Multiple sequence alignment - TraesCS5A01G281400

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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 TraesCS5A01G281400 chr5A 100.000 5724 0 0 1 5724 490422799 490417076 0.000000e+00 10571.0
1 TraesCS5A01G281400 chr5A 81.995 1183 185 20 2994 4155 490594826 490593651 0.000000e+00 979.0
2 TraesCS5A01G281400 chr5A 80.851 1175 203 15 2992 4149 490652557 490651388 0.000000e+00 904.0
3 TraesCS5A01G281400 chr5A 81.481 972 147 20 3212 4155 490321264 490320298 0.000000e+00 767.0
4 TraesCS5A01G281400 chr5A 84.248 565 66 15 1810 2359 490420408 490419852 3.930000e-146 529.0
5 TraesCS5A01G281400 chr5A 84.248 565 66 15 2392 2948 490420990 490420441 3.930000e-146 529.0
6 TraesCS5A01G281400 chr5A 94.397 232 13 0 279 510 490339963 490339732 1.960000e-94 357.0
7 TraesCS5A01G281400 chr5A 81.849 292 41 6 877 1166 579846996 579847277 9.590000e-58 235.0
8 TraesCS5A01G281400 chr5A 87.603 121 7 4 900 1018 490340080 490339966 3.600000e-27 134.0
9 TraesCS5A01G281400 chr5A 91.071 56 3 1 4165 4218 618604468 618604523 2.210000e-09 75.0
10 TraesCS5A01G281400 chr5D 93.888 5530 235 41 1 5478 387696716 387691238 0.000000e+00 8244.0
11 TraesCS5A01G281400 chr5D 81.826 1183 188 18 2992 4155 387706733 387705559 0.000000e+00 968.0
12 TraesCS5A01G281400 chr5D 80.632 950 167 10 3001 3935 387713355 387712408 0.000000e+00 719.0
13 TraesCS5A01G281400 chr5D 83.652 575 69 16 2392 2948 387694923 387694356 8.500000e-143 518.0
14 TraesCS5A01G281400 chr5D 83.929 560 60 14 1811 2359 387694322 387693782 5.120000e-140 508.0
15 TraesCS5A01G281400 chr5D 83.301 521 76 8 3212 3725 387661696 387661180 2.410000e-128 470.0
16 TraesCS5A01G281400 chr5D 93.878 49 2 1 1330 1377 459576771 459576723 7.960000e-09 73.1
17 TraesCS5A01G281400 chr5B 93.988 3210 121 20 2206 5381 466028230 466025059 0.000000e+00 4793.0
18 TraesCS5A01G281400 chr5B 93.112 1234 63 13 1 1217 466030467 466029239 0.000000e+00 1788.0
19 TraesCS5A01G281400 chr5B 93.501 954 56 5 1222 2170 466029182 466028230 0.000000e+00 1413.0
20 TraesCS5A01G281400 chr5B 82.025 1185 184 21 2992 4155 466173354 466172178 0.000000e+00 981.0
21 TraesCS5A01G281400 chr5B 81.346 1174 194 15 2992 4143 466222258 466221088 0.000000e+00 931.0
22 TraesCS5A01G281400 chr5B 81.098 656 104 13 3509 4149 466004337 466003687 1.840000e-139 507.0
23 TraesCS5A01G281400 chr5B 83.288 371 47 9 2392 2753 466028590 466028226 1.540000e-85 327.0
24 TraesCS5A01G281400 chr5B 86.328 256 28 6 4227 4478 466221080 466220828 7.310000e-69 272.0
25 TraesCS5A01G281400 chr5B 85.385 260 29 6 3209 3464 466004605 466004351 1.580000e-65 261.0
26 TraesCS5A01G281400 chr5B 81.507 292 39 8 877 1165 564213742 564213463 5.770000e-55 226.0
27 TraesCS5A01G281400 chr5B 91.391 151 9 2 5369 5515 466008628 466008478 2.700000e-48 204.0
28 TraesCS5A01G281400 chr5B 83.007 153 20 3 877 1027 564452608 564452460 3.600000e-27 134.0
29 TraesCS5A01G281400 chr5B 93.878 49 2 1 1330 1377 563715060 563715012 7.960000e-09 73.1
30 TraesCS5A01G281400 chr5B 93.750 48 2 1 1331 1377 563728191 563728144 2.860000e-08 71.3
31 TraesCS5A01G281400 chr5B 95.349 43 2 0 1387 1429 563724207 563724165 1.030000e-07 69.4
32 TraesCS5A01G281400 chr5B 95.349 43 2 0 1387 1429 563744143 563744101 1.030000e-07 69.4
33 TraesCS5A01G281400 chrUn 93.750 48 2 1 1331 1377 232948187 232948140 2.860000e-08 71.3
34 TraesCS5A01G281400 chrUn 95.349 43 2 0 1387 1429 479663785 479663827 1.030000e-07 69.4


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 TraesCS5A01G281400 chr5A 490417076 490422799 5723 True 3876.333333 10571 89.498667 1 5724 3 chr5A.!!$R5 5723
1 TraesCS5A01G281400 chr5A 490593651 490594826 1175 True 979.000000 979 81.995000 2994 4155 1 chr5A.!!$R2 1161
2 TraesCS5A01G281400 chr5A 490651388 490652557 1169 True 904.000000 904 80.851000 2992 4149 1 chr5A.!!$R3 1157
3 TraesCS5A01G281400 chr5A 490320298 490321264 966 True 767.000000 767 81.481000 3212 4155 1 chr5A.!!$R1 943
4 TraesCS5A01G281400 chr5D 387691238 387696716 5478 True 3090.000000 8244 87.156333 1 5478 3 chr5D.!!$R5 5477
5 TraesCS5A01G281400 chr5D 387705559 387706733 1174 True 968.000000 968 81.826000 2992 4155 1 chr5D.!!$R2 1163
6 TraesCS5A01G281400 chr5D 387712408 387713355 947 True 719.000000 719 80.632000 3001 3935 1 chr5D.!!$R3 934
7 TraesCS5A01G281400 chr5D 387661180 387661696 516 True 470.000000 470 83.301000 3212 3725 1 chr5D.!!$R1 513
8 TraesCS5A01G281400 chr5B 466025059 466030467 5408 True 2080.250000 4793 90.972250 1 5381 4 chr5B.!!$R7 5380
9 TraesCS5A01G281400 chr5B 466172178 466173354 1176 True 981.000000 981 82.025000 2992 4155 1 chr5B.!!$R1 1163
10 TraesCS5A01G281400 chr5B 466220828 466222258 1430 True 601.500000 931 83.837000 2992 4478 2 chr5B.!!$R8 1486
11 TraesCS5A01G281400 chr5B 466003687 466008628 4941 True 324.000000 507 85.958000 3209 5515 3 chr5B.!!$R6 2306

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
