Multiple sequence alignment - TraesCS5A01G324000

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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 TraesCS5A01G324000 chr5A 100.000 2788 0 0 2060 4847 535557402 535554615 0.000000e+00 5149.0
1 TraesCS5A01G324000 chr5A 100.000 1849 0 0 1 1849 535559461 535557613 0.000000e+00 3415.0
2 TraesCS5A01G324000 chr5A 87.690 788 93 4 3559 4345 482486895 482486111 0.000000e+00 915.0
3 TraesCS5A01G324000 chr5A 83.811 488 75 4 4361 4846 535520926 535520441 1.230000e-125 460.0
4 TraesCS5A01G324000 chr5B 95.341 1567 68 3 285 1849 508733063 508731500 0.000000e+00 2484.0
5 TraesCS5A01G324000 chr5B 92.523 642 37 6 2301 2941 508730710 508730079 0.000000e+00 909.0
6 TraesCS5A01G324000 chr5B 89.216 306 32 1 4355 4660 508729961 508729657 9.840000e-102 381.0
7 TraesCS5A01G324000 chr5B 90.146 274 14 4 1 271 508774225 508773962 1.290000e-90 344.0
8 TraesCS5A01G324000 chr5B 86.282 277 12 10 2060 2311 508731450 508731175 1.330000e-70 278.0
9 TraesCS5A01G324000 chr5D 94.128 1124 60 4 728 1849 422003527 422002408 0.000000e+00 1705.0
10 TraesCS5A01G324000 chr5D 88.766 997 70 17 2060 3027 422002358 422001375 0.000000e+00 1182.0
11 TraesCS5A01G324000 chr5D 86.152 816 108 4 3544 4355 85909698 85908884 0.000000e+00 876.0
12 TraesCS5A01G324000 chr5D 93.103 493 34 0 4355 4847 422001373 422000881 0.000000e+00 723.0
13 TraesCS5A01G324000 chr5D 87.250 549 43 15 140 688 422004113 422003592 6.940000e-168 601.0
14 TraesCS5A01G324000 chr5D 79.430 316 52 9 2545 2855 422012391 422012084 1.370000e-50 211.0
15 TraesCS5A01G324000 chr5D 90.714 140 11 2 3 142 422004350 422004213 8.280000e-43 185.0
16 TraesCS5A01G324000 chr2A 88.409 811 91 2 3544 4351 593500894 593500084 0.000000e+00 974.0
17 TraesCS5A01G324000 chr2A 95.745 47 2 0 636 682 738207399 738207353 5.200000e-10 76.8
18 TraesCS5A01G324000 chr3D 87.164 818 99 5 3533 4345 346127458 346126642 0.000000e+00 924.0
19 TraesCS5A01G324000 chr3D 86.999 823 99 6 3533 4351 3850770 3849952 0.000000e+00 920.0
20 TraesCS5A01G324000 chr3D 85.294 782 112 2 3533 4311 118199337 118200118 0.000000e+00 804.0
21 TraesCS5A01G324000 chr2B 86.925 826 102 4 3533 4355 489943667 489944489 0.000000e+00 922.0
22 TraesCS5A01G324000 chr2B 87.647 170 17 2 3363 3531 463381040 463381206 1.380000e-45 195.0
23 TraesCS5A01G324000 chr2B 87.662 154 16 3 3378 3530 489943469 489943620 4.990000e-40 176.0
24 TraesCS5A01G324000 chr7A 86.441 826 109 2 3533 4355 539999776 540000601 0.000000e+00 902.0
25 TraesCS5A01G324000 chr7A 77.672 421 53 20 3140 3523 104726002 104725586 8.170000e-53 219.0
26 TraesCS5A01G324000 chr7A 81.323 257 45 3 3129 3384 665115135 665114881 6.360000e-49 206.0
27 TraesCS5A01G324000 chr7A 80.226 177 27 6 3251 3422 3541512 3541339 5.090000e-25 126.0
28 TraesCS5A01G324000 chr1A 85.836 819 108 4 3544 4355 418919796 418920613 0.000000e+00 863.0
29 TraesCS5A01G324000 chr4A 81.818 462 62 5 3087 3536 703622465 703622916 7.660000e-98 368.0
30 TraesCS5A01G324000 chr4A 78.988 257 51 3 3129 3384 638646600 638646346 6.450000e-39 172.0
31 TraesCS5A01G324000 chr4D 82.213 253 41 4 3129 3379 502064557 502064807 1.060000e-51 215.0
32 TraesCS5A01G324000 chr4D 83.019 159 23 4 3228 3384 494103740 494103896 1.820000e-29 141.0
33 TraesCS5A01G324000 chrUn 80.556 252 46 3 3134 3384 74776090 74776339 1.780000e-44 191.0
34 TraesCS5A01G324000 chr2D 82.273 220 36 3 3166 3384 423305578 423305795 2.300000e-43 187.0
35 TraesCS5A01G324000 chr2D 79.767 257 36 13 3129 3384 6107452 6107693 6.450000e-39 172.0
36 TraesCS5A01G324000 chr1D 79.091 220 44 2 3161 3379 394846945 394847163 3.020000e-32 150.0
37 TraesCS5A01G324000 chr1D 94.118 51 1 2 3335 3384 59894567 59894518 5.200000e-10 76.8
38 TraesCS5A01G324000 chr4B 75.862 348 45 13 3038 3383 636679936 636679626 1.820000e-29 141.0
39 TraesCS5A01G324000 chr4B 89.888 89 8 1 3448 3536 636650802 636650715 3.960000e-21 113.0
40 TraesCS5A01G324000 chr6B 82.540 126 16 6 3415 3536 441052018 441051895 6.630000e-19 106.0
41 TraesCS5A01G324000 chr7D 96.078 51 0 2 3335 3384 446928929 446928880 1.120000e-11 82.4


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 TraesCS5A01G324000 chr5A 535554615 535559461 4846 True 4282.0 5149 100.0000 1 4847 2 chr5A.!!$R3 4846
1 TraesCS5A01G324000 chr5A 482486111 482486895 784 True 915.0 915 87.6900 3559 4345 1 chr5A.!!$R1 786
2 TraesCS5A01G324000 chr5B 508729657 508733063 3406 True 1013.0 2484 90.8405 285 4660 4 chr5B.!!$R2 4375
3 TraesCS5A01G324000 chr5D 422000881 422004350 3469 True 879.2 1705 90.7922 3 4847 5 chr5D.!!$R3 4844
4 TraesCS5A01G324000 chr5D 85908884 85909698 814 True 876.0 876 86.1520 3544 4355 1 chr5D.!!$R1 811
5 TraesCS5A01G324000 chr2A 593500084 593500894 810 True 974.0 974 88.4090 3544 4351 1 chr2A.!!$R1 807
6 TraesCS5A01G324000 chr3D 346126642 346127458 816 True 924.0 924 87.1640 3533 4345 1 chr3D.!!$R2 812
7 TraesCS5A01G324000 chr3D 3849952 3850770 818 True 920.0 920 86.9990 3533 4351 1 chr3D.!!$R1 818
8 TraesCS5A01G324000 chr3D 118199337 118200118 781 False 804.0 804 85.2940 3533 4311 1 chr3D.!!$F1 778
9 TraesCS5A01G324000 chr2B 489943469 489944489 1020 False 549.0 922 87.2935 3378 4355 2 chr2B.!!$F2 977
10 TraesCS5A01G324000 chr7A 539999776 540000601 825 False 902.0 902 86.4410 3533 4355 1 chr7A.!!$F1 822
11 TraesCS5A01G324000 chr1A 418919796 418920613 817 False 863.0 863 85.8360 3544 4355 1 chr1A.!!$F1 811

