Multiple sequence alignment - TraesCS3D01G170500

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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 TraesCS3D01G170500 chr3D 100.000 6717 0 0 1 6717 149552031 149545315 0.000000e+00 12405.0
1 TraesCS3D01G170500 chr3D 90.347 1036 97 1 2538 3573 149763592 149764624 0.000000e+00 1356.0
2 TraesCS3D01G170500 chr3D 95.117 471 15 5 5482 5949 149767058 149767523 0.000000e+00 736.0
3 TraesCS3D01G170500 chr3D 87.184 632 58 11 3582 4201 149764801 149765421 0.000000e+00 697.0
4 TraesCS3D01G170500 chr3D 86.565 588 48 12 3486 4063 149234478 149233912 2.660000e-173 619.0
5 TraesCS3D01G170500 chr3D 86.395 588 49 10 3486 4063 147325099 147325665 1.240000e-171 614.0
6 TraesCS3D01G170500 chr3D 84.201 557 53 9 3509 4055 149208005 149207474 6.010000e-140 508.0
7 TraesCS3D01G170500 chr3D 83.662 557 56 11 3509 4055 147332805 147333336 6.050000e-135 492.0
8 TraesCS3D01G170500 chr3D 85.655 481 43 15 3063 3533 360693470 360693006 3.640000e-132 483.0
9 TraesCS3D01G170500 chr3D 88.533 375 39 3 2978 3350 152696507 152696879 1.030000e-122 451.0
10 TraesCS3D01G170500 chr3D 86.544 379 30 13 5574 5949 149207364 149207004 1.360000e-106 398.0
11 TraesCS3D01G170500 chr3D 83.630 281 41 3 2225 2505 149763320 149763595 6.680000e-65 259.0
12 TraesCS3D01G170500 chr3D 99.057 106 1 0 6612 6717 147334561 147334666 2.470000e-44 191.0
13 TraesCS3D01G170500 chr3D 100.000 103 0 0 6615 6717 149206246 149206144 2.470000e-44 191.0
14 TraesCS3D01G170500 chr3D 93.421 76 5 0 6115 6190 141412169 141412094 5.510000e-21 113.0
15 TraesCS3D01G170500 chr3D 95.082 61 3 0 3366 3426 152701116 152701176 5.540000e-16 97.1
16 TraesCS3D01G170500 chr3D 87.324 71 4 5 4132 4201 147333360 147333426 7.220000e-10 76.8
17 TraesCS3D01G170500 chr3D 89.655 58 3 3 4145 4201 149207439 149207384 3.360000e-08 71.3
18 TraesCS3D01G170500 chr3D 94.872 39 2 0 4208 4246 223477131 223477169 2.020000e-05 62.1
19 TraesCS3D01G170500 chr3D 96.774 31 1 0 3353 3383 152701077 152701107 1.200000e-02 52.8
20 TraesCS3D01G170500 chr3A 96.347 4271 133 14 625 4881 166930995 166926734 0.000000e+00 7001.0
21 TraesCS3D01G170500 chr3A 91.796 1548 77 20 5049 6552 166926232 166924691 0.000000e+00 2109.0
22 TraesCS3D01G170500 chr3A 88.978 871 78 5 2538 3407 181135567 181134714 0.000000e+00 1061.0
23 TraesCS3D01G170500 chr3A 94.017 468 19 5 5485 5949 181107799 181107338 0.000000e+00 701.0
24 TraesCS3D01G170500 chr3A 86.551 632 60 12 3582 4201 181110045 181109427 0.000000e+00 673.0
25 TraesCS3D01G170500 chr3A 89.135 451 39 5 4 454 167672919 167672479 2.740000e-153 553.0
26 TraesCS3D01G170500 chr3A 87.696 382 36 6 2978 3350 177893695 177893316 1.030000e-117 435.0
27 TraesCS3D01G170500 chr3A 92.672 232 8 2 6493 6716 166924719 166924489 6.500000e-85 326.0
28 TraesCS3D01G170500 chr3A 92.899 169 11 1 3405 3573 181110389 181110222 1.870000e-60 244.0
29 TraesCS3D01G170500 chr3A 92.908 141 9 1 451 591 166932287 166932148 3.180000e-48 204.0
30 TraesCS3D01G170500 chr3A 86.316 95 13 0 6115 6209 159834464 159834370 3.310000e-18 104.0
31 TraesCS3D01G170500 chr3A 93.651 63 4 0 3367 3429 177889409 177889347 1.990000e-15 95.3
32 TraesCS3D01G170500 chr3A 84.211 95 14 1 6115 6209 159441377 159441284 2.580000e-14 91.6
33 TraesCS3D01G170500 chr3A 97.143 35 1 0 4212 4246 283094820 283094786 7.270000e-05 60.2
34 TraesCS3D01G170500 chr3A 100.000 31 0 0 3353 3383 177889449 177889419 2.620000e-04 58.4
35 TraesCS3D01G170500 chr3B 96.430 2913 86 7 713 3611 221987719 221984811 0.000000e+00 4787.0
36 TraesCS3D01G170500 chr3B 89.077 1474 79 33 5013 6408 221982996 221981527 0.000000e+00 1755.0
37 TraesCS3D01G170500 chr3B 89.719 924 53 20 5523 6408 221914962 221914043 0.000000e+00 1142.0
38 TraesCS3D01G170500 chr3B 96.769 681 20 2 3603 4283 221984767 221984089 0.000000e+00 1134.0
39 TraesCS3D01G170500 chr3B 90.192 887 52 14 5007 5861 221468748 221467865 0.000000e+00 1123.0
40 TraesCS3D01G170500 chr3B 87.974 923 67 22 5523 6409 215387702 215386788 0.000000e+00 1050.0
41 TraesCS3D01G170500 chr3B 93.838 568 28 2 5523 6090 215116175 215115615 0.000000e+00 848.0
