Multiple sequence alignment - TraesCS1A01G272600

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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 TraesCS1A01G272600 chr1A 100.000 3993 0 0 1 3993 465525805 465521813 0.000000e+00 7374
1 TraesCS1A01G272600 chr1A 97.704 392 6 3 127 516 126538469 126538859 0.000000e+00 671
2 TraesCS1A01G272600 chr1A 94.301 386 3 4 127 509 518655823 518656192 1.240000e-159 573
3 TraesCS1A01G272600 chr1A 99.270 137 1 0 1 137 126538425 126538561 8.570000e-62 248
4 TraesCS1A01G272600 chr1A 99.270 137 1 0 1 137 518649634 518649770 8.570000e-62 248
5 TraesCS1A01G272600 chr1A 99.270 137 1 0 1 137 518653816 518653952 8.570000e-62 248
6 TraesCS1A01G272600 chr1A 99.270 137 1 0 1 137 518655779 518655915 8.570000e-62 248
7 TraesCS1A01G272600 chr1B 88.994 1263 70 25 2041 3260 491264910 491263674 0.000000e+00 1498
8 TraesCS1A01G272600 chr1B 91.825 893 32 12 1097 1983 491266356 491265499 0.000000e+00 1206
9 TraesCS1A01G272600 chr1B 93.143 525 6 4 1 510 31470334 31469825 0.000000e+00 743
10 TraesCS1A01G272600 chr1B 88.945 398 22 9 3271 3662 491263609 491263228 4.670000e-129 472
11 TraesCS1A01G272600 chr1B 96.479 284 5 4 227 509 222291500 222291779 7.820000e-127 464
12 TraesCS1A01G272600 chr1B 86.161 224 17 6 3704 3919 491263164 491262947 3.100000e-56 230
13 TraesCS1A01G272600 chr1B 94.690 113 6 0 795 907 491266645 491266533 4.100000e-40 176
14 TraesCS1A01G272600 chr1D 88.924 1264 71 21 2041 3249 366224410 366225659 0.000000e+00 1495
15 TraesCS1A01G272600 chr1D 90.824 752 32 18 890 1637 366223279 366223997 0.000000e+00 972
16 TraesCS1A01G272600 chr1D 91.051 257 16 4 1775 2030 366224019 366224269 1.370000e-89 340
17 TraesCS1A01G272600 chr1D 85.616 292 23 7 3260 3549 366225724 366225998 5.050000e-74 289
18 TraesCS1A01G272600 chr1D 87.045 247 14 7 508 752 366222651 366222881 3.060000e-66 263
19 TraesCS1A01G272600 chr1D 82.545 275 12 11 3746 3993 366226163 366226428 4.040000e-50 209
20 TraesCS1A01G272600 chr1D 89.796 147 13 2 751 896 366222908 366223053 1.890000e-43 187
21 TraesCS1A01G272600 chr6B 99.023 512 4 1 1 511 696085386 696085897 0.000000e+00 917
22 TraesCS1A01G272600 chr6A 99.214 509 3 1 1 508 70604622 70605130 0.000000e+00 917
23 TraesCS1A01G272600 chr3A 99.214 509 3 1 1 508 657268312 657268820 0.000000e+00 917
24 TraesCS1A01G272600 chr3A 98.517 472 6 1 39 509 74441604 74442075 0.000000e+00 832
25 TraesCS1A01G272600 chr3A 92.966 526 4 6 1 509 657267667 657268176 0.000000e+00 736
26 TraesCS1A01G272600 chr3A 95.455 286 8 4 227 511 210131148 210131429 6.090000e-123 451
27 TraesCS1A01G272600 chr3A 83.367 499 60 19 1021 1510 628302159 628302643 1.320000e-119 440
28 TraesCS1A01G272600 chr3A 89.011 91 10 0 2570 2660 628304300 628304390 3.260000e-21 113
29 TraesCS1A01G272600 chr2A 93.524 525 3 5 1 509 3426787 3427296 0.000000e+00 752
30 TraesCS1A01G272600 chr2A 91.029 379 26 6 138 509 608899781 608899404 4.610000e-139 505
31 TraesCS1A01G272600 chr2A 98.188 276 4 1 241 516 608899938 608899664 7.760000e-132 481
32 TraesCS1A01G272600 chr3B 83.436 489 63 16 1021 1502 648103071 648103548 4.740000e-119 438
33 TraesCS1A01G272600 chr3B 86.667 90 12 0 2571 2660 648105003 648105092 2.540000e-17 100
34 TraesCS1A01G272600 chr3D 83.096 491 61 18 1021 1502 485357871 485358348 1.030000e-115 427
35 TraesCS1A01G272600 chr3D 86.813 91 12 0 2570 2660 485359816 485359906 7.060000e-18 102
36 TraesCS1A01G272600 chrUn 99.270 137 1 0 1 137 407837346 407837210 8.570000e-62 248


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 TraesCS1A01G272600 chr1A 465521813 465525805 3992 True 7374.000000 7374 100.000000 1 3993 1 chr1A.!!$R1 3992
1 TraesCS1A01G272600 chr1A 518653816 518656192 2376 False 356.333333 573 97.613667 1 509 3 chr1A.!!$F3 508
2 TraesCS1A01G272600 chr1B 31469825 31470334 509 True 743.000000 743 93.143000 1 510 1 chr1B.!!$R1 509
3 TraesCS1A01G272600 chr1B 491262947 491266645 3698 True 716.400000 1498 90.123000 795 3919 5 chr1B.!!$R2 3124
4 TraesCS1A01G272600 chr1D 366222651 366226428 3777 False 536.428571 1495 87.971571 508 3993 7 chr1D.!!$F1 3485
5 TraesCS1A01G272600 chr6B 696085386 696085897 511 False 917.000000 917 99.023000 1 511 1 chr6B.!!$F1 510
