Multiple sequence alignment - TraesCS4D01G079200

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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 TraesCS4D01G079200 chr4D 100.000 6373 0 0 1 6373 53236642 53243014 0.000000e+00 11769
1 TraesCS4D01G079200 chr4A 94.916 3226 143 7 905 4109 543740318 543737093 0.000000e+00 5029
2 TraesCS4D01G079200 chr4A 89.373 781 54 14 1 758 543741242 543740468 0.000000e+00 955
3 TraesCS4D01G079200 chr4A 91.105 697 40 5 4108 4798 543737022 543736342 0.000000e+00 924
4 TraesCS4D01G079200 chr4A 95.181 332 14 1 5065 5394 543735972 543735641 2.040000e-144 523
5 TraesCS4D01G079200 chr4A 96.178 314 11 1 6060 6373 543734981 543734669 4.410000e-141 512
6 TraesCS4D01G079200 chr4A 82.765 557 52 16 5471 6010 543735642 543735113 2.090000e-124 457
7 TraesCS4D01G079200 chr4B 94.294 3295 145 18 840 4113 78021942 78025214 0.000000e+00 5003
8 TraesCS4D01G079200 chr4B 92.182 857 45 9 1 836 78021032 78021887 0.000000e+00 1192
9 TraesCS4D01G079200 chr4B 90.249 882 52 18 4826 5694 78026013 78026873 0.000000e+00 1122
10 TraesCS4D01G079200 chr4B 96.058 685 18 3 5691 6373 78027127 78027804 0.000000e+00 1107
11 TraesCS4D01G079200 chr4B 90.725 690 35 11 4120 4798 78025251 78025922 0.000000e+00 893
12 TraesCS4D01G079200 chr1B 84.553 492 41 16 5894 6373 68249192 68249660 7.530000e-124 455
13 TraesCS4D01G079200 chr1A 88.854 323 30 4 6057 6373 48725208 48725530 5.990000e-105 392
14 TraesCS4D01G079200 chr1D 87.774 319 27 5 6067 6373 48458398 48458716 4.700000e-96 363
15 TraesCS4D01G079200 chr2B 75.762 689 89 31 1057 1706 384321228 384321877 6.290000e-70 276


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 TraesCS4D01G079200 chr4D 53236642 53243014 6372 False 11769.0 11769 100.000000 1 6373 1 chr4D.!!$F1 6372
1 TraesCS4D01G079200 chr4A 543734669 543741242 6573 True 1400.0 5029 91.586333 1 6373 6 chr4A.!!$R1 6372
2 TraesCS4D01G079200 chr4B 78021032 78027804 6772 False 1863.4 5003 92.701600 1 6373 5 chr4B.!!$F1 6372
3 TraesCS4D01G079200 chr2B 384321228 384321877 649 False 276.0 276 75.762000 1057 1706 1 chr2B.!!$F1 649

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
707 732 0.248012 TCGCCTCGGCATTTGAGTTA 59.752 50.0 8.87 0.0 42.06 2.24 F
1632 1751 0.030101 GGACGCTGCTAGAGTGCTAG 59.970 60.0 0.00 0.0 45.63 3.42 F
1708 1827 0.818296 GCAGTCAGTATGTCGTCCCT 59.182 55.0 0.00 0.0 37.40 4.20 F
3553 3678 0.613260 TTACTGATGGCGGTCTTGCT 59.387 50.0 0.00 0.0 34.79 3.91 F
4383 4590 0.325296 CCTACCCACAGGACTGCCTA 60.325 60.0 0.00 0.0 44.80 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1801 1920 0.810031 CCGCAATCCCGTCTAACTGG 60.810 60.000 0.00 0.0 0.00 4.00 R
3423 3548 1.121407 CACAGACTCCCTGACACCCA 61.121 60.000 0.00 0.0 45.78 4.51 R
3705 3832 3.537874 GGCGATGACCGGGCTAGT 61.538 66.667 9.82 0.0 39.04 2.57 R
4408 4615 0.039764 AGACCGTGAGATGGGAGACA 59.960 55.000 0.00 0.0 0.00 3.41 R
6236 6916 0.462581 TGCGGCTCACTCATGATTCC 60.463 55.000 0.00 0.0 33.22 3.01 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
93 94 1.094073 CCCTCTGCGGATTTGAGCTG 61.094 60.000 0.00 0.00 33.16 4.24
156 157 2.400399 CACTTGGCTGAAATGTTGCAG 58.600 47.619 0.00 0.00 35.28 4.41
176 177 0.457851 CAGGAAGAGGCGGTAGACAG 59.542 60.000 0.00 0.00 0.00 3.51
290 291 7.280876 ACCGCAGTATTTCCATATATGCTTATG 59.719 37.037 7.24 1.21 32.24 1.90
411 413 4.070716 GCCACCATTTAGAGATGAGATGG 58.929 47.826 0.00 0.00 42.28 3.51
415 417 6.465464 CCACCATTTAGAGATGAGATGGACAT 60.465 42.308 7.61 0.00 39.66 3.06
427 429 8.312564 AGATGAGATGGACATGATGTAACATAG 58.687 37.037 13.14 0.00 31.12 2.23
428 430 7.365497 TGAGATGGACATGATGTAACATAGT 57.635 36.000 13.14 6.16 31.12 2.12
429 431 8.477419 TGAGATGGACATGATGTAACATAGTA 57.523 34.615 13.14 3.16 31.12 1.82
439 450 9.981114 CATGATGTAACATAGTATTGTCCTGTA 57.019 33.333 0.00 0.00 0.00 2.74
456 467 4.471747 TCCTGTAATGTATGTGGCAGGTTA 59.528 41.667 8.05 0.00 42.77 2.85
555 569 6.077322 ACCCATTGATTCTTTCTTCCTCAAA 58.923 36.000 0.00 0.00 30.39 2.69
567 581 8.621286 TCTTTCTTCCTCAAATGTAACAAGAAC 58.379 33.333 0.00 0.00 30.17 3.01
569 583 7.730364 TCTTCCTCAAATGTAACAAGAACTC 57.270 36.000 0.00 0.00 0.00 3.01
