Multiple sequence alignment - TraesCS7A01G299600

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 TraesCS7A01G299600 chr7A 100.000 5535 0 0 1 5535 410726006 410731540 0.000000e+00 10222.0
1 TraesCS7A01G299600 chr7B 97.263 4202 88 8 659 4857 316007030 316002853 0.000000e+00 7097.0
2 TraesCS7A01G299600 chr7B 88.156 667 59 10 1 649 3922839 3923503 0.000000e+00 776.0
3 TraesCS7A01G299600 chr7B 100.000 76 0 0 5460 5535 648072221 648072296 2.080000e-29 141.0
4 TraesCS7A01G299600 chr7D 95.368 4447 134 22 660 5097 369862056 369857673 0.000000e+00 7005.0
5 TraesCS7A01G299600 chr7D 87.113 194 16 8 5280 5464 369856493 369856300 1.560000e-50 211.0
6 TraesCS7A01G299600 chr5A 84.566 1244 105 24 1899 3108 546806463 546807653 0.000000e+00 1153.0
7 TraesCS7A01G299600 chr5A 85.572 804 86 15 3138 3939 546807650 546808425 0.000000e+00 815.0
8 TraesCS7A01G299600 chr5A 100.000 76 0 0 5460 5535 581401495 581401570 2.080000e-29 141.0
9 TraesCS7A01G299600 chr5A 91.837 49 2 2 1034 1081 660799247 660799294 3.580000e-07 67.6
10 TraesCS7A01G299600 chr5A 89.796 49 5 0 1033 1081 317248163 317248115 4.630000e-06 63.9
11 TraesCS7A01G299600 chr1D 92.966 654 41 2 1 649 432545333 432545986 0.000000e+00 948.0
12 TraesCS7A01G299600 chr4A 92.649 653 42 4 1 648 650844793 650845444 0.000000e+00 935.0
13 TraesCS7A01G299600 chr6B 89.401 651 60 2 1 650 578943960 578943318 0.000000e+00 811.0
14 TraesCS7A01G299600 chr6B 98.734 79 1 0 5457 5535 362954858 362954936 2.080000e-29 141.0
15 TraesCS7A01G299600 chr4B 91.185 363 27 2 1 359 22197613 22197252 6.440000e-134 488.0
16 TraesCS7A01G299600 chr4B 91.497 294 24 1 357 649 22178296 22178003 2.400000e-108 403.0
17 TraesCS7A01G299600 chr4B 93.478 46 1 2 1037 1081 611553508 611553464 3.580000e-07 67.6
18 TraesCS7A01G299600 chr3A 93.082 159 10 1 1892 2049 431817916 431818074 1.200000e-56 231.0
19 TraesCS7A01G299600 chr3A 98.718 78 1 0 5458 5535 461965662 461965739 7.480000e-29 139.0
20 TraesCS7A01G299600 chr3D 90.132 152 13 2 1899 2049 302935220 302935070 4.370000e-46 196.0
21 TraesCS7A01G299600 chr3B 93.814 97 3 3 5440 5535 249095898 249095992 5.780000e-30 143.0
22 TraesCS7A01G299600 chr3B 100.000 76 0 0 5460 5535 161710073 161710148 2.080000e-29 141.0
23 TraesCS7A01G299600 chr2B 100.000 76 0 0 5460 5535 727321561 727321636 2.080000e-29 141.0
24 TraesCS7A01G299600 chr1B 100.000 76 0 0 5460 5535 88878457 88878532 2.080000e-29 141.0
25 TraesCS7A01G299600 chr1B 97.500 80 1 1 5456 5535 565659839 565659761 9.670000e-28 135.0
26 TraesCS7A01G299600 chr4D 93.478 46 1 2 1037 1081 481912556 481912512 3.580000e-07 67.6
27 TraesCS7A01G299600 chr5D 89.796 49 5 0 1033 1081 238066220 238066268 4.630000e-06 63.9
28 TraesCS7A01G299600 chr5D 100.000 32 0 0 1039 1070 481183790 481183821 5.990000e-05 60.2
29 TraesCS7A01G299600 chr5B 89.796 49 5 0 1033 1081 267779275 267779227 4.630000e-06 63.9


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 TraesCS7A01G299600 chr7A 410726006 410731540 5534 False 10222 10222 100.0000 1 5535 1 chr7A.!!$F1 5534
1 TraesCS7A01G299600 chr7B 316002853 316007030 4177 True 7097 7097 97.2630 659 4857 1 chr7B.!!$R1 4198
2 TraesCS7A01G299600 chr7B 3922839 3923503 664 False 776 776 88.1560 1 649 1 chr7B.!!$F1 648
3 TraesCS7A01G299600 chr7D 369856300 369862056 5756 True 3608 7005 91.2405 660 5464 2 chr7D.!!$R1 4804
4 TraesCS7A01G299600 chr5A 546806463 546808425 1962 False 984 1153 85.0690 1899 3939 2 chr5A.!!$F3 2040
5 TraesCS7A01G299600 chr1D 432545333 432545986 653 False 948 948 92.9660 1 649 1 chr1D.!!$F1 648
6 TraesCS7A01G299600 chr4A 650844793 650845444 651 False 935 935 92.6490 1 648 1 chr4A.!!$F1 647
7 TraesCS7A01G299600 chr6B 578943318 578943960 642 True 811 811 89.4010 1 650 1 chr6B.!!$R1 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
650 671 0.462375 GGAAACCAAACACGCCCTTT 59.538 50.000 0.00 0.0 0.00 3.11 F
654 675 0.673437 ACCAAACACGCCCTTTGATG 59.327 50.000 2.48 0.0 31.32 3.07 F
655 676 0.958091 CCAAACACGCCCTTTGATGA 59.042 50.000 2.48 0.0 31.32 2.92 F
664 685 1.224592 CCTTTGATGACTCCCCCGG 59.775 63.158 0.00 0.0 0.00 5.73 F
1863 1890 1.534476 TGGGTACTGGAAGGCGACA 60.534 57.895 0.00 0.0 39.30 4.35 F
3091 3153 0.176910 GTTCTCTGTAGGCTCAGGGC 59.823 60.000 12.09 0.0 36.03 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1863 1890 0.119155 TGATGACCCTGTCCTTCCCT 59.881 55.000 0.00 0.00 0.00 4.20 R
2067 2118 3.076621 CAGAATCTAACAGCACTGCCAA 58.923 45.455 0.00 0.00 0.00 4.52 R
2186 2238 6.960992 CGGATTTGTACTGTGTTGATTATGTG 59.039 38.462 0.00 0.00 0.00 3.21 R
2816 2869 6.261118 CAAATTCATGAGACCCGAGATTTTC 58.739 40.000 0.00 0.00 0.00 2.29 R
3874 3936 0.906756 TCCTCACCTCAGCTTCCAGG 60.907 60.000 2.08 2.08 35.69 4.45 R
5155 5221 0.110486 GCTCCGATCTCTCTCCCTCT 59.890 60.000 0.00 0.00 0.00 3.69 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
21 22 4.003788 CGACGAGTTGGCTGGGGT 62.004 66.667 0.00 0.00 0.00 4.95
25 26 1.373435 CGAGTTGGCTGGGGTGTAA 59.627 57.895 0.00 0.00 0.00 2.41
