Multiple sequence alignment - TraesCS3D01G227500

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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 TraesCS3D01G227500 chr3D 100.000 8627 0 0 1 8627 309667194 309658568 0.000000e+00 15932.0
1 TraesCS3D01G227500 chr3D 82.515 509 39 18 8141 8627 174057450 174057930 1.350000e-107 401.0
2 TraesCS3D01G227500 chr3D 81.446 415 41 21 8211 8622 4355674 4355293 3.030000e-79 307.0
3 TraesCS3D01G227500 chr3B 94.332 3070 108 23 5113 8144 411835194 411838235 0.000000e+00 4645.0
4 TraesCS3D01G227500 chr3B 96.904 1389 40 1 2896 4281 411833364 411834752 0.000000e+00 2324.0
5 TraesCS3D01G227500 chr3B 91.907 1594 51 31 1318 2874 411831819 411833371 0.000000e+00 2158.0
6 TraesCS3D01G227500 chr3B 96.574 467 6 4 634 1094 411831003 411831465 0.000000e+00 765.0
7 TraesCS3D01G227500 chr3B 95.370 216 8 1 31 244 411830791 411831006 8.290000e-90 342.0
8 TraesCS3D01G227500 chr3B 97.727 44 1 0 1 44 411828254 411828297 9.290000e-10 76.8
9 TraesCS3D01G227500 chr3A 95.688 2180 65 9 2228 4391 429328422 429326256 0.000000e+00 3478.0
10 TraesCS3D01G227500 chr3A 95.744 1856 47 11 6313 8144 429325087 429323240 0.000000e+00 2961.0
11 TraesCS3D01G227500 chr3A 94.003 1184 44 6 5113 6276 429326263 429325087 0.000000e+00 1768.0
12 TraesCS3D01G227500 chr3A 90.782 998 38 20 1220 2180 429329396 429328416 0.000000e+00 1284.0
13 TraesCS3D01G227500 chr3A 93.460 734 35 4 4392 5112 695773843 695774576 0.000000e+00 1077.0
14 TraesCS3D01G227500 chr3A 94.372 231 11 1 1 229 429330048 429329818 3.830000e-93 353.0
15 TraesCS3D01G227500 chr3A 97.368 38 1 0 634 671 429329798 429329761 2.010000e-06 65.8
16 TraesCS3D01G227500 chr7A 94.114 1546 63 11 5682 7202 453710164 453711706 0.000000e+00 2326.0
17 TraesCS3D01G227500 chr7A 86.842 760 75 10 4387 5123 639789168 639788411 0.000000e+00 826.0
18 TraesCS3D01G227500 chr7A 95.259 232 11 0 404 635 241796441 241796210 1.370000e-97 368.0
19 TraesCS3D01G227500 chr7A 97.647 170 4 0 244 413 241798394 241798225 8.470000e-75 292.0
20 TraesCS3D01G227500 chr6D 97.383 726 11 2 4392 5113 72344586 72345307 0.000000e+00 1229.0
21 TraesCS3D01G227500 chr6D 87.668 746 68 10 4391 5112 99595427 99596172 0.000000e+00 846.0
22 TraesCS3D01G227500 chr6D 85.024 414 46 9 3706 4110 26404131 26404537 2.900000e-109 407.0
23 TraesCS3D01G227500 chr6D 84.026 313 30 7 2416 2714 155547124 155546818 5.100000e-72 283.0
24 TraesCS3D01G227500 chr6D 87.179 234 25 3 4161 4391 26404549 26404780 2.390000e-65 261.0
25 TraesCS3D01G227500 chr6D 93.103 87 6 0 5870 5956 163831028 163830942 2.530000e-25 128.0
26 TraesCS3D01G227500 chr6D 87.037 108 11 3 5850 5956 427344960 427344855 1.520000e-22 119.0
27 TraesCS3D01G227500 chr2A 94.173 738 30 4 4392 5116 635895945 635895208 0.000000e+00 1112.0
28 TraesCS3D01G227500 chr2A 86.685 368 21 4 244 611 768944613 768944952 4.890000e-102 383.0
29 TraesCS3D01G227500 chr2D 94.360 727 28 3 4388 5112 118043133 118043848 0.000000e+00 1103.0
30 TraesCS3D01G227500 chr2D 86.957 506 41 8 8144 8627 103019620 103020122 5.890000e-151 545.0
31 TraesCS3D01G227500 chr2D 86.905 504 36 14 8144 8626 600331877 600332371 9.850000e-149 538.0
32 TraesCS3D01G227500 chr2D 85.462 509 51 6 8141 8627 623445867 623446374 7.730000e-140 508.0
33 TraesCS3D01G227500 chr2D 92.308 91 6 1 5867 5956 150380743 150380653 2.530000e-25 128.0
34 TraesCS3D01G227500 chr2D 100.000 33 0 0 1583 1615 596903294 596903326 2.600000e-05 62.1
35 TraesCS3D01G227500 chr7D 95.756 589 23 2 4391 4977 604648509 604647921 0.000000e+00 948.0
36 TraesCS3D01G227500 chr7D 86.318 497 54 12 8142 8627 204878865 204879358 5.930000e-146 529.0
37 TraesCS3D01G227500 chr7D 80.464 517 54 18 8142 8627 36350922 36351422 1.380000e-92 351.0
38 TraesCS3D01G227500 chr7D 80.671 507 34 20 8144 8627 6794965 6795430 1.390000e-87 335.0
39 TraesCS3D01G227500 chr1D 88.243 740 67 9 4392 5112 250404249 250404987 0.000000e+00 867.0
40 TraesCS3D01G227500 chr1D 87.230 509 41 7 8142 8627 229583356 229583863 7.560000e-155 558.0
41 TraesCS3D01G227500 chr1D 86.957 506 34 12 8144 8627 449659545 449659050 2.740000e-149 540.0
42 TraesCS3D01G227500 chr1D 86.282 503 43 9 8143 8623 84781322 84781820 2.760000e-144 523.0
43 TraesCS3D01G227500 chr1D 82.911 474 46 9 8144 8595 476861307 476860847 2.260000e-105 394.0
44 TraesCS3D01G227500 chr4D 87.684 747 66 11 4392 5113 479510300 479509555 0.000000e+00 846.0
45 TraesCS3D01G227500 chr4D 97.222 36 1 0 1583 1618 166493596 166493561 2.600000e-05 62.1
46 TraesCS3D01G227500 chr1A 87.618 743 69 10 4392 5112 324708101 324707360 0.000000e+00 841.0
47 TraesCS3D01G227500 chr5D 87.248 745 71 9 4392 5112 374502175 374502919 0.000000e+00 828.0
48 TraesCS3D01G227500 chr5D 84.149 511 45 9 8144 8627 425075161 425074660 6.100000e-126 462.0
49 TraesCS3D01G227500 chr5D 82.249 507 39 19 8144 8627 525175471 525174993 2.920000e-104 390.0
50 TraesCS3D01G227500 chr4A 92.393 539 28 3 4392 4918 254959827 254959290 0.000000e+00 756.0
