Multiple sequence alignment - TraesCS1D01G275600

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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 TraesCS1D01G275600 chr1D 100.000 6907 0 0 1 6907 371663990 371657084 0.000000e+00 12755.0
1 TraesCS1D01G275600 chr1B 95.839 5720 163 25 691 6389 496100831 496095166 0.000000e+00 9175.0
2 TraesCS1D01G275600 chr1B 83.521 534 32 17 6376 6907 496095136 496094657 1.370000e-121 448.0
3 TraesCS1D01G275600 chr1B 93.525 139 4 3 552 690 162036340 162036473 1.170000e-47 202.0
4 TraesCS1D01G275600 chr1A 96.385 3541 94 13 2772 6295 471324116 471320593 0.000000e+00 5799.0
5 TraesCS1D01G275600 chr1A 95.333 1157 46 8 1620 2774 471325361 471324211 0.000000e+00 1831.0
6 TraesCS1D01G275600 chr1A 93.722 908 32 6 692 1596 471326242 471325357 0.000000e+00 1338.0
7 TraesCS1D01G275600 chr1A 86.448 487 21 16 6433 6907 471320508 471320055 6.220000e-135 492.0
8 TraesCS1D01G275600 chr3D 98.919 555 5 1 1 554 578284814 578284260 0.000000e+00 990.0
9 TraesCS1D01G275600 chr3D 92.073 164 8 1 6271 6434 187836469 187836311 6.970000e-55 226.0
10 TraesCS1D01G275600 chr2B 94.394 553 31 0 2 554 622480170 622480722 0.000000e+00 850.0
11 TraesCS1D01G275600 chr2B 91.018 167 9 3 6268 6434 366017682 366017522 3.240000e-53 220.0
12 TraesCS1D01G275600 chr2B 94.203 138 4 1 553 690 26997111 26996978 2.520000e-49 207.0
13 TraesCS1D01G275600 chr2B 93.525 139 5 2 553 691 18143925 18144059 3.270000e-48 204.0
14 TraesCS1D01G275600 chr2B 93.478 138 5 1 553 690 120238578 120238711 1.170000e-47 202.0
15 TraesCS1D01G275600 chr7A 93.271 535 25 4 1 524 285417175 285417709 0.000000e+00 778.0
16 TraesCS1D01G275600 chr7A 90.244 246 12 2 309 554 602087782 602088015 1.870000e-80 311.0
17 TraesCS1D01G275600 chr7A 91.515 165 9 2 6270 6434 494786828 494786987 9.020000e-54 222.0
18 TraesCS1D01G275600 chr7A 91.071 168 10 2 6267 6434 498937371 498937209 9.020000e-54 222.0
19 TraesCS1D01G275600 chr5B 85.025 808 64 21 2701 3478 509687617 509686837 0.000000e+00 769.0
20 TraesCS1D01G275600 chr5B 89.011 182 12 4 6270 6450 536228870 536228696 1.170000e-52 219.0
21 TraesCS1D01G275600 chr7B 84.777 808 66 21 2701 3478 726106566 726105786 0.000000e+00 758.0
22 TraesCS1D01G275600 chr7B 85.918 561 70 8 2189 2745 749298538 749299093 2.150000e-164 590.0
23 TraesCS1D01G275600 chr7B 89.125 423 36 8 2327 2745 408937297 408937713 1.030000e-142 518.0
24 TraesCS1D01G275600 chr7D 84.406 808 69 17 2701 3478 53681718 53680938 0.000000e+00 741.0
25 TraesCS1D01G275600 chr6B 84.425 809 65 23 2701 3478 547719173 547719951 0.000000e+00 739.0
26 TraesCS1D01G275600 chr6B 92.857 140 6 1 553 692 624792670 624792805 4.220000e-47 200.0
27 TraesCS1D01G275600 chr2A 86.643 554 66 7 2197 2748 160836456 160835909 2.130000e-169 606.0
28 TraesCS1D01G275600 chr6A 86.232 552 39 15 2 553 603431736 603432250 1.300000e-156 564.0
29 TraesCS1D01G275600 chr2D 89.437 426 36 7 2327 2748 352981327 352980907 4.740000e-146 529.0
30 TraesCS1D01G275600 chr2D 91.018 167 9 3 6268 6434 296364046 296364206 3.240000e-53 220.0
31 TraesCS1D01G275600 chr2D 93.478 138 5 1 553 690 58657817 58657684 1.170000e-47 202.0
32 TraesCS1D01G275600 chr2D 97.436 39 1 0 2830 2868 352980845 352980807 4.470000e-07 67.6
33 TraesCS1D01G275600 chr3B 88.732 426 39 7 2327 2748 68462444 68462024 4.780000e-141 512.0
34 TraesCS1D01G275600 chr3B 88.889 423 38 7 2327 2745 778243751 778244168 4.780000e-141 512.0
35 TraesCS1D01G275600 chrUn 88.652 423 39 8 2327 2745 387670480 387670897 2.220000e-139 507.0
36 TraesCS1D01G275600 chr5A 88.652 423 39 8 2327 2745 216669718 216669301 2.220000e-139 507.0
37 TraesCS1D01G275600 chr4B 88.263 426 41 7 2327 2748 203527894 203527474 1.030000e-137 501.0
38 TraesCS1D01G275600 chr4B 91.156 147 7 3 553 699 649630155 649630015 1.970000e-45 195.0
39 TraesCS1D01G275600 chr4A 91.040 346 29 2 219 563 470132442 470132098 3.770000e-127 466.0
40 TraesCS1D01G275600 chr4A 94.203 138 4 1 553 690 652092351 652092484 2.520000e-49 207.0
41 TraesCS1D01G275600 chr4A 94.203 138 4 1 553 690 652104255 652104388 2.520000e-49 207.0
42 TraesCS1D01G275600 chr4D 92.121 165 8 2 6270 6434 117421353 117421194 1.940000e-55 228.0
43 TraesCS1D01G275600 chr3A 92.073 164 8 1 6271 6434 238686210 238686368 6.970000e-55 226.0


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 TraesCS1D01G275600 chr1D 371657084 371663990 6906 True 12755.0 12755 100.0000 1 6907 1 chr1D.!!$R1 6906
1 TraesCS1D01G275600 chr1B 496094657 496100831 6174 True 4811.5 9175 89.6800 691 6907 2 chr1B.!!$R1 6216