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
512 614 0.734942 CGTCGTTCCATACAAGGCGT 60.735 55.0 0.00 0.0 0.00 5.68 F
1074 1212 1.164411 TGTCATTGGCGCAACCTAAG 58.836 50.0 10.83 0.0 40.22 2.18 F
1787 1927 0.391793 TGGAAACACTGTGTGCGTGA 60.392 50.0 15.11 0.0 36.98 4.35 F
3110 3790 0.109039 GACTCGCTCCTCTCCAACAC 60.109 60.0 0.00 0.0 0.00 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1438 1576 0.180406 GGGCTCCAACACACCGATAT 59.820 55.0 0.0 0.0 0.00 1.63 R
2928 3575 0.254178 ATTCAGCGGACCAATGCTCT 59.746 50.0 0.0 0.0 40.03 4.09 R
3185 3865 0.043485 AGGAAGGAGGAAGAGACCCC 59.957 60.0 0.0 0.0 0.00 4.95 R
4447 5179 0.107831 TCCACCTTCGGACCAACAAG 59.892 55.0 0.0 0.0 0.00 3.16 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
30 31 2.039746 TGGAATCGGAAGTGTCCACAAT 59.960 45.455 0.00 0.00 45.26 2.71
32 33 2.403252 ATCGGAAGTGTCCACAATCC 57.597 50.000 10.56 10.56 45.26 3.01
35 36 2.901192 TCGGAAGTGTCCACAATCCTAA 59.099 45.455 15.75 5.83 45.26 2.69
36 37 3.517901 TCGGAAGTGTCCACAATCCTAAT 59.482 43.478 15.75 0.00 45.26 1.73
71 72 1.202031 GCTAATTGTTGGAAGCGACCG 60.202 52.381 0.00 0.00 0.00 4.79
88 89 4.567959 GCGACCGGTAATAAAGCTAAGAAA 59.432 41.667 7.34 0.00 0.00 2.52
91 92 7.042523 GCGACCGGTAATAAAGCTAAGAAAATA 60.043 37.037 7.34 0.00 0.00 1.40
138 139 8.911247 ATGTTTAAAGTTCATTTTCCGCTATC 57.089 30.769 0.00 0.00 32.01 2.08
153 255 5.741011 TCCGCTATCTATGTTCCAAAAGTT 58.259 37.500 0.00 0.00 0.00 2.66
158 260 7.464710 CGCTATCTATGTTCCAAAAGTTCTCAC 60.465 40.741 0.00 0.00 0.00 3.51
162 264 7.004086 TCTATGTTCCAAAAGTTCTCACCAAT 58.996 34.615 0.00 0.00 0.00 3.16
171 273 7.095523 CCAAAAGTTCTCACCAATTGCAATTAG 60.096 37.037 23.69 19.11 0.00 1.73
174 276 5.183904 AGTTCTCACCAATTGCAATTAGGAC 59.816 40.000 30.65 24.80 0.00 3.85
178 280 2.831526 ACCAATTGCAATTAGGACCACC 59.168 45.455 30.65 0.00 0.00 4.61
179 281 2.159254 CCAATTGCAATTAGGACCACCG 60.159 50.000 23.69 8.61 41.83 4.94
180 282 1.102978 ATTGCAATTAGGACCACCGC 58.897 50.000 5.99 0.00 41.83 5.68
186 288 2.869503 ATTAGGACCACCGCAAGCCG 62.870 60.000 0.00 0.00 41.83 5.52
225 327 7.310671 GCCTCCCTGACTATGATTAATCATGTA 60.311 40.741 32.15 17.71 46.34 2.29
248 350 8.714179 TGTAGTACTACAATTTCATTTGGTTCG 58.286 33.333 29.20 0.00 42.49 3.95
257 359 7.116233 ACAATTTCATTTGGTTCGAACATTAGC 59.884 33.333 28.24 12.04 0.00 3.09
262 364 7.151308 TCATTTGGTTCGAACATTAGCAATTT 58.849 30.769 28.24 11.09 0.00 1.82
271 373 6.692249 TCGAACATTAGCAATTTACATGCATG 59.308 34.615 25.09 25.09 46.22 4.06
434 536 4.873817 TGTGATTCTGATGGCACTTTTTG 58.126 39.130 0.00 0.00 32.69 2.44
443 545 5.347342 TGATGGCACTTTTTGTTACAACAG 58.653 37.500 0.00 0.00 40.50 3.16
512 614 0.734942 CGTCGTTCCATACAAGGCGT 60.735 55.000 0.00 0.00 0.00 5.68
534 636 5.440685 GTCATATATTTTGGACGAAAGCGG 58.559 41.667 0.00 0.00 43.17 5.52
560 662 3.197549 ACAACAACCCAAAAGCAAGATGT 59.802 39.130 0.00 0.00 0.00 3.06
642 744 7.548427 GTCTAGTGTCAAAAAGTAATACTCCCC 59.452 40.741 0.00 0.00 0.00 4.81
719 821 8.142994 ACTAAAGGTGCGTGAATTAATATGAG 57.857 34.615 0.00 0.00 0.00 2.90
773 911 8.748412 TGCCATTTTATTTGTAAGATTACTGCT 58.252 29.630 4.50 0.00 34.77 4.24
1074 1212 1.164411 TGTCATTGGCGCAACCTAAG 58.836 50.000 10.83 0.00 40.22 2.18
1121 1259 4.141413 TGACATTGAGATTCCCTACCCATG 60.141 45.833 0.00 0.00 0.00 3.66
1130 1268 1.394266 CCCTACCCATGTGGCATTGC 61.394 60.000 0.00 0.00 37.83 3.56
1298 1436 8.818141 TCATATTGCTACAATTCTAGTACAGC 57.182 34.615 0.00 0.00 0.00 4.40
1419 1557 7.178573 TGGGATACATTTACACAGGAAAATCA 58.821 34.615 0.00 0.00 39.74 2.57
1438 1576 3.715287 TCAAGGTATGTAGCAGGGTGTA 58.285 45.455 0.00 0.00 0.00 2.90
1485 1623 2.202349 GCAAATGGCTCGTGCGTC 60.202 61.111 3.02 0.00 40.82 5.19
1517 1655 2.028203 GCTGCCAAAACACCATTACCAT 60.028 45.455 0.00 0.00 0.00 3.55
1538 1676 3.287222 TGGGATTAACAAGCTACCATGC 58.713 45.455 0.00 0.00 0.00 4.06
1675 1815 5.872617 CACGACAAGGTTCAATGATACCTAA 59.127 40.000 14.37 0.00 43.88 2.69
1723 1863 3.900601 ACTGGGCAATTGGAAATGTAACA 59.099 39.130 7.72 0.00 0.00 2.41
1777 1917 1.878102 GCATGTCGGACTGGAAACACT 60.878 52.381 9.88 0.00 35.60 3.55
1787 1927 0.391793 TGGAAACACTGTGTGCGTGA 60.392 50.000 15.11 0.00 36.98 4.35
1819 1959 5.786121 ATGGCTTAGGGTATCTATGCAAT 57.214 39.130 0.00 4.75 45.54 3.56
2126 2270 7.721286 ATCCGAATAGAGAAATGCAAAGTAG 57.279 36.000 0.00 0.00 0.00 2.57
2218 2387 7.123547 TGTTGGAAAAACTGTAAAGGAGAACAT 59.876 33.333 0.00 0.00 0.00 2.71
2246 2415 6.348622 CGTCATACTCAAGTCTTGTACTCACT 60.349 42.308 12.30 0.00 37.50 3.41
2453 3097 6.168270 AGAAGCCTAGATCAAGTGGTATTC 57.832 41.667 0.00 1.54 0.00 1.75
2515 3159 8.190326 TCTTATCTTACCTCAAAAGTCTCACA 57.810 34.615 0.00 0.00 0.00 3.58
2525 3170 5.500234 TCAAAAGTCTCACATGGGATTAGG 58.500 41.667 0.00 0.00 0.00 2.69
2526 3171 5.014123 TCAAAAGTCTCACATGGGATTAGGT 59.986 40.000 0.00 0.00 0.00 3.08
2527 3172 4.494091 AAGTCTCACATGGGATTAGGTG 57.506 45.455 0.00 0.00 33.92 4.00
2528 3173 3.454858 AGTCTCACATGGGATTAGGTGT 58.545 45.455 0.00 0.00 34.26 4.16
2682 3327 3.706086 AGGAAACAAACTCTTGCACCAAT 59.294 39.130 0.00 0.00 35.84 3.16
2703 3348 6.410853 CCAATGGATTGATAGGTAAACCTCCT 60.411 42.308 4.57 0.00 42.01 3.69
2721 3366 4.566488 CCTCCTGAAGTTATCACCTTGCTT 60.566 45.833 0.00 0.00 33.47 3.91
2739 3384 7.773690 ACCTTGCTTTATTCGTCTTATAACCAT 59.226 33.333 0.00 0.00 0.00 3.55
2743 3388 8.609176 TGCTTTATTCGTCTTATAACCATTGAC 58.391 33.333 0.00 0.00 0.00 3.18
2823 3469 3.715628 ATGTTTTGGTGAGAGCAACAC 57.284 42.857 0.00 0.00 42.51 3.32
