Multiple sequence alignment - TraesCS4A01G056100

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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 TraesCS4A01G056100 chr4A 100.000 5153 0 0 1 5153 47096437 47101589 0.000000e+00 9516
1 TraesCS4A01G056100 chr4D 91.953 2647 146 29 1 2628 416942864 416940266 0.000000e+00 3646
2 TraesCS4A01G056100 chr4D 95.593 1316 52 4 2700 4012 416940261 416938949 0.000000e+00 2104
3 TraesCS4A01G056100 chr4D 88.992 645 44 12 3995 4633 416938823 416938200 0.000000e+00 773
4 TraesCS4A01G056100 chr4D 86.456 539 47 14 4633 5153 416938009 416937479 7.490000e-158 568
5 TraesCS4A01G056100 chr4D 94.118 85 3 2 2628 2712 123359021 123359103 1.510000e-25 128
6 TraesCS4A01G056100 chr4D 88.298 94 9 2 3101 3192 416940032 416939939 1.520000e-20 111
7 TraesCS4A01G056100 chr4B 93.239 1908 106 13 732 2628 514064282 514062387 0.000000e+00 2787
8 TraesCS4A01G056100 chr4B 91.210 1331 72 20 2700 4012 514062382 514061079 0.000000e+00 1768
9 TraesCS4A01G056100 chr4B 90.167 600 45 9 3948 4536 514061077 514060481 0.000000e+00 769
10 TraesCS4A01G056100 chr4B 87.237 619 46 17 80 692 514065554 514064963 0.000000e+00 675
11 TraesCS4A01G056100 chr4B 83.308 653 57 25 4537 5153 514060437 514059801 5.830000e-154 555
12 TraesCS4A01G056100 chr4B 96.471 85 3 0 1 85 514417262 514417178 1.930000e-29 141
13 TraesCS4A01G056100 chr4B 92.857 84 4 2 3111 3192 514062143 514062060 2.520000e-23 121
14 TraesCS4A01G056100 chr4B 86.916 107 7 4 593 692 514064916 514064810 4.220000e-21 113
15 TraesCS4A01G056100 chrUn 94.118 85 3 2 2628 2712 390053372 390053454 1.510000e-25 128
16 TraesCS4A01G056100 chr7D 93.182 88 4 2 2628 2715 307072732 307072647 1.510000e-25 128
17 TraesCS4A01G056100 chr7D 93.182 88 4 2 2628 2715 382021294 382021209 1.510000e-25 128
18 TraesCS4A01G056100 chr2D 93.182 88 4 2 2628 2715 17975033 17974948 1.510000e-25 128
19 TraesCS4A01G056100 chr2D 94.118 85 3 2 2628 2712 429496683 429496765 1.510000e-25 128
20 TraesCS4A01G056100 chr1B 94.118 85 3 2 2628 2712 49831185 49831267 1.510000e-25 128
21 TraesCS4A01G056100 chr1B 94.118 85 3 2 2628 2712 338995007 338995089 1.510000e-25 128
22 TraesCS4A01G056100 chr1B 93.182 88 4 2 2628 2715 683706096 683706011 1.510000e-25 128


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 TraesCS4A01G056100 chr4A 47096437 47101589 5152 False 9516.000000 9516 100.000000 1 5153 1 chr4A.!!$F1 5152
1 TraesCS4A01G056100 chr4D 416937479 416942864 5385 True 1440.400000 3646 90.258400 1 5153 5 chr4D.!!$R1 5152
2 TraesCS4A01G056100 chr4B 514059801 514065554 5753 True 969.714286 2787 89.276286 80 5153 7 chr4B.!!$R2 5073

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
433 434 0.165727 ACATAACACACATGCGCGTG 59.834 50.0 27.53 27.53 42.81 5.34 F
655 814 0.244450 CGGGCCTACGTGTTGAACTA 59.756 55.0 0.84 0.00 0.00 2.24 F
2317 2986 0.095935 GCTATATTGCCTGATGCGCG 59.904 55.0 0.00 0.00 45.60 6.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1857 2521 0.312102 GTGAACTGCAAAGCCTGGTC 59.688 55.0 0.0 0.0 0.0 4.02 R
2640 3309 0.038892 GCGGTAGAGTCGTGGAAACA 60.039 55.0 0.0 0.0 38.7 2.83 R
4191 5028 0.179100 TGCTCTGCGGCTCTTGATAC 60.179 55.0 0.0 0.0 0.0 2.24 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
24 25 2.104111 TCGTCTCAGTTCATGTTTGGGT 59.896 45.455 0.00 0.00 0.00 4.51
64 65 8.694540 CAATTGGAGGAATATGTGATGGTTTAA 58.305 33.333 0.00 0.00 0.00 1.52
103 104 4.909696 TGTCAATGTTGGTTAGGTTGTG 57.090 40.909 0.00 0.00 0.00 3.33
121 122 3.476552 TGTGGTCTTAAACTGCAAGAGG 58.523 45.455 0.00 0.00 37.43 3.69
183 184 1.011968 TGAATCGTGGTAGCGCACAC 61.012 55.000 11.47 14.83 0.00 3.82
265 266 2.286294 CGTGCAATCAGAGTAATGGAGC 59.714 50.000 0.00 0.00 0.00 4.70
266 267 3.273434 GTGCAATCAGAGTAATGGAGCA 58.727 45.455 0.00 0.00 0.00 4.26
267 268 3.881688 GTGCAATCAGAGTAATGGAGCAT 59.118 43.478 0.00 0.00 0.00 3.79
268 269 4.337555 GTGCAATCAGAGTAATGGAGCATT 59.662 41.667 0.00 0.00 37.80 3.56
269 270 4.577693 TGCAATCAGAGTAATGGAGCATTC 59.422 41.667 0.00 0.00 35.54 2.67
270 271 4.820716 GCAATCAGAGTAATGGAGCATTCT 59.179 41.667 0.00 0.00 35.54 2.40
271 272 5.994054 GCAATCAGAGTAATGGAGCATTCTA 59.006 40.000 0.00 0.00 35.54 2.10
286 287 5.423015 AGCATTCTACATTCGACAAGATGT 58.577 37.500 5.81 5.81 0.00 3.06
