Multiple sequence alignment - TraesCS5B01G353100

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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 TraesCS5B01G353100 chr5B 100.000 3271 0 0 1 3271 532865112 532861842 0.000000e+00 6041.0
1 TraesCS5B01G353100 chr5B 97.368 190 4 1 2818 3006 447830851 447830662 4.070000e-84 322.0
2 TraesCS5B01G353100 chr5D 92.716 2430 157 10 1 2422 438357394 438354977 0.000000e+00 3489.0
3 TraesCS5B01G353100 chr5D 93.135 539 26 5 2294 2822 438355040 438354503 0.000000e+00 780.0
4 TraesCS5B01G353100 chr5D 93.657 268 14 1 3004 3271 438354505 438354241 6.580000e-107 398.0
5 TraesCS5B01G353100 chr5D 97.340 188 4 1 2820 3006 121102663 121102476 5.270000e-83 318.0
6 TraesCS5B01G353100 chr5D 97.340 188 4 1 2820 3006 130661324 130661511 5.270000e-83 318.0
7 TraesCS5B01G353100 chr5A 91.554 2510 169 24 1 2497 553375211 553372732 0.000000e+00 3421.0
8 TraesCS5B01G353100 chr5A 94.340 530 28 2 2294 2822 553372862 553372334 0.000000e+00 811.0
9 TraesCS5B01G353100 chr5A 85.650 446 52 8 1511 1947 556697864 556698306 2.970000e-125 459.0
10 TraesCS5B01G353100 chr5A 85.650 446 52 8 1511 1947 556702779 556703221 2.970000e-125 459.0
11 TraesCS5B01G353100 chr5A 93.657 268 17 0 3004 3271 553372336 553372069 5.080000e-108 401.0
12 TraesCS5B01G353100 chr5A 82.072 251 34 8 2578 2822 673510947 673511192 1.540000e-48 204.0
13 TraesCS5B01G353100 chr3D 88.924 632 57 9 2196 2822 134663651 134663028 0.000000e+00 767.0
14 TraesCS5B01G353100 chr3D 78.674 905 112 48 1942 2822 611429753 611430600 8.040000e-146 527.0
15 TraesCS5B01G353100 chr3D 78.065 620 85 30 1942 2547 611426236 611426818 8.690000e-91 344.0
16 TraesCS5B01G353100 chr3D 95.897 195 6 2 2820 3013 142708775 142708582 6.810000e-82 315.0
17 TraesCS5B01G353100 chr3D 94.146 205 10 2 2805 3008 71527535 71527738 8.810000e-81 311.0
18 TraesCS5B01G353100 chr3D 80.140 428 64 8 2133 2547 595095782 595095363 1.910000e-77 300.0
19 TraesCS5B01G353100 chr3D 86.184 152 16 5 3003 3150 542915667 542915517 3.380000e-35 159.0
20 TraesCS5B01G353100 chr3D 86.620 142 16 3 3003 3142 491633161 491633021 1.570000e-33 154.0
21 TraesCS5B01G353100 chr2B 84.507 568 70 13 1942 2495 527664299 527664862 2.220000e-151 545.0
22 TraesCS5B01G353100 chr2B 86.111 144 19 1 3004 3146 527665203 527665346 1.570000e-33 154.0
23 TraesCS5B01G353100 chr2B 85.263 95 6 3 2734 2820 415053102 415053196 1.250000e-14 91.6
24 TraesCS5B01G353100 chr2A 84.331 568 71 13 1942 2495 717808400 717808963 1.030000e-149 540.0
25 TraesCS5B01G353100 chr2A 85.417 144 20 1 3004 3146 181788804 181788661 7.310000e-32 148.0
26 TraesCS5B01G353100 chr2A 96.774 62 2 0 2759 2820 464162243 464162304 1.610000e-18 104.0
27 TraesCS5B01G353100 chr2A 95.745 47 2 0 675 721 4010701 4010747 3.500000e-10 76.8
28 TraesCS5B01G353100 chr4A 83.803 568 74 13 1942 2495 519799948 519800511 1.040000e-144 523.0
29 TraesCS5B01G353100 chr4A 87.528 441 39 5 1514 1947 613999901 613999470 2.270000e-136 496.0
30 TraesCS5B01G353100 chr4A 88.725 408 36 8 1540 1947 519797077 519797474 1.050000e-134 490.0
31 TraesCS5B01G353100 chr1B 84.270 534 65 14 1977 2495 112755070 112754541 1.350000e-138 503.0
32 TraesCS5B01G353100 chr1B 80.588 680 86 25 1942 2607 25833914 25834561 1.760000e-132 483.0
33 TraesCS5B01G353100 chr3A 87.528 441 39 5 1514 1947 57513970 57513539 2.270000e-136 496.0
34 TraesCS5B01G353100 chr3A 83.459 532 60 17 1945 2463 57502570 57502054 1.370000e-128 470.0
35 TraesCS5B01G353100 chr1A 83.146 534 68 12 1942 2460 19986138 19986664 4.940000e-128 468.0
36 TraesCS5B01G353100 chr1A 95.960 198 6 2 2818 3013 582559669 582559472 1.460000e-83 320.0
37 TraesCS5B01G353100 chr1A 86.429 140 18 1 3004 3142 19986963 19987102 5.650000e-33 152.0
38 TraesCS5B01G353100 chr7A 85.553 443 50 9 1514 1947 60710829 60710392 4.980000e-123 451.0
39 TraesCS5B01G353100 chr7A 94.554 202 9 2 2807 3007 106297241 106297441 8.810000e-81 311.0
40 TraesCS5B01G353100 chr7A 86.429 140 19 0 3003 3142 691475050 691474911 1.570000e-33 154.0
41 TraesCS5B01G353100 chr4B 85.235 447 52 10 1511 1947 16676630 16677072 6.440000e-122 448.0
42 TraesCS5B01G353100 chr1D 78.442 552 80 19 2133 2667 432578554 432579083 1.130000e-84 324.0
43 TraesCS5B01G353100 chr1D 96.842 190 5 1 2819 3007 176953158 176952969 1.890000e-82 316.0
44 TraesCS5B01G353100 chr1D 86.111 144 16 4 3005 3146 165650129 165649988 5.650000e-33 152.0
45 TraesCS5B01G353100 chr4D 96.875 192 5 1 2820 3010 503922022 503922213 1.460000e-83 320.0
