Multiple sequence alignment - TraesCS1A01G046000

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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 TraesCS1A01G046000 chr1A 100.000 3751 0 0 1 3751 27325246 27328996 0.000000e+00 6927.0
1 TraesCS1A01G046000 chr1A 94.976 418 17 4 3142 3557 511219238 511219653 0.000000e+00 652.0
2 TraesCS1A01G046000 chr1A 100.000 241 0 0 607 847 563181804 563182044 2.660000e-121 446.0
3 TraesCS1A01G046000 chr7A 97.800 1091 17 1 866 1956 35627879 35628962 0.000000e+00 1875.0
4 TraesCS1A01G046000 chr7A 97.054 611 16 2 1 610 701574393 701573784 0.000000e+00 1027.0
5 TraesCS1A01G046000 chr7A 98.547 413 3 3 3142 3552 558102635 558102224 0.000000e+00 726.0
6 TraesCS1A01G046000 chr7A 94.673 413 19 2 3142 3552 640497004 640496593 4.090000e-179 638.0
7 TraesCS1A01G046000 chr7A 90.306 392 21 3 2610 2992 35628957 35629340 7.240000e-137 497.0
8 TraesCS1A01G046000 chr7A 97.095 241 7 0 607 847 672531506 672531746 1.250000e-109 407.0
9 TraesCS1A01G046000 chr7A 97.095 241 7 0 607 847 672715841 672716081 1.250000e-109 407.0
10 TraesCS1A01G046000 chr7A 95.902 244 10 0 606 849 486921280 486921037 2.720000e-106 396.0
11 TraesCS1A01G046000 chr7A 82.567 413 39 11 866 1278 35708968 35708589 2.160000e-87 333.0
12 TraesCS1A01G046000 chr7A 92.611 203 9 2 3553 3750 35630031 35630232 1.700000e-73 287.0
13 TraesCS1A01G046000 chr7A 87.500 256 17 3 2017 2270 254887986 254888228 7.930000e-72 281.0
14 TraesCS1A01G046000 chr7A 94.545 55 3 0 3053 3107 705305884 705305830 6.680000e-13 86.1
15 TraesCS1A01G046000 chr7D 94.268 1099 38 6 866 1956 36200591 36199510 0.000000e+00 1657.0
16 TraesCS1A01G046000 chr7D 91.768 328 18 1 2610 2928 36199515 36199188 7.390000e-122 448.0
17 TraesCS1A01G046000 chr7D 93.627 204 6 3 3553 3750 36198798 36198596 7.880000e-77 298.0
18 TraesCS1A01G046000 chr7D 88.350 206 22 2 2937 3141 36198993 36198789 2.890000e-61 246.0
19 TraesCS1A01G046000 chrUn 94.259 1080 49 3 877 1956 194662974 194664040 0.000000e+00 1639.0
20 TraesCS1A01G046000 chrUn 87.389 563 39 14 2610 3141 194664035 194664596 5.320000e-173 617.0
21 TraesCS1A01G046000 chrUn 90.244 205 11 5 3553 3750 194664587 194664789 3.720000e-65 259.0
22 TraesCS1A01G046000 chrUn 94.118 51 2 1 3056 3105 90282621 90282671 4.020000e-10 76.8
23 TraesCS1A01G046000 chr4B 99.016 610 6 0 1 610 238175594 238176203 0.000000e+00 1094.0
24 TraesCS1A01G046000 chr4B 98.525 610 9 0 1 610 312777765 312777156 0.000000e+00 1077.0
25 TraesCS1A01G046000 chr4B 87.179 273 21 2 2017 2287 647674769 647675029 7.880000e-77 298.0
26 TraesCS1A01G046000 chr4B 87.179 273 21 2 2017 2287 647676088 647676348 7.880000e-77 298.0
27 TraesCS1A01G046000 chr5B 98.191 608 11 0 3 610 311955128 311954521 0.000000e+00 1062.0
28 TraesCS1A01G046000 chr5B 94.888 626 15 3 1 610 696412995 696413619 0.000000e+00 963.0
29 TraesCS1A01G046000 chr5B 90.134 598 48 3 24 610 275181048 275180451 0.000000e+00 767.0
30 TraesCS1A01G046000 chr5B 93.598 328 20 1 1964 2290 611857549 611857222 4.350000e-134 488.0
31 TraesCS1A01G046000 chr5B 93.578 327 20 1 1964 2290 611858856 611858531 1.570000e-133 486.0
32 TraesCS1A01G046000 chr5B 90.909 55 5 0 3053 3107 664025345 664025399 1.440000e-09 75.0
33 TraesCS1A01G046000 chr5B 88.333 60 6 1 3053 3112 316708878 316708936 1.870000e-08 71.3
34 TraesCS1A01G046000 chr4A 97.545 611 14 1 1 610 590260254 590259644 0.000000e+00 1044.0
35 TraesCS1A01G046000 chr4A 100.000 242 0 0 607 848 696534262 696534021 7.390000e-122 448.0
36 TraesCS1A01G046000 chr4A 84.300 293 43 3 2320 2609 214200292 214200000 2.210000e-72 283.0
37 TraesCS1A01G046000 chr4A 84.043 282 44 1 2329 2609 214197871 214197590 1.720000e-68 270.0
38 TraesCS1A01G046000 chr6D 90.299 670 49 3 1956 2609 443238544 443237875 0.000000e+00 863.0
39 TraesCS1A01G046000 chr6D 86.316 285 38 1 2331 2614 358395533 358395817 3.640000e-80 309.0
40 TraesCS1A01G046000 chr2B 92.568 592 38 3 24 610 57910614 57911204 0.000000e+00 845.0
41 TraesCS1A01G046000 chr2B 100.000 243 0 0 605 847 705019498 705019740 2.050000e-122 449.0
42 TraesCS1A01G046000 chr2B 87.390 341 26 3 1963 2287 795768797 795769136 3.540000e-100 375.0
43 TraesCS1A01G046000 chr7B 98.039 459 7 2 1 458 372341803 372342260 0.000000e+00 797.0
44 TraesCS1A01G046000 chr7B 94.928 414 17 4 3142 3554 693399748 693399338 0.000000e+00 645.0
45 TraesCS1A01G046000 chr7B 86.957 276 22 2 2017 2290 747793207 747792944 7.880000e-77 298.0
