Multiple sequence alignment - TraesCS2B01G090700

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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 TraesCS2B01G090700 chr2B 100.000 3135 0 0 410 3544 52122468 52125602 0.000000e+00 5790.0
1 TraesCS2B01G090700 chr2B 90.063 1117 86 10 1350 2444 51706579 51705466 0.000000e+00 1424.0
2 TraesCS2B01G090700 chr2B 91.089 202 16 1 3223 3424 51703644 51703445 4.510000e-69 272.0
3 TraesCS2B01G090700 chr2B 85.477 241 33 2 2057 2297 51070984 51071222 2.110000e-62 250.0
4 TraesCS2B01G090700 chr2B 100.000 127 0 0 1 127 52122059 52122185 5.910000e-58 235.0
5 TraesCS2B01G090700 chr2B 78.740 381 40 25 959 1327 51706992 51706641 2.140000e-52 217.0
6 TraesCS2B01G090700 chr2A 88.238 2525 211 28 944 3395 33564385 33561874 0.000000e+00 2939.0
7 TraesCS2B01G090700 chr2A 90.633 1121 80 12 1350 2448 33382261 33381144 0.000000e+00 1465.0
8 TraesCS2B01G090700 chr2A 86.059 1119 136 6 1350 2449 33343986 33342869 0.000000e+00 1184.0
9 TraesCS2B01G090700 chr2A 82.095 592 53 12 2787 3366 33554711 33554161 1.160000e-124 457.0
10 TraesCS2B01G090700 chr2A 87.342 79 9 1 3427 3504 33552349 33552271 4.870000e-14 89.8
11 TraesCS2B01G090700 chr2A 90.000 60 5 1 2359 2418 33557943 33557885 3.790000e-10 76.8
12 TraesCS2B01G090700 chr2A 100.000 29 0 0 3472 3500 33560266 33560238 2.000000e-03 54.7
13 TraesCS2B01G090700 chr2D 89.429 2119 156 29 1350 3419 31729617 31727518 0.000000e+00 2610.0
14 TraesCS2B01G090700 chr2D 90.412 1116 84 8 1350 2444 31608107 31606994 0.000000e+00 1447.0
15 TraesCS2B01G090700 chr2D 86.514 1179 132 12 1353 2505 31561227 31560050 0.000000e+00 1271.0
16 TraesCS2B01G090700 chr2D 91.912 408 22 4 944 1343 31730061 31729657 8.590000e-156 560.0
17 TraesCS2B01G090700 chr2D 91.089 202 18 0 3223 3424 31606665 31606464 1.250000e-69 274.0
18 TraesCS2B01G090700 chr2D 76.943 386 42 30 959 1327 31608542 31608187 3.640000e-40 176.0
19 TraesCS2B01G090700 chr2D 90.816 98 9 0 1 98 31730900 31730803 7.980000e-27 132.0
20 TraesCS2B01G090700 chr2D 87.850 107 7 1 1040 1140 346045621 346045727 1.730000e-23 121.0
21 TraesCS2B01G090700 chr2D 100.000 44 0 0 3461 3504 31606456 31606413 8.150000e-12 82.4
22 TraesCS2B01G090700 chrUn 84.781 1071 140 7 1393 2444 17252922 17253988 0.000000e+00 1053.0
23 TraesCS2B01G090700 chr7D 80.066 908 155 19 1415 2301 154376804 154377706 0.000000e+00 651.0


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 TraesCS2B01G090700 chr2B 52122059 52125602 3543 False 3012.500000 5790 100.000000 1 3544 2 chr2B.!!$F2 3543
1 TraesCS2B01G090700 chr2B 51703445 51706992 3547 True 637.666667 1424 86.630667 959 3424 3 chr2B.!!$R1 2465
2 TraesCS2B01G090700 chr2A 33381144 33382261 1117 True 1465.000000 1465 90.633000 1350 2448 1 chr2A.!!$R2 1098
3 TraesCS2B01G090700 chr2A 33342869 33343986 1117 True 1184.000000 1184 86.059000 1350 2449 1 chr2A.!!$R1 1099
4 TraesCS2B01G090700 chr2A 33552271 33564385 12114 True 723.460000 2939 89.535000 944 3504 5 chr2A.!!$R3 2560
5 TraesCS2B01G090700 chr2D 31560050 31561227 1177 True 1271.000000 1271 86.514000 1353 2505 1 chr2D.!!$R1 1152
6 TraesCS2B01G090700 chr2D 31727518 31730900 3382 True 1100.666667 2610 90.719000 1 3419 3 chr2D.!!$R3 3418
7 TraesCS2B01G090700 chr2D 31606413 31608542 2129 True 494.850000 1447 89.611000 959 3504 4 chr2D.!!$R2 2545
8 TraesCS2B01G090700 chrUn 17252922 17253988 1066 False 1053.000000 1053 84.781000 1393 2444 1 chrUn.!!$F1 1051
9 TraesCS2B01G090700 chr7D 154376804 154377706 902 False 651.000000 651 80.066000 1415 2301 1 chr7D.!!$F1 886

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
767 768 0.034863 ACGGCCATTAACGACCCAAT 60.035 50.0 2.24 0.0 0.00 3.16 F
1089 1131 0.107312 CCTCAGGCATCCTTGTCCAG 60.107 60.0 0.00 0.0 0.00 3.86 F
2151 2282 0.389948 GTCGCGATGGTGACCTCTTT 60.390 55.0 14.06 0.0 45.75 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2133 2264 0.389817 CAAAGAGGTCACCATCGCGA 60.390 55.0 13.09 13.09 0.00 5.87 R
2348 2479 0.517316 GGCCTTCTTGCTGTTACGTG 59.483 55.0 0.00 0.00 0.00 4.49 R
3458 14487 0.035056 CCCTCCTGGATTCAAAGCGT 60.035 55.0 0.00 0.00 35.39 5.07 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
31 32 0.690762 AGGGCGTGTACTTTCCATGT 59.309 50.000 0.00 0.00 0.00 3.21
39 40 5.006358 GCGTGTACTTTCCATGTTAGGTATG 59.994 44.000 0.00 0.00 0.00 2.39
40 41 6.334989 CGTGTACTTTCCATGTTAGGTATGA 58.665 40.000 0.00 0.00 0.00 2.15
55 56 8.700973 TGTTAGGTATGATGTTGCTGATAGTTA 58.299 33.333 0.00 0.00 0.00 2.24
60 61 9.884465 GGTATGATGTTGCTGATAGTTATTTTC 57.116 33.333 0.00 0.00 0.00 2.29
126 127 9.132923 AGTCCTTTTCTTTACTTTAAAAGAGGG 57.867 33.333 8.04 4.71 44.15 4.30
431 432 4.660168 GCCCTCTATCCATTGATTGATGT 58.340 43.478 0.00 0.00 33.30 3.06
432 433 5.809001 GCCCTCTATCCATTGATTGATGTA 58.191 41.667 0.00 0.00 33.30 2.29
433 434 5.645497 GCCCTCTATCCATTGATTGATGTAC 59.355 44.000 0.00 0.00 33.30 2.90
434 435 6.176183 CCCTCTATCCATTGATTGATGTACC 58.824 44.000 0.00 0.00 33.30 3.34
435 436 5.871524 CCTCTATCCATTGATTGATGTACCG 59.128 44.000 0.00 0.00 33.30 4.02
