Multiple sequence alignment - TraesCS5A01G446900

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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 TraesCS5A01G446900 chr5A 100.000 3367 0 0 1 3367 626289078 626285712 0.000000e+00 6218.0
1 TraesCS5A01G446900 chr5A 100.000 589 0 0 3562 4150 626285517 626284929 0.000000e+00 1088.0
2 TraesCS5A01G446900 chr5A 97.963 589 12 0 3562 4150 671169898 671170486 0.000000e+00 1022.0
3 TraesCS5A01G446900 chr5A 98.450 129 0 1 3241 3367 626280604 626280476 4.170000e-55 226.0
4 TraesCS5A01G446900 chr5A 98.425 127 1 1 3241 3367 282590564 282590439 5.400000e-54 222.0
5 TraesCS5A01G446900 chr5A 97.674 129 2 1 3239 3367 40477262 40477389 1.940000e-53 220.0
6 TraesCS5A01G446900 chr5D 91.759 2609 196 10 621 3226 500976778 500979370 0.000000e+00 3609.0
7 TraesCS5A01G446900 chr5B 90.993 2609 209 15 621 3221 622512462 622515052 0.000000e+00 3493.0
8 TraesCS5A01G446900 chr5B 76.592 628 99 30 3 599 106786616 106787226 6.740000e-78 302.0
9 TraesCS5A01G446900 chr5B 84.437 302 23 13 1 279 112540043 112539743 4.090000e-70 276.0
10 TraesCS5A01G446900 chr5B 82.877 292 39 9 219 506 267278584 267278868 6.890000e-63 252.0
11 TraesCS5A01G446900 chr5B 99.213 127 0 1 3241 3367 390710197 390710322 1.160000e-55 228.0
12 TraesCS5A01G446900 chr5B 82.422 256 35 9 257 506 267271787 267272038 9.040000e-52 215.0
13 TraesCS5A01G446900 chr7A 98.132 589 11 0 3562 4150 667933812 667934400 0.000000e+00 1027.0
14 TraesCS5A01G446900 chr7A 97.963 589 12 0 3562 4150 548361575 548362163 0.000000e+00 1022.0
15 TraesCS5A01G446900 chr7A 76.271 531 76 25 7 507 301699082 301698572 1.930000e-58 237.0
16 TraesCS5A01G446900 chr7A 95.588 136 3 3 3233 3367 548361403 548361536 9.040000e-52 215.0
17 TraesCS5A01G446900 chr3B 98.132 589 11 0 3562 4150 177080744 177081332 0.000000e+00 1027.0
18 TraesCS5A01G446900 chr3B 77.169 438 79 17 1 421 685101694 685101261 6.940000e-58 235.0
19 TraesCS5A01G446900 chr3B 85.542 166 21 3 258 421 685117252 685117088 1.980000e-38 171.0
20 TraesCS5A01G446900 chr6A 97.963 589 12 0 3562 4150 101569172 101568584 0.000000e+00 1022.0
21 TraesCS5A01G446900 chr6A 76.694 605 90 36 1 571 88603119 88603706 5.250000e-74 289.0
22 TraesCS5A01G446900 chr6A 77.467 537 70 25 1 507 606756750 606757265 1.470000e-69 274.0
23 TraesCS5A01G446900 chr6A 98.425 127 1 1 3241 3367 66387746 66387621 5.400000e-54 222.0
24 TraesCS5A01G446900 chr6A 98.425 127 1 1 3241 3367 495423837 495423712 5.400000e-54 222.0
25 TraesCS5A01G446900 chr4B 97.963 589 12 0 3562 4150 117052332 117051744 0.000000e+00 1022.0
26 TraesCS5A01G446900 chr4B 97.963 589 12 0 3562 4150 249082141 249082729 0.000000e+00 1022.0
27 TraesCS5A01G446900 chr4B 97.963 589 12 0 3562 4150 316661895 316661307 0.000000e+00 1022.0
28 TraesCS5A01G446900 chr1B 97.963 589 12 0 3562 4150 121026707 121027295 0.000000e+00 1022.0
29 TraesCS5A01G446900 chrUn 92.706 425 30 1 1021 1444 476596539 476596115 2.740000e-171 612.0
30 TraesCS5A01G446900 chrUn 84.615 65 7 3 202 265 82597011 82596949 1.250000e-05 62.1
31 TraesCS5A01G446900 chr7D 88.258 528 29 7 3 499 556185894 556185369 5.940000e-168 601.0
32 TraesCS5A01G446900 chr7D 90.935 353 29 3 258 608 556207995 556207644 4.860000e-129 472.0
33 TraesCS5A01G446900 chr7D 78.936 451 65 16 3 429 255014278 255013834 3.160000e-71 279.0
34 TraesCS5A01G446900 chr6B 80.000 590 74 34 1 558 67417306 67417883 3.010000e-106 396.0
35 TraesCS5A01G446900 chr6B 84.718 301 23 9 1 279 632852040 632851741 3.160000e-71 279.0
36 TraesCS5A01G446900 chr6B 77.406 478 61 29 1 449 346978801 346979260 1.490000e-59 241.0
37 TraesCS5A01G446900 chr6B 79.167 360 59 13 208 557 573335486 573335839 6.940000e-58 235.0
38 TraesCS5A01G446900 chr6B 84.507 71 8 3 196 265 513623665 513623733 2.680000e-07 67.6
39 TraesCS5A01G446900 chr7B 78.484 488 97 5 1675 2155 685072911 685072425 3.110000e-81 313.0
40 TraesCS5A01G446900 chr7B 87.273 165 19 2 259 421 557152602 557152766 1.970000e-43 187.0
41 TraesCS5A01G446900 chr7B 100.000 32 0 0 242 273 328787330 328787361 4.480000e-05 60.2
42 TraesCS5A01G446900 chr4A 77.593 540 80 28 2 507 501894930 501895462 5.250000e-74 289.0
43 TraesCS5A01G446900 chr4A 77.654 537 70 25 1 507 68146463 68145947 8.780000e-72 281.0
44 TraesCS5A01G446900 chr2A 87.037 270 12 11 26 273 492388299 492388567 2.440000e-72 283.0
45 TraesCS5A01G446900 chr2A 84.249 273 22 7 1 252 87666318 87666590 3.200000e-61 246.0
46 TraesCS5A01G446900 chr2A 98.425 127 1 1 3241 3367 98134462 98134587 5.400000e-54 222.0
