Multiple sequence alignment - TraesCS6A01G130100

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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 TraesCS6A01G130100 chr6A 100.000 3663 0 0 1 3663 101857540 101861202 0.000000e+00 6765.0
1 TraesCS6A01G130100 chr6A 77.947 263 55 3 3379 3638 478311407 478311145 1.050000e-35 161.0
2 TraesCS6A01G130100 chr6D 92.276 1696 99 20 1982 3663 84649014 84650691 0.000000e+00 2377.0
3 TraesCS6A01G130100 chr6D 94.615 947 47 4 784 1729 84647935 84648878 0.000000e+00 1463.0
4 TraesCS6A01G130100 chr6D 94.211 950 45 7 784 1729 85626632 85625689 0.000000e+00 1441.0
5 TraesCS6A01G130100 chr6D 93.417 957 54 6 1982 2932 85625559 85624606 0.000000e+00 1410.0
6 TraesCS6A01G130100 chr6D 91.565 735 56 5 2930 3663 85612151 85611422 0.000000e+00 1009.0
7 TraesCS6A01G130100 chr6D 89.308 636 47 11 1 627 85631933 85631310 0.000000e+00 778.0
8 TraesCS6A01G130100 chr6D 90.391 281 23 3 1 280 84647364 84647641 2.080000e-97 366.0
9 TraesCS6A01G130100 chr6D 87.500 200 15 4 433 624 84647638 84647835 4.760000e-54 222.0
10 TraesCS6A01G130100 chr6D 88.333 180 17 4 1 179 254962072 254962248 2.870000e-51 213.0
11 TraesCS6A01G130100 chr6D 80.000 175 26 7 226 396 462527446 462527615 1.790000e-23 121.0
12 TraesCS6A01G130100 chr6B 93.333 1080 66 2 1976 3049 160899993 160901072 0.000000e+00 1591.0
13 TraesCS6A01G130100 chr6B 94.937 948 43 3 784 1729 160899049 160899993 0.000000e+00 1480.0
14 TraesCS6A01G130100 chr6B 92.077 568 43 2 3097 3663 160901071 160901637 0.000000e+00 798.0
15 TraesCS6A01G130100 chr6B 82.288 813 129 9 784 1585 31016443 31015635 0.000000e+00 689.0
16 TraesCS6A01G130100 chr6B 81.550 813 135 9 784 1585 31513137 31513945 0.000000e+00 656.0
17 TraesCS6A01G130100 chr6B 92.691 301 11 2 344 633 160898649 160898949 1.220000e-114 424.0
18 TraesCS6A01G130100 chr6B 80.460 174 22 9 226 393 705154770 705154937 4.970000e-24 122.0
19 TraesCS6A01G130100 chrUn 83.560 809 118 9 784 1581 95188124 95188928 0.000000e+00 743.0
20 TraesCS6A01G130100 chr5D 80.277 867 132 29 874 1720 520839463 520840310 5.200000e-173 617.0
21 TraesCS6A01G130100 chr5D 81.946 709 109 17 871 1569 520805300 520805999 1.900000e-162 582.0
22 TraesCS6A01G130100 chr5D 76.849 622 130 9 2042 2650 520840583 520841203 4.530000e-89 339.0
23 TraesCS6A01G130100 chr5D 86.161 224 28 3 1738 1959 142316623 142316401 4.730000e-59 239.0
24 TraesCS6A01G130100 chr5D 84.444 180 26 2 1 179 495139931 495140109 3.760000e-40 176.0
25 TraesCS6A01G130100 chr5D 76.277 274 53 11 3380 3647 469430367 469430634 6.380000e-28 135.0
26 TraesCS6A01G130100 chr5D 100.000 29 0 0 151 179 445883129 445883157 2.000000e-03 54.7
27 TraesCS6A01G130100 chr5A 79.698 862 147 21 876 1715 649365194 649366049 6.770000e-167 597.0
28 TraesCS6A01G130100 chr5B 76.603 624 134 8 2042 2653 656727376 656727999 2.110000e-87 333.0
29 TraesCS6A01G130100 chr5B 78.922 204 38 3 225 426 557279607 557279407 2.290000e-27 134.0
30 TraesCS6A01G130100 chr1A 86.301 219 27 3 1745 1961 311326846 311327063 6.120000e-58 235.0
31 TraesCS6A01G130100 chr2B 85.398 226 30 3 1738 1961 464096264 464096040 7.910000e-57 231.0
32 TraesCS6A01G130100 chr2A 85.217 230 29 4 1734 1961 9106951 9107177 7.910000e-57 231.0
33 TraesCS6A01G130100 chr2A 84.444 180 24 4 1 179 588996744 588996920 1.350000e-39 174.0
34 TraesCS6A01G130100 chr7D 85.022 227 28 6 1738 1961 210446721 210446498 3.680000e-55 226.0
35 TraesCS6A01G130100 chr7D 84.615 234 28 8 1738 1967 312351334 312351105 3.680000e-55 226.0
36 TraesCS6A01G130100 chr2D 84.549 233 30 6 1738 1967 5870570 5870341 3.680000e-55 226.0
37 TraesCS6A01G130100 chr2D 78.277 267 52 5 3382 3644 159596173 159596437 2.260000e-37 167.0
38 TraesCS6A01G130100 chr1D 84.279 229 33 3 1735 1961 175169324 175169551 1.710000e-53 220.0
39 TraesCS6A01G130100 chr1D 86.000 200 22 6 1 197 10034307 10034111 3.710000e-50 209.0
40 TraesCS6A01G130100 chr1D 85.500 200 23 6 1 197 9928304 9928500 1.720000e-48 204.0
41 TraesCS6A01G130100 chr4B 83.333 240 36 4 1735 1971 625913565 625913803 6.160000e-53 219.0
42 TraesCS6A01G130100 chr1B 84.656 189 23 6 1 186 216522587 216522402 2.250000e-42 183.0
43 TraesCS6A01G130100 chr1B 77.941 272 55 5 3379 3647 297454944 297455213 8.140000e-37 165.0
44 TraesCS6A01G130100 chr1B 78.873 213 43 2 3379 3589 669074732 669074944 3.810000e-30 143.0
45 TraesCS6A01G130100 chr3D 84.530 181 23 4 1 179 580329597 580329774 1.350000e-39 174.0
46 TraesCS6A01G130100 chr3A 77.528 267 54 4 3376 3637 496047424 496047689 4.900000e-34 156.0


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 TraesCS6A01G130100 chr6A 101857540 101861202 3662 False 6765.00 6765 100.0000 1 3663 1 chr6A.!!$F1 3662
1 TraesCS6A01G130100 chr6D 85624606 85626632 2026 True 1425.50 1441 93.8140 784 2932 2 chr6D.!!$R3 2148
