Multiple sequence alignment - TraesCS7D01G471700

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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 TraesCS7D01G471700 chr7D 100.000 6401 0 0 1 6401 585309185 585302785 0.000000e+00 11821.0
1 TraesCS7D01G471700 chr7A 87.871 3133 214 84 430 3485 675402001 675398958 0.000000e+00 3528.0
2 TraesCS7D01G471700 chr7A 92.786 1303 75 10 4609 5902 675397802 675396510 0.000000e+00 1868.0
3 TraesCS7D01G471700 chr7A 92.287 1141 54 13 3472 4608 675398940 675397830 0.000000e+00 1589.0
4 TraesCS7D01G471700 chr7A 84.926 471 40 17 5960 6401 675396516 675396048 1.270000e-121 448.0
5 TraesCS7D01G471700 chr7A 94.811 212 10 1 1 212 675402614 675402404 4.780000e-86 329.0
6 TraesCS7D01G471700 chr7B 88.371 2898 159 75 676 3485 653900212 653897405 0.000000e+00 3321.0
7 TraesCS7D01G471700 chr7B 94.049 1294 48 7 4609 5902 653896235 653894971 0.000000e+00 1936.0
8 TraesCS7D01G471700 chr7B 93.700 1127 47 7 3483 4608 653897371 653896268 0.000000e+00 1666.0
9 TraesCS7D01G471700 chr7B 85.174 661 41 27 1 616 653901346 653900698 5.450000e-175 625.0
10 TraesCS7D01G471700 chr7B 84.355 473 40 12 5960 6401 653894977 653894508 3.540000e-117 433.0
11 TraesCS7D01G471700 chr5D 95.199 1208 56 2 4695 5902 532656051 532654846 0.000000e+00 1908.0
12 TraesCS7D01G471700 chr5D 93.182 1056 57 3 3472 4526 532657192 532656151 0.000000e+00 1537.0
13 TraesCS7D01G471700 chr5D 95.481 686 27 4 2692 3374 532657953 532657269 0.000000e+00 1092.0
14 TraesCS7D01G471700 chr5D 100.000 48 0 0 3432 3479 532657269 532657222 8.840000e-14 89.8
15 TraesCS7D01G471700 chr6A 84.821 112 15 1 3498 3607 26326414 26326303 1.890000e-20 111.0


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 TraesCS7D01G471700 chr7D 585302785 585309185 6400 True 11821.0 11821 100.0000 1 6401 1 chr7D.!!$R1 6400
1 TraesCS7D01G471700 chr7A 675396048 675402614 6566 True 1552.4 3528 90.5362 1 6401 5 chr7A.!!$R1 6400
2 TraesCS7D01G471700 chr7B 653894508 653901346 6838 True 1596.2 3321 89.1298 1 6401 5 chr7B.!!$R1 6400
3 TraesCS7D01G471700 chr5D 532654846 532657953 3107 True 1156.7 1908 95.9655 2692 5902 4 chr5D.!!$R1 3210

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
724 1387 0.034767 CCCATCCATCCATCCATCCG 60.035 60.0 0.00 0.00 0.00 4.18 F
1882 2633 0.322008 CCAAGGACTGACCAAGAGCC 60.322 60.0 0.00 0.00 42.04 4.70 F
1939 2698 0.394899 GGATCCTGGCCCTGTTTCTG 60.395 60.0 3.84 0.00 0.00 3.02 F
3622 4446 1.166531 ACAAAGGACGGCTTGCTGAC 61.167 55.0 8.57 1.79 0.00 3.51 F
3938 4763 0.948678 ACATGTACGCCAACACAACC 59.051 50.0 0.00 0.00 30.75 3.77 F
4603 5433 0.179092 CATCAGTCGATGCAGAGCCA 60.179 55.0 0.00 0.00 42.54 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1914 2673 0.106519 CAGGGCCAGGATCCGAAAAT 60.107 55.000 6.18 0.0 0.00 1.82 R
3156 3933 0.179200 GGCACCGAATTACAGCAACG 60.179 55.000 0.00 0.0 0.00 4.10 R
3625 4449 1.008538 CTTCACCGCCACAAACTGC 60.009 57.895 0.00 0.0 0.00 4.40 R
4564 5394 0.035725 CAAGCAGCCAGTCTGATGGA 60.036 55.000 0.00 0.0 45.72 3.41 R
5181 6049 0.580578 CATTCTGCGATTGAGGCGAG 59.419 55.000 0.00 0.0 0.00 5.03 R
5519 6388 0.951040 CAGGGAGGCAAACGACAGAC 60.951 60.000 0.00 0.0 0.00 3.51 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
59 60 1.600916 GGAAAGGCACGGCTCACTT 60.601 57.895 0.00 0.00 0.00 3.16
141 142 0.039617 TTGCGCAAAGGATCAAACCG 60.040 50.000 22.78 0.00 34.73 4.44
169 170 4.949098 CTTAATCGCCCCGCCCCC 62.949 72.222 0.00 0.00 0.00 5.40
251 357 2.816672 GGCCAGAAAGGAAGAAGACAAG 59.183 50.000 0.00 0.00 41.22 3.16
265 371 5.181748 AGAAGACAAGCATACCATCAAGAC 58.818 41.667 0.00 0.00 0.00 3.01
290 396 7.075009 ACCCACTAATTATATTGTCTTCCCCAT 59.925 37.037 0.00 0.00 0.00 4.00
311 417 2.311287 CCAACTCTGGTATGCCCCT 58.689 57.895 0.00 0.00 38.00 4.79
326 432 2.750657 CCCTCTCCCCCTGCATCAC 61.751 68.421 0.00 0.00 0.00 3.06
327 433 1.692042 CCTCTCCCCCTGCATCACT 60.692 63.158 0.00 0.00 0.00 3.41
456 659 2.338785 GCCTTGTCTTGGCCTGAGC 61.339 63.158 3.32 0.00 44.32 4.26
544 778 0.041833 CCTTCTCTCTCCCCCACTCA 59.958 60.000 0.00 0.00 0.00 3.41
545 779 1.190643 CTTCTCTCTCCCCCACTCAC 58.809 60.000 0.00 0.00 0.00 3.51
546 780 0.787084 TTCTCTCTCCCCCACTCACT 59.213 55.000 0.00 0.00 0.00 3.41
