Multiple sequence alignment - TraesCS2A01G135700

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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 TraesCS2A01G135700 chr2A 100.000 5554 0 0 1 5554 81770348 81764795 0.000000e+00 10257
1 TraesCS2A01G135700 chr2A 99.060 638 5 1 1 637 768290439 768289802 0.000000e+00 1144
2 TraesCS2A01G135700 chr2A 98.507 67 0 1 4871 4937 81765423 81765358 3.520000e-22 117
3 TraesCS2A01G135700 chr2A 98.507 67 0 1 4926 4991 81765478 81765412 3.520000e-22 117
4 TraesCS2A01G135700 chr2D 96.431 2886 74 13 2055 4935 81313492 81310631 0.000000e+00 4732
5 TraesCS2A01G135700 chr2D 88.310 941 53 15 843 1745 81314938 81314017 0.000000e+00 1075
6 TraesCS2A01G135700 chr2D 93.243 148 7 3 1910 2056 81313932 81313787 1.210000e-51 215
7 TraesCS2A01G135700 chr2D 95.192 104 2 2 5454 5554 81310273 81310170 1.600000e-35 161
8 TraesCS2A01G135700 chr2B 93.349 1654 80 15 2564 4198 133024757 133023115 0.000000e+00 2418
9 TraesCS2A01G135700 chr2B 86.882 1052 67 29 745 1750 133027269 133026243 0.000000e+00 1112
10 TraesCS2A01G135700 chr2B 91.626 621 38 5 1956 2563 133025409 133024790 0.000000e+00 846
11 TraesCS2A01G135700 chr2B 90.830 578 31 11 4359 4929 133023114 133022552 0.000000e+00 754
12 TraesCS2A01G135700 chr2B 82.472 445 34 16 5019 5452 133022536 133022125 3.180000e-92 350
13 TraesCS2A01G135700 chr2B 97.458 118 3 0 1843 1960 133025698 133025581 9.430000e-48 202
14 TraesCS2A01G135700 chr2B 93.750 96 5 1 1752 1847 133025949 133025855 5.800000e-30 143
15 TraesCS2A01G135700 chr2B 85.833 120 8 4 5435 5554 133022110 133022000 9.770000e-23 119
16 TraesCS2A01G135700 chr4B 94.432 916 41 7 2600 3510 526965790 526964880 0.000000e+00 1400
17 TraesCS2A01G135700 chr4B 98.589 638 8 1 1 637 27318560 27317923 0.000000e+00 1127
18 TraesCS2A01G135700 chr4B 92.230 296 20 1 3510 3802 526963253 526962958 3.100000e-112 416
19 TraesCS2A01G135700 chr6A 93.319 943 55 4 2866 3802 611871781 611870841 0.000000e+00 1386
20 TraesCS2A01G135700 chr6A 98.746 638 6 2 1 637 270621875 270621239 0.000000e+00 1133
21 TraesCS2A01G135700 chr6A 92.208 308 17 4 2564 2868 611885985 611885682 3.980000e-116 429
22 TraesCS2A01G135700 chr6A 92.025 163 13 0 4200 4362 101317237 101317399 4.330000e-56 230
23 TraesCS2A01G135700 chr4A 99.529 637 3 0 1 637 10602215 10601579 0.000000e+00 1160
24 TraesCS2A01G135700 chr4A 98.905 639 5 2 1 637 610405127 610404489 0.000000e+00 1140
25 TraesCS2A01G135700 chr5B 99.373 638 3 1 1 638 670759209 670759845 0.000000e+00 1155
26 TraesCS2A01G135700 chr7B 98.744 637 7 1 1 637 457861912 457861277 0.000000e+00 1131
27 TraesCS2A01G135700 chr3B 98.592 639 8 1 1 638 480061581 480060943 0.000000e+00 1129
28 TraesCS2A01G135700 chr3B 98.592 639 8 1 1 638 571287467 571288105 0.000000e+00 1129
29 TraesCS2A01G135700 chr5A 92.727 165 11 1 4200 4363 320214404 320214240 2.590000e-58 237
30 TraesCS2A01G135700 chr4D 93.168 161 11 0 4200 4360 421331073 421331233 2.590000e-58 237
31 TraesCS2A01G135700 chr4D 92.593 162 12 0 4200 4361 64390472 64390633 3.350000e-57 233
32 TraesCS2A01G135700 chr3A 91.765 170 14 0 4193 4362 600920849 600921018 2.590000e-58 237
33 TraesCS2A01G135700 chr1A 92.593 162 12 0 4200 4361 39438839 39439000 3.350000e-57 233
34 TraesCS2A01G135700 chr6D 89.617 183 17 2 4184 4365 467802447 467802266 1.200000e-56 231
35 TraesCS2A01G135700 chr3D 92.073 164 13 0 4200 4363 128214008 128214171 1.200000e-56 231


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 TraesCS2A01G135700 chr2A 81764795 81770348 5553 True 10257.00 10257 100.000 1 5554 1 chr2A.!!$R1 5553
1 TraesCS2A01G135700 chr2A 768289802 768290439 637 True 1144.00 1144 99.060 1 637 1 chr2A.!!$R2 636
2 TraesCS2A01G135700 chr2D 81310170 81314938 4768 True 1545.75 4732 93.294 843 5554 4 chr2D.!!$R1 4711
3 TraesCS2A01G135700 chr2B 133022000 133027269 5269 True 743.00 2418 90.275 745 5554 8 chr2B.!!$R1 4809
4 TraesCS2A01G135700 chr4B 27317923 27318560 637 True 1127.00 1127 98.589 1 637 1 chr4B.!!$R1 636
5 TraesCS2A01G135700 chr4B 526962958 526965790 2832 True 908.00 1400 93.331 2600 3802 2 chr4B.!!$R2 1202
6 TraesCS2A01G135700 chr6A 611870841 611871781 940 True 1386.00 1386 93.319 2866 3802 1 chr6A.!!$R2 936
7 TraesCS2A01G135700 chr6A 270621239 270621875 636 True 1133.00 1133 98.746 1 637 1 chr6A.!!$R1 636
8 TraesCS2A01G135700 chr4A 10601579 10602215 636 True 1160.00 1160 99.529 1 637 1 chr4A.!!$R1 636
9 TraesCS2A01G135700 chr4A 610404489 610405127 638 True 1140.00 1140 98.905 1 637 1 chr4A.!!$R2 636
10 TraesCS2A01G135700 chr5B 670759209 670759845 636 False 1155.00 1155 99.373 1 638 1 chr5B.!!$F1 637
11 TraesCS2A01G135700 chr7B 457861277 457861912 635 True 1131.00 1131 98.744 1 637 1 chr7B.!!$R1 636
