Multiple sequence alignment - TraesCS3D01G413200

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 TraesCS3D01G413200 chr3D 100.000 8258 0 0 1 8258 525723639 525731896 0.000000e+00 15250
1 TraesCS3D01G413200 chr3D 95.062 81 2 1 2885 2963 105260760 105260680 8.700000e-25 126
2 TraesCS3D01G413200 chr3D 91.398 93 2 4 2883 2969 112712670 112712762 1.130000e-23 122
3 TraesCS3D01G413200 chr3B 95.665 4521 143 21 251 4741 694018779 694023276 0.000000e+00 7214
4 TraesCS3D01G413200 chr3B 96.932 1760 40 4 4998 6757 694023274 694025019 0.000000e+00 2939
5 TraesCS3D01G413200 chr3B 92.330 691 38 12 7049 7726 694025511 694026199 0.000000e+00 968
6 TraesCS3D01G413200 chr3B 89.535 430 21 5 7725 8135 694026407 694026831 2.640000e-144 523
7 TraesCS3D01G413200 chr3B 94.855 311 7 1 6753 7054 694025130 694025440 2.090000e-130 477
8 TraesCS3D01G413200 chr3B 92.655 177 13 0 17 193 694018601 694018777 1.060000e-63 255
9 TraesCS3D01G413200 chr3B 97.619 126 3 0 8133 8258 694026867 694026992 5.020000e-52 217
10 TraesCS3D01G413200 chr3A 92.378 2834 116 33 4863 7680 659937833 659940582 0.000000e+00 3945
11 TraesCS3D01G413200 chr3A 93.484 2394 95 15 530 2889 659933761 659936127 0.000000e+00 3500
12 TraesCS3D01G413200 chr3A 93.163 1726 83 18 2964 4681 659936126 659937824 0.000000e+00 2501
13 TraesCS3D01G413200 chr3A 92.493 373 26 2 17 387 659929526 659929898 4.390000e-147 532
14 TraesCS3D01G413200 chr3A 84.296 433 18 16 7726 8135 659940663 659941068 2.180000e-100 377
15 TraesCS3D01G413200 chr3A 97.638 127 3 0 8132 8258 659941103 659941229 1.400000e-52 219
16 TraesCS3D01G413200 chr1D 95.122 82 3 1 2886 2966 479730247 479730166 2.420000e-25 128
17 TraesCS3D01G413200 chr1D 91.954 87 3 2 2888 2970 476449370 476449456 1.460000e-22 119
18 TraesCS3D01G413200 chr5D 93.023 86 4 1 2885 2968 389245501 389245416 3.130000e-24 124
19 TraesCS3D01G413200 chr4B 94.937 79 4 0 2888 2966 172508806 172508728 3.130000e-24 124
20 TraesCS3D01G413200 chrUn 90.217 92 8 1 2888 2979 65136769 65136679 1.460000e-22 119
21 TraesCS3D01G413200 chr1B 89.474 95 9 1 2886 2979 327481295 327481201 1.460000e-22 119


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 TraesCS3D01G413200 chr3D 525723639 525731896 8257 False 15250.000000 15250 100.000000 1 8258 1 chr3D.!!$F2 8257
1 TraesCS3D01G413200 chr3B 694018601 694026992 8391 False 1799.000000 7214 94.227286 17 8258 7 chr3B.!!$F1 8241
2 TraesCS3D01G413200 chr3A 659929526 659941229 11703 False 1845.666667 3945 92.242000 17 8258 6 chr3A.!!$F1 8241

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
346 349 0.177604 ACCCCGTCGTTTTGTGTACA 59.822 50.000 0.0 0.0 0.00 2.90 F
600 4338 0.667792 GCAGTCGCCGAGAAGAAACT 60.668 55.000 0.0 0.0 0.00 2.66 F
2203 5988 0.833949 TCCGCATATACCAGCAACCA 59.166 50.000 0.0 0.0 0.00 3.67 F
3142 6929 1.069022 GCAATCGCTTCTTTGTCTGCA 60.069 47.619 0.0 0.0 34.30 4.41 F
4823 8624 0.033504 CACAGCCGTGTCTGGTTAGT 59.966 55.000 0.0 0.0 38.41 2.24 F
4865 8666 0.034574 TCAGGCACACAACACCAACT 60.035 50.000 0.0 0.0 0.00 3.16 F
6205 10014 0.112995 TCCATCTTTGCTTGCCCAGT 59.887 50.000 0.0 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1335 5102 0.238817 TCAACGTAAATTGGTGGCGC 59.761 50.000 0.00 0.0 0.00 6.53 R
2267 6052 0.664761 ATGCATTCCGAAGCATTCCG 59.335 50.000 10.48 0.0 43.81 4.30 R
3303 7092 0.392998 ATGAGCTGGTAGCCAAACCG 60.393 55.000 0.00 0.0 43.77 4.44 R
4846 8647 0.034574 AGTTGGTGTTGTGTGCCTGA 60.035 50.000 0.00 0.0 0.00 3.86 R
6205 10014 0.394762 AGGTAGTCGGCGTGTATGGA 60.395 55.000 6.85 0.0 0.00 3.41 R
6607 10418 1.133668 ACCTTCAGCTTGGAGCAGTTT 60.134 47.619 2.47 0.0 45.56 2.66 R
7741 11996 0.253044 TACCATCTTGAGGCCACAGC 59.747 55.000 5.01 0.0 38.76 4.40 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
48 49 2.043953 GATTCCCCCGCCAAGCTT 60.044 61.111 0.00 0.00 0.00 3.74
56 57 1.084370 CCCGCCAAGCTTTAGAGACG 61.084 60.000 0.00 0.00 0.00 4.18
72 73 4.272100 CGATTTCGTGGACCGGTT 57.728 55.556 9.42 0.00 37.11 4.44
94 95 1.216710 GCACTCCAGCGCTCTAGTT 59.783 57.895 16.55 2.58 0.00 2.24
169 170 3.548770 CTCTGGAAGCATAGAAATGGCA 58.451 45.455 0.00 0.00 33.38 4.92
185 186 0.248784 GGCAGCATTTTCGATGGCTC 60.249 55.000 0.00 0.00 43.81 4.70
209 210 1.276421 CCTCTCCGTCAACCAACTCAT 59.724 52.381 0.00 0.00 0.00 2.90
210 211 2.496070 CCTCTCCGTCAACCAACTCATA 59.504 50.000 0.00 0.00 0.00 2.15
218 219 5.171476 CGTCAACCAACTCATAGAGACAAT 58.829 41.667 0.31 0.00 33.32 2.71
301 304 6.992715 GGCATAGGCTGATTTAGTTTTCTAGA 59.007 38.462 0.00 0.00 40.87 2.43
321 324 5.753721 AGAGTTGAGCAGTCCTATTCTTT 57.246 39.130 0.00 0.00 0.00 2.52
325 328 6.174049 AGTTGAGCAGTCCTATTCTTTTACC 58.826 40.000 0.00 0.00 0.00 2.85
329 332 3.869832 GCAGTCCTATTCTTTTACCGACC 59.130 47.826 0.00 0.00 0.00 4.79
346 349 0.177604 ACCCCGTCGTTTTGTGTACA 59.822 50.000 0.00 0.00 0.00 2.90
351 354 4.178540 CCCGTCGTTTTGTGTACATATCT 58.821 43.478 0.00 0.00 0.00 1.98
383 2290 5.940470 ACACATTGACCTTGTATTTCTCTCC 59.060 40.000 0.00 0.00 0.00 3.71
