Multiple sequence alignment - TraesCS2A01G153500

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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 TraesCS2A01G153500 chr2A 100.000 3025 0 0 1 3025 101402765 101399741 0.000000e+00 5587.0
1 TraesCS2A01G153500 chr2D 85.842 1561 115 43 1452 2947 102298042 102296523 0.000000e+00 1561.0
2 TraesCS2A01G153500 chr2D 92.066 668 46 5 728 1391 102298730 102298066 0.000000e+00 933.0
3 TraesCS2A01G153500 chr2D 87.846 650 51 18 1 648 102299445 102298822 0.000000e+00 737.0
4 TraesCS2A01G153500 chr2D 87.834 337 32 3 2644 2980 102288208 102287881 1.320000e-103 387.0
5 TraesCS2A01G153500 chr2D 95.000 60 1 2 2938 2997 102296220 102296163 3.210000e-15 93.5
6 TraesCS2A01G153500 chr2D 97.368 38 1 0 2988 3025 102287501 102287464 7.000000e-07 65.8
7 TraesCS2A01G153500 chr2B 86.134 714 59 21 1 694 153675739 153675046 0.000000e+00 734.0
8 TraesCS2A01G153500 chr2B 93.926 461 24 3 935 1391 153674881 153674421 0.000000e+00 693.0
9 TraesCS2A01G153500 chr2B 91.324 438 36 2 1572 2009 153674258 153673823 5.580000e-167 597.0
10 TraesCS2A01G153500 chr2B 84.642 573 54 18 2087 2632 153673620 153673055 9.540000e-150 540.0
11 TraesCS2A01G153500 chr2B 86.040 351 29 10 2644 2992 153672749 153672417 2.870000e-95 359.0
12 TraesCS2A01G153500 chr1A 91.837 49 4 0 686 734 135969833 135969785 5.410000e-08 69.4
13 TraesCS2A01G153500 chr4B 100.000 36 0 0 687 722 66169551 66169516 1.950000e-07 67.6
14 TraesCS2A01G153500 chr7B 97.368 38 1 0 687 724 541686214 541686251 7.000000e-07 65.8
15 TraesCS2A01G153500 chr7B 97.368 38 1 0 687 724 542980777 542980814 7.000000e-07 65.8
16 TraesCS2A01G153500 chr4D 97.297 37 1 0 686 722 360763041 360763077 2.520000e-06 63.9
17 TraesCS2A01G153500 chr3D 89.583 48 4 1 691 738 502949425 502949471 3.260000e-05 60.2
18 TraesCS2A01G153500 chr4A 94.595 37 2 0 686 722 104095730 104095694 1.170000e-04 58.4
19 TraesCS2A01G153500 chr3A 97.059 34 1 0 691 724 57807832 57807799 1.170000e-04 58.4
20 TraesCS2A01G153500 chr5A 89.130 46 2 2 690 732 375575837 375575882 2.000000e-03 54.7


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 TraesCS2A01G153500 chr2A 101399741 101402765 3024 True 5587.000 5587 100.0000 1 3025 1 chr2A.!!$R1 3024
1 TraesCS2A01G153500 chr2D 102296163 102299445 3282 True 831.125 1561 90.1885 1 2997 4 chr2D.!!$R2 2996
2 TraesCS2A01G153500 chr2D 102287464 102288208 744 True 226.400 387 92.6010 2644 3025 2 chr2D.!!$R1 381
3 TraesCS2A01G153500 chr2B 153672417 153675739 3322 True 584.600 734 88.4132 1 2992 5 chr2B.!!$R1 2991

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
199 207 0.95104 GTCACGCCTTGGGAACTCTG 60.951 60.0 0.0 0.0 0.0 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2040 2193 0.030705 TGGAGGAAGAGGATGGGAGG 60.031 60.0 0.0 0.0 0.0 4.3 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
39 40 4.000988 CGCTTTCTGTTACACCTGGTATT 58.999 43.478 0.00 0.00 0.00 1.89
40 41 5.172934 CGCTTTCTGTTACACCTGGTATTA 58.827 41.667 0.00 0.00 0.00 0.98
157 165 6.935167 ACTAAAATGCCTTTGTTAATGGGAG 58.065 36.000 0.00 0.00 29.82 4.30
199 207 0.951040 GTCACGCCTTGGGAACTCTG 60.951 60.000 0.00 0.00 0.00 3.35
221 229 1.806542 ACTAACTCATTGGCTGTTGCG 59.193 47.619 0.00 0.00 40.82 4.85
244 252 4.081322 TGGGTACAAGTTTTGTCTCTCC 57.919 45.455 0.00 0.00 44.12 3.71
245 253 3.456644 TGGGTACAAGTTTTGTCTCTCCA 59.543 43.478 0.00 0.80 44.12 3.86
271 310 6.206829 GGACCAGTTTTGTTTGTAGCTAATCT 59.793 38.462 0.00 0.00 0.00 2.40
272 311 7.389607 GGACCAGTTTTGTTTGTAGCTAATCTA 59.610 37.037 0.00 0.00 0.00 1.98
273 312 8.685838 ACCAGTTTTGTTTGTAGCTAATCTAA 57.314 30.769 0.00 0.00 0.00 2.10
274 313 8.784043 ACCAGTTTTGTTTGTAGCTAATCTAAG 58.216 33.333 0.00 0.00 0.00 2.18
275 314 8.784043 CCAGTTTTGTTTGTAGCTAATCTAAGT 58.216 33.333 0.00 0.00 0.00 2.24
282 321 9.944376 TGTTTGTAGCTAATCTAAGTTTCATCT 57.056 29.630 0.00 0.00 0.00 2.90
286 325 9.751542 TGTAGCTAATCTAAGTTTCATCTTAGC 57.248 33.333 0.00 0.00 43.60 3.09
287 326 9.751542 GTAGCTAATCTAAGTTTCATCTTAGCA 57.248 33.333 12.33 0.00 43.60 3.49
289 328 9.270640 AGCTAATCTAAGTTTCATCTTAGCATG 57.729 33.333 12.33 0.00 43.60 4.06
290 329 9.050601 GCTAATCTAAGTTTCATCTTAGCATGT 57.949 33.333 8.15 0.00 43.60 3.21
