Multiple sequence alignment - TraesCS1D01G195100

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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 TraesCS1D01G195100 chr1D 100.000 4051 0 0 1 4051 273814892 273818942 0.000000e+00 7481.0
1 TraesCS1D01G195100 chr1D 89.024 164 15 3 1348 1510 193504381 193504542 2.470000e-47 200.0
2 TraesCS1D01G195100 chr1A 91.510 2026 98 33 522 2504 345787566 345789560 0.000000e+00 2721.0
3 TraesCS1D01G195100 chr1A 96.211 1003 29 5 2604 3600 345789555 345790554 0.000000e+00 1633.0
4 TraesCS1D01G195100 chr1A 89.753 527 27 13 1 515 345787003 345787514 0.000000e+00 649.0
5 TraesCS1D01G195100 chr1A 87.629 291 33 1 3607 3894 345790814 345791104 6.490000e-88 335.0
6 TraesCS1D01G195100 chr1A 92.500 120 7 1 2492 2609 474171112 474171231 1.940000e-38 171.0
7 TraesCS1D01G195100 chr1B 93.996 1449 58 4 2604 4051 373146599 373148019 0.000000e+00 2167.0
8 TraesCS1D01G195100 chr1B 90.568 1548 75 34 1 1519 373144080 373145585 0.000000e+00 1984.0
9 TraesCS1D01G195100 chr1B 92.483 1011 37 12 1511 2504 373145616 373146604 0.000000e+00 1410.0
10 TraesCS1D01G195100 chr1B 97.222 108 3 0 2500 2607 626498570 626498463 2.490000e-42 183.0
11 TraesCS1D01G195100 chr1B 95.370 108 5 0 2500 2607 57618242 57618135 5.380000e-39 172.0
12 TraesCS1D01G195100 chr4D 90.184 163 12 4 1344 1504 74079344 74079504 4.100000e-50 209.0
13 TraesCS1D01G195100 chr3D 90.968 155 10 4 1351 1503 315480426 315480578 5.310000e-49 206.0
14 TraesCS1D01G195100 chr5D 89.157 166 8 9 1351 1511 233044443 233044603 8.880000e-47 198.0
15 TraesCS1D01G195100 chr5D 95.495 111 5 0 2497 2607 547057208 547057318 1.160000e-40 178.0
16 TraesCS1D01G195100 chr6D 88.485 165 15 4 1342 1504 392273064 392273226 3.190000e-46 196.0
17 TraesCS1D01G195100 chr6D 87.719 171 18 3 1351 1520 410398430 410398262 3.190000e-46 196.0
18 TraesCS1D01G195100 chr6B 87.719 171 18 3 1351 1520 617176733 617176565 3.190000e-46 196.0
19 TraesCS1D01G195100 chr7D 93.913 115 5 2 2494 2607 35557845 35557958 5.380000e-39 172.0
20 TraesCS1D01G195100 chr7D 88.235 51 6 0 494 544 424917784 424917734 1.220000e-05 62.1
21 TraesCS1D01G195100 chr7D 89.583 48 5 0 494 541 502342306 502342353 1.220000e-05 62.1
22 TraesCS1D01G195100 chr5B 95.370 108 5 0 2500 2607 511610850 511610743 5.380000e-39 172.0
23 TraesCS1D01G195100 chr5B 93.023 43 3 0 492 534 458055389 458055431 3.380000e-06 63.9
24 TraesCS1D01G195100 chr5A 92.500 120 7 1 2492 2609 367605501 367605382 1.940000e-38 171.0
25 TraesCS1D01G195100 chr3B 93.860 114 5 2 2499 2612 630305544 630305433 1.940000e-38 171.0
26 TraesCS1D01G195100 chr7B 91.667 120 8 1 2492 2609 44762875 44762994 9.010000e-37 165.0
27 TraesCS1D01G195100 chr4B 97.674 43 1 0 492 534 603518488 603518446 1.560000e-09 75.0
28 TraesCS1D01G195100 chr3A 81.818 77 11 2 495 569 1250623 1250548 1.220000e-05 62.1
29 TraesCS1D01G195100 chr3A 81.818 77 11 2 495 569 1264334 1264259 1.220000e-05 62.1
30 TraesCS1D01G195100 chr2A 89.583 48 5 0 494 541 504837538 504837585 1.220000e-05 62.1
31 TraesCS1D01G195100 chr2B 83.582 67 8 3 467 533 110829703 110829640 4.370000e-05 60.2


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 TraesCS1D01G195100 chr1D 273814892 273818942 4050 False 7481.000000 7481 100.00000 1 4051 1 chr1D.!!$F2 4050
1 TraesCS1D01G195100 chr1A 345787003 345791104 4101 False 1334.500000 2721 91.27575 1 3894 4 chr1A.!!$F2 3893
2 TraesCS1D01G195100 chr1B 373144080 373148019 3939 False 1853.666667 2167 92.34900 1 4051 3 chr1B.!!$F1 4050

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
660 721 0.030908 GAGTTAGTGCGGATCCGGAG 59.969 60.0 33.98 8.59 41.08 4.63 F
2523 2667 0.108019 ACCTCCGTCCGAAAAAGCTT 59.892 50.0 0.00 0.00 0.00 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2589 2733 0.038744 AGTACTCCCTCCGTCCGAAA 59.961 55.0 0.0 0.0 0.00 3.46 R
4000 4407 0.980423 GACTCAGCCCTGAAGGAAGT 59.020 55.0 0.0 0.0 39.39 3.01 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
49 54 1.060729 TCCGACTTTGTTGGATGGGA 58.939 50.000 2.73 0.00 40.82 4.37
50 55 1.633432 TCCGACTTTGTTGGATGGGAT 59.367 47.619 2.73 0.00 40.82 3.85
52 57 2.164219 CCGACTTTGTTGGATGGGATTG 59.836 50.000 0.00 0.00 39.36 2.67
53 58 2.164219 CGACTTTGTTGGATGGGATTGG 59.836 50.000 0.00 0.00 0.00 3.16
56 61 3.246094 ACTTTGTTGGATGGGATTGGGAT 60.246 43.478 0.00 0.00 0.00 3.85
57 62 3.488355 TTGTTGGATGGGATTGGGATT 57.512 42.857 0.00 0.00 0.00 3.01
58 63 3.030873 TGTTGGATGGGATTGGGATTC 57.969 47.619 0.00 0.00 0.00 2.52