421 2328 5.470777 TGGTACGCAAGCTTTACTTATTTGT 59.529 36.000 0.00 0.00 45.62 2.83
427 2334 6.088085 CGCAAGCTTTACTTATTTGTGGAAAG 59.912 38.462 0.00 0.00 36.04 2.62
430 2337 9.185192 CAAGCTTTACTTATTTGTGGAAAGAAG 57.815 33.333 0.00 0.00 43.26 2.85
463 2370 1.142748 CGGTGCCAACTGCCAAAAA 59.857 52.632 0.00 0.00 40.16 1.94
494 2401 4.026744 AGAAAGTAGTGAGCTGAGCCATA 58.973 43.478 0.00 0.00 0.00 2.74
506 2413 1.281577 TGAGCCATATCTGCACACCAA 59.718 47.619 0.00 0.00 0.00 3.67
598 4336 4.261888 GCAGTCGCCGAGAAGAAA 57.738 55.556 0.00 0.00 0.00 2.52
599 4337 1.782181 GCAGTCGCCGAGAAGAAAC 59.218 57.895 0.00 0.00 0.00 2.78
600 4338 0.667792 GCAGTCGCCGAGAAGAAACT 60.668 55.000 0.00 0.00 0.00 2.66
601 4339 1.341606 CAGTCGCCGAGAAGAAACTC 58.658 55.000 0.00 0.00 0.00 3.01
737 4488 2.040606 TGGGAGGGTAGAGGCACC 59.959 66.667 0.00 0.00 37.91 5.01
1102 4864 1.662446 CGTTGGCCTGCTTTGCTTG 60.662 57.895 3.32 0.00 0.00 4.01
1157 4919 3.389662 CACCATTTTGGCCCCGGG 61.390 66.667 15.80 15.80 42.67 5.73
1357 5126 3.168193 CGCCACCAATTTACGTTGAATC 58.832 45.455 0.00 0.00 0.00 2.52
1628 5397 4.504514 GCCATCTGCTTCCTATGAGAATGA 60.505 45.833 0.00 0.00 36.87 2.57
1665 5434 2.029020 CAGAGTCACCGGATTTCTGTCA 60.029 50.000 9.46 0.00 35.02 3.58
1814 5583 2.828520 ACGATGATTGGAGAGGCGATAT 59.171 45.455 0.00 0.00 0.00 1.63
1966 5735 5.184287 TCGTTGAGTCAAGTACATGGTATCA 59.816 40.000 5.62 0.00 0.00 2.15
1989 5758 6.209986 TCAAGCAATCCAGTTCATTTTCATCT 59.790 34.615 0.00 0.00 0.00 2.90
2143 5928 6.139048 TCTTTTAACCTTTGTTTCTTCCCG 57.861 37.500 0.00 0.00 35.87 5.14
2203 5988 0.833949 TCCGCATATACCAGCAACCA 59.166 50.000 0.00 0.00 0.00 3.67
2251 6036 6.431234 AGTTCTAAAGTTGCTGATGGTTTAGG 59.569 38.462 0.00 0.00 33.41 2.69
2267 6052 7.275888 TGGTTTAGGTCATGATGCAAATATC 57.724 36.000 0.00 0.00 0.00 1.63
2390 6175 6.322201 GGCCATCTTTTCTTGATTCTATTGGA 59.678 38.462 0.00 0.00 0.00 3.53
2447 6232 3.520569 TGAACCTTCAAAAGCAAGCAAC 58.479 40.909 0.00 0.00 33.55 4.17
2518 6303 2.126467 CCAACAATCCACGCAAAACAG 58.874 47.619 0.00 0.00 0.00 3.16
2589 6374 1.202927 AGGGGCCATATGACAATTCCG 60.203 52.381 4.39 0.00 0.00 4.30
2820 6607 7.986889 TGACAGCAAGCATAATATGAAGAGTAA 59.013 33.333 4.14 0.00 0.00 2.24
2921 6708 7.288672 CGTCCCATAATATAAGAGCGTTTTTC 58.711 38.462 0.00 0.00 0.00 2.29
2933 6720 3.006940 AGCGTTTTTCACACTTGTCAGA 58.993 40.909 0.00 0.00 0.00 3.27
2942 6729 4.832248 TCACACTTGTCAGAAACACTCTT 58.168 39.130 0.00 0.00 37.70 2.85
3009 6796 7.703328 AGTTGTGACTAAATTAACTGTTGGTG 58.297 34.615 2.69 0.00 33.32 4.17
3054 6841 2.434336 AGAGGTTGCACCGCAGATTATA 59.566 45.455 10.59 0.00 44.90 0.98
3142 6929 1.069022 GCAATCGCTTCTTTGTCTGCA 60.069 47.619 0.00 0.00 34.30 4.41
3210 6998 8.783093 CAGATTTCTAACCAACACACTCATAAA 58.217 33.333 0.00 0.00 0.00 1.40
3303 7092 3.672808 ACATAATGCTCATAGCTGCTCC 58.327 45.455 4.91 0.00 42.97 4.70
3323 7112 1.383523 GGTTTGGCTACCAGCTCATC 58.616 55.000 4.76 0.00 41.99 2.92
3463 7252 5.518848 TGTGCATGTTCACAGAATTTTCT 57.481 34.783 2.41 0.00 41.57 2.52
3681 7477 1.738099 CGAGTTTCGCTGTCCCAGG 60.738 63.158 0.00 0.00 31.14 4.45
3682 7478 1.671742 GAGTTTCGCTGTCCCAGGA 59.328 57.895 0.00 0.00 31.21 3.86
3683 7479 0.390472 GAGTTTCGCTGTCCCAGGAG 60.390 60.000 0.00 0.00 31.21 3.69
3685 7481 0.250338 GTTTCGCTGTCCCAGGAGTT 60.250 55.000 0.00 0.00 31.21 3.01
3687 7483 0.832135 TTCGCTGTCCCAGGAGTTCT 60.832 55.000 0.00 0.00 31.21 3.01
3688 7484 1.079543 CGCTGTCCCAGGAGTTCTG 60.080 63.158 0.00 0.00 43.00 3.02
3690 7486 1.298014 CTGTCCCAGGAGTTCTGCC 59.702 63.158 0.00 0.00 42.05 4.85
3691 7487 1.152030 TGTCCCAGGAGTTCTGCCT 60.152 57.895 0.00 0.00 42.05 4.75
3692 7488 0.768221 TGTCCCAGGAGTTCTGCCTT 60.768 55.000 0.00 0.00 42.05 4.35
3693 7489 0.322008 GTCCCAGGAGTTCTGCCTTG 60.322 60.000 0.00 0.00 42.05 3.61
3694 7490 0.768221 TCCCAGGAGTTCTGCCTTGT 60.768 55.000 0.00 0.00 42.05 3.16
3758 7554 5.499004 AGTGGTTGCCTACTAATTCTCAA 57.501 39.130 0.00 0.00 0.00 3.02
3948 7744 7.434492 AGATCATCAAATTCTTCCATGAATGC 58.566 34.615 0.00 0.00 36.84 3.56
4639 8440 9.467258 AAAATGAGTTGTTTTGAGTATGTGATG 57.533 29.630 0.00 0.00 0.00 3.07
4730 8531 0.168128 GCAGCACGTCACATAAACCC 59.832 55.000 0.00 0.00 0.00 4.11
4738 8539 2.778299 GTCACATAAACCCAGTCTGCA 58.222 47.619 0.00 0.00 0.00 4.41
4739 8540 3.146066 GTCACATAAACCCAGTCTGCAA 58.854 45.455 0.00 0.00 0.00 4.08
4740 8541 3.189287 GTCACATAAACCCAGTCTGCAAG 59.811 47.826 0.00 0.00 0.00 4.01
4741 8542 3.149196 CACATAAACCCAGTCTGCAAGT 58.851 45.455 0.00 0.00 33.76 3.16
4742 8543 3.189287 CACATAAACCCAGTCTGCAAGTC 59.811 47.826 0.00 0.00 33.76 3.01
4743 8544 3.073062 ACATAAACCCAGTCTGCAAGTCT 59.927 43.478 0.00 0.00 30.65 3.24
4744 8545 2.736670 AAACCCAGTCTGCAAGTCTT 57.263 45.000 0.00 0.00 26.98 3.01
4745 8546 1.972872 AACCCAGTCTGCAAGTCTTG 58.027 50.000 8.31 8.31 26.98 3.02
4746 8547 0.109342 ACCCAGTCTGCAAGTCTTGG 59.891 55.000 14.40 0.00 40.05 3.61
4747 8548 0.607489 CCCAGTCTGCAAGTCTTGGG 60.607 60.000 14.40 1.94 41.07 4.12
4748 8549 0.397941 CCAGTCTGCAAGTCTTGGGA 59.602 55.000 14.40 0.00 26.98 4.37
