Multiple sequence alignment - TraesCS3D01G422700

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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 TraesCS3D01G422700 chr3D 100.000 4665 0 0 1 4665 535406790 535402126 0.000000e+00 8615.0
1 TraesCS3D01G422700 chr3D 77.249 189 41 2 353 539 8676690 8676502 4.940000e-20 110.0
2 TraesCS3D01G422700 chr3D 73.568 227 48 9 360 580 495483929 495484149 5.010000e-10 76.8
3 TraesCS3D01G422700 chr3B 92.588 2469 109 40 1887 4322 706759232 706756805 0.000000e+00 3478.0
4 TraesCS3D01G422700 chr3B 95.287 1952 63 15 1948 3877 706191127 706189183 0.000000e+00 3068.0
5 TraesCS3D01G422700 chr3B 92.364 956 36 14 922 1865 706760317 706759387 0.000000e+00 1327.0
6 TraesCS3D01G422700 chr3B 91.603 655 26 9 922 1571 706192120 706191490 0.000000e+00 878.0
7 TraesCS3D01G422700 chr3B 86.996 446 22 12 3930 4374 706187901 706187491 1.970000e-128 470.0
8 TraesCS3D01G422700 chr3B 89.429 350 28 5 585 926 706760701 706760353 2.580000e-117 433.0
9 TraesCS3D01G422700 chr3B 89.674 184 13 4 1683 1865 706191446 706191268 3.630000e-56 230.0
10 TraesCS3D01G422700 chr3B 95.294 85 3 1 30 113 706778989 706778905 2.930000e-27 134.0
11 TraesCS3D01G422700 chr3B 97.778 45 1 0 3900 3944 706189042 706188998 1.390000e-10 78.7
12 TraesCS3D01G422700 chr3B 91.304 46 4 0 522 567 132401202 132401247 3.900000e-06 63.9
13 TraesCS3D01G422700 chr3A 94.546 2017 77 13 1887 3877 670550414 670548405 0.000000e+00 3085.0
14 TraesCS3D01G422700 chr3A 87.689 1324 73 27 584 1865 670551838 670550563 0.000000e+00 1459.0
15 TraesCS3D01G422700 chr3A 81.353 606 83 21 1 582 670552483 670551884 2.540000e-127 466.0
16 TraesCS3D01G422700 chr3A 95.489 266 11 1 4159 4423 670547771 670547506 1.550000e-114 424.0
17 TraesCS3D01G422700 chr3A 92.884 267 17 2 3900 4166 670548270 670548006 2.040000e-103 387.0
18 TraesCS3D01G422700 chr3A 81.991 211 23 7 4457 4665 670547506 670547309 1.040000e-36 165.0
19 TraesCS3D01G422700 chr7A 79.730 222 40 5 360 579 43250553 43250771 6.250000e-34 156.0
20 TraesCS3D01G422700 chr7D 77.436 195 41 3 391 582 622606987 622606793 3.820000e-21 113.0
21 TraesCS3D01G422700 chr6B 77.297 185 37 3 397 579 229707481 229707662 2.300000e-18 104.0
22 TraesCS3D01G422700 chr6D 76.042 192 38 7 391 579 290322875 290322689 4.970000e-15 93.5
23 TraesCS3D01G422700 chr5D 76.111 180 39 4 366 542 562028599 562028421 1.790000e-14 91.6
24 TraesCS3D01G422700 chr2A 77.848 158 27 7 395 548 717575810 717575963 1.790000e-14 91.6
25 TraesCS3D01G422700 chr7B 87.692 65 7 1 391 455 492496949 492496886 1.800000e-09 75.0
26 TraesCS3D01G422700 chr2D 77.419 124 26 2 427 548 579947617 579947494 6.470000e-09 73.1


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 TraesCS3D01G422700 chr3D 535402126 535406790 4664 True 8615.000000 8615 100.000000 1 4665 1 chr3D.!!$R2 4664
1 TraesCS3D01G422700 chr3B 706756805 706760701 3896 True 1746.000000 3478 91.460333 585 4322 3 chr3B.!!$R3 3737
2 TraesCS3D01G422700 chr3B 706187491 706192120 4629 True 944.940000 3068 92.267600 922 4374 5 chr3B.!!$R2 3452
3 TraesCS3D01G422700 chr3A 670547309 670552483 5174 True 997.666667 3085 88.992000 1 4665 6 chr3A.!!$R1 4664

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
416 437 0.252558 ACCCCTATGGACACCTTCGT 60.253 55.000 0.0 0.0 38.0 3.85 F
1334 1478 0.179018 GGCACCAGGTCAGTTCTTGT 60.179 55.000 0.0 0.0 0.0 3.16 F
1493 1643 0.536006 GTGGCTGTTGACTCCTGCTT 60.536 55.000 0.0 0.0 0.0 3.91 F
2693 2999 1.211212 TGCCAATCATACTGCTCTGCT 59.789 47.619 0.0 0.0 0.0 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1424 1572 0.311790 ACTACGAAACCGCAGACGAA 59.688 50.000 0.0 0.0 43.93 3.85 R
2425 2731 0.933097 CCTTCCTGATTGCGACATCG 59.067 55.000 0.0 0.0 43.27 3.84 R
3343 3649 2.586245 CTGATGGAAGGCAGCGGA 59.414 61.111 0.0 0.0 0.00 5.54 R
4441 6248 0.037590 TTGGCAGCTTACCGGTCATT 59.962 50.000 12.4 0.0 0.00 2.57 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
59 64 9.774742 GACTTTAGCTTTGTTATGTATCTTTGG 57.225 33.333 0.00 0.00 0.00 3.28
60 65 8.244113 ACTTTAGCTTTGTTATGTATCTTTGGC 58.756 33.333 0.00 0.00 0.00 4.52
121 127 5.278061 TCCAATAAGTTACTAGCTCACCCT 58.722 41.667 0.00 0.00 0.00 4.34
126 135 9.444600 CAATAAGTTACTAGCTCACCCTAAAAA 57.555 33.333 0.00 0.00 0.00 1.94
169 178 9.135843 CAACAAGTTACTAGTATGTTCGAATCA 57.864 33.333 14.60 1.76 32.25 2.57
181 190 5.193663 TGTTCGAATCATTGGCAAAGAAA 57.806 34.783 9.41 0.00 0.00 2.52
183 192 6.045318 TGTTCGAATCATTGGCAAAGAAAAA 58.955 32.000 9.41 0.00 0.00 1.94