2 TraesCS6A01G130100 chr6D 84647364 84650691 3327 False 1107.00 2377 91.1955 1 3663 4 chr6D.!!$F3 3662
3 TraesCS6A01G130100 chr6D 85611422 85612151 729 True 1009.00 1009 91.5650 2930 3663 1 chr6D.!!$R1 733
4 TraesCS6A01G130100 chr6D 85631310 85631933 623 True 778.00 778 89.3080 1 627 1 chr6D.!!$R2 626
5 TraesCS6A01G130100 chr6B 160898649 160901637 2988 False 1073.25 1591 93.2595 344 3663 4 chr6B.!!$F3 3319
6 TraesCS6A01G130100 chr6B 31015635 31016443 808 True 689.00 689 82.2880 784 1585 1 chr6B.!!$R1 801
7 TraesCS6A01G130100 chr6B 31513137 31513945 808 False 656.00 656 81.5500 784 1585 1 chr6B.!!$F1 801
8 TraesCS6A01G130100 chrUn 95188124 95188928 804 False 743.00 743 83.5600 784 1581 1 chrUn.!!$F1 797
9 TraesCS6A01G130100 chr5D 520805300 520805999 699 False 582.00 582 81.9460 871 1569 1 chr5D.!!$F4 698
10 TraesCS6A01G130100 chr5D 520839463 520841203 1740 False 478.00 617 78.5630 874 2650 2 chr5D.!!$F5 1776
11 TraesCS6A01G130100 chr5A 649365194 649366049 855 False 597.00 597 79.6980 876 1715 1 chr5A.!!$F1 839
12 TraesCS6A01G130100 chr5B 656727376 656727999 623 False 333.00 333 76.6030 2042 2653 1 chr5B.!!$F1 611

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
735 748 0.032416 GGGAGGGTCCAGTACTGCTA 60.032 60.0 17.86 4.69 38.64 3.49 F
1657 1726 0.094216 CTTCGTTGATGTGCTGCTCG 59.906 55.0 0.00 0.00 0.00 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2132 2261 0.182775 ACCTCGGCTTGAAGTTTGGT 59.817 50.0 0.0 0.0 0.0 3.67 R
3025 3175 0.251916 TGCCGGTAGAAAGGATGGTG 59.748 55.0 1.9 0.0 0.0 4.17 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
43 44 8.786937 ATATTCACGATTTCAAATATGTGCAC 57.213 30.769 10.75 10.75 0.00 4.57
98 99 5.576447 TTGACAGCGATAGTGTATCTTCA 57.424 39.130 0.00 0.00 39.35 3.02
110 111 4.945543 AGTGTATCTTCATGATGCAGCAAA 59.054 37.500 9.54 0.00 45.85 3.68
113 114 6.198403 GTGTATCTTCATGATGCAGCAAAATG 59.802 38.462 9.54 2.64 45.85 2.32
122 123 1.001068 TGCAGCAAAATGTGGTCATGG 59.999 47.619 0.00 0.00 35.13 3.66
190 192 8.517056 GGCCTTTTTGCTAGTTAGTAAATAACA 58.483 33.333 0.00 0.00 45.34 2.41
227 229 7.555554 AGCATTGTCTTATGTTGAAGATAAGCT 59.444 33.333 15.06 7.54 39.14 3.74
239 241 8.311109 TGTTGAAGATAAGCTACATGTAAGTCA 58.689 33.333 7.06 0.00 0.00 3.41
240 242 8.812329 GTTGAAGATAAGCTACATGTAAGTCAG 58.188 37.037 7.06 0.00 0.00 3.51
243 245 6.276847 AGATAAGCTACATGTAAGTCAGCAC 58.723 40.000 17.50 7.70 34.65 4.40
259 261 5.925969 AGTCAGCACGAAAATTTATTTTGGG 59.074 36.000 12.49 5.55 39.86 4.12
276 278 3.149005 TGGGTAAGTCGATTTTTGGCT 57.851 42.857 0.00 0.00 0.00 4.75
298 300 8.598916 TGGCTATTATATTAAAGATCCAACGGA 58.401 33.333 0.00 0.00 35.55 4.69
309 311 4.911390 AGATCCAACGGATGTTCTTCTTT 58.089 39.130 0.00 0.00 43.27 2.52
310 312 4.938226 AGATCCAACGGATGTTCTTCTTTC 59.062 41.667 0.00 0.00 43.27 2.62
311 313 4.351874 TCCAACGGATGTTCTTCTTTCT 57.648 40.909 0.00 0.00 35.72 2.52
312 314 4.714632 TCCAACGGATGTTCTTCTTTCTT 58.285 39.130 0.00 0.00 35.72 2.52
313 315 4.755123 TCCAACGGATGTTCTTCTTTCTTC 59.245 41.667 0.00 0.00 35.72 2.87
314 316 4.757149 CCAACGGATGTTCTTCTTTCTTCT 59.243 41.667 0.00 0.00 35.72 2.85
315 317 5.239525 CCAACGGATGTTCTTCTTTCTTCTT 59.760 40.000 0.00 0.00 35.72 2.52
320 322 5.645929 GGATGTTCTTCTTTCTTCTTCCTCC 59.354 44.000 0.00 0.00 0.00 4.30
336 338 1.632920 CCTCCAGCTTTCTTCCTCCTT 59.367 52.381 0.00 0.00 0.00 3.36
337 339 2.355615 CCTCCAGCTTTCTTCCTCCTTC 60.356 54.545 0.00 0.00 0.00 3.46
341 343 3.693578 CCAGCTTTCTTCCTCCTTCATTC 59.306 47.826 0.00 0.00 0.00 2.67
342 344 4.330250 CAGCTTTCTTCCTCCTTCATTCA 58.670 43.478 0.00 0.00 0.00 2.57
372 374 6.265876 TCCTTCCACAAAATTAACTTACCCAC 59.734 38.462 0.00 0.00 0.00 4.61
458 464 3.562505 GCAGGTGGATAAGATACGTACG 58.437 50.000 15.01 15.01 0.00 3.67
461 467 5.683859 CAGGTGGATAAGATACGTACGTAC 58.316 45.833 28.99 21.22 33.01 3.67
513 519 4.020218 TCGATGGAGAAATTCAAGTCCACT 60.020 41.667 4.82 0.00 41.88 4.00
516 522 5.560722 TGGAGAAATTCAAGTCCACTACA 57.439 39.130 0.00 0.00 34.03 2.74
525 531 5.266733 TCAAGTCCACTACAACTAAACGT 57.733 39.130 0.00 0.00 0.00 3.99
545 551 3.142174 GTTGAACAGAAGTGGAGAAGGG 58.858 50.000 0.00 0.00 0.00 3.95
633 646 4.897509 TGGTCAGAAGATCACAGTGATT 57.102 40.909 17.43 3.17 37.20 2.57
634 647 4.825422 TGGTCAGAAGATCACAGTGATTC 58.175 43.478 17.43 12.42 37.20 2.52
635 648 4.529769 TGGTCAGAAGATCACAGTGATTCT 59.470 41.667 17.43 14.41 37.20 2.40
636 649 5.108517 GGTCAGAAGATCACAGTGATTCTC 58.891 45.833 17.43 15.45 37.20 2.87
637 650 5.105392 GGTCAGAAGATCACAGTGATTCTCT 60.105 44.000 17.43 17.21 37.20 3.10
638 651 5.806502 GTCAGAAGATCACAGTGATTCTCTG 59.193 44.000 29.54 29.54 41.85 3.35
639 652 5.479724 TCAGAAGATCACAGTGATTCTCTGT 59.520 40.000 31.40 14.10 45.43 3.41
640 653 6.660949 TCAGAAGATCACAGTGATTCTCTGTA 59.339 38.462 31.40 23.19 43.14 2.74
641 654 6.751425 CAGAAGATCACAGTGATTCTCTGTAC 59.249 42.308 28.35 13.57 43.14 2.90
