Multiple sequence alignment - TraesCS6B01G257700

Loading Multiple Alignment...

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 TraesCS6B01G257700 chr6B 100.000 3545 0 0 1 3545 462133127 462136671 0.000000e+00 6547
1 TraesCS6B01G257700 chr6B 95.882 510 21 0 3036 3545 124081339 124081848 0.000000e+00 826
2 TraesCS6B01G257700 chr6B 95.882 510 21 0 3036 3545 552131979 552132488 0.000000e+00 826
3 TraesCS6B01G257700 chr6B 95.703 512 22 0 3034 3545 346318333 346317822 0.000000e+00 824
4 TraesCS6B01G257700 chr6B 95.294 510 24 0 3036 3545 502314517 502314008 0.000000e+00 809
5 TraesCS6B01G257700 chr6A 97.541 2074 41 4 970 3035 420410750 420408679 0.000000e+00 3539
6 TraesCS6B01G257700 chr6A 86.591 440 38 11 161 595 420411323 420410900 1.930000e-127 466
7 TraesCS6B01G257700 chr6A 98.246 114 2 0 35 148 420411501 420411388 2.160000e-47 200
8 TraesCS6B01G257700 chr6A 81.283 187 15 7 771 955 420410899 420410731 2.220000e-27 134
9 TraesCS6B01G257700 chr6D 96.913 2073 53 4 970 3034 299055592 299057661 0.000000e+00 3463
10 TraesCS6B01G257700 chr6D 85.167 627 46 25 37 642 299054754 299055354 1.820000e-167 599
11 TraesCS6B01G257700 chr6D 82.993 294 25 9 664 955 299055341 299055611 3.540000e-60 243
12 TraesCS6B01G257700 chr4B 95.490 510 23 0 3036 3545 408982386 408981877 0.000000e+00 815
13 TraesCS6B01G257700 chr4B 95.108 511 25 0 3035 3545 423039883 423040393 0.000000e+00 806
14 TraesCS6B01G257700 chr2B 95.490 510 23 0 3036 3545 214826355 214825846 0.000000e+00 815
15 TraesCS6B01G257700 chr5B 95.108 511 25 0 3035 3545 94094074 94094584 0.000000e+00 806
16 TraesCS6B01G257700 chr5B 95.098 510 25 0 3036 3545 291075370 291075879 0.000000e+00 804


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 TraesCS6B01G257700 chr6B 462133127 462136671 3544 False 6547.00 6547 100.000000 1 3545 1 chr6B.!!$F2 3544
1 TraesCS6B01G257700 chr6B 124081339 124081848 509 False 826.00 826 95.882000 3036 3545 1 chr6B.!!$F1 509
2 TraesCS6B01G257700 chr6B 552131979 552132488 509 False 826.00 826 95.882000 3036 3545 1 chr6B.!!$F3 509
3 TraesCS6B01G257700 chr6B 346317822 346318333 511 True 824.00 824 95.703000 3034 3545 1 chr6B.!!$R1 511
4 TraesCS6B01G257700 chr6B 502314008 502314517 509 True 809.00 809 95.294000 3036 3545 1 chr6B.!!$R2 509
5 TraesCS6B01G257700 chr6A 420408679 420411501 2822 True 1084.75 3539 90.915250 35 3035 4 chr6A.!!$R1 3000
6 TraesCS6B01G257700 chr6D 299054754 299057661 2907 False 1435.00 3463 88.357667 37 3034 3 chr6D.!!$F1 2997
7 TraesCS6B01G257700 chr4B 408981877 408982386 509 True 815.00 815 95.490000 3036 3545 1 chr4B.!!$R1 509
8 TraesCS6B01G257700 chr4B 423039883 423040393 510 False 806.00 806 95.108000 3035 3545 1 chr4B.!!$F1 510
9 TraesCS6B01G257700 chr2B 214825846 214826355 509 True 815.00 815 95.490000 3036 3545 1 chr2B.!!$R1 509
10 TraesCS6B01G257700 chr5B 94094074 94094584 510 False 806.00 806 95.108000 3035 3545 1 chr5B.!!$F1 510
11 TraesCS6B01G257700 chr5B 291075370 291075879 509 False 804.00 804 95.098000 3036 3545 1 chr5B.!!$F2 509

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
953 1012 0.036671 AAAAGATCACGACCGTCCCC 60.037 55.0 0.0 0.0 0.0 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2704 2768 1.621107 CGCCATGTTGATTTCAGTGC 58.379 50.0 0.0 0.0 0.0 4.4 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
