Multiple sequence alignment - TraesCS1B01G104500

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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 TraesCS1B01G104500 chr1B 100.000 4906 0 0 1 4906 115283282 115278377 0.000000e+00 9060.0
1 TraesCS1B01G104500 chr1B 100.000 40 0 0 271 310 115282932 115282893 1.890000e-09 75.0
2 TraesCS1B01G104500 chr1B 100.000 40 0 0 351 390 115283012 115282973 1.890000e-09 75.0
3 TraesCS1B01G104500 chr1A 91.975 2106 116 20 2822 4906 72784011 72781938 0.000000e+00 2904.0
4 TraesCS1B01G104500 chr1A 89.436 2073 149 40 351 2378 72786488 72784441 0.000000e+00 2551.0
5 TraesCS1B01G104500 chr1A 93.249 237 14 1 74 310 72786683 72786449 1.010000e-91 348.0
6 TraesCS1B01G104500 chr1A 84.848 231 18 9 2380 2605 72784322 72784104 2.970000e-52 217.0
7 TraesCS1B01G104500 chr1A 97.674 43 1 0 2780 2822 497499672 497499630 1.890000e-09 75.0
8 TraesCS1B01G104500 chr1D 93.711 1765 89 14 3152 4906 72904745 72902993 0.000000e+00 2625.0
9 TraesCS1B01G104500 chr1D 92.204 1783 90 22 637 2396 72907375 72905619 0.000000e+00 2477.0
10 TraesCS1B01G104500 chr1D 87.858 1013 81 19 1399 2388 73053404 73052411 0.000000e+00 1151.0
11 TraesCS1B01G104500 chr1D 91.781 292 24 0 1091 1382 73054391 73054100 1.640000e-109 407.0
12 TraesCS1B01G104500 chr1D 91.919 198 13 2 3282 3479 73051525 73051331 1.740000e-69 274.0
13 TraesCS1B01G104500 chr1D 85.294 170 20 2 3027 3196 73051762 73051598 2.350000e-38 171.0
14 TraesCS1B01G104500 chr1D 95.652 46 2 0 358 403 72907990 72907945 1.890000e-09 75.0
15 TraesCS1B01G104500 chr1D 100.000 37 0 0 2927 2963 72904859 72904823 8.810000e-08 69.4
16 TraesCS1B01G104500 chr5D 76.389 216 48 1 1465 1677 357065010 357064795 4.010000e-21 113.0
17 TraesCS1B01G104500 chr5D 95.833 48 1 1 2781 2828 533870007 533870053 5.270000e-10 76.8
18 TraesCS1B01G104500 chr2D 76.233 223 47 5 1458 1677 79686562 79686781 4.010000e-21 113.0
19 TraesCS1B01G104500 chr2D 95.652 46 1 1 2781 2826 476956821 476956865 6.810000e-09 73.1
20 TraesCS1B01G104500 chr2B 76.364 220 46 5 1467 1683 131180637 131180853 4.010000e-21 113.0
21 TraesCS1B01G104500 chr5B 76.279 215 38 10 1465 1677 422040316 422040113 8.690000e-18 102.0
22 TraesCS1B01G104500 chr5B 92.308 52 3 1 2781 2832 324309523 324309573 6.810000e-09 73.1
23 TraesCS1B01G104500 chr5A 76.056 213 42 7 1465 1677 458561799 458561596 8.690000e-18 102.0
24 TraesCS1B01G104500 chr2A 75.463 216 47 5 1465 1677 80264564 80264776 3.120000e-17 100.0
25 TraesCS1B01G104500 chr7B 97.619 42 1 0 2781 2822 618073115 618073074 6.810000e-09 73.1
26 TraesCS1B01G104500 chr7B 93.617 47 3 0 2776 2822 617879044 617878998 2.450000e-08 71.3
27 TraesCS1B01G104500 chr7A 95.652 46 1 1 2781 2826 98084959 98085003 6.810000e-09 73.1
28 TraesCS1B01G104500 chr3A 100.000 39 0 0 2781 2819 726128662 726128700 6.810000e-09 73.1
29 TraesCS1B01G104500 chrUn 91.667 48 2 2 2772 2819 89133307 89133352 1.140000e-06 65.8
30 TraesCS1B01G104500 chr6D 100.000 35 0 0 1918 1952 305277379 305277413 1.140000e-06 65.8
31 TraesCS1B01G104500 chr6B 100.000 35 0 0 1918 1952 471307694 471307660 1.140000e-06 65.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G104500 chr1B 115278377 115283282 4905 True 3070.00 9060 100.00000 1 4906 3 chr1B.!!$R1 4905
1 TraesCS1B01G104500 chr1A 72781938 72786683 4745 True 1505.00 2904 89.87700 74 4906 4 chr1A.!!$R2 4832
2 TraesCS1B01G104500 chr1D 72902993 72907990 4997 True 1311.60 2625 95.39175 358 4906 4 chr1D.!!$R1 4548
3 TraesCS1B01G104500 chr1D 73051331 73054391 3060 True 500.75 1151 89.21300 1091 3479 4 chr1D.!!$R2 2388

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
56 57 0.038892 CACAGGTGCAAGCATGGAAC 60.039 55.0 0.00 0.0 36.26 3.62 F
1173 1566 1.108776 TGTACTCCGGCTACATCACC 58.891 55.0 0.00 0.0 0.00 4.02 F
1965 3057 0.666274 TCTGCAACATCACGTCGTCC 60.666 55.0 0.00 0.0 0.00 4.79 F
3393 5104 0.389391 ACAAGATACTCCATCGGCGG 59.611 55.0 7.21 0.0 38.81 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1397 1790 0.093705 GTGACGTCGATCAAGCAAGC 59.906 55.0 11.62 0.0 0.00 4.01 R
2046 3161 0.178938 TCAAAAAGCAGCATGGGGGA 60.179 50.0 0.00 0.0 35.86 4.81 R
3513 5224 0.878416 GTGGTCTATTTGCACGCCAA 59.122 50.0 0.00 0.0 0.00 4.52 R
4285 6026 0.461870 CATTACCAGCAGTGCGGCTA 60.462 55.0 21.05 12.3 43.68 3.93 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
18 19 3.284197 ACTGTGGTGAAGCGTACAC 57.716 52.632 0.00 0.00 37.51 2.90
19 20 0.596600 ACTGTGGTGAAGCGTACACG 60.597 55.000 0.00 0.00 38.90 4.49
34 35 5.198116 CGTACACGCATATTCTTTGTTCA 57.802 39.130 0.00 0.00 0.00 3.18
35 36 5.013236 CGTACACGCATATTCTTTGTTCAC 58.987 41.667 0.00 0.00 0.00 3.18
36 37 5.163992 CGTACACGCATATTCTTTGTTCACT 60.164 40.000 0.00 0.00 0.00 3.41
37 38 5.283060 ACACGCATATTCTTTGTTCACTC 57.717 39.130 0.00 0.00 0.00 3.51
38 39 4.754618 ACACGCATATTCTTTGTTCACTCA 59.245 37.500 0.00 0.00 0.00 3.41
39 40 5.082059 CACGCATATTCTTTGTTCACTCAC 58.918 41.667 0.00 0.00 0.00 3.51
