Multiple sequence alignment - TraesCS1D01G302200

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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 TraesCS1D01G302200 chr1D 100.000 5842 0 0 1 5842 400018266 400012425 0.000000e+00 10789.0
1 TraesCS1D01G302200 chr1D 98.611 144 2 0 3883 4026 400014282 400014139 7.510000e-64 255.0
2 TraesCS1D01G302200 chr1D 98.611 144 2 0 3985 4128 400014384 400014241 7.510000e-64 255.0
3 TraesCS1D01G302200 chr1D 94.545 110 6 0 34 143 400018342 400018233 2.800000e-38 171.0
4 TraesCS1D01G302200 chr1D 100.000 30 0 0 5 34 400018153 400018124 8.180000e-04 56.5
5 TraesCS1D01G302200 chr1B 92.615 3155 145 38 778 3898 536709799 536706699 0.000000e+00 4455.0
6 TraesCS1D01G302200 chr1B 92.323 1003 60 13 4159 5151 536706674 536705679 0.000000e+00 1410.0
7 TraesCS1D01G302200 chr1B 90.710 775 51 12 4 776 536710596 536709841 0.000000e+00 1013.0
8 TraesCS1D01G302200 chr1B 88.122 362 31 5 1309 1660 635830911 635831270 2.520000e-113 420.0
9 TraesCS1D01G302200 chr1B 85.200 250 16 6 1104 1352 101247218 101247447 2.720000e-58 237.0
10 TraesCS1D01G302200 chr1B 92.308 130 10 0 6 135 536710703 536710574 1.000000e-42 185.0
11 TraesCS1D01G302200 chr1B 97.872 47 1 0 5212 5258 536705678 536705632 1.350000e-11 82.4
12 TraesCS1D01G302200 chr1B 100.000 29 0 0 6 34 536710485 536710457 3.000000e-03 54.7
13 TraesCS1D01G302200 chr1A 93.480 2178 78 23 4 2129 496444226 496442061 0.000000e+00 3177.0
14 TraesCS1D01G302200 chr1A 95.163 1199 38 10 4127 5320 496440013 496438830 0.000000e+00 1875.0
15 TraesCS1D01G302200 chr1A 98.212 839 13 2 2694 3530 496441443 496440605 0.000000e+00 1465.0
16 TraesCS1D01G302200 chr1A 96.097 538 21 0 2125 2662 496441981 496441444 0.000000e+00 878.0
17 TraesCS1D01G302200 chr1A 97.429 389 5 1 3526 3914 496440570 496440187 0.000000e+00 658.0
18 TraesCS1D01G302200 chr1A 91.525 118 10 0 26 143 496444313 496444196 4.680000e-36 163.0
19 TraesCS1D01G302200 chr1A 94.186 86 4 1 3896 3981 496439980 496440064 4.750000e-26 130.0
20 TraesCS1D01G302200 chr1A 94.186 86 4 1 3998 4083 496439980 496440064 4.750000e-26 130.0
21 TraesCS1D01G302200 chr1A 97.368 38 1 0 4091 4128 496440117 496440080 1.360000e-06 65.8
22 TraesCS1D01G302200 chr1A 100.000 30 0 0 6 35 496444115 496444086 8.180000e-04 56.5
23 TraesCS1D01G302200 chr7B 89.626 1282 93 12 1579 2844 333364579 333363322 0.000000e+00 1594.0
24 TraesCS1D01G302200 chr7B 89.505 1010 79 10 1579 2578 102797939 102796947 0.000000e+00 1253.0
25 TraesCS1D01G302200 chr7B 92.475 598 26 8 2875 3470 333363324 333362744 0.000000e+00 837.0
26 TraesCS1D01G302200 chr7B 91.472 598 31 8 2875 3470 102784622 102784043 0.000000e+00 804.0
27 TraesCS1D01G302200 chr7B 88.122 362 31 5 1309 1660 600922463 600922104 2.520000e-113 420.0
28 TraesCS1D01G302200 chr7B 87.845 362 32 5 1309 1660 608180869 608180510 1.170000e-111 414.0
29 TraesCS1D01G302200 chr7B 80.962 520 79 13 5329 5842 379207967 379207462 1.530000e-105 394.0
30 TraesCS1D01G302200 chr7B 89.706 272 13 7 2581 2844 102784884 102784620 3.370000e-87 333.0
31 TraesCS1D01G302200 chr7B 85.656 244 14 7 1110 1352 535230923 535230700 2.720000e-58 237.0
32 TraesCS1D01G302200 chr7B 85.200 250 16 9 1104 1352 721431299 721431528 2.720000e-58 237.0
33 TraesCS1D01G302200 chr7B 93.182 88 6 0 3899 3986 162120811 162120898 4.750000e-26 130.0
34 TraesCS1D01G302200 chr7B 93.182 88 6 0 4001 4088 162120811 162120898 4.750000e-26 130.0
35 TraesCS1D01G302200 chr4B 88.787 981 79 12 1579 2551 617879614 617878657 0.000000e+00 1173.0
36 TraesCS1D01G302200 chr4B 91.639 598 28 10 2875 3470 617876471 617875894 0.000000e+00 808.0
37 TraesCS1D01G302200 chr4B 90.252 318 16 8 2535 2844 617876779 617876469 9.120000e-108 401.0
38 TraesCS1D01G302200 chr4B 81.705 481 71 12 5329 5805 386465234 386465701 9.180000e-103 385.0
39 TraesCS1D01G302200 chr4B 80.000 515 89 12 5329 5842 124494847 124495348 9.250000e-98 368.0
40 TraesCS1D01G302200 chr4B 85.246 244 15 9 1110 1352 35026940 35026717 1.270000e-56 231.0
41 TraesCS1D01G302200 chr6A 87.931 754 68 12 1465 2205 87534441 87533698 0.000000e+00 867.0
42 TraesCS1D01G302200 chr7A 87.434 756 70 12 1465 2205 310580685 310581430 0.000000e+00 846.0
43 TraesCS1D01G302200 chr7A 87.335 758 69 12 1465 2205 653265289 653266036 0.000000e+00 843.0
44 TraesCS1D01G302200 chr4A 87.434 756 70 12 1465 2205 101822914 101822169 0.000000e+00 846.0
45 TraesCS1D01G302200 chr4A 86.640 756 76 12 1465 2205 682036189 682036934 0.000000e+00 813.0
46 TraesCS1D01G302200 chr4A 89.698 398 29 8 429 818 721670777 721671170 1.130000e-136 497.0
47 TraesCS1D01G302200 chr4A 82.949 434 63 9 5400 5830 175003239 175003664 1.190000e-101 381.0
48 TraesCS1D01G302200 chr3A 88.714 381 27 11 1270 1640 38993333 38992959 8.930000e-123 451.0
49 TraesCS1D01G302200 chr3A 87.397 365 31 7 1309 1663 452377035 452376676 7.050000e-109 405.0
50 TraesCS1D01G302200 chr3A 93.182 88 6 0 4001 4088 470095779 470095692 4.750000e-26 130.0
51 TraesCS1D01G302200 chr3A 93.182 88 6 0 3899 3986 470095779 470095692 4.750000e-26 130.0
52 TraesCS1D01G302200 chr3A 96.875 32 1 0 1225 1256 38993363 38993332 3.000000e-03 54.7
53 TraesCS1D01G302200 chr3A 100.000 28 0 0 4101 4128 724600965 724600938 1.100000e-02 52.8
54 TraesCS1D01G302200 chr7D 83.750 480 66 7 5329 5804 517336830 517337301 1.490000e-120 444.0