389 390 0.618458 AGTATTGGGCGCTCCTCAAA 59.382 50.000 3.94 0.00 36.20 2.69
398 399 2.279741 GCGCTCCTCAAACACATCATA 58.720 47.619 0.00 0.00 0.00 2.15
402 403 3.691118 GCTCCTCAAACACATCATAGCAA 59.309 43.478 0.00 0.00 0.00 3.91
408 409 5.798132 TCAAACACATCATAGCAAGAGTCT 58.202 37.500 0.00 0.00 0.00 3.24
416 417 6.548993 ACATCATAGCAAGAGTCTCATCTACA 59.451 38.462 1.94 0.00 0.00 2.74
417 418 7.233144 ACATCATAGCAAGAGTCTCATCTACAT 59.767 37.037 1.94 0.00 0.00 2.29
425 426 7.315890 CAAGAGTCTCATCTACATAACACACA 58.684 38.462 1.94 0.00 0.00 3.72
426 427 7.652524 AGAGTCTCATCTACATAACACACAT 57.347 36.000 1.94 0.00 0.00 3.21
427 428 7.487484 AGAGTCTCATCTACATAACACACATG 58.513 38.462 1.94 0.00 0.00 3.21
428 429 6.045318 AGTCTCATCTACATAACACACATGC 58.955 40.000 0.00 0.00 0.00 4.06
429 430 5.043248 TCTCATCTACATAACACACATGCG 58.957 41.667 0.00 0.00 0.00 4.73
430 431 3.555547 TCATCTACATAACACACATGCGC 59.444 43.478 0.00 0.00 0.00 6.09
431 432 1.923864 TCTACATAACACACATGCGCG 59.076 47.619 0.00 0.00 0.00 6.86
432 433 1.658596 CTACATAACACACATGCGCGT 59.341 47.619 8.43 0.00 0.00 6.01
433 434 0.165727 ACATAACACACATGCGCGTG 59.834 50.000 27.53 27.53 42.81 5.34
462 463 2.621338 CAGTATGTTCGGTGCATCAGT 58.379 47.619 0.00 0.00 0.00 3.41
481 482 2.434336 AGTGCATTTATAGCCGGACTCA 59.566 45.455 5.05 0.00 0.00 3.41
507 508 2.368192 CCTCCCCCTACATGCCCA 60.368 66.667 0.00 0.00 0.00 5.36
509 510 3.096495 TCCCCCTACATGCCCAGC 61.096 66.667 0.00 0.00 0.00 4.85
559 560 0.738975 CCTCGACCTAGACGAATGCA 59.261 55.000 11.66 0.00 39.23 3.96
583 584 4.481112 CGGCCGCAAATGTCTGGC 62.481 66.667 14.67 0.00 46.82 4.85
655 814 0.244450 CGGGCCTACGTGTTGAACTA 59.756 55.000 0.84 0.00 0.00 2.24
692 851 2.759560 AATTGATGCGGGCCACCC 60.760 61.111 4.39 0.00 41.09 4.61
751 1409 3.303132 CGCTTACCGAATTTACATCTGCC 60.303 47.826 0.00 0.00 40.02 4.85
766 1424 3.249189 GCCCCCTCACTGACACCA 61.249 66.667 0.00 0.00 0.00 4.17
790 1448 3.626924 ACCACTCTGGCCCGTCAC 61.627 66.667 0.00 0.00 42.67 3.67
905 1563 1.378646 CCTTTTCCTTCTCCGCCCC 60.379 63.158 0.00 0.00 0.00 5.80
920 1578 4.091939 CCCGTTCCCCGTTCCCTC 62.092 72.222 0.00 0.00 33.66 4.30
960 1618 1.248101 CCCCACCCAATCGAAACCAC 61.248 60.000 0.00 0.00 0.00 4.16
1359 2020 2.815647 CTCGTGGCGAAGAAGGGC 60.816 66.667 0.00 0.00 34.74 5.19
1519 2183 1.000993 GAGGAGCAGGAGTCCCAGA 59.999 63.158 5.25 0.00 34.21 3.86
1547 2211 2.815647 GGCCGACGAGGAAGCAAG 60.816 66.667 0.00 0.00 45.00 4.01
1561 2225 3.047280 CAAGCAGTGCCGCCGTTA 61.047 61.111 12.58 0.00 0.00 3.18
1569 2233 2.338984 GCCGCCGTTATCGAGGAT 59.661 61.111 10.50 0.00 39.71 3.24
1577 2241 1.822062 CGTTATCGAGGATGGGGAGGA 60.822 57.143 0.00 0.00 39.71 3.71
1578 2242 1.896465 GTTATCGAGGATGGGGAGGAG 59.104 57.143 0.00 0.00 0.00 3.69
1580 2244 2.393710 ATCGAGGATGGGGAGGAGGG 62.394 65.000 0.00 0.00 0.00 4.30
1582 2246 2.967014 AGGATGGGGAGGAGGGGT 60.967 66.667 0.00 0.00 0.00 4.95
1583 2247 2.448736 GGATGGGGAGGAGGGGTC 60.449 72.222 0.00 0.00 0.00 4.46
1584 2248 2.706071 GATGGGGAGGAGGGGTCT 59.294 66.667 0.00 0.00 0.00 3.85
1666 2330 1.802508 CGATGAACAGCGTGCCAGATA 60.803 52.381 4.30 0.00 35.24 1.98
1728 2392 2.420890 CTGCTCTCCATCTCCGGC 59.579 66.667 0.00 0.00 0.00 6.13
1854 2518 2.358898 GTCCGATTTCATGAACATGGGG 59.641 50.000 20.62 13.70 39.24 4.96
1857 2521 1.067516 GATTTCATGAACATGGGGCCG 59.932 52.381 7.89 0.00 39.24 6.13
1899 2563 0.963962 ATGGCAAGAGCAACAGGTTG 59.036 50.000 7.77 7.77 44.61 3.77
1924 2588 4.323417 TGATACCAGCAAACAAACGAGAT 58.677 39.130 0.00 0.00 0.00 2.75
1970 2636 5.009010 TGCTGATCAAAGTTTGTTCCTCTTC 59.991 40.000 19.29 8.17 0.00 2.87
1972 2638 6.567511 GCTGATCAAAGTTTGTTCCTCTTCTC 60.568 42.308 19.29 5.25 0.00 2.87
2035 2701 2.723209 CGTAACGTGAGGATGCGATAA 58.277 47.619 0.00 0.00 33.50 1.75
2038 2704 1.112113 ACGTGAGGATGCGATAACCT 58.888 50.000 0.00 0.00 36.68 3.50
2066 2734 2.159043 TCTGCTCTACTGTTAGCCATGC 60.159 50.000 10.99 0.00 37.97 4.06
2083 2751 4.382040 GCCATGCTTGTTCTGTACTCTCTA 60.382 45.833 0.00 0.00 0.00 2.43
2090 2758 7.931407 TGCTTGTTCTGTACTCTCTAAATTCAA 59.069 33.333 0.00 0.00 0.00 2.69
2113 2781 7.825761 TCAATGTCTATTTGCTCTTTGATCTGA 59.174 33.333 0.00 0.00 0.00 3.27
2219 2887 9.474313 AGGTGAATAACAAAATCTTTGGCTATA 57.526 29.630 4.30 0.00 0.00 1.31
