Multiple sequence alignment - TraesCS2A01G012000

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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 TraesCS2A01G012000 chr2A 100.000 5774 0 0 1 5774 4616009 4621782 0.000000e+00 10663.0
1 TraesCS2A01G012000 chr2A 96.237 1196 36 4 1 1195 4527647 4528834 0.000000e+00 1951.0
2 TraesCS2A01G012000 chr2A 96.023 1207 34 8 1 1195 4595217 4596421 0.000000e+00 1951.0
3 TraesCS2A01G012000 chr2A 78.000 200 36 5 1547 1739 4349534 4349336 1.020000e-22 119.0
4 TraesCS2A01G012000 chr2D 87.661 2958 200 77 1 2899 5923150 5926001 0.000000e+00 3288.0
5 TraesCS2A01G012000 chr2D 91.746 1466 70 15 3667 5103 5927140 5928583 0.000000e+00 1989.0
6 TraesCS2A01G012000 chr2D 92.210 629 36 5 3090 3705 5926521 5927149 0.000000e+00 878.0
7 TraesCS2A01G012000 chr2D 76.368 457 65 24 4664 5096 6201032 6201469 7.580000e-49 206.0
8 TraesCS2A01G012000 chr2D 83.626 171 26 2 4268 4436 6151494 6151664 5.990000e-35 159.0
9 TraesCS2A01G012000 chr2B 87.496 2943 199 67 1 2878 5478321 5481159 0.000000e+00 3240.0
10 TraesCS2A01G012000 chr2B 81.044 1245 114 50 3090 4269 5481351 5482538 0.000000e+00 880.0
11 TraesCS2A01G012000 chr2B 91.482 587 34 5 4507 5088 5550904 5551479 0.000000e+00 793.0
12 TraesCS2A01G012000 chr2B 90.824 534 30 7 3090 3611 5543200 5543726 0.000000e+00 697.0
13 TraesCS2A01G012000 chr2B 88.255 596 37 5 3936 4520 5549024 5549597 0.000000e+00 682.0
14 TraesCS2A01G012000 chr2B 92.516 481 27 2 2232 2704 5542215 5542694 0.000000e+00 680.0
15 TraesCS2A01G012000 chr2B 81.778 675 72 33 4434 5088 5483095 5483738 8.580000e-143 518.0
16 TraesCS2A01G012000 chr2B 93.080 289 18 2 3626 3913 5544260 5544547 6.920000e-114 422.0
17 TraesCS2A01G012000 chr2B 91.045 268 18 4 1913 2178 84047539 84047802 1.980000e-94 357.0
18 TraesCS2A01G012000 chr2B 91.732 254 15 3 2205 2452 84047785 84048038 1.190000e-91 348.0
19 TraesCS2A01G012000 chr2B 90.058 171 17 0 2694 2864 5542851 5543021 7.530000e-54 222.0
20 TraesCS2A01G012000 chr2B 90.123 81 7 1 1933 2012 5059956 5059876 2.850000e-18 104.0
21 TraesCS2A01G012000 chr2B 90.411 73 7 0 685 757 179399345 179399417 4.760000e-16 97.1
22 TraesCS2A01G012000 chr2B 75.936 187 37 5 1547 1726 5579550 5579735 7.970000e-14 89.8
23 TraesCS2A01G012000 chrUn 96.730 1101 32 4 1 1100 176237444 176236347 0.000000e+00 1831.0
24 TraesCS2A01G012000 chr7D 90.922 683 52 2 5101 5774 598722861 598722180 0.000000e+00 909.0
25 TraesCS2A01G012000 chr7D 86.869 99 7 4 5102 5198 159642093 159642187 7.910000e-19 106.0
26 TraesCS2A01G012000 chr3B 90.922 683 53 2 5101 5774 244977307 244977989 0.000000e+00 909.0
27 TraesCS2A01G012000 chr3B 90.643 684 54 2 5100 5774 744218236 744217554 0.000000e+00 900.0
28 TraesCS2A01G012000 chr3B 90.602 681 55 1 5103 5774 174453054 174452374 0.000000e+00 894.0
29 TraesCS2A01G012000 chr3B 92.537 268 14 4 1913 2178 797654700 797654963 4.220000e-101 379.0
30 TraesCS2A01G012000 chr3B 92.520 254 13 2 2205 2452 797654946 797655199 5.500000e-95 359.0
31 TraesCS2A01G012000 chr3B 90.909 209 17 2 1013 1220 754354951 754354744 4.410000e-71 279.0
32 TraesCS2A01G012000 chr3D 90.643 684 53 2 5100 5774 614468960 614469641 0.000000e+00 898.0
33 TraesCS2A01G012000 chr7B 90.511 685 56 1 5099 5774 215970860 215970176 0.000000e+00 896.0
34 TraesCS2A01G012000 chr7B 92.079 202 14 2 1013 1213 686328791 686328991 3.410000e-72 283.0
35 TraesCS2A01G012000 chr6A 90.616 682 55 3 5102 5774 570490748 570490067 0.000000e+00 896.0
36 TraesCS2A01G012000 chr6A 85.526 76 9 2 682 757 571844475 571844548 1.720000e-10 78.7
37 TraesCS2A01G012000 chr1D 90.058 684 58 5 5100 5774 220422106 220422788 0.000000e+00 878.0
38 TraesCS2A01G012000 chr1D 89.796 686 61 4 5098 5774 424924959 424924274 0.000000e+00 870.0
39 TraesCS2A01G012000 chr1D 77.703 444 72 12 5127 5558 488677656 488678084 4.470000e-61 246.0
40 TraesCS2A01G012000 chr7A 84.548 686 89 5 5101 5774 330795631 330796311 0.000000e+00 664.0
41 TraesCS2A01G012000 chr7A 84.402 686 93 5 5101 5774 330750254 330750937 0.000000e+00 662.0
42 TraesCS2A01G012000 chr7A 83.007 153 12 9 5098 5237 158665818 158665667 6.070000e-25 126.0
43 TraesCS2A01G012000 chr4A 86.949 590 65 2 5101 5678 691505957 691505368 0.000000e+00 652.0
44 TraesCS2A01G012000 chr4A 88.462 338 28 6 5098 5425 628090700 628091036 1.170000e-106 398.0