40 41 4.754618 ACGCATATTCTTTGTTCACTCACA 59.245 37.500 0.00 0.00 0.00 3.58
41 42 5.106948 ACGCATATTCTTTGTTCACTCACAG 60.107 40.000 0.00 0.00 0.00 3.66
42 43 5.634896 GCATATTCTTTGTTCACTCACAGG 58.365 41.667 0.00 0.00 0.00 4.00
43 44 5.182001 GCATATTCTTTGTTCACTCACAGGT 59.818 40.000 0.00 0.00 0.00 4.00
44 45 6.605849 CATATTCTTTGTTCACTCACAGGTG 58.394 40.000 0.00 0.00 38.44 4.00
45 46 2.288666 TCTTTGTTCACTCACAGGTGC 58.711 47.619 0.00 0.00 37.16 5.01
46 47 2.016318 CTTTGTTCACTCACAGGTGCA 58.984 47.619 0.00 0.00 37.16 4.57
47 48 2.121291 TTGTTCACTCACAGGTGCAA 57.879 45.000 0.00 0.00 37.16 4.08
48 49 1.667236 TGTTCACTCACAGGTGCAAG 58.333 50.000 0.00 0.00 37.16 4.01
49 50 0.308993 GTTCACTCACAGGTGCAAGC 59.691 55.000 0.00 0.00 37.16 4.01
50 51 0.107263 TTCACTCACAGGTGCAAGCA 60.107 50.000 0.00 0.00 37.16 3.91
51 52 0.109153 TCACTCACAGGTGCAAGCAT 59.891 50.000 0.00 0.00 37.16 3.79
52 53 0.240145 CACTCACAGGTGCAAGCATG 59.760 55.000 0.00 0.00 36.26 4.06
53 54 0.892358 ACTCACAGGTGCAAGCATGG 60.892 55.000 0.00 0.00 36.26 3.66
54 55 0.607217 CTCACAGGTGCAAGCATGGA 60.607 55.000 0.00 0.00 36.26 3.41
55 56 0.178995 TCACAGGTGCAAGCATGGAA 60.179 50.000 0.00 0.00 36.26 3.53
56 57 0.038892 CACAGGTGCAAGCATGGAAC 60.039 55.000 0.00 0.00 36.26 3.62
122 123 7.273320 TCCTTCATACGTAGTTCATCTAAGG 57.727 40.000 0.08 5.33 37.78 2.69
150 151 7.919313 ATCTTTAAATTCACATAGCAATGCG 57.081 32.000 0.00 0.00 36.50 4.73
161 162 2.774799 GCAATGCGCGGGGAAATCT 61.775 57.895 8.83 0.00 0.00 2.40
167 168 1.441729 CGCGGGGAAATCTCTAGCA 59.558 57.895 0.00 0.00 0.00 3.49
174 175 4.202264 CGGGGAAATCTCTAGCAGTTATGT 60.202 45.833 0.00 0.00 0.00 2.29
180 181 9.771534 GGAAATCTCTAGCAGTTATGTAAATCT 57.228 33.333 0.00 0.00 0.00 2.40
261 262 6.980416 AGATTAGAAACGGACTATTAGCCT 57.020 37.500 0.00 0.00 0.00 4.58
310 311 7.706607 CGATACAGTTTCTTATCTTCCATGTCA 59.293 37.037 0.00 0.00 0.00 3.58
312 313 7.856145 ACAGTTTCTTATCTTCCATGTCATC 57.144 36.000 0.00 0.00 0.00 2.92
314 315 8.105829 ACAGTTTCTTATCTTCCATGTCATCTT 58.894 33.333 0.00 0.00 0.00 2.40
315 316 8.396390 CAGTTTCTTATCTTCCATGTCATCTTG 58.604 37.037 0.00 0.00 0.00 3.02
316 317 8.105829 AGTTTCTTATCTTCCATGTCATCTTGT 58.894 33.333 0.00 0.00 0.00 3.16
317 318 7.854557 TTCTTATCTTCCATGTCATCTTGTG 57.145 36.000 0.00 0.00 0.00 3.33
318 319 7.186570 TCTTATCTTCCATGTCATCTTGTGA 57.813 36.000 0.00 0.00 0.00 3.58
329 330 4.001618 TCATCTTGTGACCGAAATGACA 57.998 40.909 0.00 0.00 0.00 3.58
330 331 4.384940 TCATCTTGTGACCGAAATGACAA 58.615 39.130 0.00 0.00 0.00 3.18
331 332 5.003160 TCATCTTGTGACCGAAATGACAAT 58.997 37.500 0.00 0.00 0.00 2.71
332 333 4.747540 TCTTGTGACCGAAATGACAATG 57.252 40.909 0.00 0.00 0.00 2.82
333 334 4.133820 TCTTGTGACCGAAATGACAATGT 58.866 39.130 0.00 0.00 0.00 2.71
334 335 4.578516 TCTTGTGACCGAAATGACAATGTT 59.421 37.500 0.00 0.00 0.00 2.71
335 336 5.760743 TCTTGTGACCGAAATGACAATGTTA 59.239 36.000 0.00 0.00 0.00 2.41
336 337 5.351233 TGTGACCGAAATGACAATGTTAC 57.649 39.130 0.00 0.00 0.00 2.50
337 338 4.816925 TGTGACCGAAATGACAATGTTACA 59.183 37.500 0.00 0.00 0.00 2.41
338 339 5.297029 TGTGACCGAAATGACAATGTTACAA 59.703 36.000 0.00 0.00 0.00 2.41
339 340 6.016693 TGTGACCGAAATGACAATGTTACAAT 60.017 34.615 0.00 0.00 0.00 2.71
340 341 6.523201 GTGACCGAAATGACAATGTTACAATC 59.477 38.462 0.00 0.00 0.00 2.67
341 342 5.949735 ACCGAAATGACAATGTTACAATCC 58.050 37.500 0.00 0.00 0.00 3.01
342 343 5.475220 ACCGAAATGACAATGTTACAATCCA 59.525 36.000 0.00 0.00 0.00 3.41
343 344 6.029607 CCGAAATGACAATGTTACAATCCAG 58.970 40.000 0.00 0.00 0.00 3.86
344 345 5.512788 CGAAATGACAATGTTACAATCCAGC 59.487 40.000 0.00 0.00 0.00 4.85
345 346 5.981088 AATGACAATGTTACAATCCAGCA 57.019 34.783 0.00 0.00 0.00 4.41
346 347 5.981088 ATGACAATGTTACAATCCAGCAA 57.019 34.783 0.00 0.00 0.00 3.91
347 348 5.981088 TGACAATGTTACAATCCAGCAAT 57.019 34.783 0.00 0.00 0.00 3.56
348 349 5.953183 TGACAATGTTACAATCCAGCAATC 58.047 37.500 0.00 0.00 0.00 2.67
349 350 5.476254 TGACAATGTTACAATCCAGCAATCA 59.524 36.000 0.00 0.00 0.00 2.57
350 351 6.153170 TGACAATGTTACAATCCAGCAATCAT 59.847 34.615 0.00 0.00 0.00 2.45
351 352 6.334989 ACAATGTTACAATCCAGCAATCATG 58.665 36.000 0.00 0.00 0.00 3.07
367 368 2.646930 TCATGCTTTCAGGCAATCGAT 58.353 42.857 0.00 0.00 45.68 3.59
400 401 3.520696 TCTTCCATGTCCTTTCCTCTGA 58.479 45.455 0.00 0.00 0.00 3.27
403 404 2.568956 TCCATGTCCTTTCCTCTGACTG 59.431 50.000 0.00 0.00 0.00 3.51
405 406 3.594134 CATGTCCTTTCCTCTGACTGTC 58.406 50.000 0.00 0.00 0.00 3.51
408 724 3.322254 TGTCCTTTCCTCTGACTGTCTTC 59.678 47.826 9.51 0.00 0.00 2.87
419 735 4.765339 TCTGACTGTCTTCTGACCGAAATA 59.235 41.667 9.51 0.00 42.28 1.40
436 752 6.128007 ACCGAAATAACAATGTCACAATCCTC 60.128 38.462 0.00 0.00 0.00 3.71
438 754 6.094048 CGAAATAACAATGTCACAATCCTCCT 59.906 38.462 0.00 0.00 0.00 3.69
441 757 4.213564 ACAATGTCACAATCCTCCTCTC 57.786 45.455 0.00 0.00 0.00 3.20
484 803 2.175530 ACGTCGATAGTCTTTGCTCG 57.824 50.000 0.00 0.00 37.40 5.03