12 TraesCS2A01G135700 chr3B 480060943 480061581 638 True 1129.00 1129 98.592 1 638 1 chr3B.!!$R1 637
13 TraesCS2A01G135700 chr3B 571287467 571288105 638 False 1129.00 1129 98.592 1 638 1 chr3B.!!$F1 637

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
878 904 0.602060 GGACCTAACGATCGATCCCC 59.398 60.000 24.34 10.76 0.00 4.81 F
1339 1411 0.036388 TGAATCCGTTCACCAGCTCC 60.036 55.000 0.00 0.00 39.36 4.70 F
1440 1513 0.467290 TTGCTCTTGCCCGGAGTTTT 60.467 50.000 0.73 0.00 38.71 2.43 F
1731 1818 0.951558 CAAGGTAGCCAACGCAAACT 59.048 50.000 0.00 0.00 37.52 2.66 F
2157 3169 1.009829 CTGGCTATGTCGAGCAAACC 58.990 55.000 0.00 0.00 44.76 3.27 F
2717 3765 1.063174 CTGCAGATGCGCCTTAACTTC 59.937 52.381 8.42 0.00 45.83 3.01 F
2771 3819 2.550606 CGAGTAGCGCTCTCCTTTATCT 59.449 50.000 16.34 0.00 41.98 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1827 2207 0.940126 GACTAGAATGCATGGCACCG 59.060 55.000 0.00 0.00 43.04 4.94 R
2729 3777 1.876156 CTGTCACTCCCAAACAAGCTC 59.124 52.381 0.00 0.00 0.00 4.09 R
2771 3819 2.361757 CACATGGTCCAGAGCAAACAAA 59.638 45.455 3.33 0.00 42.53 2.83 R
3100 4155 3.673809 GGTAGCTCTCTTGTTGTGTTACG 59.326 47.826 0.00 0.00 0.00 3.18 R
4097 6791 0.871722 TCGCAATCAGTTCAAACGGG 59.128 50.000 0.00 0.00 0.00 5.28 R
4502 7201 0.803117 TCTCTGTACTCTTGACCGCG 59.197 55.000 0.00 0.00 0.00 6.46 R
4650 7349 0.855995 GAATAGAAAGAGCTCGCGGC 59.144 55.000 6.13 9.11 42.19 6.53 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
240 242 3.117398 TCGGAGGAAGTAATAGCCCTACA 60.117 47.826 0.00 0.00 29.96 2.74
638 642 3.458118 CCTAGGTACATGTCCCCATCAAA 59.542 47.826 0.00 0.00 0.00 2.69
639 643 3.366052 AGGTACATGTCCCCATCAAAC 57.634 47.619 0.00 0.00 0.00 2.93
640 644 2.647299 AGGTACATGTCCCCATCAAACA 59.353 45.455 0.00 0.00 0.00 2.83
641 645 3.269381 AGGTACATGTCCCCATCAAACAT 59.731 43.478 0.00 0.00 34.03 2.71
642 646 3.632145 GGTACATGTCCCCATCAAACATC 59.368 47.826 0.00 0.00 31.43 3.06
643 647 3.454719 ACATGTCCCCATCAAACATCA 57.545 42.857 0.00 0.00 31.43 3.07
644 648 3.091545 ACATGTCCCCATCAAACATCAC 58.908 45.455 0.00 0.00 31.43 3.06
645 649 3.245371 ACATGTCCCCATCAAACATCACT 60.245 43.478 0.00 0.00 31.43 3.41
646 650 2.794103 TGTCCCCATCAAACATCACTG 58.206 47.619 0.00 0.00 0.00 3.66
647 651 1.474077 GTCCCCATCAAACATCACTGC 59.526 52.381 0.00 0.00 0.00 4.40
648 652 0.819582 CCCCATCAAACATCACTGCC 59.180 55.000 0.00 0.00 0.00 4.85
649 653 1.617804 CCCCATCAAACATCACTGCCT 60.618 52.381 0.00 0.00 0.00 4.75
650 654 2.173519 CCCATCAAACATCACTGCCTT 58.826 47.619 0.00 0.00 0.00 4.35
651 655 3.355378 CCCATCAAACATCACTGCCTTA 58.645 45.455 0.00 0.00 0.00 2.69
652 656 3.763360 CCCATCAAACATCACTGCCTTAA 59.237 43.478 0.00 0.00 0.00 1.85
653 657 4.380867 CCCATCAAACATCACTGCCTTAAC 60.381 45.833 0.00 0.00 0.00 2.01
654 658 4.218200 CCATCAAACATCACTGCCTTAACA 59.782 41.667 0.00 0.00 0.00 2.41
655 659 5.105635 CCATCAAACATCACTGCCTTAACAT 60.106 40.000 0.00 0.00 0.00 2.71
656 660 5.627499 TCAAACATCACTGCCTTAACATC 57.373 39.130 0.00 0.00 0.00 3.06
657 661 5.316167 TCAAACATCACTGCCTTAACATCT 58.684 37.500 0.00 0.00 0.00 2.90
658 662 5.769662 TCAAACATCACTGCCTTAACATCTT 59.230 36.000 0.00 0.00 0.00 2.40
659 663 5.633830 AACATCACTGCCTTAACATCTTG 57.366 39.130 0.00 0.00 0.00 3.02
660 664 4.910195 ACATCACTGCCTTAACATCTTGA 58.090 39.130 0.00 0.00 0.00 3.02
661 665 5.503927 ACATCACTGCCTTAACATCTTGAT 58.496 37.500 0.00 0.00 0.00 2.57
662 666 5.948162 ACATCACTGCCTTAACATCTTGATT 59.052 36.000 0.00 0.00 0.00 2.57
663 667 6.435277 ACATCACTGCCTTAACATCTTGATTT 59.565 34.615 0.00 0.00 0.00 2.17
664 668 6.899393 TCACTGCCTTAACATCTTGATTTT 57.101 33.333 0.00 0.00 0.00 1.82
665 669 7.288810 TCACTGCCTTAACATCTTGATTTTT 57.711 32.000 0.00 0.00 0.00 1.94
666 670 7.370383 TCACTGCCTTAACATCTTGATTTTTC 58.630 34.615 0.00 0.00 0.00 2.29
667 671 7.231317 TCACTGCCTTAACATCTTGATTTTTCT 59.769 33.333 0.00 0.00 0.00 2.52
668 672 7.869429 CACTGCCTTAACATCTTGATTTTTCTT 59.131 33.333 0.00 0.00 0.00 2.52
669 673 8.424133 ACTGCCTTAACATCTTGATTTTTCTTT 58.576 29.630 0.00 0.00 0.00 2.52
670 674 9.264719 CTGCCTTAACATCTTGATTTTTCTTTT 57.735 29.630 0.00 0.00 0.00 2.27
671 675 9.044150 TGCCTTAACATCTTGATTTTTCTTTTG 57.956 29.630 0.00 0.00 0.00 2.44
672 676 9.260002 GCCTTAACATCTTGATTTTTCTTTTGA 57.740 29.630 0.00 0.00 0.00 2.69
704 708 9.670719 TTTCAAAACTTTTCAAACATGGTTTTC 57.329 25.926 0.00 0.00 35.58 2.29
705 709 8.383318 TCAAAACTTTTCAAACATGGTTTTCA 57.617 26.923 0.00 0.00 35.58 2.69
706 710 9.007901 TCAAAACTTTTCAAACATGGTTTTCAT 57.992 25.926 0.00 0.00 35.58 2.57
749 753 9.676861 TGATTTTCATGTGATATTCTCTTGTCT 57.323 29.630 0.00 0.00 0.00 3.41
752 756 9.506018 TTTTCATGTGATATTCTCTTGTCTTGA 57.494 29.630 0.00 0.00 0.00 3.02
753 757 8.484641 TTCATGTGATATTCTCTTGTCTTGAC 57.515 34.615 0.00 0.00 0.00 3.18
754 758 7.614494 TCATGTGATATTCTCTTGTCTTGACA 58.386 34.615 0.00 0.00 0.00 3.58
