Multiple sequence alignment - TraesCS2A01G425000

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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 TraesCS2A01G425000 chr2A 100.000 3427 0 0 1 3427 678963347 678966773 0.000000e+00 6329.0
1 TraesCS2A01G425000 chr2A 81.410 156 29 0 3271 3426 733680567 733680722 9.980000e-26 128.0
2 TraesCS2A01G425000 chr2A 92.222 90 6 1 2803 2891 65084813 65084902 3.590000e-25 126.0
3 TraesCS2A01G425000 chr2B 86.556 2819 152 75 258 2920 637574776 637577523 0.000000e+00 2896.0
4 TraesCS2A01G425000 chr2B 93.878 294 16 2 3134 3426 637582383 637582675 3.140000e-120 442.0
5 TraesCS2A01G425000 chr2B 87.166 187 23 1 3240 3426 637764825 637765010 9.640000e-51 211.0
6 TraesCS2A01G425000 chr2B 87.166 187 23 1 3240 3426 638261804 638261989 9.640000e-51 211.0
7 TraesCS2A01G425000 chr2B 93.798 129 8 0 56 184 637574515 637574643 9.700000e-46 195.0
8 TraesCS2A01G425000 chr2B 84.492 187 28 1 3240 3426 637993189 637993374 2.100000e-42 183.0
9 TraesCS2A01G425000 chr2B 91.200 125 10 1 2922 3045 637582034 637582158 5.880000e-38 169.0
10 TraesCS2A01G425000 chr2B 85.714 133 19 0 3295 3427 638755012 638755144 1.280000e-29 141.0
11 TraesCS2A01G425000 chr2D 84.879 2070 122 83 480 2429 536151820 536153818 0.000000e+00 1912.0
12 TraesCS2A01G425000 chr2D 92.270 608 23 9 2449 3042 536153886 536154483 0.000000e+00 841.0
13 TraesCS2A01G425000 chr2D 92.201 359 18 6 3072 3427 536154616 536154967 1.840000e-137 499.0
14 TraesCS2A01G425000 chr2D 90.675 311 22 5 1 307 536151415 536151722 1.140000e-109 407.0
15 TraesCS2A01G425000 chr2D 84.507 142 21 1 3286 3426 536506152 536506293 4.610000e-29 139.0
16 TraesCS2A01G425000 chr2D 80.220 182 36 0 3244 3425 536381664 536381845 1.660000e-28 137.0
17 TraesCS2A01G425000 chr2D 90.196 102 6 1 337 434 536151721 536151822 2.780000e-26 130.0
18 TraesCS2A01G425000 chr2D 100.000 28 0 0 2426 2453 536153839 536153866 6.000000e-03 52.8
19 TraesCS2A01G425000 chr5A 83.200 250 40 2 2018 2266 565395159 565395407 9.570000e-56 228.0
20 TraesCS2A01G425000 chr5A 97.059 34 1 0 2209 2242 702459801 702459834 1.330000e-04 58.4
21 TraesCS2A01G425000 chr5B 82.540 252 38 6 2018 2266 545405753 545406001 2.070000e-52 217.0
22 TraesCS2A01G425000 chr6D 92.857 84 6 0 2798 2881 427344947 427344864 4.640000e-24 122.0
23 TraesCS2A01G425000 chr6B 91.011 89 7 1 2803 2890 13827613 13827525 6.010000e-23 119.0
24 TraesCS2A01G425000 chr6B 86.408 103 12 2 2803 2903 122970909 122970807 1.010000e-20 111.0
25 TraesCS2A01G425000 chr6A 91.765 85 7 0 2798 2882 572128780 572128696 6.010000e-23 119.0
26 TraesCS2A01G425000 chr1D 91.011 89 6 2 2797 2885 87661028 87661114 6.010000e-23 119.0
27 TraesCS2A01G425000 chr7D 90.110 91 8 1 2803 2892 167548507 167548417 2.160000e-22 117.0
28 TraesCS2A01G425000 chr1A 88.542 96 10 1 2798 2892 518662753 518662848 7.770000e-22 115.0
29 TraesCS2A01G425000 chr3D 78.261 138 25 4 2134 2267 414637684 414637548 2.190000e-12 84.2
30 TraesCS2A01G425000 chr3B 80.172 116 18 4 2134 2245 540476583 540476469 7.880000e-12 82.4
31 TraesCS2A01G425000 chr3A 77.778 135 25 4 2134 2264 535727692 535727825 1.020000e-10 78.7
32 TraesCS2A01G425000 chr4D 87.719 57 7 0 2209 2265 506216839 506216783 2.210000e-07 67.6


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 TraesCS2A01G425000 chr2A 678963347 678966773 3426 False 6329.0 6329 100.0000 1 3427 1 chr2A.!!$F2 3426
1 TraesCS2A01G425000 chr2B 637574515 637577523 3008 False 1545.5 2896 90.1770 56 2920 2 chr2B.!!$F5 2864
2 TraesCS2A01G425000 chr2B 637582034 637582675 641 False 305.5 442 92.5390 2922 3426 2 chr2B.!!$F6 504
3 TraesCS2A01G425000 chr2D 536151415 536154967 3552 False 640.3 1912 91.7035 1 3427 6 chr2D.!!$F3 3426

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
156 157 0.102481 AGTACGCGCCTGTTATGGAG 59.898 55.0 5.73 0.0 0.0 3.86 F
1219 1498 0.104120 TGGAGTGAACACAGTGTCGG 59.896 55.0 6.67 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1919 2268 0.032017 GCCACCTCCTCCTTCTCCTA 60.032 60.0 0.00 0.00 0.0 2.94 R
3173 3782 0.032267 GGATACAGCCGGCAGTAGAC 59.968 60.0 31.45 26.05 0.0 2.59 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
61 62 4.033709 AGTAGAACCTGGCTCATGTGTAT 58.966 43.478 0.00 0.00 0.00 2.29
76 77 5.414454 TCATGTGTATTTGGCTGAGTAAACC 59.586 40.000 0.00 0.00 0.00 3.27
85 86 1.160137 CTGAGTAAACCTGTGGCAGC 58.840 55.000 0.00 0.00 0.00 5.25
86 87 0.764890 TGAGTAAACCTGTGGCAGCT 59.235 50.000 0.00 0.00 0.00 4.24
