Multiple sequence alignment - TraesCS3D01G250700

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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 TraesCS3D01G250700 chr3D 100.000 4047 0 0 1 4047 350877962 350873916 0.000000e+00 7474.0
1 TraesCS3D01G250700 chr3D 90.155 579 54 3 3159 3736 50831860 50831284 0.000000e+00 750.0
2 TraesCS3D01G250700 chr3A 95.238 2394 77 12 708 3089 468733628 468731260 0.000000e+00 3755.0
3 TraesCS3D01G250700 chr3A 91.124 890 77 1 3158 4047 683475150 683476037 0.000000e+00 1205.0
4 TraesCS3D01G250700 chr3A 87.669 665 73 5 2 661 468736881 468736221 0.000000e+00 765.0
5 TraesCS3D01G250700 chr3B 94.704 2417 105 10 729 3143 449446812 449444417 0.000000e+00 3733.0
6 TraesCS3D01G250700 chr3B 90.044 914 66 10 3156 4045 203704804 203703892 0.000000e+00 1160.0
7 TraesCS3D01G250700 chr3B 90.878 581 49 4 3156 3736 656735407 656735983 0.000000e+00 776.0
8 TraesCS3D01G250700 chr3B 84.592 662 81 9 6 661 449481890 449481244 4.410000e-179 638.0
9 TraesCS3D01G250700 chr7D 90.022 922 66 10 3151 4047 562819408 562820328 0.000000e+00 1170.0
10 TraesCS3D01G250700 chr1A 89.542 918 71 2 3152 4045 2864798 2863882 0.000000e+00 1140.0
11 TraesCS3D01G250700 chr5D 89.583 912 67 10 3156 4044 510060175 510061081 0.000000e+00 1133.0
12 TraesCS3D01G250700 chr5D 90.427 585 55 1 3152 3736 431251054 431250471 0.000000e+00 769.0
13 TraesCS3D01G250700 chr2B 88.865 916 76 3 3156 4047 374022599 374023512 0.000000e+00 1103.0
14 TraesCS3D01G250700 chr2B 89.634 820 61 3 3252 4047 110429468 110430287 0.000000e+00 1022.0
15 TraesCS3D01G250700 chr2B 89.008 837 70 11 3228 4047 158625110 158625941 0.000000e+00 1016.0
16 TraesCS3D01G250700 chr2B 90.034 592 58 1 3145 3736 484928890 484928300 0.000000e+00 765.0
17 TraesCS3D01G250700 chr2B 84.746 59 9 0 598 656 425730811 425730869 4.370000e-05 60.2
18 TraesCS3D01G250700 chr4D 88.827 895 87 9 3152 4045 343554264 343553382 0.000000e+00 1086.0
19 TraesCS3D01G250700 chr2D 87.649 923 82 12 3156 4047 621975445 621974524 0.000000e+00 1044.0
20 TraesCS3D01G250700 chr4B 90.208 674 64 2 3156 3828 21193128 21193800 0.000000e+00 878.0
21 TraesCS3D01G250700 chr6B 90.068 584 54 4 3153 3736 534929296 534929875 0.000000e+00 754.0
22 TraesCS3D01G250700 chr6D 91.304 46 4 0 1 46 47087383 47087338 3.380000e-06 63.9
23 TraesCS3D01G250700 chr5A 89.362 47 5 0 1 47 120936513 120936467 4.370000e-05 60.2


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 TraesCS3D01G250700 chr3D 350873916 350877962 4046 True 7474 7474 100.0000 1 4047 1 chr3D.!!$R2 4046
