Multiple sequence alignment - TraesCS2A01G101400

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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 TraesCS2A01G101400 chr2A 100.000 3957 0 0 1 3957 54475275 54471319 0.000000e+00 7308.0
1 TraesCS2A01G101400 chr2A 79.916 1190 132 53 1872 3035 54112545 54113653 0.000000e+00 774.0
2 TraesCS2A01G101400 chr2A 87.988 641 61 10 1124 1761 54012291 54012918 0.000000e+00 743.0
3 TraesCS2A01G101400 chr2A 82.010 806 89 28 1876 2656 54012980 54013754 5.580000e-178 634.0
4 TraesCS2A01G101400 chr2A 85.533 553 65 9 1216 1761 54111937 54112481 7.420000e-157 564.0
5 TraesCS2A01G101400 chr2A 79.487 117 11 8 1081 1194 54111830 54111936 1.970000e-08 71.3
6 TraesCS2A01G101400 chr2B 87.220 2942 213 66 754 3648 83955798 83952973 0.000000e+00 3199.0
7 TraesCS2A01G101400 chr2B 81.672 1615 199 41 1080 2680 82851599 82853130 0.000000e+00 1253.0
8 TraesCS2A01G101400 chr2B 87.482 711 59 20 2 706 83956566 83955880 0.000000e+00 793.0
9 TraesCS2A01G101400 chr2B 81.189 1026 100 41 1874 2873 82361935 82362893 0.000000e+00 739.0
10 TraesCS2A01G101400 chr2B 86.897 580 66 8 1164 1741 82361285 82361856 3.330000e-180 641.0
11 TraesCS2A01G101400 chr2B 83.460 659 66 19 2096 2742 82714879 82715506 1.230000e-159 573.0
12 TraesCS2A01G101400 chr2B 85.744 477 58 7 1265 1741 82714081 82714547 2.750000e-136 496.0
13 TraesCS2A01G101400 chr2B 83.854 192 19 7 1082 1272 82713707 82713887 5.260000e-39 172.0
14 TraesCS2A01G101400 chr2B 81.818 242 11 13 3741 3957 83952958 83952725 5.260000e-39 172.0
15 TraesCS2A01G101400 chr2D 89.093 2338 126 46 754 3043 53648606 53650862 0.000000e+00 2785.0
16 TraesCS2A01G101400 chr2D 87.627 687 65 11 1080 1761 52851943 52852614 0.000000e+00 780.0
17 TraesCS2A01G101400 chr2D 88.310 633 59 9 1131 1761 52646920 52647539 0.000000e+00 745.0
18 TraesCS2A01G101400 chr2D 83.827 742 76 21 2096 2816 52852942 52853660 0.000000e+00 665.0
19 TraesCS2A01G101400 chr2D 81.345 788 89 27 2096 2869 52647867 52648610 4.400000e-164 588.0
20 TraesCS2A01G101400 chr2D 91.337 404 31 4 25 427 53647664 53648064 2.080000e-152 549.0
21 TraesCS2A01G101400 chr2D 86.268 284 26 7 424 703 53648250 53648524 2.990000e-76 296.0
22 TraesCS2A01G101400 chr2D 81.857 237 12 12 3744 3957 53651532 53651760 1.890000e-38 171.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G101400 chr2A 54471319 54475275 3956 True 7308.000000 7308 100.000000 1 3957 1 chr2A.!!$R1 3956
1 TraesCS2A01G101400 chr2A 54012291 54013754 1463 False 688.500000 743 84.999000 1124 2656 2 chr2A.!!$F1 1532
2 TraesCS2A01G101400 chr2A 54111830 54113653 1823 False 469.766667 774 81.645333 1081 3035 3 chr2A.!!$F2 1954
3 TraesCS2A01G101400 chr2B 83952725 83956566 3841 True 1388.000000 3199 85.506667 2 3957 3 chr2B.!!$R1 3955
4 TraesCS2A01G101400 chr2B 82851599 82853130 1531 False 1253.000000 1253 81.672000 1080 2680 1 chr2B.!!$F1 1600
5 TraesCS2A01G101400 chr2B 82361285 82362893 1608 False 690.000000 739 84.043000 1164 2873 2 chr2B.!!$F2 1709
6 TraesCS2A01G101400 chr2B 82713707 82715506 1799 False 413.666667 573 84.352667 1082 2742 3 chr2B.!!$F3 1660
7 TraesCS2A01G101400 chr2D 53647664 53651760 4096 False 950.250000 2785 87.138750 25 3957 4 chr2D.!!$F3 3932
8 TraesCS2A01G101400 chr2D 52851943 52853660 1717 False 722.500000 780 85.727000 1080 2816 2 chr2D.!!$F2 1736
9 TraesCS2A01G101400 chr2D 52646920 52648610 1690 False 666.500000 745 84.827500 1131 2869 2 chr2D.!!$F1 1738

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
668 862 0.179134 CAAGTCGTCTCGGTCCATCC 60.179 60.0 0.0 0.00 0.0 3.51 F
2280 2890 0.179111 CTACTTCTTCATGCCGGCGA 60.179 55.0 23.9 11.45 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2440 3056 0.813184 TATCACGAACGAGGTGTCCC 59.187 55.0 0.14 0.0 36.76 4.46 R
3751 4452 0.107508 ATCACGCCCATCCAACTGAG 60.108 55.0 0.00 0.0 0.00 3.35 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
19 20 2.686558 CAATGGGTGATATTTCGCGG 57.313 50.000 6.13 0.00 32.95 6.46
20 21 1.946768 CAATGGGTGATATTTCGCGGT 59.053 47.619 6.13 0.00 32.95 5.68
21 22 1.593196 ATGGGTGATATTTCGCGGTG 58.407 50.000 6.13 0.00 32.95 4.94
39 40 3.188100 TCGCAGCGCATTTCCTCG 61.188 61.111 10.87 1.76 0.00 4.63
41 42 4.543084 GCAGCGCATTTCCTCGGC 62.543 66.667 11.47 0.00 0.00 5.54
100 101 5.994668 TCAAGCATTTGGTTTGGATTTTACC 59.005 36.000 0.00 0.00 38.17 2.85
