Multiple sequence alignment - TraesCS5B01G296800

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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 TraesCS5B01G296800 chr5B 100.000 3197 0 0 1 3197 479815135 479818331 0.000000e+00 5904.0
1 TraesCS5B01G296800 chr5A 88.433 1340 95 32 1617 2910 505490064 505491389 0.000000e+00 1561.0
2 TraesCS5B01G296800 chr5A 93.405 925 36 2 681 1580 505489136 505490060 0.000000e+00 1347.0
3 TraesCS5B01G296800 chr5A 92.170 613 30 9 1 596 505488239 505488850 0.000000e+00 850.0
4 TraesCS5B01G296800 chr5A 90.055 181 17 1 3018 3197 505491427 505491607 1.920000e-57 233.0
5 TraesCS5B01G296800 chr5A 72.185 906 169 44 1355 2218 505352661 505353525 1.940000e-47 200.0
6 TraesCS5B01G296800 chr2A 79.130 1356 231 32 909 2221 47796127 47794781 0.000000e+00 889.0
7 TraesCS5B01G296800 chr2A 78.346 1270 224 29 960 2185 47829292 47828030 0.000000e+00 774.0
8 TraesCS5B01G296800 chr2A 76.108 1218 231 31 1040 2221 47779822 47778629 1.650000e-162 582.0
9 TraesCS5B01G296800 chr2B 78.550 1338 233 34 928 2221 69036068 69034741 0.000000e+00 832.0
10 TraesCS5B01G296800 chr2B 77.123 1307 246 32 960 2221 69003759 69005057 0.000000e+00 708.0
11 TraesCS5B01G296800 chr5D 95.983 473 19 0 1035 1507 399928140 399928612 0.000000e+00 769.0
12 TraesCS5B01G296800 chr5D 97.222 180 3 1 864 1041 399909918 399910097 1.440000e-78 303.0
13 TraesCS5B01G296800 chr5D 76.964 560 95 15 969 1496 399735672 399736229 4.040000e-74 289.0
14 TraesCS5B01G296800 chr5D 72.498 1149 200 59 1144 2218 399792889 399793995 6.800000e-67 265.0
15 TraesCS5B01G296800 chr5D 74.952 523 99 20 1721 2218 399736436 399736951 8.990000e-51 211.0
16 TraesCS5B01G296800 chr2D 77.837 1304 230 31 960 2221 43988225 43986939 0.000000e+00 752.0
17 TraesCS5B01G296800 chr2D 77.329 1138 214 28 1050 2153 43974757 43975884 1.620000e-177 632.0
18 TraesCS5B01G296800 chr7A 84.583 240 33 4 1 237 563503377 563503615 5.330000e-58 235.0
19 TraesCS5B01G296800 chr7A 85.526 228 27 6 14 237 263716186 263715961 1.920000e-57 233.0
20 TraesCS5B01G296800 chr7A 76.617 201 37 8 39 237 625711308 625711500 5.640000e-18 102.0
21 TraesCS5B01G296800 chr7B 85.377 212 27 4 1 209 526425720 526425930 1.930000e-52 217.0
22 TraesCS5B01G296800 chr7B 88.966 145 12 4 80 222 223173235 223173093 3.280000e-40 176.0
23 TraesCS5B01G296800 chr7B 85.156 128 12 7 58 182 87169485 87169362 1.200000e-24 124.0
24 TraesCS5B01G296800 chr7D 80.786 229 34 7 9 233 129802462 129802684 1.520000e-38 171.0
25 TraesCS5B01G296800 chr7D 76.923 195 37 5 39 233 544366667 544366853 1.570000e-18 104.0
26 TraesCS5B01G296800 chr7D 86.792 53 7 0 1355 1407 601439289 601439237 3.440000e-05 60.2
27 TraesCS5B01G296800 chr1A 80.124 161 23 7 1 159 591710458 591710611 9.370000e-21 111.0
28 TraesCS5B01G296800 chr1B 73.958 192 42 5 1955 2138 180552276 180552085 1.590000e-08 71.3


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 TraesCS5B01G296800 chr5B 479815135 479818331 3196 False 5904.00 5904 100.00000 1 3197 1 chr5B.!!$F1 3196
1 TraesCS5B01G296800 chr5A 505488239 505491607 3368 False 997.75 1561 91.01575 1 3197 4 chr5A.!!$F2 3196
2 TraesCS5B01G296800 chr2A 47794781 47796127 1346 True 889.00 889 79.13000 909 2221 1 chr2A.!!$R2 1312
3 TraesCS5B01G296800 chr2A 47828030 47829292 1262 True 774.00 774 78.34600 960 2185 1 chr2A.!!$R3 1225
4 TraesCS5B01G296800 chr2A 47778629 47779822 1193 True 582.00 582 76.10800 1040 2221 1 chr2A.!!$R1 1181
5 TraesCS5B01G296800 chr2B 69034741 69036068 1327 True 832.00 832 78.55000 928 2221 1 chr2B.!!$R1 1293
6 TraesCS5B01G296800 chr2B 69003759 69005057 1298 False 708.00 708 77.12300 960 2221 1 chr2B.!!$F1 1261
7 TraesCS5B01G296800 chr5D 399792889 399793995 1106 False 265.00 265 72.49800 1144 2218 1 chr5D.!!$F1 1074
8 TraesCS5B01G296800 chr5D 399735672 399736951 1279 False 250.00 289 75.95800 969 2218 2 chr5D.!!$F4 1249
9 TraesCS5B01G296800 chr2D 43986939 43988225 1286 True 752.00 752 77.83700 960 2221 1 chr2D.!!$R1 1261
10 TraesCS5B01G296800 chr2D 43974757 43975884 1127 False 632.00 632 77.32900 1050 2153 1 chr2D.!!$F1 1103

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
643 661 0.109226 GGTGCGCCTAGATCCGTATC 60.109 60.0 9.68 0.0 0.0 2.24 F
671 689 0.310854 CCACACCTCCTTTTTCACGC 59.689 55.0 0.00 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1465 1764 0.034896 ACCCAAAGCACTCGGTACTG 59.965 55.0 0.00 0.0 0.00 2.74 R
2374 2755 0.391228 TGCTCAAGCTGTCCGTGTAA 59.609 50.0 3.32 0.0 42.66 2.41 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
37 38 3.717400 TGCATGAGAATCCTCTACGAC 57.283 47.619 0.00 0.00 40.10 4.34
94 103 8.586570 TTAAATCACCTTGCATTTTAGTTGTG 57.413 30.769 0.00 0.00 0.00 3.33
101 110 2.036862 TGCATTTTAGTTGTGCCATGCA 59.963 40.909 0.55 0.55 43.56 3.96
102 111 2.669434 GCATTTTAGTTGTGCCATGCAG 59.331 45.455 0.00 0.00 40.08 4.41
169 182 8.918202 TCACATAGTTTAAATGGTGAAGACTT 57.082 30.769 10.03 0.00 0.00 3.01
239 252 1.883084 CAAGCGAGGTATGGTCCGC 60.883 63.158 0.00 0.00 47.00 5.54
246 259 2.296471 CGAGGTATGGTCCGCTTTAGAT 59.704 50.000 0.00 0.00 0.00 1.98
289 302 5.523188 TGGCATGACTTCAAATCAACAAAAC 59.477 36.000 0.00 0.00 0.00 2.43