547 781 0.333312 TCTCTCTCCCCCACTCACTC 59.667 60.000 0.00 0.00 0.00 3.51
548 782 0.334676 CTCTCTCCCCCACTCACTCT 59.665 60.000 0.00 0.00 0.00 3.24
549 783 0.787084 TCTCTCCCCCACTCACTCTT 59.213 55.000 0.00 0.00 0.00 2.85
550 784 1.150135 TCTCTCCCCCACTCACTCTTT 59.850 52.381 0.00 0.00 0.00 2.52
551 785 1.552792 CTCTCCCCCACTCACTCTTTC 59.447 57.143 0.00 0.00 0.00 2.62
552 786 0.615850 CTCCCCCACTCACTCTTTCC 59.384 60.000 0.00 0.00 0.00 3.13
553 787 0.840722 TCCCCCACTCACTCTTTCCC 60.841 60.000 0.00 0.00 0.00 3.97
554 788 0.842467 CCCCCACTCACTCTTTCCCT 60.842 60.000 0.00 0.00 0.00 4.20
555 789 0.615850 CCCCACTCACTCTTTCCCTC 59.384 60.000 0.00 0.00 0.00 4.30
556 790 1.650528 CCCACTCACTCTTTCCCTCT 58.349 55.000 0.00 0.00 0.00 3.69
653 890 1.770294 TTCAAAAAGAACCGCCACCT 58.230 45.000 0.00 0.00 0.00 4.00
655 892 0.313987 CAAAAAGAACCGCCACCTCC 59.686 55.000 0.00 0.00 0.00 4.30
658 895 4.658786 AGAACCGCCACCTCCCCT 62.659 66.667 0.00 0.00 0.00 4.79
659 896 4.410400 GAACCGCCACCTCCCCTG 62.410 72.222 0.00 0.00 0.00 4.45
685 1348 1.073284 GCCTACGATCCTCTCTCCTCT 59.927 57.143 0.00 0.00 0.00 3.69
716 1379 2.689175 GTTGCCCCCATCCATCCA 59.311 61.111 0.00 0.00 0.00 3.41
717 1380 1.233949 GTTGCCCCCATCCATCCAT 59.766 57.895 0.00 0.00 0.00 3.41
718 1381 0.829182 GTTGCCCCCATCCATCCATC 60.829 60.000 0.00 0.00 0.00 3.51
719 1382 2.022538 TTGCCCCCATCCATCCATCC 62.023 60.000 0.00 0.00 0.00 3.51
720 1383 2.472463 GCCCCCATCCATCCATCCA 61.472 63.158 0.00 0.00 0.00 3.41
721 1384 1.807771 GCCCCCATCCATCCATCCAT 61.808 60.000 0.00 0.00 0.00 3.41
722 1385 0.333993 CCCCCATCCATCCATCCATC 59.666 60.000 0.00 0.00 0.00 3.51
723 1386 0.333993 CCCCATCCATCCATCCATCC 59.666 60.000 0.00 0.00 0.00 3.51
724 1387 0.034767 CCCATCCATCCATCCATCCG 60.035 60.000 0.00 0.00 0.00 4.18
725 1388 0.694771 CCATCCATCCATCCATCCGT 59.305 55.000 0.00 0.00 0.00 4.69
726 1389 1.339438 CCATCCATCCATCCATCCGTC 60.339 57.143 0.00 0.00 0.00 4.79
756 1419 1.002201 TCCATTTTCTTGGTCGCCGTA 59.998 47.619 0.00 0.00 38.01 4.02
774 1437 1.134371 GTACAGAGCTCAATCCACCCC 60.134 57.143 17.77 0.00 0.00 4.95
777 1440 0.548682 AGAGCTCAATCCACCCCAGT 60.549 55.000 17.77 0.00 0.00 4.00
778 1441 1.204146 GAGCTCAATCCACCCCAGTA 58.796 55.000 9.40 0.00 0.00 2.74
779 1442 0.912486 AGCTCAATCCACCCCAGTAC 59.088 55.000 0.00 0.00 0.00 2.73
780 1443 0.912486 GCTCAATCCACCCCAGTACT 59.088 55.000 0.00 0.00 0.00 2.73
781 1444 1.134371 GCTCAATCCACCCCAGTACTC 60.134 57.143 0.00 0.00 0.00 2.59
798 1461 4.845580 CCTGCCTACCAGCCGCTG 62.846 72.222 13.82 13.82 40.36 5.18
810 1485 2.786495 GCCGCTGCTGCTAGTAGGA 61.786 63.158 14.03 5.88 36.97 2.94
841 1539 0.324943 CCGGTGATTCCAGTTGGAGT 59.675 55.000 0.51 0.00 46.36 3.85
845 1543 3.676324 CGGTGATTCCAGTTGGAGTAGTC 60.676 52.174 0.51 0.00 46.36 2.59
846 1544 3.515901 GGTGATTCCAGTTGGAGTAGTCT 59.484 47.826 0.51 0.00 46.36 3.24
847 1545 4.499183 GTGATTCCAGTTGGAGTAGTCTG 58.501 47.826 0.51 0.00 46.36 3.51
848 1546 4.021016 GTGATTCCAGTTGGAGTAGTCTGT 60.021 45.833 0.51 0.00 46.36 3.41
849 1547 5.185249 GTGATTCCAGTTGGAGTAGTCTGTA 59.815 44.000 0.51 0.00 46.36 2.74
852 1550 2.166664 CCAGTTGGAGTAGTCTGTAGCC 59.833 54.545 0.00 0.00 37.39 3.93
853 1551 3.093057 CAGTTGGAGTAGTCTGTAGCCT 58.907 50.000 0.00 0.00 0.00 4.58
854 1552 3.129638 CAGTTGGAGTAGTCTGTAGCCTC 59.870 52.174 0.00 0.00 0.00 4.70
855 1553 3.010808 AGTTGGAGTAGTCTGTAGCCTCT 59.989 47.826 0.00 0.00 0.00 3.69
905 1603 2.043248 GCGGTGGGAGGAGGAGTA 60.043 66.667 0.00 0.00 0.00 2.59
920 1618 1.544691 GGAGTAGTCGTCCTTGCTGAA 59.455 52.381 0.00 0.00 0.00 3.02
941 1639 1.469335 TTTCGTCAAGCTCGGTCCCT 61.469 55.000 0.00 0.00 0.00 4.20
952 1650 3.391382 GGTCCCTGTCCCTGTCCG 61.391 72.222 0.00 0.00 0.00 4.79
953 1651 3.391382 GTCCCTGTCCCTGTCCGG 61.391 72.222 0.00 0.00 0.00 5.14
980 1682 2.075426 AACTTCTTGGCAGCGGCAAC 62.075 55.000 11.88 0.00 42.98 4.17
1038 1745 5.788014 AGGTATCCTTCTTCTTCTTCAACCT 59.212 40.000 0.00 0.00 0.00 3.50
1042 1759 3.254411 CCTTCTTCTTCTTCAACCTTGGC 59.746 47.826 0.00 0.00 0.00 4.52
1170 1887 4.269523 TTGAACCTGCAGGCGGCT 62.270 61.111 33.06 14.75 45.15 5.52
1284 2007 3.753272 TGCTTTCCTCATTTGTACTGCTC 59.247 43.478 0.00 0.00 0.00 4.26
