Multiple sequence alignment - TraesCS2D01G345000

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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 TraesCS2D01G345000 chr2D 100.000 4185 0 0 1 4185 440969851 440965667 0.000000e+00 7729
1 TraesCS2D01G345000 chr2D 85.457 2111 202 43 837 2878 440784210 440782136 0.000000e+00 2100
2 TraesCS2D01G345000 chr2D 83.377 385 35 15 3180 3552 440781370 440781003 3.120000e-86 329
3 TraesCS2D01G345000 chr2A 93.718 2770 93 32 805 3570 584579357 584576665 0.000000e+00 4076
4 TraesCS2D01G345000 chr2A 85.388 2101 205 52 837 2878 584523253 584521196 0.000000e+00 2085
5 TraesCS2D01G345000 chr2A 86.164 318 32 7 2874 3189 584521152 584520845 2.410000e-87 333
6 TraesCS2D01G345000 chr2A 86.275 306 24 8 3181 3485 584520461 584520173 2.430000e-82 316
7 TraesCS2D01G345000 chr2A 73.263 763 160 33 991 1743 584518509 584517781 5.410000e-59 239
8 TraesCS2D01G345000 chr2A 93.007 143 7 3 3608 3748 584576661 584576520 5.480000e-49 206
9 TraesCS2D01G345000 chr2B 91.894 1653 91 19 2125 3746 518758898 518757258 0.000000e+00 2270
10 TraesCS2D01G345000 chr2B 85.863 1733 147 40 837 2504 518753871 518752172 0.000000e+00 1753
11 TraesCS2D01G345000 chr2B 90.323 1333 82 21 805 2117 518760264 518758959 0.000000e+00 1703
12 TraesCS2D01G345000 chr2B 87.469 806 98 2 1 803 758672565 758673370 0.000000e+00 926
13 TraesCS2D01G345000 chr2B 90.494 263 23 2 2929 3189 518751627 518751365 3.100000e-91 346
14 TraesCS2D01G345000 chr1B 90.421 689 66 0 116 804 514569312 514568624 0.000000e+00 907
15 TraesCS2D01G345000 chr1B 85.872 814 112 1 1 811 430679548 430678735 0.000000e+00 863
16 TraesCS2D01G345000 chr1B 84.634 423 54 9 3768 4184 573746969 573747386 1.080000e-110 411
17 TraesCS2D01G345000 chr6B 87.166 787 100 1 1 787 581845733 581844948 0.000000e+00 893
18 TraesCS2D01G345000 chr7B 86.137 743 98 2 50 792 242723152 242722415 0.000000e+00 797
19 TraesCS2D01G345000 chr7B 85.377 424 45 15 3768 4185 496886354 496886766 1.390000e-114 424
20 TraesCS2D01G345000 chr3B 84.596 805 121 2 1 803 753959128 753959931 0.000000e+00 797
21 TraesCS2D01G345000 chr5D 87.081 418 47 5 3771 4185 293423880 293423467 2.280000e-127 466
22 TraesCS2D01G345000 chr5A 88.000 375 39 5 3768 4140 674997801 674997431 4.970000e-119 438
23 TraesCS2D01G345000 chr1A 87.234 376 43 4 3768 4140 15376390 15376017 1.390000e-114 424
24 TraesCS2D01G345000 chr4D 86.413 368 41 7 3768 4131 355819250 355819612 1.090000e-105 394
25 TraesCS2D01G345000 chr3A 86.150 361 44 6 3784 4140 52052764 52053122 6.560000e-103 385
26 TraesCS2D01G345000 chr3A 85.596 361 46 6 3784 4140 51601028 51601386 1.420000e-99 374
27 TraesCS2D01G345000 chr7D 84.282 369 46 9 3768 4133 251037731 251037372 2.390000e-92 350


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 TraesCS2D01G345000 chr2D 440965667 440969851 4184 True 7729.00 7729 100.0000 1 4185 1 chr2D.!!$R1 4184
1 TraesCS2D01G345000 chr2D 440781003 440784210 3207 True 1214.50 2100 84.4170 837 3552 2 chr2D.!!$R2 2715
2 TraesCS2D01G345000 chr2A 584576520 584579357 2837 True 2141.00 4076 93.3625 805 3748 2 chr2A.!!$R2 2943
3 TraesCS2D01G345000 chr2A 584517781 584523253 5472 True 743.25 2085 82.7725 837 3485 4 chr2A.!!$R1 2648
4 TraesCS2D01G345000 chr2B 518751365 518760264 8899 True 1518.00 2270 89.6435 805 3746 4 chr2B.!!$R1 2941
5 TraesCS2D01G345000 chr2B 758672565 758673370 805 False 926.00 926 87.4690 1 803 1 chr2B.!!$F1 802
6 TraesCS2D01G345000 chr1B 514568624 514569312 688 True 907.00 907 90.4210 116 804 1 chr1B.!!$R2 688
7 TraesCS2D01G345000 chr1B 430678735 430679548 813 True 863.00 863 85.8720 1 811 1 chr1B.!!$R1 810
8 TraesCS2D01G345000 chr6B 581844948 581845733 785 True 893.00 893 87.1660 1 787 1 chr6B.!!$R1 786
9 TraesCS2D01G345000 chr7B 242722415 242723152 737 True 797.00 797 86.1370 50 792 1 chr7B.!!$R1 742
10 TraesCS2D01G345000 chr3B 753959128 753959931 803 False 797.00 797 84.5960 1 803 1 chr3B.!!$F1 802

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
21 22 0.318955 GCACAATGGCAAGGTGTGTC 60.319 55.0 22.4 14.71 43.65 3.67 F
318 320 0.321298 TACAAGCCAGACCGAAAGCC 60.321 55.0 0.0 0.00 0.00 4.35 F
1879 1930 0.114168 CCAGATGGTTGGGTTGGGAA 59.886 55.0 0.0 0.00 34.46 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1274 1304 0.605589 CGTAGATCTGGAGGGGCATC 59.394 60.0 5.18 0.0 0.0 3.91 R
2038 2117 0.178961 ACAAAACCCTTGGCCTCCTC 60.179 55.0 3.32 0.0 0.0 3.71 R
3859 5694 0.030504 CAACACGACCAATGCTGCAA 59.969 50.0 6.36 0.0 0.0 4.08 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
