Multiple sequence alignment - TraesCS1B01G046300

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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 TraesCS1B01G046300 chr1B 100.000 4791 0 0 1 4791 26190114 26185324 0.000000e+00 8848.0
1 TraesCS1B01G046300 chr1B 88.859 377 37 3 4022 4398 26168838 26168467 4.370000e-125 459.0
2 TraesCS1B01G046300 chr1B 89.754 244 15 8 4445 4683 20453703 20453465 2.170000e-78 303.0
3 TraesCS1B01G046300 chr1B 80.930 215 15 3 4600 4789 80190349 80190562 3.860000e-31 147.0
4 TraesCS1B01G046300 chr1B 80.930 215 15 3 4600 4789 217508450 217508237 3.860000e-31 147.0
5 TraesCS1B01G046300 chr1A 91.900 3210 191 44 1501 4683 20091762 20094929 0.000000e+00 4423.0
6 TraesCS1B01G046300 chr1A 87.139 692 40 21 778 1443 20091015 20091683 0.000000e+00 739.0
7 TraesCS1B01G046300 chr1A 82.074 781 80 26 4017 4789 20101764 20102492 3.170000e-171 612.0
8 TraesCS1B01G046300 chr1A 88.843 242 21 4 4445 4683 565237214 565237452 4.690000e-75 292.0
9 TraesCS1B01G046300 chr1A 83.489 321 38 12 312 629 20082224 20082532 7.850000e-73 285.0
10 TraesCS1B01G046300 chr1D 91.121 2185 118 29 2530 4683 18066755 18068894 0.000000e+00 2891.0
11 TraesCS1B01G046300 chr1D 92.268 957 59 11 1482 2431 18065772 18066720 0.000000e+00 1343.0
12 TraesCS1B01G046300 chr1D 87.432 732 43 26 736 1443 18065003 18065709 0.000000e+00 797.0
13 TraesCS1B01G046300 chr1D 91.875 480 32 6 1 475 18064392 18064869 0.000000e+00 664.0
14 TraesCS1B01G046300 chr1D 89.767 430 38 4 4015 4443 18074833 18075257 3.260000e-151 545.0
15 TraesCS1B01G046300 chr4B 83.932 529 76 5 1873 2400 20228700 20228180 9.260000e-137 497.0
16 TraesCS1B01G046300 chr4B 78.641 103 19 3 470 571 14837247 14837147 1.110000e-06 65.8
17 TraesCS1B01G046300 chr5B 83.333 372 32 7 4445 4789 272997468 272997100 2.780000e-82 316.0
18 TraesCS1B01G046300 chr5B 83.333 372 32 7 4445 4789 557738500 557738868 2.780000e-82 316.0
19 TraesCS1B01G046300 chr5B 82.192 365 35 7 4452 4789 50773613 50773974 2.180000e-73 287.0
20 TraesCS1B01G046300 chr5B 88.430 242 22 4 4445 4683 335976204 335975966 2.180000e-73 287.0
21 TraesCS1B01G046300 chr6A 82.796 372 34 7 4445 4789 596281363 596281731 6.020000e-79 305.0
22 TraesCS1B01G046300 chr6A 80.930 215 15 3 4600 4789 413645339 413645126 3.860000e-31 147.0
23 TraesCS1B01G046300 chr3B 89.669 242 19 4 4445 4683 806384320 806384082 2.170000e-78 303.0
24 TraesCS1B01G046300 chr3B 89.256 242 20 4 4445 4683 89816796 89817034 1.010000e-76 298.0
25 TraesCS1B01G046300 chr3B 88.750 240 21 4 4445 4681 219134052 219133816 6.070000e-74 289.0
26 TraesCS1B01G046300 chr7B 85.946 185 24 2 1073 1257 725844198 725844380 3.780000e-46 196.0
27 TraesCS1B01G046300 chr2A 80.930 215 15 3 4600 4789 642795188 642795401 3.860000e-31 147.0
28 TraesCS1B01G046300 chr6B 80.465 215 16 3 4600 4789 53199754 53199541 1.800000e-29 141.0
29 TraesCS1B01G046300 chr3D 84.337 83 7 4 1180 1257 182658520 182658439 5.140000e-10 76.8
30 TraesCS1B01G046300 chr3A 95.122 41 2 0 530 570 14205303 14205343 1.110000e-06 65.8


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 TraesCS1B01G046300 chr1B 26185324 26190114 4790 True 8848.00 8848 100.0000 1 4791 1 chr1B.!!$R3 4790
1 TraesCS1B01G046300 chr1A 20091015 20094929 3914 False 2581.00 4423 89.5195 778 4683 2 chr1A.!!$F4 3905
2 TraesCS1B01G046300 chr1A 20101764 20102492 728 False 612.00 612 82.0740 4017 4789 1 chr1A.!!$F2 772
3 TraesCS1B01G046300 chr1D 18064392 18068894 4502 False 1423.75 2891 90.6740 1 4683 4 chr1D.!!$F2 4682
4 TraesCS1B01G046300 chr4B 20228180 20228700 520 True 497.00 497 83.9320 1873 2400 1 chr4B.!!$R2 527

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
627 632 0.106619 CGGAGGCACTACTACTCCCT 60.107 60.0 0.00 0.00 46.32 4.20 F
1329 1374 0.036010 CAAATCAGGTCGCCTGGTCT 60.036 55.0 20.90 3.06 45.38 3.85 F
1475 1588 0.036294 CCTCCCTTCCGACAAGTTCC 60.036 60.0 0.00 0.00 0.00 3.62 F
2772 2900 0.037447 AGCAGTTCAGGGCCTCTTTC 59.963 55.0 0.95 0.00 0.00 2.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2407 2535 0.514691 GCTGAACTTCAAGACTGCGG 59.485 55.0 0.00 0.00 0.00 5.69 R
2819 2947 0.106708 GTGTGTGCAGGACTCAAGGA 59.893 55.0 0.00 0.00 30.00 3.36 R
2822 2950 0.541392 AGTGTGTGTGCAGGACTCAA 59.459 50.0 0.00 0.00 30.00 3.02 R
4771 4956 0.101579 TGATCTGCCATGCATTTGCG 59.898 50.0 12.08 7.97 45.83 4.85 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
60 62 8.428186 AATTCATAAAAATTGCGAGCATCATT 57.572 26.923 0.00 0.00 33.17 2.57
69 71 4.811555 TGCGAGCATCATTTTATACACC 57.188 40.909 0.00 0.00 33.17 4.16
99 101 1.080093 GGTGCTCCGTGTTGATCGA 60.080 57.895 0.00 0.00 0.00 3.59
130 132 2.050144 TCATATGAGGAGCCCTTGGAC 58.950 52.381 0.00 0.00 31.76 4.02
137 139 2.282462 AGCCCTTGGACCTTTGCG 60.282 61.111 0.00 0.00 0.00 4.85
158 160 3.491342 GAAAAGCCCCTTCAAGAGTCTT 58.509 45.455 0.00 0.00 0.00 3.01
168 170 7.112779 CCCCTTCAAGAGTCTTGTAATTACAT 58.887 38.462 27.83 4.15 35.89 2.29
169 171 7.066284 CCCCTTCAAGAGTCTTGTAATTACATG 59.934 40.741 27.83 19.56 35.89 3.21
184 186 1.372501 ACATGTAGGTCCAAGGGCTT 58.627 50.000 0.00 0.00 0.00 4.35
187 189 1.742308 TGTAGGTCCAAGGGCTTCTT 58.258 50.000 0.00 0.00 35.79 2.52
194 196 3.137360 GGTCCAAGGGCTTCTTAGATGAT 59.863 47.826 0.00 0.00 33.68 2.45
229 231 1.374252 AACAACGGAGCTAGCACGG 60.374 57.895 27.70 22.47 0.00 4.94
251 253 5.354234 CGGAGCACCTGATATTTACTTGTTT 59.646 40.000 0.00 0.00 0.00 2.83
254 256 7.145932 AGCACCTGATATTTACTTGTTTCAC 57.854 36.000 0.00 0.00 0.00 3.18
