Multiple sequence alignment - TraesCS3B01G040300

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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 TraesCS3B01G040300 chr3B 100.000 4507 0 0 1 4507 19873504 19868998 0.000000e+00 8323.0
1 TraesCS3B01G040300 chr3B 100.000 29 0 0 4479 4507 783141494 783141466 2.000000e-03 54.7
2 TraesCS3B01G040300 chr3D 87.802 4394 259 124 212 4478 13585691 13581448 0.000000e+00 4889.0
3 TraesCS3B01G040300 chr3D 86.667 180 8 4 1 171 13585871 13585699 7.700000e-43 185.0
4 TraesCS3B01G040300 chr3A 86.598 4574 284 160 74 4462 23392252 23396681 0.000000e+00 4747.0
5 TraesCS3B01G040300 chr6A 100.000 31 0 0 4477 4507 32792612 32792582 1.750000e-04 58.4
6 TraesCS3B01G040300 chr6B 100.000 29 0 0 4479 4507 509258671 509258699 2.000000e-03 54.7
7 TraesCS3B01G040300 chr2B 100.000 29 0 0 4479 4507 93157668 93157640 2.000000e-03 54.7


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 TraesCS3B01G040300 chr3B 19868998 19873504 4506 True 8323 8323 100.0000 1 4507 1 chr3B.!!$R1 4506
1 TraesCS3B01G040300 chr3D 13581448 13585871 4423 True 2537 4889 87.2345 1 4478 2 chr3D.!!$R1 4477
2 TraesCS3B01G040300 chr3A 23392252 23396681 4429 False 4747 4747 86.5980 74 4462 1 chr3A.!!$F1 4388

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
781 881 0.036010 GCTTGTTAGCAGCTCCTCCA 60.036 55.0 0.0 0.0 46.95 3.86 F
1723 1903 0.032217 AGAAGAGGAGCCAGAGGAGG 60.032 60.0 0.0 0.0 0.00 4.30 F
2679 2891 0.036671 GGAACTACACCACCTTCCGG 60.037 60.0 0.0 0.0 0.00 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2446 2646 0.314618 TGCACAACACACATGCATCC 59.685 50.0 0.0 0.0 44.17 3.51 R
3250 3521 0.247736 GAGCCGGCTCTTCTTCTGAA 59.752 55.0 42.5 0.0 39.80 3.02 R
3786 4067 0.040870 CCGTCGTCATCTCATCTCCG 60.041 60.0 0.0 0.0 0.00 4.63 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
56 66 4.592351 AGATTGATGTGAGGTGCTAGCTAT 59.408 41.667 17.23 1.02 0.00 2.97
57 67 4.327982 TTGATGTGAGGTGCTAGCTATC 57.672 45.455 17.23 11.38 0.00 2.08
60 70 2.587522 TGTGAGGTGCTAGCTATCGAT 58.412 47.619 17.23 2.16 0.00 3.59
61 71 2.294512 TGTGAGGTGCTAGCTATCGATG 59.705 50.000 17.23 0.00 0.00 3.84
63 73 2.163509 GAGGTGCTAGCTATCGATGGA 58.836 52.381 17.23 0.00 0.00 3.41
66 76 0.523519 TGCTAGCTATCGATGGAGCG 59.476 55.000 17.23 2.15 43.72 5.03
67 77 0.800300 GCTAGCTATCGATGGAGCGC 60.800 60.000 13.60 8.41 43.72 5.92
68 78 0.522286 CTAGCTATCGATGGAGCGCG 60.522 60.000 13.60 0.00 43.72 6.86
69 79 1.235281 TAGCTATCGATGGAGCGCGT 61.235 55.000 13.60 0.00 43.72 6.01
70 80 1.661821 GCTATCGATGGAGCGCGTT 60.662 57.895 13.60 0.00 0.00 4.84
71 81 0.386858 GCTATCGATGGAGCGCGTTA 60.387 55.000 13.60 0.00 0.00 3.18
72 82 1.732732 GCTATCGATGGAGCGCGTTAT 60.733 52.381 13.60 0.00 0.00 1.89
178 188 2.832201 GGCCCTGCCTCTTCATGC 60.832 66.667 0.00 0.00 46.69 4.06
180 190 2.123982 CCCTGCCTCTTCATGCCC 60.124 66.667 0.00 0.00 0.00 5.36
181 191 2.123982 CCTGCCTCTTCATGCCCC 60.124 66.667 0.00 0.00 0.00 5.80
202 212 5.640147 CCCCCAAATAATTATCAGTAGGCA 58.360 41.667 0.00 0.00 0.00 4.75
203 213 5.476945 CCCCCAAATAATTATCAGTAGGCAC 59.523 44.000 0.00 0.00 0.00 5.01
204 214 6.306987 CCCCAAATAATTATCAGTAGGCACT 58.693 40.000 0.00 0.00 46.37 4.40
205 215 6.431234 CCCCAAATAATTATCAGTAGGCACTC 59.569 42.308 0.00 0.00 41.75 3.51
206 216 6.431234 CCCAAATAATTATCAGTAGGCACTCC 59.569 42.308 0.00 0.00 41.75 3.85
207 217 6.431234 CCAAATAATTATCAGTAGGCACTCCC 59.569 42.308 0.00 0.00 41.75 4.30
208 218 6.763715 AATAATTATCAGTAGGCACTCCCA 57.236 37.500 0.00 0.00 41.75 4.37
209 219 6.763715 ATAATTATCAGTAGGCACTCCCAA 57.236 37.500 0.00 0.00 41.75 4.12
210 220 5.653255 AATTATCAGTAGGCACTCCCAAT 57.347 39.130 0.00 0.00 41.75 3.16
214 224 5.653255 ATCAGTAGGCACTCCCAATAATT 57.347 39.130 0.00 0.00 41.75 1.40
217 227 7.865530 TCAGTAGGCACTCCCAATAATTATA 57.134 36.000 0.00 0.00 41.75 0.98
238 248 3.142174 AGTTTGTTTACTGCTCAGCTCC 58.858 45.455 0.00 0.00 0.00 4.70
239 249 3.142174 GTTTGTTTACTGCTCAGCTCCT 58.858 45.455 0.00 0.00 0.00 3.69
240 250 2.751166 TGTTTACTGCTCAGCTCCTC 57.249 50.000 0.00 0.00 0.00 3.71
241 251 2.251818 TGTTTACTGCTCAGCTCCTCT 58.748 47.619 0.00 0.00 0.00 3.69
242 252 2.634940 TGTTTACTGCTCAGCTCCTCTT 59.365 45.455 0.00 0.00 0.00 2.85
243 253 2.999355 GTTTACTGCTCAGCTCCTCTTG 59.001 50.000 0.00 0.00 0.00 3.02
259 290 6.641723 GCTCCTCTTGTCGTAATAATTACTCC 59.358 42.308 0.00 0.00 33.98 3.85
260 291 7.047460 TCCTCTTGTCGTAATAATTACTCCC 57.953 40.000 0.00 0.00 33.98 4.30
309 346 4.457834 TCGTCCCATCTTCTCTTTTCTC 57.542 45.455 0.00 0.00 0.00 2.87
310 347 4.090090 TCGTCCCATCTTCTCTTTTCTCT 58.910 43.478 0.00 0.00 0.00 3.10
311 348 4.528596 TCGTCCCATCTTCTCTTTTCTCTT 59.471 41.667 0.00 0.00 0.00 2.85
312 349 4.867608 CGTCCCATCTTCTCTTTTCTCTTC 59.132 45.833 0.00 0.00 0.00 2.87
313 350 5.337169 CGTCCCATCTTCTCTTTTCTCTTCT 60.337 44.000 0.00 0.00 0.00 2.85
373 410 9.901172 CCCATGATATGATATGAAAATCTCTCA 57.099 33.333 0.00 0.00 0.00 3.27
389 426 5.576563 TCTCTCAAAACCACCTTTATGGA 57.423 39.130 0.00 0.00 43.02 3.41
391 428 4.069304 TCTCAAAACCACCTTTATGGACG 58.931 43.478 0.00 0.00 43.02 4.79
392 429 3.150767 TCAAAACCACCTTTATGGACGG 58.849 45.455 0.00 0.00 43.02 4.79
