Multiple sequence alignment - TraesCS4B01G235800

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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 TraesCS4B01G235800 chr4B 100.000 3503 0 0 1 3503 492226331 492222829 0.000000e+00 6469.0
1 TraesCS4B01G235800 chr4B 96.685 181 3 3 3199 3377 20487535 20487356 7.350000e-77 298.0
2 TraesCS4B01G235800 chr4A 93.525 3243 144 30 4 3212 56512216 56509006 0.000000e+00 4765.0
3 TraesCS4B01G235800 chr4A 98.214 56 1 0 3370 3425 56509011 56508956 8.000000e-17 99.0
4 TraesCS4B01G235800 chr4D 93.493 2797 105 31 458 3212 399190805 399188044 0.000000e+00 4085.0
5 TraesCS4B01G235800 chr4D 96.429 56 2 0 3370 3425 399188049 399187994 3.720000e-15 93.5
6 TraesCS4B01G235800 chr7A 84.211 817 84 34 125 918 60636478 60637272 0.000000e+00 752.0
7 TraesCS4B01G235800 chr7A 77.033 492 65 34 437 917 712087521 712087975 4.520000e-59 239.0
8 TraesCS4B01G235800 chr7A 100.000 82 0 0 3422 3503 642732931 642732850 6.060000e-33 152.0
9 TraesCS4B01G235800 chr7A 90.323 93 9 0 2781 2873 195397790 195397882 4.750000e-24 122.0
10 TraesCS4B01G235800 chr7A 88.679 53 5 1 866 917 468584078 468584130 2.920000e-06 63.9
11 TraesCS4B01G235800 chr2D 84.629 579 63 20 118 681 601985870 601986437 1.420000e-153 553.0
12 TraesCS4B01G235800 chr2D 91.579 95 7 1 2789 2883 61023708 61023801 2.840000e-26 130.0
13 TraesCS4B01G235800 chr5A 84.574 564 64 22 143 691 413890706 413891261 3.980000e-149 538.0
14 TraesCS4B01G235800 chr5A 79.211 760 100 36 149 886 123287533 123286810 3.160000e-130 475.0
15 TraesCS4B01G235800 chr1D 83.416 603 70 26 336 918 378734627 378734035 1.850000e-147 532.0
16 TraesCS4B01G235800 chr1D 96.629 178 5 1 3208 3384 403374992 403375169 9.510000e-76 294.0
17 TraesCS4B01G235800 chr1D 84.848 198 21 9 737 931 25677141 25676950 1.280000e-44 191.0
18 TraesCS4B01G235800 chr1D 96.591 88 3 0 3416 3503 43298893 43298806 2.820000e-31 147.0
19 TraesCS4B01G235800 chr7B 85.686 503 51 16 216 710 159030194 159029705 8.670000e-141 510.0
20 TraesCS4B01G235800 chr7B 91.304 92 8 0 2790 2881 51082135 51082044 3.670000e-25 126.0
21 TraesCS4B01G235800 chr7B 77.401 177 29 8 742 917 436701420 436701586 1.040000e-15 95.3
22 TraesCS4B01G235800 chr6D 84.190 525 57 19 407 917 311244472 311244984 1.460000e-133 486.0
23 TraesCS4B01G235800 chr7D 81.051 628 85 30 108 715 399450791 399451404 1.470000e-128 470.0
24 TraesCS4B01G235800 chr7D 93.182 88 4 1 2787 2874 407262108 407262193 1.020000e-25 128.0
25 TraesCS4B01G235800 chr3B 97.714 175 4 0 3198 3372 246303840 246304014 5.680000e-78 302.0
26 TraesCS4B01G235800 chr3B 96.591 176 6 0 3205 3380 631573593 631573768 3.420000e-75 292.0
27 TraesCS4B01G235800 chr3B 92.308 91 7 0 2785 2875 482487890 482487800 2.840000e-26 130.0
28 TraesCS4B01G235800 chr2B 98.817 169 2 0 3206 3374 237980466 237980298 5.680000e-78 302.0
29 TraesCS4B01G235800 chr2B 98.788 165 2 0 3208 3372 23589257 23589093 9.510000e-76 294.0
30 TraesCS4B01G235800 chr2B 79.521 459 58 23 255 682 676757278 676757731 9.510000e-76 294.0
31 TraesCS4B01G235800 chr2A 98.802 167 2 0 3208 3374 199082316 199082150 7.350000e-77 298.0
32 TraesCS4B01G235800 chr1A 97.126 174 5 0 3199 3372 554877232 554877405 9.510000e-76 294.0
33 TraesCS4B01G235800 chr1A 91.398 93 8 0 2783 2875 568391294 568391202 1.020000e-25 128.0
34 TraesCS4B01G235800 chr6B 97.126 174 4 1 3208 3381 18163055 18162883 3.420000e-75 292.0
35 TraesCS4B01G235800 chr6B 97.647 85 2 0 3419 3503 715773221 715773305 2.820000e-31 147.0
36 TraesCS4B01G235800 chr3D 81.229 293 39 12 628 918 367306593 367306871 4.550000e-54 222.0
37 TraesCS4B01G235800 chr3D 94.565 92 5 0 3412 3503 469375470 469375561 3.640000e-30 143.0
38 TraesCS4B01G235800 chr3D 90.526 95 9 0 2790 2884 389633215 389633121 3.670000e-25 126.0
39 TraesCS4B01G235800 chrUn 100.000 82 0 0 3422 3503 11031659 11031740 6.060000e-33 152.0
40 TraesCS4B01G235800 chr1B 98.824 85 1 0 3419 3503 98989872 98989956 6.060000e-33 152.0
41 TraesCS4B01G235800 chr1B 98.795 83 1 0 3421 3503 71638881 71638963 7.830000e-32 148.0
42 TraesCS4B01G235800 chr3A 95.506 89 4 0 3415 3503 126854220 126854132 3.640000e-30 143.0
43 TraesCS4B01G235800 chr6A 91.176 102 8 1 3402 3503 494467129 494467229 1.700000e-28 137.0


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 TraesCS4B01G235800 chr4B 492222829 492226331 3502 True 6469.00 6469 100.0000 1 3503 1 chr4B.!!$R2 3502
1 TraesCS4B01G235800 chr4A 56508956 56512216 3260 True 2432.00 4765 95.8695 4 3425 2 chr4A.!!$R1 3421