46 TraesCS5B01G353100 chr6B 77.644 331 57 11 2133 2462 656204522 656204836 5.570000e-43 185.0
47 TraesCS5B01G353100 chr3B 83.036 112 14 3 2716 2822 59328646 59328535 2.690000e-16 97.1


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 TraesCS5B01G353100 chr5B 532861842 532865112 3270 True 6041.000000 6041 100.000000 1 3271 1 chr5B.!!$R2 3270
1 TraesCS5B01G353100 chr5D 438354241 438357394 3153 True 1555.666667 3489 93.169333 1 3271 3 chr5D.!!$R2 3270
2 TraesCS5B01G353100 chr5A 553372069 553375211 3142 True 1544.333333 3421 93.183667 1 3271 3 chr5A.!!$R1 3270
3 TraesCS5B01G353100 chr3D 134663028 134663651 623 True 767.000000 767 88.924000 2196 2822 1 chr3D.!!$R1 626
4 TraesCS5B01G353100 chr3D 611426236 611430600 4364 False 435.500000 527 78.369500 1942 2822 2 chr3D.!!$F2 880
5 TraesCS5B01G353100 chr2B 527664299 527665346 1047 False 349.500000 545 85.309000 1942 3146 2 chr2B.!!$F2 1204
6 TraesCS5B01G353100 chr2A 717808400 717808963 563 False 540.000000 540 84.331000 1942 2495 1 chr2A.!!$F3 553
7 TraesCS5B01G353100 chr4A 519797077 519800511 3434 False 506.500000 523 86.264000 1540 2495 2 chr4A.!!$F1 955
8 TraesCS5B01G353100 chr1B 112754541 112755070 529 True 503.000000 503 84.270000 1977 2495 1 chr1B.!!$R1 518
9 TraesCS5B01G353100 chr1B 25833914 25834561 647 False 483.000000 483 80.588000 1942 2607 1 chr1B.!!$F1 665
10 TraesCS5B01G353100 chr3A 57502054 57502570 516 True 470.000000 470 83.459000 1945 2463 1 chr3A.!!$R1 518
11 TraesCS5B01G353100 chr1A 19986138 19987102 964 False 310.000000 468 84.787500 1942 3142 2 chr1A.!!$F1 1200
12 TraesCS5B01G353100 chr1D 432578554 432579083 529 False 324.000000 324 78.442000 2133 2667 1 chr1D.!!$F1 534

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
205 210 0.034337 TGGTACGCCGAAGCTTTTCT 59.966 50.0 0.0 0.0 37.67 2.52 F
500 505 0.036732 TGATGTGGTGGTGAAGCTCC 59.963 55.0 0.0 0.0 0.00 4.70 F
904 911 0.253327 AAACCGGCCTCAATCTCTCC 59.747 55.0 0.0 0.0 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1891 1898 0.173481 GCTATCACTGTGCCACTCGA 59.827 55.000 2.12 0.0 0.0 4.04 R
2071 4557 0.583438 GCATGTATGGCAGCAGTACG 59.417 55.000 0.00 0.0 0.0 3.67 R
2520 8723 1.072331 ACATCCGGGCTCATATCCAAC 59.928 52.381 0.00 0.0 0.0 3.77 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
26 27 3.543680 TGGCAGGAGTGTAGAATAAGC 57.456 47.619 0.00 0.00 0.00 3.09
55 56 6.656270 TCTGCACCATTATATTGCCTAGATTG 59.344 38.462 0.00 0.00 35.26 2.67
100 101 3.123804 CCAGGAGTTATCGCACATGTAC 58.876 50.000 0.00 0.00 0.00 2.90
116 117 5.064579 CACATGTACGCACTAATGGATTGAA 59.935 40.000 0.00 0.00 0.00 2.69
145 146 6.426633 TCGAATGTACATTGTTCACACATTCT 59.573 34.615 25.42 7.52 46.81 2.40
173 178 1.069432 CATTATGAGCTGGTCGCATGC 60.069 52.381 7.91 7.91 42.61 4.06
188 193 1.452651 ATGCGACCTGAAGGCATGG 60.453 57.895 0.00 0.00 45.04 3.66
205 210 0.034337 TGGTACGCCGAAGCTTTTCT 59.966 50.000 0.00 0.00 37.67 2.52
321 326 7.093354 TGTCAAGTGAGACAAGCTAAGATTAG 58.907 38.462 0.00 0.00 44.92 1.73
347 352 3.843422 TCCCTTTCAAATGCTTTGGAGA 58.157 40.909 8.23 0.00 40.98 3.71
409 414 9.515020 GATTCTTTCTTTGTTTAACATGACACA 57.485 29.630 0.00 0.00 0.00 3.72
468 473 9.262358 CTACACCTTAGTATTAGCAAGGATTTC 57.738 37.037 6.60 0.00 41.18 2.17
496 501 2.794103 TCCAATGATGTGGTGGTGAAG 58.206 47.619 0.00 0.00 39.88 3.02
500 505 0.036732 TGATGTGGTGGTGAAGCTCC 59.963 55.000 0.00 0.00 0.00 4.70
521 526 4.015084 CCCATTTGTCTTCAATGCTCTCT 58.985 43.478 0.00 0.00 33.32 3.10
525 530 6.127703 CCATTTGTCTTCAATGCTCTCTGAAT 60.128 38.462 0.00 0.00 33.32 2.57
551 556 4.841813 TGTGGGAAGGTTCTACATCAGTTA 59.158 41.667 0.00 0.00 0.00 2.24
565 570 3.604875 TCAGTTATTCCTCCCACGAAC 57.395 47.619 0.00 0.00 0.00 3.95
592 597 2.762969 TTTCCGATGGGGCCACACTG 62.763 60.000 11.75 5.32 34.94 3.66
593 598 4.033776 CCGATGGGGCCACACTGT 62.034 66.667 11.75 0.00 0.00 3.55
594 599 2.034066 CGATGGGGCCACACTGTT 59.966 61.111 11.75 0.00 0.00 3.16
667 673 4.634004 CCGCTATTCAGAACATTGTGGTTA 59.366 41.667 0.00 0.00 0.00 2.85
790 796 2.415625 CCGTCGGTTCTGTTAGGAGAAG 60.416 54.545 2.08 0.00 32.53 2.85
808 814 7.310072 GGAGAAGCCTTTAAAGTCTACATTC 57.690 40.000 14.03 1.49 0.00 2.67
819 825 5.344743 AAGTCTACATTCACCGATGTCAT 57.655 39.130 0.00 0.00 40.54 3.06
869 875 5.036117 TGTCCATAATAAGCAGGAGAACC 57.964 43.478 0.00 0.00 0.00 3.62
899 906 2.710902 GCCCAAACCGGCCTCAATC 61.711 63.158 0.00 0.00 43.66 2.67
904 911 0.253327 AAACCGGCCTCAATCTCTCC 59.747 55.000 0.00 0.00 0.00 3.71
925 932 2.052690 CGAGTCCTGACCCCGTGAT 61.053 63.158 0.00 0.00 0.00 3.06
939 946 2.154462 CCGTGATTTGTGCTCCTTTCT 58.846 47.619 0.00 0.00 0.00 2.52