101 102 5.559148 AGCATTTGGTTTGGATTTTACCA 57.441 34.783 0.00 0.00 40.06 3.25
111 112 4.112634 TGGATTTTACCACAAGGCTTCT 57.887 40.909 0.00 0.00 39.06 2.85
134 135 5.358298 ACAGTCTCCGTTAGAAATTTTGC 57.642 39.130 0.00 0.00 35.47 3.68
146 147 5.873179 AGAAATTTTGCCTCGTCGATAAA 57.127 34.783 0.00 0.00 0.00 1.40
165 166 1.045407 ATCCGCGGATTTACCAGCTA 58.955 50.000 34.60 5.94 38.90 3.32
173 174 1.211949 GATTTACCAGCTACCAGGCCA 59.788 52.381 5.01 0.00 0.00 5.36
180 181 0.252742 AGCTACCAGGCCAGGTTACT 60.253 55.000 26.59 19.31 43.08 2.24
217 218 1.204792 GCATTTTCACGTGCCGTTTT 58.795 45.000 11.67 0.00 38.32 2.43
218 219 2.223502 TGCATTTTCACGTGCCGTTTTA 60.224 40.909 11.67 0.00 38.32 1.52
219 220 2.983803 GCATTTTCACGTGCCGTTTTAT 59.016 40.909 11.67 0.00 38.32 1.40
223 224 1.205568 CACGTGCCGTTTTATGCGT 59.794 52.632 0.82 0.00 38.32 5.24
230 231 1.958417 CCGTTTTATGCGTTGTCCAC 58.042 50.000 0.00 0.00 0.00 4.02
284 285 0.467384 AGAGGACAAGCATGGATCGG 59.533 55.000 0.00 0.00 0.00 4.18
314 315 1.744114 GCCCGGTGAGAAAAGGATCTC 60.744 57.143 0.00 0.00 44.96 2.75
315 316 1.834263 CCCGGTGAGAAAAGGATCTCT 59.166 52.381 0.00 0.00 44.98 3.10
316 317 2.419297 CCCGGTGAGAAAAGGATCTCTG 60.419 54.545 0.00 0.00 44.98 3.35
317 318 2.234908 CCGGTGAGAAAAGGATCTCTGT 59.765 50.000 0.00 0.00 44.98 3.41
346 347 3.486108 CGATTTAACCCTCGATTCGACAG 59.514 47.826 4.29 1.94 37.05 3.51
354 355 2.508891 CGATTCGACAGCGCAGACC 61.509 63.158 11.47 0.00 37.46 3.85
385 386 2.257676 GCCGGAACTCGTCGAACT 59.742 61.111 5.05 0.00 37.11 3.01
471 661 2.678190 GCCACAGTAGAAGGCGAATTCT 60.678 50.000 3.52 7.57 42.20 2.40
472 662 3.600388 CCACAGTAGAAGGCGAATTCTT 58.400 45.455 3.52 0.00 40.08 2.52
529 719 3.057174 ACACACAAAAACAGCGGAGAAAA 60.057 39.130 0.00 0.00 0.00 2.29
543 736 2.913590 GGAGAAAACTGACGCGTACTAC 59.086 50.000 13.97 0.00 0.00 2.73
544 737 3.365767 GGAGAAAACTGACGCGTACTACT 60.366 47.826 13.97 5.57 0.00 2.57
545 738 4.142816 GGAGAAAACTGACGCGTACTACTA 60.143 45.833 13.97 0.00 0.00 1.82
546 739 4.967437 AGAAAACTGACGCGTACTACTAG 58.033 43.478 13.97 6.65 0.00 2.57
547 740 4.453819 AGAAAACTGACGCGTACTACTAGT 59.546 41.667 13.97 7.32 0.00 2.57
548 741 5.639506 AGAAAACTGACGCGTACTACTAGTA 59.360 40.000 13.97 1.89 0.00 1.82
549 742 5.462034 AAACTGACGCGTACTACTAGTAG 57.538 43.478 25.30 25.30 39.04 2.57
551 744 4.499183 ACTGACGCGTACTACTAGTAGTT 58.501 43.478 34.30 19.83 43.35 2.24
552 745 5.651530 ACTGACGCGTACTACTAGTAGTTA 58.348 41.667 34.30 19.91 43.35 2.24
553 746 5.746245 ACTGACGCGTACTACTAGTAGTTAG 59.254 44.000 34.30 27.69 43.35 2.34
556 749 4.742659 ACGCGTACTACTAGTAGTTAGAGC 59.257 45.833 34.30 28.87 43.35 4.09
558 751 4.742659 GCGTACTACTAGTAGTTAGAGCGT 59.257 45.833 34.30 14.85 43.35 5.07
559 752 5.915758 GCGTACTACTAGTAGTTAGAGCGTA 59.084 44.000 34.30 15.58 43.35 4.42
589 782 2.040544 CCGGCACCATCACTTCCAC 61.041 63.158 0.00 0.00 0.00 4.02
621 814 2.412847 GGTTCAGCCGTTGAAATCTTCG 60.413 50.000 0.00 0.00 46.85 3.79
625 818 1.908066 GCCGTTGAAATCTTCGCCGT 61.908 55.000 0.00 0.00 0.00 5.68
643 837 1.858458 CGTCGCGTGTGGATAATCATT 59.142 47.619 5.77 0.00 0.00 2.57
644 838 2.347568 CGTCGCGTGTGGATAATCATTG 60.348 50.000 5.77 0.00 0.00 2.82
645 839 2.032894 GTCGCGTGTGGATAATCATTGG 60.033 50.000 5.77 0.00 0.00 3.16
646 840 1.939934 CGCGTGTGGATAATCATTGGT 59.060 47.619 0.00 0.00 0.00 3.67
647 841 2.286359 CGCGTGTGGATAATCATTGGTG 60.286 50.000 0.00 0.00 0.00 4.17
665 859 2.649034 GCAAGTCGTCTCGGTCCA 59.351 61.111 0.00 0.00 0.00 4.02
668 862 0.179134 CAAGTCGTCTCGGTCCATCC 60.179 60.000 0.00 0.00 0.00 3.51
670 864 1.139095 GTCGTCTCGGTCCATCCAC 59.861 63.158 0.00 0.00 35.57 4.02
679 873 3.770040 TCCATCCACGCCGTCTGG 61.770 66.667 4.14 4.14 38.77 3.86
707 919 4.647424 AAACTAGCTGGAGAGATCGAAG 57.353 45.455 3.17 0.00 0.00 3.79
710 922 4.783055 ACTAGCTGGAGAGATCGAAGTAA 58.217 43.478 3.17 0.00 0.00 2.24
712 924 5.652891 ACTAGCTGGAGAGATCGAAGTAAAA 59.347 40.000 3.17 0.00 0.00 1.52
713 925 5.407407 AGCTGGAGAGATCGAAGTAAAAA 57.593 39.130 0.00 0.00 0.00 1.94
748 960 8.530311 AGATTATAGCAGATGATTACACAGAGG 58.470 37.037 0.00 0.00 0.00 3.69
751 963 5.627182 AGCAGATGATTACACAGAGGAAT 57.373 39.130 0.00 0.00 0.00 3.01
752 964 6.737720 AGCAGATGATTACACAGAGGAATA 57.262 37.500 0.00 0.00 0.00 1.75
799 1066 3.369242 TCATTTGGACATGCTCATCCA 57.631 42.857 0.00 0.00 43.42 3.41
802 1069 2.704464 TTGGACATGCTCATCCAGAG 57.296 50.000 3.28 0.00 45.66 3.35