30 31 0.485099 TTGGCTGGGGTGTAAATGGT 59.515 50.000 0.00 0.00 0.00 3.55
395 400 2.683933 GGGGAGGGAGCTTCGACA 60.684 66.667 0.00 0.00 0.00 4.35
399 404 1.251527 GGAGGGAGCTTCGACAGTGA 61.252 60.000 0.00 0.00 0.00 3.41
404 409 2.355837 GCTTCGACAGTGACGGCA 60.356 61.111 14.72 0.00 0.00 5.69
428 433 1.153349 GGGTTGGGTGCTCGATCTC 60.153 63.158 0.00 0.00 0.00 2.75
460 480 7.118496 AGAGAGAAGAGAAAAAGAAGACACA 57.882 36.000 0.00 0.00 0.00 3.72
462 482 7.069331 AGAGAGAAGAGAAAAAGAAGACACAGA 59.931 37.037 0.00 0.00 0.00 3.41
465 485 7.560368 AGAAGAGAAAAAGAAGACACAGAAGA 58.440 34.615 0.00 0.00 0.00 2.87
503 523 1.828660 CCAGGCTCGGAGATACGGT 60.829 63.158 9.69 0.00 33.89 4.83
527 547 2.125350 CTGCGTTCCTCTCAGCCC 60.125 66.667 0.00 0.00 0.00 5.19
607 627 4.685165 CCAAACACATTCGATTTTGCATGA 59.315 37.500 0.00 0.00 0.00 3.07
650 671 0.462375 GGAAACCAAACACGCCCTTT 59.538 50.000 0.00 0.00 0.00 3.11
651 672 1.566404 GAAACCAAACACGCCCTTTG 58.434 50.000 0.00 0.00 0.00 2.77
652 673 1.135333 GAAACCAAACACGCCCTTTGA 59.865 47.619 2.48 0.00 31.32 2.69
653 674 1.408969 AACCAAACACGCCCTTTGAT 58.591 45.000 2.48 0.00 31.32 2.57
654 675 0.673437 ACCAAACACGCCCTTTGATG 59.327 50.000 2.48 0.00 31.32 3.07
655 676 0.958091 CCAAACACGCCCTTTGATGA 59.042 50.000 2.48 0.00 31.32 2.92
656 677 1.335872 CCAAACACGCCCTTTGATGAC 60.336 52.381 2.48 0.00 31.32 3.06
657 678 1.608590 CAAACACGCCCTTTGATGACT 59.391 47.619 0.00 0.00 31.32 3.41
664 685 1.224592 CCTTTGATGACTCCCCCGG 59.775 63.158 0.00 0.00 0.00 5.73
1186 1208 4.082523 GTACTGCCGCTCCTGCCA 62.083 66.667 0.00 0.00 35.36 4.92
1391 1413 3.064820 CGTTGCTGTTCTTGTAACCACTT 59.935 43.478 0.00 0.00 0.00 3.16
1594 1620 2.238084 TCCCTCGATGCCTGCTATAT 57.762 50.000 0.00 0.00 0.00 0.86
1595 1621 3.382083 TCCCTCGATGCCTGCTATATA 57.618 47.619 0.00 0.00 0.00 0.86
1596 1622 3.024547 TCCCTCGATGCCTGCTATATAC 58.975 50.000 0.00 0.00 0.00 1.47
1597 1623 2.760650 CCCTCGATGCCTGCTATATACA 59.239 50.000 0.00 0.00 0.00 2.29
1598 1624 3.181482 CCCTCGATGCCTGCTATATACAG 60.181 52.174 0.00 5.73 34.82 2.74
1648 1674 1.796151 CGATTTGGTGCGATGCAGT 59.204 52.632 0.00 0.00 40.08 4.40
1863 1890 1.534476 TGGGTACTGGAAGGCGACA 60.534 57.895 0.00 0.00 39.30 4.35
2067 2118 9.838339 TCTATCTGTTTCTTTCTCAGTTTTTCT 57.162 29.630 0.00 0.00 0.00 2.52
2154 2206 5.071788 TGACCAACATCTTCTGAAACCTACT 59.928 40.000 0.00 0.00 0.00 2.57
2816 2869 4.503910 TCACCTAATTGATTCACAGACGG 58.496 43.478 0.00 0.00 0.00 4.79
2872 2925 1.527034 CCCCCATGTTATCGCATGAG 58.473 55.000 0.00 0.00 46.65 2.90
3091 3153 0.176910 GTTCTCTGTAGGCTCAGGGC 59.823 60.000 12.09 0.00 36.03 5.19
3382 3444 2.203972 CTCAACAGGGCATTGCACCG 62.204 60.000 7.41 0.00 28.43 4.94
3437 3499 6.435591 TGATGTCAATGTTGAGAGTAGAGAGT 59.564 38.462 0.00 0.00 37.98 3.24
3439 3501 5.536538 TGTCAATGTTGAGAGTAGAGAGTGT 59.463 40.000 0.00 0.00 37.98 3.55
3462 3524 4.212143 TGACCAGAGATGAACATGAAGG 57.788 45.455 0.00 0.00 0.00 3.46
3469 3531 5.581479 CAGAGATGAACATGAAGGTGAAGAG 59.419 44.000 0.00 0.00 0.00 2.85
3492 3554 7.971168 AGAGTCAGATATTGTAACTTCGAAGTG 59.029 37.037 30.33 14.13 39.66 3.16
3582 3644 1.589196 GGCGCCGTGCTCTAACTAG 60.589 63.158 12.58 0.00 45.43 2.57
3628 3690 2.026729 TGCTCAATCAACGGGGATTACA 60.027 45.455 3.87 1.71 35.79 2.41
3701 3763 0.609957 TGCTGAGGCAACAGGGATTG 60.610 55.000 12.21 0.00 46.36 2.67
3753 3815 6.881065 AGTTCAAGCACAGATAGCTCATTTAA 59.119 34.615 0.00 0.00 42.53 1.52
3874 3936 2.293399 ACATGGAAGTGAAAACGAAGGC 59.707 45.455 0.00 0.00 0.00 4.35
3908 3970 4.528987 AGGTGAGGACTTCTTTCTTACTCC 59.471 45.833 0.00 0.00 0.00 3.85
3981 4043 9.930693 GATGTCCTAGGGTTAGTTTCATTATAG 57.069 37.037 9.46 0.00 0.00 1.31
4002 4064 3.055094 AGAATGCGTGGAAGGTGTCTTAT 60.055 43.478 0.00 0.00 32.52 1.73
4006 4068 3.252215 TGCGTGGAAGGTGTCTTATTTTG 59.748 43.478 0.00 0.00 32.52 2.44
4079 4141 1.749063 CTGCATGACAATGATGCCTGT 59.251 47.619 0.00 0.00 44.76 4.00
4107 4169 5.063944 CGAGCTGCAGTTTGTAATCTATGTT 59.936 40.000 16.64 0.00 0.00 2.71
4180 4242 2.174639 TGTGGACACAAACTTCCCTGAT 59.825 45.455 2.08 0.00 38.56 2.90
4261 4323 8.642935 AGTCTGCTGAGCTATTATACATCTTA 57.357 34.615 5.83 0.00 0.00 2.10
4417 4479 0.321671 GCAAGCAGGAGTGTGGTCTA 59.678 55.000 0.00 0.00 0.00 2.59
4456 4518 0.701147 CAAGGAAGAGGGGAGGCTTT 59.299 55.000 0.00 0.00 0.00 3.51
4483 4545 2.093500 ACGCATGATCTTGCCAGTTCTA 60.093 45.455 23.52 0.00 39.52 2.10
4662 4724 1.263217 CGAAGTGTTTGTTCCCCTTCG 59.737 52.381 5.82 5.82 45.49 3.79
4781 4843 6.463995 TGCTAGTTTTTGTTTTCCTGTCAT 57.536 33.333 0.00 0.00 0.00 3.06
4783 4845 6.096141 TGCTAGTTTTTGTTTTCCTGTCATCA 59.904 34.615 0.00 0.00 0.00 3.07
4808 4870 0.313987 GTTGGCAACCAGGTTGTAGC 59.686 55.000 29.46 17.61 44.40 3.58
4867 4929 7.044798 GTCTGAACCTAATTAGATCTGTTGCT 58.955 38.462 14.28 0.00 0.00 3.91
4876 4938 9.770097 CTAATTAGATCTGTTGCTGATCCTTTA 57.230 33.333 6.64 7.19 38.86 1.85
4878 4940 8.845413 ATTAGATCTGTTGCTGATCCTTTATC 57.155 34.615 5.18 0.00 38.86 1.75
4885 4947 6.632909 TGTTGCTGATCCTTTATCCATTTTG 58.367 36.000 0.00 0.00 33.22 2.44