942 949 2.160417 GTGATTTGTGCTCCTTTCTCCG 59.840 50.000 0.00 0.00 0.00 4.63
1033 1040 2.948720 GCCGCAGAGGGAGACAACT 61.949 63.158 0.00 0.00 41.48 3.16
1045 1052 2.678324 GAGACAACTCCAAGGAAGACG 58.322 52.381 0.00 0.00 37.19 4.18
1053 1060 1.481056 CCAAGGAAGACGACCAGGGT 61.481 60.000 0.00 0.00 0.00 4.34
1153 1160 3.998672 GGTCGGTTGAGGGTGCGA 61.999 66.667 0.00 0.00 0.00 5.10
1154 1161 2.264794 GTCGGTTGAGGGTGCGAT 59.735 61.111 0.00 0.00 0.00 4.58
1169 1176 2.577059 GATTGAGGGTGCCGACGA 59.423 61.111 0.00 0.00 0.00 4.20
1174 1181 0.467474 TGAGGGTGCCGACGAGATAT 60.467 55.000 0.00 0.00 0.00 1.63
1178 1185 1.068741 GGGTGCCGACGAGATATCTTT 59.931 52.381 6.70 0.00 0.00 2.52
1189 1196 1.486310 AGATATCTTTCGCAGGTGGCA 59.514 47.619 0.00 0.00 45.17 4.92
1192 1199 0.674895 ATCTTTCGCAGGTGGCAGTC 60.675 55.000 0.00 0.00 45.17 3.51
1232 1239 3.936203 TCAAGGCGCGGAAGTGGT 61.936 61.111 8.83 0.00 43.14 4.16
1245 1252 3.357079 GTGGTTGGGTGCTCTGCG 61.357 66.667 0.00 0.00 0.00 5.18
1275 1282 1.229400 TAAAGACTCCGGCCAGGGT 60.229 57.895 2.24 0.00 41.52 4.34
1312 1319 1.300931 GCACGTGCTTCAGACCAGA 60.301 57.895 32.55 0.00 38.21 3.86
1315 1322 2.091112 CGTGCTTCAGACCAGAGCG 61.091 63.158 0.00 0.00 0.00 5.03
1341 1348 0.727398 GTTTGTCCTCGGCTACATGC 59.273 55.000 0.00 0.00 41.94 4.06
1342 1349 0.739462 TTTGTCCTCGGCTACATGCG 60.739 55.000 0.00 0.00 44.05 4.73
1354 1361 0.805711 TACATGCGCGTGTCCAGATG 60.806 55.000 36.69 17.73 33.62 2.90
1377 1384 4.439837 GGGTAAGTGTCATTCGTAGGAGTC 60.440 50.000 0.00 0.00 0.00 3.36
1388 1395 2.094182 TCGTAGGAGTCCAAGTGAATGC 60.094 50.000 12.86 0.00 0.00 3.56
1391 1398 2.508526 AGGAGTCCAAGTGAATGCAAC 58.491 47.619 12.86 0.00 31.10 4.17
1393 1400 3.327757 AGGAGTCCAAGTGAATGCAACTA 59.672 43.478 12.86 0.00 31.10 2.24
1443 1450 9.173939 GAATGCAATGTTAGTAGCAATACATTC 57.826 33.333 16.18 16.18 38.71 2.67
1652 1659 7.484975 AGGACATACGATGTTTTTGTTTTGAA 58.515 30.769 0.00 0.00 45.03 2.69
1656 1663 9.360093 ACATACGATGTTTTTGTTTTGAAAAGA 57.640 25.926 0.00 0.00 41.63 2.52
1687 1694 7.429340 CGATTGTGACTTGACAAATTATAAGGC 59.571 37.037 0.00 0.00 39.25 4.35
1779 1786 6.718912 TGATGGTGATCTTAAAACATGTCCAA 59.281 34.615 0.00 0.00 0.00 3.53
1826 1833 7.487484 TGATGCTTATGTTTGAAAAACACTCA 58.513 30.769 7.66 4.74 32.37 3.41
1877 1884 2.698855 ATTGTGATCCCTCTGAACCG 57.301 50.000 0.00 0.00 0.00 4.44
1889 1896 3.322254 CCTCTGAACCGTATGAGCCTATT 59.678 47.826 0.00 0.00 0.00 1.73
1891 1898 5.186021 CCTCTGAACCGTATGAGCCTATTAT 59.814 44.000 0.00 0.00 0.00 1.28
1901 1908 2.035961 TGAGCCTATTATCGAGTGGCAC 59.964 50.000 10.29 10.29 45.42 5.01
1971 4457 5.104982 ACAAACAAGAGAAATGCAAAAGGGA 60.105 36.000 0.00 0.00 0.00 4.20
2041 4527 9.973450 TTATGCATAGTTAATGTTGTTGTTTGT 57.027 25.926 6.50 0.00 37.93 2.83
2099 4585 1.826096 TGCCATACATGCACTGCAATT 59.174 42.857 8.03 0.27 43.62 2.32
2100 4586 2.234168 TGCCATACATGCACTGCAATTT 59.766 40.909 8.03 0.00 43.62 1.82
2101 4587 2.605818 GCCATACATGCACTGCAATTTG 59.394 45.455 8.03 4.66 43.62 2.32
2102 4588 3.676598 GCCATACATGCACTGCAATTTGA 60.677 43.478 8.03 0.00 43.62 2.69
2366 8448 6.128902 CGTGTATGTGAACCTAAAGTCACTTC 60.129 42.308 0.00 0.00 34.51 3.01
2392 8536 6.592607 TGTGCTACTCATGTCATGCATATATG 59.407 38.462 8.45 8.45 35.74 1.78
2403 8547 6.372381 TGTCATGCATATATGTATGGACTTGC 59.628 38.462 31.22 19.28 46.54 4.01
2409 8553 7.765819 TGCATATATGTATGGACTTGCACTATC 59.234 37.037 14.14 0.00 38.49 2.08
2499 8656 9.778741 GAACTCATATATGTGAACCTGGATTTA 57.221 33.333 19.07 0.00 0.00 1.40
2659 8871 7.777440 AGGTTCTGCCCAATTTTTGAATTAAAA 59.223 29.630 0.00 0.00 38.26 1.52
2687 8908 7.394016 TGAAATACTTGTGTGTGGAGATATGT 58.606 34.615 0.00 0.00 0.00 2.29
2823 9047 9.865321 AAATCATCTTTTCATGTGTCATTTAGG 57.135 29.630 0.00 0.00 0.00 2.69
2824 9048 7.395190 TCATCTTTTCATGTGTCATTTAGGG 57.605 36.000 0.00 0.00 0.00 3.53
2825 9049 6.377996 TCATCTTTTCATGTGTCATTTAGGGG 59.622 38.462 0.00 0.00 0.00 4.79
2826 9050 5.016173 TCTTTTCATGTGTCATTTAGGGGG 58.984 41.667 0.00 0.00 0.00 5.40
2827 9051 4.396357 TTTCATGTGTCATTTAGGGGGT 57.604 40.909 0.00 0.00 0.00 4.95
2828 9052 3.364460 TCATGTGTCATTTAGGGGGTG 57.636 47.619 0.00 0.00 0.00 4.61
2829 9053 2.647299 TCATGTGTCATTTAGGGGGTGT 59.353 45.455 0.00 0.00 0.00 4.16
2830 9054 3.075283 TCATGTGTCATTTAGGGGGTGTT 59.925 43.478 0.00 0.00 0.00 3.32
2831 9055 3.603965 TGTGTCATTTAGGGGGTGTTT 57.396 42.857 0.00 0.00 0.00 2.83
2832 9056 3.226777 TGTGTCATTTAGGGGGTGTTTG 58.773 45.455 0.00 0.00 0.00 2.93
2833 9057 2.560981 GTGTCATTTAGGGGGTGTTTGG 59.439 50.000 0.00 0.00 0.00 3.28
2834 9058 2.178106 TGTCATTTAGGGGGTGTTTGGT 59.822 45.455 0.00 0.00 0.00 3.67
