Multiple sequence alignment - TraesCS3A01G205900

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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 TraesCS3A01G205900 chr3A 100.000 5398 0 0 1 5398 362342447 362337050 0.000000e+00 9969.0
1 TraesCS3A01G205900 chr3A 85.266 319 34 6 5092 5398 600043831 600043514 3.140000e-82 316.0
2 TraesCS3A01G205900 chr3A 94.545 110 6 0 4903 5012 688901911 688902020 2.590000e-38 171.0
3 TraesCS3A01G205900 chr3A 86.885 61 8 0 588 648 9817147 9817087 9.700000e-08 69.4
4 TraesCS3A01G205900 chr3A 86.885 61 7 1 588 648 9818379 9818320 3.490000e-07 67.6
5 TraesCS3A01G205900 chr3B 94.111 2700 84 16 649 3302 373134786 373132116 0.000000e+00 4036.0
6 TraesCS3A01G205900 chr3B 94.359 1560 56 15 3352 4904 373132118 373130584 0.000000e+00 2364.0
7 TraesCS3A01G205900 chr3B 90.281 391 24 3 5009 5398 373130585 373130208 2.900000e-137 499.0
8 TraesCS3A01G205900 chr3D 93.891 2701 74 22 649 3302 277135579 277138235 0.000000e+00 3989.0
9 TraesCS3A01G205900 chr3D 96.287 1562 49 2 3352 4904 277138233 277139794 0.000000e+00 2555.0
10 TraesCS3A01G205900 chr3D 91.282 390 20 3 5009 5398 277139793 277140168 2.230000e-143 520.0
11 TraesCS3A01G205900 chr3D 87.500 64 8 0 587 650 473754479 473754542 2.090000e-09 75.0
12 TraesCS3A01G205900 chr2A 90.017 601 48 5 1 590 537126828 537126229 0.000000e+00 767.0
13 TraesCS3A01G205900 chr2A 89.916 595 49 5 1 585 381084918 381084325 0.000000e+00 756.0
14 TraesCS3A01G205900 chr2A 92.373 118 8 1 4893 5010 449280147 449280031 3.340000e-37 167.0
15 TraesCS3A01G205900 chr2A 86.885 61 8 0 5092 5152 613340101 613340041 9.700000e-08 69.4
16 TraesCS3A01G205900 chr7D 89.765 596 54 6 1 590 49589082 49588488 0.000000e+00 756.0
17 TraesCS3A01G205900 chr7D 89.632 598 53 6 1 590 581276075 581276671 0.000000e+00 752.0
18 TraesCS3A01G205900 chr7D 95.370 108 4 1 4903 5010 60693373 60693479 2.590000e-38 171.0
19 TraesCS3A01G205900 chr7D 92.920 113 8 0 4903 5015 271752842 271752954 1.200000e-36 165.0
20 TraesCS3A01G205900 chr7D 80.822 73 14 0 579 651 30531040 30530968 2.100000e-04 58.4
21 TraesCS3A01G205900 chr5D 89.684 601 50 6 1 590 410072428 410073027 0.000000e+00 756.0
22 TraesCS3A01G205900 chr5D 83.871 62 8 2 591 651 335214451 335214511 2.100000e-04 58.4
23 TraesCS3A01G205900 chr5A 89.649 599 52 6 1 590 534233131 534233728 0.000000e+00 754.0
24 TraesCS3A01G205900 chr4D 89.667 600 51 6 1 590 72144553 72143955 0.000000e+00 754.0
25 TraesCS3A01G205900 chr4D 89.517 601 51 6 1 590 355681541 355680942 0.000000e+00 750.0
26 TraesCS3A01G205900 chr4D 93.750 112 7 0 4899 5010 494123007 494122896 9.300000e-38 169.0
27 TraesCS3A01G205900 chr1D 89.649 599 53 4 1 590 309944626 309944028 0.000000e+00 754.0
28 TraesCS3A01G205900 chr1D 84.762 315 34 8 5094 5398 309632923 309632613 2.440000e-78 303.0
29 TraesCS3A01G205900 chr1D 95.370 108 5 0 4903 5010 465596804 465596911 7.190000e-39 172.0
30 TraesCS3A01G205900 chr1D 90.196 51 3 2 603 652 378550470 378550519 1.250000e-06 65.8
31 TraesCS3A01G205900 chr1A 84.444 315 33 9 5094 5398 389251830 389251522 4.090000e-76 296.0
32 TraesCS3A01G205900 chr5B 87.903 248 26 4 5147 5391 711818273 711818519 6.840000e-74 289.0
33 TraesCS3A01G205900 chr5B 87.500 248 27 4 5147 5391 711820337 711820583 3.180000e-72 283.0
34 TraesCS3A01G205900 chr5B 87.045 247 29 3 5147 5391 711766183 711766428 5.330000e-70 276.0
35 TraesCS3A01G205900 chr5B 87.045 247 29 3 5147 5391 711814148 711814393 5.330000e-70 276.0
36 TraesCS3A01G205900 chrUn 96.296 108 4 0 4903 5010 94181871 94181978 1.540000e-40 178.0
37 TraesCS3A01G205900 chr6B 96.296 108 4 0 4903 5010 506127983 506128090 1.540000e-40 178.0
38 TraesCS3A01G205900 chr2B 90.833 120 11 0 4903 5022 464021308 464021427 1.560000e-35 161.0
39 TraesCS3A01G205900 chr2B 87.879 66 6 2 586 650 737693832 737693768 5.800000e-10 76.8
40 TraesCS3A01G205900 chr6A 84.615 65 10 0 588 652 615055920 615055984 1.250000e-06 65.8
41 TraesCS3A01G205900 chr7B 84.375 64 10 0 588 651 478730481 478730544 4.510000e-06 63.9


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G205900 chr3A 362337050 362342447 5397 True 9969.000000 9969 100.000000 1 5398 1 chr3A.!!$R1 5397
1 TraesCS3A01G205900 chr3B 373130208 373134786 4578 True 2299.666667 4036 92.917000 649 5398 3 chr3B.!!$R1 4749
2 TraesCS3A01G205900 chr3D 277135579 277140168 4589 False 2354.666667 3989 93.820000 649 5398 3 chr3D.!!$F2 4749
3 TraesCS3A01G205900 chr2A 537126229 537126828 599 True 767.000000 767 90.017000 1 590 1 chr2A.!!$R3 589
4 TraesCS3A01G205900 chr2A 381084325 381084918 593 True 756.000000 756 89.916000 1 585 1 chr2A.!!$R1 584
5 TraesCS3A01G205900 chr7D 49588488 49589082 594 True 756.000000 756 89.765000 1 590 1 chr7D.!!$R2 589
6 TraesCS3A01G205900 chr7D 581276075 581276671 596 False 752.000000 752 89.632000 1 590 1 chr7D.!!$F3 589
7 TraesCS3A01G205900 chr5D 410072428 410073027 599 False 756.000000 756 89.684000 1 590 1 chr5D.!!$F2 589
8 TraesCS3A01G205900 chr5A 534233131 534233728 597 False 754.000000 754 89.649000 1 590 1 chr5A.!!$F1 589
9 TraesCS3A01G205900 chr4D 72143955 72144553 598 True 754.000000 754 89.667000 1 590 1 chr4D.!!$R1 589
10 TraesCS3A01G205900 chr4D 355680942 355681541 599 True 750.000000 750 89.517000 1 590 1 chr4D.!!$R2 589
