Multiple sequence alignment - TraesCS3D01G188600

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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 TraesCS3D01G188600 chr3D 100.000 5557 0 0 1 5557 175409284 175403728 0.000000e+00 10262.0
1 TraesCS3D01G188600 chr3D 86.911 382 50 0 3998 4379 185792427 185792808 3.980000e-116 429.0
2 TraesCS3D01G188600 chr3D 90.000 110 6 4 998 1102 185790122 185790231 2.700000e-28 137.0
3 TraesCS3D01G188600 chr3D 95.062 81 4 0 2423 2503 422517903 422517983 1.620000e-25 128.0
4 TraesCS3D01G188600 chr3B 93.109 1756 59 13 3835 5557 254776773 254775047 0.000000e+00 2516.0
5 TraesCS3D01G188600 chr3B 94.191 878 39 5 1660 2529 254779339 254778466 0.000000e+00 1328.0
6 TraesCS3D01G188600 chr3B 94.647 822 38 5 21 841 691323919 691323103 0.000000e+00 1269.0
7 TraesCS3D01G188600 chr3B 94.151 701 24 5 930 1623 254780030 254779340 0.000000e+00 1051.0
8 TraesCS3D01G188600 chr3B 92.615 650 37 4 2842 3490 254777684 254777045 0.000000e+00 924.0
9 TraesCS3D01G188600 chr3B 91.515 330 24 3 2518 2847 254778283 254777958 8.490000e-123 451.0
10 TraesCS3D01G188600 chr3B 87.173 382 49 0 3998 4379 266566512 266566893 8.550000e-118 435.0
11 TraesCS3D01G188600 chr3B 94.583 240 13 0 3595 3834 254777046 254776807 6.800000e-99 372.0
12 TraesCS3D01G188600 chr3B 92.258 155 12 0 2842 2996 254777878 254777724 2.610000e-53 220.0
13 TraesCS3D01G188600 chr3B 90.654 107 6 4 998 1102 266563873 266563977 7.510000e-29 139.0
14 TraesCS3D01G188600 chr3B 95.062 81 4 0 2423 2503 242209627 242209547 1.620000e-25 128.0
15 TraesCS3D01G188600 chr3B 95.062 81 4 0 2423 2503 550641664 550641744 1.620000e-25 128.0
16 TraesCS3D01G188600 chr3B 84.746 118 1 5 836 937 254781541 254781425 9.850000e-18 102.0
17 TraesCS3D01G188600 chr3A 91.812 1380 60 15 839 2184 215482392 215481032 0.000000e+00 1873.0
18 TraesCS3D01G188600 chr3A 92.792 763 29 14 3937 4696 215479627 215478888 0.000000e+00 1081.0
19 TraesCS3D01G188600 chr3A 87.048 664 52 20 2860 3501 215481009 215480358 0.000000e+00 719.0
20 TraesCS3D01G188600 chr3A 85.933 654 50 21 4838 5478 215474852 215474228 0.000000e+00 660.0
21 TraesCS3D01G188600 chr3A 86.911 382 50 0 3998 4379 246042253 246041872 3.980000e-116 429.0
22 TraesCS3D01G188600 chr3A 89.575 259 16 5 3595 3844 215480359 215480103 8.980000e-83 318.0
23 TraesCS3D01G188600 chr3A 90.351 114 11 0 3835 3948 215480079 215479966 3.470000e-32 150.0
24 TraesCS3D01G188600 chr3A 95.349 86 4 0 4744 4829 215478423 215478338 2.700000e-28 137.0
25 TraesCS3D01G188600 chr3A 95.062 81 4 0 2423 2503 353624512 353624592 1.620000e-25 128.0
26 TraesCS3D01G188600 chr3A 93.651 63 3 1 5495 5557 215474073 215474012 5.930000e-15 93.5
27 TraesCS3D01G188600 chr2D 98.039 816 15 1 21 835 536221467 536222282 0.000000e+00 1417.0
28 TraesCS3D01G188600 chr2D 95.110 818 37 3 21 835 374140133 374140950 0.000000e+00 1286.0
29 TraesCS3D01G188600 chr2D 96.203 79 3 0 1000 1078 49875921 49875999 4.520000e-26 130.0
30 TraesCS3D01G188600 chr4D 97.188 818 20 3 21 836 65863438 65862622 0.000000e+00 1380.0
31 TraesCS3D01G188600 chr4D 95.159 847 17 4 1 835 19152636 19151802 0.000000e+00 1315.0
32 TraesCS3D01G188600 chr4D 100.000 31 0 0 1 31 65863470 65863440 2.160000e-04 58.4
33 TraesCS3D01G188600 chr1D 96.944 818 24 1 21 837 108776452 108775635 0.000000e+00 1371.0
34 TraesCS3D01G188600 chr1D 96.368 826 25 5 21 842 10791252 10790428 0.000000e+00 1354.0
35 TraesCS3D01G188600 chr1D 94.811 848 19 5 1 835 58455170 58454335 0.000000e+00 1299.0
36 TraesCS3D01G188600 chr1D 90.695 849 32 7 1 835 466333282 466332467 0.000000e+00 1086.0
37 TraesCS3D01G188600 chr1D 97.500 80 2 0 999 1078 404139954 404139875 2.700000e-28 137.0
38 TraesCS3D01G188600 chr1D 95.062 81 4 0 2423 2503 211684850 211684930 1.620000e-25 128.0
39 TraesCS3D01G188600 chr1D 100.000 31 0 0 1 31 10791284 10791254 2.160000e-04 58.4
40 TraesCS3D01G188600 chr1D 100.000 31 0 0 1 31 108776484 108776454 2.160000e-04 58.4
41 TraesCS3D01G188600 chr7D 96.695 817 26 1 21 836 30325237 30326053 0.000000e+00 1358.0
42 TraesCS3D01G188600 chr7D 96.206 817 28 3 21 835 607565964 607565149 0.000000e+00 1334.0
43 TraesCS3D01G188600 chr7D 98.969 97 1 0 3500 3596 621015981 621015885 2.060000e-39 174.0
44 TraesCS3D01G188600 chr7D 94.495 109 3 2 3500 3608 545397634 545397529 1.240000e-36 165.0
45 TraesCS3D01G188600 chr5B 96.206 817 24 6 21 835 12569115 12569926 0.000000e+00 1330.0
46 TraesCS3D01G188600 chr5B 98.980 98 1 0 3500 3597 693583898 693583801 5.720000e-40 176.0
47 TraesCS3D01G188600 chr5B 96.226 106 2 2 3500 3604 51031111 51031215 7.400000e-39 172.0
48 TraesCS3D01G188600 chr4B 90.382 863 52 14 1 836 539944837 539943979 0.000000e+00 1105.0
49 TraesCS3D01G188600 chr4B 98.020 101 2 0 3500 3600 21198651 21198751 5.720000e-40 176.0
50 TraesCS3D01G188600 chr6A 94.419 215 11 1 28 241 531070349 531070563 4.150000e-86 329.0
