Multiple sequence alignment - TraesCS2B01G429800

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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 TraesCS2B01G429800 chr2B 100.000 4138 0 0 1 4138 617139832 617143969 0.000000e+00 7642.0
1 TraesCS2B01G429800 chr2B 79.882 338 59 7 2075 2409 617528170 617527839 5.350000e-59 239.0
2 TraesCS2B01G429800 chr2B 86.420 81 11 0 246 326 549039797 549039717 5.700000e-14 89.8
3 TraesCS2B01G429800 chr2B 78.986 138 23 4 2461 2594 799251511 799251376 5.700000e-14 89.8
4 TraesCS2B01G429800 chr2A 92.752 3270 129 35 922 4138 668532077 668528863 0.000000e+00 4626.0
5 TraesCS2B01G429800 chr2A 81.609 1131 182 18 2055 3170 668922702 668923821 0.000000e+00 913.0
6 TraesCS2B01G429800 chr2A 81.432 1131 184 19 2055 3170 669109788 669108669 0.000000e+00 902.0
7 TraesCS2B01G429800 chr2A 87.812 681 38 16 1 645 668538684 668538013 0.000000e+00 756.0
8 TraesCS2B01G429800 chr2A 90.291 206 14 4 707 909 668532265 668532063 8.820000e-67 265.0
9 TraesCS2B01G429800 chr2A 80.178 338 58 7 2075 2409 668926840 668927171 1.150000e-60 244.0
10 TraesCS2B01G429800 chr2A 79.880 333 58 7 2080 2409 669105585 669105259 6.920000e-58 235.0
11 TraesCS2B01G429800 chr2A 74.269 342 56 17 246 565 276254853 276255184 9.400000e-22 115.0
12 TraesCS2B01G429800 chr2A 90.278 72 6 1 493 564 615527459 615527389 4.400000e-15 93.5
13 TraesCS2B01G429800 chr2A 78.986 138 23 4 2461 2594 767788998 767788863 5.700000e-14 89.8
14 TraesCS2B01G429800 chr2D 94.203 2812 113 19 922 3698 523160788 523163584 0.000000e+00 4244.0
15 TraesCS2B01G429800 chr2D 83.165 1087 155 20 2079 3151 523358876 523357804 0.000000e+00 968.0
16 TraesCS2B01G429800 chr2D 94.670 469 14 4 3680 4138 523163600 523164067 0.000000e+00 717.0
17 TraesCS2B01G429800 chr2D 80.178 338 58 5 2075 2409 523309904 523309573 1.150000e-60 244.0
18 TraesCS2B01G429800 chr2D 93.878 49 2 1 855 903 523160743 523160790 5.740000e-09 73.1
19 TraesCS2B01G429800 chr6B 77.211 588 66 36 3 558 179038379 179037828 8.760000e-72 281.0
20 TraesCS2B01G429800 chr6B 85.714 84 6 5 483 564 19324802 19324723 2.650000e-12 84.2
21 TraesCS2B01G429800 chr6B 85.185 81 8 3 483 563 699610831 699610907 3.430000e-11 80.5
22 TraesCS2B01G429800 chr1D 72.505 531 102 27 66 564 81732021 81731503 9.330000e-27 132.0
23 TraesCS2B01G429800 chr7B 82.000 150 20 5 418 564 64025645 64025500 2.020000e-23 121.0
24 TraesCS2B01G429800 chr4D 71.780 528 106 25 66 561 142762016 142762532 4.370000e-20 110.0
25 TraesCS2B01G429800 chr1B 73.977 342 54 20 246 564 366270463 366270134 5.660000e-19 106.0
26 TraesCS2B01G429800 chr5D 92.647 68 4 1 501 568 109564474 109564408 3.400000e-16 97.1
27 TraesCS2B01G429800 chr5D 73.392 342 56 21 246 564 422769292 422769621 1.220000e-15 95.3
28 TraesCS2B01G429800 chrUn 81.513 119 18 4 2456 2573 31552466 31552581 1.220000e-15 95.3
29 TraesCS2B01G429800 chrUn 78.986 138 23 4 2461 2594 31527550 31527415 5.700000e-14 89.8
30 TraesCS2B01G429800 chrUn 86.842 76 8 2 490 564 75455686 75455760 2.650000e-12 84.2


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 TraesCS2B01G429800 chr2B 617139832 617143969 4137 False 7642.000000 7642 100.000000 1 4138 1 chr2B.!!$F1 4137
1 TraesCS2B01G429800 chr2A 668528863 668532265 3402 True 2445.500000 4626 91.521500 707 4138 2 chr2A.!!$R4 3431
2 TraesCS2B01G429800 chr2A 668538013 668538684 671 True 756.000000 756 87.812000 1 645 1 chr2A.!!$R2 644
3 TraesCS2B01G429800 chr2A 668922702 668927171 4469 False 578.500000 913 80.893500 2055 3170 2 chr2A.!!$F2 1115
4 TraesCS2B01G429800 chr2A 669105259 669109788 4529 True 568.500000 902 80.656000 2055 3170 2 chr2A.!!$R5 1115
5 TraesCS2B01G429800 chr2D 523160743 523164067 3324 False 1678.033333 4244 94.250333 855 4138 3 chr2D.!!$F1 3283
6 TraesCS2B01G429800 chr2D 523357804 523358876 1072 True 968.000000 968 83.165000 2079 3151 1 chr2D.!!$R2 1072
7 TraesCS2B01G429800 chr6B 179037828 179038379 551 True 281.000000 281 77.211000 3 558 1 chr6B.!!$R2 555

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
473 508 0.032130 TCTTGTCTGGTGCAGTCGTC 59.968 55.0 0.0 0.0 32.61 4.20 F
654 691 0.036388 ATGCGAAGGAAAAGCCGAGA 60.036 50.0 0.0 0.0 43.43 4.04 F