11 TraesCS3A01G205900 chr1D 309944028 309944626 598 True 754.000000 754 89.649000 1 590 1 chr1D.!!$R2 589
12 TraesCS3A01G205900 chr5B 711814148 711820583 6435 False 282.666667 289 87.482667 5147 5391 3 chr5B.!!$F2 244

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
978 1013 0.248743 CGCGCGTAGACCCTAATTCA 60.249 55.000 24.19 0.00 0.00 2.57 F
2019 2102 0.332632 AGCATGTTACCAGGGCACAT 59.667 50.000 0.00 0.63 0.00 3.21 F
2571 2655 1.265635 TCCTTCACGATGTTTTTGGCG 59.734 47.619 0.00 0.00 0.00 5.69 F
3954 4057 0.676466 GGACCATGATGGCGAACACA 60.676 55.000 12.25 0.00 42.67 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2594 2678 0.179089 CTATCCGCTGCTGTGCTCTT 60.179 55.000 0.00 0.0 0.0 2.85 R
3337 3431 1.352017 AGCACCAATGGACATCACTGA 59.648 47.619 6.16 0.0 0.0 3.41 R
3986 4089 1.693627 TGCCGGCAAGGTTTTTAAGA 58.306 45.000 30.74 0.0 43.7 2.10 R
4934 5037 1.134521 TGCACCTTGTCTGAAACGTCT 60.135 47.619 0.00 0.0 0.0 4.18 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
22 23 3.746045 TGGAAGGCTATATTCGGACAC 57.254 47.619 0.00 0.00 0.00 3.67
56 57 3.861113 CGAGTGATTCGGGTATTTTTCGA 59.139 43.478 0.00 0.00 45.54 3.71
87 88 3.521937 AGAGTTATGGGAATTCGTTGGGA 59.478 43.478 0.00 0.00 0.00 4.37
231 247 5.973124 TCTCCCTCATTTCCTTCTTTCCTAT 59.027 40.000 0.00 0.00 0.00 2.57
293 309 5.252397 TCCTAGTAGGACTCCTTACACTTGA 59.748 44.000 15.33 0.00 40.06 3.02
300 316 1.666553 CCTTACACTTGACGCGCCA 60.667 57.895 5.73 0.00 0.00 5.69
367 385 2.727103 GGCACCTTAAAGGCACACA 58.273 52.632 0.00 0.00 39.63 3.72
369 387 1.000274 GGCACCTTAAAGGCACACAAG 60.000 52.381 0.00 0.00 39.63 3.16
379 399 7.201785 CCTTAAAGGCACACAAGTTTCTCTTAA 60.202 37.037 0.00 0.00 34.66 1.85
434 456 5.473846 CACCTCGGTCATATCATAGTAGTGT 59.526 44.000 0.00 0.00 0.00 3.55
552 574 1.134699 GGGACATCATCGAGCTGAACA 60.135 52.381 0.00 0.00 0.00 3.18
557 579 2.749280 TCATCGAGCTGAACATGTGT 57.251 45.000 0.00 0.00 0.00 3.72
569 591 2.462456 ACATGTGTTGATCGCAGAGT 57.538 45.000 0.00 0.00 43.63 3.24
598 620 7.880059 GTACGTTTGGTACTTGAACTCTAAT 57.120 36.000 0.00 0.00 46.50 1.73
601 623 6.987992 ACGTTTGGTACTTGAACTCTAATGAA 59.012 34.615 0.00 0.00 0.00 2.57
602 624 7.042254 ACGTTTGGTACTTGAACTCTAATGAAC 60.042 37.037 0.00 0.00 0.00 3.18
603 625 7.170998 CGTTTGGTACTTGAACTCTAATGAACT 59.829 37.037 0.00 0.00 0.00 3.01
604 626 7.962964 TTGGTACTTGAACTCTAATGAACTG 57.037 36.000 0.00 0.00 0.00 3.16
605 627 7.297936 TGGTACTTGAACTCTAATGAACTGA 57.702 36.000 0.00 0.00 0.00 3.41
606 628 7.378966 TGGTACTTGAACTCTAATGAACTGAG 58.621 38.462 0.00 0.00 0.00 3.35
607 629 7.232737 TGGTACTTGAACTCTAATGAACTGAGA 59.767 37.037 0.00 0.00 0.00 3.27
609 631 9.646427 GTACTTGAACTCTAATGAACTGAGAAT 57.354 33.333 0.00 0.00 0.00 2.40
611 633 9.646427 ACTTGAACTCTAATGAACTGAGAATAC 57.354 33.333 0.00 0.00 0.00 1.89
612 634 9.092876 CTTGAACTCTAATGAACTGAGAATACC 57.907 37.037 0.00 0.00 0.00 2.73
613 635 8.134202 TGAACTCTAATGAACTGAGAATACCA 57.866 34.615 0.00 0.00 0.00 3.25
614 636 8.035394 TGAACTCTAATGAACTGAGAATACCAC 58.965 37.037 0.00 0.00 0.00 4.16
616 638 8.824756 ACTCTAATGAACTGAGAATACCACTA 57.175 34.615 0.00 0.00 0.00 2.74
617 639 9.427821 ACTCTAATGAACTGAGAATACCACTAT 57.572 33.333 0.00 0.00 0.00 2.12
618 640 9.906660 CTCTAATGAACTGAGAATACCACTATC 57.093 37.037 0.00 0.00 0.00 2.08
619 641 8.861086 TCTAATGAACTGAGAATACCACTATCC 58.139 37.037 0.00 0.00 0.00 2.59
621 643 5.529289 TGAACTGAGAATACCACTATCCCT 58.471 41.667 0.00 0.00 0.00 4.20
622 644 5.964477 TGAACTGAGAATACCACTATCCCTT 59.036 40.000 0.00 0.00 0.00 3.95
623 645 6.443849 TGAACTGAGAATACCACTATCCCTTT 59.556 38.462 0.00 0.00 0.00 3.11
625 647 7.989947 ACTGAGAATACCACTATCCCTTTAA 57.010 36.000 0.00 0.00 0.00 1.52
626 648 7.793036 ACTGAGAATACCACTATCCCTTTAAC 58.207 38.462 0.00 0.00 0.00 2.01
627 649 7.133133 TGAGAATACCACTATCCCTTTAACC 57.867 40.000 0.00 0.00 0.00 2.85
629 651 7.349859 TGAGAATACCACTATCCCTTTAACCAT 59.650 37.037 0.00 0.00 0.00 3.55
630 652 7.746703 AGAATACCACTATCCCTTTAACCATC 58.253 38.462 0.00 0.00 0.00 3.51
631 653 4.790718 ACCACTATCCCTTTAACCATCC 57.209 45.455 0.00 0.00 0.00 3.51
632 654 4.116113 ACCACTATCCCTTTAACCATCCA 58.884 43.478 0.00 0.00 0.00 3.41
635 657 4.887655 CACTATCCCTTTAACCATCCAACC 59.112 45.833 0.00 0.00 0.00 3.77
637 659 3.163616 TCCCTTTAACCATCCAACCAC 57.836 47.619 0.00 0.00 0.00 4.16
638 660 2.447429 TCCCTTTAACCATCCAACCACA 59.553 45.455 0.00 0.00 0.00 4.17
639 661 2.825532 CCCTTTAACCATCCAACCACAG 59.174 50.000 0.00 0.00 0.00 3.66
640 662 2.825532 CCTTTAACCATCCAACCACAGG 59.174 50.000 0.00 0.00 0.00 4.00
641 663 3.496331 CTTTAACCATCCAACCACAGGT 58.504 45.455 0.00 0.00 37.65 4.00
656 678 1.202879 ACAGGTTGATTCGCTTCCCAA 60.203 47.619 0.00 0.00 0.00 4.12
662 684 5.067805 AGGTTGATTCGCTTCCCAAATTATC 59.932 40.000 0.00 0.00 0.00 1.75
675 697 3.550820 CAAATTATCCCCGTGATGGTCA 58.449 45.455 0.00 0.00 34.76 4.02
685 707 0.665835 GTGATGGTCACGGCAAACAA 59.334 50.000 0.00 0.00 37.67 2.83
688 710 1.066303 GATGGTCACGGCAAACAACAA 59.934 47.619 0.00 0.00 0.00 2.83
718 740 5.604758 TTCTCTGGATCTTGATACACCAG 57.395 43.478 0.00 0.00 46.33 4.00
735 757 0.518636 CAGGTCACCAGCATCAAACG 59.481 55.000 0.00 0.00 0.00 3.60
750 772 4.413495 TCAAACGTGTATTTTAGCCTGC 57.587 40.909 0.00 0.00 0.00 4.85
753 775 2.268298 ACGTGTATTTTAGCCTGCTCG 58.732 47.619 0.00 0.00 0.00 5.03
796 819 2.480845 GCATCGTTAAGGCCGAAGTAT 58.519 47.619 0.00 0.00 37.93 2.12
