Multiple sequence alignment - TraesCS7A01G363800

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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 TraesCS7A01G363800 chr7A 100.000 2866 0 0 622 3487 538359391 538362256 0.000000e+00 5293.0
1 TraesCS7A01G363800 chr7A 100.000 344 0 0 1 344 538358770 538359113 1.370000e-178 636.0
2 TraesCS7A01G363800 chr7A 97.468 158 4 0 2956 3113 83784994 83784837 1.600000e-68 270.0
3 TraesCS7A01G363800 chr7A 96.610 118 4 0 847 964 538355261 538355144 2.750000e-46 196.0
4 TraesCS7A01G363800 chr7D 92.051 1975 121 20 997 2949 461777936 461775976 0.000000e+00 2745.0
5 TraesCS7A01G363800 chr7D 87.535 361 28 12 3132 3487 461775972 461775624 5.420000e-108 401.0
6 TraesCS7A01G363800 chr7B 91.896 1962 128 19 971 2914 484594592 484592644 0.000000e+00 2713.0
7 TraesCS7A01G363800 chr7B 84.143 391 33 15 3116 3487 484592607 484592227 5.540000e-93 351.0
8 TraesCS7A01G363800 chr7B 97.674 172 4 0 173 344 91466247 91466418 2.630000e-76 296.0
9 TraesCS7A01G363800 chr7B 90.698 43 4 0 764 806 414717343 414717301 1.350000e-04 58.4
10 TraesCS7A01G363800 chr4D 94.940 336 15 2 2 336 321958808 321958474 3.080000e-145 525.0
11 TraesCS7A01G363800 chr4D 94.805 231 11 1 668 898 321958103 321957874 3.310000e-95 359.0
12 TraesCS7A01G363800 chr4D 98.137 161 3 0 2953 3113 23322883 23322723 7.370000e-72 281.0
13 TraesCS7A01G363800 chr4D 94.915 118 6 0 847 964 321966517 321966634 5.940000e-43 185.0
14 TraesCS7A01G363800 chr3B 92.308 351 19 1 2 344 704005154 704004804 3.130000e-135 492.0
15 TraesCS7A01G363800 chr3B 93.907 279 17 0 695 973 704004407 704004129 4.160000e-114 422.0
16 TraesCS7A01G363800 chr3B 98.256 172 3 0 173 344 157873150 157872979 5.660000e-78 302.0
17 TraesCS7A01G363800 chr3B 98.485 132 2 0 2 133 102651859 102651990 2.090000e-57 233.0
18 TraesCS7A01G363800 chr3B 94.891 137 6 1 668 804 157872535 157872400 2.730000e-51 213.0
19 TraesCS7A01G363800 chr3B 95.312 128 5 1 673 800 102652290 102652416 5.900000e-48 202.0
20 TraesCS7A01G363800 chr3B 92.800 125 9 0 847 971 102651698 102651574 7.690000e-42 182.0
21 TraesCS7A01G363800 chr3B 98.361 61 1 0 73 133 157873220 157873160 1.320000e-19 108.0
22 TraesCS7A01G363800 chr5A 91.954 348 20 2 2 341 414824117 414824464 6.770000e-132 481.0
23 TraesCS7A01G363800 chr5A 90.476 336 31 1 629 964 414824557 414824891 3.190000e-120 442.0
24 TraesCS7A01G363800 chr5A 93.220 118 8 0 847 964 414820030 414819913 1.290000e-39 174.0
25 TraesCS7A01G363800 chr1A 90.909 352 22 4 2 344 392491001 392490651 6.820000e-127 464.0
26 TraesCS7A01G363800 chr1A 86.686 353 28 5 622 974 392490561 392490228 1.180000e-99 374.0
27 TraesCS7A01G363800 chr1A 88.983 118 13 0 847 964 392494640 392494757 2.800000e-31 147.0
28 TraesCS7A01G363800 chr5B 96.532 173 4 2 173 344 12074388 12074559 5.700000e-73 285.0
29 TraesCS7A01G363800 chr5B 97.468 158 4 0 2956 3113 574956605 574956448 1.600000e-68 270.0
30 TraesCS7A01G363800 chr5B 93.571 140 6 3 661 800 458709533 458709669 4.560000e-49 206.0
31 TraesCS7A01G363800 chr5B 91.964 112 5 4 661 772 12074669 12074776 1.680000e-33 154.0
32 TraesCS7A01G363800 chr5B 98.276 58 1 0 73 130 12074318 12074375 6.160000e-18 102.0
33 TraesCS7A01G363800 chr6B 95.930 172 7 0 173 344 714076153 714076324 2.650000e-71 279.0
34 TraesCS7A01G363800 chr6B 95.930 172 7 0 173 344 717199109 717198938 2.650000e-71 279.0
35 TraesCS7A01G363800 chr6B 93.519 108 6 1 668 775 717198823 717198717 3.600000e-35 159.0
36 TraesCS7A01G363800 chr5D 97.516 161 4 0 2953 3113 62177116 62177276 3.430000e-70 276.0
37 TraesCS7A01G363800 chr2D 97.484 159 4 0 2956 3114 459298859 459298701 4.430000e-69 272.0
38 TraesCS7A01G363800 chr3D 96.894 161 5 0 2953 3113 376923800 376923640 1.600000e-68 270.0
39 TraesCS7A01G363800 chr3D 96.894 161 5 0 2953 3113 422517631 422517791 1.600000e-68 270.0
40 TraesCS7A01G363800 chr1D 96.894 161 5 0 2953 3113 86918523 86918683 1.600000e-68 270.0
41 TraesCS7A01G363800 chr3A 94.706 170 9 0 2953 3122 77542447 77542616 7.420000e-67 265.0
42 TraesCS7A01G363800 chr2A 81.452 124 19 4 852 973 767527860 767527981 7.970000e-17 99.0


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 TraesCS7A01G363800 chr7A 538358770 538362256 3486 False 2964.500000 5293 100.000000 1 3487 2 chr7A.!!$F1 3486
1 TraesCS7A01G363800 chr7D 461775624 461777936 2312 True 1573.000000 2745 89.793000 997 3487 2 chr7D.!!$R1 2490
2 TraesCS7A01G363800 chr7B 484592227 484594592 2365 True 1532.000000 2713 88.019500 971 3487 2 chr7B.!!$R2 2516
3 TraesCS7A01G363800 chr4D 321957874 321958808 934 True 442.000000 525 94.872500 2 898 2 chr4D.!!$R2 896
4 TraesCS7A01G363800 chr3B 704004129 704005154 1025 True 457.000000 492 93.107500 2 973 2 chr3B.!!$R3 971
5 TraesCS7A01G363800 chr3B 102651859 102652416 557 False 217.500000 233 96.898500 2 800 2 chr3B.!!$F1 798