546 548 0.036732 TGCACCCATCACAAGAGGTC 59.963 55.0 0.00 0.0 0.00 3.85 F
1681 1759 0.533491 CACCTTGTGATGCAATGGGG 59.467 55.0 0.00 0.0 36.36 4.96 F
2407 2506 1.243902 TTGATTGGACTTGTTCCCGC 58.756 50.0 0.00 0.0 45.17 6.13 F
2731 2834 0.321564 TCTGGCTTGTGGAACCGATG 60.322 55.0 0.00 0.0 34.36 3.84 F
4187 6407 0.171007 TCGAAAAGGGTAGTACCGCG 59.829 55.0 13.27 0.0 39.83 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2537 2639 0.460987 GACCATCTCGACAAGCCAGG 60.461 60.0 0.00 0.0 0.00 4.45 R
2572 2674 0.331616 AAAGGGCTAGGGCAAATCGT 59.668 50.0 0.00 0.0 40.87 3.73 R
3843 6050 0.821301 TTTCAACATCTGGCGCACCA 60.821 50.0 10.83 0.0 46.51 4.17 R
4505 6727 0.248784 GGTTTATCGACGCTACGCCT 60.249 55.0 0.00 0.0 0.00 5.52 R
5605 7868 0.032130 TCTCACGCTCGCTTCAGTTT 59.968 50.0 0.00 0.0 0.00 2.66 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
19 20 0.179004 TTGTCGCCCATCACTTTGGT 60.179 50.000 0.00 0.00 34.77 3.67
40 41 5.359576 TGGTTACTGCTTTGTTGATCAAACT 59.640 36.000 10.35 0.00 40.56 2.66
67 68 4.932200 AGGAACTTTCATCGCTCTTACAAG 59.068 41.667 0.00 0.00 27.25 3.16
76 77 3.770666 TCGCTCTTACAAGCACATCTAC 58.229 45.455 0.00 0.00 42.62 2.59
154 155 2.495669 CCGGCCAATCACAAAATAACCT 59.504 45.455 2.24 0.00 0.00 3.50
155 156 3.428862 CCGGCCAATCACAAAATAACCTC 60.429 47.826 2.24 0.00 0.00 3.85
250 252 2.198827 ATGTCATGTTCTTTGCCGGA 57.801 45.000 5.05 0.00 0.00 5.14
337 339 2.770802 AGCAATCACAGTCCATCTAGCT 59.229 45.455 0.00 0.00 0.00 3.32
423 425 3.064545 GCAACCTTCCAAGAAGATCATCG 59.935 47.826 5.92 0.00 0.00 3.84
507 509 2.029380 GCCATCAAGCCCTAAAAACGTT 60.029 45.455 0.00 0.00 0.00 3.99
546 548 0.036732 TGCACCCATCACAAGAGGTC 59.963 55.000 0.00 0.00 0.00 3.85
566 568 2.230508 TCTGCCTGTGTAGTTTACTCCG 59.769 50.000 0.00 0.00 0.00 4.63
678 680 5.567138 AGTTTCTCAAAGGTGTTCACAAG 57.433 39.130 5.32 0.00 0.00 3.16
716 718 2.700897 AGTAGTACATGATGGGGCAGTC 59.299 50.000 0.00 0.00 0.00 3.51
918 939 3.068881 GCCCGCAGCCCATCTATA 58.931 61.111 0.00 0.00 34.35 1.31
988 1010 2.558795 GGCTCTATCTCTAACATCGGCA 59.441 50.000 0.00 0.00 0.00 5.69
1095 1117 2.801631 CCCTCGTCCCCATCTCAGC 61.802 68.421 0.00 0.00 0.00 4.26
1235 1310 5.545723 CAGTTTAGGATCATGGATAGGTCCT 59.454 44.000 0.00 0.00 45.32 3.85
1297 1373 3.221771 TGTTTGCTTGTGCTTGTATCCT 58.778 40.909 0.00 0.00 40.48 3.24
1299 1375 4.099266 TGTTTGCTTGTGCTTGTATCCTTT 59.901 37.500 0.00 0.00 40.48 3.11
1301 1377 4.935352 TGCTTGTGCTTGTATCCTTTTT 57.065 36.364 0.00 0.00 40.48 1.94
1354 1432 3.181476 ACCCAGATGTCTGCAAACAAAAC 60.181 43.478 0.00 0.00 42.47 2.43
1357 1435 2.034558 AGATGTCTGCAAACAAAACGGG 59.965 45.455 0.00 0.00 31.81 5.28
1385 1463 2.821378 TGCCAACAAGATGATGGTTCTG 59.179 45.455 8.22 0.00 41.74 3.02
1394 1472 2.425143 TGATGGTTCTGAAGATGGCC 57.575 50.000 0.00 0.00 0.00 5.36
1395 1473 1.634973 TGATGGTTCTGAAGATGGCCA 59.365 47.619 8.56 8.56 0.00 5.36
1405 1483 4.473196 TCTGAAGATGGCCAAGTTATACCA 59.527 41.667 10.96 0.00 36.43 3.25
1557 1635 4.265893 ACCACCAAAATATGCGATGTGTA 58.734 39.130 0.00 0.00 0.00 2.90
1662 1740 1.839424 ACATTTTCTGCCCTAGCCAC 58.161 50.000 0.00 0.00 38.69 5.01
1680 1758 1.259609 ACACCTTGTGATGCAATGGG 58.740 50.000 0.49 0.00 36.96 4.00
1681 1759 0.533491 CACCTTGTGATGCAATGGGG 59.467 55.000 0.00 0.00 36.36 4.96
1765 1844 9.219603 TGATTTTTCTCCAAGAATACACTACAG 57.780 33.333 0.00 0.00 33.67 2.74
1791 1870 5.239306 TGAGAGAATACACTTGGCACTTTTG 59.761 40.000 0.00 0.00 0.00 2.44
1815 1894 6.700960 TGTTTGCAAGACATTGTTAATTGGAG 59.299 34.615 0.00 0.00 38.76 3.86
1825 1904 5.523438 TTGTTAATTGGAGTTGTTCCCAC 57.477 39.130 0.00 0.00 46.19 4.61
1960 2039 3.508793 CAGAATTGAAGTTCACCATGGCT 59.491 43.478 13.04 0.00 0.00 4.75
1961 2040 3.760684 AGAATTGAAGTTCACCATGGCTC 59.239 43.478 13.04 0.00 0.00 4.70
1962 2041 2.957402 TTGAAGTTCACCATGGCTCT 57.043 45.000 13.04 2.05 0.00 4.09
1980 2060 1.895798 TCTTGCTTGTCGAGATGGTCT 59.104 47.619 0.00 0.00 30.24 3.85
2140 2220 1.262417 TCACCGTCATGTCTGGCTTA 58.738 50.000 0.00 0.00 0.00 3.09
2176 2256 8.924511 AGAAATGGATATGTGGTTTACCTATG 57.075 34.615 0.00 0.00 36.82 2.23
2177 2257 7.944554 AGAAATGGATATGTGGTTTACCTATGG 59.055 37.037 0.00 0.00 36.82 2.74
2178 2258 7.401060 AATGGATATGTGGTTTACCTATGGA 57.599 36.000 0.00 0.00 36.82 3.41
2180 2260 6.147473 TGGATATGTGGTTTACCTATGGAGA 58.853 40.000 0.00 0.00 36.82 3.71
2182 2262 7.128109 TGGATATGTGGTTTACCTATGGAGAAA 59.872 37.037 0.00 0.00 36.82 2.52
2183 2263 7.996644 GGATATGTGGTTTACCTATGGAGAAAA 59.003 37.037 0.00 0.00 36.82 2.29
2184 2264 8.980481 ATATGTGGTTTACCTATGGAGAAAAG 57.020 34.615 0.00 0.00 36.82 2.27
2192 2283 9.569167 GTTTACCTATGGAGAAAAGTAAAATGC 57.431 33.333 0.00 0.00 33.06 3.56
2196 2287 7.397192 ACCTATGGAGAAAAGTAAAATGCACAT 59.603 33.333 0.00 0.00 0.00 3.21
2256 2348 3.872603 TGACGTGGCAGCCTGGTT 61.873 61.111 14.15 0.00 0.00 3.67
2356 2455 6.906157 AATAATTTGGCCTATGTGGATGAG 57.094 37.500 3.32 0.00 38.35 2.90
2407 2506 1.243902 TTGATTGGACTTGTTCCCGC 58.756 50.000 0.00 0.00 45.17 6.13
2437 2536 9.017509 ACCATGTTAGGCAAATCATATTCTATG 57.982 33.333 0.00 0.00 0.00 2.23