42 TraesCS3D01G170500 chr3B 93.684 570 30 4 5523 6090 221753622 221753057 0.000000e+00 848.0
43 TraesCS3D01G170500 chr3B 90.581 637 48 4 4350 4982 221983898 221983270 0.000000e+00 833.0
44 TraesCS3D01G170500 chr3B 90.312 609 48 7 6115 6717 215115546 215114943 0.000000e+00 787.0
45 TraesCS3D01G170500 chr3B 88.971 544 37 6 6180 6717 221750790 221750264 0.000000e+00 651.0
46 TraesCS3D01G170500 chr3B 91.134 485 34 7 4154 4632 221469290 221468809 0.000000e+00 649.0
47 TraesCS3D01G170500 chr3B 86.577 596 62 11 3063 3649 469633136 469632550 5.680000e-180 641.0
48 TraesCS3D01G170500 chr3B 87.444 446 45 7 80 523 221989250 221988814 2.800000e-138 503.0
49 TraesCS3D01G170500 chr3B 84.201 557 42 18 5889 6409 221467871 221467325 3.620000e-137 499.0
50 TraesCS3D01G170500 chr3B 84.615 494 48 11 3572 4063 215589080 215588613 3.670000e-127 466.0
51 TraesCS3D01G170500 chr3B 86.792 371 35 6 2978 3343 223525936 223526297 1.050000e-107 401.0
52 TraesCS3D01G170500 chr3B 95.745 141 4 2 4023 4162 221478744 221478605 6.780000e-55 226.0
53 TraesCS3D01G170500 chr3B 95.455 110 5 0 6608 6717 221466974 221466865 6.920000e-40 176.0
54 TraesCS3D01G170500 chr3B 95.455 110 5 0 6608 6717 221981081 221980972 6.920000e-40 176.0
55 TraesCS3D01G170500 chr3B 94.545 110 6 0 6608 6717 221913611 221913502 3.220000e-38 171.0
56 TraesCS3D01G170500 chr3B 97.030 101 2 1 6618 6717 215573230 215573130 1.160000e-37 169.0
57 TraesCS3D01G170500 chr3B 95.402 87 4 0 3487 3573 215589327 215589241 9.080000e-29 139.0
58 TraesCS3D01G170500 chr3B 95.082 61 3 0 3366 3426 223557456 223557516 5.540000e-16 97.1
59 TraesCS3D01G170500 chr3B 87.324 71 9 0 4212 4282 317613028 317612958 1.550000e-11 82.4
60 TraesCS3D01G170500 chr3B 97.059 34 1 0 626 659 221987732 221987699 2.620000e-04 58.4
61 TraesCS3D01G170500 chrUn 87.129 101 9 4 4192 4288 79949246 79949146 1.980000e-20 111.0
62 TraesCS3D01G170500 chr6A 84.615 104 10 6 4190 4288 7167076 7167178 1.540000e-16 99.0
63 TraesCS3D01G170500 chr5D 80.435 138 18 3 5385 5522 324781871 324781999 5.540000e-16 97.1
64 TraesCS3D01G170500 chr4A 83.146 89 14 1 4201 4288 610111309 610111221 5.580000e-11 80.5
65 TraesCS3D01G170500 chr4A 89.831 59 5 1 5415 5472 610111194 610111252 2.600000e-09 75.0


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 TraesCS3D01G170500 chr3D 149545315 149552031 6716 True 12405.000000 12405 100.000000 1 6717 1 chr3D.!!$R3 6716
1 TraesCS3D01G170500 chr3D 149763320 149767523 4203 False 762.000000 1356 89.069500 2225 5949 4 chr3D.!!$F5 3724
2 TraesCS3D01G170500 chr3D 149233912 149234478 566 True 619.000000 619 86.565000 3486 4063 1 chr3D.!!$R2 577
3 TraesCS3D01G170500 chr3D 147325099 147325665 566 False 614.000000 614 86.395000 3486 4063 1 chr3D.!!$F1 577
4 TraesCS3D01G170500 chr3D 149206144 149208005 1861 True 292.075000 508 90.100000 3509 6717 4 chr3D.!!$R5 3208
5 TraesCS3D01G170500 chr3D 147332805 147334666 1861 False 253.266667 492 90.014333 3509 6717 3 chr3D.!!$F4 3208
6 TraesCS3D01G170500 chr3A 166924489 166932287 7798 True 2410.000000 7001 93.430750 451 6716 4 chr3A.!!$R6 6265
7 TraesCS3D01G170500 chr3A 181134714 181135567 853 True 1061.000000 1061 88.978000 2538 3407 1 chr3A.!!$R4 869
8 TraesCS3D01G170500 chr3A 181107338 181110389 3051 True 539.333333 701 91.155667 3405 5949 3 chr3A.!!$R8 2544
9 TraesCS3D01G170500 chr3B 221980972 221989250 8278 True 1320.914286 4787 93.259286 80 6717 7 chr3B.!!$R11 6637
10 TraesCS3D01G170500 chr3B 215386788 215387702 914 True 1050.000000 1050 87.974000 5523 6409 1 chr3B.!!$R1 886
11 TraesCS3D01G170500 chr3B 215114943 215116175 1232 True 817.500000 848 92.075000 5523 6717 2 chr3B.!!$R6 1194
12 TraesCS3D01G170500 chr3B 221750264 221753622 3358 True 749.500000 848 91.327500 5523 6717 2 chr3B.!!$R9 1194
13 TraesCS3D01G170500 chr3B 221913502 221914962 1460 True 656.500000 1142 92.132000 5523 6717 2 chr3B.!!$R10 1194
14 TraesCS3D01G170500 chr3B 469632550 469633136 586 True 641.000000 641 86.577000 3063 3649 1 chr3B.!!$R5 586
15 TraesCS3D01G170500 chr3B 221466865 221469290 2425 True 611.750000 1123 90.245500 4154 6717 4 chr3B.!!$R8 2563