1308 2031 0.322098 TGCCCCGGTGTGAGTAATTG 60.322 55.000 0.00 0.00 0.00 2.32
1310 2033 0.616371 CCCCGGTGTGAGTAATTGGA 59.384 55.000 0.00 0.00 0.00 3.53
1311 2034 1.211949 CCCCGGTGTGAGTAATTGGAT 59.788 52.381 0.00 0.00 0.00 3.41
1316 2039 4.199310 CGGTGTGAGTAATTGGATGGATT 58.801 43.478 0.00 0.00 0.00 3.01
1322 2045 6.070021 TGTGAGTAATTGGATGGATTCTCTGT 60.070 38.462 0.00 0.00 0.00 3.41
1351 2074 1.205655 CTGATTCTCCTGCCTCGTCAA 59.794 52.381 0.00 0.00 0.00 3.18
1401 2128 7.591006 TTAGTAACCACTAAATTCGAGCTTG 57.409 36.000 0.00 0.00 42.87 4.01
1403 2130 6.694447 AGTAACCACTAAATTCGAGCTTGTA 58.306 36.000 0.00 0.00 31.45 2.41
1404 2131 6.812160 AGTAACCACTAAATTCGAGCTTGTAG 59.188 38.462 0.00 0.00 31.45 2.74
1406 2133 6.276832 ACCACTAAATTCGAGCTTGTAGTA 57.723 37.500 0.00 0.00 0.00 1.82
1415 2142 7.907214 ATTCGAGCTTGTAGTATTTCTTTGT 57.093 32.000 0.00 0.00 0.00 2.83
1416 2143 6.946229 TCGAGCTTGTAGTATTTCTTTGTC 57.054 37.500 0.00 0.00 0.00 3.18
1418 2145 7.152645 TCGAGCTTGTAGTATTTCTTTGTCTT 58.847 34.615 0.00 0.00 0.00 3.01
1437 2164 5.241506 TGTCTTGTCTCATTTCAACCAATCC 59.758 40.000 0.00 0.00 0.00 3.01
1459 2187 6.395629 TCCTCAAGGACTTAATTCGTGTTAG 58.604 40.000 0.00 0.00 39.78 2.34
1474 2202 2.796593 GTGTTAGTACCACACGTGTTCC 59.203 50.000 20.79 7.00 35.50 3.62
1475 2203 2.429971 TGTTAGTACCACACGTGTTCCA 59.570 45.455 20.79 3.37 0.00 3.53
1476 2204 3.054878 GTTAGTACCACACGTGTTCCAG 58.945 50.000 20.79 10.71 0.00 3.86
1477 2205 1.405872 AGTACCACACGTGTTCCAGA 58.594 50.000 20.79 0.00 0.00 3.86
1478 2206 1.068127 AGTACCACACGTGTTCCAGAC 59.932 52.381 20.79 12.56 0.00 3.51
1534 2269 4.836125 TTTGATTTGAACAGAGGCAGTC 57.164 40.909 0.00 0.00 0.00 3.51
1684 2431 6.489361 AGACTGACGGAGAGTTTAGTCTTTTA 59.511 38.462 0.00 0.00 46.25 1.52
1802 2549 4.597004 AGACTGATGGCATGTCAAATTCT 58.403 39.130 17.22 2.20 33.56 2.40
1829 2576 8.574737 CCCAAATTTAATTTGCCTCATTTCAAA 58.425 29.630 21.14 0.00 46.27 2.69
1882 2633 0.322008 CCAAGGACTGACCAAGAGCC 60.322 60.000 0.00 0.00 42.04 4.70
1938 2697 1.915078 CGGATCCTGGCCCTGTTTCT 61.915 60.000 10.75 0.00 0.00 2.52
1939 2698 0.394899 GGATCCTGGCCCTGTTTCTG 60.395 60.000 3.84 0.00 0.00 3.02
1980 2739 3.286353 TGAGCTGTCTCCTGTATCTCTG 58.714 50.000 0.00 0.00 38.58 3.35
2001 2760 5.046910 TGCAAATAAAAGACTGCTAGCAC 57.953 39.130 14.93 5.11 35.78 4.40
2018 2777 1.275010 GCACGTCAAATTCCCCCAAAT 59.725 47.619 0.00 0.00 0.00 2.32
2055 2816 4.768968 CCAAAATCCCTGAAGTTGACATCT 59.231 41.667 0.00 0.00 0.00 2.90
2057 2818 6.604795 CCAAAATCCCTGAAGTTGACATCTAT 59.395 38.462 0.00 0.00 0.00 1.98
2062 2823 8.915057 ATCCCTGAAGTTGACATCTATATTTG 57.085 34.615 0.00 0.00 0.00 2.32
2063 2824 7.861629 TCCCTGAAGTTGACATCTATATTTGT 58.138 34.615 0.00 0.00 0.00 2.83
2064 2825 8.988060 TCCCTGAAGTTGACATCTATATTTGTA 58.012 33.333 0.00 0.00 0.00 2.41
2065 2826 9.784531 CCCTGAAGTTGACATCTATATTTGTAT 57.215 33.333 0.00 0.00 0.00 2.29
2086 2847 5.852282 ATATTTGTTTATCAGCACCCACC 57.148 39.130 0.00 0.00 0.00 4.61
2101 2862 1.273327 CCCACCTGATCCTTTTGCAAC 59.727 52.381 0.00 0.00 0.00 4.17
2105 2866 3.441572 CACCTGATCCTTTTGCAACTAGG 59.558 47.826 17.13 17.13 0.00 3.02
2271 3040 1.622811 GGGGTTGGCAAATCAACATGA 59.377 47.619 0.00 0.00 46.29 3.07
2371 3140 2.710096 TAGAATAGGGCCTTGTGTGC 57.290 50.000 13.45 0.00 0.00 4.57
2421 3190 2.192624 CAGCGGGTTTTGTCTTGTTTG 58.807 47.619 0.00 0.00 0.00 2.93
2426 3195 4.498345 GCGGGTTTTGTCTTGTTTGTCATA 60.498 41.667 0.00 0.00 0.00 2.15
2484 3253 3.636300 AGTTTTGTTGCCATGCAGACTTA 59.364 39.130 0.00 0.00 40.61 2.24
2497 3266 2.703416 CAGACTTATTGTGGCTGCTCA 58.297 47.619 0.00 0.00 0.00 4.26
2518 3288 5.643664 TCATGCTGATTGTGTAAATCTTGC 58.356 37.500 0.00 5.15 0.00 4.01
2606 3376 3.142838 GATGTGGGCTGCGGCAAT 61.143 61.111 21.31 6.90 40.87 3.56
2617 3387 3.887868 CGGCAATAGCGGGTTGGC 61.888 66.667 12.86 12.86 45.48 4.52
2635 3405 4.405671 AGCTGATGCCGCTGTGCT 62.406 61.111 0.00 0.00 40.80 4.40
2728 3498 2.624838 ACAAAGAGGTGCCTGAAATGTG 59.375 45.455 0.00 0.00 0.00 3.21
2786 3559 2.363147 GACCAGAGCTCTCCCCGT 60.363 66.667 14.96 7.63 0.00 5.28
2960 3733 2.649034 GTGACGTTCCCTCAGCGA 59.351 61.111 0.00 0.00 0.00 4.93
3156 3933 5.350640 GGTAACATGCAACACTAACTCCTAC 59.649 44.000 0.00 0.00 0.00 3.18