21 22 0.318955 GCACAATGGCAAGGTGTGTC 60.319 55.000 22.40 14.71 43.65 3.67
27 28 2.203337 GCAAGGTGTGTCTGGGCA 60.203 61.111 0.00 0.00 0.00 5.36
122 123 6.630071 TGATGAAAGACTCGTTATCACATGA 58.370 36.000 0.00 0.00 0.00 3.07
173 175 2.620234 CCATCTGGTGGGCTAGGAA 58.380 57.895 0.00 0.00 44.79 3.36
201 203 5.005740 GCCATTCATGAGCAGATATACCAA 58.994 41.667 0.00 0.00 0.00 3.67
208 210 3.201930 TGAGCAGATATACCAAAGCCCAA 59.798 43.478 0.00 0.00 0.00 4.12
318 320 0.321298 TACAAGCCAGACCGAAAGCC 60.321 55.000 0.00 0.00 0.00 4.35
396 400 3.649986 GGAGCGTGTGCAGCGTTT 61.650 61.111 11.48 1.99 46.23 3.60
413 417 5.349817 CAGCGTTTTGTAGAGATGAGAATGT 59.650 40.000 0.00 0.00 0.00 2.71
452 458 1.276705 TGCTCTGGTAATACACGGCAA 59.723 47.619 0.00 0.00 0.00 4.52
537 543 6.577103 TCTTCACCTACAAGACATCATCATC 58.423 40.000 0.00 0.00 0.00 2.92
542 548 4.813161 CCTACAAGACATCATCATCGCTTT 59.187 41.667 0.00 0.00 0.00 3.51
619 626 4.688413 GGCCGATAATCAGAGAGATTTCAC 59.312 45.833 0.00 0.00 44.48 3.18
623 630 6.276091 CGATAATCAGAGAGATTTCACACCA 58.724 40.000 0.00 0.00 44.48 4.17
724 731 0.846015 TTCATTGGATCAGGGGCGAT 59.154 50.000 0.00 0.00 0.00 4.58
738 745 1.476488 GGGCGATATGTTTGGTTGCTT 59.524 47.619 0.00 0.00 0.00 3.91
741 748 3.181487 GGCGATATGTTTGGTTGCTTCAT 60.181 43.478 0.00 0.00 0.00 2.57
753 760 2.538512 TGCTTCATCCTCATGATCCG 57.461 50.000 0.00 0.00 38.89 4.18
772 779 7.100409 TGATCCGTTTTGTATCTCACAACATA 58.900 34.615 0.00 0.00 46.80 2.29
776 783 5.965334 CGTTTTGTATCTCACAACATATGGC 59.035 40.000 7.80 0.00 46.80 4.40
780 787 6.682423 TGTATCTCACAACATATGGCTTTG 57.318 37.500 7.80 5.39 32.95 2.77
794 801 7.561356 ACATATGGCTTTGGAGTAATAAAGCTT 59.439 33.333 17.77 0.00 44.96 3.74
1225 1253 4.179599 CCCCCTCCTCCTCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
1451 1493 2.799917 CGAGACCTCTAAATTCCGGCTG 60.800 54.545 0.00 0.00 0.00 4.85
1469 1511 3.059982 CAGGTCTTCCAGGTCGCA 58.940 61.111 0.00 0.00 35.89 5.10
1545 1588 1.798813 GAACCAGTGGCTGACGTTTAG 59.201 52.381 9.78 0.00 32.44 1.85
1550 1593 3.386486 CAGTGGCTGACGTTTAGTGTAA 58.614 45.455 0.00 0.00 32.44 2.41
1743 1786 7.493645 CCTGATATTCTAATCGATGCAAGCATA 59.506 37.037 7.64 0.00 36.70 3.14
1879 1930 0.114168 CCAGATGGTTGGGTTGGGAA 59.886 55.000 0.00 0.00 34.46 3.97
1880 1931 1.273211 CCAGATGGTTGGGTTGGGAAT 60.273 52.381 0.00 0.00 34.46 3.01
1881 1932 2.102578 CAGATGGTTGGGTTGGGAATC 58.897 52.381 0.00 0.00 0.00 2.52
1887 1938 4.093011 TGGTTGGGTTGGGAATCATAAAG 58.907 43.478 0.00 0.00 0.00 1.85
2117 2196 5.580691 CGCAATAGTAAGGACACAATCTTGA 59.419 40.000 0.00 0.00 0.00 3.02
2118 2197 6.258727 CGCAATAGTAAGGACACAATCTTGAT 59.741 38.462 0.00 0.00 0.00 2.57
2119 2198 7.201644 CGCAATAGTAAGGACACAATCTTGATT 60.202 37.037 0.00 0.00 0.00 2.57
2120 2199 8.125448 GCAATAGTAAGGACACAATCTTGATTC 58.875 37.037 0.00 0.00 0.00 2.52
2121 2200 9.388506 CAATAGTAAGGACACAATCTTGATTCT 57.611 33.333 0.00 0.00 0.00 2.40
2122 2201 9.965902 AATAGTAAGGACACAATCTTGATTCTT 57.034 29.630 0.00 0.00 0.00 2.52
2290 2455 5.299279 ACTGTTAGGTCATGTTGGTTTCTTG 59.701 40.000 0.00 0.00 0.00 3.02
2516 2684 6.136857 AGTAGGTTGGACATATCAGAAGCTA 58.863 40.000 0.00 0.00 32.09 3.32
2559 2728 8.131847 TGATGCTATATAGTCTGCTTCAGATT 57.868 34.615 11.38 0.00 42.73 2.40
2579 2748 9.283768 TCAGATTTGTTGCTTTCAGAGTTAATA 57.716 29.630 0.00 0.00 0.00 0.98
2745 2917 5.627499 TTGCAACACTCATATCAGTTTCC 57.373 39.130 0.00 0.00 0.00 3.13
2831 3003 4.301072 AGGAAGCTGCATTGGTTAAGTA 57.699 40.909 1.02 0.00 0.00 2.24
2938 3159 4.058817 CGACAAAACACTAGGAGCTCTTT 58.941 43.478 14.64 5.09 0.00 2.52
3039 3262 6.897966 TGGTACTCTAGGTTCTGATGATCTTT 59.102 38.462 0.00 0.00 0.00 2.52
3074 3297 1.136147 CAGCTGCCTCGCATTCAAC 59.864 57.895 0.00 0.00 38.13 3.18
3077 3300 1.580845 GCTGCCTCGCATTCAACACT 61.581 55.000 0.00 0.00 38.13 3.55
3172 3395 6.287525 TGCTGGAAAATATGTGACATATCGA 58.712 36.000 17.59 4.26 0.00 3.59
3200 3868 3.834813 TGTCTGAGCTCCACTACATTCTT 59.165 43.478 12.15 0.00 0.00 2.52
3201 3869 4.180057 GTCTGAGCTCCACTACATTCTTG 58.820 47.826 12.15 0.00 0.00 3.02
3396 4065 7.886405 AGACGTAGATTTCAGTAGTTTTTCC 57.114 36.000 0.00 0.00 0.00 3.13
3474 4152 0.796927 GCGGAGTTCAACTTAGTGCC 59.203 55.000 0.00 0.00 0.00 5.01
3494 4172 3.507622 GCCCCTGTATTTATCTGAATGGC 59.492 47.826 0.00 0.00 0.00 4.40
3499 4177 6.150641 CCCTGTATTTATCTGAATGGCATGAG 59.849 42.308 0.00 0.00 0.00 2.90
3525 4211 3.007635 CCTTCTGGGACCGTTGTTTATC 58.992 50.000 0.00 0.00 37.23 1.75
3527 4213 3.604875 TCTGGGACCGTTGTTTATCTC 57.395 47.619 0.00 0.00 0.00 2.75
3729 4819 8.072567 GCAATTGTAGAGATAAAACAGCCATAG 58.927 37.037 7.40 0.00 0.00 2.23