6 TraesCS7A01G363800 chr3B 157872400 157873220 820 True 207.666667 302 97.169333 73 804 3 chr3B.!!$R2 731
7 TraesCS7A01G363800 chr5A 414824117 414824891 774 False 461.500000 481 91.215000 2 964 2 chr5A.!!$F1 962
8 TraesCS7A01G363800 chr1A 392490228 392491001 773 True 419.000000 464 88.797500 2 974 2 chr1A.!!$R1 972

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
794 1277 1.974957 TGGATACGTATGGATGTGGGG 59.025 52.381 13.97 0.0 42.51 4.96 F
1386 1869 0.169009 GGATTGCCTGACAAAGACGC 59.831 55.000 0.00 0.0 42.86 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2177 2669 0.389817 TCTGTCCAGACCAAATCGCG 60.390 55.0 0.0 0.0 31.41 5.87 R
2991 3510 0.034896 GGCTGTTTCCAGGACTCGAA 59.965 55.0 0.0 0.0 39.22 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
732 1215 2.052690 CGTGAGTCGGGGTGGAGAT 61.053 63.158 0.00 0.00 35.71 2.75
794 1277 1.974957 TGGATACGTATGGATGTGGGG 59.025 52.381 13.97 0.00 42.51 4.96
870 1353 8.829746 TGGAGAAAATGGCATAGATAGATGTAT 58.170 33.333 0.00 0.00 0.00 2.29
898 1381 6.096846 GGAAGTTGTAGTGGCATATTTCCAAT 59.903 38.462 0.00 0.24 35.01 3.16
904 1387 5.014808 AGTGGCATATTTCCAATTTGAGC 57.985 39.130 0.00 0.00 35.01 4.26
908 1391 7.041107 GTGGCATATTTCCAATTTGAGCTTTA 58.959 34.615 0.00 0.00 35.01 1.85
919 1402 7.559533 TCCAATTTGAGCTTTAGTAATGGCATA 59.440 33.333 0.00 0.00 0.00 3.14
928 1411 7.561356 AGCTTTAGTAATGGCATATTTCCAACT 59.439 33.333 0.00 0.00 37.13 3.16
930 1413 8.815565 TTTAGTAATGGCATATTTCCAACTCA 57.184 30.769 0.00 0.00 37.13 3.41
931 1414 6.699575 AGTAATGGCATATTTCCAACTCAC 57.300 37.500 0.00 0.00 37.13 3.51
964 1447 3.826729 GTGGCATAGATCCAATTAACCCC 59.173 47.826 0.00 0.00 35.01 4.95
966 1449 4.082125 GGCATAGATCCAATTAACCCCTG 58.918 47.826 0.00 0.00 0.00 4.45
1159 1642 1.542175 CATCCTCCTCTCCCCGGTA 59.458 63.158 0.00 0.00 0.00 4.02
1261 1744 4.465446 TCCTCCTCCGCCTCCCTG 62.465 72.222 0.00 0.00 0.00 4.45
1386 1869 0.169009 GGATTGCCTGACAAAGACGC 59.831 55.000 0.00 0.00 42.86 5.19
1408 1891 0.995024 CTGATGTCCCCTGGGAGTTT 59.005 55.000 16.20 0.00 46.16 2.66
1429 1912 3.377656 GAGGAGTTCCACGAGCCA 58.622 61.111 0.28 0.00 38.89 4.75
1446 1929 1.669760 CACCGCCGTGGCTTAAAGA 60.670 57.895 9.55 0.00 43.94 2.52
1456 1939 1.706287 GGCTTAAAGAAGAGGCGGCG 61.706 60.000 0.51 0.51 34.25 6.46
1502 1985 2.790791 CCTCTCGATTGCCGGAGCT 61.791 63.158 5.05 0.00 40.80 4.09
1510 1993 2.563013 ATTGCCGGAGCTTGATGCCT 62.563 55.000 5.05 0.00 44.23 4.75
1550 2042 3.555966 GGGGATGGTTTAGATGGAGTTG 58.444 50.000 0.00 0.00 0.00 3.16
1579 2071 1.617536 TCTGGGGCTGGAGCAAGAT 60.618 57.895 0.20 0.00 44.36 2.40
1594 2086 6.183360 TGGAGCAAGATGAGTATTCGTTCATA 60.183 38.462 0.00 0.00 34.33 2.15
1596 2088 6.573434 AGCAAGATGAGTATTCGTTCATACA 58.427 36.000 0.00 0.00 34.33 2.29
1597 2089 6.699204 AGCAAGATGAGTATTCGTTCATACAG 59.301 38.462 0.00 0.00 34.33 2.74
1598 2090 6.074088 GCAAGATGAGTATTCGTTCATACAGG 60.074 42.308 5.40 0.00 34.33 4.00
1628 2120 2.344203 CGTGCTCCTTCTCCTCCGT 61.344 63.158 0.00 0.00 0.00 4.69
1633 2125 0.753848 CTCCTTCTCCTCCGTCTCCC 60.754 65.000 0.00 0.00 0.00 4.30
1639 2131 2.284699 CCTCCGTCTCCCCCACTT 60.285 66.667 0.00 0.00 0.00 3.16
1654 2146 2.884639 CCCACTTGGAAATTCAGTCGTT 59.115 45.455 0.00 0.00 37.39 3.85
1659 2151 6.072728 CCACTTGGAAATTCAGTCGTTCATAA 60.073 38.462 0.00 0.00 37.39 1.90
1681 2173 2.362077 GGCTCTAGCTCTGAAGAAGGAG 59.638 54.545 1.39 0.00 41.70 3.69
1691 2183 5.395546 GCTCTGAAGAAGGAGATTGAGATGT 60.396 44.000 0.00 0.00 0.00 3.06
1700 2192 5.022122 AGGAGATTGAGATGTCAGAGTCAA 58.978 41.667 0.00 0.00 32.98 3.18
1783 2275 4.677584 CTGAGGCAGTACTTAGCTTAGTG 58.322 47.826 15.47 5.10 0.00 2.74
1832 2324 3.571401 AGTGAGGGTTCTGCTTTCAAATG 59.429 43.478 0.00 0.00 0.00 2.32
1867 2359 1.690352 GATGGGATGCATGGAAAAGGG 59.310 52.381 2.46 0.00 0.00 3.95
1892 2384 2.872245 GCACTTGTGCTGTGTTCTCTTA 59.128 45.455 17.36 0.00 37.70 2.10
1893 2385 3.499918 GCACTTGTGCTGTGTTCTCTTAT 59.500 43.478 17.36 0.00 37.70 1.73
1900 2392 3.130516 TGCTGTGTTCTCTTATCCTACCG 59.869 47.826 0.00 0.00 0.00 4.02
1948 2440 4.321718 CTTCATCTGGTCTTCTTTCTGCA 58.678 43.478 0.00 0.00 0.00 4.41
2067 2559 0.792640 GTGCTCACACGGATTGTCAG 59.207 55.000 0.00 0.00 35.67 3.51
2071 2563 0.320374 TCACACGGATTGTCAGGGAC 59.680 55.000 0.00 0.00 35.67 4.46
2129 2621 0.322906 GTTGCTTTCAGGGGAGGAGG 60.323 60.000 0.00 0.00 0.00 4.30
2135 2627 0.855855 TTCAGGGGAGGAGGGAGAGA 60.856 60.000 0.00 0.00 0.00 3.10
2146 2638 2.112190 GAGGGAGAGAGGAAACCGATT 58.888 52.381 0.00 0.00 0.00 3.34
2177 2669 1.963515 AGCATCGGGAAAATATTGGCC 59.036 47.619 0.00 0.00 0.00 5.36
2274 2766 2.099263 GCACCATCGAGAAGCTAGTGTA 59.901 50.000 0.00 0.00 0.00 2.90
2332 2824 6.019075 AGTCGCTTAAATTTGGCAACTTTTTC 60.019 34.615 18.77 8.97 37.61 2.29
2391 2883 5.998363 AGATTCACAGGGTTTTACTTGAGAC 59.002 40.000 0.00 0.00 0.00 3.36
