Multiple sequence alignment - TraesCS1B01G272200

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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 TraesCS1B01G272200 chr1B 100.000 6484 0 0 1 6484 478261718 478255235 0.000000e+00 11974.0
1 TraesCS1B01G272200 chr1B 83.742 775 89 13 4686 5453 478080854 478080110 0.000000e+00 699.0
2 TraesCS1B01G272200 chr1B 86.542 483 54 8 3844 4323 478096227 478095753 7.450000e-144 521.0
3 TraesCS1B01G272200 chr1B 87.566 378 42 4 3230 3605 478097034 478096660 3.590000e-117 433.0
4 TraesCS1B01G272200 chr1B 80.541 555 55 29 100 611 478432905 478432361 1.710000e-100 377.0
5 TraesCS1B01G272200 chr1B 82.160 213 20 10 3039 3233 478255480 478255268 4.020000e-37 167.0
6 TraesCS1B01G272200 chr1B 82.160 213 20 10 6239 6451 478258680 478258486 4.020000e-37 167.0
7 TraesCS1B01G272200 chr1B 81.988 161 19 6 704 861 478408531 478408378 1.900000e-25 128.0
8 TraesCS1B01G272200 chr1B 100.000 47 0 0 6191 6237 478255483 478255437 3.220000e-13 87.9
9 TraesCS1B01G272200 chr1B 100.000 47 0 0 6236 6282 478255528 478255482 3.220000e-13 87.9
10 TraesCS1B01G272200 chr1B 97.561 41 1 0 3039 3079 478255525 478255485 3.240000e-08 71.3
11 TraesCS1B01G272200 chr1B 97.561 41 1 0 6194 6234 478258680 478258640 3.240000e-08 71.3
12 TraesCS1B01G272200 chr1A 89.175 4702 275 96 2 4600 455823816 455819246 0.000000e+00 5648.0
13 TraesCS1B01G272200 chr1A 92.205 898 52 7 4644 5526 455819254 455818360 0.000000e+00 1254.0
14 TraesCS1B01G272200 chr1A 89.122 524 48 7 3230 3749 455663991 455663473 1.520000e-180 643.0
15 TraesCS1B01G272200 chr1A 79.580 524 97 9 5539 6056 539708900 539709419 3.690000e-97 366.0
16 TraesCS1B01G272200 chr1A 88.350 309 29 4 5931 6237 455808205 455807902 1.330000e-96 364.0
17 TraesCS1B01G272200 chr1A 90.726 248 18 2 6239 6484 455807947 455807703 6.270000e-85 326.0
18 TraesCS1B01G272200 chr1A 83.568 213 17 6 6239 6451 455820787 455820593 3.990000e-42 183.0
19 TraesCS1B01G272200 chr1A 97.561 41 1 0 6194 6234 455820787 455820747 3.240000e-08 71.3
20 TraesCS1B01G272200 chr1D 91.456 2973 143 43 1012 3949 355474116 355471220 0.000000e+00 3980.0
21 TraesCS1B01G272200 chr1D 92.188 832 49 5 4643 5461 355470475 355469647 0.000000e+00 1162.0
22 TraesCS1B01G272200 chr1D 93.814 582 31 5 4044 4624 355471026 355470449 0.000000e+00 870.0
23 TraesCS1B01G272200 chr1D 87.198 703 67 11 5543 6237 355469538 355468851 0.000000e+00 778.0
24 TraesCS1B01G272200 chr1D 83.871 775 88 15 4686 5453 355439128 355438384 0.000000e+00 704.0
25 TraesCS1B01G272200 chr1D 88.302 530 45 12 478 994 355474689 355474164 2.570000e-173 619.0
26 TraesCS1B01G272200 chr1D 86.902 481 49 12 3846 4323 355440748 355440279 1.600000e-145 527.0
27 TraesCS1B01G272200 chr1D 90.840 393 26 5 49 433 355475283 355474893 9.640000e-143 518.0
28 TraesCS1B01G272200 chr1D 89.459 351 31 4 3230 3577 355441474 355441127 7.720000e-119 438.0
29 TraesCS1B01G272200 chr1D 92.580 283 20 1 4319 4600 355439438 355439156 7.830000e-109 405.0
30 TraesCS1B01G272200 chr1D 94.821 251 11 1 6236 6484 355468899 355468649 2.190000e-104 390.0
31 TraesCS1B01G272200 chr1D 83.721 215 15 8 3039 3233 355468896 355468682 1.110000e-42 185.0
32 TraesCS1B01G272200 chr1D 92.857 42 3 0 5485 5526 355469644 355469603 1.950000e-05 62.1
33 TraesCS1B01G272200 chr1D 88.235 51 3 3 5459 5508 345444560 345444512 2.530000e-04 58.4
34 TraesCS1B01G272200 chr3D 82.064 1221 156 34 2769 3948 2095965 2097163 0.000000e+00 983.0
35 TraesCS1B01G272200 chr3D 79.113 541 95 14 5526 6056 20370564 20370032 2.220000e-94 357.0
36 TraesCS1B01G272200 chr3D 88.142 253 25 3 4331 4579 2097882 2098133 4.920000e-76 296.0
37 TraesCS1B01G272200 chr3D 100.000 28 0 0 6451 6478 550311998 550312025 1.200000e-02 52.8
38 TraesCS1B01G272200 chr3A 80.884 769 101 25 2582 3325 6898311 6897564 1.220000e-156 564.0
39 TraesCS1B01G272200 chr3A 78.323 632 86 25 3339 3948 6894539 6893937 1.720000e-95 361.0
40 TraesCS1B01G272200 chrUn 79.961 509 89 8 5545 6045 171268401 171267898 4.780000e-96 363.0
41 TraesCS1B01G272200 chr6D 79.615 520 94 9 5544 6056 159786153 159785639 4.780000e-96 363.0
42 TraesCS1B01G272200 chr2A 79.884 517 87 13 5549 6056 761145021 761144513 4.780000e-96 363.0
43 TraesCS1B01G272200 chr6A 79.693 522 88 15 5544 6056 103275566 103276078 1.720000e-95 361.0
44 TraesCS1B01G272200 chr6A 100.000 28 0 0 6451 6478 18699034 18699061 1.200000e-02 52.8
45 TraesCS1B01G272200 chr5D 79.350 523 96 9 5541 6056 424878304 424878821 2.220000e-94 357.0
46 TraesCS1B01G272200 chr5D 90.164 61 5 1 5458 5517 119680336 119680276 1.940000e-10 78.7
47 TraesCS1B01G272200 chr5D 100.000 28 0 0 6451 6478 123889328 123889301 1.200000e-02 52.8
48 TraesCS1B01G272200 chr5B 78.889 540 99 11 5526 6056 707449965 707449432 1.030000e-92 351.0
49 TraesCS1B01G272200 chr5B 89.855 69 5 2 5459 5526 219085333 219085266 3.220000e-13 87.9
50 TraesCS1B01G272200 chr5B 89.091 55 5 1 5464 5517 71377131 71377185 4.200000e-07 67.6
51 TraesCS1B01G272200 chr2B 89.855 69 6 1 5459 5526 463434700 463434632 3.220000e-13 87.9
52 TraesCS1B01G272200 chr2B 100.000 29 0 0 5466 5494 685271679 685271651 3.000000e-03 54.7
53 TraesCS1B01G272200 chr7D 100.000 34 0 0 6451 6484 500785577 500785544 5.430000e-06 63.9
54 TraesCS1B01G272200 chr7D 97.143 35 1 0 6450 6484 500802712 500802678 7.020000e-05 60.2
55 TraesCS1B01G272200 chr2D 100.000 29 0 0 6450 6478 544934666 544934638 3.000000e-03 54.7
