Multiple sequence alignment - TraesCS7B01G405900

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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 TraesCS7B01G405900 chr7B 100.000 5258 0 0 1 5258 674202384 674197127 0.000000e+00 9710.0
1 TraesCS7B01G405900 chr7B 92.997 357 25 0 3458 3814 674226218 674226574 6.030000e-144 521.0
2 TraesCS7B01G405900 chr7B 90.763 249 16 6 3867 4113 674226682 674226925 5.080000e-85 326.0
3 TraesCS7B01G405900 chr7D 91.258 2528 125 31 2787 5258 596096477 596093990 0.000000e+00 3356.0
4 TraesCS7B01G405900 chr7D 90.867 427 21 5 682 1104 596096876 596096464 1.650000e-154 556.0
5 TraesCS7B01G405900 chr7D 96.000 150 6 0 516 665 596098143 596097994 1.460000e-60 244.0
6 TraesCS7B01G405900 chr7D 87.597 129 15 1 3 131 596098682 596098555 1.180000e-31 148.0
7 TraesCS7B01G405900 chr7D 81.564 179 9 7 240 418 596098453 596098299 5.530000e-25 126.0
8 TraesCS7B01G405900 chr7D 89.412 85 5 2 4449 4529 618044424 618044508 2.590000e-18 104.0
9 TraesCS7B01G405900 chr3B 96.095 1690 39 5 1102 2772 32805202 32803521 0.000000e+00 2730.0
10 TraesCS7B01G405900 chr3B 85.882 85 11 1 4863 4946 819011277 819011193 7.250000e-14 89.8
11 TraesCS7B01G405900 chr5B 95.860 1691 37 6 1104 2775 466784768 466783092 0.000000e+00 2704.0
12 TraesCS7B01G405900 chr5B 88.527 1656 144 22 1104 2755 13080453 13078840 0.000000e+00 1964.0
13 TraesCS7B01G405900 chr5B 88.880 1205 103 21 1104 2286 458942282 458941087 0.000000e+00 1454.0
14 TraesCS7B01G405900 chr5B 74.974 963 213 24 2845 3796 50470187 50469242 8.140000e-113 418.0
15 TraesCS7B01G405900 chr1B 93.909 1691 33 16 1102 2773 35280251 35278612 0.000000e+00 2488.0
16 TraesCS7B01G405900 chr1B 88.235 119 6 5 5144 5258 468217663 468217777 9.180000e-28 135.0
17 TraesCS7B01G405900 chr1B 79.375 160 27 5 4791 4946 674493999 674494156 2.000000e-19 108.0
18 TraesCS7B01G405900 chr5A 96.985 1360 25 3 1102 2446 672511187 672512545 0.000000e+00 2270.0
19 TraesCS7B01G405900 chr5A 93.528 309 9 2 2468 2772 672512605 672512906 2.890000e-122 449.0
20 TraesCS7B01G405900 chr5A 81.034 116 17 4 4834 4947 825601 825713 2.610000e-13 87.9
21 TraesCS7B01G405900 chr2B 89.849 1586 115 17 1209 2773 765028433 765029993 0.000000e+00 1995.0
22 TraesCS7B01G405900 chr4A 94.025 1339 39 15 1097 2417 741179260 741180575 0.000000e+00 1991.0
23 TraesCS7B01G405900 chr4A 96.793 1185 21 4 1104 2272 513353954 513352771 0.000000e+00 1962.0
24 TraesCS7B01G405900 chr4A 92.035 226 11 1 2441 2666 513352442 513352224 1.420000e-80 311.0
25 TraesCS7B01G405900 chr4A 80.000 150 18 10 4390 4529 617449263 617449116 3.350000e-17 100.0
26 TraesCS7B01G405900 chr6B 97.126 1183 19 2 1104 2271 52227993 52226811 0.000000e+00 1982.0
27 TraesCS7B01G405900 chr6B 96.679 271 5 1 2503 2769 52226503 52226233 1.040000e-121 448.0
28 TraesCS7B01G405900 chr6B 88.333 120 4 6 5144 5258 637180572 637180458 9.180000e-28 135.0
29 TraesCS7B01G405900 chr6A 96.774 1178 23 2 1100 2262 135004653 135003476 0.000000e+00 1951.0
30 TraesCS7B01G405900 chr6A 95.833 216 5 1 2562 2773 135003092 135002877 3.900000e-91 346.0
31 TraesCS7B01G405900 chr6A 90.789 76 3 3 4458 4529 573139793 573139868 1.210000e-16 99.0
32 TraesCS7B01G405900 chr6A 90.789 76 3 2 4458 4529 573150417 573150342 1.210000e-16 99.0
33 TraesCS7B01G405900 chr4B 90.791 1466 114 9 1105 2555 664310093 664311552 0.000000e+00 1940.0
34 TraesCS7B01G405900 chr4B 81.208 149 25 2 4789 4934 495124274 495124422 3.330000e-22 117.0
35 TraesCS7B01G405900 chr7A 94.090 643 25 4 3244 3881 689260719 689260085 0.000000e+00 965.0
36 TraesCS7B01G405900 chr7A 93.982 565 23 3 540 1104 689261636 689261083 0.000000e+00 845.0
37 TraesCS7B01G405900 chr7A 93.817 372 23 0 2787 3158 689261096 689260725 1.280000e-155 560.0
38 TraesCS7B01G405900 chr7A 89.041 438 30 9 3923 4342 689260083 689259646 1.300000e-145 527.0
39 TraesCS7B01G405900 chr7A 88.083 193 9 4 44 235 689261960 689261781 3.190000e-52 217.0
40 TraesCS7B01G405900 chr7A 82.895 152 20 5 4788 4934 485615337 485615487 1.190000e-26 132.0
41 TraesCS7B01G405900 chr7A 85.859 99 10 3 5144 5240 689255647 689255551 9.320000e-18 102.0
42 TraesCS7B01G405900 chr3A 87.624 404 32 10 2023 2409 63060384 63060786 2.230000e-123 453.0
43 TraesCS7B01G405900 chr3A 88.571 105 6 5 4459 4557 726723016 726723120 7.150000e-24 122.0
44 TraesCS7B01G405900 chr3A 89.412 85 5 2 4449 4529 9991608 9991692 2.590000e-18 104.0
45 TraesCS7B01G405900 chr5D 75.078 963 212 24 2845 3796 47333308 47332363 1.750000e-114 424.0
46 TraesCS7B01G405900 chr5D 90.000 80 2 5 4458 4531 94049037 94049116 1.210000e-16 99.0
47 TraesCS7B01G405900 chr1A 96.341 246 5 1 2532 2773 542367577 542367332 8.200000e-108 401.0