393 430 3.150767 CAAAACCACCTTTATGGACGGA 58.849 45.455 0.00 0.00 43.02 4.69
394 431 2.484742 AACCACCTTTATGGACGGAC 57.515 50.000 0.00 0.00 43.02 4.79
395 432 0.248289 ACCACCTTTATGGACGGACG 59.752 55.000 0.00 0.00 43.02 4.79
396 433 0.461339 CCACCTTTATGGACGGACGG 60.461 60.000 0.00 0.00 43.02 4.79
399 436 1.411612 ACCTTTATGGACGGACGGATC 59.588 52.381 0.00 0.00 39.71 3.36
401 438 0.249155 TTTATGGACGGACGGATCGC 60.249 55.000 0.00 0.00 0.00 4.58
460 497 3.516981 TCTTCGCTTTGATCTCTCCAG 57.483 47.619 0.00 0.00 0.00 3.86
482 533 1.625818 GCCACTTTCCTCTCTCTGGAA 59.374 52.381 0.00 0.00 41.33 3.53
609 702 2.309528 TACACATCATCGGAGGTTGC 57.690 50.000 0.97 0.00 35.53 4.17
623 723 1.444119 GGTTGCTTTGCCACTCGTCA 61.444 55.000 0.00 0.00 0.00 4.35
624 724 0.317020 GTTGCTTTGCCACTCGTCAC 60.317 55.000 0.00 0.00 0.00 3.67
625 725 0.463654 TTGCTTTGCCACTCGTCACT 60.464 50.000 0.00 0.00 0.00 3.41
667 767 1.835483 GATGCGTAATGGGAGCAGCG 61.835 60.000 0.00 0.00 44.55 5.18
696 796 2.894731 TGCTCTTCCTCTTCTTCTCCA 58.105 47.619 0.00 0.00 0.00 3.86
697 797 2.564947 TGCTCTTCCTCTTCTTCTCCAC 59.435 50.000 0.00 0.00 0.00 4.02
698 798 2.093711 GCTCTTCCTCTTCTTCTCCACC 60.094 54.545 0.00 0.00 0.00 4.61
739 839 2.203337 TGTTTGGCTCGCAGGCTT 60.203 55.556 10.22 0.00 41.96 4.35
753 853 0.924823 AGGCTTCTTCTCATGGCCAT 59.075 50.000 14.09 14.09 44.60 4.40
754 854 1.030457 GGCTTCTTCTCATGGCCATG 58.970 55.000 35.76 35.76 42.08 3.66
755 855 1.030457 GCTTCTTCTCATGGCCATGG 58.970 55.000 38.81 29.65 39.24 3.66
756 856 1.030457 CTTCTTCTCATGGCCATGGC 58.970 55.000 38.81 29.47 39.24 4.40
781 881 0.036010 GCTTGTTAGCAGCTCCTCCA 60.036 55.000 0.00 0.00 46.95 3.86
930 1045 2.492090 CTCTTCGCCCGACTCCAG 59.508 66.667 0.00 0.00 0.00 3.86
931 1046 2.282958 TCTTCGCCCGACTCCAGT 60.283 61.111 0.00 0.00 0.00 4.00
932 1047 2.182030 CTTCGCCCGACTCCAGTC 59.818 66.667 0.00 0.00 41.47 3.51
933 1048 2.282958 TTCGCCCGACTCCAGTCT 60.283 61.111 5.21 0.00 42.66 3.24
934 1049 2.272918 CTTCGCCCGACTCCAGTCTC 62.273 65.000 5.21 0.00 42.66 3.36
935 1050 3.827898 CGCCCGACTCCAGTCTCC 61.828 72.222 5.21 0.00 42.66 3.71
936 1051 2.680352 GCCCGACTCCAGTCTCCA 60.680 66.667 5.21 0.00 42.66 3.86
990 1122 9.046296 ACTGATTAAGTAATTATTGCTCCTTCG 57.954 33.333 0.00 0.00 37.36 3.79
995 1127 7.497925 AAGTAATTATTGCTCCTTCGATTCC 57.502 36.000 0.00 0.00 0.00 3.01
996 1128 6.591935 AGTAATTATTGCTCCTTCGATTCCA 58.408 36.000 0.00 0.00 0.00 3.53
997 1129 7.054124 AGTAATTATTGCTCCTTCGATTCCAA 58.946 34.615 0.00 0.00 0.00 3.53
1022 1154 1.796617 GCATGCTCACGAATTTCTGCC 60.797 52.381 11.37 0.00 0.00 4.85
1199 1331 2.181021 GGCCGTGTACGAGGACAG 59.819 66.667 5.91 0.00 43.02 3.51
1232 1364 2.696566 TTGGCGACGAAGCAAAGAA 58.303 47.368 0.00 0.00 39.27 2.52
1233 1365 1.234821 TTGGCGACGAAGCAAAGAAT 58.765 45.000 0.00 0.00 39.27 2.40
1234 1366 0.796312 TGGCGACGAAGCAAAGAATC 59.204 50.000 0.00 0.00 39.27 2.52
1257 1389 1.336755 CACCTTTTGTACACTGGTGCC 59.663 52.381 20.86 0.00 41.09 5.01
1383 1515 2.202756 GAGGACCACCGCATCGAC 60.203 66.667 0.00 0.00 41.83 4.20
1386 1518 3.188786 GACCACCGCATCGACAGC 61.189 66.667 1.74 1.74 0.00 4.40
1431 1563 4.974438 ACCGTGGCCCAGGAGGAA 62.974 66.667 19.17 0.00 38.24 3.36
1442 1574 0.987294 CAGGAGGAAGAAGAGGCCAA 59.013 55.000 5.01 0.00 0.00 4.52
1446 1578 0.988063 AGGAAGAAGAGGCCAAGGTC 59.012 55.000 5.01 0.00 0.00 3.85
1453 1585 2.915659 AGGCCAAGGTCGACGTGA 60.916 61.111 12.13 0.00 0.00 4.35
1472 1616 4.444838 CGACGACGGCATCCCCAA 62.445 66.667 0.00 0.00 35.72 4.12
1524 1668 4.059459 GCCGCGTCGTTGTCACTG 62.059 66.667 4.92 0.00 0.00 3.66
1527 1671 2.661866 GCGTCGTTGTCACTGCCT 60.662 61.111 0.00 0.00 0.00 4.75
1562 1706 4.202264 CGTTCAAGGCAATCTCCTAGGTAT 60.202 45.833 9.08 0.87 34.82 2.73
1563 1707 4.963318 TCAAGGCAATCTCCTAGGTATG 57.037 45.455 9.08 5.20 34.82 2.39
1573 1733 8.972127 GCAATCTCCTAGGTATGTATATTCTCA 58.028 37.037 9.08 0.00 0.00 3.27
1656 1824 1.743252 GAGGCAACGAAGCAGAGGG 60.743 63.158 6.23 0.00 46.39 4.30
1710 1881 1.067821 GACGGGCATGGAGTAGAAGAG 59.932 57.143 0.00 0.00 0.00 2.85
1723 1903 0.032217 AGAAGAGGAGCCAGAGGAGG 60.032 60.000 0.00 0.00 0.00 4.30
1726 1906 1.457455 GAGGAGCCAGAGGAGGAGG 60.457 68.421 0.00 0.00 0.00 4.30
1727 1907 1.938596 AGGAGCCAGAGGAGGAGGA 60.939 63.158 0.00 0.00 0.00 3.71
1728 1908 1.457455 GGAGCCAGAGGAGGAGGAG 60.457 68.421 0.00 0.00 0.00 3.69
1729 1909 1.457455 GAGCCAGAGGAGGAGGAGG 60.457 68.421 0.00 0.00 0.00 4.30
1730 1910 1.938596 AGCCAGAGGAGGAGGAGGA 60.939 63.158 0.00 0.00 0.00 3.71
1731 1911 1.457455 GCCAGAGGAGGAGGAGGAG 60.457 68.421 0.00 0.00 0.00 3.69
1732 1912 1.943730 GCCAGAGGAGGAGGAGGAGA 61.944 65.000 0.00 0.00 0.00 3.71
1733 1913 0.106217 CCAGAGGAGGAGGAGGAGAC 60.106 65.000 0.00 0.00 0.00 3.36
1734 1914 0.465460 CAGAGGAGGAGGAGGAGACG 60.465 65.000 0.00 0.00 0.00 4.18
2257 2441 2.677979 GCCCGCGTTTCCAGTTCTC 61.678 63.158 4.92 0.00 0.00 2.87
2310 2494 7.500559 GGCTCAATGGAGAATTCTTATTACACT 59.499 37.037 9.87 0.00 44.26 3.55
2315 2499 7.265599 TGGAGAATTCTTATTACACTTCCCA 57.734 36.000 9.87 4.79 0.00 4.37
2317 2501 8.336235 TGGAGAATTCTTATTACACTTCCCAAT 58.664 33.333 9.87 0.00 0.00 3.16
2318 2502 9.847224 GGAGAATTCTTATTACACTTCCCAATA 57.153 33.333 9.87 0.00 0.00 1.90