4886 4948 6.211184 TGTTGCTGATCCTTTATCCATTTTGT 59.789 34.615 0.00 0.00 33.22 2.83
4887 4949 7.395772 TGTTGCTGATCCTTTATCCATTTTGTA 59.604 33.333 0.00 0.00 33.22 2.41
4888 4950 7.333528 TGCTGATCCTTTATCCATTTTGTAC 57.666 36.000 0.00 0.00 33.22 2.90
4916 4978 1.516161 TGCAGTTGCTTAGCAGTCAG 58.484 50.000 7.08 3.54 40.61 3.51
4917 4979 0.167689 GCAGTTGCTTAGCAGTCAGC 59.832 55.000 7.08 9.64 40.61 4.26
4918 4980 2.476725 GCAGTTGCTTAGCAGTCAGCA 61.477 52.381 17.67 0.00 44.43 4.41
4920 4982 0.519077 GTTGCTTAGCAGTCAGCACC 59.481 55.000 7.08 0.00 45.77 5.01
4927 4989 3.349006 CAGTCAGCACCGGCACAC 61.349 66.667 0.00 0.00 44.61 3.82
4928 4990 3.860605 AGTCAGCACCGGCACACA 61.861 61.111 0.00 0.00 44.61 3.72
4929 4991 2.669569 GTCAGCACCGGCACACAT 60.670 61.111 0.00 0.00 44.61 3.21
4930 4992 2.358615 TCAGCACCGGCACACATC 60.359 61.111 0.00 0.00 44.61 3.06
4931 4993 2.359107 CAGCACCGGCACACATCT 60.359 61.111 0.00 0.00 44.61 2.90
4932 4994 2.359107 AGCACCGGCACACATCTG 60.359 61.111 0.00 0.00 44.61 2.90
4933 4995 3.434319 GCACCGGCACACATCTGG 61.434 66.667 0.00 0.00 40.72 3.86
4934 4996 2.032528 CACCGGCACACATCTGGT 59.967 61.111 0.00 0.00 43.67 4.00
4939 5001 1.468520 CCGGCACACATCTGGTAAAAG 59.531 52.381 0.00 0.00 0.00 2.27
4942 5004 3.252215 CGGCACACATCTGGTAAAAGAAA 59.748 43.478 0.00 0.00 0.00 2.52
4944 5006 4.982295 GGCACACATCTGGTAAAAGAAAAC 59.018 41.667 0.00 0.00 0.00 2.43
4961 5023 5.176592 AGAAAACCAGATAAGGTAAGTCGC 58.823 41.667 0.00 0.00 42.25 5.19
4969 5031 0.896940 AAGGTAAGTCGCGTCCCTGA 60.897 55.000 5.77 0.00 0.00 3.86
4970 5032 1.153881 GGTAAGTCGCGTCCCTGAC 60.154 63.158 5.77 4.10 35.33 3.51
4993 5057 1.815421 CCGCAGCGGCTGAAATACT 60.815 57.895 32.72 0.00 41.17 2.12
4995 5059 0.577269 CGCAGCGGCTGAAATACTAC 59.423 55.000 32.72 11.61 38.10 2.73
5071 5137 0.179092 GTAATTAGCGTCCCTGCCGT 60.179 55.000 0.00 0.00 34.65 5.68
5072 5138 0.103572 TAATTAGCGTCCCTGCCGTC 59.896 55.000 0.00 0.00 34.65 4.79
5097 5163 1.373812 GTGGTTCAACCCTACCGCT 59.626 57.895 3.42 0.00 40.83 5.52
5099 5165 0.834687 TGGTTCAACCCTACCGCTCT 60.835 55.000 3.42 0.00 37.50 4.09
5100 5166 0.323957 GGTTCAACCCTACCGCTCTT 59.676 55.000 0.00 0.00 30.04 2.85
5101 5167 1.271217 GGTTCAACCCTACCGCTCTTT 60.271 52.381 0.00 0.00 30.04 2.52
5102 5168 2.074576 GTTCAACCCTACCGCTCTTTC 58.925 52.381 0.00 0.00 0.00 2.62
5103 5169 0.611714 TCAACCCTACCGCTCTTTCC 59.388 55.000 0.00 0.00 0.00 3.13
5104 5170 0.613777 CAACCCTACCGCTCTTTCCT 59.386 55.000 0.00 0.00 0.00 3.36
5105 5171 0.903236 AACCCTACCGCTCTTTCCTC 59.097 55.000 0.00 0.00 0.00 3.71
5106 5172 0.976590 ACCCTACCGCTCTTTCCTCC 60.977 60.000 0.00 0.00 0.00 4.30
5107 5173 0.688087 CCCTACCGCTCTTTCCTCCT 60.688 60.000 0.00 0.00 0.00 3.69
5108 5174 0.747852 CCTACCGCTCTTTCCTCCTC 59.252 60.000 0.00 0.00 0.00 3.71
5109 5175 1.686741 CCTACCGCTCTTTCCTCCTCT 60.687 57.143 0.00 0.00 0.00 3.69
5110 5176 1.679153 CTACCGCTCTTTCCTCCTCTC 59.321 57.143 0.00 0.00 0.00 3.20
5111 5177 0.973496 ACCGCTCTTTCCTCCTCTCC 60.973 60.000 0.00 0.00 0.00 3.71
5112 5178 0.686112 CCGCTCTTTCCTCCTCTCCT 60.686 60.000 0.00 0.00 0.00 3.69
5113 5179 0.744281 CGCTCTTTCCTCCTCTCCTC 59.256 60.000 0.00 0.00 0.00 3.71
5114 5180 1.119684 GCTCTTTCCTCCTCTCCTCC 58.880 60.000 0.00 0.00 0.00 4.30
5115 5181 1.788229 CTCTTTCCTCCTCTCCTCCC 58.212 60.000 0.00 0.00 0.00 4.30
5116 5182 0.340208 TCTTTCCTCCTCTCCTCCCC 59.660 60.000 0.00 0.00 0.00 4.81
5117 5183 0.692756 CTTTCCTCCTCTCCTCCCCC 60.693 65.000 0.00 0.00 0.00 5.40
5118 5184 1.162951 TTTCCTCCTCTCCTCCCCCT 61.163 60.000 0.00 0.00 0.00 4.79
5119 5185 1.595058 TTCCTCCTCTCCTCCCCCTC 61.595 65.000 0.00 0.00 0.00 4.30
5120 5186 2.018086 CCTCCTCTCCTCCCCCTCT 61.018 68.421 0.00 0.00 0.00 3.69
5121 5187 0.703056 CCTCCTCTCCTCCCCCTCTA 60.703 65.000 0.00 0.00 0.00 2.43
5122 5188 1.236708 CTCCTCTCCTCCCCCTCTAA 58.763 60.000 0.00 0.00 0.00 2.10
5123 5189 1.146982 CTCCTCTCCTCCCCCTCTAAG 59.853 61.905 0.00 0.00 0.00 2.18
5124 5190 0.471022 CCTCTCCTCCCCCTCTAAGC 60.471 65.000 0.00 0.00 0.00 3.09
5125 5191 0.560688 CTCTCCTCCCCCTCTAAGCT 59.439 60.000 0.00 0.00 0.00 3.74
5126 5192 0.558712 TCTCCTCCCCCTCTAAGCTC 59.441 60.000 0.00 0.00 0.00 4.09
5127 5193 0.560688 CTCCTCCCCCTCTAAGCTCT 59.439 60.000 0.00 0.00 0.00 4.09
5128 5194 1.783979 CTCCTCCCCCTCTAAGCTCTA 59.216 57.143 0.00 0.00 0.00 2.43
5129 5195 1.783979 TCCTCCCCCTCTAAGCTCTAG 59.216 57.143 0.00 0.00 0.00 2.43
5130 5196 1.501604 CCTCCCCCTCTAAGCTCTAGT 59.498 57.143 0.00 0.00 0.00 2.57
5131 5197 2.090999 CCTCCCCCTCTAAGCTCTAGTT 60.091 54.545 0.00 0.00 0.00 2.24
5132 5198 3.227614 CTCCCCCTCTAAGCTCTAGTTC 58.772 54.545 0.00 0.00 0.00 3.01
5133 5199 2.860041 TCCCCCTCTAAGCTCTAGTTCT 59.140 50.000 0.00 0.00 0.00 3.01
5134 5200 4.052922 TCCCCCTCTAAGCTCTAGTTCTA 58.947 47.826 0.00 0.00 0.00 2.10
5135 5201 4.105057 TCCCCCTCTAAGCTCTAGTTCTAG 59.895 50.000 0.00 0.83 0.00 2.43
5136 5202 4.403734 CCCCTCTAAGCTCTAGTTCTAGG 58.596 52.174 6.96 0.00 0.00 3.02
5137 5203 4.403734 CCCTCTAAGCTCTAGTTCTAGGG 58.596 52.174 6.96 4.87 35.53 3.53
