Multiple sequence alignment - TraesCS7A01G560100

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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 TraesCS7A01G560100 chr7A 100.000 5084 0 0 1 5084 731961425 731966508 0.000000e+00 9389.0
1 TraesCS7A01G560100 chr7A 84.226 1008 82 35 1 973 731956172 731957137 0.000000e+00 909.0
2 TraesCS7A01G560100 chr7A 81.048 248 22 18 5 230 538912552 538912308 1.880000e-39 174.0
3 TraesCS7A01G560100 chr7B 92.323 1511 78 11 605 2113 741719631 741718157 0.000000e+00 2113.0
4 TraesCS7A01G560100 chr7B 90.497 926 81 7 3404 4325 741716879 741715957 0.000000e+00 1216.0
5 TraesCS7A01G560100 chr7B 86.667 420 31 13 2979 3387 741717430 741717025 4.670000e-120 442.0
6 TraesCS7A01G560100 chr7B 93.243 296 18 2 2638 2932 741717736 741717442 7.820000e-118 435.0
7 TraesCS7A01G560100 chr7B 88.406 69 8 0 4733 4801 1816007 1816075 3.260000e-12 84.2
8 TraesCS7A01G560100 chr7B 84.000 75 12 0 4732 4806 20762764 20762838 7.060000e-09 73.1
9 TraesCS7A01G560100 chr7D 93.979 1362 56 7 773 2113 634412380 634411024 0.000000e+00 2037.0
10 TraesCS7A01G560100 chr7D 90.141 923 68 8 3407 4328 634409578 634408678 0.000000e+00 1179.0
11 TraesCS7A01G560100 chr7D 91.917 767 55 7 4322 5084 634408642 634407879 0.000000e+00 1066.0
12 TraesCS7A01G560100 chr7D 85.767 815 54 23 2589 3387 634410492 634409724 0.000000e+00 806.0
13 TraesCS7A01G560100 chr7D 82.111 777 58 25 5 748 634413421 634412693 1.580000e-164 590.0
14 TraesCS7A01G560100 chr7D 78.235 170 20 7 76 230 617060565 617060398 5.420000e-15 93.5
15 TraesCS7A01G560100 chr7D 82.243 107 14 4 10 112 56543634 56543529 2.520000e-13 87.9
16 TraesCS7A01G560100 chr5D 92.299 896 63 2 1006 1901 412352092 412352981 0.000000e+00 1267.0
17 TraesCS7A01G560100 chr5D 86.364 88 12 0 4714 4801 538536095 538536008 4.190000e-16 97.1
18 TraesCS7A01G560100 chr5D 85.227 88 13 0 4714 4801 538535328 538535241 1.950000e-14 91.6
19 TraesCS7A01G560100 chr5D 84.270 89 13 1 4714 4801 538535082 538534994 9.070000e-13 86.1
20 TraesCS7A01G560100 chr5D 81.373 102 12 6 5 102 511937255 511937157 5.460000e-10 76.8
21 TraesCS7A01G560100 chr5A 91.880 899 64 4 1006 1901 524217500 524218392 0.000000e+00 1247.0
22 TraesCS7A01G560100 chr5A 88.158 76 4 5 5 79 534663016 534663087 9.070000e-13 86.1
23 TraesCS7A01G560100 chr5B 91.000 900 73 5 1006 1901 496485119 496486014 0.000000e+00 1206.0
24 TraesCS7A01G560100 chr4A 85.484 434 54 8 3794 4221 6891838 6891408 1.300000e-120 444.0
25 TraesCS7A01G560100 chr4A 83.740 123 7 7 121 230 182121642 182121520 2.500000e-18 104.0
26 TraesCS7A01G560100 chr4A 85.556 90 13 0 4711 4800 702691976 702692065 1.510000e-15 95.3
27 TraesCS7A01G560100 chr4A 79.195 149 14 11 97 230 501712767 501712913 2.520000e-13 87.9
28 TraesCS7A01G560100 chr4A 100.000 30 0 0 4830 4859 30316404 30316375 7.110000e-04 56.5
29 TraesCS7A01G560100 chr4D 85.057 435 54 10 3794 4221 462839769 462839339 2.810000e-117 433.0
30 TraesCS7A01G560100 chr4B 84.897 437 53 11 3794 4221 578038760 578039192 3.640000e-116 429.0
31 TraesCS7A01G560100 chr4B 90.000 70 4 3 5 73 498512030 498511963 2.520000e-13 87.9
32 TraesCS7A01G560100 chr4B 87.342 79 7 3 5 82 649753286 649753362 2.520000e-13 87.9
33 TraesCS7A01G560100 chr2B 79.767 257 27 16 5 242 130928825 130928575 4.070000e-36 163.0
34 TraesCS7A01G560100 chr2B 82.734 139 11 7 106 232 37446929 37447066 1.500000e-20 111.0
35 TraesCS7A01G560100 chr6D 84.058 138 13 6 1 131 296691516 296691651 1.920000e-24 124.0
36 TraesCS7A01G560100 chr6D 87.273 110 7 5 126 228 410155699 410155808 8.940000e-23 119.0
37 TraesCS7A01G560100 chr6D 84.545 110 9 4 126 228 410155000 410155108 9.010000e-18 102.0
38 TraesCS7A01G560100 chr6D 86.585 82 11 0 5 86 128909312 128909393 1.950000e-14 91.6
39 TraesCS7A01G560100 chr6D 84.884 86 13 0 4716 4801 82467367 82467452 2.520000e-13 87.9
40 TraesCS7A01G560100 chr3D 84.252 127 7 5 121 234 378054175 378054049 1.500000e-20 111.0
41 TraesCS7A01G560100 chr3A 81.457 151 11 8 106 241 127915034 127915182 1.940000e-19 108.0
42 TraesCS7A01G560100 chr3A 82.014 139 10 9 106 230 708069599 708069736 2.500000e-18 104.0
43 TraesCS7A01G560100 chr3A 85.057 87 11 2 4723 4807 681026572 681026658 2.520000e-13 87.9
44 TraesCS7A01G560100 chr3A 100.000 31 0 0 4829 4859 691701062 691701092 1.980000e-04 58.4
45 TraesCS7A01G560100 chr1B 75.954 262 33 27 1 239 297013736 297013482 1.940000e-19 108.0
46 TraesCS7A01G560100 chr2D 74.274 241 52 9 1197 1430 605910251 605910014 5.420000e-15 93.5


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 TraesCS7A01G560100 chr7A 731961425 731966508 5083 False 9389.0 9389 100.0000 1 5084 1 chr7A.!!$F2 5083
1 TraesCS7A01G560100 chr7A 731956172 731957137 965 False 909.0 909 84.2260 1 973 1 chr7A.!!$F1 972
2 TraesCS7A01G560100 chr7B 741715957 741719631 3674 True 1051.5 2113 90.6825 605 4325 4 chr7B.!!$R1 3720
3 TraesCS7A01G560100 chr7D 634407879 634413421 5542 True 1135.6 2037 88.7830 5 5084 5 chr7D.!!$R3 5079
4 TraesCS7A01G560100 chr5D 412352092 412352981 889 False 1267.0 1267 92.2990 1006 1901 1 chr5D.!!$F1 895
5 TraesCS7A01G560100 chr5A 524217500 524218392 892 False 1247.0 1247 91.8800 1006 1901 1 chr5A.!!$F1 895
6 TraesCS7A01G560100 chr5B 496485119 496486014 895 False 1206.0 1206 91.0000 1006 1901 1 chr5B.!!$F1 895

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