2354 2538 0.661187 TGTTCCTCGACGCACGTTAC 60.661 55.000 0.00 0.00 43.13 2.50
2355 2539 0.661187 GTTCCTCGACGCACGTTACA 60.661 55.000 0.00 0.00 43.13 2.41
2358 2542 1.468127 TCCTCGACGCACGTTACATAA 59.532 47.619 0.00 0.00 43.13 1.90
2361 2545 3.360533 CTCGACGCACGTTACATAATCT 58.639 45.455 0.00 0.00 43.13 2.40
2362 2546 4.521010 CTCGACGCACGTTACATAATCTA 58.479 43.478 0.00 0.00 43.13 1.98
2363 2547 4.521010 TCGACGCACGTTACATAATCTAG 58.479 43.478 0.00 0.00 43.13 2.43
2364 2548 3.117507 CGACGCACGTTACATAATCTAGC 59.882 47.826 0.00 0.00 37.22 3.42
2365 2549 3.378339 ACGCACGTTACATAATCTAGCC 58.622 45.455 0.00 0.00 0.00 3.93
2366 2550 2.729882 CGCACGTTACATAATCTAGCCC 59.270 50.000 0.00 0.00 0.00 5.19
2367 2551 3.552273 CGCACGTTACATAATCTAGCCCT 60.552 47.826 0.00 0.00 0.00 5.19
2368 2552 4.320714 CGCACGTTACATAATCTAGCCCTA 60.321 45.833 0.00 0.00 0.00 3.53
2369 2553 5.621555 CGCACGTTACATAATCTAGCCCTAT 60.622 44.000 0.00 0.00 0.00 2.57
2370 2554 6.403964 CGCACGTTACATAATCTAGCCCTATA 60.404 42.308 0.00 0.00 0.00 1.31
2373 2557 9.871238 CACGTTACATAATCTAGCCCTATAAAT 57.129 33.333 0.00 0.00 0.00 1.40
2384 2568 9.911788 ATCTAGCCCTATAAATCATTACATTGG 57.088 33.333 0.00 0.00 0.00 3.16
2385 2569 8.890472 TCTAGCCCTATAAATCATTACATTGGT 58.110 33.333 0.00 0.00 0.00 3.67
2386 2570 7.765695 AGCCCTATAAATCATTACATTGGTG 57.234 36.000 0.00 0.00 0.00 4.17
2388 2572 8.444783 AGCCCTATAAATCATTACATTGGTGTA 58.555 33.333 0.00 0.00 39.77 2.90
2446 2646 1.293924 GGCTGAAGGATGATGACGTG 58.706 55.000 0.00 0.00 0.00 4.49
2679 2891 0.036671 GGAACTACACCACCTTCCGG 60.037 60.000 0.00 0.00 0.00 5.14
2799 3014 2.373938 GTTCATGGAGAACGAGCCG 58.626 57.895 0.00 0.00 46.36 5.52
2850 3065 0.103208 CCCGGATGAAGAACTCCTCG 59.897 60.000 0.73 0.00 0.00 4.63
2853 3068 0.179070 GGATGAAGAACTCCTCGCCC 60.179 60.000 0.00 0.00 0.00 6.13
2868 3083 3.019003 GCCCAAGCTGCTCCTCGTA 62.019 63.158 1.00 0.00 35.50 3.43
2885 3100 3.607741 TCGTACCAGAGTTCAGAGGTAG 58.392 50.000 0.00 0.00 37.30 3.18
2886 3101 2.097791 CGTACCAGAGTTCAGAGGTAGC 59.902 54.545 0.00 0.00 37.30 3.58
2887 3102 1.562783 ACCAGAGTTCAGAGGTAGCC 58.437 55.000 0.00 0.00 31.32 3.93
2888 3103 1.203187 ACCAGAGTTCAGAGGTAGCCA 60.203 52.381 0.00 0.00 31.32 4.75
2889 3104 1.902508 CCAGAGTTCAGAGGTAGCCAA 59.097 52.381 0.00 0.00 0.00 4.52
2890 3105 2.503356 CCAGAGTTCAGAGGTAGCCAAT 59.497 50.000 0.00 0.00 0.00 3.16
2891 3106 3.529533 CAGAGTTCAGAGGTAGCCAATG 58.470 50.000 0.00 0.00 0.00 2.82
2892 3107 2.093235 AGAGTTCAGAGGTAGCCAATGC 60.093 50.000 0.00 0.00 37.95 3.56
2893 3108 1.630369 AGTTCAGAGGTAGCCAATGCA 59.370 47.619 0.00 0.00 41.13 3.96
2894 3109 2.240667 AGTTCAGAGGTAGCCAATGCAT 59.759 45.455 0.00 0.00 41.13 3.96
2896 3111 1.202568 TCAGAGGTAGCCAATGCATCG 60.203 52.381 0.00 0.00 41.13 3.84
2897 3112 1.123077 AGAGGTAGCCAATGCATCGA 58.877 50.000 0.00 0.00 41.13 3.59
2898 3113 1.486310 AGAGGTAGCCAATGCATCGAA 59.514 47.619 0.00 0.00 41.13 3.71
2899 3114 2.105477 AGAGGTAGCCAATGCATCGAAT 59.895 45.455 0.00 0.00 41.13 3.34
2901 3116 4.065088 GAGGTAGCCAATGCATCGAATAA 58.935 43.478 0.00 0.00 41.13 1.40
2903 3118 5.072741 AGGTAGCCAATGCATCGAATAATT 58.927 37.500 0.00 0.00 41.13 1.40
2906 3121 6.968904 GGTAGCCAATGCATCGAATAATTATG 59.031 38.462 0.00 0.00 41.13 1.90
2907 3122 6.822667 AGCCAATGCATCGAATAATTATGA 57.177 33.333 0.00 0.00 41.13 2.15
2908 3123 7.400599 AGCCAATGCATCGAATAATTATGAT 57.599 32.000 0.00 0.00 41.13 2.45
2910 3125 8.308931 AGCCAATGCATCGAATAATTATGATTT 58.691 29.630 0.00 0.00 41.13 2.17
2911 3126 8.377681 GCCAATGCATCGAATAATTATGATTTG 58.622 33.333 0.00 1.52 37.47 2.32
2912 3127 8.865978 CCAATGCATCGAATAATTATGATTTGG 58.134 33.333 0.00 6.16 32.63 3.28
2913 3128 9.414295 CAATGCATCGAATAATTATGATTTGGT 57.586 29.630 0.00 0.00 0.00 3.67
2916 3131 9.283768 TGCATCGAATAATTATGATTTGGTACT 57.716 29.630 0.00 0.00 0.00 2.73
2917 3132 9.546909 GCATCGAATAATTATGATTTGGTACTG 57.453 33.333 0.00 0.00 0.00 2.74
2918 3133 9.546909 CATCGAATAATTATGATTTGGTACTGC 57.453 33.333 0.00 0.00 0.00 4.40
2920 3135 9.283768 TCGAATAATTATGATTTGGTACTGCAT 57.716 29.630 0.00 0.00 0.00 3.96
2953 3193 9.318041 CTAGTTTTGTTCGTGATTAATCAAGTG 57.682 33.333 24.55 15.87 38.75 3.16
2954 3194 7.703328 AGTTTTGTTCGTGATTAATCAAGTGT 58.297 30.769 24.55 5.49 38.75 3.55
2955 3195 7.643764 AGTTTTGTTCGTGATTAATCAAGTGTG 59.356 33.333 24.55 11.88 38.75 3.82
2956 3196 6.852858 TTGTTCGTGATTAATCAAGTGTGA 57.147 33.333 24.55 13.55 38.75 3.58
2957 3197 6.223138 TGTTCGTGATTAATCAAGTGTGAC 57.777 37.500 24.55 19.20 38.75 3.67
2958 3198 5.989168 TGTTCGTGATTAATCAAGTGTGACT 59.011 36.000 24.55 0.00 38.75 3.41
2959 3199 6.145534 TGTTCGTGATTAATCAAGTGTGACTC 59.854 38.462 24.55 8.52 38.75 3.36
2960 3200 5.778862 TCGTGATTAATCAAGTGTGACTCA 58.221 37.500 24.55 6.26 38.75 3.41
2961 3201 5.633601 TCGTGATTAATCAAGTGTGACTCAC 59.366 40.000 24.55 8.74 46.46 3.51
2973 3213 3.076621 TGTGACTCACTGATTGAATGGC 58.923 45.455 10.54 0.00 35.11 4.40
2979 3219 4.337555 ACTCACTGATTGAATGGCTAATGC 59.662 41.667 0.00 0.00 32.21 3.56
3108 3348 1.134371 GGAGCCACTACCAGATGTTCC 60.134 57.143 0.00 0.00 0.00 3.62
3193 3433 0.396435 AACAAGGCCGTGAGTGATCA 59.604 50.000 26.25 0.00 0.00 2.92
