Multiple sequence alignment - TraesCS7B01G401800

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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 TraesCS7B01G401800 chr7B 100.000 4519 0 0 1 4519 668028944 668033462 0.000000e+00 8346
1 TraesCS7B01G401800 chr7B 94.175 103 2 3 2710 2808 662625355 662625457 2.180000e-33 154
2 TraesCS7B01G401800 chr7A 91.853 2455 103 53 335 2712 685833892 685831458 0.000000e+00 3336
3 TraesCS7B01G401800 chr7A 93.346 1052 48 8 2792 3839 685831461 685830428 0.000000e+00 1535
4 TraesCS7B01G401800 chr7A 93.452 336 22 0 1 336 685834263 685833928 2.430000e-137 499
5 TraesCS7B01G401800 chr7A 88.636 176 15 2 4251 4424 685781016 685780844 4.580000e-50 209
6 TraesCS7B01G401800 chr7A 88.068 176 16 2 4251 4424 685797013 685796841 2.130000e-48 204
7 TraesCS7B01G401800 chr7A 88.068 176 16 2 4251 4424 685814050 685813878 2.130000e-48 204
8 TraesCS7B01G401800 chr7A 88.068 176 16 2 4251 4424 685829975 685829803 2.130000e-48 204
9 TraesCS7B01G401800 chr7A 86.932 176 18 2 4251 4424 685734657 685734485 4.610000e-45 193
10 TraesCS7B01G401800 chr7D 96.582 1726 53 1 993 2712 593121527 593119802 0.000000e+00 2856
11 TraesCS7B01G401800 chr7D 95.743 1010 26 5 2792 3799 593119805 593118811 0.000000e+00 1611
12 TraesCS7B01G401800 chr7D 86.397 691 28 10 349 997 593122217 593121551 0.000000e+00 695
13 TraesCS7B01G401800 chr7D 82.741 591 63 24 3850 4423 593118673 593118105 1.460000e-134 490
14 TraesCS7B01G401800 chr7D 92.857 336 21 1 1 336 593122594 593122262 6.800000e-133 484
15 TraesCS7B01G401800 chr5D 92.132 394 17 4 1065 1452 3523869 3523484 1.110000e-150 544
16 TraesCS7B01G401800 chr5D 97.351 302 8 0 1523 1824 3523057 3522756 8.670000e-142 514
17 TraesCS7B01G401800 chr5D 95.960 99 3 1 2703 2800 17391248 17391150 4.680000e-35 159
18 TraesCS7B01G401800 chr6B 100.000 87 0 0 2709 2795 716607871 716607785 1.300000e-35 161
19 TraesCS7B01G401800 chr5B 83.420 193 13 8 1220 1412 426541775 426541602 1.300000e-35 161
20 TraesCS7B01G401800 chr4B 98.876 89 1 0 2707 2795 624748470 624748558 4.680000e-35 159
21 TraesCS7B01G401800 chr6A 96.842 95 2 1 2701 2795 68511246 68511339 1.680000e-34 158
22 TraesCS7B01G401800 chr3B 94.231 104 4 2 2693 2795 52905272 52905170 1.680000e-34 158
23 TraesCS7B01G401800 chrUn 94.949 99 3 2 2705 2802 132121236 132121139 2.180000e-33 154
24 TraesCS7B01G401800 chr4A 94.949 99 4 1 2703 2801 503221570 503221667 2.180000e-33 154
25 TraesCS7B01G401800 chr1B 92.453 106 6 2 2690 2794 654313679 654313575 2.820000e-32 150
26 TraesCS7B01G401800 chr2A 87.129 101 13 0 1332 1432 723835961 723835861 1.030000e-21 115


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 TraesCS7B01G401800 chr7B 668028944 668033462 4518 False 8346.0 8346 100.00000 1 4519 1 chr7B.!!$F2 4518
1 TraesCS7B01G401800 chr7A 685829803 685834263 4460 True 1393.5 3336 91.67975 1 4424 4 chr7A.!!$R5 4423
2 TraesCS7B01G401800 chr7D 593118105 593122594 4489 True 1227.2 2856 90.86400 1 4423 5 chr7D.!!$R1 4422
3 TraesCS7B01G401800 chr5D 3522756 3523869 1113 True 529.0 544 94.74150 1065 1824 2 chr5D.!!$R2 759

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
38 39 1.001378 CTTGCAGCTACAAAACGGCTT 60.001 47.619 0.11 0.00 33.74 4.35 F
644 731 1.002033 CTGCAGCTGTTTTCTGACACC 60.002 52.381 16.64 0.00 33.54 4.16 F
664 751 1.062148 CGTCTCATGCTCATGTGCTTG 59.938 52.381 22.71 22.71 39.72 4.01 F
2085 2588 0.758734 CCATGATCGACAAGGGGCTA 59.241 55.000 0.00 0.00 34.17 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1989 2492 0.301687 GCTCATTGTATGTGACGGCG 59.698 55.000 4.8 4.8 0.0 6.46 R
2083 2586 0.865769 GTGAACGTGTTGGGCAGTAG 59.134 55.000 0.0 0.0 0.0 2.57 R
2127 2630 1.383799 CACCTTCCCAGCATTCCCA 59.616 57.895 0.0 0.0 0.0 4.37 R
3605 4112 0.035458 AATATGCTACGCTCCCCTGC 59.965 55.000 0.0 0.0 0.0 4.85 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
38 39 1.001378 CTTGCAGCTACAAAACGGCTT 60.001 47.619 0.11 0.00 33.74 4.35
44 45 2.808543 AGCTACAAAACGGCTTCAAGAG 59.191 45.455 0.00 0.00 31.81 2.85
90 91 2.203788 AGGACAACTCCGAGGGCA 60.204 61.111 0.00 0.00 42.22 5.36
151 152 2.046892 CCACGGTCAAGGCAGAGG 60.047 66.667 0.00 0.00 0.00 3.69
228 229 2.365370 CCAGAGAGGAGGCCTGCT 60.365 66.667 28.97 28.97 41.22 4.24
252 253 1.301677 GGCTGAAGAAGGCGAAGTGG 61.302 60.000 0.00 0.00 42.32 4.00
279 280 2.505819 ACTGGATCCTGTTCATGGGTAC 59.494 50.000 17.95 0.00 0.00 3.34