755 759 8.262933 TCATGTGATATTCTCTTGTCTTGACAT 58.737 33.333 4.18 0.00 0.00 3.06
756 760 9.538508 CATGTGATATTCTCTTGTCTTGACATA 57.461 33.333 4.18 0.00 0.00 2.29
786 792 5.910166 CCTCATTTATCTCGTGTCGAACTAG 59.090 44.000 0.00 0.00 34.74 2.57
805 811 1.153066 TGTGTTCGAGCCAAGCCAA 60.153 52.632 0.00 0.00 0.00 4.52
806 812 1.165907 TGTGTTCGAGCCAAGCCAAG 61.166 55.000 0.00 0.00 0.00 3.61
807 813 2.260869 TGTTCGAGCCAAGCCAAGC 61.261 57.895 0.00 0.00 0.00 4.01
808 814 2.672996 TTCGAGCCAAGCCAAGCC 60.673 61.111 0.00 0.00 0.00 4.35
809 815 3.490031 TTCGAGCCAAGCCAAGCCA 62.490 57.895 0.00 0.00 0.00 4.75
810 816 2.974692 TTCGAGCCAAGCCAAGCCAA 62.975 55.000 0.00 0.00 0.00 4.52
811 817 2.968206 GAGCCAAGCCAAGCCAAG 59.032 61.111 0.00 0.00 0.00 3.61
812 818 3.292500 GAGCCAAGCCAAGCCAAGC 62.293 63.158 0.00 0.00 0.00 4.01
813 819 4.383861 GCCAAGCCAAGCCAAGCC 62.384 66.667 0.00 0.00 0.00 4.35
814 820 2.918802 CCAAGCCAAGCCAAGCCA 60.919 61.111 0.00 0.00 0.00 4.75
834 840 2.686835 GGAGGCAGCAGGGAGAGT 60.687 66.667 0.00 0.00 0.00 3.24
878 904 0.602060 GGACCTAACGATCGATCCCC 59.398 60.000 24.34 10.76 0.00 4.81
881 907 2.101917 GACCTAACGATCGATCCCCAAA 59.898 50.000 24.34 0.68 0.00 3.28
902 928 0.667184 CCATCAAACCTTTGCGTGCC 60.667 55.000 0.00 0.00 38.05 5.01
940 977 4.087892 CCCTCCCCTCACTGCGTG 62.088 72.222 2.79 2.79 34.45 5.34
941 978 4.767255 CCTCCCCTCACTGCGTGC 62.767 72.222 4.15 0.00 32.98 5.34
1054 1091 2.276740 CCTCCGGGGTACGTACCT 59.723 66.667 36.70 0.00 45.72 3.08
1176 1232 4.712425 CGTCGACGCCCCTTTCGT 62.712 66.667 26.59 0.00 43.49 3.85
1189 1255 3.540367 TTTCGTGTTCCCCCGGAGC 62.540 63.158 0.73 0.00 33.44 4.70
1339 1411 0.036388 TGAATCCGTTCACCAGCTCC 60.036 55.000 0.00 0.00 39.36 4.70
1367 1439 2.297033 GCACCAATGCCAGAGAAAGAAA 59.703 45.455 0.00 0.00 46.97 2.52
1368 1440 3.056322 GCACCAATGCCAGAGAAAGAAAT 60.056 43.478 0.00 0.00 46.97 2.17
1440 1513 0.467290 TTGCTCTTGCCCGGAGTTTT 60.467 50.000 0.73 0.00 38.71 2.43
1445 1518 3.081804 CTCTTGCCCGGAGTTTTAACAT 58.918 45.455 0.73 0.00 0.00 2.71
1459 1532 7.855904 GGAGTTTTAACATATTTGTATGCCTCG 59.144 37.037 0.00 0.00 34.06 4.63
1488 1561 3.676646 GCCTGCTAGCTGATTTTTGTTTG 59.323 43.478 21.96 3.41 0.00 2.93
1496 1575 7.223777 GCTAGCTGATTTTTGTTTGGTTTTGTA 59.776 33.333 7.70 0.00 0.00 2.41
1525 1604 2.196595 AGGCCTGGTAGCTGAATTACA 58.803 47.619 3.11 0.00 0.00 2.41
1541 1621 5.351740 TGAATTACACGTGAAACACTTGTCA 59.648 36.000 25.01 9.45 41.78 3.58
1552 1632 6.037172 GTGAAACACTTGTCACTGTACATCTT 59.963 38.462 0.00 0.00 40.82 2.40
1683 1770 1.450312 GGTCCAGCTGTTCCCATCG 60.450 63.158 13.81 0.00 0.00 3.84
1710 1797 1.912417 ACTATCTCGCGCTTATCCCT 58.088 50.000 5.56 0.00 0.00 4.20
1731 1818 0.951558 CAAGGTAGCCAACGCAAACT 59.048 50.000 0.00 0.00 37.52 2.66
1750 1838 6.074676 GCAAACTGATCTTTGTTGCACTTTAG 60.075 38.462 14.80 0.00 34.19 1.85
1804 2184 6.069684 CCAGTTTTAAATGCAATTTTGGCA 57.930 33.333 0.00 0.00 46.10 4.92
1827 2207 3.187227 CAGTGGTGATAGTTTGTGAGTGC 59.813 47.826 0.00 0.00 0.00 4.40
1931 2472 4.381566 GGTGCACACAAAATTAAAGCTACG 59.618 41.667 20.43 0.00 0.00 3.51
1945 2486 5.532025 AAAGCTACGTATCTTGCTTGTTC 57.468 39.130 17.40 0.00 43.80 3.18
1960 2501 6.072112 TGCTTGTTCTGAAATGAAGTTACC 57.928 37.500 0.00 0.00 0.00 2.85
1961 2502 5.009610 TGCTTGTTCTGAAATGAAGTTACCC 59.990 40.000 0.00 0.00 0.00 3.69
2053 3056 6.855836 ACATGTTAGATGTTTGGCATACTTG 58.144 36.000 9.46 0.00 38.06 3.16
2157 3169 1.009829 CTGGCTATGTCGAGCAAACC 58.990 55.000 0.00 0.00 44.76 3.27
2196 3208 3.340814 TCCTCTCATCTTTGTCAAGGC 57.659 47.619 0.00 0.00 0.00 4.35
2197 3209 2.639347 TCCTCTCATCTTTGTCAAGGCA 59.361 45.455 0.00 0.00 0.00 4.75
2386 3400 2.740981 CACTGTGTGAGAGATTGCCTTC 59.259 50.000 0.00 0.00 35.23 3.46
2393 3407 4.074970 GTGAGAGATTGCCTTCTCCAAAA 58.925 43.478 8.87 0.00 42.63 2.44
2439 3454 8.897752 AGCTTTTAGATGGTTAGCTATGAAAAG 58.102 33.333 11.75 11.75 40.19 2.27
2443 3458 9.920946 TTTAGATGGTTAGCTATGAAAAGGAAT 57.079 29.630 0.00 0.00 0.00 3.01
2499 3514 4.778213 TTTGGATAGGGAGTGAATCAGG 57.222 45.455 0.00 0.00 0.00 3.86
2532 3549 5.471456 GCAATGTCTCTGGTTATAGATTGGG 59.529 44.000 0.00 0.00 0.00 4.12
2630 3678 7.714377 GTGGAAATATCTGTGAGAAGTGATGAT 59.286 37.037 0.00 0.00 0.00 2.45
2631 3679 8.927411 TGGAAATATCTGTGAGAAGTGATGATA 58.073 33.333 0.00 0.00 0.00 2.15
2632 3680 9.770097 GGAAATATCTGTGAGAAGTGATGATAA 57.230 33.333 0.00 0.00 0.00 1.75
2717 3765 1.063174 CTGCAGATGCGCCTTAACTTC 59.937 52.381 8.42 0.00 45.83 3.01
2729 3777 4.201851 CGCCTTAACTTCAGGATCATGTTG 60.202 45.833 7.33 4.25 32.41 3.33
2771 3819 2.550606 CGAGTAGCGCTCTCCTTTATCT 59.449 50.000 16.34 0.00 41.98 1.98
3242 4297 3.997681 GCTACACTCCTCTTTCTGGTTTC 59.002 47.826 0.00 0.00 0.00 2.78
3335 4390 4.396478 GTGCTGAAGATTAAGGGAAAGGTC 59.604 45.833 0.00 0.00 0.00 3.85
