Multiple sequence alignment - TraesCS6D01G120100

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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 TraesCS6D01G120100 chr6D 100.000 4003 0 0 1 4003 85093881 85089879 0.000000e+00 7393.0
1 TraesCS6D01G120100 chr6D 91.304 161 11 3 3309 3468 453191632 453191790 2.420000e-52 217.0
2 TraesCS6D01G120100 chr6D 80.952 168 29 3 2185 2352 85105127 85105291 3.250000e-26 130.0
3 TraesCS6D01G120100 chr6D 83.099 142 19 4 2211 2351 85100089 85100226 1.510000e-24 124.0
4 TraesCS6D01G120100 chr6D 75.419 179 39 4 1663 1839 85099751 85099926 9.220000e-12 82.4
5 TraesCS6D01G120100 chr6A 90.292 1813 102 30 1538 3305 101999580 102001363 0.000000e+00 2305.0
6 TraesCS6D01G120100 chr6A 91.638 586 24 12 971 1539 101999061 101999638 0.000000e+00 787.0
7 TraesCS6D01G120100 chr6A 90.809 544 43 6 3465 4003 102001358 102001899 0.000000e+00 721.0
8 TraesCS6D01G120100 chr6A 89.474 456 17 16 482 929 101998617 101999049 7.560000e-152 547.0
9 TraesCS6D01G120100 chr6A 92.453 159 8 3 3306 3464 145188615 145188769 1.450000e-54 224.0
10 TraesCS6D01G120100 chr6A 91.925 161 11 2 3306 3465 440537718 440537559 1.450000e-54 224.0
11 TraesCS6D01G120100 chr6A 83.234 167 25 1 2185 2351 101991371 101991208 2.490000e-32 150.0
12 TraesCS6D01G120100 chr6A 80.114 176 32 2 2184 2356 101991690 101991515 1.170000e-25 128.0
13 TraesCS6D01G120100 chr6A 83.621 116 14 5 278 389 330805224 330805338 1.970000e-18 104.0
14 TraesCS6D01G120100 chr6A 87.097 93 11 1 257 349 608383896 608383987 1.970000e-18 104.0
15 TraesCS6D01G120100 chr6B 92.328 1525 99 9 1538 3058 161494330 161495840 0.000000e+00 2152.0
16 TraesCS6D01G120100 chr6B 87.155 1378 96 32 203 1546 161493064 161494394 0.000000e+00 1489.0
17 TraesCS6D01G120100 chr6B 88.026 618 63 9 2423 3036 161497898 161498508 0.000000e+00 721.0
18 TraesCS6D01G120100 chr6B 87.668 446 46 7 3564 4003 161498931 161499373 9.920000e-141 510.0
19 TraesCS6D01G120100 chr6B 94.000 100 5 1 104 203 161492920 161493018 2.490000e-32 150.0
20 TraesCS6D01G120100 chr6B 80.500 200 30 8 2178 2371 161458995 161458799 1.160000e-30 145.0
21 TraesCS6D01G120100 chr6B 82.143 168 27 1 2185 2352 161458670 161458506 1.500000e-29 141.0
22 TraesCS6D01G120100 chr6B 80.814 172 26 6 2182 2351 161462982 161462816 1.170000e-25 128.0
23 TraesCS6D01G120100 chr6B 83.065 124 14 5 163 285 641674182 641674065 5.470000e-19 106.0
24 TraesCS6D01G120100 chr6B 75.978 179 38 5 1663 1839 161463285 161463110 1.980000e-13 87.9
25 TraesCS6D01G120100 chr6B 85.897 78 11 0 2040 2117 161268754 161268677 2.560000e-12 84.2
26 TraesCS6D01G120100 chr1D 93.038 158 7 3 3308 3464 112352033 112352187 1.120000e-55 228.0
27 TraesCS6D01G120100 chr1D 82.222 135 18 6 203 334 420554622 420554491 1.180000e-20 111.0
28 TraesCS6D01G120100 chr2A 92.949 156 10 1 3309 3464 59640682 59640836 4.030000e-55 226.0
29 TraesCS6D01G120100 chr7B 93.377 151 7 2 3300 3450 94186870 94187017 1.870000e-53 220.0
30 TraesCS6D01G120100 chr7B 84.545 110 13 3 175 284 478835141 478835036 5.470000e-19 106.0
31 TraesCS6D01G120100 chr7B 83.621 116 14 5 278 389 245015623 245015737 1.970000e-18 104.0
32 TraesCS6D01G120100 chr7B 84.259 108 13 3 177 284 657549126 657549023 7.080000e-18 102.0
33 TraesCS6D01G120100 chr3D 91.195 159 11 3 3307 3464 504989334 504989490 3.130000e-51 213.0
34 TraesCS6D01G120100 chr3D 85.849 106 11 3 181 286 613409988 613409887 4.230000e-20 110.0
35 TraesCS6D01G120100 chr3D 83.962 106 14 3 278 381 307237110 307237214 9.160000e-17 99.0
36 TraesCS6D01G120100 chr2D 90.000 170 7 7 3309 3469 474662607 474662775 1.130000e-50 211.0
37 TraesCS6D01G120100 chr2D 83.929 112 9 7 278 381 372927010 372927120 9.160000e-17 99.0
38 TraesCS6D01G120100 chr4D 89.017 173 12 6 3299 3468 491693049 491692881 1.460000e-49 207.0
39 TraesCS6D01G120100 chr7A 92.593 81 6 0 203 283 61816002 61815922 2.530000e-22 117.0
40 TraesCS6D01G120100 chr7A 82.114 123 15 7 278 394 422141615 422141494 9.160000e-17 99.0
41 TraesCS6D01G120100 chr1A 90.361 83 8 0 203 285 238655867 238655785 4.230000e-20 110.0
42 TraesCS6D01G120100 chr5B 84.071 113 14 3 180 292 81177018 81177126 5.470000e-19 106.0
43 TraesCS6D01G120100 chr7D 82.906 117 13 7 278 389 374085228 374085114 9.160000e-17 99.0


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 TraesCS6D01G120100 chr6D 85089879 85093881 4002 True 7393.0 7393 100.00000 1 4003 1 chr6D.!!$R1 4002
1 TraesCS6D01G120100 chr6A 101998617 102001899 3282 False 1090.0 2305 90.55325 482 4003 4 chr6A.!!$F4 3521
2 TraesCS6D01G120100 chr6B 161492920 161499373 6453 False 1004.4 2152 89.83540 104 4003 5 chr6B.!!$F1 3899

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
519 568 0.102120 TGAAACTTTTGCACGCAGGG 59.898 50.0 0.0 0.0 0.00 4.45 F
2129 2220 0.106519 AACCAACCTGAAGCAGCAGT 60.107 50.0 0.0 0.0 34.06 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2242 2336 0.173481 CGAGCCACCGAGAATTCTCA 59.827 55.0 29.93 0.0 43.0 3.27 R
