Multiple sequence alignment - TraesCS1A01G362500

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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 TraesCS1A01G362500 chr1A 100.000 3834 0 0 1 3834 543066408 543070241 0.000000e+00 7081.0
1 TraesCS1A01G362500 chr1A 86.730 422 51 4 1941 2361 543187035 543187452 7.500000e-127 464.0
2 TraesCS1A01G362500 chr1A 82.151 437 63 7 3050 3472 543188493 543188928 1.010000e-95 361.0
3 TraesCS1A01G362500 chr1A 83.237 346 52 4 2011 2354 543170390 543170731 2.880000e-81 313.0
4 TraesCS1A01G362500 chr1A 78.862 492 56 26 1315 1799 543186011 543186461 4.850000e-74 289.0
5 TraesCS1A01G362500 chr1A 93.458 107 6 1 1439 1545 543190605 543190710 1.430000e-34 158.0
6 TraesCS1A01G362500 chr1A 84.733 131 20 0 3050 3180 543193342 543193472 8.640000e-27 132.0
7 TraesCS1A01G362500 chr1A 89.109 101 8 2 1315 1412 543190438 543190538 5.200000e-24 122.0
8 TraesCS1A01G362500 chr1B 88.839 2437 177 33 821 3236 612892893 612895255 0.000000e+00 2905.0
9 TraesCS1A01G362500 chr1B 89.303 617 55 4 3219 3834 612895276 612895882 0.000000e+00 763.0
10 TraesCS1A01G362500 chr1B 89.425 539 21 13 1 531 612892386 612892896 0.000000e+00 647.0
11 TraesCS1A01G362500 chr1B 93.333 300 15 3 526 821 418414479 418414777 4.550000e-119 438.0
12 TraesCS1A01G362500 chr1B 80.124 322 47 8 2119 2433 612901340 612901651 1.390000e-54 224.0
13 TraesCS1A01G362500 chr1D 90.336 2142 147 22 1726 3834 447259575 447261689 0.000000e+00 2754.0
14 TraesCS1A01G362500 chr1D 92.556 806 38 10 821 1624 447258782 447259567 0.000000e+00 1136.0
15 TraesCS1A01G362500 chr1D 91.867 541 13 11 1 531 447258266 447258785 0.000000e+00 726.0
16 TraesCS1A01G362500 chr1D 83.237 519 71 6 3050 3553 447443833 447444350 2.700000e-126 462.0
17 TraesCS1A01G362500 chr1D 83.333 438 57 6 3050 3472 447366554 447366990 1.290000e-104 390.0
18 TraesCS1A01G362500 chr1D 83.239 352 54 4 2011 2361 447282798 447283145 6.180000e-83 318.0
19 TraesCS1A01G362500 chr1D 82.934 334 39 10 2029 2361 447337884 447338200 6.270000e-73 285.0
20 TraesCS1A01G362500 chr1D 89.189 185 12 4 1376 1552 447334878 447335062 1.390000e-54 224.0
21 TraesCS1A01G362500 chr1D 82.126 207 30 3 2234 2433 447317189 447317395 1.830000e-38 171.0
22 TraesCS1A01G362500 chr1D 96.117 103 4 0 1439 1541 447368677 447368779 6.590000e-38 169.0
23 TraesCS1A01G362500 chr1D 85.156 128 19 0 3050 3177 447377883 447378010 8.640000e-27 132.0
24 TraesCS1A01G362500 chr1D 88.350 103 9 2 1315 1414 447368510 447368612 1.870000e-23 121.0
25 TraesCS1A01G362500 chr1D 100.000 33 0 0 3608 3640 447444801 447444833 1.150000e-05 62.1
26 TraesCS1A01G362500 chr2B 97.643 297 2 3 530 821 784782138 784782434 4.420000e-139 505.0
27 TraesCS1A01G362500 chr7B 97.306 297 3 3 530 821 337593406 337593702 2.060000e-137 499.0
28 TraesCS1A01G362500 chr7B 82.043 323 34 10 2000 2321 65343350 65343649 1.770000e-63 254.0
29 TraesCS1A01G362500 chr5B 97.306 297 3 3 530 821 375130845 375130549 2.060000e-137 499.0
30 TraesCS1A01G362500 chr7A 96.633 297 5 3 530 821 619577517 619577221 4.450000e-134 488.0
31 TraesCS1A01G362500 chr7A 84.667 300 32 7 2023 2321 41059412 41059126 1.740000e-73 287.0
32 TraesCS1A01G362500 chr6A 96.633 297 4 4 530 820 604571831 604572127 4.450000e-134 488.0
33 TraesCS1A01G362500 chr6A 83.775 302 33 6 2002 2301 531463095 531462808 4.880000e-69 272.0
34 TraesCS1A01G362500 chr3A 95.960 297 7 3 530 821 470711337 470711633 9.640000e-131 477.0
35 TraesCS1A01G362500 chr2A 94.276 297 11 5 530 821 447140273 447139978 2.100000e-122 449.0
36 TraesCS1A01G362500 chr6D 94.218 294 13 2 530 819 176229719 176229426 2.720000e-121 446.0
37 TraesCS1A01G362500 chr3B 83.282 323 40 4 2000 2321 261178581 261178272 6.270000e-73 285.0
38 TraesCS1A01G362500 chr6B 83.498 303 36 4 2000 2301 114458837 114458548 1.760000e-68 270.0
39 TraesCS1A01G362500 chr4D 81.633 98 16 2 1325 1421 419158889 419158793 3.180000e-11 80.5
40 TraesCS1A01G362500 chr4B 81.633 98 16 2 1325 1421 516956809 516956713 3.180000e-11 80.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G362500 chr1A 543066408 543070241 3833 False 7081.000000 7081 100.000000 1 3834 1 chr1A.!!$F1 3833
1 TraesCS1A01G362500 chr1A 543186011 543193472 7461 False 254.333333 464 85.840500 1315 3472 6 chr1A.!!$F3 2157
2 TraesCS1A01G362500 chr1B 612892386 612895882 3496 False 1438.333333 2905 89.189000 1 3834 3 chr1B.!!$F3 3833
3 TraesCS1A01G362500 chr1D 447258266 447261689 3423 False 1538.666667 2754 91.586333 1 3834 3 chr1D.!!$F4 3833
4 TraesCS1A01G362500 chr1D 447443833 447444833 1000 False 262.050000 462 91.618500 3050 3640 2 chr1D.!!$F7 590
5 TraesCS1A01G362500 chr1D 447334878 447338200 3322 False 254.500000 285 86.061500 1376 2361 2 chr1D.!!$F5 985
