Multiple sequence alignment - TraesCS5D01G183100

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5D01G183100 chr5D 100.000 4773 0 0 1 4773 284972910 284977682 0.000000e+00 8815.0
1 TraesCS5D01G183100 chr5D 98.611 72 1 0 4560 4631 284977404 284977475 1.390000e-25 128.0
2 TraesCS5D01G183100 chr5D 98.611 72 1 0 4495 4566 284977469 284977540 1.390000e-25 128.0
3 TraesCS5D01G183100 chr5A 95.400 2674 93 21 1558 4223 376545804 376548455 0.000000e+00 4229.0
4 TraesCS5D01G183100 chr5A 95.155 1486 39 14 1 1474 376544336 376545800 0.000000e+00 2314.0
5 TraesCS5D01G183100 chr5A 92.029 138 11 0 4276 4413 376548455 376548592 1.360000e-45 195.0
6 TraesCS5D01G183100 chr5B 96.685 2383 61 11 562 2939 322277295 322279664 0.000000e+00 3947.0
7 TraesCS5D01G183100 chr5B 95.798 1428 33 8 3009 4409 322279687 322281114 0.000000e+00 2279.0
8 TraesCS5D01G183100 chr5B 94.707 529 25 1 35 560 322276679 322277207 0.000000e+00 819.0
9 TraesCS5D01G183100 chr5B 82.400 125 21 1 4638 4762 275366587 275366464 1.820000e-19 108.0
10 TraesCS5D01G183100 chr5B 76.271 177 35 7 4575 4748 447009456 447009284 2.370000e-13 87.9
11 TraesCS5D01G183100 chr5B 100.000 34 0 0 2940 2973 322279654 322279687 3.990000e-06 63.9
12 TraesCS5D01G183100 chr2B 79.310 203 41 1 4560 4762 225693647 225693848 1.790000e-29 141.0
13 TraesCS5D01G183100 chr2B 81.102 127 20 4 4638 4762 26119733 26119609 1.090000e-16 99.0
14 TraesCS5D01G183100 chr3D 80.142 141 27 1 4574 4714 352078421 352078560 2.350000e-18 104.0
15 TraesCS5D01G183100 chr1B 76.963 191 37 6 4575 4762 435175003 435174817 8.450000e-18 102.0
16 TraesCS5D01G183100 chr7D 76.263 198 38 8 4566 4759 398059951 398060143 3.930000e-16 97.1
17 TraesCS5D01G183100 chr3B 76.879 173 35 4 4581 4751 29366339 29366170 5.090000e-15 93.5
18 TraesCS5D01G183100 chr3B 76.163 172 36 5 4581 4750 7123439 7123271 8.510000e-13 86.1


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 TraesCS5D01G183100 chr5D 284972910 284977682 4772 False 3023.666667 8815 99.074000 1 4773 3 chr5D.!!$F1 4772
1 TraesCS5D01G183100 chr5A 376544336 376548592 4256 False 2246.000000 4229 94.194667 1 4413 3 chr5A.!!$F1 4412
2 TraesCS5D01G183100 chr5B 322276679 322281114 4435 False 1777.225000 3947 96.797500 35 4409 4 chr5B.!!$F1 4374

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
377 384 0.032130 GTGTTGCCTCTGTGACTCGA 59.968 55.000 0.00 0.00 0.00 4.04 F
734 827 1.290955 CATGTTGCAAGCTGGTGGG 59.709 57.895 0.00 0.00 0.00 4.61 F
780 873 1.308069 ATGTCACGGCACCTTCATGC 61.308 55.000 0.00 0.00 45.34 4.06 F
781 874 1.672356 GTCACGGCACCTTCATGCT 60.672 57.895 0.00 0.00 45.38 3.79 F
2288 2387 2.223735 GGCATGGCATGAGATGAAAGTG 60.224 50.000 30.69 1.49 0.00 3.16 F
3586 3689 0.246635 ACGATGAACCGCTGCTAACT 59.753 50.000 0.00 0.00 0.00 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1789 1886 2.205022 AGTGCCAGCAGAAGCATAAA 57.795 45.000 0.00 0.00 45.49 1.40 R
2377 2476 0.599991 AGCATGTGTTTGTCGAGCGA 60.600 50.000 0.00 0.00 0.00 4.93 R
2433 2533 5.132502 TCATTAGATTATGGTTGCACCCTG 58.867 41.667 0.57 0.00 37.50 4.45 R
2738 2840 9.185192 GACACTAATTCCAAAAGTGAAATTGAG 57.815 33.333 11.38 0.00 42.59 3.02 R
3634 3737 0.322975 GTCTCTTTGCTGCCCTCTCA 59.677 55.000 0.00 0.00 0.00 3.27 R
4651 4782 0.023732 CAGTAAATGCGTCGACAGCG 59.976 55.000 17.16 2.55 37.44 5.18 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
28 29 4.439837 GGAGCTACCGTTTTCCTGTACTAG 60.440 50.000 0.00 0.00 0.00 2.57
29 30 3.119209 AGCTACCGTTTTCCTGTACTAGC 60.119 47.826 0.00 0.00 0.00 3.42
30 31 2.358939 ACCGTTTTCCTGTACTAGCG 57.641 50.000 0.00 0.00 0.00 4.26
31 32 1.615392 ACCGTTTTCCTGTACTAGCGT 59.385 47.619 0.00 0.00 0.00 5.07
32 33 2.036346 ACCGTTTTCCTGTACTAGCGTT 59.964 45.455 0.00 0.00 0.00 4.84
33 34 2.665052 CCGTTTTCCTGTACTAGCGTTC 59.335 50.000 0.00 0.00 0.00 3.95
97 101 1.001633 TGGAACGTTGGCTAGAGGTTC 59.998 52.381 5.00 0.38 39.75 3.62
227 234 2.109181 GCCACCACCTCGCCTATC 59.891 66.667 0.00 0.00 0.00 2.08
377 384 0.032130 GTGTTGCCTCTGTGACTCGA 59.968 55.000 0.00 0.00 0.00 4.04
442 449 8.659527 TGGAATGATGAGATAAAGGTATTAGCA 58.340 33.333 0.00 0.00 0.00 3.49
560 567 6.461648 GGCTGTTAGTGCTCTCAGTATTATCA 60.462 42.308 6.41 0.00 0.00 2.15
566 659 7.270757 AGTGCTCTCAGTATTATCAGTACTG 57.729 40.000 17.17 17.17 46.56 2.74
630 723 5.045797 GTGGTTAGTCTTCCCTGAAATACCT 60.046 44.000 0.00 0.00 0.00 3.08
651 744 4.463891 CCTGGGTTCTGTATGAAAATTGCT 59.536 41.667 0.00 0.00 36.30 3.91
734 827 1.290955 CATGTTGCAAGCTGGTGGG 59.709 57.895 0.00 0.00 0.00 4.61
775 868 2.747446 GTGAAATATGTCACGGCACCTT 59.253 45.455 10.28 0.00 38.68 3.50
776 869 3.006940 TGAAATATGTCACGGCACCTTC 58.993 45.455 0.00 0.00 0.00 3.46
777 870 2.779755 AATATGTCACGGCACCTTCA 57.220 45.000 0.00 0.00 0.00 3.02