492 811 1.221414 AGTCTTTGCTCGCTCACAAC 58.779 50.000 0.00 0.00 0.00 3.32
549 869 6.196079 AGCTTTTGATTTCGTATCCTTTCC 57.804 37.500 0.00 0.00 0.00 3.13
556 876 8.662781 TTGATTTCGTATCCTTTCCTTCATAG 57.337 34.615 0.00 0.00 0.00 2.23
557 877 7.792032 TGATTTCGTATCCTTTCCTTCATAGT 58.208 34.615 0.00 0.00 0.00 2.12
558 878 8.920174 TGATTTCGTATCCTTTCCTTCATAGTA 58.080 33.333 0.00 0.00 0.00 1.82
561 881 7.834881 TCGTATCCTTTCCTTCATAGTACAT 57.165 36.000 0.00 0.00 0.00 2.29
594 914 9.354673 TCTAAAATCAATCTTTCAAACTCCTGT 57.645 29.630 0.00 0.00 0.00 4.00
597 917 6.749923 ATCAATCTTTCAAACTCCTGTAGC 57.250 37.500 0.00 0.00 0.00 3.58
598 918 5.620206 TCAATCTTTCAAACTCCTGTAGCA 58.380 37.500 0.00 0.00 0.00 3.49
599 919 6.061441 TCAATCTTTCAAACTCCTGTAGCAA 58.939 36.000 0.00 0.00 0.00 3.91
600 920 5.948992 ATCTTTCAAACTCCTGTAGCAAC 57.051 39.130 0.00 0.00 0.00 4.17
601 921 3.807622 TCTTTCAAACTCCTGTAGCAACG 59.192 43.478 0.00 0.00 0.00 4.10
602 922 2.902705 TCAAACTCCTGTAGCAACGT 57.097 45.000 0.00 0.00 0.00 3.99
617 937 1.608590 CAACGTGCAGGGAAAATCACT 59.391 47.619 11.67 0.00 0.00 3.41
620 940 2.038557 ACGTGCAGGGAAAATCACTAGT 59.961 45.455 11.67 0.00 0.00 2.57
623 943 4.876107 CGTGCAGGGAAAATCACTAGTATT 59.124 41.667 0.00 0.00 0.00 1.89
625 985 6.128007 CGTGCAGGGAAAATCACTAGTATTTT 60.128 38.462 16.34 16.34 38.82 1.82
627 987 8.398665 GTGCAGGGAAAATCACTAGTATTTTAG 58.601 37.037 16.35 11.16 36.82 1.85
629 989 8.613482 GCAGGGAAAATCACTAGTATTTTAGAC 58.387 37.037 16.35 12.13 36.82 2.59
630 990 9.892130 CAGGGAAAATCACTAGTATTTTAGACT 57.108 33.333 16.35 13.26 36.82 3.24
675 1039 1.301677 TTACACGCGCCAATCATGCA 61.302 50.000 5.73 0.00 0.00 3.96
810 1176 4.645136 GTCACAATCCTCCCCTTAATTTCC 59.355 45.833 0.00 0.00 0.00 3.13
822 1188 3.259064 CTTAATTTCCTTCTCCGTCGCA 58.741 45.455 0.00 0.00 0.00 5.10
823 1189 1.439679 AATTTCCTTCTCCGTCGCAC 58.560 50.000 0.00 0.00 0.00 5.34
856 1223 8.976986 AGCTCAATAAACTGAAATCAATCAAC 57.023 30.769 0.00 0.00 0.00 3.18
904 1276 3.361977 GCGTGCGGTCCAAACCAT 61.362 61.111 0.00 0.00 46.86 3.55
1016 1391 4.716784 AGTAAGCATGAGAACTATGACCCA 59.283 41.667 0.00 0.00 0.00 4.51
1058 1442 4.265056 GGTGGCCGTGGTCTTGGT 62.265 66.667 0.00 0.00 0.00 3.67
1173 1566 1.108776 TGTACTCCGGCTACATCACC 58.891 55.000 0.00 0.00 0.00 4.02
1393 1786 2.663196 GTAGGTGCCCAGTCGCTT 59.337 61.111 0.00 0.00 0.00 4.68
1394 1787 1.741770 GTAGGTGCCCAGTCGCTTG 60.742 63.158 0.00 0.00 0.00 4.01
1395 1788 3.605749 TAGGTGCCCAGTCGCTTGC 62.606 63.158 0.00 0.00 0.00 4.01
1422 2500 2.159960 GCTTGATCGACGTCACTGTTTC 60.160 50.000 17.16 3.23 0.00 2.78
1452 2530 4.202357 TGCGCTTCTAATGGTGGAGAATAT 60.202 41.667 9.73 0.00 31.45 1.28
1455 2533 6.572509 GCGCTTCTAATGGTGGAGAATATCTA 60.573 42.308 0.00 0.00 31.45 1.98
1456 2534 7.378966 CGCTTCTAATGGTGGAGAATATCTAA 58.621 38.462 0.00 0.00 31.45 2.10
1457 2535 7.872993 CGCTTCTAATGGTGGAGAATATCTAAA 59.127 37.037 0.00 0.00 31.45 1.85
1458 2536 9.732130 GCTTCTAATGGTGGAGAATATCTAAAT 57.268 33.333 0.00 0.00 31.45 1.40
1530 2610 2.633481 GTTCTCCTACACCAACACCTCT 59.367 50.000 0.00 0.00 0.00 3.69
1965 3057 0.666274 TCTGCAACATCACGTCGTCC 60.666 55.000 0.00 0.00 0.00 4.79
1975 3067 2.501222 CGTCGTCCTCGTCGTTGG 60.501 66.667 0.00 0.00 41.73 3.77
1977 3069 4.394078 TCGTCCTCGTCGTTGGCG 62.394 66.667 4.77 4.77 38.33 5.69
2041 3156 4.702081 AGACTCCGTGCGTGCGTC 62.702 66.667 0.00 0.00 0.00 5.19
2045 3160 4.325304 TCCGTGCGTGCGTCGTTA 62.325 61.111 0.00 0.00 42.13 3.18
2046 3161 3.176578 CCGTGCGTGCGTCGTTAT 61.177 61.111 0.00 0.00 42.13 1.89
2072 3187 3.491276 CCATGCTGCTTTTTGAAGTGACA 60.491 43.478 0.00 0.00 0.00 3.58
2116 3231 4.489771 CCATGGCTGACCGGGTCC 62.490 72.222 23.81 10.47 39.70 4.46
2302 3417 0.745845 ACAGGGAGCTTATTGCAGCG 60.746 55.000 0.00 0.00 45.24 5.18
2308 3423 2.838974 GCTTATTGCAGCGGGCCTC 61.839 63.158 0.84 0.00 43.89 4.70
2320 3435 1.380380 GGGCCTCAGGATTTGGGTG 60.380 63.158 0.84 0.00 0.00 4.61
2332 3447 2.341846 TTTGGGTGTTCAGGTCAGAC 57.658 50.000 0.00 0.00 0.00 3.51
2344 3459 4.168101 TCAGGTCAGACCATTCCTAGTTT 58.832 43.478 22.31 0.00 41.95 2.66
2347 3462 4.162509 AGGTCAGACCATTCCTAGTTTAGC 59.837 45.833 22.31 0.00 41.95 3.09
2418 3702 4.686554 ACACGTTTGCTTCAGTAATCTCTC 59.313 41.667 0.00 0.00 0.00 3.20
2421 3705 5.349817 ACGTTTGCTTCAGTAATCTCTCATG 59.650 40.000 0.00 0.00 0.00 3.07
2423 3707 6.257411 CGTTTGCTTCAGTAATCTCTCATGAT 59.743 38.462 0.00 0.00 0.00 2.45
2424 3708 7.408123 GTTTGCTTCAGTAATCTCTCATGATG 58.592 38.462 0.00 0.00 0.00 3.07
2425 3709 6.475596 TGCTTCAGTAATCTCTCATGATGA 57.524 37.500 0.00 0.00 0.00 2.92
2426 3710 6.514063 TGCTTCAGTAATCTCTCATGATGAG 58.486 40.000 16.15 16.15 45.59 2.90
2444 3728 2.269172 GAGCTGTTTCGCTAGGGTAAC 58.731 52.381 18.54 18.54 41.08 2.50
2468 3884 7.778083 ACCTTTAACCTTTTCTTTTGACGAAT 58.222 30.769 0.00 0.00 0.00 3.34
2540 3958 3.670359 GCGTATGCATCGGGTTATACGTA 60.670 47.826 0.19 0.00 45.92 3.57
2592 4010 7.945033 TGTCTTGAATTTTAGGACATTTTGC 57.055 32.000 2.54 0.00 32.91 3.68
2612 4032 3.330701 TGCTCTTCCATTTTAGGACACCT 59.669 43.478 0.00 0.00 37.42 4.00
