Multiple sequence alignment - TraesCS6D01G250500

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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 TraesCS6D01G250500 chr6D 100.000 3640 0 0 1 3640 354221978 354225617 0.000000e+00 6722.0
1 TraesCS6D01G250500 chr6D 97.980 99 2 0 656 754 430998560 430998462 4.830000e-39 172.0
2 TraesCS6D01G250500 chr6B 89.943 2794 128 75 921 3640 524065096 524062382 0.000000e+00 3461.0
3 TraesCS6D01G250500 chr6B 88.504 635 36 14 13 625 524067438 524066819 0.000000e+00 734.0
4 TraesCS6D01G250500 chr6B 97.647 170 3 1 750 919 524066740 524066572 1.280000e-74 291.0
5 TraesCS6D01G250500 chr6B 91.791 134 1 5 625 758 130306045 130306168 1.040000e-40 178.0
6 TraesCS6D01G250500 chr6B 93.333 120 4 4 656 774 267021870 267021754 1.340000e-39 174.0
7 TraesCS6D01G250500 chr6B 97.368 38 1 0 490 527 706510112 706510149 8.440000e-07 65.8
8 TraesCS6D01G250500 chr6B 95.122 41 1 1 617 656 585252856 585252816 3.030000e-06 63.9
9 TraesCS6D01G250500 chr6B 97.297 37 1 0 617 653 585264888 585264852 3.030000e-06 63.9
10 TraesCS6D01G250500 chr6A 89.508 2640 119 57 741 3296 488063500 488060935 0.000000e+00 3195.0
11 TraesCS6D01G250500 chr6A 85.301 449 28 14 51 491 488068302 488067884 2.600000e-116 429.0
12 TraesCS6D01G250500 chr6A 90.881 318 22 1 3330 3640 488060937 488060620 1.560000e-113 420.0
13 TraesCS6D01G250500 chr2D 93.722 223 14 0 1542 1764 557258876 557259098 5.820000e-88 335.0
14 TraesCS6D01G250500 chr2D 88.318 214 21 3 1216 1429 557258359 557258568 1.680000e-63 254.0
15 TraesCS6D01G250500 chr2B 87.383 214 23 3 1216 1429 664933394 664933603 3.630000e-60 243.0
16 TraesCS6D01G250500 chr2B 97.143 35 1 0 621 655 317028385 317028419 3.930000e-05 60.2
17 TraesCS6D01G250500 chr2A 86.916 214 24 3 1216 1429 697289555 697289764 1.690000e-58 237.0
18 TraesCS6D01G250500 chr7A 82.960 223 36 2 1542 1763 573097002 573096781 2.220000e-47 200.0
19 TraesCS6D01G250500 chr7A 93.600 125 6 2 2628 2750 288910814 288910690 6.210000e-43 185.0
20 TraesCS6D01G250500 chr7B 82.456 228 38 2 1538 1764 533570544 533570318 7.970000e-47 198.0
21 TraesCS6D01G250500 chr7B 97.222 36 1 0 621 656 34707571 34707606 1.090000e-05 62.1
22 TraesCS6D01G250500 chr7D 82.511 223 39 0 1542 1764 505603597 505603375 2.870000e-46 196.0
23 TraesCS6D01G250500 chr7D 90.441 136 2 6 626 761 600970970 600971094 6.250000e-38 169.0
24 TraesCS6D01G250500 chr7D 87.838 148 6 7 625 771 123785074 123784938 2.910000e-36 163.0
25 TraesCS6D01G250500 chr5D 91.852 135 1 2 624 758 420228165 420228289 2.890000e-41 180.0
26 TraesCS6D01G250500 chr4B 95.327 107 3 2 656 761 148210448 148210553 6.250000e-38 169.0
27 TraesCS6D01G250500 chr4B 77.519 129 19 6 624 752 4716686 4716804 6.520000e-08 69.4
28 TraesCS6D01G250500 chr4B 100.000 32 0 0 624 655 655776134 655776165 3.930000e-05 60.2
29 TraesCS6D01G250500 chr3B 90.441 136 2 3 624 759 796433199 796433075 6.250000e-38 169.0
30 TraesCS6D01G250500 chr3B 90.076 131 3 1 625 755 786144010 786143890 1.050000e-35 161.0
31 TraesCS6D01G250500 chr1D 88.406 138 12 4 624 758 215066349 215066213 2.910000e-36 163.0
32 TraesCS6D01G250500 chr5B 81.618 136 15 3 624 759 558627327 558627202 1.790000e-18 104.0


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 TraesCS6D01G250500 chr6D 354221978 354225617 3639 False 6722.000000 6722 100.000000 1 3640 1 chr6D.!!$F1 3639
1 TraesCS6D01G250500 chr6B 524062382 524067438 5056 True 1495.333333 3461 92.031333 13 3640 3 chr6B.!!$R4 3627
2 TraesCS6D01G250500 chr6A 488060620 488063500 2880 True 1807.500000 3195 90.194500 741 3640 2 chr6A.!!$R2 2899
3 TraesCS6D01G250500 chr2D 557258359 557259098 739 False 294.500000 335 91.020000 1216 1764 2 chr2D.!!$F1 548

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
537 559 0.028902 GCACGTCTTGAAAAAGCGGT 59.971 50.0 0.00 0.0 0.00 5.68 F
649 672 0.030369 CCTCCGTCCGGAAATACTCG 59.970 60.0 5.23 3.9 44.66 4.18 F
1522 3260 0.110509 CTTGACTGATGCGTGTGTGC 60.111 55.0 0.00 0.0 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1911 3670 0.036952 CCGCTCTCTTCTTCTTGCCA 60.037 55.0 0.0 0.0 0.0 4.92 R
2609 4422 0.179078 GAGCCACTCAGCCAGATCAG 60.179 60.0 0.0 0.0 0.0 2.90 R
3147 4977 0.031716 TGATCCTCTCCCACTCCCTG 60.032 60.0 0.0 0.0 0.0 4.45 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
172 174 4.314440 ACGCATGCACGGGTGAGT 62.314 61.111 19.57 1.22 37.37 3.41