4749 8550 1.004044 CCAGTCTGCAAGTCTTGGGAT 59.996 52.381 14.40 0.00 26.98 3.85
4750 8551 2.553904 CCAGTCTGCAAGTCTTGGGATT 60.554 50.000 14.40 0.00 26.98 3.01
4751 8552 3.152341 CAGTCTGCAAGTCTTGGGATTT 58.848 45.455 14.40 0.00 26.98 2.17
4752 8553 3.057736 CAGTCTGCAAGTCTTGGGATTTG 60.058 47.826 14.40 0.00 40.60 2.32
4753 8554 3.149196 GTCTGCAAGTCTTGGGATTTGA 58.851 45.455 14.40 0.00 40.24 2.69
4754 8555 3.569701 GTCTGCAAGTCTTGGGATTTGAA 59.430 43.478 14.40 0.00 40.24 2.69
4755 8556 3.569701 TCTGCAAGTCTTGGGATTTGAAC 59.430 43.478 14.40 0.00 40.24 3.18
4756 8557 3.565307 TGCAAGTCTTGGGATTTGAACT 58.435 40.909 14.40 0.00 40.24 3.01
4757 8558 3.569701 TGCAAGTCTTGGGATTTGAACTC 59.430 43.478 14.40 0.00 40.24 3.01
4758 8559 3.057245 GCAAGTCTTGGGATTTGAACTCC 60.057 47.826 14.40 0.00 40.24 3.85
4759 8560 4.144297 CAAGTCTTGGGATTTGAACTCCA 58.856 43.478 4.52 0.00 40.24 3.86
4760 8561 4.026356 AGTCTTGGGATTTGAACTCCAG 57.974 45.455 3.91 0.00 34.24 3.86
4761 8562 3.395941 AGTCTTGGGATTTGAACTCCAGT 59.604 43.478 3.91 0.00 34.24 4.00
4762 8563 3.753797 GTCTTGGGATTTGAACTCCAGTC 59.246 47.826 3.91 0.00 34.24 3.51
4763 8564 2.472695 TGGGATTTGAACTCCAGTCG 57.527 50.000 3.91 0.00 34.24 4.18
4764 8565 1.697432 TGGGATTTGAACTCCAGTCGT 59.303 47.619 3.91 0.00 34.24 4.34
4765 8566 2.901192 TGGGATTTGAACTCCAGTCGTA 59.099 45.455 3.91 0.00 34.24 3.43
4766 8567 3.517901 TGGGATTTGAACTCCAGTCGTAT 59.482 43.478 3.91 0.00 34.24 3.06
4767 8568 4.120589 GGGATTTGAACTCCAGTCGTATC 58.879 47.826 3.91 0.00 34.24 2.24
4768 8569 4.120589 GGATTTGAACTCCAGTCGTATCC 58.879 47.826 0.00 0.00 32.72 2.59
4769 8570 4.382685 GGATTTGAACTCCAGTCGTATCCA 60.383 45.833 0.00 0.00 32.72 3.41
4770 8571 3.868757 TTGAACTCCAGTCGTATCCAG 57.131 47.619 0.00 0.00 0.00 3.86
4771 8572 2.100197 TGAACTCCAGTCGTATCCAGG 58.900 52.381 0.00 0.00 0.00 4.45
4772 8573 2.100989 GAACTCCAGTCGTATCCAGGT 58.899 52.381 0.00 0.00 0.00 4.00
4773 8574 2.233305 ACTCCAGTCGTATCCAGGTT 57.767 50.000 0.00 0.00 0.00 3.50
4774 8575 2.100989 ACTCCAGTCGTATCCAGGTTC 58.899 52.381 0.00 0.00 0.00 3.62
4775 8576 2.100197 CTCCAGTCGTATCCAGGTTCA 58.900 52.381 0.00 0.00 0.00 3.18
4776 8577 2.695666 CTCCAGTCGTATCCAGGTTCAT 59.304 50.000 0.00 0.00 0.00 2.57
4777 8578 2.693591 TCCAGTCGTATCCAGGTTCATC 59.306 50.000 0.00 0.00 0.00 2.92
4778 8579 2.430694 CCAGTCGTATCCAGGTTCATCA 59.569 50.000 0.00 0.00 0.00 3.07
4779 8580 3.448686 CAGTCGTATCCAGGTTCATCAC 58.551 50.000 0.00 0.00 0.00 3.06
4780 8581 3.096852 AGTCGTATCCAGGTTCATCACA 58.903 45.455 0.00 0.00 0.00 3.58
4781 8582 3.706594 AGTCGTATCCAGGTTCATCACAT 59.293 43.478 0.00 0.00 0.00 3.21
4782 8583 4.051922 GTCGTATCCAGGTTCATCACATC 58.948 47.826 0.00 0.00 0.00 3.06
4783 8584 3.960755 TCGTATCCAGGTTCATCACATCT 59.039 43.478 0.00 0.00 0.00 2.90
4784 8585 4.405680 TCGTATCCAGGTTCATCACATCTT 59.594 41.667 0.00 0.00 0.00 2.40
4785 8586 5.596772 TCGTATCCAGGTTCATCACATCTTA 59.403 40.000 0.00 0.00 0.00 2.10
4786 8587 5.923114 CGTATCCAGGTTCATCACATCTTAG 59.077 44.000 0.00 0.00 0.00 2.18
4787 8588 5.965033 ATCCAGGTTCATCACATCTTAGT 57.035 39.130 0.00 0.00 0.00 2.24
4788 8589 7.255486 CGTATCCAGGTTCATCACATCTTAGTA 60.255 40.741 0.00 0.00 0.00 1.82
4789 8590 7.623999 ATCCAGGTTCATCACATCTTAGTAT 57.376 36.000 0.00 0.00 0.00 2.12
4790 8591 7.055667 TCCAGGTTCATCACATCTTAGTATC 57.944 40.000 0.00 0.00 0.00 2.24
4791 8592 6.841229 TCCAGGTTCATCACATCTTAGTATCT 59.159 38.462 0.00 0.00 0.00 1.98
4792 8593 7.345653 TCCAGGTTCATCACATCTTAGTATCTT 59.654 37.037 0.00 0.00 0.00 2.40
4793 8594 8.642432 CCAGGTTCATCACATCTTAGTATCTTA 58.358 37.037 0.00 0.00 0.00 2.10
4794 8595 9.469807 CAGGTTCATCACATCTTAGTATCTTAC 57.530 37.037 0.00 0.00 0.00 2.34
4795 8596 9.427821 AGGTTCATCACATCTTAGTATCTTACT 57.572 33.333 0.00 0.00 42.68 2.24
4802 8603 9.610705 TCACATCTTAGTATCTTACTAACGAGT 57.389 33.333 3.59 0.00 44.05 4.18
4803 8604 9.653067 CACATCTTAGTATCTTACTAACGAGTG 57.347 37.037 3.59 7.87 44.05 3.51
4804 8605 8.344098 ACATCTTAGTATCTTACTAACGAGTGC 58.656 37.037 3.59 0.00 44.05 4.40
4805 8606 7.854557 TCTTAGTATCTTACTAACGAGTGCA 57.145 36.000 3.59 0.00 44.05 4.57
4806 8607 7.692088 TCTTAGTATCTTACTAACGAGTGCAC 58.308 38.462 9.40 9.40 44.05 4.57
4807 8608 5.892160 AGTATCTTACTAACGAGTGCACA 57.108 39.130 21.04 0.00 37.23 4.57
4808 8609 5.881447 AGTATCTTACTAACGAGTGCACAG 58.119 41.667 21.04 15.01 37.23 3.66
4809 8610 2.942710 TCTTACTAACGAGTGCACAGC 58.057 47.619 21.04 9.69 36.28 4.40
4810 8611 1.993370 CTTACTAACGAGTGCACAGCC 59.007 52.381 21.04 6.73 36.28 4.85
4811 8612 0.109458 TACTAACGAGTGCACAGCCG 60.109 55.000 21.04 20.23 36.28 5.52
4812 8613 1.372997 CTAACGAGTGCACAGCCGT 60.373 57.895 21.04 20.88 36.77 5.68
4813 8614 1.617755 CTAACGAGTGCACAGCCGTG 61.618 60.000 24.90 14.18 46.56 4.94
4814 8615 2.358193 TAACGAGTGCACAGCCGTGT 62.358 55.000 24.90 18.47 45.50 4.49
4815 8616 3.406361 CGAGTGCACAGCCGTGTC 61.406 66.667 21.04 4.70 45.50 3.67
4816 8617 2.029666 GAGTGCACAGCCGTGTCT 59.970 61.111 21.04 1.05 45.50 3.41