3196 3436 1.134580 CAAGGCCGTGAGTGATCAGAT 60.135 52.381 14.14 0.00 0.00 2.90
3221 3461 2.357327 TCTTACGTACGTGCAAGCAT 57.643 45.000 30.25 3.43 0.00 3.79
3222 3462 1.989864 TCTTACGTACGTGCAAGCATG 59.010 47.619 30.25 12.42 38.78 4.06
3241 3512 4.089065 GCATGATGCTTTCTGAACGTTTTC 59.911 41.667 10.72 0.00 40.96 2.29
3440 3711 2.203126 GAGAAGATGGGCCGGCTG 60.203 66.667 28.56 0.00 0.00 4.85
3512 3787 4.193334 CCCGCGCACTGAGATCGA 62.193 66.667 8.75 0.00 0.00 3.59
3513 3788 2.026734 CCGCGCACTGAGATCGAT 59.973 61.111 8.75 0.00 0.00 3.59
3514 3789 2.013483 CCGCGCACTGAGATCGATC 61.013 63.158 17.91 17.91 0.00 3.69
3515 3790 1.009108 CGCGCACTGAGATCGATCT 60.009 57.895 27.63 27.63 40.50 2.75
3536 3811 0.796312 CCATCACAAAACCTCCGTCG 59.204 55.000 0.00 0.00 0.00 5.12
3590 3865 5.240844 TGCAACCTAGCTACTTTTCCTTTTC 59.759 40.000 0.00 0.00 34.99 2.29
3597 3872 8.894731 CCTAGCTACTTTTCCTTTTCCTTTATC 58.105 37.037 0.00 0.00 0.00 1.75
3662 3939 5.461526 AGCGACAAAAGAAAAGATAAAGCC 58.538 37.500 0.00 0.00 0.00 4.35
3748 4029 9.265901 ACTAGTGGTAGTACAATATACTACGTG 57.734 37.037 14.82 7.87 46.53 4.49
3750 4031 6.016777 AGTGGTAGTACAATATACTACGTGCC 60.017 42.308 14.82 5.33 46.53 5.01
3786 4067 1.129624 CGAGATCGATCGGACTCATCC 59.870 57.143 27.64 13.48 43.02 3.51
3878 4160 2.610232 GCCCGTTTCCGTCTTGTAGTTA 60.610 50.000 0.00 0.00 0.00 2.24
3879 4161 3.248266 CCCGTTTCCGTCTTGTAGTTAG 58.752 50.000 0.00 0.00 0.00 2.34
3880 4162 3.305608 CCCGTTTCCGTCTTGTAGTTAGT 60.306 47.826 0.00 0.00 0.00 2.24
3881 4163 4.301628 CCGTTTCCGTCTTGTAGTTAGTT 58.698 43.478 0.00 0.00 0.00 2.24
3927 4209 4.286101 CTGACATACGCACACAGAGATAG 58.714 47.826 0.00 0.00 0.00 2.08
3928 4210 3.945285 TGACATACGCACACAGAGATAGA 59.055 43.478 0.00 0.00 0.00 1.98
3929 4211 4.035675 TGACATACGCACACAGAGATAGAG 59.964 45.833 0.00 0.00 0.00 2.43
3931 4213 4.824537 ACATACGCACACAGAGATAGAGAT 59.175 41.667 0.00 0.00 0.00 2.75
3932 4214 5.998363 ACATACGCACACAGAGATAGAGATA 59.002 40.000 0.00 0.00 0.00 1.98
3933 4215 6.148645 ACATACGCACACAGAGATAGAGATAG 59.851 42.308 0.00 0.00 0.00 2.08
3934 4216 4.709250 ACGCACACAGAGATAGAGATAGA 58.291 43.478 0.00 0.00 0.00 1.98
3935 4217 4.754618 ACGCACACAGAGATAGAGATAGAG 59.245 45.833 0.00 0.00 0.00 2.43
3936 4218 4.994217 CGCACACAGAGATAGAGATAGAGA 59.006 45.833 0.00 0.00 0.00 3.10
3937 4219 5.120674 CGCACACAGAGATAGAGATAGAGAG 59.879 48.000 0.00 0.00 0.00 3.20
3938 4220 6.230472 GCACACAGAGATAGAGATAGAGAGA 58.770 44.000 0.00 0.00 0.00 3.10
3939 4221 6.369890 GCACACAGAGATAGAGATAGAGAGAG 59.630 46.154 0.00 0.00 0.00 3.20
3964 4246 1.277557 AGAGATATTGGGATCGGCAGC 59.722 52.381 0.00 0.00 0.00 5.25
3965 4247 1.002430 GAGATATTGGGATCGGCAGCA 59.998 52.381 0.00 0.00 0.00 4.41
3967 4249 1.002430 GATATTGGGATCGGCAGCAGA 59.998 52.381 0.00 0.00 0.00 4.26
4007 4296 3.007398 TGACACAACCCAAAGCAAAAGTT 59.993 39.130 0.00 0.00 0.00 2.66
4041 4334 4.752879 GACAAGCACGGCCGGCTA 62.753 66.667 32.15 0.00 41.66 3.93
4042 4335 4.760047 ACAAGCACGGCCGGCTAG 62.760 66.667 32.15 22.69 41.66 3.42
4048 4341 3.702048 ACGGCCGGCTAGCTTTGA 61.702 61.111 31.76 0.00 0.00 2.69
4050 4343 1.069090 CGGCCGGCTAGCTTTGATA 59.931 57.895 28.56 0.00 0.00 2.15
4051 4344 0.320771 CGGCCGGCTAGCTTTGATAT 60.321 55.000 28.56 0.00 0.00 1.63
4054 4347 2.939103 GGCCGGCTAGCTTTGATATATG 59.061 50.000 28.56 0.00 0.00 1.78
4056 4349 4.382685 GGCCGGCTAGCTTTGATATATGTA 60.383 45.833 28.56 0.00 0.00 2.29
4057 4350 4.567159 GCCGGCTAGCTTTGATATATGTAC 59.433 45.833 22.15 0.00 0.00 2.90
4058 4351 5.720202 CCGGCTAGCTTTGATATATGTACA 58.280 41.667 15.72 0.00 0.00 2.90
4072 4365 8.949177 TGATATATGTACATGCATTGCTTTAGG 58.051 33.333 18.81 0.00 0.00 2.69
4113 4407 1.515736 CTCGGCTTTACGGACGGAC 60.516 63.158 0.00 0.00 38.41 4.79
4276 4578 1.423395 AGAAAAAGCAGTCTCGCTCG 58.577 50.000 0.00 0.00 42.89 5.03
4277 4579 0.179238 GAAAAAGCAGTCTCGCTCGC 60.179 55.000 0.00 0.00 42.89 5.03
4278 4580 0.880278 AAAAAGCAGTCTCGCTCGCA 60.880 50.000 0.00 0.00 42.89 5.10
4279 4581 1.287730 AAAAGCAGTCTCGCTCGCAG 61.288 55.000 0.00 0.00 42.89 5.18
4319 4621 1.585668 CTCTGCGTTTATGTCTGCGAG 59.414 52.381 0.00 0.00 0.00 5.03
4320 4622 1.201414 TCTGCGTTTATGTCTGCGAGA 59.799 47.619 0.00 0.00 0.00 4.04
4365 4667 3.211963 GCGCTATGGCCAGTTGGG 61.212 66.667 13.05 12.93 40.85 4.12
4373 4675 1.227674 GGCCAGTTGGGAGATAGCG 60.228 63.158 0.00 0.00 40.01 4.26
4441 4747 6.581171 TTTTGGGTTGCAGATTTTTGTTTT 57.419 29.167 0.00 0.00 0.00 2.43
4456 4762 1.269413 TGTTTTCGAGAGGGTGTCGAC 60.269 52.381 9.11 9.11 45.76 4.20
4478 4784 5.938322 ACGTTGGTGCTGATAAACATTAAG 58.062 37.500 0.00 0.00 0.00 1.85
4479 4785 5.703592 ACGTTGGTGCTGATAAACATTAAGA 59.296 36.000 0.00 0.00 0.00 2.10
4480 4786 6.128282 ACGTTGGTGCTGATAAACATTAAGAG 60.128 38.462 0.00 0.00 0.00 2.85
4481 4787 5.818136 TGGTGCTGATAAACATTAAGAGC 57.182 39.130 0.00 0.00 0.00 4.09
4482 4788 5.252547 TGGTGCTGATAAACATTAAGAGCA 58.747 37.500 0.00 0.00 0.00 4.26
4483 4789 5.355071 TGGTGCTGATAAACATTAAGAGCAG 59.645 40.000 0.00 0.00 0.00 4.24
4484 4790 5.355350 GGTGCTGATAAACATTAAGAGCAGT 59.645 40.000 0.00 0.00 0.00 4.40
4485 4791 6.253746 GTGCTGATAAACATTAAGAGCAGTG 58.746 40.000 0.00 0.00 0.00 3.66