256 258 7.023575 GCACCTGATATTTACTTGTTTCACAG 58.976 38.462 0.00 0.00 0.00 3.66
257 259 7.308589 GCACCTGATATTTACTTGTTTCACAGT 60.309 37.037 0.00 0.00 0.00 3.55
293 295 6.432936 CCATTGTCTTACCATCATTTCATCG 58.567 40.000 0.00 0.00 0.00 3.84
306 309 4.278170 TCATTTCATCGGCAAAAACAGTCT 59.722 37.500 0.00 0.00 0.00 3.24
342 345 1.496857 TGAATGGGTTCCACCACAAGA 59.503 47.619 0.00 0.00 44.72 3.02
348 351 2.558359 GGGTTCCACCACAAGAAATCTG 59.442 50.000 0.00 0.00 41.02 2.90
366 369 7.707893 AGAAATCTGACCATCAAGTTGTTTTTG 59.292 33.333 2.11 0.00 0.00 2.44
368 371 4.952957 TCTGACCATCAAGTTGTTTTTGGA 59.047 37.500 17.58 3.70 0.00 3.53
369 372 5.598005 TCTGACCATCAAGTTGTTTTTGGAT 59.402 36.000 17.58 7.35 0.00 3.41
370 373 6.098124 TCTGACCATCAAGTTGTTTTTGGATT 59.902 34.615 17.58 3.37 0.00 3.01
424 427 6.324522 TGAACAAAAACATGTTTTACGCTG 57.675 33.333 31.18 26.52 43.31 5.18
429 432 2.919666 ACATGTTTTACGCTGGCATC 57.080 45.000 0.00 0.00 0.00 3.91
500 505 3.981211 CCAATGGTTGAGTGGTTTGAAG 58.019 45.455 0.00 0.00 34.90 3.02
501 506 3.636300 CCAATGGTTGAGTGGTTTGAAGA 59.364 43.478 0.00 0.00 34.90 2.87
502 507 4.261741 CCAATGGTTGAGTGGTTTGAAGAG 60.262 45.833 0.00 0.00 34.90 2.85
511 516 1.142870 TGGTTTGAAGAGGGAGTGGTG 59.857 52.381 0.00 0.00 0.00 4.17
515 520 0.178921 TGAAGAGGGAGTGGTGCTCT 60.179 55.000 0.00 0.00 43.62 4.09
526 531 4.329545 GTGCTCTCGGCCCACCAA 62.330 66.667 0.00 0.00 40.92 3.67
528 533 2.282180 GCTCTCGGCCCACCAAAA 60.282 61.111 0.00 0.00 34.57 2.44
535 540 1.762957 TCGGCCCACCAAAAATCAAAA 59.237 42.857 0.00 0.00 34.57 2.44
537 542 2.484594 CGGCCCACCAAAAATCAAAACT 60.485 45.455 0.00 0.00 34.57 2.66
547 552 6.593770 ACCAAAAATCAAAACTCAGGTTTGAC 59.406 34.615 20.36 0.00 43.90 3.18
569 574 6.363577 ACGCTTTGGTGTCTCATTAATATG 57.636 37.500 0.00 0.00 0.00 1.78
570 575 6.112734 ACGCTTTGGTGTCTCATTAATATGA 58.887 36.000 0.00 0.00 38.45 2.15
597 602 7.758495 ACTTTATATTTCACAACGTTCCCATC 58.242 34.615 0.00 0.00 0.00 3.51
608 613 0.938008 GTTCCCATCGATCGCCTTTC 59.062 55.000 11.09 0.00 0.00 2.62
610 615 1.956170 CCCATCGATCGCCTTTCGG 60.956 63.158 11.09 3.94 39.05 4.30
611 616 1.067416 CCATCGATCGCCTTTCGGA 59.933 57.895 11.09 0.00 39.05 4.55
622 627 2.580966 CCTTTCGGAGGCACTACTAC 57.419 55.000 0.00 0.00 41.55 2.73
623 628 2.100989 CCTTTCGGAGGCACTACTACT 58.899 52.381 0.00 0.00 41.55 2.57
624 629 2.099427 CCTTTCGGAGGCACTACTACTC 59.901 54.545 0.00 0.00 41.55 2.59
627 632 0.106619 CGGAGGCACTACTACTCCCT 60.107 60.000 0.00 0.00 46.32 4.20
628 633 1.694844 GGAGGCACTACTACTCCCTC 58.305 60.000 0.00 0.00 43.93 4.30
630 635 2.442502 GGAGGCACTACTACTCCCTCTA 59.557 54.545 5.13 0.00 43.93 2.43
631 636 3.074836 GGAGGCACTACTACTCCCTCTAT 59.925 52.174 5.13 0.00 43.93 1.98
633 638 4.732065 AGGCACTACTACTCCCTCTATTC 58.268 47.826 0.00 0.00 36.02 1.75
634 639 3.827876 GGCACTACTACTCCCTCTATTCC 59.172 52.174 0.00 0.00 0.00 3.01
636 641 5.141910 GCACTACTACTCCCTCTATTCCTT 58.858 45.833 0.00 0.00 0.00 3.36
637 642 5.599242 GCACTACTACTCCCTCTATTCCTTT 59.401 44.000 0.00 0.00 0.00 3.11
638 643 6.098552 GCACTACTACTCCCTCTATTCCTTTT 59.901 42.308 0.00 0.00 0.00 2.27
639 644 7.364851 GCACTACTACTCCCTCTATTCCTTTTT 60.365 40.741 0.00 0.00 0.00 1.94
640 645 9.198475 CACTACTACTCCCTCTATTCCTTTTTA 57.802 37.037 0.00 0.00 0.00 1.52
641 646 9.779951 ACTACTACTCCCTCTATTCCTTTTTAA 57.220 33.333 0.00 0.00 0.00 1.52
647 652 9.822727 ACTCCCTCTATTCCTTTTTAAATTCAA 57.177 29.630 0.00 0.00 0.00 2.69
668 673 8.924511 TTCAAGACCATTTCTAAGATTTGAGT 57.075 30.769 0.00 0.00 32.51 3.41
713 718 9.524106 TGAATGTATGTAGACGTATTTTAGTGG 57.476 33.333 0.00 0.00 0.00 4.00
714 719 8.882415 AATGTATGTAGACGTATTTTAGTGGG 57.118 34.615 0.00 0.00 0.00 4.61
715 720 6.275335 TGTATGTAGACGTATTTTAGTGGGC 58.725 40.000 0.00 0.00 0.00 5.36
716 721 4.804868 TGTAGACGTATTTTAGTGGGCA 57.195 40.909 0.00 0.00 0.00 5.36
717 722 4.751060 TGTAGACGTATTTTAGTGGGCAG 58.249 43.478 0.00 0.00 0.00 4.85
718 723 4.463539 TGTAGACGTATTTTAGTGGGCAGA 59.536 41.667 0.00 0.00 0.00 4.26
719 724 4.755266 AGACGTATTTTAGTGGGCAGAT 57.245 40.909 0.00 0.00 0.00 2.90
720 725 5.099042 AGACGTATTTTAGTGGGCAGATT 57.901 39.130 0.00 0.00 0.00 2.40
721 726 5.116882 AGACGTATTTTAGTGGGCAGATTC 58.883 41.667 0.00 0.00 0.00 2.52
722 727 4.839121 ACGTATTTTAGTGGGCAGATTCA 58.161 39.130 0.00 0.00 0.00 2.57
723 728 4.634443 ACGTATTTTAGTGGGCAGATTCAC 59.366 41.667 0.00 0.00 0.00 3.18
724 729 4.035208 CGTATTTTAGTGGGCAGATTCACC 59.965 45.833 0.00 0.00 34.67 4.02
729 734 4.415783 GGGCAGATTCACCCGTTT 57.584 55.556 0.00 0.00 36.07 3.60
730 735 2.653557 GGGCAGATTCACCCGTTTT 58.346 52.632 0.00 0.00 36.07 2.43
731 736 0.243636 GGGCAGATTCACCCGTTTTG 59.756 55.000 0.00 0.00 36.07 2.44
732 737 0.388520 GGCAGATTCACCCGTTTTGC 60.389 55.000 0.00 0.00 0.00 3.68
733 738 0.388520 GCAGATTCACCCGTTTTGCC 60.389 55.000 0.00 0.00 0.00 4.52
734 739 0.958091 CAGATTCACCCGTTTTGCCA 59.042 50.000 0.00 0.00 0.00 4.92
740 745 3.601685 CCCGTTTTGCCACCGCTT 61.602 61.111 0.00 0.00 35.36 4.68
766 771 4.742201 TCGTGAAGCAGCCGCCTC 62.742 66.667 0.00 0.00 39.83 4.70
914 925 2.231478 ACACGATACTCCACAGTTCCAG 59.769 50.000 0.00 0.00 33.62 3.86
915 926 1.204941 ACGATACTCCACAGTTCCAGC 59.795 52.381 0.00 0.00 33.62 4.85
916 927 1.471676 CGATACTCCACAGTTCCAGCC 60.472 57.143 0.00 0.00 33.62 4.85
917 928 0.912486 ATACTCCACAGTTCCAGCCC 59.088 55.000 0.00 0.00 33.62 5.19
918 929 1.541310 TACTCCACAGTTCCAGCCCG 61.541 60.000 0.00 0.00 33.62 6.13