173 175 3.792047 CGCATGCACGGGTGAGTG 61.792 66.667 19.57 1.63 44.47 3.51
174 176 2.358615 GCATGCACGGGTGAGTGA 60.359 61.111 14.21 0.00 44.43 3.41
175 177 2.393768 GCATGCACGGGTGAGTGAG 61.394 63.158 14.21 0.00 44.43 3.51
181 183 2.262915 CGGGTGAGTGAGTGAGGC 59.737 66.667 0.00 0.00 0.00 4.70
196 198 2.049627 GAGGCTGCATCCGATCCCTT 62.050 60.000 2.29 0.00 0.00 3.95
201 203 0.758734 TGCATCCGATCCCTTTCGAT 59.241 50.000 0.00 0.00 41.62 3.59
215 217 0.322456 TTCGATCCACTTGCTTGGGG 60.322 55.000 0.00 0.00 37.24 4.96
223 226 0.613012 ACTTGCTTGGGGAGAATGGC 60.613 55.000 0.00 0.00 0.00 4.40
298 301 6.019075 GTGGTAACTTTTGTGCCATTTTTCTC 60.019 38.462 0.00 0.00 39.35 2.87
304 307 4.488126 TTGTGCCATTTTTCTCTCTTCG 57.512 40.909 0.00 0.00 0.00 3.79
316 319 1.999024 CTCTCTTCGCTTTTGAGAGCC 59.001 52.381 6.34 0.00 44.53 4.70
318 321 0.317160 TCTTCGCTTTTGAGAGCCGA 59.683 50.000 0.00 0.00 39.51 5.54
336 339 0.385598 GAGAAAACGTGGGCTTTCGC 60.386 55.000 5.12 2.44 36.78 4.70
337 340 0.818040 AGAAAACGTGGGCTTTCGCT 60.818 50.000 5.12 0.00 36.78 4.93
338 341 0.869730 GAAAACGTGGGCTTTCGCTA 59.130 50.000 0.00 0.00 36.09 4.26
367 370 2.595095 CGCCTATTTGGGGGCTGA 59.405 61.111 0.00 0.00 45.57 4.26
368 371 1.526917 CGCCTATTTGGGGGCTGAG 60.527 63.158 0.00 0.00 45.57 3.35
369 372 1.922821 GCCTATTTGGGGGCTGAGA 59.077 57.895 0.00 0.00 44.48 3.27
370 373 0.179006 GCCTATTTGGGGGCTGAGAG 60.179 60.000 0.00 0.00 44.48 3.20
371 374 0.179006 CCTATTTGGGGGCTGAGAGC 60.179 60.000 0.00 0.00 41.46 4.09
382 385 2.985957 GCTGAGAGCCTGAGAAAGAT 57.014 50.000 0.00 0.00 34.48 2.40
400 403 2.164219 AGATAAGTGTTGGGCAAATGCG 59.836 45.455 0.00 0.00 43.26 4.73
417 425 0.034616 GCGATGGAATCTCCCAGAGG 59.965 60.000 0.00 0.00 42.58 3.69
418 426 0.683973 CGATGGAATCTCCCAGAGGG 59.316 60.000 0.00 0.00 42.58 4.30
446 454 3.553597 CGGAGCCAAGATACGACTC 57.446 57.895 0.00 0.00 0.00 3.36
449 457 2.223829 CGGAGCCAAGATACGACTCAAT 60.224 50.000 0.00 0.00 0.00 2.57
450 458 3.126831 GGAGCCAAGATACGACTCAATG 58.873 50.000 0.00 0.00 0.00 2.82
451 459 3.430929 GGAGCCAAGATACGACTCAATGT 60.431 47.826 0.00 0.00 0.00 2.71
452 460 4.202121 GGAGCCAAGATACGACTCAATGTA 60.202 45.833 0.00 0.00 0.00 2.29
453 461 4.938080 AGCCAAGATACGACTCAATGTAG 58.062 43.478 0.00 0.00 0.00 2.74
456 466 6.096423 AGCCAAGATACGACTCAATGTAGTAA 59.904 38.462 0.00 0.00 39.51 2.24
476 486 1.951209 TGAATGGAGGGAGTGCAGTA 58.049 50.000 0.00 0.00 0.00 2.74
535 557 2.221055 AGTAGCACGTCTTGAAAAAGCG 59.779 45.455 0.00 0.00 0.00 4.68
537 559 0.028902 GCACGTCTTGAAAAAGCGGT 59.971 50.000 0.00 0.00 0.00 5.68
570 593 2.844281 CTTAGCACTCGCAAAAGAAGC 58.156 47.619 0.00 0.00 42.27 3.86
581 604 2.069165 AAAAGAAGCGTGCCCTCCCT 62.069 55.000 0.00 0.00 0.00 4.20
635 658 2.823147 ACGCGAGTACTCCCTCCG 60.823 66.667 15.93 15.57 46.88 4.63
636 659 2.823147 CGCGAGTACTCCCTCCGT 60.823 66.667 17.23 0.00 0.00 4.69
637 660 2.821688 CGCGAGTACTCCCTCCGTC 61.822 68.421 17.23 2.08 0.00 4.79
638 661 2.479750 GCGAGTACTCCCTCCGTCC 61.480 68.421 17.23 0.00 0.00 4.79
639 662 2.178890 CGAGTACTCCCTCCGTCCG 61.179 68.421 17.23 0.00 0.00 4.79
640 663 1.823041 GAGTACTCCCTCCGTCCGG 60.823 68.421 12.13 0.00 0.00 5.14
641 664 2.262774 GAGTACTCCCTCCGTCCGGA 62.263 65.000 12.13 0.00 42.90 5.14
642 665 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
643 666 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
645 668 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
646 669 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
647 670 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
648 671 0.388294 CCCTCCGTCCGGAAATACTC 59.612 60.000 5.23 0.00 44.66 2.59
649 672 0.030369 CCTCCGTCCGGAAATACTCG 59.970 60.000 5.23 3.90 44.66 4.18
650 673 0.737219 CTCCGTCCGGAAATACTCGT 59.263 55.000 5.23 0.00 44.66 4.18
651 674 0.734889 TCCGTCCGGAAATACTCGTC 59.265 55.000 5.23 0.00 42.05 4.20
652 675 0.590732 CCGTCCGGAAATACTCGTCG 60.591 60.000 5.23 1.25 37.50 5.12
653 676 0.374758 CGTCCGGAAATACTCGTCGA 59.625 55.000 5.23 0.00 0.00 4.20
655 678 2.728846 CGTCCGGAAATACTCGTCGAAA 60.729 50.000 5.23 0.00 0.00 3.46
656 679 2.595977 GTCCGGAAATACTCGTCGAAAC 59.404 50.000 5.23 0.00 0.00 2.78
657 680 2.489329 TCCGGAAATACTCGTCGAAACT 59.511 45.455 0.00 0.00 0.00 2.66
658 681 2.850647 CCGGAAATACTCGTCGAAACTC 59.149 50.000 0.00 0.00 0.00 3.01
659 682 2.525096 CGGAAATACTCGTCGAAACTCG 59.475 50.000 0.00 0.00 42.10 4.18
660 683 3.496155 GGAAATACTCGTCGAAACTCGT 58.504 45.455 0.00 0.00 41.35 4.18