2252 2921 2.890814 AGTGGGCAAGTCAGTAGTAGT 58.109 47.619 0.00 0.00 0.00 2.73
2258 2927 5.127194 TGGGCAAGTCAGTAGTAGTAGATTG 59.873 44.000 0.00 0.00 0.00 2.67
2265 2934 8.982091 AGTCAGTAGTAGTAGATTGAGCATTA 57.018 34.615 0.00 0.00 0.00 1.90
2293 2962 7.642978 GCATTCAGCAGTCAAAATAATCTACTG 59.357 37.037 0.00 0.00 44.79 2.74
2317 2986 0.095935 GCTATATTGCCTGATGCGCG 59.904 55.000 0.00 0.00 45.60 6.86
2318 2987 1.713597 CTATATTGCCTGATGCGCGA 58.286 50.000 12.10 0.00 45.60 5.87
2321 2990 1.308047 TATTGCCTGATGCGCGAATT 58.692 45.000 12.10 0.00 45.60 2.17
2328 2997 2.342354 CCTGATGCGCGAATTGTTTTTC 59.658 45.455 12.10 0.00 0.00 2.29
2329 2998 3.236816 CTGATGCGCGAATTGTTTTTCT 58.763 40.909 12.10 0.00 0.00 2.52
2330 2999 3.233578 TGATGCGCGAATTGTTTTTCTC 58.766 40.909 12.10 0.00 0.00 2.87
2347 3016 4.447138 TTCTCTAACAGCAAAGGGGAAA 57.553 40.909 0.00 0.00 0.00 3.13
2388 3057 7.725844 AGTTTATTCAGAAAGTCCAGGAAATGT 59.274 33.333 0.00 0.00 0.00 2.71
2467 3136 2.783135 TGAGCCTGAGGTTTGTCATTC 58.217 47.619 0.00 0.00 0.00 2.67
2469 3138 2.746362 GAGCCTGAGGTTTGTCATTCTG 59.254 50.000 0.00 0.00 0.00 3.02
2472 3141 4.018960 AGCCTGAGGTTTGTCATTCTGTAT 60.019 41.667 0.00 0.00 0.00 2.29
2480 3149 7.048512 AGGTTTGTCATTCTGTATAGCCTAAC 58.951 38.462 0.00 0.00 0.00 2.34
2539 3208 8.910944 TCTGGTATAACATACTAGTTCTTGGAC 58.089 37.037 0.00 0.00 33.07 4.02
2589 3258 9.507280 GTCAAAACTGATATATGACACATTTGG 57.493 33.333 0.00 0.00 40.02 3.28
2629 3298 9.754382 CCTTTGGAATATAACAATGAATGAAGG 57.246 33.333 0.00 0.00 0.00 3.46
2639 3308 9.865321 ATAACAATGAATGAAGGAATCAACAAG 57.135 29.630 0.00 0.00 42.54 3.16
2640 3309 7.294017 ACAATGAATGAAGGAATCAACAAGT 57.706 32.000 0.00 0.00 42.54 3.16
2641 3310 7.149973 ACAATGAATGAAGGAATCAACAAGTG 58.850 34.615 0.00 0.00 42.54 3.16
2642 3311 6.906157 ATGAATGAAGGAATCAACAAGTGT 57.094 33.333 0.00 0.00 42.54 3.55
2643 3312 6.713762 TGAATGAAGGAATCAACAAGTGTT 57.286 33.333 0.00 0.00 42.54 3.32
2644 3313 7.111247 TGAATGAAGGAATCAACAAGTGTTT 57.889 32.000 0.00 0.00 42.54 2.83
2645 3314 7.202526 TGAATGAAGGAATCAACAAGTGTTTC 58.797 34.615 0.00 0.00 42.54 2.78
2650 3319 4.545823 GAATCAACAAGTGTTTCCACGA 57.454 40.909 0.00 0.00 46.56 4.35
2651 3320 3.963383 ATCAACAAGTGTTTCCACGAC 57.037 42.857 0.00 0.00 46.56 4.34
2652 3321 2.980568 TCAACAAGTGTTTCCACGACT 58.019 42.857 0.00 0.00 46.56 4.18
2653 3322 2.933906 TCAACAAGTGTTTCCACGACTC 59.066 45.455 0.00 0.00 46.56 3.36
2654 3323 2.936498 CAACAAGTGTTTCCACGACTCT 59.064 45.455 0.00 0.00 46.56 3.24
2655 3324 4.116961 CAACAAGTGTTTCCACGACTCTA 58.883 43.478 0.00 0.00 46.56 2.43
2656 3325 3.714391 ACAAGTGTTTCCACGACTCTAC 58.286 45.455 0.00 0.00 46.56 2.59
2657 3326 3.057734 CAAGTGTTTCCACGACTCTACC 58.942 50.000 0.00 0.00 46.56 3.18
2658 3327 1.268899 AGTGTTTCCACGACTCTACCG 59.731 52.381 0.00 0.00 46.56 4.02
2659 3328 0.038892 TGTTTCCACGACTCTACCGC 60.039 55.000 0.00 0.00 0.00 5.68
2660 3329 0.735287 GTTTCCACGACTCTACCGCC 60.735 60.000 0.00 0.00 0.00 6.13
2661 3330 1.880819 TTTCCACGACTCTACCGCCC 61.881 60.000 0.00 0.00 0.00 6.13
2662 3331 4.189188 CCACGACTCTACCGCCCG 62.189 72.222 0.00 0.00 0.00 6.13
2663 3332 4.189188 CACGACTCTACCGCCCGG 62.189 72.222 4.96 4.96 42.03 5.73
2668 3337 3.861797 CTCTACCGCCCGGCCAAT 61.862 66.667 2.24 0.00 39.32 3.16
2669 3338 3.809374 CTCTACCGCCCGGCCAATC 62.809 68.421 2.24 0.00 39.32 2.67
2670 3339 4.929707 CTACCGCCCGGCCAATCC 62.930 72.222 2.24 0.00 39.32 3.01
2675 3344 3.140814 GCCCGGCCAATCCTGTTC 61.141 66.667 2.24 0.00 0.00 3.18
2676 3345 2.440247 CCCGGCCAATCCTGTTCC 60.440 66.667 2.24 0.00 0.00 3.62
2677 3346 2.354729 CCGGCCAATCCTGTTCCA 59.645 61.111 2.24 0.00 0.00 3.53
2678 3347 2.046285 CCGGCCAATCCTGTTCCAC 61.046 63.158 2.24 0.00 0.00 4.02
2679 3348 1.002134 CGGCCAATCCTGTTCCACT 60.002 57.895 2.24 0.00 0.00 4.00
2680 3349 1.308069 CGGCCAATCCTGTTCCACTG 61.308 60.000 2.24 0.00 0.00 3.66
2681 3350 0.038166 GGCCAATCCTGTTCCACTGA 59.962 55.000 0.00 0.00 0.00 3.41
2682 3351 1.547675 GGCCAATCCTGTTCCACTGAA 60.548 52.381 0.00 0.00 0.00 3.02
2683 3352 2.450476 GCCAATCCTGTTCCACTGAAT 58.550 47.619 0.00 0.00 31.98 2.57
2684 3353 2.165030 GCCAATCCTGTTCCACTGAATG 59.835 50.000 0.00 0.00 31.98 2.67
2685 3354 2.165030 CCAATCCTGTTCCACTGAATGC 59.835 50.000 0.00 0.00 31.98 3.56
2686 3355 2.134789 ATCCTGTTCCACTGAATGCC 57.865 50.000 0.00 0.00 31.98 4.40