51 TraesCS3D01G227500 chr4A 86.667 510 42 8 8139 8627 55563584 55564088 7.620000e-150 542.0
52 TraesCS3D01G227500 chr5A 94.987 399 17 2 241 637 462886699 462887096 2.640000e-174 623.0
53 TraesCS3D01G227500 chr6A 86.437 494 43 11 8144 8627 214185715 214185236 3.570000e-143 520.0
54 TraesCS3D01G227500 chr6A 82.748 313 34 6 2416 2714 209374687 209374381 2.390000e-65 261.0
55 TraesCS3D01G227500 chr5B 84.706 510 41 15 8142 8627 429362271 429361775 7.840000e-130 475.0
56 TraesCS3D01G227500 chr5B 94.186 86 5 0 5871 5956 62940408 62940323 1.950000e-26 132.0
57 TraesCS3D01G227500 chr2B 80.247 405 53 12 2182 2570 185883845 185883452 6.590000e-71 279.0
58 TraesCS3D01G227500 chr2B 88.021 192 12 7 1616 1802 185884147 185883962 5.240000e-52 217.0
59 TraesCS3D01G227500 chr2B 92.308 91 5 2 5866 5956 600748981 600749069 2.530000e-25 128.0
60 TraesCS3D01G227500 chr6B 94.186 86 5 0 5871 5956 472612060 472612145 1.950000e-26 132.0
61 TraesCS3D01G227500 chr4B 100.000 33 0 0 1583 1615 222698296 222698328 2.600000e-05 62.1
62 TraesCS3D01G227500 chr4B 97.222 36 1 0 1583 1618 222739874 222739909 2.600000e-05 62.1


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 TraesCS3D01G227500 chr3D 309658568 309667194 8626 True 15932.000000 15932 100.0000 1 8627 1 chr3D.!!$R2 8626
1 TraesCS3D01G227500 chr3B 411828254 411838235 9981 False 1718.466667 4645 95.4690 1 8144 6 chr3B.!!$F1 8143
2 TraesCS3D01G227500 chr3A 429323240 429330048 6808 True 1651.633333 3478 94.6595 1 8144 6 chr3A.!!$R1 8143
3 TraesCS3D01G227500 chr3A 695773843 695774576 733 False 1077.000000 1077 93.4600 4392 5112 1 chr3A.!!$F1 720
4 TraesCS3D01G227500 chr7A 453710164 453711706 1542 False 2326.000000 2326 94.1140 5682 7202 1 chr7A.!!$F1 1520
5 TraesCS3D01G227500 chr7A 639788411 639789168 757 True 826.000000 826 86.8420 4387 5123 1 chr7A.!!$R1 736
6 TraesCS3D01G227500 chr7A 241796210 241798394 2184 True 330.000000 368 96.4530 244 635 2 chr7A.!!$R2 391
7 TraesCS3D01G227500 chr6D 72344586 72345307 721 False 1229.000000 1229 97.3830 4392 5113 1 chr6D.!!$F1 721
8 TraesCS3D01G227500 chr6D 99595427 99596172 745 False 846.000000 846 87.6680 4391 5112 1 chr6D.!!$F2 721
9 TraesCS3D01G227500 chr6D 26404131 26404780 649 False 334.000000 407 86.1015 3706 4391 2 chr6D.!!$F3 685
10 TraesCS3D01G227500 chr2A 635895208 635895945 737 True 1112.000000 1112 94.1730 4392 5116 1 chr2A.!!$R1 724
11 TraesCS3D01G227500 chr2D 118043133 118043848 715 False 1103.000000 1103 94.3600 4388 5112 1 chr2D.!!$F2 724
12 TraesCS3D01G227500 chr2D 103019620 103020122 502 False 545.000000 545 86.9570 8144 8627 1 chr2D.!!$F1 483
13 TraesCS3D01G227500 chr2D 623445867 623446374 507 False 508.000000 508 85.4620 8141 8627 1 chr2D.!!$F5 486
14 TraesCS3D01G227500 chr7D 604647921 604648509 588 True 948.000000 948 95.7560 4391 4977 1 chr7D.!!$R1 586
15 TraesCS3D01G227500 chr7D 36350922 36351422 500 False 351.000000 351 80.4640 8142 8627 1 chr7D.!!$F2 485
16 TraesCS3D01G227500 chr1D 250404249 250404987 738 False 867.000000 867 88.2430 4392 5112 1 chr1D.!!$F3 720
17 TraesCS3D01G227500 chr1D 229583356 229583863 507 False 558.000000 558 87.2300 8142 8627 1 chr1D.!!$F2 485
18 TraesCS3D01G227500 chr4D 479509555 479510300 745 True 846.000000 846 87.6840 4392 5113 1 chr4D.!!$R2 721
19 TraesCS3D01G227500 chr1A 324707360 324708101 741 True 841.000000 841 87.6180 4392 5112 1 chr1A.!!$R1 720
20 TraesCS3D01G227500 chr5D 374502175 374502919 744 False 828.000000 828 87.2480 4392 5112 1 chr5D.!!$F1 720
21 TraesCS3D01G227500 chr5D 425074660 425075161 501 True 462.000000 462 84.1490 8144 8627 1 chr5D.!!$R1 483
22 TraesCS3D01G227500 chr4A 254959290 254959827 537 True 756.000000 756 92.3930 4392 4918 1 chr4A.!!$R1 526
23 TraesCS3D01G227500 chr4A 55563584 55564088 504 False 542.000000 542 86.6670 8139 8627 1 chr4A.!!$F1 488
24 TraesCS3D01G227500 chr2B 185883452 185884147 695 True 248.000000 279 84.1340 1616 2570 2 chr2B.!!$R1 954

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
251 2761 0.107017 GCAAGAGGCTAAGGGCATGA 60.107 55.000 0.00 0.00 44.01 3.07 F
1102 5411 0.107017 CTACACCCAGGCCATTGAGG 60.107 60.000 5.01 1.66 41.84 3.86 F
1172 5481 0.250901 AAGCTGGGCAGTTACACTGG 60.251 55.000 6.05 0.00 46.01 4.00 F
2341 6840 0.252239 TCCTCTTCAGCCTAGTGCCA 60.252 55.000 0.21 0.00 42.71 4.92 F
2342 6841 0.835941 CCTCTTCAGCCTAGTGCCAT 59.164 55.000 0.21 0.00 42.71 4.40 F
2347 6846 0.983467 TCAGCCTAGTGCCATGAACA 59.017 50.000 0.00 0.00 42.71 3.18 F
2351 6850 1.202336 GCCTAGTGCCATGAACAATGC 60.202 52.381 0.00 0.00 34.67 3.56 F
3842 8370 2.159841 CGTATTGCTGGTGAGTCAAACG 60.160 50.000 0.00 0.00 0.00 3.60 F
5115 10022 1.858910 ACCCATTGCCATCCCTATTGA 59.141 47.619 0.00 0.00 0.00 2.57 F
5140 10047 2.274437 CACCTCATTCACATCGTCAGG 58.726 52.381 0.00 0.00 0.00 3.86 F
5805 10718 2.446435 GGCACATACAGGTTTCCACAT 58.554 47.619 0.00 0.00 0.00 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1561 6012 0.098728 GTCAACACCTGCACACACAC 59.901 55.000 0.0 0.0 0.00 3.82 R