51 TraesCS3D01G188600 chr6A 94.419 215 11 1 28 241 554927971 554928185 4.150000e-86 329.0
52 TraesCS3D01G188600 chr6A 96.296 81 3 0 2423 2503 178890687 178890607 3.490000e-27 134.0
53 TraesCS3D01G188600 chr7B 98.000 100 2 0 3499 3598 562993065 562993164 2.060000e-39 174.0
54 TraesCS3D01G188600 chr7B 95.413 109 2 2 3500 3608 589348415 589348310 2.660000e-38 171.0
55 TraesCS3D01G188600 chr2A 97.980 99 2 0 3498 3596 16263575 16263673 7.400000e-39 172.0
56 TraesCS3D01G188600 chr2A 96.203 79 3 0 1000 1078 51582360 51582438 4.520000e-26 130.0
57 TraesCS3D01G188600 chr2A 91.209 91 7 1 2423 2512 437970523 437970613 7.560000e-24 122.0
58 TraesCS3D01G188600 chr4A 95.238 105 5 0 3495 3599 666944578 666944682 3.440000e-37 167.0
59 TraesCS3D01G188600 chr2B 96.203 79 3 0 1000 1078 77168977 77169055 4.520000e-26 130.0
60 TraesCS3D01G188600 chr1B 96.203 79 3 0 1000 1078 543500052 543499974 4.520000e-26 130.0
61 TraesCS3D01G188600 chr6B 95.062 81 4 0 2423 2503 337237239 337237159 1.620000e-25 128.0


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 TraesCS3D01G188600 chr3D 175403728 175409284 5556 True 10262.0000 10262 100.000000 1 5557 1 chr3D.!!$R1 5556
1 TraesCS3D01G188600 chr3D 185790122 185792808 2686 False 283.0000 429 88.455500 998 4379 2 chr3D.!!$F2 3381
2 TraesCS3D01G188600 chr3B 691323103 691323919 816 True 1269.0000 1269 94.647000 21 841 1 chr3B.!!$R2 820
3 TraesCS3D01G188600 chr3B 254775047 254781541 6494 True 870.5000 2516 92.146000 836 5557 8 chr3B.!!$R3 4721
4 TraesCS3D01G188600 chr3B 266563873 266566893 3020 False 287.0000 435 88.913500 998 4379 2 chr3B.!!$F2 3381
5 TraesCS3D01G188600 chr3A 215474012 215482392 8380 True 628.9375 1873 90.813875 839 5557 8 chr3A.!!$R2 4718
6 TraesCS3D01G188600 chr2D 536221467 536222282 815 False 1417.0000 1417 98.039000 21 835 1 chr2D.!!$F3 814
7 TraesCS3D01G188600 chr2D 374140133 374140950 817 False 1286.0000 1286 95.110000 21 835 1 chr2D.!!$F2 814
8 TraesCS3D01G188600 chr4D 19151802 19152636 834 True 1315.0000 1315 95.159000 1 835 1 chr4D.!!$R1 834
9 TraesCS3D01G188600 chr4D 65862622 65863470 848 True 719.2000 1380 98.594000 1 836 2 chr4D.!!$R2 835
10 TraesCS3D01G188600 chr1D 58454335 58455170 835 True 1299.0000 1299 94.811000 1 835 1 chr1D.!!$R1 834
11 TraesCS3D01G188600 chr1D 466332467 466333282 815 True 1086.0000 1086 90.695000 1 835 1 chr1D.!!$R3 834
12 TraesCS3D01G188600 chr1D 108775635 108776484 849 True 714.7000 1371 98.472000 1 837 2 chr1D.!!$R5 836
13 TraesCS3D01G188600 chr1D 10790428 10791284 856 True 706.2000 1354 98.184000 1 842 2 chr1D.!!$R4 841
14 TraesCS3D01G188600 chr7D 30325237 30326053 816 False 1358.0000 1358 96.695000 21 836 1 chr7D.!!$F1 815
15 TraesCS3D01G188600 chr7D 607565149 607565964 815 True 1334.0000 1334 96.206000 21 835 1 chr7D.!!$R2 814
16 TraesCS3D01G188600 chr5B 12569115 12569926 811 False 1330.0000 1330 96.206000 21 835 1 chr5B.!!$F1 814
17 TraesCS3D01G188600 chr4B 539943979 539944837 858 True 1105.0000 1105 90.382000 1 836 1 chr4B.!!$R1 835

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
578 613 0.466124 GAAGACGGAATGGGGAGAGG 59.534 60.000 0.00 0.00 0.00 3.69 F
1307 3435 0.105039 GTAGATCTCGCACCCCCTTG 59.895 60.000 0.00 0.00 0.00 3.61 F
1363 3491 0.601046 TGTCTTTCCAGCGCTGTCAG 60.601 55.000 33.75 24.75 0.00 3.51 F
1478 3613 1.673920 GGCTGTTTGGTCGTTCTTTCA 59.326 47.619 0.00 0.00 0.00 2.69 F
2139 4289 1.962807 ACTTGCATGTTGCCAGCTTAA 59.037 42.857 0.00 0.00 44.23 1.85 F
3462 7681 1.302033 CTGACTGTGGCCAGGTGAC 60.302 63.158 5.11 0.00 43.36 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1428 3556 0.250234 TTCGCTATGACAGGCAGCTT 59.750 50.0 0.0 0.00 33.03 3.74 R
2901 6885 1.600023 TCAGTACCAAAGCCCAAACG 58.400 50.0 0.0 0.00 0.00 3.60 R
3097 7276 1.890876 TGGGTCCGTCAGAACAAATG 58.109 50.0 0.0 0.00 31.73 2.32 R
3407 7624 0.459489 TTGCCCACTTGAAACACTGC 59.541 50.0 0.0 0.00 0.00 4.40 R
3489 7716 0.034283 GGAGGGAGTAGTCACCGACT 60.034 60.0 0.0 1.75 45.54 4.18 R
5089 13639 0.166597 TGCTTGAGATTTCTTGCGCG 59.833 50.0 0.0 0.00 0.00 6.86 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
506 528 2.411701 CAAGCCGTCGCCGATCTA 59.588 61.111 0.00 0.00 35.63 1.98
578 613 0.466124 GAAGACGGAATGGGGAGAGG 59.534 60.000 0.00 0.00 0.00 3.69
751 801 2.273449 GCACCTGGTGGATCTGGG 59.727 66.667 27.02 0.42 37.04 4.45
752 802 2.273449 CACCTGGTGGATCTGGGC 59.727 66.667 19.23 0.00 37.04 5.36
753 803 3.402681 ACCTGGTGGATCTGGGCG 61.403 66.667 0.00 0.00 37.04 6.13
754 804 4.864334 CCTGGTGGATCTGGGCGC 62.864 72.222 0.00 0.00 34.57 6.53
757 807 4.241555 GGTGGATCTGGGCGCGAT 62.242 66.667 12.10 0.00 0.00 4.58
758 808 2.663188 GTGGATCTGGGCGCGATC 60.663 66.667 12.10 19.75 37.21 3.69
759 809 4.284860 TGGATCTGGGCGCGATCG 62.285 66.667 12.10 11.69 38.49 3.69
798 860 2.340328 GGAATCAGCCGCCCGTTTT 61.340 57.895 0.00 0.00 0.00 2.43
