Multiple sequence alignment - TraesCS1B01G320000

Loading Multiple Alignment...

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 TraesCS1B01G320000 chr1B 100.000 4121 0 0 1 4121 544133516 544129396 0.000000e+00 7611.0
1 TraesCS1B01G320000 chr1B 90.164 61 3 2 1276 1333 544132192 544132132 4.420000e-10 76.8
2 TraesCS1B01G320000 chr1B 90.164 61 3 2 1325 1385 544132241 544132184 4.420000e-10 76.8
3 TraesCS1B01G320000 chr1D 94.043 3794 149 35 231 3983 404493249 404489492 0.000000e+00 5683.0
4 TraesCS1B01G320000 chr1D 84.058 138 10 1 13 150 404493408 404493283 5.590000e-24 122.0
5 TraesCS1B01G320000 chr1A 93.136 2739 132 29 1276 3983 499981459 499978746 0.000000e+00 3965.0
6 TraesCS1B01G320000 chr1A 87.643 1311 90 33 109 1385 499982671 499981399 0.000000e+00 1458.0
7 TraesCS1B01G320000 chr1A 98.077 52 1 0 1334 1385 499981502 499981451 1.580000e-14 91.6
8 TraesCS1B01G320000 chr1A 86.885 61 5 2 1276 1333 499981407 499981347 9.560000e-07 65.8
9 TraesCS1B01G320000 chr4D 90.411 73 7 0 1657 1729 452550053 452549981 3.390000e-16 97.1
10 TraesCS1B01G320000 chr4A 90.411 73 7 0 1657 1729 14357048 14357120 3.390000e-16 97.1


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 TraesCS1B01G320000 chr1B 544129396 544133516 4120 True 2588.2 7611 93.442667 1 4121 3 chr1B.!!$R1 4120
1 TraesCS1B01G320000 chr1D 404489492 404493408 3916 True 2902.5 5683 89.050500 13 3983 2 chr1D.!!$R1 3970
2 TraesCS1B01G320000 chr1A 499978746 499982671 3925 True 1395.1 3965 91.435250 109 3983 4 chr1A.!!$R1 3874

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
228 229 0.100146 GCTTATGAGCTGTGCCTTGC 59.900 55.0 1.49 0.0 45.65 4.01 F
289 290 0.109597 GTTGGAATTCTGTGCTGGCG 60.110 55.0 5.23 0.0 0.00 5.69 F
1413 1505 0.308993 GAACCTTGTCAGCAGCACAC 59.691 55.0 0.00 0.0 0.00 3.82 F
2607 2723 0.111639 TACTTGGGTGGGTTCCTTGC 59.888 55.0 0.00 0.0 0.00 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1693 1797 0.954452 GCAGACACAGTTCCAAAGGG 59.046 55.0 0.00 0.0 0.00 3.95 R
1881 1985 1.167851 CTGGCACACCCATTACAGTG 58.832 55.0 0.00 0.0 44.33 3.66 R
2950 3067 0.179111 GACAGATCATCCAACCGCGA 60.179 55.0 8.23 0.0 0.00 5.87 R
4060 4201 0.033228 CAGAGGCCGATGCTAGAAGG 59.967 60.0 0.00 0.0 37.74 3.46 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
33 34 3.748048 TGTGAATTTTCTGGAGCTTCTCG 59.252 43.478 0.00 0.00 0.00 4.04
47 48 2.611292 GCTTCTCGTGAGATTCCATTGG 59.389 50.000 0.00 0.00 40.84 3.16
52 53 1.399440 CGTGAGATTCCATTGGCTGTG 59.601 52.381 0.00 0.00 0.00 3.66
68 69 3.660571 TGGCCTGTGGGTGGATGG 61.661 66.667 3.32 0.00 34.45 3.51
69 70 3.661648 GGCCTGTGGGTGGATGGT 61.662 66.667 0.00 0.00 34.45 3.55
70 71 2.440599 GCCTGTGGGTGGATGGTT 59.559 61.111 0.00 0.00 34.45 3.67
76 77 1.073763 TGTGGGTGGATGGTTGAAGAG 59.926 52.381 0.00 0.00 0.00 2.85
84 85 3.279434 GGATGGTTGAAGAGCGGTATTT 58.721 45.455 0.00 0.00 0.00 1.40
85 86 4.080807 TGGATGGTTGAAGAGCGGTATTTA 60.081 41.667 0.00 0.00 0.00 1.40
86 87 4.879545 GGATGGTTGAAGAGCGGTATTTAA 59.120 41.667 0.00 0.00 0.00 1.52
87 88 5.355910 GGATGGTTGAAGAGCGGTATTTAAA 59.644 40.000 0.55 0.00 0.00 1.52
88 89 6.127842 GGATGGTTGAAGAGCGGTATTTAAAA 60.128 38.462 0.55 0.00 0.00 1.52
89 90 6.636562 TGGTTGAAGAGCGGTATTTAAAAA 57.363 33.333 0.55 0.00 0.00 1.94
168 169 2.006772 CGAAGCTTGGTATGGCGAC 58.993 57.895 2.10 0.00 0.00 5.19
169 170 1.752501 CGAAGCTTGGTATGGCGACG 61.753 60.000 2.10 0.00 0.00 5.12
170 171 2.036764 GAAGCTTGGTATGGCGACGC 62.037 60.000 12.43 12.43 0.00 5.19
207 208 6.478512 TTTCCTTGCTCATAAACCTGTTTT 57.521 33.333 0.00 0.00 34.23 2.43
210 211 3.658757 TGCTCATAAACCTGTTTTGGC 57.341 42.857 0.00 6.20 34.23 4.52
228 229 0.100146 GCTTATGAGCTGTGCCTTGC 59.900 55.000 1.49 0.00 45.65 4.01
245 246 0.749091 TGCTGCTGTGCTGACTTGTT 60.749 50.000 0.00 0.00 0.00 2.83
263 264 0.175760 TTCGATTCTGAGGCCGGAAG 59.824 55.000 5.05 0.00 40.68 3.46
278 279 1.304962 GAAGGGCCGGGTTGGAATT 60.305 57.895 2.18 0.00 42.00 2.17
279 280 1.304962 AAGGGCCGGGTTGGAATTC 60.305 57.895 2.18 0.00 42.00 2.17
289 290 0.109597 GTTGGAATTCTGTGCTGGCG 60.110 55.000 5.23 0.00 0.00 5.69
339 341 1.226575 CGATTCGACCTGCAGCGTA 60.227 57.895 8.66 1.48 0.00 4.42
364 369 4.741321 TTTGCCCATCCAGATTCATTTC 57.259 40.909 0.00 0.00 0.00 2.17
386 393 2.538222 TGTGGATCATTTGCCATGGTT 58.462 42.857 14.67 0.00 36.41 3.67
410 417 4.631813 GTCTAGTGACTTCGATTGGCATTT 59.368 41.667 0.00 0.00 39.94 2.32
412 419 2.489329 AGTGACTTCGATTGGCATTTGG 59.511 45.455 0.00 0.00 0.00 3.28
451 470 2.564771 TGCAGTTCTATGGCAGCATAC 58.435 47.619 0.00 0.00 32.95 2.39
452 471 2.093021 TGCAGTTCTATGGCAGCATACA 60.093 45.455 0.00 0.00 32.95 2.29
512 531 5.301551 TCTTCCTCTGTTGCTTGCAAATTTA 59.698 36.000 9.75 0.00 0.00 1.40
538 561 3.791320 TCTTCCTACCATGTGGAGTTCT 58.209 45.455 5.96 0.00 38.94 3.01
592 616 7.214467 TCATGTGATTTGGAGAGGTTAAAAC 57.786 36.000 0.00 0.00 0.00 2.43
599 623 7.391554 TGATTTGGAGAGGTTAAAACTCATCTG 59.608 37.037 10.14 0.00 37.43 2.90
612 639 9.990360 TTAAAACTCATCTGTACATCTGTAACA 57.010 29.630 0.00 0.00 31.52 2.41