59 64 1.956477 GTTGGATGGGATTGGGATTCG 59.044 52.381 0.00 0.00 0.00 3.34
60 65 1.517238 TGGATGGGATTGGGATTCGA 58.483 50.000 0.00 0.00 0.00 3.71
61 66 2.065007 TGGATGGGATTGGGATTCGAT 58.935 47.619 0.00 0.00 0.00 3.59
75 80 0.538516 TTCGATTGTGGTTGGGTGGG 60.539 55.000 0.00 0.00 0.00 4.61
175 182 3.938334 GACCCAGATTCTCTTCTTTCTGC 59.062 47.826 0.00 0.00 35.38 4.26
191 201 9.979578 CTTCTTTCTGCTAGCCTATATATATGG 57.020 37.037 13.29 2.22 0.00 2.74
317 333 1.145803 GAACGCCACCTGACTGTAAC 58.854 55.000 0.00 0.00 0.00 2.50
324 340 3.317993 GCCACCTGACTGTAACATGTTTT 59.682 43.478 17.78 0.00 0.00 2.43
329 345 6.147821 CACCTGACTGTAACATGTTTTCCTAG 59.852 42.308 17.78 10.34 0.00 3.02
331 347 6.934645 CCTGACTGTAACATGTTTTCCTAGAA 59.065 38.462 17.78 0.00 0.00 2.10
358 374 2.110967 CGACCTGCTGAGCCATTGG 61.111 63.158 0.23 0.00 0.00 3.16
392 409 3.787785 CGAGAGCTGTAGACTGTAGAGA 58.212 50.000 0.00 0.00 0.00 3.10
393 410 3.802139 CGAGAGCTGTAGACTGTAGAGAG 59.198 52.174 0.00 0.00 0.00 3.20
395 412 5.450826 CGAGAGCTGTAGACTGTAGAGAGTA 60.451 48.000 0.00 0.00 0.00 2.59
396 413 5.914033 AGAGCTGTAGACTGTAGAGAGTAG 58.086 45.833 0.00 0.00 0.00 2.57
397 414 5.659525 AGAGCTGTAGACTGTAGAGAGTAGA 59.340 44.000 0.00 0.00 0.00 2.59
398 415 5.914033 AGCTGTAGACTGTAGAGAGTAGAG 58.086 45.833 0.00 0.00 0.00 2.43
399 416 5.424252 AGCTGTAGACTGTAGAGAGTAGAGT 59.576 44.000 0.00 0.00 0.00 3.24
400 417 6.608405 AGCTGTAGACTGTAGAGAGTAGAGTA 59.392 42.308 0.00 0.00 0.00 2.59
401 418 6.921857 GCTGTAGACTGTAGAGAGTAGAGTAG 59.078 46.154 0.00 0.00 0.00 2.57
417 434 4.954875 AGAGTAGATAGCACCATTTGAGC 58.045 43.478 0.00 0.00 0.00 4.26
442 459 4.466015 GCTCCACCCCATGATAAAGAAAAA 59.534 41.667 0.00 0.00 0.00 1.94
549 610 5.724854 AGGGAGTACCAGCTAGAATTTGTAA 59.275 40.000 0.00 0.00 43.89 2.41
573 634 5.010922 ACAAAATCAGCAACATTGAAGGCTA 59.989 36.000 0.00 0.00 34.25 3.93
575 636 5.726980 AATCAGCAACATTGAAGGCTAAA 57.273 34.783 0.00 0.00 34.25 1.85
576 637 4.771590 TCAGCAACATTGAAGGCTAAAG 57.228 40.909 0.00 0.00 34.25 1.85
577 638 4.144297 TCAGCAACATTGAAGGCTAAAGT 58.856 39.130 0.00 0.00 34.25 2.66
578 639 4.022935 TCAGCAACATTGAAGGCTAAAGTG 60.023 41.667 0.00 0.00 34.25 3.16
579 640 3.256631 AGCAACATTGAAGGCTAAAGTGG 59.743 43.478 0.00 0.00 34.25 4.00
580 641 3.578688 CAACATTGAAGGCTAAAGTGGC 58.421 45.455 0.00 0.00 0.00 5.01
581 642 1.812571 ACATTGAAGGCTAAAGTGGCG 59.187 47.619 0.00 0.00 37.59 5.69
582 643 2.083774 CATTGAAGGCTAAAGTGGCGA 58.916 47.619 0.00 0.00 37.59 5.54
583 644 1.808411 TTGAAGGCTAAAGTGGCGAG 58.192 50.000 0.00 0.00 37.59 5.03
584 645 0.685097 TGAAGGCTAAAGTGGCGAGT 59.315 50.000 0.00 0.00 37.59 4.18
585 646 1.071699 TGAAGGCTAAAGTGGCGAGTT 59.928 47.619 0.00 0.00 37.59 3.01
586 647 2.300723 TGAAGGCTAAAGTGGCGAGTTA 59.699 45.455 0.00 0.00 37.59 2.24
587 648 2.674796 AGGCTAAAGTGGCGAGTTAG 57.325 50.000 0.00 0.00 37.59 2.34
588 649 1.900486 AGGCTAAAGTGGCGAGTTAGT 59.100 47.619 0.00 0.00 37.59 2.24
589 650 2.000447 GGCTAAAGTGGCGAGTTAGTG 59.000 52.381 0.00 0.00 0.00 2.74
660 721 0.030908 GAGTTAGTGCGGATCCGGAG 59.969 60.000 33.98 8.59 41.08 4.63
678 739 3.666902 CGGAGTAACGTGGCAGAAATTTG 60.667 47.826 0.00 0.00 0.00 2.32
743 804 2.598098 AATACCCGTTACGCCCCTGC 62.598 60.000 0.00 0.00 0.00 4.85
787 848 1.144496 GGCCGTAAATACCAGCGGA 59.856 57.895 5.99 0.00 46.33 5.54
1117 1194 0.684805 CGTCCAGTAAGCCTCCTCCT 60.685 60.000 0.00 0.00 0.00 3.69
1118 1195 1.116308 GTCCAGTAAGCCTCCTCCTC 58.884 60.000 0.00 0.00 0.00 3.71
1119 1196 0.710588 TCCAGTAAGCCTCCTCCTCA 59.289 55.000 0.00 0.00 0.00 3.86
1171 1254 1.332144 ACGCCGTAAAGGATGGGCTA 61.332 55.000 0.00 0.00 45.00 3.93
1237 1320 2.207229 GGGAAGGGCGTGCCTTTTT 61.207 57.895 9.77 2.93 35.44 1.94
1261 1344 1.299976 GGCGAGAGTGGATTTGGGT 59.700 57.895 0.00 0.00 0.00 4.51
1280 1363 3.428862 GGGTGTTTATTGGCTTGGATTCG 60.429 47.826 0.00 0.00 0.00 3.34
1355 1438 9.244292 GGAGGAAATATTTTAAGAAACACTCCT 57.756 33.333 1.43 0.00 36.30 3.69
1369 1452 3.490348 ACACTCCTTCCCTTCACAAATG 58.510 45.455 0.00 0.00 0.00 2.32
1378 1461 6.209391 CCTTCCCTTCACAAATGTAAAGATGT 59.791 38.462 0.00 0.00 0.00 3.06
1462 1550 5.791336 TCAGTCCACATGTAGTCCATATC 57.209 43.478 0.00 0.00 30.71 1.63
1539 1666 2.582052 CCAGCTTTTGGTACTGGTTCA 58.418 47.619 0.00 0.00 44.91 3.18
1562 1689 4.900635 ATCCTGCCATTCGTAAAATGTC 57.099 40.909 0.00 0.00 0.00 3.06
1580 1707 2.029918 TGTCGTCAGAGTTCCATCACAG 60.030 50.000 0.00 0.00 0.00 3.66
1601 1735 7.771826 TCACAGTATTGTAGGTTTATTAAGGCC 59.228 37.037 0.00 0.00 35.25 5.19
