Multiple sequence alignment - TraesCS2A01G255200

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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 TraesCS2A01G255200 chr2A 100.000 5579 0 0 1 5579 389443834 389438256 0.000000e+00 10303.0
1 TraesCS2A01G255200 chr2A 88.496 226 16 1 2436 2651 466393272 466393047 1.190000e-66 265.0
2 TraesCS2A01G255200 chr2A 95.413 109 5 0 2650 2758 389441077 389441185 2.070000e-39 174.0
3 TraesCS2A01G255200 chr2A 95.745 47 2 0 5266 5312 60776575 60776529 5.990000e-10 76.8
4 TraesCS2A01G255200 chr2D 93.546 2882 110 30 2751 5579 308482625 308479767 0.000000e+00 4222.0
5 TraesCS2A01G255200 chr2D 91.950 1441 51 11 1270 2651 308484052 308482618 0.000000e+00 1958.0
6 TraesCS2A01G255200 chr2D 93.280 1250 32 9 1 1228 308485338 308484119 0.000000e+00 1796.0
7 TraesCS2A01G255200 chr2B 94.368 2095 76 20 2751 4820 359614932 359617009 0.000000e+00 3177.0
8 TraesCS2A01G255200 chr2B 94.444 1278 31 8 1 1274 359612336 359613577 0.000000e+00 1930.0
9 TraesCS2A01G255200 chr2B 94.502 1164 39 12 1510 2651 359613779 359614939 0.000000e+00 1772.0
10 TraesCS2A01G255200 chr2B 90.026 782 47 14 4820 5579 359618862 359619634 0.000000e+00 983.0
11 TraesCS2A01G255200 chr2B 92.308 169 11 2 1270 1437 359613612 359613779 7.220000e-59 239.0
12 TraesCS2A01G255200 chr2B 94.783 115 5 1 2650 2763 541090339 541090453 1.600000e-40 178.0
13 TraesCS2A01G255200 chr2B 93.860 114 7 0 2648 2761 541090449 541090336 7.430000e-39 172.0
14 TraesCS2A01G255200 chr5B 89.381 226 14 1 2436 2651 713043087 713043312 5.510000e-70 276.0
15 TraesCS2A01G255200 chr5B 94.068 118 4 3 2648 2764 556160203 556160318 5.740000e-40 176.0
16 TraesCS2A01G255200 chr5B 93.103 116 6 1 2649 2762 508629541 508629656 9.610000e-38 169.0
17 TraesCS2A01G255200 chr1A 89.381 226 14 1 2436 2651 334073801 334074026 5.510000e-70 276.0
18 TraesCS2A01G255200 chr7D 88.938 226 15 1 2436 2651 307061775 307062000 2.560000e-68 270.0
19 TraesCS2A01G255200 chr7D 82.828 99 15 1 5479 5577 463970641 463970545 2.770000e-13 87.9
20 TraesCS2A01G255200 chr7D 96.154 52 2 0 5264 5315 40136204 40136153 9.960000e-13 86.1
21 TraesCS2A01G255200 chr7D 92.982 57 4 0 5480 5536 88177076 88177020 3.580000e-12 84.2
22 TraesCS2A01G255200 chr7A 88.938 226 15 1 2436 2651 120825727 120825952 2.560000e-68 270.0
23 TraesCS2A01G255200 chr7A 91.270 126 8 2 2641 2765 657371983 657371860 9.610000e-38 169.0
24 TraesCS2A01G255200 chr7A 79.412 102 17 4 5261 5362 78137436 78137339 1.000000e-07 69.4
25 TraesCS2A01G255200 chr6B 89.862 217 12 4 2445 2651 525681282 525681066 2.560000e-68 270.0
26 TraesCS2A01G255200 chr7B 88.496 226 16 1 2436 2651 743110316 743110541 1.190000e-66 265.0
27 TraesCS2A01G255200 chr7B 93.750 112 7 0 2647 2758 624570152 624570263 9.610000e-38 169.0
28 TraesCS2A01G255200 chr4D 89.401 217 13 4 2445 2651 123581696 123581480 1.190000e-66 265.0
29 TraesCS2A01G255200 chr4D 88.940 217 14 4 2445 2651 123370759 123370543 5.540000e-65 259.0
30 TraesCS2A01G255200 chr1B 89.401 217 13 1 2445 2651 339007231 339007015 1.190000e-66 265.0
31 TraesCS2A01G255200 chr3A 88.053 226 17 4 2436 2651 51929992 51930217 5.540000e-65 259.0
32 TraesCS2A01G255200 chr1D 94.643 112 6 0 2650 2761 465974453 465974342 2.070000e-39 174.0
33 TraesCS2A01G255200 chr1D 80.208 96 14 3 5269 5360 237809617 237809523 3.610000e-07 67.6
34 TraesCS2A01G255200 chr5A 90.698 129 8 2 2647 2773 544309666 544309540 9.610000e-38 169.0
35 TraesCS2A01G255200 chr6A 93.878 49 3 0 5252 5300 413061373 413061325 2.160000e-09 75.0
36 TraesCS2A01G255200 chr6D 87.931 58 7 0 5244 5301 446899910 446899967 1.000000e-07 69.4
37 TraesCS2A01G255200 chr3B 82.857 70 10 2 5244 5312 727155072 727155140 1.680000e-05 62.1


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 TraesCS2A01G255200 chr2A 389438256 389443834 5578 True 10303.000000 10303 100.000000 1 5579 1 chr2A.!!$R2 5578
1 TraesCS2A01G255200 chr2D 308479767 308485338 5571 True 2658.666667 4222 92.925333 1 5579 3 chr2D.!!$R1 5578
2 TraesCS2A01G255200 chr2B 359612336 359619634 7298 False 1620.200000 3177 93.129600 1 5579 5 chr2B.!!$F2 5578

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
92 93 0.742505 CATCGGATGTGCATGGCTTT 59.257 50.0 9.85 0.0 0.00 3.51 F