48 TraesCS7B01G405900 chr1A 92.105 76 2 2 4458 4529 501032166 501032241 2.590000e-18 104.0
49 TraesCS7B01G405900 chrUn 84.153 183 16 12 4376 4546 97636705 97636886 1.170000e-36 165.0
50 TraesCS7B01G405900 chr2D 80.368 163 15 13 4377 4529 650052882 650053037 2.000000e-19 108.0
51 TraesCS7B01G405900 chr6D 88.235 85 6 2 4449 4529 402949031 402949115 1.210000e-16 99.0
52 TraesCS7B01G405900 chr6D 89.610 77 3 4 4458 4529 447911558 447911634 5.610000e-15 93.5
53 TraesCS7B01G405900 chr6D 89.610 77 3 4 4458 4529 453944091 453944015 5.610000e-15 93.5
54 TraesCS7B01G405900 chr6D 88.462 78 3 4 4458 4529 82099486 82099409 7.250000e-14 89.8
55 TraesCS7B01G405900 chr4D 78.659 164 23 10 4377 4529 8072055 8072217 1.210000e-16 99.0
56 TraesCS7B01G405900 chr4D 88.372 86 5 4 4449 4529 233148903 233148988 1.210000e-16 99.0
57 TraesCS7B01G405900 chr4D 88.235 85 6 2 4449 4529 479679536 479679620 1.210000e-16 99.0
58 TraesCS7B01G405900 chr4D 85.000 80 9 3 4870 4946 485060803 485060724 1.570000e-10 78.7
59 TraesCS7B01G405900 chr4D 85.915 71 7 3 4879 4946 485038847 485038777 7.300000e-09 73.1
60 TraesCS7B01G405900 chr1D 78.125 160 32 2 4790 4946 484250444 484250603 1.210000e-16 99.0
61 TraesCS7B01G405900 chr1D 89.610 77 3 4 4458 4529 490037220 490037296 5.610000e-15 93.5
62 TraesCS7B01G405900 chr3D 84.706 85 12 1 4863 4946 608566566 608566482 3.370000e-12 84.2


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 TraesCS7B01G405900 chr7B 674197127 674202384 5257 True 9710.0 9710 100.0000 1 5258 1 chr7B.!!$R1 5257
1 TraesCS7B01G405900 chr7B 674226218 674226925 707 False 423.5 521 91.8800 3458 4113 2 chr7B.!!$F1 655
2 TraesCS7B01G405900 chr7D 596093990 596098682 4692 True 886.0 3356 89.4572 3 5258 5 chr7D.!!$R1 5255
3 TraesCS7B01G405900 chr3B 32803521 32805202 1681 True 2730.0 2730 96.0950 1102 2772 1 chr3B.!!$R1 1670
4 TraesCS7B01G405900 chr5B 466783092 466784768 1676 True 2704.0 2704 95.8600 1104 2775 1 chr5B.!!$R4 1671
5 TraesCS7B01G405900 chr5B 13078840 13080453 1613 True 1964.0 1964 88.5270 1104 2755 1 chr5B.!!$R1 1651
6 TraesCS7B01G405900 chr5B 458941087 458942282 1195 True 1454.0 1454 88.8800 1104 2286 1 chr5B.!!$R3 1182
7 TraesCS7B01G405900 chr5B 50469242 50470187 945 True 418.0 418 74.9740 2845 3796 1 chr5B.!!$R2 951
8 TraesCS7B01G405900 chr1B 35278612 35280251 1639 True 2488.0 2488 93.9090 1102 2773 1 chr1B.!!$R1 1671
9 TraesCS7B01G405900 chr5A 672511187 672512906 1719 False 1359.5 2270 95.2565 1102 2772 2 chr5A.!!$F2 1670
10 TraesCS7B01G405900 chr2B 765028433 765029993 1560 False 1995.0 1995 89.8490 1209 2773 1 chr2B.!!$F1 1564
11 TraesCS7B01G405900 chr4A 741179260 741180575 1315 False 1991.0 1991 94.0250 1097 2417 1 chr4A.!!$F1 1320
12 TraesCS7B01G405900 chr4A 513352224 513353954 1730 True 1136.5 1962 94.4140 1104 2666 2 chr4A.!!$R2 1562
13 TraesCS7B01G405900 chr6B 52226233 52227993 1760 True 1215.0 1982 96.9025 1104 2769 2 chr6B.!!$R2 1665
14 TraesCS7B01G405900 chr6A 135002877 135004653 1776 True 1148.5 1951 96.3035 1100 2773 2 chr6A.!!$R2 1673
15 TraesCS7B01G405900 chr4B 664310093 664311552 1459 False 1940.0 1940 90.7910 1105 2555 1 chr4B.!!$F2 1450
16 TraesCS7B01G405900 chr7A 689255551 689261960 6409 True 536.0 965 90.8120 44 5240 6 chr7A.!!$R1 5196
17 TraesCS7B01G405900 chr5D 47332363 47333308 945 True 424.0 424 75.0780 2845 3796 1 chr5D.!!$R1 951

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
40 41 0.037419 TACGAAAGGGGCAACGGTAC 60.037 55.0 0.0 0.0 37.60 3.34 F
1719 2992 0.032117 ATCCATCGGTCTCCCAGTCA 60.032 55.0 0.0 0.0 0.00 3.41 F
3307 4823 0.327924 TCCAGCGACCATTGTCCAAT 59.672 50.0 0.0 0.0 38.32 3.16 F
3912 5518 0.388006 TGTGTCGATGTGCCTGTACG 60.388 55.0 0.0 0.0 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1745 3018 0.526662 TTCGCGTCTTTCTCCTCCTC 59.473 55.000 5.77 0.0 0.00 3.71 R
3655 5179 1.065491 TGAGCTGCGGGAACATGTAAT 60.065 47.619 0.00 0.0 0.00 1.89 R
4159 5765 0.827925 AGCGCCGGGAGAATCTCATA 60.828 55.000 12.79 0.0 32.47 2.15 R
4868 8723 1.274447 GGTATACCCACCTCCGTATGC 59.726 57.143 11.17 0.0 35.55 3.14 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
30 31 4.281182 ACATAGTAGGCAGATACGAAAGGG 59.719 45.833 0.00 0.00 0.00 3.95
31 32 2.040178 AGTAGGCAGATACGAAAGGGG 58.960 52.381 0.00 0.00 0.00 4.79
33 34 1.223487 GGCAGATACGAAAGGGGCA 59.777 57.895 0.00 0.00 0.00 5.36
34 35 0.393808 GGCAGATACGAAAGGGGCAA 60.394 55.000 0.00 0.00 0.00 4.52
37 38 0.107848 AGATACGAAAGGGGCAACGG 60.108 55.000 0.00 0.00 37.60 4.44
38 39 0.392060 GATACGAAAGGGGCAACGGT 60.392 55.000 0.00 0.00 37.60 4.83
39 40 0.903942 ATACGAAAGGGGCAACGGTA 59.096 50.000 0.00 0.00 37.60 4.02
40 41 0.037419 TACGAAAGGGGCAACGGTAC 60.037 55.000 0.00 0.00 37.60 3.34