1713 1769 0.245539 TCAAATCGGACGAGGTGGAC 59.754 55.0 0.0 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2061 2123 0.252881 AGCCATCAGAGGGGAAGACA 60.253 55.000 2.61 0.0 0.00 3.41 R
2251 2315 2.106074 GCGATTGTGATCCACGGCA 61.106 57.895 0.00 0.0 37.14 5.69 R
3468 4387 1.207329 GGCAGTATCTCCTTCAACCGT 59.793 52.381 0.00 0.0 0.00 4.83 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
36 37 1.401539 CCTAGCTTGCGGCAAAGAAAC 60.402 52.381 17.13 4.31 44.79 2.78
47 48 2.034053 GGCAAAGAAACGATGTTGGACA 59.966 45.455 0.00 0.00 0.00 4.02
59 60 2.589442 TGGACAACCAACGGCGTC 60.589 61.111 15.17 0.00 43.91 5.19
60 61 3.708734 GGACAACCAACGGCGTCG 61.709 66.667 15.17 8.42 38.06 5.12
61 62 4.364409 GACAACCAACGGCGTCGC 62.364 66.667 15.17 9.22 40.63 5.19
101 110 1.523938 GCCCGTTCTATGACCAGGC 60.524 63.158 0.00 0.00 0.00 4.85
131 140 4.219802 ACGATCGACATCTATTACTTGCG 58.780 43.478 24.34 0.00 0.00 4.85
158 167 1.797933 CGCTCGACAGGTCTGTTCG 60.798 63.158 5.02 9.95 45.05 3.95
163 172 0.243907 CGACAGGTCTGTTCGGTCAT 59.756 55.000 5.02 0.00 45.05 3.06
168 177 1.691976 AGGTCTGTTCGGTCATCACAA 59.308 47.619 0.00 0.00 0.00 3.33
173 182 4.024048 GTCTGTTCGGTCATCACAAACAAT 60.024 41.667 0.00 0.00 32.40 2.71
208 217 2.435059 GACGCCAGACCAAGAGGC 60.435 66.667 0.00 0.00 44.89 4.70
209 218 3.959991 GACGCCAGACCAAGAGGCC 62.960 68.421 0.00 0.00 45.56 5.19
312 329 3.306166 GTGGAAATACAGGAACGACATCG 59.694 47.826 0.00 0.00 46.33 3.84
313 330 2.284417 GGAAATACAGGAACGACATCGC 59.716 50.000 0.14 0.00 44.43 4.58
320 337 0.442699 GGAACGACATCGCCTTCAAC 59.557 55.000 0.14 0.00 44.43 3.18
323 340 2.785258 GACATCGCCTTCAACGGC 59.215 61.111 0.00 0.00 46.68 5.68
330 347 4.481112 CCTTCAACGGCGCATGGC 62.481 66.667 10.83 0.00 42.51 4.40
372 389 0.110238 GCTTGAGCAAATCGACGCAA 60.110 50.000 6.14 0.00 41.59 4.85
404 421 1.078143 GAGGGCATCGGAACTGCTT 60.078 57.895 3.82 0.00 39.60 3.91
406 423 1.078143 GGGCATCGGAACTGCTTCT 60.078 57.895 3.82 0.00 39.60 2.85
421 456 2.166459 TGCTTCTGGTTAGAGTGGATCG 59.834 50.000 0.00 0.00 33.70 3.69
459 494 1.156736 GTTAGCATGCGGTGTCTTGT 58.843 50.000 13.01 0.00 0.00 3.16
462 497 0.952497 AGCATGCGGTGTCTTGTCTG 60.952 55.000 13.01 0.00 0.00 3.51
473 508 0.032130 TCTTGTCTGGTGCAGTCGTC 59.968 55.000 0.00 0.00 32.61 4.20
559 594 6.766084 GTCATTCTTGACGTATCCTTGAAAG 58.234 40.000 0.00 0.00 42.66 2.62
562 597 7.659799 TCATTCTTGACGTATCCTTGAAAGAAA 59.340 33.333 0.00 0.00 36.20 2.52
563 598 7.795482 TTCTTGACGTATCCTTGAAAGAAAA 57.205 32.000 0.00 0.00 31.26 2.29
564 599 7.186021 TCTTGACGTATCCTTGAAAGAAAAC 57.814 36.000 0.00 0.00 0.00 2.43
565 600 5.934935 TGACGTATCCTTGAAAGAAAACC 57.065 39.130 0.00 0.00 0.00 3.27
566 601 5.369833 TGACGTATCCTTGAAAGAAAACCA 58.630 37.500 0.00 0.00 0.00 3.67
567 602 6.001460 TGACGTATCCTTGAAAGAAAACCAT 58.999 36.000 0.00 0.00 0.00 3.55
568 603 7.162761 TGACGTATCCTTGAAAGAAAACCATA 58.837 34.615 0.00 0.00 0.00 2.74
569 604 7.662258 TGACGTATCCTTGAAAGAAAACCATAA 59.338 33.333 0.00 0.00 0.00 1.90
570 605 8.040716 ACGTATCCTTGAAAGAAAACCATAAG 57.959 34.615 0.00 0.00 0.00 1.73
571 606 7.881232 ACGTATCCTTGAAAGAAAACCATAAGA 59.119 33.333 0.00 0.00 0.00 2.10
575 610 9.764363 ATCCTTGAAAGAAAACCATAAGAAAAC 57.236 29.630 0.00 0.00 0.00 2.43
585 620 8.821147 AAAACCATAAGAAAACCGATTAAACC 57.179 30.769 0.00 0.00 0.00 3.27
596 631 1.944709 CGATTAAACCCGGACCAATCC 59.055 52.381 0.73 0.00 42.28 3.01
599 634 2.203470 TAAACCCGGACCAATCCAAC 57.797 50.000 0.73 0.00 46.67 3.77
608 643 3.340034 GGACCAATCCAACGAATACACA 58.660 45.455 0.00 0.00 45.47 3.72
645 682 2.075355 AACCCACCCATGCGAAGGAA 62.075 55.000 0.00 0.00 0.00 3.36
646 683 1.304052 CCCACCCATGCGAAGGAAA 60.304 57.895 0.00 0.00 0.00 3.13
647 684 0.897863 CCCACCCATGCGAAGGAAAA 60.898 55.000 0.00 0.00 0.00 2.29
648 685 0.527565 CCACCCATGCGAAGGAAAAG 59.472 55.000 0.00 0.00 0.00 2.27
649 686 0.109132 CACCCATGCGAAGGAAAAGC 60.109 55.000 0.00 0.00 0.00 3.51
650 687 1.250840 ACCCATGCGAAGGAAAAGCC 61.251 55.000 0.00 0.00 0.00 4.35
651 688 1.137404 CCATGCGAAGGAAAAGCCG 59.863 57.895 0.00 0.00 43.43 5.52
652 689 1.305219 CCATGCGAAGGAAAAGCCGA 61.305 55.000 0.00 0.00 43.43 5.54
653 690 0.097674 CATGCGAAGGAAAAGCCGAG 59.902 55.000 0.00 0.00 43.43 4.63