611 625 5.494632 AGTTTTGTAGGCAACACTGTAAC 57.505 39.130 0.00 0.00 42.16 2.50
624 638 3.802139 ACACTGTAACGACATGTTGTGAG 59.198 43.478 19.55 16.48 42.01 3.51
707 732 0.248012 TCGCCTCGGCATTTGAGTTA 59.752 50.000 8.87 0.00 42.06 2.24
724 749 3.829948 AGTTAAATCGTCGCGAAAGAGA 58.170 40.909 12.06 8.94 39.99 3.10
788 813 4.226168 AGAAATGGAGTTTCAGGGGTAGAG 59.774 45.833 3.68 0.00 46.97 2.43
792 817 1.555533 GAGTTTCAGGGGTAGAGTGGG 59.444 57.143 0.00 0.00 0.00 4.61
813 841 5.416013 TGGGTAAATATGATTTCGTGCAACA 59.584 36.000 0.00 0.00 35.74 3.33
815 843 6.809196 GGGTAAATATGATTTCGTGCAACAAA 59.191 34.615 0.00 0.00 35.74 2.83
816 844 7.201401 GGGTAAATATGATTTCGTGCAACAAAC 60.201 37.037 0.00 0.00 35.74 2.93
830 858 3.758554 GCAACAAACTGGACATGATACCT 59.241 43.478 0.00 0.00 0.00 3.08
836 864 2.501723 ACTGGACATGATACCTGGTGAC 59.498 50.000 10.23 3.88 0.00 3.67
838 866 3.960755 CTGGACATGATACCTGGTGACTA 59.039 47.826 10.23 0.00 0.00 2.59
850 929 9.614792 GATACCTGGTGACTATACAAAAATTCT 57.385 33.333 10.23 0.00 0.00 2.40
880 959 9.078990 ACCTCTAAACCTAAAAATTTGAAGGAG 57.921 33.333 20.55 10.99 33.16 3.69
882 961 7.590279 TCTAAACCTAAAAATTTGAAGGAGCG 58.410 34.615 20.55 9.47 33.16 5.03
884 963 5.121221 ACCTAAAAATTTGAAGGAGCGTG 57.879 39.130 20.55 0.30 33.16 5.34
890 969 5.358298 AAATTTGAAGGAGCGTGTACTTC 57.642 39.130 5.23 5.23 40.67 3.01
908 987 7.280205 GTGTACTTCTTTTCCAGAGAGAAACAA 59.720 37.037 0.00 0.00 35.53 2.83
912 991 5.940617 TCTTTTCCAGAGAGAAACAATGGA 58.059 37.500 0.00 0.00 38.26 3.41
913 992 6.000219 TCTTTTCCAGAGAGAAACAATGGAG 59.000 40.000 0.00 0.00 40.93 3.86
914 993 3.988976 TCCAGAGAGAAACAATGGAGG 57.011 47.619 0.00 0.00 35.16 4.30
915 994 3.520696 TCCAGAGAGAAACAATGGAGGA 58.479 45.455 0.00 0.00 35.16 3.71
1029 1108 4.168291 CTCCTTGCTCGGCCCCTC 62.168 72.222 0.00 0.00 0.00 4.30
1235 1314 3.535962 GCTCTCCAGCTCCCCTCG 61.536 72.222 0.00 0.00 43.09 4.63
1264 1343 3.286725 TACGACCCCCTCCCCCTT 61.287 66.667 0.00 0.00 0.00 3.95
1267 1346 3.021880 GACCCCCTCCCCCTTTCC 61.022 72.222 0.00 0.00 0.00 3.13
1277 1356 1.758592 CCCCTTTCCACCTCGTCAA 59.241 57.895 0.00 0.00 0.00 3.18
1423 1539 3.600388 AGTGCAGTGTAATTCAGCTACC 58.400 45.455 0.00 0.00 0.00 3.18
1442 1558 6.827762 AGCTACCTCGTCATACTAACTTAACT 59.172 38.462 0.00 0.00 0.00 2.24
1453 1569 8.768397 TCATACTAACTTAACTGGGATGAATGT 58.232 33.333 0.00 0.00 0.00 2.71
1589 1706 1.280746 CTCAAGTTGTGCCGCACTG 59.719 57.895 23.52 13.67 35.11 3.66
1632 1751 0.030101 GGACGCTGCTAGAGTGCTAG 59.970 60.000 0.00 0.00 45.63 3.42
1684 1803 2.533266 TGTGCTCAGGTCTTTCACTC 57.467 50.000 0.00 0.00 0.00 3.51
1708 1827 0.818296 GCAGTCAGTATGTCGTCCCT 59.182 55.000 0.00 0.00 37.40 4.20
1810 1929 1.805945 CGAGCACGGCCAGTTAGAC 60.806 63.158 2.24 0.00 35.72 2.59
1816 1935 1.262640 ACGGCCAGTTAGACGGGATT 61.263 55.000 2.24 0.00 35.32 3.01
1861 1980 1.591594 CGATGGGATAAGCACGCGT 60.592 57.895 5.58 5.58 0.00 6.01
1875 1994 4.785453 GCGTGAGGGCCTCTTGGG 62.785 72.222 32.28 19.30 38.36 4.12
1963 2082 1.672881 GTATGGGATGCACTGCAAGAC 59.327 52.381 8.03 2.99 43.62 3.01
1966 2085 1.589716 GGGATGCACTGCAAGACACC 61.590 60.000 8.03 6.86 43.62 4.16
2092 2211 5.491982 AGTATCATCCTGGTTGTTTCTGTC 58.508 41.667 4.76 0.00 0.00 3.51
2146 2265 1.814429 TCAGGGACCTGGACAAAGAA 58.186 50.000 17.75 0.00 43.75 2.52
2188 2307 1.345415 GTTACAAGGGACGGGTTCAGA 59.655 52.381 0.00 0.00 0.00 3.27
2239 2358 1.127951 GGTGACGTTGTCCATTTAGCG 59.872 52.381 0.00 0.00 0.00 4.26
2473 2592 3.054875 TCACTGAAGGTGGGAATGATGAG 60.055 47.826 0.00 0.00 45.38 2.90
2725 2844 1.153289 ACTGAGCCTTGCCTATGCG 60.153 57.895 0.00 0.00 41.78 4.73
2893 3012 4.658063 ACACCTTGGAATTTAACGATCCA 58.342 39.130 0.00 0.10 41.36 3.41
3087 3212 3.258228 ACAAACAAAAACGGCAGGAAAG 58.742 40.909 0.00 0.00 0.00 2.62
3097 3222 3.335579 ACGGCAGGAAAGTAAGATTGTC 58.664 45.455 0.00 0.00 0.00 3.18
3154 3279 3.764434 TGACTGTTATTCTCGAGCTTCCT 59.236 43.478 7.81 0.00 0.00 3.36
3163 3288 2.430610 CGAGCTTCCTGGAGGAGGG 61.431 68.421 10.38 1.10 46.36 4.30
3269 3394 4.524328 CCCTTGATAAGAAAACTGCCAACT 59.476 41.667 0.00 0.00 0.00 3.16
3319 3444 3.671971 CGAGTGAAGCTCTTAGGACACTG 60.672 52.174 0.00 0.00 41.98 3.66