3386 4441 6.025749 TCTGTTTGATGTTATCGTCTGACT 57.974 37.500 6.21 0.00 0.00 3.41
3724 6410 9.425248 TTCTGGATTTGATAGCCTTCATATTTT 57.575 29.630 0.00 0.00 0.00 1.82
4092 6786 6.237901 AGCTTGTGGAATCTATGTTGTTACA 58.762 36.000 0.00 0.00 38.95 2.41
4097 6791 6.597672 TGTGGAATCTATGTTGTTACACCATC 59.402 38.462 0.00 0.00 36.15 3.51
4212 6911 2.787473 TATGCCACTCCCTCTGTTTG 57.213 50.000 0.00 0.00 0.00 2.93
4261 6960 8.411991 TTCAATATGGACTACATACGGATGTA 57.588 34.615 19.32 19.32 44.77 2.29
4502 7201 1.379576 ATTGGCTGAGAAGCTGGCC 60.380 57.895 0.00 0.00 44.31 5.36
4566 7265 6.136541 ACAAAGTTTGAGCCTTCTACAAAG 57.863 37.500 22.23 0.00 34.86 2.77
4568 7267 6.183360 ACAAAGTTTGAGCCTTCTACAAAGAC 60.183 38.462 22.23 0.00 34.86 3.01
4576 7275 2.338500 CTTCTACAAAGACGACCTGCC 58.662 52.381 0.00 0.00 0.00 4.85
4579 7278 2.103432 TCTACAAAGACGACCTGCCAAA 59.897 45.455 0.00 0.00 0.00 3.28
4643 7342 0.250513 GAGGACAAGGGAGCATCGTT 59.749 55.000 0.00 0.00 34.37 3.85
4650 7349 2.106683 GGGAGCATCGTTGGTTCGG 61.107 63.158 0.00 0.00 34.37 4.30
4802 7510 1.129624 TGTTAGCACAATTTAGCCGCG 59.870 47.619 0.00 0.00 0.00 6.46
4803 7511 0.098025 TTAGCACAATTTAGCCGCGC 59.902 50.000 0.00 0.00 0.00 6.86
4804 7512 1.021920 TAGCACAATTTAGCCGCGCA 61.022 50.000 8.75 0.00 0.00 6.09
4830 7538 3.378427 ACTGCTGAGAGTTTTTCGCTTTT 59.622 39.130 0.00 0.00 0.00 2.27
4845 7553 2.547642 CGCTTTTCATTTTTGAGGCCCA 60.548 45.455 0.00 0.00 0.00 5.36
4846 7554 3.069289 GCTTTTCATTTTTGAGGCCCAG 58.931 45.455 0.00 0.00 0.00 4.45
4847 7555 2.837532 TTTCATTTTTGAGGCCCAGC 57.162 45.000 0.00 0.00 0.00 4.85
4899 7608 2.606795 CCGCATTGGTTTGTTTGTCGAT 60.607 45.455 0.00 0.00 0.00 3.59
4900 7609 2.656422 CGCATTGGTTTGTTTGTCGATC 59.344 45.455 0.00 0.00 0.00 3.69
4901 7610 2.986479 GCATTGGTTTGTTTGTCGATCC 59.014 45.455 0.00 0.00 0.00 3.36
4902 7611 3.233578 CATTGGTTTGTTTGTCGATCCG 58.766 45.455 0.00 0.00 0.00 4.18
4903 7612 1.956297 TGGTTTGTTTGTCGATCCGT 58.044 45.000 0.00 0.00 0.00 4.69
4904 7613 2.290464 TGGTTTGTTTGTCGATCCGTT 58.710 42.857 0.00 0.00 0.00 4.44
4905 7614 2.683867 TGGTTTGTTTGTCGATCCGTTT 59.316 40.909 0.00 0.00 0.00 3.60
4906 7615 3.040099 GGTTTGTTTGTCGATCCGTTTG 58.960 45.455 0.00 0.00 0.00 2.93
4907 7616 3.242804 GGTTTGTTTGTCGATCCGTTTGA 60.243 43.478 0.00 0.00 0.00 2.69
4908 7617 4.533222 GTTTGTTTGTCGATCCGTTTGAT 58.467 39.130 0.00 0.00 36.01 2.57
4909 7618 4.822036 TTGTTTGTCGATCCGTTTGATT 57.178 36.364 0.00 0.00 32.41 2.57
4910 7619 4.398549 TGTTTGTCGATCCGTTTGATTC 57.601 40.909 0.00 0.00 32.41 2.52
4911 7620 4.062293 TGTTTGTCGATCCGTTTGATTCT 58.938 39.130 0.00 0.00 32.41 2.40
4912 7621 5.231702 TGTTTGTCGATCCGTTTGATTCTA 58.768 37.500 0.00 0.00 32.41 2.10
4913 7622 5.872617 TGTTTGTCGATCCGTTTGATTCTAT 59.127 36.000 0.00 0.00 32.41 1.98
4914 7623 6.035650 TGTTTGTCGATCCGTTTGATTCTATC 59.964 38.462 0.00 0.00 32.41 2.08
4915 7624 5.515797 TGTCGATCCGTTTGATTCTATCT 57.484 39.130 0.00 0.00 32.41 1.98
4916 7625 5.281727 TGTCGATCCGTTTGATTCTATCTG 58.718 41.667 0.00 0.00 32.41 2.90
4917 7626 4.149046 GTCGATCCGTTTGATTCTATCTGC 59.851 45.833 0.00 0.00 32.41 4.26
4918 7627 4.038042 TCGATCCGTTTGATTCTATCTGCT 59.962 41.667 0.00 0.00 32.41 4.24
4919 7628 4.747108 CGATCCGTTTGATTCTATCTGCTT 59.253 41.667 0.00 0.00 32.41 3.91
4920 7629 5.332883 CGATCCGTTTGATTCTATCTGCTTG 60.333 44.000 0.00 0.00 32.41 4.01
4921 7630 5.084818 TCCGTTTGATTCTATCTGCTTGA 57.915 39.130 0.00 0.00 0.00 3.02
4922 7631 5.487433 TCCGTTTGATTCTATCTGCTTGAA 58.513 37.500 0.00 0.00 0.00 2.69
4923 7632 6.115446 TCCGTTTGATTCTATCTGCTTGAAT 58.885 36.000 0.00 0.00 32.90 2.57
4924 7633 6.599244 TCCGTTTGATTCTATCTGCTTGAATT 59.401 34.615 0.00 0.00 30.78 2.17
4925 7634 7.768582 TCCGTTTGATTCTATCTGCTTGAATTA 59.231 33.333 0.00 0.00 30.78 1.40
4926 7635 8.562892 CCGTTTGATTCTATCTGCTTGAATTAT 58.437 33.333 0.00 0.00 30.78 1.28
4927 7636 9.378597 CGTTTGATTCTATCTGCTTGAATTATG 57.621 33.333 0.00 0.00 30.78 1.90
4930 7639 9.842775 TTGATTCTATCTGCTTGAATTATGAGT 57.157 29.630 0.00 0.00 30.78 3.41
4931 7640 9.842775 TGATTCTATCTGCTTGAATTATGAGTT 57.157 29.630 0.00 0.00 30.78 3.01
4933 7642 7.488187 TCTATCTGCTTGAATTATGAGTTGC 57.512 36.000 0.00 0.00 0.00 4.17
4934 7643 4.970662 TCTGCTTGAATTATGAGTTGCC 57.029 40.909 0.00 0.00 0.00 4.52
4935 7644 3.374988 TCTGCTTGAATTATGAGTTGCCG 59.625 43.478 0.00 0.00 0.00 5.69
4936 7645 2.159393 TGCTTGAATTATGAGTTGCCGC 60.159 45.455 0.00 0.00 0.00 6.53
4937 7646 2.159393 GCTTGAATTATGAGTTGCCGCA 60.159 45.455 0.00 0.00 0.00 5.69
4938 7647 3.489738 GCTTGAATTATGAGTTGCCGCAT 60.490 43.478 0.00 0.00 35.18 4.73
4939 7648 4.675510 CTTGAATTATGAGTTGCCGCATT 58.324 39.130 0.00 0.00 32.94 3.56
4940 7649 4.031418 TGAATTATGAGTTGCCGCATTG 57.969 40.909 0.00 0.00 32.94 2.82
4941 7650 3.181488 TGAATTATGAGTTGCCGCATTGG 60.181 43.478 0.00 0.00 42.50 3.16