45 TraesCS2A01G012000 chr4A 92.164 268 15 4 1913 2178 733543424 733543687 1.960000e-99 374.0
46 TraesCS2A01G012000 chr4A 92.126 254 14 2 2205 2452 733543670 733543923 2.560000e-93 353.0
47 TraesCS2A01G012000 chr1B 89.053 338 28 1 5098 5426 1814548 1814885 1.500000e-110 411.0
48 TraesCS2A01G012000 chr1B 91.626 203 15 2 1013 1214 657390952 657391153 4.410000e-71 279.0
49 TraesCS2A01G012000 chr1B 91.781 73 6 0 685 757 409604909 409604837 1.020000e-17 102.0
50 TraesCS2A01G012000 chr4B 91.388 209 16 2 1013 1220 27847619 27847412 9.470000e-73 285.0
51 TraesCS2A01G012000 chr4B 92.118 203 14 2 1013 1214 620640228 620640429 9.470000e-73 285.0
52 TraesCS2A01G012000 chr3A 87.671 73 6 2 685 756 629668968 629668898 1.330000e-11 82.4


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 TraesCS2A01G012000 chr2A 4616009 4621782 5773 False 10663.000000 10663 100.000000 1 5774 1 chr2A.!!$F3 5773
1 TraesCS2A01G012000 chr2A 4527647 4528834 1187 False 1951.000000 1951 96.237000 1 1195 1 chr2A.!!$F1 1194
2 TraesCS2A01G012000 chr2A 4595217 4596421 1204 False 1951.000000 1951 96.023000 1 1195 1 chr2A.!!$F2 1194
3 TraesCS2A01G012000 chr2D 5923150 5928583 5433 False 2051.666667 3288 90.539000 1 5103 3 chr2D.!!$F3 5102
4 TraesCS2A01G012000 chr2B 5478321 5483738 5417 False 1546.000000 3240 83.439333 1 5088 3 chr2B.!!$F3 5087
5 TraesCS2A01G012000 chr2B 5549024 5551479 2455 False 737.500000 793 89.868500 3936 5088 2 chr2B.!!$F5 1152
6 TraesCS2A01G012000 chr2B 5542215 5544547 2332 False 505.250000 697 91.619500 2232 3913 4 chr2B.!!$F4 1681
7 TraesCS2A01G012000 chrUn 176236347 176237444 1097 True 1831.000000 1831 96.730000 1 1100 1 chrUn.!!$R1 1099
8 TraesCS2A01G012000 chr7D 598722180 598722861 681 True 909.000000 909 90.922000 5101 5774 1 chr7D.!!$R1 673
9 TraesCS2A01G012000 chr3B 244977307 244977989 682 False 909.000000 909 90.922000 5101 5774 1 chr3B.!!$F1 673
10 TraesCS2A01G012000 chr3B 744217554 744218236 682 True 900.000000 900 90.643000 5100 5774 1 chr3B.!!$R2 674
11 TraesCS2A01G012000 chr3B 174452374 174453054 680 True 894.000000 894 90.602000 5103 5774 1 chr3B.!!$R1 671
12 TraesCS2A01G012000 chr3D 614468960 614469641 681 False 898.000000 898 90.643000 5100 5774 1 chr3D.!!$F1 674
13 TraesCS2A01G012000 chr7B 215970176 215970860 684 True 896.000000 896 90.511000 5099 5774 1 chr7B.!!$R1 675
14 TraesCS2A01G012000 chr6A 570490067 570490748 681 True 896.000000 896 90.616000 5102 5774 1 chr6A.!!$R1 672
15 TraesCS2A01G012000 chr1D 220422106 220422788 682 False 878.000000 878 90.058000 5100 5774 1 chr1D.!!$F1 674
16 TraesCS2A01G012000 chr1D 424924274 424924959 685 True 870.000000 870 89.796000 5098 5774 1 chr1D.!!$R1 676
17 TraesCS2A01G012000 chr7A 330795631 330796311 680 False 664.000000 664 84.548000 5101 5774 1 chr7A.!!$F2 673
18 TraesCS2A01G012000 chr7A 330750254 330750937 683 False 662.000000 662 84.402000 5101 5774 1 chr7A.!!$F1 673
19 TraesCS2A01G012000 chr4A 691505368 691505957 589 True 652.000000 652 86.949000 5101 5678 1 chr4A.!!$R1 577

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
883 935 0.250234 GCAGCCACTAGACCACATGA 59.750 55.0 0.00 0.0 0.00 3.07 F
1344 1417 0.237235 TCACAACTTTGCGCCGATTC 59.763 50.0 4.18 0.0 0.00 2.52 F
2941 3208 0.250553 CCCTCGTGCTGGGTTTGTTA 60.251 55.0 0.00 0.0 39.82 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2473 2560 0.250295 TGTAGCTTGTGAGTGCCACC 60.250 55.0 0.00 0.00 45.09 4.61 R
2963 3230 0.621571 CCCCCTCCCACTTCATGAGA 60.622 60.0 0.00 0.00 0.00 3.27 R
4777 7739 0.104671 GAGCATCTCTCCAGGTGAGC 59.895 60.0 13.06 3.71 41.18 4.26 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
54 55 7.601856 ACCTGAAATAAATCGAGAAAAATGCA 58.398 30.769 0.00 0.00 0.00 3.96
97 101 0.253160 TCTGTTGGGCTGGGGATACT 60.253 55.000 0.00 0.00 0.00 2.12
115 119 6.326843 GGGATACTACTGTTCTCCTAACCATT 59.673 42.308 0.00 0.00 31.43 3.16
348 361 2.984562 TCATTAGATGCAAGGAACGCA 58.015 42.857 0.00 0.00 44.94 5.24
366 379 5.613358 ACGCAAAAATTCCTCTTCTACTG 57.387 39.130 0.00 0.00 0.00 2.74
629 651 3.545822 GGCAAGCACAAAAACATTTTCCG 60.546 43.478 0.00 0.00 0.00 4.30
883 935 0.250234 GCAGCCACTAGACCACATGA 59.750 55.000 0.00 0.00 0.00 3.07
1240 1313 3.160585 CCTGCTCCAGGTCCAACA 58.839 61.111 3.09 0.00 45.82 3.33
