Multiple sequence alignment - TraesCS5B01G435000

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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 TraesCS5B01G435000 chr5B 100.000 2848 0 0 1 2848 609597763 609600610 0.000000e+00 5260.0
1 TraesCS5B01G435000 chr5B 87.302 315 32 4 2500 2814 609927593 609927899 1.260000e-93 353.0
2 TraesCS5B01G435000 chr5B 87.179 273 27 4 2500 2767 609935499 609935768 1.280000e-78 303.0
3 TraesCS5B01G435000 chr5B 98.742 159 1 1 2351 2508 609935246 609935404 6.010000e-72 281.0
4 TraesCS5B01G435000 chr5B 80.286 350 51 13 2154 2497 609927154 609927491 6.090000e-62 248.0
5 TraesCS5B01G435000 chr5B 93.750 48 3 0 2053 2100 609604625 609604672 3.940000e-09 73.1
6 TraesCS5B01G435000 chr5B 93.750 48 3 0 2053 2100 609926851 609926898 3.940000e-09 73.1
7 TraesCS5B01G435000 chr5A 91.251 1143 63 16 732 1855 616878432 616879556 0.000000e+00 1522.0
8 TraesCS5B01G435000 chr5A 90.080 373 30 4 2138 2508 616879847 616880214 7.140000e-131 477.0
9 TraesCS5B01G435000 chr5A 90.805 348 25 5 2500 2847 616909540 616909880 2.590000e-125 459.0
10 TraesCS5B01G435000 chr5A 89.112 349 31 1 2500 2848 616880309 616880650 7.290000e-116 427.0
11 TraesCS5B01G435000 chr5A 88.406 345 33 5 2500 2844 616914296 616914633 2.640000e-110 409.0
12 TraesCS5B01G435000 chr5A 84.987 373 24 17 2157 2508 616909084 616909445 1.620000e-92 350.0
13 TraesCS5B01G435000 chr5A 88.112 286 23 6 2500 2781 616919658 616919936 2.120000e-86 329.0
14 TraesCS5B01G435000 chr5A 97.484 159 3 1 2351 2508 616914043 616914201 1.300000e-68 270.0
15 TraesCS5B01G435000 chr5A 93.711 159 9 1 2351 2508 616919405 616919563 1.320000e-58 237.0
16 TraesCS5B01G435000 chr5A 91.139 158 9 3 1 155 616877450 616877605 2.880000e-50 209.0
17 TraesCS5B01G435000 chr5D 89.138 1206 67 31 699 1855 493833319 493834509 0.000000e+00 1443.0
18 TraesCS5B01G435000 chr5D 91.196 443 27 8 50 480 493832738 493833180 2.440000e-165 592.0
19 TraesCS5B01G435000 chr5D 88.189 381 31 4 2138 2508 493834817 493835193 2.600000e-120 442.0
20 TraesCS5B01G435000 chr5D 92.704 233 17 0 2531 2763 493835494 493835726 1.260000e-88 337.0
21 TraesCS5B01G435000 chr5D 91.213 239 18 2 2507 2742 494042254 494042016 3.540000e-84 322.0
22 TraesCS5B01G435000 chr5D 87.589 282 24 6 2503 2780 494053084 494052810 1.650000e-82 316.0
23 TraesCS5B01G435000 chr5D 96.104 154 6 0 2351 2504 494053340 494053187 4.710000e-63 252.0
24 TraesCS5B01G435000 chr5D 96.226 106 3 1 474 578 493833203 493833308 3.770000e-39 172.0
25 TraesCS5B01G435000 chr5D 83.077 130 9 6 1982 2099 493834589 493834717 3.880000e-19 106.0
26 TraesCS5B01G435000 chr3D 86.828 372 31 8 977 1334 471044606 471044239 1.590000e-107 399.0
27 TraesCS5B01G435000 chr1A 76.419 229 54 0 1591 1819 99234881 99235109 1.070000e-24 124.0
28 TraesCS5B01G435000 chr7A 80.137 146 27 2 1009 1153 707975723 707975579 1.080000e-19 108.0
29 TraesCS5B01G435000 chr7A 80.000 145 29 0 1009 1153 708116337 708116193 1.080000e-19 108.0
30 TraesCS5B01G435000 chr1B 79.710 138 28 0 1591 1728 133481979 133482116 1.810000e-17 100.0
31 TraesCS5B01G435000 chr1B 77.160 162 37 0 1567 1728 133032942 133033103 8.400000e-16 95.3
32 TraesCS5B01G435000 chr1D 74.554 224 57 0 1567 1790 80817474 80817697 6.490000e-17 99.0
33 TraesCS5B01G435000 chr7B 81.416 113 19 2 1042 1153 713181804 713181693 1.090000e-14 91.6
34 TraesCS5B01G435000 chr7B 85.542 83 10 2 1010 1090 708091327 708091245 5.060000e-13 86.1


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 TraesCS5B01G435000 chr5B 609597763 609600610 2847 False 5260.000000 5260 100.000000 1 2848 1 chr5B.!!$F1 2847
1 TraesCS5B01G435000 chr5B 609935246 609935768 522 False 292.000000 303 92.960500 2351 2767 2 chr5B.!!$F4 416
2 TraesCS5B01G435000 chr5B 609926851 609927899 1048 False 224.700000 353 87.112667 2053 2814 3 chr5B.!!$F3 761
3 TraesCS5B01G435000 chr5A 616877450 616880650 3200 False 658.750000 1522 90.395500 1 2848 4 chr5A.!!$F1 2847
4 TraesCS5B01G435000 chr5A 616909084 616909880 796 False 404.500000 459 87.896000 2157 2847 2 chr5A.!!$F2 690
5 TraesCS5B01G435000 chr5A 616914043 616914633 590 False 339.500000 409 92.945000 2351 2844 2 chr5A.!!$F3 493
6 TraesCS5B01G435000 chr5A 616919405 616919936 531 False 283.000000 329 90.911500 2351 2781 2 chr5A.!!$F4 430
7 TraesCS5B01G435000 chr5D 493832738 493835726 2988 False 515.333333 1443 90.088333 50 2763 6 chr5D.!!$F1 2713
8 TraesCS5B01G435000 chr5D 494052810 494053340 530 True 284.000000 316 91.846500 2351 2780 2 chr5D.!!$R2 429

