Multiple sequence alignment - TraesCS6A01G274200

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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 TraesCS6A01G274200 chr6A 100.000 7559 0 0 1 7559 500512281 500504723 0.000000e+00 13959.0
1 TraesCS6A01G274200 chr6A 88.506 87 9 1 5626 5712 4415628 4415713 3.730000e-18 104.0
2 TraesCS6A01G274200 chr6D 92.231 4338 236 37 1 4278 358983530 358979234 0.000000e+00 6050.0
3 TraesCS6A01G274200 chr6D 92.493 1745 63 23 5793 7511 358977857 358976155 0.000000e+00 2435.0
4 TraesCS6A01G274200 chr6D 92.526 1271 61 17 4360 5628 358979235 358977997 0.000000e+00 1790.0
5 TraesCS6A01G274200 chr6B 93.624 2588 94 23 3026 5600 540594622 540592093 0.000000e+00 3799.0
6 TraesCS6A01G274200 chr6B 93.366 2035 74 19 3144 5170 560191698 560193679 0.000000e+00 2953.0
7 TraesCS6A01G274200 chr6B 91.653 1821 73 26 5724 7513 540591984 540590212 0.000000e+00 2447.0
8 TraesCS6A01G274200 chr6B 92.130 1728 82 25 738 2442 540597245 540595549 0.000000e+00 2388.0
9 TraesCS6A01G274200 chr6B 91.719 1582 74 23 5724 7273 560197237 560198793 0.000000e+00 2143.0
10 TraesCS6A01G274200 chr6B 94.952 931 33 7 926 1850 560188786 560189708 0.000000e+00 1447.0
11 TraesCS6A01G274200 chr6B 95.245 715 28 4 2422 3132 540595446 540594734 0.000000e+00 1127.0
12 TraesCS6A01G274200 chr6B 95.098 714 25 7 2422 3132 560190676 560191382 0.000000e+00 1116.0
13 TraesCS6A01G274200 chr6B 94.649 598 31 1 1846 2442 560189977 560190574 0.000000e+00 926.0
14 TraesCS6A01G274200 chr6B 96.714 426 10 2 5167 5591 560196399 560196821 0.000000e+00 706.0
15 TraesCS6A01G274200 chr6B 78.879 696 107 24 1 664 560187185 560187872 1.160000e-117 435.0
16 TraesCS6A01G274200 chr6B 78.818 694 110 21 1 664 540598277 540597591 4.190000e-117 433.0
17 TraesCS6A01G274200 chr6B 93.023 129 5 3 3026 3151 560191384 560191511 1.300000e-42 185.0
18 TraesCS6A01G274200 chr6B 100.000 53 0 0 7288 7340 560198782 560198834 1.740000e-16 99.0
19 TraesCS6A01G274200 chr5B 91.089 101 7 2 3295 3394 34252084 34252183 1.320000e-27 135.0
20 TraesCS6A01G274200 chr5B 90.805 87 7 1 5625 5711 375770503 375770588 1.720000e-21 115.0
21 TraesCS6A01G274200 chr7B 78.509 228 32 10 280 492 700605285 700605510 4.760000e-27 134.0
22 TraesCS6A01G274200 chr7B 86.916 107 13 1 3288 3394 539218274 539218379 1.330000e-22 119.0
23 TraesCS6A01G274200 chr1A 93.182 88 6 0 4277 4364 304031888 304031975 6.160000e-26 130.0
24 TraesCS6A01G274200 chr5D 89.320 103 10 1 3296 3398 556009428 556009327 2.210000e-25 128.0
25 TraesCS6A01G274200 chr1D 91.954 87 6 1 5626 5712 402722639 402722724 3.700000e-23 121.0
26 TraesCS6A01G274200 chr1D 90.698 86 7 1 5626 5711 58438787 58438871 6.200000e-21 113.0
27 TraesCS6A01G274200 chr2A 91.765 85 7 0 4277 4361 608647274 608647358 1.330000e-22 119.0
28 TraesCS6A01G274200 chr5A 94.595 74 4 0 4288 4361 564602374 564602301 1.720000e-21 115.0
29 TraesCS6A01G274200 chr4A 89.247 93 9 1 4277 4369 90592900 90592991 1.720000e-21 115.0
30 TraesCS6A01G274200 chr4A 87.640 89 9 2 5623 5711 732377141 732377055 1.340000e-17 102.0
31 TraesCS6A01G274200 chr3D 85.714 105 14 1 3298 3401 305448661 305448557 8.020000e-20 110.0
32 TraesCS6A01G274200 chr2B 89.412 85 8 1 5627 5711 7855059 7854976 1.040000e-18 106.0
33 TraesCS6A01G274200 chr2B 85.714 98 12 2 5619 5715 607246236 607246140 1.340000e-17 102.0
34 TraesCS6A01G274200 chr2D 87.097 93 10 1 3298 3390 145890407 145890497 3.730000e-18 104.0
35 TraesCS6A01G274200 chr2D 88.506 87 9 1 5626 5712 538943507 538943422 3.730000e-18 104.0
36 TraesCS6A01G274200 chr2D 87.356 87 9 2 5626 5711 99658123 99658208 1.740000e-16 99.0
37 TraesCS6A01G274200 chr1B 83.333 102 16 1 3298 3399 601489770 601489870 8.080000e-15 93.5


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 TraesCS6A01G274200 chr6A 500504723 500512281 7558 True 13959.000000 13959 100.000000 1 7559 1 chr6A.!!$R1 7558
1 TraesCS6A01G274200 chr6D 358976155 358983530 7375 True 3425.000000 6050 92.416667 1 7511 3 chr6D.!!$R1 7510
2 TraesCS6A01G274200 chr6B 540590212 540598277 8065 True 2038.800000 3799 90.294000 1 7513 5 chr6B.!!$R1 7512
3 TraesCS6A01G274200 chr6B 560187185 560198834 11649 False 1112.222222 2953 93.155556 1 7340 9 chr6B.!!$F1 7339

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
148 151 0.883153 TACGCTAGAACCGCACTTCA 59.117 50.000 0.00 0.0 0.00 3.02 F
728 793 0.957395 CGCATGCCCAGTCTGTTCTT 60.957 55.000 13.15 0.0 0.00 2.52 F
1350 2087 0.520404 GTACTTGAGGTGCTCGACGA 59.480 55.000 0.00 0.0 32.35 4.20 F
1799 2544 0.820871 GGTGGTTGTTGCCTTGTTGA 59.179 50.000 0.00 0.0 0.00 3.18 F
1875 2893 1.070914 TGTGGCGAATGTACCAAGTGA 59.929 47.619 0.00 0.0 37.79 3.41 F
2852 4012 2.150390 TGTTTGCTATGCTGCTCGAAA 58.850 42.857 0.00 0.0 0.00 3.46 F