938 1270 0.179225 CGCGAACCAAGAACCGATTG 60.179 55.0 0.0 0.0 0.00 2.67 F
2457 2949 0.439985 CTCGACATTGTGTTGCGGAG 59.560 55.0 0.0 0.0 31.81 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2484 2976 0.456312 GAGTGCCGTCGTACTTCCAG 60.456 60.0 1.58 0.0 34.75 3.86 R
4348 5049 0.252881 TCCTCCTGGAAGTCCATGCT 60.253 55.0 0.00 0.0 46.46 3.79 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
64 65 4.021192 TGCATGAAAAAGAGACCCATTTCC 60.021 41.667 0.00 0.00 32.21 3.13
234 259 5.339008 TGTGCGGGGTATCATCTATTATC 57.661 43.478 0.00 0.00 0.00 1.75
237 262 6.070251 TGTGCGGGGTATCATCTATTATCAAT 60.070 38.462 0.00 0.00 0.00 2.57
239 264 7.985184 GTGCGGGGTATCATCTATTATCAATAA 59.015 37.037 0.00 0.00 0.00 1.40
299 324 7.408543 AGAATCCAGAAATTCAGAGAAATCCA 58.591 34.615 0.00 0.00 37.98 3.41
333 358 6.072452 CCTTTTTCCAGTTAGAGATGACAACC 60.072 42.308 0.00 0.00 0.00 3.77
360 385 8.553459 AGTATCCTGACTTGAACAACAATTAG 57.447 34.615 0.00 0.00 37.88 1.73
521 555 2.108700 CAGCATAAAAATACGGTGCGC 58.891 47.619 0.00 0.00 40.54 6.09
683 719 7.203910 AGAGAATAAAATACTGTAGACGCAGG 58.796 38.462 0.00 0.00 40.59 4.85
720 756 1.281419 TCCAGGCCATCTACCGAAAA 58.719 50.000 5.01 0.00 0.00 2.29
730 766 1.278127 TCTACCGAAAAAGAGCCCCAG 59.722 52.381 0.00 0.00 0.00 4.45
739 775 3.532641 AAAGAGCCCCAGAAGACAAAT 57.467 42.857 0.00 0.00 0.00 2.32
920 1252 0.317479 CCCCGCCTATAAACCTCTCG 59.683 60.000 0.00 0.00 0.00 4.04
936 1268 0.736325 CTCGCGAACCAAGAACCGAT 60.736 55.000 11.33 0.00 0.00 4.18
938 1270 0.179225 CGCGAACCAAGAACCGATTG 60.179 55.000 0.00 0.00 0.00 2.67
946 1278 3.887621 CAAGAACCGATTGGAGTAGGA 57.112 47.619 5.81 0.00 39.21 2.94
986 1318 0.606673 GGAGGCTTTCTTGGTCGCTT 60.607 55.000 0.00 0.00 0.00 4.68
1512 1859 4.477975 CTCACCGAGGCCGACGAC 62.478 72.222 22.80 2.51 38.22 4.34
1809 2156 0.673956 GGTTCTCCAAGGCGTTCCTC 60.674 60.000 0.00 0.00 43.40 3.71
1815 2162 1.667830 CAAGGCGTTCCTCTGCGAA 60.668 57.895 0.00 0.00 43.40 4.70
1902 2249 3.394836 ACGCCCTTCTGCCCTCTC 61.395 66.667 0.00 0.00 0.00 3.20
1909 2256 2.507471 CCCTTCTGCCCTCTCAGTTAAT 59.493 50.000 0.00 0.00 35.63 1.40
1911 2258 4.568592 CCCTTCTGCCCTCTCAGTTAATTT 60.569 45.833 0.00 0.00 35.63 1.82
1939 2286 7.520451 TTATTATCGTCCAGTGTACTAGCAT 57.480 36.000 0.00 0.00 0.00 3.79
1991 2339 7.490725 GCATACCTCAAGACACAGCATATATAG 59.509 40.741 0.00 0.00 0.00 1.31
2051 2399 6.238759 GGAGGTAATTATGTTGCACTTGATCC 60.239 42.308 0.00 0.00 0.00 3.36
2082 2430 2.933495 TCGAGAAACGATCGGTTCAT 57.067 45.000 38.80 26.71 46.45 2.57
2116 2541 3.369261 CCAGAGATCAAGAGTGGAACCTG 60.369 52.174 0.00 0.00 37.80 4.00
2118 2543 3.260380 AGAGATCAAGAGTGGAACCTGTG 59.740 47.826 0.00 0.00 37.80 3.66
2181 2642 9.857656 TTTTTCTATCTTGCTCATAATGGAGAT 57.142 29.630 0.00 0.00 37.05 2.75
2182 2643 9.499479 TTTTCTATCTTGCTCATAATGGAGATC 57.501 33.333 0.00 0.00 37.05 2.75
2183 2644 7.180322 TCTATCTTGCTCATAATGGAGATCC 57.820 40.000 0.00 0.00 37.05 3.36
2195 2672 5.674052 AATGGAGATCCGAGGATAATGAG 57.326 43.478 4.36 0.00 39.43 2.90
2244 2726 8.427902 ACCAGCTCTGATGAATATGAATACTA 57.572 34.615 0.00 0.00 0.00 1.82
2245 2727 8.310382 ACCAGCTCTGATGAATATGAATACTAC 58.690 37.037 0.00 0.00 0.00 2.73
2246 2728 8.530311 CCAGCTCTGATGAATATGAATACTACT 58.470 37.037 0.00 0.00 0.00 2.57
2247 2729 9.926158 CAGCTCTGATGAATATGAATACTACTT 57.074 33.333 0.00 0.00 0.00 2.24
2248 2730 9.926158 AGCTCTGATGAATATGAATACTACTTG 57.074 33.333 0.00 0.00 0.00 3.16
2249 2731 8.655092 GCTCTGATGAATATGAATACTACTTGC 58.345 37.037 0.00 0.00 0.00 4.01
2250 2732 9.702494 CTCTGATGAATATGAATACTACTTGCA 57.298 33.333 0.00 0.00 0.00 4.08
2267 2749 5.478407 ACTTGCAATTTATGGTAAGGCAAC 58.522 37.500 0.00 0.00 36.04 4.17
2320 2802 4.321008 GCAGGATAATTGCATGATCAGGTG 60.321 45.833 9.42 0.19 41.17 4.00
2322 2804 5.181433 CAGGATAATTGCATGATCAGGTGAG 59.819 44.000 9.42 0.00 0.00 3.51
2324 2806 5.048921 GGATAATTGCATGATCAGGTGAGTG 60.049 44.000 9.42 0.00 0.00 3.51
2325 2807 3.639672 ATTGCATGATCAGGTGAGTGA 57.360 42.857 9.42 0.00 0.00 3.41
2326 2808 2.685850 TGCATGATCAGGTGAGTGAG 57.314 50.000 9.42 0.00 0.00 3.51
2327 2809 1.904537 TGCATGATCAGGTGAGTGAGT 59.095 47.619 9.42 0.00 0.00 3.41
2332 2823 4.521130 TGATCAGGTGAGTGAGTACAAC 57.479 45.455 0.00 0.00 0.00 3.32
2335 2826 4.955811 TCAGGTGAGTGAGTACAACAAT 57.044 40.909 0.00 0.00 0.00 2.71
2339 2830 4.821805 AGGTGAGTGAGTACAACAATTTGG 59.178 41.667 0.78 0.00 37.00 3.28
2389 2881 5.302823 AGAATTGGCTACTTTGCTGAGTTTT 59.697 36.000 0.00 0.00 0.00 2.43
2390 2882 5.535753 ATTGGCTACTTTGCTGAGTTTTT 57.464 34.783 0.00 0.00 0.00 1.94
2420 2912 5.570234 TTTTGAAACGGAACTACTTTGCT 57.430 34.783 0.00 0.00 0.00 3.91
2421 2913 4.545823 TTGAAACGGAACTACTTTGCTG 57.454 40.909 0.00 0.00 0.00 4.41
2422 2914 3.799366 TGAAACGGAACTACTTTGCTGA 58.201 40.909 0.00 0.00 0.00 4.26
2423 2915 3.807622 TGAAACGGAACTACTTTGCTGAG 59.192 43.478 0.00 0.00 0.00 3.35
2424 2916 3.470645 AACGGAACTACTTTGCTGAGT 57.529 42.857 0.00 0.00 0.00 3.41
2425 2917 3.470645 ACGGAACTACTTTGCTGAGTT 57.529 42.857 0.00 0.00 36.14 3.01
2426 2918 3.805207 ACGGAACTACTTTGCTGAGTTT 58.195 40.909 0.00 0.00 33.61 2.66
2427 2919 3.808174 ACGGAACTACTTTGCTGAGTTTC 59.192 43.478 0.00 0.00 33.61 2.78
2428 2920 3.120991 CGGAACTACTTTGCTGAGTTTCG 60.121 47.826 0.71 0.71 43.56 3.46
2429 2921 4.056050 GGAACTACTTTGCTGAGTTTCGA 58.944 43.478 0.00 0.00 33.61 3.71
2436 2928 5.305585 ACTTTGCTGAGTTTCGAGGATAAA 58.694 37.500 0.00 0.00 0.00 1.40