30 31 2.189594 TGGAACAGCATCTTGGACAG 57.810 50.000 0.00 0.00 0.00 3.51
31 32 1.271543 TGGAACAGCATCTTGGACAGG 60.272 52.381 0.00 0.00 0.00 4.00
32 33 1.003580 GGAACAGCATCTTGGACAGGA 59.996 52.381 0.00 0.00 0.00 3.86
33 34 2.354259 GAACAGCATCTTGGACAGGAG 58.646 52.381 0.00 0.00 0.00 3.69
140 141 8.766476 TCTCAAGATATTTTCTTCTCATCCACT 58.234 33.333 0.00 0.00 42.98 4.00
148 149 7.849804 TTTTCTTCTCATCCACTATAAGCAC 57.150 36.000 0.00 0.00 0.00 4.40
149 150 5.537300 TCTTCTCATCCACTATAAGCACC 57.463 43.478 0.00 0.00 0.00 5.01
150 151 4.038042 TCTTCTCATCCACTATAAGCACCG 59.962 45.833 0.00 0.00 0.00 4.94
151 152 3.562182 TCTCATCCACTATAAGCACCGA 58.438 45.455 0.00 0.00 0.00 4.69
152 153 3.570125 TCTCATCCACTATAAGCACCGAG 59.430 47.826 0.00 0.00 0.00 4.63
154 155 3.704566 TCATCCACTATAAGCACCGAGTT 59.295 43.478 0.00 0.00 0.00 3.01
155 156 4.161565 TCATCCACTATAAGCACCGAGTTT 59.838 41.667 0.00 0.00 0.00 2.66
156 157 3.857052 TCCACTATAAGCACCGAGTTTG 58.143 45.455 0.00 0.00 0.00 2.93
158 159 4.161565 TCCACTATAAGCACCGAGTTTGAT 59.838 41.667 0.00 0.00 0.00 2.57
159 160 4.876107 CCACTATAAGCACCGAGTTTGATT 59.124 41.667 0.00 0.00 0.00 2.57
167 220 2.157668 CACCGAGTTTGATTTCCAGACG 59.842 50.000 0.00 0.00 35.26 4.18
193 246 5.421212 TGCATGGCATTTGTTTTCTTTTC 57.579 34.783 0.00 0.00 31.71 2.29
194 247 5.124645 TGCATGGCATTTGTTTTCTTTTCT 58.875 33.333 0.00 0.00 31.71 2.52
195 248 5.589452 TGCATGGCATTTGTTTTCTTTTCTT 59.411 32.000 0.00 0.00 31.71 2.52
235 289 7.875554 TGCTATTTGATACTACTTGTTGACACA 59.124 33.333 0.00 0.00 0.00 3.72
283 337 2.961741 AGATGATGACAGTGCCGATAGT 59.038 45.455 0.00 0.00 0.00 2.12
284 338 2.584492 TGATGACAGTGCCGATAGTG 57.416 50.000 0.00 0.00 0.00 2.74
327 381 4.803426 GAGACCTGCCGCCTGACG 62.803 72.222 0.00 0.00 43.15 4.35
340 394 1.301716 CTGACGAGGGTGGTTGTGG 60.302 63.158 0.00 0.00 0.00 4.17
342 396 1.125093 TGACGAGGGTGGTTGTGGAT 61.125 55.000 0.00 0.00 0.00 3.41
343 397 0.673644 GACGAGGGTGGTTGTGGATG 60.674 60.000 0.00 0.00 0.00 3.51
344 398 1.125093 ACGAGGGTGGTTGTGGATGA 61.125 55.000 0.00 0.00 0.00 2.92
345 399 0.673644 CGAGGGTGGTTGTGGATGAC 60.674 60.000 0.00 0.00 0.00 3.06
349 403 1.435577 GGTGGTTGTGGATGACGTAC 58.564 55.000 0.00 0.00 0.00 3.67
350 404 1.270412 GGTGGTTGTGGATGACGTACA 60.270 52.381 0.00 0.00 0.00 2.90
351 405 1.796459 GTGGTTGTGGATGACGTACAC 59.204 52.381 2.77 2.77 35.75 2.90
360 414 4.639824 GACGTACACGGCTGAACA 57.360 55.556 0.00 0.00 45.57 3.18
367 421 1.237285 ACACGGCTGAACAATGGAGC 61.237 55.000 0.00 0.00 0.00 4.70
375 429 0.169009 GAACAATGGAGCGGACAAGC 59.831 55.000 0.00 0.00 37.41 4.01
385 439 2.551270 GGACAAGCGCAACACTCG 59.449 61.111 11.47 0.00 0.00 4.18
398 452 0.247736 ACACTCGGATCTTCCTGCAC 59.752 55.000 0.00 0.00 33.30 4.57
403 457 1.077429 GGATCTTCCTGCACCCCAC 60.077 63.158 0.00 0.00 32.53 4.61
411 465 1.222936 CTGCACCCCACTCTCATCC 59.777 63.158 0.00 0.00 0.00 3.51
412 466 1.229625 TGCACCCCACTCTCATCCT 60.230 57.895 0.00 0.00 0.00 3.24
461 515 8.474025 TGTCTGGTTATTTTTGTCAAATCTGTT 58.526 29.630 0.00 0.00 0.00 3.16
462 516 9.959749 GTCTGGTTATTTTTGTCAAATCTGTTA 57.040 29.630 0.00 0.00 0.00 2.41
497 551 7.391148 ACCTATAATTAGTTGCAACACTTGG 57.609 36.000 30.11 20.34 0.00 3.61