6 TraesCS1A01G362500 chr1D 447366554 447368779 2225 False 226.666667 390 89.266667 1315 3472 3 chr1D.!!$F6 2157

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
541 552 0.035056 ACGATTCAGGCCTCCTTTGG 60.035 55.000 0.0 0.0 0.00 3.28 F
1267 1282 0.597637 ACCGTGCGTCTTCTTGTCAG 60.598 55.000 0.0 0.0 0.00 3.51 F
1844 2407 1.002468 CCTGAAAGTTCACTTGGCACG 60.002 52.381 0.0 0.0 36.12 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1632 1667 0.957395 AACCAGAACATGCGAGCAGG 60.957 55.000 8.25 8.25 0.0 4.85 R
2289 5350 2.224329 TGCTCAGTTGCTTACGGGTTTA 60.224 45.455 0.00 0.00 0.0 2.01 R
3749 10697 0.963962 TCTCCCGGACACTACAACAC 59.036 55.000 0.73 0.00 0.0 3.32 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
35 36 6.406400 CCGGCTAAAATAAACATCCATTCCAA 60.406 38.462 0.00 0.00 0.00 3.53
100 101 2.034687 CCTGCCCCTTGACCTGTG 59.965 66.667 0.00 0.00 0.00 3.66
102 103 3.496309 CTGCCCCTTGACCTGTGCA 62.496 63.158 0.00 0.00 0.00 4.57
200 201 2.043625 GGGACCCGAAACCAAAACC 58.956 57.895 0.00 0.00 0.00 3.27
201 202 1.466025 GGGACCCGAAACCAAAACCC 61.466 60.000 0.00 0.00 0.00 4.11
202 203 0.756070 GGACCCGAAACCAAAACCCA 60.756 55.000 0.00 0.00 0.00 4.51
203 204 1.112950 GACCCGAAACCAAAACCCAA 58.887 50.000 0.00 0.00 0.00 4.12
204 205 1.481363 GACCCGAAACCAAAACCCAAA 59.519 47.619 0.00 0.00 0.00 3.28
205 206 1.907255 ACCCGAAACCAAAACCCAAAA 59.093 42.857 0.00 0.00 0.00 2.44
206 207 2.305052 ACCCGAAACCAAAACCCAAAAA 59.695 40.909 0.00 0.00 0.00 1.94
212 213 4.359434 AACCAAAACCCAAAAAGTGTGT 57.641 36.364 0.00 0.00 0.00 3.72
224 225 6.292488 CCCAAAAAGTGTGTTAGTACAGTACG 60.292 42.308 5.02 0.00 33.25 3.67
256 260 4.110493 GTGCCGGACACTGATAGC 57.890 61.111 18.16 0.00 46.41 2.97
262 266 1.150567 CGGACACTGATAGCAGCAGC 61.151 60.000 8.16 0.00 46.26 5.25
334 339 3.635373 ACAAAGGAGGCATGCATGATTAG 59.365 43.478 30.64 12.29 0.00 1.73
335 340 3.870538 AAGGAGGCATGCATGATTAGA 57.129 42.857 30.64 0.00 0.00 2.10
336 341 3.137446 AGGAGGCATGCATGATTAGAC 57.863 47.619 30.64 13.60 0.00 2.59
337 342 2.440627 AGGAGGCATGCATGATTAGACA 59.559 45.455 30.64 0.00 0.00 3.41
512 523 1.379977 AGGATTCTCGAGGACGGCA 60.380 57.895 13.56 0.00 40.21 5.69
517 528 2.835431 CTCGAGGACGGCAGGGAT 60.835 66.667 3.91 0.00 40.21 3.85
527 538 2.757124 GGCAGGGATGGGGACGATT 61.757 63.158 0.00 0.00 0.00 3.34
528 539 1.227973 GCAGGGATGGGGACGATTC 60.228 63.158 0.00 0.00 0.00 2.52
529 540 1.983119 GCAGGGATGGGGACGATTCA 61.983 60.000 0.00 0.00 0.00 2.57
530 541 0.107456 CAGGGATGGGGACGATTCAG 59.893 60.000 0.00 0.00 0.00 3.02
531 542 1.056700 AGGGATGGGGACGATTCAGG 61.057 60.000 0.00 0.00 0.00 3.86
532 543 1.227973 GGATGGGGACGATTCAGGC 60.228 63.158 0.00 0.00 0.00 4.85
533 544 1.227973 GATGGGGACGATTCAGGCC 60.228 63.158 0.00 0.00 39.05 5.19
534 545 1.694169 ATGGGGACGATTCAGGCCT 60.694 57.895 0.00 0.00 39.91 5.19
535 546 1.700042 ATGGGGACGATTCAGGCCTC 61.700 60.000 0.00 0.00 41.36 4.70
536 547 2.506472 GGGACGATTCAGGCCTCC 59.494 66.667 0.00 0.00 39.91 4.30
537 548 2.066999 GGGACGATTCAGGCCTCCT 61.067 63.158 0.00 0.00 39.91 3.69
538 549 1.627297 GGGACGATTCAGGCCTCCTT 61.627 60.000 0.00 0.00 39.91 3.36
539 550 0.253327 GGACGATTCAGGCCTCCTTT 59.747 55.000 0.00 0.00 36.04 3.11
540 551 1.373570 GACGATTCAGGCCTCCTTTG 58.626 55.000 0.00 0.00 0.00 2.77
541 552 0.035056 ACGATTCAGGCCTCCTTTGG 60.035 55.000 0.00 0.00 0.00 3.28
542 553 0.035056 CGATTCAGGCCTCCTTTGGT 60.035 55.000 0.00 0.00 0.00 3.67
543 554 1.614317 CGATTCAGGCCTCCTTTGGTT 60.614 52.381 0.00 0.00 0.00 3.67
544 555 2.095461 GATTCAGGCCTCCTTTGGTTC 58.905 52.381 0.00 0.00 0.00 3.62
545 556 0.850100 TTCAGGCCTCCTTTGGTTCA 59.150 50.000 0.00 0.00 0.00 3.18
546 557 1.075601 TCAGGCCTCCTTTGGTTCAT 58.924 50.000 0.00 0.00 0.00 2.57
547 558 2.274542 TCAGGCCTCCTTTGGTTCATA 58.725 47.619 0.00 0.00 0.00 2.15
548 559 2.239654 TCAGGCCTCCTTTGGTTCATAG 59.760 50.000 0.00 0.00 0.00 2.23
549 560 1.566231 AGGCCTCCTTTGGTTCATAGG 59.434 52.381 0.00 0.00 34.61 2.57
550 561 1.564348 GGCCTCCTTTGGTTCATAGGA 59.436 52.381 0.00 6.86 38.81 2.94
551 562 2.175715 GGCCTCCTTTGGTTCATAGGAT 59.824 50.000 0.00 0.00 39.94 3.24
552 563 3.394606 GGCCTCCTTTGGTTCATAGGATA 59.605 47.826 0.00 0.00 39.94 2.59
553 564 4.505742 GGCCTCCTTTGGTTCATAGGATAG 60.506 50.000 0.00 4.66 39.94 2.08
554 565 4.505742 GCCTCCTTTGGTTCATAGGATAGG 60.506 50.000 7.38 7.57 39.94 2.57
555 566 4.907875 CCTCCTTTGGTTCATAGGATAGGA 59.092 45.833 7.38 0.00 39.94 2.94
556 567 5.369699 CCTCCTTTGGTTCATAGGATAGGAA 59.630 44.000 7.38 0.00 39.94 3.36
557 568 6.044871 CCTCCTTTGGTTCATAGGATAGGAAT 59.955 42.308 7.38 0.00 43.72 3.01
558 569 7.237679 CCTCCTTTGGTTCATAGGATAGGAATA 59.762 40.741 7.38 0.00 43.72 1.75
559 570 8.575736 TCCTTTGGTTCATAGGATAGGAATAA 57.424 34.615 3.54 0.00 43.72 1.40