798 821 3.799232 GCATCGTTAAGGCCGAAGTATCT 60.799 47.826 0.00 0.00 37.93 1.98
827 850 7.201145 AGCTAACGGTATTACATTACACTCTG 58.799 38.462 0.00 0.00 0.00 3.35
828 851 6.420008 GCTAACGGTATTACATTACACTCTGG 59.580 42.308 0.00 0.00 0.00 3.86
829 852 4.690122 ACGGTATTACATTACACTCTGGC 58.310 43.478 0.00 0.00 0.00 4.85
960 995 2.672996 CAACCCAGCCAACTCCCG 60.673 66.667 0.00 0.00 0.00 5.14
978 1013 0.248743 CGCGCGTAGACCCTAATTCA 60.249 55.000 24.19 0.00 0.00 2.57
985 1020 4.258543 CGTAGACCCTAATTCAAAGGCAA 58.741 43.478 0.00 0.00 32.34 4.52
1191 1226 2.967615 GCCGCTGCGAACCCTATC 60.968 66.667 25.45 0.00 0.00 2.08
1203 1238 0.393944 ACCCTATCTGCGACGAGTCA 60.394 55.000 0.00 0.00 0.00 3.41
1395 1430 2.268920 GAGCATCAAGTGGCCGGA 59.731 61.111 5.05 0.00 33.17 5.14
2016 2099 2.041081 ACTAAAGCATGTTACCAGGGCA 59.959 45.455 0.00 0.00 0.00 5.36
2019 2102 0.332632 AGCATGTTACCAGGGCACAT 59.667 50.000 0.00 0.63 0.00 3.21
2495 2579 7.425606 GTTTCACTACCATTTGAGTTCAACAT 58.574 34.615 0.00 0.00 35.28 2.71
2557 2641 9.003145 TCCTTCTGGAATATTAATCTTCCTTCA 57.997 33.333 24.97 10.80 41.29 3.02
2571 2655 1.265635 TCCTTCACGATGTTTTTGGCG 59.734 47.619 0.00 0.00 0.00 5.69
2594 2678 6.855403 GCGTATAGAAAAACAAACGGGTTAAA 59.145 34.615 0.00 0.00 0.00 1.52
2718 2802 1.889170 GCCAGCAGGTAAGCTTTTCTT 59.111 47.619 3.20 0.00 43.70 2.52
3181 3275 2.944129 AGTTTTTAGGTCTGCCTGCAA 58.056 42.857 0.00 0.00 46.47 4.08
3187 3281 1.959042 AGGTCTGCCTGCAATATTCG 58.041 50.000 0.00 0.00 45.05 3.34
3299 3393 9.838339 ATAAACCATCTTTCAAGAACTATCGAT 57.162 29.630 2.16 2.16 38.77 3.59
3301 3395 6.536731 CCATCTTTCAAGAACTATCGATGG 57.463 41.667 8.54 7.88 40.23 3.51
3302 3396 5.049818 CCATCTTTCAAGAACTATCGATGGC 60.050 44.000 8.54 0.00 39.89 4.40
3304 3398 4.142249 TCTTTCAAGAACTATCGATGGCGA 60.142 41.667 8.54 0.00 40.71 5.54
3306 3400 6.904621 TCTTTCAAGAACTATCGATGGCGATT 60.905 38.462 8.54 0.00 42.33 3.34
3307 3401 8.324110 TCTTTCAAGAACTATCGATGGCGATTT 61.324 37.037 8.54 0.00 42.33 2.17
3316 3410 4.497473 TCGATGGCGATTTTGAACTTTT 57.503 36.364 0.00 0.00 42.51 2.27
3318 3412 6.189677 TCGATGGCGATTTTGAACTTTTAT 57.810 33.333 0.00 0.00 42.51 1.40
3319 3413 6.027131 TCGATGGCGATTTTGAACTTTTATG 58.973 36.000 0.00 0.00 42.51 1.90
3321 3415 6.307800 CGATGGCGATTTTGAACTTTTATGTT 59.692 34.615 0.00 0.00 40.82 2.71
3324 3418 7.625553 TGGCGATTTTGAACTTTTATGTTTTG 58.374 30.769 0.00 0.00 0.00 2.44
3326 3420 7.122550 GCGATTTTGAACTTTTATGTTTTGCA 58.877 30.769 0.00 0.00 0.00 4.08
3327 3421 7.637907 GCGATTTTGAACTTTTATGTTTTGCAA 59.362 29.630 0.00 0.00 0.00 4.08
3328 3422 9.146270 CGATTTTGAACTTTTATGTTTTGCAAG 57.854 29.630 0.00 0.00 0.00 4.01
3330 3424 9.986833 ATTTTGAACTTTTATGTTTTGCAAGAC 57.013 25.926 12.97 12.97 0.00 3.01
3331 3425 7.532682 TTGAACTTTTATGTTTTGCAAGACC 57.467 32.000 16.71 1.75 0.00 3.85
3332 3426 6.634805 TGAACTTTTATGTTTTGCAAGACCA 58.365 32.000 16.71 7.35 0.00 4.02
3333 3427 7.271511 TGAACTTTTATGTTTTGCAAGACCAT 58.728 30.769 16.71 13.45 0.00 3.55
3334 3428 8.417106 TGAACTTTTATGTTTTGCAAGACCATA 58.583 29.630 16.71 12.57 0.00 2.74
3335 3429 9.255304 GAACTTTTATGTTTTGCAAGACCATAA 57.745 29.630 16.71 16.82 0.00 1.90
3337 3431 8.421002 ACTTTTATGTTTTGCAAGACCATAACT 58.579 29.630 16.71 5.72 30.16 2.24
3340 3434 5.437289 TGTTTTGCAAGACCATAACTCAG 57.563 39.130 16.71 0.00 30.96 3.35
3342 3436 5.215160 GTTTTGCAAGACCATAACTCAGTG 58.785 41.667 8.90 0.00 0.00 3.66
3344 3438 4.558226 TGCAAGACCATAACTCAGTGAT 57.442 40.909 0.00 0.00 0.00 3.06
3345 3439 4.256110 TGCAAGACCATAACTCAGTGATG 58.744 43.478 0.00 0.00 0.00 3.07
3346 3440 4.256920 GCAAGACCATAACTCAGTGATGT 58.743 43.478 1.13 0.00 0.00 3.06
3347 3441 4.331168 GCAAGACCATAACTCAGTGATGTC 59.669 45.833 1.13 0.00 0.00 3.06
3348 3442 4.744795 AGACCATAACTCAGTGATGTCC 57.255 45.455 1.13 0.00 0.00 4.02
3349 3443 4.096681 AGACCATAACTCAGTGATGTCCA 58.903 43.478 1.13 0.00 0.00 4.02
3540 3637 8.696410 TTACATTCCTTTCTGTTTGTTTTGAC 57.304 30.769 0.00 0.00 0.00 3.18
3849 3952 1.028868 GCCAACTGCAGATGGTCCTC 61.029 60.000 35.14 20.07 39.81 3.71
3887 3990 4.769688 AGAAATCTGATGCGTCATTGGTA 58.230 39.130 9.53 0.00 32.98 3.25
3920 4023 2.890442 GCAGAGAGCAAACAAGTAGC 57.110 50.000 0.00 0.00 44.79 3.58
3932 4035 2.350522 ACAAGTAGCCAGAAAGCATCG 58.649 47.619 0.00 0.00 34.23 3.84
3933 4036 1.667724 CAAGTAGCCAGAAAGCATCGG 59.332 52.381 0.00 0.00 34.23 4.18
3952 4055 1.449423 CGGACCATGATGGCGAACA 60.449 57.895 12.25 0.00 42.67 3.18
3954 4057 0.676466 GGACCATGATGGCGAACACA 60.676 55.000 12.25 0.00 42.67 3.72
3986 4089 5.193679 GCTCCTACCAAACATTACTCCATT 58.806 41.667 0.00 0.00 0.00 3.16
4162 4265 6.647334 TGGCAGTAAACATCAGAATTTTGA 57.353 33.333 0.54 0.54 0.00 2.69
4195 4298 3.739209 GCTGCAGAAGGGGATAAAAATGC 60.739 47.826 20.43 0.00 0.00 3.56
4218 4321 6.127647 TGCCATTCCAAATAAACAGAGATCAC 60.128 38.462 0.00 0.00 0.00 3.06
4219 4322 6.127647 GCCATTCCAAATAAACAGAGATCACA 60.128 38.462 0.00 0.00 0.00 3.58
4235 4338 3.676291 TCACATCCACTGTTCGATGAA 57.324 42.857 17.25 6.20 38.53 2.57
4246 4349 6.293626 CCACTGTTCGATGAAAAGAACTCATT 60.294 38.462 3.81 0.00 44.95 2.57
4392 4495 3.438360 GAATTCTTATTTGGTGCTGGCG 58.562 45.455 0.00 0.00 0.00 5.69
4524 4627 3.181480 TGTTTTGGTACTTTTGGCTCAGC 60.181 43.478 0.00 0.00 0.00 4.26
4574 4677 7.383102 ACTGCTATTTTTGGTAGATCAACAG 57.617 36.000 0.00 0.00 0.00 3.16
4611 4714 5.560148 CAGTGATGCGTATAGTTTTTGGTC 58.440 41.667 0.00 0.00 0.00 4.02