3161 5940 0.181350 ACATCCCGGCTCTTCATTCC 59.819 55.0 0.00 0.0 0.0 3.01 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 27 9.672673 TTCCAAATCCAAATTAAAGAAACACAA 57.327 25.926 0.00 0.00 0.00 3.33
27 28 9.672673 TCCAAATCCAAATTAAAGAAACACAAA 57.327 25.926 0.00 0.00 0.00 2.83
61 62 5.741388 ATGTGGATAAAAGTCGATCTTGC 57.259 39.130 0.00 0.00 36.40 4.01
62 63 4.574892 TGTGGATAAAAGTCGATCTTGCA 58.425 39.130 0.00 0.00 36.40 4.08
63 64 5.185454 TGTGGATAAAAGTCGATCTTGCAT 58.815 37.500 0.00 0.00 36.40 3.96
64 65 5.647658 TGTGGATAAAAGTCGATCTTGCATT 59.352 36.000 0.00 0.00 36.40 3.56
65 66 6.821160 TGTGGATAAAAGTCGATCTTGCATTA 59.179 34.615 0.00 0.00 36.40 1.90
66 67 7.335673 TGTGGATAAAAGTCGATCTTGCATTAA 59.664 33.333 0.00 0.00 36.40 1.40
67 68 8.345565 GTGGATAAAAGTCGATCTTGCATTAAT 58.654 33.333 0.00 0.00 36.40 1.40
68 69 8.902806 TGGATAAAAGTCGATCTTGCATTAATT 58.097 29.630 0.00 0.00 36.40 1.40
69 70 9.736023 GGATAAAAGTCGATCTTGCATTAATTT 57.264 29.630 0.00 0.00 36.40 1.82
72 73 6.875926 AAGTCGATCTTGCATTAATTTTGC 57.124 33.333 6.20 6.20 40.55 3.68
73 74 6.199937 AGTCGATCTTGCATTAATTTTGCT 57.800 33.333 12.56 0.00 40.77 3.91
74 75 6.261118 AGTCGATCTTGCATTAATTTTGCTC 58.739 36.000 12.56 3.50 40.77 4.26
75 76 5.170270 GTCGATCTTGCATTAATTTTGCTCG 59.830 40.000 12.56 12.43 40.77 5.03
76 77 4.085924 CGATCTTGCATTAATTTTGCTCGC 60.086 41.667 12.56 0.00 40.77 5.03
77 78 4.171663 TCTTGCATTAATTTTGCTCGCA 57.828 36.364 12.56 0.00 40.77 5.10
78 79 4.554292 TCTTGCATTAATTTTGCTCGCAA 58.446 34.783 12.56 0.00 40.77 4.85
79 80 4.987285 TCTTGCATTAATTTTGCTCGCAAA 59.013 33.333 12.62 12.62 43.23 3.68
90 91 5.388225 TTTGCTCGCAAAATCTTTGAAAC 57.612 34.783 14.09 0.00 42.16 2.78
91 92 4.305989 TGCTCGCAAAATCTTTGAAACT 57.694 36.364 3.35 0.00 0.00 2.66
92 93 5.431420 TGCTCGCAAAATCTTTGAAACTA 57.569 34.783 3.35 0.00 0.00 2.24
93 94 6.012658 TGCTCGCAAAATCTTTGAAACTAT 57.987 33.333 3.35 0.00 0.00 2.12
94 95 6.446318 TGCTCGCAAAATCTTTGAAACTATT 58.554 32.000 3.35 0.00 0.00 1.73
95 96 6.363088 TGCTCGCAAAATCTTTGAAACTATTG 59.637 34.615 3.35 0.00 0.00 1.90
96 97 6.183360 GCTCGCAAAATCTTTGAAACTATTGG 60.183 38.462 3.35 0.00 0.00 3.16
97 98 6.976088 TCGCAAAATCTTTGAAACTATTGGA 58.024 32.000 3.35 0.00 0.00 3.53
98 99 7.083858 TCGCAAAATCTTTGAAACTATTGGAG 58.916 34.615 3.35 0.00 0.00 3.86
99 100 6.863126 CGCAAAATCTTTGAAACTATTGGAGT 59.137 34.615 3.35 0.00 41.56 3.85
121 122 8.718734 GGAGTTACGGATATCAATTTTGTATCC 58.281 37.037 4.83 15.01 37.63 2.59
125 126 6.053005 ACGGATATCAATTTTGTATCCACGT 58.947 36.000 19.98 14.43 39.10 4.49
128 129 8.221100 CGGATATCAATTTTGTATCCACGTAAG 58.779 37.037 19.98 0.00 39.10 2.34
158 159 7.116376 AGGATATCAATTTTGTAGTCATACGCG 59.884 37.037 3.53 3.53 34.39 6.01
211 258 9.601217 TCTCTCTGTTCCTAAGTAAATAAATGC 57.399 33.333 0.00 0.00 0.00 3.56
213 260 7.494625 TCTCTGTTCCTAAGTAAATAAATGCCG 59.505 37.037 0.00 0.00 0.00 5.69
218 265 5.066764 TCCTAAGTAAATAAATGCCGCAACC 59.933 40.000 0.00 0.00 0.00 3.77
219 266 3.414549 AGTAAATAAATGCCGCAACCG 57.585 42.857 0.00 0.00 0.00 4.44
221 268 3.940221 AGTAAATAAATGCCGCAACCGTA 59.060 39.130 0.00 0.00 0.00 4.02
280 327 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
287 334 1.502039 TGGGACGGAGGGAGTACATAT 59.498 52.381 0.00 0.00 0.00 1.78
292 339 3.890147 GACGGAGGGAGTACATATGAAGT 59.110 47.826 10.38 0.00 0.00 3.01
298 345 7.385205 CGGAGGGAGTACATATGAAGTAAAATG 59.615 40.741 10.38 0.00 0.00 2.32
380 429 8.011290 AGCTTATACTTAGAAATGGAGGGAGTA 58.989 37.037 0.00 0.00 0.00 2.59
384 433 8.980832 ATACTTAGAAATGGAGGGAGTATCAT 57.019 34.615 0.00 0.00 36.25 2.45
386 435 8.429237 ACTTAGAAATGGAGGGAGTATCATAG 57.571 38.462 0.00 0.00 36.25 2.23
387 436 8.013667 ACTTAGAAATGGAGGGAGTATCATAGT 58.986 37.037 0.00 0.00 36.25 2.12
412 461 9.463443 GTATAAATTAATGAACAGGAACCATGC 57.537 33.333 0.00 0.00 0.00 4.06
421 470 2.299867 ACAGGAACCATGCCAATGTTTC 59.700 45.455 0.00 0.00 35.15 2.78
429 478 3.244146 CCATGCCAATGTTTCAAACCTCA 60.244 43.478 0.00 0.00 31.27 3.86
452 501 3.495001 GCTTCCATTCCATAGAACGCTAC 59.505 47.826 0.00 0.00 33.97 3.58
518 567 1.587946 GTTGAAACTTTTGCACGCAGG 59.412 47.619 0.00 0.00 0.00 4.85
519 568 0.102120 TGAAACTTTTGCACGCAGGG 59.898 50.000 0.00 0.00 0.00 4.45
520 569 1.215014 GAAACTTTTGCACGCAGGGC 61.215 55.000 0.00 0.00 0.00 5.19
521 570 1.954362 AAACTTTTGCACGCAGGGCA 61.954 50.000 1.27 1.27 40.00 5.36
553 602 3.724478 TGGACTCTCTCTCTCTCTCTCT 58.276 50.000 0.00 0.00 0.00 3.10
554 603 3.706594 TGGACTCTCTCTCTCTCTCTCTC 59.293 52.174 0.00 0.00 0.00 3.20
555 604 3.964031 GGACTCTCTCTCTCTCTCTCTCT 59.036 52.174 0.00 0.00 0.00 3.10
556 605 4.202202 GGACTCTCTCTCTCTCTCTCTCTG 60.202 54.167 0.00 0.00 0.00 3.35
557 606 4.357325 ACTCTCTCTCTCTCTCTCTCTGT 58.643 47.826 0.00 0.00 0.00 3.41
558 607 4.404073 ACTCTCTCTCTCTCTCTCTCTGTC 59.596 50.000 0.00 0.00 0.00 3.51
559 608 4.614475 TCTCTCTCTCTCTCTCTCTGTCT 58.386 47.826 0.00 0.00 0.00 3.41