56 TraesCS1B01G272200 chr4D 100.000 28 0 0 6451 6478 297361596 297361569 1.200000e-02 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 TraesCS1B01G272200 chr1B 478255235 478261718 6483 True 11974.000000 11974 100.000000 1 6484 1 chr1B.!!$R2 6483
1 TraesCS1B01G272200 chr1B 478080110 478080854 744 True 699.000000 699 83.742000 4686 5453 1 chr1B.!!$R1 767
2 TraesCS1B01G272200 chr1B 478095753 478097034 1281 True 477.000000 521 87.054000 3230 4323 2 chr1B.!!$R5 1093
3 TraesCS1B01G272200 chr1B 478432361 478432905 544 True 377.000000 377 80.541000 100 611 1 chr1B.!!$R4 511
4 TraesCS1B01G272200 chr1A 455818360 455823816 5456 True 1789.075000 5648 90.627250 2 6451 4 chr1A.!!$R3 6449
5 TraesCS1B01G272200 chr1A 455663473 455663991 518 True 643.000000 643 89.122000 3230 3749 1 chr1A.!!$R1 519
6 TraesCS1B01G272200 chr1A 539708900 539709419 519 False 366.000000 366 79.580000 5539 6056 1 chr1A.!!$F1 517
7 TraesCS1B01G272200 chr1A 455807703 455808205 502 True 345.000000 364 89.538000 5931 6484 2 chr1A.!!$R2 553
8 TraesCS1B01G272200 chr1D 355468649 355475283 6634 True 951.566667 3980 90.577444 49 6484 9 chr1D.!!$R3 6435
9 TraesCS1B01G272200 chr1D 355438384 355441474 3090 True 518.500000 704 88.203000 3230 5453 4 chr1D.!!$R2 2223
10 TraesCS1B01G272200 chr3D 2095965 2098133 2168 False 639.500000 983 85.103000 2769 4579 2 chr3D.!!$F2 1810
11 TraesCS1B01G272200 chr3D 20370032 20370564 532 True 357.000000 357 79.113000 5526 6056 1 chr3D.!!$R1 530
12 TraesCS1B01G272200 chr3A 6893937 6898311 4374 True 462.500000 564 79.603500 2582 3948 2 chr3A.!!$R1 1366
13 TraesCS1B01G272200 chrUn 171267898 171268401 503 True 363.000000 363 79.961000 5545 6045 1 chrUn.!!$R1 500
14 TraesCS1B01G272200 chr6D 159785639 159786153 514 True 363.000000 363 79.615000 5544 6056 1 chr6D.!!$R1 512
15 TraesCS1B01G272200 chr2A 761144513 761145021 508 True 363.000000 363 79.884000 5549 6056 1 chr2A.!!$R1 507
16 TraesCS1B01G272200 chr6A 103275566 103276078 512 False 361.000000 361 79.693000 5544 6056 1 chr6A.!!$F2 512
17 TraesCS1B01G272200 chr5D 424878304 424878821 517 False 357.000000 357 79.350000 5541 6056 1 chr5D.!!$F1 515
18 TraesCS1B01G272200 chr5B 707449432 707449965 533 True 351.000000 351 78.889000 5526 6056 1 chr5B.!!$R2 530

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
25 26 0.097674 ACGCGTTACTACCGTAGCAG 59.902 55.0 5.58 0.0 32.12 4.24 F
706 948 0.251787 ATTTTCCACTGACCCCTGCC 60.252 55.0 0.00 0.0 0.00 4.85 F
1352 1658 0.032130 TCTTATCGGCCGTGCTCATC 59.968 55.0 27.15 0.0 0.00 2.92 F
1666 1974 0.398381 CATGGGTAATTGGGTGGGGG 60.398 60.0 0.00 0.0 0.00 5.40 F
3483 6862 0.254107 TAGCCCCTTTCCATTCCCCT 60.254 55.0 0.00 0.0 0.00 4.79 F
3701 7096 0.321298 TGCTGCGGGTTTTAGAGTCC 60.321 55.0 0.00 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1352 1658 0.107508 ACGGAGCAGTCAATGGATGG 60.108 55.0 0.00 0.00 0.00 3.51 R
1646 1954 0.398381 CCCCACCCAATTACCCATGG 60.398 60.0 4.14 4.14 36.42 3.66 R
3092 3438 0.536460 AGGGCGTTGTTAACCCACAG 60.536 55.0 2.48 0.00 46.88 3.66 R
3594 6988 1.355971 TCGCATACGAGGAAAGCAAC 58.644 50.0 0.00 0.00 45.12 4.17 R
5159 10139 0.329596 CAACCTTAGCAGAAGGCCCT 59.670 55.0 15.45 0.00 46.50 5.19 R
5689 10730 0.246910 TTCAAGGCGGCGTGTATACA 59.753 50.0 23.04 0.08 0.00 2.29 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 1.466773 GCACGCGTTACTACCGTAGC 61.467 60.000 10.22 1.14 32.46 3.58
25 26 0.097674 ACGCGTTACTACCGTAGCAG 59.902 55.000 5.58 0.00 32.12 4.24
27 28 1.820092 GCGTTACTACCGTAGCAGTC 58.180 55.000 5.42 0.00 0.00 3.51
32 33 5.043903 CGTTACTACCGTAGCAGTCTACTA 58.956 45.833 5.42 0.00 42.30 1.82
33 34 5.174761 CGTTACTACCGTAGCAGTCTACTAG 59.825 48.000 5.42 0.00 42.30 2.57
34 35 4.751767 ACTACCGTAGCAGTCTACTAGT 57.248 45.455 5.42 0.00 42.30 2.57
35 36 5.860941 ACTACCGTAGCAGTCTACTAGTA 57.139 43.478 5.42 1.89 42.30 1.82
36 37 5.596845 ACTACCGTAGCAGTCTACTAGTAC 58.403 45.833 5.42 0.00 42.30 2.73
39 40 3.244814 CCGTAGCAGTCTACTAGTACGTG 59.755 52.174 16.25 0.00 42.30 4.49
40 41 3.244814 CGTAGCAGTCTACTAGTACGTGG 59.755 52.174 0.00 0.00 42.30 4.94
41 42 3.347077 AGCAGTCTACTAGTACGTGGT 57.653 47.619 0.00 0.00 0.00 4.16
42 43 4.478206 AGCAGTCTACTAGTACGTGGTA 57.522 45.455 0.00 0.00 0.00 3.25
43 44 4.187694 AGCAGTCTACTAGTACGTGGTAC 58.812 47.826 0.00 0.00 39.10 3.34
45 46 4.033817 GCAGTCTACTAGTACGTGGTACAG 59.966 50.000 0.00 6.34 41.80 2.74
46 47 5.174395 CAGTCTACTAGTACGTGGTACAGT 58.826 45.833 0.00 10.77 41.80 3.55
59 71 7.515957 ACGTGGTACAGTATAATTTTCGAAG 57.484 36.000 0.00 0.00 41.80 3.79
90 102 7.132213 CGACTTTTATTTCTGCTTTTCTGTCA 58.868 34.615 0.00 0.00 0.00 3.58
192 209 2.281761 GTCCAGCCACACACCAGG 60.282 66.667 0.00 0.00 0.00 4.45
193 210 2.772191 TCCAGCCACACACCAGGT 60.772 61.111 0.00 0.00 0.00 4.00
276 295 2.125552 CATCTGTTCCGCTCGGCA 60.126 61.111 2.96 0.00 34.68 5.69
541 778 1.202054 GGTTCAGTCGAGAGCTACGTC 60.202 57.143 11.51 7.16 0.00 4.34
616 858 1.071567 GTTGCTGTCTCGCGGACTAC 61.072 60.000 22.40 16.33 44.74 2.73
630 872 1.275291 GGACTACACTAGCAGCACCAA 59.725 52.381 0.00 0.00 0.00 3.67
700 942 1.541588 GCCACTGATTTTCCACTGACC 59.458 52.381 0.00 0.00 0.00 4.02
701 943 2.162681 CCACTGATTTTCCACTGACCC 58.837 52.381 0.00 0.00 0.00 4.46
702 944 2.162681 CACTGATTTTCCACTGACCCC 58.837 52.381 0.00 0.00 0.00 4.95
703 945 2.065799 ACTGATTTTCCACTGACCCCT 58.934 47.619 0.00 0.00 0.00 4.79
704 946 2.224867 ACTGATTTTCCACTGACCCCTG 60.225 50.000 0.00 0.00 0.00 4.45
705 947 1.177401 GATTTTCCACTGACCCCTGC 58.823 55.000 0.00 0.00 0.00 4.85
706 948 0.251787 ATTTTCCACTGACCCCTGCC 60.252 55.000 0.00 0.00 0.00 4.85