4486 4792 5.163723 TGCTGATAAACATTAAGAGCAGTGC 60.164 40.000 7.13 7.13 0.00 4.40
4487 4793 5.065731 GCTGATAAACATTAAGAGCAGTGCT 59.934 40.000 19.86 19.86 43.88 4.40
4488 4794 6.258727 GCTGATAAACATTAAGAGCAGTGCTA 59.741 38.462 19.77 1.93 39.88 3.49
4489 4795 7.041508 GCTGATAAACATTAAGAGCAGTGCTAT 60.042 37.037 19.77 13.17 39.88 2.97
4490 4796 9.481340 CTGATAAACATTAAGAGCAGTGCTATA 57.519 33.333 19.77 11.75 39.88 1.31
4491 4797 9.261180 TGATAAACATTAAGAGCAGTGCTATAC 57.739 33.333 19.77 5.83 39.88 1.47
4492 4798 6.589830 AAACATTAAGAGCAGTGCTATACG 57.410 37.500 19.77 10.32 39.88 3.06
4493 4799 4.621991 ACATTAAGAGCAGTGCTATACGG 58.378 43.478 19.77 8.99 39.88 4.02
4494 4800 4.341235 ACATTAAGAGCAGTGCTATACGGA 59.659 41.667 19.77 2.16 39.88 4.69
4495 4801 2.873133 AAGAGCAGTGCTATACGGAC 57.127 50.000 19.77 3.33 39.88 4.79
4496 4802 0.663688 AGAGCAGTGCTATACGGACG 59.336 55.000 19.77 0.00 39.88 4.79
4497 4803 0.661552 GAGCAGTGCTATACGGACGA 59.338 55.000 19.77 0.00 39.88 4.20
4498 4804 1.267261 GAGCAGTGCTATACGGACGAT 59.733 52.381 19.77 0.00 39.88 3.73
4499 4805 2.483106 GAGCAGTGCTATACGGACGATA 59.517 50.000 19.77 0.00 39.88 2.92
4500 4806 2.882761 AGCAGTGCTATACGGACGATAA 59.117 45.455 18.11 0.00 36.99 1.75
4501 4807 3.317149 AGCAGTGCTATACGGACGATAAA 59.683 43.478 18.11 0.00 36.99 1.40
4502 4808 4.022242 AGCAGTGCTATACGGACGATAAAT 60.022 41.667 18.11 0.00 36.99 1.40
4503 4809 5.182570 AGCAGTGCTATACGGACGATAAATA 59.817 40.000 18.11 0.00 36.99 1.40
4504 4810 6.034591 GCAGTGCTATACGGACGATAAATAT 58.965 40.000 8.18 0.00 39.22 1.28
4505 4811 6.020599 GCAGTGCTATACGGACGATAAATATG 60.021 42.308 8.18 0.00 39.22 1.78
4506 4812 6.472486 CAGTGCTATACGGACGATAAATATGG 59.528 42.308 0.00 0.00 39.22 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.002900 TCGCTTTGTTGTGCTACTTGC 60.003 47.619 0.00 0.00 43.25 4.01
16 17 1.439365 CTCGCTCGCTTTGTTGTGC 60.439 57.895 0.00 0.00 0.00 4.57
56 66 0.179121 AACATAACGCGCTCCATCGA 60.179 50.000 5.73 0.00 0.00 3.59
57 67 1.483316 TAACATAACGCGCTCCATCG 58.517 50.000 5.73 0.00 0.00 3.84
60 70 2.101082 TGGTATAACATAACGCGCTCCA 59.899 45.455 5.73 0.00 0.00 3.86
61 71 2.746269 TGGTATAACATAACGCGCTCC 58.254 47.619 5.73 0.00 0.00 4.70
63 73 3.310501 GGTTTGGTATAACATAACGCGCT 59.689 43.478 5.73 0.00 0.00 5.92
66 76 3.546616 GCGGGTTTGGTATAACATAACGC 60.547 47.826 12.98 12.98 34.26 4.84
67 77 3.302610 CGCGGGTTTGGTATAACATAACG 60.303 47.826 0.00 0.00 0.00 3.18
68 78 3.002553 CCGCGGGTTTGGTATAACATAAC 59.997 47.826 20.10 0.00 0.00 1.89
69 79 3.204526 CCGCGGGTTTGGTATAACATAA 58.795 45.455 20.10 0.00 0.00 1.90
70 80 2.170187 ACCGCGGGTTTGGTATAACATA 59.830 45.455 31.76 0.00 36.50 2.29
71 81 1.065272 ACCGCGGGTTTGGTATAACAT 60.065 47.619 31.76 0.00 36.50 2.71
72 82 0.324285 ACCGCGGGTTTGGTATAACA 59.676 50.000 31.76 0.00 36.50 2.41
111 121 1.206610 AGCCTATATGCGAGATGCCAG 59.793 52.381 0.00 0.00 45.60 4.85
113 123 2.393271 AAGCCTATATGCGAGATGCC 57.607 50.000 0.00 0.00 45.60 4.40
180 190 6.306987 AGTGCCTACTGATAATTATTTGGGG 58.693 40.000 0.00 4.63 35.34 4.96
181 191 6.431234 GGAGTGCCTACTGATAATTATTTGGG 59.569 42.308 0.00 0.84 37.25 4.12
184 194 7.149202 TGGGAGTGCCTACTGATAATTATTT 57.851 36.000 1.06 0.00 37.25 1.40
185 195 6.763715 TGGGAGTGCCTACTGATAATTATT 57.236 37.500 1.06 0.00 37.25 1.40
187 197 6.763715 ATTGGGAGTGCCTACTGATAATTA 57.236 37.500 1.06 0.00 37.25 1.40
188 198 5.653255 ATTGGGAGTGCCTACTGATAATT 57.347 39.130 1.06 0.00 37.25 1.40
189 199 6.763715 TTATTGGGAGTGCCTACTGATAAT 57.236 37.500 1.06 0.00 37.25 1.28
190 200 6.763715 ATTATTGGGAGTGCCTACTGATAA 57.236 37.500 1.06 0.25 37.25 1.75
191 201 6.763715 AATTATTGGGAGTGCCTACTGATA 57.236 37.500 1.06 0.00 37.25 2.15
192 202 5.653255 AATTATTGGGAGTGCCTACTGAT 57.347 39.130 1.06 0.00 37.25 2.90
193 203 6.763715 ATAATTATTGGGAGTGCCTACTGA 57.236 37.500 1.06 0.00 37.25 3.41
194 204 7.680730 ACTATAATTATTGGGAGTGCCTACTG 58.319 38.462 2.68 0.00 37.25 2.74
195 205 7.873699 ACTATAATTATTGGGAGTGCCTACT 57.126 36.000 2.68 0.00 40.66 2.57
196 206 8.784043 CAAACTATAATTATTGGGAGTGCCTAC 58.216 37.037 2.68 0.00 0.00 3.18
197 207 8.499406 ACAAACTATAATTATTGGGAGTGCCTA 58.501 33.333 2.68 0.00 0.00 3.93
198 208 7.354312 ACAAACTATAATTATTGGGAGTGCCT 58.646 34.615 2.68 0.00 0.00 4.75
199 209 7.582667 ACAAACTATAATTATTGGGAGTGCC 57.417 36.000 2.68 0.00 0.00 5.01
210 220 9.667107 AGCTGAGCAGTAAACAAACTATAATTA 57.333 29.630 7.39 0.00 0.00 1.40
214 224 6.070767 AGGAGCTGAGCAGTAAACAAACTATA 60.071 38.462 7.39 0.00 0.00 1.31
217 227 3.142174 GGAGCTGAGCAGTAAACAAACT 58.858 45.455 7.39 0.00 0.00 2.66
238 248 7.713750 TCTGGGAGTAATTATTACGACAAGAG 58.286 38.462 9.16 3.52 41.01 2.85
239 249 7.649533 TCTGGGAGTAATTATTACGACAAGA 57.350 36.000 9.16 10.83 41.01 3.02
240 250 8.888579 AATCTGGGAGTAATTATTACGACAAG 57.111 34.615 9.16 9.03 41.01 3.16
241 251 9.754382 GTAATCTGGGAGTAATTATTACGACAA 57.246 33.333 9.16 0.49 41.01 3.18
242 252 9.139734 AGTAATCTGGGAGTAATTATTACGACA 57.860 33.333 9.16 8.67 41.01 4.35
243 253 9.978044 AAGTAATCTGGGAGTAATTATTACGAC 57.022 33.333 9.16 7.79 41.01 4.34
259 290 3.378427 GGGTTAGCAAGCAAGTAATCTGG 59.622 47.826 0.00 0.00 0.00 3.86
260 291 4.095483 CAGGGTTAGCAAGCAAGTAATCTG 59.905 45.833 0.00 0.00 0.00 2.90