661 684 3.541523 GGAAATACTCGTCGAAACTCGTC 59.458 47.826 0.00 0.00 41.35 4.20
671 694 2.407361 TCGAAACTCGTCGAAGAAATGC 59.593 45.455 1.95 0.00 46.52 3.56
672 695 2.154963 CGAAACTCGTCGAAGAAATGCA 59.845 45.455 1.95 0.00 43.86 3.96
673 696 3.181530 CGAAACTCGTCGAAGAAATGCAT 60.182 43.478 1.95 0.00 43.86 3.96
674 697 4.031314 CGAAACTCGTCGAAGAAATGCATA 59.969 41.667 0.00 0.00 43.86 3.14
675 698 5.444087 CGAAACTCGTCGAAGAAATGCATAA 60.444 40.000 0.00 0.00 43.86 1.90
676 699 5.856126 AACTCGTCGAAGAAATGCATAAA 57.144 34.783 0.00 0.00 39.69 1.40
677 700 5.856126 ACTCGTCGAAGAAATGCATAAAA 57.144 34.783 0.00 0.00 39.69 1.52
678 701 6.236017 ACTCGTCGAAGAAATGCATAAAAA 57.764 33.333 0.00 0.00 39.69 1.94
680 703 6.742718 ACTCGTCGAAGAAATGCATAAAAATG 59.257 34.615 0.00 0.00 39.69 2.32
681 704 6.836953 TCGTCGAAGAAATGCATAAAAATGA 58.163 32.000 0.00 0.00 39.69 2.57
682 705 7.301789 TCGTCGAAGAAATGCATAAAAATGAA 58.698 30.769 0.00 0.00 39.69 2.57
685 708 8.863049 GTCGAAGAAATGCATAAAAATGAATGT 58.137 29.630 0.00 0.00 39.69 2.71
725 748 6.929625 ACATCTAGATACATCCATTTCTCCG 58.070 40.000 4.54 0.00 0.00 4.63
726 749 6.721668 ACATCTAGATACATCCATTTCTCCGA 59.278 38.462 4.54 0.00 0.00 4.55
727 750 6.576662 TCTAGATACATCCATTTCTCCGAC 57.423 41.667 0.00 0.00 0.00 4.79
728 751 4.244425 AGATACATCCATTTCTCCGACG 57.756 45.455 0.00 0.00 0.00 5.12
729 752 3.889538 AGATACATCCATTTCTCCGACGA 59.110 43.478 0.00 0.00 0.00 4.20
730 753 2.586258 ACATCCATTTCTCCGACGAG 57.414 50.000 0.00 0.00 37.48 4.18
731 754 1.825474 ACATCCATTTCTCCGACGAGT 59.175 47.619 0.00 0.00 37.40 4.18
732 755 3.021695 ACATCCATTTCTCCGACGAGTA 58.978 45.455 0.00 0.00 37.40 2.59
733 756 3.637229 ACATCCATTTCTCCGACGAGTAT 59.363 43.478 0.00 0.00 37.40 2.12
734 757 4.099573 ACATCCATTTCTCCGACGAGTATT 59.900 41.667 0.00 0.00 37.40 1.89
735 758 4.730949 TCCATTTCTCCGACGAGTATTT 57.269 40.909 0.00 0.00 37.40 1.40
736 759 4.679662 TCCATTTCTCCGACGAGTATTTC 58.320 43.478 0.00 0.00 37.40 2.17
737 760 3.802685 CCATTTCTCCGACGAGTATTTCC 59.197 47.826 0.00 0.00 37.40 3.13
738 761 2.838386 TTCTCCGACGAGTATTTCCG 57.162 50.000 0.00 0.00 37.40 4.30
739 762 1.019673 TCTCCGACGAGTATTTCCGG 58.980 55.000 0.00 0.00 41.36 5.14
740 763 1.019673 CTCCGACGAGTATTTCCGGA 58.980 55.000 0.00 0.00 45.74 5.14
741 764 0.734889 TCCGACGAGTATTTCCGGAC 59.265 55.000 1.83 0.00 43.47 4.79
742 765 0.590732 CCGACGAGTATTTCCGGACG 60.591 60.000 1.83 5.89 42.49 4.79
743 766 0.590732 CGACGAGTATTTCCGGACGG 60.591 60.000 1.83 3.96 0.00 4.79
744 767 0.734889 GACGAGTATTTCCGGACGGA 59.265 55.000 1.83 9.76 43.52 4.69
745 768 0.737219 ACGAGTATTTCCGGACGGAG 59.263 55.000 13.64 3.15 46.06 4.63
746 769 0.030369 CGAGTATTTCCGGACGGAGG 59.970 60.000 13.64 0.00 46.06 4.30
930 2430 1.750778 CACTTTCCACAAGCCACAAGT 59.249 47.619 0.00 0.00 0.00 3.16
1095 2597 2.776370 TAGACCACGCGTCCCCTCTT 62.776 60.000 9.86 0.00 43.08 2.85
1133 2635 2.380081 CCGCCACGGTAAACTGATC 58.620 57.895 0.00 0.00 42.73 2.92
1135 2637 1.674817 CCGCCACGGTAAACTGATCTT 60.675 52.381 0.00 0.00 42.73 2.40
1138 2640 3.335579 GCCACGGTAAACTGATCTTCTT 58.664 45.455 0.00 0.00 0.00 2.52
1139 2641 3.125316 GCCACGGTAAACTGATCTTCTTG 59.875 47.826 0.00 0.00 0.00 3.02
1140 2642 4.566004 CCACGGTAAACTGATCTTCTTGA 58.434 43.478 0.00 0.00 0.00 3.02
1143 2645 4.631813 ACGGTAAACTGATCTTCTTGATGC 59.368 41.667 0.00 0.00 35.14 3.91
1148 2650 5.893897 AACTGATCTTCTTGATGCTTTCC 57.106 39.130 0.00 0.00 35.14 3.13
1151 2653 3.693085 TGATCTTCTTGATGCTTTCCTGC 59.307 43.478 0.00 0.00 35.14 4.85
1154 2656 1.171308 TCTTGATGCTTTCCTGCTGC 58.829 50.000 0.00 0.00 0.00 5.25
1156 2658 0.885879 TTGATGCTTTCCTGCTGCTG 59.114 50.000 0.00 0.00 0.00 4.41
1168 2681 1.002033 CTGCTGCTGTGTTTCTTGGTC 60.002 52.381 0.00 0.00 0.00 4.02
1520 3258 1.502231 GTCTTGACTGATGCGTGTGT 58.498 50.000 0.00 0.00 0.00 3.72
1521 3259 1.193203 GTCTTGACTGATGCGTGTGTG 59.807 52.381 0.00 0.00 0.00 3.82
1522 3260 0.110509 CTTGACTGATGCGTGTGTGC 60.111 55.000 0.00 0.00 0.00 4.57
1836 3579 2.860293 CTTGTAACCAGCACGGCG 59.140 61.111 4.80 4.80 39.03 6.46
1843 3586 2.357517 CCAGCACGGCGTCTTCTT 60.358 61.111 10.85 0.00 0.00 2.52
1848 3595 4.065281 ACGGCGTCTTCTTCCCCG 62.065 66.667 6.77 0.00 44.19 5.73
1854 3601 0.528684 CGTCTTCTTCCCCGCAGATC 60.529 60.000 0.00 0.00 0.00 2.75
1941 3700 3.991536 GAGAGCGGCGGTCAAGGAC 62.992 68.421 36.27 19.39 31.89 3.85
2134 3893 0.377554 CGTGGAGTACTAGGACAGCG 59.622 60.000 8.10 2.21 0.00 5.18
2307 4076 6.017605 CAGTTTGTTGCAGACTCTTCAGTTAT 60.018 38.462 0.00 0.00 30.63 1.89