292 305 6.035866 GCATGACTTCAAATCAACAAAACACA 59.964 34.615 0.00 0.00 0.00 3.72
320 333 6.832900 TGCAACATGGATGAGGTGAAAATATA 59.167 34.615 0.00 0.00 0.00 0.86
321 334 7.013559 TGCAACATGGATGAGGTGAAAATATAG 59.986 37.037 0.00 0.00 0.00 1.31
454 467 7.917003 TGGTACAATGGCATATCATAGTACAT 58.083 34.615 0.00 0.00 33.99 2.29
462 475 8.593945 TGGCATATCATAGTACATCATACTGA 57.406 34.615 0.00 0.00 0.00 3.41
508 521 9.291664 TGAAACCACGTGTAAAAGAAATTTTAG 57.708 29.630 15.65 0.00 32.27 1.85
630 648 2.346099 TTTTGCTTAATCAGGTGCGC 57.654 45.000 0.00 0.00 0.00 6.09
631 649 0.525761 TTTGCTTAATCAGGTGCGCC 59.474 50.000 8.71 8.71 0.00 6.53
633 651 0.539518 TGCTTAATCAGGTGCGCCTA 59.460 50.000 20.73 8.22 44.97 3.93
634 652 1.221414 GCTTAATCAGGTGCGCCTAG 58.779 55.000 20.73 13.68 44.97 3.02
635 653 1.202533 GCTTAATCAGGTGCGCCTAGA 60.203 52.381 20.73 18.52 44.97 2.43
636 654 2.548920 GCTTAATCAGGTGCGCCTAGAT 60.549 50.000 20.73 19.88 44.97 1.98
637 655 3.321497 CTTAATCAGGTGCGCCTAGATC 58.679 50.000 20.73 0.00 44.97 2.75
638 656 0.394565 AATCAGGTGCGCCTAGATCC 59.605 55.000 20.73 0.00 44.97 3.36
639 657 1.810606 ATCAGGTGCGCCTAGATCCG 61.811 60.000 20.73 5.52 44.97 4.18
640 658 2.442272 AGGTGCGCCTAGATCCGT 60.442 61.111 19.65 0.00 44.90 4.69
641 659 1.152819 AGGTGCGCCTAGATCCGTA 60.153 57.895 19.65 0.00 44.90 4.02
642 660 0.539901 AGGTGCGCCTAGATCCGTAT 60.540 55.000 19.65 0.00 44.90 3.06
643 661 0.109226 GGTGCGCCTAGATCCGTATC 60.109 60.000 9.68 0.00 0.00 2.24
644 662 0.109226 GTGCGCCTAGATCCGTATCC 60.109 60.000 4.18 0.00 31.98 2.59
645 663 0.538746 TGCGCCTAGATCCGTATCCA 60.539 55.000 4.18 0.00 31.98 3.41
646 664 0.601558 GCGCCTAGATCCGTATCCAA 59.398 55.000 0.00 0.00 31.98 3.53
647 665 1.000506 GCGCCTAGATCCGTATCCAAA 59.999 52.381 0.00 0.00 31.98 3.28
648 666 2.547218 GCGCCTAGATCCGTATCCAAAA 60.547 50.000 0.00 0.00 31.98 2.44
649 667 3.724374 CGCCTAGATCCGTATCCAAAAA 58.276 45.455 0.00 0.00 31.98 1.94
668 686 5.948742 AAAAATCCACACCTCCTTTTTCA 57.051 34.783 0.00 0.00 0.00 2.69
669 687 4.937201 AAATCCACACCTCCTTTTTCAC 57.063 40.909 0.00 0.00 0.00 3.18
670 688 1.961793 TCCACACCTCCTTTTTCACG 58.038 50.000 0.00 0.00 0.00 4.35
671 689 0.310854 CCACACCTCCTTTTTCACGC 59.689 55.000 0.00 0.00 0.00 5.34
672 690 1.308998 CACACCTCCTTTTTCACGCT 58.691 50.000 0.00 0.00 0.00 5.07
673 691 1.264288 CACACCTCCTTTTTCACGCTC 59.736 52.381 0.00 0.00 0.00 5.03
674 692 1.141053 ACACCTCCTTTTTCACGCTCT 59.859 47.619 0.00 0.00 0.00 4.09
675 693 2.367567 ACACCTCCTTTTTCACGCTCTA 59.632 45.455 0.00 0.00 0.00 2.43
676 694 3.181458 ACACCTCCTTTTTCACGCTCTAA 60.181 43.478 0.00 0.00 0.00 2.10
677 695 3.813166 CACCTCCTTTTTCACGCTCTAAA 59.187 43.478 0.00 0.00 0.00 1.85
678 696 4.274950 CACCTCCTTTTTCACGCTCTAAAA 59.725 41.667 0.00 0.00 0.00 1.52
679 697 5.048713 CACCTCCTTTTTCACGCTCTAAAAT 60.049 40.000 0.00 0.00 0.00 1.82
680 698 6.148811 CACCTCCTTTTTCACGCTCTAAAATA 59.851 38.462 0.00 0.00 0.00 1.40
681 699 6.884836 ACCTCCTTTTTCACGCTCTAAAATAT 59.115 34.615 0.00 0.00 0.00 1.28
682 700 7.148239 ACCTCCTTTTTCACGCTCTAAAATATG 60.148 37.037 0.00 0.00 0.00 1.78
786 1005 2.120909 CAGATCCGCCGCCCAAATT 61.121 57.895 0.00 0.00 0.00 1.82
823 1042 0.605589 CTCGGAGCACTTTGACCTCT 59.394 55.000 0.00 0.00 0.00 3.69
828 1047 2.614229 GGAGCACTTTGACCTCTTCTCC 60.614 54.545 0.00 0.00 33.09 3.71
833 1052 2.300437 ACTTTGACCTCTTCTCCCTTCG 59.700 50.000 0.00 0.00 0.00 3.79
945 1188 3.117888 GGCTCCATCCTTACATTTCCTCA 60.118 47.826 0.00 0.00 0.00 3.86
1140 1394 2.908073 GCAAAGTGCCACCTCCACG 61.908 63.158 0.00 0.00 37.42 4.94
1225 1491 2.680913 CCGCAGAAAACCAGCCTCG 61.681 63.158 0.00 0.00 0.00 4.63
1412 1711 1.303888 TACGGACGCCTCAGAACCT 60.304 57.895 0.00 0.00 0.00 3.50
1465 1764 3.758931 GGCACAAACCATCCGGGC 61.759 66.667 0.00 0.00 42.05 6.13
1498 1815 1.124780 TTGGGTCTCTTGTCCGACAA 58.875 50.000 13.29 13.29 36.54 3.18
1593 1910 1.429021 CATCCGGCAACCAACATCG 59.571 57.895 0.00 0.00 0.00 3.84
1596 1913 1.963855 CCGGCAACCAACATCGTCA 60.964 57.895 0.00 0.00 0.00 4.35
1764 2084 2.030363 TGAAACATTCCGGTTGATGTGC 60.030 45.455 17.22 13.78 0.00 4.57
1912 2250 2.290896 TGGTCCTTCAAGCATCGGATTT 60.291 45.455 0.00 0.00 0.00 2.17
2075 2446 1.807142 GAAAAGCGAAGAGGACCAAGG 59.193 52.381 0.00 0.00 0.00 3.61
2095 2466 1.269723 GCAAGAACTTGTGGCTTACCC 59.730 52.381 14.62 0.00 42.31 3.69
2197 2568 5.723887 CCTCCATTCTTCATAGGGCTATAGT 59.276 44.000 0.84 0.00 0.00 2.12
2198 2569 6.214412 CCTCCATTCTTCATAGGGCTATAGTT 59.786 42.308 0.84 0.00 0.00 2.24
2253 2625 9.751542 CGGTGTGAGAATTATTCTAGATAACTT 57.248 33.333 7.52 0.00 40.87 2.66
2276 2648 7.337942 ACTTTTGTCATTGTTCTCAGTTCTTCT 59.662 33.333 0.00 0.00 0.00 2.85
2282 2654 9.657121 GTCATTGTTCTCAGTTCTTCTTTTTAG 57.343 33.333 0.00 0.00 0.00 1.85
2283 2655 9.396022 TCATTGTTCTCAGTTCTTCTTTTTAGT 57.604 29.630 0.00 0.00 0.00 2.24
2317 2698 7.156876 AGAATTTAACGCTTTGGATGATTCA 57.843 32.000 0.00 0.00 0.00 2.57
2325 2706 5.295292 ACGCTTTGGATGATTCAGTATTCTG 59.705 40.000 0.00 0.00 42.54 3.02
2343 2724 1.876156 CTGAAACTGCTTCTGTCCACC 59.124 52.381 0.00 0.00 34.86 4.61
2344 2725 1.239347 GAAACTGCTTCTGTCCACCC 58.761 55.000 0.00 0.00 0.00 4.61