1674 1808 9.950680 GGCAAAACATATATATACATACCATGC 57.049 33.333 0.00 1.38 0.00 4.06
1771 1905 0.466189 CACGCCTAAGGGGATGCATT 60.466 55.000 0.00 0.00 39.07 3.56
1801 1935 1.207329 GAGCCCCGTCAGATTGTAAGT 59.793 52.381 0.00 0.00 0.00 2.24
1825 1959 2.689553 TCAAGGATTATGCGCTGACA 57.310 45.000 9.73 0.00 0.00 3.58
1864 1998 5.132648 AGGACATAGGATTTCCATGTGCTTA 59.867 40.000 20.07 0.00 44.73 3.09
1879 2013 7.665559 TCCATGTGCTTAGTATCAATATTTCCC 59.334 37.037 0.00 0.00 0.00 3.97
1880 2014 7.448161 CCATGTGCTTAGTATCAATATTTCCCA 59.552 37.037 0.00 0.00 0.00 4.37
1881 2015 8.509690 CATGTGCTTAGTATCAATATTTCCCAG 58.490 37.037 0.00 0.00 0.00 4.45
1882 2016 7.801104 TGTGCTTAGTATCAATATTTCCCAGA 58.199 34.615 0.00 0.00 0.00 3.86
1883 2017 8.271458 TGTGCTTAGTATCAATATTTCCCAGAA 58.729 33.333 0.00 0.00 0.00 3.02
1884 2018 8.778358 GTGCTTAGTATCAATATTTCCCAGAAG 58.222 37.037 0.00 0.00 0.00 2.85
1885 2019 8.713971 TGCTTAGTATCAATATTTCCCAGAAGA 58.286 33.333 0.00 0.00 0.00 2.87
1886 2020 9.732130 GCTTAGTATCAATATTTCCCAGAAGAT 57.268 33.333 0.00 0.00 0.00 2.40
1906 2040 4.777896 AGATTTTCTAGTGCACTACCAGGA 59.222 41.667 22.67 15.10 0.00 3.86
1912 2046 1.344763 AGTGCACTACCAGGAAGTGTC 59.655 52.381 20.16 0.00 45.01 3.67
1913 2047 1.070134 GTGCACTACCAGGAAGTGTCA 59.930 52.381 10.32 1.78 45.01 3.58
1935 2069 8.267183 TGTCACACACTATCTATTGATTGGATT 58.733 33.333 0.00 0.00 34.32 3.01
2143 2277 7.094377 TGTCTATGGTCTTACAGCCAAAAATTC 60.094 37.037 0.00 0.00 38.38 2.17
2299 2433 6.155910 CACTTATCAGCTACATATCCCTCCAT 59.844 42.308 0.00 0.00 0.00 3.41
2328 2462 6.374417 TCCCTCAGTTCTTAAAACTGCTAT 57.626 37.500 18.14 0.00 45.34 2.97
2356 2490 5.418840 CAGTTACATAATCAGCCCAAAACCT 59.581 40.000 0.00 0.00 0.00 3.50
2437 2581 8.246180 CACATTTTGGCTTTGTGTATCTCTATT 58.754 33.333 0.00 0.00 36.77 1.73
2498 2642 7.147724 CCAGTCTGTACCCTGTTTAGATATCAA 60.148 40.741 5.32 0.00 0.00 2.57
2499 2643 7.923344 CAGTCTGTACCCTGTTTAGATATCAAG 59.077 40.741 5.32 0.00 0.00 3.02
2500 2644 7.620094 AGTCTGTACCCTGTTTAGATATCAAGT 59.380 37.037 5.32 0.00 0.00 3.16
2501 2645 8.910944 GTCTGTACCCTGTTTAGATATCAAGTA 58.089 37.037 5.32 0.00 0.00 2.24
2502 2646 8.910944 TCTGTACCCTGTTTAGATATCAAGTAC 58.089 37.037 5.32 5.40 0.00 2.73
2503 2647 8.834004 TGTACCCTGTTTAGATATCAAGTACT 57.166 34.615 5.32 0.00 0.00 2.73
2504 2648 9.925545 TGTACCCTGTTTAGATATCAAGTACTA 57.074 33.333 5.32 0.00 0.00 1.82
2506 2650 8.247666 ACCCTGTTTAGATATCAAGTACTACC 57.752 38.462 5.32 0.00 0.00 3.18
2507 2651 8.066247 ACCCTGTTTAGATATCAAGTACTACCT 58.934 37.037 5.32 0.00 0.00 3.08
2508 2652 8.578151 CCCTGTTTAGATATCAAGTACTACCTC 58.422 40.741 5.32 0.00 0.00 3.85
2509 2653 8.578151 CCTGTTTAGATATCAAGTACTACCTCC 58.422 40.741 5.32 0.00 0.00 4.30
2510 2654 8.162878 TGTTTAGATATCAAGTACTACCTCCG 57.837 38.462 5.32 0.00 0.00 4.63
2511 2655 7.776969 TGTTTAGATATCAAGTACTACCTCCGT 59.223 37.037 5.32 0.00 0.00 4.69
2512 2656 7.976135 TTAGATATCAAGTACTACCTCCGTC 57.024 40.000 5.32 0.00 0.00 4.79
2513 2657 5.315348 AGATATCAAGTACTACCTCCGTCC 58.685 45.833 5.32 0.00 0.00 4.79
2514 2658 1.742761 TCAAGTACTACCTCCGTCCG 58.257 55.000 0.00 0.00 0.00 4.79
2515 2659 1.278985 TCAAGTACTACCTCCGTCCGA 59.721 52.381 0.00 0.00 0.00 4.55
2516 2660 2.086869 CAAGTACTACCTCCGTCCGAA 58.913 52.381 0.00 0.00 0.00 4.30
2517 2661 2.489329 CAAGTACTACCTCCGTCCGAAA 59.511 50.000 0.00 0.00 0.00 3.46
2518 2662 2.795329 AGTACTACCTCCGTCCGAAAA 58.205 47.619 0.00 0.00 0.00 2.29
2519 2663 3.157087 AGTACTACCTCCGTCCGAAAAA 58.843 45.455 0.00 0.00 0.00 1.94
2520 2664 2.738013 ACTACCTCCGTCCGAAAAAG 57.262 50.000 0.00 0.00 0.00 2.27
2521 2665 1.337541 ACTACCTCCGTCCGAAAAAGC 60.338 52.381 0.00 0.00 0.00 3.51
2522 2666 0.971386 TACCTCCGTCCGAAAAAGCT 59.029 50.000 0.00 0.00 0.00 3.74
2523 2667 0.108019 ACCTCCGTCCGAAAAAGCTT 59.892 50.000 0.00 0.00 0.00 3.74
2524 2668 0.517316 CCTCCGTCCGAAAAAGCTTG 59.483 55.000 0.00 0.00 0.00 4.01
2525 2669 1.226746 CTCCGTCCGAAAAAGCTTGT 58.773 50.000 0.00 0.00 0.00 3.16
2526 2670 1.194772 CTCCGTCCGAAAAAGCTTGTC 59.805 52.381 0.00 0.00 0.00 3.18
2527 2671 0.237498 CCGTCCGAAAAAGCTTGTCC 59.763 55.000 0.00 0.00 0.00 4.02
2528 2672 0.237498 CGTCCGAAAAAGCTTGTCCC 59.763 55.000 0.00 0.00 0.00 4.46
2529 2673 1.605753 GTCCGAAAAAGCTTGTCCCT 58.394 50.000 0.00 0.00 0.00 4.20
2530 2674 1.535896 GTCCGAAAAAGCTTGTCCCTC 59.464 52.381 0.00 0.00 0.00 4.30
2531 2675 1.142060 TCCGAAAAAGCTTGTCCCTCA 59.858 47.619 0.00 0.00 0.00 3.86
2532 2676 1.953686 CCGAAAAAGCTTGTCCCTCAA 59.046 47.619 0.00 0.00 34.61 3.02