4721 4824 5.415701 CACTTCCAACTGCATATGGTACTTT 59.584 40.000 15.35 0.00 37.94 2.66
4730 4833 7.056635 ACTGCATATGGTACTTTCATTTAGCT 58.943 34.615 4.56 0.00 0.00 3.32
4747 4850 9.955208 TCATTTAGCTAATCATTTGTAGCATTG 57.045 29.630 7.08 0.00 44.29 2.82
4855 4958 1.593196 TGGAAGTTGCTCCGAGTTTG 58.407 50.000 0.00 0.00 38.44 2.93
4862 4965 3.258372 AGTTGCTCCGAGTTTGATGAGTA 59.742 43.478 0.00 0.00 0.00 2.59
4866 4969 3.785486 CTCCGAGTTTGATGAGTATGCA 58.215 45.455 0.00 0.00 0.00 3.96
4904 5007 5.548406 ACCTTGTCATAGTTGAGGTGTTAC 58.452 41.667 0.00 0.00 29.35 2.50
4905 5008 5.307196 ACCTTGTCATAGTTGAGGTGTTACT 59.693 40.000 0.00 0.00 29.35 2.24
4906 5009 5.869888 CCTTGTCATAGTTGAGGTGTTACTC 59.130 44.000 0.00 0.00 37.99 2.59
4907 5010 5.401531 TGTCATAGTTGAGGTGTTACTCC 57.598 43.478 0.00 0.00 36.66 3.85
4908 5011 4.222145 TGTCATAGTTGAGGTGTTACTCCC 59.778 45.833 0.00 0.00 36.66 4.30
4909 5012 4.466726 GTCATAGTTGAGGTGTTACTCCCT 59.533 45.833 0.00 0.00 36.66 4.20
4910 5013 4.710375 TCATAGTTGAGGTGTTACTCCCTC 59.290 45.833 12.53 12.53 46.20 4.30
4911 5014 3.261818 AGTTGAGGTGTTACTCCCTCT 57.738 47.619 17.72 3.52 46.17 3.69
4912 5015 2.900546 AGTTGAGGTGTTACTCCCTCTG 59.099 50.000 17.72 0.00 46.17 3.35
4913 5016 2.633481 GTTGAGGTGTTACTCCCTCTGT 59.367 50.000 17.72 0.00 46.17 3.41
4914 5017 2.972348 TGAGGTGTTACTCCCTCTGTT 58.028 47.619 17.72 0.00 46.17 3.16
4915 5018 2.897969 TGAGGTGTTACTCCCTCTGTTC 59.102 50.000 17.72 3.24 46.17 3.18
4916 5019 2.897969 GAGGTGTTACTCCCTCTGTTCA 59.102 50.000 12.27 0.00 43.29 3.18
4917 5020 2.633481 AGGTGTTACTCCCTCTGTTCAC 59.367 50.000 0.00 0.00 0.00 3.18
4918 5021 2.633481 GGTGTTACTCCCTCTGTTCACT 59.367 50.000 0.00 0.00 0.00 3.41
4919 5022 3.071167 GGTGTTACTCCCTCTGTTCACTT 59.929 47.826 0.00 0.00 0.00 3.16
4920 5023 4.308265 GTGTTACTCCCTCTGTTCACTTC 58.692 47.826 0.00 0.00 0.00 3.01
4921 5024 4.039366 GTGTTACTCCCTCTGTTCACTTCT 59.961 45.833 0.00 0.00 0.00 2.85
4922 5025 5.243283 GTGTTACTCCCTCTGTTCACTTCTA 59.757 44.000 0.00 0.00 0.00 2.10
4923 5026 6.017192 TGTTACTCCCTCTGTTCACTTCTAT 58.983 40.000 0.00 0.00 0.00 1.98
4924 5027 7.122353 GTGTTACTCCCTCTGTTCACTTCTATA 59.878 40.741 0.00 0.00 0.00 1.31
4925 5028 7.672660 TGTTACTCCCTCTGTTCACTTCTATAA 59.327 37.037 0.00 0.00 0.00 0.98
4926 5029 6.783708 ACTCCCTCTGTTCACTTCTATAAG 57.216 41.667 0.00 0.00 38.77 1.73
4927 5030 6.494952 ACTCCCTCTGTTCACTTCTATAAGA 58.505 40.000 0.00 0.00 36.50 2.10
4928 5031 6.378848 ACTCCCTCTGTTCACTTCTATAAGAC 59.621 42.308 0.00 0.00 36.50 3.01
4929 5032 5.657302 TCCCTCTGTTCACTTCTATAAGACC 59.343 44.000 0.00 0.00 36.50 3.85
4930 5033 5.659079 CCCTCTGTTCACTTCTATAAGACCT 59.341 44.000 0.00 0.00 36.50 3.85
4931 5034 6.155393 CCCTCTGTTCACTTCTATAAGACCTT 59.845 42.308 0.00 0.00 36.50 3.50
4932 5035 7.038659 CCTCTGTTCACTTCTATAAGACCTTG 58.961 42.308 0.00 0.00 36.50 3.61
4933 5036 7.093727 CCTCTGTTCACTTCTATAAGACCTTGA 60.094 40.741 0.00 0.00 36.50 3.02
4934 5037 8.190326 TCTGTTCACTTCTATAAGACCTTGAA 57.810 34.615 0.00 0.00 36.50 2.69
4935 5038 8.307483 TCTGTTCACTTCTATAAGACCTTGAAG 58.693 37.037 0.00 0.00 39.72 3.02
4936 5039 8.190326 TGTTCACTTCTATAAGACCTTGAAGA 57.810 34.615 12.41 4.43 37.94 2.87
4937 5040 8.088981 TGTTCACTTCTATAAGACCTTGAAGAC 58.911 37.037 12.41 4.66 37.94 3.01
4938 5041 6.853720 TCACTTCTATAAGACCTTGAAGACG 58.146 40.000 12.41 6.69 37.94 4.18
4939 5042 6.433404 TCACTTCTATAAGACCTTGAAGACGT 59.567 38.462 12.41 0.00 37.94 4.34
4940 5043 7.039923 TCACTTCTATAAGACCTTGAAGACGTT 60.040 37.037 12.41 0.00 37.94 3.99
4941 5044 7.599245 CACTTCTATAAGACCTTGAAGACGTTT 59.401 37.037 12.41 0.00 37.94 3.60
4942 5045 7.813627 ACTTCTATAAGACCTTGAAGACGTTTC 59.186 37.037 12.41 0.00 37.94 2.78
4943 5046 7.223260 TCTATAAGACCTTGAAGACGTTTCA 57.777 36.000 8.47 8.47 0.00 2.69
4944 5047 7.313646 TCTATAAGACCTTGAAGACGTTTCAG 58.686 38.462 11.25 6.01 0.00 3.02
4945 5048 4.402056 AAGACCTTGAAGACGTTTCAGA 57.598 40.909 11.25 5.10 0.00 3.27
4946 5049 3.718815 AGACCTTGAAGACGTTTCAGAC 58.281 45.455 11.25 4.71 0.00 3.51
4947 5050 3.132289 AGACCTTGAAGACGTTTCAGACA 59.868 43.478 11.25 0.70 0.00 3.41
4948 5051 3.869065 ACCTTGAAGACGTTTCAGACAA 58.131 40.909 11.25 0.00 0.00 3.18
4949 5052 3.871594 ACCTTGAAGACGTTTCAGACAAG 59.128 43.478 11.25 0.00 34.85 3.16
4950 5053 3.248602 CCTTGAAGACGTTTCAGACAAGG 59.751 47.826 16.68 16.68 43.89 3.61
4951 5054 3.536956 TGAAGACGTTTCAGACAAGGT 57.463 42.857 8.47 0.00 0.00 3.50
4952 5055 3.194861 TGAAGACGTTTCAGACAAGGTG 58.805 45.455 8.47 0.00 0.00 4.00
4953 5056 1.583054 AGACGTTTCAGACAAGGTGC 58.417 50.000 0.00 0.00 0.00 5.01
4954 5057 1.134521 AGACGTTTCAGACAAGGTGCA 60.135 47.619 0.00 0.00 0.00 4.57
4955 5058 1.668751 GACGTTTCAGACAAGGTGCAA 59.331 47.619 0.00 0.00 0.00 4.08
4956 5059 2.088423 ACGTTTCAGACAAGGTGCAAA 58.912 42.857 0.00 0.00 0.00 3.68
4957 5060 2.097466 ACGTTTCAGACAAGGTGCAAAG 59.903 45.455 0.00 0.00 0.00 2.77
4958 5061 2.097466 CGTTTCAGACAAGGTGCAAAGT 59.903 45.455 0.00 0.00 0.00 2.66
4959 5062 3.311322 CGTTTCAGACAAGGTGCAAAGTA 59.689 43.478 0.00 0.00 0.00 2.24
4960 5063 4.552767 CGTTTCAGACAAGGTGCAAAGTAG 60.553 45.833 0.00 0.00 0.00 2.57
4961 5064 2.494059 TCAGACAAGGTGCAAAGTAGC 58.506 47.619 0.00 0.00 0.00 3.58
4962 5065 2.104792 TCAGACAAGGTGCAAAGTAGCT 59.895 45.455 0.00 0.00 34.99 3.32
4963 5066 2.481952 CAGACAAGGTGCAAAGTAGCTC 59.518 50.000 0.00 0.00 34.99 4.09