2 TraesCS4B01G235800 chr4D 399187994 399190805 2811 True 2089.25 4085 94.9610 458 3425 2 chr4D.!!$R1 2967
3 TraesCS4B01G235800 chr7A 60636478 60637272 794 False 752.00 752 84.2110 125 918 1 chr7A.!!$F1 793
4 TraesCS4B01G235800 chr2D 601985870 601986437 567 False 553.00 553 84.6290 118 681 1 chr2D.!!$F2 563
5 TraesCS4B01G235800 chr5A 413890706 413891261 555 False 538.00 538 84.5740 143 691 1 chr5A.!!$F1 548
6 TraesCS4B01G235800 chr5A 123286810 123287533 723 True 475.00 475 79.2110 149 886 1 chr5A.!!$R1 737
7 TraesCS4B01G235800 chr1D 378734035 378734627 592 True 532.00 532 83.4160 336 918 1 chr1D.!!$R3 582
8 TraesCS4B01G235800 chr6D 311244472 311244984 512 False 486.00 486 84.1900 407 917 1 chr6D.!!$F1 510
9 TraesCS4B01G235800 chr7D 399450791 399451404 613 False 470.00 470 81.0510 108 715 1 chr7D.!!$F1 607

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
73 74 0.542467 TAGGGTACGCAAGGTGTCCA 60.542 55.0 12.95 0.0 46.39 4.02 F
1812 2204 0.905337 AGGGTGAAGAGGGGAAGACG 60.905 60.0 0.00 0.0 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1974 2366 0.538287 GCACCCTCCAAAGCTCAAGT 60.538 55.000 0.0 0.0 0.00 3.16 R
3308 3725 1.131693 CACGTGACTACATACGGAGCA 59.868 52.381 10.9 0.0 44.07 4.26 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
30 31 1.832167 TTCAAGGTGGTGCAAGGGC 60.832 57.895 0.00 0.00 41.68 5.19
31 32 3.305516 CAAGGTGGTGCAAGGGCC 61.306 66.667 0.00 0.00 40.13 5.80
70 71 1.262640 CCCTAGGGTACGCAAGGTGT 61.263 60.000 20.88 0.00 46.39 4.16
73 74 0.542467 TAGGGTACGCAAGGTGTCCA 60.542 55.000 12.95 0.00 46.39 4.02
85 86 2.203862 TGTCCATGTGGTCCCCGA 60.204 61.111 0.00 0.00 36.34 5.14
102 103 2.757917 AGCAGGTCCTCTCGAGCC 60.758 66.667 7.81 2.77 40.01 4.70
103 104 4.200283 GCAGGTCCTCTCGAGCCG 62.200 72.222 7.81 0.69 40.01 5.52
104 105 3.522731 CAGGTCCTCTCGAGCCGG 61.523 72.222 7.81 10.84 40.01 6.13
105 106 4.824515 AGGTCCTCTCGAGCCGGG 62.825 72.222 7.81 9.87 40.01 5.73
108 109 4.377760 TCCTCTCGAGCCGGGGTT 62.378 66.667 7.81 0.00 0.00 4.11
109 110 3.391382 CCTCTCGAGCCGGGGTTT 61.391 66.667 7.81 0.00 0.00 3.27
110 111 2.663196 CTCTCGAGCCGGGGTTTT 59.337 61.111 7.81 0.00 0.00 2.43
112 113 1.889530 CTCTCGAGCCGGGGTTTTCT 61.890 60.000 7.81 0.00 0.00 2.52
126 127 5.064198 CGGGGTTTTCTTTTGTTTTTCCTTC 59.936 40.000 0.00 0.00 0.00 3.46
302 321 8.973835 TGTTTTCGTTTTCACTCTACATTTTT 57.026 26.923 0.00 0.00 0.00 1.94
445 466 9.645059 TCAACATTTTCAAATACTTGTTCAACA 57.355 25.926 0.00 0.00 33.94 3.33
565 759 8.722342 TTGTTCAACATTTTTCTAATACTCGC 57.278 30.769 0.00 0.00 0.00 5.03
567 761 8.564574 TGTTCAACATTTTTCTAATACTCGCTT 58.435 29.630 0.00 0.00 0.00 4.68
810 1188 6.406370 ACAAGAACAGGAAAAAGGAAAAAGG 58.594 36.000 0.00 0.00 0.00 3.11
856 1234 4.864334 CTGGGCCGGTCCATCTGC 62.864 72.222 31.80 0.00 36.05 4.26
929 1309 4.351054 CGCCCCATGCCTATCCCC 62.351 72.222 0.00 0.00 36.24 4.81
931 1311 3.650950 CCCCATGCCTATCCCCCG 61.651 72.222 0.00 0.00 0.00 5.73
1276 1668 3.070018 GCAGAGTTATTATCGCAGCCAT 58.930 45.455 0.00 0.00 0.00 4.40
1299 1691 0.912486 CTCCTGAAATCCTTCCCCGT 59.088 55.000 0.00 0.00 0.00 5.28
1420 1812 1.734477 CAGCCTGTCTGTTCGTCGG 60.734 63.158 0.00 0.00 38.02 4.79
1623 2015 4.564110 GGGGGCGCAGATGGTACC 62.564 72.222 10.83 4.43 0.00 3.34
1645 2037 0.969149 TATCCATCGCCTAGCTGTGG 59.031 55.000 0.00 0.00 0.00 4.17
1812 2204 0.905337 AGGGTGAAGAGGGGAAGACG 60.905 60.000 0.00 0.00 0.00 4.18
1974 2366 3.449018 GTGCAACAGAGGAGAAGGAGATA 59.551 47.826 0.00 0.00 36.32 1.98
2043 2435 6.604396 TGATGATATCTTTGTGCCAACTCAAT 59.396 34.615 3.98 0.00 0.00 2.57
2058 2450 2.916703 AATGGGTTGCGCTTGCCA 60.917 55.556 9.73 0.00 38.03 4.92
2475 2867 1.327303 TCTCGCCCAACTGCAATTTT 58.673 45.000 0.00 0.00 0.00 1.82
2633 3025 5.651530 TCAGATCCTATGTCTTGTCGTTTC 58.348 41.667 0.00 0.00 0.00 2.78
2780 3191 2.234143 TCGGTATCAGCTCTCATCTGG 58.766 52.381 0.00 0.00 32.63 3.86
2826 3237 8.902540 TCCATATTAATTGTCGCTGATTTAGT 57.097 30.769 0.00 0.00 0.00 2.24
2853 3264 7.700656 ACAAAGTTGTACTAAATCAGCAACAAC 59.299 33.333 7.81 7.81 45.77 3.32
3209 3626 8.662141 TCAAGCTATCCTCGTTTTATTTTGTAC 58.338 33.333 0.00 0.00 0.00 2.90
3210 3627 8.665685 CAAGCTATCCTCGTTTTATTTTGTACT 58.334 33.333 0.00 0.00 0.00 2.73
3211 3628 8.421673 AGCTATCCTCGTTTTATTTTGTACTC 57.578 34.615 0.00 0.00 0.00 2.59
3212 3629 7.494952 AGCTATCCTCGTTTTATTTTGTACTCC 59.505 37.037 0.00 0.00 0.00 3.85
3213 3630 6.997239 ATCCTCGTTTTATTTTGTACTCCC 57.003 37.500 0.00 0.00 0.00 4.30
3214 3631 6.117975 TCCTCGTTTTATTTTGTACTCCCT 57.882 37.500 0.00 0.00 0.00 4.20
3215 3632 6.168389 TCCTCGTTTTATTTTGTACTCCCTC 58.832 40.000 0.00 0.00 0.00 4.30