2398 2890 2.226674 GGTTTTACTTGAGACAGCTGCC 59.773 50.000 15.27 1.42 0.00 4.85
2416 2908 1.404035 GCCGAGACAACCAACACTTTT 59.596 47.619 0.00 0.00 0.00 2.27
2480 2972 8.450578 TTGAAGTGATGTCTTGAGTGTTTAAT 57.549 30.769 0.00 0.00 0.00 1.40
2500 2992 1.281867 TGATAAACTCCTGGTGGGCTG 59.718 52.381 0.33 0.00 34.39 4.85
2502 2994 1.422977 TAAACTCCTGGTGGGCTGCA 61.423 55.000 0.50 0.00 34.39 4.41
2530 3022 8.850156 GCCATTCAGATTAACCAAGTATGTAAT 58.150 33.333 0.00 0.00 0.00 1.89
2540 3032 9.968870 TTAACCAAGTATGTAATTGTTTGGAAC 57.031 29.630 7.95 0.00 38.67 3.62
2541 3033 7.589958 ACCAAGTATGTAATTGTTTGGAACA 57.410 32.000 7.95 0.00 38.67 3.18
2542 3034 7.430441 ACCAAGTATGTAATTGTTTGGAACAC 58.570 34.615 7.95 0.00 41.97 3.32
2544 3036 7.594758 CCAAGTATGTAATTGTTTGGAACACTG 59.405 37.037 0.00 0.00 41.97 3.66
2589 3082 5.179555 GGACAGCTTTTGTAGTTCGAGAAAT 59.820 40.000 0.00 0.00 41.05 2.17
2670 3164 9.335891 CAAAGTACATAATTTTGTTATGCACGA 57.664 29.630 6.85 0.00 35.10 4.35
2693 3190 5.343249 ACTCAAGTGCAACAATTGACTTTC 58.657 37.500 13.59 0.00 42.20 2.62
2738 3235 9.053840 GTTAAGTATAGGATTTCTTGTAAGGGC 57.946 37.037 0.00 0.00 0.00 5.19
2751 3248 3.476552 TGTAAGGGCTGTCTTTGACTTG 58.523 45.455 0.00 0.00 33.15 3.16
2767 3264 3.565482 TGACTTGTGAAATGGACAGCTTC 59.435 43.478 0.00 0.00 0.00 3.86
2774 3271 4.757149 GTGAAATGGACAGCTTCTGTAGTT 59.243 41.667 0.00 0.00 45.44 2.24
2794 3291 6.279513 AGTTCCAGAAACAATTGAACAACA 57.720 33.333 13.59 0.00 40.56 3.33
2795 3292 6.877236 AGTTCCAGAAACAATTGAACAACAT 58.123 32.000 13.59 0.00 40.56 2.71
2796 3293 6.757947 AGTTCCAGAAACAATTGAACAACATG 59.242 34.615 13.59 0.00 40.56 3.21
2797 3294 6.462552 TCCAGAAACAATTGAACAACATGA 57.537 33.333 13.59 0.00 0.00 3.07
2798 3295 7.053316 TCCAGAAACAATTGAACAACATGAT 57.947 32.000 13.59 0.00 0.00 2.45
2799 3296 6.924612 TCCAGAAACAATTGAACAACATGATG 59.075 34.615 13.59 0.00 0.00 3.07
2807 3310 8.468399 ACAATTGAACAACATGATGCATATACA 58.532 29.630 13.59 0.00 0.00 2.29
2819 3322 7.806409 TGATGCATATACACAAAGTAGCAAT 57.194 32.000 0.00 0.00 35.74 3.56
2895 3406 2.751259 GCAGCAAGATTGGAGATTGTCA 59.249 45.455 0.00 0.00 0.00 3.58
2903 3414 7.416438 GCAAGATTGGAGATTGTCATGAAATCT 60.416 37.037 22.35 22.35 45.01 2.40
2922 3433 9.083422 TGAAATCTAGGATGTCCAGTATAAGAG 57.917 37.037 1.30 0.00 38.89 2.85
2926 3437 8.642935 TCTAGGATGTCCAGTATAAGAGAATG 57.357 38.462 1.30 0.00 38.89 2.67
2928 3439 9.253832 CTAGGATGTCCAGTATAAGAGAATGAT 57.746 37.037 1.30 0.00 38.89 2.45
2950 3469 9.884636 ATGATTAAGCCAGTTTAATTTTAACCC 57.115 29.630 1.72 0.00 34.31 4.11
2951 3470 8.030106 TGATTAAGCCAGTTTAATTTTAACCCG 58.970 33.333 1.72 0.00 34.31 5.28
2955 3474 5.048294 AGCCAGTTTAATTTTAACCCGAGTG 60.048 40.000 0.00 0.00 0.00 3.51
2956 3475 5.705902 CCAGTTTAATTTTAACCCGAGTGG 58.294 41.667 0.00 0.00 41.37 4.00
2966 3485 3.625745 CCCGAGTGGTAAAGCTGTT 57.374 52.632 0.00 0.00 0.00 3.16
2967 3486 1.156736 CCCGAGTGGTAAAGCTGTTG 58.843 55.000 0.00 0.00 0.00 3.33
2968 3487 0.517316 CCGAGTGGTAAAGCTGTTGC 59.483 55.000 0.00 0.00 40.05 4.17
2969 3488 0.517316 CGAGTGGTAAAGCTGTTGCC 59.483 55.000 8.21 8.21 40.80 4.52
2970 3489 1.878102 CGAGTGGTAAAGCTGTTGCCT 60.878 52.381 13.72 0.00 40.80 4.75
2971 3490 2.230660 GAGTGGTAAAGCTGTTGCCTT 58.769 47.619 13.72 5.67 40.80 4.35
2972 3491 1.956477 AGTGGTAAAGCTGTTGCCTTG 59.044 47.619 13.72 0.00 40.80 3.61
2973 3492 1.681264 GTGGTAAAGCTGTTGCCTTGT 59.319 47.619 13.72 0.00 40.80 3.16
2974 3493 1.680735 TGGTAAAGCTGTTGCCTTGTG 59.319 47.619 13.72 0.00 40.80 3.33
2975 3494 1.953686 GGTAAAGCTGTTGCCTTGTGA 59.046 47.619 7.98 0.00 40.80 3.58
2976 3495 2.287608 GGTAAAGCTGTTGCCTTGTGAC 60.288 50.000 7.98 0.00 40.80 3.67
2977 3496 0.746659 AAAGCTGTTGCCTTGTGACC 59.253 50.000 0.00 0.00 40.80 4.02
2978 3497 0.395586 AAGCTGTTGCCTTGTGACCA 60.396 50.000 0.00 0.00 40.80 4.02
2979 3498 0.178981 AGCTGTTGCCTTGTGACCAT 60.179 50.000 0.00 0.00 40.80 3.55
2980 3499 0.038892 GCTGTTGCCTTGTGACCATG 60.039 55.000 0.00 0.00 0.00 3.66
2981 3500 1.608055 CTGTTGCCTTGTGACCATGA 58.392 50.000 0.00 0.00 0.00 3.07
2982 3501 1.538512 CTGTTGCCTTGTGACCATGAG 59.461 52.381 0.00 0.00 0.00 2.90
2983 3502 0.883833 GTTGCCTTGTGACCATGAGG 59.116 55.000 0.00 0.00 42.21 3.86
2993 3512 4.617875 CCATGAGGTCACGGGTTC 57.382 61.111 0.00 0.00 0.00 3.62
2994 3513 1.447838 CCATGAGGTCACGGGTTCG 60.448 63.158 0.00 0.00 43.02 3.95
2995 3514 1.589630 CATGAGGTCACGGGTTCGA 59.410 57.895 0.00 0.00 40.11 3.71
2996 3515 0.458543 CATGAGGTCACGGGTTCGAG 60.459 60.000 0.00 0.00 40.11 4.04
2997 3516 0.898789 ATGAGGTCACGGGTTCGAGT 60.899 55.000 0.00 0.00 40.11 4.18
2998 3517 1.212229 GAGGTCACGGGTTCGAGTC 59.788 63.158 0.00 0.00 40.11 3.36
2999 3518 2.210341 GAGGTCACGGGTTCGAGTCC 62.210 65.000 0.82 0.82 40.11 3.85
3000 3519 2.273912 GGTCACGGGTTCGAGTCCT 61.274 63.158 8.28 0.00 40.11 3.85
3001 3520 1.080705 GTCACGGGTTCGAGTCCTG 60.081 63.158 13.65 13.65 40.11 3.86