55 TraesCS1D01G302200 chr4D 82.364 516 76 10 5329 5842 434281564 434281062 8.990000e-118 435.0
56 TraesCS1D01G302200 chr2B 82.759 493 74 7 5329 5820 770229883 770230365 4.180000e-116 429.0
57 TraesCS1D01G302200 chr2B 82.556 493 75 7 5329 5820 770196848 770197330 1.950000e-114 424.0
58 TraesCS1D01G302200 chr2A 82.922 486 70 8 5329 5812 673026507 673026033 5.410000e-115 425.0
59 TraesCS1D01G302200 chr2A 87.387 111 12 2 3979 4088 53078394 53078503 6.150000e-25 126.0
60 TraesCS1D01G302200 chrUn 87.293 362 34 5 1309 1660 349787385 349787026 2.540000e-108 403.0
61 TraesCS1D01G302200 chrUn 92.308 91 6 1 3900 3990 15903921 15904010 1.710000e-25 128.0
62 TraesCS1D01G302200 chrUn 92.308 91 6 1 4002 4092 15903921 15904010 1.710000e-25 128.0
63 TraesCS1D01G302200 chr3D 79.278 526 68 19 5326 5841 387361719 387362213 4.360000e-86 329.0
64 TraesCS1D01G302200 chr3D 85.494 324 19 10 1225 1539 141488594 141488898 4.400000e-81 313.0
65 TraesCS1D01G302200 chr3D 85.032 314 19 11 1039 1352 440054569 440054284 1.590000e-75 294.0
66 TraesCS1D01G302200 chr3D 100.000 29 0 0 4100 4128 11578654 11578626 3.000000e-03 54.7
67 TraesCS1D01G302200 chr2D 85.185 324 20 10 1225 1539 431523620 431523316 2.040000e-79 307.0
68 TraesCS1D01G302200 chr2D 93.103 87 6 0 3900 3986 74149828 74149742 1.710000e-25 128.0
69 TraesCS1D01G302200 chr5B 86.066 244 13 10 1110 1352 508608666 508608443 5.850000e-60 243.0
70 TraesCS1D01G302200 chr5B 90.659 182 15 2 429 609 468933674 468933494 2.100000e-59 241.0
71 TraesCS1D01G302200 chr5B 94.186 86 5 0 4002 4087 166379182 166379097 1.320000e-26 132.0
72 TraesCS1D01G302200 chr5B 94.186 86 5 0 3900 3985 166379182 166379097 1.320000e-26 132.0
73 TraesCS1D01G302200 chr3B 86.066 244 13 10 1110 1352 773733177 773732954 5.850000e-60 243.0
74 TraesCS1D01G302200 chr3B 85.246 244 15 11 1110 1352 154413816 154413593 1.270000e-56 231.0
75 TraesCS1D01G302200 chr3B 100.000 28 0 0 4101 4128 541579971 541579944 1.100000e-02 52.8
76 TraesCS1D01G302200 chr6D 80.192 313 47 12 5495 5806 398743936 398744234 2.740000e-53 220.0
77 TraesCS1D01G302200 chr5A 94.253 87 5 0 3900 3986 600439751 600439837 3.670000e-27 134.0
78 TraesCS1D01G302200 chr5A 94.253 87 5 0 4002 4088 600439751 600439837 3.670000e-27 134.0
79 TraesCS1D01G302200 chr6B 84.091 132 18 3 3998 4128 163968040 163967911 2.210000e-24 124.0
80 TraesCS1D01G302200 chr6B 83.582 134 19 3 3896 4028 163968040 163967909 7.950000e-24 122.0
81 TraesCS1D01G302200 chr5D 100.000 29 0 0 4100 4128 312136069 312136097 3.000000e-03 54.7


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 TraesCS1D01G302200 chr1D 400012425 400018266 5841 True 10789.000000 10789 100.000000 1 5842 1 chr1D.!!$R1 5841
1 TraesCS1D01G302200 chr1B 536705632 536710703 5071 True 1200.016667 4455 94.304667 4 5258 6 chr1B.!!$R1 5254
2 TraesCS1D01G302200 chr1A 496438830 496444313 5483 True 1042.287500 3177 96.159250 4 5320 8 chr1A.!!$R1 5316
3 TraesCS1D01G302200 chr7B 102796947 102797939 992 True 1253.000000 1253 89.505000 1579 2578 1 chr7B.!!$R1 999
4 TraesCS1D01G302200 chr7B 333362744 333364579 1835 True 1215.500000 1594 91.050500 1579 3470 2 chr7B.!!$R7 1891
5 TraesCS1D01G302200 chr7B 102784043 102784884 841 True 568.500000 804 90.589000 2581 3470 2 chr7B.!!$R6 889
6 TraesCS1D01G302200 chr7B 379207462 379207967 505 True 394.000000 394 80.962000 5329 5842 1 chr7B.!!$R2 513
7 TraesCS1D01G302200 chr4B 617875894 617879614 3720 True 794.000000 1173 90.226000 1579 3470 3 chr4B.!!$R2 1891
8 TraesCS1D01G302200 chr4B 124494847 124495348 501 False 368.000000 368 80.000000 5329 5842 1 chr4B.!!$F1 513
9 TraesCS1D01G302200 chr6A 87533698 87534441 743 True 867.000000 867 87.931000 1465 2205 1 chr6A.!!$R1 740
10 TraesCS1D01G302200 chr7A 310580685 310581430 745 False 846.000000 846 87.434000 1465 2205 1 chr7A.!!$F1 740
11 TraesCS1D01G302200 chr7A 653265289 653266036 747 False 843.000000 843 87.335000 1465 2205 1 chr7A.!!$F2 740
12 TraesCS1D01G302200 chr4A 101822169 101822914 745 True 846.000000 846 87.434000 1465 2205 1 chr4A.!!$R1 740
13 TraesCS1D01G302200 chr4A 682036189 682036934 745 False 813.000000 813 86.640000 1465 2205 1 chr4A.!!$F2 740
14 TraesCS1D01G302200 chr4D 434281062 434281564 502 True 435.000000 435 82.364000 5329 5842 1 chr4D.!!$R1 513

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
28 29 1.066858 CGTCAACTCTAGGGTGCATGT 60.067 52.381 0.00 0.0 31.53 3.21 F
691 803 1.201647 CAAGACATGCCTCTTGCTTGG 59.798 52.381 11.78 0.0 46.51 3.61 F
1660 1852 0.036010 AGCCCTCTGTGTATGTGTGC 60.036 55.000 0.00 0.0 0.00 4.57 F
1668 1860 1.202475 TGTGTATGTGTGCGTGTGTCT 60.202 47.619 0.00 0.0 0.00 3.41 F
2110 2309 1.541147 TGATGGTTGCAGCTACTTTGC 59.459 47.619 6.94 0.0 41.86 3.68 F
3938 6234 1.375551 AAGTGTCGCGGTTTTGAACT 58.624 45.000 6.13 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1043 1198 0.466124 GAACGGGAGGAAGATGAGGG 59.534 60.0 0.00 0.0 0.00 4.30 R
2415 2700 0.250770 AGGGAAAGGCGGAACAGAAC 60.251 55.0 0.00 0.0 0.00 3.01 R
3264 5455 1.747709 ATGGCAAGCAGAGTAAGCAG 58.252 50.0 0.00 0.0 0.00 4.24 R
3656 5895 2.025981 CAGGGGATCATCCAAGTGTTCA 60.026 50.0 5.89 0.0 38.64 3.18 R
4108 6428 2.287915 CGCACTTATTTTGGATCGGAGG 59.712 50.0 0.00 0.0 0.00 4.30 R