309 346 1.473434 GGGCCCAACGTGATCTAGAAG 60.473 57.143 19.95 0.00 0.00 2.85
310 347 0.539986 GGGCCCAACGTGATCTAGAA 59.460 55.000 19.95 0.00 0.00 2.10
311 348 1.335132 GGGGCCCAACGTGATCTAGA 61.335 60.000 26.86 0.00 0.00 2.43
312 349 1.146263 GGGGCCCAACGTGATCTAG 59.854 63.158 26.86 0.00 0.00 2.43
313 350 0.986019 ATGGGGCCCAACGTGATCTA 60.986 55.000 32.57 0.70 36.95 1.98
373 410 3.151554 GTCCGTCCATAAAGGTGGTTTT 58.848 45.455 0.00 0.00 40.27 2.43
375 412 1.338389 CGTCCGTCCATAAAGGTGGTT 60.338 52.381 0.00 0.00 40.27 3.67
460 497 0.739112 CAGAGAGAGGAAAGTGGCGC 60.739 60.000 0.00 0.00 0.00 6.53
482 533 1.039233 ACACTGGCTTGCTGCTTTGT 61.039 50.000 0.00 1.70 42.39 2.83
609 702 0.861837 GACAGTGACGAGTGGCAAAG 59.138 55.000 0.00 0.00 29.72 2.77
667 767 0.459411 GAGGAAGAGCAAGACGAGCC 60.459 60.000 0.00 0.00 0.00 4.70
674 774 3.260380 TGGAGAAGAAGAGGAAGAGCAAG 59.740 47.826 0.00 0.00 0.00 4.01
739 839 4.993307 GCCATGGCCATGAGAAGA 57.007 55.556 41.32 1.69 41.20 2.87
756 856 3.044059 GCTGCTAACAAGCCGCTGG 62.044 63.158 6.54 0.00 40.93 4.85
757 857 2.482374 GCTGCTAACAAGCCGCTG 59.518 61.111 6.54 0.00 40.93 5.18
761 861 0.746204 GGAGGAGCTGCTAACAAGCC 60.746 60.000 8.12 0.00 0.00 4.35
930 1045 2.775032 TAACCTTGCGCGGTGGAGAC 62.775 60.000 17.86 0.00 37.36 3.36
931 1046 2.501223 CTAACCTTGCGCGGTGGAGA 62.501 60.000 17.86 6.03 37.36 3.71
932 1047 2.047655 TAACCTTGCGCGGTGGAG 60.048 61.111 17.86 4.23 37.36 3.86
933 1048 2.047655 CTAACCTTGCGCGGTGGA 60.048 61.111 17.86 4.98 37.36 4.02
934 1049 2.358247 ACTAACCTTGCGCGGTGG 60.358 61.111 8.83 9.49 37.36 4.61
935 1050 2.860293 CACTAACCTTGCGCGGTG 59.140 61.111 8.83 0.07 37.36 4.94
936 1051 2.162338 TAGCACTAACCTTGCGCGGT 62.162 55.000 8.83 0.95 45.15 5.68
1022 1154 1.060713 CACGTACGCAGAAGAAGTGG 58.939 55.000 16.72 0.00 0.00 4.00
1058 1190 4.922026 GGTTGTCACGGCCACGGT 62.922 66.667 2.24 0.00 46.48 4.83
1080 1212 0.739561 CCTTCCCGGAGTTACTCTCG 59.260 60.000 12.41 13.08 43.60 4.04
1167 1299 1.446272 GGCCTCGTCGAACCAGAAG 60.446 63.158 8.69 0.00 0.00 2.85
1232 1364 4.985538 ACCAGTGTACAAAAGGTGATGAT 58.014 39.130 12.76 0.00 0.00 2.45
1233 1365 4.431416 ACCAGTGTACAAAAGGTGATGA 57.569 40.909 12.76 0.00 0.00 2.92
1329 1461 2.737376 GAGACGCGGTTGGTGGAC 60.737 66.667 12.47 0.00 0.00 4.02
1418 1550 0.911525 CTCTTCTTCCTCCTGGGCCA 60.912 60.000 5.85 5.85 34.39 5.36
1429 1561 0.608640 TCGACCTTGGCCTCTTCTTC 59.391 55.000 3.32 0.00 0.00 2.87
1431 1563 1.878656 CGTCGACCTTGGCCTCTTCT 61.879 60.000 10.58 0.00 0.00 2.85
1517 1661 4.517285 GGAATCATTCTTAGGCAGTGACA 58.483 43.478 0.00 0.00 0.00 3.58
1524 1668 4.035675 CCTTGAACGGAATCATTCTTAGGC 59.964 45.833 0.00 0.00 0.00 3.93
1527 1671 4.584874 TGCCTTGAACGGAATCATTCTTA 58.415 39.130 0.00 0.00 0.00 2.10
1573 1733 6.702329 AGTGACCGATGAAAAAGAAGATAGT 58.298 36.000 0.00 0.00 0.00 2.12
1576 1736 6.234177 AGAAGTGACCGATGAAAAAGAAGAT 58.766 36.000 0.00 0.00 0.00 2.40
1577 1737 5.611374 AGAAGTGACCGATGAAAAAGAAGA 58.389 37.500 0.00 0.00 0.00 2.87
1710 1881 1.457455 CTCCTCCTCCTCTGGCTCC 60.457 68.421 0.00 0.00 0.00 4.70
1739 1919 3.894547 TTCACCTCGGGAAAGCCGC 62.895 63.158 0.00 0.00 33.83 6.53
1749 1929 2.030562 ACCAACCGCTTCACCTCG 59.969 61.111 0.00 0.00 0.00 4.63
1752 1932 1.098712 TGTTCACCAACCGCTTCACC 61.099 55.000 0.00 0.00 0.00 4.02
2095 2275 7.609918 TCAATTTGGCAGTAAACAATCTAGCTA 59.390 33.333 0.00 0.00 0.00 3.32
2096 2276 6.434028 TCAATTTGGCAGTAAACAATCTAGCT 59.566 34.615 0.00 0.00 0.00 3.32
2097 2277 6.620678 TCAATTTGGCAGTAAACAATCTAGC 58.379 36.000 0.00 0.00 0.00 3.42
2098 2278 9.079833 CAATCAATTTGGCAGTAAACAATCTAG 57.920 33.333 0.00 0.00 0.00 2.43
2099 2279 8.584157 ACAATCAATTTGGCAGTAAACAATCTA 58.416 29.630 0.00 0.00 39.80 1.98
2244 2428 0.784778 GTCGCAGAGAACTGGAAACG 59.215 55.000 0.00 0.00 43.62 3.60
2245 2429 0.784778 CGTCGCAGAGAACTGGAAAC 59.215 55.000 0.00 0.00 43.62 2.78
2257 2441 2.680913 CCCCTGAAAAGCGTCGCAG 61.681 63.158 21.09 7.28 0.00 5.18
2358 2542 9.911788 CCAATGTAATGATTTATAGGGCTAGAT 57.088 33.333 0.00 0.00 0.00 1.98
2361 2545 8.444783 ACACCAATGTAATGATTTATAGGGCTA 58.555 33.333 0.00 0.00 37.26 3.93
2362 2546 7.297614 ACACCAATGTAATGATTTATAGGGCT 58.702 34.615 0.00 0.00 37.26 5.19
2363 2547 7.524717 ACACCAATGTAATGATTTATAGGGC 57.475 36.000 0.00 0.00 37.26 5.19
2377 2561 7.675962 GGAACACTATTGTTACACCAATGTA 57.324 36.000 3.38 0.00 46.43 2.29
2378 2562 6.569179 GGAACACTATTGTTACACCAATGT 57.431 37.500 3.38 0.00 46.43 2.71
2446 2646 0.314618 TGCACAACACACATGCATCC 59.685 50.000 0.00 0.00 44.17 3.51
2505 2711 2.863853 CGTGATCCGCTGCGACATG 61.864 63.158 25.45 19.61 0.00 3.21
2695 2910 1.596203 CCATCATCGTGCCGCTGAT 60.596 57.895 7.73 7.73 42.18 2.90
2739 2954 4.329545 TGGAACTCCTGCGCCACC 62.330 66.667 4.18 0.00 36.82 4.61
2850 3065 3.019003 TACGAGGAGCAGCTTGGGC 62.019 63.158 0.00 0.00 39.06 5.36
2853 3068 0.459237 CTGGTACGAGGAGCAGCTTG 60.459 60.000 0.00 0.00 38.06 4.01
2868 3083 1.203187 TGGCTACCTCTGAACTCTGGT 60.203 52.381 0.00 0.00 36.66 4.00
2885 3100 8.377681 CAAATCATAATTATTCGATGCATTGGC 58.622 33.333 14.12 0.00 41.68 4.52
2886 3101 8.865978 CCAAATCATAATTATTCGATGCATTGG 58.134 33.333 14.12 3.25 33.59 3.16
