Multiple sequence alignment - TraesCS2A01G258900

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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 TraesCS2A01G258900 chr2A 100.000 8602 0 0 1 8602 406776805 406768204 0.000000e+00 15886.0
1 TraesCS2A01G258900 chr2A 93.590 78 5 0 6785 6862 75652872 75652795 5.460000e-22 117.0
2 TraesCS2A01G258900 chr2D 96.458 4376 106 28 2 4365 323639780 323644118 0.000000e+00 7177.0
3 TraesCS2A01G258900 chr2D 96.202 4107 101 18 4522 8602 323644115 323648192 0.000000e+00 6669.0
4 TraesCS2A01G258900 chr2B 94.643 2931 108 27 2 2918 391759198 391762093 0.000000e+00 4497.0
5 TraesCS2A01G258900 chr2B 93.527 1514 65 13 5255 6755 391766299 391767792 0.000000e+00 2222.0
6 TraesCS2A01G258900 chr2B 96.724 1282 38 2 6854 8131 391767804 391769085 0.000000e+00 2132.0
7 TraesCS2A01G258900 chr2B 97.659 1196 28 0 4064 5259 391763486 391764681 0.000000e+00 2054.0
8 TraesCS2A01G258900 chr2B 94.931 1085 35 5 2934 4006 391762415 391763491 0.000000e+00 1681.0
9 TraesCS2A01G258900 chr2B 88.453 459 22 10 8174 8602 391769172 391769629 7.650000e-145 525.0
10 TraesCS2A01G258900 chr5D 94.595 74 4 0 6783 6856 389245425 389245498 1.960000e-21 115.0
11 TraesCS2A01G258900 chr5D 87.671 73 7 2 5286 5357 220689572 220689643 5.530000e-12 84.2
12 TraesCS2A01G258900 chr3D 94.595 74 4 0 6783 6856 105151051 105151124 1.960000e-21 115.0
13 TraesCS2A01G258900 chr3D 94.444 72 4 0 6783 6854 105151118 105151047 2.540000e-20 111.0
14 TraesCS2A01G258900 chr3D 93.243 74 5 0 6783 6856 105182936 105183009 9.130000e-20 110.0
15 TraesCS2A01G258900 chr3D 91.026 78 6 1 6783 6860 105461204 105461128 4.250000e-18 104.0
16 TraesCS2A01G258900 chr1D 93.243 74 4 1 6783 6856 479730173 479730245 3.280000e-19 108.0
17 TraesCS2A01G258900 chr1D 90.123 81 5 3 5286 5364 437730878 437730957 1.530000e-17 102.0
18 TraesCS2A01G258900 chr6A 91.250 80 2 1 6783 6857 610518799 610518878 4.250000e-18 104.0
19 TraesCS2A01G258900 chr6A 82.222 90 15 1 2731 2819 227099490 227099579 9.260000e-10 76.8
20 TraesCS2A01G258900 chr1B 88.764 89 2 7 5283 5366 593145004 593145089 1.530000e-17 102.0
21 TraesCS2A01G258900 chr5B 79.845 129 22 4 5268 5393 243422141 243422268 3.310000e-14 91.6
22 TraesCS2A01G258900 chrUn 81.111 90 16 1 2731 2819 105614382 105614293 4.310000e-08 71.3
23 TraesCS2A01G258900 chr5A 81.111 90 16 1 2731 2819 554217412 554217323 4.310000e-08 71.3


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 TraesCS2A01G258900 chr2A 406768204 406776805 8601 True 15886.000000 15886 100.000000 1 8602 1 chr2A.!!$R2 8601
1 TraesCS2A01G258900 chr2D 323639780 323648192 8412 False 6923.000000 7177 96.330000 2 8602 2 chr2D.!!$F1 8600
2 TraesCS2A01G258900 chr2B 391759198 391769629 10431 False 2185.166667 4497 94.322833 2 8602 6 chr2B.!!$F1 8600

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
422 431 0.472471 GGGATTATGTCGGCCCTTCA 59.528 55.000 0.00 0.0 37.59 3.02 F
1949 1964 0.603065 GGTTTGCACCTGTTGGATCC 59.397 55.000 4.20 4.2 40.44 3.36 F
2595 2612 0.313987 GCAGGTAAGTGGTGTTTGGC 59.686 55.000 0.00 0.0 0.00 4.52 F
3702 4037 2.187958 CCATCCCTAGTGGTTCACTCA 58.812 52.381 3.65 0.0 41.21 3.41 F
4984 5481 0.182299 GCAAGGCTGCTTATCCCTCT 59.818 55.000 0.00 0.0 45.74 3.69 F
5388 7519 1.344065 TAGGTTTGACCGAGCAAGGA 58.656 50.000 4.39 0.0 44.90 3.36 F
6424 8560 2.697751 AGCTTATGTGCCTAGTCTCCTG 59.302 50.000 0.00 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2043 2058 0.244450 AGCATGGATGTTGCCAAACG 59.756 50.000 0.00 0.00 42.16 3.60 R
3139 3464 4.044946 TGATGAATTTCCACCATCACCA 57.955 40.909 0.00 0.00 40.96 4.17 R
4186 4523 0.241749 CTTTCGGAAGCTGCAATGCA 59.758 50.000 7.99 7.99 36.92 3.96 R
5282 7402 1.075374 CACTCCAATCCCTTCCAACCA 59.925 52.381 0.00 0.00 0.00 3.67 R
5914 8046 0.171007 CCAAAACATGCAGGCTACCG 59.829 55.000 0.00 0.00 0.00 4.02 R
6839 8984 1.880941 AGGTACTCCTTCCATCCCAC 58.119 55.000 0.00 0.00 42.12 4.61 R
8343 10538 0.603707 CTCCTTCCGTGAGCAAAGCA 60.604 55.000 0.00 0.00 0.00 3.91 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