5287 7619 0.326618 CCTCCCACCTCCCATGTACT 60.327 60.0 0.00 0.0 0.00 2.73 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
27 28 1.204704 TCGTCAACTCTAGGGTGCATG 59.795 52.381 0.00 0.00 31.53 4.06
28 29 1.066858 CGTCAACTCTAGGGTGCATGT 60.067 52.381 0.00 0.00 31.53 3.21
78 79 4.339872 ACGACACTATCCTATCTCGAGT 57.660 45.455 13.13 2.46 0.00 4.18
112 222 5.747565 CCGAAACATGCATGTCGTTATTAT 58.252 37.500 31.45 11.57 40.80 1.28
113 223 6.565060 GCCGAAACATGCATGTCGTTATTATA 60.565 38.462 31.45 0.00 40.80 0.98
253 364 3.481388 GCTATCGTCGGTTCTCGTAAAAG 59.519 47.826 0.00 0.00 40.32 2.27
306 417 7.148373 TGTGACACAAACTTTGTTTCTAGTACC 60.148 37.037 17.59 4.15 43.23 3.34
347 458 2.041216 AGGGCCACCGAATTCTAAAACT 59.959 45.455 6.18 0.00 43.47 2.66
370 481 4.102524 TGTTGGCTATATTACCACCAGAGG 59.897 45.833 0.00 0.00 35.10 3.69
452 563 5.473504 ACAATCACATTACACACCCTCTTTC 59.526 40.000 0.00 0.00 0.00 2.62
564 676 1.947456 GGGAGGTGGTAATTTCGCATC 59.053 52.381 0.00 0.00 0.00 3.91
565 677 1.947456 GGAGGTGGTAATTTCGCATCC 59.053 52.381 9.03 9.03 38.20 3.51
580 692 1.888512 GCATCCAGCAAAACAGAGGAA 59.111 47.619 0.00 0.00 44.79 3.36
657 769 5.389098 GCACATTAATTCACAGCAAAGCTTG 60.389 40.000 0.00 0.00 36.40 4.01
691 803 1.201647 CAAGACATGCCTCTTGCTTGG 59.798 52.381 11.78 0.00 46.51 3.61
752 864 2.810164 GACTGGTAGTCCTCTTCTGGT 58.190 52.381 0.00 0.00 39.28 4.00
753 865 2.494073 GACTGGTAGTCCTCTTCTGGTG 59.506 54.545 0.00 0.00 39.28 4.17
770 882 8.269317 TCTTCTGGTGGTAGTAAAAAGAGAAAA 58.731 33.333 0.00 0.00 0.00 2.29
975 1130 3.185797 CCACCGTACCGAGAAAAGAAAAG 59.814 47.826 0.00 0.00 0.00 2.27
1475 1655 2.123769 TGCAGCAAGCTGTTGGGT 60.124 55.556 21.75 0.00 45.24 4.51
1505 1685 1.946650 CCTCGATTCGCTTCCTCGC 60.947 63.158 0.00 0.00 32.62 5.03
1660 1852 0.036010 AGCCCTCTGTGTATGTGTGC 60.036 55.000 0.00 0.00 0.00 4.57
1668 1860 1.202475 TGTGTATGTGTGCGTGTGTCT 60.202 47.619 0.00 0.00 0.00 3.41
1726 1918 6.531594 TGATTCATACGATTCTTCAGTGTCAC 59.468 38.462 0.00 0.00 0.00 3.67
1967 2162 1.668419 GCGCATCCAGAGGTAATTGT 58.332 50.000 0.30 0.00 0.00 2.71
2048 2245 5.466728 TCGCATCAGCTGGTAATTAATCTTC 59.533 40.000 15.13 0.00 39.10 2.87
2052 2249 7.646922 GCATCAGCTGGTAATTAATCTTCAAAG 59.353 37.037 15.13 0.00 37.91 2.77
2110 2309 1.541147 TGATGGTTGCAGCTACTTTGC 59.459 47.619 6.94 0.00 41.86 3.68
2179 2463 1.570813 TGCGATAAGTTGCATCCTCG 58.429 50.000 0.00 0.00 39.83 4.63
2210 2494 5.791336 TCTGATCGCATGGTATTCTTAGT 57.209 39.130 0.00 0.00 0.00 2.24
2236 2520 4.393062 CGTAGTCGTAGTCTCACCCTTAAA 59.607 45.833 0.00 0.00 0.00 1.52
2249 2533 6.608002 TCTCACCCTTAAACCTATCTCTCTTC 59.392 42.308 0.00 0.00 0.00 2.87
2328 2612 8.424133 AGAATTGCTACCTGAATTTTCTGTTTT 58.576 29.630 0.00 0.00 0.00 2.43
2330 2614 5.288804 TGCTACCTGAATTTTCTGTTTTGC 58.711 37.500 0.00 0.00 0.00 3.68
2415 2700 8.576442 ACTGAAAACATATACAGGTTCCTTTTG 58.424 33.333 0.00 0.00 35.08 2.44
2471 2756 4.768583 TGCTGAAAATTGGCAAGTCTTTT 58.231 34.783 5.96 7.88 32.79 2.27
2481 2766 8.785329 AATTGGCAAGTCTTTTTCTTAAAACA 57.215 26.923 5.96 0.00 0.00 2.83
2851 5038 3.921119 ATGAGACTTGAAATGCGCAAA 57.079 38.095 17.11 2.38 0.00 3.68
2855 5042 3.236816 AGACTTGAAATGCGCAAATTCG 58.763 40.909 25.02 17.70 0.00 3.34
2866 5054 2.092055 GCGCAAATTCGGTGGATTTTTC 59.908 45.455 0.30 0.00 0.00 2.29
3444 5644 4.160329 TCTTGTATGGAACCTCACTCTGT 58.840 43.478 0.00 0.00 0.00 3.41
3909 6156 7.032580 CAGAGATTAGCATTATACTCCCTTCG 58.967 42.308 0.00 0.00 0.00 3.79
3913 6209 4.810191 AGCATTATACTCCCTTCGATCC 57.190 45.455 0.00 0.00 0.00 3.36
3937 6233 3.531262 ATAAGTGTCGCGGTTTTGAAC 57.469 42.857 6.13 0.00 0.00 3.18
3938 6234 1.375551 AAGTGTCGCGGTTTTGAACT 58.624 45.000 6.13 0.00 0.00 3.01
3939 6235 2.228138 AGTGTCGCGGTTTTGAACTA 57.772 45.000 6.13 0.00 0.00 2.24
3940 6236 2.553086 AGTGTCGCGGTTTTGAACTAA 58.447 42.857 6.13 0.00 0.00 2.24
3941 6237 2.542595 AGTGTCGCGGTTTTGAACTAAG 59.457 45.455 6.13 0.00 0.00 2.18
3942 6238 1.868498 TGTCGCGGTTTTGAACTAAGG 59.132 47.619 6.13 0.00 0.00 2.69
3943 6239 1.869132 GTCGCGGTTTTGAACTAAGGT 59.131 47.619 6.13 0.00 0.00 3.50
3944 6240 2.288729 GTCGCGGTTTTGAACTAAGGTT 59.711 45.455 6.13 0.00 38.52 3.50
3945 6241 3.494251 GTCGCGGTTTTGAACTAAGGTTA 59.506 43.478 6.13 0.00 35.58 2.85
3946 6242 3.742369 TCGCGGTTTTGAACTAAGGTTAG 59.258 43.478 6.13 0.00 35.58 2.34
3947 6243 3.495753 CGCGGTTTTGAACTAAGGTTAGT 59.504 43.478 0.00 0.00 45.43 2.24
3967 6263 8.836959 GTTAGTTCAACCTTAGTTCAAAACTG 57.163 34.615 2.65 0.00 42.84 3.16
3968 6264 5.891451 AGTTCAACCTTAGTTCAAAACTGC 58.109 37.500 2.65 0.00 42.84 4.40
3969 6265 5.417580 AGTTCAACCTTAGTTCAAAACTGCA 59.582 36.000 2.65 0.00 42.84 4.41
3970 6266 5.906113 TCAACCTTAGTTCAAAACTGCAA 57.094 34.783 2.65 0.00 42.84 4.08
3971 6267 5.646606 TCAACCTTAGTTCAAAACTGCAAC 58.353 37.500 2.65 0.00 42.84 4.17
3972 6268 5.184096 TCAACCTTAGTTCAAAACTGCAACA 59.816 36.000 2.65 0.00 42.84 3.33
3973 6269 4.993905 ACCTTAGTTCAAAACTGCAACAC 58.006 39.130 2.65 0.00 42.84 3.32
3974 6270 4.705023 ACCTTAGTTCAAAACTGCAACACT 59.295 37.500 2.65 0.00 42.84 3.55
3975 6271 5.185056 ACCTTAGTTCAAAACTGCAACACTT 59.815 36.000 2.65 0.00 42.84 3.16
3976 6272 6.376018 ACCTTAGTTCAAAACTGCAACACTTA 59.624 34.615 2.65 0.00 42.84 2.24
3977 6273 7.094118 ACCTTAGTTCAAAACTGCAACACTTAA 60.094 33.333 2.65 0.00 42.84 1.85
3978 6274 7.920682 CCTTAGTTCAAAACTGCAACACTTAAT 59.079 33.333 2.65 0.00 42.84 1.40
