Multiple sequence alignment - TraesCS7A01G464800

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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 TraesCS7A01G464800 chr7A 100.000 5694 0 0 1 5694 661282265 661276572 0.000000e+00 10515
1 TraesCS7A01G464800 chr7A 84.545 2847 194 107 994 3708 660495298 660498030 0.000000e+00 2593
2 TraesCS7A01G464800 chr7A 91.738 581 41 5 4146 4720 660498174 660498753 0.000000e+00 800
3 TraesCS7A01G464800 chr7A 79.048 630 44 49 280 830 660494480 660495100 9.080000e-93 351
4 TraesCS7A01G464800 chr7A 94.286 105 4 1 3836 3938 660498071 660498175 5.900000e-35 159
5 TraesCS7A01G464800 chr7D 90.572 4211 182 71 639 4750 571977627 571973533 0.000000e+00 5378
6 TraesCS7A01G464800 chr7D 86.796 1492 100 40 2139 3573 571480115 571481566 0.000000e+00 1574
7 TraesCS7A01G464800 chr7D 81.506 1979 147 91 280 2121 571478177 571480073 0.000000e+00 1424
8 TraesCS7A01G464800 chr7D 92.616 623 37 3 19 632 571978522 571977900 0.000000e+00 887
9 TraesCS7A01G464800 chr7D 93.127 582 32 6 4146 4720 571481819 571482399 0.000000e+00 846
10 TraesCS7A01G464800 chr7D 84.259 216 23 9 5283 5490 571972906 571972694 3.480000e-47 200
11 TraesCS7A01G464800 chr7D 94.340 106 4 1 3835 3938 571481715 571481820 1.640000e-35 161
12 TraesCS7A01G464800 chr7B 90.342 3800 163 77 258 3934 628737316 628733598 0.000000e+00 4796
13 TraesCS7A01G464800 chr7B 86.068 2828 183 102 994 3708 627611027 627613756 0.000000e+00 2844
14 TraesCS7A01G464800 chr7B 94.479 797 37 7 3959 4750 628733603 628732809 0.000000e+00 1221
15 TraesCS7A01G464800 chr7B 88.818 939 60 20 4761 5678 628732829 628731915 0.000000e+00 1110
16 TraesCS7A01G464800 chr7B 93.276 580 30 5 4146 4720 627613899 627614474 0.000000e+00 846
17 TraesCS7A01G464800 chr7B 80.822 584 51 26 280 814 627610214 627610785 8.890000e-108 401
18 TraesCS7A01G464800 chr7B 93.396 106 5 2 3835 3938 627613795 627613900 7.640000e-34 156
19 TraesCS7A01G464800 chr2A 85.039 127 16 3 1004 1128 708058375 708058500 5.990000e-25 126


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 TraesCS7A01G464800 chr7A 661276572 661282265 5693 True 10515.000000 10515 100.00000 1 5694 1 chr7A.!!$R1 5693
1 TraesCS7A01G464800 chr7A 660494480 660498753 4273 False 975.750000 2593 87.40425 280 4720 4 chr7A.!!$F1 4440
2 TraesCS7A01G464800 chr7D 571972694 571978522 5828 True 2155.000000 5378 89.14900 19 5490 3 chr7D.!!$R1 5471
3 TraesCS7A01G464800 chr7D 571478177 571482399 4222 False 1001.250000 1574 88.94225 280 4720 4 chr7D.!!$F1 4440
4 TraesCS7A01G464800 chr7B 628731915 628737316 5401 True 2375.666667 4796 91.21300 258 5678 3 chr7B.!!$R1 5420
5 TraesCS7A01G464800 chr7B 627610214 627614474 4260 False 1061.750000 2844 88.39050 280 4720 4 chr7B.!!$F1 4440

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
878 1308 0.383231 GCTGCTGCTTCTTGTGTTGT 59.617 50.0 8.53 0.00 36.03 3.32 F
1347 1845 0.535335 TGCATGAGTACTTCGGTCCC 59.465 55.0 0.00 0.00 0.00 4.46 F
1860 2434 0.322975 CTGCTAGTGGCTGGAGTTGT 59.677 55.0 0.00 0.00 42.39 3.32 F
2939 3639 0.806492 GAAGTACGCTACAGGCCAGC 60.806 60.0 5.01 4.08 37.74 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1820 2385 0.401738 ATGCACACAGCCACCTTAGT 59.598 50.000 0.00 0.00 44.83 2.24 R
2919 3619 0.818296 CTGGCCTGTAGCGTACTTCT 59.182 55.000 3.32 0.00 45.17 2.85 R
3423 4143 1.129809 GCGAATGTCACGTGAACCG 59.870 57.895 21.95 20.13 44.03 4.44 R
4835 5604 0.534412 AGACGCCATCAGTTCTGAGG 59.466 55.000 8.47 7.92 0.00 3.86 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
59 60 5.242393 ACTGTTTACTGAATGCAAATGAGCT 59.758 36.000 0.00 0.00 34.99 4.09
67 68 0.828762 TGCAAATGAGCTTGGGCACT 60.829 50.000 0.00 0.00 41.70 4.40
81 82 4.248174 TGGGCACTGAATTGAATATCCA 57.752 40.909 0.00 0.00 0.00 3.41
83 84 5.210430 TGGGCACTGAATTGAATATCCATT 58.790 37.500 0.00 0.00 0.00 3.16
85 86 6.183360 TGGGCACTGAATTGAATATCCATTTC 60.183 38.462 0.00 0.00 0.00 2.17
86 87 5.916883 GGCACTGAATTGAATATCCATTTCG 59.083 40.000 0.00 0.00 32.24 3.46
125 126 9.483916 TTCTTGACAAGAATAATTCTGTACGAA 57.516 29.630 23.67 0.00 42.31 3.85
133 134 8.912787 AGAATAATTCTGTACGAACTACACAG 57.087 34.615 0.00 0.00 38.91 3.66
149 150 1.208776 CACAGACCATCAGAGATGCCA 59.791 52.381 1.52 0.00 0.00 4.92
165 166 2.810164 TGCCATAAACCAAACCCCTAC 58.190 47.619 0.00 0.00 0.00 3.18