2537 2639 6.486253 TCATAGAGTTGAAGTTCACAATGC 57.514 37.500 4.68 0.00 0.00 3.56
2582 2684 7.116376 CGATATGGACATATATACGATTTGCCC 59.884 40.741 4.88 0.00 34.36 5.36
2583 2685 5.755409 TGGACATATATACGATTTGCCCT 57.245 39.130 0.00 0.00 0.00 5.19
2599 2701 1.615919 GCCCTAGCCCTTTGTTAAGCA 60.616 52.381 0.00 0.00 0.00 3.91
2607 2709 6.375945 AGCCCTTTGTTAAGCAAAATTTTG 57.624 33.333 23.74 23.74 45.35 2.44
2725 2828 1.877680 CGTCATGTCTGGCTTGTGGAA 60.878 52.381 0.00 0.00 0.00 3.53
2731 2834 0.321564 TCTGGCTTGTGGAACCGATG 60.322 55.000 0.00 0.00 34.36 3.84
2786 2889 5.574891 ATGGATAAAAGTAAATGCGCACA 57.425 34.783 14.90 0.57 0.00 4.57
2804 2907 3.405831 CACATATGGCATGTTCGATCCT 58.594 45.455 10.98 0.00 0.00 3.24
2945 3048 6.906157 AATAATTTGGCCTATGTGGATGAG 57.094 37.500 3.32 0.00 38.35 2.90
3271 3378 1.137479 CCGGCATTGGCATGAAGAAAT 59.863 47.619 11.10 0.00 43.71 2.17
3274 3381 3.798337 CGGCATTGGCATGAAGAAATTAC 59.202 43.478 11.10 0.00 43.71 1.89
3503 5681 1.531365 CTGGGCTTGGTTGCTGGAA 60.531 57.895 0.00 0.00 0.00 3.53
3726 5925 2.243736 TCCAAACCTCTCCACCTTTTGT 59.756 45.455 0.00 0.00 0.00 2.83
3843 6050 1.303398 TCGGACCGAGCTTCTGTCT 60.303 57.895 13.88 0.00 32.25 3.41
3902 6109 7.732025 TCGCCTAATGAGGTATATTCTGAAAA 58.268 34.615 0.00 0.00 45.78 2.29
4185 6405 4.990426 TCTTTTTCGAAAAGGGTAGTACCG 59.010 41.667 26.48 0.84 39.83 4.02
4187 6407 0.171007 TCGAAAAGGGTAGTACCGCG 59.829 55.000 13.27 0.00 39.83 6.46
4238 6458 5.448768 CCAAGTTATCTCATCTTGCAAGCAG 60.449 44.000 21.99 15.92 37.72 4.24
4358 6580 1.478510 CTCTGAGACGGCTACCACAAT 59.521 52.381 0.00 0.00 0.00 2.71
4363 6585 1.480954 AGACGGCTACCACAATACAGG 59.519 52.381 0.00 0.00 0.00 4.00
4447 6669 3.768215 TGGCATGCCACATTATTGAGAAA 59.232 39.130 35.59 7.49 41.89 2.52
4456 6678 5.065090 CCACATTATTGAGAAAGCGACATCA 59.935 40.000 0.00 0.00 0.00 3.07
4504 6726 4.459089 GGCTGTCGGAGTCCTGGC 62.459 72.222 7.77 3.08 0.00 4.85
4505 6727 3.695606 GCTGTCGGAGTCCTGGCA 61.696 66.667 7.77 7.81 0.00 4.92
4606 6828 0.107214 CTATGTGGGGTCGTGGCATT 60.107 55.000 0.00 0.00 0.00 3.56
4685 6907 3.100658 TCGGAGTCGTGTTTGAAATCA 57.899 42.857 0.00 0.00 37.69 2.57
4699 6921 1.099879 AAATCATCGAGCCCTGCAGC 61.100 55.000 8.66 0.00 0.00 5.25
4807 7029 0.798776 CAGGTCTGCAAACGATGGTC 59.201 55.000 0.00 0.00 0.00 4.02
4820 7042 2.881074 CGATGGTCGTGTGAGATTTCT 58.119 47.619 0.00 0.00 34.72 2.52
4943 7166 2.929531 TGACTTTGCTGCGTTTTTCA 57.070 40.000 0.00 0.00 0.00 2.69
5075 7303 7.305820 GCTTATGAATCTCATTGATTTTGTGCG 60.306 37.037 0.00 0.00 44.70 5.34
5135 7364 4.281898 GTTGGAGCTTCCTACTGGTTTA 57.718 45.455 8.67 0.00 38.86 2.01
5151 7380 6.690530 ACTGGTTTATGGATTGTGAACAATG 58.309 36.000 13.21 0.00 45.72 2.82
5201 7430 3.842923 CCTCGCCGTCTGCTCCAT 61.843 66.667 0.00 0.00 38.05 3.41
5330 7593 2.285827 TTGTTGTTGCAAAACCTCCG 57.714 45.000 0.00 0.00 0.00 4.63
5334 7597 1.082104 GTTGCAAAACCTCCGCTCG 60.082 57.895 0.00 0.00 0.00 5.03
5392 7655 5.585047 GCGTCTCAATACTTACATCCCTTTT 59.415 40.000 0.00 0.00 0.00 2.27
5393 7656 6.238130 GCGTCTCAATACTTACATCCCTTTTC 60.238 42.308 0.00 0.00 0.00 2.29
5396 7659 7.065923 GTCTCAATACTTACATCCCTTTTCCAC 59.934 40.741 0.00 0.00 0.00 4.02
5406 7669 6.980577 ACATCCCTTTTCCACCATCTTTATA 58.019 36.000 0.00 0.00 0.00 0.98
5455 7718 2.820037 GGGGCGACAAGTAGCAGC 60.820 66.667 7.57 0.00 32.66 5.25
5460 7723 1.568612 GCGACAAGTAGCAGCTGCAA 61.569 55.000 38.24 0.00 45.16 4.08
5470 7733 2.564975 AGCTGCAACGCTGAATGC 59.435 55.556 1.02 0.00 39.16 3.56
5478 7741 2.523015 CAACGCTGAATGCCAATCTTC 58.477 47.619 0.00 0.00 38.78 2.87
5479 7742 2.119801 ACGCTGAATGCCAATCTTCT 57.880 45.000 0.00 0.00 38.78 2.85
5480 7743 2.440409 ACGCTGAATGCCAATCTTCTT 58.560 42.857 0.00 0.00 38.78 2.52
5481 7744 2.821969 ACGCTGAATGCCAATCTTCTTT 59.178 40.909 0.00 0.00 38.78 2.52
5482 7745 3.119708 ACGCTGAATGCCAATCTTCTTTC 60.120 43.478 0.00 0.00 38.78 2.62
5483 7746 3.128242 CGCTGAATGCCAATCTTCTTTCT 59.872 43.478 0.00 0.00 38.78 2.52
5484 7747 4.380233 CGCTGAATGCCAATCTTCTTTCTT 60.380 41.667 0.00 0.00 38.78 2.52
5485 7748 5.163723 CGCTGAATGCCAATCTTCTTTCTTA 60.164 40.000 0.00 0.00 38.78 2.10
5486 7749 6.264088 GCTGAATGCCAATCTTCTTTCTTAG 58.736 40.000 0.00 0.00 35.15 2.18
5487 7750 6.679884 GCTGAATGCCAATCTTCTTTCTTAGG 60.680 42.308 0.00 0.00 35.15 2.69
5488 7751 6.248433 TGAATGCCAATCTTCTTTCTTAGGT 58.752 36.000 0.00 0.00 0.00 3.08
5489 7752 6.721208 TGAATGCCAATCTTCTTTCTTAGGTT 59.279 34.615 0.00 0.00 0.00 3.50
5490 7753 6.765915 ATGCCAATCTTCTTTCTTAGGTTC 57.234 37.500 0.00 0.00 0.00 3.62
5491 7754 5.010282 TGCCAATCTTCTTTCTTAGGTTCC 58.990 41.667 0.00 0.00 0.00 3.62
5492 7755 4.399618 GCCAATCTTCTTTCTTAGGTTCCC 59.600 45.833 0.00 0.00 0.00 3.97
5493 7756 4.950475 CCAATCTTCTTTCTTAGGTTCCCC 59.050 45.833 0.00 0.00 0.00 4.81
5494 7757 5.281245 CCAATCTTCTTTCTTAGGTTCCCCT 60.281 44.000 0.00 0.00 45.51 4.79
5495 7758 6.069615 CCAATCTTCTTTCTTAGGTTCCCCTA 60.070 42.308 0.00 0.00 42.66 3.53
5497 7760 6.370186 TCTTCTTTCTTAGGTTCCCCTAAC 57.630 41.667 0.00 0.00 46.27 2.34