3979 6275 9.301153 CTTAGTTCAAAACTGCAACACTTAATT 57.699 29.630 2.65 0.00 42.84 1.40
3980 6276 9.646427 TTAGTTCAAAACTGCAACACTTAATTT 57.354 25.926 2.65 0.00 42.84 1.82
3981 6277 7.962917 AGTTCAAAACTGCAACACTTAATTTG 58.037 30.769 0.00 0.00 41.01 2.32
3982 6278 6.900568 TCAAAACTGCAACACTTAATTTGG 57.099 33.333 0.00 0.00 0.00 3.28
3983 6279 6.634805 TCAAAACTGCAACACTTAATTTGGA 58.365 32.000 0.00 0.00 0.00 3.53
3984 6280 7.271511 TCAAAACTGCAACACTTAATTTGGAT 58.728 30.769 0.00 0.00 0.00 3.41
3985 6281 7.437862 TCAAAACTGCAACACTTAATTTGGATC 59.562 33.333 0.00 0.00 0.00 3.36
3986 6282 5.391312 ACTGCAACACTTAATTTGGATCC 57.609 39.130 4.20 4.20 0.00 3.36
3987 6283 4.832266 ACTGCAACACTTAATTTGGATCCA 59.168 37.500 11.44 11.44 0.00 3.41
3988 6284 5.047802 ACTGCAACACTTAATTTGGATCCAG 60.048 40.000 15.53 4.62 0.00 3.86
3989 6285 5.076182 TGCAACACTTAATTTGGATCCAGA 58.924 37.500 15.53 11.56 0.00 3.86
3990 6286 5.538053 TGCAACACTTAATTTGGATCCAGAA 59.462 36.000 15.53 12.52 0.00 3.02
4009 6305 8.045720 TCCAGAAATTAGCATTATACTCCCTT 57.954 34.615 0.00 0.00 0.00 3.95
4023 6319 9.726438 ATTATACTCCCTTCGATCCAAAATAAG 57.274 33.333 0.00 0.00 0.00 1.73
4030 6326 2.601314 TCGATCCAAAATAAGTGTCGCG 59.399 45.455 0.00 0.00 0.00 5.87
4047 6367 3.494251 GTCGCGGTTTTGAACTAAGGTTA 59.506 43.478 6.13 0.00 35.58 2.85
4048 6368 3.742369 TCGCGGTTTTGAACTAAGGTTAG 59.258 43.478 6.13 0.00 35.58 2.34
4049 6369 3.495753 CGCGGTTTTGAACTAAGGTTAGT 59.504 43.478 0.00 0.00 45.43 2.24
4071 6391 5.417580 AGTTCAACCTTAGTTCAAAACTGCA 59.582 36.000 2.65 0.00 42.84 4.41
4073 6393 5.646606 TCAACCTTAGTTCAAAACTGCAAC 58.353 37.500 2.65 0.00 42.84 4.17
4074 6394 5.184096 TCAACCTTAGTTCAAAACTGCAACA 59.816 36.000 2.65 0.00 42.84 3.33
4075 6395 4.993905 ACCTTAGTTCAAAACTGCAACAC 58.006 39.130 2.65 0.00 42.84 3.32
4076 6396 4.705023 ACCTTAGTTCAAAACTGCAACACT 59.295 37.500 2.65 0.00 42.84 3.55
4077 6397 5.185056 ACCTTAGTTCAAAACTGCAACACTT 59.815 36.000 2.65 0.00 42.84 3.16
4078 6398 6.376018 ACCTTAGTTCAAAACTGCAACACTTA 59.624 34.615 2.65 0.00 42.84 2.24
4079 6399 7.094118 ACCTTAGTTCAAAACTGCAACACTTAA 60.094 33.333 2.65 0.00 42.84 1.85
4080 6400 7.920682 CCTTAGTTCAAAACTGCAACACTTAAT 59.079 33.333 2.65 0.00 42.84 1.40
4081 6401 9.301153 CTTAGTTCAAAACTGCAACACTTAATT 57.699 29.630 2.65 0.00 42.84 1.40
4082 6402 9.646427 TTAGTTCAAAACTGCAACACTTAATTT 57.354 25.926 2.65 0.00 42.84 1.82
4083 6403 7.962917 AGTTCAAAACTGCAACACTTAATTTG 58.037 30.769 0.00 0.00 41.01 2.32
4084 6404 6.900568 TCAAAACTGCAACACTTAATTTGG 57.099 33.333 0.00 0.00 0.00 3.28
4085 6405 6.634805 TCAAAACTGCAACACTTAATTTGGA 58.365 32.000 0.00 0.00 0.00 3.53
4086 6406 7.271511 TCAAAACTGCAACACTTAATTTGGAT 58.728 30.769 0.00 0.00 0.00 3.41
4087 6407 7.437862 TCAAAACTGCAACACTTAATTTGGATC 59.562 33.333 0.00 0.00 0.00 3.36
4088 6408 5.391312 ACTGCAACACTTAATTTGGATCC 57.609 39.130 4.20 4.20 0.00 3.36
4089 6409 4.832266 ACTGCAACACTTAATTTGGATCCA 59.168 37.500 11.44 11.44 0.00 3.41
4090 6410 5.047802 ACTGCAACACTTAATTTGGATCCAG 60.048 40.000 15.53 4.62 0.00 3.86
4091 6411 5.076182 TGCAACACTTAATTTGGATCCAGA 58.924 37.500 15.53 11.56 0.00 3.86
4092 6412 5.538053 TGCAACACTTAATTTGGATCCAGAA 59.462 36.000 15.53 12.52 0.00 3.02
4093 6413 6.041409 TGCAACACTTAATTTGGATCCAGAAA 59.959 34.615 15.53 8.01 0.00 2.52
4094 6414 7.099120 GCAACACTTAATTTGGATCCAGAAAT 58.901 34.615 15.53 10.19 0.00 2.17
4095 6415 7.603784 GCAACACTTAATTTGGATCCAGAAATT 59.396 33.333 22.19 22.19 36.14 1.82
4098 6418 8.470002 ACACTTAATTTGGATCCAGAAATTAGC 58.530 33.333 22.21 0.00 36.11 3.09
4099 6419 8.469200 CACTTAATTTGGATCCAGAAATTAGCA 58.531 33.333 22.21 13.41 36.11 3.49
4100 6420 9.205513 ACTTAATTTGGATCCAGAAATTAGCAT 57.794 29.630 22.21 13.91 36.11 3.79
4106 6426 9.866655 TTTGGATCCAGAAATTAGCATTATACT 57.133 29.630 15.53 0.00 0.00 2.12
4107 6427 9.507329 TTGGATCCAGAAATTAGCATTATACTC 57.493 33.333 15.53 0.00 0.00 2.59
4108 6428 8.103305 TGGATCCAGAAATTAGCATTATACTCC 58.897 37.037 11.44 0.00 0.00 3.85
4109 6429 7.554476 GGATCCAGAAATTAGCATTATACTCCC 59.446 40.741 6.95 0.00 0.00 4.30
4110 6430 7.633018 TCCAGAAATTAGCATTATACTCCCT 57.367 36.000 0.00 0.00 0.00 4.20
4111 6431 7.680730 TCCAGAAATTAGCATTATACTCCCTC 58.319 38.462 0.00 0.00 0.00 4.30
4112 6432 6.881602 CCAGAAATTAGCATTATACTCCCTCC 59.118 42.308 0.00 0.00 0.00 4.30
4113 6433 6.591834 CAGAAATTAGCATTATACTCCCTCCG 59.408 42.308 0.00 0.00 0.00 4.63
4114 6434 6.497259 AGAAATTAGCATTATACTCCCTCCGA 59.503 38.462 0.00 0.00 0.00 4.55
4115 6435 6.875972 AATTAGCATTATACTCCCTCCGAT 57.124 37.500 0.00 0.00 0.00 4.18
4116 6436 5.916661 TTAGCATTATACTCCCTCCGATC 57.083 43.478 0.00 0.00 0.00 3.69
4117 6437 3.100671 AGCATTATACTCCCTCCGATCC 58.899 50.000 0.00 0.00 0.00 3.36
4118 6438 2.832129 GCATTATACTCCCTCCGATCCA 59.168 50.000 0.00 0.00 0.00 3.41
4119 6439 3.260884 GCATTATACTCCCTCCGATCCAA 59.739 47.826 0.00 0.00 0.00 3.53
4120 6440 4.262894 GCATTATACTCCCTCCGATCCAAA 60.263 45.833 0.00 0.00 0.00 3.28
4121 6441 5.744887 GCATTATACTCCCTCCGATCCAAAA 60.745 44.000 0.00 0.00 0.00 2.44
4122 6442 6.476378 CATTATACTCCCTCCGATCCAAAAT 58.524 40.000 0.00 0.00 0.00 1.82
4123 6443 7.620880 CATTATACTCCCTCCGATCCAAAATA 58.379 38.462 0.00 0.00 0.00 1.40
4124 6444 7.621006 TTATACTCCCTCCGATCCAAAATAA 57.379 36.000 0.00 0.00 0.00 1.40
4125 6445 4.423625 ACTCCCTCCGATCCAAAATAAG 57.576 45.455 0.00 0.00 0.00 1.73
