Multiple sequence alignment - TraesCS2B01G118000

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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 TraesCS2B01G118000 chr2B 100.000 5022 0 0 1 5022 81764235 81759214 0.000000e+00 9274.0
1 TraesCS2B01G118000 chr2D 91.877 2659 115 31 2385 4993 52233209 52230602 0.000000e+00 3620.0
2 TraesCS2B01G118000 chr2D 88.736 1811 143 43 4 1777 52235866 52234080 0.000000e+00 2158.0
3 TraesCS2B01G118000 chr2D 94.073 658 18 8 1756 2393 52234017 52233361 0.000000e+00 979.0
4 TraesCS2B01G118000 chr2A 94.570 1989 87 12 2385 4353 53788563 53786576 0.000000e+00 3055.0
5 TraesCS2B01G118000 chr2A 92.692 1560 79 17 855 2393 53790255 53788710 0.000000e+00 2217.0
6 TraesCS2B01G118000 chr2A 89.957 468 18 14 4499 4943 53786492 53786031 1.210000e-160 577.0
7 TraesCS2B01G118000 chr3D 84.255 235 29 7 518 746 394193664 394193432 6.540000e-54 222.0
8 TraesCS2B01G118000 chr3D 95.918 49 1 1 352 399 591123644 591123596 1.500000e-10 78.7
9 TraesCS2B01G118000 chr5B 94.118 68 3 1 516 583 590647638 590647704 8.890000e-18 102.0
10 TraesCS2B01G118000 chr5B 94.118 68 3 1 516 583 590738143 590738209 8.890000e-18 102.0
11 TraesCS2B01G118000 chr5D 82.796 93 14 2 516 607 119910448 119910357 1.160000e-11 82.4
12 TraesCS2B01G118000 chr1A 76.433 157 25 7 517 669 116711643 116711791 1.940000e-09 75.0
13 TraesCS2B01G118000 chr3B 87.037 54 6 1 346 398 448755607 448755554 5.430000e-05 60.2


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 TraesCS2B01G118000 chr2B 81759214 81764235 5021 True 9274.000000 9274 100.000000 1 5022 1 chr2B.!!$R1 5021
1 TraesCS2B01G118000 chr2D 52230602 52235866 5264 True 2252.333333 3620 91.562000 4 4993 3 chr2D.!!$R1 4989
2 TraesCS2B01G118000 chr2A 53786031 53790255 4224 True 1949.666667 3055 92.406333 855 4943 3 chr2A.!!$R1 4088

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
873 901 0.108329 ATCCGACCCGCTTAACAGTG 60.108 55.0 0.00 0.0 0.00 3.66 F
1153 1181 0.036306 TTCTCCCCCTTTCAGTTCGC 59.964 55.0 0.00 0.0 0.00 4.70 F
1261 1289 1.481871 TTCCTCTCCCGTATGGACAC 58.518 55.0 1.27 0.0 38.61 3.67 F
3067 3371 0.533032 GCAAGAGTAAGAGCTCCGGT 59.467 55.0 10.93 0.0 36.20 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2044 2169 1.380302 GGGCACAGGTGAGTCCAAT 59.620 57.895 3.1 0.0 39.02 3.16 R
2126 2251 1.880027 GACATGGTCTGGTTTGTGGTC 59.120 52.381 0.0 0.0 0.00 4.02 R
3171 3475 0.478072 AGTGGCATCAGACCCAAACA 59.522 50.000 0.0 0.0 31.90 2.83 R
4313 4645 0.108804 TCCTCGGCTGATTCGTGTTC 60.109 55.000 0.0 0.0 0.00 3.18 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
31 32 9.538508 CATCAATAGTTGACACTCTCATTCATA 57.461 33.333 0.00 0.00 43.48 2.15
64 66 2.631160 ATTTGACCGTGTTCACTCCA 57.369 45.000 1.53 0.00 0.00 3.86
65 67 1.658994 TTTGACCGTGTTCACTCCAC 58.341 50.000 1.53 0.00 0.00 4.02
66 68 0.537653 TTGACCGTGTTCACTCCACA 59.462 50.000 1.53 0.00 33.00 4.17
79 81 3.580022 TCACTCCACAGACACATGAGAAT 59.420 43.478 0.00 0.00 0.00 2.40
80 82 3.931468 CACTCCACAGACACATGAGAATC 59.069 47.826 0.00 0.00 0.00 2.52
116 118 5.816258 TGTGAAATCAATGCAAAAGCTTTGA 59.184 32.000 13.54 17.28 37.92 2.69
128 130 7.208777 TGCAAAAGCTTTGATTGTTCTATTGA 58.791 30.769 13.54 0.00 0.00 2.57
167 169 6.259638 TGTTGTCAGGTTAATCACGAAAAAC 58.740 36.000 0.00 0.00 0.00 2.43
170 172 4.211794 GTCAGGTTAATCACGAAAAACCGA 59.788 41.667 0.00 6.42 44.90 4.69
176 178 6.418523 GGTTAATCACGAAAAACCGAACAAAT 59.581 34.615 0.00 0.00 32.69 2.32
191 195 5.277974 CCGAACAAATGATACATCCATGACC 60.278 44.000 0.00 0.00 0.00 4.02
203 207 3.474798 TCCATGACCAAGACTACTCCT 57.525 47.619 0.00 0.00 0.00 3.69
204 208 3.099905 TCCATGACCAAGACTACTCCTG 58.900 50.000 0.00 0.00 0.00 3.86
210 214 1.347707 CCAAGACTACTCCTGCCAACA 59.652 52.381 0.00 0.00 0.00 3.33
215 219 1.488812 ACTACTCCTGCCAACAACACA 59.511 47.619 0.00 0.00 0.00 3.72
218 222 1.133823 ACTCCTGCCAACAACACATCA 60.134 47.619 0.00 0.00 0.00 3.07
237 241 4.782019 TCAAACTCAACAAAAGCACACT 57.218 36.364 0.00 0.00 0.00 3.55
239 243 6.260870 TCAAACTCAACAAAAGCACACTAA 57.739 33.333 0.00 0.00 0.00 2.24
241 245 4.632538 ACTCAACAAAAGCACACTAACC 57.367 40.909 0.00 0.00 0.00 2.85
244 248 3.630312 TCAACAAAAGCACACTAACCTCC 59.370 43.478 0.00 0.00 0.00 4.30
245 249 2.218603 ACAAAAGCACACTAACCTCCG 58.781 47.619 0.00 0.00 0.00 4.63
266 281 2.746279 AACACAAACCCACTCCATCA 57.254 45.000 0.00 0.00 0.00 3.07
273 288 1.632589 ACCCACTCCATCAAAAAGCC 58.367 50.000 0.00 0.00 0.00 4.35
279 294 2.554032 ACTCCATCAAAAAGCCGACTTG 59.446 45.455 0.00 0.00 35.85 3.16
282 297 0.240945 ATCAAAAAGCCGACTTGCCG 59.759 50.000 0.00 0.00 35.85 5.69
326 341 4.595762 TGTTAACATATACTCCCTCCGC 57.404 45.455 3.59 0.00 0.00 5.54
