Multiple sequence alignment - TraesCS4D01G213800

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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 TraesCS4D01G213800 chr4D 100.000 3024 0 0 1 3024 366689498 366692521 0.000000e+00 5585.0
1 TraesCS4D01G213800 chr4D 92.937 269 18 1 1 269 75409332 75409599 1.020000e-104 390.0
2 TraesCS4D01G213800 chr4B 89.819 2377 112 52 640 2957 451488856 451491161 0.000000e+00 2929.0
3 TraesCS4D01G213800 chr4B 86.740 543 51 7 2 544 451459251 451459772 4.340000e-163 584.0
4 TraesCS4D01G213800 chr4A 91.743 1526 60 27 644 2139 98560866 98559377 0.000000e+00 2060.0
5 TraesCS4D01G213800 chr4A 87.912 637 40 21 2247 2855 98559204 98558577 0.000000e+00 715.0
6 TraesCS4D01G213800 chr4A 89.333 75 5 1 2953 3024 98558527 98558453 1.150000e-14 91.6
7 TraesCS4D01G213800 chr2D 94.030 268 15 1 2 269 47439108 47439374 3.630000e-109 405.0
8 TraesCS4D01G213800 chr6D 93.657 268 16 1 2 269 302032131 302032397 1.690000e-107 399.0
9 TraesCS4D01G213800 chr6B 93.657 268 15 2 2 269 590442417 590442682 1.690000e-107 399.0
10 TraesCS4D01G213800 chr5A 93.091 275 16 2 2 273 313792878 313793152 1.690000e-107 399.0
11 TraesCS4D01G213800 chr3D 92.565 269 19 1 1 269 410297175 410297442 4.730000e-103 385.0
12 TraesCS4D01G213800 chr3D 92.251 271 20 1 2 272 379728887 379728618 1.700000e-102 383.0
13 TraesCS4D01G213800 chr3A 91.941 273 22 0 2 274 557720586 557720314 1.700000e-102 383.0
14 TraesCS4D01G213800 chr5D 82.043 323 48 7 274 589 487865914 487866233 1.790000e-67 267.0
15 TraesCS4D01G213800 chr5D 76.737 331 57 9 274 587 393607204 393607531 1.860000e-37 167.0
16 TraesCS4D01G213800 chr5D 76.503 183 42 1 397 578 381150609 381150791 6.900000e-17 99.0
17 TraesCS4D01G213800 chr5B 80.793 328 47 9 274 588 537859062 537858738 3.010000e-60 243.0
18 TraesCS4D01G213800 chr5B 83.475 236 31 3 355 589 537839493 537839265 2.360000e-51 213.0
19 TraesCS4D01G213800 chr7D 82.533 229 29 3 357 584 2445105 2444887 1.110000e-44 191.0
20 TraesCS4D01G213800 chr2A 83.621 116 17 2 476 590 92492991 92492877 1.150000e-19 108.0
21 TraesCS4D01G213800 chr1A 100.000 32 0 0 603 634 271435784 271435815 3.260000e-05 60.2


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 TraesCS4D01G213800 chr4D 366689498 366692521 3023 False 5585.000000 5585 100.000000 1 3024 1 chr4D.!!$F2 3023
1 TraesCS4D01G213800 chr4B 451488856 451491161 2305 False 2929.000000 2929 89.819000 640 2957 1 chr4B.!!$F2 2317
2 TraesCS4D01G213800 chr4B 451459251 451459772 521 False 584.000000 584 86.740000 2 544 1 chr4B.!!$F1 542
3 TraesCS4D01G213800 chr4A 98558453 98560866 2413 True 955.533333 2060 89.662667 644 3024 3 chr4A.!!$R1 2380

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
609 610 0.107643 GCAGAGGCTGGGTAATCCTC 59.892 60.0 0.00 0.00 45.11 3.71 F
681 682 0.373716 CTGAACGCCTGCGGATAAAC 59.626 55.0 16.63 1.49 44.69 2.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1477 1490 1.075601 ACAATGCAGGGGAAGAAGGA 58.924 50.0 0.0 0.0 0.0 3.36 R
2670 2837 0.178975 AGTAGAGGCGATGGGAGGAG 60.179 60.0 0.0 0.0 0.0 3.69 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 9.410556 TGTTTTAGGACTATCGTTACACTTAAC 57.589 33.333 0.00 0.00 35.17 2.01
57 58 9.623350 GTTACACTTAACGATATCCTAAGATCC 57.377 37.037 19.17 5.54 33.67 3.36
65 66 4.857588 CGATATCCTAAGATCCGGAAAACG 59.142 45.833 9.01 0.00 36.75 3.60
75 76 1.002659 TCCGGAAAACGTGATCACCAT 59.997 47.619 20.03 5.85 42.24 3.55
80 81 3.252215 GGAAAACGTGATCACCATCAACA 59.748 43.478 20.03 0.00 40.90 3.33
88 89 1.896220 TCACCATCAACACTTGAGCC 58.104 50.000 0.00 0.00 43.98 4.70
92 93 0.798776 CATCAACACTTGAGCCGGTC 59.201 55.000 1.90 0.00 43.98 4.79
132 133 8.723311 CAAGAACCTATTGTTTACCGTTTATCA 58.277 33.333 0.00 0.00 37.29 2.15
149 150 7.341446 CGTTTATCATTTCACACGTGCATATA 58.659 34.615 17.22 1.64 0.00 0.86
156 157 7.748683 TCATTTCACACGTGCATATAAGTTTTC 59.251 33.333 17.22 0.00 0.00 2.29
161 162 6.091577 CACACGTGCATATAAGTTTTCCACTA 59.908 38.462 17.22 0.00 32.94 2.74
188 189 6.364568 TGCATATTACAGGATCATAGCAGT 57.635 37.500 0.00 0.00 0.00 4.40
197 198 7.724490 ACAGGATCATAGCAGTTATAGCATA 57.276 36.000 0.00 0.00 0.00 3.14
271 272 5.957771 TGTCTCTAGGGCATACTTTCAAT 57.042 39.130 0.00 0.00 0.00 2.57
275 276 6.706716 GTCTCTAGGGCATACTTTCAATAACC 59.293 42.308 0.00 0.00 0.00 2.85
276 277 6.385759 TCTCTAGGGCATACTTTCAATAACCA 59.614 38.462 0.00 0.00 0.00 3.67
368 369 1.074471 TAGGGATGGGAGTGAGGGC 60.074 63.158 0.00 0.00 0.00 5.19
371 372 3.866582 GATGGGAGTGAGGGCCGG 61.867 72.222 0.00 0.00 0.00 6.13
431 432 4.986587 CGCCGTCACCGTTGTCGA 62.987 66.667 0.61 0.00 36.51 4.20
434 435 2.732094 CGTCACCGTTGTCGACCC 60.732 66.667 14.12 2.44 36.51 4.46
435 436 2.732094 GTCACCGTTGTCGACCCG 60.732 66.667 14.12 14.90 39.71 5.28
445 446 1.226323 GTCGACCCGTGAGTGATCG 60.226 63.158 3.51 0.00 0.00 3.69