3216 3633 5.353400 CCTCGTTTTATTTTGTACTCCCTCC 59.647 44.000 0.00 0.00 0.00 4.30
3217 3634 4.931002 TCGTTTTATTTTGTACTCCCTCCG 59.069 41.667 0.00 0.00 0.00 4.63
3218 3635 4.692155 CGTTTTATTTTGTACTCCCTCCGT 59.308 41.667 0.00 0.00 0.00 4.69
3219 3636 5.179929 CGTTTTATTTTGTACTCCCTCCGTT 59.820 40.000 0.00 0.00 0.00 4.44
3220 3637 6.605849 GTTTTATTTTGTACTCCCTCCGTTC 58.394 40.000 0.00 0.00 0.00 3.95
3221 3638 2.845363 TTTTGTACTCCCTCCGTTCC 57.155 50.000 0.00 0.00 0.00 3.62
3222 3639 0.978907 TTTGTACTCCCTCCGTTCCC 59.021 55.000 0.00 0.00 0.00 3.97
3223 3640 0.178926 TTGTACTCCCTCCGTTCCCA 60.179 55.000 0.00 0.00 0.00 4.37
3224 3641 0.178926 TGTACTCCCTCCGTTCCCAA 60.179 55.000 0.00 0.00 0.00 4.12
3225 3642 0.978907 GTACTCCCTCCGTTCCCAAA 59.021 55.000 0.00 0.00 0.00 3.28
3226 3643 1.558294 GTACTCCCTCCGTTCCCAAAT 59.442 52.381 0.00 0.00 0.00 2.32
3227 3644 1.961133 ACTCCCTCCGTTCCCAAATA 58.039 50.000 0.00 0.00 0.00 1.40
3228 3645 2.271777 ACTCCCTCCGTTCCCAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
3229 3646 2.850568 ACTCCCTCCGTTCCCAAATAAT 59.149 45.455 0.00 0.00 0.00 1.28
3230 3647 3.268595 ACTCCCTCCGTTCCCAAATAATT 59.731 43.478 0.00 0.00 0.00 1.40
3231 3648 3.626930 TCCCTCCGTTCCCAAATAATTG 58.373 45.455 0.00 0.00 36.25 2.32
3232 3649 3.010808 TCCCTCCGTTCCCAAATAATTGT 59.989 43.478 0.00 0.00 34.60 2.71
3233 3650 3.380320 CCCTCCGTTCCCAAATAATTGTC 59.620 47.826 0.00 0.00 34.60 3.18
3234 3651 4.270008 CCTCCGTTCCCAAATAATTGTCT 58.730 43.478 0.00 0.00 34.60 3.41
3235 3652 4.705023 CCTCCGTTCCCAAATAATTGTCTT 59.295 41.667 0.00 0.00 34.60 3.01
3236 3653 5.185056 CCTCCGTTCCCAAATAATTGTCTTT 59.815 40.000 0.00 0.00 34.60 2.52
3237 3654 6.262193 TCCGTTCCCAAATAATTGTCTTTC 57.738 37.500 0.00 0.00 34.60 2.62
3238 3655 6.007703 TCCGTTCCCAAATAATTGTCTTTCT 58.992 36.000 0.00 0.00 34.60 2.52
3239 3656 7.169591 TCCGTTCCCAAATAATTGTCTTTCTA 58.830 34.615 0.00 0.00 34.60 2.10
3240 3657 7.335924 TCCGTTCCCAAATAATTGTCTTTCTAG 59.664 37.037 0.00 0.00 34.60 2.43
3241 3658 6.967199 CGTTCCCAAATAATTGTCTTTCTAGC 59.033 38.462 0.00 0.00 34.60 3.42
3242 3659 7.258441 GTTCCCAAATAATTGTCTTTCTAGCC 58.742 38.462 0.00 0.00 34.60 3.93
3243 3660 6.489603 TCCCAAATAATTGTCTTTCTAGCCA 58.510 36.000 0.00 0.00 34.60 4.75
3244 3661 7.125391 TCCCAAATAATTGTCTTTCTAGCCAT 58.875 34.615 0.00 0.00 34.60 4.40
3245 3662 7.285401 TCCCAAATAATTGTCTTTCTAGCCATC 59.715 37.037 0.00 0.00 34.60 3.51
3246 3663 7.286316 CCCAAATAATTGTCTTTCTAGCCATCT 59.714 37.037 0.00 0.00 34.60 2.90
3247 3664 8.348507 CCAAATAATTGTCTTTCTAGCCATCTC 58.651 37.037 0.00 0.00 34.60 2.75
3248 3665 8.896744 CAAATAATTGTCTTTCTAGCCATCTCA 58.103 33.333 0.00 0.00 0.00 3.27
3249 3666 9.466497 AAATAATTGTCTTTCTAGCCATCTCAA 57.534 29.630 0.00 0.00 0.00 3.02
3250 3667 9.466497 AATAATTGTCTTTCTAGCCATCTCAAA 57.534 29.630 0.00 0.00 0.00 2.69
3251 3668 7.951347 AATTGTCTTTCTAGCCATCTCAAAT 57.049 32.000 0.00 0.00 0.00 2.32
3252 3669 6.748333 TTGTCTTTCTAGCCATCTCAAATG 57.252 37.500 0.00 0.00 0.00 2.32
3253 3670 5.188434 TGTCTTTCTAGCCATCTCAAATGG 58.812 41.667 0.00 0.00 41.99 3.16
3254 3671 5.045651 TGTCTTTCTAGCCATCTCAAATGGA 60.046 40.000 8.23 0.00 41.64 3.41
3255 3672 5.295540 GTCTTTCTAGCCATCTCAAATGGAC 59.704 44.000 8.23 0.19 41.64 4.02
3256 3673 5.190528 TCTTTCTAGCCATCTCAAATGGACT 59.809 40.000 8.23 7.12 41.64 3.85
3257 3674 6.384015 TCTTTCTAGCCATCTCAAATGGACTA 59.616 38.462 8.23 7.79 41.64 2.59
3258 3675 5.537300 TCTAGCCATCTCAAATGGACTAC 57.463 43.478 8.23 0.00 41.64 2.73
3259 3676 4.962362 TCTAGCCATCTCAAATGGACTACA 59.038 41.667 8.23 0.00 41.64 2.74
3260 3677 4.574674 AGCCATCTCAAATGGACTACAA 57.425 40.909 8.23 0.00 41.64 2.41
3261 3678 4.265073 AGCCATCTCAAATGGACTACAAC 58.735 43.478 8.23 0.00 41.64 3.32
3262 3679 4.009675 GCCATCTCAAATGGACTACAACA 58.990 43.478 8.23 0.00 41.64 3.33
3263 3680 4.641989 GCCATCTCAAATGGACTACAACAT 59.358 41.667 8.23 0.00 41.64 2.71
3264 3681 5.822519 GCCATCTCAAATGGACTACAACATA 59.177 40.000 8.23 0.00 41.64 2.29
3265 3682 6.238484 GCCATCTCAAATGGACTACAACATAC 60.238 42.308 8.23 0.00 41.64 2.39
3266 3683 6.018751 CCATCTCAAATGGACTACAACATACG 60.019 42.308 0.00 0.00 41.64 3.06
3267 3684 5.416083 TCTCAAATGGACTACAACATACGG 58.584 41.667 0.00 0.00 0.00 4.02
3268 3685 5.186215 TCTCAAATGGACTACAACATACGGA 59.814 40.000 0.00 0.00 0.00 4.69
3269 3686 5.984725 TCAAATGGACTACAACATACGGAT 58.015 37.500 0.00 0.00 0.00 4.18
3270 3687 5.815222 TCAAATGGACTACAACATACGGATG 59.185 40.000 5.94 5.94 39.16 3.51
3272 3689 6.474140 AATGGACTACAACATACGGATGTA 57.526 37.500 15.10 0.00 45.93 2.29