4488 6077 3.694072 TGTCAGTTTTGGACTTCTGGTTG 59.306 43.478 0.00 0.0 36.10 3.77 F
5435 9754 0.105142 ACCCCGGCCTATGATGTACT 60.105 55.000 0.00 0.0 0.00 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1333 2070 0.387929 TTTCGTCGAGCACCTCAAGT 59.612 50.000 0.00 0.00 0.00 3.16 R
1875 2893 0.403271 ACAGGCCATGAAAGCAGAGT 59.597 50.000 5.01 0.00 0.00 3.24 R
2844 4004 3.113322 GTCGCATACACTATTTCGAGCA 58.887 45.455 0.00 0.00 0.00 4.26 R
3108 4382 3.258622 AGCACTAGGACCAACTGAGTTAC 59.741 47.826 0.00 0.00 0.00 2.50 R
3175 4753 5.158141 TCTCAAGGTAGGATTCCTATGCAT 58.842 41.667 15.44 3.79 38.48 3.96 R
4527 6116 1.003438 GATCGAATTCAAAGCGCCTCC 60.003 52.381 2.29 0.00 0.00 4.30 R
5694 10394 0.255318 ATGTACTCCCTCCGTCTCGT 59.745 55.000 0.00 0.00 0.00 4.18 R
6898 11707 0.038892 ACTACGGCACTAACACGGTG 60.039 55.000 6.58 6.58 37.70 4.94 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
26 28 2.047274 ACGAGTGATGGCGGTTGG 60.047 61.111 0.00 0.00 0.00 3.77
27 29 2.264480 CGAGTGATGGCGGTTGGA 59.736 61.111 0.00 0.00 0.00 3.53
33 35 1.823899 GATGGCGGTTGGATGTCCC 60.824 63.158 0.00 0.00 34.29 4.46
66 69 2.408565 GGACCCCTGTTCATGGAGATA 58.591 52.381 0.00 0.00 0.00 1.98
73 76 3.244009 CCTGTTCATGGAGATAGACGCAT 60.244 47.826 0.00 0.00 0.00 4.73
96 99 3.130227 GCCGAAGAGGAGGCGTAT 58.870 61.111 0.00 0.00 44.22 3.06
113 116 4.141965 TGCGACCGCGGATGACAT 62.142 61.111 35.90 8.10 45.51 3.06
116 119 1.300156 CGACCGCGGATGACATCAT 60.300 57.895 35.90 5.18 39.70 2.45
148 151 0.883153 TACGCTAGAACCGCACTTCA 59.117 50.000 0.00 0.00 0.00 3.02
178 181 1.406341 GCCACAACCACGAGGCTAATA 60.406 52.381 0.00 0.00 43.70 0.98
179 182 2.937873 GCCACAACCACGAGGCTAATAA 60.938 50.000 0.00 0.00 43.70 1.40
188 191 4.442706 CACGAGGCTAATAAGTCCATGTT 58.557 43.478 0.00 0.00 0.00 2.71
196 199 2.357327 TAAGTCCATGTTCGACACCG 57.643 50.000 3.83 0.00 32.41 4.94
338 378 3.366396 GGAAGACAGGACATAGGAGACA 58.634 50.000 0.00 0.00 0.00 3.41
339 379 3.131400 GGAAGACAGGACATAGGAGACAC 59.869 52.174 0.00 0.00 0.00 3.67
349 389 1.557099 TAGGAGACACACTTCGCCAT 58.443 50.000 0.00 0.00 37.90 4.40
416 456 7.167468 GCTTTTGTTTAGTTGAAATGTGTCGAT 59.833 33.333 0.00 0.00 0.00 3.59
464 510 3.119637 CCGGTTTGCATAAATTTCGTCCT 60.120 43.478 0.00 0.00 0.00 3.85
507 553 3.703001 ATATATATATGCGGGCCTGGC 57.297 47.619 15.02 11.05 0.00 4.85
517 563 3.492353 GGCCTGGCTGGATGGCTA 61.492 66.667 19.68 0.00 45.45 3.93
523 569 2.742116 GGCTGGATGGCTAACCCGA 61.742 63.158 0.00 0.00 38.32 5.14
555 604 6.764379 TGTCCACTCACAAATACAATGTCTA 58.236 36.000 0.00 0.00 0.00 2.59
557 606 7.549134 TGTCCACTCACAAATACAATGTCTATC 59.451 37.037 0.00 0.00 0.00 2.08
574 623 4.873827 GTCTATCATAAGGGTTTGCGTTGA 59.126 41.667 0.00 0.00 0.00 3.18
595 644 9.329913 CGTTGAAGATGTCCTTACAAAATAAAG 57.670 33.333 0.00 0.00 39.58 1.85
664 714 1.940613 GAAGAAACAACCGTGAGCACT 59.059 47.619 0.00 0.00 0.00 4.40
728 793 0.957395 CGCATGCCCAGTCTGTTCTT 60.957 55.000 13.15 0.00 0.00 2.52
853 1339 4.161942 TGGCCAATACAATTCCATTCAAGG 59.838 41.667 0.61 0.00 0.00 3.61
987 1715 7.182761 CAGTATAAATGAAGAAGGAAAGCGTG 58.817 38.462 0.00 0.00 0.00 5.34
1026 1757 4.346709 TCAAAATTTCCCCAAAACTCCTCC 59.653 41.667 0.00 0.00 0.00 4.30
1299 2036 2.805353 CTCGTGCGTCCCGTGAAG 60.805 66.667 0.00 0.00 0.00 3.02
1307 2044 2.933287 TCCCGTGAAGTGCCCCAT 60.933 61.111 0.00 0.00 0.00 4.00
1333 2070 0.597568 ATTTGCTTGCTTGCTGCGTA 59.402 45.000 0.00 0.00 46.63 4.42
1350 2087 0.520404 GTACTTGAGGTGCTCGACGA 59.480 55.000 0.00 0.00 32.35 4.20
1395 2132 3.498071 CAGGGTGGTGGTGGTGGT 61.498 66.667 0.00 0.00 0.00 4.16
1413 2150 1.376683 TGTGGCCTTGGTATGCGAC 60.377 57.895 3.32 0.00 36.83 5.19
1556 2293 3.424703 CAATCCCACTGTTCCTGTTCAT 58.575 45.455 0.00 0.00 0.00 2.57
1593 2334 2.082231 TGCGACCTGTGTACTAGACTC 58.918 52.381 0.00 0.00 0.00 3.36
1594 2335 2.290134 TGCGACCTGTGTACTAGACTCT 60.290 50.000 0.00 0.00 0.00 3.24
1645 2386 2.366916 CGGCAGAAGAGGGAGATTACAT 59.633 50.000 0.00 0.00 0.00 2.29
1646 2387 3.574396 CGGCAGAAGAGGGAGATTACATA 59.426 47.826 0.00 0.00 0.00 2.29
1647 2388 4.559704 CGGCAGAAGAGGGAGATTACATAC 60.560 50.000 0.00 0.00 0.00 2.39
1685 2426 2.618053 CTCGTAGCATCCTTTTTCGGT 58.382 47.619 0.00 0.00 0.00 4.69
1698 2439 5.708230 TCCTTTTTCGGTTGCATATAGTTGT 59.292 36.000 0.00 0.00 0.00 3.32
1723 2464 3.133362 CGGTACTTTATGGGGAGCTTGTA 59.867 47.826 0.00 0.00 0.00 2.41
1757 2498 6.350949 GGGTTAGTCAATGGCATGTACAATTT 60.351 38.462 0.00 0.00 0.00 1.82
1758 2499 7.096551 GGTTAGTCAATGGCATGTACAATTTT 58.903 34.615 0.00 0.00 0.00 1.82
1764 2505 8.673711 GTCAATGGCATGTACAATTTTAGTAGA 58.326 33.333 0.00 0.00 0.00 2.59
1765 2506 9.407380 TCAATGGCATGTACAATTTTAGTAGAT 57.593 29.630 0.00 0.00 0.00 1.98
1799 2544 0.820871 GGTGGTTGTTGCCTTGTTGA 59.179 50.000 0.00 0.00 0.00 3.18
1824 2569 3.485947 TGTTGCGGCATCTGAATTAAC 57.514 42.857 2.28 0.00 0.00 2.01