47 TraesCS5A01G446900 chr2A 83.408 223 30 6 391 607 492388679 492388900 2.530000e-47 200.0
48 TraesCS5A01G446900 chr2A 83.036 224 31 6 391 608 492383584 492383806 3.270000e-46 196.0
49 TraesCS5A01G446900 chr2A 81.250 224 35 5 391 608 87661631 87661853 1.530000e-39 174.0
50 TraesCS5A01G446900 chr2B 93.373 166 11 0 1 166 438432736 438432901 3.200000e-61 246.0
51 TraesCS5A01G446900 chr3D 98.425 127 1 1 3241 3367 199108843 199108968 5.400000e-54 222.0
52 TraesCS5A01G446900 chr4D 94.444 36 2 0 238 273 157422834 157422799 5.800000e-04 56.5


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 TraesCS5A01G446900 chr5A 626284929 626289078 4149 True 3653.0 6218 100.0000 1 4150 2 chr5A.!!$R3 4149
1 TraesCS5A01G446900 chr5A 671169898 671170486 588 False 1022.0 1022 97.9630 3562 4150 1 chr5A.!!$F2 588
2 TraesCS5A01G446900 chr5D 500976778 500979370 2592 False 3609.0 3609 91.7590 621 3226 1 chr5D.!!$F1 2605
3 TraesCS5A01G446900 chr5B 622512462 622515052 2590 False 3493.0 3493 90.9930 621 3221 1 chr5B.!!$F5 2600
4 TraesCS5A01G446900 chr5B 106786616 106787226 610 False 302.0 302 76.5920 3 599 1 chr5B.!!$F1 596
5 TraesCS5A01G446900 chr7A 667933812 667934400 588 False 1027.0 1027 98.1320 3562 4150 1 chr7A.!!$F1 588
6 TraesCS5A01G446900 chr7A 548361403 548362163 760 False 618.5 1022 96.7755 3233 4150 2 chr7A.!!$F2 917
7 TraesCS5A01G446900 chr7A 301698572 301699082 510 True 237.0 237 76.2710 7 507 1 chr7A.!!$R1 500
8 TraesCS5A01G446900 chr3B 177080744 177081332 588 False 1027.0 1027 98.1320 3562 4150 1 chr3B.!!$F1 588
9 TraesCS5A01G446900 chr6A 101568584 101569172 588 True 1022.0 1022 97.9630 3562 4150 1 chr6A.!!$R2 588
10 TraesCS5A01G446900 chr6A 88603119 88603706 587 False 289.0 289 76.6940 1 571 1 chr6A.!!$F1 570
11 TraesCS5A01G446900 chr6A 606756750 606757265 515 False 274.0 274 77.4670 1 507 1 chr6A.!!$F2 506
12 TraesCS5A01G446900 chr4B 117051744 117052332 588 True 1022.0 1022 97.9630 3562 4150 1 chr4B.!!$R1 588
13 TraesCS5A01G446900 chr4B 249082141 249082729 588 False 1022.0 1022 97.9630 3562 4150 1 chr4B.!!$F1 588
14 TraesCS5A01G446900 chr4B 316661307 316661895 588 True 1022.0 1022 97.9630 3562 4150 1 chr4B.!!$R2 588
15 TraesCS5A01G446900 chr1B 121026707 121027295 588 False 1022.0 1022 97.9630 3562 4150 1 chr1B.!!$F1 588
16 TraesCS5A01G446900 chr7D 556185369 556185894 525 True 601.0 601 88.2580 3 499 1 chr7D.!!$R2 496
17 TraesCS5A01G446900 chr6B 67417306 67417883 577 False 396.0 396 80.0000 1 558 1 chr6B.!!$F1 557
18 TraesCS5A01G446900 chr4A 501894930 501895462 532 False 289.0 289 77.5930 2 507 1 chr4A.!!$F1 505
19 TraesCS5A01G446900 chr4A 68145947 68146463 516 True 281.0 281 77.6540 1 507 1 chr4A.!!$R1 506
20 TraesCS5A01G446900 chr2A 492388299 492388900 601 False 241.5 283 85.2225 26 607 2 chr2A.!!$F5 581

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
602 730 0.105658 TTCTATAGCAGAGGGGGCGT 60.106 55.0 0.00 0.00 33.83 5.68 F
1253 1385 0.035630 AGCCTTGATGTCCTGCAGAC 60.036 55.0 17.39 12.09 46.51 3.51 F
2324 2457 0.035056 ATGTGGAAGGAAGGGCGAAG 60.035 55.0 0.00 0.00 0.00 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1533 1666 0.387929 TCCAGTTTTCGACGCTCACT 59.612 50.0 0.0 0.0 0.0 3.41 R
2677 2810 0.392706 TGGACTGCAACTCGTGTCAT 59.607 50.0 4.2 0.0 0.0 3.06 R
3152 3285 1.072266 AGTACCTTCCAACCCATGCA 58.928 50.0 0.0 0.0 0.0 3.96 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
300 353 3.064134 TCACTCGAACTAGCTTGATCTCG 59.936 47.826 1.04 7.35 0.00 4.04
334 387 4.133013 AGTTTGTTGTCTCGGTTACAGT 57.867 40.909 0.00 0.00 0.00 3.55
341 395 3.921677 TGTCTCGGTTACAGTGGAATTC 58.078 45.455 0.00 0.00 0.00 2.17
359 451 6.382570 TGGAATTCGGATTACAAAATGGGAAT 59.617 34.615 0.00 0.00 33.12 3.01
360 452 7.561722 TGGAATTCGGATTACAAAATGGGAATA 59.438 33.333 0.00 0.00 33.12 1.75
365 459 5.530915 CGGATTACAAAATGGGAATAGCTGA 59.469 40.000 0.00 0.00 0.00 4.26
377 472 5.115480 GGGAATAGCTGAAGAGAAGAACTG 58.885 45.833 0.00 0.00 0.00 3.16
384 479 4.826556 CTGAAGAGAAGAACTGGGGTAAG 58.173 47.826 0.00 0.00 0.00 2.34
412 532 1.883021 CCGTTTGCCTTGATCCACC 59.117 57.895 0.00 0.00 0.00 4.61
514 642 4.280019 GGGTTGGGCCGTCTGGTT 62.280 66.667 0.00 0.00 38.44 3.67
525 653 1.874345 CGTCTGGTTCGTGGTAGCCT 61.874 60.000 0.00 0.00 0.00 4.58
587 715 3.786809 CGCTTGTCGGTGTCTTCTA 57.213 52.632 0.00 0.00 33.78 2.10
589 717 3.416119 CGCTTGTCGGTGTCTTCTATA 57.584 47.619 0.00 0.00 33.78 1.31
602 730 0.105658 TTCTATAGCAGAGGGGGCGT 60.106 55.000 0.00 0.00 33.83 5.68