184 193 6.019156 TGTTCGAATCATTGGCAAAGAAAAAC 60.019 34.615 9.41 11.04 0.00 2.43
246 255 9.899661 TTGATTATATCTTCTTTTTCCCTTCGA 57.100 29.630 0.00 0.00 0.00 3.71
268 277 1.878953 AAGACACGGCACAAAGGTAG 58.121 50.000 0.00 0.00 0.00 3.18
274 283 1.148310 CGGCACAAAGGTAGACACTG 58.852 55.000 0.00 0.00 0.00 3.66
275 284 1.270094 CGGCACAAAGGTAGACACTGA 60.270 52.381 0.00 0.00 0.00 3.41
281 290 6.338146 GCACAAAGGTAGACACTGATATACA 58.662 40.000 0.00 0.00 0.00 2.29
291 300 5.246203 AGACACTGATATACACACCAACACT 59.754 40.000 0.00 0.00 0.00 3.55
307 316 2.125350 CTCACCCTCGCAAGCCTC 60.125 66.667 0.00 0.00 37.18 4.70
317 326 0.393537 CGCAAGCCTCCAATCCTTCT 60.394 55.000 0.00 0.00 0.00 2.85
324 333 5.574970 AGCCTCCAATCCTTCTATTTAGG 57.425 43.478 0.00 0.00 0.00 2.69
359 368 8.725212 ATAAATACAAATAGACGTAGACGCTC 57.275 34.615 1.14 0.00 44.43 5.03
360 369 5.746307 ATACAAATAGACGTAGACGCTCA 57.254 39.130 1.14 0.00 44.43 4.26
361 370 4.634184 ACAAATAGACGTAGACGCTCAT 57.366 40.909 1.14 0.00 44.43 2.90
362 371 5.746307 ACAAATAGACGTAGACGCTCATA 57.254 39.130 1.14 0.00 44.43 2.15
363 372 5.508872 ACAAATAGACGTAGACGCTCATAC 58.491 41.667 1.14 0.00 44.43 2.39
364 373 4.745837 AATAGACGTAGACGCTCATACC 57.254 45.455 1.14 0.00 44.43 2.73
365 374 1.307097 AGACGTAGACGCTCATACCC 58.693 55.000 1.14 0.00 44.43 3.69
371 392 1.394618 AGACGCTCATACCCTCACTC 58.605 55.000 0.00 0.00 0.00 3.51
376 397 4.663334 ACGCTCATACCCTCACTCATATA 58.337 43.478 0.00 0.00 0.00 0.86
380 401 6.533012 CGCTCATACCCTCACTCATATAAATG 59.467 42.308 0.00 0.00 0.00 2.32
382 403 7.315066 TCATACCCTCACTCATATAAATGCA 57.685 36.000 0.00 0.00 32.76 3.96
384 405 5.372343 ACCCTCACTCATATAAATGCACA 57.628 39.130 0.00 0.00 32.76 4.57
393 414 7.482743 CACTCATATAAATGCACACAAGAACAC 59.517 37.037 0.00 0.00 32.76 3.32
394 415 7.391554 ACTCATATAAATGCACACAAGAACACT 59.608 33.333 0.00 0.00 32.76 3.55
397 418 8.882736 CATATAAATGCACACAAGAACACTCTA 58.117 33.333 0.00 0.00 0.00 2.43
401 422 2.767505 CACACAAGAACACTCTACCCC 58.232 52.381 0.00 0.00 0.00 4.95
406 427 3.775316 ACAAGAACACTCTACCCCTATGG 59.225 47.826 0.00 0.00 41.37 2.74
408 429 3.644335 AGAACACTCTACCCCTATGGAC 58.356 50.000 0.00 0.00 38.00 4.02
411 432 2.040178 CACTCTACCCCTATGGACACC 58.960 57.143 0.00 0.00 38.00 4.16
413 434 2.318207 ACTCTACCCCTATGGACACCTT 59.682 50.000 0.00 0.00 38.00 3.50
414 435 2.966516 CTCTACCCCTATGGACACCTTC 59.033 54.545 0.00 0.00 38.00 3.46
416 437 0.252558 ACCCCTATGGACACCTTCGT 60.253 55.000 0.00 0.00 38.00 3.85
421 442 2.159226 CCTATGGACACCTTCGTGAGAC 60.159 54.545 0.00 0.00 43.14 3.36
441 462 1.600957 CTAAGCCGGCACATCATCTTG 59.399 52.381 31.54 2.80 0.00 3.02
450 471 4.992951 CGGCACATCATCTTGAGATTGATA 59.007 41.667 0.90 0.00 31.21 2.15
457 478 9.458727 ACATCATCTTGAGATTGATAAAGTTGT 57.541 29.630 0.90 0.00 31.21 3.32
465 486 7.796838 TGAGATTGATAAAGTTGTCAAAGACG 58.203 34.615 7.22 0.00 40.76 4.18
466 487 6.603095 AGATTGATAAAGTTGTCAAAGACGC 58.397 36.000 7.22 0.00 40.76 5.19
467 488 6.428159 AGATTGATAAAGTTGTCAAAGACGCT 59.572 34.615 7.22 0.00 40.76 5.07
470 491 6.791303 TGATAAAGTTGTCAAAGACGCTTTT 58.209 32.000 17.81 9.63 39.29 2.27
471 492 6.690957 TGATAAAGTTGTCAAAGACGCTTTTG 59.309 34.615 17.81 6.01 39.29 2.44
472 493 2.797491 AGTTGTCAAAGACGCTTTTGC 58.203 42.857 7.21 4.40 37.83 3.68
482 503 2.556287 GCTTTTGCAGTCGACGGG 59.444 61.111 17.45 11.50 46.58 5.28
484 505 1.597027 CTTTTGCAGTCGACGGGGT 60.597 57.895 17.45 0.00 0.00 4.95
485 506 1.841663 CTTTTGCAGTCGACGGGGTG 61.842 60.000 17.45 7.95 0.00 4.61
486 507 2.596553 TTTTGCAGTCGACGGGGTGT 62.597 55.000 17.45 0.00 0.00 4.16
487 508 2.981977 TTTGCAGTCGACGGGGTGTC 62.982 60.000 17.45 0.78 44.53 3.67
490 511 2.675772 AGTCGACGGGGTGTCTCC 60.676 66.667 10.46 0.00 45.87 3.71
491 512 2.987547 GTCGACGGGGTGTCTCCA 60.988 66.667 0.00 0.00 45.87 3.86
506 530 2.234908 GTCTCCACCACTAAGCTCACAT 59.765 50.000 0.00 0.00 0.00 3.21
509 533 2.028112 TCCACCACTAAGCTCACATCAC 60.028 50.000 0.00 0.00 0.00 3.06
517 541 2.550830 AGCTCACATCACCGAAAAGT 57.449 45.000 0.00 0.00 0.00 2.66
520 544 2.808543 GCTCACATCACCGAAAAGTCTT 59.191 45.455 0.00 0.00 0.00 3.01
549 573 0.589729 CAGAAAAATGCGATCGCCGG 60.590 55.000 35.12 16.43 41.09 6.13
556 580 2.890474 GCGATCGCCGGTGTCAAT 60.890 61.111 29.48 0.28 39.04 2.57
561 585 2.285602 CGATCGCCGGTGTCAATTTTAG 60.286 50.000 16.01 0.00 33.91 1.85
567 591 4.004982 GCCGGTGTCAATTTTAGGACTTA 58.995 43.478 1.90 0.00 35.11 2.24
