Multiple sequence alignment - TraesCS2A01G289500

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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 TraesCS2A01G289500 chr2A 100.000 4862 0 0 1 4862 498085280 498090141 0.000000e+00 8979
1 TraesCS2A01G289500 chr2D 97.084 3738 79 10 936 4660 367990574 367994294 0.000000e+00 6272
2 TraesCS2A01G289500 chr2D 93.114 944 29 16 1 919 367989653 367990585 0.000000e+00 1351
3 TraesCS2A01G289500 chr2B 96.639 3749 93 11 933 4660 436992013 436995749 0.000000e+00 6194
4 TraesCS2A01G289500 chr2B 93.823 939 33 13 1 919 436991095 436992028 0.000000e+00 1389
5 TraesCS2A01G289500 chr2B 96.552 203 3 2 4653 4852 138125647 138125446 2.800000e-87 333
6 TraesCS2A01G289500 chr4A 85.349 430 63 0 1673 2102 5405427 5405856 3.450000e-121 446
7 TraesCS2A01G289500 chr4A 98.947 190 1 1 4650 4839 710743524 710743712 6.030000e-89 339
8 TraesCS2A01G289500 chr4B 84.884 430 65 0 1673 2102 581537724 581537295 7.470000e-118 435
9 TraesCS2A01G289500 chr4B 98.958 192 0 2 4651 4842 455621445 455621634 4.660000e-90 342
10 TraesCS2A01G289500 chr6B 98.969 194 0 2 4646 4839 475722677 475722868 3.600000e-91 346
11 TraesCS2A01G289500 chr7A 98.964 193 0 2 4650 4842 105168995 105168805 1.300000e-90 344
12 TraesCS2A01G289500 chr1A 99.468 188 1 0 4655 4842 583789132 583789319 4.660000e-90 342
13 TraesCS2A01G289500 chr3A 97.059 204 2 3 4640 4839 642038956 642038753 1.680000e-89 340
14 TraesCS2A01G289500 chr4D 98.947 190 0 2 4651 4840 478512182 478512369 6.030000e-89 339
15 TraesCS2A01G289500 chr1B 98.947 190 0 2 4650 4839 110622812 110622999 6.030000e-89 339


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 TraesCS2A01G289500 chr2A 498085280 498090141 4861 False 8979.0 8979 100.000 1 4862 1 chr2A.!!$F1 4861
1 TraesCS2A01G289500 chr2D 367989653 367994294 4641 False 3811.5 6272 95.099 1 4660 2 chr2D.!!$F1 4659
2 TraesCS2A01G289500 chr2B 436991095 436995749 4654 False 3791.5 6194 95.231 1 4660 2 chr2B.!!$F1 4659

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
929 956 0.387565 GGTGAAGCTTTTCCCGCAAA 59.612 50.000 0.0 0.0 0.00 3.68 F
2745 2777 1.070601 CGTGCATAGATCCACCATCCA 59.929 52.381 0.0 0.0 30.71 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2915 2947 3.230976 TCACTCATGTGGTGTAGACTGT 58.769 45.455 16.51 0.0 43.94 3.55 R
4721 4773 0.177141 GGCTGCGTACAATAGACCCA 59.823 55.000 0.00 0.0 0.00 4.51 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
67 68 3.763097 TCATCGCATGCCAAGTTTAAG 57.237 42.857 13.15 0.00 0.00 1.85
129 130 1.861542 TTCCATTCCAACAAGCGCCG 61.862 55.000 2.29 0.00 0.00 6.46
146 147 1.375396 CGGGACAGCACGAATTCCA 60.375 57.895 0.00 0.00 45.89 3.53
155 156 2.079925 GCACGAATTCCAGAGCTTCTT 58.920 47.619 0.00 0.00 0.00 2.52
173 174 6.595716 AGCTTCTTAACATAGCCACAAAGTAG 59.404 38.462 0.00 0.00 35.53 2.57
175 176 6.614694 TCTTAACATAGCCACAAAGTAGGA 57.385 37.500 0.00 0.00 0.00 2.94
176 177 7.011499 TCTTAACATAGCCACAAAGTAGGAA 57.989 36.000 0.00 0.00 0.00 3.36
178 179 7.940137 TCTTAACATAGCCACAAAGTAGGAAAA 59.060 33.333 0.00 0.00 0.00 2.29
179 180 6.575162 AACATAGCCACAAAGTAGGAAAAG 57.425 37.500 0.00 0.00 0.00 2.27
180 181 5.010282 ACATAGCCACAAAGTAGGAAAAGG 58.990 41.667 0.00 0.00 0.00 3.11
181 182 3.876309 AGCCACAAAGTAGGAAAAGGA 57.124 42.857 0.00 0.00 0.00 3.36
183 184 4.542697 AGCCACAAAGTAGGAAAAGGAAA 58.457 39.130 0.00 0.00 0.00 3.13
184 185 4.584743 AGCCACAAAGTAGGAAAAGGAAAG 59.415 41.667 0.00 0.00 0.00 2.62
185 186 4.583073 GCCACAAAGTAGGAAAAGGAAAGA 59.417 41.667 0.00 0.00 0.00 2.52
353 374 0.767375 TGGCCAATCCTAGATGAGCC 59.233 55.000 0.61 9.95 39.41 4.70
365 386 2.636830 AGATGAGCCACACAGCAATAC 58.363 47.619 0.00 0.00 34.23 1.89
368 389 1.000896 AGCCACACAGCAATACCCC 60.001 57.895 0.00 0.00 34.23 4.95
595 616 2.233922 TCCTCCATCAGTTCCTTCGTTC 59.766 50.000 0.00 0.00 0.00 3.95
614 635 3.676291 TCGATTGTGACATTGTCTCCA 57.324 42.857 17.26 11.08 33.15 3.86
805 832 6.849697 TCCTAATGTTAATATGACCCTCCAGT 59.150 38.462 0.00 0.00 0.00 4.00
817 844 0.890996 CCTCCAGTTGTTCCAGTGGC 60.891 60.000 3.51 0.00 0.00 5.01
919 946 5.425196 AATGGCAAATAATGGTGAAGCTT 57.575 34.783 0.00 0.00 0.00 3.74
920 947 4.888326 TGGCAAATAATGGTGAAGCTTT 57.112 36.364 0.00 0.00 0.00 3.51