3423 3548 4.161565 TGGTATTAAAGATCCTGTGCGTCT 59.838 41.667 0.00 0.00 0.00 4.18
3469 3594 3.057548 CGGTCTGCTGGCATTGCA 61.058 61.111 11.39 1.25 38.81 4.08
3553 3678 0.613260 TTACTGATGGCGGTCTTGCT 59.387 50.000 0.00 0.00 34.79 3.91
3650 3775 6.405176 CCATTCCTCTGTTTTATCTTGGCTTC 60.405 42.308 0.00 0.00 0.00 3.86
3684 3811 5.129980 TCCATCTAGTGAATTCTCATGTGCT 59.870 40.000 7.05 0.00 33.05 4.40
3705 3832 5.221561 TGCTAGTCTTGTGCAACTAAAGGTA 60.222 40.000 0.00 0.00 38.04 3.08
3714 3841 2.740904 GCAACTAAAGGTACTAGCCCGG 60.741 54.545 0.00 0.00 38.49 5.73
3717 3844 2.291800 ACTAAAGGTACTAGCCCGGTCA 60.292 50.000 0.00 0.00 38.49 4.02
3748 3875 4.136796 TGATAAGCTTGCACTTGTGAAGT 58.863 39.130 9.86 0.00 44.06 3.01
3880 4007 6.014647 ACTGAGGTAATAACACCACTGAGTA 58.985 40.000 4.20 0.00 41.40 2.59
3894 4021 4.386954 CCACTGAGTAATGCATACATAGCG 59.613 45.833 0.00 0.00 36.94 4.26
3928 4055 8.298140 GTCGTGGCTTATACTATACATTTCTCT 58.702 37.037 0.00 0.00 0.00 3.10
3966 4094 1.969923 TGAAGGGATGTTTGGCTTTGG 59.030 47.619 0.00 0.00 0.00 3.28
4083 4212 4.761739 TGCTGGTGAATCTAGAAACCAAAG 59.238 41.667 19.94 13.38 41.98 2.77
4114 4315 1.822425 TCTGGTTCCTGGGTTGGTAA 58.178 50.000 0.00 0.00 0.00 2.85
4138 4339 5.930135 AGCCTTCTCTAAGTTTTTGACAGA 58.070 37.500 0.00 0.00 0.00 3.41
4149 4350 4.162131 AGTTTTTGACAGACATTTGCCCTT 59.838 37.500 0.00 0.00 0.00 3.95
4156 4363 5.009610 TGACAGACATTTGCCCTTTAAGTTC 59.990 40.000 0.00 0.00 0.00 3.01
4164 4371 8.306761 ACATTTGCCCTTTAAGTTCATCTTAAG 58.693 33.333 0.00 0.00 45.54 1.85
4168 4375 6.093404 GCCCTTTAAGTTCATCTTAAGTTGC 58.907 40.000 8.43 0.00 45.54 4.17
4169 4376 6.071896 GCCCTTTAAGTTCATCTTAAGTTGCT 60.072 38.462 8.43 0.00 45.54 3.91
4347 4554 2.096248 CTAGTCAACTTCTCCTCCGCT 58.904 52.381 0.00 0.00 0.00 5.52
4363 4570 3.788937 TCCGCTTGCTTTACAGGTATAC 58.211 45.455 0.00 0.00 0.00 1.47
4369 4576 5.608449 CTTGCTTTACAGGTATACCCTACC 58.392 45.833 18.65 0.00 43.86 3.18
4370 4577 3.969312 TGCTTTACAGGTATACCCTACCC 59.031 47.826 18.65 2.41 43.86 3.69
4371 4578 3.969312 GCTTTACAGGTATACCCTACCCA 59.031 47.826 18.65 0.00 43.86 4.51
4372 4579 4.202295 GCTTTACAGGTATACCCTACCCAC 60.202 50.000 18.65 0.44 43.86 4.61
4373 4580 4.623510 TTACAGGTATACCCTACCCACA 57.376 45.455 18.65 0.00 43.86 4.17
4374 4581 3.042059 ACAGGTATACCCTACCCACAG 57.958 52.381 18.65 0.67 43.86 3.66
4375 4582 2.326428 CAGGTATACCCTACCCACAGG 58.674 57.143 18.65 0.00 43.86 4.00
4376 4583 2.090943 CAGGTATACCCTACCCACAGGA 60.091 54.545 18.65 0.00 43.86 3.86
4377 4584 2.090887 AGGTATACCCTACCCACAGGAC 60.091 54.545 18.65 0.00 43.87 3.85
4378 4585 2.090887 GGTATACCCTACCCACAGGACT 60.091 54.545 11.17 0.00 38.00 3.85
4379 4586 2.176247 ATACCCTACCCACAGGACTG 57.824 55.000 0.00 0.00 38.00 3.51
4380 4587 0.616679 TACCCTACCCACAGGACTGC 60.617 60.000 0.00 0.00 38.00 4.40
4381 4588 2.670148 CCCTACCCACAGGACTGCC 61.670 68.421 0.00 0.00 38.00 4.85
4383 4590 0.325296 CCTACCCACAGGACTGCCTA 60.325 60.000 0.00 0.00 44.80 3.93
4384 4591 0.824759 CTACCCACAGGACTGCCTAC 59.175 60.000 0.00 0.00 44.80 3.18
4432 4639 3.201487 TCTCCCATCTCACGGTCTACTAA 59.799 47.826 0.00 0.00 0.00 2.24
4480 4692 1.269051 GCCGTTCAACTTCTTTGGGTG 60.269 52.381 0.00 0.00 35.69 4.61
4558 4770 2.206576 ACTTGATGGAGAAAGCACCC 57.793 50.000 0.00 0.00 0.00 4.61
4645 4857 2.936498 CCAATTCACCGTCATCTGGTAC 59.064 50.000 0.00 0.00 37.72 3.34
4750 4962 1.476891 GTCTTCTGCCAGGTATGTCGA 59.523 52.381 0.00 0.00 0.00 4.20
4753 4965 0.817654 TCTGCCAGGTATGTCGACTG 59.182 55.000 17.92 5.93 0.00 3.51
4759 4971 2.617308 CCAGGTATGTCGACTGTCGTAT 59.383 50.000 27.16 22.96 41.35 3.06
4763 4975 6.078479 CAGGTATGTCGACTGTCGTATAATC 58.922 44.000 27.16 19.40 41.35 1.75
4764 4976 5.078084 GGTATGTCGACTGTCGTATAATCG 58.922 45.833 27.16 2.58 41.35 3.34
4769 4981 3.181178 TCGACTGTCGTATAATCGTCTCG 59.819 47.826 27.16 0.00 41.35 4.04
4775 4987 5.872635 TGTCGTATAATCGTCTCGTCTTTT 58.127 37.500 0.00 0.00 0.00 2.27
4781 4993 7.377928 CGTATAATCGTCTCGTCTTTTACCATT 59.622 37.037 0.00 0.00 0.00 3.16
4789 5001 6.851330 GTCTCGTCTTTTACCATTGTTTCTTG 59.149 38.462 0.00 0.00 0.00 3.02
4800 5012 7.272037 ACCATTGTTTCTTGTAAAGTACCAG 57.728 36.000 0.00 0.00 46.34 4.00
4801 5013 6.264518 ACCATTGTTTCTTGTAAAGTACCAGG 59.735 38.462 0.00 0.00 46.34 4.45