454 455 2.579787 GAGTGATCGGCCACGTCG 60.580 66.667 2.24 0.00 41.67 5.12
471 472 3.708239 CGTCGAAACGCTCTTAGAAAAC 58.292 45.455 0.00 0.00 42.82 2.43
479 480 4.557205 ACGCTCTTAGAAAACGAATCAGT 58.443 39.130 6.08 0.00 0.00 3.41
480 481 4.386049 ACGCTCTTAGAAAACGAATCAGTG 59.614 41.667 6.08 0.00 0.00 3.66
481 482 4.386049 CGCTCTTAGAAAACGAATCAGTGT 59.614 41.667 0.00 0.00 0.00 3.55
482 483 5.107453 CGCTCTTAGAAAACGAATCAGTGTT 60.107 40.000 0.00 0.00 0.00 3.32
483 484 6.564125 CGCTCTTAGAAAACGAATCAGTGTTT 60.564 38.462 0.00 0.00 39.84 2.83
485 486 7.644157 GCTCTTAGAAAACGAATCAGTGTTTTT 59.356 33.333 4.77 0.00 45.47 1.94
486 487 8.835467 TCTTAGAAAACGAATCAGTGTTTTTG 57.165 30.769 4.77 0.00 45.47 2.44
487 488 5.949233 AGAAAACGAATCAGTGTTTTTGC 57.051 34.783 4.77 0.00 45.47 3.68
488 489 4.803613 AGAAAACGAATCAGTGTTTTTGCC 59.196 37.500 4.77 0.00 45.47 4.52
489 490 3.791973 AACGAATCAGTGTTTTTGCCA 57.208 38.095 0.00 0.00 0.00 4.92
490 491 3.078594 ACGAATCAGTGTTTTTGCCAC 57.921 42.857 0.00 0.00 0.00 5.01
499 500 4.244862 AGTGTTTTTGCCACTGTCAAAAG 58.755 39.130 7.26 0.00 42.24 2.27
501 502 5.047660 AGTGTTTTTGCCACTGTCAAAAGTA 60.048 36.000 7.26 0.79 42.24 2.24
529 530 3.520569 GGTGCAAAGTGTCACATTTTGT 58.479 40.909 22.56 0.00 41.14 2.83
530 531 4.677584 GGTGCAAAGTGTCACATTTTGTA 58.322 39.130 22.56 17.48 41.14 2.41
533 534 6.237808 GGTGCAAAGTGTCACATTTTGTAAAG 60.238 38.462 22.56 2.42 41.14 1.85
534 535 6.310224 GTGCAAAGTGTCACATTTTGTAAAGT 59.690 34.615 22.56 0.00 41.14 2.66
535 536 7.486551 GTGCAAAGTGTCACATTTTGTAAAGTA 59.513 33.333 22.56 4.90 41.14 2.24
536 537 8.029522 TGCAAAGTGTCACATTTTGTAAAGTAA 58.970 29.630 22.56 2.90 41.14 2.24
537 538 9.030301 GCAAAGTGTCACATTTTGTAAAGTAAT 57.970 29.630 22.56 0.00 41.14 1.89
539 540 9.528018 AAAGTGTCACATTTTGTAAAGTAATGG 57.472 29.630 5.62 0.00 34.40 3.16
540 541 8.232913 AGTGTCACATTTTGTAAAGTAATGGT 57.767 30.769 5.62 0.00 34.40 3.55
541 542 8.691797 AGTGTCACATTTTGTAAAGTAATGGTT 58.308 29.630 5.62 0.00 34.40 3.67
542 543 9.308318 GTGTCACATTTTGTAAAGTAATGGTTT 57.692 29.630 0.00 0.00 34.40 3.27
543 544 9.877178 TGTCACATTTTGTAAAGTAATGGTTTT 57.123 25.926 0.00 0.00 34.40 2.43
551 552 7.355332 TGTAAAGTAATGGTTTTACGAGAGC 57.645 36.000 0.00 0.00 40.77 4.09
552 553 7.156673 TGTAAAGTAATGGTTTTACGAGAGCT 58.843 34.615 0.00 0.00 40.77 4.09
553 554 6.481954 AAAGTAATGGTTTTACGAGAGCTG 57.518 37.500 0.00 0.00 0.00 4.24
554 555 3.933332 AGTAATGGTTTTACGAGAGCTGC 59.067 43.478 0.00 0.00 0.00 5.25
555 556 1.359848 ATGGTTTTACGAGAGCTGCG 58.640 50.000 0.00 0.00 0.00 5.18
556 557 0.315886 TGGTTTTACGAGAGCTGCGA 59.684 50.000 12.04 0.00 0.00 5.10
557 558 0.714439 GGTTTTACGAGAGCTGCGAC 59.286 55.000 12.04 0.61 0.00 5.19
558 559 0.362512 GTTTTACGAGAGCTGCGACG 59.637 55.000 12.04 12.53 0.00 5.12
559 560 1.342082 TTTTACGAGAGCTGCGACGC 61.342 55.000 14.19 14.19 0.00 5.19
560 561 2.196382 TTTACGAGAGCTGCGACGCT 62.196 55.000 22.08 0.00 44.33 5.07
561 562 1.363885 TTACGAGAGCTGCGACGCTA 61.364 55.000 22.08 6.60 41.08 4.26
562 563 1.363885 TACGAGAGCTGCGACGCTAA 61.364 55.000 22.08 0.00 41.08 3.09
563 564 2.218239 CGAGAGCTGCGACGCTAAC 61.218 63.158 22.08 10.16 41.08 2.34
575 576 3.448076 CGCTAACGTGGTGGTTTTG 57.552 52.632 0.00 0.00 33.53 2.44
576 577 0.658897 CGCTAACGTGGTGGTTTTGT 59.341 50.000 0.00 0.00 33.53 2.83
577 578 1.595976 CGCTAACGTGGTGGTTTTGTG 60.596 52.381 0.00 0.00 33.53 3.33
578 579 1.862411 GCTAACGTGGTGGTTTTGTGC 60.862 52.381 0.00 0.00 0.00 4.57
579 580 1.402259 CTAACGTGGTGGTTTTGTGCA 59.598 47.619 0.00 0.00 0.00 4.57
580 581 0.820871 AACGTGGTGGTTTTGTGCAT 59.179 45.000 0.00 0.00 0.00 3.96
581 582 0.820871 ACGTGGTGGTTTTGTGCATT 59.179 45.000 0.00 0.00 0.00 3.56
582 583 1.205893 ACGTGGTGGTTTTGTGCATTT 59.794 42.857 0.00 0.00 0.00 2.32
583 584 2.275318 CGTGGTGGTTTTGTGCATTTT 58.725 42.857 0.00 0.00 0.00 1.82
584 585 3.119101 ACGTGGTGGTTTTGTGCATTTTA 60.119 39.130 0.00 0.00 0.00 1.52
585 586 3.244111 CGTGGTGGTTTTGTGCATTTTAC 59.756 43.478 0.00 0.00 0.00 2.01
586 587 4.438148 GTGGTGGTTTTGTGCATTTTACT 58.562 39.130 0.00 0.00 0.00 2.24
587 588 4.506288 GTGGTGGTTTTGTGCATTTTACTC 59.494 41.667 0.00 0.00 0.00 2.59
588 589 4.160439 TGGTGGTTTTGTGCATTTTACTCA 59.840 37.500 0.00 0.00 0.00 3.41
589 590 5.163364 TGGTGGTTTTGTGCATTTTACTCAT 60.163 36.000 0.00 0.00 0.00 2.90
590 591 5.177327 GGTGGTTTTGTGCATTTTACTCATG 59.823 40.000 0.00 0.00 0.00 3.07
591 592 4.749099 TGGTTTTGTGCATTTTACTCATGC 59.251 37.500 0.00 0.00 46.25 4.06
602 603 2.996395 CTCATGCAGAGGCTGGGT 59.004 61.111 0.00 0.00 40.84 4.51
603 604 2.215191 CTCATGCAGAGGCTGGGTA 58.785 57.895 0.00 0.00 40.84 3.69
604 605 0.543277 CTCATGCAGAGGCTGGGTAA 59.457 55.000 0.00 0.00 40.84 2.85
605 606 1.142465 CTCATGCAGAGGCTGGGTAAT 59.858 52.381 0.00 0.00 40.84 1.89
606 607 1.141657 TCATGCAGAGGCTGGGTAATC 59.858 52.381 0.00 0.00 41.91 1.75
607 608 0.475906 ATGCAGAGGCTGGGTAATCC 59.524 55.000 0.00 0.00 41.91 3.01