921 948 5.226194 TGGCAAATAATGGTGAAGCTTTT 57.774 34.783 0.00 0.00 0.00 2.27
922 949 5.237048 TGGCAAATAATGGTGAAGCTTTTC 58.763 37.500 0.00 0.00 0.00 2.29
923 950 4.631377 GGCAAATAATGGTGAAGCTTTTCC 59.369 41.667 0.00 7.16 0.00 3.13
924 951 4.631377 GCAAATAATGGTGAAGCTTTTCCC 59.369 41.667 15.15 9.77 0.00 3.97
925 952 4.718940 AATAATGGTGAAGCTTTTCCCG 57.281 40.909 15.15 0.00 0.00 5.14
926 953 0.603065 AATGGTGAAGCTTTTCCCGC 59.397 50.000 15.15 3.69 0.00 6.13
927 954 0.539438 ATGGTGAAGCTTTTCCCGCA 60.539 50.000 15.15 0.00 0.00 5.69
928 955 0.753479 TGGTGAAGCTTTTCCCGCAA 60.753 50.000 15.15 0.00 0.00 4.85
929 956 0.387565 GGTGAAGCTTTTCCCGCAAA 59.612 50.000 0.00 0.00 0.00 3.68
930 957 1.202475 GGTGAAGCTTTTCCCGCAAAA 60.202 47.619 0.00 0.00 32.77 2.44
940 967 3.828875 TTCCCGCAAAAGAAAAATGGT 57.171 38.095 0.00 0.00 0.00 3.55
941 968 3.104843 TCCCGCAAAAGAAAAATGGTG 57.895 42.857 0.00 0.00 0.00 4.17
942 969 2.695666 TCCCGCAAAAGAAAAATGGTGA 59.304 40.909 0.00 0.00 0.00 4.02
943 970 3.133003 TCCCGCAAAAGAAAAATGGTGAA 59.867 39.130 0.00 0.00 0.00 3.18
944 971 3.494251 CCCGCAAAAGAAAAATGGTGAAG 59.506 43.478 0.00 0.00 0.00 3.02
945 972 3.059665 CCGCAAAAGAAAAATGGTGAAGC 60.060 43.478 0.00 0.00 0.00 3.86
946 973 3.555139 CGCAAAAGAAAAATGGTGAAGCA 59.445 39.130 0.00 0.00 0.00 3.91
1288 1315 2.287769 ACCACAAAGGCAAAAACATGC 58.712 42.857 0.00 0.00 45.67 4.06
1427 1454 8.792831 AACGTACGTATAAAGACAGATTATGG 57.207 34.615 23.12 0.00 0.00 2.74
1445 1472 8.353684 AGATTATGGTATTAGTGAGTCTGAACG 58.646 37.037 0.00 0.00 0.00 3.95
1521 1548 1.283029 CTGTCATGATTCACCCCAGGT 59.717 52.381 0.00 0.00 35.62 4.00
1523 1550 1.561542 GTCATGATTCACCCCAGGTCT 59.438 52.381 0.00 0.00 31.02 3.85
1524 1551 2.771943 GTCATGATTCACCCCAGGTCTA 59.228 50.000 0.00 0.00 31.02 2.59
1525 1552 3.041211 TCATGATTCACCCCAGGTCTAG 58.959 50.000 0.00 0.00 31.02 2.43
1526 1553 2.642171 TGATTCACCCCAGGTCTAGT 57.358 50.000 0.00 0.00 31.02 2.57
1539 1570 8.566109 ACCCCAGGTCTAGTTAATTTATTTCAT 58.434 33.333 0.00 0.00 0.00 2.57
1640 1671 2.158957 GGATGAAAGTAGGATGCGGACA 60.159 50.000 0.00 0.00 0.00 4.02
1667 1699 4.722194 CAACAATCTGTTAACATCACCCG 58.278 43.478 9.13 0.00 38.77 5.28
2404 2436 9.703892 ATTTTCTAGAGATTTGAGTGGATATCG 57.296 33.333 0.00 0.00 0.00 2.92
2509 2541 5.527026 ATCCATAGGAATTTGGGAGGATC 57.473 43.478 0.00 0.00 34.34 3.36
2549 2581 9.578439 CAGATGAACCTAAAGGAAAATTTCATC 57.422 33.333 20.90 20.90 44.51 2.92
2606 2638 5.058490 CCTTTGACCTAAAAGAACCGTGTA 58.942 41.667 0.00 0.00 39.12 2.90
2654 2686 2.806608 ACAAAACAAGCCAGCATCAG 57.193 45.000 0.00 0.00 0.00 2.90
2745 2777 1.070601 CGTGCATAGATCCACCATCCA 59.929 52.381 0.00 0.00 30.71 3.41
2833 2865 3.132925 ACATGATGTTTTGCCAAGTTGC 58.867 40.909 0.00 0.00 0.00 4.17
2918 2950 3.191078 CCTTCTCCAGGCAATCTACAG 57.809 52.381 0.00 0.00 35.13 2.74
2919 2951 2.503356 CCTTCTCCAGGCAATCTACAGT 59.497 50.000 0.00 0.00 35.13 3.55
2920 2952 3.431486 CCTTCTCCAGGCAATCTACAGTC 60.431 52.174 0.00 0.00 35.13 3.51
2962 2994 6.205464 ACAATCACAAGTGTAACCATCTGAAG 59.795 38.462 0.00 0.00 37.80 3.02
2991 3023 9.490663 CCGATATTTACAAACTGACATTTCTTC 57.509 33.333 0.00 0.00 0.00 2.87
3087 3119 2.751806 CTCCAGAATCAACCAAAGCCTC 59.248 50.000 0.00 0.00 0.00 4.70
3125 3157 1.114119 TTGCATGGCCAACAGCAGAA 61.114 50.000 24.02 12.73 46.50 3.02
3151 3183 1.518572 CCGCACACGATACCTGGTC 60.519 63.158 0.63 0.00 43.93 4.02
3167 3199 1.064825 GGTCCAGACTCTTCCCCAAA 58.935 55.000 0.00 0.00 0.00 3.28
3423 3455 4.177026 CAAAGACCAGTGAAGATCCTACG 58.823 47.826 0.00 0.00 0.00 3.51
3470 3502 4.069304 CCGAACTATTTCACCACCAAAGA 58.931 43.478 0.00 0.00 0.00 2.52
3480 3512 2.231964 CACCACCAAAGATCACATTGGG 59.768 50.000 21.70 13.75 45.59 4.12
3590 3622 1.480137 GACTGGTAGCTGCATGAGACT 59.520 52.381 3.61 0.00 0.00 3.24
4033 4077 6.064846 TGAAATTCTGAAAACTGAGCTGAC 57.935 37.500 0.00 0.00 0.00 3.51
4049 4093 2.276201 CTGACACAAAACTGACACGGA 58.724 47.619 0.00 0.00 0.00 4.69
4097 4141 9.748708 TGGTATTGCATTCAATAAGAATAAAGC 57.251 29.630 0.00 0.00 45.06 3.51
4208 4253 6.822667 ATGTTATGACTTCAATGACAAGCA 57.177 33.333 0.00 0.00 0.00 3.91
4430 4477 0.847373 TTTGTGGGCCAGTACAAGGA 59.153 50.000 6.40 4.10 37.98 3.36
4580 4629 5.108517 CAAAAGCTTTAGTGTTTCCTTGCA 58.891 37.500 13.10 0.00 0.00 4.08