1112 2778 5.059161 TCTGTTCTCCTCTTTCAACATGTG 58.941 41.667 0.00 0.00 0.00 3.21
1143 3179 1.144969 TTTGCACGACTCCATTCGAC 58.855 50.000 0.00 0.00 41.78 4.20
1196 3324 2.517450 GCACTGGCGCGTAGATGTC 61.517 63.158 17.30 0.00 0.00 3.06
1301 3429 1.339610 AGATGCAGTAGATCTCGCACC 59.660 52.381 14.54 7.14 34.79 5.01
1302 3430 0.390860 ATGCAGTAGATCTCGCACCC 59.609 55.000 14.54 0.00 34.79 4.61
1307 3435 0.105039 GTAGATCTCGCACCCCCTTG 59.895 60.000 0.00 0.00 0.00 3.61
1350 3478 4.922206 TGGCTCCATACATTCTTGTCTTT 58.078 39.130 0.00 0.00 37.28 2.52
1363 3491 0.601046 TGTCTTTCCAGCGCTGTCAG 60.601 55.000 33.75 24.75 0.00 3.51
1428 3556 2.411701 CGTTCCGGCTGATCGCTA 59.588 61.111 0.00 0.00 39.13 4.26
1434 3562 2.593134 CGGCTGATCGCTAAGCTGC 61.593 63.158 8.94 0.00 38.86 5.25
1478 3613 1.673920 GGCTGTTTGGTCGTTCTTTCA 59.326 47.619 0.00 0.00 0.00 2.69
1742 3878 2.092323 TGGGTCACTAGTCATCAGTCG 58.908 52.381 0.00 0.00 0.00 4.18
1747 3885 3.623960 GTCACTAGTCATCAGTCGCTACT 59.376 47.826 0.00 0.00 35.91 2.57
1748 3886 3.872182 TCACTAGTCATCAGTCGCTACTC 59.128 47.826 0.00 0.00 31.97 2.59
1762 3900 6.647481 CAGTCGCTACTCTCTAGATTTAGCTA 59.353 42.308 18.27 9.92 35.24 3.32
1886 4032 4.163458 ACCGACTTGGAATTTATCTAGGCA 59.837 41.667 0.00 0.00 42.00 4.75
1972 4118 6.398234 TGGCTTAAACTGCACATTTTCTTA 57.602 33.333 0.00 0.00 0.00 2.10
1981 4127 7.275888 ACTGCACATTTTCTTATCAGTGAAA 57.724 32.000 0.00 0.00 32.77 2.69
1989 4135 9.199982 CATTTTCTTATCAGTGAAAGCAACATT 57.800 29.630 0.00 0.00 34.29 2.71
2035 4181 2.462723 TGCTATGGTGGTGCTAGTGTA 58.537 47.619 0.00 0.00 0.00 2.90
2087 4233 8.664992 TGATGGCTGGAATAGTTATTGGTATTA 58.335 33.333 0.00 0.00 0.00 0.98
2130 4280 5.978919 ACATGTTGAAGTAACTTGCATGTTG 59.021 36.000 24.00 9.49 44.15 3.33
2139 4289 1.962807 ACTTGCATGTTGCCAGCTTAA 59.037 42.857 0.00 0.00 44.23 1.85
2339 4495 8.519526 CATTTTGGTTATGCAAAAGTACCTAGA 58.480 33.333 0.00 0.00 34.36 2.43
2363 4519 3.575805 AGGACCAAAATGCTTGAAGGAA 58.424 40.909 0.00 0.00 0.00 3.36
2416 4572 7.206687 TGATTCTTCAAAAACACCACCATTAC 58.793 34.615 0.00 0.00 0.00 1.89
2425 4581 4.062490 ACACCACCATTACTCTAGAGGT 57.938 45.455 23.50 9.64 0.00 3.85
2434 4590 5.393787 CCATTACTCTAGAGGTTGCGTACAA 60.394 44.000 23.50 4.15 0.00 2.41
2478 4634 3.052082 CTGGACCCTGCACAAGCG 61.052 66.667 0.00 0.00 46.23 4.68
2551 4901 4.134379 TGAATGTGTTTGTTGGCATGTT 57.866 36.364 0.00 0.00 0.00 2.71
2552 4902 3.869832 TGAATGTGTTTGTTGGCATGTTG 59.130 39.130 0.00 0.00 0.00 3.33
2553 4903 3.540314 ATGTGTTTGTTGGCATGTTGT 57.460 38.095 0.00 0.00 0.00 3.32
2554 4904 4.662468 ATGTGTTTGTTGGCATGTTGTA 57.338 36.364 0.00 0.00 0.00 2.41
2555 4905 4.662468 TGTGTTTGTTGGCATGTTGTAT 57.338 36.364 0.00 0.00 0.00 2.29
2568 4918 8.201242 TGGCATGTTGTATGAGGACTAATATA 57.799 34.615 0.00 0.00 0.00 0.86
2605 4955 4.287067 AGGTCTAAAGAAATGTCCTCTGCA 59.713 41.667 0.00 0.00 0.00 4.41
2626 5672 6.215121 TGCAACTTTGATTGTGTAGATTTGG 58.785 36.000 0.00 0.00 31.83 3.28
2713 6612 8.970859 ACATTTGAACTTTCTAGGATCCATAG 57.029 34.615 15.82 12.48 0.00 2.23
2782 6681 8.884124 AAGAGGATTCTCAAATATGTTTCCAA 57.116 30.769 3.21 0.00 42.34 3.53
2827 6726 5.356882 TTTCTTGCGATAGAAAACTGTGG 57.643 39.130 9.19 0.00 40.25 4.17
2828 6727 2.742053 TCTTGCGATAGAAAACTGTGGC 59.258 45.455 0.00 0.00 39.76 5.01
2830 6729 2.710377 TGCGATAGAAAACTGTGGCAT 58.290 42.857 0.00 0.00 39.76 4.40
2837 6736 6.252015 CGATAGAAAACTGTGGCATTGATTTG 59.748 38.462 0.00 0.00 39.76 2.32
2847 6746 5.301551 TGTGGCATTGATTTGTGAAGTACTT 59.698 36.000 8.13 8.13 0.00 2.24
2848 6747 5.630680 GTGGCATTGATTTGTGAAGTACTTG 59.369 40.000 14.14 0.00 0.00 3.16
2850 6749 5.221880 GCATTGATTTGTGAAGTACTTGCA 58.778 37.500 14.14 9.02 0.00 4.08
2851 6750 5.691305 GCATTGATTTGTGAAGTACTTGCAA 59.309 36.000 14.14 14.44 0.00 4.08
2891 6875 6.941857 TGCTGTAATAGGTCACATGTCTTAA 58.058 36.000 0.00 0.00 0.00 1.85
2901 6885 7.731054 AGGTCACATGTCTTAATCTTCTATCC 58.269 38.462 0.00 0.00 0.00 2.59
2931 6915 5.348986 GCTTTGGTACTGATCAAGTCGATA 58.651 41.667 0.00 0.00 40.56 2.92
3093 7272 7.920160 AAATTCCAGATGAAGAAAGAGACTC 57.080 36.000 0.00 0.00 36.14 3.36
3097 7276 7.164230 TCCAGATGAAGAAAGAGACTCTAAC 57.836 40.000 5.14 3.19 0.00 2.34
3235 7422 8.294577 CCCAAAAGTTAGTTATGTTCTTGTACC 58.705 37.037 0.00 0.00 0.00 3.34
3282 7469 6.965500 GCTTCATGATGTGTTCATTACTTCTG 59.035 38.462 10.05 0.00 42.62 3.02
3320 7507 4.997565 TGATTTTGAAGATTCGCCCATTC 58.002 39.130 0.00 0.00 0.00 2.67
3321 7508 4.706476 TGATTTTGAAGATTCGCCCATTCT 59.294 37.500 0.00 0.00 0.00 2.40
3323 7510 6.376864 TGATTTTGAAGATTCGCCCATTCTTA 59.623 34.615 0.00 0.00 30.11 2.10
3407 7624 7.782644 TGGGTTTTTGTATTCCCATCTAATAGG 59.217 37.037 0.00 0.00 44.07 2.57
3460 7679 2.033141 CCTGACTGTGGCCAGGTG 59.967 66.667 5.11 1.01 43.71 4.00
3461 7680 2.519622 CCTGACTGTGGCCAGGTGA 61.520 63.158 5.11 1.00 43.71 4.02
3462 7681 1.302033 CTGACTGTGGCCAGGTGAC 60.302 63.158 5.11 0.00 43.36 3.67
