Multiple sequence alignment - TraesCS7A01G431600

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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 TraesCS7A01G431600 chr7A 100.000 7337 0 0 1 7337 625634655 625641991 0.000000e+00 13501.0
1 TraesCS7A01G431600 chr7A 95.277 741 17 13 5738 6469 625673079 625673810 0.000000e+00 1158.0
2 TraesCS7A01G431600 chr7A 85.672 670 84 7 6671 7337 631653563 631652903 0.000000e+00 695.0
3 TraesCS7A01G431600 chr7A 95.388 412 17 2 6927 7337 625674354 625674764 0.000000e+00 654.0
4 TraesCS7A01G431600 chr7A 83.140 688 80 19 6666 7337 632186931 632187598 4.900000e-166 595.0
5 TraesCS7A01G431600 chr7A 85.164 519 60 8 6824 7337 630670690 630671196 3.920000e-142 516.0
6 TraesCS7A01G431600 chr7A 80.769 468 61 21 2646 3100 625636829 625637280 9.120000e-89 339.0
7 TraesCS7A01G431600 chr7A 80.769 468 61 20 2175 2626 625637300 625637754 9.120000e-89 339.0
8 TraesCS7A01G431600 chr7D 96.837 2940 55 19 3539 6467 543727409 543730321 0.000000e+00 4879.0
9 TraesCS7A01G431600 chr7D 91.931 1326 38 15 2223 3525 543726008 543727287 0.000000e+00 1792.0
10 TraesCS7A01G431600 chr7D 89.163 1421 66 34 709 2102 543724645 543726004 0.000000e+00 1690.0
11 TraesCS7A01G431600 chr7D 91.921 755 48 8 6588 7337 543730478 543731224 0.000000e+00 1044.0
12 TraesCS7A01G431600 chr7D 85.987 628 77 10 1 621 543723944 543724567 0.000000e+00 662.0
13 TraesCS7A01G431600 chr7D 84.783 598 74 8 6740 7337 530431786 530431206 1.060000e-162 584.0
14 TraesCS7A01G431600 chr7D 84.571 525 64 10 6744 7266 548324005 548324514 8.500000e-139 505.0
15 TraesCS7A01G431600 chr7D 80.694 461 55 24 2186 2626 543726433 543726879 1.970000e-85 327.0
16 TraesCS7A01G431600 chr7D 95.349 43 2 0 663 705 543724576 543724618 1.320000e-07 69.4
17 TraesCS7A01G431600 chr6B 95.692 2925 102 11 3549 6469 694676963 694679867 0.000000e+00 4682.0
18 TraesCS7A01G431600 chr6B 90.207 2032 141 27 770 2778 694673974 694675970 0.000000e+00 2597.0
19 TraesCS7A01G431600 chr6B 92.544 845 50 5 6497 7337 694679951 694680786 0.000000e+00 1199.0
20 TraesCS7A01G431600 chr6B 78.826 1601 323 12 4286 5881 151129791 151131380 0.000000e+00 1064.0
21 TraesCS7A01G431600 chr6B 86.897 725 47 18 2816 3525 694675965 694676656 0.000000e+00 769.0
22 TraesCS7A01G431600 chr6B 81.279 641 70 30 1 622 694673272 694673881 2.400000e-129 473.0
23 TraesCS7A01G431600 chr6B 80.000 460 54 21 2658 3100 694675380 694675818 9.250000e-79 305.0
24 TraesCS7A01G431600 chr6B 82.105 285 30 14 2347 2622 694675965 694676237 2.660000e-54 224.0
25 TraesCS7A01G431600 chr6B 84.699 183 20 5 1350 1531 151127292 151127467 7.570000e-40 176.0
26 TraesCS7A01G431600 chr6B 91.250 80 6 1 2186 2264 694675849 694675928 2.800000e-19 108.0
27 TraesCS7A01G431600 chr6A 79.250 1600 318 12 4286 5881 93813292 93814881 0.000000e+00 1103.0
28 TraesCS7A01G431600 chr6A 84.699 183 20 5 1350 1531 93810416 93810591 7.570000e-40 176.0
29 TraesCS7A01G431600 chr1D 93.343 691 34 5 6653 7337 110904297 110904981 0.000000e+00 1011.0
30 TraesCS7A01G431600 chr1D 82.824 262 18 10 6213 6469 110896372 110896611 7.460000e-50 209.0
31 TraesCS7A01G431600 chr1B 93.658 473 24 3 6865 7337 169024299 169024765 0.000000e+00 702.0
32 TraesCS7A01G431600 chr1B 87.749 351 18 14 6542 6872 169013501 169013846 3.210000e-103 387.0
33 TraesCS7A01G431600 chr1B 89.286 196 13 5 6213 6406 169011256 169011445 9.510000e-59 239.0
34 TraesCS7A01G431600 chr6D 83.938 193 22 6 1350 1541 78264794 78264978 7.570000e-40 176.0


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 TraesCS7A01G431600 chr7A 625634655 625641991 7336 False 13501.000000 13501 100.000000 1 7337 1 chr7A.!!$F1 7336
1 TraesCS7A01G431600 chr7A 625673079 625674764 1685 False 906.000000 1158 95.332500 5738 7337 2 chr7A.!!$F5 1599
2 TraesCS7A01G431600 chr7A 631652903 631653563 660 True 695.000000 695 85.672000 6671 7337 1 chr7A.!!$R1 666
3 TraesCS7A01G431600 chr7A 632186931 632187598 667 False 595.000000 595 83.140000 6666 7337 1 chr7A.!!$F3 671
4 TraesCS7A01G431600 chr7A 630670690 630671196 506 False 516.000000 516 85.164000 6824 7337 1 chr7A.!!$F2 513
5 TraesCS7A01G431600 chr7A 625636829 625637754 925 False 339.000000 339 80.769000 2175 3100 2 chr7A.!!$F4 925
6 TraesCS7A01G431600 chr7D 543723944 543731224 7280 False 1494.771429 4879 90.268857 1 7337 7 chr7D.!!$F2 7336
7 TraesCS7A01G431600 chr7D 530431206 530431786 580 True 584.000000 584 84.783000 6740 7337 1 chr7D.!!$R1 597
8 TraesCS7A01G431600 chr7D 548324005 548324514 509 False 505.000000 505 84.571000 6744 7266 1 chr7D.!!$F1 522
9 TraesCS7A01G431600 chr6B 694673272 694680786 7514 False 1294.625000 4682 87.496750 1 7337 8 chr6B.!!$F2 7336
10 TraesCS7A01G431600 chr6B 151127292 151131380 4088 False 620.000000 1064 81.762500 1350 5881 2 chr6B.!!$F1 4531
