Multiple sequence alignment - TraesCS4A01G342200

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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 TraesCS4A01G342200 chr4A 100.000 6277 0 0 1 6277 622174640 622180916 0.000000e+00 11592.0
1 TraesCS4A01G342200 chr4A 78.235 510 56 39 970 1446 622248259 622247772 6.200000e-70 276.0
2 TraesCS4A01G342200 chr4A 84.112 214 19 3 1318 1531 622246097 622245899 6.420000e-45 193.0
3 TraesCS4A01G342200 chr4A 76.585 410 58 17 1790 2163 622245796 622245389 2.310000e-44 191.0
4 TraesCS4A01G342200 chr5B 92.040 2613 151 29 2 2599 689900114 689902684 0.000000e+00 3620.0
5 TraesCS4A01G342200 chr5B 91.012 2659 120 35 2993 5596 689903139 689905733 0.000000e+00 3476.0
6 TraesCS4A01G342200 chr5B 89.414 444 30 7 2659 3086 689902691 689903133 1.540000e-150 544.0
7 TraesCS4A01G342200 chr5B 86.453 406 28 14 5876 6260 689906637 689907036 2.710000e-113 420.0
8 TraesCS4A01G342200 chr5B 84.211 247 16 12 5625 5868 689906064 689906290 1.060000e-52 219.0
9 TraesCS4A01G342200 chr5B 85.586 111 14 2 1309 1418 689882011 689882120 1.430000e-21 115.0
10 TraesCS4A01G342200 chr5D 91.336 2620 135 44 2 2599 546826227 546823678 0.000000e+00 3496.0
11 TraesCS4A01G342200 chr5D 92.011 1890 79 24 2646 4499 546823676 546821823 0.000000e+00 2588.0
12 TraesCS4A01G342200 chr5D 89.593 1057 76 20 4518 5550 546821838 546820792 0.000000e+00 1312.0
13 TraesCS4A01G342200 chr5D 83.059 425 29 20 5876 6277 546819908 546819504 4.660000e-91 346.0
14 TraesCS4A01G342200 chr5D 76.433 471 38 33 971 1432 546682611 546683017 2.990000e-43 187.0
15 TraesCS4A01G342200 chr3B 80.263 456 60 12 3281 3728 806244739 806244306 3.650000e-82 316.0
16 TraesCS4A01G342200 chr3A 88.764 178 19 1 3270 3446 729155899 729155722 3.810000e-52 217.0
17 TraesCS4A01G342200 chr7A 83.163 196 32 1 3260 3454 11756326 11756521 1.800000e-40 178.0
18 TraesCS4A01G342200 chr7D 82.143 196 34 1 3260 3454 12307156 12307351 3.890000e-37 167.0
19 TraesCS4A01G342200 chr6D 95.122 41 2 0 4893 4933 142149661 142149701 1.460000e-06 65.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G342200 chr4A 622174640 622180916 6276 False 11592.0 11592 100.00000 1 6277 1 chr4A.!!$F1 6276
1 TraesCS4A01G342200 chr4A 622245389 622248259 2870 True 220.0 276 79.64400 970 2163 3 chr4A.!!$R1 1193
2 TraesCS4A01G342200 chr5B 689900114 689907036 6922 False 1655.8 3620 88.62600 2 6260 5 chr5B.!!$F2 6258
3 TraesCS4A01G342200 chr5D 546819504 546826227 6723 True 1935.5 3496 88.99975 2 6277 4 chr5D.!!$R1 6275

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
32 33 0.321346 TCTTTGCCATGTCGAGCTCA 59.679 50.000 15.4 0.0 0.00 4.26 F
215 216 0.469070 GCTCCATCATCTGGCTGAGT 59.531 55.000 0.0 0.0 45.52 3.41 F
1638 1700 0.630673 TCTATGGTTTGGCAGGGCAT 59.369 50.000 0.0 0.0 0.00 4.40 F
1712 1774 0.976641 ATTTCGAGAGGGTGACTGCA 59.023 50.000 0.0 0.0 0.00 4.41 F
1808 1870 1.064906 CCTGACAGTGATGCCTGGATT 60.065 52.381 0.0 0.0 36.75 3.01 F
2258 2361 1.068588 GGGAACTCAAAACAGGCAACC 59.931 52.381 0.0 0.0 37.17 3.77 F
2532 2639 1.336240 GCAGGCATTCTTTGGACACAC 60.336 52.381 0.0 0.0 0.00 3.82 F
2896 3014 1.550976 GAGGAAGAAGAAGCCCTCGAA 59.449 52.381 0.0 0.0 36.26 3.71 F
4409 4865 0.179119 GCATGATTCAGTGGCTTGGC 60.179 55.000 0.0 0.0 0.00 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1872 1936 0.924823 ATTTCAGAGGAGCCCTGCAT 59.075 50.000 0.00 0.00 31.76 3.96 R
1949 2020 2.097142 GCTCTGAAACAATGCTGGCTAG 59.903 50.000 0.00 0.00 0.00 3.42 R
2506 2613 0.529378 CAAAGAATGCCTGCCAGGTC 59.471 55.000 13.35 5.41 37.80 3.85 R
2650 2758 0.947660 CACGCCGCATAGCATCATCT 60.948 55.000 0.00 0.00 0.00 2.90 R
3567 3998 1.112113 GAATGAGGAGCCGTACCTGA 58.888 55.000 0.00 0.00 37.93 3.86 R
4201 4656 1.064505 CCTTCTAATGGCGTGCATGTG 59.935 52.381 7.93 0.00 0.00 3.21 R
4408 4864 0.391130 TTCCTGTACCTGTGATGCGC 60.391 55.000 0.00 0.00 0.00 6.09 R
4775 5238 1.862602 GCCGTGGAACCATGAACACC 61.863 60.000 13.85 0.00 35.09 4.16 R
5400 5893 0.246360 TCGTGAATCGTGTGGCTGAT 59.754 50.000 0.00 0.00 40.80 2.90 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
32 33 0.321346 TCTTTGCCATGTCGAGCTCA 59.679 50.000 15.40 0.00 0.00 4.26
66 67 2.152013 GAAATCGATCAGCGCGCTCC 62.152 60.000 34.28 21.62 40.61 4.70
202 203 2.765807 CTCCACTCCCCGCTCCAT 60.766 66.667 0.00 0.00 0.00 3.41
211 212 2.815945 CCCGCTCCATCATCTGGCT 61.816 63.158 0.00 0.00 45.52 4.75
215 216 0.469070 GCTCCATCATCTGGCTGAGT 59.531 55.000 0.00 0.00 45.52 3.41
227 228 4.079850 CTGAGTGCCTCCGCTGCT 62.080 66.667 0.00 0.00 35.36 4.24
228 229 4.074526 TGAGTGCCTCCGCTGCTC 62.075 66.667 0.00 0.00 37.84 4.26
536 543 4.031719 ATCTCGATCGCGGCCTCG 62.032 66.667 9.35 9.35 38.28 4.63
578 585 4.436998 GACACGGCCGAGGTCCAG 62.437 72.222 35.90 13.98 0.00 3.86
788 795 1.377725 GTGTCCACTCCCATGGCAG 60.378 63.158 6.09 2.72 39.85 4.85
789 796 2.439156 GTCCACTCCCATGGCAGC 60.439 66.667 6.09 0.00 39.85 5.25
790 797 2.934932 TCCACTCCCATGGCAGCA 60.935 61.111 6.09 0.00 39.85 4.41
791 798 2.439701 CCACTCCCATGGCAGCAG 60.440 66.667 6.09 0.00 31.52 4.24
792 799 2.672908 CACTCCCATGGCAGCAGA 59.327 61.111 6.09 0.00 0.00 4.26
793 800 1.451567 CACTCCCATGGCAGCAGAG 60.452 63.158 6.09 9.81 0.00 3.35