4964 5067 2.104792 AGACAAGGTGCAAAGTAGCTCA 59.895 45.455 0.00 0.00 34.99 4.26
4965 5068 3.077359 GACAAGGTGCAAAGTAGCTCAT 58.923 45.455 0.00 0.00 34.99 2.90
4966 5069 3.490348 ACAAGGTGCAAAGTAGCTCATT 58.510 40.909 0.00 0.00 33.06 2.57
4967 5070 3.891366 ACAAGGTGCAAAGTAGCTCATTT 59.109 39.130 0.00 0.00 30.83 2.32
4968 5071 4.342092 ACAAGGTGCAAAGTAGCTCATTTT 59.658 37.500 0.00 0.00 30.83 1.82
4969 5072 4.773323 AGGTGCAAAGTAGCTCATTTTC 57.227 40.909 0.00 0.00 34.99 2.29
4970 5073 4.144297 AGGTGCAAAGTAGCTCATTTTCA 58.856 39.130 0.00 0.00 34.99 2.69
4971 5074 4.217118 AGGTGCAAAGTAGCTCATTTTCAG 59.783 41.667 0.00 0.00 34.99 3.02
4972 5075 4.022849 GGTGCAAAGTAGCTCATTTTCAGT 60.023 41.667 0.00 0.00 34.99 3.41
4973 5076 5.507985 GGTGCAAAGTAGCTCATTTTCAGTT 60.508 40.000 0.00 0.00 34.99 3.16
4974 5077 5.400485 GTGCAAAGTAGCTCATTTTCAGTTG 59.600 40.000 0.00 0.00 34.99 3.16
4975 5078 5.067674 TGCAAAGTAGCTCATTTTCAGTTGT 59.932 36.000 0.00 0.00 34.99 3.32
4976 5079 5.626955 GCAAAGTAGCTCATTTTCAGTTGTC 59.373 40.000 0.00 0.00 0.00 3.18
4977 5080 6.514048 GCAAAGTAGCTCATTTTCAGTTGTCT 60.514 38.462 0.00 0.00 0.00 3.41
4978 5081 6.551385 AAGTAGCTCATTTTCAGTTGTCTG 57.449 37.500 0.00 0.00 42.54 3.51
4996 5099 8.695355 GTTGTCTGAAACGACTTATAAAAGTG 57.305 34.615 0.00 0.00 46.09 3.16
4997 5100 8.545420 GTTGTCTGAAACGACTTATAAAAGTGA 58.455 33.333 0.00 0.00 46.09 3.41
4998 5101 8.651391 TGTCTGAAACGACTTATAAAAGTGAA 57.349 30.769 0.00 0.00 46.09 3.18
4999 5102 8.545420 TGTCTGAAACGACTTATAAAAGTGAAC 58.455 33.333 0.00 0.00 46.09 3.18
5000 5103 7.734726 GTCTGAAACGACTTATAAAAGTGAACG 59.265 37.037 0.00 0.00 46.09 3.95
5001 5104 6.879962 TGAAACGACTTATAAAAGTGAACGG 58.120 36.000 0.00 0.00 46.09 4.44
5002 5105 6.700960 TGAAACGACTTATAAAAGTGAACGGA 59.299 34.615 0.00 0.00 46.09 4.69
5003 5106 6.701432 AACGACTTATAAAAGTGAACGGAG 57.299 37.500 0.00 0.00 46.09 4.63
5004 5107 5.166398 ACGACTTATAAAAGTGAACGGAGG 58.834 41.667 0.00 0.00 46.09 4.30
5005 5108 4.565564 CGACTTATAAAAGTGAACGGAGGG 59.434 45.833 0.00 0.00 46.09 4.30
5006 5109 5.622914 CGACTTATAAAAGTGAACGGAGGGA 60.623 44.000 0.00 0.00 46.09 4.20
5007 5110 5.731591 ACTTATAAAAGTGAACGGAGGGAG 58.268 41.667 0.00 0.00 44.40 4.30
5008 5111 5.247792 ACTTATAAAAGTGAACGGAGGGAGT 59.752 40.000 0.00 0.00 44.40 3.85
5009 5112 6.438425 ACTTATAAAAGTGAACGGAGGGAGTA 59.562 38.462 0.00 0.00 44.40 2.59
5022 5125 7.961326 ACGGAGGGAGTAGTAATTTTTAGTA 57.039 36.000 0.00 0.00 0.00 1.82
5139 5242 4.052229 CGAGCCCCTATACGCCCG 62.052 72.222 0.00 0.00 0.00 6.13
5140 5243 2.916181 GAGCCCCTATACGCCCGT 60.916 66.667 0.00 0.00 0.00 5.28
5141 5244 3.222354 GAGCCCCTATACGCCCGTG 62.222 68.421 3.22 0.00 0.00 4.94
5142 5245 4.309950 GCCCCTATACGCCCGTGG 62.310 72.222 3.22 0.00 0.00 4.94
5143 5246 2.522436 CCCCTATACGCCCGTGGA 60.522 66.667 3.22 0.00 0.00 4.02
5144 5247 2.732658 CCCTATACGCCCGTGGAC 59.267 66.667 3.22 0.00 0.00 4.02
5145 5248 2.333938 CCTATACGCCCGTGGACG 59.666 66.667 3.22 0.00 39.44 4.79
5146 5249 2.354305 CTATACGCCCGTGGACGC 60.354 66.667 3.22 0.00 38.18 5.19
5193 5296 4.320641 GCATCAAAACTTGGCATTTGCAAT 60.321 37.500 0.00 0.00 44.36 3.56
5194 5297 4.815040 TCAAAACTTGGCATTTGCAATG 57.185 36.364 0.00 2.13 44.36 2.82
5244 5347 2.734346 GCAAACACATGCACGCCC 60.734 61.111 0.00 0.00 45.70 6.13
5246 5349 1.661197 CAAACACATGCACGCCCAC 60.661 57.895 0.00 0.00 0.00 4.61
5284 5388 4.749245 AGCTTAGTGCACACAAATACAC 57.251 40.909 21.04 0.00 45.94 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 6.992715 CGAATTCCCATAACTCTCAGGTATTT 59.007 38.462 0.00 0.00 0.00 1.40
63 64 4.513442 CCAACGAATTCCCATAACTCTCA 58.487 43.478 0.00 0.00 0.00 3.27
72 73 1.702957 ACTTCTCCCAACGAATTCCCA 59.297 47.619 0.00 0.00 0.00 4.37
87 88 5.044105 AGCCCAATAAGACCCATTAACTTCT 60.044 40.000 0.00 0.00 0.00 2.85
284 300 0.314618 TAGTGGCGCGTCAAGTGTAA 59.685 50.000 18.26 0.00 0.00 2.41
356 374 6.038936 GGTTAAGAGAAACTTGTGTGCCTTTA 59.961 38.462 0.00 0.00 39.38 1.85
367 385 2.542595 CGCACACGGTTAAGAGAAACTT 59.457 45.455 0.00 0.00 37.88 2.66
369 387 2.572173 CGCACACGGTTAAGAGAAAC 57.428 50.000 0.00 0.00 34.97 2.78
552 574 1.466167 GCAACTCTGCGATCAACACAT 59.534 47.619 0.00 0.00 39.20 3.21
581 603 7.232737 TCTCAGTTCATTAGAGTTCAAGTACCA 59.767 37.037 0.00 0.00 0.00 3.25
590 612 8.140112 AGTGGTATTCTCAGTTCATTAGAGTT 57.860 34.615 0.00 0.00 0.00 3.01
591 613 7.726033 AGTGGTATTCTCAGTTCATTAGAGT 57.274 36.000 0.00 0.00 0.00 3.24
592 614 9.906660 GATAGTGGTATTCTCAGTTCATTAGAG 57.093 37.037 0.00 0.00 0.00 2.43
593 615 8.861086 GGATAGTGGTATTCTCAGTTCATTAGA 58.139 37.037 0.00 0.00 0.00 2.10
594 616 8.091449 GGGATAGTGGTATTCTCAGTTCATTAG 58.909 40.741 0.00 0.00 0.00 1.73
596 618 6.617371 AGGGATAGTGGTATTCTCAGTTCATT 59.383 38.462 0.00 0.00 0.00 2.57
597 619 6.146760 AGGGATAGTGGTATTCTCAGTTCAT 58.853 40.000 0.00 0.00 0.00 2.57
598 620 5.529289 AGGGATAGTGGTATTCTCAGTTCA 58.471 41.667 0.00 0.00 0.00 3.18
601 623 7.147532 GGTTAAAGGGATAGTGGTATTCTCAGT 60.148 40.741 0.00 0.00 0.00 3.41
602 624 7.147549 TGGTTAAAGGGATAGTGGTATTCTCAG 60.148 40.741 0.00 0.00 0.00 3.35
603 625 6.674861 TGGTTAAAGGGATAGTGGTATTCTCA 59.325 38.462 0.00 0.00 0.00 3.27
604 626 7.133133 TGGTTAAAGGGATAGTGGTATTCTC 57.867 40.000 0.00 0.00 0.00 2.87
605 627 7.202195 GGATGGTTAAAGGGATAGTGGTATTCT 60.202 40.741 0.00 0.00 0.00 2.40
606 628 6.940867 GGATGGTTAAAGGGATAGTGGTATTC 59.059 42.308 0.00 0.00 0.00 1.75