46 TraesCS1A01G046000 chr7B 86.909 275 22 2 2018 2290 747794525 747794263 2.830000e-76 296.0
47 TraesCS1A01G046000 chr7B 82.534 292 49 2 2320 2609 747257689 747257398 4.810000e-64 255.0
48 TraesCS1A01G046000 chr7B 87.283 173 22 0 2331 2503 748602787 748602615 8.220000e-47 198.0
49 TraesCS1A01G046000 chr3A 88.815 599 51 11 26 610 728894811 728894215 0.000000e+00 721.0
50 TraesCS1A01G046000 chr3A 100.000 242 0 0 606 847 208637672 208637431 7.390000e-122 448.0
51 TraesCS1A01G046000 chr3A 85.345 116 15 2 2347 2460 731516498 731516383 6.580000e-23 119.0
52 TraesCS1A01G046000 chr5A 96.411 418 8 7 3142 3556 510497343 510497756 0.000000e+00 682.0
53 TraesCS1A01G046000 chr5A 96.356 247 7 2 606 851 505223423 505223668 4.510000e-109 405.0
54 TraesCS1A01G046000 chr5A 96.356 247 7 2 606 851 505225359 505225604 4.510000e-109 405.0
55 TraesCS1A01G046000 chr2A 94.749 419 20 2 3134 3552 61475974 61475558 0.000000e+00 651.0
56 TraesCS1A01G046000 chr6A 95.146 412 18 2 3141 3552 574236887 574237296 0.000000e+00 649.0
57 TraesCS1A01G046000 chr2D 94.258 418 18 5 3142 3559 600408206 600408617 5.290000e-178 634.0
58 TraesCS1A01G046000 chr2D 88.743 382 37 3 2062 2438 87358727 87358347 2.640000e-126 462.0
59 TraesCS1A01G046000 chr2D 94.118 51 2 1 3056 3105 32017668 32017618 4.020000e-10 76.8
60 TraesCS1A01G046000 chr6B 93.088 434 27 3 3124 3554 5679232 5678799 1.900000e-177 632.0
61 TraesCS1A01G046000 chr1B 92.669 341 17 1 1956 2288 49862852 49863192 5.630000e-133 484.0
62 TraesCS1A01G046000 chr3B 87.259 259 31 1 2351 2609 810547344 810547600 1.020000e-75 294.0
63 TraesCS1A01G046000 chr3B 94.595 74 4 0 1956 2029 36433007 36433080 8.510000e-22 115.0
64 TraesCS1A01G046000 chr3B 94.595 74 4 0 1956 2029 36434336 36434409 8.510000e-22 115.0
65 TraesCS1A01G046000 chr3B 92.453 53 4 0 3053 3105 708518257 708518205 4.020000e-10 76.8
66 TraesCS1A01G046000 chr5D 86.517 267 35 1 2345 2610 133164027 133163761 3.660000e-75 292.0
67 TraesCS1A01G046000 chr5D 91.525 59 5 0 3053 3111 282007066 282007124 8.640000e-12 82.4
68 TraesCS1A01G046000 chr3D 84.752 282 41 2 2329 2609 553931057 553930777 7.930000e-72 281.0
69 TraesCS1A01G046000 chr1D 85.714 259 35 1 2351 2609 468051780 468051524 4.770000e-69 272.0


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 TraesCS1A01G046000 chr1A 27325246 27328996 3750 False 6927.000000 6927 100.000000 1 3751 1 chr1A.!!$F1 3750
1 TraesCS1A01G046000 chr7A 701573784 701574393 609 True 1027.000000 1027 97.054000 1 610 1 chr7A.!!$R5 609
2 TraesCS1A01G046000 chr7A 35627879 35630232 2353 False 886.333333 1875 93.572333 866 3750 3 chr7A.!!$F4 2884
3 TraesCS1A01G046000 chr7D 36198596 36200591 1995 True 662.250000 1657 92.003250 866 3750 4 chr7D.!!$R1 2884
4 TraesCS1A01G046000 chrUn 194662974 194664789 1815 False 838.333333 1639 90.630667 877 3750 3 chrUn.!!$F2 2873
5 TraesCS1A01G046000 chr4B 238175594 238176203 609 False 1094.000000 1094 99.016000 1 610 1 chr4B.!!$F1 609
6 TraesCS1A01G046000 chr4B 312777156 312777765 609 True 1077.000000 1077 98.525000 1 610 1 chr4B.!!$R1 609
7 TraesCS1A01G046000 chr4B 647674769 647676348 1579 False 298.000000 298 87.179000 2017 2287 2 chr4B.!!$F2 270
8 TraesCS1A01G046000 chr5B 311954521 311955128 607 True 1062.000000 1062 98.191000 3 610 1 chr5B.!!$R2 607
9 TraesCS1A01G046000 chr5B 696412995 696413619 624 False 963.000000 963 94.888000 1 610 1 chr5B.!!$F3 609
10 TraesCS1A01G046000 chr5B 275180451 275181048 597 True 767.000000 767 90.134000 24 610 1 chr5B.!!$R1 586
11 TraesCS1A01G046000 chr5B 611857222 611858856 1634 True 487.000000 488 93.588000 1964 2290 2 chr5B.!!$R3 326
12 TraesCS1A01G046000 chr4A 590259644 590260254 610 True 1044.000000 1044 97.545000 1 610 1 chr4A.!!$R1 609
13 TraesCS1A01G046000 chr4A 214197590 214200292 2702 True 276.500000 283 84.171500 2320 2609 2 chr4A.!!$R3 289
14 TraesCS1A01G046000 chr6D 443237875 443238544 669 True 863.000000 863 90.299000 1956 2609 1 chr6D.!!$R1 653
15 TraesCS1A01G046000 chr2B 57910614 57911204 590 False 845.000000 845 92.568000 24 610 1 chr2B.!!$F1 586
16 TraesCS1A01G046000 chr7B 747792944 747794525 1581 True 297.000000 298 86.933000 2017 2290 2 chr7B.!!$R4 273
17 TraesCS1A01G046000 chr3A 728894215 728894811 596 True 721.000000 721 88.815000 26 610 1 chr3A.!!$R2 584
18 TraesCS1A01G046000 chr5A 505223423 505225604 2181 False 405.000000 405 96.356000 606 851 2 chr5A.!!$F2 245

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