294 333 9.757227 ATCTAAGTTTCATCTTAGCATGTACTC 57.243 33.333 8.15 0.00 43.60 2.59
295 334 8.198109 TCTAAGTTTCATCTTAGCATGTACTCC 58.802 37.037 8.15 0.00 43.60 3.85
296 335 5.352284 AGTTTCATCTTAGCATGTACTCCG 58.648 41.667 0.00 0.00 0.00 4.63
304 343 3.454371 AGCATGTACTCCGTATGTTCC 57.546 47.619 0.00 0.00 0.00 3.62
312 351 2.231964 ACTCCGTATGTTCCGTAAAGCA 59.768 45.455 0.00 0.00 0.00 3.91
313 352 3.118884 ACTCCGTATGTTCCGTAAAGCAT 60.119 43.478 0.00 0.00 0.00 3.79
319 358 6.421501 CCGTATGTTCCGTAAAGCATATGTTA 59.578 38.462 4.29 0.00 32.11 2.41
320 359 7.358931 CCGTATGTTCCGTAAAGCATATGTTAG 60.359 40.741 4.29 0.00 32.11 2.34
322 361 6.656314 TGTTCCGTAAAGCATATGTTAGTG 57.344 37.500 4.29 0.00 0.00 2.74
326 365 6.046593 TCCGTAAAGCATATGTTAGTGAAGG 58.953 40.000 4.29 0.00 0.00 3.46
330 369 7.224753 CGTAAAGCATATGTTAGTGAAGGATGT 59.775 37.037 4.29 0.00 0.00 3.06
342 388 4.042809 AGTGAAGGATGTGGTGGTCATTTA 59.957 41.667 0.00 0.00 0.00 1.40
344 390 4.764823 TGAAGGATGTGGTGGTCATTTAAC 59.235 41.667 0.00 0.00 0.00 2.01
349 395 6.603201 AGGATGTGGTGGTCATTTAACTAATG 59.397 38.462 0.00 0.00 44.14 1.90
362 408 8.335532 CATTTAACTAATGAAACAGTGGAGGA 57.664 34.615 0.00 0.00 45.35 3.71
435 481 1.135972 GTCAGTATGTGTGGCTTTGCG 60.136 52.381 0.00 0.00 37.40 4.85
446 492 2.919494 GCTTTGCGTGTGAAGGGGG 61.919 63.158 0.00 0.00 0.00 5.40
467 513 2.436173 GGAGGGAATGTGAACTAGGGAG 59.564 54.545 0.00 0.00 0.00 4.30
472 518 4.518249 GGAATGTGAACTAGGGAGAAAGG 58.482 47.826 0.00 0.00 0.00 3.11
480 526 6.428465 GTGAACTAGGGAGAAAGGAAGAAAAG 59.572 42.308 0.00 0.00 0.00 2.27
502 548 4.665009 AGGGTCATTCTGCATAGGGAAATA 59.335 41.667 0.00 0.00 0.00 1.40
516 563 7.972277 GCATAGGGAAATAATGTGCAAGATATG 59.028 37.037 0.00 0.00 32.07 1.78
547 594 4.645535 AGAAGCAGTGACTTAGCAATGAA 58.354 39.130 7.91 0.00 36.04 2.57
548 595 4.694509 AGAAGCAGTGACTTAGCAATGAAG 59.305 41.667 7.91 0.00 36.04 3.02
555 602 4.938226 GTGACTTAGCAATGAAGCTTAGGT 59.062 41.667 0.00 0.00 43.70 3.08
572 619 1.070758 AGGTTTGCACAGTGATCGACT 59.929 47.619 4.15 0.00 34.02 4.18
614 661 5.128205 TGATTCAAGTCATTCTGCATAGGG 58.872 41.667 0.00 0.00 0.00 3.53
615 662 4.842531 TTCAAGTCATTCTGCATAGGGA 57.157 40.909 0.00 0.00 0.00 4.20
620 667 3.054139 AGTCATTCTGCATAGGGAAAGCA 60.054 43.478 0.00 0.00 36.72 3.91
629 676 3.274288 CATAGGGAAAGCAGAACAGGAC 58.726 50.000 0.00 0.00 0.00 3.85
705 785 6.639686 TGACTTAAAGTTGTACTAAGTGAGCG 59.360 38.462 8.69 0.00 29.76 5.03
706 786 6.742109 ACTTAAAGTTGTACTAAGTGAGCGA 58.258 36.000 4.23 0.00 28.79 4.93
707 787 6.640092 ACTTAAAGTTGTACTAAGTGAGCGAC 59.360 38.462 4.23 0.00 28.79 5.19
709 789 4.579454 AGTTGTACTAAGTGAGCGACAA 57.421 40.909 0.00 0.00 33.84 3.18
710 790 4.547532 AGTTGTACTAAGTGAGCGACAAG 58.452 43.478 0.00 0.00 35.84 3.16
711 791 4.037684 AGTTGTACTAAGTGAGCGACAAGT 59.962 41.667 0.00 0.00 35.84 3.16
712 792 5.240183 AGTTGTACTAAGTGAGCGACAAGTA 59.760 40.000 2.57 0.00 36.71 2.24
713 793 5.694231 TGTACTAAGTGAGCGACAAGTAA 57.306 39.130 0.00 0.00 30.99 2.24
714 794 6.263516 TGTACTAAGTGAGCGACAAGTAAT 57.736 37.500 0.00 0.00 30.99 1.89
715 795 7.381766 TGTACTAAGTGAGCGACAAGTAATA 57.618 36.000 0.00 0.00 30.99 0.98
716 796 7.993101 TGTACTAAGTGAGCGACAAGTAATAT 58.007 34.615 0.00 0.00 30.99 1.28
717 797 7.913821 TGTACTAAGTGAGCGACAAGTAATATG 59.086 37.037 0.00 0.00 30.99 1.78
718 798 6.273825 ACTAAGTGAGCGACAAGTAATATGG 58.726 40.000 0.00 0.00 0.00 2.74
719 799 5.339008 AAGTGAGCGACAAGTAATATGGA 57.661 39.130 0.00 0.00 0.00 3.41
720 800 5.537300 AGTGAGCGACAAGTAATATGGAT 57.463 39.130 0.00 0.00 0.00 3.41
721 801 5.533482 AGTGAGCGACAAGTAATATGGATC 58.467 41.667 0.00 0.00 0.00 3.36
722 802 4.383052 GTGAGCGACAAGTAATATGGATCG 59.617 45.833 0.00 0.00 0.00 3.69
723 803 3.914312 AGCGACAAGTAATATGGATCGG 58.086 45.455 0.00 0.00 0.00 4.18
724 804 2.993899 GCGACAAGTAATATGGATCGGG 59.006 50.000 0.00 0.00 0.00 5.14
725 805 3.305813 GCGACAAGTAATATGGATCGGGA 60.306 47.826 0.00 0.00 0.00 5.14
726 806 4.486090 CGACAAGTAATATGGATCGGGAG 58.514 47.826 0.00 0.00 0.00 4.30
763 843 6.577427 CGTCCTTTATTGTGACTTAAGCAAAC 59.423 38.462 1.29 0.00 0.00 2.93
766 846 6.863126 CCTTTATTGTGACTTAAGCAAACCAG 59.137 38.462 1.29 0.00 0.00 4.00