4817 8618 2.280389 AGTGCACAGCCGTGTCTG 60.280 61.111 21.04 0.00 45.50 3.51
4818 8619 3.349006 GTGCACAGCCGTGTCTGG 61.349 66.667 13.17 0.00 45.50 3.86
4819 8620 3.860605 TGCACAGCCGTGTCTGGT 61.861 61.111 1.33 0.00 45.50 4.00
4820 8621 2.591715 GCACAGCCGTGTCTGGTT 60.592 61.111 1.33 0.00 45.50 3.67
4821 8622 1.301401 GCACAGCCGTGTCTGGTTA 60.301 57.895 1.33 0.00 45.50 2.85
4822 8623 1.291877 GCACAGCCGTGTCTGGTTAG 61.292 60.000 1.33 0.00 45.50 2.34
4823 8624 0.033504 CACAGCCGTGTCTGGTTAGT 59.966 55.000 0.00 0.00 38.41 2.24
4824 8625 0.756903 ACAGCCGTGTCTGGTTAGTT 59.243 50.000 0.00 0.00 38.36 2.24
4825 8626 1.148310 CAGCCGTGTCTGGTTAGTTG 58.852 55.000 0.00 0.00 0.00 3.16
4826 8627 0.602905 AGCCGTGTCTGGTTAGTTGC 60.603 55.000 0.00 0.00 0.00 4.17
4827 8628 1.897398 GCCGTGTCTGGTTAGTTGCG 61.897 60.000 0.00 0.00 0.00 4.85
4828 8629 1.491563 CGTGTCTGGTTAGTTGCGC 59.508 57.895 0.00 0.00 0.00 6.09
4829 8630 1.218875 CGTGTCTGGTTAGTTGCGCA 61.219 55.000 5.66 5.66 0.00 6.09
4830 8631 0.941542 GTGTCTGGTTAGTTGCGCAA 59.058 50.000 21.02 21.02 0.00 4.85
4831 8632 0.941542 TGTCTGGTTAGTTGCGCAAC 59.058 50.000 39.29 39.29 41.45 4.17
4854 8655 2.857186 TTTCTAGCATGTCAGGCACA 57.143 45.000 12.67 0.00 40.18 4.57
4855 8656 2.099141 TTCTAGCATGTCAGGCACAC 57.901 50.000 12.67 0.00 38.04 3.82
4856 8657 0.975887 TCTAGCATGTCAGGCACACA 59.024 50.000 12.67 0.00 38.04 3.72
4857 8658 1.347378 TCTAGCATGTCAGGCACACAA 59.653 47.619 12.67 0.00 38.04 3.33
4858 8659 1.466167 CTAGCATGTCAGGCACACAAC 59.534 52.381 12.67 0.00 38.04 3.32
4859 8660 0.466007 AGCATGTCAGGCACACAACA 60.466 50.000 12.67 0.00 38.04 3.33
4860 8661 0.318107 GCATGTCAGGCACACAACAC 60.318 55.000 4.24 0.00 38.04 3.32
4861 8662 0.311790 CATGTCAGGCACACAACACC 59.688 55.000 0.00 0.00 38.04 4.16
4862 8663 0.106769 ATGTCAGGCACACAACACCA 60.107 50.000 0.00 0.00 38.04 4.17
4863 8664 0.322906 TGTCAGGCACACAACACCAA 60.323 50.000 0.00 0.00 0.00 3.67
4864 8665 0.100503 GTCAGGCACACAACACCAAC 59.899 55.000 0.00 0.00 0.00 3.77
4865 8666 0.034574 TCAGGCACACAACACCAACT 60.035 50.000 0.00 0.00 0.00 3.16
4866 8667 0.381801 CAGGCACACAACACCAACTC 59.618 55.000 0.00 0.00 0.00 3.01
4867 8668 0.751643 AGGCACACAACACCAACTCC 60.752 55.000 0.00 0.00 0.00 3.85
4868 8669 1.355210 GCACACAACACCAACTCCG 59.645 57.895 0.00 0.00 0.00 4.63
4891 8692 5.220951 CGTATGCTATCTGGCCTCAGTATAG 60.221 48.000 3.32 5.28 41.59 1.31
4892 8693 2.828520 TGCTATCTGGCCTCAGTATAGC 59.171 50.000 19.54 19.54 45.06 2.97
4926 8727 8.518151 TTTATGTTCATTGTAGCAATGTTGTG 57.482 30.769 17.83 0.00 0.00 3.33
4938 8739 4.039004 AGCAATGTTGTGTCCAGCATTTAA 59.961 37.500 2.58 0.00 46.44 1.52
4948 8749 4.072131 GTCCAGCATTTAACCAGAGTTGA 58.928 43.478 0.00 0.00 36.68 3.18
4949 8750 4.154918 GTCCAGCATTTAACCAGAGTTGAG 59.845 45.833 0.00 0.00 36.68 3.02
4951 8752 3.755378 CAGCATTTAACCAGAGTTGAGCT 59.245 43.478 0.00 0.00 36.68 4.09
4986 8787 2.154462 CAAGGTGCAGAACTGGGTAAG 58.846 52.381 3.99 0.00 0.00 2.34
5159 8960 7.149202 TGGGCATATAGAGTTGGAAATAACT 57.851 36.000 0.00 0.00 43.24 2.24
5160 8961 8.270137 TGGGCATATAGAGTTGGAAATAACTA 57.730 34.615 0.00 0.00 40.78 2.24
5161 8962 8.719596 TGGGCATATAGAGTTGGAAATAACTAA 58.280 33.333 0.00 0.00 40.78 2.24
5162 8963 9.000486 GGGCATATAGAGTTGGAAATAACTAAC 58.000 37.037 0.00 0.00 40.78 2.34
5661 9464 8.737168 TGAGAATCATATGTTAACTTCCCAAG 57.263 34.615 7.22 0.00 42.56 3.61
5776 9585 4.502282 CGTCAGCATCTTCAATCTACTGTC 59.498 45.833 0.00 0.00 0.00 3.51
5834 9643 8.615878 TTTAGTTTAGCACATACAGACAACAT 57.384 30.769 0.00 0.00 0.00 2.71
5858 9667 5.239963 TGTTTTCCACTAAACTTTCCGATCC 59.760 40.000 0.00 0.00 38.52 3.36
5865 9674 3.502123 AAACTTTCCGATCCTGGTCAA 57.498 42.857 0.00 0.00 0.00 3.18
5995 9804 5.009811 GGAATAAGACAGGTAGCGTGTAGAT 59.990 44.000 0.00 0.00 32.46 1.98
6041 9850 5.417580 TGCCACCATTTGACTTTTAGTATCC 59.582 40.000 0.00 0.00 0.00 2.59
6042 9851 5.417580 GCCACCATTTGACTTTTAGTATCCA 59.582 40.000 0.00 0.00 0.00 3.41
6133 9942 7.702348 GGTAAATGTCATAGAAAAACCATCAGC 59.298 37.037 0.00 0.00 0.00 4.26
6205 10014 0.112995 TCCATCTTTGCTTGCCCAGT 59.887 50.000 0.00 0.00 0.00 4.00
6446 10255 4.261825 CCTTGATGTCGGAGGTAATCTCTC 60.262 50.000 0.00 0.00 42.10 3.20
6458 10268 5.516984 AGGTAATCTCTCGAGTTTTAGGGA 58.483 41.667 13.13 0.00 0.00 4.20
6464 10274 6.696441 TCTCTCGAGTTTTAGGGATACTTC 57.304 41.667 13.13 0.00 0.00 3.01
6483 10293 4.758674 ACTTCCTCACATCAATGAGTTGTG 59.241 41.667 9.95 9.95 43.99 3.33
6484 10294 4.356405 TCCTCACATCAATGAGTTGTGT 57.644 40.909 14.38 0.00 44.54 3.72
6607 10418 2.757314 AGCACTGAGAATCGAGTCATCA 59.243 45.455 16.10 13.76 38.61 3.07
6665 10476 8.603181 GCACATTTGTTTCAGTTAATTTTGTCT 58.397 29.630 0.00 0.00 0.00 3.41
6685 10496 3.910627 TCTAGGGCTTTTCTTCCTGAACT 59.089 43.478 0.00 0.00 33.88 3.01
7134 11148 2.939103 GCGTTACATCCAGAAATGCTCT 59.061 45.455 0.00 0.00 33.37 4.09
7224 11240 2.717639 TAATGAAGCTCTTCCCTGGC 57.282 50.000 7.12 0.00 38.77 4.85
7251 11267 3.022287 CGTCGCACCAGCAAACTT 58.978 55.556 0.00 0.00 42.27 2.66
