Multiple sequence alignment - TraesCS2A01G496000

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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 TraesCS2A01G496000 chr2A 100.000 4823 0 0 1 4823 727196867 727192045 0.000000e+00 8907.0
1 TraesCS2A01G496000 chr2D 94.002 4185 182 34 126 4262 592639859 592635696 0.000000e+00 6274.0
2 TraesCS2A01G496000 chr2D 74.833 1200 280 20 2405 3595 644170765 644169579 1.540000e-144 523.0
3 TraesCS2A01G496000 chr2D 91.051 257 20 3 4568 4823 592635307 592635053 1.290000e-90 344.0
4 TraesCS2A01G496000 chr2B 95.849 3782 137 9 485 4262 718608331 718604566 0.000000e+00 6096.0
5 TraesCS2A01G496000 chr2B 73.425 730 158 26 2603 3322 792954739 792955442 1.730000e-59 241.0
6 TraesCS2A01G496000 chr2B 84.047 257 18 11 4568 4823 718604206 718603972 4.860000e-55 226.0
7 TraesCS2A01G496000 chr2B 80.935 278 22 18 240 489 718608626 718608352 1.770000e-44 191.0
8 TraesCS2A01G496000 chr4A 72.551 2379 545 83 1895 4219 498987888 498985564 0.000000e+00 676.0
9 TraesCS2A01G496000 chr3A 72.768 1781 441 41 1881 3639 36301075 36302833 3.260000e-156 562.0
10 TraesCS2A01G496000 chr3A 74.673 995 224 23 2708 3689 36290744 36291723 2.690000e-112 416.0
11 TraesCS2A01G496000 chr3D 72.706 1711 420 40 1929 3614 26301727 26303415 3.310000e-146 529.0
12 TraesCS2A01G496000 chr3D 75.497 1106 244 24 2589 3682 26292331 26293421 2.570000e-142 516.0
13 TraesCS2A01G496000 chr3D 75.816 980 216 18 2712 3682 26282919 26283886 1.210000e-130 477.0
14 TraesCS2A01G496000 chr3D 71.944 1775 449 47 1881 3632 26221675 26219927 1.570000e-129 473.0
15 TraesCS2A01G496000 chrUn 72.028 1859 454 55 1859 3687 75442341 75444163 4.340000e-135 492.0
16 TraesCS2A01G496000 chr3B 74.977 1107 248 25 2589 3682 43850568 43851658 2.610000e-132 483.0
17 TraesCS2A01G496000 chr6B 84.507 71 11 0 2720 2790 718564270 718564340 2.410000e-08 71.3
18 TraesCS2A01G496000 chr6B 78.846 104 22 0 2694 2797 718564466 718564569 2.410000e-08 71.3


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 TraesCS2A01G496000 chr2A 727192045 727196867 4822 True 8907 8907 100.000000 1 4823 1 chr2A.!!$R1 4822
1 TraesCS2A01G496000 chr2D 592635053 592639859 4806 True 3309 6274 92.526500 126 4823 2 chr2D.!!$R2 4697
2 TraesCS2A01G496000 chr2D 644169579 644170765 1186 True 523 523 74.833000 2405 3595 1 chr2D.!!$R1 1190
3 TraesCS2A01G496000 chr2B 718603972 718608626 4654 True 2171 6096 86.943667 240 4823 3 chr2B.!!$R1 4583
4 TraesCS2A01G496000 chr2B 792954739 792955442 703 False 241 241 73.425000 2603 3322 1 chr2B.!!$F1 719
5 TraesCS2A01G496000 chr4A 498985564 498987888 2324 True 676 676 72.551000 1895 4219 1 chr4A.!!$R1 2324
6 TraesCS2A01G496000 chr3A 36301075 36302833 1758 False 562 562 72.768000 1881 3639 1 chr3A.!!$F2 1758
7 TraesCS2A01G496000 chr3A 36290744 36291723 979 False 416 416 74.673000 2708 3689 1 chr3A.!!$F1 981
8 TraesCS2A01G496000 chr3D 26301727 26303415 1688 False 529 529 72.706000 1929 3614 1 chr3D.!!$F3 1685
9 TraesCS2A01G496000 chr3D 26292331 26293421 1090 False 516 516 75.497000 2589 3682 1 chr3D.!!$F2 1093
10 TraesCS2A01G496000 chr3D 26282919 26283886 967 False 477 477 75.816000 2712 3682 1 chr3D.!!$F1 970
11 TraesCS2A01G496000 chr3D 26219927 26221675 1748 True 473 473 71.944000 1881 3632 1 chr3D.!!$R1 1751
12 TraesCS2A01G496000 chrUn 75442341 75444163 1822 False 492 492 72.028000 1859 3687 1 chrUn.!!$F1 1828
13 TraesCS2A01G496000 chr3B 43850568 43851658 1090 False 483 483 74.977000 2589 3682 1 chr3B.!!$F1 1093

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
51 52 0.462789 CAAATAGGGGCGGAGTACGT 59.537 55.0 0.00 0.0 46.52 3.57 F
1233 1325 0.389948 GACATCGCGTCACTTCCCTT 60.390 55.0 5.77 0.0 44.69 3.95 F
2244 2339 0.390860 CGGAATGGCTAGGGACTCTG 59.609 60.0 0.00 0.0 41.75 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1498 1590 0.037447 AGGCTTTGAAGGTGAGGAGC 59.963 55.0 0.0 0.0 0.0 4.70 R
2829 2925 0.182537 TCCCATCCACCCATAAAGCG 59.817 55.0 0.0 0.0 0.0 4.68 R
4128 4246 1.734655 TCCTCCAAGATATGCCTCCC 58.265 55.0 0.0 0.0 0.0 4.30 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
24 25 7.595819 AAAGTGGAACCTCAAAATACATGAA 57.404 32.000 0.00 0.00 37.80 2.57
25 26 7.781324 AAGTGGAACCTCAAAATACATGAAT 57.219 32.000 0.00 0.00 37.80 2.57