302 303 2.526304 TCTGCAAACTAGCTTCACGT 57.474 45.000 0.00 0.00 34.99 4.49
306 307 1.878953 CAAACTAGCTTCACGTGGGT 58.121 50.000 17.00 8.75 0.00 4.51
313 314 1.293498 CTTCACGTGGGTGGAGGAG 59.707 63.158 17.00 0.00 44.70 3.69
400 440 2.737180 ACTGACAGGGCGACAGTG 59.263 61.111 7.51 0.00 46.72 3.66
444 484 4.142049 GGACTGGTCTGAATCTCTTGTAGG 60.142 50.000 0.67 0.00 0.00 3.18
596 683 1.881973 GTTCCATGTGTGACACTGCAT 59.118 47.619 17.47 8.52 35.11 3.96
598 685 2.585330 TCCATGTGTGACACTGCATTT 58.415 42.857 17.47 0.00 35.11 2.32
603 690 2.751806 TGTGTGACACTGCATTTGTTCA 59.248 40.909 17.47 3.80 35.11 3.18
606 693 1.337703 TGACACTGCATTTGTTCAGCC 59.662 47.619 2.81 0.00 33.80 4.85
644 731 1.002033 CTGCAGCTGTTTTCTGACACC 60.002 52.381 16.64 0.00 33.54 4.16
663 750 1.366679 CGTCTCATGCTCATGTGCTT 58.633 50.000 19.60 11.36 39.72 3.91
664 751 1.062148 CGTCTCATGCTCATGTGCTTG 59.938 52.381 22.71 22.71 39.72 4.01
677 764 2.726633 TGTGCTTGTTTTTAGCTTCGC 58.273 42.857 0.00 0.00 39.38 4.70
710 797 6.379988 TGTCAGTACTGATAGAATAACCAGCA 59.620 38.462 27.54 13.31 42.18 4.41
711 798 6.697892 GTCAGTACTGATAGAATAACCAGCAC 59.302 42.308 27.54 6.64 42.18 4.40
712 799 6.379988 TCAGTACTGATAGAATAACCAGCACA 59.620 38.462 21.74 0.00 34.14 4.57
715 802 5.423015 ACTGATAGAATAACCAGCACACAG 58.577 41.667 0.00 0.00 0.00 3.66
717 804 4.469586 TGATAGAATAACCAGCACACAGGA 59.530 41.667 0.00 0.00 0.00 3.86
718 805 3.340814 AGAATAACCAGCACACAGGAG 57.659 47.619 0.00 0.00 0.00 3.69
719 806 1.740025 GAATAACCAGCACACAGGAGC 59.260 52.381 0.00 0.00 0.00 4.70
737 829 1.937546 GCGGCAGGTGGATCTTTTGG 61.938 60.000 0.00 0.00 0.00 3.28
771 863 6.211384 TGGTAGTTCAGATTCAGATCAAGTGA 59.789 38.462 0.00 0.00 34.60 3.41
802 902 3.004419 CGCAGGTAGACAGATATTCCGAA 59.996 47.826 0.00 0.00 0.00 4.30
887 987 3.508840 CGTCATCCTTTGCCGCCC 61.509 66.667 0.00 0.00 0.00 6.13
1206 1341 3.625897 CGGACCCACCAGCAGACA 61.626 66.667 0.00 0.00 38.90 3.41
1267 1402 4.806339 CCTTCCTCTCCCCGGCCT 62.806 72.222 0.00 0.00 0.00 5.19
1485 1620 2.887568 CTGGAGATGGTCGTGCGC 60.888 66.667 0.00 0.00 0.00 6.09
1547 2050 3.490759 CGACGAAATGCCGCTGCT 61.491 61.111 0.70 0.00 38.71 4.24
1548 2051 2.401195 GACGAAATGCCGCTGCTC 59.599 61.111 0.70 0.00 38.71 4.26
1908 2411 1.134371 GTCACCTACAATGCCCTCCTC 60.134 57.143 0.00 0.00 0.00 3.71
2067 2570 2.877691 GCCAAATGCCTCGACACC 59.122 61.111 0.00 0.00 0.00 4.16
2075 2578 1.319614 TGCCTCGACACCATGATCGA 61.320 55.000 13.63 13.63 44.68 3.59
2083 2586 1.097547 CACCATGATCGACAAGGGGC 61.098 60.000 11.92 0.00 41.13 5.80
2085 2588 0.758734 CCATGATCGACAAGGGGCTA 59.241 55.000 0.00 0.00 34.17 3.93
2127 2630 2.869801 CAACACCATAATGACGGCGTAT 59.130 45.455 14.74 4.95 0.00 3.06
2136 2639 1.227556 GACGGCGTATGGGAATGCT 60.228 57.895 14.74 0.00 0.00 3.79
2157 2660 4.379243 AAGGTGGACGAGGCGCTG 62.379 66.667 7.64 0.00 0.00 5.18
2208 2711 2.873472 GTTTGTCCCATACACGAACACA 59.127 45.455 0.00 0.00 38.00 3.72
2267 2770 2.663630 TTCGCGGCGATGCTAGAGAC 62.664 60.000 26.95 0.00 35.23 3.36
2457 2960 1.366111 CTTATGGCCGGTGTGGTTCG 61.366 60.000 1.90 0.00 41.21 3.95
2496 2999 4.965814 AGATGTATGATGAAATGACCGCT 58.034 39.130 0.00 0.00 0.00 5.52
2635 3138 2.416836 CCCAACGACATGTCATACTCGT 60.417 50.000 24.93 13.81 41.00 4.18
2708 3211 3.090037 TCGAGAAGGAAGTCTACCAAGG 58.910 50.000 0.00 0.00 0.00 3.61
2709 3212 2.826725 CGAGAAGGAAGTCTACCAAGGT 59.173 50.000 0.00 0.00 0.00 3.50
2710 3213 4.015084 CGAGAAGGAAGTCTACCAAGGTA 58.985 47.826 0.00 0.00 0.00 3.08
2711 3214 4.142425 CGAGAAGGAAGTCTACCAAGGTAC 60.142 50.000 0.00 0.00 0.00 3.34
2713 3216 5.018149 AGAAGGAAGTCTACCAAGGTACTC 58.982 45.833 0.00 0.00 38.49 2.59
2714 3217 3.710724 AGGAAGTCTACCAAGGTACTCC 58.289 50.000 0.00 0.36 38.49 3.85
2715 3218 2.765135 GGAAGTCTACCAAGGTACTCCC 59.235 54.545 0.00 0.00 38.49 4.30
2717 3220 3.385314 AGTCTACCAAGGTACTCCCTC 57.615 52.381 0.00 0.00 45.47 4.30
2718 3221 2.024177 AGTCTACCAAGGTACTCCCTCC 60.024 54.545 0.00 0.00 45.47 4.30
2719 3222 1.064166 TCTACCAAGGTACTCCCTCCG 60.064 57.143 0.00 0.00 45.47 4.63
2720 3223 0.706433 TACCAAGGTACTCCCTCCGT 59.294 55.000 0.00 0.00 45.47 4.69
2721 3224 0.706433 ACCAAGGTACTCCCTCCGTA 59.294 55.000 0.00 0.00 45.47 4.02
2722 3225 1.077663 ACCAAGGTACTCCCTCCGTAA 59.922 52.381 0.00 0.00 45.47 3.18
2723 3226 2.181975 CCAAGGTACTCCCTCCGTAAA 58.818 52.381 0.00 0.00 45.47 2.01
2724 3227 2.093816 CCAAGGTACTCCCTCCGTAAAC 60.094 54.545 0.00 0.00 45.47 2.01
2725 3228 2.830321 CAAGGTACTCCCTCCGTAAACT 59.170 50.000 0.00 0.00 45.47 2.66