51 52 3.621892 AACGGTACCTCGAGCACGC 62.622 63.158 10.90 1.11 39.58 5.34
132 133 3.382832 AACACGGGAGAGGGCGAG 61.383 66.667 0.00 0.00 0.00 5.03
133 134 4.680537 ACACGGGAGAGGGCGAGT 62.681 66.667 0.00 0.00 0.00 4.18
134 135 3.382832 CACGGGAGAGGGCGAGTT 61.383 66.667 0.00 0.00 0.00 3.01
135 136 2.603776 ACGGGAGAGGGCGAGTTT 60.604 61.111 0.00 0.00 0.00 2.66
136 137 1.304713 ACGGGAGAGGGCGAGTTTA 60.305 57.895 0.00 0.00 0.00 2.01
137 138 0.901580 ACGGGAGAGGGCGAGTTTAA 60.902 55.000 0.00 0.00 0.00 1.52
138 139 0.248289 CGGGAGAGGGCGAGTTTAAA 59.752 55.000 0.00 0.00 0.00 1.52
139 140 1.338389 CGGGAGAGGGCGAGTTTAAAA 60.338 52.381 0.00 0.00 0.00 1.52
140 141 2.082231 GGGAGAGGGCGAGTTTAAAAC 58.918 52.381 0.00 0.00 0.00 2.43
141 142 2.551504 GGGAGAGGGCGAGTTTAAAACA 60.552 50.000 0.00 0.00 0.00 2.83
142 143 3.344515 GGAGAGGGCGAGTTTAAAACAT 58.655 45.455 0.00 0.00 0.00 2.71
143 144 3.127030 GGAGAGGGCGAGTTTAAAACATG 59.873 47.826 0.00 0.00 0.00 3.21
152 153 3.151554 AGTTTAAAACATGGGGTCGGTC 58.848 45.455 0.00 0.00 0.00 4.79
210 211 4.047059 GTCCACGTTCGCCGGAGA 62.047 66.667 5.05 3.81 42.24 3.71
211 212 3.296836 TCCACGTTCGCCGGAGAA 61.297 61.111 17.34 17.34 42.24 2.87
215 216 2.266627 ACGTTCGCCGGAGAAGAGT 61.267 57.895 21.74 19.93 42.24 3.24
218 219 2.646175 TTCGCCGGAGAAGAGTGGG 61.646 63.158 17.34 0.00 0.00 4.61
275 367 2.436292 CTGCACCCTGCTCTGCTC 60.436 66.667 0.00 0.00 45.31 4.26
292 384 2.289565 GCTCCGATTTCTAGGGTTTGG 58.710 52.381 0.00 0.00 0.00 3.28
323 415 2.107953 GGTCATCTCCTCGCCTGC 59.892 66.667 0.00 0.00 0.00 4.85
326 418 1.687146 TCATCTCCTCGCCTGCCTT 60.687 57.895 0.00 0.00 0.00 4.35
327 419 1.523258 CATCTCCTCGCCTGCCTTG 60.523 63.158 0.00 0.00 0.00 3.61
328 420 3.397613 ATCTCCTCGCCTGCCTTGC 62.398 63.158 0.00 0.00 0.00 4.01
366 458 1.205064 CGCGCTGAACCACTTCAAG 59.795 57.895 5.56 0.00 35.92 3.02
385 477 1.605971 GACACCCGGTCTTCCTCCTC 61.606 65.000 0.00 0.00 43.46 3.71
392 484 1.536943 GGTCTTCCTCCTCGCACAGT 61.537 60.000 0.00 0.00 0.00 3.55
398 490 3.075005 TCCTCGCACAGTAGGGGC 61.075 66.667 0.00 0.00 33.40 5.80
400 492 4.514577 CTCGCACAGTAGGGGCCG 62.515 72.222 0.00 0.00 0.00 6.13
433 525 3.382832 CACGCCCGGTCTTCCTCT 61.383 66.667 0.00 0.00 0.00 3.69
447 547 2.503382 CCTCTAGGCGGCCTCTTCC 61.503 68.421 27.65 0.00 34.61 3.46
448 548 1.456705 CTCTAGGCGGCCTCTTCCT 60.457 63.158 27.65 2.54 34.61 3.36
449 549 1.455959 TCTAGGCGGCCTCTTCCTC 60.456 63.158 27.65 0.00 34.61 3.71
450 550 1.456705 CTAGGCGGCCTCTTCCTCT 60.457 63.158 27.65 0.79 34.61 3.69
451 551 1.001760 TAGGCGGCCTCTTCCTCTT 59.998 57.895 27.65 0.00 34.61 2.85
452 552 1.043673 TAGGCGGCCTCTTCCTCTTC 61.044 60.000 27.65 0.00 34.61 2.87
453 553 2.202810 GCGGCCTCTTCCTCTTCG 60.203 66.667 0.00 0.00 0.00 3.79
454 554 2.496817 CGGCCTCTTCCTCTTCGG 59.503 66.667 0.00 0.00 0.00 4.30
455 555 2.352032 CGGCCTCTTCCTCTTCGGT 61.352 63.158 0.00 0.00 0.00 4.69
456 556 1.219393 GGCCTCTTCCTCTTCGGTG 59.781 63.158 0.00 0.00 0.00 4.94
462 562 0.969894 CTTCCTCTTCGGTGACAGGT 59.030 55.000 0.00 0.00 0.00 4.00
463 563 1.344763 CTTCCTCTTCGGTGACAGGTT 59.655 52.381 0.00 0.00 0.00 3.50
464 564 1.420430 TCCTCTTCGGTGACAGGTTT 58.580 50.000 0.00 0.00 0.00 3.27
465 565 1.343465 TCCTCTTCGGTGACAGGTTTC 59.657 52.381 0.00 0.00 0.00 2.78
467 567 1.344763 CTCTTCGGTGACAGGTTTCCT 59.655 52.381 0.00 0.00 0.00 3.36
468 568 1.766496 TCTTCGGTGACAGGTTTCCTT 59.234 47.619 0.00 0.00 0.00 3.36
469 569 2.143925 CTTCGGTGACAGGTTTCCTTC 58.856 52.381 0.00 0.00 0.00 3.46
470 570 1.420430 TCGGTGACAGGTTTCCTTCT 58.580 50.000 0.00 0.00 0.00 2.85
471 571 1.343465 TCGGTGACAGGTTTCCTTCTC 59.657 52.381 0.00 0.00 0.00 2.87
472 572 1.344763 CGGTGACAGGTTTCCTTCTCT 59.655 52.381 0.00 0.00 0.00 3.10
473 573 2.561419 CGGTGACAGGTTTCCTTCTCTA 59.439 50.000 0.00 0.00 0.00 2.43
474 574 3.614390 CGGTGACAGGTTTCCTTCTCTAC 60.614 52.174 0.00 0.00 0.00 2.59
477 577 4.020128 GTGACAGGTTTCCTTCTCTACCAT 60.020 45.833 0.00 0.00 33.02 3.55
478 578 4.597507 TGACAGGTTTCCTTCTCTACCATT 59.402 41.667 0.00 0.00 33.02 3.16
479 579 5.073144 TGACAGGTTTCCTTCTCTACCATTT 59.927 40.000 0.00 0.00 33.02 2.32
480 580 5.953571 ACAGGTTTCCTTCTCTACCATTTT 58.046 37.500 0.00 0.00 33.02 1.82
481 581 6.373759 ACAGGTTTCCTTCTCTACCATTTTT 58.626 36.000 0.00 0.00 33.02 1.94
482 582 7.523415 ACAGGTTTCCTTCTCTACCATTTTTA 58.477 34.615 0.00 0.00 33.02 1.52
484 584 9.681062 CAGGTTTCCTTCTCTACCATTTTTATA 57.319 33.333 0.00 0.00 33.02 0.98
485 585 9.907229 AGGTTTCCTTCTCTACCATTTTTATAG 57.093 33.333 0.00 0.00 33.02 1.31
486 586 9.121658 GGTTTCCTTCTCTACCATTTTTATAGG 57.878 37.037 0.00 0.00 0.00 2.57
487 587 9.901172 GTTTCCTTCTCTACCATTTTTATAGGA 57.099 33.333 0.00 0.00 0.00 2.94