2345 2726 0.550914 AAACTGCTTCTGTCCACCCA 59.449 50.000 0.00 0.00 0.00 4.51
2346 2727 0.550914 AACTGCTTCTGTCCACCCAA 59.449 50.000 0.00 0.00 0.00 4.12
2354 2735 3.304911 TCTGTCCACCCAAATTGTCAA 57.695 42.857 0.00 0.00 0.00 3.18
2356 2737 4.222336 TCTGTCCACCCAAATTGTCAAAT 58.778 39.130 0.00 0.00 0.00 2.32
2366 2747 7.856894 CACCCAAATTGTCAAATCACATTTTTC 59.143 33.333 0.00 0.00 30.86 2.29
2367 2748 7.774625 ACCCAAATTGTCAAATCACATTTTTCT 59.225 29.630 0.00 0.00 30.86 2.52
2368 2749 8.623030 CCCAAATTGTCAAATCACATTTTTCTT 58.377 29.630 0.00 0.00 30.86 2.52
2381 2762 8.789881 TCACATTTTTCTTTACAATTACACGG 57.210 30.769 0.00 0.00 0.00 4.94
2382 2763 8.622157 TCACATTTTTCTTTACAATTACACGGA 58.378 29.630 0.00 0.00 0.00 4.69
2383 2764 8.687301 CACATTTTTCTTTACAATTACACGGAC 58.313 33.333 0.00 0.00 0.00 4.79
2384 2765 8.407064 ACATTTTTCTTTACAATTACACGGACA 58.593 29.630 0.00 0.00 0.00 4.02
2385 2766 8.901748 CATTTTTCTTTACAATTACACGGACAG 58.098 33.333 0.00 0.00 0.00 3.51
2386 2767 5.600908 TTCTTTACAATTACACGGACAGC 57.399 39.130 0.00 0.00 0.00 4.40
2391 2773 3.067106 ACAATTACACGGACAGCTTGAG 58.933 45.455 0.00 0.00 0.00 3.02
2412 2794 2.352715 GCAACTGCCCTGAAATTGTACC 60.353 50.000 0.00 0.00 34.31 3.34
2423 2805 3.067461 TGAAATTGTACCAGTGTTGTGCC 59.933 43.478 0.00 0.00 0.00 5.01
2427 2809 2.660572 TGTACCAGTGTTGTGCCAATT 58.339 42.857 0.00 0.00 0.00 2.32
2428 2810 2.360483 TGTACCAGTGTTGTGCCAATTG 59.640 45.455 0.00 0.00 0.00 2.32
2440 2822 2.560542 GTGCCAATTGGGAACACATACA 59.439 45.455 25.73 8.92 45.73 2.29
2447 2829 7.160726 CCAATTGGGAACACATACAGATTTTT 58.839 34.615 17.36 0.00 42.67 1.94
2448 2830 7.331687 CCAATTGGGAACACATACAGATTTTTC 59.668 37.037 17.36 0.00 42.67 2.29
2463 2846 1.834188 TTTTCCGATCCTTCCCTTGC 58.166 50.000 0.00 0.00 0.00 4.01
2489 2872 5.650703 TCCTTTTCCCGTTTCCAGAATAATC 59.349 40.000 0.00 0.00 0.00 1.75
2490 2873 5.652452 CCTTTTCCCGTTTCCAGAATAATCT 59.348 40.000 0.00 0.00 35.88 2.40
2491 2874 6.826741 CCTTTTCCCGTTTCCAGAATAATCTA 59.173 38.462 0.00 0.00 33.50 1.98
2492 2875 7.201705 CCTTTTCCCGTTTCCAGAATAATCTAC 60.202 40.741 0.00 0.00 33.50 2.59
2495 2880 6.895782 TCCCGTTTCCAGAATAATCTACAAT 58.104 36.000 0.00 0.00 33.50 2.71
2526 2919 8.455682 GTTATGCTTATGGTAAAGTAGCAAACA 58.544 33.333 0.00 0.00 44.12 2.83
2559 2952 9.178758 ACAAATTATTCCCTACACTTCATTCTC 57.821 33.333 0.00 0.00 0.00 2.87
2565 2958 7.589958 TTCCCTACACTTCATTCTCTATCTC 57.410 40.000 0.00 0.00 0.00 2.75
2567 2960 7.358263 TCCCTACACTTCATTCTCTATCTCTT 58.642 38.462 0.00 0.00 0.00 2.85
2568 2961 7.841729 TCCCTACACTTCATTCTCTATCTCTTT 59.158 37.037 0.00 0.00 0.00 2.52
2569 2962 7.925483 CCCTACACTTCATTCTCTATCTCTTTG 59.075 40.741 0.00 0.00 0.00 2.77
2570 2963 7.437862 CCTACACTTCATTCTCTATCTCTTTGC 59.562 40.741 0.00 0.00 0.00 3.68
2571 2964 6.705302 ACACTTCATTCTCTATCTCTTTGCA 58.295 36.000 0.00 0.00 0.00 4.08
2572 2965 6.593382 ACACTTCATTCTCTATCTCTTTGCAC 59.407 38.462 0.00 0.00 0.00 4.57
2573 2966 6.036953 CACTTCATTCTCTATCTCTTTGCACC 59.963 42.308 0.00 0.00 0.00 5.01
2595 2988 6.821160 CACCAAATTTTACTGTTGGAAAGGTT 59.179 34.615 8.58 0.00 43.82 3.50
2605 2998 5.823045 ACTGTTGGAAAGGTTCTTACAAGAG 59.177 40.000 14.48 14.48 43.13 2.85
2609 3002 5.445964 TGGAAAGGTTCTTACAAGAGCTTT 58.554 37.500 13.47 13.47 41.99 3.51
2610 3003 5.891551 TGGAAAGGTTCTTACAAGAGCTTTT 59.108 36.000 13.23 13.23 44.13 2.27
2616 3009 5.631096 GGTTCTTACAAGAGCTTTTCAATGC 59.369 40.000 5.90 0.00 36.61 3.56
2617 3010 6.208644 GTTCTTACAAGAGCTTTTCAATGCA 58.791 36.000 0.00 0.00 36.22 3.96
2621 3014 5.917541 ACAAGAGCTTTTCAATGCATTTG 57.082 34.783 9.83 5.89 36.61 2.32
2629 3022 6.539464 AGCTTTTCAATGCATTTGTTGAGAAA 59.461 30.769 9.83 12.11 35.91 2.52
2630 3023 7.066043 AGCTTTTCAATGCATTTGTTGAGAAAA 59.934 29.630 21.88 21.88 35.91 2.29
2644 3037 4.229304 TGAGAAAAAGGTTCAGTGTGGA 57.771 40.909 0.00 0.00 0.00 4.02
2647 3040 5.105917 TGAGAAAAAGGTTCAGTGTGGAAAC 60.106 40.000 0.00 0.00 34.66 2.78
2649 3042 5.245075 AGAAAAAGGTTCAGTGTGGAAACAA 59.755 36.000 0.00 0.00 46.06 2.83
2661 3054 8.999431 TCAGTGTGGAAACAACTTTAAGATATC 58.001 33.333 0.00 0.00 46.06 1.63
2663 3056 9.003658 AGTGTGGAAACAACTTTAAGATATCTG 57.996 33.333 5.86 0.00 46.06 2.90
2664 3057 8.784043 GTGTGGAAACAACTTTAAGATATCTGT 58.216 33.333 5.86 0.00 46.06 3.41
2665 3058 8.783093 TGTGGAAACAACTTTAAGATATCTGTG 58.217 33.333 5.86 1.27 46.06 3.66
2696 3104 6.426646 ACATCTAACAGAAGACAAAGACCT 57.573 37.500 0.00 0.00 0.00 3.85
2698 3106 5.871396 TCTAACAGAAGACAAAGACCTGT 57.129 39.130 0.00 0.00 39.49 4.00
2706 3114 6.316390 CAGAAGACAAAGACCTGTGTTTACTT 59.684 38.462 9.48 9.48 33.30 2.24
2709 3117 6.885922 AGACAAAGACCTGTGTTTACTTAGT 58.114 36.000 0.00 0.00 0.00 2.24
2740 3148 8.807667 AATTCTTTTCAGATTTTGTAGTGCTG 57.192 30.769 0.00 0.00 0.00 4.41
2748 3156 6.716628 TCAGATTTTGTAGTGCTGGATCTTTT 59.283 34.615 0.00 0.00 0.00 2.27
2749 3157 7.231317 TCAGATTTTGTAGTGCTGGATCTTTTT 59.769 33.333 0.00 0.00 0.00 1.94
2750 3158 8.514594 CAGATTTTGTAGTGCTGGATCTTTTTA 58.485 33.333 0.00 0.00 0.00 1.52
2751 3159 8.515414 AGATTTTGTAGTGCTGGATCTTTTTAC 58.485 33.333 0.00 0.00 0.00 2.01
2761 3169 9.476202 GTGCTGGATCTTTTTACAGTAAATTTT 57.524 29.630 6.58 0.00 33.62 1.82