16 TraesCS3D01G170500 chr3B 215588613 215589327 714 True 302.500000 466 90.008500 3487 4063 2 chr3B.!!$R7 576

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
433 434 0.251341 TTTTTGCAGCCTCTCCCTCC 60.251 55.000 0.00 0.0 0.00 4.30 F
1095 3178 1.544724 AGCTCTTCTCGCTGAGACTT 58.455 50.000 7.61 0.0 38.51 3.01 F
1531 3628 0.174845 TTCGGGATAGTGCGTTCCAG 59.825 55.000 0.00 0.0 33.43 3.86 F
3034 5133 1.975680 AGTGAGGGAAAAAGAGGCGTA 59.024 47.619 0.00 0.0 0.00 4.42 F
4347 6712 0.256464 TTTGACCACGTTGACCCCTT 59.744 50.000 0.00 0.0 0.00 3.95 F
5102 8036 0.039074 AGCGAGTGTGGTCGAAGAAG 60.039 55.000 0.00 0.0 42.85 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1510 3607 0.175073 GGAACGCACTATCCCGAACT 59.825 55.000 0.00 0.0 0.00 3.01 R
2653 4751 0.986527 AGTGTGTGATGCCTGGATGA 59.013 50.000 0.00 0.0 0.00 2.92 R
3042 5141 1.147817 ACCCTTCATTGCTCCCAGTTT 59.852 47.619 0.00 0.0 0.00 2.66 R
4415 6899 0.177141 GACATGGCCGGTAGCTGTTA 59.823 55.000 1.90 0.0 43.05 2.41 R
5435 9121 0.898326 CCCACACCCTTAACTTGCCC 60.898 60.000 0.00 0.0 0.00 5.36 R
6015 9879 2.353376 CAACCGTTGTTGCTGGCG 60.353 61.111 2.87 0.0 44.86 5.69 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 9.834628 GACGGATTTTATTCATAGTTCAAAACA 57.165 29.630 0.00 0.00 0.00 2.83
37 38 9.952030 TTCATAGTTCAAAACATGAGGTATACA 57.048 29.630 5.01 0.00 39.77 2.29
38 39 9.952030 TCATAGTTCAAAACATGAGGTATACAA 57.048 29.630 5.01 0.00 39.77 2.41
40 41 7.145932 AGTTCAAAACATGAGGTATACAAGC 57.854 36.000 5.01 0.00 39.77 4.01
41 42 6.714810 AGTTCAAAACATGAGGTATACAAGCA 59.285 34.615 5.01 0.00 39.77 3.91
42 43 7.230510 AGTTCAAAACATGAGGTATACAAGCAA 59.769 33.333 5.01 0.00 39.77 3.91
43 44 7.701539 TCAAAACATGAGGTATACAAGCAAT 57.298 32.000 5.01 0.00 33.04 3.56
44 45 8.121305 TCAAAACATGAGGTATACAAGCAATT 57.879 30.769 5.01 0.00 33.04 2.32
45 46 8.584157 TCAAAACATGAGGTATACAAGCAATTT 58.416 29.630 5.01 2.94 33.04 1.82
46 47 8.863049 CAAAACATGAGGTATACAAGCAATTTC 58.137 33.333 5.01 0.00 0.00 2.17
47 48 6.363577 ACATGAGGTATACAAGCAATTTCG 57.636 37.500 5.01 0.00 0.00 3.46
48 49 5.296780 ACATGAGGTATACAAGCAATTTCGG 59.703 40.000 5.01 0.00 0.00 4.30
49 50 4.196193 TGAGGTATACAAGCAATTTCGGG 58.804 43.478 5.01 0.00 0.00 5.14
50 51 4.080807 TGAGGTATACAAGCAATTTCGGGA 60.081 41.667 5.01 0.00 0.00 5.14
51 52 4.850680 AGGTATACAAGCAATTTCGGGAA 58.149 39.130 5.01 0.00 0.00 3.97
52 53 5.445964 AGGTATACAAGCAATTTCGGGAAT 58.554 37.500 5.01 0.00 0.00 3.01
53 54 5.891551 AGGTATACAAGCAATTTCGGGAATT 59.108 36.000 5.01 0.00 38.49 2.17
54 55 7.057894 AGGTATACAAGCAATTTCGGGAATTA 58.942 34.615 5.01 0.00 35.79 1.40
55 56 7.724061 AGGTATACAAGCAATTTCGGGAATTAT 59.276 33.333 5.01 0.00 35.79 1.28
56 57 8.021396 GGTATACAAGCAATTTCGGGAATTATC 58.979 37.037 5.01 0.00 35.79 1.75
57 58 5.262588 ACAAGCAATTTCGGGAATTATCC 57.737 39.130 0.00 0.00 45.77 2.59
69 70 4.917906 GGAATTATCCCTAGCCACAGAT 57.082 45.455 0.00 0.00 40.10 2.90
70 71 4.583871 GGAATTATCCCTAGCCACAGATG 58.416 47.826 0.00 0.00 40.10 2.90
71 72 4.566488 GGAATTATCCCTAGCCACAGATGG 60.566 50.000 0.00 0.00 43.80 3.51
72 73 6.990620 GGAATTATCCCTAGCCACAGATGGT 61.991 48.000 0.00 0.00 43.28 3.55
73 74 8.925233 GGAATTATCCCTAGCCACAGATGGTG 62.925 50.000 0.00 0.00 43.28 4.17
88 89 1.982660 TGGTGTCCTATAGCCTCTCG 58.017 55.000 0.00 0.00 0.00 4.04
89 90 1.249407 GGTGTCCTATAGCCTCTCGG 58.751 60.000 0.00 0.00 0.00 4.63
93 94 1.887854 GTCCTATAGCCTCTCGGTTCC 59.112 57.143 0.00 0.00 0.00 3.62
94 95 1.203025 TCCTATAGCCTCTCGGTTCCC 60.203 57.143 0.00 0.00 0.00 3.97
105 106 4.620437 GGTTCCCGAAACGCAAAC 57.380 55.556 0.00 0.00 38.87 2.93
121 122 3.372060 GCAAACAGACACTAGCAAAACC 58.628 45.455 0.00 0.00 0.00 3.27
123 124 3.577805 AACAGACACTAGCAAAACCCT 57.422 42.857 0.00 0.00 0.00 4.34
150 151 4.342092 TCCTGTGATTGATCTCGCTCATAA 59.658 41.667 0.00 0.00 0.00 1.90
189 190 3.355378 TGCAGTCCCCTTGTTGATATTG 58.645 45.455 0.00 0.00 0.00 1.90
190 191 3.245229 TGCAGTCCCCTTGTTGATATTGT 60.245 43.478 0.00 0.00 0.00 2.71
192 193 4.335594 GCAGTCCCCTTGTTGATATTGTAC 59.664 45.833 0.00 0.00 0.00 2.90
194 195 5.943416 CAGTCCCCTTGTTGATATTGTACAA 59.057 40.000 11.41 11.41 0.00 2.41
195 196 5.944007 AGTCCCCTTGTTGATATTGTACAAC 59.056 40.000 11.22 0.00 44.21 3.32