2824 3470 1.400142 TGTTTTGGTGAGAGCAACACG 59.600 47.619 0.00 0.00 42.51 4.49
2843 3489 5.278604 ACACGGTAGTTTTCTTTTCATTGC 58.721 37.500 0.00 0.00 0.00 3.56
2844 3490 4.679654 CACGGTAGTTTTCTTTTCATTGCC 59.320 41.667 0.00 0.00 0.00 4.52
2845 3491 4.583073 ACGGTAGTTTTCTTTTCATTGCCT 59.417 37.500 0.00 0.00 0.00 4.75
2863 3510 2.619074 GCCTGGCAATGTAGAGAGGTTT 60.619 50.000 15.17 0.00 0.00 3.27
2965 3645 6.195244 CGCTGAATCTAAAAACAATGGAATCG 59.805 38.462 0.00 0.00 0.00 3.34
3038 3718 4.741928 AAAAACTATTCACACCCCTCCT 57.258 40.909 0.00 0.00 0.00 3.69
3039 3719 4.302559 AAAACTATTCACACCCCTCCTC 57.697 45.455 0.00 0.00 0.00 3.71
3040 3720 1.880941 ACTATTCACACCCCTCCTCC 58.119 55.000 0.00 0.00 0.00 4.30
3041 3721 1.132500 CTATTCACACCCCTCCTCCC 58.868 60.000 0.00 0.00 0.00 4.30
3042 3722 0.722676 TATTCACACCCCTCCTCCCT 59.277 55.000 0.00 0.00 0.00 4.20
3043 3723 0.621862 ATTCACACCCCTCCTCCCTC 60.622 60.000 0.00 0.00 0.00 4.30
3044 3724 3.077556 CACACCCCTCCTCCCTCG 61.078 72.222 0.00 0.00 0.00 4.63
3045 3725 3.273654 ACACCCCTCCTCCCTCGA 61.274 66.667 0.00 0.00 0.00 4.04
3046 3726 2.760385 CACCCCTCCTCCCTCGAC 60.760 72.222 0.00 0.00 0.00 4.20
3047 3727 4.444081 ACCCCTCCTCCCTCGACG 62.444 72.222 0.00 0.00 0.00 5.12
3048 3728 4.444081 CCCCTCCTCCCTCGACGT 62.444 72.222 0.00 0.00 0.00 4.34
3049 3729 3.141488 CCCTCCTCCCTCGACGTG 61.141 72.222 0.00 0.00 0.00 4.49
3050 3730 3.827898 CCTCCTCCCTCGACGTGC 61.828 72.222 0.00 0.00 0.00 5.34
3051 3731 3.827898 CTCCTCCCTCGACGTGCC 61.828 72.222 0.00 0.00 0.00 5.01
3075 3755 3.688159 GTACGTCACGGGTGCCCT 61.688 66.667 0.35 0.00 0.00 5.19
3076 3756 2.035469 TACGTCACGGGTGCCCTA 59.965 61.111 0.35 0.00 0.00 3.53
3077 3757 2.048023 TACGTCACGGGTGCCCTAG 61.048 63.158 0.35 0.00 0.00 3.02
3078 3758 2.482796 TACGTCACGGGTGCCCTAGA 62.483 60.000 0.35 0.30 0.00 2.43
3079 3759 2.423898 CGTCACGGGTGCCCTAGAT 61.424 63.158 5.64 0.00 0.00 1.98
3080 3760 1.442148 GTCACGGGTGCCCTAGATC 59.558 63.158 5.64 0.00 0.00 2.75
3081 3761 2.125326 TCACGGGTGCCCTAGATCG 61.125 63.158 5.64 0.00 0.00 3.69
3082 3762 2.125326 CACGGGTGCCCTAGATCGA 61.125 63.158 5.64 0.00 0.00 3.59
3083 3763 1.152525 ACGGGTGCCCTAGATCGAT 60.153 57.895 0.00 0.00 0.00 3.59
3084 3764 1.290324 CGGGTGCCCTAGATCGATG 59.710 63.158 0.54 0.00 0.00 3.84
3085 3765 1.674057 GGGTGCCCTAGATCGATGG 59.326 63.158 0.54 0.00 0.00 3.51
3086 3766 1.004440 GGTGCCCTAGATCGATGGC 60.004 63.158 15.67 15.67 44.27 4.40
3087 3767 1.004440 GTGCCCTAGATCGATGGCC 60.004 63.158 18.76 0.00 43.35 5.36
3088 3768 1.459348 TGCCCTAGATCGATGGCCA 60.459 57.895 18.76 8.56 43.35 5.36
3089 3769 1.294780 GCCCTAGATCGATGGCCAG 59.705 63.158 13.05 0.00 37.94 4.85
3090 3770 1.294780 CCCTAGATCGATGGCCAGC 59.705 63.158 12.07 12.07 0.00 4.85
3091 3771 1.080230 CCTAGATCGATGGCCAGCG 60.080 63.158 36.52 36.52 42.20 5.18
3096 3776 4.193334 TCGATGGCCAGCGACTCG 62.193 66.667 39.97 28.31 44.77 4.18
3107 3787 3.592070 CGACTCGCTCCTCTCCAA 58.408 61.111 0.00 0.00 0.00 3.53
3108 3788 1.137825 CGACTCGCTCCTCTCCAAC 59.862 63.158 0.00 0.00 0.00 3.77
3109 3789 1.587043 CGACTCGCTCCTCTCCAACA 61.587 60.000 0.00 0.00 0.00 3.33
3110 3790 0.109039 GACTCGCTCCTCTCCAACAC 60.109 60.000 0.00 0.00 0.00 3.32
3111 3791 0.540830 ACTCGCTCCTCTCCAACACT 60.541 55.000 0.00 0.00 0.00 3.55
3112 3792 0.605589 CTCGCTCCTCTCCAACACTT 59.394 55.000 0.00 0.00 0.00 3.16
3113 3793 0.603569 TCGCTCCTCTCCAACACTTC 59.396 55.000 0.00 0.00 0.00 3.01
3114 3794 0.390472 CGCTCCTCTCCAACACTTCC 60.390 60.000 0.00 0.00 0.00 3.46
3115 3795 0.980423 GCTCCTCTCCAACACTTCCT 59.020 55.000 0.00 0.00 0.00 3.36
3116 3796 1.066502 GCTCCTCTCCAACACTTCCTC 60.067 57.143 0.00 0.00 0.00 3.71
3117 3797 1.552792 CTCCTCTCCAACACTTCCTCC 59.447 57.143 0.00 0.00 0.00 4.30
3118 3798 0.615850 CCTCTCCAACACTTCCTCCC 59.384 60.000 0.00 0.00 0.00 4.30
3119 3799 0.615850 CTCTCCAACACTTCCTCCCC 59.384 60.000 0.00 0.00 0.00 4.81
3120 3800 0.840722 TCTCCAACACTTCCTCCCCC 60.841 60.000 0.00 0.00 0.00 5.40
3198 3878 3.839432 CGGCGGGGTCTCTTCCTC 61.839 72.222 0.00 0.00 0.00 3.71
3199 3879 3.471806 GGCGGGGTCTCTTCCTCC 61.472 72.222 0.00 0.00 0.00 4.30
3200 3880 2.364448 GCGGGGTCTCTTCCTCCT 60.364 66.667 0.00 0.00 0.00 3.69
3201 3881 1.990614 GCGGGGTCTCTTCCTCCTT 60.991 63.158 0.00 0.00 0.00 3.36
3202 3882 1.962321 GCGGGGTCTCTTCCTCCTTC 61.962 65.000 0.00 0.00 0.00 3.46
3203 3883 1.331399 CGGGGTCTCTTCCTCCTTCC 61.331 65.000 0.00 0.00 0.00 3.46
3204 3884 0.043485 GGGGTCTCTTCCTCCTTCCT 59.957 60.000 0.00 0.00 0.00 3.36
3205 3885 1.556002 GGGGTCTCTTCCTCCTTCCTT 60.556 57.143 0.00 0.00 0.00 3.36
3206 3886 2.270858 GGGTCTCTTCCTCCTTCCTTT 58.729 52.381 0.00 0.00 0.00 3.11
3207 3887 2.026729 GGGTCTCTTCCTCCTTCCTTTG 60.027 54.545 0.00 0.00 0.00 2.77
3208 3888 2.026729 GGTCTCTTCCTCCTTCCTTTGG 60.027 54.545 0.00 0.00 0.00 3.28
3209 3889 2.640332 GTCTCTTCCTCCTTCCTTTGGT 59.360 50.000 0.00 0.00 0.00 3.67
3210 3890 2.907042 TCTCTTCCTCCTTCCTTTGGTC 59.093 50.000 0.00 0.00 0.00 4.02
3211 3891 2.639839 CTCTTCCTCCTTCCTTTGGTCA 59.360 50.000 0.00 0.00 0.00 4.02
3212 3892 3.260205 TCTTCCTCCTTCCTTTGGTCAT 58.740 45.455 0.00 0.00 0.00 3.06
3213 3893 3.264450 TCTTCCTCCTTCCTTTGGTCATC 59.736 47.826 0.00 0.00 0.00 2.92
3214 3894 1.555075 TCCTCCTTCCTTTGGTCATCG 59.445 52.381 0.00 0.00 0.00 3.84
3215 3895 1.279271 CCTCCTTCCTTTGGTCATCGT 59.721 52.381 0.00 0.00 0.00 3.73
3216 3896 2.350522 CTCCTTCCTTTGGTCATCGTG 58.649 52.381 0.00 0.00 0.00 4.35
