Multiple sequence alignment - TraesCS1D01G305900

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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 TraesCS1D01G305900 chr1D 100.000 5478 0 0 1 5478 403240527 403235050 0.000000e+00 10117.0
1 TraesCS1D01G305900 chr1B 92.488 2689 115 47 837 3457 541470793 541468124 0.000000e+00 3766.0
2 TraesCS1D01G305900 chr1B 92.462 1048 52 13 3987 5009 541467294 541466249 0.000000e+00 1472.0
3 TraesCS1D01G305900 chr1B 96.732 459 14 1 3482 3940 541467973 541467516 0.000000e+00 763.0
4 TraesCS1D01G305900 chr1A 90.355 2312 122 46 854 3129 498455030 498452784 0.000000e+00 2940.0
5 TraesCS1D01G305900 chr1A 85.797 1387 94 42 4005 5317 498451673 498450316 0.000000e+00 1375.0
6 TraesCS1D01G305900 chr1A 90.240 625 51 5 1 621 532265000 532265618 0.000000e+00 808.0
7 TraesCS1D01G305900 chr1A 95.942 345 12 1 3127 3469 498452670 498452326 4.790000e-155 558.0
8 TraesCS1D01G305900 chr1A 96.624 237 8 0 3482 3718 498452281 498452045 1.430000e-105 394.0
9 TraesCS1D01G305900 chr1A 100.000 36 0 0 5443 5478 124179843 124179808 3.540000e-07 67.6
10 TraesCS1D01G305900 chr7D 89.136 856 72 10 1 843 228021421 228022268 0.000000e+00 1046.0
11 TraesCS1D01G305900 chr7D 89.581 835 65 12 1 821 562104281 562105107 0.000000e+00 1040.0
12 TraesCS1D01G305900 chr7D 87.443 876 69 18 1 844 22343449 22342583 0.000000e+00 970.0
13 TraesCS1D01G305900 chr7D 85.829 875 69 23 1 844 10748065 10748915 0.000000e+00 878.0
14 TraesCS1D01G305900 chr7D 100.000 36 0 0 5443 5478 80280930 80280895 3.540000e-07 67.6
15 TraesCS1D01G305900 chr6D 89.064 823 66 11 32 841 161387391 161386580 0.000000e+00 1000.0
16 TraesCS1D01G305900 chr6D 100.000 31 0 0 5284 5314 452132757 452132787 2.130000e-04 58.4
17 TraesCS1D01G305900 chr4B 88.544 838 73 8 1 825 645454559 645453732 0.000000e+00 994.0
18 TraesCS1D01G305900 chr4B 94.000 100 4 2 3915 4013 468666863 468666765 3.420000e-32 150.0
19 TraesCS1D01G305900 chr2B 88.056 854 80 10 1 841 45548362 45547518 0.000000e+00 992.0
20 TraesCS1D01G305900 chr2B 89.356 357 23 10 497 843 577423244 577422893 8.430000e-118 435.0
21 TraesCS1D01G305900 chr2B 94.845 97 3 2 3918 4013 182712413 182712508 3.420000e-32 150.0
22 TraesCS1D01G305900 chr2B 89.381 113 10 2 3918 4028 715924896 715925008 2.060000e-29 141.0
23 TraesCS1D01G305900 chr2B 89.091 55 6 0 5422 5476 697718476 697718422 9.850000e-08 69.4
24 TraesCS1D01G305900 chr2B 97.222 36 1 0 5443 5478 568027793 568027758 1.650000e-05 62.1
25 TraesCS1D01G305900 chr7A 87.086 875 73 17 1 844 9973803 9974668 0.000000e+00 953.0
26 TraesCS1D01G305900 chr7A 93.204 103 4 2 3905 4006 690096080 690095980 1.230000e-31 148.0
27 TraesCS1D01G305900 chr7A 85.714 63 9 0 5416 5478 101438340 101438402 3.540000e-07 67.6
28 TraesCS1D01G305900 chr7B 87.470 830 75 19 1 816 110694410 110695224 0.000000e+00 929.0
29 TraesCS1D01G305900 chr7B 100.000 35 0 0 5443 5477 493006746 493006712 1.270000e-06 65.8
30 TraesCS1D01G305900 chr7B 96.970 33 1 0 5446 5478 428924688 428924656 7.670000e-04 56.5
31 TraesCS1D01G305900 chrUn 86.674 878 64 24 1 847 141694517 141693662 0.000000e+00 924.0
32 TraesCS1D01G305900 chr4A 86.156 874 82 16 1 844 727903421 727902557 0.000000e+00 907.0
33 TraesCS1D01G305900 chr2A 86.085 848 94 12 10 843 100894053 100893216 0.000000e+00 891.0
34 TraesCS1D01G305900 chr2A 95.876 97 2 2 3914 4009 18339513 18339608 7.350000e-34 156.0
35 TraesCS1D01G305900 chr5B 85.414 857 94 18 1 843 421154996 421154157 0.000000e+00 861.0
36 TraesCS1D01G305900 chr5B 90.854 164 15 0 1760 1923 650546192 650546355 2.570000e-53 220.0
37 TraesCS1D01G305900 chr5B 94.175 103 3 3 3914 4014 550925184 550925083 2.640000e-33 154.0
38 TraesCS1D01G305900 chr5B 92.523 107 6 2 3905 4009 101418376 101418270 9.500000e-33 152.0
39 TraesCS1D01G305900 chr3B 87.801 582 44 8 273 841 752882150 752881583 0.000000e+00 656.0
40 TraesCS1D01G305900 chr3B 94.545 165 9 0 1759 1923 581026437 581026601 7.040000e-64 255.0
41 TraesCS1D01G305900 chr3B 90.551 127 12 0 3207 3333 581029964 581030090 9.440000e-38 169.0
42 TraesCS1D01G305900 chr3B 87.719 57 7 0 5422 5478 422494444 422494388 3.540000e-07 67.6
43 TraesCS1D01G305900 chr6B 86.473 584 52 9 273 843 554554834 554554265 2.800000e-172 616.0
44 TraesCS1D01G305900 chr3D 95.152 165 8 0 1759 1923 443258968 443259132 1.510000e-65 261.0
45 TraesCS1D01G305900 chr3D 89.706 136 12 2 3207 3340 443259706 443259841 7.300000e-39 172.0
46 TraesCS1D01G305900 chr3A 93.939 165 10 0 1759 1923 584276533 584276697 3.280000e-62 250.0
47 TraesCS1D01G305900 chr3A 91.339 127 11 0 3207 3333 584277248 584277374 2.030000e-39 174.0
48 TraesCS1D01G305900 chr3A 100.000 36 0 0 5443 5478 137634 137669 3.540000e-07 67.6
49 TraesCS1D01G305900 chr5A 91.463 164 14 0 1760 1923 645261070 645261233 5.520000e-55 226.0
50 TraesCS1D01G305900 chr5A 76.429 140 31 2 5182 5320 666236837 666236975 2.120000e-09 75.0
51 TraesCS1D01G305900 chr5A 97.368 38 1 0 5275 5312 3078612 3078649 1.270000e-06 65.8
52 TraesCS1D01G305900 chr5D 90.854 164 15 0 1760 1923 517840464 517840627 2.570000e-53 220.0
53 TraesCS1D01G305900 chr5D 97.753 89 2 0 3921 4009 373834945 373835033 2.640000e-33 154.0
54 TraesCS1D01G305900 chr2D 88.957 163 16 2 1760 1922 277672710 277672870 3.350000e-47 200.0
55 TraesCS1D01G305900 chr2D 95.833 96 2 2 3917 4011 174430743 174430837 2.640000e-33 154.0


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 TraesCS1D01G305900 chr1D 403235050 403240527 5477 True 10117.000000 10117 100.0000 1 5478 1 chr1D.!!$R1 5477