4942 7651 1.832883 TTATGAGTTGCCGCATTGGT 58.167 45.000 0.00 0.00 41.21 3.67
4943 7652 1.832883 TATGAGTTGCCGCATTGGTT 58.167 45.000 0.00 0.00 41.21 3.67
4944 7653 0.968405 ATGAGTTGCCGCATTGGTTT 59.032 45.000 0.00 0.00 41.21 3.27
4977 7686 5.487433 TCCGTTTGATTCTATCTGCTTGAA 58.513 37.500 0.00 0.00 0.00 2.69
4989 7698 4.556942 TCTGCTTGAATTATGATTGCCG 57.443 40.909 0.00 0.00 0.00 5.69
4990 7699 3.047796 CTGCTTGAATTATGATTGCCGC 58.952 45.455 0.00 0.00 0.00 6.53
4995 7704 2.287644 TGAATTATGATTGCCGCGAGTG 59.712 45.455 8.23 0.00 0.00 3.51
4996 7705 0.588252 ATTATGATTGCCGCGAGTGC 59.412 50.000 8.23 2.45 37.91 4.40
5010 7719 0.596083 GAGTGCGAGATGACCGATGG 60.596 60.000 0.00 0.00 0.00 3.51
5035 7744 4.058817 GTCTTAGAAGGTGTTGTGGTGAG 58.941 47.826 0.00 0.00 0.00 3.51
5065 7774 9.693739 AATTGGTAGTGATTGGTAAATGACATA 57.306 29.630 0.00 0.00 32.82 2.29
5176 7897 2.656002 CTACTCGGATTCAGACCCTCA 58.344 52.381 0.00 0.00 0.00 3.86
5181 7902 1.202580 CGGATTCAGACCCTCATGTCC 60.203 57.143 0.00 0.00 35.83 4.02
5219 7940 8.089115 AGTAAGATTTCTTCGAGTTCTTTTGG 57.911 34.615 0.00 0.00 37.40 3.28
5224 7945 8.251026 AGATTTCTTCGAGTTCTTTTGGTTTTT 58.749 29.630 0.00 0.00 0.00 1.94
5227 7948 9.863845 TTTCTTCGAGTTCTTTTGGTTTTTATT 57.136 25.926 0.00 0.00 0.00 1.40
5228 7949 9.863845 TTCTTCGAGTTCTTTTGGTTTTTATTT 57.136 25.926 0.00 0.00 0.00 1.40
5229 7950 9.863845 TCTTCGAGTTCTTTTGGTTTTTATTTT 57.136 25.926 0.00 0.00 0.00 1.82
5232 7953 8.384365 TCGAGTTCTTTTGGTTTTTATTTTTGC 58.616 29.630 0.00 0.00 0.00 3.68
5236 7957 8.942924 GTTCTTTTGGTTTTTATTTTTGCATCG 58.057 29.630 0.00 0.00 0.00 3.84
5237 7958 8.425577 TCTTTTGGTTTTTATTTTTGCATCGA 57.574 26.923 0.00 0.00 0.00 3.59
5238 7959 8.883731 TCTTTTGGTTTTTATTTTTGCATCGAA 58.116 25.926 0.00 0.00 0.00 3.71
5239 7960 9.157259 CTTTTGGTTTTTATTTTTGCATCGAAG 57.843 29.630 0.00 0.00 0.00 3.79
5240 7961 8.425577 TTTGGTTTTTATTTTTGCATCGAAGA 57.574 26.923 0.00 0.00 45.75 2.87
5241 7962 8.425577 TTGGTTTTTATTTTTGCATCGAAGAA 57.574 26.923 0.00 0.00 43.58 2.52
5242 7963 8.600449 TGGTTTTTATTTTTGCATCGAAGAAT 57.400 26.923 0.00 0.00 43.58 2.40
5243 7964 9.050601 TGGTTTTTATTTTTGCATCGAAGAATT 57.949 25.926 0.00 0.00 43.58 2.17
5244 7965 9.877137 GGTTTTTATTTTTGCATCGAAGAATTT 57.123 25.926 0.00 0.00 43.58 1.82
5248 7969 8.824159 TTATTTTTGCATCGAAGAATTTTCCA 57.176 26.923 0.00 0.00 43.58 3.53
5249 7970 6.768029 TTTTTGCATCGAAGAATTTTCCAG 57.232 33.333 0.00 0.00 43.58 3.86
5250 7971 3.492421 TGCATCGAAGAATTTTCCAGC 57.508 42.857 0.00 0.00 43.58 4.85
5251 7972 3.084039 TGCATCGAAGAATTTTCCAGCT 58.916 40.909 0.00 0.00 43.58 4.24
5252 7973 3.119743 TGCATCGAAGAATTTTCCAGCTG 60.120 43.478 6.78 6.78 43.58 4.24
5253 7974 3.432782 CATCGAAGAATTTTCCAGCTGC 58.567 45.455 8.66 0.00 43.58 5.25
5254 7975 1.812571 TCGAAGAATTTTCCAGCTGCC 59.187 47.619 8.66 0.00 0.00 4.85
5255 7976 1.135286 CGAAGAATTTTCCAGCTGCCC 60.135 52.381 8.66 0.00 0.00 5.36
5256 7977 1.205655 GAAGAATTTTCCAGCTGCCCC 59.794 52.381 8.66 0.00 0.00 5.80
5257 7978 0.114954 AGAATTTTCCAGCTGCCCCA 59.885 50.000 8.66 0.00 0.00 4.96
5304 8031 8.020819 GTGCAATTTATTATGTGTATGCGGTAT 58.979 33.333 0.00 0.00 35.40 2.73
5324 8051 6.183360 CGGTATGTGTAGCATGTTGTAACATT 60.183 38.462 7.48 0.00 46.95 2.71
5329 8056 4.691216 TGTAGCATGTTGTAACATTGCGTA 59.309 37.500 7.48 7.11 46.95 4.42
5338 8065 0.942410 AACATTGCGTACGCGTCTGT 60.942 50.000 32.65 29.07 45.51 3.41
5343 8070 1.804326 GCGTACGCGTCTGTGGAAT 60.804 57.895 26.17 0.00 40.81 3.01
5345 8072 0.365523 CGTACGCGTCTGTGGAATTG 59.634 55.000 18.63 0.00 0.00 2.32
5354 8081 3.255642 CGTCTGTGGAATTGAAATGGGTT 59.744 43.478 0.00 0.00 0.00 4.11
5412 8139 2.535984 GTCATTACGGCGAGTGATCAAG 59.464 50.000 16.62 0.00 0.00 3.02
5413 8140 2.165641 TCATTACGGCGAGTGATCAAGT 59.834 45.455 16.62 0.00 0.00 3.16
5416 8143 1.878953 ACGGCGAGTGATCAAGTTTT 58.121 45.000 16.62 0.00 0.00 2.43
5439 8166 6.913873 TTTTACTTTAGAACAAGCGAGTGT 57.086 33.333 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
638 642 4.910195 TCAAGATGTTAAGGCAGTGATGT 58.090 39.130 0.00 0.00 0.00 3.06
639 643 6.446781 AATCAAGATGTTAAGGCAGTGATG 57.553 37.500 0.00 0.00 0.00 3.07
640 644 7.472334 AAAATCAAGATGTTAAGGCAGTGAT 57.528 32.000 0.00 0.00 0.00 3.06
641 645 6.899393 AAAATCAAGATGTTAAGGCAGTGA 57.101 33.333 0.00 0.00 0.00 3.41
642 646 7.373493 AGAAAAATCAAGATGTTAAGGCAGTG 58.627 34.615 0.00 0.00 0.00 3.66
643 647 7.530426 AGAAAAATCAAGATGTTAAGGCAGT 57.470 32.000 0.00 0.00 0.00 4.40
644 648 8.822652 AAAGAAAAATCAAGATGTTAAGGCAG 57.177 30.769 0.00 0.00 0.00 4.85
645 649 9.044150 CAAAAGAAAAATCAAGATGTTAAGGCA 57.956 29.630 0.00 0.00 0.00 4.75
646 650 9.260002 TCAAAAGAAAAATCAAGATGTTAAGGC 57.740 29.630 0.00 0.00 0.00 4.35
678 682 9.670719 GAAAACCATGTTTGAAAAGTTTTGAAA 57.329 25.926 5.36 7.25 37.50 2.69
679 683 8.840321 TGAAAACCATGTTTGAAAAGTTTTGAA 58.160 25.926 5.36 0.04 37.50 2.69