570 594 6.376177 CCGGTGTCAATTTTAGGACTTAAAC 58.624 40.000 0.00 0.00 35.11 2.01
571 595 6.206048 CCGGTGTCAATTTTAGGACTTAAACT 59.794 38.462 0.00 0.00 35.11 2.66
572 596 7.295930 CGGTGTCAATTTTAGGACTTAAACTC 58.704 38.462 0.00 0.00 35.11 3.01
575 599 9.052759 GTGTCAATTTTAGGACTTAAACTCTGA 57.947 33.333 0.00 0.00 35.11 3.27
576 600 9.793259 TGTCAATTTTAGGACTTAAACTCTGAT 57.207 29.630 0.00 0.00 35.11 2.90
582 650 4.362677 AGGACTTAAACTCTGATGGGCTA 58.637 43.478 0.00 0.00 0.00 3.93
625 693 1.014352 GTATGCCACGTGGTTGATCC 58.986 55.000 33.92 17.61 37.57 3.36
645 714 2.621998 CCATCATTCTGCCAGATTCCAC 59.378 50.000 0.00 0.00 0.00 4.02
720 793 1.683011 CCACCCCGAATCTCAAAGCAT 60.683 52.381 0.00 0.00 0.00 3.79
745 818 1.564348 ACGGAGCTGATTTAACCCCAT 59.436 47.619 0.00 0.00 0.00 4.00
752 825 1.318576 GATTTAACCCCATCCAGCCG 58.681 55.000 0.00 0.00 0.00 5.52
777 852 2.421314 CTCCCACCGCATCGCATA 59.579 61.111 0.00 0.00 0.00 3.14
778 853 1.004560 CTCCCACCGCATCGCATAT 60.005 57.895 0.00 0.00 0.00 1.78
803 888 2.347114 CTCGCATCACCCACACCA 59.653 61.111 0.00 0.00 0.00 4.17
804 889 2.031919 TCGCATCACCCACACCAC 59.968 61.111 0.00 0.00 0.00 4.16
805 890 3.422303 CGCATCACCCACACCACG 61.422 66.667 0.00 0.00 0.00 4.94
806 891 3.737172 GCATCACCCACACCACGC 61.737 66.667 0.00 0.00 0.00 5.34
807 892 3.422303 CATCACCCACACCACGCG 61.422 66.667 3.53 3.53 0.00 6.01
833 918 2.892374 CCGGCTTCAATTTTTCCATCC 58.108 47.619 0.00 0.00 0.00 3.51
838 923 3.429085 CTTCAATTTTTCCATCCGCTCG 58.571 45.455 0.00 0.00 0.00 5.03
990 1129 2.035237 CTCTTATAACCCCGCGCCCA 62.035 60.000 0.00 0.00 0.00 5.36
1334 1478 0.179018 GGCACCAGGTCAGTTCTTGT 60.179 55.000 0.00 0.00 0.00 3.16
1424 1572 5.826737 CCAATCTCAAGTCTTTAGGCATCAT 59.173 40.000 0.00 0.00 0.00 2.45
1439 1587 0.999406 ATCATTCGTCTGCGGTTTCG 59.001 50.000 0.00 0.00 38.89 3.46
1488 1638 1.510480 GCACTGTGGCTGTTGACTCC 61.510 60.000 10.21 0.00 0.00 3.85
1493 1643 0.536006 GTGGCTGTTGACTCCTGCTT 60.536 55.000 0.00 0.00 0.00 3.91
1594 1753 3.748568 GTCTGGTTGGTGATCTTTGTCTC 59.251 47.826 0.00 0.00 0.00 3.36
1615 1775 6.979238 GTCTCTTATGCACGTTCCTACTAATT 59.021 38.462 0.00 0.00 0.00 1.40
1628 1788 5.054477 TCCTACTAATTACAAATCTGCGGC 58.946 41.667 0.00 0.00 0.00 6.53
1629 1789 4.213482 CCTACTAATTACAAATCTGCGGCC 59.787 45.833 0.00 0.00 0.00 6.13
1723 1884 9.905713 TTAATAAATCACTCTTCTATGGTGCTT 57.094 29.630 0.00 0.00 0.00 3.91
1726 1887 5.690464 ATCACTCTTCTATGGTGCTTCTT 57.310 39.130 0.00 0.00 0.00 2.52
1761 1922 2.771089 CAGGAAGTGCTTACTGCTCAA 58.229 47.619 10.82 0.00 43.75 3.02
1852 2013 5.964958 TTTCAGAAGAAAGCATGGTAAGG 57.035 39.130 0.00 0.00 38.76 2.69
1853 2014 4.640771 TCAGAAGAAAGCATGGTAAGGT 57.359 40.909 0.00 0.00 0.00 3.50
1854 2015 4.579869 TCAGAAGAAAGCATGGTAAGGTC 58.420 43.478 0.00 0.00 0.00 3.85
1885 2152 4.908601 TGAGCTGGGAAGAAATGTCTTA 57.091 40.909 0.00 0.00 44.42 2.10
1991 2293 4.202050 CCACTGCTCAAGTTTAAGTTGCTT 60.202 41.667 7.59 0.00 36.83 3.91
2068 2371 5.863935 GGTCATGCTTTCTTCATTAAACCAC 59.136 40.000 0.00 0.00 0.00 4.16
2120 2423 5.182487 TGCTGACAACAACTCAAAAGACTA 58.818 37.500 0.00 0.00 0.00 2.59
2121 2424 5.822519 TGCTGACAACAACTCAAAAGACTAT 59.177 36.000 0.00 0.00 0.00 2.12
2122 2425 6.017934 TGCTGACAACAACTCAAAAGACTATC 60.018 38.462 0.00 0.00 0.00 2.08
2123 2426 6.566753 GCTGACAACAACTCAAAAGACTATCC 60.567 42.308 0.00 0.00 0.00 2.59
2223 2528 9.769677 ACCTATCAGTATATGTGGCTATTCTTA 57.230 33.333 0.00 0.00 0.00 2.10
2266 2571 7.504238 AGAGTAGACCGATCATTCTACAATCTT 59.496 37.037 23.29 9.76 44.58 2.40
2324 2630 1.974957 TGTCTCCAGTCCATTCCGAAA 59.025 47.619 0.00 0.00 0.00 3.46
2382 2688 3.988379 TTGTCCTTCTGATTGTGTTGC 57.012 42.857 0.00 0.00 0.00 4.17
2425 2731 2.011222 CATGGTTCCATTTGGCAATGC 58.989 47.619 0.00 0.00 38.88 3.56
2693 2999 1.211212 TGCCAATCATACTGCTCTGCT 59.789 47.619 0.00 0.00 0.00 4.24
2729 3035 5.927954 TGCCTTTCAAGCAAATTCATTTC 57.072 34.783 0.00 0.00 37.28 2.17
2738 3044 8.470040 TCAAGCAAATTCATTTCTAAAGATGC 57.530 30.769 0.00 0.00 0.00 3.91
3343 3649 2.614013 ACCCCCATCTCCGCCTTT 60.614 61.111 0.00 0.00 0.00 3.11
3708 4032 5.358725 GGTGGTGTACTATAATTTGGGGTTG 59.641 44.000 0.00 0.00 0.00 3.77
3774 4098 1.714794 CGTGTGAGACTGAATGGGTC 58.285 55.000 0.00 0.00 0.00 4.46
3887 4232 8.485392 TCATCTCATATGTATGTTTCAACTGGA 58.515 33.333 15.64 0.00 35.26 3.86
3893 4238 5.181690 TGTATGTTTCAACTGGAACTTGC 57.818 39.130 2.65 1.11 34.56 4.01
3970 5530 6.799926 ACAGCAAACACACTCAAAAATTTT 57.200 29.167 0.00 0.00 0.00 1.82
3984 5544 8.387354 ACTCAAAAATTTTCAAAACCGTCAATC 58.613 29.630 3.41 0.00 0.00 2.67