11 TraesCS7A01G431600 chr6A 93810416 93814881 4465 False 639.500000 1103 81.974500 1350 5881 2 chr6A.!!$F1 4531
12 TraesCS7A01G431600 chr1D 110904297 110904981 684 False 1011.000000 1011 93.343000 6653 7337 1 chr1D.!!$F2 684
13 TraesCS7A01G431600 chr1B 169011256 169013846 2590 False 313.000000 387 88.517500 6213 6872 2 chr1B.!!$F2 659

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
216 220 0.246635 CGGGAAAGGAAGAAGAGCGA 59.753 55.000 0.00 0.0 0.00 4.93 F
1272 1337 0.178935 GATGGAGGAGGAGGAGGAGG 60.179 65.000 0.00 0.0 0.00 4.30 F
1662 1734 0.528017 TGCTACGTCCTGAGCTTCTG 59.472 55.000 9.31 0.0 39.54 3.02 F
2113 2188 1.351017 TGAATTCTCCCTTGGTTCGCT 59.649 47.619 7.05 0.0 0.00 4.93 F
3910 6180 0.953471 TGCCGTACAACTGTGCATCC 60.953 55.000 0.00 0.0 0.00 3.51 F
5155 7645 0.109153 GGTTAGTTGTGTTCGGGGGT 59.891 55.000 0.00 0.0 0.00 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1782 1855 0.107165 GGCACAGGGAATCCTACACC 60.107 60.000 0.00 0.00 42.67 4.16 R
2088 2163 4.320494 CGAACCAAGGGAGAATTCAAACAG 60.320 45.833 8.44 0.00 0.00 3.16 R
3427 5408 6.642131 TCAGAAACTCAAAATAACAAGCATGC 59.358 34.615 10.51 10.51 0.00 4.06 R
3939 6272 1.471327 GCCAGCAAAAGACAGCAAACA 60.471 47.619 0.00 0.00 0.00 2.83 R
5623 8113 0.317269 CTGGCAAACTCACAGCAACG 60.317 55.000 0.00 0.00 0.00 4.10 R
6677 11284 0.812811 ACTGCGTAGGATGCATGCTG 60.813 55.000 28.88 18.60 39.71 4.41 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
55 56 1.749063 TGTCGTATCAGATCGCAAGGT 59.251 47.619 0.00 0.00 38.47 3.50
57 58 3.568430 TGTCGTATCAGATCGCAAGGTAT 59.432 43.478 0.00 0.00 38.47 2.73
58 59 4.758165 TGTCGTATCAGATCGCAAGGTATA 59.242 41.667 0.00 0.00 38.47 1.47
164 168 2.509336 GATGAGGCCACCGACACG 60.509 66.667 5.01 0.00 0.00 4.49
195 199 3.020984 GAGAATGAGACGAAGGAGGAGT 58.979 50.000 0.00 0.00 0.00 3.85
214 218 0.321653 TGCGGGAAAGGAAGAAGAGC 60.322 55.000 0.00 0.00 0.00 4.09
215 219 1.362406 GCGGGAAAGGAAGAAGAGCG 61.362 60.000 0.00 0.00 0.00 5.03
216 220 0.246635 CGGGAAAGGAAGAAGAGCGA 59.753 55.000 0.00 0.00 0.00 4.93
217 221 1.728068 GGGAAAGGAAGAAGAGCGAC 58.272 55.000 0.00 0.00 0.00 5.19
219 223 2.070028 GGAAAGGAAGAAGAGCGACAC 58.930 52.381 0.00 0.00 0.00 3.67
221 225 2.910688 AAGGAAGAAGAGCGACACAA 57.089 45.000 0.00 0.00 0.00 3.33
241 245 1.107945 TTGACCTCAGTGTGACGACA 58.892 50.000 0.00 0.00 0.00 4.35
251 255 1.081641 GTGACGACACCGACGATGT 60.082 57.895 6.77 0.00 40.74 3.06
255 259 2.261671 GACACCGACGATGTGGCT 59.738 61.111 0.00 0.00 38.75 4.75
265 269 1.897133 ACGATGTGGCTAGTGGTGTAA 59.103 47.619 0.00 0.00 0.00 2.41
266 270 2.500098 ACGATGTGGCTAGTGGTGTAAT 59.500 45.455 0.00 0.00 0.00 1.89
267 271 2.866156 CGATGTGGCTAGTGGTGTAATG 59.134 50.000 0.00 0.00 0.00 1.90
276 280 4.155826 GCTAGTGGTGTAATGCATTGTTGA 59.844 41.667 22.27 0.00 0.00 3.18
287 291 8.620416 TGTAATGCATTGTTGATAGAATGGTAC 58.380 33.333 22.27 6.55 35.99 3.34
288 292 6.639632 ATGCATTGTTGATAGAATGGTACC 57.360 37.500 4.43 4.43 35.99 3.34
293 297 3.050619 GTTGATAGAATGGTACCGAGCG 58.949 50.000 7.57 0.00 0.00 5.03
338 342 2.291089 TGCATGATTGGGATATGGCGAT 60.291 45.455 0.00 0.00 0.00 4.58
354 358 1.377202 GATGCCTTGACTTGCCCGA 60.377 57.895 0.00 0.00 0.00 5.14
388 392 1.743394 CGGTGGAAAATCAAGGCCTAC 59.257 52.381 5.16 0.00 0.00 3.18
391 395 4.686122 CGGTGGAAAATCAAGGCCTACTAT 60.686 45.833 5.16 0.00 0.00 2.12
412 416 0.805614 GCGGAAGGAAGAAAAGGAGC 59.194 55.000 0.00 0.00 0.00 4.70
413 417 1.882352 GCGGAAGGAAGAAAAGGAGCA 60.882 52.381 0.00 0.00 0.00 4.26
415 419 1.815613 GGAAGGAAGAAAAGGAGCAGC 59.184 52.381 0.00 0.00 0.00 5.25
416 420 2.508526 GAAGGAAGAAAAGGAGCAGCA 58.491 47.619 0.00 0.00 0.00 4.41
417 421 2.197283 AGGAAGAAAAGGAGCAGCAG 57.803 50.000 0.00 0.00 0.00 4.24
418 422 0.525311 GGAAGAAAAGGAGCAGCAGC 59.475 55.000 0.00 0.00 42.56 5.25
421 425 1.696063 AGAAAAGGAGCAGCAGCAAA 58.304 45.000 3.17 0.00 45.49 3.68
422 426 1.612463 AGAAAAGGAGCAGCAGCAAAG 59.388 47.619 3.17 0.00 45.49 2.77
426 430 2.034687 GAGCAGCAGCAAAGGGGA 59.965 61.111 3.17 0.00 45.49 4.81
428 432 1.593296 GAGCAGCAGCAAAGGGGAAG 61.593 60.000 3.17 0.00 45.49 3.46
429 433 2.643232 GCAGCAGCAAAGGGGAAGG 61.643 63.158 0.00 0.00 41.58 3.46
432 436 2.681421 CAGCAAAGGGGAAGGGGC 60.681 66.667 0.00 0.00 0.00 5.80
434 438 4.360405 GCAAAGGGGAAGGGGCGA 62.360 66.667 0.00 0.00 0.00 5.54
446 460 3.491208 GGGGCGACACTACTAGAGA 57.509 57.895 0.00 0.00 0.00 3.10
461 475 0.693049 AGAGAAACAAGATGCGGGGT 59.307 50.000 0.00 0.00 0.00 4.95
483 498 4.336889 TTTTCATGGTCTGAGTTCGACT 57.663 40.909 0.00 0.00 34.68 4.18
493 508 4.321217 GTCTGAGTTCGACTTTGTACATCG 59.679 45.833 10.41 10.41 37.20 3.84
494 509 4.023450 TCTGAGTTCGACTTTGTACATCGT 60.023 41.667 14.98 7.16 37.16 3.73
501 516 3.241773 CGACTTTGTACATCGTCATGCAG 60.242 47.826 19.09 4.96 32.57 4.41
512 527 1.201954 CGTCATGCAGAACATTCGGTG 60.202 52.381 0.00 0.00 36.64 4.94
539 554 4.200283 GCGACGGAGCAGAGGAGG 62.200 72.222 0.00 0.00 37.05 4.30
