Multiple sequence alignment - TraesCS3D01G148000

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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 TraesCS3D01G148000 chr3D 100.000 6232 0 0 1 6232 112699622 112693391 0.000000e+00 11509
1 TraesCS3D01G148000 chr3B 93.639 3160 133 34 3091 6232 163663177 163660068 0.000000e+00 4660
2 TraesCS3D01G148000 chr3B 88.052 2377 153 50 1 2337 163665940 163663655 0.000000e+00 2695
3 TraesCS3D01G148000 chr3B 84.304 395 35 19 2721 3092 163663641 163663251 1.650000e-95 361
4 TraesCS3D01G148000 chr3A 87.978 1439 110 27 1462 2865 108380399 108378989 0.000000e+00 1640
5 TraesCS3D01G148000 chr3A 93.700 873 52 3 3597 4467 108378134 108377263 0.000000e+00 1304
6 TraesCS3D01G148000 chr3A 91.868 910 44 20 4504 5406 108377179 108376293 0.000000e+00 1243
7 TraesCS3D01G148000 chr3A 91.719 797 31 18 689 1460 108381220 108380434 0.000000e+00 1074
8 TraesCS3D01G148000 chr3A 85.544 754 76 23 5497 6232 108375957 108375219 0.000000e+00 758
9 TraesCS3D01G148000 chr3A 85.962 577 57 9 2977 3532 108378714 108378141 4.160000e-166 595
10 TraesCS3D01G148000 chr7D 83.372 427 41 6 3223 3646 453305509 453305908 9.870000e-98 368
11 TraesCS3D01G148000 chr7D 75.862 232 35 14 1199 1409 60079481 60079712 1.430000e-16 99
12 TraesCS3D01G148000 chr2D 83.059 425 42 5 3223 3644 442449190 442449587 5.940000e-95 359
13 TraesCS3D01G148000 chr7B 78.571 476 91 11 3944 4417 2494275 2494741 2.820000e-78 303
14 TraesCS3D01G148000 chr7B 78.151 476 94 10 3944 4417 2512627 2513094 1.700000e-75 294
15 TraesCS3D01G148000 chr7A 75.983 229 37 11 1199 1409 64466099 64466327 1.110000e-17 102


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 TraesCS3D01G148000 chr3D 112693391 112699622 6231 True 11509.000000 11509 100.000000 1 6232 1 chr3D.!!$R1 6231
1 TraesCS3D01G148000 chr3B 163660068 163665940 5872 True 2572.000000 4660 88.665000 1 6232 3 chr3B.!!$R1 6231
2 TraesCS3D01G148000 chr3A 108375219 108381220 6001 True 1102.333333 1640 89.461833 689 6232 6 chr3A.!!$R1 5543

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
334 338 0.034574 TGGGCGCACCATATCTTGTT 60.035 50.000 7.46 0.00 46.80 2.83 F
585 589 0.092351 CGTGCGTCCGTATTGTGTTC 59.908 55.000 0.00 0.00 0.00 3.18 F
1752 1820 0.521735 GCAGTAGCCCGGTTTCTTTG 59.478 55.000 0.00 0.00 33.58 2.77 F
2535 2647 1.344114 GCATTTTTGGCACCTTCTGGA 59.656 47.619 0.00 0.00 37.04 3.86 F
4023 4385 0.180406 CACTGGGCCGGCTACTTAAT 59.820 55.000 28.56 2.58 0.00 1.40 F
4675 5121 1.837947 TTGGTGCATTGCCAAGGCT 60.838 52.632 15.65 0.00 40.69 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1623 1685 0.037326 ATCAAGAACCGAAGAGCGCA 60.037 50.000 11.47 0.0 39.11 6.09 R
1775 1843 0.038435 CCATGCATGTGCCAACGAAA 60.038 50.000 24.58 0.0 41.18 3.46 R
2676 2788 1.105457 ATGCATCATGAACCCGGTTG 58.895 50.000 7.78 0.0 0.00 3.77 R
4459 4824 1.342496 TCTGAAGAGGTGTGCTCTGTG 59.658 52.381 0.00 0.0 0.00 3.66 R
4921 5382 0.106918 AGTCCAGAGTAGAGAGGCGG 60.107 60.000 0.00 0.0 0.00 6.13 R
6197 6978 1.008538 CAGGCAAGTGAAACGCCAC 60.009 57.895 2.06 0.0 44.57 5.01 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
72 73 2.269241 GGAGAACTTCCCGCCAGG 59.731 66.667 0.00 0.00 40.37 4.45
94 95 0.039618 TCAATGGGGGTGGAAGAAGC 59.960 55.000 0.00 0.00 0.00 3.86
99 100 2.747855 GGGTGGAAGAAGCGGCAG 60.748 66.667 1.45 0.00 0.00 4.85
107 108 3.819188 GAAGCGGCAGGATTCTGG 58.181 61.111 2.40 0.00 41.19 3.86
124 125 1.757118 CTGGCTCGAATTGACTCCCTA 59.243 52.381 0.00 0.00 0.00 3.53
127 128 1.480954 GCTCGAATTGACTCCCTACCA 59.519 52.381 0.00 0.00 0.00 3.25
170 171 2.836154 GTGGTGAAGGGGCAGTCA 59.164 61.111 0.00 0.00 0.00 3.41
178 179 2.107378 TGAAGGGGCAGTCATTACACAA 59.893 45.455 0.00 0.00 0.00 3.33
180 181 1.705186 AGGGGCAGTCATTACACAAGT 59.295 47.619 0.00 0.00 0.00 3.16
210 211 1.306397 TCCATGGAGCTCAGGCAGA 60.306 57.895 17.19 2.26 41.70 4.26
307 311 2.424956 GCCAAGAGAGCCTACATTTTGG 59.575 50.000 0.00 0.00 37.30 3.28
312 316 3.330701 AGAGAGCCTACATTTTGGTTCCA 59.669 43.478 0.00 0.00 34.69 3.53
313 317 4.018050 AGAGAGCCTACATTTTGGTTCCAT 60.018 41.667 0.00 0.00 34.69 3.41
314 318 4.019174 AGAGCCTACATTTTGGTTCCATG 58.981 43.478 0.00 0.00 34.69 3.66
318 322 3.195396 CCTACATTTTGGTTCCATGTGGG 59.805 47.826 10.48 10.48 41.49 4.61
332 336 4.557554 TGGGCGCACCATATCTTG 57.442 55.556 7.46 0.00 46.80 3.02
333 337 1.607071 TGGGCGCACCATATCTTGT 59.393 52.632 7.46 0.00 46.80 3.16
334 338 0.034574 TGGGCGCACCATATCTTGTT 60.035 50.000 7.46 0.00 46.80 2.83
335 339 0.663153 GGGCGCACCATATCTTGTTC 59.337 55.000 10.83 0.00 39.85 3.18
336 340 1.378531 GGCGCACCATATCTTGTTCA 58.621 50.000 10.83 0.00 35.26 3.18
351 355 4.701651 TCTTGTTCATCTCGAATTTGCCAT 59.298 37.500 0.00 0.00 35.63 4.40
354 358 3.003394 TCATCTCGAATTTGCCATGGT 57.997 42.857 14.67 0.00 0.00 3.55
367 371 2.969262 TGCCATGGTATCCGATGAACTA 59.031 45.455 14.67 0.00 0.00 2.24