3002 3521 2.261671 CACGGGTTCGAGTCCTGG 59.738 66.667 17.72 9.36 40.11 4.45
3003 3522 2.116772 ACGGGTTCGAGTCCTGGA 59.883 61.111 17.72 0.00 40.11 3.86
3004 3523 1.532316 ACGGGTTCGAGTCCTGGAA 60.532 57.895 17.72 0.00 40.11 3.53
3005 3524 1.117142 ACGGGTTCGAGTCCTGGAAA 61.117 55.000 17.72 0.00 40.11 3.13
3006 3525 0.669625 CGGGTTCGAGTCCTGGAAAC 60.670 60.000 0.00 0.00 39.00 2.78
3007 3526 0.395312 GGGTTCGAGTCCTGGAAACA 59.605 55.000 8.95 0.00 36.84 2.83
3018 3537 3.025924 TGGAAACAGCCTCTTGCAG 57.974 52.632 0.00 0.00 44.83 4.41
3019 3538 0.473755 TGGAAACAGCCTCTTGCAGA 59.526 50.000 0.00 0.00 44.83 4.26
3020 3539 1.133823 TGGAAACAGCCTCTTGCAGAA 60.134 47.619 0.00 0.00 44.83 3.02
3021 3540 1.956477 GGAAACAGCCTCTTGCAGAAA 59.044 47.619 0.00 0.00 44.83 2.52
3022 3541 2.560105 GGAAACAGCCTCTTGCAGAAAT 59.440 45.455 0.00 0.00 44.83 2.17
3023 3542 3.572584 GAAACAGCCTCTTGCAGAAATG 58.427 45.455 0.00 0.00 44.83 2.32
3024 3543 0.886563 ACAGCCTCTTGCAGAAATGC 59.113 50.000 0.00 0.00 44.83 3.56
3025 3544 0.885879 CAGCCTCTTGCAGAAATGCA 59.114 50.000 0.00 0.00 44.83 3.96
3026 3545 1.135373 CAGCCTCTTGCAGAAATGCAG 60.135 52.381 2.87 0.00 46.21 4.41
3027 3546 0.172803 GCCTCTTGCAGAAATGCAGG 59.827 55.000 6.04 6.04 46.21 4.85
3028 3547 0.815734 CCTCTTGCAGAAATGCAGGG 59.184 55.000 11.70 8.10 46.21 4.45
3029 3548 1.615116 CCTCTTGCAGAAATGCAGGGA 60.615 52.381 11.70 9.29 46.21 4.20
3030 3549 2.165167 CTCTTGCAGAAATGCAGGGAA 58.835 47.619 11.70 0.00 46.21 3.97
3031 3550 2.559668 CTCTTGCAGAAATGCAGGGAAA 59.440 45.455 11.70 0.00 46.21 3.13
3032 3551 2.559668 TCTTGCAGAAATGCAGGGAAAG 59.440 45.455 11.70 3.07 46.21 2.62
3033 3552 1.259609 TGCAGAAATGCAGGGAAAGG 58.740 50.000 0.00 0.00 40.23 3.11
3034 3553 0.108472 GCAGAAATGCAGGGAAAGGC 60.108 55.000 0.00 0.00 34.41 4.35
3035 3554 1.553706 CAGAAATGCAGGGAAAGGCT 58.446 50.000 0.00 0.00 0.00 4.58
3036 3555 1.203994 CAGAAATGCAGGGAAAGGCTG 59.796 52.381 0.00 0.00 0.00 4.85
3037 3556 0.108472 GAAATGCAGGGAAAGGCTGC 60.108 55.000 0.00 0.00 43.67 5.25
3038 3557 1.880819 AAATGCAGGGAAAGGCTGCG 61.881 55.000 0.00 0.00 46.05 5.18
3039 3558 3.574074 ATGCAGGGAAAGGCTGCGT 62.574 57.895 0.00 0.00 46.05 5.24
3040 3559 2.046314 GCAGGGAAAGGCTGCGTA 60.046 61.111 0.00 0.00 34.32 4.42
3041 3560 2.399356 GCAGGGAAAGGCTGCGTAC 61.399 63.158 0.00 0.00 34.32 3.67
3042 3561 1.003839 CAGGGAAAGGCTGCGTACA 60.004 57.895 0.00 0.00 0.00 2.90
3043 3562 0.605319 CAGGGAAAGGCTGCGTACAA 60.605 55.000 0.00 0.00 0.00 2.41
3044 3563 0.109723 AGGGAAAGGCTGCGTACAAA 59.890 50.000 0.00 0.00 0.00 2.83
3045 3564 0.955905 GGGAAAGGCTGCGTACAAAA 59.044 50.000 0.00 0.00 0.00 2.44
3046 3565 1.068541 GGGAAAGGCTGCGTACAAAAG 60.069 52.381 0.00 0.00 0.00 2.27
3047 3566 1.877443 GGAAAGGCTGCGTACAAAAGA 59.123 47.619 0.00 0.00 0.00 2.52
3048 3567 2.350484 GGAAAGGCTGCGTACAAAAGAC 60.350 50.000 0.00 0.00 0.00 3.01
3049 3568 1.235724 AAGGCTGCGTACAAAAGACC 58.764 50.000 0.00 0.00 0.00 3.85
3050 3569 0.605589 AGGCTGCGTACAAAAGACCC 60.606 55.000 0.00 0.00 0.00 4.46
3051 3570 0.887387 GGCTGCGTACAAAAGACCCA 60.887 55.000 0.00 0.00 0.00 4.51
3052 3571 0.948678 GCTGCGTACAAAAGACCCAA 59.051 50.000 0.00 0.00 0.00 4.12
3053 3572 1.335496 GCTGCGTACAAAAGACCCAAA 59.665 47.619 0.00 0.00 0.00 3.28
3054 3573 2.604614 GCTGCGTACAAAAGACCCAAAG 60.605 50.000 0.00 0.00 0.00 2.77
3055 3574 2.616842 CTGCGTACAAAAGACCCAAAGT 59.383 45.455 0.00 0.00 0.00 2.66
3056 3575 2.356382 TGCGTACAAAAGACCCAAAGTG 59.644 45.455 0.00 0.00 0.00 3.16
3057 3576 2.287368 GCGTACAAAAGACCCAAAGTGG 60.287 50.000 0.00 0.00 37.25 4.00
3058 3577 2.946990 CGTACAAAAGACCCAAAGTGGT 59.053 45.455 0.00 0.00 42.79 4.16
3063 3582 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
3064 3583 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
3065 3584 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
3066 3585 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
3067 3586 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
3068 3587 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
3069 3588 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
3070 3589 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
3071 3590 3.714001 GTGGTCGGACCCTTCCCC 61.714 72.222 23.81 0.00 38.99 4.81
3078 3597 4.735599 GACCCTTCCCCGGACCCT 62.736 72.222 0.73 0.00 0.00 4.34
3105 3624 2.203070 GGAGCTACATGCACCGGG 60.203 66.667 6.32 0.00 42.21 5.73
3106 3625 2.897350 GAGCTACATGCACCGGGC 60.897 66.667 6.32 7.25 45.94 6.13
3107 3626 3.391665 GAGCTACATGCACCGGGCT 62.392 63.158 6.32 0.81 45.94 5.19
3108 3627 3.204827 GCTACATGCACCGGGCTG 61.205 66.667 6.32 9.21 45.15 4.85
3109 3628 3.204827 CTACATGCACCGGGCTGC 61.205 66.667 6.32 8.50 45.15 5.25
3110 3629 4.794648 TACATGCACCGGGCTGCC 62.795 66.667 11.05 11.05 45.15 4.85
3115 3634 4.506255 GCACCGGGCTGCCCTAAT 62.506 66.667 33.39 16.93 42.67 1.73