806 1073 0.545171 ACATGCTCATCCAGAGGGTG 59.455 55.000 0.00 0.00 44.86 4.61
810 1079 0.908198 GCTCATCCAGAGGGTGAAGT 59.092 55.000 0.11 0.00 44.86 3.01
865 1134 7.307989 CGGAGCAATTAATCACCATTAAGTAGG 60.308 40.741 0.00 0.00 37.78 3.18
878 1147 0.846693 AAGTAGGGGCTAAGCATGGG 59.153 55.000 0.00 0.00 0.00 4.00
896 1169 1.385528 GGGGTGCGGTAAATAAGTGG 58.614 55.000 0.00 0.00 0.00 4.00
972 1245 2.034305 ACGCCAGTCCGTAGCTATAAAG 59.966 50.000 0.00 0.00 40.08 1.85
1007 1281 1.363744 CGCTCCATTCCAGTGTTCTC 58.636 55.000 0.00 0.00 0.00 2.87
1032 1306 1.062587 CCAAAGCGTCCGATCAATCAC 59.937 52.381 0.00 0.00 0.00 3.06
1041 1315 4.548916 CGTCCGATCAATCACAGAAAATCG 60.549 45.833 0.00 0.00 36.63 3.34
1056 1330 4.284746 AGAAAATCGTCCCTCCATATCTCC 59.715 45.833 0.00 0.00 0.00 3.71
1077 1351 0.459489 CAGCTCTTCTTCCTCCTCCG 59.541 60.000 0.00 0.00 0.00 4.63
1078 1352 0.333312 AGCTCTTCTTCCTCCTCCGA 59.667 55.000 0.00 0.00 0.00 4.55
1104 1379 1.326213 CCTCAGCTCCCGTGTCATCT 61.326 60.000 0.00 0.00 0.00 2.90
1113 1388 1.276421 CCCGTGTCATCTGGTTCTTCT 59.724 52.381 0.00 0.00 0.00 2.85
1116 1391 2.996621 CGTGTCATCTGGTTCTTCTTCC 59.003 50.000 0.00 0.00 0.00 3.46
1117 1392 3.306364 CGTGTCATCTGGTTCTTCTTCCT 60.306 47.826 0.00 0.00 0.00 3.36
1119 1394 3.903714 TGTCATCTGGTTCTTCTTCCTCA 59.096 43.478 0.00 0.00 0.00 3.86
1120 1395 4.020751 TGTCATCTGGTTCTTCTTCCTCAG 60.021 45.833 0.00 0.00 0.00 3.35
1122 1397 5.028802 TCATCTGGTTCTTCTTCCTCAGAT 58.971 41.667 0.00 0.00 41.06 2.90
1123 1398 6.097554 GTCATCTGGTTCTTCTTCCTCAGATA 59.902 42.308 0.00 0.00 39.17 1.98
1124 1399 6.323482 TCATCTGGTTCTTCTTCCTCAGATAG 59.677 42.308 0.00 0.00 39.17 2.08
1125 1400 4.404073 TCTGGTTCTTCTTCCTCAGATAGC 59.596 45.833 0.00 0.00 0.00 2.97
1126 1401 3.131223 TGGTTCTTCTTCCTCAGATAGCG 59.869 47.826 0.00 0.00 0.00 4.26
1127 1402 3.381908 GGTTCTTCTTCCTCAGATAGCGA 59.618 47.826 0.00 0.00 0.00 4.93
1128 1403 4.142138 GGTTCTTCTTCCTCAGATAGCGAA 60.142 45.833 0.00 0.00 0.00 4.70
1129 1404 4.909696 TCTTCTTCCTCAGATAGCGAAG 57.090 45.455 0.00 0.00 35.48 3.79
1146 1441 2.226912 CGAAGAAGGCTAGTAGATCCGG 59.773 54.545 0.00 0.00 0.00 5.14
1147 1442 3.224269 GAAGAAGGCTAGTAGATCCGGT 58.776 50.000 0.00 0.00 0.00 5.28
1397 1895 4.244802 CGAGGCGAGAGGAGCGTC 62.245 72.222 0.00 1.39 43.55 5.19
1577 2093 1.900545 GACGGGGAAGGACAAGGAGG 61.901 65.000 0.00 0.00 0.00 4.30
1648 2164 2.693762 CGTCTTCTACACCGGCCGA 61.694 63.158 30.73 5.11 0.00 5.54
1774 2290 2.981400 TCGATTTTGCTTTTCCGTCC 57.019 45.000 0.00 0.00 0.00 4.79
1775 2291 2.222886 TCGATTTTGCTTTTCCGTCCA 58.777 42.857 0.00 0.00 0.00 4.02
1903 2425 2.098233 TCGCGCTCCGGATTTGTTC 61.098 57.895 3.57 0.00 37.59 3.18
1937 2466 5.828299 TTTTCCTCGTGTTGTTTTCTCAT 57.172 34.783 0.00 0.00 0.00 2.90
2081 2610 1.211190 GTACGCCTTCCTCGACGTT 59.789 57.895 1.75 0.00 39.78 3.99
2088 2671 0.237761 CTTCCTCGACGTTGACGACT 59.762 55.000 10.87 0.00 43.02 4.18
2090 2673 0.236711 TCCTCGACGTTGACGACTTC 59.763 55.000 10.87 0.00 43.02 3.01
2280 2890 0.179111 CTACTTCTTCATGCCGGCGA 60.179 55.000 23.90 11.45 0.00 5.54
2347 2957 2.192443 CATGGGGGAGCAGCAGAG 59.808 66.667 0.00 0.00 0.00 3.35
2423 3039 4.415332 TCGCTCGGCTTCGACACC 62.415 66.667 0.00 0.00 38.07 4.16
2459 3078 0.813184 GGGACACCTCGTTCGTGATA 59.187 55.000 6.34 0.00 35.17 2.15
2468 3087 0.095935 CGTTCGTGATACCGTCGTCT 59.904 55.000 0.00 0.00 0.00 4.18
2497 3122 0.385029 CTCGATCTGGAGGAGCTGTG 59.615 60.000 0.00 0.00 0.00 3.66
2584 3211 4.500116 GGACCGGAGCGTCTCAGC 62.500 72.222 9.46 0.00 33.07 4.26
2596 3223 0.742635 GTCTCAGCTTGCTGGTAGCC 60.743 60.000 20.62 0.25 41.51 3.93
2602 3231 1.139853 AGCTTGCTGGTAGCCATAGAC 59.860 52.381 0.00 0.00 41.51 2.59
2657 3291 9.643693 ATTGATTAGTTGCTTCATTAACTTTGG 57.356 29.630 0.00 0.00 38.11 3.28
2658 3292 8.177119 TGATTAGTTGCTTCATTAACTTTGGT 57.823 30.769 0.00 0.00 38.11 3.67
2659 3293 8.637986 TGATTAGTTGCTTCATTAACTTTGGTT 58.362 29.630 0.00 0.00 38.11 3.67
2717 3351 2.579787 GGAGGATCGTCGCGTGTG 60.580 66.667 5.77 0.00 34.37 3.82
2751 3397 2.789917 CAAGGCATGTGAGCGAGC 59.210 61.111 0.00 0.00 34.64 5.03
2775 3425 7.513968 GCGAGTGCTGATTAATCTTAATTAGG 58.486 38.462 16.24 2.03 37.28 2.69
2776 3426 7.360438 GCGAGTGCTGATTAATCTTAATTAGGG 60.360 40.741 16.24 0.81 37.28 3.53
2777 3427 7.657761 CGAGTGCTGATTAATCTTAATTAGGGT 59.342 37.037 16.24 0.00 37.28 4.34