603 731 0.827925 TCTATAGCAGAGGGGGCGTG 60.828 60.000 0.00 0.00 36.08 5.34
604 732 0.827925 CTATAGCAGAGGGGGCGTGA 60.828 60.000 0.00 0.00 36.08 4.35
605 733 1.113517 TATAGCAGAGGGGGCGTGAC 61.114 60.000 0.00 0.00 36.08 3.67
606 734 3.771531 TATAGCAGAGGGGGCGTGACA 62.772 57.143 0.00 0.00 36.08 3.58
607 735 4.101448 GCAGAGGGGGCGTGACAT 62.101 66.667 0.00 0.00 0.00 3.06
608 736 2.731571 GCAGAGGGGGCGTGACATA 61.732 63.158 0.00 0.00 0.00 2.29
609 737 2.044806 GCAGAGGGGGCGTGACATAT 62.045 60.000 0.00 0.00 0.00 1.78
610 738 0.469917 CAGAGGGGGCGTGACATATT 59.530 55.000 0.00 0.00 0.00 1.28
611 739 0.469917 AGAGGGGGCGTGACATATTG 59.530 55.000 0.00 0.00 0.00 1.90
612 740 0.180406 GAGGGGGCGTGACATATTGT 59.820 55.000 0.00 0.00 0.00 2.71
613 741 0.623723 AGGGGGCGTGACATATTGTT 59.376 50.000 0.00 0.00 0.00 2.83
614 742 0.738389 GGGGGCGTGACATATTGTTG 59.262 55.000 0.00 0.00 0.00 3.33
615 743 1.680555 GGGGGCGTGACATATTGTTGA 60.681 52.381 0.00 0.00 0.00 3.18
616 744 2.297701 GGGGCGTGACATATTGTTGAT 58.702 47.619 0.00 0.00 0.00 2.57
617 745 2.290641 GGGGCGTGACATATTGTTGATC 59.709 50.000 0.00 0.00 0.00 2.92
618 746 2.290641 GGGCGTGACATATTGTTGATCC 59.709 50.000 0.00 0.00 0.00 3.36
619 747 2.032894 GGCGTGACATATTGTTGATCCG 60.033 50.000 0.00 0.00 0.00 4.18
640 768 3.265791 GTGCTTAGCAGTGATGTAAGCT 58.734 45.455 22.55 4.54 45.89 3.74
651 780 2.038952 TGATGTAAGCTCTGGCAGTTGT 59.961 45.455 15.27 1.35 41.70 3.32
654 783 0.764890 TAAGCTCTGGCAGTTGTGGT 59.235 50.000 15.27 6.44 41.70 4.16
658 787 2.121564 CTCTGGCAGTTGTGGTTGCG 62.122 60.000 15.27 0.00 41.17 4.85
661 790 3.595758 GCAGTTGTGGTTGCGGCT 61.596 61.111 0.00 0.00 0.00 5.52
663 792 3.595758 AGTTGTGGTTGCGGCTGC 61.596 61.111 11.65 11.65 43.20 5.25
664 793 3.595758 GTTGTGGTTGCGGCTGCT 61.596 61.111 20.27 0.00 43.34 4.24
665 794 3.286751 TTGTGGTTGCGGCTGCTC 61.287 61.111 20.27 11.66 43.34 4.26
666 795 3.772853 TTGTGGTTGCGGCTGCTCT 62.773 57.895 20.27 0.00 43.34 4.09
667 796 3.730761 GTGGTTGCGGCTGCTCTG 61.731 66.667 20.27 0.00 43.34 3.35
832 961 8.828644 TCATTGATGAAACACAGGAAATTTTTG 58.171 29.630 0.00 0.00 33.08 2.44
902 1034 1.092921 AGAAACGAACTTGGCACGCA 61.093 50.000 0.00 0.00 0.00 5.24
973 1105 4.706476 CAGTGGGAAAGATAATTGGCAGAA 59.294 41.667 0.00 0.00 0.00 3.02
976 1108 6.044682 GTGGGAAAGATAATTGGCAGAAATG 58.955 40.000 0.00 0.00 0.00 2.32
978 1110 6.097270 TGGGAAAGATAATTGGCAGAAATGAG 59.903 38.462 0.00 0.00 0.00 2.90
1011 1143 5.163581 GGACATAAGAACAATGCTTCATGCT 60.164 40.000 0.00 0.00 43.37 3.79
1089 1221 3.827625 TGCACAATATGTTTGTAACGCC 58.172 40.909 0.00 0.00 0.00 5.68
1129 1261 3.139077 GAGAAAGAGGAAAGGAAACGCA 58.861 45.455 0.00 0.00 0.00 5.24
1231 1363 7.283127 CAGCTTCAGGTAAAAAGGCTGAATATA 59.717 37.037 6.21 0.00 34.20 0.86
1245 1377 6.959671 GCTGAATATACTAGCCTTGATGTC 57.040 41.667 0.00 0.00 0.00 3.06
1246 1378 5.872070 GCTGAATATACTAGCCTTGATGTCC 59.128 44.000 0.00 0.00 0.00 4.02
1253 1385 0.035630 AGCCTTGATGTCCTGCAGAC 60.036 55.000 17.39 12.09 46.51 3.51
1269 1401 6.545666 TCCTGCAGACAAAACTAAAGAATGAA 59.454 34.615 17.39 0.00 0.00 2.57
1277 1409 9.665264 GACAAAACTAAAGAATGAACTAAGTGG 57.335 33.333 0.00 0.00 0.00 4.00
1319 1452 5.711506 ACTTGATGATATCTGGTGCAACAAA 59.288 36.000 5.64 0.00 39.98 2.83
1323 1456 6.261603 TGATGATATCTGGTGCAACAAAGATC 59.738 38.462 5.64 5.69 39.91 2.75
1326 1459 0.890683 CTGGTGCAACAAAGATCCCC 59.109 55.000 5.64 0.00 39.98 4.81
1331 1464 2.165030 GTGCAACAAAGATCCCCATGAG 59.835 50.000 0.00 0.00 36.32 2.90
1334 1467 2.426024 CAACAAAGATCCCCATGAGCAG 59.574 50.000 0.00 0.00 0.00 4.24
1352 1485 3.127081 CAGAATCTGCAACGGTTGATG 57.873 47.619 24.20 14.61 0.00 3.07
1362 1495 2.723124 ACGGTTGATGTTTCCATTGC 57.277 45.000 0.00 0.00 0.00 3.56
1411 1544 5.046878 TCCTAGCCACAAGTCGAAATAAAGA 60.047 40.000 0.00 0.00 0.00 2.52
1421 1554 5.343249 AGTCGAAATAAAGATGCATTTGCC 58.657 37.500 0.00 0.00 41.18 4.52
1423 1556 4.095632 TCGAAATAAAGATGCATTTGCCGA 59.904 37.500 0.00 1.58 41.18 5.54
1435 1568 2.691409 TTTGCCGATCTAAGTCCTGG 57.309 50.000 0.00 0.00 0.00 4.45
1436 1569 0.178068 TTGCCGATCTAAGTCCTGGC 59.822 55.000 0.00 0.00 42.76 4.85
1437 1570 1.069935 GCCGATCTAAGTCCTGGCC 59.930 63.158 0.00 0.00 36.51 5.36
1447 1580 1.303561 GTCCTGGCCTGACATGCAA 60.304 57.895 17.78 0.00 32.91 4.08
1463 1596 5.018809 ACATGCAATTCTGTTCCAATACCT 58.981 37.500 0.00 0.00 0.00 3.08
1478 1611 6.903516 TCCAATACCTGACTTGAATGATGAT 58.096 36.000 0.00 0.00 0.00 2.45
1485 1618 6.114089 CCTGACTTGAATGATGATGACTTCT 58.886 40.000 0.00 0.00 0.00 2.85