4126 6446 3.780850 ACTCCCTCCGATCCAAAATAAGT 59.219 43.478 0.00 0.00 0.00 2.24
4127 6447 4.130118 CTCCCTCCGATCCAAAATAAGTG 58.870 47.826 0.00 0.00 0.00 3.16
4128 6448 2.618709 CCCTCCGATCCAAAATAAGTGC 59.381 50.000 0.00 0.00 0.00 4.40
4129 6449 2.287915 CCTCCGATCCAAAATAAGTGCG 59.712 50.000 0.00 0.00 0.00 5.34
4130 6450 2.285083 TCCGATCCAAAATAAGTGCGG 58.715 47.619 0.00 0.00 38.89 5.69
4153 6473 3.877508 CACTTATTTTGGATCGGAGGGAC 59.122 47.826 0.00 0.00 0.00 4.46
4182 6502 2.650322 TCGCTTGATTGTATTTCCCCC 58.350 47.619 0.00 0.00 0.00 5.40
4258 6580 7.380423 AGAGCAGTACTAATTATTCACCCAT 57.620 36.000 0.00 0.00 0.00 4.00
4280 6602 8.736244 CCCATTAAAGCTAAAGCAGTAGTTTTA 58.264 33.333 4.54 9.95 45.16 1.52
4327 6653 2.024414 AGTGTGGTTTCAGAAAGGCAC 58.976 47.619 12.85 12.85 0.00 5.01
4434 6761 2.856032 CAACTCCGTGAGCTTGCG 59.144 61.111 4.21 4.21 32.04 4.85
4521 6848 4.228097 CATCAAGGCGGCGCTTCG 62.228 66.667 32.30 14.95 0.00 3.79
4860 7187 0.674895 GTTGCTGTGGGCTAGAGTGG 60.675 60.000 0.00 0.00 42.39 4.00
4890 7217 5.934935 TTTATCCGACTTTGGTGACTTTC 57.065 39.130 0.00 0.00 0.00 2.62
4931 7258 5.733620 TGGGAGTAGTGTTTACCAGTTAG 57.266 43.478 0.00 0.00 0.00 2.34
4932 7259 5.149976 TGGGAGTAGTGTTTACCAGTTAGT 58.850 41.667 0.00 0.00 0.00 2.24
4933 7260 6.314120 TGGGAGTAGTGTTTACCAGTTAGTA 58.686 40.000 0.00 0.00 0.00 1.82
4971 7298 2.689785 GCCGTAGTGCTGCATTGCA 61.690 57.895 11.50 11.50 41.05 4.08
5076 7403 3.107402 TCTTATGAGGGTCACAGAGCT 57.893 47.619 0.00 0.00 0.00 4.09
5097 7425 2.238521 GCAGTCTTCATCAACCCCAAA 58.761 47.619 0.00 0.00 0.00 3.28
5192 7524 3.465403 CAGCTCCTCCTGGGACCG 61.465 72.222 0.00 0.00 39.58 4.79
5251 7583 4.148825 GCACGAGGAGATGGCGGT 62.149 66.667 0.00 0.00 0.00 5.68
5264 7596 0.913205 TGGCGGTGGTGTATTATGGT 59.087 50.000 0.00 0.00 0.00 3.55
5272 7604 3.881089 GTGGTGTATTATGGTAAGGTGGC 59.119 47.826 0.00 0.00 0.00 5.01
5278 7610 1.285280 TATGGTAAGGTGGCAGCAGT 58.715 50.000 20.04 8.77 0.00 4.40
5348 7680 1.523154 GGGCATCTTCAACGGCAACA 61.523 55.000 0.00 0.00 0.00 3.33
5374 7706 1.994885 TTTCCTCCCGCATCCATCCC 61.995 60.000 0.00 0.00 0.00 3.85
5445 7778 1.663695 ACGCTAGCCGCATACATTTT 58.336 45.000 9.66 0.00 41.76 1.82
5446 7779 1.330521 ACGCTAGCCGCATACATTTTG 59.669 47.619 9.66 0.00 41.76 2.44
5448 7781 2.224079 CGCTAGCCGCATACATTTTGAT 59.776 45.455 9.66 0.00 39.08 2.57
5449 7782 3.303990 CGCTAGCCGCATACATTTTGATT 60.304 43.478 9.66 0.00 39.08 2.57
5529 7863 3.875134 GACGGATTTCATACAAACCGGAT 59.125 43.478 9.46 0.00 43.76 4.18
5536 7870 4.671880 TCATACAAACCGGATGAAAACG 57.328 40.909 9.46 0.00 0.00 3.60
5562 7896 8.629132 GGTTACGTTTTGGACATATTTTTAACG 58.371 33.333 0.00 0.00 41.81 3.18
5582 7916 6.986424 AACGAAAAAGCTAAAACTATGTGC 57.014 33.333 0.00 0.00 0.00 4.57
5583 7917 6.067263 ACGAAAAAGCTAAAACTATGTGCA 57.933 33.333 0.00 0.00 0.00 4.57
5584 7918 5.912955 ACGAAAAAGCTAAAACTATGTGCAC 59.087 36.000 10.75 10.75 0.00 4.57
5585 7919 5.912396 CGAAAAAGCTAAAACTATGTGCACA 59.088 36.000 24.08 24.08 0.00 4.57
5600 7934 1.736282 CACAGTGCGCATACGGTCA 60.736 57.895 15.91 0.00 40.57 4.02
5624 7958 0.179000 GAGCTCCATTCCCACGACAT 59.821 55.000 0.87 0.00 0.00 3.06
5651 7985 1.202734 ACTATGCTAGTCTACGGCCGA 60.203 52.381 35.90 14.96 32.47 5.54
5692 8026 4.100084 CCCATGTCCGGCAGCTCA 62.100 66.667 0.00 0.00 0.00 4.26
5696 8030 0.529337 CATGTCCGGCAGCTCACTAG 60.529 60.000 0.00 0.00 0.00 2.57
5708 8042 1.067821 GCTCACTAGCTAGATTGCCGT 59.932 52.381 27.45 0.27 45.85 5.68
5715 8049 0.461961 GCTAGATTGCCGTGAGTCCT 59.538 55.000 0.00 0.00 0.00 3.85
5783 8118 0.173481 CATCGGAGCGACAAAGAGGA 59.827 55.000 0.00 0.00 39.18 3.71
5796 8131 1.557269 AAGAGGATGCTTCAGCCGGT 61.557 55.000 1.90 0.00 45.56 5.28
5816 8152 1.001393 GGGAAGGGCATTTCCGTGA 60.001 57.895 12.19 0.00 46.19 4.35
5830 8166 2.978824 GTGAAGCTCAGGCGGGTA 59.021 61.111 0.00 0.00 44.37 3.69
5831 8167 1.448013 GTGAAGCTCAGGCGGGTAC 60.448 63.158 0.00 0.00 44.37 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.353704 CCCTAGAGTTGACGATGTGCAA 60.354 50.000 0.00 0.00 0.00 4.08
4 5 1.204941 GCACCCTAGAGTTGACGATGT 59.795 52.381 0.00 0.00 0.00 3.06
5 6 1.204704 TGCACCCTAGAGTTGACGATG 59.795 52.381 0.00 0.00 0.00 3.84
6 7 1.557099 TGCACCCTAGAGTTGACGAT 58.443 50.000 0.00 0.00 0.00 3.73
7 8 1.204704 CATGCACCCTAGAGTTGACGA 59.795 52.381 0.00 0.00 0.00 4.20
8 9 1.066858 ACATGCACCCTAGAGTTGACG 60.067 52.381 0.00 0.00 0.00 4.35
9 10 2.028112 TCACATGCACCCTAGAGTTGAC 60.028 50.000 0.00 0.00 0.00 3.18
10 11 2.028112 GTCACATGCACCCTAGAGTTGA 60.028 50.000 0.00 0.00 0.00 3.18
11 12 2.350522 GTCACATGCACCCTAGAGTTG 58.649 52.381 0.00 0.00 0.00 3.16
12 13 1.279271 GGTCACATGCACCCTAGAGTT 59.721 52.381 3.39 0.00 0.00 3.01
27 28 2.685388 GGTAGGTCGTAACTAGGGTCAC 59.315 54.545 0.00 0.00 0.00 3.67
28 29 2.357154 GGGTAGGTCGTAACTAGGGTCA 60.357 54.545 0.00 0.00 0.00 4.02
78 79 0.249953 ATGTTTCGGCACACCACGTA 60.250 50.000 0.00 0.00 34.57 3.57
112 222 2.426024 GCACCCTAGAGTTGACGATGTA 59.574 50.000 0.00 0.00 0.00 2.29
113 223 1.204941 GCACCCTAGAGTTGACGATGT 59.795 52.381 0.00 0.00 0.00 3.06
253 364 6.676950 AGATAGTCGTGATGTGATGATCTTC 58.323 40.000 1.67 1.67 0.00 2.87
306 417 2.561037 GGGTTTGAGCGGTTGGTGG 61.561 63.158 0.00 0.00 0.00 4.61
543 655 0.391927 TGCGAAATTACCACCTCCCG 60.392 55.000 0.00 0.00 0.00 5.14