196 197 5.944007 GTCCCCTTGTTGATATTGTACAACT 59.056 40.000 11.22 0.84 44.25 3.16
197 198 6.433093 GTCCCCTTGTTGATATTGTACAACTT 59.567 38.462 11.22 0.64 44.25 2.66
198 199 6.657541 TCCCCTTGTTGATATTGTACAACTTC 59.342 38.462 11.22 11.12 44.25 3.01
199 200 6.432783 CCCCTTGTTGATATTGTACAACTTCA 59.567 38.462 11.22 13.58 44.25 3.02
200 201 7.040062 CCCCTTGTTGATATTGTACAACTTCAA 60.040 37.037 22.05 22.05 44.25 2.69
230 231 7.596749 GCAATAGTATGCGATAATTAGGTGT 57.403 36.000 0.00 0.00 36.45 4.16
232 233 7.117812 GCAATAGTATGCGATAATTAGGTGTGT 59.882 37.037 0.00 0.00 36.45 3.72
246 247 1.339151 GGTGTGTGAGATTGAGGTCCC 60.339 57.143 0.00 0.00 0.00 4.46
247 248 1.347707 GTGTGTGAGATTGAGGTCCCA 59.652 52.381 0.00 0.00 0.00 4.37
268 269 0.524816 GCAATGCGAGTGCCTCATTG 60.525 55.000 9.15 9.15 45.80 2.82
272 273 1.354506 GCGAGTGCCTCATTGCATC 59.645 57.895 0.00 0.00 44.30 3.91
338 339 2.394563 GCAGAAGCTCCCACGAAGC 61.395 63.158 0.00 0.00 40.14 3.86
341 342 2.048127 AAGCTCCCACGAAGCGAC 60.048 61.111 0.00 0.00 44.59 5.19
359 360 1.426215 GACCCTCCTCCTCCCTACTAG 59.574 61.905 0.00 0.00 0.00 2.57
362 363 1.203001 CCTCCTCCTCCCTACTAGCAG 60.203 61.905 0.00 0.00 0.00 4.24
380 381 1.130054 AGTCACCTCTGCACCCATGT 61.130 55.000 0.00 0.00 0.00 3.21
390 391 1.446445 CACCCATGTTGCAATGGCG 60.446 57.895 12.80 9.08 45.03 5.69
393 394 1.314534 CCCATGTTGCAATGGCGAGA 61.315 55.000 12.80 0.00 45.03 4.04
408 409 1.332195 CGAGATAGCCCACCATCAGA 58.668 55.000 0.00 0.00 0.00 3.27
409 410 1.271934 CGAGATAGCCCACCATCAGAG 59.728 57.143 0.00 0.00 0.00 3.35
411 412 2.298729 GAGATAGCCCACCATCAGAGTC 59.701 54.545 0.00 0.00 0.00 3.36
420 421 4.096984 CCCACCATCAGAGTCTATTTTTGC 59.903 45.833 0.00 0.00 0.00 3.68
433 434 0.251341 TTTTTGCAGCCTCTCCCTCC 60.251 55.000 0.00 0.00 0.00 4.30
434 435 2.142292 TTTTGCAGCCTCTCCCTCCC 62.142 60.000 0.00 0.00 0.00 4.30
435 436 3.569361 TTGCAGCCTCTCCCTCCCT 62.569 63.158 0.00 0.00 0.00 4.20
436 437 3.160748 GCAGCCTCTCCCTCCCTC 61.161 72.222 0.00 0.00 0.00 4.30
437 438 2.837291 CAGCCTCTCCCTCCCTCG 60.837 72.222 0.00 0.00 0.00 4.63
438 439 3.351885 AGCCTCTCCCTCCCTCGT 61.352 66.667 0.00 0.00 0.00 4.18
454 455 4.830600 TCCCTCGTGTGCAATCTATATACA 59.169 41.667 0.00 0.00 0.00 2.29
465 466 6.923508 TGCAATCTATATACAAACCGTCTGAG 59.076 38.462 0.00 0.00 0.00 3.35
470 471 7.058525 TCTATATACAAACCGTCTGAGAAGGA 58.941 38.462 21.20 0.00 34.89 3.36
471 472 2.821991 ACAAACCGTCTGAGAAGGAG 57.178 50.000 21.20 12.01 34.89 3.69
484 485 2.492484 GAGAAGGAGTAAGCGAAGGACA 59.508 50.000 0.00 0.00 0.00 4.02
485 486 2.897969 AGAAGGAGTAAGCGAAGGACAA 59.102 45.455 0.00 0.00 0.00 3.18
527 528 5.517904 GCATCAGCTATTTTCAGGTCAATC 58.482 41.667 0.00 0.00 37.91 2.67
662 2743 6.260271 AGTTGGGCTTCTATAACGAAATTAGC 59.740 38.462 0.00 0.00 0.00 3.09
663 2744 5.061179 TGGGCTTCTATAACGAAATTAGCC 58.939 41.667 0.00 0.00 37.93 3.93
693 2774 9.616156 TTAGGCAAATATAACGAAATTAGTGGA 57.384 29.630 0.00 0.00 0.00 4.02
700 2781 2.277084 ACGAAATTAGTGGATGCGGTC 58.723 47.619 0.00 0.00 0.00 4.79
790 2873 1.926561 CAGCAGTTGCATAGTCGCTA 58.073 50.000 6.90 0.00 45.16 4.26
798 2881 1.954382 TGCATAGTCGCTACCCACTAG 59.046 52.381 0.00 0.00 0.00 2.57
884 2967 4.992511 TTTTCCCCGCACCGACCG 62.993 66.667 0.00 0.00 0.00 4.79
1026 3109 4.254492 GGCCGTGTTCTCTAGATTTCTTT 58.746 43.478 0.00 0.00 0.00 2.52
1057 3140 8.519799 TTCTTCATCTGTTTCCTTGTAAGTTT 57.480 30.769 0.00 0.00 0.00 2.66
1095 3178 1.544724 AGCTCTTCTCGCTGAGACTT 58.455 50.000 7.61 0.00 38.51 3.01
1189 3272 2.366916 CCTGGAGCTGATTAATCTCGGT 59.633 50.000 16.24 12.18 0.00 4.69
1190 3273 3.574396 CCTGGAGCTGATTAATCTCGGTA 59.426 47.826 16.24 0.00 0.00 4.02
1218 3301 6.155049 TGGTGGTTAGGTCTTGGTTAGTATAC 59.845 42.308 0.00 0.00 0.00 1.47
1283 3376 9.372369 GACTGATTAGGATTAATTTATCTCCGG 57.628 37.037 0.00 0.00 32.87 5.14
1284 3377 8.322091 ACTGATTAGGATTAATTTATCTCCGGG 58.678 37.037 0.00 0.00 32.87 5.73
1320 3413 2.584835 TCCATGTCCCTTTCTTGGTG 57.415 50.000 0.00 0.00 33.61 4.17
1358 3451 5.986135 GTGTAGAGCATTTGGACTATACTGG 59.014 44.000 0.00 0.00 32.96 4.00
1510 3607 9.897744 CTTTGCTTACAAATCATTCTGTTAGAA 57.102 29.630 0.00 0.00 44.54 2.10