2816 3466 4.624125 GCTAGGAGGCATCTGTAGTTTGTT 60.624 45.833 0.00 0.00 0.00 2.83
2817 3467 4.373156 AGGAGGCATCTGTAGTTTGTTT 57.627 40.909 0.00 0.00 0.00 2.83
2818 3468 4.074970 AGGAGGCATCTGTAGTTTGTTTG 58.925 43.478 0.00 0.00 0.00 2.93
2819 3469 3.821033 GGAGGCATCTGTAGTTTGTTTGT 59.179 43.478 0.00 0.00 0.00 2.83
2820 3470 5.001232 GGAGGCATCTGTAGTTTGTTTGTA 58.999 41.667 0.00 0.00 0.00 2.41
2821 3471 5.106673 GGAGGCATCTGTAGTTTGTTTGTAC 60.107 44.000 0.00 0.00 0.00 2.90
2822 3472 5.373222 AGGCATCTGTAGTTTGTTTGTACA 58.627 37.500 0.00 0.00 0.00 2.90
2823 3473 6.003950 AGGCATCTGTAGTTTGTTTGTACAT 58.996 36.000 0.00 0.00 33.44 2.29
2824 3474 7.165485 AGGCATCTGTAGTTTGTTTGTACATA 58.835 34.615 0.00 0.00 33.44 2.29
2825 3475 7.829211 AGGCATCTGTAGTTTGTTTGTACATAT 59.171 33.333 0.00 0.00 33.44 1.78
2889 3542 3.432890 GGTGAATTGGAGGGTGAGAGATC 60.433 52.174 0.00 0.00 0.00 2.75
2906 3559 3.288964 AGATCATACCGAGACCGAGTTT 58.711 45.455 0.00 0.00 38.22 2.66
2957 3610 8.946797 ATGGAAATGAATTATTCCCCTTCTAG 57.053 34.615 12.26 0.00 43.66 2.43
2958 3611 8.113114 TGGAAATGAATTATTCCCCTTCTAGA 57.887 34.615 12.26 0.00 43.66 2.43
2959 3612 8.736675 TGGAAATGAATTATTCCCCTTCTAGAT 58.263 33.333 12.26 0.00 43.66 1.98
2960 3613 9.018582 GGAAATGAATTATTCCCCTTCTAGATG 57.981 37.037 2.22 0.00 39.36 2.90
3017 3673 1.106285 GTCATGGTTGATTCTGGGGC 58.894 55.000 0.00 0.00 33.56 5.80
3023 3679 1.044790 GTTGATTCTGGGGCCATGGG 61.045 60.000 15.13 0.00 0.00 4.00
3051 3742 0.515564 GGTTTTGTGTCCGATGACCG 59.484 55.000 0.00 0.00 41.01 4.79
3052 3743 1.223187 GTTTTGTGTCCGATGACCGT 58.777 50.000 0.00 0.00 41.01 4.83
3062 3753 0.320421 CGATGACCGTGTGTTTCCCT 60.320 55.000 0.00 0.00 0.00 4.20
3068 3759 1.278127 ACCGTGTGTTTCCCTATCCAG 59.722 52.381 0.00 0.00 0.00 3.86
3072 3763 3.356290 GTGTGTTTCCCTATCCAGCATT 58.644 45.455 0.00 0.00 0.00 3.56
3078 3769 3.497103 TCCCTATCCAGCATTGATGTG 57.503 47.619 0.68 0.00 0.00 3.21
3135 3826 1.155889 TTGAAGCGCACAATCACGAT 58.844 45.000 11.47 0.00 0.00 3.73
3166 3857 6.608808 GGTACAACTGTAGTTCTATCCCCTTA 59.391 42.308 0.00 0.00 35.83 2.69
3173 3864 4.090027 AGTTCTATCCCCTTACCCTGTT 57.910 45.455 0.00 0.00 0.00 3.16
3179 3870 0.328258 CCCCTTACCCTGTTGAGGTG 59.672 60.000 0.00 0.00 38.36 4.00
3232 3925 3.781307 TCGGGATGGTTCTGGCCG 61.781 66.667 0.00 0.00 0.00 6.13
3233 3926 4.096003 CGGGATGGTTCTGGCCGT 62.096 66.667 0.00 0.00 0.00 5.68
3234 3927 2.438434 GGGATGGTTCTGGCCGTG 60.438 66.667 0.00 0.00 0.00 4.94
3235 3928 2.668632 GGATGGTTCTGGCCGTGA 59.331 61.111 0.00 0.00 0.00 4.35
3239 3932 0.107508 ATGGTTCTGGCCGTGAGATG 60.108 55.000 0.00 0.00 0.00 2.90
3296 3989 4.410099 AGATTTTGAAGCTCCCAATCACA 58.590 39.130 2.83 0.00 0.00 3.58
3308 4001 1.673626 CCAATCACAAAGCCATGGCAC 60.674 52.381 37.18 10.61 44.88 5.01
3327 4020 2.203437 GCGGTTGTTCCAACCCCT 60.203 61.111 17.94 0.00 36.99 4.79
3328 4021 2.265904 GCGGTTGTTCCAACCCCTC 61.266 63.158 17.94 6.33 36.99 4.30
3329 4022 1.602605 CGGTTGTTCCAACCCCTCC 60.603 63.158 17.94 0.00 36.99 4.30
3330 4023 1.228769 GGTTGTTCCAACCCCTCCC 60.229 63.158 13.92 0.00 34.26 4.30
3331 4024 1.228769 GTTGTTCCAACCCCTCCCC 60.229 63.158 0.00 0.00 0.00 4.81
3332 4025 1.388217 TTGTTCCAACCCCTCCCCT 60.388 57.895 0.00 0.00 0.00 4.79
3333 4026 1.002242 TTGTTCCAACCCCTCCCCTT 61.002 55.000 0.00 0.00 0.00 3.95
3334 4027 1.383019 GTTCCAACCCCTCCCCTTC 59.617 63.158 0.00 0.00 0.00 3.46
3335 4028 1.072538 TTCCAACCCCTCCCCTTCA 60.073 57.895 0.00 0.00 0.00 3.02
3336 4029 0.703056 TTCCAACCCCTCCCCTTCAA 60.703 55.000 0.00 0.00 0.00 2.69
3339 4032 1.203300 CCAACCCCTCCCCTTCAATTT 60.203 52.381 0.00 0.00 0.00 1.82
3360 4053 1.064979 CCTTGTATAGGCCACGGGTTT 60.065 52.381 5.01 0.00 37.17 3.27
3370 4063 1.343142 GCCACGGGTTTGATTTTCCTT 59.657 47.619 0.00 0.00 0.00 3.36
3381 4076 9.529325 GGGTTTGATTTTCCTTAATATAGCAAC 57.471 33.333 0.00 0.00 0.00 4.17
3474 4171 5.402270 GCGTTAGCAAAATCTTCATGTTTGT 59.598 36.000 7.36 0.00 44.35 2.83
3488 4185 5.890334 TCATGTTTGTTTCCACTTCACTTC 58.110 37.500 0.00 0.00 0.00 3.01
3509 4206 3.372822 TCAAAGCGTAATCATTTCCGTCC 59.627 43.478 0.00 0.00 0.00 4.79
3534 4233 4.551702 AAAACCCTAACCATTTCCATGC 57.448 40.909 0.00 0.00 0.00 4.06
3543 4242 4.730949 ACCATTTCCATGCTGAAGATTG 57.269 40.909 0.00 0.00 0.00 2.67
3563 4262 0.371989 TGAATACAAATCGCGTGCGG 59.628 50.000 14.89 0.33 40.25 5.69
3600 4299 9.915629 TGTGGTGTATTTTTATGGTAAATTCAC 57.084 29.630 0.00 0.00 40.01 3.18