1875 2893 1.070914 TGTGGCGAATGTACCAAGTGA 59.929 47.619 0.00 0.00 37.79 3.41
1901 2919 2.421424 GCTTTCATGGCCTGTTGTCTAG 59.579 50.000 3.32 0.84 0.00 2.43
1912 2930 5.454755 GGCCTGTTGTCTAGCCTTGATAATA 60.455 44.000 0.00 0.00 42.34 0.98
1925 2943 8.034313 AGCCTTGATAATATACTGAACTGGAA 57.966 34.615 0.00 0.00 0.00 3.53
2056 3074 6.312918 TCCTCTAATCTTAACAAACGCATGTC 59.687 38.462 0.00 0.00 31.81 3.06
2120 3138 5.447010 GCACAGTTTAGAAGAGCATGTCATC 60.447 44.000 0.00 0.00 0.00 2.92
2343 3364 9.610104 TTATGTCTAGTATCCTATTTAGGCCAA 57.390 33.333 5.01 0.00 43.31 4.52
2567 3712 7.588497 AATTTACAAGAAAGAAGAGTTGCCT 57.412 32.000 0.00 0.00 0.00 4.75
2756 3901 6.827641 CACGTTATGCCGTTATAATAGCAAT 58.172 36.000 14.15 7.64 39.45 3.56
2787 3932 6.149474 GGTATTACATATCCACATGAGTTGGC 59.851 42.308 0.00 0.00 0.00 4.52
2824 3984 7.462109 TGTTTACTAACTTTGCATGCTTTTG 57.538 32.000 20.33 8.93 35.24 2.44
2844 4004 3.689347 TGTTCTCCATGTTTGCTATGCT 58.311 40.909 0.00 0.00 0.00 3.79
2852 4012 2.150390 TGTTTGCTATGCTGCTCGAAA 58.850 42.857 0.00 0.00 0.00 3.46
2920 4080 4.377841 CCTGAATCTTTGTTCTGTTCTCGC 60.378 45.833 0.00 0.00 0.00 5.03
3108 4382 6.702282 GCTTGTAAGATAGCTGGGTAGTAAAG 59.298 42.308 0.00 0.00 34.57 1.85
3122 4506 6.162079 GGGTAGTAAAGTAACTCAGTTGGTC 58.838 44.000 0.00 0.00 0.00 4.02
3457 5035 8.182227 GGAGTACCAAGTATTTGCTTAAACATC 58.818 37.037 0.00 0.00 35.97 3.06
3523 5101 5.055812 TGATTTGTCTTTGTTGCCAATTCC 58.944 37.500 0.00 0.00 0.00 3.01
4278 5865 8.537223 CATCTTGCTAATTTTCATGCATGTTAC 58.463 33.333 25.43 11.61 35.27 2.50
4287 5874 5.372343 TTCATGCATGTTACTACCTCCAT 57.628 39.130 25.43 0.00 0.00 3.41
4290 5877 3.792401 TGCATGTTACTACCTCCATTCG 58.208 45.455 0.00 0.00 0.00 3.34
4349 5936 5.189180 GCCCCAGCATCTTATATTTAGGAG 58.811 45.833 0.00 0.00 39.53 3.69
4351 5938 6.070194 GCCCCAGCATCTTATATTTAGGAGTA 60.070 42.308 0.00 0.00 39.53 2.59
4488 6077 3.694072 TGTCAGTTTTGGACTTCTGGTTG 59.306 43.478 0.00 0.00 36.10 3.77
4527 6116 7.065120 AGATCTCTAAGATGAGGGTTGAATG 57.935 40.000 0.00 0.00 34.53 2.67
4543 6132 2.164219 TGAATGGAGGCGCTTTGAATTC 59.836 45.455 7.64 11.06 0.00 2.17
4683 6272 7.928307 AATACATCAAGCACACTTAATGTCT 57.072 32.000 0.00 0.00 40.14 3.41
4911 6501 9.577110 TTTGTCATCATGATATGCTTTTCTTTC 57.423 29.630 8.15 0.00 0.00 2.62
4912 6502 8.515695 TGTCATCATGATATGCTTTTCTTTCT 57.484 30.769 8.15 0.00 0.00 2.52
4913 6503 8.963725 TGTCATCATGATATGCTTTTCTTTCTT 58.036 29.630 8.15 0.00 0.00 2.52
5094 6689 2.569059 CACGATCTGATCCTGCCATTT 58.431 47.619 11.84 0.00 0.00 2.32
5227 9546 1.005975 GGATTTCGATGTTCGTGCTCG 60.006 52.381 0.81 0.81 41.35 5.03
5390 9709 7.170658 GTCCTACTCGTACAGAACTAATCGTAT 59.829 40.741 0.00 0.00 0.00 3.06
5421 9740 7.284489 TCCTCAAAAGAAATTAATCATACCCCG 59.716 37.037 0.00 0.00 0.00 5.73
5434 9753 1.636148 TACCCCGGCCTATGATGTAC 58.364 55.000 0.00 0.00 0.00 2.90
5435 9754 0.105142 ACCCCGGCCTATGATGTACT 60.105 55.000 0.00 0.00 0.00 2.73
5436 9755 0.608640 CCCCGGCCTATGATGTACTC 59.391 60.000 0.00 0.00 0.00 2.59
5437 9756 0.608640 CCCGGCCTATGATGTACTCC 59.391 60.000 0.00 0.00 0.00 3.85
5456 9775 3.542648 TCCGTGGTCTATCTGTGTAGAG 58.457 50.000 0.00 0.00 36.14 2.43
5591 9910 5.823045 ACTCACTGTTTTTCTCCCAGTTTAG 59.177 40.000 0.00 0.00 37.34 1.85
5625 10325 4.753516 TGATGGGACGTAATTCTGTCAT 57.246 40.909 10.95 0.00 36.83 3.06
5626 10326 5.862678 TGATGGGACGTAATTCTGTCATA 57.137 39.130 10.95 1.75 36.83 2.15
5627 10327 5.597806 TGATGGGACGTAATTCTGTCATAC 58.402 41.667 10.95 3.31 36.83 2.39
5628 10328 5.362717 TGATGGGACGTAATTCTGTCATACT 59.637 40.000 10.95 0.00 36.83 2.12
5629 10329 5.258456 TGGGACGTAATTCTGTCATACTC 57.742 43.478 10.95 0.00 36.83 2.59
5630 10330 4.098960 TGGGACGTAATTCTGTCATACTCC 59.901 45.833 10.95 4.59 36.83 3.85
5631 10331 4.501058 GGGACGTAATTCTGTCATACTCCC 60.501 50.000 10.95 0.00 36.83 4.30
5632 10332 4.341520 GGACGTAATTCTGTCATACTCCCT 59.658 45.833 10.95 0.00 36.83 4.20
5633 10333 5.507650 GGACGTAATTCTGTCATACTCCCTC 60.508 48.000 10.95 0.00 36.83 4.30
5634 10334 4.341520 ACGTAATTCTGTCATACTCCCTCC 59.658 45.833 0.00 0.00 0.00 4.30
5635 10335 4.556898 CGTAATTCTGTCATACTCCCTCCG 60.557 50.000 0.00 0.00 0.00 4.63
5636 10336 2.526888 TTCTGTCATACTCCCTCCGT 57.473 50.000 0.00 0.00 0.00 4.69
5637 10337 2.054232 TCTGTCATACTCCCTCCGTC 57.946 55.000 0.00 0.00 0.00 4.79
5638 10338 1.564818 TCTGTCATACTCCCTCCGTCT 59.435 52.381 0.00 0.00 0.00 4.18
5639 10339 1.950909 CTGTCATACTCCCTCCGTCTC 59.049 57.143 0.00 0.00 0.00 3.36
5640 10340 1.283905 TGTCATACTCCCTCCGTCTCA 59.716 52.381 0.00 0.00 0.00 3.27
5641 10341 2.091830 TGTCATACTCCCTCCGTCTCAT 60.092 50.000 0.00 0.00 0.00 2.90
5642 10342 3.137728 TGTCATACTCCCTCCGTCTCATA 59.862 47.826 0.00 0.00 0.00 2.15
5643 10343 4.142790 GTCATACTCCCTCCGTCTCATAA 58.857 47.826 0.00 0.00 0.00 1.90