2614 4034 4.876679 GCTCTTCCATTTTAGGACACCTAC 59.123 45.833 0.00 0.00 35.63 3.18
2615 4035 5.429130 CTCTTCCATTTTAGGACACCTACC 58.571 45.833 0.00 0.00 35.63 3.18
2637 4156 6.889198 ACCTACTCTGCATATTAGCTTTGAA 58.111 36.000 0.00 0.00 34.99 2.69
2643 4162 7.076842 TCTGCATATTAGCTTTGAACAAGTC 57.923 36.000 0.00 0.00 34.99 3.01
2644 4163 6.881065 TCTGCATATTAGCTTTGAACAAGTCT 59.119 34.615 0.00 0.00 34.99 3.24
2647 4166 8.615211 TGCATATTAGCTTTGAACAAGTCTATG 58.385 33.333 0.00 0.00 34.99 2.23
2648 4167 8.072567 GCATATTAGCTTTGAACAAGTCTATGG 58.927 37.037 0.00 0.00 0.00 2.74
2649 4168 8.562892 CATATTAGCTTTGAACAAGTCTATGGG 58.437 37.037 0.00 0.00 0.00 4.00
2668 4213 9.967451 TCTATGGGAAATAATACAAACTTCACA 57.033 29.630 0.00 0.00 34.15 3.58
2732 4297 7.984050 TGTATTGATTTGTTGTTGTGGATGTTT 59.016 29.630 0.00 0.00 0.00 2.83
2733 4298 6.659361 TTGATTTGTTGTTGTGGATGTTTG 57.341 33.333 0.00 0.00 0.00 2.93
2822 4393 9.752961 GGTAAGCTACCTACAAAAATTTGAAAA 57.247 29.630 12.54 0.00 45.52 2.29
2920 4491 6.367969 CAGTACTAAATGACAACAGGTACACC 59.632 42.308 0.00 0.00 33.00 4.16
2975 4644 4.776349 TCAGCCAGTTAACAAGAGAAACA 58.224 39.130 8.61 0.00 0.00 2.83
2981 4650 5.049818 CCAGTTAACAAGAGAAACAGCAGAG 60.050 44.000 8.61 0.00 0.00 3.35
3001 4670 2.812591 AGAATGCACTGCTTTGACTGAG 59.187 45.455 6.87 0.00 0.00 3.35
3078 4754 8.506921 TCCACATTTATTCATAACATTCCCCTA 58.493 33.333 0.00 0.00 0.00 3.53
3102 4778 4.331968 TGACCCGTCAGCTCAAAATTAAT 58.668 39.130 0.00 0.00 34.14 1.40
3138 4814 1.409381 CCCTGGGCATCTCTTTTCCTC 60.409 57.143 0.00 0.00 0.00 3.71
3154 4830 1.754803 TCCTCACATAATTCGCGTCCT 59.245 47.619 5.77 0.00 0.00 3.85
3264 4975 4.389992 AGCTGACGTTGTTGTTGATCTATG 59.610 41.667 0.00 0.00 0.00 2.23
3343 5054 1.231221 TGTGTTTATTTCGCAGCGGT 58.769 45.000 16.42 4.18 0.00 5.68
3393 5104 0.389391 ACAAGATACTCCATCGGCGG 59.611 55.000 7.21 0.00 38.81 6.13
3513 5224 4.774660 AGAATCATTGAGATGCTCTGGT 57.225 40.909 0.00 0.00 38.28 4.00
3518 5229 0.674581 TTGAGATGCTCTGGTTGGCG 60.675 55.000 0.00 0.00 0.00 5.69
3530 5241 0.170339 GGTTGGCGTGCAAATAGACC 59.830 55.000 0.00 0.00 0.00 3.85
3541 5253 4.096382 GTGCAAATAGACCACATAACAGGG 59.904 45.833 0.00 0.00 0.00 4.45
3587 5299 7.989741 CCTTCTCCTATCATTTTCTTAGCTTGA 59.010 37.037 0.00 0.00 0.00 3.02
3638 5355 2.566833 TTACACTCCTGCATGCAACT 57.433 45.000 22.88 0.85 0.00 3.16
3658 5375 6.389091 CAACTTGCCAGCAAACATTTAGATA 58.611 36.000 6.52 0.00 35.33 1.98
3670 5387 9.173939 GCAAACATTTAGATATCACATTAGTGC 57.826 33.333 5.32 2.23 45.49 4.40
3687 5404 9.294030 ACATTAGTGCGTGTTATTAACTACTAC 57.706 33.333 7.99 3.28 0.00 2.73
3743 5460 3.191371 GTGATGGATTTGTTGACCAGGTC 59.809 47.826 13.35 13.35 37.12 3.85
3797 5514 2.048127 GTGTCCGTCAGAGGTGCC 60.048 66.667 0.00 0.00 0.00 5.01
3818 5535 1.616921 CCATGAGGTTCCCCTGCAT 59.383 57.895 0.00 0.00 42.86 3.96
3847 5564 0.091344 CAAGCGCTCGTACTGTTTCG 59.909 55.000 12.06 0.00 0.00 3.46
3864 5581 2.125106 GGTACTTCCTGCAGGGCG 60.125 66.667 32.23 23.86 35.41 6.13
3887 5604 2.050350 CATGCCAGGCCAGACCAAG 61.050 63.158 9.64 0.00 43.14 3.61
3944 5665 8.879759 GGAAGTCAAATAGTAATTTCGATGTGA 58.120 33.333 0.00 0.00 32.87 3.58
3945 5666 9.907576 GAAGTCAAATAGTAATTTCGATGTGAG 57.092 33.333 0.00 0.00 32.87 3.51
4022 5748 9.301897 CCTGGATAGCTAGTATATATGCACATA 57.698 37.037 0.00 0.00 0.00 2.29
4054 5793 6.706055 GATTTATCGAGAATATGGACGCAA 57.294 37.500 0.00 0.00 0.00 4.85
4055 5794 7.117241 GATTTATCGAGAATATGGACGCAAA 57.883 36.000 0.00 0.00 0.00 3.68
4056 5795 6.525121 TTTATCGAGAATATGGACGCAAAG 57.475 37.500 0.00 0.00 0.00 2.77
4057 5796 2.201732 TCGAGAATATGGACGCAAAGC 58.798 47.619 0.00 0.00 0.00 3.51
4058 5797 1.933181 CGAGAATATGGACGCAAAGCA 59.067 47.619 0.00 0.00 0.00 3.91
4059 5798 2.285834 CGAGAATATGGACGCAAAGCAC 60.286 50.000 0.00 0.00 0.00 4.40
4060 5799 2.017049 AGAATATGGACGCAAAGCACC 58.983 47.619 0.00 0.00 0.00 5.01
4061 5800 1.742831 GAATATGGACGCAAAGCACCA 59.257 47.619 7.21 7.21 38.48 4.17
4062 5801 1.832883 ATATGGACGCAAAGCACCAA 58.167 45.000 8.49 1.44 37.91 3.67
4063 5802 0.878416 TATGGACGCAAAGCACCAAC 59.122 50.000 8.49 0.00 37.91 3.77
4121 5862 4.080969 ACAGACTTGATACGAACGACTC 57.919 45.455 0.14 0.00 0.00 3.36
4152 5893 6.347483 CCGATAAGATTGATGTCTCTGCAATG 60.347 42.308 0.00 0.00 32.80 2.82
4155 5896 6.829229 AAGATTGATGTCTCTGCAATGAAA 57.171 33.333 0.00 0.00 32.80 2.69
4181 5922 8.345565 AGTTTAAGTAGCAACATCAAAACAGAG 58.654 33.333 0.00 0.00 0.00 3.35
4184 5925 3.996150 AGCAACATCAAAACAGAGTGG 57.004 42.857 0.00 0.00 0.00 4.00
4191 5932 1.490490 TCAAAACAGAGTGGCAGGAGT 59.510 47.619 0.00 0.00 0.00 3.85
4193 5934 2.689983 CAAAACAGAGTGGCAGGAGTTT 59.310 45.455 0.00 0.00 0.00 2.66
4195 5936 0.398318 ACAGAGTGGCAGGAGTTTCC 59.602 55.000 0.00 0.00 36.58 3.13
4211 5952 3.117663 AGTTTCCCTCACCAGCAACTTAA 60.118 43.478 0.00 0.00 0.00 1.85
4216 5957 4.162320 TCCCTCACCAGCAACTTAAGATAG 59.838 45.833 10.09 0.00 0.00 2.08
4217 5958 3.873952 CCTCACCAGCAACTTAAGATAGC 59.126 47.826 10.09 9.69 0.00 2.97