436 437 5.793817 TCTATCCATTGATTGATGTACCGG 58.206 41.667 0.00 0.00 29.50 5.28
437 438 3.207265 TCCATTGATTGATGTACCGGG 57.793 47.619 6.32 0.00 0.00 5.73
438 439 2.158682 TCCATTGATTGATGTACCGGGG 60.159 50.000 6.32 0.00 0.00 5.73
439 440 2.229792 CATTGATTGATGTACCGGGGG 58.770 52.381 6.32 0.00 0.00 5.40
440 441 1.585895 TTGATTGATGTACCGGGGGA 58.414 50.000 6.32 0.00 0.00 4.81
441 442 1.128200 TGATTGATGTACCGGGGGAG 58.872 55.000 6.32 0.00 0.00 4.30
442 443 0.396811 GATTGATGTACCGGGGGAGG 59.603 60.000 6.32 0.00 37.30 4.30
443 444 1.060163 ATTGATGTACCGGGGGAGGG 61.060 60.000 6.32 0.00 35.02 4.30
444 445 2.847715 GATGTACCGGGGGAGGGG 60.848 72.222 6.32 0.00 35.02 4.79
445 446 4.509412 ATGTACCGGGGGAGGGGG 62.509 72.222 6.32 0.00 35.02 5.40
460 461 4.825679 GGGGGTAGCCCTCTGCCT 62.826 72.222 28.67 0.00 42.03 4.75
461 462 2.285868 GGGGTAGCCCTCTGCCTA 59.714 66.667 23.31 0.00 44.66 3.93
462 463 1.152008 GGGGTAGCCCTCTGCCTAT 60.152 63.158 23.31 0.00 44.66 2.57
463 464 1.195442 GGGGTAGCCCTCTGCCTATC 61.195 65.000 23.31 0.00 44.66 2.08
464 465 1.195442 GGGTAGCCCTCTGCCTATCC 61.195 65.000 0.00 0.00 43.66 2.59
465 466 0.471971 GGTAGCCCTCTGCCTATCCA 60.472 60.000 0.00 0.00 41.30 3.41
466 467 0.972883 GTAGCCCTCTGCCTATCCAG 59.027 60.000 0.00 0.00 42.71 3.86
467 468 0.563173 TAGCCCTCTGCCTATCCAGT 59.437 55.000 0.00 0.00 42.71 4.00
468 469 1.053264 AGCCCTCTGCCTATCCAGTG 61.053 60.000 0.00 0.00 42.71 3.66
469 470 1.050988 GCCCTCTGCCTATCCAGTGA 61.051 60.000 0.00 0.00 34.47 3.41
470 471 1.047002 CCCTCTGCCTATCCAGTGAG 58.953 60.000 0.00 0.00 34.47 3.51
471 472 1.690845 CCCTCTGCCTATCCAGTGAGT 60.691 57.143 0.00 0.00 34.47 3.41
472 473 2.424957 CCCTCTGCCTATCCAGTGAGTA 60.425 54.545 0.00 0.00 34.47 2.59
473 474 2.625790 CCTCTGCCTATCCAGTGAGTAC 59.374 54.545 0.00 0.00 34.47 2.73
474 475 2.292016 CTCTGCCTATCCAGTGAGTACG 59.708 54.545 0.00 0.00 34.47 3.67
475 476 0.744874 TGCCTATCCAGTGAGTACGC 59.255 55.000 0.00 0.00 0.00 4.42
476 477 0.744874 GCCTATCCAGTGAGTACGCA 59.255 55.000 0.00 0.00 0.00 5.24
477 478 1.136305 GCCTATCCAGTGAGTACGCAA 59.864 52.381 0.00 0.00 0.00 4.85
478 479 2.224066 GCCTATCCAGTGAGTACGCAAT 60.224 50.000 0.00 0.00 0.00 3.56
479 480 3.741388 GCCTATCCAGTGAGTACGCAATT 60.741 47.826 0.00 0.00 0.00 2.32
480 481 4.500887 GCCTATCCAGTGAGTACGCAATTA 60.501 45.833 0.00 0.00 0.00 1.40
481 482 5.784177 CCTATCCAGTGAGTACGCAATTAT 58.216 41.667 0.00 0.00 0.00 1.28
482 483 5.864474 CCTATCCAGTGAGTACGCAATTATC 59.136 44.000 0.00 0.00 0.00 1.75
483 484 5.537300 ATCCAGTGAGTACGCAATTATCT 57.463 39.130 0.00 0.00 0.00 1.98
484 485 5.339008 TCCAGTGAGTACGCAATTATCTT 57.661 39.130 0.00 0.00 0.00 2.40
485 486 5.109210 TCCAGTGAGTACGCAATTATCTTG 58.891 41.667 0.00 0.00 0.00 3.02
486 487 4.870426 CCAGTGAGTACGCAATTATCTTGT 59.130 41.667 0.00 0.00 0.00 3.16
487 488 6.040247 CCAGTGAGTACGCAATTATCTTGTA 58.960 40.000 0.00 0.00 0.00 2.41
488 489 6.701841 CCAGTGAGTACGCAATTATCTTGTAT 59.298 38.462 0.00 0.00 0.00 2.29
489 490 7.224753 CCAGTGAGTACGCAATTATCTTGTATT 59.775 37.037 0.00 0.00 0.00 1.89
490 491 8.058328 CAGTGAGTACGCAATTATCTTGTATTG 58.942 37.037 0.00 0.00 35.39 1.90
491 492 7.764443 AGTGAGTACGCAATTATCTTGTATTGT 59.236 33.333 0.00 0.00 34.88 2.71
492 493 8.056571 GTGAGTACGCAATTATCTTGTATTGTC 58.943 37.037 0.00 0.00 34.88 3.18
493 494 7.762159 TGAGTACGCAATTATCTTGTATTGTCA 59.238 33.333 0.00 0.00 34.88 3.58
494 495 8.487313 AGTACGCAATTATCTTGTATTGTCAA 57.513 30.769 0.00 0.00 34.88 3.18
495 496 8.604035 AGTACGCAATTATCTTGTATTGTCAAG 58.396 33.333 0.00 0.00 44.08 3.02
496 497 7.377766 ACGCAATTATCTTGTATTGTCAAGT 57.622 32.000 6.38 0.00 43.44 3.16
497 498 8.487313 ACGCAATTATCTTGTATTGTCAAGTA 57.513 30.769 6.38 0.00 43.44 2.24
498 499 9.109393 ACGCAATTATCTTGTATTGTCAAGTAT 57.891 29.630 6.38 2.95 43.44 2.12
499 500 9.586150 CGCAATTATCTTGTATTGTCAAGTATC 57.414 33.333 6.38 0.00 43.44 2.24
520 521 3.199946 TCAAGTTCCAGACAAAGTCCACT 59.800 43.478 0.00 0.00 32.18 4.00
521 522 4.407621 TCAAGTTCCAGACAAAGTCCACTA 59.592 41.667 0.00 0.00 32.18 2.74
523 524 5.568620 AGTTCCAGACAAAGTCCACTAAT 57.431 39.130 0.00 0.00 32.18 1.73
524 525 5.308825 AGTTCCAGACAAAGTCCACTAATG 58.691 41.667 0.00 0.00 32.18 1.90
525 526 5.071788 AGTTCCAGACAAAGTCCACTAATGA 59.928 40.000 0.00 0.00 32.18 2.57
526 527 5.560722 TCCAGACAAAGTCCACTAATGAA 57.439 39.130 0.00 0.00 32.18 2.57
527 528 5.935945 TCCAGACAAAGTCCACTAATGAAA 58.064 37.500 0.00 0.00 32.18 2.69
532 533 4.142902 ACAAAGTCCACTAATGAAATCGCG 60.143 41.667 0.00 0.00 0.00 5.87
539 540 5.818336 TCCACTAATGAAATCGCGGAATTTA 59.182 36.000 6.13 0.00 0.00 1.40
541 542 6.238374 CCACTAATGAAATCGCGGAATTTACT 60.238 38.462 6.13 0.00 0.00 2.24
544 545 4.857871 TGAAATCGCGGAATTTACTGAG 57.142 40.909 6.13 0.00 0.00 3.35
581 582 2.538449 GCGAAGTTCAGAAACAACTCGA 59.462 45.455 3.32 0.00 36.85 4.04
601 602 0.655733 CGTTGTGTTTGGCGAGTTCT 59.344 50.000 0.00 0.00 0.00 3.01
606 607 1.940613 GTGTTTGGCGAGTTCTGTTCT 59.059 47.619 0.00 0.00 0.00 3.01
615 616 3.528009 GAGTTCTGTTCTCGGCAAAAG 57.472 47.619 0.00 0.00 0.00 2.27
616 617 2.872858 GAGTTCTGTTCTCGGCAAAAGT 59.127 45.455 0.00 0.00 0.00 2.66