642 655 6.663093 AGAAGATCACAGTGATTCTCTGTACT 59.337 38.462 17.43 14.80 43.14 2.73
643 656 6.449635 AGATCACAGTGATTCTCTGTACTC 57.550 41.667 17.43 16.53 43.14 2.59
644 657 4.686839 TCACAGTGATTCTCTGTACTCG 57.313 45.455 18.22 8.68 43.14 4.18
645 658 4.324267 TCACAGTGATTCTCTGTACTCGA 58.676 43.478 18.22 10.50 43.14 4.04
646 659 4.944317 TCACAGTGATTCTCTGTACTCGAT 59.056 41.667 18.22 0.00 43.14 3.59
667 680 1.813178 CACTCTTCTCGACCAGCTACA 59.187 52.381 0.00 0.00 0.00 2.74
668 681 2.229062 CACTCTTCTCGACCAGCTACAA 59.771 50.000 0.00 0.00 0.00 2.41
669 682 2.891580 ACTCTTCTCGACCAGCTACAAA 59.108 45.455 0.00 0.00 0.00 2.83
670 683 3.511934 ACTCTTCTCGACCAGCTACAAAT 59.488 43.478 0.00 0.00 0.00 2.32
671 684 4.705507 ACTCTTCTCGACCAGCTACAAATA 59.294 41.667 0.00 0.00 0.00 1.40
672 685 4.995124 TCTTCTCGACCAGCTACAAATAC 58.005 43.478 0.00 0.00 0.00 1.89
673 686 3.416119 TCTCGACCAGCTACAAATACG 57.584 47.619 0.00 0.00 0.00 3.06
674 687 3.011818 TCTCGACCAGCTACAAATACGA 58.988 45.455 0.00 0.00 0.00 3.43
675 688 3.064958 TCTCGACCAGCTACAAATACGAG 59.935 47.826 0.00 0.00 44.36 4.18
676 689 2.751259 TCGACCAGCTACAAATACGAGT 59.249 45.455 0.00 0.00 0.00 4.18
677 690 3.940852 TCGACCAGCTACAAATACGAGTA 59.059 43.478 0.00 0.00 0.00 2.59
678 691 4.033684 CGACCAGCTACAAATACGAGTAC 58.966 47.826 0.00 0.00 0.00 2.73
679 692 4.437794 CGACCAGCTACAAATACGAGTACA 60.438 45.833 0.00 0.00 0.00 2.90
680 693 5.589192 GACCAGCTACAAATACGAGTACAT 58.411 41.667 0.00 0.00 0.00 2.29
681 694 5.974108 ACCAGCTACAAATACGAGTACATT 58.026 37.500 0.00 0.00 0.00 2.71
682 695 6.403878 ACCAGCTACAAATACGAGTACATTT 58.596 36.000 0.00 0.00 0.00 2.32
683 696 7.549839 ACCAGCTACAAATACGAGTACATTTA 58.450 34.615 0.00 0.00 0.00 1.40
684 697 8.036575 ACCAGCTACAAATACGAGTACATTTAA 58.963 33.333 0.00 0.00 0.00 1.52
685 698 8.325997 CCAGCTACAAATACGAGTACATTTAAC 58.674 37.037 0.00 0.00 0.00 2.01
686 699 9.084164 CAGCTACAAATACGAGTACATTTAACT 57.916 33.333 0.00 0.00 0.00 2.24
687 700 9.649167 AGCTACAAATACGAGTACATTTAACTT 57.351 29.630 0.00 0.00 0.00 2.66
724 737 0.901580 TACGACACCAAGGGAGGGTC 60.902 60.000 0.00 0.00 36.19 4.46
726 739 1.846124 GACACCAAGGGAGGGTCCA 60.846 63.158 0.00 0.00 38.64 4.02
727 740 1.842381 GACACCAAGGGAGGGTCCAG 61.842 65.000 0.00 0.00 38.64 3.86
728 741 1.847968 CACCAAGGGAGGGTCCAGT 60.848 63.158 0.00 0.00 38.64 4.00
730 743 0.546988 ACCAAGGGAGGGTCCAGTAC 60.547 60.000 0.00 0.00 38.64 2.73
731 744 0.252742 CCAAGGGAGGGTCCAGTACT 60.253 60.000 0.00 0.00 38.64 2.73
732 745 0.905357 CAAGGGAGGGTCCAGTACTG 59.095 60.000 16.34 16.34 38.64 2.74
733 746 0.910088 AAGGGAGGGTCCAGTACTGC 60.910 60.000 17.86 4.63 38.64 4.40
734 747 1.306226 GGGAGGGTCCAGTACTGCT 60.306 63.158 17.86 8.86 38.64 4.24
735 748 0.032416 GGGAGGGTCCAGTACTGCTA 60.032 60.000 17.86 4.69 38.64 3.49
736 749 1.112950 GGAGGGTCCAGTACTGCTAC 58.887 60.000 17.86 16.11 36.28 3.58
737 750 0.739561 GAGGGTCCAGTACTGCTACG 59.260 60.000 17.86 3.92 0.00 3.51
738 751 1.141234 GGGTCCAGTACTGCTACGC 59.859 63.158 17.86 19.36 0.00 4.42
739 752 1.226603 GGTCCAGTACTGCTACGCG 60.227 63.158 17.86 3.53 0.00 6.01
740 753 1.872679 GTCCAGTACTGCTACGCGC 60.873 63.158 17.86 0.00 39.77 6.86
741 754 2.044555 TCCAGTACTGCTACGCGCT 61.045 57.895 17.86 0.00 40.11 5.92
742 755 0.745486 TCCAGTACTGCTACGCGCTA 60.745 55.000 17.86 0.00 40.11 4.26
743 756 0.317103 CCAGTACTGCTACGCGCTAG 60.317 60.000 17.86 8.71 40.11 3.42
744 757 0.377554 CAGTACTGCTACGCGCTAGT 59.622 55.000 10.54 8.23 40.11 2.57
745 758 1.596260 CAGTACTGCTACGCGCTAGTA 59.404 52.381 10.54 7.15 40.11 1.82
746 759 1.596727 AGTACTGCTACGCGCTAGTAC 59.403 52.381 23.57 23.57 44.48 2.73
747 760 1.328680 GTACTGCTACGCGCTAGTACA 59.671 52.381 24.91 12.96 44.08 2.90
748 761 0.806868 ACTGCTACGCGCTAGTACAA 59.193 50.000 5.73 0.00 40.11 2.41
749 762 1.189403 CTGCTACGCGCTAGTACAAC 58.811 55.000 5.73 0.00 40.11 3.32
750 763 0.806868 TGCTACGCGCTAGTACAACT 59.193 50.000 5.73 0.00 40.11 3.16
751 764 2.009051 TGCTACGCGCTAGTACAACTA 58.991 47.619 5.73 0.00 40.11 2.24
760 773 2.133281 TAGTACAACTAGAGCCGGCA 57.867 50.000 31.54 7.07 0.00 5.69
802 836 7.004691 TGCTACCACTATTGCTCTATCTCTTA 58.995 38.462 0.00 0.00 0.00 2.10
844 884 3.353836 CGGGCAACAACCACGAGG 61.354 66.667 0.00 0.00 39.06 4.63
1450 1498 4.383602 CGTTTGGCGGGTTCAGCG 62.384 66.667 0.00 0.00 36.85 5.18
1601 1667 2.985847 GGCACAGGAGCAACACCC 60.986 66.667 0.00 0.00 35.83 4.61
1629 1698 4.628766 CACGATCAGCAAGAAGATCAAGAA 59.371 41.667 0.00 0.00 40.45 2.52
1630 1699 4.869297 ACGATCAGCAAGAAGATCAAGAAG 59.131 41.667 0.00 0.00 40.45 2.85
1631 1700 5.107824 CGATCAGCAAGAAGATCAAGAAGA 58.892 41.667 0.00 0.00 40.45 2.87
1644 1713 4.920640 TCAAGAAGAGACAGACTTCGTT 57.079 40.909 0.00 0.00 45.51 3.85
1653 1722 2.138320 ACAGACTTCGTTGATGTGCTG 58.862 47.619 0.00 0.00 0.00 4.41
1657 1726 0.094216 CTTCGTTGATGTGCTGCTCG 59.906 55.000 0.00 0.00 0.00 5.03