5498 7761 5.847817 TCTTCTTTCTTAGGTTCCCCTAACA 59.152 40.000 0.00 0.00 46.27 2.41
5499 7762 6.330778 TCTTCTTTCTTAGGTTCCCCTAACAA 59.669 38.462 0.00 0.00 46.27 2.83
5500 7763 6.518516 TCTTTCTTAGGTTCCCCTAACAAA 57.481 37.500 0.00 0.60 46.27 2.83
5501 7764 7.098845 TCTTTCTTAGGTTCCCCTAACAAAT 57.901 36.000 3.46 0.00 46.27 2.32
5502 7765 7.532199 TCTTTCTTAGGTTCCCCTAACAAATT 58.468 34.615 3.46 0.00 46.27 1.82
5503 7766 8.008332 TCTTTCTTAGGTTCCCCTAACAAATTT 58.992 33.333 3.46 0.00 46.27 1.82
5504 7767 8.555896 TTTCTTAGGTTCCCCTAACAAATTTT 57.444 30.769 0.00 0.00 46.27 1.82
5505 7768 9.657728 TTTCTTAGGTTCCCCTAACAAATTTTA 57.342 29.630 0.00 0.00 46.27 1.52
5506 7769 9.657728 TTCTTAGGTTCCCCTAACAAATTTTAA 57.342 29.630 0.00 0.00 46.27 1.52
5507 7770 9.304335 TCTTAGGTTCCCCTAACAAATTTTAAG 57.696 33.333 0.00 0.00 46.27 1.85
5508 7771 9.304335 CTTAGGTTCCCCTAACAAATTTTAAGA 57.696 33.333 0.00 0.00 46.27 2.10
5509 7772 9.657728 TTAGGTTCCCCTAACAAATTTTAAGAA 57.342 29.630 0.00 0.00 46.27 2.52
5510 7773 8.555896 AGGTTCCCCTAACAAATTTTAAGAAA 57.444 30.769 0.00 0.00 40.19 2.52
5511 7774 8.994500 AGGTTCCCCTAACAAATTTTAAGAAAA 58.006 29.630 0.00 0.00 40.19 2.29
5512 7775 9.048446 GGTTCCCCTAACAAATTTTAAGAAAAC 57.952 33.333 0.00 0.00 40.08 2.43
5513 7776 9.826574 GTTCCCCTAACAAATTTTAAGAAAACT 57.173 29.630 0.00 0.00 38.05 2.66
5574 7837 8.812513 ATCTAAACAAAGGTGAATGATCATCA 57.187 30.769 9.06 6.23 39.28 3.07
5575 7838 8.634335 TCTAAACAAAGGTGAATGATCATCAA 57.366 30.769 9.06 0.00 39.28 2.57
5576 7839 8.514594 TCTAAACAAAGGTGAATGATCATCAAC 58.485 33.333 9.06 11.27 39.28 3.18
5577 7840 5.300969 ACAAAGGTGAATGATCATCAACG 57.699 39.130 9.06 2.65 39.28 4.10
5578 7841 4.156556 ACAAAGGTGAATGATCATCAACGG 59.843 41.667 9.06 9.04 39.28 4.44
5579 7842 2.923121 AGGTGAATGATCATCAACGGG 58.077 47.619 9.06 0.00 39.28 5.28
5580 7843 1.949525 GGTGAATGATCATCAACGGGG 59.050 52.381 9.06 0.00 36.64 5.73
5581 7844 2.643551 GTGAATGATCATCAACGGGGT 58.356 47.619 9.06 0.00 38.01 4.95
5582 7845 2.355756 GTGAATGATCATCAACGGGGTG 59.644 50.000 9.06 0.00 38.01 4.61
5583 7846 1.334869 GAATGATCATCAACGGGGTGC 59.665 52.381 9.06 0.00 0.00 5.01
5584 7847 0.466189 ATGATCATCAACGGGGTGCC 60.466 55.000 1.18 0.00 0.00 5.01
5585 7848 1.224592 GATCATCAACGGGGTGCCT 59.775 57.895 0.00 0.00 0.00 4.75
5586 7849 0.815615 GATCATCAACGGGGTGCCTC 60.816 60.000 0.00 0.00 0.00 4.70
5587 7850 1.274703 ATCATCAACGGGGTGCCTCT 61.275 55.000 0.00 0.00 0.00 3.69
5588 7851 1.002134 CATCAACGGGGTGCCTCTT 60.002 57.895 0.00 0.00 0.00 2.85
5589 7852 0.609131 CATCAACGGGGTGCCTCTTT 60.609 55.000 0.00 0.00 0.00 2.52
5590 7853 0.609131 ATCAACGGGGTGCCTCTTTG 60.609 55.000 1.33 1.33 0.00 2.77
5591 7854 2.115266 AACGGGGTGCCTCTTTGG 59.885 61.111 0.00 0.00 39.35 3.28
5592 7855 2.763645 AACGGGGTGCCTCTTTGGT 61.764 57.895 0.00 0.00 38.35 3.67
5593 7856 2.115266 CGGGGTGCCTCTTTGGTT 59.885 61.111 0.00 0.00 38.35 3.67
5594 7857 1.971695 CGGGGTGCCTCTTTGGTTC 60.972 63.158 0.00 0.00 38.35 3.62
5595 7858 1.606601 GGGGTGCCTCTTTGGTTCC 60.607 63.158 0.00 0.00 38.35 3.62
5596 7859 1.606601 GGGTGCCTCTTTGGTTCCC 60.607 63.158 0.00 0.00 41.03 3.97
5597 7860 1.460699 GGTGCCTCTTTGGTTCCCT 59.539 57.895 0.00 0.00 38.35 4.20
5598 7861 0.895559 GGTGCCTCTTTGGTTCCCTG 60.896 60.000 0.00 0.00 38.35 4.45
5599 7862 1.228552 TGCCTCTTTGGTTCCCTGC 60.229 57.895 0.00 0.00 38.35 4.85
5600 7863 1.979155 GCCTCTTTGGTTCCCTGCC 60.979 63.158 0.00 0.00 38.35 4.85
5601 7864 1.460255 CCTCTTTGGTTCCCTGCCA 59.540 57.895 0.00 0.00 0.00 4.92
5602 7865 0.178964 CCTCTTTGGTTCCCTGCCAA 60.179 55.000 0.00 0.00 43.51 4.52
5603 7866 1.251251 CTCTTTGGTTCCCTGCCAAG 58.749 55.000 0.00 0.00 45.47 3.61
5604 7867 0.178964 TCTTTGGTTCCCTGCCAAGG 60.179 55.000 0.00 0.00 45.47 3.61
5606 7869 5.908990 CTCTTTGGTTCCCTGCCAAGGAA 62.909 52.174 9.54 0.00 46.58 3.36
5615 7878 0.239347 CTGCCAAGGAAACTGAAGCG 59.761 55.000 0.00 0.00 42.68 4.68
5616 7879 0.179032 TGCCAAGGAAACTGAAGCGA 60.179 50.000 0.00 0.00 42.68 4.93
5617 7880 0.519077 GCCAAGGAAACTGAAGCGAG 59.481 55.000 0.00 0.00 42.68 5.03
5618 7881 0.519077 CCAAGGAAACTGAAGCGAGC 59.481 55.000 0.00 0.00 42.68 5.03
5619 7882 0.164647 CAAGGAAACTGAAGCGAGCG 59.835 55.000 0.00 0.00 42.68 5.03
5620 7883 0.249911 AAGGAAACTGAAGCGAGCGT 60.250 50.000 0.00 0.00 42.68 5.07
5621 7884 0.946221 AGGAAACTGAAGCGAGCGTG 60.946 55.000 0.00 0.00 41.13 5.34
5622 7885 0.944311 GGAAACTGAAGCGAGCGTGA 60.944 55.000 0.00 0.00 0.00 4.35
5623 7886 0.436531 GAAACTGAAGCGAGCGTGAG 59.563 55.000 0.00 0.00 0.00 3.51
5624 7887 0.032130 AAACTGAAGCGAGCGTGAGA 59.968 50.000 4.52 0.00 0.00 3.27
5625 7888 0.387878 AACTGAAGCGAGCGTGAGAG 60.388 55.000 4.52 0.00 0.00 3.20
5626 7889 1.515952 CTGAAGCGAGCGTGAGAGG 60.516 63.158 0.00 0.00 0.00 3.69
5627 7890 2.206515 CTGAAGCGAGCGTGAGAGGT 62.207 60.000 0.00 0.00 0.00 3.85
5628 7891 1.515304 GAAGCGAGCGTGAGAGGTC 60.515 63.158 0.00 0.00 35.48 3.85
5629 7892 2.201436 GAAGCGAGCGTGAGAGGTCA 62.201 60.000 0.00 0.00 38.44 4.02
5638 7901 2.244946 TGAGAGGTCACGTCTCACG 58.755 57.895 23.37 0.00 46.07 4.35