3784 5619 2.364970 TGGGGACAAAATCAAGCAGTTG 59.635 45.455 0.00 0.00 37.44 3.16
3787 5622 3.259123 GGGACAAAATCAAGCAGTTGGAT 59.741 43.478 0.00 0.00 34.09 3.41
3788 5623 4.240096 GGACAAAATCAAGCAGTTGGATG 58.760 43.478 0.00 0.00 34.09 3.51
3790 5625 4.874970 ACAAAATCAAGCAGTTGGATGTC 58.125 39.130 0.00 0.00 34.09 3.06
3791 5626 4.586001 ACAAAATCAAGCAGTTGGATGTCT 59.414 37.500 0.00 0.00 34.09 3.41
3794 5629 5.382618 AATCAAGCAGTTGGATGTCTTTC 57.617 39.130 0.00 0.00 34.09 2.62
3798 5633 4.363991 AGCAGTTGGATGTCTTTCTCTT 57.636 40.909 0.00 0.00 0.00 2.85
3799 5634 4.723309 AGCAGTTGGATGTCTTTCTCTTT 58.277 39.130 0.00 0.00 0.00 2.52
3800 5635 5.136105 AGCAGTTGGATGTCTTTCTCTTTT 58.864 37.500 0.00 0.00 0.00 2.27
3801 5636 5.595952 AGCAGTTGGATGTCTTTCTCTTTTT 59.404 36.000 0.00 0.00 0.00 1.94
3822 5657 7.846644 TTTTTGCAACAATGATCTTGTTTCT 57.153 28.000 15.99 0.12 40.30 2.52
3823 5658 6.831727 TTTGCAACAATGATCTTGTTTCTG 57.168 33.333 15.99 10.19 40.30 3.02
3825 5660 6.146601 TGCAACAATGATCTTGTTTCTGAA 57.853 33.333 15.99 3.88 40.30 3.02
3826 5661 6.571605 TGCAACAATGATCTTGTTTCTGAAA 58.428 32.000 15.99 0.00 40.30 2.69
3827 5662 6.476380 TGCAACAATGATCTTGTTTCTGAAAC 59.524 34.615 22.94 22.94 40.30 2.78
3829 5664 7.096312 GCAACAATGATCTTGTTTCTGAAACTC 60.096 37.037 27.75 19.21 40.30 3.01
3833 5668 7.814264 ATGATCTTGTTTCTGAAACTCTTGT 57.186 32.000 27.75 13.91 41.90 3.16
3835 5670 8.731275 TGATCTTGTTTCTGAAACTCTTGTAA 57.269 30.769 27.75 15.05 41.90 2.41
3836 5671 8.612619 TGATCTTGTTTCTGAAACTCTTGTAAC 58.387 33.333 27.75 14.77 41.90 2.50
3838 5673 7.748847 TCTTGTTTCTGAAACTCTTGTAACAC 58.251 34.615 27.75 4.53 41.90 3.32
3840 5675 7.072177 TGTTTCTGAAACTCTTGTAACACAG 57.928 36.000 27.75 0.00 41.90 3.66
3841 5676 6.876789 TGTTTCTGAAACTCTTGTAACACAGA 59.123 34.615 27.75 5.66 41.90 3.41
3843 5678 8.398665 GTTTCTGAAACTCTTGTAACACAGATT 58.601 33.333 22.55 0.00 38.35 2.40
3844 5679 7.482654 TCTGAAACTCTTGTAACACAGATTG 57.517 36.000 0.00 0.00 0.00 2.67
3845 5680 7.047891 TCTGAAACTCTTGTAACACAGATTGT 58.952 34.615 0.00 0.00 41.74 2.71
3875 5710 1.850377 TTTTTGCAGCATTGGTCGTG 58.150 45.000 0.00 0.00 0.00 4.35
3876 5711 0.743688 TTTTGCAGCATTGGTCGTGT 59.256 45.000 0.00 0.00 0.00 4.49
3878 5713 0.030504 TTGCAGCATTGGTCGTGTTG 59.969 50.000 0.00 0.00 0.00 3.33
3880 5715 0.661187 GCAGCATTGGTCGTGTTGTG 60.661 55.000 0.00 0.00 31.44 3.33
3881 5716 0.040157 CAGCATTGGTCGTGTTGTGG 60.040 55.000 0.00 0.00 0.00 4.17
3882 5717 0.179032 AGCATTGGTCGTGTTGTGGA 60.179 50.000 0.00 0.00 0.00 4.02
3885 5817 2.288152 GCATTGGTCGTGTTGTGGAATT 60.288 45.455 0.00 0.00 0.00 2.17
3916 5848 4.604843 CAACATATGTCGTGTTGCAGAT 57.395 40.909 9.23 0.00 46.64 2.90
3917 5849 4.973396 CAACATATGTCGTGTTGCAGATT 58.027 39.130 9.23 0.00 46.64 2.40
3918 5850 5.393124 CAACATATGTCGTGTTGCAGATTT 58.607 37.500 9.23 0.00 46.64 2.17
3919 5851 5.627499 ACATATGTCGTGTTGCAGATTTT 57.373 34.783 1.41 0.00 0.00 1.82
3920 5852 6.012658 ACATATGTCGTGTTGCAGATTTTT 57.987 33.333 1.41 0.00 0.00 1.94
3970 8078 8.947055 AACAAAGATATTGTTGCAGAAAAACT 57.053 26.923 5.82 0.00 40.70 2.66
3971 8079 8.947055 ACAAAGATATTGTTGCAGAAAAACTT 57.053 26.923 0.00 0.00 0.00 2.66
3975 8083 6.985645 AGATATTGTTGCAGAAAAACTTTGCA 59.014 30.769 0.00 0.00 45.28 4.08
3982 8101 3.553105 GCAGAAAAACTTTGCAACTGAGG 59.447 43.478 13.41 0.00 37.75 3.86
3986 8105 5.127682 AGAAAAACTTTGCAACTGAGGTGAT 59.872 36.000 0.00 0.00 0.00 3.06
3987 8106 3.996150 AACTTTGCAACTGAGGTGATG 57.004 42.857 0.00 0.00 0.00 3.07
3993 8112 2.983402 CAACTGAGGTGATGTTGCAG 57.017 50.000 0.00 0.00 35.39 4.41
3996 8115 4.256110 CAACTGAGGTGATGTTGCAGATA 58.744 43.478 0.00 0.00 35.39 1.98
3997 8116 4.767578 ACTGAGGTGATGTTGCAGATAT 57.232 40.909 0.00 0.00 0.00 1.63
3998 8117 5.108187 ACTGAGGTGATGTTGCAGATATT 57.892 39.130 0.00 0.00 0.00 1.28
4024 8143 8.792830 TTTTCTTTGTCTTCACCTCTATATGG 57.207 34.615 0.00 0.00 0.00 2.74
4025 8144 7.496346 TTCTTTGTCTTCACCTCTATATGGT 57.504 36.000 0.00 0.00 38.53 3.55
4035 8154 5.057843 ACCTCTATATGGTGTTACGGAGA 57.942 43.478 0.00 0.00 36.30 3.71
4036 8155 5.452255 ACCTCTATATGGTGTTACGGAGAA 58.548 41.667 0.00 0.00 36.30 2.87
4037 8156 5.895534 ACCTCTATATGGTGTTACGGAGAAA 59.104 40.000 0.00 0.00 36.30 2.52
4038 8157 6.183360 ACCTCTATATGGTGTTACGGAGAAAC 60.183 42.308 0.00 0.00 36.30 2.78
4039 8158 6.040616 CCTCTATATGGTGTTACGGAGAAACT 59.959 42.308 0.00 0.00 0.00 2.66
4040 8159 7.414222 TCTATATGGTGTTACGGAGAAACTT 57.586 36.000 0.00 0.00 0.00 2.66
4041 8160 8.523915 TCTATATGGTGTTACGGAGAAACTTA 57.476 34.615 0.00 0.00 0.00 2.24