176 177 3.118223 CCAAACCCCTACATCTTCCTCTC 60.118 52.174 0.00 0.00 0.00 3.20
185 186 1.220236 CATCTTCCTCTCCCTCCCTCT 59.780 57.143 0.00 0.00 0.00 3.69
378 408 1.618837 GGAAGATATGTGCCCGCTAGA 59.381 52.381 0.00 0.00 0.00 2.43
830 1227 2.236644 TCCTCGATATCCCTCTCGGTAG 59.763 54.545 0.00 0.00 35.64 3.18
877 1307 3.174790 GCTGCTGCTTCTTGTGTTG 57.825 52.632 8.53 0.00 36.03 3.33
878 1308 0.383231 GCTGCTGCTTCTTGTGTTGT 59.617 50.000 8.53 0.00 36.03 3.32
879 1309 1.862815 GCTGCTGCTTCTTGTGTTGTG 60.863 52.381 8.53 0.00 36.03 3.33
880 1310 1.402968 CTGCTGCTTCTTGTGTTGTGT 59.597 47.619 0.00 0.00 0.00 3.72
966 1421 4.220163 TCCGAGGGGATCCGAGGG 62.220 72.222 5.45 4.56 37.43 4.30
1056 1515 2.840753 GGGCTTCAGGTTCCACCCA 61.841 63.158 0.00 0.00 39.75 4.51
1298 1785 3.329386 TGCTTGTGTGATCAGTTCTAGC 58.671 45.455 15.49 15.49 0.00 3.42
1302 1789 3.838120 TGTGTGATCAGTTCTAGCTTCG 58.162 45.455 0.00 0.00 0.00 3.79
1347 1845 0.535335 TGCATGAGTACTTCGGTCCC 59.465 55.000 0.00 0.00 0.00 4.46
1386 1888 7.447238 TCTGTTGATTTAATTTCTTCTCCCGTT 59.553 33.333 0.00 0.00 0.00 4.44
1389 1891 6.919721 TGATTTAATTTCTTCTCCCGTTTGG 58.080 36.000 0.00 0.00 0.00 3.28
1390 1892 4.776795 TTAATTTCTTCTCCCGTTTGGC 57.223 40.909 0.00 0.00 0.00 4.52
1391 1893 2.586648 ATTTCTTCTCCCGTTTGGCT 57.413 45.000 0.00 0.00 0.00 4.75
1411 1913 4.377841 GGCTGCTGCTGATTCGTAATTATC 60.378 45.833 15.64 0.00 39.59 1.75
1466 1969 6.184789 TCCCCTTAAAAATATATCGCATCCC 58.815 40.000 0.00 0.00 0.00 3.85
1547 2061 7.846592 CGTTTCTAAACAGACAAGTCTTCTTTC 59.153 37.037 0.00 0.00 37.98 2.62
1640 2174 4.100529 GTGTGTAAGCATGCATGATTGTC 58.899 43.478 34.19 26.25 36.98 3.18
1820 2385 4.405358 AGTTTCCTTCAGTTGCATCCAAAA 59.595 37.500 0.00 0.00 31.68 2.44
1860 2434 0.322975 CTGCTAGTGGCTGGAGTTGT 59.677 55.000 0.00 0.00 42.39 3.32
1945 2548 2.419574 GCTTCCCATACCGCTAGAAACA 60.420 50.000 0.00 0.00 0.00 2.83
1946 2549 3.869065 CTTCCCATACCGCTAGAAACAA 58.131 45.455 0.00 0.00 0.00 2.83
1947 2550 3.255969 TCCCATACCGCTAGAAACAAC 57.744 47.619 0.00 0.00 0.00 3.32
1949 2552 2.093128 CCCATACCGCTAGAAACAACCT 60.093 50.000 0.00 0.00 0.00 3.50
1952 2555 4.094442 CCATACCGCTAGAAACAACCTTTC 59.906 45.833 0.00 0.00 0.00 2.62
1954 2557 2.158726 ACCGCTAGAAACAACCTTTCCA 60.159 45.455 0.00 0.00 0.00 3.53
1955 2558 2.225727 CCGCTAGAAACAACCTTTCCAC 59.774 50.000 0.00 0.00 0.00 4.02
1956 2559 2.225727 CGCTAGAAACAACCTTTCCACC 59.774 50.000 0.00 0.00 0.00 4.61
1957 2560 3.487372 GCTAGAAACAACCTTTCCACCT 58.513 45.455 0.00 0.00 0.00 4.00
1958 2561 3.889538 GCTAGAAACAACCTTTCCACCTT 59.110 43.478 0.00 0.00 0.00 3.50
1963 2566 2.945456 ACAACCTTTCCACCTTTCCTC 58.055 47.619 0.00 0.00 0.00 3.71
2029 2647 4.340381 CCCATGCTTTTCTCCCTCTTTATG 59.660 45.833 0.00 0.00 0.00 1.90
2030 2648 4.340381 CCATGCTTTTCTCCCTCTTTATGG 59.660 45.833 0.00 0.00 0.00 2.74
2031 2649 4.657814 TGCTTTTCTCCCTCTTTATGGT 57.342 40.909 0.00 0.00 0.00 3.55
2032 2650 4.589908 TGCTTTTCTCCCTCTTTATGGTC 58.410 43.478 0.00 0.00 0.00 4.02
2034 2652 4.324641 GCTTTTCTCCCTCTTTATGGTCCT 60.325 45.833 0.00 0.00 0.00 3.85
2035 2653 5.104485 GCTTTTCTCCCTCTTTATGGTCCTA 60.104 44.000 0.00 0.00 0.00 2.94
2037 2655 7.525158 TTTTCTCCCTCTTTATGGTCCTAAT 57.475 36.000 0.00 0.00 0.00 1.73
2038 2656 7.525158 TTTCTCCCTCTTTATGGTCCTAATT 57.475 36.000 0.00 0.00 0.00 1.40
2039 2657 8.632731 TTTCTCCCTCTTTATGGTCCTAATTA 57.367 34.615 0.00 0.00 0.00 1.40
2040 2658 7.613551 TCTCCCTCTTTATGGTCCTAATTAC 57.386 40.000 0.00 0.00 0.00 1.89
2041 2659 6.557633 TCTCCCTCTTTATGGTCCTAATTACC 59.442 42.308 0.00 0.00 37.53 2.85
2042 2660 5.306160 TCCCTCTTTATGGTCCTAATTACCG 59.694 44.000 0.00 0.00 40.08 4.02
2104 2723 8.095792 AGGCAAGATAATATTCAGAGTGAGATG 58.904 37.037 0.00 0.00 0.00 2.90
2146 2800 6.229936 ACTACTGTAGACTGTAGAGAGAGG 57.770 45.833 24.92 6.19 45.49 3.69
2235 2897 9.784531 CAAGGGATGAATACATATAGTTTCTGT 57.215 33.333 0.00 0.00 36.82 3.41
2268 2930 8.219546 TCTACAATGAGAACAAAATTCACACA 57.780 30.769 0.00 0.00 0.00 3.72
2394 3059 1.133575 CCTGTTCATCCCATGCCATCT 60.134 52.381 0.00 0.00 0.00 2.90
2421 3086 1.217689 CCCCCAATTTGCCTGATCCTA 59.782 52.381 0.00 0.00 0.00 2.94
2446 3111 2.639065 GAAATTCACAGCCCACGGATA 58.361 47.619 0.00 0.00 0.00 2.59
2594 3261 5.431765 TCACAAGAATAGGAAAGATGCCTC 58.568 41.667 0.00 0.00 36.96 4.70
2597 3264 2.370189 AGAATAGGAAAGATGCCTCCCG 59.630 50.000 0.00 0.00 36.96 5.14