119 121 4.758251 CGGTCGCTGATGGGTGCA 62.758 66.667 0.00 0.00 0.00 4.57
121 123 2.690778 GGTCGCTGATGGGTGCAAC 61.691 63.158 0.00 0.00 0.00 4.17
160 162 1.876156 CTTCGCTTCTCTTTTGGTGCT 59.124 47.619 0.00 0.00 0.00 4.40
162 164 1.202639 TCGCTTCTCTTTTGGTGCTCA 60.203 47.619 0.00 0.00 0.00 4.26
163 165 1.603802 CGCTTCTCTTTTGGTGCTCAA 59.396 47.619 0.00 0.00 0.00 3.02
267 274 7.011950 TCGAATGCCATGGTTACTAGTTTAATG 59.988 37.037 14.67 0.82 0.00 1.90
379 387 5.016051 TGAATCTGCATCAAGTAGTCCTC 57.984 43.478 0.00 0.00 0.00 3.71
399 407 4.024556 CCTCCTCAGTTTATTTATGCAGCG 60.025 45.833 0.00 0.00 0.00 5.18
400 409 4.765273 TCCTCAGTTTATTTATGCAGCGA 58.235 39.130 0.00 0.00 0.00 4.93
411 420 5.375417 TTTATGCAGCGAATGGGATTATG 57.625 39.130 0.00 0.00 0.00 1.90
422 431 0.472471 GGGATTATGTCGGCCCTTCA 59.528 55.000 0.00 0.00 37.59 3.02
567 576 3.788227 TTGGTTCTTGACTACAGGCAT 57.212 42.857 0.00 0.00 0.00 4.40
596 605 1.673168 CTCTGGCAAACTATCTGGGC 58.327 55.000 0.00 0.00 0.00 5.36
699 708 9.930158 AGTTGTTGGTATAATTATAACACCCAT 57.070 29.630 20.46 6.29 35.73 4.00
728 737 2.368875 ACTTCCGTCTTGGTCACAGAAT 59.631 45.455 0.00 0.00 39.52 2.40
853 864 6.664816 TCCTAAATTCATGCATCAACTCCTTT 59.335 34.615 0.00 0.00 0.00 3.11
973 988 8.772705 CATATCATTTCTCTGAGAAAAGTAGCC 58.227 37.037 30.16 0.00 46.08 3.93
1116 1131 2.287849 ACACTCGAGGCATATCATGACG 60.288 50.000 18.41 0.00 45.18 4.35
1422 1437 9.793259 AGTTGTTAGGAGAACTGAATTATCAAA 57.207 29.630 0.00 0.00 37.91 2.69
1732 1747 6.721704 ATTGCTCCTGGGAAGATTAATTTC 57.278 37.500 0.00 0.00 0.00 2.17
1949 1964 0.603065 GGTTTGCACCTGTTGGATCC 59.397 55.000 4.20 4.20 40.44 3.36
2043 2058 7.702772 TCGTCTACTCTTTGCTCTCATATTTTC 59.297 37.037 0.00 0.00 0.00 2.29
2249 2264 4.447054 CGCAGTGCATGTTTTATTCCAAAA 59.553 37.500 16.83 0.00 0.00 2.44
2381 2398 9.300681 TCAGAAAACATATGAAACCAGATTTCT 57.699 29.630 10.38 8.58 46.05 2.52
2516 2533 4.271049 ACATCGGCTGATTTATTCAAGACG 59.729 41.667 4.93 0.00 36.16 4.18
2595 2612 0.313987 GCAGGTAAGTGGTGTTTGGC 59.686 55.000 0.00 0.00 0.00 4.52
2885 2902 9.547753 CACCTTCTTAGCATGTGTATTACTATT 57.452 33.333 0.00 0.00 0.00 1.73
2923 2940 8.031864 GGTAAGATACTAGGATGTCACATCATG 58.968 40.741 19.61 10.57 0.00 3.07
3097 3422 6.573434 TGACGATGTGCTCTATGACTATTTT 58.427 36.000 0.00 0.00 0.00 1.82
3300 3625 5.858581 GCACCATGTTAATCAGTTTTGACTC 59.141 40.000 0.00 0.00 35.83 3.36
3580 3915 9.005777 TCTAGTAAATTATGAGTTTTTGCCGTT 57.994 29.630 0.00 0.00 0.00 4.44
3702 4037 2.187958 CCATCCCTAGTGGTTCACTCA 58.812 52.381 3.65 0.00 41.21 3.41
3704 4039 3.200825 CCATCCCTAGTGGTTCACTCAAT 59.799 47.826 3.65 0.00 41.21 2.57
4007 4342 5.485209 ACGTCTCATTTTACCTCCTTTCT 57.515 39.130 0.00 0.00 0.00 2.52
4008 4343 6.600882 ACGTCTCATTTTACCTCCTTTCTA 57.399 37.500 0.00 0.00 0.00 2.10
4009 4344 7.184067 ACGTCTCATTTTACCTCCTTTCTAT 57.816 36.000 0.00 0.00 0.00 1.98
4010 4345 7.042335 ACGTCTCATTTTACCTCCTTTCTATG 58.958 38.462 0.00 0.00 0.00 2.23
4012 4347 7.565680 GTCTCATTTTACCTCCTTTCTATGGA 58.434 38.462 0.00 0.00 0.00 3.41
4013 4348 8.214364 GTCTCATTTTACCTCCTTTCTATGGAT 58.786 37.037 0.00 0.00 32.56 3.41
4014 4349 8.781951 TCTCATTTTACCTCCTTTCTATGGATT 58.218 33.333 0.00 0.00 32.56 3.01
4186 4523 3.904339 TGCCTCAGAGGAAGAGTTACTTT 59.096 43.478 21.89 0.00 37.67 2.66
4302 4639 5.250200 ACTTTGTCGGAATAAGGTGCATTA 58.750 37.500 0.00 0.00 0.00 1.90
4361 4698 7.508977 TGGATTTTTCCATTACTTCTGTTTCCT 59.491 33.333 0.00 0.00 34.33 3.36
4362 4699 7.814587 GGATTTTTCCATTACTTCTGTTTCCTG 59.185 37.037 0.00 0.00 0.00 3.86
4363 4700 7.654022 TTTTTCCATTACTTCTGTTTCCTGT 57.346 32.000 0.00 0.00 0.00 4.00
4364 4701 7.654022 TTTTCCATTACTTCTGTTTCCTGTT 57.346 32.000 0.00 0.00 0.00 3.16
4365 4702 7.654022 TTTCCATTACTTCTGTTTCCTGTTT 57.346 32.000 0.00 0.00 0.00 2.83
4366 4703 7.654022 TTCCATTACTTCTGTTTCCTGTTTT 57.346 32.000 0.00 0.00 0.00 2.43
4367 4704 7.654022 TCCATTACTTCTGTTTCCTGTTTTT 57.346 32.000 0.00 0.00 0.00 1.94
4368 4705 7.712797 TCCATTACTTCTGTTTCCTGTTTTTC 58.287 34.615 0.00 0.00 0.00 2.29
4369 4706 7.340743 TCCATTACTTCTGTTTCCTGTTTTTCA 59.659 33.333 0.00 0.00 0.00 2.69
4370 4707 7.978975 CCATTACTTCTGTTTCCTGTTTTTCAA 59.021 33.333 0.00 0.00 0.00 2.69