707 949 1.360393 TTTTCCACTGACCCCTGCCT 61.360 55.000 0.00 0.00 0.00 4.75
708 950 1.779061 TTTCCACTGACCCCTGCCTC 61.779 60.000 0.00 0.00 0.00 4.70
709 951 4.087892 CCACTGACCCCTGCCTCG 62.088 72.222 0.00 0.00 0.00 4.63
710 952 2.997315 CACTGACCCCTGCCTCGA 60.997 66.667 0.00 0.00 0.00 4.04
711 953 2.681778 ACTGACCCCTGCCTCGAG 60.682 66.667 5.13 5.13 0.00 4.04
712 954 4.154347 CTGACCCCTGCCTCGAGC 62.154 72.222 6.99 3.23 44.14 5.03
732 986 5.104259 AGCCAGTTTAGGAAGGTAATGAG 57.896 43.478 0.00 0.00 0.00 2.90
734 988 4.080526 GCCAGTTTAGGAAGGTAATGAGGA 60.081 45.833 0.00 0.00 0.00 3.71
754 1011 2.608090 GACATACCTTTGACGCTAAGCC 59.392 50.000 0.00 0.00 0.00 4.35
759 1024 0.723981 CTTTGACGCTAAGCCTGAGC 59.276 55.000 0.00 0.00 40.32 4.26
760 1025 0.673644 TTTGACGCTAAGCCTGAGCC 60.674 55.000 0.00 0.00 41.25 4.70
761 1026 1.544825 TTGACGCTAAGCCTGAGCCT 61.545 55.000 0.00 0.00 41.25 4.58
762 1027 1.227118 GACGCTAAGCCTGAGCCTC 60.227 63.158 0.00 0.00 41.25 4.70
763 1028 1.949847 GACGCTAAGCCTGAGCCTCA 61.950 60.000 0.00 0.00 41.25 3.86
764 1029 1.227205 CGCTAAGCCTGAGCCTCAG 60.227 63.158 14.99 14.99 43.91 3.35
765 1030 1.523484 GCTAAGCCTGAGCCTCAGC 60.523 63.158 16.49 11.53 42.98 4.26
800 1065 3.074412 CCACACTGTTTTCCTCGCTAAT 58.926 45.455 0.00 0.00 0.00 1.73
866 1131 3.942748 TCTTTTAATGGCATCCACGGTAC 59.057 43.478 0.00 0.00 35.80 3.34
870 1135 1.789523 ATGGCATCCACGGTACTACT 58.210 50.000 0.00 0.00 35.80 2.57
875 1140 3.251972 GGCATCCACGGTACTACTACTAC 59.748 52.174 0.00 0.00 0.00 2.73
876 1141 4.133078 GCATCCACGGTACTACTACTACT 58.867 47.826 0.00 0.00 0.00 2.57
877 1142 4.024218 GCATCCACGGTACTACTACTACTG 60.024 50.000 0.00 0.00 0.00 2.74
952 1218 1.967597 GAGCTAAGCAAACGACGGCC 61.968 60.000 0.00 0.00 0.00 6.13
959 1237 1.374252 CAAACGACGGCCAGCTACT 60.374 57.895 2.24 0.00 0.00 2.57
961 1239 0.604578 AAACGACGGCCAGCTACTAA 59.395 50.000 2.24 0.00 0.00 2.24
964 1242 1.664321 CGACGGCCAGCTACTAACCT 61.664 60.000 2.24 0.00 0.00 3.50
966 1244 0.324460 ACGGCCAGCTACTAACCTCT 60.324 55.000 2.24 0.00 0.00 3.69
975 1255 2.829023 CTACTAACCTCTTCCACCCCA 58.171 52.381 0.00 0.00 0.00 4.96
976 1256 1.359168 ACTAACCTCTTCCACCCCAC 58.641 55.000 0.00 0.00 0.00 4.61
981 1261 4.209620 TCTTCCACCCCACCCCCA 62.210 66.667 0.00 0.00 0.00 4.96
1267 1570 3.753294 AGGTAATCCGTCATCCATCAC 57.247 47.619 0.00 0.00 39.05 3.06
1335 1641 0.466555 CGTCCCCTTCGATCTCCTCT 60.467 60.000 0.00 0.00 0.00 3.69
1350 1656 1.437573 CTCTTATCGGCCGTGCTCA 59.562 57.895 27.15 5.24 0.00 4.26
1351 1657 0.032678 CTCTTATCGGCCGTGCTCAT 59.967 55.000 27.15 13.56 0.00 2.90
1352 1658 0.032130 TCTTATCGGCCGTGCTCATC 59.968 55.000 27.15 0.00 0.00 2.92
1354 1660 1.681486 TTATCGGCCGTGCTCATCCA 61.681 55.000 27.15 1.58 0.00 3.41
1403 1710 3.329231 CGGCTGCAGACGTTCAAA 58.671 55.556 33.82 0.00 42.66 2.69
1590 1898 5.386958 AGAAAGTGCTAGTATGTCGACAA 57.613 39.130 24.13 9.30 0.00 3.18
1591 1899 5.779922 AGAAAGTGCTAGTATGTCGACAAA 58.220 37.500 24.13 7.67 0.00 2.83
1592 1900 6.220930 AGAAAGTGCTAGTATGTCGACAAAA 58.779 36.000 24.13 11.24 0.00 2.44
1593 1901 6.874134 AGAAAGTGCTAGTATGTCGACAAAAT 59.126 34.615 24.13 13.23 0.00 1.82
1608 1916 5.067936 TCGACAAAATAAATTGTGGTGGTGT 59.932 36.000 0.00 0.00 43.31 4.16
1618 1926 2.972505 GGTGGTGTGGTCTGTGCG 60.973 66.667 0.00 0.00 0.00 5.34
1624 1932 1.014352 GTGTGGTCTGTGCGAAAAGT 58.986 50.000 0.00 0.00 0.00 2.66
1633 1941 1.800586 TGTGCGAAAAGTGCATCTCTC 59.199 47.619 0.00 0.00 45.34 3.20
1634 1942 2.072298 GTGCGAAAAGTGCATCTCTCT 58.928 47.619 0.00 0.00 45.34 3.10
1635 1943 2.481952 GTGCGAAAAGTGCATCTCTCTT 59.518 45.455 0.00 0.00 45.34 2.85
1636 1944 3.058639 GTGCGAAAAGTGCATCTCTCTTT 60.059 43.478 0.00 0.00 45.34 2.52
1637 1945 4.152402 GTGCGAAAAGTGCATCTCTCTTTA 59.848 41.667 0.00 0.00 45.34 1.85
1638 1946 4.937620 TGCGAAAAGTGCATCTCTCTTTAT 59.062 37.500 0.00 0.00 37.48 1.40
1639 1947 5.063944 TGCGAAAAGTGCATCTCTCTTTATC 59.936 40.000 0.00 0.00 37.48 1.75
1640 1948 5.503194 GCGAAAAGTGCATCTCTCTTTATCC 60.503 44.000 0.00 0.00 37.48 2.59
1646 1954 3.137533 GCATCTCTCTTTATCCCTGCAC 58.862 50.000 0.00 0.00 0.00 4.57
1666 1974 0.398381 CATGGGTAATTGGGTGGGGG 60.398 60.000 0.00 0.00 0.00 5.40
1667 1975 2.042333 GGGTAATTGGGTGGGGGC 60.042 66.667 0.00 0.00 0.00 5.80
1717 2026 7.125053 ACTGTTCCCCTGAAAAATAGTCAAAAA 59.875 33.333 0.00 0.00 30.79 1.94
1722 2031 7.176690 TCCCCTGAAAAATAGTCAAAAAGCTAG 59.823 37.037 0.00 0.00 0.00 3.42
1743 2069 8.568794 AGCTAGTACTCTTTTTGAATTTTGACC 58.431 33.333 0.00 0.00 0.00 4.02
1747 2073 6.908870 ACTCTTTTTGAATTTTGACCTTGC 57.091 33.333 0.00 0.00 0.00 4.01
1748 2074 6.405538 ACTCTTTTTGAATTTTGACCTTGCA 58.594 32.000 0.00 0.00 0.00 4.08
1750 2076 7.011669 ACTCTTTTTGAATTTTGACCTTGCATG 59.988 33.333 0.00 0.00 0.00 4.06
1753 2079 4.686191 TGAATTTTGACCTTGCATGGTT 57.314 36.364 23.88 8.30 41.00 3.67
1754 2080 4.378774 TGAATTTTGACCTTGCATGGTTG 58.621 39.130 23.88 0.00 41.00 3.77
1757 2083 5.743636 ATTTTGACCTTGCATGGTTGTAT 57.256 34.783 23.88 12.86 41.00 2.29
1760 2086 4.835284 TGACCTTGCATGGTTGTATCTA 57.165 40.909 23.88 4.35 41.00 1.98
1763 2089 4.718961 ACCTTGCATGGTTGTATCTATCC 58.281 43.478 18.18 0.00 36.89 2.59
1776 2102 4.347876 TGTATCTATCCTCCATGTTGGGTG 59.652 45.833 0.00 0.00 38.32 4.61
1778 2104 4.002256 TCTATCCTCCATGTTGGGTGTA 57.998 45.455 0.00 0.00 38.32 2.90
1779 2105 4.367166 TCTATCCTCCATGTTGGGTGTAA 58.633 43.478 0.00 0.00 38.32 2.41
1780 2106 2.871096 TCCTCCATGTTGGGTGTAAC 57.129 50.000 0.00 0.00 38.32 2.50
2115 2443 4.354587 CAAACTGTGGCTGTCTCTTTTTC 58.645 43.478 0.00 0.00 0.00 2.29