1358 1421 0.987613 TGCCCTCATATCAGTGGCCA 60.988 55.0 0.00 0.0 41.46 5.36 F
2662 2783 0.033306 AGGAAGTACTCCCTCCGTCC 60.033 60.0 0.00 0.0 46.81 4.79 F
3390 3512 0.485099 ATTGCACCAAAGGTACCCCA 59.515 50.0 8.74 0.0 32.11 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1388 1451 0.184933 TGGAACTTGTTGACAGGGGG 59.815 55.0 0.00 0.00 0.00 5.40 R
2740 2861 0.030909 TATACTCCCTCCGCCCCAAA 60.031 55.0 0.00 0.00 0.00 3.28 R
3586 3710 0.317479 ATCCAATACGCCTACGCTCC 59.683 55.0 0.00 0.00 45.53 4.70 R
5176 7192 0.035820 TGGTGTCCGGACATTTAGGC 60.036 55.0 38.11 23.98 43.97 3.93 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
92 93 0.742505 CATCGGATGTGCATGGCTTT 59.257 50.000 9.85 0.00 0.00 3.51
97 98 1.824230 GGATGTGCATGGCTTTGGTTA 59.176 47.619 0.00 0.00 0.00 2.85
952 976 2.813908 GCCTTCGTCGACCGCATT 60.814 61.111 10.58 0.00 36.19 3.56
961 985 2.126228 GACCGCATTGTCGTCGGA 60.126 61.111 6.91 0.00 45.53 4.55
962 986 2.126071 ACCGCATTGTCGTCGGAG 60.126 61.111 6.91 0.00 45.53 4.63
963 987 3.554692 CCGCATTGTCGTCGGAGC 61.555 66.667 0.00 0.00 45.53 4.70
964 988 3.902063 CGCATTGTCGTCGGAGCG 61.902 66.667 0.00 0.00 39.17 5.03
965 989 4.210304 GCATTGTCGTCGGAGCGC 62.210 66.667 0.00 0.00 0.00 5.92
966 990 3.554692 CATTGTCGTCGGAGCGCC 61.555 66.667 2.29 0.00 0.00 6.53
967 991 3.760035 ATTGTCGTCGGAGCGCCT 61.760 61.111 2.29 0.00 0.00 5.52
968 992 3.296709 ATTGTCGTCGGAGCGCCTT 62.297 57.895 2.29 0.00 0.00 4.35
969 993 3.909258 TTGTCGTCGGAGCGCCTTC 62.909 63.158 2.29 0.00 0.00 3.46
981 1005 2.813908 GCCTTCGTCGACCGCATT 60.814 61.111 10.58 0.00 36.19 3.56
982 1006 3.081133 CCTTCGTCGACCGCATTG 58.919 61.111 10.58 0.00 36.19 2.82
983 1007 1.736645 CCTTCGTCGACCGCATTGT 60.737 57.895 10.58 0.00 36.19 2.71
984 1008 1.683790 CCTTCGTCGACCGCATTGTC 61.684 60.000 10.58 0.00 36.19 3.18
1115 1139 2.668550 GTCGCAGCGTCCCCTTTT 60.669 61.111 15.93 0.00 0.00 2.27
1264 1288 7.227512 AGGAGTTGTCATTTAACAGAAACAGAG 59.772 37.037 0.00 0.00 0.00 3.35
1265 1289 7.226720 GGAGTTGTCATTTAACAGAAACAGAGA 59.773 37.037 0.00 0.00 0.00 3.10
1284 1347 5.122082 CAGAGAGAAAAGAAGCTTGACCATC 59.878 44.000 2.10 0.00 0.00 3.51
1285 1348 4.978099 AGAGAAAAGAAGCTTGACCATCA 58.022 39.130 2.10 0.00 0.00 3.07
1287 1350 4.723309 AGAAAAGAAGCTTGACCATCACT 58.277 39.130 2.10 0.00 0.00 3.41
1297 1360 3.382083 TGACCATCACTCACCTAGCTA 57.618 47.619 0.00 0.00 0.00 3.32
1314 1377 1.194772 GCTAGTTTCAAGACGGTGCAC 59.805 52.381 8.80 8.80 0.00 4.57
1346 1409 2.297033 GCTTGAAATGAAAGTGCCCTCA 59.703 45.455 0.00 0.00 0.00 3.86
1355 1418 3.209410 GAAAGTGCCCTCATATCAGTGG 58.791 50.000 0.00 0.00 0.00 4.00
1358 1421 0.987613 TGCCCTCATATCAGTGGCCA 60.988 55.000 0.00 0.00 41.46 5.36
1379 1442 4.218200 CCAACCATGACAATCACAAGCTTA 59.782 41.667 0.00 0.00 0.00 3.09
1381 1444 4.655963 ACCATGACAATCACAAGCTTAGT 58.344 39.130 0.00 0.00 0.00 2.24
1386 1449 8.338259 CCATGACAATCACAAGCTTAGTTATAC 58.662 37.037 0.00 0.00 0.00 1.47
1387 1450 8.882736 CATGACAATCACAAGCTTAGTTATACA 58.117 33.333 0.00 0.00 0.00 2.29
1388 1451 8.251750 TGACAATCACAAGCTTAGTTATACAC 57.748 34.615 0.00 0.00 0.00 2.90
1452 1515 3.141398 CTGTTTAACCTCAGCAAGCTCA 58.859 45.455 0.00 0.00 0.00 4.26
1453 1516 3.550820 TGTTTAACCTCAGCAAGCTCAA 58.449 40.909 0.00 0.00 0.00 3.02
1454 1517 3.315191 TGTTTAACCTCAGCAAGCTCAAC 59.685 43.478 0.00 0.00 0.00 3.18
1455 1518 3.492102 TTAACCTCAGCAAGCTCAACT 57.508 42.857 0.00 0.00 0.00 3.16
1456 1519 1.889545 AACCTCAGCAAGCTCAACTC 58.110 50.000 0.00 0.00 0.00 3.01
1528 1611 9.278734 GTTTTAGTTGTCTAAGCTGCATTTATC 57.721 33.333 1.02 0.00 37.44 1.75
1535 1618 6.481313 TGTCTAAGCTGCATTTATCTGATGTC 59.519 38.462 1.02 0.00 0.00 3.06
1549 1632 5.739752 TCTGATGTCTTTTCACACTGTTG 57.260 39.130 0.00 0.00 0.00 3.33
1561 1650 9.825972 CTTTTCACACTGTTGTATACCTATTTG 57.174 33.333 0.00 0.00 33.30 2.32
1623 1740 9.151471 GCAAACTCTGAAGTAGTGTATTTCATA 57.849 33.333 0.00 0.00 34.53 2.15
1706 1827 3.198068 CAACTCGTTGACATATCCCCAG 58.802 50.000 3.77 0.00 42.93 4.45
1709 1830 3.711704 ACTCGTTGACATATCCCCAGATT 59.288 43.478 0.00 0.00 33.67 2.40
1721 1842 2.093658 TCCCCAGATTGCGAAAGTAGTC 60.094 50.000 0.00 0.00 32.81 2.59
2276 2397 2.365293 AGAACATTGGTGGAGCAAAACC 59.635 45.455 0.00 0.00 36.96 3.27
2315 2436 7.277396 CCTTTTTGGATAGGCATCAATGATTT 58.723 34.615 0.00 0.00 38.35 2.17