942 953 3.666253 CCCGGCCACGAAACCAAC 61.666 66.667 2.24 0.00 44.60 3.77
943 954 4.020378 CCGGCCACGAAACCAACG 62.020 66.667 2.24 0.00 44.60 4.10
944 955 2.968156 CGGCCACGAAACCAACGA 60.968 61.111 2.24 0.00 44.60 3.85
945 956 2.943653 GGCCACGAAACCAACGAG 59.056 61.111 0.00 0.00 34.70 4.18
946 957 2.251371 GCCACGAAACCAACGAGC 59.749 61.111 0.00 0.00 34.70 5.03
947 958 2.549282 CCACGAAACCAACGAGCG 59.451 61.111 0.00 0.00 34.70 5.03
948 959 2.549282 CACGAAACCAACGAGCGG 59.451 61.111 0.00 0.00 34.70 5.52
950 961 2.663852 CGAAACCAACGAGCGGGT 60.664 61.111 0.00 0.00 39.65 5.28
952 963 2.593436 AAACCAACGAGCGGGTGG 60.593 61.111 12.66 12.66 37.50 4.61
953 964 2.999739 GAAACCAACGAGCGGGTGGA 63.000 60.000 19.96 0.00 37.50 4.02
957 982 3.382832 AACGAGCGGGTGGAGAGG 61.383 66.667 0.00 0.00 0.00 3.69
1023 1048 1.535202 GATGGCGGGGAGATCCTCT 60.535 63.158 0.00 0.00 33.13 3.69
1281 1322 1.923148 CCCTCCCCAATTCACTTACCT 59.077 52.381 0.00 0.00 0.00 3.08
1282 1327 2.357154 CCCTCCCCAATTCACTTACCTG 60.357 54.545 0.00 0.00 0.00 4.00
1309 1354 2.046285 GTCCCCAAATCCACAGCGG 61.046 63.158 0.00 0.00 0.00 5.52
1310 1355 3.451894 CCCCAAATCCACAGCGGC 61.452 66.667 0.00 0.00 33.14 6.53
1316 1361 1.067706 CAAATCCACAGCGGCAAATCA 60.068 47.619 1.45 0.00 33.14 2.57
1317 1362 0.813184 AATCCACAGCGGCAAATCAG 59.187 50.000 1.45 0.00 33.14 2.90
1328 1373 1.648467 GCAAATCAGGTCGCCTGGTC 61.648 60.000 20.90 4.02 45.38 4.02
1329 1374 0.036010 CAAATCAGGTCGCCTGGTCT 60.036 55.000 20.90 3.06 45.38 3.85
1341 1386 1.446792 CTGGTCTGATTGCGAGCGT 60.447 57.895 0.00 0.00 0.00 5.07
1360 1405 0.107263 TGAATTGCATGCCTCGGCTA 60.107 50.000 16.68 0.00 42.51 3.93
1363 1408 0.399454 ATTGCATGCCTCGGCTAGAT 59.601 50.000 16.68 0.00 42.51 1.98
1368 1413 2.141517 CATGCCTCGGCTAGATTCTTG 58.858 52.381 9.65 0.00 42.51 3.02
1371 1434 1.866063 GCCTCGGCTAGATTCTTGTCG 60.866 57.143 14.58 14.58 35.88 4.35
1379 1442 5.562890 CGGCTAGATTCTTGTCGTCATCATA 60.563 44.000 12.89 0.00 30.74 2.15
1412 1475 2.094575 ACGATGCTGCGCGTAATTTTAA 59.905 40.909 16.77 0.00 39.21 1.52
1472 1585 1.430992 TTTCCTCCCTTCCGACAAGT 58.569 50.000 0.00 0.00 0.00 3.16
1473 1586 1.430992 TTCCTCCCTTCCGACAAGTT 58.569 50.000 0.00 0.00 0.00 2.66
1474 1587 0.974383 TCCTCCCTTCCGACAAGTTC 59.026 55.000 0.00 0.00 0.00 3.01
1475 1588 0.036294 CCTCCCTTCCGACAAGTTCC 60.036 60.000 0.00 0.00 0.00 3.62
1476 1589 0.685097 CTCCCTTCCGACAAGTTCCA 59.315 55.000 0.00 0.00 0.00 3.53
1477 1590 0.395312 TCCCTTCCGACAAGTTCCAC 59.605 55.000 0.00 0.00 0.00 4.02
1478 1591 0.107831 CCCTTCCGACAAGTTCCACA 59.892 55.000 0.00 0.00 0.00 4.17
1479 1592 1.512926 CCTTCCGACAAGTTCCACAG 58.487 55.000 0.00 0.00 0.00 3.66
1480 1593 0.868406 CTTCCGACAAGTTCCACAGC 59.132 55.000 0.00 0.00 0.00 4.40
1481 1594 0.534203 TTCCGACAAGTTCCACAGCC 60.534 55.000 0.00 0.00 0.00 4.85
1482 1595 1.966451 CCGACAAGTTCCACAGCCC 60.966 63.158 0.00 0.00 0.00 5.19
1483 1596 1.966451 CGACAAGTTCCACAGCCCC 60.966 63.158 0.00 0.00 0.00 5.80
1484 1597 1.456287 GACAAGTTCCACAGCCCCT 59.544 57.895 0.00 0.00 0.00 4.79
1485 1598 0.178990 GACAAGTTCCACAGCCCCTT 60.179 55.000 0.00 0.00 0.00 3.95
1498 1611 2.622962 CCCCTTTCGGCGTGTTTCC 61.623 63.158 6.85 0.00 0.00 3.13
1518 1633 2.172717 CCGGAGATAAGTGTTGGGGAAT 59.827 50.000 0.00 0.00 0.00 3.01
1527 1642 0.760945 TGTTGGGGAATTTTGGCCGT 60.761 50.000 0.00 0.00 0.00 5.68
1547 1662 3.302870 CGTTTTGTGTTCGTCGATTTCCT 60.303 43.478 0.00 0.00 0.00 3.36
1560 1675 4.985409 GTCGATTTCCTAGGATTAGCTGTG 59.015 45.833 13.57 0.00 0.00 3.66
1588 1703 1.593006 CTCACTGACGTGTGGTTTGTC 59.407 52.381 0.00 0.00 41.89 3.18
1590 1705 0.463116 ACTGACGTGTGGTTTGTCCC 60.463 55.000 0.00 0.00 34.77 4.46
1613 1730 7.611467 TCCCGATTTCATGATTATCCCTTATTG 59.389 37.037 0.00 0.00 0.00 1.90
1616 1733 8.180267 CGATTTCATGATTATCCCTTATTGAGC 58.820 37.037 0.00 0.00 0.00 4.26
1627 1744 4.019141 TCCCTTATTGAGCCTACGGAAAAA 60.019 41.667 0.00 0.00 0.00 1.94
1633 1750 3.167485 TGAGCCTACGGAAAAACTAGGA 58.833 45.455 0.00 0.00 30.11 2.94
1654 1771 4.878971 GGATTTCTTTTCTCAGGCCTACTC 59.121 45.833 3.98 0.00 0.00 2.59
1716 1836 1.346395 ACTGTCAATCGTTGGCACCTA 59.654 47.619 1.68 0.00 40.96 3.08
1717 1837 1.732259 CTGTCAATCGTTGGCACCTAC 59.268 52.381 1.68 0.00 40.96 3.18
1719 1839 2.290008 TGTCAATCGTTGGCACCTACAT 60.290 45.455 2.30 0.00 40.96 2.29
1720 1840 3.055747 TGTCAATCGTTGGCACCTACATA 60.056 43.478 2.30 0.00 40.96 2.29
1722 1842 4.574828 GTCAATCGTTGGCACCTACATAAT 59.425 41.667 2.30 0.00 34.79 1.28
1724 1844 5.295787 TCAATCGTTGGCACCTACATAATTC 59.704 40.000 2.30 0.00 0.00 2.17
1725 1845 4.481368 TCGTTGGCACCTACATAATTCT 57.519 40.909 2.30 0.00 0.00 2.40
1726 1846 4.188462 TCGTTGGCACCTACATAATTCTG 58.812 43.478 2.30 0.00 0.00 3.02
1727 1847 3.938963 CGTTGGCACCTACATAATTCTGT 59.061 43.478 1.79 1.79 0.00 3.41
1728 1848 5.105269 TCGTTGGCACCTACATAATTCTGTA 60.105 40.000 3.90 3.90 0.00 2.74
1729 1849 5.006358 CGTTGGCACCTACATAATTCTGTAC 59.994 44.000 0.00 0.00 0.00 2.90
1754 1874 3.985008 TCTGCTCGCTGTTAAAGTGTTA 58.015 40.909 0.00 0.00 37.67 2.41
1796 1916 9.508567 GCCTGATTTTTCATGTTAATCTTACTC 57.491 33.333 13.96 0.00 31.25 2.59
1806 1926 2.751166 AATCTTACTCTGTGCACGCT 57.249 45.000 13.13 0.00 0.00 5.07
1966 2091 9.468532 CTTATCATCATTGTCGTCTAAATCTCA 57.531 33.333 0.00 0.00 0.00 3.27
2054 2180 2.586079 CGCTCGCCGTCCATCAAT 60.586 61.111 0.00 0.00 0.00 2.57
2108 2234 1.815408 GCCATGTGCCCTTCGTCATAT 60.815 52.381 0.00 0.00 0.00 1.78
2216 2342 1.334160 TGCACGGTGAGGACTTCTTA 58.666 50.000 13.29 0.00 0.00 2.10