4662 4714 5.964958 TCAGCACAGAAAAGAATAAAGGG 57.035 39.130 0.00 0.00 0.00 3.95
4663 4715 4.218417 TCAGCACAGAAAAGAATAAAGGGC 59.782 41.667 0.00 0.00 0.00 5.19
4664 4716 4.022068 CAGCACAGAAAAGAATAAAGGGCA 60.022 41.667 0.00 0.00 0.00 5.36
4665 4717 4.219288 AGCACAGAAAAGAATAAAGGGCAG 59.781 41.667 0.00 0.00 0.00 4.85
4666 4718 4.488879 CACAGAAAAGAATAAAGGGCAGC 58.511 43.478 0.00 0.00 0.00 5.25
4667 4719 3.511540 ACAGAAAAGAATAAAGGGCAGCC 59.488 43.478 1.26 1.26 0.00 4.85
4668 4720 3.099905 AGAAAAGAATAAAGGGCAGCCC 58.900 45.455 24.90 24.90 45.90 5.19
4679 4731 2.045045 GCAGCCCCAGTGCATGTA 60.045 61.111 0.00 0.00 40.86 2.29
4680 4732 2.117156 GCAGCCCCAGTGCATGTAG 61.117 63.158 0.00 0.00 40.86 2.74
4681 4733 2.117156 CAGCCCCAGTGCATGTAGC 61.117 63.158 0.00 0.00 45.96 3.58
4682 4734 2.273449 GCCCCAGTGCATGTAGCT 59.727 61.111 0.00 0.00 45.94 3.32
4683 4735 1.821332 GCCCCAGTGCATGTAGCTC 60.821 63.158 0.00 0.00 45.94 4.09
4684 4736 1.153086 CCCCAGTGCATGTAGCTCC 60.153 63.158 0.00 0.00 45.94 4.70
4685 4737 1.153086 CCCAGTGCATGTAGCTCCC 60.153 63.158 0.00 0.00 45.94 4.30
4686 4738 1.522355 CCAGTGCATGTAGCTCCCG 60.522 63.158 0.00 0.00 45.94 5.14
4687 4739 2.176273 CAGTGCATGTAGCTCCCGC 61.176 63.158 0.00 0.00 45.94 6.13
4689 4741 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
4690 4742 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
4691 4743 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
4692 4744 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
4695 4747 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
4707 4759 4.785453 GCGCAGGGTCTGGGGAAG 62.785 72.222 0.30 0.00 43.28 3.46
4708 4760 4.101448 CGCAGGGTCTGGGGAAGG 62.101 72.222 4.35 0.00 40.11 3.46
4709 4761 3.732849 GCAGGGTCTGGGGAAGGG 61.733 72.222 0.00 0.00 31.21 3.95
4710 4762 2.204151 CAGGGTCTGGGGAAGGGT 60.204 66.667 0.00 0.00 0.00 4.34
4711 4763 2.125225 AGGGTCTGGGGAAGGGTC 59.875 66.667 0.00 0.00 0.00 4.46
4712 4764 3.015753 GGGTCTGGGGAAGGGTCC 61.016 72.222 0.00 0.00 44.10 4.46
4713 4765 3.400054 GGTCTGGGGAAGGGTCCG 61.400 72.222 0.00 0.00 46.04 4.79
4714 4766 2.284405 GTCTGGGGAAGGGTCCGA 60.284 66.667 0.00 0.00 46.04 4.55
4715 4767 2.284405 TCTGGGGAAGGGTCCGAC 60.284 66.667 0.00 0.00 46.04 4.79
4716 4768 3.400054 CTGGGGAAGGGTCCGACC 61.400 72.222 9.30 9.30 46.04 4.79
4717 4769 4.257810 TGGGGAAGGGTCCGACCA 62.258 66.667 19.43 0.00 46.04 4.02
4718 4770 3.714001 GGGGAAGGGTCCGACCAC 61.714 72.222 19.43 8.70 46.04 4.16
4719 4771 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
4720 4772 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
4721 4773 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
4722 4774 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
4723 4775 0.605589 GAAGGGTCCGACCACTTTGG 60.606 60.000 19.43 0.00 41.02 3.28
4724 4776 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
4725 4777 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
4735 4787 3.934068 ACCACTTTGGGTCTATTGTACG 58.066 45.455 0.00 0.00 43.37 3.67
4736 4788 2.676342 CCACTTTGGGTCTATTGTACGC 59.324 50.000 0.00 0.00 32.67 4.42
4737 4789 3.331150 CACTTTGGGTCTATTGTACGCA 58.669 45.455 0.00 0.00 37.94 5.24
4738 4790 3.370978 CACTTTGGGTCTATTGTACGCAG 59.629 47.826 0.00 0.00 40.36 5.18
4739 4791 2.018542 TTGGGTCTATTGTACGCAGC 57.981 50.000 0.00 0.00 40.36 5.25
4740 4792 0.177141 TGGGTCTATTGTACGCAGCC 59.823 55.000 0.00 0.00 35.18 4.85
4741 4793 0.464452 GGGTCTATTGTACGCAGCCT 59.536 55.000 0.00 0.00 0.00 4.58
4742 4794 1.134491 GGGTCTATTGTACGCAGCCTT 60.134 52.381 0.00 0.00 0.00 4.35
4743 4795 2.629051 GGTCTATTGTACGCAGCCTTT 58.371 47.619 0.00 0.00 0.00 3.11
4744 4796 2.608090 GGTCTATTGTACGCAGCCTTTC 59.392 50.000 0.00 0.00 0.00 2.62
4745 4797 2.608090 GTCTATTGTACGCAGCCTTTCC 59.392 50.000 0.00 0.00 0.00 3.13
4746 4798 1.940613 CTATTGTACGCAGCCTTTCCC 59.059 52.381 0.00 0.00 0.00 3.97
4747 4799 0.328258 ATTGTACGCAGCCTTTCCCT 59.672 50.000 0.00 0.00 0.00 4.20
4748 4800 0.978151 TTGTACGCAGCCTTTCCCTA 59.022 50.000 0.00 0.00 0.00 3.53
4749 4801 0.248289 TGTACGCAGCCTTTCCCTAC 59.752 55.000 0.00 0.00 0.00 3.18
4750 4802 0.248289 GTACGCAGCCTTTCCCTACA 59.752 55.000 0.00 0.00 0.00 2.74
4751 4803 1.134491 GTACGCAGCCTTTCCCTACAT 60.134 52.381 0.00 0.00 0.00 2.29
