Multiple sequence alignment - TraesCS7B01G241600

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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 TraesCS7B01G241600 chr7B 100.000 4002 0 0 1 4002 449549459 449545458 0.000000e+00 7391.0
1 TraesCS7B01G241600 chr7B 82.119 151 23 4 4 152 246626089 246625941 4.200000e-25 126.0
2 TraesCS7B01G241600 chr7B 100.000 29 0 0 3918 3946 11552198 11552226 2.000000e-03 54.7
3 TraesCS7B01G241600 chr7A 86.916 1926 157 35 535 2405 483964896 483966781 0.000000e+00 2073.0
4 TraesCS7B01G241600 chr7A 92.584 418 25 3 2740 3157 483970898 483971309 2.660000e-166 595.0
5 TraesCS7B01G241600 chr7A 91.089 202 17 1 2506 2707 483966825 483967025 5.100000e-69 272.0
6 TraesCS7B01G241600 chr7A 80.921 152 23 6 4 152 423567831 423567979 9.090000e-22 115.0
7 TraesCS7B01G241600 chr7D 92.968 711 33 4 1698 2401 433070656 433071356 0.000000e+00 1020.0
8 TraesCS7B01G241600 chr7D 93.912 657 31 2 2705 3352 433071657 433072313 0.000000e+00 983.0
9 TraesCS7B01G241600 chr7D 87.995 808 54 21 921 1710 433069832 433070614 0.000000e+00 915.0
10 TraesCS7B01G241600 chr7D 85.913 575 49 16 3431 4002 433072545 433073090 5.760000e-163 584.0
11 TraesCS7B01G241600 chr7D 93.548 186 11 1 2521 2706 433071421 433071605 3.940000e-70 276.0
12 TraesCS7B01G241600 chr7D 80.381 367 36 13 155 495 433068672 433069028 3.090000e-61 246.0
13 TraesCS7B01G241600 chr7D 82.550 298 16 13 592 879 433069181 433069452 3.110000e-56 230.0
14 TraesCS7B01G241600 chr7D 92.308 156 8 4 1 154 433068472 433068625 6.730000e-53 219.0
15 TraesCS7B01G241600 chr5A 89.381 113 9 2 217 326 371679693 371679805 5.390000e-29 139.0
16 TraesCS7B01G241600 chr2A 87.611 113 11 2 217 326 10154219 10154331 1.170000e-25 128.0
17 TraesCS7B01G241600 chr2A 81.481 135 22 3 21 153 723197281 723197148 1.520000e-19 108.0
18 TraesCS7B01G241600 chr2A 97.143 35 1 0 3912 3946 97560911 97560945 4.320000e-05 60.2
19 TraesCS7B01G241600 chr2A 100.000 29 0 0 3918 3946 611047124 611047152 2.000000e-03 54.7
20 TraesCS7B01G241600 chr4A 82.119 151 23 4 4 152 60348501 60348649 4.200000e-25 126.0
21 TraesCS7B01G241600 chr1D 77.487 191 43 0 2038 2228 455766270 455766080 9.090000e-22 115.0
22 TraesCS7B01G241600 chr4D 85.714 63 7 2 3919 3980 546816 546877 9.280000e-07 65.8
23 TraesCS7B01G241600 chr1A 84.127 63 6 3 3918 3979 494152007 494152066 1.550000e-04 58.4
24 TraesCS7B01G241600 chr6B 88.889 45 5 0 3919 3963 687505034 687504990 5.590000e-04 56.5
25 TraesCS7B01G241600 chrUn 100.000 29 0 0 3918 3946 43402883 43402911 2.000000e-03 54.7
26 TraesCS7B01G241600 chr5D 100.000 28 0 0 3919 3946 62480547 62480520 7.000000e-03 52.8


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 TraesCS7B01G241600 chr7B 449545458 449549459 4001 True 7391.000 7391 100.000000 1 4002 1 chr7B.!!$R2 4001
1 TraesCS7B01G241600 chr7A 483964896 483971309 6413 False 980.000 2073 90.196333 535 3157 3 chr7A.!!$F2 2622
2 TraesCS7B01G241600 chr7D 433068472 433073090 4618 False 559.125 1020 88.696875 1 4002 8 chr7D.!!$F1 4001

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
496 571 0.039035 TGTTTATGACAGGGGTGGCC 59.961 55.0 0.0 0.0 33.4 5.36 F
2026 2626 0.035915 GGCTGTCTTCCTTGTCCTCC 60.036 60.0 0.0 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2408 3008 0.108329 AATAACTGACGTGGCGGAGG 60.108 55.0 0.0 0.0 0.0 4.30 R
3370 7851 0.250727 CACTCTCTTTCCCCCGCAAA 60.251 55.0 0.0 0.0 0.0 3.68 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
64 66 2.877786 TGCTTGTCACATTGTGTACTGG 59.122 45.455 16.06 10.42 34.79 4.00
69 71 3.386402 TGTCACATTGTGTACTGGAGTGA 59.614 43.478 16.06 0.00 34.79 3.41
98 100 8.970691 AATCAGTTGATTAAAAGATTTCACGG 57.029 30.769 5.59 0.00 42.48 4.94
102 105 9.030301 CAGTTGATTAAAAGATTTCACGGTTTT 57.970 29.630 0.00 0.00 0.00 2.43
122 125 7.164803 GGTTTTACAATTGATTGATGGGGAAA 58.835 34.615 13.59 0.00 40.14 3.13
123 126 7.828717 GGTTTTACAATTGATTGATGGGGAAAT 59.171 33.333 13.59 0.00 40.14 2.17
171 220 2.673775 TGCACAATTGAAGGGAGGAA 57.326 45.000 13.59 0.00 0.00 3.36
183 232 9.498039 AATTGAAGGGAGGAATTGAATATCTTT 57.502 29.630 0.00 0.00 0.00 2.52
215 264 9.255029 ACCCATATACTTTATAATTGAATGGCC 57.745 33.333 0.00 0.00 0.00 5.36
221 285 9.959721 ATACTTTATAATTGAATGGCCGATACT 57.040 29.630 0.00 0.00 0.00 2.12
224 288 2.568623 ATTGAATGGCCGATACTCCC 57.431 50.000 0.00 0.00 0.00 4.30
238 302 5.472137 CCGATACTCCCTTGTTTTTCTTTGA 59.528 40.000 0.00 0.00 0.00 2.69
256 320 8.578308 TTCTTTGAAAGAAGCATTACACATTG 57.422 30.769 15.81 0.00 42.31 2.82
294 361 3.766051 TCATCTAGCACAGTCACTCATGT 59.234 43.478 0.00 0.00 0.00 3.21
295 362 3.857549 TCTAGCACAGTCACTCATGTC 57.142 47.619 0.00 0.00 0.00 3.06
313 380 5.306937 TCATGTCTTGTAGACTGGAAGGAAA 59.693 40.000 8.18 0.00 45.27 3.13
316 383 7.496346 TGTCTTGTAGACTGGAAGGAAATAT 57.504 36.000 8.18 0.00 45.27 1.28
367 434 7.698836 AACAAATTCTTGATGTGTACTTTGC 57.301 32.000 0.00 0.00 35.05 3.68
368 435 6.215845 ACAAATTCTTGATGTGTACTTTGCC 58.784 36.000 0.00 0.00 34.33 4.52
371 446 4.032960 TCTTGATGTGTACTTTGCCCAT 57.967 40.909 0.00 0.00 0.00 4.00
384 459 0.963355 TGCCCATAAACCGCCACTTC 60.963 55.000 0.00 0.00 0.00 3.01