607 629 6.391649 TGGATGGTTAAAGGGATAGTGGTATT 59.608 38.462 0.00 0.00 0.00 1.89
609 631 5.290335 TGGATGGTTAAAGGGATAGTGGTA 58.710 41.667 0.00 0.00 0.00 3.25
610 632 4.116113 TGGATGGTTAAAGGGATAGTGGT 58.884 43.478 0.00 0.00 0.00 4.16
611 633 4.788925 TGGATGGTTAAAGGGATAGTGG 57.211 45.455 0.00 0.00 0.00 4.00
612 634 4.887655 GGTTGGATGGTTAAAGGGATAGTG 59.112 45.833 0.00 0.00 0.00 2.74
613 635 4.542525 TGGTTGGATGGTTAAAGGGATAGT 59.457 41.667 0.00 0.00 0.00 2.12
614 636 4.887655 GTGGTTGGATGGTTAAAGGGATAG 59.112 45.833 0.00 0.00 0.00 2.08
616 638 3.076785 TGTGGTTGGATGGTTAAAGGGAT 59.923 43.478 0.00 0.00 0.00 3.85
617 639 2.447429 TGTGGTTGGATGGTTAAAGGGA 59.553 45.455 0.00 0.00 0.00 4.20
618 640 2.825532 CTGTGGTTGGATGGTTAAAGGG 59.174 50.000 0.00 0.00 0.00 3.95
619 641 2.825532 CCTGTGGTTGGATGGTTAAAGG 59.174 50.000 0.00 0.00 0.00 3.11
621 643 3.603965 ACCTGTGGTTGGATGGTTAAA 57.396 42.857 0.00 0.00 27.29 1.52
622 644 3.603965 AACCTGTGGTTGGATGGTTAA 57.396 42.857 0.71 0.00 45.07 2.01
635 657 0.804989 GGGAAGCGAATCAACCTGTG 59.195 55.000 0.00 0.00 0.00 3.66
637 659 1.533625 TTGGGAAGCGAATCAACCTG 58.466 50.000 0.00 0.00 0.00 4.00
638 660 2.286365 TTTGGGAAGCGAATCAACCT 57.714 45.000 0.00 0.00 0.00 3.50
639 661 3.592898 AATTTGGGAAGCGAATCAACC 57.407 42.857 0.00 0.00 0.00 3.77
640 662 5.281727 GGATAATTTGGGAAGCGAATCAAC 58.718 41.667 0.00 0.00 0.00 3.18
641 663 4.340950 GGGATAATTTGGGAAGCGAATCAA 59.659 41.667 0.00 0.00 0.00 2.57
642 664 3.888930 GGGATAATTTGGGAAGCGAATCA 59.111 43.478 0.00 0.00 0.00 2.57
643 665 3.255888 GGGGATAATTTGGGAAGCGAATC 59.744 47.826 0.00 0.00 0.00 2.52
644 666 3.230976 GGGGATAATTTGGGAAGCGAAT 58.769 45.455 0.00 0.00 0.00 3.34
645 667 2.661718 GGGGATAATTTGGGAAGCGAA 58.338 47.619 0.00 0.00 0.00 4.70
646 668 1.476110 CGGGGATAATTTGGGAAGCGA 60.476 52.381 0.00 0.00 0.00 4.93
647 669 0.951558 CGGGGATAATTTGGGAAGCG 59.048 55.000 0.00 0.00 0.00 4.68
656 678 3.208747 GTGACCATCACGGGGATAATT 57.791 47.619 0.00 0.00 37.67 1.40
675 697 1.226547 CGCAGTTGTTGTTTGCCGT 60.227 52.632 0.00 0.00 34.42 5.68
685 707 0.468226 TCCAGAGAAACCGCAGTTGT 59.532 50.000 0.00 0.00 35.97 3.32
688 710 1.270907 AGATCCAGAGAAACCGCAGT 58.729 50.000 0.00 0.00 0.00 4.40
718 740 0.238289 CACGTTTGATGCTGGTGACC 59.762 55.000 0.00 0.00 0.00 4.02
735 757 1.330829 GGCGAGCAGGCTAAAATACAC 59.669 52.381 0.00 0.00 42.90 2.90
818 841 2.606519 AGGCGGGCCAGAGTGTAA 60.607 61.111 12.97 0.00 38.92 2.41
829 852 3.801997 ATGGAAGGCAGAGGCGGG 61.802 66.667 0.00 0.00 42.47 6.13
960 995 1.930567 TTGAATTAGGGTCTACGCGC 58.069 50.000 5.73 0.00 0.00 6.86
962 997 2.612672 GCCTTTGAATTAGGGTCTACGC 59.387 50.000 0.00 0.00 33.19 4.42
978 1013 1.682087 GCGAGGGATTAGGTTGCCTTT 60.682 52.381 0.00 0.00 37.60 3.11
985 1020 0.399949 TCCATGGCGAGGGATTAGGT 60.400 55.000 6.96 0.00 0.00 3.08
1191 1226 1.730902 CTGTGGTGACTCGTCGCAG 60.731 63.158 12.12 5.10 41.60 5.18
1437 1472 0.389166 CAGTCTCACGGCAGAGGTTC 60.389 60.000 4.38 0.00 36.30 3.62
1441 1476 1.287730 GCAACAGTCTCACGGCAGAG 61.288 60.000 0.00 0.00 36.97 3.35
1552 1587 4.602107 TGTTCATCATCATTGACCACCAT 58.398 39.130 0.00 0.00 33.85 3.55
2016 2099 8.579006 ACAATTTCATCATAACTGACAACATGT 58.421 29.630 0.00 0.00 33.22 3.21
2019 2102 7.230309 TCCACAATTTCATCATAACTGACAACA 59.770 33.333 0.00 0.00 33.22 3.33
2109 2192 8.950210 ACATGTGAAGAAACATCTAATAACCAG 58.050 33.333 0.00 0.00 38.75 4.00
2245 2328 5.415389 TGATGGAATTTGAGCAAGAAATCGA 59.585 36.000 0.00 0.00 0.00 3.59
2246 2329 5.514204 GTGATGGAATTTGAGCAAGAAATCG 59.486 40.000 0.00 0.00 0.00 3.34
2258 2341 7.092079 TCTAAAAGTGCATGTGATGGAATTTG 58.908 34.615 4.61 0.00 45.62 2.32
2557 2641 5.866335 TTTCTATACGCCAAAAACATCGT 57.134 34.783 0.00 0.00 38.75 3.73
2571 2655 9.949174 TCTTTTAACCCGTTTGTTTTTCTATAC 57.051 29.630 0.00 0.00 0.00 1.47
2594 2678 0.179089 CTATCCGCTGCTGTGCTCTT 60.179 55.000 0.00 0.00 0.00 2.85
2718 2802 3.068873 GTGAACAATAAGTTGGTGGCCAA 59.931 43.478 7.24 0.00 41.51 4.52
2902 2996 3.552875 ACAGCTCCTCGCAATACTACTA 58.447 45.455 0.00 0.00 42.61 1.82
2903 2997 2.379972 ACAGCTCCTCGCAATACTACT 58.620 47.619 0.00 0.00 42.61 2.57
2908 3002 5.651530 GCTATAATACAGCTCCTCGCAATA 58.348 41.667 0.00 0.00 42.61 1.90
3169 3263 1.668419 ACGAATATTGCAGGCAGACC 58.332 50.000 0.00 0.00 0.00 3.85
3187 3281 8.773645 TGCACTAATATCACAGTAATGCATAAC 58.226 33.333 0.00 0.00 0.00 1.89
3299 3393 7.625553 CAAAACATAAAAGTTCAAAATCGCCA 58.374 30.769 0.00 0.00 0.00 5.69
3301 3395 7.122550 TGCAAAACATAAAAGTTCAAAATCGC 58.877 30.769 0.00 0.00 0.00 4.58
3302 3396 9.146270 CTTGCAAAACATAAAAGTTCAAAATCG 57.854 29.630 0.00 0.00 0.00 3.34
3304 3398 9.986833 GTCTTGCAAAACATAAAAGTTCAAAAT 57.013 25.926 0.00 0.00 0.00 1.82
3306 3400 7.604164 TGGTCTTGCAAAACATAAAAGTTCAAA 59.396 29.630 5.08 0.00 0.00 2.69
3307 3401 7.099764 TGGTCTTGCAAAACATAAAAGTTCAA 58.900 30.769 5.08 0.00 0.00 2.69
3308 3402 6.634805 TGGTCTTGCAAAACATAAAAGTTCA 58.365 32.000 5.08 0.00 0.00 3.18
3309 3403 7.713764 ATGGTCTTGCAAAACATAAAAGTTC 57.286 32.000 5.08 0.00 0.00 3.01
3310 3404 9.040939 GTTATGGTCTTGCAAAACATAAAAGTT 57.959 29.630 22.43 4.05 36.23 2.66
3311 3405 8.421002 AGTTATGGTCTTGCAAAACATAAAAGT 58.579 29.630 22.43 13.58 36.23 2.66
3312 3406 8.816640 AGTTATGGTCTTGCAAAACATAAAAG 57.183 30.769 22.43 2.71 36.23 2.27
3314 3408 7.946207 TGAGTTATGGTCTTGCAAAACATAAA 58.054 30.769 22.43 12.16 36.23 1.40