2617 3285 4.453819 CCCGCAATCAATAGATCTCCTTTC 59.546 45.833 0.00 0.00 31.90 2.62
2673 3341 9.077885 CCTGTTATGCAATTACCTATTAATGGT 57.922 33.333 12.34 12.34 41.28 3.55
2708 3376 5.646360 TGCCTTACTTAAATGTGGCTCTAAC 59.354 40.000 0.00 0.00 40.82 2.34
2714 3382 6.461640 ACTTAAATGTGGCTCTAACGTTAGT 58.538 36.000 29.36 13.27 32.61 2.24
2715 3383 7.605449 ACTTAAATGTGGCTCTAACGTTAGTA 58.395 34.615 29.36 17.60 32.61 1.82
2716 3384 7.758528 ACTTAAATGTGGCTCTAACGTTAGTAG 59.241 37.037 29.36 24.58 32.61 2.57
2784 3478 1.400846 GTGGATGCACATCTTGAGCAG 59.599 52.381 13.07 0.00 46.30 4.24
2919 3619 5.046807 GGTACTTCTACAGCTTAAGGGACAA 60.047 44.000 4.29 0.00 0.00 3.18
2939 3639 0.806492 GAAGTACGCTACAGGCCAGC 60.806 60.000 5.01 4.08 37.74 4.85
3064 3764 6.012333 TGTTTTATGAAGGTAGAGCCCCTAAA 60.012 38.462 0.00 0.00 38.26 1.85
3156 3856 7.308229 GCCACTCAAGGTAAGCATCATTATAAG 60.308 40.741 0.00 0.00 0.00 1.73
3211 3912 3.526899 TGATACTCCACTCTTTTCCCCA 58.473 45.455 0.00 0.00 0.00 4.96
3213 3914 4.164221 TGATACTCCACTCTTTTCCCCATC 59.836 45.833 0.00 0.00 0.00 3.51
3265 3970 8.606754 AATGCATCATATGGATAGAGAGTAGT 57.393 34.615 0.00 0.00 40.66 2.73
3271 3976 6.435591 TCATATGGATAGAGAGTAGTGCAAGG 59.564 42.308 2.13 0.00 0.00 3.61
3282 3987 1.915141 AGTGCAAGGAATTCCACCAG 58.085 50.000 26.22 13.14 38.89 4.00
3423 4143 9.459640 GTATGGACTAAAGAAACAAAAACCTTC 57.540 33.333 0.00 0.00 0.00 3.46
3554 4274 5.106237 GCATATGGCCTCTCAATTCAAGATC 60.106 44.000 3.32 0.00 36.11 2.75
3555 4275 4.792513 ATGGCCTCTCAATTCAAGATCT 57.207 40.909 3.32 0.00 0.00 2.75
3556 4276 5.901413 ATGGCCTCTCAATTCAAGATCTA 57.099 39.130 3.32 0.00 0.00 1.98
3557 4277 5.287674 TGGCCTCTCAATTCAAGATCTAG 57.712 43.478 3.32 0.00 0.00 2.43
3623 4358 4.546829 GGTAGGTCACCAAGTTGACATA 57.453 45.455 3.87 0.00 46.68 2.29
3708 4443 2.959507 AAAAGCTGGTGTGGTTTGTC 57.040 45.000 0.00 0.00 37.65 3.18
3798 4538 7.405469 TGTTCATTGTGTTAATGATTGTTGC 57.595 32.000 3.47 0.00 36.63 4.17
3819 4559 0.702316 AATTAGTTGGGCCGGGTTCT 59.298 50.000 2.18 0.00 0.00 3.01
3977 4724 4.699735 TGCAAATTATCGACTCACACCAAT 59.300 37.500 0.00 0.00 0.00 3.16
4069 4823 9.700831 ATGGCTAAGTAATTTCAGTATTTTCCT 57.299 29.630 0.00 0.00 0.00 3.36
4119 4875 7.054491 ACTCATACTCAACCTTTGCAAAAAT 57.946 32.000 13.84 0.92 0.00 1.82
4214 4977 6.878317 TCATTCATCTTCCAGTCTAACGATT 58.122 36.000 0.00 0.00 0.00 3.34
4270 5035 3.053170 ACTGGGTCTTGTGTAGGGTTTTT 60.053 43.478 0.00 0.00 0.00 1.94
4297 5062 1.047002 CCAGGACAACCATTGCCAAA 58.953 50.000 0.00 0.00 38.94 3.28
4301 5066 1.347378 GGACAACCATTGCCAAACCAT 59.653 47.619 0.00 0.00 35.97 3.55
4396 5164 2.806945 TTGACCATCCTGGAATGTCC 57.193 50.000 19.98 8.18 40.96 4.02
4494 5262 1.069204 CTCGATGAACATCCCGGTGAT 59.931 52.381 0.00 0.00 34.40 3.06
4708 5477 5.104735 ACTCAGTTGATTTTCTAGCTAGGGG 60.105 44.000 20.58 2.99 0.00 4.79
4734 5503 7.880160 ATTATTGCTAGTGCTACCAATCAAA 57.120 32.000 3.76 0.00 40.48 2.69
4735 5504 5.824904 ATTGCTAGTGCTACCAATCAAAG 57.175 39.130 0.00 0.00 40.48 2.77
4736 5505 4.551702 TGCTAGTGCTACCAATCAAAGA 57.448 40.909 0.00 0.00 40.48 2.52
4737 5506 5.102953 TGCTAGTGCTACCAATCAAAGAT 57.897 39.130 0.00 0.00 40.48 2.40
4738 5507 5.118990 TGCTAGTGCTACCAATCAAAGATC 58.881 41.667 0.00 0.00 40.48 2.75
4739 5508 5.104776 TGCTAGTGCTACCAATCAAAGATCT 60.105 40.000 0.00 0.00 40.48 2.75
4740 5509 6.098266 TGCTAGTGCTACCAATCAAAGATCTA 59.902 38.462 0.00 0.00 40.48 1.98
4741 5510 6.422400 GCTAGTGCTACCAATCAAAGATCTAC 59.578 42.308 0.00 0.00 36.03 2.59
4742 5511 6.299805 AGTGCTACCAATCAAAGATCTACA 57.700 37.500 0.00 0.00 0.00 2.74
4743 5512 6.893583 AGTGCTACCAATCAAAGATCTACAT 58.106 36.000 0.00 0.00 0.00 2.29
4744 5513 7.341805 AGTGCTACCAATCAAAGATCTACATT 58.658 34.615 0.00 0.00 0.00 2.71
4745 5514 7.831193 AGTGCTACCAATCAAAGATCTACATTT 59.169 33.333 0.00 0.00 0.00 2.32
4746 5515 8.462016 GTGCTACCAATCAAAGATCTACATTTT 58.538 33.333 0.00 0.00 0.00 1.82
4747 5516 8.677300 TGCTACCAATCAAAGATCTACATTTTC 58.323 33.333 0.00 0.00 0.00 2.29
4748 5517 8.897752 GCTACCAATCAAAGATCTACATTTTCT 58.102 33.333 0.00 0.00 0.00 2.52
4750 5519 8.286191 ACCAATCAAAGATCTACATTTTCTCC 57.714 34.615 0.00 0.00 0.00 3.71
4751 5520 7.890127 ACCAATCAAAGATCTACATTTTCTCCA 59.110 33.333 0.00 0.00 0.00 3.86
4752 5521 8.186821 CCAATCAAAGATCTACATTTTCTCCAC 58.813 37.037 0.00 0.00 0.00 4.02