4752 4804 0.328258 ACGCAGCCTTTCCCTACATT 59.672 50.000 0.00 0.00 0.00 2.71
4753 4805 1.271926 ACGCAGCCTTTCCCTACATTT 60.272 47.619 0.00 0.00 0.00 2.32
4754 4806 1.401905 CGCAGCCTTTCCCTACATTTC 59.598 52.381 0.00 0.00 0.00 2.17
4755 4807 2.728007 GCAGCCTTTCCCTACATTTCT 58.272 47.619 0.00 0.00 0.00 2.52
4756 4808 2.424956 GCAGCCTTTCCCTACATTTCTG 59.575 50.000 0.00 0.00 0.00 3.02
4757 4809 2.424956 CAGCCTTTCCCTACATTTCTGC 59.575 50.000 0.00 0.00 0.00 4.26
4758 4810 2.041620 AGCCTTTCCCTACATTTCTGCA 59.958 45.455 0.00 0.00 0.00 4.41
4759 4811 2.825532 GCCTTTCCCTACATTTCTGCAA 59.174 45.455 0.00 0.00 0.00 4.08
4760 4812 3.119352 GCCTTTCCCTACATTTCTGCAAG 60.119 47.826 0.00 0.00 0.00 4.01
4761 4813 4.335416 CCTTTCCCTACATTTCTGCAAGA 58.665 43.478 0.00 0.00 44.68 3.02
4771 4823 3.329300 TCTGCAAGAGGCTGTTTCC 57.671 52.632 0.00 0.00 38.67 3.13
4772 4824 0.473755 TCTGCAAGAGGCTGTTTCCA 59.526 50.000 0.00 0.00 38.67 3.53
4773 4825 0.879765 CTGCAAGAGGCTGTTTCCAG 59.120 55.000 0.00 0.00 45.15 3.86
4774 4826 0.538057 TGCAAGAGGCTGTTTCCAGG 60.538 55.000 0.00 0.00 45.15 4.45
4775 4827 0.250901 GCAAGAGGCTGTTTCCAGGA 60.251 55.000 0.00 0.00 39.22 3.86
4776 4828 1.528129 CAAGAGGCTGTTTCCAGGAC 58.472 55.000 0.00 0.00 39.22 3.85
4777 4829 1.072965 CAAGAGGCTGTTTCCAGGACT 59.927 52.381 0.00 0.00 39.22 3.85
4778 4830 1.439543 AGAGGCTGTTTCCAGGACTT 58.560 50.000 0.00 0.00 39.22 3.01
4779 4831 1.072965 AGAGGCTGTTTCCAGGACTTG 59.927 52.381 0.00 0.00 39.22 3.16
4780 4832 1.072331 GAGGCTGTTTCCAGGACTTGA 59.928 52.381 0.00 0.00 39.22 3.02
4781 4833 1.494721 AGGCTGTTTCCAGGACTTGAA 59.505 47.619 0.00 0.00 39.22 2.69
4782 4834 1.609072 GGCTGTTTCCAGGACTTGAAC 59.391 52.381 0.00 0.00 39.22 3.18
4783 4835 1.609072 GCTGTTTCCAGGACTTGAACC 59.391 52.381 0.00 0.00 39.22 3.62
4784 4836 2.230660 CTGTTTCCAGGACTTGAACCC 58.769 52.381 0.00 0.00 34.90 4.11
4785 4837 1.235724 GTTTCCAGGACTTGAACCCG 58.764 55.000 0.00 0.00 0.00 5.28
4786 4838 0.841289 TTTCCAGGACTTGAACCCGT 59.159 50.000 0.00 0.00 0.00 5.28
4787 4839 0.107831 TTCCAGGACTTGAACCCGTG 59.892 55.000 0.00 0.00 0.00 4.94
4788 4840 0.761323 TCCAGGACTTGAACCCGTGA 60.761 55.000 0.00 0.00 0.00 4.35
4789 4841 0.602905 CCAGGACTTGAACCCGTGAC 60.603 60.000 0.00 0.00 0.00 3.67
4790 4842 0.602905 CAGGACTTGAACCCGTGACC 60.603 60.000 0.00 0.00 0.00 4.02
4791 4843 0.763223 AGGACTTGAACCCGTGACCT 60.763 55.000 0.00 0.00 0.00 3.85
4792 4844 0.320508 GGACTTGAACCCGTGACCTC 60.321 60.000 0.00 0.00 0.00 3.85
4793 4845 0.391597 GACTTGAACCCGTGACCTCA 59.608 55.000 0.00 0.00 0.00 3.86
4794 4846 1.002087 GACTTGAACCCGTGACCTCAT 59.998 52.381 0.00 0.00 0.00 2.90
4795 4847 1.270839 ACTTGAACCCGTGACCTCATG 60.271 52.381 0.00 0.00 0.00 3.07
4806 4858 2.154139 ACCTCATGGTCACAAGGCA 58.846 52.632 0.00 0.00 44.78 4.75
4807 4859 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.00 0.00 44.78 4.85
4808 4860 1.310933 CCTCATGGTCACAAGGCAGC 61.311 60.000 0.00 0.00 0.00 5.25
4809 4861 0.607217 CTCATGGTCACAAGGCAGCA 60.607 55.000 0.00 0.00 0.00 4.41
4810 4862 0.607217 TCATGGTCACAAGGCAGCAG 60.607 55.000 0.00 0.00 0.00 4.24
4811 4863 1.975407 ATGGTCACAAGGCAGCAGC 60.975 57.895 0.00 0.00 41.10 5.25
4812 4864 2.282040 GGTCACAAGGCAGCAGCT 60.282 61.111 0.00 0.00 41.70 4.24
4813 4865 1.900498 GGTCACAAGGCAGCAGCTT 60.900 57.895 0.00 0.00 41.70 3.74
4814 4866 1.458639 GGTCACAAGGCAGCAGCTTT 61.459 55.000 0.00 0.00 41.17 3.51
4815 4867 1.238439 GTCACAAGGCAGCAGCTTTA 58.762 50.000 0.00 0.00 38.07 1.85
4816 4868 1.068954 GTCACAAGGCAGCAGCTTTAC 60.069 52.381 0.00 0.00 38.07 2.01
4817 4869 0.242017 CACAAGGCAGCAGCTTTACC 59.758 55.000 0.00 0.00 38.07 2.85
4818 4870 0.178992 ACAAGGCAGCAGCTTTACCA 60.179 50.000 0.00 0.00 38.07 3.25
4819 4871 0.242017 CAAGGCAGCAGCTTTACCAC 59.758 55.000 0.00 0.00 38.07 4.16
4820 4872 0.111253 AAGGCAGCAGCTTTACCACT 59.889 50.000 0.00 0.00 38.40 4.00
4821 4873 0.607489 AGGCAGCAGCTTTACCACTG 60.607 55.000 0.00 0.00 41.70 3.66
4825 4877 2.870372 CAGCTTTACCACTGCGCC 59.130 61.111 4.18 0.00 0.00 6.53
4826 4878 1.965930 CAGCTTTACCACTGCGCCA 60.966 57.895 4.18 0.00 0.00 5.69
4827 4879 1.228124 AGCTTTACCACTGCGCCAA 60.228 52.632 4.18 0.00 0.00 4.52
4828 4880 1.210155 GCTTTACCACTGCGCCAAG 59.790 57.895 4.18 0.00 0.00 3.61
4829 4881 1.875963 CTTTACCACTGCGCCAAGG 59.124 57.895 4.18 6.21 0.00 3.61