3116 3635 2.203209 CACCGGGCTGCCCTAATC 60.203 66.667 33.39 8.98 42.67 1.75
3117 3636 2.366972 ACCGGGCTGCCCTAATCT 60.367 61.111 33.39 9.64 42.67 2.40
3118 3637 2.001269 ACCGGGCTGCCCTAATCTT 61.001 57.895 33.39 9.66 42.67 2.40
3119 3638 0.693092 ACCGGGCTGCCCTAATCTTA 60.693 55.000 33.39 0.00 42.67 2.10
3120 3639 0.472471 CCGGGCTGCCCTAATCTTAA 59.528 55.000 33.39 0.00 42.67 1.85
3121 3640 1.594331 CGGGCTGCCCTAATCTTAAC 58.406 55.000 33.39 5.18 42.67 2.01
3122 3641 1.141053 CGGGCTGCCCTAATCTTAACT 59.859 52.381 33.39 0.00 42.67 2.24
3123 3642 2.576615 GGGCTGCCCTAATCTTAACTG 58.423 52.381 30.42 0.00 41.34 3.16
3124 3643 2.576615 GGCTGCCCTAATCTTAACTGG 58.423 52.381 7.66 0.00 0.00 4.00
3125 3644 2.172717 GGCTGCCCTAATCTTAACTGGA 59.827 50.000 7.66 0.00 0.00 3.86
3126 3645 3.471680 GCTGCCCTAATCTTAACTGGAG 58.528 50.000 0.00 0.00 0.00 3.86
3127 3646 3.118223 GCTGCCCTAATCTTAACTGGAGT 60.118 47.826 0.00 0.00 0.00 3.85
3128 3647 4.626529 GCTGCCCTAATCTTAACTGGAGTT 60.627 45.833 0.00 0.00 41.73 3.01
3129 3648 5.501156 CTGCCCTAATCTTAACTGGAGTTT 58.499 41.667 0.00 0.00 39.31 2.66
3130 3649 6.630203 TGCCCTAATCTTAACTGGAGTTTA 57.370 37.500 0.00 0.00 39.31 2.01
3131 3650 7.023171 TGCCCTAATCTTAACTGGAGTTTAA 57.977 36.000 0.00 0.00 39.31 1.52
3132 3651 7.110155 TGCCCTAATCTTAACTGGAGTTTAAG 58.890 38.462 0.00 1.09 39.31 1.85
3133 3652 7.110810 GCCCTAATCTTAACTGGAGTTTAAGT 58.889 38.462 0.00 0.00 39.31 2.24
3134 3653 7.280428 GCCCTAATCTTAACTGGAGTTTAAGTC 59.720 40.741 0.00 0.00 39.31 3.01
3164 3683 9.090692 CAATTATCCAATGGTCAATTTCAGTTC 57.909 33.333 0.00 0.00 0.00 3.01
3184 3716 4.894252 TCTACCTACCCAAGACCATAGT 57.106 45.455 0.00 0.00 0.00 2.12
3186 3718 5.206587 TCTACCTACCCAAGACCATAGTTC 58.793 45.833 0.00 0.00 0.00 3.01
3189 3721 3.068307 CCTACCCAAGACCATAGTTCTCG 59.932 52.174 0.00 0.00 0.00 4.04
3195 3727 4.115516 CAAGACCATAGTTCTCGATGTGG 58.884 47.826 0.00 0.00 0.00 4.17
3199 3731 5.241949 AGACCATAGTTCTCGATGTGGTATC 59.758 44.000 5.29 0.00 39.86 2.24
3208 3740 6.101650 TCTCGATGTGGTATCTATGCATTT 57.898 37.500 3.54 0.00 0.00 2.32
3306 3841 5.592104 TCGCTGTTAACCATGATTCTCTA 57.408 39.130 2.48 0.00 0.00 2.43
3348 3883 4.722700 GGTGCCCAGGTCATGCGT 62.723 66.667 0.00 0.00 0.00 5.24
3380 3915 4.402793 TCAGTTAGCTCATGAGTAGGTTCC 59.597 45.833 23.38 5.42 0.00 3.62
3385 3920 2.815478 CTCATGAGTAGGTTCCGCTTC 58.185 52.381 14.95 0.00 0.00 3.86
3387 3922 2.832129 TCATGAGTAGGTTCCGCTTCTT 59.168 45.455 0.00 0.00 0.00 2.52
3389 3924 3.314541 TGAGTAGGTTCCGCTTCTTTC 57.685 47.619 0.00 0.00 0.00 2.62
3390 3925 2.028385 TGAGTAGGTTCCGCTTCTTTCC 60.028 50.000 0.00 0.00 0.00 3.13
3391 3926 1.278413 AGTAGGTTCCGCTTCTTTCCC 59.722 52.381 0.00 0.00 0.00 3.97
3396 3933 1.131303 TTCCGCTTCTTTCCCCCTCA 61.131 55.000 0.00 0.00 0.00 3.86
3410 3947 2.224695 CCCCCTCAAACCGAGTAGTTTT 60.225 50.000 0.00 0.00 40.48 2.43
3426 3963 7.952637 CGAGTAGTTTTTGCTCTTGAACTAATC 59.047 37.037 10.69 10.69 42.04 1.75
3429 3966 6.442112 AGTTTTTGCTCTTGAACTAATCAGC 58.558 36.000 0.00 0.00 39.77 4.26
3432 3969 2.028112 TGCTCTTGAACTAATCAGCCGT 60.028 45.455 0.00 0.00 39.77 5.68
3435 3972 2.301870 TCTTGAACTAATCAGCCGTGGT 59.698 45.455 0.00 0.00 39.77 4.16
3436 3973 2.380084 TGAACTAATCAGCCGTGGTC 57.620 50.000 0.00 0.00 33.04 4.02
3437 3974 1.899814 TGAACTAATCAGCCGTGGTCT 59.100 47.619 0.00 0.00 33.04 3.85
3438 3975 2.094182 TGAACTAATCAGCCGTGGTCTC 60.094 50.000 0.00 0.00 33.04 3.36
3439 3976 0.456221 ACTAATCAGCCGTGGTCTCG 59.544 55.000 0.00 0.00 0.00 4.04
3440 3977 0.456221 CTAATCAGCCGTGGTCTCGT 59.544 55.000 0.00 0.00 0.00 4.18
3441 3978 0.172578 TAATCAGCCGTGGTCTCGTG 59.827 55.000 0.00 0.00 0.00 4.35
3442 3979 2.507110 AATCAGCCGTGGTCTCGTGG 62.507 60.000 0.00 0.00 0.00 4.94
3443 3980 3.680786 CAGCCGTGGTCTCGTGGA 61.681 66.667 0.00 0.00 0.00 4.02
3444 3981 2.680352 AGCCGTGGTCTCGTGGAT 60.680 61.111 0.00 0.00 0.00 3.41
3445 3982 2.264794 GCCGTGGTCTCGTGGATT 59.735 61.111 0.00 0.00 0.00 3.01
3452 3989 2.693591 GTGGTCTCGTGGATTGGAGATA 59.306 50.000 0.00 0.00 41.04 1.98
3461 3998 6.223852 TCGTGGATTGGAGATATTTTCTAGC 58.776 40.000 0.00 0.00 33.74 3.42
3462 3999 5.991606 CGTGGATTGGAGATATTTTCTAGCA 59.008 40.000 0.00 0.00 33.74 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.680619 AGCGGTAGGAAATCATATGTGAAA 58.319 37.500 1.90 0.00 38.01 2.69
171 180 0.251297 CTGAACCTCATGCCCCAACA 60.251 55.000 0.00 0.00 0.00 3.33
732 1215 4.019792 AGCACACACACATCTTATCCAA 57.980 40.909 0.00 0.00 0.00 3.53
870 1353 1.072266 ATGCCACTACAACTTCCCCA 58.928 50.000 0.00 0.00 0.00 4.96
898 1381 8.413229 GGAAATATGCCATTACTAAAGCTCAAA 58.587 33.333 0.00 0.00 0.00 2.69
904 1387 8.902806 TGAGTTGGAAATATGCCATTACTAAAG 58.097 33.333 0.00 0.00 34.90 1.85
908 1391 5.296780 CGTGAGTTGGAAATATGCCATTACT 59.703 40.000 0.00 1.30 34.90 2.24
919 1402 7.138736 CACTACAATTTTCGTGAGTTGGAAAT 58.861 34.615 0.00 0.00 32.67 2.17