2687 3356 0.038166 TCCTGTTCCACTGAATGCCC 59.962 55.000 0.00 0.00 31.98 5.36
2688 3357 0.038744 CCTGTTCCACTGAATGCCCT 59.961 55.000 0.00 0.00 31.98 5.19
2689 3358 1.457346 CTGTTCCACTGAATGCCCTC 58.543 55.000 0.00 0.00 31.98 4.30
2690 3359 0.038166 TGTTCCACTGAATGCCCTCC 59.962 55.000 0.00 0.00 31.98 4.30
2691 3360 0.681243 GTTCCACTGAATGCCCTCCC 60.681 60.000 0.00 0.00 31.98 4.30
2692 3361 0.846427 TTCCACTGAATGCCCTCCCT 60.846 55.000 0.00 0.00 0.00 4.20
2693 3362 0.846427 TCCACTGAATGCCCTCCCTT 60.846 55.000 0.00 0.00 0.00 3.95
2694 3363 0.040204 CCACTGAATGCCCTCCCTTT 59.960 55.000 0.00 0.00 0.00 3.11
2695 3364 1.550869 CCACTGAATGCCCTCCCTTTT 60.551 52.381 0.00 0.00 0.00 2.27
2733 3402 9.706691 CATATATTCGTTTGGTTCAGTATACCT 57.293 33.333 0.00 0.00 36.60 3.08
2840 3509 7.486407 AATTCCTGGAGTTGAATAGCAAAAT 57.514 32.000 3.38 0.00 38.44 1.82
2869 3538 9.466497 ACATGATGTTAAAATCAATACTCCTGT 57.534 29.630 12.34 7.53 39.90 4.00
2870 3539 9.726232 CATGATGTTAAAATCAATACTCCTGTG 57.274 33.333 12.34 0.00 39.90 3.66
2971 3640 7.613022 TCTTGGAGATGAATAGCAAAAATGACT 59.387 33.333 0.00 0.00 0.00 3.41
2974 3643 9.241919 TGGAGATGAATAGCAAAAATGACTTAA 57.758 29.630 0.00 0.00 0.00 1.85
3081 3751 3.876914 AGATCGAAGCTTGTTGTTTGTGA 59.123 39.130 2.10 0.00 0.00 3.58
3095 3765 3.181498 TGTTTGTGAATGCTGTGACTGTG 60.181 43.478 0.00 0.00 0.00 3.66
3096 3766 2.330440 TGTGAATGCTGTGACTGTGT 57.670 45.000 0.00 0.00 0.00 3.72
3109 3779 4.256920 GTGACTGTGTTCTTATGGCATCT 58.743 43.478 1.65 0.00 0.00 2.90
3202 3874 3.815856 TTTTCTTTGGTGCATGCTGAA 57.184 38.095 20.33 10.28 0.00 3.02
3269 3941 7.389607 GCATAACTTTTGTACCTGGTTCTCTTA 59.610 37.037 3.84 0.00 0.00 2.10
3354 4026 7.044798 ACCTCTATTTTCACTAGTGCTTGATC 58.955 38.462 18.45 0.00 0.00 2.92
3510 4196 5.024785 AGCCTTATTTCAGTGGTACTAGC 57.975 43.478 0.00 0.00 0.00 3.42
3512 4198 3.802685 CCTTATTTCAGTGGTACTAGCGC 59.197 47.826 0.00 0.00 0.00 5.92
3533 4219 5.171695 GCGCGAGTCTTTTACACTCTATTAG 59.828 44.000 12.10 0.00 38.55 1.73
3625 4311 2.067013 GGGAGCGTCAACAGAAGTTAC 58.933 52.381 0.00 0.00 35.85 2.50
3732 4418 3.489738 CCAAAAAGTGAACACCTGCTCTG 60.490 47.826 1.11 0.00 0.00 3.35
3733 4419 1.312815 AAAGTGAACACCTGCTCTGC 58.687 50.000 1.11 0.00 0.00 4.26
3792 4478 9.669353 AATAACTCATTGCAATAATGATTCGAC 57.331 29.630 12.53 0.00 36.23 4.20
3820 4506 9.669887 TTACCTGTTTAGTTTTCACTAGTTGAA 57.330 29.630 0.00 0.00 42.83 2.69
3834 4520 8.740123 TCACTAGTTGAAAGTTGTCCATTTAA 57.260 30.769 0.00 0.00 0.00 1.52
3979 4668 9.672086 GAGACTGACTGAACATACACTATAATC 57.328 37.037 0.00 0.00 0.00 1.75
3987 4676 7.334858 TGAACATACACTATAATCTGTGGCAA 58.665 34.615 0.00 0.00 38.39 4.52
4000 4832 9.860650 ATAATCTGTGGCAATTAACTACCAATA 57.139 29.630 0.00 0.00 33.03 1.90
4018 4850 9.956720 CTACCAATAAATTCATCTTTCACCATC 57.043 33.333 0.00 0.00 0.00 3.51
4020 4852 7.339212 ACCAATAAATTCATCTTTCACCATCGA 59.661 33.333 0.00 0.00 0.00 3.59
4021 4853 7.645340 CCAATAAATTCATCTTTCACCATCGAC 59.355 37.037 0.00 0.00 0.00 4.20
4022 4854 7.864108 ATAAATTCATCTTTCACCATCGACA 57.136 32.000 0.00 0.00 0.00 4.35
4024 4856 2.621338 TCATCTTTCACCATCGACAGC 58.379 47.619 0.00 0.00 0.00 4.40
4025 4857 2.234661 TCATCTTTCACCATCGACAGCT 59.765 45.455 0.00 0.00 0.00 4.24
4026 4858 2.084610 TCTTTCACCATCGACAGCTG 57.915 50.000 13.48 13.48 0.00 4.24
4027 4859 1.618343 TCTTTCACCATCGACAGCTGA 59.382 47.619 23.35 0.00 0.00 4.26
4029 4861 2.768253 TTCACCATCGACAGCTGATT 57.232 45.000 23.35 0.00 0.00 2.57
4030 4862 2.014335 TCACCATCGACAGCTGATTG 57.986 50.000 23.35 11.37 0.00 2.67
4031 4863 1.012086 CACCATCGACAGCTGATTGG 58.988 55.000 23.35 21.09 0.00 3.16
4032 4864 0.745845 ACCATCGACAGCTGATTGGC 60.746 55.000 23.35 3.06 0.00 4.52
4035 4867 1.263484 CATCGACAGCTGATTGGCATC 59.737 52.381 23.35 4.27 34.17 3.91
4040 4873 3.313249 CGACAGCTGATTGGCATCAAATA 59.687 43.478 23.35 0.00 39.04 1.40
4054 4887 8.286191 TGGCATCAAATACATGTTGTGTTATA 57.714 30.769 2.30 0.00 42.29 0.98
4122 4959 6.540189 GTGAATGATGGCTGACAGTTACTATT 59.460 38.462 3.99 0.82 0.00 1.73
4183 5020 0.516322 CGCAAGCAACGTGTATGTCG 60.516 55.000 0.00 0.00 0.00 4.35
4184 5021 0.787787 GCAAGCAACGTGTATGTCGA 59.212 50.000 0.00 0.00 0.00 4.20
4191 5028 1.629013 ACGTGTATGTCGACTGCATG 58.371 50.000 17.92 18.11 0.00 4.06