654 691 0.036388 ATGCGAAGGAAAAGCCGAGA 60.036 50.000 0.00 0.00 43.43 4.04
655 692 0.670546 TGCGAAGGAAAAGCCGAGAG 60.671 55.000 0.00 0.00 43.43 3.20
656 693 1.972027 GCGAAGGAAAAGCCGAGAGC 61.972 60.000 0.00 0.00 43.43 4.09
657 694 1.362406 CGAAGGAAAAGCCGAGAGCC 61.362 60.000 0.00 0.00 45.47 4.70
658 695 0.321653 GAAGGAAAAGCCGAGAGCCA 60.322 55.000 0.00 0.00 45.47 4.75
659 696 0.322008 AAGGAAAAGCCGAGAGCCAG 60.322 55.000 0.00 0.00 45.47 4.85
660 697 2.402572 GGAAAAGCCGAGAGCCAGC 61.403 63.158 0.00 0.00 45.47 4.85
661 698 2.743928 AAAAGCCGAGAGCCAGCG 60.744 61.111 0.00 0.00 45.47 5.18
667 704 4.544689 CGAGAGCCAGCGGACGAG 62.545 72.222 0.00 0.00 0.00 4.18
668 705 3.134792 GAGAGCCAGCGGACGAGA 61.135 66.667 0.00 0.00 0.00 4.04
669 706 2.676822 AGAGCCAGCGGACGAGAA 60.677 61.111 0.00 0.00 0.00 2.87
670 707 2.214181 GAGAGCCAGCGGACGAGAAA 62.214 60.000 0.00 0.00 0.00 2.52
671 708 1.374252 GAGCCAGCGGACGAGAAAA 60.374 57.895 0.00 0.00 0.00 2.29
672 709 0.949105 GAGCCAGCGGACGAGAAAAA 60.949 55.000 0.00 0.00 0.00 1.94
673 710 1.206831 GCCAGCGGACGAGAAAAAC 59.793 57.895 0.00 0.00 0.00 2.43
674 711 1.503818 GCCAGCGGACGAGAAAAACA 61.504 55.000 0.00 0.00 0.00 2.83
675 712 0.941542 CCAGCGGACGAGAAAAACAA 59.058 50.000 0.00 0.00 0.00 2.83
676 713 1.332375 CCAGCGGACGAGAAAAACAAA 59.668 47.619 0.00 0.00 0.00 2.83
677 714 2.372350 CAGCGGACGAGAAAAACAAAC 58.628 47.619 0.00 0.00 0.00 2.93
678 715 1.004292 AGCGGACGAGAAAAACAAACG 60.004 47.619 0.00 0.00 0.00 3.60
679 716 1.918543 GCGGACGAGAAAAACAAACGG 60.919 52.381 0.00 0.00 0.00 4.44
680 717 1.593933 CGGACGAGAAAAACAAACGGA 59.406 47.619 0.00 0.00 0.00 4.69
681 718 2.030701 CGGACGAGAAAAACAAACGGAA 59.969 45.455 0.00 0.00 0.00 4.30
682 719 3.485546 CGGACGAGAAAAACAAACGGAAA 60.486 43.478 0.00 0.00 0.00 3.13
683 720 3.787634 GGACGAGAAAAACAAACGGAAAC 59.212 43.478 0.00 0.00 0.00 2.78
695 732 2.186125 GGAAACGGGTCGGCCTAG 59.814 66.667 5.77 2.77 34.45 3.02
696 733 2.653087 GGAAACGGGTCGGCCTAGT 61.653 63.158 5.77 3.54 34.45 2.57
697 734 1.322538 GGAAACGGGTCGGCCTAGTA 61.323 60.000 5.77 0.00 34.45 1.82
698 735 0.532115 GAAACGGGTCGGCCTAGTAA 59.468 55.000 5.77 0.00 34.45 2.24
699 736 0.975887 AAACGGGTCGGCCTAGTAAA 59.024 50.000 5.77 0.00 34.45 2.01
700 737 0.247460 AACGGGTCGGCCTAGTAAAC 59.753 55.000 5.77 0.00 34.45 2.01
701 738 0.613012 ACGGGTCGGCCTAGTAAACT 60.613 55.000 5.77 0.00 34.45 2.66
702 739 1.340991 ACGGGTCGGCCTAGTAAACTA 60.341 52.381 5.77 0.00 34.45 2.24
703 740 1.066152 CGGGTCGGCCTAGTAAACTAC 59.934 57.143 5.77 0.00 34.45 2.73
704 741 2.102578 GGGTCGGCCTAGTAAACTACA 58.897 52.381 5.77 0.00 34.45 2.74
705 742 2.697229 GGGTCGGCCTAGTAAACTACAT 59.303 50.000 5.77 0.00 34.45 2.29
739 776 1.075425 CAGGCGAGACTTGCTTCGAG 61.075 60.000 14.42 0.00 0.00 4.04
741 778 1.445238 GCGAGACTTGCTTCGAGCT 60.445 57.895 7.49 0.00 42.97 4.09
770 810 3.798014 AGCGAGATATAGCATTTGCGCG 61.798 50.000 0.00 0.00 46.74 6.86
795 835 0.386113 GCCTCCTGTCGGTATGTCTC 59.614 60.000 0.00 0.00 0.00 3.36
803 843 4.138290 CTGTCGGTATGTCTCCATCTACT 58.862 47.826 0.00 0.00 32.29 2.57
833 873 3.519579 CCGAGGCTGAGATGCAATATAG 58.480 50.000 0.00 0.00 34.04 1.31
834 874 3.194329 CCGAGGCTGAGATGCAATATAGA 59.806 47.826 0.00 0.00 34.04 1.98
835 875 4.422840 CGAGGCTGAGATGCAATATAGAG 58.577 47.826 0.00 0.00 34.04 2.43
842 882 6.346477 TGAGATGCAATATAGAGTACACCC 57.654 41.667 0.00 0.00 0.00 4.61
845 885 2.631062 TGCAATATAGAGTACACCCCCG 59.369 50.000 0.00 0.00 0.00 5.73
855 895 1.502527 TACACCCCCGCCCATCTTTT 61.503 55.000 0.00 0.00 0.00 2.27
856 896 2.052104 CACCCCCGCCCATCTTTTC 61.052 63.158 0.00 0.00 0.00 2.29
885 925 2.611518 CCTAGCAAAGACCGTCTCTTG 58.388 52.381 0.35 9.63 39.36 3.02
899 939 5.830991 ACCGTCTCTTGCTCTATCTAAATCT 59.169 40.000 0.00 0.00 0.00 2.40
900 940 6.999272 ACCGTCTCTTGCTCTATCTAAATCTA 59.001 38.462 0.00 0.00 0.00 1.98
901 941 7.502895 ACCGTCTCTTGCTCTATCTAAATCTAA 59.497 37.037 0.00 0.00 0.00 2.10
902 942 8.353684 CCGTCTCTTGCTCTATCTAAATCTAAA 58.646 37.037 0.00 0.00 0.00 1.85
903 943 9.393249 CGTCTCTTGCTCTATCTAAATCTAAAG 57.607 37.037 0.00 0.00 0.00 1.85
904 944 9.691362 GTCTCTTGCTCTATCTAAATCTAAAGG 57.309 37.037 0.00 0.00 0.00 3.11
905 945 9.647918 TCTCTTGCTCTATCTAAATCTAAAGGA 57.352 33.333 0.00 0.00 0.00 3.36
