Multiple sequence alignment - TraesCS3A01G159500

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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 TraesCS3A01G159500 chr3A 100.000 4573 0 0 1 4573 159346339 159350911 0.000000e+00 8445.0
1 TraesCS3A01G159500 chr3A 82.682 179 25 4 4000 4174 641865792 641865616 2.200000e-33 154.0
2 TraesCS3A01G159500 chr3A 89.431 123 8 2 491 608 159344330 159344208 2.850000e-32 150.0
3 TraesCS3A01G159500 chr3A 85.034 147 18 4 4026 4169 199695642 199695497 3.690000e-31 147.0
4 TraesCS3A01G159500 chr3D 94.089 3434 151 29 600 4001 141178582 141181995 0.000000e+00 5169.0
5 TraesCS3A01G159500 chr3D 87.805 246 19 5 4279 4517 141182020 141182261 1.250000e-70 278.0
6 TraesCS3A01G159500 chr3D 86.250 80 11 0 4203 4282 303354610 303354531 2.270000e-13 87.9
7 TraesCS3A01G159500 chr3B 95.510 1893 67 11 600 2487 202899033 202900912 0.000000e+00 3009.0
8 TraesCS3A01G159500 chr3B 89.922 1548 115 25 2468 4001 202900924 202902444 0.000000e+00 1956.0
9 TraesCS3A01G159500 chr3B 93.333 240 14 2 4279 4517 202902470 202902708 2.020000e-93 353.0
10 TraesCS3A01G159500 chr3B 83.158 95 15 1 4189 4282 250133625 250133719 8.150000e-13 86.1
11 TraesCS3A01G159500 chr5A 94.399 607 26 4 2 606 298258974 298258374 0.000000e+00 926.0
12 TraesCS3A01G159500 chr6A 92.282 609 39 8 1 605 21160402 21159798 0.000000e+00 857.0
13 TraesCS3A01G159500 chr7D 90.980 643 20 9 1 605 36515519 36514877 0.000000e+00 832.0
14 TraesCS3A01G159500 chr6D 75.635 394 63 25 189 578 56298933 56299297 1.020000e-36 165.0
15 TraesCS3A01G159500 chr6D 84.564 149 19 4 4026 4172 423084180 423084326 1.330000e-30 145.0
16 TraesCS3A01G159500 chr6D 91.892 74 5 1 4208 4280 393661924 393661997 8.090000e-18 102.0
17 TraesCS3A01G159500 chr6D 84.270 89 10 2 9 97 29986949 29986865 2.930000e-12 84.2
18 TraesCS3A01G159500 chr6D 86.111 72 10 0 4209 4280 57579363 57579434 1.360000e-10 78.7
19 TraesCS3A01G159500 chr7A 86.301 146 16 4 4026 4168 684926049 684926193 6.130000e-34 156.0
20 TraesCS3A01G159500 chr1D 86.207 145 14 6 4026 4166 355206071 355206213 7.920000e-33 152.0
21 TraesCS3A01G159500 chr2D 85.616 146 17 4 4026 4169 81004776 81004919 2.850000e-32 150.0
22 TraesCS3A01G159500 chr2D 84.932 146 19 3 4026 4169 81325503 81325359 1.330000e-30 145.0
23 TraesCS3A01G159500 chr2D 84.459 148 17 5 4026 4168 52690246 52690392 1.720000e-29 141.0
24 TraesCS3A01G159500 chr1B 84.828 145 18 4 4026 4168 623195702 623195844 4.770000e-30 143.0
25 TraesCS3A01G159500 chr4A 86.047 86 8 3 9 94 607414810 607414891 6.300000e-14 89.8
26 TraesCS3A01G159500 chr1A 77.703 148 27 4 29 175 537057593 537057735 8.150000e-13 86.1
27 TraesCS3A01G159500 chr5B 86.567 67 8 1 29 94 643801026 643801092 6.350000e-09 73.1
28 TraesCS3A01G159500 chr5B 86.567 67 8 1 29 94 643906073 643906139 6.350000e-09 73.1
29 TraesCS3A01G159500 chr6B 97.222 36 1 0 534 569 506878419 506878384 1.370000e-05 62.1


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 TraesCS3A01G159500 chr3A 159346339 159350911 4572 False 8445.000000 8445 100.000000 1 4573 1 chr3A.!!$F1 4572
1 TraesCS3A01G159500 chr3D 141178582 141182261 3679 False 2723.500000 5169 90.947000 600 4517 2 chr3D.!!$F1 3917
2 TraesCS3A01G159500 chr3B 202899033 202902708 3675 False 1772.666667 3009 92.921667 600 4517 3 chr3B.!!$F2 3917
3 TraesCS3A01G159500 chr5A 298258374 298258974 600 True 926.000000 926 94.399000 2 606 1 chr5A.!!$R1 604
4 TraesCS3A01G159500 chr6A 21159798 21160402 604 True 857.000000 857 92.282000 1 605 1 chr6A.!!$R1 604
5 TraesCS3A01G159500 chr7D 36514877 36515519 642 True 832.000000 832 90.980000 1 605 1 chr7D.!!$R1 604

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
668 710 0.336737 CCCCTCGCCCCTATCTATCT 59.663 60.000 0.00 0.0 0.00 1.98 F
876 919 0.949105 TTGTTTTCTCGGCGCTCCTC 60.949 55.000 7.64 0.0 0.00 3.71 F
1232 1276 1.267732 CGGTCTGCATTTCTCGATTGC 60.268 52.381 0.00 0.0 35.66 3.56 F