4371 4708 8.807581 CATTACTTCTGTTTCCTGTTTTTCAAC 58.192 33.333 0.00 0.00 0.00 3.18
4372 4709 6.339587 ACTTCTGTTTCCTGTTTTTCAACA 57.660 33.333 0.00 0.00 40.82 3.33
4373 4710 6.156519 ACTTCTGTTTCCTGTTTTTCAACAC 58.843 36.000 0.00 0.00 38.03 3.32
4374 4711 5.713792 TCTGTTTCCTGTTTTTCAACACA 57.286 34.783 0.00 0.00 38.03 3.72
4375 4712 5.465935 TCTGTTTCCTGTTTTTCAACACAC 58.534 37.500 0.00 0.00 38.03 3.82
4376 4713 5.010112 TCTGTTTCCTGTTTTTCAACACACA 59.990 36.000 0.00 0.00 38.03 3.72
4377 4714 5.226396 TGTTTCCTGTTTTTCAACACACAG 58.774 37.500 0.00 0.00 38.03 3.66
4378 4715 5.221342 TGTTTCCTGTTTTTCAACACACAGT 60.221 36.000 0.00 0.00 38.03 3.55
4379 4716 5.461032 TTCCTGTTTTTCAACACACAGTT 57.539 34.783 0.00 0.00 38.03 3.16
4396 4733 8.833493 ACACACAGTTGTTTAATTACTTCTACC 58.167 33.333 0.00 0.00 31.66 3.18
4397 4734 8.832521 CACACAGTTGTTTAATTACTTCTACCA 58.167 33.333 0.00 0.00 31.66 3.25
4398 4735 9.569122 ACACAGTTGTTTAATTACTTCTACCAT 57.431 29.630 0.00 0.00 28.43 3.55
4399 4736 9.825972 CACAGTTGTTTAATTACTTCTACCATG 57.174 33.333 0.00 0.00 0.00 3.66
4400 4737 9.569122 ACAGTTGTTTAATTACTTCTACCATGT 57.431 29.630 0.00 0.00 0.00 3.21
4403 4740 9.983804 GTTGTTTAATTACTTCTACCATGTAGC 57.016 33.333 0.00 0.00 0.00 3.58
4404 4741 9.953565 TTGTTTAATTACTTCTACCATGTAGCT 57.046 29.630 0.00 0.00 0.00 3.32
4405 4742 9.378551 TGTTTAATTACTTCTACCATGTAGCTG 57.621 33.333 0.00 0.00 0.00 4.24
4406 4743 9.595823 GTTTAATTACTTCTACCATGTAGCTGA 57.404 33.333 0.00 0.00 0.00 4.26
4407 4744 9.595823 TTTAATTACTTCTACCATGTAGCTGAC 57.404 33.333 0.00 0.00 0.00 3.51
4408 4745 7.425224 AATTACTTCTACCATGTAGCTGACT 57.575 36.000 0.00 0.00 0.00 3.41
4409 4746 8.534954 AATTACTTCTACCATGTAGCTGACTA 57.465 34.615 0.00 0.00 0.00 2.59
4410 4747 7.949690 TTACTTCTACCATGTAGCTGACTAA 57.050 36.000 0.00 0.00 0.00 2.24
4411 4748 8.534954 TTACTTCTACCATGTAGCTGACTAAT 57.465 34.615 0.00 0.00 0.00 1.73
4412 4749 9.636789 TTACTTCTACCATGTAGCTGACTAATA 57.363 33.333 0.00 0.00 0.00 0.98
4413 4750 7.942990 ACTTCTACCATGTAGCTGACTAATAC 58.057 38.462 0.00 0.00 0.00 1.89
4414 4751 7.780745 ACTTCTACCATGTAGCTGACTAATACT 59.219 37.037 0.00 0.00 0.00 2.12
4415 4752 9.286170 CTTCTACCATGTAGCTGACTAATACTA 57.714 37.037 0.00 0.00 0.00 1.82
4416 4753 9.636789 TTCTACCATGTAGCTGACTAATACTAA 57.363 33.333 0.00 0.00 0.00 2.24
4417 4754 9.286170 TCTACCATGTAGCTGACTAATACTAAG 57.714 37.037 0.00 0.00 0.00 2.18
4418 4755 9.286170 CTACCATGTAGCTGACTAATACTAAGA 57.714 37.037 0.00 0.00 0.00 2.10
4419 4756 8.713708 ACCATGTAGCTGACTAATACTAAGAT 57.286 34.615 0.00 0.00 0.00 2.40
4420 4757 8.580720 ACCATGTAGCTGACTAATACTAAGATG 58.419 37.037 0.00 0.00 0.00 2.90
4421 4758 8.580720 CCATGTAGCTGACTAATACTAAGATGT 58.419 37.037 0.00 0.00 0.00 3.06
4422 4759 9.619316 CATGTAGCTGACTAATACTAAGATGTC 57.381 37.037 0.00 0.00 0.00 3.06
4423 4760 8.982091 TGTAGCTGACTAATACTAAGATGTCT 57.018 34.615 0.00 0.00 0.00 3.41
4427 4764 9.062524 AGCTGACTAATACTAAGATGTCTAGTG 57.937 37.037 0.00 0.00 0.00 2.74
4428 4765 9.058174 GCTGACTAATACTAAGATGTCTAGTGA 57.942 37.037 0.00 0.00 0.00 3.41
4433 4770 9.953697 CTAATACTAAGATGTCTAGTGAACACC 57.046 37.037 1.11 0.00 0.00 4.16
4434 4771 5.312120 ACTAAGATGTCTAGTGAACACCG 57.688 43.478 1.11 0.00 0.00 4.94
4435 4772 5.008331 ACTAAGATGTCTAGTGAACACCGA 58.992 41.667 1.11 0.00 0.00 4.69
4436 4773 4.866508 AAGATGTCTAGTGAACACCGAA 57.133 40.909 1.11 0.00 0.00 4.30
4437 4774 4.866508 AGATGTCTAGTGAACACCGAAA 57.133 40.909 1.11 0.00 0.00 3.46
4438 4775 4.810790 AGATGTCTAGTGAACACCGAAAG 58.189 43.478 1.11 0.00 0.00 2.62
4439 4776 2.750948 TGTCTAGTGAACACCGAAAGC 58.249 47.619 1.11 0.00 0.00 3.51
4440 4777 2.101750 TGTCTAGTGAACACCGAAAGCA 59.898 45.455 1.11 0.00 0.00 3.91
4441 4778 3.128349 GTCTAGTGAACACCGAAAGCAA 58.872 45.455 1.11 0.00 0.00 3.91
4442 4779 3.746492 GTCTAGTGAACACCGAAAGCAAT 59.254 43.478 1.11 0.00 0.00 3.56
4443 4780 4.927425 GTCTAGTGAACACCGAAAGCAATA 59.073 41.667 1.11 0.00 0.00 1.90
4444 4781 5.581085 GTCTAGTGAACACCGAAAGCAATAT 59.419 40.000 1.11 0.00 0.00 1.28
4445 4782 6.755141 GTCTAGTGAACACCGAAAGCAATATA 59.245 38.462 1.11 0.00 0.00 0.86