1286 1359 4.133078 GCTCATCTCCCTGTAATTTCTGG 58.867 47.826 1.54 1.54 0.00 3.86
1304 1377 2.594962 GCTGTGTTGACCGGACGTG 61.595 63.158 9.46 0.00 0.00 4.49
1344 1417 0.237235 TCACAACTTTGCGCCGATTC 59.763 50.000 4.18 0.00 0.00 2.52
1363 1436 4.914312 TTCGTTTACCTGTTAGCATTCG 57.086 40.909 0.00 0.00 0.00 3.34
1394 1467 7.515957 CGTATTCGTATCCTGTTTGTAGTTT 57.484 36.000 0.00 0.00 0.00 2.66
1396 1469 7.896274 CGTATTCGTATCCTGTTTGTAGTTTTG 59.104 37.037 0.00 0.00 0.00 2.44
1397 1470 7.972832 ATTCGTATCCTGTTTGTAGTTTTGA 57.027 32.000 0.00 0.00 0.00 2.69
1400 1473 8.385898 TCGTATCCTGTTTGTAGTTTTGATTT 57.614 30.769 0.00 0.00 0.00 2.17
1401 1474 8.500773 TCGTATCCTGTTTGTAGTTTTGATTTC 58.499 33.333 0.00 0.00 0.00 2.17
1402 1475 8.286800 CGTATCCTGTTTGTAGTTTTGATTTCA 58.713 33.333 0.00 0.00 0.00 2.69
1403 1476 9.959749 GTATCCTGTTTGTAGTTTTGATTTCAA 57.040 29.630 0.00 0.00 0.00 2.69
1464 1542 8.470805 TGTACTCAAATTTGCCTTCTTTTGTTA 58.529 29.630 13.54 0.00 32.33 2.41
1484 1562 7.461182 TGTTATTTACAAAGAACAGGGGATG 57.539 36.000 10.06 0.00 42.94 3.51
1485 1563 6.435904 TGTTATTTACAAAGAACAGGGGATGG 59.564 38.462 10.06 0.00 42.94 3.51
1486 1564 4.733077 TTTACAAAGAACAGGGGATGGA 57.267 40.909 0.00 0.00 0.00 3.41
1487 1565 4.946160 TTACAAAGAACAGGGGATGGAT 57.054 40.909 0.00 0.00 0.00 3.41
1488 1566 6.395780 TTTACAAAGAACAGGGGATGGATA 57.604 37.500 0.00 0.00 0.00 2.59
1489 1567 4.946160 ACAAAGAACAGGGGATGGATAA 57.054 40.909 0.00 0.00 0.00 1.75
1490 1568 4.600062 ACAAAGAACAGGGGATGGATAAC 58.400 43.478 0.00 0.00 0.00 1.89
1497 1575 3.254960 CAGGGGATGGATAACTGGAGAT 58.745 50.000 0.00 0.00 0.00 2.75
1529 1607 1.402062 GCTAACTGCTTTTGCTGCTCC 60.402 52.381 0.00 0.00 46.47 4.70
1530 1608 2.157738 CTAACTGCTTTTGCTGCTCCT 58.842 47.619 0.00 0.00 46.47 3.69
1531 1609 0.672342 AACTGCTTTTGCTGCTCCTG 59.328 50.000 0.00 0.00 46.47 3.86
1676 1754 1.674057 CGTCTCCTGCACTTTCCCT 59.326 57.895 0.00 0.00 0.00 4.20
1760 1838 2.616376 CCGGTTGACAACTTGACATCAA 59.384 45.455 17.52 0.00 0.00 2.57
1773 1851 7.992180 ACTTGACATCAAAATTTTGTGTCTC 57.008 32.000 34.84 24.64 42.64 3.36
1830 1908 5.357742 TCTTTGCCAGCAGTTATCATAGA 57.642 39.130 0.00 0.00 0.00 1.98
1858 1936 0.941542 TTGTTGCAACGGTAGACTGC 59.058 50.000 23.79 0.00 36.60 4.40
1864 1942 1.394917 GCAACGGTAGACTGCAGAATG 59.605 52.381 23.35 6.18 36.09 2.67
1913 1991 7.164230 TCACAAAAGTTACATGGTTCAAAGT 57.836 32.000 0.00 0.00 0.00 2.66
1922 2000 8.621286 AGTTACATGGTTCAAAGTAAAGTTGAG 58.379 33.333 0.00 0.00 36.41 3.02
1925 2003 5.906113 TGGTTCAAAGTAAAGTTGAGCAA 57.094 34.783 3.91 0.00 37.79 3.91
1939 2017 1.839994 TGAGCAAGCTAAGCATAGGGT 59.160 47.619 12.91 0.00 0.00 4.34
1951 2029 1.745653 GCATAGGGTTTGAGGTTGAGC 59.254 52.381 0.00 0.00 0.00 4.26
1995 2073 9.739276 ACATCAGTATTCTCACAATCCTTTTAA 57.261 29.630 0.00 0.00 0.00 1.52
2040 2119 1.446016 ACTTCTACCCTTGTTGCCCT 58.554 50.000 0.00 0.00 0.00 5.19
2063 2144 7.710475 CCCTTGATTGTTTCAACACTAACAAAT 59.290 33.333 0.00 0.00 44.58 2.32
2158 2241 9.222916 CAGTACAGTTACAGTAAACTATCATCG 57.777 37.037 0.00 0.00 37.61 3.84
2173 2256 5.755375 ACTATCATCGTACTGGAGCAAAATG 59.245 40.000 0.00 0.00 0.00 2.32
2187 2270 1.872313 CAAAATGCAACAACGGCCAAT 59.128 42.857 2.24 0.00 0.00 3.16
2482 2569 2.717639 ACTGAATATGGGTGGCACTC 57.282 50.000 18.45 15.20 0.00 3.51
2525 2625 4.497300 GCACATTGTTGGCATTATGAAGT 58.503 39.130 0.00 0.00 0.00 3.01
2536 2636 5.174395 GGCATTATGAAGTCGATATGCTCT 58.826 41.667 0.00 0.00 34.55 4.09
2637 2737 3.375699 CATTACCTACCTGTGGACCTCT 58.624 50.000 0.00 0.00 0.00 3.69
2650 2750 2.158813 TGGACCTCTCAAGTGAAACCAC 60.159 50.000 0.00 0.00 37.80 4.16
2715 2982 2.159099 CGTGCCTAGTCTTGCTGGATAA 60.159 50.000 0.00 0.00 0.00 1.75
2752 3019 5.917462 TGGTATGTGACTATTGTGGATGAG 58.083 41.667 0.00 0.00 0.00 2.90
2852 3119 3.222173 AGTAGGCAACAACAATGGTCA 57.778 42.857 0.00 0.00 41.41 4.02
2857 3124 2.297033 GGCAACAACAATGGTCAGACAT 59.703 45.455 2.17 0.00 0.00 3.06
2900 3167 7.544622 TGTACTGTACATCATAGTTCTTGTCC 58.455 38.462 16.26 0.00 32.89 4.02
2901 3168 6.859112 ACTGTACATCATAGTTCTTGTCCT 57.141 37.500 0.00 0.00 0.00 3.85
2902 3169 7.956328 ACTGTACATCATAGTTCTTGTCCTA 57.044 36.000 0.00 0.00 0.00 2.94
2903 3170 8.540507 ACTGTACATCATAGTTCTTGTCCTAT 57.459 34.615 0.00 0.00 0.00 2.57
2904 3171 8.634444 ACTGTACATCATAGTTCTTGTCCTATC 58.366 37.037 0.00 0.00 0.00 2.08