560 609 4.646945 TCTCTCTCTCTCTCTCTCTGTCTC 59.353 50.000 0.00 0.00 0.00 3.36
568 617 2.430694 TCTCTCTCTGTCTCCTCTCTCG 59.569 54.545 0.00 0.00 0.00 4.04
569 618 1.134521 TCTCTCTGTCTCCTCTCTCGC 60.135 57.143 0.00 0.00 0.00 5.03
570 619 0.615850 TCTCTGTCTCCTCTCTCGCA 59.384 55.000 0.00 0.00 0.00 5.10
571 620 1.003696 TCTCTGTCTCCTCTCTCGCAA 59.996 52.381 0.00 0.00 0.00 4.85
572 621 1.815613 CTCTGTCTCCTCTCTCGCAAA 59.184 52.381 0.00 0.00 0.00 3.68
749 804 2.020720 TCACGCAAGAAAGGCTTTTGA 58.979 42.857 14.66 9.64 43.62 2.69
868 923 2.424956 GCTTCACCCATCACAATCTTCC 59.575 50.000 0.00 0.00 0.00 3.46
889 944 8.826765 TCTTCCCTCTACATAGTTCAATTTTCT 58.173 33.333 0.00 0.00 0.00 2.52
905 960 9.929722 TTCAATTTTCTCGTATTATTTCATCCG 57.070 29.630 0.00 0.00 0.00 4.18
906 961 9.104965 TCAATTTTCTCGTATTATTTCATCCGT 57.895 29.630 0.00 0.00 0.00 4.69
979 1035 3.163616 TCTCGGGTAAAAATGGCCTTT 57.836 42.857 3.32 0.00 0.00 3.11
1131 1204 3.497405 CCTCTCTCTCTCTCATCCTCCTG 60.497 56.522 0.00 0.00 0.00 3.86
1151 1224 3.261677 CCTCCCCGAAAACCCCCA 61.262 66.667 0.00 0.00 0.00 4.96
1576 1658 4.821589 CCGCTCCGGCACTTCTCC 62.822 72.222 0.00 0.00 41.17 3.71
1577 1659 3.764466 CGCTCCGGCACTTCTCCT 61.764 66.667 0.00 0.00 38.60 3.69
1578 1660 2.125350 GCTCCGGCACTTCTCCTG 60.125 66.667 0.00 0.00 38.54 3.86
1579 1661 2.125350 CTCCGGCACTTCTCCTGC 60.125 66.667 0.00 0.00 0.00 4.85
1580 1662 3.997064 CTCCGGCACTTCTCCTGCG 62.997 68.421 0.00 0.00 35.31 5.18
1581 1663 4.379243 CCGGCACTTCTCCTGCGT 62.379 66.667 0.00 0.00 35.31 5.24
1582 1664 3.114616 CGGCACTTCTCCTGCGTG 61.115 66.667 0.00 0.00 35.31 5.34
1583 1665 2.743928 GGCACTTCTCCTGCGTGG 60.744 66.667 0.00 0.00 35.31 4.94
1584 1666 2.743928 GCACTTCTCCTGCGTGGG 60.744 66.667 0.00 0.00 36.20 4.61
1585 1667 2.743928 CACTTCTCCTGCGTGGGC 60.744 66.667 0.00 0.00 40.52 5.36
1586 1668 4.379243 ACTTCTCCTGCGTGGGCG 62.379 66.667 0.00 0.00 44.10 6.13
1587 1669 4.069232 CTTCTCCTGCGTGGGCGA 62.069 66.667 0.00 0.00 44.10 5.54
1621 1703 4.101448 GAGTCGTGCCCAGGCCAT 62.101 66.667 5.01 0.00 41.09 4.40
2129 2220 0.106519 AACCAACCTGAAGCAGCAGT 60.107 50.000 0.00 0.00 34.06 4.40
2233 2327 4.569023 TACGCGGCGCAGATCAGG 62.569 66.667 32.61 15.83 0.00 3.86
2242 2336 4.457496 CAGATCAGGCACGCCGGT 62.457 66.667 1.90 0.00 41.95 5.28
2471 2565 2.976494 AAACCTCAACCAGCCACCCG 62.976 60.000 0.00 0.00 0.00 5.28
2526 2620 2.202797 CATGGACCTCGCCGACAG 60.203 66.667 0.00 0.00 0.00 3.51
2614 2708 4.980805 GTGTTCGCCGACCTGCCA 62.981 66.667 0.00 0.00 0.00 4.92
2659 2753 1.556911 GAGCTCCTCAAGGACATGGAA 59.443 52.381 0.87 0.00 39.78 3.53
2691 2785 2.288334 TGATGGCTTGATTTGTGTGTGC 60.288 45.455 0.00 0.00 0.00 4.57
2710 2804 1.349259 CTCGTCCGGCGTAAAACAGG 61.349 60.000 16.00 0.00 42.13 4.00
2783 2910 7.866393 AGCTGATCAAATTCTCTTTTGTTTGAG 59.134 33.333 0.00 0.00 41.97 3.02
2801 2928 6.427853 TGTTTGAGTATGAGGAAACATGAGTG 59.572 38.462 0.00 0.00 0.00 3.51
2854 2981 8.432805 AGGTAATGTTATCTCTTACCCATGAAG 58.567 37.037 0.00 0.00 43.52 3.02
2859 2986 4.803329 ATCTCTTACCCATGAAGCCATT 57.197 40.909 0.00 0.00 0.00 3.16
2994 3122 5.403466 GGTTTTGAACTGATGAATTGAGCAC 59.597 40.000 0.00 0.00 0.00 4.40
3000 3128 3.004629 ACTGATGAATTGAGCACGCAAAA 59.995 39.130 0.00 0.00 0.00 2.44
3043 3172 5.596836 AAATGGTGATATGTGCGGAAAAT 57.403 34.783 0.00 0.00 0.00 1.82
3051 3180 1.309950 TGTGCGGAAAATTCGGTGAA 58.690 45.000 3.19 0.00 0.00 3.18
3087 5864 5.456548 TTAGTGAGATGTGTAACCGACAA 57.543 39.130 0.00 0.00 40.66 3.18
3131 5908 6.588348 TCATGACTAAATTACATGTCGCAG 57.412 37.500 0.00 0.00 41.14 5.18
3161 5940 8.099364 ACACCTAATTTAGTCAGAAATGTGTG 57.901 34.615 8.88 5.75 34.61 3.82
3179 5959 0.181114 TGGAATGAAGAGCCGGGATG 59.819 55.000 2.18 0.00 0.00 3.51
3201 5981 8.829612 GGATGTGAAATGTTTGTGAAAAATTCT 58.170 29.630 0.00 0.00 0.00 2.40
3263 6044 5.649782 ATTCAGCTGTTTTAGTTCCCATG 57.350 39.130 14.67 0.00 0.00 3.66
3296 6176 7.607223 ACATATTTGGATGAATTTGTTGTTGGG 59.393 33.333 0.00 0.00 30.39 4.12
3297 6177 3.399440 TGGATGAATTTGTTGTTGGGC 57.601 42.857 0.00 0.00 0.00 5.36
3298 6178 2.702478 TGGATGAATTTGTTGTTGGGCA 59.298 40.909 0.00 0.00 0.00 5.36
3299 6179 3.327172 TGGATGAATTTGTTGTTGGGCAT 59.673 39.130 0.00 0.00 0.00 4.40
3300 6180 4.529769 TGGATGAATTTGTTGTTGGGCATA 59.470 37.500 0.00 0.00 0.00 3.14
3301 6181 5.189342 TGGATGAATTTGTTGTTGGGCATAT 59.811 36.000 0.00 0.00 0.00 1.78
3304 6184 7.201635 GGATGAATTTGTTGTTGGGCATATTTC 60.202 37.037 0.00 0.00 0.00 2.17
3305 6185 5.636965 TGAATTTGTTGTTGGGCATATTTCG 59.363 36.000 0.00 0.00 0.00 3.46
3307 6187 4.855715 TTGTTGTTGGGCATATTTCGAA 57.144 36.364 0.00 0.00 0.00 3.71
3308 6188 4.167554 TGTTGTTGGGCATATTTCGAAC 57.832 40.909 0.00 0.00 0.00 3.95
3311 6191 3.417101 TGTTGGGCATATTTCGAACAGT 58.583 40.909 0.00 0.00 30.36 3.55
3312 6192 3.823873 TGTTGGGCATATTTCGAACAGTT 59.176 39.130 0.00 0.00 30.36 3.16
3314 6194 4.433186 TGGGCATATTTCGAACAGTTTG 57.567 40.909 0.00 0.00 0.00 2.93