1151 1195 0.867329 GCATTGATTTCCGCTTCCGC 60.867 55.000 0.00 0.00 0.00 5.54
1213 1257 2.100584 GAGAACATGCTGTCGGAGATCT 59.899 50.000 0.00 0.00 40.67 2.75
1216 1260 1.827344 ACATGCTGTCGGAGATCTTGA 59.173 47.619 0.00 0.00 40.67 3.02
1217 1261 2.159128 ACATGCTGTCGGAGATCTTGAG 60.159 50.000 0.00 0.00 40.67 3.02
1218 1262 0.820226 TGCTGTCGGAGATCTTGAGG 59.180 55.000 0.00 0.00 40.67 3.86
1219 1263 0.820871 GCTGTCGGAGATCTTGAGGT 59.179 55.000 0.00 0.00 40.67 3.85
1220 1264 1.470632 GCTGTCGGAGATCTTGAGGTG 60.471 57.143 0.00 0.00 40.67 4.00
1222 1266 1.272480 TGTCGGAGATCTTGAGGTGGA 60.272 52.381 0.00 0.00 40.67 4.02
1223 1267 1.825474 GTCGGAGATCTTGAGGTGGAA 59.175 52.381 0.00 0.00 40.67 3.53
1224 1268 2.103373 TCGGAGATCTTGAGGTGGAAG 58.897 52.381 0.00 0.00 0.00 3.46
1226 1270 1.556911 GGAGATCTTGAGGTGGAAGCA 59.443 52.381 0.00 0.00 36.26 3.91
1227 1271 2.172293 GGAGATCTTGAGGTGGAAGCAT 59.828 50.000 0.00 0.00 36.26 3.79
1242 1286 2.905415 AGCATGAGGGGACAAAATCA 57.095 45.000 0.00 0.00 0.00 2.57
1283 1327 4.411927 GAGATGGTTAGGGCTGAGATCTA 58.588 47.826 0.00 0.00 0.00 1.98
1310 1354 5.008217 CCTTACTCAGTCGTATCTCCAAGAG 59.992 48.000 0.00 0.00 0.00 2.85
1356 1400 3.634283 GAAGCTGAGGATTAGCGACTAC 58.366 50.000 0.00 0.00 45.61 2.73
1374 1418 1.080230 CAGCAGTGACGAGGTCCAG 60.080 63.158 0.00 0.00 0.00 3.86
1401 1445 2.106477 TGGATAACATGTGCAGCGAA 57.894 45.000 0.00 0.00 0.00 4.70
1410 1454 1.090728 TGTGCAGCGAAGTGACAAAA 58.909 45.000 0.00 0.00 0.00 2.44
1440 1484 3.458857 AGATGATGGAGAAGGTGCAGAAT 59.541 43.478 0.00 0.00 0.00 2.40
1442 1486 4.142609 TGATGGAGAAGGTGCAGAATAC 57.857 45.455 0.00 0.00 0.00 1.89
1443 1487 3.776969 TGATGGAGAAGGTGCAGAATACT 59.223 43.478 0.00 0.00 0.00 2.12
1452 1496 3.126831 GGTGCAGAATACTGAGATTCCG 58.873 50.000 0.00 0.00 46.03 4.30
1476 1520 1.181786 AAGAGCCAGTCTCGGAGAAG 58.818 55.000 9.72 5.55 46.44 2.85
1544 1588 4.660938 AACCAAGACGCAGGGGCC 62.661 66.667 0.00 0.00 36.38 5.80
1554 1598 2.794028 GCAGGGGCCGACCTACTAC 61.794 68.421 0.00 0.00 39.34 2.73
1587 1631 4.075682 TGAATGCAATCTTCAACGGGTTA 58.924 39.130 2.94 0.00 29.96 2.85
1600 1644 1.279271 ACGGGTTAGATCAGCTTTGCT 59.721 47.619 0.00 0.00 40.77 3.91
1604 1648 2.356125 GGTTAGATCAGCTTTGCTCCCA 60.356 50.000 0.00 0.00 36.40 4.37
1623 1679 6.442541 TCCCAGTTGGATCTTAGTTACAAA 57.557 37.500 0.00 0.00 38.61 2.83
1629 1685 8.877779 CAGTTGGATCTTAGTTACAAATCTCAG 58.122 37.037 0.00 0.00 0.00 3.35
1631 1687 8.874816 GTTGGATCTTAGTTACAAATCTCAGTC 58.125 37.037 0.00 0.00 0.00 3.51
1638 1694 6.334102 AGTTACAAATCTCAGTCGTTCTCT 57.666 37.500 0.00 0.00 0.00 3.10
1639 1695 7.450124 AGTTACAAATCTCAGTCGTTCTCTA 57.550 36.000 0.00 0.00 0.00 2.43
1644 1700 4.893424 ATCTCAGTCGTTCTCTAAGCTC 57.107 45.455 0.00 0.00 0.00 4.09
1650 1706 4.619336 CAGTCGTTCTCTAAGCTCTTCAAC 59.381 45.833 0.00 0.00 0.00 3.18
1656 1712 3.125487 TCTCTAAGCTCTTCAACGAGTCG 59.875 47.826 11.85 11.85 33.55 4.18
1657 1713 2.812591 TCTAAGCTCTTCAACGAGTCGT 59.187 45.455 13.56 13.56 43.97 4.34
1704 1760 6.543736 GTTAAGAACCAGAATCAAATCGGAC 58.456 40.000 0.00 0.00 0.00 4.79
1713 1769 0.245539 TCAAATCGGACGAGGTGGAC 59.754 55.000 0.00 0.00 0.00 4.02
1724 1780 4.034258 GGTGGACGAGACGCGACA 62.034 66.667 15.93 1.00 44.57 4.35
1736 1792 4.260212 CGAGACGCGACAAATAATTTCCAT 60.260 41.667 15.93 0.00 44.57 3.41
1737 1793 4.908736 AGACGCGACAAATAATTTCCATG 58.091 39.130 15.93 0.00 0.00 3.66
1740 1796 4.201910 ACGCGACAAATAATTTCCATGGAG 60.202 41.667 15.93 3.04 0.00 3.86
1758 1814 1.078567 GACTCTGGAGGCAGCCAAG 60.079 63.158 15.80 8.37 37.52 3.61
1759 1815 1.835927 GACTCTGGAGGCAGCCAAGT 61.836 60.000 15.80 8.61 37.52 3.16
1793 1849 1.804748 GTCGCCGAAGATTTCCACTTT 59.195 47.619 0.00 0.00 0.00 2.66
1838 1894 1.683319 GGAAACCAAGGAGATGGGAGC 60.683 57.143 0.00 0.00 45.18 4.70
1867 1923 1.153469 GAGAAGCTCAGGAAGGCCG 60.153 63.158 0.00 0.00 39.96 6.13
1880 1936 1.331756 GAAGGCCGTGATGCACAATAG 59.668 52.381 0.00 0.00 33.40 1.73
1926 1982 2.717044 CCGTCGTGGCTGGGTATCA 61.717 63.158 0.00 0.00 0.00 2.15
1961 2017 7.005296 AGATTATACGGTACCTTCACAGAGAT 58.995 38.462 10.90 0.00 0.00 2.75
1978 2034 6.870439 CACAGAGATGAGTGAGTAAACATTCA 59.130 38.462 0.00 0.00 39.88 2.57