794 908 3.103447 TCATGTATACTCAGCTGCAGC 57.897 47.619 31.53 31.53 42.49 5.25
802 916 2.082231 ACTCAGCTGCAGCACTATTTG 58.918 47.619 38.24 26.19 45.16 2.32
873 988 5.577164 CCATCCTTTACTGTGACTTAACTCG 59.423 44.000 0.00 0.00 0.00 4.18
878 993 6.257193 CCTTTACTGTGACTTAACTCGTTTGT 59.743 38.462 0.00 0.00 0.00 2.83
888 1003 8.279800 TGACTTAACTCGTTTGTGTTGATTATG 58.720 33.333 0.00 0.00 34.02 1.90
900 1015 9.693739 TTTGTGTTGATTATGTACCCATCTTAT 57.306 29.630 0.00 0.00 32.29 1.73
963 1078 3.559171 GGTTACTGTGATCTTGGGAAGCA 60.559 47.826 0.00 0.00 0.00 3.91
965 1080 1.701847 ACTGTGATCTTGGGAAGCACT 59.298 47.619 0.00 0.00 34.29 4.40
992 1109 4.462133 AGGTCGCTGCTTCTATAGAGTTA 58.538 43.478 2.02 0.00 0.00 2.24
994 1111 5.182380 AGGTCGCTGCTTCTATAGAGTTATC 59.818 44.000 2.02 0.00 0.00 1.75
1314 1431 1.195448 CGCCAGACATTTGACAGTGTC 59.805 52.381 16.68 16.68 43.85 3.67
1342 1459 1.135689 GGCTTAATGAACTGCACGGTG 60.136 52.381 3.15 3.15 0.00 4.94
1346 1463 1.800805 AATGAACTGCACGGTGAGAG 58.199 50.000 13.29 9.06 0.00 3.20
1348 1465 2.029844 GAACTGCACGGTGAGAGCC 61.030 63.158 13.29 0.00 35.49 4.70
1356 1473 1.045407 ACGGTGAGAGCCAACACTTA 58.955 50.000 0.00 0.00 37.22 2.24
1362 1479 2.104792 TGAGAGCCAACACTTAGCTTGT 59.895 45.455 0.00 0.00 36.87 3.16
1366 1483 4.036852 AGAGCCAACACTTAGCTTGTTTTC 59.963 41.667 0.00 0.14 36.87 2.29
1370 1487 5.660460 CCAACACTTAGCTTGTTTTCCTTT 58.340 37.500 0.00 0.00 34.91 3.11
1371 1488 5.748630 CCAACACTTAGCTTGTTTTCCTTTC 59.251 40.000 0.00 0.00 34.91 2.62
1378 1499 4.200092 AGCTTGTTTTCCTTTCTCGAACT 58.800 39.130 0.00 0.00 0.00 3.01
1383 1504 7.117956 GCTTGTTTTCCTTTCTCGAACTAGTAT 59.882 37.037 0.00 0.00 0.00 2.12
1386 1507 8.311836 TGTTTTCCTTTCTCGAACTAGTATCAT 58.688 33.333 0.00 0.00 0.00 2.45
1391 1512 9.132923 TCCTTTCTCGAACTAGTATCATAATGT 57.867 33.333 0.00 0.00 0.00 2.71
1406 1527 9.051679 GTATCATAATGTATGTTACAAGGTGCA 57.948 33.333 9.88 0.00 42.76 4.57
1407 1528 7.929941 TCATAATGTATGTTACAAGGTGCAA 57.070 32.000 0.00 0.00 42.76 4.08
1408 1529 8.341892 TCATAATGTATGTTACAAGGTGCAAA 57.658 30.769 0.00 0.00 42.76 3.68
1409 1530 8.458052 TCATAATGTATGTTACAAGGTGCAAAG 58.542 33.333 0.00 0.00 42.76 2.77
1410 1531 4.497473 TGTATGTTACAAGGTGCAAAGC 57.503 40.909 0.00 0.00 35.38 3.51
1411 1532 3.254657 TGTATGTTACAAGGTGCAAAGCC 59.745 43.478 0.00 0.00 35.38 4.35
1412 1533 1.036707 TGTTACAAGGTGCAAAGCCC 58.963 50.000 0.00 0.00 0.00 5.19
1413 1534 1.328279 GTTACAAGGTGCAAAGCCCT 58.672 50.000 0.00 0.00 32.23 5.19
1414 1535 2.158593 TGTTACAAGGTGCAAAGCCCTA 60.159 45.455 0.00 0.00 31.07 3.53
1415 1536 3.089284 GTTACAAGGTGCAAAGCCCTAT 58.911 45.455 0.00 0.00 31.07 2.57
1416 1537 1.549203 ACAAGGTGCAAAGCCCTATG 58.451 50.000 0.00 0.00 31.07 2.23
1417 1538 1.203050 ACAAGGTGCAAAGCCCTATGT 60.203 47.619 0.00 0.00 31.07 2.29
1418 1539 2.041081 ACAAGGTGCAAAGCCCTATGTA 59.959 45.455 0.00 0.00 31.07 2.29
1419 1540 2.420058 AGGTGCAAAGCCCTATGTAC 57.580 50.000 0.00 0.00 29.87 2.90
1420 1541 1.014352 GGTGCAAAGCCCTATGTACG 58.986 55.000 0.00 0.00 33.60 3.67
1421 1542 1.677820 GGTGCAAAGCCCTATGTACGT 60.678 52.381 0.00 0.00 33.60 3.57
1422 1543 2.419021 GGTGCAAAGCCCTATGTACGTA 60.419 50.000 0.00 0.00 33.60 3.57
1423 1544 2.864343 GTGCAAAGCCCTATGTACGTAG 59.136 50.000 14.24 14.24 0.00 3.51
1425 1546 3.700539 TGCAAAGCCCTATGTACGTAGTA 59.299 43.478 18.62 0.00 45.11 1.82
1442 1563 6.802608 ACGTAGTAACTGCTATGCATTAAGA 58.197 36.000 3.54 0.00 41.94 2.10
1443 1564 7.262772 ACGTAGTAACTGCTATGCATTAAGAA 58.737 34.615 3.54 0.00 41.94 2.52
1444 1565 7.435488 ACGTAGTAACTGCTATGCATTAAGAAG 59.565 37.037 3.54 3.35 41.94 2.85
1450 1571 2.620115 GCTATGCATTAAGAAGCAGGCA 59.380 45.455 3.54 0.00 44.94 4.75
1455 1576 2.672195 GCATTAAGAAGCAGGCACCAAC 60.672 50.000 0.00 0.00 0.00 3.77
1481 1602 1.811176 GCAAAGCACAAATGGCCAAGT 60.811 47.619 10.96 6.23 0.00 3.16
1494 1625 1.013596 GCCAAGTGCCAAACCAAAAC 58.986 50.000 0.00 0.00 0.00 2.43
1500 1631 3.078097 AGTGCCAAACCAAAACCAAAAC 58.922 40.909 0.00 0.00 0.00 2.43
1507 1638 6.377780 CCAAACCAAAACCAAAACAAAAGAG 58.622 36.000 0.00 0.00 0.00 2.85
1515 1646 8.435430 CAAAACCAAAACAAAAGAGAAGAGAAC 58.565 33.333 0.00 0.00 0.00 3.01
1516 1647 6.208988 ACCAAAACAAAAGAGAAGAGAACC 57.791 37.500 0.00 0.00 0.00 3.62