2726 3229 4.019174 CAAGGTACTCCCTCCGTAAACTA 58.981 47.826 0.00 0.00 45.47 2.24
2727 3230 4.322057 AGGTACTCCCTCCGTAAACTAA 57.678 45.455 0.00 0.00 40.71 2.24
2728 3231 4.876580 AGGTACTCCCTCCGTAAACTAAT 58.123 43.478 0.00 0.00 40.71 1.73
2729 3232 6.018433 AGGTACTCCCTCCGTAAACTAATA 57.982 41.667 0.00 0.00 40.71 0.98
2730 3233 6.618501 AGGTACTCCCTCCGTAAACTAATAT 58.381 40.000 0.00 0.00 40.71 1.28
2731 3234 7.759607 AGGTACTCCCTCCGTAAACTAATATA 58.240 38.462 0.00 0.00 40.71 0.86
2732 3235 8.227507 AGGTACTCCCTCCGTAAACTAATATAA 58.772 37.037 0.00 0.00 40.71 0.98
2733 3236 8.518702 GGTACTCCCTCCGTAAACTAATATAAG 58.481 40.741 0.00 0.00 0.00 1.73
2734 3237 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
2735 3238 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
2736 3239 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
2737 3240 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
2738 3241 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
2739 3242 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
2740 3243 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
2741 3244 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
2742 3245 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
2743 3246 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
2757 3260 9.570488 AAGAGCGTTTAGAATACTAAAGTAGTG 57.430 33.333 0.00 0.00 45.42 2.74
2758 3261 8.954350 AGAGCGTTTAGAATACTAAAGTAGTGA 58.046 33.333 0.00 0.00 45.42 3.41
2759 3262 9.733219 GAGCGTTTAGAATACTAAAGTAGTGAT 57.267 33.333 0.00 0.00 45.42 3.06
2760 3263 9.733219 AGCGTTTAGAATACTAAAGTAGTGATC 57.267 33.333 0.00 0.00 45.42 2.92
2761 3264 9.733219 GCGTTTAGAATACTAAAGTAGTGATCT 57.267 33.333 0.00 4.67 45.42 2.75
2790 3293 8.777578 TGCTCTTATATTAGTTTACAGAGGGA 57.222 34.615 0.00 0.00 0.00 4.20
3005 3508 2.437895 TCGATCGAGCAGTCCGGT 60.438 61.111 15.15 0.00 0.00 5.28
3118 3621 2.607750 GACCTCCCAGTCCCAGCA 60.608 66.667 0.00 0.00 0.00 4.41
3119 3622 2.608988 ACCTCCCAGTCCCAGCAG 60.609 66.667 0.00 0.00 0.00 4.24
3120 3623 4.106925 CCTCCCAGTCCCAGCAGC 62.107 72.222 0.00 0.00 0.00 5.25
3121 3624 3.324930 CTCCCAGTCCCAGCAGCA 61.325 66.667 0.00 0.00 0.00 4.41
3122 3625 3.324930 TCCCAGTCCCAGCAGCAG 61.325 66.667 0.00 0.00 0.00 4.24
3407 3910 3.704231 CTGCAGGGCCAAGCGGTAT 62.704 63.158 18.48 0.00 32.54 2.73
3601 4108 4.664150 TGGGTGATTTCCAAGTTTTGAC 57.336 40.909 0.00 0.00 0.00 3.18
3602 4109 4.026744 TGGGTGATTTCCAAGTTTTGACA 58.973 39.130 0.00 0.00 0.00 3.58
3603 4110 4.099266 TGGGTGATTTCCAAGTTTTGACAG 59.901 41.667 0.00 0.00 0.00 3.51
3604 4111 4.501400 GGGTGATTTCCAAGTTTTGACAGG 60.501 45.833 0.00 0.00 0.00 4.00
3605 4112 4.501400 GGTGATTTCCAAGTTTTGACAGGG 60.501 45.833 0.00 0.00 0.00 4.45
3705 4212 8.193250 TCCTCGCATTCTTACAAAGTTATTAC 57.807 34.615 0.00 0.00 0.00 1.89
3706 4213 8.038944 TCCTCGCATTCTTACAAAGTTATTACT 58.961 33.333 0.00 0.00 35.68 2.24
3707 4214 9.309516 CCTCGCATTCTTACAAAGTTATTACTA 57.690 33.333 0.00 0.00 33.17 1.82
3745 4252 4.504858 GCTGTACAGTTGTTAGCCTATGT 58.495 43.478 23.44 0.00 33.65 2.29
3774 4282 2.552315 TGAATTTTGAGGTGCTTCGGAC 59.448 45.455 0.00 0.00 0.00 4.79
3792 4300 2.227556 GACGTATCGTTTGGTTTTGCG 58.772 47.619 0.00 0.00 41.37 4.85
3799 4307 3.827625 TCGTTTGGTTTTGCGGAATATG 58.172 40.909 0.00 0.00 0.00 1.78
3800 4308 3.253677 TCGTTTGGTTTTGCGGAATATGT 59.746 39.130 0.00 0.00 0.00 2.29
3801 4309 4.454847 TCGTTTGGTTTTGCGGAATATGTA 59.545 37.500 0.00 0.00 0.00 2.29
3802 4310 4.555747 CGTTTGGTTTTGCGGAATATGTAC 59.444 41.667 0.00 0.00 0.00 2.90
3803 4311 5.462405 GTTTGGTTTTGCGGAATATGTACA 58.538 37.500 0.00 0.00 0.00 2.90
3805 4313 5.242069 TGGTTTTGCGGAATATGTACATG 57.758 39.130 18.81 2.15 0.00 3.21
3818 4356 2.862541 TGTACATGAAGCAGCAAGGTT 58.137 42.857 0.00 0.00 41.46 3.50
3830 4368 1.676967 CAAGGTTGAGCTGCTCCCC 60.677 63.158 25.61 23.27 0.00 4.81
3833 4371 1.228552 GGTTGAGCTGCTCCCCAAA 60.229 57.895 25.61 11.26 0.00 3.28
3835 4373 1.260544 GTTGAGCTGCTCCCCAAATT 58.739 50.000 25.61 0.00 0.00 1.82
3836 4374 1.203287 GTTGAGCTGCTCCCCAAATTC 59.797 52.381 25.61 0.00 0.00 2.17
3837 4375 0.700564 TGAGCTGCTCCCCAAATTCT 59.299 50.000 25.61 0.00 0.00 2.40
3838 4376 1.915489 TGAGCTGCTCCCCAAATTCTA 59.085 47.619 25.61 1.03 0.00 2.10
3839 4377 2.293170 GAGCTGCTCCCCAAATTCTAC 58.707 52.381 18.80 0.00 0.00 2.59
3840 4378 1.918957 AGCTGCTCCCCAAATTCTACT 59.081 47.619 0.00 0.00 0.00 2.57
3841 4379 2.019984 GCTGCTCCCCAAATTCTACTG 58.980 52.381 0.00 0.00 0.00 2.74