955 1511 2.359975 GTTCACTCCCGGCCTTGG 60.360 66.667 0.0 0.5 0.00 3.61 F
2105 2790 0.528924 TTGTAGCCATACAGCGACGT 59.471 50.000 0.0 0.0 42.72 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2310 2995 0.599558 AAGCGTGCGTGTAGGTCTAA 59.40 50.0 0.0 0.0 0.0 2.10 R
3536 8793 0.109723 TCACGGAGGGGAACTTTTGG 59.89 55.0 0.0 0.0 0.0 3.28 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
629 660 7.020270 TGGTACTCCCTCCTTCCATCTATATAA 59.980 40.741 0.00 0.00 0.00 0.98
743 775 4.449743 TCCTTTCACTTACGAATTTGACGG 59.550 41.667 0.00 0.00 34.93 4.79
744 776 3.799137 TTCACTTACGAATTTGACGGC 57.201 42.857 0.00 0.00 34.93 5.68
806 838 8.208224 TCTAACATTTGGTCAAAGTTAGTCTCA 58.792 33.333 24.34 14.57 39.54 3.27
847 879 7.064229 CCTATATAGATGGAAGGAGGGAGTAC 58.936 46.154 11.53 0.00 0.00 2.73
848 880 6.744802 ATATAGATGGAAGGAGGGAGTACT 57.255 41.667 0.00 0.00 0.00 2.73
849 881 7.848821 ATATAGATGGAAGGAGGGAGTACTA 57.151 40.000 0.00 0.00 0.00 1.82
850 882 6.744802 ATAGATGGAAGGAGGGAGTACTAT 57.255 41.667 0.00 0.00 0.00 2.12
851 883 5.005628 AGATGGAAGGAGGGAGTACTATC 57.994 47.826 0.00 0.00 0.00 2.08
852 884 3.225177 TGGAAGGAGGGAGTACTATCG 57.775 52.381 0.00 0.00 0.00 2.92
855 887 3.553904 GAAGGAGGGAGTACTATCGTGT 58.446 50.000 0.00 0.00 0.00 4.49
857 889 4.785346 AGGAGGGAGTACTATCGTGTAA 57.215 45.455 0.00 0.00 0.00 2.41
859 891 5.703310 AGGAGGGAGTACTATCGTGTAATT 58.297 41.667 0.00 0.00 0.00 1.40
863 1242 7.230309 GGAGGGAGTACTATCGTGTAATTAACT 59.770 40.741 0.00 0.00 0.00 2.24
955 1511 2.359975 GTTCACTCCCGGCCTTGG 60.360 66.667 0.00 0.50 0.00 3.61
986 1542 2.530701 CACCACACTCTTCCTACTCCT 58.469 52.381 0.00 0.00 0.00 3.69
1332 1999 4.414956 ATCCTCCCGCACCTCCCA 62.415 66.667 0.00 0.00 0.00 4.37
1355 2022 2.186903 GTCCATCACCGCGGTCAT 59.813 61.111 31.80 21.45 0.00 3.06
2021 2704 2.783228 TTTTTCTGGCGACCAACGT 58.217 47.368 0.00 0.00 44.60 3.99
2036 2719 2.739287 CGTCCCGGCGCTTAAACA 60.739 61.111 7.64 0.00 0.00 2.83
2040 2723 3.436924 CCGGCGCTTAAACACCCC 61.437 66.667 7.64 0.00 0.00 4.95
2050 2735 4.037565 CGCTTAAACACCCCTTTTCTTTCT 59.962 41.667 0.00 0.00 0.00 2.52
2058 2743 1.271656 CCCTTTTCTTTCTGCTGGCTG 59.728 52.381 0.00 0.00 0.00 4.85
2105 2790 0.528924 TTGTAGCCATACAGCGACGT 59.471 50.000 0.00 0.00 42.72 4.34
2122 2807 1.450312 GTAGCGCCCATGCAACTCT 60.450 57.895 2.29 0.00 37.32 3.24
2158 2843 2.289547 GCACGTACACAACAAACTCCAT 59.710 45.455 0.00 0.00 0.00 3.41
2165 2850 5.726980 ACACAACAAACTCCATATGCATT 57.273 34.783 3.54 0.00 0.00 3.56
2392 3167 1.154016 CGTCCAACGAGCTCGACAT 60.154 57.895 40.58 23.16 46.05 3.06
2398 3173 2.262211 CAACGAGCTCGACATCATCAA 58.738 47.619 40.58 0.00 43.02 2.57
2405 3298 2.467838 CTCGACATCATCAATGCGTCT 58.532 47.619 9.33 0.00 39.12 4.18
2410 3303 3.538591 ACATCATCAATGCGTCTCACAT 58.461 40.909 0.00 0.00 39.12 3.21
2517 3466 1.080093 CGACCACACACGCCTACAT 60.080 57.895 0.00 0.00 0.00 2.29
2518 3467 0.669318 CGACCACACACGCCTACATT 60.669 55.000 0.00 0.00 0.00 2.71
2531 6032 1.290203 CTACATTGCGATCTTGCCGT 58.710 50.000 0.00 0.00 0.00 5.68
2586 6153 1.008881 GACGCGTCTGACACTGACA 60.009 57.895 31.12 0.00 33.00 3.58
2625 6192 0.877213 ACAAGGTGTACGTGTTCGCC 60.877 55.000 0.00 5.00 38.71 5.54
2748 6315 1.073923 ACGATCAAAGGCTTGAAGGGT 59.926 47.619 0.00 0.00 44.64 4.34
2786 6353 3.434319 CGGCAGCAGAAACGGCAT 61.434 61.111 0.00 0.00 31.84 4.40
2986 8230 4.065088 TGTTAGCTTTTCTGGCTAGTGTG 58.935 43.478 0.00 0.00 42.22 3.82
3013 8257 6.888105 TCACTCTTTCAGGATATAATGCACA 58.112 36.000 0.00 0.00 0.00 4.57
3016 8260 6.765036 ACTCTTTCAGGATATAATGCACACTG 59.235 38.462 0.00 0.00 0.00 3.66
3045 8289 9.651718 GAATAATAATTACCGACAAAGAAGCTG 57.348 33.333 0.00 0.00 0.00 4.24
3047 8291 1.144969 TTACCGACAAAGAAGCTGCG 58.855 50.000 0.00 0.00 0.00 5.18
3141 8398 7.041721 TGCTGTGATTAGTATGTGAAGTTAGG 58.958 38.462 0.00 0.00 0.00 2.69
3142 8399 6.480320 GCTGTGATTAGTATGTGAAGTTAGGG 59.520 42.308 0.00 0.00 0.00 3.53
3143 8400 6.884832 TGTGATTAGTATGTGAAGTTAGGGG 58.115 40.000 0.00 0.00 0.00 4.79
3144 8401 6.670464 TGTGATTAGTATGTGAAGTTAGGGGA 59.330 38.462 0.00 0.00 0.00 4.81
3147 8404 8.778059 TGATTAGTATGTGAAGTTAGGGGAAAT 58.222 33.333 0.00 0.00 0.00 2.17
3150 8407 7.504926 AGTATGTGAAGTTAGGGGAAATACA 57.495 36.000 0.00 0.00 0.00 2.29
3152 8409 5.836024 TGTGAAGTTAGGGGAAATACACT 57.164 39.130 0.00 0.00 0.00 3.55
3153 8410 6.195600 TGTGAAGTTAGGGGAAATACACTT 57.804 37.500 0.00 0.00 0.00 3.16
3154 8411 6.001460 TGTGAAGTTAGGGGAAATACACTTG 58.999 40.000 0.00 0.00 0.00 3.16
3155 8412 6.002082 GTGAAGTTAGGGGAAATACACTTGT 58.998 40.000 0.00 0.00 0.00 3.16