1517 1648 5.714806 ACCAAAACAAAAGAGAAGAGAACCA 59.285 36.000 0.00 0.00 0.00 3.67
1520 1651 7.276438 CCAAAACAAAAGAGAAGAGAACCAAAG 59.724 37.037 0.00 0.00 0.00 2.77
1532 1668 6.524101 AGAGAACCAAAGCAAAACTAAACA 57.476 33.333 0.00 0.00 0.00 2.83
1533 1669 6.330278 AGAGAACCAAAGCAAAACTAAACAC 58.670 36.000 0.00 0.00 0.00 3.32
1553 1689 3.059597 CACAGTTAGAGCAGGTCAAAACG 60.060 47.826 1.66 5.58 31.66 3.60
1559 1695 2.364324 AGAGCAGGTCAAAACGTAGACA 59.636 45.455 14.92 0.00 36.50 3.41
1561 1697 4.219944 AGAGCAGGTCAAAACGTAGACATA 59.780 41.667 14.92 0.00 36.50 2.29
1563 1699 3.617263 GCAGGTCAAAACGTAGACATAGG 59.383 47.826 14.92 2.25 36.50 2.57
1564 1700 4.817517 CAGGTCAAAACGTAGACATAGGT 58.182 43.478 14.92 0.00 36.50 3.08
1565 1701 5.622914 GCAGGTCAAAACGTAGACATAGGTA 60.623 44.000 14.92 0.00 36.50 3.08
1566 1702 6.034591 CAGGTCAAAACGTAGACATAGGTAG 58.965 44.000 14.92 0.00 36.50 3.18
1567 1703 4.802563 GGTCAAAACGTAGACATAGGTAGC 59.197 45.833 14.92 0.00 36.50 3.58
1595 1748 4.212214 GTCTTGAGCTAGTTGGTTGTCTTG 59.788 45.833 0.00 0.00 0.00 3.02
1598 1751 3.323691 TGAGCTAGTTGGTTGTCTTGCTA 59.676 43.478 0.00 0.00 41.17 3.49
1631 1784 5.760253 CCCTAGCAACATAGATTGGTTACAG 59.240 44.000 0.00 0.00 40.62 2.74
1633 1786 6.480320 CCTAGCAACATAGATTGGTTACAGTC 59.520 42.308 0.00 0.00 40.62 3.51
1645 1798 5.766150 TGGTTACAGTCTGGTTTGATTTG 57.234 39.130 4.53 0.00 0.00 2.32
1700 1853 1.813513 ACCTCCAAACAGCTCATTCG 58.186 50.000 0.00 0.00 0.00 3.34
1709 1862 3.272574 ACAGCTCATTCGGACATGAAT 57.727 42.857 0.00 0.00 39.10 2.57
1827 1980 1.623311 TCTTCATGGAAACCTCAGCGA 59.377 47.619 0.00 0.00 0.00 4.93
1865 2018 0.318107 CAGCAGCTTTCCAAACCGTG 60.318 55.000 0.00 0.00 0.00 4.94
2037 2190 2.353889 TCGTCGTAGAGCATGTAAGACC 59.646 50.000 0.00 0.00 39.51 3.85
2038 2191 2.541178 CGTCGTAGAGCATGTAAGACCC 60.541 54.545 0.00 0.00 39.51 4.46
2039 2192 2.029623 TCGTAGAGCATGTAAGACCCC 58.970 52.381 0.00 0.00 0.00 4.95
2040 2193 1.068741 CGTAGAGCATGTAAGACCCCC 59.931 57.143 0.00 0.00 0.00 5.40
2072 2225 3.010584 TCTTCCTCCATTTTTCTCCTGGG 59.989 47.826 0.00 0.00 0.00 4.45
2073 2226 1.640670 TCCTCCATTTTTCTCCTGGGG 59.359 52.381 0.00 0.00 0.00 4.96
2084 2362 5.796502 TTTCTCCTGGGGTATGAAGAAAT 57.203 39.130 0.00 0.00 0.00 2.17
2085 2363 4.778213 TCTCCTGGGGTATGAAGAAATG 57.222 45.455 0.00 0.00 0.00 2.32
2093 2371 4.498009 GGGGTATGAAGAAATGCATCGTTG 60.498 45.833 0.00 0.00 0.00 4.10
2096 2374 4.771590 ATGAAGAAATGCATCGTTGTGT 57.228 36.364 0.00 0.00 0.00 3.72
2097 2375 4.145876 TGAAGAAATGCATCGTTGTGTC 57.854 40.909 0.00 0.00 0.00 3.67
2100 2378 2.095567 AGAAATGCATCGTTGTGTCTGC 60.096 45.455 0.00 0.00 35.21 4.26
2105 2383 1.730121 GCATCGTTGTGTCTGCCATTG 60.730 52.381 0.00 0.00 0.00 2.82
2265 2557 7.308348 CGCCTTCTTCATCAAAAGGTAAAAGTA 60.308 37.037 2.64 0.00 41.37 2.24
2395 2700 6.148976 GTGTAAAGAGGAAAACTATGTCACCC 59.851 42.308 0.00 0.00 0.00 4.61
2433 2738 2.425143 TCATTCCACATCCTTCTGCC 57.575 50.000 0.00 0.00 0.00 4.85
2434 2739 1.064463 TCATTCCACATCCTTCTGCCC 60.064 52.381 0.00 0.00 0.00 5.36
2435 2740 0.259938 ATTCCACATCCTTCTGCCCC 59.740 55.000 0.00 0.00 0.00 5.80
2467 2772 2.096218 CCACGCTTTTACTGTTCTCAGC 60.096 50.000 0.00 0.00 44.77 4.26
2473 2781 3.728076 TTTACTGTTCTCAGCTCACGT 57.272 42.857 0.00 0.00 44.77 4.49
2506 2815 5.454755 CCTCATATGGTAAACTTCGGTCCAT 60.455 44.000 2.13 0.00 41.10 3.41
2516 2825 3.822940 ACTTCGGTCCATGGTTGTAAAA 58.177 40.909 12.58 0.00 0.00 1.52
2517 2826 4.208746 ACTTCGGTCCATGGTTGTAAAAA 58.791 39.130 12.58 0.00 0.00 1.94
2518 2827 4.037089 ACTTCGGTCCATGGTTGTAAAAAC 59.963 41.667 12.58 0.00 0.00 2.43
2519 2828 3.822940 TCGGTCCATGGTTGTAAAAACT 58.177 40.909 12.58 0.00 0.00 2.66
2523 2832 4.217767 GGTCCATGGTTGTAAAAACTCTCC 59.782 45.833 12.58 0.00 0.00 3.71
2531 2843 3.054878 TGTAAAAACTCTCCGCGAACTC 58.945 45.455 8.23 0.00 0.00 3.01
2532 2844 1.137513 AAAAACTCTCCGCGAACTCG 58.862 50.000 8.23 0.00 43.27 4.18
2539 2851 4.462417 CCGCGAACTCGAGCTCGT 62.462 66.667 31.77 16.80 43.02 4.18
2541 2853 1.225936 CGCGAACTCGAGCTCGTTA 60.226 57.895 31.77 16.31 43.02 3.18
2542 2854 1.188769 CGCGAACTCGAGCTCGTTAG 61.189 60.000 31.77 26.20 43.02 2.34
2551 2863 0.595310 GAGCTCGTTAGATCCACGCC 60.595 60.000 9.66 4.46 37.57 5.68