3842 4380 2.619074 GCTGCTCCCCAAATTCTACTGT 60.619 50.000 0.00 0.00 0.00 3.55
3843 4381 3.012518 CTGCTCCCCAAATTCTACTGTG 58.987 50.000 0.00 0.00 0.00 3.66
3845 4383 2.879756 GCTCCCCAAATTCTACTGTGCA 60.880 50.000 0.00 0.00 0.00 4.57
3846 4384 3.624777 CTCCCCAAATTCTACTGTGCAT 58.375 45.455 0.00 0.00 0.00 3.96
3847 4385 3.620488 TCCCCAAATTCTACTGTGCATC 58.380 45.455 0.00 0.00 0.00 3.91
3855 4453 6.674694 AATTCTACTGTGCATCATTCTCAC 57.325 37.500 0.00 0.00 0.00 3.51
3871 4469 1.805345 CTCACTTGCTGAAGCCTGAAG 59.195 52.381 0.00 0.00 41.18 3.02
3892 4491 2.455674 CAACCTGTGCAGTAGCTGTA 57.544 50.000 0.00 0.00 42.74 2.74
3898 4501 3.118992 CCTGTGCAGTAGCTGTATCTGAA 60.119 47.826 0.00 0.00 42.74 3.02
3904 4507 2.355132 AGTAGCTGTATCTGAACCGTCG 59.645 50.000 0.00 0.00 0.00 5.12
3908 4511 0.108992 TGTATCTGAACCGTCGGTGC 60.109 55.000 19.67 17.84 35.34 5.01
3912 4515 0.948623 TCTGAACCGTCGGTGCAATG 60.949 55.000 25.28 15.10 41.31 2.82
3916 4519 1.532007 GAACCGTCGGTGCAATGTTTA 59.468 47.619 19.67 0.00 35.34 2.01
3922 4525 1.626321 TCGGTGCAATGTTTAGGGAGA 59.374 47.619 0.00 0.00 0.00 3.71
3929 4532 4.462483 TGCAATGTTTAGGGAGATCAAACC 59.538 41.667 0.00 0.00 32.42 3.27
3944 4547 2.437651 TCAAACCCTGTCATGTCACTCA 59.562 45.455 0.00 0.00 0.00 3.41
3947 4550 2.889512 ACCCTGTCATGTCACTCACTA 58.110 47.619 0.00 0.00 0.00 2.74
3948 4551 2.828520 ACCCTGTCATGTCACTCACTAG 59.171 50.000 0.00 0.00 0.00 2.57
3978 4581 1.024046 ACACACTTGCACGCTGTCAA 61.024 50.000 0.00 0.00 0.00 3.18
3979 4582 0.308684 CACACTTGCACGCTGTCAAT 59.691 50.000 0.00 0.00 0.00 2.57
3986 4589 0.179240 GCACGCTGTCAATTCAGTCG 60.179 55.000 8.41 8.41 39.16 4.18
3997 4600 1.830587 ATTCAGTCGCCTGGCTGTGA 61.831 55.000 17.92 13.12 39.31 3.58
4030 4633 6.953520 ACAGATTTTATTCTGGGTGATTTCCA 59.046 34.615 6.43 0.00 46.04 3.53
4038 4641 2.965147 CTGGGTGATTTCCAGGTTTTGT 59.035 45.455 2.40 0.00 45.95 2.83
4041 4644 3.578282 GGGTGATTTCCAGGTTTTGTCAT 59.422 43.478 0.00 0.00 0.00 3.06
4042 4645 4.040339 GGGTGATTTCCAGGTTTTGTCATT 59.960 41.667 0.00 0.00 0.00 2.57
4043 4646 5.230182 GGTGATTTCCAGGTTTTGTCATTC 58.770 41.667 0.00 0.00 0.00 2.67
4044 4647 5.011023 GGTGATTTCCAGGTTTTGTCATTCT 59.989 40.000 0.00 0.00 0.00 2.40
4045 4648 6.152379 GTGATTTCCAGGTTTTGTCATTCTC 58.848 40.000 0.00 0.00 0.00 2.87
4046 4649 5.832595 TGATTTCCAGGTTTTGTCATTCTCA 59.167 36.000 0.00 0.00 0.00 3.27
4047 4650 6.323482 TGATTTCCAGGTTTTGTCATTCTCAA 59.677 34.615 0.00 0.00 0.00 3.02
4048 4651 5.772825 TTCCAGGTTTTGTCATTCTCAAG 57.227 39.130 0.00 0.00 0.00 3.02
4049 4652 3.569701 TCCAGGTTTTGTCATTCTCAAGC 59.430 43.478 0.00 0.00 0.00 4.01
4051 4654 3.003689 CAGGTTTTGTCATTCTCAAGCGT 59.996 43.478 0.00 0.00 0.00 5.07
4052 4655 3.251004 AGGTTTTGTCATTCTCAAGCGTC 59.749 43.478 0.00 0.00 0.00 5.19
4054 4657 4.214437 GTTTTGTCATTCTCAAGCGTCTG 58.786 43.478 0.00 0.00 0.00 3.51
4064 4694 3.127721 TCTCAAGCGTCTGTATGTCTGAG 59.872 47.826 0.00 0.00 0.00 3.35
4082 4712 4.099113 TCTGAGTTGCTCCAGATGATGTAG 59.901 45.833 0.00 0.00 0.00 2.74
4083 4713 3.771479 TGAGTTGCTCCAGATGATGTAGT 59.229 43.478 0.00 0.00 0.00 2.73
4140 4778 0.392193 ATCCTCAGTTGCTGAAGCCG 60.392 55.000 0.00 0.00 40.18 5.52
4147 4785 0.603975 GTTGCTGAAGCCGGAAGTCT 60.604 55.000 5.05 0.00 41.18 3.24
4180 4818 2.310052 AGGAGTAGCCAATCCTGCTTTT 59.690 45.455 0.00 0.00 44.42 2.27
4183 4821 2.027192 AGTAGCCAATCCTGCTTTTCGA 60.027 45.455 0.00 0.00 40.23 3.71
4196 4834 0.614294 TTTTCGATTACGGCCCCTCA 59.386 50.000 0.00 0.00 40.21 3.86
4197 4835 0.108041 TTTCGATTACGGCCCCTCAC 60.108 55.000 0.00 0.00 40.21 3.51
4198 4836 1.963464 TTCGATTACGGCCCCTCACC 61.963 60.000 0.00 0.00 40.21 4.02
4199 4837 2.432300 CGATTACGGCCCCTCACCT 61.432 63.158 0.00 0.00 35.72 4.00
4202 4840 2.833151 ATTACGGCCCCTCACCTCCA 62.833 60.000 0.00 0.00 0.00 3.86
4210 4848 2.659063 CCTCACCTCCATCCGTGCA 61.659 63.158 0.00 0.00 0.00 4.57
4230 4868 3.056607 GCATAATCTTTGGCCACACACTT 60.057 43.478 3.88 0.00 0.00 3.16
4232 4870 0.675633 ATCTTTGGCCACACACTTGC 59.324 50.000 3.88 0.00 0.00 4.01
4234 4872 0.528249 CTTTGGCCACACACTTGCAC 60.528 55.000 3.88 0.00 0.00 4.57
4237 4875 1.066257 GGCCACACACTTGCACAAG 59.934 57.895 8.82 8.82 43.79 3.16
4248 4886 2.098117 ACTTGCACAAGCTGTCAACTTC 59.902 45.455 10.26 0.00 41.99 3.01
4266 4904 3.181445 ACTTCCTTGGCTACACACATTCA 60.181 43.478 0.00 0.00 0.00 2.57
4319 4957 0.450983 GGACAGTTCCTCGGTACTCG 59.549 60.000 0.00 0.00 39.13 4.18