2892 2980 0.972883 GGCAGACAACTCTCAGGACT 59.027 55.000 0.00 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2182 2232 1.134340 ACCTTGTACGACACAAAGCCA 60.134 47.619 8.32 0.0 46.37 4.75 R
2689 2775 1.071471 CCGTGTGGGCTCTGAAACT 59.929 57.895 0.00 0.0 0.00 2.66 R
3010 3101 0.033504 TTCACGAACTGCTGGAGACC 59.966 55.000 2.24 0.0 0.00 3.85 R
3755 3857 0.099436 GGTTGCTTCATCCGTCATGC 59.901 55.000 0.00 0.0 31.70 4.06 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
371 403 1.765657 GGATCTCCTGGAGCTGGCT 60.766 63.158 19.08 0.00 0.00 4.75
476 518 4.929479 AGGGGCAAGTTTGTCATTATACA 58.071 39.130 0.00 0.00 33.59 2.29
500 542 1.270414 ACCCATCTGACAGAGGGCAG 61.270 60.000 27.23 18.14 44.39 4.85
513 555 2.641815 AGAGGGCAGAAGATCAAAGTGT 59.358 45.455 0.00 0.00 0.00 3.55
580 622 9.349713 TGACAAATAGTGAAAGTCCAAAGTAAT 57.650 29.630 0.00 0.00 0.00 1.89
668 710 0.336737 CCCCTCGCCCCTATCTATCT 59.663 60.000 0.00 0.00 0.00 1.98
669 711 1.569548 CCCCTCGCCCCTATCTATCTA 59.430 57.143 0.00 0.00 0.00 1.98
670 712 2.178106 CCCCTCGCCCCTATCTATCTAT 59.822 54.545 0.00 0.00 0.00 1.98
671 713 3.492337 CCCTCGCCCCTATCTATCTATC 58.508 54.545 0.00 0.00 0.00 2.08
698 740 4.101077 CTGGCCCCTCCCCTCTCT 62.101 72.222 0.00 0.00 0.00 3.10
858 900 3.653164 TCTTCAAAAGCCCTCCCTTTTT 58.347 40.909 0.00 0.00 41.67 1.94
859 901 3.387699 TCTTCAAAAGCCCTCCCTTTTTG 59.612 43.478 3.27 3.27 41.67 2.44
876 919 0.949105 TTGTTTTCTCGGCGCTCCTC 60.949 55.000 7.64 0.00 0.00 3.71
970 1013 2.602676 GCTAGGCTGGTTGGTGGGA 61.603 63.158 0.00 0.00 0.00 4.37
1129 1173 2.233186 AGCCTCAAGGTACTACGTTTCC 59.767 50.000 0.00 0.00 38.49 3.13
1149 1193 2.045926 GCGCCTCACCCTTCACAT 60.046 61.111 0.00 0.00 0.00 3.21
1232 1276 1.267732 CGGTCTGCATTTCTCGATTGC 60.268 52.381 0.00 0.00 35.66 3.56
1317 1361 2.780010 CCCCTATGTCCCTGTCAATCTT 59.220 50.000 0.00 0.00 0.00 2.40
1453 1502 4.517832 GTCCTTCTTTTTCCGTACCATGTT 59.482 41.667 0.00 0.00 0.00 2.71
1466 1515 5.290158 CCGTACCATGTTGTTGTATGTCTAC 59.710 44.000 0.00 0.00 0.00 2.59
1683 1733 1.386525 GGCCTCACGTATACGGTGGA 61.387 60.000 27.62 19.69 44.95 4.02
2020 2070 3.099362 CAACTCGCACAGATCTACGTAC 58.901 50.000 0.00 0.00 0.00 3.67
2029 2079 4.557690 CACAGATCTACGTACGGTCTTTTG 59.442 45.833 21.06 12.90 0.00 2.44
2042 2092 9.219497 CGTACGGTCTTTTGTTTTGTTTAATTA 57.781 29.630 7.57 0.00 0.00 1.40
2052 2102 8.514136 TTGTTTTGTTTAATTATTCAGCTCCG 57.486 30.769 0.00 0.00 0.00 4.63
2056 2106 6.417191 TGTTTAATTATTCAGCTCCGTGTC 57.583 37.500 0.00 0.00 0.00 3.67
2061 2111 6.710597 AATTATTCAGCTCCGTGTCTACTA 57.289 37.500 0.00 0.00 0.00 1.82
2128 2178 2.368875 ACTTGTCTTCTGTAGGGTGGTG 59.631 50.000 0.00 0.00 0.00 4.17
2182 2232 2.423577 GTTAGCACGGTTGACCATCTT 58.576 47.619 0.51 0.00 35.14 2.40
2185 2235 1.875963 CACGGTTGACCATCTTGGC 59.124 57.895 0.51 0.00 42.67 4.52
2405 2460 3.571401 CCCATTTGAGTCTATGGCATTCC 59.429 47.826 4.78 0.00 40.00 3.01
2444 2499 6.314400 GGTTAATATGTCGCACAAGTCCTAAA 59.686 38.462 0.00 0.00 0.00 1.85
2490 2576 3.869065 TGTAGAGGGTAAAGATTTGCCG 58.131 45.455 6.38 0.00 42.95 5.69
2584 2670 7.201696 CGTTACATATTACCAGGCAAATTCACT 60.202 37.037 0.00 0.00 0.00 3.41
2585 2671 6.455360 ACATATTACCAGGCAAATTCACTG 57.545 37.500 0.00 0.00 0.00 3.66
2661 2747 2.288948 TGTTGTTCCGTTGTATAGGCGT 60.289 45.455 0.00 0.00 0.00 5.68
2689 2775 1.347707 GTGGAATCCGCTATCCATCCA 59.652 52.381 5.44 0.00 46.78 3.41
2753 2839 3.319137 AAATGCGCAAGTCTCAGTCTA 57.681 42.857 17.11 0.00 41.68 2.59
2766 2852 6.535540 AGTCTCAGTCTAGTAAGTTCACTGA 58.464 40.000 7.67 7.67 40.89 3.41
2788 2874 7.060383 TGAATTTCTGAGTTCTGAGTTCTCT 57.940 36.000 0.00 0.00 0.00 3.10
2892 2980 0.972883 GGCAGACAACTCTCAGGACT 59.027 55.000 0.00 0.00 0.00 3.85
2932 3020 7.439157 TTGTGGATCAAAGTGTTCATAAGAG 57.561 36.000 0.00 0.00 32.64 2.85
3010 3101 2.022129 GCAGGAGTGTCCGTTCACG 61.022 63.158 0.00 0.00 42.75 4.35
3149 3241 6.533730 AGTATTCTGACCTCACATTTGAACA 58.466 36.000 0.00 0.00 0.00 3.18