4446 4783 7.438459 GTCTAGTGAACACCGAAAGCAATATAT 59.562 37.037 1.11 0.00 0.00 0.86
4447 4784 6.363577 AGTGAACACCGAAAGCAATATATG 57.636 37.500 1.11 0.00 0.00 1.78
4471 4808 8.846943 TGCTGACAAATATCTTCTTTTGTAGA 57.153 30.769 1.40 0.00 43.95 2.59
4472 4809 9.453572 TGCTGACAAATATCTTCTTTTGTAGAT 57.546 29.630 1.40 0.00 43.95 1.98
4484 4821 9.280456 TCTTCTTTTGTAGATATAACCCCTTCT 57.720 33.333 0.00 0.00 31.54 2.85
4485 4822 9.549078 CTTCTTTTGTAGATATAACCCCTTCTC 57.451 37.037 0.00 0.00 31.54 2.87
4486 4823 8.030913 TCTTTTGTAGATATAACCCCTTCTCC 57.969 38.462 0.00 0.00 0.00 3.71
4487 4824 7.626084 TCTTTTGTAGATATAACCCCTTCTCCA 59.374 37.037 0.00 0.00 0.00 3.86
4488 4825 6.996180 TTGTAGATATAACCCCTTCTCCAG 57.004 41.667 0.00 0.00 0.00 3.86
4489 4826 6.039415 TGTAGATATAACCCCTTCTCCAGT 57.961 41.667 0.00 0.00 0.00 4.00
4490 4827 7.170554 TGTAGATATAACCCCTTCTCCAGTA 57.829 40.000 0.00 0.00 0.00 2.74
4491 4828 7.776745 TGTAGATATAACCCCTTCTCCAGTAT 58.223 38.462 0.00 0.00 0.00 2.12
4492 4829 8.908095 TGTAGATATAACCCCTTCTCCAGTATA 58.092 37.037 0.00 0.00 0.00 1.47
4493 4830 9.411189 GTAGATATAACCCCTTCTCCAGTATAG 57.589 40.741 0.00 0.00 0.00 1.31
4494 4831 7.423341 AGATATAACCCCTTCTCCAGTATAGG 58.577 42.308 0.00 0.00 0.00 2.57
4495 4832 3.797671 AACCCCTTCTCCAGTATAGGT 57.202 47.619 0.00 0.00 0.00 3.08
4496 4833 3.047695 ACCCCTTCTCCAGTATAGGTG 57.952 52.381 0.00 0.00 0.00 4.00
4497 4834 2.330216 CCCCTTCTCCAGTATAGGTGG 58.670 57.143 0.00 0.00 36.28 4.61
4498 4835 2.090719 CCCCTTCTCCAGTATAGGTGGA 60.091 54.545 4.10 4.10 42.06 4.02
4499 4836 3.632645 CCCCTTCTCCAGTATAGGTGGAA 60.633 52.174 5.46 0.00 43.68 3.53
4500 4837 4.037927 CCCTTCTCCAGTATAGGTGGAAA 58.962 47.826 5.46 3.35 43.68 3.13
4501 4838 4.473559 CCCTTCTCCAGTATAGGTGGAAAA 59.526 45.833 5.46 0.00 43.68 2.29
4502 4839 5.396884 CCCTTCTCCAGTATAGGTGGAAAAG 60.397 48.000 9.08 9.08 43.68 2.27
4503 4840 5.189934 CCTTCTCCAGTATAGGTGGAAAAGT 59.810 44.000 12.93 0.00 43.68 2.66
4504 4841 6.296489 CCTTCTCCAGTATAGGTGGAAAAGTT 60.296 42.308 12.93 0.00 43.68 2.66
4505 4842 6.697641 TCTCCAGTATAGGTGGAAAAGTTT 57.302 37.500 5.46 0.00 43.68 2.66
4506 4843 6.708285 TCTCCAGTATAGGTGGAAAAGTTTC 58.292 40.000 5.46 0.00 43.68 2.78
4843 5340 5.838529 CATCATTTTATGAGGCATTCTGCA 58.161 37.500 1.09 0.00 42.68 4.41
4984 5481 0.182299 GCAAGGCTGCTTATCCCTCT 59.818 55.000 0.00 0.00 45.74 3.69
5229 5726 7.120923 TCCCACAGGTCAGTTATACTTATTC 57.879 40.000 0.00 0.00 0.00 1.75
5282 7402 8.670521 ATCTTCATTTTCCTAAGGGATTGTTT 57.329 30.769 0.00 0.00 41.87 2.83
5308 7439 2.024941 GGAAGGGATTGGAGTGGATTGT 60.025 50.000 0.00 0.00 0.00 2.71
5382 7513 3.447586 TCTCCAGAATAGGTTTGACCGAG 59.552 47.826 0.00 0.00 44.90 4.63
5388 7519 1.344065 TAGGTTTGACCGAGCAAGGA 58.656 50.000 4.39 0.00 44.90 3.36
5448 7579 6.603237 TGAAAATTCGACATATGCCACTAG 57.397 37.500 1.58 0.00 0.00 2.57
5520 7651 5.046520 ACTTGGAAGGTCATACTGAGTTACC 60.047 44.000 0.00 0.00 0.00 2.85
5581 7712 4.319177 AGCACCTATATTCCTCGCAAATC 58.681 43.478 0.00 0.00 0.00 2.17
5608 7740 7.232118 CCTGACAAAGGGAGTTTTTATTGAT 57.768 36.000 0.00 0.00 43.15 2.57
5706 7838 6.211384 TGATCTAATCCTGACTCTTGTTCACA 59.789 38.462 0.00 0.00 0.00 3.58
5894 8026 5.830457 TCATTTGTACCATCCAAACTCACAA 59.170 36.000 0.00 0.00 34.85 3.33
6258 8394 4.832248 TGAAGTGGCTAGACGAAATTGAT 58.168 39.130 0.00 0.00 0.00 2.57
6424 8560 2.697751 AGCTTATGTGCCTAGTCTCCTG 59.302 50.000 0.00 0.00 0.00 3.86
6564 8700 4.559300 CGGTCAATGGAAAGTGAGCATTTT 60.559 41.667 6.24 0.00 41.31 1.82
6801 8941 7.946219 TGAAGTACTCCGTCCCATAATATAAGA 59.054 37.037 0.00 0.00 0.00 2.10
6803 8943 7.468496 AGTACTCCGTCCCATAATATAAGAGT 58.532 38.462 0.00 0.00 36.18 3.24
6839 8984 8.656849 ACTAGTGTCAAAAACGCTCTTATATTG 58.343 33.333 0.00 0.00 45.69 1.90
6844 8989 5.941058 TCAAAAACGCTCTTATATTGTGGGA 59.059 36.000 0.00 0.00 0.00 4.37
6845 8990 6.601613 TCAAAAACGCTCTTATATTGTGGGAT 59.398 34.615 0.00 0.00 0.00 3.85
6846 8991 6.377327 AAAACGCTCTTATATTGTGGGATG 57.623 37.500 0.00 0.00 0.00 3.51
6849 8994 4.102524 ACGCTCTTATATTGTGGGATGGAA 59.897 41.667 0.00 0.00 0.00 3.53