3156 8413 6.001460 TGAAGTTAGGGGAAATACACTTGTG 58.999 40.000 0.00 0.00 0.00 3.33
3157 8414 5.578157 AGTTAGGGGAAATACACTTGTGT 57.422 39.130 11.30 11.30 0.00 3.72
3158 8415 5.948842 AGTTAGGGGAAATACACTTGTGTT 58.051 37.500 11.80 0.00 0.00 3.32
3160 8417 3.763057 AGGGGAAATACACTTGTGTTCC 58.237 45.455 11.80 12.10 40.20 3.62
3161 8418 3.397955 AGGGGAAATACACTTGTGTTCCT 59.602 43.478 17.42 8.39 40.49 3.36
3162 8419 3.506067 GGGGAAATACACTTGTGTTCCTG 59.494 47.826 17.42 0.00 40.49 3.86
3163 8420 3.506067 GGGAAATACACTTGTGTTCCTGG 59.494 47.826 17.42 0.00 40.49 4.45
3164 8421 4.142038 GGAAATACACTTGTGTTCCTGGT 58.858 43.478 11.80 0.00 38.98 4.00
3165 8422 4.023193 GGAAATACACTTGTGTTCCTGGTG 60.023 45.833 11.80 0.00 38.98 4.17
3166 8423 2.631160 TACACTTGTGTTCCTGGTGG 57.369 50.000 11.80 0.00 32.88 4.61
3168 8425 1.841277 ACACTTGTGTTCCTGGTGGTA 59.159 47.619 0.00 0.00 32.88 3.25
3169 8426 2.441750 ACACTTGTGTTCCTGGTGGTAT 59.558 45.455 0.00 0.00 32.88 2.73
3170 8427 3.649023 ACACTTGTGTTCCTGGTGGTATA 59.351 43.478 0.00 0.00 32.88 1.47
3171 8428 4.288626 ACACTTGTGTTCCTGGTGGTATAT 59.711 41.667 0.00 0.00 32.88 0.86
3172 8429 4.635765 CACTTGTGTTCCTGGTGGTATATG 59.364 45.833 0.00 0.00 34.23 1.78
3173 8430 3.275617 TGTGTTCCTGGTGGTATATGC 57.724 47.619 0.00 0.00 34.23 3.14
3174 8431 2.573915 TGTGTTCCTGGTGGTATATGCA 59.426 45.455 0.00 0.00 34.23 3.96
3175 8432 2.943033 GTGTTCCTGGTGGTATATGCAC 59.057 50.000 0.00 0.00 34.23 4.57
3176 8433 2.092646 TGTTCCTGGTGGTATATGCACC 60.093 50.000 0.00 0.00 39.20 5.01
3177 8434 1.136828 TCCTGGTGGTATATGCACCC 58.863 55.000 0.00 1.81 37.84 4.61
3178 8435 1.140312 CCTGGTGGTATATGCACCCT 58.860 55.000 0.00 0.00 37.84 4.34
3179 8436 2.090437 TCCTGGTGGTATATGCACCCTA 60.090 50.000 0.00 0.00 37.84 3.53
3180 8437 2.912956 CCTGGTGGTATATGCACCCTAT 59.087 50.000 0.00 0.00 37.84 2.57
3181 8438 4.101114 CCTGGTGGTATATGCACCCTATA 58.899 47.826 0.00 0.00 37.84 1.31
3182 8439 4.721776 CCTGGTGGTATATGCACCCTATAT 59.278 45.833 0.00 0.00 37.84 0.86
3183 8440 5.396772 CCTGGTGGTATATGCACCCTATATG 60.397 48.000 0.00 0.00 37.84 1.78
3184 8441 4.473196 TGGTGGTATATGCACCCTATATGG 59.527 45.833 0.00 0.00 37.84 2.74
3261 8518 8.850454 TGACAAAATACTTGACTTACTTTTGC 57.150 30.769 0.00 0.00 37.18 3.68
3262 8519 8.462811 TGACAAAATACTTGACTTACTTTTGCA 58.537 29.630 0.00 0.00 37.18 4.08
3263 8520 8.628882 ACAAAATACTTGACTTACTTTTGCAC 57.371 30.769 0.00 0.00 37.18 4.57
3264 8521 8.466798 ACAAAATACTTGACTTACTTTTGCACT 58.533 29.630 0.00 0.00 37.18 4.40
3265 8522 9.944663 CAAAATACTTGACTTACTTTTGCACTA 57.055 29.630 0.00 0.00 29.95 2.74
3267 8524 8.904099 AATACTTGACTTACTTTTGCACTAGT 57.096 30.769 5.34 5.34 0.00 2.57
3268 8525 9.991906 AATACTTGACTTACTTTTGCACTAGTA 57.008 29.630 0.00 3.57 0.00 1.82
3271 8528 9.991906 ACTTGACTTACTTTTGCACTAGTATAA 57.008 29.630 7.69 0.00 0.00 0.98
3279 8536 7.758495 ACTTTTGCACTAGTATAAAAATCCCG 58.242 34.615 13.97 7.58 0.00 5.14
3280 8537 7.608761 ACTTTTGCACTAGTATAAAAATCCCGA 59.391 33.333 13.97 0.00 0.00 5.14
3281 8538 6.913873 TTGCACTAGTATAAAAATCCCGAC 57.086 37.500 0.00 0.00 0.00 4.79
3282 8539 5.045215 TGCACTAGTATAAAAATCCCGACG 58.955 41.667 0.00 0.00 0.00 5.12
3283 8540 5.163530 TGCACTAGTATAAAAATCCCGACGA 60.164 40.000 0.00 0.00 0.00 4.20
3284 8541 5.750067 GCACTAGTATAAAAATCCCGACGAA 59.250 40.000 0.00 0.00 0.00 3.85
3285 8542 6.256321 GCACTAGTATAAAAATCCCGACGAAA 59.744 38.462 0.00 0.00 0.00 3.46
3286 8543 7.201548 GCACTAGTATAAAAATCCCGACGAAAA 60.202 37.037 0.00 0.00 0.00 2.29
3287 8544 8.658609 CACTAGTATAAAAATCCCGACGAAAAA 58.341 33.333 0.00 0.00 0.00 1.94
3310 8567 3.782889 AACAAAAGTTGACCTCACAGC 57.217 42.857 0.00 0.00 0.00 4.40
3311 8568 2.722094 ACAAAAGTTGACCTCACAGCA 58.278 42.857 0.00 0.00 0.00 4.41
3312 8569 3.088532 ACAAAAGTTGACCTCACAGCAA 58.911 40.909 0.00 0.00 0.00 3.91
3313 8570 3.509575 ACAAAAGTTGACCTCACAGCAAA 59.490 39.130 0.00 0.00 0.00 3.68
3314 8571 4.021544 ACAAAAGTTGACCTCACAGCAAAA 60.022 37.500 0.00 0.00 0.00 2.44
3315 8572 4.799564 AAAGTTGACCTCACAGCAAAAA 57.200 36.364 0.00 0.00 0.00 1.94
3354 8611 9.542462 TTTGCTATTATAGGTCACTATTCACAC 57.458 33.333 1.12 0.00 40.35 3.82
3355 8612 8.478775 TGCTATTATAGGTCACTATTCACACT 57.521 34.615 1.12 0.00 40.35 3.55
3356 8613 9.582648 TGCTATTATAGGTCACTATTCACACTA 57.417 33.333 1.12 0.00 40.35 2.74
3363 8620 9.765795 ATAGGTCACTATTCACACTATTTTAGC 57.234 33.333 0.00 0.00 36.51 3.09
3364 8621 7.048512 AGGTCACTATTCACACTATTTTAGCC 58.951 38.462 0.00 0.00 0.00 3.93