3170 3947 3.508762 ACTCCTACGTTGCTGTAATTCG 58.491 45.455 0.00 0.00 0.00 3.34
3248 4026 3.651803 TGCCGTAAAGAAATGGGTTTG 57.348 42.857 0.00 0.00 0.00 2.93
3251 4029 4.216687 TGCCGTAAAGAAATGGGTTTGTAG 59.783 41.667 0.00 0.00 0.00 2.74
3350 4131 4.385825 TGTTACTGGTTGCTAGTTGGAAG 58.614 43.478 0.00 0.00 0.00 3.46
3362 4144 5.248477 TGCTAGTTGGAAGATTCAAGTACCT 59.752 40.000 0.00 0.00 0.00 3.08
3377 4159 6.539173 TCAAGTACCTGACCACATTATTGTT 58.461 36.000 0.00 0.00 32.34 2.83
3378 4160 6.429692 TCAAGTACCTGACCACATTATTGTTG 59.570 38.462 0.00 0.00 32.34 3.33
3390 4172 7.094377 ACCACATTATTGTTGTCAGTTATCACC 60.094 37.037 0.00 0.00 32.34 4.02
3391 4173 7.094420 CCACATTATTGTTGTCAGTTATCACCA 60.094 37.037 0.00 0.00 32.34 4.17
3394 4176 7.994425 TTATTGTTGTCAGTTATCACCATGT 57.006 32.000 0.00 0.00 0.00 3.21
3395 4177 9.679661 ATTATTGTTGTCAGTTATCACCATGTA 57.320 29.630 0.00 0.00 0.00 2.29
3396 4178 6.795098 TTGTTGTCAGTTATCACCATGTAC 57.205 37.500 0.00 0.00 0.00 2.90
3479 4303 8.502738 ACCATATGATGTGGAAACCTAATAGTT 58.497 33.333 15.50 0.00 39.12 2.24
3481 4305 9.784531 CATATGATGTGGAAACCTAATAGTTCT 57.215 33.333 0.00 0.00 0.00 3.01
3562 4386 6.425114 GCCTGACATCTGAATGTACGATATTT 59.575 38.462 0.00 0.00 46.20 1.40
3612 4436 1.429463 GCTGAGGTGTACAAAGGACG 58.571 55.000 0.00 0.00 0.00 4.79
3622 4446 1.166531 ACAAAGGACGGCTTGCTGAC 61.167 55.000 8.57 1.79 0.00 3.51
3730 4554 1.791103 CGCACGTCAACCACCCAAAT 61.791 55.000 0.00 0.00 0.00 2.32
3897 4722 1.006220 CGGTGGCTTCCAAAAAGGC 60.006 57.895 4.55 4.55 42.45 4.35
3938 4763 0.948678 ACATGTACGCCAACACAACC 59.051 50.000 0.00 0.00 30.75 3.77
3999 4824 7.743400 CGTTGAGTGCATATTAAGCTCATAATG 59.257 37.037 2.21 0.00 36.29 1.90
4000 4825 7.137490 TGAGTGCATATTAAGCTCATAATGC 57.863 36.000 13.99 13.99 32.09 3.56
4001 4826 6.711645 TGAGTGCATATTAAGCTCATAATGCA 59.288 34.615 17.71 17.71 32.09 3.96
4002 4827 6.906659 AGTGCATATTAAGCTCATAATGCAC 58.093 36.000 30.42 30.42 41.16 4.57
4003 4828 6.713903 AGTGCATATTAAGCTCATAATGCACT 59.286 34.615 32.53 32.53 43.45 4.40
4004 4829 7.020010 GTGCATATTAAGCTCATAATGCACTC 58.980 38.462 30.34 17.23 39.56 3.51
4005 4830 6.711645 TGCATATTAAGCTCATAATGCACTCA 59.288 34.615 17.71 1.89 0.00 3.41
4006 4831 7.392393 TGCATATTAAGCTCATAATGCACTCAT 59.608 33.333 17.71 0.00 33.53 2.90
4007 4832 8.886719 GCATATTAAGCTCATAATGCACTCATA 58.113 33.333 15.31 0.00 31.46 2.15
4185 5015 4.842531 TTATCTGATCAGGTGCAAAGGA 57.157 40.909 22.42 0.25 0.00 3.36
4303 5133 6.541641 ACAGAGACATCAAGGCTTCAAATATC 59.458 38.462 0.00 0.00 33.72 1.63
4327 5157 8.263940 TCCTTTTAACTGAAGATTATCAACCG 57.736 34.615 0.00 0.00 0.00 4.44
4564 5394 7.830697 TCCATGTTCATGATGACTTCATACTTT 59.169 33.333 13.51 0.00 43.40 2.66
4568 5398 7.830697 TGTTCATGATGACTTCATACTTTCCAT 59.169 33.333 0.00 0.00 43.40 3.41
4603 5433 0.179092 CATCAGTCGATGCAGAGCCA 60.179 55.000 0.00 0.00 42.54 4.75
4742 5604 0.376852 CGGATGTGTTTGCATACGGG 59.623 55.000 2.77 0.00 46.29 5.28
4961 5829 9.079833 CGAAAACATAAAGAAGGATAGTTACGA 57.920 33.333 0.00 0.00 0.00 3.43
4980 5848 2.935201 CGAGCTTCTGGAATCCTTTGAG 59.065 50.000 0.00 0.00 0.00 3.02
5162 6030 1.270094 CGGCCTAGCATGAAATCGGTA 60.270 52.381 0.00 0.00 0.00 4.02
5181 6049 1.620822 AAGTGATTTGGGTGCACCTC 58.379 50.000 33.91 23.60 41.11 3.85
5325 6193 1.026718 CCCCAATGTTCGACTCCTGC 61.027 60.000 0.00 0.00 0.00 4.85
5402 6270 2.110835 TGCGCTGGAGCAGTGAAA 59.889 55.556 9.73 0.00 43.78 2.69
5448 6317 3.369756 TCGGCATCTTTTTGTACATCGTC 59.630 43.478 0.00 0.00 0.00 4.20
5472 6341 4.971282 ACTATCTTCATTGTGATCCTCCCA 59.029 41.667 0.00 0.00 0.00 4.37
5519 6388 5.718607 TGTATGGATAGATGTGAGGGATCAG 59.281 44.000 0.00 0.00 0.00 2.90
5539 6408 1.071471 CTGTCGTTTGCCTCCCTGT 59.929 57.895 0.00 0.00 0.00 4.00
5606 6475 6.813152 TGTATGTTGTGATACTGTGATCTGTG 59.187 38.462 0.00 0.00 31.15 3.66
5663 6532 4.169059 TGTCACAATTCCTCATATGGGG 57.831 45.455 16.26 16.26 0.00 4.96
5692 6561 6.836007 TGCTTAGAGATAGAAGAGTGGAATGA 59.164 38.462 0.00 0.00 0.00 2.57
5748 6618 6.208599 GTCCTTGTTATGACCTTCCATTTTCA 59.791 38.462 0.00 0.00 0.00 2.69
5801 6671 8.201554 TGATGAATAAGTTCAGTTACTGCATC 57.798 34.615 7.61 11.77 46.75 3.91
5884 6754 9.737844 AAATGCCTTAAATATTTGACATTGGTT 57.262 25.926 11.05 0.00 0.00 3.67