1488 1621 9.978044 CTGACTTGAATGATGATGACTTCTATA 57.022 33.333 0.00 0.00 0.00 1.31
1522 1655 4.521639 GCATTATGCATTGGGAAGATCAGA 59.478 41.667 12.80 0.00 44.26 3.27
1523 1656 5.564259 GCATTATGCATTGGGAAGATCAGAC 60.564 44.000 12.80 0.00 44.26 3.51
1528 1661 2.231716 TTGGGAAGATCAGACCTCGA 57.768 50.000 0.00 0.00 0.00 4.04
1533 1666 2.690497 GGAAGATCAGACCTCGATGACA 59.310 50.000 0.00 0.00 0.00 3.58
1534 1667 3.243367 GGAAGATCAGACCTCGATGACAG 60.243 52.174 0.00 0.00 0.00 3.51
1536 1669 2.687425 AGATCAGACCTCGATGACAGTG 59.313 50.000 0.00 0.00 0.00 3.66
1537 1670 2.200373 TCAGACCTCGATGACAGTGA 57.800 50.000 0.00 0.00 0.00 3.41
1540 1673 0.524392 GACCTCGATGACAGTGAGCG 60.524 60.000 0.00 0.00 0.00 5.03
1542 1675 0.524392 CCTCGATGACAGTGAGCGTC 60.524 60.000 0.00 0.00 0.00 5.19
1545 1678 0.454452 CGATGACAGTGAGCGTCGAA 60.454 55.000 20.04 0.00 44.03 3.71
1556 1689 2.288825 TGAGCGTCGAAAACTGGAAGAT 60.289 45.455 0.00 0.00 37.43 2.40
1604 1737 1.816679 GGGGTTACCTTTAGCGGCG 60.817 63.158 0.51 0.51 36.80 6.46
1627 1760 1.982395 CCGTGGGAGGACAGCTACA 60.982 63.158 0.00 0.00 0.00 2.74
1633 1766 3.068873 GTGGGAGGACAGCTACATAGAAG 59.931 52.174 0.00 0.00 0.00 2.85
1635 1768 3.961408 GGGAGGACAGCTACATAGAAGAA 59.039 47.826 0.00 0.00 0.00 2.52
1644 1777 9.587772 GACAGCTACATAGAAGAAAAGATGTTA 57.412 33.333 0.00 0.00 34.08 2.41
1661 1794 2.897969 TGTTAGGTTCTGGAGGAGTGTC 59.102 50.000 0.00 0.00 0.00 3.67
1662 1795 2.897969 GTTAGGTTCTGGAGGAGTGTCA 59.102 50.000 0.00 0.00 0.00 3.58
1692 1825 3.304928 GGACCTTTTGAACGAGACGACTA 60.305 47.826 0.00 0.00 0.00 2.59
1708 1841 2.428890 CGACTAGAGCTCTTTGGTGGAT 59.571 50.000 23.84 0.00 0.00 3.41
1805 1938 3.921677 ACGTGATGGGTTAGTACAGTTG 58.078 45.455 0.00 0.00 0.00 3.16
1815 1948 2.185004 AGTACAGTTGTGGATGGCAC 57.815 50.000 0.00 0.00 0.00 5.01
1845 1978 7.515841 CGTTTATAGAGACAACTAATGCTGCAG 60.516 40.741 10.11 10.11 0.00 4.41
2142 2275 2.286831 CGCACTCTCATCATTGATTGCC 60.287 50.000 12.39 0.00 32.41 4.52
2220 2353 0.388520 GAAATTGCGGGTGCTGGTTC 60.389 55.000 0.00 0.00 43.34 3.62
2222 2355 1.526575 AATTGCGGGTGCTGGTTCTG 61.527 55.000 0.00 0.00 43.34 3.02
2243 2376 0.659957 GTTTCTCCGCAGATGATGGC 59.340 55.000 0.00 0.00 0.00 4.40
2299 2432 9.733556 TCTGTTAAAGCATCTAAGGTATTTTGA 57.266 29.630 0.00 0.00 0.00 2.69
2300 2433 9.774742 CTGTTAAAGCATCTAAGGTATTTTGAC 57.225 33.333 0.00 0.00 0.00 3.18
2315 2448 7.947890 AGGTATTTTGACTTTAATGTGGAAGGA 59.052 33.333 0.00 0.00 0.00 3.36
2318 2451 6.648879 TTTGACTTTAATGTGGAAGGAAGG 57.351 37.500 0.00 0.00 0.00 3.46
2321 2454 2.122783 TTAATGTGGAAGGAAGGGCG 57.877 50.000 0.00 0.00 0.00 6.13
2323 2456 0.404040 AATGTGGAAGGAAGGGCGAA 59.596 50.000 0.00 0.00 0.00 4.70
2324 2457 0.035056 ATGTGGAAGGAAGGGCGAAG 60.035 55.000 0.00 0.00 0.00 3.79
2363 2496 6.598064 ACAGTATTACCAAGCTTTACCACATC 59.402 38.462 0.00 0.00 0.00 3.06
2375 2508 1.885049 ACCACATCCAGGTGCTAGAT 58.115 50.000 0.00 0.00 38.13 1.98
2547 2680 0.100146 GGGGTACGAGCTACGACAAG 59.900 60.000 11.64 0.00 45.77 3.16
2560 2693 4.560108 GCTACGACAAGTGAAGGACCTAAA 60.560 45.833 0.00 0.00 0.00 1.85
2574 2707 2.884639 GACCTAAACAAGCTTGAAGGCA 59.115 45.455 32.50 11.33 32.95 4.75
2656 2789 1.597854 CACACAAGGAGCGGCTGAA 60.598 57.895 7.50 0.00 0.00 3.02
2658 2791 0.465460 ACACAAGGAGCGGCTGAAAA 60.465 50.000 7.50 0.00 0.00 2.29
2677 2810 3.806949 AAAACTTGCACTATCCTGGGA 57.193 42.857 0.00 0.00 0.00 4.37
2681 2814 2.171448 ACTTGCACTATCCTGGGATGAC 59.829 50.000 11.98 0.50 36.17 3.06
2753 2886 5.046529 CCACCGAAATATCTTGAGAGACTG 58.953 45.833 0.00 0.00 33.99 3.51
2776 2909 3.100207 AGTTGGGGATTACCATGGTTG 57.900 47.619 25.38 0.00 40.91 3.77
2779 2912 1.286553 TGGGGATTACCATGGTTGGAC 59.713 52.381 25.38 11.51 46.92 4.02
2844 2977 2.892373 TTTGCGTAATCTTTGGCTCG 57.108 45.000 0.00 0.00 0.00 5.03
2866 2999 2.856032 CTGCAGCCGACTTGAACG 59.144 61.111 0.00 0.00 0.00 3.95
2916 3049 3.670627 GCATCTTCGTTGGTTTAGGCTTG 60.671 47.826 0.00 0.00 0.00 4.01
2917 3050 2.500229 TCTTCGTTGGTTTAGGCTTGG 58.500 47.619 0.00 0.00 0.00 3.61
3008 3141 1.535462 CGTTGCCCGAATATCCAATCC 59.465 52.381 0.00 0.00 39.56 3.01
3015 3148 3.181434 CCCGAATATCCAATCCCTTCCAA 60.181 47.826 0.00 0.00 0.00 3.53
3037 3170 0.911525 CTGCCCTCCTCCCTTGAGAA 60.912 60.000 0.00 0.00 41.42 2.87
3043 3176 3.416156 CCTCCTCCCTTGAGAAGTTTTG 58.584 50.000 0.00 0.00 41.42 2.44
3054 3187 0.234884 GAAGTTTTGTCTCACGGCCG 59.765 55.000 26.86 26.86 0.00 6.13
3058 3191 3.758973 TTTGTCTCACGGCCGGCAA 62.759 57.895 31.76 21.12 0.00 4.52
3089 3222 4.201208 CATGAGGTCATGCGTAACAATC 57.799 45.455 7.02 0.00 45.92 2.67