3365 8622 6.821665 GGTCACTATTCACACTATTTTAGCCA 59.178 38.462 0.00 0.00 0.00 4.75
3366 8623 7.335924 GGTCACTATTCACACTATTTTAGCCAA 59.664 37.037 0.00 0.00 0.00 4.52
3367 8624 8.726988 GTCACTATTCACACTATTTTAGCCAAA 58.273 33.333 0.00 0.00 0.00 3.28
3368 8625 9.290988 TCACTATTCACACTATTTTAGCCAAAA 57.709 29.630 0.00 0.00 38.00 2.44
3369 8626 9.906660 CACTATTCACACTATTTTAGCCAAAAA 57.093 29.630 0.00 0.00 41.21 1.94
3374 8631 9.606631 TTCACACTATTTTAGCCAAAAATTTGT 57.393 25.926 11.38 11.68 43.75 2.83
3375 8632 9.255304 TCACACTATTTTAGCCAAAAATTTGTC 57.745 29.630 11.38 0.00 43.75 3.18
3376 8633 9.260002 CACACTATTTTAGCCAAAAATTTGTCT 57.740 29.630 11.38 0.28 43.75 3.41
3377 8634 9.830975 ACACTATTTTAGCCAAAAATTTGTCTT 57.169 25.926 11.38 0.00 43.75 3.01
3444 8701 8.842358 TTTTTCTCACGAATACAATAGAAGGT 57.158 30.769 0.00 0.00 0.00 3.50
3445 8702 8.475331 TTTTCTCACGAATACAATAGAAGGTC 57.525 34.615 0.00 0.00 0.00 3.85
3446 8703 6.769134 TCTCACGAATACAATAGAAGGTCA 57.231 37.500 0.00 0.00 0.00 4.02
3447 8704 7.165460 TCTCACGAATACAATAGAAGGTCAA 57.835 36.000 0.00 0.00 0.00 3.18
3448 8705 7.258441 TCTCACGAATACAATAGAAGGTCAAG 58.742 38.462 0.00 0.00 0.00 3.02
3449 8706 6.931838 TCACGAATACAATAGAAGGTCAAGT 58.068 36.000 0.00 0.00 0.00 3.16
3450 8707 7.383687 TCACGAATACAATAGAAGGTCAAGTT 58.616 34.615 0.00 0.00 0.00 2.66
3451 8708 7.876068 TCACGAATACAATAGAAGGTCAAGTTT 59.124 33.333 0.00 0.00 0.00 2.66
3452 8709 9.146984 CACGAATACAATAGAAGGTCAAGTTTA 57.853 33.333 0.00 0.00 0.00 2.01
3453 8710 9.886132 ACGAATACAATAGAAGGTCAAGTTTAT 57.114 29.630 0.00 0.00 0.00 1.40
3488 8745 8.716646 ATTTTCAGGAATTTTCGACTTTTTGT 57.283 26.923 0.00 0.00 0.00 2.83
3489 8746 8.541133 TTTTCAGGAATTTTCGACTTTTTGTT 57.459 26.923 0.00 0.00 0.00 2.83
3490 8747 7.518731 TTCAGGAATTTTCGACTTTTTGTTG 57.481 32.000 0.00 0.00 0.00 3.33
3491 8748 6.857956 TCAGGAATTTTCGACTTTTTGTTGA 58.142 32.000 0.00 0.00 37.30 3.18
3492 8749 7.316640 TCAGGAATTTTCGACTTTTTGTTGAA 58.683 30.769 0.00 0.00 44.79 2.69
3493 8750 7.978975 TCAGGAATTTTCGACTTTTTGTTGAAT 59.021 29.630 0.00 0.00 45.50 2.57
3494 8751 8.603181 CAGGAATTTTCGACTTTTTGTTGAATT 58.397 29.630 0.00 0.00 45.50 2.17
3495 8752 9.810545 AGGAATTTTCGACTTTTTGTTGAATTA 57.189 25.926 0.00 0.00 45.50 1.40
3496 8753 9.843874 GGAATTTTCGACTTTTTGTTGAATTAC 57.156 29.630 0.00 0.00 45.50 1.89
3529 8786 4.156455 CCATATAGGGTGCATATGTCCC 57.844 50.000 22.23 22.23 41.36 4.46
3530 8787 3.117888 CCATATAGGGTGCATATGTCCCC 60.118 52.174 24.48 21.88 41.95 4.81
3531 8788 2.132303 ATAGGGTGCATATGTCCCCA 57.868 50.000 24.95 17.03 41.95 4.96
3532 8789 2.132303 TAGGGTGCATATGTCCCCAT 57.868 50.000 24.95 14.11 41.95 4.00
3533 8790 2.132303 AGGGTGCATATGTCCCCATA 57.868 50.000 24.95 0.00 41.95 2.74
3534 8791 1.988107 AGGGTGCATATGTCCCCATAG 59.012 52.381 24.95 0.00 41.95 2.23
3535 8792 1.985159 GGGTGCATATGTCCCCATAGA 59.015 52.381 20.72 0.00 36.99 1.98
3536 8793 2.290323 GGGTGCATATGTCCCCATAGAC 60.290 54.545 20.72 0.00 36.99 2.59
3537 8794 2.290323 GGTGCATATGTCCCCATAGACC 60.290 54.545 4.29 0.00 36.99 3.85
3538 8795 2.371841 GTGCATATGTCCCCATAGACCA 59.628 50.000 4.29 0.00 36.99 4.02
3539 8796 3.052329 TGCATATGTCCCCATAGACCAA 58.948 45.455 4.29 0.00 36.99 3.67
3540 8797 3.461458 TGCATATGTCCCCATAGACCAAA 59.539 43.478 4.29 0.00 36.99 3.28
3541 8798 4.079500 TGCATATGTCCCCATAGACCAAAA 60.080 41.667 4.29 0.00 36.99 2.44
3542 8799 4.520492 GCATATGTCCCCATAGACCAAAAG 59.480 45.833 4.29 0.00 36.99 2.27
3543 8800 5.694995 CATATGTCCCCATAGACCAAAAGT 58.305 41.667 0.00 0.00 36.99 2.66
3544 8801 4.675063 ATGTCCCCATAGACCAAAAGTT 57.325 40.909 0.00 0.00 35.83 2.66
3545 8802 4.028993 TGTCCCCATAGACCAAAAGTTC 57.971 45.455 0.00 0.00 35.83 3.01
3546 8803 3.245122 TGTCCCCATAGACCAAAAGTTCC 60.245 47.826 0.00 0.00 35.83 3.62
3547 8804 2.310647 TCCCCATAGACCAAAAGTTCCC 59.689 50.000 0.00 0.00 0.00 3.97
3548 8805 2.623239 CCCCATAGACCAAAAGTTCCCC 60.623 54.545 0.00 0.00 0.00 4.81
3549 8806 2.311841 CCCATAGACCAAAAGTTCCCCT 59.688 50.000 0.00 0.00 0.00 4.79
3550 8807 3.621558 CCATAGACCAAAAGTTCCCCTC 58.378 50.000 0.00 0.00 0.00 4.30
3551 8808 3.621558 CATAGACCAAAAGTTCCCCTCC 58.378 50.000 0.00 0.00 0.00 4.30
3552 8809 0.400594 AGACCAAAAGTTCCCCTCCG 59.599 55.000 0.00 0.00 0.00 4.63
3553 8810 0.109913 GACCAAAAGTTCCCCTCCGT 59.890 55.000 0.00 0.00 0.00 4.69
3554 8811 0.179001 ACCAAAAGTTCCCCTCCGTG 60.179 55.000 0.00 0.00 0.00 4.94
3555 8812 0.109723 CCAAAAGTTCCCCTCCGTGA 59.890 55.000 0.00 0.00 0.00 4.35
3556 8813 1.477923 CCAAAAGTTCCCCTCCGTGAA 60.478 52.381 0.00 0.00 0.00 3.18