680 684 8.383318 TGAAAACCATGTTTGAAAAGTTTTGA 57.617 26.923 5.36 0.00 37.50 2.69
681 685 9.063739 CATGAAAACCATGTTTGAAAAGTTTTG 57.936 29.630 5.36 0.00 45.83 2.44
723 727 9.676861 AGACAAGAGAATATCACATGAAAATCA 57.323 29.630 0.00 0.00 0.00 2.57
726 730 9.506018 TCAAGACAAGAGAATATCACATGAAAA 57.494 29.630 0.00 0.00 0.00 2.29
727 731 8.939929 GTCAAGACAAGAGAATATCACATGAAA 58.060 33.333 0.00 0.00 0.00 2.69
728 732 8.096414 TGTCAAGACAAGAGAATATCACATGAA 58.904 33.333 0.00 0.00 38.56 2.57
729 733 7.614494 TGTCAAGACAAGAGAATATCACATGA 58.386 34.615 0.00 0.00 38.56 3.07
730 734 7.838771 TGTCAAGACAAGAGAATATCACATG 57.161 36.000 0.00 0.00 38.56 3.21
732 736 9.942850 TTTATGTCAAGACAAGAGAATATCACA 57.057 29.630 7.02 0.00 45.41 3.58
770 774 2.812591 ACACACTAGTTCGACACGAGAT 59.187 45.455 12.26 0.00 37.14 2.75
786 792 1.444119 TTGGCTTGGCTCGAACACAC 61.444 55.000 0.00 0.00 0.00 3.82
812 818 3.795041 CCCTGCTGCCTCCTCTGG 61.795 72.222 0.00 0.00 0.00 3.86
813 819 2.686470 TCCCTGCTGCCTCCTCTG 60.686 66.667 0.00 0.00 0.00 3.35
814 820 2.365370 CTCCCTGCTGCCTCCTCT 60.365 66.667 0.00 0.00 0.00 3.69
822 828 2.427245 CGGGGTACTCTCCCTGCTG 61.427 68.421 4.41 0.00 45.60 4.41
834 840 1.607178 TCGACTGGCTTTCGGGGTA 60.607 57.895 8.18 0.00 37.09 3.69
839 845 2.434359 GGGGTCGACTGGCTTTCG 60.434 66.667 16.46 2.40 37.85 3.46
878 904 2.134346 CGCAAAGGTTTGATGGGTTTG 58.866 47.619 6.63 0.00 40.55 2.93
881 907 0.673437 CACGCAAAGGTTTGATGGGT 59.327 50.000 6.63 0.00 40.55 4.51
1053 1090 1.541672 GAGAGAGGGGGAGGAGGAG 59.458 68.421 0.00 0.00 0.00 3.69
1054 1091 2.015726 GGAGAGAGGGGGAGGAGGA 61.016 68.421 0.00 0.00 0.00 3.71
1151 1206 4.849329 GGCGTCGACGGGTGCTAG 62.849 72.222 36.13 9.21 40.23 3.42
1199 1265 0.749454 GAATTCCACGGCCAGCATCT 60.749 55.000 2.24 0.00 0.00 2.90
1258 1330 0.531090 ACTCAGCCACGCGTTTACAA 60.531 50.000 10.22 0.00 0.00 2.41
1300 1372 3.632604 TCAGCTATCCAACTCTAGAACCG 59.367 47.826 0.00 0.00 0.00 4.44
1440 1513 6.426633 CACATCCGAGGCATACAAATATGTTA 59.573 38.462 0.00 0.00 40.45 2.41
1445 1518 3.738982 CCACATCCGAGGCATACAAATA 58.261 45.455 0.00 0.00 0.00 1.40
1459 1532 1.525535 CAGCTAGCAGGCCACATCC 60.526 63.158 18.83 0.00 0.00 3.51
1471 1544 7.538303 ACAAAACCAAACAAAAATCAGCTAG 57.462 32.000 0.00 0.00 0.00 3.42
1488 1561 3.832490 AGGCCTTTCCTCAATACAAAACC 59.168 43.478 0.00 0.00 43.20 3.27
1496 1575 1.064389 GCTACCAGGCCTTTCCTCAAT 60.064 52.381 0.00 0.00 45.52 2.57
1525 1604 2.695359 ACAGTGACAAGTGTTTCACGT 58.305 42.857 0.00 0.00 45.71 4.49
1541 1621 1.204941 GGACGGCTCAAGATGTACAGT 59.795 52.381 0.33 0.00 0.00 3.55
1552 1632 1.893062 CATCTGTCAGGACGGCTCA 59.107 57.895 3.34 0.00 37.60 4.26
1683 1770 1.944676 CGCGAGATAGTTGACGGCC 60.945 63.158 0.00 0.00 0.00 6.13
1710 1797 1.103987 TTTGCGTTGGCTACCTTGCA 61.104 50.000 0.00 0.00 40.82 4.08
1731 1818 6.293407 GCTGTACTAAAGTGCAACAAAGATCA 60.293 38.462 2.54 0.00 40.02 2.92
1766 2146 1.068753 CTGGCACTCTAGATGGGCG 59.931 63.158 9.41 3.76 0.00 6.13
1769 2149 6.678900 GCATTTAAAACTGGCACTCTAGATGG 60.679 42.308 0.00 0.00 0.00 3.51
1804 2184 4.380531 CACTCACAAACTATCACCACTGT 58.619 43.478 0.00 0.00 0.00 3.55
1820 2200 4.107051 GCATGGCACCGCACTCAC 62.107 66.667 5.89 0.00 0.00 3.51
1827 2207 0.940126 GACTAGAATGCATGGCACCG 59.060 55.000 0.00 0.00 43.04 4.94
1931 2472 7.588512 ACTTCATTTCAGAACAAGCAAGATAC 58.411 34.615 0.00 0.00 0.00 2.24
1945 2486 6.796705 AAACTACGGGTAACTTCATTTCAG 57.203 37.500 0.00 0.00 0.00 3.02
1981 2698 3.788937 AGGCATGCTTAACATTCATTGC 58.211 40.909 18.92 0.00 36.64 3.56
2053 3056 9.813446 AATTCCAAAGAAAATAGAAGCATGATC 57.187 29.630 0.00 0.00 35.09 2.92
2157 3169 3.267031 AGGAAGAACTTACCCCTGGAATG 59.733 47.826 0.00 0.00 0.00 2.67
2196 3208 8.243289 ACAAAAGAACAAATCAAAACTCTGTG 57.757 30.769 0.00 0.00 0.00 3.66
2323 3337 5.636121 TCACATACAGTTACTTTAGTTGCCG 59.364 40.000 0.00 0.00 0.00 5.69
2386 3400 5.050490 CCACCTCGTCTACATATTTTGGAG 58.950 45.833 0.00 0.00 37.67 3.86
2393 3407 3.741388 GCTTTGCCACCTCGTCTACATAT 60.741 47.826 0.00 0.00 0.00 1.78
2439 3454 3.933332 ACTAGTTTGAGTAAGCGCATTCC 59.067 43.478 11.47 0.00 0.00 3.01
2443 3458 8.712285 ATTAATTACTAGTTTGAGTAAGCGCA 57.288 30.769 11.47 0.00 43.38 6.09
2499 3514 2.684881 CCAGAGACATTGCAACCATACC 59.315 50.000 0.00 0.00 0.00 2.73
2559 3607 8.801913 GTTGCTCAGCATAAATGAAGATTAAAC 58.198 33.333 0.00 0.00 38.76 2.01
2630 3678 4.574421 GTGCCATACACTGCATATGTGTTA 59.426 41.667 14.54 3.31 45.11 2.41
2631 3679 3.378112 GTGCCATACACTGCATATGTGTT 59.622 43.478 14.54 2.11 45.11 3.32
2717 3765 4.482386 CAAACAAGCTCAACATGATCCTG 58.518 43.478 0.00 0.00 0.00 3.86
2729 3777 1.876156 CTGTCACTCCCAAACAAGCTC 59.124 52.381 0.00 0.00 0.00 4.09
2757 3805 4.154918 AGCAAACAAAGATAAAGGAGAGCG 59.845 41.667 0.00 0.00 0.00 5.03
2771 3819 2.361757 CACATGGTCCAGAGCAAACAAA 59.638 45.455 3.33 0.00 42.53 2.83