4127 5688 3.392616 AGAAATACCCCATCTGTAGCCAG 59.607 47.826 0.00 0.00 40.25 4.85
4144 5705 5.695851 AGCCAGAAGTATTTGTGAACAAG 57.304 39.130 0.00 0.00 37.15 3.16
4305 6111 9.461312 ACAGTGTAACACCAATGTCATAATAAT 57.539 29.630 0.00 0.00 39.21 1.28
4325 6131 8.669946 AATAATCATTTTTGAACCAAAACCGT 57.330 26.923 4.55 0.00 42.02 4.83
4333 6139 1.599606 AACCAAAACCGTGCAGTGCA 61.600 50.000 15.37 15.37 35.60 4.57
4359 6166 2.804527 CAACACACTGTCATCAGACCAG 59.195 50.000 2.17 0.00 44.33 4.00
4381 6188 4.651503 AGAGCTAGCTGCCTAAGTAATGAA 59.348 41.667 24.99 0.00 44.23 2.57
4407 6214 4.756642 CACATGAAACACAGATACAGTGGT 59.243 41.667 0.00 0.00 41.21 4.16
4422 6229 2.930040 CAGTGGTCTGTAATAGCCAACG 59.070 50.000 0.00 0.00 35.38 4.10
4423 6230 2.093658 AGTGGTCTGTAATAGCCAACGG 60.094 50.000 0.00 0.00 35.38 4.44
4424 6231 2.093869 GTGGTCTGTAATAGCCAACGGA 60.094 50.000 0.00 0.00 35.38 4.69
4425 6232 2.769663 TGGTCTGTAATAGCCAACGGAT 59.230 45.455 0.00 0.00 33.74 4.18
4426 6233 3.962063 TGGTCTGTAATAGCCAACGGATA 59.038 43.478 0.00 0.00 33.74 2.59
4427 6234 4.202182 TGGTCTGTAATAGCCAACGGATAC 60.202 45.833 0.00 0.00 33.74 2.24
4428 6235 4.304939 GTCTGTAATAGCCAACGGATACC 58.695 47.826 0.00 0.00 33.74 2.73
4429 6236 3.962063 TCTGTAATAGCCAACGGATACCA 59.038 43.478 0.00 0.00 0.00 3.25
4430 6237 4.406326 TCTGTAATAGCCAACGGATACCAA 59.594 41.667 0.00 0.00 0.00 3.67
4431 6238 5.100344 TGTAATAGCCAACGGATACCAAA 57.900 39.130 0.00 0.00 0.00 3.28
4432 6239 5.498393 TGTAATAGCCAACGGATACCAAAA 58.502 37.500 0.00 0.00 0.00 2.44
4433 6240 5.944599 TGTAATAGCCAACGGATACCAAAAA 59.055 36.000 0.00 0.00 0.00 1.94
4434 6241 6.603997 TGTAATAGCCAACGGATACCAAAAAT 59.396 34.615 0.00 0.00 0.00 1.82
4435 6242 5.767816 ATAGCCAACGGATACCAAAAATC 57.232 39.130 0.00 0.00 0.00 2.17
4436 6243 3.426615 AGCCAACGGATACCAAAAATCA 58.573 40.909 0.00 0.00 0.00 2.57
4437 6244 3.829601 AGCCAACGGATACCAAAAATCAA 59.170 39.130 0.00 0.00 0.00 2.57
4438 6245 4.282195 AGCCAACGGATACCAAAAATCAAA 59.718 37.500 0.00 0.00 0.00 2.69
4439 6246 4.387559 GCCAACGGATACCAAAAATCAAAC 59.612 41.667 0.00 0.00 0.00 2.93
4440 6247 5.778862 CCAACGGATACCAAAAATCAAACT 58.221 37.500 0.00 0.00 0.00 2.66
4441 6248 6.570764 GCCAACGGATACCAAAAATCAAACTA 60.571 38.462 0.00 0.00 0.00 2.24
4442 6249 7.371936 CCAACGGATACCAAAAATCAAACTAA 58.628 34.615 0.00 0.00 0.00 2.24
4443 6250 8.032451 CCAACGGATACCAAAAATCAAACTAAT 58.968 33.333 0.00 0.00 0.00 1.73
4444 6251 8.859156 CAACGGATACCAAAAATCAAACTAATG 58.141 33.333 0.00 0.00 0.00 1.90
4445 6252 8.343168 ACGGATACCAAAAATCAAACTAATGA 57.657 30.769 0.00 0.00 0.00 2.57
4446 6253 8.241367 ACGGATACCAAAAATCAAACTAATGAC 58.759 33.333 0.00 0.00 30.82 3.06
4447 6254 7.700656 CGGATACCAAAAATCAAACTAATGACC 59.299 37.037 0.00 0.00 30.82 4.02
4448 6255 7.700656 GGATACCAAAAATCAAACTAATGACCG 59.299 37.037 0.00 0.00 30.82 4.79
4449 6256 5.778862 ACCAAAAATCAAACTAATGACCGG 58.221 37.500 0.00 0.00 30.82 5.28
4450 6257 5.303333 ACCAAAAATCAAACTAATGACCGGT 59.697 36.000 6.92 6.92 30.82 5.28
4451 6258 6.490721 ACCAAAAATCAAACTAATGACCGGTA 59.509 34.615 7.34 0.00 30.82 4.02
4452 6259 7.014422 ACCAAAAATCAAACTAATGACCGGTAA 59.986 33.333 7.34 0.00 30.82 2.85
4453 6260 7.540745 CCAAAAATCAAACTAATGACCGGTAAG 59.459 37.037 7.34 5.57 30.82 2.34
4454 6261 5.813080 AATCAAACTAATGACCGGTAAGC 57.187 39.130 7.34 0.00 30.82 3.09
4455 6262 4.546829 TCAAACTAATGACCGGTAAGCT 57.453 40.909 7.34 0.00 0.00 3.74
4464 6271 1.170290 ACCGGTAAGCTGCCAAACAC 61.170 55.000 4.49 0.00 0.00 3.32
4469 6276 3.123050 GGTAAGCTGCCAAACACAAAAG 58.877 45.455 0.00 0.00 0.00 2.27
4472 6279 1.207811 AGCTGCCAAACACAAAAGCTT 59.792 42.857 0.00 0.00 37.74 3.74
4477 6284 2.223089 GCCAAACACAAAAGCTTGCAAG 60.223 45.455 22.44 22.44 35.84 4.01
4517 6324 5.925189 AAATTCAAAATCGCCGATTAACG 57.075 34.783 13.43 4.85 42.18 3.18
4528 6335 2.241259 CGATTAACGGTGCCACAAAG 57.759 50.000 0.00 0.00 38.46 2.77
4529 6336 1.727857 CGATTAACGGTGCCACAAAGC 60.728 52.381 0.00 0.00 38.46 3.51
4530 6337 0.239879 ATTAACGGTGCCACAAAGCG 59.760 50.000 0.00 0.00 43.79 4.68
4531 6338 2.395367 TTAACGGTGCCACAAAGCGC 62.395 55.000 0.00 0.00 42.03 5.92
4535 6342 4.705519 GTGCCACAAAGCGCGCAT 62.706 61.111 35.10 20.88 35.57 4.73
4536 6343 3.052686 TGCCACAAAGCGCGCATA 61.053 55.556 35.10 0.98 34.65 3.14
4537 6344 2.576847 GCCACAAAGCGCGCATAC 60.577 61.111 35.10 11.16 0.00 2.39
4538 6345 2.866750 CCACAAAGCGCGCATACA 59.133 55.556 35.10 0.00 0.00 2.29
4539 6346 1.208870 CCACAAAGCGCGCATACAA 59.791 52.632 35.10 0.00 0.00 2.41