3612 4311 3.506067 GGTAAATTCACCCTTCACCACAG 59.494 47.826 0.00 0.00 31.91 3.66
3613 4312 2.292828 AATTCACCCTTCACCACAGG 57.707 50.000 0.00 0.00 0.00 4.00
3628 4327 1.470098 CACAGGGCTTTCTTCGATTGG 59.530 52.381 0.00 0.00 0.00 3.16
3659 4358 2.712709 TCATCCGTGGGCGAAAATTTA 58.287 42.857 0.00 0.00 41.33 1.40
3660 4359 3.283751 TCATCCGTGGGCGAAAATTTAT 58.716 40.909 0.00 0.00 41.33 1.40
3661 4360 4.452825 TCATCCGTGGGCGAAAATTTATA 58.547 39.130 0.00 0.00 41.33 0.98
3696 4395 9.823647 TTTCTTACAAAATTGTTGGCTCAATTA 57.176 25.926 16.66 4.29 44.10 1.40
3724 4425 4.301072 TTTTAGGCTATGTTGGCTCAGT 57.699 40.909 0.00 0.00 42.90 3.41
3725 4426 4.301072 TTTAGGCTATGTTGGCTCAGTT 57.699 40.909 0.00 0.00 42.90 3.16
3726 4427 2.887151 AGGCTATGTTGGCTCAGTTT 57.113 45.000 0.00 0.00 38.54 2.66
3727 4428 3.160679 AGGCTATGTTGGCTCAGTTTT 57.839 42.857 0.00 0.00 38.54 2.43
3728 4429 3.500343 AGGCTATGTTGGCTCAGTTTTT 58.500 40.909 0.00 0.00 38.54 1.94
3754 4455 8.613060 TTTTTAATGCAAAATATGTTGGCTCA 57.387 26.923 7.74 0.00 36.04 4.26
3755 4456 7.830940 TTTAATGCAAAATATGTTGGCTCAG 57.169 32.000 7.74 0.00 0.00 3.35
3831 4555 4.520846 GCGCGCAGGAATCCAACG 62.521 66.667 29.10 5.79 0.00 4.10
3837 4561 0.526211 GCAGGAATCCAACGGTTTCC 59.474 55.000 12.98 12.98 46.46 3.13
3838 4562 1.173913 CAGGAATCCAACGGTTTCCC 58.826 55.000 16.02 3.03 46.99 3.97
3866 4590 2.564771 CATGCGTGTACCCAATCATCT 58.435 47.619 0.00 0.00 0.00 2.90
3867 4591 2.309528 TGCGTGTACCCAATCATCTC 57.690 50.000 0.00 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.946768 ACCGCGAAATATCACCCATTG 59.053 47.619 8.23 0.00 0.00 2.82
2 3 1.134220 ACACCGCGAAATATCACCCAT 60.134 47.619 8.23 0.00 0.00 4.00
17 18 3.982424 GAAATGCGCTGCGACACCG 62.982 63.158 28.07 0.00 39.16 4.94
18 19 2.202349 GAAATGCGCTGCGACACC 60.202 61.111 28.07 8.44 0.00 4.16
19 20 2.202349 GGAAATGCGCTGCGACAC 60.202 61.111 28.07 8.84 0.00 3.67
20 21 2.358615 AGGAAATGCGCTGCGACA 60.359 55.556 28.07 22.33 0.00 4.35
21 22 2.401195 GAGGAAATGCGCTGCGAC 59.599 61.111 28.07 17.26 0.00 5.19
39 40 3.556549 CCAATTGCATTGCGCGCC 61.557 61.111 30.77 13.91 46.97 6.53
41 42 1.518102 GTATTCCAATTGCATTGCGCG 59.482 47.619 0.00 0.00 46.97 6.86
100 101 2.672478 CGGAGACTGTAGAAGCCTTGTG 60.672 54.545 0.00 0.00 0.00 3.33
101 102 1.546476 CGGAGACTGTAGAAGCCTTGT 59.454 52.381 0.00 0.00 0.00 3.16
111 112 5.410439 GGCAAAATTTCTAACGGAGACTGTA 59.590 40.000 0.00 0.00 32.31 2.74
134 135 1.002250 CCGCGGATTTATCGACGAGG 61.002 60.000 24.07 0.00 39.70 4.63
146 147 1.045407 TAGCTGGTAAATCCGCGGAT 58.955 50.000 34.60 34.60 39.43 4.18
165 166 0.473886 AGTGAGTAACCTGGCCTGGT 60.474 55.000 27.60 27.60 43.11 4.00
173 174 4.444536 TGTTTTTACGCAGTGAGTAACCT 58.555 39.130 17.68 0.00 45.73 3.50
217 218 0.179121 CCGCTAGTGGACAACGCATA 60.179 55.000 17.96 0.00 0.00 3.14
218 219 1.447838 CCGCTAGTGGACAACGCAT 60.448 57.895 17.96 0.00 0.00 4.73
219 220 2.048597 CCGCTAGTGGACAACGCA 60.049 61.111 17.96 0.00 0.00 5.24
223 224 1.525718 TACGTGCCGCTAGTGGACAA 61.526 55.000 26.74 7.59 0.00 3.18
230 231 2.578713 CCACGTACGTGCCGCTAG 60.579 66.667 36.76 21.34 44.16 3.42
314 315 3.606687 AGGGTTAAATCGCAAGGTACAG 58.393 45.455 0.00 0.00 38.47 2.74
315 316 3.602483 GAGGGTTAAATCGCAAGGTACA 58.398 45.455 0.00 0.00 38.47 2.90
316 317 2.606272 CGAGGGTTAAATCGCAAGGTAC 59.394 50.000 0.00 0.00 38.47 3.34
317 318 2.496871 TCGAGGGTTAAATCGCAAGGTA 59.503 45.455 2.09 0.00 38.79 3.08
382 383 5.353956 GCCACACAAAATTCAGGAAAAAGTT 59.646 36.000 0.00 0.00 0.00 2.66
383 384 4.875536 GCCACACAAAATTCAGGAAAAAGT 59.124 37.500 0.00 0.00 0.00 2.66
385 386 4.874966 CAGCCACACAAAATTCAGGAAAAA 59.125 37.500 0.00 0.00 0.00 1.94
464 654 2.531912 CGATGACTCGTCCAAGAATTCG 59.468 50.000 0.00 0.00 40.07 3.34
471 661 2.577059 GGCCGATGACTCGTCCAA 59.423 61.111 0.00 0.00 42.42 3.53
472 662 3.822192 CGGCCGATGACTCGTCCA 61.822 66.667 24.07 0.00 43.01 4.02
501 691 2.529151 GCTGTTTTTGTGTGTGACCAG 58.471 47.619 0.00 0.00 0.00 4.00
529 719 4.116747 ACTACTAGTAGTACGCGTCAGT 57.883 45.455 29.96 12.84 43.98 3.41
536 726 6.085718 CGTACGCTCTAACTACTAGTAGTACG 59.914 46.154 30.89 27.34 44.96 3.67
543 736 5.230850 CGTACGTACGCTCTAACTACTAG 57.769 47.826 32.36 4.27 43.14 2.57
558 751 2.037702 TGCCGGTGCTACGTACGTA 61.038 57.895 25.41 25.41 38.71 3.57
559 752 3.364441 TGCCGGTGCTACGTACGT 61.364 61.111 25.98 25.98 38.71 3.57