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
667 1264 0.029834 CGGGAAATGCAGCTATGTGC 59.970 55.0 0.00 0.0 44.27 4.57 F
684 1281 0.238817 TGCGCGCGTCCTTTTTATTT 59.761 45.0 32.35 0.0 0.00 1.40 F
876 1495 0.595095 GGTGTACGACGTCTTGGACT 59.405 55.0 14.70 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1580 2234 0.66178 CGCCGATGATCTTCTCGTCC 60.662 60.0 6.99 0.84 36.68 4.79 R
1703 2357 0.89694 AGTAGTGCGTCTCGGGGAAA 60.897 55.0 0.00 0.00 0.00 3.13 R
2615 3809 0.93031 CCCGTGCATGAACTACATCG 59.070 55.0 7.72 0.00 37.07 3.84 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
179 739 4.662468 TGCTTTTTCCAGCACATTTACA 57.338 36.364 0.00 0.00 45.14 2.41
188 748 3.306225 CCAGCACATTTACACAGCCAAAT 60.306 43.478 0.00 0.00 0.00 2.32
230 791 4.395231 GCCATACTTGTAGGAAAAGTGACC 59.605 45.833 0.00 0.00 38.32 4.02
294 856 6.966534 ATTAAATTTCCAGTGGAGCATAGG 57.033 37.500 12.67 0.00 31.21 2.57
360 926 3.253432 CCTGCAATCATGACCATCAGATG 59.747 47.826 14.15 3.04 0.00 2.90
416 984 5.804473 CGCCATGTTGCAATTTCTTGTTATA 59.196 36.000 0.59 0.00 34.69 0.98
427 995 9.865321 GCAATTTCTTGTTATATATCATGGCAT 57.135 29.630 0.00 0.00 34.69 4.40
434 1002 7.977789 TGTTATATATCATGGCATTTCGTGT 57.022 32.000 0.00 0.00 0.00 4.49
437 1005 0.099259 ATCATGGCATTTCGTGTGCG 59.901 50.000 0.00 0.00 43.40 5.34
448 1016 3.118454 GTGTGCGACATGTCCCCG 61.118 66.667 20.03 10.54 0.00 5.73
475 1043 8.528917 AGGTTTTTGTGTTTTTCTGAAACTAC 57.471 30.769 1.58 5.16 0.00 2.73
488 1085 7.766219 TTCTGAAACTACTAGTGTTGTTCAC 57.234 36.000 5.39 6.93 46.46 3.18
597 1194 6.718454 TTTTGATTATTGCCGACAAAATGG 57.282 33.333 0.00 0.00 39.77 3.16
599 1196 5.398603 TGATTATTGCCGACAAAATGGTT 57.601 34.783 0.00 0.00 39.77 3.67
600 1197 5.788450 TGATTATTGCCGACAAAATGGTTT 58.212 33.333 0.00 0.00 39.77 3.27
601 1198 5.866633 TGATTATTGCCGACAAAATGGTTTC 59.133 36.000 0.00 0.00 39.77 2.78
602 1199 2.126914 TTGCCGACAAAATGGTTTCG 57.873 45.000 0.00 0.00 31.21 3.46
603 1200 0.318275 TGCCGACAAAATGGTTTCGC 60.318 50.000 0.00 0.00 0.00 4.70
604 1201 0.039527 GCCGACAAAATGGTTTCGCT 60.040 50.000 0.00 0.00 0.00 4.93
605 1202 1.963747 CCGACAAAATGGTTTCGCTC 58.036 50.000 0.00 0.00 0.00 5.03
606 1203 1.265635 CCGACAAAATGGTTTCGCTCA 59.734 47.619 0.00 0.00 0.00 4.26
607 1204 2.095263 CCGACAAAATGGTTTCGCTCAT 60.095 45.455 0.00 0.00 0.00 2.90
608 1205 3.564511 CGACAAAATGGTTTCGCTCATT 58.435 40.909 0.00 0.00 35.37 2.57
609 1206 3.603770 CGACAAAATGGTTTCGCTCATTC 59.396 43.478 0.00 0.00 33.03 2.67
610 1207 3.913089 ACAAAATGGTTTCGCTCATTCC 58.087 40.909 0.00 0.00 33.03 3.01
611 1208 3.253230 CAAAATGGTTTCGCTCATTCCC 58.747 45.455 0.00 0.00 33.03 3.97
612 1209 2.514458 AATGGTTTCGCTCATTCCCT 57.486 45.000 0.00 0.00 0.00 4.20
613 1210 2.044123 ATGGTTTCGCTCATTCCCTC 57.956 50.000 0.00 0.00 0.00 4.30
614 1211 0.984230 TGGTTTCGCTCATTCCCTCT 59.016 50.000 0.00 0.00 0.00 3.69
615 1212 1.066143 TGGTTTCGCTCATTCCCTCTC 60.066 52.381 0.00 0.00 0.00 3.20
616 1213 1.657822 GTTTCGCTCATTCCCTCTCC 58.342 55.000 0.00 0.00 0.00 3.71
617 1214 0.175760 TTTCGCTCATTCCCTCTCCG 59.824 55.000 0.00 0.00 0.00 4.63
618 1215 1.676678 TTCGCTCATTCCCTCTCCGG 61.677 60.000 0.00 0.00 0.00 5.14
619 1216 2.110006 GCTCATTCCCTCTCCGGC 59.890 66.667 0.00 0.00 0.00 6.13
620 1217 2.419198 CTCATTCCCTCTCCGGCG 59.581 66.667 0.00 0.00 0.00 6.46
621 1218 3.154473 TCATTCCCTCTCCGGCGG 61.154 66.667 22.51 22.51 0.00 6.13
622 1219 3.154473 CATTCCCTCTCCGGCGGA 61.154 66.667 29.14 29.14 0.00 5.54
623 1220 2.365105 ATTCCCTCTCCGGCGGAA 60.365 61.111 30.59 18.82 39.89 4.30
624 1221 1.993391 ATTCCCTCTCCGGCGGAAA 60.993 57.895 30.59 20.74 39.07 3.13
625 1222 1.972660 ATTCCCTCTCCGGCGGAAAG 61.973 60.000 30.59 26.35 39.07 2.62
626 1223 4.162690 CCCTCTCCGGCGGAAAGG 62.163 72.222 36.07 36.07 39.56 3.11
627 1224 3.391382 CCTCTCCGGCGGAAAGGT 61.391 66.667 34.97 0.00 35.32 3.50
628 1225 2.663196 CTCTCCGGCGGAAAGGTT 59.337 61.111 30.59 0.00 0.00 3.50
629 1226 1.741770 CTCTCCGGCGGAAAGGTTG 60.742 63.158 30.59 17.01 0.00 3.77
630 1227 2.746277 CTCCGGCGGAAAGGTTGG 60.746 66.667 30.59 12.56 0.00 3.77
631 1228 3.546714 CTCCGGCGGAAAGGTTGGT 62.547 63.158 30.59 0.00 0.00 3.67
632 1229 2.596338 CCGGCGGAAAGGTTGGTT 60.596 61.111 24.41 0.00 0.00 3.67
633 1230 2.622962 CCGGCGGAAAGGTTGGTTC 61.623 63.158 24.41 0.00 0.00 3.62
634 1231 2.951458 GGCGGAAAGGTTGGTTCG 59.049 61.111 0.00 0.00 0.00 3.95
635 1232 2.254350 GCGGAAAGGTTGGTTCGC 59.746 61.111 0.00 0.00 0.00 4.70