3273 3690 6.665992 ATGGACTACAACATACGGATGTAT 57.334 37.500 15.10 8.21 45.93 2.29
3288 3705 9.692749 ATACGGATGTATGTAGACATGTTTTAG 57.307 33.333 0.00 0.00 40.18 1.85
3289 3706 7.778083 ACGGATGTATGTAGACATGTTTTAGA 58.222 34.615 0.00 0.00 40.18 2.10
3290 3707 7.921214 ACGGATGTATGTAGACATGTTTTAGAG 59.079 37.037 0.00 0.00 40.18 2.43
3291 3708 7.921214 CGGATGTATGTAGACATGTTTTAGAGT 59.079 37.037 0.00 0.00 40.18 3.24
3292 3709 9.035607 GGATGTATGTAGACATGTTTTAGAGTG 57.964 37.037 0.00 0.00 40.18 3.51
3293 3710 9.587772 GATGTATGTAGACATGTTTTAGAGTGT 57.412 33.333 0.00 0.00 40.18 3.55
3299 3716 9.856488 TGTAGACATGTTTTAGAGTGTAGATTC 57.144 33.333 0.00 0.00 0.00 2.52
3300 3717 9.856488 GTAGACATGTTTTAGAGTGTAGATTCA 57.144 33.333 0.00 0.00 0.00 2.57
3301 3718 8.764524 AGACATGTTTTAGAGTGTAGATTCAC 57.235 34.615 0.00 0.00 38.46 3.18
3312 3729 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
3313 3730 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
3314 3731 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
3315 3732 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
3316 3733 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
3317 3734 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
3318 3735 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
3319 3736 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
3320 3737 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
3321 3738 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
3322 3739 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
3323 3740 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
3324 3741 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
3325 3742 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
3326 3743 2.554806 TTGCTCCGTATGTAGTCACG 57.445 50.000 0.00 0.00 37.89 4.35
3327 3744 1.456296 TGCTCCGTATGTAGTCACGT 58.544 50.000 0.00 0.00 36.44 4.49
3328 3745 1.131693 TGCTCCGTATGTAGTCACGTG 59.868 52.381 9.94 9.94 36.44 4.49
3329 3746 1.131883 GCTCCGTATGTAGTCACGTGT 59.868 52.381 16.51 0.00 36.44 4.49
3330 3747 2.415090 GCTCCGTATGTAGTCACGTGTT 60.415 50.000 16.51 7.97 36.44 3.32
3331 3748 3.168963 CTCCGTATGTAGTCACGTGTTG 58.831 50.000 16.51 0.00 36.44 3.33
3332 3749 2.813172 TCCGTATGTAGTCACGTGTTGA 59.187 45.455 16.51 0.00 36.44 3.18
3333 3750 3.252944 TCCGTATGTAGTCACGTGTTGAA 59.747 43.478 16.51 0.00 35.39 2.69
3334 3751 3.982701 CCGTATGTAGTCACGTGTTGAAA 59.017 43.478 16.51 0.31 35.39 2.69
3335 3752 4.624024 CCGTATGTAGTCACGTGTTGAAAT 59.376 41.667 16.51 8.06 35.39 2.17
3336 3753 5.220154 CCGTATGTAGTCACGTGTTGAAATC 60.220 44.000 16.51 2.15 35.39 2.17
3337 3754 5.571741 CGTATGTAGTCACGTGTTGAAATCT 59.428 40.000 16.51 6.52 35.39 2.40
3338 3755 6.237227 CGTATGTAGTCACGTGTTGAAATCTC 60.237 42.308 16.51 0.56 35.39 2.75
3339 3756 5.196341 TGTAGTCACGTGTTGAAATCTCT 57.804 39.130 16.51 4.33 35.39 3.10
3340 3757 6.321848 TGTAGTCACGTGTTGAAATCTCTA 57.678 37.500 16.51 3.48 35.39 2.43
3341 3758 6.379386 TGTAGTCACGTGTTGAAATCTCTAG 58.621 40.000 16.51 0.00 35.39 2.43
3342 3759 5.707242 AGTCACGTGTTGAAATCTCTAGA 57.293 39.130 16.51 0.00 35.39 2.43
3343 3760 6.085555 AGTCACGTGTTGAAATCTCTAGAA 57.914 37.500 16.51 0.00 35.39 2.10
3344 3761 6.513180 AGTCACGTGTTGAAATCTCTAGAAA 58.487 36.000 16.51 0.00 35.39 2.52
3345 3762 6.642950 AGTCACGTGTTGAAATCTCTAGAAAG 59.357 38.462 16.51 0.00 35.39 2.62
3346 3763 6.641314 GTCACGTGTTGAAATCTCTAGAAAGA 59.359 38.462 16.51 0.00 35.39 2.52
3347 3764 6.641314 TCACGTGTTGAAATCTCTAGAAAGAC 59.359 38.462 16.51 0.00 0.00 3.01
3348 3765 6.420903 CACGTGTTGAAATCTCTAGAAAGACA 59.579 38.462 7.58 0.00 0.00 3.41
3349 3766 6.984474 ACGTGTTGAAATCTCTAGAAAGACAA 59.016 34.615 0.00 0.00 0.00 3.18
3350 3767 7.657761 ACGTGTTGAAATCTCTAGAAAGACAAT 59.342 33.333 0.00 0.00 0.00 2.71
3351 3768 8.499162 CGTGTTGAAATCTCTAGAAAGACAATT 58.501 33.333 0.00 0.00 0.00 2.32
3363 3780 9.595823 TCTAGAAAGACAATTATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
3364 3781 9.595823 CTAGAAAGACAATTATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
3365 3782 8.494016 AGAAAGACAATTATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
3366 3783 7.553044 AGAAAGACAATTATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
3367 3784 5.681639 AGACAATTATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
3368 3785 5.427481 AGACAATTATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
3369 3786 5.681639 ACAATTATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
3370 3787 5.191124 ACAATTATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