4830 4882 2.200170 CTTTACCACTGCGCCAAGGC 62.200 60.000 4.18 0.00 37.85 4.35
4831 4883 2.690653 TTTACCACTGCGCCAAGGCT 62.691 55.000 4.18 0.00 39.32 4.58
4832 4884 3.605749 TACCACTGCGCCAAGGCTC 62.606 63.158 4.18 1.20 39.32 4.70
4844 4896 2.123632 AGGCTCCCCTTCTCAGCA 59.876 61.111 0.00 0.00 38.74 4.41
4845 4897 2.270527 GGCTCCCCTTCTCAGCAC 59.729 66.667 0.00 0.00 34.62 4.40
4846 4898 2.596851 GGCTCCCCTTCTCAGCACA 61.597 63.158 0.00 0.00 34.62 4.57
4847 4899 1.078567 GCTCCCCTTCTCAGCACAG 60.079 63.158 0.00 0.00 33.06 3.66
4848 4900 1.548357 GCTCCCCTTCTCAGCACAGA 61.548 60.000 0.00 0.00 33.06 3.41
4849 4901 0.979665 CTCCCCTTCTCAGCACAGAA 59.020 55.000 0.00 0.00 0.00 3.02
4850 4902 1.349026 CTCCCCTTCTCAGCACAGAAA 59.651 52.381 0.00 0.00 31.86 2.52
4851 4903 1.774254 TCCCCTTCTCAGCACAGAAAA 59.226 47.619 0.00 0.00 31.86 2.29
4852 4904 2.157738 CCCCTTCTCAGCACAGAAAAG 58.842 52.381 0.00 0.00 31.86 2.27
4853 4905 2.224621 CCCCTTCTCAGCACAGAAAAGA 60.225 50.000 0.00 0.00 31.86 2.52
4854 4906 3.480470 CCCTTCTCAGCACAGAAAAGAA 58.520 45.455 0.00 0.00 31.86 2.52
4855 4907 4.077822 CCCTTCTCAGCACAGAAAAGAAT 58.922 43.478 0.00 0.00 31.86 2.40
4856 4908 5.248640 CCCTTCTCAGCACAGAAAAGAATA 58.751 41.667 0.00 0.00 31.86 1.75
4857 4909 5.707298 CCCTTCTCAGCACAGAAAAGAATAA 59.293 40.000 0.00 0.00 31.86 1.40
4858 4910 6.207417 CCCTTCTCAGCACAGAAAAGAATAAA 59.793 38.462 0.00 0.00 31.86 1.40
4859 4911 7.255590 CCCTTCTCAGCACAGAAAAGAATAAAA 60.256 37.037 0.00 0.00 31.86 1.52
4860 4912 8.137437 CCTTCTCAGCACAGAAAAGAATAAAAA 58.863 33.333 0.00 0.00 31.86 1.94
4861 4913 9.178427 CTTCTCAGCACAGAAAAGAATAAAAAG 57.822 33.333 0.00 0.00 31.86 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 1.720781 AAGCTGGGAGCATTTTGGTT 58.279 45.000 0.00 0.00 45.56 3.67
67 68 4.567959 GCTTGTTGGAATGGAAATGTATGC 59.432 41.667 0.00 0.00 0.00 3.14
129 130 0.036388 TCTGGAATTCGTGCTGTCCC 60.036 55.000 0.00 0.00 0.00 4.46
146 147 4.826274 TGTGGCTATGTTAAGAAGCTCT 57.174 40.909 0.00 0.00 36.48 4.09
155 156 6.657541 CCTTTTCCTACTTTGTGGCTATGTTA 59.342 38.462 0.00 0.00 0.00 2.41
197 215 8.561536 TTCCTTTCCTTTCCTTTTCCTATTTT 57.438 30.769 0.00 0.00 0.00 1.82
353 374 0.965363 GGGTGGGGTATTGCTGTGTG 60.965 60.000 0.00 0.00 0.00 3.82
365 386 0.633921 TTGATGGTTATGGGGTGGGG 59.366 55.000 0.00 0.00 0.00 4.96
368 389 5.937975 AGAAAATTGATGGTTATGGGGTG 57.062 39.130 0.00 0.00 0.00 4.61
805 832 2.151502 TTTTGAGGCCACTGGAACAA 57.848 45.000 5.01 0.00 38.70 2.83
817 844 9.708222 CGTTGATTGATCTAATAGTTTTTGAGG 57.292 33.333 0.00 0.00 0.00 3.86
883 910 3.118905 TGCCATTAAACAGCCAAAACC 57.881 42.857 0.00 0.00 0.00 3.27
884 911 5.687770 ATTTGCCATTAAACAGCCAAAAC 57.312 34.783 0.00 0.00 0.00 2.43
885 912 7.094463 CCATTATTTGCCATTAAACAGCCAAAA 60.094 33.333 0.00 0.00 0.00 2.44
919 946 3.873952 CACCATTTTTCTTTTGCGGGAAA 59.126 39.130 0.00 0.00 0.00 3.13
920 947 3.133003 TCACCATTTTTCTTTTGCGGGAA 59.867 39.130 0.00 0.00 0.00 3.97
921 948 2.695666 TCACCATTTTTCTTTTGCGGGA 59.304 40.909 0.00 0.00 0.00 5.14
922 949 3.104843 TCACCATTTTTCTTTTGCGGG 57.895 42.857 0.00 0.00 0.00 6.13
923 950 3.059665 GCTTCACCATTTTTCTTTTGCGG 60.060 43.478 0.00 0.00 0.00 5.69
924 951 3.555139 TGCTTCACCATTTTTCTTTTGCG 59.445 39.130 0.00 0.00 0.00 4.85
925 952 5.163774 TGTTGCTTCACCATTTTTCTTTTGC 60.164 36.000 0.00 0.00 0.00 3.68
926 953 6.092533 ACTGTTGCTTCACCATTTTTCTTTTG 59.907 34.615 0.00 0.00 0.00 2.44
927 954 6.172630 ACTGTTGCTTCACCATTTTTCTTTT 58.827 32.000 0.00 0.00 0.00 2.27
928 955 5.733676 ACTGTTGCTTCACCATTTTTCTTT 58.266 33.333 0.00 0.00 0.00 2.52
929 956 5.343307 ACTGTTGCTTCACCATTTTTCTT 57.657 34.783 0.00 0.00 0.00 2.52
930 957 5.343307 AACTGTTGCTTCACCATTTTTCT 57.657 34.783 0.00 0.00 0.00 2.52
931 958 5.462068 GGTAACTGTTGCTTCACCATTTTTC 59.538 40.000 8.49 0.00 0.00 2.29
932 959 5.356426 GGTAACTGTTGCTTCACCATTTTT 58.644 37.500 8.49 0.00 0.00 1.94
933 960 4.499019 CGGTAACTGTTGCTTCACCATTTT 60.499 41.667 8.49 0.00 0.00 1.82
934 961 3.004315 CGGTAACTGTTGCTTCACCATTT 59.996 43.478 8.49 0.00 0.00 2.32
935 962 2.552315 CGGTAACTGTTGCTTCACCATT 59.448 45.455 8.49 0.00 0.00 3.16
936 963 2.151202 CGGTAACTGTTGCTTCACCAT 58.849 47.619 8.49 0.00 0.00 3.55
937 964 1.139256 TCGGTAACTGTTGCTTCACCA 59.861 47.619 8.49 0.00 0.00 4.17