2453 2945 4.851558 GGATAAAACTCGACATTGTGTTGC 59.148 41.667 0.00 0.00 31.81 4.17
2454 2946 2.383298 AAACTCGACATTGTGTTGCG 57.617 45.000 0.00 0.00 31.81 4.85
2457 2949 0.439985 CTCGACATTGTGTTGCGGAG 59.560 55.000 0.00 0.00 31.81 4.63
2460 2952 2.094442 TCGACATTGTGTTGCGGAGATA 60.094 45.455 0.00 0.00 31.81 1.98
2477 2969 5.741388 GAGATATGTTCTCGGCAAACAAT 57.259 39.130 1.87 0.00 41.51 2.71
2484 2976 1.810151 TCTCGGCAAACAATACTTGGC 59.190 47.619 0.00 0.00 43.80 4.52
2495 2994 3.259876 ACAATACTTGGCTGGAAGTACGA 59.740 43.478 0.00 0.00 40.41 3.43
2506 3005 1.403780 GGAAGTACGACGGCACTCATT 60.404 52.381 0.00 0.00 0.00 2.57
2519 3018 4.379813 CGGCACTCATTAATTTGCTGAGTT 60.380 41.667 13.61 0.00 45.49 3.01
2520 3019 5.473039 GGCACTCATTAATTTGCTGAGTTT 58.527 37.500 12.12 0.00 45.49 2.66
2521 3020 5.928264 GGCACTCATTAATTTGCTGAGTTTT 59.072 36.000 12.12 0.00 45.49 2.43
2522 3021 6.424812 GGCACTCATTAATTTGCTGAGTTTTT 59.575 34.615 12.12 0.00 45.49 1.94
2523 3022 7.598493 GGCACTCATTAATTTGCTGAGTTTTTA 59.402 33.333 12.12 0.00 45.49 1.52
2524 3023 9.143631 GCACTCATTAATTTGCTGAGTTTTTAT 57.856 29.630 12.12 0.00 45.49 1.40
2536 3035 9.555727 TTGCTGAGTTTTTATAACTAGACACTT 57.444 29.630 0.00 0.00 0.00 3.16
2550 3049 6.646267 ACTAGACACTTGACAAACACCTAAA 58.354 36.000 0.00 0.00 0.00 1.85
2551 3050 5.813080 AGACACTTGACAAACACCTAAAC 57.187 39.130 0.00 0.00 0.00 2.01
2552 3051 5.497474 AGACACTTGACAAACACCTAAACT 58.503 37.500 0.00 0.00 0.00 2.66
2553 3052 6.646267 AGACACTTGACAAACACCTAAACTA 58.354 36.000 0.00 0.00 0.00 2.24
2554 3053 7.107542 AGACACTTGACAAACACCTAAACTAA 58.892 34.615 0.00 0.00 0.00 2.24
2555 3054 7.608761 AGACACTTGACAAACACCTAAACTAAA 59.391 33.333 0.00 0.00 0.00 1.85
2556 3055 7.532571 ACACTTGACAAACACCTAAACTAAAC 58.467 34.615 0.00 0.00 0.00 2.01
2557 3056 7.175293 ACACTTGACAAACACCTAAACTAAACA 59.825 33.333 0.00 0.00 0.00 2.83
2558 3057 7.696453 CACTTGACAAACACCTAAACTAAACAG 59.304 37.037 0.00 0.00 0.00 3.16
2559 3058 6.126568 TGACAAACACCTAAACTAAACAGC 57.873 37.500 0.00 0.00 0.00 4.40
2560 3059 5.066764 TGACAAACACCTAAACTAAACAGCC 59.933 40.000 0.00 0.00 0.00 4.85
2561 3060 5.198207 ACAAACACCTAAACTAAACAGCCT 58.802 37.500 0.00 0.00 0.00 4.58
2562 3061 5.655090 ACAAACACCTAAACTAAACAGCCTT 59.345 36.000 0.00 0.00 0.00 4.35
2563 3062 6.153851 ACAAACACCTAAACTAAACAGCCTTT 59.846 34.615 0.00 0.00 0.00 3.11
2564 3063 5.767816 ACACCTAAACTAAACAGCCTTTG 57.232 39.130 0.00 0.00 0.00 2.77
2565 3064 4.037565 ACACCTAAACTAAACAGCCTTTGC 59.962 41.667 0.00 0.00 37.95 3.68
2566 3065 3.572682 ACCTAAACTAAACAGCCTTTGCC 59.427 43.478 0.00 0.00 38.69 4.52
2567 3066 2.793278 AAACTAAACAGCCTTTGCCG 57.207 45.000 0.00 0.00 38.69 5.69
2568 3067 1.975660 AACTAAACAGCCTTTGCCGA 58.024 45.000 0.00 0.00 38.69 5.54
2569 3068 1.975660 ACTAAACAGCCTTTGCCGAA 58.024 45.000 0.00 0.00 38.69 4.30
2570 3069 1.607148 ACTAAACAGCCTTTGCCGAAC 59.393 47.619 0.00 0.00 38.69 3.95
2571 3070 1.880027 CTAAACAGCCTTTGCCGAACT 59.120 47.619 0.00 0.00 38.69 3.01
2572 3071 1.111277 AAACAGCCTTTGCCGAACTT 58.889 45.000 0.00 0.00 38.69 2.66
2573 3072 0.668535 AACAGCCTTTGCCGAACTTC 59.331 50.000 0.00 0.00 38.69 3.01
2574 3073 1.207593 CAGCCTTTGCCGAACTTCG 59.792 57.895 4.07 4.07 40.07 3.79
2587 3086 3.910648 CGAACTTCGGGAAACTAGAACT 58.089 45.455 3.06 0.00 36.00 3.01
2591 3090 3.254892 CTTCGGGAAACTAGAACTCAGC 58.745 50.000 0.00 0.00 0.00 4.26
2606 3105 3.387397 ACTCAGCAAACTACCACGTTAC 58.613 45.455 0.00 0.00 0.00 2.50
2609 3108 3.991773 TCAGCAAACTACCACGTTACATC 59.008 43.478 0.00 0.00 0.00 3.06
2635 3134 2.398036 CGTAAACGGCGGTGCATC 59.602 61.111 13.24 0.00 35.37 3.91
2657 3156 4.705507 TCACGGTAAGATCTTTCTGCTAGT 59.294 41.667 14.36 2.38 30.72 2.57
2723 3222 3.480668 GTGCATGTGTTCACGTGTTTTAC 59.519 43.478 16.51 11.07 0.00 2.01
2728 3227 5.359716 TGTGTTCACGTGTTTTACTTTGT 57.640 34.783 16.51 0.00 0.00 2.83
2862 3369 1.068083 CGACGGGATCTCACATGGG 59.932 63.158 0.00 0.00 0.00 4.00
2883 3390 1.776662 TAACGTGAGCTAGCCATCCT 58.223 50.000 12.13 0.00 0.00 3.24
2884 3391 1.776662 AACGTGAGCTAGCCATCCTA 58.223 50.000 12.13 0.00 0.00 2.94
2885 3392 2.002505 ACGTGAGCTAGCCATCCTAT 57.997 50.000 12.13 0.00 0.00 2.57
2886 3393 1.615883 ACGTGAGCTAGCCATCCTATG 59.384 52.381 12.13 0.00 0.00 2.23
2887 3394 1.615883 CGTGAGCTAGCCATCCTATGT 59.384 52.381 12.13 0.00 0.00 2.29
2889 3396 3.397482 GTGAGCTAGCCATCCTATGTTG 58.603 50.000 12.13 0.00 0.00 3.33
2891 3398 3.906218 TGAGCTAGCCATCCTATGTTGAT 59.094 43.478 12.13 0.00 0.00 2.57
2895 3402 5.046735 AGCTAGCCATCCTATGTTGATACTG 60.047 44.000 12.13 0.00 0.00 2.74
2903 3411 7.015098 CCATCCTATGTTGATACTGTTCTCTCT 59.985 40.741 0.00 0.00 0.00 3.10
2934 3447 9.559958 CATAATATAAGATCGTTTTTGGCATCC 57.440 33.333 0.00 0.00 0.00 3.51
2935 3448 7.823745 AATATAAGATCGTTTTTGGCATCCT 57.176 32.000 0.00 0.00 0.00 3.24
2936 3449 5.757850 ATAAGATCGTTTTTGGCATCCTC 57.242 39.130 0.00 0.00 0.00 3.71
2938 3451 1.064060 GATCGTTTTTGGCATCCTCCG 59.936 52.381 0.00 0.00 0.00 4.63
2945 3458 3.249189 GGCATCCTCCGCCCCATA 61.249 66.667 0.00 0.00 44.22 2.74
2948 3461 0.618458 GCATCCTCCGCCCCATAATA 59.382 55.000 0.00 0.00 0.00 0.98
2950 3463 2.941415 GCATCCTCCGCCCCATAATAAG 60.941 54.545 0.00 0.00 0.00 1.73
2952 3465 2.915869 TCCTCCGCCCCATAATAAGAT 58.084 47.619 0.00 0.00 0.00 2.40
2953 3466 4.069312 TCCTCCGCCCCATAATAAGATA 57.931 45.455 0.00 0.00 0.00 1.98
2954 3467 4.030913 TCCTCCGCCCCATAATAAGATAG 58.969 47.826 0.00 0.00 0.00 2.08