4540 6347 0.386605 CCACAAAGCGCGCATACAAA 60.387 50.000 35.10 0.00 0.00 2.83
4541 6348 0.976963 CACAAAGCGCGCATACAAAG 59.023 50.000 35.10 17.03 0.00 2.77
4542 6349 0.729140 ACAAAGCGCGCATACAAAGC 60.729 50.000 35.10 0.00 0.00 3.51
4543 6350 0.728803 CAAAGCGCGCATACAAAGCA 60.729 50.000 35.10 0.00 0.00 3.91
4550 6357 1.792993 GCGCATACAAAGCAGCTTCAG 60.793 52.381 8.48 7.06 0.00 3.02
4552 6359 2.095567 CGCATACAAAGCAGCTTCAGTT 60.096 45.455 8.48 0.00 0.00 3.16
4554 6361 3.190118 GCATACAAAGCAGCTTCAGTTCT 59.810 43.478 8.48 0.00 0.00 3.01
4567 6374 4.787882 GCTTCAGTTCTGTTTCTGCAACTC 60.788 45.833 0.00 0.00 36.21 3.01
4571 6378 4.333649 CAGTTCTGTTTCTGCAACTCTGAA 59.666 41.667 0.00 0.00 36.21 3.02
4580 6387 0.954452 GCAACTCTGAACCACCCAAG 59.046 55.000 0.00 0.00 0.00 3.61
4581 6388 1.750682 GCAACTCTGAACCACCCAAGT 60.751 52.381 0.00 0.00 0.00 3.16
4584 6391 3.487120 ACTCTGAACCACCCAAGTAAC 57.513 47.619 0.00 0.00 0.00 2.50
4616 6423 8.006298 TCCTTTTATTTTGCAGAGAAGAAACA 57.994 30.769 0.00 0.00 0.00 2.83
4630 6438 6.382570 AGAGAAGAAACACCACATCTATAGCT 59.617 38.462 0.00 0.00 0.00 3.32
4639 6447 7.897864 ACACCACATCTATAGCTAGAATTACC 58.102 38.462 0.00 0.00 37.52 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 64 8.841444 ATGAATAACTGAAAATTACATGACGC 57.159 30.769 0.00 0.00 0.00 5.19
138 147 9.925268 CGAACATACTAGTAACTTGTTGTTTTT 57.075 29.630 19.99 1.19 39.89 1.94
139 148 9.316730 TCGAACATACTAGTAACTTGTTGTTTT 57.683 29.630 19.99 1.78 39.89 2.43
159 168 4.844998 TTCTTTGCCAATGATTCGAACA 57.155 36.364 0.00 1.02 0.00 3.18
163 172 5.463061 AGTGTTTTTCTTTGCCAATGATTCG 59.537 36.000 0.00 0.00 0.00 3.34
169 178 5.585844 CCTTTGAGTGTTTTTCTTTGCCAAT 59.414 36.000 0.00 0.00 0.00 3.16
181 190 1.569072 ACCCTCCACCTTTGAGTGTTT 59.431 47.619 0.00 0.00 35.93 2.83
183 192 1.222567 AACCCTCCACCTTTGAGTGT 58.777 50.000 0.00 0.00 35.93 3.55
184 193 2.552373 GGTAACCCTCCACCTTTGAGTG 60.552 54.545 0.00 0.00 37.51 3.51
239 248 0.237498 GCCGTGTCTTTTTCGAAGGG 59.763 55.000 0.00 0.00 0.00 3.95
244 253 2.108700 CTTTGTGCCGTGTCTTTTTCG 58.891 47.619 0.00 0.00 0.00 3.46
246 255 1.822371 ACCTTTGTGCCGTGTCTTTTT 59.178 42.857 0.00 0.00 0.00 1.94
255 264 1.148310 CAGTGTCTACCTTTGTGCCG 58.852 55.000 0.00 0.00 0.00 5.69
268 277 5.479306 AGTGTTGGTGTGTATATCAGTGTC 58.521 41.667 0.00 0.00 0.00 3.67
274 283 4.081087 AGGGTGAGTGTTGGTGTGTATATC 60.081 45.833 0.00 0.00 0.00 1.63
275 284 3.844211 AGGGTGAGTGTTGGTGTGTATAT 59.156 43.478 0.00 0.00 0.00 0.86
281 290 1.445942 CGAGGGTGAGTGTTGGTGT 59.554 57.895 0.00 0.00 0.00 4.16
291 300 3.706373 GGAGGCTTGCGAGGGTGA 61.706 66.667 2.37 0.00 0.00 4.02
335 344 7.696755 TGAGCGTCTACGTCTATTTGTATTTA 58.303 34.615 4.24 0.00 42.22 1.40
337 346 6.127810 TGAGCGTCTACGTCTATTTGTATT 57.872 37.500 4.24 0.00 42.22 1.89
340 349 4.634184 ATGAGCGTCTACGTCTATTTGT 57.366 40.909 4.24 0.00 42.22 2.83
341 350 4.910456 GGTATGAGCGTCTACGTCTATTTG 59.090 45.833 4.24 0.00 42.22 2.32
342 351 4.023365 GGGTATGAGCGTCTACGTCTATTT 60.023 45.833 4.24 0.00 42.22 1.40
344 353 3.072944 GGGTATGAGCGTCTACGTCTAT 58.927 50.000 4.24 0.00 42.22 1.98
345 354 2.103771 AGGGTATGAGCGTCTACGTCTA 59.896 50.000 4.24 0.00 42.22 2.59
346 355 1.134159 AGGGTATGAGCGTCTACGTCT 60.134 52.381 4.24 2.04 42.22 4.18
347 356 1.263752 GAGGGTATGAGCGTCTACGTC 59.736 57.143 4.24 1.90 42.22 4.34
348 357 1.307097 GAGGGTATGAGCGTCTACGT 58.693 55.000 4.24 0.00 42.22 3.57
349 358 1.002684 GTGAGGGTATGAGCGTCTACG 60.003 57.143 0.00 0.00 43.27 3.51
350 359 2.291190 GAGTGAGGGTATGAGCGTCTAC 59.709 54.545 0.81 0.00 32.36 2.59
351 360 2.092592 TGAGTGAGGGTATGAGCGTCTA 60.093 50.000 0.81 0.00 32.36 2.59
353 362 1.103803 TGAGTGAGGGTATGAGCGTC 58.896 55.000 0.00 0.00 0.00 5.19
354 363 1.781786 ATGAGTGAGGGTATGAGCGT 58.218 50.000 0.00 0.00 0.00 5.07
355 364 5.644977 TTATATGAGTGAGGGTATGAGCG 57.355 43.478 0.00 0.00 0.00 5.03
356 365 6.314896 GCATTTATATGAGTGAGGGTATGAGC 59.685 42.308 0.00 0.00 33.37 4.26
357 366 7.332926 GTGCATTTATATGAGTGAGGGTATGAG 59.667 40.741 0.00 0.00 33.37 2.90
358 367 7.161404 GTGCATTTATATGAGTGAGGGTATGA 58.839 38.462 0.00 0.00 33.37 2.15
359 368 6.936335 TGTGCATTTATATGAGTGAGGGTATG 59.064 38.462 0.00 0.00 33.37 2.39
360 369 6.936900 GTGTGCATTTATATGAGTGAGGGTAT 59.063 38.462 0.00 0.00 33.37 2.73
361 370 6.126911 TGTGTGCATTTATATGAGTGAGGGTA 60.127 38.462 0.00 0.00 33.37 3.69
362 371 5.126067 GTGTGCATTTATATGAGTGAGGGT 58.874 41.667 0.00 0.00 33.37 4.34
363 372 5.125356 TGTGTGCATTTATATGAGTGAGGG 58.875 41.667 0.00 0.00 33.37 4.30