2118 2446 3.209410 CTGTGGCTGTCTCTTTTTCTGT 58.791 45.455 0.00 0.00 0.00 3.41
2119 2447 2.945008 TGTGGCTGTCTCTTTTTCTGTG 59.055 45.455 0.00 0.00 0.00 3.66
2123 2451 2.749800 GCTGTCTCTTTTTCTGTGGGGT 60.750 50.000 0.00 0.00 0.00 4.95
2124 2452 2.880890 CTGTCTCTTTTTCTGTGGGGTG 59.119 50.000 0.00 0.00 0.00 4.61
2161 2489 3.581024 CCATTGAGTTGGTTGGATGTG 57.419 47.619 0.00 0.00 31.74 3.21
2162 2490 2.231964 CCATTGAGTTGGTTGGATGTGG 59.768 50.000 0.00 0.00 31.74 4.17
2183 2511 3.562609 GGGCAGTTGGAATTAGGTACCAA 60.563 47.826 15.94 6.95 40.68 3.67
2184 2512 4.278310 GGCAGTTGGAATTAGGTACCAAT 58.722 43.478 15.94 9.06 43.89 3.16
2185 2513 5.442391 GGCAGTTGGAATTAGGTACCAATA 58.558 41.667 15.94 0.00 43.89 1.90
2186 2514 5.298527 GGCAGTTGGAATTAGGTACCAATAC 59.701 44.000 15.94 7.04 43.89 1.89
2208 2536 3.061563 CCATTGTGATTTTTGAGCATGCG 59.938 43.478 13.01 0.00 0.00 4.73
2209 2537 2.350899 TGTGATTTTTGAGCATGCGG 57.649 45.000 13.01 0.00 0.00 5.69
2273 2601 5.880054 AGATTATTTGGACCAAACAGACG 57.120 39.130 21.85 0.00 36.13 4.18
2334 2665 7.341030 TGTTGTCAATCTTAGGATGTGATGAT 58.659 34.615 0.00 0.00 31.75 2.45
2455 2786 6.166982 GGGTATCATAAAGCCATAGACAGAC 58.833 44.000 0.00 0.00 34.56 3.51
2544 2875 5.006165 GCTATGTCACTGTGCTGATTAACTC 59.994 44.000 2.12 0.00 0.00 3.01
2697 3033 7.281100 CCCACTCCTTCAGTCTTAAATAATGTC 59.719 40.741 0.00 0.00 30.26 3.06
2717 3055 7.772332 ATGTCGAGTTTCTATCCATGTAAAC 57.228 36.000 0.00 0.00 33.11 2.01
2816 3154 5.023533 TGATGTCCCTTGAAGCTATACAC 57.976 43.478 0.00 0.00 0.00 2.90
2925 3267 1.203994 ACTTATCAGTTACGGCGCTGT 59.796 47.619 27.38 27.38 34.57 4.40
3092 3438 4.924305 ATCACAATGCCAATGATGTACC 57.076 40.909 0.00 0.00 31.84 3.34
3107 3453 2.836262 TGTACCTGTGGGTTAACAACG 58.164 47.619 8.10 2.60 44.73 4.10
3118 3473 1.944709 GTTAACAACGCCCTCTTGTGT 59.055 47.619 0.00 0.00 32.07 3.72
3175 3536 4.455533 CAGCATTGTTTAGAGCCACTACAA 59.544 41.667 0.00 0.00 33.45 2.41
3189 3550 4.096382 GCCACTACAATTGTAACAGGATGG 59.904 45.833 24.10 20.18 43.62 3.51
3333 3694 7.255766 GCAATCATGAGGTCTTCTATCAGACTA 60.256 40.741 0.09 0.00 42.63 2.59
3337 6709 9.868160 TCATGAGGTCTTCTATCAGACTAAATA 57.132 33.333 0.00 0.00 42.63 1.40
3357 6729 9.184062 CTAAATATATGTTGCGAAATTGCATGT 57.816 29.630 0.00 0.00 45.78 3.21
3479 6858 7.061054 ACTAACTAATTAGCCCCTTTCCATTC 58.939 38.462 12.54 0.00 41.48 2.67
3483 6862 0.254107 TAGCCCCTTTCCATTCCCCT 60.254 55.000 0.00 0.00 0.00 4.79
3595 6989 5.629079 GCTTGTAATAAGCTGAACTTGGT 57.371 39.130 4.50 0.00 39.58 3.67
3611 7005 1.448985 TGGTTGCTTTCCTCGTATGC 58.551 50.000 0.00 0.00 0.00 3.14
3701 7096 0.321298 TGCTGCGGGTTTTAGAGTCC 60.321 55.000 0.00 0.00 0.00 3.85
3719 7114 5.482878 AGAGTCCGATTTTAAGAAGGTGGTA 59.517 40.000 0.00 0.00 0.00 3.25
3735 7130 2.103263 GTGGTAGGGATAAGGTGAGCAG 59.897 54.545 0.00 0.00 0.00 4.24
3762 7157 9.046296 AGAGTATCACACAAGTTTCTACTTTTG 57.954 33.333 0.00 0.00 44.10 2.44
3826 7581 4.937620 TCAACTCATGTCTATTCCAAGCAC 59.062 41.667 0.00 0.00 0.00 4.40
3833 7588 4.910195 TGTCTATTCCAAGCACAACTCAT 58.090 39.130 0.00 0.00 0.00 2.90
3921 7677 5.708948 TGAATGTTAATGGTAAGTTGCAGC 58.291 37.500 0.00 0.00 0.00 5.25
3927 7683 3.641434 ATGGTAAGTTGCAGCTCATCT 57.359 42.857 2.60 0.00 0.00 2.90
3952 7708 7.561021 TTTTCTGAACAGCACTTGTATACAA 57.439 32.000 17.16 17.16 39.73 2.41
3986 8072 4.637276 TGTTCGAGCCACTTTCAGAATTA 58.363 39.130 0.00 0.00 0.00 1.40
3987 8073 5.060506 TGTTCGAGCCACTTTCAGAATTAA 58.939 37.500 0.00 0.00 0.00 1.40
4127 8216 3.032017 ACAGAACCTGTCATGAGAACG 57.968 47.619 0.00 0.00 41.21 3.95
4152 8241 2.852449 TGTTCCGCAAGATGGTTTACA 58.148 42.857 0.00 0.00 43.02 2.41
4153 8242 2.550606 TGTTCCGCAAGATGGTTTACAC 59.449 45.455 0.00 0.00 43.02 2.90
4156 8245 3.857052 TCCGCAAGATGGTTTACACTAG 58.143 45.455 0.00 0.00 43.02 2.57
4324 8447 4.881019 ACATTCGCTATGAGCCTCTTAT 57.119 40.909 4.63 0.00 38.18 1.73
4325 8448 5.984695 ACATTCGCTATGAGCCTCTTATA 57.015 39.130 4.63 0.00 38.18 0.98
4326 8449 5.715070 ACATTCGCTATGAGCCTCTTATAC 58.285 41.667 4.63 0.00 38.18 1.47
4327 8450 5.478679 ACATTCGCTATGAGCCTCTTATACT 59.521 40.000 4.63 0.00 38.18 2.12
4329 8452 3.191581 TCGCTATGAGCCTCTTATACTGC 59.808 47.826 0.00 0.00 38.18 4.40
4330 8453 3.674682 CGCTATGAGCCTCTTATACTGCC 60.675 52.174 0.00 0.00 38.18 4.85
4331 8454 3.368948 GCTATGAGCCTCTTATACTGCCC 60.369 52.174 0.00 0.00 34.48 5.36
4516 9487 1.866015 TCGTCCTGTTCCTGATCCAT 58.134 50.000 0.00 0.00 0.00 3.41
4558 9529 5.011329 TGCCTTTGAGATTGCATTCTTCTTT 59.989 36.000 12.17 0.00 0.00 2.52
4624 9596 9.590451 TTTAAATTACGTTCGGTGAAGATCTAT 57.410 29.630 0.00 0.00 0.00 1.98
4625 9597 9.590451 TTAAATTACGTTCGGTGAAGATCTATT 57.410 29.630 0.00 0.00 0.00 1.73
4626 9598 8.488651 AAATTACGTTCGGTGAAGATCTATTT 57.511 30.769 0.00 0.00 0.00 1.40
4627 9599 8.488651 AATTACGTTCGGTGAAGATCTATTTT 57.511 30.769 0.00 0.00 0.00 1.82
4628 9600 7.894376 TTACGTTCGGTGAAGATCTATTTTT 57.106 32.000 0.00 0.00 0.00 1.94
4667 9639 8.980481 ATTTAAATTATGGTCGGTGAAGATCT 57.020 30.769 0.00 0.00 0.00 2.75
4829 9808 2.549754 CAAAGCGAACATGACCTTGTCT 59.450 45.455 0.00 0.00 33.15 3.41
4936 9915 0.531090 TGTAACACAGGTGCGACCAC 60.531 55.000 7.86 0.00 41.95 4.16
4968 9948 7.148869 CGACATCGTAAAATGTTTCTAGTGTCA 60.149 37.037 0.00 0.00 39.93 3.58
5159 10139 3.842925 GAGCCCCGTTGGTTCTGCA 62.843 63.158 0.00 0.00 40.97 4.41
5180 10160 1.680249 GGGCCTTCTGCTAAGGTTGAG 60.680 57.143 16.64 0.00 39.60 3.02
5199 10179 3.680786 TGGTGAGACGACCAGCGG 61.681 66.667 0.00 0.00 46.49 5.52
5318 10298 2.912967 CTGCAATGAAAGCACTTAAGCG 59.087 45.455 1.29 0.00 40.15 4.68
