Multiple sequence alignment - TraesCS3D01G085200

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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 TraesCS3D01G085200 chr3D 100.000 3690 0 0 1 3690 42894647 42898336 0.000000e+00 6815.0
1 TraesCS3D01G085200 chr3D 94.681 94 5 0 3263 3356 378534737 378534644 2.970000e-31 147.0
2 TraesCS3D01G085200 chr3D 98.734 79 1 0 3612 3690 42904337 42904415 1.380000e-29 141.0
3 TraesCS3D01G085200 chr3D 96.386 83 3 0 3608 3690 539350178 539350096 1.790000e-28 137.0
4 TraesCS3D01G085200 chr3D 97.468 79 2 0 3612 3690 539344015 539343937 6.430000e-28 135.0
5 TraesCS3D01G085200 chr3D 96.203 79 3 0 3612 3690 597235773 597235851 2.990000e-26 130.0
6 TraesCS3D01G085200 chr3D 97.619 42 1 0 3354 3395 8195066 8195025 5.110000e-09 73.1
7 TraesCS3D01G085200 chr3A 91.233 3308 185 50 1 3260 54930679 54933929 0.000000e+00 4405.0
8 TraesCS3D01G085200 chr3A 93.379 438 26 3 461 897 54936912 54937347 0.000000e+00 645.0
9 TraesCS3D01G085200 chr3A 87.886 421 48 2 1 418 54936498 54936918 3.310000e-135 492.0
10 TraesCS3D01G085200 chr3A 94.118 102 5 1 3263 3364 59827736 59827836 1.770000e-33 154.0
11 TraesCS3D01G085200 chr3A 93.137 102 6 1 3263 3364 59825327 59825227 8.260000e-32 148.0
12 TraesCS3D01G085200 chr3B 93.111 1292 48 17 1988 3262 66820208 66821475 0.000000e+00 1855.0
13 TraesCS3D01G085200 chr3B 95.721 818 31 4 1 817 66806889 66807703 0.000000e+00 1314.0
14 TraesCS3D01G085200 chr3B 94.414 734 37 1 812 1541 66816781 66817514 0.000000e+00 1125.0
15 TraesCS3D01G085200 chr3B 98.052 462 9 0 1536 1997 66819565 66820026 0.000000e+00 804.0
16 TraesCS3D01G085200 chr3B 95.588 272 10 2 3349 3619 18041238 18041508 5.660000e-118 435.0
17 TraesCS3D01G085200 chr3B 96.226 265 9 1 3356 3619 65916143 65916407 2.040000e-117 433.0
18 TraesCS3D01G085200 chr6B 85.921 554 77 1 28 580 9980191 9979638 1.140000e-164 590.0
19 TraesCS3D01G085200 chr6B 84.838 554 76 7 30 581 9503350 9503897 5.390000e-153 551.0
20 TraesCS3D01G085200 chr6B 90.385 52 4 1 3355 3405 623337685 623337634 2.380000e-07 67.6
21 TraesCS3D01G085200 chrUn 85.791 556 77 2 28 582 75930823 75931377 4.110000e-164 588.0
22 TraesCS3D01G085200 chr5B 96.981 265 7 1 3356 3619 273255543 273255807 9.400000e-121 444.0
23 TraesCS3D01G085200 chr5B 92.308 52 3 1 3355 3405 210228811 210228760 5.110000e-09 73.1
24 TraesCS3D01G085200 chr2B 95.472 265 11 1 3356 3619 25610355 25610619 4.410000e-114 422.0
25 TraesCS3D01G085200 chr1D 82.110 436 72 5 142 576 477760540 477760970 5.820000e-98 368.0
26 TraesCS3D01G085200 chr1D 92.553 94 7 0 3263 3356 298601098 298601005 6.430000e-28 135.0
27 TraesCS3D01G085200 chr1D 96.250 80 3 0 3611 3690 438281190 438281111 8.320000e-27 132.0
28 TraesCS3D01G085200 chr1D 96.203 79 3 0 3612 3690 438275151 438275073 2.990000e-26 130.0
29 TraesCS3D01G085200 chr2D 80.952 441 74 9 141 576 144413928 144413493 1.270000e-89 340.0
30 TraesCS3D01G085200 chr2D 97.500 80 2 0 3611 3690 165179889 165179968 1.790000e-28 137.0
31 TraesCS3D01G085200 chr2D 97.468 79 2 0 3612 3690 165186112 165186190 6.430000e-28 135.0
32 TraesCS3D01G085200 chr2D 97.468 79 2 0 3612 3690 586936854 586936776 6.430000e-28 135.0
33 TraesCS3D01G085200 chr2D 91.489 94 8 0 3263 3356 225310224 225310131 2.990000e-26 130.0
34 TraesCS3D01G085200 chr7D 80.726 441 78 5 140 578 622280720 622281155 1.640000e-88 337.0
35 TraesCS3D01G085200 chr7D 92.857 98 6 1 3260 3356 561597753 561597656 1.380000e-29 141.0
36 TraesCS3D01G085200 chr7D 83.495 103 14 2 2863 2965 530943269 530943368 3.920000e-15 93.5
37 TraesCS3D01G085200 chr7A 96.454 141 4 1 3480 3619 47999008 47998868 7.970000e-57 231.0
38 TraesCS3D01G085200 chr7A 79.720 143 24 3 2823 2965 611471256 611471393 8.430000e-17 99.0
39 TraesCS3D01G085200 chr5A 94.681 94 5 0 3263 3356 561650051 561650144 2.970000e-31 147.0
40 TraesCS3D01G085200 chr1B 94.624 93 5 0 3263 3355 402001251 402001159 1.070000e-30 145.0
41 TraesCS3D01G085200 chr1B 88.889 54 5 1 3354 3406 158447389 158447336 8.550000e-07 65.8
42 TraesCS3D01G085200 chr5D 91.489 94 8 0 3263 3356 447945986 447945893 2.990000e-26 130.0
43 TraesCS3D01G085200 chr4A 87.500 56 6 1 3352 3406 609566452 609566507 3.080000e-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 TraesCS3D01G085200 chr3D 42894647 42898336 3689 False 6815.000000 6815 100.000000 1 3690 1 chr3D.!!$F1 3689
1 TraesCS3D01G085200 chr3A 54930679 54937347 6668 False 1847.333333 4405 90.832667 1 3260 3 chr3A.!!$F2 3259
2 TraesCS3D01G085200 chr3B 66806889 66807703 814 False 1314.000000 1314 95.721000 1 817 1 chr3B.!!$F3 816
3 TraesCS3D01G085200 chr3B 66816781 66821475 4694 False 1261.333333 1855 95.192333 812 3262 3 chr3B.!!$F4 2450