2905 3172 7.952671 TGTACATCATAGTTCTTGTCCTATCC 58.047 38.462 0.00 0.00 0.00 2.59
2906 3173 7.563556 TGTACATCATAGTTCTTGTCCTATCCA 59.436 37.037 0.00 0.00 0.00 3.41
2907 3174 7.060383 ACATCATAGTTCTTGTCCTATCCAG 57.940 40.000 0.00 0.00 0.00 3.86
2908 3175 6.613271 ACATCATAGTTCTTGTCCTATCCAGT 59.387 38.462 0.00 0.00 0.00 4.00
2909 3176 6.716934 TCATAGTTCTTGTCCTATCCAGTC 57.283 41.667 0.00 0.00 0.00 3.51
2910 3177 6.436027 TCATAGTTCTTGTCCTATCCAGTCT 58.564 40.000 0.00 0.00 0.00 3.24
2911 3178 7.583625 TCATAGTTCTTGTCCTATCCAGTCTA 58.416 38.462 0.00 0.00 0.00 2.59
2912 3179 8.228206 TCATAGTTCTTGTCCTATCCAGTCTAT 58.772 37.037 0.00 0.00 0.00 1.98
2913 3180 6.723298 AGTTCTTGTCCTATCCAGTCTATG 57.277 41.667 0.00 0.00 0.00 2.23
2930 3197 2.126189 GGTACGTGACCCTCGTGC 60.126 66.667 0.00 3.30 43.25 5.34
2931 3198 2.633509 GGTACGTGACCCTCGTGCT 61.634 63.158 0.00 0.00 43.25 4.40
2932 3199 1.443872 GTACGTGACCCTCGTGCTG 60.444 63.158 0.00 0.00 41.62 4.41
2933 3200 2.632544 TACGTGACCCTCGTGCTGG 61.633 63.158 0.00 0.00 41.62 4.85
2939 3206 2.113139 CCCTCGTGCTGGGTTTGT 59.887 61.111 0.00 0.00 39.82 2.83
2940 3207 1.528309 CCCTCGTGCTGGGTTTGTT 60.528 57.895 0.00 0.00 39.82 2.83
2941 3208 0.250553 CCCTCGTGCTGGGTTTGTTA 60.251 55.000 0.00 0.00 39.82 2.41
2942 3209 0.872388 CCTCGTGCTGGGTTTGTTAC 59.128 55.000 0.00 0.00 0.00 2.50
2943 3210 0.872388 CTCGTGCTGGGTTTGTTACC 59.128 55.000 0.00 0.00 46.99 2.85
2967 3234 9.679661 ACCAACAATGTAAACATGTATATCTCA 57.320 29.630 0.00 0.00 36.56 3.27
2975 3242 9.546428 TGTAAACATGTATATCTCATGAAGTGG 57.454 33.333 20.42 0.00 43.47 4.00
2976 3243 8.993121 GTAAACATGTATATCTCATGAAGTGGG 58.007 37.037 20.42 0.00 43.47 4.61
2977 3244 7.379059 AACATGTATATCTCATGAAGTGGGA 57.621 36.000 20.42 0.00 43.47 4.37
2978 3245 7.002250 ACATGTATATCTCATGAAGTGGGAG 57.998 40.000 20.42 0.00 41.63 4.30
2979 3246 6.013898 ACATGTATATCTCATGAAGTGGGAGG 60.014 42.308 20.42 0.00 41.63 4.30
2980 3247 4.840680 TGTATATCTCATGAAGTGGGAGGG 59.159 45.833 0.00 0.00 41.63 4.30
2981 3248 1.516110 ATCTCATGAAGTGGGAGGGG 58.484 55.000 0.00 0.00 41.63 4.79
2982 3249 0.621571 TCTCATGAAGTGGGAGGGGG 60.622 60.000 0.00 0.00 30.47 5.40
2997 3264 3.778250 GGGGGTCCTTGCCTTAAAA 57.222 52.632 0.00 0.00 0.00 1.52
2998 3265 2.018355 GGGGGTCCTTGCCTTAAAAA 57.982 50.000 0.00 0.00 0.00 1.94
2999 3266 2.546899 GGGGGTCCTTGCCTTAAAAAT 58.453 47.619 0.00 0.00 0.00 1.82
3000 3267 2.236146 GGGGGTCCTTGCCTTAAAAATG 59.764 50.000 0.00 0.00 0.00 2.32
3001 3268 2.903784 GGGGTCCTTGCCTTAAAAATGT 59.096 45.455 0.00 0.00 0.00 2.71
3002 3269 4.090819 GGGGTCCTTGCCTTAAAAATGTA 58.909 43.478 0.00 0.00 0.00 2.29
3003 3270 4.714802 GGGGTCCTTGCCTTAAAAATGTAT 59.285 41.667 0.00 0.00 0.00 2.29
3008 3476 7.330946 GGTCCTTGCCTTAAAAATGTATTCAAC 59.669 37.037 0.00 0.00 0.00 3.18
3046 3514 9.477484 CTTTAGTATTATCGGTTGTTCTAGCAT 57.523 33.333 0.00 0.00 0.00 3.79
3047 3515 9.472361 TTTAGTATTATCGGTTGTTCTAGCATC 57.528 33.333 0.00 0.00 0.00 3.91
3079 3547 5.047590 GGGGATTTATTTTTCAGTGTCGGTT 60.048 40.000 0.00 0.00 0.00 4.44
3088 3556 1.134521 TCAGTGTCGGTTGCTTCAACT 60.135 47.619 9.23 0.00 43.14 3.16
3119 3721 6.635030 AGGAATTAGTTCAAACTCAACCAC 57.365 37.500 0.00 0.00 40.37 4.16
3121 3723 6.039382 AGGAATTAGTTCAAACTCAACCACAC 59.961 38.462 0.00 0.00 40.37 3.82
3538 4152 5.314923 ACATGTGTTATGGTTCTTCATGC 57.685 39.130 0.00 0.00 35.92 4.06
3600 4214 7.788867 ACCATAATGTTTCATCAATTATCCCCA 59.211 33.333 0.00 0.00 0.00 4.96
3604 4218 5.579047 TGTTTCATCAATTATCCCCACTGT 58.421 37.500 0.00 0.00 0.00 3.55
3611 4225 2.335681 TTATCCCCACTGTGAGGTCA 57.664 50.000 9.86 0.00 0.00 4.02
3615 4229 2.626785 TCCCCACTGTGAGGTCAATTA 58.373 47.619 9.86 0.00 0.00 1.40
3616 4230 3.189606 TCCCCACTGTGAGGTCAATTAT 58.810 45.455 9.86 0.00 0.00 1.28
3617 4231 3.591527 TCCCCACTGTGAGGTCAATTATT 59.408 43.478 9.86 0.00 0.00 1.40
3618 4232 4.044065 TCCCCACTGTGAGGTCAATTATTT 59.956 41.667 9.86 0.00 0.00 1.40
3619 4233 4.772100 CCCCACTGTGAGGTCAATTATTTT 59.228 41.667 9.86 0.00 0.00 1.82
3670 4807 8.011290 ACTATGTTAGTAGTAGATTGGATGGGT 58.989 37.037 0.00 0.00 37.23 4.51
3676 4813 4.236527 AGTAGATTGGATGGGTTTGGAC 57.763 45.455 0.00 0.00 0.00 4.02
3692 4865 5.491982 GTTTGGACTGGATTGACTATCTGT 58.508 41.667 0.00 0.00 33.53 3.41
3934 5114 4.422073 TGGGCTAGATTGTAGTGGAATG 57.578 45.455 0.00 0.00 0.00 2.67