571 586 1.158227 TCCATGCTTTTGGGGGCTT 59.842 52.632 0.00 0.00 37.37 4.35
572 587 0.473501 TCCATGCTTTTGGGGGCTTT 60.474 50.000 0.00 0.00 37.37 3.51
578 593 3.180507 TGCTTTTGGGGGCTTTTGATAT 58.819 40.909 0.00 0.00 0.00 1.63
579 594 3.586618 TGCTTTTGGGGGCTTTTGATATT 59.413 39.130 0.00 0.00 0.00 1.28
587 602 3.103742 GGGCTTTTGATATTCCCAACCA 58.896 45.455 0.00 0.00 36.96 3.67
597 612 1.394618 TTCCCAACCAGAAAACCACG 58.605 50.000 0.00 0.00 0.00 4.94
622 642 7.306213 GCCTAGAAGTTTCAAACAAATCCTAC 58.694 38.462 2.41 0.00 0.00 3.18
623 643 7.175119 GCCTAGAAGTTTCAAACAAATCCTACT 59.825 37.037 2.41 0.00 0.00 2.57
624 644 8.722394 CCTAGAAGTTTCAAACAAATCCTACTC 58.278 37.037 2.41 0.00 0.00 2.59
625 645 7.511959 AGAAGTTTCAAACAAATCCTACTCC 57.488 36.000 2.41 0.00 0.00 3.85
626 646 5.941948 AGTTTCAAACAAATCCTACTCCG 57.058 39.130 2.41 0.00 0.00 4.63
627 647 4.760204 AGTTTCAAACAAATCCTACTCCGG 59.240 41.667 2.41 0.00 0.00 5.14
628 648 4.627284 TTCAAACAAATCCTACTCCGGA 57.373 40.909 2.93 2.93 37.50 5.14
630 650 5.174037 TCAAACAAATCCTACTCCGGAAT 57.826 39.130 5.23 0.00 36.49 3.01
631 651 6.302535 TCAAACAAATCCTACTCCGGAATA 57.697 37.500 5.23 0.00 36.49 1.75
632 652 6.346096 TCAAACAAATCCTACTCCGGAATAG 58.654 40.000 13.08 13.08 36.49 1.73
633 653 6.155565 TCAAACAAATCCTACTCCGGAATAGA 59.844 38.462 21.28 8.46 36.49 1.98
634 654 6.555463 AACAAATCCTACTCCGGAATAGAA 57.445 37.500 21.28 0.17 36.49 2.10
635 655 6.749036 ACAAATCCTACTCCGGAATAGAAT 57.251 37.500 21.28 3.22 36.49 2.40
636 656 7.850935 ACAAATCCTACTCCGGAATAGAATA 57.149 36.000 21.28 6.77 36.49 1.75
637 657 7.668492 ACAAATCCTACTCCGGAATAGAATAC 58.332 38.462 21.28 0.00 36.49 1.89
638 658 7.289317 ACAAATCCTACTCCGGAATAGAATACA 59.711 37.037 21.28 0.32 36.49 2.29
639 659 7.469537 AATCCTACTCCGGAATAGAATACAG 57.530 40.000 21.28 3.53 36.49 2.74
640 660 6.196918 TCCTACTCCGGAATAGAATACAGA 57.803 41.667 21.28 5.92 0.00 3.41
641 661 6.791371 TCCTACTCCGGAATAGAATACAGAT 58.209 40.000 21.28 0.00 0.00 2.90
642 662 7.239438 TCCTACTCCGGAATAGAATACAGATT 58.761 38.462 21.28 0.00 0.00 2.40
643 663 7.176865 TCCTACTCCGGAATAGAATACAGATTG 59.823 40.741 21.28 0.66 0.00 2.67
644 664 6.102897 ACTCCGGAATAGAATACAGATTGG 57.897 41.667 5.23 0.00 0.00 3.16
645 665 5.602978 ACTCCGGAATAGAATACAGATTGGT 59.397 40.000 5.23 0.00 0.00 3.67
646 666 6.099845 ACTCCGGAATAGAATACAGATTGGTT 59.900 38.462 5.23 0.00 0.00 3.67
647 667 6.895782 TCCGGAATAGAATACAGATTGGTTT 58.104 36.000 0.00 0.00 0.00 3.27
648 668 7.343357 TCCGGAATAGAATACAGATTGGTTTT 58.657 34.615 0.00 0.00 0.00 2.43
649 669 7.832187 TCCGGAATAGAATACAGATTGGTTTTT 59.168 33.333 0.00 0.00 0.00 1.94
696 716 8.416329 AGCTGAAATTCAACTCATTTGTAAAGT 58.584 29.630 0.00 0.00 36.49 2.66
705 725 5.313712 ACTCATTTGTAAAGTGGGTGTAGG 58.686 41.667 0.00 0.00 46.24 3.18
707 727 3.512219 TTTGTAAAGTGGGTGTAGGGG 57.488 47.619 0.00 0.00 0.00 4.79
708 728 1.364269 TGTAAAGTGGGTGTAGGGGG 58.636 55.000 0.00 0.00 0.00 5.40
709 729 1.132462 TGTAAAGTGGGTGTAGGGGGA 60.132 52.381 0.00 0.00 0.00 4.81
711 731 0.845102 AAAGTGGGTGTAGGGGGAGG 60.845 60.000 0.00 0.00 0.00 4.30
714 734 4.837421 GGGTGTAGGGGGAGGGGG 62.837 77.778 0.00 0.00 0.00 5.40
715 735 3.702623 GGTGTAGGGGGAGGGGGA 61.703 72.222 0.00 0.00 0.00 4.81
716 736 2.366569 GTGTAGGGGGAGGGGGAC 60.367 72.222 0.00 0.00 0.00 4.46
717 737 2.877383 TGTAGGGGGAGGGGGACA 60.877 66.667 0.00 0.00 0.00 4.02
718 738 2.457794 GTAGGGGGAGGGGGACAA 59.542 66.667 0.00 0.00 0.00 3.18
719 739 1.230050 GTAGGGGGAGGGGGACAAA 60.230 63.158 0.00 0.00 0.00 2.83
722 742 2.035155 GGGGAGGGGGACAAAACG 59.965 66.667 0.00 0.00 0.00 3.60
723 743 2.531601 GGGGAGGGGGACAAAACGA 61.532 63.158 0.00 0.00 0.00 3.85
724 744 1.303074 GGGAGGGGGACAAAACGAC 60.303 63.158 0.00 0.00 0.00 4.34
726 746 1.670083 GAGGGGGACAAAACGACGG 60.670 63.158 0.00 0.00 0.00 4.79
727 747 3.359523 GGGGGACAAAACGACGGC 61.360 66.667 0.00 0.00 0.00 5.68
728 748 3.359523 GGGGACAAAACGACGGCC 61.360 66.667 0.00 0.00 0.00 6.13
729 749 2.592287 GGGACAAAACGACGGCCA 60.592 61.111 2.24 0.00 0.00 5.36
731 751 2.181521 GGACAAAACGACGGCCACA 61.182 57.895 2.24 0.00 0.00 4.17
732 752 1.010462 GACAAAACGACGGCCACAC 60.010 57.895 2.24 0.00 0.00 3.82
733 753 2.330041 CAAAACGACGGCCACACC 59.670 61.111 2.24 0.00 0.00 4.16
734 754 2.124653 AAAACGACGGCCACACCA 60.125 55.556 2.24 0.00 39.03 4.17
879 926 3.770040 CATCCACCGAGCGGGACA 61.770 66.667 14.07 0.00 39.97 4.02
977 1039 0.614979 CTCTTTCTCCCCTCCCACGA 60.615 60.000 0.00 0.00 0.00 4.35
1022 1084 4.066139 GAGCCCCAGCCCACCATT 62.066 66.667 0.00 0.00 41.25 3.16
1023 1085 4.066139 AGCCCCAGCCCACCATTC 62.066 66.667 0.00 0.00 41.25 2.67
1030 1092 3.346734 GCCCACCATTCCCTCCCA 61.347 66.667 0.00 0.00 0.00 4.37
1031 1093 3.010144 CCCACCATTCCCTCCCAG 58.990 66.667 0.00 0.00 0.00 4.45
1033 1095 1.609783 CCACCATTCCCTCCCAGTC 59.390 63.158 0.00 0.00 0.00 3.51