938 965 1.873698 TCGGTAACTGTTGCTTCACC 58.126 50.000 8.49 4.21 0.00 4.02
939 966 2.806244 ACATCGGTAACTGTTGCTTCAC 59.194 45.455 8.49 0.00 0.00 3.18
940 967 3.120321 ACATCGGTAACTGTTGCTTCA 57.880 42.857 8.49 0.00 0.00 3.02
941 968 3.810373 CAACATCGGTAACTGTTGCTTC 58.190 45.455 8.49 0.00 43.88 3.86
942 969 3.896648 CAACATCGGTAACTGTTGCTT 57.103 42.857 8.49 0.00 43.88 3.91
946 973 4.330944 TCTGTCAACATCGGTAACTGTT 57.669 40.909 0.00 0.00 36.04 3.16
1288 1315 1.303309 GGATCCATCTTTCGTGCCAG 58.697 55.000 6.95 0.00 0.00 4.85
1336 1363 0.598065 GAACCACTCCATGTTGGCAC 59.402 55.000 5.38 0.00 37.47 5.01
1384 1411 9.017669 ACGTACGTTTCTAATCAACTTGATATC 57.982 33.333 16.72 0.00 35.76 1.63
1427 1454 6.787225 AGTGATCGTTCAGACTCACTAATAC 58.213 40.000 2.40 0.00 41.47 1.89
1445 1472 8.068380 GTGAAAGTAGGTTGTTTACAAGTGATC 58.932 37.037 0.00 0.00 36.39 2.92
1539 1570 6.757173 TGGCTTAGAGCTATTTATTACCCA 57.243 37.500 0.00 0.00 41.99 4.51
1640 1671 5.182001 GTGATGTTAACAGATTGTTGCTCCT 59.818 40.000 14.65 0.00 41.30 3.69
1667 1699 4.913924 GCACAATGAACAAGATGAACAGAC 59.086 41.667 0.00 0.00 0.00 3.51
2404 2436 5.814764 TCCTTCGAGTCTATGACAACTAC 57.185 43.478 0.46 0.00 34.60 2.73
2509 2541 5.655532 AGGTTCATCTGATTCAAAGGAATGG 59.344 40.000 0.00 0.00 43.69 3.16
2549 2581 9.331282 AAAGAATTTCGTAGGATTCTAATCCAG 57.669 33.333 20.95 12.83 46.34 3.86
2606 2638 6.601613 TGTAATTGAATTTCTAGCCGGTGAAT 59.398 34.615 1.90 0.00 0.00 2.57
2694 2726 4.632688 GCATGCATGGCAGAAAATAAACTT 59.367 37.500 27.34 0.00 43.65 2.66
2745 2777 4.646492 GTGGCAAGGATATTCAGGTGAAAT 59.354 41.667 0.00 0.00 37.61 2.17
2914 2946 4.403734 TCACTCATGTGGTGTAGACTGTA 58.596 43.478 16.51 0.00 43.94 2.74
2915 2947 3.230976 TCACTCATGTGGTGTAGACTGT 58.769 45.455 16.51 0.00 43.94 3.55
2916 2948 3.942130 TCACTCATGTGGTGTAGACTG 57.058 47.619 16.51 0.00 43.94 3.51
2917 2949 3.641436 TGTTCACTCATGTGGTGTAGACT 59.359 43.478 16.51 0.00 43.94 3.24
2918 2950 3.990092 TGTTCACTCATGTGGTGTAGAC 58.010 45.455 16.51 14.28 43.94 2.59
2919 2951 4.681074 TTGTTCACTCATGTGGTGTAGA 57.319 40.909 16.51 7.37 43.94 2.59
2920 2952 4.996758 TGATTGTTCACTCATGTGGTGTAG 59.003 41.667 16.51 0.00 43.94 2.74
2962 2994 5.539582 TGTCAGTTTGTAAATATCGGCAC 57.460 39.130 0.00 0.00 0.00 5.01
2991 3023 7.334921 TCCTTTCTGTAACAATATTGTAACGGG 59.665 37.037 21.07 14.23 41.31 5.28
3087 3119 3.136123 CTTCCCACCATGGCAGCG 61.136 66.667 13.04 0.00 35.79 5.18
3125 3157 2.268298 GTATCGTGTGCGGAAAGATGT 58.732 47.619 1.39 0.00 38.89 3.06
3151 3183 3.285484 CATCATTTGGGGAAGAGTCTGG 58.715 50.000 0.00 0.00 0.00 3.86
3167 3199 1.098050 GAAGTTTCCGGCTGCATCAT 58.902 50.000 0.50 0.00 0.00 2.45
3201 3233 2.100197 CCCAGATGGTCGTCTGAACTA 58.900 52.381 18.69 0.00 46.77 2.24
3470 3502 4.105217 TGCCAGAAGATATCCCAATGTGAT 59.895 41.667 0.00 0.00 0.00 3.06
3480 3512 4.161377 GTCCCTAGGATGCCAGAAGATATC 59.839 50.000 11.48 0.00 32.73 1.63
3590 3622 1.354031 TCCAAGGCACTGCATTAGGAA 59.646 47.619 13.65 2.99 40.86 3.36
3813 3845 3.487711 GCTCAGATTTCTGCTGCTCATTG 60.488 47.826 14.01 0.00 43.46 2.82
4033 4077 2.006888 ACTGTCCGTGTCAGTTTTGTG 58.993 47.619 0.00 0.00 42.50 3.33
4049 4093 4.516698 CAGATTTCTGTAAAGCCACACTGT 59.483 41.667 0.00 0.00 39.09 3.55
4117 4161 3.244491 GCACTCTCTATTCCAGCATCCAT 60.244 47.826 0.00 0.00 0.00 3.41
4430 4477 0.603569 CCAGTAGTGACGCCTGAAGT 59.396 55.000 0.00 0.00 0.00 3.01
4545 4594 6.307318 CACTAAAGCTTTTGTCTTGATGCATC 59.693 38.462 21.07 20.14 0.00 3.91
4661 4713 3.643595 TACATGCACTGGGGCTGCC 62.644 63.158 11.05 11.05 33.36 4.85
4662 4714 2.045045 TACATGCACTGGGGCTGC 60.045 61.111 0.00 0.00 35.03 5.25
4663 4715 2.117156 GCTACATGCACTGGGGCTG 61.117 63.158 0.00 0.00 42.31 4.85
4664 4716 2.262774 GAGCTACATGCACTGGGGCT 62.263 60.000 13.29 13.29 45.94 5.19
4665 4717 1.821332 GAGCTACATGCACTGGGGC 60.821 63.158 0.00 0.00 45.94 5.80
4666 4718 1.153086 GGAGCTACATGCACTGGGG 60.153 63.158 0.00 0.00 45.94 4.96
4667 4719 1.153086 GGGAGCTACATGCACTGGG 60.153 63.158 0.00 0.00 45.94 4.45
4668 4720 1.522355 CGGGAGCTACATGCACTGG 60.522 63.158 0.00 0.00 45.94 4.00
4669 4721 4.115279 CGGGAGCTACATGCACTG 57.885 61.111 0.00 0.00 45.94 3.66
4690 4742 4.785453 CTTCCCCAGACCCTGCGC 62.785 72.222 0.00 0.00 0.00 6.09