3949 5129 2.159099 TGGAATGTAGCAGGTTAGCTCG 60.159 50.000 0.00 0.00 45.26 5.03
3954 5134 3.349927 TGTAGCAGGTTAGCTCGTAGAA 58.650 45.455 0.00 0.00 45.26 2.10
3966 5146 9.804758 GGTTAGCTCGTAGAAGCATATTTATAT 57.195 33.333 0.00 0.00 34.09 0.86
4049 5246 5.659463 TGTTGCTTGCTTTTTCACTGTTAT 58.341 33.333 0.00 0.00 0.00 1.89
4050 5247 6.105333 TGTTGCTTGCTTTTTCACTGTTATT 58.895 32.000 0.00 0.00 0.00 1.40
4051 5248 7.261325 TGTTGCTTGCTTTTTCACTGTTATTA 58.739 30.769 0.00 0.00 0.00 0.98
4052 5249 7.761704 TGTTGCTTGCTTTTTCACTGTTATTAA 59.238 29.630 0.00 0.00 0.00 1.40
4078 5275 6.543831 ACTGCCTGAACTATTAATGGCTTTAG 59.456 38.462 12.06 5.55 40.82 1.85
4210 5422 6.098982 AGTGGGTAGATCTATGTTGGAAAGAG 59.901 42.308 5.57 0.00 0.00 2.85
4213 5425 6.271159 GGGTAGATCTATGTTGGAAAGAGGAT 59.729 42.308 5.57 0.00 0.00 3.24
4214 5426 7.455008 GGGTAGATCTATGTTGGAAAGAGGATA 59.545 40.741 5.57 0.00 0.00 2.59
4215 5427 9.041354 GGTAGATCTATGTTGGAAAGAGGATAT 57.959 37.037 5.57 0.00 0.00 1.63
4354 5963 0.965866 TGCAGTGGAGGTAGAGGTCG 60.966 60.000 0.00 0.00 0.00 4.79
4382 5991 1.073923 CTTGACTAGGGCCAACTTGGT 59.926 52.381 6.18 0.00 40.46 3.67
4421 6030 1.713937 TTGTCCGCTGTGCTGTGTTG 61.714 55.000 0.00 0.00 0.00 3.33
4424 6033 2.179547 CCGCTGTGCTGTGTTGTCA 61.180 57.895 0.00 0.00 0.00 3.58
4514 7473 3.834489 ATCTCGCATCATCTGTTTCCT 57.166 42.857 0.00 0.00 0.00 3.36
4573 7532 4.489810 CGACTGGGAGATACTCATAATGC 58.510 47.826 0.00 0.00 31.08 3.56
4614 7573 0.322456 CCGAAGATGGGAAGCACCAA 60.322 55.000 0.00 0.00 45.13 3.67
4689 7651 3.650950 AGGACATGCAAGCCCCGT 61.651 61.111 0.00 0.00 0.00 5.28
4690 7652 2.270850 GGACATGCAAGCCCCGTA 59.729 61.111 0.00 0.00 0.00 4.02
4691 7653 2.112815 GGACATGCAAGCCCCGTAC 61.113 63.158 0.00 0.00 0.00 3.67
4692 7654 1.376683 GACATGCAAGCCCCGTACA 60.377 57.895 0.00 0.00 0.00 2.90
4693 7655 0.958382 GACATGCAAGCCCCGTACAA 60.958 55.000 0.00 0.00 0.00 2.41
4694 7656 1.241315 ACATGCAAGCCCCGTACAAC 61.241 55.000 0.00 0.00 0.00 3.32
4701 7663 4.360964 CCCCGTACAACGCCGACA 62.361 66.667 0.00 0.00 40.91 4.35
4710 7672 4.555709 ACGCCGACACCAAAGCCA 62.556 61.111 0.00 0.00 0.00 4.75
4720 7682 1.000274 CACCAAAGCCAAAGCCTACAC 60.000 52.381 0.00 0.00 41.25 2.90
4774 7736 0.967887 TCCGGCTCAGGAGAAGTGAG 60.968 60.000 0.00 0.00 43.77 3.51
4777 7739 0.823460 GGCTCAGGAGAAGTGAGGAG 59.177 60.000 0.00 0.00 41.60 3.69
4976 7953 3.578272 TGTTTGTTTCGCGGCGCT 61.578 55.556 30.54 0.00 0.00 5.92
4978 7955 4.320928 TTTGTTTCGCGGCGCTGG 62.321 61.111 30.54 15.69 0.00 4.85
4996 7973 3.741344 GCTGGCCATACTACGAAATACTG 59.259 47.826 5.51 0.00 0.00 2.74
5081 8063 9.264719 GATCTCAAATTCTTTTGTTGGTTCATT 57.735 29.630 0.00 0.00 42.37 2.57
5255 8254 7.403312 TCAAGATTGAAGAAACCTTTGAACA 57.597 32.000 0.00 0.00 33.55 3.18
5437 8437 1.153168 CGAATCAGACCGGGGCAAT 60.153 57.895 6.32 0.00 0.00 3.56
5544 8546 2.325082 GCGAACCCAGCACACGATT 61.325 57.895 0.00 0.00 34.19 3.34
5589 8591 2.300433 GCATACCACAATCTGCATCCA 58.700 47.619 0.00 0.00 34.77 3.41
5609 8611 2.637872 CACTCCTGAACTACCTCCCAAA 59.362 50.000 0.00 0.00 0.00 3.28
5734 8736 4.989279 ACTGATTTTCAAATCCATCCCG 57.011 40.909 9.33 0.00 43.19 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 7.601856 TGCATTTTTCTCGATTTATTTCAGGT 58.398 30.769 0.00 0.00 0.00 4.00
78 82 0.253160 AGTATCCCCAGCCCAACAGA 60.253 55.000 0.00 0.00 0.00 3.41
97 101 7.103641 GTGATTGAATGGTTAGGAGAACAGTA 58.896 38.462 0.00 0.00 0.00 2.74
115 119 3.536570 TCACGAACCAAACTGTGATTGA 58.463 40.909 0.00 0.00 36.50 2.57
348 361 4.906618 TCGGCAGTAGAAGAGGAATTTTT 58.093 39.130 0.00 0.00 0.00 1.94
366 379 2.594541 CGAGCTAAATGACCTCGGC 58.405 57.895 0.00 0.00 43.33 5.54
518 540 9.235537 GTGCTGCAAAAATGTTATTTTTGAAAT 57.764 25.926 29.47 3.98 46.62 2.17
669 715 5.905913 AGAGGGAGTAGTATAATTGCCTTGT 59.094 40.000 0.00 0.00 30.25 3.16
883 935 5.337250 GGGCCCTTTCGTTCTTATGATTTTT 60.337 40.000 17.04 0.00 0.00 1.94
1258 1331 2.043852 AGGGAGATGAGCGACGGT 60.044 61.111 0.00 0.00 0.00 4.83
1260 1333 0.738975 TTACAGGGAGATGAGCGACG 59.261 55.000 0.00 0.00 0.00 5.12
1268 1341 3.525199 ACAGCCAGAAATTACAGGGAGAT 59.475 43.478 0.00 0.00 0.00 2.75
1286 1359 2.279918 ACGTCCGGTCAACACAGC 60.280 61.111 0.00 0.00 0.00 4.40
1304 1377 3.936772 TTGGGCGCATCTGGGTTCC 62.937 63.158 10.83 0.00 0.00 3.62
1344 1417 4.657075 AACGAATGCTAACAGGTAAACG 57.343 40.909 0.00 0.00 0.00 3.60