3463 7682 1.762522 CTGACTGTGGCCAGGTGACT 61.763 60.000 5.11 0.00 43.36 3.41
3488 7715 5.104527 AGTCTGACTACTCTAGATGCTGACT 60.105 44.000 8.91 4.02 33.92 3.41
3489 7716 6.099125 AGTCTGACTACTCTAGATGCTGACTA 59.901 42.308 8.91 0.00 35.25 2.59
3490 7717 6.423905 GTCTGACTACTCTAGATGCTGACTAG 59.576 46.154 0.00 0.00 38.76 2.57
3491 7718 6.099125 TCTGACTACTCTAGATGCTGACTAGT 59.901 42.308 0.00 0.00 38.59 2.57
3492 7719 6.285224 TGACTACTCTAGATGCTGACTAGTC 58.715 44.000 16.32 16.32 38.59 2.59
3493 7720 5.294356 ACTACTCTAGATGCTGACTAGTCG 58.706 45.833 17.85 13.20 38.59 4.18
3494 7721 3.472652 ACTCTAGATGCTGACTAGTCGG 58.527 50.000 24.89 24.89 38.59 4.79
3495 7722 3.118186 ACTCTAGATGCTGACTAGTCGGT 60.118 47.826 28.26 13.25 38.59 4.69
3496 7723 3.206964 TCTAGATGCTGACTAGTCGGTG 58.793 50.000 28.26 16.95 38.59 4.94
3497 7724 2.130272 AGATGCTGACTAGTCGGTGA 57.870 50.000 28.26 17.84 38.23 4.02
3498 7725 1.746220 AGATGCTGACTAGTCGGTGAC 59.254 52.381 28.26 19.62 38.23 3.67
3499 7726 1.746220 GATGCTGACTAGTCGGTGACT 59.254 52.381 28.26 13.48 45.54 3.41
3500 7727 2.484742 TGCTGACTAGTCGGTGACTA 57.515 50.000 28.26 10.86 41.51 2.59
3501 7728 2.082231 TGCTGACTAGTCGGTGACTAC 58.918 52.381 28.26 13.93 41.51 2.73
3502 7729 2.290134 TGCTGACTAGTCGGTGACTACT 60.290 50.000 28.26 0.00 41.51 2.57
3503 7730 2.352342 GCTGACTAGTCGGTGACTACTC 59.648 54.545 28.26 9.26 41.51 2.59
3504 7731 2.937799 CTGACTAGTCGGTGACTACTCC 59.062 54.545 21.64 0.00 41.51 3.85
3505 7732 2.287769 GACTAGTCGGTGACTACTCCC 58.712 57.143 7.22 0.00 41.51 4.30
3506 7733 1.914798 ACTAGTCGGTGACTACTCCCT 59.085 52.381 2.65 0.00 41.51 4.20
3507 7734 2.093021 ACTAGTCGGTGACTACTCCCTC 60.093 54.545 2.65 0.00 41.51 4.30
3508 7735 0.034283 AGTCGGTGACTACTCCCTCC 60.034 60.000 0.00 0.00 41.51 4.30
3509 7736 1.077930 TCGGTGACTACTCCCTCCG 60.078 63.158 0.00 0.00 39.40 4.63
3510 7737 1.378250 CGGTGACTACTCCCTCCGT 60.378 63.158 0.00 0.00 34.38 4.69
3511 7738 1.375098 CGGTGACTACTCCCTCCGTC 61.375 65.000 0.00 0.00 34.38 4.79
3512 7739 1.036481 GGTGACTACTCCCTCCGTCC 61.036 65.000 0.00 0.00 0.00 4.79
3513 7740 1.036481 GTGACTACTCCCTCCGTCCC 61.036 65.000 0.00 0.00 0.00 4.46
3514 7741 1.305623 GACTACTCCCTCCGTCCCA 59.694 63.158 0.00 0.00 0.00 4.37
3515 7742 0.324091 GACTACTCCCTCCGTCCCAA 60.324 60.000 0.00 0.00 0.00 4.12
3516 7743 0.115745 ACTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
3517 7744 1.272807 CTACTCCCTCCGTCCCAAAA 58.727 55.000 0.00 0.00 0.00 2.44
3518 7745 1.838077 CTACTCCCTCCGTCCCAAAAT 59.162 52.381 0.00 0.00 0.00 1.82
3519 7746 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
3520 7747 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
3521 7748 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
3522 7749 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
3523 7750 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
3524 7751 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
3525 7752 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
3526 7753 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
3527 7754 3.933332 CTCCGTCCCAAAATAAGTGTCTC 59.067 47.826 0.00 0.00 0.00 3.36
3528 7755 3.325425 TCCGTCCCAAAATAAGTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
3529 7756 4.069304 CCGTCCCAAAATAAGTGTCTCAA 58.931 43.478 0.00 0.00 0.00 3.02
3530 7757 4.154195 CCGTCCCAAAATAAGTGTCTCAAG 59.846 45.833 0.00 0.00 0.00 3.02
3531 7758 4.378459 CGTCCCAAAATAAGTGTCTCAAGC 60.378 45.833 0.00 0.00 0.00 4.01
3532 7759 4.762251 GTCCCAAAATAAGTGTCTCAAGCT 59.238 41.667 0.00 0.00 0.00 3.74
3533 7760 5.241728 GTCCCAAAATAAGTGTCTCAAGCTT 59.758 40.000 0.00 0.00 0.00 3.74
3534 7761 6.430000 GTCCCAAAATAAGTGTCTCAAGCTTA 59.570 38.462 0.00 0.00 0.00 3.09
3535 7762 6.655003 TCCCAAAATAAGTGTCTCAAGCTTAG 59.345 38.462 0.00 0.00 0.00 2.18
3536 7763 6.431234 CCCAAAATAAGTGTCTCAAGCTTAGT 59.569 38.462 0.00 0.00 0.00 2.24
3537 7764 7.606456 CCCAAAATAAGTGTCTCAAGCTTAGTA 59.394 37.037 0.00 0.00 0.00 1.82
3538 7765 8.443937 CCAAAATAAGTGTCTCAAGCTTAGTAC 58.556 37.037 0.00 0.00 0.00 2.73
3539 7766 8.988934 CAAAATAAGTGTCTCAAGCTTAGTACA 58.011 33.333 0.00 0.36 0.00 2.90
3540 7767 9.555727 AAAATAAGTGTCTCAAGCTTAGTACAA 57.444 29.630 0.00 0.00 0.00 2.41
3541 7768 8.535690 AATAAGTGTCTCAAGCTTAGTACAAC 57.464 34.615 0.00 0.00 0.00 3.32
3542 7769 5.793030 AGTGTCTCAAGCTTAGTACAACT 57.207 39.130 0.00 0.00 0.00 3.16
3543 7770 6.163135 AGTGTCTCAAGCTTAGTACAACTT 57.837 37.500 0.00 0.00 0.00 2.66
3544 7771 6.583562 AGTGTCTCAAGCTTAGTACAACTTT 58.416 36.000 0.00 0.00 0.00 2.66
3545 7772 7.723324 AGTGTCTCAAGCTTAGTACAACTTTA 58.277 34.615 0.00 0.00 0.00 1.85
3546 7773 8.368668 AGTGTCTCAAGCTTAGTACAACTTTAT 58.631 33.333 0.00 0.00 0.00 1.40
3547 7774 9.635520 GTGTCTCAAGCTTAGTACAACTTTATA 57.364 33.333 0.00 0.00 0.00 0.98
3548 7775 9.635520 TGTCTCAAGCTTAGTACAACTTTATAC 57.364 33.333 0.00 0.00 0.00 1.47