5893 6763 5.643379 ATTTGACATTGGTTGCTCGTAAT 57.357 34.783 0.00 0.00 0.00 1.89
5894 6764 6.751514 ATTTGACATTGGTTGCTCGTAATA 57.248 33.333 0.00 0.00 0.00 0.98
5895 6765 6.751514 TTTGACATTGGTTGCTCGTAATAT 57.248 33.333 0.00 0.00 0.00 1.28
5896 6766 7.851387 TTTGACATTGGTTGCTCGTAATATA 57.149 32.000 0.00 0.00 0.00 0.86
5897 6767 8.445275 TTTGACATTGGTTGCTCGTAATATAT 57.555 30.769 0.00 0.00 0.00 0.86
5898 6768 9.549078 TTTGACATTGGTTGCTCGTAATATATA 57.451 29.630 0.00 0.00 0.00 0.86
5899 6769 9.719355 TTGACATTGGTTGCTCGTAATATATAT 57.281 29.630 0.00 0.00 0.00 0.86
6004 6878 9.739276 AATGTATGGAACTACAAAAAGATGAGA 57.261 29.630 0.00 0.00 35.37 3.27
6015 6889 9.661187 CTACAAAAAGATGAGACATATTGCATC 57.339 33.333 0.00 0.00 37.88 3.91
6033 6907 5.765176 TGCATCTTTCATTTTCACAGTGAG 58.235 37.500 2.82 0.00 0.00 3.51
6038 6912 4.990543 TTCATTTTCACAGTGAGCTACG 57.009 40.909 2.82 0.00 0.00 3.51
6048 6922 2.094894 CAGTGAGCTACGGCAAATTCTG 59.905 50.000 0.00 0.00 41.70 3.02
6106 6980 3.057245 GGCAAGAAGGCAAAGGAAGTAAG 60.057 47.826 0.00 0.00 43.51 2.34
6108 6982 4.320567 GCAAGAAGGCAAAGGAAGTAAGAC 60.321 45.833 0.00 0.00 0.00 3.01
6122 6999 5.992217 GGAAGTAAGACACAGAGACATTGTT 59.008 40.000 0.00 0.00 0.00 2.83
6132 7009 6.262944 ACACAGAGACATTGTTCTTGCAAATA 59.737 34.615 0.00 0.00 31.63 1.40
6133 7010 6.580041 CACAGAGACATTGTTCTTGCAAATAC 59.420 38.462 0.00 1.98 31.63 1.89
6137 7014 6.672147 AGACATTGTTCTTGCAAATACAGAC 58.328 36.000 0.00 0.00 31.63 3.51
6141 7018 8.629158 ACATTGTTCTTGCAAATACAGACTTTA 58.371 29.630 0.00 0.00 31.63 1.85
6161 7038 8.974060 ACTTTACCATATACATTGGTTACCTG 57.026 34.615 2.07 0.00 45.19 4.00
6163 7040 9.621629 CTTTACCATATACATTGGTTACCTGAA 57.378 33.333 2.07 0.00 45.19 3.02
6212 7114 0.615331 TGACCTTCTGCTGGACATCC 59.385 55.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.153229 GTCCTACAACCATCGCCCC 60.153 63.158 0.00 0.00 0.00 5.80
38 39 3.435186 GAGCCGTGCCTTTCCTGC 61.435 66.667 0.00 0.00 0.00 4.85
59 60 0.479378 GTAGGGTTTGGGTGTTGGGA 59.521 55.000 0.00 0.00 0.00 4.37
141 142 1.268743 GGCGATTAAGCTTGATGGTGC 60.269 52.381 8.68 9.36 37.29 5.01
169 170 6.149308 TGGATTAGATGTTGCTGTTAGTGTTG 59.851 38.462 0.00 0.00 0.00 3.33
251 357 2.717639 AGTGGGTCTTGATGGTATGC 57.282 50.000 0.00 0.00 0.00 3.14
265 371 6.848069 TGGGGAAGACAATATAATTAGTGGG 58.152 40.000 0.00 0.00 0.00 4.61
307 413 3.174265 GATGCAGGGGGAGAGGGG 61.174 72.222 0.00 0.00 0.00 4.79
311 417 0.689080 GAGAGTGATGCAGGGGGAGA 60.689 60.000 0.00 0.00 0.00 3.71
427 614 1.972588 AGACAAGGCTGGGGAATACT 58.027 50.000 0.00 0.00 0.00 2.12
428 615 2.369394 CAAGACAAGGCTGGGGAATAC 58.631 52.381 0.00 0.00 0.00 1.89
544 778 2.356741 CGGAGAGAGAGAGGGAAAGAGT 60.357 54.545 0.00 0.00 0.00 3.24
545 779 2.297701 CGGAGAGAGAGAGGGAAAGAG 58.702 57.143 0.00 0.00 0.00 2.85
546 780 1.636519 ACGGAGAGAGAGAGGGAAAGA 59.363 52.381 0.00 0.00 0.00 2.52
547 781 2.137810 ACGGAGAGAGAGAGGGAAAG 57.862 55.000 0.00 0.00 0.00 2.62
548 782 3.954904 CAATACGGAGAGAGAGAGGGAAA 59.045 47.826 0.00 0.00 0.00 3.13
549 783 3.053544 ACAATACGGAGAGAGAGAGGGAA 60.054 47.826 0.00 0.00 0.00 3.97
550 784 2.510382 ACAATACGGAGAGAGAGAGGGA 59.490 50.000 0.00 0.00 0.00 4.20
551 785 2.938838 ACAATACGGAGAGAGAGAGGG 58.061 52.381 0.00 0.00 0.00 4.30
552 786 3.002862 CGAACAATACGGAGAGAGAGAGG 59.997 52.174 0.00 0.00 0.00 3.69
553 787 3.547214 GCGAACAATACGGAGAGAGAGAG 60.547 52.174 0.00 0.00 0.00 3.20
554 788 2.355132 GCGAACAATACGGAGAGAGAGA 59.645 50.000 0.00 0.00 0.00 3.10
555 789 2.356382 AGCGAACAATACGGAGAGAGAG 59.644 50.000 0.00 0.00 0.00 3.20
556 790 2.097629 CAGCGAACAATACGGAGAGAGA 59.902 50.000 0.00 0.00 0.00 3.10
658 895 3.845259 GGATCGTAGGCCGGTGCA 61.845 66.667 1.90 0.00 38.02 4.57
659 896 3.501458 GAGGATCGTAGGCCGGTGC 62.501 68.421 1.90 0.00 38.46 5.01
661 898 1.528776 GAGAGGATCGTAGGCCGGT 60.529 63.158 1.90 0.00 42.67 5.28
663 900 1.238625 GGAGAGAGGATCGTAGGCCG 61.239 65.000 0.00 0.00 42.67 6.13
664 901 0.111639 AGGAGAGAGGATCGTAGGCC 59.888 60.000 0.00 0.00 42.67 5.19
665 902 1.073284 AGAGGAGAGAGGATCGTAGGC 59.927 57.143 0.00 0.00 42.67 3.93
668 905 2.040939 ACGAGAGGAGAGAGGATCGTA 58.959 52.381 0.00 0.00 41.17 3.43
669 906 0.834612 ACGAGAGGAGAGAGGATCGT 59.165 55.000 0.00 0.00 42.67 3.73