7256 9401 4.642437 TGCAGTTGACAAGGTAACATCAAA 59.358 37.500 0.00 0.00 37.08 2.69
7274 9419 7.604549 ACATCAAAATATTCAACATGCTCACA 58.395 30.769 0.00 0.00 0.00 3.58
7321 9466 6.191657 TGCATTGAATGGTACTCCTATCAT 57.808 37.500 7.35 0.00 32.35 2.45
7322 9467 6.604171 TGCATTGAATGGTACTCCTATCATT 58.396 36.000 7.35 0.00 36.54 2.57
7743 9892 0.103755 TGCCTTCAGCTCTCTATGCG 59.896 55.000 0.00 0.00 44.23 4.73
7841 9990 7.651027 ATGGATGGAGGAAACATAGAAAAAG 57.349 36.000 0.00 0.00 0.00 2.27
7874 10023 8.583296 TCATCAGATAGATTGTATTCTGAGTGG 58.417 37.037 7.45 1.27 37.59 4.00
7878 10027 8.583296 CAGATAGATTGTATTCTGAGTGGATGA 58.417 37.037 0.00 0.00 0.00 2.92
8010 10159 6.409524 TTTTCTGTAGAAGGAACCGAGTTA 57.590 37.500 0.00 0.00 35.21 2.24
8054 10203 4.265073 GTTACTCTGGTGCCATTGATTCT 58.735 43.478 0.00 0.00 0.00 2.40
8131 10282 6.715280 TCTCATTGCCTGGAGAATATAATCC 58.285 40.000 0.00 0.10 37.23 3.01
8141 10292 7.320384 TGGAGAATATAATCCTCATTCAGCA 57.680 36.000 7.46 0.00 36.50 4.41
8156 10319 6.927416 TCATTCAGCAAAGCATCTTAACATT 58.073 32.000 0.00 0.00 0.00 2.71
8208 10403 3.120616 CACAAAGCAGCAACGATTCATTG 59.879 43.478 0.00 0.00 0.00 2.82
8292 10487 5.840267 CGAAAATTCCAAAGTTTGCAAATCG 59.160 36.000 16.21 11.59 0.00 3.34
8307 10502 3.378427 GCAAATCGGTAGCTTCTCCAATT 59.622 43.478 0.00 0.00 0.00 2.32
8363 10558 0.603975 GCTTTGCTCACGGAAGGAGT 60.604 55.000 0.00 0.00 34.83 3.85
8403 10599 3.794028 GCTATATAAAGGCTCGATCTGCG 59.206 47.826 0.00 0.00 42.69 5.18
8447 10652 2.307768 TCGAGGCCAAGGTAGATACAG 58.692 52.381 5.01 0.00 0.00 2.74
8448 10653 2.032620 CGAGGCCAAGGTAGATACAGT 58.967 52.381 5.01 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.168788 ACGCAATGCAAGATGGAACG 59.831 50.000 5.91 0.00 0.00 3.95
160 162 3.948719 GTGCCGGGGACAGGTTGA 61.949 66.667 14.36 0.00 0.00 3.18
312 319 4.574674 TGTATGACAGCATCTCCCTTTT 57.425 40.909 0.00 0.00 35.94 2.27
331 339 9.462606 AGTCGGATTAAAGGATTCTTAAATTGT 57.537 29.630 0.00 0.00 32.01 2.71
379 387 5.484173 TTCGCTGCATAAATAAACTGAGG 57.516 39.130 0.00 0.00 0.00 3.86
399 407 1.073923 AGGGCCGACATAATCCCATTC 59.926 52.381 0.00 0.00 41.22 2.67
400 409 1.149101 AGGGCCGACATAATCCCATT 58.851 50.000 0.00 0.00 41.22 3.16
411 420 2.664436 CGAAACGTGAAGGGCCGAC 61.664 63.158 0.00 0.00 0.00 4.79
637 646 5.379187 TCCCAGTAGCACATATACTTCGTA 58.621 41.667 0.00 0.00 31.05 3.43
639 648 4.848562 TCCCAGTAGCACATATACTTCG 57.151 45.455 0.00 0.00 31.05 3.79
640 649 5.934625 CCAATCCCAGTAGCACATATACTTC 59.065 44.000 0.00 0.00 31.05 3.01
642 651 5.155161 TCCAATCCCAGTAGCACATATACT 58.845 41.667 0.00 0.00 33.74 2.12
645 654 4.352001 ACATCCAATCCCAGTAGCACATAT 59.648 41.667 0.00 0.00 0.00 1.78
646 655 3.716353 ACATCCAATCCCAGTAGCACATA 59.284 43.478 0.00 0.00 0.00 2.29
647 656 2.511218 ACATCCAATCCCAGTAGCACAT 59.489 45.455 0.00 0.00 0.00 3.21
648 657 1.915489 ACATCCAATCCCAGTAGCACA 59.085 47.619 0.00 0.00 0.00 4.57
649 658 2.717639 ACATCCAATCCCAGTAGCAC 57.282 50.000 0.00 0.00 0.00 4.40
650 659 4.853468 TTTACATCCAATCCCAGTAGCA 57.147 40.909 0.00 0.00 0.00 3.49
651 660 6.534634 ACTATTTACATCCAATCCCAGTAGC 58.465 40.000 0.00 0.00 0.00 3.58
652 661 7.993183 ACAACTATTTACATCCAATCCCAGTAG 59.007 37.037 0.00 0.00 0.00 2.57
687 696 8.145767 CGGAAGTATCAAGTATGGGTGTTATAA 58.854 37.037 0.00 0.00 0.00 0.98
708 717 2.526304 TTCTGTGACCAAGACGGAAG 57.474 50.000 0.00 0.00 34.46 3.46
748 759 8.554528 CAGTACCACAGTGATGATGATAAATTC 58.445 37.037 0.62 0.00 0.00 2.17
761 772 4.404394 TGAAGAGAAACAGTACCACAGTGA 59.596 41.667 0.62 0.00 0.00 3.41
853 864 5.718146 TGTTGTCAGAATTCAGCAAAACAA 58.282 33.333 8.44 3.73 0.00 2.83
949 963 7.851228 TGGCTACTTTTCTCAGAGAAATGATA 58.149 34.615 31.36 21.76 43.06 2.15
973 988 9.559958 CCAAGAAATGTTGCTTTAAGTACTATG 57.440 33.333 0.00 0.00 0.00 2.23
1116 1131 0.746659 GGCACCCAATTATCACTGCC 59.253 55.000 0.00 0.00 37.62 4.85
1369 1384 8.978874 AATGTGGTACATGCATAAAGATTCTA 57.021 30.769 0.00 0.00 44.52 2.10
1382 1397 7.822334 TCTCCTAACAACTTAATGTGGTACATG 59.178 37.037 0.00 0.00 44.52 3.21
1432 1447 2.942376 CCAAGCGACATACCTGCAATTA 59.058 45.455 0.00 0.00 0.00 1.40