364 373 6.539826 TCTTGTGTGCATTTATATGAGTGAGG 59.460 38.462 0.00 0.00 33.37 3.86
365 374 7.543947 TCTTGTGTGCATTTATATGAGTGAG 57.456 36.000 0.00 0.00 33.37 3.51
371 392 7.755591 AGAGTGTTCTTGTGTGCATTTATATG 58.244 34.615 0.00 0.00 34.76 1.78
376 397 4.275936 GGTAGAGTGTTCTTGTGTGCATTT 59.724 41.667 0.00 0.00 34.79 2.32
380 401 2.143925 GGGTAGAGTGTTCTTGTGTGC 58.856 52.381 0.00 0.00 34.79 4.57
382 403 2.690840 AGGGGTAGAGTGTTCTTGTGT 58.309 47.619 0.00 0.00 34.79 3.72
384 405 3.775316 CCATAGGGGTAGAGTGTTCTTGT 59.225 47.826 0.00 0.00 34.79 3.16
393 414 2.777459 AGGTGTCCATAGGGGTAGAG 57.223 55.000 0.00 0.00 38.11 2.43
394 415 2.688817 CGAAGGTGTCCATAGGGGTAGA 60.689 54.545 0.00 0.00 38.11 2.59
397 418 0.252558 ACGAAGGTGTCCATAGGGGT 60.253 55.000 0.00 0.00 38.11 4.95
401 422 2.755655 AGTCTCACGAAGGTGTCCATAG 59.244 50.000 0.00 0.00 44.68 2.23
406 427 2.597520 GCTTAGTCTCACGAAGGTGTC 58.402 52.381 0.00 0.00 44.68 3.67
408 429 1.732732 CGGCTTAGTCTCACGAAGGTG 60.733 57.143 0.00 0.00 45.78 4.00
411 432 0.802607 GCCGGCTTAGTCTCACGAAG 60.803 60.000 22.15 0.00 34.54 3.79
413 434 1.974875 TGCCGGCTTAGTCTCACGA 60.975 57.895 29.70 0.00 0.00 4.35
414 435 1.805945 GTGCCGGCTTAGTCTCACG 60.806 63.158 29.70 0.00 0.00 4.35
416 437 0.175760 GATGTGCCGGCTTAGTCTCA 59.824 55.000 29.70 14.55 0.00 3.27
421 442 1.600957 CAAGATGATGTGCCGGCTTAG 59.399 52.381 29.70 2.27 0.00 2.18
441 462 6.738649 GCGTCTTTGACAACTTTATCAATCTC 59.261 38.462 0.00 0.00 34.87 2.75
450 471 3.612423 GCAAAAGCGTCTTTGACAACTTT 59.388 39.130 13.44 8.80 38.98 2.66
457 478 1.003972 CGACTGCAAAAGCGTCTTTGA 60.004 47.619 13.44 1.51 38.35 2.69
462 483 1.154836 CGTCGACTGCAAAAGCGTC 60.155 57.895 14.70 0.00 0.00 5.19
465 486 2.556287 CCCGTCGACTGCAAAAGC 59.444 61.111 14.70 0.00 0.00 3.51
466 487 1.597027 ACCCCGTCGACTGCAAAAG 60.597 57.895 14.70 0.00 0.00 2.27
467 488 1.890041 CACCCCGTCGACTGCAAAA 60.890 57.895 14.70 0.00 0.00 2.44
470 491 3.986006 GACACCCCGTCGACTGCA 61.986 66.667 14.70 0.00 34.19 4.41
484 505 1.618837 GTGAGCTTAGTGGTGGAGACA 59.381 52.381 0.00 0.00 38.70 3.41
485 506 1.618837 TGTGAGCTTAGTGGTGGAGAC 59.381 52.381 0.00 0.00 0.00 3.36
486 507 2.009681 TGTGAGCTTAGTGGTGGAGA 57.990 50.000 0.00 0.00 0.00 3.71
487 508 2.234661 TGATGTGAGCTTAGTGGTGGAG 59.765 50.000 0.00 0.00 0.00 3.86
490 511 2.350522 GGTGATGTGAGCTTAGTGGTG 58.649 52.381 0.00 0.00 0.00 4.17
491 512 1.066858 CGGTGATGTGAGCTTAGTGGT 60.067 52.381 0.00 0.00 0.00 4.16
497 521 2.808543 GACTTTTCGGTGATGTGAGCTT 59.191 45.455 0.00 0.00 0.00 3.74
499 523 2.417719 AGACTTTTCGGTGATGTGAGC 58.582 47.619 0.00 0.00 0.00 4.26
501 525 8.610248 TTATTTAAGACTTTTCGGTGATGTGA 57.390 30.769 0.00 0.00 0.00 3.58
520 544 8.742188 GCGATCGCATTTTTCTGAATTTATTTA 58.258 29.630 33.89 0.00 41.49 1.40
532 556 0.861450 CACCGGCGATCGCATTTTTC 60.861 55.000 38.00 20.34 44.11 2.29
533 557 1.136565 CACCGGCGATCGCATTTTT 59.863 52.632 38.00 16.57 44.11 1.94
543 567 1.002201 TCCTAAAATTGACACCGGCGA 59.998 47.619 9.30 0.00 0.00 5.54
545 569 2.433436 AGTCCTAAAATTGACACCGGC 58.567 47.619 0.00 0.00 33.89 6.13
549 573 9.052759 TCAGAGTTTAAGTCCTAAAATTGACAC 57.947 33.333 0.00 0.00 33.89 3.67
556 580 5.944007 GCCCATCAGAGTTTAAGTCCTAAAA 59.056 40.000 0.00 0.00 31.22 1.52
561 585 3.636153 AGCCCATCAGAGTTTAAGTCC 57.364 47.619 0.00 0.00 0.00 3.85
567 591 8.689972 CAAAATCTAAATAGCCCATCAGAGTTT 58.310 33.333 0.00 0.00 32.43 2.66
570 594 7.500227 TGTCAAAATCTAAATAGCCCATCAGAG 59.500 37.037 0.00 0.00 0.00 3.35
571 595 7.345691 TGTCAAAATCTAAATAGCCCATCAGA 58.654 34.615 0.00 0.00 0.00 3.27
572 596 7.572523 TGTCAAAATCTAAATAGCCCATCAG 57.427 36.000 0.00 0.00 0.00 2.90
575 599 6.131961 AGCTGTCAAAATCTAAATAGCCCAT 58.868 36.000 0.00 0.00 0.00 4.00
576 600 5.509498 AGCTGTCAAAATCTAAATAGCCCA 58.491 37.500 0.00 0.00 0.00 5.36
625 693 3.284617 TGTGGAATCTGGCAGAATGATG 58.715 45.455 22.84 0.00 39.69 3.07
645 714 9.401873 CTCATTTATTGTGTGCCATGTATAATG 57.598 33.333 0.00 0.00 0.00 1.90
720 793 0.326595 TTAAATCAGCTCCGTGGCCA 59.673 50.000 0.00 0.00 0.00 5.36
745 818 2.043852 GAGGAGAGACCGGCTGGA 60.044 66.667 21.41 0.00 44.74 3.86
752 825 3.462678 GCGGTGGGAGGAGAGACC 61.463 72.222 0.00 0.00 39.35 3.85
775 850 0.117140 TGATGCGAGGGAGGGGATAT 59.883 55.000 0.00 0.00 0.00 1.63
777 852 2.143419 GTGATGCGAGGGAGGGGAT 61.143 63.158 0.00 0.00 0.00 3.85
778 853 2.764128 GTGATGCGAGGGAGGGGA 60.764 66.667 0.00 0.00 0.00 4.81
807 892 2.171209 AAAATTGAAGCCGGCTGCCC 62.171 55.000 33.60 22.28 42.71 5.36