3217 3897 1.003118 TCCTTCCTTTGGTCATCGTGG 59.997 52.381 0.00 0.00 0.00 4.94
3218 3898 0.804989 CTTCCTTTGGTCATCGTGGC 59.195 55.000 0.00 0.00 0.00 5.01
3219 3899 0.953471 TTCCTTTGGTCATCGTGGCG 60.953 55.000 0.00 0.00 0.00 5.69
3220 3900 2.398554 CCTTTGGTCATCGTGGCGG 61.399 63.158 0.00 0.00 0.00 6.13
3221 3901 3.039202 CTTTGGTCATCGTGGCGGC 62.039 63.158 0.00 0.00 0.00 6.53
3222 3902 3.834013 TTTGGTCATCGTGGCGGCA 62.834 57.895 7.97 7.97 0.00 5.69
3223 3903 3.620419 TTGGTCATCGTGGCGGCAT 62.620 57.895 17.19 0.00 0.00 4.40
3224 3904 3.272334 GGTCATCGTGGCGGCATC 61.272 66.667 17.19 8.25 0.00 3.91
3225 3905 2.511373 GTCATCGTGGCGGCATCA 60.511 61.111 17.19 4.90 0.00 3.07
3226 3906 1.889105 GTCATCGTGGCGGCATCAT 60.889 57.895 17.19 7.42 0.00 2.45
3227 3907 1.888638 TCATCGTGGCGGCATCATG 60.889 57.895 17.19 19.45 0.00 3.07
3228 3908 2.592574 ATCGTGGCGGCATCATGG 60.593 61.111 17.19 2.71 0.00 3.66
3229 3909 4.854924 TCGTGGCGGCATCATGGG 62.855 66.667 17.19 0.80 0.00 4.00
3231 3911 3.211963 GTGGCGGCATCATGGGTC 61.212 66.667 17.19 0.00 0.00 4.46
3232 3912 4.854924 TGGCGGCATCATGGGTCG 62.855 66.667 7.97 7.75 0.00 4.79
3235 3915 4.552365 CGGCATCATGGGTCGGCT 62.552 66.667 4.66 0.00 0.00 5.52
3236 3916 2.828868 GGCATCATGGGTCGGCTA 59.171 61.111 0.00 0.00 0.00 3.93
3237 3917 1.376466 GGCATCATGGGTCGGCTAT 59.624 57.895 0.00 0.00 0.00 2.97
3238 3918 0.957395 GGCATCATGGGTCGGCTATG 60.957 60.000 0.00 0.00 0.00 2.23
3239 3919 1.580845 GCATCATGGGTCGGCTATGC 61.581 60.000 0.00 0.00 33.69 3.14
3240 3920 1.004560 ATCATGGGTCGGCTATGCG 60.005 57.895 0.00 0.00 0.00 4.73
3241 3921 2.454832 ATCATGGGTCGGCTATGCGG 62.455 60.000 0.00 0.00 0.00 5.69
3242 3922 4.626081 ATGGGTCGGCTATGCGGC 62.626 66.667 0.00 0.00 0.00 6.53
3271 3951 2.892425 CGGCGTCTGGCTGGATTC 60.892 66.667 0.00 0.00 44.68 2.52
3272 3952 2.586792 GGCGTCTGGCTGGATTCT 59.413 61.111 0.00 0.00 42.94 2.40
3273 3953 1.522580 GGCGTCTGGCTGGATTCTC 60.523 63.158 0.00 0.00 42.94 2.87
3274 3954 1.880340 GCGTCTGGCTGGATTCTCG 60.880 63.158 0.00 0.00 39.11 4.04
3275 3955 1.809869 CGTCTGGCTGGATTCTCGA 59.190 57.895 0.00 0.00 0.00 4.04
3276 3956 0.387202 CGTCTGGCTGGATTCTCGAT 59.613 55.000 0.00 0.00 0.00 3.59
3277 3957 1.863267 GTCTGGCTGGATTCTCGATG 58.137 55.000 0.00 0.00 0.00 3.84
3278 3958 0.755079 TCTGGCTGGATTCTCGATGG 59.245 55.000 0.00 0.00 0.00 3.51
3279 3959 0.883814 CTGGCTGGATTCTCGATGGC 60.884 60.000 0.00 0.00 0.00 4.40
3280 3960 1.958205 GGCTGGATTCTCGATGGCG 60.958 63.158 0.00 0.00 39.35 5.69
3281 3961 1.958205 GCTGGATTCTCGATGGCGG 60.958 63.158 0.00 0.00 38.28 6.13
3282 3962 1.301244 CTGGATTCTCGATGGCGGG 60.301 63.158 0.00 0.00 40.06 6.13
3283 3963 2.031163 GGATTCTCGATGGCGGGG 59.969 66.667 0.00 0.00 38.91 5.73
3284 3964 2.507854 GGATTCTCGATGGCGGGGA 61.508 63.158 0.00 0.00 38.91 4.81
3285 3965 1.301009 GATTCTCGATGGCGGGGAC 60.301 63.158 0.00 0.00 38.91 4.46
3297 3977 4.547367 GGGGACGGCTGGATTCGG 62.547 72.222 0.00 0.00 0.00 4.30
3305 3985 3.854669 CTGGATTCGGCGGCCTCT 61.855 66.667 18.34 0.52 0.00 3.69
3306 3986 3.391665 CTGGATTCGGCGGCCTCTT 62.392 63.158 18.34 0.32 0.00 2.85
3307 3987 2.897350 GGATTCGGCGGCCTCTTG 60.897 66.667 18.34 0.81 0.00 3.02
3308 3988 2.897350 GATTCGGCGGCCTCTTGG 60.897 66.667 18.34 0.39 0.00 3.61
3318 3998 2.818132 CCTCTTGGCTAGGAGGCG 59.182 66.667 15.40 0.00 44.78 5.52
3319 3999 2.801631 CCTCTTGGCTAGGAGGCGG 61.802 68.421 15.40 0.00 44.78 6.13
3320 4000 2.038975 TCTTGGCTAGGAGGCGGT 59.961 61.111 0.00 0.00 44.78 5.68
3321 4001 2.187946 CTTGGCTAGGAGGCGGTG 59.812 66.667 0.00 0.00 44.78 4.94
3322 4002 3.391665 CTTGGCTAGGAGGCGGTGG 62.392 68.421 0.00 0.00 44.78 4.61
3323 4003 4.715130 TGGCTAGGAGGCGGTGGT 62.715 66.667 0.00 0.00 44.78 4.16
3324 4004 4.162690 GGCTAGGAGGCGGTGGTG 62.163 72.222 0.00 0.00 0.00 4.17
3325 4005 4.840005 GCTAGGAGGCGGTGGTGC 62.840 72.222 0.00 0.00 0.00 5.01
3326 4006 3.390521 CTAGGAGGCGGTGGTGCA 61.391 66.667 0.00 0.00 36.28 4.57
3327 4007 2.687200 TAGGAGGCGGTGGTGCAT 60.687 61.111 0.00 0.00 36.28 3.96
3328 4008 2.650813 CTAGGAGGCGGTGGTGCATC 62.651 65.000 0.00 0.00 44.47 3.91
3330 4010 4.760047 GAGGCGGTGGTGCATCGT 62.760 66.667 0.00 0.00 40.42 3.73
3334 4014 3.422303 CGGTGGTGCATCGTGGTG 61.422 66.667 0.00 0.00 32.87 4.17
3335 4015 3.055719 GGTGGTGCATCGTGGTGG 61.056 66.667 0.00 0.00 0.00 4.61
3336 4016 3.737172 GTGGTGCATCGTGGTGGC 61.737 66.667 0.00 0.00 0.00 5.01
3363 4043 4.399395 GGGGTTTCGGTCGGGGTC 62.399 72.222 0.00 0.00 0.00 4.46
3364 4044 4.747529 GGGTTTCGGTCGGGGTCG 62.748 72.222 0.00 0.00 37.82 4.79
3365 4045 3.994853 GGTTTCGGTCGGGGTCGT 61.995 66.667 0.00 0.00 37.69 4.34
3366 4046 2.431430 GTTTCGGTCGGGGTCGTC 60.431 66.667 0.00 0.00 37.69 4.20
3367 4047 2.598394 TTTCGGTCGGGGTCGTCT 60.598 61.111 0.00 0.00 37.69 4.18
3368 4048 2.629656 TTTCGGTCGGGGTCGTCTC 61.630 63.158 0.00 0.00 37.69 3.36
3371 4051 2.827642 GGTCGGGGTCGTCTCGAT 60.828 66.667 6.75 0.00 38.42 3.59
3372 4052 2.714387 GTCGGGGTCGTCTCGATC 59.286 66.667 6.75 0.00 38.42 3.69
3373 4053 1.818785 GTCGGGGTCGTCTCGATCT 60.819 63.158 6.75 0.00 37.15 2.75
3374 4054 1.523258 TCGGGGTCGTCTCGATCTC 60.523 63.158 2.60 0.00 37.15 2.75
3375 4055 3.023950 GGGGTCGTCTCGATCTCG 58.976 66.667 2.60 0.00 37.15 4.04
3390 4070 3.471244 CTCGATCTGGGACGTCGCC 62.471 68.421 27.39 20.43 35.48 5.54
3450 4130 3.691342 CGTGGGCTTGGTCTCGGA 61.691 66.667 0.00 0.00 0.00 4.55
3454 4134 2.283529 GGGCTTGGTCTCGGAGTCA 61.284 63.158 4.69 2.58 0.00 3.41