516 570 2.352342 TGGACGAAACGGTTTTGTTCTC 59.648 45.455 25.46 18.27 37.39 2.87
553 611 8.589629 GTCGTTTACTTATTCTTTTCTGCGATA 58.410 33.333 0.00 0.00 0.00 2.92
554 612 9.309516 TCGTTTACTTATTCTTTTCTGCGATAT 57.690 29.630 0.00 0.00 0.00 1.63
565 623 6.597672 TCTTTTCTGCGATATAGGAGCAAAAA 59.402 34.615 4.23 4.51 40.63 1.94
579 637 5.098211 GGAGCAAAAATTTCAGATTCTCCG 58.902 41.667 0.00 0.00 0.00 4.63
595 653 4.707030 TCTCCGTCGTTTTCTGCTTATA 57.293 40.909 0.00 0.00 0.00 0.98
596 654 5.258456 TCTCCGTCGTTTTCTGCTTATAT 57.742 39.130 0.00 0.00 0.00 0.86
597 655 5.041287 TCTCCGTCGTTTTCTGCTTATATG 58.959 41.667 0.00 0.00 0.00 1.78
598 656 4.751060 TCCGTCGTTTTCTGCTTATATGT 58.249 39.130 0.00 0.00 0.00 2.29
599 657 5.172934 TCCGTCGTTTTCTGCTTATATGTT 58.827 37.500 0.00 0.00 0.00 2.71
600 658 5.062934 TCCGTCGTTTTCTGCTTATATGTTG 59.937 40.000 0.00 0.00 0.00 3.33
601 659 5.163893 CCGTCGTTTTCTGCTTATATGTTGT 60.164 40.000 0.00 0.00 0.00 3.32
602 660 5.728049 CGTCGTTTTCTGCTTATATGTTGTG 59.272 40.000 0.00 0.00 0.00 3.33
603 661 6.021596 GTCGTTTTCTGCTTATATGTTGTGG 58.978 40.000 0.00 0.00 0.00 4.17
604 662 5.935206 TCGTTTTCTGCTTATATGTTGTGGA 59.065 36.000 0.00 0.00 0.00 4.02
605 663 6.021596 CGTTTTCTGCTTATATGTTGTGGAC 58.978 40.000 0.00 0.00 0.00 4.02
606 664 6.128282 CGTTTTCTGCTTATATGTTGTGGACT 60.128 38.462 0.00 0.00 0.00 3.85
687 745 7.008628 CAGATCGCATAATTTTGTGAAAACCTC 59.991 37.037 14.72 8.48 39.39 3.85
715 773 4.806936 CAGCTTCCTGCAGTTCCA 57.193 55.556 13.81 0.00 45.94 3.53
716 774 2.251600 CAGCTTCCTGCAGTTCCAC 58.748 57.895 13.81 0.00 45.94 4.02
717 775 1.073897 AGCTTCCTGCAGTTCCACC 59.926 57.895 13.81 0.00 45.94 4.61
721 779 2.879756 GCTTCCTGCAGTTCCACCATTA 60.880 50.000 13.81 0.00 42.31 1.90
731 789 5.473504 GCAGTTCCACCATTAAGAAGAGAAA 59.526 40.000 0.00 0.00 0.00 2.52
732 790 6.016276 GCAGTTCCACCATTAAGAAGAGAAAA 60.016 38.462 0.00 0.00 0.00 2.29
744 802 9.807921 ATTAAGAAGAGAAAATTGGTCCAGTTA 57.192 29.630 0.00 0.00 0.00 2.24
746 804 6.842676 AGAAGAGAAAATTGGTCCAGTTAGT 58.157 36.000 0.00 0.00 0.00 2.24
754 812 4.781775 TTGGTCCAGTTAGTGAGGAAAA 57.218 40.909 0.00 0.00 32.30 2.29
763 821 1.001393 GTGAGGAAAATCGGGCCCA 60.001 57.895 24.92 9.77 0.00 5.36
778 836 1.795768 GCCCAAAAGCCTTACAAAGC 58.204 50.000 0.00 0.00 0.00 3.51
787 845 0.616891 CCTTACAAAGCCCCGGTACT 59.383 55.000 0.00 0.00 0.00 2.73
790 848 0.609662 TACAAAGCCCCGGTACTGAC 59.390 55.000 2.31 0.00 0.00 3.51
805 863 1.699656 CTGACGCAGATTTCGCAGGG 61.700 60.000 1.18 0.00 32.44 4.45
810 868 2.044946 AGATTTCGCAGGGTGGCC 60.045 61.111 0.00 0.00 0.00 5.36
826 884 1.685355 GGCCCAGTTGGTTTTGCAGT 61.685 55.000 0.00 0.00 36.04 4.40
861 919 2.333926 TGTATGAACTCGAAACGGCTG 58.666 47.619 0.00 0.00 0.00 4.85
862 920 1.060698 GTATGAACTCGAAACGGCTGC 59.939 52.381 0.00 0.00 0.00 5.25
863 921 0.602638 ATGAACTCGAAACGGCTGCA 60.603 50.000 0.50 0.00 0.00 4.41
864 922 1.221466 TGAACTCGAAACGGCTGCAG 61.221 55.000 10.11 10.11 0.00 4.41
865 923 2.500183 GAACTCGAAACGGCTGCAGC 62.500 60.000 30.88 30.88 41.14 5.25
866 924 3.043713 CTCGAAACGGCTGCAGCA 61.044 61.111 37.63 16.33 44.36 4.41
867 925 2.358615 TCGAAACGGCTGCAGCAT 60.359 55.556 37.63 23.73 44.36 3.79
868 926 2.099062 CGAAACGGCTGCAGCATC 59.901 61.111 37.63 26.38 44.36 3.91
869 927 2.099062 GAAACGGCTGCAGCATCG 59.901 61.111 37.63 32.55 44.36 3.84