141 142 5.240183 TGCTATATGGTACGGTCTTGAGTAC 59.760 44.000 0.00 0.00 41.64 2.73
156 157 0.102481 AGTACGCGCCTGTTATGGAG 59.898 55.000 5.73 0.00 0.00 3.86
221 327 4.835284 TGATGTTGCTTGGGTACTGATA 57.165 40.909 0.00 0.00 0.00 2.15
225 335 6.936335 TGATGTTGCTTGGGTACTGATATATG 59.064 38.462 0.00 0.00 0.00 1.78
231 341 7.168219 TGCTTGGGTACTGATATATGAATTCC 58.832 38.462 2.27 0.00 0.00 3.01
243 353 2.074729 TGAATTCCGGGGTTGTTGTT 57.925 45.000 0.00 0.00 0.00 2.83
244 354 2.389715 TGAATTCCGGGGTTGTTGTTT 58.610 42.857 0.00 0.00 0.00 2.83
245 355 3.563223 TGAATTCCGGGGTTGTTGTTTA 58.437 40.909 0.00 0.00 0.00 2.01
248 358 5.773680 TGAATTCCGGGGTTGTTGTTTATTA 59.226 36.000 0.00 0.00 0.00 0.98
249 359 6.437793 TGAATTCCGGGGTTGTTGTTTATTAT 59.562 34.615 0.00 0.00 0.00 1.28
250 360 6.860790 ATTCCGGGGTTGTTGTTTATTATT 57.139 33.333 0.00 0.00 0.00 1.40
251 361 5.646577 TCCGGGGTTGTTGTTTATTATTG 57.353 39.130 0.00 0.00 0.00 1.90
294 404 4.826733 TGAAAAGAAAAGGCAGATACAGCA 59.173 37.500 0.00 0.00 0.00 4.41
312 422 2.162681 GCAGGTATCAGCCAGTTGTTT 58.837 47.619 0.00 0.00 0.00 2.83
316 426 2.228822 GGTATCAGCCAGTTGTTTGGTG 59.771 50.000 0.00 0.00 40.49 4.17
324 434 2.292016 CCAGTTGTTTGGTGCGTTGATA 59.708 45.455 0.00 0.00 33.38 2.15
346 456 1.777101 GCATGTAAAAGGCGTGCAAA 58.223 45.000 4.83 0.00 45.32 3.68
347 457 2.131183 GCATGTAAAAGGCGTGCAAAA 58.869 42.857 4.83 0.00 45.32 2.44
352 462 4.233789 TGTAAAAGGCGTGCAAAATGATC 58.766 39.130 0.00 0.00 0.00 2.92
373 483 5.791336 TCACATATCGCACTAGGAAAGAT 57.209 39.130 0.00 0.00 0.00 2.40
434 548 2.732282 CGTGAAAGAGAGCAGCGATGTA 60.732 50.000 1.22 0.00 0.00 2.29
435 549 3.452474 GTGAAAGAGAGCAGCGATGTAT 58.548 45.455 1.22 0.00 0.00 2.29
436 550 4.611943 GTGAAAGAGAGCAGCGATGTATA 58.388 43.478 1.22 0.00 0.00 1.47
437 551 4.679197 GTGAAAGAGAGCAGCGATGTATAG 59.321 45.833 1.22 0.00 0.00 1.31
438 552 4.339530 TGAAAGAGAGCAGCGATGTATAGT 59.660 41.667 1.22 0.00 0.00 2.12
439 553 4.927978 AAGAGAGCAGCGATGTATAGTT 57.072 40.909 1.22 0.00 0.00 2.24
440 554 4.927978 AGAGAGCAGCGATGTATAGTTT 57.072 40.909 1.22 0.00 0.00 2.66
441 555 4.865776 AGAGAGCAGCGATGTATAGTTTC 58.134 43.478 1.22 0.00 0.00 2.78
442 556 4.582656 AGAGAGCAGCGATGTATAGTTTCT 59.417 41.667 1.22 0.00 0.00 2.52
443 557 5.068460 AGAGAGCAGCGATGTATAGTTTCTT 59.932 40.000 1.22 0.00 0.00 2.52
444 558 5.046529 AGAGCAGCGATGTATAGTTTCTTG 58.953 41.667 1.22 0.00 0.00 3.02
445 559 4.759782 AGCAGCGATGTATAGTTTCTTGT 58.240 39.130 1.22 0.00 0.00 3.16
446 560 5.902681 AGCAGCGATGTATAGTTTCTTGTA 58.097 37.500 1.22 0.00 0.00 2.41
447 561 6.338146 AGCAGCGATGTATAGTTTCTTGTAA 58.662 36.000 1.22 0.00 0.00 2.41
448 562 6.255887 AGCAGCGATGTATAGTTTCTTGTAAC 59.744 38.462 1.22 0.00 0.00 2.50
449 563 6.035650 GCAGCGATGTATAGTTTCTTGTAACA 59.964 38.462 1.22 0.00 0.00 2.41
450 564 7.391786 CAGCGATGTATAGTTTCTTGTAACAC 58.608 38.462 0.00 0.00 0.00 3.32
451 565 6.534079 AGCGATGTATAGTTTCTTGTAACACC 59.466 38.462 0.00 0.00 0.00 4.16
452 566 6.534079 GCGATGTATAGTTTCTTGTAACACCT 59.466 38.462 0.00 0.00 0.00 4.00
453 567 7.464178 GCGATGTATAGTTTCTTGTAACACCTG 60.464 40.741 0.00 0.00 0.00 4.00
454 568 7.758076 CGATGTATAGTTTCTTGTAACACCTGA 59.242 37.037 0.00 0.00 0.00 3.86
455 569 9.431887 GATGTATAGTTTCTTGTAACACCTGAA 57.568 33.333 0.00 0.00 0.00 3.02
456 570 8.827177 TGTATAGTTTCTTGTAACACCTGAAG 57.173 34.615 0.00 0.00 0.00 3.02
457 571 8.426489 TGTATAGTTTCTTGTAACACCTGAAGT 58.574 33.333 0.00 0.00 0.00 3.01
458 572 7.964604 ATAGTTTCTTGTAACACCTGAAGTC 57.035 36.000 0.00 0.00 0.00 3.01
459 573 5.741011 AGTTTCTTGTAACACCTGAAGTCA 58.259 37.500 0.00 0.00 0.00 3.41
460 574 6.357367 AGTTTCTTGTAACACCTGAAGTCAT 58.643 36.000 0.00 0.00 0.00 3.06
461 575 6.260936 AGTTTCTTGTAACACCTGAAGTCATG 59.739 38.462 0.00 0.00 0.00 3.07
462 576 5.545063 TCTTGTAACACCTGAAGTCATGA 57.455 39.130 0.00 0.00 0.00 3.07
463 577 5.541845 TCTTGTAACACCTGAAGTCATGAG 58.458 41.667 0.00 0.00 0.00 2.90
464 578 4.955811 TGTAACACCTGAAGTCATGAGT 57.044 40.909 0.00 0.00 0.00 3.41
465 579 6.266786 TCTTGTAACACCTGAAGTCATGAGTA 59.733 38.462 2.79 0.00 0.00 2.59
466 580 6.025749 TGTAACACCTGAAGTCATGAGTAG 57.974 41.667 2.79 0.00 0.00 2.57
467 581 5.773176 TGTAACACCTGAAGTCATGAGTAGA 59.227 40.000 2.79 0.00 0.00 2.59
468 582 6.437477 TGTAACACCTGAAGTCATGAGTAGAT 59.563 38.462 2.79 0.00 0.00 1.98
469 583 7.614192 TGTAACACCTGAAGTCATGAGTAGATA 59.386 37.037 2.79 0.00 0.00 1.98
470 584 6.458232 ACACCTGAAGTCATGAGTAGATAC 57.542 41.667 2.79 0.00 0.00 2.24
471 585 5.361285 ACACCTGAAGTCATGAGTAGATACC 59.639 44.000 2.79 0.00 0.00 2.73