1983 2039 8.261492 AGATGAGTGAGTAAACATTCATTCAC 57.739 34.615 0.00 0.00 43.58 3.18
2053 2115 8.385858 GCATGTATCAACATACTGCATACATAG 58.614 37.037 4.08 2.00 44.70 2.23
2061 2123 9.920133 CAACATACTGCATACATAGTCTCTAAT 57.080 33.333 0.00 0.00 0.00 1.73
2177 2241 3.801050 CACTCTGCAGATTTACTCCATCG 59.199 47.826 18.63 3.13 0.00 3.84
2188 2252 9.319143 CAGATTTACTCCATCGAAGTTAAAGAT 57.681 33.333 0.00 0.00 0.00 2.40
2214 2278 3.515602 AGATGTTCCAGGCTTGAAGTT 57.484 42.857 0.56 0.00 0.00 2.66
2251 2315 0.731417 GCGTGATTGCTGCAAGAGAT 59.269 50.000 20.72 3.38 34.07 2.75
2316 2380 6.547510 AGGAATAACTGCCAAATACTCAATCC 59.452 38.462 0.00 0.00 0.00 3.01
2324 2388 4.384647 GCCAAATACTCAATCCAGAGGTCT 60.385 45.833 0.00 0.00 39.97 3.85
2430 2496 2.923121 ACACATATCAAGCGATTGCCT 58.077 42.857 8.91 0.85 44.31 4.75
2508 2574 1.071471 CACTTGACTGGCCCGTCTT 59.929 57.895 25.36 9.37 35.00 3.01
2677 2749 4.711355 AGGCTTATGCACAATGGTGTTAAT 59.289 37.500 1.31 0.00 46.95 1.40
2771 2843 4.490743 CAAGTCTTTTCAAAAACGGTGGT 58.509 39.130 0.00 0.00 0.00 4.16
2961 3033 4.154195 GTGGAACGCTTGAAGTTGTCATAT 59.846 41.667 0.00 0.00 35.70 1.78
3070 3148 2.741228 GCGACTCTGAGCTGGAAATCAT 60.741 50.000 4.19 0.00 0.00 2.45
3083 3161 4.922206 TGGAAATCATAGTTGCTTGGTCT 58.078 39.130 0.00 0.00 0.00 3.85
3089 3217 2.724977 TAGTTGCTTGGTCTCGTCTG 57.275 50.000 0.00 0.00 0.00 3.51
3163 3292 1.063174 CTCAGGCGTTATGAAAGCTGC 59.937 52.381 0.00 0.00 0.00 5.25
3468 4387 6.721208 ACTTATCTCCCAAGATTCTTGCAAAA 59.279 34.615 19.04 6.57 42.39 2.44
3515 4453 1.816863 ATCTCGCCAACACAGTCCGT 61.817 55.000 0.00 0.00 0.00 4.69
3726 4965 6.055588 GCTTTATAGGAGACAATTGTGCCTA 58.944 40.000 26.74 26.74 36.64 3.93
3732 4971 4.079253 GGAGACAATTGTGCCTAAAAGGA 58.921 43.478 17.58 0.00 37.67 3.36
3739 4978 2.334977 TGTGCCTAAAAGGAGTCTCCA 58.665 47.619 21.26 0.00 39.61 3.86
3794 5033 0.380378 GTGTGCTGAAGCGTTTTCCA 59.620 50.000 0.00 0.00 45.83 3.53
3886 6363 7.588512 AGATTAATCACTTGTTCTTTGCAGAC 58.411 34.615 17.56 0.00 0.00 3.51
4029 6513 0.594796 GGACAAGTGCGGCAACAAAG 60.595 55.000 3.23 0.00 0.00 2.77
4031 6515 1.319614 ACAAGTGCGGCAACAAAGGT 61.320 50.000 3.23 0.00 0.00 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 0.036164 TGCCGCAAGCTAGGAAAAGA 59.964 50.000 6.95 0.00 44.23 2.52
19 20 1.008538 CGTTTCTTTGCCGCAAGCT 60.009 52.632 5.83 0.00 44.23 3.74
78 87 1.166531 GGTCATAGAACGGGCATGCC 61.167 60.000 29.47 29.47 0.00 4.40
85 94 1.883084 GCGCCTGGTCATAGAACGG 60.883 63.158 0.00 0.00 0.00 4.44
131 140 1.413767 CCTGTCGAGCGTGTATGCAC 61.414 60.000 3.51 3.51 41.97 4.57
141 150 1.444553 CCGAACAGACCTGTCGAGC 60.445 63.158 17.20 4.06 44.13 5.03
158 167 3.509575 TGCCCTAATTGTTTGTGATGACC 59.490 43.478 0.00 0.00 0.00 4.02
163 172 2.298729 GGCTTGCCCTAATTGTTTGTGA 59.701 45.455 0.00 0.00 0.00 3.58
168 177 0.116143 TGGGGCTTGCCCTAATTGTT 59.884 50.000 27.45 0.00 0.00 2.83
173 182 2.763215 CAGTGGGGCTTGCCCTAA 59.237 61.111 27.45 15.14 0.00 2.69
201 210 1.672356 CCACCAGTTCGGCCTCTTG 60.672 63.158 0.00 0.00 39.03 3.02
208 217 2.959030 TCAGAGATATCCACCAGTTCGG 59.041 50.000 0.00 0.00 42.50 4.30
209 218 4.142160 TGTTCAGAGATATCCACCAGTTCG 60.142 45.833 0.00 0.00 0.00 3.95
313 330 4.481112 GCCATGCGCCGTTGAAGG 62.481 66.667 4.18 0.00 0.00 3.46
323 340 4.256180 GAGGGTAGGGGCCATGCG 62.256 72.222 4.39 0.00 0.00 4.73
328 345 3.483869 CAGCAGAGGGTAGGGGCC 61.484 72.222 0.00 0.00 0.00 5.80
330 347 1.306141 TGTCAGCAGAGGGTAGGGG 60.306 63.158 0.00 0.00 0.00 4.79
331 348 1.901085 GTGTCAGCAGAGGGTAGGG 59.099 63.158 0.00 0.00 0.00 3.53
332 349 1.513158 CGTGTCAGCAGAGGGTAGG 59.487 63.158 0.00 0.00 0.00 3.18
333 350 1.251527 ACCGTGTCAGCAGAGGGTAG 61.252 60.000 0.00 0.00 0.00 3.18
334 351 1.228769 ACCGTGTCAGCAGAGGGTA 60.229 57.895 0.00 0.00 0.00 3.69
335 352 2.524394 ACCGTGTCAGCAGAGGGT 60.524 61.111 0.00 0.00 0.00 4.34
362 379 1.175983 TTTGGCCCTTTGCGTCGATT 61.176 50.000 0.00 0.00 42.61 3.34
368 385 1.300853 CCAGTTTTGGCCCTTTGCG 60.301 57.895 0.00 0.00 42.61 4.85
372 389 1.156095 CCCTCCAGTTTTGGCCCTT 59.844 57.895 0.00 0.00 44.63 3.95
404 421 2.496070 CAACCGATCCACTCTAACCAGA 59.504 50.000 0.00 0.00 0.00 3.86
406 423 2.496070 CTCAACCGATCCACTCTAACCA 59.504 50.000 0.00 0.00 0.00 3.67