2326 2447 4.478699 CATCAATGATTTCGCAGTGTTGT 58.521 39.130 0.00 0.00 35.53 3.32
2367 2488 5.106237 ACCGATCTAACACTGAACTACTGAC 60.106 44.000 0.00 0.00 0.00 3.51
2408 2529 7.872113 ATTTCTTGTAATTCTGGGAGATGTC 57.128 36.000 0.00 0.00 0.00 3.06
2491 2612 2.119801 AGTAGGTTGATGGCTTGCAG 57.880 50.000 0.00 0.00 0.00 4.41
2527 2648 0.395586 TTGGCCTTGCTTGTGTGTCT 60.396 50.000 3.32 0.00 0.00 3.41
2589 2710 7.040686 ACCAATAGTCACCAAATTTATATCGGC 60.041 37.037 0.00 0.00 0.00 5.54
2651 2772 4.957296 TCTTCAAGTGGTCAAGGAAGTAC 58.043 43.478 0.00 0.00 37.02 2.73
2652 2773 4.654262 TCTTCAAGTGGTCAAGGAAGTACT 59.346 41.667 0.00 0.00 37.02 2.73
2653 2774 4.602340 TCAAGTGGTCAAGGAAGTACTC 57.398 45.455 0.00 0.00 0.00 2.59
2654 2775 3.323979 TCAAGTGGTCAAGGAAGTACTCC 59.676 47.826 0.00 0.00 45.81 3.85
2655 2776 2.258109 AGTGGTCAAGGAAGTACTCCC 58.742 52.381 0.00 0.00 46.81 4.30
2656 2777 2.158143 AGTGGTCAAGGAAGTACTCCCT 60.158 50.000 0.00 0.00 46.81 4.20
2657 2778 2.234168 GTGGTCAAGGAAGTACTCCCTC 59.766 54.545 0.00 0.00 46.81 4.30
2658 2779 1.832366 GGTCAAGGAAGTACTCCCTCC 59.168 57.143 0.00 2.10 46.81 4.30
2659 2780 1.477295 GTCAAGGAAGTACTCCCTCCG 59.523 57.143 0.00 0.00 46.81 4.63
2660 2781 1.076677 TCAAGGAAGTACTCCCTCCGT 59.923 52.381 0.00 0.00 46.81 4.69
2661 2782 1.477295 CAAGGAAGTACTCCCTCCGTC 59.523 57.143 0.00 0.00 46.81 4.79
2662 2783 0.033306 AGGAAGTACTCCCTCCGTCC 60.033 60.000 0.00 0.00 46.81 4.79
2663 2784 0.033306 GGAAGTACTCCCTCCGTCCT 60.033 60.000 0.00 0.00 38.44 3.85
2664 2785 1.213926 GGAAGTACTCCCTCCGTCCTA 59.786 57.143 0.00 0.00 38.44 2.94
2665 2786 2.357569 GGAAGTACTCCCTCCGTCCTAA 60.358 54.545 0.00 0.00 38.44 2.69
2666 2787 3.359950 GAAGTACTCCCTCCGTCCTAAA 58.640 50.000 0.00 0.00 0.00 1.85
2667 2788 3.463048 AGTACTCCCTCCGTCCTAAAA 57.537 47.619 0.00 0.00 0.00 1.52
2668 2789 3.991683 AGTACTCCCTCCGTCCTAAAAT 58.008 45.455 0.00 0.00 0.00 1.82
2669 2790 4.359996 AGTACTCCCTCCGTCCTAAAATT 58.640 43.478 0.00 0.00 0.00 1.82
2670 2791 3.908643 ACTCCCTCCGTCCTAAAATTC 57.091 47.619 0.00 0.00 0.00 2.17
2671 2792 3.451890 ACTCCCTCCGTCCTAAAATTCT 58.548 45.455 0.00 0.00 0.00 2.40
2672 2793 3.844804 ACTCCCTCCGTCCTAAAATTCTT 59.155 43.478 0.00 0.00 0.00 2.52
2673 2794 4.192317 CTCCCTCCGTCCTAAAATTCTTG 58.808 47.826 0.00 0.00 0.00 3.02
2674 2795 3.585732 TCCCTCCGTCCTAAAATTCTTGT 59.414 43.478 0.00 0.00 0.00 3.16
2675 2796 3.939592 CCCTCCGTCCTAAAATTCTTGTC 59.060 47.826 0.00 0.00 0.00 3.18
2676 2797 4.323562 CCCTCCGTCCTAAAATTCTTGTCT 60.324 45.833 0.00 0.00 0.00 3.41
2677 2798 5.246307 CCTCCGTCCTAAAATTCTTGTCTT 58.754 41.667 0.00 0.00 0.00 3.01
2678 2799 6.403878 CCTCCGTCCTAAAATTCTTGTCTTA 58.596 40.000 0.00 0.00 0.00 2.10
2679 2800 6.535508 CCTCCGTCCTAAAATTCTTGTCTTAG 59.464 42.308 0.00 0.00 0.00 2.18
2680 2801 7.235935 TCCGTCCTAAAATTCTTGTCTTAGA 57.764 36.000 0.00 0.00 0.00 2.10
2681 2802 7.848128 TCCGTCCTAAAATTCTTGTCTTAGAT 58.152 34.615 0.00 0.00 0.00 1.98
2682 2803 8.319146 TCCGTCCTAAAATTCTTGTCTTAGATT 58.681 33.333 0.00 0.00 0.00 2.40
2683 2804 8.947115 CCGTCCTAAAATTCTTGTCTTAGATTT 58.053 33.333 0.00 0.00 0.00 2.17
2684 2805 9.760660 CGTCCTAAAATTCTTGTCTTAGATTTG 57.239 33.333 0.00 0.00 0.00 2.32
2695 2816 9.582431 TCTTGTCTTAGATTTGTCTAAATACGG 57.418 33.333 0.26 0.99 36.66 4.02
2696 2817 9.582431 CTTGTCTTAGATTTGTCTAAATACGGA 57.418 33.333 0.26 0.00 36.66 4.69
2698 2819 9.529325 TGTCTTAGATTTGTCTAAATACGGATG 57.471 33.333 0.26 0.00 36.66 3.51
2699 2820 9.530633 GTCTTAGATTTGTCTAAATACGGATGT 57.469 33.333 0.26 0.00 36.66 3.06
2704 2825 9.698309 AGATTTGTCTAAATACGGATGTATCAG 57.302 33.333 0.00 0.00 40.42 2.90
2705 2826 9.692749 GATTTGTCTAAATACGGATGTATCAGA 57.307 33.333 0.00 0.00 40.42 3.27
2723 2844 9.292195 TGTATCAGATACATCCGTATTTAGACA 57.708 33.333 17.93 0.00 40.60 3.41
2727 2848 9.692749 TCAGATACATCCGTATTTAGACAAATC 57.307 33.333 0.00 0.00 38.48 2.17
2728 2849 9.698309 CAGATACATCCGTATTTAGACAAATCT 57.302 33.333 0.00 0.00 38.48 2.40
2733 2854 9.530633 ACATCCGTATTTAGACAAATCTAAGAC 57.469 33.333 0.00 0.83 45.93 3.01
2734 2855 9.529325 CATCCGTATTTAGACAAATCTAAGACA 57.471 33.333 9.81 0.00 45.93 3.41
2736 2857 9.582431 TCCGTATTTAGACAAATCTAAGACAAG 57.418 33.333 9.81 3.88 45.93 3.16
2737 2858 9.582431 CCGTATTTAGACAAATCTAAGACAAGA 57.418 33.333 9.81 0.00 45.93 3.02
2745 2866 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