928 1411 5.483811 TCTATGCCACTACAATTTTCGTGA 58.516 37.500 0.00 0.00 0.00 4.35
930 1413 5.527582 GGATCTATGCCACTACAATTTTCGT 59.472 40.000 0.00 0.00 0.00 3.85
931 1414 5.527214 TGGATCTATGCCACTACAATTTTCG 59.473 40.000 0.00 0.00 0.00 3.46
964 1447 3.799035 CGATTCCCGCGATTTTATTCAG 58.201 45.455 8.23 0.00 0.00 3.02
989 1472 0.033228 TTGCAAATTGGTTGGGAGCG 59.967 50.000 0.00 0.00 37.73 5.03
993 1476 2.289010 GGTCTCTTGCAAATTGGTTGGG 60.289 50.000 0.00 0.00 37.73 4.12
995 1478 3.068590 AGTGGTCTCTTGCAAATTGGTTG 59.931 43.478 0.00 0.00 40.50 3.77
1142 1625 1.542679 GTACCGGGGAGAGGAGGAT 59.457 63.158 6.32 0.00 0.00 3.24
1386 1869 1.003442 TCCCAGGGGACATCAGGAG 59.997 63.158 5.33 0.00 39.76 3.69
1464 1947 2.358737 GCCACGGAAGGACAGGTG 60.359 66.667 0.00 0.00 0.00 4.00
1465 1948 2.526873 AGCCACGGAAGGACAGGT 60.527 61.111 0.00 0.00 0.00 4.00
1522 2005 3.374012 TAAACCATCCCCGCCGACG 62.374 63.158 0.00 0.00 39.67 5.12
1524 2007 1.052124 ATCTAAACCATCCCCGCCGA 61.052 55.000 0.00 0.00 0.00 5.54
1529 2012 3.555966 CAACTCCATCTAAACCATCCCC 58.444 50.000 0.00 0.00 0.00 4.81
1550 2042 2.972819 GCCCCAGAGACTCCAACCC 61.973 68.421 0.00 0.00 0.00 4.11
1579 2071 5.198207 TCCTCCTGTATGAACGAATACTCA 58.802 41.667 0.00 0.00 34.66 3.41
1594 2086 3.322466 CGCCCAACCTCCTCCTGT 61.322 66.667 0.00 0.00 0.00 4.00
1596 2088 3.322466 CACGCCCAACCTCCTCCT 61.322 66.667 0.00 0.00 0.00 3.69
1598 2090 3.959991 GAGCACGCCCAACCTCCTC 62.960 68.421 0.00 0.00 0.00 3.71
1628 2120 2.041620 CTGAATTTCCAAGTGGGGGAGA 59.958 50.000 0.00 0.00 35.46 3.71
1633 2125 2.504367 ACGACTGAATTTCCAAGTGGG 58.496 47.619 0.00 0.00 35.41 4.61
1639 2131 4.394920 GCCTTATGAACGACTGAATTTCCA 59.605 41.667 0.00 0.00 0.00 3.53
1654 2146 4.797743 TCTTCAGAGCTAGAGCCTTATGA 58.202 43.478 0.00 0.00 43.38 2.15
1659 2151 2.024464 TCCTTCTTCAGAGCTAGAGCCT 60.024 50.000 0.00 0.00 43.38 4.58
1681 2173 7.249147 CCAAAATTGACTCTGACATCTCAATC 58.751 38.462 0.00 0.00 33.21 2.67
1691 2183 3.149196 GAGCACCCAAAATTGACTCTGA 58.851 45.455 0.00 0.00 0.00 3.27
1700 2192 1.538687 GCCTGCTGAGCACCCAAAAT 61.539 55.000 1.40 0.00 33.79 1.82
1723 2215 4.110482 GGCAGAGATCATGCAAATTGTTC 58.890 43.478 20.48 0.00 45.68 3.18
1768 2260 2.832129 TGGCTGCACTAAGCTAAGTACT 59.168 45.455 0.50 0.00 45.94 2.73
1832 2324 1.409427 CCCATCTTCCTCGAGTACCAC 59.591 57.143 12.31 0.00 0.00 4.16
1892 2384 4.351127 AGGTCAAGTAACTTCGGTAGGAT 58.649 43.478 0.00 0.00 0.00 3.24
1893 2385 3.771216 AGGTCAAGTAACTTCGGTAGGA 58.229 45.455 0.00 0.00 0.00 2.94
1900 2392 5.527582 TGCTCTTTGAAGGTCAAGTAACTTC 59.472 40.000 0.00 0.00 37.70 3.01
1948 2440 3.338249 ACGTTTGCAGACATCTAATGCT 58.662 40.909 8.25 0.00 40.62 3.79
2067 2559 0.458669 CAAAGGATGCATGCAGTCCC 59.541 55.000 29.81 26.21 32.31 4.46
2129 2621 3.336138 ACAAATCGGTTTCCTCTCTCC 57.664 47.619 0.00 0.00 0.00 3.71
2135 2627 3.279434 GAGGCATACAAATCGGTTTCCT 58.721 45.455 0.00 0.00 0.00 3.36
2177 2669 0.389817 TCTGTCCAGACCAAATCGCG 60.390 55.000 0.00 0.00 31.41 5.87
2274 2766 9.085645 ACTTTATTGCCATATCATCAATCATGT 57.914 29.630 0.00 0.00 33.66 3.21
2332 2824 4.966005 TTCGAGACGAAGCACAGG 57.034 55.556 2.48 0.00 41.05 4.00
2391 2883 1.597854 TTGGTTGTCTCGGCAGCTG 60.598 57.895 10.11 10.11 0.00 4.24
2416 2908 7.719633 AGTTTGACCAGAATAGCTTTAGTCAAA 59.280 33.333 16.45 16.45 41.48 2.69
2431 2923 2.281484 GGCCGCAGTTTGACCAGA 60.281 61.111 0.00 0.00 0.00 3.86
2432 2924 2.281761 AGGCCGCAGTTTGACCAG 60.282 61.111 0.00 0.00 0.00 4.00
2480 2972 1.281867 CAGCCCACCAGGAGTTTATCA 59.718 52.381 0.00 0.00 38.24 2.15
2486 2978 2.937689 ATGCAGCCCACCAGGAGT 60.938 61.111 0.00 0.00 38.24 3.85
2500 2992 4.142093 ACTTGGTTAATCTGAATGGCATGC 60.142 41.667 9.90 9.90 0.00 4.06
2502 2994 6.835488 ACATACTTGGTTAATCTGAATGGCAT 59.165 34.615 0.00 0.00 0.00 4.40
2530 3022 6.049149 TCAAACAAAACAGTGTTCCAAACAA 58.951 32.000 9.40 0.00 44.16 2.83
2533 3025 7.736447 AAATCAAACAAAACAGTGTTCCAAA 57.264 28.000 9.40 0.00 40.86 3.28
2534 3026 7.736447 AAAATCAAACAAAACAGTGTTCCAA 57.264 28.000 9.40 0.00 40.86 3.53
2589 3082 8.806146 TGCTACTCTGTATATATGAAGCAATGA 58.194 33.333 10.21 0.00 34.75 2.57
2644 3138 9.335891 TCGTGCATAACAAAATTATGTACTTTG 57.664 29.630 19.06 9.18 42.15 2.77
2647 3141 8.263940 AGTCGTGCATAACAAAATTATGTACT 57.736 30.769 19.06 10.70 42.15 2.73
2668 3162 3.002656 AGTCAATTGTTGCACTTGAGTCG 59.997 43.478 5.13 0.00 33.48 4.18
2670 3164 4.989279 AAGTCAATTGTTGCACTTGAGT 57.011 36.364 5.13 3.68 37.98 3.41
2693 3190 8.673626 ACTTAACTGAACATAAATTCATTGCG 57.326 30.769 0.00 0.00 37.93 4.85
2730 3227 3.118038 ACAAGTCAAAGACAGCCCTTACA 60.118 43.478 0.00 0.00 34.60 2.41
2738 3235 5.066375 TGTCCATTTCACAAGTCAAAGACAG 59.934 40.000 0.00 0.00 34.60 3.51
2751 3248 4.319177 ACTACAGAAGCTGTCCATTTCAC 58.681 43.478 2.97 0.00 41.21 3.18
2767 3264 7.026631 TGTTCAATTGTTTCTGGAACTACAG 57.973 36.000 5.13 0.00 38.82 2.74
2774 3271 6.462552 TCATGTTGTTCAATTGTTTCTGGA 57.537 33.333 5.13 0.00 0.00 3.86