3247 3339 2.937873 GCAGGTTCGCCAATACCAACTA 60.938 50.000 0.00 0.00 40.60 2.24
3248 3340 3.541632 CAGGTTCGCCAATACCAACTAT 58.458 45.455 0.00 0.00 40.60 2.12
3254 3346 3.137544 TCGCCAATACCAACTATTCCCAT 59.862 43.478 0.00 0.00 0.00 4.00
3370 3462 9.444600 TCTTTCTGTTTAACAGTGTATTATCCC 57.555 33.333 22.36 0.00 46.03 3.85
3384 3476 4.983671 ATTATCCCGAAGCCAGTTTTTC 57.016 40.909 0.00 0.00 0.00 2.29
3388 3480 2.158667 TCCCGAAGCCAGTTTTTCTTCT 60.159 45.455 0.00 0.00 35.35 2.85
3402 3494 8.760569 CAGTTTTTCTTCTCTCTAGTTTCTGAC 58.239 37.037 0.00 0.00 0.00 3.51
3456 3549 1.204941 AGGTGCAGTCCGACTATGAAC 59.795 52.381 0.00 0.00 0.00 3.18
3482 3575 3.261897 AGAAAGAGCGGGAGAAAAGATCA 59.738 43.478 0.00 0.00 0.00 2.92
3588 3681 6.208988 AGTACTGATCGCTGAAATGTCTTA 57.791 37.500 0.00 0.00 0.00 2.10
3591 3686 5.105752 ACTGATCGCTGAAATGTCTTAGAC 58.894 41.667 5.27 5.27 0.00 2.59
3656 3758 4.464244 TGTTCGAGATCTCAGACCAAATCT 59.536 41.667 22.31 0.00 38.66 2.40
3768 3870 1.980951 GCAAGCGCATGACGGATGAA 61.981 55.000 18.15 0.00 43.93 2.57
3769 3871 0.027194 CAAGCGCATGACGGATGAAG 59.973 55.000 11.47 0.00 43.93 3.02
3770 3872 1.709147 AAGCGCATGACGGATGAAGC 61.709 55.000 11.47 5.49 43.93 3.86
3783 3885 3.689161 CGGATGAAGCAACCAAATACAGA 59.311 43.478 0.00 0.00 0.00 3.41
3786 3888 3.485394 TGAAGCAACCAAATACAGAGCA 58.515 40.909 0.00 0.00 0.00 4.26
3787 3889 3.503363 TGAAGCAACCAAATACAGAGCAG 59.497 43.478 0.00 0.00 0.00 4.24
3800 3912 3.099905 ACAGAGCAGCTTCAGTACCATA 58.900 45.455 0.00 0.00 0.00 2.74
3808 3920 3.134804 AGCTTCAGTACCATACCATCACC 59.865 47.826 0.00 0.00 0.00 4.02
3829 3941 3.627577 CCTACATCCATTTCCCGTTTCTG 59.372 47.826 0.00 0.00 0.00 3.02
3891 4003 3.003689 AGTGTCATTTTCCTCTGTTTGCG 59.996 43.478 0.00 0.00 0.00 4.85
3964 4077 2.146724 AGTGGTAGCACAGTGGGCA 61.147 57.895 25.75 2.37 0.00 5.36
3972 4085 1.660560 GCACAGTGGGCATGGATGAC 61.661 60.000 13.88 0.00 34.16 3.06
3984 4097 2.734276 TGGATGACGACAAATGACGA 57.266 45.000 11.87 0.00 37.02 4.20
3985 4098 3.245518 TGGATGACGACAAATGACGAT 57.754 42.857 11.87 0.00 37.02 3.73
3999 4112 7.110155 ACAAATGACGATGTCCCTAAACTAAT 58.890 34.615 0.00 0.00 0.00 1.73
4000 4113 8.262227 ACAAATGACGATGTCCCTAAACTAATA 58.738 33.333 0.00 0.00 0.00 0.98
4001 4114 8.548721 CAAATGACGATGTCCCTAAACTAATAC 58.451 37.037 0.00 0.00 0.00 1.89
4002 4115 7.598759 ATGACGATGTCCCTAAACTAATACT 57.401 36.000 0.00 0.00 0.00 2.12
4003 4116 7.414222 TGACGATGTCCCTAAACTAATACTT 57.586 36.000 0.00 0.00 0.00 2.24
4004 4117 7.486647 TGACGATGTCCCTAAACTAATACTTC 58.513 38.462 0.00 0.00 0.00 3.01
4005 4118 6.814043 ACGATGTCCCTAAACTAATACTTCC 58.186 40.000 0.00 0.00 0.00 3.46
4006 4119 6.610425 ACGATGTCCCTAAACTAATACTTCCT 59.390 38.462 0.00 0.00 0.00 3.36
4007 4120 7.146648 CGATGTCCCTAAACTAATACTTCCTC 58.853 42.308 0.00 0.00 0.00 3.71
4008 4121 6.803366 TGTCCCTAAACTAATACTTCCTCC 57.197 41.667 0.00 0.00 0.00 4.30
4009 4122 5.361857 TGTCCCTAAACTAATACTTCCTCCG 59.638 44.000 0.00 0.00 0.00 4.63
4010 4123 5.362143 GTCCCTAAACTAATACTTCCTCCGT 59.638 44.000 0.00 0.00 0.00 4.69
4011 4124 5.960202 TCCCTAAACTAATACTTCCTCCGTT 59.040 40.000 0.00 0.00 0.00 4.44
4012 4125 6.097412 TCCCTAAACTAATACTTCCTCCGTTC 59.903 42.308 0.00 0.00 0.00 3.95
4013 4126 6.279123 CCTAAACTAATACTTCCTCCGTTCC 58.721 44.000 0.00 0.00 0.00 3.62
4014 4127 6.097981 CCTAAACTAATACTTCCTCCGTTCCT 59.902 42.308 0.00 0.00 0.00 3.36
4015 4128 7.286316 CCTAAACTAATACTTCCTCCGTTCCTA 59.714 40.741 0.00 0.00 0.00 2.94
4016 4129 7.486407 AAACTAATACTTCCTCCGTTCCTAA 57.514 36.000 0.00 0.00 0.00 2.69
4017 4130 7.486407 AACTAATACTTCCTCCGTTCCTAAA 57.514 36.000 0.00 0.00 0.00 1.85
4018 4131 7.672122 ACTAATACTTCCTCCGTTCCTAAAT 57.328 36.000 0.00 0.00 0.00 1.40
4019 4132 8.773033 ACTAATACTTCCTCCGTTCCTAAATA 57.227 34.615 0.00 0.00 0.00 1.40
4020 4133 8.637099 ACTAATACTTCCTCCGTTCCTAAATAC 58.363 37.037 0.00 0.00 0.00 1.89
4021 4134 4.382345 ACTTCCTCCGTTCCTAAATACG 57.618 45.455 0.00 0.00 37.50 3.06