5138 5204 4.141111 CCCTCTAAGCTCTAGTTCTAGGGT 60.141 50.000 8.29 2.58 37.05 4.34
5139 5205 5.067954 CCTCTAAGCTCTAGTTCTAGGGTC 58.932 50.000 8.29 2.03 0.00 4.46
5140 5206 4.706035 TCTAAGCTCTAGTTCTAGGGTCG 58.294 47.826 8.29 0.00 0.00 4.79
5141 5207 3.369242 AAGCTCTAGTTCTAGGGTCGT 57.631 47.619 8.29 0.00 0.00 4.34
5142 5208 2.645802 AGCTCTAGTTCTAGGGTCGTG 58.354 52.381 8.29 0.00 0.00 4.35
5143 5209 2.026075 AGCTCTAGTTCTAGGGTCGTGT 60.026 50.000 8.29 0.00 0.00 4.49
5144 5210 3.199508 AGCTCTAGTTCTAGGGTCGTGTA 59.800 47.826 8.29 0.00 0.00 2.90
5145 5211 3.944015 GCTCTAGTTCTAGGGTCGTGTAA 59.056 47.826 8.29 0.00 0.00 2.41
5146 5212 4.579753 GCTCTAGTTCTAGGGTCGTGTAAT 59.420 45.833 8.29 0.00 0.00 1.89
5147 5213 5.762218 GCTCTAGTTCTAGGGTCGTGTAATA 59.238 44.000 8.29 0.00 0.00 0.98
5148 5214 6.293353 GCTCTAGTTCTAGGGTCGTGTAATAC 60.293 46.154 8.29 0.00 0.00 1.89
5149 5215 6.058183 TCTAGTTCTAGGGTCGTGTAATACC 58.942 44.000 6.96 0.00 34.85 2.73
5156 5222 3.175109 GGTCGTGTAATACCCAGGAAG 57.825 52.381 0.00 0.00 0.00 3.46
5157 5223 2.762327 GGTCGTGTAATACCCAGGAAGA 59.238 50.000 0.00 0.00 0.00 2.87
5158 5224 3.181478 GGTCGTGTAATACCCAGGAAGAG 60.181 52.174 0.00 0.00 0.00 2.85
5159 5225 3.028850 TCGTGTAATACCCAGGAAGAGG 58.971 50.000 0.00 0.00 0.00 3.69
5168 5234 2.773525 CCAGGAAGAGGGAGAGAGAT 57.226 55.000 0.00 0.00 0.00 2.75
5169 5235 2.597455 CCAGGAAGAGGGAGAGAGATC 58.403 57.143 0.00 0.00 0.00 2.75
5170 5236 2.229792 CAGGAAGAGGGAGAGAGATCG 58.770 57.143 0.00 0.00 0.00 3.69
5171 5237 1.144913 AGGAAGAGGGAGAGAGATCGG 59.855 57.143 0.00 0.00 0.00 4.18
5172 5238 1.144093 GGAAGAGGGAGAGAGATCGGA 59.856 57.143 0.00 0.00 0.00 4.55
5173 5239 2.504367 GAAGAGGGAGAGAGATCGGAG 58.496 57.143 0.00 0.00 0.00 4.63
5174 5240 0.110486 AGAGGGAGAGAGATCGGAGC 59.890 60.000 0.00 0.00 0.00 4.70
5175 5241 0.893727 GAGGGAGAGAGATCGGAGCC 60.894 65.000 0.00 0.00 0.00 4.70
5176 5242 2.265182 GGGAGAGAGATCGGAGCCG 61.265 68.421 1.74 1.74 41.35 5.52
5186 5252 1.987855 TCGGAGCCGAGATTTGGGT 60.988 57.895 7.66 0.00 44.01 4.51
5201 5267 2.419739 GGGTGAGGACGAGAGGAGC 61.420 68.421 0.00 0.00 0.00 4.70
5207 5273 2.716017 GGACGAGAGGAGCAGGTGG 61.716 68.421 0.00 0.00 0.00 4.61
5225 5291 3.181526 GGGGGATGAAGCAACAGAG 57.818 57.895 0.00 0.00 0.00 3.35
5227 5293 0.329596 GGGGATGAAGCAACAGAGGT 59.670 55.000 0.00 0.00 0.00 3.85
5228 5294 1.272147 GGGGATGAAGCAACAGAGGTT 60.272 52.381 0.00 0.00 37.87 3.50
5280 5378 1.086696 CCTAACAGTGGCATCGTTGG 58.913 55.000 12.99 10.41 0.00 3.77
5291 5389 3.467803 GGCATCGTTGGCTTAAGTATCT 58.532 45.455 12.43 0.00 44.68 1.98
5303 6449 5.337330 GGCTTAAGTATCTACCACACACACT 60.337 44.000 4.02 0.00 0.00 3.55
5320 6466 0.973632 ACTCGACATGGGCTTACACA 59.026 50.000 0.00 0.00 0.00 3.72
5321 6467 1.346395 ACTCGACATGGGCTTACACAA 59.654 47.619 0.00 0.00 0.00 3.33
5326 6472 3.938963 CGACATGGGCTTACACAAGTTAT 59.061 43.478 0.00 0.00 34.00 1.89
5360 6506 3.215151 CCAGAAGACTCGTAGGCTATGA 58.785 50.000 15.36 15.36 27.04 2.15
5369 6515 1.754803 CGTAGGCTATGACCCAACTCA 59.245 52.381 8.06 0.00 0.00 3.41
5370 6516 2.167693 CGTAGGCTATGACCCAACTCAA 59.832 50.000 8.06 0.00 0.00 3.02
5372 6518 4.683400 CGTAGGCTATGACCCAACTCAAAT 60.683 45.833 8.06 0.00 0.00 2.32
5373 6519 3.891049 AGGCTATGACCCAACTCAAATC 58.109 45.455 0.00 0.00 0.00 2.17
5374 6520 2.952310 GGCTATGACCCAACTCAAATCC 59.048 50.000 0.00 0.00 0.00 3.01
5378 6524 0.521735 GACCCAACTCAAATCCGTGC 59.478 55.000 0.00 0.00 0.00 5.34
5379 6525 0.179004 ACCCAACTCAAATCCGTGCA 60.179 50.000 0.00 0.00 0.00 4.57
5396 6549 2.297625 CAGTTCGTGCACTCGTGTT 58.702 52.632 16.19 0.00 0.00 3.32
5425 6579 0.248289 TTAGGTGCTGCTACCGGAAC 59.752 55.000 9.46 0.00 45.56 3.62
5426 6580 1.610554 TAGGTGCTGCTACCGGAACC 61.611 60.000 9.46 3.86 45.37 3.62
5460 6615 2.348998 CCCTTCTTGAGGCGCAGT 59.651 61.111 10.83 0.00 44.85 4.40
5464 6619 0.601046 CTTCTTGAGGCGCAGTGTCA 60.601 55.000 10.83 2.99 0.00 3.58
5465 6620 0.880278 TTCTTGAGGCGCAGTGTCAC 60.880 55.000 10.83 0.00 0.00 3.67
5466 6621 1.595109 CTTGAGGCGCAGTGTCACA 60.595 57.895 10.83 0.00 0.00 3.58
5467 6622 1.835483 CTTGAGGCGCAGTGTCACAC 61.835 60.000 10.83 0.00 34.10 3.82
5468 6623 3.044305 GAGGCGCAGTGTCACACC 61.044 66.667 10.83 1.17 34.49 4.16
5469 6624 4.626081 AGGCGCAGTGTCACACCC 62.626 66.667 10.83 0.00 34.49 4.61
5470 6625 4.626081 GGCGCAGTGTCACACCCT 62.626 66.667 10.83 0.00 34.49 4.34
5471 6626 2.342279 GCGCAGTGTCACACCCTA 59.658 61.111 3.66 0.00 34.49 3.53
5472 6627 1.738099 GCGCAGTGTCACACCCTAG 60.738 63.158 3.66 0.00 34.49 3.02
5473 6628 1.738099 CGCAGTGTCACACCCTAGC 60.738 63.158 3.66 3.26 34.49 3.42
5474 6629 1.674057 GCAGTGTCACACCCTAGCT 59.326 57.895 3.66 0.00 34.49 3.32
5475 6630 0.895530 GCAGTGTCACACCCTAGCTA 59.104 55.000 3.66 0.00 34.49 3.32
5476 6631 1.134965 GCAGTGTCACACCCTAGCTAG 60.135 57.143 14.20 14.20 34.49 3.42
5477 6632 2.171840 CAGTGTCACACCCTAGCTAGT 58.828 52.381 19.31 0.00 34.49 2.57
5478 6633 2.164624 CAGTGTCACACCCTAGCTAGTC 59.835 54.545 19.31 2.23 34.49 2.59
5479 6634 2.168496 GTGTCACACCCTAGCTAGTCA 58.832 52.381 19.31 4.53 0.00 3.41