559 671 0.169672 CCTCTGTTTTGCTGGATGCG 59.830 55.000 0.00 0.00 46.63 4.73
564 676 2.301346 AGTGTTCCTCTGTTTTGCTGG 58.699 47.619 0.00 0.00 0.00 4.85
565 677 3.876914 TGTAGTGTTCCTCTGTTTTGCTG 59.123 43.478 0.00 0.00 0.00 4.41
657 769 4.974275 GCATGTCTTGATATTGTGCACATC 59.026 41.667 22.39 16.03 0.00 3.06
691 803 5.979517 GTGAATAAATTCCTACCATTGCTGC 59.020 40.000 0.00 0.00 35.97 5.25
776 888 1.022735 AGATACGCACCGGTCTACTG 58.977 55.000 2.59 0.00 0.00 2.74
782 937 4.508128 CGCCAGATACGCACCGGT 62.508 66.667 0.00 0.00 0.00 5.28
975 1130 1.741528 TTTTTCGCCTCGTATTCCCC 58.258 50.000 0.00 0.00 0.00 4.81
1043 1198 0.466124 GAACGGGAGGAAGATGAGGG 59.534 60.000 0.00 0.00 0.00 4.30
1475 1655 1.404391 GAATCGAGGCTCTCACCGTTA 59.596 52.381 13.50 0.00 33.69 3.18
1653 1845 1.070134 ACCTAAGACACACGCACACAT 59.930 47.619 0.00 0.00 0.00 3.21
1660 1852 4.748102 TGCTTTAAAGACCTAAGACACACG 59.252 41.667 19.48 0.00 0.00 4.49
1668 1860 7.253905 ACTACTCCATGCTTTAAAGACCTAA 57.746 36.000 19.48 0.20 0.00 2.69
1726 1918 5.740099 ACGAAAACGTACATGAAAAACTTGG 59.260 36.000 0.00 0.00 0.00 3.61
1967 2162 8.146412 CCTCATGTCATCATCAGATAACTAACA 58.854 37.037 0.00 0.00 31.88 2.41
2048 2245 8.327941 TCTTGTGTATCATTCTTTCTCCTTTG 57.672 34.615 0.00 0.00 0.00 2.77
2052 2249 7.278875 AGGATCTTGTGTATCATTCTTTCTCC 58.721 38.462 0.00 0.00 0.00 3.71
2110 2309 5.448438 ACACAAGTACACAATTAACATGCG 58.552 37.500 0.00 0.00 0.00 4.73
2236 2520 6.992664 AGTATGCAATGAAGAGAGATAGGT 57.007 37.500 0.00 0.00 0.00 3.08
2276 2560 1.226717 CTCAGCTTACGCCTCGGAC 60.227 63.158 0.00 0.00 36.60 4.79
2365 2649 5.102313 GCACTGCAACTTTGTTAGAAACTT 58.898 37.500 0.00 0.00 0.00 2.66
2415 2700 0.250770 AGGGAAAGGCGGAACAGAAC 60.251 55.000 0.00 0.00 0.00 3.01
2471 2756 4.237976 TCCACCTGGTGTGTTTTAAGAA 57.762 40.909 24.32 0.00 43.85 2.52
2481 2766 2.000048 ACCCAATTATCCACCTGGTGT 59.000 47.619 24.32 10.41 36.34 4.16
2671 4850 7.837863 TCCAGTTTACAGTCTTCCATAGTAAG 58.162 38.462 0.00 0.00 0.00 2.34
2851 5038 5.782893 TTGTTCAGAAAAATCCACCGAAT 57.217 34.783 0.00 0.00 0.00 3.34
2855 5042 6.816140 TGTCTTTTTGTTCAGAAAAATCCACC 59.184 34.615 0.00 0.00 34.97 4.61
2866 5054 3.786048 GCGTCAAGTGTCTTTTTGTTCAG 59.214 43.478 0.00 0.00 0.00 3.02
3264 5455 1.747709 ATGGCAAGCAGAGTAAGCAG 58.252 50.000 0.00 0.00 0.00 4.24
3265 5456 2.237143 AGTATGGCAAGCAGAGTAAGCA 59.763 45.455 0.00 0.00 0.00 3.91
3266 5457 2.911484 AGTATGGCAAGCAGAGTAAGC 58.089 47.619 0.00 0.00 0.00 3.09
3267 5458 4.256920 ACAAGTATGGCAAGCAGAGTAAG 58.743 43.478 0.00 0.00 0.00 2.34
3268 5459 4.286297 ACAAGTATGGCAAGCAGAGTAA 57.714 40.909 0.00 0.00 0.00 2.24
3269 5460 3.981071 ACAAGTATGGCAAGCAGAGTA 57.019 42.857 0.00 0.00 0.00 2.59
3270 5461 2.867109 ACAAGTATGGCAAGCAGAGT 57.133 45.000 0.00 0.00 0.00 3.24
3271 5462 3.076621 TGAACAAGTATGGCAAGCAGAG 58.923 45.455 0.00 0.00 0.00 3.35
3272 5463 3.076621 CTGAACAAGTATGGCAAGCAGA 58.923 45.455 0.00 0.00 0.00 4.26
3473 5673 9.929180 ATTTCAGATATGTATAGTTGCATACGT 57.071 29.630 0.00 0.00 33.92 3.57
3546 5785 6.490381 AGAAGATCAGTACTGTACACAACTGA 59.510 38.462 26.20 26.20 43.61 3.41
3554 5793 7.818642 ACACACTAAGAAGATCAGTACTGTAC 58.181 38.462 21.99 16.17 0.00 2.90
3555 5794 7.997773 ACACACTAAGAAGATCAGTACTGTA 57.002 36.000 21.99 9.79 0.00 2.74
3556 5795 6.902771 ACACACTAAGAAGATCAGTACTGT 57.097 37.500 21.99 9.95 0.00 3.55
3557 5796 7.371159 TGAACACACTAAGAAGATCAGTACTG 58.629 38.462 17.17 17.17 0.00 2.74
3558 5797 7.526142 TGAACACACTAAGAAGATCAGTACT 57.474 36.000 0.00 0.00 0.00 2.73
3656 5895 2.025981 CAGGGGATCATCCAAGTGTTCA 60.026 50.000 5.89 0.00 38.64 3.18
3909 6156 2.676342 ACCGCGACACTTATTTTGGATC 59.324 45.455 8.23 0.00 0.00 3.36
3913 6209 4.283678 TCAAAACCGCGACACTTATTTTG 58.716 39.130 8.23 12.05 38.03 2.44
3942 6238 7.431376 GCAGTTTTGAACTAAGGTTGAACTAAC 59.569 37.037 0.00 0.00 40.46 2.34
3943 6239 7.121463 TGCAGTTTTGAACTAAGGTTGAACTAA 59.879 33.333 0.00 0.00 40.46 2.24
3944 6240 6.600032 TGCAGTTTTGAACTAAGGTTGAACTA 59.400 34.615 0.00 0.00 40.46 2.24
3945 6241 5.417580 TGCAGTTTTGAACTAAGGTTGAACT 59.582 36.000 0.00 0.00 40.46 3.01
3946 6242 5.646606 TGCAGTTTTGAACTAAGGTTGAAC 58.353 37.500 0.00 0.00 40.46 3.18
3947 6243 5.906113 TGCAGTTTTGAACTAAGGTTGAA 57.094 34.783 0.00 0.00 40.46 2.69
3948 6244 5.184096 TGTTGCAGTTTTGAACTAAGGTTGA 59.816 36.000 0.00 0.00 40.46 3.18
3949 6245 5.288472 GTGTTGCAGTTTTGAACTAAGGTTG 59.712 40.000 0.00 0.00 40.46 3.77
3950 6246 5.185056 AGTGTTGCAGTTTTGAACTAAGGTT 59.815 36.000 0.00 0.00 40.46 3.50
3951 6247 4.705023 AGTGTTGCAGTTTTGAACTAAGGT 59.295 37.500 0.00 0.00 40.46 3.50
3952 6248 5.248870 AGTGTTGCAGTTTTGAACTAAGG 57.751 39.130 0.00 0.00 40.46 2.69
3953 6249 8.856490 ATTAAGTGTTGCAGTTTTGAACTAAG 57.144 30.769 0.00 0.00 40.46 2.18
3954 6250 9.646427 AAATTAAGTGTTGCAGTTTTGAACTAA 57.354 25.926 0.00 0.00 40.46 2.24
3955 6251 9.081997 CAAATTAAGTGTTGCAGTTTTGAACTA 57.918 29.630 0.00 0.00 40.46 2.24
3956 6252 7.064490 CCAAATTAAGTGTTGCAGTTTTGAACT 59.936 33.333 0.00 0.00 44.06 3.01
3957 6253 7.064016 TCCAAATTAAGTGTTGCAGTTTTGAAC 59.936 33.333 0.00 0.00 0.00 3.18
3958 6254 7.099764 TCCAAATTAAGTGTTGCAGTTTTGAA 58.900 30.769 0.00 0.00 0.00 2.69
3959 6255 6.634805 TCCAAATTAAGTGTTGCAGTTTTGA 58.365 32.000 0.00 0.00 0.00 2.69
3960 6256 6.900568 TCCAAATTAAGTGTTGCAGTTTTG 57.099 33.333 0.00 0.00 0.00 2.44
3961 6257 6.705825 GGATCCAAATTAAGTGTTGCAGTTTT 59.294 34.615 6.95 0.00 0.00 2.43