4065 4178 7.921214 AGACATTCCAATAACTGACTACATACG 59.079 37.037 0.00 0.00 0.00 3.06
4066 4179 7.778083 ACATTCCAATAACTGACTACATACGA 58.222 34.615 0.00 0.00 0.00 3.43
4067 4180 8.255206 ACATTCCAATAACTGACTACATACGAA 58.745 33.333 0.00 0.00 0.00 3.85
4068 4181 9.093970 CATTCCAATAACTGACTACATACGAAA 57.906 33.333 0.00 0.00 0.00 3.46
4069 4182 9.832445 ATTCCAATAACTGACTACATACGAAAT 57.168 29.630 0.00 0.00 0.00 2.17
4070 4183 8.642908 TCCAATAACTGACTACATACGAAATG 57.357 34.615 0.00 0.00 0.00 2.32
4071 4184 8.471609 TCCAATAACTGACTACATACGAAATGA 58.528 33.333 9.04 0.00 0.00 2.57
4072 4185 9.093970 CCAATAACTGACTACATACGAAATGAA 57.906 33.333 9.04 0.00 0.00 2.57
4076 4189 8.771920 AACTGACTACATACGAAATGAAATGA 57.228 30.769 9.04 0.00 0.00 2.57
4077 4190 8.412608 ACTGACTACATACGAAATGAAATGAG 57.587 34.615 9.04 3.28 0.00 2.90
4078 4191 8.035394 ACTGACTACATACGAAATGAAATGAGT 58.965 33.333 9.04 4.83 0.00 3.41
4079 4192 8.185003 TGACTACATACGAAATGAAATGAGTG 57.815 34.615 9.04 0.00 0.00 3.51
4080 4193 8.032451 TGACTACATACGAAATGAAATGAGTGA 58.968 33.333 9.04 0.00 0.00 3.41
4081 4194 8.771920 ACTACATACGAAATGAAATGAGTGAA 57.228 30.769 9.04 0.00 0.00 3.18
4082 4195 9.383519 ACTACATACGAAATGAAATGAGTGAAT 57.616 29.630 9.04 0.00 0.00 2.57
4164 4277 8.415392 AAAAGACTTATATTTAGGAAGGGGGA 57.585 34.615 0.00 0.00 0.00 4.81
4165 4278 7.634526 AAGACTTATATTTAGGAAGGGGGAG 57.365 40.000 0.00 0.00 0.00 4.30
4188 4302 7.726033 AGTAGATCCACTGTAATCTTCTGTT 57.274 36.000 9.36 0.00 34.21 3.16
4189 4303 8.140112 AGTAGATCCACTGTAATCTTCTGTTT 57.860 34.615 9.36 0.00 34.21 2.83
4190 4304 8.037758 AGTAGATCCACTGTAATCTTCTGTTTG 58.962 37.037 9.36 0.00 34.21 2.93
4191 4305 6.773638 AGATCCACTGTAATCTTCTGTTTGT 58.226 36.000 0.00 0.00 0.00 2.83
4192 4306 7.907389 AGATCCACTGTAATCTTCTGTTTGTA 58.093 34.615 0.00 0.00 0.00 2.41
4193 4307 8.375506 AGATCCACTGTAATCTTCTGTTTGTAA 58.624 33.333 0.00 0.00 0.00 2.41
4194 4308 8.918202 ATCCACTGTAATCTTCTGTTTGTAAA 57.082 30.769 0.00 0.00 0.00 2.01
4195 4309 8.740123 TCCACTGTAATCTTCTGTTTGTAAAA 57.260 30.769 0.00 0.00 0.00 1.52
4196 4310 9.349713 TCCACTGTAATCTTCTGTTTGTAAAAT 57.650 29.630 0.00 0.00 0.00 1.82
4206 4320 9.261180 TCTTCTGTTTGTAAAATACTGTCTCTG 57.739 33.333 0.00 0.00 0.00 3.35
4207 4321 8.958119 TTCTGTTTGTAAAATACTGTCTCTGT 57.042 30.769 0.00 0.00 0.00 3.41
4295 4409 7.002276 AGAGGGAGTACTAAGAGAAATAGAGC 58.998 42.308 0.00 0.00 0.00 4.09
4327 4441 3.016736 CAGTAATCCCAACATGGACACC 58.983 50.000 0.00 0.00 40.96 4.16
4360 4480 2.436646 CGCATCCCAGTGACCCAC 60.437 66.667 0.00 0.00 34.10 4.61
4382 4502 0.539051 CCCAGCTCCAACAGAGTAGG 59.461 60.000 0.00 0.00 45.21 3.18
4412 4532 1.760875 CGAGCCCACTAGCCCCTTA 60.761 63.158 0.00 0.00 0.00 2.69
4507 4628 1.029408 TGTTGGTTTGCGTGTCAGCT 61.029 50.000 0.00 0.00 38.13 4.24
4517 4638 1.461127 GCGTGTCAGCTAACTTTCCAG 59.539 52.381 0.00 0.00 0.00 3.86
4518 4639 1.461127 CGTGTCAGCTAACTTTCCAGC 59.539 52.381 0.00 0.00 38.09 4.85
4519 4640 1.807142 GTGTCAGCTAACTTTCCAGCC 59.193 52.381 0.00 0.00 38.61 4.85
4520 4641 1.419762 TGTCAGCTAACTTTCCAGCCA 59.580 47.619 0.00 0.00 38.61 4.75
4521 4642 2.158682 TGTCAGCTAACTTTCCAGCCAA 60.159 45.455 0.00 0.00 38.61 4.52
4522 4643 2.884639 GTCAGCTAACTTTCCAGCCAAA 59.115 45.455 0.00 0.00 38.61 3.28
4523 4644 3.507622 GTCAGCTAACTTTCCAGCCAAAT 59.492 43.478 0.00 0.00 38.61 2.32
4524 4645 4.021981 GTCAGCTAACTTTCCAGCCAAATT 60.022 41.667 0.00 0.00 38.61 1.82
4525 4646 4.588528 TCAGCTAACTTTCCAGCCAAATTT 59.411 37.500 0.00 0.00 38.61 1.82
4526 4647 5.070313 TCAGCTAACTTTCCAGCCAAATTTT 59.930 36.000 0.00 0.00 38.61 1.82
4527 4648 5.759763 CAGCTAACTTTCCAGCCAAATTTTT 59.240 36.000 0.00 0.00 38.61 1.94
4547 4668 5.425577 TTTTTAGCACAGTACAAATCGCA 57.574 34.783 0.00 0.00 0.00 5.10
4548 4669 5.425577 TTTTAGCACAGTACAAATCGCAA 57.574 34.783 0.00 0.00 0.00 4.85
4549 4670 5.425577 TTTAGCACAGTACAAATCGCAAA 57.574 34.783 0.00 0.00 0.00 3.68