617 618 4.056050 GAGTTCTGTTCTCGGCAAAAGTA 58.944 43.478 0.00 0.00 0.00 2.24
621 622 3.069016 TCTGTTCTCGGCAAAAGTACTCA 59.931 43.478 0.00 0.00 0.00 3.41
623 624 2.080286 TCTCGGCAAAAGTACTCAGC 57.920 50.000 0.00 0.34 0.00 4.26
632 633 3.669251 AAAGTACTCAGCTGGACAGTC 57.331 47.619 15.13 4.90 0.00 3.51
633 634 2.294449 AGTACTCAGCTGGACAGTCA 57.706 50.000 15.13 0.00 0.00 3.41
635 636 3.169099 AGTACTCAGCTGGACAGTCATT 58.831 45.455 15.13 0.00 0.00 2.57
645 646 4.337555 GCTGGACAGTCATTAGCAATCATT 59.662 41.667 15.14 0.00 34.64 2.57
675 676 5.411361 TGCGAGTTTCTATTATTGTGCACTT 59.589 36.000 19.41 8.24 0.00 3.16
678 679 6.955963 CGAGTTTCTATTATTGTGCACTTGAC 59.044 38.462 19.41 2.73 0.00 3.18
693 694 8.194104 TGTGCACTTGACAAACATTTAAATAGT 58.806 29.630 19.41 0.00 0.00 2.12
707 708 8.303876 ACATTTAAATAGTCATTGCGGAGTTTT 58.696 29.630 0.00 0.00 0.00 2.43
736 737 6.619801 ACTTTTAACTCAGCAAACTACCAG 57.380 37.500 0.00 0.00 0.00 4.00
737 738 5.531287 ACTTTTAACTCAGCAAACTACCAGG 59.469 40.000 0.00 0.00 0.00 4.45
753 754 0.958876 CAGGGTTAGGTGAAACGGCC 60.959 60.000 0.00 0.00 38.12 6.13
754 755 1.073548 GGGTTAGGTGAAACGGCCA 59.926 57.895 2.24 0.00 38.12 5.36
755 756 0.323087 GGGTTAGGTGAAACGGCCAT 60.323 55.000 2.24 0.00 38.12 4.40
756 757 1.541379 GGTTAGGTGAAACGGCCATT 58.459 50.000 2.24 0.00 38.12 3.16
757 758 2.618559 GGGTTAGGTGAAACGGCCATTA 60.619 50.000 2.24 0.00 38.12 1.90
758 759 3.083293 GGTTAGGTGAAACGGCCATTAA 58.917 45.455 2.24 0.00 38.12 1.40
759 760 3.119743 GGTTAGGTGAAACGGCCATTAAC 60.120 47.826 2.24 0.00 38.12 2.01
760 761 1.161843 AGGTGAAACGGCCATTAACG 58.838 50.000 2.24 0.00 38.12 3.18
761 762 1.158434 GGTGAAACGGCCATTAACGA 58.842 50.000 2.24 0.00 38.12 3.85
762 763 1.135888 GGTGAAACGGCCATTAACGAC 60.136 52.381 2.24 0.00 38.12 4.34
763 764 1.135888 GTGAAACGGCCATTAACGACC 60.136 52.381 2.24 0.00 0.00 4.79
764 765 0.448990 GAAACGGCCATTAACGACCC 59.551 55.000 2.24 0.00 0.00 4.46
765 766 0.250814 AAACGGCCATTAACGACCCA 60.251 50.000 2.24 0.00 0.00 4.51
766 767 0.250814 AACGGCCATTAACGACCCAA 60.251 50.000 2.24 0.00 0.00 4.12
767 768 0.034863 ACGGCCATTAACGACCCAAT 60.035 50.000 2.24 0.00 0.00 3.16
768 769 1.209990 ACGGCCATTAACGACCCAATA 59.790 47.619 2.24 0.00 0.00 1.90
769 770 2.158726 ACGGCCATTAACGACCCAATAT 60.159 45.455 2.24 0.00 0.00 1.28
770 771 2.882137 CGGCCATTAACGACCCAATATT 59.118 45.455 2.24 0.00 0.00 1.28
771 772 4.066490 CGGCCATTAACGACCCAATATTA 58.934 43.478 2.24 0.00 0.00 0.98
772 773 4.083696 CGGCCATTAACGACCCAATATTAC 60.084 45.833 2.24 0.00 0.00 1.89
773 774 4.822896 GGCCATTAACGACCCAATATTACA 59.177 41.667 0.00 0.00 0.00 2.41
774 775 5.475564 GGCCATTAACGACCCAATATTACAT 59.524 40.000 0.00 0.00 0.00 2.29
775 776 6.378582 GCCATTAACGACCCAATATTACATG 58.621 40.000 0.00 0.00 0.00 3.21
776 777 6.205853 GCCATTAACGACCCAATATTACATGA 59.794 38.462 0.00 0.00 0.00 3.07
777 778 7.581476 CCATTAACGACCCAATATTACATGAC 58.419 38.462 0.00 0.00 0.00 3.06
778 779 7.227711 CCATTAACGACCCAATATTACATGACA 59.772 37.037 0.00 0.00 0.00 3.58
779 780 7.542534 TTAACGACCCAATATTACATGACAC 57.457 36.000 0.00 0.00 0.00 3.67
780 781 5.092554 ACGACCCAATATTACATGACACA 57.907 39.130 0.00 0.00 0.00 3.72
781 782 4.873827 ACGACCCAATATTACATGACACAC 59.126 41.667 0.00 0.00 0.00 3.82
782 783 5.116180 CGACCCAATATTACATGACACACT 58.884 41.667 0.00 0.00 0.00 3.55
783 784 6.127281 ACGACCCAATATTACATGACACACTA 60.127 38.462 0.00 0.00 0.00 2.74
784 785 6.759356 CGACCCAATATTACATGACACACTAA 59.241 38.462 0.00 0.00 0.00 2.24
785 786 7.441157 CGACCCAATATTACATGACACACTAAT 59.559 37.037 0.00 0.00 0.00 1.73
786 787 8.450578 ACCCAATATTACATGACACACTAATG 57.549 34.615 0.00 0.00 0.00 1.90
787 788 7.013274 ACCCAATATTACATGACACACTAATGC 59.987 37.037 0.00 0.00 0.00 3.56
797 798 7.391554 ACATGACACACTAATGCTTCACTAATT 59.608 33.333 0.00 0.00 0.00 1.40
798 799 7.364522 TGACACACTAATGCTTCACTAATTC 57.635 36.000 0.00 0.00 0.00 2.17
809 810 8.757982 ATGCTTCACTAATTCAATTACTGGAT 57.242 30.769 0.00 0.00 0.00 3.41
812 813 6.844696 TCACTAATTCAATTACTGGATCGC 57.155 37.500 0.00 0.00 0.00 4.58
878 879 2.035321 GCTATGACTAGAGGCCACAGAC 59.965 54.545 5.01 0.00 0.00 3.51
884 885 3.775654 GAGGCCACAGACCTCCGG 61.776 72.222 5.01 0.00 46.81 5.14
885 886 4.316823 AGGCCACAGACCTCCGGA 62.317 66.667 5.01 2.93 28.76 5.14
886 887 3.319198 GGCCACAGACCTCCGGAA 61.319 66.667 5.23 0.00 0.00 4.30
887 888 2.047179 GCCACAGACCTCCGGAAC 60.047 66.667 5.23 0.00 0.00 3.62
889 890 2.214216 CCACAGACCTCCGGAACCA 61.214 63.158 5.23 0.00 0.00 3.67
890 891 1.293498 CACAGACCTCCGGAACCAG 59.707 63.158 5.23 0.00 0.00 4.00
891 892 2.266055 CAGACCTCCGGAACCAGC 59.734 66.667 5.23 0.00 0.00 4.85
892 893 2.120718 AGACCTCCGGAACCAGCT 59.879 61.111 5.23 0.00 0.00 4.24
894 895 3.003763 ACCTCCGGAACCAGCTCC 61.004 66.667 5.23 0.00 0.00 4.70
895 896 2.685380 CCTCCGGAACCAGCTCCT 60.685 66.667 5.23 0.00 32.82 3.69
896 897 2.726351 CCTCCGGAACCAGCTCCTC 61.726 68.421 5.23 0.00 32.82 3.71
897 898 1.684049 CTCCGGAACCAGCTCCTCT 60.684 63.158 5.23 0.00 32.82 3.69
898 899 1.954362 CTCCGGAACCAGCTCCTCTG 61.954 65.000 5.23 0.00 42.49 3.35
899 900 1.984570 CCGGAACCAGCTCCTCTGA 60.985 63.158 0.00 0.00 45.72 3.27