778 871 3.281727 AATATGTCACGGCACCTTCAT 57.718 42.857 0.00 0.00 0.00 2.57
779 872 2.022764 TATGTCACGGCACCTTCATG 57.977 50.000 0.00 0.00 0.00 3.07
780 873 1.308069 ATGTCACGGCACCTTCATGC 61.308 55.000 0.00 0.00 45.34 4.06
781 874 1.672356 GTCACGGCACCTTCATGCT 60.672 57.895 0.00 0.00 45.38 3.79
841 934 4.370049 CAAATTGTTGGTGATCACTGCAA 58.630 39.130 24.50 23.13 0.00 4.08
983 1077 4.035278 AGTCTAATCGTAGCAACTCAGC 57.965 45.455 0.00 0.00 0.00 4.26
1055 1149 2.660572 TGGACCAAACAGCAAAGCTAA 58.339 42.857 0.00 0.00 36.40 3.09
1151 1245 3.072944 GCGGTCCTGATAGTACGTATCT 58.927 50.000 0.00 0.66 38.77 1.98
1161 1255 7.308649 CCTGATAGTACGTATCTACACTGCAAT 60.309 40.741 0.00 0.00 38.77 3.56
1479 1576 7.233632 TCATATAAGCTTGGAATAAGCATGGT 58.766 34.615 9.86 0.00 45.30 3.55
2220 2319 9.862149 ATGGATCCTCGTATGTATACACATATA 57.138 33.333 14.23 0.00 46.62 0.86
2288 2387 2.223735 GGCATGGCATGAGATGAAAGTG 60.224 50.000 30.69 1.49 0.00 3.16
2614 2716 5.934043 TGATATAGCTTCAAACCGATCCATG 59.066 40.000 0.00 0.00 0.00 3.66
2738 2840 1.535896 GCGACCTTTTTCTTGGAGACC 59.464 52.381 0.00 0.00 0.00 3.85
2819 2921 5.935789 CAGTTTTTCCTAGGGACGTTTGATA 59.064 40.000 9.46 0.00 0.00 2.15
2928 3031 5.219226 TCGAAGTAAGTTTTTGTTTGCGA 57.781 34.783 0.00 0.00 0.00 5.10
3098 3201 5.185249 ACTTCCACGCTTCTTCTAGTAATGA 59.815 40.000 0.00 0.00 0.00 2.57
3099 3202 5.654603 TCCACGCTTCTTCTAGTAATGAA 57.345 39.130 0.00 0.00 0.00 2.57
3102 3205 5.812642 CCACGCTTCTTCTAGTAATGAATGT 59.187 40.000 0.00 0.00 0.00 2.71
3247 3350 4.644685 AGCGGTAAATGCATCAATAACCTT 59.355 37.500 0.00 0.00 33.85 3.50
3454 3557 1.742768 GAGCGATCAGTTCCCCGAT 59.257 57.895 0.00 0.00 0.00 4.18
3586 3689 0.246635 ACGATGAACCGCTGCTAACT 59.753 50.000 0.00 0.00 0.00 2.24
3634 3737 2.028130 CCTACTCTCAGTCCGAAGCAT 58.972 52.381 0.00 0.00 0.00 3.79
3652 3755 1.065636 CATGAGAGGGCAGCAAAGAGA 60.066 52.381 0.00 0.00 0.00 3.10
3661 3764 0.320247 CAGCAAAGAGACAGCGAGGT 60.320 55.000 0.00 0.00 0.00 3.85
3667 3770 1.062845 GAGACAGCGAGGTAGCGAC 59.937 63.158 0.00 0.00 43.00 5.19
3724 3827 2.031595 GCATATCTTCGAGTCGAGCTCA 60.032 50.000 15.88 0.00 44.33 4.26
4205 4316 7.596749 AATCCTAAGTCAACATCTACAAACG 57.403 36.000 0.00 0.00 0.00 3.60
4292 4423 6.039616 TGTGGAATACAAACTTGAAACTTGC 58.960 36.000 0.00 0.00 36.06 4.01
4323 4454 3.074390 TCCATTTGGACATATAGGGCCTG 59.926 47.826 18.53 1.87 39.78 4.85
4461 4592 4.511617 TTTTGCGGCATCTGTTAATTCA 57.488 36.364 2.28 0.00 0.00 2.57
4462 4593 4.511617 TTTGCGGCATCTGTTAATTCAA 57.488 36.364 2.28 0.00 0.00 2.69
4463 4594 4.717233 TTGCGGCATCTGTTAATTCAAT 57.283 36.364 2.28 0.00 0.00 2.57
4464 4595 4.031418 TGCGGCATCTGTTAATTCAATG 57.969 40.909 0.00 0.00 0.00 2.82
4465 4596 3.181488 TGCGGCATCTGTTAATTCAATGG 60.181 43.478 0.00 0.00 0.00 3.16
4466 4597 3.181487 GCGGCATCTGTTAATTCAATGGT 60.181 43.478 0.00 0.00 0.00 3.55
4467 4598 4.036262 GCGGCATCTGTTAATTCAATGGTA 59.964 41.667 0.00 0.00 0.00 3.25
4468 4599 5.278463 GCGGCATCTGTTAATTCAATGGTAT 60.278 40.000 0.00 0.00 0.00 2.73
4469 4600 6.144854 CGGCATCTGTTAATTCAATGGTATG 58.855 40.000 0.00 0.00 0.00 2.39
4470 4601 6.017192 CGGCATCTGTTAATTCAATGGTATGA 60.017 38.462 0.00 0.00 0.00 2.15
4471 4602 7.365741 GGCATCTGTTAATTCAATGGTATGAG 58.634 38.462 0.00 0.00 0.00 2.90
4472 4603 7.365741 GCATCTGTTAATTCAATGGTATGAGG 58.634 38.462 0.00 0.00 0.00 3.86
4473 4604 6.942532 TCTGTTAATTCAATGGTATGAGGC 57.057 37.500 0.00 0.00 0.00 4.70
4474 4605 5.827797 TCTGTTAATTCAATGGTATGAGGCC 59.172 40.000 0.00 0.00 0.00 5.19
4475 4606 5.514169 TGTTAATTCAATGGTATGAGGCCA 58.486 37.500 5.01 0.00 40.68 5.36
4477 4608 7.293828 TGTTAATTCAATGGTATGAGGCCATA 58.706 34.615 5.01 0.00 45.21 2.74
4478 4609 7.949565 TGTTAATTCAATGGTATGAGGCCATAT 59.050 33.333 5.01 0.35 45.21 1.78
4479 4610 8.462016 GTTAATTCAATGGTATGAGGCCATATC 58.538 37.037 5.01 0.00 45.21 1.63
4480 4611 4.574674 TCAATGGTATGAGGCCATATCC 57.425 45.455 5.01 0.85 45.21 2.59
4481 4612 3.915711 TCAATGGTATGAGGCCATATCCA 59.084 43.478 5.01 7.36 45.21 3.41
4482 4613 4.353489 TCAATGGTATGAGGCCATATCCAA 59.647 41.667 5.01 0.00 45.21 3.53
4483 4614 3.788227 TGGTATGAGGCCATATCCAAC 57.212 47.619 5.01 0.00 35.90 3.77
4484 4615 2.038426 TGGTATGAGGCCATATCCAACG 59.962 50.000 5.01 0.00 35.90 4.10
4485 4616 2.076863 GTATGAGGCCATATCCAACGC 58.923 52.381 5.01 0.00 37.56 4.84
4486 4617 0.473755 ATGAGGCCATATCCAACGCA 59.526 50.000 5.01 0.00 0.00 5.24
4487 4618 0.463654 TGAGGCCATATCCAACGCAC 60.464 55.000 5.01 0.00 0.00 5.34
4488 4619 0.179045 GAGGCCATATCCAACGCACT 60.179 55.000 5.01 0.00 0.00 4.40
4489 4620 0.464373 AGGCCATATCCAACGCACTG 60.464 55.000 5.01 0.00 0.00 3.66
4490 4621 0.463654 GGCCATATCCAACGCACTGA 60.464 55.000 0.00 0.00 0.00 3.41