1 TraesCS1D01G305900 chr1B 541466249 541470793 4544 True 2000.333333 3766 93.8940 837 5009 3 chr1B.!!$R1 4172
2 TraesCS1D01G305900 chr1A 498450316 498455030 4714 True 1316.750000 2940 92.1795 854 5317 4 chr1A.!!$R2 4463
3 TraesCS1D01G305900 chr1A 532265000 532265618 618 False 808.000000 808 90.2400 1 621 1 chr1A.!!$F1 620
4 TraesCS1D01G305900 chr7D 228021421 228022268 847 False 1046.000000 1046 89.1360 1 843 1 chr7D.!!$F2 842
5 TraesCS1D01G305900 chr7D 562104281 562105107 826 False 1040.000000 1040 89.5810 1 821 1 chr7D.!!$F3 820
6 TraesCS1D01G305900 chr7D 22342583 22343449 866 True 970.000000 970 87.4430 1 844 1 chr7D.!!$R1 843
7 TraesCS1D01G305900 chr7D 10748065 10748915 850 False 878.000000 878 85.8290 1 844 1 chr7D.!!$F1 843
8 TraesCS1D01G305900 chr6D 161386580 161387391 811 True 1000.000000 1000 89.0640 32 841 1 chr6D.!!$R1 809
9 TraesCS1D01G305900 chr4B 645453732 645454559 827 True 994.000000 994 88.5440 1 825 1 chr4B.!!$R2 824
10 TraesCS1D01G305900 chr2B 45547518 45548362 844 True 992.000000 992 88.0560 1 841 1 chr2B.!!$R1 840
11 TraesCS1D01G305900 chr7A 9973803 9974668 865 False 953.000000 953 87.0860 1 844 1 chr7A.!!$F1 843
12 TraesCS1D01G305900 chr7B 110694410 110695224 814 False 929.000000 929 87.4700 1 816 1 chr7B.!!$F1 815
13 TraesCS1D01G305900 chrUn 141693662 141694517 855 True 924.000000 924 86.6740 1 847 1 chrUn.!!$R1 846
14 TraesCS1D01G305900 chr4A 727902557 727903421 864 True 907.000000 907 86.1560 1 844 1 chr4A.!!$R1 843
15 TraesCS1D01G305900 chr2A 100893216 100894053 837 True 891.000000 891 86.0850 10 843 1 chr2A.!!$R1 833
16 TraesCS1D01G305900 chr5B 421154157 421154996 839 True 861.000000 861 85.4140 1 843 1 chr5B.!!$R2 842
17 TraesCS1D01G305900 chr3B 752881583 752882150 567 True 656.000000 656 87.8010 273 841 1 chr3B.!!$R2 568
18 TraesCS1D01G305900 chr3B 581026437 581030090 3653 False 212.000000 255 92.5480 1759 3333 2 chr3B.!!$F1 1574
19 TraesCS1D01G305900 chr6B 554554265 554554834 569 True 616.000000 616 86.4730 273 843 1 chr6B.!!$R1 570
20 TraesCS1D01G305900 chr3D 443258968 443259841 873 False 216.500000 261 92.4290 1759 3340 2 chr3D.!!$F1 1581
21 TraesCS1D01G305900 chr3A 584276533 584277374 841 False 212.000000 250 92.6390 1759 3333 2 chr3A.!!$F2 1574

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
832 895 0.165727 CACATGCGTTGCACGTACAT 59.834 50.0 9.76 4.11 44.73 2.29 F
1478 1550 0.107703 ATTTGAGGAATCTGCCGCGA 60.108 50.0 8.23 0.00 0.00 5.87 F
1934 4277 0.804933 CGGTAAGCCCACTTCTACGC 60.805 60.0 0.00 0.00 37.33 4.42 F
2637 5727 0.243095 AACCACGACTCCTAGCGAAC 59.757 55.0 0.00 0.00 0.00 3.95 F
4169 7949 0.595588 CATTGCCAACAAGGTGCGTA 59.404 50.0 0.00 0.00 39.69 4.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2464 5526 0.603707 ACACGCCTGAATCTGTGTGG 60.604 55.000 16.77 4.54 44.99 4.17 R
2626 5716 1.202302 TGATTCAGCGTTCGCTAGGAG 60.202 52.381 18.99 7.56 39.76 3.69 R
3725 7149 3.040990 TCGTAAAAATATGGCGCAACG 57.959 42.857 10.83 4.56 0.00 4.10 R
4359 8142 0.962356 AGAGAAAATGCACAGGCGGG 60.962 55.000 0.00 0.00 45.35 6.13 R
5347 9202 0.034896 TTCAGACCGGTTTGAGGAGC 59.965 55.000 25.04 2.65 0.00 4.70 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
23 24 3.083349 CCGCCCCTCACATCTCCA 61.083 66.667 0.00 0.00 0.00 3.86
242 281 2.110578 TCGGATCATCATGGACACTGT 58.889 47.619 0.00 0.00 0.00 3.55
251 290 0.832135 ATGGACACTGTCTGGACCGT 60.832 55.000 9.08 0.00 32.47 4.83
442 483 7.441017 CACTAAAAATTGAACCCAAATCAGGA 58.559 34.615 0.00 0.00 35.67 3.86
471 512 4.322080 AACTAAACCAAAAGCAGCCTTC 57.678 40.909 0.00 0.00 0.00 3.46
473 514 4.725490 ACTAAACCAAAAGCAGCCTTCTA 58.275 39.130 0.00 0.00 0.00 2.10
502 546 7.008901 CACACATTCAGCAGTTATTAAGCATTG 59.991 37.037 0.00 0.00 0.00 2.82
528 572 2.921121 CGTGCGCTATGAAACAACTAGA 59.079 45.455 9.73 0.00 0.00 2.43
529 573 3.000674 CGTGCGCTATGAAACAACTAGAG 60.001 47.826 9.73 0.00 0.00 2.43
536 580 6.757010 CGCTATGAAACAACTAGAGGTTACAT 59.243 38.462 0.00 3.11 36.23 2.29
549 593 9.830186 ACTAGAGGTTACATAGTGATATGGAAT 57.170 33.333 0.00 0.00 33.30 3.01
609 654 7.485810 TGATTTCAATGGATTGTGCTTAGATG 58.514 34.615 0.00 0.00 38.84 2.90
653 708 3.281975 TATGTGCCCCCTCCCCTGT 62.282 63.158 0.00 0.00 0.00 4.00
829 892 1.499049 TTACACATGCGTTGCACGTA 58.501 45.000 9.76 6.30 44.73 3.57
832 895 0.165727 CACATGCGTTGCACGTACAT 59.834 50.000 9.76 4.11 44.73 2.29
844 907 7.357043 GCGTTGCACGTACATATTTACTAGTAG 60.357 40.741 2.23 0.00 44.73 2.57
845 908 7.357043 CGTTGCACGTACATATTTACTAGTAGC 60.357 40.741 2.23 0.00 36.74 3.58
846 909 7.030075 TGCACGTACATATTTACTAGTAGCA 57.970 36.000 2.23 2.15 0.00 3.49
847 910 6.914215 TGCACGTACATATTTACTAGTAGCAC 59.086 38.462 2.23 0.00 0.00 4.40
885 954 7.587037 TGTCAAAAGAGAAATTGAATCACCT 57.413 32.000 0.00 0.00 37.31 4.00
888 957 8.020244 GTCAAAAGAGAAATTGAATCACCTCTC 58.980 37.037 7.12 7.12 37.31 3.20
897 966 7.929941 AATTGAATCACCTCTCTTTTCTACC 57.070 36.000 0.00 0.00 0.00 3.18
1258 1330 1.043116 ACCATTCGCCGGATCTCTCA 61.043 55.000 5.05 0.00 0.00 3.27
1262 1334 0.970937 TTCGCCGGATCTCTCACCTT 60.971 55.000 5.05 0.00 0.00 3.50
1273 1345 2.038329 TCACCTTCCCCCGTCGAT 59.962 61.111 0.00 0.00 0.00 3.59
1279 1351 2.930777 CTTCCCCCGTCGATCCTCCT 62.931 65.000 0.00 0.00 0.00 3.69
1315 1387 1.202940 TCCATCTCTGATCCGATCGGT 60.203 52.381 32.15 20.11 36.98 4.69
1316 1388 1.615883 CCATCTCTGATCCGATCGGTT 59.384 52.381 32.15 25.10 36.98 4.44
