Multiple sequence alignment - TraesCS1A01G151000

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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 TraesCS1A01G151000 chr1A 100.000 3743 0 0 1 3743 259048417 259052159 0.000000e+00 6913.0
1 TraesCS1A01G151000 chr1A 89.033 538 57 2 1 537 530149602 530150138 0.000000e+00 665.0
2 TraesCS1A01G151000 chr1D 98.402 1314 8 6 1564 2875 204026801 204028103 0.000000e+00 2298.0
3 TraesCS1A01G151000 chr1D 96.398 694 15 9 3054 3743 204033741 204034428 0.000000e+00 1134.0
4 TraesCS1A01G151000 chr1D 97.475 594 13 2 802 1395 204023862 204024453 0.000000e+00 1013.0
5 TraesCS1A01G151000 chr1D 87.896 537 65 0 1 537 66379160 66378624 1.900000e-177 632.0
6 TraesCS1A01G151000 chr1D 92.388 381 19 8 2875 3251 204033367 204033741 5.500000e-148 534.0
7 TraesCS1A01G151000 chr1D 98.485 198 3 0 1379 1576 204025306 204025503 2.140000e-92 350.0
8 TraesCS1A01G151000 chr1D 93.000 100 7 0 541 640 204023608 204023707 3.010000e-31 147.0
9 TraesCS1A01G151000 chr1D 94.937 79 4 0 635 713 204023785 204023863 1.410000e-24 124.0
10 TraesCS1A01G151000 chr1B 91.960 1306 55 15 839 2134 299437864 299439129 0.000000e+00 1784.0
11 TraesCS1A01G151000 chr1B 92.165 753 20 15 2134 2869 299439515 299440245 0.000000e+00 1027.0
12 TraesCS1A01G151000 chr1B 87.918 538 64 1 1 537 360985535 360986072 1.900000e-177 632.0
13 TraesCS1A01G151000 chr1B 88.000 300 32 2 3448 3743 299440946 299441245 5.950000e-93 351.0
14 TraesCS1A01G151000 chr1B 81.609 87 13 3 715 800 483877822 483877738 6.710000e-08 69.4
15 TraesCS1A01G151000 chr6A 93.123 538 36 1 1 537 117418633 117418096 0.000000e+00 787.0
16 TraesCS1A01G151000 chr6A 89.572 537 54 2 2 537 609628593 609628058 0.000000e+00 680.0
17 TraesCS1A01G151000 chr6A 88.930 542 51 4 1 537 367774133 367774670 0.000000e+00 660.0
18 TraesCS1A01G151000 chr2A 91.620 537 45 0 1 537 37219588 37220124 0.000000e+00 743.0
19 TraesCS1A01G151000 chr2A 90.075 534 52 1 4 537 434978887 434978355 0.000000e+00 691.0
20 TraesCS1A01G151000 chr2A 87.917 240 21 8 2862 3093 110894103 110894342 3.680000e-70 276.0
21 TraesCS1A01G151000 chr2B 88.476 538 60 2 1 537 115893189 115892653 0.000000e+00 649.0
22 TraesCS1A01G151000 chr4A 87.119 295 33 4 1000 1294 4818083 4818372 2.790000e-86 329.0
23 TraesCS1A01G151000 chr4A 90.187 214 17 3 2881 3090 537525287 537525500 3.680000e-70 276.0