3502 4182 3.550431 GGCAGCTGGGCGGATCTA 61.550 66.667 17.12 0.00 33.57 1.98
3505 4185 2.123854 AGCTGGGCGGATCTACGA 60.124 61.111 0.00 0.00 35.47 3.43
3520 4200 4.920640 TCTACGAGATTCCATCCTTGTC 57.079 45.455 0.00 0.00 0.00 3.18
3530 4210 1.352352 CCATCCTTGTCTGGTCCTTGT 59.648 52.381 0.00 0.00 0.00 3.16
3531 4211 2.224867 CCATCCTTGTCTGGTCCTTGTT 60.225 50.000 0.00 0.00 0.00 2.83
3538 4262 2.301870 TGTCTGGTCCTTGTTAGCGATT 59.698 45.455 0.00 0.00 0.00 3.34
3542 4266 2.224426 TGGTCCTTGTTAGCGATTGTGT 60.224 45.455 0.00 0.00 0.00 3.72
3551 4275 2.869233 AGCGATTGTGTTGCTTTTGT 57.131 40.000 0.00 0.00 45.60 2.83
3676 4402 0.464036 GACTATGGTCATGGCGGACA 59.536 55.000 4.04 0.00 41.75 4.02
3677 4403 1.070758 GACTATGGTCATGGCGGACAT 59.929 52.381 4.04 0.00 41.75 3.06
3709 4435 1.790755 TGATGTCGTTTCCTTGTCGG 58.209 50.000 0.00 0.00 0.00 4.79
3740 4466 2.186826 GCAGTTTGCGTGACCAGGT 61.187 57.895 0.00 0.00 31.71 4.00
3752 4478 1.613630 ACCAGGTTCGGGATGCTCT 60.614 57.895 0.00 0.00 0.00 4.09
3815 4541 2.541178 CGGCGTTCTTAGTATCGCTTCT 60.541 50.000 0.00 0.00 46.37 2.85
3935 4665 3.793144 GCGCTGCGGAGTTTCAGG 61.793 66.667 24.61 0.00 0.00 3.86
3950 4680 2.927856 AGGGATGGGCGTGTGTGA 60.928 61.111 0.00 0.00 0.00 3.58
4011 4741 4.849329 CGTCGACGGTAGGCCTGC 62.849 72.222 29.70 15.51 35.37 4.85
4049 4779 5.310857 TGAGTACCTGCTCTAGAGATGGATA 59.689 44.000 27.50 17.18 36.51 2.59
4050 4780 5.566469 AGTACCTGCTCTAGAGATGGATAC 58.434 45.833 27.50 23.45 0.00 2.24
4123 4853 1.476085 CAATTCCGGCATTGTGGCTTA 59.524 47.619 17.51 0.00 41.25 3.09
4160 4890 6.260936 CGGCTTTAGATGTTAGGATTTGATGT 59.739 38.462 0.00 0.00 0.00 3.06
4197 4927 1.971167 GGCTCGGACATTTGGCACA 60.971 57.895 0.00 0.00 0.00 4.57
4198 4928 1.315257 GGCTCGGACATTTGGCACAT 61.315 55.000 0.00 0.00 39.30 3.21
4335 5067 0.325016 TCCAGATGCAGAGGCTGAGA 60.325 55.000 0.00 4.07 41.91 3.27
4416 5148 9.662947 AGTTATTATTGGACTAAGTTGTGGTAC 57.337 33.333 0.00 0.00 0.00 3.34
4439 5171 6.181908 ACTGGGGTTCTATTTATTGCGTTAA 58.818 36.000 0.00 0.00 0.00 2.01
4454 5186 4.363999 TGCGTTAATTTCAACCTTGTTGG 58.636 39.130 7.08 0.00 42.93 3.77
4523 5255 2.650322 TCCGCAGAAACAAAGGTCTTT 58.350 42.857 0.00 0.00 0.00 2.52
4582 5314 7.431249 CCATGCATAGCACTGAAATATTTTCT 58.569 34.615 0.00 0.00 43.04 2.52
4590 5322 7.325694 AGCACTGAAATATTTTCTTTGGATGG 58.674 34.615 1.43 0.00 0.00 3.51
4608 5340 0.885879 GGGTTAGAAAAGGCAACCGG 59.114 55.000 0.00 0.00 42.21 5.28
4644 5376 2.166459 CACGCATTCTAGGTCTTGGAGA 59.834 50.000 0.00 0.00 0.00 3.71
4674 5406 6.377996 GGTACCGTTTACAAGGGGATTTTATT 59.622 38.462 0.00 0.00 40.69 1.40
4679 5411 9.563748 CCGTTTACAAGGGGATTTTATTAGATA 57.436 33.333 0.00 0.00 32.85 1.98
4709 5441 3.769300 GGTGGCCATAAAGAAGTCCAAAT 59.231 43.478 9.72 0.00 0.00 2.32
4714 5446 5.279960 GGCCATAAAGAAGTCCAAATTGGTT 60.280 40.000 12.28 0.00 39.03 3.67
4775 5507 7.557724 TGCCATTATGTCACAAATCAATCATT 58.442 30.769 0.00 0.00 0.00 2.57
4777 5509 7.707464 GCCATTATGTCACAAATCAATCATTGA 59.293 33.333 1.59 1.59 45.01 2.57
4834 5566 3.746492 CAGAGGTACCTTTGCTTGTGTAC 59.254 47.826 18.72 0.25 34.28 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.127730 GGACACTTCCGATTCCACAATTTTAT 60.128 38.462 0.00 0.00 29.98 1.40
1 2 5.182380 GGACACTTCCGATTCCACAATTTTA 59.818 40.000 0.00 0.00 29.98 1.52
10 11 2.178912 TTGTGGACACTTCCGATTCC 57.821 50.000 3.91 0.00 46.37 3.01
14 15 1.348064 AGGATTGTGGACACTTCCGA 58.652 50.000 14.78 0.00 46.37 4.55
18 19 9.396022 CATTAGTAATTAGGATTGTGGACACTT 57.604 33.333 3.91 0.00 0.00 3.16
36 37 8.946085 CCAACAATTAGCTCTGAACATTAGTAA 58.054 33.333 0.00 0.00 0.00 2.24
109 110 7.812669 AGCGGAAAATGAACTTTAAACATTAGG 59.187 33.333 3.69 0.00 34.48 2.69
118 119 8.958119 ACATAGATAGCGGAAAATGAACTTTA 57.042 30.769 0.00 0.00 0.00 1.85
138 139 6.633500 TTGGTGAGAACTTTTGGAACATAG 57.367 37.500 0.00 0.00 39.30 2.23
153 255 4.016444 GGTCCTAATTGCAATTGGTGAGA 58.984 43.478 30.43 18.60 0.00 3.27
158 260 2.159254 CGGTGGTCCTAATTGCAATTGG 60.159 50.000 30.43 27.28 0.00 3.16
162 264 0.250945 TGCGGTGGTCCTAATTGCAA 60.251 50.000 0.00 0.00 0.00 4.08
179 281 0.955919 AACTCTACAAGGCGGCTTGC 60.956 55.000 41.51 0.00 45.38 4.01
180 282 0.798776 CAACTCTACAAGGCGGCTTG 59.201 55.000 40.40 40.40 39.98 4.01
225 327 7.972832 TCGAACCAAATGAAATTGTAGTACT 57.027 32.000 0.00 0.00 36.10 2.73
231 333 7.116233 GCTAATGTTCGAACCAAATGAAATTGT 59.884 33.333 24.78 0.00 36.10 2.71
239 341 8.085296 TGTAAATTGCTAATGTTCGAACCAAAT 58.915 29.630 24.78 11.56 0.00 2.32
248 350 6.292488 GGCATGCATGTAAATTGCTAATGTTC 60.292 38.462 26.79 4.67 40.77 3.18
257 359 4.061357 TCCATGGCATGCATGTAAATTG 57.939 40.909 26.79 16.48 0.00 2.32
262 364 4.757019 AAATTTCCATGGCATGCATGTA 57.243 36.364 26.79 16.96 0.00 2.29
271 373 8.253113 TCTCTCAATTTCTAAAATTTCCATGGC 58.747 33.333 6.96 0.00 0.00 4.40
434 536 6.966021 ACATGTGAATTACCACTGTTGTAAC 58.034 36.000 6.62 0.00 37.89 2.50
443 545 5.824624 AGATCCATGACATGTGAATTACCAC 59.175 40.000 14.26 0.00 37.55 4.16
494 596 0.997196 GACGCCTTGTATGGAACGAC 59.003 55.000 0.00 0.00 0.00 4.34
512 614 4.024387 GCCGCTTTCGTCCAAAATATATGA 60.024 41.667 0.00 0.00 0.00 2.15
532 634 2.890847 TTTTGGGTTGTTGTGCGCCG 62.891 55.000 4.18 0.00 0.00 6.46
534 636 1.761244 GCTTTTGGGTTGTTGTGCGC 61.761 55.000 0.00 0.00 0.00 6.09
607 709 7.639945 ACTTTTTGACACTAGACAAAGCATAC 58.360 34.615 0.00 0.00 39.73 2.39
642 744 6.151648 AGCAACATCAATTAATATGGATCGGG 59.848 38.462 3.80 0.00 0.00 5.14
689 791 5.352643 AATTCACGCACCTTTAGTACAAC 57.647 39.130 0.00 0.00 0.00 3.32