2794 3291 7.806409 TTGCTACTTTGTGTATATGCATCAT 57.194 32.000 0.19 0.00 32.42 2.45
2795 3292 7.806409 ATTGCTACTTTGTGTATATGCATCA 57.194 32.000 0.19 0.00 32.42 3.07
2895 3406 9.607333 TCTTATACTGGACATCCTAGATTTCAT 57.393 33.333 0.00 0.00 36.82 2.57
2903 3414 9.607333 AATCATTCTCTTATACTGGACATCCTA 57.393 33.333 0.00 0.00 36.82 2.94
2926 3437 8.245491 TCGGGTTAAAATTAAACTGGCTTAATC 58.755 33.333 9.32 0.00 37.33 1.75
2928 3439 7.231115 ACTCGGGTTAAAATTAAACTGGCTTAA 59.769 33.333 9.32 0.00 37.33 1.85
2949 3468 0.517316 GCAACAGCTTTACCACTCGG 59.483 55.000 0.00 0.00 38.77 4.63
2950 3469 0.517316 GGCAACAGCTTTACCACTCG 59.483 55.000 0.00 0.00 0.00 4.18
2951 3470 1.897560 AGGCAACAGCTTTACCACTC 58.102 50.000 0.00 0.00 41.41 3.51
2955 3474 1.953686 TCACAAGGCAACAGCTTTACC 59.046 47.619 0.00 0.00 41.41 2.85
2956 3475 2.287608 GGTCACAAGGCAACAGCTTTAC 60.288 50.000 0.00 0.00 41.41 2.01
2957 3476 1.953686 GGTCACAAGGCAACAGCTTTA 59.046 47.619 0.00 0.00 41.41 1.85
2958 3477 0.746659 GGTCACAAGGCAACAGCTTT 59.253 50.000 0.00 0.00 41.41 3.51
2960 3479 0.178981 ATGGTCACAAGGCAACAGCT 60.179 50.000 0.00 0.00 41.41 4.24
2961 3480 0.038892 CATGGTCACAAGGCAACAGC 60.039 55.000 0.00 0.00 41.41 4.40
2962 3481 1.538512 CTCATGGTCACAAGGCAACAG 59.461 52.381 0.00 0.00 41.41 3.16
2963 3482 1.608055 CTCATGGTCACAAGGCAACA 58.392 50.000 0.00 0.00 41.41 3.33
2964 3483 0.883833 CCTCATGGTCACAAGGCAAC 59.116 55.000 0.00 0.00 0.00 4.17
2965 3484 0.478072 ACCTCATGGTCACAAGGCAA 59.522 50.000 0.00 0.00 44.78 4.52
2966 3485 2.154139 ACCTCATGGTCACAAGGCA 58.846 52.632 0.00 0.00 44.78 4.75
2977 3496 0.458543 CTCGAACCCGTGACCTCATG 60.459 60.000 0.00 0.00 37.05 3.07
2978 3497 0.898789 ACTCGAACCCGTGACCTCAT 60.899 55.000 0.00 0.00 37.05 2.90
2979 3498 1.521450 GACTCGAACCCGTGACCTCA 61.521 60.000 0.00 0.00 37.05 3.86
2980 3499 1.212229 GACTCGAACCCGTGACCTC 59.788 63.158 0.00 0.00 37.05 3.85
2981 3500 2.273912 GGACTCGAACCCGTGACCT 61.274 63.158 0.00 0.00 39.62 3.85
2982 3501 2.260743 GGACTCGAACCCGTGACC 59.739 66.667 0.00 0.00 37.08 4.02
2983 3502 1.080705 CAGGACTCGAACCCGTGAC 60.081 63.158 4.92 0.00 37.05 3.67
2984 3503 2.273179 CCAGGACTCGAACCCGTGA 61.273 63.158 4.92 0.00 37.05 4.35
2985 3504 1.812686 TTCCAGGACTCGAACCCGTG 61.813 60.000 0.00 0.64 37.05 4.94
2986 3505 1.117142 TTTCCAGGACTCGAACCCGT 61.117 55.000 0.00 0.00 37.05 5.28
2987 3506 0.669625 GTTTCCAGGACTCGAACCCG 60.670 60.000 0.00 0.00 37.07 5.28
2988 3507 0.395312 TGTTTCCAGGACTCGAACCC 59.605 55.000 0.00 0.12 0.00 4.11
2989 3508 1.797025 CTGTTTCCAGGACTCGAACC 58.203 55.000 0.00 0.64 34.90 3.62
2990 3509 1.149148 GCTGTTTCCAGGACTCGAAC 58.851 55.000 0.00 0.00 39.22 3.95
2991 3510 0.034896 GGCTGTTTCCAGGACTCGAA 59.965 55.000 0.00 0.00 39.22 3.71
2992 3511 0.832135 AGGCTGTTTCCAGGACTCGA 60.832 55.000 0.00 0.00 39.22 4.04
2993 3512 0.390472 GAGGCTGTTTCCAGGACTCG 60.390 60.000 0.00 0.00 39.22 4.18
2994 3513 0.980423 AGAGGCTGTTTCCAGGACTC 59.020 55.000 0.00 0.00 39.22 3.36
2995 3514 1.072965 CAAGAGGCTGTTTCCAGGACT 59.927 52.381 0.00 0.00 39.22 3.85
2996 3515 1.528129 CAAGAGGCTGTTTCCAGGAC 58.472 55.000 0.00 0.00 39.22 3.85
2997 3516 0.250901 GCAAGAGGCTGTTTCCAGGA 60.251 55.000 0.00 0.00 39.22 3.86
2998 3517 0.538057 TGCAAGAGGCTGTTTCCAGG 60.538 55.000 0.00 0.00 45.15 4.45
2999 3518 0.879765 CTGCAAGAGGCTGTTTCCAG 59.120 55.000 0.00 0.00 45.15 3.86
3000 3519 0.473755 TCTGCAAGAGGCTGTTTCCA 59.526 50.000 0.00 0.00 38.67 3.53
3001 3520 3.329300 TCTGCAAGAGGCTGTTTCC 57.671 52.632 0.00 0.00 38.67 3.13
3016 3535 1.203994 CAGCCTTTCCCTGCATTTCTG 59.796 52.381 0.00 0.00 0.00 3.02
3017 3536 1.553706 CAGCCTTTCCCTGCATTTCT 58.446 50.000 0.00 0.00 0.00 2.52
3024 3543 0.605319 TTGTACGCAGCCTTTCCCTG 60.605 55.000 0.00 0.00 0.00 4.45
3025 3544 0.109723 TTTGTACGCAGCCTTTCCCT 59.890 50.000 0.00 0.00 0.00 4.20
3026 3545 0.955905 TTTTGTACGCAGCCTTTCCC 59.044 50.000 0.00 0.00 0.00 3.97
3027 3546 1.877443 TCTTTTGTACGCAGCCTTTCC 59.123 47.619 0.00 0.00 0.00 3.13
3028 3547 2.350484 GGTCTTTTGTACGCAGCCTTTC 60.350 50.000 0.00 0.00 0.00 2.62
3029 3548 1.607148 GGTCTTTTGTACGCAGCCTTT 59.393 47.619 0.00 0.00 0.00 3.11
3030 3549 1.235724 GGTCTTTTGTACGCAGCCTT 58.764 50.000 0.00 0.00 0.00 4.35
3031 3550 0.605589 GGGTCTTTTGTACGCAGCCT 60.606 55.000 0.00 0.00 0.00 4.58
3032 3551 0.887387 TGGGTCTTTTGTACGCAGCC 60.887 55.000 0.00 0.00 35.18 4.85
3033 3552 0.948678 TTGGGTCTTTTGTACGCAGC 59.051 50.000 0.00 0.00 40.36 5.25
3034 3553 2.616842 ACTTTGGGTCTTTTGTACGCAG 59.383 45.455 0.00 0.00 40.36 5.18
3035 3554 2.356382 CACTTTGGGTCTTTTGTACGCA 59.644 45.455 0.00 0.00 37.94 5.24
3036 3555 2.287368 CCACTTTGGGTCTTTTGTACGC 60.287 50.000 0.00 0.00 32.67 4.42
3037 3556 2.946990 ACCACTTTGGGTCTTTTGTACG 59.053 45.455 0.00 0.00 43.37 3.67
3047 3566 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