421 456 1.473278 ACTGCTCGCTACTACTCAACC 59.527 52.381 0.00 0.00 0.00 3.77
447 482 1.227527 CACCAGACAAGACACCGCA 60.228 57.895 0.00 0.00 0.00 5.69
459 494 1.174078 TTACCGACGACTGCACCAGA 61.174 55.000 0.00 0.00 35.18 3.86
462 497 0.172803 AGATTACCGACGACTGCACC 59.827 55.000 0.00 0.00 0.00 5.01
473 508 6.160664 ACATTCGTTTACAACAGATTACCG 57.839 37.500 0.00 0.00 0.00 4.02
546 581 8.263940 TCTTATGGTTTTCTTTCAAGGATACG 57.736 34.615 0.00 0.00 46.39 3.06
559 594 8.918658 GGTTTAATCGGTTTTCTTATGGTTTTC 58.081 33.333 0.00 0.00 0.00 2.29
562 597 6.349528 CGGGTTTAATCGGTTTTCTTATGGTT 60.350 38.462 0.00 0.00 0.00 3.67
563 598 5.124297 CGGGTTTAATCGGTTTTCTTATGGT 59.876 40.000 0.00 0.00 0.00 3.55
564 599 5.449451 CCGGGTTTAATCGGTTTTCTTATGG 60.449 44.000 0.00 0.00 41.23 2.74
565 600 5.354792 TCCGGGTTTAATCGGTTTTCTTATG 59.645 40.000 0.00 0.00 45.79 1.90
566 601 5.355071 GTCCGGGTTTAATCGGTTTTCTTAT 59.645 40.000 0.00 0.00 45.79 1.73
567 602 4.694982 GTCCGGGTTTAATCGGTTTTCTTA 59.305 41.667 0.00 0.00 45.79 2.10
568 603 3.503363 GTCCGGGTTTAATCGGTTTTCTT 59.497 43.478 0.00 0.00 45.79 2.52
569 604 3.076621 GTCCGGGTTTAATCGGTTTTCT 58.923 45.455 0.00 0.00 45.79 2.52
570 605 2.162208 GGTCCGGGTTTAATCGGTTTTC 59.838 50.000 0.00 3.51 45.79 2.29
571 606 2.161855 GGTCCGGGTTTAATCGGTTTT 58.838 47.619 0.00 0.00 45.79 2.43
575 610 1.944709 GATTGGTCCGGGTTTAATCGG 59.055 52.381 0.00 6.19 46.89 4.18
596 631 6.954944 TCCTTTCTTTTCTGTGTATTCGTTG 58.045 36.000 0.00 0.00 0.00 4.10
599 634 8.850454 TTTTTCCTTTCTTTTCTGTGTATTCG 57.150 30.769 0.00 0.00 0.00 3.34
645 682 4.767255 CCGCTGGCTCTCGGCTTT 62.767 66.667 0.38 0.00 45.36 3.51
650 687 4.544689 CTCGTCCGCTGGCTCTCG 62.545 72.222 0.00 0.00 0.00 4.04
651 688 2.214181 TTTCTCGTCCGCTGGCTCTC 62.214 60.000 0.00 0.00 0.00 3.20
652 689 1.816863 TTTTCTCGTCCGCTGGCTCT 61.817 55.000 0.00 0.00 0.00 4.09
653 690 0.949105 TTTTTCTCGTCCGCTGGCTC 60.949 55.000 0.00 0.00 0.00 4.70
654 691 1.070786 TTTTTCTCGTCCGCTGGCT 59.929 52.632 0.00 0.00 0.00 4.75
655 692 1.206831 GTTTTTCTCGTCCGCTGGC 59.793 57.895 0.00 0.00 0.00 4.85
656 693 0.941542 TTGTTTTTCTCGTCCGCTGG 59.058 50.000 0.00 0.00 0.00 4.85
657 694 2.372350 GTTTGTTTTTCTCGTCCGCTG 58.628 47.619 0.00 0.00 0.00 5.18
658 695 1.004292 CGTTTGTTTTTCTCGTCCGCT 60.004 47.619 0.00 0.00 0.00 5.52
659 696 1.382163 CGTTTGTTTTTCTCGTCCGC 58.618 50.000 0.00 0.00 0.00 5.54
660 697 1.593933 TCCGTTTGTTTTTCTCGTCCG 59.406 47.619 0.00 0.00 0.00 4.79
661 698 3.678915 TTCCGTTTGTTTTTCTCGTCC 57.321 42.857 0.00 0.00 0.00 4.79
662 699 3.476024 CGTTTCCGTTTGTTTTTCTCGTC 59.524 43.478 0.00 0.00 0.00 4.20
663 700 3.419004 CGTTTCCGTTTGTTTTTCTCGT 58.581 40.909 0.00 0.00 0.00 4.18
664 701 2.779471 CCGTTTCCGTTTGTTTTTCTCG 59.221 45.455 0.00 0.00 0.00 4.04
665 702 3.110358 CCCGTTTCCGTTTGTTTTTCTC 58.890 45.455 0.00 0.00 0.00 2.87
666 703 2.492881 ACCCGTTTCCGTTTGTTTTTCT 59.507 40.909 0.00 0.00 0.00 2.52
667 704 2.853594 GACCCGTTTCCGTTTGTTTTTC 59.146 45.455 0.00 0.00 0.00 2.29
668 705 2.731654 CGACCCGTTTCCGTTTGTTTTT 60.732 45.455 0.00 0.00 0.00 1.94
669 706 1.202166 CGACCCGTTTCCGTTTGTTTT 60.202 47.619 0.00 0.00 0.00 2.43
670 707 0.377905 CGACCCGTTTCCGTTTGTTT 59.622 50.000 0.00 0.00 0.00 2.83
671 708 1.438562 CCGACCCGTTTCCGTTTGTT 61.439 55.000 0.00 0.00 0.00 2.83
672 709 1.888638 CCGACCCGTTTCCGTTTGT 60.889 57.895 0.00 0.00 0.00 2.83
673 710 2.940561 CCGACCCGTTTCCGTTTG 59.059 61.111 0.00 0.00 0.00 2.93
674 711 2.974148 GCCGACCCGTTTCCGTTT 60.974 61.111 0.00 0.00 0.00 3.60
675 712 4.994471 GGCCGACCCGTTTCCGTT 62.994 66.667 0.00 0.00 0.00 4.44
677 714 3.711541 CTAGGCCGACCCGTTTCCG 62.712 68.421 0.00 0.00 39.21 4.30
678 715 1.322538 TACTAGGCCGACCCGTTTCC 61.323 60.000 0.00 0.00 39.21 3.13
679 716 0.532115 TTACTAGGCCGACCCGTTTC 59.468 55.000 0.00 0.00 39.21 2.78
680 717 0.975887 TTTACTAGGCCGACCCGTTT 59.024 50.000 0.00 0.00 39.21 3.60
681 718 0.247460 GTTTACTAGGCCGACCCGTT 59.753 55.000 0.00 0.00 39.21 4.44
682 719 0.613012 AGTTTACTAGGCCGACCCGT 60.613 55.000 0.00 0.00 39.21 5.28
683 720 1.066152 GTAGTTTACTAGGCCGACCCG 59.934 57.143 0.00 0.00 39.21 5.28
684 721 2.102578 TGTAGTTTACTAGGCCGACCC 58.897 52.381 0.00 0.00 36.11 4.46
685 722 3.382546 TCATGTAGTTTACTAGGCCGACC 59.617 47.826 0.00 0.00 0.00 4.79