2348 6847 0.523072 GCAGTCGTTGTTCATGGCAT 59.477 50.000 0.0 0.0 0.00 4.40 R
2350 6849 1.210155 GGCAGTCGTTGTTCATGGC 59.790 57.895 0.0 0.0 0.00 4.40 R
4141 8676 1.447643 CCCCCGAAGATGTAGCTGG 59.552 63.158 0.0 0.0 0.00 4.85 R
4375 9252 7.398618 TGCCATCCCTAGAAATCAAACATAAAA 59.601 33.333 0.0 0.0 0.00 1.52 R
4389 9266 2.128771 GCAAAACTGCCATCCCTAGA 57.871 50.000 0.0 0.0 0.00 2.43 R
4640 9524 4.868171 TGGACGATTTAAGGAATTGAGACG 59.132 41.667 0.0 0.0 33.92 4.18 R
5945 10860 0.406750 TCCGTCAGTTACTCCCTCCA 59.593 55.000 0.0 0.0 0.00 3.86 R
5956 10871 1.759445 CCTCATTCCATCTCCGTCAGT 59.241 52.381 0.0 0.0 0.00 3.41 R
5957 10872 1.759445 ACCTCATTCCATCTCCGTCAG 59.241 52.381 0.0 0.0 0.00 3.51 R
8052 13013 0.458669 TCTCGGTAAATCGTGCTCCC 59.541 55.000 0.0 0.0 0.00 4.30 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
131 2639 0.530870 TCCATTGACGACGCACAACA 60.531 50.000 9.57 0.00 0.00 3.33
167 2675 2.046411 ACATGGCGCCGATGACAA 60.046 55.556 32.04 13.40 0.00 3.18
175 2683 2.004583 CGCCGATGACAACCTTCTTA 57.995 50.000 0.00 0.00 0.00 2.10
180 2688 3.195825 CCGATGACAACCTTCTTACTCCT 59.804 47.826 0.00 0.00 0.00 3.69
191 2699 7.893124 ACCTTCTTACTCCTTAATCACGATA 57.107 36.000 0.00 0.00 0.00 2.92
251 2761 0.107017 GCAAGAGGCTAAGGGCATGA 60.107 55.000 0.00 0.00 44.01 3.07
331 2841 3.835395 GGAGGAGAGAGGAGAAAAAGACA 59.165 47.826 0.00 0.00 0.00 3.41
385 2895 0.252467 AGGTAGCAGCTTGAGGGAGT 60.252 55.000 0.00 0.00 0.00 3.85
424 4727 1.199789 CAAATGTGGTAGTGCATGCGT 59.800 47.619 14.09 5.32 0.00 5.24
449 4752 0.787084 TTGGGAGAGAGGGAGAGTGT 59.213 55.000 0.00 0.00 0.00 3.55
465 4768 5.359194 AGAGTGTGTGGAAGAAGAAAAGA 57.641 39.130 0.00 0.00 0.00 2.52
509 4812 5.121454 CGAGAAAAAGATGGGAAGTGAGAAG 59.879 44.000 0.00 0.00 0.00 2.85
541 4844 2.231964 ACGTCACAAGGCTATCGGTTAA 59.768 45.455 0.00 0.00 0.00 2.01
555 4858 7.222031 GGCTATCGGTTAAATTGAATGAAAACC 59.778 37.037 6.54 6.54 34.38 3.27
562 4865 5.761818 AAATTGAATGAAAACCGAATCGC 57.238 34.783 0.00 0.00 0.00 4.58
594 4897 3.507162 TGTTGTGATGATGTGGAGGTT 57.493 42.857 0.00 0.00 0.00 3.50
610 4913 1.250840 GGTTTTGGGGCAGCACTAGG 61.251 60.000 0.00 0.00 0.00 3.02
631 4934 1.205179 TGATGCCACCATTGTTCATGC 59.795 47.619 0.00 0.00 0.00 4.06
664 4967 4.795278 GCAATGATGATTCGTGAAACTTCC 59.205 41.667 0.00 0.00 31.75 3.46
785 5094 0.666274 CTTGCCATGCACTGCAACTG 60.666 55.000 17.99 2.60 43.62 3.16
878 5187 3.719144 GCCGTTTAACCGCACGCT 61.719 61.111 3.73 0.00 34.98 5.07
902 5211 3.887716 CTCAATCCAATCCAATCAGTCCC 59.112 47.826 0.00 0.00 0.00 4.46
1094 5403 2.496817 CGAGCTCTACACCCAGGC 59.503 66.667 12.85 0.00 0.00 4.85
1095 5404 2.904131 GAGCTCTACACCCAGGCC 59.096 66.667 6.43 0.00 0.00 5.19
1096 5405 1.990060 GAGCTCTACACCCAGGCCA 60.990 63.158 5.01 0.00 0.00 5.36
1097 5406 1.307343 AGCTCTACACCCAGGCCAT 60.307 57.895 5.01 0.00 0.00 4.40
1098 5407 0.916358 AGCTCTACACCCAGGCCATT 60.916 55.000 5.01 0.00 0.00 3.16
1099 5408 0.749454 GCTCTACACCCAGGCCATTG 60.749 60.000 5.01 0.00 0.00 2.82
1100 5409 0.911769 CTCTACACCCAGGCCATTGA 59.088 55.000 5.01 0.00 0.00 2.57
1101 5410 0.911769 TCTACACCCAGGCCATTGAG 59.088 55.000 5.01 0.00 0.00 3.02
1102 5411 0.107017 CTACACCCAGGCCATTGAGG 60.107 60.000 5.01 1.66 41.84 3.86
1127 5436 3.766691 GGCCACCGCGGAACTCTA 61.767 66.667 35.90 0.00 36.56 2.43
1128 5437 2.508663 GCCACCGCGGAACTCTAC 60.509 66.667 35.90 9.75 36.56 2.59
1129 5438 2.202570 CCACCGCGGAACTCTACG 60.203 66.667 35.90 8.76 36.56 3.51
1136 5445 2.101770 GGAACTCTACGCCGACCG 59.898 66.667 0.00 0.00 44.21 4.79
1137 5446 2.401766 GGAACTCTACGCCGACCGA 61.402 63.158 0.00 0.00 41.02 4.69
1138 5447 1.062206 GAACTCTACGCCGACCGAG 59.938 63.158 0.00 0.00 41.02 4.63
1139 5448 2.916479 GAACTCTACGCCGACCGAGC 62.916 65.000 0.00 0.00 41.02 5.03
1140 5449 4.253257 CTCTACGCCGACCGAGCC 62.253 72.222 0.00 0.00 41.02 4.70
1155 5464 3.818787 GCCCAGGCGCACATCAAG 61.819 66.667 10.83 0.00 0.00 3.02
1156 5465 3.818787 CCCAGGCGCACATCAAGC 61.819 66.667 10.83 0.00 0.00 4.01
1157 5466 2.749044 CCAGGCGCACATCAAGCT 60.749 61.111 10.83 0.00 0.00 3.74
1158 5467 2.483745 CAGGCGCACATCAAGCTG 59.516 61.111 10.83 0.00 0.00 4.24
1159 5468 2.749044 AGGCGCACATCAAGCTGG 60.749 61.111 10.83 0.00 0.00 4.85
1160 5469 3.818787 GGCGCACATCAAGCTGGG 61.819 66.667 10.83 0.00 0.00 4.45
1161 5470 4.487412 GCGCACATCAAGCTGGGC 62.487 66.667 0.30 0.00 42.29 5.36
1162 5471 3.057548 CGCACATCAAGCTGGGCA 61.058 61.111 0.00 0.00 46.14 5.36
1163 5472 2.882876 GCACATCAAGCTGGGCAG 59.117 61.111 0.00 0.00 45.14 4.85
1164 5473 1.975407 GCACATCAAGCTGGGCAGT 60.975 57.895 0.00 0.00 45.14 4.40
1165 5474 1.530013 GCACATCAAGCTGGGCAGTT 61.530 55.000 0.00 0.00 45.14 3.16
1166 5475 1.825090 CACATCAAGCTGGGCAGTTA 58.175 50.000 0.00 0.00 0.00 2.24
1167 5476 1.470098 CACATCAAGCTGGGCAGTTAC 59.530 52.381 0.00 0.00 0.00 2.50
1168 5477 1.073763 ACATCAAGCTGGGCAGTTACA 59.926 47.619 0.00 0.00 0.00 2.41
1169 5478 1.470098 CATCAAGCTGGGCAGTTACAC 59.530 52.381 0.00 0.00 0.00 2.90
1170 5479 0.764890 TCAAGCTGGGCAGTTACACT 59.235 50.000 0.00 0.00 0.00 3.55
1172 5481 0.250901 AAGCTGGGCAGTTACACTGG 60.251 55.000 6.05 0.00 46.01 4.00
