 34.783 7.12 0.00 40.14 2.57
468 476 7.795482 AATACATGATTTGCCCAATTGATTG 57.205 32.000 7.12 0.00 37.52 2.67
469 477 8.810990 AAAATACATGATTTGCCCAATTGATT 57.189 26.923 7.12 0.00 37.82 2.57
502 1075 5.907391 GGTTCTATGTCGACTTTTGTGTTTG 59.093 40.000 17.92 0.00 0.00 2.93
507 1080 5.995282 TGATTGGTTCTATGTCGACTTTTGT 59.005 36.000 17.92 0.49 0.00 2.83
515 2946 5.056480 TGGCTTATGATTGGTTCTATGTCG 58.944 41.667 0.00 0.00 0.00 4.35
550 2981 2.069273 CAAGAGGGCTACAAAGTGTCG 58.931 52.381 0.00 0.00 0.00 4.35
578 3009 1.285280 ACATGGGATTCGGTTCTGGA 58.715 50.000 0.00 0.00 0.00 3.86
583 3014 2.870175 TGTGAAACATGGGATTCGGTT 58.130 42.857 0.00 0.00 45.67 4.44
596 3027 2.221055 ACTCGTCGCTTTCATGTGAAAC 59.779 45.455 4.16 2.19 38.94 2.78
607 3038 1.404391 ACGATGGATAACTCGTCGCTT 59.596 47.619 5.73 0.00 44.21 4.68
608 3039 1.022735 ACGATGGATAACTCGTCGCT 58.977 50.000 5.73 0.00 44.21 4.93
609 3040 1.836383 AACGATGGATAACTCGTCGC 58.164 50.000 5.73 0.00 46.59 5.19
641 3078 1.125384 CGTTGTCAAACCGGTGATACG 59.875 52.381 8.52 12.41 34.43 3.06
654 3091 4.063967 ATCGGCGCCTCGTTGTCA 62.064 61.111 26.68 0.00 0.00 3.58
691 3129 2.491693 CCAAATATTGCAGTGGACCGTT 59.508 45.455 0.00 0.00 32.54 4.44
695 3133 3.450578 CATGCCAAATATTGCAGTGGAC 58.549 45.455 7.90 1.26 41.46 4.02
696 3134 2.159071 GCATGCCAAATATTGCAGTGGA 60.159 45.455 6.36 0.00 41.46 4.02
700 3138 2.869801 CAAGGCATGCCAAATATTGCAG 59.130 45.455 37.18 8.14 41.46 4.41
715 3153 2.291209 ACAATGTGGATGACAAGGCA 57.709 45.000 0.00 0.00 38.36 4.75
716 3154 3.319755 CAAACAATGTGGATGACAAGGC 58.680 45.455 0.00 0.00 38.36 4.35
717 3155 3.321682 ACCAAACAATGTGGATGACAAGG 59.678 43.478 0.00 0.00 38.36 3.61
718 3156 4.037803 TGACCAAACAATGTGGATGACAAG 59.962 41.667 0.00 0.00 38.36 3.16
719 3157 3.956848 TGACCAAACAATGTGGATGACAA 59.043 39.130 0.00 0.00 38.36 3.18
720 3158 3.560105 TGACCAAACAATGTGGATGACA 58.440 40.909 0.00 0.00 39.62 3.58
721 3159 3.569701 ACTGACCAAACAATGTGGATGAC 59.430 43.478 0.00 0.00 39.62 3.06
722 3160 3.820467 GACTGACCAAACAATGTGGATGA 59.180 43.478 0.00 0.00 39.62 2.92
723 3161 3.057315 GGACTGACCAAACAATGTGGATG 60.057 47.826 0.00 0.00 39.62 3.51
726 3164 1.613437 GGGACTGACCAAACAATGTGG 59.387 52.381 0.00 0.00 42.28 4.17
745 3186 2.035632 GGATACAGGGTGAGAGACAGG 58.964 57.143 0.00 0.00 0.00 4.00
746 3187 2.739943 TGGATACAGGGTGAGAGACAG 58.260 52.381 0.00 0.00 46.17 3.51
760 3201 5.559148 AAGATTGGGAGTCAGATGGATAC 57.441 43.478 0.00 0.00 0.00 2.24
761 3202 7.878621 ATTAAGATTGGGAGTCAGATGGATA 57.121 36.000 0.00 0.00 0.00 2.59
771 3214 6.710295 GGCAAAACAAAATTAAGATTGGGAGT 59.290 34.615 7.64 0.00 0.00 3.85
773 3216 6.000840 GGGCAAAACAAAATTAAGATTGGGA 58.999 36.000 7.64 0.00 0.00 4.37