794 801 1.614525 ACTCCCATGGCAGCAGAGA 60.615 57.895 18.51 3.62 0.00 3.10
795 802 1.146485 CTCCCATGGCAGCAGAGAG 59.854 63.158 6.09 1.55 0.00 3.20
796 803 2.516460 CCCATGGCAGCAGAGAGC 60.516 66.667 6.09 0.00 46.19 4.09
818 827 2.281484 GCCGCAGAGGAACCAACA 60.281 61.111 0.00 0.00 45.00 3.33
850 863 2.012673 GATAAGCTTCAGCCCAGTGTG 58.987 52.381 0.00 0.00 43.38 3.82
871 884 1.683365 AATTGGGCCGCAATGCTCT 60.683 52.632 17.06 2.68 31.16 4.09
881 894 4.473520 AATGCTCTCGTGGGCCGG 62.474 66.667 6.92 0.00 37.11 6.13
1556 1615 0.808125 TTCGGTTCATTTGGGCATCG 59.192 50.000 0.00 0.00 0.00 3.84
1638 1700 0.630673 TCTATGGTTTGGCAGGGCAT 59.369 50.000 0.00 0.00 0.00 4.40
1712 1774 0.976641 ATTTCGAGAGGGTGACTGCA 59.023 50.000 0.00 0.00 0.00 4.41
1808 1870 1.064906 CCTGACAGTGATGCCTGGATT 60.065 52.381 0.00 0.00 36.75 3.01
1867 1931 5.689068 GTGGCTTCATATGCTCAATTTTAGC 59.311 40.000 0.00 3.09 40.50 3.09
1872 1936 7.255590 GCTTCATATGCTCAATTTTAGCCCTTA 60.256 37.037 0.00 0.00 39.30 2.69
1895 1959 2.883386 GCAGGGCTCCTCTGAAATTATG 59.117 50.000 0.00 0.00 34.36 1.90
1949 2020 6.142320 CGTTGGTTAAATCAAAGCTGAACTTC 59.858 38.462 0.00 0.00 37.75 3.01
1969 2041 3.603532 TCTAGCCAGCATTGTTTCAGAG 58.396 45.455 0.00 0.00 0.00 3.35
1981 2053 3.538591 TGTTTCAGAGCATATGCCTCTG 58.461 45.455 30.91 30.91 42.35 3.35
2005 2080 3.626217 ACATGATGTGACATAGCTTGCAG 59.374 43.478 0.00 0.00 0.00 4.41
2011 2086 2.675348 GTGACATAGCTTGCAGGAAGTC 59.325 50.000 0.00 1.91 33.73 3.01
2020 2095 4.702131 AGCTTGCAGGAAGTCGATTAATTT 59.298 37.500 0.00 0.00 33.73 1.82
2055 2134 4.280789 ACCATCCTAGAAGGTGATACCA 57.719 45.455 0.28 0.00 41.95 3.25
2056 2135 4.832492 ACCATCCTAGAAGGTGATACCAT 58.168 43.478 0.28 0.00 41.95 3.55
2110 2205 7.856145 ATATCAAGACAACAATCTGGTCTTC 57.144 36.000 3.48 0.00 45.94 2.87
2221 2324 5.724328 ACGACATTAATCTCAGACATGTGT 58.276 37.500 1.15 0.00 0.00 3.72
2258 2361 1.068588 GGGAACTCAAAACAGGCAACC 59.931 52.381 0.00 0.00 37.17 3.77
2308 2412 4.260985 CTCATTGTACATGCCTGTGGTTA 58.739 43.478 4.73 0.00 36.79 2.85
2372 2478 9.184523 CATAAGGGTGAAGGTGTATTCAATTAA 57.815 33.333 0.00 0.00 40.72 1.40
2473 2580 6.871844 TCTTCTGTCATTCTATGAAGGTCTG 58.128 40.000 0.00 0.00 41.69 3.51
2495 2602 9.712359 GTCTGTTTAGAATAGTCGTTTGTTTTT 57.288 29.630 0.00 0.00 34.01 1.94
2520 2627 2.056223 GCATGACCTGGCAGGCATT 61.056 57.895 33.04 14.66 44.30 3.56
2532 2639 1.336240 GCAGGCATTCTTTGGACACAC 60.336 52.381 0.00 0.00 0.00 3.82
2551 2658 6.930731 ACACACTGGAAAAGTAAATGTGTTT 58.069 32.000 1.43 0.00 38.49 2.83
2595 2703 3.748048 CGTTTGTTCTCCATCATGTGTCT 59.252 43.478 0.00 0.00 0.00 3.41
2599 2707 5.169992 TGTTCTCCATCATGTGTCTTCAT 57.830 39.130 0.00 0.00 0.00 2.57
2600 2708 5.181009 TGTTCTCCATCATGTGTCTTCATC 58.819 41.667 0.00 0.00 0.00 2.92
2601 2709 4.412796 TCTCCATCATGTGTCTTCATCC 57.587 45.455 0.00 0.00 0.00 3.51
2602 2710 4.035814 TCTCCATCATGTGTCTTCATCCT 58.964 43.478 0.00 0.00 0.00 3.24
2603 2711 4.127907 CTCCATCATGTGTCTTCATCCTG 58.872 47.826 0.00 0.00 0.00 3.86
2604 2712 3.118149 TCCATCATGTGTCTTCATCCTGG 60.118 47.826 0.00 0.00 32.32 4.45
2605 2713 3.211865 CATCATGTGTCTTCATCCTGGG 58.788 50.000 0.00 0.00 0.00 4.45
2606 2714 2.550175 TCATGTGTCTTCATCCTGGGA 58.450 47.619 0.00 0.00 0.00 4.37
2607 2715 2.502947 TCATGTGTCTTCATCCTGGGAG 59.497 50.000 0.00 0.00 0.00 4.30
2608 2716 2.325661 TGTGTCTTCATCCTGGGAGA 57.674 50.000 0.00 0.00 0.00 3.71
2609 2717 2.619931 TGTGTCTTCATCCTGGGAGAA 58.380 47.619 0.00 0.00 0.00 2.87
2610 2718 3.184628 TGTGTCTTCATCCTGGGAGAAT 58.815 45.455 0.00 0.00 0.00 2.40
2611 2719 3.588842 TGTGTCTTCATCCTGGGAGAATT 59.411 43.478 0.00 0.00 0.00 2.17
2612 2720 3.944015 GTGTCTTCATCCTGGGAGAATTG 59.056 47.826 0.00 0.00 0.00 2.32
2613 2721 3.588842 TGTCTTCATCCTGGGAGAATTGT 59.411 43.478 0.00 0.00 0.00 2.71
2614 2722 4.782691 TGTCTTCATCCTGGGAGAATTGTA 59.217 41.667 0.00 0.00 0.00 2.41
2615 2723 5.429762 TGTCTTCATCCTGGGAGAATTGTAT 59.570 40.000 0.00 0.00 0.00 2.29
2616 2724 5.762218 GTCTTCATCCTGGGAGAATTGTATG 59.238 44.000 0.00 0.00 0.00 2.39
2617 2725 4.090761 TCATCCTGGGAGAATTGTATGC 57.909 45.455 0.00 0.00 0.00 3.14
2618 2726 3.718434 TCATCCTGGGAGAATTGTATGCT 59.282 43.478 0.00 0.00 0.00 3.79
2619 2727 3.565764 TCCTGGGAGAATTGTATGCTG 57.434 47.619 0.00 0.00 0.00 4.41
2620 2728 1.952296 CCTGGGAGAATTGTATGCTGC 59.048 52.381 0.00 0.00 0.00 5.25
2621 2729 2.646930 CTGGGAGAATTGTATGCTGCA 58.353 47.619 4.13 4.13 0.00 4.41
2622 2730 3.018856 CTGGGAGAATTGTATGCTGCAA 58.981 45.455 6.36 0.00 0.00 4.08
2623 2731 3.634504 TGGGAGAATTGTATGCTGCAAT 58.365 40.909 6.36 0.00 38.09 3.56
2624 2732 4.790937 TGGGAGAATTGTATGCTGCAATA 58.209 39.130 6.36 0.00 35.73 1.90
2625 2733 5.387788 TGGGAGAATTGTATGCTGCAATAT 58.612 37.500 6.36 0.00 35.73 1.28
2626 2734 5.834742 TGGGAGAATTGTATGCTGCAATATT 59.165 36.000 6.36 4.10 35.73 1.28
2627 2735 6.154445 GGGAGAATTGTATGCTGCAATATTG 58.846 40.000 6.36 11.27 35.73 1.90
2628 2736 6.016024 GGGAGAATTGTATGCTGCAATATTGA 60.016 38.462 19.73 3.79 35.73 2.57
2629 2737 7.082602 GGAGAATTGTATGCTGCAATATTGAG 58.917 38.462 19.73 13.56 35.73 3.02
2630 2738 7.255381 GGAGAATTGTATGCTGCAATATTGAGT 60.255 37.037 19.73 2.27 35.73 3.41