4550 4671 3.268013 AGCACAGTACAAATCGCAAAC 57.732 42.857 0.00 0.00 0.00 2.93
4551 4672 2.616376 AGCACAGTACAAATCGCAAACA 59.384 40.909 0.00 0.00 0.00 2.83
4552 4673 2.719046 GCACAGTACAAATCGCAAACAC 59.281 45.455 0.00 0.00 0.00 3.32
4553 4674 3.548014 GCACAGTACAAATCGCAAACACT 60.548 43.478 0.00 0.00 0.00 3.55
4554 4675 4.211389 CACAGTACAAATCGCAAACACTC 58.789 43.478 0.00 0.00 0.00 3.51
4555 4676 3.874543 ACAGTACAAATCGCAAACACTCA 59.125 39.130 0.00 0.00 0.00 3.41
4556 4677 4.515191 ACAGTACAAATCGCAAACACTCAT 59.485 37.500 0.00 0.00 0.00 2.90
4557 4678 4.847757 CAGTACAAATCGCAAACACTCATG 59.152 41.667 0.00 0.00 0.00 3.07
4558 4679 2.664916 ACAAATCGCAAACACTCATGC 58.335 42.857 0.00 0.00 39.17 4.06
4559 4680 2.034432 ACAAATCGCAAACACTCATGCA 59.966 40.909 0.00 0.00 42.68 3.96
4560 4681 3.247442 CAAATCGCAAACACTCATGCAT 58.753 40.909 0.00 0.00 42.68 3.96
4561 4682 4.082841 ACAAATCGCAAACACTCATGCATA 60.083 37.500 0.00 0.00 42.68 3.14
4562 4683 3.680642 ATCGCAAACACTCATGCATAC 57.319 42.857 0.00 0.00 42.68 2.39
4563 4684 2.421619 TCGCAAACACTCATGCATACA 58.578 42.857 0.00 0.00 42.68 2.29
4564 4685 2.159430 TCGCAAACACTCATGCATACAC 59.841 45.455 0.00 0.00 42.68 2.90
4565 4686 2.095819 CGCAAACACTCATGCATACACA 60.096 45.455 0.00 0.00 42.68 3.72
4566 4687 3.236816 GCAAACACTCATGCATACACAC 58.763 45.455 0.00 0.00 42.12 3.82
4567 4688 3.304592 GCAAACACTCATGCATACACACA 60.305 43.478 0.00 0.00 42.12 3.72
4568 4689 4.616604 GCAAACACTCATGCATACACACAT 60.617 41.667 0.00 0.00 42.12 3.21
4569 4690 4.690184 AACACTCATGCATACACACATG 57.310 40.909 0.00 0.00 44.05 3.21
4570 4691 3.678289 ACACTCATGCATACACACATGT 58.322 40.909 0.00 0.00 43.34 3.21
4571 4692 4.831107 ACACTCATGCATACACACATGTA 58.169 39.130 0.00 0.00 45.37 2.29
4572 4693 4.631377 ACACTCATGCATACACACATGTAC 59.369 41.667 0.00 0.00 44.11 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
371 403 3.449227 CTGTAGGAGACGGCGGCA 61.449 66.667 18.30 0.00 0.00 5.69
431 471 3.138304 CCGAACAGATTGACCAGAAACA 58.862 45.455 0.00 0.00 0.00 2.83
556 598 8.576442 CCATTACTTTGGACTTTCACTATTTGT 58.424 33.333 0.00 0.00 39.25 2.83
698 740 3.490933 GCTAGTGATTGGTAGCGACATGA 60.491 47.826 0.00 0.00 32.79 3.07
817 859 3.736482 GAGGCGCCGTGTACTCTCG 62.736 68.421 23.20 0.00 0.00 4.04
858 900 1.374252 GAGGAGCGCCGAGAAAACA 60.374 57.895 2.29 0.00 39.96 2.83
859 901 2.445438 CGAGGAGCGCCGAGAAAAC 61.445 63.158 2.29 0.00 39.96 2.43
917 960 0.744874 CTCGCCAAGATTCTCCGGTA 59.255 55.000 0.00 0.00 0.00 4.02
1129 1173 4.020617 TGAAGGGTGAGGCGCAGG 62.021 66.667 10.83 0.00 0.00 4.85
1143 1187 2.268920 GCCTCGGAGCCATGTGAA 59.731 61.111 0.00 0.00 0.00 3.18
1144 1188 4.147449 CGCCTCGGAGCCATGTGA 62.147 66.667 0.00 0.00 0.00 3.58
1149 1193 4.838152 GATTGCGCCTCGGAGCCA 62.838 66.667 4.18 0.00 40.18 4.75
1436 1485 4.927422 ACAACAACATGGTACGGAAAAAG 58.073 39.130 0.00 0.00 0.00 2.27
1437 1486 4.985538 ACAACAACATGGTACGGAAAAA 57.014 36.364 0.00 0.00 0.00 1.94
1438 1487 5.531659 ACATACAACAACATGGTACGGAAAA 59.468 36.000 0.00 0.00 0.00 2.29
1453 1502 8.067751 AGCAATAGAAGAGTAGACATACAACA 57.932 34.615 0.00 0.00 34.07 3.33
1466 1515 6.769822 ACCCAATTATGTGAGCAATAGAAGAG 59.230 38.462 0.00 0.00 0.00 2.85
1499 1548 1.824852 GAAAGGTTGGGCCATTACAGG 59.175 52.381 7.26 0.00 40.61 4.00
1683 1733 7.063780 CAGTTCAAACTTCAAATGAGCAAAAGT 59.936 33.333 0.00 0.00 37.08 2.66
2029 2079 7.593644 ACACGGAGCTGAATAATTAAACAAAAC 59.406 33.333 0.00 0.00 0.00 2.43
2042 2092 3.243569 GCATAGTAGACACGGAGCTGAAT 60.244 47.826 0.00 0.00 0.00 2.57
2046 2096 1.678627 CAGCATAGTAGACACGGAGCT 59.321 52.381 0.00 0.00 32.42 4.09
2048 2098 2.025155 ACCAGCATAGTAGACACGGAG 58.975 52.381 0.00 0.00 0.00 4.63
2049 2099 2.139323 ACCAGCATAGTAGACACGGA 57.861 50.000 0.00 0.00 0.00 4.69
2050 2100 2.961526 AACCAGCATAGTAGACACGG 57.038 50.000 0.00 0.00 0.00 4.94
2052 2102 6.395629 TCTGTTTAACCAGCATAGTAGACAC 58.604 40.000 0.00 0.00 32.32 3.67