900 901 1.216710 CGGAACCAGCTCCTCTGAC 59.783 63.158 0.00 0.00 45.72 3.51
902 903 0.908198 GGAACCAGCTCCTCTGACAT 59.092 55.000 0.00 0.00 45.72 3.06
904 905 2.159028 GGAACCAGCTCCTCTGACATAC 60.159 54.545 0.00 0.00 45.72 2.39
905 906 1.107114 ACCAGCTCCTCTGACATACG 58.893 55.000 0.00 0.00 45.72 3.06
908 909 1.068250 GCTCCTCTGACATACGGCC 59.932 63.158 0.00 0.00 0.00 6.13
909 910 1.676678 GCTCCTCTGACATACGGCCA 61.677 60.000 2.24 0.00 0.00 5.36
911 912 1.414181 CTCCTCTGACATACGGCCAAT 59.586 52.381 2.24 0.00 0.00 3.16
912 913 1.138859 TCCTCTGACATACGGCCAATG 59.861 52.381 12.45 12.45 0.00 2.82
913 914 0.940126 CTCTGACATACGGCCAATGC 59.060 55.000 13.68 8.23 0.00 3.56
915 916 1.093972 CTGACATACGGCCAATGCAA 58.906 50.000 13.68 3.35 40.13 4.08
916 917 1.472082 CTGACATACGGCCAATGCAAA 59.528 47.619 13.68 1.24 40.13 3.68
917 918 1.889170 TGACATACGGCCAATGCAAAA 59.111 42.857 13.68 0.00 40.13 2.44
918 919 2.094803 TGACATACGGCCAATGCAAAAG 60.095 45.455 13.68 0.00 40.13 2.27
920 921 1.476085 CATACGGCCAATGCAAAAGGA 59.524 47.619 2.24 0.00 40.13 3.36
971 1009 0.322277 ATGGTGGAGTGAAGCTGCTG 60.322 55.000 1.35 0.00 36.43 4.41
1012 1050 5.050972 CGACGCAAAAGGAAGATATACCTTC 60.051 44.000 0.00 0.00 44.44 3.46
1013 1051 5.990668 ACGCAAAAGGAAGATATACCTTCT 58.009 37.500 6.80 0.00 44.44 2.85
1014 1052 6.415573 ACGCAAAAGGAAGATATACCTTCTT 58.584 36.000 6.80 0.00 44.44 2.52
1028 1066 4.130286 ACCTTCTTCCATTCATCTCGTC 57.870 45.455 0.00 0.00 0.00 4.20
1029 1067 3.118592 ACCTTCTTCCATTCATCTCGTCC 60.119 47.826 0.00 0.00 0.00 4.79
1089 1131 0.107312 CCTCAGGCATCCTTGTCCAG 60.107 60.000 0.00 0.00 0.00 3.86
1092 1134 2.437281 CTCAGGCATCCTTGTCCAGTAT 59.563 50.000 0.00 0.00 0.00 2.12
1107 1149 2.289882 CCAGTATCGATGCCATGGACAT 60.290 50.000 18.40 18.17 0.00 3.06
1297 1352 7.417911 GGAAGAATCATGGCGGATATGAGTATA 60.418 40.741 0.00 0.00 37.91 1.47
1343 1401 0.749818 TGCGCAACTCCAAGGTGAAA 60.750 50.000 8.16 0.00 33.95 2.69
1346 1404 1.264288 CGCAACTCCAAGGTGAAACTC 59.736 52.381 0.00 0.00 33.95 3.01
1348 1406 2.930950 CAACTCCAAGGTGAAACTCCA 58.069 47.619 0.00 0.00 33.95 3.86
1537 1649 2.656069 GGACTTGCTGCCGGACCTA 61.656 63.158 5.05 0.00 0.00 3.08
1630 1742 2.430921 CACCTCGTGTGCCTCGTC 60.431 66.667 0.00 0.00 38.34 4.20
1789 1901 1.737735 CGGCGATGTGCTCAACAGA 60.738 57.895 0.00 0.00 43.64 3.41
1915 2027 1.641577 GCTTCATCTACGTCGCCTTT 58.358 50.000 0.00 0.00 0.00 3.11
1930 2042 2.720758 CTTTCAGGAGCGTGCGACG 61.721 63.158 4.61 4.61 45.88 5.12
2112 2243 4.592192 CGCCGGATCGTCATGCCT 62.592 66.667 5.05 0.00 0.00 4.75
2151 2282 0.389948 GTCGCGATGGTGACCTCTTT 60.390 55.000 14.06 0.00 45.75 2.52
2304 2435 4.712425 GCGCGGGACTACGTGTGT 62.712 66.667 8.83 0.00 45.40 3.72
2305 2436 2.049802 CGCGGGACTACGTGTGTT 60.050 61.111 0.00 0.00 39.35 3.32
2347 2478 1.463214 TTGGAGGAGAAGGCCCACA 60.463 57.895 0.00 0.00 0.00 4.17
2348 2479 1.779061 TTGGAGGAGAAGGCCCACAC 61.779 60.000 0.00 0.00 0.00 3.82
2356 2487 0.533308 GAAGGCCCACACACGTAACA 60.533 55.000 0.00 0.00 0.00 2.41
2372 2503 3.437795 CAGCAAGAAGGCCCAGCG 61.438 66.667 0.00 0.00 0.00 5.18
2391 2522 1.524355 CGCATGACATCCGTCTCATTC 59.476 52.381 0.00 0.00 43.06 2.67
2741 2903 6.198966 CCTTCGGAAACTTCATTTCTTTTGTG 59.801 38.462 0.00 0.00 45.32 3.33
2747 2909 7.641020 GGAAACTTCATTTCTTTTGTGCATTTG 59.359 33.333 0.00 0.00 45.32 2.32
2792 2955 4.217118 GTCTTGTCTCTTGTAAGGTACCGA 59.783 45.833 6.18 0.00 0.00 4.69
2810 2973 5.717078 ACCGAGTCAGTTTCTGTTATGTA 57.283 39.130 0.00 0.00 32.61 2.29
2842 3005 3.578716 GCCTAAGTATCTGATGGGCTACA 59.421 47.826 0.00 0.00 35.73 2.74
2843 3006 4.223923 GCCTAAGTATCTGATGGGCTACAT 59.776 45.833 0.00 0.00 44.18 2.29
2868 3031 2.656947 TAGTTGCAAAGGGCTGAGTT 57.343 45.000 0.00 0.00 45.15 3.01
2906 3070 9.774413 AAATGTATAGTAGGCATAGTTTGGTAC 57.226 33.333 0.00 0.00 0.00 3.34
3000 3169 3.449737 TGATAAACCACTCCCCTAGTTCG 59.550 47.826 0.00 0.00 35.76 3.95
3011 3180 2.418334 CCCCTAGTTCGTGCTTCCTTAC 60.418 54.545 0.00 0.00 0.00 2.34
3022 3191 4.290969 GTGCTTCCTTACAAAGAGTTTGC 58.709 43.478 0.00 0.00 44.39 3.68
3129 3604 5.545658 TTCATTTCTTTGAGATACCACGC 57.454 39.130 0.00 0.00 0.00 5.34
3138 3613 1.067212 GAGATACCACGCGGTCATCTT 59.933 52.381 12.47 0.00 44.71 2.40
3250 4810 0.319405 ACCACGGTTTACTCGGGAAG 59.681 55.000 0.00 0.00 31.91 3.46
3267 4827 4.203226 GGGAAGACAAGATGGAGATTTCC 58.797 47.826 0.00 0.00 44.31 3.13
3366 12669 8.810652 AAATCTCGAAGATAAGATGAGCTTAC 57.189 34.615 0.00 0.00 41.64 2.34
3421 14450 5.912360 CGAAGCTTGCATATAGATGTTCA 57.088 39.130 2.10 0.00 35.30 3.18
3424 14453 3.496130 AGCTTGCATATAGATGTTCACGC 59.504 43.478 0.00 0.00 35.30 5.34
3425 14454 3.248363 GCTTGCATATAGATGTTCACGCA 59.752 43.478 0.00 0.00 35.30 5.24
3426 14455 4.766007 CTTGCATATAGATGTTCACGCAC 58.234 43.478 0.00 0.00 35.30 5.34
3427 14456 3.791245 TGCATATAGATGTTCACGCACA 58.209 40.909 0.00 0.00 35.30 4.57
3428 14457 3.803778 TGCATATAGATGTTCACGCACAG 59.196 43.478 0.00 0.00 35.30 3.66
3429 14458 3.363378 GCATATAGATGTTCACGCACAGC 60.363 47.826 0.00 0.00 35.30 4.40
3431 14460 2.455674 TAGATGTTCACGCACAGCTT 57.544 45.000 6.13 0.00 40.56 3.74