1320 1392 2.099263 TCTCTGATCCGATCGGTTGTTC 59.901 50.000 32.15 22.97 36.98 3.18
1348 1420 4.272504 GGCCGATTCGTGATCTTATTTTGA 59.727 41.667 5.20 0.00 32.30 2.69
1362 1434 5.414144 TCTTATTTTGATGTTGCCGTGATCA 59.586 36.000 0.00 0.00 0.00 2.92
1369 1441 2.225467 TGTTGCCGTGATCATGTTCAA 58.775 42.857 13.81 13.29 0.00 2.69
1377 1449 3.551485 CGTGATCATGTTCAATCTGCGTA 59.449 43.478 8.04 0.00 0.00 4.42
1382 1454 3.932710 TCATGTTCAATCTGCGTAGTTCC 59.067 43.478 0.00 0.00 0.00 3.62
1383 1455 3.678056 TGTTCAATCTGCGTAGTTCCT 57.322 42.857 0.00 0.00 0.00 3.36
1418 1490 5.295950 GTGTTCGATCTCATTCATCATCCT 58.704 41.667 0.00 0.00 0.00 3.24
1478 1550 0.107703 ATTTGAGGAATCTGCCGCGA 60.108 50.000 8.23 0.00 0.00 5.87
1509 1581 2.626780 GGTCGGCCCAGCTTTGTTC 61.627 63.158 0.00 0.00 0.00 3.18
1510 1582 1.600916 GTCGGCCCAGCTTTGTTCT 60.601 57.895 0.00 0.00 0.00 3.01
1656 1728 1.906574 AGTTGGGTGGCTTCGATTCTA 59.093 47.619 0.00 0.00 0.00 2.10
1660 1732 1.757699 GGGTGGCTTCGATTCTAGAGT 59.242 52.381 0.00 0.00 0.00 3.24
1735 1817 0.955905 GTTGACGCCTTGGCCTTAAA 59.044 50.000 3.32 0.00 0.00 1.52
1741 1823 2.029380 ACGCCTTGGCCTTAAATTTGTC 60.029 45.455 3.32 0.00 0.00 3.18
1757 1839 2.031258 TGTCTCGTTTGGTTTCAGCA 57.969 45.000 0.00 0.00 0.00 4.41
1926 2008 1.029947 CCCACAATCGGTAAGCCCAC 61.030 60.000 0.00 0.00 0.00 4.61
1932 4275 3.195661 CAATCGGTAAGCCCACTTCTAC 58.804 50.000 0.00 0.00 37.33 2.59
1934 4277 0.804933 CGGTAAGCCCACTTCTACGC 60.805 60.000 0.00 0.00 37.33 4.42
1967 4311 4.852134 TGCAGCATGTTGTTTATCTTGT 57.148 36.364 11.44 0.00 39.31 3.16
2026 5079 2.353406 GCTTTAGCTTAGGACCGTGTGA 60.353 50.000 0.00 0.00 38.21 3.58
2085 5139 6.245408 ACCAATTTAGTGCAAAGATGGTCTA 58.755 36.000 0.00 0.00 42.38 2.59
2139 5193 7.369803 TGACAATGAAGATAACTTGAAGCTC 57.630 36.000 0.00 0.00 36.39 4.09
2221 5275 5.748592 ACTTTCTGTAAATGAACTTCACGC 58.251 37.500 0.00 0.00 0.00 5.34
2296 5353 5.705609 TGTTGTCCAAAAGAAGCCTAATC 57.294 39.130 0.00 0.00 0.00 1.75
2297 5354 5.136828 TGTTGTCCAAAAGAAGCCTAATCA 58.863 37.500 0.00 0.00 0.00 2.57
2410 5467 3.055530 CAGTCAAGGCAGGATAGACTGTT 60.056 47.826 11.55 0.00 46.72 3.16
2412 5469 4.777896 AGTCAAGGCAGGATAGACTGTTTA 59.222 41.667 0.00 0.00 40.59 2.01
2464 5526 6.039941 AGGTGTGTTAGCTCTATCATAGTGAC 59.960 42.308 0.00 0.00 29.16 3.67
2528 5592 1.153168 AAGGCGTGTCAGCACTGTT 60.153 52.632 0.00 0.00 43.16 3.16
2584 5670 8.169977 ACACTAACTCATGTCATTTTGATTGT 57.830 30.769 0.00 0.00 0.00 2.71
2586 5672 8.908678 CACTAACTCATGTCATTTTGATTGTTG 58.091 33.333 0.00 0.00 0.00 3.33
2607 5697 8.755696 TGTTGCTTATATTGGATGAAAACAAC 57.244 30.769 0.00 0.00 34.58 3.32
2637 5727 0.243095 AACCACGACTCCTAGCGAAC 59.757 55.000 0.00 0.00 0.00 3.95
2661 5751 5.620654 CGCTGAATCATTCATTCCAAAGTGT 60.621 40.000 0.00 0.00 40.44 3.55
2707 5813 1.000274 GGTGTTTGACCTTGACATGCC 60.000 52.381 0.00 0.00 42.25 4.40
2710 5816 1.956477 GTTTGACCTTGACATGCCTGT 59.044 47.619 0.00 0.00 38.67 4.00
2976 6083 4.349930 AGGACAAGGTAAGCAAAGTTCCTA 59.650 41.667 0.00 0.00 0.00 2.94
2987 6094 4.706962 AGCAAAGTTCCTAAAGGCCAATAG 59.293 41.667 5.01 6.69 34.44 1.73
3005 6114 5.049543 CCAATAGTTTTTGTTTGGCCACATG 60.050 40.000 3.88 0.00 32.88 3.21
3010 6119 1.333177 TTGTTTGGCCACATGTACCC 58.667 50.000 3.88 10.08 0.00 3.69
3350 6648 5.112129 AGGTATCACCACAGGGAATAAAC 57.888 43.478 0.00 0.00 41.95 2.01
3430 6728 3.181478 CCTTCACTAGGTTGTCGGATACC 60.181 52.174 0.00 4.58 39.39 2.73
3725 7149 3.123050 GGTGAATGAAAGTTTGTGCACC 58.877 45.455 15.69 10.53 37.91 5.01
3829 7415 4.566360 AGGAACAAAAACATGAAACGCTTG 59.434 37.500 0.00 0.00 0.00 4.01
3830 7416 3.923827 ACAAAAACATGAAACGCTTGC 57.076 38.095 0.00 0.00 0.00 4.01
3831 7417 2.281234 ACAAAAACATGAAACGCTTGCG 59.719 40.909 13.70 13.70 0.00 4.85
3864 7461 4.471386 AGCATTGTCTTGAGGTGGTACTAT 59.529 41.667 0.00 0.00 0.00 2.12
3930 7532 1.541233 GCATCCAACATACTCCCTCCG 60.541 57.143 0.00 0.00 0.00 4.63
3936 7538 1.486211 ACATACTCCCTCCGTTCCAG 58.514 55.000 0.00 0.00 0.00 3.86
3940 7542 2.544844 ACTCCCTCCGTTCCAGAATA 57.455 50.000 0.00 0.00 0.00 1.75
3941 7543 2.389715 ACTCCCTCCGTTCCAGAATAG 58.610 52.381 0.00 0.00 0.00 1.73
3943 7545 3.235200 CTCCCTCCGTTCCAGAATAGAT 58.765 50.000 0.00 0.00 0.00 1.98
3944 7546 2.965831 TCCCTCCGTTCCAGAATAGATG 59.034 50.000 0.00 0.00 0.00 2.90
3945 7547 2.965831 CCCTCCGTTCCAGAATAGATGA 59.034 50.000 0.00 0.00 0.00 2.92
3947 7549 3.243907 CCTCCGTTCCAGAATAGATGACC 60.244 52.174 0.00 0.00 0.00 4.02
3948 7550 2.698797 TCCGTTCCAGAATAGATGACCC 59.301 50.000 0.00 0.00 0.00 4.46
3950 7552 3.118408 CCGTTCCAGAATAGATGACCCAA 60.118 47.826 0.00 0.00 0.00 4.12
3951 7553 4.444876 CCGTTCCAGAATAGATGACCCAAT 60.445 45.833 0.00 0.00 0.00 3.16
3952 7554 5.126067 CGTTCCAGAATAGATGACCCAATT 58.874 41.667 0.00 0.00 0.00 2.32
3953 7555 5.590259 CGTTCCAGAATAGATGACCCAATTT 59.410 40.000 0.00 0.00 0.00 1.82
3955 7557 7.260603 GTTCCAGAATAGATGACCCAATTTTG 58.739 38.462 0.00 0.00 0.00 2.44
3957 7559 7.638444 TCCAGAATAGATGACCCAATTTTGTA 58.362 34.615 0.00 0.00 0.00 2.41
3958 7560 7.556275 TCCAGAATAGATGACCCAATTTTGTAC 59.444 37.037 0.00 0.00 0.00 2.90
3959 7561 7.557719 CCAGAATAGATGACCCAATTTTGTACT 59.442 37.037 0.00 0.00 0.00 2.73
3960 7562 9.613428 CAGAATAGATGACCCAATTTTGTACTA 57.387 33.333 0.00 0.00 0.00 1.82
3963 7565 9.975218 AATAGATGACCCAATTTTGTACTAACT 57.025 29.630 0.00 0.00 0.00 2.24
3964 7566 9.975218 ATAGATGACCCAATTTTGTACTAACTT 57.025 29.630 0.00 0.00 0.00 2.66
3965 7567 8.706322 AGATGACCCAATTTTGTACTAACTTT 57.294 30.769 0.00 0.00 0.00 2.66