701 803 4.743151 TCCGACTCATATTAATTCACGCAC 59.257 41.667 0.00 0.00 0.00 5.34
719 821 1.521450 TTCTGGTCAGTCCGTCCGAC 61.521 60.000 0.00 0.00 42.32 4.79
809 947 8.702163 AACAACAACCTGAAAAATAAGAACAG 57.298 30.769 0.00 0.00 0.00 3.16
1121 1259 2.609350 CACAACCAATAGCAATGCCAC 58.391 47.619 0.00 0.00 0.00 5.01
1230 1368 2.930385 ATTGACCGCGGGATGCTGAG 62.930 60.000 31.76 0.00 43.27 3.35
1298 1436 2.097680 AGGGCGCAAATCCATTTTTG 57.902 45.000 10.83 0.00 39.16 2.44
1313 1451 3.767131 TGCTAAGTAAAAATCCCAAGGGC 59.233 43.478 0.00 0.00 34.68 5.19
1413 1551 4.949856 CACCCTGCTACATACCTTGATTTT 59.050 41.667 0.00 0.00 0.00 1.82
1419 1557 5.185249 CGATATACACCCTGCTACATACCTT 59.815 44.000 0.00 0.00 0.00 3.50
1438 1576 0.180406 GGGCTCCAACACACCGATAT 59.820 55.000 0.00 0.00 0.00 1.63
1517 1655 3.287222 GCATGGTAGCTTGTTAATCCCA 58.713 45.455 9.28 0.00 0.00 4.37
1538 1676 5.411977 AGGTAGTCGACATCATAGAATACGG 59.588 44.000 19.50 0.00 35.19 4.02
1675 1815 4.906537 ACCGGTTGCCGCCCTTTT 62.907 61.111 0.00 0.00 46.86 2.27
1723 1863 1.830587 TTCTGCTCGCCACCTCACAT 61.831 55.000 0.00 0.00 0.00 3.21
1787 1927 2.750814 CCCTAAGCCATTGGGTGAATT 58.249 47.619 8.43 0.00 35.32 2.17
1819 1959 1.412710 CCTTGGTATCCGCTAGAGCAA 59.587 52.381 1.89 0.00 42.21 3.91
2069 2209 5.183530 TGCATATATGAGAGGGGAAATGG 57.816 43.478 17.10 0.00 0.00 3.16
2141 2285 6.284459 ACTCGATTCTCAAGAGACAAAACTT 58.716 36.000 0.00 0.00 37.14 2.66
2199 2343 6.293698 ACGGTATGTTCTCCTTTACAGTTTT 58.706 36.000 0.00 0.00 0.00 2.43
2200 2344 5.861727 ACGGTATGTTCTCCTTTACAGTTT 58.138 37.500 0.00 0.00 0.00 2.66
2201 2345 5.011329 TGACGGTATGTTCTCCTTTACAGTT 59.989 40.000 0.00 0.00 0.00 3.16
2203 2347 5.068234 TGACGGTATGTTCTCCTTTACAG 57.932 43.478 0.00 0.00 0.00 2.74
2205 2349 6.803642 AGTATGACGGTATGTTCTCCTTTAC 58.196 40.000 0.00 0.00 0.00 2.01
2218 2387 5.942236 AGTACAAGACTTGAGTATGACGGTA 59.058 40.000 21.95 0.00 33.13 4.02
2504 3148 5.222130 ACACCTAATCCCATGTGAGACTTTT 60.222 40.000 0.00 0.00 33.08 2.27
2534 3179 4.637091 TGACATGTGCAGTGAATATCCAAG 59.363 41.667 1.15 0.00 0.00 3.61
2541 3186 5.047590 ACATTCATTGACATGTGCAGTGAAT 60.048 36.000 25.52 25.52 46.72 2.57
2551 3196 6.373186 ACTATGCTCACATTCATTGACATG 57.627 37.500 0.00 0.00 37.74 3.21
2604 3249 9.184523 CAATGGTATCCTCCAACTATGTTTTAA 57.815 33.333 0.00 0.00 41.09 1.52
2605 3250 8.333235 ACAATGGTATCCTCCAACTATGTTTTA 58.667 33.333 0.00 0.00 41.09 1.52
2703 3348 6.653320 ACGAATAAAGCAAGGTGATAACTTCA 59.347 34.615 0.00 0.00 0.00 3.02
2721 3366 9.438228 TGTTGTCAATGGTTATAAGACGAATAA 57.562 29.630 0.00 0.00 32.08 1.40
2823 3469 4.917415 CAGGCAATGAAAAGAAAACTACCG 59.083 41.667 0.00 0.00 0.00 4.02
2824 3470 5.230182 CCAGGCAATGAAAAGAAAACTACC 58.770 41.667 0.00 0.00 0.00 3.18
2843 3489 3.356529 AAACCTCTCTACATTGCCAGG 57.643 47.619 0.00 0.00 0.00 4.45
2844 3490 4.074970 ACAAAACCTCTCTACATTGCCAG 58.925 43.478 0.00 0.00 0.00 4.85
2845 3491 4.072131 GACAAAACCTCTCTACATTGCCA 58.928 43.478 0.00 0.00 0.00 4.92
2928 3575 0.254178 ATTCAGCGGACCAATGCTCT 59.746 50.000 0.00 0.00 40.03 4.09
2930 3577 0.254178 AGATTCAGCGGACCAATGCT 59.746 50.000 0.00 0.00 43.58 3.79
3019 3699 2.576648 GGAGGAGGGGTGTGAATAGTTT 59.423 50.000 0.00 0.00 0.00 2.66
3020 3700 2.197465 GGAGGAGGGGTGTGAATAGTT 58.803 52.381 0.00 0.00 0.00 2.24
3022 3702 1.132500 GGGAGGAGGGGTGTGAATAG 58.868 60.000 0.00 0.00 0.00 1.73
3024 3704 0.621862 GAGGGAGGAGGGGTGTGAAT 60.622 60.000 0.00 0.00 0.00 2.57
3025 3705 1.229529 GAGGGAGGAGGGGTGTGAA 60.230 63.158 0.00 0.00 0.00 3.18
3026 3706 2.450243 GAGGGAGGAGGGGTGTGA 59.550 66.667 0.00 0.00 0.00 3.58
3027 3707 3.077556 CGAGGGAGGAGGGGTGTG 61.078 72.222 0.00 0.00 0.00 3.82
3028 3708 3.273654 TCGAGGGAGGAGGGGTGT 61.274 66.667 0.00 0.00 0.00 4.16
3029 3709 2.760385 GTCGAGGGAGGAGGGGTG 60.760 72.222 0.00 0.00 0.00 4.61
3030 3710 4.444081 CGTCGAGGGAGGAGGGGT 62.444 72.222 0.00 0.00 0.00 4.95
3031 3711 4.444081 ACGTCGAGGGAGGAGGGG 62.444 72.222 10.27 0.00 0.00 4.79
3032 3712 3.141488 CACGTCGAGGGAGGAGGG 61.141 72.222 10.27 0.00 0.00 4.30
3033 3713 3.827898 GCACGTCGAGGGAGGAGG 61.828 72.222 10.27 0.00 0.00 4.30
3034 3714 3.827898 GGCACGTCGAGGGAGGAG 61.828 72.222 10.27 0.00 0.00 3.69
3069 3749 4.683432 GCCATCGATCTAGGGCAC 57.317 61.111 17.17 0.00 45.60 5.01
3071 3751 1.294780 CTGGCCATCGATCTAGGGC 59.705 63.158 14.10 14.10 45.57 5.19
3072 3752 1.294780 GCTGGCCATCGATCTAGGG 59.705 63.158 5.51 0.00 0.00 3.53
3073 3753 1.080230 CGCTGGCCATCGATCTAGG 60.080 63.158 24.25 0.06 0.00 3.02
3074 3754 0.387878 GTCGCTGGCCATCGATCTAG 60.388 60.000 31.94 7.50 37.06 2.43
3075 3755 0.823769 AGTCGCTGGCCATCGATCTA 60.824 55.000 31.94 9.48 37.06 1.98
3076 3756 2.081425 GAGTCGCTGGCCATCGATCT 62.081 60.000 31.94 27.48 37.06 2.75
3077 3757 1.663074 GAGTCGCTGGCCATCGATC 60.663 63.158 31.94 24.18 37.06 3.69
3078 3758 2.419198 GAGTCGCTGGCCATCGAT 59.581 61.111 31.94 20.99 37.06 3.59
3079 3759 4.193334 CGAGTCGCTGGCCATCGA 62.193 66.667 26.79 26.79 35.47 3.59
3090 3770 1.137825 GTTGGAGAGGAGCGAGTCG 59.862 63.158 8.54 8.54 0.00 4.18
3091 3771 0.109039 GTGTTGGAGAGGAGCGAGTC 60.109 60.000 0.00 0.00 0.00 3.36
3092 3772 0.540830 AGTGTTGGAGAGGAGCGAGT 60.541 55.000 0.00 0.00 0.00 4.18
3093 3773 0.605589 AAGTGTTGGAGAGGAGCGAG 59.394 55.000 0.00 0.00 0.00 5.03
3094 3774 0.603569 GAAGTGTTGGAGAGGAGCGA 59.396 55.000 0.00 0.00 0.00 4.93
3095 3775 0.390472 GGAAGTGTTGGAGAGGAGCG 60.390 60.000 0.00 0.00 0.00 5.03
3096 3776 0.980423 AGGAAGTGTTGGAGAGGAGC 59.020 55.000 0.00 0.00 0.00 4.70