2631 2739 8.004087 AGAATTGTATGCTGCAATATTGAGTT 57.996 30.769 19.73 8.13 35.73 3.01
2632 2740 9.123902 AGAATTGTATGCTGCAATATTGAGTTA 57.876 29.630 19.73 2.80 35.73 2.24
2633 2741 9.903682 GAATTGTATGCTGCAATATTGAGTTAT 57.096 29.630 19.73 9.62 35.73 1.89
2667 2775 1.713597 TTAGATGATGCTATGCGGCG 58.286 50.000 0.51 0.51 34.52 6.46
2681 2789 4.668576 ATGCGGCGTGATAAATTATCTG 57.331 40.909 9.37 7.71 36.17 2.90
2689 2797 6.874134 GGCGTGATAAATTATCTGTATCCTGT 59.126 38.462 13.45 0.00 36.17 4.00
2725 2833 9.965902 ATAATGGAAATAAGGCTAGTAGGAATG 57.034 33.333 0.00 0.00 0.00 2.67
2797 2913 8.916062 TCATAATGTTATCAAAATGCCTCATGT 58.084 29.630 0.00 0.00 0.00 3.21
2869 2987 5.703730 AGGTAATTTCCTCGGGTTTGATA 57.296 39.130 0.00 0.00 31.32 2.15
2896 3014 1.550976 GAGGAAGAAGAAGCCCTCGAA 59.449 52.381 0.00 0.00 36.26 3.71
2902 3020 2.569404 AGAAGAAGCCCTCGAAGTTGAT 59.431 45.455 0.00 0.00 0.00 2.57
2944 3062 2.069165 GAGGTGCACTTTCCAGGGGT 62.069 60.000 17.98 0.00 0.00 4.95
2959 3077 1.600916 GGGTTGTGTGCAGGTCTCC 60.601 63.158 0.00 0.00 0.00 3.71
2964 3082 2.427095 GTTGTGTGCAGGTCTCCTTTTT 59.573 45.455 0.00 0.00 0.00 1.94
2966 3084 2.297701 GTGTGCAGGTCTCCTTTTTCA 58.702 47.619 0.00 0.00 0.00 2.69
2968 3086 2.092429 TGTGCAGGTCTCCTTTTTCAGT 60.092 45.455 0.00 0.00 0.00 3.41
2971 3089 3.632145 TGCAGGTCTCCTTTTTCAGTTTC 59.368 43.478 0.00 0.00 0.00 2.78
2972 3090 3.632145 GCAGGTCTCCTTTTTCAGTTTCA 59.368 43.478 0.00 0.00 0.00 2.69
2983 3101 9.748708 TCCTTTTTCAGTTTCATAAGAAATGTG 57.251 29.630 0.00 0.00 44.87 3.21
2985 3103 7.945033 TTTTCAGTTTCATAAGAAATGTGCC 57.055 32.000 0.00 0.00 44.87 5.01
2988 3106 5.716228 TCAGTTTCATAAGAAATGTGCCCAT 59.284 36.000 0.00 0.00 44.87 4.00
3099 3517 8.526978 GTCACTTATCCATCATCTTCTATGCTA 58.473 37.037 0.00 0.00 0.00 3.49
3100 3518 8.526978 TCACTTATCCATCATCTTCTATGCTAC 58.473 37.037 0.00 0.00 0.00 3.58
3102 3520 4.790765 TCCATCATCTTCTATGCTACGG 57.209 45.455 0.00 0.00 0.00 4.02
3104 3522 4.460731 TCCATCATCTTCTATGCTACGGAG 59.539 45.833 0.00 0.00 0.00 4.63
3150 3574 9.654663 GTGTCACTATCTTAAGACCAGTTTTAT 57.345 33.333 15.63 0.00 0.00 1.40
3204 3628 6.239217 AGTACCTTCATGCTATGTCATCAA 57.761 37.500 0.00 0.00 0.00 2.57
3221 3645 5.694006 GTCATCAATCTGCTGGATAGTACAC 59.306 44.000 0.00 0.00 33.71 2.90
3340 3764 7.736447 GGAAGAGATCCGTTTCATGATAAAT 57.264 36.000 0.00 0.00 38.79 1.40
3412 3836 3.134804 AGGCTATAGAAATTGTCGGTGCT 59.865 43.478 3.21 0.00 0.00 4.40
3567 3998 5.796424 ATGGACACTTCATTTGCTTCTTT 57.204 34.783 0.00 0.00 0.00 2.52
3612 4043 7.117812 CCGCTTTGTCGGTGATTATTTAGATAT 59.882 37.037 0.00 0.00 44.18 1.63
3676 4107 2.288961 CAATTGATGCCTTGGACTGC 57.711 50.000 0.00 0.00 0.00 4.40
3728 4159 7.227910 GTGGTCTTTTAAGGTATGTCTTGTTCA 59.772 37.037 0.00 0.00 0.00 3.18
3739 4170 7.041098 AGGTATGTCTTGTTCATGTTTCACTTC 60.041 37.037 0.00 0.00 0.00 3.01
3740 4171 6.698008 ATGTCTTGTTCATGTTTCACTTCA 57.302 33.333 0.00 0.00 0.00 3.02
3741 4172 6.122850 TGTCTTGTTCATGTTTCACTTCAG 57.877 37.500 0.00 0.00 0.00 3.02
3742 4173 5.879777 TGTCTTGTTCATGTTTCACTTCAGA 59.120 36.000 0.00 0.00 0.00 3.27
3743 4174 6.037500 TGTCTTGTTCATGTTTCACTTCAGAG 59.962 38.462 0.00 0.00 0.00 3.35
3752 4183 6.486253 TGTTTCACTTCAGAGCAATGTATC 57.514 37.500 0.00 0.00 0.00 2.24
3765 4196 8.068380 CAGAGCAATGTATCACAGTATTTCATG 58.932 37.037 0.00 0.00 0.00 3.07
3965 4398 6.322712 TGTTTACCTAACAAGCCATGAAGTTT 59.677 34.615 0.00 0.00 43.58 2.66
4023 4460 5.911752 TCAAACACAAGTGGCAAACATTAT 58.088 33.333 5.08 0.00 34.19 1.28
4096 4551 7.775053 TGCCCCTATCATTTATTTTATGTCC 57.225 36.000 0.00 0.00 0.00 4.02
4097 4552 6.432783 TGCCCCTATCATTTATTTTATGTCCG 59.567 38.462 0.00 0.00 0.00 4.79
4098 4553 6.433093 GCCCCTATCATTTATTTTATGTCCGT 59.567 38.462 0.00 0.00 0.00 4.69
4099 4554 7.361799 GCCCCTATCATTTATTTTATGTCCGTC 60.362 40.741 0.00 0.00 0.00 4.79
4100 4555 7.148474 CCCCTATCATTTATTTTATGTCCGTCG 60.148 40.741 0.00 0.00 0.00 5.12
4101 4556 7.601130 CCCTATCATTTATTTTATGTCCGTCGA 59.399 37.037 0.00 0.00 0.00 4.20
4102 4557 8.433126 CCTATCATTTATTTTATGTCCGTCGAC 58.567 37.037 5.18 5.18 39.66 4.20
4103 4558 6.592798 TCATTTATTTTATGTCCGTCGACC 57.407 37.500 10.58 0.00 38.32 4.79
4104 4559 6.107343 TCATTTATTTTATGTCCGTCGACCA 58.893 36.000 10.58 2.35 38.32 4.02
4105 4560 6.594547 TCATTTATTTTATGTCCGTCGACCAA 59.405 34.615 10.58 0.00 38.32 3.67
4106 4561 6.988622 TTTATTTTATGTCCGTCGACCAAT 57.011 33.333 10.58 1.22 38.32 3.16
4107 4562 8.552865 CATTTATTTTATGTCCGTCGACCAATA 58.447 33.333 10.58 0.24 38.32 1.90
4108 4563 8.489990 TTTATTTTATGTCCGTCGACCAATAA 57.510 30.769 10.58 6.41 38.32 1.40
4109 4564 6.988622 ATTTTATGTCCGTCGACCAATAAA 57.011 33.333 10.58 11.60 38.32 1.40
4184 4639 7.348080 TGAGGTCTAACATGATAAGTAGTGG 57.652 40.000 0.00 0.00 0.00 4.00
4195 4650 7.937394 ACATGATAAGTAGTGGCCTAAAATACC 59.063 37.037 3.32 0.00 0.00 2.73
4196 4651 7.685849 TGATAAGTAGTGGCCTAAAATACCT 57.314 36.000 3.32 0.00 0.00 3.08
4197 4652 8.786710 TGATAAGTAGTGGCCTAAAATACCTA 57.213 34.615 3.32 0.00 0.00 3.08
4198 4653 9.216148 TGATAAGTAGTGGCCTAAAATACCTAA 57.784 33.333 3.32 0.00 0.00 2.69
4201 4656 8.571461 AAGTAGTGGCCTAAAATACCTAAAAC 57.429 34.615 3.32 0.00 0.00 2.43