4 TraesCS3D01G085200 chr6B 9979638 9980191 553 True 590.000000 590 85.921000 28 580 1 chr6B.!!$R1 552
5 TraesCS3D01G085200 chr6B 9503350 9503897 547 False 551.000000 551 84.838000 30 581 1 chr6B.!!$F1 551
6 TraesCS3D01G085200 chrUn 75930823 75931377 554 False 588.000000 588 85.791000 28 582 1 chrUn.!!$F1 554

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
209 213 0.598065 GTGGTGGCATCTTGTCCAAC 59.402 55.0 0.0 0.0 40.42 3.77 F
999 1005 0.035725 CTCTGAAGGTGGCTGCATCA 60.036 55.0 0.5 0.0 0.00 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1270 1280 0.749649 GAGGCATCCTGTCTGACGAT 59.250 55.000 2.98 0.0 28.93 3.73 R
2731 4999 2.095461 AGTCTCACATAAGCTGCTCGA 58.905 47.619 1.00 0.0 0.00 4.04 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
26 29 2.227626 TCAGAGAGAGAAAGAGTGCACG 59.772 50.000 12.01 0.00 0.00 5.34
77 80 3.592814 CGCCGCCGATCTACCTCA 61.593 66.667 0.00 0.00 36.29 3.86
114 117 2.146724 CATGGAGGCCGGGTGGATA 61.147 63.158 2.18 0.00 37.49 2.59
209 213 0.598065 GTGGTGGCATCTTGTCCAAC 59.402 55.000 0.00 0.00 40.42 3.77
466 471 2.184322 CCGTCGACATGGTCTGGG 59.816 66.667 17.16 1.66 0.00 4.45
541 546 2.969950 AGGTGCTTTGTACTGTCTGGTA 59.030 45.455 0.00 0.00 0.00 3.25
555 560 8.947115 GTACTGTCTGGTATTTCTTTTAATGCT 58.053 33.333 0.00 0.00 0.00 3.79
621 626 1.847798 AACCCTAAGCCACCATGCGA 61.848 55.000 0.00 0.00 36.02 5.10
709 714 2.526077 TCGAACGACTGAAATGATCCG 58.474 47.619 0.00 0.00 0.00 4.18
869 875 7.161404 TCTTGCATCTACATAACCATGGTATC 58.839 38.462 20.12 1.57 36.39 2.24
977 983 5.084519 AGGCGACCTACCATATTTGATCTA 58.915 41.667 0.00 0.00 28.47 1.98
989 995 8.552296 ACCATATTTGATCTAAACTCTGAAGGT 58.448 33.333 0.00 0.00 0.00 3.50
999 1005 0.035725 CTCTGAAGGTGGCTGCATCA 60.036 55.000 0.50 0.00 0.00 3.07
1116 1126 0.832135 TCCTCCTCAAGCTCCGTTGT 60.832 55.000 0.00 0.00 0.00 3.32
1402 1413 1.003003 GGAGAAGAGCTGCCTTGAAGT 59.997 52.381 7.89 0.00 0.00 3.01
1426 1437 4.443266 GCTTCGAGAGCGCCACCT 62.443 66.667 2.29 0.00 42.46 4.00
1462 1473 2.653087 GGGTTCCTCCGCCTTACGT 61.653 63.158 0.00 0.00 41.42 3.57
1857 3924 0.034896 ACCTACAACGGCTTGTCCTG 59.965 55.000 5.75 0.81 41.15 3.86
1997 4067 7.093902 CCCGGTGAGTTCATGTATACTATGTAT 60.094 40.741 0.00 0.00 0.00 2.29
1998 4068 8.953313 CCGGTGAGTTCATGTATACTATGTATA 58.047 37.037 4.17 0.00 0.00 1.47
1999 4069 9.989869 CGGTGAGTTCATGTATACTATGTATAG 57.010 37.037 4.17 0.00 36.46 1.31
2080 4341 5.650703 TCTCATACGAACTGACAGGACATAA 59.349 40.000 7.51 0.00 0.00 1.90
2423 4689 5.072193 TCAGGTTGTATATGTGATCAGCCAT 59.928 40.000 0.00 0.00 34.46 4.40
2516 4782 4.977963 GTGAACATGAAATCAGTGTTGTGG 59.022 41.667 0.00 0.00 36.30 4.17
2576 4842 7.494625 GGATGACAGTAAATTTCCATTACTCGA 59.505 37.037 0.00 0.00 40.65 4.04
2730 4998 3.073678 CGGTCCATTGATTGTCAGTTGA 58.926 45.455 0.00 0.00 0.00 3.18
2731 4999 3.691118 CGGTCCATTGATTGTCAGTTGAT 59.309 43.478 0.00 0.00 0.00 2.57
2800 5074 2.988010 TTTGTGAGTGCTCTGTCAGT 57.012 45.000 0.00 0.00 0.00 3.41
2835 5113 1.997669 GCGTGTAGCTGCTAGTTTCT 58.002 50.000 10.13 0.00 44.04 2.52
2888 5166 7.609918 ACTGATACTTGGTATGCATTTTGTGTA 59.390 33.333 3.54 4.36 0.00 2.90
2916 5198 7.119846 GGTAACTTTATGCCTCATGCCTATTAG 59.880 40.741 0.00 0.00 40.16 1.73
2966 5248 5.244626 AGTTTGAGAAATTGGCATGCTACTT 59.755 36.000 18.92 9.45 0.00 2.24
2967 5249 6.434028 AGTTTGAGAAATTGGCATGCTACTTA 59.566 34.615 18.92 0.00 0.00 2.24
2968 5250 6.832520 TTGAGAAATTGGCATGCTACTTAA 57.167 33.333 18.92 5.14 0.00 1.85
2969 5251 7.408756 TTGAGAAATTGGCATGCTACTTAAT 57.591 32.000 18.92 4.27 0.00 1.40
3041 5323 7.877097 TCAGTATGTTGGAAAATGAAAAATGGG 59.123 33.333 0.00 0.00 37.40 4.00
3112 5394 2.159572 CCGAAAATTTGGGTCTAGTGCG 60.160 50.000 0.00 0.00 0.00 5.34
3114 5396 3.181520 CGAAAATTTGGGTCTAGTGCGAG 60.182 47.826 0.00 0.00 0.00 5.03
3119 5401 4.740235 GGTCTAGTGCGAGCCATC 57.260 61.111 0.00 0.00 0.00 3.51
3120 5402 1.068250 GGTCTAGTGCGAGCCATCC 59.932 63.158 0.00 0.00 0.00 3.51
3121 5403 1.676678 GGTCTAGTGCGAGCCATCCA 61.677 60.000 0.00 0.00 0.00 3.41
3122 5404 0.175760 GTCTAGTGCGAGCCATCCAA 59.824 55.000 0.00 0.00 0.00 3.53
3123 5405 0.461548 TCTAGTGCGAGCCATCCAAG 59.538 55.000 0.00 0.00 0.00 3.61
3245 5531 3.242870 CGAGCAATTCATACAAAGCCTCC 60.243 47.826 0.00 0.00 0.00 4.30
3264 5550 3.543680 CCGATGAGGAACAATAGGTGT 57.456 47.619 0.00 0.00 45.00 4.16
3325 5611 5.501156 GGATTTGATCCTACCTTGTCTTGT 58.499 41.667 0.00 0.00 46.19 3.16
3326 5612 6.650120 GGATTTGATCCTACCTTGTCTTGTA 58.350 40.000 0.00 0.00 46.19 2.41
3327 5613 6.539103 GGATTTGATCCTACCTTGTCTTGTAC 59.461 42.308 0.00 0.00 46.19 2.90
3328 5614 6.681729 TTTGATCCTACCTTGTCTTGTACT 57.318 37.500 0.00 0.00 0.00 2.73