3097 3777 1.552792 GGAGGAAGTGTTGGAGAGGAG 59.447 57.143 0.00 0.00 0.00 3.69
3098 3778 1.645710 GGAGGAAGTGTTGGAGAGGA 58.354 55.000 0.00 0.00 0.00 3.71
3099 3779 0.615850 GGGAGGAAGTGTTGGAGAGG 59.384 60.000 0.00 0.00 0.00 3.69
3100 3780 0.615850 GGGGAGGAAGTGTTGGAGAG 59.384 60.000 0.00 0.00 0.00 3.20
3101 3781 0.840722 GGGGGAGGAAGTGTTGGAGA 60.841 60.000 0.00 0.00 0.00 3.71
3102 3782 1.685820 GGGGGAGGAAGTGTTGGAG 59.314 63.158 0.00 0.00 0.00 3.86
3103 3783 3.916184 GGGGGAGGAAGTGTTGGA 58.084 61.111 0.00 0.00 0.00 3.53
3181 3861 3.839432 GAGGAAGAGACCCCGCCG 61.839 72.222 0.00 0.00 0.00 6.46
3182 3862 3.471806 GGAGGAAGAGACCCCGCC 61.472 72.222 0.00 0.00 35.32 6.13
3183 3863 1.962321 GAAGGAGGAAGAGACCCCGC 61.962 65.000 0.00 0.00 0.00 6.13
3184 3864 1.331399 GGAAGGAGGAAGAGACCCCG 61.331 65.000 0.00 0.00 0.00 5.73
3185 3865 0.043485 AGGAAGGAGGAAGAGACCCC 59.957 60.000 0.00 0.00 0.00 4.95
3186 3866 1.959710 AAGGAAGGAGGAAGAGACCC 58.040 55.000 0.00 0.00 0.00 4.46
3187 3867 2.026729 CCAAAGGAAGGAGGAAGAGACC 60.027 54.545 0.00 0.00 0.00 3.85
3188 3868 2.640332 ACCAAAGGAAGGAGGAAGAGAC 59.360 50.000 0.00 0.00 0.00 3.36
3189 3869 2.907042 GACCAAAGGAAGGAGGAAGAGA 59.093 50.000 0.00 0.00 0.00 3.10
3190 3870 2.639839 TGACCAAAGGAAGGAGGAAGAG 59.360 50.000 0.00 0.00 0.00 2.85
3191 3871 2.701551 TGACCAAAGGAAGGAGGAAGA 58.298 47.619 0.00 0.00 0.00 2.87
3192 3872 3.615155 GATGACCAAAGGAAGGAGGAAG 58.385 50.000 0.00 0.00 0.00 3.46
3193 3873 2.027192 CGATGACCAAAGGAAGGAGGAA 60.027 50.000 0.00 0.00 0.00 3.36
3194 3874 1.555075 CGATGACCAAAGGAAGGAGGA 59.445 52.381 0.00 0.00 0.00 3.71
3195 3875 1.279271 ACGATGACCAAAGGAAGGAGG 59.721 52.381 0.00 0.00 0.00 4.30
3196 3876 2.350522 CACGATGACCAAAGGAAGGAG 58.649 52.381 0.00 0.00 0.00 3.69
3197 3877 1.003118 CCACGATGACCAAAGGAAGGA 59.997 52.381 0.00 0.00 0.00 3.36
3198 3878 1.453155 CCACGATGACCAAAGGAAGG 58.547 55.000 0.00 0.00 0.00 3.46
3199 3879 0.804989 GCCACGATGACCAAAGGAAG 59.195 55.000 0.00 0.00 0.00 3.46
3200 3880 0.953471 CGCCACGATGACCAAAGGAA 60.953 55.000 0.00 0.00 0.00 3.36
3201 3881 1.375396 CGCCACGATGACCAAAGGA 60.375 57.895 0.00 0.00 0.00 3.36
3202 3882 2.398554 CCGCCACGATGACCAAAGG 61.399 63.158 0.00 0.00 0.00 3.11
3203 3883 3.039202 GCCGCCACGATGACCAAAG 62.039 63.158 0.00 0.00 0.00 2.77
3204 3884 3.053291 GCCGCCACGATGACCAAA 61.053 61.111 0.00 0.00 0.00 3.28
3205 3885 3.620419 ATGCCGCCACGATGACCAA 62.620 57.895 0.00 0.00 0.00 3.67
3206 3886 4.094646 ATGCCGCCACGATGACCA 62.095 61.111 0.00 0.00 0.00 4.02
3207 3887 3.272334 GATGCCGCCACGATGACC 61.272 66.667 0.00 0.00 0.00 4.02
3208 3888 1.889105 ATGATGCCGCCACGATGAC 60.889 57.895 0.00 0.00 0.00 3.06
3209 3889 1.888638 CATGATGCCGCCACGATGA 60.889 57.895 0.00 0.00 0.00 2.92
3210 3890 2.635338 CATGATGCCGCCACGATG 59.365 61.111 0.00 0.00 0.00 3.84
3211 3891 2.592574 CCATGATGCCGCCACGAT 60.593 61.111 0.00 0.00 0.00 3.73
3212 3892 4.854924 CCCATGATGCCGCCACGA 62.855 66.667 0.00 0.00 0.00 4.35
3214 3894 3.211963 GACCCATGATGCCGCCAC 61.212 66.667 0.00 0.00 0.00 5.01
3215 3895 4.854924 CGACCCATGATGCCGCCA 62.855 66.667 0.00 0.00 0.00 5.69
3218 3898 2.454832 ATAGCCGACCCATGATGCCG 62.455 60.000 0.00 0.00 0.00 5.69
3219 3899 0.957395 CATAGCCGACCCATGATGCC 60.957 60.000 0.00 0.00 0.00 4.40
3220 3900 1.580845 GCATAGCCGACCCATGATGC 61.581 60.000 0.00 0.00 33.59 3.91
3221 3901 1.293963 CGCATAGCCGACCCATGATG 61.294 60.000 0.00 0.00 0.00 3.07
3222 3902 1.004560 CGCATAGCCGACCCATGAT 60.005 57.895 0.00 0.00 0.00 2.45
3223 3903 2.421314 CGCATAGCCGACCCATGA 59.579 61.111 0.00 0.00 0.00 3.07
3224 3904 2.666190 CCGCATAGCCGACCCATG 60.666 66.667 0.00 0.00 0.00 3.66
3225 3905 4.626081 GCCGCATAGCCGACCCAT 62.626 66.667 0.00 0.00 0.00 4.00
3254 3934 2.892425 GAATCCAGCCAGACGCCG 60.892 66.667 0.00 0.00 38.78 6.46
3255 3935 1.522580 GAGAATCCAGCCAGACGCC 60.523 63.158 0.00 0.00 38.78 5.68
3256 3936 1.880340 CGAGAATCCAGCCAGACGC 60.880 63.158 0.00 0.00 37.98 5.19
3257 3937 0.387202 ATCGAGAATCCAGCCAGACG 59.613 55.000 0.00 0.00 0.00 4.18
3258 3938 1.539929 CCATCGAGAATCCAGCCAGAC 60.540 57.143 0.00 0.00 0.00 3.51
3259 3939 0.755079 CCATCGAGAATCCAGCCAGA 59.245 55.000 0.00 0.00 0.00 3.86
3260 3940 0.883814 GCCATCGAGAATCCAGCCAG 60.884 60.000 0.00 0.00 0.00 4.85
3261 3941 1.146930 GCCATCGAGAATCCAGCCA 59.853 57.895 0.00 0.00 0.00 4.75
3262 3942 1.958205 CGCCATCGAGAATCCAGCC 60.958 63.158 0.00 0.00 38.10 4.85
3263 3943 1.958205 CCGCCATCGAGAATCCAGC 60.958 63.158 0.00 0.00 38.10 4.85
3264 3944 1.301244 CCCGCCATCGAGAATCCAG 60.301 63.158 0.00 0.00 38.10 3.86
3265 3945 2.807107 CCCCGCCATCGAGAATCCA 61.807 63.158 0.00 0.00 38.10 3.41
3266 3946 2.031163 CCCCGCCATCGAGAATCC 59.969 66.667 0.00 0.00 38.10 3.01
3267 3947 1.301009 GTCCCCGCCATCGAGAATC 60.301 63.158 0.00 0.00 38.10 2.52
3268 3948 2.822399 GTCCCCGCCATCGAGAAT 59.178 61.111 0.00 0.00 38.10 2.40
3269 3949 3.833645 CGTCCCCGCCATCGAGAA 61.834 66.667 0.00 0.00 38.10 2.87
3279 3959 4.891727 CGAATCCAGCCGTCCCCG 62.892 72.222 0.00 0.00 0.00 5.73
3280 3960 4.547367 CCGAATCCAGCCGTCCCC 62.547 72.222 0.00 0.00 0.00 4.81
3288 3968 3.391665 AAGAGGCCGCCGAATCCAG 62.392 63.158 1.49 0.00 0.00 3.86
3289 3969 3.399181 AAGAGGCCGCCGAATCCA 61.399 61.111 1.49 0.00 0.00 3.41
3290 3970 2.897350 CAAGAGGCCGCCGAATCC 60.897 66.667 1.49 0.00 0.00 3.01
3291 3971 2.897350 CCAAGAGGCCGCCGAATC 60.897 66.667 1.49 0.00 0.00 2.52
3302 3982 2.060980 ACCGCCTCCTAGCCAAGAG 61.061 63.158 0.00 0.00 0.00 2.85