1388 1461 9.210426 CGCATACTACATTGAAATCAAAACTAC 57.790 33.333 0.00 0.00 39.55 2.73
1389 1462 8.941977 ACGCATACTACATTGAAATCAAAACTA 58.058 29.630 0.00 0.00 39.55 2.24
1390 1463 7.750458 CACGCATACTACATTGAAATCAAAACT 59.250 33.333 0.00 0.00 39.55 2.66
1392 1465 6.526325 GCACGCATACTACATTGAAATCAAAA 59.474 34.615 0.00 0.00 39.55 2.44
1393 1466 6.027131 GCACGCATACTACATTGAAATCAAA 58.973 36.000 0.00 0.00 39.55 2.69
1394 1467 5.353956 AGCACGCATACTACATTGAAATCAA 59.646 36.000 0.00 0.00 40.51 2.57
1396 1469 5.235186 AGAGCACGCATACTACATTGAAATC 59.765 40.000 0.00 0.00 0.00 2.17
1397 1470 5.118990 AGAGCACGCATACTACATTGAAAT 58.881 37.500 0.00 0.00 0.00 2.17
1400 1473 3.801114 AGAGCACGCATACTACATTGA 57.199 42.857 0.00 0.00 0.00 2.57
1401 1474 3.544834 GCAAGAGCACGCATACTACATTG 60.545 47.826 0.00 0.00 41.58 2.82
1402 1475 2.609459 GCAAGAGCACGCATACTACATT 59.391 45.455 0.00 0.00 41.58 2.71
1403 1476 2.159043 AGCAAGAGCACGCATACTACAT 60.159 45.455 0.00 0.00 45.49 2.29
1464 1542 5.269554 TCCATCCCCTGTTCTTTGTAAAT 57.730 39.130 0.00 0.00 0.00 1.40
1468 1546 4.292306 AGTTATCCATCCCCTGTTCTTTGT 59.708 41.667 0.00 0.00 0.00 2.83
1470 1548 4.325344 CCAGTTATCCATCCCCTGTTCTTT 60.325 45.833 0.00 0.00 0.00 2.52
1476 1554 2.694397 TCTCCAGTTATCCATCCCCTG 58.306 52.381 0.00 0.00 0.00 4.45
1483 1561 2.694397 CCCCTCATCTCCAGTTATCCA 58.306 52.381 0.00 0.00 0.00 3.41
1484 1562 1.349357 GCCCCTCATCTCCAGTTATCC 59.651 57.143 0.00 0.00 0.00 2.59
1485 1563 1.349357 GGCCCCTCATCTCCAGTTATC 59.651 57.143 0.00 0.00 0.00 1.75
1486 1564 1.345422 TGGCCCCTCATCTCCAGTTAT 60.345 52.381 0.00 0.00 0.00 1.89
1487 1565 0.044092 TGGCCCCTCATCTCCAGTTA 59.956 55.000 0.00 0.00 0.00 2.24
1488 1566 1.229951 TGGCCCCTCATCTCCAGTT 60.230 57.895 0.00 0.00 0.00 3.16
1489 1567 1.692042 CTGGCCCCTCATCTCCAGT 60.692 63.158 0.00 0.00 40.79 4.00
1490 1568 2.450320 CCTGGCCCCTCATCTCCAG 61.450 68.421 0.00 0.00 44.25 3.86
1497 1575 3.015145 GTTAGCCCTGGCCCCTCA 61.015 66.667 4.13 0.00 43.17 3.86
1529 1607 0.249155 CCTGGCTGCAACAACAACAG 60.249 55.000 0.50 0.00 34.48 3.16
1530 1608 1.815196 CCTGGCTGCAACAACAACA 59.185 52.632 0.50 0.00 0.00 3.33
1531 1609 1.592400 GCCTGGCTGCAACAACAAC 60.592 57.895 12.43 0.00 0.00 3.32
1794 1872 6.183360 TGCTGGCAAAGATTTATCTGAATCAG 60.183 38.462 3.38 3.38 38.27 2.90
1848 1926 2.654749 TGTCATTCTGCAGTCTACCG 57.345 50.000 14.67 0.00 0.00 4.02
1851 1929 6.365520 TCTAGGTATGTCATTCTGCAGTCTA 58.634 40.000 14.67 0.76 0.00 2.59
1864 1942 9.364989 GAGCAAATATCAGAATCTAGGTATGTC 57.635 37.037 0.00 0.00 0.00 3.06
1913 1991 5.586243 CCTATGCTTAGCTTGCTCAACTTTA 59.414 40.000 5.60 0.00 0.00 1.85
1922 2000 3.016736 TCAAACCCTATGCTTAGCTTGC 58.983 45.455 5.60 0.00 0.00 4.01
1925 2003 2.846827 ACCTCAAACCCTATGCTTAGCT 59.153 45.455 5.60 0.00 0.00 3.32
1951 2029 1.089920 GTTGCATAGTGAGCACCAGG 58.910 55.000 0.00 0.00 42.54 4.45
2156 2239 2.177394 TGCATTTTGCTCCAGTACGA 57.823 45.000 0.75 0.00 45.31 3.43
2157 2240 2.031245 TGTTGCATTTTGCTCCAGTACG 60.031 45.455 0.75 0.00 45.31 3.67
2158 2241 3.641437 TGTTGCATTTTGCTCCAGTAC 57.359 42.857 0.75 0.00 45.31 2.73
2161 2244 1.788308 CGTTGTTGCATTTTGCTCCAG 59.212 47.619 0.75 0.00 45.31 3.86
2173 2256 2.738139 GCCATTGGCCGTTGTTGC 60.738 61.111 17.28 0.00 44.06 4.17
2187 2270 5.139727 CCCAATAGTTGATCTTTATGGCCA 58.860 41.667 8.56 8.56 0.00 5.36
2309 2396 6.187682 ACTAGGTATGGAAATTTGGGAACAG 58.812 40.000 0.00 0.00 44.54 3.16
2473 2560 0.250295 TGTAGCTTGTGAGTGCCACC 60.250 55.000 0.00 0.00 45.09 4.61
2482 2569 0.953727 TTGCCTTGCTGTAGCTTGTG 59.046 50.000 5.38 0.00 42.66 3.33
2525 2625 5.048013 CCACAACATAGGTAGAGCATATCGA 60.048 44.000 0.00 0.00 0.00 3.59
2650 2750 7.520451 AAACAGATATCCCACATCAATCATG 57.480 36.000 0.00 0.00 38.64 3.07
2715 2982 4.826733 TCACATACCAACAGCATTCAAAGT 59.173 37.500 0.00 0.00 0.00 2.66
2803 3070 4.294970 AGGTGATCTAAAGGGAAAATGGGT 59.705 41.667 0.00 0.00 0.00 4.51
2878 3145 6.859112 AGGACAAGAACTATGATGTACAGT 57.141 37.500 0.33 0.00 0.00 3.55
2879 3146 8.085296 GGATAGGACAAGAACTATGATGTACAG 58.915 40.741 0.33 0.00 30.43 2.74
2886 3153 6.436027 AGACTGGATAGGACAAGAACTATGA 58.564 40.000 0.00 0.00 30.43 2.15
2914 3181 1.443872 CAGCACGAGGGTCACGTAC 60.444 63.158 0.00 0.00 42.07 3.67
2915 3182 2.632544 CCAGCACGAGGGTCACGTA 61.633 63.158 0.00 0.00 42.07 3.57