26 27 7.161773 AGTGGAACCTCAAAATACATGAATG 57.838 36.000 0.00 0.00 37.80 2.67
27 28 6.721208 AGTGGAACCTCAAAATACATGAATGT 59.279 34.615 0.00 0.95 40.79 2.71
28 29 7.029563 GTGGAACCTCAAAATACATGAATGTC 58.970 38.462 0.00 0.00 41.97 3.06
29 30 6.718912 TGGAACCTCAAAATACATGAATGTCA 59.281 34.615 0.00 0.00 41.97 3.58
30 31 7.396907 TGGAACCTCAAAATACATGAATGTCAT 59.603 33.333 0.00 0.00 41.97 3.06
31 32 8.902806 GGAACCTCAAAATACATGAATGTCATA 58.097 33.333 0.00 0.00 41.97 2.15
32 33 9.722056 GAACCTCAAAATACATGAATGTCATAC 57.278 33.333 0.00 0.00 41.97 2.39
33 34 8.806429 ACCTCAAAATACATGAATGTCATACA 57.194 30.769 0.00 0.00 41.97 2.29
34 35 9.241919 ACCTCAAAATACATGAATGTCATACAA 57.758 29.630 0.00 0.00 41.97 2.41
41 42 8.868522 ATACATGAATGTCATACAAATAGGGG 57.131 34.615 0.00 0.00 41.97 4.79
42 43 5.536161 ACATGAATGTCATACAAATAGGGGC 59.464 40.000 0.00 0.00 34.28 5.80
43 44 4.133820 TGAATGTCATACAAATAGGGGCG 58.866 43.478 0.00 0.00 0.00 6.13
44 45 2.631160 TGTCATACAAATAGGGGCGG 57.369 50.000 0.00 0.00 0.00 6.13
45 46 2.120312 TGTCATACAAATAGGGGCGGA 58.880 47.619 0.00 0.00 0.00 5.54
46 47 2.104111 TGTCATACAAATAGGGGCGGAG 59.896 50.000 0.00 0.00 0.00 4.63
47 48 2.104281 GTCATACAAATAGGGGCGGAGT 59.896 50.000 0.00 0.00 0.00 3.85
48 49 3.322828 GTCATACAAATAGGGGCGGAGTA 59.677 47.826 0.00 0.00 0.00 2.59
49 50 3.322828 TCATACAAATAGGGGCGGAGTAC 59.677 47.826 0.00 0.00 0.00 2.73
51 52 0.462789 CAAATAGGGGCGGAGTACGT 59.537 55.000 0.00 0.00 46.52 3.57
52 53 1.682854 CAAATAGGGGCGGAGTACGTA 59.317 52.381 0.00 0.00 46.52 3.57
53 54 2.298163 CAAATAGGGGCGGAGTACGTAT 59.702 50.000 0.00 0.00 46.52 3.06
54 55 2.299326 ATAGGGGCGGAGTACGTATT 57.701 50.000 0.00 0.00 46.52 1.89
55 56 2.949177 TAGGGGCGGAGTACGTATTA 57.051 50.000 0.00 0.00 46.52 0.98
56 57 2.299326 AGGGGCGGAGTACGTATTAT 57.701 50.000 0.00 0.00 46.52 1.28
57 58 2.601905 AGGGGCGGAGTACGTATTATT 58.398 47.619 0.00 0.00 46.52 1.40
58 59 3.766545 AGGGGCGGAGTACGTATTATTA 58.233 45.455 0.00 0.00 46.52 0.98
59 60 4.347607 AGGGGCGGAGTACGTATTATTAT 58.652 43.478 0.00 0.00 46.52 1.28
60 61 4.159135 AGGGGCGGAGTACGTATTATTATG 59.841 45.833 0.00 0.00 46.52 1.90
61 62 4.158394 GGGGCGGAGTACGTATTATTATGA 59.842 45.833 0.00 0.00 46.52 2.15
62 63 5.163478 GGGGCGGAGTACGTATTATTATGAT 60.163 44.000 0.00 0.00 46.52 2.45
63 64 6.335777 GGGCGGAGTACGTATTATTATGATT 58.664 40.000 0.00 0.00 46.52 2.57
64 65 7.416664 GGGGCGGAGTACGTATTATTATGATTA 60.417 40.741 0.00 0.00 46.52 1.75
65 66 8.139989 GGGCGGAGTACGTATTATTATGATTAT 58.860 37.037 0.00 0.00 46.52 1.28
66 67 9.525409 GGCGGAGTACGTATTATTATGATTATT 57.475 33.333 0.00 0.00 46.52 1.40
101 102 8.791327 AATCACTTTCTTTGTTGAAATTTGGT 57.209 26.923 0.00 0.00 35.68 3.67
102 103 7.826260 TCACTTTCTTTGTTGAAATTTGGTC 57.174 32.000 0.00 0.00 35.68 4.02
103 104 7.382110 TCACTTTCTTTGTTGAAATTTGGTCA 58.618 30.769 0.00 0.00 35.68 4.02
104 105 7.875041 TCACTTTCTTTGTTGAAATTTGGTCAA 59.125 29.630 0.00 0.00 35.68 3.18
105 106 8.667463 CACTTTCTTTGTTGAAATTTGGTCAAT 58.333 29.630 0.00 0.00 37.34 2.57
106 107 8.667463 ACTTTCTTTGTTGAAATTTGGTCAATG 58.333 29.630 0.00 1.29 37.34 2.82
107 108 6.601741 TCTTTGTTGAAATTTGGTCAATGC 57.398 33.333 0.00 0.00 37.34 3.56
108 109 6.347696 TCTTTGTTGAAATTTGGTCAATGCT 58.652 32.000 0.00 0.00 37.34 3.79
109 110 5.987777 TTGTTGAAATTTGGTCAATGCTG 57.012 34.783 0.00 0.00 37.34 4.41
110 111 3.808726 TGTTGAAATTTGGTCAATGCTGC 59.191 39.130 0.00 0.00 37.34 5.25
111 112 4.060205 GTTGAAATTTGGTCAATGCTGCT 58.940 39.130 0.00 0.00 37.34 4.24
112 113 5.221402 TGTTGAAATTTGGTCAATGCTGCTA 60.221 36.000 0.00 0.00 37.34 3.49
113 114 4.808558 TGAAATTTGGTCAATGCTGCTAC 58.191 39.130 0.00 0.00 0.00 3.58
114 115 4.523943 TGAAATTTGGTCAATGCTGCTACT 59.476 37.500 0.00 0.00 0.00 2.57
115 116 5.709631 TGAAATTTGGTCAATGCTGCTACTA 59.290 36.000 0.00 0.00 0.00 1.82
116 117 6.208402 TGAAATTTGGTCAATGCTGCTACTAA 59.792 34.615 0.00 0.00 0.00 2.24
117 118 6.780457 AATTTGGTCAATGCTGCTACTAAT 57.220 33.333 0.00 0.00 0.00 1.73
118 119 5.818136 TTTGGTCAATGCTGCTACTAATC 57.182 39.130 0.00 0.00 0.00 1.75
119 120 4.486125 TGGTCAATGCTGCTACTAATCA 57.514 40.909 0.00 0.00 0.00 2.57
120 121 4.191544 TGGTCAATGCTGCTACTAATCAC 58.808 43.478 0.00 0.00 0.00 3.06
121 122 3.561725 GGTCAATGCTGCTACTAATCACC 59.438 47.826 0.00 0.00 0.00 4.02
122 123 3.246226 GTCAATGCTGCTACTAATCACCG 59.754 47.826 0.00 0.00 0.00 4.94