670 907 2.823924 TACGAGAGGAGAGAGGATCG 57.176 55.000 0.00 0.00 42.67 3.69
671 908 7.696992 AATTAATACGAGAGGAGAGAGGATC 57.303 40.000 0.00 0.00 0.00 3.36
672 909 7.094549 CGAAATTAATACGAGAGGAGAGAGGAT 60.095 40.741 8.61 0.00 0.00 3.24
673 910 6.205076 CGAAATTAATACGAGAGGAGAGAGGA 59.795 42.308 8.61 0.00 0.00 3.71
674 911 6.375377 CGAAATTAATACGAGAGGAGAGAGG 58.625 44.000 8.61 0.00 0.00 3.69
680 1343 4.807304 GCAACCGAAATTAATACGAGAGGA 59.193 41.667 13.89 0.00 0.00 3.71
716 1379 2.365105 ACGGGTGGACGGATGGAT 60.365 61.111 0.00 0.00 38.39 3.41
717 1380 3.072468 GACGGGTGGACGGATGGA 61.072 66.667 0.00 0.00 38.39 3.41
718 1381 4.157120 GGACGGGTGGACGGATGG 62.157 72.222 0.00 0.00 38.39 3.51
719 1382 3.075005 AGGACGGGTGGACGGATG 61.075 66.667 0.00 0.00 38.39 3.51
720 1383 2.758737 GAGGACGGGTGGACGGAT 60.759 66.667 0.00 0.00 38.39 4.18
723 1386 2.180159 AAATGGAGGACGGGTGGACG 62.180 60.000 0.00 0.00 40.31 4.79
724 1387 0.037734 AAAATGGAGGACGGGTGGAC 59.962 55.000 0.00 0.00 0.00 4.02
725 1388 0.326927 GAAAATGGAGGACGGGTGGA 59.673 55.000 0.00 0.00 0.00 4.02
726 1389 0.328258 AGAAAATGGAGGACGGGTGG 59.672 55.000 0.00 0.00 0.00 4.61
756 1419 0.842030 TGGGGTGGATTGAGCTCTGT 60.842 55.000 16.19 2.93 0.00 3.41
777 1440 1.756950 CGGCTGGTAGGCAGGAGTA 60.757 63.158 3.29 0.00 41.44 2.59
778 1441 3.077556 CGGCTGGTAGGCAGGAGT 61.078 66.667 3.29 0.00 41.44 3.85
779 1442 4.537433 GCGGCTGGTAGGCAGGAG 62.537 72.222 0.00 0.00 41.44 3.69
781 1444 4.845580 CAGCGGCTGGTAGGCAGG 62.846 72.222 22.11 0.00 41.44 4.85
798 1461 1.281899 CAAACGCTCCTACTAGCAGC 58.718 55.000 0.00 0.00 42.91 5.25
807 1482 2.357517 CGGACAGCAAACGCTCCT 60.358 61.111 0.00 0.00 37.77 3.69
810 1485 2.731691 ATCACCGGACAGCAAACGCT 62.732 55.000 9.46 0.00 41.67 5.07
814 1489 0.109532 TGGAATCACCGGACAGCAAA 59.890 50.000 9.46 0.00 42.61 3.68
841 1539 5.190925 AGAGAAGAGAAGAGGCTACAGACTA 59.809 44.000 0.00 0.00 30.09 2.59
845 1543 4.704540 TGAAGAGAAGAGAAGAGGCTACAG 59.295 45.833 0.00 0.00 0.00 2.74
846 1544 4.667573 TGAAGAGAAGAGAAGAGGCTACA 58.332 43.478 0.00 0.00 0.00 2.74
847 1545 5.652994 TTGAAGAGAAGAGAAGAGGCTAC 57.347 43.478 0.00 0.00 0.00 3.58
848 1546 5.395103 GCATTGAAGAGAAGAGAAGAGGCTA 60.395 44.000 0.00 0.00 0.00 3.93
849 1547 4.623647 GCATTGAAGAGAAGAGAAGAGGCT 60.624 45.833 0.00 0.00 0.00 4.58
852 1550 4.742417 TCGCATTGAAGAGAAGAGAAGAG 58.258 43.478 0.00 0.00 0.00 2.85
853 1551 4.381398 CCTCGCATTGAAGAGAAGAGAAGA 60.381 45.833 10.07 0.00 36.65 2.87
854 1552 3.864583 CCTCGCATTGAAGAGAAGAGAAG 59.135 47.826 10.07 0.00 36.65 2.85
855 1553 3.511540 TCCTCGCATTGAAGAGAAGAGAA 59.488 43.478 10.07 0.00 36.65 2.87
901 1599 2.229302 ACTTCAGCAAGGACGACTACTC 59.771 50.000 0.00 0.00 33.37 2.59
905 1603 2.484889 GAAACTTCAGCAAGGACGACT 58.515 47.619 0.00 0.00 33.37 4.18
920 1618 0.319641 GGACCGAGCTTGACGAAACT 60.320 55.000 1.22 0.00 0.00 2.66
952 1650 1.581447 CCAAGAAGTTCGCTTGCCC 59.419 57.895 0.00 0.00 41.00 5.36
953 1651 1.081175 GCCAAGAAGTTCGCTTGCC 60.081 57.895 0.00 0.00 41.00 4.52
955 1653 0.386478 GCTGCCAAGAAGTTCGCTTG 60.386 55.000 0.00 0.00 41.77 4.01
980 1682 4.382470 CCATTATATCCCTCCTCTGCTTCG 60.382 50.000 0.00 0.00 0.00 3.79
1031 1738 1.600636 CCTCAGCGCCAAGGTTGAA 60.601 57.895 15.76 0.00 0.00 2.69
1228 1948 4.821589 GGCGCTCACCTTCCTCGG 62.822 72.222 7.64 0.00 0.00 4.63
1308 2031 3.457749 AGGAGGAAACAGAGAATCCATCC 59.542 47.826 0.00 0.00 35.62 3.51
1310 2033 4.163839 CAGAGGAGGAAACAGAGAATCCAT 59.836 45.833 0.00 0.00 35.62 3.41
1311 2034 3.517100 CAGAGGAGGAAACAGAGAATCCA 59.483 47.826 0.00 0.00 35.62 3.41
1316 2039 4.682563 AGAATCAGAGGAGGAAACAGAGA 58.317 43.478 0.00 0.00 0.00 3.10
1322 2045 2.503356 GCAGGAGAATCAGAGGAGGAAA 59.497 50.000 0.00 0.00 36.25 3.13
1351 2074 0.473326 GAGGGATCCTGCAATCTGCT 59.527 55.000 12.58 0.00 45.31 4.24
1383 2106 5.148651 ACTACAAGCTCGAATTTAGTGGT 57.851 39.130 0.00 0.00 0.00 4.16
1384 2107 7.772332 AATACTACAAGCTCGAATTTAGTGG 57.228 36.000 0.00 0.00 0.00 4.00
1395 2122 8.089115 ACAAGACAAAGAAATACTACAAGCTC 57.911 34.615 0.00 0.00 0.00 4.09
1400 2127 9.778741 AATGAGACAAGACAAAGAAATACTACA 57.221 29.630 0.00 0.00 0.00 2.74
1403 2130 9.342308 TGAAATGAGACAAGACAAAGAAATACT 57.658 29.630 0.00 0.00 0.00 2.12