2056 2106 5.294552 GCCTTCTGTTTAACCAGCATAGTAG 59.705 44.000 0.00 0.00 32.32 2.57
2061 2111 3.160679 AGCCTTCTGTTTAACCAGCAT 57.839 42.857 0.00 0.00 32.32 3.79
2128 2178 4.678742 ACTGCGTAGTCTTTTAAACTCGTC 59.321 41.667 0.00 0.00 28.79 4.20
2170 2220 1.963515 ACAAAGCCAAGATGGTCAACC 59.036 47.619 0.00 0.00 40.46 3.77
2182 2232 1.134340 ACCTTGTACGACACAAAGCCA 60.134 47.619 8.32 0.00 46.37 4.75
2185 2235 2.828877 TCCACCTTGTACGACACAAAG 58.171 47.619 8.32 5.58 46.37 2.77
2319 2374 9.567848 GAAGTTAGAGAACATAGACAGAAAGAG 57.432 37.037 0.00 0.00 38.10 2.85
2372 2427 2.158415 ACTCAAATGGGGGCATAGATGG 60.158 50.000 0.00 0.00 0.00 3.51
2405 2460 7.246674 ACATATTAACCAAGTTATCTGTGCG 57.753 36.000 0.00 0.00 0.00 5.34
2444 2499 5.046448 ACCATGTGAAATAATGTTGCCACAT 60.046 36.000 0.00 0.00 46.34 3.21
2490 2576 1.304381 TCCTGGTCAATTGCCTGCC 60.304 57.895 16.52 9.70 0.00 4.85
2584 2670 6.648879 AAAGCACTAGAAACAAAATAGGCA 57.351 33.333 0.00 0.00 0.00 4.75
2585 2671 7.590279 TGTAAAGCACTAGAAACAAAATAGGC 58.410 34.615 0.00 0.00 0.00 3.93
2620 2706 8.213518 ACAACAATTATCTATACAGCACAAGG 57.786 34.615 0.00 0.00 0.00 3.61
2661 2747 6.669631 TGGATAGCGGATTCCACTATATCTA 58.330 40.000 12.24 4.88 37.10 1.98
2689 2775 1.071471 CCGTGTGGGCTCTGAAACT 59.929 57.895 0.00 0.00 0.00 2.66
2753 2839 8.207545 AGAACTCAGAAATTCAGTGAACTTACT 58.792 33.333 7.96 3.06 0.00 2.24
2766 2852 8.415950 TCTAGAGAACTCAGAACTCAGAAATT 57.584 34.615 4.64 0.00 33.69 1.82
2788 2874 7.692460 AAAATCAATGACACAGCAATCTCTA 57.308 32.000 0.00 0.00 0.00 2.43
2892 2980 2.223595 CCACAATAACACGCAAACCACA 60.224 45.455 0.00 0.00 0.00 4.17
2932 3020 2.297701 TGACAAAGAACAGTCAAGGGC 58.702 47.619 0.00 0.00 41.42 5.19
3010 3101 0.033504 TTCACGAACTGCTGGAGACC 59.966 55.000 2.24 0.00 0.00 3.85
3071 3162 1.599542 GGTGATGGTGATTTAGCTCGC 59.400 52.381 0.00 0.00 0.00 5.03
3162 3254 2.490903 AGAAGCTGCGCATTCAAAGAAT 59.509 40.909 22.09 1.63 0.00 2.40
3247 3339 2.603008 CGCCAGGGGAATGGGAAT 59.397 61.111 0.00 0.00 40.97 3.01
3248 3340 4.440829 GCGCCAGGGGAATGGGAA 62.441 66.667 7.95 0.00 40.97 3.97
3254 3346 4.161295 CAGATCGCGCCAGGGGAA 62.161 66.667 7.95 0.00 41.37 3.97
3366 3458 2.586648 AGAAAAACTGGCTTCGGGAT 57.413 45.000 0.00 0.00 0.00 3.85
3370 3462 4.061596 AGAGAGAAGAAAAACTGGCTTCG 58.938 43.478 0.00 0.00 42.07 3.79
3384 3476 5.614923 TCACGTCAGAAACTAGAGAGAAG 57.385 43.478 0.00 0.00 0.00 2.85
3388 3480 5.125097 GGGTTATCACGTCAGAAACTAGAGA 59.875 44.000 0.00 0.00 0.00 3.10
3402 3494 1.207089 TCTCTGCAAGGGGTTATCACG 59.793 52.381 0.00 0.00 32.73 4.35
3456 3549 0.321671 TTCTCCCGCTCTTTCTGGTG 59.678 55.000 0.00 0.00 0.00 4.17
3482 3575 1.910276 GAAGCCCCTGCCTTTGCTT 60.910 57.895 0.00 0.00 46.07 3.91
3588 3681 2.241176 TGGTCAACAAGGAACAAGGTCT 59.759 45.455 0.00 0.00 29.94 3.85
3591 3686 3.891366 AGATTGGTCAACAAGGAACAAGG 59.109 43.478 0.01 0.00 46.71 3.61
3656 3758 8.432013 ACACAAGCTATATGTATGAAGGAATGA 58.568 33.333 0.00 0.00 0.00 2.57
3755 3857 0.099436 GGTTGCTTCATCCGTCATGC 59.901 55.000 0.00 0.00 31.70 4.06
3762 3864 4.439289 GCTCTGTATTTGGTTGCTTCATCC 60.439 45.833 0.00 0.00 0.00 3.51
3763 3865 4.156556 TGCTCTGTATTTGGTTGCTTCATC 59.843 41.667 0.00 0.00 0.00 2.92
3768 3870 1.815003 GCTGCTCTGTATTTGGTTGCT 59.185 47.619 0.00 0.00 0.00 3.91
3769 3871 1.815003 AGCTGCTCTGTATTTGGTTGC 59.185 47.619 0.00 0.00 0.00 4.17
3770 3872 3.503363 TGAAGCTGCTCTGTATTTGGTTG 59.497 43.478 1.00 0.00 0.00 3.77
3783 3885 2.187958 TGGTATGGTACTGAAGCTGCT 58.812 47.619 0.00 0.00 0.00 4.24
3786 3888 3.134804 GGTGATGGTATGGTACTGAAGCT 59.865 47.826 0.00 0.00 0.00 3.74
3787 3889 3.134804 AGGTGATGGTATGGTACTGAAGC 59.865 47.826 0.00 0.00 0.00 3.86
3800 3912 3.117512 GGGAAATGGATGTAGGTGATGGT 60.118 47.826 0.00 0.00 0.00 3.55
3808 3920 4.094887 CACAGAAACGGGAAATGGATGTAG 59.905 45.833 0.00 0.00 0.00 2.74
3829 3941 4.689612 TTGGTATCAAGATCTAGGCCAC 57.310 45.455 5.01 0.00 0.00 5.01
3891 4003 1.421485 CGACAAGATCGCCAACAGC 59.579 57.895 0.00 0.00 45.52 4.40