833 918 1.878522 ATTAAGAGCACGGCGAGCG 60.879 57.895 22.71 7.48 37.01 5.03
838 923 1.032114 AAGCCCATTAAGAGCACGGC 61.032 55.000 0.00 0.00 36.62 5.68
1424 1572 0.311790 ACTACGAAACCGCAGACGAA 59.688 50.000 0.00 0.00 43.93 3.85
1439 1587 1.171308 TCACCACTGCCTACGACTAC 58.829 55.000 0.00 0.00 0.00 2.73
1488 1638 1.269517 GGACAGATCCGAGCTAAGCAG 60.270 57.143 0.00 0.00 34.48 4.24
1594 1753 7.997107 TGTAATTAGTAGGAACGTGCATAAG 57.003 36.000 0.00 0.00 0.00 1.73
1615 1775 1.276705 TGTACTGGCCGCAGATTTGTA 59.723 47.619 0.00 0.00 0.00 2.41
1715 1875 2.233271 CACCAACAGAAGAAGCACCAT 58.767 47.619 0.00 0.00 0.00 3.55
1723 1884 2.886523 CCTGATTTGCACCAACAGAAGA 59.113 45.455 9.83 0.00 0.00 2.87
1726 1887 2.655090 TCCTGATTTGCACCAACAGA 57.345 45.000 9.83 0.00 0.00 3.41
1761 1922 3.490348 ACACAACTTTAGGCAGCTTCAT 58.510 40.909 0.00 0.00 0.00 2.57
1868 2135 6.881065 TCATGAACTAAGACATTTCTTCCCAG 59.119 38.462 0.00 0.00 41.48 4.45
1884 2151 9.443323 TTCGATCCAACTATTTTTCATGAACTA 57.557 29.630 7.89 0.00 0.00 2.24
1885 2152 7.921786 TCGATCCAACTATTTTTCATGAACT 57.078 32.000 7.89 0.00 0.00 3.01
2068 2371 4.736126 CCTAAAGGGGCAACTAAAATGG 57.264 45.455 0.00 0.00 0.00 3.16
2092 2395 3.082698 TGAGTTGTTGTCAGCAAATGC 57.917 42.857 7.11 0.00 42.49 3.56
2111 2414 6.426328 GGAGCTATGTGATGGATAGTCTTTTG 59.574 42.308 0.00 0.00 0.00 2.44
2120 2423 2.824936 CTCGAGGAGCTATGTGATGGAT 59.175 50.000 3.91 0.00 0.00 3.41
2121 2424 2.158608 TCTCGAGGAGCTATGTGATGGA 60.159 50.000 13.56 0.00 0.00 3.41
2122 2425 2.030363 GTCTCGAGGAGCTATGTGATGG 60.030 54.545 13.56 0.00 0.00 3.51
2123 2426 2.884012 AGTCTCGAGGAGCTATGTGATG 59.116 50.000 13.56 0.00 0.00 3.07
2230 2535 6.127101 TGATCGGTCTACTCTAGGAATTGAA 58.873 40.000 0.00 0.00 0.00 2.69
2249 2554 7.706281 ACAAGCTAAGATTGTAGAATGATCG 57.294 36.000 0.00 0.00 39.06 3.69
2281 2586 6.053650 CACTTCATGATGCTGGAAGATAAGA 58.946 40.000 8.45 0.00 40.28 2.10
2283 2588 5.748402 ACACTTCATGATGCTGGAAGATAA 58.252 37.500 8.45 0.00 40.28 1.75
2382 2688 4.301072 TCCCACTTTGTTCCTCTTATGG 57.699 45.455 0.00 0.00 0.00 2.74
2425 2731 0.933097 CCTTCCTGATTGCGACATCG 59.067 55.000 0.00 0.00 43.27 3.84
2729 3035 7.633621 ACATATGTCAAACATCGCATCTTTAG 58.366 34.615 1.41 0.00 39.88 1.85
3277 3583 3.850098 CTGCCCCGCTGACAGGTTT 62.850 63.158 4.26 0.00 0.00 3.27
3343 3649 2.586245 CTGATGGAAGGCAGCGGA 59.414 61.111 0.00 0.00 0.00 5.54
3677 4001 7.039644 CCAAATTATAGTACACCACCCAAACAA 60.040 37.037 0.00 0.00 0.00 2.83
3708 4032 1.318576 CTCTGGACAACCACCAAACC 58.681 55.000 0.00 0.00 41.77 3.27
3774 4098 3.763097 ATGCACATCCAACAATACACG 57.237 42.857 0.00 0.00 0.00 4.49
3801 4126 6.212388 AGTCTGCCTTATTATAGGACCATCAG 59.788 42.308 0.00 0.00 37.50 2.90
3887 4232 5.010012 CAGGGTTAGTTTGATTCAGCAAGTT 59.990 40.000 0.00 0.00 0.00 2.66
3893 4238 4.566004 TCGTCAGGGTTAGTTTGATTCAG 58.434 43.478 0.00 0.00 0.00 3.02
3970 5530 1.863491 CGGCGATTGACGGTTTTGA 59.137 52.632 0.00 0.00 45.13 2.69
4127 5688 7.798982 GCTGTAGTTCTTGTTCACAAATACTTC 59.201 37.037 10.12 7.25 35.15 3.01
4144 5705 5.586243 TGCATATTTCTTCAGGCTGTAGTTC 59.414 40.000 18.91 0.00 0.00 3.01
4305 6111 3.619038 GCACGGTTTTGGTTCAAAAATGA 59.381 39.130 7.29 0.00 43.50 2.57
4359 6166 4.592485 TCATTACTTAGGCAGCTAGCTC 57.408 45.455 16.15 9.87 44.79 4.09
4381 6188 6.149973 CCACTGTATCTGTGTTTCATGTGATT 59.850 38.462 0.00 0.00 32.65 2.57
4407 6214 3.962063 TGGTATCCGTTGGCTATTACAGA 59.038 43.478 0.00 0.00 0.00 3.41
4422 6229 7.700656 CGGTCATTAGTTTGATTTTTGGTATCC 59.299 37.037 0.00 0.00 0.00 2.59
4423 6230 7.700656 CCGGTCATTAGTTTGATTTTTGGTATC 59.299 37.037 0.00 0.00 0.00 2.24
4424 6231 7.177744 ACCGGTCATTAGTTTGATTTTTGGTAT 59.822 33.333 0.00 0.00 0.00 2.73
4425 6232 6.490721 ACCGGTCATTAGTTTGATTTTTGGTA 59.509 34.615 0.00 0.00 0.00 3.25
4426 6233 5.303333 ACCGGTCATTAGTTTGATTTTTGGT 59.697 36.000 0.00 0.00 0.00 3.67
4427 6234 5.778862 ACCGGTCATTAGTTTGATTTTTGG 58.221 37.500 0.00 0.00 0.00 3.28
4428 6235 7.061789 GCTTACCGGTCATTAGTTTGATTTTTG 59.938 37.037 12.40 0.00 0.00 2.44
4429 6236 7.039993 AGCTTACCGGTCATTAGTTTGATTTTT 60.040 33.333 12.40 0.00 0.00 1.94
4430 6237 6.433093 AGCTTACCGGTCATTAGTTTGATTTT 59.567 34.615 12.40 0.00 0.00 1.82
4431 6238 5.944007 AGCTTACCGGTCATTAGTTTGATTT 59.056 36.000 12.40 0.00 0.00 2.17
4432 6239 5.354234 CAGCTTACCGGTCATTAGTTTGATT 59.646 40.000 12.40 0.00 0.00 2.57
4433 6240 4.876107 CAGCTTACCGGTCATTAGTTTGAT 59.124 41.667 12.40 0.00 0.00 2.57
4434 6241 4.250464 CAGCTTACCGGTCATTAGTTTGA 58.750 43.478 12.40 0.00 0.00 2.69