371 375 3.746045 TGGTATCCGATGAACTAAGCC 57.254 47.619 0.00 0.00 0.00 4.35
387 391 4.823276 CCGAGTAGGCAGAGCTTG 57.177 61.111 0.00 0.00 0.00 4.01
402 406 1.496403 GCTTGCCGTATAGTTCCGCC 61.496 60.000 0.00 0.00 0.00 6.13
418 422 2.767352 CCGGGGGTCCAAATCCAA 59.233 61.111 0.00 0.00 0.00 3.53
444 448 2.292918 TGGAGTCTAGGCATAGGGTGTT 60.293 50.000 5.42 0.00 0.00 3.32
479 483 3.243168 GCAGTTTGCTCTTGTGTTCATGA 60.243 43.478 0.00 0.00 40.96 3.07
480 484 4.734402 GCAGTTTGCTCTTGTGTTCATGAA 60.734 41.667 3.38 3.38 40.96 2.57
481 485 5.526115 CAGTTTGCTCTTGTGTTCATGAAT 58.474 37.500 12.12 0.00 0.00 2.57
482 486 5.628193 CAGTTTGCTCTTGTGTTCATGAATC 59.372 40.000 12.12 8.81 0.00 2.52
483 487 5.300034 AGTTTGCTCTTGTGTTCATGAATCA 59.700 36.000 12.12 11.28 0.00 2.57
484 488 5.970317 TTGCTCTTGTGTTCATGAATCAT 57.030 34.783 12.12 0.00 0.00 2.45
485 489 7.175467 AGTTTGCTCTTGTGTTCATGAATCATA 59.825 33.333 12.12 7.31 0.00 2.15
486 490 7.634671 TTGCTCTTGTGTTCATGAATCATAT 57.365 32.000 12.12 0.00 0.00 1.78
487 491 7.634671 TGCTCTTGTGTTCATGAATCATATT 57.365 32.000 12.12 0.00 0.00 1.28
488 492 8.058667 TGCTCTTGTGTTCATGAATCATATTT 57.941 30.769 12.12 0.00 0.00 1.40
489 493 8.525316 TGCTCTTGTGTTCATGAATCATATTTT 58.475 29.630 12.12 0.00 0.00 1.82
490 494 9.362539 GCTCTTGTGTTCATGAATCATATTTTT 57.637 29.630 12.12 0.00 0.00 1.94
538 542 6.638096 TTGACATGATTGTGTTCAGTGAAT 57.362 33.333 9.18 0.00 35.79 2.57
540 544 5.106987 TGACATGATTGTGTTCAGTGAATCG 60.107 40.000 9.18 0.00 35.79 3.34
545 549 4.794248 TTGTGTTCAGTGAATCGACTTG 57.206 40.909 9.18 0.00 0.00 3.16
547 551 4.939271 TGTGTTCAGTGAATCGACTTGTA 58.061 39.130 9.18 0.00 0.00 2.41
551 555 5.462068 TGTTCAGTGAATCGACTTGTAGTTG 59.538 40.000 9.18 0.00 0.00 3.16
552 556 5.447624 TCAGTGAATCGACTTGTAGTTGA 57.552 39.130 0.00 0.00 42.43 3.18
563 567 5.929992 CGACTTGTAGTTGAATGGTTAGGAA 59.070 40.000 0.00 0.00 31.05 3.36
566 570 3.998341 TGTAGTTGAATGGTTAGGAACGC 59.002 43.478 0.00 0.00 0.00 4.84
569 573 1.434555 TGAATGGTTAGGAACGCGTG 58.565 50.000 14.98 0.00 0.00 5.34
571 575 1.632046 AATGGTTAGGAACGCGTGCG 61.632 55.000 14.98 13.39 46.03 5.34
581 585 3.176578 CGCGTGCGTCCGTATTGT 61.177 61.111 6.00 0.00 34.35 2.71
582 586 2.394136 GCGTGCGTCCGTATTGTG 59.606 61.111 0.00 0.00 0.00 3.33
583 587 2.377310 GCGTGCGTCCGTATTGTGT 61.377 57.895 0.00 0.00 0.00 3.72
584 588 1.893168 GCGTGCGTCCGTATTGTGTT 61.893 55.000 0.00 0.00 0.00 3.32
585 589 0.092351 CGTGCGTCCGTATTGTGTTC 59.908 55.000 0.00 0.00 0.00 3.18
586 590 1.425412 GTGCGTCCGTATTGTGTTCT 58.575 50.000 0.00 0.00 0.00 3.01
587 591 1.796459 GTGCGTCCGTATTGTGTTCTT 59.204 47.619 0.00 0.00 0.00 2.52
623 627 7.199766 TGATTGTGTTCATAGTTTTGGTGTTC 58.800 34.615 0.00 0.00 0.00 3.18
634 638 3.605946 TGGTGTTCCAAAACCAGCT 57.394 47.368 0.00 0.00 41.56 4.24
635 639 2.738587 TGGTGTTCCAAAACCAGCTA 57.261 45.000 0.00 0.00 41.56 3.32
636 640 2.582052 TGGTGTTCCAAAACCAGCTAG 58.418 47.619 0.00 0.00 41.56 3.42
657 661 5.852282 AGTAGGTTGCAATTTTGTGAGTT 57.148 34.783 0.59 0.00 0.00 3.01
664 668 2.468777 GCAATTTTGTGAGTTGAGCGTG 59.531 45.455 0.00 0.00 0.00 5.34
665 669 3.044986 CAATTTTGTGAGTTGAGCGTGG 58.955 45.455 0.00 0.00 0.00 4.94
671 675 0.756294 TGAGTTGAGCGTGGAAAGGA 59.244 50.000 0.00 0.00 0.00 3.36
792 800 2.945008 TCATCATGGCGTTGGATTCTTC 59.055 45.455 0.00 0.00 0.00 2.87
793 801 1.750193 TCATGGCGTTGGATTCTTCC 58.250 50.000 0.00 0.00 42.94 3.46
858 868 0.894141 CGCCACATGGATCCCAAAAA 59.106 50.000 9.90 0.00 36.95 1.94
862 872 3.007831 GCCACATGGATCCCAAAAAGAAA 59.992 43.478 9.90 0.00 36.95 2.52
863 873 4.824289 CCACATGGATCCCAAAAAGAAAG 58.176 43.478 9.90 0.00 36.95 2.62
865 875 5.011943 CCACATGGATCCCAAAAAGAAAGAA 59.988 40.000 9.90 0.00 36.95 2.52
868 878 7.172019 CACATGGATCCCAAAAAGAAAGAAAAG 59.828 37.037 9.90 0.00 36.95 2.27
871 881 7.500141 TGGATCCCAAAAAGAAAGAAAAGAAG 58.500 34.615 9.90 0.00 0.00 2.85
874 884 9.599866 GATCCCAAAAAGAAAGAAAAGAAGAAA 57.400 29.630 0.00 0.00 0.00 2.52
896 906 8.504815 AGAAAGAATAGAAACTTCGTAAAAGGC 58.495 33.333 0.00 0.00 0.00 4.35
898 908 7.365840 AGAATAGAAACTTCGTAAAAGGCAG 57.634 36.000 0.00 0.00 0.00 4.85
899 909 6.371825 AGAATAGAAACTTCGTAAAAGGCAGG 59.628 38.462 0.00 0.00 0.00 4.85
968 985 4.938756 ACCCCCACTCCCCAGCAA 62.939 66.667 0.00 0.00 0.00 3.91
1444 1473 7.346471 TGCTTCCTTGCTTAAATTCTACCTAT 58.654 34.615 0.00 0.00 0.00 2.57
1446 1475 7.255277 GCTTCCTTGCTTAAATTCTACCTATGG 60.255 40.741 0.00 0.00 0.00 2.74
1448 1477 5.241728 CCTTGCTTAAATTCTACCTATGGCC 59.758 44.000 0.00 0.00 0.00 5.36
1451 1480 4.202577 GCTTAAATTCTACCTATGGCCCCT 60.203 45.833 0.00 0.00 0.00 4.79
1623 1685 4.086457 AGCAATTCCTCCCGTTTATGTTT 58.914 39.130 0.00 0.00 0.00 2.83
1750 1818 0.605589 GTGCAGTAGCCCGGTTTCTT 60.606 55.000 0.00 0.00 41.13 2.52
1752 1820 0.521735 GCAGTAGCCCGGTTTCTTTG 59.478 55.000 0.00 0.00 33.58 2.77
1753 1821 1.892209 CAGTAGCCCGGTTTCTTTGT 58.108 50.000 0.00 0.00 0.00 2.83