7359 11376 6.116126 AGAAGTTGTATAGTGGAGCCATTTC 58.884 40.000 0.00 0.00 0.00 2.17
7483 11500 9.713684 TCATTTCCTCCCATCTTATATTTTGTT 57.286 29.630 0.00 0.00 0.00 2.83
7556 11573 3.243602 ACGGTTGTACCAAAGGCATTTTC 60.244 43.478 0.00 0.00 38.47 2.29
7574 11591 6.538381 GCATTTTCCTTTTCTTTCCAAACTCA 59.462 34.615 0.00 0.00 0.00 3.41
7613 11630 9.941664 CTATTTTCCATGTTAACAGAAGCATAG 57.058 33.333 14.65 15.24 0.00 2.23
7614 11631 7.994425 TTTTCCATGTTAACAGAAGCATAGA 57.006 32.000 14.65 0.00 0.00 1.98
7615 11632 7.994425 TTTCCATGTTAACAGAAGCATAGAA 57.006 32.000 14.65 5.19 0.00 2.10
7616 11633 7.615582 TTCCATGTTAACAGAAGCATAGAAG 57.384 36.000 14.65 0.00 0.00 2.85
7688 11717 5.695851 ACAGATTGAAATGAGTGGACAAC 57.304 39.130 0.00 0.00 0.00 3.32
7706 11751 4.900664 ACAACACACTAAAACGCAACTAC 58.099 39.130 0.00 0.00 0.00 2.73
7720 11765 7.618964 AACGCAACTACATACATACGATTAG 57.381 36.000 0.00 0.00 0.00 1.73
7723 11768 6.523546 CGCAACTACATACATACGATTAGGAG 59.476 42.308 0.00 0.00 0.00 3.69
7740 11995 8.338259 CGATTAGGAGAATTGTAAGTGAATTGG 58.662 37.037 0.00 0.00 0.00 3.16
7741 11996 7.938140 TTAGGAGAATTGTAAGTGAATTGGG 57.062 36.000 0.00 0.00 0.00 4.12
7820 12079 7.113544 GCGGCAGCATATTTTTATTAAGAGAAC 59.886 37.037 3.18 0.00 44.35 3.01
7858 12117 6.813152 AGTCAGTTCAAACAAAATTTGACCAG 59.187 34.615 13.19 0.00 38.05 4.00
7882 12143 5.586643 GCCTAAATTTCAGTCTTCTACAGGG 59.413 44.000 0.00 0.00 0.00 4.45
7909 12170 5.649782 AAAACATGAATAACCTGCTCTGG 57.350 39.130 0.00 0.00 0.00 3.86
7943 12221 1.060937 GTTGCGCGTCTAATGCAGG 59.939 57.895 8.43 0.00 40.15 4.85
7969 12247 1.896220 TGGCAAACAGAAGAAGCGAT 58.104 45.000 0.00 0.00 0.00 4.58
7993 12271 2.432510 AGGCATGCTGGACTACTACTTC 59.567 50.000 18.92 0.00 0.00 3.01
8088 12366 0.247736 GTCCTCGTCTTCAGTGGCAT 59.752 55.000 0.00 0.00 0.00 4.40
8187 12503 2.980233 GAGCTGTGCCGCAAAGGT 60.980 61.111 15.20 15.20 43.70 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.059994 CAACGCGAGAATGAGCAGC 59.940 57.895 15.93 0.00 0.00 5.25
1 2 1.016130 ACCAACGCGAGAATGAGCAG 61.016 55.000 15.93 0.00 0.00 4.24
2 3 1.005037 ACCAACGCGAGAATGAGCA 60.005 52.632 15.93 0.00 0.00 4.26
3 4 1.421485 CACCAACGCGAGAATGAGC 59.579 57.895 15.93 0.00 0.00 4.26
4 5 1.291184 TGCACCAACGCGAGAATGAG 61.291 55.000 15.93 3.89 33.35 2.90
5 6 1.291184 CTGCACCAACGCGAGAATGA 61.291 55.000 15.93 0.00 33.35 2.57
6 7 1.133253 CTGCACCAACGCGAGAATG 59.867 57.895 15.93 6.99 33.35 2.67
7 8 2.034879 CCTGCACCAACGCGAGAAT 61.035 57.895 15.93 0.00 33.35 2.40
8 9 2.664851 CCTGCACCAACGCGAGAA 60.665 61.111 15.93 0.00 33.35 2.87
218 219 4.415332 GACGCGCCTCCTGACGAA 62.415 66.667 5.73 0.00 0.00 3.85
301 304 6.174049 GGTAAAAGAATAGGACTGCTCAACT 58.826 40.000 0.00 0.00 0.00 3.16
329 332 4.178540 AGATATGTACACAAAACGACGGG 58.821 43.478 0.00 0.00 0.00 5.28
346 349 9.383519 CAAGGTCAATGTGTTACACTTAGATAT 57.616 33.333 16.79 0.00 35.11 1.63
351 354 8.911918 AATACAAGGTCAATGTGTTACACTTA 57.088 30.769 16.79 0.00 35.11 2.24
383 2290 4.126437 TGCGTACCATTCATTGATAGGTG 58.874 43.478 16.57 6.11 33.91 4.00
421 2328 1.374947 CTCCGGTGCCTTCTTTCCA 59.625 57.895 0.00 0.00 0.00 3.53
427 2334 1.012486 CGTGTTACTCCGGTGCCTTC 61.012 60.000 0.00 0.00 0.00 3.46
430 2337 2.433664 CCGTGTTACTCCGGTGCC 60.434 66.667 0.00 0.00 39.38 5.01
463 2370 7.275920 TCAGCTCACTACTTTCTTCTTCTTTT 58.724 34.615 0.00 0.00 0.00 2.27
467 2374 4.625311 GCTCAGCTCACTACTTTCTTCTTC 59.375 45.833 0.00 0.00 0.00 2.87
553 4291 1.300388 CGTCAGGTTCGGTTTCGGT 60.300 57.895 0.00 0.00 36.95 4.69
596 4334 2.418609 GCTTTGCTGGTGGTTTGAGTTT 60.419 45.455 0.00 0.00 0.00 2.66
597 4335 1.136891 GCTTTGCTGGTGGTTTGAGTT 59.863 47.619 0.00 0.00 0.00 3.01
598 4336 0.746659 GCTTTGCTGGTGGTTTGAGT 59.253 50.000 0.00 0.00 0.00 3.41
599 4337 0.746063 TGCTTTGCTGGTGGTTTGAG 59.254 50.000 0.00 0.00 0.00 3.02
600 4338 0.746063 CTGCTTTGCTGGTGGTTTGA 59.254 50.000 0.00 0.00 0.00 2.69
601 4339 0.877213 GCTGCTTTGCTGGTGGTTTG 60.877 55.000 0.00 0.00 0.00 2.93
737 4488 3.637432 TCTTATTTTTGGTGCGTGCTTG 58.363 40.909 0.00 0.00 0.00 4.01
859 4612 4.292178 GAGGGGCGAGATCTGGCG 62.292 72.222 21.52 11.16 35.01 5.69
1171 4933 2.159282 GCAGCACATCCAATTTCTCCTG 60.159 50.000 0.00 0.00 0.00 3.86
1319 5086 0.676736 GCGCAGAGGCCTAGATAACT 59.323 55.000 4.42 0.00 36.38 2.24
1335 5102 0.238817 TCAACGTAAATTGGTGGCGC 59.761 50.000 0.00 0.00 0.00 6.53
1343 5112 6.094325 TGCCGAATTAGGATTCAACGTAAATT 59.906 34.615 9.03 0.00 41.43 1.82
1357 5126 3.374058 ACTCAAAATCGTGCCGAATTAGG 59.626 43.478 0.00 0.00 39.99 2.69
1628 5397 1.421646 CTCTGGAAGAAGTGGTTGGGT 59.578 52.381 0.00 0.00 46.34 4.51
1665 5434 3.788227 TCTGCAACTACAGGACCATTT 57.212 42.857 0.00 0.00 38.26 2.32
1773 5542 4.343814 TCGTGATGCCCATTAACTAGATCA 59.656 41.667 0.00 0.00 0.00 2.92
1820 5589 4.407296 CAGGACTGAGCTCTACCCTTTTAT 59.593 45.833 16.19 0.00 0.00 1.40
1852 5621 6.749118 GCACTTAATTTAGATGTCAAAGGCAG 59.251 38.462 0.00 0.00 0.00 4.85
1853 5622 6.208402 TGCACTTAATTTAGATGTCAAAGGCA 59.792 34.615 0.00 0.00 0.00 4.75
1854 5623 6.620678 TGCACTTAATTTAGATGTCAAAGGC 58.379 36.000 0.00 0.00 0.00 4.35