4435 6242 3.181510 GCAGCTTACCGGTCATTAGTTTG 60.182 47.826 12.40 8.85 0.00 2.93
4436 6243 3.007635 GCAGCTTACCGGTCATTAGTTT 58.992 45.455 12.40 0.00 0.00 2.66
4437 6244 2.629051 GCAGCTTACCGGTCATTAGTT 58.371 47.619 12.40 0.00 0.00 2.24
4438 6245 1.134491 GGCAGCTTACCGGTCATTAGT 60.134 52.381 12.40 0.00 0.00 2.24
4439 6246 1.134521 TGGCAGCTTACCGGTCATTAG 60.135 52.381 12.40 5.93 0.00 1.73
4440 6247 0.906066 TGGCAGCTTACCGGTCATTA 59.094 50.000 12.40 0.00 0.00 1.90
4441 6248 0.037590 TTGGCAGCTTACCGGTCATT 59.962 50.000 12.40 0.00 0.00 2.57
4442 6249 0.037590 TTTGGCAGCTTACCGGTCAT 59.962 50.000 12.40 0.00 0.00 3.06
4443 6250 0.887387 GTTTGGCAGCTTACCGGTCA 60.887 55.000 12.40 0.00 0.00 4.02
4444 6251 0.887387 TGTTTGGCAGCTTACCGGTC 60.887 55.000 12.40 0.00 0.00 4.79
4445 6252 1.149627 TGTTTGGCAGCTTACCGGT 59.850 52.632 13.98 13.98 0.00 5.28
4446 6253 1.169661 TGTGTTTGGCAGCTTACCGG 61.170 55.000 0.00 0.00 0.00 5.28
4447 6254 0.665835 TTGTGTTTGGCAGCTTACCG 59.334 50.000 0.00 0.00 0.00 4.02
4448 6255 2.880963 TTTGTGTTTGGCAGCTTACC 57.119 45.000 0.00 0.00 0.00 2.85
4449 6256 2.539688 GCTTTTGTGTTTGGCAGCTTAC 59.460 45.455 0.00 0.00 0.00 2.34
4450 6257 2.430332 AGCTTTTGTGTTTGGCAGCTTA 59.570 40.909 0.00 0.00 0.00 3.09
4451 6258 1.207811 AGCTTTTGTGTTTGGCAGCTT 59.792 42.857 0.00 0.00 0.00 3.74
4452 6259 0.826062 AGCTTTTGTGTTTGGCAGCT 59.174 45.000 0.00 0.00 0.00 4.24
4453 6260 1.328374 CAAGCTTTTGTGTTTGGCAGC 59.672 47.619 0.00 0.00 0.00 5.25
4454 6261 1.328374 GCAAGCTTTTGTGTTTGGCAG 59.672 47.619 0.00 0.00 0.00 4.85
4455 6262 1.338484 TGCAAGCTTTTGTGTTTGGCA 60.338 42.857 0.00 0.00 0.00 4.92
4509 6316 1.727857 GCTTTGTGGCACCGTTAATCG 60.728 52.381 16.26 0.00 39.52 3.34
4510 6317 1.727857 CGCTTTGTGGCACCGTTAATC 60.728 52.381 16.26 0.00 0.00 1.75
4511 6318 0.239879 CGCTTTGTGGCACCGTTAAT 59.760 50.000 16.26 0.00 0.00 1.40
4512 6319 1.649815 CGCTTTGTGGCACCGTTAA 59.350 52.632 16.26 0.00 0.00 2.01
4514 6321 4.264638 GCGCTTTGTGGCACCGTT 62.265 61.111 16.26 0.00 0.00 4.44
4522 6329 0.976963 CTTTGTATGCGCGCTTTGTG 59.023 50.000 33.29 12.23 0.00 3.33
4523 6330 0.729140 GCTTTGTATGCGCGCTTTGT 60.729 50.000 33.29 17.39 0.00 2.83
4524 6331 0.728803 TGCTTTGTATGCGCGCTTTG 60.729 50.000 33.29 15.30 0.00 2.77
4525 6332 0.454957 CTGCTTTGTATGCGCGCTTT 60.455 50.000 33.29 21.61 0.00 3.51
4527 6334 2.787249 CTGCTTTGTATGCGCGCT 59.213 55.556 33.29 19.73 0.00 5.92
4528 6335 2.855728 AAGCTGCTTTGTATGCGCGC 62.856 55.000 27.26 27.26 36.00 6.86
4529 6336 0.858961 GAAGCTGCTTTGTATGCGCG 60.859 55.000 17.10 0.00 36.00 6.86
4530 6337 0.168788 TGAAGCTGCTTTGTATGCGC 59.831 50.000 17.10 0.00 0.00 6.09
4531 6338 1.466167 ACTGAAGCTGCTTTGTATGCG 59.534 47.619 17.10 3.20 0.00 4.73
4532 6339 3.190118 AGAACTGAAGCTGCTTTGTATGC 59.810 43.478 17.10 11.02 0.00 3.14
4533 6340 4.214971 ACAGAACTGAAGCTGCTTTGTATG 59.785 41.667 17.10 19.08 35.57 2.39
4534 6341 4.392940 ACAGAACTGAAGCTGCTTTGTAT 58.607 39.130 17.10 8.38 35.57 2.29
4535 6342 3.808728 ACAGAACTGAAGCTGCTTTGTA 58.191 40.909 17.10 5.64 35.57 2.41
4536 6343 2.648059 ACAGAACTGAAGCTGCTTTGT 58.352 42.857 17.10 15.01 35.57 2.83
4537 6344 3.705043 AACAGAACTGAAGCTGCTTTG 57.295 42.857 17.10 14.39 35.57 2.77
4538 6345 3.950395 AGAAACAGAACTGAAGCTGCTTT 59.050 39.130 17.10 0.00 35.57 3.51
4539 6346 3.314635 CAGAAACAGAACTGAAGCTGCTT 59.685 43.478 15.92 15.92 36.38 3.91
4540 6347 2.877168 CAGAAACAGAACTGAAGCTGCT 59.123 45.455 8.87 0.00 36.38 4.24
4541 6348 2.604132 GCAGAAACAGAACTGAAGCTGC 60.604 50.000 20.56 20.56 40.57 5.25
4542 6349 2.615447 TGCAGAAACAGAACTGAAGCTG 59.385 45.455 8.87 11.74 36.38 4.24
4543 6350 2.923121 TGCAGAAACAGAACTGAAGCT 58.077 42.857 8.87 0.00 36.38 3.74
4550 6357 4.496507 GGTTCAGAGTTGCAGAAACAGAAC 60.497 45.833 12.55 12.55 41.53 3.01
4552 6359 3.206150 GGTTCAGAGTTGCAGAAACAGA 58.794 45.455 0.00 0.00 41.61 3.41
4554 6361 2.682856 GTGGTTCAGAGTTGCAGAAACA 59.317 45.455 0.00 0.00 41.61 2.83
4567 6374 2.227194 GGTGTTACTTGGGTGGTTCAG 58.773 52.381 0.00 0.00 0.00 3.02
4571 6378 0.994591 TGGGGTGTTACTTGGGTGGT 60.995 55.000 0.00 0.00 0.00 4.16
4580 6387 5.872617 GCAAAATAAAAGGATGGGGTGTTAC 59.127 40.000 0.00 0.00 0.00 2.50
4581 6388 5.544176 TGCAAAATAAAAGGATGGGGTGTTA 59.456 36.000 0.00 0.00 0.00 2.41
4584 6391 4.222588 TCTGCAAAATAAAAGGATGGGGTG 59.777 41.667 0.00 0.00 0.00 4.61
4616 6423 6.153000 CGGGTAATTCTAGCTATAGATGTGGT 59.847 42.308 3.21 0.00 37.86 4.16


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

AutoCloner maintained by Alex Coulton.