608 609 0.621571 TGCAGAGGCTGGGTAATCCT 60.622 55.000 0.00 0.00 41.91 3.24
609 610 0.107643 GCAGAGGCTGGGTAATCCTC 59.892 60.000 0.00 0.00 45.11 3.71
610 611 0.761802 CAGAGGCTGGGTAATCCTCC 59.238 60.000 0.00 0.00 45.73 4.30
611 612 0.644937 AGAGGCTGGGTAATCCTCCT 59.355 55.000 0.00 0.00 45.73 3.69
612 613 1.010170 AGAGGCTGGGTAATCCTCCTT 59.990 52.381 0.00 0.00 45.73 3.36
613 614 1.847088 GAGGCTGGGTAATCCTCCTTT 59.153 52.381 0.00 0.00 40.29 3.11
614 615 2.242452 GAGGCTGGGTAATCCTCCTTTT 59.758 50.000 0.00 0.00 40.29 2.27
615 616 2.242452 AGGCTGGGTAATCCTCCTTTTC 59.758 50.000 0.00 0.00 36.34 2.29
616 617 2.242452 GGCTGGGTAATCCTCCTTTTCT 59.758 50.000 0.00 0.00 36.20 2.52
617 618 3.458487 GGCTGGGTAATCCTCCTTTTCTA 59.542 47.826 0.00 0.00 36.20 2.10
618 619 4.079958 GGCTGGGTAATCCTCCTTTTCTAA 60.080 45.833 0.00 0.00 36.20 2.10
619 620 5.399152 GGCTGGGTAATCCTCCTTTTCTAAT 60.399 44.000 0.00 0.00 36.20 1.73
620 621 6.183361 GGCTGGGTAATCCTCCTTTTCTAATA 60.183 42.308 0.00 0.00 36.20 0.98
621 622 7.287810 GCTGGGTAATCCTCCTTTTCTAATAA 58.712 38.462 0.00 0.00 36.20 1.40
622 623 7.778382 GCTGGGTAATCCTCCTTTTCTAATAAA 59.222 37.037 0.00 0.00 36.20 1.40
623 624 9.695155 CTGGGTAATCCTCCTTTTCTAATAAAA 57.305 33.333 0.00 0.00 36.20 1.52
681 682 0.373716 CTGAACGCCTGCGGATAAAC 59.626 55.000 16.63 1.49 44.69 2.01
682 683 1.022451 TGAACGCCTGCGGATAAACC 61.022 55.000 16.63 0.00 44.69 3.27
683 684 1.003112 AACGCCTGCGGATAAACCA 60.003 52.632 16.63 0.00 44.69 3.67
684 685 1.303091 AACGCCTGCGGATAAACCAC 61.303 55.000 16.63 0.00 44.69 4.16
685 686 2.808958 CGCCTGCGGATAAACCACG 61.809 63.158 3.07 0.00 38.90 4.94
686 687 2.469516 GCCTGCGGATAAACCACGG 61.470 63.158 0.00 0.00 38.90 4.94
762 769 4.135153 CCTGGCCTCTCGTCCGTG 62.135 72.222 3.32 0.00 0.00 4.94
763 770 4.135153 CTGGCCTCTCGTCCGTGG 62.135 72.222 3.32 0.00 0.00 4.94
764 771 4.988716 TGGCCTCTCGTCCGTGGT 62.989 66.667 3.32 0.00 0.00 4.16
765 772 4.131088 GGCCTCTCGTCCGTGGTC 62.131 72.222 0.00 0.00 0.00 4.02
766 773 4.131088 GCCTCTCGTCCGTGGTCC 62.131 72.222 0.00 0.00 0.00 4.46
767 774 3.812019 CCTCTCGTCCGTGGTCCG 61.812 72.222 0.00 0.00 0.00 4.79
768 775 3.054503 CTCTCGTCCGTGGTCCGT 61.055 66.667 1.88 0.00 33.66 4.69
779 786 3.374318 TGGTCCGTCCATCTTCTCA 57.626 52.632 0.00 0.00 41.93 3.27
840 847 3.246226 CGCGGATATTTTCTCCTCACAAG 59.754 47.826 0.00 0.00 0.00 3.16
977 990 1.398739 CCGCCGCATAACAATACACAA 59.601 47.619 0.00 0.00 0.00 3.33
982 995 3.412654 CGCATAACAATACACAACACCG 58.587 45.455 0.00 0.00 0.00 4.94
983 996 3.123790 CGCATAACAATACACAACACCGA 59.876 43.478 0.00 0.00 0.00 4.69
984 997 4.647964 GCATAACAATACACAACACCGAG 58.352 43.478 0.00 0.00 0.00 4.63
1270 1283 2.266055 GAAGCCCACTCCGAGGTG 59.734 66.667 0.00 0.00 37.00 4.00
1310 1323 4.282449 TCCTGTTCATCAAAACCTCTCGTA 59.718 41.667 0.00 0.00 0.00 3.43
1316 1329 6.769134 TCATCAAAACCTCTCGTAGATACA 57.231 37.500 0.00 0.00 33.89 2.29
1474 1487 1.071299 AAGCAGCATCACACGGTCA 59.929 52.632 0.00 0.00 0.00 4.02
1477 1490 1.230635 GCAGCATCACACGGTCACTT 61.231 55.000 0.00 0.00 0.00 3.16
1487 1500 0.685660 ACGGTCACTTCCTTCTTCCC 59.314 55.000 0.00 0.00 0.00 3.97
1593 1609 1.746615 CATCAAGGTGGACAGGCCG 60.747 63.158 0.00 0.00 40.66 6.13
1725 1742 1.044611 GACAGATACTGCCCCTCTCC 58.955 60.000 0.00 0.00 34.37 3.71
1847 1872 1.819632 CCGGGCAATGGTCTACAGC 60.820 63.158 0.00 0.00 0.00 4.40
1849 1874 1.302949 GGGCAATGGTCTACAGCCA 59.697 57.895 0.00 0.00 41.06 4.75
1853 1878 2.094675 GCAATGGTCTACAGCCAACAT 58.905 47.619 0.00 0.00 39.72 2.71
1855 1880 3.346315 CAATGGTCTACAGCCAACATCA 58.654 45.455 0.00 0.00 39.72 3.07
1856 1881 3.939740 ATGGTCTACAGCCAACATCAT 57.060 42.857 0.00 0.00 39.72 2.45
1886 1916 0.534203 ATGCGTGTGACTTCCGGTTT 60.534 50.000 0.00 0.00 0.00 3.27
1977 2022 1.208535 ACTTGTCAAACTCGTGGGTCA 59.791 47.619 0.00 0.00 0.00 4.02
1986 2031 1.144093 ACTCGTGGGTCATTTTGGGAA 59.856 47.619 0.00 0.00 0.00 3.97
2009 2054 3.251729 CCTGTGTTGTGGAACTGAATGAG 59.748 47.826 0.00 0.00 38.04 2.90
2068 2114 1.000359 AACTGCCCCCATACCAAGC 60.000 57.895 0.00 0.00 0.00 4.01
2079 2125 3.691609 CCCATACCAAGCAGAAGAGAAAC 59.308 47.826 0.00 0.00 0.00 2.78
2080 2126 3.691609 CCATACCAAGCAGAAGAGAAACC 59.308 47.826 0.00 0.00 0.00 3.27
2081 2127 4.326826 CATACCAAGCAGAAGAGAAACCA 58.673 43.478 0.00 0.00 0.00 3.67
2082 2128 3.515602 ACCAAGCAGAAGAGAAACCAT 57.484 42.857 0.00 0.00 0.00 3.55
2083 2129 4.640771 ACCAAGCAGAAGAGAAACCATA 57.359 40.909 0.00 0.00 0.00 2.74
2084 2130 4.583871 ACCAAGCAGAAGAGAAACCATAG 58.416 43.478 0.00 0.00 0.00 2.23
2085 2131 3.944015 CCAAGCAGAAGAGAAACCATAGG 59.056 47.826 0.00 0.00 0.00 2.57
2086 2132 4.323792 CCAAGCAGAAGAGAAACCATAGGA 60.324 45.833 0.00 0.00 0.00 2.94
2087 2133 5.435291 CAAGCAGAAGAGAAACCATAGGAT 58.565 41.667 0.00 0.00 0.00 3.24
2088 2134 6.408548 CCAAGCAGAAGAGAAACCATAGGATA 60.409 42.308 0.00 0.00 0.00 2.59