795 3238 0.740737 GATCCGATTTGGTTGCTGGG 59.259 55.000 0.00 0.00 39.52 4.45
938 3384 2.415010 CGGCAGAGAGATCGGGTG 59.585 66.667 0.00 0.00 0.00 4.61
939 3385 3.532155 GCGGCAGAGAGATCGGGT 61.532 66.667 0.00 0.00 0.00 5.28
940 3386 4.292178 GGCGGCAGAGAGATCGGG 62.292 72.222 3.07 0.00 0.00 5.14
941 3387 4.637489 CGGCGGCAGAGAGATCGG 62.637 72.222 10.53 0.00 0.00 4.18
1491 3939 1.000607 GTGAAGGTGAGCGTGTACTCA 60.001 52.381 0.00 0.00 44.32 3.41
1493 3941 0.039437 CGTGAAGGTGAGCGTGTACT 60.039 55.000 0.00 0.00 0.00 2.73
1494 3942 1.007336 CCGTGAAGGTGAGCGTGTAC 61.007 60.000 0.00 0.00 34.51 2.90
1711 4159 3.120442 GCAAGCAAGCAACCAAATCAATC 60.120 43.478 0.00 0.00 0.00 2.67
1733 4181 3.496331 ACCTGTAACCACCAAATTCAGG 58.504 45.455 0.00 0.00 44.23 3.86
1764 4213 5.879237 ACATACTGCATGTAACCAAATTCG 58.121 37.500 0.00 0.00 46.34 3.34
1780 4233 7.959651 GCACTCTAACAAAATTCAGACATACTG 59.040 37.037 0.00 0.00 46.97 2.74
1807 4262 5.210715 CAAAAATTCAGTCTGACAGCAGTC 58.789 41.667 10.88 1.64 45.19 3.51
1829 4284 1.208052 GAAGCAGAGCAGGTATCCACA 59.792 52.381 0.00 0.00 0.00 4.17
1861 4316 0.804364 TCGGTCAGCAATGCAATGTC 59.196 50.000 8.35 0.00 0.00 3.06
1879 4334 3.424433 GCAAGCAAGCAAGCAAATCAATC 60.424 43.478 3.19 0.00 36.85 2.67
1909 4364 2.618709 GGCAAACTTCTGCAACTGTACT 59.381 45.455 0.00 0.00 44.52 2.73
1943 4430 1.105457 ACAGCAAGCAAGCACTCAAA 58.895 45.000 3.19 0.00 36.85 2.69
1962 4450 7.760794 CAGATAGGCATGCAACTCAATTTTTAA 59.239 33.333 21.36 0.00 0.00 1.52
1970 4458 3.632643 TTCAGATAGGCATGCAACTCA 57.367 42.857 21.36 0.00 0.00 3.41
1971 4459 5.511234 AAATTCAGATAGGCATGCAACTC 57.489 39.130 21.36 11.94 0.00 3.01
1999 4500 1.965935 TCTAACAGCAAGCAAGCACA 58.034 45.000 3.19 0.00 36.85 4.57
2023 4537 5.886960 AAATTCAGACAGGCATGTAACTC 57.113 39.130 2.88 0.00 40.68 3.01
2036 4633 4.259930 GCAAGCACACAACAAAATTCAGAC 60.260 41.667 0.00 0.00 0.00 3.51
2101 4698 2.034558 AGCACCCAACAAAATTCAGACG 59.965 45.455 0.00 0.00 0.00 4.18
2152 4749 7.849804 AAATGCAGGTAGACATGTAACTAAG 57.150 36.000 0.00 0.00 0.00 2.18
2168 4765 0.393820 AGCACCCAACAAAATGCAGG 59.606 50.000 0.00 0.00 40.63 4.85
2459 5064 1.377333 GGAAGTACTGGCTGGCCAC 60.377 63.158 10.55 0.00 41.89 5.01
2479 5084 6.150474 TGTTCGATTGGAGTAAAAGGGAAATC 59.850 38.462 0.00 0.00 0.00 2.17
2509 5114 2.480759 GCTATGGCTTGTCATTGGCTTG 60.481 50.000 0.00 0.00 35.22 4.01
2703 5313 5.288952 GGTAAACTCGTGCTCAGATAAGAAC 59.711 44.000 0.00 0.00 0.00 3.01
2704 5314 5.408356 GGTAAACTCGTGCTCAGATAAGAA 58.592 41.667 0.00 0.00 0.00 2.52
2706 5316 4.113354 GGGTAAACTCGTGCTCAGATAAG 58.887 47.826 0.00 0.00 0.00 1.73
2781 5392 2.289010 GGGTGAGCAGGAAAAACCAATG 60.289 50.000 0.00 0.00 42.04 2.82
2827 5439 0.106669 GGGGAAGGGCATCAAGGTAC 60.107 60.000 0.00 0.00 0.00 3.34