1774 1842 2.220479 TGATCTCATCAGCTTGCTCG 57.780 50.000 0.00 0.00 33.59 5.03
1775 1843 1.479730 TGATCTCATCAGCTTGCTCGT 59.520 47.619 0.00 0.00 33.59 4.18
1807 1883 3.263937 ACATGCATGGCTTAACCCAAAAT 59.736 39.130 29.41 1.17 38.61 1.82
1808 1884 4.469227 ACATGCATGGCTTAACCCAAAATA 59.531 37.500 29.41 0.00 38.61 1.40
1809 1885 4.734398 TGCATGGCTTAACCCAAAATAG 57.266 40.909 0.00 0.00 38.61 1.73
1810 1886 3.118811 TGCATGGCTTAACCCAAAATAGC 60.119 43.478 0.00 0.00 38.61 2.97
1827 1917 4.762289 ATAGCCTAGTTGGAGACCTTTG 57.238 45.455 0.00 0.00 38.35 2.77
1828 1918 1.630878 AGCCTAGTTGGAGACCTTTGG 59.369 52.381 0.00 0.00 38.35 3.28
1834 1924 1.546029 GTTGGAGACCTTTGGATTGGC 59.454 52.381 0.00 0.00 0.00 4.52
1864 1958 3.562182 ACCAAACTTAAGACCCAACCAG 58.438 45.455 10.09 0.00 0.00 4.00
1873 1967 4.994756 CCCAACCAGCCACCCACC 62.995 72.222 0.00 0.00 0.00 4.61
1923 2017 1.661341 CCCTGCTTTCTCTGGAATCG 58.339 55.000 0.00 0.00 0.00 3.34
1940 2034 4.210746 GGAATCGGTCGGTTTATTAGCTTC 59.789 45.833 0.00 0.00 0.00 3.86
1958 2052 6.502136 AGCTTCTATTTAAGTTTCACCAGC 57.498 37.500 0.00 0.00 0.00 4.85
1995 2091 3.118408 GCCTTTTGACTTTCCCCACTTTT 60.118 43.478 0.00 0.00 0.00 2.27
2026 2125 8.518702 AGATCTTTTCTTGTTATCTTCTTTGCC 58.481 33.333 0.00 0.00 0.00 4.52
2083 2185 1.449246 GCTGATGGCTTCGAGCTGT 60.449 57.895 0.00 0.00 41.99 4.40
2126 2228 3.565516 GTTTTCTTGCCTTTGATCGGTC 58.434 45.455 0.00 0.00 0.00 4.79
2138 2240 4.695217 TTGATCGGTCTTTTTGTATGGC 57.305 40.909 0.00 0.00 0.00 4.40
2153 2255 6.449635 TTGTATGGCAATAACAGTGATTCC 57.550 37.500 0.00 0.00 31.07 3.01
2199 2301 4.014406 GTGGGAAAAAGGAACCATATCGT 58.986 43.478 0.00 0.00 35.13 3.73
2206 2308 8.463607 GGAAAAAGGAACCATATCGTCAATTAA 58.536 33.333 0.00 0.00 0.00 1.40
2221 2323 6.257630 TCGTCAATTAATTCGCTGATCAATCA 59.742 34.615 0.00 0.00 35.16 2.57
2222 2324 6.355405 CGTCAATTAATTCGCTGATCAATCAC 59.645 38.462 0.00 0.00 32.50 3.06
2278 2386 5.109903 AGTGTATGCGAAAGGTGTTCTATC 58.890 41.667 0.00 0.00 0.00 2.08
2280 2388 4.868171 TGTATGCGAAAGGTGTTCTATCAC 59.132 41.667 0.00 0.00 37.57 3.06
2343 2455 5.540719 TGATATTGTGGGACGGTACATCATA 59.459 40.000 0.00 0.00 0.00 2.15
2346 2458 3.035363 TGTGGGACGGTACATCATATGT 58.965 45.455 1.90 0.00 46.92 2.29
2387 2499 9.853555 TTATTGATGCATTTTTGAAGTAACGAT 57.146 25.926 0.00 0.00 0.00 3.73
2475 2587 3.440173 CCTGATGAGTGCATACCGTTTTT 59.560 43.478 0.00 0.00 34.11 1.94
2480 2592 3.628032 TGAGTGCATACCGTTTTTCACAA 59.372 39.130 0.00 0.00 0.00 3.33
2483 2595 4.037446 AGTGCATACCGTTTTTCACAACAT 59.963 37.500 0.00 0.00 0.00 2.71
2486 2598 4.979197 GCATACCGTTTTTCACAACATGAA 59.021 37.500 0.00 0.00 45.92 2.57
2503 2615 6.560253 ACATGAACATTTGTCTGTAGGTTC 57.440 37.500 0.00 0.00 36.18 3.62
2531 2643 2.095617 GCAATGCATTTTTGGCACCTTC 60.096 45.455 9.83 0.00 45.23 3.46
2535 2647 1.344114 GCATTTTTGGCACCTTCTGGA 59.656 47.619 0.00 0.00 37.04 3.86
2546 2658 2.886523 CACCTTCTGGATTTCTTGTGCA 59.113 45.455 0.00 0.00 37.04 4.57
2548 2660 2.229784 CCTTCTGGATTTCTTGTGCACC 59.770 50.000 15.69 0.00 34.57 5.01
2565 2677 3.831911 TGCACCCCTCTTATTTTTCCTTG 59.168 43.478 0.00 0.00 0.00 3.61
2571 2683 6.213397 ACCCCTCTTATTTTTCCTTGGAATTG 59.787 38.462 2.65 0.00 0.00 2.32
2608 2720 8.334632 CGAGTTTTTAATTTGCAGTTGGAATTT 58.665 29.630 0.00 0.54 0.00 1.82
2618 2730 9.956640 ATTTGCAGTTGGAATTTATTGGAAATA 57.043 25.926 8.29 0.00 35.68 1.40
2635 2747 4.765339 GGAAATAGCCTTTTGGTACACTGT 59.235 41.667 0.00 0.00 39.29 3.55
2712 2824 3.804036 TGCATTACCTTAATCCTCACGG 58.196 45.455 0.00 0.00 0.00 4.94
2713 2825 3.452990 TGCATTACCTTAATCCTCACGGA 59.547 43.478 0.00 0.00 45.16 4.69
2734 2846 5.050363 CGGAATATCTTGGTTACCGACAATG 60.050 44.000 0.00 0.00 41.09 2.82
2816 2928 6.208840 AGGTTCCCTGGTGAAATAAGTTAA 57.791 37.500 0.00 0.00 29.57 2.01
2821 2934 7.801893 TCCCTGGTGAAATAAGTTAACTCTA 57.198 36.000 8.95 4.47 0.00 2.43
2823 2936 8.265055 TCCCTGGTGAAATAAGTTAACTCTATG 58.735 37.037 8.95 0.00 0.00 2.23
2824 2937 8.047310 CCCTGGTGAAATAAGTTAACTCTATGT 58.953 37.037 8.95 4.65 0.00 2.29
2825 2938 9.099454 CCTGGTGAAATAAGTTAACTCTATGTC 57.901 37.037 8.95 12.85 0.00 3.06
2921 3149 7.201316 GCAAATTTTAATAGTGTACAAGCACGG 60.201 37.037 0.00 0.00 43.61 4.94
2928 3156 2.139917 GTGTACAAGCACGGAACATGA 58.860 47.619 0.00 0.00 0.00 3.07
2932 3160 3.559238 ACAAGCACGGAACATGATTTC 57.441 42.857 0.00 0.00 15.17 2.17
2938 3171 4.154195 AGCACGGAACATGATTTCTAACAC 59.846 41.667 0.00 0.00 0.00 3.32
2988 3270 9.216117 TCACTTCTAACTTAATTTAAGCCTCAC 57.784 33.333 14.67 0.00 39.39 3.51
3010 3292 6.659242 TCACTCTGTTTCTTTTTCTTCTGGTT 59.341 34.615 0.00 0.00 0.00 3.67
3027 3309 9.807921 TCTTCTGGTTTCTCTTAATAAATGGTT 57.192 29.630 0.00 0.00 0.00 3.67
3074 3356 9.130312 CAAAGACTAGCTTACTACAGTAACTTG 57.870 37.037 0.00 5.23 35.75 3.16
3092 3425 8.466798 AGTAACTTGTTTGCACATTCTTACTTT 58.533 29.630 0.00 0.00 30.07 2.66