2 TraesCS1D01G275600 chr1A 471320055 471326242 6187 True 2365.0 5799 92.9720 692 6907 4 chr1A.!!$R1 6215
3 TraesCS1D01G275600 chr3D 578284260 578284814 554 True 990.0 990 98.9190 1 554 1 chr3D.!!$R2 553
4 TraesCS1D01G275600 chr2B 622480170 622480722 552 False 850.0 850 94.3940 2 554 1 chr2B.!!$F3 552
5 TraesCS1D01G275600 chr7A 285417175 285417709 534 False 778.0 778 93.2710 1 524 1 chr7A.!!$F1 523
6 TraesCS1D01G275600 chr5B 509686837 509687617 780 True 769.0 769 85.0250 2701 3478 1 chr5B.!!$R1 777
7 TraesCS1D01G275600 chr7B 726105786 726106566 780 True 758.0 758 84.7770 2701 3478 1 chr7B.!!$R1 777
8 TraesCS1D01G275600 chr7B 749298538 749299093 555 False 590.0 590 85.9180 2189 2745 1 chr7B.!!$F2 556
9 TraesCS1D01G275600 chr7D 53680938 53681718 780 True 741.0 741 84.4060 2701 3478 1 chr7D.!!$R1 777
10 TraesCS1D01G275600 chr6B 547719173 547719951 778 False 739.0 739 84.4250 2701 3478 1 chr6B.!!$F1 777
11 TraesCS1D01G275600 chr2A 160835909 160836456 547 True 606.0 606 86.6430 2197 2748 1 chr2A.!!$R1 551
12 TraesCS1D01G275600 chr6A 603431736 603432250 514 False 564.0 564 86.2320 2 553 1 chr6A.!!$F1 551
13 TraesCS1D01G275600 chr2D 352980807 352981327 520 True 298.3 529 93.4365 2327 2868 2 chr2D.!!$R2 541

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
571 588 0.035458 AAGGAAAGGGACAGACGCTG 59.965 55.000 5.47 5.47 41.58 5.18 F
632 649 0.458889 TATGGTCGGTGCTTACGTGC 60.459 55.000 0.00 0.00 0.00 5.34 F
638 655 0.668096 CGGTGCTTACGTGCCTTGTA 60.668 55.000 0.00 0.00 0.00 2.41 F
1330 1359 0.738975 CGACTTCGAGATGCCAGGTA 59.261 55.000 0.00 0.00 43.02 3.08 F
2149 2180 0.925558 TTGAAGATGCCATGCCCCTA 59.074 50.000 0.00 0.00 0.00 3.53 F
3098 3270 1.786937 TTGCCTTGCCTTTTCTTCCA 58.213 45.000 0.00 0.00 0.00 3.53 F
3213 3385 2.724977 TCAAGCTACCTGTCTTCACG 57.275 50.000 0.00 0.00 0.00 4.35 F
3266 3439 3.112580 CTGCAAAGTTTTGTAACCCACG 58.887 45.455 6.48 0.00 40.24 4.94 F
4403 4595 3.815401 AGCCAACTGAAACATGTACTGTC 59.185 43.478 0.00 0.00 36.98 3.51 F
5659 5851 1.466950 TCTCGGCGCTTAATTTGTTGG 59.533 47.619 7.64 0.00 0.00 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2149 2180 1.343985 ACAGGGGCCAAAAAGGAAAGT 60.344 47.619 4.39 0.00 41.22 2.66 R
2272 2305 3.384532 CCAGGGCAGCGGCAATTT 61.385 61.111 11.88 0.00 43.71 1.82 R
2551 2588 4.386711 AGAAACAGTTGGTACTTAGGCAC 58.613 43.478 0.00 0.00 30.26 5.01 R
3266 3439 1.898574 CAGGTCAGTGGCACCCAAC 60.899 63.158 15.27 9.92 34.18 3.77 R
4083 4275 0.035317 CAGCAGGTTCTGTGTGCCTA 59.965 55.000 0.00 0.00 37.98 3.93 R
4788 4980 2.684001 TCCTAGGGTGTGCATTAACG 57.316 50.000 9.46 0.00 0.00 3.18 R
5141 5333 5.366829 AAATTACGTACCTGAAAAGGCAC 57.633 39.130 0.00 0.00 0.00 5.01 R
5544 5736 2.027745 GGAAGTGAAGGATCAGCAGTCA 60.028 50.000 0.00 0.00 35.88 3.41 R
5740 5932 0.107643 TTGTCCTCCACGCACAATCA 59.892 50.000 0.00 0.00 0.00 2.57 R
6678 6921 0.183492 TGGTGGCATCAGGGAATAGC 59.817 55.000 0.00 0.00 0.00 2.97 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
93 98 2.016704 GATCGTATGTCGCTGCCGG 61.017 63.158 0.00 0.00 39.67 6.13
149 154 4.096681 CCATACTGGCCAGGTGATCTATA 58.903 47.826 35.42 16.96 0.00 1.31
569 586 1.605753 AAAAGGAAAGGGACAGACGC 58.394 50.000 0.00 0.00 0.00 5.19
570 587 0.765510 AAAGGAAAGGGACAGACGCT 59.234 50.000 0.00 0.00 43.65 5.07
571 588 0.035458 AAGGAAAGGGACAGACGCTG 59.965 55.000 5.47 5.47 41.58 5.18
572 589 1.376037 GGAAAGGGACAGACGCTGG 60.376 63.158 10.80 0.00 41.58 4.85
573 590 1.371558 GAAAGGGACAGACGCTGGT 59.628 57.895 10.80 0.00 41.58 4.00
574 591 0.606604 GAAAGGGACAGACGCTGGTA 59.393 55.000 10.80 0.00 41.58 3.25
575 592 1.207329 GAAAGGGACAGACGCTGGTAT 59.793 52.381 10.80 0.00 41.58 2.73
576 593 1.276622 AAGGGACAGACGCTGGTATT 58.723 50.000 10.80 0.00 41.58 1.89
577 594 1.276622 AGGGACAGACGCTGGTATTT 58.723 50.000 10.80 0.00 40.28 1.40
578 595 1.628846 AGGGACAGACGCTGGTATTTT 59.371 47.619 10.80 0.00 40.28 1.82
579 596 1.737793 GGGACAGACGCTGGTATTTTG 59.262 52.381 10.80 0.00 35.51 2.44
580 597 1.130561 GGACAGACGCTGGTATTTTGC 59.869 52.381 10.80 0.00 35.51 3.68
581 598 1.804151 GACAGACGCTGGTATTTTGCA 59.196 47.619 10.80 0.00 35.51 4.08
582 599 2.420022 GACAGACGCTGGTATTTTGCAT 59.580 45.455 10.80 0.00 35.51 3.96
583 600 3.605634 ACAGACGCTGGTATTTTGCATA 58.394 40.909 10.80 0.00 35.51 3.14
584 601 3.623060 ACAGACGCTGGTATTTTGCATAG 59.377 43.478 10.80 0.00 35.51 2.23
585 602 3.871006 CAGACGCTGGTATTTTGCATAGA 59.129 43.478 0.00 0.00 0.00 1.98
586 603 4.332543 CAGACGCTGGTATTTTGCATAGAA 59.667 41.667 0.00 0.00 0.00 2.10