1 TraesCS3D01G250700 chr3D 50831284 50831860 576 True 750 750 90.1550 3159 3736 1 chr3D.!!$R1 577
2 TraesCS3D01G250700 chr3A 468731260 468736881 5621 True 2260 3755 91.4535 2 3089 2 chr3A.!!$R1 3087
3 TraesCS3D01G250700 chr3A 683475150 683476037 887 False 1205 1205 91.1240 3158 4047 1 chr3A.!!$F1 889
4 TraesCS3D01G250700 chr3B 449444417 449446812 2395 True 3733 3733 94.7040 729 3143 1 chr3B.!!$R2 2414
5 TraesCS3D01G250700 chr3B 203703892 203704804 912 True 1160 1160 90.0440 3156 4045 1 chr3B.!!$R1 889
6 TraesCS3D01G250700 chr3B 656735407 656735983 576 False 776 776 90.8780 3156 3736 1 chr3B.!!$F1 580
7 TraesCS3D01G250700 chr3B 449481244 449481890 646 True 638 638 84.5920 6 661 1 chr3B.!!$R3 655
8 TraesCS3D01G250700 chr7D 562819408 562820328 920 False 1170 1170 90.0220 3151 4047 1 chr7D.!!$F1 896
9 TraesCS3D01G250700 chr1A 2863882 2864798 916 True 1140 1140 89.5420 3152 4045 1 chr1A.!!$R1 893
10 TraesCS3D01G250700 chr5D 510060175 510061081 906 False 1133 1133 89.5830 3156 4044 1 chr5D.!!$F1 888
11 TraesCS3D01G250700 chr5D 431250471 431251054 583 True 769 769 90.4270 3152 3736 1 chr5D.!!$R1 584
12 TraesCS3D01G250700 chr2B 374022599 374023512 913 False 1103 1103 88.8650 3156 4047 1 chr2B.!!$F3 891
13 TraesCS3D01G250700 chr2B 110429468 110430287 819 False 1022 1022 89.6340 3252 4047 1 chr2B.!!$F1 795
14 TraesCS3D01G250700 chr2B 158625110 158625941 831 False 1016 1016 89.0080 3228 4047 1 chr2B.!!$F2 819
15 TraesCS3D01G250700 chr2B 484928300 484928890 590 True 765 765 90.0340 3145 3736 1 chr2B.!!$R1 591
16 TraesCS3D01G250700 chr4D 343553382 343554264 882 True 1086 1086 88.8270 3152 4045 1 chr4D.!!$R1 893
17 TraesCS3D01G250700 chr2D 621974524 621975445 921 True 1044 1044 87.6490 3156 4047 1 chr2D.!!$R1 891
18 TraesCS3D01G250700 chr4B 21193128 21193800 672 False 878 878 90.2080 3156 3828 1 chr4B.!!$F1 672
19 TraesCS3D01G250700 chr6B 534929296 534929875 579 False 754 754 90.0680 3153 3736 1 chr6B.!!$F1 583

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
638 646 0.108281 GAACGGGGCAGGAGTTAGAC 60.108 60.000 0.00 0.00 0.0 2.59 F
990 3555 0.254178 TCCAAGCCCTGCAATCTCTC 59.746 55.000 0.00 0.00 0.0 3.20 F
1377 3942 1.154263 CCGTGACGTCGACTTCTCC 60.154 63.158 21.04 11.61 0.0 3.71 F
1651 4216 1.295423 GGTAACAAGCTCAGCGGGA 59.705 57.895 0.00 0.00 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1599 4164 0.935898 CAGCTAGCTTTGGCATCGAG 59.064 55.000 16.46 0.00 41.70 4.04 R
2956 5521 1.601171 AGCTTGCGATGGAGAAGCT 59.399 52.632 8.14 8.14 45.99 3.74 R
3016 5581 0.251922 AGGCGGTGGTAGACTTGGTA 60.252 55.000 0.00 0.00 0.00 3.25 R