4244 5985 6.090358 GTGTAATCTTAAGAAGTTGCACGCTA 59.910 38.462 18.23 0.00 31.57 4.26
4285 6026 4.411256 TGTAAGGAAGAAAACTGGACGT 57.589 40.909 0.00 0.00 0.00 4.34
4292 6033 0.947180 GAAAACTGGACGTAGCCGCA 60.947 55.000 0.00 0.00 37.70 5.69
4352 6093 0.246086 CCGCCTTGGCAAAGCAATTA 59.754 50.000 19.90 0.00 31.51 1.40
4408 6149 2.516888 CCACAGGACCTCCGGTTGT 61.517 63.158 0.00 0.00 41.69 3.32
4469 6210 0.725784 CCGCATTGACACTTTCACGC 60.726 55.000 0.00 0.00 32.26 5.34
4502 6243 5.661458 TCACCTCTAAGTAGCATACAAAGC 58.339 41.667 0.00 0.00 46.26 3.51
4560 6301 1.242076 AATGTCTGCACCAAGACTGC 58.758 50.000 5.54 0.00 45.69 4.40
4561 6302 0.109153 ATGTCTGCACCAAGACTGCA 59.891 50.000 5.54 0.00 45.69 4.41
4605 6347 1.738350 CAGAAGCATGAACAGCAGGAG 59.262 52.381 0.00 0.00 0.00 3.69
4650 6392 8.045507 TCGGAAGTAGACTACTCATTCTCTAAA 58.954 37.037 15.49 0.00 38.26 1.85
4662 6404 7.965045 ACTCATTCTCTAAAAGACGCAATAAC 58.035 34.615 0.00 0.00 32.27 1.89
4709 6451 5.955488 TGAAATTCGTTTCAGAAACCAACA 58.045 33.333 18.58 5.91 38.14 3.33
4722 6464 8.001881 TCAGAAACCAACAGCTTAACAAAATA 57.998 30.769 0.00 0.00 0.00 1.40
4723 6465 8.470805 TCAGAAACCAACAGCTTAACAAAATAA 58.529 29.630 0.00 0.00 0.00 1.40
4724 6466 8.539674 CAGAAACCAACAGCTTAACAAAATAAC 58.460 33.333 0.00 0.00 0.00 1.89
4725 6467 8.254508 AGAAACCAACAGCTTAACAAAATAACA 58.745 29.630 0.00 0.00 0.00 2.41
4726 6468 8.779354 AAACCAACAGCTTAACAAAATAACAA 57.221 26.923 0.00 0.00 0.00 2.83
4855 6598 2.293677 TTGCACTCTACCTACATGCG 57.706 50.000 0.00 0.00 39.18 4.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.596600 CGTGTACGCTTCACCACAGT 60.597 55.000 4.67 0.00 32.86 3.55
1 2 2.141781 CGTGTACGCTTCACCACAG 58.858 57.895 4.67 0.00 32.86 3.66
2 3 4.329619 CGTGTACGCTTCACCACA 57.670 55.556 4.67 0.00 32.86 4.17
12 13 5.013236 GTGAACAAAGAATATGCGTGTACG 58.987 41.667 0.00 0.00 43.27 3.67
13 14 6.128661 TGAGTGAACAAAGAATATGCGTGTAC 60.129 38.462 0.00 0.00 0.00 2.90
14 15 5.929415 TGAGTGAACAAAGAATATGCGTGTA 59.071 36.000 0.00 0.00 0.00 2.90
15 16 4.754618 TGAGTGAACAAAGAATATGCGTGT 59.245 37.500 0.00 0.00 0.00 4.49
16 17 5.082059 GTGAGTGAACAAAGAATATGCGTG 58.918 41.667 0.00 0.00 0.00 5.34
17 18 4.754618 TGTGAGTGAACAAAGAATATGCGT 59.245 37.500 0.00 0.00 0.00 5.24
18 19 5.281693 TGTGAGTGAACAAAGAATATGCG 57.718 39.130 0.00 0.00 0.00 4.73
19 20 5.182001 ACCTGTGAGTGAACAAAGAATATGC 59.818 40.000 0.00 0.00 0.00 3.14
20 21 6.605849 CACCTGTGAGTGAACAAAGAATATG 58.394 40.000 0.00 0.00 40.34 1.78
21 22 5.182001 GCACCTGTGAGTGAACAAAGAATAT 59.818 40.000 0.51 0.00 40.34 1.28
22 23 4.515191 GCACCTGTGAGTGAACAAAGAATA 59.485 41.667 0.51 0.00 40.34 1.75
23 24 3.316308 GCACCTGTGAGTGAACAAAGAAT 59.684 43.478 0.51 0.00 40.34 2.40
24 25 2.682856 GCACCTGTGAGTGAACAAAGAA 59.317 45.455 0.51 0.00 40.34 2.52
25 26 2.288666 GCACCTGTGAGTGAACAAAGA 58.711 47.619 0.51 0.00 40.34 2.52
26 27 2.016318 TGCACCTGTGAGTGAACAAAG 58.984 47.619 0.51 0.00 40.34 2.77
27 28 2.121291 TGCACCTGTGAGTGAACAAA 57.879 45.000 0.51 0.00 40.34 2.83
28 29 2.016318 CTTGCACCTGTGAGTGAACAA 58.984 47.619 0.51 0.00 40.34 2.83
29 30 1.667236 CTTGCACCTGTGAGTGAACA 58.333 50.000 0.51 0.00 40.34 3.18
30 31 0.308993 GCTTGCACCTGTGAGTGAAC 59.691 55.000 0.51 0.00 40.34 3.18
31 32 0.107263 TGCTTGCACCTGTGAGTGAA 60.107 50.000 0.51 0.00 40.34 3.18
32 33 0.109153 ATGCTTGCACCTGTGAGTGA 59.891 50.000 0.51 0.00 40.34 3.41
33 34 0.240145 CATGCTTGCACCTGTGAGTG 59.760 55.000 0.51 0.00 40.88 3.51
34 35 0.892358 CCATGCTTGCACCTGTGAGT 60.892 55.000 0.51 0.00 0.00 3.41
35 36 0.607217 TCCATGCTTGCACCTGTGAG 60.607 55.000 0.51 0.00 0.00 3.51
36 37 0.178995 TTCCATGCTTGCACCTGTGA 60.179 50.000 0.51 0.00 0.00 3.58
37 38 0.038892 GTTCCATGCTTGCACCTGTG 60.039 55.000 0.00 0.00 0.00 3.66
38 39 0.467844 TGTTCCATGCTTGCACCTGT 60.468 50.000 0.00 0.00 0.00 4.00
39 40 0.892755 ATGTTCCATGCTTGCACCTG 59.107 50.000 0.00 0.00 0.00 4.00
40 41 1.636148 AATGTTCCATGCTTGCACCT 58.364 45.000 0.00 0.00 0.00 4.00
41 42 2.460757 AAATGTTCCATGCTTGCACC 57.539 45.000 0.00 0.00 0.00 5.01
42 43 3.187022 GGAAAAATGTTCCATGCTTGCAC 59.813 43.478 0.00 0.00 38.45 4.57
43 44 3.181457 TGGAAAAATGTTCCATGCTTGCA 60.181 39.130 0.00 0.00 43.17 4.08
44 45 3.401182 TGGAAAAATGTTCCATGCTTGC 58.599 40.909 0.00 0.00 43.17 4.01
126 127 6.418819 GCGCATTGCTATGTGAATTTAAAGAT 59.581 34.615 23.04 0.00 43.45 2.40
138 139 2.884997 TTCCCCGCGCATTGCTATGT 62.885 55.000 8.75 0.00 43.27 2.29
150 151 0.466124 ACTGCTAGAGATTTCCCCGC 59.534 55.000 0.00 0.00 0.00 6.13
174 175 7.094592 TGGCACGTGAAAAATGACATAGATTTA 60.095 33.333 22.23 0.00 0.00 1.40
180 181 4.457257 TGATGGCACGTGAAAAATGACATA 59.543 37.500 22.23 0.00 42.26 2.29
229 230 9.945904 ATAGTCCGTTTCTAATCTTTCTCTTTT 57.054 29.630 0.00 0.00 0.00 2.27
230 231 9.945904 AATAGTCCGTTTCTAATCTTTCTCTTT 57.054 29.630 0.00 0.00 0.00 2.52
310 311 4.761739 ACATTGTCATTTCGGTCACAAGAT 59.238 37.500 0.00 0.00 32.44 2.40
312 313 4.488126 ACATTGTCATTTCGGTCACAAG 57.512 40.909 0.00 0.00 32.44 3.16