1404 2131 9.950680 TTGAAATGAGACAAGACAAAGAAATAC 57.049 29.630 0.00 0.00 0.00 1.89
1406 2133 7.922811 GGTTGAAATGAGACAAGACAAAGAAAT 59.077 33.333 0.00 0.00 0.00 2.17
1413 2140 5.241506 GGATTGGTTGAAATGAGACAAGACA 59.758 40.000 0.00 0.00 0.00 3.41
1414 2141 5.474876 AGGATTGGTTGAAATGAGACAAGAC 59.525 40.000 0.00 0.00 0.00 3.01
1415 2142 5.634118 AGGATTGGTTGAAATGAGACAAGA 58.366 37.500 0.00 0.00 0.00 3.02
1416 2143 5.474532 TGAGGATTGGTTGAAATGAGACAAG 59.525 40.000 0.00 0.00 0.00 3.16
1418 2145 4.984295 TGAGGATTGGTTGAAATGAGACA 58.016 39.130 0.00 0.00 0.00 3.41
1437 2164 7.275123 GGTACTAACACGAATTAAGTCCTTGAG 59.725 40.741 6.26 0.00 0.00 3.02
1459 2187 1.068127 AGTCTGGAACACGTGTGGTAC 59.932 52.381 24.16 15.56 34.19 3.34
1478 2206 3.475566 TGTCAGTTCTTGGACTGGAAG 57.524 47.619 8.98 0.00 45.54 3.46
1519 2247 1.618343 TCATCGACTGCCTCTGTTCAA 59.382 47.619 0.00 0.00 0.00 2.69
1521 2249 2.593346 ATCATCGACTGCCTCTGTTC 57.407 50.000 0.00 0.00 0.00 3.18
1611 2357 5.503634 TGAACTCTTGAGGATTGGAATGA 57.496 39.130 2.55 0.00 0.00 2.57
1616 2362 6.154445 CACAAATTGAACTCTTGAGGATTGG 58.846 40.000 0.00 0.00 0.00 3.16
1659 2406 4.023726 AGACTAAACTCTCCGTCAGTCT 57.976 45.455 0.00 0.00 38.27 3.24
1817 2564 4.541973 ATTCTTGGGTTTGAAATGAGGC 57.458 40.909 0.00 0.00 0.00 4.70
1829 2576 3.390639 TGGCACAAATTCAATTCTTGGGT 59.609 39.130 0.00 0.00 31.92 4.51
1861 2612 1.072331 GCTCTTGGTCAGTCCTTGGAA 59.928 52.381 0.00 0.00 37.07 3.53
1914 2673 0.106519 CAGGGCCAGGATCCGAAAAT 60.107 55.000 6.18 0.00 0.00 1.82
1938 2697 8.691797 AGCTCAACCTAAAATTTAAAACAGTCA 58.308 29.630 0.00 0.00 0.00 3.41
1939 2698 8.968242 CAGCTCAACCTAAAATTTAAAACAGTC 58.032 33.333 0.00 0.00 0.00 3.51
1980 2739 4.091424 CGTGCTAGCAGTCTTTTATTTGC 58.909 43.478 20.03 0.00 36.83 3.68
2001 2760 3.595173 GGAAATTTGGGGGAATTTGACG 58.405 45.455 0.00 0.00 38.85 4.35
2018 2777 3.310288 GGATTTTGGTAGGGGATGGGAAA 60.310 47.826 0.00 0.00 0.00 3.13
2062 2823 6.546034 AGGTGGGTGCTGATAAACAAATATAC 59.454 38.462 0.00 0.00 0.00 1.47
2063 2824 6.545666 CAGGTGGGTGCTGATAAACAAATATA 59.454 38.462 0.00 0.00 0.00 0.86
2064 2825 5.360714 CAGGTGGGTGCTGATAAACAAATAT 59.639 40.000 0.00 0.00 0.00 1.28
2065 2826 4.704540 CAGGTGGGTGCTGATAAACAAATA 59.295 41.667 0.00 0.00 0.00 1.40
2066 2827 3.511146 CAGGTGGGTGCTGATAAACAAAT 59.489 43.478 0.00 0.00 0.00 2.32
2070 2831 2.489938 TCAGGTGGGTGCTGATAAAC 57.510 50.000 0.00 0.00 0.00 2.01
2072 2833 1.490490 GGATCAGGTGGGTGCTGATAA 59.510 52.381 0.00 0.00 37.88 1.75
2073 2834 1.131638 GGATCAGGTGGGTGCTGATA 58.868 55.000 0.00 0.00 37.88 2.15
2077 2838 0.779997 AAAAGGATCAGGTGGGTGCT 59.220 50.000 0.00 0.00 0.00 4.40
2086 2847 2.424956 GGCCTAGTTGCAAAAGGATCAG 59.575 50.000 25.98 6.70 31.64 2.90
2105 2866 0.251077 CAGGGGCATCTAGGATTGGC 60.251 60.000 6.35 6.35 37.66 4.52
2371 3140 3.416277 CGCAAGGTACAAATCATTGTCG 58.584 45.455 0.00 0.00 46.78 4.35
2408 3177 5.359576 ACCAGCTATGACAAACAAGACAAAA 59.640 36.000 0.00 0.00 0.00 2.44
2421 3190 2.200373 AACCAACCACCAGCTATGAC 57.800 50.000 0.00 0.00 0.00 3.06
2426 3195 1.111277 GACAAAACCAACCACCAGCT 58.889 50.000 0.00 0.00 0.00 4.24
2484 3253 0.323087 TCAGCATGAGCAGCCACAAT 60.323 50.000 0.00 0.00 42.56 2.71
2497 3266 5.909621 AGCAAGATTTACACAATCAGCAT 57.090 34.783 11.91 0.06 34.53 3.79
2606 3376 2.669133 ATCAGCTGCCAACCCGCTA 61.669 57.895 9.47 0.00 31.80 4.26
2635 3405 1.205655 CCTCACTTGGATCTTCGCTCA 59.794 52.381 0.00 0.00 0.00 4.26
2786 3559 1.227234 CGATATGTCCAGCACGGCA 60.227 57.895 0.00 0.00 33.14 5.69
3156 3933 0.179200 GGCACCGAATTACAGCAACG 60.179 55.000 0.00 0.00 0.00 4.10
3248 4026 5.643777 AGTGAAATCATGGCAGTACAACTAC 59.356 40.000 0.00 0.00 0.00 2.73
3251 4029 4.455533 TCAGTGAAATCATGGCAGTACAAC 59.544 41.667 0.00 0.00 0.00 3.32
3350 4131 7.336931 ACAATAATGTGGTCAGGTACTTGAATC 59.663 37.037 9.54 6.01 38.69 2.52
3377 4159 7.832685 ACTAGTAGTACATGGTGATAACTGACA 59.167 37.037 0.00 0.00 0.00 3.58
3378 4160 8.223177 ACTAGTAGTACATGGTGATAACTGAC 57.777 38.462 0.00 0.00 0.00 3.51
3390 4172 9.640963 ACAAGCTAAAGAAACTAGTAGTACATG 57.359 33.333 2.50 0.00 0.00 3.21
3391 4173 9.857957 GACAAGCTAAAGAAACTAGTAGTACAT 57.142 33.333 2.50 0.00 0.00 2.29
3394 4176 8.413309 TGGACAAGCTAAAGAAACTAGTAGTA 57.587 34.615 2.50 0.00 0.00 1.82