4753 5522 7.872113 ATCAAAGATCTACATTTTCTCCACC 57.128 36.000 0.00 0.00 0.00 4.61
4754 5523 6.180472 TCAAAGATCTACATTTTCTCCACCC 58.820 40.000 0.00 0.00 0.00 4.61
4755 5524 4.408182 AGATCTACATTTTCTCCACCCG 57.592 45.455 0.00 0.00 0.00 5.28
4756 5525 2.396590 TCTACATTTTCTCCACCCGC 57.603 50.000 0.00 0.00 0.00 6.13
4757 5526 1.626321 TCTACATTTTCTCCACCCGCA 59.374 47.619 0.00 0.00 0.00 5.69
4758 5527 2.039216 TCTACATTTTCTCCACCCGCAA 59.961 45.455 0.00 0.00 0.00 4.85
4759 5528 1.698506 ACATTTTCTCCACCCGCAAA 58.301 45.000 0.00 0.00 0.00 3.68
4760 5529 2.035632 ACATTTTCTCCACCCGCAAAA 58.964 42.857 0.00 0.00 0.00 2.44
4761 5530 2.432510 ACATTTTCTCCACCCGCAAAAA 59.567 40.909 0.00 0.00 0.00 1.94
4762 5531 3.070878 ACATTTTCTCCACCCGCAAAAAT 59.929 39.130 0.00 0.00 31.54 1.82
4763 5532 4.282195 ACATTTTCTCCACCCGCAAAAATA 59.718 37.500 0.00 0.00 30.58 1.40
4764 5533 4.939052 TTTTCTCCACCCGCAAAAATAA 57.061 36.364 0.00 0.00 0.00 1.40
4765 5534 4.939052 TTTCTCCACCCGCAAAAATAAA 57.061 36.364 0.00 0.00 0.00 1.40
4787 5556 6.830873 AAGATCTACATTTTCTTGCAAGCT 57.169 33.333 21.99 5.34 0.00 3.74
4808 5577 1.226542 CTCCTGCATGACTGGGCAT 59.773 57.895 0.00 0.00 39.65 4.40
4835 5604 7.319646 TCAGCCAAACACAACAAATATTATCC 58.680 34.615 0.00 0.00 0.00 2.59
4852 5628 0.904865 TCCCTCAGAACTGATGGCGT 60.905 55.000 17.23 0.00 42.70 5.68
4971 5754 1.278985 GTGTGACCATGTCCCAGATCA 59.721 52.381 0.00 0.00 0.00 2.92
4974 5757 0.181350 GACCATGTCCCAGATCACCC 59.819 60.000 0.00 0.00 0.00 4.61
4975 5758 0.549902 ACCATGTCCCAGATCACCCA 60.550 55.000 0.00 0.00 0.00 4.51
5036 5819 0.108138 AAGTTTCAGGATCTCCGGCG 60.108 55.000 0.00 0.00 42.08 6.46
5037 5820 2.174319 GTTTCAGGATCTCCGGCGC 61.174 63.158 0.00 0.00 42.08 6.53
5055 5839 0.869880 GCAATGGCCCGTAAAATCGC 60.870 55.000 0.00 0.00 0.00 4.58
5147 5931 1.291033 ACTAGACCACCTCCAGGCATA 59.709 52.381 0.00 0.00 39.32 3.14
5148 5932 2.090494 ACTAGACCACCTCCAGGCATAT 60.090 50.000 0.00 0.00 39.32 1.78
5223 6252 2.478879 GGTTGTTTTCCCTGTGTTGTCG 60.479 50.000 0.00 0.00 0.00 4.35
5262 6291 6.385649 TCAATATCGCTACATGTACACTCA 57.614 37.500 0.08 0.00 0.00 3.41
5287 6316 3.568430 TGTATGGTACTGTAGATCTGCGG 59.432 47.826 17.19 17.19 0.00 5.69
5336 6365 2.409241 TACTGCTGTGTGTACGCGCA 62.409 55.000 20.62 20.62 35.71 6.09
5359 6388 6.512415 GCACTGATTTTGCGAAATAGCTAGAT 60.512 38.462 12.01 0.00 35.65 1.98
5365 6400 2.965831 TGCGAAATAGCTAGATGGGACT 59.034 45.455 0.00 0.00 38.13 3.85
5387 6422 4.304110 TGACAGTCAAAAGTCGATGGTAC 58.696 43.478 0.00 0.00 37.58 3.34
5408 6452 0.537143 ATTGCAACCGAAGCAGTGGA 60.537 50.000 0.00 0.00 43.75 4.02
5440 6484 2.129555 GAGGAAAGCAGGGACAGCCA 62.130 60.000 0.00 0.00 43.90 4.75
5450 6494 2.217038 GGACAGCCACTCCAGGTCA 61.217 63.158 0.00 0.00 0.00 4.02
5490 6537 4.093291 CTCGCCAGCCTCCAAGCT 62.093 66.667 0.00 0.00 46.45 3.74
5491 6538 4.087892 TCGCCAGCCTCCAAGCTC 62.088 66.667 0.00 0.00 42.61 4.09
5493 6540 4.039092 GCCAGCCTCCAAGCTCCA 62.039 66.667 0.00 0.00 42.61 3.86
5494 6541 2.271497 CCAGCCTCCAAGCTCCAG 59.729 66.667 0.00 0.00 42.61 3.86
5495 6542 2.296365 CCAGCCTCCAAGCTCCAGA 61.296 63.158 0.00 0.00 42.61 3.86
5496 6543 1.681666 CAGCCTCCAAGCTCCAGAA 59.318 57.895 0.00 0.00 42.61 3.02
5497 6544 0.676151 CAGCCTCCAAGCTCCAGAAC 60.676 60.000 0.00 0.00 42.61 3.01
5498 6545 1.743252 GCCTCCAAGCTCCAGAACG 60.743 63.158 0.00 0.00 0.00 3.95
5516 6563 5.182190 CAGAACGAGCTCTAGCCTCATAATA 59.818 44.000 12.85 0.00 43.38 0.98
5517 6564 5.414454 AGAACGAGCTCTAGCCTCATAATAG 59.586 44.000 12.85 0.00 43.38 1.73
5518 6565 4.912586 ACGAGCTCTAGCCTCATAATAGA 58.087 43.478 12.85 0.00 43.38 1.98
5567 6614 6.057321 TGTTATTATTCTGTTCGAAGGGGT 57.943 37.500 0.00 0.00 34.56 4.95
5568 6615 7.185318 TGTTATTATTCTGTTCGAAGGGGTA 57.815 36.000 0.00 0.00 34.56 3.69
5598 6645 9.541143 GATAGGAGGAAGAAAAGAATACAAGAG 57.459 37.037 0.00 0.00 0.00 2.85
5614 6661 2.751806 CAAGAGGATGGGCTTTTCACTC 59.248 50.000 0.00 0.00 0.00 3.51
5661 6708 4.271533 TGTCATGAACAAGTGAACGGTTAC 59.728 41.667 0.00 0.00 34.03 2.50
5672 6719 2.869801 TGAACGGTTACAAGAACAGCTG 59.130 45.455 13.48 13.48 0.00 4.24
5675 6722 1.195448 CGGTTACAAGAACAGCTGCTG 59.805 52.381 27.02 27.02 37.52 4.41
5678 6725 4.003648 GGTTACAAGAACAGCTGCTGTAT 58.996 43.478 33.11 22.42 44.62 2.29
5679 6726 5.175859 GGTTACAAGAACAGCTGCTGTATA 58.824 41.667 33.11 17.89 44.62 1.47