3097 3230 2.665649 TGCGTAACAATCGGACATCT 57.334 45.000 0.00 0.00 0.00 2.90
3118 3251 4.826733 TCTAAACTGGCAAAAGATTCAGCA 59.173 37.500 0.00 0.00 0.00 4.41
3130 3263 4.422073 AGATTCAGCACATTCCCGATAA 57.578 40.909 0.00 0.00 0.00 1.75
3131 3264 4.780815 AGATTCAGCACATTCCCGATAAA 58.219 39.130 0.00 0.00 0.00 1.40
3132 3265 4.576463 AGATTCAGCACATTCCCGATAAAC 59.424 41.667 0.00 0.00 0.00 2.01
3133 3266 3.627395 TCAGCACATTCCCGATAAACT 57.373 42.857 0.00 0.00 0.00 2.66
3138 3271 6.601613 TCAGCACATTCCCGATAAACTTATTT 59.398 34.615 0.00 0.00 0.00 1.40
3140 3273 7.220683 CAGCACATTCCCGATAAACTTATTTTG 59.779 37.037 0.00 0.00 0.00 2.44
3142 3275 6.475402 CACATTCCCGATAAACTTATTTTGCC 59.525 38.462 0.00 0.00 0.00 4.52
3144 3277 6.844097 TTCCCGATAAACTTATTTTGCCTT 57.156 33.333 0.00 0.00 0.00 4.35
3145 3278 6.844097 TCCCGATAAACTTATTTTGCCTTT 57.156 33.333 0.00 0.00 0.00 3.11
3172 3305 2.270858 TGCATGGGTTGGAAGGTACTA 58.729 47.619 0.00 0.00 38.49 1.82
3174 3307 2.026636 GCATGGGTTGGAAGGTACTACA 60.027 50.000 0.00 0.00 38.49 2.74
3175 3308 3.371595 GCATGGGTTGGAAGGTACTACAT 60.372 47.826 0.00 0.00 38.49 2.29
3177 3310 3.798515 TGGGTTGGAAGGTACTACATCT 58.201 45.455 0.00 0.00 38.49 2.90
3178 3311 3.517901 TGGGTTGGAAGGTACTACATCTG 59.482 47.826 0.00 0.00 38.49 2.90
3179 3312 3.532542 GGTTGGAAGGTACTACATCTGC 58.467 50.000 0.00 0.00 38.49 4.26
3180 3313 3.055385 GGTTGGAAGGTACTACATCTGCA 60.055 47.826 0.00 0.00 38.49 4.41
3183 3316 5.435686 TGGAAGGTACTACATCTGCAAAT 57.564 39.130 0.00 0.00 38.49 2.32
3198 3331 5.358922 TCTGCAAATTCCTTTGTTCCTTTG 58.641 37.500 0.00 0.00 43.07 2.77
3206 3340 4.134563 TCCTTTGTTCCTTTGTGTAGCTC 58.865 43.478 0.00 0.00 0.00 4.09
3212 3346 5.479306 TGTTCCTTTGTGTAGCTCTATGAC 58.521 41.667 0.00 0.00 0.00 3.06
3214 3348 5.073311 TCCTTTGTGTAGCTCTATGACAC 57.927 43.478 9.34 9.34 43.06 3.67
3228 3362 9.539825 AGCTCTATGACACATGTTAATTAAGAG 57.460 33.333 0.00 6.10 0.00 2.85
3229 3363 9.319143 GCTCTATGACACATGTTAATTAAGAGT 57.681 33.333 16.29 2.23 0.00 3.24
3231 3365 9.516314 TCTATGACACATGTTAATTAAGAGTCG 57.484 33.333 0.00 0.00 0.00 4.18
3232 3366 6.961359 TGACACATGTTAATTAAGAGTCGG 57.039 37.500 0.00 0.00 0.00 4.79
3233 3367 6.460781 TGACACATGTTAATTAAGAGTCGGT 58.539 36.000 0.00 0.00 0.00 4.69
3234 3368 7.604549 TGACACATGTTAATTAAGAGTCGGTA 58.395 34.615 0.00 0.00 0.00 4.02
3235 3369 8.255206 TGACACATGTTAATTAAGAGTCGGTAT 58.745 33.333 0.00 0.00 0.00 2.73
3236 3370 8.420374 ACACATGTTAATTAAGAGTCGGTATG 57.580 34.615 0.00 0.00 0.00 2.39
3237 3371 8.255206 ACACATGTTAATTAAGAGTCGGTATGA 58.745 33.333 0.00 0.00 0.00 2.15
3238 3372 9.261180 CACATGTTAATTAAGAGTCGGTATGAT 57.739 33.333 0.00 0.00 0.00 2.45
3251 3385 8.361139 AGAGTCGGTATGATTTGTTAGGAATAG 58.639 37.037 0.00 0.00 0.00 1.73
3330 3464 3.473113 ACATATGCAGGAAAACCCCTT 57.527 42.857 1.58 0.00 33.38 3.95
3603 3738 3.445096 AGAGATAAAAGCCATGTTGTGCC 59.555 43.478 0.00 0.00 0.00 5.01
3682 3817 1.869767 GAGCAATAACCTGATCCTGCG 59.130 52.381 0.00 0.00 35.00 5.18
3943 4078 1.918262 TCCAGGCAATGAGAGAACCAT 59.082 47.619 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 2.656651 CGATCTGGAGAAGCGCGG 60.657 66.667 8.83 0.00 0.00 6.46
300 353 4.351192 ACAACAAACTTGAATTCGTGAGC 58.649 39.130 0.04 0.00 0.00 4.26
317 370 2.033372 TCCACTGTAACCGAGACAACA 58.967 47.619 0.00 0.00 0.00 3.33
334 387 5.265191 TCCCATTTTGTAATCCGAATTCCA 58.735 37.500 0.00 0.00 0.00 3.53
341 395 5.530915 TCAGCTATTCCCATTTTGTAATCCG 59.469 40.000 0.00 0.00 0.00 4.18
359 451 2.834549 CCCCAGTTCTTCTCTTCAGCTA 59.165 50.000 0.00 0.00 0.00 3.32
360 452 1.627834 CCCCAGTTCTTCTCTTCAGCT 59.372 52.381 0.00 0.00 0.00 4.24
365 459 3.008485 CAGCTTACCCCAGTTCTTCTCTT 59.992 47.826 0.00 0.00 0.00 2.85
412 532 1.068753 CTGACTGGCTAGGCATCCG 59.931 63.158 20.56 10.92 42.26 4.18
454 580 0.032813 CCCAATGAAGCCCAGGTGAT 60.033 55.000 0.00 0.00 0.00 3.06
457 585 1.384191 GACCCAATGAAGCCCAGGT 59.616 57.895 0.00 0.00 0.00 4.00
508 636 1.053424 AAAGGCTACCACGAACCAGA 58.947 50.000 0.00 0.00 0.00 3.86
510 638 0.250553 CCAAAGGCTACCACGAACCA 60.251 55.000 0.00 0.00 0.00 3.67
587 715 2.041922 TCACGCCCCCTCTGCTAT 60.042 61.111 0.00 0.00 0.00 2.97
602 730 3.872696 AGCACGGATCAACAATATGTCA 58.127 40.909 0.00 0.00 0.00 3.58
603 731 4.882671 AAGCACGGATCAACAATATGTC 57.117 40.909 0.00 0.00 0.00 3.06
604 732 4.273480 GCTAAGCACGGATCAACAATATGT 59.727 41.667 0.00 0.00 0.00 2.29
605 733 4.273235 TGCTAAGCACGGATCAACAATATG 59.727 41.667 0.00 0.00 31.71 1.78
606 734 4.450976 TGCTAAGCACGGATCAACAATAT 58.549 39.130 0.00 0.00 31.71 1.28