695 733 9.679661 AAAGATTTGTTTTTCTTGGTTATGGTT 57.320 25.926 0.00 0.00 32.65 3.67
809 847 5.047660 AGACTTAGCAACTTCTCGACATCTT 60.048 40.000 0.00 0.00 0.00 2.40
888 926 2.159653 CGTACCAGAAAATGCTCAGTGC 60.160 50.000 0.00 0.00 43.25 4.40
920 958 4.794169 ACATTTTGCCGTCAACTTGATAC 58.206 39.130 0.00 0.00 30.75 2.24
1126 1164 7.775093 AGCATGTAAGTAATATTGGAGCTTTCA 59.225 33.333 0.00 2.82 0.00 2.69
1131 1169 5.440610 AGTAATATTGGAGCTTTCAGTGGG 58.559 41.667 0.00 0.00 0.00 4.61
1150 1188 2.025699 GGGTCCAACATAAGCAACCCTA 60.026 50.000 1.10 0.00 42.54 3.53
1179 1217 0.688487 TAGGGAGTGGGAAACAACGG 59.312 55.000 0.00 0.00 0.00 4.44
1182 1220 1.515521 GGAGTGGGAAACAACGGCTG 61.516 60.000 0.00 0.00 0.00 4.85
1413 1505 0.308993 GAACCTTGTCAGCAGCACAC 59.691 55.000 0.00 0.00 0.00 3.82
1471 1563 3.475566 TGCATATCTAGAACCTGCACC 57.524 47.619 18.09 0.00 37.88 5.01
1475 1567 2.409948 ATCTAGAACCTGCACCTTGC 57.590 50.000 0.00 0.00 45.29 4.01
1510 1602 5.532032 TCGAATCCATTGTGTATCATGCATT 59.468 36.000 0.00 0.00 0.00 3.56
1564 1660 8.537049 TTCCAAATGTTTATGAAGCAGATTTG 57.463 30.769 0.00 0.00 0.00 2.32
1667 1771 4.738252 CCTCATGTTTCAATGATTCATGCG 59.262 41.667 17.13 13.30 36.03 4.73
1693 1797 8.934507 AGTCTGCTAGAAGTTGTTAATATGAC 57.065 34.615 0.00 0.00 0.00 3.06
1821 1925 6.878389 TGAAGTACACAAGATACAATGCATCA 59.122 34.615 0.00 0.00 0.00 3.07
1881 1985 4.496360 GAGCAACACCTAAAGGAGTACTC 58.504 47.826 14.87 14.87 38.05 2.59
1896 2000 4.495422 GAGTACTCACTGTAATGGGTGTG 58.505 47.826 18.20 0.00 33.07 3.82
1899 2003 0.767998 TCACTGTAATGGGTGTGCCA 59.232 50.000 0.00 0.00 36.17 4.92
1902 2006 0.327924 CTGTAATGGGTGTGCCAGGA 59.672 55.000 0.00 0.00 36.17 3.86
1943 2047 3.766545 AGAGCCATTTGCAGGTAAAGAA 58.233 40.909 0.00 0.00 44.83 2.52
1952 2056 6.560253 TTTGCAGGTAAAGAATGTCTCTTC 57.440 37.500 0.00 0.00 44.00 2.87
2154 2259 5.885352 AGCTTTGGTTTTTAAAATTGGCAGT 59.115 32.000 0.55 0.00 0.00 4.40
2273 2378 5.176406 CACATGATTGTATCCTCTGCTAACG 59.824 44.000 0.00 0.00 33.76 3.18
2279 2384 1.041437 ATCCTCTGCTAACGTAGGCC 58.959 55.000 0.00 0.00 0.00 5.19
2306 2412 8.518430 TTTAAGCTGGTTGATATCATGCTAAA 57.482 30.769 17.35 14.92 0.00 1.85
2417 2524 0.250901 AGCGGCTCCATGAACAACTT 60.251 50.000 0.00 0.00 0.00 2.66
2431 2538 4.097741 TGAACAACTTGAGGTTTGTGATGG 59.902 41.667 0.00 0.00 35.74 3.51
2511 2618 4.737054 CCACATCCATGCTGTACTTTTTC 58.263 43.478 0.00 0.00 0.00 2.29
2512 2619 4.218200 CCACATCCATGCTGTACTTTTTCA 59.782 41.667 0.00 0.00 0.00 2.69
2607 2723 0.111639 TACTTGGGTGGGTTCCTTGC 59.888 55.000 0.00 0.00 0.00 4.01
2766 2883 9.593134 AAGACTAGACTAAATCATCACATGTTC 57.407 33.333 0.00 0.00 0.00 3.18
2950 3067 4.446371 CATACAGCCTTCTCCGAAGAAAT 58.554 43.478 5.24 0.00 40.95 2.17
3042 3159 1.396653 GCCCATGGGATCAAGAACTG 58.603 55.000 36.00 3.15 37.50 3.16
3136 3253 4.835056 AGTCATAAAGCAAAGCCTTCCTTT 59.165 37.500 7.80 7.80 44.45 3.11
3167 3284 7.661847 AGGAAACACTTCTGAGTTATTAACCTG 59.338 37.037 2.92 0.71 32.54 4.00
3284 3401 4.247258 ACTAAGTGTTGTTGTCGTTGTCA 58.753 39.130 0.00 0.00 0.00 3.58
3354 3471 3.282885 CCAGTTAGCAATCCCCTTCTTC 58.717 50.000 0.00 0.00 0.00 2.87
3394 3511 5.821204 ACTGAAACATGTAGCAAGAAACAC 58.179 37.500 0.00 0.00 0.00 3.32
3396 3513 6.127758 ACTGAAACATGTAGCAAGAAACACAA 60.128 34.615 0.00 0.00 0.00 3.33
3397 3514 6.625362 TGAAACATGTAGCAAGAAACACAAA 58.375 32.000 0.00 0.00 0.00 2.83
3398 3515 6.751425 TGAAACATGTAGCAAGAAACACAAAG 59.249 34.615 0.00 0.00 0.00 2.77
3474 3592 3.744660 ACATTCCTGTTCAGTTCAGTCC 58.255 45.455 0.00 0.00 28.70 3.85
3658 3776 5.105392 AGCACTGAACAATGTTCCTTTCAAA 60.105 36.000 21.75 2.16 0.00 2.69
3660 3778 5.232838 CACTGAACAATGTTCCTTTCAAAGC 59.767 40.000 21.75 0.00 0.00 3.51
3661 3779 5.105392 ACTGAACAATGTTCCTTTCAAAGCA 60.105 36.000 21.75 0.72 0.00 3.91
3663 3781 6.347696 TGAACAATGTTCCTTTCAAAGCATT 58.652 32.000 21.75 0.00 0.00 3.56
3664 3782 6.258287 TGAACAATGTTCCTTTCAAAGCATTG 59.742 34.615 21.75 19.49 44.83 2.82
3665 3783 4.512571 ACAATGTTCCTTTCAAAGCATTGC 59.487 37.500 20.38 0.00 43.82 3.56
3666 3784 2.741612 TGTTCCTTTCAAAGCATTGCG 58.258 42.857 2.38 0.00 36.45 4.85
3667 3785 2.100584 TGTTCCTTTCAAAGCATTGCGT 59.899 40.909 2.38 0.00 36.45 5.24
3669 3787 3.451141 TCCTTTCAAAGCATTGCGTTT 57.549 38.095 7.10 4.02 36.45 3.60
3670 3788 4.576216 TCCTTTCAAAGCATTGCGTTTA 57.424 36.364 7.10 0.00 36.45 2.01
3671 3789 4.295051 TCCTTTCAAAGCATTGCGTTTAC 58.705 39.130 7.10 0.00 36.45 2.01
3672 3790 3.119463 CCTTTCAAAGCATTGCGTTTACG 59.881 43.478 7.10 0.00 43.27 3.18
3674 3792 3.181826 TCAAAGCATTGCGTTTACGAG 57.818 42.857 7.10 0.00 41.87 4.18
3675 3793 2.095969 TCAAAGCATTGCGTTTACGAGG 60.096 45.455 7.10 0.00 41.87 4.63
3676 3794 1.519408 AAGCATTGCGTTTACGAGGT 58.481 45.000 6.44 0.00 43.02 3.85
3677 3795 1.519408 AGCATTGCGTTTACGAGGTT 58.481 45.000 6.44 0.00 43.02 3.50
3678 3796 1.196808 AGCATTGCGTTTACGAGGTTG 59.803 47.619 6.44 0.00 43.02 3.77
3679 3797 1.727857 GCATTGCGTTTACGAGGTTGG 60.728 52.381 6.44 0.00 43.02 3.77
3680 3798 1.533731 CATTGCGTTTACGAGGTTGGT 59.466 47.619 6.44 0.00 43.02 3.67