3432 14461 1.151668 AGATGTTCACGCACAGCTTC 58.848 50.000 0.00 0.00 40.56 3.86
3433 14462 0.867746 GATGTTCACGCACAGCTTCA 59.132 50.000 0.00 0.00 30.04 3.02
3434 14463 1.466167 GATGTTCACGCACAGCTTCAT 59.534 47.619 0.00 0.00 30.04 2.57
3435 14464 1.308047 TGTTCACGCACAGCTTCATT 58.692 45.000 0.00 0.00 0.00 2.57
3436 14465 1.675483 TGTTCACGCACAGCTTCATTT 59.325 42.857 0.00 0.00 0.00 2.32
3437 14466 2.098934 TGTTCACGCACAGCTTCATTTT 59.901 40.909 0.00 0.00 0.00 1.82
3438 14467 3.115554 GTTCACGCACAGCTTCATTTTT 58.884 40.909 0.00 0.00 0.00 1.94
3459 14488 6.808008 TTTTTCTCTCTGAATGGTCATGAC 57.192 37.500 17.91 17.91 34.24 3.06
3505 14589 3.473647 ATGCTGCAGGGCGAGCTA 61.474 61.111 17.12 0.00 35.15 3.32
3506 14590 2.815945 ATGCTGCAGGGCGAGCTAT 61.816 57.895 17.12 0.00 35.15 2.97
3507 14591 1.475169 ATGCTGCAGGGCGAGCTATA 61.475 55.000 17.12 0.00 35.15 1.31
3508 14592 1.294780 GCTGCAGGGCGAGCTATAT 59.705 57.895 17.12 0.00 32.81 0.86
3509 14593 0.532573 GCTGCAGGGCGAGCTATATA 59.467 55.000 17.12 0.00 32.81 0.86
3510 14594 1.137872 GCTGCAGGGCGAGCTATATAT 59.862 52.381 17.12 0.00 32.81 0.86
3511 14595 2.362397 GCTGCAGGGCGAGCTATATATA 59.638 50.000 17.12 0.00 32.81 0.86
3512 14596 3.006323 GCTGCAGGGCGAGCTATATATAT 59.994 47.826 17.12 0.00 32.81 0.86
3513 14597 4.218635 GCTGCAGGGCGAGCTATATATATA 59.781 45.833 17.12 2.49 32.81 0.86
3514 14598 5.105554 GCTGCAGGGCGAGCTATATATATAT 60.106 44.000 17.12 10.10 32.81 0.86
3515 14599 6.095580 GCTGCAGGGCGAGCTATATATATATA 59.904 42.308 17.12 11.21 32.81 0.86
3516 14600 7.201866 GCTGCAGGGCGAGCTATATATATATAT 60.202 40.741 17.12 17.37 32.81 0.86
3517 14601 9.343539 CTGCAGGGCGAGCTATATATATATATA 57.656 37.037 17.68 17.68 31.69 0.86
3518 14602 9.695155 TGCAGGGCGAGCTATATATATATATAA 57.305 33.333 18.75 5.80 32.44 0.98
3535 14619 2.624316 TAATAGGGTCGCGCTATTCG 57.376 50.000 22.62 0.00 43.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.950909 TGGAAAGTACACGCCCTTTTG 59.049 47.619 0.00 0.00 31.30 2.44
19 20 8.612619 CAACATCATACCTAACATGGAAAGTAC 58.387 37.037 0.00 0.00 0.00 2.73
22 23 6.319658 AGCAACATCATACCTAACATGGAAAG 59.680 38.462 0.00 0.00 0.00 2.62
39 40 6.914757 GCCAGAAAATAACTATCAGCAACATC 59.085 38.462 0.00 0.00 0.00 3.06
40 41 6.377996 TGCCAGAAAATAACTATCAGCAACAT 59.622 34.615 0.00 0.00 0.00 2.71
55 56 3.636300 TGCTAAGTTGTGTGCCAGAAAAT 59.364 39.130 0.00 0.00 0.00 1.82
60 61 2.553602 TCATTGCTAAGTTGTGTGCCAG 59.446 45.455 0.00 0.00 0.00 4.85
61 62 2.580962 TCATTGCTAAGTTGTGTGCCA 58.419 42.857 0.00 0.00 0.00 4.92
409 410 4.660168 ACATCAATCAATGGATAGAGGGC 58.340 43.478 0.00 0.00 32.09 5.19
410 411 6.176183 GGTACATCAATCAATGGATAGAGGG 58.824 44.000 0.00 0.00 32.09 4.30
411 412 5.871524 CGGTACATCAATCAATGGATAGAGG 59.128 44.000 0.00 0.00 32.09 3.69
412 413 5.871524 CCGGTACATCAATCAATGGATAGAG 59.128 44.000 0.00 0.00 32.09 2.43
413 414 5.279960 CCCGGTACATCAATCAATGGATAGA 60.280 44.000 0.00 0.00 32.09 1.98
414 415 4.937620 CCCGGTACATCAATCAATGGATAG 59.062 45.833 0.00 0.00 32.09 2.08
415 416 4.263287 CCCCGGTACATCAATCAATGGATA 60.263 45.833 0.00 0.00 32.09 2.59
416 417 3.498481 CCCCGGTACATCAATCAATGGAT 60.498 47.826 0.00 0.00 34.43 3.41
417 418 2.158682 CCCCGGTACATCAATCAATGGA 60.159 50.000 0.00 0.00 0.00 3.41
418 419 2.229792 CCCCGGTACATCAATCAATGG 58.770 52.381 0.00 0.00 0.00 3.16
419 420 2.158682 TCCCCCGGTACATCAATCAATG 60.159 50.000 0.00 0.00 0.00 2.82
420 421 2.106511 CTCCCCCGGTACATCAATCAAT 59.893 50.000 0.00 0.00 0.00 2.57
421 422 1.488812 CTCCCCCGGTACATCAATCAA 59.511 52.381 0.00 0.00 0.00 2.57
422 423 1.128200 CTCCCCCGGTACATCAATCA 58.872 55.000 0.00 0.00 0.00 2.57
423 424 0.396811 CCTCCCCCGGTACATCAATC 59.603 60.000 0.00 0.00 0.00 2.67
424 425 1.060163 CCCTCCCCCGGTACATCAAT 61.060 60.000 0.00 0.00 0.00 2.57
425 426 1.691337 CCCTCCCCCGGTACATCAA 60.691 63.158 0.00 0.00 0.00 2.57
426 427 2.041301 CCCTCCCCCGGTACATCA 60.041 66.667 0.00 0.00 0.00 3.07
427 428 2.847715 CCCCTCCCCCGGTACATC 60.848 72.222 0.00 0.00 0.00 3.06
428 429 4.509412 CCCCCTCCCCCGGTACAT 62.509 72.222 0.00 0.00 0.00 2.29
450 451 1.050988 TCACTGGATAGGCAGAGGGC 61.051 60.000 0.00 0.00 43.74 5.19
451 452 1.047002 CTCACTGGATAGGCAGAGGG 58.953 60.000 0.00 0.00 0.00 4.30
452 453 1.786937 ACTCACTGGATAGGCAGAGG 58.213 55.000 0.00 0.00 0.00 3.69
453 454 2.292016 CGTACTCACTGGATAGGCAGAG 59.708 54.545 0.00 0.00 0.00 3.35
454 455 2.298610 CGTACTCACTGGATAGGCAGA 58.701 52.381 0.00 0.00 0.00 4.26
455 456 1.269309 GCGTACTCACTGGATAGGCAG 60.269 57.143 0.00 0.00 31.61 4.85
456 457 0.744874 GCGTACTCACTGGATAGGCA 59.255 55.000 0.00 0.00 31.61 4.75
457 458 0.744874 TGCGTACTCACTGGATAGGC 59.255 55.000 0.00 0.00 0.00 3.93
458 459 3.735237 ATTGCGTACTCACTGGATAGG 57.265 47.619 0.00 0.00 0.00 2.57
459 460 6.682746 AGATAATTGCGTACTCACTGGATAG 58.317 40.000 0.00 0.00 0.00 2.08
460 461 6.650427 AGATAATTGCGTACTCACTGGATA 57.350 37.500 0.00 0.00 0.00 2.59
461 462 5.537300 AGATAATTGCGTACTCACTGGAT 57.463 39.130 0.00 0.00 0.00 3.41
462 463 5.109210 CAAGATAATTGCGTACTCACTGGA 58.891 41.667 0.00 0.00 0.00 3.86
463 464 4.870426 ACAAGATAATTGCGTACTCACTGG 59.130 41.667 0.00 0.00 0.00 4.00