24 TraesCS1A01G151000 chr4A 87.083 240 24 6 2862 3094 706640307 706640546 7.970000e-67 265.0
25 TraesCS1A01G151000 chr4A 90.909 132 12 0 2221 2352 4820648 4820779 1.070000e-40 178.0
26 TraesCS1A01G151000 chr4B 86.780 295 34 4 1000 1294 582827319 582827030 1.300000e-84 324.0
27 TraesCS1A01G151000 chr4D 85.085 295 39 4 1000 1294 465760882 465760593 2.830000e-76 296.0
28 TraesCS1A01G151000 chr4D 88.971 136 15 0 2221 2356 465759982 465759847 6.430000e-38 169.0
29 TraesCS1A01G151000 chr3D 91.667 216 14 4 2880 3093 43676488 43676701 2.830000e-76 296.0
30 TraesCS1A01G151000 chr6D 91.509 212 16 1 2882 3093 23080488 23080697 1.320000e-74 291.0
31 TraesCS1A01G151000 chr7D 89.954 219 16 5 2880 3092 87234535 87234753 1.020000e-70 278.0
32 TraesCS1A01G151000 chr3A 89.908 218 17 4 2881 3093 740441345 740441128 3.680000e-70 276.0
33 TraesCS1A01G151000 chr7B 87.295 244 22 8 2862 3096 184195076 184195319 1.710000e-68 270.0
34 TraesCS1A01G151000 chr7B 96.875 32 1 0 770 801 483219031 483219062 2.000000e-03 54.7


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 TraesCS1A01G151000 chr1A 259048417 259052159 3742 False 6913.0 6913 100.000000 1 3743 1 chr1A.!!$F1 3742
1 TraesCS1A01G151000 chr1A 530149602 530150138 536 False 665.0 665 89.033000 1 537 1 chr1A.!!$F2 536
2 TraesCS1A01G151000 chr1D 204033367 204034428 1061 False 834.0 1134 94.393000 2875 3743 2 chr1D.!!$F2 868
3 TraesCS1A01G151000 chr1D 204023608 204028103 4495 False 786.4 2298 96.459800 541 2875 5 chr1D.!!$F1 2334
4 TraesCS1A01G151000 chr1D 66378624 66379160 536 True 632.0 632 87.896000 1 537 1 chr1D.!!$R1 536
5 TraesCS1A01G151000 chr1B 299437864 299441245 3381 False 1054.0 1784 90.708333 839 3743 3 chr1B.!!$F2 2904
6 TraesCS1A01G151000 chr1B 360985535 360986072 537 False 632.0 632 87.918000 1 537 1 chr1B.!!$F1 536
7 TraesCS1A01G151000 chr6A 117418096 117418633 537 True 787.0 787 93.123000 1 537 1 chr6A.!!$R1 536
8 TraesCS1A01G151000 chr6A 609628058 609628593 535 True 680.0 680 89.572000 2 537 1 chr6A.!!$R2 535
9 TraesCS1A01G151000 chr6A 367774133 367774670 537 False 660.0 660 88.930000 1 537 1 chr6A.!!$F1 536
10 TraesCS1A01G151000 chr2A 37219588 37220124 536 False 743.0 743 91.620000 1 537 1 chr2A.!!$F1 536
11 TraesCS1A01G151000 chr2A 434978355 434978887 532 True 691.0 691 90.075000 4 537 1 chr2A.!!$R1 533