3681 3799 1.666054 TTGCGTTTACGAGGTTGGTT 58.334 45.000 6.44 0.00 43.02 3.67
3682 3800 0.938713 TGCGTTTACGAGGTTGGTTG 59.061 50.000 6.44 0.00 43.02 3.77
3683 3801 0.939419 GCGTTTACGAGGTTGGTTGT 59.061 50.000 6.44 0.00 43.02 3.32
3684 3802 2.134346 GCGTTTACGAGGTTGGTTGTA 58.866 47.619 6.44 0.00 43.02 2.41
3685 3803 2.096762 GCGTTTACGAGGTTGGTTGTAC 60.097 50.000 6.44 0.00 43.02 2.90
3686 3804 3.383761 CGTTTACGAGGTTGGTTGTACT 58.616 45.455 0.00 0.00 43.02 2.73
3687 3805 4.545610 CGTTTACGAGGTTGGTTGTACTA 58.454 43.478 0.00 0.00 43.02 1.82
3688 3806 5.163513 CGTTTACGAGGTTGGTTGTACTAT 58.836 41.667 0.00 0.00 43.02 2.12
3689 3807 5.634859 CGTTTACGAGGTTGGTTGTACTATT 59.365 40.000 0.00 0.00 43.02 1.73
3690 3808 6.146021 CGTTTACGAGGTTGGTTGTACTATTT 59.854 38.462 0.00 0.00 43.02 1.40
3691 3809 7.328249 CGTTTACGAGGTTGGTTGTACTATTTA 59.672 37.037 0.00 0.00 43.02 1.40
3692 3810 8.435430 GTTTACGAGGTTGGTTGTACTATTTAC 58.565 37.037 0.00 0.00 0.00 2.01
3693 3811 5.163513 ACGAGGTTGGTTGTACTATTTACG 58.836 41.667 0.00 0.00 0.00 3.18
3761 3879 2.816087 CACAGGCTTTCAATGCTAGTGT 59.184 45.455 10.42 3.76 33.80 3.55
3789 3925 5.009631 CAGAATCACATACCTTGGGTTGAA 58.990 41.667 0.00 0.00 37.09 2.69
3897 4038 2.040544 CGTGGAGGCGGATGCTTTT 61.041 57.895 0.00 0.00 42.25 2.27
3911 4052 5.220265 CGGATGCTTTTGTACATGCATTTTC 60.220 40.000 23.12 15.63 44.80 2.29
3915 4056 4.804108 CTTTTGTACATGCATTTTCCCGA 58.196 39.130 0.00 0.00 0.00 5.14
3932 4073 5.698741 TCCCGATCATGCCAGATAATAAT 57.301 39.130 0.00 0.00 0.00 1.28
3943 4084 6.591001 TGCCAGATAATAATTCACAGCTGTA 58.409 36.000 21.20 5.19 0.00 2.74
3985 4126 8.841444 AAAACTATTAGCATCAAAGCATTACG 57.159 30.769 0.00 0.00 36.85 3.18
3986 4127 7.553881 AACTATTAGCATCAAAGCATTACGT 57.446 32.000 0.00 0.00 36.85 3.57
3987 4128 7.553881 ACTATTAGCATCAAAGCATTACGTT 57.446 32.000 0.00 0.00 36.85 3.99
3988 4129 7.985476 ACTATTAGCATCAAAGCATTACGTTT 58.015 30.769 0.00 0.00 36.85 3.60
3989 4130 8.122952 ACTATTAGCATCAAAGCATTACGTTTC 58.877 33.333 0.00 0.00 36.85 2.78
3990 4131 4.096732 AGCATCAAAGCATTACGTTTCC 57.903 40.909 0.00 0.00 36.85 3.13
3991 4132 2.845967 GCATCAAAGCATTACGTTTCCG 59.154 45.455 0.00 0.00 40.83 4.30
3992 4133 3.425404 CATCAAAGCATTACGTTTCCGG 58.575 45.455 0.00 0.00 38.78 5.14
3993 4134 2.768698 TCAAAGCATTACGTTTCCGGA 58.231 42.857 0.00 0.00 38.78 5.14
3994 4135 2.739913 TCAAAGCATTACGTTTCCGGAG 59.260 45.455 3.34 0.00 38.78 4.63
3995 4136 2.739913 CAAAGCATTACGTTTCCGGAGA 59.260 45.455 3.34 0.00 38.78 3.71
3996 4137 2.005971 AGCATTACGTTTCCGGAGAC 57.994 50.000 15.04 15.04 38.78 3.36
3997 4138 1.274167 AGCATTACGTTTCCGGAGACA 59.726 47.619 23.53 6.04 38.78 3.41
3998 4139 2.093658 AGCATTACGTTTCCGGAGACAT 60.094 45.455 23.53 12.42 38.78 3.06
3999 4140 2.284417 GCATTACGTTTCCGGAGACATC 59.716 50.000 23.53 4.91 38.78 3.06
4000 4141 3.517602 CATTACGTTTCCGGAGACATCA 58.482 45.455 23.53 1.47 38.78 3.07
4001 4142 2.933495 TACGTTTCCGGAGACATCAG 57.067 50.000 23.53 10.52 38.78 2.90
4002 4143 0.966920 ACGTTTCCGGAGACATCAGT 59.033 50.000 23.53 11.13 38.78 3.41
4003 4144 2.165167 ACGTTTCCGGAGACATCAGTA 58.835 47.619 23.53 0.00 38.78 2.74
4004 4145 2.163815 ACGTTTCCGGAGACATCAGTAG 59.836 50.000 23.53 8.83 38.78 2.57
4005 4146 2.422479 CGTTTCCGGAGACATCAGTAGA 59.578 50.000 23.53 0.00 0.00 2.59
4006 4147 3.119602 CGTTTCCGGAGACATCAGTAGAA 60.120 47.826 23.53 0.00 0.00 2.10
4007 4148 4.174762 GTTTCCGGAGACATCAGTAGAAC 58.825 47.826 19.71 5.90 0.00 3.01
4008 4149 3.081710 TCCGGAGACATCAGTAGAACA 57.918 47.619 0.00 0.00 0.00 3.18
4009 4150 3.632333 TCCGGAGACATCAGTAGAACAT 58.368 45.455 0.00 0.00 0.00 2.71
4010 4151 4.788679 TCCGGAGACATCAGTAGAACATA 58.211 43.478 0.00 0.00 0.00 2.29
4011 4152 4.822350 TCCGGAGACATCAGTAGAACATAG 59.178 45.833 0.00 0.00 0.00 2.23
4012 4153 4.580995 CCGGAGACATCAGTAGAACATAGT 59.419 45.833 0.00 0.00 0.00 2.12
4013 4154 5.067936 CCGGAGACATCAGTAGAACATAGTT 59.932 44.000 0.00 0.00 0.00 2.24
4014 4155 6.405953 CCGGAGACATCAGTAGAACATAGTTT 60.406 42.308 0.00 0.00 0.00 2.66
4015 4156 6.693545 CGGAGACATCAGTAGAACATAGTTTC 59.306 42.308 0.00 0.00 0.00 2.78
4016 4157 6.981559 GGAGACATCAGTAGAACATAGTTTCC 59.018 42.308 0.00 0.00 0.00 3.13
4017 4158 6.565234 AGACATCAGTAGAACATAGTTTCCG 58.435 40.000 0.00 0.00 0.00 4.30
4018 4159 5.661458 ACATCAGTAGAACATAGTTTCCGG 58.339 41.667 0.00 0.00 0.00 5.14
4019 4160 5.421056 ACATCAGTAGAACATAGTTTCCGGA 59.579 40.000 0.00 0.00 0.00 5.14
4020 4161 5.578005 TCAGTAGAACATAGTTTCCGGAG 57.422 43.478 3.34 0.00 0.00 4.63
4021 4162 5.258841 TCAGTAGAACATAGTTTCCGGAGA 58.741 41.667 3.34 0.00 0.00 3.71
4022 4163 5.125097 TCAGTAGAACATAGTTTCCGGAGAC 59.875 44.000 17.16 17.16 0.00 3.36
4023 4164 5.014858 AGTAGAACATAGTTTCCGGAGACA 58.985 41.667 25.51 12.76 0.00 3.41
4024 4165 5.657302 AGTAGAACATAGTTTCCGGAGACAT 59.343 40.000 25.51 14.32 0.00 3.06
4025 4166 5.012328 AGAACATAGTTTCCGGAGACATC 57.988 43.478 25.51 14.80 0.00 3.06
4026 4167 4.466370 AGAACATAGTTTCCGGAGACATCA 59.534 41.667 25.51 11.51 0.00 3.07
4027 4168 4.392921 ACATAGTTTCCGGAGACATCAG 57.607 45.455 25.51 14.64 0.00 2.90
