Multiple sequence alignment - TraesCS5A01G548500

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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 TraesCS5A01G548500 chr5A 100.000 3170 0 0 1 3170 702500830 702503999 0.000000e+00 5854.0
1 TraesCS5A01G548500 chr5A 93.333 45 3 0 3039 3083 44998158 44998114 2.040000e-07 67.6
2 TraesCS5A01G548500 chr4D 89.223 2459 117 57 661 3021 506204488 506206896 0.000000e+00 2937.0
3 TraesCS5A01G548500 chr4D 85.882 680 59 14 1 658 506203758 506204422 0.000000e+00 689.0
4 TraesCS5A01G548500 chr4B 88.740 1048 64 28 1334 2374 662401433 662402433 0.000000e+00 1232.0
5 TraesCS5A01G548500 chr4B 85.667 600 42 19 1 583 662399603 662400175 2.720000e-165 592.0
6 TraesCS5A01G548500 chr4B 93.857 293 14 2 966 1256 662401027 662401317 3.750000e-119 438.0
7 TraesCS5A01G548500 chr4B 89.688 320 20 8 661 971 662400336 662400651 2.290000e-106 396.0
8 TraesCS5A01G548500 chr7D 81.718 547 90 8 1592 2133 462673548 462674089 6.240000e-122 448.0
9 TraesCS5A01G548500 chr7B 81.569 548 91 8 1591 2133 485833421 485833963 8.070000e-121 444.0
10 TraesCS5A01G548500 chr7A 81.387 548 92 8 1591 2133 537518283 537517741 3.750000e-119 438.0
11 TraesCS5A01G548500 chr2D 95.122 41 2 0 3043 3083 15592205 15592245 7.340000e-07 65.8


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 TraesCS5A01G548500 chr5A 702500830 702503999 3169 False 5854.0 5854 100.0000 1 3170 1 chr5A.!!$F1 3169
1 TraesCS5A01G548500 chr4D 506203758 506206896 3138 False 1813.0 2937 87.5525 1 3021 2 chr4D.!!$F1 3020
2 TraesCS5A01G548500 chr4B 662399603 662402433 2830 False 664.5 1232 89.4880 1 2374 4 chr4B.!!$F1 2373
3 TraesCS5A01G548500 chr7D 462673548 462674089 541 False 448.0 448 81.7180 1592 2133 1 chr7D.!!$F1 541
4 TraesCS5A01G548500 chr7B 485833421 485833963 542 False 444.0 444 81.5690 1591 2133 1 chr7B.!!$F1 542
5 TraesCS5A01G548500 chr7A 537517741 537518283 542 True 438.0 438 81.3870 1591 2133 1 chr7A.!!$R1 542

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
905 1024 0.838987 GACCCACCCCACTCCTACAA 60.839 60.0 0.0 0.0 0.0 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2198 2762 0.099791 CTCGAACTCGGAGCTTCCTC 59.9 60.0 4.58 0.0 40.29 3.71 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
130 135 2.239402 TGGTGGATCAAGCAGCTGATTA 59.761 45.455 18.24 6.61 36.15 1.75
134 139 5.506982 GGTGGATCAAGCAGCTGATTAATTC 60.507 44.000 18.24 8.20 36.15 2.17
171 176 3.102097 GCGTAGGCTCCATTGCAC 58.898 61.111 0.00 0.00 35.83 4.57
172 177 1.745115 GCGTAGGCTCCATTGCACA 60.745 57.895 0.00 0.00 35.83 4.57
173 178 1.305219 GCGTAGGCTCCATTGCACAA 61.305 55.000 0.00 0.00 35.83 3.33
174 179 1.164411 CGTAGGCTCCATTGCACAAA 58.836 50.000 0.00 0.00 34.04 2.83
175 180 1.539388 CGTAGGCTCCATTGCACAAAA 59.461 47.619 0.00 0.00 34.04 2.44
176 181 2.030363 CGTAGGCTCCATTGCACAAAAA 60.030 45.455 0.00 0.00 34.04 1.94
207 212 1.501582 AAGGTCCAGGCTAGGCTAAG 58.498 55.000 19.78 13.47 0.00 2.18
222 227 3.025262 GGCTAAGGTAGTGCAGTACTCT 58.975 50.000 26.66 19.75 40.89 3.24
223 228 3.447944 GGCTAAGGTAGTGCAGTACTCTT 59.552 47.826 26.66 25.98 40.89 2.85
242 255 3.852307 TATGTACCGGCCGGCCAC 61.852 66.667 43.58 37.14 39.32 5.01
274 287 4.463879 CCGCTCAGGTCAGCCAGG 62.464 72.222 0.00 0.00 35.84 4.45
276 289 4.792804 GCTCAGGTCAGCCAGGCC 62.793 72.222 8.22 0.00 44.66 5.19
436 452 2.285220 GCGATTTGCATACGATGACAGT 59.715 45.455 10.87 0.00 45.45 3.55
451 467 5.590259 CGATGACAGTTCCTTAATTTGGGAT 59.410 40.000 0.85 0.00 0.00 3.85
453 469 5.016173 TGACAGTTCCTTAATTTGGGATGG 58.984 41.667 0.85 0.00 0.00 3.51
454 470 4.352893 ACAGTTCCTTAATTTGGGATGGG 58.647 43.478 0.85 0.00 0.00 4.00
479 495 7.042119 GGTGTTTAAAATGGTCAAATGTTCAGG 60.042 37.037 0.00 0.00 0.00 3.86
485 501 2.971330 TGGTCAAATGTTCAGGCCAATT 59.029 40.909 5.01 0.00 0.00 2.32
486 502 3.006752 TGGTCAAATGTTCAGGCCAATTC 59.993 43.478 5.01 0.00 0.00 2.17
508 525 3.435601 CCCCTGAATTTGGTCCATCTAGG 60.436 52.174 0.00 0.00 39.47 3.02
518 535 7.546250 TTTGGTCCATCTAGGCAAATTAAAA 57.454 32.000 0.00 0.00 37.29 1.52
531 548 8.947055 AGGCAAATTAAAATTACATTAGCTGG 57.053 30.769 0.00 0.00 0.00 4.85
555 572 4.408182 AGTATTCCCTCCGTCTCAAATG 57.592 45.455 0.00 0.00 0.00 2.32
558 575 3.887621 TTCCCTCCGTCTCAAATGTAG 57.112 47.619 0.00 0.00 0.00 2.74
559 576 2.816411 TCCCTCCGTCTCAAATGTAGT 58.184 47.619 0.00 0.00 0.00 2.73
563 591 4.885907 CCCTCCGTCTCAAATGTAGTACTA 59.114 45.833 0.00 0.00 0.00 1.82
564 592 5.221009 CCCTCCGTCTCAAATGTAGTACTAC 60.221 48.000 23.58 23.58 36.63 2.73
566 594 5.178061 TCCGTCTCAAATGTAGTACTACGA 58.822 41.667 24.36 15.64 38.85 3.43
569 597 5.261661 GTCTCAAATGTAGTACTACGACGG 58.738 45.833 24.36 15.49 38.85 4.79
574 602 6.922957 TCAAATGTAGTACTACGACGGTTTTT 59.077 34.615 24.36 13.33 38.85 1.94