2835 9059 3.236047 GTCATTTAGGGGGTGTTTGGTT 58.764 45.455 0.00 0.00 0.00 3.67
2836 9060 3.257375 GTCATTTAGGGGGTGTTTGGTTC 59.743 47.826 0.00 0.00 0.00 3.62
2837 9061 3.117093 TCATTTAGGGGGTGTTTGGTTCA 60.117 43.478 0.00 0.00 0.00 3.18
2838 9062 2.668144 TTAGGGGGTGTTTGGTTCAG 57.332 50.000 0.00 0.00 0.00 3.02
2839 9063 1.822425 TAGGGGGTGTTTGGTTCAGA 58.178 50.000 0.00 0.00 0.00 3.27
2840 9064 0.930726 AGGGGGTGTTTGGTTCAGAA 59.069 50.000 0.00 0.00 0.00 3.02
2841 9065 1.133482 AGGGGGTGTTTGGTTCAGAAG 60.133 52.381 0.00 0.00 0.00 2.85
2842 9066 1.411074 GGGGGTGTTTGGTTCAGAAGT 60.411 52.381 0.00 0.00 0.00 3.01
2843 9067 1.954382 GGGGTGTTTGGTTCAGAAGTC 59.046 52.381 0.00 0.00 0.00 3.01
2844 9068 1.954382 GGGTGTTTGGTTCAGAAGTCC 59.046 52.381 0.00 0.00 0.00 3.85
2845 9069 2.422945 GGGTGTTTGGTTCAGAAGTCCT 60.423 50.000 0.00 0.00 0.00 3.85
2846 9070 3.181448 GGGTGTTTGGTTCAGAAGTCCTA 60.181 47.826 0.00 0.00 0.00 2.94
2847 9071 4.065789 GGTGTTTGGTTCAGAAGTCCTAG 58.934 47.826 0.00 0.00 0.00 3.02
2848 9072 4.065789 GTGTTTGGTTCAGAAGTCCTAGG 58.934 47.826 0.82 0.82 0.00 3.02
2849 9073 3.971305 TGTTTGGTTCAGAAGTCCTAGGA 59.029 43.478 7.62 7.62 0.00 2.94
2850 9074 4.202326 TGTTTGGTTCAGAAGTCCTAGGAC 60.202 45.833 31.29 31.29 44.86 3.85
2906 9130 7.696992 CTCTCCAGTAGAGTCTTTTTCTAGT 57.303 40.000 0.00 0.00 45.85 2.57
2907 9131 7.690952 TCTCCAGTAGAGTCTTTTTCTAGTC 57.309 40.000 0.00 0.00 43.71 2.59
2908 9132 6.660094 TCTCCAGTAGAGTCTTTTTCTAGTCC 59.340 42.308 0.00 0.00 43.71 3.85
2909 9133 5.715753 TCCAGTAGAGTCTTTTTCTAGTCCC 59.284 44.000 0.00 0.00 30.30 4.46
2910 9134 5.717654 CCAGTAGAGTCTTTTTCTAGTCCCT 59.282 44.000 0.00 0.00 30.30 4.20
2911 9135 6.350612 CCAGTAGAGTCTTTTTCTAGTCCCTG 60.351 46.154 0.00 0.00 30.30 4.45
2912 9136 6.209788 CAGTAGAGTCTTTTTCTAGTCCCTGT 59.790 42.308 0.00 0.00 30.30 4.00
2913 9137 7.393796 CAGTAGAGTCTTTTTCTAGTCCCTGTA 59.606 40.741 0.00 0.00 30.30 2.74
2914 9138 6.844097 AGAGTCTTTTTCTAGTCCCTGTAG 57.156 41.667 0.00 0.00 0.00 2.74
2915 9139 6.553857 AGAGTCTTTTTCTAGTCCCTGTAGA 58.446 40.000 0.00 0.00 0.00 2.59
2916 9140 7.011382 AGAGTCTTTTTCTAGTCCCTGTAGAA 58.989 38.462 0.00 0.00 35.21 2.10
2917 9141 7.509659 AGAGTCTTTTTCTAGTCCCTGTAGAAA 59.490 37.037 1.96 1.96 42.24 2.52
2923 9147 5.997384 TCTAGTCCCTGTAGAAAAAGTCC 57.003 43.478 0.00 0.00 0.00 3.85
2924 9148 4.776308 TCTAGTCCCTGTAGAAAAAGTCCC 59.224 45.833 0.00 0.00 0.00 4.46
2925 9149 3.599348 AGTCCCTGTAGAAAAAGTCCCT 58.401 45.455 0.00 0.00 0.00 4.20
2926 9150 3.583526 AGTCCCTGTAGAAAAAGTCCCTC 59.416 47.826 0.00 0.00 0.00 4.30
2927 9151 2.910977 TCCCTGTAGAAAAAGTCCCTCC 59.089 50.000 0.00 0.00 0.00 4.30
2928 9152 2.026169 CCCTGTAGAAAAAGTCCCTCCC 60.026 54.545 0.00 0.00 0.00 4.30
2929 9153 2.354805 CCTGTAGAAAAAGTCCCTCCCG 60.355 54.545 0.00 0.00 0.00 5.14
2930 9154 2.302157 CTGTAGAAAAAGTCCCTCCCGT 59.698 50.000 0.00 0.00 0.00 5.28
2931 9155 2.707257 TGTAGAAAAAGTCCCTCCCGTT 59.293 45.455 0.00 0.00 0.00 4.44
2932 9156 3.136992 TGTAGAAAAAGTCCCTCCCGTTT 59.863 43.478 0.00 0.00 0.00 3.60
2933 9157 2.583143 AGAAAAAGTCCCTCCCGTTTG 58.417 47.619 0.00 0.00 0.00 2.93
2934 9158 1.611977 GAAAAAGTCCCTCCCGTTTGG 59.388 52.381 0.00 0.00 0.00 3.28
2935 9159 0.554305 AAAAGTCCCTCCCGTTTGGT 59.446 50.000 0.00 0.00 34.77 3.67
2936 9160 0.554305 AAAGTCCCTCCCGTTTGGTT 59.446 50.000 0.00 0.00 34.77 3.67
2937 9161 0.109913 AAGTCCCTCCCGTTTGGTTC 59.890 55.000 0.00 0.00 34.77 3.62
2938 9162 1.303074 GTCCCTCCCGTTTGGTTCC 60.303 63.158 0.00 0.00 34.77 3.62
2939 9163 1.462627 TCCCTCCCGTTTGGTTCCT 60.463 57.895 0.00 0.00 34.77 3.36
2940 9164 0.178897 TCCCTCCCGTTTGGTTCCTA 60.179 55.000 0.00 0.00 34.77 2.94
2941 9165 0.252197 CCCTCCCGTTTGGTTCCTAG 59.748 60.000 0.00 0.00 34.77 3.02
2942 9166 0.252197 CCTCCCGTTTGGTTCCTAGG 59.748 60.000 0.82 0.82 34.77 3.02
2943 9167 0.252197 CTCCCGTTTGGTTCCTAGGG 59.748 60.000 9.46 0.00 40.16 3.53
2944 9168 0.178897 TCCCGTTTGGTTCCTAGGGA 60.179 55.000 9.46 0.00 44.85 4.20
2945 9169 0.035725 CCCGTTTGGTTCCTAGGGAC 60.036 60.000 12.35 12.35 41.26 4.46
2946 9170 0.981943 CCGTTTGGTTCCTAGGGACT 59.018 55.000 20.08 0.00 46.37 3.85
2947 9171 1.350019 CCGTTTGGTTCCTAGGGACTT 59.650 52.381 20.08 0.00 41.75 3.01
2948 9172 2.614734 CCGTTTGGTTCCTAGGGACTTC 60.615 54.545 20.08 4.83 41.75 3.01
2949 9173 2.302157 CGTTTGGTTCCTAGGGACTTCT 59.698 50.000 20.08 0.00 41.75 2.85
2950 9174 3.244457 CGTTTGGTTCCTAGGGACTTCTT 60.244 47.826 20.08 0.00 41.75 2.52
2951 9175 4.020839 CGTTTGGTTCCTAGGGACTTCTTA 60.021 45.833 20.08 0.00 41.75 2.10