4042 8161 9.139734 TCTATATGGTGTTACGGAGAAACTTAT 57.860 33.333 0.00 0.00 0.00 1.73
4043 8162 9.193133 CTATATGGTGTTACGGAGAAACTTATG 57.807 37.037 0.00 0.00 0.00 1.90
4044 8163 3.998341 TGGTGTTACGGAGAAACTTATGC 59.002 43.478 0.00 0.00 0.00 3.14
4045 8164 3.998341 GGTGTTACGGAGAAACTTATGCA 59.002 43.478 0.00 0.00 0.00 3.96
4046 8165 4.453136 GGTGTTACGGAGAAACTTATGCAA 59.547 41.667 0.00 0.00 0.00 4.08
4047 8166 5.379827 GTGTTACGGAGAAACTTATGCAAC 58.620 41.667 0.00 0.00 0.00 4.17
4048 8167 5.049954 GTGTTACGGAGAAACTTATGCAACA 60.050 40.000 0.00 0.00 0.00 3.33
4049 8168 5.703592 TGTTACGGAGAAACTTATGCAACAT 59.296 36.000 0.00 0.00 0.00 2.71
4050 8169 6.874664 TGTTACGGAGAAACTTATGCAACATA 59.125 34.615 0.00 0.00 0.00 2.29
4051 8170 7.388224 TGTTACGGAGAAACTTATGCAACATAA 59.612 33.333 0.00 0.52 0.00 1.90
4052 8171 6.178239 ACGGAGAAACTTATGCAACATAAC 57.822 37.500 0.00 0.00 0.00 1.89
4053 8172 5.938125 ACGGAGAAACTTATGCAACATAACT 59.062 36.000 0.00 0.00 0.00 2.24
4054 8173 6.128282 ACGGAGAAACTTATGCAACATAACTG 60.128 38.462 0.00 0.00 0.00 3.16
4055 8174 6.092122 CGGAGAAACTTATGCAACATAACTGA 59.908 38.462 0.00 0.00 0.00 3.41
4056 8175 7.201644 CGGAGAAACTTATGCAACATAACTGAT 60.202 37.037 0.00 0.00 0.00 2.90
4057 8176 7.912250 GGAGAAACTTATGCAACATAACTGATG 59.088 37.037 0.00 0.00 41.79 3.07
4076 8195 7.588512 ACTGATGTTGTAGAAATCTTTCTTGC 58.411 34.615 10.24 5.54 44.70 4.01
4077 8196 7.229306 ACTGATGTTGTAGAAATCTTTCTTGCA 59.771 33.333 10.24 7.70 44.70 4.08
4078 8197 7.939782 TGATGTTGTAGAAATCTTTCTTGCAA 58.060 30.769 10.24 12.23 44.70 4.08
4079 8198 7.862372 TGATGTTGTAGAAATCTTTCTTGCAAC 59.138 33.333 25.62 25.62 44.70 4.17
4083 8202 9.334693 GTTGTAGAAATCTTTCTTGCAACATAG 57.665 33.333 26.40 0.00 46.51 2.23
4084 8203 8.621532 TGTAGAAATCTTTCTTGCAACATAGT 57.378 30.769 10.24 0.00 44.70 2.12
4085 8204 9.719355 TGTAGAAATCTTTCTTGCAACATAGTA 57.281 29.630 10.24 0.00 44.70 1.82
4088 8207 9.678260 AGAAATCTTTCTTGCAACATAGTAGAT 57.322 29.630 0.00 0.00 44.70 1.98
4089 8208 9.713740 GAAATCTTTCTTGCAACATAGTAGATG 57.286 33.333 0.00 0.00 34.41 2.90
4090 8209 8.798859 AATCTTTCTTGCAACATAGTAGATGT 57.201 30.769 0.00 0.00 0.00 3.06
4091 8210 8.798859 ATCTTTCTTGCAACATAGTAGATGTT 57.201 30.769 0.00 0.00 42.38 2.71
4103 8222 9.593134 AACATAGTAGATGTTGCAAAACAAAAA 57.407 25.926 0.00 0.00 40.82 1.94
4104 8223 9.030301 ACATAGTAGATGTTGCAAAACAAAAAC 57.970 29.630 0.00 0.00 40.82 2.43
4105 8224 9.029243 CATAGTAGATGTTGCAAAACAAAAACA 57.971 29.630 0.00 0.00 40.82 2.83
4106 8225 7.289587 AGTAGATGTTGCAAAACAAAAACAC 57.710 32.000 0.00 0.00 40.82 3.32
4107 8226 5.544136 AGATGTTGCAAAACAAAAACACC 57.456 34.783 0.00 0.00 40.82 4.16
4108 8227 4.999950 AGATGTTGCAAAACAAAAACACCA 59.000 33.333 0.00 0.00 40.82 4.17
4109 8228 4.474226 TGTTGCAAAACAAAAACACCAC 57.526 36.364 0.00 0.00 40.82 4.16
4110 8229 4.130118 TGTTGCAAAACAAAAACACCACT 58.870 34.783 0.00 0.00 40.82 4.00
4111 8230 5.297547 TGTTGCAAAACAAAAACACCACTA 58.702 33.333 0.00 0.00 40.82 2.74
4112 8231 5.934625 TGTTGCAAAACAAAAACACCACTAT 59.065 32.000 0.00 0.00 40.82 2.12
4113 8232 7.097192 TGTTGCAAAACAAAAACACCACTATA 58.903 30.769 0.00 0.00 40.82 1.31
4114 8233 7.276658 TGTTGCAAAACAAAAACACCACTATAG 59.723 33.333 0.00 0.00 40.82 1.31
4115 8234 6.868622 TGCAAAACAAAAACACCACTATAGT 58.131 32.000 0.00 0.00 0.00 2.12
4116 8235 7.324178 TGCAAAACAAAAACACCACTATAGTT 58.676 30.769 1.56 0.00 0.00 2.24
4117 8236 7.489757 TGCAAAACAAAAACACCACTATAGTTC 59.510 33.333 1.56 0.00 0.00 3.01
4118 8237 7.305763 GCAAAACAAAAACACCACTATAGTTCG 60.306 37.037 1.56 0.00 0.00 3.95
4119 8238 5.934935 ACAAAAACACCACTATAGTTCGG 57.065 39.130 1.56 5.15 0.00 4.30
4120 8239 4.214758 ACAAAAACACCACTATAGTTCGGC 59.785 41.667 1.56 0.00 0.00 5.54
4121 8240 2.288961 AACACCACTATAGTTCGGCG 57.711 50.000 1.56 0.00 0.00 6.46
4122 8241 0.179119 ACACCACTATAGTTCGGCGC 60.179 55.000 1.56 0.00 0.00 6.53
4123 8242 1.065273 ACCACTATAGTTCGGCGCG 59.935 57.895 0.00 0.00 0.00 6.86
4124 8243 1.357690 CCACTATAGTTCGGCGCGA 59.642 57.895 12.10 0.00 0.00 5.87
4125 8244 0.660595 CCACTATAGTTCGGCGCGAG 60.661 60.000 12.10 2.11 37.14 5.03
4138 8257 2.263540 GCGAGCCCGTCAAAGGTA 59.736 61.111 0.00 0.00 38.24 3.08
4139 8258 1.810030 GCGAGCCCGTCAAAGGTAG 60.810 63.158 0.00 0.00 38.24 3.18
4140 8259 1.888018 CGAGCCCGTCAAAGGTAGA 59.112 57.895 0.00 0.00 0.00 2.59
4141 8260 0.179134 CGAGCCCGTCAAAGGTAGAG 60.179 60.000 0.00 0.00 0.00 2.43
4142 8261 1.183549 GAGCCCGTCAAAGGTAGAGA 58.816 55.000 0.00 0.00 0.00 3.10
4143 8262 1.135333 GAGCCCGTCAAAGGTAGAGAG 59.865 57.143 0.00 0.00 0.00 3.20
4144 8263 1.183549 GCCCGTCAAAGGTAGAGAGA 58.816 55.000 0.00 0.00 0.00 3.10