644 676 9.443323 TGGTCGATTGAAGTAATATTTTTCTCA 57.557 29.630 0.00 0.00 0.00 3.27
659 691 7.742556 ATTTTTCTCAATCATCCTAGCTAGC 57.257 36.000 15.74 6.62 0.00 3.42
660 692 6.491714 TTTTCTCAATCATCCTAGCTAGCT 57.508 37.500 23.12 23.12 0.00 3.32
661 693 7.603180 TTTTCTCAATCATCCTAGCTAGCTA 57.397 36.000 22.85 22.85 0.00 3.32
678 775 7.942990 AGCTAGCTACTTTTACAATAGACGAT 58.057 34.615 17.69 0.00 0.00 3.73
690 787 3.895232 ATAGACGATCTTGCAACCACT 57.105 42.857 0.00 0.00 0.00 4.00
719 819 5.243954 TGTCTTTTTCTCTAGAGTAGCAGCA 59.756 40.000 19.21 8.98 0.00 4.41
727 827 5.473162 TCTCTAGAGTAGCAGCAAGATCATC 59.527 44.000 19.21 0.00 0.00 2.92
728 828 5.136105 TCTAGAGTAGCAGCAAGATCATCA 58.864 41.667 0.00 0.00 0.00 3.07
759 859 1.137282 TCTGCGCGTACCATCCATAAA 59.863 47.619 8.43 0.00 0.00 1.40
761 861 2.548057 CTGCGCGTACCATCCATAAAAT 59.452 45.455 8.43 0.00 0.00 1.82
821 923 1.067364 AGCTCATCATCAGTCTCAGCG 59.933 52.381 0.00 0.00 0.00 5.18
827 929 2.094675 TCATCAGTCTCAGCGATCACA 58.905 47.619 0.00 0.00 0.00 3.58
905 1024 0.838987 GACCCACCCCACTCCTACAA 60.839 60.000 0.00 0.00 0.00 2.41
973 1469 1.437625 CACACACACACACACACTCA 58.562 50.000 0.00 0.00 0.00 3.41
983 1479 1.139058 ACACACACTCAACTCCACTCC 59.861 52.381 0.00 0.00 0.00 3.85
987 1483 1.414181 ACACTCAACTCCACTCCACTG 59.586 52.381 0.00 0.00 0.00 3.66
988 1484 1.051812 ACTCAACTCCACTCCACTGG 58.948 55.000 0.00 0.00 0.00 4.00
989 1485 1.342074 CTCAACTCCACTCCACTGGA 58.658 55.000 0.00 0.00 38.05 3.86
1026 1527 3.619242 CGATGATGATGCAGATTAGGCCT 60.619 47.826 11.78 11.78 0.00 5.19
1097 1598 3.730761 GCTGCAGCAGGGTCGTTG 61.731 66.667 33.36 0.00 41.59 4.10
1260 1761 1.959848 CAGCTCAGGTCAGTCACGA 59.040 57.895 0.00 0.00 0.00 4.35
1302 1858 8.021396 TGCATGATTACTCATATGTACGTAGTC 58.979 37.037 1.90 9.45 39.44 2.59
1310 1866 6.602406 ACTCATATGTACGTAGTCCTCAAGTT 59.398 38.462 1.90 0.00 43.93 2.66
1329 1887 7.092079 TCAAGTTTGCAATAGTTGGATGATTG 58.908 34.615 19.80 0.00 34.37 2.67
1330 1888 6.839124 AGTTTGCAATAGTTGGATGATTGA 57.161 33.333 0.00 0.00 33.28 2.57
1331 1889 7.414222 AGTTTGCAATAGTTGGATGATTGAT 57.586 32.000 0.00 0.00 33.28 2.57
1332 1890 7.844009 AGTTTGCAATAGTTGGATGATTGATT 58.156 30.769 0.00 0.00 33.28 2.57
1368 1926 7.859377 CACCTAACAAATCATGCTGCTAATTAG 59.141 37.037 8.20 8.20 0.00 1.73
1372 1930 6.489675 ACAAATCATGCTGCTAATTAGTTCG 58.510 36.000 13.91 4.30 0.00 3.95
1381 1939 5.163982 GCTGCTAATTAGTTCGTTCTTCGTT 60.164 40.000 13.91 0.00 40.80 3.85
1382 1940 6.148270 TGCTAATTAGTTCGTTCTTCGTTG 57.852 37.500 13.91 0.00 40.80 4.10
1383 1941 5.013859 GCTAATTAGTTCGTTCTTCGTTGC 58.986 41.667 13.91 0.00 40.80 4.17
1385 1943 1.411394 TAGTTCGTTCTTCGTTGCCG 58.589 50.000 0.00 0.00 40.80 5.69
1386 1944 0.249155 AGTTCGTTCTTCGTTGCCGA 60.249 50.000 0.00 0.00 42.41 5.54
1389 1947 1.504359 TCGTTCTTCGTTGCCGATTT 58.496 45.000 0.00 0.00 43.80 2.17
1503 2061 1.404391 CACCGCCTTCTACGTCAGTAT 59.596 52.381 0.00 0.00 31.58 2.12
1504 2062 2.615447 CACCGCCTTCTACGTCAGTATA 59.385 50.000 0.00 0.00 31.58 1.47
1506 2064 4.453478 CACCGCCTTCTACGTCAGTATATA 59.547 45.833 0.00 0.00 31.58 0.86
1507 2065 4.453819 ACCGCCTTCTACGTCAGTATATAC 59.546 45.833 4.60 4.60 31.58 1.47
1508 2066 4.142730 CCGCCTTCTACGTCAGTATATACC 60.143 50.000 9.32 0.00 31.58 2.73
1509 2067 4.694509 CGCCTTCTACGTCAGTATATACCT 59.305 45.833 9.32 0.00 31.58 3.08
1510 2068 5.163874 CGCCTTCTACGTCAGTATATACCTC 60.164 48.000 9.32 0.21 31.58 3.85
1511 2069 5.123661 GCCTTCTACGTCAGTATATACCTCC 59.876 48.000 9.32 0.00 31.58 4.30
1512 2070 5.647225 CCTTCTACGTCAGTATATACCTCCC 59.353 48.000 9.32 0.00 31.58 4.30
1513 2071 6.445451 TTCTACGTCAGTATATACCTCCCT 57.555 41.667 9.32 0.00 31.58 4.20
1516 2074 5.321934 ACGTCAGTATATACCTCCCTTCT 57.678 43.478 9.32 0.00 0.00 2.85
1541 2102 1.084289 CCCTCCGACGACCATTTTTC 58.916 55.000 0.00 0.00 0.00 2.29
1545 2106 2.147958 TCCGACGACCATTTTTCCTTG 58.852 47.619 0.00 0.00 0.00 3.61
1561 2122 6.985188 TTTCCTTGTTGGATCGATCTTAAG 57.015 37.500 23.96 19.63 45.68 1.85
1573 2134 8.696374 TGGATCGATCTTAAGTTCTTAACTGAT 58.304 33.333 23.96 5.80 41.91 2.90
1971 2532 0.908180 ACTACCGCTACCAGCCCTTT 60.908 55.000 0.00 0.00 38.18 3.11
1989 2550 0.768622 TTGTGTCCGGGTTCAAGGAT 59.231 50.000 0.00 0.00 38.97 3.24
2160 2724 2.582978 GACCGCTCCAACTACCCC 59.417 66.667 0.00 0.00 0.00 4.95
2170 2734 0.179108 CAACTACCCCGAGTGCTAGC 60.179 60.000 8.10 8.10 0.00 3.42
2177 2741 1.361993 CCGAGTGCTAGCCTGCTAG 59.638 63.158 19.48 19.48 46.41 3.42
2333 2919 4.386867 AGTGTGATCGATACGGTGATTT 57.613 40.909 0.00 0.00 0.00 2.17
2334 2920 4.360563 AGTGTGATCGATACGGTGATTTC 58.639 43.478 0.00 0.00 0.00 2.17
2335 2921 4.098044 AGTGTGATCGATACGGTGATTTCT 59.902 41.667 0.00 0.00 0.00 2.52
2338 2924 4.441415 GTGATCGATACGGTGATTTCTGTC 59.559 45.833 0.00 0.00 0.00 3.51