1051 1113 2.854076 CCAGCCCCAAACCTCCTT 59.146 61.111 0.00 0.00 0.00 3.36
1053 1115 1.675641 CAGCCCCAAACCTCCTTCG 60.676 63.158 0.00 0.00 0.00 3.79
1270 1335 0.856982 GAGATGGAGGAGGAGGAGGA 59.143 60.000 0.00 0.00 0.00 3.71
1271 1336 0.859760 AGATGGAGGAGGAGGAGGAG 59.140 60.000 0.00 0.00 0.00 3.69
1272 1337 0.178935 GATGGAGGAGGAGGAGGAGG 60.179 65.000 0.00 0.00 0.00 4.30
1273 1338 0.631998 ATGGAGGAGGAGGAGGAGGA 60.632 60.000 0.00 0.00 0.00 3.71
1274 1339 1.292941 TGGAGGAGGAGGAGGAGGAG 61.293 65.000 0.00 0.00 0.00 3.69
1275 1340 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
1276 1341 2.018086 AGGAGGAGGAGGAGGAGGG 61.018 68.421 0.00 0.00 0.00 4.30
1277 1342 2.612251 GAGGAGGAGGAGGAGGGG 59.388 72.222 0.00 0.00 0.00 4.79
1337 1408 4.522975 GGCGGGGGATTTGGAGGG 62.523 72.222 0.00 0.00 0.00 4.30
1338 1409 3.416880 GCGGGGGATTTGGAGGGA 61.417 66.667 0.00 0.00 0.00 4.20
1339 1410 2.768022 GCGGGGGATTTGGAGGGAT 61.768 63.158 0.00 0.00 0.00 3.85
1340 1411 1.423794 GCGGGGGATTTGGAGGGATA 61.424 60.000 0.00 0.00 0.00 2.59
1341 1412 0.693049 CGGGGGATTTGGAGGGATAG 59.307 60.000 0.00 0.00 0.00 2.08
1342 1413 1.076438 GGGGGATTTGGAGGGATAGG 58.924 60.000 0.00 0.00 0.00 2.57
1588 1660 5.384063 TTCGTGCATGTATTGTTGGAATT 57.616 34.783 5.68 0.00 0.00 2.17
1607 1679 4.630644 ATTGATGCCACTTAGGATCGAT 57.369 40.909 0.00 0.00 41.22 3.59
1626 1698 7.641802 GGATCGATCAGAGCTTAATTTTTGTTC 59.358 37.037 25.93 0.00 35.20 3.18
1629 1701 6.797033 CGATCAGAGCTTAATTTTTGTTCGTT 59.203 34.615 0.00 0.00 0.00 3.85
1630 1702 7.323656 CGATCAGAGCTTAATTTTTGTTCGTTT 59.676 33.333 0.00 0.00 0.00 3.60
1632 1704 6.695278 TCAGAGCTTAATTTTTGTTCGTTTGG 59.305 34.615 0.00 0.00 0.00 3.28
1633 1705 6.695278 CAGAGCTTAATTTTTGTTCGTTTGGA 59.305 34.615 0.00 0.00 0.00 3.53
1635 1707 8.573035 AGAGCTTAATTTTTGTTCGTTTGGATA 58.427 29.630 0.00 0.00 0.00 2.59
1636 1708 9.187455 GAGCTTAATTTTTGTTCGTTTGGATAA 57.813 29.630 0.00 0.00 0.00 1.75
1645 1717 3.859411 TCGTTTGGATAATTGGGTTGC 57.141 42.857 0.00 0.00 0.00 4.17
1661 1733 1.067495 GTTGCTACGTCCTGAGCTTCT 60.067 52.381 9.31 0.00 39.54 2.85
1662 1734 0.528017 TGCTACGTCCTGAGCTTCTG 59.472 55.000 9.31 0.00 39.54 3.02
1733 1806 8.196771 TCTTCGGTTTACACTCTACTTGTTAAA 58.803 33.333 0.00 0.00 0.00 1.52
1749 1822 4.927422 TGTTAAAACGCTTCTTCTTTGGG 58.073 39.130 0.00 0.00 0.00 4.12
1782 1855 1.724623 CTGTGACGTGGGTTCGTTATG 59.275 52.381 0.00 0.00 44.21 1.90
1821 1894 3.803368 GCCTGTTTGTGCTTATTTGGCTT 60.803 43.478 0.00 0.00 35.44 4.35
1824 1897 3.559242 TGTTTGTGCTTATTTGGCTTTGC 59.441 39.130 0.00 0.00 0.00 3.68
1865 1938 7.612266 CATTGTTTGCTTTCTGTTAACAGTTC 58.388 34.615 29.83 18.76 44.12 3.01
1881 1954 4.890088 ACAGTTCCTACAAATGCTCGTAA 58.110 39.130 0.00 0.00 0.00 3.18
1892 1965 2.561733 TGCTCGTAAGACTTCCGATG 57.438 50.000 3.16 0.30 45.01 3.84
1905 1978 1.889545 TCCGATGATTTGTGTGCACA 58.110 45.000 17.42 17.42 39.98 4.57
1923 1996 7.061094 GTGTGCACAAAATAGATTGAAGTTAGC 59.939 37.037 23.59 0.00 34.38 3.09
2031 2104 8.718656 ACCATATCTTGAGGCTTTATTTACTCT 58.281 33.333 0.00 0.00 0.00 3.24
2076 2151 4.252073 CATCTTGGCCTGATATGCTAGTC 58.748 47.826 3.32 0.00 0.00 2.59
2088 2163 2.113860 TGCTAGTCTTGGAACCATGC 57.886 50.000 0.00 0.00 0.00 4.06
2103 2178 2.827921 ACCATGCTGTTTGAATTCTCCC 59.172 45.455 7.05 0.00 0.00 4.30
2105 2180 3.512724 CCATGCTGTTTGAATTCTCCCTT 59.487 43.478 7.05 0.00 0.00 3.95
2107 2182 2.892852 TGCTGTTTGAATTCTCCCTTGG 59.107 45.455 7.05 0.00 0.00 3.61
2109 2184 3.321968 GCTGTTTGAATTCTCCCTTGGTT 59.678 43.478 7.05 0.00 0.00 3.67
2110 2185 4.559502 GCTGTTTGAATTCTCCCTTGGTTC 60.560 45.833 7.05 0.00 0.00 3.62
2111 2186 3.568007 TGTTTGAATTCTCCCTTGGTTCG 59.432 43.478 7.05 0.00 0.00 3.95
2112 2187 1.821216 TGAATTCTCCCTTGGTTCGC 58.179 50.000 7.05 0.00 0.00 4.70
2113 2188 1.351017 TGAATTCTCCCTTGGTTCGCT 59.649 47.619 7.05 0.00 0.00 4.93
2114 2189 2.569853 TGAATTCTCCCTTGGTTCGCTA 59.430 45.455 7.05 0.00 0.00 4.26
2131 2206 6.036735 GGTTCGCTAACTTTGTATCTAATGCA 59.963 38.462 0.73 0.00 35.81 3.96
2135 2210 6.495706 GCTAACTTTGTATCTAATGCAACCC 58.504 40.000 0.00 0.00 34.59 4.11
2137 2212 7.148069 GCTAACTTTGTATCTAATGCAACCCTT 60.148 37.037 0.00 0.00 34.59 3.95
2153 2228 5.241728 GCAACCCTTCAAGATTGACTTAACT 59.758 40.000 5.74 0.00 36.83 2.24
2154 2229 6.568653 GCAACCCTTCAAGATTGACTTAACTC 60.569 42.308 5.74 0.00 36.83 3.01
2155 2230 6.441088 ACCCTTCAAGATTGACTTAACTCT 57.559 37.500 0.00 0.00 36.83 3.24
2156 2231 6.234177 ACCCTTCAAGATTGACTTAACTCTG 58.766 40.000 0.00 0.00 36.83 3.35
2168 2243 6.783162 TGACTTAACTCTGATACTTCTACGC 58.217 40.000 0.00 0.00 0.00 4.42
3295 5265 7.186594 TGAGGGACCCATAGATATCTGTATACT 59.813 40.741 14.60 3.92 0.00 2.12
3296 5266 8.654751 AGGGACCCATAGATATCTGTATACTA 57.345 38.462 14.60 0.00 0.00 1.82
3297 5267 8.504409 AGGGACCCATAGATATCTGTATACTAC 58.496 40.741 14.60 0.92 0.00 2.73
3298 5268 7.444792 GGGACCCATAGATATCTGTATACTACG 59.555 44.444 15.79 0.00 0.00 3.51