491 648 9.907229 CCTTCTCTACCATTTTTATAGGAAGTT 57.093 33.333 0.00 0.00 29.93 2.66
499 656 8.101419 ACCATTTTTATAGGAAGTTCTTCTCGT 58.899 33.333 11.53 1.64 0.00 4.18
508 665 1.000283 AGTTCTTCTCGTCCTGCTGTG 60.000 52.381 0.00 0.00 0.00 3.66
509 666 0.319900 TTCTTCTCGTCCTGCTGTGC 60.320 55.000 0.00 0.00 0.00 4.57
510 667 1.181741 TCTTCTCGTCCTGCTGTGCT 61.182 55.000 0.00 0.00 0.00 4.40
511 668 0.735632 CTTCTCGTCCTGCTGTGCTC 60.736 60.000 0.00 0.00 0.00 4.26
512 669 1.181741 TTCTCGTCCTGCTGTGCTCT 61.182 55.000 0.00 0.00 0.00 4.09
513 670 0.322546 TCTCGTCCTGCTGTGCTCTA 60.323 55.000 0.00 0.00 0.00 2.43
514 671 0.179150 CTCGTCCTGCTGTGCTCTAC 60.179 60.000 0.00 0.00 0.00 2.59
552 709 1.265095 CCATAACCTTAGCGCTGCATG 59.735 52.381 22.90 12.95 0.00 4.06
573 730 9.900710 TGCATGTTTAATACGTTTATGAAAACT 57.099 25.926 0.00 0.00 42.39 2.66
686 1957 1.895131 GTCCCAACCAAACTGATGCAT 59.105 47.619 0.00 0.00 0.00 3.96
687 1958 2.299867 GTCCCAACCAAACTGATGCATT 59.700 45.455 0.00 0.00 0.00 3.56
688 1959 2.971330 TCCCAACCAAACTGATGCATTT 59.029 40.909 0.00 0.00 0.00 2.32
689 1960 3.390639 TCCCAACCAAACTGATGCATTTT 59.609 39.130 0.00 0.00 0.00 1.82
690 1961 4.136051 CCCAACCAAACTGATGCATTTTT 58.864 39.130 0.00 0.00 0.00 1.94
724 1995 6.759272 TCTGTGTTGCTCACTATCTAAACTT 58.241 36.000 12.23 0.00 46.27 2.66
771 2042 5.200483 TCCTCAAACATCACCTTGTTCTTT 58.800 37.500 0.00 0.00 38.85 2.52
803 2074 0.461870 TGGGCAATCATCGAACGAGG 60.462 55.000 2.48 2.48 0.00 4.63
978 2249 8.546322 TCCTAAACTAATAGGTTTCCTTCCTTC 58.454 37.037 0.00 0.00 42.63 3.46
1719 2992 0.032117 ATCCATCGGTCTCCCAGTCA 60.032 55.000 0.00 0.00 0.00 3.41
2105 3395 1.135915 GCAACAACCAACACCACATCA 59.864 47.619 0.00 0.00 0.00 3.07
2639 4132 1.228154 GAAGAAACCCACCGCCACT 60.228 57.895 0.00 0.00 0.00 4.00
2779 4295 2.264794 CGGGGTCGGGAAAGAGTG 59.735 66.667 0.00 0.00 0.00 3.51
2780 4296 2.580601 CGGGGTCGGGAAAGAGTGT 61.581 63.158 0.00 0.00 0.00 3.55
2781 4297 1.252904 CGGGGTCGGGAAAGAGTGTA 61.253 60.000 0.00 0.00 0.00 2.90
2782 4298 0.535797 GGGGTCGGGAAAGAGTGTAG 59.464 60.000 0.00 0.00 0.00 2.74
2783 4299 1.264295 GGGTCGGGAAAGAGTGTAGT 58.736 55.000 0.00 0.00 0.00 2.73
2784 4300 1.622312 GGGTCGGGAAAGAGTGTAGTT 59.378 52.381 0.00 0.00 0.00 2.24
2785 4301 2.038164 GGGTCGGGAAAGAGTGTAGTTT 59.962 50.000 0.00 0.00 0.00 2.66
2786 4302 3.324117 GGTCGGGAAAGAGTGTAGTTTC 58.676 50.000 0.00 0.00 32.79 2.78
2792 4308 5.434352 GGAAAGAGTGTAGTTTCCCAAAC 57.566 43.478 2.92 0.00 44.12 2.93
2805 4321 4.320608 TTCCCAAACTGAGTTTCAATGC 57.679 40.909 7.75 0.00 33.10 3.56
2840 4356 2.091665 CCTAGGCATGGAGGGAAACAAT 60.092 50.000 0.00 0.00 0.00 2.71
2917 4433 5.661056 AGGTTGTCGACAATCTTGAGATA 57.339 39.130 33.21 6.70 44.32 1.98
2923 4439 9.267096 GTTGTCGACAATCTTGAGATAAAATTC 57.733 33.333 31.81 10.55 38.24 2.17
2947 4463 6.530534 TCGTATTTGAGAGCAAGCTAGTTTAC 59.469 38.462 0.00 0.00 35.04 2.01
3001 4517 4.105858 TCCTCCCGGACTAAGAATCTATCA 59.894 45.833 0.73 0.00 33.30 2.15
3058 4574 3.560636 AGGAATCATTACAGGTTCCCG 57.439 47.619 2.53 0.00 40.75 5.14
3075 4591 5.009310 GGTTCCCGTTTGAACTTTTAGACAT 59.991 40.000 8.87 0.00 43.31 3.06
3145 4661 1.301160 AACCACCCCCTTCCCAGTTT 61.301 55.000 0.00 0.00 0.00 2.66
3146 4662 1.076727 CCACCCCCTTCCCAGTTTC 59.923 63.158 0.00 0.00 0.00 2.78
3197 4713 2.742053 CTCCATTTACTCAACACCACCG 59.258 50.000 0.00 0.00 0.00 4.94
3307 4823 0.327924 TCCAGCGACCATTGTCCAAT 59.672 50.000 0.00 0.00 38.32 3.16
3319 4835 4.384098 CCATTGTCCAATCTGCAGTACCTA 60.384 45.833 14.67 0.00 0.00 3.08
3330 4846 6.360370 TCTGCAGTACCTAAGAGTCAAATT 57.640 37.500 14.67 0.00 0.00 1.82
3410 4926 1.421646 GGGACTGCATACCTATTGCCT 59.578 52.381 8.78 0.00 39.39 4.75
3510 5026 1.205417 CAATGGGCTTCCACATGTTCC 59.795 52.381 0.00 0.00 44.44 3.62
3597 5117 8.220755 TCTAGGTTGTGCAATATGGTTTTATC 57.779 34.615 0.00 0.00 0.00 1.75
3655 5179 4.226384 ACTACATGGACATCAGATAGCCA 58.774 43.478 0.00 6.00 0.00 4.75
3702 5226 6.183360 GCATCTGCAGATAATATTGGCTGTAG 60.183 42.308 28.27 20.95 40.82 2.74
3877 5483 5.684704 TGACCTTTTATCAGGATGCTTAGG 58.315 41.667 0.00 0.00 37.39 2.69
3882 5488 2.355010 ATCAGGATGCTTAGGGTTGC 57.645 50.000 0.00 0.00 34.76 4.17
3891 5497 1.726853 CTTAGGGTTGCTTCACTCGG 58.273 55.000 0.00 0.00 0.00 4.63
3897 5503 0.814010 GTTGCTTCACTCGGGTGTGT 60.814 55.000 16.53 0.00 43.41 3.72
3898 5504 0.531974 TTGCTTCACTCGGGTGTGTC 60.532 55.000 16.53 5.99 43.41 3.67
3905 5511 2.048597 TCGGGTGTGTCGATGTGC 60.049 61.111 0.00 0.00 0.00 4.57
3908 5514 2.034879 GGGTGTGTCGATGTGCCTG 61.035 63.158 0.00 0.00 0.00 4.85
3911 5517 1.068474 GTGTGTCGATGTGCCTGTAC 58.932 55.000 0.00 0.00 0.00 2.90
3912 5518 0.388006 TGTGTCGATGTGCCTGTACG 60.388 55.000 0.00 0.00 0.00 3.67
3913 5519 0.388134 GTGTCGATGTGCCTGTACGT 60.388 55.000 0.00 0.00 0.00 3.57