870 928 4.107051 AAACGGCTGCAGCATCGC 62.107 61.111 37.63 20.56 44.36 4.58
876 934 4.309347 CTGCAGCATCGCCGCATC 62.309 66.667 0.00 0.00 34.63 3.91
925 984 1.074872 GTAGCCCGTCGTTGTAGCAC 61.075 60.000 0.00 0.00 0.00 4.40
927 986 2.340809 CCCGTCGTTGTAGCACCA 59.659 61.111 0.00 0.00 0.00 4.17
934 993 1.273886 TCGTTGTAGCACCAGCATGTA 59.726 47.619 0.00 0.00 45.49 2.29
935 994 2.073056 CGTTGTAGCACCAGCATGTAA 58.927 47.619 0.00 0.00 45.49 2.41
944 1003 3.728864 GCACCAGCATGTAAAAGATCACG 60.729 47.826 0.00 0.00 41.58 4.35
945 1004 3.684305 CACCAGCATGTAAAAGATCACGA 59.316 43.478 0.00 0.00 0.00 4.35
946 1005 3.684788 ACCAGCATGTAAAAGATCACGAC 59.315 43.478 0.00 0.00 0.00 4.34
947 1006 3.063997 CCAGCATGTAAAAGATCACGACC 59.936 47.826 0.00 0.00 0.00 4.79
948 1007 2.930040 AGCATGTAAAAGATCACGACCG 59.070 45.455 0.00 0.00 0.00 4.79
949 1008 2.671396 GCATGTAAAAGATCACGACCGT 59.329 45.455 0.00 0.00 0.00 4.83
950 1009 3.241995 GCATGTAAAAGATCACGACCGTC 60.242 47.826 0.00 0.00 0.00 4.79
951 1010 2.950433 TGTAAAAGATCACGACCGTCC 58.050 47.619 0.00 0.00 0.00 4.79
952 1011 2.265683 GTAAAAGATCACGACCGTCCC 58.734 52.381 0.00 0.00 0.00 4.46
953 1012 0.036671 AAAAGATCACGACCGTCCCC 60.037 55.000 0.00 0.00 0.00 4.81
954 1013 0.903454 AAAGATCACGACCGTCCCCT 60.903 55.000 0.00 0.00 0.00 4.79
955 1014 1.321074 AAGATCACGACCGTCCCCTC 61.321 60.000 0.00 0.00 0.00 4.30
956 1015 2.036731 ATCACGACCGTCCCCTCA 59.963 61.111 0.00 0.00 0.00 3.86
957 1016 1.601419 GATCACGACCGTCCCCTCAA 61.601 60.000 0.00 0.00 0.00 3.02
958 1017 1.189524 ATCACGACCGTCCCCTCAAA 61.190 55.000 0.00 0.00 0.00 2.69
959 1018 1.070105 CACGACCGTCCCCTCAAAA 59.930 57.895 0.00 0.00 0.00 2.44
960 1019 0.533308 CACGACCGTCCCCTCAAAAA 60.533 55.000 0.00 0.00 0.00 1.94
1017 1076 1.142748 GATGCAGACCACTCGAGGG 59.857 63.158 18.41 13.63 0.00 4.30
1025 1084 2.060383 CCACTCGAGGGGCAGATCA 61.060 63.158 23.36 0.00 0.00 2.92
1026 1085 1.617018 CCACTCGAGGGGCAGATCAA 61.617 60.000 23.36 0.00 0.00 2.57
1179 1243 0.042581 TCATCACCTCTGGCCACCTA 59.957 55.000 0.00 0.00 0.00 3.08
1363 1427 2.282958 TCCTCCACTCGTTCGCCT 60.283 61.111 0.00 0.00 0.00 5.52
1962 2026 1.368579 GGTGTTTGCTGCAATGCCT 59.631 52.632 16.77 0.00 0.00 4.75
1980 2044 3.745975 TGCCTGTGAAAAACATCTACTCG 59.254 43.478 0.00 0.00 38.39 4.18
2001 2065 4.386867 GTGGAACTCGATGATTACTGGA 57.613 45.455 0.00 0.00 0.00 3.86
2124 2188 1.404851 GCTTGTAGCCACTCAGGTCTC 60.405 57.143 0.00 0.00 40.61 3.36
2127 2191 0.889306 GTAGCCACTCAGGTCTCGTT 59.111 55.000 0.00 0.00 40.61 3.85
2649 2713 1.021202 TGTGCTGAAACAAACCTCCG 58.979 50.000 0.00 0.00 0.00 4.63
2704 2768 1.672363 TGCCTGATTTCTTATGCTGCG 59.328 47.619 0.00 0.00 0.00 5.18
2722 2786 1.621107 CGCACTGAAATCAACATGGC 58.379 50.000 0.00 0.00 0.00 4.40
2843 2910 8.434661 CGGCATGCATATTTGTAATTAAATTCC 58.565 33.333 21.36 0.00 32.79 3.01
2893 2960 3.726557 TCATGAGGCTCAGGTTCATTT 57.273 42.857 26.34 3.04 29.48 2.32
2924 2991 0.727398 GCAACCTGTCCGTATGCTTC 59.273 55.000 0.00 0.00 34.29 3.86
3040 3107 9.730420 ATGTGTTTATCAAAGTTTCTGTGTTAC 57.270 29.630 0.00 0.00 0.00 2.50
3516 3583 2.750350 CTGTTCTTGGCCGGGTCT 59.250 61.111 2.18 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.386299 CCAAGATGCTGTTCCAGTATATTACTC 59.614 40.741 2.64 0.00 36.27 2.59