2956 3469 4.225267 CCTCCGCCCCATAATAAGATAGTT 59.775 45.833 0.00 0.00 0.00 2.24
2957 3470 5.280521 CCTCCGCCCCATAATAAGATAGTTT 60.281 44.000 0.00 0.00 0.00 2.66
2958 3471 6.195600 TCCGCCCCATAATAAGATAGTTTT 57.804 37.500 0.00 0.00 0.00 2.43
2959 3472 6.607019 TCCGCCCCATAATAAGATAGTTTTT 58.393 36.000 0.00 0.00 0.00 1.94
2960 3473 7.747690 TCCGCCCCATAATAAGATAGTTTTTA 58.252 34.615 0.00 0.00 0.00 1.52
2961 3474 8.387813 TCCGCCCCATAATAAGATAGTTTTTAT 58.612 33.333 0.00 0.00 0.00 1.40
2962 3475 8.458843 CCGCCCCATAATAAGATAGTTTTTATG 58.541 37.037 0.00 0.00 32.57 1.90
2963 3476 9.010029 CGCCCCATAATAAGATAGTTTTTATGT 57.990 33.333 0.00 0.00 31.43 2.29
3077 3591 2.159653 GGTTGCTGTATTCTGTTGCTCG 60.160 50.000 0.00 0.00 0.00 5.03
3100 3614 2.223572 CCATAGGGCAATGAAACGAAGC 60.224 50.000 0.00 0.00 0.00 3.86
3157 3671 0.251608 TGTCCGGGTCAGATGACAGA 60.252 55.000 14.52 5.58 46.47 3.41
3166 3682 3.129462 GGTCAGATGACAGAATCTCGACA 59.871 47.826 14.52 0.00 46.47 4.35
3180 3696 2.688446 TCTCGACAAGTGAACACTGACT 59.312 45.455 8.25 0.00 41.58 3.41
3210 3726 0.534412 AGCCAGATTCGAGTCCACTG 59.466 55.000 4.05 0.00 0.00 3.66
3211 3727 1.086634 GCCAGATTCGAGTCCACTGC 61.087 60.000 4.05 0.00 0.00 4.40
3241 3757 4.626042 CGTTGATCTTTCTCCCATCCTAG 58.374 47.826 0.00 0.00 0.00 3.02
3271 3787 2.191375 CATCAGGTGCGCATCCCT 59.809 61.111 19.01 15.99 0.00 4.20
3275 3791 2.765807 AGGTGCGCATCCCTAGCT 60.766 61.111 19.01 2.50 0.00 3.32
3325 3842 7.015877 GTGAACGAGTTCCAAGAATTTGATAC 58.984 38.462 12.76 0.00 38.77 2.24
3326 3843 6.934645 TGAACGAGTTCCAAGAATTTGATACT 59.065 34.615 12.76 0.00 38.77 2.12
3327 3844 8.092068 TGAACGAGTTCCAAGAATTTGATACTA 58.908 33.333 12.76 0.00 38.77 1.82
3328 3845 8.480643 AACGAGTTCCAAGAATTTGATACTAG 57.519 34.615 0.00 0.00 36.36 2.57
3353 3875 0.732880 ATCGAGGTCAAGAACGTGCG 60.733 55.000 0.00 0.00 0.00 5.34
3354 3876 1.660575 CGAGGTCAAGAACGTGCGT 60.661 57.895 0.00 0.00 0.00 5.24
3355 3877 0.386352 CGAGGTCAAGAACGTGCGTA 60.386 55.000 0.00 0.00 0.00 4.42
3356 3878 1.731424 CGAGGTCAAGAACGTGCGTAT 60.731 52.381 0.00 0.00 0.00 3.06
3357 3879 2.334838 GAGGTCAAGAACGTGCGTATT 58.665 47.619 0.00 0.00 0.00 1.89
3358 3880 3.504863 GAGGTCAAGAACGTGCGTATTA 58.495 45.455 0.00 0.00 0.00 0.98
3395 3974 7.686438 AATGTGACATGCAAGTGTATTCTTA 57.314 32.000 0.00 0.00 31.16 2.10
3468 4120 2.110213 GTGTGACGGGACCAAGCA 59.890 61.111 0.00 0.00 0.00 3.91
3544 4196 3.411446 TGCCTCGTCAACAGATCAAATT 58.589 40.909 0.00 0.00 0.00 1.82
3571 4224 7.381766 TCATAAATGTTTGGATCAGACTGTG 57.618 36.000 1.59 0.00 0.00 3.66
3641 4295 3.458189 GTCCGTATGTCTGAAATCCCAG 58.542 50.000 0.00 0.00 35.55 4.45
3650 4304 0.404040 TGAAATCCCAGAAACCGGCT 59.596 50.000 0.00 0.00 0.00 5.52
3656 4310 1.007387 CCAGAAACCGGCTGCAAAC 60.007 57.895 0.00 0.00 32.06 2.93
3721 4375 0.243636 GCCCACCCAAATTCAAGTCG 59.756 55.000 0.00 0.00 0.00 4.18
3726 4380 1.202879 ACCCAAATTCAAGTCGGAGCA 60.203 47.619 0.00 0.00 0.00 4.26
3741 4395 0.523072 GAGCACACGCATTTGGACAT 59.477 50.000 0.00 0.00 42.27 3.06
3746 4400 1.069296 ACACGCATTTGGACATTCACG 60.069 47.619 0.00 0.00 0.00 4.35
3758 4412 1.959985 ACATTCACGCCATTGTTTCCA 59.040 42.857 0.00 0.00 0.00 3.53
3773 4427 2.359354 CCACGCGAAATCCCACCA 60.359 61.111 15.93 0.00 0.00 4.17
3781 4435 2.417243 GCGAAATCCCACCATTTTCCAG 60.417 50.000 0.00 0.00 0.00 3.86
3783 4437 4.013728 CGAAATCCCACCATTTTCCAGTA 58.986 43.478 0.00 0.00 0.00 2.74
3803 4457 4.807304 AGTACAGTGTTACCTTTTGTGACG 59.193 41.667 0.00 0.00 36.29 4.35
3813 4469 7.874016 TGTTACCTTTTGTGACGAATAGTGTAT 59.126 33.333 0.00 0.00 36.29 2.29
3814 4470 9.357652 GTTACCTTTTGTGACGAATAGTGTATA 57.642 33.333 0.00 0.00 0.00 1.47
3816 4472 8.248117 ACCTTTTGTGACGAATAGTGTATAAC 57.752 34.615 0.00 0.00 0.00 1.89
3818 4474 6.874297 TTTGTGACGAATAGTGTATAACCG 57.126 37.500 0.00 0.00 0.00 4.44
3820 4476 4.142425 TGTGACGAATAGTGTATAACCGCA 60.142 41.667 0.00 0.00 0.00 5.69
3821 4477 4.205792 GTGACGAATAGTGTATAACCGCAC 59.794 45.833 0.00 0.00 35.98 5.34
3822 4478 4.096833 TGACGAATAGTGTATAACCGCACT 59.903 41.667 0.00 0.00 46.33 4.40
3850 4506 8.877864 TCAATTATCAGATACTGGTGGTTTTT 57.122 30.769 0.00 0.00 31.51 1.94
3886 4542 8.922931 AAATGTTTATTCCAGCCTGAAAAATT 57.077 26.923 0.00 0.00 0.00 1.82
3910 4567 6.033341 TGTTTTGCACCTTATTTCGCATATC 58.967 36.000 0.00 0.00 33.71 1.63
3913 4570 6.539649 TTGCACCTTATTTCGCATATCTAC 57.460 37.500 0.00 0.00 33.71 2.59
3975 4632 9.337396 AGACTTCATAGTACAATGACAAAAACA 57.663 29.630 0.00 0.00 35.63 2.83
4062 4720 4.196193 TCTTTTCTTTCGAACCTGCAGAA 58.804 39.130 17.39 0.69 0.00 3.02
4159 4817 2.933495 TAGTCTGACGAACAATCCCG 57.067 50.000 1.52 0.00 0.00 5.14
4207 4865 7.994425 TTCTCTTACAAGGTAAATGCATCAA 57.006 32.000 0.00 0.00 0.00 2.57
4208 4866 7.377766 TCTCTTACAAGGTAAATGCATCAAC 57.622 36.000 0.00 0.73 0.00 3.18
4317 4976 5.163744 CCAAACTGCATTCTCTCTTGATCAG 60.164 44.000 0.00 0.00 0.00 2.90
4341 5042 8.417106 CAGTGAACACATATAGTCTCTTATGGT 58.583 37.037 7.68 1.89 31.46 3.55
4348 5049 9.599866 CACATATAGTCTCTTATGGTTGTCAAA 57.400 33.333 7.35 0.00 31.46 2.69
4358 5059 2.665165 TGGTTGTCAAAGCATGGACTT 58.335 42.857 0.00 0.00 38.83 3.01
4372 5073 1.203300 TGGACTTCCAGGAGGACATCA 60.203 52.381 5.36 0.00 45.73 3.07
4386 5087 3.199946 AGGACATCACGTACCCAAATGAT 59.800 43.478 0.00 0.00 31.93 2.45
4399 5100 3.567164 CCCAAATGATCCGAGATCAAAGG 59.433 47.826 16.96 16.76 0.00 3.11
4411 5113 4.479619 GAGATCAAAGGTCAATGTTGTGC 58.520 43.478 0.00 0.00 0.00 4.57