4202 4657 7.692172 AGTAGTGGCCTAAAATACCTAAAACA 58.308 34.615 3.32 0.00 0.00 2.83
4203 4658 6.829229 AGTGGCCTAAAATACCTAAAACAC 57.171 37.500 3.32 0.00 0.00 3.32
4245 4700 6.535508 GGTGGTGTCTATATGTTCTGAACTTC 59.464 42.308 20.18 4.13 0.00 3.01
4408 4864 1.404391 GAGCATGATTCAGTGGCTTGG 59.596 52.381 0.00 0.00 34.44 3.61
4409 4865 0.179119 GCATGATTCAGTGGCTTGGC 60.179 55.000 0.00 0.00 0.00 4.52
4483 4941 3.888930 GGAGTTCATCTGTTTGTTCCCAA 59.111 43.478 0.00 0.00 0.00 4.12
4570 5028 6.462552 TGAACATTGTTGGAGTGATCAAAA 57.537 33.333 6.80 0.00 0.00 2.44
4581 5039 6.969366 TGGAGTGATCAAAATATATTTGGCG 58.031 36.000 11.42 4.23 0.00 5.69
4651 5109 3.701542 TGAGGATGCGTCACTTAGAAGAT 59.298 43.478 8.47 0.00 0.00 2.40
4679 5137 8.822805 AGAAGAGGTACCACAATACTATGAAAA 58.177 33.333 15.94 0.00 0.00 2.29
4727 5190 5.061064 CAGTTATGCACAGAAGTAGAACGAC 59.939 44.000 0.00 0.00 0.00 4.34
4734 5197 7.372714 TGCACAGAAGTAGAACGACTAAAATA 58.627 34.615 0.00 0.00 32.49 1.40
4739 5202 9.182933 CAGAAGTAGAACGACTAAAATATAGCC 57.817 37.037 0.00 0.00 32.49 3.93
4742 5205 8.108551 AGTAGAACGACTAAAATATAGCCGAT 57.891 34.615 0.00 0.00 32.49 4.18
4775 5238 2.960819 AGTAGTTTTGCCTGTCTAGCG 58.039 47.619 0.00 0.00 0.00 4.26
4810 5273 0.798776 CGGCCACTCACTGAATTGTC 59.201 55.000 2.24 0.00 0.00 3.18
4817 5280 4.330250 CACTCACTGAATTGTCTTGGGAT 58.670 43.478 0.00 0.00 0.00 3.85
4841 5305 7.838079 TTGGCAAATATAGCAATCCTACATT 57.162 32.000 0.00 0.00 0.00 2.71
4873 5337 8.245701 TGTTAAATTTTGGTTTTCAGTGTGAC 57.754 30.769 0.00 0.00 0.00 3.67
4891 5356 4.520111 TGTGACTCAACCAATGATTGAAGG 59.480 41.667 6.76 0.00 37.44 3.46
4933 5398 3.778629 AGCCTAATAAACCGGAAAGGAGA 59.221 43.478 9.46 0.00 45.00 3.71
4936 5401 5.628433 GCCTAATAAACCGGAAAGGAGAGAA 60.628 44.000 9.46 0.00 45.00 2.87
5055 5531 2.092429 GGTCCTAATCCCATGCTGTCAA 60.092 50.000 0.00 0.00 0.00 3.18
5056 5532 3.209410 GTCCTAATCCCATGCTGTCAAG 58.791 50.000 0.00 0.00 0.00 3.02
5171 5648 2.413239 CGAGTTGTGGCACATGATTGTC 60.413 50.000 22.73 10.56 44.52 3.18
5195 5672 3.782523 AGTATTCATCCCAGAGGCTCAAA 59.217 43.478 18.26 0.00 0.00 2.69
5207 5684 5.278218 CCAGAGGCTCAAAAGAGAAACTTTC 60.278 44.000 18.26 0.00 46.55 2.62
5242 5719 4.962155 ACTTGGTTACTTCCAGAAGACAG 58.038 43.478 14.19 1.00 40.79 3.51
5255 5732 2.939103 AGAAGACAGCGCCAATAATGAC 59.061 45.455 2.29 0.00 0.00 3.06
5317 5794 4.400036 CATCTGTGTGATGTGTGAACAG 57.600 45.455 0.00 0.00 45.55 3.16
5318 5795 3.541996 TCTGTGTGATGTGTGAACAGT 57.458 42.857 0.00 0.00 39.39 3.55
5319 5796 4.664150 TCTGTGTGATGTGTGAACAGTA 57.336 40.909 0.00 0.00 39.39 2.74
5320 5797 5.017294 TCTGTGTGATGTGTGAACAGTAA 57.983 39.130 0.00 0.00 39.39 2.24
5321 5798 4.808895 TCTGTGTGATGTGTGAACAGTAAC 59.191 41.667 0.00 0.00 39.39 2.50
5360 5851 3.627577 CGGATATTTGTTTCCCTGACCAG 59.372 47.826 0.00 0.00 0.00 4.00
5388 5881 3.504906 AGCAATGTGTGAGACCAATTCAG 59.495 43.478 0.00 0.00 0.00 3.02
5391 5884 5.336213 GCAATGTGTGAGACCAATTCAGAAT 60.336 40.000 0.00 0.00 0.00 2.40
5400 5893 6.720748 TGAGACCAATTCAGAATTTCCATGAA 59.279 34.615 5.58 4.21 37.36 2.57
5402 5895 7.779073 AGACCAATTCAGAATTTCCATGAATC 58.221 34.615 5.58 4.17 41.56 2.52
5410 5903 4.159135 AGAATTTCCATGAATCAGCCACAC 59.841 41.667 0.00 0.00 0.00 3.82
5434 5927 6.804534 GATTCACGATCGATGAAGGATATC 57.195 41.667 24.34 15.77 39.36 1.63
5436 5929 5.302357 TCACGATCGATGAAGGATATCTG 57.698 43.478 24.34 4.58 0.00 2.90
5439 5932 4.142491 ACGATCGATGAAGGATATCTGCTC 60.142 45.833 24.34 0.00 0.00 4.26
5442 5935 5.735285 TCGATGAAGGATATCTGCTCAAT 57.265 39.130 2.05 0.00 0.00 2.57
5468 5961 5.574891 AATAAACACACACACACACACAT 57.425 34.783 0.00 0.00 0.00 3.21
5556 6049 4.415881 AAGGGTTGTGTGCATCGATATA 57.584 40.909 0.00 0.00 0.00 0.86
5557 6050 3.728845 AGGGTTGTGTGCATCGATATAC 58.271 45.455 0.00 0.57 0.00 1.47
5558 6051 3.388024 AGGGTTGTGTGCATCGATATACT 59.612 43.478 0.00 0.00 0.00 2.12
5559 6052 4.587262 AGGGTTGTGTGCATCGATATACTA 59.413 41.667 0.00 0.00 0.00 1.82
5596 6089 1.267121 TGCCTCTCCACTGTAACCTC 58.733 55.000 0.00 0.00 0.00 3.85
5598 6091 1.478916 GCCTCTCCACTGTAACCTCTC 59.521 57.143 0.00 0.00 0.00 3.20
5599 6092 1.746220 CCTCTCCACTGTAACCTCTCG 59.254 57.143 0.00 0.00 0.00 4.04
5600 6093 2.438411 CTCTCCACTGTAACCTCTCGT 58.562 52.381 0.00 0.00 0.00 4.18
5601 6094 3.607741 CTCTCCACTGTAACCTCTCGTA 58.392 50.000 0.00 0.00 0.00 3.43
5603 6096 3.262660 TCTCCACTGTAACCTCTCGTAGA 59.737 47.826 0.00 0.00 0.00 2.59
5604 6097 4.080469 TCTCCACTGTAACCTCTCGTAGAT 60.080 45.833 0.00 0.00 33.89 1.98
5606 6099 5.938279 TCCACTGTAACCTCTCGTAGATAT 58.062 41.667 0.00 0.00 33.89 1.63
5607 6100 7.015974 TCTCCACTGTAACCTCTCGTAGATATA 59.984 40.741 0.00 0.00 33.89 0.86
5608 6101 6.933521 TCCACTGTAACCTCTCGTAGATATAC 59.066 42.308 0.00 0.00 33.89 1.47
5609 6102 6.935771 CCACTGTAACCTCTCGTAGATATACT 59.064 42.308 0.00 0.00 33.89 2.12
5611 6104 9.656040 CACTGTAACCTCTCGTAGATATACTAT 57.344 37.037 0.00 0.00 33.89 2.12
5673 6488 1.615883 CACCTCCTCGTAGCTGCATAT 59.384 52.381 1.02 0.00 0.00 1.78
5675 6490 1.671261 CCTCCTCGTAGCTGCATATGC 60.671 57.143 21.09 21.09 42.50 3.14
5701 6516 5.722263 AGATGATTGACAAGAGACAGTGAG 58.278 41.667 0.00 0.00 0.00 3.51
5732 6549 4.025040 TGGCATTTCTGTCTCTCAACAT 57.975 40.909 0.00 0.00 0.00 2.71