2952 9176 5.489249 GTTTGGTTCCTAGGGACTTCTTAG 58.511 45.833 20.08 0.00 41.75 2.18
2953 9177 3.721021 TGGTTCCTAGGGACTTCTTAGG 58.279 50.000 20.08 0.00 41.75 2.69
2954 9178 3.039743 GGTTCCTAGGGACTTCTTAGGG 58.960 54.545 20.08 0.00 41.75 3.53
2955 9179 3.310435 GGTTCCTAGGGACTTCTTAGGGA 60.310 52.174 20.08 0.00 41.75 4.20
2956 9180 3.684408 TCCTAGGGACTTCTTAGGGAC 57.316 52.381 9.46 0.00 41.75 4.46
2957 9181 3.208173 TCCTAGGGACTTCTTAGGGACT 58.792 50.000 9.46 0.00 41.75 3.85
2958 9182 3.601537 TCCTAGGGACTTCTTAGGGACTT 59.398 47.826 9.46 0.00 39.49 3.01
2959 9183 4.046876 TCCTAGGGACTTCTTAGGGACTTT 59.953 45.833 9.46 0.00 39.49 2.66
2960 9184 4.783763 CCTAGGGACTTCTTAGGGACTTTT 59.216 45.833 0.00 0.00 39.49 2.27
2961 9185 5.251005 CCTAGGGACTTCTTAGGGACTTTTT 59.749 44.000 0.00 0.00 39.49 1.94
2962 9186 5.244189 AGGGACTTCTTAGGGACTTTTTC 57.756 43.478 0.00 0.00 34.75 2.29
2963 9187 4.914581 AGGGACTTCTTAGGGACTTTTTCT 59.085 41.667 0.00 0.00 34.75 2.52
2964 9188 6.089502 AGGGACTTCTTAGGGACTTTTTCTA 58.910 40.000 0.00 0.00 34.75 2.10
2965 9189 6.213802 AGGGACTTCTTAGGGACTTTTTCTAG 59.786 42.308 0.00 0.00 34.75 2.43
2966 9190 6.013553 GGGACTTCTTAGGGACTTTTTCTAGT 60.014 42.308 0.00 0.00 41.75 2.57
2967 9191 7.098477 GGACTTCTTAGGGACTTTTTCTAGTC 58.902 42.308 0.00 0.00 43.05 2.59
2968 9192 7.038870 GGACTTCTTAGGGACTTTTTCTAGTCT 60.039 40.741 0.00 0.00 43.26 3.24
2969 9193 8.265108 ACTTCTTAGGGACTTTTTCTAGTCTT 57.735 34.615 0.00 0.00 43.26 3.01
2970 9194 8.715842 ACTTCTTAGGGACTTTTTCTAGTCTTT 58.284 33.333 0.00 0.00 43.26 2.52
2971 9195 8.904099 TTCTTAGGGACTTTTTCTAGTCTTTG 57.096 34.615 0.00 0.00 43.26 2.77
2972 9196 7.450903 TCTTAGGGACTTTTTCTAGTCTTTGG 58.549 38.462 0.00 0.00 43.26 3.28
2973 9197 4.986783 AGGGACTTTTTCTAGTCTTTGGG 58.013 43.478 0.00 0.00 43.26 4.12
2974 9198 4.663592 AGGGACTTTTTCTAGTCTTTGGGA 59.336 41.667 0.00 0.00 43.26 4.37
2975 9199 4.760715 GGGACTTTTTCTAGTCTTTGGGAC 59.239 45.833 0.00 0.00 43.26 4.46
2977 9201 8.358596 AGGGACTTTTTCTAGTCTTTGGGACTA 61.359 40.741 0.00 5.55 46.03 2.59
2993 9217 3.782656 GACTAAAAAGTCCCTGACCCA 57.217 47.619 0.00 0.00 32.18 4.51
2994 9218 4.094830 GACTAAAAAGTCCCTGACCCAA 57.905 45.455 0.00 0.00 32.18 4.12
2995 9219 4.466827 GACTAAAAAGTCCCTGACCCAAA 58.533 43.478 0.00 0.00 32.18 3.28
2996 9220 4.212716 ACTAAAAAGTCCCTGACCCAAAC 58.787 43.478 0.00 0.00 32.18 2.93
2997 9221 2.838637 AAAAGTCCCTGACCCAAACA 57.161 45.000 0.00 0.00 32.18 2.83
2998 9222 2.067365 AAAGTCCCTGACCCAAACAC 57.933 50.000 0.00 0.00 32.18 3.32
2999 9223 0.185175 AAGTCCCTGACCCAAACACC 59.815 55.000 0.00 0.00 32.18 4.16
3000 9224 1.228459 GTCCCTGACCCAAACACCC 60.228 63.158 0.00 0.00 0.00 4.61
3001 9225 2.117423 CCCTGACCCAAACACCCC 59.883 66.667 0.00 0.00 0.00 4.95
3002 9226 2.117423 CCTGACCCAAACACCCCC 59.883 66.667 0.00 0.00 0.00 5.40
3003 9227 2.469765 CCTGACCCAAACACCCCCT 61.470 63.158 0.00 0.00 0.00 4.79
3004 9228 1.541672 CTGACCCAAACACCCCCTT 59.458 57.895 0.00 0.00 0.00 3.95
3005 9229 0.774908 CTGACCCAAACACCCCCTTA 59.225 55.000 0.00 0.00 0.00 2.69
3006 9230 1.146152 CTGACCCAAACACCCCCTTAA 59.854 52.381 0.00 0.00 0.00 1.85
3007 9231 1.574339 TGACCCAAACACCCCCTTAAA 59.426 47.619 0.00 0.00 0.00 1.52
3020 9244 6.183361 ACACCCCCTTAAAACCATTAGTACTT 60.183 38.462 0.00 0.00 0.00 2.24
3049 9273 1.142060 TGGAAGTGTCACAACGGGAAT 59.858 47.619 5.62 0.00 0.00 3.01
3055 9279 5.622770 AGTGTCACAACGGGAATAAATTC 57.377 39.130 5.62 0.00 36.08 2.17
3092 9316 9.909644 GTTAGATAAGGAAGAAAAAGTTTTCCC 57.090 33.333 11.90 7.92 45.84 3.97
3093 9317 9.649316 TTAGATAAGGAAGAAAAAGTTTTCCCA 57.351 29.630 11.90 0.00 45.84 4.37
3101 9325 7.201609 GGAAGAAAAAGTTTTCCCATGTCAAAC 60.202 37.037 11.90 0.00 45.84 2.93
3142 9367 7.781056 TGCCAATGTTAAATAAGGAATTCTCC 58.219 34.615 5.23 0.00 42.81 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 8.043113 TCTAGGCAATATAATGGTGCAGAATAG 58.957 37.037 0.00 0.00 40.12 1.73
33 34 6.207417 ACACAATCTAGGCAATATAATGGTGC 59.793 38.462 0.00 0.00 37.55 5.01
44 45 9.764363 CTTCTTATGTATACACAATCTAGGCAA 57.236 33.333 7.96 0.00 38.42 4.52
55 56 7.146648 GGTCAGGTAGCTTCTTATGTATACAC 58.853 42.308 7.96 0.00 0.00 2.90
62 63 4.065321 CCTGGTCAGGTAGCTTCTTATG 57.935 50.000 8.78 0.00 43.61 1.90
91 92 2.276201 TCCATTAGTGCGTACATGTGC 58.724 47.619 9.11 6.17 0.00 4.57
100 101 4.507756 TCGAAGATTCAATCCATTAGTGCG 59.492 41.667 0.00 0.00 0.00 5.34
116 117 6.426633 TGTGTGAACAATGTACATTCGAAGAT 59.573 34.615 18.25 2.31 35.04 2.40
145 146 5.564848 GCGACCAGCTCATAATGTGATACTA 60.565 44.000 0.00 0.00 44.04 1.82
173 178 0.806102 CGTACCATGCCTTCAGGTCG 60.806 60.000 0.00 0.00 36.87 4.79