2746 2867 7.670364 ACAAATCTAAGACAAGAATTTTGGGG 58.330 34.615 0.00 0.00 33.04 4.96
2747 2868 5.921962 ATCTAAGACAAGAATTTTGGGGC 57.078 39.130 5.68 0.00 0.00 5.80
2748 2869 3.756434 TCTAAGACAAGAATTTTGGGGCG 59.244 43.478 5.68 0.00 0.00 6.13
2749 2870 1.256812 AGACAAGAATTTTGGGGCGG 58.743 50.000 5.68 0.00 0.00 6.13
2750 2871 1.203001 AGACAAGAATTTTGGGGCGGA 60.203 47.619 5.68 0.00 0.00 5.54
2751 2872 1.202348 GACAAGAATTTTGGGGCGGAG 59.798 52.381 5.68 0.00 0.00 4.63
2752 2873 0.532115 CAAGAATTTTGGGGCGGAGG 59.468 55.000 0.00 0.00 0.00 4.30
2753 2874 0.614697 AAGAATTTTGGGGCGGAGGG 60.615 55.000 0.00 0.00 0.00 4.30
2754 2875 1.000145 GAATTTTGGGGCGGAGGGA 60.000 57.895 0.00 0.00 0.00 4.20
2755 2876 1.000359 AATTTTGGGGCGGAGGGAG 60.000 57.895 0.00 0.00 0.00 4.30
2756 2877 1.800229 AATTTTGGGGCGGAGGGAGT 61.800 55.000 0.00 0.00 0.00 3.85
2757 2878 0.917333 ATTTTGGGGCGGAGGGAGTA 60.917 55.000 0.00 0.00 0.00 2.59
2811 2932 7.099120 GCTTCAGGAAACATGGTATTGAAAAT 58.901 34.615 0.00 0.00 0.00 1.82
2840 2961 0.522180 AGAACTCAGTCGTAGGTGCG 59.478 55.000 0.00 0.00 0.00 5.34
2903 3025 3.319122 GGCACTTTGATGACAAAAGAGGT 59.681 43.478 6.62 0.00 43.92 3.85
2916 3038 4.202253 ACAAAAGAGGTGGGAAAAGCAATC 60.202 41.667 0.00 0.00 0.00 2.67
2941 3063 1.133790 GAAGAATTTGGCGCTGCTCAT 59.866 47.619 7.64 0.00 0.00 2.90
2981 3103 8.409358 AGTAAAATTTGTAAATCTGTGGCTCT 57.591 30.769 0.00 0.00 0.00 4.09
3132 3254 9.462174 TGTTTGTGCTTCATAATTAGAACAAAG 57.538 29.630 11.09 2.93 45.76 2.77
3135 3257 8.621532 TGTGCTTCATAATTAGAACAAAGTCT 57.378 30.769 0.00 0.00 26.89 3.24
3152 3274 7.781056 ACAAAGTCTGTGTTGAAAATAATGGT 58.219 30.769 0.00 0.00 36.69 3.55
3390 3512 0.485099 ATTGCACCAAAGGTACCCCA 59.515 50.000 8.74 0.00 32.11 4.96
3402 3524 8.571345 ACCAAAGGTACCCCATAAATAATTAGT 58.429 33.333 8.74 0.00 32.11 2.24
3524 3647 6.712095 TGATCTGTTGAACATGCTCTTTAACT 59.288 34.615 0.00 0.00 0.00 2.24
3593 3717 6.229936 ACCTTTTGTATCTAATGGAGCGTA 57.770 37.500 0.00 0.00 0.00 4.42
3594 3718 6.281405 ACCTTTTGTATCTAATGGAGCGTAG 58.719 40.000 0.00 0.00 0.00 3.51
3595 3719 5.696724 CCTTTTGTATCTAATGGAGCGTAGG 59.303 44.000 0.00 0.00 0.00 3.18
3597 3721 2.228103 TGTATCTAATGGAGCGTAGGCG 59.772 50.000 1.05 0.00 46.35 5.52
3598 3722 1.329256 ATCTAATGGAGCGTAGGCGT 58.671 50.000 1.05 0.00 46.35 5.68
3633 3757 4.940046 AGTTCTGATGTATGGCTTGTTGAG 59.060 41.667 0.00 0.00 0.00 3.02
3655 3779 6.043854 AGAGTTGACCCTTCTCATTTCTAC 57.956 41.667 0.00 0.00 0.00 2.59
3826 3951 5.537188 TCACCATGTTTTACAATGCTTTCC 58.463 37.500 0.00 0.00 0.00 3.13
3861 3986 6.594159 GTGTAGGTACATCATAAGTGCAGTTT 59.406 38.462 12.95 0.00 38.63 2.66
3879 4004 8.482429 GTGCAGTTTGTTTCAAATCTCATTAAG 58.518 33.333 0.00 0.00 0.00 1.85
3880 4005 7.169645 TGCAGTTTGTTTCAAATCTCATTAAGC 59.830 33.333 0.00 0.00 0.00 3.09
3881 4006 7.359514 GCAGTTTGTTTCAAATCTCATTAAGCC 60.360 37.037 0.00 0.00 0.00 4.35
3882 4007 6.863126 AGTTTGTTTCAAATCTCATTAAGCCG 59.137 34.615 0.00 0.00 0.00 5.52
3985 4110 2.170166 GACATTGGGAAGGTCATTGCA 58.830 47.619 0.00 0.00 41.54 4.08
4017 4142 2.827190 CATGGGCTGCAGCATCGT 60.827 61.111 37.63 26.43 44.36 3.73
4052 4177 0.242825 CAGCGTCAAGTACTTCCGGA 59.757 55.000 20.02 0.00 0.00 5.14
4136 4261 5.518847 CGATACAATGTGGATGTTCTACGTT 59.481 40.000 0.00 0.00 37.53 3.99
4202 4327 0.462789 TCTTATCGAGTTTCCCCGGC 59.537 55.000 0.00 0.00 0.00 6.13
4358 4483 3.129287 GTGGCCAACAGGATAAACATGAG 59.871 47.826 7.24 0.00 34.19 2.90
4428 4553 3.213402 GAGGCCGTCGAGAGGAGG 61.213 72.222 10.77 0.00 0.00 4.30
4568 4709 5.473039 CAAGAAACAAGAATTCCATGTCCC 58.527 41.667 13.20 9.09 0.00 4.46
4580 4722 2.567169 TCCATGTCCCTGACTTGTAGTG 59.433 50.000 8.66 0.00 36.42 2.74
4672 4816 2.979240 GACTCCAAAGTCCTAAGCCAG 58.021 52.381 0.00 0.00 45.26 4.85
4803 4951 0.109597 CTGGTTCGGCATGAAAGCAC 60.110 55.000 0.00 0.00 38.60 4.40
4810 4958 1.331756 CGGCATGAAAGCACCTCATAC 59.668 52.381 0.00 0.00 32.20 2.39
4828 6829 8.865090 ACCTCATACAAAATTTCATTTACACCA 58.135 29.630 0.00 0.00 0.00 4.17
4915 6930 4.825085 GGATACACAGGAAAAACAAGGACA 59.175 41.667 0.00 0.00 0.00 4.02
4927 6942 5.596836 AAACAAGGACAAAATTCAGCTGA 57.403 34.783 13.74 13.74 0.00 4.26
4933 6948 4.279420 AGGACAAAATTCAGCTGAAACTCC 59.721 41.667 31.55 25.60 37.61 3.85
4952 6967 2.023404 TCCCAGCTAGAGAATACCCACA 60.023 50.000 0.00 0.00 0.00 4.17