636 1233 2.548295 GCGGAAAGGTTGGTTCGCA 61.548 57.895 0.00 0.00 0.00 5.10
637 1234 1.281656 CGGAAAGGTTGGTTCGCAC 59.718 57.895 0.00 0.00 0.00 5.34
638 1235 1.164041 CGGAAAGGTTGGTTCGCACT 61.164 55.000 0.00 0.00 0.00 4.40
639 1236 0.310854 GGAAAGGTTGGTTCGCACTG 59.689 55.000 0.00 0.00 0.00 3.66
640 1237 0.310854 GAAAGGTTGGTTCGCACTGG 59.689 55.000 0.00 0.00 0.00 4.00
641 1238 1.106944 AAAGGTTGGTTCGCACTGGG 61.107 55.000 0.00 0.00 0.00 4.45
642 1239 2.203294 GGTTGGTTCGCACTGGGT 60.203 61.111 0.00 0.00 0.00 4.51
643 1240 1.071814 GGTTGGTTCGCACTGGGTA 59.928 57.895 0.00 0.00 0.00 3.69
644 1241 0.322187 GGTTGGTTCGCACTGGGTAT 60.322 55.000 0.00 0.00 0.00 2.73
645 1242 1.084289 GTTGGTTCGCACTGGGTATC 58.916 55.000 0.00 0.00 0.00 2.24
646 1243 0.035820 TTGGTTCGCACTGGGTATCC 60.036 55.000 0.00 0.00 0.00 2.59
647 1244 1.153229 GGTTCGCACTGGGTATCCC 60.153 63.158 0.00 0.00 45.71 3.85
657 1254 1.228459 GGGTATCCCCGGGAAATGC 60.228 63.158 26.32 18.14 42.41 3.56
658 1255 1.534697 GGTATCCCCGGGAAATGCA 59.465 57.895 26.32 0.00 34.34 3.96
659 1256 0.537371 GGTATCCCCGGGAAATGCAG 60.537 60.000 26.32 2.41 34.34 4.41
660 1257 1.150536 TATCCCCGGGAAATGCAGC 59.849 57.895 26.32 0.00 34.34 5.25
661 1258 1.352622 TATCCCCGGGAAATGCAGCT 61.353 55.000 26.32 0.00 34.34 4.24
662 1259 1.352622 ATCCCCGGGAAATGCAGCTA 61.353 55.000 26.32 0.00 34.34 3.32
663 1260 1.151450 CCCCGGGAAATGCAGCTAT 59.849 57.895 26.32 0.00 0.00 2.97
664 1261 1.174712 CCCCGGGAAATGCAGCTATG 61.175 60.000 26.32 0.00 0.00 2.23
665 1262 0.466189 CCCGGGAAATGCAGCTATGT 60.466 55.000 18.48 0.00 0.00 2.29
666 1263 0.664761 CCGGGAAATGCAGCTATGTG 59.335 55.000 0.00 0.00 0.00 3.21
667 1264 0.029834 CGGGAAATGCAGCTATGTGC 59.970 55.000 0.00 0.00 44.27 4.57
677 1274 2.885644 CTATGTGCGCGCGTCCTT 60.886 61.111 32.35 20.52 0.00 3.36
678 1275 2.433491 TATGTGCGCGCGTCCTTT 60.433 55.556 32.35 14.95 0.00 3.11
679 1276 1.966493 CTATGTGCGCGCGTCCTTTT 61.966 55.000 32.35 13.87 0.00 2.27
680 1277 1.570347 TATGTGCGCGCGTCCTTTTT 61.570 50.000 32.35 12.27 0.00 1.94
681 1278 1.570347 ATGTGCGCGCGTCCTTTTTA 61.570 50.000 32.35 9.67 0.00 1.52
682 1279 1.133869 GTGCGCGCGTCCTTTTTAT 59.866 52.632 32.35 0.00 0.00 1.40
683 1280 0.453782 GTGCGCGCGTCCTTTTTATT 60.454 50.000 32.35 0.00 0.00 1.40
684 1281 0.238817 TGCGCGCGTCCTTTTTATTT 59.761 45.000 32.35 0.00 0.00 1.40
685 1282 1.333115 GCGCGCGTCCTTTTTATTTT 58.667 45.000 32.35 0.00 0.00 1.82
686 1283 1.717113 GCGCGCGTCCTTTTTATTTTT 59.283 42.857 32.35 0.00 0.00 1.94
687 1284 2.222202 GCGCGCGTCCTTTTTATTTTTC 60.222 45.455 32.35 4.24 0.00 2.29
688 1285 2.024759 CGCGCGTCCTTTTTATTTTTCG 59.975 45.455 24.19 0.00 0.00 3.46
689 1286 2.975193 GCGCGTCCTTTTTATTTTTCGT 59.025 40.909 8.43 0.00 0.00 3.85
690 1287 3.057221 GCGCGTCCTTTTTATTTTTCGTC 59.943 43.478 8.43 0.00 0.00 4.20
691 1288 3.293605 CGCGTCCTTTTTATTTTTCGTCG 59.706 43.478 0.00 0.00 0.00 5.12
692 1289 4.213674 GCGTCCTTTTTATTTTTCGTCGT 58.786 39.130 0.00 0.00 0.00 4.34
693 1290 4.316513 GCGTCCTTTTTATTTTTCGTCGTC 59.683 41.667 0.00 0.00 0.00 4.20
694 1291 4.543177 CGTCCTTTTTATTTTTCGTCGTCG 59.457 41.667 0.00 0.00 38.55 5.12
695 1292 4.842376 GTCCTTTTTATTTTTCGTCGTCGG 59.158 41.667 1.55 0.00 37.69 4.79
696 1293 4.083908 TCCTTTTTATTTTTCGTCGTCGGG 60.084 41.667 1.55 0.00 37.69 5.14
697 1294 4.319694 CCTTTTTATTTTTCGTCGTCGGGT 60.320 41.667 1.55 0.00 37.69 5.28
729 1326 1.976132 ATCCACACATCCCTGCCGAG 61.976 60.000 0.00 0.00 0.00 4.63
730 1327 2.821366 CACACATCCCTGCCGAGC 60.821 66.667 0.00 0.00 0.00 5.03
770 1380 2.868899 AGCTGCTTATTAATCAGGGCC 58.131 47.619 0.00 0.00 0.00 5.80
802 1417 2.847133 GACAATTCAGACGACGACTAGC 59.153 50.000 0.00 0.00 0.00 3.42
814 1429 1.811359 ACGACTAGCTGTCCACACTAC 59.189 52.381 0.00 0.00 42.49 2.73
876 1495 0.595095 GGTGTACGACGTCTTGGACT 59.405 55.000 14.70 0.00 0.00 3.85
893 1512 4.974399 TGGACTTTTCCTTCTTTCTCCTC 58.026 43.478 0.00 0.00 43.31 3.71
894 1513 4.202472 TGGACTTTTCCTTCTTTCTCCTCC 60.202 45.833 0.00 0.00 43.31 4.30
895 1514 4.328536 GACTTTTCCTTCTTTCTCCTCCC 58.671 47.826 0.00 0.00 0.00 4.30
896 1515 3.984090 ACTTTTCCTTCTTTCTCCTCCCT 59.016 43.478 0.00 0.00 0.00 4.20
897 1516 4.042311 ACTTTTCCTTCTTTCTCCTCCCTC 59.958 45.833 0.00 0.00 0.00 4.30
898 1517 3.569135 TTCCTTCTTTCTCCTCCCTCT 57.431 47.619 0.00 0.00 0.00 3.69
926 1547 3.146066 GGCATGCCGTATAAATCAAGGA 58.854 45.455 23.48 0.00 0.00 3.36
929 1550 2.479837 TGCCGTATAAATCAAGGAGCG 58.520 47.619 0.00 0.00 0.00 5.03
979 1604 0.982852 AGGGGAGCATCGTCATCCAA 60.983 55.000 0.00 0.00 34.62 3.53