560 571 9.182642 TCCTTTGGTTCATAGGATAGGAATAAT 57.817 33.333 3.54 0.00 43.72 1.28
589 600 9.844257 AGGAATAAGAAAATCATAGGAAGTGAG 57.156 33.333 0.00 0.00 0.00 3.51
590 601 9.838339 GGAATAAGAAAATCATAGGAAGTGAGA 57.162 33.333 0.00 0.00 0.00 3.27
594 605 8.729805 AAGAAAATCATAGGAAGTGAGATGAC 57.270 34.615 0.00 0.00 31.41 3.06
595 606 7.855375 AGAAAATCATAGGAAGTGAGATGACA 58.145 34.615 0.00 0.00 31.41 3.58
596 607 8.492782 AGAAAATCATAGGAAGTGAGATGACAT 58.507 33.333 0.00 0.00 31.41 3.06
597 608 8.447924 AAAATCATAGGAAGTGAGATGACATG 57.552 34.615 0.00 0.00 31.41 3.21
598 609 4.953667 TCATAGGAAGTGAGATGACATGC 58.046 43.478 0.00 0.00 0.00 4.06
599 610 4.406649 TCATAGGAAGTGAGATGACATGCA 59.593 41.667 0.00 0.00 0.00 3.96
600 611 3.928005 AGGAAGTGAGATGACATGCAT 57.072 42.857 0.00 0.00 40.77 3.96
615 626 8.929260 ATGACATGCATCTCAAATCCTATAAA 57.071 30.769 8.81 0.00 28.85 1.40
616 627 8.387190 TGACATGCATCTCAAATCCTATAAAG 57.613 34.615 1.73 0.00 0.00 1.85
617 628 8.212995 TGACATGCATCTCAAATCCTATAAAGA 58.787 33.333 1.73 0.00 0.00 2.52
618 629 8.985315 ACATGCATCTCAAATCCTATAAAGAA 57.015 30.769 0.00 0.00 0.00 2.52
619 630 9.412460 ACATGCATCTCAAATCCTATAAAGAAA 57.588 29.630 0.00 0.00 0.00 2.52
620 631 9.894783 CATGCATCTCAAATCCTATAAAGAAAG 57.105 33.333 0.00 0.00 0.00 2.62
621 632 9.857656 ATGCATCTCAAATCCTATAAAGAAAGA 57.142 29.630 0.00 0.00 0.00 2.52
622 633 9.334947 TGCATCTCAAATCCTATAAAGAAAGAG 57.665 33.333 0.00 0.00 0.00 2.85
623 634 9.553064 GCATCTCAAATCCTATAAAGAAAGAGA 57.447 33.333 0.00 0.00 33.54 3.10
641 652 9.775854 AGAAAGAGATGTCATTTGATGTATAGG 57.224 33.333 0.00 0.00 0.00 2.57
642 653 9.770097 GAAAGAGATGTCATTTGATGTATAGGA 57.230 33.333 0.00 0.00 0.00 2.94
646 657 9.814899 GAGATGTCATTTGATGTATAGGATAGG 57.185 37.037 0.00 0.00 0.00 2.57
647 658 9.552695 AGATGTCATTTGATGTATAGGATAGGA 57.447 33.333 0.00 0.00 0.00 2.94
672 683 6.603940 TTTTTCCATTGCTAGGCTAATGTT 57.396 33.333 7.50 0.00 33.52 2.71
673 684 6.603940 TTTTCCATTGCTAGGCTAATGTTT 57.396 33.333 7.50 0.00 33.52 2.83
674 685 6.603940 TTTCCATTGCTAGGCTAATGTTTT 57.396 33.333 7.50 0.00 33.52 2.43
675 686 6.603940 TTCCATTGCTAGGCTAATGTTTTT 57.396 33.333 7.50 0.00 33.52 1.94
703 714 9.599866 CCCTTTAAAATGTGAAGGATTAATTCC 57.400 33.333 0.00 0.00 45.85 3.01
730 741 6.607004 CCTACGTAGGAATAGGAATCCATT 57.393 41.667 33.93 0.00 46.63 3.16
731 742 6.631962 CCTACGTAGGAATAGGAATCCATTC 58.368 44.000 33.93 8.71 46.63 2.67
746 757 7.290110 GAATCCATTCCTATAAACCAAAGGG 57.710 40.000 0.00 0.00 41.29 3.95
747 758 4.542697 TCCATTCCTATAAACCAAAGGGC 58.457 43.478 0.00 0.00 37.90 5.19
748 759 4.231890 TCCATTCCTATAAACCAAAGGGCT 59.768 41.667 0.00 0.00 37.90 5.19
749 760 4.962362 CCATTCCTATAAACCAAAGGGCTT 59.038 41.667 0.00 0.00 37.90 4.35
750 761 5.069119 CCATTCCTATAAACCAAAGGGCTTC 59.931 44.000 0.00 0.00 37.90 3.86
751 762 4.938575 TCCTATAAACCAAAGGGCTTCA 57.061 40.909 0.00 0.00 37.90 3.02
752 763 5.263872 TCCTATAAACCAAAGGGCTTCAA 57.736 39.130 0.00 0.00 37.90 2.69
753 764 5.646215 TCCTATAAACCAAAGGGCTTCAAA 58.354 37.500 0.00 0.00 37.90 2.69
754 765 5.714806 TCCTATAAACCAAAGGGCTTCAAAG 59.285 40.000 0.00 0.00 37.90 2.77
755 766 4.890158 ATAAACCAAAGGGCTTCAAAGG 57.110 40.909 0.00 0.00 37.90 3.11
756 767 2.470057 AACCAAAGGGCTTCAAAGGA 57.530 45.000 0.00 0.00 37.90 3.36
757 768 2.470057 ACCAAAGGGCTTCAAAGGAA 57.530 45.000 0.00 0.00 37.90 3.36
758 769 2.976440 ACCAAAGGGCTTCAAAGGAAT 58.024 42.857 0.00 0.00 37.90 3.01
759 770 3.317406 ACCAAAGGGCTTCAAAGGAATT 58.683 40.909 0.00 0.00 37.90 2.17
760 771 3.716353 ACCAAAGGGCTTCAAAGGAATTT 59.284 39.130 0.00 0.00 37.90 1.82
761 772 4.165950 ACCAAAGGGCTTCAAAGGAATTTT 59.834 37.500 0.00 0.00 37.90 1.82
762 773 5.132502 CCAAAGGGCTTCAAAGGAATTTTT 58.867 37.500 0.00 0.00 31.34 1.94
763 774 5.239306 CCAAAGGGCTTCAAAGGAATTTTTC 59.761 40.000 0.00 0.00 31.34 2.29
764 775 5.894298 AAGGGCTTCAAAGGAATTTTTCT 57.106 34.783 0.00 0.00 31.34 2.52
765 776 6.994421 AAGGGCTTCAAAGGAATTTTTCTA 57.006 33.333 0.00 0.00 31.34 2.10
766 777 6.346477 AGGGCTTCAAAGGAATTTTTCTAC 57.654 37.500 0.00 0.00 31.34 2.59
767 778 5.048013 AGGGCTTCAAAGGAATTTTTCTACG 60.048 40.000 0.00 0.00 31.34 3.51
768 779 5.048294 GGGCTTCAAAGGAATTTTTCTACGA 60.048 40.000 0.00 0.00 31.34 3.43
769 780 6.443792 GGCTTCAAAGGAATTTTTCTACGAA 58.556 36.000 0.00 0.00 31.34 3.85
770 781 6.921307 GGCTTCAAAGGAATTTTTCTACGAAA 59.079 34.615 0.00 0.00 31.34 3.46
771 782 7.598869 GGCTTCAAAGGAATTTTTCTACGAAAT 59.401 33.333 0.00 0.00 31.34 2.17
772 783 8.978539 GCTTCAAAGGAATTTTTCTACGAAATT 58.021 29.630 0.00 0.00 38.89 1.82
784 795 6.920569 TTCTACGAAATTCCTATCCTTTGC 57.079 37.500 0.00 0.00 0.00 3.68
785 796 5.984725 TCTACGAAATTCCTATCCTTTGCA 58.015 37.500 0.00 0.00 0.00 4.08
786 797 6.411376 TCTACGAAATTCCTATCCTTTGCAA 58.589 36.000 0.00 0.00 0.00 4.08