4802 5014 6.294508 CCATTGTTTCTTGTAAAGTACCAGGG 60.295 42.308 0.00 0.00 46.34 4.45
4803 5015 4.721132 TGTTTCTTGTAAAGTACCAGGGG 58.279 43.478 0.00 0.00 46.34 4.79
4805 5017 2.340731 TCTTGTAAAGTACCAGGGGCA 58.659 47.619 0.00 0.00 46.34 5.36
4806 5018 2.304761 TCTTGTAAAGTACCAGGGGCAG 59.695 50.000 0.00 0.00 46.34 4.85
4807 5019 2.032965 TGTAAAGTACCAGGGGCAGA 57.967 50.000 0.00 0.00 0.00 4.26
4809 5021 2.712087 TGTAAAGTACCAGGGGCAGAAA 59.288 45.455 0.00 0.00 0.00 2.52
4810 5022 2.586648 AAAGTACCAGGGGCAGAAAG 57.413 50.000 0.00 0.00 0.00 2.62
4811 5023 0.698818 AAGTACCAGGGGCAGAAAGG 59.301 55.000 0.00 0.00 0.00 3.11
4812 5024 0.178873 AGTACCAGGGGCAGAAAGGA 60.179 55.000 0.00 0.00 0.00 3.36
4814 5026 0.178873 TACCAGGGGCAGAAAGGAGT 60.179 55.000 0.00 0.00 0.00 3.85
4815 5027 1.068352 ACCAGGGGCAGAAAGGAGTT 61.068 55.000 0.00 0.00 0.00 3.01
4816 5028 0.610232 CCAGGGGCAGAAAGGAGTTG 60.610 60.000 0.00 0.00 0.00 3.16
4817 5029 0.401738 CAGGGGCAGAAAGGAGTTGA 59.598 55.000 0.00 0.00 0.00 3.18
4818 5030 1.005215 CAGGGGCAGAAAGGAGTTGAT 59.995 52.381 0.00 0.00 0.00 2.57
4821 5033 3.333680 AGGGGCAGAAAGGAGTTGATAAA 59.666 43.478 0.00 0.00 0.00 1.40
4822 5034 4.017130 AGGGGCAGAAAGGAGTTGATAAAT 60.017 41.667 0.00 0.00 0.00 1.40
4843 5119 7.604657 AAATACTAGAACCAGATAGAGTGGG 57.395 40.000 0.00 0.00 39.65 4.61
4845 5121 4.538738 ACTAGAACCAGATAGAGTGGGAC 58.461 47.826 0.00 0.00 39.65 4.46
4846 5122 3.767309 AGAACCAGATAGAGTGGGACT 57.233 47.619 0.00 0.00 39.65 3.85
4848 5124 4.798882 AGAACCAGATAGAGTGGGACTAG 58.201 47.826 0.00 0.00 39.65 2.57
4849 5125 3.603965 ACCAGATAGAGTGGGACTAGG 57.396 52.381 0.00 0.00 39.65 3.02
4850 5126 3.132056 ACCAGATAGAGTGGGACTAGGA 58.868 50.000 0.00 0.00 39.65 2.94
4852 5128 4.171044 ACCAGATAGAGTGGGACTAGGATT 59.829 45.833 0.00 0.00 39.65 3.01
4853 5129 5.375956 ACCAGATAGAGTGGGACTAGGATTA 59.624 44.000 0.00 0.00 39.65 1.75
4854 5130 6.047359 ACCAGATAGAGTGGGACTAGGATTAT 59.953 42.308 0.00 0.00 39.65 1.28
4855 5131 6.605594 CCAGATAGAGTGGGACTAGGATTATC 59.394 46.154 0.00 0.00 0.00 1.75
4856 5132 7.178573 CAGATAGAGTGGGACTAGGATTATCA 58.821 42.308 0.00 0.00 0.00 2.15
4859 5135 5.970289 AGAGTGGGACTAGGATTATCATCA 58.030 41.667 0.00 0.00 0.00 3.07
4864 5140 8.125081 AGTGGGACTAGGATTATCATCATATGA 58.875 37.037 8.10 8.10 44.55 2.15
4953 5232 2.294233 TCTGAAATGCCAACAGAAGTGC 59.706 45.455 0.00 0.00 37.66 4.40
4955 5234 2.223782 TGAAATGCCAACAGAAGTGCAC 60.224 45.455 9.40 9.40 36.41 4.57
4975 5254 5.098211 GCACAATTTCTTGCAGAGGATTAC 58.902 41.667 0.00 0.00 38.68 1.89
4978 5257 7.201767 GCACAATTTCTTGCAGAGGATTACTAT 60.202 37.037 0.00 0.00 38.68 2.12
4986 5265 6.676990 TGCAGAGGATTACTATGATGTGAT 57.323 37.500 0.00 0.00 40.90 3.06
5021 5300 7.654022 TTGGGATCTCTGTTTTGTTTTTACT 57.346 32.000 0.00 0.00 0.00 2.24
5032 5311 6.701841 TGTTTTGTTTTTACTGTGTTCAAGCA 59.298 30.769 0.00 0.00 0.00 3.91
5046 5365 6.476380 TGTGTTCAAGCAGAATCAAACAATTC 59.524 34.615 0.00 0.00 38.76 2.17
5048 5367 4.229096 TCAAGCAGAATCAAACAATTCGC 58.771 39.130 0.00 0.00 40.00 4.70
5050 5372 3.829948 AGCAGAATCAAACAATTCGCTG 58.170 40.909 11.99 0.00 40.53 5.18
5056 5378 7.059212 CAGAATCAAACAATTCGCTGTTTTTC 58.941 34.615 7.19 9.23 45.10 2.29
5058 5380 6.753897 ATCAAACAATTCGCTGTTTTTCTC 57.246 33.333 7.19 0.00 45.10 2.87
5059 5381 5.040635 TCAAACAATTCGCTGTTTTTCTCC 58.959 37.500 7.19 0.00 45.10 3.71
5060 5382 4.918810 AACAATTCGCTGTTTTTCTCCT 57.081 36.364 0.00 0.00 36.05 3.69
5062 5384 4.860072 ACAATTCGCTGTTTTTCTCCTTC 58.140 39.130 0.00 0.00 0.00 3.46
5063 5385 4.338118 ACAATTCGCTGTTTTTCTCCTTCA 59.662 37.500 0.00 0.00 0.00 3.02
5086 5410 2.086869 CATGGCTCCGTTTTGATCTGT 58.913 47.619 0.00 0.00 0.00 3.41
5087 5411 1.522668 TGGCTCCGTTTTGATCTGTG 58.477 50.000 0.00 0.00 0.00 3.66
5248 5572 0.755327 GACTTTGCCAACACCACCCT 60.755 55.000 0.00 0.00 0.00 4.34
5273 5597 1.302285 CCAGCTCCAGTGGCTCATT 59.698 57.895 3.51 0.00 38.03 2.57
5330 5654 2.287427 CGCCATGATCAAGCTCATTTCC 60.287 50.000 16.42 0.00 33.59 3.13
5394 5718 9.534565 TGTAGACTAGAGCAAAATATCATCAAC 57.465 33.333 0.00 0.00 0.00 3.18
5395 5719 9.534565 GTAGACTAGAGCAAAATATCATCAACA 57.465 33.333 0.00 0.00 0.00 3.33