4194 5031 3.181490 ACGTGTATGTCGACTGCATGTAT 60.181 43.478 21.60 8.50 0.00 2.29
4213 5053 2.202851 AAGAGCCGCAGAGCATCG 60.203 61.111 0.00 0.00 42.67 3.84
4239 5079 2.225019 CACGCATGATTTAGATGCTCCC 59.775 50.000 0.00 0.00 43.45 4.30
4309 5152 1.534729 GGTCTTTGTAGCTTGGGTGG 58.465 55.000 0.00 0.00 0.00 4.61
4316 5159 0.250513 GTAGCTTGGGTGGTCTCCAG 59.749 60.000 0.00 0.00 35.48 3.86
4408 5252 3.304190 GGGTTAAACCAGCTTGTTGTACG 60.304 47.826 4.11 0.00 41.02 3.67
4412 5256 2.150397 ACCAGCTTGTTGTACGAGAC 57.850 50.000 0.00 0.00 31.05 3.36
4630 5517 9.453572 GTATGGAATGAATATGGATCAAGCTTA 57.546 33.333 0.00 0.00 0.00 3.09
4633 5520 8.388589 TGGAATGAATATGGATCAAGCTTATCT 58.611 33.333 0.00 0.00 0.00 1.98
4634 5521 8.675504 GGAATGAATATGGATCAAGCTTATCTG 58.324 37.037 0.00 0.00 0.00 2.90
4646 5725 7.124573 TCAAGCTTATCTGTATGCTAAAGGA 57.875 36.000 0.00 0.00 39.58 3.36
4658 5737 1.066430 GCTAAAGGACACACCGGATCA 60.066 52.381 9.46 0.00 44.74 2.92
4759 5845 8.187480 ACTATGTATGCGTATCATTTTGCAAAA 58.813 29.630 25.76 25.76 41.22 2.44
4772 5858 9.287373 ATCATTTTGCAAAATGGTCATTTTACT 57.713 25.926 42.54 22.57 44.16 2.24
4815 5911 1.668101 GACTTCTGTCTCCGCGGGAT 61.668 60.000 27.83 5.08 39.94 3.85
4827 5923 1.546029 CCGCGGGATTGAGATGAGATA 59.454 52.381 20.10 0.00 0.00 1.98
4830 5926 3.367806 CGCGGGATTGAGATGAGATATGT 60.368 47.826 0.00 0.00 0.00 2.29
4831 5927 4.142381 CGCGGGATTGAGATGAGATATGTA 60.142 45.833 0.00 0.00 0.00 2.29
4842 5939 8.633561 TGAGATGAGATATGTACAACGAGATTT 58.366 33.333 0.00 0.00 0.00 2.17
4846 5943 8.420374 TGAGATATGTACAACGAGATTTTTCC 57.580 34.615 0.00 0.00 0.00 3.13
4883 6003 4.025979 ACAGAGAAAGTCGCTTTAAACACG 60.026 41.667 5.08 0.47 33.49 4.49
4888 6008 2.909076 GTCGCTTTAAACACGACGAA 57.091 45.000 18.10 0.00 45.52 3.85
4889 6009 3.223186 GTCGCTTTAAACACGACGAAA 57.777 42.857 18.10 0.00 45.52 3.46
4890 6010 3.596319 GTCGCTTTAAACACGACGAAAA 58.404 40.909 18.10 0.00 45.52 2.29
4891 6011 4.021169 GTCGCTTTAAACACGACGAAAAA 58.979 39.130 18.10 0.00 45.52 1.94
4892 6012 4.667504 GTCGCTTTAAACACGACGAAAAAT 59.332 37.500 18.10 0.00 45.52 1.82
4893 6013 5.840267 GTCGCTTTAAACACGACGAAAAATA 59.160 36.000 18.10 0.00 45.52 1.40
4894 6014 5.840267 TCGCTTTAAACACGACGAAAAATAC 59.160 36.000 0.00 0.00 0.00 1.89
4895 6015 5.616383 CGCTTTAAACACGACGAAAAATACA 59.384 36.000 0.00 0.00 0.00 2.29
4896 6016 6.301372 CGCTTTAAACACGACGAAAAATACAT 59.699 34.615 0.00 0.00 0.00 2.29
4897 6017 7.149256 CGCTTTAAACACGACGAAAAATACATT 60.149 33.333 0.00 0.00 0.00 2.71
4898 6018 8.473796 GCTTTAAACACGACGAAAAATACATTT 58.526 29.630 0.00 0.00 0.00 2.32
5048 6168 0.744281 CACGCCCAACCACTTTCTTT 59.256 50.000 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 5.063204 TCTAACACCCAAACATGAACTGAG 58.937 41.667 0.00 0.00 0.00 3.35
24 25 4.326826 CTCCAATTGTGCCTTCTCTAACA 58.673 43.478 4.43 0.00 0.00 2.41
64 65 6.698008 TTGACATGTTCTCACATCACTTTT 57.302 33.333 0.00 0.00 42.14 2.27
103 104 5.281727 CAAAACCTCTTGCAGTTTAAGACC 58.718 41.667 2.60 0.00 35.19 3.85
121 122 4.756084 AGCTCTATGACAAGTGCAAAAC 57.244 40.909 0.00 0.00 38.22 2.43
160 161 2.080693 TGCGCTACCACGATTCAAAAT 58.919 42.857 9.73 0.00 34.06 1.82
207 208 7.683746 ACAATTTTGTGTGTTTCTTATGCAAC 58.316 30.769 0.00 0.00 40.49 4.17
220 221 4.503734 ACATTTCAGCGACAATTTTGTGTG 59.496 37.500 0.00 0.00 42.43 3.82
265 266 8.357796 ACATACATCTTGTCGAATGTAGAATG 57.642 34.615 11.99 9.48 33.65 2.67
266 267 8.581057 GACATACATCTTGTCGAATGTAGAAT 57.419 34.615 11.99 2.47 34.67 2.40
267 268 7.987268 GACATACATCTTGTCGAATGTAGAA 57.013 36.000 11.99 0.00 34.67 2.10
286 287 2.159099 GCACTGATGAACTCCCGACATA 60.159 50.000 0.00 0.00 0.00 2.29
296 297 0.889186 AACCGGTGGCACTGATGAAC 60.889 55.000 27.61 2.75 0.00 3.18
389 390 5.363292 AGATGAGACTCTTGCTATGATGTGT 59.637 40.000 3.68 0.00 0.00 3.72
398 399 6.153510 TGTGTTATGTAGATGAGACTCTTGCT 59.846 38.462 3.68 1.26 0.00 3.91
402 403 7.487484 CATGTGTGTTATGTAGATGAGACTCT 58.513 38.462 3.68 0.00 0.00 3.24
408 409 3.555547 GCGCATGTGTGTTATGTAGATGA 59.444 43.478 0.30 0.00 0.00 2.92
431 432 2.348498 CGAACATACTGTGTGTGTGCAC 60.348 50.000 10.75 10.75 41.14 4.57
432 433 1.864082 CGAACATACTGTGTGTGTGCA 59.136 47.619 11.02 0.00 41.14 4.57
433 434 1.194547 CCGAACATACTGTGTGTGTGC 59.805 52.381 11.02 3.67 41.14 4.57
443 444 2.621338 CACTGATGCACCGAACATACT 58.379 47.619 0.00 0.00 0.00 2.12