3914 5520 1.135603 GTGTCGATGTGCCTGTACGTA 60.136 52.381 0.00 0.00 0.00 3.57
3915 5521 1.540707 TGTCGATGTGCCTGTACGTAA 59.459 47.619 0.00 0.00 0.00 3.18
3916 5522 1.916000 GTCGATGTGCCTGTACGTAAC 59.084 52.381 0.00 0.00 0.00 2.50
3917 5523 1.540707 TCGATGTGCCTGTACGTAACA 59.459 47.619 0.00 0.00 36.42 2.41
4029 5635 6.231211 ACACAAATACCTACACCTGAAGAAG 58.769 40.000 0.00 0.00 0.00 2.85
4041 5647 2.681848 CCTGAAGAAGATGCATGTCACC 59.318 50.000 2.46 0.00 0.00 4.02
4056 5662 0.608035 TCACCGGATTCAAAGCCACC 60.608 55.000 9.46 0.00 32.95 4.61
4092 5698 2.289072 ACTCCTGTTTCATGTCGTGGAG 60.289 50.000 16.65 16.65 43.56 3.86
4114 5720 1.663173 GCCCCTGCGATAGAGACTC 59.337 63.158 0.00 0.00 39.76 3.36
4116 5722 1.243902 CCCCTGCGATAGAGACTCTC 58.756 60.000 8.64 0.00 39.76 3.20
4117 5723 0.871722 CCCTGCGATAGAGACTCTCG 59.128 60.000 8.64 8.97 35.36 4.04
4139 5745 4.565166 CGCCGTAGATACAATTCAAAGACA 59.435 41.667 0.00 0.00 0.00 3.41
4156 5762 8.078060 TCAAAGACAGTATGATCTGTTGGATA 57.922 34.615 0.98 0.00 46.81 2.59
4159 5765 7.609097 AGACAGTATGATCTGTTGGATACAT 57.391 36.000 0.98 0.00 46.81 2.29
4265 5871 3.371965 TCTACCTTCTGTAAAGGCCGAT 58.628 45.455 0.00 0.00 41.10 4.18
4323 5947 3.081061 ACTGAAATCGCTATTGTTGGCA 58.919 40.909 0.00 0.00 0.00 4.92
4353 5994 3.838120 TGTGTTCTCTATGTTGCTCGAG 58.162 45.455 8.45 8.45 0.00 4.04
4455 6921 0.392060 ACCGGTCAAAATAGCCCGAC 60.392 55.000 0.00 0.00 43.01 4.79
4462 6928 4.022676 GGTCAAAATAGCCCGACAGAAAAA 60.023 41.667 0.00 0.00 0.00 1.94
4513 7186 5.940192 ATTTGACGCACTACAAAAGATGA 57.060 34.783 0.00 0.00 39.01 2.92
4541 7214 5.941555 AAACTTAGACATAGGAGGTGAGG 57.058 43.478 0.00 0.00 0.00 3.86
4563 7236 4.058797 GCAGGTGGTTAGTGCGTT 57.941 55.556 0.00 0.00 0.00 4.84
4564 7237 3.220447 GCAGGTGGTTAGTGCGTTA 57.780 52.632 0.00 0.00 0.00 3.18
4565 7238 1.734163 GCAGGTGGTTAGTGCGTTAT 58.266 50.000 0.00 0.00 0.00 1.89
4566 7239 2.896168 GCAGGTGGTTAGTGCGTTATA 58.104 47.619 0.00 0.00 0.00 0.98
4567 7240 3.463944 GCAGGTGGTTAGTGCGTTATAT 58.536 45.455 0.00 0.00 0.00 0.86
4568 7241 3.875134 GCAGGTGGTTAGTGCGTTATATT 59.125 43.478 0.00 0.00 0.00 1.28
4570 7243 5.729454 GCAGGTGGTTAGTGCGTTATATTTG 60.729 44.000 0.00 0.00 0.00 2.32
4571 7244 5.583061 CAGGTGGTTAGTGCGTTATATTTGA 59.417 40.000 0.00 0.00 0.00 2.69
4573 7246 6.315393 AGGTGGTTAGTGCGTTATATTTGAAG 59.685 38.462 0.00 0.00 0.00 3.02
4574 7247 5.963586 GTGGTTAGTGCGTTATATTTGAAGC 59.036 40.000 0.00 0.00 0.00 3.86
4575 7248 5.644206 TGGTTAGTGCGTTATATTTGAAGCA 59.356 36.000 0.00 0.00 0.00 3.91
4582 7255 7.459394 TGCGTTATATTTGAAGCACTACTAC 57.541 36.000 0.00 0.00 0.00 2.73
4583 7256 7.036829 TGCGTTATATTTGAAGCACTACTACA 58.963 34.615 0.00 0.00 0.00 2.74
4585 7258 8.385111 GCGTTATATTTGAAGCACTACTACAAA 58.615 33.333 0.00 0.00 35.49 2.83
4604 7277 9.554724 ACTACAAATATTTGACGCTTATGTTTG 57.445 29.630 30.18 10.43 40.55 2.93
4720 8231 7.864108 AAAAATGAAGGGAAAAAGACCAAAG 57.136 32.000 0.00 0.00 0.00 2.77
4768 8622 5.624344 ATGAGAAGATGCACAACAAGAAG 57.376 39.130 0.00 0.00 0.00 2.85
4769 8623 3.251729 TGAGAAGATGCACAACAAGAAGC 59.748 43.478 0.00 0.00 0.00 3.86
4844 8698 0.174845 CCGGAAGAATCGGCTGTGTA 59.825 55.000 0.00 0.00 41.07 2.90
4868 8723 1.917955 CTATGTACAACTCGTGTGCCG 59.082 52.381 0.00 0.00 41.81 5.69
4934 8789 0.036590 TGTACGGTTTGTAAGGGGGC 59.963 55.000 0.00 0.00 34.07 5.80
5016 8871 7.201929 GGGTTGGTGGTCTTAAAATAAACAAGA 60.202 37.037 0.00 0.00 0.00 3.02
5023 8878 6.492429 GGTCTTAAAATAAACAAGAGGGGTGT 59.508 38.462 0.00 0.00 0.00 4.16
5183 10016 2.380084 TGGTTATCTTGTGTCGCCTC 57.620 50.000 0.00 0.00 0.00 4.70
5194 10027 0.460459 TGTCGCCTCGTTGTTGTTGA 60.460 50.000 0.00 0.00 0.00 3.18
5195 10028 0.042448 GTCGCCTCGTTGTTGTTGAC 60.042 55.000 0.00 0.00 0.00 3.18
5196 10029 0.179094 TCGCCTCGTTGTTGTTGACT 60.179 50.000 0.00 0.00 0.00 3.41
5197 10030 0.655733 CGCCTCGTTGTTGTTGACTT 59.344 50.000 0.00 0.00 0.00 3.01
5198 10031 1.594518 CGCCTCGTTGTTGTTGACTTG 60.595 52.381 0.00 0.00 0.00 3.16
5199 10032 1.859998 GCCTCGTTGTTGTTGACTTGC 60.860 52.381 0.00 0.00 0.00 4.01
5200 10033 1.670811 CCTCGTTGTTGTTGACTTGCT 59.329 47.619 0.00 0.00 0.00 3.91
5240 10073 4.042311 AGAGTTGTGTCTCTAGGTCTCAGA 59.958 45.833 0.00 0.00 42.18 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.434340 TCGTATCTGCCTACTATGTGATTGAT 59.566 38.462 0.00 0.00 0.00 2.57
10 11 3.228453 CCCCTTTCGTATCTGCCTACTA 58.772 50.000 0.00 0.00 0.00 1.82
21 22 0.037419 GTACCGTTGCCCCTTTCGTA 60.037 55.000 0.00 0.00 0.00 3.43
23 24 2.036571 GGTACCGTTGCCCCTTTCG 61.037 63.158 0.00 0.00 0.00 3.46
30 31 2.508663 GCTCGAGGTACCGTTGCC 60.509 66.667 15.58 0.00 0.00 4.52
31 32 2.092882 GTGCTCGAGGTACCGTTGC 61.093 63.158 15.58 10.39 0.00 4.17