3132 3488 6.101650 TCTTTTGTTGTCTCTGATGCTCTA 57.898 37.500 0.00 0.00 0.00 2.43
3143 3499 3.194329 TCTGATGCTCTACTCACAACAGG 59.806 47.826 0.00 0.00 0.00 4.00
3154 3510 2.684881 CTCACAACAGGGTTATGATGGC 59.315 50.000 0.00 0.00 0.00 4.40
3172 3528 5.429435 TGATGGCCCATATGCTAGAATCATA 59.571 40.000 0.00 0.00 0.00 2.15
3173 3529 5.363562 TGGCCCATATGCTAGAATCATAG 57.636 43.478 0.00 0.00 30.84 2.23
3174 3530 4.133078 GGCCCATATGCTAGAATCATAGC 58.867 47.826 0.00 0.00 46.86 2.97
3196 3552 5.801947 AGCGCAATTTAATTTTACTGCTCTG 59.198 36.000 11.47 0.00 0.00 3.35
3199 3555 6.033831 CGCAATTTAATTTTACTGCTCTGTGG 59.966 38.462 0.00 0.00 0.00 4.17
3200 3556 7.090173 GCAATTTAATTTTACTGCTCTGTGGA 58.910 34.615 0.00 0.00 0.00 4.02
3217 3573 5.070847 TCTGTGGATATTCAGCTCTATGCAA 59.929 40.000 0.00 0.00 45.94 4.08
3218 3574 5.872963 TGTGGATATTCAGCTCTATGCAAT 58.127 37.500 0.00 0.00 45.94 3.56
3230 3588 2.032426 TCTATGCAATGTGCTTGATGCG 59.968 45.455 0.00 0.00 45.31 4.73
3237 3595 3.029810 TGCTTGATGCGCACGTTT 58.970 50.000 14.90 0.00 46.63 3.60
3299 3660 4.090090 CTGGTCTCTCTGGGACTAAAGAA 58.910 47.826 0.00 0.00 34.47 2.52
3350 3711 1.963338 GCTGCTTGCTGGTTCGACT 60.963 57.895 0.00 0.00 38.95 4.18
3398 3759 3.393089 ACTTGTGTTGTTGTTGGCAAA 57.607 38.095 0.00 0.00 36.22 3.68
3408 3769 5.268118 TGTTGTTGGCAAATGTGATGTTA 57.732 34.783 0.00 0.00 36.22 2.41
3409 3770 5.046529 TGTTGTTGGCAAATGTGATGTTAC 58.953 37.500 0.00 0.00 36.22 2.50
3487 3848 3.873910 AGTTGTCACCCTGTATGTATGC 58.126 45.455 0.00 0.00 0.00 3.14
3545 3907 6.777526 TGGTTGTTTTGTAAATTATGCAGC 57.222 33.333 0.00 0.00 0.00 5.25
3547 3909 6.423302 TGGTTGTTTTGTAAATTATGCAGCAG 59.577 34.615 0.00 0.00 0.00 4.24
3548 3910 6.644592 GGTTGTTTTGTAAATTATGCAGCAGA 59.355 34.615 0.00 0.00 0.00 4.26
3552 3914 7.871973 TGTTTTGTAAATTATGCAGCAGAATGT 59.128 29.630 15.94 13.03 39.31 2.71
3578 3940 9.624697 TTGTCAATTTTTATCTCGAAAGGAATG 57.375 29.630 0.00 0.00 0.00 2.67
3582 3944 9.090692 CAATTTTTATCTCGAAAGGAATGCAAT 57.909 29.630 0.00 0.00 0.00 3.56
3583 3945 8.638685 ATTTTTATCTCGAAAGGAATGCAATG 57.361 30.769 0.00 0.00 0.00 2.82
3585 3947 3.071874 TCTCGAAAGGAATGCAATGGT 57.928 42.857 0.00 0.00 0.00 3.55
3586 3948 2.749076 TCTCGAAAGGAATGCAATGGTG 59.251 45.455 0.00 0.00 0.00 4.17
3587 3949 2.749076 CTCGAAAGGAATGCAATGGTGA 59.251 45.455 0.00 0.00 0.00 4.02
3633 3995 9.693739 AATGTTTGATATGATTGTACCCTGTTA 57.306 29.630 0.00 0.00 0.00 2.41
3699 4061 3.817084 ACGAATCATGGCCATATCTGTTG 59.183 43.478 20.30 5.82 0.00 3.33
3756 4118 3.790437 CTCACCATGGGGAGCGCT 61.790 66.667 30.71 11.27 38.05 5.92
3788 4150 3.765511 TGCTGGCTCTAATTGCTTCATTT 59.234 39.130 0.00 0.00 0.00 2.32
3869 4231 4.171754 GAGGCTGCAAATGATGAAAAGAC 58.828 43.478 0.50 0.00 0.00 3.01
4023 4385 0.180406 CACTGGGCCGGCTACTTAAT 59.820 55.000 28.56 2.58 0.00 1.40
4068 4430 4.566987 ACGTCATAAGAAAGTGAGGTTCC 58.433 43.478 0.00 0.00 39.59 3.62
4119 4482 2.100197 AGCACAGCATTCATGAGCATT 58.900 42.857 9.38 0.00 36.81 3.56
4166 4531 2.227388 CTGCAGGTTGTTCCACAAGATC 59.773 50.000 5.57 0.00 39.00 2.75
4459 4824 5.753921 CCGATCCCTGTAAACAGAAATAGAC 59.246 44.000 11.69 0.00 46.59 2.59
4515 4953 8.528044 AATAACTTTCACTAGGGAAACACAAA 57.472 30.769 16.31 1.46 33.48 2.83
4657 5103 2.600769 AGCGTCGAGAACCCTGGT 60.601 61.111 0.00 0.00 0.00 4.00
4675 5121 1.837947 TTGGTGCATTGCCAAGGCT 60.838 52.632 15.65 0.00 40.69 4.58
4918 5379 6.436261 GTGAAACTCCTTAGCTTGTAAAACC 58.564 40.000 0.00 0.00 0.00 3.27
4919 5380 5.237779 TGAAACTCCTTAGCTTGTAAAACCG 59.762 40.000 0.00 0.00 0.00 4.44
4920 5381 4.347360 ACTCCTTAGCTTGTAAAACCGT 57.653 40.909 0.00 0.00 0.00 4.83
4921 5382 4.313282 ACTCCTTAGCTTGTAAAACCGTC 58.687 43.478 0.00 0.00 0.00 4.79
4922 5383 3.667360 TCCTTAGCTTGTAAAACCGTCC 58.333 45.455 0.00 0.00 0.00 4.79
4923 5384 2.414138 CCTTAGCTTGTAAAACCGTCCG 59.586 50.000 0.00 0.00 0.00 4.79
4924 5385 1.431496 TAGCTTGTAAAACCGTCCGC 58.569 50.000 0.00 0.00 0.00 5.54
4991 5452 0.533491 TTCGCTTGCAGGTATACGGT 59.467 50.000 0.00 0.00 0.00 4.83
5012 5473 1.002900 GGTGTGACCATGAACAACACG 60.003 52.381 0.00 0.00 38.42 4.49
5072 5533 0.540830 AGCTGACGTGGGACTTCTCT 60.541 55.000 0.00 0.00 0.00 3.10
5269 5730 1.003866 GGACACACGCTTGAGTTTGAC 60.004 52.381 0.00 0.00 0.00 3.18
5421 5883 4.340097 TGTGTGTTCTCTTCTCTTCGGTAA 59.660 41.667 0.00 0.00 0.00 2.85
5426 5888 4.720649 TCTCTTCTCTTCGGTAATGGTG 57.279 45.455 0.00 0.00 0.00 4.17
5432 5894 8.070034 TCTTCTCTTCGGTAATGGTGTATTAA 57.930 34.615 0.00 0.00 33.22 1.40
5478 5941 6.851222 GCTACATGCTAGAAATAAGCTTGA 57.149 37.500 9.86 0.00 43.94 3.02
5480 5943 6.703607 GCTACATGCTAGAAATAAGCTTGAGA 59.296 38.462 9.86 0.00 43.94 3.27
5481 5944 7.387397 GCTACATGCTAGAAATAAGCTTGAGAT 59.613 37.037 9.86 0.00 43.94 2.75
5482 5945 9.270640 CTACATGCTAGAAATAAGCTTGAGATT 57.729 33.333 9.86 0.00 43.94 2.40
5513 6256 7.069950 ACCTATTTTATCTGGATTTTGCCCTTC 59.930 37.037 0.00 0.00 0.00 3.46