12 TraesCS1A01G151000 chr2B 115892653 115893189 536 True 649.0 649 88.476000 1 537 1 chr2B.!!$R1 536
13 TraesCS1A01G151000 chr4A 4818083 4820779 2696 False 253.5 329 89.014000 1000 2352 2 chr4A.!!$F3 1352
14 TraesCS1A01G151000 chr4D 465759847 465760882 1035 True 232.5 296 87.028000 1000 2356 2 chr4D.!!$R1 1356

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
546 556 0.105760 ATTTGGTGGACACAAGGCCA 60.106 50.0 5.01 0.0 0.00 5.36 F
547 557 0.324738 TTTGGTGGACACAAGGCCAA 60.325 50.0 5.01 0.0 37.42 4.52 F
681 774 0.391263 ATCTTGTTCCGCGAGTTCCC 60.391 55.0 8.23 0.0 0.00 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1538 2517 2.948979 TGGTAGAAGGTTGCTGTTTGTG 59.051 45.455 0.0 0.0 0.0 3.33 R
2144 4453 6.618811 ACAGACAGATCAATTTTGCAATCTC 58.381 36.000 0.0 0.0 0.0 2.75 R
2827 7162 5.364446 TCATGCCAGAAAAGCCATTATTCAT 59.636 36.000 0.0 0.0 0.0 2.57 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
27 28 1.810030 GGTCGGCGATGAGGTTGTC 60.810 63.158 14.79 0.00 0.00 3.18
36 37 2.607187 GATGAGGTTGTCGATGACGTT 58.393 47.619 0.00 0.00 40.69 3.99
45 46 1.600957 GTCGATGACGTTCCGATCCTA 59.399 52.381 10.20 0.00 40.69 2.94
49 50 0.256752 TGACGTTCCGATCCTAGGGA 59.743 55.000 9.46 0.00 35.55 4.20
80 81 0.745845 CCGCCAGAGCTGCAAGTATT 60.746 55.000 1.02 0.00 36.60 1.89
180 181 1.923395 TTCAGGCGAGGACCCCAAT 60.923 57.895 0.00 0.00 0.00 3.16
237 243 0.813184 CATGGATTTCCGCAAGCAGT 59.187 50.000 0.00 0.00 39.43 4.40
243 249 0.179032 TTTCCGCAAGCAGTTCAGGA 60.179 50.000 0.00 0.00 0.00 3.86
280 286 3.637273 GGCCCCCAACAGTCTCGT 61.637 66.667 0.00 0.00 0.00 4.18
286 292 0.393077 CCCAACAGTCTCGTGGAAGT 59.607 55.000 0.50 0.00 0.00 3.01
441 447 4.037803 CCGTGAATCCATTGCCATATGAAA 59.962 41.667 3.65 0.00 0.00 2.69
450 456 5.279607 CCATTGCCATATGAAAATCCGGATT 60.280 40.000 24.27 24.27 0.00 3.01
492 502 5.459505 TCCCAAATCAAACTAAAGGGTTCA 58.540 37.500 0.00 0.00 36.24 3.18
495 505 5.538433 CCAAATCAAACTAAAGGGTTCAGGA 59.462 40.000 0.00 0.00 0.00 3.86
504 514 3.637184 GGGTTCAGGAGCCGTTAAA 57.363 52.632 0.00 0.00 35.94 1.52
505 515 1.900245 GGGTTCAGGAGCCGTTAAAA 58.100 50.000 0.00 0.00 35.94 1.52
506 516 2.232399 GGGTTCAGGAGCCGTTAAAAA 58.768 47.619 0.00 0.00 35.94 1.94
526 536 2.202824 CGATGGCCGCGTAAAGGA 60.203 61.111 4.92 0.00 0.00 3.36
537 547 2.413634 CGCGTAAAGGAATTTGGTGGAC 60.414 50.000 0.00 0.00 0.00 4.02