1732 1747 3.131933 ACTGATGACCTGGAAGAGATTCG 59.868 47.826 0.00 0.00 34.07 3.34
1949 1964 3.119316 ACAGAAGAGGATAGTCACTTGCG 60.119 47.826 0.00 0.00 0.00 4.85
2043 2058 0.244450 AGCATGGATGTTGCCAAACG 59.756 50.000 0.00 0.00 42.16 3.60
2516 2533 3.557595 CAGAGACCATAAGATCAAACGCC 59.442 47.826 0.00 0.00 0.00 5.68
2901 2918 7.009550 AGACATGATGTGACATCCTAGTATCT 58.990 38.462 21.68 12.76 0.00 1.98
3097 3422 7.777910 TCAAACCAAAGGTCTTCTCTTTCATTA 59.222 33.333 0.00 0.00 33.12 1.90
3139 3464 4.044946 TGATGAATTTCCACCATCACCA 57.955 40.909 0.00 0.00 40.96 4.17
3432 3766 9.561069 CTAGAACATTGGTGGCTATATAAGTTT 57.439 33.333 0.00 0.00 0.00 2.66
3641 3976 9.480053 GCTAATGTGCAAATGATAACCAAATAT 57.520 29.630 0.00 0.00 0.00 1.28
3647 3982 5.894807 ACAGCTAATGTGCAAATGATAACC 58.105 37.500 0.00 0.00 41.91 2.85
3748 4083 7.501225 CGAAGGGTTTGGATACCTACATATTTT 59.499 37.037 0.00 0.00 38.30 1.82
4007 4342 8.088365 CCTTACATACTTGACATCGAATCCATA 58.912 37.037 0.00 0.00 0.00 2.74
4008 4343 6.931281 CCTTACATACTTGACATCGAATCCAT 59.069 38.462 0.00 0.00 0.00 3.41
4009 4344 6.097696 TCCTTACATACTTGACATCGAATCCA 59.902 38.462 0.00 0.00 0.00 3.41
4010 4345 6.513180 TCCTTACATACTTGACATCGAATCC 58.487 40.000 0.00 0.00 0.00 3.01
4012 4347 7.782049 TCTTCCTTACATACTTGACATCGAAT 58.218 34.615 0.00 0.00 0.00 3.34
4013 4348 7.165460 TCTTCCTTACATACTTGACATCGAA 57.835 36.000 0.00 0.00 0.00 3.71
4014 4349 6.769134 TCTTCCTTACATACTTGACATCGA 57.231 37.500 0.00 0.00 0.00 3.59
4060 4397 4.697828 GGCAAGGAAACAAACAAAGGAAAA 59.302 37.500 0.00 0.00 0.00 2.29
4186 4523 0.241749 CTTTCGGAAGCTGCAATGCA 59.758 50.000 7.99 7.99 36.92 3.96
4302 4639 2.488836 AGGATAAACAGGGGACGGAAT 58.511 47.619 0.00 0.00 0.00 3.01
4370 4707 8.833493 GGTAGAAGTAATTAAACAACTGTGTGT 58.167 33.333 0.00 0.00 38.27 3.72
4371 4708 8.832521 TGGTAGAAGTAATTAAACAACTGTGTG 58.167 33.333 0.00 0.00 38.27 3.82
4372 4709 8.967664 TGGTAGAAGTAATTAAACAACTGTGT 57.032 30.769 0.00 0.00 40.75 3.72
4373 4710 9.825972 CATGGTAGAAGTAATTAAACAACTGTG 57.174 33.333 0.00 0.00 0.00 3.66
4374 4711 9.569122 ACATGGTAGAAGTAATTAAACAACTGT 57.431 29.630 0.00 0.00 0.00 3.55
4377 4714 9.983804 GCTACATGGTAGAAGTAATTAAACAAC 57.016 33.333 7.55 0.00 0.00 3.32
4378 4715 9.953565 AGCTACATGGTAGAAGTAATTAAACAA 57.046 29.630 7.55 0.00 0.00 2.83
4379 4716 9.378551 CAGCTACATGGTAGAAGTAATTAAACA 57.621 33.333 7.55 0.00 0.00 2.83
4380 4717 9.595823 TCAGCTACATGGTAGAAGTAATTAAAC 57.404 33.333 7.55 0.00 0.00 2.01
4381 4718 9.595823 GTCAGCTACATGGTAGAAGTAATTAAA 57.404 33.333 7.55 0.00 0.00 1.52
4382 4719 8.978472 AGTCAGCTACATGGTAGAAGTAATTAA 58.022 33.333 7.55 0.00 0.00 1.40
4383 4720 8.534954 AGTCAGCTACATGGTAGAAGTAATTA 57.465 34.615 7.55 0.00 0.00 1.40
4384 4721 7.425224 AGTCAGCTACATGGTAGAAGTAATT 57.575 36.000 7.55 0.00 0.00 1.40
4385 4722 8.534954 TTAGTCAGCTACATGGTAGAAGTAAT 57.465 34.615 7.55 0.00 0.00 1.89
4386 4723 7.949690 TTAGTCAGCTACATGGTAGAAGTAA 57.050 36.000 7.55 3.42 0.00 2.24
4387 4724 9.064706 GTATTAGTCAGCTACATGGTAGAAGTA 57.935 37.037 7.55 0.00 0.00 2.24
4388 4725 7.780745 AGTATTAGTCAGCTACATGGTAGAAGT 59.219 37.037 7.55 0.00 0.00 3.01
4389 4726 8.172352 AGTATTAGTCAGCTACATGGTAGAAG 57.828 38.462 7.55 0.00 0.00 2.85
4390 4727 9.636789 TTAGTATTAGTCAGCTACATGGTAGAA 57.363 33.333 7.55 0.00 0.00 2.10
4391 4728 9.286170 CTTAGTATTAGTCAGCTACATGGTAGA 57.714 37.037 7.55 0.00 0.00 2.59
4392 4729 9.286170 TCTTAGTATTAGTCAGCTACATGGTAG 57.714 37.037 0.00 0.00 0.00 3.18
4393 4730 9.809395 ATCTTAGTATTAGTCAGCTACATGGTA 57.191 33.333 0.00 0.00 0.00 3.25
4394 4731 8.580720 CATCTTAGTATTAGTCAGCTACATGGT 58.419 37.037 0.00 0.00 0.00 3.55
4395 4732 8.580720 ACATCTTAGTATTAGTCAGCTACATGG 58.419 37.037 0.00 0.00 0.00 3.66
4396 4733 9.619316 GACATCTTAGTATTAGTCAGCTACATG 57.381 37.037 0.00 0.00 0.00 3.21
4397 4734 9.581289 AGACATCTTAGTATTAGTCAGCTACAT 57.419 33.333 0.00 0.00 0.00 2.29
4398 4735 8.982091 AGACATCTTAGTATTAGTCAGCTACA 57.018 34.615 0.00 0.00 0.00 2.74
4401 4738 9.062524 CACTAGACATCTTAGTATTAGTCAGCT 57.937 37.037 0.00 0.00 0.00 4.24
4402 4739 9.058174 TCACTAGACATCTTAGTATTAGTCAGC 57.942 37.037 0.00 0.00 0.00 4.26