4320 4958 0.179169 GACAGTTCCTCGGTACTCGC 60.179 60.000 0.00 0.00 39.05 5.03
4338 4982 2.510238 GCCCACGCTGCTACTCTG 60.510 66.667 0.00 0.00 0.00 3.35
4343 4987 0.801451 CACGCTGCTACTCTGCTCTG 60.801 60.000 0.00 0.00 37.48 3.35
4420 5064 3.027675 GCCCTGTCCGTTCTACCCC 62.028 68.421 0.00 0.00 0.00 4.95
4424 5068 0.679002 CTGTCCGTTCTACCCCTCGA 60.679 60.000 0.00 0.00 0.00 4.04
4425 5069 0.033796 TGTCCGTTCTACCCCTCGAT 60.034 55.000 0.00 0.00 0.00 3.59
4426 5070 0.667453 GTCCGTTCTACCCCTCGATC 59.333 60.000 0.00 0.00 0.00 3.69
4427 5071 0.816825 TCCGTTCTACCCCTCGATCG 60.817 60.000 9.36 9.36 0.00 3.69
4428 5072 0.816825 CCGTTCTACCCCTCGATCGA 60.817 60.000 18.32 18.32 0.00 3.59
4429 5073 1.236628 CGTTCTACCCCTCGATCGAT 58.763 55.000 19.78 6.20 0.00 3.59
4430 5074 1.197264 CGTTCTACCCCTCGATCGATC 59.803 57.143 19.78 15.68 0.00 3.69
4431 5075 2.506444 GTTCTACCCCTCGATCGATCT 58.494 52.381 19.78 5.87 0.00 2.75
4432 5076 2.476126 TCTACCCCTCGATCGATCTC 57.524 55.000 19.78 0.00 0.00 2.75
4433 5077 1.080298 CTACCCCTCGATCGATCTCG 58.920 60.000 19.78 12.75 39.99 4.04
4434 5078 0.395686 TACCCCTCGATCGATCTCGT 59.604 55.000 19.78 14.18 39.62 4.18
4435 5079 0.465824 ACCCCTCGATCGATCTCGTT 60.466 55.000 19.78 0.00 39.62 3.85
4436 5080 0.238817 CCCCTCGATCGATCTCGTTC 59.761 60.000 19.78 0.00 39.62 3.95
4437 5081 1.231221 CCCTCGATCGATCTCGTTCT 58.769 55.000 19.78 0.00 39.62 3.01
4438 5082 2.414806 CCCTCGATCGATCTCGTTCTA 58.585 52.381 19.78 0.00 39.62 2.10
4439 5083 2.158058 CCCTCGATCGATCTCGTTCTAC 59.842 54.545 19.78 0.00 39.62 2.59
4440 5084 2.158058 CCTCGATCGATCTCGTTCTACC 59.842 54.545 19.78 0.00 39.62 3.18
4441 5085 2.141517 TCGATCGATCTCGTTCTACCC 58.858 52.381 22.43 0.00 39.62 3.69
4442 5086 1.136308 CGATCGATCTCGTTCTACCCG 60.136 57.143 22.43 2.22 40.80 5.28
4443 5087 1.197264 GATCGATCTCGTTCTACCCGG 59.803 57.143 18.29 0.00 40.80 5.73
4444 5088 1.008767 CGATCTCGTTCTACCCGGC 60.009 63.158 0.00 0.00 34.11 6.13
4445 5089 1.008767 GATCTCGTTCTACCCGGCG 60.009 63.158 0.00 0.00 0.00 6.46
4446 5090 2.403671 GATCTCGTTCTACCCGGCGG 62.404 65.000 21.46 21.46 0.00 6.13
4447 5091 4.867599 CTCGTTCTACCCGGCGGC 62.868 72.222 23.20 4.39 0.00 6.53
4466 5110 4.477975 GACGGCGACACGAGGGAG 62.478 72.222 16.62 0.00 37.61 4.30
4481 5125 4.681978 GAGGGCGCCACACGTTCT 62.682 66.667 30.85 14.42 46.11 3.01
4482 5126 4.988598 AGGGCGCCACACGTTCTG 62.989 66.667 30.85 0.00 46.11 3.02
4486 5130 3.345808 CGCCACACGTTCTGGGTG 61.346 66.667 10.42 3.87 41.15 4.61
4487 5131 3.660111 GCCACACGTTCTGGGTGC 61.660 66.667 10.42 0.00 38.98 5.01
4488 5132 2.978010 CCACACGTTCTGGGTGCC 60.978 66.667 1.51 0.00 38.98 5.01
4489 5133 2.111043 CACACGTTCTGGGTGCCT 59.889 61.111 0.00 0.00 38.98 4.75
4490 5134 1.961277 CACACGTTCTGGGTGCCTC 60.961 63.158 0.00 0.00 38.98 4.70
4491 5135 2.358737 CACGTTCTGGGTGCCTCC 60.359 66.667 0.00 0.00 0.00 4.30
4492 5136 2.847234 ACGTTCTGGGTGCCTCCA 60.847 61.111 0.00 0.00 38.11 3.86
4493 5137 2.358737 CGTTCTGGGTGCCTCCAC 60.359 66.667 0.00 0.00 41.32 4.02
4494 5138 2.358737 GTTCTGGGTGCCTCCACG 60.359 66.667 0.00 0.00 43.00 4.94
4495 5139 3.636231 TTCTGGGTGCCTCCACGG 61.636 66.667 0.00 0.00 43.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 1.800805 CTTTCTTCTGCGGCTCTTGA 58.199 50.000 0.00 0.00 0.00 3.02
44 45 0.179153 GGATTGCTTTCTTCTGCGGC 60.179 55.000 0.00 0.00 0.00 6.53
90 91 4.181010 ATGGCGGGCGAATCTGCT 62.181 61.111 0.00 0.00 38.94 4.24
111 112 4.111016 CCGAGTCTGCGGCGTGTA 62.111 66.667 9.37 0.00 45.38 2.90
151 152 1.798813 CGTTTGCTCTACCAGGTTGAC 59.201 52.381 0.00 0.00 0.00 3.18
160 161 0.801067 ATCGGCGTCGTTTGCTCTAC 60.801 55.000 10.18 0.00 37.69 2.59
228 229 2.959484 CGCCTTCTTCAGCCTCCCA 61.959 63.158 0.00 0.00 0.00 4.37
236 237 0.108585 AAGCCACTTCGCCTTCTTCA 59.891 50.000 0.00 0.00 0.00 3.02
246 247 2.237392 AGGATCCAGTACAAGCCACTTC 59.763 50.000 15.82 0.00 0.00 3.01
252 253 3.334583 TGAACAGGATCCAGTACAAGC 57.665 47.619 15.82 1.30 0.00 4.01
258 259 1.673767 ACCCATGAACAGGATCCAGT 58.326 50.000 15.82 9.70 0.00 4.00
279 280 3.363378 CGTGAAGCTAGTTTGCAGAAGTG 60.363 47.826 0.00 0.00 34.99 3.16
302 303 0.690762 GTAACAAGCTCCTCCACCCA 59.309 55.000 0.00 0.00 0.00 4.51
306 307 1.053424 AACGGTAACAAGCTCCTCCA 58.947 50.000 0.00 0.00 0.00 3.86
313 314 2.415512 GTCAGGATCAACGGTAACAAGC 59.584 50.000 0.00 0.00 0.00 4.01
399 439 1.546923 CACTGAAATTCCATGGCAGCA 59.453 47.619 6.96 0.00 0.00 4.41
400 440 1.820519 TCACTGAAATTCCATGGCAGC 59.179 47.619 6.96 0.00 0.00 5.25