5644 10344 4.767928 GTCATACTCCCTCCGTCTCATAAT 59.232 45.833 0.00 0.00 0.00 1.28
5645 10345 4.767409 TCATACTCCCTCCGTCTCATAATG 59.233 45.833 0.00 0.00 0.00 1.90
5646 10346 3.033659 ACTCCCTCCGTCTCATAATGT 57.966 47.619 0.00 0.00 0.00 2.71
5647 10347 4.180377 ACTCCCTCCGTCTCATAATGTA 57.820 45.455 0.00 0.00 0.00 2.29
5648 10348 4.543689 ACTCCCTCCGTCTCATAATGTAA 58.456 43.478 0.00 0.00 0.00 2.41
5649 10349 4.585162 ACTCCCTCCGTCTCATAATGTAAG 59.415 45.833 0.00 0.00 0.00 2.34
5650 10350 4.800023 TCCCTCCGTCTCATAATGTAAGA 58.200 43.478 0.00 0.00 0.00 2.10
5651 10351 5.394738 TCCCTCCGTCTCATAATGTAAGAT 58.605 41.667 0.00 0.00 0.00 2.40
5652 10352 5.243954 TCCCTCCGTCTCATAATGTAAGATG 59.756 44.000 0.00 0.00 0.00 2.90
5653 10353 5.011125 CCCTCCGTCTCATAATGTAAGATGT 59.989 44.000 0.00 0.00 0.00 3.06
5654 10354 6.463049 CCCTCCGTCTCATAATGTAAGATGTT 60.463 42.308 0.00 0.00 0.00 2.71
5655 10355 6.986817 CCTCCGTCTCATAATGTAAGATGTTT 59.013 38.462 0.00 0.00 0.00 2.83
5656 10356 8.141909 CCTCCGTCTCATAATGTAAGATGTTTA 58.858 37.037 0.00 0.00 0.00 2.01
5657 10357 9.698309 CTCCGTCTCATAATGTAAGATGTTTAT 57.302 33.333 0.00 0.00 0.00 1.40
5677 10377 9.990360 TGTTTATTGAATCTAGTGTAGTGTCAA 57.010 29.630 0.00 0.00 35.64 3.18
5701 10401 7.579425 AAAAACGTTTTTACATTACGAGACG 57.421 32.000 31.82 0.00 38.50 4.18
5702 10402 4.891277 ACGTTTTTACATTACGAGACGG 57.109 40.909 0.00 0.00 38.56 4.79
5703 10403 4.545610 ACGTTTTTACATTACGAGACGGA 58.454 39.130 0.00 0.00 38.56 4.69
5704 10404 4.618489 ACGTTTTTACATTACGAGACGGAG 59.382 41.667 0.00 0.00 38.56 4.63
5705 10405 4.030977 CGTTTTTACATTACGAGACGGAGG 59.969 45.833 0.00 0.00 37.47 4.30
5706 10406 3.788333 TTTACATTACGAGACGGAGGG 57.212 47.619 0.00 0.00 0.00 4.30
5707 10407 2.715749 TACATTACGAGACGGAGGGA 57.284 50.000 0.00 0.00 0.00 4.20
5708 10408 1.390565 ACATTACGAGACGGAGGGAG 58.609 55.000 0.00 0.00 0.00 4.30
5709 10409 1.340795 ACATTACGAGACGGAGGGAGT 60.341 52.381 0.00 0.00 0.00 3.85
5710 10410 2.092753 ACATTACGAGACGGAGGGAGTA 60.093 50.000 0.00 0.00 0.00 2.59
5711 10411 2.029838 TTACGAGACGGAGGGAGTAC 57.970 55.000 0.00 0.00 0.00 2.73
5712 10412 0.904649 TACGAGACGGAGGGAGTACA 59.095 55.000 0.00 0.00 0.00 2.90
5713 10413 0.255318 ACGAGACGGAGGGAGTACAT 59.745 55.000 0.00 0.00 0.00 2.29
5714 10414 1.340795 ACGAGACGGAGGGAGTACATT 60.341 52.381 0.00 0.00 0.00 2.71
5715 10415 2.092753 ACGAGACGGAGGGAGTACATTA 60.093 50.000 0.00 0.00 0.00 1.90
5716 10416 2.290093 CGAGACGGAGGGAGTACATTAC 59.710 54.545 0.00 0.00 0.00 1.89
5717 10417 3.285484 GAGACGGAGGGAGTACATTACA 58.715 50.000 0.00 0.00 0.00 2.41
5718 10418 3.890147 GAGACGGAGGGAGTACATTACAT 59.110 47.826 0.00 0.00 0.00 2.29
5719 10419 3.890147 AGACGGAGGGAGTACATTACATC 59.110 47.826 0.00 0.00 0.00 3.06
5720 10420 3.890147 GACGGAGGGAGTACATTACATCT 59.110 47.826 0.00 0.00 0.00 2.90
5721 10421 5.057843 ACGGAGGGAGTACATTACATCTA 57.942 43.478 0.00 0.00 0.00 1.98
5722 10422 5.071370 ACGGAGGGAGTACATTACATCTAG 58.929 45.833 0.00 0.00 0.00 2.43
5744 10444 5.178797 AGTACATTACATCTCTGCAACACC 58.821 41.667 0.00 0.00 0.00 4.16
5855 10628 1.444836 TGCTACGTTTGCACCCATAC 58.555 50.000 11.10 0.00 35.31 2.39
5858 10631 2.419021 GCTACGTTTGCACCCATACCTA 60.419 50.000 0.00 0.00 0.00 3.08
5914 10690 8.049721 ACCTAATCTTGTCTTTCCAGAATAAGG 58.950 37.037 0.00 0.00 31.11 2.69
6120 10924 1.078709 CACTGAACTATGCCGTGTGG 58.921 55.000 0.00 0.00 38.77 4.17
6165 10973 1.247567 GTGGTCCATTCTTGTGGGTG 58.752 55.000 0.00 0.00 39.80 4.61
6179 10987 1.032014 TGGGTGAAGCAAAGCAGAAC 58.968 50.000 0.00 0.00 0.00 3.01
6199 11007 2.140717 CTTCCGCTTGAACTAAACGGT 58.859 47.619 0.00 0.00 44.17 4.83
6200 11008 1.787012 TCCGCTTGAACTAAACGGTC 58.213 50.000 0.00 0.00 44.17 4.79
6323 11131 2.494918 CAGGACCCCATCGACGAC 59.505 66.667 0.00 0.00 0.00 4.34
6469 11278 5.050295 CCCAAAACTAGAGTGAAGAACGAAC 60.050 44.000 0.00 0.00 0.00 3.95
7024 11833 4.988598 ACGCCCAGCACGGTGAAG 62.989 66.667 13.29 2.70 36.85 3.02
7165 11974 1.226547 GCCTCTCGTGCTCTCGAAG 60.227 63.158 0.00 0.00 39.34 3.79
7275 12084 4.559063 CGGGGCAGAGGCAGATGG 62.559 72.222 0.00 0.00 43.71 3.51
7276 12085 3.092511 GGGGCAGAGGCAGATGGA 61.093 66.667 0.00 0.00 43.71 3.41
7277 12086 2.509916 GGGCAGAGGCAGATGGAG 59.490 66.667 0.00 0.00 43.71 3.86
7278 12087 2.203181 GGCAGAGGCAGATGGAGC 60.203 66.667 0.00 0.00 43.71 4.70
7279 12088 2.588314 GCAGAGGCAGATGGAGCG 60.588 66.667 0.00 0.00 40.72 5.03
7280 12089 2.108566 CAGAGGCAGATGGAGCGG 59.891 66.667 0.00 0.00 0.00 5.52
7281 12090 3.160047 AGAGGCAGATGGAGCGGG 61.160 66.667 0.00 0.00 0.00 6.13
7282 12091 4.247380 GAGGCAGATGGAGCGGGG 62.247 72.222 0.00 0.00 0.00 5.73
7286 12095 3.473647 CAGATGGAGCGGGGCAGA 61.474 66.667 0.00 0.00 0.00 4.26
7287 12096 3.160047 AGATGGAGCGGGGCAGAG 61.160 66.667 0.00 0.00 0.00 3.35
7288 12097 4.247380 GATGGAGCGGGGCAGAGG 62.247 72.222 0.00 0.00 0.00 3.69