4407 4744 9.953697 GGTGTTCACTAGACATCTTAGTATTAG 57.046 37.037 0.00 0.00 0.00 1.73
4408 4745 8.618677 CGGTGTTCACTAGACATCTTAGTATTA 58.381 37.037 0.00 0.00 0.00 0.98
4409 4746 7.338703 TCGGTGTTCACTAGACATCTTAGTATT 59.661 37.037 0.00 0.00 0.00 1.89
4410 4747 6.827251 TCGGTGTTCACTAGACATCTTAGTAT 59.173 38.462 0.00 0.00 0.00 2.12
4411 4748 6.175471 TCGGTGTTCACTAGACATCTTAGTA 58.825 40.000 0.00 0.00 0.00 1.82
4412 4749 5.008331 TCGGTGTTCACTAGACATCTTAGT 58.992 41.667 0.00 0.00 0.00 2.24
4413 4750 5.562506 TCGGTGTTCACTAGACATCTTAG 57.437 43.478 0.00 0.00 0.00 2.18
4414 4751 5.970317 TTCGGTGTTCACTAGACATCTTA 57.030 39.130 0.00 0.00 0.00 2.10
4415 4752 4.866508 TTCGGTGTTCACTAGACATCTT 57.133 40.909 0.00 0.00 0.00 2.40
4416 4753 4.810790 CTTTCGGTGTTCACTAGACATCT 58.189 43.478 0.00 0.00 0.00 2.90
4417 4754 3.368236 GCTTTCGGTGTTCACTAGACATC 59.632 47.826 0.00 0.00 0.00 3.06
4418 4755 3.244078 TGCTTTCGGTGTTCACTAGACAT 60.244 43.478 0.00 0.00 0.00 3.06
4419 4756 2.101750 TGCTTTCGGTGTTCACTAGACA 59.898 45.455 0.00 0.00 0.00 3.41
4420 4757 2.750948 TGCTTTCGGTGTTCACTAGAC 58.249 47.619 0.00 0.00 0.00 2.59
4421 4758 3.462483 TTGCTTTCGGTGTTCACTAGA 57.538 42.857 0.00 1.18 0.00 2.43
4422 4759 7.567571 CATATATTGCTTTCGGTGTTCACTAG 58.432 38.462 2.98 0.00 0.00 2.57
4423 4760 7.477144 CATATATTGCTTTCGGTGTTCACTA 57.523 36.000 2.98 0.00 0.00 2.74
4424 4761 6.363577 CATATATTGCTTTCGGTGTTCACT 57.636 37.500 2.98 0.00 0.00 3.41
4445 4782 9.453572 TCTACAAAAGAAGATATTTGTCAGCAT 57.546 29.630 7.11 0.00 44.16 3.79
4446 4783 8.846943 TCTACAAAAGAAGATATTTGTCAGCA 57.153 30.769 7.11 0.00 44.16 4.41
4458 4795 9.280456 AGAAGGGGTTATATCTACAAAAGAAGA 57.720 33.333 0.00 0.00 37.89 2.87
4459 4796 9.549078 GAGAAGGGGTTATATCTACAAAAGAAG 57.451 37.037 0.00 0.00 37.89 2.85
4460 4797 8.491958 GGAGAAGGGGTTATATCTACAAAAGAA 58.508 37.037 0.00 0.00 37.89 2.52
4461 4798 7.626084 TGGAGAAGGGGTTATATCTACAAAAGA 59.374 37.037 0.00 0.00 39.02 2.52
4462 4799 7.802117 TGGAGAAGGGGTTATATCTACAAAAG 58.198 38.462 0.00 0.00 29.94 2.27
4463 4800 7.404980 ACTGGAGAAGGGGTTATATCTACAAAA 59.595 37.037 0.00 0.00 32.56 2.44
4464 4801 6.906901 ACTGGAGAAGGGGTTATATCTACAAA 59.093 38.462 0.00 0.00 32.56 2.83
4465 4802 6.449956 ACTGGAGAAGGGGTTATATCTACAA 58.550 40.000 0.00 0.00 32.56 2.41
4466 4803 6.039415 ACTGGAGAAGGGGTTATATCTACA 57.961 41.667 0.00 0.00 32.05 2.74
4467 4804 9.411189 CTATACTGGAGAAGGGGTTATATCTAC 57.589 40.741 0.00 0.00 0.00 2.59
4468 4805 8.566979 CCTATACTGGAGAAGGGGTTATATCTA 58.433 40.741 0.00 0.00 0.00 1.98
4469 4806 7.020781 ACCTATACTGGAGAAGGGGTTATATCT 59.979 40.741 0.00 0.00 33.16 1.98
4470 4807 7.124448 CACCTATACTGGAGAAGGGGTTATATC 59.876 44.444 0.00 0.00 33.16 1.63
4471 4808 6.960542 CACCTATACTGGAGAAGGGGTTATAT 59.039 42.308 0.00 0.00 33.16 0.86
4472 4809 6.320518 CACCTATACTGGAGAAGGGGTTATA 58.679 44.000 0.00 0.00 33.16 0.98
4473 4810 5.155905 CACCTATACTGGAGAAGGGGTTAT 58.844 45.833 0.00 0.00 33.16 1.89
4474 4811 4.553678 CACCTATACTGGAGAAGGGGTTA 58.446 47.826 0.00 0.00 33.16 2.85
4475 4812 3.385115 CACCTATACTGGAGAAGGGGTT 58.615 50.000 0.00 0.00 33.16 4.11
4476 4813 2.360423 CCACCTATACTGGAGAAGGGGT 60.360 54.545 0.00 0.00 29.98 4.95
4477 4814 2.090719 TCCACCTATACTGGAGAAGGGG 60.091 54.545 0.00 0.00 32.52 4.79
4478 4815 3.330126 TCCACCTATACTGGAGAAGGG 57.670 52.381 0.00 0.00 32.52 3.95
4479 4816 5.189934 ACTTTTCCACCTATACTGGAGAAGG 59.810 44.000 19.65 10.44 46.94 3.46
4481 4818 6.697641 AACTTTTCCACCTATACTGGAGAA 57.302 37.500 0.00 0.00 39.06 2.87
4482 4819 6.697641 AAACTTTTCCACCTATACTGGAGA 57.302 37.500 0.00 0.00 39.06 3.71
4483 4820 6.986904 GAAACTTTTCCACCTATACTGGAG 57.013 41.667 0.00 0.00 39.06 3.86
4497 4834 8.882736 ACAAAGAAATCAACATGGAAACTTTTC 58.117 29.630 0.00 0.00 36.46 2.29
4498 4835 8.791327 ACAAAGAAATCAACATGGAAACTTTT 57.209 26.923 0.00 0.00 0.00 2.27
4499 4836 8.791327 AACAAAGAAATCAACATGGAAACTTT 57.209 26.923 0.00 0.00 0.00 2.66
4501 4838 9.696917 GATAACAAAGAAATCAACATGGAAACT 57.303 29.630 0.00 0.00 0.00 2.66
4502 4839 9.474920 TGATAACAAAGAAATCAACATGGAAAC 57.525 29.630 0.00 0.00 0.00 2.78
4520 4857 9.495572 GGAACCAACCAAATAAAATGATAACAA 57.504 29.630 0.00 0.00 0.00 2.83