2796 3209 0.250684 TGGAGGCGACTTCATTGCAA 60.251 50.000 0.00 0.00 42.58 4.08
2801 3214 1.994779 GGCGACTTCATTGCAAAATGG 59.005 47.619 1.71 0.00 39.86 3.16
2807 3220 6.324819 CGACTTCATTGCAAAATGGTAAGAT 58.675 36.000 1.71 0.00 0.00 2.40
2818 3231 5.772393 AAATGGTAAGATCACCCACAGTA 57.228 39.130 0.00 0.00 37.84 2.74
2828 3241 8.934023 AAGATCACCCACAGTAAAGAAAATAA 57.066 30.769 0.00 0.00 0.00 1.40
2834 3247 9.981114 CACCCACAGTAAAGAAAATAAGAAAAT 57.019 29.630 0.00 0.00 0.00 1.82
2846 3259 4.725790 ATAAGAAAATCTGGTTGCTGGC 57.274 40.909 0.00 0.00 0.00 4.85
2848 3261 0.968405 GAAAATCTGGTTGCTGGCCA 59.032 50.000 4.71 4.71 34.42 5.36
2850 3263 0.971386 AAATCTGGTTGCTGGCCAAG 59.029 50.000 7.01 0.00 35.32 3.61
2869 3284 4.321974 CCAAGCATTTTCACCCCTTACTTC 60.322 45.833 0.00 0.00 0.00 3.01
2877 3292 0.178912 ACCCCTTACTTCGACCACCT 60.179 55.000 0.00 0.00 0.00 4.00
2878 3293 0.981943 CCCCTTACTTCGACCACCTT 59.018 55.000 0.00 0.00 0.00 3.50
2893 3308 3.993736 ACCACCTTTTGCAAATATTTCGC 59.006 39.130 13.65 12.76 0.00 4.70
2900 3315 7.219344 ACCTTTTGCAAATATTTCGCGTATAAC 59.781 33.333 13.65 0.00 0.00 1.89
2910 3325 0.785979 CGCGTATAACAATACCGGGC 59.214 55.000 6.32 0.00 0.00 6.13
2911 3326 1.868469 GCGTATAACAATACCGGGCA 58.132 50.000 6.32 0.00 0.00 5.36
2912 3327 2.211806 GCGTATAACAATACCGGGCAA 58.788 47.619 6.32 0.00 0.00 4.52
2913 3328 2.809696 GCGTATAACAATACCGGGCAAT 59.190 45.455 6.32 0.00 0.00 3.56
2914 3329 3.251487 GCGTATAACAATACCGGGCAATT 59.749 43.478 6.32 0.00 0.00 2.32
2915 3330 4.612033 GCGTATAACAATACCGGGCAATTC 60.612 45.833 6.32 0.00 0.00 2.17
2916 3331 4.753107 CGTATAACAATACCGGGCAATTCT 59.247 41.667 6.32 0.00 0.00 2.40
2917 3332 5.237779 CGTATAACAATACCGGGCAATTCTT 59.762 40.000 6.32 0.00 0.00 2.52
2918 3333 3.866883 AACAATACCGGGCAATTCTTG 57.133 42.857 6.32 0.99 0.00 3.02
2919 3334 3.080300 ACAATACCGGGCAATTCTTGA 57.920 42.857 6.32 0.00 0.00 3.02
2920 3335 3.426615 ACAATACCGGGCAATTCTTGAA 58.573 40.909 6.32 0.00 0.00 2.69
2921 3336 3.829601 ACAATACCGGGCAATTCTTGAAA 59.170 39.130 6.32 0.00 0.00 2.69
2922 3337 4.282195 ACAATACCGGGCAATTCTTGAAAA 59.718 37.500 6.32 0.00 0.00 2.29
2923 3338 2.812358 ACCGGGCAATTCTTGAAAAC 57.188 45.000 6.32 0.00 0.00 2.43
2924 3339 2.035632 ACCGGGCAATTCTTGAAAACA 58.964 42.857 6.32 0.00 0.00 2.83
2925 3340 2.632512 ACCGGGCAATTCTTGAAAACAT 59.367 40.909 6.32 0.00 0.00 2.71
2926 3341 3.253230 CCGGGCAATTCTTGAAAACATC 58.747 45.455 0.00 0.00 0.00 3.06
2927 3342 3.056607 CCGGGCAATTCTTGAAAACATCT 60.057 43.478 0.00 0.00 0.00 2.90
2928 3343 4.168760 CGGGCAATTCTTGAAAACATCTC 58.831 43.478 0.00 0.00 0.00 2.75
2929 3344 4.321156 CGGGCAATTCTTGAAAACATCTCA 60.321 41.667 0.00 0.00 0.00 3.27
2930 3345 4.925646 GGGCAATTCTTGAAAACATCTCAC 59.074 41.667 0.00 0.00 0.00 3.51
2931 3346 4.618489 GGCAATTCTTGAAAACATCTCACG 59.382 41.667 0.00 0.00 0.00 4.35
2932 3347 5.215160 GCAATTCTTGAAAACATCTCACGT 58.785 37.500 0.00 0.00 0.00 4.49
2933 3348 5.116074 GCAATTCTTGAAAACATCTCACGTG 59.884 40.000 9.94 9.94 0.00 4.49
2934 3349 6.201517 CAATTCTTGAAAACATCTCACGTGT 58.798 36.000 16.51 0.00 0.00 4.49
2935 3350 5.811399 TTCTTGAAAACATCTCACGTGTT 57.189 34.783 16.51 0.00 41.28 3.32
2936 3351 6.912203 TTCTTGAAAACATCTCACGTGTTA 57.088 33.333 16.51 5.20 38.76 2.41
2937 3352 6.281848 TCTTGAAAACATCTCACGTGTTAC 57.718 37.500 16.51 1.44 38.76 2.50
2938 3353 5.235616 TCTTGAAAACATCTCACGTGTTACC 59.764 40.000 16.51 0.00 38.76 2.85
2939 3354 4.443621 TGAAAACATCTCACGTGTTACCA 58.556 39.130 16.51 1.31 38.76 3.25
2940 3355 4.876679 TGAAAACATCTCACGTGTTACCAA 59.123 37.500 16.51 0.00 38.76 3.67
2941 3356 5.007234 TGAAAACATCTCACGTGTTACCAAG 59.993 40.000 16.51 4.28 38.76 3.61
2942 3357 3.040147 ACATCTCACGTGTTACCAAGG 57.960 47.619 16.51 1.30 0.00 3.61
2943 3358 2.631062 ACATCTCACGTGTTACCAAGGA 59.369 45.455 16.51 3.12 0.00 3.36
2958 3373 2.440539 AAGGACTACTTGCAGACACG 57.559 50.000 0.00 0.00 38.21 4.49
2965 3380 1.978542 ACTTGCAGACACGATACGAC 58.021 50.000 0.00 0.00 0.00 4.34
2971 3386 1.063616 CAGACACGATACGACGGATGT 59.936 52.381 0.00 0.00 37.61 3.06
2977 3392 2.286831 ACGATACGACGGATGTCATGTC 60.287 50.000 0.00 0.00 45.80 3.06
2981 3396 3.967886 GACGGATGTCATGTCGGAT 57.032 52.632 9.18 0.00 44.82 4.18
2983 3398 3.577649 GACGGATGTCATGTCGGATAT 57.422 47.619 9.18 0.00 44.82 1.63
2984 3399 3.245797 GACGGATGTCATGTCGGATATG 58.754 50.000 8.29 8.29 44.82 1.78
2985 3400 2.890945 ACGGATGTCATGTCGGATATGA 59.109 45.455 12.69 12.69 32.44 2.15
2986 3401 3.511540 ACGGATGTCATGTCGGATATGAT 59.488 43.478 18.50 5.75 36.96 2.45
2987 3402 3.861689 CGGATGTCATGTCGGATATGATG 59.138 47.826 18.50 5.48 36.96 3.07
2988 3403 4.619160 CGGATGTCATGTCGGATATGATGT 60.619 45.833 18.50 11.29 36.96 3.06
2989 3404 4.867047 GGATGTCATGTCGGATATGATGTC 59.133 45.833 18.50 17.39 36.96 3.06
2990 3405 3.900941 TGTCATGTCGGATATGATGTCG 58.099 45.455 18.50 0.00 36.96 4.35
2991 3406 2.663602 GTCATGTCGGATATGATGTCGC 59.336 50.000 18.50 4.11 36.96 5.19
2992 3407 2.295909 TCATGTCGGATATGATGTCGCA 59.704 45.455 12.69 0.00 30.03 5.10
2993 3408 2.134201 TGTCGGATATGATGTCGCAC 57.866 50.000 0.00 0.00 0.00 5.34
2994 3409 1.681264 TGTCGGATATGATGTCGCACT 59.319 47.619 0.00 0.00 0.00 4.40