3461 6031 0.532573 CCACTATCCACTGCAGTCGT 59.467 55.000 18.64 8.39 0.00 4.34 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
26 27 0.323725 ATTCGCAATGGCCTGGAAGT 60.324 50.000 3.32 0.00 36.38 3.01
29 30 1.097547 CGCAATGGCCTGGAAGTAGG 61.098 60.000 3.32 0.00 40.95 3.18
55 56 2.059786 CGCATCCCCCAGCCATTTT 61.060 57.895 0.00 0.00 0.00 1.82
80 81 0.321653 CCCTCTACGCTGCCAAAAGT 60.322 55.000 0.00 0.00 0.00 2.66
89 90 1.580845 CTGCCAAAAGTGCTCCTCCG 61.581 60.000 0.00 0.00 0.00 4.63
109 110 3.191581 CCGCTTCGTATATCTCCATCAGT 59.808 47.826 0.00 0.00 0.00 3.41
140 141 0.601311 GGAGTATCGCTGCATCCACC 60.601 60.000 0.00 0.00 35.45 4.61
149 150 2.352422 GCATCCACCTGTCAGCCA 59.648 61.111 0.00 0.00 0.00 4.75
158 159 1.242076 CCTGTCAGCCAAAAGACCAG 58.758 55.000 0.00 0.00 33.89 4.00
175 176 1.995484 CCAGCATTATCGGCTATCACG 59.005 52.381 0.00 0.00 40.23 4.35
179 180 2.663602 GCATTATCGGCTATCACGTCTG 59.336 50.000 0.00 0.00 0.00 3.51
198 199 4.038642 GTCTGGAGCCTTAATCTGGTCTAG 59.961 50.000 0.00 0.00 0.00 2.43
201 202 3.134804 GGAGCCTTAATCTGGTCTAGCAA 59.865 47.826 0.00 0.00 0.00 3.91
216 217 1.076705 GCAAGTCCCCCAATCCTCC 60.077 63.158 0.00 0.00 0.00 4.30
218 219 0.704076 CAAGTCCCCCAATCCTCCAA 59.296 55.000 0.00 0.00 0.00 3.53
219 220 1.288932 CAAGTCCCCCAATCCTCCAAT 59.711 52.381 0.00 0.00 0.00 3.16
221 222 2.136026 AGTCCCCCAATCCTCCAATAC 58.864 52.381 0.00 0.00 0.00 1.89
233 234 7.946776 CCAATCCTCCAATACTCCAAAAGATAT 59.053 37.037 0.00 0.00 0.00 1.63
234 235 9.007901 CAATCCTCCAATACTCCAAAAGATATC 57.992 37.037 0.00 0.00 0.00 1.63
247 248 8.537728 TCCAAAAGATATCAGCCATAAAACAT 57.462 30.769 5.32 0.00 0.00 2.71
263 264 9.912634 CCATAAAACATTTTATATAGGCAGGTG 57.087 33.333 8.84 0.00 40.37 4.00
319 321 5.456921 TTTCTGCATTTTCCTCTCCCTAT 57.543 39.130 0.00 0.00 0.00 2.57
357 362 8.064222 CCTATGTTCAATTTCATACGACATGAC 58.936 37.037 0.00 0.00 0.00 3.06
360 365 4.196193 TCAATTTCATACGACATGACCCC 58.804 43.478 0.00 0.00 0.00 4.95
375 380 9.062524 CGACATGACCCCATTTCTATATTTTTA 57.937 33.333 0.00 0.00 29.55 1.52
377 382 9.936329 ACATGACCCCATTTCTATATTTTTACT 57.064 29.630 0.00 0.00 0.00 2.24
457 465 4.533815 AATCTGATGACCTCAGGTACGTA 58.466 43.478 0.00 0.00 44.90 3.57
465 473 1.133575 CCTCAGGTACGTAGGATCCCA 60.134 57.143 8.55 0.00 37.31 4.37
498 506 2.030893 GGCAATTATTCGCTGCAGCATA 60.031 45.455 36.03 24.19 42.21 3.14
503 511 4.898829 TTATTCGCTGCAGCATAACAAT 57.101 36.364 36.03 24.53 42.21 2.71
504 512 3.788333 ATTCGCTGCAGCATAACAATT 57.212 38.095 36.03 13.13 42.21 2.32
506 514 3.574284 TCGCTGCAGCATAACAATTTT 57.426 38.095 36.03 0.00 42.21 1.82
507 515 3.911868 TCGCTGCAGCATAACAATTTTT 58.088 36.364 36.03 0.00 42.21 1.94