3964 4077 3.245518 TCGTCATTTGTCGTCATCCAT 57.754 42.857 0.00 0.00 0.00 3.41
3972 4085 2.010145 AGGGACATCGTCATTTGTCG 57.990 50.000 0.00 0.00 42.51 4.35
3984 4097 6.041751 CGGAGGAAGTATTAGTTTAGGGACAT 59.958 42.308 0.00 0.00 0.00 3.06
3985 4098 5.361857 CGGAGGAAGTATTAGTTTAGGGACA 59.638 44.000 0.00 0.00 0.00 4.02
3999 4112 5.505173 CGTATTTAGGAACGGAGGAAGTA 57.495 43.478 0.00 0.00 35.51 2.24
4000 4113 4.382345 CGTATTTAGGAACGGAGGAAGT 57.618 45.455 0.00 0.00 35.51 3.01
4008 4121 5.860716 GCCTTATACTCCGTATTTAGGAACG 59.139 44.000 14.14 0.00 37.32 3.95
4009 4122 6.990798 AGCCTTATACTCCGTATTTAGGAAC 58.009 40.000 14.14 3.66 37.32 3.62
4010 4123 7.607615 AAGCCTTATACTCCGTATTTAGGAA 57.392 36.000 14.14 0.00 37.32 3.36
4011 4124 7.607615 AAAGCCTTATACTCCGTATTTAGGA 57.392 36.000 14.14 0.00 34.19 2.94
4012 4125 8.672823 AAAAAGCCTTATACTCCGTATTTAGG 57.327 34.615 9.01 9.01 34.81 2.69
4039 4152 7.921214 CGTATGTAGTCAGTTATTGGAATGTCT 59.079 37.037 0.00 0.00 0.00 3.41
4040 4153 7.919091 TCGTATGTAGTCAGTTATTGGAATGTC 59.081 37.037 0.00 0.00 0.00 3.06
4041 4154 7.778083 TCGTATGTAGTCAGTTATTGGAATGT 58.222 34.615 0.00 0.00 0.00 2.71
4042 4155 8.642908 TTCGTATGTAGTCAGTTATTGGAATG 57.357 34.615 0.00 0.00 0.00 2.67
4043 4156 9.832445 ATTTCGTATGTAGTCAGTTATTGGAAT 57.168 29.630 0.00 0.00 0.00 3.01
4044 4157 9.093970 CATTTCGTATGTAGTCAGTTATTGGAA 57.906 33.333 0.00 0.00 0.00 3.53
4045 4158 8.471609 TCATTTCGTATGTAGTCAGTTATTGGA 58.528 33.333 1.38 0.00 0.00 3.53
4046 4159 8.642908 TCATTTCGTATGTAGTCAGTTATTGG 57.357 34.615 1.38 0.00 0.00 3.16
4050 4163 9.863845 TCATTTCATTTCGTATGTAGTCAGTTA 57.136 29.630 1.38 0.00 0.00 2.24
4051 4164 8.771920 TCATTTCATTTCGTATGTAGTCAGTT 57.228 30.769 1.38 0.00 0.00 3.16
4052 4165 8.035394 ACTCATTTCATTTCGTATGTAGTCAGT 58.965 33.333 1.38 0.00 0.00 3.41
4053 4166 8.323854 CACTCATTTCATTTCGTATGTAGTCAG 58.676 37.037 1.38 0.00 0.00 3.51
4054 4167 8.032451 TCACTCATTTCATTTCGTATGTAGTCA 58.968 33.333 1.38 0.00 0.00 3.41
4055 4168 8.407457 TCACTCATTTCATTTCGTATGTAGTC 57.593 34.615 1.38 0.00 0.00 2.59
4056 4169 8.771920 TTCACTCATTTCATTTCGTATGTAGT 57.228 30.769 1.38 0.00 0.00 2.73
4063 4176 9.383519 AGTGTATATTCACTCATTTCATTTCGT 57.616 29.630 9.03 0.00 44.07 3.85
4138 4251 8.852894 TCCCCCTTCCTAAATATAAGTCTTTTT 58.147 33.333 0.00 0.00 0.00 1.94
4139 4252 8.415392 TCCCCCTTCCTAAATATAAGTCTTTT 57.585 34.615 0.00 0.00 0.00 2.27
4140 4253 7.632164 ACTCCCCCTTCCTAAATATAAGTCTTT 59.368 37.037 0.00 0.00 0.00 2.52
4141 4254 7.147195 ACTCCCCCTTCCTAAATATAAGTCTT 58.853 38.462 0.00 0.00 0.00 3.01
4142 4255 6.704792 ACTCCCCCTTCCTAAATATAAGTCT 58.295 40.000 0.00 0.00 0.00 3.24
4143 4256 7.954620 TCTACTCCCCCTTCCTAAATATAAGTC 59.045 40.741 0.00 0.00 0.00 3.01
4144 4257 7.844566 TCTACTCCCCCTTCCTAAATATAAGT 58.155 38.462 0.00 0.00 0.00 2.24
4145 4258 8.919018 ATCTACTCCCCCTTCCTAAATATAAG 57.081 38.462 0.00 0.00 0.00 1.73
4146 4259 7.905106 GGATCTACTCCCCCTTCCTAAATATAA 59.095 40.741 0.00 0.00 38.19 0.98
4147 4260 7.021295 TGGATCTACTCCCCCTTCCTAAATATA 59.979 40.741 0.00 0.00 44.23 0.86
4148 4261 6.183361 TGGATCTACTCCCCCTTCCTAAATAT 60.183 42.308 0.00 0.00 44.23 1.28
4149 4262 5.138996 TGGATCTACTCCCCCTTCCTAAATA 59.861 44.000 0.00 0.00 44.23 1.40
4150 4263 4.077387 TGGATCTACTCCCCCTTCCTAAAT 60.077 45.833 0.00 0.00 44.23 1.40
4151 4264 3.276578 TGGATCTACTCCCCCTTCCTAAA 59.723 47.826 0.00 0.00 44.23 1.85
4152 4265 2.869689 TGGATCTACTCCCCCTTCCTAA 59.130 50.000 0.00 0.00 44.23 2.69
4153 4266 2.179424 GTGGATCTACTCCCCCTTCCTA 59.821 54.545 1.27 0.00 44.23 2.94
4154 4267 1.062044 GTGGATCTACTCCCCCTTCCT 60.062 57.143 1.27 0.00 44.23 3.36
4155 4268 1.062044 AGTGGATCTACTCCCCCTTCC 60.062 57.143 5.80 0.00 44.23 3.46
4156 4269 2.043227 CAGTGGATCTACTCCCCCTTC 58.957 57.143 9.05 0.00 44.23 3.46
4157 4270 1.366435 ACAGTGGATCTACTCCCCCTT 59.634 52.381 9.05 0.00 44.23 3.95
4158 4271 1.019650 ACAGTGGATCTACTCCCCCT 58.980 55.000 9.05 0.00 44.23 4.79