2995 3410 2.882137 TGTCGGATATGATGTCGCACTA 59.118 45.455 0.00 0.00 0.00 2.74
2996 3411 3.316868 TGTCGGATATGATGTCGCACTAA 59.683 43.478 0.00 0.00 0.00 2.24
2997 3412 4.022329 TGTCGGATATGATGTCGCACTAAT 60.022 41.667 0.00 0.00 0.00 1.73
2998 3413 4.559251 GTCGGATATGATGTCGCACTAATC 59.441 45.833 0.00 0.00 0.00 1.75
2999 3414 3.859961 CGGATATGATGTCGCACTAATCC 59.140 47.826 0.00 0.00 0.00 3.01
3000 3415 4.618227 CGGATATGATGTCGCACTAATCCA 60.618 45.833 0.00 0.00 32.85 3.41
3001 3416 5.423015 GGATATGATGTCGCACTAATCCAT 58.577 41.667 0.00 0.00 33.39 3.41
3002 3417 6.573434 GGATATGATGTCGCACTAATCCATA 58.427 40.000 0.00 0.00 33.39 2.74
3003 3418 7.041721 GGATATGATGTCGCACTAATCCATAA 58.958 38.462 0.00 0.00 33.39 1.90
3004 3419 7.549134 GGATATGATGTCGCACTAATCCATAAA 59.451 37.037 0.00 0.00 33.39 1.40
3005 3420 5.984233 TGATGTCGCACTAATCCATAAAC 57.016 39.130 0.00 0.00 0.00 2.01
3006 3421 5.670485 TGATGTCGCACTAATCCATAAACT 58.330 37.500 0.00 0.00 0.00 2.66
3007 3422 5.523552 TGATGTCGCACTAATCCATAAACTG 59.476 40.000 0.00 0.00 0.00 3.16
3008 3423 5.079689 TGTCGCACTAATCCATAAACTGA 57.920 39.130 0.00 0.00 0.00 3.41
3009 3424 4.868171 TGTCGCACTAATCCATAAACTGAC 59.132 41.667 0.00 0.00 0.00 3.51
3010 3425 5.109903 GTCGCACTAATCCATAAACTGACT 58.890 41.667 0.00 0.00 0.00 3.41
3011 3426 5.005779 GTCGCACTAATCCATAAACTGACTG 59.994 44.000 0.00 0.00 0.00 3.51
3012 3427 4.260375 CGCACTAATCCATAAACTGACTGC 60.260 45.833 0.00 0.00 0.00 4.40
3013 3428 4.635765 GCACTAATCCATAAACTGACTGCA 59.364 41.667 0.00 0.00 0.00 4.41
3014 3429 5.123820 GCACTAATCCATAAACTGACTGCAA 59.876 40.000 0.00 0.00 0.00 4.08
3015 3430 6.676456 GCACTAATCCATAAACTGACTGCAAG 60.676 42.308 0.00 0.00 42.29 4.01
3016 3431 5.882557 ACTAATCCATAAACTGACTGCAAGG 59.117 40.000 0.00 0.00 39.30 3.61
3040 3455 6.887002 GGAAACTTCCTAAAATCTCAGGTGAT 59.113 38.462 0.97 0.00 44.11 3.06
3077 3492 1.269936 GCATGACATTTATGCCCTGCC 60.270 52.381 0.00 0.00 43.88 4.85
3079 3494 0.034574 TGACATTTATGCCCTGCCGT 60.035 50.000 0.00 0.00 0.00 5.68
3080 3495 1.210722 TGACATTTATGCCCTGCCGTA 59.789 47.619 0.00 0.00 0.00 4.02
3091 3506 1.002087 CCCTGCCGTAACTGTTCTCTT 59.998 52.381 0.00 0.00 0.00 2.85
3094 3509 3.589988 CTGCCGTAACTGTTCTCTTGAT 58.410 45.455 0.00 0.00 0.00 2.57
3097 3512 2.673368 CCGTAACTGTTCTCTTGATGCC 59.327 50.000 0.00 0.00 0.00 4.40
3115 3531 1.471287 GCCGGTGGTCTGTTATTTTCC 59.529 52.381 1.90 0.00 0.00 3.13
3117 3533 3.418047 CCGGTGGTCTGTTATTTTCCTT 58.582 45.455 0.00 0.00 0.00 3.36
3119 3535 4.082949 CCGGTGGTCTGTTATTTTCCTTTC 60.083 45.833 0.00 0.00 0.00 2.62
3132 3548 5.982890 TTTTCCTTTCCTTCATCCATCAC 57.017 39.130 0.00 0.00 0.00 3.06
3133 3549 4.934797 TTCCTTTCCTTCATCCATCACT 57.065 40.909 0.00 0.00 0.00 3.41
3143 3559 6.655003 TCCTTCATCCATCACTTTCTGTAAAC 59.345 38.462 0.00 0.00 0.00 2.01
3184 3600 0.675837 GGATCAGCAGCTGCAACTCA 60.676 55.000 38.24 18.10 45.16 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 93 3.636300 AGTTCTGCATGGCACAACTAAAA 59.364 39.130 9.61 0.00 43.67 1.52
94 103 4.082571 ACTTACATGAAAGTTCTGCATGGC 60.083 41.667 0.00 0.00 42.70 4.40
212 225 4.389576 CCTCGCTTGTTGCCGCAC 62.390 66.667 0.00 0.00 38.78 5.34
246 259 4.342378 TGCCATGCTTTAGGTTGTTGTTTA 59.658 37.500 0.00 0.00 0.00 2.01
289 302 2.159296 CCTCATCCATGTTGCATGTGTG 60.159 50.000 8.11 6.53 0.00 3.82
292 305 2.097036 CACCTCATCCATGTTGCATGT 58.903 47.619 8.11 0.00 0.00 3.21
320 333 8.216423 ACCATGAAGATATCTTAAATCTGTGCT 58.784 33.333 17.94 0.00 36.11 4.40
321 334 8.388484 ACCATGAAGATATCTTAAATCTGTGC 57.612 34.615 17.94 3.33 36.11 4.57
437 450 8.593945 TCAGTATGATGTACTATGATATGCCA 57.406 34.615 0.00 0.00 42.56 4.92
482 495 9.291664 CTAAAATTTCTTTTACACGTGGTTTCA 57.708 29.630 21.57 0.00 36.09 2.69
540 558 6.607004 ACATAGCCTACCATAATACTCCAC 57.393 41.667 0.00 0.00 0.00 4.02
553 571 4.616181 ATTTGCGACAAACATAGCCTAC 57.384 40.909 7.08 0.00 0.00 3.18
557 575 6.526325 TGAAACATATTTGCGACAAACATAGC 59.474 34.615 7.08 0.00 0.00 2.97
610 628 2.609244 GGCGCACCTGATTAAGCAAAAA 60.609 45.455 10.83 0.00 0.00 1.94
611 629 1.067915 GGCGCACCTGATTAAGCAAAA 60.068 47.619 10.83 0.00 0.00 2.44
612 630 0.525761 GGCGCACCTGATTAAGCAAA 59.474 50.000 10.83 0.00 0.00 3.68
613 631 2.179764 GGCGCACCTGATTAAGCAA 58.820 52.632 10.83 0.00 0.00 3.91
614 632 3.903783 GGCGCACCTGATTAAGCA 58.096 55.556 10.83 0.00 0.00 3.91
624 642 0.109226 GATACGGATCTAGGCGCACC 60.109 60.000 10.83 1.23 0.00 5.01
625 643 0.109226 GGATACGGATCTAGGCGCAC 60.109 60.000 10.83 0.00 32.15 5.34
626 644 0.538746 TGGATACGGATCTAGGCGCA 60.539 55.000 10.83 0.00 42.51 6.09
627 645 0.601558 TTGGATACGGATCTAGGCGC 59.398 55.000 7.75 0.00 42.51 6.53
628 646 3.380479 TTTTGGATACGGATCTAGGCG 57.620 47.619 7.75 0.00 42.51 5.52
646 664 5.670485 GTGAAAAAGGAGGTGTGGATTTTT 58.330 37.500 0.00 0.00 36.17 1.94
647 665 4.202111 CGTGAAAAAGGAGGTGTGGATTTT 60.202 41.667 0.00 0.00 0.00 1.82
648 666 3.317993 CGTGAAAAAGGAGGTGTGGATTT 59.682 43.478 0.00 0.00 0.00 2.17
649 667 2.884639 CGTGAAAAAGGAGGTGTGGATT 59.115 45.455 0.00 0.00 0.00 3.01
650 668 2.504367 CGTGAAAAAGGAGGTGTGGAT 58.496 47.619 0.00 0.00 0.00 3.41
651 669 1.961793 CGTGAAAAAGGAGGTGTGGA 58.038 50.000 0.00 0.00 0.00 4.02