1173 5482 1.073199 GCTGGGCAGTTACACTGGT 59.927 57.895 6.05 0.00 46.01 4.00
1174 5483 1.237285 GCTGGGCAGTTACACTGGTG 61.237 60.000 6.05 0.00 46.01 4.17
1175 5484 1.228124 TGGGCAGTTACACTGGTGC 60.228 57.895 6.05 0.00 46.01 5.01
1176 5485 2.325082 GGGCAGTTACACTGGTGCG 61.325 63.158 6.05 0.00 46.01 5.34
1177 5486 1.597027 GGCAGTTACACTGGTGCGT 60.597 57.895 6.05 0.00 46.01 5.24
1178 5487 1.569493 GCAGTTACACTGGTGCGTG 59.431 57.895 6.05 0.00 46.01 5.34
1179 5488 1.157870 GCAGTTACACTGGTGCGTGT 61.158 55.000 6.05 2.00 46.01 4.49
1180 5489 1.295792 CAGTTACACTGGTGCGTGTT 58.704 50.000 1.66 0.00 45.27 3.32
1181 5490 1.668751 CAGTTACACTGGTGCGTGTTT 59.331 47.619 1.66 0.00 45.27 2.83
1182 5491 1.937899 AGTTACACTGGTGCGTGTTTC 59.062 47.619 1.66 0.00 45.27 2.78
1183 5492 1.003223 GTTACACTGGTGCGTGTTTCC 60.003 52.381 1.66 0.00 45.27 3.13
1184 5493 0.533308 TACACTGGTGCGTGTTTCCC 60.533 55.000 1.66 0.00 45.27 3.97
1185 5494 2.590575 ACTGGTGCGTGTTTCCCG 60.591 61.111 0.00 0.00 0.00 5.14
1191 5500 3.733960 GCGTGTTTCCCGCCTTCC 61.734 66.667 0.00 0.00 45.20 3.46
1192 5501 3.053896 CGTGTTTCCCGCCTTCCC 61.054 66.667 0.00 0.00 0.00 3.97
1193 5502 2.675423 GTGTTTCCCGCCTTCCCC 60.675 66.667 0.00 0.00 0.00 4.81
1194 5503 2.856988 TGTTTCCCGCCTTCCCCT 60.857 61.111 0.00 0.00 0.00 4.79
1195 5504 2.045242 GTTTCCCGCCTTCCCCTC 60.045 66.667 0.00 0.00 0.00 4.30
1196 5505 3.335729 TTTCCCGCCTTCCCCTCC 61.336 66.667 0.00 0.00 0.00 4.30
1197 5506 3.883822 TTTCCCGCCTTCCCCTCCT 62.884 63.158 0.00 0.00 0.00 3.69
1198 5507 4.798682 TCCCGCCTTCCCCTCCTC 62.799 72.222 0.00 0.00 0.00 3.71
1255 5564 1.401905 GCCGAACCCTGTCATGATTTC 59.598 52.381 0.00 0.00 0.00 2.17
1260 5569 1.439353 CCCTGTCATGATTTCCCGCG 61.439 60.000 0.00 0.00 0.00 6.46
1285 5594 0.394565 GTGGATGGAATCGCTAGGCT 59.605 55.000 0.00 0.00 46.86 4.58
1286 5595 0.681733 TGGATGGAATCGCTAGGCTC 59.318 55.000 0.00 0.00 46.86 4.70
1287 5596 0.972883 GGATGGAATCGCTAGGCTCT 59.027 55.000 0.00 0.00 46.86 4.09
1288 5597 1.067213 GGATGGAATCGCTAGGCTCTC 60.067 57.143 0.00 0.00 46.86 3.20
1289 5598 1.892474 GATGGAATCGCTAGGCTCTCT 59.108 52.381 0.00 0.00 31.13 3.10
1290 5599 2.658807 TGGAATCGCTAGGCTCTCTA 57.341 50.000 0.00 0.00 0.00 2.43
1291 5600 2.509569 TGGAATCGCTAGGCTCTCTAG 58.490 52.381 0.00 0.00 46.33 2.43
1292 5601 1.816224 GGAATCGCTAGGCTCTCTAGG 59.184 57.143 0.00 0.00 44.32 3.02
1315 5624 1.942657 CCCCTATGAGATGTTTGCGTG 59.057 52.381 0.00 0.00 0.00 5.34
1344 5783 2.159043 GGGAGCAGATGAGTTCGATTCA 60.159 50.000 3.02 3.02 0.00 2.57
1394 5841 6.271566 GGTTCTAGGTTAGTTATGGAGTTCG 58.728 44.000 0.00 0.00 0.00 3.95
1423 5870 3.306613 AGTTAGGCCCTAATAAGCTCGT 58.693 45.455 6.46 0.00 0.00 4.18
1453 5903 2.854185 CGTTCCGAATCCTTACGTTACC 59.146 50.000 0.00 0.00 0.00 2.85
1478 5928 4.980805 TGCGCCCAAGTGTCGGTC 62.981 66.667 4.18 0.00 0.00 4.79
1492 5943 2.106683 CGGTCGGTCAAAGATGGGC 61.107 63.158 0.00 0.00 0.00 5.36
1560 6011 2.549064 TGTCAGCACACATAGCTTGT 57.451 45.000 0.00 0.00 41.14 3.16
1602 6053 4.039488 ACGTACAAGTGTGTTGAATCCCTA 59.961 41.667 0.00 0.00 39.30 3.53
1604 6055 5.642063 CGTACAAGTGTGTTGAATCCCTAAT 59.358 40.000 0.00 0.00 39.30 1.73
1651 6104 0.733150 GTTTGCATAGGCGAGGGAAC 59.267 55.000 0.00 0.00 45.35 3.62
1853 6323 7.920682 GGTTGTTATGTTGTTGATTTCTGTTCT 59.079 33.333 0.00 0.00 0.00 3.01
2025 6508 5.590530 TGCAGTTCAGTATTTGGTTGTTT 57.409 34.783 0.00 0.00 0.00 2.83
2050 6533 8.795786 TGCACATCTTGTTTTATTACTTGTTC 57.204 30.769 0.00 0.00 0.00 3.18
2087 6570 7.177216 TGAATTGTTGCATAGAACTCCATTTCT 59.823 33.333 0.00 0.00 39.28 2.52
2088 6571 5.885230 TGTTGCATAGAACTCCATTTCTG 57.115 39.130 0.00 0.00 36.48 3.02
2289 6788 6.615617 TGCTATCCTCCTGAAGTTAGATACT 58.384 40.000 0.00 0.00 39.32 2.12
2340 6839 0.905357 TTCCTCTTCAGCCTAGTGCC 59.095 55.000 0.21 0.00 42.71 5.01
2341 6840 0.252239 TCCTCTTCAGCCTAGTGCCA 60.252 55.000 0.21 0.00 42.71 4.92
2342 6841 0.835941 CCTCTTCAGCCTAGTGCCAT 59.164 55.000 0.21 0.00 42.71 4.40
2343 6842 1.474677 CCTCTTCAGCCTAGTGCCATG 60.475 57.143 0.21 0.00 42.71 3.66
2344 6843 1.483827 CTCTTCAGCCTAGTGCCATGA 59.516 52.381 0.00 0.00 42.71 3.07
2345 6844 1.908619 TCTTCAGCCTAGTGCCATGAA 59.091 47.619 0.00 4.42 42.71 2.57
2346 6845 2.012673 CTTCAGCCTAGTGCCATGAAC 58.987 52.381 0.00 0.00 42.71 3.18
2347 6846 0.983467 TCAGCCTAGTGCCATGAACA 59.017 50.000 0.00 0.00 42.71 3.18
2348 6847 1.350684 TCAGCCTAGTGCCATGAACAA 59.649 47.619 0.00 0.00 42.71 2.83
2349 6848 2.025981 TCAGCCTAGTGCCATGAACAAT 60.026 45.455 0.00 0.00 42.71 2.71
2350 6849 2.098607 CAGCCTAGTGCCATGAACAATG 59.901 50.000 0.00 0.00 42.71 2.82
2351 6850 1.202336 GCCTAGTGCCATGAACAATGC 60.202 52.381 0.00 0.00 34.67 3.56
2363 6862 2.620585 TGAACAATGCCATGAACAACGA 59.379 40.909 0.00 0.00 0.00 3.85
2506 7017 6.931281 GCCACTGCTTGATATACTAGAAATCA 59.069 38.462 0.00 0.00 33.53 2.57
2593 7104 7.615582 TCGAATGCTTCATAAATTGAGAACT 57.384 32.000 0.00 0.00 35.27 3.01
2878 7403 2.375174 AGCACCTAATCCCTGTTTGTCA 59.625 45.455 0.00 0.00 0.00 3.58