4028 4169 3.769844 ACATAGTTTCCGGAGACATCAGT 59.230 43.478 25.51 15.21 0.00 3.41
4029 4170 4.954202 ACATAGTTTCCGGAGACATCAGTA 59.046 41.667 25.51 10.23 0.00 2.74
4030 4171 5.067936 ACATAGTTTCCGGAGACATCAGTAG 59.932 44.000 25.51 10.91 0.00 2.57
4031 4172 3.698289 AGTTTCCGGAGACATCAGTAGA 58.302 45.455 25.51 0.00 0.00 2.59
4032 4173 4.282496 AGTTTCCGGAGACATCAGTAGAT 58.718 43.478 25.51 0.00 33.87 1.98
4033 4174 4.339814 AGTTTCCGGAGACATCAGTAGATC 59.660 45.833 25.51 0.00 30.20 2.75
4034 4175 2.865079 TCCGGAGACATCAGTAGATCC 58.135 52.381 0.00 0.00 30.20 3.36
4035 4176 2.443632 TCCGGAGACATCAGTAGATCCT 59.556 50.000 0.00 0.00 30.20 3.24
4036 4177 3.117474 TCCGGAGACATCAGTAGATCCTT 60.117 47.826 0.00 0.00 30.20 3.36
4037 4178 4.104261 TCCGGAGACATCAGTAGATCCTTA 59.896 45.833 0.00 0.00 30.20 2.69
4038 4179 4.216687 CCGGAGACATCAGTAGATCCTTAC 59.783 50.000 0.00 0.00 30.20 2.34
4039 4180 4.083749 CGGAGACATCAGTAGATCCTTACG 60.084 50.000 0.00 0.00 30.20 3.18
4040 4181 4.216687 GGAGACATCAGTAGATCCTTACGG 59.783 50.000 0.00 0.00 30.20 4.02
4041 4182 5.050126 AGACATCAGTAGATCCTTACGGA 57.950 43.478 0.00 0.00 45.16 4.69
4042 4183 5.446860 AGACATCAGTAGATCCTTACGGAA 58.553 41.667 0.00 0.00 44.02 4.30
4043 4184 5.533154 AGACATCAGTAGATCCTTACGGAAG 59.467 44.000 0.00 0.00 44.02 3.46
4044 4185 5.446860 ACATCAGTAGATCCTTACGGAAGA 58.553 41.667 9.60 0.00 44.02 2.87
4045 4186 5.892119 ACATCAGTAGATCCTTACGGAAGAA 59.108 40.000 9.60 0.00 44.02 2.52
4046 4187 6.551601 ACATCAGTAGATCCTTACGGAAGAAT 59.448 38.462 9.60 0.00 44.02 2.40
4047 4188 6.636562 TCAGTAGATCCTTACGGAAGAATC 57.363 41.667 9.60 3.01 44.02 2.52
4048 4189 5.238868 TCAGTAGATCCTTACGGAAGAATCG 59.761 44.000 9.60 0.00 44.02 3.34
4049 4190 4.519730 AGTAGATCCTTACGGAAGAATCGG 59.480 45.833 9.60 0.00 44.02 4.18
4050 4191 3.563223 AGATCCTTACGGAAGAATCGGA 58.437 45.455 9.60 0.00 44.02 4.55
4051 4192 4.153411 AGATCCTTACGGAAGAATCGGAT 58.847 43.478 9.60 3.00 44.02 4.18
4052 4193 4.218852 AGATCCTTACGGAAGAATCGGATC 59.781 45.833 9.60 12.88 44.02 3.36
4053 4194 3.293337 TCCTTACGGAAGAATCGGATCA 58.707 45.455 9.60 0.00 36.03 2.92
4054 4195 3.895656 TCCTTACGGAAGAATCGGATCAT 59.104 43.478 9.60 0.00 36.03 2.45
4055 4196 4.022242 TCCTTACGGAAGAATCGGATCATC 60.022 45.833 9.60 0.00 36.03 2.92
4056 4197 4.262036 CCTTACGGAAGAATCGGATCATCA 60.262 45.833 9.60 0.00 34.25 3.07
4057 4198 3.819564 ACGGAAGAATCGGATCATCAA 57.180 42.857 0.00 0.00 0.00 2.57
4058 4199 3.722147 ACGGAAGAATCGGATCATCAAG 58.278 45.455 0.00 0.00 0.00 3.02
4059 4200 2.478134 CGGAAGAATCGGATCATCAAGC 59.522 50.000 0.00 0.00 0.00 4.01
4060 4201 2.810852 GGAAGAATCGGATCATCAAGCC 59.189 50.000 0.00 0.00 0.00 4.35
4061 4202 2.557920 AGAATCGGATCATCAAGCCC 57.442 50.000 0.00 0.00 0.00 5.19
4062 4203 2.053244 AGAATCGGATCATCAAGCCCT 58.947 47.619 0.00 0.00 0.00 5.19
4063 4204 2.441001 AGAATCGGATCATCAAGCCCTT 59.559 45.455 0.00 0.00 0.00 3.95
4064 4205 2.557920 ATCGGATCATCAAGCCCTTC 57.442 50.000 0.00 0.00 0.00 3.46
4065 4206 1.500474 TCGGATCATCAAGCCCTTCT 58.500 50.000 0.00 0.00 0.00 2.85
4066 4207 2.677914 TCGGATCATCAAGCCCTTCTA 58.322 47.619 0.00 0.00 0.00 2.10
4067 4208 2.630098 TCGGATCATCAAGCCCTTCTAG 59.370 50.000 0.00 0.00 0.00 2.43
4068 4209 2.777094 GGATCATCAAGCCCTTCTAGC 58.223 52.381 0.00 0.00 0.00 3.42
4069 4210 2.105477 GGATCATCAAGCCCTTCTAGCA 59.895 50.000 0.00 0.00 0.00 3.49
4070 4211 3.244840 GGATCATCAAGCCCTTCTAGCAT 60.245 47.826 0.00 0.00 0.00 3.79
4071 4212 3.482156 TCATCAAGCCCTTCTAGCATC 57.518 47.619 0.00 0.00 0.00 3.91
4072 4213 2.141517 CATCAAGCCCTTCTAGCATCG 58.858 52.381 0.00 0.00 0.00 3.84
4073 4214 0.465705 TCAAGCCCTTCTAGCATCGG 59.534 55.000 0.00 0.00 0.00 4.18
4074 4215 1.147153 AAGCCCTTCTAGCATCGGC 59.853 57.895 0.00 0.00 40.03 5.54
4075 4216 2.281139 GCCCTTCTAGCATCGGCC 60.281 66.667 0.00 0.00 42.56 6.13
4076 4217 2.812619 GCCCTTCTAGCATCGGCCT 61.813 63.158 0.00 0.00 42.56 5.19
4077 4218 1.369321 CCCTTCTAGCATCGGCCTC 59.631 63.158 0.00 0.00 42.56 4.70
4078 4219 1.118356 CCCTTCTAGCATCGGCCTCT 61.118 60.000 0.00 0.00 42.56 3.69
4079 4220 0.033228 CCTTCTAGCATCGGCCTCTG 59.967 60.000 0.00 0.00 42.56 3.35
4080 4221 0.033228 CTTCTAGCATCGGCCTCTGG 59.967 60.000 0.00 0.00 42.56 3.86
4081 4222 0.397114 TTCTAGCATCGGCCTCTGGA 60.397 55.000 0.00 0.00 42.56 3.86
4082 4223 0.825425 TCTAGCATCGGCCTCTGGAG 60.825 60.000 0.00 0.00 42.56 3.86
4083 4224 0.825425 CTAGCATCGGCCTCTGGAGA 60.825 60.000 0.00 0.00 42.56 3.71
4084 4225 0.397114 TAGCATCGGCCTCTGGAGAA 60.397 55.000 0.00 0.00 42.56 2.87
4085 4226 1.522580 GCATCGGCCTCTGGAGAAC 60.523 63.158 0.00 0.00 0.00 3.01
4086 4227 1.900351 CATCGGCCTCTGGAGAACA 59.100 57.895 0.00 0.00 0.00 3.18
4087 4228 0.250234 CATCGGCCTCTGGAGAACAA 59.750 55.000 0.00 0.00 0.00 2.83
4088 4229 0.539051 ATCGGCCTCTGGAGAACAAG 59.461 55.000 0.00 0.00 0.00 3.16
4089 4230 1.078848 CGGCCTCTGGAGAACAAGG 60.079 63.158 0.00 0.00 33.30 3.61
4090 4231 1.301293 GGCCTCTGGAGAACAAGGG 59.699 63.158 0.00 0.00 31.82 3.95