587 604 5.008019 CAGACGCTGGTATTTTGCATAGAAT 59.992 40.000 0.00 0.00 0.00 2.40
588 605 5.590259 AGACGCTGGTATTTTGCATAGAATT 59.410 36.000 0.00 0.00 0.00 2.17
589 606 6.095440 AGACGCTGGTATTTTGCATAGAATTT 59.905 34.615 0.00 0.00 0.00 1.82
590 607 6.630071 ACGCTGGTATTTTGCATAGAATTTT 58.370 32.000 0.00 0.00 0.00 1.82
591 608 7.096551 ACGCTGGTATTTTGCATAGAATTTTT 58.903 30.769 0.00 0.00 0.00 1.94
618 635 9.685276 TTATCTTTTCATTCAGTCATGTATGGT 57.315 29.630 0.00 0.00 35.53 3.55
619 636 7.615582 TCTTTTCATTCAGTCATGTATGGTC 57.384 36.000 0.00 0.00 35.53 4.02
620 637 6.313658 TCTTTTCATTCAGTCATGTATGGTCG 59.686 38.462 0.00 0.00 35.53 4.79
621 638 4.058721 TCATTCAGTCATGTATGGTCGG 57.941 45.455 0.00 0.00 35.53 4.79
622 639 3.450817 TCATTCAGTCATGTATGGTCGGT 59.549 43.478 0.00 0.00 35.53 4.69
623 640 2.959507 TCAGTCATGTATGGTCGGTG 57.040 50.000 0.00 0.00 0.00 4.94
624 641 1.134818 TCAGTCATGTATGGTCGGTGC 60.135 52.381 0.00 0.00 0.00 5.01
625 642 1.134699 CAGTCATGTATGGTCGGTGCT 60.135 52.381 0.00 0.00 0.00 4.40
626 643 1.555075 AGTCATGTATGGTCGGTGCTT 59.445 47.619 0.00 0.00 0.00 3.91
627 644 2.764010 AGTCATGTATGGTCGGTGCTTA 59.236 45.455 0.00 0.00 0.00 3.09
628 645 2.864343 GTCATGTATGGTCGGTGCTTAC 59.136 50.000 0.00 0.00 0.00 2.34
629 646 1.858458 CATGTATGGTCGGTGCTTACG 59.142 52.381 0.00 0.00 0.00 3.18
630 647 0.889994 TGTATGGTCGGTGCTTACGT 59.110 50.000 0.00 0.00 0.00 3.57
631 648 1.274596 GTATGGTCGGTGCTTACGTG 58.725 55.000 0.00 0.00 0.00 4.49
632 649 0.458889 TATGGTCGGTGCTTACGTGC 60.459 55.000 0.00 0.00 0.00 5.34
633 650 3.116531 GGTCGGTGCTTACGTGCC 61.117 66.667 0.00 0.00 0.00 5.01
634 651 2.048503 GTCGGTGCTTACGTGCCT 60.049 61.111 0.00 0.00 0.00 4.75
635 652 1.666872 GTCGGTGCTTACGTGCCTT 60.667 57.895 0.00 0.00 0.00 4.35
636 653 1.666553 TCGGTGCTTACGTGCCTTG 60.667 57.895 0.00 0.00 0.00 3.61
637 654 1.959226 CGGTGCTTACGTGCCTTGT 60.959 57.895 0.00 0.00 0.00 3.16
638 655 0.668096 CGGTGCTTACGTGCCTTGTA 60.668 55.000 0.00 0.00 0.00 2.41
639 656 1.515081 GGTGCTTACGTGCCTTGTAA 58.485 50.000 0.00 0.00 0.00 2.41
640 657 1.196127 GGTGCTTACGTGCCTTGTAAC 59.804 52.381 0.00 0.00 0.00 2.50
641 658 2.140717 GTGCTTACGTGCCTTGTAACT 58.859 47.619 0.00 0.00 0.00 2.24
642 659 2.546789 GTGCTTACGTGCCTTGTAACTT 59.453 45.455 0.00 0.00 0.00 2.66
643 660 2.546368 TGCTTACGTGCCTTGTAACTTG 59.454 45.455 0.00 0.00 0.00 3.16
644 661 2.803956 GCTTACGTGCCTTGTAACTTGA 59.196 45.455 0.00 0.00 0.00 3.02
645 662 3.435671 GCTTACGTGCCTTGTAACTTGAT 59.564 43.478 0.00 0.00 0.00 2.57
646 663 4.435651 GCTTACGTGCCTTGTAACTTGATC 60.436 45.833 0.00 0.00 0.00 2.92
647 664 3.402628 ACGTGCCTTGTAACTTGATCT 57.597 42.857 0.00 0.00 0.00 2.75
648 665 3.740115 ACGTGCCTTGTAACTTGATCTT 58.260 40.909 0.00 0.00 0.00 2.40
649 666 4.134563 ACGTGCCTTGTAACTTGATCTTT 58.865 39.130 0.00 0.00 0.00 2.52
650 667 5.302360 ACGTGCCTTGTAACTTGATCTTTA 58.698 37.500 0.00 0.00 0.00 1.85
651 668 5.938125 ACGTGCCTTGTAACTTGATCTTTAT 59.062 36.000 0.00 0.00 0.00 1.40
652 669 6.430000 ACGTGCCTTGTAACTTGATCTTTATT 59.570 34.615 0.00 0.00 0.00 1.40
653 670 6.961554 CGTGCCTTGTAACTTGATCTTTATTC 59.038 38.462 0.00 0.00 0.00 1.75
654 671 7.148407 CGTGCCTTGTAACTTGATCTTTATTCT 60.148 37.037 0.00 0.00 0.00 2.40
655 672 9.162764 GTGCCTTGTAACTTGATCTTTATTCTA 57.837 33.333 0.00 0.00 0.00 2.10
656 673 9.905713 TGCCTTGTAACTTGATCTTTATTCTAT 57.094 29.630 0.00 0.00 0.00 1.98
684 701 8.780846 AAATGAGACACGTATTACCATGTAAA 57.219 30.769 0.00 0.00 0.00 2.01
685 702 8.780846 AATGAGACACGTATTACCATGTAAAA 57.219 30.769 0.00 0.00 0.00 1.52
686 703 8.780846 ATGAGACACGTATTACCATGTAAAAA 57.219 30.769 0.00 0.00 0.00 1.94
804 832 4.379082 GGTGACGTATTTTAAACCCAGCAG 60.379 45.833 0.00 0.00 0.00 4.24
811 839 1.350071 TTAAACCCAGCAGGACCGTA 58.650 50.000 0.00 0.00 39.89 4.02
845 873 3.554731 GTGCGGCTTAGATAAACCTGTAC 59.445 47.826 0.00 0.00 0.00 2.90
846 874 3.196039 TGCGGCTTAGATAAACCTGTACA 59.804 43.478 0.00 0.00 0.00 2.90
1093 1122 1.982395 ATCTCCGTGACGCCCTTCA 60.982 57.895 0.00 0.00 0.00 3.02
1330 1359 0.738975 CGACTTCGAGATGCCAGGTA 59.261 55.000 0.00 0.00 43.02 3.08
1331 1360 1.268794 CGACTTCGAGATGCCAGGTAG 60.269 57.143 0.00 0.00 43.02 3.18
1354 1383 1.075659 GCCTGCCTCCCTTTCTGTT 59.924 57.895 0.00 0.00 0.00 3.16
1415 1444 2.158475 TGAGTTGGTTTCTCATGGCCTT 60.158 45.455 3.32 0.00 37.07 4.35
1416 1445 2.489722 GAGTTGGTTTCTCATGGCCTTC 59.510 50.000 3.32 0.00 32.79 3.46
1417 1446 2.158475 AGTTGGTTTCTCATGGCCTTCA 60.158 45.455 3.32 0.00 0.00 3.02