3315 6195 3.823873 TGGGCATATTTCGAACAGTTTGT 59.176 39.130 0.00 0.00 0.00 2.83
3316 6196 4.083003 TGGGCATATTTCGAACAGTTTGTC 60.083 41.667 0.00 0.00 0.00 3.18
3317 6197 4.156008 GGGCATATTTCGAACAGTTTGTCT 59.844 41.667 0.00 0.00 0.00 3.41
3318 6198 5.353123 GGGCATATTTCGAACAGTTTGTCTA 59.647 40.000 0.00 0.00 0.00 2.59
3319 6199 6.128117 GGGCATATTTCGAACAGTTTGTCTAA 60.128 38.462 0.00 0.00 0.00 2.10
3320 6200 7.415206 GGGCATATTTCGAACAGTTTGTCTAAT 60.415 37.037 0.00 3.00 0.00 1.73
3321 6201 7.968405 GGCATATTTCGAACAGTTTGTCTAATT 59.032 33.333 0.00 0.00 0.00 1.40
3322 6202 9.000018 GCATATTTCGAACAGTTTGTCTAATTC 58.000 33.333 0.00 0.00 0.00 2.17
3325 6205 6.912203 TTCGAACAGTTTGTCTAATTCACA 57.088 33.333 0.00 0.00 0.00 3.58
3326 6206 7.490962 TTCGAACAGTTTGTCTAATTCACAT 57.509 32.000 0.00 0.00 0.00 3.21
3327 6207 7.117241 TCGAACAGTTTGTCTAATTCACATC 57.883 36.000 0.15 0.00 0.00 3.06
3328 6208 6.929049 TCGAACAGTTTGTCTAATTCACATCT 59.071 34.615 0.15 0.00 0.00 2.90
3329 6209 8.085909 TCGAACAGTTTGTCTAATTCACATCTA 58.914 33.333 0.15 0.00 0.00 1.98
3330 6210 8.376203 CGAACAGTTTGTCTAATTCACATCTAG 58.624 37.037 0.00 0.00 0.00 2.43
3331 6211 9.424319 GAACAGTTTGTCTAATTCACATCTAGA 57.576 33.333 0.00 0.00 0.00 2.43
3332 6212 9.950496 AACAGTTTGTCTAATTCACATCTAGAT 57.050 29.630 0.00 0.00 0.00 1.98
3333 6213 9.376075 ACAGTTTGTCTAATTCACATCTAGATG 57.624 33.333 27.63 27.63 44.15 2.90
3361 6241 7.849804 TTTTAAGGATGTCACATCTAAGCTC 57.150 36.000 17.46 0.00 0.00 4.09
3362 6242 4.414337 AAGGATGTCACATCTAAGCTCC 57.586 45.455 17.46 0.18 0.00 4.70
3363 6243 2.703007 AGGATGTCACATCTAAGCTCCC 59.297 50.000 17.46 0.00 0.00 4.30
3364 6244 2.435805 GGATGTCACATCTAAGCTCCCA 59.564 50.000 17.46 0.00 0.00 4.37
3365 6245 3.462021 GATGTCACATCTAAGCTCCCAC 58.538 50.000 10.81 0.00 0.00 4.61
3366 6246 2.256306 TGTCACATCTAAGCTCCCACA 58.744 47.619 0.00 0.00 0.00 4.17
3367 6247 2.637382 TGTCACATCTAAGCTCCCACAA 59.363 45.455 0.00 0.00 0.00 3.33
3368 6248 3.072330 TGTCACATCTAAGCTCCCACAAA 59.928 43.478 0.00 0.00 0.00 2.83
3369 6249 4.263462 TGTCACATCTAAGCTCCCACAAAT 60.263 41.667 0.00 0.00 0.00 2.32
3370 6250 5.045942 TGTCACATCTAAGCTCCCACAAATA 60.046 40.000 0.00 0.00 0.00 1.40
3371 6251 6.058183 GTCACATCTAAGCTCCCACAAATAT 58.942 40.000 0.00 0.00 0.00 1.28
3372 6252 7.147567 TGTCACATCTAAGCTCCCACAAATATA 60.148 37.037 0.00 0.00 0.00 0.86
3373 6253 7.880195 GTCACATCTAAGCTCCCACAAATATAT 59.120 37.037 0.00 0.00 0.00 0.86
3374 6254 9.100197 TCACATCTAAGCTCCCACAAATATATA 57.900 33.333 0.00 0.00 0.00 0.86
3375 6255 9.725019 CACATCTAAGCTCCCACAAATATATAA 57.275 33.333 0.00 0.00 0.00 0.98
3378 6258 8.792830 TCTAAGCTCCCACAAATATATAATGC 57.207 34.615 0.00 0.00 0.00 3.56
3379 6259 8.382405 TCTAAGCTCCCACAAATATATAATGCA 58.618 33.333 0.00 0.00 0.00 3.96
3380 6260 9.182214 CTAAGCTCCCACAAATATATAATGCAT 57.818 33.333 0.00 0.00 0.00 3.96
3382 6262 9.532494 AAGCTCCCACAAATATATAATGCATAA 57.468 29.630 0.00 0.00 0.00 1.90
3383 6263 9.532494 AGCTCCCACAAATATATAATGCATAAA 57.468 29.630 0.00 0.00 0.00 1.40
3384 6264 9.573133 GCTCCCACAAATATATAATGCATAAAC 57.427 33.333 0.00 0.00 0.00 2.01
3440 6320 3.470709 CACAAACAGAGTGGACATCAGT 58.529 45.455 0.00 0.00 33.43 3.41
3441 6321 3.879295 CACAAACAGAGTGGACATCAGTT 59.121 43.478 0.00 0.00 33.43 3.16
3442 6322 4.336433 CACAAACAGAGTGGACATCAGTTT 59.664 41.667 0.00 0.00 37.00 2.66
3443 6323 5.527214 CACAAACAGAGTGGACATCAGTTTA 59.473 40.000 0.00 0.00 35.12 2.01
3444 6324 5.760253 ACAAACAGAGTGGACATCAGTTTAG 59.240 40.000 0.00 0.00 35.12 1.85
3445 6325 5.808366 AACAGAGTGGACATCAGTTTAGA 57.192 39.130 0.00 0.00 0.00 2.10
3446 6326 6.365970 AACAGAGTGGACATCAGTTTAGAT 57.634 37.500 0.00 0.00 0.00 1.98
3458 6338 6.867550 CATCAGTTTAGATGTGTCCTAGACA 58.132 40.000 0.00 0.00 40.35 3.41
3459 6339 6.516739 TCAGTTTAGATGTGTCCTAGACAG 57.483 41.667 0.00 0.00 43.57 3.51
3460 6340 6.246163 TCAGTTTAGATGTGTCCTAGACAGA 58.754 40.000 0.00 0.00 43.57 3.41
3461 6341 6.151312 TCAGTTTAGATGTGTCCTAGACAGAC 59.849 42.308 0.00 0.00 43.57 3.51
3462 6342 5.419471 AGTTTAGATGTGTCCTAGACAGACC 59.581 44.000 0.00 0.00 43.57 3.85
3463 6343 2.741145 AGATGTGTCCTAGACAGACCC 58.259 52.381 0.00 0.00 43.57 4.46
3464 6344 2.313342 AGATGTGTCCTAGACAGACCCT 59.687 50.000 0.00 0.00 43.57 4.34
3465 6345 3.528078 AGATGTGTCCTAGACAGACCCTA 59.472 47.826 0.00 0.00 43.57 3.53
3466 6346 4.169068 AGATGTGTCCTAGACAGACCCTAT 59.831 45.833 0.00 0.00 43.57 2.57
3467 6347 4.332683 TGTGTCCTAGACAGACCCTATT 57.667 45.455 0.00 0.00 43.57 1.73
3468 6348 4.684724 TGTGTCCTAGACAGACCCTATTT 58.315 43.478 0.00 0.00 43.57 1.40
3469 6349 4.710375 TGTGTCCTAGACAGACCCTATTTC 59.290 45.833 0.00 0.00 43.57 2.17
3470 6350 3.952323 TGTCCTAGACAGACCCTATTTCG 59.048 47.826 0.00 0.00 37.67 3.46
3471 6351 4.205587 GTCCTAGACAGACCCTATTTCGA 58.794 47.826 0.00 0.00 32.09 3.71
3472 6352 4.643784 GTCCTAGACAGACCCTATTTCGAA 59.356 45.833 0.00 0.00 32.09 3.71
3473 6353 5.126707 GTCCTAGACAGACCCTATTTCGAAA 59.873 44.000 13.91 13.91 32.09 3.46