5744 6561 5.413523 TGTCTCTCAACATTGTGATGGATTG 59.586 40.000 0.00 0.00 37.60 2.67
5747 6564 7.281774 GTCTCTCAACATTGTGATGGATTGTAT 59.718 37.037 0.00 0.00 37.60 2.29
5750 6567 8.892723 TCTCAACATTGTGATGGATTGTATTAC 58.107 33.333 0.00 0.00 37.60 1.89
5866 6683 5.959618 CATCCATGCATGATCATTACAGT 57.040 39.130 28.31 0.00 0.00 3.55
5869 6686 3.305131 CCATGCATGATCATTACAGTGCC 60.305 47.826 28.31 0.00 0.00 5.01
5873 6690 3.120408 GCATGATCATTACAGTGCCGATC 60.120 47.826 5.16 0.00 34.40 3.69
5876 6693 4.309933 TGATCATTACAGTGCCGATCATC 58.690 43.478 9.19 0.00 38.00 2.92
5877 6694 3.111853 TCATTACAGTGCCGATCATCC 57.888 47.619 0.00 0.00 0.00 3.51
5905 7073 1.738099 CAGGTGAAGAAGTCGGCGG 60.738 63.158 7.21 0.00 0.00 6.13
5909 7077 0.389948 GTGAAGAAGTCGGCGGTGAT 60.390 55.000 7.21 0.00 0.00 3.06
5922 7090 2.100631 GGTGATGAAGGCCACGTCG 61.101 63.158 5.01 0.00 34.30 5.12
5923 7091 2.100631 GTGATGAAGGCCACGTCGG 61.101 63.158 5.01 0.00 38.11 4.79
5924 7092 2.511600 GATGAAGGCCACGTCGGG 60.512 66.667 5.01 0.00 34.06 5.14
5943 7111 2.483745 GACGACGATGACCGCTGA 59.516 61.111 0.00 0.00 43.32 4.26
5950 7118 3.005539 ATGACCGCTGACTGGCCT 61.006 61.111 3.32 0.00 0.00 5.19
6065 7239 1.533625 GTGCATGAGGTTGCCAGTTA 58.466 50.000 0.00 0.00 42.06 2.24
6066 7240 2.094675 GTGCATGAGGTTGCCAGTTAT 58.905 47.619 0.00 0.00 42.06 1.89
6067 7241 2.493278 GTGCATGAGGTTGCCAGTTATT 59.507 45.455 0.00 0.00 42.06 1.40
6069 7243 4.339247 GTGCATGAGGTTGCCAGTTATTAT 59.661 41.667 0.00 0.00 42.06 1.28
6071 7245 4.823989 GCATGAGGTTGCCAGTTATTATCT 59.176 41.667 0.00 0.00 36.60 1.98
6072 7246 5.049129 GCATGAGGTTGCCAGTTATTATCTC 60.049 44.000 0.00 0.00 36.60 2.75
6078 7252 7.501844 AGGTTGCCAGTTATTATCTCTCTTAC 58.498 38.462 0.00 0.00 0.00 2.34
6079 7253 7.125811 AGGTTGCCAGTTATTATCTCTCTTACA 59.874 37.037 0.00 0.00 0.00 2.41
6082 7256 9.905713 TTGCCAGTTATTATCTCTCTTACAATT 57.094 29.630 0.00 0.00 0.00 2.32
6083 7257 9.330063 TGCCAGTTATTATCTCTCTTACAATTG 57.670 33.333 3.24 3.24 0.00 2.32
6100 7292 2.046283 TTGAACGAGTAGAGCGTGTG 57.954 50.000 0.00 0.00 41.75 3.82
6123 7316 4.132441 TAACGTACCCCGCCGCAG 62.132 66.667 0.00 0.00 41.42 5.18
6187 7380 2.355837 GCACCAGCTTGACGACGA 60.356 61.111 0.00 0.00 37.91 4.20
6260 7458 0.890996 CTCCACCCCTCTGCAAACAC 60.891 60.000 0.00 0.00 0.00 3.32
6266 7464 4.724697 CTCTGCAAACACGCGCCG 62.725 66.667 5.73 0.00 33.35 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.232303 GCAAAGACGGTGTTCGACAG 59.768 55.000 0.00 0.00 42.43 3.51
17 18 1.902765 ATGGTGAGCTCGACATGGCA 61.903 55.000 18.70 8.20 0.00 4.92
224 225 2.738521 GGCGAGTTCAAGCGAGCA 60.739 61.111 0.00 0.00 0.00 4.26
227 228 4.357947 AGCGGCGAGTTCAAGCGA 62.358 61.111 12.98 0.00 0.00 4.93
228 229 3.843240 GAGCGGCGAGTTCAAGCG 61.843 66.667 12.98 0.00 0.00 4.68
231 232 4.735132 CCGGAGCGGCGAGTTCAA 62.735 66.667 12.98 0.00 41.17 2.69
504 511 1.766143 GAGATGTTCGCGGACATGGC 61.766 60.000 36.57 22.78 40.21 4.40
578 585 4.072088 CGCAAGAACGTCGTGGCC 62.072 66.667 0.00 0.00 43.02 5.36
788 795 3.194308 GCGGCTCAAGCTCTCTGC 61.194 66.667 1.46 0.00 41.70 4.26
789 796 1.810441 CTGCGGCTCAAGCTCTCTG 60.810 63.158 0.00 0.00 41.70 3.35
790 797 1.947597 CTCTGCGGCTCAAGCTCTCT 61.948 60.000 0.00 0.00 41.70 3.10
791 798 1.519013 CTCTGCGGCTCAAGCTCTC 60.519 63.158 0.00 0.00 41.70 3.20
792 799 2.578128 CTCTGCGGCTCAAGCTCT 59.422 61.111 0.00 0.00 41.70 4.09
793 800 2.511145 CCTCTGCGGCTCAAGCTC 60.511 66.667 0.00 0.00 41.70 4.09
794 801 2.587247 TTCCTCTGCGGCTCAAGCT 61.587 57.895 0.00 0.00 41.70 3.74
795 802 2.046892 TTCCTCTGCGGCTCAAGC 60.047 61.111 0.00 0.00 41.14 4.01
796 803 1.743252 GGTTCCTCTGCGGCTCAAG 60.743 63.158 0.00 0.00 0.00 3.02
798 805 2.515979 TTGGTTCCTCTGCGGCTCA 61.516 57.895 0.00 0.00 0.00 4.26
896 909 2.294791 TGTGTATTCTTTTGTTGGGCCG 59.705 45.455 0.00 0.00 0.00 6.13
940 953 1.336755 CCCTTCTCTCTCTAGCTTCGC 59.663 57.143 0.00 0.00 0.00 4.70
1029 1051 4.521062 AGCAGCGGCAGGATCGAC 62.521 66.667 12.44 0.00 44.61 4.20
1402 1461 4.504916 CTGGCCGAGGAGCACGAG 62.505 72.222 0.00 0.00 0.00 4.18
1638 1700 2.076100 CTGCCTCGCATTGTTAGTCAA 58.924 47.619 0.00 0.00 38.13 3.18
1712 1774 1.024579 CAAAACCGGCAGGCGTAGAT 61.025 55.000 16.17 0.00 42.76 1.98
1777 1839 3.786553 TCACTGTCAGGGTAGGTAACAT 58.213 45.455 1.07 0.00 41.41 2.71
1872 1936 0.924823 ATTTCAGAGGAGCCCTGCAT 59.075 50.000 0.00 0.00 31.76 3.96
1895 1959 5.009210 TGAACCCAAATAACTTGCACACTAC 59.991 40.000 0.00 0.00 33.27 2.73
1949 2020 2.097142 GCTCTGAAACAATGCTGGCTAG 59.903 50.000 0.00 0.00 0.00 3.42
1969 2041 4.153655 CACATCATGTACAGAGGCATATGC 59.846 45.833 19.79 19.79 41.14 3.14
1981 2053 4.571984 TGCAAGCTATGTCACATCATGTAC 59.428 41.667 0.00 0.00 0.00 2.90
2046 2125 2.965831 TCTGCTACCTGATGGTATCACC 59.034 50.000 0.00 0.00 46.67 4.02
2055 2134 5.212532 CAGCTAAATCTCTGCTACCTGAT 57.787 43.478 0.00 0.00 35.05 2.90
2056 2135 4.662468 CAGCTAAATCTCTGCTACCTGA 57.338 45.455 0.00 0.00 35.05 3.86
2096 2191 8.375506 TCTATGTTGTTAGAAGACCAGATTGTT 58.624 33.333 0.00 0.00 0.00 2.83
2164 2259 4.899502 CCTAGGGCAATGGTAATAGACTG 58.100 47.826 0.00 0.00 0.00 3.51
2221 2324 3.266477 TCCCAAATCCCAAAATGACCA 57.734 42.857 0.00 0.00 0.00 4.02