2533 2677 2.360801 CCGAAAAAGCTTGTCCCTCAAA 59.639 45.455 0.00 0.00 35.48 2.69
2534 2678 3.005791 CCGAAAAAGCTTGTCCCTCAAAT 59.994 43.478 0.00 0.00 35.48 2.32
2535 2679 3.983344 CGAAAAAGCTTGTCCCTCAAATG 59.017 43.478 0.00 0.00 35.48 2.32
2536 2680 4.309933 GAAAAAGCTTGTCCCTCAAATGG 58.690 43.478 0.00 0.00 35.48 3.16
2537 2681 2.978156 AAGCTTGTCCCTCAAATGGA 57.022 45.000 0.00 0.00 35.48 3.41
2538 2682 3.463048 AAGCTTGTCCCTCAAATGGAT 57.537 42.857 0.00 0.00 35.48 3.41
2539 2683 2.731572 AGCTTGTCCCTCAAATGGATG 58.268 47.619 0.00 0.00 35.48 3.51
2540 2684 2.042162 AGCTTGTCCCTCAAATGGATGT 59.958 45.455 0.00 0.00 35.48 3.06
2541 2685 3.266772 AGCTTGTCCCTCAAATGGATGTA 59.733 43.478 0.00 0.00 35.48 2.29
2542 2686 4.079558 AGCTTGTCCCTCAAATGGATGTAT 60.080 41.667 0.00 0.00 35.48 2.29
2543 2687 4.276926 GCTTGTCCCTCAAATGGATGTATC 59.723 45.833 0.00 0.00 35.48 2.24
2544 2688 5.688807 CTTGTCCCTCAAATGGATGTATCT 58.311 41.667 0.00 0.00 35.48 1.98
2545 2689 6.688922 GCTTGTCCCTCAAATGGATGTATCTA 60.689 42.308 0.00 0.00 35.48 1.98
2546 2690 6.425210 TGTCCCTCAAATGGATGTATCTAG 57.575 41.667 0.00 0.00 33.65 2.43
2547 2691 5.221722 TGTCCCTCAAATGGATGTATCTAGC 60.222 44.000 0.00 0.00 33.65 3.42
2548 2692 4.907269 TCCCTCAAATGGATGTATCTAGCA 59.093 41.667 0.00 0.00 0.00 3.49
2549 2693 4.999950 CCCTCAAATGGATGTATCTAGCAC 59.000 45.833 0.00 0.00 0.00 4.40
2550 2694 5.221803 CCCTCAAATGGATGTATCTAGCACT 60.222 44.000 0.00 0.00 0.00 4.40
2551 2695 6.014242 CCCTCAAATGGATGTATCTAGCACTA 60.014 42.308 0.00 0.00 0.00 2.74
2552 2696 7.445121 CCTCAAATGGATGTATCTAGCACTAA 58.555 38.462 0.00 0.00 0.00 2.24
2553 2697 7.386299 CCTCAAATGGATGTATCTAGCACTAAC 59.614 40.741 0.00 0.00 0.00 2.34
2554 2698 8.023021 TCAAATGGATGTATCTAGCACTAACT 57.977 34.615 0.00 0.00 0.00 2.24
2555 2699 8.486210 TCAAATGGATGTATCTAGCACTAACTT 58.514 33.333 0.00 0.00 0.00 2.66
2556 2700 8.554528 CAAATGGATGTATCTAGCACTAACTTG 58.445 37.037 0.00 0.00 0.00 3.16
2557 2701 6.161855 TGGATGTATCTAGCACTAACTTGG 57.838 41.667 0.00 0.00 0.00 3.61
2558 2702 5.661312 TGGATGTATCTAGCACTAACTTGGT 59.339 40.000 0.00 0.00 0.00 3.67
2559 2703 5.986135 GGATGTATCTAGCACTAACTTGGTG 59.014 44.000 0.97 0.97 37.70 4.17
2572 2716 8.039603 CACTAACTTGGTGCTAAATACATTCA 57.960 34.615 0.00 0.00 0.00 2.57
2573 2717 8.677300 CACTAACTTGGTGCTAAATACATTCAT 58.323 33.333 0.00 0.00 0.00 2.57
2574 2718 9.243105 ACTAACTTGGTGCTAAATACATTCATT 57.757 29.630 0.00 0.00 0.00 2.57
2576 2720 8.761575 AACTTGGTGCTAAATACATTCATTTG 57.238 30.769 0.00 0.00 30.84 2.32
2577 2721 8.121305 ACTTGGTGCTAAATACATTCATTTGA 57.879 30.769 0.00 0.00 30.84 2.69
2578 2722 8.246180 ACTTGGTGCTAAATACATTCATTTGAG 58.754 33.333 0.00 0.00 30.84 3.02
2579 2723 7.099266 TGGTGCTAAATACATTCATTTGAGG 57.901 36.000 0.00 0.00 30.84 3.86
2580 2724 6.096705 TGGTGCTAAATACATTCATTTGAGGG 59.903 38.462 0.00 0.00 30.84 4.30
2581 2725 6.321181 GGTGCTAAATACATTCATTTGAGGGA 59.679 38.462 0.00 0.00 30.84 4.20
2582 2726 7.196331 GTGCTAAATACATTCATTTGAGGGAC 58.804 38.462 0.00 0.00 30.84 4.46
2583 2727 6.889177 TGCTAAATACATTCATTTGAGGGACA 59.111 34.615 0.00 0.00 30.84 4.02
2584 2728 7.395772 TGCTAAATACATTCATTTGAGGGACAA 59.604 33.333 0.00 0.00 36.65 3.18
2585 2729 7.917505 GCTAAATACATTCATTTGAGGGACAAG 59.082 37.037 0.00 0.00 39.77 3.16
2586 2730 5.841957 ATACATTCATTTGAGGGACAAGC 57.158 39.130 0.00 0.00 39.77 4.01
2587 2731 3.771216 ACATTCATTTGAGGGACAAGCT 58.229 40.909 0.00 0.00 39.77 3.74
2588 2732 4.154942 ACATTCATTTGAGGGACAAGCTT 58.845 39.130 0.00 0.00 39.77 3.74
2589 2733 4.590222 ACATTCATTTGAGGGACAAGCTTT 59.410 37.500 0.00 0.00 39.77 3.51
2590 2734 5.070847 ACATTCATTTGAGGGACAAGCTTTT 59.929 36.000 0.00 0.00 39.77 2.27
2591 2735 5.612725 TTCATTTGAGGGACAAGCTTTTT 57.387 34.783 0.00 0.00 39.77 1.94
2592 2736 5.200368 TCATTTGAGGGACAAGCTTTTTC 57.800 39.130 0.00 0.00 39.77 2.29
2593 2737 3.708563 TTTGAGGGACAAGCTTTTTCG 57.291 42.857 0.00 0.00 39.77 3.46
2594 2738 1.604604 TGAGGGACAAGCTTTTTCGG 58.395 50.000 0.00 0.00 0.00 4.30
2595 2739 1.142060 TGAGGGACAAGCTTTTTCGGA 59.858 47.619 0.00 0.00 0.00 4.55
2596 2740 1.535896 GAGGGACAAGCTTTTTCGGAC 59.464 52.381 0.00 0.00 0.00 4.79
2597 2741 0.237498 GGGACAAGCTTTTTCGGACG 59.763 55.000 0.00 0.00 0.00 4.79
2598 2742 0.237498 GGACAAGCTTTTTCGGACGG 59.763 55.000 0.00 0.00 0.00 4.79
2599 2743 1.223187 GACAAGCTTTTTCGGACGGA 58.777 50.000 0.00 0.00 0.00 4.69
2600 2744 1.194772 GACAAGCTTTTTCGGACGGAG 59.805 52.381 0.00 0.00 0.00 4.63
2601 2745 0.517316 CAAGCTTTTTCGGACGGAGG 59.483 55.000 0.00 0.00 0.00 4.30