5649 7912 0.575390 CGTCTCACGTGTGTTTCACC 59.425 55.000 16.51 0.00 43.51 4.02
5650 7913 0.575390 GTCTCACGTGTGTTTCACCG 59.425 55.000 16.51 8.38 43.51 4.94
5651 7914 1.149361 TCTCACGTGTGTTTCACCGC 61.149 55.000 16.51 0.00 43.51 5.68
5652 7915 2.101209 CTCACGTGTGTTTCACCGCC 62.101 60.000 16.51 0.00 43.51 6.13
5653 7916 3.266376 ACGTGTGTTTCACCGCCG 61.266 61.111 0.00 6.48 43.51 6.46
5654 7917 3.266376 CGTGTGTTTCACCGCCGT 61.266 61.111 0.00 0.00 43.51 5.68
5655 7918 2.629763 GTGTGTTTCACCGCCGTC 59.370 61.111 0.00 0.00 40.84 4.79
5656 7919 2.589442 TGTGTTTCACCGCCGTCC 60.589 61.111 0.00 0.00 32.73 4.79
5657 7920 3.708734 GTGTTTCACCGCCGTCCG 61.709 66.667 0.00 0.00 0.00 4.79
5658 7921 3.914117 TGTTTCACCGCCGTCCGA 61.914 61.111 0.00 0.00 40.02 4.55
5659 7922 2.433664 GTTTCACCGCCGTCCGAT 60.434 61.111 0.00 0.00 40.02 4.18
5660 7923 2.030958 GTTTCACCGCCGTCCGATT 61.031 57.895 0.00 0.00 40.02 3.34
5661 7924 0.737019 GTTTCACCGCCGTCCGATTA 60.737 55.000 0.00 0.00 40.02 1.75
5662 7925 0.737019 TTTCACCGCCGTCCGATTAC 60.737 55.000 0.00 0.00 40.02 1.89
5663 7926 2.561549 TTCACCGCCGTCCGATTACC 62.562 60.000 0.00 0.00 40.02 2.85
5664 7927 3.069946 ACCGCCGTCCGATTACCA 61.070 61.111 0.00 0.00 40.02 3.25
5665 7928 2.279252 CCGCCGTCCGATTACCAG 60.279 66.667 0.00 0.00 40.02 4.00
5666 7929 2.493030 CGCCGTCCGATTACCAGT 59.507 61.111 0.00 0.00 40.02 4.00
5667 7930 1.876714 CGCCGTCCGATTACCAGTG 60.877 63.158 0.00 0.00 40.02 3.66
5668 7931 2.171725 GCCGTCCGATTACCAGTGC 61.172 63.158 0.00 0.00 0.00 4.40
5669 7932 1.515954 CCGTCCGATTACCAGTGCT 59.484 57.895 0.00 0.00 0.00 4.40
5670 7933 0.108329 CCGTCCGATTACCAGTGCTT 60.108 55.000 0.00 0.00 0.00 3.91
5671 7934 1.674817 CCGTCCGATTACCAGTGCTTT 60.675 52.381 0.00 0.00 0.00 3.51
5672 7935 1.659098 CGTCCGATTACCAGTGCTTTC 59.341 52.381 0.00 0.00 0.00 2.62
5673 7936 2.674177 CGTCCGATTACCAGTGCTTTCT 60.674 50.000 0.00 0.00 0.00 2.52
5674 7937 3.428452 CGTCCGATTACCAGTGCTTTCTA 60.428 47.826 0.00 0.00 0.00 2.10
5675 7938 4.694339 GTCCGATTACCAGTGCTTTCTAT 58.306 43.478 0.00 0.00 0.00 1.98
5676 7939 5.116882 GTCCGATTACCAGTGCTTTCTATT 58.883 41.667 0.00 0.00 0.00 1.73
5677 7940 5.585047 GTCCGATTACCAGTGCTTTCTATTT 59.415 40.000 0.00 0.00 0.00 1.40
5678 7941 6.093633 GTCCGATTACCAGTGCTTTCTATTTT 59.906 38.462 0.00 0.00 0.00 1.82
5679 7942 6.315393 TCCGATTACCAGTGCTTTCTATTTTC 59.685 38.462 0.00 0.00 0.00 2.29
5680 7943 6.316390 CCGATTACCAGTGCTTTCTATTTTCT 59.684 38.462 0.00 0.00 0.00 2.52
5681 7944 7.148239 CCGATTACCAGTGCTTTCTATTTTCTT 60.148 37.037 0.00 0.00 0.00 2.52
5682 7945 8.237267 CGATTACCAGTGCTTTCTATTTTCTTT 58.763 33.333 0.00 0.00 0.00 2.52
5683 7946 9.914131 GATTACCAGTGCTTTCTATTTTCTTTT 57.086 29.630 0.00 0.00 0.00 2.27
5684 7947 9.914131 ATTACCAGTGCTTTCTATTTTCTTTTC 57.086 29.630 0.00 0.00 0.00 2.29
5685 7948 7.588497 ACCAGTGCTTTCTATTTTCTTTTCT 57.412 32.000 0.00 0.00 0.00 2.52
5686 7949 8.011844 ACCAGTGCTTTCTATTTTCTTTTCTT 57.988 30.769 0.00 0.00 0.00 2.52
5687 7950 8.138074 ACCAGTGCTTTCTATTTTCTTTTCTTC 58.862 33.333 0.00 0.00 0.00 2.87
5688 7951 8.355913 CCAGTGCTTTCTATTTTCTTTTCTTCT 58.644 33.333 0.00 0.00 0.00 2.85
5689 7952 9.392021 CAGTGCTTTCTATTTTCTTTTCTTCTC 57.608 33.333 0.00 0.00 0.00 2.87
5690 7953 9.348476 AGTGCTTTCTATTTTCTTTTCTTCTCT 57.652 29.630 0.00 0.00 0.00 3.10
5691 7954 9.958234 GTGCTTTCTATTTTCTTTTCTTCTCTT 57.042 29.630 0.00 0.00 0.00 2.85
5699 7962 8.744568 ATTTTCTTTTCTTCTCTTCTCTGTGT 57.255 30.769 0.00 0.00 0.00 3.72
5700 7963 9.838339 ATTTTCTTTTCTTCTCTTCTCTGTGTA 57.162 29.630 0.00 0.00 0.00 2.90
5701 7964 8.649973 TTTCTTTTCTTCTCTTCTCTGTGTAC 57.350 34.615 0.00 0.00 0.00 2.90
5702 7965 7.348080 TCTTTTCTTCTCTTCTCTGTGTACA 57.652 36.000 0.00 0.00 0.00 2.90
5703 7966 7.203910 TCTTTTCTTCTCTTCTCTGTGTACAC 58.796 38.462 19.36 19.36 0.00 2.90
5704 7967 6.465439 TTTCTTCTCTTCTCTGTGTACACA 57.535 37.500 26.37 26.37 39.32 3.72
5712 7975 4.889807 TGTGTACACAGGGGTTGC 57.110 55.556 24.62 0.00 36.21 4.17
5713 7976 1.149627 TGTGTACACAGGGGTTGCC 59.850 57.895 24.62 0.00 36.21 4.52
5714 7977 1.349542 TGTGTACACAGGGGTTGCCT 61.350 55.000 24.62 0.00 36.21 4.75
5715 7978 0.179001 GTGTACACAGGGGTTGCCTT 60.179 55.000 21.14 0.00 0.00 4.35
5716 7979 0.553819 TGTACACAGGGGTTGCCTTT 59.446 50.000 0.00 0.00 0.00 3.11
5717 7980 1.063567 TGTACACAGGGGTTGCCTTTT 60.064 47.619 0.00 0.00 0.00 2.27
5718 7981 2.175069 TGTACACAGGGGTTGCCTTTTA 59.825 45.455 0.00 0.00 0.00 1.52
5719 7982 2.694616 ACACAGGGGTTGCCTTTTAT 57.305 45.000 0.00 0.00 0.00 1.40
5720 7983 2.525368 ACACAGGGGTTGCCTTTTATC 58.475 47.619 0.00 0.00 0.00 1.75
5721 7984 1.472480 CACAGGGGTTGCCTTTTATCG 59.528 52.381 0.00 0.00 0.00 2.92
5722 7985 1.353022 ACAGGGGTTGCCTTTTATCGA 59.647 47.619 0.00 0.00 0.00 3.59
5723 7986 2.017049 CAGGGGTTGCCTTTTATCGAG 58.983 52.381 0.00 0.00 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 5.344743 AAGAGCGATGAAAGTTCCTGATA 57.655 39.130 0.00 0.00 0.00 2.15
67 68 2.860735 GACATGAACTCCGTAGATGTGC 59.139 50.000 0.00 0.00 0.00 4.57