2945 7470 3.206150 GGTCTGCTCTTTGTCAAACTCA 58.794 45.455 0.00 0.00 0.00 3.41
3264 7789 5.216614 AGTGTTCTTCTTGGGTAGAGAAC 57.783 43.478 7.86 7.86 39.21 3.01
3288 7813 9.868277 AACACATAAATCTCTCTTAGTCTCAAG 57.132 33.333 0.00 0.00 0.00 3.02
3294 7819 3.687212 TCTCTCTTAGTCTCAAGTGCTCG 59.313 47.826 0.00 0.00 0.00 5.03
3608 8136 2.269241 CCTTCGGAAGGGGTCAGC 59.731 66.667 25.98 0.00 45.27 4.26
3632 8160 3.956233 TGCATTTATTCGCTTCATCAGC 58.044 40.909 0.00 0.00 46.31 4.26
3842 8370 2.159841 CGTATTGCTGGTGAGTCAAACG 60.160 50.000 0.00 0.00 0.00 3.60
3914 8442 7.095060 GGCATGCCATAATAGGAATATATGTCG 60.095 40.741 32.08 0.00 35.81 4.35
3969 8497 6.456988 CGTTCTGTTAAAATCTCCCATAGCAC 60.457 42.308 0.00 0.00 0.00 4.40
4193 8728 4.258702 CTACAACTGTGGCTACTGAAGT 57.741 45.455 13.97 12.61 0.00 3.01
4361 9238 7.616528 CCATTTAAATTTGGGGGACATCTAT 57.383 36.000 0.00 0.00 0.00 1.98
4375 9252 7.257053 GGGGGACATCTATTACATCCACTAAAT 60.257 40.741 0.00 0.00 33.07 1.40
4640 9524 2.633481 CAACTCCTATGGCCTACCCTAC 59.367 54.545 3.32 0.00 33.59 3.18
4794 9698 2.040178 GACCACCACCTCCCACTATAG 58.960 57.143 0.00 0.00 0.00 1.31
5114 10021 2.386829 ACCCATTGCCATCCCTATTG 57.613 50.000 0.00 0.00 0.00 1.90
5115 10022 1.858910 ACCCATTGCCATCCCTATTGA 59.141 47.619 0.00 0.00 0.00 2.57
5116 10023 2.452047 ACCCATTGCCATCCCTATTGAT 59.548 45.455 0.00 0.00 0.00 2.57
5140 10047 2.274437 CACCTCATTCACATCGTCAGG 58.726 52.381 0.00 0.00 0.00 3.86
5163 10070 4.980434 GGGTGTGCGTAATACTAGTGTATG 59.020 45.833 5.39 4.60 39.16 2.39
5173 10080 9.125906 CGTAATACTAGTGTATGTAAGGAATGC 57.874 37.037 5.39 0.00 39.16 3.56
5406 10313 4.563184 CGTGTTGACTAATCTAGCTTCACC 59.437 45.833 0.00 0.00 0.00 4.02
5485 10392 4.773013 TCGTCTGTTTTCAAAGGTACCTT 58.227 39.130 21.96 21.96 37.98 3.50
5500 10407 9.067986 CAAAGGTACCTTCTCATCTTTTTAACT 57.932 33.333 27.24 3.06 34.84 2.24
5519 10426 8.500753 TTTAACTTGTATGTGGCTACTTATGG 57.499 34.615 0.64 0.00 0.00 2.74
5532 10439 5.163519 GGCTACTTATGGACACAATGCAAAT 60.164 40.000 0.00 0.00 29.34 2.32
5589 10496 3.007506 TGCATCGTTTGGTAAGAGAAGGA 59.992 43.478 0.00 0.00 0.00 3.36
5590 10497 4.000988 GCATCGTTTGGTAAGAGAAGGAA 58.999 43.478 0.00 0.00 0.00 3.36
5591 10498 4.093556 GCATCGTTTGGTAAGAGAAGGAAG 59.906 45.833 0.00 0.00 0.00 3.46
5592 10499 4.267349 TCGTTTGGTAAGAGAAGGAAGG 57.733 45.455 0.00 0.00 0.00 3.46
5657 10564 7.412137 AAAAGCATAGTTCTCATGTTTTTGC 57.588 32.000 8.46 0.00 41.93 3.68
5662 10569 6.744537 GCATAGTTCTCATGTTTTTGCTAGTG 59.255 38.462 0.00 0.00 0.00 2.74
5805 10718 2.446435 GGCACATACAGGTTTCCACAT 58.554 47.619 0.00 0.00 0.00 3.21
5806 10719 3.616219 GGCACATACAGGTTTCCACATA 58.384 45.455 0.00 0.00 0.00 2.29
5840 10753 7.706179 ACAAACAACTTTGGAAGTACATGATTG 59.294 33.333 0.00 10.08 41.91 2.67
6094 11027 7.821359 TGATCTGCTGATAAAGTAGGATATTGC 59.179 37.037 6.02 0.00 39.01 3.56
6132 11065 1.478105 GATTGCTAAGGGCCCAAGTTG 59.522 52.381 27.56 10.87 40.92 3.16
6173 11106 5.012239 ACACATGGTCAATAGTTCATTGCT 58.988 37.500 0.00 0.00 43.28 3.91
6332 11266 3.899360 CCATTGTTCCCTAATGCATGGAT 59.101 43.478 0.00 0.00 34.88 3.41
6347 11281 5.231702 TGCATGGATGTTGTTGAAAATCAG 58.768 37.500 0.00 0.00 28.21 2.90
6350 11284 6.347079 GCATGGATGTTGTTGAAAATCAGTTG 60.347 38.462 0.00 0.00 28.21 3.16
6422 11356 4.357142 GGTTGAGCTATTGCACATTCATG 58.643 43.478 1.12 0.00 39.36 3.07
6668 11605 5.675575 GCTGTGATTGAGCTTTTGTATGGAG 60.676 44.000 0.00 0.00 33.37 3.86
6669 11606 4.701651 TGTGATTGAGCTTTTGTATGGAGG 59.298 41.667 0.00 0.00 0.00 4.30
6782 11719 4.149511 TCCTGACATGACAGTCAACAAA 57.850 40.909 21.04 0.00 46.90 2.83
6904 11841 2.877168 CCTAAGCTTGCAGAATGGCTAG 59.123 50.000 9.86 0.00 39.22 3.42
7061 12000 6.039270 TCTGGGTTAGTGTTATATTGCATTGC 59.961 38.462 0.46 0.46 0.00 3.56
7086 12025 6.239120 CCTTCCATTTGTCACTGAAACATTCT 60.239 38.462 0.00 0.00 0.00 2.40
7262 12203 2.092914 ACTGCCCTACTACCATTGAAGC 60.093 50.000 0.00 0.00 0.00 3.86
7279 12220 6.889301 TTGAAGCTTCTCATGATTTTGAGT 57.111 33.333 26.09 0.00 43.02 3.41
7482 12425 4.083643 GGTCACAACACAACTGAGATCATG 60.084 45.833 0.00 0.00 0.00 3.07
7510 12453 3.937706 ACTTGCTGTCTGAACATATCTGC 59.062 43.478 0.00 0.00 34.13 4.26
7935 12879 2.553602 TGAAATCTGCGCATCACACTTT 59.446 40.909 12.24 4.64 0.00 2.66
8015 12959 7.931407 TGATTGTCTCAGAAAGTTAGCAGTTAA 59.069 33.333 0.00 0.00 0.00 2.01
8017 12961 7.891183 TGTCTCAGAAAGTTAGCAGTTAATC 57.109 36.000 0.00 0.00 0.00 1.75
8019 12963 8.097038 TGTCTCAGAAAGTTAGCAGTTAATCAT 58.903 33.333 0.00 0.00 0.00 2.45
8020 12964 9.587772 GTCTCAGAAAGTTAGCAGTTAATCATA 57.412 33.333 0.00 0.00 0.00 2.15
8044 13005 3.744660 AGAAAAGAGCGGAATCACTGTT 58.255 40.909 0.00 0.00 0.00 3.16
8052 13013 2.346803 CGGAATCACTGTTGTGGTAGG 58.653 52.381 0.00 0.00 43.94 3.18
8073 13034 1.135199 GGAGCACGATTTACCGAGACA 60.135 52.381 0.00 0.00 0.00 3.41
8103 13064 2.299013 TGTGTTTCTACCATCGTGAGCT 59.701 45.455 0.00 0.00 0.00 4.09
8115 13076 1.890489 TCGTGAGCTGCAGTACCTTTA 59.110 47.619 16.64 0.00 0.00 1.85
8121 13082 2.372172 AGCTGCAGTACCTTTAGTTGGT 59.628 45.455 16.64 0.00 41.28 3.67