2217 2343 1.272490 TGCACGGTGAGGACTTCTTAG 59.728 52.381 13.29 0.00 0.00 2.18
2226 2352 0.905357 GGACTTCTTAGCCTGCCTCA 59.095 55.000 0.00 0.00 0.00 3.86
2402 2530 3.515104 TCACTGATGGCATGTAAGTCTCA 59.485 43.478 3.81 0.00 0.00 3.27
2407 2535 3.526931 TGGCATGTAAGTCTCACTAGC 57.473 47.619 0.00 0.00 0.00 3.42
2412 2540 1.472878 TGTAAGTCTCACTAGCCGCAG 59.527 52.381 0.00 0.00 0.00 5.18
2418 2546 0.528017 CTCACTAGCCGCAGTCTTGA 59.472 55.000 0.00 0.00 0.00 3.02
2426 2554 0.514691 CCGCAGTCTTGAAGTTCAGC 59.485 55.000 5.56 4.90 0.00 4.26
2471 2599 6.729187 AGCATTAACTTCACTTTTGACACTC 58.271 36.000 0.00 0.00 0.00 3.51
2474 2602 7.679638 GCATTAACTTCACTTTTGACACTCTGT 60.680 37.037 0.00 0.00 0.00 3.41
2488 2616 6.078202 GACACTCTGTCTGCTGCTATAATA 57.922 41.667 0.00 0.00 43.73 0.98
2514 2642 3.755965 TGCTGCGTATTACAAATGGTG 57.244 42.857 0.00 0.00 0.00 4.17
2516 2644 3.504134 TGCTGCGTATTACAAATGGTGTT 59.496 39.130 0.00 0.00 41.98 3.32
2599 2727 3.071479 GGAACTGTTGCATACGAAGGAA 58.929 45.455 7.20 0.00 0.00 3.36
2650 2778 2.225805 TGCTACCTTAGGTCCTTCCCTT 60.226 50.000 7.39 0.00 37.09 3.95
2749 2877 6.317140 TGTTCAGATTGGAACTAGATGAATGC 59.683 38.462 0.00 0.00 45.74 3.56
2772 2900 0.037447 AGCAGTTCAGGGCCTCTTTC 59.963 55.000 0.95 0.00 0.00 2.62
2776 2904 1.003355 TTCAGGGCCTCTTTCTGCG 60.003 57.895 0.95 0.00 0.00 5.18
2819 2947 3.244181 GGCCACCATCAACTTTGACAATT 60.244 43.478 0.00 0.00 40.49 2.32
2822 2950 4.281688 CCACCATCAACTTTGACAATTCCT 59.718 41.667 0.00 0.00 40.49 3.36
2911 3039 3.181451 TGAGAACACTCAAGGACTGCAAT 60.181 43.478 0.00 0.00 37.66 3.56
3138 3266 7.267857 GCATTTTAATCCTCCTTTGCTGTTAT 58.732 34.615 0.00 0.00 0.00 1.89
3176 3304 7.710676 ATTCTGCTCTCTTTTACTCTGAGTA 57.289 36.000 13.34 13.34 0.00 2.59
3441 3581 1.804326 GATCGTCAACCGTGGACCG 60.804 63.158 0.16 0.00 37.94 4.79
3454 3594 0.469331 TGGACCGGACACAGAACTCT 60.469 55.000 9.46 0.00 0.00 3.24
3477 3617 1.480545 GTTGCCAACCCTGTTGAACTT 59.519 47.619 8.47 0.00 0.00 2.66
3489 3629 2.002018 TTGAACTTGCCGGGAAGGGT 62.002 55.000 35.08 24.25 41.48 4.34
3523 3663 5.355350 GTGTTCTATGATGCTACTTTGGCTT 59.645 40.000 0.00 0.00 0.00 4.35
3582 3722 8.135529 AGAGTTACAACCTAATTGAAAAAGTGC 58.864 33.333 0.00 0.00 41.23 4.40
3583 3723 7.777095 AGTTACAACCTAATTGAAAAAGTGCA 58.223 30.769 0.00 0.00 41.23 4.57
3588 3728 8.955388 ACAACCTAATTGAAAAAGTGCAAAATT 58.045 25.926 0.00 0.00 41.23 1.82
3599 3739 9.255304 GAAAAAGTGCAAAATTAGTCCACAATA 57.745 29.630 0.00 0.00 0.00 1.90
3625 3765 8.488668 AGAGTTAGTGTTTACTGTTTCCCTTTA 58.511 33.333 0.00 0.00 37.78 1.85
3658 3798 1.841302 AAATCGGGAGACAGGCAGCA 61.841 55.000 0.00 0.00 44.82 4.41
3816 3956 5.745227 ACTCGGTTTGTATCTCCATGAATT 58.255 37.500 0.00 0.00 0.00 2.17
3852 3994 1.609239 CCATCCAGTAGGCAGCCAA 59.391 57.895 15.80 0.00 33.74 4.52
3873 4015 6.038271 GCCAATGTATCCAGTTAGTTAACCTG 59.962 42.308 0.88 2.77 36.88 4.00
3878 4020 4.267349 TCCAGTTAGTTAACCTGCTGAC 57.733 45.455 17.23 2.12 36.88 3.51
3964 4106 1.134431 CCAAACTTGCTGGCCAAACTT 60.134 47.619 7.01 0.00 31.94 2.66
3965 4107 2.631267 CAAACTTGCTGGCCAAACTTT 58.369 42.857 7.01 0.00 31.94 2.66
3980 4122 4.524328 CCAAACTTTTCTTCATAGTGCCCT 59.476 41.667 0.00 0.00 0.00 5.19
3992 4134 4.082523 TGCCCTGTACCTCGCAGC 62.083 66.667 0.00 0.00 32.93 5.25
4000 4142 2.423898 TACCTCGCAGCTACCAGCC 61.424 63.158 0.00 0.00 43.77 4.85
4006 4164 2.984623 CAGCTACCAGCCTCAGCA 59.015 61.111 0.00 0.00 43.77 4.41
4014 4172 3.644606 AGCCTCAGCACTGTGGGG 61.645 66.667 17.85 10.46 42.71 4.96
4020 4178 3.889692 AGCACTGTGGGGGTGTGG 61.890 66.667 10.21 0.00 37.07 4.17
4094 4252 6.053632 TGTTGCAGGATTTCAGAGAGAATA 57.946 37.500 0.00 0.00 35.83 1.75
4114 4272 0.647410 CTATGGTCAGCAAACGAGCG 59.353 55.000 0.00 0.00 40.15 5.03
4123 4281 3.036084 AAACGAGCGCAGGACACG 61.036 61.111 11.47 7.83 0.00 4.49
4152 4310 2.703007 ACTATGTCTCTTGGATGCCTCC 59.297 50.000 0.22 0.22 42.45 4.30
4171 4329 5.448654 CCTCCAAAATATCTTCATGTGGGA 58.551 41.667 0.00 0.00 0.00 4.37
4184 4343 5.957842 TCATGTGGGAAGTGTTGTAAATC 57.042 39.130 0.00 0.00 0.00 2.17
4257 4416 2.352805 GTCCTCTTGCCCACCCAG 59.647 66.667 0.00 0.00 0.00 4.45
4290 4449 2.424956 GGTTGGAGGCTCAATCATTGTC 59.575 50.000 17.69 0.00 0.00 3.18
4336 4495 2.887790 TGCTGACGCAGATCCTACT 58.112 52.632 10.46 0.00 42.25 2.57
4369 4528 7.011016 TGTTGTAGATTAATGTAGAATGTGCCG 59.989 37.037 5.63 0.00 0.00 5.69
4377 4549 0.108186 TAGAATGTGCCGTCTGCCTG 60.108 55.000 0.00 0.00 40.16 4.85
4378 4550 3.044059 GAATGTGCCGTCTGCCTGC 62.044 63.158 0.00 0.00 40.16 4.85
4384 4556 4.767255 CCGTCTGCCTGCCTCACC 62.767 72.222 0.00 0.00 0.00 4.02
4385 4557 4.767255 CGTCTGCCTGCCTCACCC 62.767 72.222 0.00 0.00 0.00 4.61
4386 4558 4.767255 GTCTGCCTGCCTCACCCG 62.767 72.222 0.00 0.00 0.00 5.28
4408 4580 1.223211 GCTCCCTTCCTGCCTTCTC 59.777 63.158 0.00 0.00 0.00 2.87
4434 4606 5.818136 TGATTACTGCTTTGCCAATAGAC 57.182 39.130 0.00 0.00 0.00 2.59
4442 4614 4.821805 TGCTTTGCCAATAGACTATTAGGC 59.178 41.667 25.94 25.94 40.05 3.93
4443 4615 4.216472 GCTTTGCCAATAGACTATTAGGCC 59.784 45.833 27.69 17.48 39.47 5.19
4444 4616 3.678056 TGCCAATAGACTATTAGGCCG 57.322 47.619 27.69 11.73 39.47 6.13
4445 4617 2.289444 TGCCAATAGACTATTAGGCCGC 60.289 50.000 27.69 17.13 39.47 6.53
4446 4618 2.028020 GCCAATAGACTATTAGGCCGCT 60.028 50.000 24.09 0.00 36.86 5.52
4447 4619 3.557264 GCCAATAGACTATTAGGCCGCTT 60.557 47.826 24.09 0.00 36.86 4.68
4448 4620 4.642429 CCAATAGACTATTAGGCCGCTTT 58.358 43.478 7.40 0.00 0.00 3.51