3418 5399 6.314784 CAAAGTTTGGAAGGCTTAATCGTAG 58.685 40.000 7.78 0.00 0.00 3.51
3420 5401 5.801380 AGTTTGGAAGGCTTAATCGTAGAA 58.199 37.500 0.00 0.00 43.58 2.10
3422 5403 5.416271 TTGGAAGGCTTAATCGTAGAAGT 57.584 39.130 0.00 0.00 43.58 3.01
3424 5405 6.534475 TGGAAGGCTTAATCGTAGAAGTTA 57.466 37.500 0.00 0.00 43.58 2.24
3425 5406 7.120923 TGGAAGGCTTAATCGTAGAAGTTAT 57.879 36.000 0.00 0.00 43.58 1.89
3427 5408 7.494625 TGGAAGGCTTAATCGTAGAAGTTATTG 59.505 37.037 0.00 0.00 43.58 1.90
3428 5409 6.846325 AGGCTTAATCGTAGAAGTTATTGC 57.154 37.500 0.00 0.00 43.58 3.56
3429 5410 6.346096 AGGCTTAATCGTAGAAGTTATTGCA 58.654 36.000 0.00 0.00 43.58 4.08
3430 5411 6.992715 AGGCTTAATCGTAGAAGTTATTGCAT 59.007 34.615 0.00 0.00 43.58 3.96
3431 5412 7.041780 AGGCTTAATCGTAGAAGTTATTGCATG 60.042 37.037 0.00 0.00 43.58 4.06
3432 5413 6.575201 GCTTAATCGTAGAAGTTATTGCATGC 59.425 38.462 11.82 11.82 43.58 4.06
3433 5414 7.519008 GCTTAATCGTAGAAGTTATTGCATGCT 60.519 37.037 20.33 1.26 43.58 3.79
3434 5415 6.683974 AATCGTAGAAGTTATTGCATGCTT 57.316 33.333 20.33 9.09 43.58 3.91
3435 5416 5.469373 TCGTAGAAGTTATTGCATGCTTG 57.531 39.130 20.33 0.00 0.00 4.01
3436 5417 4.935205 TCGTAGAAGTTATTGCATGCTTGT 59.065 37.500 20.33 7.25 0.00 3.16
3437 5418 5.411361 TCGTAGAAGTTATTGCATGCTTGTT 59.589 36.000 20.33 3.73 0.00 2.83
3910 6180 0.953471 TGCCGTACAACTGTGCATCC 60.953 55.000 0.00 0.00 0.00 3.51
3931 6264 6.271488 TCCTGACCATGAACATTGAATTTC 57.729 37.500 0.00 0.00 0.00 2.17
3953 6286 8.825667 TTTCTTAAAGTTGTTTGCTGTCTTTT 57.174 26.923 0.00 0.00 32.01 2.27
3977 6310 5.704053 TGCTGGCATTCTACATCATTATGAG 59.296 40.000 0.29 0.00 36.54 2.90
4067 6400 4.021368 CCAAGGGGTCCTTATGATACTACG 60.021 50.000 0.00 0.00 42.67 3.51
4903 7393 1.529010 CACCCTGGAAGCTGTTGCA 60.529 57.895 0.00 0.00 42.74 4.08
4918 7408 3.229293 TGTTGCATGGAGGAAATTGACA 58.771 40.909 0.00 0.00 0.00 3.58
5119 7609 1.059913 GCTGGGGCCATACACTATCT 58.940 55.000 4.39 0.00 0.00 1.98
5155 7645 0.109153 GGTTAGTTGTGTTCGGGGGT 59.891 55.000 0.00 0.00 0.00 4.95
5503 7993 1.228533 GTCCTCTCCGACTACGATCC 58.771 60.000 0.00 0.00 42.66 3.36
5623 8113 1.134965 CCACCTCCTCGTCTTGATCAC 60.135 57.143 0.00 0.00 0.00 3.06
5656 8146 0.474854 TGCCAGGGGGAAGAGTGTTA 60.475 55.000 0.00 0.00 35.59 2.41
6099 8591 0.179067 CCGGGGTTGCTCGCTTTATA 60.179 55.000 0.00 0.00 0.00 0.98
6100 8592 1.542547 CCGGGGTTGCTCGCTTTATAT 60.543 52.381 0.00 0.00 0.00 0.86
6127 8622 9.338622 GTAGCTAATGGGTAGTGATATGTTTTT 57.661 33.333 0.00 0.00 31.78 1.94
6285 8781 2.160721 TGTACAGATGACCCCTCTCC 57.839 55.000 0.00 0.00 0.00 3.71
6416 8917 6.996282 AGGTAAGCTTATTAGTTGTGTGTGTT 59.004 34.615 9.88 0.00 0.00 3.32
6483 10967 6.842437 ACAGTTCTTCTCTAGCACTGATAA 57.158 37.500 10.70 0.00 46.98 1.75
6484 10968 7.233389 ACAGTTCTTCTCTAGCACTGATAAA 57.767 36.000 10.70 0.00 46.98 1.40
6485 10969 7.093992 ACAGTTCTTCTCTAGCACTGATAAAC 58.906 38.462 10.70 0.00 46.98 2.01
6486 10970 7.093354 CAGTTCTTCTCTAGCACTGATAAACA 58.907 38.462 0.00 0.00 46.98 2.83
6487 10971 7.763528 CAGTTCTTCTCTAGCACTGATAAACAT 59.236 37.037 0.00 0.00 46.98 2.71
6491 11044 7.547019 TCTTCTCTAGCACTGATAAACATTGTG 59.453 37.037 0.00 0.00 32.78 3.33
6553 11111 2.240667 AGATCCTAGCCTGCACAACATT 59.759 45.455 0.00 0.00 0.00 2.71
6584 11146 5.640147 ACAATTCCATTACAGGAGAAACCA 58.360 37.500 0.00 0.00 39.25 3.67
6585 11147 5.476945 ACAATTCCATTACAGGAGAAACCAC 59.523 40.000 0.00 0.00 39.25 4.16
6586 11148 3.713826 TCCATTACAGGAGAAACCACC 57.286 47.619 0.00 0.00 42.04 4.61
6646 11233 8.055181 ACAAAACATATCATCATCTTGTACCCT 58.945 33.333 0.00 0.00 0.00 4.34
6648 11235 9.561069 AAAACATATCATCATCTTGTACCCTAC 57.439 33.333 0.00 0.00 0.00 3.18
6650 11237 3.728076 TCATCATCTTGTACCCTACGC 57.272 47.619 0.00 0.00 0.00 4.42
6651 11238 3.028130 TCATCATCTTGTACCCTACGCA 58.972 45.455 0.00 0.00 0.00 5.24
6677 11284 4.110482 GTGATGACGTAGAATGGTGGTAC 58.890 47.826 0.00 0.00 0.00 3.34
6696 11303 0.812811 CAGCATGCATCCTACGCAGT 60.813 55.000 21.98 0.00 43.88 4.40
6697 11304 0.752658 AGCATGCATCCTACGCAGTA 59.247 50.000 21.98 0.00 43.88 2.74
6839 11455 4.821589 GCTCCTCCGGGAACAGCG 62.822 72.222 0.00 0.00 41.69 5.18
6921 11544 2.995482 CGTGCGCGTGAATCCTAC 59.005 61.111 12.43 0.00 0.00 3.18
6968 11591 2.636412 CGGAAGAGCTGGTCGACCA 61.636 63.158 34.13 34.13 45.30 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 7.125356 AGGAATTTTGTTCGGAGTATACCTACT 59.875 37.037 0.00 0.00 40.98 2.57
22 23 7.504924 TCTGATACGACAACAAAGGAATTTT 57.495 32.000 0.00 0.00 0.00 1.82
37 38 5.704053 TCTTATACCTTGCGATCTGATACGA 59.296 40.000 11.74 0.00 0.00 3.43
43 44 6.266168 AGATCTCTTATACCTTGCGATCTG 57.734 41.667 0.00 0.00 35.95 2.90
55 56 7.964867 TCTCCTTCCTCCTCTAGATCTCTTATA 59.035 40.741 0.00 0.00 0.00 0.98
57 58 6.154645 TCTCCTTCCTCCTCTAGATCTCTTA 58.845 44.000 0.00 0.00 0.00 2.10
58 59 4.981647 TCTCCTTCCTCCTCTAGATCTCTT 59.018 45.833 0.00 0.00 0.00 2.85