3371 3788 6.384886 ACAATTATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
3386 3803 7.177041 ACGGAGGGAGTATTCTATAAGTCAATC 59.823 40.741 0.00 0.00 0.00 2.67
3425 3842 2.795231 ATGCAATGCTGTCAGGTACT 57.205 45.000 6.82 0.00 43.88 2.73
3426 3843 2.099141 TGCAATGCTGTCAGGTACTC 57.901 50.000 6.82 0.00 34.60 2.59
3427 3844 1.339055 TGCAATGCTGTCAGGTACTCC 60.339 52.381 6.82 0.00 34.60 3.85
3428 3845 2.014068 GCAATGCTGTCAGGTACTCCC 61.014 57.143 0.00 0.00 34.60 4.30
3430 3847 1.490574 ATGCTGTCAGGTACTCCCTC 58.509 55.000 1.14 0.00 43.86 4.30
3431 3848 0.614979 TGCTGTCAGGTACTCCCTCC 60.615 60.000 1.14 0.00 43.86 4.30
3432 3849 1.668101 GCTGTCAGGTACTCCCTCCG 61.668 65.000 1.14 0.00 43.86 4.63
3433 3850 0.323542 CTGTCAGGTACTCCCTCCGT 60.324 60.000 0.00 0.00 43.86 4.69
3434 3851 0.323178 TGTCAGGTACTCCCTCCGTC 60.323 60.000 0.00 0.00 43.86 4.79
3435 3852 1.036481 GTCAGGTACTCCCTCCGTCC 61.036 65.000 0.00 0.00 43.86 4.79
3436 3853 1.757340 CAGGTACTCCCTCCGTCCC 60.757 68.421 0.00 0.00 43.86 4.46
3437 3854 2.243888 AGGTACTCCCTCCGTCCCA 61.244 63.158 0.00 0.00 40.71 4.37
3438 3855 1.305549 GGTACTCCCTCCGTCCCAA 60.306 63.158 0.00 0.00 0.00 4.12
3439 3856 0.906282 GGTACTCCCTCCGTCCCAAA 60.906 60.000 0.00 0.00 0.00 3.28
3440 3857 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
3441 3858 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
3442 3859 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
3443 3860 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
3444 3861 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
3445 3862 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
3446 3863 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
3447 3864 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
3448 3865 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
3449 3866 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
3450 3867 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
3451 3868 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
3452 3869 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
3453 3870 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
3454 3871 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
3455 3872 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
3456 3873 7.335924 CCGTCCCAAAATTCTTGTCTTAGATTA 59.664 37.037 0.00 0.00 0.00 1.75
3457 3874 8.391106 CGTCCCAAAATTCTTGTCTTAGATTAG 58.609 37.037 0.00 0.00 0.00 1.73
3458 3875 9.232473 GTCCCAAAATTCTTGTCTTAGATTAGT 57.768 33.333 0.00 0.00 0.00 2.24
3459 3876 9.449719 TCCCAAAATTCTTGTCTTAGATTAGTC 57.550 33.333 0.00 0.00 0.00 2.59
3460 3877 9.454859 CCCAAAATTCTTGTCTTAGATTAGTCT 57.545 33.333 0.00 0.00 38.52 3.24
3468 3885 9.491675 TCTTGTCTTAGATTAGTCTAGATACGG 57.508 37.037 0.00 0.00 38.17 4.02
3469 3886 9.491675 CTTGTCTTAGATTAGTCTAGATACGGA 57.508 37.037 0.00 0.00 38.17 4.69
3471 3888 9.438228 TGTCTTAGATTAGTCTAGATACGGATG 57.562 37.037 0.00 0.00 38.17 3.51
3472 3889 9.439500 GTCTTAGATTAGTCTAGATACGGATGT 57.561 37.037 0.00 0.00 38.17 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.806542 CACCTTGAACCGATTCCACTG 59.193 52.381 0.00 0.00 33.49 3.66
1 2 1.271379 CCACCTTGAACCGATTCCACT 60.271 52.381 0.00 0.00 33.49 4.00
5 6 0.521735 GCACCACCTTGAACCGATTC 59.478 55.000 0.00 0.00 35.18 2.52
9 10 1.654220 CTTGCACCACCTTGAACCG 59.346 57.895 0.00 0.00 0.00 4.44
10 11 1.463553 CCCTTGCACCACCTTGAACC 61.464 60.000 0.00 0.00 0.00 3.62
11 12 2.041153 CCCTTGCACCACCTTGAAC 58.959 57.895 0.00 0.00 0.00 3.18
30 31 2.044650 CACCTGCTCATGTGGGGG 60.045 66.667 0.00 0.00 0.00 5.40
31 32 2.753043 GCACCTGCTCATGTGGGG 60.753 66.667 7.26 0.00 38.21 4.96
54 55 0.542467 TGGACACCTTGCGTACCCTA 60.542 55.000 0.00 0.00 0.00 3.53
55 56 1.198759 ATGGACACCTTGCGTACCCT 61.199 55.000 0.00 0.00 0.00 4.34
58 59 0.796312 CACATGGACACCTTGCGTAC 59.204 55.000 0.00 0.00 32.73 3.67
59 60 0.321210 CCACATGGACACCTTGCGTA 60.321 55.000 0.00 0.00 37.39 4.42
60 61 1.600636 CCACATGGACACCTTGCGT 60.601 57.895 0.00 0.00 37.39 5.24
61 62 1.577328 GACCACATGGACACCTTGCG 61.577 60.000 4.53 0.00 38.94 4.85
85 86 2.757917 GGCTCGAGAGGACCTGCT 60.758 66.667 18.75 0.00 0.00 4.24
100 101 2.319136 AAACAAAAGAAAACCCCGGC 57.681 45.000 0.00 0.00 0.00 6.13
102 103 4.509616 AGGAAAAACAAAAGAAAACCCCG 58.490 39.130 0.00 0.00 0.00 5.73
103 104 6.093495 CAGAAGGAAAAACAAAAGAAAACCCC 59.907 38.462 0.00 0.00 0.00 4.95
104 105 6.653320 ACAGAAGGAAAAACAAAAGAAAACCC 59.347 34.615 0.00 0.00 0.00 4.11
105 106 7.667043 ACAGAAGGAAAAACAAAAGAAAACC 57.333 32.000 0.00 0.00 0.00 3.27
106 107 9.594038 GAAACAGAAGGAAAAACAAAAGAAAAC 57.406 29.630 0.00 0.00 0.00 2.43