621 814 1.818221 GATTATCCACACGCGACGGC 61.818 60.000 15.93 0.00 0.00 5.68
625 818 2.209273 CCAATGATTATCCACACGCGA 58.791 47.619 15.93 0.00 0.00 5.87
633 827 3.003689 CGACTTGCCACCAATGATTATCC 59.996 47.826 0.00 0.00 0.00 2.59
643 837 2.338620 CGAGACGACTTGCCACCA 59.661 61.111 0.00 0.00 0.00 4.17
644 838 2.432628 CCGAGACGACTTGCCACC 60.433 66.667 0.00 0.00 0.00 4.61
645 839 1.733399 GACCGAGACGACTTGCCAC 60.733 63.158 0.00 0.00 0.00 5.01
646 840 2.649034 GACCGAGACGACTTGCCA 59.351 61.111 0.00 0.00 0.00 4.92
647 841 2.126031 GGACCGAGACGACTTGCC 60.126 66.667 0.00 0.00 0.00 4.52
679 873 4.256920 TCTCTCCAGCTAGTTTTTCATGC 58.743 43.478 0.00 0.00 0.00 4.06
683 877 5.000012 TCGATCTCTCCAGCTAGTTTTTC 58.000 43.478 0.00 0.00 0.00 2.29
712 924 9.950496 ATCATCTGCTATAATCTTACCGAATTT 57.050 29.630 0.00 0.00 0.00 1.82
713 925 9.950496 AATCATCTGCTATAATCTTACCGAATT 57.050 29.630 0.00 0.00 0.00 2.17
715 927 9.856488 GTAATCATCTGCTATAATCTTACCGAA 57.144 33.333 0.00 0.00 0.00 4.30
716 928 9.020731 TGTAATCATCTGCTATAATCTTACCGA 57.979 33.333 0.00 0.00 0.00 4.69
717 929 9.077674 GTGTAATCATCTGCTATAATCTTACCG 57.922 37.037 0.00 0.00 0.00 4.02
718 930 9.929180 TGTGTAATCATCTGCTATAATCTTACC 57.071 33.333 0.00 0.00 0.00 2.85
721 933 9.926158 CTCTGTGTAATCATCTGCTATAATCTT 57.074 33.333 0.00 0.00 0.00 2.40
722 934 8.530311 CCTCTGTGTAATCATCTGCTATAATCT 58.470 37.037 0.00 0.00 0.00 2.40
723 935 8.526978 TCCTCTGTGTAATCATCTGCTATAATC 58.473 37.037 0.00 0.00 0.00 1.75
724 936 8.427902 TCCTCTGTGTAATCATCTGCTATAAT 57.572 34.615 0.00 0.00 0.00 1.28
725 937 7.839680 TCCTCTGTGTAATCATCTGCTATAA 57.160 36.000 0.00 0.00 0.00 0.98
726 938 7.839680 TTCCTCTGTGTAATCATCTGCTATA 57.160 36.000 0.00 0.00 0.00 1.31
727 939 6.737720 TTCCTCTGTGTAATCATCTGCTAT 57.262 37.500 0.00 0.00 0.00 2.97
728 940 6.737720 ATTCCTCTGTGTAATCATCTGCTA 57.262 37.500 0.00 0.00 0.00 3.49
729 941 5.627182 ATTCCTCTGTGTAATCATCTGCT 57.373 39.130 0.00 0.00 0.00 4.24
730 942 7.976135 AATATTCCTCTGTGTAATCATCTGC 57.024 36.000 0.00 0.00 0.00 4.26
784 1050 0.835276 CCTCTGGATGAGCATGTCCA 59.165 55.000 3.02 3.02 42.03 4.02
799 1066 5.710567 GGTAAATTAAAGCACTTCACCCTCT 59.289 40.000 0.00 0.00 0.00 3.69
802 1069 4.729595 CGGTAAATTAAAGCACTTCACCC 58.270 43.478 0.00 0.00 0.00 4.61
806 1073 3.120095 ACGGCGGTAAATTAAAGCACTTC 60.120 43.478 13.24 0.00 0.00 3.01
810 1079 2.095161 CCAACGGCGGTAAATTAAAGCA 60.095 45.455 13.24 0.00 0.00 3.91
861 1130 1.456287 CCCCATGCTTAGCCCCTAC 59.544 63.158 0.29 0.00 0.00 3.18
865 1134 2.123726 CACCCCCATGCTTAGCCC 60.124 66.667 0.29 0.00 0.00 5.19
878 1147 1.340308 ACCCACTTATTTACCGCACCC 60.340 52.381 0.00 0.00 0.00 4.61
896 1169 2.104859 GGGCTCGGCGAGTTTTACC 61.105 63.158 34.41 26.03 31.39 2.85
1007 1281 1.982073 GATCGGACGCTTTGGGCTTG 61.982 60.000 0.00 0.00 39.13 4.01
1032 1306 5.220710 AGATATGGAGGGACGATTTTCTG 57.779 43.478 0.00 0.00 0.00 3.02
1041 1315 1.650528 CTGGGGAGATATGGAGGGAC 58.349 60.000 0.00 0.00 0.00 4.46
1056 1330 0.829990 GAGGAGGAAGAAGAGCTGGG 59.170 60.000 0.00 0.00 0.00 4.45
1077 1351 1.760480 GGGAGCTGAGGAGGAGGTC 60.760 68.421 0.00 0.00 37.25 3.85
1078 1352 2.366570 GGGAGCTGAGGAGGAGGT 59.633 66.667 0.00 0.00 0.00 3.85
1104 1379 3.131223 CGCTATCTGAGGAAGAAGAACCA 59.869 47.826 0.00 0.00 38.79 3.67
1113 1388 2.101582 GCCTTCTTCGCTATCTGAGGAA 59.898 50.000 0.00 0.00 31.63 3.36
1116 1391 3.568007 ACTAGCCTTCTTCGCTATCTGAG 59.432 47.826 0.00 0.00 38.14 3.35
1117 1392 3.556999 ACTAGCCTTCTTCGCTATCTGA 58.443 45.455 0.00 0.00 38.14 3.27
1119 1394 4.975631 TCTACTAGCCTTCTTCGCTATCT 58.024 43.478 0.00 0.00 38.14 1.98
1120 1395 5.163693 GGATCTACTAGCCTTCTTCGCTATC 60.164 48.000 0.00 0.00 38.14 2.08
1122 1397 4.073549 GGATCTACTAGCCTTCTTCGCTA 58.926 47.826 0.00 0.00 37.79 4.26
1123 1398 2.888414 GGATCTACTAGCCTTCTTCGCT 59.112 50.000 0.00 0.00 40.45 4.93
1124 1399 2.350964 CGGATCTACTAGCCTTCTTCGC 60.351 54.545 0.00 0.00 0.00 4.70
1125 1400 2.226912 CCGGATCTACTAGCCTTCTTCG 59.773 54.545 0.00 0.00 0.00 3.79
1126 1401 3.224269 ACCGGATCTACTAGCCTTCTTC 58.776 50.000 9.46 0.00 0.00 2.87
1127 1402 3.224269 GACCGGATCTACTAGCCTTCTT 58.776 50.000 9.46 0.00 0.00 2.52
1128 1403 2.811136 CGACCGGATCTACTAGCCTTCT 60.811 54.545 9.46 0.00 0.00 2.85
1129 1404 1.536331 CGACCGGATCTACTAGCCTTC 59.464 57.143 9.46 0.00 0.00 3.46
1159 1454 2.879462 GTCACGTCCGACATCGCC 60.879 66.667 0.00 0.00 38.18 5.54
1237 1532 1.818363 CTCCTCGTCGGTCGGATGA 60.818 63.158 2.66 2.66 38.36 2.92