5583 6343 5.159209 GTGAGAGAGAAAATTGCATTGTGG 58.841 41.667 0.00 0.00 0.00 4.17
5631 6395 0.801251 CACAAGCTAGCTGTGAAGCC 59.199 55.000 28.62 0.00 39.64 4.35
5756 6520 2.623416 GCCTGGACCATACATAAAAGCC 59.377 50.000 0.00 0.00 0.00 4.35
5799 6566 1.634702 CTCTACTTCACTTCGCCAGC 58.365 55.000 0.00 0.00 0.00 4.85
5800 6567 0.246635 TCTACTTCACTTCGCCAGCC 59.753 55.000 0.00 0.00 0.00 4.85
5802 6569 0.037326 TACTTCACTTCGCCAGCCAG 60.037 55.000 0.00 0.00 0.00 4.85
5803 6570 1.004560 CTTCACTTCGCCAGCCAGA 60.005 57.895 0.00 0.00 0.00 3.86
5804 6571 0.603707 CTTCACTTCGCCAGCCAGAA 60.604 55.000 0.00 0.00 0.00 3.02
5805 6572 0.179032 TTCACTTCGCCAGCCAGAAA 60.179 50.000 0.00 0.00 0.00 2.52
5806 6573 0.036732 TCACTTCGCCAGCCAGAAAT 59.963 50.000 0.00 0.00 0.00 2.17
5807 6574 0.169672 CACTTCGCCAGCCAGAAATG 59.830 55.000 0.00 0.00 0.00 2.32
5808 6575 0.036732 ACTTCGCCAGCCAGAAATGA 59.963 50.000 0.00 0.00 0.00 2.57
5809 6576 1.167851 CTTCGCCAGCCAGAAATGAA 58.832 50.000 0.00 0.00 0.00 2.57
5810 6577 0.881118 TTCGCCAGCCAGAAATGAAC 59.119 50.000 0.00 0.00 0.00 3.18
5811 6578 0.250684 TCGCCAGCCAGAAATGAACA 60.251 50.000 0.00 0.00 0.00 3.18
5812 6579 0.813184 CGCCAGCCAGAAATGAACAT 59.187 50.000 0.00 0.00 0.00 2.71
5813 6580 1.468565 CGCCAGCCAGAAATGAACATG 60.469 52.381 0.00 0.00 0.00 3.21
5814 6581 1.134907 GCCAGCCAGAAATGAACATGG 60.135 52.381 0.00 0.00 35.84 3.66
5841 6621 6.318648 GGCTCAGTAAATTGAACCATATCACA 59.681 38.462 0.00 0.00 34.24 3.58
5875 6655 3.568007 TGGCAGTGAAAAACATGTCCTAC 59.432 43.478 0.00 0.00 0.00 3.18
5876 6656 3.821033 GGCAGTGAAAAACATGTCCTACT 59.179 43.478 0.00 0.00 0.00 2.57
6052 6833 3.222855 CGCTCGGGGCTCTCTCAT 61.223 66.667 0.00 0.00 39.13 2.90
6141 6922 0.176680 TCCCGAGCTGATCAAGAAGC 59.823 55.000 0.00 0.00 39.82 3.86
6172 6953 0.319383 ACAGTCAGAGCAAGCTCACG 60.319 55.000 22.68 13.67 44.99 4.35
6197 6978 2.743636 TTACAGGGTTCAGAAGAGCG 57.256 50.000 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 1.845809 GACAACAAGAGGCGCCACAG 61.846 60.000 31.54 20.99 0.00 3.66
33 34 0.111061 AGGCACTCCAGCAATGACAA 59.889 50.000 0.00 0.00 35.83 3.18
67 68 2.841044 CCCCCATTGATGCCTGGC 60.841 66.667 12.87 12.87 0.00 4.85
72 73 0.033208 TCTTCCACCCCCATTGATGC 60.033 55.000 0.00 0.00 0.00 3.91
94 95 2.578163 TTCGAGCCAGAATCCTGCCG 62.578 60.000 0.00 0.00 39.07 5.69
99 100 2.869192 GAGTCAATTCGAGCCAGAATCC 59.131 50.000 4.95 0.00 39.69 3.01
107 108 1.480954 TGGTAGGGAGTCAATTCGAGC 59.519 52.381 0.00 0.00 0.00 5.03
111 112 3.828875 CTCCTGGTAGGGAGTCAATTC 57.171 52.381 2.65 0.00 45.65 2.17
124 125 1.588239 TTCCATGATGCTCTCCTGGT 58.412 50.000 0.00 0.00 39.83 4.00
127 128 3.434739 GGTTCATTCCATGATGCTCTCCT 60.435 47.826 0.00 0.00 39.39 3.69
136 137 1.024046 CACGGCGGTTCATTCCATGA 61.024 55.000 13.24 0.00 37.55 3.07
151 152 3.901797 GACTGCCCCTTCACCACGG 62.902 68.421 0.00 0.00 0.00 4.94
153 154 0.251341 AATGACTGCCCCTTCACCAC 60.251 55.000 0.00 0.00 0.00 4.16
154 155 1.004277 GTAATGACTGCCCCTTCACCA 59.996 52.381 0.00 0.00 0.00 4.17
165 166 3.498397 GTCACCCACTTGTGTAATGACTG 59.502 47.826 15.67 0.00 37.51 3.51
170 171 1.418637 ACGGTCACCCACTTGTGTAAT 59.581 47.619 0.00 0.00 37.51 1.89
178 179 1.229209 ATGGAGACGGTCACCCACT 60.229 57.895 19.81 9.35 0.00 4.00
180 181 2.290287 CCATGGAGACGGTCACCCA 61.290 63.158 19.81 19.75 0.00 4.51
210 211 0.393944 CATGACTCCATGTGCCAGCT 60.394 55.000 0.00 0.00 43.90 4.24
211 212 1.381928 CCATGACTCCATGTGCCAGC 61.382 60.000 0.00 0.00 46.68 4.85
212 213 0.750546 CCCATGACTCCATGTGCCAG 60.751 60.000 0.00 0.00 46.68 4.85
213 214 1.303948 CCCATGACTCCATGTGCCA 59.696 57.895 0.00 0.00 46.68 4.92
214 215 1.454479 CCCCATGACTCCATGTGCC 60.454 63.158 0.00 0.00 46.68 5.01
215 216 2.123428 GCCCCATGACTCCATGTGC 61.123 63.158 0.00 0.00 46.68 4.57
216 217 1.454479 GGCCCCATGACTCCATGTG 60.454 63.158 0.00 0.00 46.68 3.21
217 218 1.929860 CTGGCCCCATGACTCCATGT 61.930 60.000 0.00 0.00 46.68 3.21
272 273 1.077787 TTGGCCGGTGCTCCATAAG 60.078 57.895 1.90 0.00 37.74 1.73
307 311 3.747976 GGTGCGCCCACATGGAAC 61.748 66.667 4.45 0.00 43.88 3.62
318 322 2.874701 AGATGAACAAGATATGGTGCGC 59.125 45.455 0.00 0.00 0.00 6.09
331 335 3.129113 CCATGGCAAATTCGAGATGAACA 59.871 43.478 0.00 0.00 40.00 3.18
332 336 3.129287 ACCATGGCAAATTCGAGATGAAC 59.871 43.478 13.04 0.00 40.00 3.18
333 337 3.355378 ACCATGGCAAATTCGAGATGAA 58.645 40.909 13.04 0.00 41.81 2.57
334 338 3.003394 ACCATGGCAAATTCGAGATGA 57.997 42.857 13.04 0.00 0.00 2.92
335 339 4.083110 GGATACCATGGCAAATTCGAGATG 60.083 45.833 13.04 0.00 0.00 2.90
336 340 4.074970 GGATACCATGGCAAATTCGAGAT 58.925 43.478 13.04 0.00 0.00 2.75
351 355 2.035449 CGGCTTAGTTCATCGGATACCA 59.965 50.000 0.00 0.00 0.00 3.25
354 358 3.220110 ACTCGGCTTAGTTCATCGGATA 58.780 45.455 0.00 0.00 0.00 2.59
371 375 4.100981 GCAAGCTCTGCCTACTCG 57.899 61.111 9.03 0.00 46.13 4.18
380 384 1.067212 CGGAACTATACGGCAAGCTCT 59.933 52.381 0.00 0.00 0.00 4.09