2572 2890 1.329599 GGTTTTACCGATCGGACATGC 59.670 52.381 39.55 23.63 38.96 4.06
2573 2891 2.004017 GTTTTACCGATCGGACATGCA 58.996 47.619 39.55 15.34 38.96 3.96
2604 2935 7.009907 GCACTGAAATGGCAGAAAATAATCTTC 59.990 37.037 0.00 0.00 39.20 2.87
2641 3236 5.321102 ACATTCAGTACTTTGCCATTACCA 58.679 37.500 0.00 0.00 0.00 3.25
2642 3237 5.772672 ACATTCAGTACTTTGCCATTACCAA 59.227 36.000 0.00 0.00 0.00 3.67
2657 3281 1.295423 CCAAGTGTGGGTACGAGGG 59.705 63.158 0.00 0.00 41.77 4.30
2673 3297 1.903183 GAGGGCTCTCTAACCAAGTGT 59.097 52.381 6.27 0.00 37.07 3.55
2677 3301 2.418884 GGCTCTCTAACCAAGTGTAGCC 60.419 54.545 0.00 0.00 36.15 3.93
2755 3379 6.083098 TGTGTGATTTTGTACCATCCAAAG 57.917 37.500 0.00 0.00 33.67 2.77
2772 3396 1.590932 AAGCTCATGCGATGGATGAC 58.409 50.000 0.00 0.00 45.42 3.06
2802 3426 4.317839 GCAGTACCGACACATTATAAAGCG 60.318 45.833 0.00 0.00 0.00 4.68
2818 3448 1.838112 AGCGGAGAAAATCATGGCAA 58.162 45.000 0.00 0.00 0.00 4.52
2819 3449 2.381911 AGCGGAGAAAATCATGGCAAT 58.618 42.857 0.00 0.00 0.00 3.56
2841 3471 2.668550 GTGTCCCCGGAACAGTGC 60.669 66.667 0.73 0.00 0.00 4.40
2846 3476 2.671070 CCCGGAACAGTGCCATCT 59.329 61.111 0.73 0.00 0.00 2.90
2847 3477 1.450312 CCCGGAACAGTGCCATCTC 60.450 63.158 0.73 0.00 0.00 2.75
2848 3478 1.296392 CCGGAACAGTGCCATCTCA 59.704 57.895 0.00 0.00 0.00 3.27
2849 3479 0.107508 CCGGAACAGTGCCATCTCAT 60.108 55.000 0.00 0.00 0.00 2.90
2850 3480 1.293924 CGGAACAGTGCCATCTCATC 58.706 55.000 0.00 0.00 0.00 2.92
2851 3481 1.134580 CGGAACAGTGCCATCTCATCT 60.135 52.381 0.00 0.00 0.00 2.90
2852 3482 2.101415 CGGAACAGTGCCATCTCATCTA 59.899 50.000 0.00 0.00 0.00 1.98
2853 3483 3.726607 GGAACAGTGCCATCTCATCTAG 58.273 50.000 0.00 0.00 0.00 2.43
2933 3565 2.605837 TAACCGAATGATTGCCGCTA 57.394 45.000 0.00 0.00 0.00 4.26
2953 3896 3.577805 AGGTAAAAAGTGACAGCACCT 57.422 42.857 0.00 0.00 46.32 4.00
3016 4331 2.086094 CATCAGCAAGTACATGTGCCA 58.914 47.619 9.11 0.00 41.88 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.612212 CAGGTGTAACAGAAAGCGTTGT 59.388 45.455 0.00 0.00 39.98 3.32
39 40 3.201930 TCCTGCCAATAGTTGCCTTGATA 59.798 43.478 0.00 0.00 0.00 2.15
40 41 2.025037 TCCTGCCAATAGTTGCCTTGAT 60.025 45.455 0.00 0.00 0.00 2.57
199 207 3.181520 CGCAACAGCCAATGAGTTAGTAC 60.182 47.826 0.00 0.00 0.00 2.73
221 229 4.275196 GGAGAGACAAAACTTGTACCCAAC 59.725 45.833 0.00 0.00 45.52 3.77
244 252 3.632145 AGCTACAAACAAAACTGGTCCTG 59.368 43.478 0.00 0.00 0.00 3.86
245 253 3.898482 AGCTACAAACAAAACTGGTCCT 58.102 40.909 0.00 0.00 0.00 3.85
271 310 6.978659 CGGAGTACATGCTAAGATGAAACTTA 59.021 38.462 0.00 0.00 0.00 2.24
272 311 5.812642 CGGAGTACATGCTAAGATGAAACTT 59.187 40.000 0.00 0.00 0.00 2.66
273 312 5.105310 ACGGAGTACATGCTAAGATGAAACT 60.105 40.000 0.00 0.00 41.94 2.66
274 313 5.109903 ACGGAGTACATGCTAAGATGAAAC 58.890 41.667 0.00 0.00 41.94 2.78
275 314 5.339008 ACGGAGTACATGCTAAGATGAAA 57.661 39.130 0.00 0.00 41.94 2.69
292 331 2.883574 TGCTTTACGGAACATACGGAG 58.116 47.619 0.00 0.00 35.23 4.63
293 332 3.530265 ATGCTTTACGGAACATACGGA 57.470 42.857 0.00 0.00 35.23 4.69
294 333 4.748102 ACATATGCTTTACGGAACATACGG 59.252 41.667 1.58 0.00 35.23 4.02
295 334 5.900339 ACATATGCTTTACGGAACATACG 57.100 39.130 1.58 0.00 37.36 3.06
296 335 8.273557 CACTAACATATGCTTTACGGAACATAC 58.726 37.037 1.58 0.00 0.00 2.39
304 343 7.224753 ACATCCTTCACTAACATATGCTTTACG 59.775 37.037 1.58 0.00 0.00 3.18
312 351 5.191722 ACCACCACATCCTTCACTAACATAT 59.808 40.000 0.00 0.00 0.00 1.78
313 352 4.534500 ACCACCACATCCTTCACTAACATA 59.466 41.667 0.00 0.00 0.00 2.29
319 358 1.434188 TGACCACCACATCCTTCACT 58.566 50.000 0.00 0.00 0.00 3.41
320 359 2.496899 ATGACCACCACATCCTTCAC 57.503 50.000 0.00 0.00 0.00 3.18
322 361 5.010282 AGTTAAATGACCACCACATCCTTC 58.990 41.667 0.00 0.00 0.00 3.46
342 388 7.067494 GCATATTCCTCCACTGTTTCATTAGTT 59.933 37.037 0.00 0.00 0.00 2.24
344 390 6.016777 GGCATATTCCTCCACTGTTTCATTAG 60.017 42.308 0.00 0.00 0.00 1.73
349 395 3.891049 AGGCATATTCCTCCACTGTTTC 58.109 45.455 0.00 0.00 0.00 2.78
446 492 2.436173 CTCCCTAGTTCACATTCCCTCC 59.564 54.545 0.00 0.00 0.00 4.30
467 513 5.565637 GCAGAATGACCCTTTTCTTCCTTTC 60.566 44.000 0.00 0.00 39.69 2.62
472 518 5.067023 CCTATGCAGAATGACCCTTTTCTTC 59.933 44.000 0.00 0.00 39.69 2.87