4691 4743 4.101448 CCTTCCCCAGACCCTGCG 62.101 72.222 0.00 0.00 0.00 5.18
4692 4744 3.732849 CCCTTCCCCAGACCCTGC 61.733 72.222 0.00 0.00 0.00 4.85
4693 4745 2.204151 ACCCTTCCCCAGACCCTG 60.204 66.667 0.00 0.00 0.00 4.45
4694 4746 2.125225 GACCCTTCCCCAGACCCT 59.875 66.667 0.00 0.00 0.00 4.34
4695 4747 3.015753 GGACCCTTCCCCAGACCC 61.016 72.222 0.00 0.00 35.57 4.46
4696 4748 3.400054 CGGACCCTTCCCCAGACC 61.400 72.222 0.00 0.00 38.99 3.85
4697 4749 2.284405 TCGGACCCTTCCCCAGAC 60.284 66.667 0.00 0.00 38.99 3.51
4698 4750 2.284405 GTCGGACCCTTCCCCAGA 60.284 66.667 0.00 0.00 38.99 3.86
4699 4751 3.400054 GGTCGGACCCTTCCCCAG 61.400 72.222 16.55 0.00 38.99 4.45
4700 4752 4.257810 TGGTCGGACCCTTCCCCA 62.258 66.667 23.81 0.69 38.99 4.96
4701 4753 3.714001 GTGGTCGGACCCTTCCCC 61.714 72.222 23.81 0.00 38.99 4.81
4702 4754 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
4703 4755 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
4704 4756 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
4705 4757 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
4706 4758 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
4707 4759 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
4708 4760 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
4709 4761 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
4714 4766 3.867216 GCGTACAATAGACCCAAAGTGGT 60.867 47.826 0.00 0.00 42.79 4.16
4715 4767 2.676342 GCGTACAATAGACCCAAAGTGG 59.324 50.000 0.00 0.00 37.25 4.00
4716 4768 3.331150 TGCGTACAATAGACCCAAAGTG 58.669 45.455 0.00 0.00 0.00 3.16
4717 4769 3.596214 CTGCGTACAATAGACCCAAAGT 58.404 45.455 0.00 0.00 0.00 2.66
4718 4770 2.351726 GCTGCGTACAATAGACCCAAAG 59.648 50.000 0.00 0.00 0.00 2.77
4719 4771 2.352388 GCTGCGTACAATAGACCCAAA 58.648 47.619 0.00 0.00 0.00 3.28
4720 4772 1.406341 GGCTGCGTACAATAGACCCAA 60.406 52.381 0.00 0.00 0.00 4.12
4721 4773 0.177141 GGCTGCGTACAATAGACCCA 59.823 55.000 0.00 0.00 0.00 4.51
4722 4774 0.464452 AGGCTGCGTACAATAGACCC 59.536 55.000 0.00 0.00 0.00 4.46
4723 4775 2.311124 AAGGCTGCGTACAATAGACC 57.689 50.000 0.00 0.00 0.00 3.85
4724 4776 2.608090 GGAAAGGCTGCGTACAATAGAC 59.392 50.000 0.00 0.00 0.00 2.59
4725 4777 2.419574 GGGAAAGGCTGCGTACAATAGA 60.420 50.000 0.00 0.00 0.00 1.98
4726 4778 1.940613 GGGAAAGGCTGCGTACAATAG 59.059 52.381 0.00 0.00 0.00 1.73
4727 4779 1.557832 AGGGAAAGGCTGCGTACAATA 59.442 47.619 0.00 0.00 0.00 1.90
4728 4780 0.328258 AGGGAAAGGCTGCGTACAAT 59.672 50.000 0.00 0.00 0.00 2.71
4729 4781 0.978151 TAGGGAAAGGCTGCGTACAA 59.022 50.000 0.00 0.00 0.00 2.41
4730 4782 0.248289 GTAGGGAAAGGCTGCGTACA 59.752 55.000 0.00 0.00 36.89 2.90
4731 4783 0.248289 TGTAGGGAAAGGCTGCGTAC 59.752 55.000 0.00 0.00 37.28 3.67
4732 4784 1.200519 ATGTAGGGAAAGGCTGCGTA 58.799 50.000 0.00 0.00 0.00 4.42
4733 4785 0.328258 AATGTAGGGAAAGGCTGCGT 59.672 50.000 0.00 0.00 0.00 5.24
4734 4786 1.401905 GAAATGTAGGGAAAGGCTGCG 59.598 52.381 0.00 0.00 0.00 5.18
4735 4787 2.424956 CAGAAATGTAGGGAAAGGCTGC 59.575 50.000 0.00 0.00 0.00 5.25
4736 4788 2.424956 GCAGAAATGTAGGGAAAGGCTG 59.575 50.000 0.00 0.00 0.00 4.85
4737 4789 2.041620 TGCAGAAATGTAGGGAAAGGCT 59.958 45.455 0.00 0.00 0.00 4.58
4738 4790 2.446435 TGCAGAAATGTAGGGAAAGGC 58.554 47.619 0.00 0.00 0.00 4.35
4739 4791 4.335416 TCTTGCAGAAATGTAGGGAAAGG 58.665 43.478 0.00 0.00 0.00 3.11
4740 4792 4.397417 CCTCTTGCAGAAATGTAGGGAAAG 59.603 45.833 0.00 0.00 0.00 2.62
4741 4793 4.335416 CCTCTTGCAGAAATGTAGGGAAA 58.665 43.478 0.00 0.00 0.00 3.13
4742 4794 3.873801 GCCTCTTGCAGAAATGTAGGGAA 60.874 47.826 0.00 0.00 40.77 3.97
4743 4795 2.356125 GCCTCTTGCAGAAATGTAGGGA 60.356 50.000 0.00 0.00 40.77 4.20
4744 4796 2.019984 GCCTCTTGCAGAAATGTAGGG 58.980 52.381 0.00 0.00 40.77 3.53
4745 4797 2.681848 CAGCCTCTTGCAGAAATGTAGG 59.318 50.000 0.00 0.00 44.83 3.18
4746 4798 3.341823 ACAGCCTCTTGCAGAAATGTAG 58.658 45.455 0.00 0.00 44.83 2.74
4747 4799 3.423539 ACAGCCTCTTGCAGAAATGTA 57.576 42.857 0.00 0.00 44.83 2.29
4748 4800 2.283145 ACAGCCTCTTGCAGAAATGT 57.717 45.000 0.00 0.00 44.83 2.71
4749 4801 3.572584 GAAACAGCCTCTTGCAGAAATG 58.427 45.455 0.00 0.00 44.83 2.32
4750 4802 2.560105 GGAAACAGCCTCTTGCAGAAAT 59.440 45.455 0.00 0.00 44.83 2.17
4751 4803 1.956477 GGAAACAGCCTCTTGCAGAAA 59.044 47.619 0.00 0.00 44.83 2.52