3048 3567 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
3049 3568 0.605589 GAAGGGTCCGACCACTTTGG 60.606 60.000 19.43 0.00 41.02 3.28
3050 3569 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
3051 3570 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
3052 3571 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
3053 3572 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
3054 3573 3.714001 GGGGAAGGGTCCGACCAC 61.714 72.222 19.43 8.70 46.04 4.16
3061 3580 4.735599 AGGGTCCGGGGAAGGGTC 62.736 72.222 0.00 0.00 0.00 4.46
3077 3596 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
3080 3599 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
3081 3600 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
3082 3601 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
3083 3602 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
3089 3608 2.897350 GCCCGGTGCATGTAGCTC 60.897 66.667 11.25 0.00 45.94 4.09
3090 3609 3.402681 AGCCCGGTGCATGTAGCT 61.403 61.111 15.92 4.82 45.94 3.32
3091 3610 3.204827 CAGCCCGGTGCATGTAGC 61.205 66.667 15.92 2.56 44.83 3.58
3092 3611 3.204827 GCAGCCCGGTGCATGTAG 61.205 66.667 13.70 0.91 43.41 2.74
3093 3612 4.794648 GGCAGCCCGGTGCATGTA 62.795 66.667 19.47 0.00 45.93 2.29
3103 3622 2.576615 CAGTTAAGATTAGGGCAGCCC 58.423 52.381 24.90 24.90 45.90 5.19
3104 3623 2.172717 TCCAGTTAAGATTAGGGCAGCC 59.827 50.000 1.26 1.26 0.00 4.85
3105 3624 3.118223 ACTCCAGTTAAGATTAGGGCAGC 60.118 47.826 0.00 0.00 0.00 5.25
3106 3625 4.762289 ACTCCAGTTAAGATTAGGGCAG 57.238 45.455 0.00 0.00 0.00 4.85
3107 3626 5.514500 AAACTCCAGTTAAGATTAGGGCA 57.486 39.130 0.00 0.00 37.25 5.36
3108 3627 7.110810 ACTTAAACTCCAGTTAAGATTAGGGC 58.889 38.462 10.13 0.00 37.25 5.19
3109 3628 8.541234 AGACTTAAACTCCAGTTAAGATTAGGG 58.459 37.037 10.13 0.00 37.25 3.53
3120 3639 9.668497 GGATAATTGTTAGACTTAAACTCCAGT 57.332 33.333 0.00 0.00 0.00 4.00
3121 3640 9.667107 TGGATAATTGTTAGACTTAAACTCCAG 57.333 33.333 0.00 0.00 28.58 3.86
3128 3647 9.967451 TGACCATTGGATAATTGTTAGACTTAA 57.033 29.630 10.37 0.00 0.00 1.85
3129 3648 9.967451 TTGACCATTGGATAATTGTTAGACTTA 57.033 29.630 10.37 0.00 0.00 2.24
3130 3649 8.877864 TTGACCATTGGATAATTGTTAGACTT 57.122 30.769 10.37 0.00 0.00 3.01
3131 3650 9.479549 AATTGACCATTGGATAATTGTTAGACT 57.520 29.630 10.37 0.00 0.00 3.24
3148 3667 6.415573 GGTAGGTAGAACTGAAATTGACCAT 58.584 40.000 0.00 0.00 0.00 3.55
3164 3683 5.209659 AGAACTATGGTCTTGGGTAGGTAG 58.790 45.833 0.00 0.00 0.00 3.18
3184 3716 5.728637 ATGCATAGATACCACATCGAGAA 57.271 39.130 0.00 0.00 0.00 2.87
3186 3718 5.928264 TCAAATGCATAGATACCACATCGAG 59.072 40.000 0.00 0.00 0.00 4.04
3208 3740 8.410673 TTTAACAAACTACCATTAAGGCATCA 57.589 30.769 0.00 0.00 43.14 3.07
3250 3782 9.520515 ACAAATCCTACACTGATAGAAAAACAT 57.479 29.630 0.00 0.00 0.00 2.71
3282 3817 6.161855 AGAGAATCATGGTTAACAGCGATA 57.838 37.500 8.10 0.00 37.82 2.92
3306 3841 5.555017 GGAACATATCTGTGTGCCTATGAT 58.445 41.667 0.00 0.00 43.43 2.45
3340 3875 4.410492 ACTGAATCTGAAAACGCATGAC 57.590 40.909 0.00 0.00 0.00 3.06
3348 3883 7.164122 ACTCATGAGCTAACTGAATCTGAAAA 58.836 34.615 22.83 0.00 0.00 2.29
3380 3915 0.881796 GTTTGAGGGGGAAAGAAGCG 59.118 55.000 0.00 0.00 0.00 4.68
3385 3920 3.249687 CTCGGTTTGAGGGGGAAAG 57.750 57.895 0.00 0.00 41.29 2.62
3396 3933 4.879545 TCAAGAGCAAAAACTACTCGGTTT 59.120 37.500 0.00 0.00 40.59 3.27
3410 3947 3.002791 CGGCTGATTAGTTCAAGAGCAA 58.997 45.455 0.00 0.00 32.78 3.91
3426 3963 2.507110 AATCCACGAGACCACGGCTG 62.507 60.000 0.00 0.00 37.61 4.85
3429 3966 1.447838 CCAATCCACGAGACCACGG 60.448 63.158 0.00 0.00 37.61 4.94
3432 3969 1.866015 ATCTCCAATCCACGAGACCA 58.134 50.000 0.00 0.00 37.94 4.02
3435 3972 6.485830 AGAAAATATCTCCAATCCACGAGA 57.514 37.500 0.00 0.00 39.38 4.04
3436 3973 6.367422 GCTAGAAAATATCTCCAATCCACGAG 59.633 42.308 0.00 0.00 39.71 4.18
3437 3974 6.183360 TGCTAGAAAATATCTCCAATCCACGA 60.183 38.462 0.00 0.00 39.71 4.35
3438 3975 5.991606 TGCTAGAAAATATCTCCAATCCACG 59.008 40.000 0.00 0.00 39.71 4.94
3439 3976 6.767902 TGTGCTAGAAAATATCTCCAATCCAC 59.232 38.462 0.00 0.00 39.71 4.02
3440 3977 6.899089 TGTGCTAGAAAATATCTCCAATCCA 58.101 36.000 0.00 0.00 39.71 3.41
3441 3978 7.992754 ATGTGCTAGAAAATATCTCCAATCC 57.007 36.000 0.00 0.00 39.71 3.01
3442 3979 9.494271 TGTATGTGCTAGAAAATATCTCCAATC 57.506 33.333 0.00 0.00 39.71 2.67
3444 3981 9.276590 CATGTATGTGCTAGAAAATATCTCCAA 57.723 33.333 0.00 0.00 39.71 3.53
3445 3982 8.432013 ACATGTATGTGCTAGAAAATATCTCCA 58.568 33.333 0.00 0.00 40.03 3.86
3452 3989 7.394359 ACAGGAAACATGTATGTGCTAGAAAAT 59.606 33.333 0.00 0.00 41.61 1.82
3461 3998 6.801539 ACAGTAACAGGAAACATGTATGTG 57.198 37.500 0.00 0.00 41.61 3.21
3462 3999 7.817418 AAACAGTAACAGGAAACATGTATGT 57.183 32.000 0.00 0.00 44.20 2.29


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

AutoCloner maintained by Alex Coulton.