4091 4232 1.377856 GCCTCTGGAGAACAAGGGC 60.378 63.158 0.00 0.00 38.81 5.19
4092 4233 1.846712 GCCTCTGGAGAACAAGGGCT 61.847 60.000 0.00 0.00 41.03 5.19
4093 4234 0.695347 CCTCTGGAGAACAAGGGCTT 59.305 55.000 0.00 0.00 0.00 4.35
4094 4235 1.612726 CCTCTGGAGAACAAGGGCTTG 60.613 57.143 0.00 0.00 45.58 4.01
4095 4236 0.250901 TCTGGAGAACAAGGGCTTGC 60.251 55.000 0.00 0.00 44.03 4.01
4096 4237 0.251077 CTGGAGAACAAGGGCTTGCT 60.251 55.000 0.00 0.00 44.03 3.91
4097 4238 0.538057 TGGAGAACAAGGGCTTGCTG 60.538 55.000 0.00 0.00 44.03 4.41
4098 4239 1.583477 GAGAACAAGGGCTTGCTGC 59.417 57.895 0.00 0.00 44.03 5.25
4099 4240 2.192608 GAGAACAAGGGCTTGCTGCG 62.193 60.000 0.00 0.00 44.03 5.18
4100 4241 2.203337 AACAAGGGCTTGCTGCGA 60.203 55.556 0.00 0.00 44.03 5.10
4101 4242 2.463675 GAACAAGGGCTTGCTGCGAC 62.464 60.000 0.00 0.00 44.03 5.19
4102 4243 2.979676 CAAGGGCTTGCTGCGACA 60.980 61.111 0.00 0.00 44.05 4.35
4103 4244 2.034687 AAGGGCTTGCTGCGACAT 59.965 55.556 0.00 0.00 44.05 3.06
4104 4245 2.338015 AAGGGCTTGCTGCGACATG 61.338 57.895 0.00 0.00 44.05 3.21
4105 4246 3.818787 GGGCTTGCTGCGACATGG 61.819 66.667 0.00 0.00 44.05 3.66
4106 4247 3.818787 GGCTTGCTGCGACATGGG 61.819 66.667 0.00 0.00 44.05 4.00
4107 4248 2.747460 GCTTGCTGCGACATGGGA 60.747 61.111 0.00 0.00 0.00 4.37
4108 4249 2.117156 GCTTGCTGCGACATGGGAT 61.117 57.895 0.00 0.00 0.00 3.85
4109 4250 0.815213 GCTTGCTGCGACATGGGATA 60.815 55.000 0.00 0.00 0.00 2.59
4110 4251 1.224075 CTTGCTGCGACATGGGATAG 58.776 55.000 0.00 0.00 0.00 2.08
4111 4252 0.829990 TTGCTGCGACATGGGATAGA 59.170 50.000 0.00 0.00 0.00 1.98
4112 4253 0.104855 TGCTGCGACATGGGATAGAC 59.895 55.000 0.00 0.00 0.00 2.59
4113 4254 0.390860 GCTGCGACATGGGATAGACT 59.609 55.000 0.00 0.00 0.00 3.24
4114 4255 1.202580 GCTGCGACATGGGATAGACTT 60.203 52.381 0.00 0.00 0.00 3.01
4115 4256 2.477825 CTGCGACATGGGATAGACTTG 58.522 52.381 0.00 0.00 0.00 3.16
4116 4257 1.138859 TGCGACATGGGATAGACTTGG 59.861 52.381 0.00 0.00 0.00 3.61
4117 4258 1.871080 CGACATGGGATAGACTTGGC 58.129 55.000 0.00 0.00 0.00 4.52
4118 4259 1.869754 CGACATGGGATAGACTTGGCG 60.870 57.143 0.00 0.00 38.00 5.69
4119 4260 0.179045 ACATGGGATAGACTTGGCGC 60.179 55.000 0.00 0.00 0.00 6.53
4120 4261 0.886490 CATGGGATAGACTTGGCGCC 60.886 60.000 22.73 22.73 0.00 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.940470 CCAGAAAATTCACACTAACTAGGCT 59.060 40.000 0.00 0.00 0.00 4.58
1 2 5.938125 TCCAGAAAATTCACACTAACTAGGC 59.062 40.000 0.00 0.00 0.00 3.93
2 3 6.092807 GCTCCAGAAAATTCACACTAACTAGG 59.907 42.308 0.00 0.00 0.00 3.02
3 4 6.876257 AGCTCCAGAAAATTCACACTAACTAG 59.124 38.462 0.00 0.00 0.00 2.57
4 5 6.769512 AGCTCCAGAAAATTCACACTAACTA 58.230 36.000 0.00 0.00 0.00 2.24
5 6 5.625150 AGCTCCAGAAAATTCACACTAACT 58.375 37.500 0.00 0.00 0.00 2.24
6 7 5.948992 AGCTCCAGAAAATTCACACTAAC 57.051 39.130 0.00 0.00 0.00 2.34
7 8 6.299141 AGAAGCTCCAGAAAATTCACACTAA 58.701 36.000 0.00 0.00 0.00 2.24
8 9 5.869579 AGAAGCTCCAGAAAATTCACACTA 58.130 37.500 0.00 0.00 0.00 2.74
9 10 4.723309 AGAAGCTCCAGAAAATTCACACT 58.277 39.130 0.00 0.00 0.00 3.55
10 11 4.377841 CGAGAAGCTCCAGAAAATTCACAC 60.378 45.833 0.00 0.00 0.00 3.82
11 12 3.748048 CGAGAAGCTCCAGAAAATTCACA 59.252 43.478 0.00 0.00 0.00 3.58
15 16 3.999663 CTCACGAGAAGCTCCAGAAAATT 59.000 43.478 0.00 0.00 0.00 1.82
33 34 1.747355 CCACAGCCAATGGAATCTCAC 59.253 52.381 2.05 0.00 39.87 3.51
52 53 3.224007 AACCATCCACCCACAGGCC 62.224 63.158 0.00 0.00 36.11 5.19
61 62 0.321653 ACCGCTCTTCAACCATCCAC 60.322 55.000 0.00 0.00 0.00 4.02
91 92 4.273318 GTGATCTCCCTGCCTATGTTTTT 58.727 43.478 0.00 0.00 0.00 1.94
92 93 3.682718 CGTGATCTCCCTGCCTATGTTTT 60.683 47.826 0.00 0.00 0.00 2.43
93 94 2.158900 CGTGATCTCCCTGCCTATGTTT 60.159 50.000 0.00 0.00 0.00 2.83
94 95 1.414181 CGTGATCTCCCTGCCTATGTT 59.586 52.381 0.00 0.00 0.00 2.71
95 96 1.043816 CGTGATCTCCCTGCCTATGT 58.956 55.000 0.00 0.00 0.00 2.29
96 97 1.043816 ACGTGATCTCCCTGCCTATG 58.956 55.000 0.00 0.00 0.00 2.23
161 162 1.282570 CAAAACACTGCGTCGCCAT 59.717 52.632 15.88 0.00 0.00 4.40
165 166 2.425124 CGCCAAAACACTGCGTCG 60.425 61.111 0.00 0.00 43.12 5.12
169 170 1.000274 AGGAAATCGCCAAAACACTGC 60.000 47.619 0.00 0.00 0.00 4.40
170 171 3.052036 CAAGGAAATCGCCAAAACACTG 58.948 45.455 0.00 0.00 0.00 3.66
180 181 3.378427 AGGTTTATGAGCAAGGAAATCGC 59.622 43.478 0.00 0.00 0.00 4.58
210 211 1.400846 CAGCAAGGCACAGCTCATAAG 59.599 52.381 0.00 0.00 39.83 1.73
224 225 0.040336 CAAGTCAGCACAGCAGCAAG 60.040 55.000 0.00 0.00 36.85 4.01
228 229 0.234106 CGAACAAGTCAGCACAGCAG 59.766 55.000 0.00 0.00 0.00 4.24
245 246 1.676678 CCTTCCGGCCTCAGAATCGA 61.677 60.000 0.00 0.00 0.00 3.59
263 264 2.052104 CAGAATTCCAACCCGGCCC 61.052 63.158 0.65 0.00 33.14 5.80
268 269 0.890683 CCAGCACAGAATTCCAACCC 59.109 55.000 0.65 0.00 0.00 4.11
289 290 1.589727 GCCATACGCAAATGCCAGC 60.590 57.895 0.00 0.00 37.91 4.85
294 295 1.093972 TCACAGGCCATACGCAAATG 58.906 50.000 5.01 0.00 40.31 2.32
300 301 0.668535 TCGAGATCACAGGCCATACG 59.331 55.000 5.01 0.00 0.00 3.06
301 302 2.669670 CGATCGAGATCACAGGCCATAC 60.670 54.545 10.26 0.00 37.69 2.39