2089 2135 6.418057 AGCAGAAGAGAAACCATAGGATAG 57.582 41.667 0.00 0.00 0.00 2.08
2090 2136 5.306678 AGCAGAAGAGAAACCATAGGATAGG 59.693 44.000 0.00 0.00 0.00 2.57
2091 2137 5.305644 GCAGAAGAGAAACCATAGGATAGGA 59.694 44.000 0.00 0.00 0.00 2.94
2092 2138 6.013812 GCAGAAGAGAAACCATAGGATAGGAT 60.014 42.308 0.00 0.00 0.00 3.24
2093 2139 7.474079 GCAGAAGAGAAACCATAGGATAGGATT 60.474 40.741 0.00 0.00 0.00 3.01
2094 2140 9.094578 CAGAAGAGAAACCATAGGATAGGATTA 57.905 37.037 0.00 0.00 0.00 1.75
2139 2190 2.101582 GAGAGGCGAAGACACATGGTAT 59.898 50.000 0.00 0.00 39.87 2.73
2160 2295 7.491372 TGGTATTATTTTTCTGTGCGTAGAGAG 59.509 37.037 0.00 0.00 0.00 3.20
2164 2304 9.988815 ATTATTTTTCTGTGCGTAGAGAGATAT 57.011 29.630 0.00 0.54 0.00 1.63
2190 2330 3.684788 GCAAGTACACATACACCAGGAAG 59.315 47.826 0.00 0.00 33.30 3.46
2199 2339 2.016905 ACACCAGGAAGCTCAGTAGT 57.983 50.000 0.00 0.00 0.00 2.73
2200 2340 3.170991 ACACCAGGAAGCTCAGTAGTA 57.829 47.619 0.00 0.00 0.00 1.82
2201 2341 3.093057 ACACCAGGAAGCTCAGTAGTAG 58.907 50.000 0.00 0.00 0.00 2.57
2203 2343 2.043252 ACCAGGAAGCTCAGTAGTAGGT 59.957 50.000 0.00 0.00 0.00 3.08
2204 2344 3.268856 ACCAGGAAGCTCAGTAGTAGGTA 59.731 47.826 0.00 0.00 0.00 3.08
2206 2346 4.710375 CCAGGAAGCTCAGTAGTAGGTAAA 59.290 45.833 0.00 0.00 0.00 2.01
2210 2363 7.285858 CAGGAAGCTCAGTAGTAGGTAAATACT 59.714 40.741 0.00 0.00 39.35 2.12
2221 2374 4.910458 AGGTAAATACTCCTGCAAGTGT 57.090 40.909 1.14 0.00 32.29 3.55
2222 2375 5.242795 AGGTAAATACTCCTGCAAGTGTT 57.757 39.130 1.14 0.00 32.67 3.32
2223 2376 5.631119 AGGTAAATACTCCTGCAAGTGTTT 58.369 37.500 15.00 15.00 41.57 2.83
2224 2377 6.068670 AGGTAAATACTCCTGCAAGTGTTTT 58.931 36.000 15.62 10.71 40.01 2.43
2225 2378 6.549736 AGGTAAATACTCCTGCAAGTGTTTTT 59.450 34.615 15.62 12.52 40.01 1.94
2243 2396 3.721868 TCCCCGAGGAATCCACAC 58.278 61.111 0.61 0.00 40.08 3.82
2244 2397 1.993391 TCCCCGAGGAATCCACACC 60.993 63.158 0.61 0.00 40.08 4.16
2245 2398 1.995626 CCCCGAGGAATCCACACCT 60.996 63.158 0.61 0.00 39.41 4.00
2246 2399 1.221840 CCCGAGGAATCCACACCTG 59.778 63.158 0.61 0.00 36.57 4.00
2247 2400 1.450312 CCGAGGAATCCACACCTGC 60.450 63.158 0.61 0.00 36.57 4.85
2248 2401 1.811266 CGAGGAATCCACACCTGCG 60.811 63.158 0.61 0.00 36.57 5.18
2249 2402 1.450312 GAGGAATCCACACCTGCGG 60.450 63.158 0.61 0.00 36.57 5.69
2250 2403 1.899437 GAGGAATCCACACCTGCGGA 61.899 60.000 0.61 0.00 36.57 5.54
2251 2404 1.002624 GGAATCCACACCTGCGGAA 60.003 57.895 0.00 0.00 34.22 4.30
2252 2405 0.394352 GGAATCCACACCTGCGGAAT 60.394 55.000 0.00 0.00 34.22 3.01
2253 2406 1.463674 GAATCCACACCTGCGGAATT 58.536 50.000 0.00 0.00 34.22 2.17
2254 2407 1.818674 GAATCCACACCTGCGGAATTT 59.181 47.619 0.00 0.00 34.22 1.82
2255 2408 1.923356 ATCCACACCTGCGGAATTTT 58.077 45.000 0.00 0.00 34.22 1.82
2256 2409 1.698506 TCCACACCTGCGGAATTTTT 58.301 45.000 0.00 0.00 0.00 1.94
2257 2410 2.865079 TCCACACCTGCGGAATTTTTA 58.135 42.857 0.00 0.00 0.00 1.52
2258 2411 2.554893 TCCACACCTGCGGAATTTTTAC 59.445 45.455 0.00 0.00 0.00 2.01
2259 2412 2.556622 CCACACCTGCGGAATTTTTACT 59.443 45.455 0.00 0.00 0.00 2.24
2260 2413 3.564511 CACACCTGCGGAATTTTTACTG 58.435 45.455 0.00 0.00 0.00 2.74
2285 2438 1.902938 TTGATTGATGTTGGCACGGA 58.097 45.000 0.00 0.00 0.00 4.69
2660 2827 2.285144 TCCCGAACTCCTTCCCCC 60.285 66.667 0.00 0.00 0.00 5.40
2679 2846 4.888325 CGCCCCTCCTCCTCCCAT 62.888 72.222 0.00 0.00 0.00 4.00
2680 2847 2.851588 GCCCCTCCTCCTCCCATC 60.852 72.222 0.00 0.00 0.00 3.51
2681 2848 2.525381 CCCCTCCTCCTCCCATCG 60.525 72.222 0.00 0.00 0.00 3.84
2682 2849 3.237741 CCCTCCTCCTCCCATCGC 61.238 72.222 0.00 0.00 0.00 4.58
2683 2850 3.237741 CCTCCTCCTCCCATCGCC 61.238 72.222 0.00 0.00 0.00 5.54
2684 2851 2.123077 CTCCTCCTCCCATCGCCT 60.123 66.667 0.00 0.00 0.00 5.52
2685 2852 2.123251 TCCTCCTCCCATCGCCTC 60.123 66.667 0.00 0.00 0.00 4.70
2686 2853 2.123077 CCTCCTCCCATCGCCTCT 60.123 66.667 0.00 0.00 0.00 3.69
2687 2854 1.153989 CCTCCTCCCATCGCCTCTA 59.846 63.158 0.00 0.00 0.00 2.43
2688 2855 1.182385 CCTCCTCCCATCGCCTCTAC 61.182 65.000 0.00 0.00 0.00 2.59
2689 2856 0.178975 CTCCTCCCATCGCCTCTACT 60.179 60.000 0.00 0.00 0.00 2.57
2690 2857 1.074084 CTCCTCCCATCGCCTCTACTA 59.926 57.143 0.00 0.00 0.00 1.82
2702 2869 2.213499 CCTCTACTATTTGCTTGGGCG 58.787 52.381 0.00 0.00 42.25 6.13
2704 2871 1.134220 TCTACTATTTGCTTGGGCGGG 60.134 52.381 0.00 0.00 42.25 6.13
2705 2872 0.750182 TACTATTTGCTTGGGCGGGC 60.750 55.000 0.00 0.00 42.25 6.13
2706 2873 1.754234 CTATTTGCTTGGGCGGGCT 60.754 57.895 0.26 0.00 42.25 5.19
2707 2874 2.008268 CTATTTGCTTGGGCGGGCTG 62.008 60.000 0.26 0.00 42.25 4.85
2739 2953 0.250234 TCTCTGCGGGGTTCAAGATG 59.750 55.000 0.00 0.00 0.00 2.90
2741 2955 0.911769 TCTGCGGGGTTCAAGATGAT 59.088 50.000 0.00 0.00 0.00 2.45
2742 2956 2.103094 CTCTGCGGGGTTCAAGATGATA 59.897 50.000 0.00 0.00 0.00 2.15
2744 2958 2.874701 CTGCGGGGTTCAAGATGATAAG 59.125 50.000 0.00 0.00 0.00 1.73