5067 7082 6.057533 TCATCCAATGTGTTCATATGGACTC 58.942 40.000 15.27 11.99 40.41 3.36
5159 7175 4.034510 GCTGAATTTAGGACATCTCCAACG 59.965 45.833 0.00 0.00 39.39 4.10
5220 7236 1.268352 CGCGTCCAAATTCCCAGAAAA 59.732 47.619 0.00 0.00 0.00 2.29
5222 7238 2.296190 GCGTCCAAATTCCCAGAAAACT 59.704 45.455 0.00 0.00 0.00 2.66
5224 7240 3.305335 CGTCCAAATTCCCAGAAAACTGG 60.305 47.826 9.05 9.05 43.86 4.00
5225 7241 2.632512 TCCAAATTCCCAGAAAACTGGC 59.367 45.455 10.37 0.00 42.94 4.85
5226 7242 2.368221 CCAAATTCCCAGAAAACTGGCA 59.632 45.455 10.37 0.00 42.94 4.92
5228 7244 1.632589 ATTCCCAGAAAACTGGCACC 58.367 50.000 10.37 0.00 42.94 5.01
5230 7246 0.260230 TCCCAGAAAACTGGCACCAA 59.740 50.000 10.37 0.00 42.94 3.67
5231 7247 1.118838 CCCAGAAAACTGGCACCAAA 58.881 50.000 10.37 0.00 42.94 3.28
5232 7248 1.202521 CCCAGAAAACTGGCACCAAAC 60.203 52.381 10.37 0.00 42.94 2.93
5233 7249 1.202521 CCAGAAAACTGGCACCAAACC 60.203 52.381 3.31 0.00 37.72 3.27
5234 7250 1.119684 AGAAAACTGGCACCAAACCC 58.880 50.000 0.00 0.00 0.00 4.11
5247 7267 2.296084 AACCCAGGGGAGGTTCCA 59.704 61.111 11.37 0.00 44.42 3.53
5304 7324 2.526110 GGCCCACCCAAAACCTCT 59.474 61.111 0.00 0.00 0.00 3.69
5351 7372 2.187958 CTTCCCCACACTCTGTATCCA 58.812 52.381 0.00 0.00 0.00 3.41
5361 7382 0.264955 TCTGTATCCACTCCCTCCCC 59.735 60.000 0.00 0.00 0.00 4.81
5362 7383 0.031111 CTGTATCCACTCCCTCCCCA 60.031 60.000 0.00 0.00 0.00 4.96
5382 7403 4.690719 CGGCGGCTACCAACACCA 62.691 66.667 7.61 0.00 0.00 4.17
5386 7407 2.745037 GGCTACCAACACCACCGA 59.255 61.111 0.00 0.00 0.00 4.69
5439 7480 3.948719 GCACCGTTCCACCCCTCA 61.949 66.667 0.00 0.00 0.00 3.86
5445 7486 1.221021 GTTCCACCCCTCATCCGTC 59.779 63.158 0.00 0.00 0.00 4.79
5459 7500 4.814294 CGTCCGCTGCCCAGGTAC 62.814 72.222 0.00 0.00 0.00 3.34
5470 7511 2.440796 CAGGTACCGTCCGCCCTA 60.441 66.667 6.18 0.00 0.00 3.53
5471 7512 1.831286 CAGGTACCGTCCGCCCTAT 60.831 63.158 6.18 0.00 0.00 2.57
5472 7513 0.538057 CAGGTACCGTCCGCCCTATA 60.538 60.000 6.18 0.00 0.00 1.31
5473 7514 0.251077 AGGTACCGTCCGCCCTATAG 60.251 60.000 6.18 0.00 0.00 1.31
5497 7538 3.245346 TCCATGGCGGACACCACA 61.245 61.111 6.96 0.00 44.17 4.17
5500 7541 4.344865 ATGGCGGACACCACACCC 62.345 66.667 0.00 0.00 44.17 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 93 3.709653 ACACTTCTGACCTTGAGTAACCA 59.290 43.478 0.00 0.00 0.00 3.67
97 98 1.486310 TGCACACTTCTGACCTTGAGT 59.514 47.619 0.00 0.00 0.00 3.41
290 293 1.697432 ACCTTCGACCCAGAACAATCA 59.303 47.619 0.00 0.00 0.00 2.57
436 447 6.616237 TTTTTAACTGTTTGGGGGTTAACA 57.384 33.333 8.10 0.00 35.87 2.41
471 495 1.609555 AGCGAGGTTTAGCTCTATCCG 59.390 52.381 7.29 0.00 39.98 4.18
617 641 0.452184 TTCTGGAGACGCGATGAGAC 59.548 55.000 15.93 0.00 0.00 3.36
952 976 4.415332 GAAGGCGCTCCGACGACA 62.415 66.667 7.64 0.00 46.03 4.35
973 997 2.126228 TCCGACGACAATGCGGTC 60.126 61.111 0.00 0.00 45.02 4.79
974 998 2.126071 CTCCGACGACAATGCGGT 60.126 61.111 0.00 0.00 45.02 5.68
975 999 3.554692 GCTCCGACGACAATGCGG 61.555 66.667 0.00 0.00 46.08 5.69
976 1000 3.554692 GGCTCCGACGACAATGCG 61.555 66.667 0.00 0.00 37.29 4.73
977 1001 3.554692 CGGCTCCGACGACAATGC 61.555 66.667 1.35 0.00 42.83 3.56
978 1002 3.554692 GCGGCTCCGACGACAATG 61.555 66.667 13.11 0.00 42.83 2.82
979 1003 4.814294 GGCGGCTCCGACGACAAT 62.814 66.667 13.11 0.00 44.48 2.71
1115 1139 9.927668 AAACAGAAGAATTGAACAAGAAAAAGA 57.072 25.926 0.00 0.00 0.00 2.52
1191 1215 8.379161 CACACAAAAACAAAATTTCATTCGAGA 58.621 29.630 0.00 0.00 0.00 4.04
1259 1283 4.141620 TGGTCAAGCTTCTTTTCTCTCTGT 60.142 41.667 0.00 0.00 0.00 3.41
1264 1288 4.759183 AGTGATGGTCAAGCTTCTTTTCTC 59.241 41.667 0.00 0.00 0.00 2.87
1265 1289 4.723309 AGTGATGGTCAAGCTTCTTTTCT 58.277 39.130 0.00 0.00 0.00 2.52
1284 1347 5.164954 GTCTTGAAACTAGCTAGGTGAGTG 58.835 45.833 24.35 10.15 0.00 3.51
1285 1348 4.082679 CGTCTTGAAACTAGCTAGGTGAGT 60.083 45.833 24.35 3.17 0.00 3.41
1287 1350 3.192844 CCGTCTTGAAACTAGCTAGGTGA 59.807 47.826 24.35 8.98 0.00 4.02
1297 1360 1.967319 ATGTGCACCGTCTTGAAACT 58.033 45.000 15.69 0.00 0.00 2.66
1314 1377 8.277713 CACTTTCATTTCAAGCCTAACAAAATG 58.722 33.333 0.00 0.00 38.21 2.32
1355 1418 2.927871 GCTTGTGATTGTCATGGTTGGC 60.928 50.000 0.00 0.00 0.00 4.52
1358 1421 5.072741 ACTAAGCTTGTGATTGTCATGGTT 58.927 37.500 9.86 0.00 35.78 3.67