2308 4077 7.171508 CAGTTTGTTGCAGACTCTTCAGTTATA 59.828 37.037 0.00 0.00 30.63 0.98
2341 4110 0.388520 GGTAAAACCGTAGCGTCCGT 60.389 55.000 0.00 0.00 0.00 4.69
2342 4111 1.418373 GTAAAACCGTAGCGTCCGTT 58.582 50.000 0.00 0.00 0.00 4.44
2343 4112 2.591133 GTAAAACCGTAGCGTCCGTTA 58.409 47.619 0.00 0.00 0.00 3.18
2344 4113 2.368655 AAAACCGTAGCGTCCGTTAT 57.631 45.000 0.00 0.00 0.00 1.89
2393 4166 6.091123 ACGACGACTAAGTTTTGCAATATC 57.909 37.500 0.00 0.00 0.00 1.63
2409 4190 6.941857 TGCAATATCACTGTAGTAAACTCCA 58.058 36.000 0.00 0.00 0.00 3.86
2426 4209 3.657239 ACTCCATGCCCATATGGTTATGA 59.343 43.478 25.67 14.04 46.23 2.15
2427 4210 4.263639 ACTCCATGCCCATATGGTTATGAG 60.264 45.833 25.67 21.45 46.23 2.90
2428 4211 3.010472 TCCATGCCCATATGGTTATGAGG 59.990 47.826 25.67 17.51 46.23 3.86
2430 4213 2.065007 TGCCCATATGGTTATGAGGCT 58.935 47.619 20.46 0.00 44.34 4.58
2431 4214 2.446666 TGCCCATATGGTTATGAGGCTT 59.553 45.455 20.46 0.00 44.34 4.35
2432 4215 3.655291 TGCCCATATGGTTATGAGGCTTA 59.345 43.478 20.46 0.00 44.34 3.09
2433 4216 4.292041 TGCCCATATGGTTATGAGGCTTAT 59.708 41.667 20.46 0.00 44.34 1.73
2434 4217 4.641989 GCCCATATGGTTATGAGGCTTATG 59.358 45.833 20.46 1.06 42.67 1.90
2435 4218 5.195940 CCCATATGGTTATGAGGCTTATGG 58.804 45.833 20.46 9.62 37.94 2.74
2436 4219 4.641989 CCATATGGTTATGAGGCTTATGGC 59.358 45.833 14.09 0.00 37.94 4.40
2437 4220 3.882102 ATGGTTATGAGGCTTATGGCA 57.118 42.857 1.43 0.00 44.01 4.92
2438 4221 2.930950 TGGTTATGAGGCTTATGGCAC 58.069 47.619 1.43 0.00 44.01 5.01
2439 4222 2.509548 TGGTTATGAGGCTTATGGCACT 59.490 45.455 1.43 0.00 44.01 4.40
2440 4223 3.714280 TGGTTATGAGGCTTATGGCACTA 59.286 43.478 1.43 0.00 44.01 2.74
2441 4224 4.165180 TGGTTATGAGGCTTATGGCACTAA 59.835 41.667 1.43 0.00 44.01 2.24
2442 4225 4.757149 GGTTATGAGGCTTATGGCACTAAG 59.243 45.833 1.43 0.74 44.01 2.18
2458 4241 5.050972 GGCACTAAGTAGATCGTAAATGTGC 60.051 44.000 18.46 18.46 44.02 4.57
2459 4242 5.050972 GCACTAAGTAGATCGTAAATGTGCC 60.051 44.000 16.93 5.65 40.47 5.01
2511 4307 4.792804 GGAGCAGGAGGCCAGTGC 62.793 72.222 14.44 14.44 46.50 4.40
2673 4486 0.964700 TCTGACACTCAGCACAGAGG 59.035 55.000 0.00 0.00 43.95 3.69
2695 4508 3.447040 CCCCCATTAATGCGGCTG 58.553 61.111 12.91 5.39 0.00 4.85
2696 4509 2.730094 CCCCATTAATGCGGCTGC 59.270 61.111 11.65 11.65 43.20 5.25
2777 4594 2.363018 CTGAGGTCAGAGGCCCGA 60.363 66.667 0.00 0.00 46.59 5.14
2779 4596 2.043852 GAGGTCAGAGGCCCGAGA 60.044 66.667 0.00 0.00 0.00 4.04
2780 4597 2.043450 AGGTCAGAGGCCCGAGAG 60.043 66.667 0.00 0.00 0.00 3.20
2781 4598 2.043852 GGTCAGAGGCCCGAGAGA 60.044 66.667 0.00 0.00 0.00 3.10
2782 4599 2.124693 GGTCAGAGGCCCGAGAGAG 61.125 68.421 0.00 0.00 0.00 3.20
2783 4600 1.077357 GTCAGAGGCCCGAGAGAGA 60.077 63.158 0.00 0.00 0.00 3.10
2784 4601 1.077357 TCAGAGGCCCGAGAGAGAC 60.077 63.158 0.00 0.00 0.00 3.36
2785 4602 2.124487 AGAGGCCCGAGAGAGACG 60.124 66.667 0.00 0.00 0.00 4.18
2875 4692 0.902984 TGCGGTAGCTTCTGGAAGGA 60.903 55.000 11.61 0.00 45.42 3.36
3169 5016 0.467804 GGAGTGGGAGAGGATCAAGC 59.532 60.000 0.00 0.00 37.82 4.01
3193 5040 1.414181 AGCGCATCCAAGCTATGTACT 59.586 47.619 11.47 0.00 42.60 2.73
3206 5053 2.522271 TGTACTGTCCAGTGCACCA 58.478 52.632 14.63 3.00 46.49 4.17
3262 5109 3.188773 CGCCTCCGTATTATTCGCA 57.811 52.632 0.00 0.00 0.00 5.10
3273 5120 2.093306 TTATTCGCATAGGGCATCGG 57.907 50.000 0.00 0.00 45.17 4.18
3281 5128 2.715181 ATAGGGCATCGGCTCCTCGA 62.715 60.000 0.00 0.00 43.51 4.04
3324 5179 4.470170 TGCCACGTCGATCGACCG 62.470 66.667 35.48 30.68 41.76 4.79
3422 5277 0.890683 CCATTGGCCAGTTCCAGTTC 59.109 55.000 5.11 0.00 37.44 3.01
3440 5295 2.355837 TCTTCACTGGACACGCGC 60.356 61.111 5.73 0.00 0.00 6.86
3447 5302 2.432456 TGGACACGCGCTGATGTC 60.432 61.111 21.41 21.41 43.75 3.06
3449 5304 1.738099 GGACACGCGCTGATGTCTT 60.738 57.895 25.66 1.09 43.91 3.01
3450 5305 1.417592 GACACGCGCTGATGTCTTG 59.582 57.895 21.94 3.47 41.69 3.02
3467 5330 0.112218 TTGCTTGCTCCCCTTTGCTA 59.888 50.000 0.00 0.00 0.00 3.49
3512 5375 4.876107 GTGACATGGACCTATCAAAACGAT 59.124 41.667 0.00 0.00 38.21 3.73
3584 5474 2.534019 CGTCACTGCGTTGTGCCTT 61.534 57.895 5.30 0.00 45.60 4.35
3593 5483 1.729517 GCGTTGTGCCTTTGTGTTTTT 59.270 42.857 0.00 0.00 37.76 1.94
3594 5484 2.924290 GCGTTGTGCCTTTGTGTTTTTA 59.076 40.909 0.00 0.00 37.76 1.52
3601 5491 5.359576 TGTGCCTTTGTGTTTTTATCTCTGT 59.640 36.000 0.00 0.00 0.00 3.41