2602 2746 0.605589 AAGCTTTTTCGGACGGAGGG 60.606 55.000 0.00 0.00 0.00 4.30
2650 2794 6.662414 TGCTTGAATGTATAAAGAACCTCG 57.338 37.500 0.00 0.00 0.00 4.63
2666 2810 0.249405 CTCGATGCAAGAGAGCCTCC 60.249 60.000 15.10 0.00 37.93 4.30
2673 2817 0.676151 CAAGAGAGCCTCCAAGTGCC 60.676 60.000 0.00 0.00 0.00 5.01
3016 3162 2.640826 ACAGAGGTGAAATTAACGGGGA 59.359 45.455 0.00 0.00 0.00 4.81
3073 3219 7.648510 GTGATTTATCTGTACTGTAGCAGGTAC 59.351 40.741 2.56 2.56 35.51 3.34
3109 3256 0.975887 TTGGCTTGGAAGGAATTGGC 59.024 50.000 0.00 0.00 0.00 4.52
3119 3266 3.945285 GGAAGGAATTGGCGTGAGAATTA 59.055 43.478 0.00 0.00 0.00 1.40
3123 3270 5.010282 AGGAATTGGCGTGAGAATTAGTTT 58.990 37.500 0.00 0.00 0.00 2.66
3128 3275 8.515473 AATTGGCGTGAGAATTAGTTTAAAAC 57.485 30.769 0.00 0.00 0.00 2.43
3198 3345 1.530419 GTGGGGTGCCATGTCAACA 60.530 57.895 0.00 0.00 0.00 3.33
3205 3352 2.401766 GCCATGTCAACAGCCCTCG 61.402 63.158 0.00 0.00 0.00 4.63
3210 3357 1.069090 GTCAACAGCCCTCGTGTCA 59.931 57.895 0.00 0.00 0.00 3.58
3218 3365 1.899437 GCCCTCGTGTCATTCTGGGA 61.899 60.000 0.00 0.00 36.90 4.37
3219 3366 0.108138 CCCTCGTGTCATTCTGGGAC 60.108 60.000 0.00 0.00 36.90 4.46
3255 3402 6.126911 TGGTGATGGTTATGTATCTGTAAGCA 60.127 38.462 0.00 0.00 41.01 3.91
3344 3491 7.905604 TGATACCAGTAATCTTGTCTTGTTG 57.094 36.000 0.00 0.00 0.00 3.33
3365 3515 6.127814 TGTTGCTTGAGATTTGATCTGGAATC 60.128 38.462 0.00 1.98 40.38 2.52
3455 3606 2.346766 TGTGACCAACTGAAGCATGT 57.653 45.000 0.00 0.00 0.00 3.21
3649 4053 2.047061 AGTCAGTCAGGTTACCTTGCA 58.953 47.619 0.00 0.00 0.00 4.08
3689 4093 5.122711 CGGAGTTGTATCAAACGGGTAATTT 59.877 40.000 0.00 0.00 35.13 1.82
3700 4104 3.558033 ACGGGTAATTTCCACACAAGTT 58.442 40.909 3.30 0.00 0.00 2.66
3843 4247 7.706179 ACACAAAATCTGAACCATTTGTACTTG 59.294 33.333 11.32 5.42 42.36 3.16
4000 4407 4.641396 AGTCACCGTCTTCATCAAAATCA 58.359 39.130 0.00 0.00 0.00 2.57
4006 4413 4.697352 CCGTCTTCATCAAAATCACTTCCT 59.303 41.667 0.00 0.00 0.00 3.36
4013 4420 3.157087 TCAAAATCACTTCCTTCAGGGC 58.843 45.455 0.00 0.00 35.41 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.369756 GGACGATCGCATTACAGTTTTGA 59.630 43.478 16.60 0.00 0.00 2.69
49 54 2.760092 CCAACCACAATCGAATCCCAAT 59.240 45.455 0.00 0.00 0.00 3.16
50 55 2.166829 CCAACCACAATCGAATCCCAA 58.833 47.619 0.00 0.00 0.00 4.12
52 57 1.102978 CCCAACCACAATCGAATCCC 58.897 55.000 0.00 0.00 0.00 3.85
53 58 1.472480 CACCCAACCACAATCGAATCC 59.528 52.381 0.00 0.00 0.00 3.01
56 61 0.538516 CCCACCCAACCACAATCGAA 60.539 55.000 0.00 0.00 0.00 3.71
57 62 1.074072 CCCACCCAACCACAATCGA 59.926 57.895 0.00 0.00 0.00 3.59
58 63 1.074072 TCCCACCCAACCACAATCG 59.926 57.895 0.00 0.00 0.00 3.34
59 64 1.241315 CGTCCCACCCAACCACAATC 61.241 60.000 0.00 0.00 0.00 2.67
60 65 1.228429 CGTCCCACCCAACCACAAT 60.228 57.895 0.00 0.00 0.00 2.71
61 66 2.193517 CGTCCCACCCAACCACAA 59.806 61.111 0.00 0.00 0.00 3.33
75 80 3.482783 GCTGCTGAAGGCGACGTC 61.483 66.667 5.18 5.18 45.43 4.34
190 200 4.065789 ACAAAGCTAGCAGAACAAGTACC 58.934 43.478 18.83 0.00 0.00 3.34
191 201 5.674933 AACAAAGCTAGCAGAACAAGTAC 57.325 39.130 18.83 0.00 0.00 2.73
294 310 0.320374 CAGTCAGGTGGCGTTCCTAA 59.680 55.000 0.00 0.00 33.54 2.69
296 312 0.830444 TACAGTCAGGTGGCGTTCCT 60.830 55.000 0.00 0.00 35.45 3.36
317 333 6.309494 TCGACACGTATTTCTAGGAAAACATG 59.691 38.462 0.00 0.00 0.00 3.21
324 340 3.376234 CAGGTCGACACGTATTTCTAGGA 59.624 47.826 18.91 0.00 0.00 2.94
329 345 1.654105 CAGCAGGTCGACACGTATTTC 59.346 52.381 18.91 0.00 0.00 2.17
331 347 0.885879 TCAGCAGGTCGACACGTATT 59.114 50.000 18.91 0.00 0.00 1.89
358 374 1.905922 GCTCTCGCCAACTGTTGAGC 61.906 60.000 21.49 19.53 39.74 4.26
392 409 6.239176 GCTCAAATGGTGCTATCTACTCTACT 60.239 42.308 0.00 0.00 33.29 2.57
393 410 5.923684 GCTCAAATGGTGCTATCTACTCTAC 59.076 44.000 0.00 0.00 33.29 2.59
395 412 4.406972 TGCTCAAATGGTGCTATCTACTCT 59.593 41.667 0.00 0.00 36.94 3.24
396 413 4.697514 TGCTCAAATGGTGCTATCTACTC 58.302 43.478 0.00 0.00 36.94 2.59
397 414 4.701765 CTGCTCAAATGGTGCTATCTACT 58.298 43.478 0.00 0.00 36.94 2.57
398 415 3.249559 GCTGCTCAAATGGTGCTATCTAC 59.750 47.826 0.00 0.00 36.94 2.59
399 416 3.135348 AGCTGCTCAAATGGTGCTATCTA 59.865 43.478 0.00 0.00 36.94 1.98
400 417 2.092538 AGCTGCTCAAATGGTGCTATCT 60.093 45.455 0.00 0.00 36.94 1.98
401 418 2.290093 GAGCTGCTCAAATGGTGCTATC 59.710 50.000 24.02 0.00 36.94 2.08
417 434 2.173356 TCTTTATCATGGGGTGGAGCTG 59.827 50.000 0.00 0.00 0.00 4.24
523 560 3.983533 ATTCTAGCTGGTACTCCCTCT 57.016 47.619 0.00 0.00 0.00 3.69