427 467 3.444388 ACGTCCCTACAAGAGATTCAGAC 59.556 47.826 0.00 0.00 0.00 3.51
444 484 1.521681 GTCCAGCAGGCATACGTCC 60.522 63.158 0.00 0.00 33.74 4.79
603 690 3.347077 CCATGAGAGAAGTTCAAGGCT 57.653 47.619 5.50 0.00 0.00 4.58
606 693 2.419324 GCAGCCATGAGAGAAGTTCAAG 59.581 50.000 5.50 0.00 0.00 3.02
624 711 1.002033 GGTGTCAGAAAACAGCTGCAG 60.002 52.381 15.27 10.11 42.82 4.41
644 731 1.062148 CAAGCACATGAGCATGAGACG 59.938 52.381 17.61 4.11 41.20 4.18
677 764 6.201226 TCTATCAGTACTGACAGAGCAAAG 57.799 41.667 26.33 14.01 38.13 2.77
706 793 4.994471 TGCCGCTCCTGTGTGCTG 62.994 66.667 0.00 0.00 0.00 4.41
710 797 4.320456 CACCTGCCGCTCCTGTGT 62.320 66.667 0.00 0.00 0.00 3.72
715 802 2.543067 AAAGATCCACCTGCCGCTCC 62.543 60.000 0.00 0.00 0.00 4.70
717 804 0.962356 CAAAAGATCCACCTGCCGCT 60.962 55.000 0.00 0.00 0.00 5.52
718 805 1.508088 CAAAAGATCCACCTGCCGC 59.492 57.895 0.00 0.00 0.00 6.53
719 806 1.937546 GCCAAAAGATCCACCTGCCG 61.938 60.000 0.00 0.00 0.00 5.69
771 863 1.753078 TCTACCTGCGCCTGATCGT 60.753 57.895 4.18 0.00 0.00 3.73
850 950 2.887568 GACACGAGCGCCATCTGG 60.888 66.667 2.29 0.00 38.53 3.86
968 1068 0.456221 CAGGAAGCAGACGTACGGAT 59.544 55.000 21.06 4.25 0.00 4.18
1671 2174 2.049802 ACGTTGTAGGTGACGCGG 60.050 61.111 12.47 0.00 42.67 6.46
1839 2342 1.585006 GTCCTCGAAGAAGGCGACA 59.415 57.895 0.00 0.00 34.09 4.35
1908 2411 2.736531 GCCTTGCCAAACACCTGG 59.263 61.111 0.00 0.00 39.71 4.45
1989 2492 0.301687 GCTCATTGTATGTGACGGCG 59.698 55.000 4.80 4.80 0.00 6.46
2067 2570 1.414181 AGTAGCCCCTTGTCGATCATG 59.586 52.381 0.00 0.00 0.00 3.07
2083 2586 0.865769 GTGAACGTGTTGGGCAGTAG 59.134 55.000 0.00 0.00 0.00 2.57
2085 2588 1.822186 GGTGAACGTGTTGGGCAGT 60.822 57.895 0.00 0.00 0.00 4.40
2127 2630 1.383799 CACCTTCCCAGCATTCCCA 59.616 57.895 0.00 0.00 0.00 4.37
2136 2639 3.319198 GCCTCGTCCACCTTCCCA 61.319 66.667 0.00 0.00 0.00 4.37
2157 2660 3.782443 ATCCGGTCGAACAGGGCC 61.782 66.667 0.00 0.00 34.05 5.80
2208 2711 3.470709 CATGCCGAGGACAAGATTGTAT 58.529 45.455 0.00 0.00 42.43 2.29
2267 2770 3.187699 CTCGACATCTCCCCGAGCG 62.188 68.421 0.00 0.00 42.34 5.03
2457 2960 2.966309 CTTGAACGCGTTGGCCCTC 61.966 63.158 31.89 14.70 35.02 4.30
2469 2972 7.128331 CGGTCATTTCATCATACATCTTGAAC 58.872 38.462 0.00 0.00 0.00 3.18
2502 3005 2.044946 GTGAGGCAAGGGGCGAAT 60.045 61.111 0.00 0.00 46.16 3.34
2635 3138 2.595463 GTGGCACTGGAGCAGCAA 60.595 61.111 11.13 0.00 34.37 3.91
2708 3211 9.289782 TCTTATATTAGTTTACGGAGGGAGTAC 57.710 37.037 0.00 0.00 0.00 2.73
2709 3212 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
2710 3213 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
2711 3214 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
2712 3215 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
2713 3216 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
2714 3217 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
2715 3218 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
2716 3219 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
2717 3220 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
2731 3234 9.570488 CACTACTTTAGTATTCTAAACGCTCTT 57.430 33.333 0.76 0.00 40.05 2.85
2732 3235 8.954350 TCACTACTTTAGTATTCTAAACGCTCT 58.046 33.333 0.76 0.00 40.05 4.09
2733 3236 9.733219 ATCACTACTTTAGTATTCTAAACGCTC 57.267 33.333 0.76 0.00 40.05 5.03
2734 3237 9.733219 GATCACTACTTTAGTATTCTAAACGCT 57.267 33.333 0.76 0.00 40.05 5.07
2735 3238 9.733219 AGATCACTACTTTAGTATTCTAAACGC 57.267 33.333 0.76 0.00 40.05 4.84
2764 3267 9.381038 TCCCTCTGTAAACTAATATAAGAGCAT 57.619 33.333 0.00 0.00 0.00 3.79
2765 3268 8.777578 TCCCTCTGTAAACTAATATAAGAGCA 57.222 34.615 0.00 0.00 0.00 4.26
2766 3269 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
2770 3273 9.940974 TGGTACTCCCTCTGTAAACTAATATAA 57.059 33.333 0.00 0.00 0.00 0.98
2772 3275 9.091220 GATGGTACTCCCTCTGTAAACTAATAT 57.909 37.037 0.00 0.00 0.00 1.28
2773 3276 8.287350 AGATGGTACTCCCTCTGTAAACTAATA 58.713 37.037 0.00 0.00 37.33 0.98
2774 3277 7.133483 AGATGGTACTCCCTCTGTAAACTAAT 58.867 38.462 0.00 0.00 37.33 1.73
2775 3278 6.500336 AGATGGTACTCCCTCTGTAAACTAA 58.500 40.000 0.00 0.00 37.33 2.24
2776 3279 6.088541 AGATGGTACTCCCTCTGTAAACTA 57.911 41.667 0.00 0.00 37.33 2.24
2777 3280 4.949121 AGATGGTACTCCCTCTGTAAACT 58.051 43.478 0.00 0.00 37.33 2.66
2778 3281 5.395435 GGAAGATGGTACTCCCTCTGTAAAC 60.395 48.000 0.00 0.00 38.42 2.01
2779 3282 4.715297 GGAAGATGGTACTCCCTCTGTAAA 59.285 45.833 0.00 0.00 38.42 2.01