1522 3619 6.380274 TCATTCTGTTAGAAGTTCGGGATAGT 59.620 38.462 0.00 0.00 37.69 2.12
1524 3621 4.113354 CTGTTAGAAGTTCGGGATAGTGC 58.887 47.826 0.00 0.00 0.00 4.40
1531 3628 0.174845 TTCGGGATAGTGCGTTCCAG 59.825 55.000 0.00 0.00 33.43 3.86
1596 3693 5.927689 TCAGTTGCTGCAATTTCCTTATTTG 59.072 36.000 19.11 0.00 0.00 2.32
1792 3890 2.305635 TGGATGTGCCAGTAAGTGACAT 59.694 45.455 0.00 0.00 43.33 3.06
1985 4083 2.338785 GCAGCTTGCCTCCAAGGAC 61.339 63.158 5.68 0.00 46.77 3.85
2205 4303 3.801114 AACAAAGAGGCAAGGAACAAC 57.199 42.857 0.00 0.00 0.00 3.32
2915 5013 3.996150 AACCTCAACTCTGCATTGTTG 57.004 42.857 19.62 19.62 43.28 3.33
2965 5063 2.485903 AGCGGTATCGACTCTACAGAG 58.514 52.381 0.00 4.67 41.29 3.35
3034 5133 1.975680 AGTGAGGGAAAAAGAGGCGTA 59.024 47.619 0.00 0.00 0.00 4.42
3042 5141 4.442706 GGAAAAAGAGGCGTATCAGATCA 58.557 43.478 0.00 0.00 0.00 2.92
3165 5267 5.263599 ACAAGGAGTTTGATATGATTGCCA 58.736 37.500 0.00 0.00 39.21 4.92
3408 5515 7.038729 TGAGAGAGTTTGAGAATCTGGTTACAT 60.039 37.037 0.00 0.00 34.92 2.29
3696 6026 4.858935 TCACGAAAGAAGGCAATCTTTTG 58.141 39.130 21.86 21.86 46.77 2.44
4231 6591 4.023193 GTCCACATTACAACCCTCAACTTG 60.023 45.833 0.00 0.00 0.00 3.16
4285 6645 2.218454 CCGGTTGTCCCACACCCTA 61.218 63.158 0.00 0.00 27.10 3.53
4347 6712 0.256464 TTTGACCACGTTGACCCCTT 59.744 50.000 0.00 0.00 0.00 3.95
4415 6899 0.965866 TGTTCTCTCTCACCGGCGAT 60.966 55.000 9.30 0.00 0.00 4.58
4564 7048 2.726691 CGACACGGTCATCGGCAAC 61.727 63.158 3.90 0.00 44.45 4.17
4577 7061 4.527157 GCAACTGCAGCGGCGATC 62.527 66.667 15.27 0.00 45.35 3.69
4603 7088 3.933542 GAGCTGGAGGAGGGGGTGT 62.934 68.421 0.00 0.00 0.00 4.16
4656 7144 2.516930 CGGTTGCCATGCCCCTAG 60.517 66.667 0.00 0.00 0.00 3.02
4658 7146 1.453928 GGTTGCCATGCCCCTAGTC 60.454 63.158 0.00 0.00 0.00 2.59
4695 7183 2.289072 CCACGACTCACTGATTCCTGTT 60.289 50.000 0.00 0.00 0.00 3.16
4702 7190 4.248859 CTCACTGATTCCTGTTGTCGATT 58.751 43.478 0.00 0.00 0.00 3.34
4748 7236 3.650950 GCAGAGGAGGTTGGGGCA 61.651 66.667 0.00 0.00 0.00 5.36
4943 7506 2.561569 CTCCGGTCAGAGTTTTTGTGT 58.438 47.619 0.00 0.00 0.00 3.72
4982 7545 1.676678 GCGGTATGTGGAGGAGCAGA 61.677 60.000 0.00 0.00 0.00 4.26
4983 7546 0.387202 CGGTATGTGGAGGAGCAGAG 59.613 60.000 0.00 0.00 0.00 3.35
4984 7547 0.105778 GGTATGTGGAGGAGCAGAGC 59.894 60.000 0.00 0.00 0.00 4.09
4987 7550 1.954362 ATGTGGAGGAGCAGAGCGTC 61.954 60.000 0.00 0.00 0.00 5.19
5008 7571 3.414700 GCACGACGACAGCTTGGG 61.415 66.667 0.00 0.00 0.00 4.12
5022 7828 0.323360 CTTGGGGGCGAAAGGATTGA 60.323 55.000 0.00 0.00 0.00 2.57
5026 7832 0.464554 GGGGCGAAAGGATTGAGGAG 60.465 60.000 0.00 0.00 0.00 3.69
5035 7841 1.135094 GGATTGAGGAGGATGGCTCA 58.865 55.000 0.00 0.00 0.00 4.26
5087 8021 3.019799 AGGACATAGAAAGAGGAGCGA 57.980 47.619 0.00 0.00 0.00 4.93
5097 8031 2.282251 AGGAGCGAGTGTGGTCGA 60.282 61.111 0.00 0.00 42.85 4.20
5102 8036 0.039074 AGCGAGTGTGGTCGAAGAAG 60.039 55.000 0.00 0.00 42.85 2.85
5237 8180 0.250209 CTGTCAGGCACTTGCTCACT 60.250 55.000 0.38 0.00 41.70 3.41
5271 8458 3.277962 CTCCATGGCAAAGGAGCTT 57.722 52.632 21.59 0.00 44.37 3.74
5399 8959 4.855105 ACTCAGCAGTCAACGCAA 57.145 50.000 0.00 0.00 0.00 4.85
5405 9091 2.031769 TCAGCAGTCAACGCAATCAAAG 60.032 45.455 0.00 0.00 0.00 2.77
5435 9121 2.562738 GGGGTTGATTTCTGAACCAAGG 59.437 50.000 0.00 0.00 43.07 3.61
5455 9141 0.111639 GGCAAGTTAAGGGTGTGGGA 59.888 55.000 0.00 0.00 0.00 4.37
5545 9377 4.379603 CGTCTAGGATTACCTATTGCTCCG 60.380 50.000 0.00 0.00 46.23 4.63
5614 9447 5.564651 CGTGATTTTCTTGCACCCTTACAAT 60.565 40.000 0.00 0.00 0.00 2.71
5884 9723 0.175989 GAGTAGCTTGTTCCCCTCCG 59.824 60.000 0.00 0.00 0.00 4.63
5885 9724 0.544595 AGTAGCTTGTTCCCCTCCGT 60.545 55.000 0.00 0.00 0.00 4.69
5886 9725 0.108281 GTAGCTTGTTCCCCTCCGTC 60.108 60.000 0.00 0.00 0.00 4.79
6015 9879 1.556911 TGCAGAGGGGAGACTTGATTC 59.443 52.381 0.00 0.00 0.00 2.52
6176 10152 7.342318 CAGTTGGCTGTTTTATTCTTCAATG 57.658 36.000 0.00 0.00 37.92 2.82
6378 12452 2.664916 ACAGTTTGCATTGTCGATTGC 58.335 42.857 10.07 10.07 39.33 3.56
6391 12465 3.505680 TGTCGATTGCAATTGTAGCCTTT 59.494 39.130 23.14 0.00 0.00 3.11
6397 12471 6.238456 CGATTGCAATTGTAGCCTTTATCAGA 60.238 38.462 14.33 0.00 0.00 3.27