3612 5509 6.978080 TGTTTTTATCTCTGTGAAAACCTTGC 59.022 34.615 7.75 0.00 39.82 4.01
3616 5513 1.370414 CTGTGAAAACCTTGCGCCG 60.370 57.895 4.18 0.00 0.00 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.759459 GCCCTCCCGGATTTCTCGAT 61.759 60.000 0.73 0.00 0.00 3.59
2 3 2.432300 GCCCTCCCGGATTTCTCGA 61.432 63.158 0.73 0.00 0.00 4.04
3 4 2.044806 ATGCCCTCCCGGATTTCTCG 62.045 60.000 0.73 0.00 0.00 4.04
4 5 0.536006 CATGCCCTCCCGGATTTCTC 60.536 60.000 0.73 0.00 0.00 2.87
6 7 1.529244 CCATGCCCTCCCGGATTTC 60.529 63.158 0.73 0.00 0.00 2.17
7 8 2.603008 CCATGCCCTCCCGGATTT 59.397 61.111 0.73 0.00 0.00 2.17
8 9 3.501911 CCCATGCCCTCCCGGATT 61.502 66.667 0.73 0.00 0.00 3.01
9 10 4.843331 ACCCATGCCCTCCCGGAT 62.843 66.667 0.73 0.00 0.00 4.18
13 14 3.662117 GAACCACCCATGCCCTCCC 62.662 68.421 0.00 0.00 0.00 4.30
14 15 2.043953 GAACCACCCATGCCCTCC 60.044 66.667 0.00 0.00 0.00 4.30
15 16 2.043953 GGAACCACCCATGCCCTC 60.044 66.667 0.00 0.00 0.00 4.30
16 17 2.228841 GATGGAACCACCCATGCCCT 62.229 60.000 0.00 0.00 46.34 5.19
26 27 2.189257 CCGGCGATGATGGAACCA 59.811 61.111 9.30 0.00 0.00 3.67
60 61 0.609957 TTCTCTAGTGGCCGAACGGA 60.610 55.000 17.63 0.00 37.50 4.69
125 126 7.237871 CGCCATATATACTAGCATATCTCGTC 58.762 42.308 0.00 0.00 0.00 4.20
127 128 6.149640 ACCGCCATATATACTAGCATATCTCG 59.850 42.308 0.00 0.63 0.00 4.04
171 173 1.812922 CGGATGCAGCCTCACTCAC 60.813 63.158 20.58 0.00 0.00 3.51
172 174 1.332889 ATCGGATGCAGCCTCACTCA 61.333 55.000 20.58 0.00 0.00 3.41
173 175 0.599728 GATCGGATGCAGCCTCACTC 60.600 60.000 20.58 6.33 0.00 3.51
174 176 1.445095 GATCGGATGCAGCCTCACT 59.555 57.895 20.58 0.00 0.00 3.41
175 177 1.596477 GGATCGGATGCAGCCTCAC 60.596 63.158 20.58 9.38 0.00 3.51
181 183 0.104855 TCGAAAGGGATCGGATGCAG 59.895 55.000 11.71 0.00 42.92 4.41
196 198 0.322456 CCCCAAGCAAGTGGATCGAA 60.322 55.000 2.83 0.00 41.65 3.71
201 203 1.075601 ATTCTCCCCAAGCAAGTGGA 58.924 50.000 2.83 0.00 41.65 4.02
234 237 0.813610 CCTAATGCGTCGCCCATTGA 60.814 55.000 15.88 0.00 34.87 2.57
257 260 1.423845 CACTAACGACGCCATTGCC 59.576 57.895 0.00 0.00 0.00 4.52
298 301 0.718343 CGGCTCTCAAAAGCGAAGAG 59.282 55.000 0.00 0.00 43.45 2.85
304 307 2.663063 CGTTTTCTCGGCTCTCAAAAGC 60.663 50.000 0.00 0.00 41.73 3.51
316 319 0.110823 CGAAAGCCCACGTTTTCTCG 60.111 55.000 8.39 0.00 37.14 4.04
336 339 1.803334 TAGGCGGTGCAAAACAGTAG 58.197 50.000 0.00 0.00 0.00 2.57
337 340 2.483014 ATAGGCGGTGCAAAACAGTA 57.517 45.000 0.00 0.00 0.00 2.74
338 341 1.616159 AATAGGCGGTGCAAAACAGT 58.384 45.000 0.00 0.00 0.00 3.55
365 368 4.774726 ACACTTATCTTTCTCAGGCTCTCA 59.225 41.667 0.00 0.00 0.00 3.27
366 369 5.337578 ACACTTATCTTTCTCAGGCTCTC 57.662 43.478 0.00 0.00 0.00 3.20
367 370 5.486526 CAACACTTATCTTTCTCAGGCTCT 58.513 41.667 0.00 0.00 0.00 4.09
368 371 4.633565 CCAACACTTATCTTTCTCAGGCTC 59.366 45.833 0.00 0.00 0.00 4.70
369 372 4.566488 CCCAACACTTATCTTTCTCAGGCT 60.566 45.833 0.00 0.00 0.00 4.58
370 373 3.691609 CCCAACACTTATCTTTCTCAGGC 59.308 47.826 0.00 0.00 0.00 4.85
371 374 3.691609 GCCCAACACTTATCTTTCTCAGG 59.308 47.826 0.00 0.00 0.00 3.86
372 375 4.326826 TGCCCAACACTTATCTTTCTCAG 58.673 43.478 0.00 0.00 0.00 3.35
373 376 4.365514 TGCCCAACACTTATCTTTCTCA 57.634 40.909 0.00 0.00 0.00 3.27
381 384 2.166829 TCGCATTTGCCCAACACTTAT 58.833 42.857 0.00 0.00 37.91 1.73
382 385 1.610363 TCGCATTTGCCCAACACTTA 58.390 45.000 0.00 0.00 37.91 2.24
383 386 0.968405 ATCGCATTTGCCCAACACTT 59.032 45.000 0.00 0.00 37.91 3.16
437 445 8.916654 CCATTCATTACTACATTGAGTCGTATC 58.083 37.037 0.00 0.00 29.68 2.24
439 447 8.002984 TCCATTCATTACTACATTGAGTCGTA 57.997 34.615 0.00 0.00 0.00 3.43
440 448 6.873997 TCCATTCATTACTACATTGAGTCGT 58.126 36.000 0.00 0.00 0.00 4.34
441 449 6.422100 CCTCCATTCATTACTACATTGAGTCG 59.578 42.308 0.00 0.00 0.00 4.18
442 450 6.708054 CCCTCCATTCATTACTACATTGAGTC 59.292 42.308 0.00 0.00 0.00 3.36
444 452 6.830912 TCCCTCCATTCATTACTACATTGAG 58.169 40.000 0.00 0.00 0.00 3.02
445 453 6.386927 ACTCCCTCCATTCATTACTACATTGA 59.613 38.462 0.00 0.00 0.00 2.57
446 454 6.484643 CACTCCCTCCATTCATTACTACATTG 59.515 42.308 0.00 0.00 0.00 2.82
449 457 4.141711 GCACTCCCTCCATTCATTACTACA 60.142 45.833 0.00 0.00 0.00 2.74
450 458 4.141711 TGCACTCCCTCCATTCATTACTAC 60.142 45.833 0.00 0.00 0.00 2.73
451 459 4.037222 TGCACTCCCTCCATTCATTACTA 58.963 43.478 0.00 0.00 0.00 1.82
452 460 2.846206 TGCACTCCCTCCATTCATTACT 59.154 45.455 0.00 0.00 0.00 2.24
453 461 3.209410 CTGCACTCCCTCCATTCATTAC 58.791 50.000 0.00 0.00 0.00 1.89