652 670 0.310854 GCGTGAAAAAGGAGGTGTGG 59.689 55.000 0.00 0.00 0.00 4.17
653 671 1.264288 GAGCGTGAAAAAGGAGGTGTG 59.736 52.381 0.00 0.00 0.00 3.82
654 672 1.141053 AGAGCGTGAAAAAGGAGGTGT 59.859 47.619 0.00 0.00 0.00 4.16
655 673 1.884235 AGAGCGTGAAAAAGGAGGTG 58.116 50.000 0.00 0.00 0.00 4.00
656 674 3.764237 TTAGAGCGTGAAAAAGGAGGT 57.236 42.857 0.00 0.00 0.00 3.85
657 675 5.629079 ATTTTAGAGCGTGAAAAAGGAGG 57.371 39.130 0.00 0.00 0.00 4.30
658 676 7.693951 CACATATTTTAGAGCGTGAAAAAGGAG 59.306 37.037 0.00 0.00 0.00 3.69
659 677 7.389330 TCACATATTTTAGAGCGTGAAAAAGGA 59.611 33.333 0.00 0.00 30.88 3.36
660 678 7.481798 GTCACATATTTTAGAGCGTGAAAAAGG 59.518 37.037 0.00 0.00 35.35 3.11
661 679 7.214449 CGTCACATATTTTAGAGCGTGAAAAAG 59.786 37.037 0.00 0.00 35.35 2.27
662 680 7.012943 CGTCACATATTTTAGAGCGTGAAAAA 58.987 34.615 0.00 0.00 35.35 1.94
663 681 6.366604 TCGTCACATATTTTAGAGCGTGAAAA 59.633 34.615 0.00 0.00 35.35 2.29
664 682 5.865013 TCGTCACATATTTTAGAGCGTGAAA 59.135 36.000 0.00 0.00 35.35 2.69
665 683 5.404096 TCGTCACATATTTTAGAGCGTGAA 58.596 37.500 0.00 0.00 35.35 3.18
666 684 4.989044 TCGTCACATATTTTAGAGCGTGA 58.011 39.130 0.00 0.00 0.00 4.35
667 685 5.890110 ATCGTCACATATTTTAGAGCGTG 57.110 39.130 0.00 0.00 0.00 5.34
668 686 5.919141 GGTATCGTCACATATTTTAGAGCGT 59.081 40.000 0.00 0.00 0.00 5.07
669 687 5.345202 GGGTATCGTCACATATTTTAGAGCG 59.655 44.000 0.00 0.00 0.00 5.03
670 688 6.220930 TGGGTATCGTCACATATTTTAGAGC 58.779 40.000 0.00 0.00 0.00 4.09
671 689 8.548721 GTTTGGGTATCGTCACATATTTTAGAG 58.451 37.037 0.00 0.00 0.00 2.43
672 690 7.496591 GGTTTGGGTATCGTCACATATTTTAGA 59.503 37.037 0.00 0.00 0.00 2.10
673 691 7.255001 GGGTTTGGGTATCGTCACATATTTTAG 60.255 40.741 0.00 0.00 0.00 1.85
674 692 6.543100 GGGTTTGGGTATCGTCACATATTTTA 59.457 38.462 0.00 0.00 0.00 1.52
675 693 5.358725 GGGTTTGGGTATCGTCACATATTTT 59.641 40.000 0.00 0.00 0.00 1.82
676 694 4.885325 GGGTTTGGGTATCGTCACATATTT 59.115 41.667 0.00 0.00 0.00 1.40
677 695 4.165372 AGGGTTTGGGTATCGTCACATATT 59.835 41.667 0.00 0.00 0.00 1.28
678 696 3.714798 AGGGTTTGGGTATCGTCACATAT 59.285 43.478 0.00 0.00 0.00 1.78
679 697 3.109151 AGGGTTTGGGTATCGTCACATA 58.891 45.455 0.00 0.00 0.00 2.29
680 698 1.913419 AGGGTTTGGGTATCGTCACAT 59.087 47.619 0.00 0.00 0.00 3.21
681 699 1.354101 AGGGTTTGGGTATCGTCACA 58.646 50.000 0.00 0.00 0.00 3.58
682 700 2.353323 GAAGGGTTTGGGTATCGTCAC 58.647 52.381 0.00 0.00 0.00 3.67
782 1001 2.282180 ACCTCGCACGCCCAATTT 60.282 55.556 0.00 0.00 0.00 1.82
823 1042 2.043992 TCTTTGGACACGAAGGGAGAA 58.956 47.619 0.00 0.00 38.43 2.87
828 1047 1.566018 GGCGTCTTTGGACACGAAGG 61.566 60.000 0.00 0.00 42.21 3.46
833 1052 1.595929 TTCCGGCGTCTTTGGACAC 60.596 57.895 6.01 0.00 42.21 3.67
945 1188 5.525378 CGATTTCGATCTCTGAAAAGGGAAT 59.475 40.000 0.00 0.00 43.02 3.01
1140 1394 1.168714 GGTCCAGCATGAACTTGTCC 58.831 55.000 0.00 0.00 39.69 4.02
1225 1491 1.717194 TCGGCGTCAAAGGATAACAC 58.283 50.000 6.85 0.00 0.00 3.32
1412 1711 8.618677 CGACAATCTGGTAGTAATAGTTCAGTA 58.381 37.037 0.00 0.00 0.00 2.74
1465 1764 0.034896 ACCCAAAGCACTCGGTACTG 59.965 55.000 0.00 0.00 0.00 2.74
1498 1815 7.961325 AAAAAGTTCTGTGATTTGTGTTGTT 57.039 28.000 0.00 0.00 0.00 2.83
1580 1897 1.135689 GTGATGACGATGTTGGTTGCC 60.136 52.381 0.00 0.00 0.00 4.52
1581 1898 1.135689 GGTGATGACGATGTTGGTTGC 60.136 52.381 0.00 0.00 0.00 4.17
1593 1910 3.077359 CAGTTCCAAGGAAGGTGATGAC 58.923 50.000 0.88 0.00 34.49 3.06
1596 1913 1.272147 GCCAGTTCCAAGGAAGGTGAT 60.272 52.381 0.88 0.00 34.49 3.06
1764 2084 2.674380 GGCAACTGGGCTGGACAG 60.674 66.667 0.00 0.00 41.64 3.51
1912 2250 7.018449 TGGTGATTCATCCATCCCTGATAAATA 59.982 37.037 0.00 0.00 0.00 1.40
2075 2446 1.269723 GGGTAAGCCACAAGTTCTTGC 59.730 52.381 11.79 0.00 36.17 4.01
2197 2568 2.291209 TCCAGATGAAGCAAGGCAAA 57.709 45.000 0.00 0.00 0.00 3.68
2198 2569 2.097036 CATCCAGATGAAGCAAGGCAA 58.903 47.619 1.16 0.00 41.20 4.52
2253 2625 7.630242 AAGAAGAACTGAGAACAATGACAAA 57.370 32.000 0.00 0.00 0.00 2.83
2283 2655 9.793252 CCAAAGCGTTAAATTCTACTAGTAGTA 57.207 33.333 25.58 18.71 34.84 1.82
2285 2657 8.922058 TCCAAAGCGTTAAATTCTACTAGTAG 57.078 34.615 21.87 21.87 34.56 2.57
2294 2666 7.029563 ACTGAATCATCCAAAGCGTTAAATTC 58.970 34.615 0.00 0.00 0.00 2.17
2295 2667 6.924111 ACTGAATCATCCAAAGCGTTAAATT 58.076 32.000 0.00 0.00 0.00 1.82
2297 2669 5.957842 ACTGAATCATCCAAAGCGTTAAA 57.042 34.783 0.00 0.00 0.00 1.52
2299 2671 7.011389 CAGAATACTGAATCATCCAAAGCGTTA 59.989 37.037 0.00 0.00 46.03 3.18
2300 2672 5.882557 AGAATACTGAATCATCCAAAGCGTT 59.117 36.000 0.00 0.00 0.00 4.84
2301 2673 5.295292 CAGAATACTGAATCATCCAAAGCGT 59.705 40.000 0.00 0.00 46.03 5.07
2302 2674 5.745514 CAGAATACTGAATCATCCAAAGCG 58.254 41.667 0.00 0.00 46.03 4.68
2317 2698 5.221722 TGGACAGAAGCAGTTTCAGAATACT 60.222 40.000 0.00 0.00 38.31 2.12
2325 2706 1.239347 GGGTGGACAGAAGCAGTTTC 58.761 55.000 0.00 0.00 35.97 2.78
2356 2737 8.622157 TCCGTGTAATTGTAAAGAAAAATGTGA 58.378 29.630 0.00 0.00 0.00 3.58
2366 2747 5.178623 TCAAGCTGTCCGTGTAATTGTAAAG 59.821 40.000 0.00 0.00 0.00 1.85
2367 2748 5.057819 TCAAGCTGTCCGTGTAATTGTAAA 58.942 37.500 0.00 0.00 0.00 2.01