2258 2361 6.147164 AGTTGAACTTCATGTAACATACACCG 59.853 38.462 0.00 0.00 42.23 4.94
2316 2420 5.346822 GCTGCAATATTTTCTTGACACTTGG 59.653 40.000 0.00 0.00 0.00 3.61
2372 2478 7.907389 TCTCATTACAGGAAACTACTCACATT 58.093 34.615 0.00 0.00 40.21 2.71
2450 2557 6.638610 ACAGACCTTCATAGAATGACAGAAG 58.361 40.000 0.00 0.00 39.39 2.85
2483 2590 8.211838 GGTCATGCTAATTTAAAAACAAACGAC 58.788 33.333 0.00 0.00 0.00 4.34
2495 2602 3.554934 CCTGCCAGGTCATGCTAATTTA 58.445 45.455 1.39 0.00 0.00 1.40
2506 2613 0.529378 CAAAGAATGCCTGCCAGGTC 59.471 55.000 13.35 5.41 37.80 3.85
2520 2627 3.963129 ACTTTTCCAGTGTGTCCAAAGA 58.037 40.909 0.00 0.00 32.83 2.52
2532 2639 8.702163 AAAGACAAACACATTTACTTTTCCAG 57.298 30.769 0.00 0.00 33.62 3.86
2569 2677 4.875536 CACATGATGGAGAACAAACGGATA 59.124 41.667 0.00 0.00 0.00 2.59
2570 2678 3.691118 CACATGATGGAGAACAAACGGAT 59.309 43.478 0.00 0.00 0.00 4.18
2571 2679 3.073678 CACATGATGGAGAACAAACGGA 58.926 45.455 0.00 0.00 0.00 4.69
2572 2680 2.813754 ACACATGATGGAGAACAAACGG 59.186 45.455 0.00 0.00 0.00 4.44
2573 2681 3.748048 AGACACATGATGGAGAACAAACG 59.252 43.478 0.00 0.00 0.00 3.60
2595 2703 4.166725 AGCATACAATTCTCCCAGGATGAA 59.833 41.667 0.00 0.00 39.69 2.57
2599 2707 2.421952 GCAGCATACAATTCTCCCAGGA 60.422 50.000 0.00 0.00 0.00 3.86
2600 2708 1.952296 GCAGCATACAATTCTCCCAGG 59.048 52.381 0.00 0.00 0.00 4.45
2601 2709 2.646930 TGCAGCATACAATTCTCCCAG 58.353 47.619 0.00 0.00 0.00 4.45
2602 2710 2.804986 TGCAGCATACAATTCTCCCA 57.195 45.000 0.00 0.00 0.00 4.37
2603 2711 5.972107 ATATTGCAGCATACAATTCTCCC 57.028 39.130 0.00 0.00 38.62 4.30
2604 2712 6.973843 TCAATATTGCAGCATACAATTCTCC 58.026 36.000 10.76 0.00 38.62 3.71
2605 2713 7.646314 ACTCAATATTGCAGCATACAATTCTC 58.354 34.615 10.76 0.00 38.62 2.87
2606 2714 7.578310 ACTCAATATTGCAGCATACAATTCT 57.422 32.000 10.76 0.00 38.62 2.40
2607 2715 9.903682 ATAACTCAATATTGCAGCATACAATTC 57.096 29.630 10.76 0.00 38.62 2.17
2650 2758 0.947660 CACGCCGCATAGCATCATCT 60.948 55.000 0.00 0.00 0.00 2.90
2681 2789 6.649141 TCCATTATCGTGCAATAACAGGATAC 59.351 38.462 6.47 0.00 43.41 2.24
2689 2797 7.230510 AGCCTTATTTCCATTATCGTGCAATAA 59.769 33.333 0.00 0.00 0.00 1.40
2693 2801 4.460263 AGCCTTATTTCCATTATCGTGCA 58.540 39.130 0.00 0.00 0.00 4.57
2725 2833 3.511934 ACTCCAGTGTCACAGAGTTATCC 59.488 47.826 18.20 0.00 36.16 2.59
2869 2987 3.199727 GGGCTTCTTCTTCCTCATCTTCT 59.800 47.826 0.00 0.00 0.00 2.85
2902 3020 7.944554 CCTCCTCCCAGATATTTATTAGCAAAA 59.055 37.037 0.00 0.00 0.00 2.44
2944 3062 2.435372 AAAAGGAGACCTGCACACAA 57.565 45.000 0.00 0.00 32.13 3.33
2959 3077 8.490355 GGCACATTTCTTATGAAACTGAAAAAG 58.510 33.333 5.97 0.00 43.90 2.27
2964 3082 5.076182 TGGGCACATTTCTTATGAAACTGA 58.924 37.500 5.97 0.00 43.90 3.41
2966 3084 6.610075 AATGGGCACATTTCTTATGAAACT 57.390 33.333 8.82 0.00 44.69 2.66
2985 3103 7.604927 CCTCATAATTATTGCAATCCCAAATGG 59.395 37.037 16.86 7.23 0.00 3.16
2988 3106 6.523840 GCCTCATAATTATTGCAATCCCAAA 58.476 36.000 16.86 4.90 0.00 3.28
2991 3109 4.218417 ACGCCTCATAATTATTGCAATCCC 59.782 41.667 16.86 0.00 0.00 3.85
3000 3222 9.893305 GCTAAACAAATAACGCCTCATAATTAT 57.107 29.630 0.00 0.00 0.00 1.28
3058 3280 9.546428 TGGATAAGTGACATACAATTCATACAG 57.454 33.333 0.00 0.00 37.89 2.74
3099 3517 9.444600 ACAACAATAATTTTCTATGTACTCCGT 57.555 29.630 0.00 0.00 0.00 4.69
3100 3518 9.702726 CACAACAATAATTTTCTATGTACTCCG 57.297 33.333 0.00 0.00 0.00 4.63
3150 3574 4.623886 GCATCAGACACCCATGAAGTCTTA 60.624 45.833 10.64 5.57 40.42 2.10
3151 3575 3.871463 GCATCAGACACCCATGAAGTCTT 60.871 47.826 10.64 0.00 40.42 3.01
3152 3576 2.355513 GCATCAGACACCCATGAAGTCT 60.356 50.000 8.31 8.31 42.97 3.24
3204 3628 4.290093 TCAAGGTGTACTATCCAGCAGAT 58.710 43.478 0.00 0.00 39.15 2.90
3221 3645 3.713858 TCAACTTGCACAACATCAAGG 57.286 42.857 6.88 0.00 42.82 3.61
3301 3725 7.148154 CGGATCTCTTCCTGTACCATAGAATAG 60.148 44.444 0.00 0.00 42.99 1.73
3303 3727 5.478679 CGGATCTCTTCCTGTACCATAGAAT 59.521 44.000 0.00 0.00 42.99 2.40
3340 3764 3.877559 CATGCCTACAATCAGTTCTGGA 58.122 45.455 0.00 0.00 0.00 3.86
3373 3797 9.104713 TCTATAGCCTCATTATCTTCCATTGAA 57.895 33.333 0.00 0.00 0.00 2.69
3412 3836 5.104527 CCCCATATACTGTGAGAACCTTTCA 60.105 44.000 0.00 0.00 0.00 2.69
3495 3919 9.573166 AAATGCCATAGCTAATTAGTATTGTCA 57.427 29.630 13.91 5.79 40.80 3.58
3497 3921 9.014297 GGAAATGCCATAGCTAATTAGTATTGT 57.986 33.333 13.91 0.00 40.80 2.71
3525 3949 9.149225 TGTCCATTTACAATGTAAAAATCATGC 57.851 29.630 20.59 9.36 0.00 4.06
3567 3998 1.112113 GAATGAGGAGCCGTACCTGA 58.888 55.000 0.00 0.00 37.93 3.86
3612 4043 1.187974 CATTGCATCAAGGGGCTTCA 58.812 50.000 0.00 0.00 0.00 3.02
3676 4107 9.367444 CTAGTTTCATACTGTAACTTAGTTGGG 57.633 37.037 8.00 0.62 38.59 4.12
3728 4159 6.656270 TGATACATTGCTCTGAAGTGAAACAT 59.344 34.615 0.00 0.00 41.43 2.71
3739 4170 7.543947 TGAAATACTGTGATACATTGCTCTG 57.456 36.000 0.00 0.00 0.00 3.35
3740 4171 7.989170 TCATGAAATACTGTGATACATTGCTCT 59.011 33.333 0.00 0.00 0.00 4.09
3741 4172 8.146479 TCATGAAATACTGTGATACATTGCTC 57.854 34.615 0.00 0.00 0.00 4.26
3742 4173 8.687292 ATCATGAAATACTGTGATACATTGCT 57.313 30.769 0.00 0.00 30.03 3.91