983 1608 1.406069 GGAGCATCGTCATCCAACAGT 60.406 52.381 0.00 0.00 34.37 3.55
992 1617 3.367395 CGTCATCCAACAGTAGAGCAGAA 60.367 47.826 0.00 0.00 0.00 3.02
994 1619 3.578282 TCATCCAACAGTAGAGCAGAACA 59.422 43.478 0.00 0.00 0.00 3.18
1020 1645 3.284449 GCGCCGGTGAAGGTGTTT 61.284 61.111 21.76 0.00 43.39 2.83
1075 1700 2.204034 TGTGCCTGGAGGAGGTCA 59.796 61.111 0.00 0.00 44.97 4.02
1134 1759 4.115199 GAGCACAAGGGCCCCGAT 62.115 66.667 21.43 2.66 0.00 4.18
1160 1785 1.862201 CGCCAGAAACGTAAGAACACA 59.138 47.619 0.00 0.00 43.62 3.72
1165 1790 3.619483 CAGAAACGTAAGAACACACACCA 59.381 43.478 0.00 0.00 43.62 4.17
1166 1791 4.093703 CAGAAACGTAAGAACACACACCAA 59.906 41.667 0.00 0.00 43.62 3.67
1167 1792 4.093850 AGAAACGTAAGAACACACACCAAC 59.906 41.667 0.00 0.00 43.62 3.77
1172 1800 2.052782 AGAACACACACCAACCCTTC 57.947 50.000 0.00 0.00 0.00 3.46
1191 1830 6.153170 ACCCTTCTAGCAGAGTAGTAAGTTTC 59.847 42.308 0.00 0.00 0.00 2.78
1310 1957 2.308039 ACGCGCTTCCGTCAGTTTC 61.308 57.895 5.73 0.00 36.61 2.78
1314 1961 0.941542 CGCTTCCGTCAGTTTCCAAA 59.058 50.000 0.00 0.00 0.00 3.28
1315 1962 1.333791 CGCTTCCGTCAGTTTCCAAAC 60.334 52.381 0.00 0.00 39.17 2.93
1326 1973 7.237173 CGTCAGTTTCCAAACTCTTATTGATC 58.763 38.462 1.52 0.00 45.65 2.92
1463 2117 2.739996 CCTGCTGAGGGAAGGCGAT 61.740 63.158 0.00 0.00 33.20 4.58
1494 2148 2.745100 CCCTCGTCGACGTCTGGA 60.745 66.667 34.40 16.33 40.80 3.86
1508 2162 3.723235 CTGGATGGACGTGGAGGCG 62.723 68.421 0.00 0.00 37.94 5.52
1524 2178 4.069232 CGCTCAGCTTCGACCCCA 62.069 66.667 0.00 0.00 0.00 4.96
1525 2179 2.586792 GCTCAGCTTCGACCCCAT 59.413 61.111 0.00 0.00 0.00 4.00
1558 2212 4.415332 CTACCAGCACCGCGTCGT 62.415 66.667 4.92 0.00 0.00 4.34
1631 2285 1.078567 GCTGAGGAAGGTGCTGGAG 60.079 63.158 0.00 0.00 0.00 3.86
1645 2299 2.682494 GGAGGTGTACGAGGCCCA 60.682 66.667 0.00 0.00 0.00 5.36
1651 2305 2.184579 GTACGAGGCCCAGCTGAC 59.815 66.667 17.39 6.73 0.00 3.51
1667 2321 0.685097 TGACCAAGCACAGGTACCTC 59.315 55.000 12.84 0.33 40.09 3.85
1703 2357 2.362369 CCTCGTGGACCTCAGCCAT 61.362 63.158 0.00 0.00 37.81 4.40
1739 2393 0.180406 ACTTCATGGGGATGCCGTAC 59.820 55.000 0.00 0.00 0.00 3.67
1795 2449 2.817396 GCTGGAGGAGCTGTTCGC 60.817 66.667 0.00 0.00 45.21 4.70
1855 2509 8.208903 GGCCAAGGACTTCAATTAGTTATACTA 58.791 37.037 0.00 0.00 0.00 1.82
1856 2510 9.043079 GCCAAGGACTTCAATTAGTTATACTAC 57.957 37.037 0.00 0.00 28.93 2.73
1857 2511 9.543783 CCAAGGACTTCAATTAGTTATACTACC 57.456 37.037 0.00 0.00 28.93 3.18
1860 2514 8.925338 AGGACTTCAATTAGTTATACTACCAGG 58.075 37.037 0.00 0.00 28.93 4.45
1861 2515 8.921205 GGACTTCAATTAGTTATACTACCAGGA 58.079 37.037 0.00 0.00 28.93 3.86
1865 2519 9.880157 TTCAATTAGTTATACTACCAGGAACAC 57.120 33.333 0.00 0.00 28.93 3.32
1866 2520 8.480501 TCAATTAGTTATACTACCAGGAACACC 58.519 37.037 0.00 0.00 28.93 4.16
1867 2521 7.983166 ATTAGTTATACTACCAGGAACACCA 57.017 36.000 0.00 0.00 28.93 4.17
1868 2522 5.672421 AGTTATACTACCAGGAACACCAC 57.328 43.478 0.00 0.00 0.00 4.16
1869 2523 4.159135 AGTTATACTACCAGGAACACCACG 59.841 45.833 0.00 0.00 0.00 4.94
1870 2524 2.291209 TACTACCAGGAACACCACGA 57.709 50.000 0.00 0.00 0.00 4.35
1871 2525 1.416243 ACTACCAGGAACACCACGAA 58.584 50.000 0.00 0.00 0.00 3.85
1872 2526 1.764134 ACTACCAGGAACACCACGAAA 59.236 47.619 0.00 0.00 0.00 3.46
1873 2527 2.171027 ACTACCAGGAACACCACGAAAA 59.829 45.455 0.00 0.00 0.00 2.29
1874 2528 2.131776 ACCAGGAACACCACGAAAAA 57.868 45.000 0.00 0.00 0.00 1.94
1920 2574 8.918202 TGTTTTCTTCCAGAATGTATGTAGTT 57.082 30.769 0.00 0.00 33.67 2.24
1936 2590 9.562408 TGTATGTAGTTTGTGGTGAGAAATAAA 57.438 29.630 0.00 0.00 0.00 1.40
1944 2598 3.576550 GTGGTGAGAAATAAAAAGGGGCA 59.423 43.478 0.00 0.00 0.00 5.36
1965 2619 4.282068 CACGTATGCAATATGACTTTGGC 58.718 43.478 0.00 0.00 38.06 4.52
1967 2621 4.035558 ACGTATGCAATATGACTTTGGCTG 59.964 41.667 0.00 0.00 38.06 4.85
1968 2622 4.035558 CGTATGCAATATGACTTTGGCTGT 59.964 41.667 0.00 0.00 38.06 4.40
1969 2623 5.236263 CGTATGCAATATGACTTTGGCTGTA 59.764 40.000 0.00 0.00 38.06 2.74
1970 2624 6.073058 CGTATGCAATATGACTTTGGCTGTAT 60.073 38.462 0.00 0.00 38.06 2.29
1971 2625 5.503662 TGCAATATGACTTTGGCTGTATG 57.496 39.130 0.00 0.00 0.00 2.39
1972 2626 4.949238 TGCAATATGACTTTGGCTGTATGT 59.051 37.500 0.00 0.00 0.00 2.29
1973 2627 6.118852 TGCAATATGACTTTGGCTGTATGTA 58.881 36.000 0.00 0.00 0.00 2.29
1974 2628 6.772233 TGCAATATGACTTTGGCTGTATGTAT 59.228 34.615 0.00 0.00 0.00 2.29
1975 2629 7.936301 TGCAATATGACTTTGGCTGTATGTATA 59.064 33.333 0.00 0.00 0.00 1.47