340 355 2.352814 CCCTCCGCTCCATATTAAGTCG 60.353 54.545 0.00 0.00 0.00 4.18
341 356 2.296471 CCTCCGCTCCATATTAAGTCGT 59.704 50.000 0.00 0.00 0.00 4.34
342 357 3.243771 CCTCCGCTCCATATTAAGTCGTT 60.244 47.826 0.00 0.00 0.00 3.85
343 358 4.022589 CCTCCGCTCCATATTAAGTCGTTA 60.023 45.833 0.00 0.00 0.00 3.18
380 395 9.672673 ACTTTATGCTAAATCAGTGACACTTAT 57.327 29.630 5.04 0.08 0.00 1.73
406 422 6.126568 TGAAACGAAGGAGTAAACAAAAGG 57.873 37.500 0.00 0.00 0.00 3.11
411 427 5.469084 ACGAAGGAGTAAACAAAAGGATGAC 59.531 40.000 0.00 0.00 0.00 3.06
416 432 7.004086 AGGAGTAAACAAAAGGATGACATGAA 58.996 34.615 0.00 0.00 0.00 2.57
439 455 9.844257 TGAACCATATCATCATGTGTTTATACA 57.156 29.630 0.00 0.00 34.63 2.29
513 532 9.676195 TTTGTGACAAATCATGTGTTTATACAG 57.324 29.630 6.66 0.00 44.12 2.74
514 533 8.389779 TGTGACAAATCATGTGTTTATACAGT 57.610 30.769 0.00 0.00 44.12 3.55
516 535 7.962918 GTGACAAATCATGTGTTTATACAGTCC 59.037 37.037 0.00 0.00 44.12 3.85
535 554 5.520288 CAGTCCAAATGATAAGTACCAGACG 59.480 44.000 0.00 0.00 0.00 4.18
556 575 0.877213 GTGGCACGAAGTAACACCGT 60.877 55.000 0.00 0.00 41.61 4.83
560 579 1.068333 GCACGAAGTAACACCGTCCTA 60.068 52.381 0.00 0.00 41.61 2.94
582 601 9.235537 TCCTAACGTTTTTACAACTAAAATTGC 57.764 29.630 5.91 0.00 32.90 3.56
585 604 8.426881 AACGTTTTTACAACTAAAATTGCCAT 57.573 26.923 0.00 0.00 32.90 4.40
586 605 8.067780 ACGTTTTTACAACTAAAATTGCCATC 57.932 30.769 0.00 0.00 32.90 3.51
587 606 7.096394 ACGTTTTTACAACTAAAATTGCCATCG 60.096 33.333 0.00 0.00 32.90 3.84
588 607 7.506474 GTTTTTACAACTAAAATTGCCATCGG 58.494 34.615 0.00 0.00 32.90 4.18
593 613 6.284459 ACAACTAAAATTGCCATCGGAAAAA 58.716 32.000 0.00 0.00 32.47 1.94
633 656 3.951680 ACTGAAACTTACCACCAAACAGG 59.048 43.478 0.00 0.00 45.67 4.00
640 663 1.111277 ACCACCAAACAGGAAGTTGC 58.889 50.000 0.00 0.00 41.19 4.17
649 672 0.169672 CAGGAAGTTGCCATGCTTCG 59.830 55.000 5.16 0.00 41.29 3.79
658 681 1.611006 TGCCATGCTTCGCAACTAAAA 59.389 42.857 0.00 0.00 43.62 1.52
662 685 4.484236 CCATGCTTCGCAACTAAAATTGA 58.516 39.130 0.00 0.00 43.62 2.57
669 692 5.957842 TCGCAACTAAAATTGACATCCTT 57.042 34.783 0.00 0.00 0.00 3.36
672 695 6.876789 TCGCAACTAAAATTGACATCCTTAGA 59.123 34.615 0.00 0.00 0.00 2.10
689 712 9.778741 CATCCTTAGATAACTAAACTTGCCATA 57.221 33.333 0.00 0.00 38.01 2.74
722 745 2.423538 GGACGAAATTGCTTAGTGCCAT 59.576 45.455 0.00 0.00 42.00 4.40
724 747 4.275936 GGACGAAATTGCTTAGTGCCATAT 59.724 41.667 0.00 0.00 42.00 1.78
726 749 4.881273 ACGAAATTGCTTAGTGCCATATGA 59.119 37.500 3.65 0.00 42.00 2.15
727 750 5.532406 ACGAAATTGCTTAGTGCCATATGAT 59.468 36.000 3.65 0.00 42.00 2.45
728 751 5.854866 CGAAATTGCTTAGTGCCATATGATG 59.145 40.000 3.65 0.00 42.00 3.07
729 752 6.293571 CGAAATTGCTTAGTGCCATATGATGA 60.294 38.462 3.65 0.00 42.00 2.92
730 753 5.954296 ATTGCTTAGTGCCATATGATGAC 57.046 39.130 3.65 0.00 42.00 3.06
731 754 4.420522 TGCTTAGTGCCATATGATGACA 57.579 40.909 3.65 0.00 42.00 3.58
732 755 4.129380 TGCTTAGTGCCATATGATGACAC 58.871 43.478 3.65 7.10 42.96 3.67
750 773 3.709653 GACACCTATCAGGGTCCATACAA 59.290 47.826 0.00 0.00 40.58 2.41
763 786 6.391227 GGTCCATACAACCCAAATGATAAG 57.609 41.667 0.00 0.00 0.00 1.73
764 787 5.891551 GGTCCATACAACCCAAATGATAAGT 59.108 40.000 0.00 0.00 0.00 2.24
765 788 6.183360 GGTCCATACAACCCAAATGATAAGTG 60.183 42.308 0.00 0.00 0.00 3.16
767 790 5.451798 CCATACAACCCAAATGATAAGTGCC 60.452 44.000 0.00 0.00 0.00 5.01
804 832 4.468007 ACGACGGGTGAAAAAGGG 57.532 55.556 0.00 0.00 0.00 3.95
806 834 0.180878 ACGACGGGTGAAAAAGGGAA 59.819 50.000 0.00 0.00 0.00 3.97
807 835 0.872388 CGACGGGTGAAAAAGGGAAG 59.128 55.000 0.00 0.00 0.00 3.46
813 841 4.407621 ACGGGTGAAAAAGGGAAGAAAAAT 59.592 37.500 0.00 0.00 0.00 1.82
815 843 6.098552 ACGGGTGAAAAAGGGAAGAAAAATAA 59.901 34.615 0.00 0.00 0.00 1.40
817 845 7.659799 CGGGTGAAAAAGGGAAGAAAAATAAAT 59.340 33.333 0.00 0.00 0.00 1.40
871 899 0.529992 GGATCCGACCCGCTTAACAG 60.530 60.000 0.00 0.00 0.00 3.16
873 901 0.108329 ATCCGACCCGCTTAACAGTG 60.108 55.000 0.00 0.00 0.00 3.66
1103 1131 1.006571 TGAAGTCACGCGAGTTCCC 60.007 57.895 15.93 0.00 46.84 3.97
1117 1145 0.615850 GTTCCCACTCCCCTCTTCAG 59.384 60.000 0.00 0.00 0.00 3.02
1153 1181 0.036306 TTCTCCCCCTTTCAGTTCGC 59.964 55.000 0.00 0.00 0.00 4.70
1183 1211 5.398603 TCTGTCTGTTCTTCATCCTCTTC 57.601 43.478 0.00 0.00 0.00 2.87
1228 1256 7.276218 TGGTGCGATTTTATACAGTACAAGTAC 59.724 37.037 2.18 2.18 36.35 2.73
1239 1267 4.833380 ACAGTACAAGTACATGTCCTCTGT 59.167 41.667 20.38 20.38 38.48 3.41
1240 1268 5.304614 ACAGTACAAGTACATGTCCTCTGTT 59.695 40.000 20.38 11.54 36.96 3.16
1245 1273 5.531287 ACAAGTACATGTCCTCTGTTTTTCC 59.469 40.000 0.00 0.00 0.00 3.13
1254 1282 2.565834 CCTCTGTTTTTCCTCTCCCGTA 59.434 50.000 0.00 0.00 0.00 4.02