6502 12820 8.917088 TGAAGAAATTCAGAGAAAAATGAACCT 58.083 29.630 0.00 0.00 38.19 3.50
6503 12821 9.755804 GAAGAAATTCAGAGAAAAATGAACCTT 57.244 29.630 0.00 0.00 38.19 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.834628 TGTTTTGAACTATGAATAAAATCCGTC 57.165 29.630 0.00 0.00 0.00 4.79
11 12 9.952030 TGTATACCTCATGTTTTGAACTATGAA 57.048 29.630 0.00 0.00 32.78 2.57
12 13 9.952030 TTGTATACCTCATGTTTTGAACTATGA 57.048 29.630 0.00 0.00 32.78 2.15
14 15 8.893727 GCTTGTATACCTCATGTTTTGAACTAT 58.106 33.333 0.00 0.00 32.78 2.12
15 16 7.880713 TGCTTGTATACCTCATGTTTTGAACTA 59.119 33.333 0.00 0.00 32.78 2.24
16 17 6.714810 TGCTTGTATACCTCATGTTTTGAACT 59.285 34.615 0.00 0.00 32.78 3.01
17 18 6.908825 TGCTTGTATACCTCATGTTTTGAAC 58.091 36.000 0.00 0.00 32.78 3.18
18 19 7.517614 TTGCTTGTATACCTCATGTTTTGAA 57.482 32.000 0.00 0.00 32.78 2.69
19 20 7.701539 ATTGCTTGTATACCTCATGTTTTGA 57.298 32.000 0.00 0.00 0.00 2.69
20 21 8.761575 AAATTGCTTGTATACCTCATGTTTTG 57.238 30.769 0.00 0.00 0.00 2.44
21 22 7.754924 CGAAATTGCTTGTATACCTCATGTTTT 59.245 33.333 0.00 0.00 0.00 2.43
22 23 7.250569 CGAAATTGCTTGTATACCTCATGTTT 58.749 34.615 0.00 0.00 0.00 2.83
23 24 6.183360 CCGAAATTGCTTGTATACCTCATGTT 60.183 38.462 0.00 0.00 0.00 2.71
24 25 5.296780 CCGAAATTGCTTGTATACCTCATGT 59.703 40.000 0.00 0.00 0.00 3.21
25 26 5.277974 CCCGAAATTGCTTGTATACCTCATG 60.278 44.000 0.00 0.00 0.00 3.07
26 27 4.821805 CCCGAAATTGCTTGTATACCTCAT 59.178 41.667 0.00 0.00 0.00 2.90
27 28 4.080807 TCCCGAAATTGCTTGTATACCTCA 60.081 41.667 0.00 0.00 0.00 3.86
28 29 4.448210 TCCCGAAATTGCTTGTATACCTC 58.552 43.478 0.00 0.00 0.00 3.85
29 30 4.497291 TCCCGAAATTGCTTGTATACCT 57.503 40.909 0.00 0.00 0.00 3.08
30 31 5.767816 ATTCCCGAAATTGCTTGTATACC 57.232 39.130 0.00 0.00 0.00 2.73
31 32 8.021396 GGATAATTCCCGAAATTGCTTGTATAC 58.979 37.037 0.00 0.00 38.08 1.47
32 33 8.106247 GGATAATTCCCGAAATTGCTTGTATA 57.894 34.615 6.13 0.00 38.08 1.47
33 34 6.981722 GGATAATTCCCGAAATTGCTTGTAT 58.018 36.000 6.13 0.00 38.08 2.29
34 35 6.385649 GGATAATTCCCGAAATTGCTTGTA 57.614 37.500 6.13 0.00 38.08 2.41
35 36 5.262588 GGATAATTCCCGAAATTGCTTGT 57.737 39.130 6.13 0.00 38.08 3.16
48 49 4.566488 CCATCTGTGGCTAGGGATAATTCC 60.566 50.000 0.00 0.00 39.01 3.01
49 50 4.583871 CCATCTGTGGCTAGGGATAATTC 58.416 47.826 0.00 0.00 39.01 2.17
50 51 4.647564 CCATCTGTGGCTAGGGATAATT 57.352 45.455 0.00 0.00 39.01 1.40
64 65 3.116939 AGAGGCTATAGGACACCATCTGT 60.117 47.826 1.04 0.00 34.96 3.41
65 66 3.505386 AGAGGCTATAGGACACCATCTG 58.495 50.000 1.04 0.00 0.00 2.90
66 67 3.773560 GAGAGGCTATAGGACACCATCT 58.226 50.000 1.04 0.00 0.00 2.90
67 68 2.490115 CGAGAGGCTATAGGACACCATC 59.510 54.545 1.04 0.00 0.00 3.51
68 69 2.520069 CGAGAGGCTATAGGACACCAT 58.480 52.381 1.04 0.00 0.00 3.55
69 70 1.982660 CGAGAGGCTATAGGACACCA 58.017 55.000 1.04 0.00 0.00 4.17
89 90 0.658897 TCTGTTTGCGTTTCGGGAAC 59.341 50.000 0.00 0.00 34.82 3.62
93 94 0.655733 AGTGTCTGTTTGCGTTTCGG 59.344 50.000 0.00 0.00 0.00 4.30
94 95 2.659291 GCTAGTGTCTGTTTGCGTTTCG 60.659 50.000 0.00 0.00 0.00 3.46
101 102 3.632145 AGGGTTTTGCTAGTGTCTGTTTG 59.368 43.478 0.00 0.00 0.00 2.93
104 105 3.214328 CAAGGGTTTTGCTAGTGTCTGT 58.786 45.455 0.00 0.00 0.00 3.41
105 106 2.030805 GCAAGGGTTTTGCTAGTGTCTG 60.031 50.000 4.73 0.00 41.87 3.51
121 122 3.204526 GAGATCAATCACAGGAGCAAGG 58.795 50.000 0.00 0.00 0.00 3.61
123 124 2.897436 CGAGATCAATCACAGGAGCAA 58.103 47.619 0.00 0.00 0.00 3.91
150 151 7.417116 GGGACTGCAAAACTCATATGATTTGAT 60.417 37.037 25.61 14.92 35.34 2.57
165 166 2.151502 TCAACAAGGGGACTGCAAAA 57.848 45.000 0.00 0.00 42.68 2.44
167 168 3.737559 ATATCAACAAGGGGACTGCAA 57.262 42.857 0.00 0.00 42.68 4.08
192 193 7.096763 CGCATACTATTGCATTGATTGAAGTTG 60.097 37.037 0.00 0.00 42.91 3.16
194 195 6.260714 TCGCATACTATTGCATTGATTGAAGT 59.739 34.615 0.00 0.00 42.91 3.01
195 196 6.661669 TCGCATACTATTGCATTGATTGAAG 58.338 36.000 0.00 0.00 42.91 3.02
196 197 6.616774 TCGCATACTATTGCATTGATTGAA 57.383 33.333 0.00 0.00 42.91 2.69
197 198 6.806388 ATCGCATACTATTGCATTGATTGA 57.194 33.333 0.00 0.00 42.91 2.57
198 199 9.563898 AATTATCGCATACTATTGCATTGATTG 57.436 29.630 0.00 0.00 42.91 2.67