3966 7568 9.802039 AGATGACCCAATTTTGTACTAACTTTA 57.198 29.630 0.00 0.00 0.00 1.85
3968 7570 8.983702 TGACCCAATTTTGTACTAACTTTAGT 57.016 30.769 6.85 6.85 45.39 2.24
3982 7584 7.567458 ACTAACTTTAGTACAAAGTTGGGTCA 58.433 34.615 28.62 17.50 46.38 4.02
3984 7586 7.506328 AACTTTAGTACAAAGTTGGGTCATC 57.494 36.000 23.48 0.00 45.58 2.92
3985 7587 6.838382 ACTTTAGTACAAAGTTGGGTCATCT 58.162 36.000 14.04 0.00 37.18 2.90
4006 7783 4.966805 TCTATTTTGGAACGGAGGGAGTAT 59.033 41.667 0.00 0.00 0.00 2.12
4007 7784 6.138263 TCTATTTTGGAACGGAGGGAGTATA 58.862 40.000 0.00 0.00 0.00 1.47
4008 7785 5.906772 ATTTTGGAACGGAGGGAGTATAT 57.093 39.130 0.00 0.00 0.00 0.86
4012 7791 6.811634 TTGGAACGGAGGGAGTATATTTTA 57.188 37.500 0.00 0.00 0.00 1.52
4013 7792 7.383156 TTGGAACGGAGGGAGTATATTTTAT 57.617 36.000 0.00 0.00 0.00 1.40
4014 7793 6.765403 TGGAACGGAGGGAGTATATTTTATG 58.235 40.000 0.00 0.00 0.00 1.90
4016 7795 5.161943 ACGGAGGGAGTATATTTTATGGC 57.838 43.478 0.00 0.00 0.00 4.40
4018 7797 4.225267 CGGAGGGAGTATATTTTATGGCCT 59.775 45.833 3.32 0.00 0.00 5.19
4035 7814 4.934356 TGGCCTTTTTCCATAATGACTCT 58.066 39.130 3.32 0.00 0.00 3.24
4040 7819 7.922811 GGCCTTTTTCCATAATGACTCTATTTG 59.077 37.037 0.00 0.00 0.00 2.32
4129 7909 1.305887 AGAGGGGTTGTACGAGGGG 60.306 63.158 0.00 0.00 0.00 4.79
4169 7949 0.595588 CATTGCCAACAAGGTGCGTA 59.404 50.000 0.00 0.00 39.69 4.42
4195 7978 3.264706 TGGCCTTACTATGTGCCTTGTTA 59.735 43.478 3.32 0.00 44.32 2.41
4201 7984 7.201821 GCCTTACTATGTGCCTTGTTATTTGAT 60.202 37.037 0.00 0.00 0.00 2.57
4208 7991 6.990798 TGTGCCTTGTTATTTGATCAAATGA 58.009 32.000 33.94 26.74 40.83 2.57
4210 7993 8.095792 TGTGCCTTGTTATTTGATCAAATGATT 58.904 29.630 33.94 17.80 40.83 2.57
4243 8026 5.193099 ACTTATGGCAACTAGGTCCATTT 57.807 39.130 14.48 0.00 40.71 2.32
4253 8036 7.201705 GGCAACTAGGTCCATTTGATACTTTAC 60.202 40.741 0.00 0.00 0.00 2.01
4254 8037 7.465513 GCAACTAGGTCCATTTGATACTTTACG 60.466 40.741 0.00 0.00 0.00 3.18
4259 8042 6.938030 AGGTCCATTTGATACTTTACGAACAA 59.062 34.615 0.00 0.00 0.00 2.83
4318 8101 0.698238 AAGCTGCCACCTGGAACATA 59.302 50.000 0.00 0.00 38.20 2.29
4359 8142 6.152379 GGCAGCTTTAGTATATGAAAATGCC 58.848 40.000 15.25 15.25 38.89 4.40
4362 8145 5.473504 AGCTTTAGTATATGAAAATGCCCCG 59.526 40.000 0.00 0.00 0.00 5.73
4363 8146 5.699097 TTTAGTATATGAAAATGCCCCGC 57.301 39.130 0.00 0.00 0.00 6.13
4364 8147 2.514803 AGTATATGAAAATGCCCCGCC 58.485 47.619 0.00 0.00 0.00 6.13
4366 8149 1.331214 ATATGAAAATGCCCCGCCTG 58.669 50.000 0.00 0.00 0.00 4.85
4367 8150 0.033601 TATGAAAATGCCCCGCCTGT 60.034 50.000 0.00 0.00 0.00 4.00
4368 8151 1.606885 ATGAAAATGCCCCGCCTGTG 61.607 55.000 0.00 0.00 0.00 3.66
4369 8152 3.647649 GAAAATGCCCCGCCTGTGC 62.648 63.158 0.00 0.00 0.00 4.57
4370 8153 4.992740 AAATGCCCCGCCTGTGCA 62.993 61.111 0.00 0.00 39.68 4.57
4410 8193 9.042008 TGTTGCTACTTAGTTTTACTCTCTTTG 57.958 33.333 0.00 0.00 0.00 2.77
4411 8194 8.496751 GTTGCTACTTAGTTTTACTCTCTTTGG 58.503 37.037 0.00 0.00 0.00 3.28
4413 8196 6.874664 GCTACTTAGTTTTACTCTCTTTGGCT 59.125 38.462 0.00 0.00 0.00 4.75
4417 8200 7.993758 ACTTAGTTTTACTCTCTTTGGCTTCTT 59.006 33.333 0.00 0.00 0.00 2.52
4425 8217 2.291741 CTCTTTGGCTTCTTTTGCTCGT 59.708 45.455 0.00 0.00 0.00 4.18
4429 8221 2.020720 TGGCTTCTTTTGCTCGTTTGA 58.979 42.857 0.00 0.00 0.00 2.69
4707 8499 1.401199 GTCCGCTCTGTACTCTGTACC 59.599 57.143 5.55 0.00 0.00 3.34
4767 8559 4.085357 TGTCTTGGCATAGTTTGTCAGT 57.915 40.909 0.00 0.00 41.93 3.41
4860 8652 1.610038 TCAACTGGAAATGCTGTGCAG 59.390 47.619 0.00 0.00 43.65 4.41
4878 8670 2.428925 GGGGGCATTGCATGGTCTG 61.429 63.158 11.39 0.00 0.00 3.51
4943 8743 4.168088 ACAGTAATATTCCCCTTCCCCAAG 59.832 45.833 0.00 0.00 0.00 3.61
4988 8788 3.744426 AGGAAACGATACACCTTTCAACG 59.256 43.478 0.00 0.00 0.00 4.10
5043 8871 4.722193 CGGAGCACCTGGTTGAAT 57.278 55.556 0.00 0.00 0.00 2.57
5094 8922 8.246180 ACTCACAATTTATGACATTTTAGGCTG 58.754 33.333 0.00 0.00 0.00 4.85
5120 8975 7.166691 ACCACTTAGCTCGTTAAAGAATCTA 57.833 36.000 0.00 0.00 0.00 1.98
5141 8996 6.843752 TCTAAAGTGTTATGTGGGGAGAAAA 58.156 36.000 0.00 0.00 0.00 2.29
5195 9050 1.602237 CCTCAACACCTGGGCGTAT 59.398 57.895 0.00 0.00 0.00 3.06
5196 9051 0.744414 CCTCAACACCTGGGCGTATG 60.744 60.000 0.00 0.00 0.00 2.39
5198 9053 1.002624 CAACACCTGGGCGTATGGT 60.003 57.895 0.00 0.00 33.87 3.55
5209 9064 0.460284 GCGTATGGTCTGGTCACTGG 60.460 60.000 0.00 0.00 0.00 4.00
5217 9072 0.907704 TCTGGTCACTGGCCGGTAAT 60.908 55.000 19.20 0.00 34.14 1.89
5254 9109 1.120530 ATACGTCTCAATCCGGCCTT 58.879 50.000 0.00 0.00 0.00 4.35
5258 9113 2.093128 ACGTCTCAATCCGGCCTTAAAT 60.093 45.455 0.00 0.00 0.00 1.40
5271 9126 1.453155 CTTAAATGCCGGTGCTCACT 58.547 50.000 1.90 0.00 38.71 3.41
5273 9128 1.305219 TAAATGCCGGTGCTCACTGC 61.305 55.000 1.90 5.87 43.25 4.40
5281 9136 3.640407 TGCTCACTGCCACCCCTC 61.640 66.667 0.00 0.00 42.00 4.30
5300 9155 2.707791 CTCCTATCCAGCCCAAATCTGA 59.292 50.000 0.00 0.00 33.54 3.27
5317 9172 3.553095 GAGGCGGATATGGGGTGGC 62.553 68.421 0.00 0.00 0.00 5.01
5318 9173 4.660938 GGCGGATATGGGGTGGCC 62.661 72.222 0.00 0.00 0.00 5.36
5319 9174 4.660938 GCGGATATGGGGTGGCCC 62.661 72.222 0.00 0.00 44.51 5.80
5333 9188 4.986708 GCCCAGCCCCGGTCAAAA 62.987 66.667 0.00 0.00 0.00 2.44
5334 9189 2.203567 CCCAGCCCCGGTCAAAAA 60.204 61.111 0.00 0.00 0.00 1.94
5351 9206 1.474330 AAAATGATCCAACGGGCTCC 58.526 50.000 0.00 0.00 0.00 4.70
5352 9207 0.625849 AAATGATCCAACGGGCTCCT 59.374 50.000 0.00 0.00 0.00 3.69
5353 9208 0.181350 AATGATCCAACGGGCTCCTC 59.819 55.000 0.00 0.00 0.00 3.71