549 610 4.060205 GCCTTCAATGTTGCTGATTTTGT 58.940 39.130 0.00 0.00 0.00 2.83
573 634 1.226746 GCACACTAACTCGCCACTTT 58.773 50.000 0.00 0.00 0.00 2.66
575 636 1.372997 CGCACACTAACTCGCCACT 60.373 57.895 0.00 0.00 0.00 4.00
576 637 3.011760 GCGCACACTAACTCGCCAC 62.012 63.158 0.30 0.00 41.53 5.01
577 638 2.736995 GCGCACACTAACTCGCCA 60.737 61.111 0.30 0.00 41.53 5.69
579 640 1.837538 TTTGGCGCACACTAACTCGC 61.838 55.000 10.83 0.00 45.99 5.03
580 641 0.584396 TTTTGGCGCACACTAACTCG 59.416 50.000 10.83 0.00 0.00 4.18
581 642 2.989422 ATTTTGGCGCACACTAACTC 57.011 45.000 10.83 0.00 0.00 3.01
582 643 2.621055 TGAATTTTGGCGCACACTAACT 59.379 40.909 10.83 0.00 0.00 2.24
583 644 3.006659 TGAATTTTGGCGCACACTAAC 57.993 42.857 10.83 0.00 0.00 2.34
584 645 3.717400 TTGAATTTTGGCGCACACTAA 57.283 38.095 10.83 2.64 0.00 2.24
585 646 3.067461 ACTTTGAATTTTGGCGCACACTA 59.933 39.130 10.83 0.00 0.00 2.74
586 647 2.159114 ACTTTGAATTTTGGCGCACACT 60.159 40.909 10.83 0.00 0.00 3.55
587 648 2.200899 ACTTTGAATTTTGGCGCACAC 58.799 42.857 10.83 0.00 0.00 3.82
588 649 2.100584 AGACTTTGAATTTTGGCGCACA 59.899 40.909 10.83 1.22 0.00 4.57
589 650 2.472488 CAGACTTTGAATTTTGGCGCAC 59.528 45.455 10.83 0.00 0.00 5.34
595 656 8.397906 TCACACTACTTCAGACTTTGAATTTTG 58.602 33.333 0.00 0.00 44.48 2.44
623 684 1.860950 CTCGCCACATTAAGACGATGG 59.139 52.381 0.00 0.00 31.59 3.51
660 721 4.165779 CCATCAAATTTCTGCCACGTTAC 58.834 43.478 0.00 0.00 0.00 2.50
678 739 4.440663 GGAGAATTAAAACTGCTGCCCATC 60.441 45.833 0.00 0.00 0.00 3.51
758 819 2.526304 TTTACGGCCTATGCTAGCAG 57.474 50.000 23.89 10.83 37.74 4.24
763 824 2.550208 GCTGGTATTTACGGCCTATGCT 60.550 50.000 0.00 0.00 37.74 3.79
853 915 2.385803 GATTCCGAGTCAAGTAGGGGA 58.614 52.381 0.00 0.00 0.00 4.81
855 917 2.108168 TGGATTCCGAGTCAAGTAGGG 58.892 52.381 0.00 0.00 0.00 3.53
856 918 3.056107 TGTTGGATTCCGAGTCAAGTAGG 60.056 47.826 0.00 0.00 0.00 3.18
1261 1344 3.126171 CGACGAATCCAAGCCAATAAACA 59.874 43.478 0.00 0.00 0.00 2.83
1280 1363 5.742453 TCTGAAATTAGCGAATACACTCGAC 59.258 40.000 0.00 0.00 41.44 4.20
1329 1412 9.244292 AGGAGTGTTTCTTAAAATATTTCCTCC 57.756 33.333 0.10 5.91 32.22 4.30
1355 1438 7.432869 CAACATCTTTACATTTGTGAAGGGAA 58.567 34.615 13.32 0.00 40.66 3.97
1539 1666 5.179368 CGACATTTTACGAATGGCAGGATAT 59.821 40.000 5.54 0.00 35.41 1.63
1562 1689 2.732412 ACTGTGATGGAACTCTGACG 57.268 50.000 0.00 0.00 0.00 4.35
1580 1707 7.558161 AACGGCCTTAATAAACCTACAATAC 57.442 36.000 0.00 0.00 0.00 1.89
1601 1735 6.968904 TCAGAAACTACCGTATTAGCTAAACG 59.031 38.462 22.96 22.96 36.42 3.60
1662 1796 2.974794 TGAGCTCAGGCATGGTATGTAT 59.025 45.455 13.74 0.00 41.70 2.29
1771 1905 2.406002 GACGGGGCTCCAAAGTTCCA 62.406 60.000 1.96 0.00 0.00 3.53
1801 1935 1.024271 GCGCATAATCCTTGAAGCCA 58.976 50.000 0.30 0.00 0.00 4.75
1825 1959 4.724279 ATGTCCTTGGAACAGTTACCTT 57.276 40.909 0.00 0.00 42.39 3.50
1837 1971 4.581824 CACATGGAAATCCTATGTCCTTGG 59.418 45.833 13.64 3.20 39.64 3.61
1838 1972 4.037208 GCACATGGAAATCCTATGTCCTTG 59.963 45.833 11.92 9.40 40.61 3.61
1848 1982 6.942532 TTGATACTAAGCACATGGAAATCC 57.057 37.500 0.00 0.00 0.00 3.01
1879 2013 6.166279 TGGTAGTGCACTAGAAAATCTTCTG 58.834 40.000 26.70 0.00 42.11 3.02
1880 2014 6.360370 TGGTAGTGCACTAGAAAATCTTCT 57.640 37.500 26.70 0.00 44.37 2.85
1881 2015 5.582665 CCTGGTAGTGCACTAGAAAATCTTC 59.417 44.000 26.70 11.32 37.96 2.87
1882 2016 5.248477 TCCTGGTAGTGCACTAGAAAATCTT 59.752 40.000 26.70 0.00 37.96 2.40
1883 2017 4.777896 TCCTGGTAGTGCACTAGAAAATCT 59.222 41.667 26.70 0.29 37.96 2.40
1884 2018 5.086104 TCCTGGTAGTGCACTAGAAAATC 57.914 43.478 26.70 13.45 37.96 2.17
1885 2019 5.013183 ACTTCCTGGTAGTGCACTAGAAAAT 59.987 40.000 26.70 13.50 37.96 1.82
1886 2020 4.347000 ACTTCCTGGTAGTGCACTAGAAAA 59.653 41.667 26.70 14.73 37.96 2.29
1887 2021 3.901844 ACTTCCTGGTAGTGCACTAGAAA 59.098 43.478 26.70 13.80 37.96 2.52
1888 2022 3.258372 CACTTCCTGGTAGTGCACTAGAA 59.742 47.826 26.70 22.33 37.96 2.10
1889 2023 2.826128 CACTTCCTGGTAGTGCACTAGA 59.174 50.000 26.70 16.98 37.96 2.43
1890 2024 2.563179 ACACTTCCTGGTAGTGCACTAG 59.437 50.000 26.70 16.82 45.38 2.57
1891 2025 2.561419 GACACTTCCTGGTAGTGCACTA 59.439 50.000 27.19 22.67 45.38 2.74
1892 2026 1.344763 GACACTTCCTGGTAGTGCACT 59.655 52.381 27.19 25.12 45.38 4.40
2143 2277 5.737353 TCATAAGAAAATAGCGTTGATGCG 58.263 37.500 0.00 0.00 40.67 4.73
2328 2462 5.685520 TGGGCTGATTATGTAACTGTGTA 57.314 39.130 0.00 0.00 0.00 2.90
2437 2581 6.731292 TGCTAGATAAATGGCAGACTCTAA 57.269 37.500 0.00 0.00 0.00 2.10