472 586 5.596361 CACCTGAAGTCATGAGTAGATACCT 59.404 44.000 2.79 0.00 0.00 3.08
473 587 5.830991 ACCTGAAGTCATGAGTAGATACCTC 59.169 44.000 2.79 0.00 0.00 3.85
474 588 6.068010 CCTGAAGTCATGAGTAGATACCTCT 58.932 44.000 2.79 0.00 35.39 3.69
475 589 6.016360 CCTGAAGTCATGAGTAGATACCTCTG 60.016 46.154 2.79 0.41 32.66 3.35
476 590 5.300539 TGAAGTCATGAGTAGATACCTCTGC 59.699 44.000 2.79 0.00 34.59 4.26
477 591 5.060427 AGTCATGAGTAGATACCTCTGCT 57.940 43.478 0.00 0.00 45.85 4.24
488 602 1.356124 ACCTCTGCTCTGTCCATGTT 58.644 50.000 0.00 0.00 0.00 2.71
523 710 1.441016 CACTGCGCGCTTTCCTTTC 60.441 57.895 33.29 0.00 0.00 2.62
524 711 2.176792 CTGCGCGCTTTCCTTTCC 59.823 61.111 33.29 0.00 0.00 3.13
525 712 2.281484 TGCGCGCTTTCCTTTCCT 60.281 55.556 33.29 0.00 0.00 3.36
526 713 1.856265 CTGCGCGCTTTCCTTTCCTT 61.856 55.000 33.29 0.00 0.00 3.36
527 714 1.285950 GCGCGCTTTCCTTTCCTTT 59.714 52.632 26.67 0.00 0.00 3.11
571 760 1.668419 GACAGCCTTGTGTCTTGTGT 58.332 50.000 0.00 0.00 43.10 3.72
572 761 1.331756 GACAGCCTTGTGTCTTGTGTG 59.668 52.381 0.00 0.00 43.10 3.82
574 763 0.255890 AGCCTTGTGTCTTGTGTGGT 59.744 50.000 0.00 0.00 0.00 4.16
575 764 0.381801 GCCTTGTGTCTTGTGTGGTG 59.618 55.000 0.00 0.00 0.00 4.17
576 765 1.024271 CCTTGTGTCTTGTGTGGTGG 58.976 55.000 0.00 0.00 0.00 4.61
577 766 0.381801 CTTGTGTCTTGTGTGGTGGC 59.618 55.000 0.00 0.00 0.00 5.01
578 767 0.322906 TTGTGTCTTGTGTGGTGGCA 60.323 50.000 0.00 0.00 0.00 4.92
579 768 0.106769 TGTGTCTTGTGTGGTGGCAT 60.107 50.000 0.00 0.00 0.00 4.40
580 769 0.593128 GTGTCTTGTGTGGTGGCATC 59.407 55.000 0.00 0.00 0.00 3.91
581 770 0.182299 TGTCTTGTGTGGTGGCATCA 59.818 50.000 0.00 0.00 0.00 3.07
582 771 0.877071 GTCTTGTGTGGTGGCATCAG 59.123 55.000 0.00 0.00 0.00 2.90
583 772 0.890542 TCTTGTGTGGTGGCATCAGC 60.891 55.000 0.00 0.00 41.42 4.26
672 894 3.194542 AGGCAGAAGAAGCACACTAGTAG 59.805 47.826 0.00 0.00 0.00 2.57
685 907 3.119459 ACACTAGTAGGATGCAAGTGACG 60.119 47.826 17.08 0.00 39.93 4.35
707 929 3.479370 CGCTTCCTGGAGAAAGCG 58.521 61.111 22.35 22.35 41.88 4.68
793 1016 4.185467 ACTACATGGATCATCGATCTGC 57.815 45.455 0.00 0.00 38.91 4.26
845 1070 4.021016 TCCACTGCTTTCTTCTCCTCTTAC 60.021 45.833 0.00 0.00 0.00 2.34
857 1082 1.144057 CTCTTACCGATGGCCGCTT 59.856 57.895 0.00 0.00 36.84 4.68
858 1083 0.876342 CTCTTACCGATGGCCGCTTC 60.876 60.000 0.00 0.00 36.84 3.86
859 1084 1.887707 CTTACCGATGGCCGCTTCC 60.888 63.158 0.00 0.00 36.84 3.46
860 1085 2.587322 CTTACCGATGGCCGCTTCCA 62.587 60.000 0.00 0.00 40.97 3.53
909 1150 5.869344 TCAGCTATAATATAACAAGCGCCTG 59.131 40.000 2.29 3.24 38.23 4.85
922 1169 2.757917 GCCTGCTCCTCCTCGAGT 60.758 66.667 12.31 0.00 32.11 4.18
936 1183 0.881796 TCGAGTGGTGCAGTAGACAG 59.118 55.000 0.00 0.00 0.00 3.51
939 1186 2.159503 CGAGTGGTGCAGTAGACAGTAG 60.160 54.545 0.00 0.00 0.00 2.57
945 1192 3.128938 GGTGCAGTAGACAGTAGTAGTGG 59.871 52.174 9.78 0.00 0.00 4.00
947 1194 3.018149 GCAGTAGACAGTAGTAGTGGCT 58.982 50.000 17.57 17.57 40.69 4.75
948 1195 4.197750 GCAGTAGACAGTAGTAGTGGCTA 58.802 47.826 15.49 15.49 38.10 3.93
951 1198 2.641305 AGACAGTAGTAGTGGCTACCG 58.359 52.381 11.93 0.00 34.45 4.02
952 1199 1.674962 GACAGTAGTAGTGGCTACCGG 59.325 57.143 9.78 0.00 41.54 5.28
983 1261 2.970974 GCAGAGCAAGCAACCGACC 61.971 63.158 0.00 0.00 0.00 4.79
988 1266 2.590575 CAAGCAACCGACCGTGGT 60.591 61.111 0.00 0.00 46.67 4.16
991 1269 2.989055 AAGCAACCGACCGTGGTGAG 62.989 60.000 0.00 0.00 42.89 3.51
992 1270 2.420043 CAACCGACCGTGGTGAGT 59.580 61.111 0.00 0.00 42.89 3.41
993 1271 1.954146 CAACCGACCGTGGTGAGTG 60.954 63.158 0.00 0.00 42.89 3.51
994 1272 3.159858 AACCGACCGTGGTGAGTGG 62.160 63.158 0.00 0.00 42.89 4.00
995 1273 3.612681 CCGACCGTGGTGAGTGGT 61.613 66.667 0.00 0.00 39.12 4.16
996 1274 2.355837 CGACCGTGGTGAGTGGTG 60.356 66.667 0.00 0.00 35.75 4.17
997 1275 2.852180 CGACCGTGGTGAGTGGTGA 61.852 63.158 0.00 0.00 35.75 4.02
998 1276 1.300697 GACCGTGGTGAGTGGTGAC 60.301 63.158 0.00 0.00 35.75 3.67
1084 1362 1.198713 CCTCATGCTCTGTACCACCT 58.801 55.000 0.00 0.00 0.00 4.00
1136 1414 4.194640 CCATCCAGTGAACCAAGATACTG 58.805 47.826 0.00 0.00 40.06 2.74
1141 1419 4.625742 CCAGTGAACCAAGATACTGTAACG 59.374 45.833 0.00 0.00 39.02 3.18
1144 1422 2.288961 ACCAAGATACTGTAACGGCG 57.711 50.000 4.80 4.80 0.00 6.46
1145 1423 1.547372 ACCAAGATACTGTAACGGCGT 59.453 47.619 6.77 6.77 0.00 5.68
1146 1424 2.190981 CCAAGATACTGTAACGGCGTC 58.809 52.381 15.17 1.45 0.00 5.19