4145 8264 1.135053 GCCCGTCAAAGGTAGAGAGAC 60.135 57.143 0.00 0.00 0.00 3.36
4146 8265 2.168496 CCCGTCAAAGGTAGAGAGACA 58.832 52.381 0.00 0.00 0.00 3.41
4147 8266 2.761208 CCCGTCAAAGGTAGAGAGACAT 59.239 50.000 0.00 0.00 0.00 3.06
4148 8267 3.429547 CCCGTCAAAGGTAGAGAGACATG 60.430 52.174 0.00 0.00 0.00 3.21
4150 8269 3.182967 GTCAAAGGTAGAGAGACATGCG 58.817 50.000 0.00 0.00 0.00 4.73
4153 8272 1.107114 AGGTAGAGAGACATGCGTGG 58.893 55.000 11.36 0.00 0.00 4.94
4158 8277 2.020720 AGAGAGACATGCGTGGTCTAG 58.979 52.381 11.36 0.00 45.21 2.43
4162 8281 2.025155 AGACATGCGTGGTCTAGTAGG 58.975 52.381 11.36 0.00 43.50 3.18
4163 8282 0.460311 ACATGCGTGGTCTAGTAGGC 59.540 55.000 11.36 0.00 0.00 3.93
4168 8287 3.612251 TGGTCTAGTAGGCCACGC 58.388 61.111 19.85 0.00 43.71 5.34
4169 8288 2.412112 GGTCTAGTAGGCCACGCG 59.588 66.667 16.26 3.53 40.51 6.01
4171 8290 1.063811 GTCTAGTAGGCCACGCGTC 59.936 63.158 9.86 0.00 0.00 5.19
4175 8294 1.779025 TAGTAGGCCACGCGTCGATC 61.779 60.000 9.86 0.00 0.00 3.69
4180 8299 2.885644 CCACGCGTCGATCAAGGG 60.886 66.667 9.86 0.00 0.00 3.95
4183 8302 2.278857 CGCGTCGATCAAGGGAGG 60.279 66.667 0.00 0.00 0.00 4.30
4184 8303 2.586357 GCGTCGATCAAGGGAGGC 60.586 66.667 0.00 0.00 36.97 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.484062 GCCATCGACCATTGCCCAG 61.484 63.158 0.00 0.00 0.00 4.45
27 28 0.806102 CGAGTTCGCCATCGACCATT 60.806 55.000 0.00 0.00 45.43 3.16
58 59 1.202952 ACTGGGTTCAGACGTCTCTCT 60.203 52.381 16.96 0.00 43.49 3.10
66 67 1.618837 TGTCTAGCACTGGGTTCAGAC 59.381 52.381 0.00 0.00 43.49 3.51
122 123 1.334960 CCGAAAGCTTGACAAACGCAT 60.335 47.619 0.00 0.00 0.00 4.73
173 175 1.005097 TCTGCTCATGAATGGCCTGTT 59.995 47.619 3.32 0.00 0.00 3.16
201 203 1.005805 TGATATGTGGCTGTTGGGCTT 59.994 47.619 0.00 0.00 41.48 4.35
208 210 5.829391 TGCAGATAAAATGATATGTGGCTGT 59.171 36.000 0.00 0.00 29.68 4.40
354 356 3.056393 CCACATGTGATCTTGCCATTGTT 60.056 43.478 27.46 0.00 0.00 2.83
355 359 2.494471 CCACATGTGATCTTGCCATTGT 59.506 45.455 27.46 0.00 0.00 2.71
396 400 9.730705 AAGAAATTGACATTCTCATCTCTACAA 57.269 29.630 0.00 0.00 36.14 2.41
413 417 2.821969 GCAGAGCTTCCCAAGAAATTGA 59.178 45.455 0.00 0.00 0.00 2.57
452 458 0.874390 CATTGCCGCTACACTTGTGT 59.126 50.000 11.30 11.30 0.00 3.72
542 548 1.415374 GACGACTTGCTTTGCGTCTA 58.585 50.000 0.00 0.00 46.74 2.59
619 626 8.984891 TTACAATTAATCAAAGAAGCATGGTG 57.015 30.769 0.00 0.00 0.00 4.17
667 674 7.015098 AGCTAGTCTATCAGCATCTATGTTTGT 59.985 37.037 0.00 0.00 40.36 2.83
705 712 0.846015 ATCGCCCCTGATCCAATGAA 59.154 50.000 0.00 0.00 0.00 2.57
724 731 4.661222 TGAGGATGAAGCAACCAAACATA 58.339 39.130 0.00 0.00 0.00 2.29
738 745 4.220693 ACAAAACGGATCATGAGGATGA 57.779 40.909 0.09 0.00 42.92 2.92
741 748 5.128663 TGAGATACAAAACGGATCATGAGGA 59.871 40.000 0.09 0.00 0.00 3.71
776 783 8.023706 GGAAAGACAAGCTTTATTACTCCAAAG 58.976 37.037 0.00 0.00 46.52 2.77
780 787 8.788325 TTAGGAAAGACAAGCTTTATTACTCC 57.212 34.615 0.00 0.00 46.52 3.85
866 873 0.253327 ATTGAGGAAGAAGGGTCGGC 59.747 55.000 0.00 0.00 0.00 5.54
1047 1075 2.012237 CAGCATCTGCATCACCGTC 58.988 57.895 4.79 0.00 45.16 4.79
1155 1183 1.810030 GCGGTTGATGACGAGGTCC 60.810 63.158 0.00 0.00 0.00 4.46
1211 1239 3.430497 TCGGGGAGGAGGAGGAGG 61.430 72.222 0.00 0.00 0.00 4.30
1213 1241 4.124943 CGTCGGGGAGGAGGAGGA 62.125 72.222 0.00 0.00 0.00 3.71
1216 1244 1.001248 AAATCGTCGGGGAGGAGGA 59.999 57.895 0.00 0.00 35.54 3.71
1219 1247 2.420568 CGGAAATCGTCGGGGAGGA 61.421 63.158 0.00 0.00 0.00 3.71
1274 1304 0.605589 CGTAGATCTGGAGGGGCATC 59.394 60.000 5.18 0.00 0.00 3.91
1451 1493 2.435059 GCGACCTGGAAGACCTGC 60.435 66.667 0.00 0.00 34.07 4.85
1469 1511 1.410517 CACGAGGCATGGATGTAGAGT 59.589 52.381 0.00 0.00 0.00 3.24
1545 1588 3.233355 CTGCAGGACAGGGTTACAC 57.767 57.895 5.57 0.00 43.19 2.90
1790 1837 8.454106 AGCTATAATTGTTTGTTCACAGATGAC 58.546 33.333 0.00 0.00 33.38 3.06
2036 2115 1.074296 AAAACCCTTGGCCTCCTCCT 61.074 55.000 3.32 0.00 0.00 3.69
2037 2116 0.900182 CAAAACCCTTGGCCTCCTCC 60.900 60.000 3.32 0.00 0.00 4.30
2038 2117 0.178961 ACAAAACCCTTGGCCTCCTC 60.179 55.000 3.32 0.00 0.00 3.71
2243 2408 9.755064 CAGTTGTCATACCGAAAGTAAATTAAG 57.245 33.333 0.00 0.00 33.70 1.85
2290 2455 9.798994 ATTGTTGAATCAAGATGATTTAAGAGC 57.201 29.630 9.66 1.93 46.20 4.09
2528 2696 9.434420 GAAGCAGACTATATAGCATCATTCTTT 57.566 33.333 9.78 0.00 0.00 2.52
2559 2728 8.629158 ACAACATATTAACTCTGAAAGCAACAA 58.371 29.630 0.00 0.00 0.00 2.83
2607 2776 6.110707 CACTAACCTATGGGAAACATAACGT 58.889 40.000 0.25 0.00 41.33 3.99