8194 13156 1.875963 CCGAAAAAGAGCGGCATGT 59.124 52.632 1.45 0.00 41.17 3.21
8226 13189 1.766461 CTAGATCGGCCCTTGGGGT 60.766 63.158 7.91 0.00 46.51 4.95
8298 13283 6.251376 GGCAAATTCAAACGTAGTCATTCATC 59.749 38.462 0.00 0.00 45.00 2.92
8327 13313 0.459899 ATCATGCGGCTACAGTTCGA 59.540 50.000 0.00 0.00 0.00 3.71
8328 13314 0.179137 TCATGCGGCTACAGTTCGAG 60.179 55.000 0.00 0.00 0.00 4.04
8362 13351 4.619437 AGTTCGGCGTACAAAAAGAAAA 57.381 36.364 18.71 0.00 0.00 2.29
8376 13365 3.223435 GAAAAGACGCGCGTGCAGT 62.223 57.895 42.90 22.70 42.97 4.40
8385 13374 2.458610 CGCGTGCAGTGCATCAGAT 61.459 57.895 22.87 0.00 41.91 2.90
8463 13452 2.669569 TTCTTCTGTGCTGGGCGC 60.670 61.111 0.00 0.00 39.75 6.53
8606 13607 2.345991 GCTCCGCCAAGTACCACA 59.654 61.111 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
131 2639 2.546494 GCAGTCGTTGGCTTGTGCT 61.546 57.895 0.00 0.00 39.59 4.40
167 2675 6.793505 ATCGTGATTAAGGAGTAAGAAGGT 57.206 37.500 0.00 0.00 0.00 3.50
175 2683 6.239064 GGTGTCTGATATCGTGATTAAGGAGT 60.239 42.308 0.00 0.00 0.00 3.85
180 2688 7.107639 TCTTGGTGTCTGATATCGTGATTAA 57.892 36.000 0.00 0.00 0.00 1.40
191 2699 6.016777 GTGACTTTTTGATCTTGGTGTCTGAT 60.017 38.462 0.00 0.00 0.00 2.90
298 2808 3.073735 CTCCTCCACGGCAGCTCT 61.074 66.667 0.00 0.00 0.00 4.09
385 2895 0.976641 GTCCATGGACCACACTCTCA 59.023 55.000 31.37 0.00 39.08 3.27
449 4752 7.287061 TGGACTTTATCTTTTCTTCTTCCACA 58.713 34.615 0.00 0.00 0.00 4.17
465 4768 3.141398 CGCCATAGCACATGGACTTTAT 58.859 45.455 18.77 0.00 41.64 1.40
509 4812 0.243907 TTGTGACGTGAGCTAGCCTC 59.756 55.000 12.13 9.07 41.15 4.70
541 4844 4.804108 TGCGATTCGGTTTTCATTCAATT 58.196 34.783 8.34 0.00 0.00 2.32
555 4858 4.070581 ACAAAAATGAGACTGCGATTCG 57.929 40.909 0.62 0.62 0.00 3.34
560 4863 3.951306 TCACAACAAAAATGAGACTGCG 58.049 40.909 0.00 0.00 0.00 5.18
562 4865 7.114388 CACATCATCACAACAAAAATGAGACTG 59.886 37.037 0.00 0.00 32.09 3.51
594 4897 1.074775 CACCTAGTGCTGCCCCAAA 59.925 57.895 0.00 0.00 0.00 3.28
610 4913 2.883574 CATGAACAATGGTGGCATCAC 58.116 47.619 0.63 0.00 42.91 3.06
631 4934 5.240183 ACGAATCATCATTGCTTGATTAGGG 59.760 40.000 17.72 11.89 42.62 3.53
664 4967 1.484240 TGTTTTGCTTTTGGGACCCAG 59.516 47.619 14.35 3.32 33.81 4.45
756 5065 0.674895 GCATGGCAAGTTCTCCGTCT 60.675 55.000 0.00 0.00 0.00 4.18
818 5127 1.262640 TTCTAGAGTGTTCCGGGGGC 61.263 60.000 0.00 0.00 0.00 5.80
878 5187 3.949754 GACTGATTGGATTGGATTGAGCA 59.050 43.478 0.00 0.00 0.00 4.26
1110 5419 3.766691 TAGAGTTCCGCGGTGGCC 61.767 66.667 27.15 13.28 37.80 5.36
1111 5420 2.508663 GTAGAGTTCCGCGGTGGC 60.509 66.667 27.15 16.10 37.80 5.01
1112 5421 2.202570 CGTAGAGTTCCGCGGTGG 60.203 66.667 27.15 0.00 40.09 4.61
1113 5422 2.879462 GCGTAGAGTTCCGCGGTG 60.879 66.667 27.15 0.00 40.56 4.94
1118 5427 2.101770 GGTCGGCGTAGAGTTCCG 59.898 66.667 6.85 0.00 44.16 4.30
1119 5428 2.101770 CGGTCGGCGTAGAGTTCC 59.898 66.667 6.85 0.00 0.00 3.62
1120 5429 1.062206 CTCGGTCGGCGTAGAGTTC 59.938 63.158 6.85 0.00 0.00 3.01
1121 5430 3.048941 GCTCGGTCGGCGTAGAGTT 62.049 63.158 21.87 0.00 33.57 3.01
1122 5431 3.507009 GCTCGGTCGGCGTAGAGT 61.507 66.667 21.87 0.00 33.57 3.24
1123 5432 4.253257 GGCTCGGTCGGCGTAGAG 62.253 72.222 18.81 18.81 0.00 2.43
1136 5445 4.783621 TGATGTGCGCCTGGGCTC 62.784 66.667 4.18 2.14 39.32 4.70
1137 5446 4.349503 TTGATGTGCGCCTGGGCT 62.350 61.111 4.18 0.00 39.32 5.19
1138 5447 3.818787 CTTGATGTGCGCCTGGGC 61.819 66.667 4.18 0.82 37.85 5.36
1139 5448 3.818787 GCTTGATGTGCGCCTGGG 61.819 66.667 4.18 0.00 0.00 4.45
1140 5449 2.749044 AGCTTGATGTGCGCCTGG 60.749 61.111 4.18 0.00 35.28 4.45
1141 5450 2.483745 CAGCTTGATGTGCGCCTG 59.516 61.111 4.18 0.00 35.28 4.85
1142 5451 2.749044 CCAGCTTGATGTGCGCCT 60.749 61.111 4.18 0.00 35.28 5.52
1143 5452 3.818787 CCCAGCTTGATGTGCGCC 61.819 66.667 4.18 0.00 35.28 6.53
1144 5453 4.487412 GCCCAGCTTGATGTGCGC 62.487 66.667 0.00 0.00 35.28 6.09
1145 5454 3.047718 CTGCCCAGCTTGATGTGCG 62.048 63.158 0.00 0.00 35.28 5.34
1146 5455 1.530013 AACTGCCCAGCTTGATGTGC 61.530 55.000 0.00 0.00 0.00 4.57
1147 5456 1.470098 GTAACTGCCCAGCTTGATGTG 59.530 52.381 0.00 0.00 0.00 3.21
1148 5457 1.073763 TGTAACTGCCCAGCTTGATGT 59.926 47.619 0.00 0.00 0.00 3.06
1149 5458 1.470098 GTGTAACTGCCCAGCTTGATG 59.530 52.381 0.00 0.00 0.00 3.07
1150 5459 1.826385 GTGTAACTGCCCAGCTTGAT 58.174 50.000 0.00 0.00 0.00 2.57
1151 5460 3.322514 GTGTAACTGCCCAGCTTGA 57.677 52.632 0.00 0.00 0.00 3.02
1167 5476 2.892334 CGGGAAACACGCACCAGTG 61.892 63.158 0.00 0.00 46.83 3.66
1168 5477 2.590575 CGGGAAACACGCACCAGT 60.591 61.111 0.00 0.00 0.00 4.00
1175 5484 3.053896 GGGAAGGCGGGAAACACG 61.054 66.667 0.00 0.00 0.00 4.49
1176 5485 2.675423 GGGGAAGGCGGGAAACAC 60.675 66.667 0.00 0.00 0.00 3.32
1177 5486 2.856988 AGGGGAAGGCGGGAAACA 60.857 61.111 0.00 0.00 0.00 2.83
1178 5487 2.045242 GAGGGGAAGGCGGGAAAC 60.045 66.667 0.00 0.00 0.00 2.78
1179 5488 3.335729 GGAGGGGAAGGCGGGAAA 61.336 66.667 0.00 0.00 0.00 3.13
1180 5489 4.348495 AGGAGGGGAAGGCGGGAA 62.348 66.667 0.00 0.00 0.00 3.97
1181 5490 4.798682 GAGGAGGGGAAGGCGGGA 62.799 72.222 0.00 0.00 0.00 5.14