1976 2630 8.950210 GCAATATGACTTTGGCTGTATGTATAT 58.050 33.333 0.00 0.00 0.00 0.86
1980 2634 8.978874 ATGACTTTGGCTGTATGTATATTCAA 57.021 30.769 0.00 0.00 0.00 2.69
1983 2637 9.109393 GACTTTGGCTGTATGTATATTCAAGAA 57.891 33.333 0.00 0.00 0.00 2.52
2030 2686 9.442047 CTCACCAGACTTTCTTATCAATTTAGT 57.558 33.333 0.00 0.00 0.00 2.24
2090 2755 7.701809 GAGTATCACTACTCTGTTTTATGCC 57.298 40.000 5.70 0.00 46.97 4.40
2091 2756 7.425224 AGTATCACTACTCTGTTTTATGCCT 57.575 36.000 0.00 0.00 32.56 4.75
2103 2909 7.551585 TCTGTTTTATGCCTTGTTTTCTTTGA 58.448 30.769 0.00 0.00 0.00 2.69
2123 2929 3.698539 TGAAAAGGCACACATCAAACAGA 59.301 39.130 0.00 0.00 0.00 3.41
2124 2930 4.159321 TGAAAAGGCACACATCAAACAGAA 59.841 37.500 0.00 0.00 0.00 3.02
2125 2931 3.715628 AAGGCACACATCAAACAGAAC 57.284 42.857 0.00 0.00 0.00 3.01
2126 2932 2.653726 AGGCACACATCAAACAGAACA 58.346 42.857 0.00 0.00 0.00 3.18
2128 2934 3.115554 GGCACACATCAAACAGAACAAC 58.884 45.455 0.00 0.00 0.00 3.32
2129 2935 3.428725 GGCACACATCAAACAGAACAACA 60.429 43.478 0.00 0.00 0.00 3.33
2130 2936 3.547468 GCACACATCAAACAGAACAACAC 59.453 43.478 0.00 0.00 0.00 3.32
2131 2937 4.731720 CACACATCAAACAGAACAACACA 58.268 39.130 0.00 0.00 0.00 3.72
2132 2938 5.159925 CACACATCAAACAGAACAACACAA 58.840 37.500 0.00 0.00 0.00 3.33
2133 2939 5.632764 CACACATCAAACAGAACAACACAAA 59.367 36.000 0.00 0.00 0.00 2.83
2135 2941 6.873076 ACACATCAAACAGAACAACACAAAAT 59.127 30.769 0.00 0.00 0.00 1.82
2136 2942 7.387397 ACACATCAAACAGAACAACACAAAATT 59.613 29.630 0.00 0.00 0.00 1.82
2223 3119 2.036958 TGGAACACAACACTGACCAG 57.963 50.000 0.00 0.00 0.00 4.00
2244 3140 1.372087 CCTCCTCGCCAATGCTCAAC 61.372 60.000 0.00 0.00 34.43 3.18
2265 3161 8.050778 TCAACGCTAAACCAATATGAAAATCT 57.949 30.769 0.00 0.00 0.00 2.40
2277 3173 8.611757 CCAATATGAAAATCTAATCGTGTCACA 58.388 33.333 3.42 0.00 0.00 3.58
2278 3174 9.425893 CAATATGAAAATCTAATCGTGTCACAC 57.574 33.333 0.00 0.00 0.00 3.82
2279 3175 8.948631 ATATGAAAATCTAATCGTGTCACACT 57.051 30.769 6.33 0.00 31.34 3.55
2280 3176 6.466308 TGAAAATCTAATCGTGTCACACTG 57.534 37.500 6.33 0.00 31.34 3.66
2602 3796 2.678934 AGGACTTAGTCGGCGCCA 60.679 61.111 28.98 11.20 32.65 5.69
2640 3834 0.673644 AGTTCATGCACGGGTACAGC 60.674 55.000 0.00 0.00 0.00 4.40
2650 3844 3.755628 GGTACAGCCCGACGAGCA 61.756 66.667 3.60 0.00 0.00 4.26
2794 3991 6.071728 CCCCTTGGATTGATATTTGATAGTGC 60.072 42.308 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 9.737844 AAATTTGTAGTGGCATGGAAAATTTAT 57.262 25.926 17.48 3.86 35.25 1.40
82 86 4.339872 TTGTTTTCTGAAAGCATGGCAT 57.660 36.364 18.27 0.00 31.59 4.40
212 773 3.477530 GCTGGTCACTTTTCCTACAAGT 58.522 45.455 0.00 0.00 34.67 3.16
230 791 2.708464 GCGCAAATTTTGTTTTTCGCTG 59.292 40.909 17.87 0.93 38.48 5.18
281 843 5.882557 AGTACAAATTTCCTATGCTCCACTG 59.117 40.000 0.00 0.00 0.00 3.66
332 894 5.188163 TGATGGTCATGATTGCAGGAAAAAT 59.812 36.000 0.00 0.00 36.47 1.82
390 958 3.255725 CAAGAAATTGCAACATGGCGAT 58.744 40.909 0.00 0.00 39.59 4.58
416 984 2.031769 CGCACACGAAATGCCATGATAT 60.032 45.455 0.00 0.00 43.93 1.63
434 1002 2.717044 CCTACGGGGACATGTCGCA 61.717 63.158 35.12 19.60 43.40 5.10
437 1005 2.484742 AAAACCTACGGGGACATGTC 57.515 50.000 17.91 17.91 38.76 3.06
439 1007 2.227865 CACAAAAACCTACGGGGACATG 59.772 50.000 3.71 0.00 38.76 3.21
440 1008 2.158579 ACACAAAAACCTACGGGGACAT 60.159 45.455 3.71 0.00 38.76 3.06
448 1016 8.528917 AGTTTCAGAAAAACACAAAAACCTAC 57.471 30.769 0.00 0.00 32.81 3.18
574 1171 6.226787 ACCATTTTGTCGGCAATAATCAAAA 58.773 32.000 1.89 0.00 40.50 2.44
579 1176 4.862018 CGAAACCATTTTGTCGGCAATAAT 59.138 37.500 1.89 3.85 34.18 1.28
582 1179 2.671596 CGAAACCATTTTGTCGGCAAT 58.328 42.857 1.89 0.00 34.18 3.56
585 1182 0.039527 AGCGAAACCATTTTGTCGGC 60.040 50.000 0.00 0.00 34.13 5.54
586 1183 1.265635 TGAGCGAAACCATTTTGTCGG 59.734 47.619 0.00 0.00 34.13 4.79
589 1186 3.306019 GGGAATGAGCGAAACCATTTTGT 60.306 43.478 0.00 0.00 33.57 2.83
592 1189 2.755103 GAGGGAATGAGCGAAACCATTT 59.245 45.455 0.00 0.00 33.57 2.32
593 1190 2.025887 AGAGGGAATGAGCGAAACCATT 60.026 45.455 0.00 0.00 35.87 3.16
594 1191 1.561542 AGAGGGAATGAGCGAAACCAT 59.438 47.619 0.00 0.00 0.00 3.55
595 1192 0.984230 AGAGGGAATGAGCGAAACCA 59.016 50.000 0.00 0.00 0.00 3.67
596 1193 1.657822 GAGAGGGAATGAGCGAAACC 58.342 55.000 0.00 0.00 0.00 3.27
597 1194 1.657822 GGAGAGGGAATGAGCGAAAC 58.342 55.000 0.00 0.00 0.00 2.78
599 1196 1.676678 CCGGAGAGGGAATGAGCGAA 61.677 60.000 0.00 0.00 35.97 4.70