4843 5340 6.976934 AAAGTTGGTTTATCTGATGGTGTT 57.023 33.333 0.00 0.00 0.00 3.32
4984 5481 6.390504 ACATACCCCACTAGATTCCTCATAA 58.609 40.000 0.00 0.00 0.00 1.90
5229 5726 6.349363 GCAAGGAAGAAAACTACACCTTATGG 60.349 42.308 0.00 0.00 36.22 2.74
5282 7402 1.075374 CACTCCAATCCCTTCCAACCA 59.925 52.381 0.00 0.00 0.00 3.67
5382 7513 7.068470 AGGTATAGTACTTCACTTAGTCCTTGC 59.932 40.741 0.00 0.00 38.80 4.01
5388 7519 8.915036 CATCCAAGGTATAGTACTTCACTTAGT 58.085 37.037 0.00 0.00 38.80 2.24
5433 7564 4.508124 GGAACTTTCTAGTGGCATATGTCG 59.492 45.833 2.28 0.00 34.01 4.35
5520 7651 9.091784 ACTGAATAGCATATGTAATATTGCTCG 57.908 33.333 4.29 0.00 40.38 5.03
5608 7740 1.595794 GTCTTGGAGCGACGTTTTGAA 59.404 47.619 0.00 0.00 0.00 2.69
5665 7797 8.672815 GGATTAGATCAAAGATTATAAGCCTGC 58.327 37.037 0.00 0.00 0.00 4.85
5706 7838 8.526147 CAAGATTACACTGGAAAAGATGGAAAT 58.474 33.333 0.00 0.00 0.00 2.17
5914 8046 0.171007 CCAAAACATGCAGGCTACCG 59.829 55.000 0.00 0.00 0.00 4.02
5918 8050 2.586293 GGGCCAAAACATGCAGGCT 61.586 57.895 4.39 0.00 46.23 4.58
5992 8124 5.510671 GTTGCCAGTAAATGATTCCGTATG 58.489 41.667 0.00 0.00 0.00 2.39
6097 8231 8.593945 TTCAAAAGGGATATAACAGCAAGAAT 57.406 30.769 0.00 0.00 0.00 2.40
6258 8394 9.219603 CAGATTATGTTTCTCCAACTGAACTTA 57.780 33.333 0.00 0.00 36.21 2.24
6378 8514 4.348168 AGCTAGAACTTTTCTGGAGTGGAA 59.652 41.667 3.66 0.00 40.34 3.53
6446 8582 7.944729 TGAAGAAGCAGGAAATAAGCTAAAT 57.055 32.000 0.00 0.00 37.70 1.40
6693 8829 7.906327 TGCAATGCATCTATACTGGAATAGTA 58.094 34.615 2.72 0.00 38.85 1.82
6747 8883 9.743057 ACACAAAAGTCGAAAAATGAATTGATA 57.257 25.926 0.00 0.00 0.00 2.15
6830 8975 5.911178 ACTCCTTCCATCCCACAATATAAGA 59.089 40.000 0.00 0.00 0.00 2.10
6839 8984 1.880941 AGGTACTCCTTCCATCCCAC 58.119 55.000 0.00 0.00 42.12 4.61
6844 8989 8.742125 TGATAATTCATAGGTACTCCTTCCAT 57.258 34.615 0.00 0.00 42.12 3.41
6845 8990 8.742125 ATGATAATTCATAGGTACTCCTTCCA 57.258 34.615 0.00 0.00 40.87 3.53
6846 8991 9.041354 AGATGATAATTCATAGGTACTCCTTCC 57.959 37.037 0.00 0.00 42.73 3.46
6849 8994 9.030452 GTCAGATGATAATTCATAGGTACTCCT 57.970 37.037 0.00 0.00 42.73 3.69
6867 9012 6.957920 TTTTGATTTTGTGAGGTCAGATGA 57.042 33.333 0.00 0.00 0.00 2.92
6871 9016 7.212274 AGGAAATTTTGATTTTGTGAGGTCAG 58.788 34.615 0.00 0.00 0.00 3.51
7256 9401 7.160547 TGTGAATGTGAGCATGTTGAATATT 57.839 32.000 0.00 0.00 35.15 1.28
7274 9419 7.258441 CAATGCTGATCTGAAAAGATGTGAAT 58.742 34.615 3.42 0.00 0.00 2.57
7321 9466 9.762381 AAACCTGTATCCACCTTATATTGAAAA 57.238 29.630 0.00 0.00 0.00 2.29
7322 9467 9.762381 AAAACCTGTATCCACCTTATATTGAAA 57.238 29.630 0.00 0.00 0.00 2.69
7661 9810 5.887598 TGGATATGGGATGAAAAACTGACAG 59.112 40.000 0.00 0.00 0.00 3.51
7743 9892 2.751259 TGCAATGCTGGAGATGAAGTTC 59.249 45.455 6.82 0.00 0.00 3.01
7938 10087 7.674120 TCAGTGAAATCTACATCCAGGATATG 58.326 38.462 0.00 0.00 0.00 1.78
8010 10159 6.436843 ACGAAGCGAATTCCAGAAATAATT 57.563 33.333 0.00 0.00 34.10 1.40
8131 10282 5.946298 TGTTAAGATGCTTTGCTGAATGAG 58.054 37.500 0.00 0.00 0.00 2.90
8156 10319 5.079689 TGTGTCCATCGTTTTATAGCTGA 57.920 39.130 0.00 0.00 0.00 4.26
8208 10403 2.912624 GCTGCAGTGACACCCAAGC 61.913 63.158 16.64 5.16 0.00 4.01
8268 10463 5.840267 CGATTTGCAAACTTTGGAATTTTCG 59.160 36.000 15.41 11.17 40.72 3.46
8292 10487 4.837972 ACTTCAGAATTGGAGAAGCTACC 58.162 43.478 9.74 0.00 41.80 3.18
8307 10502 7.289549 ACATGATTATCATCTCCAGACTTCAGA 59.710 37.037 4.51 0.00 34.28 3.27
8343 10538 0.603707 CTCCTTCCGTGAGCAAAGCA 60.604 55.000 0.00 0.00 0.00 3.91
8363 10558 3.969287 AGCTGAGTGTTGAGATGCTTA 57.031 42.857 0.00 0.00 0.00 3.09
8403 10599 0.938008 GGAGCTTACGCCATTAGCAC 59.062 55.000 0.00 0.00 44.04 4.40
8447 10652 2.992543 GCGCCATGATTATCTCTCTCAC 59.007 50.000 0.00 0.00 0.00 3.51
8448 10653 2.629617 TGCGCCATGATTATCTCTCTCA 59.370 45.455 4.18 0.00 0.00 3.27
8556 10781 0.460987 GAAGATGTGGTCCAGCTCCG 60.461 60.000 0.00 0.00 39.37 4.63
8559 10784 1.599047 CGGAAGATGTGGTCCAGCT 59.401 57.895 0.00 0.00 42.98 4.24


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

AutoCloner maintained by Alex Coulton.