5433 5757 1.471119 CTGATGCTGGCCAGTGATTT 58.529 50.000 32.81 13.91 0.00 2.17
5434 5758 1.404391 CTGATGCTGGCCAGTGATTTC 59.596 52.381 32.81 21.02 0.00 2.17
5440 5764 2.942752 GCTGGCCAGTGATTTCTCATGA 60.943 50.000 32.81 0.00 32.98 3.07
5448 5772 5.470437 CCAGTGATTTCTCATGATCATGGAG 59.530 44.000 30.54 24.75 39.24 3.86
5458 5782 5.997843 TCATGATCATGGAGTCTGAACAAT 58.002 37.500 30.54 0.00 39.24 2.71
5459 5783 7.070322 TCTCATGATCATGGAGTCTGAACAATA 59.930 37.037 30.54 9.30 39.24 1.90
5518 5842 1.649171 CACGAAGAAACATCCGACTCG 59.351 52.381 0.00 0.00 0.00 4.18
5620 5944 2.931512 GCCCAGCGCAAAATAACTTA 57.068 45.000 11.47 0.00 37.47 2.24
5627 5951 6.809196 CCCAGCGCAAAATAACTTAATACAAA 59.191 34.615 11.47 0.00 0.00 2.83
5654 5978 5.418524 TGGCACACTAACTTTGCATTATGAT 59.581 36.000 0.00 0.00 38.04 2.45
5683 6008 1.649633 TGGTGTAGGGGTAGACCTCAT 59.350 52.381 0.41 0.00 42.09 2.90
5937 6535 2.737359 GCCTACAACGTACTGCATAGCA 60.737 50.000 0.00 0.00 36.92 3.49
6048 6646 3.999229 CGCAGATTTCTGAGTGGTAAC 57.001 47.619 11.70 0.00 46.59 2.50
6236 6916 1.739562 AAAGAAGCTCTCGCGCAGG 60.740 57.895 8.75 0.00 42.32 4.85
6313 6993 2.878580 CAGCTTGTCACAAACAAAGCA 58.121 42.857 8.75 0.00 46.95 3.91
6329 7009 0.745845 AGCATGCCAAGCCTAAGACG 60.746 55.000 15.66 0.00 0.00 4.18
6361 7041 1.670406 CTCTCTGCAGCGCCAACTT 60.670 57.895 9.47 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
156 157 1.142097 GTCTACCGCCTCTTCCTGC 59.858 63.158 0.00 0.00 0.00 4.85
290 291 9.533253 CAAATAATTATGGGAATTGGAGTCAAC 57.467 33.333 0.00 0.00 35.48 3.18
389 391 4.070716 CCATCTCATCTCTAAATGGTGGC 58.929 47.826 0.00 0.00 33.66 5.01
395 397 7.975608 ACATCATGTCCATCTCATCTCTAAAT 58.024 34.615 0.00 0.00 0.00 1.40
404 406 7.365497 ACTATGTTACATCATGTCCATCTCA 57.635 36.000 0.00 0.00 0.00 3.27
411 413 8.982685 CAGGACAATACTATGTTACATCATGTC 58.017 37.037 0.00 9.95 32.57 3.06
427 429 5.820423 TGCCACATACATTACAGGACAATAC 59.180 40.000 0.00 0.00 0.00 1.89
428 430 5.995446 TGCCACATACATTACAGGACAATA 58.005 37.500 0.00 0.00 0.00 1.90
429 431 4.854173 TGCCACATACATTACAGGACAAT 58.146 39.130 0.00 0.00 0.00 2.71
439 450 3.054434 TCAGCTAACCTGCCACATACATT 60.054 43.478 0.00 0.00 41.50 2.71
440 451 2.505407 TCAGCTAACCTGCCACATACAT 59.495 45.455 0.00 0.00 41.50 2.29
441 452 1.905894 TCAGCTAACCTGCCACATACA 59.094 47.619 0.00 0.00 41.50 2.29
442 453 2.678336 GTTCAGCTAACCTGCCACATAC 59.322 50.000 0.00 0.00 41.50 2.39
446 457 1.298859 CCGTTCAGCTAACCTGCCAC 61.299 60.000 0.00 0.00 41.50 5.01
456 467 1.617018 TAGAGCATGGCCGTTCAGCT 61.617 55.000 7.96 7.96 38.43 4.24
555 569 7.544622 TGCTATCTTACGAGTTCTTGTTACAT 58.455 34.615 0.00 0.00 0.00 2.29
567 581 2.359214 TGTGGCTCTGCTATCTTACGAG 59.641 50.000 0.00 0.00 0.00 4.18
569 583 2.871182 TGTGGCTCTGCTATCTTACG 57.129 50.000 0.00 0.00 0.00 3.18
611 625 0.603707 ACTGGGCTCACAACATGTCG 60.604 55.000 0.00 0.00 0.00 4.35
656 678 9.620660 ACATATTATTCTCAACAACGGAAAAAC 57.379 29.630 0.00 0.00 0.00 2.43
724 749 2.011122 TCTCTTCTGGGAAAGTCCGT 57.989 50.000 0.00 0.00 37.43 4.69
788 813 5.493133 TGCACGAAATCATATTTACCCAC 57.507 39.130 0.00 0.00 0.00 4.61
792 817 8.365210 CAGTTTGTTGCACGAAATCATATTTAC 58.635 33.333 0.00 0.00 0.00 2.01
813 841 3.587061 TCACCAGGTATCATGTCCAGTTT 59.413 43.478 0.00 0.00 0.00 2.66
815 843 2.501723 GTCACCAGGTATCATGTCCAGT 59.498 50.000 0.00 0.00 0.00 4.00
816 844 2.768527 AGTCACCAGGTATCATGTCCAG 59.231 50.000 0.00 0.00 0.00 3.86
868 947 5.063880 AGAAGTACACGCTCCTTCAAATTT 58.936 37.500 0.00 0.00 37.62 1.82
871 950 3.746045 AGAAGTACACGCTCCTTCAAA 57.254 42.857 0.00 0.00 37.62 2.69
873 952 3.746045 AAAGAAGTACACGCTCCTTCA 57.254 42.857 0.00 0.00 37.62 3.02
880 959 3.650139 TCTCTGGAAAAGAAGTACACGC 58.350 45.455 0.00 0.00 33.37 5.34
882 961 6.761714 TGTTTCTCTCTGGAAAAGAAGTACAC 59.238 38.462 0.00 0.00 37.02 2.90
884 963 7.787725 TTGTTTCTCTCTGGAAAAGAAGTAC 57.212 36.000 0.00 0.00 37.02 2.73
890 969 5.182760 CCTCCATTGTTTCTCTCTGGAAAAG 59.817 44.000 0.00 0.00 37.02 2.27
908 987 5.261040 TCTTTCACCTGAAAATCCTCCAT 57.739 39.130 2.25 0.00 42.72 3.41
912 991 9.539194 AAGATATTTCTTTCACCTGAAAATCCT 57.461 29.630 2.25 0.00 42.72 3.24
913 992 9.578439 CAAGATATTTCTTTCACCTGAAAATCC 57.422 33.333 2.25 0.00 42.72 3.01