123 124 3.118775 TCAATGCTGCTACTAATCACCGT 60.119 43.478 0.00 0.00 0.00 4.83
124 125 3.543680 ATGCTGCTACTAATCACCGTT 57.456 42.857 0.00 0.00 0.00 4.44
133 134 1.022451 TAATCACCGTTGGAAGCCGC 61.022 55.000 0.00 0.00 0.00 6.53
139 140 2.650778 GTTGGAAGCCGCCTTTGG 59.349 61.111 0.00 0.00 0.00 3.28
155 156 3.370103 CCTTTGGCTGGTTCTACGGATAA 60.370 47.826 0.00 0.00 0.00 1.75
159 160 2.633481 GGCTGGTTCTACGGATAAGGAT 59.367 50.000 0.00 0.00 0.00 3.24
167 168 4.800023 TCTACGGATAAGGATTGGACTGA 58.200 43.478 0.00 0.00 0.00 3.41
176 177 7.611855 GGATAAGGATTGGACTGAAGAAAGAAA 59.388 37.037 0.00 0.00 0.00 2.52
258 261 5.011431 GGTAGGTACTTGGTTCGCCTATAAT 59.989 44.000 0.00 0.00 41.75 1.28
361 368 1.202806 TCTGAAGGAGGTGGTGCAAAG 60.203 52.381 0.00 0.00 0.00 2.77
453 500 7.281549 TGCGTACTGTATAACTTCAGATCACTA 59.718 37.037 0.00 0.00 35.84 2.74
489 536 1.546773 TGTCCAATAAGTGGTGGGCAC 60.547 52.381 0.00 0.00 44.50 5.01
490 537 3.355077 CCAATAAGTGGTGGGCACA 57.645 52.632 0.00 0.00 43.20 4.57
747 829 5.104569 TGTCCTACACAATATCTGAATGGCA 60.105 40.000 0.00 0.00 29.30 4.92
768 852 4.202358 GCAAATTCGATTAGTAAAGCGCAC 59.798 41.667 11.47 0.00 43.95 5.34
769 853 5.320723 CAAATTCGATTAGTAAAGCGCACA 58.679 37.500 11.47 0.00 43.95 4.57
770 854 4.778842 ATTCGATTAGTAAAGCGCACAG 57.221 40.909 11.47 0.00 43.95 3.66
771 855 3.226346 TCGATTAGTAAAGCGCACAGT 57.774 42.857 11.47 0.00 43.95 3.55
772 856 3.581755 TCGATTAGTAAAGCGCACAGTT 58.418 40.909 11.47 0.00 43.95 3.16
773 857 4.735985 TCGATTAGTAAAGCGCACAGTTA 58.264 39.130 11.47 0.00 43.95 2.24
774 858 5.345702 TCGATTAGTAAAGCGCACAGTTAT 58.654 37.500 11.47 0.00 43.95 1.89
775 859 6.497437 TCGATTAGTAAAGCGCACAGTTATA 58.503 36.000 11.47 0.00 43.95 0.98
776 860 6.415867 TCGATTAGTAAAGCGCACAGTTATAC 59.584 38.462 11.47 1.75 43.95 1.47
917 1004 6.702723 CACCAACAATTCCATATATTTGCCAG 59.297 38.462 0.00 0.00 0.00 4.85
1170 1262 1.059098 TGTCCTGGAATGACAGCACT 58.941 50.000 0.00 0.00 36.54 4.40
1233 1325 0.389948 GACATCGCGTCACTTCCCTT 60.390 55.000 5.77 0.00 44.69 3.95
1261 1353 1.885163 CGGTCGAGGCTTACAAGGGT 61.885 60.000 0.00 0.00 0.00 4.34
1278 1370 2.641815 AGGGTGCATCTCTCTTTCACTT 59.358 45.455 0.00 0.00 0.00 3.16
1282 1374 3.683822 GTGCATCTCTCTTTCACTTGGAG 59.316 47.826 0.00 0.00 0.00 3.86
1371 1463 2.113774 CACCTGCAGCACCTCCAA 59.886 61.111 8.66 0.00 0.00 3.53
1498 1590 4.741321 ATCCCTACACATGCCAATTTTG 57.259 40.909 0.00 0.00 0.00 2.44
1543 1635 9.625747 TGCTGATTTCATATAACAATCTTACCA 57.374 29.630 0.00 0.00 0.00 3.25
1599 1691 4.944317 ACACTGACTCGACTTGATATCTCA 59.056 41.667 3.98 0.00 0.00 3.27
1656 1748 1.413445 GGAAATATGCCCATGCTGCAA 59.587 47.619 6.36 0.00 42.92 4.08
1666 1758 3.666274 CCCATGCTGCAATTCTTTTTCA 58.334 40.909 6.36 0.00 0.00 2.69
2244 2339 0.390860 CGGAATGGCTAGGGACTCTG 59.609 60.000 0.00 0.00 41.75 3.35
2258 2353 1.078848 CTCTGGAGAACTTGCGGGG 60.079 63.158 0.00 0.00 0.00 5.73
2277 2372 5.544650 CGGGGTATCGTATTAAGGAACAAT 58.455 41.667 0.00 0.00 0.00 2.71
2700 2796 6.989759 TCAGAAACTTGCAAGTACTCAATGTA 59.010 34.615 31.31 12.69 38.57 2.29
2706 2802 7.334090 ACTTGCAAGTACTCAATGTATCTCAT 58.666 34.615 30.25 0.00 37.52 2.90
2807 2903 3.208747 TGAAGGTGAAGTCCCAGAAAC 57.791 47.619 0.00 0.00 0.00 2.78
2811 2907 1.143073 GGTGAAGTCCCAGAAACAGGT 59.857 52.381 0.00 0.00 0.00 4.00
2829 2925 7.865706 AACAGGTATATTCAAGAATGTGACC 57.134 36.000 5.59 9.21 32.69 4.02
2841 2937 1.750193 ATGTGACCGCTTTATGGGTG 58.250 50.000 0.00 0.00 36.46 4.61
2958 3054 3.865745 CAGTGCTCAAAGTAGTAATCCCG 59.134 47.826 0.00 0.00 0.00 5.14
2973 3069 1.855295 TCCCGTTAGTCAGCATGGTA 58.145 50.000 0.00 0.00 36.16 3.25
3028 3124 2.038557 TGGAGGAGAAAACGGAAGAAGG 59.961 50.000 0.00 0.00 0.00 3.46
3042 3138 5.221661 ACGGAAGAAGGTTTACATGTCTCTT 60.222 40.000 0.00 2.04 0.00 2.85
3182 3278 4.319177 AGACTGTTGCAAGATGGAACTAC 58.681 43.478 14.38 7.09 46.83 2.73
3239 3335 3.005155 GGAGCACAAAAGAGCTTCATTGT 59.995 43.478 6.24 6.24 42.04 2.71
3263 3359 4.201783 GGAATGCAATGCTTTGAGAAATGC 60.202 41.667 15.97 0.16 34.60 3.56
3372 3468 0.685785 TGCCAAAGGGTGACTTGCAA 60.686 50.000 0.00 0.00 39.96 4.08
3435 3531 1.476488 TCAGAGCGCATTACACTAGCA 59.524 47.619 11.47 0.00 0.00 3.49
3619 3715 3.259625 TGGTCCGACACAGTCATATTTCA 59.740 43.478 0.00 0.00 32.09 2.69
3646 3742 3.072211 TCGAACTCTGCTTCTTCGACTA 58.928 45.455 0.00 0.00 40.54 2.59