1379 1442 3.253220 TGTTGACAGGGGGTGTATAACT 58.747 45.455 0.00 0.00 40.56 2.24
1381 1444 3.653836 ACTTGTTGACAGGGGGTGTATAA 59.346 43.478 0.00 0.00 40.56 0.98
1386 1449 1.318576 GAACTTGTTGACAGGGGGTG 58.681 55.000 0.00 0.00 0.00 4.61
1387 1450 0.185175 GGAACTTGTTGACAGGGGGT 59.815 55.000 0.00 0.00 0.00 4.95
1388 1451 0.184933 TGGAACTTGTTGACAGGGGG 59.815 55.000 0.00 0.00 0.00 5.40
1517 1600 6.471519 GTGAAAAGACATCAGATAAATGCAGC 59.528 38.462 0.00 0.00 0.00 5.25
1528 1611 5.490139 ACAACAGTGTGAAAAGACATCAG 57.510 39.130 0.00 0.00 36.31 2.90
1535 1618 9.825972 CAAATAGGTATACAACAGTGTGAAAAG 57.174 33.333 5.01 0.00 38.82 2.27
1561 1650 8.752766 ATCATGTCAGTTCAAATGAAATGTTC 57.247 30.769 15.91 14.82 46.51 3.18
1623 1740 3.375299 AGCGAGGAAACTACGTACGTATT 59.625 43.478 26.98 19.49 44.43 1.89
1665 1786 1.604278 GTGCTTGAACCACCTGAAGTC 59.396 52.381 0.00 0.00 0.00 3.01
1706 1827 2.605366 GGAGCAGACTACTTTCGCAATC 59.395 50.000 0.00 0.00 0.00 2.67
1709 1830 1.067565 CAGGAGCAGACTACTTTCGCA 60.068 52.381 0.00 0.00 33.41 5.10
1721 1842 1.554160 AGATCACCAGAACAGGAGCAG 59.446 52.381 0.00 0.00 0.00 4.24
2276 2397 4.159506 TCCAAAAAGGGAACTGTGAGTTTG 59.840 41.667 0.00 0.00 42.68 2.93
2315 2436 2.161078 TATGGCGGACAACACTGCGA 62.161 55.000 0.00 0.00 42.39 5.10
2326 2447 5.362717 AGATCGGTTATAATCATATGGCGGA 59.637 40.000 2.13 0.00 0.00 5.54
2434 2555 7.013655 AGACAACTTAGCATGTCAAGACAAAAT 59.986 33.333 17.15 0.00 46.55 1.82
2436 2557 5.822519 AGACAACTTAGCATGTCAAGACAAA 59.177 36.000 17.15 0.00 46.55 2.83
2446 2567 4.696479 ATAGGGGAGACAACTTAGCATG 57.304 45.455 0.00 0.00 0.00 4.06
2491 2612 0.249826 CAAAACATGTGTGTGGGGCC 60.250 55.000 0.00 0.00 38.92 5.80
2551 2672 5.433526 GTGACTATTGGTATGTTTAGGCCA 58.566 41.667 5.01 0.00 0.00 5.36
2552 2673 4.820173 GGTGACTATTGGTATGTTTAGGCC 59.180 45.833 0.00 0.00 0.00 5.19
2628 2749 4.713792 ACTTCCTTGACCACTTGAAGAT 57.286 40.909 0.00 0.00 36.72 2.40
2651 2772 4.192317 CAAGAATTTTAGGACGGAGGGAG 58.808 47.826 0.00 0.00 0.00 4.30
2652 2773 3.585732 ACAAGAATTTTAGGACGGAGGGA 59.414 43.478 0.00 0.00 0.00 4.20
2653 2774 3.939592 GACAAGAATTTTAGGACGGAGGG 59.060 47.826 0.00 0.00 0.00 4.30
2654 2775 4.833390 AGACAAGAATTTTAGGACGGAGG 58.167 43.478 0.00 0.00 0.00 4.30
2655 2776 7.321153 TCTAAGACAAGAATTTTAGGACGGAG 58.679 38.462 0.00 0.00 0.00 4.63
2656 2777 7.235935 TCTAAGACAAGAATTTTAGGACGGA 57.764 36.000 0.00 0.00 0.00 4.69
2657 2778 8.494016 AATCTAAGACAAGAATTTTAGGACGG 57.506 34.615 0.00 0.00 0.00 4.79
2658 2779 9.760660 CAAATCTAAGACAAGAATTTTAGGACG 57.239 33.333 0.00 0.00 0.00 4.79
2669 2790 9.582431 CCGTATTTAGACAAATCTAAGACAAGA 57.418 33.333 9.81 0.00 45.93 3.02
2670 2791 9.582431 TCCGTATTTAGACAAATCTAAGACAAG 57.418 33.333 9.81 3.88 45.93 3.16
2672 2793 9.529325 CATCCGTATTTAGACAAATCTAAGACA 57.471 33.333 9.81 0.00 45.93 3.41
2673 2794 9.530633 ACATCCGTATTTAGACAAATCTAAGAC 57.469 33.333 0.00 0.83 45.93 3.01
2678 2799 9.698309 CTGATACATCCGTATTTAGACAAATCT 57.302 33.333 0.00 0.00 38.48 2.40
2679 2800 9.692749 TCTGATACATCCGTATTTAGACAAATC 57.307 33.333 0.00 0.00 38.48 2.17
2683 2804 9.292195 TGTATCTGATACATCCGTATTTAGACA 57.708 33.333 23.01 1.20 40.60 3.41
2701 2822 9.692749 GATTTGTCTAAATACGGATGTATCTGA 57.307 33.333 7.66 0.00 40.42 3.27
2702 2823 9.698309 AGATTTGTCTAAATACGGATGTATCTG 57.302 33.333 0.00 0.00 40.42 2.90
2707 2828 9.530633 GTCTTAGATTTGTCTAAATACGGATGT 57.469 33.333 0.26 0.00 36.66 3.06
2708 2829 9.529325 TGTCTTAGATTTGTCTAAATACGGATG 57.471 33.333 0.26 0.00 36.66 3.51
2710 2831 9.582431 CTTGTCTTAGATTTGTCTAAATACGGA 57.418 33.333 0.26 0.00 36.66 4.69
2711 2832 9.582431 TCTTGTCTTAGATTTGTCTAAATACGG 57.418 33.333 0.26 0.99 36.66 4.02
2719 2840 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
2720 2841 7.814587 CCCCAAAATTCTTGTCTTAGATTTGTC 59.185 37.037 0.00 0.00 28.79 3.18
2721 2842 7.670364 CCCCAAAATTCTTGTCTTAGATTTGT 58.330 34.615 0.00 0.00 28.79 2.83
2722 2843 6.591448 GCCCCAAAATTCTTGTCTTAGATTTG 59.409 38.462 0.00 0.00 29.84 2.32
2723 2844 6.572314 CGCCCCAAAATTCTTGTCTTAGATTT 60.572 38.462 0.00 0.00 0.00 2.17
2724 2845 5.105756 CGCCCCAAAATTCTTGTCTTAGATT 60.106 40.000 0.00 0.00 0.00 2.40
2725 2846 4.399303 CGCCCCAAAATTCTTGTCTTAGAT 59.601 41.667 0.00 0.00 0.00 1.98
2726 2847 3.756434 CGCCCCAAAATTCTTGTCTTAGA 59.244 43.478 0.00 0.00 0.00 2.10