107 108 9.554395 AGAAACAGAAGGAAAAACAAAAGAAAA 57.446 25.926 0.00 0.00 0.00 2.29
108 109 9.554395 AAGAAACAGAAGGAAAAACAAAAGAAA 57.446 25.926 0.00 0.00 0.00 2.52
109 110 9.554395 AAAGAAACAGAAGGAAAAACAAAAGAA 57.446 25.926 0.00 0.00 0.00 2.52
110 111 9.554395 AAAAGAAACAGAAGGAAAAACAAAAGA 57.446 25.926 0.00 0.00 0.00 2.52
539 733 9.176181 GCGAGTATTAGAAAAATGTTGAACAAA 57.824 29.630 0.62 0.00 0.00 2.83
540 734 8.564574 AGCGAGTATTAGAAAAATGTTGAACAA 58.435 29.630 0.62 0.00 0.00 2.83
541 735 8.094798 AGCGAGTATTAGAAAAATGTTGAACA 57.905 30.769 0.00 0.00 0.00 3.18
542 736 8.950403 AAGCGAGTATTAGAAAAATGTTGAAC 57.050 30.769 0.00 0.00 0.00 3.18
545 739 9.820229 TGTTAAGCGAGTATTAGAAAAATGTTG 57.180 29.630 0.00 0.00 0.00 3.33
553 747 9.431887 ACTGAAATTGTTAAGCGAGTATTAGAA 57.568 29.630 0.00 0.00 0.00 2.10
920 1300 0.836400 TCAGGATTCGGGGGATAGGC 60.836 60.000 0.00 0.00 0.00 3.93
923 1303 3.178865 GGTATTCAGGATTCGGGGGATA 58.821 50.000 0.00 0.00 0.00 2.59
929 1309 1.000955 CGAGGGGTATTCAGGATTCGG 59.999 57.143 0.00 0.00 0.00 4.30
931 1311 1.605712 CGCGAGGGGTATTCAGGATTC 60.606 57.143 0.00 0.00 0.00 2.52
1080 1472 2.223803 AGGACTTCACATCGGAGAGT 57.776 50.000 0.00 0.00 43.63 3.24
1276 1668 0.541863 GGAAGGATTTCAGGAGGCGA 59.458 55.000 0.00 0.00 34.90 5.54
1299 1691 1.488390 CTGTAACCGGGCTAGGGTTA 58.512 55.000 6.32 10.03 45.65 2.85
1412 1804 2.452366 ATTTTGCGGCACCGACGAAC 62.452 55.000 14.43 0.00 42.83 3.95
1420 1812 2.919666 ATGTGTAGATTTTGCGGCAC 57.080 45.000 0.05 0.00 0.00 5.01
1623 2015 1.000163 ACAGCTAGGCGATGGATAACG 60.000 52.381 0.00 0.00 32.00 3.18
1812 2204 3.068024 TCAATGAGCAGTTCAAAACCACC 59.932 43.478 0.00 0.00 39.77 4.61
1943 2335 1.679139 CTCTGTTGCACCCACTTCAA 58.321 50.000 0.00 0.00 0.00 2.69
1974 2366 0.538287 GCACCCTCCAAAGCTCAAGT 60.538 55.000 0.00 0.00 0.00 3.16
2475 2867 2.669133 CCCTTGGCGATGACCCTCA 61.669 63.158 0.00 0.00 0.00 3.86
2611 3003 5.655488 AGAAACGACAAGACATAGGATCTG 58.345 41.667 0.00 0.00 0.00 2.90
2633 3025 4.058817 GTCATAGCAAGGAATAACCGGAG 58.941 47.826 9.46 0.00 44.74 4.63
2826 3237 8.439993 TGTTGCTGATTTAGTACAACTTTGTA 57.560 30.769 0.00 0.00 42.35 2.41
2853 3264 2.813907 ACTCCCTCCGATCCATATCAG 58.186 52.381 0.00 0.00 31.93 2.90
3042 3459 7.224297 ACAGTCCATTCTTGCTACTAAGAAAA 58.776 34.615 5.20 0.00 46.35 2.29
3139 3556 3.923017 AACTCAAAATGCCAGCAGTAC 57.077 42.857 0.00 0.00 0.00 2.73
3145 3562 4.853924 AGGTTGTAACTCAAAATGCCAG 57.146 40.909 0.00 0.00 37.81 4.85
3188 3605 7.985752 AGGGAGTACAAAATAAAACGAGGATAG 59.014 37.037 0.00 0.00 0.00 2.08
3209 3626 3.577805 ATTATTTGGGAACGGAGGGAG 57.422 47.619 0.00 0.00 0.00 4.30
3210 3627 3.010808 ACAATTATTTGGGAACGGAGGGA 59.989 43.478 2.66 0.00 37.15 4.20
3211 3628 3.361786 ACAATTATTTGGGAACGGAGGG 58.638 45.455 2.66 0.00 37.15 4.30
3212 3629 4.270008 AGACAATTATTTGGGAACGGAGG 58.730 43.478 2.66 0.00 37.15 4.30
3213 3630 5.897377 AAGACAATTATTTGGGAACGGAG 57.103 39.130 2.66 0.00 37.15 4.63
3214 3631 6.007703 AGAAAGACAATTATTTGGGAACGGA 58.992 36.000 2.66 0.00 37.15 4.69
3215 3632 6.267496 AGAAAGACAATTATTTGGGAACGG 57.733 37.500 2.66 0.00 37.15 4.44
3216 3633 6.967199 GCTAGAAAGACAATTATTTGGGAACG 59.033 38.462 0.00 0.00 37.15 3.95
3217 3634 7.093945 TGGCTAGAAAGACAATTATTTGGGAAC 60.094 37.037 0.00 0.00 38.01 3.62
3218 3635 6.951198 TGGCTAGAAAGACAATTATTTGGGAA 59.049 34.615 0.00 0.00 38.01 3.97
3219 3636 6.489603 TGGCTAGAAAGACAATTATTTGGGA 58.510 36.000 0.00 0.00 38.01 4.37
3220 3637 6.773976 TGGCTAGAAAGACAATTATTTGGG 57.226 37.500 0.00 0.00 38.01 4.12
3221 3638 8.230472 AGATGGCTAGAAAGACAATTATTTGG 57.770 34.615 0.00 0.00 46.32 3.28
3222 3639 8.896744 TGAGATGGCTAGAAAGACAATTATTTG 58.103 33.333 0.00 0.00 46.32 2.32
3223 3640 9.466497 TTGAGATGGCTAGAAAGACAATTATTT 57.534 29.630 0.00 0.00 46.32 1.40
3224 3641 9.466497 TTTGAGATGGCTAGAAAGACAATTATT 57.534 29.630 0.00 0.00 46.32 1.40
3225 3642 9.638176 ATTTGAGATGGCTAGAAAGACAATTAT 57.362 29.630 0.00 0.00 46.32 1.28
3226 3643 8.896744 CATTTGAGATGGCTAGAAAGACAATTA 58.103 33.333 0.00 0.00 46.32 1.40
3227 3644 7.147949 CCATTTGAGATGGCTAGAAAGACAATT 60.148 37.037 0.00 0.00 46.32 2.32
3228 3645 6.320672 CCATTTGAGATGGCTAGAAAGACAAT 59.679 38.462 0.00 0.00 46.32 2.71
3229 3646 5.649395 CCATTTGAGATGGCTAGAAAGACAA 59.351 40.000 0.00 0.00 46.32 3.18
3231 3648 5.295540 GTCCATTTGAGATGGCTAGAAAGAC 59.704 44.000 0.00 0.00 39.01 3.01
3232 3649 5.190528 AGTCCATTTGAGATGGCTAGAAAGA 59.809 40.000 0.00 0.00 39.01 2.52
3233 3650 5.435291 AGTCCATTTGAGATGGCTAGAAAG 58.565 41.667 0.00 0.00 39.01 2.62