464 465 7.700322 ATACAAGATAATTGCGTACTCACTG 57.300 36.000 0.00 0.00 0.00 3.66
465 466 7.764443 ACAATACAAGATAATTGCGTACTCACT 59.236 33.333 0.00 0.00 36.72 3.41
466 467 7.906160 ACAATACAAGATAATTGCGTACTCAC 58.094 34.615 0.00 0.00 36.72 3.51
467 468 7.762159 TGACAATACAAGATAATTGCGTACTCA 59.238 33.333 0.00 0.00 36.72 3.41
468 469 8.126871 TGACAATACAAGATAATTGCGTACTC 57.873 34.615 0.00 0.00 36.72 2.59
469 470 8.487313 TTGACAATACAAGATAATTGCGTACT 57.513 30.769 0.00 0.00 36.72 2.73
470 471 8.388103 ACTTGACAATACAAGATAATTGCGTAC 58.612 33.333 14.00 0.00 46.85 3.67
471 472 8.487313 ACTTGACAATACAAGATAATTGCGTA 57.513 30.769 14.00 0.00 46.85 4.42
472 473 7.377766 ACTTGACAATACAAGATAATTGCGT 57.622 32.000 14.00 0.00 46.85 5.24
473 474 9.586150 GATACTTGACAATACAAGATAATTGCG 57.414 33.333 14.00 0.00 46.85 4.85
480 481 9.167311 GGAACTTGATACTTGACAATACAAGAT 57.833 33.333 20.09 13.54 46.85 2.40
481 482 8.154203 TGGAACTTGATACTTGACAATACAAGA 58.846 33.333 20.09 0.77 46.85 3.02
483 484 8.154203 TCTGGAACTTGATACTTGACAATACAA 58.846 33.333 0.00 0.00 0.00 2.41
484 485 7.602644 GTCTGGAACTTGATACTTGACAATACA 59.397 37.037 0.00 0.00 0.00 2.29
485 486 7.602644 TGTCTGGAACTTGATACTTGACAATAC 59.397 37.037 0.00 0.00 0.00 1.89
486 487 7.676004 TGTCTGGAACTTGATACTTGACAATA 58.324 34.615 0.00 0.00 0.00 1.90
487 488 6.533730 TGTCTGGAACTTGATACTTGACAAT 58.466 36.000 0.00 0.00 0.00 2.71
488 489 5.924356 TGTCTGGAACTTGATACTTGACAA 58.076 37.500 0.00 0.00 0.00 3.18
489 490 5.545063 TGTCTGGAACTTGATACTTGACA 57.455 39.130 0.00 0.00 0.00 3.58
490 491 6.483640 ACTTTGTCTGGAACTTGATACTTGAC 59.516 38.462 0.00 0.00 0.00 3.18
491 492 6.591935 ACTTTGTCTGGAACTTGATACTTGA 58.408 36.000 0.00 0.00 0.00 3.02
492 493 6.073003 GGACTTTGTCTGGAACTTGATACTTG 60.073 42.308 0.00 0.00 32.47 3.16
493 494 5.998363 GGACTTTGTCTGGAACTTGATACTT 59.002 40.000 0.00 0.00 32.47 2.24
494 495 5.071788 TGGACTTTGTCTGGAACTTGATACT 59.928 40.000 0.00 0.00 32.47 2.12
495 496 5.179555 GTGGACTTTGTCTGGAACTTGATAC 59.820 44.000 0.00 0.00 32.47 2.24
496 497 5.071788 AGTGGACTTTGTCTGGAACTTGATA 59.928 40.000 0.00 0.00 32.47 2.15
497 498 4.137543 GTGGACTTTGTCTGGAACTTGAT 58.862 43.478 0.00 0.00 32.47 2.57
498 499 3.199946 AGTGGACTTTGTCTGGAACTTGA 59.800 43.478 0.00 0.00 32.47 3.02
499 500 3.545703 AGTGGACTTTGTCTGGAACTTG 58.454 45.455 0.00 0.00 32.47 3.16
520 521 6.537301 ACTCAGTAAATTCCGCGATTTCATTA 59.463 34.615 8.23 0.00 31.96 1.90
521 522 5.354234 ACTCAGTAAATTCCGCGATTTCATT 59.646 36.000 8.23 0.00 31.96 2.57
523 524 4.250464 ACTCAGTAAATTCCGCGATTTCA 58.750 39.130 8.23 0.00 31.96 2.69
524 525 4.859629 ACTCAGTAAATTCCGCGATTTC 57.140 40.909 8.23 1.55 31.96 2.17
525 526 4.693566 TGAACTCAGTAAATTCCGCGATTT 59.306 37.500 8.23 9.51 33.95 2.17
526 527 4.250464 TGAACTCAGTAAATTCCGCGATT 58.750 39.130 8.23 0.00 0.00 3.34
527 528 3.857052 TGAACTCAGTAAATTCCGCGAT 58.143 40.909 8.23 0.00 0.00 4.58
532 533 5.422214 TCCCTCTGAACTCAGTAAATTCC 57.578 43.478 6.61 0.00 44.12 3.01
560 561 2.538449 TCGAGTTGTTTCTGAACTTCGC 59.462 45.455 0.00 0.00 36.13 4.70
562 563 3.550678 ACGTCGAGTTGTTTCTGAACTTC 59.449 43.478 0.00 0.00 33.71 3.01
581 582 0.375803 GAACTCGCCAAACACAACGT 59.624 50.000 0.00 0.00 0.00 3.99
601 602 3.390135 CTGAGTACTTTTGCCGAGAACA 58.610 45.455 0.00 0.00 0.00 3.18
606 607 1.608025 CCAGCTGAGTACTTTTGCCGA 60.608 52.381 17.39 0.00 0.00 5.54
614 615 2.294449 TGACTGTCCAGCTGAGTACT 57.706 50.000 17.39 0.00 0.00 2.73
615 616 3.601443 AATGACTGTCCAGCTGAGTAC 57.399 47.619 17.39 10.92 0.00 2.73
616 617 3.131223 GCTAATGACTGTCCAGCTGAGTA 59.869 47.826 17.39 0.00 0.00 2.59
617 618 2.093764 GCTAATGACTGTCCAGCTGAGT 60.094 50.000 17.39 11.14 0.00 3.41
621 622 3.054875 TGATTGCTAATGACTGTCCAGCT 60.055 43.478 19.95 7.33 33.38 4.24
623 624 7.558161 TTAATGATTGCTAATGACTGTCCAG 57.442 36.000 5.17 1.40 0.00 3.86
632 633 8.343974 ACTCGCAAAATTAATGATTGCTAATG 57.656 30.769 24.97 17.64 45.48 1.90
633 634 8.931385 AACTCGCAAAATTAATGATTGCTAAT 57.069 26.923 24.97 11.07 45.48 1.73
635 636 8.243426 AGAAACTCGCAAAATTAATGATTGCTA 58.757 29.630 24.97 18.19 45.48 3.49
645 646 9.284594 GCACAATAATAGAAACTCGCAAAATTA 57.715 29.630 0.00 0.00 0.00 1.40
654 655 7.806690 TGTCAAGTGCACAATAATAGAAACTC 58.193 34.615 21.04 0.00 0.00 3.01
675 676 7.540400 CCGCAATGACTATTTAAATGTTTGTCA 59.460 33.333 19.94 19.94 37.37 3.58
678 679 7.754924 ACTCCGCAATGACTATTTAAATGTTTG 59.245 33.333 11.05 9.67 0.00 2.93
707 708 9.349145 GTAGTTTGCTGAGTTAAAAGTTTTTGA 57.651 29.630 6.10 0.00 0.00 2.69
715 716 4.825085 CCCTGGTAGTTTGCTGAGTTAAAA 59.175 41.667 0.00 0.00 0.00 1.52
716 717 4.141344 ACCCTGGTAGTTTGCTGAGTTAAA 60.141 41.667 0.00 0.00 0.00 1.52
717 718 3.393278 ACCCTGGTAGTTTGCTGAGTTAA 59.607 43.478 0.00 0.00 0.00 2.01
726 727 4.360951 TTCACCTAACCCTGGTAGTTTG 57.639 45.455 0.00 0.00 35.80 2.93
736 737 0.323087 ATGGCCGTTTCACCTAACCC 60.323 55.000 0.00 0.00 0.00 4.11
737 738 1.541379 AATGGCCGTTTCACCTAACC 58.459 50.000 3.71 0.00 0.00 2.85
753 754 8.067784 GTGTCATGTAATATTGGGTCGTTAATG 58.932 37.037 0.00 0.00 0.00 1.90
754 755 7.771361 TGTGTCATGTAATATTGGGTCGTTAAT 59.229 33.333 0.00 0.00 0.00 1.40