607 735 3.867857 TGCTAAGCACGGATCAACAATA 58.132 40.909 0.00 0.00 31.71 1.90
608 736 2.679837 CTGCTAAGCACGGATCAACAAT 59.320 45.455 0.00 0.00 33.79 2.71
609 737 2.076100 CTGCTAAGCACGGATCAACAA 58.924 47.619 0.00 0.00 33.79 2.83
610 738 1.001974 ACTGCTAAGCACGGATCAACA 59.998 47.619 0.00 0.00 33.79 3.33
611 739 1.394917 CACTGCTAAGCACGGATCAAC 59.605 52.381 0.00 0.00 33.79 3.18
612 740 1.275010 TCACTGCTAAGCACGGATCAA 59.725 47.619 0.00 0.00 33.79 2.57
613 741 0.894835 TCACTGCTAAGCACGGATCA 59.105 50.000 0.00 0.00 33.79 2.92
614 742 1.863454 CATCACTGCTAAGCACGGATC 59.137 52.381 0.00 0.00 33.79 3.36
615 743 1.208052 ACATCACTGCTAAGCACGGAT 59.792 47.619 0.00 0.00 33.79 4.18
616 744 0.608130 ACATCACTGCTAAGCACGGA 59.392 50.000 0.00 0.00 33.79 4.69
617 745 2.293677 TACATCACTGCTAAGCACGG 57.706 50.000 0.00 0.00 33.79 4.94
618 746 2.029728 GCTTACATCACTGCTAAGCACG 59.970 50.000 6.72 0.00 39.34 5.34
619 747 3.265791 AGCTTACATCACTGCTAAGCAC 58.734 45.455 12.45 0.00 40.53 4.40
640 768 2.186160 CGCAACCACAACTGCCAGA 61.186 57.895 0.00 0.00 35.01 3.86
661 790 2.089887 TTAACGGGTGTCGCAGAGCA 62.090 55.000 0.00 0.00 43.89 4.26
663 792 1.068474 CTTTAACGGGTGTCGCAGAG 58.932 55.000 0.00 0.00 43.89 3.35
664 793 0.390124 ACTTTAACGGGTGTCGCAGA 59.610 50.000 0.00 0.00 43.89 4.26
665 794 1.070175 CAACTTTAACGGGTGTCGCAG 60.070 52.381 0.00 0.00 43.89 5.18
666 795 0.938713 CAACTTTAACGGGTGTCGCA 59.061 50.000 0.00 0.00 43.89 5.10
667 796 0.385098 GCAACTTTAACGGGTGTCGC 60.385 55.000 0.00 0.00 43.89 5.19
668 797 1.223187 AGCAACTTTAACGGGTGTCG 58.777 50.000 0.00 0.00 45.88 4.35
669 798 5.063060 CAGTATAGCAACTTTAACGGGTGTC 59.937 44.000 0.00 0.00 0.00 3.67
796 925 9.390795 CTGTGTTTCATCAATGAGTTTTTCTAG 57.609 33.333 0.00 0.00 38.19 2.43
902 1034 6.129874 TCTCCAGTAGTAACATCTGCAGTAT 58.870 40.000 14.67 3.15 0.00 2.12
965 1097 4.219070 CCTGACAAATCTCATTTCTGCCAA 59.781 41.667 0.00 0.00 0.00 4.52
973 1105 7.884877 TGTTCTTATGTCCTGACAAATCTCATT 59.115 33.333 3.79 0.00 45.41 2.57
976 1108 7.672983 TTGTTCTTATGTCCTGACAAATCTC 57.327 36.000 3.79 0.00 45.41 2.75
978 1110 6.749118 GCATTGTTCTTATGTCCTGACAAATC 59.251 38.462 3.79 0.00 45.41 2.17
1011 1143 6.839124 ATGCCAACTACATCAGATTTTGAA 57.161 33.333 0.00 0.00 39.77 2.69
1089 1221 4.029520 TCTCTCCCTCTTCCTCTTTCATG 58.970 47.826 0.00 0.00 0.00 3.07
1231 1363 1.209019 CTGCAGGACATCAAGGCTAGT 59.791 52.381 5.57 0.00 0.00 2.57
1245 1377 6.317789 TCATTCTTTAGTTTTGTCTGCAGG 57.682 37.500 15.13 0.00 0.00 4.85
1246 1378 7.420800 AGTTCATTCTTTAGTTTTGTCTGCAG 58.579 34.615 7.63 7.63 0.00 4.41
1292 1425 5.876651 TGCACCAGATATCATCAAGTACT 57.123 39.130 5.32 0.00 0.00 2.73
1305 1438 2.450476 GGGATCTTTGTTGCACCAGAT 58.550 47.619 0.00 0.00 0.00 2.90
1319 1452 2.372504 CAGATTCTGCTCATGGGGATCT 59.627 50.000 0.00 0.00 0.00 2.75
1334 1467 3.559238 AACATCAACCGTTGCAGATTC 57.441 42.857 6.37 0.00 0.00 2.52
1352 1485 3.252944 CCAACCCAAATTGCAATGGAAAC 59.747 43.478 18.76 0.00 39.12 2.78
1362 1495 2.368221 TGCTTCCTTCCAACCCAAATTG 59.632 45.455 0.00 0.00 0.00 2.32
1411 1544 2.880890 GGACTTAGATCGGCAAATGCAT 59.119 45.455 7.80 0.00 44.36 3.96
1421 1554 1.067821 GTCAGGCCAGGACTTAGATCG 59.932 57.143 17.60 0.00 32.54 3.69
1423 1556 2.254152 TGTCAGGCCAGGACTTAGAT 57.746 50.000 23.12 0.00 36.26 1.98
1435 1568 2.416431 GGAACAGAATTGCATGTCAGGC 60.416 50.000 1.65 1.65 0.00 4.85
1436 1569 2.821378 TGGAACAGAATTGCATGTCAGG 59.179 45.455 0.00 0.00 0.00 3.86
1437 1570 4.508461 TTGGAACAGAATTGCATGTCAG 57.492 40.909 0.00 0.00 42.39 3.51
1447 1580 6.126863 TCAAGTCAGGTATTGGAACAGAAT 57.873 37.500 0.00 0.00 42.39 2.40
1500 1633 5.048224 GGTCTGATCTTCCCAATGCATAATG 60.048 44.000 0.00 0.00 0.00 1.90
1509 1642 2.231716 TCGAGGTCTGATCTTCCCAA 57.768 50.000 0.00 0.00 0.00 4.12
1511 1644 2.035321 GTCATCGAGGTCTGATCTTCCC 59.965 54.545 0.00 0.00 0.00 3.97
1517 1650 2.687425 CTCACTGTCATCGAGGTCTGAT 59.313 50.000 8.02 0.00 0.00 2.90
1522 1655 1.244697 ACGCTCACTGTCATCGAGGT 61.245 55.000 0.00 0.00 0.00 3.85
1523 1656 0.524392 GACGCTCACTGTCATCGAGG 60.524 60.000 0.00 0.00 36.37 4.63
1528 1661 1.792949 GTTTTCGACGCTCACTGTCAT 59.207 47.619 0.00 0.00 36.11 3.06
1533 1666 0.387929 TCCAGTTTTCGACGCTCACT 59.612 50.000 0.00 0.00 0.00 3.41
1534 1667 1.192534 CTTCCAGTTTTCGACGCTCAC 59.807 52.381 0.00 0.00 0.00 3.51
1536 1669 1.779569 TCTTCCAGTTTTCGACGCTC 58.220 50.000 0.00 0.00 0.00 5.03
1537 1670 2.457366 ATCTTCCAGTTTTCGACGCT 57.543 45.000 0.00 0.00 0.00 5.07
1540 1673 4.335594 CCCCAATATCTTCCAGTTTTCGAC 59.664 45.833 0.00 0.00 0.00 4.20