3557 8814 1.880027 CAAAAGTTCCCCTCCGTGAAG 59.120 52.381 0.00 0.00 0.00 3.02
3558 8815 1.137697 AAAGTTCCCCTCCGTGAAGT 58.862 50.000 0.00 0.00 0.00 3.01
3559 8816 1.137697 AAGTTCCCCTCCGTGAAGTT 58.862 50.000 0.00 0.00 31.07 2.66
3560 8817 2.019807 AGTTCCCCTCCGTGAAGTTA 57.980 50.000 0.00 0.00 0.00 2.24
3561 8818 1.900486 AGTTCCCCTCCGTGAAGTTAG 59.100 52.381 0.00 0.00 0.00 2.34
3562 8819 1.622312 GTTCCCCTCCGTGAAGTTAGT 59.378 52.381 0.00 0.00 0.00 2.24
3563 8820 1.553706 TCCCCTCCGTGAAGTTAGTC 58.446 55.000 0.00 0.00 0.00 2.59
3564 8821 0.172803 CCCCTCCGTGAAGTTAGTCG 59.827 60.000 0.00 0.00 0.00 4.18
3671 8930 2.899900 TCTAGTCATCCAGTGTGCAACT 59.100 45.455 0.00 0.00 40.93 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
629 660 3.057526 GTCTTGAAAAACGCATTAGGCCT 60.058 43.478 11.78 11.78 40.31 5.19
679 711 8.861033 ATTTTCACATTATGCATGTCATGTAC 57.139 30.769 10.16 0.00 43.17 2.90
729 761 0.164217 GCACGCCGTCAAATTCGTAA 59.836 50.000 0.00 0.00 33.51 3.18
743 775 2.189342 TGCAACTTAAACAAAGCACGC 58.811 42.857 0.00 0.00 38.93 5.34
744 776 3.796178 ACATGCAACTTAAACAAAGCACG 59.204 39.130 0.00 0.00 38.93 5.34
779 811 8.608844 AGACTAACTTTGACCAAATGTTAGAG 57.391 34.615 27.54 17.58 40.08 2.43
847 879 7.490000 AGAAGGTGGAGTTAATTACACGATAG 58.510 38.462 7.20 0.00 46.19 2.08
848 880 7.123098 TGAGAAGGTGGAGTTAATTACACGATA 59.877 37.037 7.20 0.00 34.78 2.92
849 881 6.070995 TGAGAAGGTGGAGTTAATTACACGAT 60.071 38.462 7.20 0.00 34.78 3.73
850 882 5.244402 TGAGAAGGTGGAGTTAATTACACGA 59.756 40.000 7.20 0.00 34.78 4.35
851 883 5.475719 TGAGAAGGTGGAGTTAATTACACG 58.524 41.667 7.20 0.00 34.78 4.49
852 884 6.698380 TCTGAGAAGGTGGAGTTAATTACAC 58.302 40.000 4.77 4.77 0.00 2.90
855 887 5.104900 GGCTCTGAGAAGGTGGAGTTAATTA 60.105 44.000 9.28 0.00 0.00 1.40
857 889 3.198853 GGCTCTGAGAAGGTGGAGTTAAT 59.801 47.826 9.28 0.00 0.00 1.40
859 891 2.180276 GGCTCTGAGAAGGTGGAGTTA 58.820 52.381 9.28 0.00 0.00 2.24
863 1242 1.076727 TCGGCTCTGAGAAGGTGGA 59.923 57.895 9.28 0.00 0.00 4.02
955 1511 1.963338 GTGTGGTGGAGCTGTCTGC 60.963 63.158 0.00 0.00 43.29 4.26
1332 1999 4.796231 GCGGTGATGGACGTCGCT 62.796 66.667 9.92 0.00 42.62 4.93
1600 2267 1.643868 TACGGGTACGCGTTCACGAT 61.644 55.000 40.24 27.26 46.04 3.73
1950 2617 2.124320 AGCGGCAACAACACACCT 60.124 55.556 1.45 0.00 0.00 4.00
1951 2618 2.117941 GAGAGCGGCAACAACACACC 62.118 60.000 1.45 0.00 0.00 4.16
1952 2619 1.160329 AGAGAGCGGCAACAACACAC 61.160 55.000 1.45 0.00 0.00 3.82
1953 2620 0.880278 GAGAGAGCGGCAACAACACA 60.880 55.000 1.45 0.00 0.00 3.72
1954 2621 0.601311 AGAGAGAGCGGCAACAACAC 60.601 55.000 1.45 0.00 0.00 3.32
2021 2704 2.358984 GGTGTTTAAGCGCCGGGA 60.359 61.111 2.29 0.00 0.00 5.14
2031 2714 4.340950 CAGCAGAAAGAAAAGGGGTGTTTA 59.659 41.667 0.00 0.00 0.00 2.01
2036 2719 2.001076 CCAGCAGAAAGAAAAGGGGT 57.999 50.000 0.00 0.00 0.00 4.95
2040 2723 2.228343 CCTCAGCCAGCAGAAAGAAAAG 59.772 50.000 0.00 0.00 0.00 2.27
2050 2735 0.983467 TGATGTAACCTCAGCCAGCA 59.017 50.000 0.00 0.00 0.00 4.41
2058 2743 5.220605 GCCTTGTAATCGTTGATGTAACCTC 60.221 44.000 0.00 0.00 35.84 3.85
2105 2790 0.744414 GAAGAGTTGCATGGGCGCTA 60.744 55.000 7.64 0.00 45.35 4.26
2114 2799 1.609635 TATCGGCCGGAAGAGTTGCA 61.610 55.000 27.83 0.77 0.00 4.08
2165 2850 2.009051 CGGATCAAGCTGCATGTGTAA 58.991 47.619 1.02 0.00 0.00 2.41
2260 2945 6.598753 TTGAGTTAGTCTGCAGTTTGTTAC 57.401 37.500 14.67 2.98 0.00 2.50
2310 2995 0.599558 AAGCGTGCGTGTAGGTCTAA 59.400 50.000 0.00 0.00 0.00 2.10
2364 3139 3.849953 GTTGGACGCGTCGGATGC 61.850 66.667 30.99 18.12 0.00 3.91
2376 3151 0.817654 ATGATGTCGAGCTCGTTGGA 59.182 50.000 33.33 13.67 40.80 3.53
2379 3154 2.654749 TTGATGATGTCGAGCTCGTT 57.345 45.000 33.33 20.25 40.80 3.85
2392 3167 2.931969 GACATGTGAGACGCATTGATGA 59.068 45.455 1.15 0.00 31.79 2.92
2398 3173 1.153568 CGGGACATGTGAGACGCAT 60.154 57.895 1.15 0.00 34.71 4.73
2517 3466 3.430862 GGCACGGCAAGATCGCAA 61.431 61.111 0.00 0.00 0.00 4.85
2518 3467 4.393155 AGGCACGGCAAGATCGCA 62.393 61.111 0.00 0.00 0.00 5.10
2522 6023 1.672356 GTGTCAGGCACGGCAAGAT 60.672 57.895 0.00 0.00 38.45 2.40
2564 6131 4.338539 GTGTCAGACGCGTCGGGT 62.339 66.667 33.32 15.47 34.09 5.28
2625 6192 3.217242 CTGGTCCTCGTTGAACAGG 57.783 57.895 12.30 7.27 44.64 4.00
2703 6270 1.516386 CTTGACGCTGACGCCGTAT 60.516 57.895 0.00 0.00 45.53 3.06
2748 6315 4.169696 CCGTCCCCATTGCCGCTA 62.170 66.667 0.00 0.00 0.00 4.26
2776 6343 1.747206 GCCACTATCCATGCCGTTTCT 60.747 52.381 0.00 0.00 0.00 2.52