388 463 1.737793 CCATAAACCGCCACTTCTCAC 59.262 52.381 0.00 0.00 0.00 3.51
408 483 4.322101 ACGCACGTGACAAAAATCTATC 57.678 40.909 22.23 0.00 0.00 2.08
409 484 3.743911 ACGCACGTGACAAAAATCTATCA 59.256 39.130 22.23 0.00 0.00 2.15
410 485 4.081761 CGCACGTGACAAAAATCTATCAC 58.918 43.478 22.23 0.00 38.46 3.06
411 486 4.143115 CGCACGTGACAAAAATCTATCACT 60.143 41.667 22.23 0.00 39.45 3.41
412 487 5.614668 CGCACGTGACAAAAATCTATCACTT 60.615 40.000 22.23 0.00 39.45 3.16
413 488 6.142817 GCACGTGACAAAAATCTATCACTTT 58.857 36.000 22.23 0.00 39.45 2.66
414 489 6.086765 GCACGTGACAAAAATCTATCACTTTG 59.913 38.462 22.23 0.00 39.45 2.77
415 490 7.351981 CACGTGACAAAAATCTATCACTTTGA 58.648 34.615 10.90 0.00 39.45 2.69
416 491 7.855409 CACGTGACAAAAATCTATCACTTTGAA 59.145 33.333 10.90 0.00 39.45 2.69
417 492 8.070171 ACGTGACAAAAATCTATCACTTTGAAG 58.930 33.333 0.00 0.00 39.45 3.02
418 493 7.535258 CGTGACAAAAATCTATCACTTTGAAGG 59.465 37.037 0.00 0.00 39.45 3.46
419 494 7.327032 GTGACAAAAATCTATCACTTTGAAGGC 59.673 37.037 0.73 0.00 38.72 4.35
431 506 4.211794 CACTTTGAAGGCAATTTTTCGCAT 59.788 37.500 0.00 0.00 33.25 4.73
447 522 1.754803 CGCATAGACCTACCACCTTCA 59.245 52.381 0.00 0.00 0.00 3.02
478 553 7.271223 GTGATCGGTTCAGACAATTTAAACATG 59.729 37.037 0.00 0.00 34.17 3.21
483 558 9.405587 CGGTTCAGACAATTTAAACATGTTTAT 57.594 29.630 27.14 14.82 35.27 1.40
495 570 1.750778 CATGTTTATGACAGGGGTGGC 59.249 52.381 0.00 0.00 42.62 5.01
496 571 0.039035 TGTTTATGACAGGGGTGGCC 59.961 55.000 0.00 0.00 33.40 5.36
497 572 0.683179 GTTTATGACAGGGGTGGCCC 60.683 60.000 0.00 0.00 44.51 5.80
520 595 1.133884 CCTGATGGGCTGATGTGACAT 60.134 52.381 0.00 0.00 0.00 3.06
522 597 3.434024 CCTGATGGGCTGATGTGACATAA 60.434 47.826 0.00 0.00 0.00 1.90
538 613 6.297080 TGACATAATAGTCAACCCCGTTAA 57.703 37.500 0.00 0.00 44.92 2.01
555 630 3.624900 GTTAAGTTTGACCGGCACTTTC 58.375 45.455 0.00 0.00 32.88 2.62
577 670 1.906574 ACGTTATGACATGTGGGACCT 59.093 47.619 1.15 0.00 0.00 3.85
585 678 1.939974 CATGTGGGACCTACATGTCG 58.060 55.000 32.35 15.28 46.37 4.35
588 681 5.843684 CATGTGGGACCTACATGTCGGTC 62.844 56.522 32.35 31.76 46.37 4.79
662 806 0.252284 ACGAACCATCTCCCTGTCCT 60.252 55.000 0.00 0.00 0.00 3.85
667 811 3.993658 ACCATCTCCCTGTCCTATACA 57.006 47.619 0.00 0.00 36.42 2.29
702 846 0.817634 CTTCCTGTGTTCGCCCACAA 60.818 55.000 8.09 0.00 44.25 3.33
760 904 2.428890 ACTGAAATTGTTTGTTCGCCCA 59.571 40.909 0.00 0.00 0.00 5.36
775 929 4.743018 CCACACCAGGGAATGACC 57.257 61.111 0.00 0.00 38.08 4.02
776 930 1.767036 CCACACCAGGGAATGACCA 59.233 57.895 0.00 0.00 41.20 4.02
777 931 0.332632 CCACACCAGGGAATGACCAT 59.667 55.000 0.00 0.00 41.20 3.55
847 1008 1.447489 CAGGAAGCGTCTCCAGCAG 60.447 63.158 0.00 0.00 38.02 4.24
848 1009 1.607756 AGGAAGCGTCTCCAGCAGA 60.608 57.895 0.00 0.00 38.02 4.26
861 1022 2.282040 GCAGAGCACCAACCAGCT 60.282 61.111 0.00 0.00 45.25 4.24
879 1040 4.800993 CCAGCTCGTCAACAACTTATCTAG 59.199 45.833 0.00 0.00 0.00 2.43
882 1043 5.361285 AGCTCGTCAACAACTTATCTAGGAT 59.639 40.000 0.00 0.00 0.00 3.24
885 1046 6.722301 TCGTCAACAACTTATCTAGGATACG 58.278 40.000 0.00 0.00 46.39 3.06
886 1047 6.317140 TCGTCAACAACTTATCTAGGATACGT 59.683 38.462 0.00 0.00 46.39 3.57
887 1048 6.632035 CGTCAACAACTTATCTAGGATACGTC 59.368 42.308 0.00 0.00 46.39 4.34
888 1049 6.916932 GTCAACAACTTATCTAGGATACGTCC 59.083 42.308 0.00 0.00 45.45 4.79
917 1416 0.388263 GTCAACGTCGTCTTCCTCCC 60.388 60.000 0.00 0.00 0.00 4.30
919 1418 2.281295 AACGTCGTCTTCCTCCCCC 61.281 63.158 0.00 0.00 0.00 5.40
940 1439 4.644685 CCCCAAGAAATACATAACACCCTG 59.355 45.833 0.00 0.00 0.00 4.45
946 1461 7.259088 AGAAATACATAACACCCTGAACTCT 57.741 36.000 0.00 0.00 0.00 3.24
948 1463 3.594603 ACATAACACCCTGAACTCTCG 57.405 47.619 0.00 0.00 0.00 4.04
953 1468 1.760613 ACACCCTGAACTCTCGTTTCA 59.239 47.619 0.00 0.00 32.39 2.69
954 1469 2.224066 ACACCCTGAACTCTCGTTTCAG 60.224 50.000 5.30 5.30 32.39 3.02
959 1474 1.618837 TGAACTCTCGTTTCAGGGGAG 59.381 52.381 0.00 0.00 32.39 4.30
976 1491 2.043852 GGAGGAGGAGGCTGTCGA 60.044 66.667 0.00 0.00 0.00 4.20
980 1495 1.216710 GGAGGAGGCTGTCGACTTG 59.783 63.158 17.92 10.70 0.00 3.16
981 1496 1.536943 GGAGGAGGCTGTCGACTTGT 61.537 60.000 17.92 0.00 0.00 3.16
982 1497 0.389166 GAGGAGGCTGTCGACTTGTG 60.389 60.000 17.92 5.67 0.00 3.33
983 1498 1.374758 GGAGGCTGTCGACTTGTGG 60.375 63.158 17.92 3.23 0.00 4.17
992 1514 3.414700 GACTTGTGGAGGCGTGCG 61.415 66.667 0.00 0.00 0.00 5.34
1170 1692 3.276091 CACCGCTTCGTGGCACAA 61.276 61.111 19.09 10.03 44.16 3.33
1337 1875 5.103000 CCGGAGTGAACTTTGATACTAGTG 58.897 45.833 5.39 0.00 0.00 2.74
1346 1884 6.195600 ACTTTGATACTAGTGGTTTTGGGA 57.804 37.500 5.39 0.00 0.00 4.37
1352 1890 6.373216 TGATACTAGTGGTTTTGGGATTTTCG 59.627 38.462 5.39 0.00 0.00 3.46
1360 1898 1.243902 TTGGGATTTTCGTGCAGGTC 58.756 50.000 6.26 0.00 0.00 3.85
1398 1936 3.385079 GATGGTTTTCATCGTCGGAAC 57.615 47.619 0.00 0.00 42.29 3.62
1440 1978 2.034685 TCTATGACCTGCATCACGCTAC 59.965 50.000 0.00 0.00 43.06 3.58
1459 1997 4.381612 GCTACCCTTGGCAAGTTAATTTCC 60.382 45.833 24.57 3.11 0.00 3.13
1471 2009 6.314784 CAAGTTAATTTCCCTTCTTACGCAG 58.685 40.000 0.00 0.00 0.00 5.18