5406 10392 8.221965 AGAAATTCGGTCCAAATAGTTTATCC 57.778 34.615 0.00 0.00 0.00 2.59
5441 10427 2.073816 GCCTAAAACTGTCGCTGCTTA 58.926 47.619 0.00 0.00 0.00 3.09
5442 10428 2.482721 GCCTAAAACTGTCGCTGCTTAA 59.517 45.455 0.00 0.00 0.00 1.85
5534 10558 2.821969 ACATGATGAGGAAGCCAAACAC 59.178 45.455 0.00 0.00 0.00 3.32
5617 10658 4.388378 AACTATGCCTAAGTCGAAGGAC 57.612 45.455 5.80 0.00 43.76 3.85
5628 10669 2.863346 CGAAGGACGTGGTGGACCA 61.863 63.158 0.00 0.00 45.30 4.02
5688 10729 0.250295 CTCTGGTCACCCGCTTCAAA 60.250 55.000 0.00 0.00 0.00 2.69
5689 10730 0.400213 TCTGGTCACCCGCTTCAAAT 59.600 50.000 0.00 0.00 0.00 2.32
5698 10739 2.933906 ACCCGCTTCAAATGTATACACG 59.066 45.455 7.96 5.30 0.00 4.49
5723 10764 5.868801 CCGCCTTGAACAACAATTGATAATT 59.131 36.000 13.59 0.00 37.88 1.40
5729 10770 9.398170 CTTGAACAACAATTGATAATTCGTTCT 57.602 29.630 13.59 0.00 37.88 3.01
5786 10827 8.748412 CATACAATGGAAAATAACCTCCAAAGA 58.252 33.333 0.00 0.00 44.77 2.52
5789 10830 5.722021 TGGAAAATAACCTCCAAAGAAGC 57.278 39.130 0.00 0.00 38.81 3.86
5790 10831 4.526650 TGGAAAATAACCTCCAAAGAAGCC 59.473 41.667 0.00 0.00 38.81 4.35
5797 10844 0.879765 CTCCAAAGAAGCCAGTGCAG 59.120 55.000 0.00 0.00 41.13 4.41
5829 10876 8.806146 ACAAAATCATTTCTACATAGCCAAAGT 58.194 29.630 0.00 0.00 0.00 2.66
5843 10890 5.193099 AGCCAAAGTGACCATAATAAGGT 57.807 39.130 0.00 0.00 43.46 3.50
5847 10894 5.590259 CCAAAGTGACCATAATAAGGTGGAG 59.410 44.000 0.00 0.00 40.09 3.86
5855 10902 1.912862 AATAAGGTGGAGGCTCCCAT 58.087 50.000 30.03 16.35 38.66 4.00
5864 10911 2.979678 TGGAGGCTCCCATCCTTATTAC 59.020 50.000 30.03 1.30 35.03 1.89
5954 11001 7.147976 GGATACAAATTGGATGCTATTTGGAC 58.852 38.462 27.81 20.07 42.96 4.02
5961 11008 2.498167 GATGCTATTTGGACGGCTGAT 58.502 47.619 0.00 0.00 0.00 2.90
6062 11109 1.006281 TCCATGCCAATTGCTCCTCTT 59.994 47.619 0.00 0.00 42.00 2.85
6071 11118 4.749099 CCAATTGCTCCTCTTCGAAGATAG 59.251 45.833 27.19 25.05 35.04 2.08
6074 11121 2.099921 TGCTCCTCTTCGAAGATAGCAC 59.900 50.000 36.90 24.01 43.31 4.40
6110 11157 6.595716 CCTGGACTTTTAGTGAAATCTTCGAT 59.404 38.462 0.00 0.00 0.00 3.59
6116 11163 8.507249 ACTTTTAGTGAAATCTTCGATTTCCAG 58.493 33.333 20.45 11.97 37.25 3.86
6121 11168 7.533426 AGTGAAATCTTCGATTTCCAGATTTG 58.467 34.615 21.03 0.00 43.95 2.32
6128 11175 7.475015 TCTTCGATTTCCAGATTTGCTTATTG 58.525 34.615 0.00 0.00 0.00 1.90
6145 11192 9.866655 TTGCTTATTGTTATCTATTGGGATCTT 57.133 29.630 0.00 0.00 0.00 2.40
6209 11256 3.635591 CCCAGATGGTATTTGAGCCTTT 58.364 45.455 0.00 0.00 0.00 3.11
6210 11257 3.633986 CCCAGATGGTATTTGAGCCTTTC 59.366 47.826 0.00 0.00 0.00 2.62
6211 11258 4.530875 CCAGATGGTATTTGAGCCTTTCT 58.469 43.478 0.00 0.00 0.00 2.52
6212 11259 4.952335 CCAGATGGTATTTGAGCCTTTCTT 59.048 41.667 0.00 0.00 0.00 2.52
6213 11260 5.163581 CCAGATGGTATTTGAGCCTTTCTTG 60.164 44.000 0.00 0.00 0.00 3.02
6214 11261 5.416952 CAGATGGTATTTGAGCCTTTCTTGT 59.583 40.000 0.00 0.00 0.00 3.16
6215 11262 6.012745 AGATGGTATTTGAGCCTTTCTTGTT 58.987 36.000 0.00 0.00 0.00 2.83
6216 11263 5.452078 TGGTATTTGAGCCTTTCTTGTTG 57.548 39.130 0.00 0.00 0.00 3.33
6217 11264 4.892934 TGGTATTTGAGCCTTTCTTGTTGT 59.107 37.500 0.00 0.00 0.00 3.32
6218 11265 5.362430 TGGTATTTGAGCCTTTCTTGTTGTT 59.638 36.000 0.00 0.00 0.00 2.83
6219 11266 6.547880 TGGTATTTGAGCCTTTCTTGTTGTTA 59.452 34.615 0.00 0.00 0.00 2.41
6220 11267 7.068839 TGGTATTTGAGCCTTTCTTGTTGTTAA 59.931 33.333 0.00 0.00 0.00 2.01
6221 11268 8.088365 GGTATTTGAGCCTTTCTTGTTGTTAAT 58.912 33.333 0.00 0.00 0.00 1.40
6250 11297 6.441093 TCACAATTCAGATGGTATTTGAGC 57.559 37.500 0.00 0.00 0.00 4.26
6251 11298 5.357878 TCACAATTCAGATGGTATTTGAGCC 59.642 40.000 0.00 0.00 0.00 4.70
6300 11347 7.012704 ACAATTCACAATGCCAGTGATATACTC 59.987 37.037 0.00 0.00 44.66 2.59
6301 11348 5.612725 TCACAATGCCAGTGATATACTCA 57.387 39.130 0.00 0.00 40.80 3.41
6309 11356 5.174395 GCCAGTGATATACTCATGGCTTAG 58.826 45.833 6.76 0.00 45.42 2.18
6328 11375 5.124617 GCTTAGCAGCAGTTATCTTTTTCCT 59.875 40.000 0.00 0.00 46.49 3.36
6356 11403 9.229784 CTTGTGCACTGAAAATCAATATATGTC 57.770 33.333 19.41 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 5.174395 ACTGTACCACGTACTAGTAGACTG 58.826 45.833 1.87 0.00 39.49 3.51
25 26 8.873215 TTATACTGTACCACGTACTAGTAGAC 57.127 38.462 1.87 0.00 39.49 2.59
32 33 7.761409 TCGAAAATTATACTGTACCACGTACT 58.239 34.615 3.79 0.00 39.49 2.73
33 34 7.969387 TCGAAAATTATACTGTACCACGTAC 57.031 36.000 0.00 0.00 39.24 3.67
34 35 7.220683 GCTTCGAAAATTATACTGTACCACGTA 59.779 37.037 0.00 0.00 0.00 3.57
35 36 6.035327 GCTTCGAAAATTATACTGTACCACGT 59.965 38.462 0.00 0.00 0.00 4.49
36 37 6.408428 GCTTCGAAAATTATACTGTACCACG 58.592 40.000 0.00 0.00 0.00 4.94
39 40 5.750067 TCCGCTTCGAAAATTATACTGTACC 59.250 40.000 0.00 0.00 0.00 3.34
40 41 6.561717 GCTCCGCTTCGAAAATTATACTGTAC 60.562 42.308 0.00 0.00 0.00 2.90
41 42 5.461078 GCTCCGCTTCGAAAATTATACTGTA 59.539 40.000 0.00 0.00 0.00 2.74
42 43 4.270325 GCTCCGCTTCGAAAATTATACTGT 59.730 41.667 0.00 0.00 0.00 3.55
43 44 4.606232 CGCTCCGCTTCGAAAATTATACTG 60.606 45.833 0.00 0.00 0.00 2.74
45 46 3.488310 TCGCTCCGCTTCGAAAATTATAC 59.512 43.478 0.00 0.00 0.00 1.47
46 47 3.488310 GTCGCTCCGCTTCGAAAATTATA 59.512 43.478 0.00 0.00 36.41 0.98
59 71 2.788065 GCAGAAATAAAAGTCGCTCCGC 60.788 50.000 0.00 0.00 0.00 5.54
90 102 3.487376 CCGCTTTGTGATTTGTATGCGAT 60.487 43.478 0.00 0.00 44.02 4.58
192 209 3.178540 AAGACCAGTCCACCGCCAC 62.179 63.158 0.00 0.00 0.00 5.01
193 210 2.847234 AAGACCAGTCCACCGCCA 60.847 61.111 0.00 0.00 0.00 5.69