2929 5542 4.480115 TGATTGAGGGGTGTCGTATAGAT 58.520 43.478 0.00 0.00 0.00 1.98
2932 5545 3.323691 CCATGATTGAGGGGTGTCGTATA 59.676 47.826 0.00 0.00 0.00 1.47
3051 5676 7.213216 TGAGTTTGCTTGCAATTTACTGATA 57.787 32.000 13.67 1.44 0.00 2.15
3113 5751 1.156736 AACTCGAATCAAACAGCCCG 58.843 50.000 0.00 0.00 0.00 6.13
3404 6043 8.617290 TTCTAGATCAACAGTAAAGGGAAAAC 57.383 34.615 0.00 0.00 0.00 2.43
3490 6132 6.902341 TCTGTTATTGCTCATGAAGTGTTTC 58.098 36.000 0.00 0.00 0.00 2.78
3496 6138 5.879223 AGAACCTCTGTTATTGCTCATGAAG 59.121 40.000 0.00 0.00 33.97 3.02
3499 6141 5.064452 GTGAGAACCTCTGTTATTGCTCATG 59.936 44.000 0.00 0.00 35.40 3.07
3502 6144 4.569943 TGTGAGAACCTCTGTTATTGCTC 58.430 43.478 0.00 0.00 33.97 4.26
3510 6152 4.101585 TCTGACATTTGTGAGAACCTCTGT 59.898 41.667 0.00 0.00 35.41 3.41
3568 6210 6.901300 GGATACTAGGGAACAGAGGATTTTT 58.099 40.000 0.00 0.00 0.00 1.94
3569 6211 6.502074 GGATACTAGGGAACAGAGGATTTT 57.498 41.667 0.00 0.00 0.00 1.82
3644 6286 2.233676 CAGTAGTGTGGGCTGTGTCATA 59.766 50.000 0.00 0.00 0.00 2.15
3687 6329 5.784750 TGAAGAAATCAGCATCGTGTTAG 57.215 39.130 0.00 0.00 33.04 2.34
3820 6463 1.447317 CCGGCACAGCTGTTTTGACT 61.447 55.000 18.94 0.00 32.22 3.41
3868 6511 1.280710 TCCATTGTGGCGTTACAGGAT 59.719 47.619 0.00 0.00 37.47 3.24
3957 6600 9.241919 AGAAACACCAACATGACATAAATATGA 57.758 29.630 0.00 0.00 37.15 2.15
4021 6664 5.376854 AAGCTACCAAACATGCAAACTAG 57.623 39.130 0.00 0.00 0.00 2.57
4044 6687 2.710377 AGTGCTGGATTGCGTATTTGA 58.290 42.857 0.00 0.00 35.36 2.69
4069 6712 0.401356 TGGCATGCACTCCTTGAGAA 59.599 50.000 21.36 0.00 33.32 2.87
4077 6720 2.906691 ACTCTAGATGGCATGCACTC 57.093 50.000 21.36 14.90 0.00 3.51
4120 6763 1.263217 GCACAACTTGAACCCAGTACG 59.737 52.381 0.00 0.00 0.00 3.67
4155 6798 8.812972 TGACATATCTACACTCAAAACTACCTT 58.187 33.333 0.00 0.00 0.00 3.50
4157 6800 8.870879 GTTGACATATCTACACTCAAAACTACC 58.129 37.037 0.00 0.00 31.64 3.18
4242 6885 3.488047 GCATGATGCGTGCTACTTGAATT 60.488 43.478 0.00 0.00 42.44 2.17
4328 6971 4.219264 TGTCCACATGTCATATGAGCAA 57.781 40.909 5.42 0.00 0.00 3.91
4430 7073 2.214181 CTCCTCCACGTGTTCCCTCG 62.214 65.000 15.65 0.00 0.00 4.63
4473 7116 2.183300 GATACCGACAGCGTGGCA 59.817 61.111 0.00 0.00 35.23 4.92
4629 7272 0.103208 GCACTATCTGTCCACCCTCG 59.897 60.000 0.00 0.00 0.00 4.63
4634 7277 2.670635 CGCAGCACTATCTGTCCAC 58.329 57.895 0.00 0.00 36.49 4.02
4662 7305 2.480244 CGATCAGCGTCATGAAGAAGGA 60.480 50.000 13.18 6.34 31.76 3.36
4803 7463 2.459555 ATCCTGGCCCCTGTATTTTG 57.540 50.000 0.00 0.00 0.00 2.44
4870 7530 3.545078 GCATTGCTGCTATTTTTCAGACG 59.455 43.478 0.16 0.00 45.32 4.18
4926 7586 1.774254 ACAACCCACTCTCACCATTCA 59.226 47.619 0.00 0.00 0.00 2.57
4931 7591 3.949113 TGTAAAAACAACCCACTCTCACC 59.051 43.478 0.00 0.00 0.00 4.02