1500 2039 2.827322 TGATTTTTCTGGGGCAGTGATG 59.173 45.455 0.00 0.00 32.61 3.07
1692 2231 1.489649 CATCCCACAGCTTCCTCAGAT 59.510 52.381 0.00 0.00 0.00 2.90
1744 2337 4.907582 GTCACCACTGTAAAATTTACACGC 59.092 41.667 13.93 0.00 0.00 5.34
1763 2356 4.270325 CACGCTTTCTAGCTTGGGTAATAC 59.730 45.833 0.00 0.00 45.51 1.89
1767 2360 5.461407 GCTTTCTAGCTTGGGTAATACGTAC 59.539 44.000 0.00 0.00 44.27 3.67
1768 2361 6.682362 GCTTTCTAGCTTGGGTAATACGTACT 60.682 42.308 0.00 0.00 44.27 2.73
1769 2362 7.469181 GCTTTCTAGCTTGGGTAATACGTACTA 60.469 40.741 0.00 0.00 44.27 1.82
1770 2363 7.880160 TTCTAGCTTGGGTAATACGTACTAA 57.120 36.000 0.00 0.00 32.80 2.24
1771 2364 7.502120 TCTAGCTTGGGTAATACGTACTAAG 57.498 40.000 0.00 0.00 33.61 2.18
1772 2365 7.056635 TCTAGCTTGGGTAATACGTACTAAGT 58.943 38.462 0.00 0.00 33.31 2.24
1773 2366 8.210946 TCTAGCTTGGGTAATACGTACTAAGTA 58.789 37.037 0.00 0.00 33.31 2.24
1779 2372 7.045416 TGGGTAATACGTACTAAGTAGAACGA 58.955 38.462 0.00 0.00 38.64 3.85
1790 2383 5.775701 ACTAAGTAGAACGATGATGGGCTAT 59.224 40.000 0.00 0.00 0.00 2.97
1791 2384 4.792521 AGTAGAACGATGATGGGCTATC 57.207 45.455 3.57 3.57 36.29 2.08
1792 2385 3.511934 AGTAGAACGATGATGGGCTATCC 59.488 47.826 8.48 0.00 34.77 2.59
1863 2456 2.830104 AGAAGTACAACAACGTCACCC 58.170 47.619 0.00 0.00 31.24 4.61
1878 2471 1.000274 TCACCCGAGATGTGATATGCG 60.000 52.381 0.00 0.00 37.80 4.73
1978 2571 1.821753 CTCTGAATCTCTGACACCCGT 59.178 52.381 0.00 0.00 0.00 5.28
2016 2616 1.246056 TGCAATGGCTGGCTGTCTTC 61.246 55.000 2.00 0.00 41.91 2.87
2026 2626 0.035915 GGCTGTCTTCCTTGTCCTCC 60.036 60.000 0.00 0.00 0.00 4.30
2028 2628 1.338579 GCTGTCTTCCTTGTCCTCCTG 60.339 57.143 0.00 0.00 0.00 3.86
2072 2672 1.357137 TTCTGTCATGGTACCTGGCA 58.643 50.000 14.36 14.80 0.00 4.92
2135 2735 1.664649 CTGCGTCGTTCTTCTGCCA 60.665 57.895 0.00 0.00 0.00 4.92
2142 2742 1.343142 TCGTTCTTCTGCCACTGCTTA 59.657 47.619 0.00 0.00 38.71 3.09
2144 2744 2.094894 CGTTCTTCTGCCACTGCTTATG 59.905 50.000 0.00 0.00 38.71 1.90
2229 2829 1.697982 GTGGAGTCCTTGGTAGGTGTT 59.302 52.381 11.33 0.00 42.60 3.32
2256 2856 4.617959 TCAGTTCAGTTACTTTCCGTCTG 58.382 43.478 0.00 0.00 0.00 3.51
2281 2881 8.093307 TGCTATAACTCTGATGATTCCTGAATC 58.907 37.037 11.99 11.99 45.55 2.52
2299 2899 0.894835 TCAAGATCACACAGCCGCTA 59.105 50.000 0.00 0.00 0.00 4.26
2408 3008 9.875691 TGGTATGATGCATAGTTTCATATACTC 57.124 33.333 0.00 0.00 35.46 2.59
2409 3009 9.319143 GGTATGATGCATAGTTTCATATACTCC 57.681 37.037 0.00 0.00 35.46 3.85
2412 3012 7.615403 TGATGCATAGTTTCATATACTCCTCC 58.385 38.462 0.00 0.00 0.00 4.30
2414 3014 4.865365 GCATAGTTTCATATACTCCTCCGC 59.135 45.833 0.00 0.00 0.00 5.54
2415 3015 5.411781 CATAGTTTCATATACTCCTCCGCC 58.588 45.833 0.00 0.00 0.00 6.13
2416 3016 3.305720 AGTTTCATATACTCCTCCGCCA 58.694 45.455 0.00 0.00 0.00 5.69
2417 3017 3.069729 AGTTTCATATACTCCTCCGCCAC 59.930 47.826 0.00 0.00 0.00 5.01
2418 3018 1.244816 TCATATACTCCTCCGCCACG 58.755 55.000 0.00 0.00 0.00 4.94
2420 3020 1.068472 CATATACTCCTCCGCCACGTC 60.068 57.143 0.00 0.00 0.00 4.34
2422 3022 1.384989 ATACTCCTCCGCCACGTCAG 61.385 60.000 0.00 0.00 0.00 3.51
2423 3023 2.759641 TACTCCTCCGCCACGTCAGT 62.760 60.000 0.00 0.00 0.00 3.41
2425 3025 1.592400 CTCCTCCGCCACGTCAGTTA 61.592 60.000 0.00 0.00 0.00 2.24
2428 3028 1.674817 CCTCCGCCACGTCAGTTATTT 60.675 52.381 0.00 0.00 0.00 1.40
2429 3029 1.659098 CTCCGCCACGTCAGTTATTTC 59.341 52.381 0.00 0.00 0.00 2.17
2430 3030 0.725117 CCGCCACGTCAGTTATTTCC 59.275 55.000 0.00 0.00 0.00 3.13
2431 3031 0.368907 CGCCACGTCAGTTATTTCCG 59.631 55.000 0.00 0.00 0.00 4.30
2432 3032 1.717194 GCCACGTCAGTTATTTCCGA 58.283 50.000 0.00 0.00 0.00 4.55
2433 3033 2.070783 GCCACGTCAGTTATTTCCGAA 58.929 47.619 0.00 0.00 0.00 4.30
2434 3034 2.159747 GCCACGTCAGTTATTTCCGAAC 60.160 50.000 0.00 0.00 0.00 3.95
2435 3035 2.091588 CCACGTCAGTTATTTCCGAACG 59.908 50.000 0.00 0.00 31.85 3.95
2436 3036 2.981805 CACGTCAGTTATTTCCGAACGA 59.018 45.455 0.00 0.00 31.85 3.85
2437 3037 3.426191 CACGTCAGTTATTTCCGAACGAA 59.574 43.478 0.00 0.00 31.85 3.85
2438 3038 3.671928 ACGTCAGTTATTTCCGAACGAAG 59.328 43.478 0.00 0.00 31.85 3.79
2439 3039 3.060363 CGTCAGTTATTTCCGAACGAAGG 59.940 47.826 0.00 0.00 31.85 3.46
2445 3045 7.223971 TCAGTTATTTCCGAACGAAGGATTATG 59.776 37.037 0.00 0.00 37.65 1.90
2449 3049 4.459390 TCCGAACGAAGGATTATGTCAA 57.541 40.909 0.00 0.00 31.86 3.18
2453 3053 7.042950 TCCGAACGAAGGATTATGTCAAAATA 58.957 34.615 0.00 0.00 31.86 1.40
2456 3056 8.388103 CGAACGAAGGATTATGTCAAAATAGTT 58.612 33.333 0.00 0.00 0.00 2.24
2490 3090 9.780186 AAATCTTATTAAGAAATACTCCCTCCG 57.220 33.333 10.07 0.00 41.63 4.63
2491 3091 7.909485 TCTTATTAAGAAATACTCCCTCCGT 57.091 36.000 3.60 0.00 33.83 4.69
2492 3092 7.949434 TCTTATTAAGAAATACTCCCTCCGTC 58.051 38.462 3.60 0.00 33.83 4.79
2493 3093 5.548181 ATTAAGAAATACTCCCTCCGTCC 57.452 43.478 0.00 0.00 0.00 4.79
2494 3094 1.790818 AGAAATACTCCCTCCGTCCC 58.209 55.000 0.00 0.00 0.00 4.46
2495 3095 1.291335 AGAAATACTCCCTCCGTCCCT 59.709 52.381 0.00 0.00 0.00 4.20
2496 3096 1.687660 GAAATACTCCCTCCGTCCCTC 59.312 57.143 0.00 0.00 0.00 4.30