1240 1535 4.025858 ACCTCCTCGTCGGTCGGA 62.026 66.667 0.00 0.00 40.32 4.55
1384 1882 4.117661 AACGGACGCTCCTCTCGC 62.118 66.667 0.00 0.00 33.30 5.03
1397 1895 0.179225 CTGCAAATCGAACCGAACGG 60.179 55.000 11.83 11.83 39.99 4.44
1741 2257 4.830765 TCGAATCTTGCGGGCGGG 62.831 66.667 0.00 0.00 0.00 6.13
1903 2425 4.455877 ACACGAGGAAAATAAGAAGCAAGG 59.544 41.667 0.00 0.00 0.00 3.61
1937 2466 3.286751 GCACGCAACAGGCAAGGA 61.287 61.111 0.00 0.00 45.17 3.36
2081 2610 2.557317 GGGTTGTTGAAGAAGTCGTCA 58.443 47.619 0.00 0.00 32.73 4.35
2088 2671 0.841289 AGGTCGGGGTTGTTGAAGAA 59.159 50.000 0.00 0.00 0.00 2.52
2090 2673 1.515521 GCAGGTCGGGGTTGTTGAAG 61.516 60.000 0.00 0.00 0.00 3.02
2100 2701 4.899239 GAGCATCGGCAGGTCGGG 62.899 72.222 0.00 0.00 44.61 5.14
2189 2790 3.785859 TGCTCCATGTCCGGCTCC 61.786 66.667 0.00 0.00 0.00 4.70
2311 2921 3.117372 CCTGGTAGGGCGAGTACG 58.883 66.667 0.00 0.00 42.93 3.67
2405 3021 2.876645 GTGTCGAAGCCGAGCGAG 60.877 66.667 0.00 0.00 46.52 5.03
2440 3056 0.813184 TATCACGAACGAGGTGTCCC 59.187 55.000 0.14 0.00 36.76 4.46
2454 3073 4.991760 CCGAGACGACGGTATCAC 57.008 61.111 0.00 0.00 46.70 3.06
2584 3211 1.539065 CCGTCTATGGCTACCAGCAAG 60.539 57.143 0.00 0.00 44.75 4.01
2596 3223 5.636837 CACCAACCAAATTAACCGTCTATG 58.363 41.667 0.00 0.00 0.00 2.23
2602 3231 3.672241 GCTAGCACCAACCAAATTAACCG 60.672 47.826 10.63 0.00 0.00 4.44
2657 3291 8.294577 CGCCTAATTAACCCAATCCTTAATAAC 58.705 37.037 0.00 0.00 0.00 1.89
2658 3292 7.040271 GCGCCTAATTAACCCAATCCTTAATAA 60.040 37.037 0.00 0.00 0.00 1.40
2659 3293 6.431852 GCGCCTAATTAACCCAATCCTTAATA 59.568 38.462 0.00 0.00 0.00 0.98
2717 3351 1.518102 CTTGCACGCATCAACAACAAC 59.482 47.619 0.00 0.00 0.00 3.32
2751 3397 7.657761 ACCCTAATTAAGATTAATCAGCACTCG 59.342 37.037 17.56 1.59 32.46 4.18
2770 3420 6.058183 GCAGTTTGATATCTCACACCCTAAT 58.942 40.000 3.98 0.00 33.40 1.73
2771 3421 5.189736 AGCAGTTTGATATCTCACACCCTAA 59.810 40.000 3.98 0.00 33.40 2.69
2772 3422 4.716784 AGCAGTTTGATATCTCACACCCTA 59.283 41.667 3.98 0.00 33.40 3.53
2773 3423 3.521126 AGCAGTTTGATATCTCACACCCT 59.479 43.478 3.98 0.00 33.40 4.34
2774 3424 3.878778 AGCAGTTTGATATCTCACACCC 58.121 45.455 3.98 0.00 33.40 4.61
2775 3425 5.053145 CCTAGCAGTTTGATATCTCACACC 58.947 45.833 3.98 0.00 33.40 4.16
2776 3426 5.907207 TCCTAGCAGTTTGATATCTCACAC 58.093 41.667 3.98 0.00 33.17 3.82
2777 3427 5.069648 CCTCCTAGCAGTTTGATATCTCACA 59.930 44.000 3.98 0.00 0.00 3.58
2841 3494 5.812642 CCCTAATCACTGAACTGTATGACAC 59.187 44.000 0.00 0.00 0.00 3.67
2843 3496 5.360591 CCCCTAATCACTGAACTGTATGAC 58.639 45.833 0.00 0.00 0.00 3.06
2868 3521 3.198635 TGATCTCTCACCCTCCAATTCAC 59.801 47.826 0.00 0.00 0.00 3.18
2889 3542 2.933495 TCAAACTCGGTCTCGGTATG 57.067 50.000 0.00 0.00 36.95 2.39
2906 3559 7.175293 TCAACACACAATCAGATTCATCAATCA 59.825 33.333 0.00 0.00 41.03 2.57
2992 3648 6.306199 CCCCAGAATCAACCATGACATATAA 58.694 40.000 0.00 0.00 38.69 0.98
3017 3673 0.326927 AAACCGTCCAGTACCCATGG 59.673 55.000 4.14 4.14 39.33 3.66
3045 3736 2.093128 GGATAGGGAAACACACGGTCAT 60.093 50.000 0.00 0.00 0.00 3.06
3047 3738 1.276989 TGGATAGGGAAACACACGGTC 59.723 52.381 0.00 0.00 0.00 4.79
3051 3742 2.489938 TGCTGGATAGGGAAACACAC 57.510 50.000 0.00 0.00 0.00 3.82
3052 3743 3.010027 TCAATGCTGGATAGGGAAACACA 59.990 43.478 0.00 0.00 0.00 3.72
3101 3792 4.201561 GCGCTTCAAAATCTTCAAGCAATC 60.202 41.667 0.00 0.00 41.17 2.67
3135 3826 3.326588 AGAACTACAGTTGTACCATGGCA 59.673 43.478 13.04 0.00 38.56 4.92
3149 3840 4.015918 ACAGGGTAAGGGGATAGAACTACA 60.016 45.833 0.00 0.00 0.00 2.74
3156 3847 2.706190 CCTCAACAGGGTAAGGGGATAG 59.294 54.545 0.00 0.00 35.89 2.08
3157 3848 2.046729 ACCTCAACAGGGTAAGGGGATA 59.953 50.000 0.00 0.00 45.53 2.59
3166 3857 3.953775 CCGCCACCTCAACAGGGT 61.954 66.667 0.00 0.00 45.53 4.34
3173 3864 0.178975 AAATCAAACCCGCCACCTCA 60.179 50.000 0.00 0.00 0.00 3.86
3179 3870 7.381408 GCTATATTTAGAAAAATCAAACCCGCC 59.619 37.037 0.00 0.00 36.67 6.13
3232 3925 4.829064 TTGCTTGGTAAACACATCTCAC 57.171 40.909 0.00 0.00 0.00 3.51
3233 3926 5.843673 TTTTGCTTGGTAAACACATCTCA 57.156 34.783 0.00 0.00 0.00 3.27
3234 3927 9.503427 GTATATTTTGCTTGGTAAACACATCTC 57.497 33.333 0.00 0.00 0.00 2.75
3235 3928 9.243105 AGTATATTTTGCTTGGTAAACACATCT 57.757 29.630 0.00 0.00 0.00 2.90
3239 3932 7.822658 TCCAGTATATTTTGCTTGGTAAACAC 58.177 34.615 0.00 0.00 0.00 3.32