1258 1286 2.907696 TGTTTTTCCTCTCCCGTATGGA 59.092 45.455 1.27 0.00 42.41 3.41
1261 1289 1.481871 TTCCTCTCCCGTATGGACAC 58.518 55.000 1.27 0.00 38.61 3.67
1274 1303 4.092968 CGTATGGACACTTGGAAAAGCTAC 59.907 45.833 0.00 0.00 0.00 3.58
1275 1304 2.858745 TGGACACTTGGAAAAGCTACC 58.141 47.619 0.00 0.00 0.00 3.18
1281 1310 2.087646 CTTGGAAAAGCTACCAGGAGC 58.912 52.381 9.82 0.00 43.19 4.70
1323 1352 7.308229 GCTTCAATCAGTTCATGTCAGTTAGTT 60.308 37.037 0.00 0.00 0.00 2.24
1325 1354 8.534333 TCAATCAGTTCATGTCAGTTAGTTAC 57.466 34.615 0.00 0.00 0.00 2.50
1331 1360 6.590292 AGTTCATGTCAGTTAGTTACGGATTG 59.410 38.462 0.00 0.00 33.49 2.67
1338 1370 8.308931 TGTCAGTTAGTTACGGATTGAATTAGT 58.691 33.333 0.00 0.00 33.49 2.24
1367 1400 1.493772 TAAGGCATATCGTTTCGGCG 58.506 50.000 0.00 0.00 0.00 6.46
1394 1427 6.482641 AGCAGCAGATTGTTAATCTAGTCATG 59.517 38.462 3.93 0.00 46.20 3.07
1408 1441 6.737720 TCTAGTCATGTGCTGGATCTTATT 57.262 37.500 0.00 0.00 0.00 1.40
1409 1442 6.753180 TCTAGTCATGTGCTGGATCTTATTC 58.247 40.000 0.00 0.00 0.00 1.75
1453 1486 6.112927 TCCCTGCTAATTTTGCATCTTTTT 57.887 33.333 5.99 0.00 39.86 1.94
1522 1555 6.016610 AGCTTTTCGATTTGTAGCTGGTTTTA 60.017 34.615 0.00 0.00 40.45 1.52
1639 1672 5.578316 TGGGTGGGTACATATAGGGATAT 57.422 43.478 0.00 0.00 0.00 1.63
1663 1696 7.676683 TGCCAATTCTCTTATCTTACCTAGT 57.323 36.000 0.00 0.00 0.00 2.57
1664 1697 8.090788 TGCCAATTCTCTTATCTTACCTAGTT 57.909 34.615 0.00 0.00 0.00 2.24
1665 1698 7.987458 TGCCAATTCTCTTATCTTACCTAGTTG 59.013 37.037 0.00 0.00 0.00 3.16
1666 1699 8.204836 GCCAATTCTCTTATCTTACCTAGTTGA 58.795 37.037 0.00 0.00 0.00 3.18
1667 1700 9.757227 CCAATTCTCTTATCTTACCTAGTTGAG 57.243 37.037 0.00 0.00 0.00 3.02
1668 1701 9.255304 CAATTCTCTTATCTTACCTAGTTGAGC 57.745 37.037 0.00 0.00 0.00 4.26
1812 1931 3.667166 GCAAAGCTCACTTTAGTTACCGC 60.667 47.826 0.00 0.00 44.41 5.68
1957 2082 6.166982 GCACAGTTACCTTTCTAGTCTGAAT 58.833 40.000 0.00 0.00 0.00 2.57
1986 2111 8.270080 TGATCCTATATAGAGCTTAACTGTCG 57.730 38.462 11.53 0.00 0.00 4.35
1995 2120 4.705507 AGAGCTTAACTGTCGTGGAATCTA 59.294 41.667 0.00 0.00 0.00 1.98
2022 2147 1.532868 GTCCGCAGCAGCAATTATAGG 59.467 52.381 0.82 0.00 42.27 2.57
2091 2216 9.077885 TGTGCTTAGTCTCAAATTTCCTAAAAT 57.922 29.630 0.00 0.00 36.64 1.82
2092 2217 9.346725 GTGCTTAGTCTCAAATTTCCTAAAATG 57.653 33.333 0.00 0.00 35.27 2.32
2094 2219 9.914131 GCTTAGTCTCAAATTTCCTAAAATGTT 57.086 29.630 0.00 0.00 35.27 2.71
2218 2350 4.761739 TCATGGGAAAATTCTGTCAGTGAC 59.238 41.667 16.68 16.68 0.00 3.67
2331 2469 4.542697 ACCATATCCCCGCAAACTAATTT 58.457 39.130 0.00 0.00 0.00 1.82
2377 2515 3.251487 TGGTACGTCTTTTTAAGCTTGCC 59.749 43.478 9.86 0.00 0.00 4.52
2412 2710 8.567948 CAAAATAAGATGTTACACACAGAAGGT 58.432 33.333 0.00 0.00 39.40 3.50
2484 2787 9.118300 AGATAGACATTCATTTCTCAAATGGTC 57.882 33.333 8.71 8.28 46.40 4.02
2497 2800 9.905713 TTTCTCAAATGGTCTTATAGCTATGTT 57.094 29.630 16.77 0.00 0.00 2.71
2610 2914 9.295825 TGTTTGTTCTATTGTCCTATCACAAAT 57.704 29.630 0.00 0.00 39.69 2.32
2647 2951 9.643693 CTTTGCCATTCATCTTGTTTAACTTAT 57.356 29.630 0.00 0.00 0.00 1.73
2725 3029 0.968405 AAAATTCATGCACACCGCCT 59.032 45.000 0.00 0.00 41.33 5.52
2798 3102 2.437651 TGTGAGAACCAGACATCCAACA 59.562 45.455 0.00 0.00 0.00 3.33
2846 3150 1.002430 CACTGGAAGCAGCTAAGACCA 59.998 52.381 0.00 2.91 37.60 4.02
2980 3284 2.503356 TCACCAACCAAGGCATTTTTGT 59.497 40.909 2.51 0.00 0.00 2.83
3065 3369 1.142778 GCGCAAGAGTAAGAGCTCCG 61.143 60.000 10.93 4.42 43.02 4.63
3067 3371 0.533032 GCAAGAGTAAGAGCTCCGGT 59.467 55.000 10.93 0.00 36.20 5.28
3079 3383 3.514309 AGAGCTCCGGTACAAACTGTAAT 59.486 43.478 10.93 0.00 34.21 1.89
3098 3402 8.723365 ACTGTAATGGTATATTGATTCCAGGAA 58.277 33.333 3.72 3.72 36.10 3.36
3130 3434 1.202330 CTCCTGGAGGTGATGCTTCT 58.798 55.000 16.19 0.00 36.34 2.85
3170 3474 5.357742 AAAGGAAAATCAACCAGCAGTTT 57.642 34.783 0.00 0.00 36.18 2.66
3171 3475 5.357742 AAGGAAAATCAACCAGCAGTTTT 57.642 34.783 0.00 0.00 36.18 2.43
3185 3489 3.068590 AGCAGTTTTGTTTGGGTCTGATG 59.931 43.478 0.00 0.00 0.00 3.07
3187 3491 2.365293 AGTTTTGTTTGGGTCTGATGCC 59.635 45.455 0.00 0.00 0.00 4.40
3305 3609 0.321122 GACCTGTCCACCTTCAGCAG 60.321 60.000 0.00 0.00 0.00 4.24
3541 3845 3.962718 CAGAAAATGGCCATGGAGGTAAT 59.037 43.478 21.63 0.00 40.61 1.89
3649 3953 0.251742 CATTGGTTTCTCCCTGGCCA 60.252 55.000 4.71 4.71 34.77 5.36
3826 4130 0.320374 TGTGGATTCCGAAGACGCTT 59.680 50.000 0.00 0.00 38.29 4.68
3889 4193 1.077716 CACCCTCGGGATTGAACCC 60.078 63.158 9.43 0.00 45.92 4.11
3911 4215 0.370273 CGAGCGTGGCATGTTTAGAC 59.630 55.000 8.75 0.00 0.00 2.59
3922 4226 0.759959 TGTTTAGACCGTTCCAGCCA 59.240 50.000 0.00 0.00 0.00 4.75