538 548 2.554893 GCGTAAAGGAATTTGGTGGACA 59.445 45.455 0.00 0.00 0.00 4.02
539 549 3.610821 GCGTAAAGGAATTTGGTGGACAC 60.611 47.826 0.00 0.00 0.00 3.67
540 550 3.566322 CGTAAAGGAATTTGGTGGACACA 59.434 43.478 4.69 0.00 0.00 3.72
541 551 4.036971 CGTAAAGGAATTTGGTGGACACAA 59.963 41.667 4.69 0.00 0.00 3.33
542 552 4.670896 AAAGGAATTTGGTGGACACAAG 57.329 40.909 4.69 0.00 0.00 3.16
543 553 2.597455 AGGAATTTGGTGGACACAAGG 58.403 47.619 4.69 0.00 0.00 3.61
544 554 1.000843 GGAATTTGGTGGACACAAGGC 59.999 52.381 4.69 0.00 0.00 4.35
545 555 1.000843 GAATTTGGTGGACACAAGGCC 59.999 52.381 0.00 0.00 0.00 5.19
546 556 0.105760 ATTTGGTGGACACAAGGCCA 60.106 50.000 5.01 0.00 0.00 5.36
547 557 0.324738 TTTGGTGGACACAAGGCCAA 60.325 50.000 5.01 0.00 37.42 4.52
548 558 0.754957 TTGGTGGACACAAGGCCAAG 60.755 55.000 5.01 0.00 35.63 3.61
582 592 2.103094 CAGACTGAACTCAACTGGTCCA 59.897 50.000 0.00 0.00 31.49 4.02
591 601 3.196685 ACTCAACTGGTCCATCTAAGAGC 59.803 47.826 0.00 0.00 0.00 4.09
593 603 1.501582 ACTGGTCCATCTAAGAGCCC 58.498 55.000 0.00 0.00 0.00 5.19
615 625 3.416156 GGATCAGGATATTCAACCAGGC 58.584 50.000 0.00 0.00 0.00 4.85
625 635 2.507407 TCAACCAGGCCATAAAGACC 57.493 50.000 5.01 0.00 0.00 3.85
640 733 6.463331 CCATAAAGACCGGCCTAATTAGTACA 60.463 42.308 11.50 0.00 0.00 2.90
677 770 0.603569 AGACATCTTGTTCCGCGAGT 59.396 50.000 8.23 0.00 0.00 4.18
681 774 0.391263 ATCTTGTTCCGCGAGTTCCC 60.391 55.000 8.23 0.00 0.00 3.97
713 806 7.872113 ACTTTCCTCCTCATCAATCAAATAC 57.128 36.000 0.00 0.00 0.00 1.89
714 807 7.637511 ACTTTCCTCCTCATCAATCAAATACT 58.362 34.615 0.00 0.00 0.00 2.12
715 808 8.772250 ACTTTCCTCCTCATCAATCAAATACTA 58.228 33.333 0.00 0.00 0.00 1.82
716 809 8.964476 TTTCCTCCTCATCAATCAAATACTAC 57.036 34.615 0.00 0.00 0.00 2.73
717 810 7.921041 TCCTCCTCATCAATCAAATACTACT 57.079 36.000 0.00 0.00 0.00 2.57
718 811 9.434275 TTCCTCCTCATCAATCAAATACTACTA 57.566 33.333 0.00 0.00 0.00 1.82
719 812 8.861086 TCCTCCTCATCAATCAAATACTACTAC 58.139 37.037 0.00 0.00 0.00 2.73
720 813 8.091449 CCTCCTCATCAATCAAATACTACTACC 58.909 40.741 0.00 0.00 0.00 3.18
721 814 8.783660 TCCTCATCAATCAAATACTACTACCT 57.216 34.615 0.00 0.00 0.00 3.08
722 815 8.861086 TCCTCATCAATCAAATACTACTACCTC 58.139 37.037 0.00 0.00 0.00 3.85
723 816 8.091449 CCTCATCAATCAAATACTACTACCTCC 58.909 40.741 0.00 0.00 0.00 4.30
724 817 7.658261 TCATCAATCAAATACTACTACCTCCG 58.342 38.462 0.00 0.00 0.00 4.63