2497 3097 0.105607 AATACTCCCTCCGTCCCTCC 60.106 60.000 0.00 0.00 0.00 4.30
2498 3098 1.294426 ATACTCCCTCCGTCCCTCCA 61.294 60.000 0.00 0.00 0.00 3.86
2499 3099 1.294426 TACTCCCTCCGTCCCTCCAT 61.294 60.000 0.00 0.00 0.00 3.41
2500 3100 2.041922 TCCCTCCGTCCCTCCATG 60.042 66.667 0.00 0.00 0.00 3.66
2501 3101 3.164269 CCCTCCGTCCCTCCATGG 61.164 72.222 4.97 4.97 0.00 3.66
2502 3102 2.041922 CCTCCGTCCCTCCATGGA 60.042 66.667 15.27 15.27 38.35 3.41
2503 3103 2.136878 CCTCCGTCCCTCCATGGAG 61.137 68.421 31.69 31.69 45.92 3.86
2504 3104 1.381872 CTCCGTCCCTCCATGGAGT 60.382 63.158 34.49 0.00 42.63 3.85
2510 3110 3.954904 CCGTCCCTCCATGGAGTATATAG 59.045 52.174 34.49 20.54 40.44 1.31
2511 3111 4.570079 CCGTCCCTCCATGGAGTATATAGT 60.570 50.000 34.49 0.00 40.44 2.12
2519 3120 7.068839 CCTCCATGGAGTATATAGTATGTGTCC 59.931 44.444 34.49 0.00 40.44 4.02
2574 3175 6.032094 GCAGCTACTATAAAACACACGACTA 58.968 40.000 0.00 0.00 0.00 2.59
2604 3205 4.390297 GTCTTTCTCTCCTTTCATCAACCG 59.610 45.833 0.00 0.00 0.00 4.44
2608 3209 5.932619 TCTCTCCTTTCATCAACCGATAA 57.067 39.130 0.00 0.00 0.00 1.75
2615 3216 7.109501 TCCTTTCATCAACCGATAATCAAAGA 58.890 34.615 0.00 0.00 0.00 2.52
2633 3234 5.771666 TCAAAGAGATGGCATTCAGAAAACT 59.228 36.000 0.00 0.00 0.00 2.66
2650 3251 5.416013 AGAAAACTAATAGTCAAAGGCTGCC 59.584 40.000 11.65 11.65 0.00 4.85
2677 3278 3.356290 AGGTGGACATATGAAAAGGCAC 58.644 45.455 10.38 0.00 0.00 5.01
2680 3281 2.754552 TGGACATATGAAAAGGCACTGC 59.245 45.455 10.38 0.00 40.86 4.40
2710 3364 4.883585 TCTTGAATCACCAATGCATAGTCC 59.116 41.667 0.00 0.00 0.00 3.85
2799 7272 9.965824 AAGACCAACAAATTACAGAAGTTATTG 57.034 29.630 0.00 0.00 29.15 1.90
2877 7350 2.183409 CGGAGGGTGAAATGCAAGG 58.817 57.895 0.00 0.00 0.00 3.61
2896 7369 3.030291 AGGGCAATCAACAACAAACTCA 58.970 40.909 0.00 0.00 0.00 3.41
3022 7495 3.433343 ACAGATGAATGCATGGTTTCCA 58.567 40.909 0.00 0.00 38.19 3.53
3083 7556 3.133901 TCATACCATGGCACTACGTGAAT 59.866 43.478 13.04 0.00 35.23 2.57
3161 7634 6.487828 AGGAATTTCATGAATGGAGAAGTCA 58.512 36.000 9.40 0.00 37.28 3.41
3235 7716 2.300967 GGAGTGATGGGCCCTGTCA 61.301 63.158 25.70 23.45 0.00 3.58
3259 7740 3.376234 CACAGACAATCCTAATGCCACAG 59.624 47.826 0.00 0.00 0.00 3.66
3269 7750 2.664402 AATGCCACAGAACTTGGAGT 57.336 45.000 0.00 0.00 36.02 3.85
3290 7771 1.412343 GGAGTTGGGTTGCAATTGTGT 59.588 47.619 0.59 0.00 0.00 3.72
3301 7782 3.206964 TGCAATTGTGTTTCGGTAGTCA 58.793 40.909 7.40 0.00 0.00 3.41
3314 7795 2.032799 CGGTAGTCAGTCTCATCTGCTC 59.967 54.545 0.00 0.00 35.63 4.26
3355 7836 3.906660 ACGCCTTCATCGTCAAAGA 57.093 47.368 0.00 0.00 34.84 2.52
3356 7837 1.714794 ACGCCTTCATCGTCAAAGAG 58.285 50.000 0.00 0.00 34.84 2.85
3357 7838 1.272490 ACGCCTTCATCGTCAAAGAGA 59.728 47.619 0.00 0.00 34.84 3.10
3358 7839 1.923204 CGCCTTCATCGTCAAAGAGAG 59.077 52.381 0.00 0.00 0.00 3.20
3359 7840 2.672478 CGCCTTCATCGTCAAAGAGAGT 60.672 50.000 0.00 0.00 0.00 3.24
3360 7841 2.670414 GCCTTCATCGTCAAAGAGAGTG 59.330 50.000 0.00 0.00 0.00 3.51
3361 7842 3.862642 GCCTTCATCGTCAAAGAGAGTGT 60.863 47.826 0.00 0.00 0.00 3.55
3362 7843 4.618460 GCCTTCATCGTCAAAGAGAGTGTA 60.618 45.833 0.00 0.00 0.00 2.90
3363 7844 5.655488 CCTTCATCGTCAAAGAGAGTGTAT 58.345 41.667 0.00 0.00 0.00 2.29
3364 7845 6.102663 CCTTCATCGTCAAAGAGAGTGTATT 58.897 40.000 0.00 0.00 0.00 1.89
3365 7846 6.591834 CCTTCATCGTCAAAGAGAGTGTATTT 59.408 38.462 0.00 0.00 0.00 1.40
3366 7847 7.118390 CCTTCATCGTCAAAGAGAGTGTATTTT 59.882 37.037 0.00 0.00 0.00 1.82
3367 7848 7.962964 TCATCGTCAAAGAGAGTGTATTTTT 57.037 32.000 0.00 0.00 0.00 1.94
3386 7867 3.831651 TTTTTGCGGGGGAAAGAGA 57.168 47.368 0.00 0.00 0.00 3.10
3387 7868 1.616159 TTTTTGCGGGGGAAAGAGAG 58.384 50.000 0.00 0.00 0.00 3.20
3388 7869 0.476771 TTTTGCGGGGGAAAGAGAGT 59.523 50.000 0.00 0.00 0.00 3.24
3389 7870 0.250727 TTTGCGGGGGAAAGAGAGTG 60.251 55.000 0.00 0.00 0.00 3.51
3390 7871 1.415672 TTGCGGGGGAAAGAGAGTGT 61.416 55.000 0.00 0.00 0.00 3.55
3391 7872 0.543410 TGCGGGGGAAAGAGAGTGTA 60.543 55.000 0.00 0.00 0.00 2.90
3392 7873 0.831307 GCGGGGGAAAGAGAGTGTAT 59.169 55.000 0.00 0.00 0.00 2.29
3393 7874 1.209747 GCGGGGGAAAGAGAGTGTATT 59.790 52.381 0.00 0.00 0.00 1.89
3394 7875 2.355818 GCGGGGGAAAGAGAGTGTATTT 60.356 50.000 0.00 0.00 0.00 1.40
3395 7876 3.270877 CGGGGGAAAGAGAGTGTATTTG 58.729 50.000 0.00 0.00 0.00 2.32
3396 7877 3.621558 GGGGGAAAGAGAGTGTATTTGG 58.378 50.000 0.00 0.00 0.00 3.28
3397 7878 3.010250 GGGGGAAAGAGAGTGTATTTGGT 59.990 47.826 0.00 0.00 0.00 3.67
3398 7879 4.226620 GGGGGAAAGAGAGTGTATTTGGTA 59.773 45.833 0.00 0.00 0.00 3.25
3399 7880 5.183969 GGGGAAAGAGAGTGTATTTGGTAC 58.816 45.833 0.00 0.00 0.00 3.34
3400 7881 5.183969 GGGAAAGAGAGTGTATTTGGTACC 58.816 45.833 4.43 4.43 32.03 3.34
3401 7882 5.183969 GGAAAGAGAGTGTATTTGGTACCC 58.816 45.833 10.07 0.00 32.03 3.69
3402 7883 4.838904 AAGAGAGTGTATTTGGTACCCC 57.161 45.455 10.07 0.00 32.03 4.95
3403 7884 3.113043 AGAGAGTGTATTTGGTACCCCC 58.887 50.000 10.07 0.00 32.03 5.40
3417 7898 4.796495 CCCCCGCCCCTTCTTTCG 62.796 72.222 0.00 0.00 0.00 3.46
3418 7899 3.712907 CCCCGCCCCTTCTTTCGA 61.713 66.667 0.00 0.00 0.00 3.71
3419 7900 2.590092 CCCGCCCCTTCTTTCGAT 59.410 61.111 0.00 0.00 0.00 3.59