755 756 7.064847 GTGTGTCATGTAATATTGGGTCGTTAA 59.935 37.037 0.00 0.00 0.00 2.01
756 757 6.535865 GTGTGTCATGTAATATTGGGTCGTTA 59.464 38.462 0.00 0.00 0.00 3.18
757 758 5.353123 GTGTGTCATGTAATATTGGGTCGTT 59.647 40.000 0.00 0.00 0.00 3.85
758 759 4.873827 GTGTGTCATGTAATATTGGGTCGT 59.126 41.667 0.00 0.00 0.00 4.34
759 760 5.116180 AGTGTGTCATGTAATATTGGGTCG 58.884 41.667 0.00 0.00 0.00 4.79
760 761 8.559536 CATTAGTGTGTCATGTAATATTGGGTC 58.440 37.037 0.00 0.00 0.00 4.46
761 762 7.013274 GCATTAGTGTGTCATGTAATATTGGGT 59.987 37.037 0.00 0.00 0.00 4.51
762 763 7.229306 AGCATTAGTGTGTCATGTAATATTGGG 59.771 37.037 0.00 0.00 0.00 4.12
763 764 8.158169 AGCATTAGTGTGTCATGTAATATTGG 57.842 34.615 0.00 0.00 0.00 3.16
764 765 9.655769 GAAGCATTAGTGTGTCATGTAATATTG 57.344 33.333 0.00 0.00 0.00 1.90
765 766 9.394767 TGAAGCATTAGTGTGTCATGTAATATT 57.605 29.630 0.00 0.00 0.00 1.28
766 767 8.830580 GTGAAGCATTAGTGTGTCATGTAATAT 58.169 33.333 0.00 0.00 0.00 1.28
767 768 8.040727 AGTGAAGCATTAGTGTGTCATGTAATA 58.959 33.333 0.00 0.00 0.00 0.98
768 769 6.881065 AGTGAAGCATTAGTGTGTCATGTAAT 59.119 34.615 0.00 0.00 0.00 1.89
769 770 6.230472 AGTGAAGCATTAGTGTGTCATGTAA 58.770 36.000 0.00 0.00 0.00 2.41
770 771 5.793817 AGTGAAGCATTAGTGTGTCATGTA 58.206 37.500 0.00 0.00 0.00 2.29
771 772 4.645535 AGTGAAGCATTAGTGTGTCATGT 58.354 39.130 0.00 0.00 0.00 3.21
772 773 6.726258 TTAGTGAAGCATTAGTGTGTCATG 57.274 37.500 0.00 0.00 0.00 3.07
773 774 7.607607 TGAATTAGTGAAGCATTAGTGTGTCAT 59.392 33.333 0.00 0.00 0.00 3.06
774 775 6.934083 TGAATTAGTGAAGCATTAGTGTGTCA 59.066 34.615 0.00 0.00 0.00 3.58
775 776 7.364522 TGAATTAGTGAAGCATTAGTGTGTC 57.635 36.000 0.00 0.00 0.00 3.67
776 777 7.744087 TTGAATTAGTGAAGCATTAGTGTGT 57.256 32.000 0.00 0.00 0.00 3.72
781 782 9.941664 CCAGTAATTGAATTAGTGAAGCATTAG 57.058 33.333 26.32 9.52 44.95 1.73
782 783 9.679661 TCCAGTAATTGAATTAGTGAAGCATTA 57.320 29.630 26.32 6.98 44.95 1.90
783 784 8.579850 TCCAGTAATTGAATTAGTGAAGCATT 57.420 30.769 26.32 0.00 44.95 3.56
784 785 8.757982 ATCCAGTAATTGAATTAGTGAAGCAT 57.242 30.769 26.32 13.72 44.95 3.79
785 786 7.011389 CGATCCAGTAATTGAATTAGTGAAGCA 59.989 37.037 26.32 12.46 44.95 3.91
786 787 7.348201 CGATCCAGTAATTGAATTAGTGAAGC 58.652 38.462 26.32 13.86 44.95 3.86
787 788 7.348201 GCGATCCAGTAATTGAATTAGTGAAG 58.652 38.462 26.32 14.96 44.95 3.02
797 798 3.126001 GGATGGCGATCCAGTAATTGA 57.874 47.619 21.74 0.00 46.93 2.57
809 810 4.013050 TGTTCAACAAATATGGATGGCGA 58.987 39.130 0.00 0.00 0.00 5.54
812 813 9.217278 TGAATTTTGTTCAACAAATATGGATGG 57.783 29.630 16.41 0.00 46.17 3.51
823 824 6.154203 TGGTAGCATGAATTTTGTTCAACA 57.846 33.333 0.00 0.00 31.55 3.33
838 839 2.176364 AGCCATTTGGAGATGGTAGCAT 59.824 45.455 7.23 7.23 46.74 3.79
863 864 3.291497 GAGGTCTGTGGCCTCTAGT 57.709 57.895 10.63 0.00 46.71 2.57
883 884 0.908198 ATGTCAGAGGAGCTGGTTCC 59.092 55.000 0.00 0.00 44.98 3.62
884 885 2.480416 CGTATGTCAGAGGAGCTGGTTC 60.480 54.545 0.00 0.00 44.98 3.62
885 886 1.478510 CGTATGTCAGAGGAGCTGGTT 59.521 52.381 0.00 0.00 44.98 3.67
886 887 1.107114 CGTATGTCAGAGGAGCTGGT 58.893 55.000 0.00 0.00 44.98 4.00
887 888 0.387202 CCGTATGTCAGAGGAGCTGG 59.613 60.000 0.00 0.00 44.98 4.85
889 890 1.395826 GGCCGTATGTCAGAGGAGCT 61.396 60.000 0.00 0.00 0.00 4.09
890 891 1.068250 GGCCGTATGTCAGAGGAGC 59.932 63.158 0.00 0.00 0.00 4.70
891 892 0.824109 TTGGCCGTATGTCAGAGGAG 59.176 55.000 0.00 0.00 0.00 3.69
892 893 1.138859 CATTGGCCGTATGTCAGAGGA 59.861 52.381 9.02 0.00 0.00 3.71
894 895 0.940126 GCATTGGCCGTATGTCAGAG 59.060 55.000 16.42 0.00 0.00 3.35
895 896 0.251634 TGCATTGGCCGTATGTCAGA 59.748 50.000 16.42 0.19 40.13 3.27
896 897 1.093972 TTGCATTGGCCGTATGTCAG 58.906 50.000 16.42 0.00 40.13 3.51
897 898 1.539157 TTTGCATTGGCCGTATGTCA 58.461 45.000 16.42 12.54 40.13 3.58
898 899 2.529151 CTTTTGCATTGGCCGTATGTC 58.471 47.619 16.42 10.64 40.13 3.06
899 900 1.204467 CCTTTTGCATTGGCCGTATGT 59.796 47.619 16.42 0.00 40.13 2.29
900 901 1.476085 TCCTTTTGCATTGGCCGTATG 59.524 47.619 12.16 12.16 40.13 2.39
902 903 1.543802 CTTCCTTTTGCATTGGCCGTA 59.456 47.619 0.00 0.00 40.13 4.02
904 905 0.318120 ACTTCCTTTTGCATTGGCCG 59.682 50.000 0.00 0.00 40.13 6.13
905 906 2.549064 AACTTCCTTTTGCATTGGCC 57.451 45.000 0.00 0.00 40.13 5.36
939 953 4.763793 CACTCCACCATCAATCAAGTTCTT 59.236 41.667 0.00 0.00 0.00 2.52
942 980 4.371624 TCACTCCACCATCAATCAAGTT 57.628 40.909 0.00 0.00 0.00 2.66
951 989 0.035630 AGCAGCTTCACTCCACCATC 60.036 55.000 0.00 0.00 0.00 3.51
971 1009 3.367025 GCGTCGGTGGAGCATATTTATAC 59.633 47.826 0.00 0.00 0.00 1.47
1012 1050 2.871182 TCGGACGAGATGAATGGAAG 57.129 50.000 0.00 0.00 0.00 3.46
1013 1051 3.603158 TTTCGGACGAGATGAATGGAA 57.397 42.857 0.00 0.00 0.00 3.53
1014 1052 3.259064 GTTTTCGGACGAGATGAATGGA 58.741 45.455 0.00 0.00 0.00 3.41
1028 1066 2.223021 CGCCATATCACACTGTTTTCGG 60.223 50.000 0.00 0.00 0.00 4.30
1029 1067 2.670905 TCGCCATATCACACTGTTTTCG 59.329 45.455 0.00 0.00 0.00 3.46
1439 1551 0.598680 GGCTCCAGATGATCGAACGG 60.599 60.000 0.00 0.00 0.00 4.44
1440 1552 0.387202 AGGCTCCAGATGATCGAACG 59.613 55.000 0.00 0.00 0.00 3.95
1630 1742 1.447838 CTCCGTCACCATGTTCCCG 60.448 63.158 0.00 0.00 0.00 5.14