1860 5629 9.638239 TTTCCAAATGCACTTAATTTAGATGTC 57.362 29.630 0.00 0.00 0.00 3.06
1966 5735 6.395629 CAGATGAAAATGAACTGGATTGCTT 58.604 36.000 0.00 0.00 0.00 3.91
1989 5758 3.437642 CTTCCCAAGAAGGTTGCCA 57.562 52.632 0.00 0.00 44.97 4.92
2143 5928 1.537202 CTTTGGAGGTAGCTGCACAAC 59.463 52.381 16.24 0.00 0.00 3.32
2186 5971 1.202639 TCCTGGTTGCTGGTATATGCG 60.203 52.381 0.00 0.00 0.00 4.73
2203 5988 7.299134 ACTACTAAAGATACTGCCATAGTCCT 58.701 38.462 0.00 0.00 40.89 3.85
2237 6022 3.998913 TCATGACCTAAACCATCAGCA 57.001 42.857 0.00 0.00 0.00 4.41
2251 6036 4.855388 GCATTCCGATATTTGCATCATGAC 59.145 41.667 0.00 0.00 35.22 3.06
2267 6052 0.664761 ATGCATTCCGAAGCATTCCG 59.335 50.000 10.48 0.00 43.81 4.30
2390 6175 3.326836 GCTGGAAGAGCTCTTTGTACT 57.673 47.619 29.02 6.75 45.21 2.73
2589 6374 3.636153 AGGCAAGGAATCAGGAAGTAC 57.364 47.619 0.00 0.00 0.00 2.73
2795 6580 6.857777 ACTCTTCATATTATGCTTGCTGTC 57.142 37.500 0.00 0.00 0.00 3.51
2921 6708 6.851222 ATAAGAGTGTTTCTGACAAGTGTG 57.149 37.500 0.00 0.00 40.65 3.82
2933 6720 7.369551 TCCGTCCCATAATATAAGAGTGTTT 57.630 36.000 0.00 0.00 0.00 2.83
2942 6729 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
3009 6796 3.916776 GGTTACGTACAGACAGCAACTAC 59.083 47.826 0.00 0.00 0.00 2.73
3054 6841 6.322201 AGTCTTGACAAACAATCAGTGGAAAT 59.678 34.615 3.49 0.00 37.88 2.17
3142 6929 7.435068 AGTAAACAATTACAAGCGACAGAAT 57.565 32.000 0.00 0.00 43.20 2.40
3210 6998 4.277515 ACTACTGTCACAGCACATCAAT 57.722 40.909 4.13 0.00 34.37 2.57
3303 7092 0.392998 ATGAGCTGGTAGCCAAACCG 60.393 55.000 0.00 0.00 43.77 4.44
3323 7112 4.310769 ACTTCTCTGTTGTCAAATCCTCG 58.689 43.478 0.00 0.00 0.00 4.63
3381 7170 3.126831 CCGTTGCCAAATTTTGTGCTAA 58.873 40.909 17.59 10.83 0.00 3.09
3463 7252 3.295093 TGATTGCAAGAAAACCTCCACA 58.705 40.909 4.94 0.00 0.00 4.17
3552 7341 6.693466 TGTGAAAACATCTCACTATTACGGA 58.307 36.000 4.74 0.00 43.03 4.69
3625 7421 7.676683 AAGTTTACTATGCCCTATCAGAAGA 57.323 36.000 0.00 0.00 0.00 2.87
3681 7477 3.477530 ACCTTAACACAAGGCAGAACTC 58.522 45.455 2.93 0.00 41.10 3.01
3682 7478 3.577805 ACCTTAACACAAGGCAGAACT 57.422 42.857 2.93 0.00 41.10 3.01
3683 7479 5.122396 CAGATACCTTAACACAAGGCAGAAC 59.878 44.000 2.93 0.00 41.10 3.01
3685 7481 4.530553 TCAGATACCTTAACACAAGGCAGA 59.469 41.667 2.93 0.00 41.10 4.26
3687 7483 4.901197 TCAGATACCTTAACACAAGGCA 57.099 40.909 2.93 0.00 41.10 4.75
3688 7484 5.246307 ACTTCAGATACCTTAACACAAGGC 58.754 41.667 2.93 0.00 41.10 4.35
3691 7487 9.841295 AGTTTAACTTCAGATACCTTAACACAA 57.159 29.630 0.00 0.00 0.00 3.33
3694 7490 9.649167 GCTAGTTTAACTTCAGATACCTTAACA 57.351 33.333 1.94 0.00 0.00 2.41
3758 7554 5.674052 ATTGAGCTTCATCACAGAGTAGT 57.326 39.130 0.00 0.00 0.00 2.73
3948 7744 9.586150 GTATTTATTCATGCTTACTGTCATTCG 57.414 33.333 0.00 0.00 0.00 3.34
4028 7829 3.628942 GTGTGCCTGATATTTGCAGATGA 59.371 43.478 0.00 0.00 35.33 2.92
4639 8440 4.523083 TGATTGTTATGAACTACAGGGGC 58.477 43.478 0.00 0.00 0.00 5.80
4699 8500 1.303561 GTGCTGCAGTTGGATGGGA 60.304 57.895 16.64 0.00 0.00 4.37
4730 8531 2.486472 ATCCCAAGACTTGCAGACTG 57.514 50.000 9.85 0.00 0.00 3.51
4738 8539 4.141158 ACTGGAGTTCAAATCCCAAGACTT 60.141 41.667 0.34 0.00 35.86 3.01
4739 8540 3.395941 ACTGGAGTTCAAATCCCAAGACT 59.604 43.478 0.34 0.00 35.86 3.24
4740 8541 3.753797 GACTGGAGTTCAAATCCCAAGAC 59.246 47.826 0.34 0.00 35.86 3.01
4741 8542 3.557054 CGACTGGAGTTCAAATCCCAAGA 60.557 47.826 0.34 0.00 35.86 3.02
4742 8543 2.744202 CGACTGGAGTTCAAATCCCAAG 59.256 50.000 0.34 0.00 35.86 3.61
4743 8544 2.105821 ACGACTGGAGTTCAAATCCCAA 59.894 45.455 0.34 0.00 35.86 4.12
4744 8545 1.697432 ACGACTGGAGTTCAAATCCCA 59.303 47.619 0.34 0.00 35.86 4.37
4745 8546 2.474410 ACGACTGGAGTTCAAATCCC 57.526 50.000 0.34 0.00 35.86 3.85
4746 8547 4.120589 GGATACGACTGGAGTTCAAATCC 58.879 47.826 0.00 0.00 37.35 3.01
4747 8548 4.755411 TGGATACGACTGGAGTTCAAATC 58.245 43.478 0.00 0.00 42.51 2.17
4748 8549 4.383118 CCTGGATACGACTGGAGTTCAAAT 60.383 45.833 0.00 0.00 42.51 2.32
4749 8550 3.056107 CCTGGATACGACTGGAGTTCAAA 60.056 47.826 0.00 0.00 42.51 2.69
4750 8551 2.496070 CCTGGATACGACTGGAGTTCAA 59.504 50.000 0.00 0.00 42.51 2.69
4751 8552 2.100197 CCTGGATACGACTGGAGTTCA 58.900 52.381 0.00 0.00 42.51 3.18
4752 8553 2.100989 ACCTGGATACGACTGGAGTTC 58.899 52.381 0.00 0.00 42.51 3.01
4753 8554 2.233305 ACCTGGATACGACTGGAGTT 57.767 50.000 0.00 0.00 42.51 3.01
4754 8555 2.100989 GAACCTGGATACGACTGGAGT 58.899 52.381 0.00 0.00 42.51 3.85
4755 8556 2.100197 TGAACCTGGATACGACTGGAG 58.900 52.381 0.00 0.00 42.51 3.86
4756 8557 2.225382 TGAACCTGGATACGACTGGA 57.775 50.000 0.00 0.00 42.51 3.86
4757 8558 2.430694 TGATGAACCTGGATACGACTGG 59.569 50.000 0.00 0.00 42.51 4.00
4758 8559 3.119137 TGTGATGAACCTGGATACGACTG 60.119 47.826 0.00 0.00 42.51 3.51
4759 8560 3.096852 TGTGATGAACCTGGATACGACT 58.903 45.455 0.00 0.00 42.51 4.18
4760 8561 3.520290 TGTGATGAACCTGGATACGAC 57.480 47.619 0.00 0.00 42.51 4.34
4761 8562 3.960755 AGATGTGATGAACCTGGATACGA 59.039 43.478 0.00 0.00 42.51 3.43