33 34 2.564975 CGTGCTCGAGGTACCGTT 59.435 61.111 15.58 0.00 39.71 4.44
34 35 4.112341 GCGTGCTCGAGGTACCGT 62.112 66.667 15.58 0.00 39.71 4.83
37 38 1.878522 CCATGCGTGCTCGAGGTAC 60.879 63.158 15.58 3.92 39.71 3.34
38 39 2.004808 CTCCATGCGTGCTCGAGGTA 62.005 60.000 15.58 0.00 39.71 3.08
39 40 3.362399 CTCCATGCGTGCTCGAGGT 62.362 63.158 15.58 0.00 39.71 3.85
40 41 2.584418 CTCCATGCGTGCTCGAGG 60.584 66.667 15.58 10.06 39.71 4.63
132 133 2.095617 CGACCGACCCCATGTTTTAAAC 60.096 50.000 0.20 0.20 0.00 2.01
133 134 2.152830 CGACCGACCCCATGTTTTAAA 58.847 47.619 0.00 0.00 0.00 1.52
134 135 1.611148 CCGACCGACCCCATGTTTTAA 60.611 52.381 0.00 0.00 0.00 1.52
135 136 0.036199 CCGACCGACCCCATGTTTTA 60.036 55.000 0.00 0.00 0.00 1.52
136 137 1.302993 CCGACCGACCCCATGTTTT 60.303 57.895 0.00 0.00 0.00 2.43
137 138 2.349755 CCGACCGACCCCATGTTT 59.650 61.111 0.00 0.00 0.00 2.83
138 139 2.926242 ACCGACCGACCCCATGTT 60.926 61.111 0.00 0.00 0.00 2.71
139 140 3.387947 GACCGACCGACCCCATGT 61.388 66.667 0.00 0.00 0.00 3.21
140 141 4.157120 GGACCGACCGACCCCATG 62.157 72.222 0.00 0.00 0.00 3.66
229 230 2.490217 CGGCTCGACTCGATTGGT 59.510 61.111 0.62 0.00 34.61 3.67
232 233 3.001902 TTGGCGGCTCGACTCGATT 62.002 57.895 11.43 0.00 35.04 3.34
234 235 4.415332 GTTGGCGGCTCGACTCGA 62.415 66.667 11.43 0.29 35.04 4.04
275 367 1.389555 GCCCAAACCCTAGAAATCGG 58.610 55.000 0.00 0.00 0.00 4.18
337 429 3.906649 CAGCGCGCGTGAGATGAC 61.907 66.667 32.35 11.90 32.68 3.06
338 430 3.625082 TTCAGCGCGCGTGAGATGA 62.625 57.895 32.35 19.82 38.56 2.92
339 431 3.181290 TTCAGCGCGCGTGAGATG 61.181 61.111 32.35 17.60 32.17 2.90
340 432 3.181967 GTTCAGCGCGCGTGAGAT 61.182 61.111 32.35 3.33 0.00 2.75
346 438 4.430423 GAAGTGGTTCAGCGCGCG 62.430 66.667 28.44 28.44 32.36 6.86
347 439 2.770587 CTTGAAGTGGTTCAGCGCGC 62.771 60.000 26.66 26.66 43.66 6.86
348 440 1.205064 CTTGAAGTGGTTCAGCGCG 59.795 57.895 0.00 0.00 43.66 6.86
349 441 0.235926 GTCTTGAAGTGGTTCAGCGC 59.764 55.000 0.00 0.00 43.66 5.92
366 458 1.605971 GAGGAGGAAGACCGGGTGTC 61.606 65.000 3.30 1.08 44.82 3.67
385 477 3.426117 CTACGGCCCCTACTGTGCG 62.426 68.421 0.00 0.00 0.00 5.34
392 484 3.031873 ACTCCCCTACGGCCCCTA 61.032 66.667 0.00 0.00 0.00 3.53
398 490 3.082579 GCAGCTCACTCCCCTACGG 62.083 68.421 0.00 0.00 0.00 4.02
400 492 1.219393 GTGCAGCTCACTCCCCTAC 59.781 63.158 8.50 0.00 42.38 3.18
418 510 2.491022 CCTAGAGGAAGACCGGGCG 61.491 68.421 6.32 0.00 41.83 6.13
420 512 2.491022 CGCCTAGAGGAAGACCGGG 61.491 68.421 6.32 0.00 41.83 5.73
421 513 2.491022 CCGCCTAGAGGAAGACCGG 61.491 68.421 0.00 0.00 41.83 5.28
422 514 3.121019 CCGCCTAGAGGAAGACCG 58.879 66.667 0.00 0.00 41.83 4.79
424 516 1.740332 GAGGCCGCCTAGAGGAAGAC 61.740 65.000 13.29 0.00 37.39 3.01
425 517 1.455959 GAGGCCGCCTAGAGGAAGA 60.456 63.158 13.29 0.00 37.39 2.87
426 518 1.045911 AAGAGGCCGCCTAGAGGAAG 61.046 60.000 13.29 0.00 37.39 3.46
427 519 1.001760 AAGAGGCCGCCTAGAGGAA 59.998 57.895 13.29 0.00 37.39 3.36
428 520 1.455959 GAAGAGGCCGCCTAGAGGA 60.456 63.158 13.29 0.00 37.39 3.71
429 521 2.503382 GGAAGAGGCCGCCTAGAGG 61.503 68.421 13.29 0.00 31.76 3.69
430 522 1.456705 AGGAAGAGGCCGCCTAGAG 60.457 63.158 13.29 0.00 31.76 2.43
433 525 1.001760 AAGAGGAAGAGGCCGCCTA 59.998 57.895 13.29 0.00 31.76 3.93
447 547 1.344763 AGGAAACCTGTCACCGAAGAG 59.655 52.381 0.00 0.00 29.57 2.85
448 548 1.420430 AGGAAACCTGTCACCGAAGA 58.580 50.000 0.00 0.00 29.57 2.87
449 549 2.143925 GAAGGAAACCTGTCACCGAAG 58.856 52.381 0.00 0.00 32.13 3.79
450 550 1.766496 AGAAGGAAACCTGTCACCGAA 59.234 47.619 0.00 0.00 32.13 4.30
451 551 1.343465 GAGAAGGAAACCTGTCACCGA 59.657 52.381 0.00 0.00 32.13 4.69
452 552 1.344763 AGAGAAGGAAACCTGTCACCG 59.655 52.381 0.00 0.00 32.13 4.94
453 553 3.306849 GGTAGAGAAGGAAACCTGTCACC 60.307 52.174 0.00 0.00 32.13 4.02
454 554 3.323979 TGGTAGAGAAGGAAACCTGTCAC 59.676 47.826 0.00 0.00 32.13 3.67
455 555 3.583228 TGGTAGAGAAGGAAACCTGTCA 58.417 45.455 0.00 0.00 32.13 3.58
456 556 4.828072 ATGGTAGAGAAGGAAACCTGTC 57.172 45.455 0.00 0.00 32.13 3.51
464 564 9.280456 ACTTCCTATAAAAATGGTAGAGAAGGA 57.720 33.333 0.00 0.00 32.77 3.36
465 565 9.907229 AACTTCCTATAAAAATGGTAGAGAAGG 57.093 33.333 0.00 0.00 32.77 3.46
472 572 9.595823 CGAGAAGAACTTCCTATAAAAATGGTA 57.404 33.333 10.41 0.00 40.33 3.25
473 573 8.101419 ACGAGAAGAACTTCCTATAAAAATGGT 58.899 33.333 10.41 0.00 40.33 3.55
474 574 8.494016 ACGAGAAGAACTTCCTATAAAAATGG 57.506 34.615 10.41 0.00 40.33 3.16
477 577 7.817962 CAGGACGAGAAGAACTTCCTATAAAAA 59.182 37.037 10.41 0.00 40.33 1.94
478 578 7.321153 CAGGACGAGAAGAACTTCCTATAAAA 58.679 38.462 10.41 0.00 40.33 1.52
479 579 6.627508 GCAGGACGAGAAGAACTTCCTATAAA 60.628 42.308 10.41 0.00 40.33 1.40