1418 1447 2.627699 GTTGGTTTCTCATGGCCTTCAA 59.372 45.455 3.32 0.00 0.00 2.69
1419 1448 3.173953 TGGTTTCTCATGGCCTTCAAT 57.826 42.857 3.32 0.00 0.00 2.57
1420 1449 2.827322 TGGTTTCTCATGGCCTTCAATG 59.173 45.455 3.32 0.00 0.00 2.82
1421 1450 2.827921 GGTTTCTCATGGCCTTCAATGT 59.172 45.455 3.32 0.00 0.00 2.71
1422 1451 4.016444 GGTTTCTCATGGCCTTCAATGTA 58.984 43.478 3.32 0.00 0.00 2.29
1423 1452 4.142381 GGTTTCTCATGGCCTTCAATGTAC 60.142 45.833 3.32 0.00 0.00 2.90
1424 1453 3.998913 TCTCATGGCCTTCAATGTACA 57.001 42.857 3.32 0.00 0.00 2.90
1425 1454 4.299586 TCTCATGGCCTTCAATGTACAA 57.700 40.909 3.32 0.00 0.00 2.41
1426 1455 4.264253 TCTCATGGCCTTCAATGTACAAG 58.736 43.478 3.32 0.00 0.00 3.16
1427 1456 4.012374 CTCATGGCCTTCAATGTACAAGT 58.988 43.478 3.32 0.00 0.00 3.16
1428 1457 3.758023 TCATGGCCTTCAATGTACAAGTG 59.242 43.478 3.32 1.17 0.00 3.16
1429 1458 3.222173 TGGCCTTCAATGTACAAGTGT 57.778 42.857 3.32 0.00 0.00 3.55
1430 1459 2.884012 TGGCCTTCAATGTACAAGTGTG 59.116 45.455 3.32 0.00 0.00 3.82
1431 1460 3.146066 GGCCTTCAATGTACAAGTGTGA 58.854 45.455 0.00 0.00 0.00 3.58
1432 1461 3.058224 GGCCTTCAATGTACAAGTGTGAC 60.058 47.826 0.00 0.00 0.00 3.67
1433 1462 3.058224 GCCTTCAATGTACAAGTGTGACC 60.058 47.826 0.00 0.00 0.00 4.02
1434 1463 3.502211 CCTTCAATGTACAAGTGTGACCC 59.498 47.826 0.00 0.00 0.00 4.46
1435 1464 3.134574 TCAATGTACAAGTGTGACCCC 57.865 47.619 0.00 0.00 0.00 4.95
1436 1465 2.439880 TCAATGTACAAGTGTGACCCCA 59.560 45.455 0.00 0.00 0.00 4.96
1439 1468 1.771854 TGTACAAGTGTGACCCCATGT 59.228 47.619 0.00 0.00 0.00 3.21
1461 1490 1.761449 TGTGTTTGTGCAGTGGATGT 58.239 45.000 0.00 0.00 0.00 3.06
1487 1516 3.649986 GTGCAGGTGACGGTGTGC 61.650 66.667 0.00 0.00 36.42 4.57
1488 1517 3.860605 TGCAGGTGACGGTGTGCT 61.861 61.111 0.00 0.00 36.84 4.40
1492 1521 4.927782 GGTGACGGTGTGCTGGCA 62.928 66.667 0.00 0.00 36.47 4.92
1596 1625 8.410673 TGTATTGCTGGAAGTTAATTTTACCA 57.589 30.769 0.00 0.00 35.30 3.25
1604 1633 6.263617 TGGAAGTTAATTTTACCAGCGAGTTT 59.736 34.615 0.00 0.00 0.00 2.66
1620 1649 3.187700 GAGTTTCATCTCGTATGGCGTT 58.812 45.455 0.00 0.00 42.13 4.84
1632 1662 3.676873 CGTATGGCGTTACCCAAGTAAGT 60.677 47.826 0.00 0.00 39.13 2.24
1647 1677 6.391537 CCAAGTAAGTCACCTAGAAGAGAAC 58.608 44.000 0.00 0.00 0.00 3.01
1652 1682 8.062536 AGTAAGTCACCTAGAAGAGAACCATAT 58.937 37.037 0.00 0.00 0.00 1.78
1656 1686 7.288158 AGTCACCTAGAAGAGAACCATATAACC 59.712 40.741 0.00 0.00 0.00 2.85
1657 1687 7.288158 GTCACCTAGAAGAGAACCATATAACCT 59.712 40.741 0.00 0.00 0.00 3.50
1702 1732 5.998454 ATAGCTCAATTTCAGTTGGATCG 57.002 39.130 0.00 0.00 0.00 3.69
1929 1960 5.727515 GCTGATTTTTGGTTGCTCAAACAAC 60.728 40.000 12.13 2.85 46.48 3.32
1935 1966 2.748461 GTTGCTCAAACAACGCTGTA 57.252 45.000 0.00 0.00 40.45 2.74
1955 1986 6.183359 GCTGTATCGTTAGTGAGTCAAGTTTC 60.183 42.308 0.00 0.00 0.00 2.78
1959 1990 3.244112 CGTTAGTGAGTCAAGTTTCCCCT 60.244 47.826 0.00 0.00 0.00 4.79
2074 2105 1.697982 GTACAAGGTCCAGTCCCTGTT 59.302 52.381 0.00 0.00 30.99 3.16
2116 2147 3.102972 TCCAGACTCAGAAGAAGATGGG 58.897 50.000 0.00 0.00 0.00 4.00
2149 2180 0.925558 TTGAAGATGCCATGCCCCTA 59.074 50.000 0.00 0.00 0.00 3.53
2199 2230 7.956328 ACAGAACTATATGGAGTGTTACAGA 57.044 36.000 0.00 0.00 0.00 3.41
2225 2256 5.652891 TGGTTTAGTCAGTCTCAGGATAGAC 59.347 44.000 0.00 0.00 45.20 2.59
2272 2305 2.308570 AGGTTGATACATGCAAGGACCA 59.691 45.455 9.83 0.00 0.00 4.02
2551 2588 6.092748 AGAGTTTTTGTACTTGCTGTTTGTG 58.907 36.000 0.00 0.00 0.00 3.33
2909 3056 3.226347 CGATTTGGCTTCGTTGAAGTTC 58.774 45.455 8.23 0.00 41.27 3.01
3097 3269 2.299867 TCATTGCCTTGCCTTTTCTTCC 59.700 45.455 0.00 0.00 0.00 3.46
3098 3270 1.786937 TTGCCTTGCCTTTTCTTCCA 58.213 45.000 0.00 0.00 0.00 3.53
3213 3385 2.724977 TCAAGCTACCTGTCTTCACG 57.275 50.000 0.00 0.00 0.00 4.35
3266 3439 3.112580 CTGCAAAGTTTTGTAACCCACG 58.887 45.455 6.48 0.00 40.24 4.94
3586 3764 9.932207 ATGTTGATAATGAATGTGTTGAATTGT 57.068 25.926 0.00 0.00 0.00 2.71
3991 4183 8.980143 TGTAAAAGCATAACTATTTTTGCTCC 57.020 30.769 10.38 2.46 45.88 4.70
4035 4227 7.201902 GGTGGATCCTATTCATTTATTGTGCAA 60.202 37.037 14.23 0.00 0.00 4.08
4375 4567 7.487829 TCATTTTTCACTTTGTTTGCTAGTGTC 59.512 33.333 0.00 0.00 40.08 3.67
4403 4595 3.815401 AGCCAACTGAAACATGTACTGTC 59.185 43.478 0.00 0.00 36.98 3.51
4788 4980 4.802999 CAGGAAAGATGTTCTGCCTTTTC 58.197 43.478 0.00 0.00 31.99 2.29
5141 5333 8.256605 CACCCAGATTACAGGATATATCTTCAG 58.743 40.741 12.42 3.35 0.00 3.02
5544 5736 8.245195 ACCAACCTTGTTGTTTACTATTCATT 57.755 30.769 6.25 0.00 0.00 2.57
5560 5752 3.986996 TCATTGACTGCTGATCCTTCA 57.013 42.857 0.00 0.00 0.00 3.02