6 TraesCS1A01G272600 chr6A 70604622 70605130 508 False 917.000000 917 99.214000 1 508 1 chr6A.!!$F1 507
7 TraesCS1A01G272600 chr3A 657267667 657268820 1153 False 826.500000 917 96.090000 1 509 2 chr3A.!!$F4 508
8 TraesCS1A01G272600 chr3A 628302159 628304390 2231 False 276.500000 440 86.189000 1021 2660 2 chr3A.!!$F3 1639
9 TraesCS1A01G272600 chr2A 3426787 3427296 509 False 752.000000 752 93.524000 1 509 1 chr2A.!!$F1 508
10 TraesCS1A01G272600 chr2A 608899404 608899938 534 True 493.000000 505 94.608500 138 516 2 chr2A.!!$R1 378
11 TraesCS1A01G272600 chr3B 648103071 648105092 2021 False 269.000000 438 85.051500 1021 2660 2 chr3B.!!$F1 1639
12 TraesCS1A01G272600 chr3D 485357871 485359906 2035 False 264.500000 427 84.954500 1021 2660 2 chr3D.!!$F1 1639

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
656 3239 0.320771 CAAACCAGACCGAGTCCAGG 60.321 60.0 9.86 9.86 35.35 4.45 F
891 3505 0.474614 GCTTATTCCTCCCCTGGTCC 59.525 60.0 0.00 0.00 0.00 4.46 F
2854 7585 0.457166 TAAAGATCGTCGTGGTGGCG 60.457 55.0 0.00 0.00 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2451 7002 2.295349 CCAAGGATGCTTGCATATGGAC 59.705 50.000 20.62 5.93 33.3 4.02 R
2884 7615 1.802960 GCGGTGCTCATGAATGGATAG 59.197 52.381 0.00 0.00 0.0 2.08 R
3833 8698 0.250166 ACTTGTTCCTGGCACGTACC 60.250 55.000 0.00 0.00 0.0 3.34 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
83 84 3.139397 AGGTGGGACAAATAAACCAGACA 59.861 43.478 0.00 0.00 44.16 3.41
436 3019 9.902196 ACGAAAATAAACCAGACGAAAATAAAT 57.098 25.926 0.00 0.00 0.00 1.40
517 3100 7.902087 ACATTAGGAGTAGAGATAAGGATTGC 58.098 38.462 0.00 0.00 0.00 3.56
534 3117 4.382754 GGATTGCTGAAACGAAATTGACAC 59.617 41.667 0.00 0.00 0.00 3.67
577 3160 2.976356 GGAAACCCTAGACGCGGT 59.024 61.111 12.47 0.00 0.00 5.68
627 3210 4.485163 GCCACTCAAATTCGTTTAGCAAT 58.515 39.130 0.00 0.00 0.00 3.56
633 3216 9.340695 CACTCAAATTCGTTTAGCAATAAATGA 57.659 29.630 0.00 0.00 34.30 2.57
635 3218 8.375717 TCAAATTCGTTTAGCAATAAATGACG 57.624 30.769 2.88 0.00 35.43 4.35
653 3236 0.666577 CGTCAAACCAGACCGAGTCC 60.667 60.000 1.06 0.00 35.07 3.85
654 3237 0.391597 GTCAAACCAGACCGAGTCCA 59.608 55.000 1.06 0.00 32.18 4.02
656 3239 0.320771 CAAACCAGACCGAGTCCAGG 60.321 60.000 9.86 9.86 35.35 4.45
657 3240 2.113243 AAACCAGACCGAGTCCAGGC 62.113 60.000 10.81 0.00 33.40 4.85
658 3241 3.775654 CCAGACCGAGTCCAGGCC 61.776 72.222 0.00 0.00 32.18 5.19
659 3242 4.135153 CAGACCGAGTCCAGGCCG 62.135 72.222 0.00 0.00 32.18 6.13
660 3243 4.361971 AGACCGAGTCCAGGCCGA 62.362 66.667 0.00 0.00 32.18 5.54
661 3244 3.379445 GACCGAGTCCAGGCCGAA 61.379 66.667 0.00 0.00 0.00 4.30
662 3245 3.644399 GACCGAGTCCAGGCCGAAC 62.644 68.421 0.00 0.00 0.00 3.95
663 3246 4.452733 CCGAGTCCAGGCCGAACC 62.453 72.222 0.00 0.00 39.61 3.62
673 3256 2.482326 GGCCGAACCTTGGAATCTG 58.518 57.895 0.00 0.00 34.51 2.90
674 3257 1.032114 GGCCGAACCTTGGAATCTGG 61.032 60.000 0.00 0.00 34.51 3.86
675 3258 1.032114 GCCGAACCTTGGAATCTGGG 61.032 60.000 0.00 0.00 0.00 4.45
683 3266 3.026694 CCTTGGAATCTGGGGAATTGTC 58.973 50.000 0.00 0.00 0.00 3.18
690 3273 1.280133 TCTGGGGAATTGTCAGCTGAG 59.720 52.381 18.89 0.82 0.00 3.35
736 3319 3.377656 GACTTCAGTCCAGGCCGA 58.622 61.111 0.00 0.00 39.07 5.54
752 3337 1.371183 CGAACTTCCTGTGGAGGCA 59.629 57.895 0.00 0.00 39.57 4.75
753 3338 0.951040 CGAACTTCCTGTGGAGGCAC 60.951 60.000 0.00 0.00 39.57 5.01
754 3339 0.606673 GAACTTCCTGTGGAGGCACC 60.607 60.000 0.00 0.00 39.57 5.01
755 3340 2.069165 AACTTCCTGTGGAGGCACCC 62.069 60.000 0.00 0.00 39.57 4.61
756 3341 3.256960 TTCCTGTGGAGGCACCCC 61.257 66.667 0.00 0.00 39.57 4.95
759 3373 2.520458 CTGTGGAGGCACCCCAAA 59.480 61.111 0.00 0.00 38.59 3.28
780 3394 2.485266 AAAGGAAAAGTTGCGAACCG 57.515 45.000 0.00 0.00 0.00 4.44
876 3490 4.124351 CCCCTCGTCGCGTGCTTA 62.124 66.667 5.77 0.00 0.00 3.09
891 3505 0.474614 GCTTATTCCTCCCCTGGTCC 59.525 60.000 0.00 0.00 0.00 4.46
1091 3937 2.081425 ATCGAGAGCCTCATCCACGC 62.081 60.000 0.00 0.00 0.00 5.34
1259 4111 3.550431 CTCCGTCGCCATCCCCAT 61.550 66.667 0.00 0.00 0.00 4.00
1260 4112 3.521529 CTCCGTCGCCATCCCCATC 62.522 68.421 0.00 0.00 0.00 3.51