480 580 5.163540 GCAGGACGAGAAGAACTTCCTATAA 60.164 44.000 10.41 0.00 40.33 0.98
481 581 4.338682 GCAGGACGAGAAGAACTTCCTATA 59.661 45.833 10.41 0.00 40.33 1.31
482 582 3.131400 GCAGGACGAGAAGAACTTCCTAT 59.869 47.826 10.41 0.00 40.33 2.57
484 584 1.273886 GCAGGACGAGAAGAACTTCCT 59.726 52.381 10.41 0.00 40.33 3.36
485 585 1.273886 AGCAGGACGAGAAGAACTTCC 59.726 52.381 10.41 2.91 40.33 3.46
486 586 2.288518 ACAGCAGGACGAGAAGAACTTC 60.289 50.000 6.46 6.46 39.78 3.01
487 587 1.689273 ACAGCAGGACGAGAAGAACTT 59.311 47.619 0.00 0.00 0.00 2.66
489 589 1.423395 CACAGCAGGACGAGAAGAAC 58.577 55.000 0.00 0.00 0.00 3.01
491 648 1.181741 AGCACAGCAGGACGAGAAGA 61.182 55.000 0.00 0.00 0.00 2.87
499 656 0.741326 GATCGTAGAGCACAGCAGGA 59.259 55.000 0.00 0.00 45.47 3.86
509 666 4.346970 CAGTGTGCTTGTAGATCGTAGAG 58.653 47.826 0.00 0.00 43.63 2.43
510 667 3.427638 GCAGTGTGCTTGTAGATCGTAGA 60.428 47.826 0.00 0.00 40.96 2.59
511 668 2.854777 GCAGTGTGCTTGTAGATCGTAG 59.145 50.000 0.00 0.00 40.96 3.51
512 669 2.416836 GGCAGTGTGCTTGTAGATCGTA 60.417 50.000 0.00 0.00 44.28 3.43
513 670 1.673033 GGCAGTGTGCTTGTAGATCGT 60.673 52.381 0.00 0.00 44.28 3.73
514 671 1.002366 GGCAGTGTGCTTGTAGATCG 58.998 55.000 0.00 0.00 44.28 3.69
618 775 1.301716 CACCACCTCCACTCAACCG 60.302 63.158 0.00 0.00 0.00 4.44
724 1995 5.725551 AAAATAGGTGGATGGTGACCATA 57.274 39.130 18.56 0.00 45.26 2.74
771 2042 2.192664 TTGCCCATTCTAACGCTGAA 57.807 45.000 0.00 0.00 0.00 3.02
816 2087 7.178274 TGTTGGTTTAATATGGACATGCTTCTT 59.822 33.333 0.00 0.00 0.00 2.52
880 2151 7.787028 ACATACCTCTGGAAGATCTTTAAGTC 58.213 38.462 9.87 0.00 45.62 3.01
1020 2291 2.944129 ACAGCCTCTTTTGCAGGTAAA 58.056 42.857 0.00 0.00 32.98 2.01
1332 2604 2.637383 GGTGAAGTCGGAGTCGCCT 61.637 63.158 12.00 0.00 40.59 5.52
1528 2800 2.299521 CTTCGGTAGTCGGATCTTCCT 58.700 52.381 0.00 0.00 39.77 3.36
1719 2992 1.680522 ATCGTCTCGGAGCAGGCAAT 61.681 55.000 0.00 0.00 0.00 3.56
1745 3018 0.526662 TTCGCGTCTTTCTCCTCCTC 59.473 55.000 5.77 0.00 0.00 3.71
2082 3357 2.415426 GGTGTTGGTTGTTGCGGG 59.585 61.111 0.00 0.00 0.00 6.13
2105 3395 1.005630 GTCTGGTGCTGCTCTTCGT 60.006 57.895 0.00 0.00 0.00 3.85
2162 3453 2.433838 TGCTCTGCTGCTTCGCTC 60.434 61.111 0.00 0.00 0.00 5.03
2782 4298 4.507756 GCATTGAAACTCAGTTTGGGAAAC 59.492 41.667 7.75 0.00 41.69 2.78
2783 4299 4.442753 GGCATTGAAACTCAGTTTGGGAAA 60.443 41.667 7.75 0.00 35.77 3.13
2784 4300 3.069443 GGCATTGAAACTCAGTTTGGGAA 59.931 43.478 7.75 0.00 35.77 3.97
2785 4301 2.627699 GGCATTGAAACTCAGTTTGGGA 59.372 45.455 7.75 0.00 35.77 4.37
2786 4302 2.364970 TGGCATTGAAACTCAGTTTGGG 59.635 45.455 7.75 0.00 35.77 4.12
2787 4303 3.731652 TGGCATTGAAACTCAGTTTGG 57.268 42.857 7.75 0.00 35.77 3.28
2788 4304 4.053295 CCTTGGCATTGAAACTCAGTTTG 58.947 43.478 7.75 0.00 35.77 2.93
2789 4305 3.960102 TCCTTGGCATTGAAACTCAGTTT 59.040 39.130 1.21 1.21 38.54 2.66
2790 4306 3.565307 TCCTTGGCATTGAAACTCAGTT 58.435 40.909 0.00 0.00 0.00 3.16
2791 4307 3.228188 TCCTTGGCATTGAAACTCAGT 57.772 42.857 0.00 0.00 0.00 3.41
2792 4308 3.760151 TGATCCTTGGCATTGAAACTCAG 59.240 43.478 0.00 0.00 0.00 3.35
2793 4309 3.765381 TGATCCTTGGCATTGAAACTCA 58.235 40.909 0.00 0.00 0.00 3.41
2794 4310 4.159135 ACATGATCCTTGGCATTGAAACTC 59.841 41.667 0.00 0.00 0.00 3.01
2795 4311 4.081862 CACATGATCCTTGGCATTGAAACT 60.082 41.667 0.00 0.00 0.00 2.66
2796 4312 4.178540 CACATGATCCTTGGCATTGAAAC 58.821 43.478 0.00 0.00 0.00 2.78
2797 4313 3.368635 GCACATGATCCTTGGCATTGAAA 60.369 43.478 0.00 0.00 0.00 2.69
2798 4314 2.166870 GCACATGATCCTTGGCATTGAA 59.833 45.455 0.00 0.00 0.00 2.69
2799 4315 1.752498 GCACATGATCCTTGGCATTGA 59.248 47.619 0.00 0.00 0.00 2.57
2805 4321 1.816961 GCCTAGGCACATGATCCTTGG 60.817 57.143 29.33 23.02 44.66 3.61
2840 4356 3.973305 TGGTCTATGAACATCTGGGCATA 59.027 43.478 0.00 0.00 0.00 3.14
2917 4433 6.259550 AGCTTGCTCTCAAATACGAATTTT 57.740 33.333 0.00 0.00 32.87 1.82
2923 4439 5.786401 AAACTAGCTTGCTCTCAAATACG 57.214 39.130 0.00 0.00 0.00 3.06
2947 4463 4.848357 ACCTTATCCAACTGTTGAGATGG 58.152 43.478 21.49 18.74 42.34 3.51
3001 4517 2.460757 GCAGTGGTGCCAAATCAAAT 57.539 45.000 0.00 0.00 44.72 2.32
3058 4574 8.784043 ACACTATCCATGTCTAAAAGTTCAAAC 58.216 33.333 0.00 0.00 0.00 2.93
3097 4613 8.450578 AACATACAAATCTGAGTTGAAGACAA 57.549 30.769 22.86 3.34 0.00 3.18
3109 4625 5.925969 GGGTGGTTTGAAACATACAAATCTG 59.074 40.000 10.53 0.00 38.62 2.90
3197 4713 6.585702 CACAAGATATTCTCGAGATCATGTCC 59.414 42.308 17.44 2.56 31.16 4.02
3307 4823 6.211584 AGAATTTGACTCTTAGGTACTGCAGA 59.788 38.462 23.35 0.48 41.52 4.26
3319 4835 2.568623 ACCCGCAGAATTTGACTCTT 57.431 45.000 0.00 0.00 0.00 2.85
3330 4846 1.207089 CTATCTTGGTGAACCCGCAGA 59.793 52.381 0.00 0.00 35.15 4.26