2727 2848 3.119495 CCGCCCCAAAATTCTTGTCTTAG 60.119 47.826 0.00 0.00 0.00 2.18
2728 2849 2.823154 CCGCCCCAAAATTCTTGTCTTA 59.177 45.455 0.00 0.00 0.00 2.10
2729 2850 1.618343 CCGCCCCAAAATTCTTGTCTT 59.382 47.619 0.00 0.00 0.00 3.01
2730 2851 1.203001 TCCGCCCCAAAATTCTTGTCT 60.203 47.619 0.00 0.00 0.00 3.41
2731 2852 1.202348 CTCCGCCCCAAAATTCTTGTC 59.798 52.381 0.00 0.00 0.00 3.18
2732 2853 1.256812 CTCCGCCCCAAAATTCTTGT 58.743 50.000 0.00 0.00 0.00 3.16
2733 2854 0.532115 CCTCCGCCCCAAAATTCTTG 59.468 55.000 0.00 0.00 0.00 3.02
2734 2855 0.614697 CCCTCCGCCCCAAAATTCTT 60.615 55.000 0.00 0.00 0.00 2.52
2735 2856 1.000359 CCCTCCGCCCCAAAATTCT 60.000 57.895 0.00 0.00 0.00 2.40
2736 2857 1.000145 TCCCTCCGCCCCAAAATTC 60.000 57.895 0.00 0.00 0.00 2.17
2737 2858 1.000359 CTCCCTCCGCCCCAAAATT 60.000 57.895 0.00 0.00 0.00 1.82
2738 2859 0.917333 TACTCCCTCCGCCCCAAAAT 60.917 55.000 0.00 0.00 0.00 1.82
2739 2860 0.917333 ATACTCCCTCCGCCCCAAAA 60.917 55.000 0.00 0.00 0.00 2.44
2740 2861 0.030909 TATACTCCCTCCGCCCCAAA 60.031 55.000 0.00 0.00 0.00 3.28
2741 2862 0.192566 ATATACTCCCTCCGCCCCAA 59.807 55.000 0.00 0.00 0.00 4.12
2742 2863 0.192566 AATATACTCCCTCCGCCCCA 59.807 55.000 0.00 0.00 0.00 4.96
2743 2864 1.359168 AAATATACTCCCTCCGCCCC 58.641 55.000 0.00 0.00 0.00 5.80
2744 2865 4.838904 ATAAAATATACTCCCTCCGCCC 57.161 45.455 0.00 0.00 0.00 6.13
2745 2866 5.105064 TGCTATAAAATATACTCCCTCCGCC 60.105 44.000 0.00 0.00 0.00 6.13
2746 2867 5.974108 TGCTATAAAATATACTCCCTCCGC 58.026 41.667 0.00 0.00 0.00 5.54
2747 2868 7.435488 CGATTGCTATAAAATATACTCCCTCCG 59.565 40.741 0.00 0.00 0.00 4.63
2748 2869 7.224949 GCGATTGCTATAAAATATACTCCCTCC 59.775 40.741 0.00 0.00 38.39 4.30
2749 2870 7.043325 CGCGATTGCTATAAAATATACTCCCTC 60.043 40.741 0.00 0.00 39.65 4.30
2750 2871 6.757010 CGCGATTGCTATAAAATATACTCCCT 59.243 38.462 0.00 0.00 39.65 4.20
2751 2872 6.509677 GCGCGATTGCTATAAAATATACTCCC 60.510 42.308 12.10 0.00 39.65 4.30
2752 2873 6.411652 GCGCGATTGCTATAAAATATACTCC 58.588 40.000 12.10 0.00 39.65 3.85
2753 2874 6.035650 TGGCGCGATTGCTATAAAATATACTC 59.964 38.462 12.10 0.00 39.65 2.59
2754 2875 5.872617 TGGCGCGATTGCTATAAAATATACT 59.127 36.000 12.10 0.00 39.65 2.12
2755 2876 6.102006 TGGCGCGATTGCTATAAAATATAC 57.898 37.500 12.10 0.00 39.65 1.47
2756 2877 6.729391 TTGGCGCGATTGCTATAAAATATA 57.271 33.333 12.10 0.00 39.65 0.86
2757 2878 5.621197 TTGGCGCGATTGCTATAAAATAT 57.379 34.783 12.10 0.00 39.65 1.28
2811 2932 5.769484 ACGACTGAGTTCTGTTTCTAAGA 57.231 39.130 0.00 0.00 0.00 2.10
2823 2944 0.240411 GACGCACCTACGACTGAGTT 59.760 55.000 0.00 0.00 36.70 3.01
2840 2961 1.117150 TACCCGAAGCCCATGTAGAC 58.883 55.000 0.00 0.00 0.00 2.59
2903 3025 5.191727 TCTTCTATGGATTGCTTTTCCCA 57.808 39.130 0.00 0.00 31.87 4.37
2916 3038 2.542411 GCAGCGCCAAATTCTTCTATGG 60.542 50.000 2.29 0.00 36.00 2.74
3007 3129 9.071276 ACTTGTATCCATTTTTATGCTATCAGG 57.929 33.333 0.00 0.00 0.00 3.86
3104 3226 9.979578 TTGTTCTAATTATGAAGCACAAACAAT 57.020 25.926 0.00 0.00 29.94 2.71
3113 3235 8.507249 ACACAGACTTTGTTCTAATTATGAAGC 58.493 33.333 0.00 0.00 38.16 3.86
3132 3254 7.379529 CAGAACACCATTATTTTCAACACAGAC 59.620 37.037 0.00 0.00 0.00 3.51
3135 3257 6.511416 CCAGAACACCATTATTTTCAACACA 58.489 36.000 0.00 0.00 0.00 3.72
3152 3274 0.836606 TGAACCTGTGAGCCAGAACA 59.163 50.000 0.00 0.00 44.49 3.18
3476 3598 7.870826 TCATAATATATTTTGTGAACAGGCCG 58.129 34.615 13.48 0.00 0.00 6.13
3477 3599 9.846248 GATCATAATATATTTTGTGAACAGGCC 57.154 33.333 13.48 0.00 31.69 5.19
3508 3630 7.437862 CCTATCAGAGAGTTAAAGAGCATGTTC 59.562 40.741 0.50 0.50 0.00 3.18
3514 3636 6.709018 ACTCCTATCAGAGAGTTAAAGAGC 57.291 41.667 0.00 0.00 40.43 4.09
3515 3637 9.403583 AGTTACTCCTATCAGAGAGTTAAAGAG 57.596 37.037 0.00 0.00 40.43 2.85
3524 3647 4.528076 AGGCAGTTACTCCTATCAGAGA 57.472 45.455 2.35 0.00 37.33 3.10
3583 3707 1.540363 CCAATACGCCTACGCTCCATT 60.540 52.381 0.00 0.00 45.53 3.16
3585 3709 1.038681 TCCAATACGCCTACGCTCCA 61.039 55.000 0.00 0.00 45.53 3.86
3586 3710 0.317479 ATCCAATACGCCTACGCTCC 59.683 55.000 0.00 0.00 45.53 4.70
3587 3711 2.150397 AATCCAATACGCCTACGCTC 57.850 50.000 0.00 0.00 45.53 5.03
3589 3713 2.480845 AGAAATCCAATACGCCTACGC 58.519 47.619 0.00 0.00 45.53 4.42
3593 3717 5.128827 TCAGAACTAGAAATCCAATACGCCT 59.871 40.000 0.00 0.00 0.00 5.52