725 818 7.287005 TCATCAATCAAATACTACTACCTCCGT 59.713 37.037 0.00 0.00 0.00 4.69
726 819 7.414222 TCAATCAAATACTACTACCTCCGTT 57.586 36.000 0.00 0.00 0.00 4.44
727 820 7.486647 TCAATCAAATACTACTACCTCCGTTC 58.513 38.462 0.00 0.00 0.00 3.95
728 821 5.841957 TCAAATACTACTACCTCCGTTCC 57.158 43.478 0.00 0.00 0.00 3.62
729 822 5.263599 TCAAATACTACTACCTCCGTTCCA 58.736 41.667 0.00 0.00 0.00 3.53
730 823 5.895534 TCAAATACTACTACCTCCGTTCCAT 59.104 40.000 0.00 0.00 0.00 3.41
731 824 7.062322 TCAAATACTACTACCTCCGTTCCATA 58.938 38.462 0.00 0.00 0.00 2.74
732 825 7.560991 TCAAATACTACTACCTCCGTTCCATAA 59.439 37.037 0.00 0.00 0.00 1.90
733 826 8.365647 CAAATACTACTACCTCCGTTCCATAAT 58.634 37.037 0.00 0.00 0.00 1.28
734 827 9.592196 AAATACTACTACCTCCGTTCCATAATA 57.408 33.333 0.00 0.00 0.00 0.98
735 828 9.765295 AATACTACTACCTCCGTTCCATAATAT 57.235 33.333 0.00 0.00 0.00 1.28
736 829 7.463961 ACTACTACCTCCGTTCCATAATATG 57.536 40.000 0.00 0.00 0.00 1.78
737 830 7.008941 ACTACTACCTCCGTTCCATAATATGT 58.991 38.462 0.00 0.00 0.00 2.29
738 831 8.166061 ACTACTACCTCCGTTCCATAATATGTA 58.834 37.037 0.00 0.00 0.00 2.29
739 832 7.844493 ACTACCTCCGTTCCATAATATGTAA 57.156 36.000 0.00 0.00 0.00 2.41
740 833 8.253867 ACTACCTCCGTTCCATAATATGTAAA 57.746 34.615 0.00 0.00 0.00 2.01
741 834 8.365647 ACTACCTCCGTTCCATAATATGTAAAG 58.634 37.037 0.00 0.00 0.00 1.85
742 835 7.133133 ACCTCCGTTCCATAATATGTAAAGT 57.867 36.000 0.00 0.00 0.00 2.66
743 836 6.990349 ACCTCCGTTCCATAATATGTAAAGTG 59.010 38.462 0.00 0.00 0.00 3.16
744 837 6.990349 CCTCCGTTCCATAATATGTAAAGTGT 59.010 38.462 0.00 0.00 0.00 3.55
745 838 7.497909 CCTCCGTTCCATAATATGTAAAGTGTT 59.502 37.037 0.00 0.00 0.00 3.32
746 839 8.795842 TCCGTTCCATAATATGTAAAGTGTTT 57.204 30.769 0.00 0.00 0.00 2.83
747 840 9.233649 TCCGTTCCATAATATGTAAAGTGTTTT 57.766 29.630 0.00 0.00 0.00 2.43
748 841 9.849166 CCGTTCCATAATATGTAAAGTGTTTTT 57.151 29.630 0.00 0.00 0.00 1.94
795 888 9.838339 AACACTTTTATATTATGAGACAGAGGG 57.162 33.333 0.00 0.00 0.00 4.30
796 889 9.213777 ACACTTTTATATTATGAGACAGAGGGA 57.786 33.333 0.00 0.00 0.00 4.20
944 1038 4.675303 CCTCACCCTCCCACCCCA 62.675 72.222 0.00 0.00 0.00 4.96
1323 1417 1.303643 CTTGTCCCACTCCCAAGGC 60.304 63.158 0.00 0.00 33.57 4.35
1538 2517 5.405269 AGTTGCTAAAATTCCGCAATGTTTC 59.595 36.000 10.78 1.21 44.35 2.78
1649 3945 5.011738 TCTGTACCCAAGTTCTTACTCAAGG 59.988 44.000 0.00 0.00 31.99 3.61