3549 7776 9.857957 GTCTCAAGCTTAGTACAACTTTATACT 57.142 33.333 0.00 0.00 35.76 2.12
3583 7810 9.673454 GTACAAAGTTAAGACACTTATTTTGGG 57.327 33.333 19.96 8.06 35.87 4.12
3584 7811 8.528044 ACAAAGTTAAGACACTTATTTTGGGA 57.472 30.769 19.96 0.00 35.87 4.37
3585 7812 8.410912 ACAAAGTTAAGACACTTATTTTGGGAC 58.589 33.333 19.96 6.58 35.87 4.46
3586 7813 6.796705 AGTTAAGACACTTATTTTGGGACG 57.203 37.500 0.00 0.00 0.00 4.79
3587 7814 5.704053 AGTTAAGACACTTATTTTGGGACGG 59.296 40.000 0.00 0.00 0.00 4.79
3588 7815 4.360951 AAGACACTTATTTTGGGACGGA 57.639 40.909 0.00 0.00 0.00 4.69
3589 7816 3.939066 AGACACTTATTTTGGGACGGAG 58.061 45.455 0.00 0.00 0.00 4.63
3590 7817 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
3591 7818 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
3592 7819 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
3593 7820 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
3638 7866 2.016905 AGTCAGGGCAGTTAGACAGT 57.983 50.000 0.00 0.00 33.56 3.55
3660 7888 3.751175 TCTGGCAATAGGTTTTCAAGTCG 59.249 43.478 0.00 0.00 0.00 4.18
3704 7932 0.764271 CAAGCCAAACCCCACCAAAT 59.236 50.000 0.00 0.00 0.00 2.32
3753 7981 2.363306 TTGGACACTGTTGGCAAGAT 57.637 45.000 0.00 0.00 28.57 2.40
3801 8037 4.060205 GTCATGCCAAATTTTTGTCAGCT 58.940 39.130 2.63 0.00 36.45 4.24
3838 8107 5.163519 ACCAAAACTTCAGTCATGACCAAAG 60.164 40.000 25.27 25.27 34.35 2.77
3852 8121 4.693283 TGACCAAAGCATTCCTATAGTCG 58.307 43.478 0.00 0.00 0.00 4.18
3923 8192 3.010472 TCTCTGGGGCATTTCATTCTTGA 59.990 43.478 0.00 0.00 0.00 3.02
3939 8208 7.761409 TCATTCTTGAACAGTATTACCATTGC 58.239 34.615 0.00 0.00 0.00 3.56
4019 8639 0.895100 GCTGCATCACCACCAAGGAA 60.895 55.000 0.00 0.00 41.22 3.36
4133 8753 4.202367 ACGATTGACTTTCCTGAGTTCCTT 60.202 41.667 0.00 0.00 0.00 3.36
4157 8777 3.270027 CCTGATGGCACGTAAGATGAAA 58.730 45.455 0.00 0.00 43.62 2.69
4163 8783 2.415512 GGCACGTAAGATGAAAGACACC 59.584 50.000 0.00 0.00 43.62 4.16
4166 8786 3.364023 CACGTAAGATGAAAGACACCGAC 59.636 47.826 0.00 0.00 43.62 4.79
4478 9126 5.503927 AGTCCAGTGAATGAACATATTGCT 58.496 37.500 0.00 0.00 0.00 3.91
4481 9129 4.277258 CAGTGAATGAACATATTGCTCGC 58.723 43.478 0.00 0.00 0.00 5.03
4482 9130 4.034858 CAGTGAATGAACATATTGCTCGCT 59.965 41.667 0.00 0.00 0.00 4.93
4483 9131 4.272018 AGTGAATGAACATATTGCTCGCTC 59.728 41.667 0.00 0.00 0.00 5.03
4484 9132 4.272018 GTGAATGAACATATTGCTCGCTCT 59.728 41.667 0.00 0.00 0.00 4.09
4485 9133 4.877823 TGAATGAACATATTGCTCGCTCTT 59.122 37.500 0.00 0.00 0.00 2.85
4486 9134 5.007039 TGAATGAACATATTGCTCGCTCTTC 59.993 40.000 0.00 0.00 0.00 2.87
4490 9138 3.878778 ACATATTGCTCGCTCTTCCTTT 58.121 40.909 0.00 0.00 0.00 3.11
4527 9175 6.699642 TGTTGAGAATTTCGTTTGGATTTTCC 59.300 34.615 0.00 0.00 36.96 3.13
4637 9291 6.802608 AGTTGCATGGATGTCTGATATTTTG 58.197 36.000 0.00 0.00 0.00 2.44
4638 9292 6.379133 AGTTGCATGGATGTCTGATATTTTGT 59.621 34.615 0.00 0.00 0.00 2.83
4639 9293 6.139048 TGCATGGATGTCTGATATTTTGTG 57.861 37.500 0.00 0.00 0.00 3.33
4640 9294 5.653330 TGCATGGATGTCTGATATTTTGTGT 59.347 36.000 0.00 0.00 0.00 3.72
4641 9295 5.975344 GCATGGATGTCTGATATTTTGTGTG 59.025 40.000 0.00 0.00 0.00 3.82
4642 9296 6.405065 GCATGGATGTCTGATATTTTGTGTGT 60.405 38.462 0.00 0.00 0.00 3.72
4643 9297 6.499234 TGGATGTCTGATATTTTGTGTGTG 57.501 37.500 0.00 0.00 0.00 3.82
4644 9298 6.003326 TGGATGTCTGATATTTTGTGTGTGT 58.997 36.000 0.00 0.00 0.00 3.72
4645 9299 6.072563 TGGATGTCTGATATTTTGTGTGTGTG 60.073 38.462 0.00 0.00 0.00 3.82
4646 9300 6.072508 GGATGTCTGATATTTTGTGTGTGTGT 60.073 38.462 0.00 0.00 0.00 3.72
4647 9301 6.058827 TGTCTGATATTTTGTGTGTGTGTG 57.941 37.500 0.00 0.00 0.00 3.82
4648 9302 5.588246 TGTCTGATATTTTGTGTGTGTGTGT 59.412 36.000 0.00 0.00 0.00 3.72
4649 9303 5.909054 GTCTGATATTTTGTGTGTGTGTGTG 59.091 40.000 0.00 0.00 0.00 3.82
4897 13446 5.450592 TGCAAAAGTCAATCTGTGCATTA 57.549 34.783 0.00 0.00 40.63 1.90
4918 13467 7.279758 GCATTATATTCTACATCTTCTCCAGCC 59.720 40.741 0.00 0.00 0.00 4.85
4943 13493 2.839228 AGTATGGCTCTTCTGTCCCTT 58.161 47.619 0.00 0.00 0.00 3.95
5062 13612 0.934496 TTGCTGGAAAACGACAGTCG 59.066 50.000 21.62 21.62 46.93 4.18
5075 13625 2.092838 CGACAGTCGCTGATTTTTCCTC 59.907 50.000 10.66 0.00 35.18 3.71
5079 13629 2.232941 AGTCGCTGATTTTTCCTCCGTA 59.767 45.455 0.00 0.00 0.00 4.02
5080 13630 2.997986 GTCGCTGATTTTTCCTCCGTAA 59.002 45.455 0.00 0.00 0.00 3.18
5089 13639 6.477360 TGATTTTTCCTCCGTAAACAAAAAGC 59.523 34.615 0.00 0.00 34.47 3.51
5124 13677 7.870509 TCTCAAGCAAGCATTATTCAACTAT 57.129 32.000 0.00 0.00 0.00 2.12
5221 13776 9.762933 AGCAAATAAAATACTTTTCAAGCTTGA 57.237 25.926 25.16 25.16 34.19 3.02
5411 13970 7.054751 ACCTAGTTATAAGTTTGATTCCCTGC 58.945 38.462 0.00 0.00 0.00 4.85
5434 13993 8.400184 TGCAATTTATTCCATCTTATCTGGAG 57.600 34.615 0.00 0.00 43.46 3.86
5468 14027 4.946772 TCCTCTGATCACACACAAAAACAA 59.053 37.500 0.00 0.00 0.00 2.83