302 303 1.541588 CGATCGAGATCACAGGCCATA 59.458 52.381 10.26 0.00 37.69 2.74
333 335 2.094286 TGGATGGGCAAAATTTACGCTG 60.094 45.455 11.15 0.00 0.00 5.18
339 341 5.703730 ATGAATCTGGATGGGCAAAATTT 57.296 34.783 0.00 0.00 0.00 1.82
364 369 2.498481 ACCATGGCAAATGATCCACAAG 59.502 45.455 13.04 0.00 34.81 3.16
446 465 3.243301 CCATTGTCCTGCATCTTGTATGC 60.243 47.826 3.05 3.05 44.76 3.14
448 467 4.458397 CTCCATTGTCCTGCATCTTGTAT 58.542 43.478 0.00 0.00 0.00 2.29
451 470 2.022195 CCTCCATTGTCCTGCATCTTG 58.978 52.381 0.00 0.00 0.00 3.02
452 471 1.918262 TCCTCCATTGTCCTGCATCTT 59.082 47.619 0.00 0.00 0.00 2.40
512 531 5.892348 ACTCCACATGGTAGGAAGAAAAAT 58.108 37.500 0.00 0.00 36.34 1.82
538 561 0.991146 TTCATCCCAGGCTGCTAACA 59.009 50.000 9.56 0.00 0.00 2.41
623 650 7.582667 AATATCCAAATAGCCAACACCTAAC 57.417 36.000 0.00 0.00 0.00 2.34
677 710 7.039313 ACAGAGAACCATAACCAAGAAAAAC 57.961 36.000 0.00 0.00 0.00 2.43
680 713 6.039270 CACAACAGAGAACCATAACCAAGAAA 59.961 38.462 0.00 0.00 0.00 2.52
683 716 4.821805 ACACAACAGAGAACCATAACCAAG 59.178 41.667 0.00 0.00 0.00 3.61
695 733 7.714813 TGAAAGACAATATTGACACAACAGAGA 59.285 33.333 22.16 0.00 0.00 3.10
792 830 7.757097 TTATCTTAAGATGTCGAGAAGTTGC 57.243 36.000 25.22 0.00 36.05 4.17
809 847 9.383519 GAAATCCCGATCAGCATATTTATCTTA 57.616 33.333 0.00 0.00 0.00 2.10
888 926 3.753842 ACGGCAAAATGTAAATACAGCG 58.246 40.909 0.00 0.00 39.92 5.18
920 958 7.011950 TGCCATCCTGTATATCTAAACAAAACG 59.988 37.037 0.00 0.00 0.00 3.60
1126 1164 2.514803 GTTGCTTATGTTGGACCCACT 58.485 47.619 0.00 0.00 0.00 4.00
1131 1169 3.951663 AGTAGGGTTGCTTATGTTGGAC 58.048 45.455 0.00 0.00 0.00 4.02
1150 1188 2.590611 TCCCACTCCCTACAGGATTAGT 59.409 50.000 0.00 0.00 46.33 2.24
1179 1217 2.297033 GAGATCAGAGGTCCATCTCAGC 59.703 54.545 10.65 0.00 41.52 4.26
1182 1220 2.956132 TGGAGATCAGAGGTCCATCTC 58.044 52.381 7.98 7.98 41.27 2.75
1301 1339 7.436970 AGAATGAACCAACAAAATAAACGGAAC 59.563 33.333 0.00 0.00 0.00 3.62
1302 1340 7.436673 CAGAATGAACCAACAAAATAAACGGAA 59.563 33.333 0.00 0.00 39.69 4.30
1303 1341 6.920758 CAGAATGAACCAACAAAATAAACGGA 59.079 34.615 0.00 0.00 39.69 4.69
1304 1342 6.346518 GCAGAATGAACCAACAAAATAAACGG 60.347 38.462 0.00 0.00 39.69 4.44
1471 1563 3.063997 GGATTCGACATACAACCAGCAAG 59.936 47.826 0.00 0.00 0.00 4.01
1475 1567 4.635765 ACAATGGATTCGACATACAACCAG 59.364 41.667 0.00 0.00 0.00 4.00
1667 1771 9.026074 GTCATATTAACAACTTCTAGCAGACTC 57.974 37.037 0.00 0.00 0.00 3.36
1693 1797 0.954452 GCAGACACAGTTCCAAAGGG 59.046 55.000 0.00 0.00 0.00 3.95
1809 1913 9.524106 CATTAACAAATGTCTGATGCATTGTAT 57.476 29.630 0.00 0.00 36.75 2.29
1881 1985 1.167851 CTGGCACACCCATTACAGTG 58.832 55.000 0.00 0.00 44.33 3.66
1896 2000 5.971202 CACGTGATAAATTGTAATTCCTGGC 59.029 40.000 10.90 0.00 0.00 4.85
1899 2003 8.786826 TCTTCACGTGATAAATTGTAATTCCT 57.213 30.769 20.80 0.00 0.00 3.36
1902 2006 7.120579 TGGCTCTTCACGTGATAAATTGTAATT 59.879 33.333 20.80 0.00 0.00 1.40
1952 2056 8.502387 GCAAATATTTATTAGCTGTCTCCTCAG 58.498 37.037 0.00 0.00 38.35 3.35
1992 2096 5.772521 ACGCAAGCAACAAGAGAAATAAAT 58.227 33.333 0.00 0.00 45.62 1.40
1994 2098 4.829064 ACGCAAGCAACAAGAGAAATAA 57.171 36.364 0.00 0.00 45.62 1.40
2013 2117 2.203800 TGCAAGGCGATACTTCTACG 57.796 50.000 0.00 0.00 0.00 3.51
2065 2169 2.223665 GCAATGAAGCATAGAAGGGCAC 60.224 50.000 0.00 0.00 0.00 5.01
2154 2259 2.435069 TCGTCCTTGGAACCTACACAAA 59.565 45.455 0.00 0.00 0.00 2.83
2273 2378 3.418047 TCAACCAGCTTAAAAGGCCTAC 58.582 45.455 5.16 0.00 0.00 3.18
2279 2384 7.035840 AGCATGATATCAACCAGCTTAAAAG 57.964 36.000 9.99 0.00 0.00 2.27
2417 2524 4.037803 CACATGTTTCCATCACAAACCTCA 59.962 41.667 0.00 0.00 33.49 3.86
2431 2538 8.807667 ATGATTCAAAGAAGTTCACATGTTTC 57.192 30.769 5.50 0.00 0.00 2.78
2512 2619 7.616711 GGAGTAAATCCCCAGCTAACAGCTT 62.617 48.000 0.00 0.00 45.84 3.74
2679 2795 9.049050 AGAATATATCTCAGAGATGGCAGATTT 57.951 33.333 21.58 6.70 35.37 2.17
2680 2796 8.612486 AGAATATATCTCAGAGATGGCAGATT 57.388 34.615 21.58 11.29 35.37 2.40
2681 2797 8.612486 AAGAATATATCTCAGAGATGGCAGAT 57.388 34.615 21.58 9.95 37.42 2.90
2682 2798 7.148103 CGAAGAATATATCTCAGAGATGGCAGA 60.148 40.741 21.58 2.84 37.42 4.26
2699 2815 5.367945 TTTAGGTTGGCTCCGAAGAATAT 57.632 39.130 0.00 0.00 0.00 1.28
2950 3067 0.179111 GACAGATCATCCAACCGCGA 60.179 55.000 8.23 0.00 0.00 5.87
2952 3069 1.398390 GTTGACAGATCATCCAACCGC 59.602 52.381 10.93 0.00 33.85 5.68
3042 3159 2.351726 GCATATGTTGGTCTTCGGACAC 59.648 50.000 4.29 0.00 46.11 3.67
3136 3253 8.974060 AATAACTCAGAAGTGTTTCCTTTGTA 57.026 30.769 0.00 0.00 35.36 2.41
3284 3401 8.902540 TTACAAAGATCTGTATGGCGAAATAT 57.097 30.769 0.00 0.00 31.96 1.28
3449 3567 5.300752 ACTGAACTGAACAGGAATGTACAG 58.699 41.667 0.33 0.00 39.38 2.74
3458 3576 3.475566 TCAAGGACTGAACTGAACAGG 57.524 47.619 6.76 0.00 39.38 4.00
3474 3592 8.778358 GGTCAATATAAGGTAAGCAGATTCAAG 58.222 37.037 0.00 0.00 0.00 3.02
3543 3661 5.560722 TCCAGAAGACAGGTTGATTTGTA 57.439 39.130 0.00 0.00 0.00 2.41