1958 4262 8.161610 CGCACAAATGTTTCACTTAATTATTGG 58.838 33.333 0.00 0.00 0.00 3.16
2136 4441 8.582437 TGGAATGTAAGAAACCGACCTATATAG 58.418 37.037 2.46 2.46 0.00 1.31
2137 4442 8.583296 GGAATGTAAGAAACCGACCTATATAGT 58.417 37.037 8.92 0.00 0.00 2.12
2171 6491 6.395426 TTGCAAAATTGATCTGTCTGTCTT 57.605 33.333 0.00 0.00 0.00 3.01
2172 6492 7.509141 TTGCAAAATTGATCTGTCTGTCTTA 57.491 32.000 0.00 0.00 0.00 2.10
2869 7204 4.798387 GCATGAATGACCGACAAATAAACC 59.202 41.667 0.00 0.00 0.00 3.27
2872 7207 6.582677 TGAATGACCGACAAATAAACCAAT 57.417 33.333 0.00 0.00 0.00 3.16
2873 7208 6.385843 TGAATGACCGACAAATAAACCAATG 58.614 36.000 0.00 0.00 0.00 2.82
2875 7210 5.114785 TGACCGACAAATAAACCAATGTG 57.885 39.130 0.00 0.00 0.00 3.21
2876 7211 4.822350 TGACCGACAAATAAACCAATGTGA 59.178 37.500 0.00 0.00 0.00 3.58
2880 7236 6.644592 ACCGACAAATAAACCAATGTGATTTG 59.355 34.615 0.00 0.00 0.00 2.32
2984 7344 1.330829 TGCGTGCACGACAAACATTTA 59.669 42.857 41.19 11.92 43.02 1.40
3104 7464 2.160417 GGCACTTTCGTTCTGATTGAGG 59.840 50.000 0.00 0.00 0.00 3.86
3279 7841 7.092079 TGTCAAATTTCATCATGATTGGACAC 58.908 34.615 5.16 0.00 38.28 3.67
3302 7864 4.407296 CCTGAGTAGCTCTAAGAAACCCAT 59.593 45.833 0.00 0.00 0.00 4.00
3320 7882 9.325198 GAAACCCATGAGAAAGTTTATTGTTTT 57.675 29.630 0.00 0.00 32.80 2.43
3371 8023 0.037326 GCCACGAGTTCCTCATGTCA 60.037 55.000 0.00 0.00 0.00 3.58
3414 8066 4.992319 CCAAACATCATGCACTTGAACATT 59.008 37.500 0.00 0.00 0.00 2.71
3418 8070 5.845103 ACATCATGCACTTGAACATTTTCA 58.155 33.333 0.00 0.00 40.14 2.69
3537 8190 4.010349 GCACTTAAGTACCAAAGCTGGAT 58.990 43.478 8.04 0.00 46.92 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 1.421346 TAGCCGTCCCTAGGATCGGA 61.421 60.000 33.12 19.11 43.64 4.55
80 81 7.598278 ACTGACGCCATTTTTAAAATATGTGA 58.402 30.769 15.00 4.68 0.00 3.58
124 125 5.181056 TCGCAATAAGCTTGTCATTCAGAAA 59.819 36.000 9.86 0.00 42.61 2.52
163 164 2.285368 ATTGGGGTCCTCGCCTGA 60.285 61.111 3.25 0.00 45.40 3.86
280 286 2.111972 AGTTCCTCTGGTCCTACTTCCA 59.888 50.000 0.00 0.00 0.00 3.53
321 327 3.266772 TGGAGGATGCTAACCACATCTTT 59.733 43.478 3.98 0.00 42.88 2.52
374 380 2.358898 GTCCGTAAGCGTAATGGACCTA 59.641 50.000 16.60 0.00 42.57 3.08
416 422 0.396139 ATGGCAATGGATTCACGGCT 60.396 50.000 0.00 0.00 0.00 5.52
421 427 6.517027 CGGATTTTCATATGGCAATGGATTCA 60.517 38.462 2.13 0.00 0.00 2.57