3420 7901 1.523938 CCCGCCCCTTCTTTCGATC 60.524 63.158 0.00 0.00 0.00 3.69
3421 7902 1.220749 CCGCCCCTTCTTTCGATCA 59.779 57.895 0.00 0.00 0.00 2.92
3422 7903 1.090052 CCGCCCCTTCTTTCGATCAC 61.090 60.000 0.00 0.00 0.00 3.06
3423 7904 1.090052 CGCCCCTTCTTTCGATCACC 61.090 60.000 0.00 0.00 0.00 4.02
3424 7905 0.748367 GCCCCTTCTTTCGATCACCC 60.748 60.000 0.00 0.00 0.00 4.61
3425 7906 0.107165 CCCCTTCTTTCGATCACCCC 60.107 60.000 0.00 0.00 0.00 4.95
3426 7907 0.912486 CCCTTCTTTCGATCACCCCT 59.088 55.000 0.00 0.00 0.00 4.79
3427 7908 1.282157 CCCTTCTTTCGATCACCCCTT 59.718 52.381 0.00 0.00 0.00 3.95
3428 7909 2.359900 CCTTCTTTCGATCACCCCTTG 58.640 52.381 0.00 0.00 0.00 3.61
3429 7910 2.290323 CCTTCTTTCGATCACCCCTTGT 60.290 50.000 0.00 0.00 0.00 3.16
3462 8096 2.026542 AGAAGGTTCCCATCGGTTTACC 60.027 50.000 0.00 0.00 0.00 2.85
3662 8296 7.575332 TTGTGCTTTTTCTGTAGTTTGAAAC 57.425 32.000 0.00 0.00 32.72 2.78
3663 8297 5.797934 TGTGCTTTTTCTGTAGTTTGAAACG 59.202 36.000 1.97 0.00 36.23 3.60
3776 8411 9.277783 CTTATGGATTTTCCTCTAATTCGTGAT 57.722 33.333 0.00 0.00 37.46 3.06
3778 8413 7.320443 TGGATTTTCCTCTAATTCGTGATTG 57.680 36.000 0.00 0.00 37.46 2.67
3783 8418 9.981114 ATTTTCCTCTAATTCGTGATTGTTTTT 57.019 25.926 0.00 0.00 0.00 1.94
3784 8419 9.458374 TTTTCCTCTAATTCGTGATTGTTTTTC 57.542 29.630 0.00 0.00 0.00 2.29
3785 8420 7.737972 TCCTCTAATTCGTGATTGTTTTTCA 57.262 32.000 0.00 0.00 0.00 2.69
3787 8422 8.792633 TCCTCTAATTCGTGATTGTTTTTCATT 58.207 29.630 0.00 0.00 0.00 2.57
3788 8423 9.410556 CCTCTAATTCGTGATTGTTTTTCATTT 57.589 29.630 0.00 0.00 0.00 2.32
3795 8430 8.918961 TCGTGATTGTTTTTCATTTAAACTGT 57.081 26.923 0.00 0.00 36.64 3.55
3796 8431 8.802856 TCGTGATTGTTTTTCATTTAAACTGTG 58.197 29.630 0.00 0.00 36.64 3.66
3797 8432 8.802856 CGTGATTGTTTTTCATTTAAACTGTGA 58.197 29.630 0.00 0.00 36.64 3.58
3897 8532 9.605955 TTGTGAACTTTTGTTATATTCGTGATG 57.394 29.630 0.00 0.00 43.66 3.07
3940 8575 8.892723 ACCTTTTTCCAAATTCATGAACTTTTC 58.107 29.630 11.07 0.00 0.00 2.29
3946 8581 8.647143 TCCAAATTCATGAACTTTTCTCAAAC 57.353 30.769 11.07 0.00 0.00 2.93
3955 8590 9.472361 CATGAACTTTTCTCAAACATCTGATTT 57.528 29.630 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 6.262944 AGCACAATGAAACATTCTGACTTGTA 59.737 34.615 0.00 0.00 0.00 2.41
22 23 5.068198 AGCACAATGAAACATTCTGACTTGT 59.932 36.000 0.00 0.00 0.00 3.16
23 24 5.526115 AGCACAATGAAACATTCTGACTTG 58.474 37.500 0.00 0.00 0.00 3.16
97 99 6.293004 TCCCCATCAATCAATTGTAAAACC 57.707 37.500 5.13 0.00 38.84 3.27
98 100 8.791327 ATTTCCCCATCAATCAATTGTAAAAC 57.209 30.769 5.13 0.00 38.84 2.43
102 105 8.474025 GTGTAATTTCCCCATCAATCAATTGTA 58.526 33.333 5.13 0.00 38.84 2.41
107 110 6.723515 TGAAGTGTAATTTCCCCATCAATCAA 59.276 34.615 0.00 0.00 30.58 2.57
145 148 5.127519 CCTCCCTTCAATTGTGCATATTCAA 59.872 40.000 5.13 0.00 0.00 2.69
190 239 8.405531 CGGCCATTCAATTATAAAGTATATGGG 58.594 37.037 2.24 0.00 0.00 4.00
203 252 3.650942 AGGGAGTATCGGCCATTCAATTA 59.349 43.478 2.24 0.00 34.37 1.40
214 263 5.472137 TCAAAGAAAAACAAGGGAGTATCGG 59.528 40.000 0.00 0.00 34.37 4.18
215 264 6.554334 TCAAAGAAAAACAAGGGAGTATCG 57.446 37.500 0.00 0.00 34.37 2.92
221 285 6.106003 GCTTCTTTCAAAGAAAAACAAGGGA 58.894 36.000 13.61 0.00 46.13 4.20
224 288 9.906111 GTAATGCTTCTTTCAAAGAAAAACAAG 57.094 29.630 13.61 2.30 46.13 3.16
238 302 4.503741 ACGCAATGTGTAATGCTTCTTT 57.496 36.364 0.00 0.00 40.39 2.52
244 308 5.509771 TGATATGAACGCAATGTGTAATGC 58.490 37.500 0.00 0.00 39.17 3.56
252 316 8.570096 AGATGAAAAATGATATGAACGCAATG 57.430 30.769 0.00 0.00 0.00 2.82
256 320 7.322222 GTGCTAGATGAAAAATGATATGAACGC 59.678 37.037 0.00 0.00 0.00 4.84
336 403 9.944663 GTACACATCAAGAATTTGTTAACTGAA 57.055 29.630 7.22 2.49 35.73 3.02
348 415 4.406456 TGGGCAAAGTACACATCAAGAAT 58.594 39.130 0.00 0.00 0.00 2.40
350 417 3.500448 TGGGCAAAGTACACATCAAGA 57.500 42.857 0.00 0.00 0.00 3.02
352 419 5.047660 GGTTTATGGGCAAAGTACACATCAA 60.048 40.000 0.00 0.00 0.00 2.57
357 424 2.414957 GCGGTTTATGGGCAAAGTACAC 60.415 50.000 0.00 0.00 0.00 2.90
367 434 1.339631 TGAGAAGTGGCGGTTTATGGG 60.340 52.381 0.00 0.00 0.00 4.00
368 435 1.737793 GTGAGAAGTGGCGGTTTATGG 59.262 52.381 0.00 0.00 0.00 2.74
371 446 0.947180 GCGTGAGAAGTGGCGGTTTA 60.947 55.000 0.00 0.00 0.00 2.01
388 463 4.081761 GTGATAGATTTTTGTCACGTGCG 58.918 43.478 11.67 0.00 32.64 5.34
403 478 7.083858 CGAAAAATTGCCTTCAAAGTGATAGA 58.916 34.615 0.00 0.00 35.56 1.98
407 482 3.801594 GCGAAAAATTGCCTTCAAAGTGA 59.198 39.130 0.00 0.00 35.56 3.41
408 483 3.555139 TGCGAAAAATTGCCTTCAAAGTG 59.445 39.130 0.00 0.00 35.56 3.16
409 484 3.791245 TGCGAAAAATTGCCTTCAAAGT 58.209 36.364 0.00 0.00 35.56 2.66
410 485 4.996062 ATGCGAAAAATTGCCTTCAAAG 57.004 36.364 0.00 0.00 35.56 2.77
411 486 5.633182 GTCTATGCGAAAAATTGCCTTCAAA 59.367 36.000 0.00 0.00 35.56 2.69
412 487 5.160641 GTCTATGCGAAAAATTGCCTTCAA 58.839 37.500 0.00 0.00 36.51 2.69
413 488 4.380444 GGTCTATGCGAAAAATTGCCTTCA 60.380 41.667 0.00 0.00 0.00 3.02
414 489 4.105486 GGTCTATGCGAAAAATTGCCTTC 58.895 43.478 0.00 0.00 0.00 3.46
415 490 3.763897 AGGTCTATGCGAAAAATTGCCTT 59.236 39.130 0.00 0.00 0.00 4.35