76 77 2.979814 TATGGGTGACATGAACTCCG 57.020 50.000 0.00 0.00 40.82 4.63
154 155 0.909610 AGCAATGGAAGAGGGTCCGA 60.910 55.000 0.00 0.00 40.96 4.55
155 156 0.462759 GAGCAATGGAAGAGGGTCCG 60.463 60.000 0.00 0.00 40.96 4.79
250 252 3.318839 CCGCCATGAATATTGTGTGGAAT 59.681 43.478 12.30 0.00 31.59 3.01
337 339 5.774690 AGTATTTGAAGATTTGAAGGTGGCA 59.225 36.000 0.00 0.00 0.00 4.92
411 413 4.714308 AGGGAAGACTTCGATGATCTTCTT 59.286 41.667 25.02 16.33 45.09 2.52
423 425 5.087391 AGTCGGAAAATAGGGAAGACTTC 57.913 43.478 6.66 6.66 34.27 3.01
507 509 1.133823 ACAATGTCTTCTGTGGGCACA 60.134 47.619 0.00 0.00 39.32 4.57
546 548 2.607187 CGGAGTAAACTACACAGGCAG 58.393 52.381 0.00 0.00 0.00 4.85
553 555 2.289840 GGGGGCGGAGTAAACTACA 58.710 57.895 0.00 0.00 0.00 2.74
579 581 3.430929 GGCGACTGATCATAAGTCACCTT 60.431 47.826 11.49 0.00 43.53 3.50
678 680 6.606395 TGTACTACTCCCATCTAGGTTTCTTC 59.394 42.308 0.00 0.00 34.66 2.87
965 987 2.414824 CCGATGTTAGAGATAGAGCCGC 60.415 54.545 0.00 0.00 0.00 6.53
988 1010 2.650813 GATGACATCGAGGCCGGCTT 62.651 60.000 28.56 21.53 36.24 4.35
1047 1069 2.203337 AGCCTTTCTGCGGTGCAA 60.203 55.556 0.00 0.00 38.41 4.08
1095 1117 1.806461 GCATCTGCATGGCTGGATGG 61.806 60.000 18.39 7.62 38.62 3.51
1274 1350 2.490328 TACAAGCACAAGCAAACAGC 57.510 45.000 0.00 0.00 45.49 4.40
1301 1377 7.759886 CGGAGTGATGATAAGAGTACAGAAAAA 59.240 37.037 0.00 0.00 0.00 1.94
1321 1397 1.275291 ACATCTGGGTACAACGGAGTG 59.725 52.381 0.00 1.89 45.00 3.51
1326 1402 1.337728 TGCAGACATCTGGGTACAACG 60.338 52.381 10.81 0.00 43.94 4.10
1354 1432 1.227823 TTGTTGGCAGAGTGACCCG 60.228 57.895 0.00 0.00 0.00 5.28
1357 1435 2.771089 TCATCTTGTTGGCAGAGTGAC 58.229 47.619 0.00 0.00 0.00 3.67
1385 1463 4.816925 GTCTGGTATAACTTGGCCATCTTC 59.183 45.833 6.09 0.00 0.00 2.87
1394 1472 5.395768 CCTCTGGAAGGTCTGGTATAACTTG 60.396 48.000 0.00 0.00 40.67 3.16
1395 1473 4.717280 CCTCTGGAAGGTCTGGTATAACTT 59.283 45.833 0.00 0.00 40.67 2.66
1662 1740 0.533491 CCCCATTGCATCACAAGGTG 59.467 55.000 0.00 0.00 42.87 4.00
1680 1758 2.751806 CCAGGAAAGCTCTGAAATGTCC 59.248 50.000 2.56 0.00 34.36 4.02
1681 1759 3.416156 ACCAGGAAAGCTCTGAAATGTC 58.584 45.455 2.56 0.00 34.36 3.06
1765 1844 4.764172 AGTGCCAAGTGTATTCTCTCATC 58.236 43.478 0.00 0.00 0.00 2.92
1791 1870 6.701400 ACTCCAATTAACAATGTCTTGCAAAC 59.299 34.615 0.00 2.76 35.69 2.93
1815 1894 5.349543 CCTAACATAGTAACGTGGGAACAAC 59.650 44.000 0.00 0.00 46.06 3.32
1886 1965 5.774498 ATTAATCATTTTCCGAGCCCTTC 57.226 39.130 0.00 0.00 0.00 3.46
1960 2039 1.895798 AGACCATCTCGACAAGCAAGA 59.104 47.619 0.00 0.00 0.00 3.02
1961 2040 2.376808 AGACCATCTCGACAAGCAAG 57.623 50.000 0.00 0.00 0.00 4.01
1962 2041 5.509670 CCATATAGACCATCTCGACAAGCAA 60.510 44.000 0.00 0.00 0.00 3.91
1980 2060 6.884295 GCTTAGGCAAACCATATGTCCATATA 59.116 38.462 1.24 0.00 39.06 0.86
2103 2183 5.023920 CGGTGAATTTGAAGTCATCATTCG 58.976 41.667 5.45 0.00 38.03 3.34
2140 2220 5.130477 ACATATCCATTTCTACCGGTTCAGT 59.870 40.000 15.04 0.00 0.00 3.41
2175 2255 5.229423 GCATGTGCATTTTACTTTTCTCCA 58.771 37.500 0.00 0.00 41.59 3.86
2176 2256 5.768333 GCATGTGCATTTTACTTTTCTCC 57.232 39.130 0.00 0.00 41.59 3.71
2256 2348 9.268268 GACAAATAGGTATCCATATTCGAAACA 57.732 33.333 0.00 0.00 0.00 2.83
2407 2506 4.955925 TGATTTGCCTAACATGGTAACG 57.044 40.909 0.00 0.00 42.51 3.18
2437 2536 2.941891 TCTTCGAAACATTGCACGAC 57.058 45.000 0.00 0.00 34.59 4.34
2439 2538 3.121696 GCTTTTCTTCGAAACATTGCACG 60.122 43.478 0.00 0.00 0.00 5.34
2537 2639 0.460987 GACCATCTCGACAAGCCAGG 60.461 60.000 0.00 0.00 0.00 4.45
2570 2672 1.435256 AGGGCTAGGGCAAATCGTAT 58.565 50.000 0.00 0.00 40.87 3.06
2571 2673 1.209621 AAGGGCTAGGGCAAATCGTA 58.790 50.000 0.00 0.00 40.87 3.43
2572 2674 0.331616 AAAGGGCTAGGGCAAATCGT 59.668 50.000 0.00 0.00 40.87 3.73
2573 2675 0.740737 CAAAGGGCTAGGGCAAATCG 59.259 55.000 0.00 0.00 40.87 3.34
2638 2740 6.796785 ATCTATTAAGCAATTTGGGCAGTT 57.203 33.333 0.00 0.00 0.00 3.16
2679 2782 9.211485 GGTGAATTTGAAGTCATCATTCAATTT 57.789 29.630 13.88 5.40 43.96 1.82
2680 2783 7.543172 CGGTGAATTTGAAGTCATCATTCAATT 59.457 33.333 13.88 3.27 43.96 2.32
2725 2828 2.426522 CGCATATCCATTTCCATCGGT 58.573 47.619 0.00 0.00 0.00 4.69
2731 2834 3.636764 AGGAAAACCGCATATCCATTTCC 59.363 43.478 6.93 6.93 43.80 3.13
2786 2889 4.356405 TTCAGGATCGAACATGCCATAT 57.644 40.909 2.11 0.00 0.00 1.78
2804 2907 6.486657 CAGTTAGGAAAACAAGGAGTCATTCA 59.513 38.462 0.00 0.00 31.25 2.57
2945 3048 3.645884 AGATGCAAACAAATCACTGCAC 58.354 40.909 0.00 0.00 46.75 4.57
3041 3145 6.371825 ACAAAAGAACGGGAGATCAGTTATTC 59.628 38.462 0.00 0.00 33.60 1.75
3271 3378 5.996513 TGTTACCATAAAGTTCAAGCCGTAA 59.003 36.000 0.00 0.00 0.00 3.18
3274 3381 5.365403 TTGTTACCATAAAGTTCAAGCCG 57.635 39.130 0.00 0.00 0.00 5.52
3694 5893 2.027377 AGAGGTTTGGAGCATCACTCTG 60.027 50.000 0.00 0.00 45.48 3.35
3726 5925 3.512329 TCGATACTAAGCCACCAAACAGA 59.488 43.478 0.00 0.00 0.00 3.41
3843 6050 0.821301 TTTCAACATCTGGCGCACCA 60.821 50.000 10.83 0.00 46.51 4.17