195 200 7.550906 ACATAAGTCATAGGTGAGAAAAGCTTC 59.449 37.037 0.00 0.00 34.36 3.86
205 210 9.559732 CCAATTGAATACATAAGTCATAGGTGA 57.440 33.333 7.12 0.00 29.89 4.02
261 266 4.417183 TGGGGGCAATACTTAATCACCATA 59.583 41.667 0.00 0.00 0.00 2.74
269 274 4.054359 ACACATTGGGGGCAATACTTAA 57.946 40.909 0.00 0.00 0.00 1.85
468 473 3.192001 CACCACATCATTGGAAGGAAGTG 59.808 47.826 3.16 3.16 39.24 3.16
496 501 2.494870 AGCATTGAAGACAAATGGGAGC 59.505 45.455 0.00 0.00 39.54 4.70
500 505 4.698780 TCAGAGAGCATTGAAGACAAATGG 59.301 41.667 0.00 0.00 39.54 3.16
521 526 1.697432 AGAACCTTCCCACACGATTCA 59.303 47.619 0.00 0.00 0.00 2.57
525 530 1.707106 TGTAGAACCTTCCCACACGA 58.293 50.000 0.00 0.00 0.00 4.35
551 556 1.489230 GGTATGGTTCGTGGGAGGAAT 59.511 52.381 0.00 0.00 0.00 3.01
605 610 4.373116 GCGGTGCCGAGGAGAACA 62.373 66.667 15.45 0.00 42.83 3.18
642 648 2.017049 ACAATGTTCTGAATAGCGGCC 58.983 47.619 0.00 0.00 0.00 6.13
673 679 9.675464 AACGGTGTTATATAAGGAATTTTCTCA 57.325 29.630 0.00 0.00 0.00 3.27
749 755 3.568443 GGGTGTGTTAGGAAGGGAAAAA 58.432 45.455 0.00 0.00 0.00 1.94
768 774 0.172803 CTCCTAACAGAACCGACGGG 59.827 60.000 20.00 2.20 40.11 5.28
790 796 4.933400 TCGGTGAATGTAGACTTTAAAGGC 59.067 41.667 19.14 16.59 0.00 4.35
793 799 7.156000 TGACATCGGTGAATGTAGACTTTAAA 58.844 34.615 0.65 0.00 39.93 1.52
833 839 0.693622 TGGACAGGGGCAATTTCGTA 59.306 50.000 0.00 0.00 0.00 3.43
836 842 5.509670 GCTTATTATGGACAGGGGCAATTTC 60.510 44.000 0.00 0.00 0.00 2.17
869 875 2.607180 CGGTTTGGGCTTTGTTTTCTTG 59.393 45.455 0.00 0.00 0.00 3.02
899 906 1.755008 GTCAGGACTCGGGGGAGAG 60.755 68.421 0.00 0.00 43.56 3.20
925 932 2.158813 AGAACGGAGAAAGGAGCACAAA 60.159 45.455 0.00 0.00 0.00 2.83
939 946 0.606604 GCTAGGTTGGACAGAACGGA 59.393 55.000 0.00 0.00 0.00 4.69
942 949 1.352156 CGCGCTAGGTTGGACAGAAC 61.352 60.000 5.56 0.00 0.00 3.01
1017 1024 4.900154 GAGTTGTCTCCCTCTGCG 57.100 61.111 0.00 0.00 34.87 5.18
1033 1040 1.192146 CCCTGGTCGTCTTCCTTGGA 61.192 60.000 0.00 0.00 0.00 3.53
1037 1044 2.584391 GCACCCTGGTCGTCTTCCT 61.584 63.158 0.00 0.00 0.00 3.36
1153 1160 1.330655 ATCTCGTCGGCACCCTCAAT 61.331 55.000 0.00 0.00 0.00 2.57
1154 1161 0.681887 TATCTCGTCGGCACCCTCAA 60.682 55.000 0.00 0.00 0.00 3.02
1169 1176 1.486310 TGCCACCTGCGAAAGATATCT 59.514 47.619 0.00 0.00 45.60 1.98
1174 1181 1.301716 GACTGCCACCTGCGAAAGA 60.302 57.895 0.00 0.00 45.60 2.52
1224 1231 0.890996 CAGAGCACCCAACCACTTCC 60.891 60.000 0.00 0.00 0.00 3.46
1226 1233 1.529244 GCAGAGCACCCAACCACTT 60.529 57.895 0.00 0.00 0.00 3.16
1297 1304 2.091112 CGCTCTGGTCTGAAGCACG 61.091 63.158 0.60 0.00 0.00 5.34
1315 1322 3.479269 CGAGGACAAACGAGCCGC 61.479 66.667 0.00 0.00 0.00 6.53
1341 1348 0.806102 CTTACCCATCTGGACACGCG 60.806 60.000 3.53 3.53 37.39 6.01
1342 1349 0.249398 ACTTACCCATCTGGACACGC 59.751 55.000 0.00 0.00 37.39 5.34
1354 1361 3.446516 ACTCCTACGAATGACACTTACCC 59.553 47.826 0.00 0.00 0.00 3.69
1377 1384 4.067896 ACAGAGTAGTTGCATTCACTTGG 58.932 43.478 0.00 0.00 0.00 3.61
1388 1395 8.378172 TGAGGAAAATACAAACAGAGTAGTTG 57.622 34.615 0.00 0.00 31.10 3.16
1391 1398 9.831737 CAAATGAGGAAAATACAAACAGAGTAG 57.168 33.333 0.00 0.00 0.00 2.57
1393 1400 8.463930 TCAAATGAGGAAAATACAAACAGAGT 57.536 30.769 0.00 0.00 0.00 3.24
1443 1450 4.763279 TGCATGATAATTGCTACTGGATGG 59.237 41.667 0.00 0.00 40.77 3.51
1532 1539 9.414295 TGAATTAAGAAGACAATTTTGCATCAG 57.586 29.630 0.00 0.00 0.00 2.90
1652 1659 5.934043 TGTCAAGTCACAATCGATGATCTTT 59.066 36.000 0.00 0.00 0.00 2.52
1656 1663 6.748333 ATTTGTCAAGTCACAATCGATGAT 57.252 33.333 0.00 0.00 36.16 2.45
1687 1694 7.439056 ACTGCTTTACAATTGATTCAACCAAAG 59.561 33.333 13.59 9.50 0.00 2.77
1772 1779 7.505585 TCTTGGTCAGAATTTACTTTTGGACAT 59.494 33.333 0.00 0.00 0.00 3.06
1779 1786 9.918630 CATCAAATCTTGGTCAGAATTTACTTT 57.081 29.630 0.00 0.00 34.16 2.66
1787 1794 6.660521 ACATAAGCATCAAATCTTGGTCAGAA 59.339 34.615 0.00 0.00 34.16 3.02
1826 1833 3.054875 TCATATGCAGCACCTTTGTCTCT 60.055 43.478 0.00 0.00 0.00 3.10
1877 1884 4.082190 TGCCACTCGATAATAGGCTCATAC 60.082 45.833 12.72 0.00 45.42 2.39
1889 1896 2.034685 GCTATCACTGTGCCACTCGATA 59.965 50.000 2.12 0.00 0.00 2.92
1891 1898 0.173481 GCTATCACTGTGCCACTCGA 59.827 55.000 2.12 0.00 0.00 4.04
1901 1908 2.654749 TGTCAGGTTCGCTATCACTG 57.345 50.000 0.00 0.00 0.00 3.66
1971 4457 7.298374 AGAATTAGGAAAGTTCACCTTTTCCT 58.702 34.615 19.02 19.02 43.47 3.36
2071 4557 0.583438 GCATGTATGGCAGCAGTACG 59.417 55.000 0.00 0.00 0.00 3.67
2146 4636 8.811994 CCTTAGGACCATTTTGATCCTTTTTAA 58.188 33.333 0.00 0.00 36.92 1.52
2216 4709 1.131638 TTGCAGGGATGGCTAGGTAG 58.868 55.000 0.00 0.00 0.00 3.18