276 295 2.172483 GAGTGTGCGACCTGGGACAT 62.172 60.000 0.00 0.00 40.44 3.06
283 302 2.214181 GACCATCGAGTGTGCGACCT 62.214 60.000 0.00 0.00 43.79 3.85
430 454 4.011517 ACGGGCCAACGTGTAGGG 62.012 66.667 4.39 0.00 46.64 3.53
456 489 4.367023 TTCAACGGAGCGACGGGG 62.367 66.667 7.92 0.02 38.39 5.73
616 858 1.825090 TTGGATTGGTGCTGCTAGTG 58.175 50.000 0.00 0.00 0.00 2.74
630 872 3.005367 GGACACGTTGGTTTGAATTGGAT 59.995 43.478 0.00 0.00 0.00 3.41
679 921 1.541588 GTCAGTGGAAAATCAGTGGCC 59.458 52.381 0.00 0.00 36.88 5.36
704 946 0.249398 TTCCTAAACTGGCTCGAGGC 59.751 55.000 30.53 30.53 41.50 4.70
705 947 1.134670 CCTTCCTAAACTGGCTCGAGG 60.135 57.143 15.58 0.00 0.00 4.63
706 948 1.550976 ACCTTCCTAAACTGGCTCGAG 59.449 52.381 8.45 8.45 0.00 4.04
707 949 1.640917 ACCTTCCTAAACTGGCTCGA 58.359 50.000 0.00 0.00 0.00 4.04
708 950 3.604875 TTACCTTCCTAAACTGGCTCG 57.395 47.619 0.00 0.00 0.00 5.03
709 951 5.099042 TCATTACCTTCCTAAACTGGCTC 57.901 43.478 0.00 0.00 0.00 4.70
710 952 4.080299 CCTCATTACCTTCCTAAACTGGCT 60.080 45.833 0.00 0.00 0.00 4.75
711 953 4.080526 TCCTCATTACCTTCCTAAACTGGC 60.081 45.833 0.00 0.00 0.00 4.85
712 954 5.045869 TGTCCTCATTACCTTCCTAAACTGG 60.046 44.000 0.00 0.00 0.00 4.00
732 986 2.608090 GCTTAGCGTCAAAGGTATGTCC 59.392 50.000 0.00 0.00 0.00 4.02
734 988 2.236395 AGGCTTAGCGTCAAAGGTATGT 59.764 45.455 0.00 0.00 0.00 2.29
754 1011 2.733669 CCTGAGGGCTGAGGCTCAG 61.734 68.421 34.76 34.76 46.90 3.35
800 1065 1.242989 TTGCATGCTCGTGGCTAAAA 58.757 45.000 20.33 0.00 42.39 1.52
866 1131 6.364435 TCGCATGATACGTACAGTAGTAGTAG 59.636 42.308 0.00 0.00 38.94 2.57
870 1135 5.525012 AGTTCGCATGATACGTACAGTAGTA 59.475 40.000 0.00 0.00 38.94 1.82
875 1140 3.691498 TCAGTTCGCATGATACGTACAG 58.309 45.455 0.00 0.00 33.84 2.74
876 1141 3.768468 TCAGTTCGCATGATACGTACA 57.232 42.857 0.00 0.00 33.84 2.90
877 1142 4.348656 TCTTCAGTTCGCATGATACGTAC 58.651 43.478 0.00 0.00 0.00 3.67
919 1184 3.404369 GCTCTTAAGCGCTGGAGC 58.596 61.111 30.18 30.18 43.07 4.70
952 1218 2.168728 GGGTGGAAGAGGTTAGTAGCTG 59.831 54.545 0.00 0.00 30.79 4.24
959 1237 0.843343 GGGTGGGGTGGAAGAGGTTA 60.843 60.000 0.00 0.00 0.00 2.85
961 1239 2.531942 GGGTGGGGTGGAAGAGGT 60.532 66.667 0.00 0.00 0.00 3.85
964 1242 4.209620 TGGGGGTGGGGTGGAAGA 62.210 66.667 0.00 0.00 0.00 2.87
1006 1286 4.435121 CCGCGTCCTGTAGTTTATTGTTTC 60.435 45.833 4.92 0.00 0.00 2.78
1185 1488 0.179089 GCACGATGATGGAGCAGACT 60.179 55.000 0.00 0.00 0.00 3.24
1335 1641 1.069090 GGATGAGCACGGCCGATAA 59.931 57.895 35.90 11.00 0.00 1.75
1350 1656 1.202734 CGGAGCAGTCAATGGATGGAT 60.203 52.381 0.00 0.00 0.00 3.41
1351 1657 0.178767 CGGAGCAGTCAATGGATGGA 59.821 55.000 0.00 0.00 0.00 3.41
1352 1658 0.107508 ACGGAGCAGTCAATGGATGG 60.108 55.000 0.00 0.00 0.00 3.51
1354 1660 0.615331 ACACGGAGCAGTCAATGGAT 59.385 50.000 0.00 0.00 0.00 3.41
1403 1710 1.004918 CGGCTTCTGGTTCTTCCGT 60.005 57.895 0.00 0.00 39.52 4.69
1575 1883 9.210426 CACAATTTATTTTGTCGACATACTAGC 57.790 33.333 20.80 0.00 37.73 3.42
1590 1898 4.898861 AGACCACACCACCACAATTTATTT 59.101 37.500 0.00 0.00 0.00 1.40
1591 1899 4.280677 CAGACCACACCACCACAATTTATT 59.719 41.667 0.00 0.00 0.00 1.40
1592 1900 3.826157 CAGACCACACCACCACAATTTAT 59.174 43.478 0.00 0.00 0.00 1.40
1593 1901 3.218453 CAGACCACACCACCACAATTTA 58.782 45.455 0.00 0.00 0.00 1.40
1608 1916 0.746204 TGCACTTTTCGCACAGACCA 60.746 50.000 0.00 0.00 33.55 4.02
1618 1926 6.038050 CAGGGATAAAGAGAGATGCACTTTTC 59.962 42.308 4.77 3.65 38.22 2.29
1624 1932 2.773661 TGCAGGGATAAAGAGAGATGCA 59.226 45.455 0.00 0.00 39.89 3.96
1640 1948 1.113788 CCAATTACCCATGGTGCAGG 58.886 55.000 11.73 0.84 36.19 4.85
1646 1954 0.398381 CCCCACCCAATTACCCATGG 60.398 60.000 4.14 4.14 36.42 3.66
1666 1974 0.528470 ACGTTCCTACTGAGAGCAGC 59.472 55.000 0.00 0.00 46.26 5.25
1667 1975 5.030258 GGAGACGTTCCTACTGAGAGCAG 62.030 56.522 8.87 0.00 44.20 4.24
1717 2026 8.568794 GGTCAAAATTCAAAAAGAGTACTAGCT 58.431 33.333 0.00 0.00 0.00 3.32
1722 2031 7.491048 TGCAAGGTCAAAATTCAAAAAGAGTAC 59.509 33.333 0.00 0.00 0.00 2.73
1743 2069 4.999950 GGAGGATAGATACAACCATGCAAG 59.000 45.833 0.00 0.00 0.00 4.01
1746 2072 4.623932 TGGAGGATAGATACAACCATGC 57.376 45.455 0.00 0.00 0.00 4.06
1748 2074 6.466326 CCAACATGGAGGATAGATACAACCAT 60.466 42.308 0.00 0.00 40.96 3.55
1750 2076 5.308825 CCAACATGGAGGATAGATACAACC 58.691 45.833 0.00 0.00 40.96 3.77
1753 2079 4.347876 CACCCAACATGGAGGATAGATACA 59.652 45.833 7.22 0.00 40.96 2.29
1754 2080 4.348168 ACACCCAACATGGAGGATAGATAC 59.652 45.833 7.22 0.00 40.96 2.24
1757 2083 2.845659 ACACCCAACATGGAGGATAGA 58.154 47.619 7.22 0.00 40.96 1.98
1760 2086 2.647299 TGTTACACCCAACATGGAGGAT 59.353 45.455 7.22 0.00 40.96 3.24
1763 2089 3.684908 TGATGTTACACCCAACATGGAG 58.315 45.455 6.22 0.00 46.53 3.86
1776 2102 3.189287 CACCAAGGAGCAGTTGATGTTAC 59.811 47.826 0.00 0.00 0.00 2.50
1778 2104 2.233271 CACCAAGGAGCAGTTGATGTT 58.767 47.619 0.00 0.00 0.00 2.71
1779 2105 1.901591 CACCAAGGAGCAGTTGATGT 58.098 50.000 0.00 0.00 0.00 3.06
1780 2106 0.524862 GCACCAAGGAGCAGTTGATG 59.475 55.000 3.56 0.00 0.00 3.07
1944 2270 0.976641 AGATGCTCCTTTGTCGGTGA 59.023 50.000 0.00 0.00 0.00 4.02
1946 2272 1.072331 ACAAGATGCTCCTTTGTCGGT 59.928 47.619 0.00 0.00 0.00 4.69
2160 2488 2.025699 GGTACCTAATTCCAACTGCCCA 60.026 50.000 4.06 0.00 0.00 5.36
2161 2489 2.025699 TGGTACCTAATTCCAACTGCCC 60.026 50.000 14.36 0.00 0.00 5.36
2162 2490 3.359695 TGGTACCTAATTCCAACTGCC 57.640 47.619 14.36 0.00 0.00 4.85
2183 2511 5.813672 GCATGCTCAAAAATCACAATGGTAT 59.186 36.000 11.37 0.00 0.00 2.73