3743 4174 9.740239 AAATCATGAAATACTGTGATACATTGC 57.260 29.630 0.00 0.00 31.49 3.56
3752 4183 9.669353 GCTACCAATAAATCATGAAATACTGTG 57.331 33.333 0.00 0.00 0.00 3.66
3765 4196 6.267496 ACCACAACAAGCTACCAATAAATC 57.733 37.500 0.00 0.00 0.00 2.17
3842 4275 5.986135 GCAGAGATGTAGTACCGATGAAAAT 59.014 40.000 0.00 0.00 0.00 1.82
3952 4385 7.288810 TCAATTAACAGAAACTTCATGGCTT 57.711 32.000 0.00 0.00 0.00 4.35
3955 4388 8.526147 AGGATTCAATTAACAGAAACTTCATGG 58.474 33.333 0.00 0.00 0.00 3.66
4023 4460 3.921104 ACCTTAGCAGAGATGGAGATGA 58.079 45.455 0.00 0.00 0.00 2.92
4092 4547 4.517952 TTACTTTATTGGTCGACGGACA 57.482 40.909 9.92 0.00 45.28 4.02
4093 4548 7.276438 AGTTTATTACTTTATTGGTCGACGGAC 59.724 37.037 9.92 0.00 36.68 4.79
4094 4549 7.276218 CAGTTTATTACTTTATTGGTCGACGGA 59.724 37.037 9.92 0.14 33.85 4.69
4095 4550 7.063780 ACAGTTTATTACTTTATTGGTCGACGG 59.936 37.037 9.92 0.00 33.85 4.79
4096 4551 7.956558 ACAGTTTATTACTTTATTGGTCGACG 58.043 34.615 9.92 0.00 33.85 5.12
4097 4552 8.106348 CGACAGTTTATTACTTTATTGGTCGAC 58.894 37.037 7.13 7.13 43.15 4.20
4098 4553 7.276218 CCGACAGTTTATTACTTTATTGGTCGA 59.724 37.037 0.00 0.00 43.15 4.20
4099 4554 7.276218 TCCGACAGTTTATTACTTTATTGGTCG 59.724 37.037 0.00 0.00 41.59 4.79
4100 4555 8.483307 TCCGACAGTTTATTACTTTATTGGTC 57.517 34.615 0.00 0.00 33.85 4.02
4101 4556 8.851541 TTCCGACAGTTTATTACTTTATTGGT 57.148 30.769 0.00 0.00 33.85 3.67
4102 4557 9.716507 CATTCCGACAGTTTATTACTTTATTGG 57.283 33.333 0.00 0.00 33.85 3.16
4106 4561 9.715121 ACTTCATTCCGACAGTTTATTACTTTA 57.285 29.630 0.00 0.00 33.85 1.85
4107 4562 8.617290 ACTTCATTCCGACAGTTTATTACTTT 57.383 30.769 0.00 0.00 33.85 2.66
4108 4563 8.617290 AACTTCATTCCGACAGTTTATTACTT 57.383 30.769 0.00 0.00 33.85 2.24
4109 4564 8.095169 AGAACTTCATTCCGACAGTTTATTACT 58.905 33.333 0.00 0.00 38.16 2.24
4131 4586 8.344831 TGAAATTATATACACATGCAGCAGAAC 58.655 33.333 0.00 0.00 0.00 3.01
4184 4639 6.530181 GTGCATGTGTTTTAGGTATTTTAGGC 59.470 38.462 0.00 0.00 0.00 3.93
4195 4650 2.634982 ATGGCGTGCATGTGTTTTAG 57.365 45.000 7.93 0.00 0.00 1.85
4196 4651 3.753797 TCTAATGGCGTGCATGTGTTTTA 59.246 39.130 7.93 1.03 0.00 1.52
4197 4652 2.556189 TCTAATGGCGTGCATGTGTTTT 59.444 40.909 7.93 0.00 0.00 2.43
4198 4653 2.158559 TCTAATGGCGTGCATGTGTTT 58.841 42.857 7.93 1.60 0.00 2.83
4199 4654 1.819928 TCTAATGGCGTGCATGTGTT 58.180 45.000 7.93 3.12 0.00 3.32
4200 4655 1.739466 CTTCTAATGGCGTGCATGTGT 59.261 47.619 7.93 0.00 0.00 3.72
4201 4656 1.064505 CCTTCTAATGGCGTGCATGTG 59.935 52.381 7.93 0.00 0.00 3.21
4202 4657 1.340017 ACCTTCTAATGGCGTGCATGT 60.340 47.619 7.93 0.00 0.00 3.21
4203 4658 1.064505 CACCTTCTAATGGCGTGCATG 59.935 52.381 0.09 0.09 0.00 4.06
4408 4864 0.391130 TTCCTGTACCTGTGATGCGC 60.391 55.000 0.00 0.00 0.00 6.09
4409 4865 2.093306 TTTCCTGTACCTGTGATGCG 57.907 50.000 0.00 0.00 0.00 4.73
4570 5028 7.721402 TGCAAAATAAGAACCGCCAAATATAT 58.279 30.769 0.00 0.00 0.00 0.86
4575 5033 3.553922 CCTGCAAAATAAGAACCGCCAAA 60.554 43.478 0.00 0.00 0.00 3.28
4581 5039 3.317150 GTGTGCCTGCAAAATAAGAACC 58.683 45.455 0.00 0.00 0.00 3.62
4651 5109 9.483489 TTCATAGTATTGTGGTACCTCTTCTAA 57.517 33.333 14.36 0.09 0.00 2.10
4727 5190 9.370126 CAACTTCGAAAATCGGCTATATTTTAG 57.630 33.333 0.00 0.00 40.88 1.85
4734 5197 5.416947 ACTACAACTTCGAAAATCGGCTAT 58.583 37.500 0.00 0.00 40.88 2.97
4739 5202 7.058016 GCAAAACTACTACAACTTCGAAAATCG 59.942 37.037 0.00 0.00 42.10 3.34
4742 5205 6.316890 AGGCAAAACTACTACAACTTCGAAAA 59.683 34.615 0.00 0.00 0.00 2.29
4775 5238 1.862602 GCCGTGGAACCATGAACACC 61.863 60.000 13.85 0.00 35.09 4.16
4810 5273 5.534207 TTGCTATATTTGCCAATCCCAAG 57.466 39.130 0.00 0.00 0.00 3.61
4817 5280 7.838079 AATGTAGGATTGCTATATTTGCCAA 57.162 32.000 2.06 0.00 0.00 4.52
4873 5337 5.184479 ACATCACCTTCAATCATTGGTTGAG 59.816 40.000 11.92 5.14 37.89 3.02
4891 5356 6.054295 AGGCTCATCTTAGAAATCACATCAC 58.946 40.000 0.00 0.00 0.00 3.06
4933 5398 8.244113 GGCTTTAGTGTGCAAATAAGTTATTCT 58.756 33.333 8.56 3.59 0.00 2.40
4936 5401 7.703058 AGGCTTTAGTGTGCAAATAAGTTAT 57.297 32.000 0.00 0.00 0.00 1.89
5036 5512 2.421952 GCTTGACAGCATGGGATTAGGA 60.422 50.000 0.00 0.00 46.49 2.94
5067 5543 9.410556 GCAAAAATTATAAGCTGAAGAGAACAA 57.589 29.630 0.00 0.00 0.00 2.83
5171 5648 1.967066 AGCCTCTGGGATGAATACTCG 59.033 52.381 0.00 0.00 33.58 4.18
5195 5672 2.528041 AGCCGTCGAAAGTTTCTCTT 57.472 45.000 13.56 0.00 38.10 2.85
5207 5684 0.661020 ACCAAGTCAAAAAGCCGTCG 59.339 50.000 0.00 0.00 0.00 5.12
5255 5732 1.145759 ACTCGCACATGTAATCGGCG 61.146 55.000 18.37 18.37 44.45 6.46
5258 5735 1.787155 GGCTACTCGCACATGTAATCG 59.213 52.381 0.00 2.87 41.67 3.34
5313 5790 7.431084 CGAGTAATGTTTTTGCAAGTTACTGTT 59.569 33.333 18.96 12.00 33.82 3.16
5316 5793 6.261381 TCCGAGTAATGTTTTTGCAAGTTACT 59.739 34.615 16.23 16.23 35.69 2.24
5317 5794 6.432107 TCCGAGTAATGTTTTTGCAAGTTAC 58.568 36.000 0.00 6.05 0.00 2.50
5318 5795 6.621316 TCCGAGTAATGTTTTTGCAAGTTA 57.379 33.333 0.00 0.00 0.00 2.24
5319 5796 5.508200 TCCGAGTAATGTTTTTGCAAGTT 57.492 34.783 0.00 0.00 0.00 2.66
5320 5797 5.705609 ATCCGAGTAATGTTTTTGCAAGT 57.294 34.783 0.00 0.00 0.00 3.16
5321 5798 8.586273 CAAATATCCGAGTAATGTTTTTGCAAG 58.414 33.333 0.00 0.00 0.00 4.01