914 993 9.080915 GCAAGATATTTCTTTCACCTGAAAATC 57.919 33.333 2.25 2.64 42.72 2.17
915 994 8.810041 AGCAAGATATTTCTTTCACCTGAAAAT 58.190 29.630 2.25 0.00 42.72 1.82
1231 1310 1.080298 GTACACGTTGGGGTCGAGG 60.080 63.158 0.00 0.00 0.00 4.63
1232 1311 1.443194 CGTACACGTTGGGGTCGAG 60.443 63.158 0.00 0.00 34.11 4.04
1235 1314 1.373371 GGTCGTACACGTTGGGGTC 60.373 63.158 1.19 0.00 40.80 4.46
1264 1343 6.260050 GCAATAATCTATTTGACGAGGTGGAA 59.740 38.462 0.00 0.00 0.00 3.53
1267 1346 5.760253 AGGCAATAATCTATTTGACGAGGTG 59.240 40.000 0.00 0.00 0.00 4.00
1423 1539 6.446781 TCCCAGTTAAGTTAGTATGACGAG 57.553 41.667 0.00 0.00 0.00 4.18
1442 1558 7.723172 TGCAATACATATACAACATTCATCCCA 59.277 33.333 0.00 0.00 0.00 4.37
1453 1569 6.707608 CAGCTTCTCCTGCAATACATATACAA 59.292 38.462 0.00 0.00 0.00 2.41
1589 1706 4.860907 CAGGCTGCATTCAAATAAGAACAC 59.139 41.667 0.00 0.00 0.00 3.32
1632 1751 3.242123 GCAACACGCTTAGAAGATGCTAC 60.242 47.826 0.00 0.00 37.77 3.58
1636 1755 1.398390 GGGCAACACGCTTAGAAGATG 59.602 52.381 0.00 0.00 41.91 2.90
1684 1803 1.474478 ACGACATACTGACTGCTCTGG 59.526 52.381 0.00 0.00 0.00 3.86
1708 1827 1.134699 CCTGCCGCTCTAACATCTTCA 60.135 52.381 0.00 0.00 0.00 3.02
1801 1920 0.810031 CCGCAATCCCGTCTAACTGG 60.810 60.000 0.00 0.00 0.00 4.00
1810 1929 1.153449 TAGCTTGTCCGCAATCCCG 60.153 57.895 0.00 0.00 33.65 5.14
1816 1935 2.126071 GTCGCTAGCTTGTCCGCA 60.126 61.111 13.93 0.00 0.00 5.69
1875 1994 2.363359 CCATAAATTTCCTGCCTCTGCC 59.637 50.000 0.00 0.00 36.33 4.85
1963 2082 3.875727 CAGCAAGGATTATCAGAGTGGTG 59.124 47.826 0.00 0.00 0.00 4.17
1966 2085 3.538591 TGCAGCAAGGATTATCAGAGTG 58.461 45.455 0.00 0.00 0.00 3.51
2038 2157 1.152138 GATGCCATCATGGGAGCCA 59.848 57.895 1.05 0.00 42.59 4.75
2092 2211 1.007336 GGTAGTCACTTGTCGCGGTG 61.007 60.000 6.13 6.58 35.06 4.94
2146 2265 7.423844 AACCTGAACAAGAATTTTCCTCTTT 57.576 32.000 0.00 0.00 30.58 2.52
2188 2307 8.492782 AGAAGATCATCTATCAATGTCCTTTGT 58.507 33.333 0.00 0.00 37.03 2.83
2234 2353 1.568504 ACCTGATCTCCAACCGCTAA 58.431 50.000 0.00 0.00 0.00 3.09
2239 2358 1.680249 GCAGGAACCTGATCTCCAACC 60.680 57.143 22.96 0.03 46.30 3.77
2473 2592 3.041508 AGTTTAACCTGAAGCGGAGTC 57.958 47.619 0.00 0.00 0.00 3.36
2569 2688 7.816031 CCATCATGATATTTCTGGCCAATTAAC 59.184 37.037 7.01 0.00 0.00 2.01
2725 2844 7.066043 GCCTTATCATTCATCATCTTCTCCATC 59.934 40.741 0.00 0.00 0.00 3.51
2876 2995 7.881232 ACTAGAAAGTGGATCGTTAAATTCCAA 59.119 33.333 0.00 0.00 41.05 3.53
2882 3001 7.929785 AGACAAACTAGAAAGTGGATCGTTAAA 59.070 33.333 0.00 0.00 35.62 1.52
2893 3012 6.987404 GGAGTTCTGAAGACAAACTAGAAAGT 59.013 38.462 0.00 0.00 37.65 2.66
3087 3212 4.327680 AGGCTCCACTTTGACAATCTTAC 58.672 43.478 0.00 0.00 0.00 2.34
3097 3222 6.089249 ACTGAATTAAAAGGCTCCACTTTG 57.911 37.500 0.00 0.00 40.36 2.77
3154 3279 2.682494 GCACGGTACCCTCCTCCA 60.682 66.667 6.25 0.00 0.00 3.86
3163 3288 1.735571 CCCTTACAATGTGCACGGTAC 59.264 52.381 13.13 0.00 0.00 3.34
3319 3444 1.926426 ATCCCCTGTAGGCAAGGCAC 61.926 60.000 0.00 0.00 0.00 5.01
3423 3548 1.121407 CACAGACTCCCTGACACCCA 61.121 60.000 0.00 0.00 45.78 4.51
3469 3594 5.327737 TGTCCCCTGTAACCATTTTAACT 57.672 39.130 0.00 0.00 0.00 2.24
3517 3642 5.898174 TCAGTAAGTATACCACATTCACGG 58.102 41.667 0.00 0.00 32.08 4.94
3553 3678 4.528206 TCTCTGAACTCAGCACCTTCAATA 59.472 41.667 1.61 0.00 43.46 1.90
3650 3775 4.837896 TCACTAGATGGATAGACTTGCG 57.162 45.455 0.00 0.00 0.00 4.85
3684 3811 6.415206 AGTACCTTTAGTTGCACAAGACTA 57.585 37.500 0.00 0.00 0.00 2.59
3705 3832 3.537874 GGCGATGACCGGGCTAGT 61.538 66.667 9.82 0.00 39.04 2.57
3714 3841 2.555199 AGCTTATCAAGTGGCGATGAC 58.445 47.619 0.00 0.00 0.00 3.06
3717 3844 1.672881 GCAAGCTTATCAAGTGGCGAT 59.327 47.619 0.00 0.00 0.00 4.58
3748 3875 1.669604 TTGGAAGTTGTGCGCAAGTA 58.330 45.000 20.14 2.75 37.28 2.24
3777 3904 2.393768 GCCATCACCAGTCACAGCG 61.394 63.158 0.00 0.00 0.00 5.18
3847 3974 4.227300 TGTTATTACCTCAGTCCCTGCAAT 59.773 41.667 0.00 0.00 0.00 3.56
3880 4007 6.135290 ACATTTCAACGCTATGTATGCATT 57.865 33.333 3.54 0.00 36.58 3.56
3894 4021 5.796350 AGTATAAGCCACGACATTTCAAC 57.204 39.130 0.00 0.00 0.00 3.18