2184 2512 5.170021 GCATGCTCAAAAATCACAATGGTA 58.830 37.500 11.37 0.00 0.00 3.25
2185 2513 3.998341 GCATGCTCAAAAATCACAATGGT 59.002 39.130 11.37 0.00 0.00 3.55
2186 2514 3.061563 CGCATGCTCAAAAATCACAATGG 59.938 43.478 17.13 0.00 0.00 3.16
2187 2515 3.061563 CCGCATGCTCAAAAATCACAATG 59.938 43.478 17.13 0.00 0.00 2.82
2188 2516 3.056678 TCCGCATGCTCAAAAATCACAAT 60.057 39.130 17.13 0.00 0.00 2.71
2208 2536 8.228464 CGAAGTCCTAAGAAAATTTAAGTGTCC 58.772 37.037 0.00 0.00 0.00 4.02
2209 2537 8.771766 ACGAAGTCCTAAGAAAATTTAAGTGTC 58.228 33.333 0.00 0.00 29.74 3.67
2334 2665 1.792273 GCAAAACAGAACAACGTCGCA 60.792 47.619 0.00 0.00 0.00 5.10
2400 2731 1.407437 CCCACTCCTTCCACATGCTAC 60.407 57.143 0.00 0.00 0.00 3.58
2455 2786 2.099098 GTGATTAAACCGGCCATCCTTG 59.901 50.000 0.00 0.00 0.00 3.61
2521 2852 5.230936 CGAGTTAATCAGCACAGTGACATAG 59.769 44.000 4.15 0.00 0.00 2.23
2522 2853 5.102313 CGAGTTAATCAGCACAGTGACATA 58.898 41.667 4.15 0.00 0.00 2.29
2576 2907 4.622220 GCAGAGCCATTTGAATGTTCCAAT 60.622 41.667 3.30 0.00 34.60 3.16
2697 3033 7.330946 TGTTCAGTTTACATGGATAGAAACTCG 59.669 37.037 0.00 1.66 39.50 4.18
2706 3042 9.685276 TCTGAATATTGTTCAGTTTACATGGAT 57.315 29.630 18.93 0.00 44.58 3.41
2707 3043 9.685276 ATCTGAATATTGTTCAGTTTACATGGA 57.315 29.630 18.93 0.00 44.58 3.41
2760 3098 6.003859 TCCCTGTTAAAACAAACACTAGGA 57.996 37.500 0.00 0.00 38.66 2.94
2761 3099 6.702716 TTCCCTGTTAAAACAAACACTAGG 57.297 37.500 0.00 0.00 38.66 3.02
2816 3154 7.493320 AGCACAAATATGAAAATATGCAACTGG 59.507 33.333 0.00 0.00 0.00 4.00
2925 3267 1.961793 GGTATTCCGTGGCTAATGCA 58.038 50.000 0.00 0.00 41.91 3.96
3092 3438 0.536460 AGGGCGTTGTTAACCCACAG 60.536 55.000 2.48 0.00 46.88 3.66
3107 3453 4.072131 TGATTTTCAGTACACAAGAGGGC 58.928 43.478 0.00 0.00 0.00 5.19
3146 3501 4.336433 TGGCTCTAAACAATGCTGCTTATC 59.664 41.667 0.00 0.00 0.00 1.75
3148 3503 3.440173 GTGGCTCTAAACAATGCTGCTTA 59.560 43.478 0.00 0.00 0.00 3.09
3189 3550 6.447162 GCCCTGCAGTTTATTATGGAATAAC 58.553 40.000 13.81 0.00 42.43 1.89
3333 3694 8.967218 GTACATGCAATTTCGCAACATATATTT 58.033 29.630 0.00 0.00 46.87 1.40
3337 6709 6.135290 AGTACATGCAATTTCGCAACATAT 57.865 33.333 0.00 0.00 46.87 1.78
3456 6832 6.370453 GGAATGGAAAGGGGCTAATTAGTTA 58.630 40.000 13.91 0.00 0.00 2.24
3479 6858 2.845363 AAAAAGAATGCTGCAAGGGG 57.155 45.000 6.36 0.00 0.00 4.79
3503 6882 9.654663 GTTTTACTTACTGATCCATAGAACTGT 57.345 33.333 0.00 0.00 32.82 3.55
3589 6972 2.922740 TACGAGGAAAGCAACCAAGT 57.077 45.000 0.00 0.00 0.00 3.16
3594 6988 1.355971 TCGCATACGAGGAAAGCAAC 58.644 50.000 0.00 0.00 45.12 4.17
3595 6989 3.824621 TCGCATACGAGGAAAGCAA 57.175 47.368 0.00 0.00 45.12 3.91
3701 7096 5.093849 TCCCTACCACCTTCTTAAAATCG 57.906 43.478 0.00 0.00 0.00 3.34
3719 7114 2.023501 ACTCTCTGCTCACCTTATCCCT 60.024 50.000 0.00 0.00 0.00 4.20
3735 7130 8.819643 AAAGTAGAAACTTGTGTGATACTCTC 57.180 34.615 0.00 0.00 45.37 3.20
3762 7157 8.904099 AAACCAGCTTGGAACAGTATATATAC 57.096 34.615 14.05 14.05 40.96 1.47
3921 7677 5.686159 AGTGCTGTTCAGAAAAAGATGAG 57.314 39.130 3.84 0.00 0.00 2.90
3927 7683 7.561021 TGTATACAAGTGCTGTTCAGAAAAA 57.439 32.000 2.20 0.00 39.64 1.94
3987 8073 3.081804 CGTCTAGGGCCAGATTGTTTTT 58.918 45.455 6.18 0.00 0.00 1.94
4000 8086 3.192844 TCTTCAAACTGTAGCGTCTAGGG 59.807 47.826 0.00 0.00 0.00 3.53
4005 8091 5.652744 TTTCTTCTTCAAACTGTAGCGTC 57.347 39.130 0.00 0.00 0.00 5.19
4078 8167 2.104451 TGCCCGTTACCAACTTAACTGA 59.896 45.455 0.00 0.00 30.87 3.41
4127 8216 1.339929 ACCATCTTGCGGAACAAAACC 59.660 47.619 0.00 0.00 37.96 3.27
4209 8302 3.834231 ACCCTGCAGATTAGCAAAATGTT 59.166 39.130 17.39 0.00 45.13 2.71
4324 8447 3.245300 ACAGAGAGTGAGTAAGGGCAGTA 60.245 47.826 0.00 0.00 0.00 2.74
4325 8448 2.175202 CAGAGAGTGAGTAAGGGCAGT 58.825 52.381 0.00 0.00 0.00 4.40
4326 8449 2.175202 ACAGAGAGTGAGTAAGGGCAG 58.825 52.381 0.00 0.00 0.00 4.85
4327 8450 2.310779 ACAGAGAGTGAGTAAGGGCA 57.689 50.000 0.00 0.00 0.00 5.36
4329 8452 3.445805 GGAGAACAGAGAGTGAGTAAGGG 59.554 52.174 0.00 0.00 0.00 3.95
4330 8453 3.445805 GGGAGAACAGAGAGTGAGTAAGG 59.554 52.174 0.00 0.00 0.00 2.69
4331 8454 4.157656 CAGGGAGAACAGAGAGTGAGTAAG 59.842 50.000 0.00 0.00 0.00 2.34
4558 9529 5.396772 CCTCAAGATGCTTACCAGTATCCAA 60.397 44.000 0.00 0.00 41.81 3.53
4642 9614 8.980481 AGATCTTCACCGACCATAATTTAAAT 57.020 30.769 0.00 0.00 0.00 1.40
4643 9615 9.893634 TTAGATCTTCACCGACCATAATTTAAA 57.106 29.630 0.00 0.00 0.00 1.52
4645 9617 9.489084 CATTAGATCTTCACCGACCATAATTTA 57.511 33.333 0.00 0.00 0.00 1.40
4646 9618 8.210946 TCATTAGATCTTCACCGACCATAATTT 58.789 33.333 0.00 0.00 0.00 1.82
4647 9619 7.657761 GTCATTAGATCTTCACCGACCATAATT 59.342 37.037 0.00 0.00 0.00 1.40
4648 9620 7.015682 AGTCATTAGATCTTCACCGACCATAAT 59.984 37.037 0.00 0.00 0.00 1.28
4649 9621 6.323996 AGTCATTAGATCTTCACCGACCATAA 59.676 38.462 0.00 0.00 0.00 1.90
4650 9622 5.833667 AGTCATTAGATCTTCACCGACCATA 59.166 40.000 0.00 0.00 0.00 2.74
4651 9623 4.651503 AGTCATTAGATCTTCACCGACCAT 59.348 41.667 0.00 0.00 0.00 3.55
4652 9624 4.023980 AGTCATTAGATCTTCACCGACCA 58.976 43.478 0.00 0.00 0.00 4.02
4653 9625 4.098044 TCAGTCATTAGATCTTCACCGACC 59.902 45.833 0.00 0.00 0.00 4.79
4654 9626 5.250235 TCAGTCATTAGATCTTCACCGAC 57.750 43.478 0.00 1.60 0.00 4.79
4655 9627 5.278022 CGATCAGTCATTAGATCTTCACCGA 60.278 44.000 0.00 0.00 38.75 4.69
4656 9628 4.914504 CGATCAGTCATTAGATCTTCACCG 59.085 45.833 0.00 0.00 38.75 4.94
4657 9629 6.078202 TCGATCAGTCATTAGATCTTCACC 57.922 41.667 0.00 0.00 38.75 4.02