480 526 3.297134 TTTCCCTATGCAGAATGACCC 57.703 47.619 0.00 0.00 39.69 4.46
516 563 6.915843 GCTAAGTCACTGCTTCTATAGAGTTC 59.084 42.308 2.02 0.00 0.00 3.01
547 594 2.638480 TCACTGTGCAAACCTAAGCT 57.362 45.000 2.12 0.00 0.00 3.74
548 595 2.159653 CGATCACTGTGCAAACCTAAGC 60.160 50.000 2.12 0.00 0.00 3.09
592 639 5.371526 TCCCTATGCAGAATGACTTGAATC 58.628 41.667 0.00 0.00 39.69 2.52
614 661 1.534595 CTGCTGTCCTGTTCTGCTTTC 59.465 52.381 0.00 0.00 0.00 2.62
615 662 1.133976 ACTGCTGTCCTGTTCTGCTTT 60.134 47.619 0.00 0.00 0.00 3.51
620 667 3.567478 AAGAAACTGCTGTCCTGTTCT 57.433 42.857 0.00 0.00 34.93 3.01
686 766 4.940463 TGTCGCTCACTTAGTACAACTTT 58.060 39.130 0.00 0.00 0.00 2.66
687 767 4.579454 TGTCGCTCACTTAGTACAACTT 57.421 40.909 0.00 0.00 0.00 2.66
694 774 6.096423 TCCATATTACTTGTCGCTCACTTAGT 59.904 38.462 0.00 0.00 0.00 2.24
695 775 6.504398 TCCATATTACTTGTCGCTCACTTAG 58.496 40.000 0.00 0.00 0.00 2.18
698 778 5.533482 GATCCATATTACTTGTCGCTCACT 58.467 41.667 0.00 0.00 0.00 3.41
699 779 4.383052 CGATCCATATTACTTGTCGCTCAC 59.617 45.833 0.00 0.00 0.00 3.51
700 780 4.546570 CGATCCATATTACTTGTCGCTCA 58.453 43.478 0.00 0.00 0.00 4.26
701 781 3.921021 CCGATCCATATTACTTGTCGCTC 59.079 47.826 0.00 0.00 0.00 5.03
703 783 2.993899 CCCGATCCATATTACTTGTCGC 59.006 50.000 0.00 0.00 0.00 5.19
705 785 5.470047 ACTCCCGATCCATATTACTTGTC 57.530 43.478 0.00 0.00 0.00 3.18
706 786 6.075984 ACTACTCCCGATCCATATTACTTGT 58.924 40.000 0.00 0.00 0.00 3.16
707 787 6.591750 ACTACTCCCGATCCATATTACTTG 57.408 41.667 0.00 0.00 0.00 3.16
709 789 8.896722 AAATACTACTCCCGATCCATATTACT 57.103 34.615 0.00 0.00 0.00 2.24
710 790 9.939802 AAAAATACTACTCCCGATCCATATTAC 57.060 33.333 0.00 0.00 0.00 1.89
763 843 8.147058 AGCTGAGTATACATGATAAGAAACTGG 58.853 37.037 5.50 0.00 0.00 4.00
766 846 7.439356 TGCAGCTGAGTATACATGATAAGAAAC 59.561 37.037 20.43 0.00 0.00 2.78
840 955 9.178758 AGTCACAGTAAAGGATGGAAAAATATC 57.821 33.333 0.00 0.00 0.00 1.63
859 974 5.062934 TCAACACAAACGAGTTAAGTCACAG 59.937 40.000 10.83 0.00 0.00 3.66
873 988 7.391148 AGATGGGTACATAATCAACACAAAC 57.609 36.000 0.00 0.00 37.47 2.93
923 1038 6.262273 CAGTAACCCTGTCAAGTTTACACAAT 59.738 38.462 0.00 0.00 36.37 2.71
924 1039 5.587043 CAGTAACCCTGTCAAGTTTACACAA 59.413 40.000 0.00 0.00 36.37 3.33
950 1065 4.195416 CCTTTCTAGTGCTTCCCAAGATC 58.805 47.826 0.00 0.00 0.00 2.75
957 1072 1.066787 AGCGACCTTTCTAGTGCTTCC 60.067 52.381 0.00 0.00 0.00 3.46
963 1078 1.896465 AGAAGCAGCGACCTTTCTAGT 59.104 47.619 0.00 0.00 0.00 2.57
965 1080 5.131067 TCTATAGAAGCAGCGACCTTTCTA 58.869 41.667 0.00 4.10 0.00 2.10
992 1109 2.224606 CACCATAAGCCATTCTGCGAT 58.775 47.619 0.00 0.00 36.02 4.58
994 1111 0.664761 CCACCATAAGCCATTCTGCG 59.335 55.000 0.00 0.00 36.02 5.18
1346 1463 3.068165 AGGAAAACAAGCTAAGTGTTGGC 59.932 43.478 3.10 0.00 39.14 4.52
1348 1465 6.564328 AGAAAGGAAAACAAGCTAAGTGTTG 58.436 36.000 3.10 0.00 39.14 3.33
1356 1473 4.200092 AGTTCGAGAAAGGAAAACAAGCT 58.800 39.130 0.00 0.00 0.00 3.74
1383 1504 7.929941 TTGCACCTTGTAACATACATTATGA 57.070 32.000 0.00 0.00 38.68 2.15
1386 1507 6.349777 GGCTTTGCACCTTGTAACATACATTA 60.350 38.462 0.00 0.00 38.68 1.90
1391 1512 2.823154 GGGCTTTGCACCTTGTAACATA 59.177 45.455 0.00 0.00 0.00 2.29
1392 1513 1.618343 GGGCTTTGCACCTTGTAACAT 59.382 47.619 0.00 0.00 0.00 2.71
1396 1517 2.041081 ACATAGGGCTTTGCACCTTGTA 59.959 45.455 0.00 0.00 38.30 2.41
1398 1519 1.549203 ACATAGGGCTTTGCACCTTG 58.451 50.000 0.00 1.40 38.30 3.61
1399 1520 2.723273 GTACATAGGGCTTTGCACCTT 58.277 47.619 0.00 0.00 38.30 3.50
1400 1521 1.406887 CGTACATAGGGCTTTGCACCT 60.407 52.381 0.00 0.00 40.89 4.00
1401 1522 1.014352 CGTACATAGGGCTTTGCACC 58.986 55.000 0.00 0.00 28.43 5.01
1404 1525 3.175109 ACTACGTACATAGGGCTTTGC 57.825 47.619 0.47 0.00 0.00 3.68
1406 1527 5.680665 GCAGTTACTACGTACATAGGGCTTT 60.681 44.000 0.47 0.00 0.00 3.51
1407 1528 4.202090 GCAGTTACTACGTACATAGGGCTT 60.202 45.833 0.47 0.00 0.00 4.35
1408 1529 3.317430 GCAGTTACTACGTACATAGGGCT 59.683 47.826 0.47 0.00 0.00 5.19
1409 1530 3.317430 AGCAGTTACTACGTACATAGGGC 59.683 47.826 0.47 0.00 0.00 5.19
1410 1531 6.609533 CATAGCAGTTACTACGTACATAGGG 58.390 44.000 0.47 0.00 0.00 3.53