1147 1425 2.159282 CCAAGATACTGTAACGGCGTCT 60.159 50.000 15.17 6.47 0.00 4.18
1148 1426 3.508762 CAAGATACTGTAACGGCGTCTT 58.491 45.455 15.17 6.78 0.00 3.01
1151 1429 5.314923 AGATACTGTAACGGCGTCTTTTA 57.685 39.130 15.17 0.00 0.00 1.52
1194 1472 1.412710 TCTCTTCTGCGTTTGAGTGGT 59.587 47.619 0.00 0.00 0.00 4.16
1197 1475 1.261619 CTTCTGCGTTTGAGTGGTGTC 59.738 52.381 0.00 0.00 0.00 3.67
1198 1476 0.176910 TCTGCGTTTGAGTGGTGTCA 59.823 50.000 0.00 0.00 0.00 3.58
1199 1477 0.304705 CTGCGTTTGAGTGGTGTCAC 59.695 55.000 0.00 0.00 43.93 3.67
1219 1498 0.104120 TGGAGTGAACACAGTGTCGG 59.896 55.000 6.67 0.00 0.00 4.79
1244 1525 0.528470 AGTGACCAGCTCTCGCTAAC 59.472 55.000 2.67 0.00 46.99 2.34
1269 1550 2.813754 TCTGTTAACCTGCATTGTGCTC 59.186 45.455 2.48 0.00 45.31 4.26
1488 1780 1.371558 GTTCTGCGTCAACCCTCCT 59.628 57.895 0.00 0.00 0.00 3.69
1821 2140 2.522193 GGAGGCGTAGGAGGAGGG 60.522 72.222 0.00 0.00 0.00 4.30
1848 2182 1.547755 TGGAGGAGAGGGAGGAGGT 60.548 63.158 0.00 0.00 0.00 3.85
1881 2230 0.930726 GAGGAGAAGGAGGAGGAGGA 59.069 60.000 0.00 0.00 0.00 3.71
1889 2238 4.150454 AGGAGGAGGAGGAGGCGG 62.150 72.222 0.00 0.00 0.00 6.13
1890 2239 4.144727 GGAGGAGGAGGAGGCGGA 62.145 72.222 0.00 0.00 0.00 5.54
1891 2240 2.520741 GAGGAGGAGGAGGCGGAG 60.521 72.222 0.00 0.00 0.00 4.63
1892 2241 4.150454 AGGAGGAGGAGGCGGAGG 62.150 72.222 0.00 0.00 0.00 4.30
1918 2267 2.835895 GAGGAGGAGGAGGCGGTC 60.836 72.222 0.00 0.00 0.00 4.79
1919 2268 3.351885 AGGAGGAGGAGGCGGTCT 61.352 66.667 0.00 0.00 0.00 3.85
1983 2332 2.258591 CCGCCGATCATCTACCCG 59.741 66.667 0.00 0.00 0.00 5.28
2266 2615 0.034896 CACCAGCGACCCAAGTAAGT 59.965 55.000 0.00 0.00 0.00 2.24
2280 2629 3.938289 AGTAAGTCCTCAAACCTCGAC 57.062 47.619 0.00 0.00 0.00 4.20
2304 2676 0.107017 CGAAAGCTCCATCCACCCAT 60.107 55.000 0.00 0.00 0.00 4.00
2310 2682 0.538977 CTCCATCCACCCATCCATGC 60.539 60.000 0.00 0.00 0.00 4.06
2311 2683 0.995132 TCCATCCACCCATCCATGCT 60.995 55.000 0.00 0.00 0.00 3.79
2312 2684 0.773014 CCATCCACCCATCCATGCTA 59.227 55.000 0.00 0.00 0.00 3.49
2313 2685 1.356738 CCATCCACCCATCCATGCTAT 59.643 52.381 0.00 0.00 0.00 2.97
2314 2686 2.443416 CATCCACCCATCCATGCTATG 58.557 52.381 0.00 0.00 0.00 2.23
2315 2687 0.111061 TCCACCCATCCATGCTATGC 59.889 55.000 0.00 0.00 0.00 3.14
2319 2691 1.182667 CCCATCCATGCTATGCCATG 58.817 55.000 0.00 0.00 41.71 3.66
2321 2693 0.530744 CATCCATGCTATGCCATGCC 59.469 55.000 0.00 0.00 40.92 4.40
2322 2694 0.113580 ATCCATGCTATGCCATGCCA 59.886 50.000 0.00 0.00 40.92 4.92
2323 2695 0.824595 TCCATGCTATGCCATGCCAC 60.825 55.000 0.00 0.00 40.92 5.01
2334 2714 1.110518 CCATGCCACTGCCATGCATA 61.111 55.000 0.00 0.00 43.49 3.14
2370 2750 5.104527 TCGATCTTGATTTCTTACCATGGGT 60.105 40.000 18.09 4.30 40.16 4.51
2399 2779 2.753296 GTCATGATCTCTGCAGGCTAC 58.247 52.381 15.13 4.51 0.00 3.58
2476 2904 0.109781 CCATTTGTTTCGAGGCCACG 60.110 55.000 17.19 17.19 0.00 4.94
2672 3111 9.923143 GACCAAATTAGTTTAGTTTAAGCCAAT 57.077 29.630 0.00 0.00 0.00 3.16
2673 3112 9.705290 ACCAAATTAGTTTAGTTTAAGCCAATG 57.295 29.630 0.00 0.00 0.00 2.82
2746 3185 2.594541 GGATTCTGTCCGATCACGC 58.405 57.895 0.00 0.00 37.23 5.34
2796 3235 3.895232 TCCAACTAAGCATCTCCAGAC 57.105 47.619 0.00 0.00 0.00 3.51
2831 3282 7.724287 ACTCCCTCCGTAAAGAAATATAAGAC 58.276 38.462 0.00 0.00 0.00 3.01
2844 3295 9.543783 AAGAAATATAAGACCGTTTAGATCACC 57.456 33.333 0.00 0.00 0.00 4.02
2845 3296 7.866393 AGAAATATAAGACCGTTTAGATCACCG 59.134 37.037 0.00 0.00 0.00 4.94
2862 3313 4.978186 TCACCGAAGTAGTCATCTAAACG 58.022 43.478 0.00 0.00 0.00 3.60
2917 3373 9.132923 ACGTGATAACTAAGATTGAGAAGGATA 57.867 33.333 0.00 0.00 0.00 2.59
2944 3400 3.279434 AGACACAAGAACCCAGTGAAAC 58.721 45.455 0.00 0.00 37.05 2.78
3010 3466 2.386661 CTACCGGAGCACTGACAAAT 57.613 50.000 9.46 0.00 0.00 2.32
3042 3498 0.319728 AGAACACGATGCAGCAGAGT 59.680 50.000 1.53 0.00 0.00 3.24
3044 3500 0.870393 AACACGATGCAGCAGAGTTG 59.130 50.000 1.53 0.00 0.00 3.16
3046 3502 0.441533 CACGATGCAGCAGAGTTGAC 59.558 55.000 1.53 0.00 0.00 3.18
3047 3503 0.033920 ACGATGCAGCAGAGTTGACA 59.966 50.000 1.53 0.00 0.00 3.58
3048 3504 0.720027 CGATGCAGCAGAGTTGACAG 59.280 55.000 1.53 0.00 0.00 3.51
3049 3505 1.085091 GATGCAGCAGAGTTGACAGG 58.915 55.000 0.00 0.00 0.00 4.00
3050 3506 0.322277 ATGCAGCAGAGTTGACAGGG 60.322 55.000 0.00 0.00 0.00 4.45
3052 3508 0.321671 GCAGCAGAGTTGACAGGGTA 59.678 55.000 0.00 0.00 0.00 3.69
3053 3509 1.270839 GCAGCAGAGTTGACAGGGTAA 60.271 52.381 0.00 0.00 0.00 2.85
3054 3510 2.693069 CAGCAGAGTTGACAGGGTAAG 58.307 52.381 0.00 0.00 0.00 2.34