4491 4622 0.657840 GCCATATCCAACGCACTGAC 59.342 55.000 0.00 0.00 0.00 3.51
4492 4623 1.299541 CCATATCCAACGCACTGACC 58.700 55.000 0.00 0.00 0.00 4.02
4493 4624 1.299541 CATATCCAACGCACTGACCC 58.700 55.000 0.00 0.00 0.00 4.46
4494 4625 0.180406 ATATCCAACGCACTGACCCC 59.820 55.000 0.00 0.00 0.00 4.95
4495 4626 1.195442 TATCCAACGCACTGACCCCA 61.195 55.000 0.00 0.00 0.00 4.96
4496 4627 2.063015 ATCCAACGCACTGACCCCAA 62.063 55.000 0.00 0.00 0.00 4.12
4497 4628 1.826054 CCAACGCACTGACCCCAAA 60.826 57.895 0.00 0.00 0.00 3.28
4498 4629 1.178534 CCAACGCACTGACCCCAAAT 61.179 55.000 0.00 0.00 0.00 2.32
4499 4630 0.039256 CAACGCACTGACCCCAAATG 60.039 55.000 0.00 0.00 0.00 2.32
4500 4631 1.178534 AACGCACTGACCCCAAATGG 61.179 55.000 0.00 0.00 0.00 3.16
4501 4632 1.603455 CGCACTGACCCCAAATGGT 60.603 57.895 0.00 0.00 42.79 3.55
4507 4638 4.966247 ACCCCAAATGGTCCAACC 57.034 55.556 0.00 0.00 39.22 3.77
4508 4639 1.228737 ACCCCAAATGGTCCAACCG 60.229 57.895 0.00 0.00 42.58 4.44
4509 4640 2.645192 CCCCAAATGGTCCAACCGC 61.645 63.158 0.00 0.00 42.58 5.68
4510 4641 2.566010 CCAAATGGTCCAACCGCG 59.434 61.111 0.00 0.00 42.58 6.46
4511 4642 2.265182 CCAAATGGTCCAACCGCGT 61.265 57.895 4.92 0.00 42.58 6.01
4512 4643 1.209127 CAAATGGTCCAACCGCGTC 59.791 57.895 4.92 0.00 42.58 5.19
4513 4644 1.969589 AAATGGTCCAACCGCGTCC 60.970 57.895 4.92 0.00 42.58 4.79
4514 4645 2.684192 AAATGGTCCAACCGCGTCCA 62.684 55.000 4.92 4.17 42.58 4.02
4515 4646 2.478335 AATGGTCCAACCGCGTCCAT 62.478 55.000 4.92 6.38 42.58 3.41
4516 4647 2.359478 GGTCCAACCGCGTCCATT 60.359 61.111 4.92 0.00 0.00 3.16
4517 4648 1.969589 GGTCCAACCGCGTCCATTT 60.970 57.895 4.92 0.00 0.00 2.32
4518 4649 1.209127 GTCCAACCGCGTCCATTTG 59.791 57.895 4.92 0.00 0.00 2.32
4519 4650 1.969064 TCCAACCGCGTCCATTTGG 60.969 57.895 4.92 9.62 40.01 3.28
4520 4651 2.566010 CAACCGCGTCCATTTGGG 59.434 61.111 4.92 0.00 35.41 4.12
4521 4652 2.675075 AACCGCGTCCATTTGGGG 60.675 61.111 4.92 0.00 43.36 4.96
4524 4655 2.124901 CGCGTCCATTTGGGGCTA 60.125 61.111 0.00 0.00 39.98 3.93
4525 4656 1.747367 CGCGTCCATTTGGGGCTAA 60.747 57.895 0.00 0.00 39.98 3.09
4526 4657 1.309499 CGCGTCCATTTGGGGCTAAA 61.309 55.000 0.00 0.00 39.98 1.85
4527 4658 0.172578 GCGTCCATTTGGGGCTAAAC 59.827 55.000 0.00 0.00 39.98 2.01
4528 4659 1.834188 CGTCCATTTGGGGCTAAACT 58.166 50.000 0.00 0.00 39.98 2.66
4529 4660 1.472480 CGTCCATTTGGGGCTAAACTG 59.528 52.381 0.00 0.00 39.98 3.16
4530 4661 1.824852 GTCCATTTGGGGCTAAACTGG 59.175 52.381 0.00 3.73 38.65 4.00
4531 4662 1.194218 CCATTTGGGGCTAAACTGGG 58.806 55.000 0.00 0.00 0.00 4.45
4532 4663 0.536724 CATTTGGGGCTAAACTGGGC 59.463 55.000 0.00 0.00 0.00 5.36
4533 4664 0.116143 ATTTGGGGCTAAACTGGGCA 59.884 50.000 0.00 0.00 0.00 5.36
4534 4665 0.830023 TTTGGGGCTAAACTGGGCAC 60.830 55.000 0.00 0.00 0.00 5.01
4535 4666 2.012824 TTGGGGCTAAACTGGGCACA 62.013 55.000 0.00 0.00 40.86 4.57
4536 4667 1.228737 GGGGCTAAACTGGGCACAA 60.229 57.895 0.00 0.00 32.86 3.33
4537 4668 0.830023 GGGGCTAAACTGGGCACAAA 60.830 55.000 0.00 0.00 32.86 2.83
4538 4669 1.266178 GGGCTAAACTGGGCACAAAT 58.734 50.000 0.00 0.00 0.00 2.32
4539 4670 1.204704 GGGCTAAACTGGGCACAAATC 59.795 52.381 0.00 0.00 0.00 2.17
4540 4671 1.135402 GGCTAAACTGGGCACAAATCG 60.135 52.381 0.00 0.00 0.00 3.34
4541 4672 1.732405 GCTAAACTGGGCACAAATCGC 60.732 52.381 0.00 0.00 0.00 4.58
4542 4673 0.519519 TAAACTGGGCACAAATCGCG 59.480 50.000 0.00 0.00 0.00 5.87
4543 4674 2.141122 AAACTGGGCACAAATCGCGG 62.141 55.000 6.13 0.00 0.00 6.46
4544 4675 4.481112 CTGGGCACAAATCGCGGC 62.481 66.667 6.13 0.00 0.00 6.53
4548 4679 4.049640 GCACAAATCGCGGCCCAA 62.050 61.111 6.13 0.00 0.00 4.12
4549 4680 2.126502 CACAAATCGCGGCCCAAC 60.127 61.111 6.13 0.00 0.00 3.77
4550 4681 3.732892 ACAAATCGCGGCCCAACG 61.733 61.111 6.13 0.00 0.00 4.10
4551 4682 3.732892 CAAATCGCGGCCCAACGT 61.733 61.111 6.13 0.00 35.98 3.99
4552 4683 3.732892 AAATCGCGGCCCAACGTG 61.733 61.111 6.13 0.00 45.04 4.49
4565 4696 1.838913 CAACGTGTGGAAGCAAAAGG 58.161 50.000 0.00 0.00 0.00 3.11
4566 4697 1.134175 CAACGTGTGGAAGCAAAAGGT 59.866 47.619 0.00 0.00 0.00 3.50
4567 4698 1.021968 ACGTGTGGAAGCAAAAGGTC 58.978 50.000 0.00 0.00 0.00 3.85
4568 4699 0.310854 CGTGTGGAAGCAAAAGGTCC 59.689 55.000 0.00 0.00 0.00 4.46
4569 4700 1.398692 GTGTGGAAGCAAAAGGTCCA 58.601 50.000 0.00 0.00 39.14 4.02
4570 4701 1.754226 GTGTGGAAGCAAAAGGTCCAA 59.246 47.619 0.00 0.00 42.97 3.53
4571 4702 1.754226 TGTGGAAGCAAAAGGTCCAAC 59.246 47.619 0.00 0.00 42.97 3.77
4572 4703 1.068588 GTGGAAGCAAAAGGTCCAACC 59.931 52.381 0.00 0.00 42.97 3.77
4573 4704 0.313987 GGAAGCAAAAGGTCCAACCG 59.686 55.000 0.00 0.00 44.90 4.44
4574 4705 0.318699 GAAGCAAAAGGTCCAACCGC 60.319 55.000 0.00 0.00 44.90 5.68
4575 4706 2.050442 GCAAAAGGTCCAACCGCG 60.050 61.111 0.00 0.00 44.90 6.46