600 1197 2.127869 CCGGAGAGGGAATGAGCGA 61.128 63.158 0.00 0.00 35.97 4.93
601 1198 2.419198 CCGGAGAGGGAATGAGCG 59.581 66.667 0.00 0.00 35.97 5.03
602 1199 2.110006 GCCGGAGAGGGAATGAGC 59.890 66.667 5.05 0.00 41.48 4.26
603 1200 2.419198 CGCCGGAGAGGGAATGAG 59.581 66.667 5.05 0.00 41.48 2.90
604 1201 3.154473 CCGCCGGAGAGGGAATGA 61.154 66.667 5.05 0.00 41.48 2.57
605 1202 2.252072 TTTCCGCCGGAGAGGGAATG 62.252 60.000 5.05 0.00 38.18 2.67
606 1203 1.972660 CTTTCCGCCGGAGAGGGAAT 61.973 60.000 15.52 0.00 38.18 3.01
607 1204 2.605295 TTTCCGCCGGAGAGGGAA 60.605 61.111 5.05 9.25 41.48 3.97
608 1205 3.075005 CTTTCCGCCGGAGAGGGA 61.075 66.667 15.52 2.12 41.48 4.20
609 1206 4.162690 CCTTTCCGCCGGAGAGGG 62.163 72.222 30.03 18.21 46.61 4.30
611 1208 1.741770 CAACCTTTCCGCCGGAGAG 60.742 63.158 16.30 16.30 34.21 3.20
612 1209 2.345991 CAACCTTTCCGCCGGAGA 59.654 61.111 5.05 0.00 31.21 3.71
613 1210 2.746277 CCAACCTTTCCGCCGGAG 60.746 66.667 5.05 0.00 31.21 4.63
614 1211 3.122727 AACCAACCTTTCCGCCGGA 62.123 57.895 5.05 0.00 0.00 5.14
615 1212 2.596338 AACCAACCTTTCCGCCGG 60.596 61.111 0.00 0.00 0.00 6.13
616 1213 2.951458 GAACCAACCTTTCCGCCG 59.049 61.111 0.00 0.00 0.00 6.46
617 1214 2.951458 CGAACCAACCTTTCCGCC 59.049 61.111 0.00 0.00 0.00 6.13
618 1215 2.254350 GCGAACCAACCTTTCCGC 59.746 61.111 0.00 0.00 0.00 5.54
619 1216 1.164041 AGTGCGAACCAACCTTTCCG 61.164 55.000 0.00 0.00 0.00 4.30
620 1217 0.310854 CAGTGCGAACCAACCTTTCC 59.689 55.000 0.00 0.00 0.00 3.13
621 1218 0.310854 CCAGTGCGAACCAACCTTTC 59.689 55.000 0.00 0.00 0.00 2.62
622 1219 1.106944 CCCAGTGCGAACCAACCTTT 61.107 55.000 0.00 0.00 0.00 3.11
623 1220 1.528309 CCCAGTGCGAACCAACCTT 60.528 57.895 0.00 0.00 0.00 3.50
624 1221 1.412453 TACCCAGTGCGAACCAACCT 61.412 55.000 0.00 0.00 0.00 3.50
625 1222 0.322187 ATACCCAGTGCGAACCAACC 60.322 55.000 0.00 0.00 0.00 3.77
626 1223 1.084289 GATACCCAGTGCGAACCAAC 58.916 55.000 0.00 0.00 0.00 3.77
627 1224 0.035820 GGATACCCAGTGCGAACCAA 60.036 55.000 0.00 0.00 0.00 3.67
628 1225 1.600107 GGATACCCAGTGCGAACCA 59.400 57.895 0.00 0.00 0.00 3.67
629 1226 4.534401 GGATACCCAGTGCGAACC 57.466 61.111 0.00 0.00 0.00 3.62
641 1238 1.172812 GCTGCATTTCCCGGGGATAC 61.173 60.000 23.50 10.73 0.00 2.24
642 1239 1.150536 GCTGCATTTCCCGGGGATA 59.849 57.895 23.50 13.25 0.00 2.59
643 1240 1.352622 TAGCTGCATTTCCCGGGGAT 61.353 55.000 23.50 12.82 0.00 3.85
644 1241 1.352622 ATAGCTGCATTTCCCGGGGA 61.353 55.000 23.50 12.99 0.00 4.81
645 1242 1.151450 ATAGCTGCATTTCCCGGGG 59.849 57.895 23.50 6.77 0.00 5.73
646 1243 0.466189 ACATAGCTGCATTTCCCGGG 60.466 55.000 16.85 16.85 0.00 5.73
647 1244 0.664761 CACATAGCTGCATTTCCCGG 59.335 55.000 1.02 0.00 0.00 5.73
648 1245 0.029834 GCACATAGCTGCATTTCCCG 59.970 55.000 1.02 0.00 41.15 5.14
649 1246 0.029834 CGCACATAGCTGCATTTCCC 59.970 55.000 1.02 0.00 42.61 3.97
650 1247 0.593263 GCGCACATAGCTGCATTTCC 60.593 55.000 0.30 0.00 42.61 3.13
651 1248 0.927083 CGCGCACATAGCTGCATTTC 60.927 55.000 8.75 0.00 42.61 2.17
652 1249 1.063006 CGCGCACATAGCTGCATTT 59.937 52.632 8.75 0.00 42.61 2.32
653 1250 2.711311 CGCGCACATAGCTGCATT 59.289 55.556 8.75 0.00 42.61 3.56
654 1251 3.945434 GCGCGCACATAGCTGCAT 61.945 61.111 29.10 0.00 42.61 3.96
657 1254 4.271170 GACGCGCGCACATAGCTG 62.271 66.667 32.58 14.51 42.61 4.24
660 1257 1.966493 AAAAGGACGCGCGCACATAG 61.966 55.000 32.58 16.92 0.00 2.23
661 1258 1.570347 AAAAAGGACGCGCGCACATA 61.570 50.000 32.58 0.00 0.00 2.29
662 1259 1.570347 TAAAAAGGACGCGCGCACAT 61.570 50.000 32.58 19.50 0.00 3.21
663 1260 1.570347 ATAAAAAGGACGCGCGCACA 61.570 50.000 32.58 6.74 0.00 4.57
664 1261 0.453782 AATAAAAAGGACGCGCGCAC 60.454 50.000 32.58 23.14 0.00 5.34
665 1262 0.238817 AAATAAAAAGGACGCGCGCA 59.761 45.000 32.58 8.37 0.00 6.09
666 1263 1.333115 AAAATAAAAAGGACGCGCGC 58.667 45.000 32.58 23.91 0.00 6.86
667 1264 2.024759 CGAAAAATAAAAAGGACGCGCG 59.975 45.455 30.96 30.96 0.00 6.86
668 1265 2.975193 ACGAAAAATAAAAAGGACGCGC 59.025 40.909 5.73 0.00 0.00 6.86
669 1266 3.293605 CGACGAAAAATAAAAAGGACGCG 59.706 43.478 3.53 3.53 0.00 6.01
670 1267 4.213674 ACGACGAAAAATAAAAAGGACGC 58.786 39.130 0.00 0.00 0.00 5.19
671 1268 4.543177 CGACGACGAAAAATAAAAAGGACG 59.457 41.667 0.00 0.00 42.66 4.79
672 1269 4.842376 CCGACGACGAAAAATAAAAAGGAC 59.158 41.667 9.28 0.00 42.66 3.85
673 1270 4.083908 CCCGACGACGAAAAATAAAAAGGA 60.084 41.667 9.28 0.00 42.66 3.36
674 1271 4.153256 CCCGACGACGAAAAATAAAAAGG 58.847 43.478 9.28 0.00 42.66 3.11
675 1272 4.775664 ACCCGACGACGAAAAATAAAAAG 58.224 39.130 9.28 0.00 42.66 2.27