164 168 4.138290 TCGTCTCATTCTCCTACCATCTC 58.862 47.826 0.00 0.00 0.00 2.75
195 199 0.321653 GCTCTTCTTCCTTTCCCGCA 60.322 55.000 0.00 0.00 0.00 5.69
214 218 2.221749 CACACTGAGGTCAATTGTGTCG 59.778 50.000 5.13 1.41 39.46 4.35
215 219 3.248602 GTCACACTGAGGTCAATTGTGTC 59.751 47.826 15.87 10.12 39.46 3.67
216 220 3.206150 GTCACACTGAGGTCAATTGTGT 58.794 45.455 15.87 8.67 41.75 3.72
217 221 2.221749 CGTCACACTGAGGTCAATTGTG 59.778 50.000 5.13 12.34 39.48 3.33
219 223 2.476619 GTCGTCACACTGAGGTCAATTG 59.523 50.000 0.00 0.00 34.22 2.32
221 225 1.686587 TGTCGTCACACTGAGGTCAAT 59.313 47.619 0.00 0.00 34.22 2.57
241 245 1.511305 CACTAGCCACATCGTCGGT 59.489 57.895 0.00 0.00 0.00 4.69
251 255 3.016031 CAATGCATTACACCACTAGCCA 58.984 45.455 12.53 0.00 0.00 4.75
255 259 7.334858 TCTATCAACAATGCATTACACCACTA 58.665 34.615 12.53 0.00 0.00 2.74
265 269 5.239306 CGGTACCATTCTATCAACAATGCAT 59.761 40.000 13.54 0.00 0.00 3.96
266 270 4.574421 CGGTACCATTCTATCAACAATGCA 59.426 41.667 13.54 0.00 0.00 3.96
267 271 4.814234 TCGGTACCATTCTATCAACAATGC 59.186 41.667 13.54 0.00 0.00 3.56
276 280 0.317479 GGCGCTCGGTACCATTCTAT 59.683 55.000 13.54 0.00 0.00 1.98
293 297 2.111582 GCTTGTAGGCTCTGCAGGC 61.112 63.158 15.13 15.77 40.98 4.85
299 303 3.302347 AAGCGCGCTTGTAGGCTCT 62.302 57.895 42.62 18.29 33.99 4.09
319 323 2.098607 GCATCGCCATATCCCAATCATG 59.901 50.000 0.00 0.00 0.00 3.07
338 342 2.281484 GTCGGGCAAGTCAAGGCA 60.281 61.111 0.00 0.00 0.00 4.75
354 358 3.766691 ACCGCCGCCATCGTAAGT 61.767 61.111 0.00 0.00 39.48 2.24
388 392 2.945668 CCTTTTCTTCCTTCCGCCATAG 59.054 50.000 0.00 0.00 0.00 2.23
391 395 0.768622 TCCTTTTCTTCCTTCCGCCA 59.231 50.000 0.00 0.00 0.00 5.69
412 416 1.980772 CCCTTCCCCTTTGCTGCTG 60.981 63.158 0.00 0.00 0.00 4.41
413 417 2.442413 CCCTTCCCCTTTGCTGCT 59.558 61.111 0.00 0.00 0.00 4.24
415 419 2.681421 GCCCCTTCCCCTTTGCTG 60.681 66.667 0.00 0.00 0.00 4.41
416 420 4.366684 CGCCCCTTCCCCTTTGCT 62.367 66.667 0.00 0.00 0.00 3.91
417 421 4.360405 TCGCCCCTTCCCCTTTGC 62.360 66.667 0.00 0.00 0.00 3.68
418 422 2.361230 GTCGCCCCTTCCCCTTTG 60.361 66.667 0.00 0.00 0.00 2.77
421 425 3.248248 TAGTGTCGCCCCTTCCCCT 62.248 63.158 0.00 0.00 0.00 4.79
422 426 2.686106 TAGTGTCGCCCCTTCCCC 60.686 66.667 0.00 0.00 0.00 4.81
426 430 1.284198 TCTCTAGTAGTGTCGCCCCTT 59.716 52.381 0.00 0.00 0.00 3.95
428 432 1.760192 TTCTCTAGTAGTGTCGCCCC 58.240 55.000 0.00 0.00 0.00 5.80
429 433 2.490903 TGTTTCTCTAGTAGTGTCGCCC 59.509 50.000 0.00 0.00 0.00 6.13
432 436 5.513495 GCATCTTGTTTCTCTAGTAGTGTCG 59.487 44.000 0.00 0.00 0.00 4.35
434 438 5.403246 CGCATCTTGTTTCTCTAGTAGTGT 58.597 41.667 0.00 0.00 0.00 3.55
446 460 2.432510 TGAAAAACCCCGCATCTTGTTT 59.567 40.909 0.00 0.00 32.62 2.83
461 475 4.703897 AGTCGAACTCAGACCATGAAAAA 58.296 39.130 0.00 0.00 37.52 1.94
483 498 4.061596 TGTTCTGCATGACGATGTACAAA 58.938 39.130 0.00 0.00 31.50 2.83
493 508 1.466360 GCACCGAATGTTCTGCATGAC 60.466 52.381 0.00 0.00 37.96 3.06
494 509 0.804364 GCACCGAATGTTCTGCATGA 59.196 50.000 0.00 0.00 37.96 3.07
501 516 1.666209 CCCCCATGCACCGAATGTTC 61.666 60.000 0.00 0.00 0.00 3.18
571 586 5.841237 TGGTTTTCTGGTTGGGAATATCAAA 59.159 36.000 0.00 0.00 0.00 2.69
572 587 5.245075 GTGGTTTTCTGGTTGGGAATATCAA 59.755 40.000 0.00 0.00 0.00 2.57
578 593 1.394618 CGTGGTTTTCTGGTTGGGAA 58.605 50.000 0.00 0.00 0.00 3.97
579 594 1.104577 GCGTGGTTTTCTGGTTGGGA 61.105 55.000 0.00 0.00 0.00 4.37
587 602 3.487120 AACTTCTAGGCGTGGTTTTCT 57.513 42.857 0.00 0.00 0.00 2.52
597 612 6.332735 AGGATTTGTTTGAAACTTCTAGGC 57.667 37.500 9.69 0.00 0.00 3.93
622 642 6.102897 ACCAATCTGTATTCTATTCCGGAG 57.897 41.667 3.34 0.00 0.00 4.63
623 643 6.494666 AACCAATCTGTATTCTATTCCGGA 57.505 37.500 0.00 0.00 0.00 5.14
624 644 7.568199 AAAACCAATCTGTATTCTATTCCGG 57.432 36.000 0.00 0.00 0.00 5.14
647 667 7.234577 AGCTCAATTTGTATTGTCCCCTAAAAA 59.765 33.333 0.00 0.00 41.54 1.94
648 668 6.723977 AGCTCAATTTGTATTGTCCCCTAAAA 59.276 34.615 0.00 0.00 41.54 1.52
649 669 6.152661 CAGCTCAATTTGTATTGTCCCCTAAA 59.847 38.462 0.00 0.00 41.54 1.85
650 670 5.652014 CAGCTCAATTTGTATTGTCCCCTAA 59.348 40.000 0.00 0.00 41.54 2.69
651 671 5.045213 TCAGCTCAATTTGTATTGTCCCCTA 60.045 40.000 0.00 0.00 41.54 3.53
652 672 4.019174 CAGCTCAATTTGTATTGTCCCCT 58.981 43.478 0.00 0.00 41.54 4.79
653 673 4.016444 TCAGCTCAATTTGTATTGTCCCC 58.984 43.478 0.00 0.00 41.54 4.81
654 674 5.643379 TTCAGCTCAATTTGTATTGTCCC 57.357 39.130 0.00 0.00 41.54 4.46
655 675 7.814107 TGAATTTCAGCTCAATTTGTATTGTCC 59.186 33.333 0.00 0.00 41.54 4.02
656 676 8.746922 TGAATTTCAGCTCAATTTGTATTGTC 57.253 30.769 0.00 0.00 41.54 3.18
657 677 8.981647 GTTGAATTTCAGCTCAATTTGTATTGT 58.018 29.630 6.04 0.00 41.54 2.71
658 678 9.199982 AGTTGAATTTCAGCTCAATTTGTATTG 57.800 29.630 9.68 0.00 42.06 1.90
696 716 4.033251 CCCCTCCCCCTACACCCA 62.033 72.222 0.00 0.00 0.00 4.51