211 212 6.040504 TCTCACACACCTAATTATCGCATACT 59.959 38.462 0.00 0.00 0.00 2.12
215 216 4.729227 TCTCACACACCTAATTATCGCA 57.271 40.909 0.00 0.00 0.00 5.10
223 224 3.260884 GGACCTCAATCTCACACACCTAA 59.739 47.826 0.00 0.00 0.00 2.69
230 231 1.279496 CCTGGGACCTCAATCTCACA 58.721 55.000 0.00 0.00 0.00 3.58
232 233 0.547471 TGCCTGGGACCTCAATCTCA 60.547 55.000 0.00 0.00 0.00 3.27
268 269 0.249322 GCATGGAAGCACATGGATGC 60.249 55.000 15.00 0.00 46.40 3.91
272 273 0.666913 GCTAGCATGGAAGCACATGG 59.333 55.000 10.63 3.48 46.40 3.66
329 330 4.452733 GGAGGGTCGCTTCGTGGG 62.453 72.222 0.00 0.00 0.00 4.61
338 339 1.152715 GTAGGGAGGAGGAGGGTCG 60.153 68.421 0.00 0.00 0.00 4.79
341 342 0.113580 GCTAGTAGGGAGGAGGAGGG 59.886 65.000 0.00 0.00 0.00 4.30
362 363 0.250901 AACATGGGTGCAGAGGTGAC 60.251 55.000 0.00 0.00 0.00 3.67
390 391 2.298729 GACTCTGATGGTGGGCTATCTC 59.701 54.545 0.00 0.00 34.22 2.75
393 394 2.485966 AGACTCTGATGGTGGGCTAT 57.514 50.000 0.00 0.00 0.00 2.97
408 409 3.615155 GGAGAGGCTGCAAAAATAGACT 58.385 45.455 0.50 0.00 34.20 3.24
409 410 2.685388 GGGAGAGGCTGCAAAAATAGAC 59.315 50.000 0.50 0.00 0.00 2.59
411 412 2.948315 GAGGGAGAGGCTGCAAAAATAG 59.052 50.000 0.50 0.00 0.00 1.73
420 421 2.837291 CGAGGGAGGGAGAGGCTG 60.837 72.222 0.00 0.00 0.00 4.85
433 434 6.073765 GGTTTGTATATAGATTGCACACGAGG 60.074 42.308 0.00 0.00 0.00 4.63
434 435 6.345803 CGGTTTGTATATAGATTGCACACGAG 60.346 42.308 0.00 0.00 0.00 4.18
435 436 5.460748 CGGTTTGTATATAGATTGCACACGA 59.539 40.000 0.00 0.00 0.00 4.35
436 437 5.233476 ACGGTTTGTATATAGATTGCACACG 59.767 40.000 0.00 0.00 0.00 4.49
437 438 6.479001 AGACGGTTTGTATATAGATTGCACAC 59.521 38.462 0.00 0.00 0.00 3.82
438 439 6.478673 CAGACGGTTTGTATATAGATTGCACA 59.521 38.462 0.00 0.00 0.00 4.57
454 455 3.306156 GCTTACTCCTTCTCAGACGGTTT 60.306 47.826 0.00 0.00 0.00 3.27
465 466 3.314541 TTGTCCTTCGCTTACTCCTTC 57.685 47.619 0.00 0.00 0.00 3.46
470 471 3.600388 CTCCATTTGTCCTTCGCTTACT 58.400 45.455 0.00 0.00 0.00 2.24
471 472 2.096013 GCTCCATTTGTCCTTCGCTTAC 59.904 50.000 0.00 0.00 0.00 2.34
484 485 2.154462 CTCGTGTTCCTTGCTCCATTT 58.846 47.619 0.00 0.00 0.00 2.32
485 486 1.813513 CTCGTGTTCCTTGCTCCATT 58.186 50.000 0.00 0.00 0.00 3.16
686 2767 2.011548 GCACATGACCGCATCCACTAA 61.012 52.381 0.00 0.00 30.68 2.24
693 2774 0.535780 CCCATAGCACATGACCGCAT 60.536 55.000 0.00 0.00 34.29 4.73
700 2781 0.396139 AGCCCAACCCATAGCACATG 60.396 55.000 0.00 0.00 0.00 3.21
790 2873 2.352032 GCTGTCGCCTCTAGTGGGT 61.352 63.158 12.65 0.00 0.00 4.51
839 2922 1.079503 CTTTCCTCTCCTTTTCCGCG 58.920 55.000 0.00 0.00 0.00 6.46
1026 3109 6.550854 ACAAGGAAACAGATGAAGAAAATGGA 59.449 34.615 0.00 0.00 0.00 3.41
1057 3140 1.687297 TACGCACCACCAAGGACACA 61.687 55.000 0.00 0.00 41.22 3.72
1095 3178 3.899052 ATATGGGAACGAGACCGAAAA 57.101 42.857 0.00 0.00 39.50 2.29
1189 3272 3.320129 ACCAAGACCTAACCACCAACTA 58.680 45.455 0.00 0.00 0.00 2.24
1190 3273 2.132686 ACCAAGACCTAACCACCAACT 58.867 47.619 0.00 0.00 0.00 3.16
1231 3324 9.965824 CACTCAAACATGGTAAAACTAGAAAAT 57.034 29.630 0.00 0.00 0.00 1.82
1238 3331 6.119536 TCAGTCACTCAAACATGGTAAAACT 58.880 36.000 0.00 0.00 0.00 2.66
1320 3413 3.490078 GCTCTACACCTGACTACATGCTC 60.490 52.174 0.00 0.00 0.00 4.26
1358 3451 2.271800 CGAGGATAAGGACACAAGCAC 58.728 52.381 0.00 0.00 0.00 4.40
1510 3607 0.175073 GGAACGCACTATCCCGAACT 59.825 55.000 0.00 0.00 0.00 3.01
1522 3619 2.101750 TCTAACAACAGACTGGAACGCA 59.898 45.455 7.51 0.00 0.00 5.24
1524 3621 3.736252 CACTCTAACAACAGACTGGAACG 59.264 47.826 7.51 0.00 0.00 3.95
1531 3628 4.811557 ACAAAGCTCACTCTAACAACAGAC 59.188 41.667 0.00 0.00 0.00 3.51
1694 3792 0.320247 AGCTCTCAGCCTGAACAACG 60.320 55.000 0.00 0.00 43.77 4.10
1753 3851 2.235650 TCCAAGCTCTCTTCACCATGAG 59.764 50.000 0.00 0.00 0.00 2.90
1985 4083 3.060895 GGTTCAGCAACGTTATCTCTTCG 59.939 47.826 0.00 0.00 32.68 3.79
2205 4303 5.183140 CCTTTGTTGTACCATTTCTACAGGG 59.817 44.000 0.00 0.00 0.00 4.45
2653 4751 0.986527 AGTGTGTGATGCCTGGATGA 59.013 50.000 0.00 0.00 0.00 2.92
2915 5013 4.155644 CAGCTCCTTTCCTCATTGAACTTC 59.844 45.833 0.00 0.00 0.00 3.01
2965 5063 4.379290 GCTTCAGTTTCTCAATCTCTTGCC 60.379 45.833 0.00 0.00 32.11 4.52