3329 5615 5.916661 TGATCCTACCTTGTCTTGTACTC 57.083 43.478 0.00 0.00 0.00 2.59
3330 5616 5.580998 TGATCCTACCTTGTCTTGTACTCT 58.419 41.667 0.00 0.00 0.00 3.24
3331 5617 6.728411 TGATCCTACCTTGTCTTGTACTCTA 58.272 40.000 0.00 0.00 0.00 2.43
3332 5618 7.179966 TGATCCTACCTTGTCTTGTACTCTAA 58.820 38.462 0.00 0.00 0.00 2.10
3334 5620 6.550163 TCCTACCTTGTCTTGTACTCTAAGT 58.450 40.000 0.00 0.00 0.00 2.24
3335 5621 7.008941 TCCTACCTTGTCTTGTACTCTAAGTT 58.991 38.462 0.00 0.00 0.00 2.66
3336 5622 7.039923 TCCTACCTTGTCTTGTACTCTAAGTTG 60.040 40.741 0.00 0.00 0.00 3.16
3337 5623 6.726490 ACCTTGTCTTGTACTCTAAGTTGA 57.274 37.500 0.00 0.00 0.00 3.18
3340 5626 7.233757 ACCTTGTCTTGTACTCTAAGTTGATCT 59.766 37.037 0.00 0.00 0.00 2.75
3343 5629 8.818141 TGTCTTGTACTCTAAGTTGATCTTTG 57.182 34.615 0.00 0.00 37.56 2.77
3344 5630 7.385205 TGTCTTGTACTCTAAGTTGATCTTTGC 59.615 37.037 0.00 0.00 37.56 3.68
3346 5632 7.385205 TCTTGTACTCTAAGTTGATCTTTGCAC 59.615 37.037 0.00 0.00 37.56 4.57
3347 5633 6.759272 TGTACTCTAAGTTGATCTTTGCACT 58.241 36.000 0.00 0.00 37.56 4.40
3348 5634 6.868864 TGTACTCTAAGTTGATCTTTGCACTC 59.131 38.462 0.00 0.00 37.56 3.51
3349 5635 5.241662 ACTCTAAGTTGATCTTTGCACTCC 58.758 41.667 0.00 0.00 37.56 3.85
3351 5637 6.211584 ACTCTAAGTTGATCTTTGCACTCCTA 59.788 38.462 0.00 0.00 37.56 2.94
3352 5638 7.093112 ACTCTAAGTTGATCTTTGCACTCCTAT 60.093 37.037 0.00 0.00 37.56 2.57
3353 5639 8.306313 TCTAAGTTGATCTTTGCACTCCTATA 57.694 34.615 0.00 0.00 37.56 1.31
3356 5642 8.894768 AAGTTGATCTTTGCACTCCTATATAC 57.105 34.615 0.00 0.00 31.57 1.47
3357 5643 8.256356 AGTTGATCTTTGCACTCCTATATACT 57.744 34.615 0.00 0.00 0.00 2.12
3358 5644 9.368416 AGTTGATCTTTGCACTCCTATATACTA 57.632 33.333 0.00 0.00 0.00 1.82
3359 5645 9.632807 GTTGATCTTTGCACTCCTATATACTAG 57.367 37.037 0.00 0.00 0.00 2.57
3361 5647 9.015367 TGATCTTTGCACTCCTATATACTAGAC 57.985 37.037 0.00 0.00 0.00 2.59
3362 5648 7.762588 TCTTTGCACTCCTATATACTAGACC 57.237 40.000 0.00 0.00 0.00 3.85
3364 5650 7.950684 TCTTTGCACTCCTATATACTAGACCAT 59.049 37.037 0.00 0.00 0.00 3.55
3365 5651 7.468141 TTGCACTCCTATATACTAGACCATG 57.532 40.000 0.00 0.00 0.00 3.66
3367 5653 7.414266 TGCACTCCTATATACTAGACCATGAT 58.586 38.462 0.00 0.00 0.00 2.45
3368 5654 8.557450 TGCACTCCTATATACTAGACCATGATA 58.443 37.037 0.00 0.00 0.00 2.15
3370 5656 9.062524 CACTCCTATATACTAGACCATGATAGC 57.937 40.741 0.00 0.00 0.00 2.97
3371 5657 7.934665 ACTCCTATATACTAGACCATGATAGCG 59.065 40.741 0.00 0.00 0.00 4.26
3372 5658 6.711194 TCCTATATACTAGACCATGATAGCGC 59.289 42.308 0.00 0.00 0.00 5.92
3373 5659 3.766676 ATACTAGACCATGATAGCGCG 57.233 47.619 0.00 0.00 0.00 6.86
3375 5661 1.067743 CTAGACCATGATAGCGCGCG 61.068 60.000 28.44 28.44 0.00 6.86
3376 5662 1.792118 TAGACCATGATAGCGCGCGT 61.792 55.000 32.35 19.20 0.00 6.01
3377 5663 2.202878 ACCATGATAGCGCGCGTT 60.203 55.556 32.35 28.79 0.00 4.84
3378 5664 2.246397 CCATGATAGCGCGCGTTG 59.754 61.111 32.35 18.44 0.00 4.10
3380 5666 3.640000 ATGATAGCGCGCGTTGCC 61.640 61.111 32.35 20.68 42.08 4.52
3402 7918 3.664107 GCGCCTGTCCATTCTATGATAA 58.336 45.455 0.00 0.00 0.00 1.75
3407 7923 6.205464 CGCCTGTCCATTCTATGATAAAATGT 59.795 38.462 0.00 0.00 0.00 2.71
3408 7924 7.255242 CGCCTGTCCATTCTATGATAAAATGTT 60.255 37.037 0.00 0.00 0.00 2.71
3409 7925 9.066892 GCCTGTCCATTCTATGATAAAATGTTA 57.933 33.333 0.00 0.00 0.00 2.41
3434 7950 8.635765 AAGAATAGTGAAAATACTTGAAGCCA 57.364 30.769 0.00 0.00 32.19 4.75
3435 7951 8.045176 AGAATAGTGAAAATACTTGAAGCCAC 57.955 34.615 0.00 0.00 32.19 5.01
3439 7955 6.872920 AGTGAAAATACTTGAAGCCACAAAA 58.127 32.000 0.00 0.00 0.00 2.44
3440 7956 6.756542 AGTGAAAATACTTGAAGCCACAAAAC 59.243 34.615 0.00 0.00 0.00 2.43
3442 7958 7.224557 GTGAAAATACTTGAAGCCACAAAACAT 59.775 33.333 0.00 0.00 0.00 2.71
3444 7960 3.457610 ACTTGAAGCCACAAAACATGG 57.542 42.857 0.00 0.00 40.50 3.66
3446 7962 3.450457 ACTTGAAGCCACAAAACATGGAA 59.550 39.130 0.00 0.00 39.87 3.53
3449 7965 5.033589 TGAAGCCACAAAACATGGAAATT 57.966 34.783 0.00 0.00 39.87 1.82
3450 7966 5.435291 TGAAGCCACAAAACATGGAAATTT 58.565 33.333 0.00 0.00 39.87 1.82
3453 7969 7.226325 TGAAGCCACAAAACATGGAAATTTAAG 59.774 33.333 0.00 0.00 39.87 1.85
3457 7973 7.643371 GCCACAAAACATGGAAATTTAAGTTTG 59.357 33.333 0.06 8.21 39.87 2.93
3458 7974 8.672815 CCACAAAACATGGAAATTTAAGTTTGT 58.327 29.630 0.06 8.65 39.87 2.83
3468 7984 9.255304 TGGAAATTTAAGTTTGTATCAACTTGC 57.745 29.630 8.72 0.00 39.36 4.01
3469 7985 9.476202 GGAAATTTAAGTTTGTATCAACTTGCT 57.524 29.630 8.72 0.00 39.36 3.91
3478 7994 9.319143 AGTTTGTATCAACTTGCTCATATAGTC 57.681 33.333 0.00 0.00 0.00 2.59
3480 7996 9.836864 TTTGTATCAACTTGCTCATATAGTCAT 57.163 29.630 0.00 0.00 0.00 3.06
3481 7997 9.481340 TTGTATCAACTTGCTCATATAGTCATC 57.519 33.333 0.00 0.00 0.00 2.92