5354 9209 0.982852 ATGATCCAACGGGCTCCTCA 60.983 55.000 0.00 0.00 0.00 3.86
5355 9210 1.198094 TGATCCAACGGGCTCCTCAA 61.198 55.000 0.00 0.00 0.00 3.02
5356 9211 0.035439 GATCCAACGGGCTCCTCAAA 60.035 55.000 0.00 0.00 0.00 2.69
5357 9212 0.322546 ATCCAACGGGCTCCTCAAAC 60.323 55.000 0.00 0.00 0.00 2.93
5358 9213 1.971695 CCAACGGGCTCCTCAAACC 60.972 63.158 0.00 0.00 0.00 3.27
5361 9216 4.016706 CGGGCTCCTCAAACCGGT 62.017 66.667 0.00 0.00 42.48 5.28
5362 9217 2.046217 GGGCTCCTCAAACCGGTC 60.046 66.667 8.04 0.00 0.00 4.79
5363 9218 2.593956 GGGCTCCTCAAACCGGTCT 61.594 63.158 8.04 0.00 0.00 3.85
5364 9219 1.376037 GGCTCCTCAAACCGGTCTG 60.376 63.158 8.04 3.73 0.00 3.51
5365 9220 1.671742 GCTCCTCAAACCGGTCTGA 59.328 57.895 10.84 10.84 0.00 3.27
5366 9221 0.034896 GCTCCTCAAACCGGTCTGAA 59.965 55.000 12.58 0.00 0.00 3.02
5367 9222 1.542547 GCTCCTCAAACCGGTCTGAAA 60.543 52.381 12.58 2.30 0.00 2.69
5368 9223 2.846193 CTCCTCAAACCGGTCTGAAAA 58.154 47.619 12.58 1.93 0.00 2.29
5369 9224 2.808543 CTCCTCAAACCGGTCTGAAAAG 59.191 50.000 12.58 8.32 0.00 2.27
5370 9225 1.266989 CCTCAAACCGGTCTGAAAAGC 59.733 52.381 12.58 0.00 0.00 3.51
5371 9226 1.266989 CTCAAACCGGTCTGAAAAGCC 59.733 52.381 12.58 0.00 0.00 4.35
5372 9227 0.313987 CAAACCGGTCTGAAAAGCCC 59.686 55.000 8.04 0.00 0.00 5.19
5373 9228 1.170290 AAACCGGTCTGAAAAGCCCG 61.170 55.000 8.04 0.00 40.12 6.13
5374 9229 3.431725 CCGGTCTGAAAAGCCCGC 61.432 66.667 0.00 0.00 39.12 6.13
5375 9230 3.788766 CGGTCTGAAAAGCCCGCG 61.789 66.667 0.00 0.00 33.20 6.46
5376 9231 4.103103 GGTCTGAAAAGCCCGCGC 62.103 66.667 0.00 0.00 0.00 6.86
5405 9260 3.214123 CGGACAGACGGCCGGATA 61.214 66.667 31.76 0.00 43.67 2.59
5406 9261 2.777972 CGGACAGACGGCCGGATAA 61.778 63.158 31.76 0.00 43.67 1.75
5407 9262 1.518774 GGACAGACGGCCGGATAAA 59.481 57.895 31.76 0.00 0.00 1.40
5408 9263 0.108041 GGACAGACGGCCGGATAAAA 60.108 55.000 31.76 0.00 0.00 1.52
5409 9264 1.676615 GGACAGACGGCCGGATAAAAA 60.677 52.381 31.76 0.00 0.00 1.94
5427 9282 2.873133 AAAGAAGCGATCTAGACGGG 57.127 50.000 13.92 0.70 37.42 5.28
5428 9283 0.386113 AAGAAGCGATCTAGACGGGC 59.614 55.000 13.92 9.33 37.42 6.13
5429 9284 0.752009 AGAAGCGATCTAGACGGGCA 60.752 55.000 13.92 0.00 36.32 5.36
5430 9285 0.595310 GAAGCGATCTAGACGGGCAC 60.595 60.000 13.92 5.43 0.00 5.01
5445 9300 1.909700 GGCACCTCAAACCATTCTCA 58.090 50.000 0.00 0.00 0.00 3.27
5446 9301 2.238521 GGCACCTCAAACCATTCTCAA 58.761 47.619 0.00 0.00 0.00 3.02
5447 9302 2.627699 GGCACCTCAAACCATTCTCAAA 59.372 45.455 0.00 0.00 0.00 2.69
5448 9303 3.552890 GGCACCTCAAACCATTCTCAAAC 60.553 47.826 0.00 0.00 0.00 2.93
5449 9304 3.853307 GCACCTCAAACCATTCTCAAACG 60.853 47.826 0.00 0.00 0.00 3.60
5450 9305 2.293399 ACCTCAAACCATTCTCAAACGC 59.707 45.455 0.00 0.00 0.00 4.84
5451 9306 2.351738 CCTCAAACCATTCTCAAACGCC 60.352 50.000 0.00 0.00 0.00 5.68
5452 9307 1.611491 TCAAACCATTCTCAAACGCCC 59.389 47.619 0.00 0.00 0.00 6.13
5453 9308 0.596082 AAACCATTCTCAAACGCCCG 59.404 50.000 0.00 0.00 0.00 6.13
5454 9309 1.241315 AACCATTCTCAAACGCCCGG 61.241 55.000 0.00 0.00 0.00 5.73
5455 9310 2.406616 CCATTCTCAAACGCCCGGG 61.407 63.158 19.09 19.09 0.00 5.73
5456 9311 2.750237 ATTCTCAAACGCCCGGGC 60.750 61.111 36.69 36.69 37.85 6.13
5457 9312 3.268103 ATTCTCAAACGCCCGGGCT 62.268 57.895 41.01 26.06 39.32 5.19
5458 9313 4.697756 TCTCAAACGCCCGGGCTG 62.698 66.667 41.01 33.95 39.32 4.85
5459 9314 4.697756 CTCAAACGCCCGGGCTGA 62.698 66.667 41.01 34.10 39.32 4.26
5471 9326 4.554036 GGCTGACCGGCATCCCTC 62.554 72.222 0.00 0.00 38.25 4.30
5472 9327 3.785859 GCTGACCGGCATCCCTCA 61.786 66.667 0.00 0.00 0.00 3.86
5473 9328 3.112205 GCTGACCGGCATCCCTCAT 62.112 63.158 0.00 0.00 0.00 2.90
5474 9329 1.758440 GCTGACCGGCATCCCTCATA 61.758 60.000 0.00 0.00 0.00 2.15
5475 9330 0.979665 CTGACCGGCATCCCTCATAT 59.020 55.000 0.00 0.00 0.00 1.78
5476 9331 0.976641 TGACCGGCATCCCTCATATC 59.023 55.000 0.00 0.00 0.00 1.63
5477 9332 0.250513 GACCGGCATCCCTCATATCC 59.749 60.000 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 2.872388 CGATGGGTAGAGGCGGCAT 61.872 63.158 13.08 1.06 0.00 4.40
227 266 2.234661 GTCCAGACAGTGTCCATGATGA 59.765 50.000 19.71 3.90 32.18 2.92
242 281 4.988716 ACGGGCAGACGGTCCAGA 62.989 66.667 4.14 0.00 43.46 3.86
251 290 2.363018 CAGAGAGGGACGGGCAGA 60.363 66.667 0.00 0.00 0.00 4.26
442 483 6.419710 GCTGCTTTTGGTTTAGTTTTACGAAT 59.580 34.615 0.00 0.00 0.00 3.34
471 512 5.746307 ATAACTGCTGAATGTGTGCATAG 57.254 39.130 0.00 0.00 36.07 2.23
473 514 6.513806 TTAATAACTGCTGAATGTGTGCAT 57.486 33.333 0.00 0.00 36.07 3.96
502 546 0.793104 GTTTCATAGCGCACGTTGGC 60.793 55.000 11.47 0.00 0.00 4.52
529 573 9.965824 CCAAAAATTCCATATCACTATGTAACC 57.034 33.333 0.00 0.00 34.12 2.85
536 580 7.013274 GCTGCTACCAAAAATTCCATATCACTA 59.987 37.037 0.00 0.00 0.00 2.74
549 593 2.107552 ACTACCCAGCTGCTACCAAAAA 59.892 45.455 8.66 0.00 0.00 1.94
609 654 2.489722 GTCCTCAGGCAGAAATCCAAAC 59.510 50.000 0.00 0.00 0.00 2.93
653 708 9.899661 AAGTAGTTAATGGTATATGCAAGTGAA 57.100 29.630 0.00 0.00 0.00 3.18
699 755 4.324563 GGTCCATCTCTTCCTTCAAATGGA 60.325 45.833 0.00 0.00 40.14 3.41
832 895 9.865321 ACAGATTTTTCGTGCTACTAGTAAATA 57.135 29.630 3.76 0.00 0.00 1.40
844 907 6.984740 TTTGACATTACAGATTTTTCGTGC 57.015 33.333 0.00 0.00 0.00 5.34
845 908 8.781067 TCTTTTGACATTACAGATTTTTCGTG 57.219 30.769 0.00 0.00 0.00 4.35
846 909 8.836413 TCTCTTTTGACATTACAGATTTTTCGT 58.164 29.630 0.00 0.00 0.00 3.85
847 910 9.663904 TTCTCTTTTGACATTACAGATTTTTCG 57.336 29.630 0.00 0.00 0.00 3.46