3315 3409 7.230510 ACTGAGTTATGGTCTTGCAAAACATAA 59.769 33.333 19.39 19.39 33.16 1.90
3316 3410 6.714810 ACTGAGTTATGGTCTTGCAAAACATA 59.285 34.615 5.08 9.67 0.00 2.29
3318 3412 4.887071 ACTGAGTTATGGTCTTGCAAAACA 59.113 37.500 5.08 3.64 0.00 2.83
3319 3413 5.008613 TCACTGAGTTATGGTCTTGCAAAAC 59.991 40.000 0.00 0.00 0.00 2.43
3321 3415 4.713553 TCACTGAGTTATGGTCTTGCAAA 58.286 39.130 0.00 0.00 0.00 3.68
3324 3418 4.256920 ACATCACTGAGTTATGGTCTTGC 58.743 43.478 11.09 0.00 0.00 4.01
3326 3420 4.532126 TGGACATCACTGAGTTATGGTCTT 59.468 41.667 11.09 0.00 0.00 3.01
3327 3421 4.096681 TGGACATCACTGAGTTATGGTCT 58.903 43.478 11.09 0.00 0.00 3.85
3328 3422 4.471904 TGGACATCACTGAGTTATGGTC 57.528 45.455 11.09 6.34 0.00 4.02
3330 3424 4.577693 CCAATGGACATCACTGAGTTATGG 59.422 45.833 11.09 0.00 0.00 2.74
3331 3425 5.065602 CACCAATGGACATCACTGAGTTATG 59.934 44.000 6.16 5.28 0.00 1.90
3332 3426 5.188434 CACCAATGGACATCACTGAGTTAT 58.812 41.667 6.16 0.00 0.00 1.89
3333 3427 4.578871 CACCAATGGACATCACTGAGTTA 58.421 43.478 6.16 0.00 0.00 2.24
3334 3428 3.415212 CACCAATGGACATCACTGAGTT 58.585 45.455 6.16 0.00 0.00 3.01
3335 3429 2.877300 GCACCAATGGACATCACTGAGT 60.877 50.000 6.16 0.00 0.00 3.41
3337 3431 1.352017 AGCACCAATGGACATCACTGA 59.648 47.619 6.16 0.00 0.00 3.41
3340 3434 2.161855 TCAAGCACCAATGGACATCAC 58.838 47.619 6.16 0.00 0.00 3.06
3342 3436 3.940209 TTTCAAGCACCAATGGACATC 57.060 42.857 6.16 0.00 0.00 3.06
3344 3438 4.661222 TCTATTTCAAGCACCAATGGACA 58.339 39.130 6.16 0.00 0.00 4.02
3345 3439 5.450965 CCATCTATTTCAAGCACCAATGGAC 60.451 44.000 6.16 0.00 34.40 4.02
3346 3440 4.646040 CCATCTATTTCAAGCACCAATGGA 59.354 41.667 6.16 0.00 34.40 3.41
3347 3441 4.403432 ACCATCTATTTCAAGCACCAATGG 59.597 41.667 0.00 0.00 37.68 3.16
3348 3442 5.587388 ACCATCTATTTCAAGCACCAATG 57.413 39.130 0.00 0.00 0.00 2.82
3349 3443 6.400568 CAAACCATCTATTTCAAGCACCAAT 58.599 36.000 0.00 0.00 0.00 3.16
3432 3529 7.609760 TTTATACTTCAGCCTTGTACACATG 57.390 36.000 0.00 0.00 0.00 3.21
3540 3637 3.424302 CGGACACCAAAACATGTCATACG 60.424 47.826 0.00 0.00 45.83 3.06
3849 3952 3.749665 TTTCTTTGCATCTGGTTTGGG 57.250 42.857 0.00 0.00 0.00 4.12
3887 3990 3.683802 CTCTCTGCCAGGTTTTTCAGAT 58.316 45.455 0.00 0.00 35.34 2.90
3920 4023 2.125147 TCCGCCGATGCTTTCTGG 60.125 61.111 0.00 0.00 34.43 3.86
3932 4035 4.545706 TCGCCATCATGGTCCGCC 62.546 66.667 5.31 0.00 40.46 6.13
3933 4036 2.513666 TTCGCCATCATGGTCCGC 60.514 61.111 5.31 0.00 40.46 5.54
3952 4055 5.221843 TGTTTGGTAGGAGCAGAAGTTATGT 60.222 40.000 0.00 0.00 0.00 2.29
3954 4057 5.499004 TGTTTGGTAGGAGCAGAAGTTAT 57.501 39.130 0.00 0.00 0.00 1.89
3986 4089 1.693627 TGCCGGCAAGGTTTTTAAGA 58.306 45.000 30.74 0.00 43.70 2.10
4115 4218 9.586435 CCATTTGTATACATATGCTTCTCGATA 57.414 33.333 23.39 0.00 35.08 2.92
4177 4280 5.453762 GGAATGGCATTTTTATCCCCTTCTG 60.454 44.000 14.93 0.00 0.00 3.02
4195 4298 7.395190 TGTGATCTCTGTTTATTTGGAATGG 57.605 36.000 0.00 0.00 0.00 3.16
4218 4321 5.180117 AGTTCTTTTCATCGAACAGTGGATG 59.820 40.000 8.07 8.07 41.40 3.51
4219 4322 5.308825 AGTTCTTTTCATCGAACAGTGGAT 58.691 37.500 0.00 0.00 41.40 3.41
4246 4349 7.224297 ACTTGGATGTGAACTAGCTTCTTTTA 58.776 34.615 0.00 0.00 0.00 1.52
4392 4495 9.747293 GTAGTGTATTCATACTTTCCTCTAACC 57.253 37.037 0.00 0.00 34.41 2.85
4466 4569 4.418973 AGCATGAACTCATACTGCAGAT 57.581 40.909 23.35 6.78 34.26 2.90
4487 4590 1.890876 AAACAAGCCGCACACTCATA 58.109 45.000 0.00 0.00 0.00 2.15
4721 4824 9.955208 CAATGCTACAAATGATTAGCTAAATGA 57.045 29.630 10.85 0.00 41.21 2.57
4730 4833 8.786898 GCTTAGATCCAATGCTACAAATGATTA 58.213 33.333 0.00 0.00 0.00 1.75
4862 4965 9.423061 GACAAGGTAACATTTAAAAATCTGCAT 57.577 29.630 0.00 0.00 41.41 3.96
4904 5007 6.183360 GGTCTTATAGAAGTGAACAGAGGGAG 60.183 46.154 0.00 0.00 34.03 4.30
4905 5008 5.657302 GGTCTTATAGAAGTGAACAGAGGGA 59.343 44.000 0.00 0.00 34.03 4.20
4906 5009 5.659079 AGGTCTTATAGAAGTGAACAGAGGG 59.341 44.000 0.00 0.00 34.03 4.30
4907 5010 6.783708 AGGTCTTATAGAAGTGAACAGAGG 57.216 41.667 0.00 0.00 34.03 3.69
4908 5011 7.831753 TCAAGGTCTTATAGAAGTGAACAGAG 58.168 38.462 0.00 0.00 34.03 3.35
4909 5012 7.776618 TCAAGGTCTTATAGAAGTGAACAGA 57.223 36.000 0.00 0.00 34.03 3.41
4910 5013 8.307483 TCTTCAAGGTCTTATAGAAGTGAACAG 58.693 37.037 0.00 0.00 37.53 3.16
4911 5014 8.088981 GTCTTCAAGGTCTTATAGAAGTGAACA 58.911 37.037 0.00 0.00 37.53 3.18
4912 5015 7.273815 CGTCTTCAAGGTCTTATAGAAGTGAAC 59.726 40.741 0.00 0.00 37.53 3.18
4913 5016 7.039923 ACGTCTTCAAGGTCTTATAGAAGTGAA 60.040 37.037 0.00 0.00 37.53 3.18
4914 5017 6.433404 ACGTCTTCAAGGTCTTATAGAAGTGA 59.567 38.462 0.00 0.00 37.53 3.41
4915 5018 6.622549 ACGTCTTCAAGGTCTTATAGAAGTG 58.377 40.000 0.00 0.00 37.53 3.16
4916 5019 6.837471 ACGTCTTCAAGGTCTTATAGAAGT 57.163 37.500 0.00 7.55 37.53 3.01
4917 5020 7.813148 TGAAACGTCTTCAAGGTCTTATAGAAG 59.187 37.037 9.68 0.00 37.60 2.85
4918 5021 7.663827 TGAAACGTCTTCAAGGTCTTATAGAA 58.336 34.615 9.68 0.00 0.00 2.10
4919 5022 7.176165 TCTGAAACGTCTTCAAGGTCTTATAGA 59.824 37.037 12.17 2.98 0.00 1.98
4920 5023 7.273815 GTCTGAAACGTCTTCAAGGTCTTATAG 59.726 40.741 12.17 1.27 0.00 1.31
4921 5024 7.088905 GTCTGAAACGTCTTCAAGGTCTTATA 58.911 38.462 12.17 0.00 0.00 0.98
4922 5025 5.927115 GTCTGAAACGTCTTCAAGGTCTTAT 59.073 40.000 12.17 0.00 0.00 1.73
4923 5026 5.163488 TGTCTGAAACGTCTTCAAGGTCTTA 60.163 40.000 12.17 0.00 0.00 2.10
4924 5027 4.120589 GTCTGAAACGTCTTCAAGGTCTT 58.879 43.478 12.17 0.00 0.00 3.01