3482 7998 8.641541 TGTATCAACTTGCTCATATAGTCATCA 58.358 33.333 0.00 0.00 0.00 3.07
3484 8000 7.117285 TCAACTTGCTCATATAGTCATCAGT 57.883 36.000 0.00 0.00 0.00 3.41
3486 8002 8.695456 TCAACTTGCTCATATAGTCATCAGTAA 58.305 33.333 0.00 0.00 0.00 2.24
3487 8003 9.486497 CAACTTGCTCATATAGTCATCAGTAAT 57.514 33.333 0.00 0.00 0.00 1.89
3488 8004 9.703892 AACTTGCTCATATAGTCATCAGTAATC 57.296 33.333 0.00 0.00 0.00 1.75
3489 8005 8.864087 ACTTGCTCATATAGTCATCAGTAATCA 58.136 33.333 0.00 0.00 0.00 2.57
3490 8006 9.702494 CTTGCTCATATAGTCATCAGTAATCAA 57.298 33.333 0.00 0.00 0.00 2.57
3532 8150 9.790389 AATAATTAGACAGTACAACTCTTCGAG 57.210 33.333 0.00 0.00 35.52 4.04
3534 8152 3.752665 AGACAGTACAACTCTTCGAGGA 58.247 45.455 0.00 0.00 33.35 3.71
3535 8153 4.142790 AGACAGTACAACTCTTCGAGGAA 58.857 43.478 0.00 0.00 33.35 3.36
3536 8154 4.023021 AGACAGTACAACTCTTCGAGGAAC 60.023 45.833 0.00 0.00 33.35 3.62
3537 8155 3.005578 ACAGTACAACTCTTCGAGGAACC 59.994 47.826 0.00 0.00 33.35 3.62
3538 8156 3.256136 CAGTACAACTCTTCGAGGAACCT 59.744 47.826 0.00 0.00 33.35 3.50
3539 8157 3.896272 AGTACAACTCTTCGAGGAACCTT 59.104 43.478 0.00 0.00 33.35 3.50
3540 8158 3.113260 ACAACTCTTCGAGGAACCTTG 57.887 47.619 0.00 3.59 33.35 3.61
3541 8159 2.224305 ACAACTCTTCGAGGAACCTTGG 60.224 50.000 8.09 0.00 33.35 3.61
3542 8160 0.977395 ACTCTTCGAGGAACCTTGGG 59.023 55.000 8.09 2.93 33.35 4.12
3543 8161 1.267121 CTCTTCGAGGAACCTTGGGA 58.733 55.000 8.09 6.44 0.00 4.37
3544 8162 1.623811 CTCTTCGAGGAACCTTGGGAA 59.376 52.381 8.09 5.77 0.00 3.97
3545 8163 2.038557 CTCTTCGAGGAACCTTGGGAAA 59.961 50.000 8.09 0.00 0.00 3.13
3547 8165 3.073946 TCTTCGAGGAACCTTGGGAAATT 59.926 43.478 8.09 0.00 0.00 1.82
3548 8166 3.518992 TCGAGGAACCTTGGGAAATTT 57.481 42.857 8.09 0.00 0.00 1.82
3549 8167 4.644163 TCGAGGAACCTTGGGAAATTTA 57.356 40.909 8.09 0.00 0.00 1.40
3550 8168 4.988029 TCGAGGAACCTTGGGAAATTTAA 58.012 39.130 8.09 0.00 0.00 1.52
3552 8170 6.723339 TCGAGGAACCTTGGGAAATTTAATA 58.277 36.000 8.09 0.00 0.00 0.98
3553 8171 6.600427 TCGAGGAACCTTGGGAAATTTAATAC 59.400 38.462 8.09 0.00 0.00 1.89
3554 8172 6.376018 CGAGGAACCTTGGGAAATTTAATACA 59.624 38.462 0.00 0.00 0.00 2.29
3555 8173 7.415206 CGAGGAACCTTGGGAAATTTAATACAG 60.415 40.741 0.00 0.00 0.00 2.74
3556 8174 7.246027 AGGAACCTTGGGAAATTTAATACAGT 58.754 34.615 0.00 0.00 0.00 3.55
3557 8175 8.395605 AGGAACCTTGGGAAATTTAATACAGTA 58.604 33.333 0.00 0.00 0.00 2.74
3558 8176 9.197306 GGAACCTTGGGAAATTTAATACAGTAT 57.803 33.333 0.00 0.00 0.00 2.12
3560 8178 9.990868 AACCTTGGGAAATTTAATACAGTATCT 57.009 29.630 0.00 0.00 0.00 1.98
3575 8193 6.286240 ACAGTATCTCAATGTAGAAGTGCA 57.714 37.500 0.00 0.00 0.00 4.57
3577 8195 6.101997 CAGTATCTCAATGTAGAAGTGCACA 58.898 40.000 21.04 0.00 0.00 4.57
3578 8196 6.591448 CAGTATCTCAATGTAGAAGTGCACAA 59.409 38.462 21.04 0.00 0.00 3.33
3579 8197 7.279536 CAGTATCTCAATGTAGAAGTGCACAAT 59.720 37.037 21.04 7.32 0.00 2.71
3580 8198 5.868043 TCTCAATGTAGAAGTGCACAATG 57.132 39.130 21.04 0.19 0.00 2.82
3587 8887 8.615211 CAATGTAGAAGTGCACAATGTATATGT 58.385 33.333 21.04 3.45 0.00 2.29
3590 8890 7.821846 TGTAGAAGTGCACAATGTATATGTTCA 59.178 33.333 21.04 1.24 0.00 3.18
3597 8897 7.008628 GTGCACAATGTATATGTTCAAAGCTTC 59.991 37.037 13.17 0.00 0.00 3.86
3598 8898 7.028962 GCACAATGTATATGTTCAAAGCTTCA 58.971 34.615 0.00 0.00 0.00 3.02
3599 8899 7.219535 GCACAATGTATATGTTCAAAGCTTCAG 59.780 37.037 0.00 0.00 0.00 3.02
3600 8900 7.699391 CACAATGTATATGTTCAAAGCTTCAGG 59.301 37.037 0.00 0.00 0.00 3.86
3601 8901 7.394359 ACAATGTATATGTTCAAAGCTTCAGGT 59.606 33.333 0.00 0.00 0.00 4.00
3603 8903 9.632638 AATGTATATGTTCAAAGCTTCAGGTAT 57.367 29.630 0.00 0.00 0.00 2.73
3609 8909 7.849804 TGTTCAAAGCTTCAGGTATAAGATC 57.150 36.000 0.00 0.00 0.00 2.75
3610 8910 7.394016 TGTTCAAAGCTTCAGGTATAAGATCA 58.606 34.615 0.00 0.00 0.00 2.92
3612 8912 8.341173 GTTCAAAGCTTCAGGTATAAGATCATG 58.659 37.037 0.00 0.00 0.00 3.07
3613 8913 7.795047 TCAAAGCTTCAGGTATAAGATCATGA 58.205 34.615 0.00 0.00 0.00 3.07
3614 8914 8.435187 TCAAAGCTTCAGGTATAAGATCATGAT 58.565 33.333 8.25 8.25 0.00 2.45
3615 8915 9.716531 CAAAGCTTCAGGTATAAGATCATGATA 57.283 33.333 8.54 0.00 0.00 2.15
3616 8916 9.941325 AAAGCTTCAGGTATAAGATCATGATAG 57.059 33.333 8.54 0.00 0.00 2.08
3623 8923 9.645128 CAGGTATAAGATCATGATAGATCCTCT 57.355 37.037 8.54 0.00 44.32 3.69
3624 8924 9.645128 AGGTATAAGATCATGATAGATCCTCTG 57.355 37.037 8.54 0.00 44.32 3.35
3625 8925 8.859090 GGTATAAGATCATGATAGATCCTCTGG 58.141 40.741 8.54 0.00 44.32 3.86
3639 8939 3.056832 TCCTCTGGATCACTAGGCTAGA 58.943 50.000 27.59 7.26 0.00 2.43
3641 8941 4.107149 TCCTCTGGATCACTAGGCTAGATT 59.893 45.833 27.59 11.38 0.00 2.40