3709 3806 7.766283 TGTCTGTTGTTCATTTTCATGTTGTA 58.234 30.769 0.00 0.00 0.00 2.41
3726 3823 7.383843 TCATGTTGTACCATATATGTTACAGCG 59.616 37.037 22.91 14.58 38.86 5.18
3735 3832 7.652105 ACCATATATGTTACAGCGTAACTTGAG 59.348 37.037 22.75 12.90 0.00 3.02
3751 3848 9.582431 CGTAACTTGAGAATGACTCCTTATTTA 57.418 33.333 0.00 0.00 44.34 1.40
3803 3900 6.074888 AACTATCGTTGTACGTGTTGTTACAC 60.075 38.462 0.00 0.00 43.14 2.90
3965 4062 5.708544 TGAATTTTCCTGCTGGGATATCAT 58.291 37.500 10.07 0.00 44.66 2.45
4002 4120 2.010145 TTGCTACAAGATCGTCCAGC 57.990 50.000 4.61 4.61 0.00 4.85
4128 4246 2.681848 CTGCAAGCCTTCATGGAGTTAG 59.318 50.000 0.00 0.00 38.35 2.34
4147 4265 1.224120 AGGGAGGCATATCTTGGAGGA 59.776 52.381 0.00 0.00 0.00 3.71
4163 4281 6.500751 TCTTGGAGGAAGATAAGGTAAACACT 59.499 38.462 0.00 0.00 35.64 3.55
4240 4358 4.804868 AAATGTCTAAATGCATGTGCCA 57.195 36.364 0.00 0.00 41.18 4.92
4249 4367 1.798283 TGCATGTGCCATTTCTTTGC 58.202 45.000 2.07 0.00 41.18 3.68
4285 4502 1.279271 AGGCGAACTAACCTGATGCTT 59.721 47.619 0.00 0.00 34.07 3.91
4293 4510 2.789409 AACCTGATGCTTGTAGTCCC 57.211 50.000 0.00 0.00 0.00 4.46
4348 4565 0.304705 CTGCTGCGAACAACGAGTTT 59.695 50.000 0.00 0.00 45.77 2.66
4349 4566 0.027455 TGCTGCGAACAACGAGTTTG 59.973 50.000 0.00 0.00 45.77 2.93
4358 4575 2.389713 CAACGAGTTTGTGGCTTCTG 57.610 50.000 0.00 0.00 0.00 3.02
4359 4576 1.939934 CAACGAGTTTGTGGCTTCTGA 59.060 47.619 0.00 0.00 0.00 3.27
4360 4577 2.325583 ACGAGTTTGTGGCTTCTGAA 57.674 45.000 0.00 0.00 0.00 3.02
4361 4578 2.851195 ACGAGTTTGTGGCTTCTGAAT 58.149 42.857 0.00 0.00 0.00 2.57
4362 4579 2.549754 ACGAGTTTGTGGCTTCTGAATG 59.450 45.455 0.00 0.00 0.00 2.67
4363 4580 2.549754 CGAGTTTGTGGCTTCTGAATGT 59.450 45.455 0.00 0.00 0.00 2.71
4364 4581 3.745975 CGAGTTTGTGGCTTCTGAATGTA 59.254 43.478 0.00 0.00 0.00 2.29
4390 4613 5.454329 GGTCAGGGTGTTCTACTACAAGTTT 60.454 44.000 0.00 0.00 0.00 2.66
4391 4614 6.239402 GGTCAGGGTGTTCTACTACAAGTTTA 60.239 42.308 0.00 0.00 0.00 2.01
4423 4647 1.283487 CTGTTGTGCAATGCGCTCA 59.717 52.632 19.95 16.33 42.18 4.26
4426 4650 0.727122 GTTGTGCAATGCGCTCAGTC 60.727 55.000 19.95 2.51 44.41 3.51
4436 4660 1.818674 TGCGCTCAGTCTCTGATGTTA 59.181 47.619 9.73 0.00 39.92 2.41
4450 4714 5.473931 TCTGATGTTACTCAAAGCAGAGTC 58.526 41.667 9.36 0.00 45.35 3.36
4460 4724 0.617413 AAGCAGAGTCTGGGTGATGG 59.383 55.000 21.54 0.00 31.21 3.51
4480 4745 2.618709 GGCTCTGGTTGGGATAATTTCG 59.381 50.000 0.00 0.00 0.00 3.46
4481 4746 2.618709 GCTCTGGTTGGGATAATTTCGG 59.381 50.000 0.00 0.00 0.00 4.30
4485 4750 4.227754 TCTGGTTGGGATAATTTCGGGTTA 59.772 41.667 0.00 0.00 0.00 2.85
4517 4782 7.933215 TTTAAGGAATTAAGTAGCTGGTTCC 57.067 36.000 0.00 1.15 36.29 3.62
4518 4783 5.514500 AAGGAATTAAGTAGCTGGTTCCA 57.486 39.130 0.00 0.00 38.02 3.53
4520 4785 5.440610 AGGAATTAAGTAGCTGGTTCCATG 58.559 41.667 0.00 0.00 38.02 3.66
4521 4786 4.036852 GGAATTAAGTAGCTGGTTCCATGC 59.963 45.833 0.00 0.00 36.13 4.06
4522 4787 4.510167 ATTAAGTAGCTGGTTCCATGCT 57.490 40.909 15.73 15.73 40.43 3.79
4523 4788 2.887151 AAGTAGCTGGTTCCATGCTT 57.113 45.000 16.32 5.81 38.15 3.91
4524 4789 2.887151 AGTAGCTGGTTCCATGCTTT 57.113 45.000 16.32 7.26 38.15 3.51
4525 4790 2.440409 AGTAGCTGGTTCCATGCTTTG 58.560 47.619 16.32 0.00 38.15 2.77
4543 4808 7.770801 TGCTTTGCATGTTACTAGTAGTATG 57.229 36.000 10.82 17.55 31.71 2.39
4544 4809 7.552459 TGCTTTGCATGTTACTAGTAGTATGA 58.448 34.615 22.58 1.58 31.71 2.15
4545 4810 8.204160 TGCTTTGCATGTTACTAGTAGTATGAT 58.796 33.333 22.58 3.77 31.71 2.45
4546 4811 8.491152 GCTTTGCATGTTACTAGTAGTATGATG 58.509 37.037 22.58 14.90 29.64 3.07
4547 4812 9.750125 CTTTGCATGTTACTAGTAGTATGATGA 57.250 33.333 22.58 11.47 29.64 2.92
4550 4815 9.696917 TGCATGTTACTAGTAGTATGATGATTG 57.303 33.333 22.58 11.59 29.64 2.67
4551 4816 8.651588 GCATGTTACTAGTAGTATGATGATTGC 58.348 37.037 22.58 15.42 29.64 3.56
4552 4817 9.920133 CATGTTACTAGTAGTATGATGATTGCT 57.080 33.333 10.82 0.00 29.64 3.91
4556 4821 9.678941 TTACTAGTAGTATGATGATTGCTTTCG 57.321 33.333 10.82 0.00 29.64 3.46
4557 4822 7.717568 ACTAGTAGTATGATGATTGCTTTCGT 58.282 34.615 0.00 0.00 0.00 3.85
4558 4823 6.834959 AGTAGTATGATGATTGCTTTCGTG 57.165 37.500 0.00 0.00 0.00 4.35
4559 4824 5.755375 AGTAGTATGATGATTGCTTTCGTGG 59.245 40.000 0.00 0.00 0.00 4.94