1658 1727 0.319469 TTCGTTGATGTGCTGCTCGA 60.319 50.000 0.00 0.00 0.00 4.04
1670 1739 0.388659 CTGCTCGATCTTCAGGAGGG 59.611 60.000 0.00 0.00 0.00 4.30
1729 1798 6.672266 TGATGGTAAATCTCCTCTCATACC 57.328 41.667 0.00 0.00 34.69 2.73
1730 1799 5.544176 TGATGGTAAATCTCCTCTCATACCC 59.456 44.000 0.00 0.00 33.46 3.69
1731 1800 5.157770 TGGTAAATCTCCTCTCATACCCT 57.842 43.478 0.00 0.00 33.46 4.34
1736 1805 7.455008 GGTAAATCTCCTCTCATACCCTCATAA 59.545 40.741 0.00 0.00 0.00 1.90
1737 1806 9.041354 GTAAATCTCCTCTCATACCCTCATAAT 57.959 37.037 0.00 0.00 0.00 1.28
1739 1808 8.602472 AATCTCCTCTCATACCCTCATAATAC 57.398 38.462 0.00 0.00 0.00 1.89
1742 1811 6.875469 TCCTCTCATACCCTCATAATACCTT 58.125 40.000 0.00 0.00 0.00 3.50
1744 1813 7.235606 TCCTCTCATACCCTCATAATACCTTTG 59.764 40.741 0.00 0.00 0.00 2.77
1745 1814 7.016661 CCTCTCATACCCTCATAATACCTTTGT 59.983 40.741 0.00 0.00 0.00 2.83
1746 1815 7.963532 TCTCATACCCTCATAATACCTTTGTC 58.036 38.462 0.00 0.00 0.00 3.18
1747 1816 7.789831 TCTCATACCCTCATAATACCTTTGTCT 59.210 37.037 0.00 0.00 0.00 3.41
1749 1818 8.210946 TCATACCCTCATAATACCTTTGTCTTG 58.789 37.037 0.00 0.00 0.00 3.02
1751 1820 5.253096 ACCCTCATAATACCTTTGTCTTGGT 59.747 40.000 0.00 0.00 40.12 3.67
1752 1821 6.187682 CCCTCATAATACCTTTGTCTTGGTT 58.812 40.000 0.00 0.00 37.74 3.67
1753 1822 6.663523 CCCTCATAATACCTTTGTCTTGGTTT 59.336 38.462 0.00 0.00 37.74 3.27
1762 1831 6.008331 ACCTTTGTCTTGGTTTATTAGTCCC 58.992 40.000 0.00 0.00 31.62 4.46
1763 1832 6.183361 ACCTTTGTCTTGGTTTATTAGTCCCT 60.183 38.462 0.00 0.00 31.62 4.20
1764 1833 6.719829 CCTTTGTCTTGGTTTATTAGTCCCTT 59.280 38.462 0.00 0.00 0.00 3.95
1765 1834 7.232737 CCTTTGTCTTGGTTTATTAGTCCCTTT 59.767 37.037 0.00 0.00 0.00 3.11
1766 1835 8.541899 TTTGTCTTGGTTTATTAGTCCCTTTT 57.458 30.769 0.00 0.00 0.00 2.27
1767 1836 7.519032 TGTCTTGGTTTATTAGTCCCTTTTG 57.481 36.000 0.00 0.00 0.00 2.44
1770 1839 9.070179 GTCTTGGTTTATTAGTCCCTTTTGTAA 57.930 33.333 0.00 0.00 0.00 2.41
1771 1840 9.816787 TCTTGGTTTATTAGTCCCTTTTGTAAT 57.183 29.630 0.00 0.00 0.00 1.89
1810 1879 9.535878 TTGACCAAATATTTAACTGACAAAACC 57.464 29.630 0.00 0.00 0.00 3.27
1811 1880 8.919145 TGACCAAATATTTAACTGACAAAACCT 58.081 29.630 0.00 0.00 0.00 3.50
1906 1975 8.859156 GTGACATGCACGAATATTTTGTTAATT 58.141 29.630 0.00 0.00 37.83 1.40
1933 2058 9.995003 AAATTTATGGTCAAAATTTAGCACAGA 57.005 25.926 5.06 0.00 42.05 3.41
1941 2066 8.863049 GGTCAAAATTTAGCACAGATTACAATG 58.137 33.333 0.00 0.00 0.00 2.82
1942 2067 8.863049 GTCAAAATTTAGCACAGATTACAATGG 58.137 33.333 0.00 0.00 0.00 3.16
1943 2068 8.801299 TCAAAATTTAGCACAGATTACAATGGA 58.199 29.630 0.00 0.00 0.00 3.41
1946 2071 6.985188 TTTAGCACAGATTACAATGGAGAC 57.015 37.500 0.00 0.00 0.00 3.36
1961 2086 4.715534 TGGAGACAAATAAACCAGGACA 57.284 40.909 0.00 0.00 37.44 4.02
1962 2087 5.055265 TGGAGACAAATAAACCAGGACAA 57.945 39.130 0.00 0.00 37.44 3.18
1963 2088 5.450453 TGGAGACAAATAAACCAGGACAAA 58.550 37.500 0.00 0.00 37.44 2.83
1964 2089 6.074648 TGGAGACAAATAAACCAGGACAAAT 58.925 36.000 0.00 0.00 37.44 2.32
1965 2090 6.015519 TGGAGACAAATAAACCAGGACAAATG 60.016 38.462 0.00 0.00 37.44 2.32
1966 2091 6.015434 GGAGACAAATAAACCAGGACAAATGT 60.015 38.462 0.00 0.00 0.00 2.71
1967 2092 7.360113 AGACAAATAAACCAGGACAAATGTT 57.640 32.000 0.00 0.00 0.00 2.71
1968 2093 7.209475 AGACAAATAAACCAGGACAAATGTTG 58.791 34.615 0.00 0.00 0.00 3.33
1970 2095 8.012957 ACAAATAAACCAGGACAAATGTTGTA 57.987 30.769 0.00 0.00 45.52 2.41
1971 2096 8.646900 ACAAATAAACCAGGACAAATGTTGTAT 58.353 29.630 0.00 0.00 45.52 2.29
1972 2097 8.924691 CAAATAAACCAGGACAAATGTTGTATG 58.075 33.333 0.00 0.00 45.52 2.39
1973 2098 7.775053 ATAAACCAGGACAAATGTTGTATGT 57.225 32.000 0.00 0.00 45.52 2.29
1974 2099 6.478512 AAACCAGGACAAATGTTGTATGTT 57.521 33.333 0.00 0.00 45.52 2.71
1975 2100 5.705609 ACCAGGACAAATGTTGTATGTTC 57.294 39.130 0.00 0.00 45.52 3.18
1976 2101 4.215399 ACCAGGACAAATGTTGTATGTTCG 59.785 41.667 0.00 0.00 45.52 3.95
1977 2102 4.215399 CCAGGACAAATGTTGTATGTTCGT 59.785 41.667 0.00 0.00 45.52 3.85
1978 2103 5.410132 CCAGGACAAATGTTGTATGTTCGTA 59.590 40.000 0.00 0.00 45.52 3.43
1985 2110 3.777478 TGTTGTATGTTCGTAGCTAGCC 58.223 45.455 12.13 0.00 0.00 3.93
2047 2176 4.503910 CTTCAGATCGAACCCATACACAA 58.496 43.478 0.00 0.00 0.00 3.33
2068 2197 1.372004 CATGTTTGTGGCAGGCACG 60.372 57.895 21.33 2.96 0.00 5.34
2132 2261 3.137484 CGAAAGCCGAACCTCATGA 57.863 52.632 0.00 0.00 41.76 3.07
2318 2450 5.049198 TGCGATATCGACGGTTATAAAGTCT 60.049 40.000 28.63 5.57 43.02 3.24
2329 2461 5.176592 GGTTATAAAGTCTCCGCTGAAACT 58.823 41.667 0.00 0.00 0.00 2.66
2417 2552 1.752198 CCGGAGAGGTTTGTGGACA 59.248 57.895 0.00 0.00 34.51 4.02
2461 2602 3.157087 GAGGGATTTTCAGTTTCTGCCA 58.843 45.455 0.00 0.00 0.00 4.92
2482 2623 2.203126 GGAGCTGGGCGAAGGATG 60.203 66.667 0.00 0.00 0.00 3.51
2614 2755 2.816087 GACTGATGTGTTTGGCATGACT 59.184 45.455 0.00 0.00 0.00 3.41