2887 3102 9.414295 ACCAAATCATAATTATTCGATGCATTG 57.586 29.630 7.70 7.70 0.00 2.82
2890 3105 9.283768 AGTACCAAATCATAATTATTCGATGCA 57.716 29.630 0.00 0.00 0.00 3.96
2891 3106 9.546909 CAGTACCAAATCATAATTATTCGATGC 57.453 33.333 0.00 0.00 0.00 3.91
2892 3107 9.546909 GCAGTACCAAATCATAATTATTCGATG 57.453 33.333 0.00 0.00 0.00 3.84
2893 3108 9.283768 TGCAGTACCAAATCATAATTATTCGAT 57.716 29.630 0.00 0.00 0.00 3.59
2894 3109 8.669946 TGCAGTACCAAATCATAATTATTCGA 57.330 30.769 0.00 0.00 0.00 3.71
2910 3125 9.073475 ACAAAACTAGATTAAAATGCAGTACCA 57.927 29.630 0.00 0.00 0.00 3.25
2911 3126 9.908152 AACAAAACTAGATTAAAATGCAGTACC 57.092 29.630 0.00 0.00 0.00 3.34
2913 3128 9.820229 CGAACAAAACTAGATTAAAATGCAGTA 57.180 29.630 0.00 0.00 0.00 2.74
2914 3129 8.349983 ACGAACAAAACTAGATTAAAATGCAGT 58.650 29.630 0.00 0.00 0.00 4.40
2915 3130 8.629986 CACGAACAAAACTAGATTAAAATGCAG 58.370 33.333 0.00 0.00 0.00 4.41
2916 3131 8.346300 TCACGAACAAAACTAGATTAAAATGCA 58.654 29.630 0.00 0.00 0.00 3.96
2917 3132 8.722342 TCACGAACAAAACTAGATTAAAATGC 57.278 30.769 0.00 0.00 0.00 3.56
2929 3144 7.643764 CACACTTGATTAATCACGAACAAAACT 59.356 33.333 24.23 1.23 36.36 2.66
2938 3178 5.847715 GTGAGTCACACTTGATTAATCACG 58.152 41.667 17.76 17.77 45.13 4.35
2953 3193 3.341823 AGCCATTCAATCAGTGAGTCAC 58.658 45.455 15.78 15.78 37.61 3.67
2954 3194 3.708403 AGCCATTCAATCAGTGAGTCA 57.292 42.857 0.00 0.00 37.61 3.41
2955 3195 5.505324 GCATTAGCCATTCAATCAGTGAGTC 60.505 44.000 0.00 0.00 34.00 3.36
2956 3196 4.337555 GCATTAGCCATTCAATCAGTGAGT 59.662 41.667 0.00 0.00 34.00 3.41
2957 3197 4.554134 CGCATTAGCCATTCAATCAGTGAG 60.554 45.833 0.00 0.00 35.78 3.51
2958 3198 3.313249 CGCATTAGCCATTCAATCAGTGA 59.687 43.478 0.00 0.00 37.52 3.41
2959 3199 3.624900 CGCATTAGCCATTCAATCAGTG 58.375 45.455 0.00 0.00 37.52 3.66
2960 3200 2.033801 GCGCATTAGCCATTCAATCAGT 59.966 45.455 0.30 0.00 37.52 3.41
2961 3201 2.033675 TGCGCATTAGCCATTCAATCAG 59.966 45.455 5.66 0.00 37.52 2.90
2963 3203 2.223548 TGTGCGCATTAGCCATTCAATC 60.224 45.455 15.91 0.00 37.52 2.67
2965 3205 1.132834 CTGTGCGCATTAGCCATTCAA 59.867 47.619 15.91 0.00 37.52 2.69
2969 3209 0.816825 CCTCTGTGCGCATTAGCCAT 60.817 55.000 15.91 0.00 37.52 4.40
2973 3213 0.461548 TCCTCCTCTGTGCGCATTAG 59.538 55.000 15.91 15.93 0.00 1.73
2979 3219 2.888863 GTCCTCCTCCTCTGTGCG 59.111 66.667 0.00 0.00 0.00 5.34
3050 3290 0.460284 ACGCCATGAACGTCCTGATC 60.460 55.000 7.78 0.00 40.28 2.92
3138 3378 1.323271 ATGACGATGGACTGGTCGCT 61.323 55.000 0.00 0.00 41.31 4.93
3149 3389 2.428530 TCTCTTGAGGGTGATGACGATG 59.571 50.000 0.00 0.00 0.00 3.84
3193 3433 5.165676 TGCACGTACGTAAGAAATTCATCT 58.834 37.500 22.34 0.00 43.62 2.90
3196 3436 4.376615 GCTTGCACGTACGTAAGAAATTCA 60.377 41.667 27.05 11.47 43.62 2.57
3221 3461 3.311322 ACGAAAACGTTCAGAAAGCATCA 59.689 39.130 0.00 0.00 32.89 3.07
3222 3462 3.659444 CACGAAAACGTTCAGAAAGCATC 59.341 43.478 0.00 0.00 32.89 3.91
3227 3471 3.181505 ACATGCACGAAAACGTTCAGAAA 60.182 39.130 0.00 0.00 32.89 2.52
3235 3479 2.980586 TCTGAAACATGCACGAAAACG 58.019 42.857 0.00 0.00 0.00 3.60
3241 3512 3.666374 GCTCTTCTTCTGAAACATGCACG 60.666 47.826 0.00 0.00 0.00 5.34
3245 3516 2.417933 CCGGCTCTTCTTCTGAAACATG 59.582 50.000 0.00 0.00 0.00 3.21
3246 3517 2.704572 CCGGCTCTTCTTCTGAAACAT 58.295 47.619 0.00 0.00 0.00 2.71
3247 3518 1.878102 GCCGGCTCTTCTTCTGAAACA 60.878 52.381 22.15 0.00 0.00 2.83
3248 3519 0.799393 GCCGGCTCTTCTTCTGAAAC 59.201 55.000 22.15 0.00 0.00 2.78
3249 3520 0.687354 AGCCGGCTCTTCTTCTGAAA 59.313 50.000 27.08 0.00 0.00 2.69
3250 3521 0.247736 GAGCCGGCTCTTCTTCTGAA 59.752 55.000 42.50 0.00 39.80 3.02
3462 3733 4.554036 GGGGTCTCGCTCCATGGC 62.554 72.222 6.96 0.00 37.78 4.40
3511 3786 3.282885 GGAGGTTTTGTGATGGGAGATC 58.717 50.000 0.00 0.00 0.00 2.75
3512 3787 2.356125 CGGAGGTTTTGTGATGGGAGAT 60.356 50.000 0.00 0.00 0.00 2.75
3513 3788 1.003118 CGGAGGTTTTGTGATGGGAGA 59.997 52.381 0.00 0.00 0.00 3.71
3514 3789 1.271379 ACGGAGGTTTTGTGATGGGAG 60.271 52.381 0.00 0.00 0.00 4.30
3515 3790 0.768622 ACGGAGGTTTTGTGATGGGA 59.231 50.000 0.00 0.00 0.00 4.37
3516 3791 1.165270 GACGGAGGTTTTGTGATGGG 58.835 55.000 0.00 0.00 0.00 4.00
3517 3792 0.796312 CGACGGAGGTTTTGTGATGG 59.204 55.000 0.00 0.00 0.00 3.51
3518 3793 1.459592 GTCGACGGAGGTTTTGTGATG 59.540 52.381 0.00 0.00 0.00 3.07
3519 3794 1.607251 GGTCGACGGAGGTTTTGTGAT 60.607 52.381 9.92 0.00 0.00 3.06
3520 3795 0.249573 GGTCGACGGAGGTTTTGTGA 60.250 55.000 9.92 0.00 0.00 3.58
3521 3796 1.554042 CGGTCGACGGAGGTTTTGTG 61.554 60.000 17.47 0.00 39.42 3.33
3522 3797 1.300388 CGGTCGACGGAGGTTTTGT 60.300 57.895 17.47 0.00 39.42 2.83
3525 3800 1.509923 GATCGGTCGACGGAGGTTT 59.490 57.895 26.73 13.21 44.45 3.27
3590 3865 8.986929 AGATAAGGTGAAGGAAATGATAAAGG 57.013 34.615 0.00 0.00 0.00 3.11
3597 3872 7.709149 AAAGGAAGATAAGGTGAAGGAAATG 57.291 36.000 0.00 0.00 0.00 2.32
3603 3878 8.628630 AAAGAGAAAAGGAAGATAAGGTGAAG 57.371 34.615 0.00 0.00 0.00 3.02
3637 3914 6.743172 GGCTTTATCTTTTCTTTTGTCGCTAG 59.257 38.462 0.00 0.00 0.00 3.42
3662 3939 2.817035 TGCCTACGCAAACACTACG 58.183 52.632 0.00 0.00 43.74 3.51
3748 4029 3.615496 TCTCGCTTCTTTTTATACACGGC 59.385 43.478 0.00 0.00 0.00 5.68