4439 5141 0.537188 AGCAGTTGTACCGGGAGATG 59.463 55.000 6.32 0.00 0.00 2.90
4476 5178 0.109039 GACCGACACTGAGAAGGAGC 60.109 60.000 0.00 0.00 0.00 4.70
4497 5199 1.892474 TCCTGTAAAATGGCCACAAGC 59.108 47.619 8.16 0.00 42.60 4.01
4509 5211 1.737735 CACAAGCCAGCGATCGACA 60.738 57.895 21.57 0.00 0.00 4.35
4514 5216 2.178273 CCAGCGATCGACACGACA 59.822 61.111 21.57 0.00 39.18 4.35
4515 5217 1.226688 CCAGCGATCGACACGACAT 60.227 57.895 21.57 0.76 39.18 3.06
4527 5229 2.586079 CGACATAGGGGCGTGCAG 60.586 66.667 0.00 0.00 0.00 4.41
4549 5251 1.498865 GCGTAGATCCATGGCCAACG 61.499 60.000 10.96 15.08 0.00 4.10
4558 5260 1.077716 ATGGCCAACGACCTAAGCC 60.078 57.895 10.96 0.00 44.13 4.35
4614 5316 2.436417 TCAAGCTTACCAAGGCACATC 58.564 47.619 0.00 0.00 0.00 3.06
4634 5336 7.187480 CACATCTGTCTGAGCTATTTGATTTG 58.813 38.462 0.00 0.00 0.00 2.32
4636 5338 5.494724 TCTGTCTGAGCTATTTGATTTGCT 58.505 37.500 0.00 0.00 38.59 3.91
4638 5340 7.278135 TCTGTCTGAGCTATTTGATTTGCTAT 58.722 34.615 0.00 0.00 35.76 2.97
4653 5355 7.784037 TGATTTGCTATGCTAAAATCAATGGT 58.216 30.769 12.46 0.00 43.64 3.55
4660 5362 3.376859 TGCTAAAATCAATGGTGCGTAGG 59.623 43.478 0.00 0.00 0.00 3.18
4668 5370 0.108329 ATGGTGCGTAGGAGTTTCGG 60.108 55.000 0.00 0.00 0.00 4.30
4676 5378 2.443416 GTAGGAGTTTCGGGGCATTTT 58.557 47.619 0.00 0.00 0.00 1.82
4691 5393 3.489738 GGCATTTTGATCTTCATGTCCGG 60.490 47.826 0.00 0.00 0.00 5.14
4697 5399 0.749454 ATCTTCATGTCCGGGCTTGC 60.749 55.000 16.71 0.00 0.00 4.01
4704 5406 2.719531 TGTCCGGGCTTGCAATAATA 57.280 45.000 7.97 0.00 0.00 0.98
4706 5408 3.357203 TGTCCGGGCTTGCAATAATAAA 58.643 40.909 7.97 0.00 0.00 1.40
4773 5475 6.663953 CGGATGAGATCTCTTTATACCCCTTA 59.336 42.308 22.95 0.00 0.00 2.69
4844 5547 4.760047 CGGAGGTCAACTGGGCCG 62.760 72.222 0.00 0.00 0.00 6.13
4863 5566 4.680237 CCCAGCAGCGAACGGTCA 62.680 66.667 0.00 0.00 0.00 4.02
4877 5580 6.982141 AGCGAACGGTCACTATAATGAAATAA 59.018 34.615 0.00 0.00 0.00 1.40
4905 5608 7.009540 GGAAAATCCAAAGAAAATCTGTATGCG 59.990 37.037 0.00 0.00 36.28 4.73
4964 5667 1.867233 CGAGCCAAACCATTAGATCGG 59.133 52.381 0.00 0.00 0.00 4.18
4993 5696 5.239306 GCTATATTGGTTAATGAGCAGCACA 59.761 40.000 0.00 0.00 36.94 4.57
4994 5697 5.762825 ATATTGGTTAATGAGCAGCACAG 57.237 39.130 0.00 0.00 37.03 3.66
5006 5709 5.494724 TGAGCAGCACAGAATTCTAAGAAT 58.505 37.500 7.86 0.00 0.00 2.40
5024 5727 9.823647 TCTAAGAATTATGAACAAGGACAGATC 57.176 33.333 0.00 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.561733 CATGCTTGCATGTTGAGAGG 57.438 50.000 23.00 0.09 0.00 3.69
234 259 8.802267 TCCTTATTTGGTCTTCCACTTTTATTG 58.198 33.333 0.00 0.00 44.22 1.90
237 262 7.291566 TGTCCTTATTTGGTCTTCCACTTTTA 58.708 34.615 0.00 0.00 44.22 1.52
239 264 5.701224 TGTCCTTATTTGGTCTTCCACTTT 58.299 37.500 0.00 0.00 44.22 2.66
244 269 7.754851 TTAGTTTGTCCTTATTTGGTCTTCC 57.245 36.000 0.00 0.00 0.00 3.46
284 309 6.382282 GGGGAATTTCTGGATTTCTCTGAATT 59.618 38.462 0.00 0.00 0.00 2.17
285 310 5.896106 GGGGAATTTCTGGATTTCTCTGAAT 59.104 40.000 0.00 0.00 0.00 2.57
286 311 5.015603 AGGGGAATTTCTGGATTTCTCTGAA 59.984 40.000 0.00 0.00 0.00 3.02
287 312 4.541714 AGGGGAATTTCTGGATTTCTCTGA 59.458 41.667 0.00 0.00 0.00 3.27
288 313 4.864726 AGGGGAATTTCTGGATTTCTCTG 58.135 43.478 0.00 0.00 0.00 3.35
289 314 5.542848 AAGGGGAATTTCTGGATTTCTCT 57.457 39.130 0.00 0.00 0.00 3.10
290 315 6.611613 AAAAGGGGAATTTCTGGATTTCTC 57.388 37.500 0.00 0.00 0.00 2.87
291 316 6.013379 GGAAAAAGGGGAATTTCTGGATTTCT 60.013 38.462 0.00 0.00 36.15 2.52
299 324 6.620429 TCTAACTGGAAAAAGGGGAATTTCT 58.380 36.000 0.00 0.00 36.15 2.52
333 358 5.639506 ATTGTTGTTCAAGTCAGGATACTCG 59.360 40.000 0.00 0.00 42.36 4.18
503 537 2.468532 AGCGCACCGTATTTTTATGC 57.531 45.000 11.47 0.00 0.00 3.14
659 695 6.074249 GCCTGCGTCTACAGTATTTTATTCTC 60.074 42.308 0.00 0.00 35.83 2.87
683 719 2.283472 GAATGGGCCGAATGTGGTGC 62.283 60.000 0.00 0.00 0.00 5.01
720 756 2.376518 TCATTTGTCTTCTGGGGCTCTT 59.623 45.455 0.00 0.00 0.00 2.85
730 766 3.561725 GGACGGATGGATCATTTGTCTTC 59.438 47.826 0.00 0.00 32.65 2.87
739 775 3.546543 GGGCGGACGGATGGATCA 61.547 66.667 0.00 0.00 0.00 2.92
920 1252 0.168128 CCAATCGGTTCTTGGTTCGC 59.832 55.000 0.00 0.00 38.67 4.70
936 1268 1.122632 TGTTGCCCGTCCTACTCCAA 61.123 55.000 0.00 0.00 0.00 3.53
938 1270 0.391263 CTTGTTGCCCGTCCTACTCC 60.391 60.000 0.00 0.00 0.00 3.85
939 1271 0.391263 CCTTGTTGCCCGTCCTACTC 60.391 60.000 0.00 0.00 0.00 2.59
946 1278 1.228154 GGTTCTCCTTGTTGCCCGT 60.228 57.895 0.00 0.00 0.00 5.28
986 1318 3.365291 GACATACGGACGGGCAGCA 62.365 63.158 0.00 0.00 0.00 4.41
999 1331 1.739667 CGGGCTCGACATGGACATA 59.260 57.895 0.00 0.00 39.00 2.29
1692 2039 4.155733 CCGGCGGTGTAGATGGCA 62.156 66.667 19.97 0.00 0.00 4.92
1923 2270 4.498345 GCTAGTCATGCTAGTACACTGGAC 60.498 50.000 18.99 0.00 46.81 4.02
1939 2286 2.897326 TCAAGGTAAGTGCAGCTAGTCA 59.103 45.455 0.00 0.00 0.00 3.41
2038 2386 1.635663 CGGACCGGATCAAGTGCAAC 61.636 60.000 9.46 0.00 0.00 4.17
2040 2388 2.264480 CGGACCGGATCAAGTGCA 59.736 61.111 9.46 0.00 0.00 4.57
2051 2399 1.985447 TTTCTCGATCCGACGGACCG 61.985 60.000 25.10 25.10 40.72 4.79
2082 2430 3.490348 TGATCTCTGGACTATGCGATCA 58.510 45.455 0.00 0.00 36.04 2.92
2166 2627 2.564504 CCTCGGATCTCCATTATGAGCA 59.435 50.000 0.00 0.00 35.14 4.26
2176 2637 5.930837 AATCTCATTATCCTCGGATCTCC 57.069 43.478 0.86 0.00 36.17 3.71
2177 2638 9.883142 AAATAAATCTCATTATCCTCGGATCTC 57.117 33.333 0.86 0.00 36.17 2.75