2366 8448 2.624636 TGCATGACATGAGTAGCACAG 58.375 47.619 19.76 0.00 0.00 3.66
2392 8536 6.749139 TCACATAGATAGTGCAAGTCCATAC 58.251 40.000 0.00 0.00 36.93 2.39
2409 8553 9.018582 TCTCACATCATATCTAGGTTCACATAG 57.981 37.037 0.00 0.00 0.00 2.23
2520 8723 1.072331 ACATCCGGGCTCATATCCAAC 59.928 52.381 0.00 0.00 0.00 3.77
2527 8730 3.297134 AACATAAACATCCGGGCTCAT 57.703 42.857 0.00 0.00 0.00 2.90
2659 8871 7.765695 ATCTCCACACACAAGTATTTCAAAT 57.234 32.000 0.00 0.00 0.00 2.32
2822 9046 1.328279 CTTCTGAACCAAACACCCCC 58.672 55.000 0.00 0.00 0.00 5.40
2823 9047 1.954382 GACTTCTGAACCAAACACCCC 59.046 52.381 0.00 0.00 0.00 4.95
2824 9048 1.954382 GGACTTCTGAACCAAACACCC 59.046 52.381 0.00 0.00 0.00 4.61
2825 9049 2.932261 AGGACTTCTGAACCAAACACC 58.068 47.619 0.58 0.00 0.00 4.16
2826 9050 4.065789 CCTAGGACTTCTGAACCAAACAC 58.934 47.826 1.05 0.00 0.00 3.32
2827 9051 3.971305 TCCTAGGACTTCTGAACCAAACA 59.029 43.478 7.62 0.00 0.00 2.83
2828 9052 4.316645 GTCCTAGGACTTCTGAACCAAAC 58.683 47.826 31.12 3.26 41.57 2.93
2829 9053 4.618920 GTCCTAGGACTTCTGAACCAAA 57.381 45.455 31.12 0.00 41.57 3.28
2883 9107 6.660094 GGACTAGAAAAAGACTCTACTGGAGA 59.340 42.308 0.00 0.00 44.45 3.71
2884 9108 6.127563 GGGACTAGAAAAAGACTCTACTGGAG 60.128 46.154 0.00 0.00 46.87 3.86
2885 9109 5.715753 GGGACTAGAAAAAGACTCTACTGGA 59.284 44.000 0.00 0.00 0.00 3.86
2886 9110 5.717654 AGGGACTAGAAAAAGACTCTACTGG 59.282 44.000 0.00 0.00 36.02 4.00
2887 9111 6.209788 ACAGGGACTAGAAAAAGACTCTACTG 59.790 42.308 0.00 0.00 36.02 2.74
2888 9112 6.316513 ACAGGGACTAGAAAAAGACTCTACT 58.683 40.000 0.00 0.00 36.02 2.57
2889 9113 6.593268 ACAGGGACTAGAAAAAGACTCTAC 57.407 41.667 0.00 0.00 36.02 2.59
2890 9114 7.696981 TCTACAGGGACTAGAAAAAGACTCTA 58.303 38.462 0.00 0.00 36.02 2.43
2891 9115 6.553857 TCTACAGGGACTAGAAAAAGACTCT 58.446 40.000 0.00 0.00 36.02 3.24
2892 9116 6.837471 TCTACAGGGACTAGAAAAAGACTC 57.163 41.667 0.00 0.00 36.02 3.36
2893 9117 7.613551 TTTCTACAGGGACTAGAAAAAGACT 57.386 36.000 0.00 0.00 37.31 3.24
2894 9118 8.672823 TTTTTCTACAGGGACTAGAAAAAGAC 57.327 34.615 16.61 0.00 46.05 3.01
2898 9122 7.222161 GGACTTTTTCTACAGGGACTAGAAAA 58.778 38.462 0.00 8.58 43.60 2.29
2899 9123 6.239800 GGGACTTTTTCTACAGGGACTAGAAA 60.240 42.308 0.00 0.00 38.08 2.52
2900 9124 5.247792 GGGACTTTTTCTACAGGGACTAGAA 59.752 44.000 0.00 0.00 36.02 2.10
2901 9125 4.776308 GGGACTTTTTCTACAGGGACTAGA 59.224 45.833 0.00 0.00 36.02 2.43
2902 9126 4.778427 AGGGACTTTTTCTACAGGGACTAG 59.222 45.833 0.00 0.00 28.08 2.57
2903 9127 4.759953 AGGGACTTTTTCTACAGGGACTA 58.240 43.478 0.00 0.00 28.08 2.59
2904 9128 3.583526 GAGGGACTTTTTCTACAGGGACT 59.416 47.826 0.00 0.00 41.55 3.85
2905 9129 3.307550 GGAGGGACTTTTTCTACAGGGAC 60.308 52.174 0.00 0.00 41.55 4.46
2906 9130 2.910977 GGAGGGACTTTTTCTACAGGGA 59.089 50.000 0.00 0.00 41.55 4.20
2907 9131 2.026169 GGGAGGGACTTTTTCTACAGGG 60.026 54.545 0.00 0.00 41.55 4.45
2908 9132 2.354805 CGGGAGGGACTTTTTCTACAGG 60.355 54.545 0.00 0.00 41.55 4.00
2909 9133 2.302157 ACGGGAGGGACTTTTTCTACAG 59.698 50.000 0.00 0.00 41.55 2.74
2910 9134 2.332117 ACGGGAGGGACTTTTTCTACA 58.668 47.619 0.00 0.00 41.55 2.74
2911 9135 3.413846 AACGGGAGGGACTTTTTCTAC 57.586 47.619 0.00 0.00 41.55 2.59
2912 9136 3.497227 CCAAACGGGAGGGACTTTTTCTA 60.497 47.826 0.00 0.00 41.55 2.10
2913 9137 2.583143 CAAACGGGAGGGACTTTTTCT 58.417 47.619 0.00 0.00 41.55 2.52
2914 9138 1.611977 CCAAACGGGAGGGACTTTTTC 59.388 52.381 0.00 0.00 41.55 2.29
2915 9139 1.063492 ACCAAACGGGAGGGACTTTTT 60.063 47.619 0.00 0.00 41.55 1.94
2916 9140 0.554305 ACCAAACGGGAGGGACTTTT 59.446 50.000 0.00 0.00 41.55 2.27
2917 9141 0.554305 AACCAAACGGGAGGGACTTT 59.446 50.000 0.00 0.00 41.55 2.66
2918 9142 0.109913 GAACCAAACGGGAGGGACTT 59.890 55.000 0.00 0.00 41.55 3.01
2920 9144 1.303074 GGAACCAAACGGGAGGGAC 60.303 63.158 0.00 0.00 41.15 4.46
2921 9145 0.178897 TAGGAACCAAACGGGAGGGA 60.179 55.000 0.00 0.00 41.15 4.20
2922 9146 0.252197 CTAGGAACCAAACGGGAGGG 59.748 60.000 0.00 0.00 41.15 4.30
2923 9147 0.252197 CCTAGGAACCAAACGGGAGG 59.748 60.000 1.05 0.00 41.15 4.30
2924 9148 0.252197 CCCTAGGAACCAAACGGGAG 59.748 60.000 11.48 0.00 41.15 4.30
2925 9149 0.178897 TCCCTAGGAACCAAACGGGA 60.179 55.000 11.48 0.00 41.15 5.14
2926 9150 0.035725 GTCCCTAGGAACCAAACGGG 60.036 60.000 11.48 0.00 44.81 5.28
2927 9151 0.981943 AGTCCCTAGGAACCAAACGG 59.018 55.000 11.48 0.00 31.38 4.44
2928 9152 2.302157 AGAAGTCCCTAGGAACCAAACG 59.698 50.000 11.48 0.00 31.38 3.60
2929 9153 4.368565 AAGAAGTCCCTAGGAACCAAAC 57.631 45.455 11.48 0.00 31.38 2.93