5680 6727 5.063564 GGTTACAAGAACAGCTGCTGTATAC 59.936 44.000 33.11 25.07 44.62 1.47
5681 6728 4.543590 ACAAGAACAGCTGCTGTATACT 57.456 40.909 33.11 26.58 44.62 2.12
5682 6729 4.499183 ACAAGAACAGCTGCTGTATACTC 58.501 43.478 33.11 25.58 44.62 2.59
5683 6730 3.810310 AGAACAGCTGCTGTATACTCC 57.190 47.619 33.11 17.87 44.62 3.85
5684 6731 2.432510 AGAACAGCTGCTGTATACTCCC 59.567 50.000 33.11 16.37 44.62 4.30
5685 6732 2.166907 ACAGCTGCTGTATACTCCCT 57.833 50.000 32.18 5.63 43.46 4.20
5686 6733 2.035632 ACAGCTGCTGTATACTCCCTC 58.964 52.381 32.18 0.00 43.46 4.30
5687 6734 1.342819 CAGCTGCTGTATACTCCCTCC 59.657 57.143 21.21 0.00 0.00 4.30
5688 6735 0.315568 GCTGCTGTATACTCCCTCCG 59.684 60.000 4.17 0.00 0.00 4.63
5689 6736 1.693627 CTGCTGTATACTCCCTCCGT 58.306 55.000 4.17 0.00 0.00 4.69
5690 6737 2.032620 CTGCTGTATACTCCCTCCGTT 58.967 52.381 4.17 0.00 0.00 4.44
5691 6738 2.029623 TGCTGTATACTCCCTCCGTTC 58.970 52.381 4.17 0.00 0.00 3.95
5692 6739 1.340568 GCTGTATACTCCCTCCGTTCC 59.659 57.143 4.17 0.00 0.00 3.62
5693 6740 2.946785 CTGTATACTCCCTCCGTTCCT 58.053 52.381 4.17 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 7.978414 TCATTTGCATTCAGTAAACAGTGAAAA 59.022 29.630 0.00 0.00 36.31 2.29
31 32 7.487484 TCATTTGCATTCAGTAAACAGTGAAA 58.513 30.769 0.00 0.00 36.31 2.69
32 33 7.036996 TCATTTGCATTCAGTAAACAGTGAA 57.963 32.000 0.00 0.00 34.59 3.18
33 34 6.631971 TCATTTGCATTCAGTAAACAGTGA 57.368 33.333 0.00 0.00 34.59 3.41
34 35 5.344128 GCTCATTTGCATTCAGTAAACAGTG 59.656 40.000 0.00 0.00 34.59 3.66
35 36 5.242393 AGCTCATTTGCATTCAGTAAACAGT 59.758 36.000 0.00 0.00 34.59 3.55
36 37 5.706916 AGCTCATTTGCATTCAGTAAACAG 58.293 37.500 0.00 0.00 34.59 3.16
37 38 5.710513 AGCTCATTTGCATTCAGTAAACA 57.289 34.783 0.00 0.00 34.59 2.83
38 39 5.346822 CCAAGCTCATTTGCATTCAGTAAAC 59.653 40.000 0.00 0.00 34.59 2.01
39 40 5.472148 CCAAGCTCATTTGCATTCAGTAAA 58.528 37.500 0.00 0.00 36.25 2.01
40 41 4.082081 CCCAAGCTCATTTGCATTCAGTAA 60.082 41.667 0.00 0.00 34.99 2.24
41 42 3.444742 CCCAAGCTCATTTGCATTCAGTA 59.555 43.478 0.00 0.00 34.99 2.74
42 43 2.232941 CCCAAGCTCATTTGCATTCAGT 59.767 45.455 0.00 0.00 34.99 3.41
43 44 2.888594 CCCAAGCTCATTTGCATTCAG 58.111 47.619 0.00 0.00 34.99 3.02
44 45 1.066716 GCCCAAGCTCATTTGCATTCA 60.067 47.619 0.00 0.00 35.50 2.57
45 46 1.066716 TGCCCAAGCTCATTTGCATTC 60.067 47.619 0.00 0.00 40.80 2.67
46 47 0.978151 TGCCCAAGCTCATTTGCATT 59.022 45.000 0.00 0.00 40.80 3.56
47 48 0.248289 GTGCCCAAGCTCATTTGCAT 59.752 50.000 0.00 0.00 40.80 3.96
52 53 2.226962 ATTCAGTGCCCAAGCTCATT 57.773 45.000 0.00 0.00 40.80 2.57
59 60 4.608269 TGGATATTCAATTCAGTGCCCAA 58.392 39.130 0.00 0.00 0.00 4.12
67 68 9.573166 AACCTATCGAAATGGATATTCAATTCA 57.427 29.630 11.55 0.93 0.00 2.57
81 82 7.876068 TGTCAAGAACTAACAACCTATCGAAAT 59.124 33.333 0.00 0.00 0.00 2.17
83 84 6.751157 TGTCAAGAACTAACAACCTATCGAA 58.249 36.000 0.00 0.00 0.00 3.71
85 86 6.866770 TCTTGTCAAGAACTAACAACCTATCG 59.133 38.462 13.00 0.00 33.83 2.92
86 87 8.603242 TTCTTGTCAAGAACTAACAACCTATC 57.397 34.615 21.59 0.00 42.31 2.08
125 126 3.131933 GCATCTCTGATGGTCTGTGTAGT 59.868 47.826 9.24 0.00 0.00 2.73
133 134 3.817647 GGTTTATGGCATCTCTGATGGTC 59.182 47.826 1.65 0.00 0.00 4.02
149 150 5.255443 AGGAAGATGTAGGGGTTTGGTTTAT 59.745 40.000 0.00 0.00 0.00 1.40
165 166 1.220236 AGAGGGAGGGAGAGGAAGATG 59.780 57.143 0.00 0.00 0.00 2.90
176 177 0.334676 AGACAGACAGAGAGGGAGGG 59.665 60.000 0.00 0.00 0.00 4.30
185 186 2.168313 TGCACACAGAAAGACAGACAGA 59.832 45.455 0.00 0.00 0.00 3.41
230 231 0.252197 GGAACTGGAAGGGTGCGTAT 59.748 55.000 0.00 0.00 39.30 3.06
231 232 1.122632 TGGAACTGGAAGGGTGCGTA 61.123 55.000 0.00 0.00 39.30 4.42
264 273 1.543429 GGTATGCTGGTATGGGCTGTC 60.543 57.143 0.00 0.00 0.00 3.51
378 408 0.037303 CGGGCTGGCCTAATCATCAT 59.963 55.000 18.81 0.00 36.10 2.45
668 1015 3.387374 ACGGCTCTACTACTAGTAGCTGA 59.613 47.826 26.54 21.91 45.93 4.26
876 1306 2.194597 GGCAGTGGGACCAACACA 59.805 61.111 0.72 0.00 41.21 3.72
877 1307 2.978010 CGGCAGTGGGACCAACAC 60.978 66.667 0.72 0.00 39.10 3.32
878 1308 3.164977 TCGGCAGTGGGACCAACA 61.165 61.111 0.72 0.00 0.00 3.33
879 1309 2.185310 ATCTCGGCAGTGGGACCAAC 62.185 60.000 0.00 0.00 0.00 3.77
880 1310 1.899437 GATCTCGGCAGTGGGACCAA 61.899 60.000 0.00 0.00 0.00 3.67
959 1414 2.768344 GCCTTGGATCCCCTCGGA 60.768 66.667 9.90 0.00 44.33 4.55