3966 4094 1.065418 CCCCACAGTTCCACTACATCC 60.065 57.143 0.00 0.00 0.00 3.51
4083 4212 8.762481 ACCCAGGAACCAGATAAATATTTTAC 57.238 34.615 5.91 1.49 0.00 2.01
4114 4315 6.261158 GTCTGTCAAAAACTTAGAGAAGGCTT 59.739 38.462 0.00 0.00 36.95 4.35
4138 4339 6.670695 AAGATGAACTTAAAGGGCAAATGT 57.329 33.333 0.00 0.00 37.03 2.71
4149 4350 9.840427 GCATAAAGCAACTTAAGATGAACTTAA 57.160 29.630 16.23 0.00 43.92 1.85
4168 4375 1.921887 CACCTGCGCAAATGCATAAAG 59.078 47.619 13.05 0.00 45.26 1.85
4169 4376 1.403914 CCACCTGCGCAAATGCATAAA 60.404 47.619 13.05 0.00 45.26 1.40
4363 4570 2.670148 GGCAGTCCTGTGGGTAGGG 61.670 68.421 0.00 0.00 38.42 3.53
4369 4576 1.274703 ATGGGTAGGCAGTCCTGTGG 61.275 60.000 0.00 0.00 44.08 4.17
4370 4577 0.107508 CATGGGTAGGCAGTCCTGTG 60.108 60.000 0.00 0.00 44.08 3.66
4371 4578 0.252696 TCATGGGTAGGCAGTCCTGT 60.253 55.000 0.00 0.00 44.08 4.00
4372 4579 1.135094 ATCATGGGTAGGCAGTCCTG 58.865 55.000 0.00 0.00 44.08 3.86
4373 4580 2.795291 TATCATGGGTAGGCAGTCCT 57.205 50.000 0.00 0.00 46.57 3.85
4374 4581 3.073062 ACAATATCATGGGTAGGCAGTCC 59.927 47.826 0.00 0.00 0.00 3.85
4375 4582 4.357918 ACAATATCATGGGTAGGCAGTC 57.642 45.455 0.00 0.00 0.00 3.51
4376 4583 4.464008 CAACAATATCATGGGTAGGCAGT 58.536 43.478 0.00 0.00 0.00 4.40
4377 4584 3.822735 CCAACAATATCATGGGTAGGCAG 59.177 47.826 0.00 0.00 0.00 4.85
4378 4585 3.204158 ACCAACAATATCATGGGTAGGCA 59.796 43.478 0.00 0.00 38.58 4.75
4379 4586 3.832527 ACCAACAATATCATGGGTAGGC 58.167 45.455 0.00 0.00 38.58 3.93
4380 4587 5.890985 TGAAACCAACAATATCATGGGTAGG 59.109 40.000 0.00 0.00 38.58 3.18
4381 4588 7.257722 GTTGAAACCAACAATATCATGGGTAG 58.742 38.462 0.00 0.00 42.52 3.18
4382 4589 7.164230 GTTGAAACCAACAATATCATGGGTA 57.836 36.000 0.00 0.00 42.52 3.69
4383 4590 6.036577 GTTGAAACCAACAATATCATGGGT 57.963 37.500 0.00 0.00 42.52 4.51
4408 4615 0.039764 AGACCGTGAGATGGGAGACA 59.960 55.000 0.00 0.00 0.00 3.41
4432 4639 1.145598 CGCATCTCCTGGCATGAGT 59.854 57.895 17.60 4.76 0.00 3.41
4480 4692 3.287867 AGGGTGTCCATGATCATGTTC 57.712 47.619 29.23 21.91 37.11 3.18
4507 4719 0.602905 GTTCGGTGGCAAGTGCTAGT 60.603 55.000 2.85 0.00 41.70 2.57
4558 4770 1.558233 ACTTCCCTGTCCTTCCTACG 58.442 55.000 0.00 0.00 0.00 3.51
4645 4857 6.051717 CACATATCTCCCTTGACTTTGTAGG 58.948 44.000 0.00 0.00 0.00 3.18
4726 4938 4.072131 GACATACCTGGCAGAAGACAAAA 58.928 43.478 17.94 0.00 27.50 2.44
4729 4941 1.204704 CGACATACCTGGCAGAAGACA 59.795 52.381 17.94 0.00 0.00 3.41
4750 4962 4.118410 AGACGAGACGATTATACGACAGT 58.882 43.478 0.00 0.00 37.03 3.55
4753 4965 6.355666 GGTAAAAGACGAGACGATTATACGAC 59.644 42.308 0.00 0.00 37.03 4.34
4759 4971 6.392354 ACAATGGTAAAAGACGAGACGATTA 58.608 36.000 0.00 0.00 0.00 1.75
4763 4975 4.985044 AACAATGGTAAAAGACGAGACG 57.015 40.909 0.00 0.00 0.00 4.18
4764 4976 6.541111 AGAAACAATGGTAAAAGACGAGAC 57.459 37.500 0.00 0.00 0.00 3.36
4769 4981 9.797556 ACTTTACAAGAAACAATGGTAAAAGAC 57.202 29.630 0.00 0.00 34.60 3.01
4775 4987 7.446013 CCTGGTACTTTACAAGAAACAATGGTA 59.554 37.037 0.00 0.00 31.03 3.25
4781 4993 4.721132 CCCCTGGTACTTTACAAGAAACA 58.279 43.478 0.00 0.00 31.03 2.83
4789 5001 3.344515 CTTTCTGCCCCTGGTACTTTAC 58.655 50.000 0.00 0.00 0.00 2.01
4798 5010 0.401738 TCAACTCCTTTCTGCCCCTG 59.598 55.000 0.00 0.00 0.00 4.45
4800 5012 3.366052 TTATCAACTCCTTTCTGCCCC 57.634 47.619 0.00 0.00 0.00 5.80
4801 5013 6.122964 AGTATTTATCAACTCCTTTCTGCCC 58.877 40.000 0.00 0.00 0.00 5.36
4802 5014 8.204836 TCTAGTATTTATCAACTCCTTTCTGCC 58.795 37.037 0.00 0.00 0.00 4.85
4803 5015 9.601217 TTCTAGTATTTATCAACTCCTTTCTGC 57.399 33.333 0.00 0.00 0.00 4.26
4806 5018 9.886132 TGGTTCTAGTATTTATCAACTCCTTTC 57.114 33.333 0.00 0.00 0.00 2.62
4807 5019 9.892130 CTGGTTCTAGTATTTATCAACTCCTTT 57.108 33.333 0.00 0.00 0.00 3.11
4809 5021 8.840200 TCTGGTTCTAGTATTTATCAACTCCT 57.160 34.615 0.00 0.00 0.00 3.69
4817 5029 9.315363 CCCACTCTATCTGGTTCTAGTATTTAT 57.685 37.037 0.00 0.00 0.00 1.40
4818 5030 8.508601 TCCCACTCTATCTGGTTCTAGTATTTA 58.491 37.037 0.00 0.00 0.00 1.40
4821 5033 6.103501 AGTCCCACTCTATCTGGTTCTAGTAT 59.896 42.308 0.00 0.00 0.00 2.12
4822 5034 5.432390 AGTCCCACTCTATCTGGTTCTAGTA 59.568 44.000 0.00 0.00 0.00 1.82