1 2 7.071196 TCCAAGATGCTGTTCCAGTATATTACT 59.929 37.037 2.64 0.00 36.27 2.24
2 3 7.171678 GTCCAAGATGCTGTTCCAGTATATTAC 59.828 40.741 2.64 0.00 36.27 1.89
3 4 7.147567 TGTCCAAGATGCTGTTCCAGTATATTA 60.148 37.037 2.64 0.00 36.27 0.98
4 5 6.058183 GTCCAAGATGCTGTTCCAGTATATT 58.942 40.000 0.00 0.00 38.21 1.28
5 6 5.130975 TGTCCAAGATGCTGTTCCAGTATAT 59.869 40.000 0.00 0.00 36.96 0.86
6 7 4.469586 TGTCCAAGATGCTGTTCCAGTATA 59.530 41.667 0.00 0.00 36.96 1.47
7 8 3.264193 TGTCCAAGATGCTGTTCCAGTAT 59.736 43.478 0.00 0.00 39.36 2.12
8 9 2.637382 TGTCCAAGATGCTGTTCCAGTA 59.363 45.455 0.00 0.00 33.43 2.74
9 10 1.421268 TGTCCAAGATGCTGTTCCAGT 59.579 47.619 0.00 0.00 33.43 4.00
10 11 2.082231 CTGTCCAAGATGCTGTTCCAG 58.918 52.381 0.00 0.00 34.12 3.86
11 12 1.271543 CCTGTCCAAGATGCTGTTCCA 60.272 52.381 0.00 0.00 0.00 3.53
12 13 1.003580 TCCTGTCCAAGATGCTGTTCC 59.996 52.381 0.00 0.00 0.00 3.62
13 14 2.289945 ACTCCTGTCCAAGATGCTGTTC 60.290 50.000 0.00 0.00 0.00 3.18
14 15 1.701847 ACTCCTGTCCAAGATGCTGTT 59.298 47.619 0.00 0.00 0.00 3.16
15 16 1.356124 ACTCCTGTCCAAGATGCTGT 58.644 50.000 0.00 0.00 0.00 4.40
16 17 2.499289 ACTACTCCTGTCCAAGATGCTG 59.501 50.000 0.00 0.00 0.00 4.41
17 18 2.826488 ACTACTCCTGTCCAAGATGCT 58.174 47.619 0.00 0.00 0.00 3.79
18 19 3.954904 TCTACTACTCCTGTCCAAGATGC 59.045 47.826 0.00 0.00 0.00 3.91
19 20 7.227873 TCTATCTACTACTCCTGTCCAAGATG 58.772 42.308 0.00 0.00 0.00 2.90
20 21 7.395525 TCTATCTACTACTCCTGTCCAAGAT 57.604 40.000 0.00 0.00 0.00 2.40
21 22 6.689433 GCTCTATCTACTACTCCTGTCCAAGA 60.689 46.154 0.00 0.00 0.00 3.02
22 23 5.472137 GCTCTATCTACTACTCCTGTCCAAG 59.528 48.000 0.00 0.00 0.00 3.61
23 24 5.132985 AGCTCTATCTACTACTCCTGTCCAA 59.867 44.000 0.00 0.00 0.00 3.53
24 25 4.661240 AGCTCTATCTACTACTCCTGTCCA 59.339 45.833 0.00 0.00 0.00 4.02
25 26 5.221762 TGAGCTCTATCTACTACTCCTGTCC 60.222 48.000 16.19 0.00 0.00 4.02
26 27 5.860611 TGAGCTCTATCTACTACTCCTGTC 58.139 45.833 16.19 0.00 0.00 3.51
27 28 5.897851 TGAGCTCTATCTACTACTCCTGT 57.102 43.478 16.19 0.00 0.00 4.00
28 29 5.705441 CCTTGAGCTCTATCTACTACTCCTG 59.295 48.000 16.19 0.00 0.00 3.86
29 30 5.609284 TCCTTGAGCTCTATCTACTACTCCT 59.391 44.000 16.19 0.00 0.00 3.69
30 31 5.871834 TCCTTGAGCTCTATCTACTACTCC 58.128 45.833 16.19 0.00 0.00 3.85
31 32 7.811117 TTTCCTTGAGCTCTATCTACTACTC 57.189 40.000 16.19 0.00 0.00 2.59
32 33 7.201875 GCTTTTCCTTGAGCTCTATCTACTACT 60.202 40.741 16.19 0.00 36.01 2.57
33 34 6.921307 GCTTTTCCTTGAGCTCTATCTACTAC 59.079 42.308 16.19 0.00 36.01 2.73
140 141 5.492895 TGGAAATCAAACTCGGTGCTTATA 58.507 37.500 0.00 0.00 0.00 0.98
148 149 1.732259 CCGTCTGGAAATCAAACTCGG 59.268 52.381 0.00 0.00 37.49 4.63
149 150 1.128692 GCCGTCTGGAAATCAAACTCG 59.871 52.381 0.00 0.00 37.49 4.18
150 151 2.151202 TGCCGTCTGGAAATCAAACTC 58.849 47.619 0.00 0.00 37.49 3.01
151 152 2.270352 TGCCGTCTGGAAATCAAACT 57.730 45.000 0.00 0.00 37.49 2.66
152 153 2.867429 CATGCCGTCTGGAAATCAAAC 58.133 47.619 0.00 0.00 37.49 2.93
154 155 0.810648 GCATGCCGTCTGGAAATCAA 59.189 50.000 6.36 0.00 37.49 2.57
155 156 0.322366 TGCATGCCGTCTGGAAATCA 60.322 50.000 16.68 0.00 37.49 2.57
156 157 1.027357 ATGCATGCCGTCTGGAAATC 58.973 50.000 16.68 0.00 37.49 2.17
158 159 1.314534 CCATGCATGCCGTCTGGAAA 61.315 55.000 21.69 0.00 37.49 3.13
159 160 1.750018 CCATGCATGCCGTCTGGAA 60.750 57.895 21.69 0.00 37.49 3.53