4014 4318 0.984230 TTTGCGTCCTTCCAGGAGAT 59.016 50.000 0.00 0.00 46.90 2.75
4024 4328 3.576118 CCTTCCAGGAGATGACGTGATAT 59.424 47.826 0.00 0.00 37.67 1.63
4098 4403 4.011966 TGATGTTGTCTGAGCACTGATT 57.988 40.909 0.00 0.00 0.00 2.57
4132 4437 3.006003 TGTTGTGCAACTGTACTATCGGA 59.994 43.478 14.97 0.00 41.67 4.55
4144 4449 6.154021 ACTGTACTATCGGAATAGTGGTGTTT 59.846 38.462 8.07 0.00 46.07 2.83
4147 4452 6.980051 ACTATCGGAATAGTGGTGTTTTTC 57.020 37.500 0.00 0.00 45.12 2.29
4173 4479 8.691661 TTTTCCTGTAATTTTCTTGTAGAGCT 57.308 30.769 0.00 0.00 0.00 4.09
4174 4480 7.907214 TTCCTGTAATTTTCTTGTAGAGCTC 57.093 36.000 5.27 5.27 0.00 4.09
4177 4483 6.183360 CCTGTAATTTTCTTGTAGAGCTCGTG 60.183 42.308 8.37 0.00 0.00 4.35
4205 4511 0.541392 CCGGGTTCATGATCAGACCA 59.459 55.000 20.76 0.00 0.00 4.02
4230 4536 5.532779 TCAGCATGTGTTTGGTTGTACAATA 59.467 36.000 12.26 1.36 37.40 1.90
4232 4538 6.143758 CAGCATGTGTTTGGTTGTACAATAAC 59.856 38.462 12.26 15.59 0.00 1.89
4311 4643 6.263168 CAGTTTACTGAGATCCACAAGGTTTT 59.737 38.462 3.80 0.00 46.59 2.43
4313 4645 3.490348 ACTGAGATCCACAAGGTTTTGG 58.510 45.455 0.00 0.00 38.66 3.28
4319 4651 1.746220 TCCACAAGGTTTTGGAACACG 59.254 47.619 0.00 0.00 39.04 4.49
4327 4659 2.607038 GGTTTTGGAACACGAATCAGCC 60.607 50.000 0.00 0.00 39.29 4.85
4330 4662 0.389817 TGGAACACGAATCAGCCGAG 60.390 55.000 0.00 0.00 0.00 4.63
4359 4691 3.202906 TCAACTCTGAAGAAAACCGGTG 58.797 45.455 8.52 0.00 0.00 4.94
4362 4694 2.169769 ACTCTGAAGAAAACCGGTGACA 59.830 45.455 8.52 1.61 0.00 3.58
4367 4699 4.204012 TGAAGAAAACCGGTGACATTTCT 58.796 39.130 21.13 21.13 42.30 2.52
4369 4701 3.551846 AGAAAACCGGTGACATTTCTGT 58.448 40.909 24.45 7.93 39.83 3.41
4371 4703 2.341846 AACCGGTGACATTTCTGTGT 57.658 45.000 8.52 0.00 35.14 3.72
4372 4704 1.593196 ACCGGTGACATTTCTGTGTG 58.407 50.000 6.12 0.00 35.14 3.82
4373 4705 1.134220 ACCGGTGACATTTCTGTGTGT 60.134 47.619 6.12 0.00 35.14 3.72
4383 4715 7.587757 GTGACATTTCTGTGTGTTTCTTGATAC 59.412 37.037 0.00 0.00 35.14 2.24
4394 4726 4.156556 TGTTTCTTGATACTTGCTGATGCC 59.843 41.667 0.00 0.00 38.71 4.40
4406 4738 1.411977 GCTGATGCCTCTGCTTCTCTA 59.588 52.381 12.51 0.00 41.63 2.43
4415 4747 3.456280 CTCTGCTTCTCTACTGGAATGC 58.544 50.000 0.00 0.00 0.00 3.56
4416 4748 2.169352 TCTGCTTCTCTACTGGAATGCC 59.831 50.000 0.00 0.00 0.00 4.40
4424 4756 2.754552 TCTACTGGAATGCCATTTGTGC 59.245 45.455 0.00 0.00 44.91 4.57
4430 4762 1.854126 GAATGCCATTTGTGCGTATGC 59.146 47.619 0.00 0.00 43.20 3.14
4440 4772 3.303605 GCGTATGCGAGTGCTGAG 58.696 61.111 7.60 0.00 43.34 3.35
4441 4773 2.864931 GCGTATGCGAGTGCTGAGC 61.865 63.158 7.60 0.00 43.34 4.26
4442 4774 1.517039 CGTATGCGAGTGCTGAGCA 60.517 57.895 1.40 1.40 45.46 4.26
4451 4783 2.340078 TGCTGAGCACCGAGTGAC 59.660 61.111 1.40 2.65 35.23 3.67
4452 4784 2.203082 TGCTGAGCACCGAGTGACT 61.203 57.895 1.40 0.00 35.23 3.41
4453 4785 0.893727 TGCTGAGCACCGAGTGACTA 60.894 55.000 1.40 0.00 35.23 2.59
4454 4786 0.456995 GCTGAGCACCGAGTGACTAC 60.457 60.000 0.00 0.00 35.23 2.73
4574 4910 3.301794 TGTGGCCTGCATTCTGATTAT 57.698 42.857 3.32 0.00 0.00 1.28
4575 4911 3.634504 TGTGGCCTGCATTCTGATTATT 58.365 40.909 3.32 0.00 0.00 1.40
4576 4912 4.790937 TGTGGCCTGCATTCTGATTATTA 58.209 39.130 3.32 0.00 0.00 0.98
4622 4958 4.665833 TTGTTCTACTACACACTGTGCT 57.334 40.909 9.20 0.00 36.98 4.40
4637 4973 3.623060 ACTGTGCTGCCTTTATATCAACG 59.377 43.478 0.00 0.00 0.00 4.10
4683 5019 0.392595 CAAGTCGTAAAGCCCCCTCC 60.393 60.000 0.00 0.00 0.00 4.30
4770 5106 1.337071 CATGCTCCACCATGCATCTTC 59.663 52.381 0.00 0.00 46.65 2.87
4772 5108 1.005097 TGCTCCACCATGCATCTTCTT 59.995 47.619 0.00 0.00 33.94 2.52
4773 5109 2.097825 GCTCCACCATGCATCTTCTTT 58.902 47.619 0.00 0.00 0.00 2.52
4774 5110 2.494870 GCTCCACCATGCATCTTCTTTT 59.505 45.455 0.00 0.00 0.00 2.27
4819 5155 3.199508 AGCATTCTAACTCTGCCACTGAT 59.800 43.478 0.00 0.00 36.56 2.90
4837 5173 6.238648 CCACTGATACGGATATTTTTGTTCCC 60.239 42.308 0.00 0.00 0.00 3.97
4838 5174 6.542370 CACTGATACGGATATTTTTGTTCCCT 59.458 38.462 0.00 0.00 0.00 4.20
4839 5175 6.542370 ACTGATACGGATATTTTTGTTCCCTG 59.458 38.462 0.00 0.00 0.00 4.45
4840 5176 5.298276 TGATACGGATATTTTTGTTCCCTGC 59.702 40.000 0.00 0.00 0.00 4.85
4865 5218 6.010294 TGCACTGAAGTAGAAGTAGTGTAC 57.990 41.667 0.00 0.00 40.52 2.90
4868 5221 7.119407 TGCACTGAAGTAGAAGTAGTGTACTAG 59.881 40.741 0.00 0.00 40.52 2.57
4869 5222 7.465989 CACTGAAGTAGAAGTAGTGTACTAGC 58.534 42.308 0.00 0.00 35.31 3.42
4870 5223 7.119407 CACTGAAGTAGAAGTAGTGTACTAGCA 59.881 40.741 0.00 0.00 35.31 3.49
4873 5231 9.848710 TGAAGTAGAAGTAGTGTACTAGCATAT 57.151 33.333 0.00 0.00 35.31 1.78
4895 5253 1.270839 CCTTGCAGGAACTCGAAAGGA 60.271 52.381 0.00 0.00 41.65 3.36