2953 4005 4.825634 CCAATGATGCTGATAATCACCTGT 59.174 41.667 0.00 0.00 36.89 4.00
3100 4155 3.673809 GGTAGCTCTCTTGTTGTGTTACG 59.326 47.826 0.00 0.00 0.00 3.18
3242 4297 3.813443 CAATCCTGACAGAACCCCATAG 58.187 50.000 3.32 0.00 0.00 2.23
3386 4441 8.472007 AGTAGGGACAAAAATAAACATGTCAA 57.528 30.769 0.00 0.00 0.00 3.18
3645 6328 9.729281 AGGAAATTCAACCGTAAACTATCTTAA 57.271 29.630 0.00 0.00 0.00 1.85
4092 6786 2.819608 CAATCAGTTCAAACGGGATGGT 59.180 45.455 4.58 0.00 31.42 3.55
4097 6791 0.871722 TCGCAATCAGTTCAAACGGG 59.128 50.000 0.00 0.00 0.00 5.28
4336 7035 5.703730 ACTCCCTCCGTTCCAAAATATAA 57.296 39.130 0.00 0.00 0.00 0.98
4340 7039 2.910977 ACTACTCCCTCCGTTCCAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
4341 7040 2.332117 ACTACTCCCTCCGTTCCAAAA 58.668 47.619 0.00 0.00 0.00 2.44
4502 7201 0.803117 TCTCTGTACTCTTGACCGCG 59.197 55.000 0.00 0.00 0.00 6.46
4566 7265 0.951558 ACAACATTTGGCAGGTCGTC 59.048 50.000 0.00 0.00 34.12 4.20
4568 7267 0.950836 TCACAACATTTGGCAGGTCG 59.049 50.000 0.00 0.00 34.12 4.79
4576 7275 3.316283 CACCGGGAATTCACAACATTTG 58.684 45.455 8.74 0.00 0.00 2.32
4579 7278 0.887933 GCACCGGGAATTCACAACAT 59.112 50.000 8.74 0.00 0.00 2.71
4631 7330 1.079127 CGAACCAACGATGCTCCCT 60.079 57.895 0.00 0.00 35.09 4.20
4650 7349 0.855995 GAATAGAAAGAGCTCGCGGC 59.144 55.000 6.13 9.11 42.19 6.53
4751 7459 1.466856 ATCATTGCACAGTTCGGCAT 58.533 45.000 0.00 0.00 40.17 4.40
4752 7460 2.009051 CTATCATTGCACAGTTCGGCA 58.991 47.619 0.00 0.00 38.46 5.69
4803 7511 3.060003 CGAAAAACTCTCAGCAGTCAGTG 60.060 47.826 0.00 0.00 0.00 3.66
4804 7512 3.126831 CGAAAAACTCTCAGCAGTCAGT 58.873 45.455 0.00 0.00 0.00 3.41
4830 7538 2.669878 GGCTGGGCCTCAAAAATGA 58.330 52.632 4.53 0.00 46.69 2.57
4847 7555 0.037303 TGCTCAAGGAAAGCCTCTGG 59.963 55.000 0.00 0.00 46.28 3.86
4848 7556 1.743958 CATGCTCAAGGAAAGCCTCTG 59.256 52.381 0.00 0.00 46.28 3.35
4855 7563 4.321452 GCAACTCATTCATGCTCAAGGAAA 60.321 41.667 0.00 0.00 37.12 3.13
4860 7568 1.469703 CGGCAACTCATTCATGCTCAA 59.530 47.619 0.00 0.00 39.94 3.02
4899 7608 5.084818 TCAAGCAGATAGAATCAAACGGA 57.915 39.130 0.00 0.00 0.00 4.69
4900 7609 5.801350 TTCAAGCAGATAGAATCAAACGG 57.199 39.130 0.00 0.00 0.00 4.44
4901 7610 9.378597 CATAATTCAAGCAGATAGAATCAAACG 57.621 33.333 0.00 0.00 31.21 3.60
4904 7613 9.842775 ACTCATAATTCAAGCAGATAGAATCAA 57.157 29.630 0.00 0.00 31.21 2.57
4905 7614 9.842775 AACTCATAATTCAAGCAGATAGAATCA 57.157 29.630 0.00 0.00 31.21 2.57
4907 7616 8.566260 GCAACTCATAATTCAAGCAGATAGAAT 58.434 33.333 0.00 0.00 33.68 2.40
4908 7617 7.012704 GGCAACTCATAATTCAAGCAGATAGAA 59.987 37.037 0.00 0.00 0.00 2.10
4909 7618 6.484643 GGCAACTCATAATTCAAGCAGATAGA 59.515 38.462 0.00 0.00 0.00 1.98
4910 7619 6.565435 CGGCAACTCATAATTCAAGCAGATAG 60.565 42.308 0.00 0.00 0.00 2.08
4911 7620 5.237127 CGGCAACTCATAATTCAAGCAGATA 59.763 40.000 0.00 0.00 0.00 1.98
4912 7621 4.036027 CGGCAACTCATAATTCAAGCAGAT 59.964 41.667 0.00 0.00 0.00 2.90
4913 7622 3.374988 CGGCAACTCATAATTCAAGCAGA 59.625 43.478 0.00 0.00 0.00 4.26
4914 7623 3.688272 CGGCAACTCATAATTCAAGCAG 58.312 45.455 0.00 0.00 0.00 4.24
4915 7624 2.159393 GCGGCAACTCATAATTCAAGCA 60.159 45.455 0.00 0.00 0.00 3.91
4916 7625 2.159393 TGCGGCAACTCATAATTCAAGC 60.159 45.455 0.00 0.00 0.00 4.01
4917 7626 3.763097 TGCGGCAACTCATAATTCAAG 57.237 42.857 0.00 0.00 0.00 3.02
4918 7627 4.422840 CAATGCGGCAACTCATAATTCAA 58.577 39.130 6.82 0.00 42.32 2.69
4919 7628 3.181488 CCAATGCGGCAACTCATAATTCA 60.181 43.478 6.82 0.00 42.32 2.57
4920 7629 3.181487 ACCAATGCGGCAACTCATAATTC 60.181 43.478 6.82 0.00 42.32 2.17
4921 7630 2.760092 ACCAATGCGGCAACTCATAATT 59.240 40.909 6.82 0.00 42.32 1.40
4922 7631 2.378038 ACCAATGCGGCAACTCATAAT 58.622 42.857 6.82 0.00 42.32 1.28
4923 7632 1.832883 ACCAATGCGGCAACTCATAA 58.167 45.000 6.82 0.00 42.32 1.90
4924 7633 1.832883 AACCAATGCGGCAACTCATA 58.167 45.000 6.82 0.00 42.32 2.15
4925 7634 0.968405 AAACCAATGCGGCAACTCAT 59.032 45.000 6.82 0.00 45.90 2.90
4926 7635 0.031857 CAAACCAATGCGGCAACTCA 59.968 50.000 6.82 0.00 39.03 3.41
4927 7636 0.031994 ACAAACCAATGCGGCAACTC 59.968 50.000 6.82 0.00 39.03 3.01
4928 7637 0.463620 AACAAACCAATGCGGCAACT 59.536 45.000 6.82 0.00 39.03 3.16
4929 7638 1.004079 CAAACAAACCAATGCGGCAAC 60.004 47.619 6.82 0.00 39.03 4.17
4930 7639 1.293924 CAAACAAACCAATGCGGCAA 58.706 45.000 6.82 0.00 39.03 4.52
4931 7640 0.176680 ACAAACAAACCAATGCGGCA 59.823 45.000 4.58 4.58 39.03 5.69
4932 7641 0.858583 GACAAACAAACCAATGCGGC 59.141 50.000 0.00 0.00 39.03 6.53
4933 7642 1.127701 CGACAAACAAACCAATGCGG 58.872 50.000 0.00 0.00 42.50 5.69
4934 7643 2.112475 TCGACAAACAAACCAATGCG 57.888 45.000 0.00 0.00 0.00 4.73
4935 7644 2.986479 GGATCGACAAACAAACCAATGC 59.014 45.455 0.00 0.00 0.00 3.56