441 447 4.634443 CGTCTGTCCTTAAAAATCCGGATT 59.366 41.667 24.27 24.27 0.00 3.01
450 456 4.717778 TGGGATATCCGTCTGTCCTTAAAA 59.282 41.667 15.69 0.00 38.76 1.52
458 464 4.771114 TTGATTTGGGATATCCGTCTGT 57.229 40.909 15.69 0.57 38.76 3.41
462 468 6.546034 CCTTTAGTTTGATTTGGGATATCCGT 59.454 38.462 15.69 1.65 38.76 4.69
492 502 0.035739 TCGCCTTTTTAACGGCTCCT 59.964 50.000 8.16 0.00 44.11 3.69
495 505 0.808755 CCATCGCCTTTTTAACGGCT 59.191 50.000 8.16 0.00 44.11 5.52
522 532 2.965147 CCTTGTGTCCACCAAATTCCTT 59.035 45.455 0.00 0.00 0.00 3.36
526 536 1.047801 GGCCTTGTGTCCACCAAATT 58.952 50.000 0.00 0.00 0.00 1.82
543 553 2.343426 GGCTAGTTGTGGGCTTGGC 61.343 63.158 0.00 0.00 0.00 4.52
544 554 0.962356 CTGGCTAGTTGTGGGCTTGG 60.962 60.000 0.00 0.00 0.00 3.61
545 555 0.036732 TCTGGCTAGTTGTGGGCTTG 59.963 55.000 0.00 0.00 0.00 4.01
546 556 0.036875 GTCTGGCTAGTTGTGGGCTT 59.963 55.000 0.00 0.00 0.00 4.35
547 557 0.838122 AGTCTGGCTAGTTGTGGGCT 60.838 55.000 0.00 0.00 0.00 5.19
548 558 0.674895 CAGTCTGGCTAGTTGTGGGC 60.675 60.000 0.00 0.00 0.00 5.36
582 592 1.148027 TCCTGATCCGGGCTCTTAGAT 59.852 52.381 0.00 0.00 0.00 1.98
591 601 2.371841 TGGTTGAATATCCTGATCCGGG 59.628 50.000 0.00 0.00 0.00 5.73
593 603 3.668447 CCTGGTTGAATATCCTGATCCG 58.332 50.000 0.00 0.00 0.00 4.18
615 625 4.969484 ACTAATTAGGCCGGTCTTTATGG 58.031 43.478 17.04 5.09 0.00 2.74
625 635 7.307751 CCATGTGTTTATGTACTAATTAGGCCG 60.308 40.741 16.73 0.00 0.00 6.13
640 733 3.270877 GTCTCTTCGGCCATGTGTTTAT 58.729 45.455 2.24 0.00 0.00 1.40
677 770 2.698274 GGAGGAAAGTTTTTGCAGGGAA 59.302 45.455 0.00 0.00 0.00 3.97
681 774 4.279169 TGATGAGGAGGAAAGTTTTTGCAG 59.721 41.667 0.00 0.00 0.00 4.41
713 806 7.463961 ACATATTATGGAACGGAGGTAGTAG 57.536 40.000 8.48 0.00 33.60 2.57
714 807 8.938801 TTACATATTATGGAACGGAGGTAGTA 57.061 34.615 8.48 0.00 33.60 1.82
715 808 7.844493 TTACATATTATGGAACGGAGGTAGT 57.156 36.000 8.48 0.00 33.60 2.73
716 809 8.365647 ACTTTACATATTATGGAACGGAGGTAG 58.634 37.037 8.48 1.63 31.51 3.18
717 810 8.145767 CACTTTACATATTATGGAACGGAGGTA 58.854 37.037 8.48 0.00 31.51 3.08
718 811 6.990349 CACTTTACATATTATGGAACGGAGGT 59.010 38.462 8.48 0.00 31.51 3.85
719 812 6.990349 ACACTTTACATATTATGGAACGGAGG 59.010 38.462 8.48 1.78 31.51 4.30
720 813 8.433421 AACACTTTACATATTATGGAACGGAG 57.567 34.615 8.48 3.52 31.51 4.63
721 814 8.795842 AAACACTTTACATATTATGGAACGGA 57.204 30.769 8.48 0.00 31.51 4.69