1261 4113 4.626081 CCGTCGCCATCCCCATCC 62.626 72.222 0.00 0.00 0.00 3.51
1391 4291 1.462627 TCGTCTTCCCCAACCCCTT 60.463 57.895 0.00 0.00 0.00 3.95
1437 4337 2.136878 CGACTGGGATCTCTGGGGG 61.137 68.421 4.33 0.00 0.00 5.40
1507 4407 2.093106 CAGTCAGGAAGGTACGTAGCT 58.907 52.381 21.15 21.15 35.17 3.32
1508 4408 3.054875 TCAGTCAGGAAGGTACGTAGCTA 60.055 47.826 26.24 8.82 33.01 3.32
1569 4469 0.602638 TCAGTTAGCTGGGTGCAACG 60.603 55.000 6.75 0.00 45.94 4.10
1615 4521 9.708092 AGTTAGAATGAACTAGTACAAACCTTC 57.292 33.333 0.00 0.00 37.90 3.46
1661 4568 7.364939 CCCCACATTGATCAGGTGAAAATATTT 60.365 37.037 23.57 0.00 34.52 1.40
1691 4598 2.101783 GTCAATTGCATGGGTGATGGA 58.898 47.619 0.00 0.00 31.99 3.41
1692 4599 2.101783 TCAATTGCATGGGTGATGGAC 58.898 47.619 0.00 0.00 30.96 4.02
1693 4600 2.104967 CAATTGCATGGGTGATGGACT 58.895 47.619 0.00 0.00 30.96 3.85
1694 4601 1.771565 ATTGCATGGGTGATGGACTG 58.228 50.000 0.00 0.00 30.96 3.51
1695 4602 0.697658 TTGCATGGGTGATGGACTGA 59.302 50.000 0.00 0.00 30.96 3.41
1696 4603 0.921166 TGCATGGGTGATGGACTGAT 59.079 50.000 0.00 0.00 31.99 2.90
1697 4604 1.315690 GCATGGGTGATGGACTGATG 58.684 55.000 0.00 0.00 31.99 3.07
1698 4605 1.977056 CATGGGTGATGGACTGATGG 58.023 55.000 0.00 0.00 0.00 3.51
1714 4621 7.332430 TGGACTGATGGTTAACAACGTTAATAG 59.668 37.037 8.10 0.00 0.00 1.73
1715 4622 7.332678 GGACTGATGGTTAACAACGTTAATAGT 59.667 37.037 8.10 0.00 0.00 2.12
1716 4623 9.357652 GACTGATGGTTAACAACGTTAATAGTA 57.642 33.333 8.10 0.00 0.00 1.82
1801 4708 1.012841 GACCTGATAACTGCTGCTGC 58.987 55.000 8.89 8.89 40.20 5.25
1803 4710 0.731417 CCTGATAACTGCTGCTGCAC 59.269 55.000 14.93 5.20 45.31 4.57
1816 4723 3.063997 GCTGCTGCACGTATTGTAGATTT 59.936 43.478 11.11 0.00 40.27 2.17
1828 4735 5.653255 ATTGTAGATTTAGCAGGGGATGT 57.347 39.130 0.00 0.00 0.00 3.06
1830 4737 6.569127 TTGTAGATTTAGCAGGGGATGTAA 57.431 37.500 0.00 0.00 0.00 2.41
1838 4745 2.852449 AGCAGGGGATGTAAATCCTTGA 59.148 45.455 11.89 0.00 40.54 3.02
1863 4771 3.767131 ACAAACCAAACAGTGTTAAGGCT 59.233 39.130 21.27 11.04 0.00 4.58
1868 4776 3.573967 CCAAACAGTGTTAAGGCTGGATT 59.426 43.478 15.71 0.00 37.07 3.01
1869 4777 4.549458 CAAACAGTGTTAAGGCTGGATTG 58.451 43.478 9.37 10.01 37.07 2.67
1870 4778 3.508845 ACAGTGTTAAGGCTGGATTGT 57.491 42.857 9.99 0.00 37.07 2.71
1871 4779 3.832527 ACAGTGTTAAGGCTGGATTGTT 58.167 40.909 9.99 0.00 37.07 2.83
1872 4780 3.569701 ACAGTGTTAAGGCTGGATTGTTG 59.430 43.478 9.99 0.00 37.07 3.33
1876 4784 6.010219 AGTGTTAAGGCTGGATTGTTGTTAT 58.990 36.000 0.00 0.00 0.00 1.89
1946 4854 9.787435 TTGCTTTACAAACTAGGATTAGAAGAA 57.213 29.630 0.00 0.00 34.56 2.52
2085 5546 3.084786 AGTGCTGTTAAATCTGGAAGGC 58.915 45.455 0.00 0.00 0.00 4.35
2232 5694 1.484240 GGCATCTCCAGTTCAGTAGCT 59.516 52.381 0.00 0.00 34.01 3.32
2451 7002 9.784824 CGATAGAAAATTTTAGATGCTCGTTAG 57.215 33.333 2.75 0.00 39.76 2.34
2454 7005 7.975750 AGAAAATTTTAGATGCTCGTTAGTCC 58.024 34.615 2.75 0.00 0.00 3.85
2464 7015 2.221981 GCTCGTTAGTCCATATGCAAGC 59.778 50.000 0.00 0.00 0.00 4.01
2467 7018 4.058124 TCGTTAGTCCATATGCAAGCATC 58.942 43.478 11.32 0.00 37.82 3.91
2479 7030 1.133853 GCAAGCATCCTTGGAGATCCT 60.134 52.381 0.00 0.00 46.77 3.24
2818 7549 1.015868 GAGCTCTGATTTGCCTGCTC 58.984 55.000 6.43 0.00 39.74 4.26
2843 7574 3.557595 GGACAAGGACATGCTAAAGATCG 59.442 47.826 0.00 0.00 0.00 3.69
2854 7585 0.457166 TAAAGATCGTCGTGGTGGCG 60.457 55.000 0.00 0.00 0.00 5.69
2861 7592 4.595538 TCGTGGTGGCGGTGACAC 62.596 66.667 0.00 0.00 41.56 3.67
2992 7723 6.034044 GCTTCCTCATAATCGCGATAAACTAG 59.966 42.308 24.00 15.31 0.00 2.57
2997 7728 5.711506 TCATAATCGCGATAAACTAGGGGTA 59.288 40.000 24.00 7.16 0.00 3.69
2998 7729 6.379133 TCATAATCGCGATAAACTAGGGGTAT 59.621 38.462 24.00 9.29 0.00 2.73
2999 7730 3.928727 TCGCGATAAACTAGGGGTATG 57.071 47.619 3.71 0.00 0.00 2.39
3001 7732 3.890756 TCGCGATAAACTAGGGGTATGAA 59.109 43.478 3.71 0.00 0.00 2.57
3008 7740 2.846950 ACTAGGGGTATGAAGGTTGCT 58.153 47.619 0.00 0.00 0.00 3.91
3043 7777 0.804933 GTCCGGAGATTTTCCCGTCG 60.805 60.000 3.06 0.00 43.63 5.12
3048 7782 1.338389 GGAGATTTTCCCGTCGAACCA 60.338 52.381 0.00 0.00 40.37 3.67
3049 7783 2.629051 GAGATTTTCCCGTCGAACCAT 58.371 47.619 0.00 0.00 0.00 3.55