211 265 9.203421 TGTGTGTCAACAAGTAGTATCAAATAG 57.797 33.333 0.00 0.00 38.27 1.73
212 266 9.549078 TTGTGTGTCAACAAGTAGTATCAAATA 57.451 29.630 0.00 0.00 38.27 1.40
217 271 7.478520 AGTTTGTGTGTCAACAAGTAGTATC 57.521 36.000 0.00 0.00 40.93 2.24
218 272 9.555727 AATAGTTTGTGTGTCAACAAGTAGTAT 57.444 29.630 0.00 0.00 40.93 2.12
219 273 8.822855 CAATAGTTTGTGTGTCAACAAGTAGTA 58.177 33.333 0.00 0.00 40.93 1.82
220 274 7.678690 GCAATAGTTTGTGTGTCAACAAGTAGT 60.679 37.037 0.00 0.00 40.93 2.73
221 275 6.632834 GCAATAGTTTGTGTGTCAACAAGTAG 59.367 38.462 0.00 0.00 40.93 2.57
283 337 2.171659 TGCTCTTGAGGTGTTTGTACCA 59.828 45.455 0.00 0.00 43.37 3.25
284 338 2.846193 TGCTCTTGAGGTGTTTGTACC 58.154 47.619 0.00 0.00 41.17 3.34
327 381 0.673644 CGTCATCCACAACCACCCTC 60.674 60.000 0.00 0.00 0.00 4.30
334 388 1.065358 CCGTGTACGTCATCCACAAC 58.935 55.000 0.00 0.00 37.74 3.32
340 394 0.989890 GTTCAGCCGTGTACGTCATC 59.010 55.000 0.00 0.00 37.74 2.92
342 396 0.102663 TTGTTCAGCCGTGTACGTCA 59.897 50.000 0.00 0.00 37.74 4.35
343 397 1.126113 CATTGTTCAGCCGTGTACGTC 59.874 52.381 0.00 0.00 37.74 4.34
344 398 1.144969 CATTGTTCAGCCGTGTACGT 58.855 50.000 3.57 0.00 37.74 3.57
345 399 0.442310 CCATTGTTCAGCCGTGTACG 59.558 55.000 0.00 0.00 39.44 3.67
349 403 1.503542 GCTCCATTGTTCAGCCGTG 59.496 57.895 0.00 0.00 0.00 4.94
350 404 2.034879 CGCTCCATTGTTCAGCCGT 61.035 57.895 0.00 0.00 0.00 5.68
351 405 2.753966 CCGCTCCATTGTTCAGCCG 61.754 63.158 0.00 0.00 0.00 5.52
367 421 2.551270 GAGTGTTGCGCTTGTCCG 59.449 61.111 9.73 0.00 0.00 4.79
375 429 0.108615 AGGAAGATCCGAGTGTTGCG 60.109 55.000 0.00 0.00 42.75 4.85
385 439 1.077429 GTGGGGTGCAGGAAGATCC 60.077 63.158 0.00 0.00 36.58 3.36
398 452 4.844349 TTTTCTTAGGATGAGAGTGGGG 57.156 45.455 0.00 0.00 0.00 4.96
434 488 8.137437 ACAGATTTGACAAAAATAACCAGACAG 58.863 33.333 4.41 0.00 0.00 3.51
436 490 8.871686 AACAGATTTGACAAAAATAACCAGAC 57.128 30.769 4.41 0.00 0.00 3.51
497 551 2.598205 CCGAGAACAAAACCGTTTCGTC 60.598 50.000 0.00 0.00 32.49 4.20
553 611 8.005192 GGAGAATCTGAAATTTTTGCTCCTAT 57.995 34.615 0.00 0.00 37.13 2.57
554 612 7.396540 GGAGAATCTGAAATTTTTGCTCCTA 57.603 36.000 0.00 0.00 37.13 2.94
555 613 6.278172 GGAGAATCTGAAATTTTTGCTCCT 57.722 37.500 0.00 0.00 37.13 3.69
577 635 5.163893 ACAACATATAAGCAGAAAACGACGG 60.164 40.000 0.00 0.00 0.00 4.79
579 637 6.021596 CCACAACATATAAGCAGAAAACGAC 58.978 40.000 0.00 0.00 0.00 4.34
595 653 2.727123 TCACCACAAGTCCACAACAT 57.273 45.000 0.00 0.00 0.00 2.71
596 654 2.727123 ATCACCACAAGTCCACAACA 57.273 45.000 0.00 0.00 0.00 3.33
597 655 3.490761 CCAAATCACCACAAGTCCACAAC 60.491 47.826 0.00 0.00 0.00 3.32
598 656 2.692557 CCAAATCACCACAAGTCCACAA 59.307 45.455 0.00 0.00 0.00 3.33
599 657 2.092158 TCCAAATCACCACAAGTCCACA 60.092 45.455 0.00 0.00 0.00 4.17
600 658 2.582052 TCCAAATCACCACAAGTCCAC 58.418 47.619 0.00 0.00 0.00 4.02
601 659 3.420893 GATCCAAATCACCACAAGTCCA 58.579 45.455 0.00 0.00 31.76 4.02
602 660 2.420022 CGATCCAAATCACCACAAGTCC 59.580 50.000 0.00 0.00 31.76 3.85
603 661 2.420022 CCGATCCAAATCACCACAAGTC 59.580 50.000 0.00 0.00 31.76 3.01
604 662 2.039746 TCCGATCCAAATCACCACAAGT 59.960 45.455 0.00 0.00 31.76 3.16
605 663 2.710377 TCCGATCCAAATCACCACAAG 58.290 47.619 0.00 0.00 31.76 3.16