722 815 9.849166 AAAAACACTTTACATATTATGGAACGG 57.151 29.630 8.48 4.46 31.51 4.44
769 862 9.838339 CCCTCTGTCTCATAATATAAAAGTGTT 57.162 33.333 0.00 0.00 0.00 3.32
770 863 9.213777 TCCCTCTGTCTCATAATATAAAAGTGT 57.786 33.333 0.00 0.00 0.00 3.55
783 876 9.213777 TGTAATTTACTATTCCCTCTGTCTCAT 57.786 33.333 7.99 0.00 0.00 2.90
784 877 8.603898 TGTAATTTACTATTCCCTCTGTCTCA 57.396 34.615 7.99 0.00 0.00 3.27
785 878 8.697292 ACTGTAATTTACTATTCCCTCTGTCTC 58.303 37.037 7.99 0.00 0.00 3.36
786 879 8.611051 ACTGTAATTTACTATTCCCTCTGTCT 57.389 34.615 7.99 0.00 0.00 3.41
787 880 9.968870 CTACTGTAATTTACTATTCCCTCTGTC 57.031 37.037 7.99 0.00 0.00 3.51
788 881 8.925338 CCTACTGTAATTTACTATTCCCTCTGT 58.075 37.037 7.99 0.00 0.00 3.41
789 882 9.144298 TCCTACTGTAATTTACTATTCCCTCTG 57.856 37.037 7.99 0.00 0.00 3.35
790 883 9.900112 ATCCTACTGTAATTTACTATTCCCTCT 57.100 33.333 7.99 0.00 0.00 3.69
934 1028 1.024579 CGAAATCGTTGGGGTGGGAG 61.025 60.000 0.00 0.00 34.11 4.30
980 1074 3.945304 ATTTGTCCGTCCGCCGTCC 62.945 63.158 0.00 0.00 33.66 4.79
1098 1192 1.874345 CGTAGACGTTGGTGAGCCCT 61.874 60.000 0.00 0.00 34.11 5.19
1323 1417 3.918294 TCGGGGATAAAACTACAAGGG 57.082 47.619 0.00 0.00 0.00 3.95
1538 2517 2.948979 TGGTAGAAGGTTGCTGTTTGTG 59.051 45.455 0.00 0.00 0.00 3.33
1997 4301 7.718272 AAGTTAGTAACAACGCAATTCTACA 57.282 32.000 15.28 0.00 33.50 2.74
2138 4443 8.701895 ACAGATCAATTTTGCAATCTCCATAAT 58.298 29.630 0.00 0.00 0.00 1.28
2144 4453 6.618811 ACAGACAGATCAATTTTGCAATCTC 58.381 36.000 0.00 0.00 0.00 2.75
2827 7162 5.364446 TCATGCCAGAAAAGCCATTATTCAT 59.636 36.000 0.00 0.00 0.00 2.57
2936 7296 0.801872 TCGCGAAATCACATTGGTGG 59.198 50.000 6.20 0.00 45.32 4.61
3219 7781 6.680810 CACTAGAACATCTTCCATGCAAAAA 58.319 36.000 0.00 0.00 0.00 1.94
3220 7782 5.335897 GCACTAGAACATCTTCCATGCAAAA 60.336 40.000 0.00 0.00 32.78 2.44
3221 7783 4.156556 GCACTAGAACATCTTCCATGCAAA 59.843 41.667 0.00 0.00 32.78 3.68
3222 7784 3.691118 GCACTAGAACATCTTCCATGCAA 59.309 43.478 0.00 0.00 32.78 4.08
3279 7841 3.769844 TGGGTTTCTTAGAGCTACTCAGG 59.230 47.826 0.00 0.00 32.06 3.86
3302 7864 7.642194 CAGTGCGTAAAACAATAAACTTTCTCA 59.358 33.333 0.00 0.00 0.00 3.27
3371 8023 3.766591 TGGGCGAAATTTCACCATGTTAT 59.233 39.130 23.24 0.00 31.01 1.89
3537 8190 2.688958 GCCTCGCTTTCTCTTACCTCTA 59.311 50.000 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.