3057 7791 1.504900 CGTCGAACCATCCGAGTGA 59.495 57.895 0.00 0.00 36.66 3.41
3058 7792 0.523546 CGTCGAACCATCCGAGTGAG 60.524 60.000 0.00 0.00 36.66 3.51
3076 7810 4.406003 AGTGAGTACAGGTTTTGTCTGACT 59.594 41.667 9.51 0.00 41.29 3.41
3082 7816 3.694566 ACAGGTTTTGTCTGACTGGTTTC 59.305 43.478 9.51 0.00 33.87 2.78
3090 7824 7.455641 TTTGTCTGACTGGTTTCTTTTGTAA 57.544 32.000 9.51 0.00 0.00 2.41
3091 7825 7.455641 TTGTCTGACTGGTTTCTTTTGTAAA 57.544 32.000 9.51 0.00 0.00 2.01
3092 7826 7.639113 TGTCTGACTGGTTTCTTTTGTAAAT 57.361 32.000 9.51 0.00 0.00 1.40
3132 7870 8.840833 ACTACTTTGAGATTTCTTCTTCTTCC 57.159 34.615 0.00 0.00 33.74 3.46
3179 7918 7.123247 GGCGTATAGTAGGGGTATAGAAAATCA 59.877 40.741 0.00 0.00 0.00 2.57
3180 7919 8.526147 GCGTATAGTAGGGGTATAGAAAATCAA 58.474 37.037 0.00 0.00 0.00 2.57
3211 7950 4.201656 GGAAATCGTACGTTCTGTAAAGGC 60.202 45.833 16.05 0.00 34.07 4.35
3221 7960 2.582052 TCTGTAAAGGCACCACTTTGG 58.418 47.619 0.00 0.00 45.02 3.28
3250 7989 5.765182 CACCTGGCTAGAATAATTTGTAGGG 59.235 44.000 0.00 0.00 31.12 3.53
3252 7991 6.069029 ACCTGGCTAGAATAATTTGTAGGGTT 60.069 38.462 0.00 0.00 31.12 4.11
3253 7992 6.263168 CCTGGCTAGAATAATTTGTAGGGTTG 59.737 42.308 0.00 0.00 31.12 3.77
3254 7993 5.592688 TGGCTAGAATAATTTGTAGGGTTGC 59.407 40.000 0.00 0.00 31.12 4.17
3255 7994 5.828328 GGCTAGAATAATTTGTAGGGTTGCT 59.172 40.000 0.00 0.00 31.12 3.91
3256 7995 6.238759 GGCTAGAATAATTTGTAGGGTTGCTG 60.239 42.308 0.00 0.00 31.12 4.41
3258 7997 4.402474 AGAATAATTTGTAGGGTTGCTGCC 59.598 41.667 0.00 0.00 0.00 4.85
3259 7998 2.309136 AATTTGTAGGGTTGCTGCCT 57.691 45.000 0.00 0.00 0.00 4.75
3261 8000 0.476338 TTTGTAGGGTTGCTGCCTCA 59.524 50.000 0.00 0.00 0.00 3.86
3262 8001 0.250727 TTGTAGGGTTGCTGCCTCAC 60.251 55.000 0.00 0.00 0.00 3.51
3263 8002 1.377333 GTAGGGTTGCTGCCTCACC 60.377 63.158 0.00 0.36 0.00 4.02
3265 8004 1.207488 TAGGGTTGCTGCCTCACCAT 61.207 55.000 13.00 9.33 0.00 3.55
3364 8166 5.633830 TTCTTGGAAGTTCTCATTGATGC 57.366 39.130 2.25 0.00 0.00 3.91
3365 8167 4.654915 TCTTGGAAGTTCTCATTGATGCA 58.345 39.130 2.25 0.00 0.00 3.96
3366 8168 5.072055 TCTTGGAAGTTCTCATTGATGCAA 58.928 37.500 2.25 0.00 0.00 4.08
3367 8169 5.182570 TCTTGGAAGTTCTCATTGATGCAAG 59.817 40.000 10.49 10.49 0.00 4.01
3368 8170 4.401022 TGGAAGTTCTCATTGATGCAAGT 58.599 39.130 2.25 0.00 0.00 3.16
3369 8171 5.559770 TGGAAGTTCTCATTGATGCAAGTA 58.440 37.500 2.25 0.00 0.00 2.24
3370 8172 6.182627 TGGAAGTTCTCATTGATGCAAGTAT 58.817 36.000 2.25 0.00 0.00 2.12
3371 8173 6.317140 TGGAAGTTCTCATTGATGCAAGTATC 59.683 38.462 2.25 0.00 0.00 2.24
3372 8174 6.238593 GGAAGTTCTCATTGATGCAAGTATCC 60.239 42.308 2.25 0.00 0.00 2.59
3373 8175 4.813161 AGTTCTCATTGATGCAAGTATCCG 59.187 41.667 0.00 0.00 0.00 4.18
3380 8182 5.794687 TTGATGCAAGTATCCGTTAACTG 57.205 39.130 3.71 0.00 0.00 3.16
3385 8187 3.000376 GCAAGTATCCGTTAACTGCGTAC 60.000 47.826 3.71 4.58 0.00 3.67
3409 8215 5.609423 TGTTGGGATGAAAAATGGTGAAAG 58.391 37.500 0.00 0.00 0.00 2.62
3413 8219 5.243730 TGGGATGAAAAATGGTGAAAGAGAC 59.756 40.000 0.00 0.00 0.00 3.36
3424 8230 1.070758 TGAAAGAGACTCACCACAGCC 59.929 52.381 5.02 0.00 0.00 4.85
3488 8294 4.207165 TCCATTTGCTGTATTTCTAGCCC 58.793 43.478 0.00 0.00 39.15 5.19
3507 8313 1.002250 CCGTCGTGTGTACTCTGCAC 61.002 60.000 0.00 0.00 37.37 4.57
3533 8339 1.860950 CCAGACCAATATTGACTCGCG 59.139 52.381 17.23 0.00 0.00 5.87
3550 8356 0.992802 GCGAGTCGTCACTGAATTCC 59.007 55.000 15.08 0.00 30.63 3.01
3558 8364 1.986378 GTCACTGAATTCCGACTGACG 59.014 52.381 2.27 0.00 42.18 4.35
3563 8369 2.600420 CTGAATTCCGACTGACGACATG 59.400 50.000 2.27 0.00 45.77 3.21
3612 8418 5.427481 TCCCGTCCTAACCTAAAATCATTCT 59.573 40.000 0.00 0.00 0.00 2.40
3613 8419 6.069847 TCCCGTCCTAACCTAAAATCATTCTT 60.070 38.462 0.00 0.00 0.00 2.52
3614 8420 6.260271 CCCGTCCTAACCTAAAATCATTCTTC 59.740 42.308 0.00 0.00 0.00 2.87
3615 8421 7.048512 CCGTCCTAACCTAAAATCATTCTTCT 58.951 38.462 0.00 0.00 0.00 2.85
3616 8422 7.553044 CCGTCCTAACCTAAAATCATTCTTCTT 59.447 37.037 0.00 0.00 0.00 2.52
3617 8423 8.604890 CGTCCTAACCTAAAATCATTCTTCTTC 58.395 37.037 0.00 0.00 0.00 2.87
3618 8424 9.674068 GTCCTAACCTAAAATCATTCTTCTTCT 57.326 33.333 0.00 0.00 0.00 2.85
3619 8425 9.892130 TCCTAACCTAAAATCATTCTTCTTCTC 57.108 33.333 0.00 0.00 0.00 2.87