3642 8942 5.313506 TCCTCTGGATCACTAGGCTAGATTA 59.686 44.000 27.59 12.31 0.00 1.75
3643 8943 5.652014 CCTCTGGATCACTAGGCTAGATTAG 59.348 48.000 27.59 14.96 0.00 1.73
3646 8946 7.116075 TCTGGATCACTAGGCTAGATTAGATC 58.884 42.308 27.59 25.94 0.00 2.75
3648 8948 5.298276 GGATCACTAGGCTAGATTAGATCCG 59.702 48.000 30.13 9.91 40.38 4.18
3649 8949 4.590918 TCACTAGGCTAGATTAGATCCGG 58.409 47.826 27.59 0.00 0.00 5.14
3650 8950 4.043059 TCACTAGGCTAGATTAGATCCGGT 59.957 45.833 27.59 0.00 0.00 5.28
3652 8952 5.944599 CACTAGGCTAGATTAGATCCGGTAA 59.055 44.000 27.59 0.00 0.00 2.85
3653 8953 6.433404 CACTAGGCTAGATTAGATCCGGTAAA 59.567 42.308 27.59 0.00 0.00 2.01
3654 8954 5.725325 AGGCTAGATTAGATCCGGTAAAC 57.275 43.478 0.00 0.00 0.00 2.01
3656 8956 4.527427 GGCTAGATTAGATCCGGTAAACCT 59.473 45.833 0.00 0.00 0.00 3.50
3657 8957 5.713861 GGCTAGATTAGATCCGGTAAACCTA 59.286 44.000 0.00 0.00 0.00 3.08
3659 8959 6.350027 GCTAGATTAGATCCGGTAAACCTACC 60.350 46.154 0.00 0.00 43.86 3.18
3660 8960 5.713807 AGATTAGATCCGGTAAACCTACCT 58.286 41.667 0.00 0.00 44.96 3.08
3661 8961 6.141790 AGATTAGATCCGGTAAACCTACCTT 58.858 40.000 0.00 0.00 44.96 3.50
3663 8963 3.447950 AGATCCGGTAAACCTACCTTGT 58.552 45.455 0.00 0.00 44.96 3.16
3664 8964 3.197116 AGATCCGGTAAACCTACCTTGTG 59.803 47.826 0.00 0.00 44.96 3.33
3665 8965 1.002315 TCCGGTAAACCTACCTTGTGC 59.998 52.381 0.00 0.00 44.96 4.57
3666 8966 1.270947 CCGGTAAACCTACCTTGTGCA 60.271 52.381 0.00 0.00 44.96 4.57
3667 8967 2.073816 CGGTAAACCTACCTTGTGCAG 58.926 52.381 0.00 0.00 44.96 4.41
3668 8968 1.810755 GGTAAACCTACCTTGTGCAGC 59.189 52.381 0.00 0.00 43.92 5.25
3669 8969 2.500229 GTAAACCTACCTTGTGCAGCA 58.500 47.619 0.00 0.00 0.00 4.41
3670 8970 1.609208 AAACCTACCTTGTGCAGCAG 58.391 50.000 0.00 0.00 0.00 4.24
3671 8971 0.474184 AACCTACCTTGTGCAGCAGT 59.526 50.000 0.00 0.00 0.00 4.40
3672 8972 1.348064 ACCTACCTTGTGCAGCAGTA 58.652 50.000 0.00 0.00 0.00 2.74
3673 8973 1.276421 ACCTACCTTGTGCAGCAGTAG 59.724 52.381 11.08 11.08 0.00 2.57
3674 8974 1.550524 CCTACCTTGTGCAGCAGTAGA 59.449 52.381 17.23 0.00 31.33 2.59
3675 8975 2.169352 CCTACCTTGTGCAGCAGTAGAT 59.831 50.000 17.23 0.00 31.33 1.98
3676 8976 2.105006 ACCTTGTGCAGCAGTAGATG 57.895 50.000 0.00 0.00 0.00 2.90
3677 8977 1.625315 ACCTTGTGCAGCAGTAGATGA 59.375 47.619 0.00 0.00 31.30 2.92
3678 8978 2.038952 ACCTTGTGCAGCAGTAGATGAA 59.961 45.455 0.00 0.00 31.30 2.57
3679 8979 2.417933 CCTTGTGCAGCAGTAGATGAAC 59.582 50.000 0.00 0.00 40.22 3.18
3680 8980 3.332919 CTTGTGCAGCAGTAGATGAACT 58.667 45.455 0.00 0.00 40.46 3.01
3681 8981 2.964740 TGTGCAGCAGTAGATGAACTC 58.035 47.619 0.00 0.00 40.46 3.01
3682 8982 1.923204 GTGCAGCAGTAGATGAACTCG 59.077 52.381 0.00 0.00 36.74 4.18
3683 8983 1.818674 TGCAGCAGTAGATGAACTCGA 59.181 47.619 0.00 0.00 31.30 4.04
3684 8984 2.159324 TGCAGCAGTAGATGAACTCGAG 60.159 50.000 11.84 11.84 31.30 4.04
3685 8985 2.458951 CAGCAGTAGATGAACTCGAGC 58.541 52.381 13.61 0.00 31.30 5.03
3686 8986 2.098934 CAGCAGTAGATGAACTCGAGCT 59.901 50.000 13.61 0.00 31.30 4.09
3687 8987 2.098934 AGCAGTAGATGAACTCGAGCTG 59.901 50.000 13.61 10.02 0.00 4.24
3688 8988 2.797792 GCAGTAGATGAACTCGAGCTGG 60.798 54.545 13.61 0.00 0.00 4.85
3689 8989 2.685388 CAGTAGATGAACTCGAGCTGGA 59.315 50.000 13.61 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 108 4.016706 GGGGCCGATATCCACCCG 62.017 72.222 17.49 0.00 43.82 5.28
209 213 1.135575 GCTGAAGCCGTGGAGATTTTG 60.136 52.381 0.00 0.00 34.31 2.44
381 385 2.437716 GGATGGGAAGCGCCGAAA 60.438 61.111 2.29 0.00 37.63 3.46
466 471 0.322546 ATGCCCTTCGTCTTCAACCC 60.323 55.000 0.00 0.00 0.00 4.11
541 546 8.435931 AAAAGGACCCTAGCATTAAAAGAAAT 57.564 30.769 0.00 0.00 0.00 2.17
621 626 3.244582 GTGGGGGTAGTTTTGGGATTTT 58.755 45.455 0.00 0.00 0.00 1.82
709 714 1.465200 GGGCGTCTATCTCTGGGTCC 61.465 65.000 0.00 0.00 0.00 4.46
977 983 0.183492 TGCAGCCACCTTCAGAGTTT 59.817 50.000 0.00 0.00 0.00 2.66
989 995 0.750546 GCTCTCCATTGATGCAGCCA 60.751 55.000 0.00 0.00 0.00 4.75
999 1005 0.465097 CCTTCGGCATGCTCTCCATT 60.465 55.000 18.92 0.00 29.71 3.16
1084 1094 0.948050 AGGAGGATCTGGATGAGGGT 59.052 55.000 0.00 0.00 33.73 4.34
1270 1280 0.749649 GAGGCATCCTGTCTGACGAT 59.250 55.000 2.98 0.00 28.93 3.73
1426 1437 3.786553 ACCCTAACCGCATATAGATCCA 58.213 45.455 0.00 0.00 0.00 3.41
1478 1489 2.473664 AAGACTGAGTCGGGCGAACG 62.474 60.000 6.99 0.00 37.67 3.95
1857 3924 8.564574 TCCTTTCCATATACGATAAATTGTTGC 58.435 33.333 0.00 0.00 0.00 4.17
1997 4067 5.356751 AGCAGTTCAACAATGACACAAACTA 59.643 36.000 0.00 0.00 34.61 2.24
1998 4068 4.158394 AGCAGTTCAACAATGACACAAACT 59.842 37.500 0.00 0.00 34.61 2.66
1999 4069 4.423732 AGCAGTTCAACAATGACACAAAC 58.576 39.130 0.00 0.00 34.61 2.93
2035 4296 5.880901 AGAGGTCACACACAAAAGGATTAT 58.119 37.500 0.00 0.00 0.00 1.28