2786 6353 1.456892 ATCCCGACGCCACTATCCA 60.457 57.895 0.00 0.00 0.00 3.41
2953 7647 9.801873 GCCAGAAAAGCTAACATTATCAAAATA 57.198 29.630 0.00 0.00 0.00 1.40
2986 8230 5.411053 GCATTATATCCTGAAAGAGTGAGCC 59.589 44.000 0.00 0.00 34.07 4.70
3013 8257 8.500753 TTTGTCGGTAATTATTATTCAGCAGT 57.499 30.769 0.00 0.00 0.00 4.40
3016 8260 9.651718 CTTCTTTGTCGGTAATTATTATTCAGC 57.348 33.333 0.00 0.00 0.00 4.26
3045 8289 2.807967 TGTATCTAGCATTGATTGGCGC 59.192 45.455 0.00 0.00 34.54 6.53
3047 8291 4.093998 CGGATGTATCTAGCATTGATTGGC 59.906 45.833 0.00 0.00 0.00 4.52
3120 8377 7.120923 TCCCCTAACTTCACATACTAATCAC 57.879 40.000 0.00 0.00 0.00 3.06
3141 8398 3.506067 CCAGGAACACAAGTGTATTTCCC 59.494 47.826 15.43 8.77 44.13 3.97
3142 8399 4.023193 CACCAGGAACACAAGTGTATTTCC 60.023 45.833 12.48 12.48 44.13 3.13
3143 8400 4.023193 CCACCAGGAACACAAGTGTATTTC 60.023 45.833 6.24 0.83 44.13 2.17
3144 8401 3.888930 CCACCAGGAACACAAGTGTATTT 59.111 43.478 6.24 0.00 44.13 1.40
3147 8404 1.841277 ACCACCAGGAACACAAGTGTA 59.159 47.619 6.24 0.00 39.84 2.90
3148 8405 0.623723 ACCACCAGGAACACAAGTGT 59.376 50.000 0.00 0.00 41.52 3.55
3149 8406 2.631160 TACCACCAGGAACACAAGTG 57.369 50.000 0.00 0.00 38.69 3.16
3150 8407 4.843728 CATATACCACCAGGAACACAAGT 58.156 43.478 0.00 0.00 38.69 3.16
3152 8409 3.009584 TGCATATACCACCAGGAACACAA 59.990 43.478 0.00 0.00 38.69 3.33
3153 8410 2.573915 TGCATATACCACCAGGAACACA 59.426 45.455 0.00 0.00 38.69 3.72
3154 8411 2.943033 GTGCATATACCACCAGGAACAC 59.057 50.000 0.00 0.00 38.69 3.32
3155 8412 3.275617 GTGCATATACCACCAGGAACA 57.724 47.619 0.00 0.00 38.69 3.18
3235 8492 9.296400 GCAAAAGTAAGTCAAGTATTTTGTCAA 57.704 29.630 9.22 0.00 38.96 3.18
3236 8493 8.462811 TGCAAAAGTAAGTCAAGTATTTTGTCA 58.537 29.630 9.22 5.94 38.96 3.58
3237 8494 8.743099 GTGCAAAAGTAAGTCAAGTATTTTGTC 58.257 33.333 9.22 3.99 38.96 3.18
3238 8495 8.466798 AGTGCAAAAGTAAGTCAAGTATTTTGT 58.533 29.630 9.22 0.00 38.96 2.83
3239 8496 8.856490 AGTGCAAAAGTAAGTCAAGTATTTTG 57.144 30.769 0.00 0.00 39.46 2.44
3241 8498 9.338622 ACTAGTGCAAAAGTAAGTCAAGTATTT 57.661 29.630 0.00 0.00 0.00 1.40
3242 8499 8.904099 ACTAGTGCAAAAGTAAGTCAAGTATT 57.096 30.769 0.00 0.00 0.00 1.89
3245 8502 9.991906 TTATACTAGTGCAAAAGTAAGTCAAGT 57.008 29.630 5.39 0.00 32.24 3.16
3253 8510 8.885722 CGGGATTTTTATACTAGTGCAAAAGTA 58.114 33.333 5.39 10.83 32.98 2.24
3254 8511 7.608761 TCGGGATTTTTATACTAGTGCAAAAGT 59.391 33.333 5.39 8.31 0.00 2.66
3255 8512 7.908601 GTCGGGATTTTTATACTAGTGCAAAAG 59.091 37.037 5.39 0.00 0.00 2.27
3256 8513 7.413219 CGTCGGGATTTTTATACTAGTGCAAAA 60.413 37.037 5.39 8.77 0.00 2.44
3257 8514 6.036300 CGTCGGGATTTTTATACTAGTGCAAA 59.964 38.462 5.39 2.65 0.00 3.68
3258 8515 5.521010 CGTCGGGATTTTTATACTAGTGCAA 59.479 40.000 5.39 0.00 0.00 4.08
3259 8516 5.045215 CGTCGGGATTTTTATACTAGTGCA 58.955 41.667 5.39 0.00 0.00 4.57
3260 8517 5.284079 TCGTCGGGATTTTTATACTAGTGC 58.716 41.667 5.39 0.00 0.00 4.40
3261 8518 7.760131 TTTCGTCGGGATTTTTATACTAGTG 57.240 36.000 5.39 0.00 0.00 2.74
3262 8519 8.776376 TTTTTCGTCGGGATTTTTATACTAGT 57.224 30.769 0.00 0.00 0.00 2.57
3287 8544 4.929211 GCTGTGAGGTCAACTTTTGTTTTT 59.071 37.500 0.00 0.00 41.35 1.94
3288 8545 4.021544 TGCTGTGAGGTCAACTTTTGTTTT 60.022 37.500 0.00 0.00 41.35 2.43
3289 8546 3.509575 TGCTGTGAGGTCAACTTTTGTTT 59.490 39.130 0.00 0.00 41.35 2.83
3290 8547 3.088532 TGCTGTGAGGTCAACTTTTGTT 58.911 40.909 0.00 0.00 44.66 2.83
3291 8548 2.722094 TGCTGTGAGGTCAACTTTTGT 58.278 42.857 0.00 0.00 0.00 2.83
3292 8549 3.781079 TTGCTGTGAGGTCAACTTTTG 57.219 42.857 0.00 0.00 0.00 2.44
3293 8550 4.799564 TTTTGCTGTGAGGTCAACTTTT 57.200 36.364 0.00 0.00 0.00 2.27
3294 8551 4.799564 TTTTTGCTGTGAGGTCAACTTT 57.200 36.364 0.00 0.00 0.00 2.66
3328 8585 9.542462 GTGTGAATAGTGACCTATAATAGCAAA 57.458 33.333 0.00 0.00 32.57 3.68
3329 8586 8.924303 AGTGTGAATAGTGACCTATAATAGCAA 58.076 33.333 0.00 0.00 32.57 3.91
3330 8587 8.478775 AGTGTGAATAGTGACCTATAATAGCA 57.521 34.615 0.00 0.00 32.57 3.49
3337 8594 9.765795 GCTAAAATAGTGTGAATAGTGACCTAT 57.234 33.333 0.00 0.00 35.33 2.57
3338 8595 8.202137 GGCTAAAATAGTGTGAATAGTGACCTA 58.798 37.037 0.00 0.00 0.00 3.08
3339 8596 7.048512 GGCTAAAATAGTGTGAATAGTGACCT 58.951 38.462 0.00 0.00 0.00 3.85
3340 8597 6.821665 TGGCTAAAATAGTGTGAATAGTGACC 59.178 38.462 0.00 0.00 0.00 4.02
3341 8598 7.843490 TGGCTAAAATAGTGTGAATAGTGAC 57.157 36.000 0.00 0.00 0.00 3.67
3342 8599 8.856153 TTTGGCTAAAATAGTGTGAATAGTGA 57.144 30.769 0.00 0.00 0.00 3.41
3343 8600 9.906660 TTTTTGGCTAAAATAGTGTGAATAGTG 57.093 29.630 8.93 0.00 35.82 2.74