676 1273 4.608000 CGACCCGACGACGAAAAATAAAAA 60.608 41.667 9.28 0.00 42.66 1.94
677 1274 3.121058 CGACCCGACGACGAAAAATAAAA 60.121 43.478 9.28 0.00 42.66 1.52
678 1275 2.408032 CGACCCGACGACGAAAAATAAA 59.592 45.455 9.28 0.00 42.66 1.40
679 1276 1.984990 CGACCCGACGACGAAAAATAA 59.015 47.619 9.28 0.00 42.66 1.40
680 1277 1.068610 ACGACCCGACGACGAAAAATA 60.069 47.619 9.28 0.00 42.66 1.40
681 1278 0.318955 ACGACCCGACGACGAAAAAT 60.319 50.000 9.28 0.00 42.66 1.82
682 1279 1.065600 ACGACCCGACGACGAAAAA 59.934 52.632 9.28 0.00 42.66 1.94
683 1280 1.658102 CACGACCCGACGACGAAAA 60.658 57.895 9.28 0.00 42.66 2.29
684 1281 2.051076 CACGACCCGACGACGAAA 60.051 61.111 9.28 0.00 42.66 3.46
685 1282 2.971959 TCACGACCCGACGACGAA 60.972 61.111 9.28 2.19 42.66 3.85
686 1283 3.716006 GTCACGACCCGACGACGA 61.716 66.667 9.28 0.00 42.66 4.20
691 1288 4.338539 AGTGCGTCACGACCCGAC 62.339 66.667 0.00 0.00 39.64 4.79
692 1289 4.034258 GAGTGCGTCACGACCCGA 62.034 66.667 0.00 0.00 39.64 5.14
693 1290 3.626680 ATGAGTGCGTCACGACCCG 62.627 63.158 0.00 0.00 38.28 5.28
694 1291 1.805945 GATGAGTGCGTCACGACCC 60.806 63.158 0.00 0.00 38.28 4.46
695 1292 1.805945 GGATGAGTGCGTCACGACC 60.806 63.158 0.00 0.00 38.28 4.79
696 1293 1.080772 TGGATGAGTGCGTCACGAC 60.081 57.895 0.00 0.00 38.28 4.34
697 1294 1.080772 GTGGATGAGTGCGTCACGA 60.081 57.895 0.00 0.00 38.28 4.35
770 1380 3.681897 GTCTGAATTGTCTACCAGCACTG 59.318 47.826 0.00 0.00 0.00 3.66
814 1429 1.593006 GTTGAAGTGAGGTGACACGTG 59.407 52.381 15.48 15.48 44.35 4.49
876 1495 4.243643 AGAGGGAGGAGAAAGAAGGAAAA 58.756 43.478 0.00 0.00 0.00 2.29
893 1512 1.446791 GCATGCCAGAGAGAGAGGG 59.553 63.158 6.36 0.00 0.00 4.30
894 1513 1.446791 GGCATGCCAGAGAGAGAGG 59.553 63.158 32.08 0.00 35.81 3.69
895 1514 1.067749 CGGCATGCCAGAGAGAGAG 59.932 63.158 34.93 12.63 35.37 3.20
896 1515 0.395724 TACGGCATGCCAGAGAGAGA 60.396 55.000 34.93 10.13 35.37 3.10
897 1516 0.678395 ATACGGCATGCCAGAGAGAG 59.322 55.000 34.93 19.51 35.37 3.20
898 1517 1.995376 TATACGGCATGCCAGAGAGA 58.005 50.000 34.93 13.85 35.37 3.10
926 1547 3.682292 GAATTCTCACGGCCCCGCT 62.682 63.158 6.63 0.00 44.19 5.52
929 1550 2.513897 CGGAATTCTCACGGCCCC 60.514 66.667 5.23 0.00 0.00 5.80
979 1604 2.630098 TGCTCTTGTTCTGCTCTACTGT 59.370 45.455 0.00 0.00 0.00 3.55
983 1608 2.679059 GCCATGCTCTTGTTCTGCTCTA 60.679 50.000 0.00 0.00 0.00 2.43
1075 1700 2.883468 CGATCTCGTACTCGGCGCT 61.883 63.158 7.64 0.00 37.69 5.92
1110 1735 1.000396 GCCCTTGTGCTCCTTGGAT 60.000 57.895 0.00 0.00 0.00 3.41
1134 1759 0.675083 TTACGTTTCTGGCGAGGTGA 59.325 50.000 0.00 0.00 0.00 4.02
1160 1785 1.625818 CTCTGCTAGAAGGGTTGGTGT 59.374 52.381 0.00 0.00 0.00 4.16
1165 1790 5.581975 ACTTACTACTCTGCTAGAAGGGTT 58.418 41.667 9.08 0.00 31.72 4.11
1166 1791 5.195848 ACTTACTACTCTGCTAGAAGGGT 57.804 43.478 8.74 8.74 34.45 4.34
1167 1792 6.532988 AAACTTACTACTCTGCTAGAAGGG 57.467 41.667 0.00 0.00 0.00 3.95
1172 1800 5.814764 TCCGAAACTTACTACTCTGCTAG 57.185 43.478 0.00 0.00 0.00 3.42
1191 1830 2.486982 CCGGTGGTAGTACTATGATCCG 59.513 54.545 20.99 20.99 36.00 4.18
1296 1943 1.947456 AGTTTGGAAACTGACGGAAGC 59.053 47.619 3.95 0.00 46.80 3.86
1356 2007 6.036083 ACGAAGATGCATATATAATTCGGTGC 59.964 38.462 20.60 7.33 41.57 5.01
1421 2075 1.444553 CTCGTCGGTCCTGTGCTTC 60.445 63.158 0.00 0.00 0.00 3.86
1463 2117 2.286121 AGGGCCGATTCCTTGGGA 60.286 61.111 0.00 0.00 0.00 4.37
1494 2148 4.148825 GAGCGCCTCCACGTCCAT 62.149 66.667 2.29 0.00 34.88 3.41
1508 2162 1.522580 GATGGGGTCGAAGCTGAGC 60.523 63.158 0.00 0.00 35.66 4.26
1524 2178 2.418746 GGTAGAACACCGAGTGCATGAT 60.419 50.000 0.00 0.00 37.63 2.45
1525 2179 1.067142 GGTAGAACACCGAGTGCATGA 60.067 52.381 0.00 0.00 37.63 3.07
1580 2234 0.661780 CGCCGATGATCTTCTCGTCC 60.662 60.000 6.99 0.84 36.68 4.79
1631 2285 3.391382 AGCTGGGCCTCGTACACC 61.391 66.667 4.53 0.00 0.00 4.16
1651 2305 1.741770 GCGAGGTACCTGTGCTTGG 60.742 63.158 22.10 0.00 0.00 3.61
1667 2321 2.203070 CTCAGGAAATCCCCGGCG 60.203 66.667 0.00 0.00 36.42 6.46
1703 2357 0.896940 AGTAGTGCGTCTCGGGGAAA 60.897 55.000 0.00 0.00 0.00 3.13
1795 2449 2.907897 CTTCTTGACGGCGGGCCTAG 62.908 65.000 13.24 6.59 0.00 3.02
1855 2509 2.131776 TTTTTCGTGGTGTTCCTGGT 57.868 45.000 0.00 0.00 34.23 4.00
1900 2554 6.878923 CCACAAACTACATACATTCTGGAAGA 59.121 38.462 0.00 0.00 44.68 2.87
1901 2555 6.655003 ACCACAAACTACATACATTCTGGAAG 59.345 38.462 0.00 0.00 0.00 3.46
1902 2556 6.429692 CACCACAAACTACATACATTCTGGAA 59.570 38.462 0.00 0.00 0.00 3.53