4576 4707 2.841160 GCAAAAGGTCCAACCGCGT 61.841 57.895 4.92 0.00 44.90 6.01
4577 4708 1.281656 CAAAAGGTCCAACCGCGTC 59.718 57.895 4.92 0.00 44.90 5.19
4578 4709 1.895231 AAAAGGTCCAACCGCGTCC 60.895 57.895 4.92 0.00 44.90 4.79
4579 4710 2.612095 AAAAGGTCCAACCGCGTCCA 62.612 55.000 4.92 0.00 44.90 4.02
4580 4711 2.406002 AAAGGTCCAACCGCGTCCAT 62.406 55.000 4.92 0.00 44.90 3.41
4581 4712 2.359478 GGTCCAACCGCGTCCATT 60.359 61.111 4.92 0.00 0.00 3.16
4582 4713 1.969589 GGTCCAACCGCGTCCATTT 60.970 57.895 4.92 0.00 0.00 2.32
4583 4714 1.209127 GTCCAACCGCGTCCATTTG 59.791 57.895 4.92 0.00 0.00 2.32
4584 4715 1.969064 TCCAACCGCGTCCATTTGG 60.969 57.895 4.92 9.62 40.01 3.28
4585 4716 2.566010 CAACCGCGTCCATTTGGG 59.434 61.111 4.92 0.00 35.41 4.12
4586 4717 2.675075 AACCGCGTCCATTTGGGG 60.675 61.111 4.92 0.00 43.36 4.96
4589 4720 2.124901 CGCGTCCATTTGGGGCTA 60.125 61.111 0.00 0.00 39.98 3.93
4590 4721 1.747367 CGCGTCCATTTGGGGCTAA 60.747 57.895 0.00 0.00 39.98 3.09
4591 4722 1.309499 CGCGTCCATTTGGGGCTAAA 61.309 55.000 0.00 0.00 39.98 1.85
4592 4723 0.172578 GCGTCCATTTGGGGCTAAAC 59.827 55.000 0.00 0.00 39.98 2.01
4593 4724 1.834188 CGTCCATTTGGGGCTAAACT 58.166 50.000 0.00 0.00 39.98 2.66
4594 4725 1.472480 CGTCCATTTGGGGCTAAACTG 59.528 52.381 0.00 0.00 39.98 3.16
4595 4726 1.824852 GTCCATTTGGGGCTAAACTGG 59.175 52.381 0.00 3.73 38.65 4.00
4596 4727 1.194218 CCATTTGGGGCTAAACTGGG 58.806 55.000 0.00 0.00 0.00 4.45
4597 4728 0.536724 CATTTGGGGCTAAACTGGGC 59.463 55.000 0.00 0.00 0.00 5.36
4598 4729 0.116143 ATTTGGGGCTAAACTGGGCA 59.884 50.000 0.00 0.00 0.00 5.36
4599 4730 0.830023 TTTGGGGCTAAACTGGGCAC 60.830 55.000 0.00 0.00 0.00 5.01
4600 4731 2.012824 TTGGGGCTAAACTGGGCACA 62.013 55.000 0.00 0.00 40.86 4.57
4601 4732 1.228737 GGGGCTAAACTGGGCACAA 60.229 57.895 0.00 0.00 32.86 3.33
4602 4733 0.830023 GGGGCTAAACTGGGCACAAA 60.830 55.000 0.00 0.00 32.86 2.83
4603 4734 1.266178 GGGCTAAACTGGGCACAAAT 58.734 50.000 0.00 0.00 0.00 2.32
4604 4735 1.204704 GGGCTAAACTGGGCACAAATC 59.795 52.381 0.00 0.00 0.00 2.17
4605 4736 1.135402 GGCTAAACTGGGCACAAATCG 60.135 52.381 0.00 0.00 0.00 3.34
4606 4737 1.732405 GCTAAACTGGGCACAAATCGC 60.732 52.381 0.00 0.00 0.00 4.58
4607 4738 0.519519 TAAACTGGGCACAAATCGCG 59.480 50.000 0.00 0.00 0.00 5.87
4608 4739 2.141122 AAACTGGGCACAAATCGCGG 62.141 55.000 6.13 0.00 0.00 6.46
4609 4740 4.481112 CTGGGCACAAATCGCGGC 62.481 66.667 6.13 0.00 0.00 6.53
4613 4744 4.049640 GCACAAATCGCGGCCCAA 62.050 61.111 6.13 0.00 0.00 4.12
4614 4745 2.126502 CACAAATCGCGGCCCAAC 60.127 61.111 6.13 0.00 0.00 3.77
4615 4746 3.732892 ACAAATCGCGGCCCAACG 61.733 61.111 6.13 0.00 0.00 4.10
4616 4747 3.732892 CAAATCGCGGCCCAACGT 61.733 61.111 6.13 0.00 35.98 3.99
4617 4748 3.732892 AAATCGCGGCCCAACGTG 61.733 61.111 6.13 0.00 45.04 4.49
4630 4761 1.838913 CAACGTGTGGAAGCAAAAGG 58.161 50.000 0.00 0.00 0.00 3.11
4631 4762 1.403679 CAACGTGTGGAAGCAAAAGGA 59.596 47.619 0.00 0.00 0.00 3.36
4632 4763 1.021968 ACGTGTGGAAGCAAAAGGAC 58.978 50.000 0.00 0.00 0.00 3.85
4633 4764 1.021202 CGTGTGGAAGCAAAAGGACA 58.979 50.000 0.00 0.00 0.00 4.02
4634 4765 1.403679 CGTGTGGAAGCAAAAGGACAA 59.596 47.619 0.00 0.00 0.00 3.18
4635 4766 2.159310 CGTGTGGAAGCAAAAGGACAAA 60.159 45.455 0.00 0.00 0.00 2.83
4636 4767 3.186909 GTGTGGAAGCAAAAGGACAAAC 58.813 45.455 0.00 0.00 0.00 2.93
4637 4768 2.159310 TGTGGAAGCAAAAGGACAAACG 60.159 45.455 0.00 0.00 0.00 3.60
4638 4769 2.096248 TGGAAGCAAAAGGACAAACGT 58.904 42.857 0.00 0.00 0.00 3.99
4639 4770 2.098443 TGGAAGCAAAAGGACAAACGTC 59.902 45.455 0.00 0.00 0.00 4.34
4661 4792 1.928653 TTTTTGTCCGCTGTCGACG 59.071 52.632 11.62 7.05 38.10 5.12
4662 4793 2.096481 TTTTTGTCCGCTGTCGACGC 62.096 55.000 18.30 18.30 38.10 5.19
4663 4794 3.776659 TTTGTCCGCTGTCGACGCA 62.777 57.895 24.54 9.69 38.10 5.24
4664 4795 3.567478 TTGTCCGCTGTCGACGCAT 62.567 57.895 24.54 0.00 38.10 4.73
4665 4796 2.809601 GTCCGCTGTCGACGCATT 60.810 61.111 24.54 0.00 38.10 3.56
4666 4797 2.048597 TCCGCTGTCGACGCATTT 60.049 55.556 24.54 0.00 38.10 2.32
4667 4798 1.074319 GTCCGCTGTCGACGCATTTA 61.074 55.000 24.54 9.64 38.10 1.40
4668 4799 1.074319 TCCGCTGTCGACGCATTTAC 61.074 55.000 24.54 5.12 38.10 2.01
4669 4800 1.076533 CCGCTGTCGACGCATTTACT 61.077 55.000 24.54 0.00 38.10 2.24
4670 4801 0.023732 CGCTGTCGACGCATTTACTG 59.976 55.000 24.54 9.00 38.10 2.74
4671 4802 3.777215 CGCTGTCGACGCATTTACTGC 62.777 57.143 24.54 9.82 42.21 4.40
4690 4821 3.579066 CCAAATTTGGGTCGCGTTT 57.421 47.368 26.87 0.00 44.70 3.60
4691 4822 1.135867 CCAAATTTGGGTCGCGTTTG 58.864 50.000 26.87 7.57 44.70 2.93
4692 4823 0.506506 CAAATTTGGGTCGCGTTTGC 59.493 50.000 10.49 0.00 37.91 3.68