2916 3183 3.991051 CCAGCACGAGGGTCACGT 61.991 66.667 0.00 0.00 44.83 4.49
2917 3184 4.742201 CCCAGCACGAGGGTCACG 62.742 72.222 0.00 0.00 41.61 4.35
2923 3190 0.872388 GTAACAAACCCAGCACGAGG 59.128 55.000 0.00 0.00 0.00 4.63
2924 3191 0.872388 GGTAACAAACCCAGCACGAG 59.128 55.000 0.00 0.00 43.16 4.18
2925 3192 3.009612 GGTAACAAACCCAGCACGA 57.990 52.632 0.00 0.00 43.16 4.35
2941 3208 9.679661 TGAGATATACATGTTTACATTGTTGGT 57.320 29.630 2.30 0.00 33.61 3.67
2949 3216 9.546428 CCACTTCATGAGATATACATGTTTACA 57.454 33.333 2.30 0.00 43.56 2.41
2950 3217 8.993121 CCCACTTCATGAGATATACATGTTTAC 58.007 37.037 2.30 0.00 43.56 2.01
2951 3218 8.933653 TCCCACTTCATGAGATATACATGTTTA 58.066 33.333 2.30 0.00 43.56 2.01
2952 3219 7.805163 TCCCACTTCATGAGATATACATGTTT 58.195 34.615 2.30 0.00 43.56 2.83
2953 3220 7.379059 TCCCACTTCATGAGATATACATGTT 57.621 36.000 2.30 0.00 43.56 2.71
2954 3221 6.013898 CCTCCCACTTCATGAGATATACATGT 60.014 42.308 2.69 2.69 43.56 3.21
2955 3222 6.404708 CCTCCCACTTCATGAGATATACATG 58.595 44.000 13.12 13.12 44.20 3.21
2956 3223 5.486775 CCCTCCCACTTCATGAGATATACAT 59.513 44.000 0.00 0.00 0.00 2.29
2957 3224 4.840680 CCCTCCCACTTCATGAGATATACA 59.159 45.833 0.00 0.00 0.00 2.29
2958 3225 4.223923 CCCCTCCCACTTCATGAGATATAC 59.776 50.000 0.00 0.00 0.00 1.47
2959 3226 4.429505 CCCCTCCCACTTCATGAGATATA 58.570 47.826 0.00 0.00 0.00 0.86
2960 3227 3.254960 CCCCTCCCACTTCATGAGATAT 58.745 50.000 0.00 0.00 0.00 1.63
2961 3228 2.694397 CCCCTCCCACTTCATGAGATA 58.306 52.381 0.00 0.00 0.00 1.98
2962 3229 1.516110 CCCCTCCCACTTCATGAGAT 58.484 55.000 0.00 0.00 0.00 2.75
2963 3230 0.621571 CCCCCTCCCACTTCATGAGA 60.622 60.000 0.00 0.00 0.00 3.27
2964 3231 1.918253 CCCCCTCCCACTTCATGAG 59.082 63.158 0.00 0.00 0.00 2.90
2965 3232 4.169452 CCCCCTCCCACTTCATGA 57.831 61.111 0.00 0.00 0.00 3.07
2979 3246 2.018355 TTTTTAAGGCAAGGACCCCC 57.982 50.000 0.00 0.00 0.00 5.40
2980 3247 2.903784 ACATTTTTAAGGCAAGGACCCC 59.096 45.455 0.00 0.00 0.00 4.95
2981 3248 5.932619 ATACATTTTTAAGGCAAGGACCC 57.067 39.130 0.00 0.00 0.00 4.46
2982 3249 6.930731 TGAATACATTTTTAAGGCAAGGACC 58.069 36.000 0.00 0.00 0.00 4.46
2983 3250 7.330946 GGTTGAATACATTTTTAAGGCAAGGAC 59.669 37.037 0.00 0.00 0.00 3.85
2984 3251 7.382898 GGTTGAATACATTTTTAAGGCAAGGA 58.617 34.615 0.00 0.00 0.00 3.36
2985 3252 6.593770 GGGTTGAATACATTTTTAAGGCAAGG 59.406 38.462 0.00 0.00 0.00 3.61
2986 3253 7.386059 AGGGTTGAATACATTTTTAAGGCAAG 58.614 34.615 0.00 0.00 0.00 4.01
2987 3254 7.015682 TGAGGGTTGAATACATTTTTAAGGCAA 59.984 33.333 0.00 0.00 0.00 4.52
2988 3255 6.495181 TGAGGGTTGAATACATTTTTAAGGCA 59.505 34.615 0.00 0.00 0.00 4.75
2989 3256 6.930731 TGAGGGTTGAATACATTTTTAAGGC 58.069 36.000 0.00 0.00 0.00 4.35
2990 3257 8.971073 AGATGAGGGTTGAATACATTTTTAAGG 58.029 33.333 0.00 0.00 0.00 2.69
2994 3261 7.603784 GCAAAGATGAGGGTTGAATACATTTTT 59.396 33.333 0.00 0.00 0.00 1.94
2995 3262 7.038799 AGCAAAGATGAGGGTTGAATACATTTT 60.039 33.333 0.00 0.00 0.00 1.82
2996 3263 6.438425 AGCAAAGATGAGGGTTGAATACATTT 59.562 34.615 0.00 0.00 0.00 2.32
2997 3264 5.954150 AGCAAAGATGAGGGTTGAATACATT 59.046 36.000 0.00 0.00 0.00 2.71
2998 3265 5.513233 AGCAAAGATGAGGGTTGAATACAT 58.487 37.500 0.00 0.00 0.00 2.29
2999 3266 4.922206 AGCAAAGATGAGGGTTGAATACA 58.078 39.130 0.00 0.00 0.00 2.29
3000 3267 5.904362 AAGCAAAGATGAGGGTTGAATAC 57.096 39.130 0.00 0.00 0.00 1.89
3001 3268 7.175104 ACTAAAGCAAAGATGAGGGTTGAATA 58.825 34.615 0.00 0.00 0.00 1.75
3002 3269 6.012745 ACTAAAGCAAAGATGAGGGTTGAAT 58.987 36.000 0.00 0.00 0.00 2.57
3003 3270 5.385198 ACTAAAGCAAAGATGAGGGTTGAA 58.615 37.500 0.00 0.00 0.00 2.69
3008 3476 7.118390 CCGATAATACTAAAGCAAAGATGAGGG 59.882 40.741 0.00 0.00 0.00 4.30
3046 3514 6.259893 TGAAAAATAAATCCCCCATCTGTGA 58.740 36.000 0.00 0.00 0.00 3.58
3047 3515 6.155049 ACTGAAAAATAAATCCCCCATCTGTG 59.845 38.462 0.00 0.00 0.00 3.66
3079 3547 6.959639 AATTCCTACTTTTGAGTTGAAGCA 57.040 33.333 0.00 0.00 0.00 3.91
3088 3556 9.621629 TGAGTTTGAACTAATTCCTACTTTTGA 57.378 29.630 0.00 0.00 39.88 2.69
3119 3721 2.050691 GTGTGCATTTGTTTAGCGGTG 58.949 47.619 0.00 0.00 0.00 4.94
3121 3723 1.269448 AGGTGTGCATTTGTTTAGCGG 59.731 47.619 0.00 0.00 0.00 5.52
3575 4189 8.090214 GTGGGGATAATTGATGAAACATTATGG 58.910 37.037 0.00 0.00 0.00 2.74
3600 4214 6.040842 ACAAGCAAAATAATTGACCTCACAGT 59.959 34.615 0.00 0.00 0.00 3.55