3410 4926 1.139654 CATCTCGGGAGCTTGATGGAA 59.860 52.381 0.00 0.00 34.40 3.53
3510 5026 6.265577 ACTGAAATTTTCAAAGTGAGGTTCG 58.734 36.000 12.62 0.35 39.58 3.95
3577 5097 8.372521 CGAAAAGATAAAACCATATTGCACAAC 58.627 33.333 0.00 0.00 0.00 3.32
3597 5117 2.913613 CAAGTTGAGCTCAGCGAAAAG 58.086 47.619 22.76 9.87 32.04 2.27
3655 5179 1.065491 TGAGCTGCGGGAACATGTAAT 60.065 47.619 0.00 0.00 0.00 1.89
3830 5436 8.030692 TCATTGAAGCAGAATCCTTAACAAATG 58.969 33.333 0.00 0.00 0.00 2.32
3891 5497 0.037697 TACAGGCACATCGACACACC 60.038 55.000 0.00 0.00 0.00 4.16
3897 5503 1.540707 TGTTACGTACAGGCACATCGA 59.459 47.619 0.00 0.00 31.68 3.59
3898 5504 1.985334 TGTTACGTACAGGCACATCG 58.015 50.000 0.00 0.00 31.68 3.84
3911 5517 9.403110 ACTGTAAAAGTAGAACATACTGTTACG 57.597 33.333 17.21 14.86 44.93 3.18
3915 5521 9.826574 TCAAACTGTAAAAGTAGAACATACTGT 57.173 29.630 0.00 0.00 38.56 3.55
3920 5526 7.230510 TGCCATCAAACTGTAAAAGTAGAACAT 59.769 33.333 0.00 0.00 38.56 2.71
3921 5527 6.544197 TGCCATCAAACTGTAAAAGTAGAACA 59.456 34.615 0.00 0.00 38.56 3.18
3922 5528 6.856426 GTGCCATCAAACTGTAAAAGTAGAAC 59.144 38.462 0.00 0.00 38.56 3.01
3932 5538 2.293122 GTGCAAGTGCCATCAAACTGTA 59.707 45.455 0.00 0.00 41.18 2.74
3933 5539 1.067516 GTGCAAGTGCCATCAAACTGT 59.932 47.619 0.00 0.00 41.18 3.55
4029 5635 1.667236 TGAATCCGGTGACATGCATC 58.333 50.000 0.00 0.00 0.00 3.91
4041 5647 1.067635 CCTTTGGTGGCTTTGAATCCG 60.068 52.381 0.00 0.00 0.00 4.18
4056 5662 0.600057 GGAGTTGAAGCTGGCCTTTG 59.400 55.000 3.32 0.00 32.78 2.77
4114 5720 5.041287 TCTTTGAATTGTATCTACGGCGAG 58.959 41.667 16.62 6.98 0.00 5.03
4116 5722 4.565166 TGTCTTTGAATTGTATCTACGGCG 59.435 41.667 4.80 4.80 0.00 6.46
4117 5723 5.581085 ACTGTCTTTGAATTGTATCTACGGC 59.419 40.000 0.00 0.00 0.00 5.68
4139 5745 9.539194 TCTCATATGTATCCAACAGATCATACT 57.461 33.333 1.90 0.00 42.70 2.12
4156 5762 1.273606 CGCCGGGAGAATCTCATATGT 59.726 52.381 12.79 0.00 32.47 2.29
4159 5765 0.827925 AGCGCCGGGAGAATCTCATA 60.828 55.000 12.79 0.00 32.47 2.15
4184 5790 1.837439 TGACAATATCAAGGGCGGAGT 59.163 47.619 0.00 0.00 33.02 3.85
4188 5794 1.140852 TCCCTGACAATATCAAGGGCG 59.859 52.381 1.50 0.00 41.81 6.13
4323 5947 6.441274 CAACATAGAGAACACAAAAGCACAT 58.559 36.000 0.00 0.00 0.00 3.21
4413 6679 8.113675 CGGTTTTTCTTCTGTTTTTAATTGGTG 58.886 33.333 0.00 0.00 0.00 4.17
4462 6928 7.937649 ACGCTAAAAATAAAGACTGGTTTTCT 58.062 30.769 0.00 0.00 0.00 2.52
4521 7194 4.611564 ACCTCACCTCCTATGTCTAAGT 57.388 45.455 0.00 0.00 0.00 2.24
4541 7214 1.287425 GCACTAACCACCTGCGATAC 58.713 55.000 0.00 0.00 0.00 2.24
4568 7241 8.440059 CGTCAAATATTTGTAGTAGTGCTTCAA 58.560 33.333 23.95 0.00 39.18 2.69
4570 7243 6.900299 GCGTCAAATATTTGTAGTAGTGCTTC 59.100 38.462 23.95 4.73 39.18 3.86
4571 7244 6.594159 AGCGTCAAATATTTGTAGTAGTGCTT 59.406 34.615 23.95 8.83 39.18 3.91
4573 7246 6.345920 AGCGTCAAATATTTGTAGTAGTGC 57.654 37.500 23.95 17.51 39.18 4.40
4574 7247 9.849607 CATAAGCGTCAAATATTTGTAGTAGTG 57.150 33.333 23.95 13.74 39.18 2.74
4575 7248 9.595823 ACATAAGCGTCAAATATTTGTAGTAGT 57.404 29.630 23.95 12.66 39.18 2.73
4578 7251 9.554724 CAAACATAAGCGTCAAATATTTGTAGT 57.445 29.630 23.95 11.22 39.18 2.73
4579 7252 9.009327 CCAAACATAAGCGTCAAATATTTGTAG 57.991 33.333 23.95 19.49 39.18 2.74
4580 7253 8.731605 TCCAAACATAAGCGTCAAATATTTGTA 58.268 29.630 23.95 11.72 39.18 2.41
4581 7254 7.598278 TCCAAACATAAGCGTCAAATATTTGT 58.402 30.769 23.95 10.06 39.18 2.83
4582 7255 8.459521 TTCCAAACATAAGCGTCAAATATTTG 57.540 30.769 20.13 20.13 39.48 2.32
4583 7256 7.759433 CCTTCCAAACATAAGCGTCAAATATTT 59.241 33.333 0.00 0.00 0.00 1.40
4585 7258 6.377146 ACCTTCCAAACATAAGCGTCAAATAT 59.623 34.615 0.00 0.00 0.00 1.28
4604 7277 3.466836 CCCTTTCTTTTTGCAACCTTCC 58.533 45.455 0.00 0.00 0.00 3.46
4706 8217 6.401688 CGTTTGGTTTTCTTTGGTCTTTTTCC 60.402 38.462 0.00 0.00 0.00 3.13
4720 8231 7.691158 TCTAGTTTCTTCTTCGTTTGGTTTTC 58.309 34.615 0.00 0.00 0.00 2.29
4797 8651 2.581354 CCTCTGTCCTCGGCCTTG 59.419 66.667 0.00 0.00 0.00 3.61
4844 8698 3.367087 GCACACGAGTTGTACATAGAGGT 60.367 47.826 0.00 0.00 35.67 3.85
4868 8723 1.274447 GGTATACCCACCTCCGTATGC 59.726 57.143 11.17 0.00 35.55 3.14
4934 8789 6.366061 TGGATTCAAGAATATGCTTCGATACG 59.634 38.462 0.00 0.00 0.00 3.06
5016 8871 2.443255 AGTGAAGTCATTCAACACCCCT 59.557 45.455 0.00 0.00 46.75 4.79
5023 8878 6.808704 CGAGTAATCTGAGTGAAGTCATTCAA 59.191 38.462 7.76 1.20 46.75 2.69
5183 10016 3.944422 AGTAGCAAGTCAACAACAACG 57.056 42.857 0.00 0.00 0.00 4.10
5198 10031 3.283751 TCTCCTGTCTCTAGCAAGTAGC 58.716 50.000 0.00 0.00 46.19 3.58
5199 10032 4.523083 ACTCTCCTGTCTCTAGCAAGTAG 58.477 47.826 0.00 0.00 0.00 2.57
5200 10033 4.577988 ACTCTCCTGTCTCTAGCAAGTA 57.422 45.455 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.