7390 12206 2.223112 CGCCCATCTTTTCACTCATTCG 60.223 50.000 0.00 0.00 0.00 3.34
7391 12207 2.749621 GCCCATCTTTTCACTCATTCGT 59.250 45.455 0.00 0.00 0.00 3.85
7392 12208 3.191371 GCCCATCTTTTCACTCATTCGTT 59.809 43.478 0.00 0.00 0.00 3.85
7393 12209 4.672801 GCCCATCTTTTCACTCATTCGTTC 60.673 45.833 0.00 0.00 0.00 3.95
7448 12264 1.594862 GAGATCTTTGAACGCATCGGG 59.405 52.381 0.00 0.00 0.00 5.14
7513 12329 1.374758 GCACAACGTCTCCCTCAGG 60.375 63.158 0.00 0.00 0.00 3.86
7514 12330 1.293498 CACAACGTCTCCCTCAGGG 59.707 63.158 1.80 1.80 46.11 4.45
7515 12331 1.152312 ACAACGTCTCCCTCAGGGT 60.152 57.895 10.50 0.00 44.74 4.34
7516 12332 0.763223 ACAACGTCTCCCTCAGGGTT 60.763 55.000 10.50 0.00 44.74 4.11
7517 12333 0.320771 CAACGTCTCCCTCAGGGTTG 60.321 60.000 10.50 2.14 44.74 3.77
7518 12334 1.481056 AACGTCTCCCTCAGGGTTGG 61.481 60.000 10.50 1.46 44.74 3.77
7519 12335 2.671682 GTCTCCCTCAGGGTTGGC 59.328 66.667 10.50 1.47 44.74 4.52
7520 12336 2.610859 TCTCCCTCAGGGTTGGCC 60.611 66.667 10.50 0.00 44.74 5.36
7521 12337 2.612115 CTCCCTCAGGGTTGGCCT 60.612 66.667 10.50 0.00 44.74 5.19
7522 12338 2.610859 TCCCTCAGGGTTGGCCTC 60.611 66.667 10.50 0.00 44.74 4.70
7523 12339 4.101448 CCCTCAGGGTTGGCCTCG 62.101 72.222 0.00 0.00 38.25 4.63
7524 12340 4.785453 CCTCAGGGTTGGCCTCGC 62.785 72.222 3.32 5.86 34.45 5.03
7536 12352 2.829003 CCTCGCCCTCACGCTCTA 60.829 66.667 0.00 0.00 0.00 2.43
7537 12353 2.409651 CTCGCCCTCACGCTCTAC 59.590 66.667 0.00 0.00 0.00 2.59
7538 12354 2.045242 TCGCCCTCACGCTCTACT 60.045 61.111 0.00 0.00 0.00 2.57
7539 12355 2.103143 CGCCCTCACGCTCTACTG 59.897 66.667 0.00 0.00 0.00 2.74
7540 12356 2.701780 CGCCCTCACGCTCTACTGT 61.702 63.158 0.00 0.00 0.00 3.55
7541 12357 1.153745 GCCCTCACGCTCTACTGTG 60.154 63.158 0.00 0.00 37.44 3.66
7542 12358 1.153745 CCCTCACGCTCTACTGTGC 60.154 63.158 0.00 0.00 36.06 4.57
7543 12359 1.599606 CCCTCACGCTCTACTGTGCT 61.600 60.000 0.00 0.00 36.06 4.40
7544 12360 0.457509 CCTCACGCTCTACTGTGCTG 60.458 60.000 0.00 0.00 36.06 4.41
7545 12361 0.242286 CTCACGCTCTACTGTGCTGT 59.758 55.000 0.00 0.00 36.06 4.40
7546 12362 0.039165 TCACGCTCTACTGTGCTGTG 60.039 55.000 0.00 0.00 37.90 3.66
7547 12363 1.373497 ACGCTCTACTGTGCTGTGC 60.373 57.895 0.00 0.00 0.00 4.57
7548 12364 1.080230 CGCTCTACTGTGCTGTGCT 60.080 57.895 0.00 0.00 0.00 4.40
7549 12365 1.349982 CGCTCTACTGTGCTGTGCTG 61.350 60.000 0.00 0.00 0.00 4.41
7550 12366 0.320247 GCTCTACTGTGCTGTGCTGT 60.320 55.000 0.00 0.00 0.00 4.40
7551 12367 1.426423 CTCTACTGTGCTGTGCTGTG 58.574 55.000 0.00 0.00 0.00 3.66
7552 12368 0.601046 TCTACTGTGCTGTGCTGTGC 60.601 55.000 0.00 0.00 0.00 4.57
7553 12369 0.602106 CTACTGTGCTGTGCTGTGCT 60.602 55.000 0.00 0.00 0.00 4.40
7554 12370 0.881600 TACTGTGCTGTGCTGTGCTG 60.882 55.000 0.00 0.00 0.00 4.41
7555 12371 3.538028 CTGTGCTGTGCTGTGCTGC 62.538 63.158 0.00 0.00 0.00 5.25
7556 12372 3.285215 GTGCTGTGCTGTGCTGCT 61.285 61.111 0.00 0.00 0.00 4.24
7557 12373 3.284449 TGCTGTGCTGTGCTGCTG 61.284 61.111 0.00 0.00 0.00 4.41
7558 12374 4.039357 GCTGTGCTGTGCTGCTGG 62.039 66.667 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 1.077787 GGACATCCAACCGCCATCA 60.078 57.895 0.00 0.00 35.64 3.07
26 28 2.511600 CTTCGCCCACGGGACATC 60.512 66.667 6.21 0.00 40.63 3.06
27 29 3.000819 TCTTCGCCCACGGGACAT 61.001 61.111 6.21 0.00 40.63 3.06
33 35 4.452733 GGTCCCTCTTCGCCCACG 62.453 72.222 0.00 0.00 42.01 4.94
41 43 0.995024 CATGAACAGGGGTCCCTCTT 59.005 55.000 8.15 0.28 46.28 2.85
66 69 2.298158 CTTCGGCCACCTATGCGTCT 62.298 60.000 2.24 0.00 0.00 4.18
73 76 1.381327 CCTCCTCTTCGGCCACCTA 60.381 63.158 2.24 0.00 0.00 3.08
96 99 4.141965 ATGTCATCCGCGGTCGCA 62.142 61.111 27.15 19.37 42.06 5.10
163 166 2.835764 TGGACTTATTAGCCTCGTGGTT 59.164 45.455 5.26 1.21 35.27 3.67
178 181 0.391597 ACGGTGTCGAACATGGACTT 59.608 50.000 0.00 0.00 40.11 3.01
179 182 1.201647 CTACGGTGTCGAACATGGACT 59.798 52.381 0.00 0.00 40.11 3.85
196 199 0.097325 CTCGAGTCTGCCGTGTCTAC 59.903 60.000 3.62 0.00 0.00 2.59
205 208 4.428615 ACTCTTTCTTACTCGAGTCTGC 57.571 45.455 23.89 0.00 31.51 4.26
349 389 0.828022 ATCTAAATGACCGTCCGCCA 59.172 50.000 0.00 0.00 0.00 5.69
353 393 7.605410 TTCAAACTAATCTAAATGACCGTCC 57.395 36.000 0.00 0.00 0.00 4.79
489 535 1.141657 CAGCCAGGCCCGCATATATAT 59.858 52.381 8.22 0.00 0.00 0.86
493 539 4.275508 CCAGCCAGGCCCGCATAT 62.276 66.667 8.22 0.00 0.00 1.78
507 553 1.410004 TACTCGGGTTAGCCATCCAG 58.590 55.000 0.00 0.00 36.17 3.86
517 563 1.549170 GTGGACAGTGATACTCGGGTT 59.451 52.381 0.00 0.00 0.00 4.11
523 569 4.955811 TTTGTGAGTGGACAGTGATACT 57.044 40.909 0.00 0.00 0.00 2.12
555 604 4.331968 TCTTCAACGCAAACCCTTATGAT 58.668 39.130 0.00 0.00 0.00 2.45
557 606 4.082787 ACATCTTCAACGCAAACCCTTATG 60.083 41.667 0.00 0.00 0.00 1.90