4936 7645 3.233578 CGGATCGACAAACAAACCAATG 58.766 45.455 0.00 0.00 0.00 2.82
4937 7646 2.882137 ACGGATCGACAAACAAACCAAT 59.118 40.909 0.00 0.00 0.00 3.16
4938 7647 2.290464 ACGGATCGACAAACAAACCAA 58.710 42.857 0.00 0.00 0.00 3.67
4939 7648 1.956297 ACGGATCGACAAACAAACCA 58.044 45.000 0.00 0.00 0.00 3.67
4940 7649 3.040099 CAAACGGATCGACAAACAAACC 58.960 45.455 0.00 0.00 0.00 3.27
4941 7650 3.942739 TCAAACGGATCGACAAACAAAC 58.057 40.909 0.00 0.00 0.00 2.93
4942 7651 4.822036 ATCAAACGGATCGACAAACAAA 57.178 36.364 0.00 0.00 0.00 2.83
4943 7652 4.513692 AGAATCAAACGGATCGACAAACAA 59.486 37.500 0.00 0.00 34.28 2.83
4944 7653 4.062293 AGAATCAAACGGATCGACAAACA 58.938 39.130 0.00 0.00 34.28 2.83
4977 7686 0.588252 GCACTCGCGGCAATCATAAT 59.412 50.000 6.13 0.00 0.00 1.28
4989 7698 2.669808 ATCGGTCATCTCGCACTCGC 62.670 60.000 0.00 0.00 35.26 5.03
4990 7699 0.932123 CATCGGTCATCTCGCACTCG 60.932 60.000 0.00 0.00 0.00 4.18
4995 7704 3.032609 CGCCATCGGTCATCTCGC 61.033 66.667 0.00 0.00 0.00 5.03
5010 7719 1.798813 CACAACACCTTCTAAGACCGC 59.201 52.381 0.00 0.00 0.00 5.68
5017 7726 5.617528 TTAACTCACCACAACACCTTCTA 57.382 39.130 0.00 0.00 0.00 2.10
5065 7774 8.807948 ATTATTTTACCACACTCAGTAGCATT 57.192 30.769 0.00 0.00 0.00 3.56
5125 7840 2.238898 GGCTGGTAGTTCCCATACAAGT 59.761 50.000 0.00 0.00 33.00 3.16
5152 7873 2.376109 GGTCTGAATCCGAGTAGGTGA 58.624 52.381 0.00 0.00 41.99 4.02
5181 7902 9.953825 GAAGAAATCTTACTTACGTATGTGTTG 57.046 33.333 20.87 12.02 36.11 3.33
5201 7922 9.863845 AATAAAAACCAAAAGAACTCGAAGAAA 57.136 25.926 0.00 0.00 34.09 2.52
5207 7928 8.171840 TGCAAAAATAAAAACCAAAAGAACTCG 58.828 29.630 0.00 0.00 0.00 4.18
5213 7934 9.157259 CTTCGATGCAAAAATAAAAACCAAAAG 57.843 29.630 0.00 0.00 0.00 2.27
5218 7939 9.877137 AAATTCTTCGATGCAAAAATAAAAACC 57.123 25.926 0.00 0.00 0.00 3.27
5224 7945 7.063308 GCTGGAAAATTCTTCGATGCAAAAATA 59.937 33.333 0.00 0.00 0.00 1.40
5227 7948 4.685628 GCTGGAAAATTCTTCGATGCAAAA 59.314 37.500 0.00 0.00 0.00 2.44
5228 7949 4.022068 AGCTGGAAAATTCTTCGATGCAAA 60.022 37.500 0.00 0.00 0.00 3.68
5229 7950 3.507233 AGCTGGAAAATTCTTCGATGCAA 59.493 39.130 0.00 0.00 0.00 4.08
5230 7951 3.084039 AGCTGGAAAATTCTTCGATGCA 58.916 40.909 0.00 0.00 0.00 3.96
5232 7953 3.432782 GCAGCTGGAAAATTCTTCGATG 58.567 45.455 17.12 0.00 0.00 3.84
5235 7956 1.135286 GGGCAGCTGGAAAATTCTTCG 60.135 52.381 17.12 0.00 0.00 3.79
5236 7957 1.205655 GGGGCAGCTGGAAAATTCTTC 59.794 52.381 17.12 0.00 0.00 2.87
5237 7958 1.269958 GGGGCAGCTGGAAAATTCTT 58.730 50.000 17.12 0.00 0.00 2.52
5238 7959 0.114954 TGGGGCAGCTGGAAAATTCT 59.885 50.000 17.12 0.00 0.00 2.40
5239 7960 0.533951 CTGGGGCAGCTGGAAAATTC 59.466 55.000 17.12 0.00 0.00 2.17
5240 7961 0.178924 ACTGGGGCAGCTGGAAAATT 60.179 50.000 17.12 0.00 34.37 1.82
5241 7962 0.613012 GACTGGGGCAGCTGGAAAAT 60.613 55.000 17.12 0.00 34.37 1.82
5242 7963 1.228552 GACTGGGGCAGCTGGAAAA 60.229 57.895 17.12 0.00 34.37 2.29
5243 7964 2.005606 TTGACTGGGGCAGCTGGAAA 62.006 55.000 17.12 0.00 34.37 3.13
5244 7965 1.792757 ATTGACTGGGGCAGCTGGAA 61.793 55.000 17.12 0.00 34.37 3.53
5245 7966 1.792757 AATTGACTGGGGCAGCTGGA 61.793 55.000 17.12 0.00 34.37 3.86
5246 7967 0.901580 AAATTGACTGGGGCAGCTGG 60.902 55.000 17.12 0.00 34.37 4.85
5247 7968 0.529378 GAAATTGACTGGGGCAGCTG 59.471 55.000 10.11 10.11 34.37 4.24
5248 7969 0.112995 TGAAATTGACTGGGGCAGCT 59.887 50.000 0.00 0.00 34.37 4.24
5249 7970 0.244721 GTGAAATTGACTGGGGCAGC 59.755 55.000 0.00 0.00 34.37 5.25
5250 7971 1.270550 GTGTGAAATTGACTGGGGCAG 59.729 52.381 0.00 0.00 37.52 4.85
5251 7972 1.133513 AGTGTGAAATTGACTGGGGCA 60.134 47.619 0.00 0.00 0.00 5.36
5252 7973 1.620822 AGTGTGAAATTGACTGGGGC 58.379 50.000 0.00 0.00 0.00 5.80
5253 7974 3.221771 TGAAGTGTGAAATTGACTGGGG 58.778 45.455 0.00 0.00 0.00 4.96
5254 7975 4.520111 TCATGAAGTGTGAAATTGACTGGG 59.480 41.667 0.00 0.00 0.00 4.45
5255 7976 5.240183 ACTCATGAAGTGTGAAATTGACTGG 59.760 40.000 0.00 0.00 36.65 4.00
5256 7977 6.309712 ACTCATGAAGTGTGAAATTGACTG 57.690 37.500 0.00 0.00 36.65 3.51
5281 8002 9.328721 CACATACCGCATACACATAATAAATTG 57.671 33.333 0.00 0.00 0.00 2.32
5297 8018 2.006169 CAACATGCTACACATACCGCA 58.994 47.619 0.00 0.00 36.64 5.69
5324 8051 2.480853 ATTCCACAGACGCGTACGCA 62.481 55.000 36.44 16.65 45.53 5.24
5329 8056 1.588674 TTTCAATTCCACAGACGCGT 58.411 45.000 13.85 13.85 0.00 6.01
5368 8095 8.042515 TGACAAAACCTATAGCCGTAAATAAGT 58.957 33.333 0.00 0.00 0.00 2.24
5385 8112 1.802365 ACTCGCCGTAATGACAAAACC 59.198 47.619 0.00 0.00 0.00 3.27
5416 8143 6.913873 ACACTCGCTTGTTCTAAAGTAAAA 57.086 33.333 0.00 0.00 0.00 1.52
5439 8166 4.036734 GGCAAAGTCATGTCAAAGTCAGAA 59.963 41.667 0.00 0.00 0.00 3.02
5480 8239 2.396590 TTCGTGGGCTTATGAGGTTC 57.603 50.000 0.00 0.00 0.00 3.62


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

AutoCloner maintained by Alex Coulton.