3620 8426 9.114952 CCTAACCTAAAATCATTCTTCTTCTCC 57.885 37.037 0.00 0.00 0.00 3.71
3621 8427 9.898152 CTAACCTAAAATCATTCTTCTTCTCCT 57.102 33.333 0.00 0.00 0.00 3.69
3622 8428 8.572855 AACCTAAAATCATTCTTCTTCTCCTG 57.427 34.615 0.00 0.00 0.00 3.86
3644 8452 4.516698 TGTTCTCCTTCACATTCTCAAAGC 59.483 41.667 0.00 0.00 0.00 3.51
3662 8470 7.177216 TCTCAAAGCATACAAACATCCATTTCT 59.823 33.333 0.00 0.00 0.00 2.52
3663 8471 7.669427 TCAAAGCATACAAACATCCATTTCTT 58.331 30.769 0.00 0.00 0.00 2.52
3664 8472 8.149647 TCAAAGCATACAAACATCCATTTCTTT 58.850 29.630 0.00 0.00 0.00 2.52
3666 8474 8.907222 AAGCATACAAACATCCATTTCTTTTT 57.093 26.923 0.00 0.00 0.00 1.94
3667 8475 8.538409 AGCATACAAACATCCATTTCTTTTTC 57.462 30.769 0.00 0.00 0.00 2.29
3668 8476 8.370182 AGCATACAAACATCCATTTCTTTTTCT 58.630 29.630 0.00 0.00 0.00 2.52
3669 8477 8.992073 GCATACAAACATCCATTTCTTTTTCTT 58.008 29.630 0.00 0.00 0.00 2.52
3697 8505 7.552050 TTTTTGAGGGAATACAAACATCCAT 57.448 32.000 0.00 0.00 36.06 3.41
3698 8506 7.552050 TTTTGAGGGAATACAAACATCCATT 57.448 32.000 0.00 0.00 36.06 3.16
3700 8508 6.773976 TGAGGGAATACAAACATCCATTTC 57.226 37.500 0.00 0.00 34.82 2.17
3701 8509 6.252233 TGAGGGAATACAAACATCCATTTCA 58.748 36.000 0.00 0.00 34.82 2.69
3706 8536 6.747280 GGAATACAAACATCCATTTCAAGTCG 59.253 38.462 0.00 0.00 33.30 4.18
3740 8594 6.073873 GCAATAGAAACTAGTAGCAGCAGATG 60.074 42.308 0.00 0.00 0.00 2.90
3741 8595 6.968263 ATAGAAACTAGTAGCAGCAGATGA 57.032 37.500 0.00 0.00 0.00 2.92
3750 8608 1.265568 GCAGCAGATGAATTGTTGCG 58.734 50.000 0.00 0.00 41.64 4.85
3772 8634 3.735037 GACGCGGTCCCCAAGATCC 62.735 68.421 12.47 0.00 0.00 3.36
3777 8639 2.124695 GTCCCCAAGATCCGTGGC 60.125 66.667 7.41 0.00 34.56 5.01
3814 8676 4.403137 TACGCCGACCCGTCAACG 62.403 66.667 0.00 0.00 42.20 4.10
3830 8695 3.373319 CGTCGGCGCATACGTACG 61.373 66.667 21.34 15.01 42.83 3.67
3831 8696 2.277501 GTCGGCGCATACGTACGT 60.278 61.111 25.98 25.98 42.83 3.57
3832 8697 2.023181 TCGGCGCATACGTACGTC 59.977 61.111 26.53 9.99 42.83 4.34
3834 8699 3.020665 GGCGCATACGTACGTCGG 61.021 66.667 26.53 18.70 44.69 4.79
3835 8700 2.277501 GCGCATACGTACGTCGGT 60.278 61.111 26.53 9.66 44.69 4.69
3836 8701 1.011242 GCGCATACGTACGTCGGTA 60.011 57.895 26.53 7.76 44.69 4.02
3837 8702 1.255635 GCGCATACGTACGTCGGTAC 61.256 60.000 26.53 9.49 44.50 3.34
3884 8749 3.113322 GGTCAAGTTTCAAAGCCGTTTC 58.887 45.455 0.00 0.00 0.00 2.78
3892 8757 0.938637 CAAAGCCGTTTCGCATTGCA 60.939 50.000 9.69 0.00 31.54 4.08
3908 8773 3.940209 TTGCAATCTAAACTTGGCCAG 57.060 42.857 5.11 2.72 0.00 4.85
3930 8818 5.350091 CAGAACAAACAACCGAAAACCAAAT 59.650 36.000 0.00 0.00 0.00 2.32
3931 8819 5.350091 AGAACAAACAACCGAAAACCAAATG 59.650 36.000 0.00 0.00 0.00 2.32
3952 8840 4.500116 GCGGGCACGAGTCTCCTC 62.500 72.222 15.48 0.00 44.60 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
436 3019 4.873817 TCGTCTGGTTTATTTTCGTCTGA 58.126 39.130 0.00 0.00 0.00 3.27
517 3100 2.546368 TCCGGTGTCAATTTCGTTTCAG 59.454 45.455 0.00 0.00 0.00 3.02
574 3157 4.436998 GCACTCCCCTCACGACCG 62.437 72.222 0.00 0.00 0.00 4.79
575 3158 2.391724 TTTGCACTCCCCTCACGACC 62.392 60.000 0.00 0.00 0.00 4.79
577 3160 0.181587 TTTTTGCACTCCCCTCACGA 59.818 50.000 0.00 0.00 0.00 4.35
627 3210 3.061322 CGGTCTGGTTTGACGTCATTTA 58.939 45.455 20.80 0.76 37.81 1.40
633 3216 0.031721 GACTCGGTCTGGTTTGACGT 59.968 55.000 0.00 0.00 37.81 4.34
635 3218 0.391597 TGGACTCGGTCTGGTTTGAC 59.608 55.000 4.41 0.00 36.31 3.18
656 3239 1.032114 CCCAGATTCCAAGGTTCGGC 61.032 60.000 0.00 0.00 0.00 5.54
657 3240 0.394352 CCCCAGATTCCAAGGTTCGG 60.394 60.000 0.00 0.00 0.00 4.30
658 3241 0.618458 TCCCCAGATTCCAAGGTTCG 59.382 55.000 0.00 0.00 0.00 3.95
659 3242 2.899303 TTCCCCAGATTCCAAGGTTC 57.101 50.000 0.00 0.00 0.00 3.62
660 3243 3.181407 ACAATTCCCCAGATTCCAAGGTT 60.181 43.478 0.00 0.00 0.00 3.50
661 3244 2.383338 ACAATTCCCCAGATTCCAAGGT 59.617 45.455 0.00 0.00 0.00 3.50
662 3245 3.026694 GACAATTCCCCAGATTCCAAGG 58.973 50.000 0.00 0.00 0.00 3.61
663 3246 3.698040 CTGACAATTCCCCAGATTCCAAG 59.302 47.826 0.00 0.00 0.00 3.61
664 3247 3.700538 CTGACAATTCCCCAGATTCCAA 58.299 45.455 0.00 0.00 0.00 3.53
665 3248 2.621407 GCTGACAATTCCCCAGATTCCA 60.621 50.000 0.00 0.00 0.00 3.53