5480 6635 2.761208 GTGTCACACCCTAGCTAGTCAT 59.239 50.000 19.31 1.55 0.00 3.06
5481 6636 2.760650 TGTCACACCCTAGCTAGTCATG 59.239 50.000 19.31 15.31 0.00 3.07
5482 6637 1.757118 TCACACCCTAGCTAGTCATGC 59.243 52.381 19.31 0.00 0.00 4.06
5483 6638 1.482182 CACACCCTAGCTAGTCATGCA 59.518 52.381 19.31 0.00 0.00 3.96
5484 6639 2.103771 CACACCCTAGCTAGTCATGCAT 59.896 50.000 19.31 0.00 0.00 3.96
5485 6640 2.366916 ACACCCTAGCTAGTCATGCATC 59.633 50.000 19.31 0.00 0.00 3.91
5486 6641 2.366590 CACCCTAGCTAGTCATGCATCA 59.633 50.000 19.31 0.00 0.00 3.07
5487 6642 2.632028 ACCCTAGCTAGTCATGCATCAG 59.368 50.000 19.31 0.07 0.00 2.90
5488 6643 2.896044 CCCTAGCTAGTCATGCATCAGA 59.104 50.000 19.31 0.00 0.00 3.27
5489 6644 3.056678 CCCTAGCTAGTCATGCATCAGAG 60.057 52.174 19.31 0.00 0.00 3.35
5490 6645 3.573538 CCTAGCTAGTCATGCATCAGAGT 59.426 47.826 19.31 0.00 0.00 3.24
5491 6646 3.455990 AGCTAGTCATGCATCAGAGTG 57.544 47.619 0.00 0.00 0.00 3.51
5492 6647 2.765135 AGCTAGTCATGCATCAGAGTGT 59.235 45.455 0.00 0.00 0.00 3.55
5493 6648 2.864946 GCTAGTCATGCATCAGAGTGTG 59.135 50.000 0.00 0.00 0.00 3.82
5494 6649 3.678252 GCTAGTCATGCATCAGAGTGTGT 60.678 47.826 0.00 0.00 0.00 3.72
5495 6650 2.696506 AGTCATGCATCAGAGTGTGTG 58.303 47.619 0.00 0.00 0.00 3.82
5496 6651 1.129998 GTCATGCATCAGAGTGTGTGC 59.870 52.381 0.00 7.56 35.17 4.57
5497 6652 1.161843 CATGCATCAGAGTGTGTGCA 58.838 50.000 15.95 15.95 43.06 4.57
5498 6653 1.743394 CATGCATCAGAGTGTGTGCAT 59.257 47.619 18.18 18.18 46.21 3.96
5499 6654 1.445871 TGCATCAGAGTGTGTGCATC 58.554 50.000 11.60 0.00 37.89 3.91
5500 6655 1.270947 TGCATCAGAGTGTGTGCATCA 60.271 47.619 11.60 0.00 37.89 3.07
5501 6656 2.014857 GCATCAGAGTGTGTGCATCAT 58.985 47.619 9.06 0.00 34.90 2.45
5502 6657 2.223272 GCATCAGAGTGTGTGCATCATG 60.223 50.000 9.06 0.00 34.90 3.07
5503 6658 2.845363 TCAGAGTGTGTGCATCATGT 57.155 45.000 0.00 0.00 0.00 3.21
5504 6659 3.130280 TCAGAGTGTGTGCATCATGTT 57.870 42.857 0.00 0.00 0.00 2.71
5505 6660 3.479489 TCAGAGTGTGTGCATCATGTTT 58.521 40.909 0.00 0.00 0.00 2.83
5506 6661 4.640364 TCAGAGTGTGTGCATCATGTTTA 58.360 39.130 0.00 0.00 0.00 2.01
5507 6662 5.062528 TCAGAGTGTGTGCATCATGTTTAA 58.937 37.500 0.00 0.00 0.00 1.52
5508 6663 5.530543 TCAGAGTGTGTGCATCATGTTTAAA 59.469 36.000 0.00 0.00 0.00 1.52
5509 6664 6.039159 TCAGAGTGTGTGCATCATGTTTAAAA 59.961 34.615 0.00 0.00 0.00 1.52
5510 6665 6.864685 CAGAGTGTGTGCATCATGTTTAAAAT 59.135 34.615 0.00 0.00 0.00 1.82
5511 6666 7.383029 CAGAGTGTGTGCATCATGTTTAAAATT 59.617 33.333 0.00 0.00 0.00 1.82
5512 6667 7.927629 AGAGTGTGTGCATCATGTTTAAAATTT 59.072 29.630 0.00 0.00 0.00 1.82
5513 6668 8.075593 AGTGTGTGCATCATGTTTAAAATTTC 57.924 30.769 0.00 0.00 0.00 2.17
5514 6669 7.171337 AGTGTGTGCATCATGTTTAAAATTTCC 59.829 33.333 0.00 0.00 0.00 3.13
5515 6670 6.988580 TGTGTGCATCATGTTTAAAATTTCCA 59.011 30.769 0.00 0.00 0.00 3.53
5516 6671 7.660617 TGTGTGCATCATGTTTAAAATTTCCAT 59.339 29.630 0.00 0.00 0.00 3.41
5517 6672 8.505625 GTGTGCATCATGTTTAAAATTTCCATT 58.494 29.630 0.00 0.00 0.00 3.16
5518 6673 9.064706 TGTGCATCATGTTTAAAATTTCCATTT 57.935 25.926 0.00 0.00 33.72 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 2.052690 GGCGTCTCCTACTGGCTGA 61.053 63.158 0.00 0.00 0.00 4.26
36 37 2.105466 GTCGTCGGCGTCTCCTACT 61.105 63.158 10.18 0.00 39.49 2.57
183 188 1.564348 GGTGTTCCTCCATACCCATGT 59.436 52.381 0.00 0.00 0.00 3.21
185 190 0.837272 CGGTGTTCCTCCATACCCAT 59.163 55.000 0.00 0.00 0.00 4.00
191 196 3.000819 TCGCCGGTGTTCCTCCAT 61.001 61.111 16.01 0.00 0.00 3.41
332 337 4.814294 CACCCGTACAGGCTCCGC 62.814 72.222 0.00 0.00 39.21 5.54
395 400 2.034066 CCCACCATTGCCGTCACT 59.966 61.111 0.00 0.00 0.00 3.41
399 404 2.600173 CCAACCCACCATTGCCGT 60.600 61.111 0.00 0.00 0.00 5.68
404 409 1.228862 GAGCACCCAACCCACCATT 60.229 57.895 0.00 0.00 0.00 3.16
428 433 3.500558 TTCTCTTCTCTCTCACGCATG 57.499 47.619 0.00 0.00 0.00 4.06
460 480 3.642705 GCGTTTGCATCCTTTTTCTTCT 58.357 40.909 0.00 0.00 42.15 2.85
462 482 2.393764 CGCGTTTGCATCCTTTTTCTT 58.606 42.857 0.00 0.00 42.97 2.52
465 485 0.319469 CCCGCGTTTGCATCCTTTTT 60.319 50.000 4.92 0.00 42.97 1.94
503 523 1.544246 TGAGAGGAACGCAGAAATCGA 59.456 47.619 0.00 0.00 0.00 3.59
527 547 0.036875 AAAAGGAACCCTCTCAGCCG 59.963 55.000 0.00 0.00 30.89 5.52
562 582 0.604511 TCCTGTGCGACGTACTCAGA 60.605 55.000 16.98 8.15 0.00 3.27
568 588 1.736365 TTGGTGTCCTGTGCGACGTA 61.736 55.000 0.00 0.00 35.40 3.57
607 627 2.573869 CACCTGTCTCGCATCCGT 59.426 61.111 0.00 0.00 35.54 4.69
618 638 3.884774 TTTCCTGGCCGCACCTGT 61.885 61.111 0.00 0.00 40.22 4.00
650 671 1.048724 GTGATCCGGGGGAGTCATCA 61.049 60.000 0.00 0.00 34.05 3.07
651 672 0.760945 AGTGATCCGGGGGAGTCATC 60.761 60.000 0.00 0.00 34.05 2.92
652 673 1.050988 CAGTGATCCGGGGGAGTCAT 61.051 60.000 0.00 0.00 34.05 3.06
653 674 1.685765 CAGTGATCCGGGGGAGTCA 60.686 63.158 0.00 0.00 34.05 3.41
654 675 3.095347 GCAGTGATCCGGGGGAGTC 62.095 68.421 0.00 0.00 34.05 3.36
655 676 3.083997 GCAGTGATCCGGGGGAGT 61.084 66.667 0.00 0.00 34.05 3.85