5360 5851 4.065088 TGGTCTCACACATTGCTAGTTTC 58.935 43.478 0.00 0.00 0.00 2.78
5388 5881 4.427312 GTGTGGCTGATTCATGGAAATTC 58.573 43.478 0.00 0.00 0.00 2.17
5391 5884 1.811965 CGTGTGGCTGATTCATGGAAA 59.188 47.619 0.00 0.00 0.00 3.13
5400 5893 0.246360 TCGTGAATCGTGTGGCTGAT 59.754 50.000 0.00 0.00 40.80 2.90
5402 5895 0.647410 GATCGTGAATCGTGTGGCTG 59.353 55.000 0.00 0.00 40.80 4.85
5434 5927 7.535258 GTGTGTGTGTTTATTTCTATTGAGCAG 59.465 37.037 0.00 0.00 0.00 4.24
5436 5929 7.323656 GTGTGTGTGTGTTTATTTCTATTGAGC 59.676 37.037 0.00 0.00 0.00 4.26
5439 5932 7.912773 TGTGTGTGTGTGTGTTTATTTCTATTG 59.087 33.333 0.00 0.00 0.00 1.90
5442 5935 6.371825 TGTGTGTGTGTGTGTGTTTATTTCTA 59.628 34.615 0.00 0.00 0.00 2.10
5468 5961 9.416794 CATGTTAGTGGCACATTTTAAACAATA 57.583 29.630 21.41 0.00 44.52 1.90
5533 6026 1.234821 TCGATGCACACAACCCTTTC 58.765 50.000 0.00 0.00 0.00 2.62
5538 6031 7.421530 AAATAGTATATCGATGCACACAACC 57.578 36.000 8.54 0.00 0.00 3.77
5614 6107 7.931948 GGTTTCTTCATCGAATCCTTCCTATTA 59.068 37.037 0.00 0.00 32.50 0.98
5615 6108 6.768381 GGTTTCTTCATCGAATCCTTCCTATT 59.232 38.462 0.00 0.00 32.50 1.73
5616 6109 6.292150 GGTTTCTTCATCGAATCCTTCCTAT 58.708 40.000 0.00 0.00 32.50 2.57
5619 6112 3.628032 GGGTTTCTTCATCGAATCCTTCC 59.372 47.826 0.00 0.00 34.60 3.46
5620 6113 4.261801 TGGGTTTCTTCATCGAATCCTTC 58.738 43.478 0.00 0.00 34.60 3.46
5622 6115 3.370953 CCTGGGTTTCTTCATCGAATCCT 60.371 47.826 0.00 0.00 34.60 3.24
5623 6116 2.945668 CCTGGGTTTCTTCATCGAATCC 59.054 50.000 0.00 0.00 33.81 3.01
5624 6117 2.945668 CCCTGGGTTTCTTCATCGAATC 59.054 50.000 3.97 0.00 0.00 2.52
5627 6120 0.618458 CCCCTGGGTTTCTTCATCGA 59.382 55.000 12.71 0.00 0.00 3.59
5628 6121 3.175133 CCCCTGGGTTTCTTCATCG 57.825 57.895 12.71 0.00 0.00 3.84
5647 6462 0.246635 GCTACGAGGAGGTGCTCAAA 59.753 55.000 0.00 0.00 31.08 2.69
5673 6488 5.981174 TGTCTCTTGTCAATCATCTATGCA 58.019 37.500 0.00 0.00 0.00 3.96
5675 6490 7.263496 TCACTGTCTCTTGTCAATCATCTATG 58.737 38.462 0.00 0.00 0.00 2.23
5676 6491 7.341512 TCTCACTGTCTCTTGTCAATCATCTAT 59.658 37.037 0.00 0.00 0.00 1.98
5677 6492 6.660949 TCTCACTGTCTCTTGTCAATCATCTA 59.339 38.462 0.00 0.00 0.00 1.98
5678 6493 5.479724 TCTCACTGTCTCTTGTCAATCATCT 59.520 40.000 0.00 0.00 0.00 2.90
5679 6494 5.718146 TCTCACTGTCTCTTGTCAATCATC 58.282 41.667 0.00 0.00 0.00 2.92
5682 6497 5.718146 TCATCTCACTGTCTCTTGTCAATC 58.282 41.667 0.00 0.00 0.00 2.67
5683 6498 5.735285 TCATCTCACTGTCTCTTGTCAAT 57.265 39.130 0.00 0.00 0.00 2.57
5684 6499 5.302823 TCTTCATCTCACTGTCTCTTGTCAA 59.697 40.000 0.00 0.00 0.00 3.18
5701 6516 6.095160 AGAGACAGAAATGCCAATTCTTCATC 59.905 38.462 0.00 0.00 34.99 2.92
5732 6549 9.429109 TCCTACTAGTAATACAATCCATCACAA 57.571 33.333 3.76 0.00 0.00 3.33
5750 6567 7.069578 TCCCTGCTAGTACATTTTTCCTACTAG 59.930 40.741 0.00 6.70 41.28 2.57
5753 6570 5.985911 TCCCTGCTAGTACATTTTTCCTAC 58.014 41.667 0.00 0.00 0.00 3.18
5755 6572 5.044846 ACATCCCTGCTAGTACATTTTTCCT 60.045 40.000 0.00 0.00 0.00 3.36
5757 6574 5.880332 TCACATCCCTGCTAGTACATTTTTC 59.120 40.000 0.00 0.00 0.00 2.29
5761 6578 4.744867 GCATCACATCCCTGCTAGTACATT 60.745 45.833 0.00 0.00 33.15 2.71
5762 6579 3.244353 GCATCACATCCCTGCTAGTACAT 60.244 47.826 0.00 0.00 33.15 2.29
5763 6580 2.103094 GCATCACATCCCTGCTAGTACA 59.897 50.000 0.00 0.00 33.15 2.90
5764 6581 2.366916 AGCATCACATCCCTGCTAGTAC 59.633 50.000 0.00 0.00 44.08 2.73
5765 6582 2.682594 AGCATCACATCCCTGCTAGTA 58.317 47.619 0.00 0.00 44.08 1.82
5766 6583 1.504912 AGCATCACATCCCTGCTAGT 58.495 50.000 0.00 0.00 44.08 2.57
5767 6584 2.634815 AAGCATCACATCCCTGCTAG 57.365 50.000 0.00 0.00 45.10 3.42
5824 6641 1.888512 GCATTTCAGCCTCAAGACCAA 59.111 47.619 0.00 0.00 0.00 3.67
5880 6697 4.697756 TTCTTCACCTGGGCGCCG 62.698 66.667 22.54 9.65 0.00 6.46
5882 6699 2.032681 ACTTCTTCACCTGGGCGC 59.967 61.111 0.00 0.00 0.00 6.53
5905 7073 2.100631 CCGACGTGGCCTTCATCAC 61.101 63.158 3.32 0.00 0.00 3.06
5924 7092 4.831307 AGCGGTCATCGTCGTCGC 62.831 66.667 0.00 0.00 45.72 5.19
5931 7099 2.887568 GCCAGTCAGCGGTCATCG 60.888 66.667 0.00 0.00 42.76 3.84
5934 7102 3.240134 GAAGGCCAGTCAGCGGTCA 62.240 63.158 5.01 0.00 0.00 4.02
5943 7111 1.599047 CGTCATCCAGAAGGCCAGT 59.401 57.895 5.01 0.00 33.74 4.00
5950 7118 2.180769 CGACGCCGTCATCCAGAA 59.819 61.111 18.40 0.00 32.09 3.02
6067 7241 9.392259 TCTACTCGTTCAATTGTAAGAGAGATA 57.608 33.333 26.34 12.82 0.00 1.98
6069 7243 7.626664 GCTCTACTCGTTCAATTGTAAGAGAGA 60.627 40.741 26.34 21.69 0.00 3.10
6071 7245 6.323266 GCTCTACTCGTTCAATTGTAAGAGA 58.677 40.000 26.34 13.74 0.00 3.10
6072 7246 5.228220 CGCTCTACTCGTTCAATTGTAAGAG 59.772 44.000 20.72 20.72 0.00 2.85
6078 7252 2.987149 ACACGCTCTACTCGTTCAATTG 59.013 45.455 0.00 0.00 38.19 2.32
6079 7253 2.987149 CACACGCTCTACTCGTTCAATT 59.013 45.455 0.00 0.00 38.19 2.32
6082 7256 0.386858 GCACACGCTCTACTCGTTCA 60.387 55.000 0.00 0.00 38.19 3.18
6083 7257 2.350833 GCACACGCTCTACTCGTTC 58.649 57.895 0.00 0.00 38.19 3.95
6105 7297 4.433877 TGCGGCGGGGTACGTTAC 62.434 66.667 9.78 0.00 46.52 2.50
6106 7298 4.132441 CTGCGGCGGGGTACGTTA 62.132 66.667 9.78 0.00 46.52 3.18


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

AutoCloner maintained by Alex Coulton.