3594 3718 5.357257 TCAGAACTAGAAATCCAATACGCC 58.643 41.667 0.00 0.00 0.00 5.68
3595 3719 6.480320 ACATCAGAACTAGAAATCCAATACGC 59.520 38.462 0.00 0.00 0.00 4.42
3633 3757 5.179533 GGTAGAAATGAGAAGGGTCAACTC 58.820 45.833 0.00 0.00 0.00 3.01
3655 3779 2.612212 CGTACCTGGAAAATTGATCGGG 59.388 50.000 0.00 0.00 0.00 5.14
3826 3951 6.872628 TGATGTACCTACACTTATCCTACG 57.127 41.667 0.00 0.00 39.30 3.51
3861 3986 4.380444 GCCGGCTTAATGAGATTTGAAACA 60.380 41.667 22.15 0.00 0.00 2.83
3879 4004 4.043200 GAGCACAACAAGGCCGGC 62.043 66.667 21.18 21.18 0.00 6.13
3880 4005 0.392998 ATAGAGCACAACAAGGCCGG 60.393 55.000 0.00 0.00 0.00 6.13
3881 4006 1.398390 GAATAGAGCACAACAAGGCCG 59.602 52.381 0.00 0.00 0.00 6.13
3882 4007 1.398390 CGAATAGAGCACAACAAGGCC 59.602 52.381 0.00 0.00 0.00 5.19
3985 4110 1.452651 CATGAGCTGCGGGTCCAAT 60.453 57.895 21.54 6.99 39.02 3.16
4052 4177 1.003580 CAAGTGGTAGATGCCCAGTGT 59.996 52.381 0.00 0.00 35.78 3.55
4136 4261 3.369052 CGCCTGAGGTACTGGTATTTTGA 60.369 47.826 0.00 0.00 41.55 2.69
4202 4327 2.987149 GGATATGAATGCGGTACACTCG 59.013 50.000 0.00 0.00 0.00 4.18
4358 4483 3.880846 GCAGCATGTACCGCAGCC 61.881 66.667 9.72 0.00 39.31 4.85
4428 4553 2.962253 CCGGCTTCGAATCTCGCC 60.962 66.667 14.47 14.47 40.21 5.54
4489 4614 0.740737 GCTACGCCATTTCCATTGCT 59.259 50.000 0.00 0.00 0.00 3.91
4514 4642 2.392662 CCTCCATCTCTTGACAGGCTA 58.607 52.381 0.00 0.00 0.00 3.93
4518 4646 1.554160 ACTGCCTCCATCTCTTGACAG 59.446 52.381 0.00 0.00 0.00 3.51
4568 4709 3.575630 ACACGTATGCACTACAAGTCAG 58.424 45.455 0.00 0.00 0.00 3.51
4580 4722 5.176958 GGAACAGGAATATGTACACGTATGC 59.823 44.000 0.00 0.00 31.70 3.14
4672 4816 0.103208 AGCAGAATCCACCGTCGATC 59.897 55.000 0.00 0.00 0.00 3.69
4803 4951 9.703892 TTGGTGTAAATGAAATTTTGTATGAGG 57.296 29.630 0.00 0.00 46.10 3.86
4810 4958 8.769891 GGTACCTTTGGTGTAAATGAAATTTTG 58.230 33.333 4.06 0.00 39.09 2.44
4878 6892 5.034852 TGTGTATCCTGTGTAATCCATGG 57.965 43.478 4.97 4.97 0.00 3.66
4883 6897 7.174253 TGTTTTTCCTGTGTATCCTGTGTAATC 59.826 37.037 0.00 0.00 0.00 1.75
4915 6930 4.861102 CTGGGAGTTTCAGCTGAATTTT 57.139 40.909 28.89 17.15 33.54 1.82
4927 6942 3.712218 GGGTATTCTCTAGCTGGGAGTTT 59.288 47.826 15.07 8.72 33.06 2.66
4933 6948 2.224161 GCTGTGGGTATTCTCTAGCTGG 60.224 54.545 0.00 0.00 0.00 4.85
5176 7192 0.035820 TGGTGTCCGGACATTTAGGC 60.036 55.000 38.11 23.98 43.97 3.93
5220 7236 2.198426 CCTGGGTTTGGTGCCAGT 59.802 61.111 0.00 0.00 0.00 4.00
5222 7238 4.232061 CCCCTGGGTTTGGTGCCA 62.232 66.667 12.71 0.00 0.00 4.92
5224 7240 2.283173 CTCCCCTGGGTTTGGTGC 60.283 66.667 12.71 0.00 36.47 5.01
5225 7241 2.018884 AACCTCCCCTGGGTTTGGTG 62.019 60.000 18.19 0.81 43.66 4.17
5226 7242 1.703597 AACCTCCCCTGGGTTTGGT 60.704 57.895 12.71 13.23 43.66 3.67
5228 7244 1.076727 GGAACCTCCCCTGGGTTTG 59.923 63.158 12.71 1.39 45.78 2.93
5231 7247 1.852626 CTTGGAACCTCCCCTGGGT 60.853 63.158 12.71 0.00 35.03 4.51
5232 7248 3.090765 CTTGGAACCTCCCCTGGG 58.909 66.667 5.50 5.50 35.03 4.45
5233 7249 2.356667 GCTTGGAACCTCCCCTGG 59.643 66.667 0.00 0.00 35.03 4.45
5234 7250 2.045926 CGCTTGGAACCTCCCCTG 60.046 66.667 0.00 0.00 35.03 4.45
5245 7265 2.128035 GACGGATATCTGAACGCTTGG 58.872 52.381 18.63 0.00 0.00 3.61
5247 7267 2.794981 CGTGACGGATATCTGAACGCTT 60.795 50.000 22.34 1.69 32.56 4.68
5288 7308 0.609406 GAGAGAGGTTTTGGGTGGGC 60.609 60.000 0.00 0.00 0.00 5.36
5304 7324 2.234300 AAGAAAAACGCAGTCCGAGA 57.766 45.000 0.00 0.00 45.00 4.04
5361 7382 3.799755 GTTGGTAGCCGCCGCTTG 61.800 66.667 4.51 0.00 45.55 4.01
5362 7383 4.323477 TGTTGGTAGCCGCCGCTT 62.323 61.111 4.51 0.00 45.55 4.68
5379 7400 0.539986 GTGGGTGATACATCGGTGGT 59.460 55.000 0.00 0.00 0.00 4.16
5380 7401 0.529773 CGTGGGTGATACATCGGTGG 60.530 60.000 0.00 0.00 0.00 4.61
5382 7403 1.143183 GCGTGGGTGATACATCGGT 59.857 57.895 0.00 0.00 0.00 4.69
5386 7407 1.396607 TAGGCGCGTGGGTGATACAT 61.397 55.000 13.84 0.00 0.00 2.29
5433 7474 4.227134 CAGCGGACGGATGAGGGG 62.227 72.222 0.00 0.00 32.47 4.79
5459 7500 3.048602 CACCTATAGGGCGGACGG 58.951 66.667 22.91 0.00 40.27 4.79
5497 7538 1.826487 GGCCAAACACTTGTCGGGT 60.826 57.895 0.00 0.00 0.00 5.28
5500 7541 2.126467 CATTTGGCCAAACACTTGTCG 58.874 47.619 32.62 10.10 32.51 4.35


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

AutoCloner maintained by Alex Coulton.