2609 2778 6.420638 ACCACTAACCTATGGGAAACATAAC 58.579 40.000 0.25 0.00 41.33 1.89
2745 2917 3.839954 GCACAAGAACGAACAAGTACACG 60.840 47.826 0.00 0.00 0.00 4.49
2831 3003 5.243060 GTGAAAGGGGTAAGCAACACTTAAT 59.757 40.000 0.00 0.00 42.50 1.40
2938 3159 8.394971 ACATTTCGCCTTATATCATTGATTGA 57.605 30.769 4.14 0.00 39.12 2.57
3039 3262 1.936656 GCTGCGTCATCACAAGACAGA 60.937 52.381 0.00 0.00 35.77 3.41
3074 3297 3.459232 TCTTGCTATTGGATCCGAGTG 57.541 47.619 7.97 3.88 0.00 3.51
3077 3300 6.127338 CCATAGTATCTTGCTATTGGATCCGA 60.127 42.308 3.49 3.49 0.00 4.55
3172 3395 4.711846 TGTAGTGGAGCTCAGACAACATAT 59.288 41.667 17.19 0.00 0.00 1.78
3200 3868 0.907486 CAGAACATCTCTGGCCCTCA 59.093 55.000 0.00 0.00 46.89 3.86
3201 3869 3.776616 CAGAACATCTCTGGCCCTC 57.223 57.895 0.00 0.00 46.89 4.30
3355 4024 4.200874 ACGTCTAGATGCTAGCTAACAGT 58.799 43.478 17.23 3.31 0.00 3.55
3396 4065 7.914537 ATTTAGCTGTGTCGAAAAAGAAAAG 57.085 32.000 0.00 0.00 0.00 2.27
3474 4152 6.005823 TCATGCCATTCAGATAAATACAGGG 58.994 40.000 0.00 0.00 0.00 4.45
3494 4172 0.106868 TCCCAGAAGGCATGCTCATG 60.107 55.000 18.92 11.18 41.60 3.07
3499 4177 2.825836 CGGTCCCAGAAGGCATGC 60.826 66.667 9.90 9.90 34.51 4.06
3525 4211 2.913613 CAGCTTTTCTTTGCTCGTGAG 58.086 47.619 0.00 0.00 37.44 3.51
3527 4213 1.268692 TGCAGCTTTTCTTTGCTCGTG 60.269 47.619 0.00 0.00 37.44 4.35
3748 4838 6.834168 TTGTCCCCATGTTTTATCTTCTTC 57.166 37.500 0.00 0.00 0.00 2.87
3751 4841 7.610865 TGATTTTGTCCCCATGTTTTATCTTC 58.389 34.615 0.00 0.00 0.00 2.87
3753 4843 7.552050 TTGATTTTGTCCCCATGTTTTATCT 57.448 32.000 0.00 0.00 0.00 1.98
3754 4844 6.313658 GCTTGATTTTGTCCCCATGTTTTATC 59.686 38.462 0.00 0.00 0.00 1.75
3755 4845 6.172630 GCTTGATTTTGTCCCCATGTTTTAT 58.827 36.000 0.00 0.00 0.00 1.40
3761 4851 2.564062 ACTGCTTGATTTTGTCCCCATG 59.436 45.455 0.00 0.00 0.00 3.66
3763 4853 2.364970 CAACTGCTTGATTTTGTCCCCA 59.635 45.455 0.00 0.00 0.00 4.96
3764 4854 2.289010 CCAACTGCTTGATTTTGTCCCC 60.289 50.000 0.00 0.00 0.00 4.81
3765 4855 2.627699 TCCAACTGCTTGATTTTGTCCC 59.372 45.455 0.00 0.00 0.00 4.46
3766 4856 4.240096 CATCCAACTGCTTGATTTTGTCC 58.760 43.478 0.00 0.00 0.00 4.02
3775 5610 4.070716 AGAGAAAGACATCCAACTGCTTG 58.929 43.478 0.00 0.00 0.00 4.01
3777 5612 4.363991 AAGAGAAAGACATCCAACTGCT 57.636 40.909 0.00 0.00 0.00 4.24
3778 5613 5.444663 AAAAGAGAAAGACATCCAACTGC 57.555 39.130 0.00 0.00 0.00 4.40
3798 5633 7.548427 TCAGAAACAAGATCATTGTTGCAAAAA 59.452 29.630 21.18 4.10 41.30 1.94
3799 5634 7.040494 TCAGAAACAAGATCATTGTTGCAAAA 58.960 30.769 21.18 0.00 41.30 2.44
3800 5635 6.571605 TCAGAAACAAGATCATTGTTGCAAA 58.428 32.000 21.18 11.71 41.30 3.68
3801 5636 6.146601 TCAGAAACAAGATCATTGTTGCAA 57.853 33.333 21.18 0.00 41.30 4.08
3802 5637 5.771153 TCAGAAACAAGATCATTGTTGCA 57.229 34.783 21.18 7.56 41.30 4.08
3803 5638 6.698766 AGTTTCAGAAACAAGATCATTGTTGC 59.301 34.615 24.85 16.78 43.79 4.17
3804 5639 8.133627 AGAGTTTCAGAAACAAGATCATTGTTG 58.866 33.333 24.85 7.28 43.79 3.33
3805 5640 8.230472 AGAGTTTCAGAAACAAGATCATTGTT 57.770 30.769 24.85 13.96 43.79 2.83
3806 5641 7.814264 AGAGTTTCAGAAACAAGATCATTGT 57.186 32.000 24.85 3.19 43.79 2.71
3807 5642 8.133627 ACAAGAGTTTCAGAAACAAGATCATTG 58.866 33.333 24.85 18.62 43.79 2.82
3808 5643 8.230472 ACAAGAGTTTCAGAAACAAGATCATT 57.770 30.769 24.85 4.55 43.79 2.57
3809 5644 7.814264 ACAAGAGTTTCAGAAACAAGATCAT 57.186 32.000 24.85 6.82 43.79 2.45
3810 5645 8.612619 GTTACAAGAGTTTCAGAAACAAGATCA 58.387 33.333 24.85 6.13 43.79 2.92
3811 5646 8.612619 TGTTACAAGAGTTTCAGAAACAAGATC 58.387 33.333 24.85 14.73 43.79 2.75
3812 5647 8.398665 GTGTTACAAGAGTTTCAGAAACAAGAT 58.601 33.333 24.85 6.97 43.79 2.40
3813 5648 7.389330 TGTGTTACAAGAGTTTCAGAAACAAGA 59.611 33.333 24.85 7.78 43.79 3.02
3814 5649 7.526608 TGTGTTACAAGAGTTTCAGAAACAAG 58.473 34.615 24.85 14.48 43.79 3.16
3815 5650 7.389330 TCTGTGTTACAAGAGTTTCAGAAACAA 59.611 33.333 24.85 9.00 43.79 2.83
3816 5651 6.876789 TCTGTGTTACAAGAGTTTCAGAAACA 59.123 34.615 24.85 3.41 43.79 2.83
3817 5652 7.303634 TCTGTGTTACAAGAGTTTCAGAAAC 57.696 36.000 17.11 17.11 41.69 2.78
3818 5653 8.397906 CAATCTGTGTTACAAGAGTTTCAGAAA 58.602 33.333 4.21 0.00 35.01 2.52
3819 5654 7.552687 ACAATCTGTGTTACAAGAGTTTCAGAA 59.447 33.333 4.21 0.00 37.01 3.02
3822 5657 7.015226 CACAATCTGTGTTACAAGAGTTTCA 57.985 36.000 0.00 0.00 43.08 2.69
3856 5691 1.135915 ACACGACCAATGCTGCAAAAA 59.864 42.857 6.36 0.00 0.00 1.94
3858 5693 0.743688 AACACGACCAATGCTGCAAA 59.256 45.000 6.36 0.00 0.00 3.68
3859 5694 0.030504 CAACACGACCAATGCTGCAA 59.969 50.000 6.36 0.00 0.00 4.08