389 393 2.337532 CCCCGGCGGAACTATACG 59.662 66.667 30.79 7.64 0.00 3.06
390 394 2.092319 GACCCCCGGCGGAACTATAC 62.092 65.000 30.79 8.03 0.00 1.47
391 395 1.833934 GACCCCCGGCGGAACTATA 60.834 63.158 30.79 0.00 0.00 1.31
392 396 3.159347 GACCCCCGGCGGAACTAT 61.159 66.667 30.79 7.76 0.00 2.12
402 406 0.394352 CTCTTGGATTTGGACCCCCG 60.394 60.000 0.00 0.00 34.29 5.73
418 422 3.245586 CCCTATGCCTAGACTCCATCTCT 60.246 52.174 0.00 0.00 39.04 3.10
431 435 2.196595 TGCTCTAAACACCCTATGCCT 58.803 47.619 0.00 0.00 0.00 4.75
435 439 5.028549 CACAGATGCTCTAAACACCCTAT 57.971 43.478 0.00 0.00 0.00 2.57
460 464 5.522456 TGATTCATGAACACAAGAGCAAAC 58.478 37.500 11.07 0.00 0.00 2.93
531 535 6.401474 CCATTCAACTACAAGTCGATTCACTG 60.401 42.308 0.00 0.00 0.00 3.66
538 542 5.244402 TCCTAACCATTCAACTACAAGTCGA 59.756 40.000 0.00 0.00 0.00 4.20
540 544 6.128634 CGTTCCTAACCATTCAACTACAAGTC 60.129 42.308 0.00 0.00 0.00 3.01
545 549 3.061697 CGCGTTCCTAACCATTCAACTAC 59.938 47.826 0.00 0.00 0.00 2.73
547 551 2.073816 CGCGTTCCTAACCATTCAACT 58.926 47.619 0.00 0.00 0.00 3.16
551 555 0.096454 GCACGCGTTCCTAACCATTC 59.904 55.000 10.22 0.00 0.00 2.67
552 556 1.632046 CGCACGCGTTCCTAACCATT 61.632 55.000 10.22 0.00 34.35 3.16
566 570 0.092351 GAACACAATACGGACGCACG 59.908 55.000 0.00 0.00 40.31 5.34
569 573 4.650545 TTTAAGAACACAATACGGACGC 57.349 40.909 0.00 0.00 0.00 5.19
623 627 2.488153 GCAACCTACTAGCTGGTTTTGG 59.512 50.000 8.46 11.14 43.27 3.28
634 638 6.544197 TCAACTCACAAAATTGCAACCTACTA 59.456 34.615 0.00 0.00 0.00 1.82
635 639 5.359576 TCAACTCACAAAATTGCAACCTACT 59.640 36.000 0.00 0.00 0.00 2.57
636 640 5.587289 TCAACTCACAAAATTGCAACCTAC 58.413 37.500 0.00 0.00 0.00 3.18
657 661 3.135994 GTTACTTTCCTTTCCACGCTCA 58.864 45.455 0.00 0.00 0.00 4.26
664 668 7.306213 GTTGAGCTATTGTTACTTTCCTTTCC 58.694 38.462 0.00 0.00 0.00 3.13
665 669 7.015877 CGTTGAGCTATTGTTACTTTCCTTTC 58.984 38.462 0.00 0.00 0.00 2.62
671 675 3.124636 CGCCGTTGAGCTATTGTTACTTT 59.875 43.478 0.00 0.00 0.00 2.66
742 746 7.918562 TGGCAAGTTAAACAAGCTAAAAGTAAG 59.081 33.333 0.00 0.00 0.00 2.34
827 837 0.474184 ATGTGGCGGGAATAGAAGGG 59.526 55.000 0.00 0.00 0.00 3.95
828 838 1.597742 CATGTGGCGGGAATAGAAGG 58.402 55.000 0.00 0.00 0.00 3.46
871 881 8.287503 TGCCTTTTACGAAGTTTCTATTCTTTC 58.712 33.333 0.00 0.00 37.78 2.62
874 884 6.371825 CCTGCCTTTTACGAAGTTTCTATTCT 59.628 38.462 0.00 0.00 37.78 2.40
955 972 1.153168 CGGTATTGCTGGGGAGTGG 60.153 63.158 0.00 0.00 0.00 4.00
1189 1218 4.504916 CTGCTCGCACTCCTCGGG 62.505 72.222 0.00 0.00 0.00 5.14
1190 1219 3.443925 TCTGCTCGCACTCCTCGG 61.444 66.667 0.00 0.00 0.00 4.63
1356 1385 1.942271 GAGGATGGGGAGGAGGAGA 59.058 63.158 0.00 0.00 0.00 3.71
1444 1473 4.344865 GCCTTGAACGAGGGGCCA 62.345 66.667 4.39 0.00 38.77 5.36
1448 1477 0.825840 TTTTGGGCCTTGAACGAGGG 60.826 55.000 4.53 0.00 37.29 4.30
1623 1685 0.037326 ATCAAGAACCGAAGAGCGCA 60.037 50.000 11.47 0.00 39.11 6.09
1661 1723 5.095145 TCCAATCAGATCAAACCAGAGAG 57.905 43.478 0.00 0.00 0.00 3.20
1662 1724 5.678583 GATCCAATCAGATCAAACCAGAGA 58.321 41.667 0.00 0.00 41.96 3.10
1768 1836 1.353804 GTGCCAACGAAACGAGCAA 59.646 52.632 0.00 0.00 34.42 3.91
1769 1837 1.163420 ATGTGCCAACGAAACGAGCA 61.163 50.000 0.00 0.00 0.00 4.26
1770 1838 0.725784 CATGTGCCAACGAAACGAGC 60.726 55.000 0.00 0.00 0.00 5.03
1771 1839 0.725784 GCATGTGCCAACGAAACGAG 60.726 55.000 0.00 0.00 34.31 4.18
1772 1840 1.281353 GCATGTGCCAACGAAACGA 59.719 52.632 0.00 0.00 34.31 3.85
1773 1841 0.387112 ATGCATGTGCCAACGAAACG 60.387 50.000 0.00 0.00 41.18 3.60
1774 1842 1.062258 CATGCATGTGCCAACGAAAC 58.938 50.000 18.91 0.00 41.18 2.78
1775 1843 0.038435 CCATGCATGTGCCAACGAAA 60.038 50.000 24.58 0.00 41.18 3.46
1807 1883 2.838202 CCAAAGGTCTCCAACTAGGCTA 59.162 50.000 0.00 0.00 37.29 3.93
1808 1884 1.630878 CCAAAGGTCTCCAACTAGGCT 59.369 52.381 0.00 0.00 37.29 4.58
1809 1885 1.628846 TCCAAAGGTCTCCAACTAGGC 59.371 52.381 0.00 0.00 37.29 3.93
1810 1886 4.265073 CAATCCAAAGGTCTCCAACTAGG 58.735 47.826 0.00 0.00 39.47 3.02
1814 1904 1.546029 GCCAATCCAAAGGTCTCCAAC 59.454 52.381 0.00 0.00 0.00 3.77
1827 1917 9.660180 TTAAGTTTGGTTATAAATTGCCAATCC 57.340 29.630 6.20 2.16 40.23 3.01
1855 1949 4.218686 GTGGGTGGCTGGTTGGGT 62.219 66.667 0.00 0.00 0.00 4.51
1873 1967 0.750182 AACACTGTTTGTCCGTGGGG 60.750 55.000 0.00 0.00 37.51 4.96
1923 2017 9.322773 ACTTAAATAGAAGCTAATAAACCGACC 57.677 33.333 0.00 0.00 0.00 4.79
1940 2034 5.473504 ACAGGTGCTGGTGAAACTTAAATAG 59.526 40.000 0.00 0.00 35.51 1.73
1958 2052 2.281761 GGCCAGTGACCACAGGTG 60.282 66.667 12.21 0.00 39.81 4.00
2026 2125 7.084486 GCAGTGGACAAAGAAAGGTAAATTAG 58.916 38.462 0.00 0.00 0.00 1.73
2083 2185 7.669089 AACCCCACAAAATTAGAGAGAAAAA 57.331 32.000 0.00 0.00 0.00 1.94
2126 2228 8.761575 AATCACTGTTATTGCCATACAAAAAG 57.238 30.769 0.00 0.00 42.86 2.27
2138 2240 8.341173 GCTATTCTCAAGGAATCACTGTTATTG 58.659 37.037 0.00 0.00 42.96 1.90