1777 1889 3.055819 GGAAGAGGTATCTGTTGAGCACA 60.056 47.826 0.00 0.00 35.37 4.57
1789 1901 0.470268 GGCCGGAGAGGAAGAGGTAT 60.470 60.000 5.05 0.00 45.00 2.73
1930 2042 1.745489 GTTGCCGTGGGAGATGGAC 60.745 63.158 0.00 0.00 31.27 4.02
2010 2141 4.435436 CGCGTGTAGGCCAGCTCA 62.435 66.667 5.01 0.00 0.00 4.26
2133 2264 0.389817 CAAAGAGGTCACCATCGCGA 60.390 55.000 13.09 13.09 0.00 5.87
2323 2454 1.276622 GCCTTCTCCTCCAACCTGTA 58.723 55.000 0.00 0.00 0.00 2.74
2324 2455 1.492993 GGCCTTCTCCTCCAACCTGT 61.493 60.000 0.00 0.00 0.00 4.00
2347 2478 1.226746 GCCTTCTTGCTGTTACGTGT 58.773 50.000 0.00 0.00 0.00 4.49
2348 2479 0.517316 GGCCTTCTTGCTGTTACGTG 59.483 55.000 0.00 0.00 0.00 4.49
2391 2522 2.502295 GGCCTATCAAAGATCCAGCTG 58.498 52.381 6.78 6.78 0.00 4.24
2781 2944 4.022503 ACAGAAACTGACTCGGTACCTTAC 60.023 45.833 10.90 0.00 35.18 2.34
2792 2955 6.331061 GTCCGATACATAACAGAAACTGACT 58.669 40.000 5.76 0.00 35.18 3.41
2810 2973 3.322254 CAGATACTTAGGCTTGGTCCGAT 59.678 47.826 0.00 0.00 0.00 4.18
2850 3013 1.133668 AGAACTCAGCCCTTTGCAACT 60.134 47.619 0.00 0.00 44.83 3.16
2882 3046 8.722622 AGTACCAAACTATGCCTACTATACAT 57.277 34.615 0.00 0.00 36.36 2.29
2883 3047 9.645128 TTAGTACCAAACTATGCCTACTATACA 57.355 33.333 0.00 0.00 40.41 2.29
2885 3049 9.872684 ACTTAGTACCAAACTATGCCTACTATA 57.127 33.333 0.00 0.00 40.41 1.31
2886 3050 8.779096 ACTTAGTACCAAACTATGCCTACTAT 57.221 34.615 0.00 0.00 40.41 2.12
2889 3053 7.110043 AGACTTAGTACCAAACTATGCCTAC 57.890 40.000 0.00 0.00 40.41 3.18
2978 3147 3.449737 CGAACTAGGGGAGTGGTTTATCA 59.550 47.826 0.00 0.00 38.87 2.15
3000 3169 4.036852 AGCAAACTCTTTGTAAGGAAGCAC 59.963 41.667 0.00 0.00 42.56 4.40
3129 3604 0.249073 ATCCGAAGCGAAGATGACCG 60.249 55.000 0.00 0.00 0.00 4.79
3138 3613 0.527113 TTTGGTCGTATCCGAAGCGA 59.473 50.000 0.00 0.00 46.26 4.93
3233 4793 1.000060 TGTCTTCCCGAGTAAACCGTG 60.000 52.381 0.00 0.00 0.00 4.94
3235 4795 2.029649 TCTTGTCTTCCCGAGTAAACCG 60.030 50.000 0.00 0.00 0.00 4.44
3267 4827 8.697846 TTACAAATCTGGACTCGTAGTTTATG 57.302 34.615 0.00 0.00 0.00 1.90
3272 4832 6.817140 GGAAATTACAAATCTGGACTCGTAGT 59.183 38.462 0.00 0.00 0.00 2.73
3274 4834 6.703319 TGGAAATTACAAATCTGGACTCGTA 58.297 36.000 0.00 0.00 0.00 3.43
3386 13728 0.179026 AGCTTCGCATGCTGGATGAT 60.179 50.000 17.13 4.83 39.56 2.45
3436 14465 5.409520 CGTCATGACCATTCAGAGAGAAAAA 59.590 40.000 20.03 0.00 40.22 1.94
3437 14466 4.931601 CGTCATGACCATTCAGAGAGAAAA 59.068 41.667 20.03 0.00 40.22 2.29
3438 14467 4.498241 CGTCATGACCATTCAGAGAGAAA 58.502 43.478 20.03 0.00 40.22 2.52
3439 14468 3.677148 GCGTCATGACCATTCAGAGAGAA 60.677 47.826 20.03 0.00 41.28 2.87
3440 14469 2.159184 GCGTCATGACCATTCAGAGAGA 60.159 50.000 20.03 0.00 34.35 3.10
3441 14470 2.159128 AGCGTCATGACCATTCAGAGAG 60.159 50.000 20.03 3.17 34.35 3.20
3442 14471 1.827344 AGCGTCATGACCATTCAGAGA 59.173 47.619 20.03 0.00 34.35 3.10
3443 14472 2.306341 AGCGTCATGACCATTCAGAG 57.694 50.000 20.03 4.61 34.35 3.35
3444 14473 2.743664 CAAAGCGTCATGACCATTCAGA 59.256 45.455 20.03 0.00 34.35 3.27
3445 14474 2.743664 TCAAAGCGTCATGACCATTCAG 59.256 45.455 20.03 6.06 34.35 3.02
3446 14475 2.777094 TCAAAGCGTCATGACCATTCA 58.223 42.857 20.03 3.34 35.73 2.57
3447 14476 3.829886 TTCAAAGCGTCATGACCATTC 57.170 42.857 20.03 7.05 0.00 2.67
3448 14477 3.129287 GGATTCAAAGCGTCATGACCATT 59.871 43.478 20.03 11.79 0.00 3.16
3449 14478 2.684881 GGATTCAAAGCGTCATGACCAT 59.315 45.455 20.03 5.95 0.00 3.55
3450 14479 2.083774 GGATTCAAAGCGTCATGACCA 58.916 47.619 20.03 0.00 0.00 4.02
3451 14480 2.083774 TGGATTCAAAGCGTCATGACC 58.916 47.619 20.03 12.53 0.00 4.02
3452 14481 2.096496 CCTGGATTCAAAGCGTCATGAC 59.904 50.000 16.21 16.21 0.00 3.06
3453 14482 2.027285 TCCTGGATTCAAAGCGTCATGA 60.027 45.455 0.00 0.00 0.00 3.07
3454 14483 2.353889 CTCCTGGATTCAAAGCGTCATG 59.646 50.000 0.00 0.00 0.00 3.07
3455 14484 2.636830 CTCCTGGATTCAAAGCGTCAT 58.363 47.619 0.00 0.00 0.00 3.06
3456 14485 1.339055 CCTCCTGGATTCAAAGCGTCA 60.339 52.381 0.00 0.00 34.57 4.35
3457 14486 1.373570 CCTCCTGGATTCAAAGCGTC 58.626 55.000 0.00 0.00 34.57 5.19
3458 14487 0.035056 CCCTCCTGGATTCAAAGCGT 60.035 55.000 0.00 0.00 35.39 5.07
3459 14488 0.253044 TCCCTCCTGGATTCAAAGCG 59.747 55.000 0.00 0.00 38.61 4.68
3509 14593 8.396390 CGAATAGCGCGACCCTATTATATATAT 58.604 37.037 12.10 0.00 36.05 0.86
3510 14594 7.745972 CGAATAGCGCGACCCTATTATATATA 58.254 38.462 12.10 0.00 36.05 0.86
3511 14595 6.609533 CGAATAGCGCGACCCTATTATATAT 58.390 40.000 12.10 0.00 36.05 0.86
3512 14596 5.993891 CGAATAGCGCGACCCTATTATATA 58.006 41.667 12.10 0.00 36.05 0.86
3513 14597 4.856664 CGAATAGCGCGACCCTATTATAT 58.143 43.478 12.10 0.00 36.05 0.86
3514 14598 4.282950 CGAATAGCGCGACCCTATTATA 57.717 45.455 12.10 0.00 36.05 0.98
3515 14599 3.146618 CGAATAGCGCGACCCTATTAT 57.853 47.619 12.10 0.00 36.05 1.28
3516 14600 2.624316 CGAATAGCGCGACCCTATTA 57.376 50.000 12.10 0.00 36.05 0.98
3517 14601 3.491581 CGAATAGCGCGACCCTATT 57.508 52.632 12.10 13.82 38.00 1.73


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

AutoCloner maintained by Alex Coulton.