2498 2642 2.496899 TTTCGGACGGAGGTAGTACT 57.503 50.000 0.00 0.00 0.00 2.73
2499 2643 3.505836 CTTTTTCGGACGGAGGTAGTAC 58.494 50.000 0.00 0.00 0.00 2.73
2500 2644 2.094545 GCTTTTTCGGACGGAGGTAGTA 60.095 50.000 0.00 0.00 0.00 1.82
2501 2645 1.337541 GCTTTTTCGGACGGAGGTAGT 60.338 52.381 0.00 0.00 0.00 2.73
2502 2646 1.067071 AGCTTTTTCGGACGGAGGTAG 60.067 52.381 0.00 0.00 0.00 3.18
2503 2647 0.971386 AGCTTTTTCGGACGGAGGTA 59.029 50.000 0.00 0.00 0.00 3.08
2504 2648 0.108019 AAGCTTTTTCGGACGGAGGT 59.892 50.000 0.00 0.00 0.00 3.85
2505 2649 0.517316 CAAGCTTTTTCGGACGGAGG 59.483 55.000 0.00 0.00 0.00 4.30
2506 2650 1.194772 GACAAGCTTTTTCGGACGGAG 59.805 52.381 0.00 0.00 0.00 4.63
2507 2651 1.223187 GACAAGCTTTTTCGGACGGA 58.777 50.000 0.00 0.00 0.00 4.69
2508 2652 0.237498 GGACAAGCTTTTTCGGACGG 59.763 55.000 0.00 0.00 0.00 4.79
2509 2653 0.237498 GGGACAAGCTTTTTCGGACG 59.763 55.000 0.00 0.00 0.00 4.79
2510 2654 1.535896 GAGGGACAAGCTTTTTCGGAC 59.464 52.381 0.00 0.00 0.00 4.79
2511 2655 1.142060 TGAGGGACAAGCTTTTTCGGA 59.858 47.619 0.00 0.00 0.00 4.55
2512 2656 1.604604 TGAGGGACAAGCTTTTTCGG 58.395 50.000 0.00 0.00 0.00 4.30
2513 2657 3.708563 TTTGAGGGACAAGCTTTTTCG 57.291 42.857 0.00 0.00 39.77 3.46
2514 2658 4.039124 TCCATTTGAGGGACAAGCTTTTTC 59.961 41.667 0.00 0.00 39.77 2.29
2515 2659 3.966665 TCCATTTGAGGGACAAGCTTTTT 59.033 39.130 0.00 0.00 39.77 1.94
2516 2660 3.575805 TCCATTTGAGGGACAAGCTTTT 58.424 40.909 0.00 0.00 39.77 2.27
2517 2661 3.243359 TCCATTTGAGGGACAAGCTTT 57.757 42.857 0.00 0.00 39.77 3.51
2518 2662 2.978156 TCCATTTGAGGGACAAGCTT 57.022 45.000 0.00 0.00 39.77 3.74
2519 2663 2.042162 ACATCCATTTGAGGGACAAGCT 59.958 45.455 0.00 0.00 39.77 3.74
2520 2664 2.450476 ACATCCATTTGAGGGACAAGC 58.550 47.619 0.00 0.00 39.77 4.01
2521 2665 5.688807 AGATACATCCATTTGAGGGACAAG 58.311 41.667 0.00 0.00 39.77 3.16
2522 2666 5.715439 AGATACATCCATTTGAGGGACAA 57.285 39.130 0.00 0.00 37.23 3.18
2523 2667 5.221722 GCTAGATACATCCATTTGAGGGACA 60.222 44.000 0.00 0.00 37.23 4.02
2524 2668 5.221722 TGCTAGATACATCCATTTGAGGGAC 60.222 44.000 0.00 0.00 37.23 4.46
2525 2669 4.907269 TGCTAGATACATCCATTTGAGGGA 59.093 41.667 0.00 0.00 39.14 4.20
2526 2670 4.999950 GTGCTAGATACATCCATTTGAGGG 59.000 45.833 0.00 0.00 0.00 4.30
2527 2671 5.862845 AGTGCTAGATACATCCATTTGAGG 58.137 41.667 0.00 0.00 0.00 3.86
2528 2672 8.147058 AGTTAGTGCTAGATACATCCATTTGAG 58.853 37.037 0.00 0.00 0.00 3.02
2529 2673 8.023021 AGTTAGTGCTAGATACATCCATTTGA 57.977 34.615 0.00 0.00 0.00 2.69
2530 2674 8.554528 CAAGTTAGTGCTAGATACATCCATTTG 58.445 37.037 0.00 0.00 0.00 2.32
2531 2675 7.716998 CCAAGTTAGTGCTAGATACATCCATTT 59.283 37.037 0.00 0.00 0.00 2.32
2532 2676 7.147479 ACCAAGTTAGTGCTAGATACATCCATT 60.147 37.037 0.00 0.00 0.00 3.16
2533 2677 6.327626 ACCAAGTTAGTGCTAGATACATCCAT 59.672 38.462 0.00 0.00 0.00 3.41
2534 2678 5.661312 ACCAAGTTAGTGCTAGATACATCCA 59.339 40.000 0.00 0.00 0.00 3.41
2535 2679 5.986135 CACCAAGTTAGTGCTAGATACATCC 59.014 44.000 0.00 0.00 0.00 3.51
2547 2691 8.039603 TGAATGTATTTAGCACCAAGTTAGTG 57.960 34.615 0.00 0.00 38.30 2.74
2548 2692 8.807948 ATGAATGTATTTAGCACCAAGTTAGT 57.192 30.769 0.00 0.00 0.00 2.24
2550 2694 9.853555 CAAATGAATGTATTTAGCACCAAGTTA 57.146 29.630 0.00 0.00 0.00 2.24
2551 2695 8.584157 TCAAATGAATGTATTTAGCACCAAGTT 58.416 29.630 0.00 0.00 0.00 2.66
2552 2696 8.121305 TCAAATGAATGTATTTAGCACCAAGT 57.879 30.769 0.00 0.00 0.00 3.16
2553 2697 7.703621 CCTCAAATGAATGTATTTAGCACCAAG 59.296 37.037 0.00 0.00 0.00 3.61
2554 2698 7.363705 CCCTCAAATGAATGTATTTAGCACCAA 60.364 37.037 0.00 0.00 0.00 3.67
2555 2699 6.096705 CCCTCAAATGAATGTATTTAGCACCA 59.903 38.462 0.00 0.00 0.00 4.17
2556 2700 6.321181 TCCCTCAAATGAATGTATTTAGCACC 59.679 38.462 0.00 0.00 0.00 5.01
2557 2701 7.148086 TGTCCCTCAAATGAATGTATTTAGCAC 60.148 37.037 0.00 0.00 0.00 4.40
2558 2702 6.889177 TGTCCCTCAAATGAATGTATTTAGCA 59.111 34.615 0.00 0.00 0.00 3.49
2559 2703 7.333528 TGTCCCTCAAATGAATGTATTTAGC 57.666 36.000 0.00 0.00 0.00 3.09
2560 2704 7.917505 GCTTGTCCCTCAAATGAATGTATTTAG 59.082 37.037 0.00 0.00 35.48 1.85
2561 2705 7.615365 AGCTTGTCCCTCAAATGAATGTATTTA 59.385 33.333 0.00 0.00 35.48 1.40
2562 2706 6.438425 AGCTTGTCCCTCAAATGAATGTATTT 59.562 34.615 0.00 0.00 35.48 1.40
2563 2707 5.954150 AGCTTGTCCCTCAAATGAATGTATT 59.046 36.000 0.00 0.00 35.48 1.89
2564 2708 5.513233 AGCTTGTCCCTCAAATGAATGTAT 58.487 37.500 0.00 0.00 35.48 2.29
2565 2709 4.922206 AGCTTGTCCCTCAAATGAATGTA 58.078 39.130 0.00 0.00 35.48 2.29