3234 3651 5.441718 AGTCCATTTGAGATGGCTAGAAA 57.558 39.130 0.00 0.00 39.01 2.52
3235 3652 5.425217 TGTAGTCCATTTGAGATGGCTAGAA 59.575 40.000 0.00 0.00 39.01 2.10
3236 3653 4.962362 TGTAGTCCATTTGAGATGGCTAGA 59.038 41.667 0.00 0.00 39.01 2.43
3237 3654 5.282055 TGTAGTCCATTTGAGATGGCTAG 57.718 43.478 0.00 0.00 39.01 3.42
3238 3655 5.045942 TGTTGTAGTCCATTTGAGATGGCTA 60.046 40.000 0.00 0.33 39.01 3.93
3239 3656 4.263462 TGTTGTAGTCCATTTGAGATGGCT 60.263 41.667 0.00 1.24 39.01 4.75
3240 3657 4.009675 TGTTGTAGTCCATTTGAGATGGC 58.990 43.478 0.00 0.00 39.01 4.40
3241 3658 6.018751 CGTATGTTGTAGTCCATTTGAGATGG 60.019 42.308 0.00 0.00 40.48 3.51
3242 3659 6.018751 CCGTATGTTGTAGTCCATTTGAGATG 60.019 42.308 0.00 0.00 0.00 2.90
3243 3660 6.049149 CCGTATGTTGTAGTCCATTTGAGAT 58.951 40.000 0.00 0.00 0.00 2.75
3244 3661 5.186215 TCCGTATGTTGTAGTCCATTTGAGA 59.814 40.000 0.00 0.00 0.00 3.27
3245 3662 5.416083 TCCGTATGTTGTAGTCCATTTGAG 58.584 41.667 0.00 0.00 0.00 3.02
3246 3663 5.408880 TCCGTATGTTGTAGTCCATTTGA 57.591 39.130 0.00 0.00 0.00 2.69
3247 3664 5.584649 ACATCCGTATGTTGTAGTCCATTTG 59.415 40.000 0.00 0.00 44.07 2.32
3248 3665 5.741011 ACATCCGTATGTTGTAGTCCATTT 58.259 37.500 0.00 0.00 44.07 2.32
3249 3666 5.353394 ACATCCGTATGTTGTAGTCCATT 57.647 39.130 0.00 0.00 44.07 3.16
3250 3667 6.455647 CATACATCCGTATGTTGTAGTCCAT 58.544 40.000 0.00 0.00 46.70 3.41
3251 3668 5.838529 CATACATCCGTATGTTGTAGTCCA 58.161 41.667 0.00 0.00 46.70 4.02
3262 3679 9.692749 CTAAAACATGTCTACATACATCCGTAT 57.307 33.333 0.00 0.00 38.01 3.06
3263 3680 8.905850 TCTAAAACATGTCTACATACATCCGTA 58.094 33.333 0.00 0.00 38.01 4.02
3264 3681 7.778083 TCTAAAACATGTCTACATACATCCGT 58.222 34.615 0.00 0.00 38.01 4.69
3265 3682 7.921214 ACTCTAAAACATGTCTACATACATCCG 59.079 37.037 0.00 0.00 38.01 4.18
3266 3683 9.035607 CACTCTAAAACATGTCTACATACATCC 57.964 37.037 0.00 0.00 38.01 3.51
3267 3684 9.587772 ACACTCTAAAACATGTCTACATACATC 57.412 33.333 0.00 0.00 38.01 3.06
3273 3690 9.856488 GAATCTACACTCTAAAACATGTCTACA 57.144 33.333 0.00 0.00 0.00 2.74
3274 3691 9.856488 TGAATCTACACTCTAAAACATGTCTAC 57.144 33.333 0.00 0.00 0.00 2.59
3275 3692 9.856488 GTGAATCTACACTCTAAAACATGTCTA 57.144 33.333 0.00 0.00 37.73 2.59
3276 3693 8.589338 AGTGAATCTACACTCTAAAACATGTCT 58.411 33.333 0.00 0.00 46.36 3.41
3277 3694 8.764524 AGTGAATCTACACTCTAAAACATGTC 57.235 34.615 0.00 0.00 46.36 3.06
3290 3707 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
3291 3708 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
3292 3709 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
3293 3710 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
3294 3711 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
3295 3712 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
3296 3713 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
3297 3714 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
3298 3715 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
3299 3716 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
3300 3717 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
3301 3718 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
3302 3719 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
3303 3720 4.259810 CGTGACTACATACGGAGCAAAATG 60.260 45.833 0.00 0.00 36.71 2.32
3304 3721 3.863424 CGTGACTACATACGGAGCAAAAT 59.137 43.478 0.00 0.00 36.71 1.82
3305 3722 3.247442 CGTGACTACATACGGAGCAAAA 58.753 45.455 0.00 0.00 36.71 2.44
3306 3723 2.229543 ACGTGACTACATACGGAGCAAA 59.770 45.455 0.00 0.00 44.07 3.68
3307 3724 1.814394 ACGTGACTACATACGGAGCAA 59.186 47.619 0.00 0.00 44.07 3.91
3308 3725 1.131693 CACGTGACTACATACGGAGCA 59.868 52.381 10.90 0.00 44.07 4.26
3309 3726 1.131883 ACACGTGACTACATACGGAGC 59.868 52.381 25.01 0.00 44.07 4.70
3310 3727 3.120095 TCAACACGTGACTACATACGGAG 60.120 47.826 25.01 0.00 44.07 4.63
3311 3728 2.813172 TCAACACGTGACTACATACGGA 59.187 45.455 25.01 1.36 44.07 4.69
3312 3729 3.206034 TCAACACGTGACTACATACGG 57.794 47.619 25.01 0.00 44.07 4.02
3313 3730 5.571741 AGATTTCAACACGTGACTACATACG 59.428 40.000 25.01 0.00 45.19 3.06
3314 3731 6.807230 AGAGATTTCAACACGTGACTACATAC 59.193 38.462 25.01 7.12 35.39 2.39
3315 3732 6.920817 AGAGATTTCAACACGTGACTACATA 58.079 36.000 25.01 1.26 35.39 2.29
3316 3733 5.784177 AGAGATTTCAACACGTGACTACAT 58.216 37.500 25.01 8.26 35.39 2.29
3317 3734 5.196341 AGAGATTTCAACACGTGACTACA 57.804 39.130 25.01 3.09 35.39 2.74
3318 3735 6.609533 TCTAGAGATTTCAACACGTGACTAC 58.390 40.000 25.01 6.63 35.39 2.73
3319 3736 6.812879 TCTAGAGATTTCAACACGTGACTA 57.187 37.500 25.01 3.25 35.39 2.59