4897 5255 0.756294 TGCAGGAACTCGAAAGGACA 59.244 50.000 0.00 0.00 34.60 4.02
4917 5275 1.234821 TGCCTGTAAAAAGCCTGTCG 58.765 50.000 0.00 0.00 0.00 4.35
4958 5316 3.320541 CACTGCAGTGGTTGGGATTTTTA 59.679 43.478 34.65 0.00 42.10 1.52
4959 5317 4.021192 CACTGCAGTGGTTGGGATTTTTAT 60.021 41.667 34.65 0.00 42.10 1.40
4983 5345 4.525487 TCTGCATTTTTGCCTCTTCTGAAT 59.475 37.500 0.00 0.00 0.00 2.57
4989 5351 6.808008 TTTTTGCCTCTTCTGAATGAGTAG 57.192 37.500 12.59 3.97 0.00 2.57
4993 5355 3.066900 GCCTCTTCTGAATGAGTAGCGTA 59.933 47.826 12.59 0.00 0.00 4.42
4994 5356 4.602995 CCTCTTCTGAATGAGTAGCGTAC 58.397 47.826 12.59 0.00 0.00 3.67
4995 5357 4.336993 CCTCTTCTGAATGAGTAGCGTACT 59.663 45.833 12.59 0.00 42.86 2.73
4996 5358 5.527951 CCTCTTCTGAATGAGTAGCGTACTA 59.472 44.000 12.59 0.00 39.59 1.82
4997 5359 6.038382 CCTCTTCTGAATGAGTAGCGTACTAA 59.962 42.308 12.59 0.00 39.59 2.24
4998 5360 6.783162 TCTTCTGAATGAGTAGCGTACTAAC 58.217 40.000 0.00 0.00 39.59 2.34
5010 5372 3.901667 CGTACTAACGCTTGGTTGATC 57.098 47.619 0.00 0.00 43.12 2.92
5011 5373 2.601763 CGTACTAACGCTTGGTTGATCC 59.398 50.000 0.00 0.00 43.12 3.36
5012 5374 2.851263 ACTAACGCTTGGTTGATCCA 57.149 45.000 0.00 0.00 45.60 3.41
5013 5375 3.350219 ACTAACGCTTGGTTGATCCAT 57.650 42.857 0.00 0.00 46.60 3.41
5014 5376 3.686016 ACTAACGCTTGGTTGATCCATT 58.314 40.909 0.00 0.00 46.60 3.16
5015 5377 3.440173 ACTAACGCTTGGTTGATCCATTG 59.560 43.478 0.00 0.00 46.60 2.82
5016 5378 1.176527 ACGCTTGGTTGATCCATTGG 58.823 50.000 0.00 0.00 46.60 3.16
5017 5379 1.271871 ACGCTTGGTTGATCCATTGGA 60.272 47.619 8.08 8.08 46.60 3.53
5018 5380 1.402968 CGCTTGGTTGATCCATTGGAG 59.597 52.381 11.78 0.00 46.60 3.86
5019 5381 1.753073 GCTTGGTTGATCCATTGGAGG 59.247 52.381 11.78 0.00 46.60 4.30
5020 5382 2.885554 GCTTGGTTGATCCATTGGAGGT 60.886 50.000 11.78 0.00 46.60 3.85
5021 5383 2.512692 TGGTTGATCCATTGGAGGTG 57.487 50.000 11.78 0.00 41.93 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.014242 TGAGAGTGTCAACTATTGATGTCCTT 60.014 38.462 0.00 0.00 42.47 3.36
1 2 5.481824 TGAGAGTGTCAACTATTGATGTCCT 59.518 40.000 0.00 0.00 42.47 3.85
2 3 5.724328 TGAGAGTGTCAACTATTGATGTCC 58.276 41.667 0.00 0.00 42.47 4.02
31 32 9.886132 AACACGGTCAAATAGACTAATTAAGAT 57.114 29.630 0.00 0.00 46.72 2.40
51 53 0.104120 TGTCTGTGGAGTGAACACGG 59.896 55.000 0.00 0.00 44.59 4.94
53 55 2.309528 TGTGTCTGTGGAGTGAACAC 57.690 50.000 0.00 0.00 39.26 3.32
89 91 4.764940 GCTTTTGCATTGATTTCACACAC 58.235 39.130 0.00 0.00 46.58 3.82
128 130 7.684529 ACCTGACAACAGATCTTCTTCTTAAT 58.315 34.615 0.00 0.00 46.03 1.40
144 146 5.684184 GGTTTTTCGTGATTAACCTGACAAC 59.316 40.000 0.00 0.00 37.61 3.32
148 150 4.378774 TCGGTTTTTCGTGATTAACCTGA 58.621 39.130 0.00 0.00 38.27 3.86
167 169 5.277974 GGTCATGGATGTATCATTTGTTCGG 60.278 44.000 0.00 0.00 0.00 4.30
170 172 6.891361 TCTTGGTCATGGATGTATCATTTGTT 59.109 34.615 0.00 0.00 0.00 2.83
176 178 5.899547 AGTAGTCTTGGTCATGGATGTATCA 59.100 40.000 0.00 0.00 0.00 2.15
191 195 2.808543 GTTGTTGGCAGGAGTAGTCTTG 59.191 50.000 5.33 5.33 32.88 3.02
203 207 2.757314 TGAGTTTGATGTGTTGTTGGCA 59.243 40.909 0.00 0.00 0.00 4.92
204 208 3.435105 TGAGTTTGATGTGTTGTTGGC 57.565 42.857 0.00 0.00 0.00 4.52
210 214 5.348451 GTGCTTTTGTTGAGTTTGATGTGTT 59.652 36.000 0.00 0.00 0.00 3.32
215 219 5.329035 AGTGTGCTTTTGTTGAGTTTGAT 57.671 34.783 0.00 0.00 0.00 2.57
218 222 5.185056 AGGTTAGTGTGCTTTTGTTGAGTTT 59.815 36.000 0.00 0.00 0.00 2.66
237 241 2.092538 TGGGTTTGTGTTTCGGAGGTTA 60.093 45.455 0.00 0.00 0.00 2.85
239 243 0.256464 TGGGTTTGTGTTTCGGAGGT 59.744 50.000 0.00 0.00 0.00 3.85
241 245 1.602377 GAGTGGGTTTGTGTTTCGGAG 59.398 52.381 0.00 0.00 0.00 4.63
244 248 1.384525 TGGAGTGGGTTTGTGTTTCG 58.615 50.000 0.00 0.00 0.00 3.46
245 249 2.955660 TGATGGAGTGGGTTTGTGTTTC 59.044 45.455 0.00 0.00 0.00 2.78
266 281 3.039134 CCGGCAAGTCGGCTTTTT 58.961 55.556 0.00 0.00 43.71 1.94
273 288 1.071605 CTTCTTTCTCCGGCAAGTCG 58.928 55.000 0.00 0.00 0.00 4.18
279 294 2.194271 CATACGACTTCTTTCTCCGGC 58.806 52.381 0.00 0.00 0.00 6.13
282 297 3.447944 AGGTCCATACGACTTCTTTCTCC 59.552 47.826 0.00 0.00 41.64 3.71
285 300 4.566987 ACAAGGTCCATACGACTTCTTTC 58.433 43.478 0.00 0.00 41.64 2.62
307 322 3.830755 GGAGCGGAGGGAGTATATGTTAA 59.169 47.826 0.00 0.00 0.00 2.01
314 329 2.930109 ATATGGAGCGGAGGGAGTAT 57.070 50.000 0.00 0.00 0.00 2.12
361 376 9.677567 TTTCAAAATAAGTGTCACTGATTTAGC 57.322 29.630 23.29 0.00 38.11 3.09
371 386 6.540914 ACTCCTTCGTTTCAAAATAAGTGTCA 59.459 34.615 0.00 0.00 0.00 3.58
380 395 7.542824 CCTTTTGTTTACTCCTTCGTTTCAAAA 59.457 33.333 0.00 0.00 33.42 2.44
382 397 6.374894 TCCTTTTGTTTACTCCTTCGTTTCAA 59.625 34.615 0.00 0.00 0.00 2.69
435 451 2.945008 CCATTCATGTTGAGCGGTGTAT 59.055 45.455 0.00 0.00 0.00 2.29