5469 14028 5.066375 TCCTCTGATCACACACAAAAACAAG 59.934 40.000 0.00 0.00 0.00 3.16
5470 14029 5.247507 TCTGATCACACACAAAAACAAGG 57.752 39.130 0.00 0.00 0.00 3.61
5491 14050 9.213777 ACAAGGAGTATAACTCTGATGGATTTA 57.786 33.333 6.99 0.00 44.46 1.40
5542 14238 4.721776 TGTCATTAGCTCCACCCTTAATCT 59.278 41.667 0.00 0.00 0.00 2.40
5550 14246 4.770795 CTCCACCCTTAATCTACACAAGG 58.229 47.826 0.00 0.00 38.86 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
496 518 1.734137 GGAGTGCTTAGATCGGCGA 59.266 57.895 13.87 13.87 0.00 5.54
742 780 4.284860 CGATCGCGCCCAGATCCA 62.285 66.667 15.33 0.00 40.91 3.41
759 809 4.005472 CCATTCGATCGCGCCAGC 62.005 66.667 11.09 0.00 37.46 4.85
760 810 4.005472 GCCATTCGATCGCGCCAG 62.005 66.667 11.09 0.00 37.46 4.85
774 836 4.802051 GCGGCTGATTCCTGGCCA 62.802 66.667 4.71 4.71 45.50 5.36
798 860 1.899534 GCCGGCCACCAACTAACAA 60.900 57.895 18.11 0.00 0.00 2.83
991 2471 2.520536 GGTCCGCCATGGCTCCTAT 61.521 63.158 33.07 0.00 39.32 2.57
1112 2778 5.346281 GGAGTCGTGCAAATCATATAGTAGC 59.654 44.000 0.00 0.00 0.00 3.58
1196 3324 1.069823 CGATCAGATCTCCCACCCAAG 59.930 57.143 8.82 0.00 0.00 3.61
1302 3430 2.881403 CCACAAGGAATGGAGACAAGGG 60.881 54.545 0.00 0.00 40.49 3.95
1428 3556 0.250234 TTCGCTATGACAGGCAGCTT 59.750 50.000 0.00 0.00 33.03 3.74
1478 3613 4.041444 AGTTGCTCCACTGAAAGAGATCTT 59.959 41.667 0.00 0.00 37.43 2.40
1696 3832 2.737039 GCTCTAGCAACCTACTCAGCAC 60.737 54.545 0.00 0.00 41.59 4.40
1742 3878 8.385898 TGTTCTAGCTAAATCTAGAGAGTAGC 57.614 38.462 18.02 18.02 43.99 3.58
1762 3900 2.345244 CCTCGCCACTGCTGTTCT 59.655 61.111 0.00 0.00 34.43 3.01
1853 3999 2.086869 TCCAAGTCGGTAGTAGTTCCG 58.913 52.381 9.21 9.21 46.93 4.30
1886 4032 4.646492 GCATCCATAGAAAAACACCCAGAT 59.354 41.667 0.00 0.00 0.00 2.90
1972 4118 4.147321 ACTCCAATGTTGCTTTCACTGAT 58.853 39.130 0.00 0.00 0.00 2.90
1981 4127 2.624838 CCAGACAAACTCCAATGTTGCT 59.375 45.455 0.00 0.00 0.00 3.91
1989 4135 1.754226 GGCAAAACCAGACAAACTCCA 59.246 47.619 0.00 0.00 38.86 3.86
2035 4181 5.748402 TGCATTCTCCATGTTATCAGTCTT 58.252 37.500 0.00 0.00 34.98 3.01
2165 4315 5.772825 ATCTTCAAACAGCAAGCAACTAA 57.227 34.783 0.00 0.00 0.00 2.24
2166 4316 5.772825 AATCTTCAAACAGCAAGCAACTA 57.227 34.783 0.00 0.00 0.00 2.24
2175 4325 5.157067 GTTGGCTAGAAATCTTCAAACAGC 58.843 41.667 0.00 0.00 0.00 4.40
2284 4440 7.528996 TTGACAATGTTTTCATGGAAGAGAT 57.471 32.000 0.00 0.00 40.79 2.75
2339 4495 3.070015 CCTTCAAGCATTTTGGTCCTTGT 59.930 43.478 0.00 0.00 36.82 3.16
2363 4519 4.762251 CCATCATTGATGCATCTGATCAGT 59.238 41.667 26.32 7.26 38.59 3.41
2416 4572 4.621886 GTCTTTTGTACGCAACCTCTAGAG 59.378 45.833 13.18 13.18 33.82 2.43
2425 4581 3.018149 ACTTTGGGTCTTTTGTACGCAA 58.982 40.909 0.00 0.00 44.85 4.85
2451 4607 3.015753 GGGTCCAGGGAAGGGTCC 61.016 72.222 0.00 0.00 44.10 4.46
2478 4634 2.125512 CCAGTGCACGTAGCTCCC 60.126 66.667 12.01 0.00 45.94 4.30
2503 4659 3.127030 GCTAGTGATACCAAAACTGCCAC 59.873 47.826 0.00 0.00 0.00 5.01
2507 4663 6.204688 TCAACAAGCTAGTGATACCAAAACTG 59.795 38.462 0.00 0.00 0.00 3.16
2512 4668 6.149308 CACATTCAACAAGCTAGTGATACCAA 59.851 38.462 0.00 0.00 0.00 3.67
2580 4930 5.123027 GCAGAGGACATTTCTTTAGACCTTG 59.877 44.000 0.00 0.00 0.00 3.61
2756 6655 9.973661 TTGGAAACATATTTGAGAATCCTCTTA 57.026 29.630 0.00 0.00 42.32 2.10
2813 6712 7.062605 CACAAATCAATGCCACAGTTTTCTATC 59.937 37.037 0.00 0.00 0.00 2.08
2823 6722 4.826733 AGTACTTCACAAATCAATGCCACA 59.173 37.500 0.00 0.00 0.00 4.17
2824 6723 5.376854 AGTACTTCACAAATCAATGCCAC 57.623 39.130 0.00 0.00 0.00 5.01
2827 6726 5.221880 TGCAAGTACTTCACAAATCAATGC 58.778 37.500 4.77 2.95 0.00 3.56
2828 6727 6.919662 AGTTGCAAGTACTTCACAAATCAATG 59.080 34.615 17.83 1.26 0.00 2.82
2830 6729 6.094742 TGAGTTGCAAGTACTTCACAAATCAA 59.905 34.615 29.99 20.63 37.59 2.57
2837 6736 5.636837 TGTTTTGAGTTGCAAGTACTTCAC 58.363 37.500 6.80 3.18 37.87 3.18
2847 6746 5.063691 CAGCAAAGATTTGTTTTGAGTTGCA 59.936 36.000 7.12 0.00 41.91 4.08
2848 6747 5.063817 ACAGCAAAGATTTGTTTTGAGTTGC 59.936 36.000 7.12 0.00 40.24 4.17
2850 6749 8.947055 ATTACAGCAAAGATTTGTTTTGAGTT 57.053 26.923 7.12 0.00 40.24 3.01
2851 6750 9.683069 CTATTACAGCAAAGATTTGTTTTGAGT 57.317 29.630 7.12 2.78 40.24 3.41
2891 6875 3.933861 AAGCCCAAACGGATAGAAGAT 57.066 42.857 0.00 0.00 0.00 2.40
2901 6885 1.600023 TCAGTACCAAAGCCCAAACG 58.400 50.000 0.00 0.00 0.00 3.60
2931 6915 9.942850 CCAGAAAATTATTTGGGTAAACATTCT 57.057 29.630 0.00 0.00 0.00 2.40
3093 7272 3.435671 GGGTCCGTCAGAACAAATGTTAG 59.564 47.826 0.00 0.00 38.56 2.34
3097 7276 1.890876 TGGGTCCGTCAGAACAAATG 58.109 50.000 0.00 0.00 31.73 2.32
3189 7368 9.930693 TTTTGGGTATTTAATGGACACAAATAC 57.069 29.630 8.51 15.89 43.84 1.89
3207 7394 8.983702 ACAAGAACATAACTAACTTTTGGGTA 57.016 30.769 0.00 0.00 0.00 3.69
3212 7399 7.227116 TGCGGTACAAGAACATAACTAACTTTT 59.773 33.333 0.00 0.00 0.00 2.27