606 664 2.869101 TCCGATCCAAATCACCACAA 57.131 45.000 0.00 0.00 31.76 3.33
652 710 5.913137 AATTATGCGATCTGTCCCAAAAA 57.087 34.783 0.00 0.00 0.00 1.94
653 711 5.913137 AAATTATGCGATCTGTCCCAAAA 57.087 34.783 0.00 0.00 0.00 2.44
654 712 5.184864 ACAAAATTATGCGATCTGTCCCAAA 59.815 36.000 0.00 0.00 0.00 3.28
655 713 4.704540 ACAAAATTATGCGATCTGTCCCAA 59.295 37.500 0.00 0.00 0.00 4.12
656 714 4.096231 CACAAAATTATGCGATCTGTCCCA 59.904 41.667 0.00 0.00 0.00 4.37
657 715 4.335315 TCACAAAATTATGCGATCTGTCCC 59.665 41.667 0.00 0.00 0.00 4.46
658 716 5.484173 TCACAAAATTATGCGATCTGTCC 57.516 39.130 0.00 0.00 0.00 4.02
659 717 7.201350 GGTTTTCACAAAATTATGCGATCTGTC 60.201 37.037 0.00 0.00 32.22 3.51
660 718 6.586082 GGTTTTCACAAAATTATGCGATCTGT 59.414 34.615 0.00 0.00 32.22 3.41
661 719 6.808212 AGGTTTTCACAAAATTATGCGATCTG 59.192 34.615 0.00 0.00 32.22 2.90
662 720 6.924111 AGGTTTTCACAAAATTATGCGATCT 58.076 32.000 0.00 0.00 32.22 2.75
663 721 6.021468 CGAGGTTTTCACAAAATTATGCGATC 60.021 38.462 0.00 0.00 32.22 3.69
664 722 5.799936 CGAGGTTTTCACAAAATTATGCGAT 59.200 36.000 0.00 0.00 32.22 4.58
665 723 5.150683 CGAGGTTTTCACAAAATTATGCGA 58.849 37.500 0.00 0.00 32.22 5.10
666 724 4.915085 ACGAGGTTTTCACAAAATTATGCG 59.085 37.500 0.00 0.00 32.22 4.73
667 725 5.918011 TGACGAGGTTTTCACAAAATTATGC 59.082 36.000 0.00 0.00 32.22 3.14
668 726 6.582295 CCTGACGAGGTTTTCACAAAATTATG 59.418 38.462 0.00 0.00 34.16 1.90
669 727 6.488683 TCCTGACGAGGTTTTCACAAAATTAT 59.511 34.615 0.00 0.00 40.76 1.28
670 728 5.823570 TCCTGACGAGGTTTTCACAAAATTA 59.176 36.000 0.00 0.00 40.76 1.40
671 729 4.642885 TCCTGACGAGGTTTTCACAAAATT 59.357 37.500 0.00 0.00 40.76 1.82
672 730 4.204012 TCCTGACGAGGTTTTCACAAAAT 58.796 39.130 0.00 0.00 40.76 1.82
687 745 2.125350 GAAGCTGCCCTCCTGACG 60.125 66.667 0.00 0.00 0.00 4.35
698 756 1.239968 GGTGGAACTGCAGGAAGCTG 61.240 60.000 19.93 0.00 45.94 4.24
701 759 1.915141 AATGGTGGAACTGCAGGAAG 58.085 50.000 19.93 0.00 36.74 3.46
710 768 7.814587 CCAATTTTCTCTTCTTAATGGTGGAAC 59.185 37.037 0.00 0.00 0.00 3.62
713 771 7.232118 ACCAATTTTCTCTTCTTAATGGTGG 57.768 36.000 0.00 0.00 0.00 4.61
714 772 7.039784 TGGACCAATTTTCTCTTCTTAATGGTG 60.040 37.037 0.00 0.00 0.00 4.17
715 773 7.010160 TGGACCAATTTTCTCTTCTTAATGGT 58.990 34.615 0.00 0.00 0.00 3.55
716 774 7.177392 ACTGGACCAATTTTCTCTTCTTAATGG 59.823 37.037 0.00 0.00 0.00 3.16
717 775 8.115490 ACTGGACCAATTTTCTCTTCTTAATG 57.885 34.615 0.00 0.00 0.00 1.90
721 779 7.229506 CACTAACTGGACCAATTTTCTCTTCTT 59.770 37.037 0.00 0.00 0.00 2.52
731 789 4.993705 TTCCTCACTAACTGGACCAATT 57.006 40.909 0.00 0.00 0.00 2.32
732 790 4.993705 TTTCCTCACTAACTGGACCAAT 57.006 40.909 0.00 0.00 0.00 3.16
744 802 1.303282 GGGCCCGATTTTCCTCACT 59.697 57.895 5.69 0.00 0.00 3.41
746 804 0.113385 TTTGGGCCCGATTTTCCTCA 59.887 50.000 19.37 0.00 0.00 3.86
778 836 1.956629 AATCTGCGTCAGTACCGGGG 61.957 60.000 6.32 0.00 32.61 5.73
787 845 1.741401 CCCTGCGAAATCTGCGTCA 60.741 57.895 0.00 0.00 34.24 4.35
790 848 2.753966 CCACCCTGCGAAATCTGCG 61.754 63.158 0.00 0.00 34.24 5.18
805 863 1.227527 GCAAAACCAACTGGGCCAC 60.228 57.895 0.00 0.00 42.05 5.01
810 868 1.956477 AGCTACTGCAAAACCAACTGG 59.044 47.619 0.00 0.00 42.74 4.00
826 884 5.476599 AGTTCATACATTTTTGGCACAGCTA 59.523 36.000 0.00 0.00 42.39 3.32