2339 2925 4.097286 TGATCGATACGGTGATTTCTGTCA 59.903 41.667 0.00 0.00 0.00 3.58
2340 2926 3.766151 TCGATACGGTGATTTCTGTCAC 58.234 45.455 0.00 0.00 46.04 3.67
2350 2937 4.447724 GTGATTTCTGTCACGTATGTGTGT 59.552 41.667 14.63 0.00 46.49 3.72
2353 2940 3.282831 TCTGTCACGTATGTGTGTGAG 57.717 47.619 14.63 6.93 45.08 3.51
2355 2942 3.237628 CTGTCACGTATGTGTGTGAGAG 58.762 50.000 14.63 5.32 45.92 3.20
2430 3023 7.013464 AGCGTACTCTGTCTAAGTTATTGCTAT 59.987 37.037 0.00 0.00 0.00 2.97
2445 3038 7.445402 AGTTATTGCTATTTGTGAGACACTTGT 59.555 33.333 0.00 0.00 35.11 3.16
2476 3069 1.838112 TGATGGACATTTGGACCTGC 58.162 50.000 0.00 0.00 0.00 4.85
2497 3090 4.418392 GCAATCTGCACCTTTTGATACAG 58.582 43.478 0.00 0.00 44.26 2.74
2534 3127 6.854381 CGAATTTTAGTACACCACCTTTTGAC 59.146 38.462 0.00 0.00 0.00 3.18
2535 3128 5.738118 TTTTAGTACACCACCTTTTGACG 57.262 39.130 0.00 0.00 0.00 4.35
2536 3129 2.994186 AGTACACCACCTTTTGACGT 57.006 45.000 0.00 0.00 0.00 4.34
2613 3231 3.492309 CCTCTCTCACTCGATTTGGATGG 60.492 52.174 0.00 0.00 0.00 3.51
2642 3260 1.917872 TTGGTGGCTGGATTGGTTAC 58.082 50.000 0.00 0.00 0.00 2.50
2644 3262 0.331616 GGTGGCTGGATTGGTTACCT 59.668 55.000 2.07 0.00 0.00 3.08
2645 3263 1.272480 GGTGGCTGGATTGGTTACCTT 60.272 52.381 2.07 0.00 0.00 3.50
2646 3264 2.525368 GTGGCTGGATTGGTTACCTTT 58.475 47.619 2.07 0.00 0.00 3.11
2647 3265 2.897326 GTGGCTGGATTGGTTACCTTTT 59.103 45.455 2.07 0.00 0.00 2.27
2648 3266 2.896685 TGGCTGGATTGGTTACCTTTTG 59.103 45.455 2.07 0.00 0.00 2.44
2649 3267 2.897326 GGCTGGATTGGTTACCTTTTGT 59.103 45.455 2.07 0.00 0.00 2.83
2650 3268 3.306019 GGCTGGATTGGTTACCTTTTGTG 60.306 47.826 2.07 0.00 0.00 3.33
2651 3269 3.860754 GCTGGATTGGTTACCTTTTGTGC 60.861 47.826 2.07 0.00 0.00 4.57
2652 3270 2.630580 TGGATTGGTTACCTTTTGTGCC 59.369 45.455 2.07 0.00 0.00 5.01
2653 3271 2.630580 GGATTGGTTACCTTTTGTGCCA 59.369 45.455 2.07 0.00 33.39 4.92
2654 3272 3.306019 GGATTGGTTACCTTTTGTGCCAG 60.306 47.826 2.07 0.00 35.63 4.85
2655 3273 2.738587 TGGTTACCTTTTGTGCCAGA 57.261 45.000 2.07 0.00 32.11 3.86
2656 3274 2.303175 TGGTTACCTTTTGTGCCAGAC 58.697 47.619 2.07 0.00 32.11 3.51
2657 3275 2.092103 TGGTTACCTTTTGTGCCAGACT 60.092 45.455 2.07 0.00 32.11 3.24
2658 3276 2.956333 GGTTACCTTTTGTGCCAGACTT 59.044 45.455 0.00 0.00 0.00 3.01
2659 3277 3.004419 GGTTACCTTTTGTGCCAGACTTC 59.996 47.826 0.00 0.00 0.00 3.01
2660 3278 2.736670 ACCTTTTGTGCCAGACTTCT 57.263 45.000 0.00 0.00 0.00 2.85
2672 3290 2.951642 CCAGACTTCTTTTTGTGCCAGA 59.048 45.455 0.00 0.00 0.00 3.86
2767 3413 0.173481 GGGCCGCCTTCTTTTCATTC 59.827 55.000 9.86 0.00 0.00 2.67
2830 3476 4.699735 TCACAGACAGACACACAAACATTT 59.300 37.500 0.00 0.00 0.00 2.32
2867 3513 6.018832 CGAAACATTGCTCCAAAAACAGAAAT 60.019 34.615 0.00 0.00 0.00 2.17
2876 3522 7.821846 TGCTCCAAAAACAGAAATTACAAACTT 59.178 29.630 0.00 0.00 0.00 2.66
2922 3568 5.109210 GCCAATTTAAGCCCAACTTACATC 58.891 41.667 0.00 0.00 40.63 3.06
2950 3596 5.120674 CACTATTCAGTGCGAGATTTGTTGA 59.879 40.000 0.00 0.00 45.44 3.18
2953 3599 5.437289 TTCAGTGCGAGATTTGTTGATTT 57.563 34.783 0.00 0.00 0.00 2.17
3021 3667 6.426327 CAACGTAGATTCATGTTGTGTCAAA 58.574 36.000 0.00 0.00 39.52 2.69
3022 3668 6.228273 ACGTAGATTCATGTTGTGTCAAAG 57.772 37.500 0.00 0.00 0.00 2.77
3023 3669 5.989168 ACGTAGATTCATGTTGTGTCAAAGA 59.011 36.000 0.00 0.00 0.00 2.52
3024 3670 6.073765 ACGTAGATTCATGTTGTGTCAAAGAC 60.074 38.462 0.00 0.00 0.00 3.01
3025 3671 6.146184 CGTAGATTCATGTTGTGTCAAAGACT 59.854 38.462 0.00 0.00 33.15 3.24
3026 3672 6.309712 AGATTCATGTTGTGTCAAAGACTG 57.690 37.500 0.00 0.00 33.15 3.51
3027 3673 5.824624 AGATTCATGTTGTGTCAAAGACTGT 59.175 36.000 0.00 0.00 33.15 3.55
3028 3674 4.880886 TCATGTTGTGTCAAAGACTGTG 57.119 40.909 0.00 0.00 33.15 3.66
3029 3675 3.627123 TCATGTTGTGTCAAAGACTGTGG 59.373 43.478 0.00 0.00 33.15 4.17
3030 3676 3.342377 TGTTGTGTCAAAGACTGTGGA 57.658 42.857 0.00 0.00 33.15 4.02
3031 3677 3.884895 TGTTGTGTCAAAGACTGTGGAT 58.115 40.909 0.00 0.00 33.15 3.41
3032 3678 3.627123 TGTTGTGTCAAAGACTGTGGATG 59.373 43.478 0.00 0.00 33.15 3.51
3033 3679 2.221169 TGTGTCAAAGACTGTGGATGC 58.779 47.619 0.00 0.00 33.15 3.91
3034 3680 2.221169 GTGTCAAAGACTGTGGATGCA 58.779 47.619 0.00 0.00 33.15 3.96
3035 3681 2.816087 GTGTCAAAGACTGTGGATGCAT 59.184 45.455 0.00 0.00 33.15 3.96
3036 3682 2.815503 TGTCAAAGACTGTGGATGCATG 59.184 45.455 2.46 0.00 33.15 4.06
3037 3683 3.076621 GTCAAAGACTGTGGATGCATGA 58.923 45.455 2.46 0.00 0.00 3.07
3038 3684 3.503363 GTCAAAGACTGTGGATGCATGAA 59.497 43.478 2.46 0.00 0.00 2.57
3039 3685 4.157289 GTCAAAGACTGTGGATGCATGAAT 59.843 41.667 2.46 0.00 0.00 2.57
3040 3686 5.355071 GTCAAAGACTGTGGATGCATGAATA 59.645 40.000 2.46 0.00 0.00 1.75
3041 3687 5.945191 TCAAAGACTGTGGATGCATGAATAA 59.055 36.000 2.46 0.00 0.00 1.40