2780 3283 4.287552 GGAAGATGGTACTCCCTCTGTAA 58.712 47.826 0.00 0.00 38.42 2.41
2781 3284 3.373877 GGGAAGATGGTACTCCCTCTGTA 60.374 52.174 9.40 0.00 38.42 2.74
2782 3285 2.627217 GGGAAGATGGTACTCCCTCTGT 60.627 54.545 9.40 0.00 38.42 3.41
2783 3286 2.043227 GGGAAGATGGTACTCCCTCTG 58.957 57.143 9.40 0.00 38.42 3.35
2784 3287 1.411787 CGGGAAGATGGTACTCCCTCT 60.412 57.143 13.64 0.00 39.74 3.69
2785 3288 1.041437 CGGGAAGATGGTACTCCCTC 58.959 60.000 13.64 0.00 38.44 4.30
2786 3289 0.635009 TCGGGAAGATGGTACTCCCT 59.365 55.000 13.64 0.00 38.44 4.20
2787 3290 1.041437 CTCGGGAAGATGGTACTCCC 58.959 60.000 7.01 7.01 37.28 4.30
2788 3291 0.389757 GCTCGGGAAGATGGTACTCC 59.610 60.000 0.00 0.00 0.00 3.85
2789 3292 1.067821 CAGCTCGGGAAGATGGTACTC 59.932 57.143 0.00 0.00 37.76 2.59
2790 3293 1.115467 CAGCTCGGGAAGATGGTACT 58.885 55.000 0.00 0.00 37.76 2.73
2861 3364 3.153270 GAACGCCCTCTCGATCCCC 62.153 68.421 0.00 0.00 0.00 4.81
3005 3508 1.758514 GATCAGGTCCGGGCTCAGA 60.759 63.158 5.77 1.47 0.00 3.27
3137 3640 3.633951 GACACCACGTCGGGTTTC 58.366 61.111 8.57 2.78 39.79 2.78
3601 4108 3.854669 CTACGCTCCCCTGCCCTG 61.855 72.222 0.00 0.00 0.00 4.45
3604 4111 1.831652 ATATGCTACGCTCCCCTGCC 61.832 60.000 0.00 0.00 0.00 4.85
3605 4112 0.035458 AATATGCTACGCTCCCCTGC 59.965 55.000 0.00 0.00 0.00 4.85
3637 4144 5.766222 CCATTTTGCAGCACTATCTTATCC 58.234 41.667 0.00 0.00 0.00 2.59
3705 4212 2.652662 GCCGAATGCGACTTTCATAG 57.347 50.000 0.00 0.00 40.82 2.23
3745 4252 5.869579 AGCACCTCAAAATTCAGACTCTTA 58.130 37.500 0.00 0.00 0.00 2.10
3774 4282 1.194997 TCCGCAAAACCAAACGATACG 59.805 47.619 0.00 0.00 0.00 3.06
3792 4300 5.278169 CCTTGCTGCTTCATGTACATATTCC 60.278 44.000 8.32 0.00 0.00 3.01
3799 4307 2.813754 TCAACCTTGCTGCTTCATGTAC 59.186 45.455 0.00 0.00 0.00 2.90
3800 4308 3.076621 CTCAACCTTGCTGCTTCATGTA 58.923 45.455 0.00 0.00 0.00 2.29
3801 4309 1.884579 CTCAACCTTGCTGCTTCATGT 59.115 47.619 0.00 0.00 0.00 3.21
3802 4310 1.402456 GCTCAACCTTGCTGCTTCATG 60.402 52.381 0.00 0.00 0.00 3.07
3803 4311 0.886563 GCTCAACCTTGCTGCTTCAT 59.113 50.000 0.00 0.00 0.00 2.57
3805 4313 2.638744 AGCTCAACCTTGCTGCTTC 58.361 52.632 0.00 0.00 38.21 3.86
3818 4356 0.700564 AGAATTTGGGGAGCAGCTCA 59.299 50.000 24.09 3.10 31.08 4.26
3830 4368 6.965500 GTGAGAATGATGCACAGTAGAATTTG 59.035 38.462 0.00 0.00 32.96 2.32
3833 4371 5.987098 AGTGAGAATGATGCACAGTAGAAT 58.013 37.500 0.00 0.00 35.08 2.40
3835 4373 5.173664 CAAGTGAGAATGATGCACAGTAGA 58.826 41.667 0.00 0.00 35.08 2.59
3836 4374 4.201792 GCAAGTGAGAATGATGCACAGTAG 60.202 45.833 0.00 0.00 37.00 2.57
3837 4375 3.686241 GCAAGTGAGAATGATGCACAGTA 59.314 43.478 0.00 0.00 37.00 2.74
3838 4376 2.486982 GCAAGTGAGAATGATGCACAGT 59.513 45.455 0.00 0.00 37.00 3.55
3839 4377 2.747989 AGCAAGTGAGAATGATGCACAG 59.252 45.455 0.00 0.00 39.42 3.66
3840 4378 2.486592 CAGCAAGTGAGAATGATGCACA 59.513 45.455 0.00 0.00 39.42 4.57
3841 4379 2.745821 TCAGCAAGTGAGAATGATGCAC 59.254 45.455 0.00 0.00 39.42 4.57
3842 4380 3.062122 TCAGCAAGTGAGAATGATGCA 57.938 42.857 0.00 0.00 39.42 3.96
3843 4381 3.731264 GCTTCAGCAAGTGAGAATGATGC 60.731 47.826 0.00 0.00 41.59 3.91
3845 4383 3.015327 GGCTTCAGCAAGTGAGAATGAT 58.985 45.455 0.30 0.00 44.36 2.45
3846 4384 2.039480 AGGCTTCAGCAAGTGAGAATGA 59.961 45.455 0.30 0.00 44.36 2.57
3847 4385 2.161808 CAGGCTTCAGCAAGTGAGAATG 59.838 50.000 0.30 0.00 44.36 2.67
3879 4478 3.190874 GGTTCAGATACAGCTACTGCAC 58.809 50.000 0.00 0.00 42.74 4.57
3892 4491 0.036388 ATTGCACCGACGGTTCAGAT 60.036 50.000 19.02 11.95 29.63 2.90
3898 4501 1.153353 CTAAACATTGCACCGACGGT 58.847 50.000 15.37 15.37 35.62 4.83
3904 4507 3.620488 TGATCTCCCTAAACATTGCACC 58.380 45.455 0.00 0.00 0.00 5.01
3908 4511 5.582689 GGGTTTGATCTCCCTAAACATTG 57.417 43.478 11.93 0.00 40.48 2.82
3922 4525 3.072915 TGAGTGACATGACAGGGTTTGAT 59.927 43.478 0.00 0.00 0.00 2.57
3929 4532 3.507622 TGACTAGTGAGTGACATGACAGG 59.492 47.826 0.00 0.00 35.45 4.00
3944 4547 3.231818 AGTGTGTAGCCAAGTGACTAGT 58.768 45.455 0.00 0.00 0.00 2.57
3947 4550 2.838736 CAAGTGTGTAGCCAAGTGACT 58.161 47.619 0.00 0.00 0.00 3.41
3948 4551 1.264288 GCAAGTGTGTAGCCAAGTGAC 59.736 52.381 0.00 0.00 0.00 3.67
3986 4589 0.819259 TGACAAACTCACAGCCAGGC 60.819 55.000 1.84 1.84 0.00 4.85
3997 4600 6.777580 ACCCAGAATAAAATCTGTGACAAACT 59.222 34.615 3.86 0.00 44.32 2.66
4030 4633 3.214328 ACGCTTGAGAATGACAAAACCT 58.786 40.909 0.00 0.00 0.00 3.50
4038 4641 4.158579 AGACATACAGACGCTTGAGAATGA 59.841 41.667 0.00 0.00 0.00 2.57