4449 4621 4.452455 CCAATAGACTATTAGGCCGCTTTG 59.548 45.833 7.40 0.00 0.00 2.77
4450 4622 1.954927 AGACTATTAGGCCGCTTTGC 58.045 50.000 0.00 0.00 0.00 3.68
4459 4631 2.482326 GCCGCTTTGCCAATAGACT 58.518 52.632 0.00 0.00 0.00 3.24
4460 4632 1.663695 GCCGCTTTGCCAATAGACTA 58.336 50.000 0.00 0.00 0.00 2.59
4461 4633 2.222027 GCCGCTTTGCCAATAGACTAT 58.778 47.619 0.00 0.00 0.00 2.12
4462 4634 2.618709 GCCGCTTTGCCAATAGACTATT 59.381 45.455 1.63 1.63 0.00 1.73
4463 4635 3.813166 GCCGCTTTGCCAATAGACTATTA 59.187 43.478 7.40 0.00 0.00 0.98
4464 4636 4.083802 GCCGCTTTGCCAATAGACTATTAG 60.084 45.833 7.40 1.98 0.00 1.73
4465 4637 4.452455 CCGCTTTGCCAATAGACTATTAGG 59.548 45.833 7.40 11.80 0.00 2.69
4466 4638 4.083802 CGCTTTGCCAATAGACTATTAGGC 60.084 45.833 25.94 25.94 40.05 3.93
4524 4700 9.956640 TGTCACCATGCATGTTATTATATATGA 57.043 29.630 24.58 9.34 0.00 2.15
4547 4726 6.644592 TGAAAAAGAAGACACTTTGTTTGTGG 59.355 34.615 0.00 0.00 39.57 4.17
4548 4727 4.718940 AAGAAGACACTTTGTTTGTGGG 57.281 40.909 0.00 0.00 39.52 4.61
4549 4728 3.963129 AGAAGACACTTTGTTTGTGGGA 58.037 40.909 0.00 0.00 39.52 4.37
4554 4733 4.638865 AGACACTTTGTTTGTGGGAAGTAC 59.361 41.667 0.00 0.00 39.52 2.73
4666 4848 1.671328 CTTGGTCATCATCAGCAGCAG 59.329 52.381 0.00 0.00 0.00 4.24
4695 4877 8.476064 TCATGCAATTTGTAACACCCATATAT 57.524 30.769 0.00 0.00 0.00 0.86
4696 4878 8.575589 TCATGCAATTTGTAACACCCATATATC 58.424 33.333 0.00 0.00 0.00 1.63
4698 4880 8.298729 TGCAATTTGTAACACCCATATATCAA 57.701 30.769 0.00 0.00 0.00 2.57
4699 4881 8.922237 TGCAATTTGTAACACCCATATATCAAT 58.078 29.630 0.00 0.00 0.00 2.57
4700 4882 9.195411 GCAATTTGTAACACCCATATATCAATG 57.805 33.333 0.00 0.00 0.00 2.82
4704 4886 8.675705 TTGTAACACCCATATATCAATGACTG 57.324 34.615 0.00 0.00 0.00 3.51
4705 4887 8.028652 TGTAACACCCATATATCAATGACTGA 57.971 34.615 0.00 0.00 38.81 3.41
4743 4928 9.722056 GCATAAACTTTGATCAATTTCGAGTAT 57.278 29.630 9.40 0.00 0.00 2.12
4751 4936 7.246674 TGATCAATTTCGAGTATTGGCTTAC 57.753 36.000 17.22 8.81 34.51 2.34
4766 4951 2.487986 GGCTTACCAGGGATGATGAAGG 60.488 54.545 0.00 0.00 35.26 3.46
4771 4956 0.466922 CAGGGATGATGAAGGTGGCC 60.467 60.000 0.00 0.00 0.00 5.36
4773 4958 2.189499 GGATGATGAAGGTGGCCGC 61.189 63.158 8.12 8.12 0.00 6.53
4789 4974 0.596600 CCGCAAATGCATGGCAGATC 60.597 55.000 19.85 0.00 43.65 2.75
4790 4975 0.101579 CGCAAATGCATGGCAGATCA 59.898 50.000 19.85 0.00 43.65 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 7.830940 AAAATGATGCTCGCAATTTTTATGA 57.169 28.000 7.94 0.00 0.00 2.15
47 48 4.260579 CGGTGTATAAAATGATGCTCGCAA 60.261 41.667 0.00 0.00 0.00 4.85
69 71 4.272504 ACACGGAGCACCATATATTTTTCG 59.727 41.667 0.00 0.00 35.59 3.46
79 81 0.740868 CGATCAACACGGAGCACCAT 60.741 55.000 0.00 0.00 35.59 3.55
99 101 4.019501 GCTCCTCATATGACCATTGGATCT 60.020 45.833 10.37 0.00 0.00 2.75
130 132 0.038251 GAAGGGGCTTTTCGCAAAGG 60.038 55.000 9.58 0.00 40.03 3.11
137 139 3.147553 AGACTCTTGAAGGGGCTTTTC 57.852 47.619 0.00 0.00 0.00 2.29
148 150 8.812972 ACCTACATGTAATTACAAGACTCTTGA 58.187 33.333 23.67 4.42 39.99 3.02
158 160 5.630539 GCCCTTGGACCTACATGTAATTACA 60.631 44.000 20.14 20.14 40.98 2.41
168 170 1.742308 AAGAAGCCCTTGGACCTACA 58.258 50.000 0.00 0.00 32.92 2.74
169 171 3.105283 TCTAAGAAGCCCTTGGACCTAC 58.895 50.000 0.00 0.00 37.44 3.18
194 196 5.222631 CGTTGTTGGATCGAGATCATATGA 58.777 41.667 8.10 8.10 39.54 2.15
229 231 7.244192 GTGAAACAAGTAAATATCAGGTGCTC 58.756 38.462 0.00 0.00 36.32 4.26
251 253 0.174845 GGCGTGGTATGCTACTGTGA 59.825 55.000 0.00 0.00 0.00 3.58
254 256 1.599071 CAATGGCGTGGTATGCTACTG 59.401 52.381 0.00 0.00 0.00 2.74
256 258 1.597663 GACAATGGCGTGGTATGCTAC 59.402 52.381 0.00 0.00 0.00 3.58
257 259 1.484653 AGACAATGGCGTGGTATGCTA 59.515 47.619 0.00 0.00 0.00 3.49
293 295 7.437862 TGTGATGAAAATTAGACTGTTTTTGCC 59.562 33.333 2.89 0.00 0.00 4.52
306 309 9.434420 GAACCCATTCAATTGTGATGAAAATTA 57.566 29.630 19.30 0.00 39.98 1.40
342 345 6.762661 CCAAAAACAACTTGATGGTCAGATTT 59.237 34.615 0.00 0.00 0.00 2.17
348 351 7.552458 AAAATCCAAAAACAACTTGATGGTC 57.448 32.000 0.00 0.00 0.00 4.02
410 413 2.158559 TGATGCCAGCGTAAAACATGT 58.841 42.857 0.00 0.00 0.00 3.21
451 456 2.349590 TCAGGTGAGATGCAATTGACG 58.650 47.619 10.34 0.00 0.00 4.35
478 483 3.025322 TCAAACCACTCAACCATTGGT 57.975 42.857 1.37 1.37 45.95 3.67
479 484 3.636300 TCTTCAAACCACTCAACCATTGG 59.364 43.478 0.00 0.00 36.39 3.16
480 485 4.261741 CCTCTTCAAACCACTCAACCATTG 60.262 45.833 0.00 0.00 0.00 2.82
481 486 3.891366 CCTCTTCAAACCACTCAACCATT 59.109 43.478 0.00 0.00 0.00 3.16
482 487 3.490348 CCTCTTCAAACCACTCAACCAT 58.510 45.455 0.00 0.00 0.00 3.55
483 488 2.422803 CCCTCTTCAAACCACTCAACCA 60.423 50.000 0.00 0.00 0.00 3.67
484 489 2.158667 TCCCTCTTCAAACCACTCAACC 60.159 50.000 0.00 0.00 0.00 3.77
485 490 3.142174 CTCCCTCTTCAAACCACTCAAC 58.858 50.000 0.00 0.00 0.00 3.18
486 491 2.777692 ACTCCCTCTTCAAACCACTCAA 59.222 45.455 0.00 0.00 0.00 3.02
487 492 2.104792 CACTCCCTCTTCAAACCACTCA 59.895 50.000 0.00 0.00 0.00 3.41
488 493 2.551071 CCACTCCCTCTTCAAACCACTC 60.551 54.545 0.00 0.00 0.00 3.51
489 494 1.421646 CCACTCCCTCTTCAAACCACT 59.578 52.381 0.00 0.00 0.00 4.00
490 495 1.143073 ACCACTCCCTCTTCAAACCAC 59.857 52.381 0.00 0.00 0.00 4.16
491 496 1.142870 CACCACTCCCTCTTCAAACCA 59.857 52.381 0.00 0.00 0.00 3.67
492 497 1.897560 CACCACTCCCTCTTCAAACC 58.102 55.000 0.00 0.00 0.00 3.27
493 498 1.202818 AGCACCACTCCCTCTTCAAAC 60.203 52.381 0.00 0.00 0.00 2.93
494 499 1.072331 GAGCACCACTCCCTCTTCAAA 59.928 52.381 0.00 0.00 39.75 2.69