705 725 2.035155 CGTTTTGTCCCCCTCCCC 59.965 66.667 0.00 0.00 0.00 4.81
707 727 1.670083 CGTCGTTTTGTCCCCCTCC 60.670 63.158 0.00 0.00 0.00 4.30
708 728 1.670083 CCGTCGTTTTGTCCCCCTC 60.670 63.158 0.00 0.00 0.00 4.30
709 729 2.428622 CCGTCGTTTTGTCCCCCT 59.571 61.111 0.00 0.00 0.00 4.79
711 731 3.359523 GGCCGTCGTTTTGTCCCC 61.360 66.667 0.00 0.00 0.00 4.81
714 734 1.010462 GTGTGGCCGTCGTTTTGTC 60.010 57.895 0.00 0.00 0.00 3.18
715 735 2.474612 GGTGTGGCCGTCGTTTTGT 61.475 57.895 0.00 0.00 0.00 2.83
716 736 2.330041 GGTGTGGCCGTCGTTTTG 59.670 61.111 0.00 0.00 0.00 2.44
717 737 2.124653 TGGTGTGGCCGTCGTTTT 60.125 55.556 0.00 0.00 41.21 2.43
718 738 2.590575 CTGGTGTGGCCGTCGTTT 60.591 61.111 0.00 0.00 41.21 3.60
719 739 4.619227 CCTGGTGTGGCCGTCGTT 62.619 66.667 0.00 0.00 41.21 3.85
830 877 4.916293 GATGGGATCTGCGGCGCA 62.916 66.667 34.06 34.06 36.92 6.09
856 903 2.501610 GCTCGGTGGATGGACCTC 59.498 66.667 0.00 0.00 39.86 3.85
860 907 4.770362 TCCCGCTCGGTGGATGGA 62.770 66.667 7.59 0.00 34.74 3.41
863 910 3.461773 CTGTCCCGCTCGGTGGAT 61.462 66.667 7.59 0.00 34.74 3.41
1021 1083 2.610859 GCTGGGACTGGGAGGGAA 60.611 66.667 0.00 0.00 0.00 3.97
1022 1084 4.741239 GGCTGGGACTGGGAGGGA 62.741 72.222 0.00 0.00 0.00 4.20
1030 1092 2.452491 AGGTTTGGGGCTGGGACT 60.452 61.111 0.00 0.00 0.00 3.85
1031 1093 2.035783 GAGGTTTGGGGCTGGGAC 59.964 66.667 0.00 0.00 0.00 4.46
1033 1095 2.788210 GAAGGAGGTTTGGGGCTGGG 62.788 65.000 0.00 0.00 0.00 4.45
1275 1340 2.936032 AAGCACCACCTCTCCCCC 60.936 66.667 0.00 0.00 0.00 5.40
1276 1341 2.352805 CAAGCACCACCTCTCCCC 59.647 66.667 0.00 0.00 0.00 4.81
1277 1342 2.352805 CCAAGCACCACCTCTCCC 59.647 66.667 0.00 0.00 0.00 4.30
1331 1402 4.533124 TCGCCGCCTATCCCTCCA 62.533 66.667 0.00 0.00 0.00 3.86
1588 1660 2.965147 TGATCGATCCTAAGTGGCATCA 59.035 45.455 22.31 0.00 35.26 3.07
1607 1679 6.695278 CCAAACGAACAAAAATTAAGCTCTGA 59.305 34.615 0.00 0.00 0.00 3.27
1626 1698 3.866883 AGCAACCCAATTATCCAAACG 57.133 42.857 0.00 0.00 0.00 3.60
1629 1701 3.942748 GACGTAGCAACCCAATTATCCAA 59.057 43.478 0.00 0.00 0.00 3.53
1630 1702 3.537580 GACGTAGCAACCCAATTATCCA 58.462 45.455 0.00 0.00 0.00 3.41
1632 1704 3.560068 CAGGACGTAGCAACCCAATTATC 59.440 47.826 0.00 0.00 0.00 1.75
1633 1705 3.199071 TCAGGACGTAGCAACCCAATTAT 59.801 43.478 0.00 0.00 0.00 1.28
1635 1707 1.349688 TCAGGACGTAGCAACCCAATT 59.650 47.619 0.00 0.00 0.00 2.32
1636 1708 0.981183 TCAGGACGTAGCAACCCAAT 59.019 50.000 0.00 0.00 0.00 3.16
1645 1717 3.011119 ACTACAGAAGCTCAGGACGTAG 58.989 50.000 0.00 0.00 0.00 3.51
1661 1733 4.617253 ATTGCTACAAGTCACCACTACA 57.383 40.909 0.00 0.00 30.14 2.74
1662 1734 5.962433 TCTATTGCTACAAGTCACCACTAC 58.038 41.667 0.00 0.00 30.14 2.73
1733 1806 0.467290 TGGCCCAAAGAAGAAGCGTT 60.467 50.000 0.00 0.00 0.00 4.84
1749 1822 2.420022 ACGTCACAGCTTGATATTTGGC 59.580 45.455 2.61 0.00 36.32 4.52
1782 1855 0.107165 GGCACAGGGAATCCTACACC 60.107 60.000 0.00 0.00 42.67 4.16
1821 1894 1.273041 TGCTACTGGAGGACTAGGCAA 60.273 52.381 0.00 0.00 0.00 4.52
1824 1897 3.034635 ACAATGCTACTGGAGGACTAGG 58.965 50.000 0.00 0.00 0.00 3.02
1865 1938 4.567159 GGAAGTCTTACGAGCATTTGTAGG 59.433 45.833 0.00 0.00 0.00 3.18
1881 1954 2.744202 GCACACAAATCATCGGAAGTCT 59.256 45.455 0.00 0.00 0.00 3.24
1947 2020 2.617308 GGGACTGATGATGCAAGACATG 59.383 50.000 8.67 0.00 39.84 3.21
2031 2104 5.071653 TGTGGTTCAGCAGCTCCAATATATA 59.928 40.000 2.87 0.00 0.00 0.86
2032 2105 4.141413 TGTGGTTCAGCAGCTCCAATATAT 60.141 41.667 2.87 0.00 0.00 0.86
2088 2163 4.320494 CGAACCAAGGGAGAATTCAAACAG 60.320 45.833 8.44 0.00 0.00 3.16
2103 2178 7.591006 TTAGATACAAAGTTAGCGAACCAAG 57.409 36.000 6.04 0.00 36.08 3.61
2105 2180 6.036735 GCATTAGATACAAAGTTAGCGAACCA 59.963 38.462 6.04 0.00 36.08 3.67
2107 2182 7.000575 TGCATTAGATACAAAGTTAGCGAAC 57.999 36.000 0.83 0.83 35.64 3.95
2109 2184 6.036735 GGTTGCATTAGATACAAAGTTAGCGA 59.963 38.462 0.00 0.00 0.00 4.93
2110 2185 6.192360 GGTTGCATTAGATACAAAGTTAGCG 58.808 40.000 0.00 0.00 0.00 4.26
2111 2186 6.318900 AGGGTTGCATTAGATACAAAGTTAGC 59.681 38.462 0.00 0.00 0.00 3.09
2112 2187 7.865706 AGGGTTGCATTAGATACAAAGTTAG 57.134 36.000 0.00 0.00 0.00 2.34
2113 2188 7.885922 TGAAGGGTTGCATTAGATACAAAGTTA 59.114 33.333 0.00 0.00 0.00 2.24
2114 2189 6.719370 TGAAGGGTTGCATTAGATACAAAGTT 59.281 34.615 0.00 0.00 0.00 2.66
2131 2206 6.712547 CAGAGTTAAGTCAATCTTGAAGGGTT 59.287 38.462 12.77 0.00 39.21 4.11
2135 2210 9.868277 AGTATCAGAGTTAAGTCAATCTTGAAG 57.132 33.333 12.77 0.00 39.21 3.02
2137 2212 9.862371 GAAGTATCAGAGTTAAGTCAATCTTGA 57.138 33.333 12.77 7.26 37.56 3.02
2153 2228 6.754702 AAACACTAGCGTAGAAGTATCAGA 57.245 37.500 0.00 0.00 0.00 3.27
2154 2229 7.201444 CCAAAAACACTAGCGTAGAAGTATCAG 60.201 40.741 0.00 0.00 0.00 2.90
2155 2230 6.588756 CCAAAAACACTAGCGTAGAAGTATCA 59.411 38.462 0.00 0.00 0.00 2.15
2156 2231 6.810182 TCCAAAAACACTAGCGTAGAAGTATC 59.190 38.462 0.00 0.00 0.00 2.24