1904 2558 5.937540 TCACCACAAACTACATACATTCTGG 59.062 40.000 0.00 0.00 0.00 3.86
1905 2559 6.873605 TCTCACCACAAACTACATACATTCTG 59.126 38.462 0.00 0.00 0.00 3.02
1906 2560 7.004555 TCTCACCACAAACTACATACATTCT 57.995 36.000 0.00 0.00 0.00 2.40
1907 2561 7.667043 TTCTCACCACAAACTACATACATTC 57.333 36.000 0.00 0.00 0.00 2.67
1908 2562 8.635765 ATTTCTCACCACAAACTACATACATT 57.364 30.769 0.00 0.00 0.00 2.71
1909 2563 9.733556 TTATTTCTCACCACAAACTACATACAT 57.266 29.630 0.00 0.00 0.00 2.29
1910 2564 9.562408 TTTATTTCTCACCACAAACTACATACA 57.438 29.630 0.00 0.00 0.00 2.29
1913 2567 9.965824 CTTTTTATTTCTCACCACAAACTACAT 57.034 29.630 0.00 0.00 0.00 2.29
1914 2568 8.410141 CCTTTTTATTTCTCACCACAAACTACA 58.590 33.333 0.00 0.00 0.00 2.74
1915 2569 7.865889 CCCTTTTTATTTCTCACCACAAACTAC 59.134 37.037 0.00 0.00 0.00 2.73
1916 2570 7.014808 CCCCTTTTTATTTCTCACCACAAACTA 59.985 37.037 0.00 0.00 0.00 2.24
1917 2571 6.183360 CCCCTTTTTATTTCTCACCACAAACT 60.183 38.462 0.00 0.00 0.00 2.66
1918 2572 5.989168 CCCCTTTTTATTTCTCACCACAAAC 59.011 40.000 0.00 0.00 0.00 2.93
1919 2573 5.454045 GCCCCTTTTTATTTCTCACCACAAA 60.454 40.000 0.00 0.00 0.00 2.83
1920 2574 4.039852 GCCCCTTTTTATTTCTCACCACAA 59.960 41.667 0.00 0.00 0.00 3.33
1944 2598 4.035558 CAGCCAAAGTCATATTGCATACGT 59.964 41.667 0.00 0.00 0.00 3.57
1956 2610 8.264347 TCTTGAATATACATACAGCCAAAGTCA 58.736 33.333 0.00 0.00 0.00 3.41
1960 2614 9.407380 ACATTCTTGAATATACATACAGCCAAA 57.593 29.630 0.00 0.00 0.00 3.28
1961 2615 8.978874 ACATTCTTGAATATACATACAGCCAA 57.021 30.769 0.00 0.00 0.00 4.52
1983 2637 9.547753 GGTGAGATGTAAAGACAATACATACAT 57.452 33.333 0.00 0.00 42.48 2.29
2030 2686 7.281774 AGCACGCTAATAAACAGAGTAGTAGTA 59.718 37.037 0.00 0.00 0.00 1.82
2031 2687 6.095160 AGCACGCTAATAAACAGAGTAGTAGT 59.905 38.462 0.00 0.00 0.00 2.73
2034 2690 5.125739 AGAGCACGCTAATAAACAGAGTAGT 59.874 40.000 0.00 0.00 0.00 2.73
2037 2693 4.177026 CAGAGCACGCTAATAAACAGAGT 58.823 43.478 0.00 0.00 0.00 3.24
2040 2696 4.928661 AACAGAGCACGCTAATAAACAG 57.071 40.909 0.00 0.00 0.00 3.16
2042 2698 5.790495 CAGAAAACAGAGCACGCTAATAAAC 59.210 40.000 0.00 0.00 0.00 2.01
2043 2699 5.699001 TCAGAAAACAGAGCACGCTAATAAA 59.301 36.000 0.00 0.00 0.00 1.40
2046 2702 3.664107 TCAGAAAACAGAGCACGCTAAT 58.336 40.909 0.00 0.00 0.00 1.73
2047 2703 3.059884 CTCAGAAAACAGAGCACGCTAA 58.940 45.455 0.00 0.00 0.00 3.09
2048 2704 2.035961 ACTCAGAAAACAGAGCACGCTA 59.964 45.455 0.00 0.00 35.28 4.26
2090 2755 5.407995 TGTGTGCCTTTTCAAAGAAAACAAG 59.592 36.000 0.56 0.00 38.28 3.16
2091 2756 5.300752 TGTGTGCCTTTTCAAAGAAAACAA 58.699 33.333 0.56 0.00 38.28 2.83
2103 2909 4.081752 TGTTCTGTTTGATGTGTGCCTTTT 60.082 37.500 0.00 0.00 0.00 2.27
2123 2929 8.621286 TGGTTGTTTTTGTAATTTTGTGTTGTT 58.379 25.926 0.00 0.00 0.00 2.83
2124 2930 8.154649 TGGTTGTTTTTGTAATTTTGTGTTGT 57.845 26.923 0.00 0.00 0.00 3.32
2125 2931 8.286097 ACTGGTTGTTTTTGTAATTTTGTGTTG 58.714 29.630 0.00 0.00 0.00 3.33
2126 2932 8.384607 ACTGGTTGTTTTTGTAATTTTGTGTT 57.615 26.923 0.00 0.00 0.00 3.32
2128 2934 8.384365 GGTACTGGTTGTTTTTGTAATTTTGTG 58.616 33.333 0.00 0.00 0.00 3.33
2129 2935 8.315482 AGGTACTGGTTGTTTTTGTAATTTTGT 58.685 29.630 0.00 0.00 37.18 2.83
2130 2936 8.710835 AGGTACTGGTTGTTTTTGTAATTTTG 57.289 30.769 0.00 0.00 37.18 2.44
2131 2937 8.755028 AGAGGTACTGGTTGTTTTTGTAATTTT 58.245 29.630 0.00 0.00 41.55 1.82
2132 2938 8.301252 AGAGGTACTGGTTGTTTTTGTAATTT 57.699 30.769 0.00 0.00 41.55 1.82
2133 2939 7.891498 AGAGGTACTGGTTGTTTTTGTAATT 57.109 32.000 0.00 0.00 41.55 1.40
2135 2941 7.706100 AAAGAGGTACTGGTTGTTTTTGTAA 57.294 32.000 0.00 0.00 41.55 2.41
2136 2942 8.983702 ATAAAGAGGTACTGGTTGTTTTTGTA 57.016 30.769 0.00 0.00 41.55 2.41
2244 3140 9.318041 CGATTAGATTTTCATATTGGTTTAGCG 57.682 33.333 0.00 0.00 0.00 4.26
2277 3173 2.806244 CGGAAATTCGTTTCCTGTCAGT 59.194 45.455 15.60 0.00 46.35 3.41
2278 3174 3.064207 TCGGAAATTCGTTTCCTGTCAG 58.936 45.455 15.60 0.00 46.35 3.51
2279 3175 3.064207 CTCGGAAATTCGTTTCCTGTCA 58.936 45.455 15.60 0.17 46.35 3.58
2280 3176 3.064931 ACTCGGAAATTCGTTTCCTGTC 58.935 45.455 15.60 0.00 46.35 3.51
2402 3314 4.148825 GGCGGCTCGTCACTCCAT 62.149 66.667 0.00 0.00 0.00 3.41
2592 3786 4.373116 AACGACATGGCGCCGACT 62.373 61.111 23.72 5.45 33.86 4.18
2615 3809 0.930310 CCCGTGCATGAACTACATCG 59.070 55.000 7.72 0.00 37.07 3.84
2751 3948 5.478503 AGGGGAAGAGAAATCCATCAATT 57.521 39.130 0.00 0.00 38.80 2.32


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

AutoCloner maintained by Alex Coulton.