4937 7597 6.976934 ATTCTCATGTAAAAACAACCCACT 57.023 33.333 0.00 0.00 0.00 4.00
4979 7647 7.493320 CCAACCATAATCTCAAATTGGACAATG 59.507 37.037 0.00 0.00 37.85 2.82
5157 7825 7.805083 ATATAGAAGTACAGAGGATTGCCAT 57.195 36.000 0.00 0.00 36.29 4.40
5182 7850 9.524496 AGCTGCATATCATTCCATTTAAGATAA 57.476 29.630 1.02 0.00 0.00 1.75
5184 7852 7.889073 AGAGCTGCATATCATTCCATTTAAGAT 59.111 33.333 1.02 0.00 0.00 2.40
5186 7854 7.361885 GGAGAGCTGCATATCATTCCATTTAAG 60.362 40.741 1.02 0.00 0.00 1.85
5187 7855 6.432162 GGAGAGCTGCATATCATTCCATTTAA 59.568 38.462 1.02 0.00 0.00 1.52
5188 7856 5.942236 GGAGAGCTGCATATCATTCCATTTA 59.058 40.000 1.02 0.00 0.00 1.40
5189 7857 4.765856 GGAGAGCTGCATATCATTCCATTT 59.234 41.667 1.02 0.00 0.00 2.32
5205 7873 1.338200 CCTAAAACACGCAGGAGAGCT 60.338 52.381 0.00 0.00 0.00 4.09
5206 7874 1.079503 CCTAAAACACGCAGGAGAGC 58.920 55.000 0.00 0.00 0.00 4.09
5241 7909 4.142315 CCTCCATGAAACCATCACAATCAC 60.142 45.833 0.00 0.00 41.93 3.06
5318 8002 9.883142 AAATTATCCCAATCTTTTCGCAAAATA 57.117 25.926 0.00 0.00 0.00 1.40
5320 8004 8.614469 AAAATTATCCCAATCTTTTCGCAAAA 57.386 26.923 0.00 0.00 0.00 2.44
5325 8009 8.863049 CACTCAAAAATTATCCCAATCTTTTCG 58.137 33.333 0.00 0.00 0.00 3.46
5331 8015 9.710900 AAAACTCACTCAAAAATTATCCCAATC 57.289 29.630 0.00 0.00 0.00 2.67
5412 8100 9.294030 CATATTTTCAGAATTGGTTTGTAGAGC 57.706 33.333 0.00 0.00 0.00 4.09
5438 8126 5.010282 AGGAACACCCATTAGTCACAAATC 58.990 41.667 0.00 0.00 37.41 2.17
5508 8196 7.538678 CGTTTCAGACTTTCCAGGAAATAATTG 59.461 37.037 15.38 11.17 30.85 2.32
5509 8197 7.593825 CGTTTCAGACTTTCCAGGAAATAATT 58.406 34.615 15.38 0.45 30.85 1.40
5510 8198 6.349363 GCGTTTCAGACTTTCCAGGAAATAAT 60.349 38.462 15.38 4.25 30.85 1.28
5525 8213 1.000506 TCACTAGTGGGCGTTTCAGAC 59.999 52.381 22.48 0.00 0.00 3.51
5529 8217 3.071479 TGAAATCACTAGTGGGCGTTTC 58.929 45.455 22.48 22.57 0.00 2.78
5536 8224 5.188434 ACCATGTCATGAAATCACTAGTGG 58.812 41.667 22.48 4.94 0.00 4.00
5539 8227 4.509230 CCGACCATGTCATGAAATCACTAG 59.491 45.833 14.67 0.00 32.09 2.57
5545 8233 2.239654 ACTCCCGACCATGTCATGAAAT 59.760 45.455 14.67 0.00 32.09 2.17
5561 8249 1.969208 CCGGGATAGGACTAAACTCCC 59.031 57.143 0.00 6.48 41.86 4.30
5580 8271 8.164070 AGAATTCCTTATATATTGTCCACACCC 58.836 37.037 0.65 0.00 0.00 4.61
5603 8307 4.835615 GCTCTAATAGGATGTGGAGGAGAA 59.164 45.833 0.00 0.00 0.00 2.87
5622 8326 1.357420 TCACTCCTCTTCTCCTGCTCT 59.643 52.381 0.00 0.00 0.00 4.09
5628 8332 3.181495 CGTGTGTATCACTCCTCTTCTCC 60.181 52.174 1.72 0.00 44.16 3.71
5638 8342 0.818296 GGAGGAGCGTGTGTATCACT 59.182 55.000 1.72 0.00 44.16 3.41


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

AutoCloner maintained by Alex Coulton.