3962 6258 6.183360 TGGATCCAAATTAAGTGTTGCAGTTT 60.183 34.615 13.46 0.00 0.00 2.66
3963 6259 5.304101 TGGATCCAAATTAAGTGTTGCAGTT 59.696 36.000 13.46 0.00 0.00 3.16
3964 6260 4.832266 TGGATCCAAATTAAGTGTTGCAGT 59.168 37.500 13.46 0.00 0.00 4.40
3965 6261 5.183713 TCTGGATCCAAATTAAGTGTTGCAG 59.816 40.000 17.00 0.00 0.00 4.41
3966 6262 5.076182 TCTGGATCCAAATTAAGTGTTGCA 58.924 37.500 17.00 0.00 0.00 4.08
3967 6263 5.643379 TCTGGATCCAAATTAAGTGTTGC 57.357 39.130 17.00 0.00 0.00 4.17
3970 6266 8.470002 GCTAATTTCTGGATCCAAATTAAGTGT 58.530 33.333 23.01 7.95 35.19 3.55
3971 6267 8.469200 TGCTAATTTCTGGATCCAAATTAAGTG 58.531 33.333 23.01 16.30 35.19 3.16
3972 6268 8.593945 TGCTAATTTCTGGATCCAAATTAAGT 57.406 30.769 23.01 14.10 35.19 2.24
3978 6274 9.866655 AGTATAATGCTAATTTCTGGATCCAAA 57.133 29.630 17.00 8.73 0.00 3.28
3979 6275 9.507329 GAGTATAATGCTAATTTCTGGATCCAA 57.493 33.333 17.00 0.60 0.00 3.53
3980 6276 8.103305 GGAGTATAATGCTAATTTCTGGATCCA 58.897 37.037 15.27 15.27 0.00 3.41
3981 6277 7.554476 GGGAGTATAATGCTAATTTCTGGATCC 59.446 40.741 4.20 4.20 0.00 3.36
3982 6278 8.325046 AGGGAGTATAATGCTAATTTCTGGATC 58.675 37.037 0.00 0.00 0.00 3.36
3983 6279 8.224620 AGGGAGTATAATGCTAATTTCTGGAT 57.775 34.615 0.00 0.00 0.00 3.41
3984 6280 7.633018 AGGGAGTATAATGCTAATTTCTGGA 57.367 36.000 0.00 0.00 0.00 3.86
3985 6281 7.118390 CGAAGGGAGTATAATGCTAATTTCTGG 59.882 40.741 0.00 0.00 0.00 3.86
3986 6282 7.872993 TCGAAGGGAGTATAATGCTAATTTCTG 59.127 37.037 0.00 0.00 0.00 3.02
3987 6283 7.963532 TCGAAGGGAGTATAATGCTAATTTCT 58.036 34.615 0.00 0.00 0.00 2.52
3988 6284 8.779354 ATCGAAGGGAGTATAATGCTAATTTC 57.221 34.615 0.00 0.00 0.00 2.17
3989 6285 7.824779 GGATCGAAGGGAGTATAATGCTAATTT 59.175 37.037 0.00 0.00 0.00 1.82
3990 6286 7.038302 TGGATCGAAGGGAGTATAATGCTAATT 60.038 37.037 0.00 0.00 0.00 1.40
4009 6305 2.601314 CGCGACACTTATTTTGGATCGA 59.399 45.455 0.00 0.00 0.00 3.59
4023 6319 2.349155 CCTTAGTTCAAAACCGCGACAC 60.349 50.000 8.23 0.00 0.00 3.67
4047 6367 5.417580 TGCAGTTTTGAACTAAGGTTGAACT 59.582 36.000 0.00 0.00 40.46 3.01
4048 6368 5.646606 TGCAGTTTTGAACTAAGGTTGAAC 58.353 37.500 0.00 0.00 40.46 3.18
4049 6369 5.906113 TGCAGTTTTGAACTAAGGTTGAA 57.094 34.783 0.00 0.00 40.46 2.69
4050 6370 5.184096 TGTTGCAGTTTTGAACTAAGGTTGA 59.816 36.000 0.00 0.00 40.46 3.18
4051 6371 5.288472 GTGTTGCAGTTTTGAACTAAGGTTG 59.712 40.000 0.00 0.00 40.46 3.77
4073 6393 8.469200 TGCTAATTTCTGGATCCAAATTAAGTG 58.531 33.333 23.01 16.30 35.19 3.16
4074 6394 8.593945 TGCTAATTTCTGGATCCAAATTAAGT 57.406 30.769 23.01 14.10 35.19 2.24
4080 6400 9.866655 AGTATAATGCTAATTTCTGGATCCAAA 57.133 29.630 17.00 8.73 0.00 3.28
4081 6401 9.507329 GAGTATAATGCTAATTTCTGGATCCAA 57.493 33.333 17.00 0.60 0.00 3.53
4082 6402 8.103305 GGAGTATAATGCTAATTTCTGGATCCA 58.897 37.037 15.27 15.27 0.00 3.41
4083 6403 7.554476 GGGAGTATAATGCTAATTTCTGGATCC 59.446 40.741 4.20 4.20 0.00 3.36
4084 6404 8.325046 AGGGAGTATAATGCTAATTTCTGGATC 58.675 37.037 0.00 0.00 0.00 3.36
4085 6405 8.224620 AGGGAGTATAATGCTAATTTCTGGAT 57.775 34.615 0.00 0.00 0.00 3.41
4086 6406 7.256691 GGAGGGAGTATAATGCTAATTTCTGGA 60.257 40.741 0.00 0.00 0.00 3.86
4087 6407 6.881602 GGAGGGAGTATAATGCTAATTTCTGG 59.118 42.308 0.00 0.00 0.00 3.86
4088 6408 6.591834 CGGAGGGAGTATAATGCTAATTTCTG 59.408 42.308 0.00 0.00 0.00 3.02
4089 6409 6.497259 TCGGAGGGAGTATAATGCTAATTTCT 59.503 38.462 0.00 0.00 0.00 2.52
4090 6410 6.698380 TCGGAGGGAGTATAATGCTAATTTC 58.302 40.000 0.00 0.00 0.00 2.17
4091 6411 6.681729 TCGGAGGGAGTATAATGCTAATTT 57.318 37.500 0.00 0.00 0.00 1.82
4092 6412 6.127026 GGATCGGAGGGAGTATAATGCTAATT 60.127 42.308 0.00 0.00 0.00 1.40
4093 6413 5.364157 GGATCGGAGGGAGTATAATGCTAAT 59.636 44.000 0.00 0.00 0.00 1.73
4094 6414 4.710375 GGATCGGAGGGAGTATAATGCTAA 59.290 45.833 0.00 0.00 0.00 3.09
4095 6415 4.264217 TGGATCGGAGGGAGTATAATGCTA 60.264 45.833 0.00 0.00 0.00 3.49
4096 6416 3.100671 GGATCGGAGGGAGTATAATGCT 58.899 50.000 0.00 0.00 0.00 3.79
4097 6417 2.832129 TGGATCGGAGGGAGTATAATGC 59.168 50.000 0.00 0.00 0.00 3.56
4098 6418 5.483685 TTTGGATCGGAGGGAGTATAATG 57.516 43.478 0.00 0.00 0.00 1.90
4099 6419 6.704056 ATTTTGGATCGGAGGGAGTATAAT 57.296 37.500 0.00 0.00 0.00 1.28
4100 6420 7.291651 ACTTATTTTGGATCGGAGGGAGTATAA 59.708 37.037 0.00 0.00 0.00 0.98
4101 6421 6.785963 ACTTATTTTGGATCGGAGGGAGTATA 59.214 38.462 0.00 0.00 0.00 1.47
4102 6422 5.607171 ACTTATTTTGGATCGGAGGGAGTAT 59.393 40.000 0.00 0.00 0.00 2.12
4103 6423 4.966805 ACTTATTTTGGATCGGAGGGAGTA 59.033 41.667 0.00 0.00 0.00 2.59
4104 6424 3.780850 ACTTATTTTGGATCGGAGGGAGT 59.219 43.478 0.00 0.00 0.00 3.85
4105 6425 4.130118 CACTTATTTTGGATCGGAGGGAG 58.870 47.826 0.00 0.00 0.00 4.30
4106 6426 3.684413 GCACTTATTTTGGATCGGAGGGA 60.684 47.826 0.00 0.00 0.00 4.20
4107 6427 2.618709 GCACTTATTTTGGATCGGAGGG 59.381 50.000 0.00 0.00 0.00 4.30
4108 6428 2.287915 CGCACTTATTTTGGATCGGAGG 59.712 50.000 0.00 0.00 0.00 4.30
4109 6429 2.287915 CCGCACTTATTTTGGATCGGAG 59.712 50.000 0.00 0.00 38.02 4.63
4110 6430 2.285083 CCGCACTTATTTTGGATCGGA 58.715 47.619 0.00 0.00 38.02 4.55
4111 6431 1.268539 GCCGCACTTATTTTGGATCGG 60.269 52.381 0.00 0.00 38.72 4.18
4112 6432 1.400142 TGCCGCACTTATTTTGGATCG 59.600 47.619 0.00 0.00 0.00 3.69
4113 6433 2.423538 AGTGCCGCACTTATTTTGGATC 59.576 45.455 20.59 0.00 42.59 3.36