4560 4825 3.879295 AGTATGATGATTGCTTTCGTGGG 59.121 43.478 0.00 0.00 0.00 4.61
4561 4826 0.810648 TGATGATTGCTTTCGTGGGC 59.189 50.000 0.00 0.00 0.00 5.36
4562 4827 0.810648 GATGATTGCTTTCGTGGGCA 59.189 50.000 0.00 0.00 36.62 5.36
4563 4828 1.406539 GATGATTGCTTTCGTGGGCAT 59.593 47.619 0.00 0.00 38.30 4.40
4564 4829 1.255882 TGATTGCTTTCGTGGGCATT 58.744 45.000 0.00 0.00 38.30 3.56
4565 4830 1.067706 TGATTGCTTTCGTGGGCATTG 60.068 47.619 0.00 0.00 38.30 2.82
4566 4831 0.968405 ATTGCTTTCGTGGGCATTGT 59.032 45.000 0.00 0.00 38.30 2.71
4599 4864 4.955811 TTGCTGGTCTAGACTCTTTTGA 57.044 40.909 21.88 1.03 0.00 2.69
4611 4876 6.426646 AGACTCTTTTGATGTAGAAGTGGT 57.573 37.500 0.00 0.00 0.00 4.16
4612 4877 6.226787 AGACTCTTTTGATGTAGAAGTGGTG 58.773 40.000 0.00 0.00 0.00 4.17
4617 4882 7.907389 TCTTTTGATGTAGAAGTGGTGACTAT 58.093 34.615 0.00 0.00 0.00 2.12
4630 4895 6.534634 AGTGGTGACTATTTTCTTACAGCTT 58.465 36.000 0.00 0.00 0.00 3.74
4650 4915 7.147759 ACAGCTTGAGCCTACATCCTATATATG 60.148 40.741 0.00 0.00 43.38 1.78
4651 4916 6.900186 AGCTTGAGCCTACATCCTATATATGT 59.100 38.462 0.00 6.22 43.38 2.29
4688 4953 8.789762 CCATGTAGAGATTAAATTGATCATGCA 58.210 33.333 0.00 0.00 0.00 3.96
4727 4992 9.634021 AGTTGAAGTTTTTAGAAAGATCTCCTT 57.366 29.630 0.00 0.00 37.10 3.36
4729 4994 9.627123 TTGAAGTTTTTAGAAAGATCTCCTTGA 57.373 29.630 0.00 0.00 37.10 3.02
4797 5062 3.009033 CCTGTCTGGAACCCTATGTTGAA 59.991 47.826 0.00 0.00 37.29 2.69
4804 5069 3.561313 GGAACCCTATGTTGAAGCAAGGA 60.561 47.826 0.00 0.00 37.29 3.36
4808 5073 2.239654 CCTATGTTGAAGCAAGGAGGGA 59.760 50.000 0.00 0.00 0.00 4.20
4809 5074 2.503895 ATGTTGAAGCAAGGAGGGAG 57.496 50.000 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 6.721208 ACATTCATGTATTTTGAGGTTCCACT 59.279 34.615 0.00 0.00 39.68 4.00
3 4 6.924111 ACATTCATGTATTTTGAGGTTCCAC 58.076 36.000 0.00 0.00 39.68 4.02
4 5 6.718912 TGACATTCATGTATTTTGAGGTTCCA 59.281 34.615 0.00 0.00 41.95 3.53
5 6 7.156876 TGACATTCATGTATTTTGAGGTTCC 57.843 36.000 0.00 0.00 41.95 3.62
6 7 9.722056 GTATGACATTCATGTATTTTGAGGTTC 57.278 33.333 0.00 0.00 41.95 3.62
7 8 9.241919 TGTATGACATTCATGTATTTTGAGGTT 57.758 29.630 0.00 0.00 41.95 3.50
8 9 8.806429 TGTATGACATTCATGTATTTTGAGGT 57.194 30.769 0.00 0.00 41.95 3.85
15 16 9.300681 CCCCTATTTGTATGACATTCATGTATT 57.699 33.333 0.00 0.00 41.95 1.89
16 17 7.394359 GCCCCTATTTGTATGACATTCATGTAT 59.606 37.037 0.00 0.00 41.95 2.29
17 18 6.714810 GCCCCTATTTGTATGACATTCATGTA 59.285 38.462 0.00 0.00 41.95 2.29
18 19 5.536161 GCCCCTATTTGTATGACATTCATGT 59.464 40.000 0.00 0.00 45.16 3.21
19 20 5.335113 CGCCCCTATTTGTATGACATTCATG 60.335 44.000 0.00 0.00 37.70 3.07
20 21 4.761739 CGCCCCTATTTGTATGACATTCAT 59.238 41.667 0.00 0.00 40.72 2.57
21 22 4.133820 CGCCCCTATTTGTATGACATTCA 58.866 43.478 0.00 0.00 0.00 2.57
22 23 3.502211 CCGCCCCTATTTGTATGACATTC 59.498 47.826 0.00 0.00 0.00 2.67
23 24 3.137544 TCCGCCCCTATTTGTATGACATT 59.862 43.478 0.00 0.00 0.00 2.71
24 25 2.708861 TCCGCCCCTATTTGTATGACAT 59.291 45.455 0.00 0.00 0.00 3.06
25 26 2.104111 CTCCGCCCCTATTTGTATGACA 59.896 50.000 0.00 0.00 0.00 3.58
26 27 2.104281 ACTCCGCCCCTATTTGTATGAC 59.896 50.000 0.00 0.00 0.00 3.06
27 28 2.404559 ACTCCGCCCCTATTTGTATGA 58.595 47.619 0.00 0.00 0.00 2.15
28 29 2.930826 ACTCCGCCCCTATTTGTATG 57.069 50.000 0.00 0.00 0.00 2.39
29 30 2.298163 CGTACTCCGCCCCTATTTGTAT 59.702 50.000 0.00 0.00 0.00 2.29
30 31 1.682854 CGTACTCCGCCCCTATTTGTA 59.317 52.381 0.00 0.00 0.00 2.41
31 32 0.462789 CGTACTCCGCCCCTATTTGT 59.537 55.000 0.00 0.00 0.00 2.83
32 33 0.462789 ACGTACTCCGCCCCTATTTG 59.537 55.000 0.00 0.00 41.42 2.32
33 34 2.071778 TACGTACTCCGCCCCTATTT 57.928 50.000 0.00 0.00 41.42 1.40
34 35 2.299326 ATACGTACTCCGCCCCTATT 57.701 50.000 0.00 0.00 41.42 1.73
35 36 2.299326 AATACGTACTCCGCCCCTAT 57.701 50.000 0.00 0.00 41.42 2.57
36 37 2.949177 TAATACGTACTCCGCCCCTA 57.051 50.000 0.00 0.00 41.42 3.53
37 38 2.299326 ATAATACGTACTCCGCCCCT 57.701 50.000 0.00 0.00 41.42 4.79
38 39 4.158394 TCATAATAATACGTACTCCGCCCC 59.842 45.833 0.00 0.00 41.42 5.80
39 40 5.314923 TCATAATAATACGTACTCCGCCC 57.685 43.478 0.00 0.00 41.42 6.13
40 41 9.525409 AATAATCATAATAATACGTACTCCGCC 57.475 33.333 0.00 0.00 41.42 6.13
75 76 9.883142 ACCAAATTTCAACAAAGAAAGTGATTA 57.117 25.926 0.00 0.00 40.49 1.75
76 77 8.791327 ACCAAATTTCAACAAAGAAAGTGATT 57.209 26.923 0.00 0.00 40.49 2.57