3034 5133 3.726557 TTGCTCCCAGTTTGATCTGAT 57.273 42.857 0.00 0.00 37.61 2.90
3042 5141 1.147817 ACCCTTCATTGCTCCCAGTTT 59.852 47.619 0.00 0.00 0.00 2.66
3165 5267 3.625348 GAGCTTGCTCCAGCCTGCT 62.625 63.158 11.24 13.14 45.92 4.24
3408 5515 9.755804 TTTGTTTGCAATGATAGTTTGTTGATA 57.244 25.926 0.00 0.00 34.18 2.15
3696 6026 2.947448 ATCGCAATGCCTTCCTTTTC 57.053 45.000 0.00 0.00 0.00 2.29
3889 6248 7.119699 TCAGAAATCACAACTCAATACATCACC 59.880 37.037 0.00 0.00 0.00 4.02
3922 6281 2.102578 GCCAAGTAAATCCACCTGCAT 58.897 47.619 0.00 0.00 0.00 3.96
4129 6489 7.446001 TGAAGAAACAAACCAGCAAAATTTT 57.554 28.000 0.00 0.00 0.00 1.82
4172 6532 1.534336 ATGCCCTCAAATTGCACGCA 61.534 50.000 0.00 3.86 37.92 5.24
4231 6591 2.396590 TGAATCCTAAACCGAGTGGC 57.603 50.000 0.00 0.00 39.70 5.01
4310 6674 3.120041 CAAACCAATCAAAACCGGTCAC 58.880 45.455 8.04 0.00 0.00 3.67
4313 6677 2.101750 GGTCAAACCAATCAAAACCGGT 59.898 45.455 0.00 0.00 38.42 5.28
4342 6707 1.064685 GGTCCCACATGTAAGAAGGGG 60.065 57.143 16.13 13.12 40.02 4.79
4397 6881 1.022735 TATCGCCGGTGAGAGAGAAC 58.977 55.000 24.04 0.00 0.00 3.01
4407 6891 1.440476 GGTAGCTGTTATCGCCGGT 59.560 57.895 1.90 0.00 0.00 5.28
4415 6899 0.177141 GACATGGCCGGTAGCTGTTA 59.823 55.000 1.90 0.00 43.05 2.41
4456 6940 2.420547 CCCTTCAATTGCAGATCGGAGA 60.421 50.000 6.67 0.00 45.75 3.71
4546 7030 2.431771 TTGCCGATGACCGTGTCG 60.432 61.111 0.00 0.00 34.95 4.35
4603 7088 1.065709 GCTTCCCACTAATTCCGACCA 60.066 52.381 0.00 0.00 0.00 4.02
4732 7220 1.225704 GATGCCCCAACCTCCTCTG 59.774 63.158 0.00 0.00 0.00 3.35
4760 7248 1.673665 CAGCCACCTTGACTGGAGC 60.674 63.158 0.00 0.00 0.00 4.70
4929 7492 0.380378 GGCGCACACAAAAACTCTGA 59.620 50.000 10.83 0.00 0.00 3.27
4967 7530 0.684479 ACGCTCTGCTCCTCCACATA 60.684 55.000 0.00 0.00 0.00 2.29
4991 7554 3.414700 CCCAAGCTGTCGTCGTGC 61.415 66.667 0.00 0.00 0.00 5.34
4992 7555 2.738521 CCCCAAGCTGTCGTCGTG 60.739 66.667 0.00 0.00 0.00 4.35
5001 7564 2.155197 AATCCTTTCGCCCCCAAGCT 62.155 55.000 0.00 0.00 0.00 3.74
5004 7567 0.323360 CTCAATCCTTTCGCCCCCAA 60.323 55.000 0.00 0.00 0.00 4.12
5008 7571 0.464554 CCTCCTCAATCCTTTCGCCC 60.465 60.000 0.00 0.00 0.00 6.13
5011 7574 2.843701 CCATCCTCCTCAATCCTTTCG 58.156 52.381 0.00 0.00 0.00 3.46
5022 7828 1.277580 CCCTTGTGAGCCATCCTCCT 61.278 60.000 0.00 0.00 39.98 3.69
5026 7832 2.048603 GCACCCTTGTGAGCCATCC 61.049 63.158 0.00 0.00 45.76 3.51
5035 7841 0.392998 GGATGTCGATGCACCCTTGT 60.393 55.000 0.00 0.00 0.00 3.16
5077 8011 1.867919 CGACCACACTCGCTCCTCTT 61.868 60.000 0.00 0.00 0.00 2.85
5087 8021 1.996798 TCTCCTTCTTCGACCACACT 58.003 50.000 0.00 0.00 0.00 3.55
5097 8031 1.908483 GCCCCACGATCTCCTTCTT 59.092 57.895 0.00 0.00 0.00 2.52
5120 8054 2.359230 GCCGGCTCTGACAAGCTT 60.359 61.111 22.15 0.00 42.13 3.74
5399 8959 2.106338 CAACCCCCTTTTTGGCTTTGAT 59.894 45.455 0.00 0.00 0.00 2.57
5405 9091 2.371841 AGAAATCAACCCCCTTTTTGGC 59.628 45.455 0.00 0.00 0.00 4.52
5435 9121 0.898326 CCCACACCCTTAACTTGCCC 60.898 60.000 0.00 0.00 0.00 5.36
5455 9141 3.181437 ACTGAGAACCCAAAACCGGTTAT 60.181 43.478 22.60 8.26 43.75 1.89
5545 9377 5.531122 TTCCTACCACACTAGCATGATAC 57.469 43.478 0.00 0.00 0.00 2.24
5591 9423 4.846779 TGTAAGGGTGCAAGAAAATCAC 57.153 40.909 0.00 0.00 0.00 3.06
5614 9447 7.040062 ACCCGACAGAAACATCAAAATCATAAA 60.040 33.333 0.00 0.00 0.00 1.40
5884 9723 3.522553 AGCAAAATCTACTGCCTACGAC 58.477 45.455 0.00 0.00 39.47 4.34
5885 9724 3.887621 AGCAAAATCTACTGCCTACGA 57.112 42.857 0.00 0.00 39.47 3.43
5886 9725 4.683832 ACTAGCAAAATCTACTGCCTACG 58.316 43.478 0.00 0.00 39.47 3.51
6015 9879 2.353376 CAACCGTTGTTGCTGGCG 60.353 61.111 2.87 0.00 44.86 5.69
6190 12231 4.443457 GCCGCATATCACCATCATATAGGT 60.443 45.833 0.00 0.00 39.10 3.08
6314 12385 3.249189 TCGTCCAAGGGGCTGCTT 61.249 61.111 0.00 0.00 0.00 3.91
6391 12465 9.316730 GGCTGCAAAATTGATAAATTTCTGATA 57.683 29.630 1.03 0.00 31.66 2.15
6397 12471 7.982761 TGAAGGCTGCAAAATTGATAAATTT 57.017 28.000 0.50 0.00 34.09 1.82
6411 12485 5.653330 TGATAAATTTCTGATGAAGGCTGCA 59.347 36.000 0.00 0.00 33.28 4.41


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

AutoCloner maintained by Alex Coulton.