3303 3983 2.038975 ACCGCCTCCTAGCCAAGA 59.961 61.111 0.00 0.00 0.00 3.02
3304 3984 2.187946 CACCGCCTCCTAGCCAAG 59.812 66.667 0.00 0.00 0.00 3.61
3305 3985 3.399181 CCACCGCCTCCTAGCCAA 61.399 66.667 0.00 0.00 0.00 4.52
3306 3986 4.715130 ACCACCGCCTCCTAGCCA 62.715 66.667 0.00 0.00 0.00 4.75
3307 3987 4.162690 CACCACCGCCTCCTAGCC 62.163 72.222 0.00 0.00 0.00 3.93
3308 3988 4.840005 GCACCACCGCCTCCTAGC 62.840 72.222 0.00 0.00 0.00 3.42
3309 3989 2.650813 GATGCACCACCGCCTCCTAG 62.651 65.000 0.00 0.00 0.00 3.02
3310 3990 2.687200 ATGCACCACCGCCTCCTA 60.687 61.111 0.00 0.00 0.00 2.94
3311 3991 4.101448 GATGCACCACCGCCTCCT 62.101 66.667 0.00 0.00 0.00 3.69
3313 3993 4.760047 ACGATGCACCACCGCCTC 62.760 66.667 0.00 0.00 0.00 4.70
3317 3997 3.422303 CACCACGATGCACCACCG 61.422 66.667 0.00 0.00 0.00 4.94
3318 3998 3.055719 CCACCACGATGCACCACC 61.056 66.667 0.00 0.00 0.00 4.61
3319 3999 3.737172 GCCACCACGATGCACCAC 61.737 66.667 0.00 0.00 0.00 4.16
3346 4026 4.399395 GACCCCGACCGAAACCCC 62.399 72.222 0.00 0.00 0.00 4.95
3347 4027 4.747529 CGACCCCGACCGAAACCC 62.748 72.222 0.00 0.00 38.22 4.11
3348 4028 3.921767 GACGACCCCGACCGAAACC 62.922 68.421 0.00 0.00 39.50 3.27
3349 4029 2.431430 GACGACCCCGACCGAAAC 60.431 66.667 0.00 0.00 39.50 2.78
3350 4030 2.598394 AGACGACCCCGACCGAAA 60.598 61.111 0.00 0.00 39.50 3.46
3351 4031 3.058160 GAGACGACCCCGACCGAA 61.058 66.667 0.00 0.00 39.50 4.30
3354 4034 2.827642 ATCGAGACGACCCCGACC 60.828 66.667 0.00 0.00 39.18 4.79
3355 4035 1.774046 GAGATCGAGACGACCCCGAC 61.774 65.000 0.00 0.00 39.18 4.79
3356 4036 1.523258 GAGATCGAGACGACCCCGA 60.523 63.158 0.00 0.00 39.18 5.14
3357 4037 2.883468 CGAGATCGAGACGACCCCG 61.883 68.421 0.00 0.00 43.02 5.73
3358 4038 1.523258 TCGAGATCGAGACGACCCC 60.523 63.158 0.00 0.00 44.22 4.95
3359 4039 4.121691 TCGAGATCGAGACGACCC 57.878 61.111 0.00 0.00 44.22 4.46
3368 4048 0.236187 GACGTCCCAGATCGAGATCG 59.764 60.000 3.51 0.00 42.48 3.69
3369 4049 0.236187 CGACGTCCCAGATCGAGATC 59.764 60.000 10.58 5.00 38.10 2.75
3370 4050 1.787057 GCGACGTCCCAGATCGAGAT 61.787 60.000 10.58 0.00 38.10 2.75
3371 4051 2.470362 GCGACGTCCCAGATCGAGA 61.470 63.158 10.58 0.00 38.10 4.04
3372 4052 2.024871 GCGACGTCCCAGATCGAG 59.975 66.667 10.58 0.00 38.10 4.04
3373 4053 3.515286 GGCGACGTCCCAGATCGA 61.515 66.667 10.58 0.00 38.10 3.59
3463 4143 3.084646 TGTCACACCCACCACCGT 61.085 61.111 0.00 0.00 0.00 4.83
3502 4182 2.169352 CCAGACAAGGATGGAATCTCGT 59.831 50.000 0.00 0.00 44.71 4.18
3505 4185 2.507471 GGACCAGACAAGGATGGAATCT 59.493 50.000 0.00 0.00 44.71 2.40
3520 4200 2.416547 CACAATCGCTAACAAGGACCAG 59.583 50.000 0.00 0.00 0.00 4.00
3530 4210 4.300189 ACAAAAGCAACACAATCGCTAA 57.700 36.364 0.00 0.00 34.11 3.09
3531 4211 3.980646 ACAAAAGCAACACAATCGCTA 57.019 38.095 0.00 0.00 34.11 4.26
3538 4262 3.499157 GGGTACGATACAAAAGCAACACA 59.501 43.478 0.00 0.00 0.00 3.72
3542 4266 4.546829 AGAGGGTACGATACAAAAGCAA 57.453 40.909 0.00 0.00 0.00 3.91
3591 4317 1.004440 GTCGCTGCTCCCTTCAACT 60.004 57.895 0.00 0.00 0.00 3.16
3632 4358 2.669113 GCGATTTTCATCAGCAGTTGCA 60.669 45.455 6.90 0.00 45.16 4.08
3676 4402 0.960364 ACATCAAAGACGCCGCCAAT 60.960 50.000 0.00 0.00 0.00 3.16
3677 4403 1.573829 GACATCAAAGACGCCGCCAA 61.574 55.000 0.00 0.00 0.00 4.52
3709 4435 1.852067 AAACTGCAACGACGATGCCC 61.852 55.000 24.68 2.03 43.16 5.36
3733 4459 1.153349 GAGCATCCCGAACCTGGTC 60.153 63.158 0.00 0.00 0.00 4.02
3740 4466 3.089874 CCCCCAGAGCATCCCGAA 61.090 66.667 0.00 0.00 33.66 4.30
3815 4541 3.943137 AACGATGCCCCCAGGAGGA 62.943 63.158 0.00 0.00 38.24 3.71
3935 4665 1.656818 CCATTCACACACGCCCATCC 61.657 60.000 0.00 0.00 0.00 3.51
3950 4680 2.108514 CATCCTGCGCGTGTCCATT 61.109 57.895 8.43 0.00 0.00 3.16
4024 4754 4.105537 TCCATCTCTAGAGCAGGTACTCAT 59.894 45.833 22.15 5.01 39.26 2.90
4026 4756 4.093472 TCCATCTCTAGAGCAGGTACTC 57.907 50.000 22.15 0.00 34.60 2.59
4123 4853 1.858739 TAAAGCCGGATGCCCCAACT 61.859 55.000 5.05 0.00 42.71 3.16
4160 4890 5.428253 GAGCCTAATACCAAACAGACATCA 58.572 41.667 0.00 0.00 0.00 3.07
4197 4927 4.837218 ACTCCTATCCCCTTGATGAAGAT 58.163 43.478 0.00 0.00 34.76 2.40
4198 4928 4.286813 ACTCCTATCCCCTTGATGAAGA 57.713 45.455 0.00 0.00 34.76 2.87
4416 5148 6.687081 TTAACGCAATAAATAGAACCCCAG 57.313 37.500 0.00 0.00 0.00 4.45
4447 5179 0.107831 TCCACCTTCGGACCAACAAG 59.892 55.000 0.00 0.00 0.00 3.16
4454 5186 0.605589 CCTTGGTTCCACCTTCGGAC 60.606 60.000 0.00 0.00 39.58 4.79
4474 5206 6.035327 GCGCCTTTCGAACTCTACTTTTAATA 59.965 38.462 0.00 0.00 41.67 0.98
4507 5239 6.207691 TCCAAGAAAAGACCTTTGTTTCTG 57.792 37.500 0.00 0.00 39.97 3.02
4523 5255 4.931601 CGATGAGATCAGTTGTTCCAAGAA 59.068 41.667 0.00 0.00 0.00 2.52
4546 5278 2.288030 GCTATGCATGGCACTTTCATCC 60.288 50.000 28.02 0.00 43.04 3.51
4582 5314 3.850752 TGCCTTTTCTAACCCATCCAAA 58.149 40.909 0.00 0.00 0.00 3.28
4590 5322 0.242825 GCCGGTTGCCTTTTCTAACC 59.757 55.000 1.90 0.00 40.29 2.85
4608 5340 1.268999 TGCGTGTGGAGTCAAAATTGC 60.269 47.619 0.00 0.00 0.00 3.56
4644 5376 2.617021 CCCTTGTAAACGGTACCATGCT 60.617 50.000 13.54 0.00 0.00 3.79
4674 5406 3.125607 CCACCACGCGCCTATCTA 58.874 61.111 5.73 0.00 0.00 1.98
4741 5473 3.621268 GTGACATAATGGCAAGCTCGTTA 59.379 43.478 0.00 0.00 36.98 3.18
4775 5507 7.011857 GCATCCAAAAAGTTTTACCACATTTCA 59.988 33.333 0.24 0.00 0.00 2.69
4777 5509 7.012232 CAGCATCCAAAAAGTTTTACCACATTT 59.988 33.333 0.24 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.