787 798 7.054124 TCTACGAAATTCCTATCCTTTGCAAT 58.946 34.615 0.00 0.00 0.00 3.56
788 799 6.530019 ACGAAATTCCTATCCTTTGCAATT 57.470 33.333 0.00 0.00 0.00 2.32
789 800 6.564328 ACGAAATTCCTATCCTTTGCAATTC 58.436 36.000 0.00 0.00 0.00 2.17
790 801 5.979517 CGAAATTCCTATCCTTTGCAATTCC 59.020 40.000 0.00 0.00 0.00 3.01
791 802 6.183360 CGAAATTCCTATCCTTTGCAATTCCT 60.183 38.462 0.00 0.00 0.00 3.36
792 803 7.013274 CGAAATTCCTATCCTTTGCAATTCCTA 59.987 37.037 0.00 0.00 0.00 2.94
793 804 7.588497 AATTCCTATCCTTTGCAATTCCTAC 57.412 36.000 0.00 0.00 0.00 3.18
794 805 5.708736 TCCTATCCTTTGCAATTCCTACA 57.291 39.130 0.00 0.00 0.00 2.74
795 806 6.073447 TCCTATCCTTTGCAATTCCTACAA 57.927 37.500 0.00 0.00 0.00 2.41
796 807 6.672593 TCCTATCCTTTGCAATTCCTACAAT 58.327 36.000 0.00 0.00 0.00 2.71
797 808 7.811282 TCCTATCCTTTGCAATTCCTACAATA 58.189 34.615 0.00 0.00 0.00 1.90
798 809 8.448008 TCCTATCCTTTGCAATTCCTACAATAT 58.552 33.333 0.00 0.00 0.00 1.28
799 810 9.082313 CCTATCCTTTGCAATTCCTACAATATT 57.918 33.333 0.00 0.00 0.00 1.28
801 812 7.346751 TCCTTTGCAATTCCTACAATATTCC 57.653 36.000 0.00 0.00 0.00 3.01
802 813 7.125391 TCCTTTGCAATTCCTACAATATTCCT 58.875 34.615 0.00 0.00 0.00 3.36
803 814 8.278639 TCCTTTGCAATTCCTACAATATTCCTA 58.721 33.333 0.00 0.00 0.00 2.94
804 815 9.082313 CCTTTGCAATTCCTACAATATTCCTAT 57.918 33.333 0.00 0.00 0.00 2.57
805 816 9.903682 CTTTGCAATTCCTACAATATTCCTATG 57.096 33.333 0.00 0.00 0.00 2.23
806 817 9.639563 TTTGCAATTCCTACAATATTCCTATGA 57.360 29.630 0.00 0.00 0.00 2.15
807 818 9.639563 TTGCAATTCCTACAATATTCCTATGAA 57.360 29.630 0.00 0.00 34.33 2.57
808 819 9.066892 TGCAATTCCTACAATATTCCTATGAAC 57.933 33.333 0.00 0.00 32.13 3.18
809 820 8.515414 GCAATTCCTACAATATTCCTATGAACC 58.485 37.037 0.00 0.00 32.13 3.62
810 821 9.573166 CAATTCCTACAATATTCCTATGAACCA 57.427 33.333 0.00 0.00 32.13 3.67
814 825 9.573166 TCCTACAATATTCCTATGAACCAAATG 57.427 33.333 0.00 0.00 32.13 2.32
815 826 9.573166 CCTACAATATTCCTATGAACCAAATGA 57.427 33.333 0.00 0.00 32.13 2.57
817 828 8.469309 ACAATATTCCTATGAACCAAATGAGG 57.531 34.615 0.00 0.00 32.13 3.86
818 829 7.014615 ACAATATTCCTATGAACCAAATGAGGC 59.985 37.037 0.00 0.00 32.13 4.70
819 830 3.297134 TCCTATGAACCAAATGAGGCC 57.703 47.619 0.00 0.00 0.00 5.19
828 839 2.290577 ACCAAATGAGGCCTCAGAGTTC 60.291 50.000 37.03 10.34 43.61 3.01
1006 1020 2.485122 GCCACCATAACGCAGCAC 59.515 61.111 0.00 0.00 0.00 4.40
1033 1047 3.324930 CCCAGCCAGTGAGCCAGA 61.325 66.667 0.00 0.00 0.00 3.86
1244 1258 2.579684 AATCGGACTGGCTCGGCTTC 62.580 60.000 0.00 0.00 0.00 3.86
1267 1282 0.597637 ACCGTGCGTCTTCTTGTCAG 60.598 55.000 0.00 0.00 0.00 3.51
1270 1285 1.583054 GTGCGTCTTCTTGTCAGGTT 58.417 50.000 0.00 0.00 0.00 3.50
1271 1286 2.750948 GTGCGTCTTCTTGTCAGGTTA 58.249 47.619 0.00 0.00 0.00 2.85
1472 1497 2.267324 GAGTGCTCTGGTCTGCCC 59.733 66.667 0.00 0.00 0.00 5.36
1573 1598 2.096860 CGCAATCTCGATGCTTCAGATG 60.097 50.000 7.80 9.20 41.64 2.90
1632 1667 5.795972 AGTCTAACCAGAGTAAGAAAAGCC 58.204 41.667 0.00 0.00 32.39 4.35
1639 1674 2.003301 GAGTAAGAAAAGCCCTGCTCG 58.997 52.381 0.00 0.00 38.25 5.03
1649 1684 2.110967 CCCTGCTCGCATGTTCTGG 61.111 63.158 0.00 0.00 0.00 3.86
1662 1697 1.079503 GTTCTGGTTCATGCCGAGAC 58.920 55.000 0.00 0.00 0.00 3.36
1698 1733 4.645535 TGTGAAAGAAACCATCCTCTCTG 58.354 43.478 0.00 0.00 0.00 3.35
1724 1759 2.159099 TCTAGGCATACAAGTTCTGGCG 60.159 50.000 0.00 0.00 40.13 5.69
1746 1781 6.016610 GGCGATTTCCCTGCAATAATAGTAAA 60.017 38.462 0.00 0.00 0.00 2.01
1786 1821 8.695456 AGTCTATGTGAATTTGGTCAAGTTTTT 58.305 29.630 0.00 0.00 0.00 1.94
1787 1822 8.755018 GTCTATGTGAATTTGGTCAAGTTTTTG 58.245 33.333 0.00 0.00 35.57 2.44
1788 1823 8.474025 TCTATGTGAATTTGGTCAAGTTTTTGT 58.526 29.630 0.00 0.00 35.73 2.83
1789 1824 7.920160 ATGTGAATTTGGTCAAGTTTTTGTT 57.080 28.000 0.00 0.00 35.73 2.83
1790 1825 7.736447 TGTGAATTTGGTCAAGTTTTTGTTT 57.264 28.000 0.00 0.00 35.73 2.83
1831 2393 4.693566 TGAATTTAGCCGTACACCTGAAAG 59.306 41.667 0.00 0.00 0.00 2.62
1844 2407 1.002468 CCTGAAAGTTCACTTGGCACG 60.002 52.381 0.00 0.00 36.12 5.34
1847 2410 1.400494 GAAAGTTCACTTGGCACGTGT 59.600 47.619 21.55 4.10 36.12 4.49
1895 2458 7.498570 AGTGTGTGGCAAAACATTCAAATTAAT 59.501 29.630 7.45 0.00 31.49 1.40
1925 2488 3.084039 ACTGAAATGACGACCATGCAAT 58.916 40.909 0.00 0.00 35.24 3.56
1947 2510 4.841441 GGGGGCAACAGATTGACA 57.159 55.556 0.00 0.00 46.84 3.58
1985 2556 9.845740 TTGTATGTACAACATTATATCCAGCTT 57.154 29.630 0.00 0.00 40.93 3.74
2003 2574 3.810386 AGCTTCCGTTTCTCTGAAAGTTC 59.190 43.478 0.00 0.00 33.76 3.01
2039 5095 5.283457 ACCAACAGATATTAGGTGAGAGC 57.717 43.478 0.00 0.00 0.00 4.09
2131 5187 2.249413 ATCGCTCTTCCAGGTGCCAG 62.249 60.000 0.00 0.00 0.00 4.85
2289 5350 3.081804 GTCCCAACTCGGAATTCACAAT 58.918 45.455 7.93 0.00 36.56 2.71