3395 4177 7.015389 ACTGGACAAGCTAAAGAAACTAGTAGT 59.985 37.037 0.00 0.00 0.00 2.73
3396 4178 7.379750 ACTGGACAAGCTAAAGAAACTAGTAG 58.620 38.462 0.00 0.00 0.00 2.57
3562 4386 7.256332 CCTCCCTTTCCGATCAAATTATCTAGA 60.256 40.741 0.00 0.00 0.00 2.43
3625 4449 1.008538 CTTCACCGCCACAAACTGC 60.009 57.895 0.00 0.00 0.00 4.40
3897 4722 9.880064 CATGTCAAGATATTTGCTCTATTTCTG 57.120 33.333 0.00 0.00 0.00 3.02
3957 4782 3.275143 TCAACGGACATCGGCATTTAAT 58.725 40.909 0.00 0.00 44.45 1.40
3966 4791 1.921243 TATGCACTCAACGGACATCG 58.079 50.000 0.00 0.00 45.88 3.84
4163 4993 5.178096 TCCTTTGCACCTGATCAGATAAA 57.822 39.130 24.62 16.01 0.00 1.40
4185 5015 1.075659 GCCTTCCACTTGAGGCCTT 59.924 57.895 6.77 0.00 41.28 4.35
4303 5133 6.967199 GCGGTTGATAATCTTCAGTTAAAAGG 59.033 38.462 0.00 0.00 0.00 3.11
4327 5157 4.321378 GCTAGCAGTAGGATTAGTACCTGC 60.321 50.000 10.63 8.01 39.74 4.85
4339 5169 2.761208 AGTGTAACAGGCTAGCAGTAGG 59.239 50.000 18.24 2.97 41.43 3.18
4564 5394 0.035725 CAAGCAGCCAGTCTGATGGA 60.036 55.000 0.00 0.00 45.72 3.41
4568 5398 0.675837 GATGCAAGCAGCCAGTCTGA 60.676 55.000 0.00 0.00 45.72 3.27
4742 5604 5.932303 TGTCACTAGTTCAAGAAGCAATACC 59.068 40.000 0.00 0.00 0.00 2.73
4935 5803 9.079833 TCGTAACTATCCTTCTTTATGTTTTCG 57.920 33.333 0.00 0.00 0.00 3.46
4961 5829 4.379302 AACTCAAAGGATTCCAGAAGCT 57.621 40.909 5.29 0.00 0.00 3.74
5162 6030 1.145738 AGAGGTGCACCCAAATCACTT 59.854 47.619 32.29 10.49 36.42 3.16
5181 6049 0.580578 CATTCTGCGATTGAGGCGAG 59.419 55.000 0.00 0.00 0.00 5.03
5325 6193 2.539953 GCGAGTGTAGTCCTCTGAATCG 60.540 54.545 0.00 0.00 32.33 3.34
5402 6270 4.394729 TCTGTCCAAAGTCGGCTAAAAAT 58.605 39.130 0.00 0.00 0.00 1.82
5448 6317 5.303971 GGGAGGATCACAATGAAGATAGTG 58.696 45.833 0.00 0.00 39.41 2.74
5519 6388 0.951040 CAGGGAGGCAAACGACAGAC 60.951 60.000 0.00 0.00 0.00 3.51
5539 6408 6.240894 AGAAATGACACCTTAGATCAGCAAA 58.759 36.000 0.00 0.00 0.00 3.68
5663 6532 6.264292 TCCACTCTTCTATCTCTAAGCATGTC 59.736 42.308 0.00 0.00 0.00 3.06
5692 6561 2.893424 ACCCTGCAGATGACCAAAATT 58.107 42.857 17.39 0.00 0.00 1.82
5801 6671 8.995220 TGTAAGCTGTAGTAGTAACCAATTTTG 58.005 33.333 0.00 0.00 0.00 2.44
5860 6730 7.280652 GCAACCAATGTCAAATATTTAAGGCAT 59.719 33.333 0.00 0.18 0.00 4.40
5989 6859 9.661187 GATGCAATATGTCTCATCTTTTTGTAG 57.339 33.333 0.00 0.00 34.19 2.74
5991 6861 8.289939 AGATGCAATATGTCTCATCTTTTTGT 57.710 30.769 0.00 0.00 41.87 2.83
5998 6872 9.745880 AAAATGAAAGATGCAATATGTCTCATC 57.254 29.630 0.00 0.00 36.49 2.92
6000 6874 8.741841 TGAAAATGAAAGATGCAATATGTCTCA 58.258 29.630 0.00 0.00 0.00 3.27
6001 6875 9.017669 GTGAAAATGAAAGATGCAATATGTCTC 57.982 33.333 0.00 0.00 0.00 3.36
6004 6878 8.308931 ACTGTGAAAATGAAAGATGCAATATGT 58.691 29.630 0.00 0.00 0.00 2.29
6015 6889 5.377358 CGTAGCTCACTGTGAAAATGAAAG 58.623 41.667 12.16 0.00 0.00 2.62
6019 6893 2.159653 GCCGTAGCTCACTGTGAAAATG 60.160 50.000 12.16 1.22 35.50 2.32
6020 6894 2.076863 GCCGTAGCTCACTGTGAAAAT 58.923 47.619 12.16 3.41 35.50 1.82
6050 6924 1.409427 AGTACTGCATAGCGGAAGTCC 59.591 52.381 4.61 0.00 38.46 3.85
6054 6928 2.871182 CAGAGTACTGCATAGCGGAA 57.129 50.000 0.00 0.00 38.46 4.30
6081 6955 3.245407 ACTTCCTTTGCCTTCTTGCCTAT 60.245 43.478 0.00 0.00 0.00 2.57
6098 6972 5.542779 ACAATGTCTCTGTGTCTTACTTCC 58.457 41.667 0.00 0.00 0.00 3.46
6099 6973 6.926272 AGAACAATGTCTCTGTGTCTTACTTC 59.074 38.462 0.00 0.00 0.00 3.01
6102 6976 6.564873 GCAAGAACAATGTCTCTGTGTCTTAC 60.565 42.308 0.00 0.00 30.24 2.34
6106 6980 3.561310 TGCAAGAACAATGTCTCTGTGTC 59.439 43.478 0.00 0.00 0.00 3.67
6108 6982 4.556942 TTGCAAGAACAATGTCTCTGTG 57.443 40.909 0.00 0.00 0.00 3.66
6152 7029 9.016438 GTTTAAGGTGAAATATTCAGGTAACCA 57.984 33.333 0.00 0.00 41.01 3.67
6163 7040 9.273016 CTGGATACGATGTTTAAGGTGAAATAT 57.727 33.333 0.00 0.00 42.51 1.28
6166 7043 5.878116 CCTGGATACGATGTTTAAGGTGAAA 59.122 40.000 0.00 0.00 42.51 2.69
6167 7044 5.188163 TCCTGGATACGATGTTTAAGGTGAA 59.812 40.000 0.00 0.00 42.51 3.18
6168 7045 4.712829 TCCTGGATACGATGTTTAAGGTGA 59.287 41.667 0.00 0.00 42.51 4.02
6169 7046 5.018539 TCCTGGATACGATGTTTAAGGTG 57.981 43.478 0.00 0.00 42.51 4.00


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

AutoCloner maintained by Alex Coulton.