595 644 6.759497 AGTCTTTATTGGCCATGTTCTTAC 57.241 37.500 6.09 0.00 0.00 2.34
604 653 2.205342 AGGGCTAGTCTTTATTGGCCA 58.795 47.619 0.00 0.00 44.44 5.36
664 714 1.808343 TCAAGTCTTAGCTCACGCGTA 59.192 47.619 13.44 0.00 42.32 4.42
669 719 3.743396 CCTGTGTTCAAGTCTTAGCTCAC 59.257 47.826 0.00 0.00 0.00 3.51
676 726 1.871080 CTCGCCTGTGTTCAAGTCTT 58.129 50.000 0.00 0.00 0.00 3.01
713 763 1.271543 CCATGAAGAACAGACTGGGCA 60.272 52.381 7.51 0.00 0.00 5.36
720 770 8.783093 CAATTTTGTAGTACCATGAAGAACAGA 58.217 33.333 0.00 0.00 0.00 3.41
728 793 8.918202 AGACTTTCAATTTTGTAGTACCATGA 57.082 30.769 0.00 0.00 0.00 3.07
812 1298 8.593945 ATTGGCCAATCAATTAAAGAGAAGTA 57.406 30.769 25.73 0.00 34.01 2.24
813 1299 6.916360 TTGGCCAATCAATTAAAGAGAAGT 57.084 33.333 16.05 0.00 0.00 3.01
814 1300 8.469200 TGTATTGGCCAATCAATTAAAGAGAAG 58.531 33.333 33.89 0.00 38.24 2.85
853 1339 4.236935 TCCGTGTGAATTTCCGTTACTAC 58.763 43.478 0.00 0.00 0.00 2.73
1026 1757 1.615384 CCTTGGCAAGAAGAAGGGGAG 60.615 57.143 28.18 3.67 33.81 4.30
1307 2044 0.680618 CAAGCAAGCAAATCCACCCA 59.319 50.000 0.00 0.00 0.00 4.51
1333 2070 0.387929 TTTCGTCGAGCACCTCAAGT 59.612 50.000 0.00 0.00 0.00 3.16
1395 2132 1.376683 GTCGCATACCAAGGCCACA 60.377 57.895 5.01 0.00 0.00 4.17
1556 2293 3.709633 AGCAGCAGACGCATCCCA 61.710 61.111 0.00 0.00 42.27 4.37
1645 2386 2.959030 AGCGGATGCATCAGAAGTAGTA 59.041 45.455 27.98 0.00 46.23 1.82
1646 2387 1.759445 AGCGGATGCATCAGAAGTAGT 59.241 47.619 27.98 4.16 46.23 2.73
1647 2388 2.402305 GAGCGGATGCATCAGAAGTAG 58.598 52.381 27.98 11.05 46.23 2.57
1685 2426 5.333299 AGTACCGTGACAACTATATGCAA 57.667 39.130 0.00 0.00 0.00 4.08
1698 2439 1.483415 GCTCCCCATAAAGTACCGTGA 59.517 52.381 0.00 0.00 0.00 4.35
1723 2464 4.398319 CCATTGACTAACCCTGAAACAGT 58.602 43.478 0.00 0.00 0.00 3.55
1758 2499 9.244292 CCACCAGCTAGTATGATTAATCTACTA 57.756 37.037 21.11 21.11 0.00 1.82
1764 2505 6.900194 ACAACCACCAGCTAGTATGATTAAT 58.100 36.000 0.00 0.00 0.00 1.40
1765 2506 6.308015 ACAACCACCAGCTAGTATGATTAA 57.692 37.500 0.00 0.00 0.00 1.40
1768 2513 4.517285 CAACAACCACCAGCTAGTATGAT 58.483 43.478 0.00 0.00 0.00 2.45
1799 2544 2.401583 TCAGATGCCGCAACAACTAT 57.598 45.000 0.00 0.00 0.00 2.12
1824 2569 1.732941 TGGCATTTGTAGCGGTACAG 58.267 50.000 24.81 15.99 40.33 2.74
1875 2893 0.403271 ACAGGCCATGAAAGCAGAGT 59.597 50.000 5.01 0.00 0.00 3.24
1901 2919 8.725148 CATTCCAGTTCAGTATATTATCAAGGC 58.275 37.037 0.00 0.00 0.00 4.35
1912 2930 4.307032 AACCAGCATTCCAGTTCAGTAT 57.693 40.909 0.00 0.00 0.00 2.12
1925 2943 5.243730 ACAGCAAAAACTACATAACCAGCAT 59.756 36.000 0.00 0.00 0.00 3.79
1993 3011 6.306356 GCAATCTGCATTTACACAACTTACAG 59.694 38.462 0.00 0.00 44.26 2.74
2056 3074 6.774354 AAAAATACACTGTGTAGTACCACG 57.226 37.500 23.35 0.00 36.14 4.94
2120 3138 1.033746 AACTGGGGCGCATCAATCAG 61.034 55.000 10.83 9.32 0.00 2.90
2343 3364 3.953542 GGATACTCTTCCACCCCAAAT 57.046 47.619 0.00 0.00 35.72 2.32
2368 3389 6.039717 ACATTGTGCAGTTATAATAGCAAGGG 59.960 38.462 14.06 8.55 38.91 3.95
2402 3423 4.651778 TCCTGAAGAACGGTTGAATGAAT 58.348 39.130 0.00 0.00 0.00 2.57
2756 3901 5.638530 TGTGGATATGTAATACCCTGCAA 57.361 39.130 0.00 0.00 0.00 4.08
2787 3932 6.157211 AGTTAGTAAACAACTCGATGGACAG 58.843 40.000 0.00 0.00 39.80 3.51
2824 3984 3.733077 GCAGCATAGCAAACATGGAGAAC 60.733 47.826 0.00 0.00 0.00 3.01
2844 4004 3.113322 GTCGCATACACTATTTCGAGCA 58.887 45.455 0.00 0.00 0.00 4.26
2852 4012 7.553881 AAAGCTATTTTGTCGCATACACTAT 57.446 32.000 0.00 0.00 38.00 2.12
2920 4080 5.121221 AGTGCCTTTTAGTCCAAAAATCG 57.879 39.130 0.00 0.00 35.71 3.34
3108 4382 3.258622 AGCACTAGGACCAACTGAGTTAC 59.741 47.826 0.00 0.00 0.00 2.50
3175 4753 5.158141 TCTCAAGGTAGGATTCCTATGCAT 58.842 41.667 15.44 3.79 38.48 3.96
3313 4891 7.408132 TGTATAGAAGCTGCGTCATTTAATC 57.592 36.000 17.46 2.71 0.00 1.75
3491 5069 7.096065 GGCAACAAAGACAAATCAGAAATACAC 60.096 37.037 0.00 0.00 0.00 2.90
3919 5505 6.822667 ACACAATGAAGATTACTCATGCAA 57.177 33.333 0.00 0.00 0.00 4.08
4030 5616 2.553602 GCCCAATTTTGCCAAAGAAAGG 59.446 45.455 0.00 0.00 0.00 3.11
4150 5736 8.120140 ACTAACTTACTAAGGTAACAGACAGG 57.880 38.462 0.88 0.00 41.41 4.00
4278 5865 8.295288 ACGTCTTATATTTACGAATGGAGGTAG 58.705 37.037 10.10 0.00 39.80 3.18
4287 5874 4.810491 GCCCCAACGTCTTATATTTACGAA 59.190 41.667 10.10 0.00 39.80 3.85
4290 5877 5.121105 ACTGCCCCAACGTCTTATATTTAC 58.879 41.667 0.00 0.00 0.00 2.01
4364 5951 8.225603 AGAAACACAGTTGTTCTGATACAATT 57.774 30.769 1.79 3.20 45.69 2.32
4450 6037 4.903054 ACTGACAAGATCAAGATGCAAGA 58.097 39.130 0.00 0.00 36.69 3.02
4451 6038 5.624344 AACTGACAAGATCAAGATGCAAG 57.376 39.130 0.00 0.00 36.69 4.01
4527 6116 1.003438 GATCGAATTCAAAGCGCCTCC 60.003 52.381 2.29 0.00 0.00 4.30
4622 6211 4.571919 TGGTTAAGTTACCAAGGTGATCG 58.428 43.478 1.07 0.00 44.97 3.69