2295 5356 5.399013 CAACTCGGAATTCACAATAAACCC 58.601 41.667 7.93 0.00 0.00 4.11
2305 5366 4.391155 TCACAATAAACCCGTAAGCAACT 58.609 39.130 0.00 0.00 0.00 3.16
2330 5391 7.436933 TGAGCATAACAGATAGATTGTACTGG 58.563 38.462 0.00 0.00 35.08 4.00
2381 5620 0.797249 CGAATCGAGCTTTCCGTCGT 60.797 55.000 0.00 0.00 37.46 4.34
2416 5655 2.508526 CCAATATAGGTTGGGCTGCTC 58.491 52.381 0.00 0.00 43.94 4.26
2554 5793 3.519107 TGCTGACAAAGATGGAGGTGATA 59.481 43.478 0.00 0.00 0.00 2.15
2565 5804 9.699410 AAAGATGGAGGTGATATGACAATTTTA 57.301 29.630 0.00 0.00 0.00 1.52
2613 5852 6.420604 CACACACTACATTTCCATTTTCCAAC 59.579 38.462 0.00 0.00 0.00 3.77
2720 5961 2.072298 CTCAGAGCTTGGCTACACAAC 58.928 52.381 0.00 0.00 39.88 3.32
2967 6210 1.402787 GTGAATCCAATCCGGCCATT 58.597 50.000 2.24 0.00 33.14 3.16
3135 6569 2.031682 GTGATCTTGTGCACAACTCCAC 60.032 50.000 27.96 25.98 35.19 4.02
3303 6788 7.382110 GCCATCTGAAAGCTATTATCTCACTA 58.618 38.462 0.00 0.00 0.00 2.74
3319 6804 6.716934 TCTCACTACATCAGAATTCTACCC 57.283 41.667 7.86 0.00 0.00 3.69
3411 6896 1.479323 GATCACATGTTGGCAGCCATT 59.521 47.619 17.09 0.00 31.53 3.16
3435 6920 0.965439 GCCACAACAAATAGGCCACA 59.035 50.000 5.01 0.00 41.25 4.17
3474 6961 4.634184 TGAAAGCTATCGTGGAGTAGTC 57.366 45.455 0.00 0.00 0.00 2.59
3480 6967 4.822896 AGCTATCGTGGAGTAGTCTAAAGG 59.177 45.833 0.00 0.00 0.00 3.11
3557 7046 2.659897 CGCTGTATGCCGCCTCTC 60.660 66.667 0.00 0.00 38.78 3.20
3653 10057 0.673985 TCAGCTTAGCACACACGTCT 59.326 50.000 7.07 0.00 0.00 4.18
3674 10078 1.963338 GATAGATGCACCCAGGCGC 60.963 63.158 0.00 0.00 36.28 6.53
3681 10085 4.690719 CACCCAGGCGCGTGGTAA 62.691 66.667 38.41 0.00 35.60 2.85
3704 10108 1.891150 GTTCCCGTGTTAGAGACCAGA 59.109 52.381 0.00 0.00 0.00 3.86
3758 10706 2.359088 GGGACCTCCGTGTTGTAGT 58.641 57.895 0.00 0.00 36.71 2.73
3788 10736 5.451242 GGAGATATAGGAACCAGCGATCATC 60.451 48.000 0.00 0.00 0.00 2.92
3789 10737 2.732412 ATAGGAACCAGCGATCATCG 57.268 50.000 1.50 1.50 43.89 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 8.531146 ACAGGTTGGAATGGATGTTTATTTTAG 58.469 33.333 0.00 0.00 0.00 1.85
100 101 1.442017 GTCAAACGTGGCCGAATGC 60.442 57.895 0.00 0.00 37.88 3.56
102 103 1.802365 GTTAGTCAAACGTGGCCGAAT 59.198 47.619 0.00 0.00 37.88 3.34
130 131 6.944945 CGCGATCGAAGATCATTAACATTTAG 59.055 38.462 21.57 0.00 45.12 1.85
190 191 4.720046 ACACACTTTTTGGGTTTTGGTTT 58.280 34.783 0.00 0.00 39.68 3.27
199 200 6.292488 CGTACTGTACTAACACACTTTTTGGG 60.292 42.308 15.35 0.00 33.17 4.12
200 201 6.476380 TCGTACTGTACTAACACACTTTTTGG 59.524 38.462 15.35 0.00 0.00 3.28
201 202 7.453980 TCGTACTGTACTAACACACTTTTTG 57.546 36.000 15.35 0.00 0.00 2.44
202 203 6.199719 GCTCGTACTGTACTAACACACTTTTT 59.800 38.462 15.35 0.00 0.00 1.94
203 204 5.689068 GCTCGTACTGTACTAACACACTTTT 59.311 40.000 15.35 0.00 0.00 2.27
204 205 5.009410 AGCTCGTACTGTACTAACACACTTT 59.991 40.000 15.35 0.00 0.00 2.66
205 206 4.518211 AGCTCGTACTGTACTAACACACTT 59.482 41.667 15.35 0.00 0.00 3.16
206 207 4.070716 AGCTCGTACTGTACTAACACACT 58.929 43.478 15.35 1.67 0.00 3.55
224 225 2.391389 GCACCGGCAGTAACAGCTC 61.391 63.158 0.00 0.00 40.72 4.09
254 258 1.879380 TGAAATTTACGTGCTGCTGCT 59.121 42.857 17.00 0.00 40.48 4.24
255 259 2.245096 CTGAAATTTACGTGCTGCTGC 58.755 47.619 8.89 8.89 40.20 5.25
256 260 3.228749 CACTGAAATTTACGTGCTGCTG 58.771 45.455 0.00 0.00 0.00 4.41
334 339 2.621338 TGCAAATCTGGATCGTCTGTC 58.379 47.619 0.00 0.00 0.00 3.51
335 340 2.768253 TGCAAATCTGGATCGTCTGT 57.232 45.000 0.00 0.00 0.00 3.41
336 341 2.289820 CCATGCAAATCTGGATCGTCTG 59.710 50.000 0.00 0.00 34.24 3.51
337 342 2.569059 CCATGCAAATCTGGATCGTCT 58.431 47.619 0.00 0.00 34.24 4.18
512 523 1.056700 CCTGAATCGTCCCCATCCCT 61.057 60.000 0.00 0.00 0.00 4.20
517 528 2.285368 AGGCCTGAATCGTCCCCA 60.285 61.111 3.11 0.00 0.00 4.96
527 538 1.075601 ATGAACCAAAGGAGGCCTGA 58.924 50.000 12.00 0.00 32.13 3.86
528 539 2.648059 CTATGAACCAAAGGAGGCCTG 58.352 52.381 12.00 0.00 32.13 4.85
529 540 1.566231 CCTATGAACCAAAGGAGGCCT 59.434 52.381 3.86 3.86 33.87 5.19
530 541 1.564348 TCCTATGAACCAAAGGAGGCC 59.436 52.381 0.00 0.00 34.46 5.19
531 542 3.584733 ATCCTATGAACCAAAGGAGGC 57.415 47.619 0.00 0.00 42.53 4.70
532 543 4.907875 TCCTATCCTATGAACCAAAGGAGG 59.092 45.833 0.00 0.00 42.53 4.30
533 544 6.500589 TTCCTATCCTATGAACCAAAGGAG 57.499 41.667 0.00 0.00 42.53 3.69
534 545 8.575736 TTATTCCTATCCTATGAACCAAAGGA 57.424 34.615 0.00 0.00 43.38 3.36
563 574 9.844257 CTCACTTCCTATGATTTTCTTATTCCT 57.156 33.333 0.00 0.00 0.00 3.36
564 575 9.838339 TCTCACTTCCTATGATTTTCTTATTCC 57.162 33.333 0.00 0.00 0.00 3.01
568 579 9.823647 GTCATCTCACTTCCTATGATTTTCTTA 57.176 33.333 0.00 0.00 31.49 2.10
569 580 8.324306 TGTCATCTCACTTCCTATGATTTTCTT 58.676 33.333 0.00 0.00 31.49 2.52
570 581 7.855375 TGTCATCTCACTTCCTATGATTTTCT 58.145 34.615 0.00 0.00 31.49 2.52