2368 2749 4.633175 TCAAGCTGTCCGTGTAATTGTAA 58.367 39.130 0.00 0.00 0.00 2.41
2371 2752 2.159653 GCTCAAGCTGTCCGTGTAATTG 60.160 50.000 0.00 0.00 38.21 2.32
2372 2753 2.076863 GCTCAAGCTGTCCGTGTAATT 58.923 47.619 0.00 0.00 38.21 1.40
2374 2755 0.391228 TGCTCAAGCTGTCCGTGTAA 59.609 50.000 3.32 0.00 42.66 2.41
2376 2757 1.146041 TTGCTCAAGCTGTCCGTGT 59.854 52.632 3.32 0.00 42.66 4.49
2377 2758 0.882042 AGTTGCTCAAGCTGTCCGTG 60.882 55.000 3.32 0.00 42.66 4.94
2378 2759 0.882042 CAGTTGCTCAAGCTGTCCGT 60.882 55.000 3.32 0.00 42.66 4.69
2379 2760 1.864862 CAGTTGCTCAAGCTGTCCG 59.135 57.895 3.32 0.00 42.66 4.79
2380 2761 1.578423 GCAGTTGCTCAAGCTGTCC 59.422 57.895 3.32 0.00 42.66 4.02
2381 2762 1.578423 GGCAGTTGCTCAAGCTGTC 59.422 57.895 3.88 7.22 42.66 3.51
2382 2763 1.900498 GGGCAGTTGCTCAAGCTGT 60.900 57.895 3.88 0.00 42.27 4.40
2383 2764 1.602888 AGGGCAGTTGCTCAAGCTG 60.603 57.895 6.77 0.00 46.01 4.24
2384 2765 1.602888 CAGGGCAGTTGCTCAAGCT 60.603 57.895 6.77 0.00 46.01 3.74
2385 2766 1.174712 TTCAGGGCAGTTGCTCAAGC 61.175 55.000 6.77 0.00 46.01 4.01
2386 2767 1.321474 TTTCAGGGCAGTTGCTCAAG 58.679 50.000 6.77 0.00 46.01 3.02
2391 2773 2.352715 GGTACAATTTCAGGGCAGTTGC 60.353 50.000 0.00 0.00 41.14 4.17
2423 2805 7.331687 GGAAAAATCTGTATGTGTTCCCAATTG 59.668 37.037 0.00 0.00 0.00 2.32
2427 2809 4.457603 CGGAAAAATCTGTATGTGTTCCCA 59.542 41.667 0.00 0.00 31.30 4.37
2428 2810 4.698304 TCGGAAAAATCTGTATGTGTTCCC 59.302 41.667 0.00 0.00 31.30 3.97
2440 2822 4.273318 CAAGGGAAGGATCGGAAAAATCT 58.727 43.478 0.00 0.00 0.00 2.40
2447 2829 0.541863 GAAGCAAGGGAAGGATCGGA 59.458 55.000 0.00 0.00 0.00 4.55
2448 2830 0.464554 GGAAGCAAGGGAAGGATCGG 60.465 60.000 0.00 0.00 0.00 4.18
2463 2846 2.858745 TCTGGAAACGGGAAAAGGAAG 58.141 47.619 0.00 0.00 37.31 3.46
2495 2880 9.268268 GCTACTTTACCATAAGCATAACACATA 57.732 33.333 0.00 0.00 33.38 2.29
2501 2886 8.568676 TGTTTGCTACTTTACCATAAGCATAA 57.431 30.769 0.00 0.00 42.34 1.90
2510 2895 9.871238 TTGTTAATTTTGTTTGCTACTTTACCA 57.129 25.926 0.00 0.00 0.00 3.25
2533 2926 9.178758 GAGAATGAAGTGTAGGGAATAATTTGT 57.821 33.333 0.00 0.00 0.00 2.83
2539 2932 9.303116 GAGATAGAGAATGAAGTGTAGGGAATA 57.697 37.037 0.00 0.00 0.00 1.75
2546 2939 7.761704 GTGCAAAGAGATAGAGAATGAAGTGTA 59.238 37.037 0.00 0.00 0.00 2.90
2559 2952 8.299570 ACAGTAAAATTTGGTGCAAAGAGATAG 58.700 33.333 0.00 0.00 36.76 2.08
2565 2958 5.814705 TCCAACAGTAAAATTTGGTGCAAAG 59.185 36.000 0.00 0.00 40.68 2.77
2567 2960 5.344743 TCCAACAGTAAAATTTGGTGCAA 57.655 34.783 0.00 0.00 40.68 4.08
2568 2961 5.344743 TTCCAACAGTAAAATTTGGTGCA 57.655 34.783 0.00 0.00 40.68 4.57
2569 2962 5.236263 CCTTTCCAACAGTAAAATTTGGTGC 59.764 40.000 0.00 0.00 40.68 5.01
2570 2963 6.345298 ACCTTTCCAACAGTAAAATTTGGTG 58.655 36.000 0.00 0.00 40.68 4.17
2571 2964 6.553953 ACCTTTCCAACAGTAAAATTTGGT 57.446 33.333 0.00 0.00 40.68 3.67
2572 2965 7.272244 AGAACCTTTCCAACAGTAAAATTTGG 58.728 34.615 0.00 0.00 41.12 3.28
2573 2966 8.716646 AAGAACCTTTCCAACAGTAAAATTTG 57.283 30.769 0.00 0.00 0.00 2.32
2595 2988 6.579666 ATGCATTGAAAAGCTCTTGTAAGA 57.420 33.333 0.00 0.00 0.00 2.10
2605 2998 5.910637 TCTCAACAAATGCATTGAAAAGC 57.089 34.783 13.82 0.00 41.85 3.51
2609 3002 6.822676 ACCTTTTTCTCAACAAATGCATTGAA 59.177 30.769 13.82 8.06 41.85 2.69
2610 3003 6.347696 ACCTTTTTCTCAACAAATGCATTGA 58.652 32.000 13.82 6.49 41.85 2.57
2611 3004 6.607735 ACCTTTTTCTCAACAAATGCATTG 57.392 33.333 13.82 9.78 44.95 2.82
2616 3009 6.813152 ACACTGAACCTTTTTCTCAACAAATG 59.187 34.615 0.00 0.00 0.00 2.32
2617 3010 6.813152 CACACTGAACCTTTTTCTCAACAAAT 59.187 34.615 0.00 0.00 0.00 2.32
2621 3014 4.398044 TCCACACTGAACCTTTTTCTCAAC 59.602 41.667 0.00 0.00 0.00 3.18
2629 3022 4.086457 AGTTGTTTCCACACTGAACCTTT 58.914 39.130 0.00 0.00 30.32 3.11
2630 3023 3.697166 AGTTGTTTCCACACTGAACCTT 58.303 40.909 0.00 0.00 30.32 3.50
2644 3037 9.520515 ACCATCACAGATATCTTAAAGTTGTTT 57.479 29.630 1.33 0.00 0.00 2.83
2677 3085 5.360591 ACACAGGTCTTTGTCTTCTGTTAG 58.639 41.667 0.00 0.00 36.66 2.34
2719 3127 6.317789 TCCAGCACTACAAAATCTGAAAAG 57.682 37.500 0.00 0.00 0.00 2.27
2724 3132 6.506500 AAAGATCCAGCACTACAAAATCTG 57.493 37.500 0.00 0.00 0.00 2.90
2761 3169 6.319405 GTCGCCTCCAAAAAGGGTAAAATATA 59.681 38.462 0.00 0.00 36.88 0.86
2774 3182 1.269448 GCAATGAAGTCGCCTCCAAAA 59.731 47.619 0.00 0.00 0.00 2.44
2781 3189 1.994779 CCATTTTGCAATGAAGTCGCC 59.005 47.619 0.00 0.00 42.35 5.54
2796 3209 4.657814 ACTGTGGGTGATCTTACCATTT 57.342 40.909 4.72 0.00 42.69 2.32
2801 3214 7.739498 TTTTCTTTACTGTGGGTGATCTTAC 57.261 36.000 0.00 0.00 0.00 2.34
2807 3220 8.754991 TTTCTTATTTTCTTTACTGTGGGTGA 57.245 30.769 0.00 0.00 0.00 4.02
2818 3231 9.264719 CAGCAACCAGATTTTCTTATTTTCTTT 57.735 29.630 0.00 0.00 0.00 2.52
2828 3241 1.260544 GGCCAGCAACCAGATTTTCT 58.739 50.000 0.00 0.00 0.00 2.52
2846 3259 3.165071 AGTAAGGGGTGAAAATGCTTGG 58.835 45.455 0.00 0.00 0.00 3.61
2848 3261 3.506067 CGAAGTAAGGGGTGAAAATGCTT 59.494 43.478 0.00 0.00 0.00 3.91
2850 3263 3.078837 TCGAAGTAAGGGGTGAAAATGC 58.921 45.455 0.00 0.00 0.00 3.56
2851 3264 3.439129 GGTCGAAGTAAGGGGTGAAAATG 59.561 47.826 0.00 0.00 0.00 2.32
2852 3265 3.073356 TGGTCGAAGTAAGGGGTGAAAAT 59.927 43.478 0.00 0.00 0.00 1.82