686 723 4.499357 CCTCATGTAGTTTACTAGGCCGAC 60.499 50.000 0.00 0.00 0.00 4.79
687 724 3.635373 CCTCATGTAGTTTACTAGGCCGA 59.365 47.826 0.00 0.00 0.00 5.54
688 725 3.243771 CCCTCATGTAGTTTACTAGGCCG 60.244 52.174 0.00 0.00 0.00 6.13
689 726 3.710165 ACCCTCATGTAGTTTACTAGGCC 59.290 47.826 0.00 0.00 0.00 5.19
690 727 6.475596 TTACCCTCATGTAGTTTACTAGGC 57.524 41.667 0.00 0.00 0.00 3.93
691 728 7.767659 GGTTTTACCCTCATGTAGTTTACTAGG 59.232 40.741 0.00 0.00 30.04 3.02
692 729 8.537858 AGGTTTTACCCTCATGTAGTTTACTAG 58.462 37.037 0.00 0.00 39.75 2.57
693 730 8.439964 AGGTTTTACCCTCATGTAGTTTACTA 57.560 34.615 0.00 0.00 39.75 1.82
694 731 7.325725 AGGTTTTACCCTCATGTAGTTTACT 57.674 36.000 0.00 0.00 39.75 2.24
695 732 7.662669 TGAAGGTTTTACCCTCATGTAGTTTAC 59.337 37.037 0.00 0.00 39.75 2.01
696 733 7.747690 TGAAGGTTTTACCCTCATGTAGTTTA 58.252 34.615 0.00 0.00 39.75 2.01
697 734 6.607019 TGAAGGTTTTACCCTCATGTAGTTT 58.393 36.000 0.00 0.00 39.75 2.66
698 735 6.195600 TGAAGGTTTTACCCTCATGTAGTT 57.804 37.500 0.00 0.00 39.75 2.24
699 736 5.280521 CCTGAAGGTTTTACCCTCATGTAGT 60.281 44.000 0.00 0.00 38.01 2.73
700 737 5.186198 CCTGAAGGTTTTACCCTCATGTAG 58.814 45.833 0.00 0.00 38.01 2.74
701 738 4.566907 GCCTGAAGGTTTTACCCTCATGTA 60.567 45.833 0.00 0.00 38.01 2.29
702 739 3.814316 GCCTGAAGGTTTTACCCTCATGT 60.814 47.826 0.00 0.00 38.01 3.21
703 740 2.755103 GCCTGAAGGTTTTACCCTCATG 59.245 50.000 0.00 0.00 38.01 3.07
704 741 2.618045 CGCCTGAAGGTTTTACCCTCAT 60.618 50.000 0.00 0.00 38.01 2.90
705 742 1.271163 CGCCTGAAGGTTTTACCCTCA 60.271 52.381 0.00 0.00 39.75 3.86
770 810 1.676678 TACCGACAGGAGGCTGATGC 61.677 60.000 0.00 0.00 41.02 3.91
775 815 0.033011 AGACATACCGACAGGAGGCT 60.033 55.000 0.00 0.00 41.02 4.58
833 873 3.087906 ATGGGCGGGGGTGTACTC 61.088 66.667 0.00 0.00 0.00 2.59
834 874 3.087906 GATGGGCGGGGGTGTACT 61.088 66.667 0.00 0.00 0.00 2.73
835 875 2.206182 AAAGATGGGCGGGGGTGTAC 62.206 60.000 0.00 0.00 0.00 2.90
842 882 3.518068 GGCGAAAAGATGGGCGGG 61.518 66.667 0.00 0.00 0.00 6.13
845 885 0.456142 GTTTCGGCGAAAAGATGGGC 60.456 55.000 33.66 17.33 33.14 5.36
855 895 0.672401 CTTTGCTAGGGTTTCGGCGA 60.672 55.000 4.99 4.99 0.00 5.54
856 896 0.672401 TCTTTGCTAGGGTTTCGGCG 60.672 55.000 0.00 0.00 0.00 6.46
920 960 8.150945 GCCCTTCTTTCTTTTCCTTTAGATTTT 58.849 33.333 0.00 0.00 0.00 1.82
1151 1195 3.194116 CCCCATCTCCAATTTTGTGTCAG 59.806 47.826 0.00 0.00 0.00 3.51
1213 1257 0.329261 CCCTCATGCTTCCACCTCAA 59.671 55.000 0.00 0.00 0.00 3.02
1216 1260 1.229951 TCCCCTCATGCTTCCACCT 60.230 57.895 0.00 0.00 0.00 4.00
1217 1261 1.077429 GTCCCCTCATGCTTCCACC 60.077 63.158 0.00 0.00 0.00 4.61
1218 1262 0.038166 TTGTCCCCTCATGCTTCCAC 59.962 55.000 0.00 0.00 0.00 4.02
1219 1263 0.776810 TTTGTCCCCTCATGCTTCCA 59.223 50.000 0.00 0.00 0.00 3.53
1220 1264 1.923356 TTTTGTCCCCTCATGCTTCC 58.077 50.000 0.00 0.00 0.00 3.46
1222 1266 3.094572 CTGATTTTGTCCCCTCATGCTT 58.905 45.455 0.00 0.00 0.00 3.91
1223 1267 2.309755 TCTGATTTTGTCCCCTCATGCT 59.690 45.455 0.00 0.00 0.00 3.79
1224 1268 2.686915 CTCTGATTTTGTCCCCTCATGC 59.313 50.000 0.00 0.00 0.00 4.06
1226 1270 3.848975 AGTCTCTGATTTTGTCCCCTCAT 59.151 43.478 0.00 0.00 0.00 2.90
1227 1271 3.251484 AGTCTCTGATTTTGTCCCCTCA 58.749 45.455 0.00 0.00 0.00 3.86
1242 1286 2.336478 CGTGGCCGACTGAGTCTCT 61.336 63.158 11.26 0.00 35.63 3.10
1283 1327 4.080469 TGGAGATACGACTGAGTAAGGAGT 60.080 45.833 0.00 0.00 0.00 3.85
1310 1354 3.016474 GCTTTCAGCTCCGTGACGC 62.016 63.158 0.00 0.00 38.45 5.19
1334 1378 1.066303 AGTCGCTAATCCTCAGCTTCG 59.934 52.381 0.00 0.00 36.86 3.79
1356 1400 1.080230 CTGGACCTCGTCACTGCTG 60.080 63.158 0.00 0.00 33.68 4.41
1394 1438 1.453148 GCAATTTTGTCACTTCGCTGC 59.547 47.619 0.00 0.00 0.00 5.25
1401 1445 3.570975 TCATCTGCAGCAATTTTGTCACT 59.429 39.130 9.47 0.00 0.00 3.41
1410 1454 3.215151 CTTCTCCATCATCTGCAGCAAT 58.785 45.455 9.47 0.00 0.00 3.56
1440 1484 2.168521 CTCTTTGCCCGGAATCTCAGTA 59.831 50.000 0.73 0.00 0.00 2.74
1442 1486 1.661341 CTCTTTGCCCGGAATCTCAG 58.339 55.000 0.73 0.00 0.00 3.35
1443 1487 0.392998 GCTCTTTGCCCGGAATCTCA 60.393 55.000 0.73 0.00 35.15 3.27
1463 1507 1.064803 CACCGATCTTCTCCGAGACTG 59.935 57.143 0.00 0.00 0.00 3.51