2036 4297 5.163248 TGAGAGGTCACACACAAAAGGATTA 60.163 40.000 0.00 0.00 0.00 1.75
2037 4298 4.137543 GAGAGGTCACACACAAAAGGATT 58.862 43.478 0.00 0.00 0.00 3.01
2038 4299 3.136443 TGAGAGGTCACACACAAAAGGAT 59.864 43.478 0.00 0.00 0.00 3.24
2039 4300 2.503765 TGAGAGGTCACACACAAAAGGA 59.496 45.455 0.00 0.00 0.00 3.36
2516 4782 2.866762 GTGCCCAACTGAATAGACGATC 59.133 50.000 0.00 0.00 0.00 3.69
2576 4842 5.506982 GCTCTTCAGCTTTGTTTTCAGTGAT 60.507 40.000 0.00 0.00 43.09 3.06
2730 4998 2.692557 AGTCTCACATAAGCTGCTCGAT 59.307 45.455 1.00 0.00 0.00 3.59
2731 4999 2.095461 AGTCTCACATAAGCTGCTCGA 58.905 47.619 1.00 0.00 0.00 4.04
2793 5067 5.064452 GCAGATGAAGATTACCAACTGACAG 59.936 44.000 0.00 0.00 35.89 3.51
2800 5074 3.937814 ACACGCAGATGAAGATTACCAA 58.062 40.909 0.00 0.00 0.00 3.67
2851 5129 9.607988 CATACCAAGTATCAGTAACAAACCATA 57.392 33.333 0.00 0.00 0.00 2.74
2852 5130 7.067008 GCATACCAAGTATCAGTAACAAACCAT 59.933 37.037 0.00 0.00 0.00 3.55
2854 5132 6.373216 TGCATACCAAGTATCAGTAACAAACC 59.627 38.462 0.00 0.00 0.00 3.27
2855 5133 7.372451 TGCATACCAAGTATCAGTAACAAAC 57.628 36.000 0.00 0.00 0.00 2.93
2856 5134 8.574251 AATGCATACCAAGTATCAGTAACAAA 57.426 30.769 0.00 0.00 0.00 2.83
2857 5135 8.574251 AAATGCATACCAAGTATCAGTAACAA 57.426 30.769 0.00 0.00 0.00 2.83
2859 5137 8.458843 ACAAAATGCATACCAAGTATCAGTAAC 58.541 33.333 0.00 0.00 0.00 2.50
2860 5138 8.458052 CACAAAATGCATACCAAGTATCAGTAA 58.542 33.333 0.00 0.00 0.00 2.24
2862 5140 6.434028 ACACAAAATGCATACCAAGTATCAGT 59.566 34.615 0.00 0.00 0.00 3.41
2863 5141 6.855836 ACACAAAATGCATACCAAGTATCAG 58.144 36.000 0.00 0.00 0.00 2.90
2865 5143 6.905076 CGTACACAAAATGCATACCAAGTATC 59.095 38.462 0.00 0.00 0.00 2.24
2868 5146 4.083003 CCGTACACAAAATGCATACCAAGT 60.083 41.667 0.00 0.00 0.00 3.16
2888 5166 2.943033 GCATGAGGCATAAAGTTACCGT 59.057 45.455 0.00 0.00 43.97 4.83
3014 5296 9.270640 CCATTTTTCATTTTCCAACATACTGAA 57.729 29.630 0.00 0.00 0.00 3.02
3020 5302 6.489700 GGTTCCCATTTTTCATTTTCCAACAT 59.510 34.615 0.00 0.00 0.00 2.71
3027 5309 7.284261 ACAAAATCGGTTCCCATTTTTCATTTT 59.716 29.630 4.82 0.00 31.22 1.82
3041 5323 3.251004 AGCAGACAAGACAAAATCGGTTC 59.749 43.478 0.00 0.00 0.00 3.62
3046 5328 5.186996 TGGAAAGCAGACAAGACAAAATC 57.813 39.130 0.00 0.00 0.00 2.17
3112 5394 0.034670 AGCTTGGACTTGGATGGCTC 60.035 55.000 0.00 0.00 0.00 4.70
3114 5396 2.355010 ATAGCTTGGACTTGGATGGC 57.645 50.000 0.00 0.00 0.00 4.40
3160 5446 6.359617 CGTGTGAAAATGACAACTATGGAAAC 59.640 38.462 0.00 0.00 0.00 2.78
3220 5506 4.572389 AGGCTTTGTATGAATTGCTCGTAG 59.428 41.667 0.00 0.00 0.00 3.51
3245 5531 4.503910 TCAACACCTATTGTTCCTCATCG 58.496 43.478 0.00 0.00 46.05 3.84
3303 5589 7.331791 AGTACAAGACAAGGTAGGATCAAATC 58.668 38.462 0.00 0.00 0.00 2.17
3304 5590 7.181125 AGAGTACAAGACAAGGTAGGATCAAAT 59.819 37.037 0.00 0.00 0.00 2.32
3305 5591 6.497259 AGAGTACAAGACAAGGTAGGATCAAA 59.503 38.462 0.00 0.00 0.00 2.69
3306 5592 6.017192 AGAGTACAAGACAAGGTAGGATCAA 58.983 40.000 0.00 0.00 0.00 2.57
3307 5593 5.580998 AGAGTACAAGACAAGGTAGGATCA 58.419 41.667 0.00 0.00 0.00 2.92
3308 5594 7.339976 ACTTAGAGTACAAGACAAGGTAGGATC 59.660 40.741 0.00 0.00 0.00 3.36
3309 5595 7.183460 ACTTAGAGTACAAGACAAGGTAGGAT 58.817 38.462 0.00 0.00 0.00 3.24
3312 5598 7.883217 TCAACTTAGAGTACAAGACAAGGTAG 58.117 38.462 0.00 0.00 0.00 3.18
3313 5599 7.828508 TCAACTTAGAGTACAAGACAAGGTA 57.171 36.000 0.00 0.00 0.00 3.08
3315 5601 7.607250 AGATCAACTTAGAGTACAAGACAAGG 58.393 38.462 0.00 0.00 0.00 3.61
3318 5604 7.385205 GCAAAGATCAACTTAGAGTACAAGACA 59.615 37.037 0.00 0.00 37.93 3.41
3319 5605 7.385205 TGCAAAGATCAACTTAGAGTACAAGAC 59.615 37.037 0.00 0.00 37.93 3.01
3320 5606 7.385205 GTGCAAAGATCAACTTAGAGTACAAGA 59.615 37.037 0.00 0.00 37.93 3.02
3321 5607 7.386299 AGTGCAAAGATCAACTTAGAGTACAAG 59.614 37.037 0.00 0.00 37.93 3.16
3322 5608 7.217200 AGTGCAAAGATCAACTTAGAGTACAA 58.783 34.615 0.00 0.00 37.93 2.41
3325 5611 6.211584 AGGAGTGCAAAGATCAACTTAGAGTA 59.788 38.462 0.00 0.00 37.93 2.59
3326 5612 5.012561 AGGAGTGCAAAGATCAACTTAGAGT 59.987 40.000 0.00 0.00 37.93 3.24
3327 5613 5.486526 AGGAGTGCAAAGATCAACTTAGAG 58.513 41.667 0.00 0.00 37.93 2.43
3328 5614 5.489792 AGGAGTGCAAAGATCAACTTAGA 57.510 39.130 0.00 0.00 37.93 2.10
3330 5616 9.982651 GTATATAGGAGTGCAAAGATCAACTTA 57.017 33.333 0.00 0.00 37.93 2.24
3331 5617 8.709308 AGTATATAGGAGTGCAAAGATCAACTT 58.291 33.333 0.00 0.00 40.98 2.66
3332 5618 8.256356 AGTATATAGGAGTGCAAAGATCAACT 57.744 34.615 0.00 0.00 0.00 3.16
3334 5620 9.588096 TCTAGTATATAGGAGTGCAAAGATCAA 57.412 33.333 0.00 0.00 0.00 2.57
3335 5621 9.015367 GTCTAGTATATAGGAGTGCAAAGATCA 57.985 37.037 0.00 0.00 0.00 2.92