3474 6354 5.360144 TCCTAGACAGACCCTATTTCGAAAG 59.640 44.000 16.80 3.20 0.00 2.62
3475 6355 3.863041 AGACAGACCCTATTTCGAAAGC 58.137 45.455 16.80 1.79 0.00 3.51
3476 6356 2.603560 GACAGACCCTATTTCGAAAGCG 59.396 50.000 16.80 9.20 39.35 4.68
3483 6363 3.063045 CCCTATTTCGAAAGCGTTACACC 59.937 47.826 16.80 0.00 38.98 4.16
3530 6412 8.622572 ACCCATGTGAAAAATATATTTTCCCT 57.377 30.769 20.86 8.31 38.92 4.20
3531 6413 9.722317 ACCCATGTGAAAAATATATTTTCCCTA 57.278 29.630 20.86 10.68 38.92 3.53
3548 6435 8.593945 TTTTCCCTATAATGCAATGAAGAACT 57.406 30.769 0.00 0.00 0.00 3.01
3561 6450 2.951642 TGAAGAACTCACAAGGGCTTTG 59.048 45.455 7.91 7.91 42.68 2.77
3634 6547 2.879756 GCCCAGGACAATGAAGCAACTA 60.880 50.000 0.00 0.00 0.00 2.24
3658 6571 6.005066 ACCTTGACATGATGATGATGGTTA 57.995 37.500 0.00 0.00 33.36 2.85
3745 6658 6.822442 TGTGTCTGGTTTATGTCTCAAGTTA 58.178 36.000 0.00 0.00 0.00 2.24
3862 6778 0.465287 ACCACTGGCTTGCCAAAAAG 59.535 50.000 15.63 6.44 0.00 2.27
3912 6829 3.029483 TGAGCCATTGCCATCCAATTA 57.971 42.857 0.00 0.00 42.15 1.40
3916 6833 4.147321 AGCCATTGCCATCCAATTACTAG 58.853 43.478 0.00 0.00 42.15 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.672673 TTGTGTTTCTTTAATTTGGATTTGGAA 57.327 25.926 0.00 0.00 0.00 3.53
1 2 9.672673 TTTGTGTTTCTTTAATTTGGATTTGGA 57.327 25.926 0.00 0.00 0.00 3.53
35 36 8.988934 GCAAGATCGACTTTTATCCACATATAA 58.011 33.333 0.00 0.00 36.61 0.98
36 37 8.147704 TGCAAGATCGACTTTTATCCACATATA 58.852 33.333 0.00 0.00 36.61 0.86
37 38 6.992123 TGCAAGATCGACTTTTATCCACATAT 59.008 34.615 0.00 0.00 36.61 1.78
38 39 6.345298 TGCAAGATCGACTTTTATCCACATA 58.655 36.000 0.00 0.00 36.61 2.29
39 40 5.185454 TGCAAGATCGACTTTTATCCACAT 58.815 37.500 0.00 0.00 36.61 3.21
40 41 4.574892 TGCAAGATCGACTTTTATCCACA 58.425 39.130 0.00 0.00 36.61 4.17
41 42 5.741388 ATGCAAGATCGACTTTTATCCAC 57.259 39.130 0.00 0.00 36.61 4.02
42 43 7.857734 TTAATGCAAGATCGACTTTTATCCA 57.142 32.000 0.00 0.00 36.61 3.41
43 44 9.736023 AAATTAATGCAAGATCGACTTTTATCC 57.264 29.630 0.00 0.00 36.61 2.59
46 47 8.859156 GCAAAATTAATGCAAGATCGACTTTTA 58.141 29.630 10.39 0.00 43.29 1.52
47 48 7.599998 AGCAAAATTAATGCAAGATCGACTTTT 59.400 29.630 15.96 0.00 46.22 2.27
48 49 7.092716 AGCAAAATTAATGCAAGATCGACTTT 58.907 30.769 15.96 0.00 46.22 2.66
49 50 6.624423 AGCAAAATTAATGCAAGATCGACTT 58.376 32.000 15.96 0.00 46.22 3.01
50 51 6.199937 AGCAAAATTAATGCAAGATCGACT 57.800 33.333 15.96 0.00 46.22 4.18
51 52 5.170270 CGAGCAAAATTAATGCAAGATCGAC 59.830 40.000 15.96 0.00 46.22 4.20
52 53 5.265477 CGAGCAAAATTAATGCAAGATCGA 58.735 37.500 15.96 0.00 46.22 3.59
53 54 4.085924 GCGAGCAAAATTAATGCAAGATCG 60.086 41.667 15.96 15.59 46.22 3.69
54 55 4.799949 TGCGAGCAAAATTAATGCAAGATC 59.200 37.500 15.96 6.15 46.22 2.75
55 56 4.746729 TGCGAGCAAAATTAATGCAAGAT 58.253 34.783 15.96 0.00 46.22 2.40
56 57 4.171663 TGCGAGCAAAATTAATGCAAGA 57.828 36.364 15.96 0.00 46.22 3.02
57 58 4.907188 TTGCGAGCAAAATTAATGCAAG 57.093 36.364 15.96 10.89 46.22 4.01
58 59 5.663795 TTTTGCGAGCAAAATTAATGCAA 57.336 30.435 26.14 6.76 46.80 4.08
68 69 5.108517 AGTTTCAAAGATTTTGCGAGCAAA 58.891 33.333 18.01 18.01 43.23 3.68
69 70 4.681744 AGTTTCAAAGATTTTGCGAGCAA 58.318 34.783 6.39 6.39 0.00 3.91
70 71 4.305989 AGTTTCAAAGATTTTGCGAGCA 57.694 36.364 0.00 0.00 0.00 4.26
71 72 6.183360 CCAATAGTTTCAAAGATTTTGCGAGC 60.183 38.462 0.00 0.00 0.00 5.03
72 73 7.083858 TCCAATAGTTTCAAAGATTTTGCGAG 58.916 34.615 0.00 0.00 0.00 5.03
73 74 6.976088 TCCAATAGTTTCAAAGATTTTGCGA 58.024 32.000 0.00 0.00 0.00 5.10
74 75 6.863126 ACTCCAATAGTTTCAAAGATTTTGCG 59.137 34.615 0.00 0.00 33.35 4.85
75 76 8.593492 AACTCCAATAGTTTCAAAGATTTTGC 57.407 30.769 0.00 0.00 46.61 3.68
77 78 9.893305 CGTAACTCCAATAGTTTCAAAGATTTT 57.107 29.630 0.00 0.00 46.61 1.82
78 79 8.512138 CCGTAACTCCAATAGTTTCAAAGATTT 58.488 33.333 0.00 0.00 46.61 2.17
79 80 7.881232 TCCGTAACTCCAATAGTTTCAAAGATT 59.119 33.333 0.00 0.00 46.61 2.40
80 81 7.391620 TCCGTAACTCCAATAGTTTCAAAGAT 58.608 34.615 0.00 0.00 46.61 2.40
81 82 6.761312 TCCGTAACTCCAATAGTTTCAAAGA 58.239 36.000 0.00 0.00 46.61 2.52
82 83 7.611213 ATCCGTAACTCCAATAGTTTCAAAG 57.389 36.000 0.00 0.00 46.61 2.77
83 84 9.321562 GATATCCGTAACTCCAATAGTTTCAAA 57.678 33.333 0.00 0.00 46.61 2.69
84 85 8.479689 TGATATCCGTAACTCCAATAGTTTCAA 58.520 33.333 0.00 0.00 46.61 2.69
85 86 8.014070 TGATATCCGTAACTCCAATAGTTTCA 57.986 34.615 0.00 0.00 46.61 2.69
86 87 8.882415 TTGATATCCGTAACTCCAATAGTTTC 57.118 34.615 0.00 0.00 46.61 2.78
87 88 9.847224 AATTGATATCCGTAACTCCAATAGTTT 57.153 29.630 0.00 0.00 46.61 2.66
89 90 9.847224 AAAATTGATATCCGTAACTCCAATAGT 57.153 29.630 0.00 0.00 41.49 2.12
91 92 9.621629 ACAAAATTGATATCCGTAACTCCAATA 57.378 29.630 0.00 0.00 0.00 1.90
92 93 8.519799 ACAAAATTGATATCCGTAACTCCAAT 57.480 30.769 0.00 0.00 0.00 3.16
93 94 7.931578 ACAAAATTGATATCCGTAACTCCAA 57.068 32.000 0.00 0.00 0.00 3.53
94 95 9.268268 GATACAAAATTGATATCCGTAACTCCA 57.732 33.333 0.00 0.00 0.00 3.86