4710 4841 2.201885 GTCGAAACGAACAGCGCG 60.202 61.111 0.00 0.00 46.04 6.86
4711 4842 4.054455 TCGAAACGAACAGCGCGC 62.054 61.111 26.66 26.66 46.04 6.86
4737 4868 4.717313 GGGACCCACGCCCTTGTC 62.717 72.222 5.33 0.00 42.56 3.18
4738 4869 4.717313 GGACCCACGCCCTTGTCC 62.717 72.222 0.00 0.00 40.40 4.02
4739 4870 3.948719 GACCCACGCCCTTGTCCA 61.949 66.667 0.00 0.00 0.00 4.02
4740 4871 4.265056 ACCCACGCCCTTGTCCAC 62.265 66.667 0.00 0.00 0.00 4.02
4743 4874 4.263572 CACGCCCTTGTCCACCCA 62.264 66.667 0.00 0.00 0.00 4.51
4744 4875 3.256960 ACGCCCTTGTCCACCCAT 61.257 61.111 0.00 0.00 0.00 4.00
4745 4876 2.751436 CGCCCTTGTCCACCCATG 60.751 66.667 0.00 0.00 0.00 3.66
4747 4878 2.362889 CCCTTGTCCACCCATGGC 60.363 66.667 6.09 0.00 46.80 4.40
4748 4879 2.362889 CCTTGTCCACCCATGGCC 60.363 66.667 6.09 0.00 46.80 5.36
4749 4880 2.362889 CTTGTCCACCCATGGCCC 60.363 66.667 6.09 0.00 46.80 5.80
4750 4881 4.358841 TTGTCCACCCATGGCCCG 62.359 66.667 6.09 0.00 46.80 6.13
4769 4900 2.181021 CCGTCGGGGATATAGCGC 59.819 66.667 2.34 0.00 38.47 5.92
4770 4901 2.341101 CCGTCGGGGATATAGCGCT 61.341 63.158 17.26 17.26 38.47 5.92
4771 4902 1.136984 CGTCGGGGATATAGCGCTC 59.863 63.158 16.34 0.00 0.00 5.03
4772 4903 1.511768 GTCGGGGATATAGCGCTCC 59.488 63.158 16.34 9.49 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 3.185330 GCTAGTACAGGAAAACGGTAGC 58.815 50.000 0.00 0.00 30.28 3.58
15 16 2.331194 GCGAACGCTAGTACAGGAAAA 58.669 47.619 11.97 0.00 38.26 2.29
28 29 0.844503 CATCCTACTAACGCGAACGC 59.155 55.000 15.93 9.20 45.53 4.84
30 31 4.025979 CCAATTCATCCTACTAACGCGAAC 60.026 45.833 15.93 0.00 0.00 3.95
31 32 4.116961 CCAATTCATCCTACTAACGCGAA 58.883 43.478 15.93 0.00 0.00 4.70
32 33 3.713288 CCAATTCATCCTACTAACGCGA 58.287 45.455 15.93 0.00 0.00 5.87
33 34 2.221055 GCCAATTCATCCTACTAACGCG 59.779 50.000 3.53 3.53 0.00 6.01
97 101 5.422145 CAAAGGGGCTGATATTTTCAAAGG 58.578 41.667 0.00 0.00 32.78 3.11
227 234 3.067106 AGACAAAACAGCACGGATACAG 58.933 45.455 0.00 0.00 0.00 2.74
377 384 6.540438 ACAAGGCAGATCAATCAAATCATT 57.460 33.333 0.00 0.00 0.00 2.57
442 449 5.047802 ACAGCCATTTTCTGTTTTCATCGAT 60.048 36.000 0.00 0.00 41.61 3.59
566 659 9.326339 GACAACGGAGAGTGTTTAATTTAATTC 57.674 33.333 0.00 0.00 30.40 2.17
630 723 8.995027 ATATAGCAATTTTCATACAGAACCCA 57.005 30.769 0.00 0.00 35.56 4.51
651 744 8.540388 ACCTCAGACAAAAAGCAGTAAGATATA 58.460 33.333 0.00 0.00 0.00 0.86
734 827 4.890581 TCACTCCCTATCTACTGAGAAAGC 59.109 45.833 0.00 0.00 34.61 3.51
949 1043 3.378742 CGATTAGACTCTAGTGCTGGTGT 59.621 47.826 0.00 0.00 0.00 4.16
983 1077 2.338015 ATTTGCTGCAGGTGAGCGG 61.338 57.895 17.12 0.00 43.77 5.52
1055 1149 2.980233 GTTGCCTCGCAGCCAAGT 60.980 61.111 0.00 0.00 40.61 3.16
1789 1886 2.205022 AGTGCCAGCAGAAGCATAAA 57.795 45.000 0.00 0.00 45.49 1.40
2010 2109 7.820648 AGCCTGTATTTCTGAAAACAGTAATG 58.179 34.615 25.73 18.31 38.10 1.90
2377 2476 0.599991 AGCATGTGTTTGTCGAGCGA 60.600 50.000 0.00 0.00 0.00 4.93
2433 2533 5.132502 TCATTAGATTATGGTTGCACCCTG 58.867 41.667 0.57 0.00 37.50 4.45
2738 2840 9.185192 GACACTAATTCCAAAAGTGAAATTGAG 57.815 33.333 11.38 0.00 42.59 3.02
2819 2921 4.511826 CACTGTAAAGAAAAAGGCTCGACT 59.488 41.667 0.00 0.00 0.00 4.18
2928 3031 2.699846 TGCTTTTGGACTGCTTTTGGAT 59.300 40.909 0.00 0.00 0.00 3.41
2997 3100 7.723616 TCCTCTGTTTTTAGAATGGACAAATCA 59.276 33.333 0.00 0.00 0.00 2.57
2998 3101 8.110860 TCCTCTGTTTTTAGAATGGACAAATC 57.889 34.615 0.00 0.00 0.00 2.17
2999 3102 8.477419 TTCCTCTGTTTTTAGAATGGACAAAT 57.523 30.769 0.00 0.00 0.00 2.32
3003 3106 9.411801 GAATTTTCCTCTGTTTTTAGAATGGAC 57.588 33.333 0.00 0.00 0.00 4.02
3098 3201 5.798132 TGTCTCTAATGCAGACTTCACATT 58.202 37.500 4.86 0.00 40.93 2.71
3099 3202 5.411831 TGTCTCTAATGCAGACTTCACAT 57.588 39.130 4.86 0.00 40.93 3.21
3102 3205 5.798132 ACAATGTCTCTAATGCAGACTTCA 58.202 37.500 4.86 0.00 40.93 3.02
3454 3557 0.787084 AGGGGTCTGTCCTCTCAGAA 59.213 55.000 0.00 0.00 45.43 3.02
3586 3689 2.618816 GGGATGACAGTTGGAATCTGCA 60.619 50.000 0.00 0.00 36.50 4.41
3634 3737 0.322975 GTCTCTTTGCTGCCCTCTCA 59.677 55.000 0.00 0.00 0.00 3.27
3652 3755 4.477975 GCGTCGCTACCTCGCTGT 62.478 66.667 10.68 0.00 45.29 4.40
3661 3764 1.226859 CGGGAATTCAGCGTCGCTA 60.227 57.895 21.25 5.66 36.40 4.26
3667 3770 2.897350 GCCTCCGGGAATTCAGCG 60.897 66.667 7.93 0.00 33.58 5.18
3724 3827 1.504275 ATTGCTGGAACTCTGGCCCT 61.504 55.000 0.00 0.00 0.00 5.19
4292 4423 1.553248 TGTCCAAATGGAGGGAGTACG 59.447 52.381 1.47 0.00 46.49 3.67
4439 4570 4.876125 TGAATTAACAGATGCCGCAAAAA 58.124 34.783 0.00 0.00 0.00 1.94
4440 4571 4.511617 TGAATTAACAGATGCCGCAAAA 57.488 36.364 0.00 0.00 0.00 2.44
4441 4572 4.511617 TTGAATTAACAGATGCCGCAAA 57.488 36.364 0.00 0.00 0.00 3.68
4442 4573 4.422840 CATTGAATTAACAGATGCCGCAA 58.577 39.130 0.00 0.00 0.00 4.85