2642 2783 6.309737 GCGTCGGAAAGAGAAGTTATTTCTTA 59.690 38.462 0.00 0.00 46.12 2.10
2672 2815 8.167345 CGAGAATGAGATGTTAATCATGCATAC 58.833 37.037 0.00 0.00 36.31 2.39
2685 2828 9.649167 TTAATCATGCATACTATCTGTCATGAG 57.351 33.333 0.00 0.00 38.87 2.90
2758 2901 3.089284 GTTTTCAAGAGGGTATGTGGGG 58.911 50.000 0.00 0.00 0.00 4.96
2761 2904 2.858644 TCAAGAGGGTATGTGGGGAAT 58.141 47.619 0.00 0.00 0.00 3.01
2788 2931 2.573462 AGGTACTCACATTCTGCCACAT 59.427 45.455 0.00 0.00 0.00 3.21
2851 2994 5.379732 TCAAACGGGTTTTATTGATGGTC 57.620 39.130 0.00 0.00 0.00 4.02
2944 3094 5.047092 CCCATGGTCATTAAGCTTGACTTTT 60.047 40.000 11.73 0.00 42.48 2.27
2945 3095 5.865552 CCATGGTCATTAAGCTTGACTTTTG 59.134 40.000 9.86 7.99 42.48 2.44
2968 3118 4.830826 AAAACATTCGACTCAGTTTCCC 57.169 40.909 0.00 0.00 33.45 3.97
2973 3123 0.538977 TCGACTCAGTTTCCCGGACT 60.539 55.000 0.73 0.00 0.00 3.85
2974 3124 0.109226 CGACTCAGTTTCCCGGACTC 60.109 60.000 0.73 0.00 0.00 3.36
2994 3144 6.209788 GGACTCCACTTATATCCACTCTAAGG 59.790 46.154 0.00 0.00 0.00 2.69
3002 3152 1.919240 TCCACTCTAAGGCTTCGTGA 58.081 50.000 19.52 10.24 0.00 4.35
3049 3199 2.642154 TCCTTTCTACCGGCAAAACA 57.358 45.000 0.00 0.00 0.00 2.83
3050 3200 2.500229 TCCTTTCTACCGGCAAAACAG 58.500 47.619 0.00 0.00 0.00 3.16
3053 3203 1.600023 TTCTACCGGCAAAACAGTGG 58.400 50.000 0.00 0.00 0.00 4.00
3067 3217 1.272648 ACAGTGGCCATGCTAAATGGT 60.273 47.619 9.72 0.00 41.17 3.55
3227 3379 5.627182 TTTACAACTACCTACCACCAACA 57.373 39.130 0.00 0.00 0.00 3.33
3248 3400 4.119862 CAACACTAGAATACATGGGACGG 58.880 47.826 0.00 0.00 0.00 4.79
3277 3429 0.741221 CGCAGCTAAGTTCTCACCCC 60.741 60.000 0.00 0.00 0.00 4.95
3282 3434 3.054802 CAGCTAAGTTCTCACCCCAAGAT 60.055 47.826 0.00 0.00 0.00 2.40
3343 3495 2.303022 ACCCTGAATTGATCTGACGTGT 59.697 45.455 0.00 0.00 0.00 4.49
3365 3517 0.034476 GGCATCAGATCTCGCCATCA 59.966 55.000 18.34 0.00 44.25 3.07
3386 3538 5.375773 TCACAAACAGATGATGAGAAACCA 58.624 37.500 0.00 0.00 0.00 3.67
3403 3555 0.679640 CCATAACCTCAGCGCCCAAA 60.680 55.000 2.29 0.00 0.00 3.28
3528 3681 4.643387 GCCTGAACACCGCCCTGT 62.643 66.667 0.00 0.00 0.00 4.00
3637 3791 3.000819 TGAGGCGAATCCACGGGT 61.001 61.111 0.00 0.00 37.29 5.28
3657 3811 4.083862 GCCGGTGTCCAGAGACCC 62.084 72.222 1.90 0.00 41.33 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 5.061933 GCATCATGAAGATACACTATCGCTG 59.938 44.000 0.00 0.00 40.12 5.18
81 82 5.167121 GCATCATGAAGATACACTATCGCT 58.833 41.667 0.00 0.00 40.12 4.93
82 83 4.925646 TGCATCATGAAGATACACTATCGC 59.074 41.667 0.00 0.00 40.12 4.58
83 84 5.061933 GCTGCATCATGAAGATACACTATCG 59.938 44.000 0.00 0.00 40.12 2.92
98 99 2.563620 TGACCACATTTTGCTGCATCAT 59.436 40.909 1.84 0.00 0.00 2.45
110 111 3.010472 TCTCCAATGACCATGACCACATT 59.990 43.478 0.00 0.00 34.15 2.71
113 114 2.787473 TCTCCAATGACCATGACCAC 57.213 50.000 0.00 0.00 0.00 4.16
146 147 1.415374 CCCGTGTGTTGTAACGAGAG 58.585 55.000 0.00 0.00 42.32 3.20
147 148 0.598158 GCCCGTGTGTTGTAACGAGA 60.598 55.000 0.00 0.00 42.32 4.04
148 149 1.562575 GGCCCGTGTGTTGTAACGAG 61.563 60.000 0.00 0.00 42.32 4.18
149 150 1.594836 GGCCCGTGTGTTGTAACGA 60.595 57.895 0.00 0.00 42.32 3.85
154 156 0.174617 CAAAAAGGCCCGTGTGTTGT 59.825 50.000 0.00 0.00 0.00 3.32
159 161 0.179001 ACTAGCAAAAAGGCCCGTGT 60.179 50.000 0.00 0.00 0.00 4.49
190 192 3.132139 CAATGCTCCGCTGCAGCT 61.132 61.111 34.22 13.71 46.71 4.24
213 215 8.311109 TGACTTACATGTAGCTTATCTTCAACA 58.689 33.333 5.56 0.00 0.00 3.33
227 229 6.795098 AATTTTCGTGCTGACTTACATGTA 57.205 33.333 0.08 0.08 0.00 2.29
229 231 8.673626 AATAAATTTTCGTGCTGACTTACATG 57.326 30.769 0.00 0.00 0.00 3.21
236 238 5.694458 ACCCAAAATAAATTTTCGTGCTGAC 59.306 36.000 0.00 0.00 37.86 3.51
239 241 7.438564 ACTTACCCAAAATAAATTTTCGTGCT 58.561 30.769 0.00 0.00 37.86 4.40
240 242 7.409980 CGACTTACCCAAAATAAATTTTCGTGC 60.410 37.037 0.00 0.00 37.86 5.34
243 245 8.905103 ATCGACTTACCCAAAATAAATTTTCG 57.095 30.769 0.00 0.00 37.86 3.46
296 298 5.645929 GGAGGAAGAAGAAAGAAGAACATCC 59.354 44.000 0.00 0.00 0.00 3.51
298 300 6.192970 TGGAGGAAGAAGAAAGAAGAACAT 57.807 37.500 0.00 0.00 0.00 2.71
309 311 3.008485 GGAAGAAAGCTGGAGGAAGAAGA 59.992 47.826 0.00 0.00 0.00 2.87
310 312 3.008923 AGGAAGAAAGCTGGAGGAAGAAG 59.991 47.826 0.00 0.00 0.00 2.85
311 313 2.982488 AGGAAGAAAGCTGGAGGAAGAA 59.018 45.455 0.00 0.00 0.00 2.52
312 314 2.569404 GAGGAAGAAAGCTGGAGGAAGA 59.431 50.000 0.00 0.00 0.00 2.87
313 315 2.355615 GGAGGAAGAAAGCTGGAGGAAG 60.356 54.545 0.00 0.00 0.00 3.46
314 316 1.630878 GGAGGAAGAAAGCTGGAGGAA 59.369 52.381 0.00 0.00 0.00 3.36
315 317 1.203364 AGGAGGAAGAAAGCTGGAGGA 60.203 52.381 0.00 0.00 0.00 3.71
320 322 4.330250 TGAATGAAGGAGGAAGAAAGCTG 58.670 43.478 0.00 0.00 0.00 4.24
336 338 6.975196 TTTTGTGGAAGGAGAAATGAATGA 57.025 33.333 0.00 0.00 0.00 2.57