2745 2959 2.222027 GCGGGGTTCAAGATGATAAGG 58.778 52.381 0.00 0.00 0.00 2.69
2746 2960 2.158813 GCGGGGTTCAAGATGATAAGGA 60.159 50.000 0.00 0.00 0.00 3.36
2747 2961 3.733337 CGGGGTTCAAGATGATAAGGAG 58.267 50.000 0.00 0.00 0.00 3.69
2748 2962 3.495100 CGGGGTTCAAGATGATAAGGAGG 60.495 52.174 0.00 0.00 0.00 4.30
2749 2963 3.481453 GGGTTCAAGATGATAAGGAGGC 58.519 50.000 0.00 0.00 0.00 4.70
2750 2964 3.137360 GGGTTCAAGATGATAAGGAGGCT 59.863 47.826 0.00 0.00 0.00 4.58
2840 3054 2.456989 CGGTGAATCTGATGCATTTGC 58.543 47.619 0.00 0.00 42.50 3.68
2849 3063 0.099436 GATGCATTTGCCGGTCTGAC 59.901 55.000 1.90 0.00 41.18 3.51
2860 3085 1.821241 CGGTCTGACGCACAACACAG 61.821 60.000 1.07 0.00 0.00 3.66
2866 3091 2.863740 CTGACGCACAACACAGTTTAGA 59.136 45.455 0.00 0.00 0.00 2.10
2923 3156 6.970640 AGAGGGATATGGATGAGTGGATTAAT 59.029 38.462 0.00 0.00 0.00 1.40
2933 3166 5.581126 TGAGTGGATTAATCAAACATGGC 57.419 39.130 17.07 6.73 29.08 4.40
2940 3173 5.335191 GGATTAATCAAACATGGCGATCTCC 60.335 44.000 17.07 0.00 0.00 3.71
2944 3178 1.091771 AAACATGGCGATCTCCTGCG 61.092 55.000 2.88 0.00 0.00 5.18
2958 3192 4.435436 TGCGCGCTGGTACCTCAG 62.435 66.667 33.29 3.98 37.79 3.35
3009 3246 3.386078 TGAGCCAAACTATTGCCAACAAA 59.614 39.130 0.00 0.00 39.77 2.83
3015 3252 6.426633 GCCAAACTATTGCCAACAAATAACTT 59.573 34.615 0.00 0.00 39.77 2.66
3017 3254 9.139174 CCAAACTATTGCCAACAAATAACTTAG 57.861 33.333 0.00 0.00 39.77 2.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.339466 GTCCTAAAACAACATTGAGGGTATGAT 59.661 37.037 0.00 0.00 0.00 2.45
42 43 4.857588 CGTTTTCCGGATCTTAGGATATCG 59.142 45.833 4.15 8.17 36.28 2.92
53 54 1.664151 GGTGATCACGTTTTCCGGATC 59.336 52.381 19.33 0.00 42.24 3.36
56 57 1.396996 GATGGTGATCACGTTTTCCGG 59.603 52.381 19.33 0.00 42.24 5.14
57 58 2.073056 TGATGGTGATCACGTTTTCCG 58.927 47.619 19.33 0.00 44.03 4.30
65 66 3.120060 GCTCAAGTGTTGATGGTGATCAC 60.120 47.826 17.91 17.91 38.38 3.06
75 76 0.468226 AAGACCGGCTCAAGTGTTGA 59.532 50.000 0.00 0.00 38.17 3.18
80 81 1.187087 CCTCTAAGACCGGCTCAAGT 58.813 55.000 0.00 0.00 0.00 3.16
92 93 3.835395 AGGTTCTTGGTCTCACCTCTAAG 59.165 47.826 0.00 0.00 39.58 2.18
106 107 8.723311 TGATAAACGGTAAACAATAGGTTCTTG 58.277 33.333 0.00 0.00 39.29 3.02
108 109 9.457436 AATGATAAACGGTAAACAATAGGTTCT 57.543 29.630 0.00 0.00 39.29 3.01
132 133 7.027161 GGAAAACTTATATGCACGTGTGAAAT 58.973 34.615 18.38 8.68 0.00 2.17
156 157 8.394971 TGATCCTGTAATATGCAATTTAGTGG 57.605 34.615 0.00 0.00 0.00 4.00
161 162 8.640063 TGCTATGATCCTGTAATATGCAATTT 57.360 30.769 0.00 0.00 0.00 1.82
173 174 6.617782 ATGCTATAACTGCTATGATCCTGT 57.382 37.500 0.00 0.00 0.00 4.00
174 175 9.440773 TTTTATGCTATAACTGCTATGATCCTG 57.559 33.333 0.00 0.00 0.00 3.86
250 251 6.706716 GGTTATTGAAAGTATGCCCTAGAGAC 59.293 42.308 0.00 0.00 0.00 3.36
251 252 6.385759 TGGTTATTGAAAGTATGCCCTAGAGA 59.614 38.462 0.00 0.00 0.00 3.10
252 253 6.483640 GTGGTTATTGAAAGTATGCCCTAGAG 59.516 42.308 0.00 0.00 0.00 2.43
253 254 6.157994 AGTGGTTATTGAAAGTATGCCCTAGA 59.842 38.462 0.00 0.00 0.00 2.43
254 255 6.357367 AGTGGTTATTGAAAGTATGCCCTAG 58.643 40.000 0.00 0.00 0.00 3.02
255 256 6.321821 AGTGGTTATTGAAAGTATGCCCTA 57.678 37.500 0.00 0.00 0.00 3.53
259 260 5.193679 AGGGAGTGGTTATTGAAAGTATGC 58.806 41.667 0.00 0.00 0.00 3.14
264 265 2.678336 GCGAGGGAGTGGTTATTGAAAG 59.322 50.000 0.00 0.00 0.00 2.62
267 268 0.539986 GGCGAGGGAGTGGTTATTGA 59.460 55.000 0.00 0.00 0.00 2.57
271 272 1.380785 ATCGGCGAGGGAGTGGTTA 60.381 57.895 17.22 0.00 0.00 2.85
275 276 2.427540 GATCCATCGGCGAGGGAGTG 62.428 65.000 40.24 22.55 45.75 3.51
276 277 2.123251 ATCCATCGGCGAGGGAGT 60.123 61.111 40.24 27.64 45.75 3.85
321 322 2.892914 CTCTCCTCTCTCGCGCGA 60.893 66.667 32.60 32.60 0.00 5.87
326 327 4.600692 TGTCTATCTCTCTCCTCTCTCG 57.399 50.000 0.00 0.00 0.00 4.04
371 372 2.435938 TGTCCGAAGCGATTGGGC 60.436 61.111 9.85 4.62 37.75 5.36
383 384 2.457778 CCGTTAATGGCCGTGTCCG 61.458 63.158 0.00 0.33 0.00 4.79
402 403 4.430765 ACGGCGAGGCACTAACGG 62.431 66.667 16.62 0.00 41.55 4.44
404 405 2.260434 TGACGGCGAGGCACTAAC 59.740 61.111 16.62 0.00 41.55 2.34
434 435 2.880879 CGTGGCCGATCACTCACG 60.881 66.667 14.25 14.25 44.98 4.35
435 436 1.805945 GACGTGGCCGATCACTCAC 60.806 63.158 0.00 0.00 37.88 3.51
445 446 3.774702 GAGCGTTTCGACGTGGCC 61.775 66.667 0.00 0.00 35.26 5.36
454 455 5.912528 TGATTCGTTTTCTAAGAGCGTTTC 58.087 37.500 0.00 0.00 0.00 2.78
464 465 5.974751 GGCAAAAACACTGATTCGTTTTCTA 59.025 36.000 0.00 0.00 42.83 2.10
471 472 3.354089 AGTGGCAAAAACACTGATTCG 57.646 42.857 0.00 0.00 46.67 3.34
479 480 4.264460 ACTTTTGACAGTGGCAAAAACA 57.736 36.364 31.28 14.83 42.59 2.83
480 481 5.810074 ACATACTTTTGACAGTGGCAAAAAC 59.190 36.000 31.28 0.00 42.59 2.43
481 482 5.971763 ACATACTTTTGACAGTGGCAAAAA 58.028 33.333 31.28 21.16 42.59 1.94
482 483 5.587289 GACATACTTTTGACAGTGGCAAAA 58.413 37.500 30.19 30.19 41.42 2.44