885 954 5.105716 CGAGAATCAGGTGGTAGAAAAGAGA 60.106 44.000 0.00 0.00 33.17 3.10
888 957 5.073311 TCGAGAATCAGGTGGTAGAAAAG 57.927 43.478 0.00 0.00 33.17 2.27
897 966 2.544685 GTGTCCATCGAGAATCAGGTG 58.455 52.381 0.00 0.00 33.17 4.00
989 1058 0.745845 AAGGCGCATAGAACTGGCAG 60.746 55.000 14.16 14.16 0.00 4.85
994 1063 0.460284 CGTGGAAGGCGCATAGAACT 60.460 55.000 10.83 0.00 0.00 3.01
995 1064 0.459585 TCGTGGAAGGCGCATAGAAC 60.460 55.000 10.83 0.00 0.00 3.01
1258 1330 2.762875 GGATCGACGGGGGAAGGT 60.763 66.667 0.00 0.00 0.00 3.50
1262 1334 3.426836 AGGAGGATCGACGGGGGA 61.427 66.667 0.00 0.00 34.37 4.81
1295 1367 1.202940 ACCGATCGGATCAGAGATGGA 60.203 52.381 39.55 0.00 38.96 3.41
1298 1370 2.311463 ACAACCGATCGGATCAGAGAT 58.689 47.619 39.55 12.74 38.96 2.75
1299 1371 1.763968 ACAACCGATCGGATCAGAGA 58.236 50.000 39.55 0.00 38.96 3.10
1348 1420 2.435422 TGAACATGATCACGGCAACAT 58.565 42.857 0.83 0.00 0.00 2.71
1362 1434 3.935203 CAGGAACTACGCAGATTGAACAT 59.065 43.478 0.00 0.00 36.02 2.71
1369 1441 1.557099 TCCACAGGAACTACGCAGAT 58.443 50.000 0.00 0.00 36.02 2.90
1377 1449 1.995626 CCCCCGATCCACAGGAACT 60.996 63.158 0.00 0.00 43.88 3.01
1382 1454 1.078426 GAACACCCCCGATCCACAG 60.078 63.158 0.00 0.00 0.00 3.66
1383 1455 2.949909 CGAACACCCCCGATCCACA 61.950 63.158 0.00 0.00 0.00 4.17
1672 1752 6.201044 CACAGGCTCGTTATAAGAATTACTGG 59.799 42.308 0.00 0.00 30.46 4.00
1673 1753 6.757010 ACACAGGCTCGTTATAAGAATTACTG 59.243 38.462 0.00 0.00 30.46 2.74
1675 1755 6.979238 AGACACAGGCTCGTTATAAGAATTAC 59.021 38.462 0.00 0.00 30.46 1.89
1724 1806 4.766404 ACGAGACAAATTTAAGGCCAAG 57.234 40.909 5.01 0.00 0.00 3.61
1735 1817 3.380004 TGCTGAAACCAAACGAGACAAAT 59.620 39.130 0.00 0.00 0.00 2.32
1741 1823 1.002468 CCTGTGCTGAAACCAAACGAG 60.002 52.381 0.00 0.00 0.00 4.18
1757 1839 2.765807 CCCCATCTCCGCTCCTGT 60.766 66.667 0.00 0.00 0.00 4.00
1926 2008 5.486095 GCAACAGAAAATTTGCGTAGAAG 57.514 39.130 0.00 0.00 38.86 2.85
1934 4277 5.201910 CAACATGCTGCAACAGAAAATTTG 58.798 37.500 6.36 0.00 32.44 2.32
2085 5139 4.526438 AATGTTATTCCTAAGGCAGGCT 57.474 40.909 0.00 0.00 45.10 4.58
2139 5193 9.636879 AATGAGACATATAATCAACTCGAGATG 57.363 33.333 21.68 18.56 0.00 2.90
2221 5275 4.843879 TGTACGTACAAATAACATGGCG 57.156 40.909 25.54 0.00 32.40 5.69
2277 5334 6.016276 GTCTTTGATTAGGCTTCTTTTGGACA 60.016 38.462 0.00 0.00 0.00 4.02
2278 5335 6.016276 TGTCTTTGATTAGGCTTCTTTTGGAC 60.016 38.462 0.00 0.00 0.00 4.02
2279 5336 6.068010 TGTCTTTGATTAGGCTTCTTTTGGA 58.932 36.000 0.00 0.00 0.00 3.53
2296 5353 8.870160 TCTTAAACATGAATGGTTTGTCTTTG 57.130 30.769 0.00 0.00 38.84 2.77
2464 5526 0.603707 ACACGCCTGAATCTGTGTGG 60.604 55.000 16.77 4.54 44.99 4.17
2550 5614 9.944376 AATGACATGAGTTAGTGTTATACTGTT 57.056 29.630 0.00 0.00 40.65 3.16
2551 5615 9.944376 AAATGACATGAGTTAGTGTTATACTGT 57.056 29.630 0.00 0.00 40.65 3.55
2564 5650 6.518493 AGCAACAATCAAAATGACATGAGTT 58.482 32.000 0.00 0.00 0.00 3.01
2566 5652 8.697846 ATAAGCAACAATCAAAATGACATGAG 57.302 30.769 0.00 0.00 0.00 2.90
2607 5697 6.205101 AGGAGTCGTGGTTACTAAACATAG 57.795 41.667 0.00 0.00 37.34 2.23
2623 5713 1.583967 CAGCGTTCGCTAGGAGTCG 60.584 63.158 18.99 2.00 39.76 4.18
2626 5716 1.202302 TGATTCAGCGTTCGCTAGGAG 60.202 52.381 18.99 7.56 39.76 3.69
2637 5727 4.796830 CACTTTGGAATGAATGATTCAGCG 59.203 41.667 13.79 0.11 43.98 5.18
2644 5734 5.139727 AGTTGGACACTTTGGAATGAATGA 58.860 37.500 0.00 0.00 27.32 2.57
2645 5735 5.009911 TGAGTTGGACACTTTGGAATGAATG 59.990 40.000 0.00 0.00 35.01 2.67
2646 5736 5.139727 TGAGTTGGACACTTTGGAATGAAT 58.860 37.500 0.00 0.00 35.01 2.57
2647 5737 4.531854 TGAGTTGGACACTTTGGAATGAA 58.468 39.130 0.00 0.00 35.01 2.57
2661 5751 3.273434 GTTATGCTGCTCATGAGTTGGA 58.727 45.455 23.38 17.03 36.63 3.53
2987 6094 3.558006 GGTACATGTGGCCAAACAAAAAC 59.442 43.478 7.24 2.00 32.81 2.43
3038 6147 4.622740 GCACCTCAGTGTAATTTCAATTGC 59.377 41.667 0.00 0.00 46.35 3.56
3150 6446 4.154195 GCACACAAGGAAAATAGATCACGT 59.846 41.667 0.00 0.00 0.00 4.49
3350 6648 4.326826 AGTGGTCTATGTGTTGACATTGG 58.673 43.478 0.00 0.00 40.05 3.16
3470 6853 6.488006 ACAAGGCAGCATCTTTACTAATATGG 59.512 38.462 0.00 0.00 0.00 2.74
3475 6858 4.009675 CCACAAGGCAGCATCTTTACTAA 58.990 43.478 0.00 0.00 0.00 2.24
3542 6966 7.941790 TCCTATAACAATAATACAGCATTGCCA 59.058 33.333 4.70 0.00 35.91 4.92
3725 7149 3.040990 TCGTAAAAATATGGCGCAACG 57.959 42.857 10.83 4.56 0.00 4.10
3731 7155 6.915843 ACGGAAATCAATCGTAAAAATATGGC 59.084 34.615 0.00 0.00 35.23 4.40
3802 7388 5.105752 CGTTTCATGTTTTTGTTCCTTCCA 58.894 37.500 0.00 0.00 0.00 3.53
3829 7415 3.448686 AGACAATGCTATACACAGACGC 58.551 45.455 0.00 0.00 0.00 5.19
3830 7416 5.102313 TCAAGACAATGCTATACACAGACG 58.898 41.667 0.00 0.00 0.00 4.18
3831 7417 5.521735 CCTCAAGACAATGCTATACACAGAC 59.478 44.000 0.00 0.00 0.00 3.51
3896 7498 3.084536 TGGATGCTGCCAAATGAGTAA 57.915 42.857 0.00 0.00 34.31 2.24
3930 7532 7.093771 ACAAAATTGGGTCATCTATTCTGGAAC 60.094 37.037 0.00 0.00 0.00 3.62
3940 7542 8.706322 AAAGTTAGTACAAAATTGGGTCATCT 57.294 30.769 0.00 0.00 0.00 2.90
3943 7545 8.983702 ACTAAAGTTAGTACAAAATTGGGTCA 57.016 30.769 1.81 0.00 41.92 4.02
3957 7559 7.567458 TGACCCAACTTTGTACTAAAGTTAGT 58.433 34.615 23.56 22.58 45.57 2.24
3958 7560 8.617290 ATGACCCAACTTTGTACTAAAGTTAG 57.383 34.615 23.56 20.79 45.57 2.34
3959 7561 8.434392 AGATGACCCAACTTTGTACTAAAGTTA 58.566 33.333 23.56 14.79 45.57 2.24
3962 7564 9.449719 AATAGATGACCCAACTTTGTACTAAAG 57.550 33.333 13.08 13.08 0.00 1.85