337 339 9.709495 TTAATTTTGTGGAAGGAGAAATGAATG 57.291 29.630 0.00 0.00 0.00 2.67
372 374 9.872757 ACGTGTAAGTTGACTAAATTTACAATG 57.127 29.630 7.48 6.60 46.39 2.82
396 398 4.932268 TTTTCCTTCCGCAATAGTTACG 57.068 40.909 0.00 0.00 0.00 3.18
458 464 0.026285 GCGCAACCATGATCACGTAC 59.974 55.000 0.30 0.00 0.00 3.67
461 467 2.404789 GGCGCAACCATGATCACG 59.595 61.111 10.83 0.00 38.86 4.35
516 522 5.180271 TCCACTTCTGTTCAACGTTTAGTT 58.820 37.500 0.00 0.00 45.45 2.24
525 531 2.487265 GCCCTTCTCCACTTCTGTTCAA 60.487 50.000 0.00 0.00 0.00 2.69
545 551 0.869880 GTTTGGAGTTTGGTGCGTGC 60.870 55.000 0.00 0.00 0.00 5.34
601 614 1.273606 CTTCTGACCACGACTGGATGT 59.726 52.381 0.00 0.00 40.55 3.06
633 646 5.092554 AGAAGAGTGATCGAGTACAGAGA 57.907 43.478 0.00 0.00 0.00 3.10
634 647 4.026062 CGAGAAGAGTGATCGAGTACAGAG 60.026 50.000 0.00 0.00 38.72 3.35
635 648 3.866327 CGAGAAGAGTGATCGAGTACAGA 59.134 47.826 0.00 0.00 38.72 3.41
636 649 3.866327 TCGAGAAGAGTGATCGAGTACAG 59.134 47.826 0.00 0.00 40.29 2.74
637 650 3.617706 GTCGAGAAGAGTGATCGAGTACA 59.382 47.826 0.00 0.00 45.25 2.90
638 651 3.001533 GGTCGAGAAGAGTGATCGAGTAC 59.998 52.174 0.00 0.00 45.25 2.73
639 652 3.196463 GGTCGAGAAGAGTGATCGAGTA 58.804 50.000 0.00 0.00 45.25 2.59
640 653 2.011222 GGTCGAGAAGAGTGATCGAGT 58.989 52.381 0.00 0.00 45.25 4.18
641 654 2.010497 TGGTCGAGAAGAGTGATCGAG 58.990 52.381 0.00 0.00 45.25 4.04
642 655 2.010497 CTGGTCGAGAAGAGTGATCGA 58.990 52.381 0.00 0.00 42.71 3.59
643 656 1.532921 GCTGGTCGAGAAGAGTGATCG 60.533 57.143 0.00 0.00 37.79 3.69
644 657 1.748493 AGCTGGTCGAGAAGAGTGATC 59.252 52.381 0.00 0.00 0.00 2.92
645 658 1.846007 AGCTGGTCGAGAAGAGTGAT 58.154 50.000 0.00 0.00 0.00 3.06
646 659 2.085320 GTAGCTGGTCGAGAAGAGTGA 58.915 52.381 0.00 0.00 0.00 3.41
692 705 5.821516 TGGTGTCGTATTTCTGTGTTTTT 57.178 34.783 0.00 0.00 0.00 1.94
693 706 5.220970 CCTTGGTGTCGTATTTCTGTGTTTT 60.221 40.000 0.00 0.00 0.00 2.43
694 707 4.274950 CCTTGGTGTCGTATTTCTGTGTTT 59.725 41.667 0.00 0.00 0.00 2.83
695 708 3.813166 CCTTGGTGTCGTATTTCTGTGTT 59.187 43.478 0.00 0.00 0.00 3.32
696 709 3.399330 CCTTGGTGTCGTATTTCTGTGT 58.601 45.455 0.00 0.00 0.00 3.72
697 710 2.742053 CCCTTGGTGTCGTATTTCTGTG 59.258 50.000 0.00 0.00 0.00 3.66
698 711 2.635915 TCCCTTGGTGTCGTATTTCTGT 59.364 45.455 0.00 0.00 0.00 3.41
699 712 3.262420 CTCCCTTGGTGTCGTATTTCTG 58.738 50.000 0.00 0.00 0.00 3.02
700 713 2.236395 CCTCCCTTGGTGTCGTATTTCT 59.764 50.000 0.00 0.00 0.00 2.52
701 714 2.629051 CCTCCCTTGGTGTCGTATTTC 58.371 52.381 0.00 0.00 0.00 2.17
727 740 8.869365 CTAGTTGTACTAGCGCGTAGCAGTAC 62.869 50.000 22.91 22.91 46.78 2.73
728 741 6.970250 CTAGTTGTACTAGCGCGTAGCAGTA 61.970 48.000 8.43 7.52 46.78 2.74
730 743 3.845303 CTAGTTGTACTAGCGCGTAGCAG 60.845 52.174 8.43 2.25 46.78 4.24
731 744 2.031314 CTAGTTGTACTAGCGCGTAGCA 59.969 50.000 8.43 0.00 46.78 3.49
732 745 2.637595 CTAGTTGTACTAGCGCGTAGC 58.362 52.381 8.43 0.00 44.22 3.58
733 746 3.604314 GCTCTAGTTGTACTAGCGCGTAG 60.604 52.174 8.43 10.89 45.71 3.51
734 747 2.286294 GCTCTAGTTGTACTAGCGCGTA 59.714 50.000 8.43 0.00 45.71 4.42
735 748 1.063764 GCTCTAGTTGTACTAGCGCGT 59.936 52.381 8.43 0.00 45.71 6.01
736 749 1.744374 GCTCTAGTTGTACTAGCGCG 58.256 55.000 11.63 0.00 45.71 6.86
738 751 1.002684 CCGGCTCTAGTTGTACTAGCG 60.003 57.143 8.63 4.61 45.93 4.26
739 752 1.269154 GCCGGCTCTAGTTGTACTAGC 60.269 57.143 22.15 1.81 45.93 3.42
741 754 2.133281 TGCCGGCTCTAGTTGTACTA 57.867 50.000 29.70 0.00 0.00 1.82
742 755 1.263356 TTGCCGGCTCTAGTTGTACT 58.737 50.000 29.70 0.00 0.00 2.73
743 756 1.933853 CATTGCCGGCTCTAGTTGTAC 59.066 52.381 29.70 0.00 0.00 2.90
744 757 1.134521 CCATTGCCGGCTCTAGTTGTA 60.135 52.381 29.70 0.00 0.00 2.41
745 758 0.392998 CCATTGCCGGCTCTAGTTGT 60.393 55.000 29.70 1.21 0.00 3.32
746 759 2.397751 CCATTGCCGGCTCTAGTTG 58.602 57.895 29.70 14.78 0.00 3.16
747 760 4.963878 CCATTGCCGGCTCTAGTT 57.036 55.556 29.70 2.60 0.00 2.24
756 769 4.481112 GTTGAGCCGCCATTGCCG 62.481 66.667 0.00 0.00 0.00 5.69
760 773 1.973281 CACTGGTTGAGCCGCCATT 60.973 57.895 0.00 0.00 41.21 3.16
773 786 2.169352 AGAGCAATAGTGGTAGCACTGG 59.831 50.000 32.44 22.79 35.00 4.00
802 836 2.283532 AGCAGCAGAGGGACGAGT 60.284 61.111 0.00 0.00 0.00 4.18
862 902 2.360350 CCATGGTTGTCCGCTGCT 60.360 61.111 2.57 0.00 36.30 4.24
991 1037 4.166888 GAGGAGCATGAGCCGCCA 62.167 66.667 0.00 0.00 43.56 5.69
1517 1565 4.593956 GTCCCATTTCCTCTTCAACTGAT 58.406 43.478 0.00 0.00 0.00 2.90
1601 1667 0.737367 TTCTTGCTGATCGTGCTCGG 60.737 55.000 8.49 0.00 37.69 4.63
1629 1698 3.858877 GCACATCAACGAAGTCTGTCTCT 60.859 47.826 0.00 0.00 45.00 3.10
1630 1699 2.410053 GCACATCAACGAAGTCTGTCTC 59.590 50.000 0.00 0.00 45.00 3.36
1631 1700 2.036475 AGCACATCAACGAAGTCTGTCT 59.964 45.455 0.00 0.00 45.00 3.41
1644 1713 1.205417 TGAAGATCGAGCAGCACATCA 59.795 47.619 2.38 0.00 0.00 3.07
1653 1722 1.045911 ACCCCTCCTGAAGATCGAGC 61.046 60.000 0.00 0.00 0.00 5.03