95 96 8.718734 GGATACAAAATTGATATCCGTAACTCC 58.281 37.037 13.81 0.00 34.65 3.85
121 122 9.840427 ACAAAATTGATATCCTTTTCTTACGTG 57.160 29.630 0.00 0.00 0.00 4.49
149 150 7.479291 ACATAAAATACAACAAACGCGTATGAC 59.521 33.333 14.46 0.00 0.00 3.06
191 192 5.648526 TGCGGCATTTATTTACTTAGGAACA 59.351 36.000 0.00 0.00 0.00 3.18
211 258 1.787012 AAGTTGTACTACGGTTGCGG 58.213 50.000 1.74 0.00 0.00 5.69
235 282 4.691216 GTCCCAGCTTTGTACTAACTTCAG 59.309 45.833 0.00 0.00 0.00 3.02
237 284 4.451435 GTGTCCCAGCTTTGTACTAACTTC 59.549 45.833 0.00 0.00 0.00 3.01
255 302 3.007635 CTCCGTCCCAAAATAAGTGTCC 58.992 50.000 0.00 0.00 0.00 4.02
354 403 6.847036 ACTCCCTCCATTTCTAAGTATAAGCT 59.153 38.462 0.00 0.00 0.00 3.74
362 411 8.429237 ACTATGATACTCCCTCCATTTCTAAG 57.571 38.462 0.00 0.00 0.00 2.18
386 435 9.463443 GCATGGTTCCTGTTCATTAATTTATAC 57.537 33.333 0.00 0.00 0.00 1.47
387 436 8.637986 GGCATGGTTCCTGTTCATTAATTTATA 58.362 33.333 0.00 0.00 0.00 0.98
396 445 2.307496 TTGGCATGGTTCCTGTTCAT 57.693 45.000 0.00 0.00 0.00 2.57
407 456 3.244146 TGAGGTTTGAAACATTGGCATGG 60.244 43.478 10.53 0.00 34.27 3.66
412 461 4.301628 GAAGCTGAGGTTTGAAACATTGG 58.698 43.478 10.53 1.48 0.00 3.16
421 470 2.517959 TGGAATGGAAGCTGAGGTTTG 58.482 47.619 0.00 0.00 0.00 2.93
429 478 2.171448 AGCGTTCTATGGAATGGAAGCT 59.829 45.455 12.40 7.70 44.80 3.74
452 501 3.871006 TCTTGTGATAGTAATTGCGCTGG 59.129 43.478 9.73 0.00 0.00 4.85
457 506 4.561606 ACGTCGTCTTGTGATAGTAATTGC 59.438 41.667 0.00 0.00 0.00 3.56
520 569 1.874231 GAGAGTCCATCTGCATGCATG 59.126 52.381 22.97 22.70 38.84 4.06
521 570 1.769465 AGAGAGTCCATCTGCATGCAT 59.231 47.619 22.97 3.95 38.84 3.96
553 602 1.911057 TTTGCGAGAGAGGAGACAGA 58.089 50.000 0.00 0.00 0.00 3.41
554 603 2.333014 GTTTTGCGAGAGAGGAGACAG 58.667 52.381 0.00 0.00 0.00 3.51
555 604 1.335964 CGTTTTGCGAGAGAGGAGACA 60.336 52.381 0.00 0.00 44.77 3.41
556 605 1.068472 TCGTTTTGCGAGAGAGGAGAC 60.068 52.381 0.00 0.00 45.68 3.36
557 606 1.244816 TCGTTTTGCGAGAGAGGAGA 58.755 50.000 0.00 0.00 45.68 3.71
558 607 3.794690 TCGTTTTGCGAGAGAGGAG 57.205 52.632 0.00 0.00 45.68 3.69
601 650 2.997980 TGCTTGTCTCTTTGTTCCACA 58.002 42.857 0.00 0.00 0.00 4.17
631 680 3.511540 ACTATCTCTTGTACAGCAGCACA 59.488 43.478 0.00 0.00 0.00 4.57
757 812 4.216042 CGACATAATGGATAGGCATTGCAA 59.784 41.667 11.39 0.00 0.00 4.08
845 900 2.719739 AGATTGTGATGGGTGAAGCTG 58.280 47.619 0.00 0.00 0.00 4.24
868 923 9.751542 ATACGAGAAAATTGAACTATGTAGAGG 57.248 33.333 0.00 0.00 0.00 3.69
889 944 9.590451 AGAAAAACTACGGATGAAATAATACGA 57.410 29.630 0.00 0.00 35.84 3.43
932 988 6.640907 GCTTCCGTTACAAAATTTCTGACATT 59.359 34.615 0.00 0.00 0.00 2.71
979 1035 4.119556 TGACTCCCTCTCTCTGAAAAGA 57.880 45.455 0.00 0.00 0.00 2.52
1024 1080 0.320946 TAGTACTGTTGCCGGTTGCC 60.321 55.000 5.39 0.00 40.16 4.52
1025 1081 0.794473 GTAGTACTGTTGCCGGTTGC 59.206 55.000 5.39 0.00 41.77 4.17
1026 1082 1.065358 CGTAGTACTGTTGCCGGTTG 58.935 55.000 5.39 0.00 0.00 3.77
1027 1083 0.675633 ACGTAGTACTGTTGCCGGTT 59.324 50.000 5.39 0.00 41.94 4.44
1028 1084 0.038892 CACGTAGTACTGTTGCCGGT 60.039 55.000 5.39 0.00 41.61 5.28
1029 1085 0.241749 TCACGTAGTACTGTTGCCGG 59.758 55.000 5.39 0.00 41.61 6.13
1040 1096 5.172934 TCTCAAACTTGTTTGTCACGTAGT 58.827 37.500 20.99 0.00 35.41 2.73
1131 1204 2.675423 GGGTTTTCGGGGAGGCAC 60.675 66.667 0.00 0.00 0.00 5.01
1151 1224 1.080434 GAGAGCGCGTGAGGTTCTT 60.080 57.895 8.43 0.00 0.00 2.52
1212 1294 1.878656 CGTCTTCTTCCTCCTGCCGT 61.879 60.000 0.00 0.00 0.00 5.68
1560 1642 3.764466 AGGAGAAGTGCCGGAGCG 61.764 66.667 5.05 0.00 44.31 5.03
1561 1643 2.125350 CAGGAGAAGTGCCGGAGC 60.125 66.667 5.05 0.00 40.48 4.70
1562 1644 2.125350 GCAGGAGAAGTGCCGGAG 60.125 66.667 5.05 0.00 34.67 4.63
1563 1645 4.069232 CGCAGGAGAAGTGCCGGA 62.069 66.667 5.05 0.00 37.67 5.14
1564 1646 4.379243 ACGCAGGAGAAGTGCCGG 62.379 66.667 0.00 0.00 37.67 6.13
1565 1647 3.114616 CACGCAGGAGAAGTGCCG 61.115 66.667 0.00 0.00 37.67 5.69
1566 1648 2.743928 CCACGCAGGAGAAGTGCC 60.744 66.667 0.00 0.00 41.22 5.01
1567 1649 2.743928 CCCACGCAGGAGAAGTGC 60.744 66.667 0.00 0.00 41.22 4.40
1568 1650 2.743928 GCCCACGCAGGAGAAGTG 60.744 66.667 0.00 0.00 41.22 3.16
1569 1651 4.379243 CGCCCACGCAGGAGAAGT 62.379 66.667 0.00 0.00 41.22 3.01
1570 1652 3.997064 CTCGCCCACGCAGGAGAAG 62.997 68.421 0.00 0.00 41.22 2.85
1571 1653 4.069232 CTCGCCCACGCAGGAGAA 62.069 66.667 0.00 0.00 41.22 2.87
1576 1658 4.457496 ACATCCTCGCCCACGCAG 62.457 66.667 0.00 0.00 39.84 5.18
1577 1659 4.451150 GACATCCTCGCCCACGCA 62.451 66.667 0.00 0.00 39.84 5.24
1579 1661 4.873129 CCGACATCCTCGCCCACG 62.873 72.222 0.00 0.00 41.46 4.94
1580 1662 4.530857 CCCGACATCCTCGCCCAC 62.531 72.222 0.00 0.00 41.46 4.61
1586 1668 4.530857 CACGGCCCCGACATCCTC 62.531 72.222 14.44 0.00 42.83 3.71
1620 1702 4.957684 CGCTCTCCGCCGCATCAT 62.958 66.667 0.00 0.00 34.21 2.45
1906 1997 1.352404 CCTCGACCTCGACTTAGCG 59.648 63.158 0.00 0.00 44.22 4.26