314 315 4.816925 TGTAACATTGTCATTTCGGTCACA 59.183 37.500 0.00 0.00 0.00 3.58
315 316 5.351233 TGTAACATTGTCATTTCGGTCAC 57.649 39.130 0.00 0.00 0.00 3.67
316 317 6.348950 GGATTGTAACATTGTCATTTCGGTCA 60.349 38.462 0.00 0.00 0.00 4.02
317 318 6.027749 GGATTGTAACATTGTCATTTCGGTC 58.972 40.000 0.00 0.00 0.00 4.79
318 319 5.475220 TGGATTGTAACATTGTCATTTCGGT 59.525 36.000 0.00 0.00 0.00 4.69
319 320 5.948588 TGGATTGTAACATTGTCATTTCGG 58.051 37.500 0.00 0.00 0.00 4.30
320 321 5.512788 GCTGGATTGTAACATTGTCATTTCG 59.487 40.000 0.00 0.00 0.00 3.46
321 322 6.389091 TGCTGGATTGTAACATTGTCATTTC 58.611 36.000 0.00 0.00 0.00 2.17
322 323 6.343716 TGCTGGATTGTAACATTGTCATTT 57.656 33.333 0.00 0.00 0.00 2.32
323 324 5.981088 TGCTGGATTGTAACATTGTCATT 57.019 34.783 0.00 0.00 0.00 2.57
324 325 5.981088 TTGCTGGATTGTAACATTGTCAT 57.019 34.783 0.00 0.00 0.00 3.06
325 326 5.476254 TGATTGCTGGATTGTAACATTGTCA 59.524 36.000 0.00 0.00 0.00 3.58
326 327 5.953183 TGATTGCTGGATTGTAACATTGTC 58.047 37.500 0.00 0.00 0.00 3.18
327 328 5.981088 TGATTGCTGGATTGTAACATTGT 57.019 34.783 0.00 0.00 0.00 2.71
328 329 5.233476 GCATGATTGCTGGATTGTAACATTG 59.767 40.000 0.00 0.00 45.77 2.82
329 330 5.353938 GCATGATTGCTGGATTGTAACATT 58.646 37.500 0.00 0.00 45.77 2.71
330 331 4.940463 GCATGATTGCTGGATTGTAACAT 58.060 39.130 0.00 0.00 45.77 2.71
331 332 4.374843 GCATGATTGCTGGATTGTAACA 57.625 40.909 0.00 0.00 45.77 2.41
344 345 3.113322 CGATTGCCTGAAAGCATGATTG 58.887 45.455 0.00 0.00 43.64 2.67
345 346 3.018856 TCGATTGCCTGAAAGCATGATT 58.981 40.909 0.00 0.00 43.64 2.57
346 347 2.646930 TCGATTGCCTGAAAGCATGAT 58.353 42.857 0.00 0.00 43.64 2.45
347 348 2.112380 TCGATTGCCTGAAAGCATGA 57.888 45.000 0.00 0.00 43.64 3.07
348 349 3.313249 TGTATCGATTGCCTGAAAGCATG 59.687 43.478 1.71 0.00 43.64 4.06
349 350 3.544684 TGTATCGATTGCCTGAAAGCAT 58.455 40.909 1.71 0.00 43.64 3.79
350 351 2.938451 CTGTATCGATTGCCTGAAAGCA 59.062 45.455 1.71 0.00 42.17 3.91
351 352 2.939103 ACTGTATCGATTGCCTGAAAGC 59.061 45.455 1.71 0.00 0.00 3.51
352 353 5.352569 AGAAACTGTATCGATTGCCTGAAAG 59.647 40.000 1.71 0.00 0.00 2.62
353 354 5.245531 AGAAACTGTATCGATTGCCTGAAA 58.754 37.500 1.71 0.00 0.00 2.69
354 355 4.832248 AGAAACTGTATCGATTGCCTGAA 58.168 39.130 1.71 0.00 0.00 3.02
355 356 4.471904 AGAAACTGTATCGATTGCCTGA 57.528 40.909 1.71 0.00 0.00 3.86
356 357 6.703607 AGATAAGAAACTGTATCGATTGCCTG 59.296 38.462 1.71 0.00 32.90 4.85
367 368 7.496346 AGGACATGGAAGATAAGAAACTGTA 57.504 36.000 0.00 0.00 0.00 2.74
400 401 5.209818 TGTTATTTCGGTCAGAAGACAGT 57.790 39.130 0.00 0.00 46.80 3.55
403 404 6.147164 TGACATTGTTATTTCGGTCAGAAGAC 59.853 38.462 0.00 0.00 44.21 3.01
405 406 6.073276 TGTGACATTGTTATTTCGGTCAGAAG 60.073 38.462 0.00 0.00 40.40 2.85
408 724 5.605564 TGTGACATTGTTATTTCGGTCAG 57.394 39.130 0.00 0.00 36.10 3.51
419 735 4.042062 TGAGAGGAGGATTGTGACATTGTT 59.958 41.667 0.00 0.00 0.00 2.83
436 752 7.133891 ACGACAGAAACAATAAATTGAGAGG 57.866 36.000 9.60 0.00 40.14 3.69
438 754 8.827177 ACTACGACAGAAACAATAAATTGAGA 57.173 30.769 9.60 0.00 40.14 3.27
469 788 1.849219 GTGAGCGAGCAAAGACTATCG 59.151 52.381 0.00 0.00 38.19 2.92
474 793 0.111089 CGTTGTGAGCGAGCAAAGAC 60.111 55.000 0.00 0.00 0.00 3.01
484 803 3.469899 TGTTTCATATGCGTTGTGAGC 57.530 42.857 0.00 0.00 0.00 4.26
584 904 1.069906 GCACGTTGCTACAGGAGTTTG 60.070 52.381 0.00 0.00 40.96 2.93
588 908 2.449548 CTGCACGTTGCTACAGGAG 58.550 57.895 10.54 0.00 45.31 3.69
592 912 0.179043 TTTCCCTGCACGTTGCTACA 60.179 50.000 10.54 0.00 45.31 2.74
593 913 0.948678 TTTTCCCTGCACGTTGCTAC 59.051 50.000 10.54 0.00 45.31 3.58
594 914 1.810151 GATTTTCCCTGCACGTTGCTA 59.190 47.619 10.54 0.00 45.31 3.49
595 915 0.598065 GATTTTCCCTGCACGTTGCT 59.402 50.000 10.54 0.00 45.31 3.91
596 916 0.313672 TGATTTTCCCTGCACGTTGC 59.686 50.000 3.44 3.44 45.29 4.17
597 917 1.608590 AGTGATTTTCCCTGCACGTTG 59.391 47.619 0.00 0.00 36.43 4.10
598 918 1.981256 AGTGATTTTCCCTGCACGTT 58.019 45.000 0.00 0.00 36.43 3.99
599 919 2.038557 ACTAGTGATTTTCCCTGCACGT 59.961 45.455 0.00 0.00 36.43 4.49
600 920 2.699954 ACTAGTGATTTTCCCTGCACG 58.300 47.619 0.00 0.00 36.43 5.34
601 921 6.759497 AAATACTAGTGATTTTCCCTGCAC 57.241 37.500 5.39 0.00 0.00 4.57
602 922 8.325787 TCTAAAATACTAGTGATTTTCCCTGCA 58.674 33.333 18.28 0.00 37.59 4.41
627 987 8.890718 GGACACAGGTTTATATAAGGAAAAGTC 58.109 37.037 0.00 2.88 0.00 3.01
629 989 9.462606 AAGGACACAGGTTTATATAAGGAAAAG 57.537 33.333 0.00 0.00 0.00 2.27
630 990 9.816787 AAAGGACACAGGTTTATATAAGGAAAA 57.183 29.630 0.00 0.00 0.00 2.29
631 991 9.816787 AAAAGGACACAGGTTTATATAAGGAAA 57.183 29.630 0.00 0.00 0.00 3.13
633 993 9.895138 GTAAAAGGACACAGGTTTATATAAGGA 57.105 33.333 0.00 0.00 0.00 3.36
634 994 9.675464 TGTAAAAGGACACAGGTTTATATAAGG 57.325 33.333 0.00 0.00 0.00 2.69
648 1008 1.205820 GGCGCGTGTAAAAGGACAC 59.794 57.895 8.43 0.00 45.19 3.67
675 1039 8.299570 AGCTTGTGATTTCGTTTCTAATCATTT 58.700 29.630 0.00 0.00 41.35 2.32
810 1176 1.797933 CGTGAGTGCGACGGAGAAG 60.798 63.158 0.00 0.00 33.08 2.85