495 500 0.687354 GAGCACCACTCCCTCTTCAA 59.313 55.000 0.00 0.00 39.75 2.69
496 501 2.366469 GAGCACCACTCCCTCTTCA 58.634 57.895 0.00 0.00 39.75 3.02
511 516 1.250840 ATTTTTGGTGGGCCGAGAGC 61.251 55.000 0.00 0.00 42.60 4.09
515 520 1.414158 TTTGATTTTTGGTGGGCCGA 58.586 45.000 0.00 0.00 37.67 5.54
526 531 4.803613 GCGTCAAACCTGAGTTTTGATTTT 59.196 37.500 8.41 0.00 43.82 1.82
528 533 3.632145 AGCGTCAAACCTGAGTTTTGATT 59.368 39.130 8.41 0.00 43.82 2.57
535 540 1.308998 CCAAAGCGTCAAACCTGAGT 58.691 50.000 0.00 0.00 30.14 3.41
537 542 1.021202 CACCAAAGCGTCAAACCTGA 58.979 50.000 0.00 0.00 0.00 3.86
547 552 6.603237 TCATATTAATGAGACACCAAAGCG 57.397 37.500 0.00 0.00 37.20 4.68
569 574 8.077386 TGGGAACGTTGTGAAATATAAAGTTTC 58.923 33.333 5.00 0.00 33.66 2.78
570 575 7.942990 TGGGAACGTTGTGAAATATAAAGTTT 58.057 30.769 5.00 0.00 33.66 2.66
575 580 6.107343 TCGATGGGAACGTTGTGAAATATAA 58.893 36.000 5.00 0.00 32.16 0.98
578 583 3.927854 TCGATGGGAACGTTGTGAAATA 58.072 40.909 5.00 0.00 32.16 1.40
579 584 2.773487 TCGATGGGAACGTTGTGAAAT 58.227 42.857 5.00 0.00 32.16 2.17
583 588 0.645355 CGATCGATGGGAACGTTGTG 59.355 55.000 10.26 0.00 36.33 3.33
588 593 0.810031 AAAGGCGATCGATGGGAACG 60.810 55.000 21.57 0.00 43.08 3.95
608 613 0.106619 AGGGAGTAGTAGTGCCTCCG 60.107 60.000 12.11 0.00 44.71 4.63
611 616 4.448054 GGAATAGAGGGAGTAGTAGTGCCT 60.448 50.000 17.38 17.38 42.52 4.75
621 626 9.822727 TTGAATTTAAAAAGGAATAGAGGGAGT 57.177 29.630 0.00 0.00 0.00 3.85
642 647 9.525826 ACTCAAATCTTAGAAATGGTCTTGAAT 57.474 29.630 0.00 0.00 37.84 2.57
643 648 8.924511 ACTCAAATCTTAGAAATGGTCTTGAA 57.075 30.769 0.00 0.00 37.84 2.69
687 692 9.524106 CCACTAAAATACGTCTACATACATTCA 57.476 33.333 0.00 0.00 0.00 2.57
688 693 8.975439 CCCACTAAAATACGTCTACATACATTC 58.025 37.037 0.00 0.00 0.00 2.67
689 694 7.440255 GCCCACTAAAATACGTCTACATACATT 59.560 37.037 0.00 0.00 0.00 2.71
690 695 6.927381 GCCCACTAAAATACGTCTACATACAT 59.073 38.462 0.00 0.00 0.00 2.29
691 696 6.127394 TGCCCACTAAAATACGTCTACATACA 60.127 38.462 0.00 0.00 0.00 2.29
692 697 6.275335 TGCCCACTAAAATACGTCTACATAC 58.725 40.000 0.00 0.00 0.00 2.39
693 698 6.321945 TCTGCCCACTAAAATACGTCTACATA 59.678 38.462 0.00 0.00 0.00 2.29
694 699 5.128171 TCTGCCCACTAAAATACGTCTACAT 59.872 40.000 0.00 0.00 0.00 2.29
695 700 4.463539 TCTGCCCACTAAAATACGTCTACA 59.536 41.667 0.00 0.00 0.00 2.74
696 701 5.002464 TCTGCCCACTAAAATACGTCTAC 57.998 43.478 0.00 0.00 0.00 2.59
697 702 5.864418 ATCTGCCCACTAAAATACGTCTA 57.136 39.130 0.00 0.00 0.00 2.59
698 703 4.755266 ATCTGCCCACTAAAATACGTCT 57.245 40.909 0.00 0.00 0.00 4.18
699 704 4.873827 TGAATCTGCCCACTAAAATACGTC 59.126 41.667 0.00 0.00 0.00 4.34
700 705 4.634443 GTGAATCTGCCCACTAAAATACGT 59.366 41.667 0.00 0.00 0.00 3.57
701 706 4.035208 GGTGAATCTGCCCACTAAAATACG 59.965 45.833 0.00 0.00 33.99 3.06
702 707 4.338400 GGGTGAATCTGCCCACTAAAATAC 59.662 45.833 8.22 0.00 44.23 1.89
703 708 4.532834 GGGTGAATCTGCCCACTAAAATA 58.467 43.478 8.22 0.00 44.23 1.40
704 709 3.365472 GGGTGAATCTGCCCACTAAAAT 58.635 45.455 8.22 0.00 44.23 1.82
705 710 2.802719 GGGTGAATCTGCCCACTAAAA 58.197 47.619 8.22 0.00 44.23 1.52
706 711 1.339631 CGGGTGAATCTGCCCACTAAA 60.340 52.381 12.38 0.00 45.07 1.85
707 712 0.251916 CGGGTGAATCTGCCCACTAA 59.748 55.000 12.38 0.00 45.07 2.24
708 713 0.907704 ACGGGTGAATCTGCCCACTA 60.908 55.000 12.38 0.00 45.07 2.74
709 714 1.779061 AACGGGTGAATCTGCCCACT 61.779 55.000 12.38 0.00 45.07 4.00
710 715 0.893727 AAACGGGTGAATCTGCCCAC 60.894 55.000 12.38 0.00 45.07 4.61
711 716 0.178975 AAAACGGGTGAATCTGCCCA 60.179 50.000 12.38 0.00 45.07 5.36
712 717 0.243636 CAAAACGGGTGAATCTGCCC 59.756 55.000 3.91 3.91 41.45 5.36
713 718 0.388520 GCAAAACGGGTGAATCTGCC 60.389 55.000 0.00 0.00 0.00 4.85
714 719 0.388520 GGCAAAACGGGTGAATCTGC 60.389 55.000 0.00 0.00 0.00 4.26
715 720 0.958091 TGGCAAAACGGGTGAATCTG 59.042 50.000 0.00 0.00 0.00 2.90
716 721 0.958822 GTGGCAAAACGGGTGAATCT 59.041 50.000 0.00 0.00 0.00 2.40
717 722 0.038618 GGTGGCAAAACGGGTGAATC 60.039 55.000 0.00 0.00 0.00 2.52
718 723 1.801309 CGGTGGCAAAACGGGTGAAT 61.801 55.000 0.00 0.00 0.00 2.57
719 724 2.482333 CGGTGGCAAAACGGGTGAA 61.482 57.895 0.00 0.00 0.00 3.18
720 725 2.902846 CGGTGGCAAAACGGGTGA 60.903 61.111 0.00 0.00 0.00 4.02
721 726 4.639171 GCGGTGGCAAAACGGGTG 62.639 66.667 9.09 0.00 39.62 4.61
722 727 4.887190 AGCGGTGGCAAAACGGGT 62.887 61.111 9.09 0.00 43.41 5.28
723 728 3.601685 AAGCGGTGGCAAAACGGG 61.602 61.111 9.09 0.00 43.41 5.28
724 729 2.354539 CAAGCGGTGGCAAAACGG 60.355 61.111 9.09 0.00 43.41 4.44
725 730 2.354539 CCAAGCGGTGGCAAAACG 60.355 61.111 0.00 0.00 41.72 3.60
928 939 2.943653 CTCGTTGGTTTCGTGGCC 59.056 61.111 0.00 0.00 0.00 5.36
943 954 3.151022 CTCCCTCTCCACCCGCTC 61.151 72.222 0.00 0.00 0.00 5.03
944 955 4.787280 CCTCCCTCTCCACCCGCT 62.787 72.222 0.00 0.00 0.00 5.52
945 956 4.779733 TCCTCCCTCTCCACCCGC 62.780 72.222 0.00 0.00 0.00 6.13
946 957 1.834822 GATCCTCCCTCTCCACCCG 60.835 68.421 0.00 0.00 0.00 5.28
947 958 1.460497 GGATCCTCCCTCTCCACCC 60.460 68.421 3.84 0.00 0.00 4.61
948 959 1.834822 CGGATCCTCCCTCTCCACC 60.835 68.421 10.75 0.00 31.13 4.61
950 961 2.609339 CCGGATCCTCCCTCTCCA 59.391 66.667 10.75 0.00 31.13 3.86
952 963 2.920384 GCCCGGATCCTCCCTCTC 60.920 72.222 10.75 0.00 31.13 3.20
953 964 4.565850 GGCCCGGATCCTCCCTCT 62.566 72.222 10.75 0.00 31.13 3.69
1246 1286 4.825679 GGGGAGGGGAGGTGGAGG 62.826 77.778 0.00 0.00 0.00 4.30
1247 1287 3.700350 AGGGGAGGGGAGGTGGAG 61.700 72.222 0.00 0.00 0.00 3.86