1907 1998 0.377905 GACCTCGACCTCGACTTAGC 59.622 60.000 0.00 0.00 44.22 3.09
1908 1999 0.651551 CGACCTCGACCTCGACTTAG 59.348 60.000 1.47 0.00 44.22 2.18
1930 2021 3.137459 ACCGGCAGAGAGCTCGAG 61.137 66.667 8.45 8.45 44.79 4.04
2129 2220 1.907739 CCTTCTTCCTCGCCATGGA 59.092 57.895 18.40 0.00 0.00 3.41
2233 2327 1.696832 GAGAATTCTCACCGGCGTGC 61.697 60.000 27.08 0.00 42.42 5.34
2242 2336 0.173481 CGAGCCACCGAGAATTCTCA 59.827 55.000 29.93 0.00 43.00 3.27
2338 2432 1.202405 GGTGGTTGCTTGAAGTTGGTG 60.202 52.381 0.00 0.00 0.00 4.17
2380 2474 3.263503 CTCCTCGCCGTCGTCAACA 62.264 63.158 0.00 0.00 36.96 3.33
2394 2488 3.083997 GGTCCATGGGCGACTCCT 61.084 66.667 13.02 0.00 34.39 3.69
2439 2533 0.317519 GAGGTTTGTTTTGGCCGTCG 60.318 55.000 0.00 0.00 0.00 5.12
2452 2546 1.152546 GGGTGGCTGGTTGAGGTTT 60.153 57.895 0.00 0.00 0.00 3.27
2487 2581 1.226717 GACTCCTCGCCGTCATCAC 60.227 63.158 0.00 0.00 0.00 3.06
2577 2671 1.366854 ATCGTCGAGCTGTGCGTCTA 61.367 55.000 0.00 0.00 0.00 2.59
2609 2703 1.080569 GCAAATCCAACGGTGGCAG 60.081 57.895 16.88 5.22 45.54 4.85
2614 2708 1.526575 CCTGCTGCAAATCCAACGGT 61.527 55.000 3.02 0.00 0.00 4.83
2681 2775 1.885388 CCGGACGAGCACACACAAA 60.885 57.895 0.00 0.00 0.00 2.83
2710 2804 1.696832 GGCCGCATTTCGTCTCTGTC 61.697 60.000 0.00 0.00 36.19 3.51
2783 2910 4.937620 TGAAGCACTCATGTTTCCTCATAC 59.062 41.667 0.00 0.00 43.42 2.39
2801 2928 6.382869 ACCAACATTATAGCTGAATGAAGC 57.617 37.500 22.92 0.00 43.88 3.86
2854 2981 1.230324 GTTCGGCTCCTCATAATGGC 58.770 55.000 0.00 0.00 0.00 4.40
2859 2986 2.499693 TGTGAATGTTCGGCTCCTCATA 59.500 45.455 0.00 0.00 0.00 2.15
3038 3167 4.865776 TCCACACATTTCACCGAATTTTC 58.134 39.130 0.00 0.00 0.00 2.29
3043 3172 4.720649 TTTTTCCACACATTTCACCGAA 57.279 36.364 0.00 0.00 0.00 4.30
3051 3180 8.084073 CACATCTCACTAATTTTTCCACACATT 58.916 33.333 0.00 0.00 0.00 2.71
3087 5864 0.828343 GCTATCCTACCGGGCTGAGT 60.828 60.000 6.32 0.00 34.39 3.41
3155 5932 1.679944 CCGGCTCTTCATTCCACACAT 60.680 52.381 0.00 0.00 0.00 3.21
3161 5940 0.181350 ACATCCCGGCTCTTCATTCC 59.819 55.000 0.00 0.00 0.00 3.01
3201 5981 4.171878 TCCCAATGTTTTGTGTGGACTA 57.828 40.909 0.00 0.00 32.54 2.59
3202 5982 3.025322 TCCCAATGTTTTGTGTGGACT 57.975 42.857 0.00 0.00 32.54 3.85
3279 6159 7.464444 CGAAATATGCCCAACAACAAATTCATC 60.464 37.037 0.00 0.00 0.00 2.92
3296 6176 8.895932 AATTAGACAAACTGTTCGAAATATGC 57.104 30.769 0.00 0.00 0.00 3.14
3299 6179 9.047371 TGTGAATTAGACAAACTGTTCGAAATA 57.953 29.630 0.00 0.00 31.70 1.40
3300 6180 7.925993 TGTGAATTAGACAAACTGTTCGAAAT 58.074 30.769 0.00 0.00 31.70 2.17
3301 6181 7.310072 TGTGAATTAGACAAACTGTTCGAAA 57.690 32.000 0.00 0.00 31.70 3.46
3304 6184 7.121974 AGATGTGAATTAGACAAACTGTTCG 57.878 36.000 0.00 0.00 31.70 3.95
3305 6185 9.424319 TCTAGATGTGAATTAGACAAACTGTTC 57.576 33.333 0.00 0.00 0.00 3.18
3307 6187 9.376075 CATCTAGATGTGAATTAGACAAACTGT 57.624 33.333 22.42 0.00 34.23 3.55
3336 6216 7.336931 GGAGCTTAGATGTGACATCCTTAAAAA 59.663 37.037 21.05 6.46 0.00 1.94
3337 6217 6.823689 GGAGCTTAGATGTGACATCCTTAAAA 59.176 38.462 21.05 8.00 0.00 1.52
3338 6218 6.349300 GGAGCTTAGATGTGACATCCTTAAA 58.651 40.000 21.05 10.18 0.00 1.52
3339 6219 5.163301 GGGAGCTTAGATGTGACATCCTTAA 60.163 44.000 21.05 13.11 0.00 1.85
3340 6220 4.345257 GGGAGCTTAGATGTGACATCCTTA 59.655 45.833 21.05 6.22 0.00 2.69
3341 6221 3.135530 GGGAGCTTAGATGTGACATCCTT 59.864 47.826 21.05 7.22 0.00 3.36
3342 6222 2.703007 GGGAGCTTAGATGTGACATCCT 59.297 50.000 21.05 11.37 0.00 3.24
3343 6223 2.435805 TGGGAGCTTAGATGTGACATCC 59.564 50.000 21.05 6.28 0.00 3.51
3344 6224 3.118629 TGTGGGAGCTTAGATGTGACATC 60.119 47.826 17.46 17.46 0.00 3.06
3345 6225 2.840038 TGTGGGAGCTTAGATGTGACAT 59.160 45.455 0.00 0.00 0.00 3.06
3346 6226 2.256306 TGTGGGAGCTTAGATGTGACA 58.744 47.619 0.00 0.00 0.00 3.58
3347 6227 3.334583 TTGTGGGAGCTTAGATGTGAC 57.665 47.619 0.00 0.00 0.00 3.67
3348 6228 4.574674 ATTTGTGGGAGCTTAGATGTGA 57.425 40.909 0.00 0.00 0.00 3.58
3349 6229 9.725019 TTATATATTTGTGGGAGCTTAGATGTG 57.275 33.333 0.00 0.00 0.00 3.21
3352 6232 9.401058 GCATTATATATTTGTGGGAGCTTAGAT 57.599 33.333 0.00 0.00 0.00 1.98
3353 6233 8.382405 TGCATTATATATTTGTGGGAGCTTAGA 58.618 33.333 0.00 0.00 0.00 2.10
3354 6234 8.565896 TGCATTATATATTTGTGGGAGCTTAG 57.434 34.615 0.00 0.00 0.00 2.18
3356 6236 9.532494 TTATGCATTATATATTTGTGGGAGCTT 57.468 29.630 3.54 0.00 0.00 3.74
3357 6237 9.532494 TTTATGCATTATATATTTGTGGGAGCT 57.468 29.630 3.54 0.00 0.00 4.09
3358 6238 9.573133 GTTTATGCATTATATATTTGTGGGAGC 57.427 33.333 3.54 0.00 0.00 4.70
3419 6299 3.470709 ACTGATGTCCACTCTGTTTGTG 58.529 45.455 0.00 0.00 35.39 3.33
3420 6300 3.845781 ACTGATGTCCACTCTGTTTGT 57.154 42.857 0.00 0.00 0.00 2.83
3421 6301 5.991606 TCTAAACTGATGTCCACTCTGTTTG 59.008 40.000 14.59 7.92 41.71 2.93
3422 6302 6.174720 TCTAAACTGATGTCCACTCTGTTT 57.825 37.500 11.33 11.33 43.11 2.83
3423 6303 5.808366 TCTAAACTGATGTCCACTCTGTT 57.192 39.130 0.00 0.00 36.66 3.16