3557 3675 4.564782 AAATGCAGAGTCATCCAGAAGA 57.435 40.909 0.00 0.00 0.00 2.87
3560 3678 3.447229 TCGTAAATGCAGAGTCATCCAGA 59.553 43.478 0.00 0.00 0.00 3.86
3642 3760 4.512571 GCAATGCTTTGAAAGGAACATTGT 59.487 37.500 24.30 1.75 43.82 2.71
3658 3776 1.196808 CAACCTCGTAAACGCAATGCT 59.803 47.619 2.94 0.00 39.60 3.79
3660 3778 1.533731 ACCAACCTCGTAAACGCAATG 59.466 47.619 0.00 0.00 39.60 2.82
3661 3779 1.886886 ACCAACCTCGTAAACGCAAT 58.113 45.000 0.00 0.00 39.60 3.56
3663 3781 0.938713 CAACCAACCTCGTAAACGCA 59.061 50.000 0.00 0.00 39.60 5.24
3664 3782 0.939419 ACAACCAACCTCGTAAACGC 59.061 50.000 0.00 0.00 39.60 4.84
3665 3783 3.383761 AGTACAACCAACCTCGTAAACG 58.616 45.455 0.00 0.00 41.45 3.60
3666 3784 7.425577 AAATAGTACAACCAACCTCGTAAAC 57.574 36.000 0.00 0.00 0.00 2.01
3667 3785 7.328249 CGTAAATAGTACAACCAACCTCGTAAA 59.672 37.037 0.00 0.00 0.00 2.01
3669 3787 6.150307 TCGTAAATAGTACAACCAACCTCGTA 59.850 38.462 0.00 0.00 0.00 3.43
3670 3788 5.048083 TCGTAAATAGTACAACCAACCTCGT 60.048 40.000 0.00 0.00 0.00 4.18
3671 3789 5.401550 TCGTAAATAGTACAACCAACCTCG 58.598 41.667 0.00 0.00 0.00 4.63
3672 3790 6.393171 ACTCGTAAATAGTACAACCAACCTC 58.607 40.000 0.00 0.00 0.00 3.85
3674 3792 7.315890 ACTACTCGTAAATAGTACAACCAACC 58.684 38.462 0.00 0.00 29.70 3.77
3726 3844 1.294659 CCTGTGCTCTGCCGAACTTC 61.295 60.000 0.00 0.00 0.00 3.01
3761 3879 4.264253 CCAAGGTATGTGATTCTGAGCAA 58.736 43.478 0.00 0.00 0.00 3.91
3887 4028 2.917701 TGCATGTACAAAAGCATCCG 57.082 45.000 14.57 0.00 31.05 4.18
3897 4038 3.615155 TGATCGGGAAAATGCATGTACA 58.385 40.909 0.00 0.00 0.00 2.90
3911 4052 5.882000 TGAATTATTATCTGGCATGATCGGG 59.118 40.000 0.00 0.00 0.00 5.14
3915 4056 6.946583 AGCTGTGAATTATTATCTGGCATGAT 59.053 34.615 0.00 0.00 0.00 2.45
3932 4073 2.101750 TCCAGAAACGTACAGCTGTGAA 59.898 45.455 29.57 7.53 0.00 3.18
3943 4084 5.638596 AGTTTTTGTTCTTCCAGAAACGT 57.361 34.783 0.00 0.00 41.65 3.99
3966 4107 6.265577 GGAAACGTAATGCTTTGATGCTAAT 58.734 36.000 0.00 0.00 0.00 1.73
3985 4126 4.174762 GTTCTACTGATGTCTCCGGAAAC 58.825 47.826 5.23 2.17 0.00 2.78
3986 4127 3.830178 TGTTCTACTGATGTCTCCGGAAA 59.170 43.478 5.23 0.00 0.00 3.13
3987 4128 3.427573 TGTTCTACTGATGTCTCCGGAA 58.572 45.455 5.23 0.00 0.00 4.30
3988 4129 3.081710 TGTTCTACTGATGTCTCCGGA 57.918 47.619 2.93 2.93 0.00 5.14
3989 4130 4.580995 ACTATGTTCTACTGATGTCTCCGG 59.419 45.833 0.00 0.00 0.00 5.14
3990 4131 5.759506 ACTATGTTCTACTGATGTCTCCG 57.240 43.478 0.00 0.00 0.00 4.63
3991 4132 6.981559 GGAAACTATGTTCTACTGATGTCTCC 59.018 42.308 0.00 0.00 0.00 3.71
3992 4133 6.693545 CGGAAACTATGTTCTACTGATGTCTC 59.306 42.308 0.00 0.00 0.00 3.36
3993 4134 6.405953 CCGGAAACTATGTTCTACTGATGTCT 60.406 42.308 0.00 0.00 0.00 3.41
3994 4135 5.749109 CCGGAAACTATGTTCTACTGATGTC 59.251 44.000 0.00 0.00 0.00 3.06
3995 4136 5.421056 TCCGGAAACTATGTTCTACTGATGT 59.579 40.000 0.00 0.00 0.00 3.06
3996 4137 5.902681 TCCGGAAACTATGTTCTACTGATG 58.097 41.667 0.00 0.00 0.00 3.07
3997 4138 5.892119 TCTCCGGAAACTATGTTCTACTGAT 59.108 40.000 5.23 0.00 0.00 2.90
3998 4139 5.125097 GTCTCCGGAAACTATGTTCTACTGA 59.875 44.000 5.23 0.00 0.00 3.41
3999 4140 5.105877 TGTCTCCGGAAACTATGTTCTACTG 60.106 44.000 9.80 0.00 0.00 2.74
4000 4141 5.014858 TGTCTCCGGAAACTATGTTCTACT 58.985 41.667 9.80 0.00 0.00 2.57
4001 4142 5.320549 TGTCTCCGGAAACTATGTTCTAC 57.679 43.478 9.80 0.00 0.00 2.59
4002 4143 5.655090 TGATGTCTCCGGAAACTATGTTCTA 59.345 40.000 9.80 0.00 0.00 2.10
4003 4144 4.466370 TGATGTCTCCGGAAACTATGTTCT 59.534 41.667 9.80 0.00 0.00 3.01
4004 4145 4.755411 TGATGTCTCCGGAAACTATGTTC 58.245 43.478 9.80 0.00 0.00 3.18
4005 4146 4.223032 ACTGATGTCTCCGGAAACTATGTT 59.777 41.667 9.80 0.00 0.00 2.71
4006 4147 3.769844 ACTGATGTCTCCGGAAACTATGT 59.230 43.478 9.80 0.40 0.00 2.29
4007 4148 4.392921 ACTGATGTCTCCGGAAACTATG 57.607 45.455 9.80 0.00 0.00 2.23
4008 4149 5.446860 TCTACTGATGTCTCCGGAAACTAT 58.553 41.667 9.80 1.00 0.00 2.12
4009 4150 4.851843 TCTACTGATGTCTCCGGAAACTA 58.148 43.478 9.80 0.00 0.00 2.24
4010 4151 3.698289 TCTACTGATGTCTCCGGAAACT 58.302 45.455 9.80 0.00 0.00 2.66
4011 4152 4.500035 GGATCTACTGATGTCTCCGGAAAC 60.500 50.000 5.23 2.17 32.19 2.78
4012 4153 3.637229 GGATCTACTGATGTCTCCGGAAA 59.363 47.826 5.23 0.00 32.19 3.13
4013 4154 3.117474 AGGATCTACTGATGTCTCCGGAA 60.117 47.826 5.23 0.00 32.19 4.30
4014 4155 2.443632 AGGATCTACTGATGTCTCCGGA 59.556 50.000 2.93 2.93 32.19 5.14
4015 4156 2.870175 AGGATCTACTGATGTCTCCGG 58.130 52.381 0.00 0.00 32.19 5.14
4016 4157 4.083749 CGTAAGGATCTACTGATGTCTCCG 60.084 50.000 0.00 0.00 32.19 4.63
4017 4158 5.365403 CGTAAGGATCTACTGATGTCTCC 57.635 47.826 0.00 0.00 32.19 3.71
4034 4175 4.871513 TGATGATCCGATTCTTCCGTAAG 58.128 43.478 0.00 0.00 0.00 2.34
4035 4176 4.929819 TGATGATCCGATTCTTCCGTAA 57.070 40.909 0.00 0.00 0.00 3.18
4036 4177 4.796290 GCTTGATGATCCGATTCTTCCGTA 60.796 45.833 0.00 0.00 0.00 4.02
4037 4178 3.722147 CTTGATGATCCGATTCTTCCGT 58.278 45.455 0.00 0.00 0.00 4.69
4038 4179 2.478134 GCTTGATGATCCGATTCTTCCG 59.522 50.000 0.00 0.00 0.00 4.30
4039 4180 2.810852 GGCTTGATGATCCGATTCTTCC 59.189 50.000 0.00 0.00 0.00 3.46