3354 7571 9.248291 CAAGTATGCAGAAAAACACAAGTAATT 57.752 29.630 0.00 0.00 0.00 1.40
3407 7624 0.459489 TTGCCCACTTGAAACACTGC 59.541 50.000 0.00 0.00 0.00 4.40
3460 7679 6.423905 CAGCATCTAGAGTAGTCAGACTAGTC 59.576 46.154 28.24 28.24 46.51 2.59
3461 7680 6.099125 TCAGCATCTAGAGTAGTCAGACTAGT 59.901 42.308 16.67 16.67 37.08 2.57
3462 7681 6.423905 GTCAGCATCTAGAGTAGTCAGACTAG 59.576 46.154 10.81 0.68 30.12 2.57
3463 7682 6.099125 AGTCAGCATCTAGAGTAGTCAGACTA 59.901 42.308 6.15 6.15 30.50 2.59
3488 7715 1.211457 GGAGGGAGTAGTCACCGACTA 59.789 57.143 0.00 0.00 41.51 2.59
3489 7716 0.034283 GGAGGGAGTAGTCACCGACT 60.034 60.000 0.00 1.75 45.54 4.18
3490 7717 1.375098 CGGAGGGAGTAGTCACCGAC 61.375 65.000 18.63 9.15 42.40 4.79
3491 7718 1.077930 CGGAGGGAGTAGTCACCGA 60.078 63.158 18.63 0.00 42.40 4.69
3492 7719 1.375098 GACGGAGGGAGTAGTCACCG 61.375 65.000 20.50 20.50 44.77 4.94
3493 7720 1.036481 GGACGGAGGGAGTAGTCACC 61.036 65.000 0.00 0.00 35.49 4.02
3494 7721 1.036481 GGGACGGAGGGAGTAGTCAC 61.036 65.000 0.00 0.00 35.49 3.67
3495 7722 1.305623 GGGACGGAGGGAGTAGTCA 59.694 63.158 0.00 0.00 35.49 3.41
3496 7723 0.324091 TTGGGACGGAGGGAGTAGTC 60.324 60.000 0.00 0.00 0.00 2.59
3497 7724 0.115745 TTTGGGACGGAGGGAGTAGT 59.884 55.000 0.00 0.00 0.00 2.73
3498 7725 1.272807 TTTTGGGACGGAGGGAGTAG 58.727 55.000 0.00 0.00 0.00 2.57
3499 7726 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
3500 7727 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
3501 7728 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
3502 7729 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
3503 7730 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
3504 7731 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
3505 7732 3.933332 GAGACACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 0.00 4.63
3506 7733 3.325425 TGAGACACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 0.00 4.69
3507 7734 3.670625 TGAGACACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 0.00 4.79
3508 7735 4.378459 GCTTGAGACACTTATTTTGGGACG 60.378 45.833 0.00 0.00 0.00 4.79
3509 7736 4.762251 AGCTTGAGACACTTATTTTGGGAC 59.238 41.667 0.00 0.00 0.00 4.46
3510 7737 4.985538 AGCTTGAGACACTTATTTTGGGA 58.014 39.130 0.00 0.00 0.00 4.37
3511 7738 5.712152 AAGCTTGAGACACTTATTTTGGG 57.288 39.130 0.00 0.00 0.00 4.12
3512 7739 7.440523 ACTAAGCTTGAGACACTTATTTTGG 57.559 36.000 9.86 0.00 0.00 3.28
3513 7740 8.988934 TGTACTAAGCTTGAGACACTTATTTTG 58.011 33.333 9.86 0.00 0.00 2.44
3514 7741 9.555727 TTGTACTAAGCTTGAGACACTTATTTT 57.444 29.630 9.86 0.00 0.00 1.82
3515 7742 8.989980 GTTGTACTAAGCTTGAGACACTTATTT 58.010 33.333 9.86 0.00 0.00 1.40
3516 7743 8.368668 AGTTGTACTAAGCTTGAGACACTTATT 58.631 33.333 9.86 0.00 0.00 1.40
3517 7744 7.897864 AGTTGTACTAAGCTTGAGACACTTAT 58.102 34.615 9.86 0.00 0.00 1.73
3518 7745 7.286215 AGTTGTACTAAGCTTGAGACACTTA 57.714 36.000 9.86 0.00 0.00 2.24
3519 7746 6.163135 AGTTGTACTAAGCTTGAGACACTT 57.837 37.500 9.86 0.00 0.00 3.16
3520 7747 5.793030 AGTTGTACTAAGCTTGAGACACT 57.207 39.130 9.86 7.29 0.00 3.55
3521 7748 6.846325 AAAGTTGTACTAAGCTTGAGACAC 57.154 37.500 9.86 7.18 0.00 3.67
3522 7749 9.635520 GTATAAAGTTGTACTAAGCTTGAGACA 57.364 33.333 9.86 7.12 0.00 3.41
3523 7750 9.857957 AGTATAAAGTTGTACTAAGCTTGAGAC 57.142 33.333 9.86 4.39 34.01 3.36
3557 7784 9.673454 CCCAAAATAAGTGTCTTAACTTTGTAC 57.327 33.333 16.72 0.00 40.77 2.90
3558 7785 9.629878 TCCCAAAATAAGTGTCTTAACTTTGTA 57.370 29.630 16.72 8.94 40.77 2.41
3559 7786 8.410912 GTCCCAAAATAAGTGTCTTAACTTTGT 58.589 33.333 16.72 0.00 40.77 2.83
3560 7787 7.589954 CGTCCCAAAATAAGTGTCTTAACTTTG 59.410 37.037 14.00 14.00 40.77 2.77
3561 7788 7.255346 CCGTCCCAAAATAAGTGTCTTAACTTT 60.255 37.037 0.00 0.00 40.77 2.66
3562 7789 6.206048 CCGTCCCAAAATAAGTGTCTTAACTT 59.794 38.462 0.00 0.00 42.89 2.66
3563 7790 5.704053 CCGTCCCAAAATAAGTGTCTTAACT 59.296 40.000 0.00 0.00 0.00 2.24
3564 7791 5.702209 TCCGTCCCAAAATAAGTGTCTTAAC 59.298 40.000 0.00 0.00 0.00 2.01
3565 7792 5.867330 TCCGTCCCAAAATAAGTGTCTTAA 58.133 37.500 0.00 0.00 0.00 1.85
3566 7793 5.484715 CTCCGTCCCAAAATAAGTGTCTTA 58.515 41.667 0.00 0.00 0.00 2.10
3567 7794 4.324267 CTCCGTCCCAAAATAAGTGTCTT 58.676 43.478 0.00 0.00 0.00 3.01
3568 7795 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
3569 7796 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
3570 7797 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
3571 7798 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
3572 7799 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
3573 7800 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
3574 7801 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
3575 7802 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
3576 7803 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
3577 7804 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