416 491 3.356290 AGGTCTATGCGAAAAATTGCCT 58.644 40.909 0.00 0.00 0.00 4.75
417 492 3.782889 AGGTCTATGCGAAAAATTGCC 57.217 42.857 0.00 0.00 0.00 4.52
418 493 4.095782 TGGTAGGTCTATGCGAAAAATTGC 59.904 41.667 0.00 0.00 0.00 3.56
419 494 5.448632 GGTGGTAGGTCTATGCGAAAAATTG 60.449 44.000 0.00 0.00 0.00 2.32
431 506 5.014858 CACTAACTGAAGGTGGTAGGTCTA 58.985 45.833 0.00 0.00 0.00 2.59
447 522 4.866508 TTGTCTGAACCGATCACTAACT 57.133 40.909 0.00 0.00 33.47 2.24
478 553 2.882170 GGCCACCCCTGTCATAAAC 58.118 57.895 0.00 0.00 0.00 2.01
500 575 0.253894 TGTCACATCAGCCCATCAGG 59.746 55.000 0.00 0.00 39.47 3.86
501 576 2.343484 ATGTCACATCAGCCCATCAG 57.657 50.000 0.00 0.00 0.00 2.90
502 577 3.929955 TTATGTCACATCAGCCCATCA 57.070 42.857 0.00 0.00 0.00 3.07
503 578 5.555017 ACTATTATGTCACATCAGCCCATC 58.445 41.667 0.00 0.00 0.00 3.51
504 579 5.072193 TGACTATTATGTCACATCAGCCCAT 59.928 40.000 0.00 0.00 41.43 4.00
505 580 4.408596 TGACTATTATGTCACATCAGCCCA 59.591 41.667 0.00 0.00 41.43 5.36
506 581 4.960938 TGACTATTATGTCACATCAGCCC 58.039 43.478 0.00 0.00 41.43 5.19
507 582 5.237344 GGTTGACTATTATGTCACATCAGCC 59.763 44.000 0.00 0.00 45.32 4.85
510 585 5.680619 GGGGTTGACTATTATGTCACATCA 58.319 41.667 0.00 0.00 45.32 3.07
513 588 3.516300 ACGGGGTTGACTATTATGTCACA 59.484 43.478 0.00 0.00 45.32 3.58
517 592 6.303903 ACTTAACGGGGTTGACTATTATGT 57.696 37.500 0.00 0.00 0.00 2.29
520 595 6.650390 GTCAAACTTAACGGGGTTGACTATTA 59.350 38.462 13.92 0.00 0.00 0.98
522 597 4.999311 GTCAAACTTAACGGGGTTGACTAT 59.001 41.667 13.92 0.00 0.00 2.12
531 606 0.885596 TGCCGGTCAAACTTAACGGG 60.886 55.000 1.90 0.00 44.39 5.28
534 609 3.065648 TGAAAGTGCCGGTCAAACTTAAC 59.934 43.478 1.90 7.29 33.09 2.01
538 613 1.404035 GTTGAAAGTGCCGGTCAAACT 59.596 47.619 1.90 0.00 33.29 2.66
555 630 2.418628 GGTCCCACATGTCATAACGTTG 59.581 50.000 11.99 0.00 0.00 4.10
616 760 1.283613 TGAGGAGGGAGAGAGTGAGAC 59.716 57.143 0.00 0.00 0.00 3.36
617 761 1.563879 CTGAGGAGGGAGAGAGTGAGA 59.436 57.143 0.00 0.00 0.00 3.27
618 762 1.284785 ACTGAGGAGGGAGAGAGTGAG 59.715 57.143 0.00 0.00 0.00 3.51
619 763 1.283613 GACTGAGGAGGGAGAGAGTGA 59.716 57.143 0.00 0.00 0.00 3.41
620 764 1.684869 GGACTGAGGAGGGAGAGAGTG 60.685 61.905 0.00 0.00 0.00 3.51
621 765 0.629058 GGACTGAGGAGGGAGAGAGT 59.371 60.000 0.00 0.00 0.00 3.24
622 766 0.926293 AGGACTGAGGAGGGAGAGAG 59.074 60.000 0.00 0.00 0.00 3.20
623 767 0.923358 GAGGACTGAGGAGGGAGAGA 59.077 60.000 0.00 0.00 0.00 3.10
662 806 4.274700 GCGGCGGCGGTCTGTATA 62.275 66.667 33.02 0.00 0.00 1.47
681 825 1.070786 TGGGCGAACACAGGAAGAC 59.929 57.895 0.00 0.00 0.00 3.01
682 826 1.070786 GTGGGCGAACACAGGAAGA 59.929 57.895 5.21 0.00 40.99 2.87
684 828 2.911928 TGTGGGCGAACACAGGAA 59.088 55.556 8.30 0.00 45.70 3.36
760 904 0.332632 CCATGGTCATTCCCTGGTGT 59.667 55.000 2.57 0.00 43.90 4.16
775 929 1.533338 GCGAAGAAGCTGCATTCCATG 60.533 52.381 1.02 0.00 0.00 3.66
776 930 0.737219 GCGAAGAAGCTGCATTCCAT 59.263 50.000 1.02 0.00 0.00 3.41
777 931 1.308069 GGCGAAGAAGCTGCATTCCA 61.308 55.000 1.02 0.00 37.29 3.53
778 932 1.431036 GGCGAAGAAGCTGCATTCC 59.569 57.895 1.02 0.00 37.29 3.01
779 933 1.431036 GGGCGAAGAAGCTGCATTC 59.569 57.895 1.02 3.15 37.29 2.67
780 934 2.048603 GGGGCGAAGAAGCTGCATT 61.049 57.895 1.02 0.00 37.29 3.56
848 1009 2.031163 GACGAGCTGGTTGGTGCT 59.969 61.111 1.83 0.00 42.82 4.40
861 1022 6.317140 ACGTATCCTAGATAAGTTGTTGACGA 59.683 38.462 0.00 0.00 0.00 4.20
862 1023 6.493116 ACGTATCCTAGATAAGTTGTTGACG 58.507 40.000 0.00 0.00 0.00 4.35
879 1040 1.797211 CGAGCAGGGAGGACGTATCC 61.797 65.000 10.22 10.22 46.69 2.59
882 1043 1.748122 GACGAGCAGGGAGGACGTA 60.748 63.158 0.00 0.00 37.32 3.57
885 1046 1.079750 GTTGACGAGCAGGGAGGAC 60.080 63.158 0.00 0.00 0.00 3.85
886 1047 2.636412 CGTTGACGAGCAGGGAGGA 61.636 63.158 0.00 0.00 43.02 3.71
887 1048 2.125912 CGTTGACGAGCAGGGAGG 60.126 66.667 0.00 0.00 43.02 4.30
888 1049 1.444553 GACGTTGACGAGCAGGGAG 60.445 63.158 10.87 0.00 43.02 4.30
889 1050 2.649034 GACGTTGACGAGCAGGGA 59.351 61.111 10.87 0.00 43.02 4.20
890 1051 2.805353 CGACGTTGACGAGCAGGG 60.805 66.667 10.87 0.00 43.02 4.45
893 1054 0.659417 GAAGACGACGTTGACGAGCA 60.659 55.000 10.51 0.00 43.02 4.26
917 1416 4.644685 CAGGGTGTTATGTATTTCTTGGGG 59.355 45.833 0.00 0.00 0.00 4.96
919 1418 6.659242 AGTTCAGGGTGTTATGTATTTCTTGG 59.341 38.462 0.00 0.00 0.00 3.61
929 1428 3.594603 ACGAGAGTTCAGGGTGTTATG 57.405 47.619 0.00 0.00 46.40 1.90
946 1461 0.614979 CTCCTCCTCCCCTGAAACGA 60.615 60.000 0.00 0.00 0.00 3.85
948 1463 0.252742 TCCTCCTCCTCCCCTGAAAC 60.253 60.000 0.00 0.00 0.00 2.78
953 1468 3.773154 GCCTCCTCCTCCTCCCCT 61.773 72.222 0.00 0.00 0.00 4.79
954 1469 3.773154 AGCCTCCTCCTCCTCCCC 61.773 72.222 0.00 0.00 0.00 4.81
959 1474 2.043852 TCGACAGCCTCCTCCTCC 60.044 66.667 0.00 0.00 0.00 4.30
976 1491 4.988598 CCGCACGCCTCCACAAGT 62.989 66.667 0.00 0.00 0.00 3.16
981 1496 4.257654 TTTTCCCGCACGCCTCCA 62.258 61.111 0.00 0.00 0.00 3.86
982 1497 3.431725 CTTTTCCCGCACGCCTCC 61.432 66.667 0.00 0.00 0.00 4.30
983 1498 1.745489 ATCTTTTCCCGCACGCCTC 60.745 57.895 0.00 0.00 0.00 4.70
992 1514 4.193334 GCGGCGGCATCTTTTCCC 62.193 66.667 9.78 0.00 39.62 3.97