4752 4804 1.133823 TGGAAACAGCCTCTTGCAGAA 60.134 47.619 0.00 0.00 44.83 3.02
4753 4805 0.473755 TGGAAACAGCCTCTTGCAGA 59.526 50.000 0.00 0.00 44.83 4.26
4754 4806 3.025924 TGGAAACAGCCTCTTGCAG 57.974 52.632 0.00 0.00 44.83 4.41
4765 4817 1.476110 CGGGTTCAAGTCCTGGAAACA 60.476 52.381 0.00 0.00 32.36 2.83
4766 4818 1.235724 CGGGTTCAAGTCCTGGAAAC 58.764 55.000 0.00 0.00 0.00 2.78
4767 4819 0.841289 ACGGGTTCAAGTCCTGGAAA 59.159 50.000 0.00 0.00 35.79 3.13
4768 4820 0.107831 CACGGGTTCAAGTCCTGGAA 59.892 55.000 0.00 0.00 35.79 3.53
4769 4821 0.761323 TCACGGGTTCAAGTCCTGGA 60.761 55.000 0.00 0.00 35.79 3.86
4770 4822 0.602905 GTCACGGGTTCAAGTCCTGG 60.603 60.000 0.00 0.00 35.79 4.45
4771 4823 0.602905 GGTCACGGGTTCAAGTCCTG 60.603 60.000 0.00 0.00 37.36 3.86
4772 4824 0.763223 AGGTCACGGGTTCAAGTCCT 60.763 55.000 0.00 0.00 0.00 3.85
4773 4825 0.320508 GAGGTCACGGGTTCAAGTCC 60.321 60.000 0.00 0.00 0.00 3.85
4774 4826 0.391597 TGAGGTCACGGGTTCAAGTC 59.608 55.000 0.00 0.00 0.00 3.01
4775 4827 1.056660 ATGAGGTCACGGGTTCAAGT 58.943 50.000 0.00 0.00 0.00 3.16
4776 4828 1.442769 CATGAGGTCACGGGTTCAAG 58.557 55.000 0.00 0.00 0.00 3.02
4777 4829 0.036164 CCATGAGGTCACGGGTTCAA 59.964 55.000 0.00 0.00 0.00 2.69
4778 4830 1.676968 CCATGAGGTCACGGGTTCA 59.323 57.895 0.00 0.00 0.00 3.18
4779 4831 4.617875 CCATGAGGTCACGGGTTC 57.382 61.111 0.00 0.00 0.00 3.62
4789 4841 1.310933 GCTGCCTTGTGACCATGAGG 61.311 60.000 0.00 0.00 42.21 3.86
4790 4842 0.607217 TGCTGCCTTGTGACCATGAG 60.607 55.000 0.00 0.00 0.00 2.90
4791 4843 0.607217 CTGCTGCCTTGTGACCATGA 60.607 55.000 0.00 0.00 0.00 3.07
4792 4844 1.880894 CTGCTGCCTTGTGACCATG 59.119 57.895 0.00 0.00 0.00 3.66
4793 4845 1.975407 GCTGCTGCCTTGTGACCAT 60.975 57.895 3.85 0.00 0.00 3.55
4794 4846 2.595463 GCTGCTGCCTTGTGACCA 60.595 61.111 3.85 0.00 0.00 4.02
4795 4847 1.458639 AAAGCTGCTGCCTTGTGACC 61.459 55.000 12.44 0.00 40.80 4.02
4796 4848 1.068954 GTAAAGCTGCTGCCTTGTGAC 60.069 52.381 12.44 0.00 40.80 3.67
4797 4849 1.238439 GTAAAGCTGCTGCCTTGTGA 58.762 50.000 12.44 0.00 40.80 3.58
4798 4850 0.242017 GGTAAAGCTGCTGCCTTGTG 59.758 55.000 12.44 0.00 40.80 3.33
4799 4851 0.178992 TGGTAAAGCTGCTGCCTTGT 60.179 50.000 12.44 0.00 40.80 3.16
4800 4852 0.242017 GTGGTAAAGCTGCTGCCTTG 59.758 55.000 12.44 0.00 40.80 3.61
4801 4853 0.111253 AGTGGTAAAGCTGCTGCCTT 59.889 50.000 12.44 8.34 40.80 4.35
4802 4854 0.607489 CAGTGGTAAAGCTGCTGCCT 60.607 55.000 12.44 2.45 40.80 4.75
4803 4855 1.878775 CAGTGGTAAAGCTGCTGCC 59.121 57.895 12.44 7.07 40.80 4.85
4808 4860 1.514678 TTGGCGCAGTGGTAAAGCTG 61.515 55.000 10.83 0.00 35.93 4.24
4809 4861 1.228124 TTGGCGCAGTGGTAAAGCT 60.228 52.632 10.83 0.00 0.00 3.74
4810 4862 1.210155 CTTGGCGCAGTGGTAAAGC 59.790 57.895 10.83 0.00 0.00 3.51
4811 4863 1.875963 CCTTGGCGCAGTGGTAAAG 59.124 57.895 10.83 0.71 0.00 1.85
4812 4864 2.265182 GCCTTGGCGCAGTGGTAAA 61.265 57.895 10.83 0.00 0.00 2.01
4813 4865 2.671619 GCCTTGGCGCAGTGGTAA 60.672 61.111 10.83 0.00 0.00 2.85
4814 4866 3.605749 GAGCCTTGGCGCAGTGGTA 62.606 63.158 10.83 0.00 0.00 3.25
4822 4874 3.689002 GAGAAGGGGAGCCTTGGCG 62.689 68.421 5.95 0.00 0.00 5.69
4823 4875 2.273776 GAGAAGGGGAGCCTTGGC 59.726 66.667 2.97 2.97 0.00 4.52
4824 4876 1.606531 CTGAGAAGGGGAGCCTTGG 59.393 63.158 0.00 0.00 0.00 3.61
4825 4877 1.077858 GCTGAGAAGGGGAGCCTTG 60.078 63.158 0.00 0.00 0.00 3.61
4826 4878 1.539869 TGCTGAGAAGGGGAGCCTT 60.540 57.895 0.00 0.00 31.31 4.35
4827 4879 2.123632 TGCTGAGAAGGGGAGCCT 59.876 61.111 0.00 0.00 31.31 4.58
4828 4880 2.270527 GTGCTGAGAAGGGGAGCC 59.729 66.667 0.00 0.00 31.31 4.70
4829 4881 1.078567 CTGTGCTGAGAAGGGGAGC 60.079 63.158 0.00 0.00 0.00 4.70
4830 4882 0.979665 TTCTGTGCTGAGAAGGGGAG 59.020 55.000 0.00 0.00 0.00 4.30
4831 4883 1.434188 TTTCTGTGCTGAGAAGGGGA 58.566 50.000 0.00 0.00 33.50 4.81
4832 4884 2.157738 CTTTTCTGTGCTGAGAAGGGG 58.842 52.381 0.00 0.00 33.50 4.79
4833 4885 3.131709 TCTTTTCTGTGCTGAGAAGGG 57.868 47.619 8.63 0.00 33.50 3.95
4834 4886 6.808008 TTATTCTTTTCTGTGCTGAGAAGG 57.192 37.500 8.63 0.00 33.50 3.46
4835 4887 9.178427 CTTTTTATTCTTTTCTGTGCTGAGAAG 57.822 33.333 3.94 3.94 33.50 2.85


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

AutoCloner maintained by Alex Coulton.