77 78 8.040132 TGACCAAATTTCAACAAAGAAAGTGAT 58.960 29.630 0.00 0.00 40.49 3.06
78 79 7.382110 TGACCAAATTTCAACAAAGAAAGTGA 58.618 30.769 0.00 0.00 40.49 3.41
79 80 7.593875 TGACCAAATTTCAACAAAGAAAGTG 57.406 32.000 0.00 0.00 40.49 3.16
80 81 8.667463 CATTGACCAAATTTCAACAAAGAAAGT 58.333 29.630 0.00 0.00 40.49 2.66
81 82 7.641020 GCATTGACCAAATTTCAACAAAGAAAG 59.359 33.333 0.00 0.00 40.49 2.62
82 83 7.336427 AGCATTGACCAAATTTCAACAAAGAAA 59.664 29.630 0.00 0.00 41.31 2.52
83 84 6.822676 AGCATTGACCAAATTTCAACAAAGAA 59.177 30.769 0.00 0.00 35.82 2.52
84 85 6.258287 CAGCATTGACCAAATTTCAACAAAGA 59.742 34.615 0.00 0.00 35.82 2.52
85 86 6.423862 CAGCATTGACCAAATTTCAACAAAG 58.576 36.000 0.00 0.00 35.82 2.77
86 87 5.220815 GCAGCATTGACCAAATTTCAACAAA 60.221 36.000 0.00 0.00 35.82 2.83
87 88 4.272991 GCAGCATTGACCAAATTTCAACAA 59.727 37.500 0.00 0.00 35.82 2.83
88 89 3.808726 GCAGCATTGACCAAATTTCAACA 59.191 39.130 0.00 0.00 35.82 3.33
89 90 4.060205 AGCAGCATTGACCAAATTTCAAC 58.940 39.130 0.00 0.00 35.82 3.18
90 91 4.339872 AGCAGCATTGACCAAATTTCAA 57.660 36.364 0.00 0.00 37.38 2.69
91 92 4.523943 AGTAGCAGCATTGACCAAATTTCA 59.476 37.500 0.00 0.00 0.00 2.69
92 93 5.064441 AGTAGCAGCATTGACCAAATTTC 57.936 39.130 0.00 0.00 0.00 2.17
93 94 6.588719 TTAGTAGCAGCATTGACCAAATTT 57.411 33.333 0.00 0.00 0.00 1.82
94 95 6.377996 TGATTAGTAGCAGCATTGACCAAATT 59.622 34.615 0.00 0.00 0.00 1.82
95 96 5.887598 TGATTAGTAGCAGCATTGACCAAAT 59.112 36.000 0.00 0.00 0.00 2.32
96 97 5.123820 GTGATTAGTAGCAGCATTGACCAAA 59.876 40.000 0.00 0.00 0.00 3.28
97 98 4.635765 GTGATTAGTAGCAGCATTGACCAA 59.364 41.667 0.00 0.00 0.00 3.67
98 99 4.191544 GTGATTAGTAGCAGCATTGACCA 58.808 43.478 0.00 0.00 0.00 4.02
99 100 3.561725 GGTGATTAGTAGCAGCATTGACC 59.438 47.826 0.00 0.00 38.04 4.02
100 101 3.246226 CGGTGATTAGTAGCAGCATTGAC 59.754 47.826 0.00 0.00 38.02 3.18
101 102 3.118775 ACGGTGATTAGTAGCAGCATTGA 60.119 43.478 0.00 0.00 38.02 2.57
102 103 3.198068 ACGGTGATTAGTAGCAGCATTG 58.802 45.455 0.00 0.00 38.02 2.82
103 104 3.543680 ACGGTGATTAGTAGCAGCATT 57.456 42.857 0.00 0.00 38.02 3.56
104 105 3.198068 CAACGGTGATTAGTAGCAGCAT 58.802 45.455 0.00 0.00 38.02 3.79
105 106 2.616960 CAACGGTGATTAGTAGCAGCA 58.383 47.619 0.00 0.00 38.02 4.41
106 107 1.933853 CCAACGGTGATTAGTAGCAGC 59.066 52.381 0.00 0.00 34.96 5.25
107 108 3.520290 TCCAACGGTGATTAGTAGCAG 57.480 47.619 0.00 0.00 0.00 4.24
108 109 3.857052 CTTCCAACGGTGATTAGTAGCA 58.143 45.455 0.00 0.00 0.00 3.49
109 110 2.608090 GCTTCCAACGGTGATTAGTAGC 59.392 50.000 0.00 0.00 0.00 3.58
110 111 3.195661 GGCTTCCAACGGTGATTAGTAG 58.804 50.000 0.00 0.00 0.00 2.57
111 112 2.417651 CGGCTTCCAACGGTGATTAGTA 60.418 50.000 0.00 0.00 0.00 1.82
112 113 1.674817 CGGCTTCCAACGGTGATTAGT 60.675 52.381 0.00 0.00 0.00 2.24
113 114 1.006832 CGGCTTCCAACGGTGATTAG 58.993 55.000 0.00 0.00 0.00 1.73
114 115 1.022451 GCGGCTTCCAACGGTGATTA 61.022 55.000 0.00 0.00 0.00 1.75
115 116 2.332654 GCGGCTTCCAACGGTGATT 61.333 57.895 0.00 0.00 0.00 2.57
116 117 2.746277 GCGGCTTCCAACGGTGAT 60.746 61.111 0.00 0.00 0.00 3.06
119 120 3.785122 AAAGGCGGCTTCCAACGGT 62.785 57.895 25.70 4.13 0.00 4.83
120 121 2.983592 AAAGGCGGCTTCCAACGG 60.984 61.111 25.70 0.00 0.00 4.44
121 122 2.255252 CAAAGGCGGCTTCCAACG 59.745 61.111 25.70 7.59 0.00 4.10
122 123 2.650778 CCAAAGGCGGCTTCCAAC 59.349 61.111 25.70 0.00 0.00 3.77
133 134 0.323629 TCCGTAGAACCAGCCAAAGG 59.676 55.000 0.00 0.00 0.00 3.11
139 140 4.058817 CAATCCTTATCCGTAGAACCAGC 58.941 47.826 0.00 0.00 0.00 4.85
147 148 5.205821 TCTTCAGTCCAATCCTTATCCGTA 58.794 41.667 0.00 0.00 0.00 4.02
149 150 4.672587 TCTTCAGTCCAATCCTTATCCG 57.327 45.455 0.00 0.00 0.00 4.18
207 208 6.165659 GACAAGCTATAATGTCAACGTGTT 57.834 37.500 10.70 0.00 44.19 3.32
208 209 5.779806 GACAAGCTATAATGTCAACGTGT 57.220 39.130 10.70 0.00 44.19 4.49
258 261 3.521560 CTTAGAGCCATACACGCTTCAA 58.478 45.455 0.00 0.00 36.48 2.69
314 317 2.223377 CCTGCGTACTTTTGTTGGAGAC 59.777 50.000 0.00 0.00 30.57 3.36
489 536 8.602328 CAAACTCAAAGATAAGCTAGACATCTG 58.398 37.037 0.00 0.00 0.00 2.90
490 537 8.317679 ACAAACTCAAAGATAAGCTAGACATCT 58.682 33.333 0.00 0.00 0.00 2.90
538 610 8.547967 TGCTGATTAGAAACTCGTAATTTCTT 57.452 30.769 13.67 1.54 42.46 2.52
544 616 7.386573 TGTTTCATGCTGATTAGAAACTCGTAA 59.613 33.333 15.23 0.00 46.03 3.18