1253 1293 2.883316 AATTGGGGAGGGGAGGGGAG 62.883 65.000 0.00 0.00 0.00 4.30
1257 1297 0.921256 AGTGAATTGGGGAGGGGAGG 60.921 60.000 0.00 0.00 0.00 4.30
1281 1322 2.104359 ATTTGGGGACATGGTGGGCA 62.104 55.000 0.00 0.00 42.32 5.36
1282 1327 1.306056 ATTTGGGGACATGGTGGGC 60.306 57.895 0.00 0.00 42.32 5.36
1316 1361 1.599047 CAATCAGACCAGGCGACCT 59.401 57.895 0.00 0.00 0.00 3.85
1317 1362 2.109126 GCAATCAGACCAGGCGACC 61.109 63.158 0.00 0.00 0.00 4.79
1328 1373 1.806511 CAATTCACGCTCGCAATCAG 58.193 50.000 0.00 0.00 0.00 2.90
1329 1374 0.179192 GCAATTCACGCTCGCAATCA 60.179 50.000 0.00 0.00 0.00 2.57
1341 1386 0.107263 TAGCCGAGGCATGCAATTCA 60.107 50.000 21.36 0.00 44.88 2.57
1360 1405 4.499865 CCCGTATGATGACGACAAGAATCT 60.500 45.833 0.00 0.00 45.82 2.40
1363 1408 2.756207 TCCCGTATGATGACGACAAGAA 59.244 45.455 0.00 0.00 45.82 2.52
1368 1413 2.404215 CCAATCCCGTATGATGACGAC 58.596 52.381 0.00 0.00 45.82 4.34
1371 1434 1.697432 TCCCCAATCCCGTATGATGAC 59.303 52.381 0.00 0.00 0.00 3.06
1379 1442 2.908015 CATCGTCCCCAATCCCGT 59.092 61.111 0.00 0.00 0.00 5.28
1498 1611 3.560636 ATTCCCCAACACTTATCTCCG 57.439 47.619 0.00 0.00 0.00 4.63
1518 1633 1.067776 ACGAACACAAAACGGCCAAAA 60.068 42.857 2.24 0.00 0.00 2.44
1527 1642 4.449743 CCTAGGAAATCGACGAACACAAAA 59.550 41.667 1.05 0.00 0.00 2.44
1547 1662 1.139654 CTGCCTGCACAGCTAATCCTA 59.860 52.381 5.62 0.00 0.00 2.94
1560 1675 3.117171 CGTCAGTGAGCTGCCTGC 61.117 66.667 0.00 0.00 42.29 4.85
1588 1703 7.611467 TCAATAAGGGATAATCATGAAATCGGG 59.389 37.037 0.00 0.00 0.00 5.14
1590 1705 8.180267 GCTCAATAAGGGATAATCATGAAATCG 58.820 37.037 0.00 0.00 0.00 3.34
1627 1744 4.538089 AGGCCTGAGAAAAGAAATCCTAGT 59.462 41.667 3.11 0.00 0.00 2.57
1633 1750 4.508662 CGAGTAGGCCTGAGAAAAGAAAT 58.491 43.478 17.99 0.00 0.00 2.17
1654 1771 2.804828 GAAAGTCAGGGGAGGTGGCG 62.805 65.000 0.00 0.00 0.00 5.69
1716 1836 5.807520 CGAGCAGAACAGTACAGAATTATGT 59.192 40.000 11.02 11.02 37.19 2.29
1717 1837 5.276584 GCGAGCAGAACAGTACAGAATTATG 60.277 44.000 0.00 0.00 0.00 1.90
1719 1839 4.082190 AGCGAGCAGAACAGTACAGAATTA 60.082 41.667 0.00 0.00 0.00 1.40
1720 1840 2.996621 GCGAGCAGAACAGTACAGAATT 59.003 45.455 0.00 0.00 0.00 2.17
1722 1842 1.613925 AGCGAGCAGAACAGTACAGAA 59.386 47.619 0.00 0.00 0.00 3.02
1724 1844 1.336332 ACAGCGAGCAGAACAGTACAG 60.336 52.381 0.00 0.00 0.00 2.74
1725 1845 0.673985 ACAGCGAGCAGAACAGTACA 59.326 50.000 0.00 0.00 0.00 2.90
1726 1846 1.784525 AACAGCGAGCAGAACAGTAC 58.215 50.000 0.00 0.00 0.00 2.73
1727 1847 3.653539 TTAACAGCGAGCAGAACAGTA 57.346 42.857 0.00 0.00 0.00 2.74
1728 1848 2.526304 TTAACAGCGAGCAGAACAGT 57.474 45.000 0.00 0.00 0.00 3.55
1729 1849 2.802816 ACTTTAACAGCGAGCAGAACAG 59.197 45.455 0.00 0.00 0.00 3.16
1754 1874 2.079158 CAGGCGACATCACTTGTGATT 58.921 47.619 12.95 5.98 39.18 2.57
1796 1916 0.800631 ATGATTGACAGCGTGCACAG 59.199 50.000 18.64 10.86 0.00 3.66
1806 1926 2.028420 AGCGCTGCTAATGATTGACA 57.972 45.000 10.39 0.00 36.99 3.58
1966 2091 4.184629 GTCTGCTAAATCCGACAAGACAT 58.815 43.478 0.00 0.00 0.00 3.06
2090 2216 1.265095 GCATATGACGAAGGGCACATG 59.735 52.381 6.97 0.00 0.00 3.21
2108 2234 1.306654 AGGGTAGAACGGGATGGCA 60.307 57.895 0.00 0.00 0.00 4.92
2226 2352 3.881688 GGATGCACAGACAATTAGAGCAT 59.118 43.478 0.00 0.00 43.17 3.79
2402 2530 0.969894 ACTTCAAGACTGCGGCTAGT 59.030 50.000 0.00 3.03 0.00 2.57
2407 2535 0.514691 GCTGAACTTCAAGACTGCGG 59.485 55.000 0.00 0.00 0.00 5.69
2412 2540 4.795278 CACAAAACAGCTGAACTTCAAGAC 59.205 41.667 23.35 0.00 0.00 3.01
2418 2546 3.119029 ACATGCACAAAACAGCTGAACTT 60.119 39.130 23.35 7.69 0.00 2.66
2426 2554 4.539870 CTTCAGGTACATGCACAAAACAG 58.460 43.478 1.79 0.00 0.00 3.16
2471 2599 7.119407 AGCAATTGATATTATAGCAGCAGACAG 59.881 37.037 10.34 0.00 0.00 3.51
2474 2602 6.128090 GCAGCAATTGATATTATAGCAGCAGA 60.128 38.462 10.34 0.00 33.95 4.26
2488 2616 5.978919 CCATTTGTAATACGCAGCAATTGAT 59.021 36.000 10.34 0.00 0.00 2.57
2514 2642 4.792521 TTATACCATGCAACCAACCAAC 57.207 40.909 0.00 0.00 0.00 3.77
2516 2644 7.563188 AGAATTATTATACCATGCAACCAACCA 59.437 33.333 0.00 0.00 0.00 3.67
2552 2680 9.039870 CCTTCAGATAGAAATATGAACTGTCAC 57.960 37.037 0.00 0.00 38.17 3.67
2650 2778 4.404394 TCCGCTGATAGGATTTCACAAGTA 59.596 41.667 0.00 0.00 31.86 2.24
2749 2877 2.125350 GGCCCTGAACTGCTCTCG 60.125 66.667 0.00 0.00 0.00 4.04
2772 2900 1.135575 GCACCTTTTTCATCTCCGCAG 60.136 52.381 0.00 0.00 0.00 5.18
2776 2904 3.192212 CCTTCTGCACCTTTTTCATCTCC 59.808 47.826 0.00 0.00 0.00 3.71
2819 2947 0.106708 GTGTGTGCAGGACTCAAGGA 59.893 55.000 0.00 0.00 30.00 3.36
2822 2950 0.541392 AGTGTGTGTGCAGGACTCAA 59.459 50.000 0.00 0.00 30.00 3.02
3157 3285 9.078753 GTAAACATACTCAGAGTAAAAGAGAGC 57.921 37.037 14.46 0.00 33.89 4.09
3176 3304 5.046878 TGAAGACGATACAGTGGGTAAACAT 60.047 40.000 0.00 0.00 35.14 2.71
3441 3581 2.033424 GGCAACAAAGAGTTCTGTGTCC 59.967 50.000 5.46 0.73 43.31 4.02
3489 3629 1.985662 ATAGAACACCCGTGGCCGA 60.986 57.895 0.00 0.00 35.63 5.54
3501 3641 6.094048 TCAAAGCCAAAGTAGCATCATAGAAC 59.906 38.462 0.00 0.00 0.00 3.01
3523 3663 1.068333 GCAGATTCCAAGCGCTTTCAA 60.068 47.619 22.51 16.23 0.00 2.69
3565 3705 9.830975 ACTAATTTTGCACTTTTTCAATTAGGT 57.169 25.926 11.99 0.00 38.03 3.08
3573 3713 7.532682 TTGTGGACTAATTTTGCACTTTTTC 57.467 32.000 11.15 0.00 36.35 2.29
3588 3728 9.305555 AGTAAACACTAACTCTATTGTGGACTA 57.694 33.333 0.00 0.00 35.02 2.59
3599 3739 6.496144 AGGGAAACAGTAAACACTAACTCT 57.504 37.500 0.00 0.00 0.00 3.24