3578 7805 1.961133 AATACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
3579 7806 1.557832 CAAATACTCCCTCCGTCCCAA 59.442 52.381 0.00 0.00 0.00 4.12
3580 7807 1.200519 CAAATACTCCCTCCGTCCCA 58.799 55.000 0.00 0.00 0.00 4.37
3581 7808 1.138464 GTCAAATACTCCCTCCGTCCC 59.862 57.143 0.00 0.00 0.00 4.46
3582 7809 1.829222 TGTCAAATACTCCCTCCGTCC 59.171 52.381 0.00 0.00 0.00 4.79
3583 7810 3.604875 TTGTCAAATACTCCCTCCGTC 57.395 47.619 0.00 0.00 0.00 4.79
3584 7811 4.569719 AATTGTCAAATACTCCCTCCGT 57.430 40.909 0.00 0.00 0.00 4.69
3585 7812 4.511826 GCTAATTGTCAAATACTCCCTCCG 59.488 45.833 0.00 0.00 0.00 4.63
3586 7813 4.822350 GGCTAATTGTCAAATACTCCCTCC 59.178 45.833 0.00 0.00 0.00 4.30
3587 7814 5.437060 TGGCTAATTGTCAAATACTCCCTC 58.563 41.667 0.00 0.00 0.00 4.30
3588 7815 5.440610 CTGGCTAATTGTCAAATACTCCCT 58.559 41.667 0.00 0.00 0.00 4.20
3589 7816 4.580580 CCTGGCTAATTGTCAAATACTCCC 59.419 45.833 0.00 0.00 0.00 4.30
3590 7817 4.036852 GCCTGGCTAATTGTCAAATACTCC 59.963 45.833 12.43 0.00 0.00 3.85
3591 7818 4.036852 GGCCTGGCTAATTGTCAAATACTC 59.963 45.833 19.68 0.00 0.00 2.59
3592 7819 3.954258 GGCCTGGCTAATTGTCAAATACT 59.046 43.478 19.68 0.00 0.00 2.12
3593 7820 3.954258 AGGCCTGGCTAATTGTCAAATAC 59.046 43.478 19.68 0.00 0.00 1.89
3629 7857 4.473477 ACCTATTGCCAGACTGTCTAAC 57.527 45.455 10.47 6.17 0.00 2.34
3638 7866 3.751175 CGACTTGAAAACCTATTGCCAGA 59.249 43.478 0.00 0.00 0.00 3.86
3660 7888 3.537580 TCAAACCAGACACACCAAGTAC 58.462 45.455 0.00 0.00 0.00 2.73
3753 7981 4.270008 GCTCCTTAGCCCACTTTCAATTA 58.730 43.478 0.00 0.00 43.40 1.40
3801 8037 5.596361 TGAAGTTTTGGTTCTTGCTTGGATA 59.404 36.000 0.00 0.00 0.00 2.59
3821 8057 4.380233 GGAATGCTTTGGTCATGACTGAAG 60.380 45.833 24.50 24.66 31.85 3.02
3838 8107 6.586844 GGTCTTAACATCGACTATAGGAATGC 59.413 42.308 4.43 0.00 0.00 3.56
3852 8121 5.965918 GCGCAATAAAAGAGGTCTTAACATC 59.034 40.000 0.30 0.00 36.45 3.06
4019 8639 0.250467 AGCGCATCACAGTTCCAAGT 60.250 50.000 11.47 0.00 0.00 3.16
4133 8753 3.449377 TCATCTTACGTGCCATCAGGTTA 59.551 43.478 0.00 0.00 41.12 2.85
4157 8777 1.377463 CTCCTCGGAGTCGGTGTCT 60.377 63.158 4.02 0.00 37.47 3.41
4478 9126 2.232452 CCTGAGAAGAAAGGAAGAGCGA 59.768 50.000 0.00 0.00 35.40 4.93
4481 9129 4.224818 ACATCCCTGAGAAGAAAGGAAGAG 59.775 45.833 0.00 0.00 35.40 2.85
4482 9130 4.171234 ACATCCCTGAGAAGAAAGGAAGA 58.829 43.478 0.00 0.00 35.40 2.87
4483 9131 4.566426 ACATCCCTGAGAAGAAAGGAAG 57.434 45.455 0.00 0.00 35.40 3.46
4484 9132 4.350816 TCAACATCCCTGAGAAGAAAGGAA 59.649 41.667 0.00 0.00 35.40 3.36
4485 9133 3.909995 TCAACATCCCTGAGAAGAAAGGA 59.090 43.478 0.00 0.00 35.40 3.36
4486 9134 4.019860 TCTCAACATCCCTGAGAAGAAAGG 60.020 45.833 0.12 0.00 44.89 3.11
4527 9175 6.795098 TGTACAAAGGTAATACAACTGCAG 57.205 37.500 13.48 13.48 0.00 4.41
4637 9291 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
4638 9292 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
4639 9293 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
4640 9294 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
4641 9295 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
4642 9296 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
4643 9297 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
4644 9298 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
4645 9299 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
4646 9300 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
4647 9301 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
4648 9302 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
4649 9303 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
4713 9367 8.406297 TGAGATGTACTACATTGTCTACATCAC 58.594 37.037 28.46 25.31 43.48 3.06
4897 13446 6.949117 ATGGCTGGAGAAGATGTAGAATAT 57.051 37.500 0.00 0.00 0.00 1.28
4918 13467 5.059833 GGGACAGAAGAGCCATACTAAATG 58.940 45.833 0.00 0.00 0.00 2.32
5062 13612 4.759516 TGTTTACGGAGGAAAAATCAGC 57.240 40.909 0.00 0.00 0.00 4.26
5075 13625 0.930742 TGCGCGCTTTTTGTTTACGG 60.931 50.000 33.29 0.00 0.00 4.02
5079 13629 1.634702 TTCTTGCGCGCTTTTTGTTT 58.365 40.000 33.29 0.00 0.00 2.83
5080 13630 1.634702 TTTCTTGCGCGCTTTTTGTT 58.365 40.000 33.29 0.00 0.00 2.83
5089 13639 0.166597 TGCTTGAGATTTCTTGCGCG 59.833 50.000 0.00 0.00 0.00 6.86
5124 13677 9.642327 CAGGACATAATTGATTTGACAAATTCA 57.358 29.630 14.46 10.81 33.44 2.57
5221 13776 6.644347 TGGTTTGTCCATTATTTGTGTTGTT 58.356 32.000 0.00 0.00 41.93 2.83
5226 13781 7.656948 ACTCATTTGGTTTGTCCATTATTTGTG 59.343 33.333 0.00 0.00 46.60 3.33
5411 13970 8.295288 GTGCTCCAGATAAGATGGAATAAATTG 58.705 37.037 0.00 0.00 46.04 2.32
5434 13993 3.373439 GTGATCAGAGGACAAATGAGTGC 59.627 47.826 0.00 0.00 0.00 4.40
5468 14027 9.213777 TGTTAAATCCATCAGAGTTATACTCCT 57.786 33.333 3.33 0.00 46.18 3.69


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

AutoCloner maintained by Alex Coulton.