2930 9154 4.534897 CCTAAGAAGTCCCTAGGAACCAAA 59.465 45.833 11.48 0.00 31.38 3.28
2931 9155 4.101856 CCTAAGAAGTCCCTAGGAACCAA 58.898 47.826 11.48 0.00 31.38 3.67
2932 9156 3.568109 CCCTAAGAAGTCCCTAGGAACCA 60.568 52.174 11.48 0.00 31.38 3.67
2933 9157 3.039743 CCCTAAGAAGTCCCTAGGAACC 58.960 54.545 11.48 0.00 31.38 3.62
2934 9158 3.705579 GTCCCTAAGAAGTCCCTAGGAAC 59.294 52.174 11.48 0.00 31.38 3.62
2935 9159 3.601537 AGTCCCTAAGAAGTCCCTAGGAA 59.398 47.826 11.48 0.00 31.38 3.36
2936 9160 3.208173 AGTCCCTAAGAAGTCCCTAGGA 58.792 50.000 11.48 0.00 0.00 2.94
2937 9161 3.691698 AGTCCCTAAGAAGTCCCTAGG 57.308 52.381 0.06 0.06 0.00 3.02
2938 9162 6.213802 AGAAAAAGTCCCTAAGAAGTCCCTAG 59.786 42.308 0.00 0.00 0.00 3.02
2939 9163 6.089502 AGAAAAAGTCCCTAAGAAGTCCCTA 58.910 40.000 0.00 0.00 0.00 3.53
2940 9164 4.914581 AGAAAAAGTCCCTAAGAAGTCCCT 59.085 41.667 0.00 0.00 0.00 4.20
2941 9165 5.244189 AGAAAAAGTCCCTAAGAAGTCCC 57.756 43.478 0.00 0.00 0.00 4.46
2942 9166 7.006865 ACTAGAAAAAGTCCCTAAGAAGTCC 57.993 40.000 0.00 0.00 0.00 3.85
2943 9167 7.898918 AGACTAGAAAAAGTCCCTAAGAAGTC 58.101 38.462 0.00 0.00 45.86 3.01
2944 9168 7.859026 AGACTAGAAAAAGTCCCTAAGAAGT 57.141 36.000 0.00 0.00 45.86 3.01
2945 9169 8.994170 CAAAGACTAGAAAAAGTCCCTAAGAAG 58.006 37.037 0.00 0.00 45.86 2.85
2946 9170 7.937394 CCAAAGACTAGAAAAAGTCCCTAAGAA 59.063 37.037 0.00 0.00 45.86 2.52
2947 9171 7.450903 CCAAAGACTAGAAAAAGTCCCTAAGA 58.549 38.462 0.00 0.00 45.86 2.10
2948 9172 6.655425 CCCAAAGACTAGAAAAAGTCCCTAAG 59.345 42.308 0.00 0.00 45.86 2.18
2949 9173 6.330778 TCCCAAAGACTAGAAAAAGTCCCTAA 59.669 38.462 0.00 0.00 45.86 2.69
2950 9174 5.847817 TCCCAAAGACTAGAAAAAGTCCCTA 59.152 40.000 0.00 0.00 45.86 3.53
2951 9175 4.663592 TCCCAAAGACTAGAAAAAGTCCCT 59.336 41.667 0.00 0.00 45.86 4.20
2952 9176 4.760715 GTCCCAAAGACTAGAAAAAGTCCC 59.239 45.833 0.00 0.00 45.86 4.46
2953 9177 5.943706 GTCCCAAAGACTAGAAAAAGTCC 57.056 43.478 0.00 0.00 45.86 3.85
2973 9197 3.782656 TGGGTCAGGGACTTTTTAGTC 57.217 47.619 0.00 0.00 34.60 2.59
2974 9198 4.212716 GTTTGGGTCAGGGACTTTTTAGT 58.787 43.478 0.00 0.00 34.60 2.24
2975 9199 4.037565 GTGTTTGGGTCAGGGACTTTTTAG 59.962 45.833 0.00 0.00 34.60 1.85
2976 9200 3.955551 GTGTTTGGGTCAGGGACTTTTTA 59.044 43.478 0.00 0.00 34.60 1.52
2977 9201 2.764010 GTGTTTGGGTCAGGGACTTTTT 59.236 45.455 0.00 0.00 34.60 1.94
2978 9202 2.384828 GTGTTTGGGTCAGGGACTTTT 58.615 47.619 0.00 0.00 34.60 2.27
2979 9203 1.411074 GGTGTTTGGGTCAGGGACTTT 60.411 52.381 0.00 0.00 34.60 2.66
2980 9204 0.185175 GGTGTTTGGGTCAGGGACTT 59.815 55.000 0.00 0.00 34.60 3.01
2981 9205 1.716028 GGGTGTTTGGGTCAGGGACT 61.716 60.000 0.00 0.00 43.88 3.85
2982 9206 1.228459 GGGTGTTTGGGTCAGGGAC 60.228 63.158 0.00 0.00 0.00 4.46
2983 9207 2.466186 GGGGTGTTTGGGTCAGGGA 61.466 63.158 0.00 0.00 0.00 4.20
2984 9208 2.117423 GGGGTGTTTGGGTCAGGG 59.883 66.667 0.00 0.00 0.00 4.45
2985 9209 2.018884 AAGGGGGTGTTTGGGTCAGG 62.019 60.000 0.00 0.00 0.00 3.86
2986 9210 0.774908 TAAGGGGGTGTTTGGGTCAG 59.225 55.000 0.00 0.00 0.00 3.51
2987 9211 1.232909 TTAAGGGGGTGTTTGGGTCA 58.767 50.000 0.00 0.00 0.00 4.02
2988 9212 2.366266 GTTTTAAGGGGGTGTTTGGGTC 59.634 50.000 0.00 0.00 0.00 4.46
2989 9213 2.400573 GTTTTAAGGGGGTGTTTGGGT 58.599 47.619 0.00 0.00 0.00 4.51
2990 9214 1.695242 GGTTTTAAGGGGGTGTTTGGG 59.305 52.381 0.00 0.00 0.00 4.12
2991 9215 2.399580 TGGTTTTAAGGGGGTGTTTGG 58.600 47.619 0.00 0.00 0.00 3.28
2992 9216 4.698201 AATGGTTTTAAGGGGGTGTTTG 57.302 40.909 0.00 0.00 0.00 2.93
2993 9217 5.469579 ACTAATGGTTTTAAGGGGGTGTTT 58.530 37.500 0.00 0.00 0.00 2.83
2994 9218 5.082633 ACTAATGGTTTTAAGGGGGTGTT 57.917 39.130 0.00 0.00 0.00 3.32
2995 9219 4.752621 ACTAATGGTTTTAAGGGGGTGT 57.247 40.909 0.00 0.00 0.00 4.16
2996 9220 5.823312 AGTACTAATGGTTTTAAGGGGGTG 58.177 41.667 0.00 0.00 0.00 4.61
2997 9221 6.473429 AAGTACTAATGGTTTTAAGGGGGT 57.527 37.500 0.00 0.00 0.00 4.95
2998 9222 8.882557 TTTAAGTACTAATGGTTTTAAGGGGG 57.117 34.615 0.00 0.00 0.00 5.40
3020 9244 6.370442 CCGTTGTGACACTTCCATCTATTTTA 59.630 38.462 7.20 0.00 0.00 1.52
3055 9279 8.948631 TCTTCCTTATCTAACAACAATGCTAG 57.051 34.615 0.00 0.00 0.00 3.42
3093 9317 7.148373 GCATAATTCTTTTGCCATGTTTGACAT 60.148 33.333 0.00 0.00 39.91 3.06
3117 9342 7.147742 GGGAGAATTCCTTATTTAACATTGGCA 60.148 37.037 0.65 0.00 43.49 4.92
3142 9367 6.273071 CGGCTTGGGATCTTTAAATTTAAGG 58.727 40.000 12.58 12.58 0.00 2.69
3197 9422 6.049263 ACACAAGAAAGAAAGAGTAAAGCG 57.951 37.500 0.00 0.00 0.00 4.68


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

AutoCloner maintained by Alex Coulton.