960 1415 4.241555 CGCCTTGGATCCCCTCGG 62.242 72.222 9.90 5.35 0.00 4.63
961 1416 3.154473 TCGCCTTGGATCCCCTCG 61.154 66.667 9.90 7.81 0.00 4.63
964 1419 3.483869 AGCTCGCCTTGGATCCCC 61.484 66.667 9.90 0.00 0.00 4.81
966 1421 2.899339 GCAGCTCGCCTTGGATCC 60.899 66.667 4.20 4.20 32.94 3.36
1232 1698 8.902540 TGGTGTAATTAAGCTACTTGGATATG 57.097 34.615 0.00 0.00 0.00 1.78
1236 1708 5.183228 GCTGGTGTAATTAAGCTACTTGGA 58.817 41.667 0.00 0.00 32.82 3.53
1267 1746 5.043248 TGATCACACAAGCATATAGACACG 58.957 41.667 0.00 0.00 0.00 4.49
1347 1845 6.639632 AAATCAACAGATAAATCATCCCCG 57.360 37.500 0.00 0.00 33.75 5.73
1386 1888 0.036483 TACGAATCAGCAGCAGCCAA 60.036 50.000 0.00 0.00 43.56 4.52
1389 1891 4.377841 GGATAATTACGAATCAGCAGCAGC 60.378 45.833 0.00 0.00 42.56 5.25
1390 1892 4.993584 AGGATAATTACGAATCAGCAGCAG 59.006 41.667 0.00 0.00 0.00 4.24
1391 1893 4.960938 AGGATAATTACGAATCAGCAGCA 58.039 39.130 0.00 0.00 0.00 4.41
1411 1913 5.082059 CGTCATCGACTTCAAATTGAAAGG 58.918 41.667 9.85 1.93 36.10 3.11
1466 1969 4.814147 ACACCGCAGAGATATCATACATG 58.186 43.478 5.32 0.00 0.00 3.21
1547 2061 8.893727 CAAGGAATTTAATTAGTACAGTGGAGG 58.106 37.037 0.00 0.00 0.00 4.30
1625 2159 3.600187 TGGGACAATCATGCATGCT 57.400 47.368 22.25 9.87 31.92 3.79
1640 2174 2.449464 TGCATGATTGAGAACCTTGGG 58.551 47.619 0.00 0.00 0.00 4.12
1778 2339 1.596260 CTACACATGCATGAGCGGAAG 59.404 52.381 32.75 15.76 46.23 3.46
1820 2385 0.401738 ATGCACACAGCCACCTTAGT 59.598 50.000 0.00 0.00 44.83 2.24
1860 2434 5.456548 TTGTCGTGGTCACTTCAGTTATA 57.543 39.130 0.00 0.00 0.00 0.98
1945 2548 3.463704 AGAAGAGGAAAGGTGGAAAGGTT 59.536 43.478 0.00 0.00 0.00 3.50
1946 2549 3.056832 AGAAGAGGAAAGGTGGAAAGGT 58.943 45.455 0.00 0.00 0.00 3.50
1947 2550 3.797559 AGAAGAGGAAAGGTGGAAAGG 57.202 47.619 0.00 0.00 0.00 3.11
1949 2552 5.766590 AGAAAAGAAGAGGAAAGGTGGAAA 58.233 37.500 0.00 0.00 0.00 3.13
1952 2555 6.773200 AGTAAAGAAAAGAAGAGGAAAGGTGG 59.227 38.462 0.00 0.00 0.00 4.61
1954 2557 7.499563 GTGAGTAAAGAAAAGAAGAGGAAAGGT 59.500 37.037 0.00 0.00 0.00 3.50
1955 2558 7.717436 AGTGAGTAAAGAAAAGAAGAGGAAAGG 59.283 37.037 0.00 0.00 0.00 3.11
1956 2559 8.669946 AGTGAGTAAAGAAAAGAAGAGGAAAG 57.330 34.615 0.00 0.00 0.00 2.62
1957 2560 9.462606 AAAGTGAGTAAAGAAAAGAAGAGGAAA 57.537 29.630 0.00 0.00 0.00 3.13
1958 2561 9.462606 AAAAGTGAGTAAAGAAAAGAAGAGGAA 57.537 29.630 0.00 0.00 0.00 3.36
2029 2647 9.773328 GTAATTAAACAAACGGTAATTAGGACC 57.227 33.333 0.00 0.00 32.87 4.46
2030 2648 9.773328 GGTAATTAAACAAACGGTAATTAGGAC 57.227 33.333 0.00 0.00 32.87 3.85
2031 2649 9.512588 TGGTAATTAAACAAACGGTAATTAGGA 57.487 29.630 0.00 0.00 32.87 2.94
2035 2653 9.344309 CGAATGGTAATTAAACAAACGGTAATT 57.656 29.630 0.00 0.00 33.27 1.40
2037 2655 8.092521 TCGAATGGTAATTAAACAAACGGTAA 57.907 30.769 14.21 0.00 0.00 2.85
2038 2656 7.664082 TCGAATGGTAATTAAACAAACGGTA 57.336 32.000 14.21 2.46 0.00 4.02
2039 2657 6.557291 TCGAATGGTAATTAAACAAACGGT 57.443 33.333 14.21 0.00 0.00 4.83
2040 2658 7.854934 TTTCGAATGGTAATTAAACAAACGG 57.145 32.000 0.00 0.00 0.00 4.44
2104 2723 7.392953 ACAGTAGTAGTAGTTACTTTGGAGGTC 59.607 40.741 0.00 0.00 42.57 3.85
2146 2800 6.149142 ACTGTGCAAGAATTTGATCTCTCTTC 59.851 38.462 0.00 0.00 36.36 2.87
2192 2854 3.430790 CCCTTGATCAAGTCTCGCATGTA 60.431 47.826 29.03 0.00 36.72 2.29
2198 2860 3.808466 TCATCCCTTGATCAAGTCTCG 57.192 47.619 29.03 16.23 36.72 4.04
2268 2930 1.366319 AAGATGGAGGCAGACAAGGT 58.634 50.000 0.00 0.00 0.00 3.50
2394 3059 5.149584 TCAGGCAAATTGGGGGAATATTA 57.850 39.130 0.00 0.00 0.00 0.98
2421 3086 2.035832 CGTGGGCTGTGAATTTCCTTTT 59.964 45.455 0.00 0.00 0.00 2.27
2427 3092 2.643551 CTATCCGTGGGCTGTGAATTT 58.356 47.619 0.00 0.00 0.00 1.82
2446 3111 5.717654 TCCTTTTTGTGTTAAGTTTGTCCCT 59.282 36.000 0.00 0.00 0.00 4.20
2594 3261 3.692257 AGGAGATCTATTGATTGCGGG 57.308 47.619 0.00 0.00 32.19 6.13
2597 3264 7.041235 CCAGAAGAAAGGAGATCTATTGATTGC 60.041 40.741 0.00 0.00 32.19 3.56
2691 3359 6.963049 ACTAACGTTAGAGCCACATTTAAG 57.037 37.500 35.60 12.14 34.84 1.85
2715 3383 9.201989 ACTTTTCCATTTTTAAGAGAAAGTCCT 57.798 29.630 0.00 0.00 0.00 3.85
2716 3384 9.249457 CACTTTTCCATTTTTAAGAGAAAGTCC 57.751 33.333 0.00 0.00 0.00 3.85
2764 3457 1.400846 CTGCTCAAGATGTGCATCCAC 59.599 52.381 8.41 0.00 44.44 4.02
2784 3478 9.338291 GAACGAAGTAATAATCTTTTTGGAACC 57.662 33.333 0.00 0.00 45.00 3.62