2199 2301 6.728200 GGTGATTGATCAGCGAATTAATTGA 58.272 36.000 5.17 0.00 44.12 2.57
2221 2323 2.420043 CGACACCAAGACACCGGT 59.580 61.111 0.00 0.00 35.27 5.28
2222 2324 2.357034 CCGACACCAAGACACCGG 60.357 66.667 0.00 0.00 0.00 5.28
2236 2338 4.141321 ACACTAGTGATGATACCTACCCGA 60.141 45.833 29.30 0.00 0.00 5.14
2237 2339 4.142790 ACACTAGTGATGATACCTACCCG 58.857 47.826 29.30 0.00 0.00 5.28
2280 2388 8.151198 CTGTAAGATGTTAGCTGACTAACCGAG 61.151 44.444 10.29 0.00 46.87 4.63
2363 2475 9.853555 TTATCGTTACTTCAAAAATGCATCAAT 57.146 25.926 0.00 0.00 0.00 2.57
2475 2587 5.833406 ACAGACAAATGTTCATGTTGTGA 57.167 34.783 3.59 0.00 35.67 3.58
2480 2592 6.205464 CAGAACCTACAGACAAATGTTCATGT 59.795 38.462 0.00 5.66 35.68 3.21
2483 2595 5.924356 TCAGAACCTACAGACAAATGTTCA 58.076 37.500 0.00 0.00 35.68 3.18
2486 2598 5.552870 ACTCAGAACCTACAGACAAATGT 57.447 39.130 0.00 0.00 37.19 2.71
2487 2599 5.334414 GCAACTCAGAACCTACAGACAAATG 60.334 44.000 0.00 0.00 0.00 2.32
2488 2600 4.757149 GCAACTCAGAACCTACAGACAAAT 59.243 41.667 0.00 0.00 0.00 2.32
2503 2615 3.364565 GCCAAAAATGCATTGCAACTCAG 60.365 43.478 16.46 6.14 43.62 3.35
2531 2643 0.890683 GGGGTGCACAAGAAATCCAG 59.109 55.000 20.43 0.00 0.00 3.86
2535 2647 2.683211 AAGAGGGGTGCACAAGAAAT 57.317 45.000 20.43 0.00 0.00 2.17
2546 2658 5.348259 TTCCAAGGAAAAATAAGAGGGGT 57.652 39.130 0.00 0.00 0.00 4.95
2548 2660 7.244886 ACAATTCCAAGGAAAAATAAGAGGG 57.755 36.000 5.52 0.00 37.69 4.30
2565 2677 2.159142 ACTCGTCGGGATGTACAATTCC 60.159 50.000 0.00 6.93 0.00 3.01
2571 2683 6.413018 AATTAAAAACTCGTCGGGATGTAC 57.587 37.500 0.00 0.00 0.00 2.90
2608 2720 7.122055 CAGTGTACCAAAAGGCTATTTCCAATA 59.878 37.037 0.00 0.00 0.00 1.90
2609 2721 6.016555 AGTGTACCAAAAGGCTATTTCCAAT 58.983 36.000 0.00 0.00 0.00 3.16
2613 2725 5.959618 ACAGTGTACCAAAAGGCTATTTC 57.040 39.130 0.00 0.00 0.00 2.17
2618 2730 3.632145 CAGAAACAGTGTACCAAAAGGCT 59.368 43.478 0.00 0.00 0.00 4.58
2657 2769 8.089597 CCCGGTTGTAAAATTTTATAAGTGGTT 58.910 33.333 22.60 0.00 0.00 3.67
2676 2788 1.105457 ATGCATCATGAACCCGGTTG 58.895 50.000 7.78 0.00 0.00 3.77
2677 2789 1.851304 AATGCATCATGAACCCGGTT 58.149 45.000 1.22 1.22 0.00 4.44
2712 2824 6.537301 TGTCATTGTCGGTAACCAAGATATTC 59.463 38.462 0.00 0.00 0.00 1.75
2713 2825 6.315393 GTGTCATTGTCGGTAACCAAGATATT 59.685 38.462 0.00 0.00 0.00 1.28
2734 2846 7.696755 TGATACATGCAAGTAATCAATGTGTC 58.303 34.615 5.81 3.75 32.05 3.67
2921 3149 5.851177 CCGTGTTGTGTTAGAAATCATGTTC 59.149 40.000 0.00 0.00 0.00 3.18
2928 3156 2.031157 GCAGCCGTGTTGTGTTAGAAAT 60.031 45.455 0.00 0.00 0.00 2.17
2932 3160 1.726791 CTAGCAGCCGTGTTGTGTTAG 59.273 52.381 0.00 0.00 0.00 2.34
2938 3171 4.808895 TCAAATATACTAGCAGCCGTGTTG 59.191 41.667 0.00 0.00 0.00 3.33
2972 3242 8.329203 AGAAACAGAGTGAGGCTTAAATTAAG 57.671 34.615 8.32 8.32 38.80 1.85
2975 3245 7.588497 AAAGAAACAGAGTGAGGCTTAAATT 57.412 32.000 0.00 0.00 0.00 1.82
2988 3270 7.766283 AGAAACCAGAAGAAAAAGAAACAGAG 58.234 34.615 0.00 0.00 0.00 3.35
3027 3309 5.607939 TGAAGTGAACACAGGAGAAGTAA 57.392 39.130 7.68 0.00 0.00 2.24
3074 3356 7.860373 TCACATACAAAGTAAGAATGTGCAAAC 59.140 33.333 8.50 0.00 44.43 2.93
3132 3488 3.873801 GCCATCATAACCCTGTTGTGAGT 60.874 47.826 11.20 0.02 0.00 3.41
3143 3499 3.091633 AGCATATGGGCCATCATAACC 57.908 47.619 25.07 6.84 33.86 2.85
3154 3510 3.806521 GCGCTATGATTCTAGCATATGGG 59.193 47.826 0.00 0.00 43.53 4.00
3172 3528 5.801947 CAGAGCAGTAAAATTAAATTGCGCT 59.198 36.000 9.73 7.51 41.26 5.92
3173 3529 5.572896 ACAGAGCAGTAAAATTAAATTGCGC 59.427 36.000 0.00 0.00 36.70 6.09
3174 3530 6.033831 CCACAGAGCAGTAAAATTAAATTGCG 59.966 38.462 0.00 0.00 36.70 4.85
3196 3552 5.704515 ACATTGCATAGAGCTGAATATCCAC 59.295 40.000 0.00 0.00 45.94 4.02
3199 3555 5.629097 GCACATTGCATAGAGCTGAATATC 58.371 41.667 0.00 0.00 44.26 1.63
3200 3556 5.624344 GCACATTGCATAGAGCTGAATAT 57.376 39.130 0.00 0.00 44.26 1.28
3230 3588 6.901887 CAGATCAGAATTATGTGTAAACGTGC 59.098 38.462 0.00 0.00 0.00 5.34
3237 3595 9.283768 ACAACAAACAGATCAGAATTATGTGTA 57.716 29.630 0.00 0.00 31.24 2.90
3262 3620 8.132362 CAGAGAGACCAGATACTGTTATAACAC 58.868 40.741 14.35 5.12 34.70 3.32
3299 3660 1.212935 AGGACCTGACTTTGTGCAGTT 59.787 47.619 0.00 0.00 0.00 3.16
3350 3711 2.050144 AGCAGGGTGAGAAGAAAGACA 58.950 47.619 0.00 0.00 0.00 3.41
3398 3759 3.187637 CACCGTTTTCCGTAACATCACAT 59.812 43.478 0.00 0.00 33.66 3.21
3408 3769 1.886886 ATAGCAACACCGTTTTCCGT 58.113 45.000 0.00 0.00 33.66 4.69
3409 3770 2.224549 TCAATAGCAACACCGTTTTCCG 59.775 45.455 0.00 0.00 0.00 4.30
3487 3848 3.111853 TCCAGACTGCAGTAACAACAG 57.888 47.619 21.73 3.51 37.45 3.16
3517 3879 9.250624 TGCATAATTTACAAAACAACCAAGTAC 57.749 29.630 0.00 0.00 0.00 2.73
3545 3907 9.611284 TTCGAGATAAAAATTGACAACATTCTG 57.389 29.630 0.00 0.00 0.00 3.02
3548 3910 9.410556 CCTTTCGAGATAAAAATTGACAACATT 57.589 29.630 0.00 0.00 0.00 2.71