4443 4574 3.181488 CCATTGAATTAACAGATGCCGCA 60.181 43.478 0.00 0.00 0.00 5.69
4444 4575 3.181487 ACCATTGAATTAACAGATGCCGC 60.181 43.478 0.00 0.00 0.00 6.53
4445 4576 4.637483 ACCATTGAATTAACAGATGCCG 57.363 40.909 0.00 0.00 0.00 5.69
4446 4577 7.275888 TCATACCATTGAATTAACAGATGCC 57.724 36.000 0.00 0.00 0.00 4.40
4447 4578 7.365741 CCTCATACCATTGAATTAACAGATGC 58.634 38.462 0.00 0.00 0.00 3.91
4448 4579 7.365741 GCCTCATACCATTGAATTAACAGATG 58.634 38.462 0.00 0.00 0.00 2.90
4449 4580 6.491403 GGCCTCATACCATTGAATTAACAGAT 59.509 38.462 0.00 0.00 0.00 2.90
4450 4581 5.827797 GGCCTCATACCATTGAATTAACAGA 59.172 40.000 0.00 0.00 0.00 3.41
4451 4582 5.593909 TGGCCTCATACCATTGAATTAACAG 59.406 40.000 3.32 0.00 30.29 3.16
4452 4583 5.514169 TGGCCTCATACCATTGAATTAACA 58.486 37.500 3.32 0.00 30.29 2.41
4453 4584 6.655078 ATGGCCTCATACCATTGAATTAAC 57.345 37.500 3.32 0.00 45.86 2.01
4454 4585 7.615365 GGATATGGCCTCATACCATTGAATTAA 59.385 37.037 3.32 0.00 45.86 1.40
4455 4586 7.118723 GGATATGGCCTCATACCATTGAATTA 58.881 38.462 3.32 0.00 45.86 1.40
4456 4587 5.954150 GGATATGGCCTCATACCATTGAATT 59.046 40.000 3.32 0.00 45.86 2.17
4457 4588 5.015497 TGGATATGGCCTCATACCATTGAAT 59.985 40.000 3.32 0.00 45.86 2.57
4458 4589 4.353489 TGGATATGGCCTCATACCATTGAA 59.647 41.667 3.32 0.00 45.86 2.69
4459 4590 3.915711 TGGATATGGCCTCATACCATTGA 59.084 43.478 3.32 0.00 45.86 2.57
4460 4591 4.305539 TGGATATGGCCTCATACCATTG 57.694 45.455 3.32 0.00 45.86 2.82
4461 4592 4.666512 GTTGGATATGGCCTCATACCATT 58.333 43.478 3.32 0.00 45.86 3.16
4463 4594 2.038426 CGTTGGATATGGCCTCATACCA 59.962 50.000 3.32 4.68 42.61 3.25
4464 4595 2.699954 CGTTGGATATGGCCTCATACC 58.300 52.381 3.32 1.79 38.53 2.73
4465 4596 2.076863 GCGTTGGATATGGCCTCATAC 58.923 52.381 3.32 0.00 38.53 2.39
4466 4597 1.696884 TGCGTTGGATATGGCCTCATA 59.303 47.619 3.32 0.00 39.85 2.15
4467 4598 0.473755 TGCGTTGGATATGGCCTCAT 59.526 50.000 3.32 0.00 37.40 2.90
4468 4599 0.463654 GTGCGTTGGATATGGCCTCA 60.464 55.000 3.32 0.00 0.00 3.86
4469 4600 0.179045 AGTGCGTTGGATATGGCCTC 60.179 55.000 3.32 0.00 0.00 4.70
4470 4601 0.464373 CAGTGCGTTGGATATGGCCT 60.464 55.000 3.32 0.00 0.00 5.19
4471 4602 0.463654 TCAGTGCGTTGGATATGGCC 60.464 55.000 0.00 0.00 0.00 5.36
4472 4603 0.657840 GTCAGTGCGTTGGATATGGC 59.342 55.000 0.00 0.00 0.00 4.40
4473 4604 1.299541 GGTCAGTGCGTTGGATATGG 58.700 55.000 0.00 0.00 0.00 2.74
4474 4605 1.299541 GGGTCAGTGCGTTGGATATG 58.700 55.000 0.00 0.00 0.00 1.78
4475 4606 0.180406 GGGGTCAGTGCGTTGGATAT 59.820 55.000 0.00 0.00 0.00 1.63
4476 4607 1.195442 TGGGGTCAGTGCGTTGGATA 61.195 55.000 0.00 0.00 0.00 2.59
4477 4608 2.063015 TTGGGGTCAGTGCGTTGGAT 62.063 55.000 0.00 0.00 0.00 3.41
4478 4609 2.272230 TTTGGGGTCAGTGCGTTGGA 62.272 55.000 0.00 0.00 0.00 3.53
4479 4610 1.178534 ATTTGGGGTCAGTGCGTTGG 61.179 55.000 0.00 0.00 0.00 3.77
4480 4611 0.039256 CATTTGGGGTCAGTGCGTTG 60.039 55.000 0.00 0.00 0.00 4.10
4481 4612 1.178534 CCATTTGGGGTCAGTGCGTT 61.179 55.000 0.00 0.00 0.00 4.84
4482 4613 1.603455 CCATTTGGGGTCAGTGCGT 60.603 57.895 0.00 0.00 0.00 5.24
4483 4614 1.603455 ACCATTTGGGGTCAGTGCG 60.603 57.895 0.96 0.00 42.91 5.34
4484 4615 4.519610 ACCATTTGGGGTCAGTGC 57.480 55.556 0.96 0.00 42.91 4.40
4490 4621 1.228737 CGGTTGGACCATTTGGGGT 60.229 57.895 0.00 0.00 46.02 4.95
4491 4622 2.645192 GCGGTTGGACCATTTGGGG 61.645 63.158 0.00 0.00 42.91 4.96
4492 4623 2.969827 GCGGTTGGACCATTTGGG 59.030 61.111 0.00 0.00 38.47 4.12
4493 4624 2.195123 GACGCGGTTGGACCATTTGG 62.195 60.000 12.47 0.00 38.47 3.28
4494 4625 1.209127 GACGCGGTTGGACCATTTG 59.791 57.895 12.47 0.00 38.47 2.32
4495 4626 1.969589 GGACGCGGTTGGACCATTT 60.970 57.895 12.47 0.00 38.47 2.32
4496 4627 2.359478 GGACGCGGTTGGACCATT 60.359 61.111 12.47 0.00 38.47 3.16
4497 4628 2.478335 AATGGACGCGGTTGGACCAT 62.478 55.000 12.47 12.09 42.17 3.55
4498 4629 2.684192 AAATGGACGCGGTTGGACCA 62.684 55.000 12.47 10.25 38.47 4.02
4499 4630 1.969589 AAATGGACGCGGTTGGACC 60.970 57.895 12.47 4.45 34.05 4.46
4500 4631 1.209127 CAAATGGACGCGGTTGGAC 59.791 57.895 12.47 0.00 0.00 4.02
4501 4632 1.969064 CCAAATGGACGCGGTTGGA 60.969 57.895 12.47 0.00 42.66 3.53
4502 4633 2.566010 CCAAATGGACGCGGTTGG 59.434 61.111 12.47 11.86 37.39 3.77
4503 4634 2.566010 CCCAAATGGACGCGGTTG 59.434 61.111 12.47 6.42 37.39 3.77
4504 4635 2.675075 CCCCAAATGGACGCGGTT 60.675 61.111 12.47 0.00 37.39 4.44
4506 4637 3.690685 TAGCCCCAAATGGACGCGG 62.691 63.158 12.47 0.00 37.39 6.46
4507 4638 1.309499 TTTAGCCCCAAATGGACGCG 61.309 55.000 3.53 3.53 37.39 6.01
4508 4639 0.172578 GTTTAGCCCCAAATGGACGC 59.827 55.000 0.00 2.27 37.39 5.19
4509 4640 1.472480 CAGTTTAGCCCCAAATGGACG 59.528 52.381 0.00 0.00 37.39 4.79
4510 4641 1.824852 CCAGTTTAGCCCCAAATGGAC 59.175 52.381 0.00 0.00 37.39 4.02