3908 6115 6.280855 TGCAAACAGCTAGTCTATACTCAA 57.719 37.500 0.00 0.00 45.94 3.02
4157 6375 9.229784 GTACTACCCTTTTCGAAAAAGAAAAAG 57.770 33.333 22.67 16.48 45.78 2.27
4238 6458 3.187227 CAGCAGTTCCACAATACACACTC 59.813 47.826 0.00 0.00 0.00 3.51
4358 6580 4.141574 ACTCTTTAGGTTGTTGTGCCTGTA 60.142 41.667 0.00 0.00 36.38 2.74
4363 6585 3.625764 TCACACTCTTTAGGTTGTTGTGC 59.374 43.478 0.00 0.00 0.00 4.57
4447 6669 2.101185 CGCTCGAGTGATGTCGCT 59.899 61.111 21.40 0.00 39.90 4.93
4456 6678 1.373497 CAAAGTGAGGCGCTCGAGT 60.373 57.895 15.13 0.00 32.35 4.18
4504 6726 0.844503 GTTTATCGACGCTACGCCTG 59.155 55.000 0.00 0.00 0.00 4.85
4505 6727 0.248784 GGTTTATCGACGCTACGCCT 60.249 55.000 0.00 0.00 0.00 5.52
4606 6828 1.979155 CGCCCTGTGAGACTCCTCA 60.979 63.158 0.00 0.00 46.48 3.86
4807 7029 1.927174 CGGCCTAAGAAATCTCACACG 59.073 52.381 0.00 0.00 0.00 4.49
4820 7042 1.888512 ACGAAACAGAGTACGGCCTAA 59.111 47.619 0.00 0.00 0.00 2.69
4943 7166 6.766944 CCTCTGATATCTCTGAAAACAGCAAT 59.233 38.462 3.98 0.00 0.00 3.56
5023 7251 1.927895 AGAGTTCGCCGCATTCTTAG 58.072 50.000 0.00 0.00 0.00 2.18
5075 7303 7.651304 CACCTTCTATATTGATCAGACTGACAC 59.349 40.741 7.47 5.95 0.00 3.67
5110 7339 3.138468 ACCAGTAGGAAGCTCCAACTTTT 59.862 43.478 5.21 0.00 39.61 2.27
5111 7340 2.711547 ACCAGTAGGAAGCTCCAACTTT 59.288 45.455 5.21 0.00 39.61 2.66
5135 7364 5.336690 GCTGTAACCATTGTTCACAATCCAT 60.337 40.000 2.01 0.00 44.10 3.41
5151 7380 1.654023 GCGGGGTTCATGCTGTAACC 61.654 60.000 5.64 5.64 43.70 2.85
5201 7430 4.487804 AGAAGGAGATGCTGGAGCTTATA 58.512 43.478 0.00 0.00 42.66 0.98
5330 7593 3.000022 GCCGAGTAGTAAATTGTTCGAGC 60.000 47.826 0.00 0.00 0.00 5.03
5334 7597 5.796350 ACATGCCGAGTAGTAAATTGTTC 57.204 39.130 0.00 0.00 0.00 3.18
5372 7635 6.318900 GGTGGAAAAGGGATGTAAGTATTGAG 59.681 42.308 0.00 0.00 0.00 3.02
5406 7669 5.447279 CCACTCATTTAGCGCGTCTTTATTT 60.447 40.000 8.43 0.00 0.00 1.40
5486 7749 9.048446 GTTTTCTTAAAATTTGTTAGGGGAACC 57.952 33.333 0.00 0.00 41.30 3.62
5487 7750 9.826574 AGTTTTCTTAAAATTTGTTAGGGGAAC 57.173 29.630 0.00 0.00 34.09 3.62
5548 7811 9.246670 TGATGATCATTCACCTTTGTTTAGATT 57.753 29.630 10.14 0.00 33.85 2.40
5549 7812 8.812513 TGATGATCATTCACCTTTGTTTAGAT 57.187 30.769 10.14 0.00 33.85 1.98
5550 7813 8.514594 GTTGATGATCATTCACCTTTGTTTAGA 58.485 33.333 10.14 0.00 33.85 2.10
5551 7814 7.482743 CGTTGATGATCATTCACCTTTGTTTAG 59.517 37.037 10.14 0.00 33.85 1.85
5552 7815 7.304735 CGTTGATGATCATTCACCTTTGTTTA 58.695 34.615 10.14 0.00 33.85 2.01
5553 7816 6.151691 CGTTGATGATCATTCACCTTTGTTT 58.848 36.000 10.14 0.00 33.85 2.83
5554 7817 5.335897 CCGTTGATGATCATTCACCTTTGTT 60.336 40.000 10.14 0.00 33.85 2.83
5555 7818 4.156556 CCGTTGATGATCATTCACCTTTGT 59.843 41.667 10.14 0.00 33.85 2.83
5556 7819 4.439153 CCCGTTGATGATCATTCACCTTTG 60.439 45.833 10.14 0.00 33.85 2.77
5557 7820 3.696051 CCCGTTGATGATCATTCACCTTT 59.304 43.478 10.14 0.00 33.85 3.11
5558 7821 3.282021 CCCGTTGATGATCATTCACCTT 58.718 45.455 10.14 0.00 33.85 3.50
5559 7822 2.421952 CCCCGTTGATGATCATTCACCT 60.422 50.000 10.14 0.00 33.85 4.00
5560 7823 1.949525 CCCCGTTGATGATCATTCACC 59.050 52.381 10.14 1.61 33.85 4.02
5561 7824 2.355756 CACCCCGTTGATGATCATTCAC 59.644 50.000 10.14 8.69 33.85 3.18
5562 7825 2.642427 CACCCCGTTGATGATCATTCA 58.358 47.619 10.14 6.69 36.00 2.57
5563 7826 1.334869 GCACCCCGTTGATGATCATTC 59.665 52.381 10.14 4.08 0.00 2.67
5564 7827 1.392589 GCACCCCGTTGATGATCATT 58.607 50.000 10.14 0.00 0.00 2.57
5565 7828 0.466189 GGCACCCCGTTGATGATCAT 60.466 55.000 8.25 8.25 0.00 2.45
5566 7829 1.077787 GGCACCCCGTTGATGATCA 60.078 57.895 0.00 0.00 0.00 2.92
5567 7830 0.815615 GAGGCACCCCGTTGATGATC 60.816 60.000 0.00 0.00 35.76 2.92
5568 7831 1.224592 GAGGCACCCCGTTGATGAT 59.775 57.895 0.00 0.00 35.76 2.45
5569 7832 1.488705 AAGAGGCACCCCGTTGATGA 61.489 55.000 0.00 0.00 35.76 2.92
5570 7833 0.609131 AAAGAGGCACCCCGTTGATG 60.609 55.000 0.00 0.00 35.76 3.07
5571 7834 0.609131 CAAAGAGGCACCCCGTTGAT 60.609 55.000 0.00 0.00 35.76 2.57
5572 7835 1.228124 CAAAGAGGCACCCCGTTGA 60.228 57.895 0.00 0.00 35.76 3.18
5573 7836 2.268076 CCAAAGAGGCACCCCGTTG 61.268 63.158 0.00 0.00 35.76 4.10
5574 7837 2.115266 CCAAAGAGGCACCCCGTT 59.885 61.111 0.00 0.00 35.76 4.44
5575 7838 2.692273 GAACCAAAGAGGCACCCCGT 62.692 60.000 0.00 0.00 43.14 5.28
5576 7839 1.971695 GAACCAAAGAGGCACCCCG 60.972 63.158 0.00 0.00 43.14 5.73
5577 7840 1.606601 GGAACCAAAGAGGCACCCC 60.607 63.158 0.00 0.00 43.14 4.95
5578 7841 4.097218 GGAACCAAAGAGGCACCC 57.903 61.111 0.00 0.00 43.14 4.61
5592 7855 0.850100 TCAGTTTCCTTGGCAGGGAA 59.150 50.000 25.46 25.46 41.25 3.97
5593 7856 0.850100 TTCAGTTTCCTTGGCAGGGA 59.150 50.000 15.22 15.22 41.25 4.20
5594 7857 1.251251 CTTCAGTTTCCTTGGCAGGG 58.749 55.000 9.81 9.81 41.25 4.45
5595 7858 0.600057 GCTTCAGTTTCCTTGGCAGG 59.400 55.000 0.00 0.00 42.50 4.85
5596 7859 0.239347 CGCTTCAGTTTCCTTGGCAG 59.761 55.000 0.00 0.00 0.00 4.85
5597 7860 0.179032 TCGCTTCAGTTTCCTTGGCA 60.179 50.000 0.00 0.00 0.00 4.92
5598 7861 0.519077 CTCGCTTCAGTTTCCTTGGC 59.481 55.000 0.00 0.00 0.00 4.52