4762 8563 4.327982 AGATGTGATGAACCTGGATACG 57.672 45.455 0.00 0.00 42.51 3.06
4763 8564 6.821388 ACTAAGATGTGATGAACCTGGATAC 58.179 40.000 0.00 0.00 0.00 2.24
4764 8565 8.727100 ATACTAAGATGTGATGAACCTGGATA 57.273 34.615 0.00 0.00 0.00 2.59
4765 8566 5.965033 ACTAAGATGTGATGAACCTGGAT 57.035 39.130 0.00 0.00 0.00 3.41
4766 8567 6.841229 AGATACTAAGATGTGATGAACCTGGA 59.159 38.462 0.00 0.00 0.00 3.86
4767 8568 7.060383 AGATACTAAGATGTGATGAACCTGG 57.940 40.000 0.00 0.00 0.00 4.45
4768 8569 9.469807 GTAAGATACTAAGATGTGATGAACCTG 57.530 37.037 0.00 0.00 0.00 4.00
4769 8570 9.427821 AGTAAGATACTAAGATGTGATGAACCT 57.572 33.333 0.00 0.00 37.23 3.50
4783 8584 7.381766 TGTGCACTCGTTAGTAAGATACTAA 57.618 36.000 19.41 6.00 46.03 2.24
4784 8585 6.457934 GCTGTGCACTCGTTAGTAAGATACTA 60.458 42.308 19.41 0.00 40.14 1.82
4785 8586 5.676584 GCTGTGCACTCGTTAGTAAGATACT 60.677 44.000 19.41 0.00 42.68 2.12
4786 8587 4.499758 GCTGTGCACTCGTTAGTAAGATAC 59.500 45.833 19.41 0.00 33.48 2.24
4787 8588 4.439700 GGCTGTGCACTCGTTAGTAAGATA 60.440 45.833 19.41 0.00 33.48 1.98
4788 8589 3.512680 GCTGTGCACTCGTTAGTAAGAT 58.487 45.455 19.41 0.00 33.48 2.40
4789 8590 2.352421 GGCTGTGCACTCGTTAGTAAGA 60.352 50.000 19.41 0.00 33.48 2.10
4790 8591 1.993370 GGCTGTGCACTCGTTAGTAAG 59.007 52.381 19.41 4.49 33.48 2.34
4791 8592 1.667756 CGGCTGTGCACTCGTTAGTAA 60.668 52.381 19.41 0.00 33.48 2.24
4792 8593 0.109458 CGGCTGTGCACTCGTTAGTA 60.109 55.000 19.41 0.00 33.48 1.82
4793 8594 1.372997 CGGCTGTGCACTCGTTAGT 60.373 57.895 19.41 0.00 35.91 2.24
4794 8595 1.372997 ACGGCTGTGCACTCGTTAG 60.373 57.895 19.41 7.61 31.38 2.34
4795 8596 1.663388 CACGGCTGTGCACTCGTTA 60.663 57.895 23.14 2.63 39.67 3.18
4796 8597 2.967076 CACGGCTGTGCACTCGTT 60.967 61.111 23.14 11.45 39.67 3.85
4805 8606 0.756903 AACTAACCAGACACGGCTGT 59.243 50.000 0.00 0.00 34.06 4.40
4806 8607 1.148310 CAACTAACCAGACACGGCTG 58.852 55.000 0.00 0.00 35.66 4.85
4807 8608 0.602905 GCAACTAACCAGACACGGCT 60.603 55.000 0.00 0.00 0.00 5.52
4808 8609 1.866925 GCAACTAACCAGACACGGC 59.133 57.895 0.00 0.00 0.00 5.68
4809 8610 1.897398 GCGCAACTAACCAGACACGG 61.897 60.000 0.30 0.00 0.00 4.94
4810 8611 1.218875 TGCGCAACTAACCAGACACG 61.219 55.000 8.16 0.00 0.00 4.49
4811 8612 0.941542 TTGCGCAACTAACCAGACAC 59.058 50.000 21.02 0.00 0.00 3.67
4812 8613 0.941542 GTTGCGCAACTAACCAGACA 59.058 50.000 38.86 5.92 38.25 3.41
4813 8614 3.748021 GTTGCGCAACTAACCAGAC 57.252 52.632 38.86 16.08 38.25 3.51
4833 8634 3.253188 GTGTGCCTGACATGCTAGAAAAA 59.747 43.478 4.30 0.00 36.78 1.94
4834 8635 2.813754 GTGTGCCTGACATGCTAGAAAA 59.186 45.455 4.30 0.00 36.78 2.29
4835 8636 2.224499 TGTGTGCCTGACATGCTAGAAA 60.224 45.455 4.30 0.00 36.78 2.52
4836 8637 1.347378 TGTGTGCCTGACATGCTAGAA 59.653 47.619 4.30 0.00 36.78 2.10
4837 8638 0.975887 TGTGTGCCTGACATGCTAGA 59.024 50.000 4.30 0.00 36.78 2.43
4838 8639 1.466167 GTTGTGTGCCTGACATGCTAG 59.534 52.381 4.30 0.00 36.78 3.42
4839 8640 1.202746 TGTTGTGTGCCTGACATGCTA 60.203 47.619 4.30 0.00 36.78 3.49
4840 8641 0.466007 TGTTGTGTGCCTGACATGCT 60.466 50.000 4.30 0.00 36.78 3.79
4841 8642 0.318107 GTGTTGTGTGCCTGACATGC 60.318 55.000 0.00 0.00 36.78 4.06
4842 8643 0.311790 GGTGTTGTGTGCCTGACATG 59.688 55.000 0.00 0.00 36.78 3.21
4843 8644 0.106769 TGGTGTTGTGTGCCTGACAT 60.107 50.000 0.00 0.00 36.78 3.06
4844 8645 0.322906 TTGGTGTTGTGTGCCTGACA 60.323 50.000 0.00 0.00 0.00 3.58
4845 8646 0.100503 GTTGGTGTTGTGTGCCTGAC 59.899 55.000 0.00 0.00 0.00 3.51
4846 8647 0.034574 AGTTGGTGTTGTGTGCCTGA 60.035 50.000 0.00 0.00 0.00 3.86
4847 8648 0.381801 GAGTTGGTGTTGTGTGCCTG 59.618 55.000 0.00 0.00 0.00 4.85
4848 8649 0.751643 GGAGTTGGTGTTGTGTGCCT 60.752 55.000 0.00 0.00 0.00 4.75
4849 8650 1.733526 GGAGTTGGTGTTGTGTGCC 59.266 57.895 0.00 0.00 0.00 5.01
4850 8651 1.355210 CGGAGTTGGTGTTGTGTGC 59.645 57.895 0.00 0.00 0.00 4.57
4851 8652 1.942677 TACGGAGTTGGTGTTGTGTG 58.057 50.000 0.00 0.00 37.78 3.82
4852 8653 2.489971 CATACGGAGTTGGTGTTGTGT 58.510 47.619 0.00 0.00 37.78 3.72
4853 8654 1.196808 GCATACGGAGTTGGTGTTGTG 59.803 52.381 0.00 0.00 37.78 3.33
4854 8655 1.071699 AGCATACGGAGTTGGTGTTGT 59.928 47.619 0.00 0.00 37.78 3.32
4855 8656 1.808411 AGCATACGGAGTTGGTGTTG 58.192 50.000 0.00 0.00 37.78 3.33
4856 8657 3.451178 AGATAGCATACGGAGTTGGTGTT 59.549 43.478 0.00 0.00 37.78 3.32
4857 8658 3.031736 AGATAGCATACGGAGTTGGTGT 58.968 45.455 0.00 0.00 37.78 4.16
4858 8659 3.384668 CAGATAGCATACGGAGTTGGTG 58.615 50.000 0.00 0.00 37.78 4.17
4859 8660 2.365617 CCAGATAGCATACGGAGTTGGT 59.634 50.000 0.00 0.00 37.78 3.67
4860 8661 2.868044 GCCAGATAGCATACGGAGTTGG 60.868 54.545 0.00 0.00 37.78 3.77
4861 8662 2.408050 GCCAGATAGCATACGGAGTTG 58.592 52.381 0.00 0.00 37.78 3.16
4862 8663 1.344763 GGCCAGATAGCATACGGAGTT 59.655 52.381 0.00 0.00 37.78 3.01
4864 8665 1.203523 GAGGCCAGATAGCATACGGAG 59.796 57.143 5.01 0.00 0.00 4.63
4865 8666 1.257743 GAGGCCAGATAGCATACGGA 58.742 55.000 5.01 0.00 0.00 4.69