887 945 1.821332 GCAATCTTCCTCCGGCCAG 60.821 63.158 2.24 0.00 0.00 4.85
915 974 1.720805 TACATGCTGGTGCTACAACG 58.279 50.000 0.00 0.00 40.48 4.10
925 984 3.063997 GGTCGTGATCTTTTACATGCTGG 59.936 47.826 0.00 0.00 0.00 4.85
927 986 2.930040 CGGTCGTGATCTTTTACATGCT 59.070 45.455 0.00 0.00 0.00 3.79
934 993 0.036671 GGGGACGGTCGTGATCTTTT 60.037 55.000 0.00 0.00 0.00 2.27
935 994 0.903454 AGGGGACGGTCGTGATCTTT 60.903 55.000 0.00 0.00 0.00 2.52
958 1017 5.627780 GCGGTCGTGATCTTTTACAATTTTT 59.372 36.000 0.00 0.00 0.00 1.94
959 1018 5.151389 GCGGTCGTGATCTTTTACAATTTT 58.849 37.500 0.00 0.00 0.00 1.82
960 1019 4.379082 GGCGGTCGTGATCTTTTACAATTT 60.379 41.667 0.00 0.00 0.00 1.82
961 1020 3.126343 GGCGGTCGTGATCTTTTACAATT 59.874 43.478 0.00 0.00 0.00 2.32
962 1021 2.676342 GGCGGTCGTGATCTTTTACAAT 59.324 45.455 0.00 0.00 0.00 2.71
963 1022 2.070783 GGCGGTCGTGATCTTTTACAA 58.929 47.619 0.00 0.00 0.00 2.41
964 1023 1.673626 GGGCGGTCGTGATCTTTTACA 60.674 52.381 0.00 0.00 0.00 2.41
965 1024 1.004595 GGGCGGTCGTGATCTTTTAC 58.995 55.000 0.00 0.00 0.00 2.01
966 1025 0.458889 CGGGCGGTCGTGATCTTTTA 60.459 55.000 0.00 0.00 0.00 1.52
967 1026 1.740296 CGGGCGGTCGTGATCTTTT 60.740 57.895 0.00 0.00 0.00 2.27
968 1027 2.125673 CGGGCGGTCGTGATCTTT 60.126 61.111 0.00 0.00 0.00 2.52
969 1028 4.814294 GCGGGCGGTCGTGATCTT 62.814 66.667 0.00 0.00 0.00 2.40
1002 1061 4.459089 GCCCCTCGAGTGGTCTGC 62.459 72.222 15.75 9.27 0.00 4.26
1005 1064 2.022240 GATCTGCCCCTCGAGTGGTC 62.022 65.000 15.75 8.41 0.00 4.02
1007 1066 1.617018 TTGATCTGCCCCTCGAGTGG 61.617 60.000 9.92 9.92 0.00 4.00
1025 1084 1.322538 GGCGAGAATGGGGCAATGTT 61.323 55.000 0.00 0.00 0.00 2.71
1026 1085 1.754234 GGCGAGAATGGGGCAATGT 60.754 57.895 0.00 0.00 0.00 2.71
1128 1192 4.864334 CGGTGGAGGATGGCTGGC 62.864 72.222 0.00 0.00 0.00 4.85
1179 1243 0.325296 TAACGGAGGTGCAGGAGGAT 60.325 55.000 0.00 0.00 0.00 3.24
1341 1405 1.878656 CGAACGAGTGGAGGAGGCTT 61.879 60.000 0.00 0.00 0.00 4.35
1809 1873 2.025719 CTCTATCGACCGCAGCAGA 58.974 57.895 0.00 0.00 0.00 4.26
1962 2026 4.951254 TCCACGAGTAGATGTTTTTCACA 58.049 39.130 0.00 0.00 40.71 3.58
1980 2044 4.113354 GTCCAGTAATCATCGAGTTCCAC 58.887 47.826 0.00 0.00 0.00 4.02
2124 2188 3.197790 CAGCGGCCCTCATCAACG 61.198 66.667 0.00 0.00 0.00 4.10
2127 2191 3.329889 AACCAGCGGCCCTCATCA 61.330 61.111 0.00 0.00 0.00 3.07
2649 2713 8.190784 CACATAAATCAAACATTTCTCCCCTAC 58.809 37.037 0.00 0.00 0.00 3.18
2704 2768 1.621107 CGCCATGTTGATTTCAGTGC 58.379 50.000 0.00 0.00 0.00 4.40
2843 2910 3.154473 TCCCGCCTCTTCCCATCG 61.154 66.667 0.00 0.00 0.00 3.84
2893 2960 5.708230 ACGGACAGGTTGCAAGAAATTATTA 59.292 36.000 0.00 0.00 0.00 0.98
3040 3107 4.218417 GCCCATTAAGCCCATTACATACTG 59.782 45.833 0.00 0.00 0.00 2.74
3045 3112 2.080654 GGCCCATTAAGCCCATTACA 57.919 50.000 0.00 0.00 45.16 2.41
3055 3122 4.105697 CCCTAAGACTAATGGGCCCATTAA 59.894 45.833 42.53 31.41 44.95 1.40
3161 3228 5.109210 TGCTTGATTCGATTGATACGTCTT 58.891 37.500 0.00 0.00 0.00 3.01
3165 3232 5.641777 TCTTGCTTGATTCGATTGATACG 57.358 39.130 0.00 0.00 0.00 3.06
3175 3242 9.866798 ATTTCCTTCTTAATTCTTGCTTGATTC 57.133 29.630 0.00 0.00 0.00 2.52
3351 3418 3.766691 GCGGGAGGCGACAAGGTA 61.767 66.667 0.00 0.00 0.00 3.08


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

AutoCloner maintained by Alex Coulton.