1411 1532 6.084925 GCATAGCAGTTACTACGTACATAGG 58.915 44.000 0.47 0.00 0.00 2.57
1412 1533 6.665465 TGCATAGCAGTTACTACGTACATAG 58.335 40.000 0.00 0.00 33.32 2.23
1413 1534 6.622833 TGCATAGCAGTTACTACGTACATA 57.377 37.500 0.00 0.00 33.32 2.29
1414 1535 5.509716 TGCATAGCAGTTACTACGTACAT 57.490 39.130 0.00 0.00 33.32 2.29
1415 1536 4.968812 TGCATAGCAGTTACTACGTACA 57.031 40.909 0.00 0.00 33.32 2.90
1416 1537 7.859377 TCTTAATGCATAGCAGTTACTACGTAC 59.141 37.037 0.00 0.00 43.65 3.67
1417 1538 7.933396 TCTTAATGCATAGCAGTTACTACGTA 58.067 34.615 0.00 0.00 43.65 3.57
1418 1539 6.802608 TCTTAATGCATAGCAGTTACTACGT 58.197 36.000 0.00 0.00 43.65 3.57
1419 1540 7.567771 GCTTCTTAATGCATAGCAGTTACTACG 60.568 40.741 12.50 0.00 43.65 3.51
1420 1541 7.224753 TGCTTCTTAATGCATAGCAGTTACTAC 59.775 37.037 15.45 0.00 43.65 2.73
1421 1542 7.272244 TGCTTCTTAATGCATAGCAGTTACTA 58.728 34.615 15.45 0.00 43.65 1.82
1422 1543 6.115446 TGCTTCTTAATGCATAGCAGTTACT 58.885 36.000 15.45 0.00 43.65 2.24
1423 1544 6.363577 TGCTTCTTAATGCATAGCAGTTAC 57.636 37.500 15.45 0.00 43.65 2.50
1428 1549 2.620115 GCCTGCTTCTTAATGCATAGCA 59.380 45.455 17.75 17.75 44.86 3.49
1429 1550 2.620115 TGCCTGCTTCTTAATGCATAGC 59.380 45.455 10.82 10.82 38.59 2.97
1430 1551 3.004106 GGTGCCTGCTTCTTAATGCATAG 59.996 47.826 0.00 0.00 38.59 2.23
1431 1552 2.951642 GGTGCCTGCTTCTTAATGCATA 59.048 45.455 0.00 0.00 38.59 3.14
1432 1553 1.753073 GGTGCCTGCTTCTTAATGCAT 59.247 47.619 0.00 0.00 38.59 3.96
1433 1554 1.176527 GGTGCCTGCTTCTTAATGCA 58.823 50.000 0.00 0.00 37.63 3.96
1434 1555 1.176527 TGGTGCCTGCTTCTTAATGC 58.823 50.000 0.00 0.00 0.00 3.56
1435 1556 2.557924 TGTTGGTGCCTGCTTCTTAATG 59.442 45.455 0.00 0.00 0.00 1.90
1436 1557 2.875296 TGTTGGTGCCTGCTTCTTAAT 58.125 42.857 0.00 0.00 0.00 1.40
1437 1558 2.356665 TGTTGGTGCCTGCTTCTTAA 57.643 45.000 0.00 0.00 0.00 1.85
1438 1559 2.229792 CTTGTTGGTGCCTGCTTCTTA 58.770 47.619 0.00 0.00 0.00 2.10
1439 1560 1.035139 CTTGTTGGTGCCTGCTTCTT 58.965 50.000 0.00 0.00 0.00 2.52
1440 1561 0.825010 CCTTGTTGGTGCCTGCTTCT 60.825 55.000 0.00 0.00 0.00 2.85
1441 1562 1.662044 CCTTGTTGGTGCCTGCTTC 59.338 57.895 0.00 0.00 0.00 3.86
1442 1563 3.860681 CCTTGTTGGTGCCTGCTT 58.139 55.556 0.00 0.00 0.00 3.91
1460 1581 0.179702 TTGGCCATTTGTGCTTTGCA 59.820 45.000 6.09 0.00 35.60 4.08
1481 1602 3.140325 TGTTTTGGTTTTGGTTTGGCA 57.860 38.095 0.00 0.00 0.00 4.92
1494 1625 6.207691 TGGTTCTCTTCTCTTTTGTTTTGG 57.792 37.500 0.00 0.00 0.00 3.28
1500 1631 5.505173 TGCTTTGGTTCTCTTCTCTTTTG 57.495 39.130 0.00 0.00 0.00 2.44
1507 1638 7.009265 GTGTTTAGTTTTGCTTTGGTTCTCTTC 59.991 37.037 0.00 0.00 0.00 2.87
1515 1646 7.254852 TCTAACTGTGTTTAGTTTTGCTTTGG 58.745 34.615 0.00 0.00 41.01 3.28
1516 1647 7.044052 GCTCTAACTGTGTTTAGTTTTGCTTTG 60.044 37.037 0.00 0.00 41.01 2.77
1517 1648 6.972901 GCTCTAACTGTGTTTAGTTTTGCTTT 59.027 34.615 0.00 0.00 41.01 3.51
1520 1651 5.816919 TGCTCTAACTGTGTTTAGTTTTGC 58.183 37.500 0.00 0.00 41.01 3.68
1532 1668 3.131396 CGTTTTGACCTGCTCTAACTGT 58.869 45.455 0.00 0.00 0.00 3.55
1533 1669 3.131396 ACGTTTTGACCTGCTCTAACTG 58.869 45.455 0.00 0.00 0.00 3.16
1580 1733 4.974591 GCAATAGCAAGACAACCAACTAG 58.025 43.478 0.00 0.00 41.58 2.57
1582 1735 3.923017 GCAATAGCAAGACAACCAACT 57.077 42.857 0.00 0.00 41.58 3.16
1595 1748 2.261215 GCTAGGGGCATGCAATAGC 58.739 57.895 23.58 23.58 41.35 2.97
1617 1770 7.016153 TCAAACCAGACTGTAACCAATCTAT 57.984 36.000 0.93 0.00 0.00 1.98
1631 1784 5.831997 AGCTAACAACAAATCAAACCAGAC 58.168 37.500 0.00 0.00 0.00 3.51
1633 1786 8.816640 ATAAAGCTAACAACAAATCAAACCAG 57.183 30.769 0.00 0.00 0.00 4.00
1645 1798 9.677567 TCAAACAAAGATGATAAAGCTAACAAC 57.322 29.630 0.00 0.00 0.00 3.32
1709 1862 2.483877 GCCAATCAGAATTGTGACGACA 59.516 45.455 7.55 0.00 40.63 4.35
1827 1980 0.109873 GTGACGTTCGACGAGTCCAT 60.110 55.000 12.95 0.00 46.05 3.41
1865 2018 4.586841 AGTATGCTGTAGATCTCCTTGACC 59.413 45.833 0.00 0.00 0.00 4.02
1991 2144 2.743928 CACCTCCCGCTGCTGTTC 60.744 66.667 0.00 0.00 0.00 3.18
2037 2190 1.772156 GGAAGAGGATGGGAGGGGG 60.772 68.421 0.00 0.00 0.00 5.40
2038 2191 0.766288 GAGGAAGAGGATGGGAGGGG 60.766 65.000 0.00 0.00 0.00 4.79
2039 2192 0.766288 GGAGGAAGAGGATGGGAGGG 60.766 65.000 0.00 0.00 0.00 4.30