5599 7862 0.519077 GCTCGCTTCAGTTTCCTTGG 59.481 55.000 0.00 0.00 0.00 3.61
5600 7863 0.164647 CGCTCGCTTCAGTTTCCTTG 59.835 55.000 0.00 0.00 0.00 3.61
5601 7864 0.249911 ACGCTCGCTTCAGTTTCCTT 60.250 50.000 0.00 0.00 0.00 3.36
5602 7865 0.946221 CACGCTCGCTTCAGTTTCCT 60.946 55.000 0.00 0.00 0.00 3.36
5603 7866 0.944311 TCACGCTCGCTTCAGTTTCC 60.944 55.000 0.00 0.00 0.00 3.13
5604 7867 0.436531 CTCACGCTCGCTTCAGTTTC 59.563 55.000 0.00 0.00 0.00 2.78
5605 7868 0.032130 TCTCACGCTCGCTTCAGTTT 59.968 50.000 0.00 0.00 0.00 2.66
5606 7869 0.387878 CTCTCACGCTCGCTTCAGTT 60.388 55.000 0.00 0.00 0.00 3.16
5607 7870 1.211449 CTCTCACGCTCGCTTCAGT 59.789 57.895 0.00 0.00 0.00 3.41
5608 7871 1.515952 CCTCTCACGCTCGCTTCAG 60.516 63.158 0.00 0.00 0.00 3.02
5609 7872 2.201436 GACCTCTCACGCTCGCTTCA 62.201 60.000 0.00 0.00 0.00 3.02
5610 7873 1.515304 GACCTCTCACGCTCGCTTC 60.515 63.158 0.00 0.00 0.00 3.86
5611 7874 2.268802 TGACCTCTCACGCTCGCTT 61.269 57.895 0.00 0.00 0.00 4.68
5612 7875 2.673341 TGACCTCTCACGCTCGCT 60.673 61.111 0.00 0.00 0.00 4.93
5613 7876 2.505118 GTGACCTCTCACGCTCGC 60.505 66.667 0.00 0.00 37.67 5.03
5620 7883 2.244946 CGTGAGACGTGACCTCTCA 58.755 57.895 9.70 9.70 41.55 3.27
5639 7902 2.589442 GGACGGCGGTGAAACACA 60.589 61.111 13.24 0.00 39.98 3.72
5640 7903 3.708734 CGGACGGCGGTGAAACAC 61.709 66.667 13.24 0.00 39.98 3.32
5641 7904 2.718747 AATCGGACGGCGGTGAAACA 62.719 55.000 13.24 0.00 39.98 2.83
5642 7905 0.737019 TAATCGGACGGCGGTGAAAC 60.737 55.000 13.24 0.00 0.00 2.78
5643 7906 0.737019 GTAATCGGACGGCGGTGAAA 60.737 55.000 13.24 0.00 0.00 2.69
5644 7907 1.153784 GTAATCGGACGGCGGTGAA 60.154 57.895 13.24 0.00 0.00 3.18
5645 7908 2.491152 GTAATCGGACGGCGGTGA 59.509 61.111 13.24 6.11 0.00 4.02
5646 7909 2.584143 GGTAATCGGACGGCGGTG 60.584 66.667 13.24 0.00 0.00 4.94
5647 7910 3.069946 TGGTAATCGGACGGCGGT 61.070 61.111 13.24 0.00 0.00 5.68
5648 7911 2.279252 CTGGTAATCGGACGGCGG 60.279 66.667 13.24 0.00 0.00 6.13
5649 7912 1.876714 CACTGGTAATCGGACGGCG 60.877 63.158 4.80 4.80 0.00 6.46
5650 7913 2.171725 GCACTGGTAATCGGACGGC 61.172 63.158 0.00 0.00 0.00 5.68
5651 7914 0.108329 AAGCACTGGTAATCGGACGG 60.108 55.000 0.00 0.00 0.00 4.79
5652 7915 1.659098 GAAAGCACTGGTAATCGGACG 59.341 52.381 0.00 0.00 0.00 4.79
5653 7916 2.973945 AGAAAGCACTGGTAATCGGAC 58.026 47.619 0.00 0.00 0.00 4.79
5654 7917 5.353394 AATAGAAAGCACTGGTAATCGGA 57.647 39.130 0.00 0.00 0.00 4.55
5655 7918 6.316390 AGAAAATAGAAAGCACTGGTAATCGG 59.684 38.462 0.00 0.00 0.00 4.18
5656 7919 7.308782 AGAAAATAGAAAGCACTGGTAATCG 57.691 36.000 0.00 0.00 0.00 3.34
5657 7920 9.914131 AAAAGAAAATAGAAAGCACTGGTAATC 57.086 29.630 0.00 0.00 0.00 1.75
5658 7921 9.914131 GAAAAGAAAATAGAAAGCACTGGTAAT 57.086 29.630 0.00 0.00 0.00 1.89
5659 7922 9.131791 AGAAAAGAAAATAGAAAGCACTGGTAA 57.868 29.630 0.00 0.00 0.00 2.85
5660 7923 8.691661 AGAAAAGAAAATAGAAAGCACTGGTA 57.308 30.769 0.00 0.00 0.00 3.25
5661 7924 7.588497 AGAAAAGAAAATAGAAAGCACTGGT 57.412 32.000 0.00 0.00 0.00 4.00
5662 7925 8.355913 AGAAGAAAAGAAAATAGAAAGCACTGG 58.644 33.333 0.00 0.00 0.00 4.00
5663 7926 9.392021 GAGAAGAAAAGAAAATAGAAAGCACTG 57.608 33.333 0.00 0.00 0.00 3.66
5664 7927 9.348476 AGAGAAGAAAAGAAAATAGAAAGCACT 57.652 29.630 0.00 0.00 0.00 4.40
5665 7928 9.958234 AAGAGAAGAAAAGAAAATAGAAAGCAC 57.042 29.630 0.00 0.00 0.00 4.40
5673 7936 9.838339 ACACAGAGAAGAGAAGAAAAGAAAATA 57.162 29.630 0.00 0.00 0.00 1.40
5674 7937 8.744568 ACACAGAGAAGAGAAGAAAAGAAAAT 57.255 30.769 0.00 0.00 0.00 1.82
5675 7938 9.099454 GTACACAGAGAAGAGAAGAAAAGAAAA 57.901 33.333 0.00 0.00 0.00 2.29
5676 7939 8.258007 TGTACACAGAGAAGAGAAGAAAAGAAA 58.742 33.333 0.00 0.00 0.00 2.52
5677 7940 7.707035 GTGTACACAGAGAAGAGAAGAAAAGAA 59.293 37.037 21.14 0.00 0.00 2.52
5678 7941 7.147897 TGTGTACACAGAGAAGAGAAGAAAAGA 60.148 37.037 24.62 0.00 36.21 2.52
5679 7942 6.980978 TGTGTACACAGAGAAGAGAAGAAAAG 59.019 38.462 24.62 0.00 36.21 2.27
5680 7943 6.873997 TGTGTACACAGAGAAGAGAAGAAAA 58.126 36.000 24.62 0.00 36.21 2.29
5681 7944 6.465439 TGTGTACACAGAGAAGAGAAGAAA 57.535 37.500 24.62 0.00 36.21 2.52
5694 7957 4.722712 AAGGCAACCCCTGTGTACACAG 62.723 54.545 38.09 38.09 45.62 3.66
5695 7958 1.149627 GGCAACCCCTGTGTACACA 59.850 57.895 26.37 26.37 39.32 3.72
5696 7959 0.179001 AAGGCAACCCCTGTGTACAC 60.179 55.000 19.36 19.36 45.62 2.90
5697 7960 0.553819 AAAGGCAACCCCTGTGTACA 59.446 50.000 0.00 0.00 45.62 2.90
5698 7961 1.699730 AAAAGGCAACCCCTGTGTAC 58.300 50.000 0.00 0.00 45.62 2.90
5699 7962 3.692690 GATAAAAGGCAACCCCTGTGTA 58.307 45.455 0.00 0.00 45.62 2.90
5700 7963 2.525368 GATAAAAGGCAACCCCTGTGT 58.475 47.619 0.00 0.00 45.62 3.72
5701 7964 1.472480 CGATAAAAGGCAACCCCTGTG 59.528 52.381 0.00 0.00 45.62 3.66
5702 7965 1.353022 TCGATAAAAGGCAACCCCTGT 59.647 47.619 0.00 0.00 45.62 4.00
5703 7966 2.017049 CTCGATAAAAGGCAACCCCTG 58.983 52.381 0.00 0.00 45.62 4.45


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

AutoCloner maintained by Alex Coulton.