4159 4272 2.769602 TACAGTGGATCTACTCCCCC 57.230 55.000 9.05 0.00 44.23 5.40
4160 4273 4.484912 AGATTACAGTGGATCTACTCCCC 58.515 47.826 9.05 0.00 44.23 4.81
4161 4274 5.836358 AGAAGATTACAGTGGATCTACTCCC 59.164 44.000 9.05 0.00 44.23 4.30
4162 4275 6.322712 ACAGAAGATTACAGTGGATCTACTCC 59.677 42.308 9.05 0.00 45.19 3.85
4163 4276 7.341445 ACAGAAGATTACAGTGGATCTACTC 57.659 40.000 9.05 0.00 32.52 2.59
4164 4277 7.726033 AACAGAAGATTACAGTGGATCTACT 57.274 36.000 5.80 5.80 32.52 2.57
4165 4278 7.819900 ACAAACAGAAGATTACAGTGGATCTAC 59.180 37.037 10.56 0.00 32.52 2.59
4269 4383 8.158789 GCTCTATTTCTCTTAGTACTCCCTCTA 58.841 40.741 0.00 0.00 0.00 2.43
4270 4384 7.002276 GCTCTATTTCTCTTAGTACTCCCTCT 58.998 42.308 0.00 0.00 0.00 3.69
4271 4385 7.002276 AGCTCTATTTCTCTTAGTACTCCCTC 58.998 42.308 0.00 0.00 0.00 4.30
4272 4386 6.775629 CAGCTCTATTTCTCTTAGTACTCCCT 59.224 42.308 0.00 0.00 0.00 4.20
4273 4387 6.548251 ACAGCTCTATTTCTCTTAGTACTCCC 59.452 42.308 0.00 0.00 0.00 4.30
4274 4388 7.576861 ACAGCTCTATTTCTCTTAGTACTCC 57.423 40.000 0.00 0.00 0.00 3.85
4276 4390 8.573035 GCATACAGCTCTATTTCTCTTAGTACT 58.427 37.037 0.00 0.00 41.15 2.73
4277 4391 8.353684 TGCATACAGCTCTATTTCTCTTAGTAC 58.646 37.037 0.00 0.00 45.94 2.73
4301 4415 4.275936 GTCCATGTTGGGATTACTGTATGC 59.724 45.833 0.00 0.00 39.62 3.14
4313 4427 0.327924 TAGCAGGTGTCCATGTTGGG 59.672 55.000 0.00 0.00 38.32 4.12
4340 4454 3.127533 GGTCACTGGGATGCGCAC 61.128 66.667 14.90 6.86 0.00 5.34
4360 4480 1.376942 CTCTGTTGGAGCTGGGCAG 60.377 63.158 0.00 0.00 35.08 4.85
4382 4502 1.079057 GGGCTCGGAGAAGTGTTCC 60.079 63.158 9.69 0.00 34.09 3.62
4412 4532 5.241728 CACGGAAGGGAAAGAAGAAGAAAAT 59.758 40.000 0.00 0.00 35.60 1.82
4447 4568 0.719465 CGCATCGTGTGGAACCTAAC 59.281 55.000 0.00 0.00 34.36 2.34
4525 4646 5.425577 TGCGATTTGTACTGTGCTAAAAA 57.574 34.783 0.00 0.00 0.00 1.94
4526 4647 5.425577 TTGCGATTTGTACTGTGCTAAAA 57.574 34.783 0.00 0.00 0.00 1.52
4527 4648 5.209240 GTTTGCGATTTGTACTGTGCTAAA 58.791 37.500 0.00 0.00 0.00 1.85
4528 4649 4.273724 TGTTTGCGATTTGTACTGTGCTAA 59.726 37.500 0.00 0.00 0.00 3.09
4529 4650 3.810386 TGTTTGCGATTTGTACTGTGCTA 59.190 39.130 0.00 0.00 0.00 3.49
4530 4651 2.616376 TGTTTGCGATTTGTACTGTGCT 59.384 40.909 0.00 0.00 0.00 4.40
4531 4652 2.719046 GTGTTTGCGATTTGTACTGTGC 59.281 45.455 0.00 0.00 0.00 4.57
4532 4653 4.209452 AGTGTTTGCGATTTGTACTGTG 57.791 40.909 0.00 0.00 0.00 3.66
4533 4654 3.874543 TGAGTGTTTGCGATTTGTACTGT 59.125 39.130 0.00 0.00 0.00 3.55
4534 4655 4.466567 TGAGTGTTTGCGATTTGTACTG 57.533 40.909 0.00 0.00 0.00 2.74
4535 4656 4.613622 GCATGAGTGTTTGCGATTTGTACT 60.614 41.667 0.00 0.00 0.00 2.73
4536 4657 3.603770 GCATGAGTGTTTGCGATTTGTAC 59.396 43.478 0.00 0.00 0.00 2.90
4537 4658 3.251972 TGCATGAGTGTTTGCGATTTGTA 59.748 39.130 0.00 0.00 41.80 2.41
4538 4659 2.034432 TGCATGAGTGTTTGCGATTTGT 59.966 40.909 0.00 0.00 41.80 2.83
4539 4660 2.663808 TGCATGAGTGTTTGCGATTTG 58.336 42.857 0.00 0.00 41.80 2.32
4540 4661 3.581024 ATGCATGAGTGTTTGCGATTT 57.419 38.095 0.00 0.00 41.80 2.17
4541 4662 3.439825 TGTATGCATGAGTGTTTGCGATT 59.560 39.130 10.16 0.00 41.80 3.34
4542 4663 3.009026 TGTATGCATGAGTGTTTGCGAT 58.991 40.909 10.16 0.00 41.80 4.58
4543 4664 2.159430 GTGTATGCATGAGTGTTTGCGA 59.841 45.455 10.16 0.00 41.80 5.10
4544 4665 2.095819 TGTGTATGCATGAGTGTTTGCG 60.096 45.455 10.16 0.00 41.80 4.85
4545 4666 3.236816 GTGTGTATGCATGAGTGTTTGC 58.763 45.455 10.16 0.00 39.33 3.68
4546 4667 4.486574 TGTGTGTATGCATGAGTGTTTG 57.513 40.909 10.16 0.00 0.00 2.93
4547 4668 4.520111 ACATGTGTGTATGCATGAGTGTTT 59.480 37.500 10.16 0.00 43.60 2.83
4548 4669 4.074259 ACATGTGTGTATGCATGAGTGTT 58.926 39.130 10.16 0.00 43.60 3.32
4549 4670 3.678289 ACATGTGTGTATGCATGAGTGT 58.322 40.909 10.16 1.98 43.60 3.55
4550 4671 5.147767 GTACATGTGTGTATGCATGAGTG 57.852 43.478 10.16 1.36 43.60 3.51


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

AutoCloner maintained by Alex Coulton.