3860 5695 1.100463 ACAACACGACCAATGCTGCA 61.100 50.000 4.13 4.13 0.00 4.41
3861 5696 0.661187 CACAACACGACCAATGCTGC 60.661 55.000 0.00 0.00 0.00 5.25
3862 5697 0.040157 CCACAACACGACCAATGCTG 60.040 55.000 0.00 0.00 0.00 4.41
3863 5698 0.179032 TCCACAACACGACCAATGCT 60.179 50.000 0.00 0.00 0.00 3.79
3864 5699 0.665835 TTCCACAACACGACCAATGC 59.334 50.000 0.00 0.00 0.00 3.56
3867 5702 5.776173 AATAAATTCCACAACACGACCAA 57.224 34.783 0.00 0.00 0.00 3.67
3868 5703 5.776173 AAATAAATTCCACAACACGACCA 57.224 34.783 0.00 0.00 0.00 4.02
3897 5829 5.627499 AAAATCTGCAACACGACATATGT 57.373 34.783 8.43 8.43 0.00 2.29
3946 5878 8.947055 AAGTTTTTCTGCAACAATATCTTTGT 57.053 26.923 0.00 0.00 0.00 2.83
3947 5879 9.640974 CAAAGTTTTTCTGCAACAATATCTTTG 57.359 29.630 12.52 12.52 33.82 2.77
3948 5880 8.337532 GCAAAGTTTTTCTGCAACAATATCTTT 58.662 29.630 0.00 0.00 36.09 2.52
3949 5881 7.495279 TGCAAAGTTTTTCTGCAACAATATCTT 59.505 29.630 0.00 0.00 42.84 2.40
3951 5883 7.176285 TGCAAAGTTTTTCTGCAACAATATC 57.824 32.000 0.00 0.00 42.84 1.63
3967 8075 3.290710 ACATCACCTCAGTTGCAAAGTT 58.709 40.909 0.00 0.00 0.00 2.66
3970 8078 3.713858 CAACATCACCTCAGTTGCAAA 57.286 42.857 0.00 0.00 36.59 3.68
3975 8083 2.936919 TCTGCAACATCACCTCAGTT 57.063 45.000 0.00 0.00 0.00 3.16
3976 8084 4.767578 ATATCTGCAACATCACCTCAGT 57.232 40.909 0.00 0.00 0.00 3.41
3977 8085 6.446781 AAAATATCTGCAACATCACCTCAG 57.553 37.500 0.00 0.00 0.00 3.35
3978 8086 6.839124 AAAAATATCTGCAACATCACCTCA 57.161 33.333 0.00 0.00 0.00 3.86
3998 8117 9.231297 CCATATAGAGGTGAAGACAAAGAAAAA 57.769 33.333 0.00 0.00 0.00 1.94
4016 8135 7.414222 AAGTTTCTCCGTAACACCATATAGA 57.586 36.000 0.00 0.00 0.00 1.98
4017 8136 9.193133 CATAAGTTTCTCCGTAACACCATATAG 57.807 37.037 0.00 0.00 0.00 1.31
4018 8137 7.654520 GCATAAGTTTCTCCGTAACACCATATA 59.345 37.037 0.00 0.00 0.00 0.86
4019 8138 6.482308 GCATAAGTTTCTCCGTAACACCATAT 59.518 38.462 0.00 0.00 0.00 1.78
4020 8139 5.813672 GCATAAGTTTCTCCGTAACACCATA 59.186 40.000 0.00 0.00 0.00 2.74
4021 8140 4.634443 GCATAAGTTTCTCCGTAACACCAT 59.366 41.667 0.00 0.00 0.00 3.55
4022 8141 3.998341 GCATAAGTTTCTCCGTAACACCA 59.002 43.478 0.00 0.00 0.00 4.17
4023 8142 3.998341 TGCATAAGTTTCTCCGTAACACC 59.002 43.478 0.00 0.00 0.00 4.16
4024 8143 5.049954 TGTTGCATAAGTTTCTCCGTAACAC 60.050 40.000 0.00 0.00 0.00 3.32
4025 8144 5.057819 TGTTGCATAAGTTTCTCCGTAACA 58.942 37.500 0.00 0.00 0.00 2.41
4026 8145 5.600908 TGTTGCATAAGTTTCTCCGTAAC 57.399 39.130 0.00 0.00 0.00 2.50
4027 8146 7.604927 AGTTATGTTGCATAAGTTTCTCCGTAA 59.395 33.333 2.22 0.00 0.00 3.18
4028 8147 7.064134 CAGTTATGTTGCATAAGTTTCTCCGTA 59.936 37.037 6.50 0.00 0.00 4.02
4029 8148 5.938125 AGTTATGTTGCATAAGTTTCTCCGT 59.062 36.000 2.22 0.00 0.00 4.69
4030 8149 6.092122 TCAGTTATGTTGCATAAGTTTCTCCG 59.908 38.462 6.50 0.00 0.00 4.63
4031 8150 7.377766 TCAGTTATGTTGCATAAGTTTCTCC 57.622 36.000 6.50 0.00 0.00 3.71
4032 8151 8.832487 CATCAGTTATGTTGCATAAGTTTCTC 57.168 34.615 6.50 0.00 0.00 2.87
4050 8169 8.078596 GCAAGAAAGATTTCTACAACATCAGTT 58.921 33.333 8.19 0.00 46.22 3.16
4051 8170 7.229306 TGCAAGAAAGATTTCTACAACATCAGT 59.771 33.333 8.19 0.00 46.22 3.41
4052 8171 7.587629 TGCAAGAAAGATTTCTACAACATCAG 58.412 34.615 8.19 0.00 46.22 2.90
4053 8172 7.509141 TGCAAGAAAGATTTCTACAACATCA 57.491 32.000 8.19 0.00 46.22 3.07
4058 8177 9.066892 ACTATGTTGCAAGAAAGATTTCTACAA 57.933 29.630 8.19 12.17 46.22 2.41
4059 8178 8.621532 ACTATGTTGCAAGAAAGATTTCTACA 57.378 30.769 8.19 9.11 46.22 2.74
4063 8182 9.713740 CATCTACTATGTTGCAAGAAAGATTTC 57.286 33.333 0.00 0.00 37.45 2.17
4064 8183 9.236006 ACATCTACTATGTTGCAAGAAAGATTT 57.764 29.630 0.00 0.00 0.00 2.17
4065 8184 8.798859 ACATCTACTATGTTGCAAGAAAGATT 57.201 30.769 0.00 0.00 0.00 2.40
4066 8185 8.798859 AACATCTACTATGTTGCAAGAAAGAT 57.201 30.769 0.00 3.99 40.37 2.40
4077 8196 9.593134 TTTTTGTTTTGCAACATCTACTATGTT 57.407 25.926 0.00 0.00 42.66 2.71
4078 8197 9.030301 GTTTTTGTTTTGCAACATCTACTATGT 57.970 29.630 0.00 0.00 42.66 2.29
4079 8198 9.029243 TGTTTTTGTTTTGCAACATCTACTATG 57.971 29.630 0.00 0.00 42.66 2.23
4080 8199 9.030301 GTGTTTTTGTTTTGCAACATCTACTAT 57.970 29.630 0.00 0.00 42.66 2.12
4081 8200 7.489757 GGTGTTTTTGTTTTGCAACATCTACTA 59.510 33.333 0.00 0.00 42.66 1.82
4082 8201 6.312672 GGTGTTTTTGTTTTGCAACATCTACT 59.687 34.615 0.00 0.00 42.66 2.57
4083 8202 6.091441 TGGTGTTTTTGTTTTGCAACATCTAC 59.909 34.615 0.00 0.00 42.66 2.59
4084 8203 6.091441 GTGGTGTTTTTGTTTTGCAACATCTA 59.909 34.615 0.00 0.00 42.66 1.98
4085 8204 4.999950 TGGTGTTTTTGTTTTGCAACATCT 59.000 33.333 0.00 0.00 42.66 2.90
4086 8205 5.085390 GTGGTGTTTTTGTTTTGCAACATC 58.915 37.500 0.00 0.00 42.66 3.06