3042 3688 6.604396 TCAAAGACTGTGGATGCATGAATAAT 59.396 34.615 2.46 0.00 0.00 1.28
3043 3689 7.774625 TCAAAGACTGTGGATGCATGAATAATA 59.225 33.333 2.46 0.00 0.00 0.98
3044 3690 7.502120 AAGACTGTGGATGCATGAATAATAC 57.498 36.000 2.46 0.00 0.00 1.89
3045 3691 6.835174 AGACTGTGGATGCATGAATAATACT 58.165 36.000 2.46 0.00 0.00 2.12
3046 3692 6.933521 AGACTGTGGATGCATGAATAATACTC 59.066 38.462 2.46 0.00 0.00 2.59
3047 3693 6.000219 ACTGTGGATGCATGAATAATACTCC 59.000 40.000 2.46 0.00 0.00 3.85
3048 3694 5.316167 TGTGGATGCATGAATAATACTCCC 58.684 41.667 2.46 0.00 0.00 4.30
3049 3695 5.073554 TGTGGATGCATGAATAATACTCCCT 59.926 40.000 2.46 0.00 0.00 4.20
3050 3696 5.645497 GTGGATGCATGAATAATACTCCCTC 59.355 44.000 2.46 0.00 0.00 4.30
3051 3697 5.549228 TGGATGCATGAATAATACTCCCTCT 59.451 40.000 2.46 0.00 0.00 3.69
3052 3698 6.730507 TGGATGCATGAATAATACTCCCTCTA 59.269 38.462 2.46 0.00 0.00 2.43
3053 3699 7.404104 TGGATGCATGAATAATACTCCCTCTAT 59.596 37.037 2.46 0.00 0.00 1.98
3054 3700 8.928448 GGATGCATGAATAATACTCCCTCTATA 58.072 37.037 2.46 0.00 0.00 1.31
3070 3716 9.360093 CTCCCTCTATAAAGAAATATAACAGCG 57.640 37.037 0.00 0.00 0.00 5.18
3071 3717 8.867097 TCCCTCTATAAAGAAATATAACAGCGT 58.133 33.333 0.00 0.00 0.00 5.07
3072 3718 9.490379 CCCTCTATAAAGAAATATAACAGCGTT 57.510 33.333 0.02 0.02 0.00 4.84
3088 3734 7.627298 AACAGCGTTTAGATTACTAGAGAGA 57.373 36.000 0.00 0.00 0.00 3.10
3089 3735 7.627298 ACAGCGTTTAGATTACTAGAGAGAA 57.373 36.000 0.00 0.00 0.00 2.87
3090 3736 8.228035 ACAGCGTTTAGATTACTAGAGAGAAT 57.772 34.615 0.00 0.00 0.00 2.40
3091 3737 9.339850 ACAGCGTTTAGATTACTAGAGAGAATA 57.660 33.333 0.00 0.00 0.00 1.75
3092 3738 9.820229 CAGCGTTTAGATTACTAGAGAGAATAG 57.180 37.037 0.00 0.00 0.00 1.73
3093 3739 9.781633 AGCGTTTAGATTACTAGAGAGAATAGA 57.218 33.333 0.00 0.00 0.00 1.98
3105 3751 8.842280 ACTAGAGAGAATAGAAAATACAGTCCG 58.158 37.037 0.00 0.00 0.00 4.79
3106 3752 6.508777 AGAGAGAATAGAAAATACAGTCCGC 58.491 40.000 0.00 0.00 0.00 5.54
3107 3753 5.602628 AGAGAATAGAAAATACAGTCCGCC 58.397 41.667 0.00 0.00 0.00 6.13
3108 3754 4.704965 AGAATAGAAAATACAGTCCGCCC 58.295 43.478 0.00 0.00 0.00 6.13
3109 3755 4.163458 AGAATAGAAAATACAGTCCGCCCA 59.837 41.667 0.00 0.00 0.00 5.36
3110 3756 4.706842 ATAGAAAATACAGTCCGCCCAT 57.293 40.909 0.00 0.00 0.00 4.00
3111 3757 2.643551 AGAAAATACAGTCCGCCCATG 58.356 47.619 0.00 0.00 0.00 3.66
3112 3758 2.026262 AGAAAATACAGTCCGCCCATGT 60.026 45.455 0.00 0.00 0.00 3.21
3113 3759 1.750193 AAATACAGTCCGCCCATGTG 58.250 50.000 0.00 0.00 0.00 3.21
3114 3760 0.618458 AATACAGTCCGCCCATGTGT 59.382 50.000 0.00 0.00 0.00 3.72
3115 3761 0.178068 ATACAGTCCGCCCATGTGTC 59.822 55.000 0.00 0.00 0.00 3.67
3116 3762 1.188871 TACAGTCCGCCCATGTGTCA 61.189 55.000 0.00 0.00 0.00 3.58
3117 3763 2.034879 CAGTCCGCCCATGTGTCAC 61.035 63.158 0.00 0.00 0.00 3.67
3118 3764 2.217038 AGTCCGCCCATGTGTCACT 61.217 57.895 4.27 0.00 0.00 3.41
3119 3765 1.741770 GTCCGCCCATGTGTCACTC 60.742 63.158 4.27 0.00 0.00 3.51
3120 3766 2.815211 CCGCCCATGTGTCACTCG 60.815 66.667 4.27 0.72 0.00 4.18
3121 3767 2.048222 CGCCCATGTGTCACTCGT 60.048 61.111 4.27 0.00 0.00 4.18
3122 3768 1.214325 CGCCCATGTGTCACTCGTA 59.786 57.895 4.27 0.00 0.00 3.43
3123 3769 1.076533 CGCCCATGTGTCACTCGTAC 61.077 60.000 4.27 0.00 0.00 3.67
3124 3770 0.246635 GCCCATGTGTCACTCGTACT 59.753 55.000 4.27 0.00 0.00 2.73
3125 3771 1.337823 GCCCATGTGTCACTCGTACTT 60.338 52.381 4.27 0.00 0.00 2.24
3126 3772 2.337583 CCCATGTGTCACTCGTACTTG 58.662 52.381 4.27 0.00 0.00 3.16
3127 3773 2.337583 CCATGTGTCACTCGTACTTGG 58.662 52.381 4.27 0.00 34.62 3.61
3128 3774 1.726791 CATGTGTCACTCGTACTTGGC 59.273 52.381 4.27 0.00 0.00 4.52
3129 3775 0.747852 TGTGTCACTCGTACTTGGCA 59.252 50.000 4.27 0.00 0.00 4.92
3130 3776 1.137282 TGTGTCACTCGTACTTGGCAA 59.863 47.619 4.27 0.00 0.00 4.52
3131 3777 2.206750 GTGTCACTCGTACTTGGCAAA 58.793 47.619 0.00 0.00 0.00 3.68
3132 3778 2.806244 GTGTCACTCGTACTTGGCAAAT 59.194 45.455 0.00 0.00 0.00 2.32
3133 3779 3.250040 GTGTCACTCGTACTTGGCAAATT 59.750 43.478 0.00 0.00 0.00 1.82
3134 3780 4.449743 GTGTCACTCGTACTTGGCAAATTA 59.550 41.667 0.00 0.00 0.00 1.40
3135 3781 5.049954 GTGTCACTCGTACTTGGCAAATTAA 60.050 40.000 0.00 0.00 0.00 1.40
3136 3782 5.703592 TGTCACTCGTACTTGGCAAATTAAT 59.296 36.000 0.00 0.00 0.00 1.40
3137 3783 6.021596 GTCACTCGTACTTGGCAAATTAATG 58.978 40.000 0.00 0.00 0.00 1.90
3138 3784 4.793216 CACTCGTACTTGGCAAATTAATGC 59.207 41.667 0.00 0.00 45.67 3.56
3156 3802 9.830975 AATTAATGCATAACTTGTAAAATCCCC 57.169 29.630 0.00 0.00 0.00 4.81
3157 3803 6.865834 AATGCATAACTTGTAAAATCCCCA 57.134 33.333 0.00 0.00 0.00 4.96
3158 3804 6.865834 ATGCATAACTTGTAAAATCCCCAA 57.134 33.333 0.00 0.00 0.00 4.12
3159 3805 6.865834 TGCATAACTTGTAAAATCCCCAAT 57.134 33.333 0.00 0.00 0.00 3.16