656 677 2.765807 AGCAGTGATCCGGGGGAG 60.766 66.667 0.00 0.00 34.05 4.30
657 678 3.083349 CAGCAGTGATCCGGGGGA 61.083 66.667 0.00 0.00 35.55 4.81
664 685 1.002430 TGAACCAGTCCAGCAGTGATC 59.998 52.381 0.00 0.00 0.00 2.92
739 760 2.236893 GTCCGTGTTTACCCCCTTGATA 59.763 50.000 0.00 0.00 0.00 2.15
1186 1208 0.986019 TCCCCACACACACAAGAGGT 60.986 55.000 0.00 0.00 0.00 3.85
1265 1287 0.248458 AGCCGCAAAACAAAGACACG 60.248 50.000 0.00 0.00 0.00 4.49
1344 1366 2.364002 ACAAAACGGGGGAGACAAAATG 59.636 45.455 0.00 0.00 0.00 2.32
1391 1413 0.601046 CGCAAGAACAGACTGGCTGA 60.601 55.000 19.29 0.00 44.44 4.26
1430 1452 2.826674 GGATCAGAATCCCCCAAACA 57.173 50.000 0.00 0.00 45.11 2.83
1595 1621 9.939424 AAAGAGGGTATACTAGAGAAATACTGT 57.061 33.333 2.25 0.00 0.00 3.55
1597 1623 9.590828 GGAAAGAGGGTATACTAGAGAAATACT 57.409 37.037 2.25 0.00 0.00 2.12
1598 1624 8.513774 CGGAAAGAGGGTATACTAGAGAAATAC 58.486 40.741 2.25 0.00 0.00 1.89
1648 1674 2.428491 CACCACGCCCAATAGTTACAA 58.572 47.619 0.00 0.00 0.00 2.41
1863 1890 0.119155 TGATGACCCTGTCCTTCCCT 59.881 55.000 0.00 0.00 0.00 4.20
2067 2118 3.076621 CAGAATCTAACAGCACTGCCAA 58.923 45.455 0.00 0.00 0.00 4.52
2186 2238 6.960992 CGGATTTGTACTGTGTTGATTATGTG 59.039 38.462 0.00 0.00 0.00 3.21
2816 2869 6.261118 CAAATTCATGAGACCCGAGATTTTC 58.739 40.000 0.00 0.00 0.00 2.29
2872 2925 5.003804 TGAAGTAGAAGCTTGTCCAAATCC 58.996 41.667 2.10 0.00 0.00 3.01
2970 3029 7.334090 AGTGTCTGCATCATACTGAACTTTAT 58.666 34.615 0.00 0.00 0.00 1.40
3049 3111 6.842163 ACAAACAAATATAAGAAGGCAGACG 58.158 36.000 0.00 0.00 0.00 4.18
3091 3153 4.257267 TGGACCATCATATAGCAACTCG 57.743 45.455 0.00 0.00 0.00 4.18
3382 3444 1.439644 CAGTAGCCGAAGCCTCCTC 59.560 63.158 0.00 0.00 41.25 3.71
3437 3499 5.937975 TCATGTTCATCTCTGGTCATACA 57.062 39.130 0.00 0.00 0.00 2.29
3439 3501 5.426509 ACCTTCATGTTCATCTCTGGTCATA 59.573 40.000 0.00 0.00 0.00 2.15
3462 3524 7.968956 TCGAAGTTACAATATCTGACTCTTCAC 59.031 37.037 0.00 0.00 33.01 3.18
3469 3531 7.813852 ACACTTCGAAGTTACAATATCTGAC 57.186 36.000 27.79 0.00 37.08 3.51
3492 3554 4.795268 TGACTCAACAGATTCACTCGTAC 58.205 43.478 0.00 0.00 0.00 3.67
3701 3763 3.430218 GCTGTGTGTCGGCTCATAATATC 59.570 47.826 0.00 0.00 44.39 1.63
3753 3815 1.227853 GCAGTCCCTTGTTCGGTGT 60.228 57.895 0.00 0.00 0.00 4.16
3874 3936 0.906756 TCCTCACCTCAGCTTCCAGG 60.907 60.000 2.08 2.08 35.69 4.45
3908 3970 5.799213 AGTCCAGTTGAAGAATTAGGTCAG 58.201 41.667 0.00 0.00 0.00 3.51
3964 4026 7.352739 CACGCATTCTATAATGAAACTAACCC 58.647 38.462 5.09 0.00 44.50 4.11
3981 4043 1.523758 AAGACACCTTCCACGCATTC 58.476 50.000 0.00 0.00 0.00 2.67
4002 4064 1.748493 GCACAGGAACAGGTCACAAAA 59.252 47.619 0.00 0.00 0.00 2.44
4006 4068 1.604278 GAAAGCACAGGAACAGGTCAC 59.396 52.381 0.00 0.00 0.00 3.67
4079 4141 2.232756 TACAAACTGCAGCTCGTTGA 57.767 45.000 15.27 1.71 0.00 3.18
4107 4169 7.651304 CCAAAACATGTTAGTATTGCTTCAACA 59.349 33.333 12.39 0.00 33.96 3.33
4180 4242 1.071299 ATGACTGTTGCCAGCGTCA 59.929 52.632 8.15 8.15 42.81 4.35
4261 4323 7.123247 AGCAGAAGCCAACAATAACAAGATAAT 59.877 33.333 0.00 0.00 43.56 1.28
4357 4419 2.169789 CGTCTTCCGCAGCCTCATG 61.170 63.158 0.00 0.00 0.00 3.07
4417 4479 1.270518 GGTGCTCTCACATGTGACTGT 60.271 52.381 24.56 0.00 44.87 3.55
4483 4545 1.668101 GGACGAGAAGAGCCACCGAT 61.668 60.000 0.00 0.00 0.00 4.18
4662 4724 3.282374 ATTTCACAGTCCCCCGCCC 62.282 63.158 0.00 0.00 0.00 6.13
4781 4843 1.608055 CTGGTTGCCAACATCTGTGA 58.392 50.000 10.18 0.00 30.80 3.58
4783 4845 0.185901 ACCTGGTTGCCAACATCTGT 59.814 50.000 10.18 0.00 30.80 3.41
4808 4870 5.048154 TCACAACAACACACATAATGGATGG 60.048 40.000 0.00 0.00 40.18 3.51
4876 4938 7.448469 ACTGCAAAGTTCTAGTACAAAATGGAT 59.552 33.333 2.11 0.00 0.00 3.41
4878 4940 6.970484 ACTGCAAAGTTCTAGTACAAAATGG 58.030 36.000 2.11 0.00 0.00 3.16
4885 4947 5.674933 AAGCAACTGCAAAGTTCTAGTAC 57.325 39.130 4.22 0.00 45.16 2.73
4886 4948 5.408604 GCTAAGCAACTGCAAAGTTCTAGTA 59.591 40.000 4.22 0.00 45.16 1.82
4887 4949 4.214332 GCTAAGCAACTGCAAAGTTCTAGT 59.786 41.667 4.22 0.00 45.16 2.57
4888 4950 4.214119 TGCTAAGCAACTGCAAAGTTCTAG 59.786 41.667 4.22 0.00 45.16 2.43
4916 4978 2.796483 TACCAGATGTGTGCCGGTGC 62.796 60.000 1.90 0.00 38.26 5.01
4917 4979 0.321210 TTACCAGATGTGTGCCGGTG 60.321 55.000 1.90 0.00 0.00 4.94
4918 4980 0.398696 TTTACCAGATGTGTGCCGGT 59.601 50.000 1.90 0.00 0.00 5.28
4920 4982 2.422597 TCTTTTACCAGATGTGTGCCG 58.577 47.619 0.00 0.00 0.00 5.69
4923 4985 6.142818 TGGTTTTCTTTTACCAGATGTGTG 57.857 37.500 0.00 0.00 39.44 3.82
4931 4993 9.292195 CTTACCTTATCTGGTTTTCTTTTACCA 57.708 33.333 0.00 0.00 41.97 3.25
4932 4994 9.293404 ACTTACCTTATCTGGTTTTCTTTTACC 57.707 33.333 0.00 0.00 41.22 2.85
4934 4996 9.211485 CGACTTACCTTATCTGGTTTTCTTTTA 57.789 33.333 0.00 0.00 41.22 1.52
4939 5001 4.032558 CGCGACTTACCTTATCTGGTTTTC 59.967 45.833 0.00 0.00 41.22 2.29
4942 5004 2.494870 ACGCGACTTACCTTATCTGGTT 59.505 45.455 15.93 0.00 41.22 3.67
4944 5006 2.543238 GGACGCGACTTACCTTATCTGG 60.543 54.545 15.93 0.00 0.00 3.86