2919 3619 0.818296 CTGGCCTGTAGCGTACTTCT 59.182 55.000 3.32 0.00 45.17 2.85
2939 3639 6.169419 TGATTCAGTTGCTCTATTTGTTCG 57.831 37.500 0.00 0.00 0.00 3.95
3064 3764 2.573915 GACCCATTCAGTCTTCTTCCCT 59.426 50.000 0.00 0.00 0.00 4.20
3079 3779 1.392589 GGAATTCGTGCATGACCCAT 58.607 50.000 8.48 0.00 0.00 4.00
3190 3891 3.526899 TGGGGAAAAGAGTGGAGTATCA 58.473 45.455 0.00 0.00 36.25 2.15
3265 3970 2.673775 TTCTGGTGGAATTCCTTGCA 57.326 45.000 24.73 1.80 36.82 4.08
3271 3976 8.519526 TGTGTACATAATTTTCTGGTGGAATTC 58.480 33.333 0.00 0.00 33.53 2.17
3282 3987 8.795786 TTCTTGCTTGTGTGTACATAATTTTC 57.204 30.769 0.00 0.00 36.53 2.29
3349 4063 9.467258 TGAAATCAAATCTGTCAAGTTTCATTC 57.533 29.630 0.00 0.00 31.62 2.67
3423 4143 1.129809 GCGAATGTCACGTGAACCG 59.870 57.895 21.95 20.13 44.03 4.44
3708 4443 7.489757 GCTAACTATCTGTTCTGGTGTCTTAAG 59.510 40.741 0.00 0.00 39.89 1.85
3758 4498 2.512692 AACATATGTTCTGGCTGCCA 57.487 45.000 21.96 21.96 31.64 4.92
3790 4530 4.682787 GGCCCAACTAATTAGCAACAATC 58.317 43.478 12.54 0.00 0.00 2.67
3791 4531 3.130340 CGGCCCAACTAATTAGCAACAAT 59.870 43.478 12.54 0.00 0.00 2.71
3792 4532 2.490115 CGGCCCAACTAATTAGCAACAA 59.510 45.455 12.54 0.00 0.00 2.83
3798 4538 2.092592 AGAACCCGGCCCAACTAATTAG 60.093 50.000 11.05 11.05 0.00 1.73
3819 4559 3.769739 AGTACAGAACATCAACAGGCA 57.230 42.857 0.00 0.00 0.00 4.75
3943 4690 9.144747 GAGTCGATAATTTGCACATACATCTAT 57.855 33.333 0.00 0.00 0.00 1.98
3944 4691 8.141268 TGAGTCGATAATTTGCACATACATCTA 58.859 33.333 0.00 0.00 0.00 1.98
3945 4692 6.986231 TGAGTCGATAATTTGCACATACATCT 59.014 34.615 0.00 0.00 0.00 2.90
3946 4693 7.065894 GTGAGTCGATAATTTGCACATACATC 58.934 38.462 0.00 0.00 0.00 3.06
3947 4694 6.538381 TGTGAGTCGATAATTTGCACATACAT 59.462 34.615 0.00 0.00 30.73 2.29
3948 4695 5.872070 TGTGAGTCGATAATTTGCACATACA 59.128 36.000 0.00 0.00 30.73 2.29
3977 4724 7.328249 GGATGCGTTGACAGAAATGATTAAAAA 59.672 33.333 0.00 0.00 0.00 1.94
4023 4774 5.708948 CCATTTTTATCTTGTTCTGGCGAA 58.291 37.500 0.00 0.00 0.00 4.70
4096 4850 9.643693 AATATTTTTGCAAAGGTTGAGTATGAG 57.356 29.630 12.41 0.00 0.00 2.90
4107 4863 4.093850 GGCAGCAGAATATTTTTGCAAAGG 59.906 41.667 20.97 12.09 40.22 3.11
4119 4875 5.889853 AGATCAAGATTTTGGCAGCAGAATA 59.110 36.000 0.00 0.00 34.97 1.75
4186 4945 3.871485 AGACTGGAAGATGAATGAGTGC 58.129 45.455 0.00 0.00 37.43 4.40
4187 4946 5.518128 CGTTAGACTGGAAGATGAATGAGTG 59.482 44.000 0.00 0.00 37.43 3.51
4198 4961 6.147821 ACACATGAAAATCGTTAGACTGGAAG 59.852 38.462 0.00 0.00 42.29 3.46
4233 4997 2.781174 ACCCAGTCCTCCTGTTTAACAA 59.219 45.455 0.00 0.00 39.74 2.83
4270 5035 4.141287 CAATGGTTGTCCTGGTCTTGTAA 58.859 43.478 0.00 0.00 34.23 2.41
4297 5062 1.136329 AGTTGCTCCCTGTGGATGGT 61.136 55.000 0.00 0.00 40.80 3.55
4301 5066 1.071699 GTTGTAGTTGCTCCCTGTGGA 59.928 52.381 0.00 0.00 38.75 4.02
4314 5079 2.549754 GCTGCACTGTCAATGTTGTAGT 59.450 45.455 0.00 0.00 0.00 2.73
4516 5284 2.172372 GTGCTGCTGCTCCTGATCG 61.172 63.158 17.00 0.00 40.48 3.69
4734 5503 3.432326 GCGGGTGGAGAAAATGTAGATCT 60.432 47.826 0.00 0.00 0.00 2.75
4735 5504 2.872858 GCGGGTGGAGAAAATGTAGATC 59.127 50.000 0.00 0.00 0.00 2.75
4736 5505 2.238646 TGCGGGTGGAGAAAATGTAGAT 59.761 45.455 0.00 0.00 0.00 1.98
4737 5506 1.626321 TGCGGGTGGAGAAAATGTAGA 59.374 47.619 0.00 0.00 0.00 2.59
4738 5507 2.107950 TGCGGGTGGAGAAAATGTAG 57.892 50.000 0.00 0.00 0.00 2.74
4739 5508 2.570415 TTGCGGGTGGAGAAAATGTA 57.430 45.000 0.00 0.00 0.00 2.29
4740 5509 1.698506 TTTGCGGGTGGAGAAAATGT 58.301 45.000 0.00 0.00 0.00 2.71
4741 5510 2.810439 TTTTGCGGGTGGAGAAAATG 57.190 45.000 0.00 0.00 0.00 2.32
4742 5511 5.476091 TTATTTTTGCGGGTGGAGAAAAT 57.524 34.783 0.00 0.00 35.06 1.82
4743 5512 4.939052 TTATTTTTGCGGGTGGAGAAAA 57.061 36.364 0.00 0.00 0.00 2.29
4744 5513 4.585162 TCTTTATTTTTGCGGGTGGAGAAA 59.415 37.500 0.00 0.00 0.00 2.52
4745 5514 4.145807 TCTTTATTTTTGCGGGTGGAGAA 58.854 39.130 0.00 0.00 0.00 2.87
4746 5515 3.757270 TCTTTATTTTTGCGGGTGGAGA 58.243 40.909 0.00 0.00 0.00 3.71
4747 5516 4.399303 AGATCTTTATTTTTGCGGGTGGAG 59.601 41.667 0.00 0.00 0.00 3.86
4748 5517 4.340617 AGATCTTTATTTTTGCGGGTGGA 58.659 39.130 0.00 0.00 0.00 4.02
4749 5518 4.718940 AGATCTTTATTTTTGCGGGTGG 57.281 40.909 0.00 0.00 0.00 4.61
4750 5519 6.189677 TGTAGATCTTTATTTTTGCGGGTG 57.810 37.500 0.00 0.00 0.00 4.61