4511 4642 1.272985 CCCAGTTTAGCCCCAAATGGA 60.273 52.381 0.00 0.00 37.39 3.41
4512 4643 1.194218 CCCAGTTTAGCCCCAAATGG 58.806 55.000 0.00 0.00 0.00 3.16
4513 4644 0.536724 GCCCAGTTTAGCCCCAAATG 59.463 55.000 0.00 0.00 0.00 2.32
4514 4645 0.116143 TGCCCAGTTTAGCCCCAAAT 59.884 50.000 0.00 0.00 0.00 2.32
4515 4646 0.830023 GTGCCCAGTTTAGCCCCAAA 60.830 55.000 0.00 0.00 0.00 3.28
4516 4647 1.228737 GTGCCCAGTTTAGCCCCAA 60.229 57.895 0.00 0.00 0.00 4.12
4517 4648 2.012824 TTGTGCCCAGTTTAGCCCCA 62.013 55.000 0.00 0.00 0.00 4.96
4518 4649 0.830023 TTTGTGCCCAGTTTAGCCCC 60.830 55.000 0.00 0.00 0.00 5.80
4519 4650 1.204704 GATTTGTGCCCAGTTTAGCCC 59.795 52.381 0.00 0.00 0.00 5.19
4520 4651 1.135402 CGATTTGTGCCCAGTTTAGCC 60.135 52.381 0.00 0.00 0.00 3.93
4521 4652 1.732405 GCGATTTGTGCCCAGTTTAGC 60.732 52.381 0.00 0.00 0.00 3.09
4522 4653 1.465689 CGCGATTTGTGCCCAGTTTAG 60.466 52.381 0.00 0.00 0.00 1.85
4523 4654 0.519519 CGCGATTTGTGCCCAGTTTA 59.480 50.000 0.00 0.00 0.00 2.01
4524 4655 1.285641 CGCGATTTGTGCCCAGTTT 59.714 52.632 0.00 0.00 0.00 2.66
4525 4656 2.625823 CCGCGATTTGTGCCCAGTT 61.626 57.895 8.23 0.00 0.00 3.16
4526 4657 3.055719 CCGCGATTTGTGCCCAGT 61.056 61.111 8.23 0.00 0.00 4.00
4527 4658 4.481112 GCCGCGATTTGTGCCCAG 62.481 66.667 8.23 0.00 0.00 4.45
4531 4662 4.049640 TTGGGCCGCGATTTGTGC 62.050 61.111 8.23 0.00 0.00 4.57
4532 4663 2.126502 GTTGGGCCGCGATTTGTG 60.127 61.111 8.23 0.00 0.00 3.33
4533 4664 3.732892 CGTTGGGCCGCGATTTGT 61.733 61.111 8.23 0.00 0.00 2.83
4534 4665 3.732892 ACGTTGGGCCGCGATTTG 61.733 61.111 23.64 0.00 0.00 2.32
4535 4666 3.732892 CACGTTGGGCCGCGATTT 61.733 61.111 23.64 2.21 0.00 2.17
4541 4672 3.353836 CTTCCACACGTTGGGCCG 61.354 66.667 14.23 0.00 46.92 6.13
4542 4673 3.670377 GCTTCCACACGTTGGGCC 61.670 66.667 14.23 0.00 46.92 5.80
4543 4674 2.010582 TTTGCTTCCACACGTTGGGC 62.011 55.000 14.23 11.64 46.92 5.36
4544 4675 0.457851 TTTTGCTTCCACACGTTGGG 59.542 50.000 14.23 6.45 46.92 4.12
4546 4677 1.134175 ACCTTTTGCTTCCACACGTTG 59.866 47.619 0.00 0.00 0.00 4.10
4547 4678 1.404035 GACCTTTTGCTTCCACACGTT 59.596 47.619 0.00 0.00 0.00 3.99
4548 4679 1.021968 GACCTTTTGCTTCCACACGT 58.978 50.000 0.00 0.00 0.00 4.49
4549 4680 0.310854 GGACCTTTTGCTTCCACACG 59.689 55.000 0.00 0.00 0.00 4.49
4550 4681 1.398692 TGGACCTTTTGCTTCCACAC 58.601 50.000 0.00 0.00 34.35 3.82
4551 4682 1.754226 GTTGGACCTTTTGCTTCCACA 59.246 47.619 0.00 0.00 39.20 4.17
4552 4683 1.068588 GGTTGGACCTTTTGCTTCCAC 59.931 52.381 0.00 0.00 39.20 4.02
4553 4684 1.408969 GGTTGGACCTTTTGCTTCCA 58.591 50.000 0.00 0.00 37.66 3.53
4554 4685 0.313987 CGGTTGGACCTTTTGCTTCC 59.686 55.000 0.00 0.00 35.66 3.46
4555 4686 0.318699 GCGGTTGGACCTTTTGCTTC 60.319 55.000 0.00 0.00 35.66 3.86
4556 4687 1.739667 GCGGTTGGACCTTTTGCTT 59.260 52.632 0.00 0.00 35.66 3.91
4557 4688 2.551912 CGCGGTTGGACCTTTTGCT 61.552 57.895 0.00 0.00 35.66 3.91
4558 4689 2.050442 CGCGGTTGGACCTTTTGC 60.050 61.111 0.00 0.00 35.66 3.68
4559 4690 1.281656 GACGCGGTTGGACCTTTTG 59.718 57.895 12.47 0.00 35.66 2.44
4560 4691 1.895231 GGACGCGGTTGGACCTTTT 60.895 57.895 12.47 0.00 35.66 2.27
4561 4692 2.281276 GGACGCGGTTGGACCTTT 60.281 61.111 12.47 0.00 35.66 3.11
4562 4693 2.406002 AATGGACGCGGTTGGACCTT 62.406 55.000 12.47 0.00 35.66 3.50
4563 4694 2.406002 AAATGGACGCGGTTGGACCT 62.406 55.000 12.47 0.00 35.66 3.85
4564 4695 1.969589 AAATGGACGCGGTTGGACC 60.970 57.895 12.47 4.45 34.05 4.46
4565 4696 1.209127 CAAATGGACGCGGTTGGAC 59.791 57.895 12.47 0.00 0.00 4.02
4566 4697 1.969064 CCAAATGGACGCGGTTGGA 60.969 57.895 12.47 0.00 42.66 3.53
4567 4698 2.566010 CCAAATGGACGCGGTTGG 59.434 61.111 12.47 11.86 37.39 3.77
4568 4699 2.566010 CCCAAATGGACGCGGTTG 59.434 61.111 12.47 6.42 37.39 3.77
4569 4700 2.675075 CCCCAAATGGACGCGGTT 60.675 61.111 12.47 0.00 37.39 4.44
4571 4702 3.690685 TAGCCCCAAATGGACGCGG 62.691 63.158 12.47 0.00 37.39 6.46
4572 4703 1.309499 TTTAGCCCCAAATGGACGCG 61.309 55.000 3.53 3.53 37.39 6.01
4573 4704 0.172578 GTTTAGCCCCAAATGGACGC 59.827 55.000 0.00 2.27 37.39 5.19
4574 4705 1.472480 CAGTTTAGCCCCAAATGGACG 59.528 52.381 0.00 0.00 37.39 4.79
4575 4706 1.824852 CCAGTTTAGCCCCAAATGGAC 59.175 52.381 0.00 0.00 37.39 4.02
4576 4707 1.272985 CCCAGTTTAGCCCCAAATGGA 60.273 52.381 0.00 0.00 37.39 3.41
4577 4708 1.194218 CCCAGTTTAGCCCCAAATGG 58.806 55.000 0.00 0.00 0.00 3.16
4578 4709 0.536724 GCCCAGTTTAGCCCCAAATG 59.463 55.000 0.00 0.00 0.00 2.32
4579 4710 0.116143 TGCCCAGTTTAGCCCCAAAT 59.884 50.000 0.00 0.00 0.00 2.32
4580 4711 0.830023 GTGCCCAGTTTAGCCCCAAA 60.830 55.000 0.00 0.00 0.00 3.28
4581 4712 1.228737 GTGCCCAGTTTAGCCCCAA 60.229 57.895 0.00 0.00 0.00 4.12