4087 8206 4.759183 AGTGGTGTTTTTGTTTTGCAACAT 59.241 33.333 0.00 0.00 42.66 2.71
4088 8207 4.130118 AGTGGTGTTTTTGTTTTGCAACA 58.870 34.783 0.00 0.00 41.39 3.33
4089 8208 4.740741 AGTGGTGTTTTTGTTTTGCAAC 57.259 36.364 0.00 0.00 36.72 4.17
4090 8209 7.324178 ACTATAGTGGTGTTTTTGTTTTGCAA 58.676 30.769 4.10 0.00 34.87 4.08
4091 8210 6.868622 ACTATAGTGGTGTTTTTGTTTTGCA 58.131 32.000 4.10 0.00 0.00 4.08
4092 8211 7.305763 CGAACTATAGTGGTGTTTTTGTTTTGC 60.306 37.037 6.06 0.00 0.00 3.68
4093 8212 7.166804 CCGAACTATAGTGGTGTTTTTGTTTTG 59.833 37.037 6.06 0.00 0.00 2.44
4094 8213 7.197703 CCGAACTATAGTGGTGTTTTTGTTTT 58.802 34.615 6.06 0.00 0.00 2.43
4095 8214 6.731164 CCGAACTATAGTGGTGTTTTTGTTT 58.269 36.000 6.06 0.00 0.00 2.83
4096 8215 5.278120 GCCGAACTATAGTGGTGTTTTTGTT 60.278 40.000 6.06 0.00 0.00 2.83
4097 8216 4.214758 GCCGAACTATAGTGGTGTTTTTGT 59.785 41.667 6.06 0.00 0.00 2.83
4098 8217 4.668177 CGCCGAACTATAGTGGTGTTTTTG 60.668 45.833 6.06 0.00 0.00 2.44
4099 8218 3.434299 CGCCGAACTATAGTGGTGTTTTT 59.566 43.478 6.06 0.00 0.00 1.94
4100 8219 2.997986 CGCCGAACTATAGTGGTGTTTT 59.002 45.455 6.06 0.00 0.00 2.43
4101 8220 2.613691 CGCCGAACTATAGTGGTGTTT 58.386 47.619 6.06 0.00 0.00 2.83
4102 8221 1.738030 GCGCCGAACTATAGTGGTGTT 60.738 52.381 18.89 0.00 34.50 3.32
4103 8222 0.179119 GCGCCGAACTATAGTGGTGT 60.179 55.000 18.89 0.32 34.50 4.16
4104 8223 1.206745 CGCGCCGAACTATAGTGGTG 61.207 60.000 15.31 15.31 35.12 4.17
4105 8224 1.065273 CGCGCCGAACTATAGTGGT 59.935 57.895 6.06 0.00 0.00 4.16
4106 8225 0.660595 CTCGCGCCGAACTATAGTGG 60.661 60.000 6.06 5.51 34.74 4.00
4107 8226 1.269444 GCTCGCGCCGAACTATAGTG 61.269 60.000 6.06 0.00 34.74 2.74
4108 8227 1.008767 GCTCGCGCCGAACTATAGT 60.009 57.895 0.00 0.00 34.74 2.12
4109 8228 3.830249 GCTCGCGCCGAACTATAG 58.170 61.111 0.00 0.00 34.74 1.31
4120 8239 3.636313 TACCTTTGACGGGCTCGCG 62.636 63.158 5.51 0.00 40.63 5.87
4121 8240 1.810030 CTACCTTTGACGGGCTCGC 60.810 63.158 5.51 0.00 40.63 5.03
4122 8241 0.179134 CTCTACCTTTGACGGGCTCG 60.179 60.000 3.27 3.27 43.02 5.03
4123 8242 1.135333 CTCTCTACCTTTGACGGGCTC 59.865 57.143 0.00 0.00 0.00 4.70
4124 8243 1.187087 CTCTCTACCTTTGACGGGCT 58.813 55.000 0.00 0.00 0.00 5.19
4125 8244 1.135053 GTCTCTCTACCTTTGACGGGC 60.135 57.143 0.00 0.00 0.00 6.13
4126 8245 2.168496 TGTCTCTCTACCTTTGACGGG 58.832 52.381 0.00 0.00 0.00 5.28
4127 8246 3.775202 CATGTCTCTCTACCTTTGACGG 58.225 50.000 0.00 0.00 0.00 4.79
4128 8247 3.182967 GCATGTCTCTCTACCTTTGACG 58.817 50.000 0.00 0.00 0.00 4.35
4129 8248 3.182967 CGCATGTCTCTCTACCTTTGAC 58.817 50.000 0.00 0.00 0.00 3.18
4130 8249 2.826128 ACGCATGTCTCTCTACCTTTGA 59.174 45.455 0.00 0.00 0.00 2.69
4131 8250 2.926200 CACGCATGTCTCTCTACCTTTG 59.074 50.000 0.00 0.00 0.00 2.77
4132 8251 2.093973 CCACGCATGTCTCTCTACCTTT 60.094 50.000 0.00 0.00 0.00 3.11
4133 8252 1.478510 CCACGCATGTCTCTCTACCTT 59.521 52.381 0.00 0.00 0.00 3.50
4134 8253 1.107114 CCACGCATGTCTCTCTACCT 58.893 55.000 0.00 0.00 0.00 3.08
4135 8254 0.818296 ACCACGCATGTCTCTCTACC 59.182 55.000 0.00 0.00 0.00 3.18
4136 8255 1.746220 AGACCACGCATGTCTCTCTAC 59.254 52.381 0.00 0.00 38.71 2.59
4137 8256 2.130272 AGACCACGCATGTCTCTCTA 57.870 50.000 0.00 0.00 38.71 2.43
4138 8257 2.020720 CTAGACCACGCATGTCTCTCT 58.979 52.381 5.47 0.00 41.97 3.10
4139 8258 1.746220 ACTAGACCACGCATGTCTCTC 59.254 52.381 0.00 0.00 41.97 3.20
4140 8259 1.840737 ACTAGACCACGCATGTCTCT 58.159 50.000 0.00 0.00 41.97 3.10
4141 8260 2.033550 CCTACTAGACCACGCATGTCTC 59.966 54.545 0.00 0.00 41.97 3.36
4142 8261 2.025155 CCTACTAGACCACGCATGTCT 58.975 52.381 0.00 7.18 44.85 3.41
4143 8262 1.536284 GCCTACTAGACCACGCATGTC 60.536 57.143 0.00 0.00 0.00 3.06
4144 8263 0.460311 GCCTACTAGACCACGCATGT 59.540 55.000 0.00 0.00 0.00 3.21
4145 8264 0.249489 GGCCTACTAGACCACGCATG 60.249 60.000 0.00 0.00 0.00 4.06
4146 8265 0.686441 TGGCCTACTAGACCACGCAT 60.686 55.000 3.32 0.00 0.00 4.73
4147 8266 1.304630 TGGCCTACTAGACCACGCA 60.305 57.895 3.32 0.00 0.00 5.24
4148 8267 1.141234 GTGGCCTACTAGACCACGC 59.859 63.158 3.32 0.00 44.02 5.34
4153 8272 1.063811 GACGCGTGGCCTACTAGAC 59.936 63.158 20.70 0.00 0.00 2.59
4156 8275 1.779025 GATCGACGCGTGGCCTACTA 61.779 60.000 20.70 0.00 0.00 1.82
4158 8277 2.654404 GATCGACGCGTGGCCTAC 60.654 66.667 20.70 0.00 0.00 3.18
4162 8281 3.554692 CCTTGATCGACGCGTGGC 61.555 66.667 20.70 3.82 0.00 5.01
4163 8282 2.885644 CCCTTGATCGACGCGTGG 60.886 66.667 20.70 17.88 0.00 4.94


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

AutoCloner maintained by Alex Coulton.