3272 3965 5.166398 GTGATTGGGAGCTTCAAAATCTTG 58.834 41.667 16.54 0.00 0.00 3.02
3296 3989 3.376078 CCGCTGTGCCATGGCTTT 61.376 61.111 35.53 0.00 42.51 3.51
3370 4063 4.406326 TCCCGACCACTTGTTGCTATATTA 59.594 41.667 0.00 0.00 0.00 0.98
3381 4076 1.666872 GAACCGTCCCGACCACTTG 60.667 63.158 0.00 0.00 0.00 3.16
3467 4164 5.913137 TGAAGTGAAGTGGAAACAAACAT 57.087 34.783 0.00 0.00 46.06 2.71
3474 4171 3.013921 ACGCTTTGAAGTGAAGTGGAAA 58.986 40.909 10.97 0.00 38.58 3.13
3534 4233 5.674148 CGCGATTTGTATTCACAATCTTCAG 59.326 40.000 0.00 0.00 44.01 3.02
3543 4242 1.442765 CGCACGCGATTTGTATTCAC 58.557 50.000 15.93 0.00 42.83 3.18
3575 4274 9.361315 GGTGAATTTACCATAAAAATACACCAC 57.639 33.333 14.26 0.00 40.54 4.16
3576 4275 8.532819 GGGTGAATTTACCATAAAAATACACCA 58.467 33.333 20.02 0.00 42.69 4.17
3577 4276 8.755028 AGGGTGAATTTACCATAAAAATACACC 58.245 33.333 20.02 7.97 42.69 4.16
3582 4281 8.318412 GGTGAAGGGTGAATTTACCATAAAAAT 58.682 33.333 20.02 0.00 42.69 1.82
3583 4282 7.290248 TGGTGAAGGGTGAATTTACCATAAAAA 59.710 33.333 20.02 0.00 40.29 1.94
3584 4283 6.782988 TGGTGAAGGGTGAATTTACCATAAAA 59.217 34.615 20.02 1.09 40.29 1.52
3589 4288 3.117474 TGTGGTGAAGGGTGAATTTACCA 60.117 43.478 20.02 0.00 42.20 3.25
3592 4291 3.761897 CCTGTGGTGAAGGGTGAATTTA 58.238 45.455 0.00 0.00 0.00 1.40
3593 4292 2.597455 CCTGTGGTGAAGGGTGAATTT 58.403 47.619 0.00 0.00 0.00 1.82
3607 4306 1.470098 CAATCGAAGAAAGCCCTGTGG 59.530 52.381 0.00 0.00 43.58 4.17
3612 4311 0.681243 AGCCCAATCGAAGAAAGCCC 60.681 55.000 0.00 0.00 43.58 5.19
3613 4312 1.177401 AAGCCCAATCGAAGAAAGCC 58.823 50.000 0.00 0.00 43.58 4.35
3628 4327 1.200020 CCACGGATGAAGAACAAAGCC 59.800 52.381 0.00 0.00 0.00 4.35
3729 4430 8.613060 TGAGCCAACATATTTTGCATTAAAAA 57.387 26.923 0.00 0.00 41.29 1.94
3730 4431 7.877097 ACTGAGCCAACATATTTTGCATTAAAA 59.123 29.630 0.00 0.00 42.10 1.52
3731 4432 7.385267 ACTGAGCCAACATATTTTGCATTAAA 58.615 30.769 0.00 0.00 0.00 1.52
3732 4433 6.934056 ACTGAGCCAACATATTTTGCATTAA 58.066 32.000 0.00 0.00 0.00 1.40
3733 4434 6.528537 ACTGAGCCAACATATTTTGCATTA 57.471 33.333 0.00 0.00 0.00 1.90
3734 4435 5.410355 ACTGAGCCAACATATTTTGCATT 57.590 34.783 0.00 0.00 0.00 3.56
3735 4436 5.172934 CAACTGAGCCAACATATTTTGCAT 58.827 37.500 0.00 0.00 0.00 3.96
3736 4437 4.558178 CAACTGAGCCAACATATTTTGCA 58.442 39.130 0.00 0.00 0.00 4.08
3737 4438 3.928375 CCAACTGAGCCAACATATTTTGC 59.072 43.478 0.00 0.00 0.00 3.68
3738 4439 5.389859 TCCAACTGAGCCAACATATTTTG 57.610 39.130 0.00 0.00 0.00 2.44
3739 4440 5.105228 CCATCCAACTGAGCCAACATATTTT 60.105 40.000 0.00 0.00 0.00 1.82
3740 4441 4.403432 CCATCCAACTGAGCCAACATATTT 59.597 41.667 0.00 0.00 0.00 1.40
3741 4442 3.956199 CCATCCAACTGAGCCAACATATT 59.044 43.478 0.00 0.00 0.00 1.28
3742 4443 3.559069 CCATCCAACTGAGCCAACATAT 58.441 45.455 0.00 0.00 0.00 1.78
3743 4444 2.357050 CCCATCCAACTGAGCCAACATA 60.357 50.000 0.00 0.00 0.00 2.29
3744 4445 1.617804 CCCATCCAACTGAGCCAACAT 60.618 52.381 0.00 0.00 0.00 2.71
3745 4446 0.251297 CCCATCCAACTGAGCCAACA 60.251 55.000 0.00 0.00 0.00 3.33
3746 4447 1.598701 GCCCATCCAACTGAGCCAAC 61.599 60.000 0.00 0.00 0.00 3.77
3747 4448 1.304381 GCCCATCCAACTGAGCCAA 60.304 57.895 0.00 0.00 0.00 4.52
3748 4449 2.356278 GCCCATCCAACTGAGCCA 59.644 61.111 0.00 0.00 0.00 4.75
3749 4450 2.825836 CGCCCATCCAACTGAGCC 60.826 66.667 0.00 0.00 0.00 4.70
3750 4451 2.045926 ACGCCCATCCAACTGAGC 60.046 61.111 0.00 0.00 0.00 4.26
3751 4452 0.107508 ATCACGCCCATCCAACTGAG 60.108 55.000 0.00 0.00 0.00 3.35
3752 4453 0.327924 AATCACGCCCATCCAACTGA 59.672 50.000 0.00 0.00 0.00 3.41
3753 4454 1.942657 CTAATCACGCCCATCCAACTG 59.057 52.381 0.00 0.00 0.00 3.16
3754 4455 1.559682 ACTAATCACGCCCATCCAACT 59.440 47.619 0.00 0.00 0.00 3.16
3755 4456 2.038387 ACTAATCACGCCCATCCAAC 57.962 50.000 0.00 0.00 0.00 3.77
3813 4537 4.520846 GTTGGATTCCTGCGCGCG 62.521 66.667 28.44 28.44 0.00 6.86
3814 4538 4.520846 CGTTGGATTCCTGCGCGC 62.521 66.667 27.26 27.26 0.00 6.86
3838 4562 3.772560 TACACGCATGCACGCACG 61.773 61.111 19.57 2.13 36.19 5.34
3839 4563 2.202171 GTACACGCATGCACGCAC 60.202 61.111 19.57 4.69 36.19 5.34
3840 4564 3.418913 GGTACACGCATGCACGCA 61.419 61.111 19.57 0.00 36.19 5.24
3841 4565 4.160635 GGGTACACGCATGCACGC 62.161 66.667 19.57 12.57 36.19 5.34


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

AutoCloner maintained by Alex Coulton.