822 1188 4.082190 TCAGTTTATTGAGCTAGCGTGAGT 60.082 41.667 9.55 0.00 0.00 3.41
823 1189 4.424626 TCAGTTTATTGAGCTAGCGTGAG 58.575 43.478 9.55 0.00 0.00 3.51
883 1255 1.370051 GTTTGGACCGCACGCTTTC 60.370 57.895 0.00 0.00 0.00 2.62
904 1276 4.647611 AGGGTTTGATTGATGTCGTTGTA 58.352 39.130 0.00 0.00 0.00 2.41
1047 1431 4.988598 AGCGCCACCAAGACCACG 62.989 66.667 2.29 0.00 0.00 4.94
1051 1435 3.414700 CGTCAGCGCCACCAAGAC 61.415 66.667 2.29 2.14 0.00 3.01
1393 1786 2.047370 TCGATCAAGCAAGCCGCA 60.047 55.556 0.00 0.00 46.13 5.69
1394 1787 2.401195 GTCGATCAAGCAAGCCGC 59.599 61.111 0.00 0.00 42.91 6.53
1395 1788 2.014093 GACGTCGATCAAGCAAGCCG 62.014 60.000 0.00 0.00 0.00 5.52
1396 1789 1.014044 TGACGTCGATCAAGCAAGCC 61.014 55.000 11.62 0.00 0.00 4.35
1397 1790 0.093705 GTGACGTCGATCAAGCAAGC 59.906 55.000 11.62 0.00 0.00 4.01
1422 2500 2.679837 ACCATTAGAAGCGCAACAGATG 59.320 45.455 11.47 8.11 0.00 2.90
1452 2530 2.029110 GGCCACTGCAAAGCAATTTAGA 60.029 45.455 0.00 0.00 38.41 2.10
1455 2533 0.469070 TGGCCACTGCAAAGCAATTT 59.531 45.000 0.00 0.00 38.41 1.82
1456 2534 0.469070 TTGGCCACTGCAAAGCAATT 59.531 45.000 3.88 0.00 38.41 2.32
1457 2535 0.249996 GTTGGCCACTGCAAAGCAAT 60.250 50.000 3.88 0.00 38.41 3.56
1458 2536 1.143620 GTTGGCCACTGCAAAGCAA 59.856 52.632 3.88 0.00 38.41 3.91
1459 2537 2.813901 GTTGGCCACTGCAAAGCA 59.186 55.556 3.88 0.00 40.13 3.91
1460 2538 2.355009 CGTTGGCCACTGCAAAGC 60.355 61.111 3.88 0.00 40.13 3.51
1530 2610 1.100510 CGGAGGTGTAGATGTCGGAA 58.899 55.000 0.00 0.00 0.00 4.30
1698 2778 1.960689 AGGTTGATGACGGGGTTTTTG 59.039 47.619 0.00 0.00 0.00 2.44
1701 2781 0.768622 TGAGGTTGATGACGGGGTTT 59.231 50.000 0.00 0.00 0.00 3.27
2041 3156 0.466189 AAGCAGCATGGGGGATAACG 60.466 55.000 0.00 0.00 35.86 3.18
2042 3157 1.780503 AAAGCAGCATGGGGGATAAC 58.219 50.000 0.00 0.00 35.86 1.89
2043 3158 2.500910 CAAAAAGCAGCATGGGGGATAA 59.499 45.455 0.00 0.00 35.86 1.75
2044 3159 2.109774 CAAAAAGCAGCATGGGGGATA 58.890 47.619 0.00 0.00 35.86 2.59
2045 3160 0.906775 CAAAAAGCAGCATGGGGGAT 59.093 50.000 0.00 0.00 35.86 3.85
2046 3161 0.178938 TCAAAAAGCAGCATGGGGGA 60.179 50.000 0.00 0.00 35.86 4.81
2113 3228 2.126189 GTGCACGGGTCGTAGGAC 60.126 66.667 0.00 7.03 38.32 3.85
2134 3249 2.434185 TACGCCGTCGAGTACCGT 60.434 61.111 0.00 5.80 39.75 4.83
2302 3417 1.380380 CACCCAAATCCTGAGGCCC 60.380 63.158 0.00 0.00 0.00 5.80
2308 3423 2.162681 GACCTGAACACCCAAATCCTG 58.837 52.381 0.00 0.00 0.00 3.86
2320 3435 3.515901 ACTAGGAATGGTCTGACCTGAAC 59.484 47.826 26.03 14.43 39.58 3.18
2332 3447 7.148086 TGCATTGTTAAGCTAAACTAGGAATGG 60.148 37.037 0.00 0.00 0.00 3.16
2344 3459 4.015764 TGCTGGAATGCATTGTTAAGCTA 58.984 39.130 18.59 8.07 38.12 3.32
2393 3677 6.398918 AGAGATTACTGAAGCAAACGTGTAT 58.601 36.000 0.00 0.00 0.00 2.29
2418 3702 2.543012 CCTAGCGAAACAGCTCATCATG 59.457 50.000 0.00 0.00 45.67 3.07
2421 3705 1.134670 ACCCTAGCGAAACAGCTCATC 60.135 52.381 0.00 0.00 45.67 2.92
2423 3707 1.552578 TACCCTAGCGAAACAGCTCA 58.447 50.000 0.00 0.00 45.67 4.26
2424 3708 2.269172 GTTACCCTAGCGAAACAGCTC 58.731 52.381 0.00 0.00 45.67 4.09
2426 3710 1.066358 AGGTTACCCTAGCGAAACAGC 60.066 52.381 0.00 0.00 40.19 4.40
2444 3728 8.642908 AATTCGTCAAAAGAAAAGGTTAAAGG 57.357 30.769 0.00 0.00 0.00 3.11
2447 3731 8.384365 GCAAAATTCGTCAAAAGAAAAGGTTAA 58.616 29.630 0.00 0.00 0.00 2.01
2448 3732 7.253817 CGCAAAATTCGTCAAAAGAAAAGGTTA 60.254 33.333 0.00 0.00 0.00 2.85
2449 3733 6.454981 CGCAAAATTCGTCAAAAGAAAAGGTT 60.455 34.615 0.00 0.00 0.00 3.50
2450 3734 5.005299 CGCAAAATTCGTCAAAAGAAAAGGT 59.995 36.000 0.00 0.00 0.00 3.50
2451 3735 5.422878 CGCAAAATTCGTCAAAAGAAAAGG 58.577 37.500 0.00 0.00 0.00 3.11
2452 3736 5.231147 TCCGCAAAATTCGTCAAAAGAAAAG 59.769 36.000 0.00 0.00 0.00 2.27
2457 3873 6.869421 AATATCCGCAAAATTCGTCAAAAG 57.131 33.333 0.00 0.00 0.00 2.27
2468 3884 6.547141 AGATTCCTGATGAAATATCCGCAAAA 59.453 34.615 0.00 0.00 36.33 2.44
2592 4010 5.189934 AGGTAGGTGTCCTAAAATGGAAGAG 59.810 44.000 0.00 0.00 37.91 2.85
2612 4032 7.597288 TCAAAGCTAATATGCAGAGTAGGTA 57.403 36.000 19.30 3.21 34.99 3.08
2614 4034 6.763135 TGTTCAAAGCTAATATGCAGAGTAGG 59.237 38.462 16.66 1.31 34.99 3.18
2615 4035 7.776933 TGTTCAAAGCTAATATGCAGAGTAG 57.223 36.000 11.29 11.29 34.99 2.57
2637 4156 9.975218 AGTTTGTATTATTTCCCATAGACTTGT 57.025 29.630 0.00 0.00 0.00 3.16
2766 4337 4.804597 ACCGCTTGGTCACAATATGTGTTA 60.805 41.667 10.03 0.00 45.05 2.41
2767 4338 4.059644 ACCGCTTGGTCACAATATGTGTT 61.060 43.478 10.03 0.00 45.05 3.32
2769 4340 2.083774 ACCGCTTGGTCACAATATGTG 58.916 47.619 4.13 4.13 45.05 3.21
2792 4363 7.328493 CAAATTTTTGTAGGTAGCTTACCAAGC 59.672 37.037 0.00 2.65 42.64 4.01
2793 4364 8.573035 TCAAATTTTTGTAGGTAGCTTACCAAG 58.427 33.333 0.00 0.00 43.62 3.61
2794 4365 8.466617 TCAAATTTTTGTAGGTAGCTTACCAA 57.533 30.769 0.00 0.00 43.62 3.67
2817 4388 9.915629 GGTTTACCACAATATGTGTTATTTTCA 57.084 29.630 9.42 0.00 46.45 2.69
2821 4392 8.113462 AGGAGGTTTACCACAATATGTGTTATT 58.887 33.333 9.42 0.00 46.45 1.40