4866 8667 0.969149 TGAGGCCAGATAGCATACGG 59.031 55.000 5.01 0.00 0.00 4.02
4867 8668 1.615883 ACTGAGGCCAGATAGCATACG 59.384 52.381 5.01 0.00 43.02 3.06
4868 8669 5.451242 GCTATACTGAGGCCAGATAGCATAC 60.451 48.000 23.08 0.00 44.58 2.39
4891 8692 8.850452 GCTACAATGAACATAAAACTAAACAGC 58.150 33.333 0.00 0.00 0.00 4.40
4892 8693 9.891828 TGCTACAATGAACATAAAACTAAACAG 57.108 29.630 0.00 0.00 0.00 3.16
4920 8721 3.291584 TGGTTAAATGCTGGACACAACA 58.708 40.909 0.00 0.00 0.00 3.33
4926 8727 4.072131 TCAACTCTGGTTAAATGCTGGAC 58.928 43.478 0.00 0.00 33.88 4.02
4938 8739 1.210478 ACACAACAGCTCAACTCTGGT 59.790 47.619 0.00 0.00 35.94 4.00
4948 8749 3.494398 CCTTGGTACAGTACACAACAGCT 60.494 47.826 12.89 0.00 42.39 4.24
4949 8750 2.806244 CCTTGGTACAGTACACAACAGC 59.194 50.000 12.89 0.00 42.39 4.40
4951 8752 3.799366 CACCTTGGTACAGTACACAACA 58.201 45.455 12.89 0.00 42.39 3.33
4986 8787 2.048603 GCCATCTTCCTGGTGGTGC 61.049 63.158 3.34 0.00 38.63 5.01
5159 8960 7.562088 AGTTTCAATTAGAGGTTGGGTTTGTTA 59.438 33.333 0.00 0.00 0.00 2.41
5160 8961 6.382859 AGTTTCAATTAGAGGTTGGGTTTGTT 59.617 34.615 0.00 0.00 0.00 2.83
5161 8962 5.897250 AGTTTCAATTAGAGGTTGGGTTTGT 59.103 36.000 0.00 0.00 0.00 2.83
5162 8963 6.405278 AGTTTCAATTAGAGGTTGGGTTTG 57.595 37.500 0.00 0.00 0.00 2.93
5227 9028 7.672240 AGCCTTATAGGAAAGCTATCAAGTAC 58.328 38.462 0.00 0.00 37.67 2.73
5267 9068 2.954989 TGTGGAAAGCAATAGTTGTGCA 59.045 40.909 0.00 0.00 44.74 4.57
5321 9123 2.203451 GGAGGATGCAGCCCATGG 60.203 66.667 19.48 4.14 33.29 3.66
5661 9464 2.429610 TGTCGTTAGCTAGTTCCATCCC 59.570 50.000 0.00 0.00 0.00 3.85
5714 9523 8.464404 ACTAGAAACTTTGCGTCTGTGTATATA 58.536 33.333 0.00 0.00 0.00 0.86
5715 9524 7.321153 ACTAGAAACTTTGCGTCTGTGTATAT 58.679 34.615 0.00 0.00 0.00 0.86
5716 9525 6.684686 ACTAGAAACTTTGCGTCTGTGTATA 58.315 36.000 0.00 0.00 0.00 1.47
5717 9526 5.539048 ACTAGAAACTTTGCGTCTGTGTAT 58.461 37.500 0.00 0.00 0.00 2.29
5718 9527 4.940463 ACTAGAAACTTTGCGTCTGTGTA 58.060 39.130 0.00 0.00 0.00 2.90
5719 9528 3.793559 ACTAGAAACTTTGCGTCTGTGT 58.206 40.909 0.00 0.00 0.00 3.72
5776 9585 3.810310 ATACCTTCTTGAAGAGCCTCG 57.190 47.619 11.53 0.00 0.00 4.63
5834 9643 5.239963 GGATCGGAAAGTTTAGTGGAAAACA 59.760 40.000 2.68 0.00 40.97 2.83
5858 9667 4.461198 AGTGTTTTTCTAGGGTTGACCAG 58.539 43.478 2.12 0.00 43.89 4.00
5865 9674 8.755028 ACAAATTACAAAGTGTTTTTCTAGGGT 58.245 29.630 0.00 0.00 0.00 4.34
5958 9767 6.868339 CCTGTCTTATTCCAAAAACACCAATC 59.132 38.462 0.00 0.00 0.00 2.67
5995 9804 4.502105 ACAATGGCATGTATAGGTCACA 57.498 40.909 0.00 0.00 0.00 3.58
6041 9850 6.583806 GCTTCTTTTCTGTCCAAACATATGTG 59.416 38.462 9.63 0.00 34.13 3.21
6042 9851 6.491403 AGCTTCTTTTCTGTCCAAACATATGT 59.509 34.615 1.41 1.41 34.13 2.29
6133 9942 3.438087 AGTTGATGCATCTCTTTTGTCGG 59.562 43.478 26.32 0.00 0.00 4.79
6205 10014 0.394762 AGGTAGTCGGCGTGTATGGA 60.395 55.000 6.85 0.00 0.00 3.41
6483 10293 5.585820 TCAAGTTAAGGTTGTTTGGGAAC 57.414 39.130 0.00 0.00 36.29 3.62
6484 10294 6.800072 AATCAAGTTAAGGTTGTTTGGGAA 57.200 33.333 0.00 0.00 0.00 3.97
6607 10418 1.133668 ACCTTCAGCTTGGAGCAGTTT 60.134 47.619 2.47 0.00 45.56 2.66
6665 10476 3.650942 TCAGTTCAGGAAGAAAAGCCCTA 59.349 43.478 0.00 0.00 38.13 3.53
6685 10496 6.501805 AGGGTACAGGCATCTTATCAATATCA 59.498 38.462 0.00 0.00 0.00 2.15
7134 11148 6.040247 CAGGCACGTATAGATAAACTGTTCA 58.960 40.000 0.00 0.00 0.00 3.18
7251 11267 5.932303 ACTAAAGCTTCATTTTCGCTAGTGA 59.068 36.000 0.70 0.70 32.90 3.41
7397 11414 5.703592 ACGTTGTATAGCTCCAACATTTTCA 59.296 36.000 18.36 0.00 40.71 2.69
7423 11440 6.821665 GGCTATTCTGTTTACTGTCCAATACA 59.178 38.462 0.00 0.00 36.42 2.29
7483 11500 2.621445 CCACCCCCAACCCATAGCA 61.621 63.158 0.00 0.00 0.00 3.49
7556 11573 9.546428 AAACATATTGAGTTTGGAAAGAAAAGG 57.454 29.630 0.00 0.00 37.76 3.11
7587 11604 9.941664 CTATGCTTCTGTTAACATGGAAAATAG 57.058 33.333 9.13 14.00 0.00 1.73
7616 11633 4.712337 TCAGAACTACTCAAGGATCCTTCC 59.288 45.833 24.67 6.34 42.96 3.46
7683 11712 4.011058 AGTTGCGTTTTAGTGTGTTGTC 57.989 40.909 0.00 0.00 0.00 3.18
7688 11717 6.218025 TGTATGTAGTTGCGTTTTAGTGTG 57.782 37.500 0.00 0.00 0.00 3.82
7698 11743 6.376177 TCCTAATCGTATGTATGTAGTTGCG 58.624 40.000 0.00 0.00 0.00 4.85
7720 11765 4.706962 AGCCCAATTCACTTACAATTCTCC 59.293 41.667 0.00 0.00 0.00 3.71
7723 11768 5.163513 CACAGCCCAATTCACTTACAATTC 58.836 41.667 0.00 0.00 0.00 2.17
7741 11996 0.253044 TACCATCTTGAGGCCACAGC 59.747 55.000 5.01 0.00 38.76 4.40
7858 12117 5.586643 CCCTGTAGAAGACTGAAATTTAGGC 59.413 44.000 0.00 0.00 0.00 3.93
7889 12150 3.019564 GCCAGAGCAGGTTATTCATGTT 58.980 45.455 0.00 0.00 39.53 2.71
7909 12170 3.301642 GCGCAACTCAGTAATCAATTTGC 59.698 43.478 0.30 0.00 35.59 3.68
7993 12271 0.951558 GTGTGCCTACCCACAACAAG 59.048 55.000 0.00 0.00 46.28 3.16
8088 12366 2.025321 GCCTTTATGGAGGAGTTTGGGA 60.025 50.000 0.69 0.00 39.25 4.37
8187 12503 4.398988 CAGCTTGCACATACCAATTTCCTA 59.601 41.667 0.00 0.00 0.00 2.94


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

AutoCloner maintained by Alex Coulton.