4582 4713 2.012824 TTGTGCCCAGTTTAGCCCCA 62.013 55.000 0.00 0.00 0.00 4.96
4583 4714 0.830023 TTTGTGCCCAGTTTAGCCCC 60.830 55.000 0.00 0.00 0.00 5.80
4584 4715 1.204704 GATTTGTGCCCAGTTTAGCCC 59.795 52.381 0.00 0.00 0.00 5.19
4585 4716 1.135402 CGATTTGTGCCCAGTTTAGCC 60.135 52.381 0.00 0.00 0.00 3.93
4586 4717 1.732405 GCGATTTGTGCCCAGTTTAGC 60.732 52.381 0.00 0.00 0.00 3.09
4587 4718 1.465689 CGCGATTTGTGCCCAGTTTAG 60.466 52.381 0.00 0.00 0.00 1.85
4588 4719 0.519519 CGCGATTTGTGCCCAGTTTA 59.480 50.000 0.00 0.00 0.00 2.01
4589 4720 1.285641 CGCGATTTGTGCCCAGTTT 59.714 52.632 0.00 0.00 0.00 2.66
4590 4721 2.625823 CCGCGATTTGTGCCCAGTT 61.626 57.895 8.23 0.00 0.00 3.16
4591 4722 3.055719 CCGCGATTTGTGCCCAGT 61.056 61.111 8.23 0.00 0.00 4.00
4592 4723 4.481112 GCCGCGATTTGTGCCCAG 62.481 66.667 8.23 0.00 0.00 4.45
4596 4727 4.049640 TTGGGCCGCGATTTGTGC 62.050 61.111 8.23 0.00 0.00 4.57
4597 4728 2.126502 GTTGGGCCGCGATTTGTG 60.127 61.111 8.23 0.00 0.00 3.33
4598 4729 3.732892 CGTTGGGCCGCGATTTGT 61.733 61.111 8.23 0.00 0.00 2.83
4599 4730 3.732892 ACGTTGGGCCGCGATTTG 61.733 61.111 23.64 0.00 0.00 2.32
4600 4731 3.732892 CACGTTGGGCCGCGATTT 61.733 61.111 23.64 2.21 0.00 2.17
4606 4737 3.353836 CTTCCACACGTTGGGCCG 61.354 66.667 14.23 0.00 46.92 6.13
4607 4738 3.670377 GCTTCCACACGTTGGGCC 61.670 66.667 14.23 0.00 46.92 5.80
4608 4739 2.010582 TTTGCTTCCACACGTTGGGC 62.011 55.000 14.23 11.64 46.92 5.36
4609 4740 0.457851 TTTTGCTTCCACACGTTGGG 59.542 50.000 14.23 6.45 46.92 4.12
4611 4742 1.403679 TCCTTTTGCTTCCACACGTTG 59.596 47.619 0.00 0.00 0.00 4.10
4612 4743 1.404035 GTCCTTTTGCTTCCACACGTT 59.596 47.619 0.00 0.00 0.00 3.99
4613 4744 1.021968 GTCCTTTTGCTTCCACACGT 58.978 50.000 0.00 0.00 0.00 4.49
4614 4745 1.021202 TGTCCTTTTGCTTCCACACG 58.979 50.000 0.00 0.00 0.00 4.49
4615 4746 3.186909 GTTTGTCCTTTTGCTTCCACAC 58.813 45.455 0.00 0.00 0.00 3.82
4616 4747 2.159310 CGTTTGTCCTTTTGCTTCCACA 60.159 45.455 0.00 0.00 0.00 4.17
4617 4748 2.159296 ACGTTTGTCCTTTTGCTTCCAC 60.159 45.455 0.00 0.00 0.00 4.02
4618 4749 2.096248 ACGTTTGTCCTTTTGCTTCCA 58.904 42.857 0.00 0.00 0.00 3.53
4619 4750 2.727777 GACGTTTGTCCTTTTGCTTCC 58.272 47.619 0.00 0.00 39.30 3.46
4643 4774 1.928653 CGTCGACAGCGGACAAAAA 59.071 52.632 17.16 0.00 38.28 1.94
4644 4775 2.591311 GCGTCGACAGCGGACAAAA 61.591 57.895 17.16 0.00 38.28 2.44
4645 4776 3.033764 GCGTCGACAGCGGACAAA 61.034 61.111 17.16 0.00 38.28 2.83
4646 4777 3.567478 ATGCGTCGACAGCGGACAA 62.567 57.895 17.16 4.33 38.28 3.18
4647 4778 3.567478 AATGCGTCGACAGCGGACA 62.567 57.895 17.16 4.68 38.28 4.02
4648 4779 1.074319 TAAATGCGTCGACAGCGGAC 61.074 55.000 17.16 0.00 38.28 4.79
4649 4780 1.074319 GTAAATGCGTCGACAGCGGA 61.074 55.000 17.16 3.12 38.28 5.54
4650 4781 1.076533 AGTAAATGCGTCGACAGCGG 61.077 55.000 17.16 0.00 38.28 5.52
4651 4782 0.023732 CAGTAAATGCGTCGACAGCG 59.976 55.000 17.16 2.55 37.44 5.18
4652 4783 0.247301 GCAGTAAATGCGTCGACAGC 60.247 55.000 17.16 19.12 46.99 4.40
4653 4784 3.858040 GCAGTAAATGCGTCGACAG 57.142 52.632 17.16 9.59 46.99 3.51
4673 4804 0.506506 GCAAACGCGACCCAAATTTG 59.493 50.000 15.93 12.51 34.17 2.32
4674 4805 2.893671 GCAAACGCGACCCAAATTT 58.106 47.368 15.93 0.00 0.00 1.82
4675 4806 4.645692 GCAAACGCGACCCAAATT 57.354 50.000 15.93 0.00 0.00 1.82
4687 4818 1.372656 CTGTTCGTTTCGACGCAAAC 58.627 50.000 10.80 10.80 34.89 2.93
4688 4819 0.315544 GCTGTTCGTTTCGACGCAAA 60.316 50.000 0.00 0.00 34.89 3.68
4689 4820 1.274476 GCTGTTCGTTTCGACGCAA 59.726 52.632 0.00 0.00 34.89 4.85
4690 4821 2.923177 CGCTGTTCGTTTCGACGCA 61.923 57.895 0.00 0.00 34.89 5.24
4691 4822 2.201885 CGCTGTTCGTTTCGACGC 60.202 61.111 0.00 0.00 34.89 5.19
4692 4823 2.201885 GCGCTGTTCGTTTCGACG 60.202 61.111 0.00 0.00 41.07 5.12
4693 4824 2.201885 CGCGCTGTTCGTTTCGAC 60.202 61.111 5.56 0.00 41.07 4.20
4694 4825 4.054455 GCGCGCTGTTCGTTTCGA 62.054 61.111 26.67 0.00 41.07 3.71
4720 4851 4.717313 GACAAGGGCGTGGGTCCC 62.717 72.222 0.00 0.00 39.40 4.46
4721 4852 4.717313 GGACAAGGGCGTGGGTCC 62.717 72.222 13.35 13.35 42.60 4.46
4722 4853 3.948719 TGGACAAGGGCGTGGGTC 61.949 66.667 4.28 4.28 0.00 4.46
4723 4854 4.265056 GTGGACAAGGGCGTGGGT 62.265 66.667 0.00 0.00 0.00 4.51
4726 4857 3.567579 ATGGGTGGACAAGGGCGTG 62.568 63.158 0.00 0.00 0.00 5.34
4727 4858 3.256960 ATGGGTGGACAAGGGCGT 61.257 61.111 0.00 0.00 0.00 5.68
4728 4859 2.751436 CATGGGTGGACAAGGGCG 60.751 66.667 0.00 0.00 0.00 6.13
4752 4883 2.181021 GCGCTATATCCCCGACGG 59.819 66.667 6.99 6.99 0.00 4.79
4753 4884 1.136984 GAGCGCTATATCCCCGACG 59.863 63.158 11.50 0.00 0.00 5.12
4754 4885 1.511768 GGAGCGCTATATCCCCGAC 59.488 63.158 11.50 0.00 0.00 4.79
4755 4886 4.013702 GGAGCGCTATATCCCCGA 57.986 61.111 11.50 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.