1048 1570 1.738099 CCTTTCCGTGCGTCCTCAG 60.738 63.158 0.00 0.00 0.00 3.35
1170 1692 1.115467 GGAGGTCCGACATCATGTCT 58.885 55.000 15.89 0.00 44.85 3.41
1294 1832 1.596934 CTCCGGGAAACTGCAGCTA 59.403 57.895 15.27 0.00 34.42 3.32
1313 1851 2.973945 AGTATCAAAGTTCACTCCGGC 58.026 47.619 0.00 0.00 0.00 6.13
1314 1852 5.103000 CACTAGTATCAAAGTTCACTCCGG 58.897 45.833 0.00 0.00 0.00 5.14
1315 1853 5.103000 CCACTAGTATCAAAGTTCACTCCG 58.897 45.833 0.00 0.00 0.00 4.63
1316 1854 6.038997 ACCACTAGTATCAAAGTTCACTCC 57.961 41.667 0.00 0.00 0.00 3.85
1317 1855 7.964604 AAACCACTAGTATCAAAGTTCACTC 57.035 36.000 0.00 0.00 0.00 3.51
1318 1856 7.228706 CCAAAACCACTAGTATCAAAGTTCACT 59.771 37.037 0.00 0.00 0.00 3.41
1319 1857 7.360361 CCAAAACCACTAGTATCAAAGTTCAC 58.640 38.462 0.00 0.00 0.00 3.18
1323 1861 6.195600 TCCCAAAACCACTAGTATCAAAGT 57.804 37.500 0.00 0.00 0.00 2.66
1337 1875 2.403259 CTGCACGAAAATCCCAAAACC 58.597 47.619 0.00 0.00 0.00 3.27
1346 1884 1.067635 GGCAATGACCTGCACGAAAAT 60.068 47.619 0.00 0.00 44.52 1.82
1352 1890 1.308069 ACGATGGCAATGACCTGCAC 61.308 55.000 0.00 0.00 44.52 4.57
1360 1898 1.514657 CGGCACAACGATGGCAATG 60.515 57.895 11.68 0.00 45.18 2.82
1393 1931 3.384789 TCCTCCTCTTGATGTATGTTCCG 59.615 47.826 0.00 0.00 0.00 4.30
1398 1936 4.098654 AGACGTTCCTCCTCTTGATGTATG 59.901 45.833 0.00 0.00 0.00 2.39
1440 1978 3.173151 AGGGAAATTAACTTGCCAAGGG 58.827 45.455 9.94 0.00 39.18 3.95
1471 2009 4.191544 GCCCCAGAAAAATCAAATTAGCC 58.808 43.478 0.00 0.00 0.00 3.93
1500 2039 1.534729 CTTAGTGACCACAAAGGGGC 58.465 55.000 2.78 0.00 43.89 5.80
1503 2042 6.431234 AGAAATAAGCTTAGTGACCACAAAGG 59.569 38.462 12.54 0.00 45.67 3.11
1506 2045 6.426937 GTCAGAAATAAGCTTAGTGACCACAA 59.573 38.462 20.21 0.00 0.00 3.33
1744 2337 6.803642 AGTACGTATTACCCAAGCTAGAAAG 58.196 40.000 0.00 0.00 0.00 2.62
1763 2356 5.450171 CCCATCATCGTTCTACTTAGTACG 58.550 45.833 8.63 8.63 44.83 3.67
1767 2360 4.592485 AGCCCATCATCGTTCTACTTAG 57.408 45.455 0.00 0.00 0.00 2.18
1768 2361 5.185249 GGATAGCCCATCATCGTTCTACTTA 59.815 44.000 0.00 0.00 35.11 2.24
1769 2362 4.021016 GGATAGCCCATCATCGTTCTACTT 60.021 45.833 0.00 0.00 35.11 2.24
1770 2363 3.511934 GGATAGCCCATCATCGTTCTACT 59.488 47.826 0.00 0.00 35.11 2.57
1771 2364 3.511934 AGGATAGCCCATCATCGTTCTAC 59.488 47.826 0.00 0.00 37.41 2.59
1772 2365 3.764434 GAGGATAGCCCATCATCGTTCTA 59.236 47.826 0.00 0.00 34.97 2.10
1773 2366 2.564947 GAGGATAGCCCATCATCGTTCT 59.435 50.000 0.00 0.00 34.97 3.01
1790 2383 3.027412 GCTCAGAGTTACAGATGGAGGA 58.973 50.000 0.00 0.00 0.00 3.71
1791 2384 3.030291 AGCTCAGAGTTACAGATGGAGG 58.970 50.000 0.00 0.00 0.00 4.30
1792 2385 5.587289 GTTAGCTCAGAGTTACAGATGGAG 58.413 45.833 0.00 0.00 0.00 3.86
1863 2456 1.331241 CCGTCGCATATCACATCTCG 58.669 55.000 0.00 0.00 0.00 4.04
2026 2626 0.316204 CCCAGCAAAAGCACCTTCAG 59.684 55.000 0.00 0.00 0.00 3.02
2028 2628 1.005748 GCCCAGCAAAAGCACCTTC 60.006 57.895 0.00 0.00 0.00 3.46
2121 2721 0.601311 AGCAGTGGCAGAAGAACGAC 60.601 55.000 0.00 0.00 44.61 4.34
2159 2759 1.112113 AGTCAGTCACCCGCGATATT 58.888 50.000 8.23 0.00 0.00 1.28
2229 2829 6.053005 ACGGAAAGTAACTGAACTGAATTGA 58.947 36.000 0.00 0.00 0.00 2.57
2256 2856 8.477984 GATTCAGGAATCATCAGAGTTATAGC 57.522 38.462 15.31 0.00 44.89 2.97
2281 2881 1.394917 GTTAGCGGCTGTGTGATCTTG 59.605 52.381 13.86 0.00 0.00 3.02
2299 2899 3.067106 CGGAGTTGTATCAAGCACAGTT 58.933 45.455 0.00 0.00 0.00 3.16
2405 3005 3.374402 CTGACGTGGCGGAGGAGT 61.374 66.667 0.00 0.00 0.00 3.85
2406 3006 1.592400 TAACTGACGTGGCGGAGGAG 61.592 60.000 0.00 0.00 0.00 3.69
2407 3007 0.968901 ATAACTGACGTGGCGGAGGA 60.969 55.000 0.00 0.00 0.00 3.71
2408 3008 0.108329 AATAACTGACGTGGCGGAGG 60.108 55.000 0.00 0.00 0.00 4.30
2409 3009 1.659098 GAAATAACTGACGTGGCGGAG 59.341 52.381 0.00 0.00 0.00 4.63
2412 3012 0.368907 CGGAAATAACTGACGTGGCG 59.631 55.000 0.00 0.00 0.00 5.69
2414 3014 2.091588 CGTTCGGAAATAACTGACGTGG 59.908 50.000 0.00 0.00 0.00 4.94
2415 3015 2.981805 TCGTTCGGAAATAACTGACGTG 59.018 45.455 0.00 0.00 0.00 4.49
2416 3016 3.287312 TCGTTCGGAAATAACTGACGT 57.713 42.857 0.00 0.00 0.00 4.34
2417 3017 3.060363 CCTTCGTTCGGAAATAACTGACG 59.940 47.826 0.00 0.00 33.34 4.35
2418 3018 4.240096 TCCTTCGTTCGGAAATAACTGAC 58.760 43.478 0.00 0.00 33.34 3.51
2420 3020 5.796350 AATCCTTCGTTCGGAAATAACTG 57.204 39.130 0.00 0.00 33.34 3.16
2422 3022 7.010738 TGACATAATCCTTCGTTCGGAAATAAC 59.989 37.037 0.00 0.00 33.34 1.89
2423 3023 7.042950 TGACATAATCCTTCGTTCGGAAATAA 58.957 34.615 0.00 0.00 33.34 1.40
2425 3025 5.424757 TGACATAATCCTTCGTTCGGAAAT 58.575 37.500 0.00 0.00 33.34 2.17
2428 3028 4.459390 TTGACATAATCCTTCGTTCGGA 57.541 40.909 0.00 0.00 34.52 4.55
2429 3029 5.539582 TTTTGACATAATCCTTCGTTCGG 57.460 39.130 0.00 0.00 0.00 4.30
2430 3030 7.906160 ACTATTTTGACATAATCCTTCGTTCG 58.094 34.615 0.00 0.00 0.00 3.95
2464 3064 9.780186 CGGAGGGAGTATTTCTTAATAAGATTT 57.220 33.333 3.28 0.00 37.38 2.17
2465 3065 8.935741 ACGGAGGGAGTATTTCTTAATAAGATT 58.064 33.333 3.28 0.00 37.38 2.40
2466 3066 8.493787 ACGGAGGGAGTATTTCTTAATAAGAT 57.506 34.615 3.28 0.00 37.38 2.40
2474 3074 2.117051 GGGACGGAGGGAGTATTTCTT 58.883 52.381 0.00 0.00 0.00 2.52