3056 3512 1.348036 GCAGAGTTGACAGGGTAAGGT 59.652 52.381 0.00 0.00 0.00 3.50
3058 3514 3.747708 GCAGAGTTGACAGGGTAAGGTTT 60.748 47.826 0.00 0.00 0.00 3.27
3059 3515 4.461198 CAGAGTTGACAGGGTAAGGTTTT 58.539 43.478 0.00 0.00 0.00 2.43
3060 3516 5.617252 CAGAGTTGACAGGGTAAGGTTTTA 58.383 41.667 0.00 0.00 0.00 1.52
3061 3517 5.469084 CAGAGTTGACAGGGTAAGGTTTTAC 59.531 44.000 0.00 0.00 38.74 2.01
3062 3518 5.131475 AGAGTTGACAGGGTAAGGTTTTACA 59.869 40.000 0.54 0.00 40.77 2.41
3065 3521 4.453751 TGACAGGGTAAGGTTTTACACAC 58.546 43.478 2.90 0.00 44.11 3.82
3066 3522 3.469739 ACAGGGTAAGGTTTTACACACG 58.530 45.455 2.90 0.00 44.11 4.49
3067 3523 2.224784 CAGGGTAAGGTTTTACACACGC 59.775 50.000 2.90 0.00 44.11 5.34
3068 3524 1.195222 GGGTAAGGTTTTACACACGCG 59.805 52.381 3.53 3.53 41.80 6.01
3069 3525 1.398832 GGTAAGGTTTTACACACGCGC 60.399 52.381 5.73 0.00 40.77 6.86
3070 3526 0.867086 TAAGGTTTTACACACGCGCC 59.133 50.000 5.73 0.00 0.00 6.53
3104 3678 4.957971 ACGAAGCTTAATTCACATCAACG 58.042 39.130 0.00 0.00 0.00 4.10
3127 3701 5.227184 CGCCGTCAAAAATCAAATAAGTAGC 59.773 40.000 0.00 0.00 0.00 3.58
3128 3702 6.090129 GCCGTCAAAAATCAAATAAGTAGCA 58.910 36.000 0.00 0.00 0.00 3.49
3130 3704 7.305474 CCGTCAAAAATCAAATAAGTAGCACT 58.695 34.615 0.00 0.00 0.00 4.40
3132 3741 9.478019 CGTCAAAAATCAAATAAGTAGCACTAG 57.522 33.333 0.00 0.00 0.00 2.57
3149 3758 5.187967 AGCACTAGTAGTATTTGTTCCTGCT 59.812 40.000 1.57 0.77 0.00 4.24
3241 3853 3.064900 AGAGAGCACCTGATTGGAAAC 57.935 47.619 0.00 0.00 39.71 2.78
3267 3879 2.367030 TTTTTCTGATTGCATGGCCG 57.633 45.000 0.00 0.00 0.00 6.13
3278 3890 4.875713 ATGGCCGGCGATGGGTTC 62.876 66.667 24.25 5.55 0.00 3.62
3293 3905 1.341089 GGGTTCCTGATCTGGGGTTTC 60.341 57.143 17.73 4.78 0.00 2.78
3323 3935 2.009051 CTGATAACTGCATTCACCGCA 58.991 47.619 0.00 0.00 37.88 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 3.303329 CCTTCACAGTTCACATTCACACG 60.303 47.826 0.00 0.00 0.00 4.49
61 62 2.582052 CCACAGGTTTACTCAGCCAAA 58.418 47.619 0.00 0.00 0.00 3.28
76 77 1.199327 CAAACATCAGAGCTGCCACAG 59.801 52.381 0.00 0.00 34.12 3.66
85 86 1.089112 TCATGCCGCAAACATCAGAG 58.911 50.000 0.00 0.00 0.00 3.35
86 87 1.199789 GTTCATGCCGCAAACATCAGA 59.800 47.619 0.00 0.00 0.00 3.27
141 142 2.173669 CACCTCCATAACAGGCGCG 61.174 63.158 0.00 0.00 33.84 6.86
156 157 4.314740 TGTTGCATTAAGTTGGTTCACC 57.685 40.909 0.00 0.00 0.00 4.02
210 316 5.188948 CCCGGAATTCATATATCAGTACCCA 59.811 44.000 0.73 0.00 0.00 4.51
211 317 5.396436 CCCCGGAATTCATATATCAGTACCC 60.396 48.000 0.73 0.00 0.00 3.69
221 327 3.976015 ACAACAACCCCGGAATTCATAT 58.024 40.909 0.73 0.00 0.00 1.78
225 335 4.794278 ATAAACAACAACCCCGGAATTC 57.206 40.909 0.73 0.00 0.00 2.17
231 341 4.081917 AGCCAATAATAAACAACAACCCCG 60.082 41.667 0.00 0.00 0.00 5.73
277 387 2.716217 ACCTGCTGTATCTGCCTTTTC 58.284 47.619 0.00 0.00 0.00 2.29
294 404 2.108250 ACCAAACAACTGGCTGATACCT 59.892 45.455 0.00 0.00 40.45 3.08
312 422 1.093972 CATGCCTTATCAACGCACCA 58.906 50.000 0.00 0.00 34.87 4.17
316 426 4.351192 CCTTTTACATGCCTTATCAACGC 58.649 43.478 0.00 0.00 0.00 4.84
324 434 0.243636 GCACGCCTTTTACATGCCTT 59.756 50.000 0.00 0.00 0.00 4.35
329 439 4.250116 TCATTTTGCACGCCTTTTACAT 57.750 36.364 0.00 0.00 0.00 2.29
335 445 1.612950 TGTGATCATTTTGCACGCCTT 59.387 42.857 0.00 0.00 35.37 4.35
346 456 5.728637 TCCTAGTGCGATATGTGATCATT 57.271 39.130 0.00 0.00 35.70 2.57
347 457 5.728637 TTCCTAGTGCGATATGTGATCAT 57.271 39.130 0.00 0.00 38.00 2.45
352 462 5.532557 TCATCTTTCCTAGTGCGATATGTG 58.467 41.667 0.00 0.00 0.00 3.21
434 548 7.506114 TGACTTCAGGTGTTACAAGAAACTAT 58.494 34.615 0.00 0.00 0.00 2.12
435 549 6.880484 TGACTTCAGGTGTTACAAGAAACTA 58.120 36.000 0.00 0.00 0.00 2.24
436 550 5.741011 TGACTTCAGGTGTTACAAGAAACT 58.259 37.500 0.00 0.00 0.00 2.66
437 551 6.260050 TCATGACTTCAGGTGTTACAAGAAAC 59.740 38.462 0.00 0.00 0.00 2.78
438 552 6.353323 TCATGACTTCAGGTGTTACAAGAAA 58.647 36.000 0.00 0.00 0.00 2.52
439 553 5.924356 TCATGACTTCAGGTGTTACAAGAA 58.076 37.500 0.00 0.00 0.00 2.52
440 554 5.070446 ACTCATGACTTCAGGTGTTACAAGA 59.930 40.000 0.00 0.00 31.55 3.02
441 555 5.300752 ACTCATGACTTCAGGTGTTACAAG 58.699 41.667 0.00 0.00 31.55 3.16
442 556 5.290493 ACTCATGACTTCAGGTGTTACAA 57.710 39.130 0.00 0.00 31.55 2.41
443 557 4.955811 ACTCATGACTTCAGGTGTTACA 57.044 40.909 0.00 0.00 31.55 2.41
444 558 6.268825 TCTACTCATGACTTCAGGTGTTAC 57.731 41.667 4.18 0.00 36.14 2.50
445 559 7.068348 GGTATCTACTCATGACTTCAGGTGTTA 59.932 40.741 4.18 0.00 36.14 2.41