5622 5814 4.427096 TTACAATACGTTGGGCATGTTG 57.573 40.909 0.00 0.00 39.70 3.33
5623 5815 2.235016 ACAATACGTTGGGCATGTTGT 58.765 42.857 0.00 0.00 39.70 3.32
5624 5816 2.625790 ACAATACGTTGGGCATGTTGTT 59.374 40.909 0.00 0.00 39.70 2.83
5625 5817 3.068873 ACAATACGTTGGGCATGTTGTTT 59.931 39.130 0.00 0.00 39.70 2.83
5626 5818 2.783828 TACGTTGGGCATGTTGTTTG 57.216 45.000 0.00 0.00 0.00 2.93
5651 5843 2.125673 GCCTGTCTCGGCGCTTAA 60.126 61.111 7.64 0.00 40.79 1.85
5659 5851 1.466950 TCTCGGCGCTTAATTTGTTGG 59.533 47.619 7.64 0.00 0.00 3.77
5747 5939 5.375417 TCACACCAAAGCTTATGATTGTG 57.625 39.130 21.24 21.24 35.04 3.33
5753 5945 2.401583 AGCTTATGATTGTGCGTGGA 57.598 45.000 0.00 0.00 0.00 4.02
5789 5981 7.962964 TTCATCGTTGTTTGAGAACTATCTT 57.037 32.000 0.00 0.00 35.54 2.40
5816 6008 3.005554 AGAGCAAGATGTTGATGGTTCG 58.994 45.455 6.80 0.00 35.46 3.95
5852 6044 7.996644 AGTGGTAATGGTTTTATATCATTCCGT 59.003 33.333 0.00 0.00 33.72 4.69
5935 6127 0.323360 GCTATGGGCTTGTGGTTCCA 60.323 55.000 0.00 0.00 38.06 3.53
5956 6148 5.003160 CCAAAGATGGTGTAGATTGTGTCA 58.997 41.667 0.00 0.00 42.18 3.58
6209 6402 8.489489 AGCAAAGATACTCATGAAAAGGATAGA 58.511 33.333 0.00 0.00 0.00 1.98
6238 6431 9.601810 ATGAGTTCCAGAGGTATACAATATACA 57.398 33.333 5.01 0.00 0.00 2.29
6382 6576 7.277098 GTGTAGATTTACTCATTTTGCTCCGTA 59.723 37.037 0.00 0.00 0.00 4.02
6385 6579 4.875544 TTACTCATTTTGCTCCGTATGC 57.124 40.909 0.00 0.00 0.00 3.14
6389 6583 2.677836 TCATTTTGCTCCGTATGCAGTC 59.322 45.455 0.00 0.00 41.71 3.51
6397 6634 2.738846 CTCCGTATGCAGTCCATATTGC 59.261 50.000 0.00 0.00 38.60 3.56
6411 6648 8.896744 CAGTCCATATTGCAATCTCTAAAAAGA 58.103 33.333 16.86 0.00 0.00 2.52
6431 6668 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
6432 6669 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
6433 6670 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
6434 6671 6.842807 AGACTTATATTTAGGAACGGAGGGAA 59.157 38.462 0.00 0.00 0.00 3.97
6469 6706 4.002982 AGTGCGAGTGAATGCAATTTCTA 58.997 39.130 0.00 0.00 43.75 2.10
6483 6720 7.379059 TGCAATTTCTAGGGAGATTCTGATA 57.621 36.000 0.00 0.00 0.00 2.15
6484 6721 7.982252 TGCAATTTCTAGGGAGATTCTGATAT 58.018 34.615 0.00 0.00 0.00 1.63
6489 6726 1.905215 AGGGAGATTCTGATATGGGCG 59.095 52.381 0.00 0.00 0.00 6.13
6490 6727 1.625818 GGGAGATTCTGATATGGGCGT 59.374 52.381 0.00 0.00 0.00 5.68
6578 6815 0.947960 TTGATTCTTGACGCCGCAAA 59.052 45.000 0.00 0.00 0.00 3.68
6622 6865 7.537306 CCTTTTTGATACGTTATGAAACAGTGG 59.463 37.037 0.00 0.00 35.16 4.00
6674 6917 2.345991 CGGCGAAAACAGGGGAGA 59.654 61.111 0.00 0.00 0.00 3.71
6675 6918 1.741770 CGGCGAAAACAGGGGAGAG 60.742 63.158 0.00 0.00 0.00 3.20
6676 6919 1.377333 GGCGAAAACAGGGGAGAGG 60.377 63.158 0.00 0.00 0.00 3.69
6677 6920 1.377333 GCGAAAACAGGGGAGAGGG 60.377 63.158 0.00 0.00 0.00 4.30
6678 6921 1.299976 CGAAAACAGGGGAGAGGGG 59.700 63.158 0.00 0.00 0.00 4.79
6680 6923 1.466186 AAAACAGGGGAGAGGGGCT 60.466 57.895 0.00 0.00 0.00 5.19
6681 6924 0.178843 AAAACAGGGGAGAGGGGCTA 60.179 55.000 0.00 0.00 0.00 3.93
6682 6925 0.046397 AAACAGGGGAGAGGGGCTAT 59.954 55.000 0.00 0.00 0.00 2.97
6684 6927 0.400670 ACAGGGGAGAGGGGCTATTC 60.401 60.000 0.00 0.00 0.00 1.75
6685 6928 1.130678 CAGGGGAGAGGGGCTATTCC 61.131 65.000 0.00 0.00 0.00 3.01
6695 6938 3.027419 GGCTATTCCCTGATGCCAC 57.973 57.895 0.00 0.00 42.79 5.01
6696 6939 0.538287 GGCTATTCCCTGATGCCACC 60.538 60.000 0.00 0.00 42.79 4.61
6697 6940 0.183492 GCTATTCCCTGATGCCACCA 59.817 55.000 0.00 0.00 0.00 4.17
6698 6941 1.816961 GCTATTCCCTGATGCCACCAG 60.817 57.143 0.00 0.00 0.00 4.00
6714 6957 0.785979 CCAGCATCAACGCTTTTTGC 59.214 50.000 0.67 0.67 41.38 3.68
6793 7036 1.098712 ACGAGATCGCTCCTCCTGAC 61.099 60.000 1.39 0.00 44.43 3.51
6801 7044 1.882989 GCTCCTCCTGACGTTGAGCT 61.883 60.000 0.00 0.00 43.85 4.09
6803 7046 0.318441 TCCTCCTGACGTTGAGCTTG 59.682 55.000 0.00 0.00 0.00 4.01
6804 7047 0.318441 CCTCCTGACGTTGAGCTTGA 59.682 55.000 0.00 0.00 0.00 3.02
6805 7048 1.671261 CCTCCTGACGTTGAGCTTGAG 60.671 57.143 0.00 0.00 0.00 3.02
6806 7049 0.319900 TCCTGACGTTGAGCTTGAGC 60.320 55.000 0.00 0.00 42.49 4.26
6807 7050 1.294659 CCTGACGTTGAGCTTGAGCC 61.295 60.000 0.00 0.00 43.38 4.70
6816 7059 2.438075 GCTTGAGCCTCCCTGCAG 60.438 66.667 6.78 6.78 34.31 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
149 154 0.905357 AAGAGCCATCTACAAGCGGT 59.095 50.000 0.00 0.00 33.45 5.68
554 571 1.376037 CCAGCGTCTGTCCCTTTCC 60.376 63.158 6.19 0.00 0.00 3.13