2480 3080 1.294426 ATGGAGGGACGGAGGGAGTA 61.294 60.000 0.00 0.00 0.00 2.59
2481 3081 2.637640 ATGGAGGGACGGAGGGAGT 61.638 63.158 0.00 0.00 0.00 3.85
2482 3082 2.136878 CATGGAGGGACGGAGGGAG 61.137 68.421 0.00 0.00 0.00 4.30
2483 3083 2.041922 CATGGAGGGACGGAGGGA 60.042 66.667 0.00 0.00 0.00 4.20
2484 3084 3.164269 CCATGGAGGGACGGAGGG 61.164 72.222 5.56 0.00 0.00 4.30
2485 3085 2.041922 TCCATGGAGGGACGGAGG 60.042 66.667 11.44 0.00 38.24 4.30
2486 3086 3.543537 CTCCATGGAGGGACGGAG 58.456 66.667 31.14 6.42 39.20 4.63
2487 3087 0.561184 ATACTCCATGGAGGGACGGA 59.439 55.000 38.54 20.02 45.88 4.69
2488 3088 2.304221 TATACTCCATGGAGGGACGG 57.696 55.000 38.54 19.07 45.88 4.79
2489 3089 4.601084 ACTATATACTCCATGGAGGGACG 58.399 47.826 38.54 24.72 45.88 4.79
2490 3090 7.068839 CACATACTATATACTCCATGGAGGGAC 59.931 44.444 38.54 0.00 45.88 4.46
2491 3091 7.126061 CACATACTATATACTCCATGGAGGGA 58.874 42.308 38.54 28.30 45.88 4.20
2492 3092 6.897966 ACACATACTATATACTCCATGGAGGG 59.102 42.308 38.54 23.85 45.88 4.30
2493 3093 7.068839 GGACACATACTATATACTCCATGGAGG 59.931 44.444 38.54 24.63 45.88 4.30
2494 3094 7.615757 TGGACACATACTATATACTCCATGGAG 59.384 40.741 35.55 35.55 46.91 3.86
2495 3095 7.396339 GTGGACACATACTATATACTCCATGGA 59.604 40.741 15.27 15.27 0.00 3.41
2496 3096 7.397476 AGTGGACACATACTATATACTCCATGG 59.603 40.741 4.97 4.97 0.00 3.66
2497 3097 8.354711 AGTGGACACATACTATATACTCCATG 57.645 38.462 5.14 0.00 0.00 3.66
2498 3098 9.463902 GTAGTGGACACATACTATATACTCCAT 57.536 37.037 5.14 0.00 32.55 3.41
2499 3099 7.886970 GGTAGTGGACACATACTATATACTCCA 59.113 40.741 5.14 0.00 32.55 3.86
2500 3100 7.065563 CGGTAGTGGACACATACTATATACTCC 59.934 44.444 5.14 0.00 32.55 3.85
2501 3101 7.413877 GCGGTAGTGGACACATACTATATACTC 60.414 44.444 5.14 0.00 32.55 2.59
2502 3102 6.373774 GCGGTAGTGGACACATACTATATACT 59.626 42.308 5.14 0.00 32.55 2.12
2503 3103 6.404074 GGCGGTAGTGGACACATACTATATAC 60.404 46.154 5.14 0.00 32.55 1.47
2504 3104 5.649395 GGCGGTAGTGGACACATACTATATA 59.351 44.000 5.14 0.00 32.55 0.86
2510 3110 0.179092 GGGCGGTAGTGGACACATAC 60.179 60.000 5.14 4.77 0.00 2.39
2511 3111 0.615261 TGGGCGGTAGTGGACACATA 60.615 55.000 5.14 0.00 0.00 2.29
2604 3205 7.741027 TCTGAATGCCATCTCTTTGATTATC 57.259 36.000 0.00 0.00 32.05 1.75
2608 3209 6.436532 AGTTTTCTGAATGCCATCTCTTTGAT 59.563 34.615 0.00 0.00 35.40 2.57
2615 3216 8.049117 TGACTATTAGTTTTCTGAATGCCATCT 58.951 33.333 0.00 0.00 0.00 2.90
2633 3234 2.026356 TGCTGGCAGCCTTTGACTATTA 60.026 45.455 34.58 10.32 41.51 0.98
2650 3251 5.240183 CCTTTTCATATGTCCACCTATGCTG 59.760 44.000 1.90 0.00 0.00 4.41
2677 3278 1.135859 GTGATTCAAGAACAGGCGCAG 60.136 52.381 10.83 3.04 0.00 5.18
2680 3281 1.522668 TGGTGATTCAAGAACAGGCG 58.477 50.000 0.00 0.00 0.00 5.52
2729 3383 6.952935 ATACAGCATAAATTAGCTAGCGAC 57.047 37.500 9.55 0.00 39.50 5.19
2790 7263 9.624697 TTATTCAACAGTTCATGCAATAACTTC 57.375 29.630 12.88 0.00 33.72 3.01
2877 7350 5.989551 ATTTGAGTTTGTTGTTGATTGCC 57.010 34.783 0.00 0.00 0.00 4.52
2896 7369 4.339247 GGCAGTGAGTTATGGTGCATATTT 59.661 41.667 0.00 0.00 35.78 1.40
3235 7716 4.202441 GTGGCATTAGGATTGTCTGTGAT 58.798 43.478 0.00 0.00 0.00 3.06
3241 7722 4.265073 AGTTCTGTGGCATTAGGATTGTC 58.735 43.478 0.00 0.00 0.00 3.18
3259 7740 1.143073 ACCCAACTCCACTCCAAGTTC 59.857 52.381 0.00 0.00 33.53 3.01
3269 7750 1.411977 CACAATTGCAACCCAACTCCA 59.588 47.619 0.00 0.00 35.99 3.86
3290 7771 3.119459 GCAGATGAGACTGACTACCGAAA 60.119 47.826 0.00 0.00 39.94 3.46
3301 7782 2.163412 GTCGAACAGAGCAGATGAGACT 59.837 50.000 0.00 0.00 0.00 3.24
3368 7849 1.133606 ACTCTCTTTCCCCCGCAAAAA 60.134 47.619 0.00 0.00 0.00 1.94
3369 7850 0.476771 ACTCTCTTTCCCCCGCAAAA 59.523 50.000 0.00 0.00 0.00 2.44
3370 7851 0.250727 CACTCTCTTTCCCCCGCAAA 60.251 55.000 0.00 0.00 0.00 3.68
3371 7852 1.374947 CACTCTCTTTCCCCCGCAA 59.625 57.895 0.00 0.00 0.00 4.85
3372 7853 0.543410 TACACTCTCTTTCCCCCGCA 60.543 55.000 0.00 0.00 0.00 5.69
3373 7854 0.831307 ATACACTCTCTTTCCCCCGC 59.169 55.000 0.00 0.00 0.00 6.13
3374 7855 3.270877 CAAATACACTCTCTTTCCCCCG 58.729 50.000 0.00 0.00 0.00 5.73
3375 7856 3.010250 ACCAAATACACTCTCTTTCCCCC 59.990 47.826 0.00 0.00 0.00 5.40
3376 7857 4.302559 ACCAAATACACTCTCTTTCCCC 57.697 45.455 0.00 0.00 0.00 4.81
3377 7858 5.183969 GGTACCAAATACACTCTCTTTCCC 58.816 45.833 7.15 0.00 35.23 3.97
3400 7881 4.796495 CGAAAGAAGGGGCGGGGG 62.796 72.222 0.00 0.00 0.00 5.40
3401 7882 3.712907 TCGAAAGAAGGGGCGGGG 61.713 66.667 0.00 0.00 37.03 5.73
3421 7902 0.261696 AGAAGGTTTGCACAAGGGGT 59.738 50.000 0.00 0.00 0.00 4.95
3422 7903 2.162681 CTAGAAGGTTTGCACAAGGGG 58.837 52.381 0.00 0.00 0.00 4.79
3423 7904 3.140325 TCTAGAAGGTTTGCACAAGGG 57.860 47.619 0.00 0.00 0.00 3.95
3424 7905 4.756084 CTTCTAGAAGGTTTGCACAAGG 57.244 45.455 22.67 0.00 34.87 3.61
3635 8269 8.594881 TTCAAACTACAGAAAAAGCACAAAAA 57.405 26.923 0.00 0.00 0.00 1.94
3762 8397 8.970691 AATGAAAAACAATCACGAATTAGAGG 57.029 30.769 0.00 0.00 0.00 3.69
3829 8464 7.981142 TCACGAATTTAAGAAAAGTTCACAGT 58.019 30.769 0.00 0.00 0.00 3.55
3830 8465 9.450807 AATCACGAATTTAAGAAAAGTTCACAG 57.549 29.630 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.