4658 9630 7.489435 TGTTTCGATCAGTCATTAGATCTTCAC 59.511 37.037 0.00 0.00 38.75 3.18
4659 9631 7.547227 TGTTTCGATCAGTCATTAGATCTTCA 58.453 34.615 0.00 0.00 38.75 3.02
4660 9632 7.993821 TGTTTCGATCAGTCATTAGATCTTC 57.006 36.000 0.00 0.00 38.75 2.87
4661 9633 8.586570 GATGTTTCGATCAGTCATTAGATCTT 57.413 34.615 0.00 0.00 38.75 2.40
4829 9808 0.865111 CATGGACGCGTCAGTTCAAA 59.135 50.000 37.26 15.46 32.66 2.69
4936 9915 8.488979 AGAAACATTTTACGATGTCGAAAAAG 57.511 30.769 9.67 10.28 39.25 2.27
5159 10139 0.329596 CAACCTTAGCAGAAGGCCCT 59.670 55.000 15.45 0.00 46.50 5.19
5180 10160 1.517257 CGCTGGTCGTCTCACCATC 60.517 63.158 0.00 0.00 45.76 3.51
5318 10298 8.562892 AGAACTATTTGCATAATGATAGCACAC 58.437 33.333 0.00 0.00 38.11 3.82
5406 10392 1.877576 TAGGCACTGACGCTGTGAGG 61.878 60.000 16.67 0.00 41.52 3.86
5462 10448 8.941977 TGAGTTAATAAAAGCGCTCTTTATTGA 58.058 29.630 32.53 27.84 41.40 2.57
5463 10449 9.554724 TTGAGTTAATAAAAGCGCTCTTTATTG 57.445 29.630 32.53 0.00 41.40 1.90
5568 10608 9.760077 CGGTCCTATATATGACTTTACTTTTGT 57.240 33.333 15.20 0.00 0.00 2.83
5587 10627 4.284178 ACTTAGGCATAGTTTCGGTCCTA 58.716 43.478 0.00 0.00 0.00 2.94
5588 10628 3.105283 ACTTAGGCATAGTTTCGGTCCT 58.895 45.455 0.00 0.00 0.00 3.85
5589 10629 3.455327 GACTTAGGCATAGTTTCGGTCC 58.545 50.000 0.00 0.00 0.00 4.46
5628 10669 3.902881 TGGCGGCATAATTTTTGGATT 57.097 38.095 7.97 0.00 0.00 3.01
5633 10674 3.134442 ACATGGATGGCGGCATAATTTTT 59.866 39.130 25.86 0.46 0.00 1.94
5636 10677 1.999648 ACATGGATGGCGGCATAATT 58.000 45.000 25.86 9.27 0.00 1.40
5688 10729 0.462375 TCAAGGCGGCGTGTATACAT 59.538 50.000 23.04 0.00 0.00 2.29
5689 10730 0.246910 TTCAAGGCGGCGTGTATACA 59.753 50.000 23.04 0.08 0.00 2.29
5698 10739 1.139163 CAATTGTTGTTCAAGGCGGC 58.861 50.000 0.00 0.00 39.55 6.53
5743 10784 2.465860 ATGCACTGGCTTTGTACGTA 57.534 45.000 0.00 0.00 41.91 3.57
5750 10791 2.806434 TCCATTGTATGCACTGGCTTT 58.194 42.857 14.29 0.00 42.93 3.51
5786 10827 4.464069 TTTGTTTTTACTGCACTGGCTT 57.536 36.364 0.00 0.00 41.91 4.35
5789 10830 7.481275 AATGATTTTGTTTTTACTGCACTGG 57.519 32.000 0.00 0.00 0.00 4.00
5790 10831 8.819974 AGAAATGATTTTGTTTTTACTGCACTG 58.180 29.630 0.00 0.00 0.00 3.66
5829 10876 3.391296 GAGCCTCCACCTTATTATGGTCA 59.609 47.826 0.00 0.00 37.27 4.02
5843 10890 2.212752 AATAAGGATGGGAGCCTCCA 57.787 50.000 13.90 0.00 38.64 3.86
5847 10894 1.697982 ACGGTAATAAGGATGGGAGCC 59.302 52.381 0.00 0.00 0.00 4.70
5896 10943 7.116075 AGTGTTGCCAATATTTATGGTCACTA 58.884 34.615 13.74 0.00 40.66 2.74
5954 11001 0.031314 ACGCTCTACATGATCAGCCG 59.969 55.000 0.00 2.87 0.00 5.52
5961 11008 1.177401 AGTCTGCACGCTCTACATGA 58.823 50.000 0.00 0.00 0.00 3.07
6080 11127 9.588096 AAGATTTCACTAAAAGTCCAGGTTATT 57.412 29.630 0.00 0.00 0.00 1.40
6081 11128 9.232473 GAAGATTTCACTAAAAGTCCAGGTTAT 57.768 33.333 0.00 0.00 0.00 1.89
6082 11129 7.386848 CGAAGATTTCACTAAAAGTCCAGGTTA 59.613 37.037 0.00 0.00 0.00 2.85
6083 11130 6.204882 CGAAGATTTCACTAAAAGTCCAGGTT 59.795 38.462 0.00 0.00 0.00 3.50
6084 11131 5.701290 CGAAGATTTCACTAAAAGTCCAGGT 59.299 40.000 0.00 0.00 0.00 4.00
6085 11132 5.932303 TCGAAGATTTCACTAAAAGTCCAGG 59.068 40.000 0.00 0.00 0.00 4.45
6089 11136 8.504005 TGGAAATCGAAGATTTCACTAAAAGTC 58.496 33.333 26.66 13.12 45.12 3.01
6134 11181 8.238631 GCACTTACGTTTTTAAAGATCCCAATA 58.761 33.333 0.00 0.00 0.00 1.90
6145 11192 6.615264 TGTACCATGCACTTACGTTTTTAA 57.385 33.333 0.00 0.00 0.00 1.52
6147 11194 5.699097 ATGTACCATGCACTTACGTTTTT 57.301 34.783 0.00 0.00 0.00 1.94
6150 11197 5.105473 ACTCTATGTACCATGCACTTACGTT 60.105 40.000 0.00 0.00 0.00 3.99
6151 11198 4.401519 ACTCTATGTACCATGCACTTACGT 59.598 41.667 0.00 0.00 0.00 3.57
6224 11271 8.623903 GCTCAAATACCATCTGAATTGTGATTA 58.376 33.333 0.00 0.00 0.00 1.75
6225 11272 7.417116 GGCTCAAATACCATCTGAATTGTGATT 60.417 37.037 0.00 0.00 0.00 2.57
6226 11273 6.040166 GGCTCAAATACCATCTGAATTGTGAT 59.960 38.462 0.00 0.00 0.00 3.06
6227 11274 5.357878 GGCTCAAATACCATCTGAATTGTGA 59.642 40.000 0.00 0.00 0.00 3.58
6228 11275 5.359009 AGGCTCAAATACCATCTGAATTGTG 59.641 40.000 0.00 0.00 0.00 3.33
6229 11276 5.513233 AGGCTCAAATACCATCTGAATTGT 58.487 37.500 0.00 0.00 0.00 2.71
6230 11277 6.461110 AAGGCTCAAATACCATCTGAATTG 57.539 37.500 0.00 0.00 0.00 2.32
6231 11278 6.894103 AGAAAGGCTCAAATACCATCTGAATT 59.106 34.615 0.00 0.00 0.00 2.17
6232 11279 6.430007 AGAAAGGCTCAAATACCATCTGAAT 58.570 36.000 0.00 0.00 0.00 2.57
6233 11280 5.819991 AGAAAGGCTCAAATACCATCTGAA 58.180 37.500 0.00 0.00 0.00 3.02
6234 11281 5.441718 AGAAAGGCTCAAATACCATCTGA 57.558 39.130 0.00 0.00 0.00 3.27
6235 11282 5.416952 ACAAGAAAGGCTCAAATACCATCTG 59.583 40.000 0.00 0.00 0.00 2.90
6236 11283 5.574188 ACAAGAAAGGCTCAAATACCATCT 58.426 37.500 0.00 0.00 0.00 2.90
6237 11284 5.904362 ACAAGAAAGGCTCAAATACCATC 57.096 39.130 0.00 0.00 0.00 3.51
6238 11285 5.539955 ACAACAAGAAAGGCTCAAATACCAT 59.460 36.000 0.00 0.00 0.00 3.55
6239 11286 4.892934 ACAACAAGAAAGGCTCAAATACCA 59.107 37.500 0.00 0.00 0.00 3.25
6240 11287 5.453567 ACAACAAGAAAGGCTCAAATACC 57.546 39.130 0.00 0.00 0.00 2.73
6270 11317 4.281435 TCACTGGCATTGTGAATTGTGATT 59.719 37.500 7.07 0.00 40.89 2.57
6309 11356 5.635417 AGAAGGAAAAAGATAACTGCTGC 57.365 39.130 0.00 0.00 0.00 5.25
6328 11375 9.791820 CATATATTGATTTTCAGTGCACAAGAA 57.208 29.630 21.04 18.96 0.00 2.52
6413 11460 1.202927 GGGCCCTGCAGCTTATTATGA 60.203 52.381 17.04 0.00 0.00 2.15
6422 11469 3.066814 CTTCTTGGGCCCTGCAGC 61.067 66.667 25.70 0.00 0.00 5.25


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

AutoCloner maintained by Alex Coulton.