436 452 2.290008 ACCATTCATGTTGAGCGGTGTA 60.290 45.455 0.00 0.00 33.28 2.90
437 453 1.167851 CCATTCATGTTGAGCGGTGT 58.832 50.000 0.00 0.00 0.00 4.16
439 455 1.909700 AACCATTCATGTTGAGCGGT 58.090 45.000 0.00 0.00 35.19 5.68
441 457 4.685169 AACTAACCATTCATGTTGAGCG 57.315 40.909 0.00 0.00 0.00 5.03
442 458 7.559590 AGATAACTAACCATTCATGTTGAGC 57.440 36.000 0.00 0.00 0.00 4.26
497 516 8.806429 TCATTTGGACTGTATAAACACATGAT 57.194 30.769 0.00 0.00 0.00 2.45
498 517 8.806429 ATCATTTGGACTGTATAAACACATGA 57.194 30.769 0.00 0.00 0.00 3.07
501 520 9.733556 ACTTATCATTTGGACTGTATAAACACA 57.266 29.630 0.00 0.00 0.00 3.72
507 526 9.429109 TCTGGTACTTATCATTTGGACTGTATA 57.571 33.333 0.00 0.00 0.00 1.47
508 527 8.204836 GTCTGGTACTTATCATTTGGACTGTAT 58.795 37.037 0.00 0.00 0.00 2.29
509 528 7.553334 GTCTGGTACTTATCATTTGGACTGTA 58.447 38.462 0.00 0.00 0.00 2.74
510 529 6.407202 GTCTGGTACTTATCATTTGGACTGT 58.593 40.000 0.00 0.00 0.00 3.55
511 530 5.520288 CGTCTGGTACTTATCATTTGGACTG 59.480 44.000 0.00 0.00 0.00 3.51
513 532 5.291128 CACGTCTGGTACTTATCATTTGGAC 59.709 44.000 0.00 0.00 0.00 4.02
514 533 5.046878 ACACGTCTGGTACTTATCATTTGGA 60.047 40.000 0.00 0.00 0.00 3.53
516 535 5.063438 CCACACGTCTGGTACTTATCATTTG 59.937 44.000 1.01 0.00 0.00 2.32
526 545 3.946907 GTGCCACACGTCTGGTAC 58.053 61.111 14.63 14.63 39.39 3.34
535 554 0.584876 GGTGTTACTTCGTGCCACAC 59.415 55.000 0.00 0.00 37.59 3.82
553 572 7.405769 TTTTAGTTGTAAAAACGTTAGGACGG 58.594 34.615 0.00 0.00 41.56 4.79
556 575 9.235537 GCAATTTTAGTTGTAAAAACGTTAGGA 57.764 29.630 0.00 0.00 40.65 2.94
560 579 7.829378 TGGCAATTTTAGTTGTAAAAACGTT 57.171 28.000 0.00 0.00 40.65 3.99
614 637 4.643334 ACTTCCTGTTTGGTGGTAAGTTTC 59.357 41.667 0.00 0.00 37.07 2.78
621 644 1.111277 GCAACTTCCTGTTTGGTGGT 58.889 50.000 0.00 0.00 36.63 4.16
622 645 0.389025 GGCAACTTCCTGTTTGGTGG 59.611 55.000 0.00 0.00 36.63 4.61
625 648 1.606224 GCATGGCAACTTCCTGTTTGG 60.606 52.381 0.00 0.00 36.63 3.28
662 685 7.630082 TGGCAAGTTTAGTTATCTAAGGATGT 58.370 34.615 0.00 0.00 37.44 3.06
691 714 2.646250 CAATTTCGTCCTCGCGTTTTT 58.354 42.857 5.77 0.00 36.96 1.94
698 721 2.222819 GCACTAAGCAATTTCGTCCTCG 60.223 50.000 0.00 0.00 44.79 4.63
699 722 3.391227 GCACTAAGCAATTTCGTCCTC 57.609 47.619 0.00 0.00 44.79 3.71
722 745 4.160329 GGACCCTGATAGGTGTCATCATA 58.840 47.826 14.28 0.00 41.42 2.15
724 747 2.292851 TGGACCCTGATAGGTGTCATCA 60.293 50.000 14.28 0.00 41.42 3.07
726 749 2.568546 TGGACCCTGATAGGTGTCAT 57.431 50.000 14.28 0.00 41.42 3.06
727 750 2.568546 ATGGACCCTGATAGGTGTCA 57.431 50.000 14.28 2.35 41.42 3.58
728 751 3.305720 TGTATGGACCCTGATAGGTGTC 58.694 50.000 7.53 7.53 41.42 3.67
729 752 3.414759 TGTATGGACCCTGATAGGTGT 57.585 47.619 0.00 0.00 41.42 4.16
730 753 3.181454 GGTTGTATGGACCCTGATAGGTG 60.181 52.174 0.00 0.00 41.42 4.00
731 754 3.046374 GGTTGTATGGACCCTGATAGGT 58.954 50.000 0.00 0.00 45.12 3.08
732 755 3.771577 GGTTGTATGGACCCTGATAGG 57.228 52.381 0.00 0.00 34.30 2.57
750 773 5.268387 TGTATTGGCACTTATCATTTGGGT 58.732 37.500 0.00 0.00 0.00 4.51
763 786 3.696898 TCGTTTGTGTTTGTATTGGCAC 58.303 40.909 0.00 0.00 0.00 5.01
764 787 4.106197 GTTCGTTTGTGTTTGTATTGGCA 58.894 39.130 0.00 0.00 0.00 4.92
765 788 4.027214 GTGTTCGTTTGTGTTTGTATTGGC 60.027 41.667 0.00 0.00 0.00 4.52
767 790 5.022653 TCGTGTTCGTTTGTGTTTGTATTG 58.977 37.500 0.00 0.00 38.33 1.90
806 834 9.906660 TTCGCACTCATTTGTATTTATTTTTCT 57.093 25.926 0.00 0.00 0.00 2.52
813 841 6.247727 TGCTTTCGCACTCATTTGTATTTA 57.752 33.333 0.00 0.00 42.25 1.40
815 843 4.379813 CCTGCTTTCGCACTCATTTGTATT 60.380 41.667 0.00 0.00 42.25 1.89
817 845 2.483877 CCTGCTTTCGCACTCATTTGTA 59.516 45.455 0.00 0.00 42.25 2.41
819 847 1.536766 TCCTGCTTTCGCACTCATTTG 59.463 47.619 0.00 0.00 42.25 2.32
822 850 2.988010 TATCCTGCTTTCGCACTCAT 57.012 45.000 0.00 0.00 42.25 2.90
823 851 2.483714 GGATATCCTGCTTTCGCACTCA 60.484 50.000 14.97 0.00 42.25 3.41
824 852 2.139118 GGATATCCTGCTTTCGCACTC 58.861 52.381 14.97 0.00 42.25 3.51
871 899 3.877508 GGTAATTGCATAGTGGTCCTCAC 59.122 47.826 0.00 0.00 46.39 3.51
873 901 3.118038 TGGGTAATTGCATAGTGGTCCTC 60.118 47.826 0.00 0.00 0.00 3.71
882 910 5.011533 ACTGCACTTTTTGGGTAATTGCATA 59.988 36.000 0.00 0.00 39.43 3.14
1103 1131 4.285863 AGTAGATTCTGAAGAGGGGAGTG 58.714 47.826 0.00 0.00 0.00 3.51
1117 1145 5.394773 GGGGAGAACAGAACAGAGTAGATTC 60.395 48.000 0.00 0.00 0.00 2.52
1153 1181 1.871080 AGAACAGACAGAGCGTTTGG 58.129 50.000 0.00 0.00 34.01 3.28
1183 1211 3.627577 ACCATTTCCTCGAATCAAATCGG 59.372 43.478 0.00 0.00 42.92 4.18
1228 1256 4.006319 GGAGAGGAAAAACAGAGGACATG 58.994 47.826 0.00 0.00 0.00 3.21
1234 1262 2.841442 ACGGGAGAGGAAAAACAGAG 57.159 50.000 0.00 0.00 0.00 3.35