555 572 0.606604 TACCAGCGTCTGTCCCTTTC 59.393 55.000 6.19 0.00 0.00 2.62
556 573 1.276622 ATACCAGCGTCTGTCCCTTT 58.723 50.000 6.19 0.00 0.00 3.11
557 574 1.276622 AATACCAGCGTCTGTCCCTT 58.723 50.000 6.19 0.00 0.00 3.95
558 575 1.276622 AAATACCAGCGTCTGTCCCT 58.723 50.000 6.19 0.00 0.00 4.20
559 576 1.737793 CAAAATACCAGCGTCTGTCCC 59.262 52.381 6.19 0.00 0.00 4.46
560 577 1.130561 GCAAAATACCAGCGTCTGTCC 59.869 52.381 6.19 0.00 0.00 4.02
561 578 1.804151 TGCAAAATACCAGCGTCTGTC 59.196 47.619 6.19 0.00 0.00 3.51
562 579 1.890876 TGCAAAATACCAGCGTCTGT 58.109 45.000 6.19 0.00 0.00 3.41
563 580 3.871006 TCTATGCAAAATACCAGCGTCTG 59.129 43.478 0.00 0.52 0.00 3.51
564 581 4.137116 TCTATGCAAAATACCAGCGTCT 57.863 40.909 0.00 0.00 0.00 4.18
565 582 4.875544 TTCTATGCAAAATACCAGCGTC 57.124 40.909 0.00 0.00 0.00 5.19
566 583 5.835113 AATTCTATGCAAAATACCAGCGT 57.165 34.783 0.00 0.00 0.00 5.07
567 584 7.524294 AAAAATTCTATGCAAAATACCAGCG 57.476 32.000 0.00 0.00 0.00 5.18
592 609 9.685276 ACCATACATGACTGAATGAAAAGATAA 57.315 29.630 0.00 0.00 0.00 1.75
593 610 9.330063 GACCATACATGACTGAATGAAAAGATA 57.670 33.333 0.00 0.00 0.00 1.98
594 611 7.011763 CGACCATACATGACTGAATGAAAAGAT 59.988 37.037 0.00 0.00 0.00 2.40
595 612 6.313658 CGACCATACATGACTGAATGAAAAGA 59.686 38.462 0.00 0.00 0.00 2.52
596 613 6.457392 CCGACCATACATGACTGAATGAAAAG 60.457 42.308 0.00 0.00 0.00 2.27
597 614 5.353956 CCGACCATACATGACTGAATGAAAA 59.646 40.000 0.00 0.00 0.00 2.29
598 615 4.875536 CCGACCATACATGACTGAATGAAA 59.124 41.667 0.00 0.00 0.00 2.69
599 616 4.081142 ACCGACCATACATGACTGAATGAA 60.081 41.667 0.00 0.00 0.00 2.57
600 617 3.450817 ACCGACCATACATGACTGAATGA 59.549 43.478 0.00 0.00 0.00 2.57
601 618 3.557185 CACCGACCATACATGACTGAATG 59.443 47.826 0.00 0.00 0.00 2.67
602 619 3.797039 CACCGACCATACATGACTGAAT 58.203 45.455 0.00 0.00 0.00 2.57
603 620 2.676750 GCACCGACCATACATGACTGAA 60.677 50.000 0.00 0.00 0.00 3.02
604 621 1.134818 GCACCGACCATACATGACTGA 60.135 52.381 0.00 0.00 0.00 3.41
605 622 1.134699 AGCACCGACCATACATGACTG 60.135 52.381 0.00 0.00 0.00 3.51
606 623 1.195115 AGCACCGACCATACATGACT 58.805 50.000 0.00 0.00 0.00 3.41
607 624 2.024176 AAGCACCGACCATACATGAC 57.976 50.000 0.00 0.00 0.00 3.06
608 625 2.480587 CGTAAGCACCGACCATACATGA 60.481 50.000 0.00 0.00 0.00 3.07
609 626 1.858458 CGTAAGCACCGACCATACATG 59.142 52.381 0.00 0.00 0.00 3.21
610 627 1.479323 ACGTAAGCACCGACCATACAT 59.521 47.619 0.00 0.00 45.62 2.29
611 628 0.889994 ACGTAAGCACCGACCATACA 59.110 50.000 0.00 0.00 45.62 2.29
612 629 1.274596 CACGTAAGCACCGACCATAC 58.725 55.000 0.00 0.00 45.62 2.39
613 630 0.458889 GCACGTAAGCACCGACCATA 60.459 55.000 0.00 0.00 45.62 2.74
614 631 1.740296 GCACGTAAGCACCGACCAT 60.740 57.895 0.00 0.00 45.62 3.55
615 632 2.356553 GCACGTAAGCACCGACCA 60.357 61.111 0.00 0.00 45.62 4.02
616 633 3.116531 GGCACGTAAGCACCGACC 61.117 66.667 0.00 0.00 45.62 4.79
617 634 1.666872 AAGGCACGTAAGCACCGAC 60.667 57.895 0.00 0.00 45.62 4.79
618 635 1.666553 CAAGGCACGTAAGCACCGA 60.667 57.895 0.00 0.00 45.62 4.69
619 636 0.668096 TACAAGGCACGTAAGCACCG 60.668 55.000 0.00 0.00 45.62 4.94
620 637 1.196127 GTTACAAGGCACGTAAGCACC 59.804 52.381 0.00 0.00 45.62 5.01
621 638 2.140717 AGTTACAAGGCACGTAAGCAC 58.859 47.619 0.00 0.00 45.62 4.40
622 639 2.536761 AGTTACAAGGCACGTAAGCA 57.463 45.000 0.00 0.00 45.62 3.91
623 640 2.803956 TCAAGTTACAAGGCACGTAAGC 59.196 45.455 0.00 0.00 45.62 3.09
625 642 4.890088 AGATCAAGTTACAAGGCACGTAA 58.110 39.130 0.00 0.00 0.00 3.18
626 643 4.530710 AGATCAAGTTACAAGGCACGTA 57.469 40.909 0.00 0.00 0.00 3.57
627 644 3.402628 AGATCAAGTTACAAGGCACGT 57.597 42.857 0.00 0.00 0.00 4.49
628 645 4.749245 AAAGATCAAGTTACAAGGCACG 57.251 40.909 0.00 0.00 0.00 5.34
629 646 8.045176 AGAATAAAGATCAAGTTACAAGGCAC 57.955 34.615 0.00 0.00 0.00 5.01
630 647 9.905713 ATAGAATAAAGATCAAGTTACAAGGCA 57.094 29.630 0.00 0.00 0.00 4.75
658 675 9.872721 TTTACATGGTAATACGTGTCTCATTTA 57.127 29.630 0.00 0.00 40.76 1.40
659 676 8.780846 TTTACATGGTAATACGTGTCTCATTT 57.219 30.769 0.00 0.00 40.76 2.32
660 677 8.780846 TTTTACATGGTAATACGTGTCTCATT 57.219 30.769 0.00 0.00 40.76 2.57
661 678 8.780846 TTTTTACATGGTAATACGTGTCTCAT 57.219 30.769 0.00 0.00 40.76 2.90
685 702 6.179756 AGGTTTTCTTCATTTGTGCCTTTTT 58.820 32.000 0.00 0.00 0.00 1.94
686 703 5.744171 AGGTTTTCTTCATTTGTGCCTTTT 58.256 33.333 0.00 0.00 0.00 2.27
687 704 5.357742 AGGTTTTCTTCATTTGTGCCTTT 57.642 34.783 0.00 0.00 0.00 3.11
688 705 5.833131 TCTAGGTTTTCTTCATTTGTGCCTT 59.167 36.000 0.00 0.00 0.00 4.35
689 706 5.385198 TCTAGGTTTTCTTCATTTGTGCCT 58.615 37.500 0.00 0.00 0.00 4.75