666 3249 2.027385 GCTGACAATTCCCCAGATTCC 58.973 52.381 0.00 0.00 0.00 3.01
667 3250 2.686915 CAGCTGACAATTCCCCAGATTC 59.313 50.000 8.42 0.00 0.00 2.52
668 3251 2.309755 TCAGCTGACAATTCCCCAGATT 59.690 45.455 13.74 0.00 0.00 2.40
669 3252 1.918262 TCAGCTGACAATTCCCCAGAT 59.082 47.619 13.74 0.00 0.00 2.90
670 3253 1.280133 CTCAGCTGACAATTCCCCAGA 59.720 52.381 13.74 0.00 0.00 3.86
671 3254 1.280133 TCTCAGCTGACAATTCCCCAG 59.720 52.381 13.74 0.00 0.00 4.45
672 3255 1.361204 TCTCAGCTGACAATTCCCCA 58.639 50.000 13.74 0.00 0.00 4.96
673 3256 2.087646 GTTCTCAGCTGACAATTCCCC 58.912 52.381 13.74 0.00 0.00 4.81
674 3257 3.064900 AGTTCTCAGCTGACAATTCCC 57.935 47.619 13.74 0.00 0.00 3.97
675 3258 3.365767 GCAAGTTCTCAGCTGACAATTCC 60.366 47.826 13.74 0.00 0.00 3.01
683 3266 3.231965 CGAAAATGCAAGTTCTCAGCTG 58.768 45.455 7.63 7.63 0.00 4.24
690 3273 0.039527 ACGGGCGAAAATGCAAGTTC 60.040 50.000 0.00 0.00 36.28 3.01
730 3313 1.831652 CTCCACAGGAAGTTCGGCCT 61.832 60.000 0.00 0.00 33.99 5.19
736 3319 1.456287 GGTGCCTCCACAGGAAGTT 59.544 57.895 0.00 0.00 43.65 2.66
759 3373 3.183754 CGGTTCGCAACTTTTCCTTTTT 58.816 40.909 0.00 0.00 0.00 1.94
789 3403 4.155733 CGGTGTGCCTGCGGGATA 62.156 66.667 18.31 0.00 33.58 2.59
875 3489 1.074775 CCGGACCAGGGGAGGAATA 60.075 63.158 0.00 0.00 0.00 1.75
876 3490 2.366972 CCGGACCAGGGGAGGAAT 60.367 66.667 0.00 0.00 0.00 3.01
907 3753 2.045143 GAGACGAGGAGGGACGGT 60.045 66.667 0.00 0.00 0.00 4.83
908 3754 3.203412 CGAGACGAGGAGGGACGG 61.203 72.222 0.00 0.00 0.00 4.79
911 3757 2.124653 GAGCGAGACGAGGAGGGA 60.125 66.667 0.00 0.00 0.00 4.20
951 3797 3.069980 GCGGCGAGATCTCAGTGGT 62.070 63.158 22.31 0.00 0.00 4.16
1209 4055 4.475135 GCGGAGGAGAAGGTGGGC 62.475 72.222 0.00 0.00 0.00 5.36
1250 4102 2.551413 GGGATGGGGATGGGGATGG 61.551 68.421 0.00 0.00 0.00 3.51
1251 4103 2.551413 GGGGATGGGGATGGGGATG 61.551 68.421 0.00 0.00 0.00 3.51
1252 4104 2.120854 GGGGATGGGGATGGGGAT 60.121 66.667 0.00 0.00 0.00 3.85
1253 4105 3.078909 ATGGGGATGGGGATGGGGA 62.079 63.158 0.00 0.00 0.00 4.81
1254 4106 2.455122 ATGGGGATGGGGATGGGG 60.455 66.667 0.00 0.00 0.00 4.96
1255 4107 2.910737 CGATGGGGATGGGGATGGG 61.911 68.421 0.00 0.00 0.00 4.00
1256 4108 2.759114 CGATGGGGATGGGGATGG 59.241 66.667 0.00 0.00 0.00 3.51
1257 4109 2.759114 CCGATGGGGATGGGGATG 59.241 66.667 0.00 0.00 38.47 3.51
1258 4110 3.260100 GCCGATGGGGATGGGGAT 61.260 66.667 0.00 0.00 38.47 3.85
1419 4319 2.136878 CCCCCAGAGATCCCAGTCG 61.137 68.421 0.00 0.00 0.00 4.18
1437 4337 2.682155 AGACGATGAAGAAGAAGGGC 57.318 50.000 0.00 0.00 0.00 5.19
1520 4420 8.771521 TGATGGACTTGGATTTCAAATGATAT 57.228 30.769 0.00 0.00 34.56 1.63
1521 4421 8.592529 TTGATGGACTTGGATTTCAAATGATA 57.407 30.769 0.00 0.00 34.56 2.15
1569 4469 8.405531 TCTAACTAATGTATTTCAAATGCAGGC 58.594 33.333 7.03 0.00 0.00 4.85
1615 4521 6.930722 GTGGGGCCTCATGAATTAAATAATTG 59.069 38.462 9.60 0.00 36.13 2.32
1618 4525 5.523588 TGTGGGGCCTCATGAATTAAATAA 58.476 37.500 9.60 0.00 0.00 1.40
1661 4568 5.772672 ACCCATGCAATTGACAAGTACTAAA 59.227 36.000 10.34 0.00 0.00 1.85
1691 4598 9.709495 TTACTATTAACGTTGTTAACCATCAGT 57.291 29.630 11.99 0.60 0.00 3.41
1801 4708 4.750098 CCCCTGCTAAATCTACAATACGTG 59.250 45.833 0.00 0.00 0.00 4.49
1803 4710 5.209818 TCCCCTGCTAAATCTACAATACG 57.790 43.478 0.00 0.00 0.00 3.06
1828 4735 8.919145 ACTGTTTGGTTTGTAATCAAGGATTTA 58.081 29.630 0.00 0.00 33.95 1.40
1830 4737 7.147742 ACACTGTTTGGTTTGTAATCAAGGATT 60.148 33.333 0.00 0.00 36.20 3.01
1838 4745 6.097696 AGCCTTAACACTGTTTGGTTTGTAAT 59.902 34.615 0.00 0.00 0.00 1.89
1863 4771 5.822519 GCTGGAGATGTATAACAACAATCCA 59.177 40.000 11.51 11.51 42.47 3.41
1868 4776 5.159273 TGTGCTGGAGATGTATAACAACA 57.841 39.130 0.00 0.00 0.00 3.33
1869 4777 6.540189 AGAATGTGCTGGAGATGTATAACAAC 59.460 38.462 0.00 0.00 0.00 3.32
1870 4778 6.653020 AGAATGTGCTGGAGATGTATAACAA 58.347 36.000 0.00 0.00 0.00 2.83
1871 4779 6.239217 AGAATGTGCTGGAGATGTATAACA 57.761 37.500 0.00 0.00 0.00 2.41
1872 4780 8.839310 ATAAGAATGTGCTGGAGATGTATAAC 57.161 34.615 0.00 0.00 0.00 1.89
1876 4784 7.112122 ACAAATAAGAATGTGCTGGAGATGTA 58.888 34.615 0.00 0.00 0.00 2.29
1946 4854 9.736023 CTCTTTTATTCTTTACAAAAGTGCACT 57.264 29.630 15.25 15.25 39.30 4.40