1657 1726 3.970640 AGATTGTACCCCTCCTGAAGATC 59.029 47.826 0.00 0.00 0.00 2.75
1658 1727 3.970640 GAGATTGTACCCCTCCTGAAGAT 59.029 47.826 0.00 0.00 0.00 2.40
1670 1739 2.497675 TGCTCTCTGGTGAGATTGTACC 59.502 50.000 4.17 0.00 46.93 3.34
1720 1789 7.967908 ACAAAGGTATTATGAGGGTATGAGAG 58.032 38.462 0.00 0.00 0.00 3.20
1729 1798 7.703058 AAACCAAGACAAAGGTATTATGAGG 57.297 36.000 0.00 0.00 37.07 3.86
1736 1805 7.832685 GGGACTAATAAACCAAGACAAAGGTAT 59.167 37.037 0.00 0.00 37.07 2.73
1737 1806 7.017850 AGGGACTAATAAACCAAGACAAAGGTA 59.982 37.037 0.00 0.00 34.36 3.08
1739 1808 6.246163 AGGGACTAATAAACCAAGACAAAGG 58.754 40.000 0.00 0.00 36.02 3.11
1742 1811 7.562088 ACAAAAGGGACTAATAAACCAAGACAA 59.438 33.333 0.00 0.00 38.49 3.18
1744 1813 7.520451 ACAAAAGGGACTAATAAACCAAGAC 57.480 36.000 0.00 0.00 38.49 3.01
1745 1814 9.816787 ATTACAAAAGGGACTAATAAACCAAGA 57.183 29.630 0.00 0.00 38.49 3.02
1784 1853 9.535878 GGTTTTGTCAGTTAAATATTTGGTCAA 57.464 29.630 11.05 5.57 0.00 3.18
1786 1855 9.758651 AAGGTTTTGTCAGTTAAATATTTGGTC 57.241 29.630 11.05 1.68 0.00 4.02
1865 1934 9.462174 CGTGCATGTCACCAAAATTTATATTAT 57.538 29.630 12.62 0.00 42.69 1.28
1866 1935 8.678199 TCGTGCATGTCACCAAAATTTATATTA 58.322 29.630 5.68 0.00 42.69 0.98
1867 1936 7.542890 TCGTGCATGTCACCAAAATTTATATT 58.457 30.769 5.68 0.00 42.69 1.28
1868 1937 7.094508 TCGTGCATGTCACCAAAATTTATAT 57.905 32.000 5.68 0.00 42.69 0.86
1869 1938 6.502136 TCGTGCATGTCACCAAAATTTATA 57.498 33.333 5.68 0.00 42.69 0.98
1870 1939 5.384063 TCGTGCATGTCACCAAAATTTAT 57.616 34.783 5.68 0.00 42.69 1.40
1871 1940 4.837896 TCGTGCATGTCACCAAAATTTA 57.162 36.364 5.68 0.00 42.69 1.40
1872 1941 3.724508 TCGTGCATGTCACCAAAATTT 57.275 38.095 5.68 0.00 42.69 1.82
1873 1942 3.724508 TTCGTGCATGTCACCAAAATT 57.275 38.095 5.68 0.00 42.69 1.82
1874 1943 3.940209 ATTCGTGCATGTCACCAAAAT 57.060 38.095 5.68 8.52 42.69 1.82
1875 1944 5.384063 AATATTCGTGCATGTCACCAAAA 57.616 34.783 5.68 7.06 42.69 2.44
1876 1945 5.384063 AAATATTCGTGCATGTCACCAAA 57.616 34.783 5.68 8.89 42.69 3.28
1877 1946 5.159925 CAAAATATTCGTGCATGTCACCAA 58.840 37.500 5.68 8.21 42.69 3.67
1878 1947 4.217334 ACAAAATATTCGTGCATGTCACCA 59.783 37.500 5.68 0.32 42.69 4.17
1879 1948 4.732784 ACAAAATATTCGTGCATGTCACC 58.267 39.130 5.68 0.00 42.69 4.02
1880 1949 7.789341 TTAACAAAATATTCGTGCATGTCAC 57.211 32.000 5.68 9.41 42.23 3.67
1881 1950 8.978564 AATTAACAAAATATTCGTGCATGTCA 57.021 26.923 5.68 0.00 0.00 3.58
1915 1984 8.863049 CATTGTAATCTGTGCTAAATTTTGACC 58.137 33.333 3.69 0.00 0.00 4.02
1916 1985 8.863049 CCATTGTAATCTGTGCTAAATTTTGAC 58.137 33.333 3.69 0.67 0.00 3.18
1917 1986 8.801299 TCCATTGTAATCTGTGCTAAATTTTGA 58.199 29.630 3.69 0.00 0.00 2.69
1918 1987 8.984891 TCCATTGTAATCTGTGCTAAATTTTG 57.015 30.769 0.00 0.00 0.00 2.44
1921 2046 7.611467 TGTCTCCATTGTAATCTGTGCTAAATT 59.389 33.333 0.00 0.00 0.00 1.82
1927 2052 5.627499 TTTGTCTCCATTGTAATCTGTGC 57.373 39.130 0.00 0.00 0.00 4.57
1928 2053 9.559958 GTTTATTTGTCTCCATTGTAATCTGTG 57.440 33.333 0.00 0.00 0.00 3.66
1932 2057 8.190784 CCTGGTTTATTTGTCTCCATTGTAATC 58.809 37.037 0.00 0.00 0.00 1.75
1933 2058 7.893302 TCCTGGTTTATTTGTCTCCATTGTAAT 59.107 33.333 0.00 0.00 0.00 1.89
1941 2066 6.015434 ACATTTGTCCTGGTTTATTTGTCTCC 60.015 38.462 0.00 0.00 0.00 3.71
1942 2067 6.981722 ACATTTGTCCTGGTTTATTTGTCTC 58.018 36.000 0.00 0.00 0.00 3.36
1943 2068 6.976934 ACATTTGTCCTGGTTTATTTGTCT 57.023 33.333 0.00 0.00 0.00 3.41
1946 2071 8.924691 CATACAACATTTGTCCTGGTTTATTTG 58.075 33.333 0.00 0.00 44.12 2.32
1949 2074 7.775053 ACATACAACATTTGTCCTGGTTTAT 57.225 32.000 0.00 0.00 44.12 1.40
1953 2078 4.215399 CGAACATACAACATTTGTCCTGGT 59.785 41.667 0.00 0.00 44.12 4.00
1954 2079 4.215399 ACGAACATACAACATTTGTCCTGG 59.785 41.667 0.00 0.00 44.12 4.45
1955 2080 5.356882 ACGAACATACAACATTTGTCCTG 57.643 39.130 0.00 0.00 44.12 3.86
1956 2081 5.121768 GCTACGAACATACAACATTTGTCCT 59.878 40.000 0.00 0.00 44.12 3.85
1957 2082 5.121768 AGCTACGAACATACAACATTTGTCC 59.878 40.000 0.00 0.00 44.12 4.02
1958 2083 6.165659 AGCTACGAACATACAACATTTGTC 57.834 37.500 0.00 0.00 44.12 3.18
1960 2085 6.185399 GCTAGCTACGAACATACAACATTTG 58.815 40.000 7.70 0.00 0.00 2.32
1961 2086 5.293569 GGCTAGCTACGAACATACAACATTT 59.706 40.000 15.72 0.00 0.00 2.32
1962 2087 4.809426 GGCTAGCTACGAACATACAACATT 59.191 41.667 15.72 0.00 0.00 2.71
1963 2088 4.099573 AGGCTAGCTACGAACATACAACAT 59.900 41.667 15.72 0.00 0.00 2.71
1964 2089 3.446161 AGGCTAGCTACGAACATACAACA 59.554 43.478 15.72 0.00 0.00 3.33
1965 2090 4.043037 AGGCTAGCTACGAACATACAAC 57.957 45.455 15.72 0.00 0.00 3.32
1966 2091 6.401047 AATAGGCTAGCTACGAACATACAA 57.599 37.500 15.72 0.00 0.00 2.41
1967 2092 7.362660 CCATAATAGGCTAGCTACGAACATACA 60.363 40.741 15.72 0.00 0.00 2.29
1968 2093 6.973474 CCATAATAGGCTAGCTACGAACATAC 59.027 42.308 15.72 0.00 0.00 2.39