462 463 2.484770 GGTGAGTCCGGCTATAAATGCA 60.485 50.000 0.00 0.00 0.00 3.96
467 468 2.093341 GGTTTGGTGAGTCCGGCTATAA 60.093 50.000 0.00 0.00 39.52 0.98
481 482 2.831951 TAGGGGGAGGGGGTTTGGT 61.832 63.158 0.00 0.00 0.00 3.67
507 508 3.374402 CAGTCAGACCGTCCGGCT 61.374 66.667 5.47 1.25 39.32 5.52
509 510 1.246056 TTACCAGTCAGACCGTCCGG 61.246 60.000 3.76 3.76 42.03 5.14
535 536 1.457346 TCGTCTAGGTCGAGGGTTTC 58.543 55.000 6.80 0.00 33.38 2.78
538 539 1.390565 CATTCGTCTAGGTCGAGGGT 58.609 55.000 9.88 1.34 38.52 4.34
540 541 0.738975 TGCATTCGTCTAGGTCGAGG 59.261 55.000 9.88 8.41 38.52 4.63
546 547 3.245797 CGGTATGATGCATTCGTCTAGG 58.754 50.000 0.00 0.00 0.00 3.02
559 560 0.465460 ACATTTGCGGCCGGTATGAT 60.465 50.000 29.38 2.19 0.00 2.45
583 584 2.512286 AGATGATGCGTGCCGGTG 60.512 61.111 1.90 0.00 0.00 4.94
602 606 2.435586 CACGGAGGCTGCTTCCAG 60.436 66.667 27.43 21.50 42.13 3.86
634 640 0.038343 GTTCAACACGTAGGCCCGTA 60.038 55.000 6.73 0.00 39.45 4.02
655 814 1.671054 CAACGGGGCTGTCACGATT 60.671 57.895 12.37 0.00 0.00 3.34
692 851 4.135153 CTCGAGTGGAGGCGTGGG 62.135 72.222 3.62 0.00 39.22 4.61
751 1409 3.072476 CCTGGTGTCAGTGAGGGG 58.928 66.667 0.00 0.00 39.31 4.79
920 1578 4.815973 TGGGAGATCGGGGGTGGG 62.816 72.222 0.00 0.00 0.00 4.61
949 1607 1.202879 TGCTTGGGAGTGGTTTCGATT 60.203 47.619 0.00 0.00 0.00 3.34
960 1618 0.675633 CAGGGTGTTTTGCTTGGGAG 59.324 55.000 0.00 0.00 0.00 4.30
1515 2176 4.168291 GCCGCTCCCTCCTTCTGG 62.168 72.222 0.00 0.00 0.00 3.86
1526 2190 4.856607 CTTCCTCGTCGGCCGCTC 62.857 72.222 23.51 15.19 36.19 5.03
1547 2211 3.925238 CGATAACGGCGGCACTGC 61.925 66.667 13.24 0.00 35.72 4.40
1561 2225 1.157276 CCTCCTCCCCATCCTCGAT 59.843 63.158 0.00 0.00 0.00 3.59
1569 2233 3.208592 ACAGACCCCTCCTCCCCA 61.209 66.667 0.00 0.00 0.00 4.96
1577 2241 2.231380 AAATCCGCCACAGACCCCT 61.231 57.895 0.00 0.00 0.00 4.79
1578 2242 2.046285 CAAATCCGCCACAGACCCC 61.046 63.158 0.00 0.00 0.00 4.95
1580 2244 1.002624 TCCAAATCCGCCACAGACC 60.003 57.895 0.00 0.00 0.00 3.85
1582 2246 1.299648 CCTCCAAATCCGCCACAGA 59.700 57.895 0.00 0.00 0.00 3.41
1583 2247 1.750399 CCCTCCAAATCCGCCACAG 60.750 63.158 0.00 0.00 0.00 3.66
1584 2248 2.354729 CCCTCCAAATCCGCCACA 59.645 61.111 0.00 0.00 0.00 4.17
1857 2521 0.312102 GTGAACTGCAAAGCCTGGTC 59.688 55.000 0.00 0.00 0.00 4.02
1863 2527 2.669364 CCATCAAGTGAACTGCAAAGC 58.331 47.619 0.00 0.00 0.00 3.51
1899 2563 3.003897 TCGTTTGTTTGCTGGTATCAACC 59.996 43.478 0.00 0.00 46.98 3.77
1924 2588 6.884295 AGCAACAACCTAGATGCAATTACTTA 59.116 34.615 0.00 0.00 41.18 2.24
2017 2683 2.691526 AGGTTATCGCATCCTCACGTTA 59.308 45.455 0.00 0.00 0.00 3.18
2045 2711 2.159043 GCATGGCTAACAGTAGAGCAGA 60.159 50.000 9.12 0.00 40.64 4.26
2046 2712 2.158986 AGCATGGCTAACAGTAGAGCAG 60.159 50.000 9.12 1.26 40.64 4.24
2047 2713 1.833630 AGCATGGCTAACAGTAGAGCA 59.166 47.619 9.12 0.00 40.64 4.26
2048 2714 2.611225 AGCATGGCTAACAGTAGAGC 57.389 50.000 0.00 0.00 36.99 4.09
2049 2715 3.866651 ACAAGCATGGCTAACAGTAGAG 58.133 45.455 0.00 0.00 38.25 2.43
2050 2716 3.981071 ACAAGCATGGCTAACAGTAGA 57.019 42.857 0.00 0.00 38.25 2.59
2059 2727 2.304180 AGAGTACAGAACAAGCATGGCT 59.696 45.455 0.00 0.00 42.56 4.75
2060 2728 2.675348 GAGAGTACAGAACAAGCATGGC 59.325 50.000 0.00 0.00 0.00 4.40
2090 2758 7.108194 TGTCAGATCAAAGAGCAAATAGACAT 58.892 34.615 0.00 0.00 0.00 3.06
2113 2781 5.395103 GCTCCTTAGTGATTCAGATGACTGT 60.395 44.000 0.00 0.00 43.81 3.55
2219 2887 3.290948 TGCCCACTAACAAACAGAACT 57.709 42.857 0.00 0.00 0.00 3.01
2252 2921 5.824097 TGCTGAATGCTTAATGCTCAATCTA 59.176 36.000 0.00 0.00 43.37 1.98
2258 2927 3.376234 TGACTGCTGAATGCTTAATGCTC 59.624 43.478 0.00 0.00 43.37 4.26
2265 2934 7.166691 AGATTATTTTGACTGCTGAATGCTT 57.833 32.000 0.00 0.00 43.37 3.91
2270 2939 9.890629 ATACAGTAGATTATTTTGACTGCTGAA 57.109 29.630 15.34 0.00 42.53 3.02
2271 2940 9.890629 AATACAGTAGATTATTTTGACTGCTGA 57.109 29.630 15.34 3.23 42.53 4.26
2285 2954 8.597167 TCAGGCAATATAGCAATACAGTAGATT 58.403 33.333 0.00 0.00 35.83 2.40
2287 2956 7.539034 TCAGGCAATATAGCAATACAGTAGA 57.461 36.000 0.00 0.00 35.83 2.59
2293 2962 4.728882 GCGCATCAGGCAATATAGCAATAC 60.729 45.833 0.30 0.00 45.17 1.89
2307 2976 1.981254 AAAACAATTCGCGCATCAGG 58.019 45.000 8.75 0.00 0.00 3.86