3160 3806 6.638610 TGCATAACTTGTAAAATCCCCAATG 58.361 36.000 0.00 0.00 0.00 2.82
3161 3807 6.212388 TGCATAACTTGTAAAATCCCCAATGT 59.788 34.615 0.00 0.00 0.00 2.71
3162 3808 7.397476 TGCATAACTTGTAAAATCCCCAATGTA 59.603 33.333 0.00 0.00 0.00 2.29
3163 3809 8.421002 GCATAACTTGTAAAATCCCCAATGTAT 58.579 33.333 0.00 0.00 0.00 2.29
3168 3814 9.707957 ACTTGTAAAATCCCCAATGTATATTCA 57.292 29.630 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
130 135 2.571870 CTTAAACGCGCGCCGGAATT 62.572 55.000 32.58 13.10 42.52 2.17
134 139 4.494400 GACTTAAACGCGCGCCGG 62.494 66.667 32.58 15.62 42.52 6.13
190 195 0.691413 ACCTTAGCCTAGCCTGGACC 60.691 60.000 0.00 0.00 0.00 4.46
207 212 5.326200 ACATACAAGAGTACTGCACTACC 57.674 43.478 0.00 0.00 37.72 3.18
222 227 2.187424 GCCGGCCGGTACATACAA 59.813 61.111 42.53 0.00 37.65 2.41
223 228 3.852307 GGCCGGCCGGTACATACA 61.852 66.667 42.53 0.00 37.65 2.29
242 255 1.327764 GAGCGGCTGAAATTCGGTTAG 59.672 52.381 7.50 0.00 34.71 2.34
271 284 0.036732 TGTCTGCTGGTTAAGGCCTG 59.963 55.000 5.69 0.00 0.00 4.85
274 287 1.897560 ACTTGTCTGCTGGTTAAGGC 58.102 50.000 0.00 0.00 0.00 4.35
276 289 4.642429 ACCTAACTTGTCTGCTGGTTAAG 58.358 43.478 0.00 0.00 0.00 1.85
278 291 4.385825 CAACCTAACTTGTCTGCTGGTTA 58.614 43.478 0.00 0.00 34.96 2.85
347 363 2.362077 GGATCCAATCCCCATGTTTTCG 59.638 50.000 6.95 0.00 43.88 3.46
373 389 8.556194 TCGCGAAAAGAATATATGCAAATAAGT 58.444 29.630 6.20 0.00 0.00 2.24
374 390 8.933438 TCGCGAAAAGAATATATGCAAATAAG 57.067 30.769 6.20 0.00 0.00 1.73
393 409 2.298158 GATTGCCTCCTCCTCGCGAA 62.298 60.000 11.33 0.00 0.00 4.70
396 412 2.110006 GGATTGCCTCCTCCTCGC 59.890 66.667 0.00 0.00 41.29 5.03
436 452 4.412060 ACACCCATCCCAAATTAAGGAA 57.588 40.909 0.76 0.00 35.30 3.36
451 467 6.240549 ACATTTGACCATTTTAAACACCCA 57.759 33.333 0.00 0.00 0.00 4.51
453 469 7.042119 CCTGAACATTTGACCATTTTAAACACC 60.042 37.037 0.00 0.00 0.00 4.16
454 470 7.518211 GCCTGAACATTTGACCATTTTAAACAC 60.518 37.037 0.00 0.00 0.00 3.32
485 501 2.287584 AGATGGACCAAATTCAGGGGA 58.712 47.619 0.00 0.00 0.00 4.81
486 502 2.834638 AGATGGACCAAATTCAGGGG 57.165 50.000 0.00 0.00 0.00 4.79
531 548 4.467198 TTGAGACGGAGGGAATACTTTC 57.533 45.455 0.00 0.00 0.00 2.62
546 563 5.163814 ACCGTCGTAGTACTACATTTGAGAC 60.164 44.000 28.03 22.87 35.87 3.36
555 572 4.793731 GCCTAAAAACCGTCGTAGTACTAC 59.206 45.833 21.06 21.06 0.00 2.73
558 575 3.838120 AGCCTAAAAACCGTCGTAGTAC 58.162 45.455 0.00 0.00 0.00 2.73
559 576 4.519540 AAGCCTAAAAACCGTCGTAGTA 57.480 40.909 0.00 0.00 0.00 1.82
563 591 3.006217 AGTCTAAGCCTAAAAACCGTCGT 59.994 43.478 0.00 0.00 0.00 4.34
564 592 3.582780 AGTCTAAGCCTAAAAACCGTCG 58.417 45.455 0.00 0.00 0.00 5.12
594 626 5.497635 AAAATTGCGCCAACTTGATTTTT 57.502 30.435 4.18 0.00 0.00 1.94
644 676 8.251383 TGTAAAAGTAGCTAGCTAGGATGATT 57.749 34.615 24.78 15.07 0.00 2.57
654 686 8.077386 AGATCGTCTATTGTAAAAGTAGCTAGC 58.923 37.037 6.62 6.62 0.00 3.42
658 690 7.010183 TGCAAGATCGTCTATTGTAAAAGTAGC 59.990 37.037 0.00 0.00 0.00 3.58
659 691 8.407457 TGCAAGATCGTCTATTGTAAAAGTAG 57.593 34.615 0.00 0.00 0.00 2.57
660 692 8.653338 GTTGCAAGATCGTCTATTGTAAAAGTA 58.347 33.333 0.00 0.00 31.78 2.24
661 693 7.360946 GGTTGCAAGATCGTCTATTGTAAAAGT 60.361 37.037 0.00 0.00 31.78 2.66
678 775 2.158623 AGACAATCCAGTGGTTGCAAGA 60.159 45.455 18.67 0.00 0.00 3.02
690 787 7.039011 TGCTACTCTAGAGAAAAAGACAATCCA 60.039 37.037 26.57 7.12 0.00 3.41
719 819 3.198635 AGAATCGGGTGTGTGATGATCTT 59.801 43.478 0.00 0.00 0.00 2.40
727 827 3.027170 GCGCAGAATCGGGTGTGTG 62.027 63.158 0.30 0.00 0.00 3.82
728 828 2.742372 GCGCAGAATCGGGTGTGT 60.742 61.111 0.30 0.00 0.00 3.72
759 859 7.546358 TGACGCATGAGGATTTTCATTTTATT 58.454 30.769 0.00 0.00 35.67 1.40
761 861 6.507958 TGACGCATGAGGATTTTCATTTTA 57.492 33.333 0.00 0.00 35.67 1.52
821 923 7.553334 TGGGAGTTAGTTATACACTTGTGATC 58.447 38.462 7.83 0.00 36.88 2.92
827 929 8.545472 TGCTAATTGGGAGTTAGTTATACACTT 58.455 33.333 0.00 0.00 36.88 3.16
894 1013 6.924060 GCTATATGTAGTGTTTGTAGGAGTGG 59.076 42.308 0.00 0.00 0.00 4.00
901 1020 6.530120 CATGGGGCTATATGTAGTGTTTGTA 58.470 40.000 0.00 0.00 0.00 2.41
905 1024 3.557054 CGCATGGGGCTATATGTAGTGTT 60.557 47.826 0.89 0.00 41.67 3.32
983 1479 3.196463 GTCATCATCTTCTGCTCCAGTG 58.804 50.000 0.00 0.00 32.61 3.66
987 1483 2.879002 TCGTCATCATCTTCTGCTCC 57.121 50.000 0.00 0.00 0.00 4.70
988 1484 3.974912 TCATCGTCATCATCTTCTGCTC 58.025 45.455 0.00 0.00 0.00 4.26
989 1485 4.038883 TCATCATCGTCATCATCTTCTGCT 59.961 41.667 0.00 0.00 0.00 4.24
991 1487 5.163943 GCATCATCATCGTCATCATCTTCTG 60.164 44.000 0.00 0.00 0.00 3.02
1026 1527 6.433093 CCATGAGATTTGAGATGGCAATATGA 59.567 38.462 0.00 0.00 0.00 2.15
1042 1543 2.774234 CTCCTACCACCACCATGAGATT 59.226 50.000 0.00 0.00 0.00 2.40