3552 3914 9.624697 CATTCCTTTCGAGATAAAAATTGACAA 57.375 29.630 0.00 0.00 0.00 3.18
3558 3920 7.707893 CCATTGCATTCCTTTCGAGATAAAAAT 59.292 33.333 0.00 0.00 0.00 1.82
3559 3921 7.035004 CCATTGCATTCCTTTCGAGATAAAAA 58.965 34.615 0.00 0.00 0.00 1.94
3573 3935 5.964758 TCAATAACTTCACCATTGCATTCC 58.035 37.500 0.00 0.00 31.21 3.01
3633 3995 1.352352 AGTTGTAATGCCAGAGCCTGT 59.648 47.619 2.18 0.00 38.69 4.00
3699 4061 2.887152 ACTGAGCAATGACAAAGGGAAC 59.113 45.455 0.00 0.00 0.00 3.62
3764 4126 3.359033 TGAAGCAATTAGAGCCAGCAAT 58.641 40.909 0.00 0.00 0.00 3.56
3773 4135 9.066892 AGTACAAGTGAAAATGAAGCAATTAGA 57.933 29.630 0.00 0.00 0.00 2.10
3788 4150 2.352421 GCAGTAGGCGAGTACAAGTGAA 60.352 50.000 0.00 0.00 0.00 3.18
3838 4200 3.831333 TCATTTGCAGCCTCCAACAAATA 59.169 39.130 0.00 0.00 39.92 1.40
3845 4207 2.219080 TTCATCATTTGCAGCCTCCA 57.781 45.000 0.00 0.00 0.00 3.86
4023 4385 2.107366 TCATTAGGTGAGCCGTCATCA 58.893 47.619 0.00 0.00 36.10 3.07
4100 4463 2.159296 TCAATGCTCATGAATGCTGTGC 60.159 45.455 8.27 1.64 34.55 4.57
4119 4482 6.763135 GTGAGCATAGACAAGGTTTCATATCA 59.237 38.462 0.00 0.00 0.00 2.15
4166 4531 1.921243 TACGGCTGTCATCATTGTCG 58.079 50.000 0.00 0.00 0.00 4.35
4459 4824 1.342496 TCTGAAGAGGTGTGCTCTGTG 59.658 52.381 0.00 0.00 0.00 3.66
4657 5103 1.837947 AGCCTTGGCAATGCACCAA 60.838 52.632 25.70 7.04 44.86 3.67
4675 5121 1.541310 CGAGAAGCAGGTACCCCACA 61.541 60.000 8.74 0.00 0.00 4.17
4915 5376 1.001145 AGTAGAGAGGCGGACGGTT 60.001 57.895 0.00 0.00 0.00 4.44
4916 5377 1.451747 GAGTAGAGAGGCGGACGGT 60.452 63.158 0.00 0.00 0.00 4.83
4917 5378 1.153127 AGAGTAGAGAGGCGGACGG 60.153 63.158 0.00 0.00 0.00 4.79
4918 5379 1.440938 CCAGAGTAGAGAGGCGGACG 61.441 65.000 0.00 0.00 0.00 4.79
4919 5380 0.107116 TCCAGAGTAGAGAGGCGGAC 60.107 60.000 0.00 0.00 0.00 4.79
4920 5381 0.107116 GTCCAGAGTAGAGAGGCGGA 60.107 60.000 0.00 0.00 0.00 5.54
4921 5382 0.106918 AGTCCAGAGTAGAGAGGCGG 60.107 60.000 0.00 0.00 0.00 6.13
4922 5383 2.623878 TAGTCCAGAGTAGAGAGGCG 57.376 55.000 0.00 0.00 0.00 5.52
4923 5384 4.159244 TCTTAGTCCAGAGTAGAGAGGC 57.841 50.000 0.00 0.00 0.00 4.70
4924 5385 5.502079 TGTTCTTAGTCCAGAGTAGAGAGG 58.498 45.833 0.00 0.00 0.00 3.69
5012 5473 2.591715 AACACGCCCAGACACAGC 60.592 61.111 0.00 0.00 0.00 4.40
5018 5479 2.281484 GCCAAGAACACGCCCAGA 60.281 61.111 0.00 0.00 0.00 3.86
5072 5533 1.511305 GATGACGAGCACCTCCGAA 59.489 57.895 0.00 0.00 0.00 4.30
5269 5730 3.138304 TGAGTCAAAAATCACGACAGGG 58.862 45.455 0.00 0.00 31.92 4.45
5314 5775 6.601613 TGGATATGAACACAATAAACACCTCC 59.398 38.462 0.00 0.00 0.00 4.30
5397 5859 3.132289 ACCGAAGAGAAGAGAACACACAA 59.868 43.478 0.00 0.00 0.00 3.33
5421 5883 6.271391 TCCTCCGGATATGTTTAATACACCAT 59.729 38.462 3.57 0.00 40.19 3.55
5426 5888 7.980099 CCAGTATCCTCCGGATATGTTTAATAC 59.020 40.741 3.57 4.83 45.08 1.89
5432 5894 3.173965 CCCAGTATCCTCCGGATATGTT 58.826 50.000 3.57 0.00 45.08 2.71
5438 5900 1.152525 GCTCCCAGTATCCTCCGGA 60.153 63.158 2.93 2.93 35.55 5.14
5439 5901 0.112606 TAGCTCCCAGTATCCTCCGG 59.887 60.000 0.00 0.00 0.00 5.14
5513 6256 4.631131 TGCCACTCCATAATCTTCATACG 58.369 43.478 0.00 0.00 0.00 3.06
5631 6395 1.105167 ATCGTGCAAGGATGGGCATG 61.105 55.000 0.00 0.00 45.94 4.06
5756 6520 2.825836 GCATGACGGAAGCAGGGG 60.826 66.667 0.00 0.00 0.00 4.79
5799 6566 2.165030 GAGCCACCATGTTCATTTCTGG 59.835 50.000 0.00 0.00 34.84 3.86
5800 6567 2.821378 TGAGCCACCATGTTCATTTCTG 59.179 45.455 0.00 0.00 0.00 3.02
5802 6569 2.821969 ACTGAGCCACCATGTTCATTTC 59.178 45.455 0.00 0.00 0.00 2.17
5803 6570 2.880443 ACTGAGCCACCATGTTCATTT 58.120 42.857 0.00 0.00 0.00 2.32
5804 6571 2.592102 ACTGAGCCACCATGTTCATT 57.408 45.000 0.00 0.00 0.00 2.57
5805 6572 3.719268 TTACTGAGCCACCATGTTCAT 57.281 42.857 0.00 0.00 0.00 2.57
5806 6573 3.500448 TTTACTGAGCCACCATGTTCA 57.500 42.857 0.00 0.00 0.00 3.18
5807 6574 4.458989 TCAATTTACTGAGCCACCATGTTC 59.541 41.667 0.00 0.00 0.00 3.18
5808 6575 4.406456 TCAATTTACTGAGCCACCATGTT 58.594 39.130 0.00 0.00 0.00 2.71
5809 6576 4.032960 TCAATTTACTGAGCCACCATGT 57.967 40.909 0.00 0.00 0.00 3.21
5810 6577 4.380867 GGTTCAATTTACTGAGCCACCATG 60.381 45.833 2.03 0.00 43.99 3.66
5811 6578 3.763897 GGTTCAATTTACTGAGCCACCAT 59.236 43.478 2.03 0.00 43.99 3.55
5812 6579 3.153919 GGTTCAATTTACTGAGCCACCA 58.846 45.455 2.03 0.00 43.99 4.17
5813 6580 3.850122 GGTTCAATTTACTGAGCCACC 57.150 47.619 2.03 0.00 43.99 4.61
5841 6621 6.478512 TTTTCACTGCCAATAAACCTTCTT 57.521 33.333 0.00 0.00 0.00 2.52
6137 6918 5.928839 TCTGACTGTAACTGATGAAAGCTTC 59.071 40.000 0.00 0.00 0.00 3.86
6141 6922 5.233225 TGCTCTGACTGTAACTGATGAAAG 58.767 41.667 0.00 0.00 0.00 2.62
6172 6953 5.703876 CTCTTCTGAACCCTGTAAAAATGC 58.296 41.667 0.00 0.00 0.00 3.56
6197 6978 1.008538 CAGGCAAGTGAAACGCCAC 60.009 57.895 2.06 0.00 44.57 5.01


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

AutoCloner maintained by Alex Coulton.