571 582 8.557864 CATGTCATCTCACTTCCTATGATTTTC 58.442 37.037 0.00 0.00 31.49 2.29
572 583 7.013083 GCATGTCATCTCACTTCCTATGATTTT 59.987 37.037 0.00 0.00 31.49 1.82
573 584 6.485984 GCATGTCATCTCACTTCCTATGATTT 59.514 38.462 0.00 0.00 31.49 2.17
574 585 5.996513 GCATGTCATCTCACTTCCTATGATT 59.003 40.000 0.00 0.00 31.49 2.57
575 586 5.071384 TGCATGTCATCTCACTTCCTATGAT 59.929 40.000 0.00 0.00 31.49 2.45
576 587 4.406649 TGCATGTCATCTCACTTCCTATGA 59.593 41.667 0.00 0.00 0.00 2.15
577 588 4.700700 TGCATGTCATCTCACTTCCTATG 58.299 43.478 0.00 0.00 0.00 2.23
578 589 5.549347 GATGCATGTCATCTCACTTCCTAT 58.451 41.667 2.46 0.00 46.29 2.57
579 590 4.953667 GATGCATGTCATCTCACTTCCTA 58.046 43.478 2.46 0.00 46.29 2.94
580 591 3.806380 GATGCATGTCATCTCACTTCCT 58.194 45.455 2.46 0.00 46.29 3.36
590 601 8.929260 TTTATAGGATTTGAGATGCATGTCAT 57.071 30.769 25.41 13.07 38.32 3.06
591 602 8.212995 TCTTTATAGGATTTGAGATGCATGTCA 58.787 33.333 21.70 21.70 0.00 3.58
592 603 8.613060 TCTTTATAGGATTTGAGATGCATGTC 57.387 34.615 16.63 16.63 0.00 3.06
593 604 8.985315 TTCTTTATAGGATTTGAGATGCATGT 57.015 30.769 2.46 0.00 0.00 3.21
594 605 9.894783 CTTTCTTTATAGGATTTGAGATGCATG 57.105 33.333 2.46 0.00 0.00 4.06
595 606 9.857656 TCTTTCTTTATAGGATTTGAGATGCAT 57.142 29.630 0.00 0.00 0.00 3.96
596 607 9.334947 CTCTTTCTTTATAGGATTTGAGATGCA 57.665 33.333 0.00 0.00 0.00 3.96
597 608 9.553064 TCTCTTTCTTTATAGGATTTGAGATGC 57.447 33.333 0.00 0.00 0.00 3.91
615 626 9.775854 CCTATACATCAAATGACATCTCTTTCT 57.224 33.333 0.00 0.00 0.00 2.52
616 627 9.770097 TCCTATACATCAAATGACATCTCTTTC 57.230 33.333 0.00 0.00 0.00 2.62
620 631 9.814899 CCTATCCTATACATCAAATGACATCTC 57.185 37.037 0.00 0.00 0.00 2.75
621 632 9.552695 TCCTATCCTATACATCAAATGACATCT 57.447 33.333 0.00 0.00 0.00 2.90
649 660 6.603940 AACATTAGCCTAGCAATGGAAAAA 57.396 33.333 12.05 0.00 34.19 1.94
650 661 6.603940 AAACATTAGCCTAGCAATGGAAAA 57.396 33.333 12.05 0.00 34.19 2.29
651 662 6.603940 AAAACATTAGCCTAGCAATGGAAA 57.396 33.333 12.05 0.00 34.19 3.13
652 663 6.603940 AAAAACATTAGCCTAGCAATGGAA 57.396 33.333 12.05 0.00 34.19 3.53
677 688 9.599866 GGAATTAATCCTTCACATTTTAAAGGG 57.400 33.333 0.00 0.00 45.56 3.95
707 718 6.607004 AATGGATTCCTATTCCTACGTAGG 57.393 41.667 32.05 32.05 45.02 3.18
722 733 6.239317 GCCCTTTGGTTTATAGGAATGGATTC 60.239 42.308 0.00 0.00 36.08 2.52
723 734 5.602561 GCCCTTTGGTTTATAGGAATGGATT 59.397 40.000 0.00 0.00 0.00 3.01
724 735 5.103086 AGCCCTTTGGTTTATAGGAATGGAT 60.103 40.000 0.00 0.00 0.00 3.41
725 736 4.231890 AGCCCTTTGGTTTATAGGAATGGA 59.768 41.667 0.00 0.00 0.00 3.41
726 737 4.546674 AGCCCTTTGGTTTATAGGAATGG 58.453 43.478 0.00 0.00 0.00 3.16
727 738 5.656416 TGAAGCCCTTTGGTTTATAGGAATG 59.344 40.000 0.00 0.00 34.87 2.67
728 739 5.837829 TGAAGCCCTTTGGTTTATAGGAAT 58.162 37.500 0.00 0.00 34.87 3.01
729 740 5.263872 TGAAGCCCTTTGGTTTATAGGAA 57.736 39.130 0.00 0.00 34.87 3.36
730 741 4.938575 TGAAGCCCTTTGGTTTATAGGA 57.061 40.909 0.00 0.00 34.87 2.94
731 742 5.105351 CCTTTGAAGCCCTTTGGTTTATAGG 60.105 44.000 0.00 0.00 34.87 2.57
732 743 5.714806 TCCTTTGAAGCCCTTTGGTTTATAG 59.285 40.000 0.00 0.00 34.87 1.31
733 744 5.646215 TCCTTTGAAGCCCTTTGGTTTATA 58.354 37.500 0.00 0.00 34.87 0.98
734 745 4.488770 TCCTTTGAAGCCCTTTGGTTTAT 58.511 39.130 0.00 0.00 34.87 1.40
735 746 3.917300 TCCTTTGAAGCCCTTTGGTTTA 58.083 40.909 0.00 0.00 34.87 2.01
736 747 2.758130 TCCTTTGAAGCCCTTTGGTTT 58.242 42.857 0.00 0.00 37.85 3.27
737 748 2.470057 TCCTTTGAAGCCCTTTGGTT 57.530 45.000 0.00 0.00 37.39 3.67
738 749 2.470057 TTCCTTTGAAGCCCTTTGGT 57.530 45.000 0.00 0.00 0.00 3.67
739 750 4.356405 AAATTCCTTTGAAGCCCTTTGG 57.644 40.909 0.00 0.00 33.05 3.28
740 751 6.057533 AGAAAAATTCCTTTGAAGCCCTTTG 58.942 36.000 0.00 0.00 33.05 2.77
741 752 6.252599 AGAAAAATTCCTTTGAAGCCCTTT 57.747 33.333 0.00 0.00 33.05 3.11
742 753 5.894298 AGAAAAATTCCTTTGAAGCCCTT 57.106 34.783 0.00 0.00 33.05 3.95
743 754 5.048013 CGTAGAAAAATTCCTTTGAAGCCCT 60.048 40.000 0.00 0.00 33.05 5.19
744 755 5.048294 TCGTAGAAAAATTCCTTTGAAGCCC 60.048 40.000 0.00 0.00 33.05 5.19
745 756 6.009115 TCGTAGAAAAATTCCTTTGAAGCC 57.991 37.500 0.00 0.00 33.05 4.35
746 757 7.924103 TTTCGTAGAAAAATTCCTTTGAAGC 57.076 32.000 0.00 0.00 45.90 3.86
758 769 8.241367 GCAAAGGATAGGAATTTCGTAGAAAAA 58.759 33.333 5.21 0.00 45.90 1.94
759 770 7.392113 TGCAAAGGATAGGAATTTCGTAGAAAA 59.608 33.333 5.21 0.00 45.90 2.29
760 771 6.882140 TGCAAAGGATAGGAATTTCGTAGAAA 59.118 34.615 5.21 0.00 45.90 2.52
761 772 6.411376 TGCAAAGGATAGGAATTTCGTAGAA 58.589 36.000 5.21 0.00 45.90 2.10
762 773 5.984725 TGCAAAGGATAGGAATTTCGTAGA 58.015 37.500 5.21 0.00 0.00 2.59
763 774 6.677781 TTGCAAAGGATAGGAATTTCGTAG 57.322 37.500 0.00 0.00 0.00 3.51
764 775 7.201785 GGAATTGCAAAGGATAGGAATTTCGTA 60.202 37.037 1.71 1.61 36.18 3.43