545 617 6.871492 TGTTTCATGCTGATTAGAAACTCGTA 59.129 34.615 15.23 0.00 46.03 3.43
747 829 5.121768 ACTGTGCGCTTTACTAATCGAATTT 59.878 36.000 9.73 0.00 0.00 1.82
978 1066 3.440173 TGGCTGGATTTCTTTGTCGAATC 59.560 43.478 0.00 0.00 0.00 2.52
1170 1262 3.071023 CACCTTCCCAGTTACAGAAGTCA 59.929 47.826 8.31 0.00 36.16 3.41
1261 1353 3.580022 TCTCCAAGTGAAAGAGAGATGCA 59.420 43.478 0.00 0.00 32.92 3.96
1498 1590 0.037447 AGGCTTTGAAGGTGAGGAGC 59.963 55.000 0.00 0.00 0.00 4.70
1543 1635 4.400529 AAAGTGAAACGGGAATTTTGCT 57.599 36.364 0.00 0.00 45.86 3.91
1599 1691 1.138859 TCGCCACTGATCCGATTTGAT 59.861 47.619 0.00 0.00 0.00 2.57
1656 1748 6.295859 GCTTATTTCCCCAGGTGAAAAAGAAT 60.296 38.462 16.37 0.36 35.52 2.40
1666 1758 3.395941 CCTGATAGCTTATTTCCCCAGGT 59.604 47.826 0.00 0.00 36.20 4.00
2244 2339 0.529992 CGATACCCCGCAAGTTCTCC 60.530 60.000 0.00 0.00 0.00 3.71
2660 2755 1.002990 CTGATGCTGCCCAGTGACA 60.003 57.895 9.96 0.00 0.00 3.58
2700 2796 6.789457 TGGATCCTGATAAGTGGTTATGAGAT 59.211 38.462 14.23 0.00 33.03 2.75
2706 2802 6.147473 TGGTATGGATCCTGATAAGTGGTTA 58.853 40.000 14.23 0.00 0.00 2.85
2807 2903 5.050091 GCGGTCACATTCTTGAATATACCTG 60.050 44.000 13.85 10.48 0.00 4.00
2811 2907 8.773645 CATAAAGCGGTCACATTCTTGAATATA 58.226 33.333 0.00 0.00 0.00 0.86
2829 2925 0.182537 TCCCATCCACCCATAAAGCG 59.817 55.000 0.00 0.00 0.00 4.68
2841 2937 0.252239 AAAGCCCCTTGTTCCCATCC 60.252 55.000 0.00 0.00 0.00 3.51
2958 3054 4.034510 GCAAGTGATACCATGCTGACTAAC 59.965 45.833 0.00 0.00 35.93 2.34
3028 3124 7.013369 ACCAAAAGAAGGAAGAGACATGTAAAC 59.987 37.037 0.00 0.00 0.00 2.01
3042 3138 4.337274 GGAAACTTTCGACCAAAAGAAGGA 59.663 41.667 1.68 0.00 38.30 3.36
3239 3335 4.603989 TTTCTCAAAGCATTGCATTCCA 57.396 36.364 11.91 0.00 36.45 3.53
3263 3359 2.658593 CTAGATTCCGGTGCCGCG 60.659 66.667 0.00 0.00 38.24 6.46
3372 3468 3.306364 CCAAAGCTGAGTACAGTAGTGCT 60.306 47.826 0.00 0.00 45.04 4.40
3435 3531 2.101249 CACCACAATGCTCAACCTTTGT 59.899 45.455 0.00 0.00 34.58 2.83
3619 3715 2.235016 AGAAGCAGAGTTCGAGTCACT 58.765 47.619 0.00 0.00 0.00 3.41
3627 3723 9.517609 TTTATTATAGTCGAAGAAGCAGAGTTC 57.482 33.333 0.00 0.00 39.69 3.01
3646 3742 9.367444 GACATATCCGATCGTTCCTTTTATTAT 57.633 33.333 15.09 0.00 0.00 1.28
3709 3806 7.494211 TCAAGTTACGCTGTAACATATATGGT 58.506 34.615 23.70 13.06 0.00 3.55
3719 3816 5.779922 AGTCATTCTCAAGTTACGCTGTAA 58.220 37.500 0.00 0.00 0.00 2.41
3965 4062 7.386059 TGTAGCAATTCAGAGTCAACAATCTA 58.614 34.615 0.00 0.00 0.00 1.98
4002 4120 3.923017 AATCTTTTTCCTTCGTGGCTG 57.077 42.857 0.00 0.00 35.26 4.85
4128 4246 1.734655 TCCTCCAAGATATGCCTCCC 58.265 55.000 0.00 0.00 0.00 4.30
4163 4281 8.042515 ACACCTACGGCATTAAAGACTAAATAA 58.957 33.333 0.00 0.00 0.00 1.40
4176 4294 2.843401 TGTACAACACCTACGGCATT 57.157 45.000 0.00 0.00 0.00 3.56
4177 4295 4.475051 TTATGTACAACACCTACGGCAT 57.525 40.909 0.00 0.00 0.00 4.40
4231 4349 8.952713 TCTTATTTGCAAAGAAATGGCACATGC 61.953 37.037 18.94 0.00 37.26 4.06
4232 4350 6.369340 TCTTATTTGCAAAGAAATGGCACATG 59.631 34.615 18.94 5.68 37.26 3.21
4240 4358 7.054491 ACTGTGGTCTTATTTGCAAAGAAAT 57.946 32.000 18.94 4.57 34.86 2.17
4249 4367 3.857052 TCGCCTACTGTGGTCTTATTTG 58.143 45.455 0.00 0.00 0.00 2.32
4285 4502 2.345991 GCAACCTGCGGGACTACA 59.654 61.111 21.41 0.00 31.71 2.74
4293 4510 0.597377 GGTTTTTGAGGCAACCTGCG 60.597 55.000 0.00 0.00 46.21 5.18
4298 4515 1.754226 TGGTCAGGTTTTTGAGGCAAC 59.246 47.619 0.00 0.00 0.00 4.17
4301 4518 1.338020 CTGTGGTCAGGTTTTTGAGGC 59.662 52.381 0.00 0.00 37.97 4.70
4328 4545 2.105960 AACTCGTTGTTCGCAGCAGC 62.106 55.000 0.00 0.00 39.67 5.25
4348 4565 3.008923 TGACCATACATTCAGAAGCCACA 59.991 43.478 0.00 0.00 0.00 4.17
4349 4566 3.609853 TGACCATACATTCAGAAGCCAC 58.390 45.455 0.00 0.00 0.00 5.01
4350 4567 3.370846 CCTGACCATACATTCAGAAGCCA 60.371 47.826 0.08 0.00 41.65 4.75
4352 4569 3.209410 CCCTGACCATACATTCAGAAGC 58.791 50.000 0.08 0.00 41.65 3.86
4353 4570 4.194640 CACCCTGACCATACATTCAGAAG 58.805 47.826 0.08 0.00 41.65 2.85
4354 4571 3.587061 ACACCCTGACCATACATTCAGAA 59.413 43.478 0.08 0.00 41.65 3.02
4355 4572 3.181329 ACACCCTGACCATACATTCAGA 58.819 45.455 0.08 0.00 41.65 3.27
4356 4573 3.634397 ACACCCTGACCATACATTCAG 57.366 47.619 0.00 0.00 39.25 3.02
4357 4574 3.587061 AGAACACCCTGACCATACATTCA 59.413 43.478 0.00 0.00 0.00 2.57