3750 4031 5.454554 TCGATCTCGCTTCTTTTTATACACG 59.545 40.000 0.00 0.00 39.60 4.49
3786 4067 0.040870 CCGTCGTCATCTCATCTCCG 60.041 60.000 0.00 0.00 0.00 4.63
3794 4075 3.314553 CTTTACAACACCGTCGTCATCT 58.685 45.455 0.00 0.00 0.00 2.90
3878 4160 1.303561 ACATCACATGCGCCCAACT 60.304 52.632 4.18 0.00 0.00 3.16
3879 4161 1.153978 CACATCACATGCGCCCAAC 60.154 57.895 4.18 0.00 0.00 3.77
3880 4162 2.341875 CCACATCACATGCGCCCAA 61.342 57.895 4.18 0.00 0.00 4.12
3881 4163 2.751036 CCACATCACATGCGCCCA 60.751 61.111 4.18 0.00 0.00 5.36
3927 4209 9.814899 CAATATCTCTCTCTCTCTCTCTATCTC 57.185 40.741 0.00 0.00 0.00 2.75
3928 4210 8.766476 CCAATATCTCTCTCTCTCTCTCTATCT 58.234 40.741 0.00 0.00 0.00 1.98
3929 4211 7.989741 CCCAATATCTCTCTCTCTCTCTCTATC 59.010 44.444 0.00 0.00 0.00 2.08
3931 4213 7.022496 TCCCAATATCTCTCTCTCTCTCTCTA 58.978 42.308 0.00 0.00 0.00 2.43
3932 4214 5.851693 TCCCAATATCTCTCTCTCTCTCTCT 59.148 44.000 0.00 0.00 0.00 3.10
3933 4215 6.126863 TCCCAATATCTCTCTCTCTCTCTC 57.873 45.833 0.00 0.00 0.00 3.20
3934 4216 6.577039 CGATCCCAATATCTCTCTCTCTCTCT 60.577 46.154 0.00 0.00 0.00 3.10
3935 4217 5.586243 CGATCCCAATATCTCTCTCTCTCTC 59.414 48.000 0.00 0.00 0.00 3.20
3936 4218 5.500234 CGATCCCAATATCTCTCTCTCTCT 58.500 45.833 0.00 0.00 0.00 3.10
3937 4219 4.640201 CCGATCCCAATATCTCTCTCTCTC 59.360 50.000 0.00 0.00 0.00 3.20
3938 4220 4.599041 CCGATCCCAATATCTCTCTCTCT 58.401 47.826 0.00 0.00 0.00 3.10
3939 4221 3.130340 GCCGATCCCAATATCTCTCTCTC 59.870 52.174 0.00 0.00 0.00 3.20
3964 4246 0.454600 ATGGTACGTACTGCCGTCTG 59.545 55.000 24.07 0.00 42.00 3.51
3965 4247 0.454600 CATGGTACGTACTGCCGTCT 59.545 55.000 24.07 0.43 42.00 4.18
3967 4249 0.108992 CACATGGTACGTACTGCCGT 60.109 55.000 24.07 13.65 44.50 5.68
3969 4251 1.067425 TGTCACATGGTACGTACTGCC 60.067 52.381 24.07 9.58 0.00 4.85
3971 4253 3.291809 TGTGTCACATGGTACGTACTG 57.708 47.619 24.07 17.70 0.00 2.74
3973 4255 2.733026 GGTTGTGTCACATGGTACGTAC 59.267 50.000 17.56 17.56 0.00 3.67
3974 4256 2.288948 GGGTTGTGTCACATGGTACGTA 60.289 50.000 6.48 0.00 0.00 3.57
3976 4258 1.153353 GGGTTGTGTCACATGGTACG 58.847 55.000 6.48 0.00 0.00 3.67
3979 4261 2.031120 CTTTGGGTTGTGTCACATGGT 58.969 47.619 6.48 0.00 0.00 3.55
3980 4262 1.269726 GCTTTGGGTTGTGTCACATGG 60.270 52.381 6.48 0.00 0.00 3.66
3982 4264 1.774110 TGCTTTGGGTTGTGTCACAT 58.226 45.000 6.48 0.00 0.00 3.21
4041 4334 7.176165 AGCAATGCATGTACATATATCAAAGCT 59.824 33.333 8.32 13.14 0.00 3.74
4042 4335 7.310664 AGCAATGCATGTACATATATCAAAGC 58.689 34.615 8.32 5.84 0.00 3.51
4043 4336 9.687210 AAAGCAATGCATGTACATATATCAAAG 57.313 29.630 8.32 0.00 0.00 2.77
4046 4339 8.949177 CCTAAAGCAATGCATGTACATATATCA 58.051 33.333 8.32 5.03 0.00 2.15
4048 4341 7.148018 GCCCTAAAGCAATGCATGTACATATAT 60.148 37.037 8.32 3.18 0.00 0.86
4050 4343 5.047802 GCCCTAAAGCAATGCATGTACATAT 60.048 40.000 8.32 0.00 0.00 1.78
4051 4344 4.278170 GCCCTAAAGCAATGCATGTACATA 59.722 41.667 8.32 0.00 0.00 2.29
4054 4347 2.689983 AGCCCTAAAGCAATGCATGTAC 59.310 45.455 8.35 0.00 34.23 2.90
4056 4349 1.856629 AGCCCTAAAGCAATGCATGT 58.143 45.000 8.35 0.00 34.23 3.21
4057 4350 2.933906 CAAAGCCCTAAAGCAATGCATG 59.066 45.455 8.35 0.00 34.23 4.06
4058 4351 2.678769 GCAAAGCCCTAAAGCAATGCAT 60.679 45.455 8.35 0.00 42.63 3.96
4072 4365 1.615392 ACACATGAGGAAAGCAAAGCC 59.385 47.619 0.00 0.00 0.00 4.35
4113 4407 1.064296 CCTTCTCGTGACCGATCCG 59.936 63.158 0.00 0.00 43.27 4.18
4151 4449 1.730121 CGTGACATGCATTTGCTGGTC 60.730 52.381 15.51 15.51 41.60 4.02
4231 4530 3.302365 GCAAAGCCAAATAGTGCAAGA 57.698 42.857 0.00 0.00 35.28 3.02
4276 4578 2.991250 TCCAAGATAAAGTCTGCCTGC 58.009 47.619 0.00 0.00 37.23 4.85
4277 4579 4.133078 GGATCCAAGATAAAGTCTGCCTG 58.867 47.826 6.95 0.00 37.23 4.85
4278 4580 4.043596 AGGATCCAAGATAAAGTCTGCCT 58.956 43.478 15.82 0.00 37.23 4.75
4279 4581 4.102367 AGAGGATCCAAGATAAAGTCTGCC 59.898 45.833 15.82 0.00 33.89 4.85
4319 4621 4.084013 ACCGCGCATATACATAGCTTTTTC 60.084 41.667 8.75 0.00 0.00 2.29
4320 4622 3.813166 ACCGCGCATATACATAGCTTTTT 59.187 39.130 8.75 0.00 0.00 1.94
4365 4667 2.352960 CTCCTTTTGTTGCCGCTATCTC 59.647 50.000 0.00 0.00 0.00 2.75
4373 4675 1.067354 CAGATGCCTCCTTTTGTTGCC 60.067 52.381 0.00 0.00 0.00 4.52
4402 4707 3.557054 CCCAAAATCAACGAGGAGACAGA 60.557 47.826 0.00 0.00 0.00 3.41
4403 4708 2.744202 CCCAAAATCAACGAGGAGACAG 59.256 50.000 0.00 0.00 0.00 3.51
4404 4709 2.105821 ACCCAAAATCAACGAGGAGACA 59.894 45.455 0.00 0.00 0.00 3.41
4405 4710 2.779506 ACCCAAAATCAACGAGGAGAC 58.220 47.619 0.00 0.00 0.00 3.36
4441 4747 1.598962 AACGTCGACACCCTCTCGA 60.599 57.895 17.16 0.00 37.82 4.04
4456 4762 6.176975 TCTTAATGTTTATCAGCACCAACG 57.823 37.500 0.00 0.00 0.00 4.10
4478 4784 0.661552 TCGTCCGTATAGCACTGCTC 59.338 55.000 6.86 0.00 40.44 4.26
4479 4785 1.319541 ATCGTCCGTATAGCACTGCT 58.680 50.000 8.95 8.95 43.41 4.24
4480 4786 2.983402 TATCGTCCGTATAGCACTGC 57.017 50.000 0.00 0.00 0.00 4.40
4481 4787 6.472486 CCATATTTATCGTCCGTATAGCACTG 59.528 42.308 0.00 0.00 0.00 3.66
4482 4788 6.561614 CCATATTTATCGTCCGTATAGCACT 58.438 40.000 0.00 0.00 0.00 4.40
4483 4789 6.807708 CCATATTTATCGTCCGTATAGCAC 57.192 41.667 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.