4874 5150 9.784531 TCTTCTCTCTTCACTGTTTTAAATGAT 57.215 29.630 0.00 0.00 0.00 2.45
4875 5151 9.613428 TTCTTCTCTCTTCACTGTTTTAAATGA 57.387 29.630 0.00 0.00 0.00 2.57
4876 5152 9.875675 CTTCTTCTCTCTTCACTGTTTTAAATG 57.124 33.333 0.00 0.00 0.00 2.32
4877 5153 9.061435 CCTTCTTCTCTCTTCACTGTTTTAAAT 57.939 33.333 0.00 0.00 0.00 1.40
4878 5154 8.047310 ACCTTCTTCTCTCTTCACTGTTTTAAA 58.953 33.333 0.00 0.00 0.00 1.52
4895 5171 1.195115 TCGCCATGCTACCTTCTTCT 58.805 50.000 0.00 0.00 0.00 2.85
4896 5172 2.246719 ATCGCCATGCTACCTTCTTC 57.753 50.000 0.00 0.00 0.00 2.87
4897 5173 2.700897 ACTATCGCCATGCTACCTTCTT 59.299 45.455 0.00 0.00 0.00 2.52
4932 5211 2.294233 GCACTTCTGTTGGCATTTCAGA 59.706 45.455 11.56 11.56 36.59 3.27
4938 5217 1.401761 TTGTGCACTTCTGTTGGCAT 58.598 45.000 19.41 0.00 38.68 4.40
4945 5224 3.708890 TGCAAGAAATTGTGCACTTCTG 58.291 40.909 19.41 13.30 45.52 3.02
4953 5232 6.506500 AGTAATCCTCTGCAAGAAATTGTG 57.493 37.500 0.00 0.00 46.34 3.33
4955 5234 8.442632 TCATAGTAATCCTCTGCAAGAAATTG 57.557 34.615 0.00 0.00 46.34 2.32
4975 5254 7.546667 CCCAAAACCAAGAAAATCACATCATAG 59.453 37.037 0.00 0.00 0.00 2.23
4978 5257 5.365025 TCCCAAAACCAAGAAAATCACATCA 59.635 36.000 0.00 0.00 0.00 3.07
4986 5265 5.208121 ACAGAGATCCCAAAACCAAGAAAA 58.792 37.500 0.00 0.00 0.00 2.29
5021 5300 4.979943 TGTTTGATTCTGCTTGAACACA 57.020 36.364 0.00 0.00 37.52 3.72
5046 5365 4.488126 TGAATGAAGGAGAAAAACAGCG 57.512 40.909 0.00 0.00 0.00 5.18
5048 5367 5.047519 AGCCATGAATGAAGGAGAAAAACAG 60.048 40.000 0.00 0.00 0.00 3.16
5050 5372 5.397142 AGCCATGAATGAAGGAGAAAAAC 57.603 39.130 0.00 0.00 0.00 2.43
5056 5378 1.134280 ACGGAGCCATGAATGAAGGAG 60.134 52.381 0.00 0.00 0.00 3.69
5058 5380 1.755179 AACGGAGCCATGAATGAAGG 58.245 50.000 0.00 0.00 0.00 3.46
5059 5381 3.191162 TCAAAACGGAGCCATGAATGAAG 59.809 43.478 0.00 0.00 0.00 3.02
5060 5382 3.153130 TCAAAACGGAGCCATGAATGAA 58.847 40.909 0.00 0.00 0.00 2.57
5062 5384 3.379372 AGATCAAAACGGAGCCATGAATG 59.621 43.478 0.00 0.00 0.00 2.67
5063 5385 3.379372 CAGATCAAAACGGAGCCATGAAT 59.621 43.478 0.00 0.00 0.00 2.57
5086 5410 2.894765 TCATTGAACACCTACGGAGACA 59.105 45.455 0.00 0.00 0.00 3.41
5087 5411 3.512680 CTCATTGAACACCTACGGAGAC 58.487 50.000 0.00 0.00 0.00 3.36
5228 5552 1.040339 GGGTGGTGTTGGCAAAGTCA 61.040 55.000 0.00 0.00 0.00 3.41
5273 5597 1.076024 AGGAAGCCAAAGAGGATGCAA 59.924 47.619 0.00 0.00 41.22 4.08
5330 5654 3.608506 CGTGTTCTTCATGAGGTTCTACG 59.391 47.826 4.57 8.13 35.23 3.51
5433 5757 4.713321 TGTTCAGACTCCATGATCATGAGA 59.287 41.667 32.71 25.14 41.20 3.27
5434 5758 5.019785 TGTTCAGACTCCATGATCATGAG 57.980 43.478 32.71 26.90 41.20 2.90
5440 5764 6.305272 ACACTATTGTTCAGACTCCATGAT 57.695 37.500 0.00 0.00 28.43 2.45
5448 5772 2.993899 CACGGGACACTATTGTTCAGAC 59.006 50.000 0.00 0.00 35.47 3.51
5458 5782 4.676986 CGATTCTTGATTCACGGGACACTA 60.677 45.833 0.00 0.00 0.00 2.74
5459 5783 3.600388 GATTCTTGATTCACGGGACACT 58.400 45.455 0.00 0.00 0.00 3.55
5565 5889 1.473258 TGGTTTTCAAGTGCAGCTGT 58.527 45.000 16.64 0.00 0.00 4.40
5620 5944 7.759433 GCAAAGTTAGTGTGCCATATTTGTATT 59.241 33.333 0.00 0.00 31.94 1.89
5627 5951 5.920193 AATGCAAAGTTAGTGTGCCATAT 57.080 34.783 0.00 0.00 37.48 1.78
5654 5978 1.847737 ACCCCTACACCAGTTGAAACA 59.152 47.619 0.00 0.00 0.00 2.83
5783 6369 7.279981 TGCTGGAACATTTGATATGTACTGTAC 59.720 37.037 10.98 10.98 38.20 2.90
5937 6535 1.898574 CGCTGCAGTTTGGGAAGGT 60.899 57.895 16.64 0.00 0.00 3.50
6042 6640 5.564651 GCAAGTACGTACTTACCAGTTACCA 60.565 44.000 34.03 0.00 44.19 3.25
6043 6641 4.859245 GCAAGTACGTACTTACCAGTTACC 59.141 45.833 34.03 13.99 44.19 2.85
6044 6642 4.859245 GGCAAGTACGTACTTACCAGTTAC 59.141 45.833 36.75 18.60 45.15 2.50
6045 6643 5.059404 GGCAAGTACGTACTTACCAGTTA 57.941 43.478 36.75 0.00 45.15 2.24
6046 6644 3.917988 GGCAAGTACGTACTTACCAGTT 58.082 45.455 36.75 17.57 45.15 3.16
6047 6645 3.582714 GGCAAGTACGTACTTACCAGT 57.417 47.619 36.75 18.20 45.15 4.00
6236 6916 0.462581 TGCGGCTCACTCATGATTCC 60.463 55.000 0.00 0.00 33.22 3.01
6263 6943 1.291588 CAGCAGCTCGTCAACCTCT 59.708 57.895 0.00 0.00 0.00 3.69
6313 6993 1.959042 CATCGTCTTAGGCTTGGCAT 58.041 50.000 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.