4040 4181 2.810852 GGGCTTGATGATCCGATTCTTC 59.189 50.000 0.00 0.00 0.00 2.87
4041 4182 2.441001 AGGGCTTGATGATCCGATTCTT 59.559 45.455 0.00 0.00 0.00 2.52
4042 4183 2.053244 AGGGCTTGATGATCCGATTCT 58.947 47.619 0.00 0.00 0.00 2.40
4043 4184 2.557920 AGGGCTTGATGATCCGATTC 57.442 50.000 0.00 0.00 0.00 2.52
4044 4185 2.441001 AGAAGGGCTTGATGATCCGATT 59.559 45.455 0.00 0.00 0.00 3.34
4045 4186 2.053244 AGAAGGGCTTGATGATCCGAT 58.947 47.619 0.00 0.00 0.00 4.18
4046 4187 1.500474 AGAAGGGCTTGATGATCCGA 58.500 50.000 0.00 0.00 0.00 4.55
4047 4188 2.869636 GCTAGAAGGGCTTGATGATCCG 60.870 54.545 0.00 0.00 0.00 4.18
4048 4189 2.105477 TGCTAGAAGGGCTTGATGATCC 59.895 50.000 0.00 0.00 0.00 3.36
4049 4190 3.482156 TGCTAGAAGGGCTTGATGATC 57.518 47.619 0.00 0.00 0.00 2.92
4050 4191 3.556633 CGATGCTAGAAGGGCTTGATGAT 60.557 47.826 0.00 0.00 0.00 2.45
4051 4192 2.224137 CGATGCTAGAAGGGCTTGATGA 60.224 50.000 0.00 0.00 0.00 2.92
4052 4193 2.141517 CGATGCTAGAAGGGCTTGATG 58.858 52.381 0.00 0.00 0.00 3.07
4053 4194 1.071385 CCGATGCTAGAAGGGCTTGAT 59.929 52.381 0.00 0.00 0.00 2.57
4054 4195 0.465705 CCGATGCTAGAAGGGCTTGA 59.534 55.000 0.00 0.00 0.00 3.02
4055 4196 1.162800 GCCGATGCTAGAAGGGCTTG 61.163 60.000 8.11 0.00 40.59 4.01
4056 4197 1.147153 GCCGATGCTAGAAGGGCTT 59.853 57.895 8.11 0.00 40.59 4.35
4057 4198 2.812619 GGCCGATGCTAGAAGGGCT 61.813 63.158 13.79 0.00 44.69 5.19
4058 4199 2.281139 GGCCGATGCTAGAAGGGC 60.281 66.667 6.99 6.99 43.01 5.19
4059 4200 1.118356 AGAGGCCGATGCTAGAAGGG 61.118 60.000 0.00 0.00 37.74 3.95
4060 4201 0.033228 CAGAGGCCGATGCTAGAAGG 59.967 60.000 0.00 0.00 37.74 3.46
4061 4202 0.033228 CCAGAGGCCGATGCTAGAAG 59.967 60.000 0.00 0.00 37.74 2.85
4062 4203 0.397114 TCCAGAGGCCGATGCTAGAA 60.397 55.000 0.00 0.00 37.74 2.10
4063 4204 0.825425 CTCCAGAGGCCGATGCTAGA 60.825 60.000 0.00 0.00 37.74 2.43
4064 4205 0.825425 TCTCCAGAGGCCGATGCTAG 60.825 60.000 0.00 1.05 37.74 3.42
4065 4206 0.397114 TTCTCCAGAGGCCGATGCTA 60.397 55.000 0.00 0.00 37.74 3.49
4066 4207 1.687146 TTCTCCAGAGGCCGATGCT 60.687 57.895 0.00 0.00 37.74 3.79
4067 4208 1.522580 GTTCTCCAGAGGCCGATGC 60.523 63.158 0.00 0.00 0.00 3.91
4068 4209 0.250234 TTGTTCTCCAGAGGCCGATG 59.750 55.000 0.00 0.00 0.00 3.84
4069 4210 0.539051 CTTGTTCTCCAGAGGCCGAT 59.461 55.000 0.00 0.00 0.00 4.18
4070 4211 1.544825 CCTTGTTCTCCAGAGGCCGA 61.545 60.000 0.00 0.00 0.00 5.54
4071 4212 1.078848 CCTTGTTCTCCAGAGGCCG 60.079 63.158 0.00 0.00 0.00 6.13
4072 4213 1.301293 CCCTTGTTCTCCAGAGGCC 59.699 63.158 0.00 0.00 0.00 5.19
4073 4214 1.377856 GCCCTTGTTCTCCAGAGGC 60.378 63.158 0.00 0.00 36.34 4.70
4074 4215 0.695347 AAGCCCTTGTTCTCCAGAGG 59.305 55.000 0.00 0.00 0.00 3.69
4075 4216 1.818642 CAAGCCCTTGTTCTCCAGAG 58.181 55.000 0.00 0.00 35.92 3.35
4076 4217 0.250901 GCAAGCCCTTGTTCTCCAGA 60.251 55.000 9.53 0.00 42.31 3.86
4077 4218 0.251077 AGCAAGCCCTTGTTCTCCAG 60.251 55.000 9.53 0.00 42.31 3.86
4078 4219 0.538057 CAGCAAGCCCTTGTTCTCCA 60.538 55.000 9.53 0.00 42.31 3.86
4079 4220 1.871126 GCAGCAAGCCCTTGTTCTCC 61.871 60.000 9.53 0.00 42.31 3.71
4080 4221 1.583477 GCAGCAAGCCCTTGTTCTC 59.417 57.895 9.53 0.00 42.31 2.87
4081 4222 2.263741 CGCAGCAAGCCCTTGTTCT 61.264 57.895 9.53 0.00 42.31 3.01
4082 4223 2.256461 CGCAGCAAGCCCTTGTTC 59.744 61.111 9.53 0.00 42.31 3.18
4083 4224 2.203337 TCGCAGCAAGCCCTTGTT 60.203 55.556 9.53 0.90 42.31 2.83
4084 4225 2.980233 GTCGCAGCAAGCCCTTGT 60.980 61.111 9.53 0.00 42.31 3.16
4085 4226 2.338015 ATGTCGCAGCAAGCCCTTG 61.338 57.895 3.70 3.70 43.14 3.61
4086 4227 2.034687 ATGTCGCAGCAAGCCCTT 59.965 55.556 0.00 0.00 41.38 3.95
4087 4228 2.749044 CATGTCGCAGCAAGCCCT 60.749 61.111 0.00 0.00 41.38 5.19
4088 4229 3.818787 CCATGTCGCAGCAAGCCC 61.819 66.667 0.00 0.00 41.38 5.19
4089 4230 3.818787 CCCATGTCGCAGCAAGCC 61.819 66.667 0.00 0.00 41.38 4.35
4090 4231 0.815213 TATCCCATGTCGCAGCAAGC 60.815 55.000 0.00 0.00 40.87 4.01
4091 4232 1.202568 TCTATCCCATGTCGCAGCAAG 60.203 52.381 0.00 0.00 0.00 4.01
4092 4233 0.829990 TCTATCCCATGTCGCAGCAA 59.170 50.000 0.00 0.00 0.00 3.91
4093 4234 0.104855 GTCTATCCCATGTCGCAGCA 59.895 55.000 0.00 0.00 0.00 4.41
4094 4235 0.390860 AGTCTATCCCATGTCGCAGC 59.609 55.000 0.00 0.00 0.00 5.25
4095 4236 2.477825 CAAGTCTATCCCATGTCGCAG 58.522 52.381 0.00 0.00 0.00 5.18
4096 4237 1.138859 CCAAGTCTATCCCATGTCGCA 59.861 52.381 0.00 0.00 0.00 5.10
4097 4238 1.871080 CCAAGTCTATCCCATGTCGC 58.129 55.000 0.00 0.00 0.00 5.19
4098 4239 1.869754 CGCCAAGTCTATCCCATGTCG 60.870 57.143 0.00 0.00 0.00 4.35
4099 4240 1.871080 CGCCAAGTCTATCCCATGTC 58.129 55.000 0.00 0.00 0.00 3.06
4100 4241 0.179045 GCGCCAAGTCTATCCCATGT 60.179 55.000 0.00 0.00 0.00 3.21
4101 4242 0.886490 GGCGCCAAGTCTATCCCATG 60.886 60.000 24.80 0.00 0.00 3.66
4102 4243 1.451936 GGCGCCAAGTCTATCCCAT 59.548 57.895 24.80 0.00 0.00 4.00
4103 4244 2.908015 GGCGCCAAGTCTATCCCA 59.092 61.111 24.80 0.00 0.00 4.37


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

AutoCloner maintained by Alex Coulton.