4358 4575 4.222124 AGAACACCCTGACCATACATTC 57.778 45.455 0.00 0.00 0.00 2.67
4359 4576 4.783227 AGTAGAACACCCTGACCATACATT 59.217 41.667 0.00 0.00 0.00 2.71
4360 4577 4.362677 AGTAGAACACCCTGACCATACAT 58.637 43.478 0.00 0.00 0.00 2.29
4361 4578 3.786553 AGTAGAACACCCTGACCATACA 58.213 45.455 0.00 0.00 0.00 2.29
4362 4579 4.708421 TGTAGTAGAACACCCTGACCATAC 59.292 45.833 0.00 0.00 0.00 2.39
4363 4580 4.938028 TGTAGTAGAACACCCTGACCATA 58.062 43.478 0.00 0.00 0.00 2.74
4364 4581 3.786553 TGTAGTAGAACACCCTGACCAT 58.213 45.455 0.00 0.00 0.00 3.55
4390 4613 4.215399 GCACAACAGTACTCCAGCAAAATA 59.785 41.667 0.00 0.00 0.00 1.40
4391 4614 3.004734 GCACAACAGTACTCCAGCAAAAT 59.995 43.478 0.00 0.00 0.00 1.82
4423 4647 5.244851 TCTGCTTTGAGTAACATCAGAGACT 59.755 40.000 0.00 0.00 34.21 3.24
4426 4650 5.477510 ACTCTGCTTTGAGTAACATCAGAG 58.522 41.667 12.99 12.99 44.53 3.35
4450 4714 0.679002 CAACCAGAGCCATCACCCAG 60.679 60.000 0.00 0.00 0.00 4.45
4460 4724 2.618709 CCGAAATTATCCCAACCAGAGC 59.381 50.000 0.00 0.00 0.00 4.09
4518 4783 8.204160 TCATACTACTAGTAACATGCAAAGCAT 58.796 33.333 14.47 0.00 41.12 3.79
4520 4785 8.491152 CATCATACTACTAGTAACATGCAAAGC 58.509 37.037 14.47 0.00 33.89 3.51
4521 4786 9.750125 TCATCATACTACTAGTAACATGCAAAG 57.250 33.333 14.47 1.50 33.89 2.77
4524 4789 9.696917 CAATCATCATACTACTAGTAACATGCA 57.303 33.333 14.47 0.00 33.89 3.96
4525 4790 8.651588 GCAATCATCATACTACTAGTAACATGC 58.348 37.037 14.47 5.29 33.89 4.06
4530 4795 9.678941 CGAAAGCAATCATCATACTACTAGTAA 57.321 33.333 3.76 0.00 33.89 2.24
4531 4796 8.847196 ACGAAAGCAATCATCATACTACTAGTA 58.153 33.333 1.89 1.89 34.82 1.82
4532 4797 7.649705 CACGAAAGCAATCATCATACTACTAGT 59.350 37.037 0.00 0.00 0.00 2.57
4533 4798 7.115520 CCACGAAAGCAATCATCATACTACTAG 59.884 40.741 0.00 0.00 0.00 2.57
4534 4799 6.923508 CCACGAAAGCAATCATCATACTACTA 59.076 38.462 0.00 0.00 0.00 1.82
4535 4800 5.755375 CCACGAAAGCAATCATCATACTACT 59.245 40.000 0.00 0.00 0.00 2.57
4536 4801 5.050091 CCCACGAAAGCAATCATCATACTAC 60.050 44.000 0.00 0.00 0.00 2.73
4537 4802 5.056480 CCCACGAAAGCAATCATCATACTA 58.944 41.667 0.00 0.00 0.00 1.82
4538 4803 3.879295 CCCACGAAAGCAATCATCATACT 59.121 43.478 0.00 0.00 0.00 2.12
4539 4804 3.548818 GCCCACGAAAGCAATCATCATAC 60.549 47.826 0.00 0.00 0.00 2.39
4540 4805 2.618241 GCCCACGAAAGCAATCATCATA 59.382 45.455 0.00 0.00 0.00 2.15
4541 4806 1.406539 GCCCACGAAAGCAATCATCAT 59.593 47.619 0.00 0.00 0.00 2.45
4542 4807 0.810648 GCCCACGAAAGCAATCATCA 59.189 50.000 0.00 0.00 0.00 3.07
4543 4808 0.810648 TGCCCACGAAAGCAATCATC 59.189 50.000 0.00 0.00 35.69 2.92
4544 4809 1.477553 ATGCCCACGAAAGCAATCAT 58.522 45.000 0.00 0.00 43.36 2.45
4545 4810 1.067706 CAATGCCCACGAAAGCAATCA 60.068 47.619 0.00 0.00 43.36 2.57
4546 4811 1.067635 ACAATGCCCACGAAAGCAATC 60.068 47.619 0.00 0.00 43.36 2.67
4547 4812 0.968405 ACAATGCCCACGAAAGCAAT 59.032 45.000 0.00 0.00 43.36 3.56
4548 4813 0.749649 AACAATGCCCACGAAAGCAA 59.250 45.000 0.00 0.00 43.36 3.91
4549 4814 0.031857 CAACAATGCCCACGAAAGCA 59.968 50.000 0.00 0.00 44.45 3.91
4550 4815 2.813100 CAACAATGCCCACGAAAGC 58.187 52.632 0.00 0.00 0.00 3.51
4578 4843 4.955811 TCAAAAGAGTCTAGACCAGCAA 57.044 40.909 19.38 0.00 0.00 3.91
4581 4846 7.397892 TCTACATCAAAAGAGTCTAGACCAG 57.602 40.000 19.38 3.72 0.00 4.00
4588 4853 6.042093 TCACCACTTCTACATCAAAAGAGTCT 59.958 38.462 0.00 0.00 0.00 3.24
4599 4864 9.654663 GTAAGAAAATAGTCACCACTTCTACAT 57.345 33.333 0.00 0.00 33.62 2.29
4611 4876 5.643777 GGCTCAAGCTGTAAGAAAATAGTCA 59.356 40.000 1.46 0.00 41.70 3.41
4612 4877 5.877564 AGGCTCAAGCTGTAAGAAAATAGTC 59.122 40.000 1.46 0.00 41.70 2.59
4617 4882 4.968259 TGTAGGCTCAAGCTGTAAGAAAA 58.032 39.130 1.46 0.00 41.70 2.29
4630 4895 9.944376 GAAAAACATATATAGGATGTAGGCTCA 57.056 33.333 0.54 0.00 36.50 4.26
4669 4934 9.823098 GTACAGATGCATGATCAATTTAATCTC 57.177 33.333 2.46 0.00 32.86 2.75
4684 4949 6.881065 ACTTCAACTTACATGTACAGATGCAT 59.119 34.615 4.68 0.00 0.00 3.96
4727 4992 7.510407 TCCAACCAAATTCCGTGTATATATCA 58.490 34.615 0.00 0.00 0.00 2.15
4729 4994 8.754991 TTTCCAACCAAATTCCGTGTATATAT 57.245 30.769 0.00 0.00 0.00 0.86
4797 5062 0.045469 ATCCCTTCTCCCTCCTTGCT 59.955 55.000 0.00 0.00 0.00 3.91
4804 5069 1.804502 TTCCCCATCCCTTCTCCCT 59.195 57.895 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.