446 560 6.127310 GGTATCTACTCATGACTTCAGGTGTT 60.127 42.308 4.18 0.00 36.14 3.32
447 561 5.361285 GGTATCTACTCATGACTTCAGGTGT 59.639 44.000 0.00 4.29 37.91 4.16
448 562 5.596361 AGGTATCTACTCATGACTTCAGGTG 59.404 44.000 0.00 0.00 0.00 4.00
449 563 5.772004 AGGTATCTACTCATGACTTCAGGT 58.228 41.667 0.00 0.00 0.00 4.00
450 564 6.016360 CAGAGGTATCTACTCATGACTTCAGG 60.016 46.154 0.00 0.00 37.43 3.86
451 565 6.514870 GCAGAGGTATCTACTCATGACTTCAG 60.515 46.154 0.00 0.00 37.43 3.02
452 566 5.300539 GCAGAGGTATCTACTCATGACTTCA 59.699 44.000 0.00 0.00 37.43 3.02
453 567 5.534654 AGCAGAGGTATCTACTCATGACTTC 59.465 44.000 0.00 0.00 37.43 3.01
454 568 5.454062 AGCAGAGGTATCTACTCATGACTT 58.546 41.667 0.00 0.00 37.43 3.01
455 569 5.060427 AGCAGAGGTATCTACTCATGACT 57.940 43.478 0.00 0.00 37.43 3.41
456 570 5.048782 CAGAGCAGAGGTATCTACTCATGAC 60.049 48.000 7.94 0.00 45.17 3.06
457 571 5.069318 CAGAGCAGAGGTATCTACTCATGA 58.931 45.833 7.94 0.00 45.17 3.07
458 572 4.826733 ACAGAGCAGAGGTATCTACTCATG 59.173 45.833 7.94 6.08 45.17 3.07
459 573 5.060427 ACAGAGCAGAGGTATCTACTCAT 57.940 43.478 7.94 0.00 45.17 2.90
460 574 4.456535 GACAGAGCAGAGGTATCTACTCA 58.543 47.826 7.94 0.00 45.17 3.41
461 575 3.818773 GGACAGAGCAGAGGTATCTACTC 59.181 52.174 0.00 0.00 43.69 2.59
462 576 3.203263 TGGACAGAGCAGAGGTATCTACT 59.797 47.826 0.00 0.00 33.22 2.57
463 577 3.556999 TGGACAGAGCAGAGGTATCTAC 58.443 50.000 0.00 0.00 33.22 2.59
464 578 3.953542 TGGACAGAGCAGAGGTATCTA 57.046 47.619 0.00 0.00 33.22 1.98
465 579 2.836636 TGGACAGAGCAGAGGTATCT 57.163 50.000 0.00 0.00 35.63 1.98
466 580 2.697751 ACATGGACAGAGCAGAGGTATC 59.302 50.000 0.00 0.00 0.00 2.24
467 581 2.756907 ACATGGACAGAGCAGAGGTAT 58.243 47.619 0.00 0.00 0.00 2.73
468 582 2.238084 ACATGGACAGAGCAGAGGTA 57.762 50.000 0.00 0.00 0.00 3.08
469 583 1.277557 GAACATGGACAGAGCAGAGGT 59.722 52.381 0.00 0.00 0.00 3.85
470 584 1.738365 CGAACATGGACAGAGCAGAGG 60.738 57.143 0.00 0.00 0.00 3.69
471 585 1.638133 CGAACATGGACAGAGCAGAG 58.362 55.000 0.00 0.00 0.00 3.35
472 586 0.390340 GCGAACATGGACAGAGCAGA 60.390 55.000 0.00 0.00 0.00 4.26
473 587 0.390866 AGCGAACATGGACAGAGCAG 60.391 55.000 0.00 0.00 0.00 4.24
474 588 0.671472 CAGCGAACATGGACAGAGCA 60.671 55.000 0.00 0.00 0.00 4.26
475 589 0.390340 TCAGCGAACATGGACAGAGC 60.390 55.000 0.00 0.00 0.00 4.09
476 590 1.354040 GTCAGCGAACATGGACAGAG 58.646 55.000 0.00 0.00 0.00 3.35
477 591 0.388520 CGTCAGCGAACATGGACAGA 60.389 55.000 0.00 0.00 41.33 3.41
478 592 0.388520 TCGTCAGCGAACATGGACAG 60.389 55.000 0.00 0.00 44.92 3.51
479 593 1.663173 TCGTCAGCGAACATGGACA 59.337 52.632 0.00 0.00 44.92 4.02
480 594 4.571250 TCGTCAGCGAACATGGAC 57.429 55.556 0.00 0.00 44.92 4.02
523 710 0.606401 TCCGCTTGCTCAAGGAAAGG 60.606 55.000 11.15 0.00 38.80 3.11
524 711 0.801251 CTCCGCTTGCTCAAGGAAAG 59.199 55.000 11.15 0.00 38.80 2.62
525 712 0.396435 TCTCCGCTTGCTCAAGGAAA 59.604 50.000 11.15 0.00 38.80 3.13
526 713 0.396435 TTCTCCGCTTGCTCAAGGAA 59.604 50.000 11.15 3.97 38.80 3.36
527 714 0.396435 TTTCTCCGCTTGCTCAAGGA 59.604 50.000 11.15 1.84 38.80 3.36
571 760 0.607217 CAACTGAGCTGATGCCACCA 60.607 55.000 0.00 0.00 40.80 4.17
572 761 1.310933 CCAACTGAGCTGATGCCACC 61.311 60.000 0.00 0.00 40.80 4.61
574 763 1.676635 GCCAACTGAGCTGATGCCA 60.677 57.895 0.00 0.00 40.80 4.92
575 764 2.413142 GGCCAACTGAGCTGATGCC 61.413 63.158 0.00 0.00 40.80 4.40
576 765 1.378250 AGGCCAACTGAGCTGATGC 60.378 57.895 5.01 0.00 40.05 3.91
672 894 1.745489 GTCCCCGTCACTTGCATCC 60.745 63.158 0.00 0.00 0.00 3.51
685 907 1.838073 TTTCTCCAGGAAGCGTCCCC 61.838 60.000 15.64 0.00 46.30 4.81
698 920 2.350868 GCCAACTCTTTTCGCTTTCTCC 60.351 50.000 0.00 0.00 0.00 3.71
707 929 2.358898 TGCTGTTGAGCCAACTCTTTTC 59.641 45.455 15.91 3.78 45.57 2.29
729 951 2.663188 GGCGACGATGATCCTGCC 60.663 66.667 0.00 2.15 35.04 4.85
754 976 6.510879 TGTAGTAGATGTAAGTGAGGTGTG 57.489 41.667 0.00 0.00 0.00 3.82
793 1016 1.541588 CGGCAGAAAGAGGAAAAAGGG 59.458 52.381 0.00 0.00 0.00 3.95
857 1082 3.458163 GCGTGGATCGGAGGTGGA 61.458 66.667 0.00 0.00 40.26 4.02
858 1083 2.907897 GAAGCGTGGATCGGAGGTGG 62.908 65.000 0.00 0.00 40.26 4.61
859 1084 1.519455 GAAGCGTGGATCGGAGGTG 60.519 63.158 0.00 0.00 40.26 4.00
860 1085 2.722201 GGAAGCGTGGATCGGAGGT 61.722 63.158 0.00 0.00 40.26 3.85
909 1150 2.888863 CACCACTCGAGGAGGAGC 59.111 66.667 26.84 0.00 37.57 4.70
922 1169 3.756963 CACTACTACTGTCTACTGCACCA 59.243 47.826 0.00 0.00 0.00 4.17
936 1183 1.403323 GACACCGGTAGCCACTACTAC 59.597 57.143 6.87 0.00 41.54 2.73