4041 4644 3.506067 TCAGACATACAGACGCTTGAGAA 59.494 43.478 0.00 0.00 0.00 2.87
4042 4645 3.081804 TCAGACATACAGACGCTTGAGA 58.918 45.455 0.00 0.00 0.00 3.27
4043 4646 3.119673 ACTCAGACATACAGACGCTTGAG 60.120 47.826 0.00 0.00 0.00 3.02
4044 4647 2.820197 ACTCAGACATACAGACGCTTGA 59.180 45.455 0.00 0.00 0.00 3.02
4045 4648 3.223423 ACTCAGACATACAGACGCTTG 57.777 47.619 0.00 0.00 0.00 4.01
4046 4649 3.579709 CAACTCAGACATACAGACGCTT 58.420 45.455 0.00 0.00 0.00 4.68
4047 4650 2.672478 GCAACTCAGACATACAGACGCT 60.672 50.000 0.00 0.00 0.00 5.07
4048 4651 1.656095 GCAACTCAGACATACAGACGC 59.344 52.381 0.00 0.00 0.00 5.19
4049 4652 3.175152 GAGCAACTCAGACATACAGACG 58.825 50.000 0.00 0.00 0.00 4.18
4051 4654 3.165071 TGGAGCAACTCAGACATACAGA 58.835 45.455 0.00 0.00 31.08 3.41
4052 4655 3.194329 TCTGGAGCAACTCAGACATACAG 59.806 47.826 0.00 0.00 31.08 2.74
4054 4657 3.876274 TCTGGAGCAACTCAGACATAC 57.124 47.619 0.00 0.00 31.08 2.39
4064 4694 5.847304 TGATACTACATCATCTGGAGCAAC 58.153 41.667 0.00 0.00 39.74 4.17
4082 4712 7.446625 AGAAACCAGCTCCATATCAAATGATAC 59.553 37.037 5.30 0.00 39.57 2.24
4083 4713 7.446319 CAGAAACCAGCTCCATATCAAATGATA 59.554 37.037 5.64 5.64 40.85 2.15
4094 4724 2.290577 GGACTTCAGAAACCAGCTCCAT 60.291 50.000 0.00 0.00 0.00 3.41
4140 4778 1.398390 CTGCCGCACATTTAGACTTCC 59.602 52.381 0.00 0.00 0.00 3.46
4147 4785 1.742411 GCTACTCCTGCCGCACATTTA 60.742 52.381 0.00 0.00 0.00 1.40
4180 4818 2.428925 GGTGAGGGGCCGTAATCGA 61.429 63.158 0.00 0.00 39.71 3.59
4183 4821 2.070650 GGAGGTGAGGGGCCGTAAT 61.071 63.158 0.00 0.00 0.00 1.89
4196 4834 2.050144 AGATTATGCACGGATGGAGGT 58.950 47.619 0.00 0.00 0.00 3.85
4197 4835 2.847327 AGATTATGCACGGATGGAGG 57.153 50.000 0.00 0.00 0.00 4.30
4198 4836 3.251729 CCAAAGATTATGCACGGATGGAG 59.748 47.826 0.00 0.00 0.00 3.86
4199 4837 3.213506 CCAAAGATTATGCACGGATGGA 58.786 45.455 0.00 0.00 0.00 3.41
4202 4840 1.956477 GGCCAAAGATTATGCACGGAT 59.044 47.619 0.00 0.00 0.00 4.18
4210 4848 3.056607 GCAAGTGTGTGGCCAAAGATTAT 60.057 43.478 7.24 0.00 0.00 1.28
4230 4868 1.024271 GGAAGTTGACAGCTTGTGCA 58.976 50.000 9.49 0.00 42.74 4.57
4232 4870 2.033801 CCAAGGAAGTTGACAGCTTGTG 59.966 50.000 9.49 4.93 38.60 3.33
4234 4872 1.000938 GCCAAGGAAGTTGACAGCTTG 60.001 52.381 9.49 0.00 38.60 4.01
4237 4875 1.807142 GTAGCCAAGGAAGTTGACAGC 59.193 52.381 0.00 0.00 38.60 4.40
4248 4886 2.485426 CACTGAATGTGTGTAGCCAAGG 59.515 50.000 0.00 0.00 41.53 3.61
4286 4924 4.142204 GGAACTGTCCAAGTACTACTAGCC 60.142 50.000 0.00 0.00 44.26 3.93
4320 4958 4.135153 AGAGTAGCAGCGTGGGCG 62.135 66.667 0.00 0.00 46.35 6.13
4327 4969 0.528249 GAGCAGAGCAGAGTAGCAGC 60.528 60.000 0.00 0.00 36.85 5.25
4396 5040 3.060020 GAACGGACAGGGCGATCGA 62.060 63.158 21.57 0.00 0.00 3.59
4406 5050 0.033796 ATCGAGGGGTAGAACGGACA 60.034 55.000 0.00 0.00 0.00 4.02
4420 5064 2.158058 GGGTAGAACGAGATCGATCGAG 59.842 54.545 23.84 18.31 45.56 4.04
4424 5068 1.236628 CCGGGTAGAACGAGATCGAT 58.763 55.000 9.58 0.00 43.02 3.59
4425 5069 1.442526 GCCGGGTAGAACGAGATCGA 61.443 60.000 9.58 0.00 43.02 3.59
4426 5070 1.008767 GCCGGGTAGAACGAGATCG 60.009 63.158 2.18 0.00 46.33 3.69
4427 5071 1.008767 CGCCGGGTAGAACGAGATC 60.009 63.158 2.18 0.00 0.00 2.75
4428 5072 2.487532 CCGCCGGGTAGAACGAGAT 61.488 63.158 2.18 0.00 0.00 2.75
4429 5073 3.136123 CCGCCGGGTAGAACGAGA 61.136 66.667 2.18 0.00 0.00 4.04
4430 5074 4.867599 GCCGCCGGGTAGAACGAG 62.868 72.222 4.77 0.00 34.97 4.18
4449 5093 4.477975 CTCCCTCGTGTCGCCGTC 62.478 72.222 0.00 0.00 0.00 4.79
4464 5108 4.681978 AGAACGTGTGGCGCCCTC 62.682 66.667 26.77 17.83 46.11 4.30
4465 5109 4.988598 CAGAACGTGTGGCGCCCT 62.989 66.667 26.77 8.89 46.11 5.19
4470 5114 3.660111 GCACCCAGAACGTGTGGC 61.660 66.667 11.07 0.00 33.24 5.01
4471 5115 2.978010 GGCACCCAGAACGTGTGG 60.978 66.667 9.79 9.79 33.61 4.17
4472 5116 1.961277 GAGGCACCCAGAACGTGTG 60.961 63.158 0.00 0.00 33.61 3.82
4473 5117 2.426023 GAGGCACCCAGAACGTGT 59.574 61.111 0.00 0.00 33.61 4.49
4474 5118 2.358737 GGAGGCACCCAGAACGTG 60.359 66.667 0.00 0.00 0.00 4.49
4475 5119 2.847234 TGGAGGCACCCAGAACGT 60.847 61.111 0.00 0.00 38.00 3.99
4476 5120 2.358737 GTGGAGGCACCCAGAACG 60.359 66.667 0.00 0.00 36.78 3.95
4477 5121 2.358737 CGTGGAGGCACCCAGAAC 60.359 66.667 0.00 0.00 36.78 3.01
4478 5122 3.636231 CCGTGGAGGCACCCAGAA 61.636 66.667 0.00 0.00 36.78 3.02


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

AutoCloner maintained by Alex Coulton.