3320 3737 5.707242 TCTAGAGATTTCAACACGTGACT 57.293 39.130 25.01 5.75 35.39 3.41
3321 3738 6.641314 TCTTTCTAGAGATTTCAACACGTGAC 59.359 38.462 25.01 4.36 35.39 3.67
3322 3739 6.641314 GTCTTTCTAGAGATTTCAACACGTGA 59.359 38.462 25.01 0.00 0.00 4.35
3323 3740 6.420903 TGTCTTTCTAGAGATTTCAACACGTG 59.579 38.462 15.48 15.48 0.00 4.49
3324 3741 6.513180 TGTCTTTCTAGAGATTTCAACACGT 58.487 36.000 0.00 0.00 0.00 4.49
3325 3742 7.408132 TTGTCTTTCTAGAGATTTCAACACG 57.592 36.000 0.00 0.00 0.00 4.49
3337 3754 9.595823 CCGTTCCTAAATAATTGTCTTTCTAGA 57.404 33.333 0.00 0.00 0.00 2.43
3338 3755 9.595823 TCCGTTCCTAAATAATTGTCTTTCTAG 57.404 33.333 0.00 0.00 0.00 2.43
3339 3756 9.595823 CTCCGTTCCTAAATAATTGTCTTTCTA 57.404 33.333 0.00 0.00 0.00 2.10
3340 3757 7.553044 CCTCCGTTCCTAAATAATTGTCTTTCT 59.447 37.037 0.00 0.00 0.00 2.52
3341 3758 7.201705 CCCTCCGTTCCTAAATAATTGTCTTTC 60.202 40.741 0.00 0.00 0.00 2.62
3342 3759 6.602009 CCCTCCGTTCCTAAATAATTGTCTTT 59.398 38.462 0.00 0.00 0.00 2.52
3343 3760 6.069847 TCCCTCCGTTCCTAAATAATTGTCTT 60.070 38.462 0.00 0.00 0.00 3.01
3344 3761 5.427481 TCCCTCCGTTCCTAAATAATTGTCT 59.573 40.000 0.00 0.00 0.00 3.41
3345 3762 5.677567 TCCCTCCGTTCCTAAATAATTGTC 58.322 41.667 0.00 0.00 0.00 3.18
3346 3763 5.191124 ACTCCCTCCGTTCCTAAATAATTGT 59.809 40.000 0.00 0.00 0.00 2.71
3347 3764 5.681639 ACTCCCTCCGTTCCTAAATAATTG 58.318 41.667 0.00 0.00 0.00 2.32
3348 3765 5.970501 ACTCCCTCCGTTCCTAAATAATT 57.029 39.130 0.00 0.00 0.00 1.40
3349 3766 7.513091 AGAATACTCCCTCCGTTCCTAAATAAT 59.487 37.037 0.00 0.00 0.00 1.28
3350 3767 6.842807 AGAATACTCCCTCCGTTCCTAAATAA 59.157 38.462 0.00 0.00 0.00 1.40
3351 3768 6.379579 AGAATACTCCCTCCGTTCCTAAATA 58.620 40.000 0.00 0.00 0.00 1.40
3352 3769 5.217400 AGAATACTCCCTCCGTTCCTAAAT 58.783 41.667 0.00 0.00 0.00 1.40
3353 3770 4.617593 AGAATACTCCCTCCGTTCCTAAA 58.382 43.478 0.00 0.00 0.00 1.85
3354 3771 4.261411 AGAATACTCCCTCCGTTCCTAA 57.739 45.455 0.00 0.00 0.00 2.69
3355 3772 3.967467 AGAATACTCCCTCCGTTCCTA 57.033 47.619 0.00 0.00 0.00 2.94
3356 3773 2.850695 AGAATACTCCCTCCGTTCCT 57.149 50.000 0.00 0.00 0.00 3.36
3357 3774 5.774184 ACTTATAGAATACTCCCTCCGTTCC 59.226 44.000 0.00 0.00 0.00 3.62
3358 3775 6.489361 TGACTTATAGAATACTCCCTCCGTTC 59.511 42.308 0.00 0.00 0.00 3.95
3359 3776 6.371278 TGACTTATAGAATACTCCCTCCGTT 58.629 40.000 0.00 0.00 0.00 4.44
3360 3777 5.950023 TGACTTATAGAATACTCCCTCCGT 58.050 41.667 0.00 0.00 0.00 4.69
3361 3778 6.896021 TTGACTTATAGAATACTCCCTCCG 57.104 41.667 0.00 0.00 0.00 4.63
3362 3779 7.540299 CGATTGACTTATAGAATACTCCCTCC 58.460 42.308 0.00 0.00 0.00 4.30
3363 3780 7.030768 GCGATTGACTTATAGAATACTCCCTC 58.969 42.308 0.00 0.00 0.00 4.30
3364 3781 6.493802 TGCGATTGACTTATAGAATACTCCCT 59.506 38.462 0.00 0.00 0.00 4.20
3365 3782 6.586844 GTGCGATTGACTTATAGAATACTCCC 59.413 42.308 0.00 0.00 0.00 4.30
3366 3783 7.371936 AGTGCGATTGACTTATAGAATACTCC 58.628 38.462 0.00 0.00 0.00 3.85
3367 3784 9.332301 GTAGTGCGATTGACTTATAGAATACTC 57.668 37.037 0.00 0.00 0.00 2.59
3368 3785 9.069082 AGTAGTGCGATTGACTTATAGAATACT 57.931 33.333 0.00 0.00 0.00 2.12
3369 3786 9.119329 CAGTAGTGCGATTGACTTATAGAATAC 57.881 37.037 0.00 0.00 0.00 1.89
3370 3787 8.847196 ACAGTAGTGCGATTGACTTATAGAATA 58.153 33.333 0.00 0.00 0.00 1.75
3371 3788 7.717568 ACAGTAGTGCGATTGACTTATAGAAT 58.282 34.615 0.00 0.00 0.00 2.40
3386 3803 5.234116 TGCATAATACATGAACAGTAGTGCG 59.766 40.000 0.00 0.00 34.14 5.34
3425 3842 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
3426 3843 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
3427 3844 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
3428 3845 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
3429 3846 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
3430 3847 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
3431 3848 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
3432 3849 9.232473 ACTAATCTAAGACAAGAATTTTGGGAC 57.768 33.333 5.68 0.00 0.00 4.46
3433 3850 9.449719 GACTAATCTAAGACAAGAATTTTGGGA 57.550 33.333 5.68 0.00 0.00 4.37
3434 3851 9.454859 AGACTAATCTAAGACAAGAATTTTGGG 57.545 33.333 5.68 0.00 31.46 4.12
3442 3859 9.491675 CCGTATCTAGACTAATCTAAGACAAGA 57.508 37.037 0.00 0.00 36.98 3.02
3443 3860 9.491675 TCCGTATCTAGACTAATCTAAGACAAG 57.508 37.037 0.00 0.00 36.98 3.16
3445 3862 9.438228 CATCCGTATCTAGACTAATCTAAGACA 57.562 37.037 0.00 0.00 36.98 3.41
3446 3863 9.439500 ACATCCGTATCTAGACTAATCTAAGAC 57.561 37.037 0.00 0.00 36.98 3.01


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

AutoCloner maintained by Alex Coulton.