483 484 4.260990 CGACATACTTTTGACAGTGGCAAA 60.261 41.667 20.42 20.42 33.76 3.68
484 485 3.249799 CGACATACTTTTGACAGTGGCAA 59.750 43.478 7.51 7.51 0.00 4.52
485 486 2.805671 CGACATACTTTTGACAGTGGCA 59.194 45.455 0.00 0.00 0.00 4.92
486 487 2.412847 GCGACATACTTTTGACAGTGGC 60.413 50.000 0.00 0.00 0.00 5.01
487 488 2.159841 CGCGACATACTTTTGACAGTGG 60.160 50.000 0.00 0.00 0.00 4.00
488 489 2.159841 CCGCGACATACTTTTGACAGTG 60.160 50.000 8.23 0.00 0.00 3.66
489 490 2.066262 CCGCGACATACTTTTGACAGT 58.934 47.619 8.23 0.00 0.00 3.55
490 491 2.066262 ACCGCGACATACTTTTGACAG 58.934 47.619 8.23 0.00 0.00 3.51
494 495 0.515127 TGCACCGCGACATACTTTTG 59.485 50.000 8.23 0.00 0.00 2.44
499 500 0.179225 CACTTTGCACCGCGACATAC 60.179 55.000 8.23 0.00 0.00 2.39
501 502 1.841663 GACACTTTGCACCGCGACAT 61.842 55.000 8.23 0.00 0.00 3.06
529 530 6.091713 GCAGCTCTCGTAAAACCATTACTTTA 59.908 38.462 0.00 0.00 0.00 1.85
530 531 5.106673 GCAGCTCTCGTAAAACCATTACTTT 60.107 40.000 0.00 0.00 0.00 2.66
533 534 3.241995 CGCAGCTCTCGTAAAACCATTAC 60.242 47.826 0.00 0.00 0.00 1.89
534 535 2.927477 CGCAGCTCTCGTAAAACCATTA 59.073 45.455 0.00 0.00 0.00 1.90
535 536 1.732259 CGCAGCTCTCGTAAAACCATT 59.268 47.619 0.00 0.00 0.00 3.16
536 537 1.067142 TCGCAGCTCTCGTAAAACCAT 60.067 47.619 5.01 0.00 0.00 3.55
537 538 0.315886 TCGCAGCTCTCGTAAAACCA 59.684 50.000 5.01 0.00 0.00 3.67
538 539 0.714439 GTCGCAGCTCTCGTAAAACC 59.286 55.000 5.01 0.00 0.00 3.27
539 540 0.362512 CGTCGCAGCTCTCGTAAAAC 59.637 55.000 5.01 0.00 0.00 2.43
540 541 1.342082 GCGTCGCAGCTCTCGTAAAA 61.342 55.000 13.44 0.00 0.00 1.52
541 542 1.800315 GCGTCGCAGCTCTCGTAAA 60.800 57.895 13.44 0.00 0.00 2.01
542 543 1.363885 TAGCGTCGCAGCTCTCGTAA 61.364 55.000 21.09 0.00 45.67 3.18
543 544 1.363885 TTAGCGTCGCAGCTCTCGTA 61.364 55.000 21.09 0.00 45.67 3.43
544 545 2.687805 TTAGCGTCGCAGCTCTCGT 61.688 57.895 21.09 0.00 45.67 4.18
545 546 2.100410 TTAGCGTCGCAGCTCTCG 59.900 61.111 21.09 0.00 45.67 4.04
546 547 2.218239 CGTTAGCGTCGCAGCTCTC 61.218 63.158 21.09 2.70 45.67 3.20
547 548 2.202492 CGTTAGCGTCGCAGCTCT 60.202 61.111 21.09 0.00 45.67 4.09
557 558 0.658897 ACAAAACCACCACGTTAGCG 59.341 50.000 0.00 0.00 44.93 4.26
558 559 1.862411 GCACAAAACCACCACGTTAGC 60.862 52.381 0.00 0.00 0.00 3.09
559 560 1.402259 TGCACAAAACCACCACGTTAG 59.598 47.619 0.00 0.00 0.00 2.34
560 561 1.460504 TGCACAAAACCACCACGTTA 58.539 45.000 0.00 0.00 0.00 3.18
561 562 0.820871 ATGCACAAAACCACCACGTT 59.179 45.000 0.00 0.00 0.00 3.99
562 563 0.820871 AATGCACAAAACCACCACGT 59.179 45.000 0.00 0.00 0.00 4.49
563 564 1.933247 AAATGCACAAAACCACCACG 58.067 45.000 0.00 0.00 0.00 4.94
578 579 3.066342 CCAGCCTCTGCATGAGTAAAATG 59.934 47.826 0.00 0.00 41.11 2.32
579 580 3.285484 CCAGCCTCTGCATGAGTAAAAT 58.715 45.455 0.00 0.00 41.11 1.82
580 581 2.618816 CCCAGCCTCTGCATGAGTAAAA 60.619 50.000 0.00 0.00 41.11 1.52
581 582 1.065199 CCCAGCCTCTGCATGAGTAAA 60.065 52.381 0.00 0.00 41.11 2.01
582 583 0.543277 CCCAGCCTCTGCATGAGTAA 59.457 55.000 0.00 0.00 41.11 2.24
583 584 0.618680 ACCCAGCCTCTGCATGAGTA 60.619 55.000 0.00 0.00 41.11 2.59
584 585 0.618680 TACCCAGCCTCTGCATGAGT 60.619 55.000 0.00 0.00 41.11 3.41
585 586 0.543277 TTACCCAGCCTCTGCATGAG 59.457 55.000 0.00 6.28 41.13 2.90
586 587 1.141657 GATTACCCAGCCTCTGCATGA 59.858 52.381 0.00 0.00 41.13 3.07
587 588 1.602311 GATTACCCAGCCTCTGCATG 58.398 55.000 0.00 0.00 41.13 4.06
588 589 0.475906 GGATTACCCAGCCTCTGCAT 59.524 55.000 0.00 0.00 41.13 3.96
589 590 0.621571 AGGATTACCCAGCCTCTGCA 60.622 55.000 0.00 0.00 37.04 4.41
590 591 0.107643 GAGGATTACCCAGCCTCTGC 59.892 60.000 0.00 0.00 43.79 4.26
591 592 0.761802 GGAGGATTACCCAGCCTCTG 59.238 60.000 6.13 0.00 45.87 3.35
592 593 0.644937 AGGAGGATTACCCAGCCTCT 59.355 55.000 6.13 0.00 45.87 3.69
593 594 1.512735 AAGGAGGATTACCCAGCCTC 58.487 55.000 0.00 0.00 45.88 4.70
594 595 1.987080 AAAGGAGGATTACCCAGCCT 58.013 50.000 0.00 0.00 41.84 4.58
595 596 2.242452 AGAAAAGGAGGATTACCCAGCC 59.758 50.000 0.00 0.00 37.41 4.85
596 597 3.653835 AGAAAAGGAGGATTACCCAGC 57.346 47.619 0.00 0.00 37.41 4.85
597 598 9.695155 TTTTATTAGAAAAGGAGGATTACCCAG 57.305 33.333 0.00 0.00 37.41 4.45
617 618 9.674068 ATGCGTGGGGTTTATTTTATTTTTATT 57.326 25.926 0.00 0.00 0.00 1.40
618 619 9.674068 AATGCGTGGGGTTTATTTTATTTTTAT 57.326 25.926 0.00 0.00 0.00 1.40
619 620 9.503399 AAATGCGTGGGGTTTATTTTATTTTTA 57.497 25.926 0.00 0.00 0.00 1.52
620 621 7.987750 AATGCGTGGGGTTTATTTTATTTTT 57.012 28.000 0.00 0.00 0.00 1.94
621 622 7.661847 TCAAATGCGTGGGGTTTATTTTATTTT 59.338 29.630 0.00 0.00 0.00 1.82
622 623 7.162082 TCAAATGCGTGGGGTTTATTTTATTT 58.838 30.769 0.00 0.00 0.00 1.40
623 624 6.702329 TCAAATGCGTGGGGTTTATTTTATT 58.298 32.000 0.00 0.00 0.00 1.40
624 625 6.287589 TCAAATGCGTGGGGTTTATTTTAT 57.712 33.333 0.00 0.00 0.00 1.40
625 626 5.715070 CTCAAATGCGTGGGGTTTATTTTA 58.285 37.500 0.00 0.00 0.00 1.52