456 466 1.293062 ACTGCACTCCCTCCATTCAT 58.707 50.000 0.00 0.00 0.00 2.57
461 471 1.229177 TGCTACTGCACTCCCTCCA 60.229 57.895 0.00 0.00 45.31 3.86
476 486 1.971357 ACTAGTAAGTGCCACACTGCT 59.029 47.619 0.15 5.79 44.62 4.24
518 528 0.028902 ACCGCTTTTTCAAGACGTGC 59.971 50.000 0.00 0.00 31.52 5.34
527 537 0.102300 AGGCACACAACCGCTTTTTC 59.898 50.000 0.00 0.00 0.00 2.29
535 557 1.602920 GCTAAGCAAAGGCACACAACC 60.603 52.381 0.00 0.00 44.61 3.77
537 559 1.397672 TGCTAAGCAAAGGCACACAA 58.602 45.000 0.00 0.00 44.61 3.33
570 593 0.108138 CTCTAAACAGGGAGGGCACG 60.108 60.000 0.00 0.00 0.00 5.34
575 598 4.033709 TCAATCCTCTCTAAACAGGGAGG 58.966 47.826 13.49 13.49 44.69 4.30
581 604 8.868522 AAATTGTGATCAATCCTCTCTAAACA 57.131 30.769 0.00 0.00 42.60 2.83
625 648 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
626 649 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
627 650 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
628 651 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
632 655 0.734889 GACGAGTATTTCCGGACGGA 59.265 55.000 1.83 9.76 43.52 4.69
633 656 0.590732 CGACGAGTATTTCCGGACGG 60.591 60.000 1.83 3.96 0.00 4.79
634 657 0.374758 TCGACGAGTATTTCCGGACG 59.625 55.000 1.83 5.89 0.00 4.79
635 658 2.549633 TTCGACGAGTATTTCCGGAC 57.450 50.000 1.83 0.00 0.00 4.79
636 659 2.489329 AGTTTCGACGAGTATTTCCGGA 59.511 45.455 0.00 0.00 0.00 5.14
637 660 2.850647 GAGTTTCGACGAGTATTTCCGG 59.149 50.000 0.00 0.00 0.00 5.14
638 661 2.525096 CGAGTTTCGACGAGTATTTCCG 59.475 50.000 0.00 0.00 43.74 4.30
639 662 3.496155 ACGAGTTTCGACGAGTATTTCC 58.504 45.455 5.38 0.00 43.74 3.13
640 663 4.718779 GACGAGTTTCGACGAGTATTTC 57.281 45.455 5.38 0.00 43.74 2.17
650 673 2.407361 GCATTTCTTCGACGAGTTTCGA 59.593 45.455 5.38 0.00 46.12 3.71
651 674 2.154963 TGCATTTCTTCGACGAGTTTCG 59.845 45.455 0.00 0.00 46.93 3.46
652 675 3.788434 TGCATTTCTTCGACGAGTTTC 57.212 42.857 0.00 0.00 0.00 2.78
653 676 5.856126 TTATGCATTTCTTCGACGAGTTT 57.144 34.783 3.54 0.00 0.00 2.66
655 678 5.856126 TTTTATGCATTTCTTCGACGAGT 57.144 34.783 3.54 0.00 0.00 4.18
656 679 6.960992 TCATTTTTATGCATTTCTTCGACGAG 59.039 34.615 3.54 0.00 0.00 4.18
657 680 6.836953 TCATTTTTATGCATTTCTTCGACGA 58.163 32.000 3.54 0.00 0.00 4.20
658 681 7.491254 TTCATTTTTATGCATTTCTTCGACG 57.509 32.000 3.54 0.00 0.00 5.12
659 682 8.863049 ACATTCATTTTTATGCATTTCTTCGAC 58.137 29.630 3.54 0.00 0.00 4.20
660 683 8.984891 ACATTCATTTTTATGCATTTCTTCGA 57.015 26.923 3.54 0.00 0.00 3.71
699 722 8.690884 CGGAGAAATGGATGTATCTAGATGTAT 58.309 37.037 15.79 9.11 0.00 2.29
701 724 6.721668 TCGGAGAAATGGATGTATCTAGATGT 59.278 38.462 15.79 1.25 0.00 3.06
702 725 7.032580 GTCGGAGAAATGGATGTATCTAGATG 58.967 42.308 15.79 0.00 39.69 2.90
703 726 6.127869 CGTCGGAGAAATGGATGTATCTAGAT 60.128 42.308 10.73 10.73 39.69 1.98
704 727 5.181433 CGTCGGAGAAATGGATGTATCTAGA 59.819 44.000 0.00 0.00 39.69 2.43
705 728 5.181433 TCGTCGGAGAAATGGATGTATCTAG 59.819 44.000 0.00 0.00 39.69 2.43
706 729 5.067954 TCGTCGGAGAAATGGATGTATCTA 58.932 41.667 0.00 0.00 39.69 1.98
707 730 3.889538 TCGTCGGAGAAATGGATGTATCT 59.110 43.478 0.00 0.00 39.69 1.98
708 731 4.230657 CTCGTCGGAGAAATGGATGTATC 58.769 47.826 0.00 0.00 43.27 2.24
709 732 3.637229 ACTCGTCGGAGAAATGGATGTAT 59.363 43.478 0.00 0.00 43.27 2.29
710 733 3.021695 ACTCGTCGGAGAAATGGATGTA 58.978 45.455 0.00 0.00 43.27 2.29
711 734 1.825474 ACTCGTCGGAGAAATGGATGT 59.175 47.619 0.00 0.00 43.27 3.06
712 735 2.586258 ACTCGTCGGAGAAATGGATG 57.414 50.000 0.00 0.00 43.27 3.51
713 736 4.939052 AATACTCGTCGGAGAAATGGAT 57.061 40.909 0.00 0.00 43.27 3.41
714 737 4.441079 GGAAATACTCGTCGGAGAAATGGA 60.441 45.833 0.00 0.00 43.27 3.41
715 738 3.802685 GGAAATACTCGTCGGAGAAATGG 59.197 47.826 0.00 0.00 43.27 3.16
716 739 3.486108 CGGAAATACTCGTCGGAGAAATG 59.514 47.826 0.00 0.00 43.27 2.32
717 740 3.490419 CCGGAAATACTCGTCGGAGAAAT 60.490 47.826 0.00 0.00 43.27 2.17
718 741 2.159338 CCGGAAATACTCGTCGGAGAAA 60.159 50.000 0.00 0.00 43.27 2.52
719 742 1.402968 CCGGAAATACTCGTCGGAGAA 59.597 52.381 0.00 0.00 43.27 2.87
720 743 1.019673 CCGGAAATACTCGTCGGAGA 58.980 55.000 0.00 0.00 43.27 3.71
721 744 1.019673 TCCGGAAATACTCGTCGGAG 58.980 55.000 0.00 0.00 43.84 4.63
722 745 0.734889 GTCCGGAAATACTCGTCGGA 59.265 55.000 5.23 0.00 46.06 4.55
723 746 0.590732 CGTCCGGAAATACTCGTCGG 60.591 60.000 5.23 0.00 41.80 4.79
724 747 0.590732 CCGTCCGGAAATACTCGTCG 60.591 60.000 5.23 1.25 37.50 5.12