939 1186 0.172803 CTGACACCGGTAGCCACTAC 59.827 60.000 6.87 0.00 36.33 2.73
945 1192 0.739561 CCTCTACTGACACCGGTAGC 59.260 60.000 6.87 2.15 46.81 3.58
947 1194 0.682209 GCCCTCTACTGACACCGGTA 60.682 60.000 6.87 0.00 33.18 4.02
948 1195 1.982938 GCCCTCTACTGACACCGGT 60.983 63.158 0.00 0.00 35.70 5.28
949 1196 1.949847 CTGCCCTCTACTGACACCGG 61.950 65.000 0.00 0.00 0.00 5.28
951 1198 0.820871 CTCTGCCCTCTACTGACACC 59.179 60.000 0.00 0.00 0.00 4.16
952 1199 0.174617 GCTCTGCCCTCTACTGACAC 59.825 60.000 0.00 0.00 0.00 3.67
983 1261 0.950555 CATGGTCACCACTCACCACG 60.951 60.000 0.00 0.00 45.61 4.94
988 1266 2.347114 CGCCATGGTCACCACTCA 59.653 61.111 14.67 0.00 35.80 3.41
994 1272 4.759096 GTTGCGCGCCATGGTCAC 62.759 66.667 30.77 9.69 0.00 3.67
996 1274 4.465512 CAGTTGCGCGCCATGGTC 62.466 66.667 30.77 12.01 0.00 4.02
1039 1317 2.189342 GAAGAAGAAGAGCATCGACGG 58.811 52.381 0.00 0.00 42.67 4.79
1041 1319 3.186119 CAGGAAGAAGAAGAGCATCGAC 58.814 50.000 0.00 0.00 42.67 4.20
1042 1320 2.417924 GCAGGAAGAAGAAGAGCATCGA 60.418 50.000 0.00 0.00 42.67 3.59
1043 1321 1.932511 GCAGGAAGAAGAAGAGCATCG 59.067 52.381 0.00 0.00 42.67 3.84
1044 1322 3.197265 GAGCAGGAAGAAGAAGAGCATC 58.803 50.000 0.00 0.00 0.00 3.91
1045 1323 2.093021 GGAGCAGGAAGAAGAAGAGCAT 60.093 50.000 0.00 0.00 0.00 3.79
1046 1324 1.277557 GGAGCAGGAAGAAGAAGAGCA 59.722 52.381 0.00 0.00 0.00 4.26
1050 1328 3.533547 CATGAGGAGCAGGAAGAAGAAG 58.466 50.000 0.00 0.00 0.00 2.85
1051 1329 2.355513 GCATGAGGAGCAGGAAGAAGAA 60.356 50.000 0.00 0.00 0.00 2.52
1105 1383 3.415087 ACTGGATGGGCTGGGAGC 61.415 66.667 0.00 0.00 41.46 4.70
1106 1384 1.565390 TTCACTGGATGGGCTGGGAG 61.565 60.000 0.00 0.00 0.00 4.30
1107 1385 1.541118 TTCACTGGATGGGCTGGGA 60.541 57.895 0.00 0.00 0.00 4.37
1108 1386 1.379044 GTTCACTGGATGGGCTGGG 60.379 63.158 0.00 0.00 0.00 4.45
1109 1387 1.379044 GGTTCACTGGATGGGCTGG 60.379 63.158 0.00 0.00 0.00 4.85
1110 1388 0.251297 TTGGTTCACTGGATGGGCTG 60.251 55.000 0.00 0.00 0.00 4.85
1111 1389 0.038744 CTTGGTTCACTGGATGGGCT 59.961 55.000 0.00 0.00 0.00 5.19
1112 1390 0.038166 TCTTGGTTCACTGGATGGGC 59.962 55.000 0.00 0.00 0.00 5.36
1113 1391 2.814805 ATCTTGGTTCACTGGATGGG 57.185 50.000 0.00 0.00 0.00 4.00
1164 1442 3.654414 ACGCAGAAGAGAAGAAACGAAT 58.346 40.909 0.00 0.00 0.00 3.34
1177 1455 1.261619 GACACCACTCAAACGCAGAAG 59.738 52.381 0.00 0.00 0.00 2.85
1198 1476 1.202417 CGACACTGTGTTCACTCCAGT 60.202 52.381 15.54 0.00 39.93 4.00
1199 1477 1.491670 CGACACTGTGTTCACTCCAG 58.508 55.000 15.54 0.00 0.00 3.86
1209 1488 1.541588 TCACTGAGATCCGACACTGTG 59.458 52.381 6.19 6.19 34.07 3.66
1219 1498 1.065401 CGAGAGCTGGTCACTGAGATC 59.935 57.143 9.78 0.00 0.00 2.75
1244 1525 3.058016 CACAATGCAGGTTAACAGACAGG 60.058 47.826 8.10 1.85 0.00 4.00
1269 1550 5.299279 ACCAACACAAAGACTCCAATTAGTG 59.701 40.000 0.00 0.00 0.00 2.74
1314 1597 0.612744 AGTTCCTCTTGCTCTGCCTC 59.387 55.000 0.00 0.00 0.00 4.70
1316 1599 0.739112 CGAGTTCCTCTTGCTCTGCC 60.739 60.000 0.00 0.00 0.00 4.85
1518 1813 4.410400 GCCGTGGAGGTGAAGGGG 62.410 72.222 0.00 0.00 43.70 4.79
1686 1993 3.039202 GAACTGCGGCGGGTTGATG 62.039 63.158 14.26 0.00 0.00 3.07
1848 2182 2.529136 CCTCCTCCACCACCACCA 60.529 66.667 0.00 0.00 0.00 4.17
1889 2238 1.529713 CCTCCTCCTCCTACGCCTC 60.530 68.421 0.00 0.00 0.00 4.70
1890 2239 2.002018 CTCCTCCTCCTCCTACGCCT 62.002 65.000 0.00 0.00 0.00 5.52
1891 2240 1.529713 CTCCTCCTCCTCCTACGCC 60.530 68.421 0.00 0.00 0.00 5.68
1892 2241 1.529713 CCTCCTCCTCCTCCTACGC 60.530 68.421 0.00 0.00 0.00 4.42
1893 2242 0.109723 CTCCTCCTCCTCCTCCTACG 59.890 65.000 0.00 0.00 0.00 3.51
1894 2243 0.481128 CCTCCTCCTCCTCCTCCTAC 59.519 65.000 0.00 0.00 0.00 3.18
1895 2244 1.365105 GCCTCCTCCTCCTCCTCCTA 61.365 65.000 0.00 0.00 0.00 2.94
1896 2245 2.710826 GCCTCCTCCTCCTCCTCCT 61.711 68.421 0.00 0.00 0.00 3.69
1897 2246 2.123033 GCCTCCTCCTCCTCCTCC 60.123 72.222 0.00 0.00 0.00 4.30
1898 2247 2.520741 CGCCTCCTCCTCCTCCTC 60.521 72.222 0.00 0.00 0.00 3.71
1918 2267 2.032151 GCCACCTCCTCCTTCTCCTAG 61.032 61.905 0.00 0.00 0.00 3.02
1919 2268 0.032017 GCCACCTCCTCCTTCTCCTA 60.032 60.000 0.00 0.00 0.00 2.94
2266 2615 0.966920 GGTCAGTCGAGGTTTGAGGA 59.033 55.000 0.00 0.00 0.00 3.71
2280 2629 0.250234 TGGATGGAGCTTTCGGTCAG 59.750 55.000 0.00 0.00 39.38 3.51
2304 2676 0.824595 GTGGCATGGCATAGCATGGA 60.825 55.000 26.07 0.00 0.00 3.41
2310 2682 3.440151 GGCAGTGGCATGGCATAG 58.560 61.111 26.07 20.41 44.71 2.23
2319 2691 1.269936 GGATTTATGCATGGCAGTGGC 60.270 52.381 10.16 10.30 43.65 5.01