2178 2639 9.664332 CAAATAAATCTCATTATCCTCGGATCT 57.336 33.333 0.86 0.00 36.17 2.75
2180 2641 9.799106 AACAAATAAATCTCATTATCCTCGGAT 57.201 29.630 3.61 3.61 38.54 4.18
2181 2642 9.627123 AAACAAATAAATCTCATTATCCTCGGA 57.373 29.630 0.00 0.00 0.00 4.55
2182 2643 9.669353 CAAACAAATAAATCTCATTATCCTCGG 57.331 33.333 0.00 0.00 0.00 4.63
2244 2726 5.245977 AGTTGCCTTACCATAAATTGCAAGT 59.754 36.000 4.94 0.00 37.85 3.16
2245 2727 5.723295 AGTTGCCTTACCATAAATTGCAAG 58.277 37.500 4.94 0.00 37.85 4.01
2246 2728 5.736951 AGTTGCCTTACCATAAATTGCAA 57.263 34.783 0.00 0.00 35.13 4.08
2247 2729 5.736951 AAGTTGCCTTACCATAAATTGCA 57.263 34.783 0.00 0.00 0.00 4.08
2248 2730 8.410141 TGTATAAGTTGCCTTACCATAAATTGC 58.590 33.333 0.00 0.00 36.03 3.56
2251 2733 9.695155 ACTTGTATAAGTTGCCTTACCATAAAT 57.305 29.630 0.00 0.00 44.57 1.40
2287 2769 5.802465 TGCAATTATCCTGCATTTTCCAAA 58.198 33.333 0.00 0.00 44.67 3.28
2311 2793 3.895041 TGTTGTACTCACTCACCTGATCA 59.105 43.478 0.00 0.00 0.00 2.92
2313 2795 4.955811 TTGTTGTACTCACTCACCTGAT 57.044 40.909 0.00 0.00 0.00 2.90
2314 2796 4.955811 ATTGTTGTACTCACTCACCTGA 57.044 40.909 0.00 0.00 0.00 3.86
2315 2797 5.277974 CCAAATTGTTGTACTCACTCACCTG 60.278 44.000 0.00 0.00 32.40 4.00
2316 2798 4.821805 CCAAATTGTTGTACTCACTCACCT 59.178 41.667 0.00 0.00 32.40 4.00
2317 2799 4.578928 ACCAAATTGTTGTACTCACTCACC 59.421 41.667 0.00 0.00 32.40 4.02
2320 2802 6.201425 TCGTTACCAAATTGTTGTACTCACTC 59.799 38.462 0.00 0.00 32.40 3.51
2322 2804 6.289745 TCGTTACCAAATTGTTGTACTCAC 57.710 37.500 0.00 0.00 32.40 3.51
2324 2806 5.467735 ACCTCGTTACCAAATTGTTGTACTC 59.532 40.000 0.00 0.00 32.40 2.59
2325 2807 5.370679 ACCTCGTTACCAAATTGTTGTACT 58.629 37.500 0.00 0.00 32.40 2.73
2326 2808 5.678132 ACCTCGTTACCAAATTGTTGTAC 57.322 39.130 0.00 0.00 32.40 2.90
2327 2809 7.798596 TTAACCTCGTTACCAAATTGTTGTA 57.201 32.000 0.00 0.00 32.40 2.41
2332 2823 6.604930 ACGATTTAACCTCGTTACCAAATTG 58.395 36.000 6.47 0.00 46.49 2.32
2335 2826 6.145371 GTGTACGATTTAACCTCGTTACCAAA 59.855 38.462 15.17 0.00 46.49 3.28
2339 2830 7.244192 AGTAGTGTACGATTTAACCTCGTTAC 58.756 38.462 15.17 14.10 46.49 2.50
2356 2848 7.039882 GCAAAGTAGCCAATTCTAGTAGTGTA 58.960 38.462 0.00 0.00 0.00 2.90
2365 2857 4.026356 ACTCAGCAAAGTAGCCAATTCT 57.974 40.909 0.00 0.00 34.23 2.40
2397 2889 5.802956 CAGCAAAGTAGTTCCGTTTCAAAAA 59.197 36.000 0.00 0.00 0.00 1.94
2400 2892 4.193090 TCAGCAAAGTAGTTCCGTTTCAA 58.807 39.130 0.00 0.00 0.00 2.69
2401 2893 3.799366 TCAGCAAAGTAGTTCCGTTTCA 58.201 40.909 0.00 0.00 0.00 2.69
2402 2894 3.808174 ACTCAGCAAAGTAGTTCCGTTTC 59.192 43.478 0.00 0.00 0.00 2.78
2406 2898 3.120991 CGAAACTCAGCAAAGTAGTTCCG 60.121 47.826 0.00 0.00 32.42 4.30
2407 2899 4.056050 TCGAAACTCAGCAAAGTAGTTCC 58.944 43.478 0.00 0.00 32.42 3.62
2408 2900 4.150804 CCTCGAAACTCAGCAAAGTAGTTC 59.849 45.833 0.00 0.00 32.42 3.01
2409 2901 4.058817 CCTCGAAACTCAGCAAAGTAGTT 58.941 43.478 0.00 0.00 35.01 2.24
2410 2902 3.321111 TCCTCGAAACTCAGCAAAGTAGT 59.679 43.478 0.00 0.00 0.00 2.73
2411 2903 3.914312 TCCTCGAAACTCAGCAAAGTAG 58.086 45.455 0.00 0.00 0.00 2.57
2412 2904 4.537135 ATCCTCGAAACTCAGCAAAGTA 57.463 40.909 0.00 0.00 0.00 2.24
2413 2905 2.910688 TCCTCGAAACTCAGCAAAGT 57.089 45.000 0.00 0.00 0.00 2.66
2414 2906 5.862924 TTTATCCTCGAAACTCAGCAAAG 57.137 39.130 0.00 0.00 0.00 2.77
2415 2907 5.763204 AGTTTTATCCTCGAAACTCAGCAAA 59.237 36.000 0.00 0.00 40.97 3.68
2416 2908 5.305585 AGTTTTATCCTCGAAACTCAGCAA 58.694 37.500 0.00 0.00 40.97 3.91
2417 2909 4.894784 AGTTTTATCCTCGAAACTCAGCA 58.105 39.130 0.00 0.00 40.97 4.41
2428 2920 6.307155 CAACACAATGTCGAGTTTTATCCTC 58.693 40.000 0.00 0.00 0.00 3.71
2429 2921 5.334879 GCAACACAATGTCGAGTTTTATCCT 60.335 40.000 0.00 0.00 0.00 3.24
2436 2928 0.586319 CCGCAACACAATGTCGAGTT 59.414 50.000 0.00 0.00 0.00 3.01
2442 2934 3.609853 ACATATCTCCGCAACACAATGT 58.390 40.909 0.00 0.00 0.00 2.71
2457 2949 6.604735 AGTATTGTTTGCCGAGAACATATC 57.395 37.500 0.00 0.00 36.92 1.63
2460 2952 4.082787 CCAAGTATTGTTTGCCGAGAACAT 60.083 41.667 0.00 0.00 46.99 2.71
2472 2964 4.000988 CGTACTTCCAGCCAAGTATTGTT 58.999 43.478 4.35 0.00 46.99 2.83
2473 2965 3.259876 TCGTACTTCCAGCCAAGTATTGT 59.740 43.478 4.35 0.00 46.99 2.71
2477 2969 1.200716 CGTCGTACTTCCAGCCAAGTA 59.799 52.381 0.00 0.00 37.75 2.24
2484 2976 0.456312 GAGTGCCGTCGTACTTCCAG 60.456 60.000 1.58 0.00 34.75 3.86
2495 2994 3.081061 TCAGCAAATTAATGAGTGCCGT 58.919 40.909 12.86 0.00 37.73 5.68
2520 3019 9.048446 GGTGTTTGTCAAGTGTCTAGTTATAAA 57.952 33.333 0.00 0.00 0.00 1.40
2521 3020 8.426489 AGGTGTTTGTCAAGTGTCTAGTTATAA 58.574 33.333 0.00 0.00 0.00 0.98
2522 3021 7.959175 AGGTGTTTGTCAAGTGTCTAGTTATA 58.041 34.615 0.00 0.00 0.00 0.98
2523 3022 6.827727 AGGTGTTTGTCAAGTGTCTAGTTAT 58.172 36.000 0.00 0.00 0.00 1.89
2524 3023 6.229936 AGGTGTTTGTCAAGTGTCTAGTTA 57.770 37.500 0.00 0.00 0.00 2.24
2525 3024 5.099042 AGGTGTTTGTCAAGTGTCTAGTT 57.901 39.130 0.00 0.00 0.00 2.24
2526 3025 4.755266 AGGTGTTTGTCAAGTGTCTAGT 57.245 40.909 0.00 0.00 0.00 2.57
2527 3026 6.761714 AGTTTAGGTGTTTGTCAAGTGTCTAG 59.238 38.462 0.00 0.00 0.00 2.43
2528 3027 6.646267 AGTTTAGGTGTTTGTCAAGTGTCTA 58.354 36.000 0.00 0.00 0.00 2.59
2529 3028 5.497474 AGTTTAGGTGTTTGTCAAGTGTCT 58.503 37.500 0.00 0.00 0.00 3.41
2530 3029 5.813080 AGTTTAGGTGTTTGTCAAGTGTC 57.187 39.130 0.00 0.00 0.00 3.67
2531 3030 7.175293 TGTTTAGTTTAGGTGTTTGTCAAGTGT 59.825 33.333 0.00 0.00 0.00 3.55