626 627 4.565022 CTCAAATGCGTGGGGTTTATTTT 58.435 39.130 0.00 0.00 0.00 1.82
627 628 3.616317 GCTCAAATGCGTGGGGTTTATTT 60.616 43.478 0.00 0.00 0.00 1.40
628 629 2.094234 GCTCAAATGCGTGGGGTTTATT 60.094 45.455 0.00 0.00 0.00 1.40
629 630 1.476488 GCTCAAATGCGTGGGGTTTAT 59.524 47.619 0.00 0.00 0.00 1.40
630 631 0.885196 GCTCAAATGCGTGGGGTTTA 59.115 50.000 0.00 0.00 0.00 2.01
631 632 1.112315 TGCTCAAATGCGTGGGGTTT 61.112 50.000 0.00 0.00 35.36 3.27
632 633 1.526575 CTGCTCAAATGCGTGGGGTT 61.527 55.000 0.00 0.00 35.36 4.11
633 634 1.973281 CTGCTCAAATGCGTGGGGT 60.973 57.895 0.00 0.00 35.36 4.95
634 635 1.243342 TTCTGCTCAAATGCGTGGGG 61.243 55.000 0.00 0.00 35.36 4.96
635 636 0.109597 GTTCTGCTCAAATGCGTGGG 60.110 55.000 0.00 0.00 35.36 4.61
636 637 0.453282 CGTTCTGCTCAAATGCGTGG 60.453 55.000 0.00 0.00 35.36 4.94
637 638 1.061799 GCGTTCTGCTCAAATGCGTG 61.062 55.000 0.00 0.00 41.73 5.34
638 639 1.207593 GCGTTCTGCTCAAATGCGT 59.792 52.632 0.00 0.00 41.73 5.24
737 744 3.687321 GAGAGGCCAGGAATGCGCA 62.687 63.158 14.96 14.96 0.00 6.09
762 769 1.187087 AGTGAGAAGATGGACGGACC 58.813 55.000 0.00 0.00 39.54 4.46
763 770 3.429135 GGTTAGTGAGAAGATGGACGGAC 60.429 52.174 0.00 0.00 0.00 4.79
764 771 2.758979 GGTTAGTGAGAAGATGGACGGA 59.241 50.000 0.00 0.00 0.00 4.69
765 772 2.159085 GGGTTAGTGAGAAGATGGACGG 60.159 54.545 0.00 0.00 0.00 4.79
766 773 2.496070 TGGGTTAGTGAGAAGATGGACG 59.504 50.000 0.00 0.00 0.00 4.79
767 774 3.680196 GCTGGGTTAGTGAGAAGATGGAC 60.680 52.174 0.00 0.00 0.00 4.02
768 775 2.501723 GCTGGGTTAGTGAGAAGATGGA 59.498 50.000 0.00 0.00 0.00 3.41
779 786 0.610232 AGGTACGTCGCTGGGTTAGT 60.610 55.000 0.00 0.00 0.00 2.24
961 974 3.123790 TCGGTGTTGTGTATTGTTATGCG 59.876 43.478 0.00 0.00 0.00 4.73
982 995 4.874977 GCTGCCGGAGCGTACCTC 62.875 72.222 5.05 3.50 44.31 3.85
1084 1097 4.778415 CTCACCGCCTCGTCCACG 62.778 72.222 0.00 0.00 41.45 4.94
1270 1283 4.148825 AGGAGATGGTGCGACCGC 62.149 66.667 7.53 7.53 42.58 5.68
1310 1323 6.010850 TCCGGCTTGTAGATTCTATGTATCT 58.989 40.000 0.00 0.00 36.39 1.98
1316 1329 2.029828 CGCTCCGGCTTGTAGATTCTAT 60.030 50.000 0.00 0.00 36.09 1.98
1354 1367 0.730265 GACAAGAAACCACACGCACA 59.270 50.000 0.00 0.00 0.00 4.57
1474 1487 1.376649 ATGCAGGGGAAGAAGGAAGT 58.623 50.000 0.00 0.00 0.00 3.01
1477 1490 1.075601 ACAATGCAGGGGAAGAAGGA 58.924 50.000 0.00 0.00 0.00 3.36
1725 1742 3.922171 ACTGCAGAAATAGAAGAGGGG 57.078 47.619 23.35 0.00 0.00 4.79
1847 1872 5.119743 CGCATCTGATGTAGTATGATGTTGG 59.880 44.000 18.19 0.00 37.44 3.77
1849 1874 5.693555 CACGCATCTGATGTAGTATGATGTT 59.306 40.000 18.19 0.00 37.44 2.71
1853 1878 4.338118 TCACACGCATCTGATGTAGTATGA 59.662 41.667 18.19 18.26 29.27 2.15
1855 1880 4.339530 AGTCACACGCATCTGATGTAGTAT 59.660 41.667 18.19 6.46 0.00 2.12
1856 1881 3.694566 AGTCACACGCATCTGATGTAGTA 59.305 43.478 18.19 3.20 0.00 1.82
1977 2022 2.433970 CCACAACACAGGTTCCCAAAAT 59.566 45.455 0.00 0.00 34.21 1.82
1986 2031 2.799126 TTCAGTTCCACAACACAGGT 57.201 45.000 0.00 0.00 34.60 4.00
2009 2054 9.614792 ACATACTTCTGATTTATTTCCTGTACC 57.385 33.333 0.00 0.00 0.00 3.34
2068 2114 6.985653 TCCTATCCTATGGTTTCTCTTCTG 57.014 41.667 0.00 0.00 0.00 3.02
2079 2125 6.041523 GCTCTAAGGCTAATCCTATCCTATGG 59.958 46.154 0.00 0.00 46.94 2.74
2080 2126 6.609212 TGCTCTAAGGCTAATCCTATCCTATG 59.391 42.308 0.00 0.00 46.94 2.23
2081 2127 6.746894 TGCTCTAAGGCTAATCCTATCCTAT 58.253 40.000 0.00 0.00 46.94 2.57
2082 2128 6.153942 TGCTCTAAGGCTAATCCTATCCTA 57.846 41.667 0.00 0.00 46.94 2.94
2083 2129 5.017093 TGCTCTAAGGCTAATCCTATCCT 57.983 43.478 0.00 0.00 46.94 3.24
2084 2130 5.746990 TTGCTCTAAGGCTAATCCTATCC 57.253 43.478 0.00 0.00 46.94 2.59
2085 2131 6.816140 GTGATTGCTCTAAGGCTAATCCTATC 59.184 42.308 3.65 0.00 46.94 2.08
2086 2132 6.270927 TGTGATTGCTCTAAGGCTAATCCTAT 59.729 38.462 3.65 0.00 46.94 2.57
2087 2133 5.602561 TGTGATTGCTCTAAGGCTAATCCTA 59.397 40.000 3.65 0.00 46.94 2.94
2089 2135 4.708177 TGTGATTGCTCTAAGGCTAATCC 58.292 43.478 3.65 0.00 33.33 3.01
2090 2136 6.874288 ATTGTGATTGCTCTAAGGCTAATC 57.126 37.500 0.00 0.00 34.07 1.75
2091 2137 6.830324 TGAATTGTGATTGCTCTAAGGCTAAT 59.170 34.615 0.00 0.00 0.00 1.73
2092 2138 6.094048 GTGAATTGTGATTGCTCTAAGGCTAA 59.906 38.462 0.00 0.00 0.00 3.09
2093 2139 5.586243 GTGAATTGTGATTGCTCTAAGGCTA 59.414 40.000 0.00 0.00 0.00 3.93
2094 2140 4.397417 GTGAATTGTGATTGCTCTAAGGCT 59.603 41.667 0.00 0.00 0.00 4.58
2110 2161 1.656095 GTCTTCGCCTCTCGTGAATTG 59.344 52.381 0.00 0.00 40.16 2.32
2125 2176 9.559958 CACAGAAAAATAATACCATGTGTCTTC 57.440 33.333 0.00 0.00 33.78 2.87
2139 2190 9.249457 CATATCTCTCTACGCACAGAAAAATAA 57.751 33.333 0.00 0.00 0.00 1.40
2160 2295 5.050091 GGTGTATGTGTACTTGCTGCATATC 60.050 44.000 1.84 0.00 0.00 1.63
2163 2303 3.009723 GGTGTATGTGTACTTGCTGCAT 58.990 45.455 1.84 0.00 0.00 3.96
2164 2304 2.224402 TGGTGTATGTGTACTTGCTGCA 60.224 45.455 0.00 0.00 0.00 4.41