2853 3266 2.438763 TGGTCGAAGTAAGGGGTGAAAA 59.561 45.455 0.00 0.00 0.00 2.29
2869 3284 4.323336 CGAAATATTTGCAAAAGGTGGTCG 59.677 41.667 17.19 15.50 0.00 4.79
2877 3292 8.449085 TTGTTATACGCGAAATATTTGCAAAA 57.551 26.923 17.19 6.25 0.00 2.44
2878 3293 8.621921 ATTGTTATACGCGAAATATTTGCAAA 57.378 26.923 15.93 15.44 0.00 3.68
2893 3308 4.753107 AGAATTGCCCGGTATTGTTATACG 59.247 41.667 0.00 0.00 37.99 3.06
2910 3325 6.692681 AACACGTGAGATGTTTTCAAGAATTG 59.307 34.615 25.01 0.00 41.72 2.32
2911 3326 6.377327 ACACGTGAGATGTTTTCAAGAATT 57.623 33.333 25.01 0.00 0.00 2.17
2912 3327 6.377327 AACACGTGAGATGTTTTCAAGAAT 57.623 33.333 25.01 0.00 36.93 2.40
2913 3328 5.811399 AACACGTGAGATGTTTTCAAGAA 57.189 34.783 25.01 0.00 36.93 2.52
2914 3329 5.235616 GGTAACACGTGAGATGTTTTCAAGA 59.764 40.000 25.01 0.00 40.68 3.02
2915 3330 5.007234 TGGTAACACGTGAGATGTTTTCAAG 59.993 40.000 25.01 0.00 46.17 3.02
2916 3331 4.876679 TGGTAACACGTGAGATGTTTTCAA 59.123 37.500 25.01 0.00 46.17 2.69
2917 3332 4.443621 TGGTAACACGTGAGATGTTTTCA 58.556 39.130 25.01 4.85 46.17 2.69
2939 3354 1.961394 TCGTGTCTGCAAGTAGTCCTT 59.039 47.619 0.00 0.00 33.76 3.36
2940 3355 1.617322 TCGTGTCTGCAAGTAGTCCT 58.383 50.000 0.00 0.00 33.76 3.85
2941 3356 2.656560 ATCGTGTCTGCAAGTAGTCC 57.343 50.000 0.00 0.00 33.76 3.85
2942 3357 3.099362 CGTATCGTGTCTGCAAGTAGTC 58.901 50.000 0.00 0.00 33.76 2.59
2943 3358 2.745821 TCGTATCGTGTCTGCAAGTAGT 59.254 45.455 0.00 0.00 33.76 2.73
2958 3373 2.307929 CGACATGACATCCGTCGTATC 58.692 52.381 16.26 0.00 45.80 2.24
2965 3380 3.575965 TCATATCCGACATGACATCCG 57.424 47.619 0.00 0.00 0.00 4.18
2971 3386 2.295909 TGCGACATCATATCCGACATGA 59.704 45.455 0.00 0.00 36.86 3.07
2977 3392 3.859961 GGATTAGTGCGACATCATATCCG 59.140 47.826 0.00 0.00 0.00 4.18
2978 3393 4.820897 TGGATTAGTGCGACATCATATCC 58.179 43.478 0.00 0.00 0.00 2.59
2979 3394 8.383619 GTTTATGGATTAGTGCGACATCATATC 58.616 37.037 0.00 0.00 0.00 1.63
2980 3395 8.097038 AGTTTATGGATTAGTGCGACATCATAT 58.903 33.333 0.00 0.00 0.00 1.78
2981 3396 7.384932 CAGTTTATGGATTAGTGCGACATCATA 59.615 37.037 0.00 0.00 0.00 2.15
2982 3397 6.203530 CAGTTTATGGATTAGTGCGACATCAT 59.796 38.462 0.00 0.00 0.00 2.45
2983 3398 5.523552 CAGTTTATGGATTAGTGCGACATCA 59.476 40.000 0.00 0.00 0.00 3.07
2984 3399 5.753438 TCAGTTTATGGATTAGTGCGACATC 59.247 40.000 0.00 0.00 0.00 3.06
2985 3400 5.523916 GTCAGTTTATGGATTAGTGCGACAT 59.476 40.000 0.00 0.00 0.00 3.06
2986 3401 4.868171 GTCAGTTTATGGATTAGTGCGACA 59.132 41.667 0.00 0.00 0.00 4.35
2987 3402 5.005779 CAGTCAGTTTATGGATTAGTGCGAC 59.994 44.000 0.00 0.00 0.00 5.19
2988 3403 5.109210 CAGTCAGTTTATGGATTAGTGCGA 58.891 41.667 0.00 0.00 0.00 5.10
2989 3404 4.260375 GCAGTCAGTTTATGGATTAGTGCG 60.260 45.833 0.00 0.00 0.00 5.34
2990 3405 4.635765 TGCAGTCAGTTTATGGATTAGTGC 59.364 41.667 0.00 0.00 31.93 4.40
2991 3406 6.183360 CCTTGCAGTCAGTTTATGGATTAGTG 60.183 42.308 0.00 0.00 0.00 2.74
2992 3407 5.882557 CCTTGCAGTCAGTTTATGGATTAGT 59.117 40.000 0.00 0.00 0.00 2.24
2993 3408 6.115446 TCCTTGCAGTCAGTTTATGGATTAG 58.885 40.000 0.00 0.00 0.00 1.73
2994 3409 6.061022 TCCTTGCAGTCAGTTTATGGATTA 57.939 37.500 0.00 0.00 0.00 1.75
2995 3410 4.922206 TCCTTGCAGTCAGTTTATGGATT 58.078 39.130 0.00 0.00 0.00 3.01
2996 3411 4.574674 TCCTTGCAGTCAGTTTATGGAT 57.425 40.909 0.00 0.00 0.00 3.41
2997 3412 4.365514 TTCCTTGCAGTCAGTTTATGGA 57.634 40.909 0.00 0.00 0.00 3.41
2998 3413 4.520492 AGTTTCCTTGCAGTCAGTTTATGG 59.480 41.667 0.00 0.00 0.00 2.74
2999 3414 5.695851 AGTTTCCTTGCAGTCAGTTTATG 57.304 39.130 0.00 0.00 0.00 1.90
3000 3415 5.241728 GGAAGTTTCCTTGCAGTCAGTTTAT 59.758 40.000 3.63 0.00 44.11 1.40
3001 3416 4.578928 GGAAGTTTCCTTGCAGTCAGTTTA 59.421 41.667 3.63 0.00 44.11 2.01
3002 3417 3.381590 GGAAGTTTCCTTGCAGTCAGTTT 59.618 43.478 3.63 0.00 44.11 2.66
3003 3418 2.952310 GGAAGTTTCCTTGCAGTCAGTT 59.048 45.455 3.63 0.00 44.11 3.16
3004 3419 2.576615 GGAAGTTTCCTTGCAGTCAGT 58.423 47.619 3.63 0.00 44.11 3.41
3016 3431 7.826744 AGATCACCTGAGATTTTAGGAAGTTTC 59.173 37.037 0.53 0.00 37.52 2.78
3040 3455 7.953005 TGTCATGCCTCCAAATTTTAATAGA 57.047 32.000 0.00 0.00 0.00 1.98
3049 3464 4.952460 GCATAAATGTCATGCCTCCAAAT 58.048 39.130 0.00 0.00 42.41 2.32
3074 3489 3.325870 CATCAAGAGAACAGTTACGGCA 58.674 45.455 0.00 0.00 0.00 5.69
3077 3492 2.345641 CGGCATCAAGAGAACAGTTACG 59.654 50.000 0.00 0.00 0.00 3.18
3079 3494 2.301870 ACCGGCATCAAGAGAACAGTTA 59.698 45.455 0.00 0.00 0.00 2.24
3080 3495 1.072331 ACCGGCATCAAGAGAACAGTT 59.928 47.619 0.00 0.00 0.00 3.16
3091 3506 0.908910 ATAACAGACCACCGGCATCA 59.091 50.000 0.00 0.00 0.00 3.07
3094 3509 2.156098 GAAAATAACAGACCACCGGCA 58.844 47.619 0.00 0.00 0.00 5.69
3097 3512 4.082949 GGAAAGGAAAATAACAGACCACCG 60.083 45.833 0.00 0.00 0.00 4.94
3115 3531 5.709164 ACAGAAAGTGATGGATGAAGGAAAG 59.291 40.000 0.00 0.00 0.00 2.62
3117 3533 5.246981 ACAGAAAGTGATGGATGAAGGAA 57.753 39.130 0.00 0.00 0.00 3.36
3119 3535 6.656693 AGTTTACAGAAAGTGATGGATGAAGG 59.343 38.462 0.00 0.00 0.00 3.46
3143 3559 7.490962 TCCAAACAGTAAATGTGACTACAAG 57.509 36.000 0.00 0.00 43.00 3.16


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

AutoCloner maintained by Alex Coulton.