2536 3035 5.066764 GGCTGTTTAGTTTAGGTGTTTGTCA 59.933 40.000 0.00 0.00 0.00 3.58
2550 3049 1.607148 GTTCGGCAAAGGCTGTTTAGT 59.393 47.619 0.00 0.00 46.81 2.24
2551 3050 1.880027 AGTTCGGCAAAGGCTGTTTAG 59.120 47.619 0.00 0.00 46.81 1.85
2552 3051 1.975660 AGTTCGGCAAAGGCTGTTTA 58.024 45.000 0.00 0.00 46.81 2.01
2553 3052 1.067060 GAAGTTCGGCAAAGGCTGTTT 59.933 47.619 0.00 0.00 46.81 2.83
2554 3053 0.668535 GAAGTTCGGCAAAGGCTGTT 59.331 50.000 0.00 0.00 46.81 3.16
2555 3054 1.507141 CGAAGTTCGGCAAAGGCTGT 61.507 55.000 17.61 0.00 46.81 4.40
2557 3056 3.655481 CGAAGTTCGGCAAAGGCT 58.345 55.556 17.61 0.00 40.87 4.58
2566 3065 3.910648 AGTTCTAGTTTCCCGAAGTTCG 58.089 45.455 18.40 18.40 40.07 3.95
2567 3066 4.879598 TGAGTTCTAGTTTCCCGAAGTTC 58.120 43.478 0.00 0.00 0.00 3.01
2568 3067 4.799917 GCTGAGTTCTAGTTTCCCGAAGTT 60.800 45.833 0.00 0.00 0.00 2.66
2569 3068 3.306156 GCTGAGTTCTAGTTTCCCGAAGT 60.306 47.826 0.00 0.00 0.00 3.01
2570 3069 3.254892 GCTGAGTTCTAGTTTCCCGAAG 58.745 50.000 0.00 0.00 0.00 3.79
2571 3070 2.631062 TGCTGAGTTCTAGTTTCCCGAA 59.369 45.455 0.00 0.00 0.00 4.30
2572 3071 2.244695 TGCTGAGTTCTAGTTTCCCGA 58.755 47.619 0.00 0.00 0.00 5.14
2573 3072 2.743636 TGCTGAGTTCTAGTTTCCCG 57.256 50.000 0.00 0.00 0.00 5.14
2574 3073 4.390264 AGTTTGCTGAGTTCTAGTTTCCC 58.610 43.478 0.00 0.00 0.00 3.97
2575 3074 5.408909 GGTAGTTTGCTGAGTTCTAGTTTCC 59.591 44.000 0.00 0.00 0.00 3.13
2576 3075 5.989777 TGGTAGTTTGCTGAGTTCTAGTTTC 59.010 40.000 0.00 0.00 0.00 2.78
2577 3076 5.758784 GTGGTAGTTTGCTGAGTTCTAGTTT 59.241 40.000 0.00 0.00 0.00 2.66
2578 3077 5.298347 GTGGTAGTTTGCTGAGTTCTAGTT 58.702 41.667 0.00 0.00 0.00 2.24
2579 3078 4.558898 CGTGGTAGTTTGCTGAGTTCTAGT 60.559 45.833 0.00 0.00 0.00 2.57
2580 3079 3.921021 CGTGGTAGTTTGCTGAGTTCTAG 59.079 47.826 0.00 0.00 0.00 2.43
2581 3080 3.319972 ACGTGGTAGTTTGCTGAGTTCTA 59.680 43.478 0.00 0.00 0.00 2.10
2582 3081 2.102588 ACGTGGTAGTTTGCTGAGTTCT 59.897 45.455 0.00 0.00 0.00 3.01
2583 3082 2.480845 ACGTGGTAGTTTGCTGAGTTC 58.519 47.619 0.00 0.00 0.00 3.01
2584 3083 2.614829 ACGTGGTAGTTTGCTGAGTT 57.385 45.000 0.00 0.00 0.00 3.01
2585 3084 2.614829 AACGTGGTAGTTTGCTGAGT 57.385 45.000 0.00 0.00 0.00 3.41
2586 3085 3.386486 TGTAACGTGGTAGTTTGCTGAG 58.614 45.455 0.00 0.00 35.70 3.35
2587 3086 3.455990 TGTAACGTGGTAGTTTGCTGA 57.544 42.857 0.00 0.00 35.70 4.26
2591 3090 4.431986 CGTTCGATGTAACGTGGTAGTTTG 60.432 45.833 0.00 0.00 45.46 2.93
2606 3105 0.636733 CGTTTACGGGTCGTTCGATG 59.363 55.000 0.00 0.00 41.54 3.84
2618 3117 2.384309 TGATGCACCGCCGTTTACG 61.384 57.895 0.00 0.00 39.44 3.18
2626 3125 0.810031 ATCTTACCGTGATGCACCGC 60.810 55.000 0.00 0.00 0.00 5.68
2629 3128 4.033358 CAGAAAGATCTTACCGTGATGCAC 59.967 45.833 8.75 0.00 32.03 4.57
2635 3134 4.800993 CACTAGCAGAAAGATCTTACCGTG 59.199 45.833 8.75 5.28 32.03 4.94
2750 3257 7.040478 CCATTTAGAAAGGAAGAACACACATGA 60.040 37.037 0.00 0.00 0.00 3.07
2862 3369 2.159085 AGGATGGCTAGCTCACGTTAAC 60.159 50.000 15.72 0.00 0.00 2.01
2883 3390 7.611855 TGAGACAGAGAGAACAGTATCAACATA 59.388 37.037 0.00 0.00 30.27 2.29
2884 3391 6.435591 TGAGACAGAGAGAACAGTATCAACAT 59.564 38.462 0.00 0.00 30.27 2.71
2885 3392 5.770162 TGAGACAGAGAGAACAGTATCAACA 59.230 40.000 0.00 0.00 30.27 3.33
2886 3393 6.260870 TGAGACAGAGAGAACAGTATCAAC 57.739 41.667 0.00 0.00 30.27 3.18
2887 3394 8.581253 TTATGAGACAGAGAGAACAGTATCAA 57.419 34.615 0.00 0.00 36.06 2.57
2920 3433 1.582610 GCGGAGGATGCCAAAAACGA 61.583 55.000 0.00 0.00 0.00 3.85
2932 3445 2.409064 TCTTATTATGGGGCGGAGGA 57.591 50.000 0.00 0.00 0.00 3.71
2933 3446 3.775316 ACTATCTTATTATGGGGCGGAGG 59.225 47.826 0.00 0.00 0.00 4.30
2934 3447 5.422214 AACTATCTTATTATGGGGCGGAG 57.578 43.478 0.00 0.00 0.00 4.63
2935 3448 5.836024 AAACTATCTTATTATGGGGCGGA 57.164 39.130 0.00 0.00 0.00 5.54
2936 3449 6.894339 AAAAACTATCTTATTATGGGGCGG 57.106 37.500 0.00 0.00 0.00 6.13
2967 3480 7.552687 TCCGTCTCACAATATAAGAGCATTTTT 59.447 33.333 0.00 0.00 0.00 1.94
2968 3481 7.047891 TCCGTCTCACAATATAAGAGCATTTT 58.952 34.615 0.00 0.00 0.00 1.82
2972 3485 4.038042 CCTCCGTCTCACAATATAAGAGCA 59.962 45.833 0.00 0.00 0.00 4.26
2976 3489 4.559704 GCTCCCTCCGTCTCACAATATAAG 60.560 50.000 0.00 0.00 0.00 1.73
2987 3500 2.160721 TAATTCTGCTCCCTCCGTCT 57.839 50.000 0.00 0.00 0.00 4.18
3077 3591 2.639065 TCGTTTCATTGCCCTATGGAC 58.361 47.619 0.00 0.00 0.00 4.02
3100 3614 4.507756 TGTTCTTTTCTGTGAGTGTCATCG 59.492 41.667 0.00 0.00 0.00 3.84
3137 3651 0.608130 CTGTCATCTGACCCGGACAA 59.392 55.000 0.73 0.00 44.15 3.18
3157 3671 4.051922 GTCAGTGTTCACTTGTCGAGATT 58.948 43.478 2.47 0.00 0.00 2.40
3166 3682 3.393800 CCGAATCAGTCAGTGTTCACTT 58.606 45.455 2.47 0.00 0.00 3.16
3210 3726 4.504826 GGAGAAAGATCAACGCTAACTAGC 59.495 45.833 0.00 0.00 45.62 3.42
3211 3727 5.044558 GGGAGAAAGATCAACGCTAACTAG 58.955 45.833 0.00 0.00 0.00 2.57
3271 3787 5.916661 AACTCAATTCGAGGTTCTAGCTA 57.083 39.130 0.00 0.00 39.23 3.32
3353 3875 8.489559 TGTCACATTTGAAACACGTACTAATAC 58.510 33.333 0.00 0.00 31.90 1.89
3354 3876 8.590719 TGTCACATTTGAAACACGTACTAATA 57.409 30.769 0.00 0.00 31.90 0.98
3355 3877 7.485418 TGTCACATTTGAAACACGTACTAAT 57.515 32.000 0.00 0.00 31.90 1.73
3356 3878 6.905544 TGTCACATTTGAAACACGTACTAA 57.094 33.333 0.00 0.00 31.90 2.24
3357 3879 6.565060 GCATGTCACATTTGAAACACGTACTA 60.565 38.462 0.00 0.00 31.90 1.82
3358 3880 5.747565 CATGTCACATTTGAAACACGTACT 58.252 37.500 0.00 0.00 31.90 2.73