1302 1858 5.183713 TCATCCAACTATTGCAAACTTGAGG 59.816 40.000 1.71 1.90 0.00 3.86
1310 1866 9.970395 GATTAATCAATCATCCAACTATTGCAA 57.030 29.630 10.68 0.00 40.35 4.08
1332 1890 8.196771 GCATGATTTGTTAGGTGAAATGGATTA 58.803 33.333 0.00 0.00 0.00 1.75
1381 1939 1.221840 GCTCCCTGAGAAATCGGCA 59.778 57.895 0.00 0.00 0.00 5.69
1382 1940 1.884926 CGCTCCCTGAGAAATCGGC 60.885 63.158 0.00 0.00 0.00 5.54
1383 1941 1.227380 CCGCTCCCTGAGAAATCGG 60.227 63.158 0.00 0.00 0.00 4.18
1385 1943 0.253327 AACCCGCTCCCTGAGAAATC 59.747 55.000 0.00 0.00 0.00 2.17
1386 1944 0.253327 GAACCCGCTCCCTGAGAAAT 59.747 55.000 0.00 0.00 0.00 2.17
1389 1947 1.535444 TTGAACCCGCTCCCTGAGA 60.535 57.895 0.00 0.00 0.00 3.27
1503 2061 2.181642 GGGGAGGAAGAAGGGAGGTATA 59.818 54.545 0.00 0.00 0.00 1.47
1504 2062 1.061268 GGGGAGGAAGAAGGGAGGTAT 60.061 57.143 0.00 0.00 0.00 2.73
1506 2064 1.083141 GGGGAGGAAGAAGGGAGGT 59.917 63.158 0.00 0.00 0.00 3.85
1507 2065 0.692756 GAGGGGAGGAAGAAGGGAGG 60.693 65.000 0.00 0.00 0.00 4.30
1508 2066 0.692756 GGAGGGGAGGAAGAAGGGAG 60.693 65.000 0.00 0.00 0.00 4.30
1509 2067 1.396594 GGAGGGGAGGAAGAAGGGA 59.603 63.158 0.00 0.00 0.00 4.20
1510 2068 2.066999 CGGAGGGGAGGAAGAAGGG 61.067 68.421 0.00 0.00 0.00 3.95
1511 2069 1.001760 TCGGAGGGGAGGAAGAAGG 59.998 63.158 0.00 0.00 0.00 3.46
1512 2070 1.668101 CGTCGGAGGGGAGGAAGAAG 61.668 65.000 0.00 0.00 0.00 2.85
1513 2071 1.681327 CGTCGGAGGGGAGGAAGAA 60.681 63.158 0.00 0.00 0.00 2.52
1516 2074 2.362120 GTCGTCGGAGGGGAGGAA 60.362 66.667 0.00 0.00 33.15 3.36
1541 2102 6.109359 AGAACTTAAGATCGATCCAACAAGG 58.891 40.000 21.66 8.42 39.47 3.61
1545 2106 8.596380 CAGTTAAGAACTTAAGATCGATCCAAC 58.404 37.037 21.66 9.01 40.46 3.77
1561 2122 6.826893 TTTTTGCTTGCATCAGTTAAGAAC 57.173 33.333 0.00 0.00 0.00 3.01
1869 2430 4.208686 ATCTCGCGCTCGGGGAAC 62.209 66.667 5.56 0.00 37.13 3.62
1971 2532 0.768622 AATCCTTGAACCCGGACACA 59.231 50.000 0.73 0.00 30.90 3.72
1989 2550 2.668212 CAGCCGGCGACCTTGAAA 60.668 61.111 23.20 0.00 0.00 2.69
2183 2747 8.855110 CGGAGCTTCCTCATCTTATATGTATAT 58.145 37.037 0.00 0.00 39.96 0.86
2184 2748 8.053355 TCGGAGCTTCCTCATCTTATATGTATA 58.947 37.037 0.00 0.00 39.96 1.47
2185 2749 6.892456 TCGGAGCTTCCTCATCTTATATGTAT 59.108 38.462 0.00 0.00 39.96 2.29
2187 2751 5.080337 TCGGAGCTTCCTCATCTTATATGT 58.920 41.667 0.00 0.00 39.96 2.29
2188 2752 5.184864 ACTCGGAGCTTCCTCATCTTATATG 59.815 44.000 4.58 0.00 39.96 1.78
2189 2753 5.329399 ACTCGGAGCTTCCTCATCTTATAT 58.671 41.667 4.58 0.00 39.96 0.86
2190 2754 4.730966 ACTCGGAGCTTCCTCATCTTATA 58.269 43.478 4.58 0.00 39.96 0.98
2191 2755 3.571590 ACTCGGAGCTTCCTCATCTTAT 58.428 45.455 4.58 0.00 39.96 1.73
2192 2756 3.019799 ACTCGGAGCTTCCTCATCTTA 57.980 47.619 4.58 0.00 39.96 2.10
2193 2757 1.859302 ACTCGGAGCTTCCTCATCTT 58.141 50.000 4.58 0.00 39.96 2.40
2194 2758 1.754226 GAACTCGGAGCTTCCTCATCT 59.246 52.381 4.58 0.00 39.96 2.90
2195 2759 1.535015 CGAACTCGGAGCTTCCTCATC 60.535 57.143 4.58 0.00 39.96 2.92
2196 2760 0.457851 CGAACTCGGAGCTTCCTCAT 59.542 55.000 4.58 0.00 39.96 2.90
2197 2761 0.608308 TCGAACTCGGAGCTTCCTCA 60.608 55.000 4.58 0.00 39.96 3.86
2198 2762 0.099791 CTCGAACTCGGAGCTTCCTC 59.900 60.000 4.58 0.00 40.29 3.71
2199 2763 1.939769 GCTCGAACTCGGAGCTTCCT 61.940 60.000 4.58 0.00 38.51 3.36
2200 2764 1.517475 GCTCGAACTCGGAGCTTCC 60.517 63.158 4.58 0.00 38.51 3.46
2201 2765 1.517475 GGCTCGAACTCGGAGCTTC 60.517 63.158 12.85 7.46 40.08 3.86
2202 2766 2.219325 CTGGCTCGAACTCGGAGCTT 62.219 60.000 12.85 0.00 40.08 3.74
2290 2876 9.091784 ACACTATACATCGTATACCGTATACTG 57.908 37.037 21.16 16.84 39.05 2.74
2291 2877 9.091784 CACACTATACATCGTATACCGTATACT 57.908 37.037 21.16 9.29 39.05 2.12
2292 2878 9.087424 TCACACTATACATCGTATACCGTATAC 57.913 37.037 15.97 15.97 38.09 1.47
2293 2879 9.822185 ATCACACTATACATCGTATACCGTATA 57.178 33.333 0.00 5.95 37.94 1.47
2294 2880 8.728337 ATCACACTATACATCGTATACCGTAT 57.272 34.615 10.44 10.44 37.94 3.06
2295 2881 7.009540 CGATCACACTATACATCGTATACCGTA 59.990 40.741 0.00 0.00 37.94 4.02
2296 2882 6.183360 CGATCACACTATACATCGTATACCGT 60.183 42.308 0.00 0.00 37.94 4.83
2333 2919 2.882137 TCTCACACACATACGTGACAGA 59.118 45.455 0.00 0.00 46.80 3.41
2334 2920 3.237628 CTCTCACACACATACGTGACAG 58.762 50.000 0.00 0.00 46.80 3.51
2335 2921 2.621526 ACTCTCACACACATACGTGACA 59.378 45.455 0.00 0.00 46.80 3.58
2339 2925 3.146847 TCAGACTCTCACACACATACGT 58.853 45.455 0.00 0.00 0.00 3.57
2340 2926 3.189495 ACTCAGACTCTCACACACATACG 59.811 47.826 0.00 0.00 0.00 3.06
2341 2927 4.480541 CACTCAGACTCTCACACACATAC 58.519 47.826 0.00 0.00 0.00 2.39
2342 2928 3.057245 GCACTCAGACTCTCACACACATA 60.057 47.826 0.00 0.00 0.00 2.29
2343 2929 2.288702 GCACTCAGACTCTCACACACAT 60.289 50.000 0.00 0.00 0.00 3.21
2350 2937 0.890996 TGCTCGCACTCAGACTCTCA 60.891 55.000 0.00 0.00 0.00 3.27