4976 5038 0.577269 GTAGTATTTCAGCCGCTGCG 59.423 55.000 16.34 16.34 44.33 5.18
5017 5081 0.885150 TTGTACCAAATGTGCGCCGA 60.885 50.000 4.18 0.00 31.26 5.54
5019 5083 2.141535 TTTTGTACCAAATGTGCGCC 57.858 45.000 4.18 0.00 31.26 6.53
5071 5137 2.970324 GTTGAACCACTGCGGCGA 60.970 61.111 12.98 0.00 39.03 5.54
5072 5138 4.025401 GGTTGAACCACTGCGGCG 62.025 66.667 9.98 0.51 38.42 6.46
5075 5141 0.953960 GGTAGGGTTGAACCACTGCG 60.954 60.000 17.27 0.00 41.02 5.18
5080 5146 0.834687 AGAGCGGTAGGGTTGAACCA 60.835 55.000 17.27 0.00 41.02 3.67
5083 5149 1.002773 GGAAAGAGCGGTAGGGTTGAA 59.997 52.381 0.00 0.00 0.00 2.69
5097 5163 0.340208 GGGGAGGAGAGGAGGAAAGA 59.660 60.000 0.00 0.00 0.00 2.52
5099 5165 1.162951 AGGGGGAGGAGAGGAGGAAA 61.163 60.000 0.00 0.00 0.00 3.13
5100 5166 1.550374 AGGGGGAGGAGAGGAGGAA 60.550 63.158 0.00 0.00 0.00 3.36
5101 5167 2.015726 GAGGGGGAGGAGAGGAGGA 61.016 68.421 0.00 0.00 0.00 3.71
5102 5168 0.703056 TAGAGGGGGAGGAGAGGAGG 60.703 65.000 0.00 0.00 0.00 4.30
5103 5169 1.146982 CTTAGAGGGGGAGGAGAGGAG 59.853 61.905 0.00 0.00 0.00 3.69
5104 5170 1.236708 CTTAGAGGGGGAGGAGAGGA 58.763 60.000 0.00 0.00 0.00 3.71
5105 5171 0.471022 GCTTAGAGGGGGAGGAGAGG 60.471 65.000 0.00 0.00 0.00 3.69
5106 5172 0.560688 AGCTTAGAGGGGGAGGAGAG 59.439 60.000 0.00 0.00 0.00 3.20
5107 5173 0.558712 GAGCTTAGAGGGGGAGGAGA 59.441 60.000 0.00 0.00 0.00 3.71
5108 5174 0.560688 AGAGCTTAGAGGGGGAGGAG 59.439 60.000 0.00 0.00 0.00 3.69
5109 5175 1.783979 CTAGAGCTTAGAGGGGGAGGA 59.216 57.143 0.00 0.00 0.00 3.71
5110 5176 1.501604 ACTAGAGCTTAGAGGGGGAGG 59.498 57.143 0.00 0.00 0.00 4.30
5111 5177 3.117284 AGAACTAGAGCTTAGAGGGGGAG 60.117 52.174 0.00 0.00 0.00 4.30
5112 5178 2.860041 AGAACTAGAGCTTAGAGGGGGA 59.140 50.000 0.00 0.00 0.00 4.81
5113 5179 3.322191 AGAACTAGAGCTTAGAGGGGG 57.678 52.381 0.00 0.00 0.00 5.40
5114 5180 4.403734 CCTAGAACTAGAGCTTAGAGGGG 58.596 52.174 10.04 0.00 35.21 4.79
5115 5181 4.141111 ACCCTAGAACTAGAGCTTAGAGGG 60.141 50.000 17.02 17.02 45.61 4.30
5116 5182 5.056553 ACCCTAGAACTAGAGCTTAGAGG 57.943 47.826 10.04 3.50 35.21 3.69
5117 5183 4.753107 CGACCCTAGAACTAGAGCTTAGAG 59.247 50.000 10.04 0.52 35.21 2.43
5118 5184 4.163839 ACGACCCTAGAACTAGAGCTTAGA 59.836 45.833 10.04 0.00 35.21 2.10
5119 5185 4.273969 CACGACCCTAGAACTAGAGCTTAG 59.726 50.000 10.04 0.00 35.21 2.18
5120 5186 4.197750 CACGACCCTAGAACTAGAGCTTA 58.802 47.826 10.04 0.00 35.21 3.09
5121 5187 3.018149 CACGACCCTAGAACTAGAGCTT 58.982 50.000 10.04 0.00 35.21 3.74
5122 5188 2.026075 ACACGACCCTAGAACTAGAGCT 60.026 50.000 10.04 0.00 35.21 4.09
5123 5189 2.367486 ACACGACCCTAGAACTAGAGC 58.633 52.381 10.04 0.00 35.21 4.09
5124 5190 6.204495 GGTATTACACGACCCTAGAACTAGAG 59.796 46.154 10.04 0.03 35.21 2.43
5125 5191 6.058183 GGTATTACACGACCCTAGAACTAGA 58.942 44.000 10.04 0.00 35.21 2.43
5126 5192 6.311055 GGTATTACACGACCCTAGAACTAG 57.689 45.833 0.00 2.23 0.00 2.57
5136 5202 2.762327 TCTTCCTGGGTATTACACGACC 59.238 50.000 0.00 0.00 34.75 4.79
5137 5203 3.181478 CCTCTTCCTGGGTATTACACGAC 60.181 52.174 0.00 0.00 0.00 4.34
5138 5204 3.028850 CCTCTTCCTGGGTATTACACGA 58.971 50.000 0.00 0.00 0.00 4.35
5139 5205 2.102588 CCCTCTTCCTGGGTATTACACG 59.897 54.545 0.00 0.00 39.82 4.49
5140 5206 3.381335 TCCCTCTTCCTGGGTATTACAC 58.619 50.000 0.00 0.00 44.84 2.90
5141 5207 3.273886 TCTCCCTCTTCCTGGGTATTACA 59.726 47.826 0.00 0.00 44.84 2.41
5142 5208 3.898741 CTCTCCCTCTTCCTGGGTATTAC 59.101 52.174 0.00 0.00 44.84 1.89
5143 5209 3.797845 TCTCTCCCTCTTCCTGGGTATTA 59.202 47.826 0.00 0.00 44.84 0.98
5144 5210 2.592512 TCTCTCCCTCTTCCTGGGTATT 59.407 50.000 0.00 0.00 44.84 1.89
5145 5211 2.178984 CTCTCTCCCTCTTCCTGGGTAT 59.821 54.545 0.00 0.00 44.84 2.73
5146 5212 1.571457 CTCTCTCCCTCTTCCTGGGTA 59.429 57.143 0.00 0.00 44.84 3.69
5147 5213 0.338120 CTCTCTCCCTCTTCCTGGGT 59.662 60.000 0.00 0.00 44.84 4.51
5148 5214 0.633921 TCTCTCTCCCTCTTCCTGGG 59.366 60.000 0.00 0.00 45.90 4.45
5149 5215 2.597455 GATCTCTCTCCCTCTTCCTGG 58.403 57.143 0.00 0.00 0.00 4.45
5150 5216 2.229792 CGATCTCTCTCCCTCTTCCTG 58.770 57.143 0.00 0.00 0.00 3.86
5151 5217 1.144913 CCGATCTCTCTCCCTCTTCCT 59.855 57.143 0.00 0.00 0.00 3.36
5152 5218 1.144093 TCCGATCTCTCTCCCTCTTCC 59.856 57.143 0.00 0.00 0.00 3.46
5153 5219 2.504367 CTCCGATCTCTCTCCCTCTTC 58.496 57.143 0.00 0.00 0.00 2.87
5154 5220 1.478654 GCTCCGATCTCTCTCCCTCTT 60.479 57.143 0.00 0.00 0.00 2.85
5155 5221 0.110486 GCTCCGATCTCTCTCCCTCT 59.890 60.000 0.00 0.00 0.00 3.69
5156 5222 0.893727 GGCTCCGATCTCTCTCCCTC 60.894 65.000 0.00 0.00 0.00 4.30
5157 5223 1.152830 GGCTCCGATCTCTCTCCCT 59.847 63.158 0.00 0.00 0.00 4.20
5158 5224 2.265182 CGGCTCCGATCTCTCTCCC 61.265 68.421 1.35 0.00 42.83 4.30
5159 5225 1.228003 TCGGCTCCGATCTCTCTCC 60.228 63.158 6.95 0.00 44.01 3.71
5160 5226 4.466133 TCGGCTCCGATCTCTCTC 57.534 61.111 6.95 0.00 44.01 3.20
5168 5234 1.987855 ACCCAAATCTCGGCTCCGA 60.988 57.895 10.84 10.84 46.87 4.55
5169 5235 1.815421 CACCCAAATCTCGGCTCCG 60.815 63.158 1.14 1.14 41.35 4.63