1542 1675 3.066760 GCCCCAATATCTTCCAGTTTTCG 59.933 47.826 0.00 0.00 0.00 3.46
1545 1678 3.269381 TCAGCCCCAATATCTTCCAGTTT 59.731 43.478 0.00 0.00 0.00 2.66
1587 1720 0.808847 CTCGCCGCTAAAGGTAACCC 60.809 60.000 0.00 0.00 37.17 4.11
1604 1737 1.592223 CTGTCCTCCCACGGTTCTC 59.408 63.158 0.00 0.00 0.00 2.87
1627 1760 8.826765 TCCAGAACCTAACATCTTTTCTTCTAT 58.173 33.333 0.00 0.00 0.00 1.98
1633 1766 5.805728 TCCTCCAGAACCTAACATCTTTTC 58.194 41.667 0.00 0.00 0.00 2.29
1635 1768 4.846940 ACTCCTCCAGAACCTAACATCTTT 59.153 41.667 0.00 0.00 0.00 2.52
1644 1777 2.103153 TTGACACTCCTCCAGAACCT 57.897 50.000 0.00 0.00 0.00 3.50
1661 1794 4.577283 TCGTTCAAAAGGTCCCTAACTTTG 59.423 41.667 3.57 3.57 37.04 2.77
1662 1795 4.784177 TCGTTCAAAAGGTCCCTAACTTT 58.216 39.130 0.00 0.00 38.48 2.66
1692 1825 2.769095 GGTAGATCCACCAAAGAGCTCT 59.231 50.000 11.45 11.45 38.55 4.09
1708 1841 3.954200 TGCTCATCAAATTGCTGGTAGA 58.046 40.909 0.00 0.00 0.00 2.59
1768 1901 6.151691 CCATCACGTTTGAAATGATGTCTTT 58.848 36.000 16.10 0.00 45.45 2.52
1792 1925 3.007635 GCCATCCACAACTGTACTAACC 58.992 50.000 0.00 0.00 0.00 2.85
1805 1938 0.878416 TAAACGCTTGTGCCATCCAC 59.122 50.000 0.00 0.00 44.90 4.02
1815 1948 7.010552 AGCATTAGTTGTCTCTATAAACGCTTG 59.989 37.037 0.00 0.00 0.00 4.01
1845 1978 5.069648 TCTGACCAACATCATACAGATCCTC 59.930 44.000 0.00 0.00 33.72 3.71
1894 2027 6.382282 TCTCTCTCCTAATTGCAGAAATGAGA 59.618 38.462 7.00 7.00 28.75 3.27
2177 2310 3.903714 TCAACCTCCTGAACATTCTCTCA 59.096 43.478 0.00 0.00 0.00 3.27
2243 2376 6.757237 ACATGCTGGAAGTGAGAAGATATAG 58.243 40.000 0.00 0.00 35.30 1.31
2299 2432 3.431415 GCCCTTCCTTCCACATTAAAGT 58.569 45.455 0.00 0.00 0.00 2.66
2300 2433 2.423538 CGCCCTTCCTTCCACATTAAAG 59.576 50.000 0.00 0.00 0.00 1.85
2303 2436 1.281419 TCGCCCTTCCTTCCACATTA 58.719 50.000 0.00 0.00 0.00 1.90
2310 2443 1.943340 CATTAGCTTCGCCCTTCCTTC 59.057 52.381 0.00 0.00 0.00 3.46
2311 2444 2.019156 GCATTAGCTTCGCCCTTCCTT 61.019 52.381 0.00 0.00 37.91 3.36
2324 2457 6.540914 TGGTAATACTGTTTGGTAGCATTAGC 59.459 38.462 0.00 0.20 42.56 3.09
2325 2458 8.500753 TTGGTAATACTGTTTGGTAGCATTAG 57.499 34.615 0.00 0.00 0.00 1.73
2330 2463 4.941873 AGCTTGGTAATACTGTTTGGTAGC 59.058 41.667 0.00 0.00 0.00 3.58
2331 2464 7.448748 AAAGCTTGGTAATACTGTTTGGTAG 57.551 36.000 0.00 0.00 0.00 3.18
2333 2466 6.208007 GGTAAAGCTTGGTAATACTGTTTGGT 59.792 38.462 0.00 0.00 0.00 3.67
2343 2476 4.929479 TGGATGTGGTAAAGCTTGGTAAT 58.071 39.130 0.00 0.00 0.00 1.89
2363 2496 7.197017 CGCTACTATAATTATCTAGCACCTGG 58.803 42.308 22.82 0.00 31.84 4.45
2375 2508 4.650588 ACCACACCACCGCTACTATAATTA 59.349 41.667 0.00 0.00 0.00 1.40
2499 2632 8.459635 TGTCTTGCTTATACTGAAGTGTACTAG 58.540 37.037 0.00 0.00 0.00 2.57
2506 2639 5.482908 CCTGTGTCTTGCTTATACTGAAGT 58.517 41.667 0.00 0.00 0.00 3.01
2547 2680 4.134563 TCAAGCTTGTTTAGGTCCTTCAC 58.865 43.478 25.19 0.00 32.17 3.18
2560 2693 3.034030 GCGTGCCTTCAAGCTTGT 58.966 55.556 25.19 0.00 43.01 3.16
2574 2707 1.760192 AGACCCGTGATACTTAGCGT 58.240 50.000 0.00 0.00 0.00 5.07
2656 2789 4.112634 TCCCAGGATAGTGCAAGTTTTT 57.887 40.909 0.00 0.00 0.00 1.94
2658 2791 3.266772 TCATCCCAGGATAGTGCAAGTTT 59.733 43.478 0.00 0.00 32.93 2.66
2664 2797 1.539065 CGTGTCATCCCAGGATAGTGC 60.539 57.143 0.00 0.00 32.93 4.40
2677 2810 0.392706 TGGACTGCAACTCGTGTCAT 59.607 50.000 4.20 0.00 0.00 3.06
2681 2814 1.143305 CTTCTGGACTGCAACTCGTG 58.857 55.000 0.00 0.00 0.00 4.35
2753 2886 2.024369 ACCATGGTAATCCCCAACTTCC 60.024 50.000 18.10 0.00 38.20 3.46
2776 2909 1.202651 CCATCCAATCTGGGTACGTCC 60.203 57.143 0.00 0.00 38.32 4.79
2777 2910 1.485066 ACCATCCAATCTGGGTACGTC 59.515 52.381 0.00 0.00 38.32 4.34
2779 2912 1.475034 CCACCATCCAATCTGGGTACG 60.475 57.143 0.00 0.00 38.32 3.67
2891 3024 2.161609 CCTAAACCAACGAAGATGCACC 59.838 50.000 0.00 0.00 0.00 5.01
2916 3049 1.080569 CGTGCCAATTGCTGAACCC 60.081 57.895 0.00 0.00 42.00 4.11
2917 3050 1.734117 GCGTGCCAATTGCTGAACC 60.734 57.895 0.00 0.00 42.00 3.62
2933 3066 1.086696 CCATATTATCGGGCAAGGCG 58.913 55.000 0.00 0.00 0.00 5.52
2934 3067 2.359900 CTCCATATTATCGGGCAAGGC 58.640 52.381 0.00 0.00 0.00 4.35
2942 3075 1.645034 CCAGCCGCTCCATATTATCG 58.355 55.000 0.00 0.00 0.00 2.92
3002 3135 0.890683 GCAGTGTTGGAAGGGATTGG 59.109 55.000 0.00 0.00 0.00 3.16
3008 3141 1.303643 GGAGGGCAGTGTTGGAAGG 60.304 63.158 0.00 0.00 0.00 3.46
3015 3148 2.208349 AAGGGAGGAGGGCAGTGT 59.792 61.111 0.00 0.00 0.00 3.55
3037 3170 1.597027 CCGGCCGTGAGACAAAACT 60.597 57.895 26.12 0.00 0.00 2.66