3658 3798 3.466791 CTCCCATTGGCGCTCCGAT 62.467 63.158 7.64 0.00 36.91 4.18
3816 3956 4.158394 GGATGGCAGTCATTCTTGCTTTTA 59.842 41.667 0.00 0.00 35.97 1.52
3938 4080 1.364901 CCAGCAAGTTTGGCACTGG 59.635 57.895 5.32 5.32 41.78 4.00
3964 4106 3.844211 AGGTACAGGGCACTATGAAGAAA 59.156 43.478 0.00 0.00 0.00 2.52
3965 4107 3.450904 AGGTACAGGGCACTATGAAGAA 58.549 45.455 0.00 0.00 0.00 2.52
3992 4134 0.390866 CACAGTGCTGAGGCTGGTAG 60.391 60.000 6.17 0.00 39.59 3.18
4000 4142 2.033141 CACCCCCACAGTGCTGAG 59.967 66.667 6.17 0.00 0.00 3.35
4014 4172 0.321346 CTTGGGAAATTGGCCACACC 59.679 55.000 3.88 6.53 39.84 4.16
4020 4178 2.167075 CCACTGATCTTGGGAAATTGGC 59.833 50.000 6.13 0.00 0.00 4.52
4094 4252 1.726853 GCTCGTTTGCTGACCATAGT 58.273 50.000 0.00 0.00 0.00 2.12
4114 4272 1.014352 AGTTTTGTCACGTGTCCTGC 58.986 50.000 16.51 3.28 0.00 4.85
4123 4281 6.621596 GCATCCAAGAGACATAGTTTTGTCAC 60.622 42.308 7.28 1.23 46.81 3.67
4152 4310 7.161773 ACACTTCCCACATGAAGATATTTTG 57.838 36.000 0.00 0.00 43.60 2.44
4171 4329 3.813166 CCCACTCACGATTTACAACACTT 59.187 43.478 0.00 0.00 0.00 3.16
4184 4343 4.002982 TCATTTCTTGATTCCCACTCACG 58.997 43.478 0.00 0.00 0.00 4.35
4236 4395 1.003233 GGTGGGCAAGAGGACAGAC 60.003 63.158 0.00 0.00 0.00 3.51
4237 4396 2.224159 GGGTGGGCAAGAGGACAGA 61.224 63.158 0.00 0.00 0.00 3.41
4238 4397 2.352805 GGGTGGGCAAGAGGACAG 59.647 66.667 0.00 0.00 0.00 3.51
4239 4398 2.449518 TGGGTGGGCAAGAGGACA 60.450 61.111 0.00 0.00 0.00 4.02
4257 4416 3.130633 GCCTCCAACCAAACATGTTTTC 58.869 45.455 21.10 0.00 0.00 2.29
4290 4449 2.080654 TCCCTTGACCCAAACAAAGG 57.919 50.000 0.00 0.00 32.13 3.11
4369 4528 4.767255 CGGGTGAGGCAGGCAGAC 62.767 72.222 0.00 0.00 0.00 3.51
4381 4553 4.785453 GAAGGGAGCAGGCGGGTG 62.785 72.222 0.00 0.00 0.00 4.61
4384 4556 4.479993 CAGGAAGGGAGCAGGCGG 62.480 72.222 0.00 0.00 0.00 6.13
4386 4558 4.811364 GGCAGGAAGGGAGCAGGC 62.811 72.222 0.00 0.00 0.00 4.85
4387 4559 2.549169 GAAGGCAGGAAGGGAGCAGG 62.549 65.000 0.00 0.00 0.00 4.85
4388 4560 1.077858 GAAGGCAGGAAGGGAGCAG 60.078 63.158 0.00 0.00 0.00 4.24
4389 4561 1.539869 AGAAGGCAGGAAGGGAGCA 60.540 57.895 0.00 0.00 0.00 4.26
4408 4580 4.614555 TTGGCAAAGCAGTAATCATACG 57.385 40.909 0.00 0.00 37.11 3.06
4442 4614 4.452455 CCTAATAGTCTATTGGCAAAGCGG 59.548 45.833 14.32 0.00 0.00 5.52
4443 4615 4.083802 GCCTAATAGTCTATTGGCAAAGCG 60.084 45.833 25.53 10.20 39.73 4.68
4444 4616 4.216472 GGCCTAATAGTCTATTGGCAAAGC 59.784 45.833 28.38 18.84 40.72 3.51
4445 4617 5.471456 CAGGCCTAATAGTCTATTGGCAAAG 59.529 44.000 28.38 20.04 40.72 2.77
4446 4618 5.104109 ACAGGCCTAATAGTCTATTGGCAAA 60.104 40.000 28.38 8.99 40.72 3.68
4447 4619 4.412199 ACAGGCCTAATAGTCTATTGGCAA 59.588 41.667 28.38 0.68 40.72 4.52
4448 4620 3.973973 ACAGGCCTAATAGTCTATTGGCA 59.026 43.478 28.38 9.52 40.72 4.92
4449 4621 4.625607 ACAGGCCTAATAGTCTATTGGC 57.374 45.455 23.97 23.97 39.48 4.52
4450 4622 5.998363 GGAAACAGGCCTAATAGTCTATTGG 59.002 44.000 3.98 11.40 0.00 3.16
4451 4623 6.708054 CAGGAAACAGGCCTAATAGTCTATTG 59.292 42.308 3.98 5.51 33.51 1.90
4452 4624 6.615726 TCAGGAAACAGGCCTAATAGTCTATT 59.384 38.462 3.98 9.98 33.51 1.73
4453 4625 6.143915 TCAGGAAACAGGCCTAATAGTCTAT 58.856 40.000 3.98 0.00 33.51 1.98
4454 4626 5.525484 TCAGGAAACAGGCCTAATAGTCTA 58.475 41.667 3.98 0.00 33.51 2.59
4455 4627 4.362677 TCAGGAAACAGGCCTAATAGTCT 58.637 43.478 3.98 0.00 33.51 3.24
4456 4628 4.755266 TCAGGAAACAGGCCTAATAGTC 57.245 45.455 3.98 0.00 33.51 2.59
4457 4629 4.475016 ACATCAGGAAACAGGCCTAATAGT 59.525 41.667 3.98 0.00 33.51 2.12
4458 4630 5.041191 ACATCAGGAAACAGGCCTAATAG 57.959 43.478 3.98 0.00 33.51 1.73
4459 4631 6.174720 CTACATCAGGAAACAGGCCTAATA 57.825 41.667 3.98 0.00 33.51 0.98
4460 4632 5.041191 CTACATCAGGAAACAGGCCTAAT 57.959 43.478 3.98 0.00 33.51 1.73
4461 4633 4.487714 CTACATCAGGAAACAGGCCTAA 57.512 45.455 3.98 0.00 33.51 2.69
4523 4699 6.090763 CCCACAAACAAAGTGTCTTCTTTTTC 59.909 38.462 0.00 0.00 35.77 2.29
4524 4700 5.931724 CCCACAAACAAAGTGTCTTCTTTTT 59.068 36.000 0.00 0.00 35.77 1.94
4544 4723 3.721035 ACTTTGTACACGTACTTCCCAC 58.279 45.455 8.69 0.00 37.00 4.61
4547 4726 4.805192 TCACAACTTTGTACACGTACTTCC 59.195 41.667 8.69 0.00 39.91 3.46
4548 4727 5.954434 TCACAACTTTGTACACGTACTTC 57.046 39.130 8.69 0.00 39.91 3.01
4549 4728 6.913873 ATTCACAACTTTGTACACGTACTT 57.086 33.333 8.69 0.00 39.91 2.24
4554 4733 7.956508 TTGTTAATTCACAACTTTGTACACG 57.043 32.000 1.01 0.00 39.91 4.49
4596 4778 4.873746 ATAAGCACGGTGTAGAGCATAT 57.126 40.909 10.24 0.00 0.00 1.78
4597 4779 4.825634 ACTATAAGCACGGTGTAGAGCATA 59.174 41.667 10.24 0.00 0.00 3.14
4602 4784 4.018490 TCCAACTATAAGCACGGTGTAGA 58.982 43.478 10.24 0.00 0.00 2.59
4609 4791 2.351726 GCTTGGTCCAACTATAAGCACG 59.648 50.000 0.00 0.00 42.35 5.34
4715 4900 8.246180 ACTCGAAATTGATCAAAGTTTATGCAT 58.754 29.630 13.09 3.79 0.00 3.96
4727 4912 6.260050 GGTAAGCCAATACTCGAAATTGATCA 59.740 38.462 17.50 0.00 36.61 2.92
4738 4923 3.391296 TCATCCCTGGTAAGCCAATACTC 59.609 47.826 0.00 0.00 45.51 2.59
4743 4928 2.204463 TCATCATCCCTGGTAAGCCAA 58.796 47.619 0.00 0.00 45.51 4.52
4751 4936 0.466922 GCCACCTTCATCATCCCTGG 60.467 60.000 0.00 0.00 0.00 4.45
4762 4947 2.125952 GCATTTGCGGCCACCTTC 60.126 61.111 2.24 0.00 0.00 3.46
4766 4951 2.509786 CCATGCATTTGCGGCCAC 60.510 61.111 2.24 0.00 45.83 5.01
4771 4956 0.101579 TGATCTGCCATGCATTTGCG 59.898 50.000 12.08 7.97 45.83 4.85


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

AutoCloner maintained by Alex Coulton.