5170 5236 0.462759 CTCACCCAAATCTCGGCTCC 60.463 60.000 0.00 0.00 0.00 4.70
5171 5237 0.462759 CCTCACCCAAATCTCGGCTC 60.463 60.000 0.00 0.00 0.00 4.70
5172 5238 0.909610 TCCTCACCCAAATCTCGGCT 60.910 55.000 0.00 0.00 0.00 5.52
5173 5239 0.744771 GTCCTCACCCAAATCTCGGC 60.745 60.000 0.00 0.00 0.00 5.54
5174 5240 0.460284 CGTCCTCACCCAAATCTCGG 60.460 60.000 0.00 0.00 0.00 4.63
5175 5241 0.530744 TCGTCCTCACCCAAATCTCG 59.469 55.000 0.00 0.00 0.00 4.04
5176 5242 1.825474 TCTCGTCCTCACCCAAATCTC 59.175 52.381 0.00 0.00 0.00 2.75
5177 5243 1.827969 CTCTCGTCCTCACCCAAATCT 59.172 52.381 0.00 0.00 0.00 2.40
5178 5244 1.134670 CCTCTCGTCCTCACCCAAATC 60.135 57.143 0.00 0.00 0.00 2.17
5179 5245 0.905357 CCTCTCGTCCTCACCCAAAT 59.095 55.000 0.00 0.00 0.00 2.32
5180 5246 0.178944 TCCTCTCGTCCTCACCCAAA 60.179 55.000 0.00 0.00 0.00 3.28
5181 5247 0.612174 CTCCTCTCGTCCTCACCCAA 60.612 60.000 0.00 0.00 0.00 4.12
5182 5248 1.000771 CTCCTCTCGTCCTCACCCA 60.001 63.158 0.00 0.00 0.00 4.51
5186 5252 1.379176 CCTGCTCCTCTCGTCCTCA 60.379 63.158 0.00 0.00 0.00 3.86
5207 5273 0.394899 CCTCTGTTGCTTCATCCCCC 60.395 60.000 0.00 0.00 0.00 5.40
5220 5286 4.288105 AGTGAATTGATCTCCAACCTCTGT 59.712 41.667 0.00 0.00 37.63 3.41
5221 5287 4.841422 AGTGAATTGATCTCCAACCTCTG 58.159 43.478 0.00 0.00 37.63 3.35
5223 5289 5.942826 AGAAAGTGAATTGATCTCCAACCTC 59.057 40.000 0.00 0.00 37.63 3.85
5224 5290 5.885465 AGAAAGTGAATTGATCTCCAACCT 58.115 37.500 0.00 0.00 37.63 3.50
5225 5291 6.581171 AAGAAAGTGAATTGATCTCCAACC 57.419 37.500 0.00 0.00 37.63 3.77
5227 5293 9.519191 TGAATAAGAAAGTGAATTGATCTCCAA 57.481 29.630 0.00 0.00 39.41 3.53
5228 5294 9.519191 TTGAATAAGAAAGTGAATTGATCTCCA 57.481 29.630 0.00 0.00 0.00 3.86
5280 5378 5.721232 AGTGTGTGTGGTAGATACTTAAGC 58.279 41.667 1.29 0.00 0.00 3.09
5291 5389 1.000394 CCATGTCGAGTGTGTGTGGTA 60.000 52.381 0.00 0.00 0.00 3.25
5303 6449 1.346395 ACTTGTGTAAGCCCATGTCGA 59.654 47.619 0.00 0.00 37.43 4.20
5320 6466 1.444672 GCCGGAGCCCGTATAACTT 59.555 57.895 5.05 0.00 46.80 2.66
5321 6467 3.135814 GCCGGAGCCCGTATAACT 58.864 61.111 5.05 0.00 46.80 2.24
5360 6506 0.179004 TGCACGGATTTGAGTTGGGT 60.179 50.000 0.00 0.00 0.00 4.51
5369 6515 1.574428 GCACGAACTGCACGGATTT 59.426 52.632 0.08 0.00 46.29 2.17
5370 6516 3.253955 GCACGAACTGCACGGATT 58.746 55.556 0.08 0.00 46.29 3.01
5378 6524 0.229753 GAACACGAGTGCACGAACTG 59.770 55.000 12.01 8.14 37.03 3.16
5379 6525 1.206745 CGAACACGAGTGCACGAACT 61.207 55.000 12.01 0.00 35.59 3.01
5396 6549 2.047274 GCACCTAACCTGCAGCGA 60.047 61.111 8.66 0.00 34.56 4.93
5437 6591 1.743252 GCCTCAAGAAGGGCGACTG 60.743 63.158 0.00 0.00 46.32 3.51
5460 6615 2.597578 TGACTAGCTAGGGTGTGACA 57.402 50.000 24.35 9.62 0.00 3.58
5464 6619 1.866015 TGCATGACTAGCTAGGGTGT 58.134 50.000 24.35 4.29 0.00 4.16
5465 6620 2.366590 TGATGCATGACTAGCTAGGGTG 59.633 50.000 24.35 18.63 0.00 4.61
5466 6621 2.632028 CTGATGCATGACTAGCTAGGGT 59.368 50.000 24.35 5.47 0.00 4.34
5467 6622 2.896044 TCTGATGCATGACTAGCTAGGG 59.104 50.000 24.35 11.76 0.00 3.53
5468 6623 3.573538 ACTCTGATGCATGACTAGCTAGG 59.426 47.826 24.35 7.95 0.00 3.02
5469 6624 4.037803 ACACTCTGATGCATGACTAGCTAG 59.962 45.833 19.44 19.44 0.00 3.42
5470 6625 3.956848 ACACTCTGATGCATGACTAGCTA 59.043 43.478 2.46 0.00 0.00 3.32
5471 6626 2.765135 ACACTCTGATGCATGACTAGCT 59.235 45.455 2.46 0.00 0.00 3.32
5472 6627 2.864946 CACACTCTGATGCATGACTAGC 59.135 50.000 2.46 0.00 0.00 3.42
5473 6628 3.864003 CACACACTCTGATGCATGACTAG 59.136 47.826 2.46 0.00 0.00 2.57
5474 6629 3.853475 CACACACTCTGATGCATGACTA 58.147 45.455 2.46 0.00 0.00 2.59
5475 6630 2.696506 CACACACTCTGATGCATGACT 58.303 47.619 2.46 0.00 0.00 3.41
5476 6631 1.129998 GCACACACTCTGATGCATGAC 59.870 52.381 2.46 0.00 34.67 3.06
5477 6632 1.270947 TGCACACACTCTGATGCATGA 60.271 47.619 2.46 0.00 37.81 3.07
5478 6633 1.161843 TGCACACACTCTGATGCATG 58.838 50.000 2.46 0.00 37.81 4.06
5479 6634 2.124277 ATGCACACACTCTGATGCAT 57.876 45.000 0.00 0.00 43.14 3.96
5480 6635 1.270947 TGATGCACACACTCTGATGCA 60.271 47.619 5.46 5.46 43.20 3.96
5481 6636 1.445871 TGATGCACACACTCTGATGC 58.554 50.000 0.00 0.00 34.95 3.91
5482 6637 3.007635 ACATGATGCACACACTCTGATG 58.992 45.455 0.00 0.00 0.00 3.07
5483 6638 3.345508 ACATGATGCACACACTCTGAT 57.654 42.857 0.00 0.00 0.00 2.90
5484 6639 2.845363 ACATGATGCACACACTCTGA 57.155 45.000 0.00 0.00 0.00 3.27
5485 6640 3.909776 AAACATGATGCACACACTCTG 57.090 42.857 0.00 0.00 0.00 3.35
5486 6641 6.389830 TTTTAAACATGATGCACACACTCT 57.610 33.333 0.00 0.00 0.00 3.24
5487 6642 7.642071 AATTTTAAACATGATGCACACACTC 57.358 32.000 0.00 0.00 0.00 3.51
5488 6643 7.171337 GGAAATTTTAAACATGATGCACACACT 59.829 33.333 0.00 0.00 0.00 3.55
5489 6644 7.042187 TGGAAATTTTAAACATGATGCACACAC 60.042 33.333 0.00 0.00 0.00 3.82
5490 6645 6.988580 TGGAAATTTTAAACATGATGCACACA 59.011 30.769 0.00 0.00 0.00 3.72
5491 6646 7.418840 TGGAAATTTTAAACATGATGCACAC 57.581 32.000 0.00 0.00 0.00 3.82
5492 6647 8.618702 AATGGAAATTTTAAACATGATGCACA 57.381 26.923 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.