1211 5520 1.059369 CAAACGAATCGAGCCGCAG 59.941 57.895 10.55 0.00 0.00 5.18
1212 5521 3.022401 GCAAACGAATCGAGCCGCA 62.022 57.895 10.55 0.00 0.00 5.69
1213 5522 2.240612 AAGCAAACGAATCGAGCCGC 62.241 55.000 10.55 6.33 0.00 6.53
1214 5523 0.996462 TAAGCAAACGAATCGAGCCG 59.004 50.000 10.55 7.56 0.00 5.52
1215 5524 2.851008 GCATAAGCAAACGAATCGAGCC 60.851 50.000 10.55 0.00 41.58 4.70
1216 5525 2.366859 GCATAAGCAAACGAATCGAGC 58.633 47.619 10.55 10.39 41.58 5.03
1217 5526 2.597505 CGGCATAAGCAAACGAATCGAG 60.598 50.000 10.55 0.00 44.61 4.04
1218 5527 1.326245 CGGCATAAGCAAACGAATCGA 59.674 47.619 10.55 0.00 44.61 3.59
1255 5564 2.896854 CATCCACATCCACGCGGG 60.897 66.667 12.47 6.05 38.37 6.13
1260 5569 0.947244 GCGATTCCATCCACATCCAC 59.053 55.000 0.00 0.00 0.00 4.02
1478 5928 1.815421 CGGAGCCCATCTTTGACCG 60.815 63.158 0.00 0.00 0.00 4.79
1492 5943 2.359975 GAGCAACCCCCAACGGAG 60.360 66.667 0.00 0.00 0.00 4.63
1560 6011 0.322008 TCAACACCTGCACACACACA 60.322 50.000 0.00 0.00 0.00 3.72
1561 6012 0.098728 GTCAACACCTGCACACACAC 59.901 55.000 0.00 0.00 0.00 3.82
1602 6053 7.690256 AGTCAACCCTAACTGTAAATGAGATT 58.310 34.615 0.00 0.00 0.00 2.40
1604 6055 6.681729 AGTCAACCCTAACTGTAAATGAGA 57.318 37.500 0.00 0.00 0.00 3.27
1651 6104 5.711506 TGCAATGCTATTCTACCCCATTATG 59.288 40.000 6.82 0.00 0.00 1.90
2025 6508 7.865385 GGAACAAGTAATAAAACAAGATGTGCA 59.135 33.333 0.00 0.00 0.00 4.57
2050 6533 8.354426 TCTATGCAACAATTCAATGATACATGG 58.646 33.333 0.00 0.00 0.00 3.66
2087 6570 7.148086 GGCATTTTACTTTACATCATGAGGACA 60.148 37.037 15.42 0.00 0.00 4.02
2088 6571 7.148086 TGGCATTTTACTTTACATCATGAGGAC 60.148 37.037 15.42 0.00 0.00 3.85
2289 6788 3.818965 TGGCCATGCTAGGACACA 58.181 55.556 0.00 0.00 43.33 3.72
2328 6827 0.983467 TGTTCATGGCACTAGGCTGA 59.017 50.000 0.00 0.00 44.01 4.26
2340 6839 3.365520 CGTTGTTCATGGCATTGTTCATG 59.634 43.478 0.00 12.69 41.35 3.07
2341 6840 3.255395 TCGTTGTTCATGGCATTGTTCAT 59.745 39.130 0.00 0.00 0.00 2.57
2342 6841 2.620585 TCGTTGTTCATGGCATTGTTCA 59.379 40.909 0.00 0.00 0.00 3.18
2343 6842 2.979813 GTCGTTGTTCATGGCATTGTTC 59.020 45.455 0.00 0.00 0.00 3.18
2344 6843 2.622942 AGTCGTTGTTCATGGCATTGTT 59.377 40.909 0.00 0.00 0.00 2.83
2345 6844 2.030893 CAGTCGTTGTTCATGGCATTGT 60.031 45.455 0.00 0.00 0.00 2.71
2346 6845 2.587956 CAGTCGTTGTTCATGGCATTG 58.412 47.619 0.00 0.00 0.00 2.82
2347 6846 1.068333 GCAGTCGTTGTTCATGGCATT 60.068 47.619 0.00 0.00 0.00 3.56
2348 6847 0.523072 GCAGTCGTTGTTCATGGCAT 59.477 50.000 0.00 0.00 0.00 4.40
2349 6848 1.514678 GGCAGTCGTTGTTCATGGCA 61.515 55.000 0.00 0.00 36.53 4.92
2350 6849 1.210155 GGCAGTCGTTGTTCATGGC 59.790 57.895 0.00 0.00 0.00 4.40
2351 6850 1.238439 AAGGCAGTCGTTGTTCATGG 58.762 50.000 0.00 0.00 0.00 3.66
2379 6881 3.643199 AATTGTTGCCAAAAACAGGGT 57.357 38.095 0.00 0.00 40.93 4.34
2386 6896 7.284034 ACCATTGATTACAAATTGTTGCCAAAA 59.716 29.630 3.17 0.00 39.54 2.44
2430 6940 4.227300 ACAGGCAACATAGGGATACTTTGA 59.773 41.667 0.00 0.00 41.41 2.69
2555 7066 5.296813 AGCATTCGAACAAATAACCTCAC 57.703 39.130 0.00 0.00 0.00 3.51
2593 7104 6.849085 TGCAGGGAATCAAATTAGCTTTTA 57.151 33.333 0.00 0.00 0.00 1.52
2777 7302 6.371548 GCACAACAATGTACCTCTTGAATCTA 59.628 38.462 6.86 0.00 37.82 1.98
2836 7361 6.798959 GTGCTAAGAAATTCTGCAAAGTACAG 59.201 38.462 9.19 0.00 35.34 2.74
2878 7403 8.157476 ACAACAAGGAAACAACTATAGATCACT 58.843 33.333 6.78 0.00 0.00 3.41
2906 7431 5.300286 GCAGACCAAGGCTTCATTAATATGT 59.700 40.000 0.00 0.00 33.34 2.29
3264 7789 9.299963 CACTTGAGACTAAGAGAGATTTATGTG 57.700 37.037 0.00 0.00 0.00 3.21
3288 7813 4.852650 GTGTTCTCTACTTAAGACGAGCAC 59.147 45.833 10.09 13.76 36.94 4.40
3404 7932 6.258727 CAGTATGTCCACAAATGTAGGTCATC 59.741 42.308 13.41 8.84 35.48 2.92
3469 7997 4.330074 GTGCGAGTACAAGCAGACAATTAT 59.670 41.667 14.28 0.00 44.70 1.28
3488 8016 4.143597 GCGCTTAGTACACTATATTGTGCG 60.144 45.833 15.90 15.84 41.30 5.34
3608 8136 4.862350 TGATGAAGCGAATAAATGCATGG 58.138 39.130 0.00 0.00 0.00 3.66
3683 8211 7.441760 AGAGCTGCATAGAATTATTCTTGTCAG 59.558 37.037 13.00 15.87 41.14 3.51
3769 8297 2.298446 CCTCGAGTCACCAGATGCATAT 59.702 50.000 12.31 0.00 0.00 1.78
3842 8370 3.917988 AGGCAATTGCTGAGCTAAAAAC 58.082 40.909 28.42 8.43 41.70 2.43
3914 8442 6.106003 ACTCAAAAATTGGGAAAACACAGAC 58.894 36.000 0.00 0.00 34.45 3.51
3969 8497 2.359981 ACTGGATGATGATGCAAGGG 57.640 50.000 0.00 0.00 28.12 3.95
4141 8676 1.447643 CCCCCGAAGATGTAGCTGG 59.552 63.158 0.00 0.00 0.00 4.85
4375 9252 7.398618 TGCCATCCCTAGAAATCAAACATAAAA 59.601 33.333 0.00 0.00 0.00 1.52
4389 9266 2.128771 GCAAAACTGCCATCCCTAGA 57.871 50.000 0.00 0.00 0.00 2.43
4640 9524 4.868171 TGGACGATTTAAGGAATTGAGACG 59.132 41.667 0.00 0.00 33.92 4.18
5114 10021 3.941483 ACGATGTGAATGAGGTGGAAATC 59.059 43.478 0.00 0.00 0.00 2.17
5115 10022 3.941483 GACGATGTGAATGAGGTGGAAAT 59.059 43.478 0.00 0.00 0.00 2.17
5116 10023 3.244387 TGACGATGTGAATGAGGTGGAAA 60.244 43.478 0.00 0.00 0.00 3.13
5140 10047 3.515330 ACACTAGTATTACGCACACCC 57.485 47.619 0.00 0.00 0.00 4.61