1476 1520 1.209504 TGAATCCCTTCCACACCGATC 59.790 52.381 0.00 0.00 0.00 3.69
1515 1559 2.508526 GTCTTGGTTGCTGATCCACTT 58.491 47.619 0.00 0.00 33.12 3.16
1516 1560 1.609061 CGTCTTGGTTGCTGATCCACT 60.609 52.381 0.00 0.00 33.12 4.00
1544 1588 6.250344 TCAATCCATATTCGTAGTAGGTCG 57.750 41.667 0.00 0.00 0.00 4.79
1587 1631 0.990374 ACTGGGAGCAAAGCTGATCT 59.010 50.000 0.00 0.00 39.88 2.75
1604 1648 8.598041 ACTGAGATTTGTAACTAAGATCCAACT 58.402 33.333 0.00 0.00 0.00 3.16
1623 1679 4.523083 AGAGCTTAGAGAACGACTGAGAT 58.477 43.478 0.00 0.00 0.00 2.75
1629 1685 3.604627 CGTTGAAGAGCTTAGAGAACGAC 59.395 47.826 11.34 0.00 37.49 4.34
1631 1687 3.822996 TCGTTGAAGAGCTTAGAGAACG 58.177 45.455 10.80 10.80 36.83 3.95
1650 1706 1.455786 GTCATGTTGACCAACGACTCG 59.544 52.381 8.18 0.00 41.37 4.18
1687 1743 2.418746 CCTCGTCCGATTTGATTCTGGT 60.419 50.000 0.00 0.00 0.00 4.00
1700 1756 2.745100 TCTCGTCCACCTCGTCCG 60.745 66.667 0.00 0.00 0.00 4.79
1704 1760 4.813526 CGCGTCTCGTCCACCTCG 62.814 72.222 0.00 0.00 0.00 4.63
1713 1769 3.061563 TGGAAATTATTTGTCGCGTCTCG 59.938 43.478 5.77 0.00 40.15 4.04
1721 1777 7.201767 CCAGAGTCTCCATGGAAATTATTTGTC 60.202 40.741 17.00 0.00 36.09 3.18
1724 1780 6.973642 TCCAGAGTCTCCATGGAAATTATTT 58.026 36.000 17.00 0.00 40.13 1.40
1736 1792 1.986757 GCTGCCTCCAGAGTCTCCA 60.987 63.158 0.00 0.00 41.77 3.86
1737 1793 2.730524 GGCTGCCTCCAGAGTCTCC 61.731 68.421 12.43 0.00 41.77 3.71
1740 1796 1.078567 CTTGGCTGCCTCCAGAGTC 60.079 63.158 21.03 0.00 41.77 3.36
1758 1814 2.022129 CGACACCTCGCACTTCCAC 61.022 63.158 0.00 0.00 31.91 4.02
1759 1815 2.338620 CGACACCTCGCACTTCCA 59.661 61.111 0.00 0.00 31.91 3.53
1793 1849 8.646004 CCTCTATCTCCAATTTTATCTCTGTGA 58.354 37.037 0.00 0.00 0.00 3.58
1845 1901 2.237392 GGCCTTCCTGAGCTTCTCTTTA 59.763 50.000 0.00 0.00 0.00 1.85
1867 1923 2.353889 CAGCCTGTCTATTGTGCATCAC 59.646 50.000 0.00 0.00 34.56 3.06
1880 1936 2.037772 TCAAAGAACTCCTCAGCCTGTC 59.962 50.000 0.00 0.00 0.00 3.51
1926 1982 6.100714 AGGTACCGTATAATCTGGACCAATTT 59.899 38.462 6.18 0.00 0.00 1.82
1961 2017 5.107104 GCGTGAATGAATGTTTACTCACTCA 60.107 40.000 0.00 0.00 32.80 3.41
1978 2034 4.541973 TGAGCAGATATATGGCGTGAAT 57.458 40.909 0.00 0.00 0.00 2.57
1983 2039 4.692155 TGAACAATGAGCAGATATATGGCG 59.308 41.667 0.00 0.00 0.00 5.69
2053 2115 4.282496 TCAGAGGGGAAGACATTAGAGAC 58.718 47.826 0.00 0.00 0.00 3.36
2061 2123 0.252881 AGCCATCAGAGGGGAAGACA 60.253 55.000 2.61 0.00 0.00 3.41
2188 2252 6.156949 ACTTCAAGCCTGGAACATCTTCTATA 59.843 38.462 0.00 0.00 38.20 1.31
2251 2315 2.106074 GCGATTGTGATCCACGGCA 61.106 57.895 0.00 0.00 37.14 5.69
2454 2520 6.380560 TCCTGCATTCACCATTCATTAATCAA 59.619 34.615 0.00 0.00 0.00 2.57
2508 2574 3.505680 GGTTCCTCACATACAATTGCACA 59.494 43.478 5.05 0.00 0.00 4.57
2677 2749 5.483231 ACTGATTCATGAAGTTCCTCTGAGA 59.517 40.000 14.54 0.00 0.00 3.27
2771 2843 4.310769 GCAGAGAGAAGCAAACAACTCTA 58.689 43.478 0.00 0.00 39.39 2.43
2912 2984 8.892723 CATAATTTTACAGAGACAACATGCCTA 58.107 33.333 0.00 0.00 0.00 3.93
2961 3033 1.409064 CCCAGACTGCGAGTTAGCATA 59.591 52.381 0.00 0.00 46.97 3.14
3070 3148 1.272490 CCAGACGAGACCAAGCAACTA 59.728 52.381 0.00 0.00 0.00 2.24
3083 3161 1.412710 AGCTTGTCTTGAACCAGACGA 59.587 47.619 0.00 0.00 45.53 4.20
3089 3217 1.967319 TCCACAGCTTGTCTTGAACC 58.033 50.000 0.00 0.00 0.00 3.62
3163 3292 5.180117 CAGAACACTGGAAATACAAGTCTGG 59.820 44.000 0.00 0.00 0.00 3.86
3392 3906 3.303791 GGTGGAACTTTGTTACTCGCTTG 60.304 47.826 0.00 0.00 36.74 4.01
3393 3907 2.876550 GGTGGAACTTTGTTACTCGCTT 59.123 45.455 0.00 0.00 36.74 4.68
3404 3918 4.948062 AAGGCTAATAGGGTGGAACTTT 57.052 40.909 0.00 0.00 36.74 2.66
3468 4387 1.207329 GGCAGTATCTCCTTCAACCGT 59.793 52.381 0.00 0.00 0.00 4.83
3726 4965 3.716872 TCCTCTTGTTGGAGACTCCTTTT 59.283 43.478 22.14 0.00 37.46 2.27
3732 4971 1.132689 AGGGTCCTCTTGTTGGAGACT 60.133 52.381 0.00 0.00 35.52 3.24
3886 6363 6.197276 CACATTTGCCTTCATAAGAGAATCG 58.803 40.000 0.00 0.00 42.67 3.34
3999 6483 2.740447 CGCACTTGTCCCCTTACTAAAC 59.260 50.000 0.00 0.00 0.00 2.01
4029 6513 4.022329 CCCAAACTAACAAGAACATCCACC 60.022 45.833 0.00 0.00 0.00 4.61
4031 6515 4.798882 ACCCAAACTAACAAGAACATCCA 58.201 39.130 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.