1254 1282 3.181434 TGGTAGCTTTTCCAAGTGTCCAT 60.181 43.478 0.00 0.00 31.86 3.41
1258 1286 2.441750 TCCTGGTAGCTTTTCCAAGTGT 59.558 45.455 0.00 0.00 33.06 3.55
1261 1289 2.087646 GCTCCTGGTAGCTTTTCCAAG 58.912 52.381 0.00 0.00 39.50 3.61
1281 1310 0.250640 AAGCAACCACAGAGAGGCAG 60.251 55.000 0.00 0.00 0.00 4.85
1285 1314 3.405831 TGATTGAAGCAACCACAGAGAG 58.594 45.455 0.00 0.00 0.00 3.20
1323 1352 6.869695 TCTTGCAGTACTAATTCAATCCGTA 58.130 36.000 0.00 0.00 0.00 4.02
1325 1354 6.851222 ATCTTGCAGTACTAATTCAATCCG 57.149 37.500 0.00 0.00 0.00 4.18
1331 1360 7.736447 ATGCCTTATCTTGCAGTACTAATTC 57.264 36.000 0.00 0.00 41.46 2.17
1338 1370 5.468540 ACGATATGCCTTATCTTGCAGTA 57.531 39.130 0.00 0.00 41.46 2.74
1377 1410 6.653020 TCCAGCACATGACTAGATTAACAAT 58.347 36.000 0.00 0.00 0.00 2.71
1378 1411 6.048732 TCCAGCACATGACTAGATTAACAA 57.951 37.500 0.00 0.00 0.00 2.83
1379 1412 5.675684 TCCAGCACATGACTAGATTAACA 57.324 39.130 0.00 0.00 0.00 2.41
1380 1413 6.520272 AGATCCAGCACATGACTAGATTAAC 58.480 40.000 0.00 0.00 0.00 2.01
1381 1414 6.737720 AGATCCAGCACATGACTAGATTAA 57.262 37.500 0.00 0.00 0.00 1.40
1394 1427 2.615912 GTGCCTGAATAAGATCCAGCAC 59.384 50.000 0.00 0.00 38.97 4.40
1408 1441 1.754745 GACTGGGACAAGTGCCTGA 59.245 57.895 21.03 0.00 41.36 3.86
1409 1442 1.669115 CGACTGGGACAAGTGCCTG 60.669 63.158 14.40 14.40 42.12 4.85
1453 1486 8.388656 ACTAACCTAACCTAATCAATCTTCCA 57.611 34.615 0.00 0.00 0.00 3.53
1522 1555 8.650143 AACCCATAAATGATACTTTGAACTGT 57.350 30.769 0.00 0.00 0.00 3.55
1639 1672 7.676683 ACTAGGTAAGATAAGAGAATTGGCA 57.323 36.000 0.00 0.00 0.00 4.92
1663 1696 4.521639 ACATCAAAATCTGCTCAAGCTCAA 59.478 37.500 3.32 0.00 42.66 3.02
1664 1697 4.077108 ACATCAAAATCTGCTCAAGCTCA 58.923 39.130 3.32 0.00 42.66 4.26
1665 1698 4.413087 CACATCAAAATCTGCTCAAGCTC 58.587 43.478 3.32 0.00 42.66 4.09
1666 1699 3.192844 CCACATCAAAATCTGCTCAAGCT 59.807 43.478 3.32 0.00 42.66 3.74
1667 1700 3.057033 ACCACATCAAAATCTGCTCAAGC 60.057 43.478 0.00 0.00 42.50 4.01
1668 1701 4.778534 ACCACATCAAAATCTGCTCAAG 57.221 40.909 0.00 0.00 0.00 3.02
1812 1931 9.450807 CTAAAAGTGAATTTGTCAAAGTACAGG 57.549 33.333 4.03 0.00 38.23 4.00
1941 2060 7.181845 AGGATCAGAAATTCAGACTAGAAAGGT 59.818 37.037 0.00 0.00 0.00 3.50
1986 2111 2.872858 GCGGACCAATCTTAGATTCCAC 59.127 50.000 4.24 0.00 0.00 4.02
1995 2120 2.042831 GCTGCTGCGGACCAATCTT 61.043 57.895 13.72 0.00 0.00 2.40
2044 2169 1.380302 GGGCACAGGTGAGTCCAAT 59.620 57.895 3.10 0.00 39.02 3.16
2126 2251 1.880027 GACATGGTCTGGTTTGTGGTC 59.120 52.381 0.00 0.00 0.00 4.02
2218 2350 7.513132 CACTCAACATATATTTCTATGTGGCG 58.487 38.462 0.00 0.00 40.57 5.69
2377 2515 7.903431 GTGTAACATCTTATTTTGTAAGAGGCG 59.097 37.037 8.79 1.58 38.47 5.52
2437 2735 7.969536 ATCTTCAATGCTTGTTATATACGCT 57.030 32.000 0.00 0.00 0.00 5.07
2473 2776 9.905713 AAAACATAGCTATAAGACCATTTGAGA 57.094 29.630 5.77 0.00 0.00 3.27
2552 2856 9.914834 ATATACAAATCCAAGTACTAAAAGCCA 57.085 29.630 0.00 0.00 0.00 4.75
2606 2910 9.853555 TGAATGGCAAAGTAACAAGTATATTTG 57.146 29.630 6.44 6.44 0.00 2.32
2610 2914 9.461312 AAGATGAATGGCAAAGTAACAAGTATA 57.539 29.630 0.00 0.00 0.00 1.47
2798 3102 4.092279 TCTGGTTCAGTCATCTCATCACT 58.908 43.478 0.00 0.00 32.61 3.41
2846 3150 4.739793 TCTTTGTTTGATCCATCACCCTT 58.260 39.130 0.00 0.00 36.36 3.95
2959 3263 2.503356 ACAAAAATGCCTTGGTTGGTGA 59.497 40.909 4.27 0.00 0.00 4.02
2980 3284 3.917629 TCCAATACCTTTGACAACCCCTA 59.082 43.478 0.00 0.00 0.00 3.53
3079 3383 5.132648 ACTGCTTCCTGGAATCAATATACCA 59.867 40.000 10.03 0.00 0.00 3.25
3130 3434 6.012337 TCCTTTATAGGCAATGGAATGACA 57.988 37.500 0.00 0.00 41.69 3.58
3170 3474 1.133513 AGTGGCATCAGACCCAAACAA 60.134 47.619 0.00 0.00 31.90 2.83
3171 3475 0.478072 AGTGGCATCAGACCCAAACA 59.522 50.000 0.00 0.00 31.90 2.83
3185 3489 2.103263 CCATGGAGTTAGGTAGAGTGGC 59.897 54.545 5.56 0.00 0.00 5.01
3187 3491 3.034635 AGCCATGGAGTTAGGTAGAGTG 58.965 50.000 18.40 0.00 0.00 3.51
3253 3557 2.189594 TTCTGGGATGTGCTGTTGAG 57.810 50.000 0.00 0.00 0.00 3.02
3305 3609 3.531538 TCCGTGGATTATCAGAAGTTGC 58.468 45.455 0.00 0.00 0.00 4.17
3560 3864 0.180171 CCTGGCATCGGTACCATTGA 59.820 55.000 13.54 1.05 34.82 2.57
3568 3872 0.107508 CACAGAATCCTGGCATCGGT 60.108 55.000 0.00 0.00 44.60 4.69
3922 4226 0.613012 GCTCCCTGCCACCAGATTTT 60.613 55.000 0.00 0.00 41.77 1.82
3949 4253 1.153647 CATGACTCGGGCTGCGTTA 60.154 57.895 0.00 0.00 0.00 3.18
4098 4403 1.338579 TGCACAACATCTACATCGCCA 60.339 47.619 0.00 0.00 0.00 5.69
4132 4437 7.418337 ACAGGAAAAGAAAAACACCACTATT 57.582 32.000 0.00 0.00 0.00 1.73
4147 4452 8.787852 AGCTCTACAAGAAAATTACAGGAAAAG 58.212 33.333 0.00 0.00 0.00 2.27
4173 4479 3.299977 CCCGGTGGAGTGTCACGA 61.300 66.667 0.00 0.00 38.46 4.35