3963 7565 9.802039 AAATAGATGACCCAACTTTGTACTAAA 57.198 29.630 0.00 0.00 0.00 1.85
3964 7566 9.802039 AAAATAGATGACCCAACTTTGTACTAA 57.198 29.630 0.00 0.00 0.00 2.24
3965 7567 9.226606 CAAAATAGATGACCCAACTTTGTACTA 57.773 33.333 0.00 0.00 0.00 1.82
3966 7568 7.176690 CCAAAATAGATGACCCAACTTTGTACT 59.823 37.037 0.00 0.00 0.00 2.73
3967 7569 7.175990 TCCAAAATAGATGACCCAACTTTGTAC 59.824 37.037 0.00 0.00 0.00 2.90
3968 7570 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
3970 7572 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
3971 7573 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
3972 7574 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
3973 7575 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
3974 7576 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
3975 7577 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
3976 7578 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
3977 7579 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
3978 7580 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
3979 7581 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
3980 7582 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
3981 7583 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
3982 7584 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
3984 7586 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
3985 7587 7.383156 AATATACTCCCTCCGTTCCAAAATA 57.617 36.000 0.00 0.00 0.00 1.40
4013 7792 4.934356 AGAGTCATTATGGAAAAAGGCCA 58.066 39.130 5.01 0.00 40.24 5.36
4014 7793 7.588497 AATAGAGTCATTATGGAAAAAGGCC 57.412 36.000 0.00 0.00 0.00 5.19
4016 7795 8.689972 AGCAAATAGAGTCATTATGGAAAAAGG 58.310 33.333 0.00 0.00 0.00 3.11
4035 7814 7.395190 AAGATCAAAGCACATGTAGCAAATA 57.605 32.000 18.31 5.80 0.00 1.40
4040 7819 6.369059 ACATAAGATCAAAGCACATGTAGC 57.631 37.500 0.00 5.03 0.00 3.58
4044 7823 8.697846 ATCAAAACATAAGATCAAAGCACATG 57.302 30.769 0.00 0.00 0.00 3.21
4169 7949 1.408822 GGCACATAGTAAGGCCAGCTT 60.409 52.381 5.01 0.00 45.70 3.74
4231 8014 7.414222 TCGTAAAGTATCAAATGGACCTAGT 57.586 36.000 0.00 0.00 0.00 2.57
4243 8026 7.915293 ACCATCAATTGTTCGTAAAGTATCA 57.085 32.000 5.13 0.00 0.00 2.15
4253 8036 8.427012 CACTAATTCAAAACCATCAATTGTTCG 58.573 33.333 5.13 0.00 0.00 3.95
4254 8037 8.223100 GCACTAATTCAAAACCATCAATTGTTC 58.777 33.333 5.13 0.00 0.00 3.18
4259 8042 7.714377 TGTTTGCACTAATTCAAAACCATCAAT 59.286 29.630 0.00 0.00 34.44 2.57
4318 8101 4.010349 GCTGCCAGGTACAGTTTATTTCT 58.990 43.478 0.00 0.00 37.47 2.52
4359 8142 0.962356 AGAGAAAATGCACAGGCGGG 60.962 55.000 0.00 0.00 45.35 6.13
4362 8145 5.105997 ACAATAGAAGAGAAAATGCACAGGC 60.106 40.000 0.00 0.00 41.68 4.85
4363 8146 6.506500 ACAATAGAAGAGAAAATGCACAGG 57.493 37.500 0.00 0.00 0.00 4.00
4364 8147 6.307318 GCAACAATAGAAGAGAAAATGCACAG 59.693 38.462 0.00 0.00 0.00 3.66
4366 8149 6.385033 AGCAACAATAGAAGAGAAAATGCAC 58.615 36.000 0.00 0.00 32.76 4.57
4367 8150 6.579666 AGCAACAATAGAAGAGAAAATGCA 57.420 33.333 0.00 0.00 32.76 3.96
4368 8151 7.756558 AGTAGCAACAATAGAAGAGAAAATGC 58.243 34.615 0.00 0.00 0.00 3.56
4371 8154 9.998106 ACTAAGTAGCAACAATAGAAGAGAAAA 57.002 29.630 0.00 0.00 0.00 2.29
4406 8189 2.781945 ACGAGCAAAAGAAGCCAAAG 57.218 45.000 0.00 0.00 0.00 2.77
4410 8193 2.774439 TCAAACGAGCAAAAGAAGCC 57.226 45.000 0.00 0.00 0.00 4.35
4411 8194 4.978580 AGAAATCAAACGAGCAAAAGAAGC 59.021 37.500 0.00 0.00 0.00 3.86
4413 8196 4.739716 GCAGAAATCAAACGAGCAAAAGAA 59.260 37.500 0.00 0.00 0.00 2.52
4417 8200 3.706802 TGCAGAAATCAAACGAGCAAA 57.293 38.095 0.00 0.00 0.00 3.68
4425 8217 4.892934 AGGTGGTTAGTTGCAGAAATCAAA 59.107 37.500 0.00 0.00 0.00 2.69
4429 8221 3.821033 GACAGGTGGTTAGTTGCAGAAAT 59.179 43.478 0.00 0.00 0.00 2.17
4707 8499 2.932234 AAGTCTGTCGGAGTGGCGG 61.932 63.158 0.00 0.00 0.00 6.13
4767 8559 6.291648 AGAGATAGCAATTCAGAAGACACA 57.708 37.500 0.00 0.00 0.00 3.72
4860 8652 2.042639 AGACCATGCAATGCCCCC 60.043 61.111 1.53 0.00 44.97 5.40
4878 8670 9.313118 CCTTCCCTAACATACAATAAAATTTGC 57.687 33.333 0.00 0.00 0.00 3.68
4887 8687 6.926630 TTTTTGCCTTCCCTAACATACAAT 57.073 33.333 0.00 0.00 0.00 2.71
4943 8743 4.752661 TTTCCAATAGCGTGTTGGTAAC 57.247 40.909 14.60 0.00 45.05 2.50
4988 8788 2.467826 GCTTCCACCTGATGCGAGC 61.468 63.158 0.00 0.00 34.83 5.03
5020 8848 2.032528 CCAGGTGCTCCGCTTCAA 59.967 61.111 0.00 0.00 39.05 2.69
5029 8857 0.681175 GGCAAATTCAACCAGGTGCT 59.319 50.000 0.00 0.00 32.61 4.40
5069 8897 7.703621 CCAGCCTAAAATGTCATAAATTGTGAG 59.296 37.037 0.00 0.00 0.00 3.51
5070 8898 7.395772 TCCAGCCTAAAATGTCATAAATTGTGA 59.604 33.333 0.00 0.00 0.00 3.58
5071 8899 7.489113 GTCCAGCCTAAAATGTCATAAATTGTG 59.511 37.037 0.00 0.00 0.00 3.33
5072 8900 7.363793 GGTCCAGCCTAAAATGTCATAAATTGT 60.364 37.037 0.00 0.00 0.00 2.71
5082 8910 3.525800 AAGTGGTCCAGCCTAAAATGT 57.474 42.857 0.00 0.00 38.35 2.71
5094 8922 4.184079 TCTTTAACGAGCTAAGTGGTCC 57.816 45.455 0.00 0.00 39.84 4.46
5148 9003 7.769507 CCCGTCTCTATATGCTCTTAGTATACA 59.230 40.741 5.50 0.00 0.00 2.29
5188 9043 1.153429 GTGACCAGACCATACGCCC 60.153 63.158 0.00 0.00 0.00 6.13
5191 9046 0.460284 GCCAGTGACCAGACCATACG 60.460 60.000 0.00 0.00 0.00 3.06
5192 9047 0.107654 GGCCAGTGACCAGACCATAC 60.108 60.000 0.00 0.00 0.00 2.39
5195 9050 3.625897 CGGCCAGTGACCAGACCA 61.626 66.667 2.24 0.00 0.00 4.02
5196 9051 4.394712 CCGGCCAGTGACCAGACC 62.395 72.222 2.24 0.00 0.00 3.85
5198 9053 0.907704 ATTACCGGCCAGTGACCAGA 60.908 55.000 0.00 0.00 0.00 3.86