3051 3184 3.119096 GAACTCCTCGTTGCCGGC 61.119 66.667 22.73 22.73 35.56 6.13
3054 3187 1.363744 CTCATGAACTCCTCGTTGCC 58.636 55.000 0.00 0.00 35.56 4.52
3058 3191 1.924731 TGACCTCATGAACTCCTCGT 58.075 50.000 0.00 0.00 0.00 4.18
3082 3215 4.873827 GCCAGTTTAGATGTCCGATTGTTA 59.126 41.667 0.00 0.00 0.00 2.41
3089 3222 3.751175 TCTTTTGCCAGTTTAGATGTCCG 59.249 43.478 0.00 0.00 0.00 4.79
3097 3230 4.340666 TGTGCTGAATCTTTTGCCAGTTTA 59.659 37.500 0.00 0.00 0.00 2.01
3118 3251 6.379988 AGGCAAAATAAGTTTATCGGGAATGT 59.620 34.615 0.00 0.00 0.00 2.71
3130 3263 8.443953 TGCATGTTAAAAAGGCAAAATAAGTT 57.556 26.923 0.00 0.00 0.00 2.66
3131 3264 8.505625 CATGCATGTTAAAAAGGCAAAATAAGT 58.494 29.630 18.91 0.00 38.08 2.24
3132 3265 7.964011 CCATGCATGTTAAAAAGGCAAAATAAG 59.036 33.333 24.58 0.00 38.08 1.73
3133 3266 7.094463 CCCATGCATGTTAAAAAGGCAAAATAA 60.094 33.333 24.58 0.00 38.08 1.40
3138 3271 3.072184 ACCCATGCATGTTAAAAAGGCAA 59.928 39.130 24.58 0.00 38.08 4.52
3140 3273 3.333029 ACCCATGCATGTTAAAAAGGC 57.667 42.857 24.58 0.00 0.00 4.35
3142 3275 4.892433 TCCAACCCATGCATGTTAAAAAG 58.108 39.130 24.58 7.82 0.00 2.27
3144 3277 4.262808 CCTTCCAACCCATGCATGTTAAAA 60.263 41.667 24.58 10.27 0.00 1.52
3145 3278 3.260380 CCTTCCAACCCATGCATGTTAAA 59.740 43.478 24.58 10.28 0.00 1.52
3150 3283 1.750778 GTACCTTCCAACCCATGCATG 59.249 52.381 20.19 20.19 0.00 4.06
3151 3284 1.640670 AGTACCTTCCAACCCATGCAT 59.359 47.619 0.00 0.00 0.00 3.96
3152 3285 1.072266 AGTACCTTCCAACCCATGCA 58.928 50.000 0.00 0.00 0.00 3.96
3153 3286 2.026636 TGTAGTACCTTCCAACCCATGC 60.027 50.000 0.00 0.00 0.00 4.06
3154 3287 3.992943 TGTAGTACCTTCCAACCCATG 57.007 47.619 0.00 0.00 0.00 3.66
3171 3304 5.774690 AGGAACAAAGGAATTTGCAGATGTA 59.225 36.000 0.79 0.00 35.42 2.29
3172 3305 4.590222 AGGAACAAAGGAATTTGCAGATGT 59.410 37.500 0.79 0.00 35.42 3.06
3174 3307 5.813513 AAGGAACAAAGGAATTTGCAGAT 57.186 34.783 0.79 0.00 35.42 2.90
3175 3308 5.104982 ACAAAGGAACAAAGGAATTTGCAGA 60.105 36.000 0.79 0.00 35.42 4.26
3177 3310 4.874966 CACAAAGGAACAAAGGAATTTGCA 59.125 37.500 0.79 0.00 35.42 4.08
3178 3311 4.875536 ACACAAAGGAACAAAGGAATTTGC 59.124 37.500 0.79 0.00 35.42 3.68
3179 3312 6.200854 GCTACACAAAGGAACAAAGGAATTTG 59.799 38.462 0.00 0.00 37.89 2.32
3180 3313 6.098266 AGCTACACAAAGGAACAAAGGAATTT 59.902 34.615 0.00 0.00 0.00 1.82
3183 3316 4.532834 AGCTACACAAAGGAACAAAGGAA 58.467 39.130 0.00 0.00 0.00 3.36
3198 3331 8.425577 AATTAACATGTGTCATAGAGCTACAC 57.574 34.615 9.34 9.34 43.00 2.90
3206 3340 8.755941 CCGACTCTTAATTAACATGTGTCATAG 58.244 37.037 0.00 0.00 0.00 2.23
3212 3346 8.642908 TCATACCGACTCTTAATTAACATGTG 57.357 34.615 0.00 0.00 0.00 3.21
3226 3360 7.599245 CCTATTCCTAACAAATCATACCGACTC 59.401 40.741 0.00 0.00 0.00 3.36
3227 3361 7.442656 CCTATTCCTAACAAATCATACCGACT 58.557 38.462 0.00 0.00 0.00 4.18
3228 3362 6.147328 GCCTATTCCTAACAAATCATACCGAC 59.853 42.308 0.00 0.00 0.00 4.79
3229 3363 6.183361 TGCCTATTCCTAACAAATCATACCGA 60.183 38.462 0.00 0.00 0.00 4.69
3230 3364 5.995282 TGCCTATTCCTAACAAATCATACCG 59.005 40.000 0.00 0.00 0.00 4.02
3231 3365 7.502561 AGTTGCCTATTCCTAACAAATCATACC 59.497 37.037 0.00 0.00 0.00 2.73
3232 3366 8.451908 AGTTGCCTATTCCTAACAAATCATAC 57.548 34.615 0.00 0.00 0.00 2.39
3233 3367 8.902806 CAAGTTGCCTATTCCTAACAAATCATA 58.097 33.333 0.00 0.00 0.00 2.15
3234 3368 7.397192 ACAAGTTGCCTATTCCTAACAAATCAT 59.603 33.333 1.81 0.00 0.00 2.45
3235 3369 6.719370 ACAAGTTGCCTATTCCTAACAAATCA 59.281 34.615 1.81 0.00 0.00 2.57
3236 3370 7.158099 ACAAGTTGCCTATTCCTAACAAATC 57.842 36.000 1.81 0.00 0.00 2.17
3237 3371 8.823220 ATACAAGTTGCCTATTCCTAACAAAT 57.177 30.769 1.81 0.00 0.00 2.32
3238 3372 8.644374 AATACAAGTTGCCTATTCCTAACAAA 57.356 30.769 1.81 0.00 0.00 2.83
3251 3385 2.689983 CCTCATGGGAATACAAGTTGCC 59.310 50.000 1.81 0.00 39.75 4.52
3330 3464 7.147337 ACCCCTTTGTATTTATCCCGTTGTATA 60.147 37.037 0.00 0.00 0.00 1.47
3580 3715 4.418392 GCACAACATGGCTTTTATCTCTG 58.582 43.478 0.00 0.00 0.00 3.35
3603 3738 1.403679 CTGACGAAGGCTCAGACTAGG 59.596 57.143 0.00 0.00 37.90 3.02
3682 3817 1.145759 TTCTATGTACGCGCTGCTGC 61.146 55.000 5.73 5.34 0.00 5.25
3693 3828 4.195225 TGGTGTTGATGCGTTCTATGTA 57.805 40.909 0.00 0.00 0.00 2.29
3909 4044 2.218603 GCCTGGAAGACGAAGAAACAA 58.781 47.619 0.00 0.00 34.07 2.83
3943 4078 6.751514 TTCTGCTTACTGTGTTTTTCTTGA 57.248 33.333 0.00 0.00 0.00 3.02
3994 4129 1.611977 CTATTCGGATGCTACGTGGGA 59.388 52.381 0.00 0.00 0.00 4.37


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

AutoCloner maintained by Alex Coulton.