3424 6304 5.728471 CATCTAAACTGATGTCCACTCTGT 58.272 41.667 0.00 0.00 39.05 3.41
3434 6314 6.867550 TGTCTAGGACACATCTAAACTGATG 58.132 40.000 0.00 0.00 46.61 3.07
3435 6315 6.892456 TCTGTCTAGGACACATCTAAACTGAT 59.108 38.462 0.00 0.00 37.67 2.90
3436 6316 6.151312 GTCTGTCTAGGACACATCTAAACTGA 59.849 42.308 0.00 0.00 37.67 3.41
3437 6317 6.326375 GTCTGTCTAGGACACATCTAAACTG 58.674 44.000 0.00 0.00 37.67 3.16
3438 6318 5.419471 GGTCTGTCTAGGACACATCTAAACT 59.581 44.000 0.00 0.00 37.67 2.66
3439 6319 5.394333 GGGTCTGTCTAGGACACATCTAAAC 60.394 48.000 0.00 0.00 37.67 2.01
3440 6320 4.710375 GGGTCTGTCTAGGACACATCTAAA 59.290 45.833 0.00 0.00 37.67 1.85
3441 6321 4.017407 AGGGTCTGTCTAGGACACATCTAA 60.017 45.833 3.18 0.00 39.36 2.10
3442 6322 3.528078 AGGGTCTGTCTAGGACACATCTA 59.472 47.826 3.18 0.00 39.36 1.98
3443 6323 2.313342 AGGGTCTGTCTAGGACACATCT 59.687 50.000 3.18 0.00 39.36 2.90
3444 6324 2.741145 AGGGTCTGTCTAGGACACATC 58.259 52.381 3.18 0.00 39.36 3.06
3445 6325 2.930109 AGGGTCTGTCTAGGACACAT 57.070 50.000 3.18 0.00 39.36 3.21
3446 6326 4.332683 AATAGGGTCTGTCTAGGACACA 57.667 45.455 3.18 0.00 39.36 3.72
3447 6327 4.202030 CGAAATAGGGTCTGTCTAGGACAC 60.202 50.000 0.00 0.00 37.67 3.67
3448 6328 3.952323 CGAAATAGGGTCTGTCTAGGACA 59.048 47.826 0.43 0.43 40.50 4.02
3449 6329 4.205587 TCGAAATAGGGTCTGTCTAGGAC 58.794 47.826 0.00 0.00 0.00 3.85
3450 6330 4.515028 TCGAAATAGGGTCTGTCTAGGA 57.485 45.455 0.00 0.00 0.00 2.94
3451 6331 5.593010 CTTTCGAAATAGGGTCTGTCTAGG 58.407 45.833 11.70 0.00 0.00 3.02
3452 6332 5.044558 GCTTTCGAAATAGGGTCTGTCTAG 58.955 45.833 11.70 0.00 0.00 2.43
3453 6333 4.439700 CGCTTTCGAAATAGGGTCTGTCTA 60.440 45.833 11.70 0.00 38.10 2.59
3454 6334 3.676324 CGCTTTCGAAATAGGGTCTGTCT 60.676 47.826 11.70 0.00 38.10 3.41
3455 6335 2.603560 CGCTTTCGAAATAGGGTCTGTC 59.396 50.000 11.70 0.00 38.10 3.51
3456 6336 2.028385 ACGCTTTCGAAATAGGGTCTGT 60.028 45.455 11.70 0.00 39.41 3.41
3457 6337 2.618053 ACGCTTTCGAAATAGGGTCTG 58.382 47.619 11.70 0.00 39.41 3.51
3458 6338 3.329929 AACGCTTTCGAAATAGGGTCT 57.670 42.857 16.93 7.57 36.65 3.85
3459 6339 3.928375 TGTAACGCTTTCGAAATAGGGTC 59.072 43.478 16.93 8.65 36.65 4.46
3460 6340 3.681417 GTGTAACGCTTTCGAAATAGGGT 59.319 43.478 11.70 12.08 38.96 4.34
3461 6341 3.063045 GGTGTAACGCTTTCGAAATAGGG 59.937 47.826 11.70 11.42 38.12 3.53
3462 6342 3.930848 AGGTGTAACGCTTTCGAAATAGG 59.069 43.478 11.70 6.26 38.12 2.57
3463 6343 4.201685 CCAGGTGTAACGCTTTCGAAATAG 60.202 45.833 11.70 10.75 38.12 1.73
3464 6344 3.680937 CCAGGTGTAACGCTTTCGAAATA 59.319 43.478 11.70 0.00 38.12 1.40
3465 6345 2.482721 CCAGGTGTAACGCTTTCGAAAT 59.517 45.455 11.70 0.00 38.12 2.17
3466 6346 1.868498 CCAGGTGTAACGCTTTCGAAA 59.132 47.619 10.71 10.71 38.12 3.46
3467 6347 1.202557 ACCAGGTGTAACGCTTTCGAA 60.203 47.619 0.00 0.00 38.12 3.71
3468 6348 0.390124 ACCAGGTGTAACGCTTTCGA 59.610 50.000 0.00 0.00 38.12 3.71
3469 6349 2.068837 TACCAGGTGTAACGCTTTCG 57.931 50.000 0.76 0.00 38.12 3.46
3470 6350 5.366829 AAAATACCAGGTGTAACGCTTTC 57.633 39.130 0.76 0.00 38.12 2.62
3471 6351 5.777850 AAAAATACCAGGTGTAACGCTTT 57.222 34.783 0.76 0.00 38.12 3.51
3528 6410 7.558161 TGTGAGTTCTTCATTGCATTATAGG 57.442 36.000 0.00 0.00 38.29 2.57
3530 6412 7.067372 CCCTTGTGAGTTCTTCATTGCATTATA 59.933 37.037 0.00 0.00 38.29 0.98
3531 6413 6.127535 CCCTTGTGAGTTCTTCATTGCATTAT 60.128 38.462 0.00 0.00 38.29 1.28
3532 6414 5.183713 CCCTTGTGAGTTCTTCATTGCATTA 59.816 40.000 0.00 0.00 38.29 1.90
3533 6415 4.021719 CCCTTGTGAGTTCTTCATTGCATT 60.022 41.667 0.00 0.00 38.29 3.56
3534 6416 3.508793 CCCTTGTGAGTTCTTCATTGCAT 59.491 43.478 0.00 0.00 38.29 3.96
3548 6435 2.356665 TGTTAGCAAAGCCCTTGTGA 57.643 45.000 0.00 0.00 37.36 3.58
3588 6500 7.959109 GCGATTTAAACTACAAATACGAAAGGT 59.041 33.333 0.00 0.00 0.00 3.50
3595 6507 6.316890 TCCTGGGCGATTTAAACTACAAATAC 59.683 38.462 0.00 0.00 0.00 1.89
3600 6512 3.008157 TGTCCTGGGCGATTTAAACTACA 59.992 43.478 0.00 0.00 0.00 2.74
3634 6547 4.863548 ACCATCATCATCATGTCAAGGTT 58.136 39.130 0.00 0.00 0.00 3.50
3658 6571 9.671279 AGTTTTCTTTGAACATCTTCCATTTTT 57.329 25.926 0.00 0.00 0.00 1.94
3697 6610 3.331150 CACAAACCTAGCATTACCGTGA 58.669 45.455 0.00 0.00 0.00 4.35
3701 6614 3.824443 ACAACCACAAACCTAGCATTACC 59.176 43.478 0.00 0.00 0.00 2.85
3706 6619 2.092646 AGACACAACCACAAACCTAGCA 60.093 45.455 0.00 0.00 0.00 3.49
3709 6622 2.240160 ACCAGACACAACCACAAACCTA 59.760 45.455 0.00 0.00 0.00 3.08
3711 6624 1.470051 ACCAGACACAACCACAAACC 58.530 50.000 0.00 0.00 0.00 3.27
3745 6658 6.786122 TGACTAGCCAAAAGTTTAATAGGGT 58.214 36.000 0.00 0.00 0.00 4.34
3893 6810 2.961062 AGTAATTGGATGGCAATGGCTC 59.039 45.455 8.59 3.20 40.87 4.70
3912 6829 3.433306 TGTGGCCAAACTATTGCTAGT 57.567 42.857 7.24 0.00 39.97 2.57
3916 6833 2.233431 TGGATTGTGGCCAAACTATTGC 59.767 45.455 7.24 0.00 35.10 3.56


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

AutoCloner maintained by Alex Coulton.