2021 5346 3.571828 TCCTAAGAAGATCGAGAGCATGG 59.428 47.826 0.00 0.00 0.00 3.66
2085 5546 4.717280 AGTCCCCCTTCTAAGAATACACTG 59.283 45.833 0.00 0.00 0.00 3.66
2425 5907 9.784824 CTAACGAGCATCTAAAATTTTCTATCG 57.215 33.333 6.72 11.69 0.00 2.92
2438 5920 4.522789 TGCATATGGACTAACGAGCATCTA 59.477 41.667 4.56 0.00 0.00 1.98
2440 6991 3.653344 TGCATATGGACTAACGAGCATC 58.347 45.455 4.56 0.00 0.00 3.91
2447 6998 4.392940 AGGATGCTTGCATATGGACTAAC 58.607 43.478 8.17 0.00 0.00 2.34
2451 7002 2.295349 CCAAGGATGCTTGCATATGGAC 59.705 50.000 20.62 5.93 33.30 4.02
2454 7005 3.483421 TCTCCAAGGATGCTTGCATATG 58.517 45.455 20.62 7.54 33.30 1.78
2529 7093 9.842775 AAGTCAGTATGTGATACATCAAATGAT 57.157 29.630 5.31 0.00 39.88 2.45
2818 7549 4.326826 TCTTTAGCATGTCCTTGTCCTTG 58.673 43.478 0.00 0.00 0.00 3.61
2827 7558 2.535984 CACGACGATCTTTAGCATGTCC 59.464 50.000 0.00 0.00 0.00 4.02
2843 7574 4.595538 TGTCACCGCCACCACGAC 62.596 66.667 0.00 0.00 34.06 4.34
2854 7585 3.071580 GCTCCATGCTAGTGTCACC 57.928 57.895 0.00 0.00 38.95 4.02
2884 7615 1.802960 GCGGTGCTCATGAATGGATAG 59.197 52.381 0.00 0.00 0.00 2.08
2992 7723 1.037579 GGCAGCAACCTTCATACCCC 61.038 60.000 0.00 0.00 0.00 4.95
2997 7728 3.434319 CGCGGCAGCAACCTTCAT 61.434 61.111 10.08 0.00 45.49 2.57
3043 7777 2.159226 CCTGTACTCACTCGGATGGTTC 60.159 54.545 0.00 0.00 0.00 3.62
3048 7782 3.323979 ACAAAACCTGTACTCACTCGGAT 59.676 43.478 0.00 0.00 36.10 4.18
3049 7783 2.696707 ACAAAACCTGTACTCACTCGGA 59.303 45.455 0.00 0.00 36.10 4.55
3057 7791 3.454812 ACCAGTCAGACAAAACCTGTACT 59.545 43.478 2.66 0.00 38.84 2.73
3058 7792 3.805207 ACCAGTCAGACAAAACCTGTAC 58.195 45.455 2.66 0.00 38.84 2.90
3132 7870 6.316390 ACGCCCTTTGATTATGTAAAGAAGAG 59.684 38.462 0.00 0.00 36.29 2.85
3179 7918 2.093658 ACGTACGATTTCCTGCTGGATT 60.094 45.455 24.41 4.25 42.81 3.01
3180 7919 1.480954 ACGTACGATTTCCTGCTGGAT 59.519 47.619 24.41 0.00 42.81 3.41
3181 7920 0.892755 ACGTACGATTTCCTGCTGGA 59.107 50.000 24.41 8.48 41.36 3.86
3182 7921 1.659098 GAACGTACGATTTCCTGCTGG 59.341 52.381 24.41 2.58 0.00 4.85
3194 7933 1.723003 GGTGCCTTTACAGAACGTACG 59.277 52.381 15.01 15.01 0.00 3.67
3195 7934 2.477754 GTGGTGCCTTTACAGAACGTAC 59.522 50.000 0.00 0.00 0.00 3.67
3221 7960 5.582689 AATTATTCTAGCCAGGTGCAAAC 57.417 39.130 0.00 0.00 44.83 2.93
3250 7989 1.604593 ACCATGGTGAGGCAGCAAC 60.605 57.895 18.99 0.00 44.96 4.17
3261 8000 3.495331 TGAAACATGCTAACACCATGGT 58.505 40.909 13.00 13.00 42.11 3.55
3262 8001 4.400251 AGATGAAACATGCTAACACCATGG 59.600 41.667 11.19 11.19 43.29 3.66
3263 8002 5.571784 AGATGAAACATGCTAACACCATG 57.428 39.130 0.00 0.00 44.28 3.66
3265 8004 6.539826 CAGATAGATGAAACATGCTAACACCA 59.460 38.462 0.00 0.00 0.00 4.17
3280 8077 1.485124 ACCGGCACACAGATAGATGA 58.515 50.000 0.00 0.00 0.00 2.92
3284 8081 2.386661 AGAAACCGGCACACAGATAG 57.613 50.000 0.00 0.00 0.00 2.08
3364 8166 4.264614 CAGTACGCAGTTAACGGATACTTG 59.735 45.833 10.11 7.44 37.78 3.16
3365 8167 4.082571 ACAGTACGCAGTTAACGGATACTT 60.083 41.667 10.11 5.24 37.78 2.24
3366 8168 3.441572 ACAGTACGCAGTTAACGGATACT 59.558 43.478 10.11 12.26 37.78 2.12
3367 8169 3.762779 ACAGTACGCAGTTAACGGATAC 58.237 45.455 10.11 10.38 37.78 2.24
3368 8170 4.168014 CAACAGTACGCAGTTAACGGATA 58.832 43.478 10.11 0.00 37.78 2.59
3369 8171 2.991190 CAACAGTACGCAGTTAACGGAT 59.009 45.455 10.11 0.00 37.78 4.18
3370 8172 2.396601 CAACAGTACGCAGTTAACGGA 58.603 47.619 10.11 0.00 37.78 4.69
3371 8173 1.458064 CCAACAGTACGCAGTTAACGG 59.542 52.381 0.90 0.90 37.78 4.44
3372 8174 1.458064 CCCAACAGTACGCAGTTAACG 59.542 52.381 0.00 0.00 37.78 3.18
3373 8175 2.758009 TCCCAACAGTACGCAGTTAAC 58.242 47.619 0.00 0.00 37.78 2.01
3380 8182 3.907894 TTTTTCATCCCAACAGTACGC 57.092 42.857 0.00 0.00 0.00 4.42
3385 8187 4.870123 TCACCATTTTTCATCCCAACAG 57.130 40.909 0.00 0.00 0.00 3.16
3409 8215 1.202698 ACTTTGGCTGTGGTGAGTCTC 60.203 52.381 0.00 0.00 0.00 3.36
3413 8219 1.102809 TGCACTTTGGCTGTGGTGAG 61.103 55.000 0.00 0.00 36.08 3.51
3424 8230 0.169672 CAATCTCCGGCTGCACTTTG 59.830 55.000 0.50 0.00 0.00 2.77
3488 8294 1.002250 GTGCAGAGTACACACGACGG 61.002 60.000 0.00 0.00 37.96 4.79
3507 8313 4.785301 AGTCAATATTGGTCTGGTCATGG 58.215 43.478 15.36 0.00 0.00 3.66