765 776 6.405842 GGAATTGCAAAGGATAGGAATTTCGT 60.406 38.462 1.71 0.00 36.18 3.85
766 777 5.979517 GGAATTGCAAAGGATAGGAATTTCG 59.020 40.000 1.71 0.00 36.18 3.46
767 778 7.117285 AGGAATTGCAAAGGATAGGAATTTC 57.883 36.000 1.71 0.00 36.18 2.17
768 779 7.619302 TGTAGGAATTGCAAAGGATAGGAATTT 59.381 33.333 1.71 0.00 36.18 1.82
769 780 7.125391 TGTAGGAATTGCAAAGGATAGGAATT 58.875 34.615 1.71 0.00 38.28 2.17
770 781 6.672593 TGTAGGAATTGCAAAGGATAGGAAT 58.327 36.000 1.71 0.00 0.00 3.01
771 782 6.073447 TGTAGGAATTGCAAAGGATAGGAA 57.927 37.500 1.71 0.00 0.00 3.36
772 783 5.708736 TGTAGGAATTGCAAAGGATAGGA 57.291 39.130 1.71 0.00 0.00 2.94
773 784 6.966534 ATTGTAGGAATTGCAAAGGATAGG 57.033 37.500 1.71 0.00 34.97 2.57
775 786 9.077885 GGAATATTGTAGGAATTGCAAAGGATA 57.922 33.333 1.71 0.00 34.97 2.59
776 787 7.786464 AGGAATATTGTAGGAATTGCAAAGGAT 59.214 33.333 1.71 0.00 34.97 3.24
777 788 7.125391 AGGAATATTGTAGGAATTGCAAAGGA 58.875 34.615 1.71 0.00 34.97 3.36
778 789 7.352079 AGGAATATTGTAGGAATTGCAAAGG 57.648 36.000 1.71 0.00 34.97 3.11
779 790 9.903682 CATAGGAATATTGTAGGAATTGCAAAG 57.096 33.333 1.71 0.00 34.97 2.77
780 791 9.639563 TCATAGGAATATTGTAGGAATTGCAAA 57.360 29.630 1.71 0.00 34.97 3.68
781 792 9.639563 TTCATAGGAATATTGTAGGAATTGCAA 57.360 29.630 0.00 0.00 35.80 4.08
782 793 9.066892 GTTCATAGGAATATTGTAGGAATTGCA 57.933 33.333 0.00 0.00 35.05 4.08
783 794 8.515414 GGTTCATAGGAATATTGTAGGAATTGC 58.485 37.037 0.00 0.00 35.05 3.56
784 795 9.573166 TGGTTCATAGGAATATTGTAGGAATTG 57.427 33.333 0.00 0.00 35.05 2.32
788 799 9.573166 CATTTGGTTCATAGGAATATTGTAGGA 57.427 33.333 0.00 0.00 35.05 2.94
789 800 9.573166 TCATTTGGTTCATAGGAATATTGTAGG 57.427 33.333 0.00 0.00 35.05 3.18
791 802 9.573166 CCTCATTTGGTTCATAGGAATATTGTA 57.427 33.333 0.00 0.00 35.05 2.41
792 803 7.014615 GCCTCATTTGGTTCATAGGAATATTGT 59.985 37.037 0.00 0.00 35.05 2.71
793 804 7.373493 GCCTCATTTGGTTCATAGGAATATTG 58.627 38.462 0.00 0.00 35.05 1.90
794 805 6.494835 GGCCTCATTTGGTTCATAGGAATATT 59.505 38.462 0.00 0.00 35.05 1.28
795 806 6.012745 GGCCTCATTTGGTTCATAGGAATAT 58.987 40.000 0.00 0.00 35.05 1.28
796 807 5.134339 AGGCCTCATTTGGTTCATAGGAATA 59.866 40.000 0.00 0.00 35.05 1.75
797 808 4.078980 AGGCCTCATTTGGTTCATAGGAAT 60.079 41.667 0.00 0.00 35.05 3.01
798 809 3.269381 AGGCCTCATTTGGTTCATAGGAA 59.731 43.478 0.00 0.00 0.00 3.36
799 810 2.852449 AGGCCTCATTTGGTTCATAGGA 59.148 45.455 0.00 0.00 0.00 2.94
800 811 3.217626 GAGGCCTCATTTGGTTCATAGG 58.782 50.000 28.43 0.00 0.00 2.57
801 812 3.881688 CTGAGGCCTCATTTGGTTCATAG 59.118 47.826 35.11 15.31 39.13 2.23
802 813 3.523157 TCTGAGGCCTCATTTGGTTCATA 59.477 43.478 35.11 8.39 39.13 2.15
803 814 2.309755 TCTGAGGCCTCATTTGGTTCAT 59.690 45.455 35.11 0.00 39.13 2.57
804 815 1.704628 TCTGAGGCCTCATTTGGTTCA 59.295 47.619 35.11 10.66 39.13 3.18
805 816 2.290577 ACTCTGAGGCCTCATTTGGTTC 60.291 50.000 35.11 5.85 39.13 3.62
806 817 1.707427 ACTCTGAGGCCTCATTTGGTT 59.293 47.619 35.11 13.91 39.13 3.67
807 818 1.366319 ACTCTGAGGCCTCATTTGGT 58.634 50.000 35.11 24.99 39.13 3.67
808 819 2.290514 TGAACTCTGAGGCCTCATTTGG 60.291 50.000 35.11 23.10 39.13 3.28
809 820 2.746362 GTGAACTCTGAGGCCTCATTTG 59.254 50.000 35.11 26.77 39.13 2.32
810 821 2.373169 TGTGAACTCTGAGGCCTCATTT 59.627 45.455 35.11 26.12 39.13 2.32
811 822 1.980765 TGTGAACTCTGAGGCCTCATT 59.019 47.619 35.11 26.06 39.13 2.57
812 823 1.554160 CTGTGAACTCTGAGGCCTCAT 59.446 52.381 35.11 21.16 39.13 2.90
813 824 0.972134 CTGTGAACTCTGAGGCCTCA 59.028 55.000 33.04 33.04 38.06 3.86
814 825 0.248843 CCTGTGAACTCTGAGGCCTC 59.751 60.000 26.78 26.78 0.00 4.70
815 826 1.835927 GCCTGTGAACTCTGAGGCCT 61.836 60.000 3.86 3.86 44.54 5.19
816 827 1.376553 GCCTGTGAACTCTGAGGCC 60.377 63.158 9.85 0.00 44.54 5.19
817 828 4.292784 GCCTGTGAACTCTGAGGC 57.707 61.111 9.85 0.00 44.10 4.70
818 829 2.421619 GAAAGCCTGTGAACTCTGAGG 58.578 52.381 9.85 0.00 0.00 3.86
819 830 2.064762 CGAAAGCCTGTGAACTCTGAG 58.935 52.381 2.45 2.45 0.00 3.35
828 839 2.145225 CGTCTGACGAAAGCCTGTG 58.855 57.895 24.86 0.00 46.05 3.66
861 872 0.468226 ACTGACACCAATCACCGTGT 59.532 50.000 0.00 0.00 45.67 4.49
972 983 3.490759 CGTGGCGGTAGCTGCAAG 61.491 66.667 3.61 0.00 44.37 4.01
1017 1031 2.046507 GTCTGGCTCACTGGCTGG 60.047 66.667 0.00 0.00 42.34 4.85
1025 1039 1.530655 TCGTGTCTGGTCTGGCTCA 60.531 57.895 0.00 0.00 0.00 4.26
1026 1040 1.080434 GTCGTGTCTGGTCTGGCTC 60.080 63.158 0.00 0.00 0.00 4.70
1027 1041 2.920645 CGTCGTGTCTGGTCTGGCT 61.921 63.158 0.00 0.00 0.00 4.75
1028 1042 2.430921 CGTCGTGTCTGGTCTGGC 60.431 66.667 0.00 0.00 0.00 4.85
1029 1043 1.081376 GTCGTCGTGTCTGGTCTGG 60.081 63.158 0.00 0.00 0.00 3.86
1030 1044 1.440518 CGTCGTCGTGTCTGGTCTG 60.441 63.158 0.00 0.00 0.00 3.51