774 802 2.375173 AAAATACGTCACCGGTCCTC 57.625 50.000 2.59 0.00 38.78 3.71
778 806 3.073678 GGGTTTAAAATACGTCACCGGT 58.926 45.455 0.00 0.00 38.78 5.28
780 808 3.425227 GCTGGGTTTAAAATACGTCACCG 60.425 47.826 0.00 0.00 40.83 4.94
804 832 2.858344 CACGTTGATGATCTTACGGTCC 59.142 50.000 19.17 0.00 38.26 4.46
811 839 0.391661 AGCCGCACGTTGATGATCTT 60.392 50.000 0.00 0.00 0.00 2.40
1415 1444 2.439880 TGGGGTCACACTTGTACATTGA 59.560 45.455 11.06 3.16 0.00 2.57
1416 1445 2.857483 TGGGGTCACACTTGTACATTG 58.143 47.619 0.00 0.00 0.00 2.82
1417 1446 3.181434 ACATGGGGTCACACTTGTACATT 60.181 43.478 0.00 0.00 0.00 2.71
1418 1447 2.375174 ACATGGGGTCACACTTGTACAT 59.625 45.455 0.00 0.00 0.00 2.29
1419 1448 1.771854 ACATGGGGTCACACTTGTACA 59.228 47.619 0.00 0.00 0.00 2.90
1420 1449 2.561478 ACATGGGGTCACACTTGTAC 57.439 50.000 0.00 0.00 0.00 2.90
1421 1450 4.042311 ACAATACATGGGGTCACACTTGTA 59.958 41.667 0.00 0.00 33.57 2.41
1422 1451 3.181434 ACAATACATGGGGTCACACTTGT 60.181 43.478 0.00 0.00 0.00 3.16
1423 1452 3.191162 CACAATACATGGGGTCACACTTG 59.809 47.826 0.00 0.00 0.00 3.16
1424 1453 3.181434 ACACAATACATGGGGTCACACTT 60.181 43.478 0.00 0.00 36.45 3.16
1425 1454 2.375174 ACACAATACATGGGGTCACACT 59.625 45.455 0.00 0.00 36.45 3.55
1426 1455 2.790433 ACACAATACATGGGGTCACAC 58.210 47.619 0.00 0.00 36.45 3.82
1427 1456 3.517296 AACACAATACATGGGGTCACA 57.483 42.857 0.00 0.00 36.45 3.58
1428 1457 3.572255 ACAAACACAATACATGGGGTCAC 59.428 43.478 0.00 0.00 36.45 3.67
1429 1458 3.571828 CACAAACACAATACATGGGGTCA 59.428 43.478 0.00 0.00 36.45 4.02
1430 1459 3.613910 GCACAAACACAATACATGGGGTC 60.614 47.826 0.00 0.00 36.45 4.46
1431 1460 2.298729 GCACAAACACAATACATGGGGT 59.701 45.455 0.00 0.00 36.45 4.95
1432 1461 2.298446 TGCACAAACACAATACATGGGG 59.702 45.455 0.00 0.00 36.45 4.96
1433 1462 3.005684 ACTGCACAAACACAATACATGGG 59.994 43.478 0.00 0.00 38.89 4.00
1434 1463 3.982701 CACTGCACAAACACAATACATGG 59.017 43.478 0.00 0.00 0.00 3.66
1435 1464 3.982701 CCACTGCACAAACACAATACATG 59.017 43.478 0.00 0.00 0.00 3.21
1436 1465 3.888323 TCCACTGCACAAACACAATACAT 59.112 39.130 0.00 0.00 0.00 2.29
1439 1468 3.888323 ACATCCACTGCACAAACACAATA 59.112 39.130 0.00 0.00 0.00 1.90
1461 1490 4.720902 CACCTGCACCATCCGCCA 62.721 66.667 0.00 0.00 0.00 5.69
1492 1521 2.584608 GCCACATAGACAGGCCGT 59.415 61.111 0.00 0.00 42.58 5.68
1620 1649 5.895807 TCTTCTAGGTGACTTACTTGGGTA 58.104 41.667 0.00 0.00 43.67 3.69
1632 1662 7.363031 AGGTTATATGGTTCTCTTCTAGGTGA 58.637 38.462 0.00 0.00 0.00 4.02
1652 1682 7.859377 CGCGTTCACTCTAATTATTCTAGGTTA 59.141 37.037 0.00 0.00 0.00 2.85
1656 1686 8.951954 ATACGCGTTCACTCTAATTATTCTAG 57.048 34.615 20.78 0.00 0.00 2.43
1702 1732 7.519002 ACATGAAGACTAGTAAACGCAAATTC 58.481 34.615 0.00 0.00 0.00 2.17
1815 1845 5.528690 CAGAACCTGAAGACATTGAAACAGA 59.471 40.000 0.00 0.00 32.44 3.41
1929 1960 3.400505 TGACTCACTAACGATACAGCG 57.599 47.619 0.00 0.00 37.29 5.18
1935 1966 4.562963 GGGGAAACTTGACTCACTAACGAT 60.563 45.833 0.00 0.00 0.00 3.73
2074 2105 5.365025 TGGAGGGATGAAAACATTTTTCACA 59.635 36.000 14.62 6.24 40.70 3.58
2149 2180 1.343985 ACAGGGGCCAAAAAGGAAAGT 60.344 47.619 4.39 0.00 41.22 2.66
2178 2209 8.204836 ACCAATCTGTAACACTCCATATAGTTC 58.795 37.037 0.00 0.00 0.00 3.01
2188 2219 6.929606 ACTGACTAAACCAATCTGTAACACTC 59.070 38.462 0.00 0.00 0.00 3.51
2199 2230 6.897966 TCTATCCTGAGACTGACTAAACCAAT 59.102 38.462 0.00 0.00 0.00 3.16
2225 2256 7.602644 TGCTCATAGGTTCACTTACAGTTAAAG 59.397 37.037 0.00 0.00 0.00 1.85
2272 2305 3.384532 CCAGGGCAGCGGCAATTT 61.385 61.111 11.88 0.00 43.71 1.82
2531 2568 4.387256 GCACACAAACAGCAAGTACAAAAA 59.613 37.500 0.00 0.00 0.00 1.94
2551 2588 4.386711 AGAAACAGTTGGTACTTAGGCAC 58.613 43.478 0.00 0.00 30.26 5.01
2909 3056 4.504858 AGCCACCACTTTCGATACTTAAG 58.495 43.478 0.00 0.00 0.00 1.85
3266 3439 1.898574 CAGGTCAGTGGCACCCAAC 60.899 63.158 15.27 9.92 34.18 3.77
3329 3502 5.414454 TCTGTCACTGCAAAGTTTTGTAACT 59.586 36.000 6.48 0.00 46.44 2.24
3586 3764 2.877786 CACATACGCTTGGCATGGATTA 59.122 45.455 2.33 0.00 0.00 1.75
3851 4034 3.592059 TCGGCAACCTACTACATTTCAC 58.408 45.455 0.00 0.00 0.00 3.18
3979 4171 9.626045 AAATAAGTTTCTTCGGAGCAAAAATAG 57.374 29.630 0.00 0.00 0.00 1.73
4035 4227 2.950781 TCTGGTGAGAAGTGTCAGACT 58.049 47.619 1.31 0.00 35.94 3.24
4083 4275 0.035317 CAGCAGGTTCTGTGTGCCTA 59.965 55.000 0.00 0.00 37.98 3.93
4346 4538 9.213799 ACTAGCAAACAAAGTGAAAAATGAAAA 57.786 25.926 0.00 0.00 0.00 2.29
4375 4567 3.507233 ACATGTTTCAGTTGGCTACATGG 59.493 43.478 15.41 1.69 46.34 3.66