5163 10070 9.023967 CAGCATAAACATTTAAGCATTCCTTAC 57.976 33.333 12.58 0.00 39.17 2.34
5214 10121 3.766151 ACATCAAATGCATTGCGAGAAG 58.234 40.909 13.82 8.58 38.98 2.85
5219 10126 3.548668 CCTACAACATCAAATGCATTGCG 59.451 43.478 13.82 7.74 38.98 4.85
5406 10313 5.718146 TCAATTGAGACACTCAGCTAGAAG 58.282 41.667 3.38 0.00 41.75 2.85
5485 10392 7.665559 AGCCACATACAAGTTAAAAAGATGAGA 59.334 33.333 0.00 0.00 0.00 3.27
5500 10407 5.046231 TGTGTCCATAAGTAGCCACATACAA 60.046 40.000 0.00 0.00 0.00 2.41
5519 10426 5.740569 CAGCATGTACTATTTGCATTGTGTC 59.259 40.000 11.36 0.00 38.84 3.67
5590 10497 8.404000 CGTGTATGTTCTGAATACTTAGTACCT 58.596 37.037 0.00 0.00 32.70 3.08
5591 10498 7.167136 GCGTGTATGTTCTGAATACTTAGTACC 59.833 40.741 0.00 0.00 32.70 3.34
5592 10499 7.699391 TGCGTGTATGTTCTGAATACTTAGTAC 59.301 37.037 0.00 0.00 32.70 2.73
5744 10655 4.343814 GGGTGGAAAATTTGTTTGAGAGGA 59.656 41.667 0.00 0.00 0.00 3.71
5816 10729 7.706179 CACAATCATGTACTTCCAAAGTTGTTT 59.294 33.333 0.00 0.00 42.81 2.83
5830 10743 6.859508 TCGTCGTTATATCCACAATCATGTAC 59.140 38.462 0.00 0.00 37.82 2.90
5840 10753 3.050619 CTGGCTTCGTCGTTATATCCAC 58.949 50.000 0.00 0.00 0.00 4.02
5925 10840 7.118390 CCCTCCATAAAGAAATATAAGAGCGTG 59.882 40.741 0.00 0.00 0.00 5.34
5945 10860 0.406750 TCCGTCAGTTACTCCCTCCA 59.593 55.000 0.00 0.00 0.00 3.86
5956 10871 1.759445 CCTCATTCCATCTCCGTCAGT 59.241 52.381 0.00 0.00 0.00 3.41
5957 10872 1.759445 ACCTCATTCCATCTCCGTCAG 59.241 52.381 0.00 0.00 0.00 3.51
5959 10874 2.035632 AGACCTCATTCCATCTCCGTC 58.964 52.381 0.00 0.00 0.00 4.79
6094 11027 7.935338 AGCAATCAATTTACTTTGTCAGTTG 57.065 32.000 0.00 0.00 36.88 3.16
6132 11065 3.818210 TGTGTATTTCCACACCACATGAC 59.182 43.478 0.00 0.00 46.73 3.06
6173 11106 4.150897 AGTTTGTCAAAGGTGCTACTCA 57.849 40.909 0.00 0.00 0.00 3.41
6332 11266 5.070770 AGCACAACTGATTTTCAACAACA 57.929 34.783 0.00 0.00 0.00 3.33
6347 11281 5.715070 ACAGTTACATAGAGAGAGCACAAC 58.285 41.667 0.00 0.00 0.00 3.32
6350 11284 7.659652 AAAAACAGTTACATAGAGAGAGCAC 57.340 36.000 0.00 0.00 0.00 4.40
6668 11605 5.046520 ACACAATTTACAGAGGGAGTAGTCC 60.047 44.000 8.22 8.22 43.05 3.85
6669 11606 6.038997 ACACAATTTACAGAGGGAGTAGTC 57.961 41.667 0.00 0.00 0.00 2.59
6772 11709 8.918658 CAGAAATCACCATATTTTTGTTGACTG 58.081 33.333 0.00 0.00 30.34 3.51
6782 11719 9.295825 TCACAAAGTACAGAAATCACCATATTT 57.704 29.630 0.00 0.00 0.00 1.40
6804 11741 5.997129 TGTGCATGAAAGTATCTTTCTCACA 59.003 36.000 23.23 23.23 34.75 3.58
6904 11841 2.789409 ACAGCCTGGGACTGAAATAC 57.211 50.000 14.55 0.00 38.55 1.89
7061 12000 4.916983 TGTTTCAGTGACAAATGGAAGG 57.083 40.909 0.00 0.00 0.00 3.46
7086 12025 5.709631 TCAGCTGCAAAACAAGGAATACATA 59.290 36.000 9.47 0.00 0.00 2.29
7279 12220 7.124147 AGTTTTTCATCCTTCTCCTGAAACAAA 59.876 33.333 0.00 0.00 38.30 2.83
7468 12409 6.336566 CAAGTAGTAGCATGATCTCAGTTGT 58.663 40.000 0.00 0.00 0.00 3.32
7469 12410 5.233902 GCAAGTAGTAGCATGATCTCAGTTG 59.766 44.000 0.00 0.00 0.00 3.16
7470 12411 5.128499 AGCAAGTAGTAGCATGATCTCAGTT 59.872 40.000 0.00 0.00 0.00 3.16
7471 12412 4.648762 AGCAAGTAGTAGCATGATCTCAGT 59.351 41.667 0.00 0.00 0.00 3.41
7472 12413 4.983538 CAGCAAGTAGTAGCATGATCTCAG 59.016 45.833 0.00 0.00 0.00 3.35
7482 12425 3.914312 TGTTCAGACAGCAAGTAGTAGC 58.086 45.455 0.00 0.00 0.00 3.58
7510 12453 2.839486 TTAGACTCCACCTGCAACAG 57.161 50.000 0.00 0.00 0.00 3.16
7923 12867 7.159437 TCAAACAAAAATAAAGTGTGATGCG 57.841 32.000 0.00 0.00 0.00 4.73
8015 12959 8.153550 AGTGATTCCGCTCTTTTCTTATATGAT 58.846 33.333 0.00 0.00 0.00 2.45
8017 12961 7.225538 ACAGTGATTCCGCTCTTTTCTTATATG 59.774 37.037 0.00 0.00 0.00 1.78
8019 12963 6.640518 ACAGTGATTCCGCTCTTTTCTTATA 58.359 36.000 0.00 0.00 0.00 0.98
8020 12964 5.491982 ACAGTGATTCCGCTCTTTTCTTAT 58.508 37.500 0.00 0.00 0.00 1.73
8021 12965 4.894784 ACAGTGATTCCGCTCTTTTCTTA 58.105 39.130 0.00 0.00 0.00 2.10
8044 13005 0.907704 AATCGTGCTCCCCTACCACA 60.908 55.000 0.00 0.00 0.00 4.17
8052 13013 0.458669 TCTCGGTAAATCGTGCTCCC 59.541 55.000 0.00 0.00 0.00 4.30
8073 13034 9.208022 CACGATGGTAGAAACACATATCATAAT 57.792 33.333 0.00 0.00 0.00 1.28
8103 13064 2.882137 GCAACCAACTAAAGGTACTGCA 59.118 45.455 0.00 0.00 40.76 4.41
8115 13076 1.331214 CACCTTCCATGCAACCAACT 58.669 50.000 0.00 0.00 0.00 3.16
8121 13082 1.425066 AGAACTCCACCTTCCATGCAA 59.575 47.619 0.00 0.00 0.00 4.08
8172 13134 2.173382 CCGCTCTTTTTCGGTGCG 59.827 61.111 0.00 0.00 43.32 5.34
8194 13156 4.077184 CTAGCGCCGGTTCACCCA 62.077 66.667 2.29 0.00 0.00 4.51
8263 13227 2.598985 AATTTGCCGCGGGTTGGA 60.599 55.556 29.38 0.00 0.00 3.53
8298 13283 2.552768 CGCATGATCGCCGGATTG 59.447 61.111 5.05 0.00 31.51 2.67
8376 13365 1.144716 GACCTCGCCATCTGATGCA 59.855 57.895 12.17 0.00 0.00 3.96
8463 13452 2.149803 TACAGAAGCCACACCGACGG 62.150 60.000 13.61 13.61 0.00 4.79
8470 13459 1.005037 CCGCAGTACAGAAGCCACA 60.005 57.895 0.00 0.00 0.00 4.17
8606 13607 4.052229 CGACGAGGCGGTCAAGGT 62.052 66.667 11.34 0.00 36.73 3.50


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

AutoCloner maintained by Alex Coulton.