1031 1045 2.614446 CCGTCGTCGTGTCTGGTCT 61.614 63.158 0.71 0.00 35.01 3.85
1032 1046 2.126965 CCGTCGTCGTGTCTGGTC 60.127 66.667 0.71 0.00 35.01 4.02
1033 1047 4.338539 GCCGTCGTCGTGTCTGGT 62.339 66.667 0.71 0.00 35.01 4.00
1361 1377 3.838271 GCGACGAGGCCCATGAGA 61.838 66.667 0.00 0.00 0.00 3.27
1465 1489 1.359848 CATGTGTTAGACGGGCAGAC 58.640 55.000 0.00 0.00 0.00 3.51
1472 1497 2.409715 CAGTCAGTGCATGTGTTAGACG 59.590 50.000 0.00 0.00 0.00 4.18
1573 1598 5.516996 TGCTACGTACAGCACATAGATAAC 58.483 41.667 8.93 0.00 46.41 1.89
1632 1667 0.957395 AACCAGAACATGCGAGCAGG 60.957 55.000 8.25 8.25 0.00 4.85
1649 1684 1.795768 TTCACTGTCTCGGCATGAAC 58.204 50.000 0.00 0.00 0.00 3.18
1698 1733 4.808364 CAGAACTTGTATGCCTAGAGAAGC 59.192 45.833 0.00 0.00 0.00 3.86
1751 1786 4.553330 ATTCACATAGACTGTCGGGTTT 57.447 40.909 1.52 0.00 35.29 3.27
1752 1787 4.553330 AATTCACATAGACTGTCGGGTT 57.447 40.909 1.52 0.00 35.29 4.11
1753 1788 4.253685 CAAATTCACATAGACTGTCGGGT 58.746 43.478 1.52 0.00 35.29 5.28
1754 1789 3.623060 CCAAATTCACATAGACTGTCGGG 59.377 47.826 1.52 0.00 35.29 5.14
1755 1790 4.253685 ACCAAATTCACATAGACTGTCGG 58.746 43.478 1.52 0.00 35.29 4.79
1761 1796 8.755018 CAAAAACTTGACCAAATTCACATAGAC 58.245 33.333 0.00 0.00 0.00 2.59
1763 1798 8.647143 ACAAAAACTTGACCAAATTCACATAG 57.353 30.769 0.00 0.00 0.00 2.23
1786 1821 7.953158 TCAGATGACAAAACAAAACAAAACA 57.047 28.000 0.00 0.00 0.00 2.83
1787 1822 9.824534 AATTCAGATGACAAAACAAAACAAAAC 57.175 25.926 0.00 0.00 0.00 2.43
1831 2393 1.355210 CCACACGTGCCAAGTGAAC 59.645 57.895 17.65 0.00 41.83 3.18
1844 2407 5.412594 TCAAATTCAGCTGAGATAACCACAC 59.587 40.000 17.43 0.00 0.00 3.82
1847 2410 6.149973 CACTTCAAATTCAGCTGAGATAACCA 59.850 38.462 17.43 0.00 0.00 3.67
1936 2499 4.630644 ATCAGACCTGTGTCAATCTGTT 57.369 40.909 0.00 0.00 44.33 3.16
1938 2501 5.240183 ACAAAATCAGACCTGTGTCAATCTG 59.760 40.000 0.00 0.00 44.33 2.90
1939 2502 5.380043 ACAAAATCAGACCTGTGTCAATCT 58.620 37.500 0.00 0.00 44.33 2.40
1947 2510 6.995686 TGTTGTACATACAAAATCAGACCTGT 59.004 34.615 6.05 0.00 46.54 4.00
1985 2556 3.463944 GTGGAACTTTCAGAGAAACGGA 58.536 45.455 0.00 0.00 0.00 4.69
2019 2590 4.742167 CACGCTCTCACCTAATATCTGTTG 59.258 45.833 0.00 0.00 0.00 3.33
2039 5095 1.202842 ACAACCTTTACTTCCCCCACG 60.203 52.381 0.00 0.00 0.00 4.94
2131 5187 4.201891 TGACTAGGAAGATCGTTAAGCGTC 60.202 45.833 0.00 0.00 42.13 5.19
2178 5234 2.864968 CTATACTAACTCATCGGCGCC 58.135 52.381 19.07 19.07 0.00 6.53
2183 5239 7.139392 TGTAAGCAAGCTATACTAACTCATCG 58.861 38.462 0.00 0.00 0.00 3.84
2289 5350 2.224329 TGCTCAGTTGCTTACGGGTTTA 60.224 45.455 0.00 0.00 0.00 2.01
2295 5356 3.926527 TCTGTTATGCTCAGTTGCTTACG 59.073 43.478 0.00 0.00 34.86 3.18
2305 5366 7.287696 TCCAGTACAATCTATCTGTTATGCTCA 59.712 37.037 0.00 0.00 0.00 4.26
2330 5391 5.405935 AAAACTATGGCCAATTTGTCCTC 57.594 39.130 10.96 0.00 0.00 3.71
2346 5408 3.304794 CGATTCGTTTGGGGCAAAAACTA 60.305 43.478 11.09 0.12 35.03 2.24
2416 5655 6.655003 GGGTATCATAGTAACCATCCACATTG 59.345 42.308 0.00 0.00 34.83 2.82
2613 5852 7.227512 AGAGAAGAAAAGGACATGTAAACACAG 59.772 37.037 0.00 0.00 0.00 3.66
2967 6210 3.996363 CAGCTGCTTCTACATGTACAACA 59.004 43.478 0.00 0.00 0.00 3.33
3020 6263 4.934001 TGCTTGCAAATTGTGAAGAAAACA 59.066 33.333 0.00 0.00 0.00 2.83
3094 6528 5.245531 TCACAAGATGGATTTTAGCGAGTT 58.754 37.500 0.00 0.00 0.00 3.01
3098 6532 5.998454 AGATCACAAGATGGATTTTAGCG 57.002 39.130 0.00 0.00 33.72 4.26
3101 6535 6.433716 TGCACAAGATCACAAGATGGATTTTA 59.566 34.615 0.00 0.00 33.72 1.52
3135 6569 9.447157 AATTTGGGTGTAAAAATATGACCATTG 57.553 29.630 0.00 0.00 0.00 2.82
3262 6747 6.173339 TCAGATGGCCAACTAAGAAGTAAAG 58.827 40.000 16.10 0.00 33.75 1.85
3303 6788 6.070995 TGAGTAAACGGGTAGAATTCTGATGT 60.071 38.462 18.47 8.22 0.00 3.06
3307 6792 7.611213 AAATGAGTAAACGGGTAGAATTCTG 57.389 36.000 18.47 3.59 0.00 3.02
3370 6855 3.327757 TCTTGAGCTGTTGTAATGGGTCT 59.672 43.478 0.00 0.00 0.00 3.85
3411 6896 1.067000 GCCTATTTGTTGTGGCATGCA 60.067 47.619 21.36 2.54 44.34 3.96
3435 6920 3.168035 TCATTGTATTGTGGGGCACTT 57.832 42.857 0.00 0.00 35.11 3.16
3474 6961 3.372440 AGAGTGCCCCATTTCCTTTAG 57.628 47.619 0.00 0.00 0.00 1.85
3480 6967 1.909700 TGACAAGAGTGCCCCATTTC 58.090 50.000 0.00 0.00 0.00 2.17
3557 7046 2.896854 CGCGGATGATGGTGTGGG 60.897 66.667 0.00 0.00 0.00 4.61
3653 10057 1.746861 CGCCTGGGTGCATCTATCAAA 60.747 52.381 0.00 0.00 0.00 2.69
3704 10108 5.246203 TGAGTCTGGTCTTAGCATAAAGTGT 59.754 40.000 0.00 0.00 0.00 3.55
3749 10697 0.963962 TCTCCCGGACACTACAACAC 59.036 55.000 0.73 0.00 0.00 3.32
3758 10706 2.178325 TGGTTCCTATATCTCCCGGACA 59.822 50.000 0.73 0.00 0.00 4.02
3788 10736 2.551912 GCCTGTTGTTGTGGGTCCG 61.552 63.158 0.00 0.00 0.00 4.79
3789 10737 1.152756 AGCCTGTTGTTGTGGGTCC 60.153 57.895 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.