4114 6434 2.446435 AGTGCCGCACTTATTTTGGAT 58.554 42.857 20.59 0.00 42.59 3.41
4115 6435 1.904287 AGTGCCGCACTTATTTTGGA 58.096 45.000 20.59 0.00 42.59 3.53
4125 6445 2.791158 CGATCCAAAATAAGTGCCGCAC 60.791 50.000 16.04 16.04 34.10 5.34
4126 6446 1.400142 CGATCCAAAATAAGTGCCGCA 59.600 47.619 0.00 0.00 0.00 5.69
4127 6447 1.268539 CCGATCCAAAATAAGTGCCGC 60.269 52.381 0.00 0.00 0.00 6.53
4128 6448 2.285083 TCCGATCCAAAATAAGTGCCG 58.715 47.619 0.00 0.00 0.00 5.69
4129 6449 2.618709 CCTCCGATCCAAAATAAGTGCC 59.381 50.000 0.00 0.00 0.00 5.01
4130 6450 2.618709 CCCTCCGATCCAAAATAAGTGC 59.381 50.000 0.00 0.00 0.00 4.40
4182 6502 7.858052 AAATAAACTTGTGAGAAATGAAGCG 57.142 32.000 0.00 0.00 0.00 4.68
4229 6551 9.982651 GGTGAATAATTAGTACTGCTCTATGAA 57.017 33.333 5.39 0.00 0.00 2.57
4232 6554 8.492415 TGGGTGAATAATTAGTACTGCTCTAT 57.508 34.615 5.39 0.00 0.00 1.98
4258 6580 9.654417 CGTTTAAAACTACTGCTTTAGCTTTAA 57.346 29.630 0.00 8.33 42.66 1.52
4327 6653 3.238108 AGGACATAAGTTCACTCTGCG 57.762 47.619 0.00 0.00 0.00 5.18
4434 6761 1.086634 GGAGCGGTGAGTTCAGCATC 61.087 60.000 11.39 8.13 44.00 3.91
4521 6848 1.376812 CCCACCGTTACTGAAGGGC 60.377 63.158 0.00 0.00 43.23 5.19
4860 7187 4.461431 ACCAAAGTCGGATAAAAATCCCAC 59.539 41.667 0.00 0.00 37.43 4.61
4890 7217 0.617413 ATTGTGGCTCAGACTCAGGG 59.383 55.000 0.00 0.00 0.00 4.45
4971 7298 2.943199 GCAGGAGAATTTAGCTGGCAGT 60.943 50.000 17.16 5.61 0.00 4.40
5076 7403 0.770499 TGGGGTTGATGAAGACTGCA 59.230 50.000 0.00 0.00 0.00 4.41
5097 7425 6.603599 GCAGTTGGGAGTTCTATTTTAGGAAT 59.396 38.462 0.00 0.00 0.00 3.01
5251 7583 3.523972 TGCCACCTTACCATAATACACCA 59.476 43.478 0.00 0.00 0.00 4.17
5264 7596 4.079446 GCAACTGCTGCCACCTTA 57.921 55.556 0.00 0.00 46.13 2.69
5278 7610 2.705658 CCTCCCATGTACTATCAGGCAA 59.294 50.000 0.00 0.00 0.00 4.52
5286 7618 1.062428 CCTCCCACCTCCCATGTACTA 60.062 57.143 0.00 0.00 0.00 1.82
5287 7619 0.326618 CCTCCCACCTCCCATGTACT 60.327 60.000 0.00 0.00 0.00 2.73
5288 7620 1.984288 GCCTCCCACCTCCCATGTAC 61.984 65.000 0.00 0.00 0.00 2.90
5320 7652 2.681848 GTTGAAGATGCCCTGATCACAG 59.318 50.000 0.00 0.00 43.12 3.66
5321 7653 2.715046 GTTGAAGATGCCCTGATCACA 58.285 47.619 0.00 0.00 0.00 3.58
5322 7654 1.667724 CGTTGAAGATGCCCTGATCAC 59.332 52.381 0.00 0.00 0.00 3.06
5323 7655 1.407299 CCGTTGAAGATGCCCTGATCA 60.407 52.381 0.00 0.00 0.00 2.92
5324 7656 1.303309 CCGTTGAAGATGCCCTGATC 58.697 55.000 0.00 0.00 0.00 2.92
5325 7657 0.749454 GCCGTTGAAGATGCCCTGAT 60.749 55.000 0.00 0.00 0.00 2.90
5326 7658 1.377202 GCCGTTGAAGATGCCCTGA 60.377 57.895 0.00 0.00 0.00 3.86
5327 7659 1.243342 TTGCCGTTGAAGATGCCCTG 61.243 55.000 0.00 0.00 0.00 4.45
5348 7680 2.285977 GATGCGGGAGGAAATTTACGT 58.714 47.619 0.00 0.00 0.00 3.57
5351 7683 3.486383 GATGGATGCGGGAGGAAATTTA 58.514 45.455 0.00 0.00 0.00 1.40
5374 7706 1.986413 CTGGTCCCCTTCTGTCCAG 59.014 63.158 0.00 0.00 39.41 3.86
5397 7730 4.530857 CTCCCGCATCCGTGTCCC 62.531 72.222 0.00 0.00 0.00 4.46
5536 7870 8.629132 CGTTAAAAATATGTCCAAAACGTAACC 58.371 33.333 0.00 0.00 35.14 2.85
5558 7892 7.588488 GTGCACATAGTTTTAGCTTTTTCGTTA 59.412 33.333 13.17 0.00 0.00 3.18
5562 7896 6.918022 ACTGTGCACATAGTTTTAGCTTTTTC 59.082 34.615 22.00 0.00 27.72 2.29
5581 7915 3.083600 GACCGTATGCGCACTGTGC 62.084 63.158 22.38 22.38 40.69 4.57
5582 7916 1.736282 TGACCGTATGCGCACTGTG 60.736 57.895 14.90 4.51 36.67 3.66
5583 7917 1.736645 GTGACCGTATGCGCACTGT 60.737 57.895 14.90 7.55 36.67 3.55
5584 7918 2.788176 CGTGACCGTATGCGCACTG 61.788 63.158 14.90 5.10 36.67 3.66
5585 7919 2.506217 CGTGACCGTATGCGCACT 60.506 61.111 14.90 4.70 36.67 4.40
5590 7924 2.954868 CTCCGCGTGACCGTATGC 60.955 66.667 4.92 0.00 36.15 3.14
5592 7926 3.122250 GAGCTCCGCGTGACCGTAT 62.122 63.158 4.92 0.00 36.15 3.06
5600 7934 4.162690 GGGAATGGAGCTCCGCGT 62.163 66.667 27.43 15.03 39.43 6.01
5635 7969 2.117156 GGTCGGCCGTAGACTAGCA 61.117 63.158 27.15 0.00 38.58 3.49
5636 7970 2.720605 GGTCGGCCGTAGACTAGC 59.279 66.667 27.15 10.67 38.58 3.42
5690 8024 2.359214 CTCACGGCAATCTAGCTAGTGA 59.641 50.000 20.10 13.75 43.72 3.41
5692 8026 2.359531 GACTCACGGCAATCTAGCTAGT 59.640 50.000 20.10 5.41 34.17 2.57
5696 8030 0.461961 AGGACTCACGGCAATCTAGC 59.538 55.000 0.00 0.00 0.00 3.42
5698 8032 0.824109 CCAGGACTCACGGCAATCTA 59.176 55.000 0.00 0.00 0.00 1.98
5699 8033 0.904865 TCCAGGACTCACGGCAATCT 60.905 55.000 0.00 0.00 0.00 2.40
5702 8036 2.583441 CCTCCAGGACTCACGGCAA 61.583 63.158 0.00 0.00 37.39 4.52
5708 8042 3.051940 AGAATATGCCTCCAGGACTCA 57.948 47.619 0.00 0.00 37.39 3.41
5715 8049 1.149101 GGGGGAAGAATATGCCTCCA 58.851 55.000 0.51 0.00 0.00 3.86
5772 8106 1.396301 GCTGAAGCATCCTCTTTGTCG 59.604 52.381 0.00 0.00 41.59 4.35
5783 8118 4.431131 CCCCACCGGCTGAAGCAT 62.431 66.667 0.00 0.00 44.36 3.79
5796 8131 2.358619 CGGAAATGCCCTTCCCCA 59.641 61.111 8.03 0.00 41.73 4.96
5805 8141 0.449388 CCTGAGCTTCACGGAAATGC 59.551 55.000 0.00 0.00 0.00 3.56
5806 8142 0.449388 GCCTGAGCTTCACGGAAATG 59.551 55.000 0.00 0.00 35.50 2.32
5807 8143 1.021390 CGCCTGAGCTTCACGGAAAT 61.021 55.000 0.00 0.00 36.60 2.17
5808 8144 1.667830 CGCCTGAGCTTCACGGAAA 60.668 57.895 0.00 0.00 36.60 3.13
5816 8152 1.001248 TAGGTACCCGCCTGAGCTT 59.999 57.895 8.74 0.00 39.60 3.74


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

AutoCloner maintained by Alex Coulton.