3336 5622 8.463607 GGTCTAGTATATAGGAGTGCAAAGATC 58.536 40.741 0.00 0.00 0.00 2.75
3337 5623 7.950684 TGGTCTAGTATATAGGAGTGCAAAGAT 59.049 37.037 0.00 0.00 0.00 2.40
3340 5626 7.728532 TCATGGTCTAGTATATAGGAGTGCAAA 59.271 37.037 0.00 0.00 0.00 3.68
3343 5629 7.889873 ATCATGGTCTAGTATATAGGAGTGC 57.110 40.000 0.00 0.00 0.00 4.40
3344 5630 9.062524 GCTATCATGGTCTAGTATATAGGAGTG 57.937 40.741 0.00 0.00 0.00 3.51
3346 5632 7.094975 GCGCTATCATGGTCTAGTATATAGGAG 60.095 44.444 0.00 0.00 0.00 3.69
3347 5633 6.711194 GCGCTATCATGGTCTAGTATATAGGA 59.289 42.308 0.00 0.00 0.00 2.94
3348 5634 6.347806 CGCGCTATCATGGTCTAGTATATAGG 60.348 46.154 5.56 0.00 0.00 2.57
3349 5635 6.594886 CGCGCTATCATGGTCTAGTATATAG 58.405 44.000 5.56 0.00 0.00 1.31
3351 5637 4.261238 GCGCGCTATCATGGTCTAGTATAT 60.261 45.833 26.67 0.00 0.00 0.86
3352 5638 3.064958 GCGCGCTATCATGGTCTAGTATA 59.935 47.826 26.67 0.00 0.00 1.47
3353 5639 2.159366 GCGCGCTATCATGGTCTAGTAT 60.159 50.000 26.67 0.00 0.00 2.12
3355 5641 0.039074 GCGCGCTATCATGGTCTAGT 60.039 55.000 26.67 0.00 0.00 2.57
3356 5642 1.067743 CGCGCGCTATCATGGTCTAG 61.068 60.000 30.48 4.24 0.00 2.43
3357 5643 1.081442 CGCGCGCTATCATGGTCTA 60.081 57.895 30.48 0.00 0.00 2.59
3358 5644 2.355126 CGCGCGCTATCATGGTCT 60.355 61.111 30.48 0.00 0.00 3.85
3359 5645 2.237751 AACGCGCGCTATCATGGTC 61.238 57.895 32.58 0.00 0.00 4.02
3361 5647 2.246397 CAACGCGCGCTATCATGG 59.754 61.111 32.58 14.15 0.00 3.66
3362 5648 2.424157 GCAACGCGCGCTATCATG 60.424 61.111 32.58 19.25 0.00 3.07
3378 5664 2.996168 ATAGAATGGACAGGCGCGGC 62.996 60.000 27.06 27.06 0.00 6.53
3380 5666 0.249447 TCATAGAATGGACAGGCGCG 60.249 55.000 0.00 0.00 0.00 6.86
3382 5668 6.205464 ACATTTTATCATAGAATGGACAGGCG 59.795 38.462 11.59 0.00 35.60 5.52
3383 5669 7.516198 ACATTTTATCATAGAATGGACAGGC 57.484 36.000 11.59 0.00 35.60 4.85
3408 7924 9.733556 TGGCTTCAAGTATTTTCACTATTCTTA 57.266 29.630 0.00 0.00 0.00 2.10
3409 7925 8.515414 GTGGCTTCAAGTATTTTCACTATTCTT 58.485 33.333 0.00 0.00 0.00 2.52
3410 7926 7.665559 TGTGGCTTCAAGTATTTTCACTATTCT 59.334 33.333 0.00 0.00 0.00 2.40
3411 7927 7.816640 TGTGGCTTCAAGTATTTTCACTATTC 58.183 34.615 0.00 0.00 0.00 1.75
3412 7928 7.759489 TGTGGCTTCAAGTATTTTCACTATT 57.241 32.000 0.00 0.00 0.00 1.73
3414 7930 7.575414 TTTGTGGCTTCAAGTATTTTCACTA 57.425 32.000 0.00 0.00 0.00 2.74
3415 7931 6.463995 TTTGTGGCTTCAAGTATTTTCACT 57.536 33.333 0.00 0.00 0.00 3.41
3418 7934 7.307337 CCATGTTTTGTGGCTTCAAGTATTTTC 60.307 37.037 0.00 0.00 0.00 2.29
3419 7935 6.482973 CCATGTTTTGTGGCTTCAAGTATTTT 59.517 34.615 0.00 0.00 0.00 1.82
3422 7938 4.832266 TCCATGTTTTGTGGCTTCAAGTAT 59.168 37.500 0.00 0.00 36.66 2.12
3423 7939 4.211125 TCCATGTTTTGTGGCTTCAAGTA 58.789 39.130 0.00 0.00 36.66 2.24
3425 7941 3.731652 TCCATGTTTTGTGGCTTCAAG 57.268 42.857 0.00 0.00 36.66 3.02
3426 7942 4.478206 TTTCCATGTTTTGTGGCTTCAA 57.522 36.364 0.00 0.00 36.66 2.69
3427 7943 4.686191 ATTTCCATGTTTTGTGGCTTCA 57.314 36.364 0.00 0.00 36.66 3.02
3428 7944 7.226523 ACTTAAATTTCCATGTTTTGTGGCTTC 59.773 33.333 0.00 0.00 36.66 3.86
3429 7945 7.053498 ACTTAAATTTCCATGTTTTGTGGCTT 58.947 30.769 0.00 0.00 36.66 4.35
3431 7947 6.859420 ACTTAAATTTCCATGTTTTGTGGC 57.141 33.333 0.00 0.00 36.66 5.01
3432 7948 8.672815 ACAAACTTAAATTTCCATGTTTTGTGG 58.327 29.630 0.00 0.00 38.11 4.17
3442 7958 9.255304 GCAAGTTGATACAAACTTAAATTTCCA 57.745 29.630 7.16 0.00 46.19 3.53
3453 7969 9.098355 TGACTATATGAGCAAGTTGATACAAAC 57.902 33.333 7.16 0.00 0.00 2.93
3457 7973 9.138062 CTGATGACTATATGAGCAAGTTGATAC 57.862 37.037 7.16 0.00 0.00 2.24
3458 7974 8.864087 ACTGATGACTATATGAGCAAGTTGATA 58.136 33.333 7.16 0.00 0.00 2.15
3459 7975 7.733969 ACTGATGACTATATGAGCAAGTTGAT 58.266 34.615 7.16 0.00 0.00 2.57
3460 7976 7.117285 ACTGATGACTATATGAGCAAGTTGA 57.883 36.000 7.16 0.00 0.00 3.18
3461 7977 8.877808 TTACTGATGACTATATGAGCAAGTTG 57.122 34.615 0.00 0.00 0.00 3.16
3463 7979 8.864087 TGATTACTGATGACTATATGAGCAAGT 58.136 33.333 0.00 0.00 0.00 3.16
3464 7980 9.702494 TTGATTACTGATGACTATATGAGCAAG 57.298 33.333 0.00 0.00 0.00 4.01
3467 7983 9.920133 TCTTTGATTACTGATGACTATATGAGC 57.080 33.333 0.00 0.00 0.00 4.26
3525 8143 1.724545 TTCCCAAGGTTCCTCGAAGA 58.275 50.000 0.00 0.00 0.00 2.87
3526 8144 2.561478 TTTCCCAAGGTTCCTCGAAG 57.439 50.000 0.00 0.00 0.00 3.79
3527 8145 3.518992 AATTTCCCAAGGTTCCTCGAA 57.481 42.857 0.00 0.00 0.00 3.71
3528 8146 3.518992 AAATTTCCCAAGGTTCCTCGA 57.481 42.857 0.00 0.00 0.00 4.04
3529 8147 5.914898 ATTAAATTTCCCAAGGTTCCTCG 57.085 39.130 0.00 0.00 0.00 4.63
3530 8148 7.396339 ACTGTATTAAATTTCCCAAGGTTCCTC 59.604 37.037 0.00 0.00 0.00 3.71
3531 8149 7.246027 ACTGTATTAAATTTCCCAAGGTTCCT 58.754 34.615 0.00 0.00 0.00 3.36
3532 8150 7.476540 ACTGTATTAAATTTCCCAAGGTTCC 57.523 36.000 0.00 0.00 0.00 3.62