2566 2710 3.771216 AGCTTGTCCCTCAAATGAATGT 58.229 40.909 0.00 0.00 35.48 2.71
2567 2711 4.796038 AAGCTTGTCCCTCAAATGAATG 57.204 40.909 0.00 0.00 35.48 2.67
2568 2712 5.813513 AAAAGCTTGTCCCTCAAATGAAT 57.186 34.783 0.00 0.00 35.48 2.57
2569 2713 5.600696 GAAAAAGCTTGTCCCTCAAATGAA 58.399 37.500 0.00 0.00 35.48 2.57
2570 2714 4.261572 CGAAAAAGCTTGTCCCTCAAATGA 60.262 41.667 0.00 0.00 35.48 2.57
2571 2715 3.983344 CGAAAAAGCTTGTCCCTCAAATG 59.017 43.478 0.00 0.00 35.48 2.32
2572 2716 3.005791 CCGAAAAAGCTTGTCCCTCAAAT 59.994 43.478 0.00 0.00 35.48 2.32
2573 2717 2.360801 CCGAAAAAGCTTGTCCCTCAAA 59.639 45.455 0.00 0.00 35.48 2.69
2574 2718 1.953686 CCGAAAAAGCTTGTCCCTCAA 59.046 47.619 0.00 0.00 34.61 3.02
2575 2719 1.142060 TCCGAAAAAGCTTGTCCCTCA 59.858 47.619 0.00 0.00 0.00 3.86
2576 2720 1.535896 GTCCGAAAAAGCTTGTCCCTC 59.464 52.381 0.00 0.00 0.00 4.30
2577 2721 1.605753 GTCCGAAAAAGCTTGTCCCT 58.394 50.000 0.00 0.00 0.00 4.20
2578 2722 0.237498 CGTCCGAAAAAGCTTGTCCC 59.763 55.000 0.00 0.00 0.00 4.46
2579 2723 0.237498 CCGTCCGAAAAAGCTTGTCC 59.763 55.000 0.00 0.00 0.00 4.02
2580 2724 1.194772 CTCCGTCCGAAAAAGCTTGTC 59.805 52.381 0.00 0.00 0.00 3.18
2581 2725 1.226746 CTCCGTCCGAAAAAGCTTGT 58.773 50.000 0.00 0.00 0.00 3.16
2582 2726 0.517316 CCTCCGTCCGAAAAAGCTTG 59.483 55.000 0.00 0.00 0.00 4.01
2583 2727 0.605589 CCCTCCGTCCGAAAAAGCTT 60.606 55.000 0.00 0.00 0.00 3.74
2584 2728 1.003718 CCCTCCGTCCGAAAAAGCT 60.004 57.895 0.00 0.00 0.00 3.74
2585 2729 1.004200 TCCCTCCGTCCGAAAAAGC 60.004 57.895 0.00 0.00 0.00 3.51
2586 2730 0.320697 ACTCCCTCCGTCCGAAAAAG 59.679 55.000 0.00 0.00 0.00 2.27
2587 2731 1.273327 GTACTCCCTCCGTCCGAAAAA 59.727 52.381 0.00 0.00 0.00 1.94
2588 2732 0.890683 GTACTCCCTCCGTCCGAAAA 59.109 55.000 0.00 0.00 0.00 2.29
2589 2733 0.038744 AGTACTCCCTCCGTCCGAAA 59.961 55.000 0.00 0.00 0.00 3.46
2590 2734 0.393537 GAGTACTCCCTCCGTCCGAA 60.394 60.000 12.13 0.00 0.00 4.30
2591 2735 1.222936 GAGTACTCCCTCCGTCCGA 59.777 63.158 12.13 0.00 0.00 4.55
2592 2736 0.465824 ATGAGTACTCCCTCCGTCCG 60.466 60.000 20.11 0.00 0.00 4.79
2593 2737 1.320507 GATGAGTACTCCCTCCGTCC 58.679 60.000 20.11 0.00 0.00 4.79
2594 2738 1.677052 GTGATGAGTACTCCCTCCGTC 59.323 57.143 20.11 7.06 0.00 4.79
2595 2739 1.005569 TGTGATGAGTACTCCCTCCGT 59.994 52.381 20.11 0.00 0.00 4.69
2596 2740 1.678627 CTGTGATGAGTACTCCCTCCG 59.321 57.143 20.11 6.07 0.00 4.63
2597 2741 2.741145 ACTGTGATGAGTACTCCCTCC 58.259 52.381 20.11 10.82 0.00 4.30
2598 2742 4.810191 AAACTGTGATGAGTACTCCCTC 57.190 45.455 20.11 16.12 0.00 4.30
2599 2743 5.334421 AGTAAACTGTGATGAGTACTCCCT 58.666 41.667 20.11 7.57 0.00 4.20
2600 2744 5.185249 TGAGTAAACTGTGATGAGTACTCCC 59.815 44.000 20.11 12.18 33.36 4.30
2601 2745 6.071840 AGTGAGTAAACTGTGATGAGTACTCC 60.072 42.308 20.11 6.32 33.36 3.85
2602 2746 6.915349 AGTGAGTAAACTGTGATGAGTACTC 58.085 40.000 16.32 16.32 34.28 2.59
2650 2794 1.065564 ACTTGGAGGCTCTCTTGCATC 60.066 52.381 15.23 0.00 42.23 3.91
2666 2810 4.634004 TGAAGTTAACATATCCGGCACTTG 59.366 41.667 8.61 0.00 0.00 3.16
2673 2817 7.228507 TGAAATCCCATGAAGTTAACATATCCG 59.771 37.037 8.61 0.00 0.00 4.18
3198 3345 1.599047 CCAGAATGACACGAGGGCT 59.401 57.895 0.00 0.00 39.69 5.19
3210 3357 6.496565 TCACCATTTAATTTGTGTCCCAGAAT 59.503 34.615 4.86 0.00 0.00 2.40
3218 3365 8.592809 ACATAACCATCACCATTTAATTTGTGT 58.407 29.630 4.86 0.00 0.00 3.72
3301 3448 7.833682 TGGTATCATAACCAGTGAATGAACAAT 59.166 33.333 0.00 0.00 44.68 2.71
3344 3491 6.696441 AAGATTCCAGATCAAATCTCAAGC 57.304 37.500 14.62 0.00 40.47 4.01
3365 3515 9.683069 AATGTTATGTTTGAGCTTTTGACTAAG 57.317 29.630 0.00 0.00 0.00 2.18
3662 4066 3.267483 CCCGTTTGATACAACTCCGAAT 58.733 45.455 0.00 0.00 0.00 3.34
3664 4068 1.619827 ACCCGTTTGATACAACTCCGA 59.380 47.619 0.00 0.00 0.00 4.55
3700 4104 1.351017 GGGATTATCCGCATCCAAGGA 59.649 52.381 5.03 0.00 42.03 3.36
3815 4219 8.257306 AGTACAAATGGTTCAGATTTTGTGTTT 58.743 29.630 9.46 0.00 41.13 2.83
3816 4220 7.781056 AGTACAAATGGTTCAGATTTTGTGTT 58.219 30.769 9.46 0.00 41.13 3.32
3843 4247 3.127030 GCTCCACAAATAACAGTACTGCC 59.873 47.826 22.90 0.00 0.00 4.85
3935 4342 1.447945 GCTCTCTGAACTGGCTTTCC 58.552 55.000 0.00 0.00 0.00 3.13
4000 4407 0.980423 GACTCAGCCCTGAAGGAAGT 59.020 55.000 0.00 0.00 39.39 3.01
4006 4413 2.550277 TGGATAGACTCAGCCCTGAA 57.450 50.000 0.00 0.00 39.39 3.02
4013 4420 4.081406 CTCCCAGAGATGGATAGACTCAG 58.919 52.174 0.00 0.00 33.69 3.35


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

AutoCloner maintained by Alex Coulton.