4751 5520 7.404671 AATGTAGATCTTTATTTTTGCGGGT 57.595 32.000 0.00 0.00 0.00 5.28
4752 5521 8.702163 AAAATGTAGATCTTTATTTTTGCGGG 57.298 30.769 17.26 0.00 30.86 6.13
4753 5522 9.573133 AGAAAATGTAGATCTTTATTTTTGCGG 57.427 29.630 21.02 0.00 34.07 5.69
4760 5529 9.578439 GCTTGCAAGAAAATGTAGATCTTTATT 57.422 29.630 30.39 0.00 31.26 1.40
4761 5530 8.964772 AGCTTGCAAGAAAATGTAGATCTTTAT 58.035 29.630 30.39 0.00 31.26 1.40
4762 5531 8.239314 CAGCTTGCAAGAAAATGTAGATCTTTA 58.761 33.333 30.39 0.00 31.26 1.85
4763 5532 7.088905 CAGCTTGCAAGAAAATGTAGATCTTT 58.911 34.615 30.39 0.00 31.26 2.52
4764 5533 6.208204 ACAGCTTGCAAGAAAATGTAGATCTT 59.792 34.615 30.39 2.34 33.83 2.40
4765 5534 5.709164 ACAGCTTGCAAGAAAATGTAGATCT 59.291 36.000 30.39 9.63 0.00 2.75
4780 5549 2.831043 TGCAGGAGACAGCTTGCA 59.169 55.556 4.41 4.41 44.30 4.08
4787 5556 1.985614 CCCAGTCATGCAGGAGACA 59.014 57.895 0.00 0.00 37.23 3.41
4808 5577 9.202273 GATAATATTTGTTGTGTTTGGCTGAAA 57.798 29.630 0.00 0.00 0.00 2.69
4835 5604 0.534412 AGACGCCATCAGTTCTGAGG 59.466 55.000 8.47 7.92 0.00 3.86
4852 5628 1.694150 CGAGATAATTGCCCTCCCAGA 59.306 52.381 0.00 0.00 0.00 3.86
4971 5754 2.357154 GCAGAATGGTTATCTGGTGGGT 60.357 50.000 5.76 0.00 43.60 4.51
4974 5757 4.012374 AGTTGCAGAATGGTTATCTGGTG 58.988 43.478 5.76 0.00 43.60 4.17
4975 5758 4.012374 CAGTTGCAGAATGGTTATCTGGT 58.988 43.478 5.76 0.00 43.60 4.00
5036 5819 0.869880 GCGATTTTACGGGCCATTGC 60.870 55.000 4.39 0.00 0.00 3.56
5037 5820 0.453793 TGCGATTTTACGGGCCATTG 59.546 50.000 4.39 0.00 0.00 2.82
5055 5839 9.971922 TGATCACATCAATATACTACTGTCTTG 57.028 33.333 0.00 0.00 36.11 3.02
5100 5884 6.755141 CAGATGCCTTTTTGATTCAATTCGAT 59.245 34.615 0.00 0.00 0.00 3.59
5113 5897 3.330701 TGGTCTAGTCCAGATGCCTTTTT 59.669 43.478 4.43 0.00 35.17 1.94
5147 5931 7.595819 TCAGGATTCACCAAGTTTTTACAAT 57.404 32.000 0.00 0.00 42.04 2.71
5148 5932 7.595819 ATCAGGATTCACCAAGTTTTTACAA 57.404 32.000 0.00 0.00 42.04 2.41
5203 6232 2.162809 ACGACAACACAGGGAAAACAAC 59.837 45.455 0.00 0.00 0.00 3.32
5262 6291 5.278512 CGCAGATCTACAGTACCATACACAT 60.279 44.000 0.00 0.00 0.00 3.21
5267 6296 3.819337 GACCGCAGATCTACAGTACCATA 59.181 47.826 0.00 0.00 0.00 2.74
5269 6298 2.022195 GACCGCAGATCTACAGTACCA 58.978 52.381 0.00 0.00 0.00 3.25
5287 6316 3.018149 AGATCGAAGACTACCAGTGGAC 58.982 50.000 18.40 4.30 42.51 4.02
5336 6365 6.017605 CCATCTAGCTATTTCGCAAAATCAGT 60.018 38.462 0.00 0.00 36.49 3.41
5359 6388 2.483013 CGACTTTTGACTGTCAGTCCCA 60.483 50.000 26.51 13.08 44.44 4.37
5365 6400 3.469008 ACCATCGACTTTTGACTGTCA 57.531 42.857 6.36 6.36 33.18 3.58
5387 6422 1.411394 CACTGCTTCGGTTGCAATTG 58.589 50.000 0.59 0.00 40.13 2.32
5398 6442 2.111384 TGGTAGATCCTCCACTGCTTC 58.889 52.381 2.79 0.00 37.07 3.86
5408 6452 4.820775 TGCTTTCCTCTATGGTAGATCCT 58.179 43.478 0.00 0.00 37.07 3.24
5422 6466 2.156098 TGGCTGTCCCTGCTTTCCT 61.156 57.895 0.00 0.00 0.00 3.36
5440 6484 2.923035 CCACCGGTGACCTGGAGT 60.923 66.667 36.07 0.00 0.00 3.85
5474 6521 4.087892 GAGCTTGGAGGCTGGCGA 62.088 66.667 0.00 0.00 43.20 5.54
5490 6537 0.033991 AGGCTAGAGCTCGTTCTGGA 60.034 55.000 8.37 0.00 41.70 3.86
5491 6538 0.383949 GAGGCTAGAGCTCGTTCTGG 59.616 60.000 8.37 0.00 41.70 3.86
5492 6539 1.098869 TGAGGCTAGAGCTCGTTCTG 58.901 55.000 8.37 0.00 41.70 3.02
5493 6540 2.065899 ATGAGGCTAGAGCTCGTTCT 57.934 50.000 8.37 4.88 41.70 3.01
5494 6541 3.992260 TTATGAGGCTAGAGCTCGTTC 57.008 47.619 8.37 3.79 41.70 3.95
5495 6542 5.182380 GTCTATTATGAGGCTAGAGCTCGTT 59.818 44.000 8.37 0.00 41.70 3.85
5496 6543 4.698304 GTCTATTATGAGGCTAGAGCTCGT 59.302 45.833 8.37 0.00 41.70 4.18
5497 6544 4.697828 TGTCTATTATGAGGCTAGAGCTCG 59.302 45.833 8.37 0.00 41.70 5.03
5498 6545 6.405731 CCATGTCTATTATGAGGCTAGAGCTC 60.406 46.154 5.27 5.27 41.70 4.09
5548 6595 8.258850 TCTTATACCCCTTCGAACAGAATAAT 57.741 34.615 0.00 0.00 38.34 1.28
5591 6638 3.330701 AGTGAAAAGCCCATCCTCTTGTA 59.669 43.478 0.00 0.00 0.00 2.41
5598 6645 2.489722 GACTTGAGTGAAAAGCCCATCC 59.510 50.000 0.00 0.00 0.00 3.51
5614 6661 6.063640 TGTTTGTCATGAATCACAGACTTG 57.936 37.500 15.53 0.00 30.73 3.16
5643 6690 4.505808 TCTTGTAACCGTTCACTTGTTCA 58.494 39.130 0.00 0.00 0.00 3.18
5661 6708 3.868077 GGAGTATACAGCAGCTGTTCTTG 59.132 47.826 32.64 11.26 42.59 3.02
5672 6719 1.340568 GGAACGGAGGGAGTATACAGC 59.659 57.143 5.50 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.