4766 4958 4.614535 CGAAAAGGCAGAACATCTTTCCTG 60.615 45.833 0.00 0.00 30.23 3.86
4788 4980 2.684001 TCCTAGGGTGTGCATTAACG 57.316 50.000 9.46 0.00 0.00 3.18
5141 5333 5.366829 AAATTACGTACCTGAAAAGGCAC 57.633 39.130 0.00 0.00 0.00 5.01
5544 5736 2.027745 GGAAGTGAAGGATCAGCAGTCA 60.028 50.000 0.00 0.00 35.88 3.41
5560 5752 0.778083 GGGGTGGAGGAAAAGGAAGT 59.222 55.000 0.00 0.00 0.00 3.01
5643 5835 1.459209 GTTGCCAACAAATTAAGCGCC 59.541 47.619 2.29 0.00 37.58 6.53
5651 5843 7.148656 GCACGATATTTTTAGTTGCCAACAAAT 60.149 33.333 10.69 9.51 37.58 2.32
5659 5851 4.981794 ACCTGCACGATATTTTTAGTTGC 58.018 39.130 0.00 0.00 0.00 4.17
5732 5924 3.081061 TCCACGCACAATCATAAGCTTT 58.919 40.909 3.20 0.00 0.00 3.51
5739 5931 0.324614 TGTCCTCCACGCACAATCAT 59.675 50.000 0.00 0.00 0.00 2.45
5740 5932 0.107643 TTGTCCTCCACGCACAATCA 59.892 50.000 0.00 0.00 0.00 2.57
5741 5933 0.798776 CTTGTCCTCCACGCACAATC 59.201 55.000 0.00 0.00 29.82 2.67
5747 5939 1.936547 GAATCATCTTGTCCTCCACGC 59.063 52.381 0.00 0.00 0.00 5.34
5753 5945 4.836825 ACAACGATGAATCATCTTGTCCT 58.163 39.130 22.96 10.57 37.50 3.85
5789 5981 6.182627 ACCATCAACATCTTGCTCTTCAATA 58.817 36.000 0.00 0.00 33.57 1.90
5816 6008 2.306847 CCATTACCACTTGCATACCCC 58.693 52.381 0.00 0.00 0.00 4.95
5852 6044 4.345257 GCTACTTCATTCCTGATACCCTCA 59.655 45.833 0.00 0.00 0.00 3.86
5935 6127 6.061441 TGTTGACACAATCTACACCATCTTT 58.939 36.000 0.00 0.00 38.02 2.52
5956 6148 7.315890 GCCATAATGTTAAAGAAAGAGCTGTT 58.684 34.615 0.00 0.00 0.00 3.16
6071 6264 3.407424 TGAGCTATTGTCACAAGCAGT 57.593 42.857 4.30 0.00 38.75 4.40
6209 6402 6.620877 TTGTATACCTCTGGAACTCATGTT 57.379 37.500 0.00 0.00 39.42 2.71
6219 6412 6.351371 CCCAGCTGTATATTGTATACCTCTGG 60.351 46.154 22.08 22.08 39.71 3.86
6261 6454 4.351407 AGAACGGAGGGAGTAGATGAGATA 59.649 45.833 0.00 0.00 0.00 1.98
6385 6579 8.896744 TCTTTTTAGAGATTGCAATATGGACTG 58.103 33.333 12.07 0.00 0.00 3.51
6411 6648 6.042897 CCTTCCCTCCGTTCCTAAATATAAGT 59.957 42.308 0.00 0.00 0.00 2.24
6421 6658 0.708802 TACTCCTTCCCTCCGTTCCT 59.291 55.000 0.00 0.00 0.00 3.36
6428 6665 3.068873 CACTGCTACATACTCCTTCCCTC 59.931 52.174 0.00 0.00 0.00 4.30
6429 6666 3.034635 CACTGCTACATACTCCTTCCCT 58.965 50.000 0.00 0.00 0.00 4.20
6430 6667 2.483889 GCACTGCTACATACTCCTTCCC 60.484 54.545 0.00 0.00 0.00 3.97
6431 6668 2.799917 CGCACTGCTACATACTCCTTCC 60.800 54.545 0.00 0.00 0.00 3.46
6432 6669 2.099263 TCGCACTGCTACATACTCCTTC 59.901 50.000 0.00 0.00 0.00 3.46
6433 6670 2.099921 CTCGCACTGCTACATACTCCTT 59.900 50.000 0.00 0.00 0.00 3.36
6434 6671 1.678627 CTCGCACTGCTACATACTCCT 59.321 52.381 0.00 0.00 0.00 3.69
6469 6706 1.905215 CGCCCATATCAGAATCTCCCT 59.095 52.381 0.00 0.00 0.00 4.20
6489 6726 3.837355 AGAATCCATTTCCCTGGCATAC 58.163 45.455 0.00 0.00 36.16 2.39
6490 6727 4.168675 AGAAGAATCCATTTCCCTGGCATA 59.831 41.667 0.00 0.00 36.16 3.14
6613 6856 6.978080 TCTGTATTTTTCTTTGCCACTGTTTC 59.022 34.615 0.00 0.00 0.00 2.78
6622 6865 6.272822 AGACCCATCTGTATTTTTCTTTGC 57.727 37.500 0.00 0.00 32.29 3.68
6677 6920 0.538287 GGTGGCATCAGGGAATAGCC 60.538 60.000 0.00 0.00 45.41 3.93
6678 6921 0.183492 TGGTGGCATCAGGGAATAGC 59.817 55.000 0.00 0.00 0.00 2.97
6680 6923 0.183492 GCTGGTGGCATCAGGGAATA 59.817 55.000 27.87 0.00 41.35 1.75
6681 6924 1.076485 GCTGGTGGCATCAGGGAAT 60.076 57.895 27.87 0.00 41.35 3.01
6682 6925 2.356278 GCTGGTGGCATCAGGGAA 59.644 61.111 27.87 0.00 41.35 3.97
6691 6934 2.146073 AAAGCGTTGATGCTGGTGGC 62.146 55.000 0.00 0.00 46.60 5.01
6692 6935 0.314935 AAAAGCGTTGATGCTGGTGG 59.685 50.000 0.00 0.00 46.60 4.61
6693 6936 1.788308 CAAAAAGCGTTGATGCTGGTG 59.212 47.619 0.00 0.00 46.60 4.17
6694 6937 1.869342 GCAAAAAGCGTTGATGCTGGT 60.869 47.619 13.59 0.00 46.60 4.00
6695 6938 0.785979 GCAAAAAGCGTTGATGCTGG 59.214 50.000 13.59 0.00 46.60 4.85
6714 6957 2.046507 AGCAGCTTTCCTCGCCAG 60.047 61.111 0.00 0.00 0.00 4.85
6793 7036 1.743252 GGGAGGCTCAAGCTCAACG 60.743 63.158 17.69 0.00 41.70 4.10
6801 7044 4.039092 GGCTGCAGGGAGGCTCAA 62.039 66.667 17.12 0.00 35.65 3.02
6803 7046 4.792804 GTGGCTGCAGGGAGGCTC 62.793 72.222 17.12 5.78 39.27 4.70
6806 7049 3.215587 AAAGGTGGCTGCAGGGAGG 62.216 63.158 17.12 0.00 0.00 4.30
6807 7050 1.676967 GAAAGGTGGCTGCAGGGAG 60.677 63.158 17.12 0.00 0.00 4.30
6816 7059 2.922335 GCATTCGTTTCTGAAAGGTGGC 60.922 50.000 18.87 16.50 0.00 5.01
6874 7122 8.600625 CAACCTTGCATTTCTCATCAAAATATG 58.399 33.333 0.00 0.00 0.00 1.78


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

AutoCloner maintained by Alex Coulton.