4174 4480 3.159858 AACCCGGTGGAGTGTCACG 62.160 63.158 0.00 0.00 38.46 4.35
4177 4483 0.673644 CATGAACCCGGTGGAGTGTC 60.674 60.000 0.00 0.00 34.81 3.67
4205 4511 3.888323 TGTACAACCAAACACATGCTGAT 59.112 39.130 0.00 0.00 0.00 2.90
4230 4536 8.980143 AAGCAACGCTATTAACAATTATTGTT 57.020 26.923 23.98 23.98 46.78 2.83
4269 4575 7.041508 CAGTAAACTGAACTCTGAAAGCAGAAT 60.042 37.037 3.99 0.00 46.89 2.40
4287 4593 5.568620 AACCTTGTGGATCTCAGTAAACT 57.431 39.130 0.00 0.00 37.04 2.66
4299 4631 1.746220 CGTGTTCCAAAACCTTGTGGA 59.254 47.619 0.00 0.00 42.27 4.02
4307 4639 2.661594 GGCTGATTCGTGTTCCAAAAC 58.338 47.619 0.00 0.00 35.85 2.43
4311 4643 0.389817 CTCGGCTGATTCGTGTTCCA 60.390 55.000 0.00 0.00 0.00 3.53
4313 4645 0.108804 TCCTCGGCTGATTCGTGTTC 60.109 55.000 0.00 0.00 0.00 3.18
4319 4651 2.093973 TGAACTTCTCCTCGGCTGATTC 60.094 50.000 0.00 0.00 0.00 2.52
4327 4659 3.924918 TCAGAGTTGAACTTCTCCTCG 57.075 47.619 0.00 0.00 0.00 4.63
4330 4662 6.238511 GGTTTTCTTCAGAGTTGAACTTCTCC 60.239 42.308 0.00 0.00 38.37 3.71
4359 4691 7.865707 AGTATCAAGAAACACACAGAAATGTC 58.134 34.615 0.00 0.00 0.00 3.06
4362 4694 7.013655 AGCAAGTATCAAGAAACACACAGAAAT 59.986 33.333 0.00 0.00 0.00 2.17
4367 4699 5.122519 TCAGCAAGTATCAAGAAACACACA 58.877 37.500 0.00 0.00 0.00 3.72
4369 4701 5.335113 GCATCAGCAAGTATCAAGAAACACA 60.335 40.000 0.00 0.00 41.58 3.72
4371 4703 4.156556 GGCATCAGCAAGTATCAAGAAACA 59.843 41.667 0.00 0.00 44.61 2.83
4372 4704 4.397417 AGGCATCAGCAAGTATCAAGAAAC 59.603 41.667 0.00 0.00 44.61 2.78
4373 4705 4.592942 AGGCATCAGCAAGTATCAAGAAA 58.407 39.130 0.00 0.00 44.61 2.52
4383 4715 0.733729 GAAGCAGAGGCATCAGCAAG 59.266 55.000 18.11 0.00 44.61 4.01
4394 4726 3.456280 GCATTCCAGTAGAGAAGCAGAG 58.544 50.000 0.00 0.00 0.00 3.35
4415 4747 0.726827 ACTCGCATACGCACAAATGG 59.273 50.000 0.00 0.00 39.84 3.16
4416 4748 1.801618 CACTCGCATACGCACAAATG 58.198 50.000 0.00 0.00 39.84 2.32
4424 4756 1.517039 TGCTCAGCACTCGCATACG 60.517 57.895 0.00 0.00 42.27 3.06
4436 4768 1.135546 CAGTAGTCACTCGGTGCTCAG 60.136 57.143 0.00 0.00 32.98 3.35
4437 4769 0.881796 CAGTAGTCACTCGGTGCTCA 59.118 55.000 0.00 0.00 32.98 4.26
4438 4770 1.135632 GTCAGTAGTCACTCGGTGCTC 60.136 57.143 0.00 0.00 32.98 4.26
4439 4771 0.882474 GTCAGTAGTCACTCGGTGCT 59.118 55.000 0.00 3.67 32.98 4.40
4440 4772 0.109226 GGTCAGTAGTCACTCGGTGC 60.109 60.000 0.00 0.00 32.98 5.01
4441 4773 1.200252 CTGGTCAGTAGTCACTCGGTG 59.800 57.143 0.00 0.00 30.46 4.94
4442 4774 1.202903 ACTGGTCAGTAGTCACTCGGT 60.203 52.381 1.24 0.00 40.43 4.69
4443 4775 1.200252 CACTGGTCAGTAGTCACTCGG 59.800 57.143 3.06 0.00 40.20 4.63
4444 4776 1.200252 CCACTGGTCAGTAGTCACTCG 59.800 57.143 3.06 0.00 40.20 4.18
4445 4777 2.029828 CACCACTGGTCAGTAGTCACTC 60.030 54.545 0.00 0.00 40.20 3.51
4446 4778 1.964223 CACCACTGGTCAGTAGTCACT 59.036 52.381 0.00 0.00 40.20 3.41
4447 4779 1.000955 CCACCACTGGTCAGTAGTCAC 59.999 57.143 0.00 0.00 40.20 3.67
4448 4780 1.338107 CCACCACTGGTCAGTAGTCA 58.662 55.000 0.00 0.00 40.20 3.41
4574 4910 0.606604 GACAGGGGCGTCTCAACTAA 59.393 55.000 0.00 0.00 32.92 2.24
4575 4911 0.251653 AGACAGGGGCGTCTCAACTA 60.252 55.000 0.00 0.00 42.70 2.24
4576 4912 1.122019 AAGACAGGGGCGTCTCAACT 61.122 55.000 0.00 0.00 45.56 3.16
4622 4958 4.982295 CAGATCGACGTTGATATAAAGGCA 59.018 41.667 18.34 0.00 0.00 4.75
4637 4973 3.129638 ACTTCCTGAGCTTACAGATCGAC 59.870 47.826 4.03 0.00 39.94 4.20
4683 5019 5.360591 AGAGCTTACCGAACCATTGATAAG 58.639 41.667 0.00 0.00 0.00 1.73
4772 5108 3.318839 CACATCTGCTGGGAACTGAAAAA 59.681 43.478 0.00 0.00 0.00 1.94
4773 5109 2.886523 CACATCTGCTGGGAACTGAAAA 59.113 45.455 0.00 0.00 0.00 2.29
4774 5110 2.158623 ACACATCTGCTGGGAACTGAAA 60.159 45.455 0.00 0.00 30.50 2.69
4819 5155 4.590918 TGCAGGGAACAAAAATATCCGTA 58.409 39.130 0.00 0.00 33.90 4.02
4837 5173 3.332919 ACTTCTACTTCAGTGCATGCAG 58.667 45.455 23.41 10.99 0.00 4.41
4838 5174 3.407424 ACTTCTACTTCAGTGCATGCA 57.593 42.857 18.46 18.46 0.00 3.96
4839 5175 4.328440 CACTACTTCTACTTCAGTGCATGC 59.672 45.833 11.82 11.82 31.14 4.06
4840 5176 5.473931 ACACTACTTCTACTTCAGTGCATG 58.526 41.667 0.00 0.00 40.17 4.06
4895 5253 2.597455 ACAGGCTTTTTACAGGCATGT 58.403 42.857 9.77 9.77 44.24 3.21
4897 5255 1.812571 CGACAGGCTTTTTACAGGCAT 59.187 47.619 0.00 0.00 41.89 4.40
4917 5275 3.694072 AGTGACAGTGAGAGTGATCTAGC 59.306 47.826 0.00 0.00 0.00 3.42
4958 5316 4.525487 TCAGAAGAGGCAAAAATGCAGAAT 59.475 37.500 2.97 0.00 36.33 2.40
4959 5317 3.890756 TCAGAAGAGGCAAAAATGCAGAA 59.109 39.130 2.97 0.00 36.33 3.02
4993 5355 2.851263 TGGATCAACCAAGCGTTAGT 57.149 45.000 0.00 0.00 46.75 2.24


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

AutoCloner maintained by Alex Coulton.