4677 6266 2.705658 TCGGCTCCCAATATCAGACATT 59.294 45.455 0.00 0.00 0.00 2.71
4683 6272 1.138859 CACAGTCGGCTCCCAATATCA 59.861 52.381 0.00 0.00 0.00 2.15
4778 6368 8.383318 ACAGTATCAGATTTATTGTGGTATGC 57.617 34.615 0.00 0.00 0.00 3.14
4872 6462 2.603075 TGACAAATTGGGAAGGAGGG 57.397 50.000 0.00 0.00 0.00 4.30
4970 6561 8.940397 TGTTCTCTGATCATATAGTCCATGTA 57.060 34.615 0.00 0.00 0.00 2.29
4981 6572 4.758773 TGCACCATGTTCTCTGATCATA 57.241 40.909 0.00 0.00 0.00 2.15
5041 6636 5.763876 AGGCCACAACTTAAATCTAGACT 57.236 39.130 5.01 0.00 0.00 3.24
5074 6669 2.251409 AATGGCAGGATCAGATCGTG 57.749 50.000 23.45 23.45 45.32 4.35
5094 6689 1.337703 GCACCAACACAAATCAGAGCA 59.662 47.619 0.00 0.00 0.00 4.26
5217 9536 0.985549 CTTGTCTAGCGAGCACGAAC 59.014 55.000 8.01 0.00 42.66 3.95
5227 9546 1.669779 CAAGGCAGCATCTTGTCTAGC 59.330 52.381 0.00 0.00 37.43 3.42
5390 9709 8.899887 ATGATTAATTTCTTTTGAGGAAGGGA 57.100 30.769 0.00 0.00 0.00 4.20
5421 9740 1.000955 CCACGGAGTACATCATAGGCC 59.999 57.143 0.00 0.00 41.61 5.19
5434 9753 3.542648 TCTACACAGATAGACCACGGAG 58.457 50.000 0.00 0.00 0.00 4.63
5435 9754 3.542648 CTCTACACAGATAGACCACGGA 58.457 50.000 0.00 0.00 0.00 4.69
5436 9755 2.033550 GCTCTACACAGATAGACCACGG 59.966 54.545 0.00 0.00 0.00 4.94
5437 9756 2.946329 AGCTCTACACAGATAGACCACG 59.054 50.000 0.00 0.00 0.00 4.94
5555 9874 3.678056 ACAGTGAGTTCGCAGGATTTA 57.322 42.857 0.00 0.00 0.00 1.40
5622 10322 4.448720 TTATGAGACGGAGGGAGTATGA 57.551 45.455 0.00 0.00 0.00 2.15
5625 10325 4.180377 ACATTATGAGACGGAGGGAGTA 57.820 45.455 0.00 0.00 0.00 2.59
5626 10326 3.033659 ACATTATGAGACGGAGGGAGT 57.966 47.619 0.00 0.00 0.00 3.85
5627 10327 4.827835 TCTTACATTATGAGACGGAGGGAG 59.172 45.833 0.00 0.00 0.00 4.30
5628 10328 4.800023 TCTTACATTATGAGACGGAGGGA 58.200 43.478 0.00 0.00 0.00 4.20
5629 10329 5.011125 ACATCTTACATTATGAGACGGAGGG 59.989 44.000 0.00 0.00 0.00 4.30
5630 10330 6.090483 ACATCTTACATTATGAGACGGAGG 57.910 41.667 0.00 0.00 0.00 4.30
5631 10331 9.698309 ATAAACATCTTACATTATGAGACGGAG 57.302 33.333 0.00 0.00 0.00 4.63
5651 10351 9.990360 TTGACACTACACTAGATTCAATAAACA 57.010 29.630 0.00 0.00 30.64 2.83
5677 10377 6.628461 CCGTCTCGTAATGTAAAAACGTTTTT 59.372 34.615 33.94 33.94 42.51 1.94
5678 10378 6.019156 TCCGTCTCGTAATGTAAAAACGTTTT 60.019 34.615 20.26 20.26 37.83 2.43
5679 10379 5.461737 TCCGTCTCGTAATGTAAAAACGTTT 59.538 36.000 7.96 7.96 37.83 3.60
5680 10380 4.981674 TCCGTCTCGTAATGTAAAAACGTT 59.018 37.500 0.00 0.00 37.83 3.99
5681 10381 4.545610 TCCGTCTCGTAATGTAAAAACGT 58.454 39.130 0.00 0.00 37.83 3.99
5682 10382 4.030977 CCTCCGTCTCGTAATGTAAAAACG 59.969 45.833 0.00 0.00 37.96 3.60
5683 10383 4.328169 CCCTCCGTCTCGTAATGTAAAAAC 59.672 45.833 0.00 0.00 0.00 2.43
5684 10384 4.220382 TCCCTCCGTCTCGTAATGTAAAAA 59.780 41.667 0.00 0.00 0.00 1.94
5685 10385 3.763360 TCCCTCCGTCTCGTAATGTAAAA 59.237 43.478 0.00 0.00 0.00 1.52
5686 10386 3.355378 TCCCTCCGTCTCGTAATGTAAA 58.645 45.455 0.00 0.00 0.00 2.01
5687 10387 2.947652 CTCCCTCCGTCTCGTAATGTAA 59.052 50.000 0.00 0.00 0.00 2.41
5688 10388 2.092753 ACTCCCTCCGTCTCGTAATGTA 60.093 50.000 0.00 0.00 0.00 2.29
5689 10389 1.340795 ACTCCCTCCGTCTCGTAATGT 60.341 52.381 0.00 0.00 0.00 2.71
5690 10390 1.390565 ACTCCCTCCGTCTCGTAATG 58.609 55.000 0.00 0.00 0.00 1.90
5691 10391 2.092753 TGTACTCCCTCCGTCTCGTAAT 60.093 50.000 0.00 0.00 0.00 1.89
5692 10392 1.278985 TGTACTCCCTCCGTCTCGTAA 59.721 52.381 0.00 0.00 0.00 3.18
5693 10393 0.904649 TGTACTCCCTCCGTCTCGTA 59.095 55.000 0.00 0.00 0.00 3.43
5694 10394 0.255318 ATGTACTCCCTCCGTCTCGT 59.745 55.000 0.00 0.00 0.00 4.18
5695 10395 1.390565 AATGTACTCCCTCCGTCTCG 58.609 55.000 0.00 0.00 0.00 4.04
5696 10396 3.285484 TGTAATGTACTCCCTCCGTCTC 58.715 50.000 0.00 0.00 0.00 3.36
5697 10397 3.377253 TGTAATGTACTCCCTCCGTCT 57.623 47.619 0.00 0.00 0.00 4.18
5698 10398 3.890147 AGATGTAATGTACTCCCTCCGTC 59.110 47.826 0.00 0.00 0.00 4.79
5699 10399 3.912248 AGATGTAATGTACTCCCTCCGT 58.088 45.455 0.00 0.00 0.00 4.69
5700 10400 5.071370 ACTAGATGTAATGTACTCCCTCCG 58.929 45.833 0.00 0.00 0.00 4.63
5701 10401 7.002879 TGTACTAGATGTAATGTACTCCCTCC 58.997 42.308 0.00 0.00 36.98 4.30
5702 10402 8.638629 ATGTACTAGATGTAATGTACTCCCTC 57.361 38.462 0.00 0.00 36.98 4.30
5713 10413 9.131791 TGCAGAGATGTAATGTACTAGATGTAA 57.868 33.333 0.00 0.00 32.25 2.41
5714 10414 8.691661 TGCAGAGATGTAATGTACTAGATGTA 57.308 34.615 0.00 0.00 0.00 2.29
5715 10415 7.588497 TGCAGAGATGTAATGTACTAGATGT 57.412 36.000 0.00 0.00 0.00 3.06
5716 10416 7.922811 TGTTGCAGAGATGTAATGTACTAGATG 59.077 37.037 0.00 0.00 0.00 2.90
5717 10417 7.923344 GTGTTGCAGAGATGTAATGTACTAGAT 59.077 37.037 0.00 0.00 0.00 1.98
5718 10418 7.258441 GTGTTGCAGAGATGTAATGTACTAGA 58.742 38.462 0.00 0.00 0.00 2.43
5719 10419 6.477033 GGTGTTGCAGAGATGTAATGTACTAG 59.523 42.308 0.00 0.00 0.00 2.57