1969 2094 6.662234 ACCATAATAGGCTAGCTACGAACATA 59.338 38.462 15.72 0.00 0.00 2.29
1970 2095 5.480772 ACCATAATAGGCTAGCTACGAACAT 59.519 40.000 15.72 0.00 0.00 2.71
1971 2096 4.831155 ACCATAATAGGCTAGCTACGAACA 59.169 41.667 15.72 0.00 0.00 3.18
1972 2097 5.388408 ACCATAATAGGCTAGCTACGAAC 57.612 43.478 15.72 0.00 0.00 3.95
1973 2098 7.528996 TTTACCATAATAGGCTAGCTACGAA 57.471 36.000 15.72 0.00 0.00 3.85
1974 2099 7.713734 ATTTACCATAATAGGCTAGCTACGA 57.286 36.000 15.72 0.00 0.00 3.43
1975 2100 9.464714 CATATTTACCATAATAGGCTAGCTACG 57.535 37.037 15.72 0.00 0.00 3.51
1976 2101 9.765795 CCATATTTACCATAATAGGCTAGCTAC 57.234 37.037 15.72 0.00 0.00 3.58
1977 2102 9.502035 ACCATATTTACCATAATAGGCTAGCTA 57.498 33.333 15.72 5.54 0.00 3.32
1978 2103 8.393959 ACCATATTTACCATAATAGGCTAGCT 57.606 34.615 15.72 3.22 0.00 3.32
2033 2162 3.334691 ACATGTCTTGTGTATGGGTTCG 58.665 45.455 0.00 0.00 37.11 3.95
2047 2176 0.467844 TGCCTGCCACAAACATGTCT 60.468 50.000 0.00 0.00 0.00 3.41
2068 2197 6.147492 ACTCGAGAACTATGTATGACGTATCC 59.853 42.308 21.68 0.00 0.00 2.59
2132 2261 0.182775 ACCTCGGCTTGAAGTTTGGT 59.817 50.000 0.00 0.00 0.00 3.67
2156 2285 0.758685 TGGCCCTTGGGTGTCTTTTG 60.759 55.000 0.00 0.00 0.00 2.44
2318 2450 0.317160 ATCACACGAGTTTCAGCGGA 59.683 50.000 0.00 0.00 0.00 5.54
2329 2461 1.717113 CAAGCGTTTACGATCACACGA 59.283 47.619 6.44 0.00 43.02 4.35
2427 2568 4.316025 AAATCCCTCCCTTTGAAATCGA 57.684 40.909 0.00 0.00 0.00 3.59
2431 2572 4.814967 ACTGAAAATCCCTCCCTTTGAAA 58.185 39.130 0.00 0.00 0.00 2.69
2461 2602 1.379044 CCTTCGCCCAGCTCCAAAT 60.379 57.895 0.00 0.00 0.00 2.32
2482 2623 2.429250 CCCAAAATTTATCCCGGGACAC 59.571 50.000 29.69 0.00 35.57 3.67
2580 2721 0.979665 ATCAGTCATATCCAGGCCCG 59.020 55.000 0.00 0.00 0.00 6.13
2583 2724 3.482156 ACACATCAGTCATATCCAGGC 57.518 47.619 0.00 0.00 0.00 4.85
2614 2755 3.587797 AACTTCTCTTTCCGACGCATA 57.412 42.857 0.00 0.00 0.00 3.14
2626 2767 7.899648 TCTCGGGATAAGAAATAACTTCTCT 57.100 36.000 0.00 0.00 44.00 3.10
2642 2783 6.425210 TGATTAACATCTCATTCTCGGGAT 57.575 37.500 0.00 0.00 0.00 3.85
2672 2815 6.279123 AGTGCACATAACTCATGACAGATAG 58.721 40.000 21.04 0.00 38.10 2.08
2685 2828 6.721571 TCTAGCTTTACAAGTGCACATAAC 57.278 37.500 21.04 4.20 0.00 1.89
2758 2901 6.276847 CAGAATGTGAGTACCTGGAGTATTC 58.723 44.000 0.00 1.27 38.00 1.75
2761 2904 3.447586 GCAGAATGTGAGTACCTGGAGTA 59.552 47.826 0.00 0.00 39.31 2.59
2788 2931 5.954757 TGGGATGAAGGTTGGTAGTTTTTA 58.045 37.500 0.00 0.00 0.00 1.52
2879 3029 3.683847 GCAAGACTTGATGAGGTAGGCAT 60.684 47.826 19.51 0.00 0.00 4.40
2944 3094 5.220970 GGGAAACTGAGTCGAATGTTTTTCA 60.221 40.000 0.00 0.00 33.49 2.69
2945 3095 5.212934 GGGAAACTGAGTCGAATGTTTTTC 58.787 41.667 0.00 0.00 33.49 2.29
2968 3118 4.145807 AGAGTGGATATAAGTGGAGTCCG 58.854 47.826 4.30 0.00 0.00 4.79
2973 3123 5.716979 AGCCTTAGAGTGGATATAAGTGGA 58.283 41.667 0.00 0.00 31.89 4.02
2974 3124 6.426646 AAGCCTTAGAGTGGATATAAGTGG 57.573 41.667 0.00 0.00 31.89 4.00
2994 3144 3.575965 AATGGTTGGAAATCACGAAGC 57.424 42.857 0.00 0.00 41.54 3.86
3025 3175 0.251916 TGCCGGTAGAAAGGATGGTG 59.748 55.000 1.90 0.00 0.00 4.17
3049 3199 1.477553 CACCATTTAGCATGGCCACT 58.522 50.000 8.16 3.79 42.82 4.00
3050 3200 0.461135 CCACCATTTAGCATGGCCAC 59.539 55.000 8.16 0.00 42.82 5.01
3053 3203 2.618709 GAGTACCACCATTTAGCATGGC 59.381 50.000 1.52 0.00 42.82 4.40
3067 3217 0.251916 CAATCAAGGGCCGAGTACCA 59.748 55.000 0.00 0.00 0.00 3.25
3227 3379 3.431766 GCCGTCCCATGTATTCTAGTGTT 60.432 47.826 0.00 0.00 0.00 3.32
3256 3408 1.351153 GGTGAGAACTTAGCTGCGAC 58.649 55.000 0.00 0.00 0.00 5.19
3259 3411 0.324943 TGGGGTGAGAACTTAGCTGC 59.675 55.000 0.00 0.00 0.00 5.25
3260 3412 2.303022 TCTTGGGGTGAGAACTTAGCTG 59.697 50.000 0.00 0.00 0.00 4.24
3277 3429 6.568869 TGTGTTTTAGGGTTTCAACATCTTG 58.431 36.000 0.00 0.00 32.00 3.02
3282 3434 6.783708 AAGATGTGTTTTAGGGTTTCAACA 57.216 33.333 0.00 0.00 0.00 3.33
3343 3495 3.085208 GGCGAGATCTGATGCCAAA 57.915 52.632 20.09 0.00 46.76 3.28
3365 3517 7.094205 GGTTATGGTTTCTCATCATCTGTTTGT 60.094 37.037 0.00 0.00 0.00 2.83
3386 3538 0.618458 TCTTTGGGCGCTGAGGTTAT 59.382 50.000 7.64 0.00 0.00 1.89
3403 3555 2.988570 ACGTAGATTCCTGTCGTCTCT 58.011 47.619 0.00 0.00 32.24 3.10
3457 3609 0.820074 GAGCTCCGATCCTCCTCGAA 60.820 60.000 0.87 0.00 41.12 3.71
3525 3678 5.001874 GGTTAGGGTTTTTAGTCCTCACAG 58.998 45.833 0.00 0.00 32.46 3.66
3528 3681 7.072834 AGTTTAGGTTAGGGTTTTTAGTCCTCA 59.927 37.037 0.00 0.00 32.46 3.86
3601 3754 2.047465 CTCTGCTTGCCGCTCTGT 60.047 61.111 0.00 0.00 40.11 3.41
3603 3756 3.317571 ACCTCTGCTTGCCGCTCT 61.318 61.111 0.00 0.00 40.11 4.09
3608 3761 2.749441 GCCTCACCTCTGCTTGCC 60.749 66.667 0.00 0.00 0.00 4.52
3620 3774 3.000819 ACCCGTGGATTCGCCTCA 61.001 61.111 0.00 0.00 37.63 3.86
3637 3791 2.117423 TCTCTGGACACCGGCTGA 59.883 61.111 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.