3604 4218 8.081633 CACTAACAAGCAAAATAATTGACCTCA 58.918 33.333 0.00 0.00 0.00 3.86
3611 4225 9.515226 TCCTCTACACTAACAAGCAAAATAATT 57.485 29.630 0.00 0.00 0.00 1.40
3615 4229 8.947115 GTATTCCTCTACACTAACAAGCAAAAT 58.053 33.333 0.00 0.00 0.00 1.82
3616 4230 7.389607 GGTATTCCTCTACACTAACAAGCAAAA 59.610 37.037 0.00 0.00 0.00 2.44
3617 4231 6.877322 GGTATTCCTCTACACTAACAAGCAAA 59.123 38.462 0.00 0.00 0.00 3.68
3618 4232 6.014070 TGGTATTCCTCTACACTAACAAGCAA 60.014 38.462 0.00 0.00 34.23 3.91
3619 4233 5.482526 TGGTATTCCTCTACACTAACAAGCA 59.517 40.000 0.00 0.00 34.23 3.91
3661 4798 1.153539 TCCAGTCCAAACCCATCCAA 58.846 50.000 0.00 0.00 0.00 3.53
3670 4807 5.762179 ACAGATAGTCAATCCAGTCCAAA 57.238 39.130 0.00 0.00 34.90 3.28
3676 4813 5.256474 ACCCAAAACAGATAGTCAATCCAG 58.744 41.667 0.00 0.00 34.90 3.86
3692 4865 0.689080 TGGCTTGCCAGAACCCAAAA 60.689 50.000 10.65 0.00 0.00 2.44
3825 5004 8.815565 TTTGGTCTATATAACAAAATCAGCCA 57.184 30.769 0.00 0.00 30.67 4.75
3934 5114 3.792794 GCTTCTACGAGCTAACCTGCTAC 60.793 52.174 0.00 0.00 44.17 3.58
3966 5146 7.228652 AGGCCAATTATAGTAAAACCCCTTA 57.771 36.000 5.01 0.00 0.00 2.69
3975 5155 9.161572 TGTCCTGTAATAGGCCAATTATAGTAA 57.838 33.333 5.01 0.84 46.87 2.24
4049 5246 6.889722 AGCCATTAATAGTTCAGGCAGTTTAA 59.110 34.615 13.08 0.00 44.34 1.52
4050 5247 6.423182 AGCCATTAATAGTTCAGGCAGTTTA 58.577 36.000 13.08 0.00 44.34 2.01
4051 5248 5.264395 AGCCATTAATAGTTCAGGCAGTTT 58.736 37.500 13.08 0.00 44.34 2.66
4052 5249 4.860022 AGCCATTAATAGTTCAGGCAGTT 58.140 39.130 13.08 0.00 44.34 3.16
4070 5267 3.857157 ACTGAAGGTCAACTAAAGCCA 57.143 42.857 0.00 0.00 0.00 4.75
4078 5275 1.261619 CAGCGACAACTGAAGGTCAAC 59.738 52.381 0.00 0.00 40.25 3.18
4214 5426 9.646522 ATGCTCCTATTTTGTACCTAAAATCAT 57.353 29.630 7.07 3.33 39.96 2.45
4302 5911 7.518731 TGCGCTGTGGAATAAAATTTATTTC 57.481 32.000 9.73 10.48 0.00 2.17
4354 5963 1.202428 GGCCCTAGTCAAGTCGTCATC 60.202 57.143 0.00 0.00 0.00 2.92
4382 5991 1.630369 AGCTGGACAGGCACTTGAATA 59.370 47.619 1.01 0.00 34.60 1.75
4441 6077 7.468441 TCAAAATGCACGACGAATAAACATAT 58.532 30.769 0.00 0.00 0.00 1.78
4514 7473 2.632377 GAAACCATGATTCCTCTGCGA 58.368 47.619 0.00 0.00 0.00 5.10
4614 7573 1.950484 GCGACCATCACCCTCATTGTT 60.950 52.381 0.00 0.00 0.00 2.83
4628 7587 2.279851 CCGTGTTGTCTGCGACCA 60.280 61.111 6.30 0.00 0.00 4.02
4689 7651 1.500512 GCTTTGGTGTCGGCGTTGTA 61.501 55.000 6.85 0.00 0.00 2.41
4690 7652 2.830285 GCTTTGGTGTCGGCGTTGT 61.830 57.895 6.85 0.00 0.00 3.32
4691 7653 2.051345 GCTTTGGTGTCGGCGTTG 60.051 61.111 6.85 0.00 0.00 4.10
4692 7654 3.284449 GGCTTTGGTGTCGGCGTT 61.284 61.111 6.85 0.00 0.00 4.84
4693 7655 4.555709 TGGCTTTGGTGTCGGCGT 62.556 61.111 6.85 0.00 0.00 5.68
4694 7656 2.731587 CTTTGGCTTTGGTGTCGGCG 62.732 60.000 0.00 0.00 0.00 6.46
4698 7660 1.269723 GTAGGCTTTGGCTTTGGTGTC 59.730 52.381 0.00 0.00 39.70 3.67
4701 7663 1.328279 GTGTAGGCTTTGGCTTTGGT 58.672 50.000 0.00 0.00 39.70 3.67
4710 7672 1.302511 CGGCACTGGTGTAGGCTTT 60.303 57.895 0.00 0.00 0.00 3.51
4774 7736 0.752054 CATCTCTCCAGGTGAGCTCC 59.248 60.000 12.15 2.19 41.18 4.70
4777 7739 0.104671 GAGCATCTCTCCAGGTGAGC 59.895 60.000 13.06 3.71 41.18 4.26
4976 7953 4.647853 AGACAGTATTTCGTAGTATGGCCA 59.352 41.667 8.56 8.56 0.00 5.36
4978 7955 7.818642 AGATAGACAGTATTTCGTAGTATGGC 58.181 38.462 0.00 0.00 0.00 4.40
4980 7957 9.814507 GTGAGATAGACAGTATTTCGTAGTATG 57.185 37.037 0.00 0.00 0.00 2.39
4996 7973 6.262601 GCAGTTCTAGTCTTGTGAGATAGAC 58.737 44.000 0.00 0.00 40.82 2.59
5139 8125 7.286087 TCGGTTACATGACTTGTACTATGGTAT 59.714 37.037 0.00 0.00 40.53 2.73
5142 8128 5.747197 GTCGGTTACATGACTTGTACTATGG 59.253 44.000 0.00 0.00 40.53 2.74
5157 8143 1.134037 AGTTTTGCCAGGTCGGTTACA 60.134 47.619 0.00 0.00 36.97 2.41
5255 8254 2.358247 GACGGGCGTTGGTGTCAT 60.358 61.111 0.00 0.00 0.00 3.06
5326 8326 0.242825 CTACGAGCTCGGGTGTGAAA 59.757 55.000 36.93 12.52 44.95 2.69
5405 8405 4.624024 GTCTGATTCGTTCAACGGTAATGA 59.376 41.667 10.69 1.13 42.81 2.57
5589 8591 2.638363 GTTTGGGAGGTAGTTCAGGAGT 59.362 50.000 0.00 0.00 0.00 3.85
5654 8656 1.203250 TGTGGTGGACCTGTATCCTCA 60.203 52.381 0.00 0.00 39.75 3.86
5734 8736 1.227176 GCGACCGGTCCTATGGTTC 60.227 63.158 28.52 1.12 38.99 3.62


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

AutoCloner maintained by Alex Coulton.