2353 2940 1.805134 GCTGCTCGCACTCAGACTC 60.805 63.158 0.00 0.00 38.92 3.36
2355 2942 2.093473 CAGCTGCTCGCACTCAGAC 61.093 63.158 0.00 0.00 42.61 3.51
2388 2978 1.896694 GCTGTCAGCCTGCTAGACT 59.103 57.895 14.27 0.00 34.48 3.24
2430 3023 3.950397 AGTTGGACAAGTGTCTCACAAA 58.050 40.909 11.07 0.00 44.20 2.83
2476 3069 5.645067 TCTCTGTATCAAAAGGTGCAGATTG 59.355 40.000 0.00 0.00 33.33 2.67
2497 3090 9.378597 GTGTACTAAAATTCGAACCTTTTTCTC 57.621 33.333 13.13 5.19 0.00 2.87
2508 3101 6.766944 TCAAAAGGTGGTGTACTAAAATTCGA 59.233 34.615 0.00 0.00 0.00 3.71
2510 3103 6.854381 CGTCAAAAGGTGGTGTACTAAAATTC 59.146 38.462 0.00 0.00 0.00 2.17
2584 3200 5.930837 AATCGAGTGAGAGAGGAAGAATT 57.069 39.130 0.00 0.00 0.00 2.17
2586 3202 4.081972 CCAAATCGAGTGAGAGAGGAAGAA 60.082 45.833 0.55 0.00 0.00 2.52
2588 3204 3.445450 TCCAAATCGAGTGAGAGAGGAAG 59.555 47.826 0.55 0.00 0.00 3.46
2613 3231 0.877213 CAGCCACCAAAAGCACAAGC 60.877 55.000 0.00 0.00 42.56 4.01
2642 3260 4.391405 AAAAGAAGTCTGGCACAAAAGG 57.609 40.909 0.00 0.00 38.70 3.11
2644 3262 4.928615 CACAAAAAGAAGTCTGGCACAAAA 59.071 37.500 0.00 0.00 38.70 2.44
2645 3263 4.493547 CACAAAAAGAAGTCTGGCACAAA 58.506 39.130 0.00 0.00 38.70 2.83
2646 3264 3.675775 GCACAAAAAGAAGTCTGGCACAA 60.676 43.478 0.00 0.00 38.70 3.33
2647 3265 2.159254 GCACAAAAAGAAGTCTGGCACA 60.159 45.455 0.00 0.00 0.00 4.57
2648 3266 2.463876 GCACAAAAAGAAGTCTGGCAC 58.536 47.619 0.00 0.00 0.00 5.01
2649 3267 1.408702 GGCACAAAAAGAAGTCTGGCA 59.591 47.619 0.00 0.00 0.00 4.92
2650 3268 1.408702 TGGCACAAAAAGAAGTCTGGC 59.591 47.619 0.00 0.00 31.92 4.85
2651 3269 2.951642 TCTGGCACAAAAAGAAGTCTGG 59.048 45.455 0.00 0.00 38.70 3.86
2652 3270 3.629398 AGTCTGGCACAAAAAGAAGTCTG 59.371 43.478 0.00 0.00 38.70 3.51
2653 3271 3.891049 AGTCTGGCACAAAAAGAAGTCT 58.109 40.909 0.00 0.00 38.70 3.24
2654 3272 4.336713 AGAAGTCTGGCACAAAAAGAAGTC 59.663 41.667 0.00 0.00 38.70 3.01
2655 3273 4.096984 CAGAAGTCTGGCACAAAAAGAAGT 59.903 41.667 0.00 0.00 38.70 3.01
2656 3274 4.336433 TCAGAAGTCTGGCACAAAAAGAAG 59.664 41.667 8.42 0.00 43.91 2.85
2657 3275 4.269183 TCAGAAGTCTGGCACAAAAAGAA 58.731 39.130 8.42 0.00 43.91 2.52
2658 3276 3.879295 CTCAGAAGTCTGGCACAAAAAGA 59.121 43.478 8.42 0.00 43.91 2.52
2659 3277 3.629398 ACTCAGAAGTCTGGCACAAAAAG 59.371 43.478 8.42 0.00 43.91 2.27
2660 3278 3.378112 CACTCAGAAGTCTGGCACAAAAA 59.622 43.478 8.42 0.00 43.91 1.94
2695 3313 4.142447 CTTCCCATGCTTCTTCATGTGAAG 60.142 45.833 14.99 14.99 45.36 3.02
2788 3434 6.936335 TCTGTGAGCTAATTGAAGTTTCATCA 59.064 34.615 0.00 0.00 37.00 3.07
2789 3435 7.095060 TGTCTGTGAGCTAATTGAAGTTTCATC 60.095 37.037 0.00 0.00 37.00 2.92
2790 3436 6.712095 TGTCTGTGAGCTAATTGAAGTTTCAT 59.288 34.615 0.00 0.00 37.00 2.57
2791 3437 6.054941 TGTCTGTGAGCTAATTGAAGTTTCA 58.945 36.000 0.00 0.00 34.92 2.69
2792 3438 6.425114 TCTGTCTGTGAGCTAATTGAAGTTTC 59.575 38.462 0.00 0.00 0.00 2.78
2793 3439 6.203723 GTCTGTCTGTGAGCTAATTGAAGTTT 59.796 38.462 0.00 0.00 0.00 2.66
2796 3442 5.119898 GTGTCTGTCTGTGAGCTAATTGAAG 59.880 44.000 0.00 0.00 0.00 3.02
2797 3443 4.991056 GTGTCTGTCTGTGAGCTAATTGAA 59.009 41.667 0.00 0.00 0.00 2.69
2799 3445 4.151335 GTGTGTCTGTCTGTGAGCTAATTG 59.849 45.833 0.00 0.00 0.00 2.32
2800 3446 4.202253 TGTGTGTCTGTCTGTGAGCTAATT 60.202 41.667 0.00 0.00 0.00 1.40
2801 3447 3.321968 TGTGTGTCTGTCTGTGAGCTAAT 59.678 43.478 0.00 0.00 0.00 1.73
2867 3513 4.752604 TCGCTATTGACAGCAAGTTTGTAA 59.247 37.500 0.00 0.00 41.88 2.41
2876 3522 4.309933 CCATTATCTCGCTATTGACAGCA 58.690 43.478 0.00 0.00 41.88 4.41
2980 3626 9.912634 ATCTACGTTGTCATGAAAATTCAAATT 57.087 25.926 0.61 0.00 41.13 1.82
3021 3667 6.835174 AGTATTATTCATGCATCCACAGTCT 58.165 36.000 0.00 0.00 0.00 3.24
3022 3668 6.148480 GGAGTATTATTCATGCATCCACAGTC 59.852 42.308 0.00 0.00 0.00 3.51
3023 3669 6.000219 GGAGTATTATTCATGCATCCACAGT 59.000 40.000 0.00 0.00 0.00 3.55
3024 3670 5.413833 GGGAGTATTATTCATGCATCCACAG 59.586 44.000 0.00 0.00 0.00 3.66
3025 3671 5.073554 AGGGAGTATTATTCATGCATCCACA 59.926 40.000 0.00 0.00 0.00 4.17
3026 3672 5.564550 AGGGAGTATTATTCATGCATCCAC 58.435 41.667 0.00 0.00 0.00 4.02
3027 3673 5.549228 AGAGGGAGTATTATTCATGCATCCA 59.451 40.000 0.00 0.00 0.00 3.41
3028 3674 6.059787 AGAGGGAGTATTATTCATGCATCC 57.940 41.667 0.00 0.00 0.00 3.51
3044 3690 9.360093 CGCTGTTATATTTCTTTATAGAGGGAG 57.640 37.037 0.00 0.00 0.00 4.30
3045 3691 8.867097 ACGCTGTTATATTTCTTTATAGAGGGA 58.133 33.333 0.00 0.00 0.00 4.20
3046 3692 9.490379 AACGCTGTTATATTTCTTTATAGAGGG 57.510 33.333 0.00 0.00 0.00 4.30
3062 3708 9.339850 TCTCTCTAGTAATCTAAACGCTGTTAT 57.660 33.333 0.00 0.00 0.00 1.89
3063 3709 8.728337 TCTCTCTAGTAATCTAAACGCTGTTA 57.272 34.615 0.00 0.00 0.00 2.41
3064 3710 7.627298 TCTCTCTAGTAATCTAAACGCTGTT 57.373 36.000 0.00 0.00 0.00 3.16