2040 2193 0.030705 TGGAGGAAGAGGATGGGAGG 60.031 60.000 0.00 0.00 0.00 4.30
2041 2194 2.115337 ATGGAGGAAGAGGATGGGAG 57.885 55.000 0.00 0.00 0.00 4.30
2042 2195 2.594536 AATGGAGGAAGAGGATGGGA 57.405 50.000 0.00 0.00 0.00 4.37
2043 2196 3.677156 AAAATGGAGGAAGAGGATGGG 57.323 47.619 0.00 0.00 0.00 4.00
2044 2197 4.864726 AGAAAAATGGAGGAAGAGGATGG 58.135 43.478 0.00 0.00 0.00 3.51
2045 2198 4.886489 GGAGAAAAATGGAGGAAGAGGATG 59.114 45.833 0.00 0.00 0.00 3.51
2046 2199 4.792972 AGGAGAAAAATGGAGGAAGAGGAT 59.207 41.667 0.00 0.00 0.00 3.24
2047 2200 4.018960 CAGGAGAAAAATGGAGGAAGAGGA 60.019 45.833 0.00 0.00 0.00 3.71
2048 2201 4.268359 CAGGAGAAAAATGGAGGAAGAGG 58.732 47.826 0.00 0.00 0.00 3.69
2049 2202 4.268359 CCAGGAGAAAAATGGAGGAAGAG 58.732 47.826 0.00 0.00 36.09 2.85
2050 2203 3.010584 CCCAGGAGAAAAATGGAGGAAGA 59.989 47.826 0.00 0.00 36.09 2.87
2053 2206 1.640670 CCCCAGGAGAAAAATGGAGGA 59.359 52.381 0.00 0.00 36.09 3.71
2072 2225 5.030295 CACAACGATGCATTTCTTCATACC 58.970 41.667 0.00 0.00 0.00 2.73
2073 2226 5.631026 ACACAACGATGCATTTCTTCATAC 58.369 37.500 0.00 0.00 0.00 2.39
2084 2362 0.606130 ATGGCAGACACAACGATGCA 60.606 50.000 0.00 0.00 40.46 3.96
2085 2363 0.523072 AATGGCAGACACAACGATGC 59.477 50.000 0.00 0.00 37.95 3.91
2093 2371 1.626654 CGACGACCAATGGCAGACAC 61.627 60.000 0.00 0.00 0.00 3.67
2096 2374 0.604073 TAACGACGACCAATGGCAGA 59.396 50.000 0.00 0.00 0.00 4.26
2097 2375 1.327460 CATAACGACGACCAATGGCAG 59.673 52.381 0.00 0.00 0.00 4.85
2100 2378 0.655733 GGCATAACGACGACCAATGG 59.344 55.000 0.00 0.00 0.00 3.16
2105 2383 0.108992 TGTCAGGCATAACGACGACC 60.109 55.000 0.00 0.00 32.17 4.79
2265 2557 3.966543 CCAACCAACCCTCGGCCT 61.967 66.667 0.00 0.00 0.00 5.19
2395 2700 0.956633 AATTGACACAGCAGCCAGTG 59.043 50.000 12.76 12.76 41.40 3.66
2434 2739 1.838073 AAGCGTGGTGTTCTAGGGGG 61.838 60.000 0.00 0.00 0.00 5.40
2435 2740 0.036306 AAAGCGTGGTGTTCTAGGGG 59.964 55.000 0.00 0.00 0.00 4.79
2442 2747 3.275999 AGAACAGTAAAAGCGTGGTGTT 58.724 40.909 0.00 0.00 0.00 3.32
2467 2772 1.739562 GAGGGCAAGCAGACGTGAG 60.740 63.158 0.00 0.00 0.00 3.51
2473 2781 1.216064 ACCATATGAGGGCAAGCAGA 58.784 50.000 3.65 0.00 0.00 4.26
2506 2815 1.868498 CGCGGAGAGTTTTTACAACCA 59.132 47.619 0.00 0.00 0.00 3.67
2516 2825 1.502640 CTCGAGTTCGCGGAGAGTT 59.497 57.895 6.13 0.00 39.60 3.01
2517 2826 3.041627 GCTCGAGTTCGCGGAGAGT 62.042 63.158 15.13 0.00 39.60 3.24
2518 2827 2.277628 GCTCGAGTTCGCGGAGAG 60.278 66.667 15.13 9.36 39.60 3.20
2519 2828 2.746671 AGCTCGAGTTCGCGGAGA 60.747 61.111 15.13 0.00 39.60 3.71
2531 2843 0.930742 GCGTGGATCTAACGAGCTCG 60.931 60.000 33.45 33.45 43.68 5.03
2532 2844 0.595310 GGCGTGGATCTAACGAGCTC 60.595 60.000 20.70 2.73 43.68 4.09
2539 2851 2.620242 GTAAAACCGGCGTGGATCTAA 58.380 47.619 6.01 0.00 42.00 2.10
2541 2853 0.392060 GGTAAAACCGGCGTGGATCT 60.392 55.000 6.01 0.00 42.00 2.75
2542 2854 2.092374 GGTAAAACCGGCGTGGATC 58.908 57.895 6.01 0.00 42.00 3.36
2572 2890 1.129251 CTGCCATTTCAGTGCTACGTG 59.871 52.381 0.00 0.00 0.00 4.49
2573 2891 1.001974 TCTGCCATTTCAGTGCTACGT 59.998 47.619 0.00 0.00 35.63 3.57
2641 3236 1.535687 AGCCCTCGTACCCACACTT 60.536 57.895 0.00 0.00 0.00 3.16
2642 3237 1.982938 GAGCCCTCGTACCCACACT 60.983 63.158 0.00 0.00 0.00 3.55
2657 3281 2.498078 AGGCTACACTTGGTTAGAGAGC 59.502 50.000 0.00 0.00 0.00 4.09
2673 3297 5.208890 TGGCTTTCAGATCTAGTTAGGCTA 58.791 41.667 15.81 0.00 0.00 3.93
2701 3325 3.129988 GCTCCATCTTCAGAAATTGTGGG 59.870 47.826 0.00 0.00 0.00 4.61
2755 3379 1.302366 TTGTCATCCATCGCATGAGC 58.698 50.000 0.00 0.00 30.72 4.26
2772 3396 0.512952 GTGTCGGTACTGCTGCTTTG 59.487 55.000 0.00 0.00 0.00 2.77
2802 3426 6.040166 ACACATCTATTGCCATGATTTTCTCC 59.960 38.462 0.00 0.00 0.00 3.71
2818 3448 1.762957 CTGTTCCGGGGACACATCTAT 59.237 52.381 3.34 0.00 0.00 1.98
2819 3449 1.191535 CTGTTCCGGGGACACATCTA 58.808 55.000 3.34 0.00 0.00 1.98
2841 3471 5.303845 TGGTGAAGATGACTAGATGAGATGG 59.696 44.000 0.00 0.00 0.00 3.51
2933 3565 3.577805 AGGTGCTGTCACTTTTTACCT 57.422 42.857 0.00 0.00 42.72 3.08
2953 3896 8.480501 AGTACTTTTCTACAGTGTTGAGGTAAA 58.519 33.333 0.00 2.18 0.00 2.01


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

AutoCloner maintained by Alex Coulton.