2822 4393 7.639378 AGGAGGTTTACCACAATATGTGTTAT 58.361 34.615 9.42 0.00 46.45 1.89
2920 4491 4.925068 TGACTCATCAGTGATGTACATCG 58.075 43.478 28.03 15.16 40.55 3.84
2981 4650 2.551459 ACTCAGTCAAAGCAGTGCATTC 59.449 45.455 19.20 0.47 0.00 2.67
3001 4670 3.321497 GGTGACATCTGAGTGAGTTCAC 58.679 50.000 4.09 4.09 46.77 3.18
3016 4689 3.704800 TGTTAATTCGGATGGGTGACA 57.295 42.857 0.00 0.00 0.00 3.58
3063 4739 4.202419 CGGGTCAATAGGGGAATGTTATGA 60.202 45.833 0.00 0.00 0.00 2.15
3121 4797 1.704628 TGTGAGGAAAAGAGATGCCCA 59.295 47.619 0.00 0.00 0.00 5.36
3138 4814 1.258982 GCTGAGGACGCGAATTATGTG 59.741 52.381 15.93 0.00 0.00 3.21
3343 5054 2.969806 GACTACCGCGTCCGTGTCA 61.970 63.158 4.92 0.00 31.99 3.58
3513 5224 0.878416 GTGGTCTATTTGCACGCCAA 59.122 50.000 0.00 0.00 0.00 4.52
3518 5229 4.096382 CCCTGTTATGTGGTCTATTTGCAC 59.904 45.833 0.00 0.00 0.00 4.57
3530 5241 4.517952 TTTTCATGTGCCCTGTTATGTG 57.482 40.909 0.00 0.00 0.00 3.21
3587 5299 5.067153 TCGGCCATGTGAATCGAATTTTTAT 59.933 36.000 2.24 0.00 0.00 1.40
3589 5301 3.192422 TCGGCCATGTGAATCGAATTTTT 59.808 39.130 2.24 0.00 0.00 1.94
3590 5302 2.752354 TCGGCCATGTGAATCGAATTTT 59.248 40.909 2.24 0.00 0.00 1.82
3591 5303 2.364632 TCGGCCATGTGAATCGAATTT 58.635 42.857 2.24 0.00 0.00 1.82
3638 5355 6.152492 TGTGATATCTAAATGTTTGCTGGCAA 59.848 34.615 3.98 3.72 0.00 4.52
3658 5375 7.843490 AGTTAATAACACGCACTAATGTGAT 57.157 32.000 5.89 0.00 46.55 3.06
3670 5387 9.992910 TGACATGTAGTAGTAGTTAATAACACG 57.007 33.333 0.00 0.00 0.00 4.49
3847 5564 2.125106 CGCCCTGCAGGAAGTACC 60.125 66.667 34.91 12.93 38.24 3.34
3887 5604 2.006772 CTAAGCCACCGTCGCATTC 58.993 57.895 0.00 0.00 0.00 2.67
3945 5666 9.070149 GCTTTATTGATGATCACTCTTGTTTTC 57.930 33.333 0.00 0.00 0.00 2.29
4051 5790 0.652071 GCTTTGTGTTGGTGCTTTGC 59.348 50.000 0.00 0.00 0.00 3.68
4052 5791 1.660104 GTGCTTTGTGTTGGTGCTTTG 59.340 47.619 0.00 0.00 0.00 2.77
4053 5792 1.274728 TGTGCTTTGTGTTGGTGCTTT 59.725 42.857 0.00 0.00 0.00 3.51
4054 5793 0.894141 TGTGCTTTGTGTTGGTGCTT 59.106 45.000 0.00 0.00 0.00 3.91
4055 5794 0.894141 TTGTGCTTTGTGTTGGTGCT 59.106 45.000 0.00 0.00 0.00 4.40
4056 5795 1.719600 TTTGTGCTTTGTGTTGGTGC 58.280 45.000 0.00 0.00 0.00 5.01
4057 5796 3.583806 TCTTTTGTGCTTTGTGTTGGTG 58.416 40.909 0.00 0.00 0.00 4.17
4058 5797 3.951775 TCTTTTGTGCTTTGTGTTGGT 57.048 38.095 0.00 0.00 0.00 3.67
4059 5798 3.993081 TGTTCTTTTGTGCTTTGTGTTGG 59.007 39.130 0.00 0.00 0.00 3.77
4060 5799 4.447054 TGTGTTCTTTTGTGCTTTGTGTTG 59.553 37.500 0.00 0.00 0.00 3.33
4061 5800 4.626042 TGTGTTCTTTTGTGCTTTGTGTT 58.374 34.783 0.00 0.00 0.00 3.32
4062 5801 4.022416 TCTGTGTTCTTTTGTGCTTTGTGT 60.022 37.500 0.00 0.00 0.00 3.72
4063 5802 4.484236 TCTGTGTTCTTTTGTGCTTTGTG 58.516 39.130 0.00 0.00 0.00 3.33
4121 5862 9.085250 CAGAGACATCAATCTTATCGGAATATG 57.915 37.037 0.00 0.00 0.00 1.78
4152 5893 9.296400 TGTTTTGATGTTGCTACTTAAACTTTC 57.704 29.630 0.00 0.00 0.00 2.62
4155 5896 8.220755 TCTGTTTTGATGTTGCTACTTAAACT 57.779 30.769 0.00 0.00 0.00 2.66
4181 5922 0.606673 GTGAGGGAAACTCCTGCCAC 60.607 60.000 0.00 0.00 46.01 5.01
4184 5925 0.322008 CTGGTGAGGGAAACTCCTGC 60.322 60.000 0.00 0.00 46.01 4.85
4191 5932 3.137544 TCTTAAGTTGCTGGTGAGGGAAA 59.862 43.478 1.63 0.00 0.00 3.13
4193 5934 2.334977 TCTTAAGTTGCTGGTGAGGGA 58.665 47.619 1.63 0.00 0.00 4.20
4195 5936 3.873952 GCTATCTTAAGTTGCTGGTGAGG 59.126 47.826 1.63 0.00 0.00 3.86
4211 5952 9.593134 CAACTTCTTAAGATTACACTGCTATCT 57.407 33.333 5.89 0.00 0.00 1.98
4216 5957 6.080406 GTGCAACTTCTTAAGATTACACTGC 58.920 40.000 5.89 10.00 0.00 4.40
4217 5958 6.299604 CGTGCAACTTCTTAAGATTACACTG 58.700 40.000 15.39 8.73 31.75 3.66
4285 6026 0.461870 CATTACCAGCAGTGCGGCTA 60.462 55.000 21.05 12.30 43.68 3.93
4292 6033 3.550820 TGTTGTCAACATTACCAGCAGT 58.449 40.909 14.48 0.00 36.25 4.40
4352 6093 5.335661 GGTTATTCGGAATGCAGACACTTTT 60.336 40.000 13.37 0.00 0.00 2.27
4408 6149 1.551560 ACGAAGTATCTGGGACCACCA 60.552 52.381 0.00 0.00 45.23 4.17
4469 6210 2.695666 ACTTAGAGGTGATGATGGACGG 59.304 50.000 0.00 0.00 0.00 4.79
4502 6243 2.978824 CCCCACCTGGTACGAGTG 59.021 66.667 0.00 3.18 0.00 3.51
4560 6301 5.508153 CGTATCATTTACCCTCTGTCTCCTG 60.508 48.000 0.00 0.00 0.00 3.86
4561 6302 4.585162 CGTATCATTTACCCTCTGTCTCCT 59.415 45.833 0.00 0.00 0.00 3.69
4562 6303 4.796618 GCGTATCATTTACCCTCTGTCTCC 60.797 50.000 0.00 0.00 0.00 3.71
4605 6347 3.063997 CCGAAGTGGATAACAGCACATTC 59.936 47.826 0.00 0.00 42.00 2.67
4634 6376 6.268825 TGCGTCTTTTAGAGAATGAGTAGT 57.731 37.500 0.00 0.00 35.79 2.73
4650 6392 5.467705 ACTCTAAGAACGTTATTGCGTCTT 58.532 37.500 17.98 9.72 45.00 3.01
4662 6404 8.922676 TCAAATTTAAGCACTACTCTAAGAACG 58.077 33.333 0.00 0.00 0.00 3.95
4693 6435 3.420839 AAGCTGTTGGTTTCTGAAACG 57.579 42.857 22.80 12.32 42.29 3.60
4777 6520 8.508883 TTTAAGAGACTACCAGAGAGACATAC 57.491 38.462 0.00 0.00 0.00 2.39


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

AutoCloner maintained by Alex Coulton.