725 748 0.734889 TCCGTCCGGAAATACTCGTC 59.265 55.000 5.23 0.00 42.05 4.20
726 749 0.737219 CTCCGTCCGGAAATACTCGT 59.263 55.000 5.23 0.00 44.66 4.18
727 750 0.030369 CCTCCGTCCGGAAATACTCG 59.970 60.000 5.23 3.90 44.66 4.18
728 751 0.388294 CCCTCCGTCCGGAAATACTC 59.612 60.000 5.23 0.00 44.66 2.59
729 752 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
730 753 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
731 754 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
732 755 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
733 756 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
734 757 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
735 758 0.982852 TAGTACTCCCTCCGTCCGGA 60.983 60.000 0.00 0.00 42.90 5.14
736 759 0.110104 ATAGTACTCCCTCCGTCCGG 59.890 60.000 0.00 0.00 0.00 5.14
737 760 2.847327 TATAGTACTCCCTCCGTCCG 57.153 55.000 0.00 0.00 0.00 4.79
738 761 5.999044 TCATATATAGTACTCCCTCCGTCC 58.001 45.833 0.00 0.00 0.00 4.79
739 762 8.407064 CAAATCATATATAGTACTCCCTCCGTC 58.593 40.741 0.00 0.00 0.00 4.79
740 763 7.147880 GCAAATCATATATAGTACTCCCTCCGT 60.148 40.741 0.00 0.00 0.00 4.69
741 764 7.147897 TGCAAATCATATATAGTACTCCCTCCG 60.148 40.741 0.00 0.00 0.00 4.63
742 765 8.079211 TGCAAATCATATATAGTACTCCCTCC 57.921 38.462 0.00 0.00 0.00 4.30
909 936 2.023673 CTTGTGGCTTGTGGAAAGTGA 58.976 47.619 0.00 0.00 0.00 3.41
930 2430 1.740296 GAGGAAAAGTAGCGCGGCA 60.740 57.895 8.83 0.00 0.00 5.69
1011 2511 0.618968 GGAGAGCAGGGGAGGAAAGA 60.619 60.000 0.00 0.00 0.00 2.52
1015 2517 4.465446 CGGGAGAGCAGGGGAGGA 62.465 72.222 0.00 0.00 0.00 3.71
1067 2569 1.498865 CGCGTGGTCTATTGCCATCC 61.499 60.000 0.00 0.00 38.40 3.51
1117 2619 2.973945 AGAAGATCAGTTTACCGTGGC 58.026 47.619 0.00 0.00 0.00 5.01
1118 2620 4.566004 TCAAGAAGATCAGTTTACCGTGG 58.434 43.478 0.00 0.00 0.00 4.94
1119 2621 5.446473 GCATCAAGAAGATCAGTTTACCGTG 60.446 44.000 0.00 0.00 33.72 4.94
1127 2629 4.942483 CAGGAAAGCATCAAGAAGATCAGT 59.058 41.667 0.00 0.00 33.72 3.41
1130 2632 3.946558 AGCAGGAAAGCATCAAGAAGATC 59.053 43.478 0.00 0.00 33.72 2.75
1131 2633 3.695060 CAGCAGGAAAGCATCAAGAAGAT 59.305 43.478 0.00 0.00 37.48 2.40
1133 2635 2.415625 GCAGCAGGAAAGCATCAAGAAG 60.416 50.000 0.00 0.00 36.85 2.85
1135 2637 1.171308 GCAGCAGGAAAGCATCAAGA 58.829 50.000 0.00 0.00 36.85 3.02
1138 2640 0.251033 ACAGCAGCAGGAAAGCATCA 60.251 50.000 0.00 0.00 36.85 3.07
1139 2641 0.170561 CACAGCAGCAGGAAAGCATC 59.829 55.000 0.00 0.00 36.85 3.91
1140 2642 0.538977 ACACAGCAGCAGGAAAGCAT 60.539 50.000 0.00 0.00 36.85 3.79
1143 2645 1.952296 AGAAACACAGCAGCAGGAAAG 59.048 47.619 0.00 0.00 0.00 2.62
1148 2650 1.002033 GACCAAGAAACACAGCAGCAG 60.002 52.381 0.00 0.00 0.00 4.24
1151 2653 1.876156 GAGGACCAAGAAACACAGCAG 59.124 52.381 0.00 0.00 0.00 4.24
1154 2656 2.135933 GTCGAGGACCAAGAAACACAG 58.864 52.381 0.00 0.00 0.00 3.66
1168 2681 1.740285 CCATTAGGACCGGTCGAGG 59.260 63.158 27.68 19.24 36.89 4.63
1200 2713 0.664166 CACGCCCAACATTGCAGTTC 60.664 55.000 0.00 0.00 0.00 3.01
1237 2750 4.689549 TTCCCCGCCTCCTCGTCA 62.690 66.667 0.00 0.00 0.00 4.35
1534 3272 4.207281 TCCGAATCTGCTCCCGCG 62.207 66.667 0.00 0.00 39.65 6.46
1535 3273 2.279784 CTCCGAATCTGCTCCCGC 60.280 66.667 0.00 0.00 0.00 6.13
1836 3579 0.528684 CGATCTGCGGGGAAGAAGAC 60.529 60.000 0.00 0.00 36.03 3.01
1843 3586 3.224324 GCCTACGATCTGCGGGGA 61.224 66.667 0.00 0.00 46.49 4.81
1872 3619 4.388499 TTCTTCCTCGGCCGGTGC 62.388 66.667 27.83 0.00 0.00 5.01
1905 3664 2.668212 TTCTTCTTGCCACCGCCG 60.668 61.111 0.00 0.00 0.00 6.46
1906 3665 1.301677 CTCTTCTTCTTGCCACCGCC 61.302 60.000 0.00 0.00 0.00 6.13
1907 3666 0.320771 TCTCTTCTTCTTGCCACCGC 60.321 55.000 0.00 0.00 0.00 5.68
1908 3667 1.719600 CTCTCTTCTTCTTGCCACCG 58.280 55.000 0.00 0.00 0.00 4.94
1909 3668 1.447945 GCTCTCTTCTTCTTGCCACC 58.552 55.000 0.00 0.00 0.00 4.61
1910 3669 1.074752 CGCTCTCTTCTTCTTGCCAC 58.925 55.000 0.00 0.00 0.00 5.01
1911 3670 0.036952 CCGCTCTCTTCTTCTTGCCA 60.037 55.000 0.00 0.00 0.00 4.92
1912 3671 1.365368 GCCGCTCTCTTCTTCTTGCC 61.365 60.000 0.00 0.00 0.00 4.52
1913 3672 1.691215 CGCCGCTCTCTTCTTCTTGC 61.691 60.000 0.00 0.00 0.00 4.01
1914 3673 1.080995 CCGCCGCTCTCTTCTTCTTG 61.081 60.000 0.00 0.00 0.00 3.02
1997 3756 4.687215 TCTGCACCACGCTGCTCC 62.687 66.667 0.00 0.00 43.06 4.70
2307 4076 4.081697 GGTTTTACCGGTGGTAACTAGCTA 60.082 45.833 19.93 0.00 46.28 3.32
2308 4077 3.306989 GGTTTTACCGGTGGTAACTAGCT 60.307 47.826 19.93 0.00 46.28 3.32