3065 3711 7.627298 TTCTCTCTAGTAATCTAAACGCTGT 57.373 36.000 0.00 0.00 0.00 4.40
3066 3712 9.820229 CTATTCTCTCTAGTAATCTAAACGCTG 57.180 37.037 0.00 0.00 0.00 5.18
3067 3713 9.781633 TCTATTCTCTCTAGTAATCTAAACGCT 57.218 33.333 0.00 0.00 0.00 5.07
3079 3725 8.842280 CGGACTGTATTTTCTATTCTCTCTAGT 58.158 37.037 0.00 0.00 0.00 2.57
3080 3726 7.806014 GCGGACTGTATTTTCTATTCTCTCTAG 59.194 40.741 0.00 0.00 0.00 2.43
3081 3727 7.255520 GGCGGACTGTATTTTCTATTCTCTCTA 60.256 40.741 0.00 0.00 0.00 2.43
3082 3728 6.461788 GGCGGACTGTATTTTCTATTCTCTCT 60.462 42.308 0.00 0.00 0.00 3.10
3083 3729 5.692654 GGCGGACTGTATTTTCTATTCTCTC 59.307 44.000 0.00 0.00 0.00 3.20
3084 3730 5.453480 GGGCGGACTGTATTTTCTATTCTCT 60.453 44.000 0.00 0.00 0.00 3.10
3085 3731 4.750598 GGGCGGACTGTATTTTCTATTCTC 59.249 45.833 0.00 0.00 0.00 2.87
3086 3732 4.163458 TGGGCGGACTGTATTTTCTATTCT 59.837 41.667 0.00 0.00 0.00 2.40
3087 3733 4.448210 TGGGCGGACTGTATTTTCTATTC 58.552 43.478 0.00 0.00 0.00 1.75
3088 3734 4.497291 TGGGCGGACTGTATTTTCTATT 57.503 40.909 0.00 0.00 0.00 1.73
3089 3735 4.141482 ACATGGGCGGACTGTATTTTCTAT 60.141 41.667 0.00 0.00 0.00 1.98
3090 3736 3.199071 ACATGGGCGGACTGTATTTTCTA 59.801 43.478 0.00 0.00 0.00 2.10
3091 3737 2.026262 ACATGGGCGGACTGTATTTTCT 60.026 45.455 0.00 0.00 0.00 2.52
3092 3738 2.097466 CACATGGGCGGACTGTATTTTC 59.903 50.000 0.00 0.00 0.00 2.29
3093 3739 2.091541 CACATGGGCGGACTGTATTTT 58.908 47.619 0.00 0.00 0.00 1.82
3094 3740 1.004277 ACACATGGGCGGACTGTATTT 59.996 47.619 0.00 0.00 0.00 1.40
3095 3741 0.618458 ACACATGGGCGGACTGTATT 59.382 50.000 0.00 0.00 0.00 1.89
3096 3742 0.178068 GACACATGGGCGGACTGTAT 59.822 55.000 0.00 0.00 0.00 2.29
3097 3743 1.188871 TGACACATGGGCGGACTGTA 61.189 55.000 0.00 0.00 0.00 2.74
3098 3744 2.347490 GACACATGGGCGGACTGT 59.653 61.111 0.00 0.00 0.00 3.55
3099 3745 2.034879 GTGACACATGGGCGGACTG 61.035 63.158 0.00 0.00 0.00 3.51
3100 3746 2.172483 GAGTGACACATGGGCGGACT 62.172 60.000 8.59 0.00 0.00 3.85
3101 3747 1.741770 GAGTGACACATGGGCGGAC 60.742 63.158 8.59 0.00 0.00 4.79
3102 3748 2.662596 GAGTGACACATGGGCGGA 59.337 61.111 8.59 0.00 0.00 5.54
3103 3749 2.220615 TACGAGTGACACATGGGCGG 62.221 60.000 8.59 0.00 0.00 6.13
3104 3750 1.076533 GTACGAGTGACACATGGGCG 61.077 60.000 8.59 5.91 0.00 6.13
3105 3751 0.246635 AGTACGAGTGACACATGGGC 59.753 55.000 8.59 0.00 0.00 5.36
3106 3752 2.337583 CAAGTACGAGTGACACATGGG 58.662 52.381 8.59 0.00 0.00 4.00
3107 3753 2.337583 CCAAGTACGAGTGACACATGG 58.662 52.381 8.59 0.00 0.00 3.66
3108 3754 1.726791 GCCAAGTACGAGTGACACATG 59.273 52.381 8.59 1.84 0.00 3.21
3109 3755 1.343142 TGCCAAGTACGAGTGACACAT 59.657 47.619 8.59 0.00 0.00 3.21
3110 3756 0.747852 TGCCAAGTACGAGTGACACA 59.252 50.000 8.59 0.00 0.00 3.72
3111 3757 1.860676 TTGCCAAGTACGAGTGACAC 58.139 50.000 0.00 0.00 0.00 3.67
3112 3758 2.605837 TTTGCCAAGTACGAGTGACA 57.394 45.000 0.00 0.00 0.00 3.58
3113 3759 5.600908 TTAATTTGCCAAGTACGAGTGAC 57.399 39.130 0.00 0.00 0.00 3.67
3114 3760 5.391523 GCATTAATTTGCCAAGTACGAGTGA 60.392 40.000 0.00 0.00 36.60 3.41
3115 3761 4.793216 GCATTAATTTGCCAAGTACGAGTG 59.207 41.667 0.00 0.00 36.60 3.51
3116 3762 4.457603 TGCATTAATTTGCCAAGTACGAGT 59.542 37.500 0.00 0.00 42.06 4.18
3117 3763 4.980590 TGCATTAATTTGCCAAGTACGAG 58.019 39.130 0.00 0.00 42.06 4.18
3118 3764 5.574891 ATGCATTAATTTGCCAAGTACGA 57.425 34.783 0.00 0.00 42.06 3.43
3119 3765 6.972328 AGTTATGCATTAATTTGCCAAGTACG 59.028 34.615 3.54 0.00 42.06 3.67
3120 3766 8.594687 CAAGTTATGCATTAATTTGCCAAGTAC 58.405 33.333 3.54 0.00 42.06 2.73
3121 3767 8.310382 ACAAGTTATGCATTAATTTGCCAAGTA 58.690 29.630 3.54 0.00 39.73 2.24
3122 3768 7.160726 ACAAGTTATGCATTAATTTGCCAAGT 58.839 30.769 3.54 0.00 39.73 3.16
3123 3769 7.599630 ACAAGTTATGCATTAATTTGCCAAG 57.400 32.000 3.54 0.00 39.73 3.61
3124 3770 9.494271 TTTACAAGTTATGCATTAATTTGCCAA 57.506 25.926 3.54 6.22 39.73 4.52
3125 3771 9.494271 TTTTACAAGTTATGCATTAATTTGCCA 57.506 25.926 3.54 0.98 39.73 4.92
3130 3776 9.830975 GGGGATTTTACAAGTTATGCATTAATT 57.169 29.630 3.54 0.00 0.00 1.40
3131 3777 8.986991 TGGGGATTTTACAAGTTATGCATTAAT 58.013 29.630 3.54 0.00 0.00 1.40
3132 3778 8.367660 TGGGGATTTTACAAGTTATGCATTAA 57.632 30.769 3.54 0.00 0.00 1.40
3133 3779 7.962995 TGGGGATTTTACAAGTTATGCATTA 57.037 32.000 3.54 0.00 0.00 1.90
3134 3780 6.865834 TGGGGATTTTACAAGTTATGCATT 57.134 33.333 3.54 0.00 0.00 3.56
3135 3781 6.865834 TTGGGGATTTTACAAGTTATGCAT 57.134 33.333 3.79 3.79 0.00 3.96
3136 3782 6.212388 ACATTGGGGATTTTACAAGTTATGCA 59.788 34.615 0.00 0.00 0.00 3.96
3137 3783 6.639563 ACATTGGGGATTTTACAAGTTATGC 58.360 36.000 0.00 0.00 0.00 3.14
3142 3788 9.707957 TGAATATACATTGGGGATTTTACAAGT 57.292 29.630 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.