3544 4196 7.448161 ACAGTCTGATCCAAACATTTATGAACA 59.552 33.333 6.91 0.00 0.00 3.18
3584 4238 3.520290 TGATTACTGTCGGTGGATGAC 57.480 47.619 0.00 0.00 36.88 3.06
3641 4295 1.082104 CTCGTTTGCAGCCGGTTTC 60.082 57.895 1.90 0.00 0.00 2.78
3721 4375 1.210155 GTCCAAATGCGTGTGCTCC 59.790 57.895 0.00 0.00 43.34 4.70
3726 4380 1.069296 CGTGAATGTCCAAATGCGTGT 60.069 47.619 0.00 0.00 0.00 4.49
3741 4395 0.309302 CGTGGAAACAATGGCGTGAA 59.691 50.000 0.00 0.00 46.06 3.18
3746 4400 0.318275 TTTCGCGTGGAAACAATGGC 60.318 50.000 5.77 0.00 46.06 4.40
3758 4412 1.201414 GAAAATGGTGGGATTTCGCGT 59.799 47.619 5.77 0.00 0.00 6.01
3773 4427 7.340999 ACAAAAGGTAACACTGTACTGGAAAAT 59.659 33.333 4.66 0.00 41.41 1.82
3781 4435 4.805192 TCGTCACAAAAGGTAACACTGTAC 59.195 41.667 0.00 0.00 41.41 2.90
3783 4437 3.864243 TCGTCACAAAAGGTAACACTGT 58.136 40.909 0.00 0.00 41.41 3.55
3803 4457 6.270815 TGAGAAGTGCGGTTATACACTATTC 58.729 40.000 0.00 0.00 46.17 1.75
3813 4469 5.972935 TCTGATAATTGAGAAGTGCGGTTA 58.027 37.500 0.00 0.00 0.00 2.85
3814 4470 4.832248 TCTGATAATTGAGAAGTGCGGTT 58.168 39.130 0.00 0.00 0.00 4.44
3816 4472 6.145209 CAGTATCTGATAATTGAGAAGTGCGG 59.855 42.308 0.00 0.00 32.44 5.69
3818 4474 6.989169 ACCAGTATCTGATAATTGAGAAGTGC 59.011 38.462 0.00 0.00 32.44 4.40
3820 4476 7.126421 ACCACCAGTATCTGATAATTGAGAAGT 59.874 37.037 0.00 0.00 32.44 3.01
3821 4477 7.504403 ACCACCAGTATCTGATAATTGAGAAG 58.496 38.462 0.00 0.00 32.44 2.85
3822 4478 7.437713 ACCACCAGTATCTGATAATTGAGAA 57.562 36.000 0.00 0.00 32.44 2.87
3850 4506 9.651913 GCTGGAATAAACATTTCTATTTTTCCA 57.348 29.630 8.60 8.60 35.74 3.53
3873 4529 4.496175 GGTGCAAAACAATTTTTCAGGCTG 60.496 41.667 8.58 8.58 32.27 4.85
3886 4542 3.717400 TGCGAAATAAGGTGCAAAACA 57.283 38.095 0.00 0.00 33.80 2.83
3994 4652 9.806448 AACACATTATACCATATATTTGAGGCA 57.194 29.630 0.00 0.00 0.00 4.75
4062 4720 7.469537 ACTCTACTGTATTAGCAAGTCTTGT 57.530 36.000 14.03 4.06 0.00 3.16
4159 4817 3.435671 CACTTCCCATCAAACCGTACTTC 59.564 47.826 0.00 0.00 0.00 3.01
4317 4976 9.035607 CAACCATAAGAGACTATATGTGTTCAC 57.964 37.037 6.88 0.00 0.00 3.18
4341 5042 2.886523 CTGGAAGTCCATGCTTTGACAA 59.113 45.455 0.00 0.00 46.46 3.18
4348 5049 0.252881 TCCTCCTGGAAGTCCATGCT 60.253 55.000 0.00 0.00 46.46 3.79
4358 5059 1.471119 GTACGTGATGTCCTCCTGGA 58.529 55.000 0.00 0.00 40.69 3.86
4366 5067 3.560068 GGATCATTTGGGTACGTGATGTC 59.440 47.826 0.00 0.00 31.86 3.06
4372 5073 2.104967 TCTCGGATCATTTGGGTACGT 58.895 47.619 0.00 0.00 0.00 3.57
4386 5087 3.981071 ACATTGACCTTTGATCTCGGA 57.019 42.857 0.00 0.00 0.00 4.55
4399 5100 3.969117 TCAAGTCAGCACAACATTGAC 57.031 42.857 0.00 0.00 41.10 3.18
4411 5113 2.476619 CGGTACAACTGCTTCAAGTCAG 59.523 50.000 7.15 7.15 36.45 3.51
4425 5127 0.325296 AGCTCCATCTCCCGGTACAA 60.325 55.000 0.00 0.00 0.00 2.41
4465 5167 4.543590 TTTTACAGGAGCTCCTTCTCAG 57.456 45.455 33.33 22.64 46.09 3.35
4476 5178 2.094545 GCTTGTGGCCATTTTACAGGAG 60.095 50.000 9.72 0.00 34.27 3.69
4489 5191 3.869272 CGATCGCTGGCTTGTGGC 61.869 66.667 0.26 0.00 40.90 5.01
4497 5199 0.028902 TATGTCGTGTCGATCGCTGG 59.971 55.000 11.09 0.00 38.42 4.85
4504 5206 2.767445 CGCCCCTATGTCGTGTCGA 61.767 63.158 0.00 0.00 0.00 4.20
4509 5211 3.371097 CTGCACGCCCCTATGTCGT 62.371 63.158 0.00 0.00 36.84 4.34
4514 5216 4.864334 GCAGCTGCACGCCCCTAT 62.864 66.667 33.36 0.00 41.59 2.57
4527 5229 1.963338 GGCCATGGATCTACGCAGC 60.963 63.158 18.40 0.00 0.00 5.25
4528 5230 0.179048 TTGGCCATGGATCTACGCAG 60.179 55.000 18.40 0.00 0.00 5.18
4529 5231 0.463654 GTTGGCCATGGATCTACGCA 60.464 55.000 18.40 0.00 0.00 5.24
4530 5232 1.498865 CGTTGGCCATGGATCTACGC 61.499 60.000 18.40 0.00 0.00 4.42
4558 5260 4.122046 CTCTTTTTGTTTCTTGGCCTTGG 58.878 43.478 3.32 0.00 0.00 3.61
4571 5273 6.550854 TGATCCTTTTGGTGATCTCTTTTTGT 59.449 34.615 0.00 0.00 38.53 2.83
4614 5316 5.814764 AGCAAATCAAATAGCTCAGACAG 57.185 39.130 0.00 0.00 30.05 3.51
4634 5336 3.976942 CGCACCATTGATTTTAGCATAGC 59.023 43.478 0.00 0.00 0.00 2.97
4636 5338 5.238432 CCTACGCACCATTGATTTTAGCATA 59.762 40.000 0.00 0.00 0.00 3.14
4638 5340 3.376859 CCTACGCACCATTGATTTTAGCA 59.623 43.478 0.00 0.00 0.00 3.49
4653 5355 2.975536 CCCCGAAACTCCTACGCA 59.024 61.111 0.00 0.00 0.00 5.24
4660 5362 2.755103 AGATCAAAATGCCCCGAAACTC 59.245 45.455 0.00 0.00 0.00 3.01
4668 5370 3.489738 CGGACATGAAGATCAAAATGCCC 60.490 47.826 0.00 0.00 0.00 5.36
4676 5378 0.911769 AAGCCCGGACATGAAGATCA 59.088 50.000 0.73 0.00 0.00 2.92
4717 5419 5.128205 GTTTAGGGGGTTATACGAAAGCAT 58.872 41.667 0.00 0.00 0.00 3.79
4724 5426 5.026038 TGATGTGTTTAGGGGGTTATACG 57.974 43.478 0.00 0.00 0.00 3.06
4728 5430 3.559597 CCGTTGATGTGTTTAGGGGGTTA 60.560 47.826 0.00 0.00 0.00 2.85
4801 5504 1.029408 AGTGCGGGCGATGCATTTTA 61.029 50.000 0.00 0.00 45.34 1.52
4897 5600 0.813610 TTGATTCCCGCCGCATACAG 60.814 55.000 0.00 0.00 0.00 2.74
4905 5608 2.696759 CCCGTGTTTGATTCCCGCC 61.697 63.158 0.00 0.00 0.00 6.13
4943 5646 2.550978 CGATCTAATGGTTTGGCTCGT 58.449 47.619 0.00 0.00 30.35 4.18
4964 5667 5.702670 TGCTCATTAACCAATATAGCTCAGC 59.297 40.000 0.00 0.00 35.14 4.26
5006 5709 6.037786 AGTTCGATCTGTCCTTGTTCATAA 57.962 37.500 0.00 0.00 0.00 1.90
5035 5739 9.838339 TTTAGAAAAGGTTGCATCCAAAAATTA 57.162 25.926 16.12 0.00 31.68 1.40
5056 5760 7.687005 ATTTTGAAAAATGTTCGCGTTTAGA 57.313 28.000 5.77 0.00 37.24 2.10


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

AutoCloner maintained by Alex Coulton.