2330 4099 2.744787 ACAGTATAACGGACGCTACG 57.255 50.000 0.00 0.00 37.36 3.51
2338 4107 6.237755 GCTGCAAGTTACTTACAGTATAACGG 60.238 42.308 21.90 1.13 37.23 4.44
2339 4108 6.530534 AGCTGCAAGTTACTTACAGTATAACG 59.469 38.462 21.90 1.75 37.23 3.18
2341 4110 7.039882 GGAGCTGCAAGTTACTTACAGTATAA 58.960 38.462 21.90 0.00 37.23 0.98
2342 4111 6.153851 TGGAGCTGCAAGTTACTTACAGTATA 59.846 38.462 21.90 7.91 37.23 1.47
2343 4112 5.046591 TGGAGCTGCAAGTTACTTACAGTAT 60.047 40.000 21.90 13.59 37.23 2.12
2344 4113 4.282449 TGGAGCTGCAAGTTACTTACAGTA 59.718 41.667 21.90 7.91 37.23 2.74
2362 4135 1.132643 ACTTAGTCGTCGTCATGGAGC 59.867 52.381 0.00 0.00 0.00 4.70
2393 4166 3.270877 GGGCATGGAGTTTACTACAGTG 58.729 50.000 0.78 1.63 40.74 3.66
2409 4190 2.651334 AGCCTCATAACCATATGGGCAT 59.349 45.455 25.55 14.60 46.94 4.40
2426 4209 4.021894 CGATCTACTTAGTGCCATAAGCCT 60.022 45.833 0.00 0.00 42.71 4.58
2427 4210 4.238514 CGATCTACTTAGTGCCATAAGCC 58.761 47.826 0.00 0.00 42.71 4.35
2428 4211 4.872664 ACGATCTACTTAGTGCCATAAGC 58.127 43.478 0.00 0.00 44.14 3.09
2430 4213 8.418662 ACATTTACGATCTACTTAGTGCCATAA 58.581 33.333 0.00 0.00 0.00 1.90
2431 4214 7.865889 CACATTTACGATCTACTTAGTGCCATA 59.134 37.037 0.00 0.00 0.00 2.74
2432 4215 6.701841 CACATTTACGATCTACTTAGTGCCAT 59.298 38.462 0.00 0.00 0.00 4.40
2433 4216 6.040247 CACATTTACGATCTACTTAGTGCCA 58.960 40.000 0.00 0.00 0.00 4.92
2434 4217 5.050972 GCACATTTACGATCTACTTAGTGCC 60.051 44.000 12.98 1.04 41.82 5.01
2435 4218 5.050972 GGCACATTTACGATCTACTTAGTGC 60.051 44.000 14.68 14.68 45.54 4.40
2436 4219 5.462398 GGGCACATTTACGATCTACTTAGTG 59.538 44.000 0.00 0.00 0.00 2.74
2437 4220 5.128171 TGGGCACATTTACGATCTACTTAGT 59.872 40.000 0.00 0.00 0.00 2.24
2438 4221 5.597806 TGGGCACATTTACGATCTACTTAG 58.402 41.667 0.00 0.00 0.00 2.18
2439 4222 5.601583 TGGGCACATTTACGATCTACTTA 57.398 39.130 0.00 0.00 0.00 2.24
2440 4223 4.481368 TGGGCACATTTACGATCTACTT 57.519 40.909 0.00 0.00 0.00 2.24
2441 4224 4.689612 ATGGGCACATTTACGATCTACT 57.310 40.909 0.00 0.00 32.00 2.57
2442 4225 5.779922 TCTATGGGCACATTTACGATCTAC 58.220 41.667 6.84 0.00 38.53 2.59
2511 4307 0.787787 CACGTACATGAACACCACCG 59.212 55.000 0.00 0.00 0.00 4.94
2609 4422 0.179078 GAGCCACTCAGCCAGATCAG 60.179 60.000 0.00 0.00 0.00 2.90
2769 4586 3.213402 CCGTCTCTCTCGGGCCTC 61.213 72.222 0.84 0.00 43.68 4.70
2776 4593 3.827898 CACCCCGCCGTCTCTCTC 61.828 72.222 0.00 0.00 0.00 3.20
2786 4603 3.799755 CAGCTAAACGCACCCCGC 61.800 66.667 0.00 0.00 42.61 6.13
2787 4604 2.047655 TCAGCTAAACGCACCCCG 60.048 61.111 0.00 0.00 42.61 5.73
2788 4605 2.388232 CGTCAGCTAAACGCACCCC 61.388 63.158 7.76 0.00 42.61 4.95
2789 4606 2.388232 CCGTCAGCTAAACGCACCC 61.388 63.158 13.75 0.00 42.61 4.61
2790 4607 2.388232 CCCGTCAGCTAAACGCACC 61.388 63.158 13.75 0.00 42.61 5.01
2853 4670 1.529152 TTCCAGAAGCTACCGCACGA 61.529 55.000 0.00 0.00 39.10 4.35
2875 4692 1.596934 ATGCGTCCCATGACTCGTT 59.403 52.632 0.00 0.00 39.47 3.85
3147 4977 0.031716 TGATCCTCTCCCACTCCCTG 60.032 60.000 0.00 0.00 0.00 4.45
3148 4978 0.719015 TTGATCCTCTCCCACTCCCT 59.281 55.000 0.00 0.00 0.00 4.20
3169 5016 1.263484 CATAGCTTGGATGCGCTTGAG 59.737 52.381 9.73 1.30 37.68 3.02
3254 5101 1.943968 GCCGATGCCCTATGCGAATAA 60.944 52.381 0.00 0.00 45.60 1.40
3262 5109 2.279069 CGAGGAGCCGATGCCCTAT 61.279 63.158 0.00 0.00 38.01 2.57
3273 5120 0.737715 ACGAAATGCTGTCGAGGAGC 60.738 55.000 9.06 9.06 41.02 4.70
3307 5154 4.470170 CGGTCGATCGACGTGGCA 62.470 66.667 34.69 4.18 45.41 4.92
3422 5277 2.375766 GCGCGTGTCCAGTGAAGAG 61.376 63.158 8.43 0.00 0.00 2.85
3440 5295 1.093159 GGGAGCAAGCAAGACATCAG 58.907 55.000 0.00 0.00 0.00 2.90
3447 5302 1.183676 AGCAAAGGGGAGCAAGCAAG 61.184 55.000 0.00 0.00 0.00 4.01
3449 5304 0.112218 TTAGCAAAGGGGAGCAAGCA 59.888 50.000 0.00 0.00 0.00 3.91
3450 5305 1.406898 GATTAGCAAAGGGGAGCAAGC 59.593 52.381 0.00 0.00 0.00 4.01
3584 5474 8.062065 AGGTTTTCACAGAGATAAAAACACAA 57.938 30.769 10.58 0.00 41.25 3.33
3593 5483 2.742053 GCGCAAGGTTTTCACAGAGATA 59.258 45.455 0.30 0.00 38.28 1.98
3594 5484 1.537202 GCGCAAGGTTTTCACAGAGAT 59.463 47.619 0.30 0.00 38.28 2.75
3601 5491 1.064946 CAACGGCGCAAGGTTTTCA 59.935 52.632 10.83 0.00 38.28 2.69
3612 5509 2.365068 CGTCTCACTGACAACGGCG 61.365 63.158 4.80 4.80 45.60 6.46
3616 5513 2.493713 AGTCACGTCTCACTGACAAC 57.506 50.000 4.66 0.00 45.60 3.32


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

AutoCloner maintained by Alex Coulton.