2321 2693 2.953648 TGAGGATTTATGCATGGCAGTG 59.046 45.455 10.16 0.00 43.65 3.66
2322 2694 3.301794 TGAGGATTTATGCATGGCAGT 57.698 42.857 10.16 0.00 43.65 4.40
2323 2695 3.824443 TCATGAGGATTTATGCATGGCAG 59.176 43.478 10.16 0.00 43.65 4.85
2334 2714 7.937942 AGAAATCAAGATCGATCATGAGGATTT 59.062 33.333 30.14 27.43 37.85 2.17
2370 2750 3.677148 GCAGAGATCATGACGGACAGAAA 60.677 47.826 0.00 0.00 0.00 2.52
2399 2779 1.717728 GTTGAACGCGCAACTGTCG 60.718 57.895 18.54 0.00 43.60 4.35
2476 2904 2.852495 TACTAAGCCTGCGGTGCTGC 62.852 60.000 8.98 0.00 39.48 5.25
2485 2913 3.954904 TCAGCTACTCCTTACTAAGCCTG 59.045 47.826 0.00 0.00 33.63 4.85
2672 3111 4.568072 ACACCAAGTTAGGCATACATCA 57.432 40.909 0.00 0.00 0.00 3.07
2673 3112 4.941263 TGAACACCAAGTTAGGCATACATC 59.059 41.667 0.00 0.00 41.51 3.06
2676 3115 3.124636 CGTGAACACCAAGTTAGGCATAC 59.875 47.826 0.00 0.00 41.51 2.39
2746 3185 5.933286 TGGAACAAAGAGTCGAGCTCGTG 62.933 52.174 33.33 24.82 42.46 4.35
2796 3235 5.587388 TTACGGAGGGAGTACTATGTTTG 57.413 43.478 0.00 0.00 0.00 2.93
2831 3282 4.142534 TGACTACTTCGGTGATCTAAACGG 60.143 45.833 0.00 0.00 0.00 4.44
2844 3295 4.911053 AGAGCGTTTAGATGACTACTTCG 58.089 43.478 0.00 0.00 0.00 3.79
2885 3341 9.610705 TCTCAATCTTAGTTATCACGTAGTACT 57.389 33.333 0.00 0.00 41.61 2.73
2889 3345 8.622157 TCCTTCTCAATCTTAGTTATCACGTAG 58.378 37.037 0.00 0.00 0.00 3.51
2917 3373 7.914427 TCACTGGGTTCTTGTGTCTATATAT 57.086 36.000 0.00 0.00 33.82 0.86
2918 3374 7.727578 TTCACTGGGTTCTTGTGTCTATATA 57.272 36.000 0.00 0.00 33.82 0.86
2919 3375 6.620877 TTCACTGGGTTCTTGTGTCTATAT 57.379 37.500 0.00 0.00 33.82 0.86
2920 3376 6.183361 TGTTTCACTGGGTTCTTGTGTCTATA 60.183 38.462 0.00 0.00 33.82 1.31
2944 3400 3.548745 TGTCCTGTCAATATGGAGCTG 57.451 47.619 0.00 0.00 0.00 4.24
3010 3466 3.271729 TCGTGTTCTTGGCTGTTTGTAA 58.728 40.909 0.00 0.00 0.00 2.41
3042 3498 4.883006 GTGTGTAAAACCTTACCCTGTCAA 59.117 41.667 0.00 0.00 37.24 3.18
3044 3500 3.495753 CGTGTGTAAAACCTTACCCTGTC 59.504 47.826 0.00 0.00 37.24 3.51
3046 3502 2.224784 GCGTGTGTAAAACCTTACCCTG 59.775 50.000 0.00 0.00 37.24 4.45
3047 3503 2.497138 GCGTGTGTAAAACCTTACCCT 58.503 47.619 0.00 0.00 37.24 4.34
3048 3504 1.195222 CGCGTGTGTAAAACCTTACCC 59.805 52.381 0.00 0.00 37.24 3.69
3049 3505 1.398832 GCGCGTGTGTAAAACCTTACC 60.399 52.381 8.43 0.00 37.24 2.85
3050 3506 1.398832 GGCGCGTGTGTAAAACCTTAC 60.399 52.381 8.43 0.00 38.34 2.34
3052 3508 0.816421 AGGCGCGTGTGTAAAACCTT 60.816 50.000 8.43 0.00 0.00 3.50
3053 3509 0.816421 AAGGCGCGTGTGTAAAACCT 60.816 50.000 8.43 0.00 0.00 3.50
3054 3510 0.867086 TAAGGCGCGTGTGTAAAACC 59.133 50.000 8.43 0.00 0.00 3.27
3056 3512 1.527736 CTGTAAGGCGCGTGTGTAAAA 59.472 47.619 8.43 0.00 0.00 1.52
3058 3514 1.286354 GCTGTAAGGCGCGTGTGTAA 61.286 55.000 8.43 0.00 0.00 2.41
3059 3515 1.735198 GCTGTAAGGCGCGTGTGTA 60.735 57.895 8.43 0.00 0.00 2.90
3060 3516 3.041940 GCTGTAAGGCGCGTGTGT 61.042 61.111 8.43 0.00 0.00 3.72
3061 3517 3.015293 CTGCTGTAAGGCGCGTGTG 62.015 63.158 8.43 0.00 34.52 3.82
3062 3518 2.507110 ATCTGCTGTAAGGCGCGTGT 62.507 55.000 8.43 0.00 34.52 4.49
3065 3521 1.540607 CGTATCTGCTGTAAGGCGCG 61.541 60.000 0.00 0.00 34.52 6.86
3066 3522 0.248907 TCGTATCTGCTGTAAGGCGC 60.249 55.000 0.00 0.00 34.52 6.53
3067 3523 2.120232 CTTCGTATCTGCTGTAAGGCG 58.880 52.381 0.00 0.00 34.52 5.52
3068 3524 1.861575 GCTTCGTATCTGCTGTAAGGC 59.138 52.381 0.00 0.00 0.00 4.35
3069 3525 3.444703 AGCTTCGTATCTGCTGTAAGG 57.555 47.619 0.00 0.00 35.54 2.69
3070 3526 7.222805 TGAATTAAGCTTCGTATCTGCTGTAAG 59.777 37.037 0.00 0.00 37.11 2.34
3104 3678 6.033513 GTGCTACTTATTTGATTTTTGACGGC 59.966 38.462 0.00 0.00 0.00 5.68
3127 3701 7.220300 CGTAAGCAGGAACAAATACTACTAGTG 59.780 40.741 5.39 0.00 0.00 2.74
3128 3702 7.256286 CGTAAGCAGGAACAAATACTACTAGT 58.744 38.462 0.00 0.00 0.00 2.57
3149 3758 0.889994 ACTCCGTGTATGTGGCGTAA 59.110 50.000 0.00 0.00 0.00 3.18
3173 3782 0.032267 GGATACAGCCGGCAGTAGAC 59.968 60.000 31.45 26.05 0.00 2.59
3214 3826 4.320788 CCAATCAGGTGCTCTCTTGAAAAC 60.321 45.833 0.00 0.00 0.00 2.43
3241 3853 5.295045 GCCATGCAATCAGAAAAATTAAGGG 59.705 40.000 0.00 0.00 0.00 3.95
3267 3879 0.533755 CAGATCAGGAACCCATCGCC 60.534 60.000 0.00 0.00 0.00 5.54
3278 3890 1.340405 CCACTGAAACCCCAGATCAGG 60.340 57.143 0.00 0.00 43.79 3.86
3293 3905 1.284657 CAGTTATCAGCGAGCCACTG 58.715 55.000 0.00 0.00 36.44 3.66
3323 3935 1.741770 GCCGAGCGAAATGGTGAGT 60.742 57.895 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.