3348 8605 9.606631 ACAAATTTTTGGCTAAAATAGTGTGAA 57.393 25.926 22.86 0.00 43.84 3.18
3349 8606 9.255304 GACAAATTTTTGGCTAAAATAGTGTGA 57.745 29.630 25.81 0.92 43.84 3.58
3423 8680 6.769134 TGACCTTCTATTGTATTCGTGAGA 57.231 37.500 0.00 0.00 39.20 3.27
3424 8681 7.036220 ACTTGACCTTCTATTGTATTCGTGAG 58.964 38.462 0.00 0.00 0.00 3.51
3425 8682 6.931838 ACTTGACCTTCTATTGTATTCGTGA 58.068 36.000 0.00 0.00 0.00 4.35
3426 8683 7.596749 AACTTGACCTTCTATTGTATTCGTG 57.403 36.000 0.00 0.00 0.00 4.35
3427 8684 9.886132 ATAAACTTGACCTTCTATTGTATTCGT 57.114 29.630 0.00 0.00 0.00 3.85
3462 8719 9.810545 ACAAAAAGTCGAAAATTCCTGAAAATA 57.189 25.926 0.00 0.00 0.00 1.40
3463 8720 8.716646 ACAAAAAGTCGAAAATTCCTGAAAAT 57.283 26.923 0.00 0.00 0.00 1.82
3464 8721 8.439286 CAACAAAAAGTCGAAAATTCCTGAAAA 58.561 29.630 0.00 0.00 0.00 2.29
3465 8722 7.815068 TCAACAAAAAGTCGAAAATTCCTGAAA 59.185 29.630 0.00 0.00 0.00 2.69
3466 8723 7.316640 TCAACAAAAAGTCGAAAATTCCTGAA 58.683 30.769 0.00 0.00 0.00 3.02
3467 8724 6.857956 TCAACAAAAAGTCGAAAATTCCTGA 58.142 32.000 0.00 0.00 0.00 3.86
3468 8725 7.518731 TTCAACAAAAAGTCGAAAATTCCTG 57.481 32.000 0.00 0.00 0.00 3.86
3469 8726 8.716646 AATTCAACAAAAAGTCGAAAATTCCT 57.283 26.923 0.00 0.00 0.00 3.36
3470 8727 9.843874 GTAATTCAACAAAAAGTCGAAAATTCC 57.156 29.630 0.00 0.00 0.00 3.01
3508 8765 3.117888 GGGGACATATGCACCCTATATGG 60.118 52.174 26.98 0.00 40.92 2.74
3509 8766 3.523157 TGGGGACATATGCACCCTATATG 59.477 47.826 26.78 6.07 43.72 1.78
3510 8767 3.814284 TGGGGACATATGCACCCTATAT 58.186 45.455 26.78 0.00 43.72 0.86
3511 8768 3.283712 TGGGGACATATGCACCCTATA 57.716 47.619 26.78 16.20 43.72 1.31
3512 8769 2.132303 TGGGGACATATGCACCCTAT 57.868 50.000 26.78 0.00 43.72 2.57
3513 8770 3.664869 TGGGGACATATGCACCCTA 57.335 52.632 26.78 21.97 43.72 3.53
3514 8771 4.518056 TGGGGACATATGCACCCT 57.482 55.556 26.78 0.12 43.72 4.34
3523 8780 4.569865 GGAACTTTTGGTCTATGGGGACAT 60.570 45.833 0.00 0.00 43.22 3.06
3524 8781 3.245122 GGAACTTTTGGTCTATGGGGACA 60.245 47.826 0.00 0.00 39.95 4.02
3525 8782 3.353557 GGAACTTTTGGTCTATGGGGAC 58.646 50.000 0.00 0.00 36.15 4.46
3526 8783 2.310647 GGGAACTTTTGGTCTATGGGGA 59.689 50.000 0.00 0.00 36.15 4.81
3527 8784 2.623239 GGGGAACTTTTGGTCTATGGGG 60.623 54.545 0.00 0.00 36.15 4.96
3528 8785 2.311841 AGGGGAACTTTTGGTCTATGGG 59.688 50.000 0.00 0.00 36.15 4.00
3529 8786 3.621558 GAGGGGAACTTTTGGTCTATGG 58.378 50.000 0.00 0.00 36.15 2.74
3530 8787 3.621558 GGAGGGGAACTTTTGGTCTATG 58.378 50.000 0.00 0.00 36.15 2.23
3531 8788 2.238898 CGGAGGGGAACTTTTGGTCTAT 59.761 50.000 0.00 0.00 36.15 1.98
3532 8789 1.626825 CGGAGGGGAACTTTTGGTCTA 59.373 52.381 0.00 0.00 36.15 2.59
3533 8790 0.400594 CGGAGGGGAACTTTTGGTCT 59.599 55.000 0.00 0.00 36.15 3.85
3534 8791 0.109913 ACGGAGGGGAACTTTTGGTC 59.890 55.000 0.00 0.00 34.82 4.02
3535 8792 0.179001 CACGGAGGGGAACTTTTGGT 60.179 55.000 0.00 0.00 0.00 3.67
3536 8793 0.109723 TCACGGAGGGGAACTTTTGG 59.890 55.000 0.00 0.00 0.00 3.28
3537 8794 1.880027 CTTCACGGAGGGGAACTTTTG 59.120 52.381 0.00 0.00 0.00 2.44
3538 8795 1.493446 ACTTCACGGAGGGGAACTTTT 59.507 47.619 0.00 0.00 0.00 2.27
3539 8796 1.137697 ACTTCACGGAGGGGAACTTT 58.862 50.000 0.00 0.00 0.00 2.66
3540 8797 1.137697 AACTTCACGGAGGGGAACTT 58.862 50.000 0.00 0.00 0.00 2.66
3541 8798 1.900486 CTAACTTCACGGAGGGGAACT 59.100 52.381 0.00 0.00 0.00 3.01
3542 8799 1.622312 ACTAACTTCACGGAGGGGAAC 59.378 52.381 0.00 0.00 0.00 3.62
3543 8800 1.897802 GACTAACTTCACGGAGGGGAA 59.102 52.381 0.00 0.00 0.00 3.97
3544 8801 1.553706 GACTAACTTCACGGAGGGGA 58.446 55.000 0.00 0.00 0.00 4.81
3545 8802 0.172803 CGACTAACTTCACGGAGGGG 59.827 60.000 0.00 0.00 0.00 4.79
3546 8803 1.171308 TCGACTAACTTCACGGAGGG 58.829 55.000 0.00 0.00 0.00 4.30
3547 8804 4.832590 ATATCGACTAACTTCACGGAGG 57.167 45.455 0.00 0.00 0.00 4.30
3548 8805 6.134730 GTGTATATCGACTAACTTCACGGAG 58.865 44.000 0.00 0.00 0.00 4.63
3549 8806 5.585844 TGTGTATATCGACTAACTTCACGGA 59.414 40.000 0.00 0.00 0.00 4.69
3550 8807 5.813717 TGTGTATATCGACTAACTTCACGG 58.186 41.667 0.00 0.00 0.00 4.94
3551 8808 7.909777 AATGTGTATATCGACTAACTTCACG 57.090 36.000 0.00 0.00 0.00 4.35
3552 8809 9.297586 TCAAATGTGTATATCGACTAACTTCAC 57.702 33.333 0.00 0.00 0.00 3.18
3553 8810 9.863845 TTCAAATGTGTATATCGACTAACTTCA 57.136 29.630 0.00 0.00 0.00 3.02
3671 8930 1.005805 ACTTGGTGCCCAGCATGATTA 59.994 47.619 16.84 0.00 41.91 1.75


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

AutoCloner maintained by Alex Coulton.