2317 2986 7.169813 CCCTTTGCTGTTAGAGAAAAACAATTC 59.830 37.037 0.00 0.00 36.46 2.17
2318 2987 6.986231 CCCTTTGCTGTTAGAGAAAAACAATT 59.014 34.615 0.00 0.00 36.46 2.32
2321 2990 4.340950 CCCCTTTGCTGTTAGAGAAAAACA 59.659 41.667 0.00 0.00 35.61 2.83
2328 2997 3.057245 GCTTTTCCCCTTTGCTGTTAGAG 60.057 47.826 0.00 0.00 0.00 2.43
2329 2998 2.890945 GCTTTTCCCCTTTGCTGTTAGA 59.109 45.455 0.00 0.00 0.00 2.10
2330 2999 2.029020 GGCTTTTCCCCTTTGCTGTTAG 60.029 50.000 0.00 0.00 0.00 2.34
2347 3016 6.872920 TGAATAAACTGTTGTTCTTTGGCTT 58.127 32.000 15.47 0.00 36.21 4.35
2388 3057 4.572389 GCGCTTCTTCTCATCCTCAATTAA 59.428 41.667 0.00 0.00 0.00 1.40
2469 3138 9.194271 GCTGTGTTATAGAAAGTTAGGCTATAC 57.806 37.037 0.00 0.00 29.48 1.47
2472 3141 6.383147 AGGCTGTGTTATAGAAAGTTAGGCTA 59.617 38.462 0.00 0.00 36.87 3.93
2480 3149 4.697352 AGTGCAAGGCTGTGTTATAGAAAG 59.303 41.667 0.00 0.00 0.00 2.62
2514 3183 8.915036 AGTCCAAGAACTAGTATGTTATACCAG 58.085 37.037 0.00 0.00 0.00 4.00
2589 3258 5.649782 TTCCAAAGGAAATCAGCATTCTC 57.350 39.130 0.00 0.00 38.93 2.87
2640 3309 0.038892 GCGGTAGAGTCGTGGAAACA 60.039 55.000 0.00 0.00 38.70 2.83
2641 3310 0.735287 GGCGGTAGAGTCGTGGAAAC 60.735 60.000 0.00 0.00 0.00 2.78
2642 3311 1.588082 GGCGGTAGAGTCGTGGAAA 59.412 57.895 0.00 0.00 0.00 3.13
2643 3312 2.345760 GGGCGGTAGAGTCGTGGAA 61.346 63.158 0.00 0.00 0.00 3.53
2644 3313 2.753043 GGGCGGTAGAGTCGTGGA 60.753 66.667 0.00 0.00 0.00 4.02
2645 3314 4.189188 CGGGCGGTAGAGTCGTGG 62.189 72.222 0.00 0.00 0.00 4.94
2646 3315 4.189188 CCGGGCGGTAGAGTCGTG 62.189 72.222 0.00 0.00 0.00 4.35
2651 3320 3.809374 GATTGGCCGGGCGGTAGAG 62.809 68.421 24.45 0.00 37.65 2.43
2652 3321 3.857038 GATTGGCCGGGCGGTAGA 61.857 66.667 24.45 1.34 37.65 2.59
2653 3322 4.929707 GGATTGGCCGGGCGGTAG 62.930 72.222 24.45 0.00 37.65 3.18
2658 3327 3.140814 GAACAGGATTGGCCGGGC 61.141 66.667 23.42 23.42 43.43 6.13
2659 3328 2.440247 GGAACAGGATTGGCCGGG 60.440 66.667 2.18 0.00 43.43 5.73
2660 3329 2.046285 GTGGAACAGGATTGGCCGG 61.046 63.158 0.00 0.00 41.80 6.13
2661 3330 1.002134 AGTGGAACAGGATTGGCCG 60.002 57.895 0.00 0.00 41.80 6.13
2662 3331 0.038166 TCAGTGGAACAGGATTGGCC 59.962 55.000 0.00 0.00 41.80 5.36
2663 3332 1.909700 TTCAGTGGAACAGGATTGGC 58.090 50.000 0.00 0.00 41.80 4.52
2664 3333 2.165030 GCATTCAGTGGAACAGGATTGG 59.835 50.000 0.00 0.00 41.80 3.16
2665 3334 2.165030 GGCATTCAGTGGAACAGGATTG 59.835 50.000 0.00 0.00 41.80 2.67
2666 3335 2.450476 GGCATTCAGTGGAACAGGATT 58.550 47.619 0.00 0.00 41.80 3.01
2667 3336 1.341383 GGGCATTCAGTGGAACAGGAT 60.341 52.381 0.00 0.00 41.80 3.24
2668 3337 0.038166 GGGCATTCAGTGGAACAGGA 59.962 55.000 0.00 0.00 41.80 3.86
2669 3338 0.038744 AGGGCATTCAGTGGAACAGG 59.961 55.000 0.00 0.00 41.80 4.00
2670 3339 1.457346 GAGGGCATTCAGTGGAACAG 58.543 55.000 0.00 0.00 41.80 3.16
2671 3340 0.038166 GGAGGGCATTCAGTGGAACA 59.962 55.000 0.00 0.00 41.43 3.18
2672 3341 0.681243 GGGAGGGCATTCAGTGGAAC 60.681 60.000 0.00 0.00 35.46 3.62
2673 3342 0.846427 AGGGAGGGCATTCAGTGGAA 60.846 55.000 0.00 0.00 37.45 3.53
2674 3343 0.846427 AAGGGAGGGCATTCAGTGGA 60.846 55.000 0.00 0.00 0.00 4.02
2675 3344 0.040204 AAAGGGAGGGCATTCAGTGG 59.960 55.000 0.00 0.00 0.00 4.00
2676 3345 1.928868 AAAAGGGAGGGCATTCAGTG 58.071 50.000 0.00 0.00 0.00 3.66
2677 3346 2.702270 AAAAAGGGAGGGCATTCAGT 57.298 45.000 0.00 0.00 0.00 3.41
2694 3363 9.644993 CAAACGAATATATGTCGCTAATGAAAA 57.355 29.630 13.64 0.00 42.27 2.29
2695 3364 8.279800 CCAAACGAATATATGTCGCTAATGAAA 58.720 33.333 13.64 0.00 42.27 2.69
2698 3367 7.117241 ACCAAACGAATATATGTCGCTAATG 57.883 36.000 13.64 9.29 42.27 1.90
2733 3402 8.540388 AGTAGCACACATTTATCTTCCTTCTAA 58.460 33.333 0.00 0.00 0.00 2.10
2735 3404 6.951971 AGTAGCACACATTTATCTTCCTTCT 58.048 36.000 0.00 0.00 0.00 2.85
3081 3751 4.456911 CCATAAGAACACAGTCACAGCATT 59.543 41.667 0.00 0.00 0.00 3.56
3095 3765 8.821894 CAAGAACTAGTAAGATGCCATAAGAAC 58.178 37.037 0.00 0.00 0.00 3.01
3096 3766 7.987458 CCAAGAACTAGTAAGATGCCATAAGAA 59.013 37.037 0.00 0.00 0.00 2.52
3243 3915 5.705905 AGAGAACCAGGTACAAAAGTTATGC 59.294 40.000 0.00 0.00 0.00 3.14
3269 3941 8.038862 ACTTATCAACCATCATAGTGATTCCT 57.961 34.615 0.00 0.00 34.28 3.36
3354 4026 1.610522 CTTTCCTTGACTGGTGGCTTG 59.389 52.381 0.00 0.00 0.00 4.01