3533 8339 2.631418 TCGGAATTCAGTGACGACTC 57.369 50.000 7.93 0.00 0.00 3.36
3550 8356 2.337583 ACCATTTCATGTCGTCAGTCG 58.662 47.619 0.00 0.00 41.41 4.18
3612 8418 3.967326 TGTGAAGGAGAACAGGAGAAGAA 59.033 43.478 0.00 0.00 0.00 2.52
3613 8419 3.576861 TGTGAAGGAGAACAGGAGAAGA 58.423 45.455 0.00 0.00 0.00 2.87
3614 8420 4.550076 ATGTGAAGGAGAACAGGAGAAG 57.450 45.455 0.00 0.00 0.00 2.85
3615 8421 4.594920 AGAATGTGAAGGAGAACAGGAGAA 59.405 41.667 0.00 0.00 0.00 2.87
3616 8422 4.163427 AGAATGTGAAGGAGAACAGGAGA 58.837 43.478 0.00 0.00 0.00 3.71
3617 8423 4.020751 TGAGAATGTGAAGGAGAACAGGAG 60.021 45.833 0.00 0.00 0.00 3.69
3618 8424 3.903714 TGAGAATGTGAAGGAGAACAGGA 59.096 43.478 0.00 0.00 0.00 3.86
3619 8425 4.277515 TGAGAATGTGAAGGAGAACAGG 57.722 45.455 0.00 0.00 0.00 4.00
3620 8426 5.334724 GCTTTGAGAATGTGAAGGAGAACAG 60.335 44.000 0.00 0.00 0.00 3.16
3621 8427 4.516698 GCTTTGAGAATGTGAAGGAGAACA 59.483 41.667 0.00 0.00 0.00 3.18
3622 8428 4.516698 TGCTTTGAGAATGTGAAGGAGAAC 59.483 41.667 0.00 0.00 0.00 3.01
3674 8482 7.552050 AATGGATGTTTGTATTCCCTCAAAA 57.448 32.000 0.00 0.00 35.73 2.44
3675 8483 7.234371 TGAAATGGATGTTTGTATTCCCTCAAA 59.766 33.333 0.00 0.00 0.00 2.69
3676 8484 6.723515 TGAAATGGATGTTTGTATTCCCTCAA 59.276 34.615 0.00 0.00 0.00 3.02
3677 8485 6.252233 TGAAATGGATGTTTGTATTCCCTCA 58.748 36.000 0.00 0.00 0.00 3.86
3678 8486 6.773976 TGAAATGGATGTTTGTATTCCCTC 57.226 37.500 0.00 0.00 0.00 4.30
3680 8488 6.935167 ACTTGAAATGGATGTTTGTATTCCC 58.065 36.000 0.00 0.00 0.00 3.97
3681 8489 6.747280 CGACTTGAAATGGATGTTTGTATTCC 59.253 38.462 0.00 0.00 0.00 3.01
3682 8490 7.305474 ACGACTTGAAATGGATGTTTGTATTC 58.695 34.615 0.00 0.00 0.00 1.75
3685 8493 5.107259 CGACGACTTGAAATGGATGTTTGTA 60.107 40.000 0.00 0.00 0.00 2.41
3687 8495 4.151070 CGACGACTTGAAATGGATGTTTG 58.849 43.478 0.00 0.00 0.00 2.93
3689 8497 3.399330 ACGACGACTTGAAATGGATGTT 58.601 40.909 0.00 0.00 0.00 2.71
3690 8498 2.993899 GACGACGACTTGAAATGGATGT 59.006 45.455 0.00 0.00 0.00 3.06
3691 8499 2.993220 TGACGACGACTTGAAATGGATG 59.007 45.455 0.00 0.00 0.00 3.51
3692 8500 3.056821 TCTGACGACGACTTGAAATGGAT 60.057 43.478 0.00 0.00 0.00 3.41
3694 8502 2.663602 CTCTGACGACGACTTGAAATGG 59.336 50.000 0.00 0.00 0.00 3.16
3697 8505 1.066454 TGCTCTGACGACGACTTGAAA 59.934 47.619 0.00 0.00 0.00 2.69
3698 8506 0.666374 TGCTCTGACGACGACTTGAA 59.334 50.000 0.00 0.00 0.00 2.69
3700 8508 1.702886 ATTGCTCTGACGACGACTTG 58.297 50.000 0.00 0.00 0.00 3.16
3701 8509 2.747989 TCTATTGCTCTGACGACGACTT 59.252 45.455 0.00 0.00 0.00 3.01
3706 8536 5.642686 ACTAGTTTCTATTGCTCTGACGAC 58.357 41.667 0.00 0.00 0.00 4.34
3765 8623 1.813513 ACAGAAAGCCACGGATCTTG 58.186 50.000 0.00 0.00 0.00 3.02
3772 8634 3.555518 GAAAAGCTAACAGAAAGCCACG 58.444 45.455 0.00 0.00 41.02 4.94
3777 8639 4.143179 CGTACCGGAAAAGCTAACAGAAAG 60.143 45.833 9.46 0.00 0.00 2.62
3814 8676 2.277501 ACGTACGTATGCGCCGAC 60.278 61.111 21.41 5.15 42.83 4.79
3819 8681 2.758356 GTACCGACGTACGTATGCG 58.242 57.895 22.87 19.94 44.93 4.73
3830 8695 1.735559 GTTCCTGGCACGTACCGAC 60.736 63.158 0.00 0.00 0.00 4.79
3831 8696 1.746322 TTGTTCCTGGCACGTACCGA 61.746 55.000 0.00 0.00 0.00 4.69
3832 8697 1.289109 CTTGTTCCTGGCACGTACCG 61.289 60.000 0.00 0.00 0.00 4.02
3833 8698 0.250166 ACTTGTTCCTGGCACGTACC 60.250 55.000 0.00 0.00 0.00 3.34
3834 8699 2.443887 TACTTGTTCCTGGCACGTAC 57.556 50.000 0.00 0.00 0.00 3.67
3835 8700 2.548493 GGTTACTTGTTCCTGGCACGTA 60.548 50.000 0.00 0.00 0.00 3.57
3836 8701 1.589803 GTTACTTGTTCCTGGCACGT 58.410 50.000 0.00 0.00 0.00 4.49
3837 8702 0.872388 GGTTACTTGTTCCTGGCACG 59.128 55.000 0.00 0.00 0.00 5.34
3838 8703 0.872388 CGGTTACTTGTTCCTGGCAC 59.128 55.000 0.00 0.00 0.00 5.01
3884 8749 2.599973 GCCAAGTTTAGATTGCAATGCG 59.400 45.455 18.59 0.00 0.00 4.73
3892 8757 5.362430 TGTTTGTTCTGGCCAAGTTTAGATT 59.638 36.000 7.01 0.00 0.00 2.40
3908 8773 5.348997 TCATTTGGTTTTCGGTTGTTTGTTC 59.651 36.000 0.00 0.00 0.00 3.18
3930 8818 2.357034 GACTCGTGCCCGCTTTCA 60.357 61.111 0.00 0.00 0.00 2.69
3931 8819 2.048127 AGACTCGTGCCCGCTTTC 60.048 61.111 0.00 0.00 0.00 2.62
3952 8840 2.356667 GGAAGGTGGCAGGAAGGG 59.643 66.667 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.