4925 5028 3.132289 TGTCTGAAACGTCTTCAAGGTCT 59.868 43.478 12.17 0.00 0.00 3.85
4926 5029 3.454375 TGTCTGAAACGTCTTCAAGGTC 58.546 45.455 12.17 3.85 0.00 3.85
4927 5030 3.536956 TGTCTGAAACGTCTTCAAGGT 57.463 42.857 12.17 0.00 0.00 3.50
4928 5031 3.248602 CCTTGTCTGAAACGTCTTCAAGG 59.751 47.826 15.07 15.07 38.64 3.61
4929 5032 3.871594 ACCTTGTCTGAAACGTCTTCAAG 59.128 43.478 12.17 10.02 0.00 3.02
4930 5033 3.621268 CACCTTGTCTGAAACGTCTTCAA 59.379 43.478 12.17 2.93 0.00 2.69
4931 5034 3.194861 CACCTTGTCTGAAACGTCTTCA 58.805 45.455 11.07 11.07 0.00 3.02
4932 5035 2.032808 GCACCTTGTCTGAAACGTCTTC 60.033 50.000 0.00 0.00 0.00 2.87
4933 5036 1.940613 GCACCTTGTCTGAAACGTCTT 59.059 47.619 0.00 0.00 0.00 3.01
4934 5037 1.134521 TGCACCTTGTCTGAAACGTCT 60.135 47.619 0.00 0.00 0.00 4.18
4935 5038 1.295792 TGCACCTTGTCTGAAACGTC 58.704 50.000 0.00 0.00 0.00 4.34
4936 5039 1.745232 TTGCACCTTGTCTGAAACGT 58.255 45.000 0.00 0.00 0.00 3.99
4937 5040 2.097466 ACTTTGCACCTTGTCTGAAACG 59.903 45.455 0.00 0.00 0.00 3.60
4938 5041 3.782889 ACTTTGCACCTTGTCTGAAAC 57.217 42.857 0.00 0.00 0.00 2.78
4939 5042 3.315191 GCTACTTTGCACCTTGTCTGAAA 59.685 43.478 0.00 0.00 0.00 2.69
4940 5043 2.878406 GCTACTTTGCACCTTGTCTGAA 59.122 45.455 0.00 0.00 0.00 3.02
4941 5044 2.104792 AGCTACTTTGCACCTTGTCTGA 59.895 45.455 0.00 0.00 34.99 3.27
4942 5045 2.481952 GAGCTACTTTGCACCTTGTCTG 59.518 50.000 0.00 0.00 34.99 3.51
4943 5046 2.104792 TGAGCTACTTTGCACCTTGTCT 59.895 45.455 0.00 0.00 34.99 3.41
4944 5047 2.494059 TGAGCTACTTTGCACCTTGTC 58.506 47.619 0.00 0.00 34.99 3.18
4945 5048 2.638480 TGAGCTACTTTGCACCTTGT 57.362 45.000 0.00 0.00 34.99 3.16
4946 5049 4.510038 AAATGAGCTACTTTGCACCTTG 57.490 40.909 0.00 0.00 34.99 3.61
4947 5050 4.584325 TGAAAATGAGCTACTTTGCACCTT 59.416 37.500 0.00 0.00 34.99 3.50
4948 5051 4.144297 TGAAAATGAGCTACTTTGCACCT 58.856 39.130 0.00 0.00 34.99 4.00
4949 5052 4.022849 ACTGAAAATGAGCTACTTTGCACC 60.023 41.667 0.00 0.00 34.99 5.01
4950 5053 5.113502 ACTGAAAATGAGCTACTTTGCAC 57.886 39.130 0.00 0.00 34.99 4.57
4951 5054 5.067674 ACAACTGAAAATGAGCTACTTTGCA 59.932 36.000 0.00 0.00 34.99 4.08
4952 5055 5.523369 ACAACTGAAAATGAGCTACTTTGC 58.477 37.500 0.00 0.00 0.00 3.68
4953 5056 6.854892 CAGACAACTGAAAATGAGCTACTTTG 59.145 38.462 0.00 0.00 46.03 2.77
4954 5057 6.963796 CAGACAACTGAAAATGAGCTACTTT 58.036 36.000 0.00 0.00 46.03 2.66
4955 5058 6.551385 CAGACAACTGAAAATGAGCTACTT 57.449 37.500 0.00 0.00 46.03 2.24
4969 5072 8.548721 ACTTTTATAAGTCGTTTCAGACAACTG 58.451 33.333 0.00 0.00 40.60 3.16
4970 5073 8.548721 CACTTTTATAAGTCGTTTCAGACAACT 58.451 33.333 0.00 0.00 42.67 3.16
4971 5074 8.545420 TCACTTTTATAAGTCGTTTCAGACAAC 58.455 33.333 0.00 0.00 42.67 3.32
4972 5075 8.651391 TCACTTTTATAAGTCGTTTCAGACAA 57.349 30.769 0.00 0.00 42.67 3.18
4973 5076 8.545420 GTTCACTTTTATAAGTCGTTTCAGACA 58.455 33.333 0.00 0.00 42.67 3.41
4974 5077 7.734726 CGTTCACTTTTATAAGTCGTTTCAGAC 59.265 37.037 0.00 0.00 42.67 3.51
4975 5078 7.095940 CCGTTCACTTTTATAAGTCGTTTCAGA 60.096 37.037 0.00 0.00 42.67 3.27
4976 5079 7.007697 CCGTTCACTTTTATAAGTCGTTTCAG 58.992 38.462 0.00 0.00 42.67 3.02
4977 5080 6.700960 TCCGTTCACTTTTATAAGTCGTTTCA 59.299 34.615 0.00 0.00 42.67 2.69
4978 5081 7.109006 TCCGTTCACTTTTATAAGTCGTTTC 57.891 36.000 0.00 0.00 42.67 2.78
4979 5082 6.146673 CCTCCGTTCACTTTTATAAGTCGTTT 59.853 38.462 0.00 0.00 42.67 3.60
4980 5083 5.636543 CCTCCGTTCACTTTTATAAGTCGTT 59.363 40.000 0.00 0.00 42.67 3.85
4981 5084 5.166398 CCTCCGTTCACTTTTATAAGTCGT 58.834 41.667 0.00 0.00 42.67 4.34
4982 5085 4.565564 CCCTCCGTTCACTTTTATAAGTCG 59.434 45.833 0.00 0.00 42.67 4.18
4983 5086 5.727434 TCCCTCCGTTCACTTTTATAAGTC 58.273 41.667 0.00 0.00 42.67 3.01
4984 5087 5.247792 ACTCCCTCCGTTCACTTTTATAAGT 59.752 40.000 0.00 0.00 45.40 2.24
4985 5088 5.731591 ACTCCCTCCGTTCACTTTTATAAG 58.268 41.667 0.00 0.00 37.40 1.73
4986 5089 5.750352 ACTCCCTCCGTTCACTTTTATAA 57.250 39.130 0.00 0.00 0.00 0.98
4987 5090 5.954150 ACTACTCCCTCCGTTCACTTTTATA 59.046 40.000 0.00 0.00 0.00 0.98
4988 5091 4.776308 ACTACTCCCTCCGTTCACTTTTAT 59.224 41.667 0.00 0.00 0.00 1.40
4989 5092 4.154942 ACTACTCCCTCCGTTCACTTTTA 58.845 43.478 0.00 0.00 0.00 1.52
4990 5093 2.970640 ACTACTCCCTCCGTTCACTTTT 59.029 45.455 0.00 0.00 0.00 2.27
4991 5094 2.606378 ACTACTCCCTCCGTTCACTTT 58.394 47.619 0.00 0.00 0.00 2.66
4992 5095 2.305858 ACTACTCCCTCCGTTCACTT 57.694 50.000 0.00 0.00 0.00 3.16
4993 5096 3.446442 TTACTACTCCCTCCGTTCACT 57.554 47.619 0.00 0.00 0.00 3.41
4994 5097 4.732672 AATTACTACTCCCTCCGTTCAC 57.267 45.455 0.00 0.00 0.00 3.18
4995 5098 5.750352 AAAATTACTACTCCCTCCGTTCA 57.250 39.130 0.00 0.00 0.00 3.18
4996 5099 7.326454 ACTAAAAATTACTACTCCCTCCGTTC 58.674 38.462 0.00 0.00 0.00 3.95
4997 5100 7.250032 ACTAAAAATTACTACTCCCTCCGTT 57.750 36.000 0.00 0.00 0.00 4.44
4998 5101 6.864151 ACTAAAAATTACTACTCCCTCCGT 57.136 37.500 0.00 0.00 0.00 4.69
4999 5102 7.775120 TGTACTAAAAATTACTACTCCCTCCG 58.225 38.462 0.00 0.00 0.00 4.63
5242 5345 3.767902 ATGTTTGTCCAAAATGGTGGG 57.232 42.857 0.00 0.00 39.03 4.61
5244 5347 5.138125 AGCTATGTTTGTCCAAAATGGTG 57.862 39.130 0.00 0.00 39.03 4.17
5246 5349 6.808212 CACTAAGCTATGTTTGTCCAAAATGG 59.192 38.462 0.00 0.00 39.43 3.16


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

AutoCloner maintained by Alex Coulton.