3460 4132 4.280425 ACCATGTGCAATGTACAATGAACA 59.720 37.500 23.91 23.91 39.36 3.18
3510 4196 5.681982 CCTAATAGAGTGTAAAAGACTCGCG 59.318 44.000 0.00 0.00 43.95 5.87
3533 4219 5.413499 TCTCAAACAGCCGTAGTTAATACC 58.587 41.667 0.00 0.00 0.00 2.73
3544 4230 5.116180 TGATACCTAAATCTCAAACAGCCG 58.884 41.667 0.00 0.00 0.00 5.52
3625 4311 4.785301 TGCCTTATCATTTCTTCCTCCTG 58.215 43.478 0.00 0.00 0.00 3.86
3732 4418 5.954296 ATCATCTATACAAGTGCCATTGC 57.046 39.130 0.00 0.00 33.28 3.56
3767 4453 8.839343 TGTCGAATCATTATTGCAATGAGTTAT 58.161 29.630 22.27 6.11 39.69 1.89
3792 4478 9.878599 CAACTAGTGAAAACTAAACAGGTAATG 57.121 33.333 0.00 0.00 0.00 1.90
3979 4668 9.301153 GAATTTATTGGTAGTTAATTGCCACAG 57.699 33.333 7.30 0.00 0.00 3.66
3993 4825 8.620416 CGATGGTGAAAGATGAATTTATTGGTA 58.380 33.333 0.00 0.00 0.00 3.25
4000 4832 5.392380 GCTGTCGATGGTGAAAGATGAATTT 60.392 40.000 0.00 0.00 0.00 1.82
4018 4850 1.089112 TTGATGCCAATCAGCTGTCG 58.911 50.000 14.67 3.19 43.64 4.35
4020 4852 4.018490 TGTATTTGATGCCAATCAGCTGT 58.982 39.130 14.67 0.00 43.64 4.40
4021 4853 4.642445 TGTATTTGATGCCAATCAGCTG 57.358 40.909 7.63 7.63 43.64 4.24
4022 4854 4.647853 ACATGTATTTGATGCCAATCAGCT 59.352 37.500 0.00 0.00 43.64 4.24
4024 4856 6.254804 CACAACATGTATTTGATGCCAATCAG 59.745 38.462 0.00 0.00 43.64 2.90
4025 4857 6.100668 CACAACATGTATTTGATGCCAATCA 58.899 36.000 0.00 0.00 41.16 2.57
4026 4858 6.101332 ACACAACATGTATTTGATGCCAATC 58.899 36.000 0.00 0.00 40.88 2.67
4027 4859 6.040209 ACACAACATGTATTTGATGCCAAT 57.960 33.333 0.00 0.00 40.88 3.16
4029 4861 5.465532 AACACAACATGTATTTGATGCCA 57.534 34.783 0.00 0.00 42.31 4.92
4030 4862 9.748708 AATATAACACAACATGTATTTGATGCC 57.251 29.630 0.00 0.00 42.31 4.40
4040 4873 9.066892 AGAGAACAACAATATAACACAACATGT 57.933 29.630 0.00 0.00 46.42 3.21
4054 4887 6.810182 GCATGCTTTGAATAGAGAACAACAAT 59.190 34.615 11.37 0.00 0.00 2.71
4060 4893 5.448360 GGTGAGCATGCTTTGAATAGAGAAC 60.448 44.000 23.61 4.38 0.00 3.01
4122 4959 1.020861 GTGACCATGCATCGCTGTCA 61.021 55.000 11.70 11.70 33.02 3.58
4174 5011 4.359706 TGATACATGCAGTCGACATACAC 58.640 43.478 19.50 2.38 0.00 2.90
4177 5014 5.514274 TCTTGATACATGCAGTCGACATA 57.486 39.130 19.50 3.45 0.00 2.29
4183 5020 1.863454 CGGCTCTTGATACATGCAGTC 59.137 52.381 0.00 0.00 0.00 3.51
4184 5021 1.945387 CGGCTCTTGATACATGCAGT 58.055 50.000 0.00 0.00 0.00 4.40
4191 5028 0.179100 TGCTCTGCGGCTCTTGATAC 60.179 55.000 0.00 0.00 0.00 2.24
4194 5031 1.153489 GATGCTCTGCGGCTCTTGA 60.153 57.895 0.00 0.00 0.00 3.02
4213 5053 4.031028 GCATCTAAATCATGCGTGTTGAC 58.969 43.478 5.68 0.00 37.51 3.18
4239 5079 3.350833 AGCTAGGCACTTGAAAGAATGG 58.649 45.455 0.00 0.00 41.75 3.16
4309 5152 3.471680 ACACAGAAGAAAAGCTGGAGAC 58.528 45.455 0.00 0.00 36.47 3.36
4316 5159 3.058914 ACGCATGTACACAGAAGAAAAGC 60.059 43.478 0.00 0.00 0.00 3.51
4322 5165 4.142924 TGCATAAACGCATGTACACAGAAG 60.143 41.667 0.00 0.00 36.86 2.85
4394 5238 1.792949 GTGTCTCGTACAACAAGCTGG 59.207 52.381 0.00 0.00 40.63 4.85
4408 5252 0.036388 TTTCCCATCTGCGGTGTCTC 60.036 55.000 0.00 0.00 0.00 3.36
4412 5256 1.462616 TGAATTTCCCATCTGCGGTG 58.537 50.000 0.00 0.00 0.00 4.94
4543 5429 4.490959 CGCTACTGACAGTAAAATTCAGCG 60.491 45.833 24.17 24.17 40.46 5.18
4630 5517 4.680708 CGGTGTGTCCTTTAGCATACAGAT 60.681 45.833 0.00 0.00 0.00 2.90
4633 5520 2.354303 CCGGTGTGTCCTTTAGCATACA 60.354 50.000 0.00 0.00 0.00 2.29
4634 5521 2.093869 TCCGGTGTGTCCTTTAGCATAC 60.094 50.000 0.00 0.00 0.00 2.39
4646 5725 1.338107 TTCTCAGTGATCCGGTGTGT 58.662 50.000 0.00 0.00 0.00 3.72
4658 5737 7.178274 ACTGTTATCTCATCTCAGTTTCTCAGT 59.822 37.037 0.00 0.00 36.17 3.41
4759 5845 8.793592 GGTTTCAGAACTTAGTAAAATGACCAT 58.206 33.333 0.00 0.00 36.03 3.55
4772 5858 7.610305 GTCATATTTCCCTGGTTTCAGAACTTA 59.390 37.037 0.00 0.00 43.49 2.24
4815 5911 7.568199 TCTCGTTGTACATATCTCATCTCAA 57.432 36.000 0.00 0.00 0.00 3.02
4853 5973 6.150318 TAAAGCGACTTTCTCTGTCTTACAG 58.850 40.000 7.89 0.50 39.72 2.74
4855 5975 7.042925 TGTTTAAAGCGACTTTCTCTGTCTTAC 60.043 37.037 7.89 0.00 35.21 2.34
4899 6019 8.844441 AAATGTATTTTTCGTCGTCTCAAAAA 57.156 26.923 5.19 5.19 34.41 1.94
5048 6168 4.286032 AGGGAATGTGCTACAGTAGTTTCA 59.714 41.667 9.42 6.69 0.00 2.69


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

AutoCloner maintained by Alex Coulton.