5720 10420 6.154534 AGGTGTTGCAGAGATGTAATGTACTA 59.845 38.462 0.00 0.00 0.00 1.82
5721 10421 5.046304 AGGTGTTGCAGAGATGTAATGTACT 60.046 40.000 0.00 0.00 0.00 2.73
5722 10422 5.178797 AGGTGTTGCAGAGATGTAATGTAC 58.821 41.667 0.00 0.00 0.00 2.90
5789 10489 7.171678 AGACTTCACCATTTCTCGAAACTAAAG 59.828 37.037 0.00 0.00 32.51 1.85
5855 10628 3.871006 TCGCATTTGTCACAGCTATTAGG 59.129 43.478 0.00 0.00 0.00 2.69
5858 10631 4.970662 ATTCGCATTTGTCACAGCTATT 57.029 36.364 0.00 0.00 0.00 1.73
5914 10690 2.109425 AGATAAAACCCTCACACGCC 57.891 50.000 0.00 0.00 0.00 5.68
5973 10750 6.327279 CATCATAAGGATGCATTCACACAT 57.673 37.500 7.96 0.00 46.35 3.21
5974 10751 5.761165 CATCATAAGGATGCATTCACACA 57.239 39.130 7.96 0.00 46.35 3.72
6063 10860 6.983307 TCAGAAGAAGAATCTAAGCTGCATAC 59.017 38.462 1.02 0.00 33.77 2.39
6135 10943 5.636903 AGAATGGACCACAATATGCTAGT 57.363 39.130 0.00 0.00 0.00 2.57
6138 10946 4.400251 CACAAGAATGGACCACAATATGCT 59.600 41.667 0.00 0.00 0.00 3.79
6139 10947 4.440525 CCACAAGAATGGACCACAATATGC 60.441 45.833 0.00 0.00 43.02 3.14
6140 10948 4.098349 CCCACAAGAATGGACCACAATATG 59.902 45.833 0.00 0.00 43.02 1.78
6165 10973 1.664302 GCGGAAGTTCTGCTTTGCTTC 60.664 52.381 26.28 0.00 45.06 3.86
6199 11007 0.378962 CCTGCAACGAAAAACACCGA 59.621 50.000 0.00 0.00 0.00 4.69
6200 11008 0.593773 CCCTGCAACGAAAAACACCG 60.594 55.000 0.00 0.00 0.00 4.94
6257 11065 1.517257 GATGACTGGACACTCGGCG 60.517 63.158 0.00 0.00 0.00 6.46
6323 11131 1.136147 GGCTGCACGAAAGCATCAG 59.864 57.895 0.50 0.00 44.68 2.90
6469 11278 1.347097 CCATCGGCGATCATAGCGTG 61.347 60.000 21.25 7.70 35.00 5.34
6559 11368 6.109156 TCATCACAGTAGCTTTTAGGTTCA 57.891 37.500 0.00 0.00 0.00 3.18
6560 11369 6.818644 TGATCATCACAGTAGCTTTTAGGTTC 59.181 38.462 0.00 0.00 0.00 3.62
6561 11370 6.711277 TGATCATCACAGTAGCTTTTAGGTT 58.289 36.000 0.00 0.00 0.00 3.50
6695 11504 4.828296 CCACCAGCATCCCCAGGC 62.828 72.222 0.00 0.00 0.00 4.85
6706 11515 2.981909 CAGCAGCACCACCACCAG 60.982 66.667 0.00 0.00 0.00 4.00
6835 11644 4.845580 AAGCCCATGCCGAGCTCG 62.846 66.667 29.06 29.06 38.69 5.03
6898 11707 0.038892 ACTACGGCACTAACACGGTG 60.039 55.000 6.58 6.58 37.70 4.94
6903 11712 2.094906 CAGCACTACTACGGCACTAACA 60.095 50.000 0.00 0.00 0.00 2.41
6907 11716 0.898789 ACCAGCACTACTACGGCACT 60.899 55.000 0.00 0.00 0.00 4.40
6991 11800 2.010582 GCGTCATCTCCTTCCTCGCT 62.011 60.000 0.00 0.00 39.26 4.93
7270 12079 3.160047 CTCTGCCCCGCTCCATCT 61.160 66.667 0.00 0.00 0.00 2.90
7271 12080 4.247380 CCTCTGCCCCGCTCCATC 62.247 72.222 0.00 0.00 0.00 3.51
7280 12089 4.486503 CTGCCTCTGCCTCTGCCC 62.487 72.222 0.00 0.00 36.33 5.36
7281 12090 3.388703 CTCTGCCTCTGCCTCTGCC 62.389 68.421 0.00 0.00 36.33 4.85
7282 12091 2.187424 CTCTGCCTCTGCCTCTGC 59.813 66.667 0.00 0.00 36.33 4.26
7283 12092 2.901813 CCTCTGCCTCTGCCTCTG 59.098 66.667 0.00 0.00 36.33 3.35
7284 12093 3.082701 GCCTCTGCCTCTGCCTCT 61.083 66.667 0.00 0.00 36.33 3.69
7519 12335 2.829003 TAGAGCGTGAGGGCGAGG 60.829 66.667 0.00 0.00 38.18 4.63
7520 12336 2.115911 AGTAGAGCGTGAGGGCGAG 61.116 63.158 0.00 0.00 38.18 5.03
7521 12337 2.045242 AGTAGAGCGTGAGGGCGA 60.045 61.111 0.00 0.00 38.18 5.54
7522 12338 2.103143 CAGTAGAGCGTGAGGGCG 59.897 66.667 0.00 0.00 38.18 6.13
7523 12339 1.153745 CACAGTAGAGCGTGAGGGC 60.154 63.158 0.00 0.00 35.02 5.19
7524 12340 1.153745 GCACAGTAGAGCGTGAGGG 60.154 63.158 0.00 0.00 35.02 4.30
7525 12341 0.457509 CAGCACAGTAGAGCGTGAGG 60.458 60.000 0.00 0.00 36.39 3.86
7526 12342 0.242286 ACAGCACAGTAGAGCGTGAG 59.758 55.000 0.00 0.00 36.39 3.51
7527 12343 0.039165 CACAGCACAGTAGAGCGTGA 60.039 55.000 0.00 0.00 37.72 4.35
7528 12344 1.621301 GCACAGCACAGTAGAGCGTG 61.621 60.000 0.00 0.00 38.13 5.34
7529 12345 1.373497 GCACAGCACAGTAGAGCGT 60.373 57.895 0.00 0.00 36.39 5.07
7530 12346 1.080230 AGCACAGCACAGTAGAGCG 60.080 57.895 0.00 0.00 36.39 5.03
7531 12347 0.320247 ACAGCACAGCACAGTAGAGC 60.320 55.000 0.00 0.00 0.00 4.09
7532 12348 1.426423 CACAGCACAGCACAGTAGAG 58.574 55.000 0.00 0.00 0.00 2.43
7533 12349 0.601046 GCACAGCACAGCACAGTAGA 60.601 55.000 0.00 0.00 0.00 2.59
7534 12350 0.602106 AGCACAGCACAGCACAGTAG 60.602 55.000 0.00 0.00 0.00 2.57
7535 12351 0.881600 CAGCACAGCACAGCACAGTA 60.882 55.000 0.00 0.00 0.00 2.74
7536 12352 2.184830 CAGCACAGCACAGCACAGT 61.185 57.895 0.00 0.00 0.00 3.55
7537 12353 2.637589 CAGCACAGCACAGCACAG 59.362 61.111 0.00 0.00 0.00 3.66
7538 12354 3.588906 GCAGCACAGCACAGCACA 61.589 61.111 0.00 0.00 0.00 4.57
7539 12355 3.285215 AGCAGCACAGCACAGCAC 61.285 61.111 0.00 0.00 36.85 4.40
7540 12356 3.284449 CAGCAGCACAGCACAGCA 61.284 61.111 0.00 0.00 36.85 4.41
7541 12357 4.039357 CCAGCAGCACAGCACAGC 62.039 66.667 0.00 0.00 36.85 4.40


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

AutoCloner maintained by Alex Coulton.