3534 8152 9.990868 AGATACTGTATTAAATTTCCCAAGGTT 57.009 29.630 1.22 0.00 0.00 3.50
3535 8153 9.628500 GAGATACTGTATTAAATTTCCCAAGGT 57.372 33.333 1.22 0.00 0.00 3.50
3536 8154 9.627123 TGAGATACTGTATTAAATTTCCCAAGG 57.373 33.333 1.22 0.00 0.00 3.61
3548 8166 9.967346 GCACTTCTACATTGAGATACTGTATTA 57.033 33.333 1.22 0.00 0.00 0.98
3549 8167 8.478066 TGCACTTCTACATTGAGATACTGTATT 58.522 33.333 1.22 0.00 0.00 1.89
3550 8168 7.923344 GTGCACTTCTACATTGAGATACTGTAT 59.077 37.037 10.32 0.00 0.00 2.29
3552 8170 6.102663 GTGCACTTCTACATTGAGATACTGT 58.897 40.000 10.32 0.00 0.00 3.55
3553 8171 6.101997 TGTGCACTTCTACATTGAGATACTG 58.898 40.000 19.41 0.00 0.00 2.74
3554 8172 6.286240 TGTGCACTTCTACATTGAGATACT 57.714 37.500 19.41 0.00 0.00 2.12
3555 8173 6.968131 TTGTGCACTTCTACATTGAGATAC 57.032 37.500 19.41 0.00 0.00 2.24
3556 8174 7.105588 ACATTGTGCACTTCTACATTGAGATA 58.894 34.615 19.41 0.00 34.22 1.98
3557 8175 5.942236 ACATTGTGCACTTCTACATTGAGAT 59.058 36.000 19.41 0.00 34.22 2.75
3558 8176 5.308014 ACATTGTGCACTTCTACATTGAGA 58.692 37.500 19.41 0.00 34.22 3.27
3559 8177 5.618056 ACATTGTGCACTTCTACATTGAG 57.382 39.130 19.41 0.00 34.22 3.02
3560 8178 8.829612 CATATACATTGTGCACTTCTACATTGA 58.170 33.333 19.41 0.00 34.22 2.57
3563 8181 8.737168 AACATATACATTGTGCACTTCTACAT 57.263 30.769 19.41 6.98 0.00 2.29
3564 8182 7.821846 TGAACATATACATTGTGCACTTCTACA 59.178 33.333 19.41 0.00 27.36 2.74
3566 8184 8.785329 TTGAACATATACATTGTGCACTTCTA 57.215 30.769 19.41 3.52 32.29 2.10
3567 8185 7.686438 TTGAACATATACATTGTGCACTTCT 57.314 32.000 19.41 0.00 32.29 2.85
3568 8186 7.008628 GCTTTGAACATATACATTGTGCACTTC 59.991 37.037 19.41 9.55 32.29 3.01
3569 8187 6.808212 GCTTTGAACATATACATTGTGCACTT 59.192 34.615 19.41 2.38 32.29 3.16
3571 8189 6.324819 AGCTTTGAACATATACATTGTGCAC 58.675 36.000 10.75 10.75 32.29 4.57
3572 8190 6.513806 AGCTTTGAACATATACATTGTGCA 57.486 33.333 0.00 0.00 30.60 4.57
3573 8191 7.028962 TGAAGCTTTGAACATATACATTGTGC 58.971 34.615 0.00 0.00 0.00 4.57
3575 8193 7.394359 ACCTGAAGCTTTGAACATATACATTGT 59.606 33.333 0.00 0.00 0.00 2.71
3577 8195 7.944729 ACCTGAAGCTTTGAACATATACATT 57.055 32.000 0.00 0.00 0.00 2.71
3587 8887 8.267183 TCATGATCTTATACCTGAAGCTTTGAA 58.733 33.333 0.00 0.00 0.00 2.69
3590 8890 9.941325 CTATCATGATCTTATACCTGAAGCTTT 57.059 33.333 12.53 0.00 0.00 3.51
3620 8920 6.480763 TCTAATCTAGCCTAGTGATCCAGAG 58.519 44.000 0.00 0.00 0.00 3.35
3621 8921 6.455690 TCTAATCTAGCCTAGTGATCCAGA 57.544 41.667 0.00 0.00 0.00 3.86
3623 8923 6.191315 GGATCTAATCTAGCCTAGTGATCCA 58.809 44.000 23.78 1.35 44.63 3.41
3624 8924 5.298276 CGGATCTAATCTAGCCTAGTGATCC 59.702 48.000 21.47 21.47 42.91 3.36
3625 8925 5.298276 CCGGATCTAATCTAGCCTAGTGATC 59.702 48.000 0.00 8.00 0.00 2.92
3627 8927 4.043059 ACCGGATCTAATCTAGCCTAGTGA 59.957 45.833 9.46 0.00 0.00 3.41
3630 8930 6.127675 GGTTTACCGGATCTAATCTAGCCTAG 60.128 46.154 9.46 0.00 0.00 3.02
3631 8931 5.713861 GGTTTACCGGATCTAATCTAGCCTA 59.286 44.000 9.46 0.00 0.00 3.93
3632 8932 4.527427 GGTTTACCGGATCTAATCTAGCCT 59.473 45.833 9.46 0.00 0.00 4.58
3633 8933 4.527427 AGGTTTACCGGATCTAATCTAGCC 59.473 45.833 9.46 0.00 42.08 3.93
3634 8934 5.725325 AGGTTTACCGGATCTAATCTAGC 57.275 43.478 9.46 0.00 42.08 3.42
3635 8935 7.155655 GGTAGGTTTACCGGATCTAATCTAG 57.844 44.000 9.46 0.00 40.02 2.43
3649 8949 2.484264 CTGCTGCACAAGGTAGGTTTAC 59.516 50.000 0.00 0.00 0.00 2.01
3650 8950 2.105821 ACTGCTGCACAAGGTAGGTTTA 59.894 45.455 0.00 0.00 0.00 2.01
3652 8952 0.474184 ACTGCTGCACAAGGTAGGTT 59.526 50.000 0.00 0.00 0.00 3.50
3653 8953 1.276421 CTACTGCTGCACAAGGTAGGT 59.724 52.381 15.26 5.73 0.00 3.08
3654 8954 1.550524 TCTACTGCTGCACAAGGTAGG 59.449 52.381 20.06 3.91 33.06 3.18
3656 8956 2.831526 TCATCTACTGCTGCACAAGGTA 59.168 45.455 0.00 0.00 0.00 3.08
3657 8957 1.625315 TCATCTACTGCTGCACAAGGT 59.375 47.619 0.00 0.00 0.00 3.50
3659 8959 3.332919 AGTTCATCTACTGCTGCACAAG 58.667 45.455 0.00 0.00 0.00 3.16
3660 8960 3.329386 GAGTTCATCTACTGCTGCACAA 58.671 45.455 0.00 0.00 0.00 3.33
3661 8961 2.672195 CGAGTTCATCTACTGCTGCACA 60.672 50.000 0.00 0.00 0.00 4.57
3663 8963 1.818674 TCGAGTTCATCTACTGCTGCA 59.181 47.619 0.88 0.88 0.00 4.41
3664 8964 2.458951 CTCGAGTTCATCTACTGCTGC 58.541 52.381 3.62 0.00 0.00 5.25
3665 8965 2.098934 AGCTCGAGTTCATCTACTGCTG 59.901 50.000 15.13 0.00 0.00 4.41
3666 8966 2.098934 CAGCTCGAGTTCATCTACTGCT 59.901 50.000 15.13 0.00 0.00 4.24
3667 8967 2.458951 CAGCTCGAGTTCATCTACTGC 58.541 52.381 15.13 0.00 0.00 4.40
3668 8968 2.685388 TCCAGCTCGAGTTCATCTACTG 59.315 50.000 15.13 9.61 0.00 2.74
3669 8969 3.006112 TCCAGCTCGAGTTCATCTACT 57.994 47.619 15.13 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.