2168 2243 9.449719 AGTCTATAACCAATCCAAAAACACTAG 57.550 33.333 0.00 0.00 0.00 2.57
3319 5289 9.249457 CACCATCATAGTAATATACTATTGGCG 57.751 37.037 19.13 11.70 46.88 5.69
3356 5337 7.966812 TCCATCACATAAATCAGTAGCACTAT 58.033 34.615 0.00 0.00 0.00 2.12
3418 5399 8.924691 TCAAAATAACAAGCATGCAATAACTTC 58.075 29.630 21.98 0.00 0.00 3.01
3420 5401 8.090214 ACTCAAAATAACAAGCATGCAATAACT 58.910 29.630 21.98 1.28 0.00 2.24
3422 5403 8.830201 AACTCAAAATAACAAGCATGCAATAA 57.170 26.923 21.98 1.00 0.00 1.40
3424 5405 7.658575 AGAAACTCAAAATAACAAGCATGCAAT 59.341 29.630 21.98 5.17 0.00 3.56
3425 5406 6.985645 AGAAACTCAAAATAACAAGCATGCAA 59.014 30.769 21.98 0.00 0.00 4.08
3427 5408 6.642131 TCAGAAACTCAAAATAACAAGCATGC 59.358 34.615 10.51 10.51 0.00 4.06
3428 5409 8.752766 ATCAGAAACTCAAAATAACAAGCATG 57.247 30.769 0.00 0.00 0.00 4.06
3430 5411 9.283768 TCTATCAGAAACTCAAAATAACAAGCA 57.716 29.630 0.00 0.00 0.00 3.91
3554 5818 7.930865 AGGCTTTATGATTATGAGAGAACAGAC 59.069 37.037 0.00 0.00 0.00 3.51
3757 6021 2.613223 GGACAAAGGTCTACAGGCTGAC 60.613 54.545 23.66 9.02 43.77 3.51
3910 6180 9.695526 TTTAAGAAATTCAATGTTCATGGTCAG 57.304 29.630 0.00 0.00 0.00 3.51
3931 6264 6.311200 AGCAAAAGACAGCAAACAACTTTAAG 59.689 34.615 0.00 0.00 31.86 1.85
3939 6272 1.471327 GCCAGCAAAAGACAGCAAACA 60.471 47.619 0.00 0.00 0.00 2.83
3953 6286 5.623169 TCATAATGATGTAGAATGCCAGCA 58.377 37.500 0.00 0.00 34.41 4.41
3977 6310 7.489113 CCTTAATTATCATGTGTGTTTTGAGGC 59.511 37.037 0.00 0.00 0.00 4.70
4067 6400 2.887151 ATATAGCCCAGGAATGCCAC 57.113 50.000 0.00 0.00 36.29 5.01
4211 6682 2.134201 AAACTACTGCGCAAAAAGCC 57.866 45.000 13.05 0.00 41.38 4.35
4903 7393 4.338879 CTCCAACTGTCAATTTCCTCCAT 58.661 43.478 0.00 0.00 0.00 3.41
4918 7408 1.757306 CTCCACTGCACCTCCAACT 59.243 57.895 0.00 0.00 0.00 3.16
5119 7609 5.826643 ACTAACCAAGATCCATTTAGGCAA 58.173 37.500 0.00 0.00 37.29 4.52
5560 8050 2.615465 CCCAGGCATTCCACTCCCA 61.615 63.158 0.00 0.00 33.74 4.37
5623 8113 0.317269 CTGGCAAACTCACAGCAACG 60.317 55.000 0.00 0.00 0.00 4.10
5656 8146 3.956199 CTGCCACTGATCCACCAAATATT 59.044 43.478 0.00 0.00 0.00 1.28
6099 8591 7.798710 ACATATCACTACCCATTAGCTACAT 57.201 36.000 0.00 0.00 0.00 2.29
6100 8592 7.612065 AACATATCACTACCCATTAGCTACA 57.388 36.000 0.00 0.00 0.00 2.74
6127 8622 6.073331 CCAAACAAACAGCAACAAGAGAAAAA 60.073 34.615 0.00 0.00 0.00 1.94
6128 8623 5.407995 CCAAACAAACAGCAACAAGAGAAAA 59.592 36.000 0.00 0.00 0.00 2.29
6129 8624 4.928615 CCAAACAAACAGCAACAAGAGAAA 59.071 37.500 0.00 0.00 0.00 2.52
6130 8625 4.021544 ACCAAACAAACAGCAACAAGAGAA 60.022 37.500 0.00 0.00 0.00 2.87
6265 8761 2.044492 AGGAGAGGGGTCATCTGTACAA 59.956 50.000 0.00 0.00 0.00 2.41
6277 8773 2.752030 TCACAGAATACAGGAGAGGGG 58.248 52.381 0.00 0.00 0.00 4.79
6285 8781 8.539770 AACTATCACAGTTTCACAGAATACAG 57.460 34.615 0.00 0.00 45.54 2.74
6361 8859 6.150474 GGAAAACTTGCTACAGCCTGTTATTA 59.850 38.462 1.02 0.00 41.18 0.98
6362 8860 5.048013 GGAAAACTTGCTACAGCCTGTTATT 60.048 40.000 1.02 6.52 41.18 1.40
6363 8861 4.459337 GGAAAACTTGCTACAGCCTGTTAT 59.541 41.667 1.02 0.00 41.18 1.89
6483 10967 4.460382 CAGCTATTTCCCTGTCACAATGTT 59.540 41.667 0.00 0.00 0.00 2.71
6484 10968 4.012374 CAGCTATTTCCCTGTCACAATGT 58.988 43.478 0.00 0.00 0.00 2.71
6485 10969 4.012374 ACAGCTATTTCCCTGTCACAATG 58.988 43.478 0.00 0.00 37.77 2.82
6486 10970 4.307032 ACAGCTATTTCCCTGTCACAAT 57.693 40.909 0.00 0.00 37.77 2.71
6487 10971 3.788227 ACAGCTATTTCCCTGTCACAA 57.212 42.857 0.00 0.00 37.77 3.33
6584 11146 5.944007 GTCAGTAATGGAATTGTACCAAGGT 59.056 40.000 0.00 0.00 40.93 3.50
6585 11147 6.180472 AGTCAGTAATGGAATTGTACCAAGG 58.820 40.000 0.00 0.00 40.93 3.61
6586 11148 8.786826 TTAGTCAGTAATGGAATTGTACCAAG 57.213 34.615 0.00 0.00 40.93 3.61
6637 11224 2.230508 TCACTTCTGCGTAGGGTACAAG 59.769 50.000 0.00 0.00 0.00 3.16
6640 11227 2.426024 TCATCACTTCTGCGTAGGGTAC 59.574 50.000 0.00 0.00 0.00 3.34
6641 11228 2.426024 GTCATCACTTCTGCGTAGGGTA 59.574 50.000 0.00 0.00 0.00 3.69
6642 11229 1.204941 GTCATCACTTCTGCGTAGGGT 59.795 52.381 0.00 0.00 0.00 4.34
6644 11231 1.135373 ACGTCATCACTTCTGCGTAGG 60.135 52.381 0.00 0.00 0.00 3.18
6646 11233 3.004862 TCTACGTCATCACTTCTGCGTA 58.995 45.455 0.00 0.00 34.38 4.42
6648 11235 2.544480 TCTACGTCATCACTTCTGCG 57.456 50.000 0.00 0.00 0.00 5.18
6650 11237 4.564372 CACCATTCTACGTCATCACTTCTG 59.436 45.833 0.00 0.00 0.00 3.02
6651 11238 4.382040 CCACCATTCTACGTCATCACTTCT 60.382 45.833 0.00 0.00 0.00 2.85
6677 11284 0.812811 ACTGCGTAGGATGCATGCTG 60.813 55.000 28.88 18.60 39.71 4.41
6696 11303 3.506096 CCGACGTCGCTGCCTCTA 61.506 66.667 31.73 0.00 38.18 2.43
6719 11332 2.110213 GTGCCCGTGGTTCACTGA 59.890 61.111 0.00 0.00 31.34 3.41
6968 11591 0.816421 CTGTTCCCGGGACAAAACGT 60.816 55.000 26.87 0.00 0.00 3.99


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

AutoCloner maintained by Alex Coulton.