5236 9091 1.766494 TAAGGCCGGATTGAGACGTA 58.234 50.000 5.05 0.00 0.00 3.57
5254 9109 1.305219 GCAGTGAGCACCGGCATTTA 61.305 55.000 0.00 0.00 44.61 1.40
5271 9126 1.384502 CTGGATAGGAGGGGTGGCA 60.385 63.158 0.00 0.00 0.00 4.92
5273 9128 2.150051 GGCTGGATAGGAGGGGTGG 61.150 68.421 0.00 0.00 0.00 4.61
5276 9131 0.993509 TTTGGGCTGGATAGGAGGGG 60.994 60.000 0.00 0.00 0.00 4.79
5281 9136 2.224719 CCTCAGATTTGGGCTGGATAGG 60.225 54.545 0.00 0.00 34.20 2.57
5300 9155 3.570212 GCCACCCCATATCCGCCT 61.570 66.667 0.00 0.00 0.00 5.52
5317 9172 2.203567 TTTTTGACCGGGGCTGGG 60.204 61.111 6.32 0.00 0.00 4.45
5337 9192 0.035439 TTTGAGGAGCCCGTTGGATC 60.035 55.000 0.00 0.00 46.70 3.36
5338 9193 0.322546 GTTTGAGGAGCCCGTTGGAT 60.323 55.000 0.00 0.00 0.00 3.41
5339 9194 1.072505 GTTTGAGGAGCCCGTTGGA 59.927 57.895 0.00 0.00 0.00 3.53
5340 9195 1.971695 GGTTTGAGGAGCCCGTTGG 60.972 63.158 0.00 0.00 0.00 3.77
5341 9196 2.325082 CGGTTTGAGGAGCCCGTTG 61.325 63.158 0.00 0.00 35.78 4.10
5342 9197 2.032071 CGGTTTGAGGAGCCCGTT 59.968 61.111 0.00 0.00 35.78 4.44
5343 9198 4.016706 CCGGTTTGAGGAGCCCGT 62.017 66.667 0.00 0.00 38.79 5.28
5344 9199 3.952628 GACCGGTTTGAGGAGCCCG 62.953 68.421 9.42 0.00 40.12 6.13
5345 9200 2.046217 GACCGGTTTGAGGAGCCC 60.046 66.667 9.42 0.00 0.00 5.19
5346 9201 1.376037 CAGACCGGTTTGAGGAGCC 60.376 63.158 20.10 0.00 0.00 4.70
5347 9202 0.034896 TTCAGACCGGTTTGAGGAGC 59.965 55.000 25.04 2.65 0.00 4.70
5348 9203 2.543777 TTTCAGACCGGTTTGAGGAG 57.456 50.000 25.04 0.47 0.00 3.69
5349 9204 2.846193 CTTTTCAGACCGGTTTGAGGA 58.154 47.619 25.04 16.33 0.00 3.71
5350 9205 1.266989 GCTTTTCAGACCGGTTTGAGG 59.733 52.381 25.04 19.50 0.00 3.86
5351 9206 1.266989 GGCTTTTCAGACCGGTTTGAG 59.733 52.381 25.04 16.25 0.00 3.02
5352 9207 1.314730 GGCTTTTCAGACCGGTTTGA 58.685 50.000 23.04 23.04 0.00 2.69
5353 9208 0.313987 GGGCTTTTCAGACCGGTTTG 59.686 55.000 18.80 18.80 39.02 2.93
5354 9209 2.728397 GGGCTTTTCAGACCGGTTT 58.272 52.632 9.42 0.00 39.02 3.27
5355 9210 4.494515 GGGCTTTTCAGACCGGTT 57.505 55.556 9.42 0.00 39.02 4.44
5359 9214 4.103103 GCGCGGGCTTTTCAGACC 62.103 66.667 18.33 0.00 46.67 3.85
5388 9243 2.287457 TTTATCCGGCCGTCTGTCCG 62.287 60.000 26.12 6.69 44.89 4.79
5389 9244 0.108041 TTTTATCCGGCCGTCTGTCC 60.108 55.000 26.12 0.00 0.00 4.02
5390 9245 1.729284 TTTTTATCCGGCCGTCTGTC 58.271 50.000 26.12 0.00 0.00 3.51
5391 9246 3.940229 TTTTTATCCGGCCGTCTGT 57.060 47.368 26.12 9.22 0.00 3.41
5406 9261 3.522553 CCCGTCTAGATCGCTTCTTTTT 58.477 45.455 0.00 0.00 35.79 1.94
5407 9262 2.738964 GCCCGTCTAGATCGCTTCTTTT 60.739 50.000 0.00 0.00 35.79 2.27
5408 9263 1.202428 GCCCGTCTAGATCGCTTCTTT 60.202 52.381 0.00 0.00 35.79 2.52
5409 9264 0.386113 GCCCGTCTAGATCGCTTCTT 59.614 55.000 0.00 0.00 35.79 2.52
5410 9265 0.752009 TGCCCGTCTAGATCGCTTCT 60.752 55.000 0.00 0.00 38.57 2.85
5411 9266 0.595310 GTGCCCGTCTAGATCGCTTC 60.595 60.000 0.00 0.00 0.00 3.86
5412 9267 1.437986 GTGCCCGTCTAGATCGCTT 59.562 57.895 0.00 0.00 0.00 4.68
5413 9268 2.491022 GGTGCCCGTCTAGATCGCT 61.491 63.158 0.00 0.00 0.00 4.93
5414 9269 2.027751 GGTGCCCGTCTAGATCGC 59.972 66.667 0.00 0.00 0.00 4.58
5415 9270 1.101635 TGAGGTGCCCGTCTAGATCG 61.102 60.000 0.00 1.64 0.00 3.69
5416 9271 1.112113 TTGAGGTGCCCGTCTAGATC 58.888 55.000 0.00 0.00 0.00 2.75
5417 9272 1.207329 GTTTGAGGTGCCCGTCTAGAT 59.793 52.381 0.00 0.00 0.00 1.98
5418 9273 0.606604 GTTTGAGGTGCCCGTCTAGA 59.393 55.000 0.00 0.00 0.00 2.43
5419 9274 0.391263 GGTTTGAGGTGCCCGTCTAG 60.391 60.000 0.00 0.00 0.00 2.43
5420 9275 1.122632 TGGTTTGAGGTGCCCGTCTA 61.123 55.000 0.00 0.00 0.00 2.59
5421 9276 1.779061 ATGGTTTGAGGTGCCCGTCT 61.779 55.000 0.00 0.00 0.00 4.18
5422 9277 0.893727 AATGGTTTGAGGTGCCCGTC 60.894 55.000 0.00 0.00 0.00 4.79
5423 9278 0.893727 GAATGGTTTGAGGTGCCCGT 60.894 55.000 0.00 0.00 0.00 5.28
5424 9279 0.609131 AGAATGGTTTGAGGTGCCCG 60.609 55.000 0.00 0.00 0.00 6.13
5425 9280 1.177401 GAGAATGGTTTGAGGTGCCC 58.823 55.000 0.00 0.00 0.00 5.36
5426 9281 1.909700 TGAGAATGGTTTGAGGTGCC 58.090 50.000 0.00 0.00 0.00 5.01
5427 9282 3.642705 GTTTGAGAATGGTTTGAGGTGC 58.357 45.455 0.00 0.00 0.00 5.01
5428 9283 3.853307 GCGTTTGAGAATGGTTTGAGGTG 60.853 47.826 0.00 0.00 0.00 4.00
5429 9284 2.293399 GCGTTTGAGAATGGTTTGAGGT 59.707 45.455 0.00 0.00 0.00 3.85
5430 9285 2.351738 GGCGTTTGAGAATGGTTTGAGG 60.352 50.000 0.00 0.00 0.00 3.86
5431 9286 2.351738 GGGCGTTTGAGAATGGTTTGAG 60.352 50.000 0.00 0.00 0.00 3.02
5432 9287 1.611491 GGGCGTTTGAGAATGGTTTGA 59.389 47.619 0.00 0.00 0.00 2.69
5433 9288 1.665735 CGGGCGTTTGAGAATGGTTTG 60.666 52.381 0.00 0.00 0.00 2.93
5434 9289 0.596082 CGGGCGTTTGAGAATGGTTT 59.404 50.000 0.00 0.00 0.00 3.27
5435 9290 1.241315 CCGGGCGTTTGAGAATGGTT 61.241 55.000 0.00 0.00 0.00 3.67
5436 9291 1.674322 CCGGGCGTTTGAGAATGGT 60.674 57.895 0.00 0.00 0.00 3.55
5437 9292 2.406616 CCCGGGCGTTTGAGAATGG 61.407 63.158 8.08 0.00 0.00 3.16
5438 9293 3.051392 GCCCGGGCGTTTGAGAATG 62.051 63.158 33.60 0.00 0.00 2.67
5439 9294 2.750237 GCCCGGGCGTTTGAGAAT 60.750 61.111 33.60 0.00 0.00 2.40
5455 9310 1.758440 TATGAGGGATGCCGGTCAGC 61.758 60.000 1.90 4.23 0.00 4.26
5456 9311 0.979665 ATATGAGGGATGCCGGTCAG 59.020 55.000 1.90 0.00 0.00 3.51
5457 9312 0.976641 GATATGAGGGATGCCGGTCA 59.023 55.000 1.90 1.38 0.00 4.02
5458 9313 0.250513 GGATATGAGGGATGCCGGTC 59.749 60.000 1.90 0.00 0.00 4.79
5459 9314 2.377136 GGATATGAGGGATGCCGGT 58.623 57.895 1.90 0.00 0.00 5.28


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

AutoCloner maintained by Alex Coulton.