2199 2339 6.368779 AACACTTGCAGGAGTATTTACCTA 57.631 37.500 1.40 0.00 34.87 3.08
2200 2340 4.910458 ACACTTGCAGGAGTATTTACCT 57.090 40.909 1.40 0.00 36.92 3.08
2201 2341 5.959618 AAACACTTGCAGGAGTATTTACC 57.040 39.130 1.40 0.00 25.26 2.85
2226 2379 1.993391 GGTGTGGATTCCTCGGGGA 60.993 63.158 0.00 0.00 40.36 4.81
2227 2380 1.995626 AGGTGTGGATTCCTCGGGG 60.996 63.158 0.00 0.00 0.00 5.73
2228 2381 1.221840 CAGGTGTGGATTCCTCGGG 59.778 63.158 3.95 0.00 30.91 5.14
2230 2383 1.811266 CGCAGGTGTGGATTCCTCG 60.811 63.158 3.95 0.00 30.91 4.63
2231 2384 4.208632 CGCAGGTGTGGATTCCTC 57.791 61.111 3.95 0.59 30.91 3.71
2244 2397 7.028962 TCAATCAATCAGTAAAAATTCCGCAG 58.971 34.615 0.00 0.00 0.00 5.18
2245 2398 6.918626 TCAATCAATCAGTAAAAATTCCGCA 58.081 32.000 0.00 0.00 0.00 5.69
2246 2399 7.992180 ATCAATCAATCAGTAAAAATTCCGC 57.008 32.000 0.00 0.00 0.00 5.54
2247 2400 9.571810 TCAATCAATCAATCAGTAAAAATTCCG 57.428 29.630 0.00 0.00 0.00 4.30
2253 2406 9.642327 CCAACATCAATCAATCAATCAGTAAAA 57.358 29.630 0.00 0.00 0.00 1.52
2254 2407 7.760794 GCCAACATCAATCAATCAATCAGTAAA 59.239 33.333 0.00 0.00 0.00 2.01
2255 2408 7.093858 TGCCAACATCAATCAATCAATCAGTAA 60.094 33.333 0.00 0.00 0.00 2.24
2256 2409 6.377712 TGCCAACATCAATCAATCAATCAGTA 59.622 34.615 0.00 0.00 0.00 2.74
2257 2410 5.186215 TGCCAACATCAATCAATCAATCAGT 59.814 36.000 0.00 0.00 0.00 3.41
2258 2411 5.518847 GTGCCAACATCAATCAATCAATCAG 59.481 40.000 0.00 0.00 0.00 2.90
2259 2412 5.412640 GTGCCAACATCAATCAATCAATCA 58.587 37.500 0.00 0.00 0.00 2.57
2260 2413 4.501559 CGTGCCAACATCAATCAATCAATC 59.498 41.667 0.00 0.00 0.00 2.67
2285 2438 2.257676 GTCTCTTCGCCGTCCGTT 59.742 61.111 0.00 0.00 38.35 4.44
2307 2465 2.415608 GCCTCCGACTGACCGATCA 61.416 63.158 0.00 0.00 0.00 2.92
2410 2577 2.347490 CACCCCGTCTGGTCCTTG 59.653 66.667 0.00 0.00 36.12 3.61
2666 2833 3.237741 GGCGATGGGAGGAGGAGG 61.238 72.222 0.00 0.00 0.00 4.30
2669 2836 1.153989 TAGAGGCGATGGGAGGAGG 59.846 63.158 0.00 0.00 0.00 4.30
2670 2837 0.178975 AGTAGAGGCGATGGGAGGAG 60.179 60.000 0.00 0.00 0.00 3.69
2671 2838 1.146452 TAGTAGAGGCGATGGGAGGA 58.854 55.000 0.00 0.00 0.00 3.71
2673 2840 3.862642 GCAAATAGTAGAGGCGATGGGAG 60.863 52.174 0.00 0.00 0.00 4.30
2675 2842 2.037772 AGCAAATAGTAGAGGCGATGGG 59.962 50.000 0.00 0.00 0.00 4.00
2676 2843 3.393089 AGCAAATAGTAGAGGCGATGG 57.607 47.619 0.00 0.00 0.00 3.51
2677 2844 3.496130 CCAAGCAAATAGTAGAGGCGATG 59.504 47.826 0.00 0.00 0.00 3.84
2678 2845 3.495100 CCCAAGCAAATAGTAGAGGCGAT 60.495 47.826 0.00 0.00 0.00 4.58
2679 2846 2.158957 CCCAAGCAAATAGTAGAGGCGA 60.159 50.000 0.00 0.00 0.00 5.54
2680 2847 2.213499 CCCAAGCAAATAGTAGAGGCG 58.787 52.381 0.00 0.00 0.00 5.52
2681 2848 1.950216 GCCCAAGCAAATAGTAGAGGC 59.050 52.381 0.00 0.00 39.53 4.70
2682 2849 2.213499 CGCCCAAGCAAATAGTAGAGG 58.787 52.381 0.00 0.00 39.83 3.69
2683 2850 2.213499 CCGCCCAAGCAAATAGTAGAG 58.787 52.381 0.00 0.00 39.83 2.43
2684 2851 1.134220 CCCGCCCAAGCAAATAGTAGA 60.134 52.381 0.00 0.00 39.83 2.59
2685 2852 1.308998 CCCGCCCAAGCAAATAGTAG 58.691 55.000 0.00 0.00 39.83 2.57
2686 2853 0.750182 GCCCGCCCAAGCAAATAGTA 60.750 55.000 0.00 0.00 39.83 1.82
2687 2854 2.052104 GCCCGCCCAAGCAAATAGT 61.052 57.895 0.00 0.00 39.83 2.12
2688 2855 1.754234 AGCCCGCCCAAGCAAATAG 60.754 57.895 0.00 0.00 39.83 1.73
2689 2856 2.051518 CAGCCCGCCCAAGCAAATA 61.052 57.895 0.00 0.00 39.83 1.40
2690 2857 3.384532 CAGCCCGCCCAAGCAAAT 61.385 61.111 0.00 0.00 39.83 2.32
2702 2869 1.066358 AGAAAGTAGTAACCGCAGCCC 60.066 52.381 0.00 0.00 0.00 5.19
2704 2871 2.924290 CAGAGAAAGTAGTAACCGCAGC 59.076 50.000 0.00 0.00 0.00 5.25
2705 2872 2.924290 GCAGAGAAAGTAGTAACCGCAG 59.076 50.000 0.00 0.00 0.00 5.18
2706 2873 2.670229 CGCAGAGAAAGTAGTAACCGCA 60.670 50.000 0.00 0.00 0.00 5.69
2707 2874 1.918609 CGCAGAGAAAGTAGTAACCGC 59.081 52.381 0.00 0.00 0.00 5.68
2708 2875 2.527100 CCGCAGAGAAAGTAGTAACCG 58.473 52.381 0.00 0.00 0.00 4.44
2710 2877 2.233186 ACCCCGCAGAGAAAGTAGTAAC 59.767 50.000 0.00 0.00 0.00 2.50
2712 2879 2.226962 ACCCCGCAGAGAAAGTAGTA 57.773 50.000 0.00 0.00 0.00 1.82
2713 2880 1.275573 GAACCCCGCAGAGAAAGTAGT 59.724 52.381 0.00 0.00 0.00 2.73
2739 2953 1.228094 GCCAGCCAGCCTCCTTATC 60.228 63.158 0.00 0.00 0.00 1.75
2741 2955 2.285668 AGCCAGCCAGCCTCCTTA 60.286 61.111 0.00 0.00 0.00 2.69
2742 2956 4.044439 CAGCCAGCCAGCCTCCTT 62.044 66.667 0.00 0.00 0.00 3.36
2759 2973 2.946762 GCAAGTCAGTTGGTCGCC 59.053 61.111 0.00 0.00 36.56 5.54
2840 3054 2.279851 TGTTGTGCGTCAGACCGG 60.280 61.111 0.00 0.00 0.00 5.28
2849 3063 1.070843 CCGTCTAAACTGTGTTGTGCG 60.071 52.381 0.00 0.00 0.00 5.34
2923 3156 2.013563 GCAGGAGATCGCCATGTTTGA 61.014 52.381 18.44 0.00 0.00 2.69
2940 3173 4.435436 TGAGGTACCAGCGCGCAG 62.435 66.667 35.10 26.46 0.00 5.18
2958 3192 1.134075 CTCACGTCTGCAGCAATGC 59.866 57.895 9.47 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.