563 571 9.856488 GTCTCATGTAACTTCTGTACTATTTGA 57.144 33.333 0.00 0.00 0.00 2.69
612 620 0.320771 ATCCCCACGAATATCTGCGC 60.321 55.000 0.00 0.00 0.00 6.09
619 627 2.960266 CACGAATATCTGCGCAAAATCG 59.040 45.455 13.05 18.57 35.36 3.34
625 633 1.511887 CTGCGCAAAATCGAACGGG 60.512 57.895 13.05 0.00 0.00 5.28
627 635 2.202427 CGCAAAATCGAACGGGGC 60.202 61.111 0.00 0.00 0.00 5.80
638 646 0.108281 GAACGGGGCAGGAGTTAGAC 60.108 60.000 0.00 0.00 0.00 2.59
639 647 1.885163 AACGGGGCAGGAGTTAGACG 61.885 60.000 0.00 0.00 0.00 4.18
661 669 6.797454 ACGAGACATAGTTATTTCTGGTCTC 58.203 40.000 0.00 0.00 41.37 3.36
662 670 6.377429 ACGAGACATAGTTATTTCTGGTCTCA 59.623 38.462 16.27 0.00 42.88 3.27
663 671 7.068839 ACGAGACATAGTTATTTCTGGTCTCAT 59.931 37.037 16.27 1.36 42.88 2.90
665 673 8.546083 AGACATAGTTATTTCTGGTCTCATCT 57.454 34.615 0.00 0.00 32.25 2.90
669 677 9.482627 CATAGTTATTTCTGGTCTCATCTAACC 57.517 37.037 0.00 0.00 36.03 2.85
670 678 7.741554 AGTTATTTCTGGTCTCATCTAACCT 57.258 36.000 0.00 0.00 36.47 3.50
672 680 8.606830 AGTTATTTCTGGTCTCATCTAACCTTT 58.393 33.333 0.00 0.00 36.47 3.11
673 681 9.232473 GTTATTTCTGGTCTCATCTAACCTTTT 57.768 33.333 0.00 0.00 36.47 2.27
674 682 9.807921 TTATTTCTGGTCTCATCTAACCTTTTT 57.192 29.630 0.00 0.00 36.47 1.94
737 3291 1.425412 TTTAAACAGAGAGCGTCCGC 58.575 50.000 2.94 2.94 42.33 5.54
890 3452 1.675483 GCCATTAATCCATCACGCACA 59.325 47.619 0.00 0.00 0.00 4.57
911 3473 0.939106 GGCCGTTGCACAATCAACAC 60.939 55.000 7.31 0.00 44.80 3.32
912 3474 0.939106 GCCGTTGCACAATCAACACC 60.939 55.000 7.31 0.00 44.80 4.16
913 3475 0.318614 CCGTTGCACAATCAACACCC 60.319 55.000 7.31 0.00 44.80 4.61
959 3524 2.285977 TGCTCTGCTGCATACATTCTG 58.714 47.619 1.31 0.00 38.12 3.02
990 3555 0.254178 TCCAAGCCCTGCAATCTCTC 59.746 55.000 0.00 0.00 0.00 3.20
1101 3666 2.030412 TCGCTGCTCGCCTTCAAA 59.970 55.556 0.00 0.00 38.27 2.69
1107 3672 3.102097 CTCGCCTTCAAATCGGCC 58.898 61.111 0.00 0.00 43.38 6.13
1261 3826 2.372690 CGTGTTGTTCTCGAGGGCG 61.373 63.158 13.56 3.52 35.42 6.13
1317 3882 2.125106 GCGGATGTCCCTTCGCTT 60.125 61.111 0.00 0.00 44.10 4.68
1377 3942 1.154263 CCGTGACGTCGACTTCTCC 60.154 63.158 21.04 11.61 0.00 3.71
1579 4144 2.089936 CGCAATTCGTTCGTCGGGA 61.090 57.895 0.00 0.00 40.32 5.14
1651 4216 1.295423 GGTAACAAGCTCAGCGGGA 59.705 57.895 0.00 0.00 0.00 5.14
1769 4334 4.724602 GCAGAGAGCGCACACCGA 62.725 66.667 11.47 0.00 40.02 4.69
1777 4342 3.842126 CGCACACCGACGCTGATG 61.842 66.667 0.00 0.00 40.02 3.07
1778 4343 3.490759 GCACACCGACGCTGATGG 61.491 66.667 0.00 0.00 0.00 3.51
1779 4344 3.490759 CACACCGACGCTGATGGC 61.491 66.667 0.00 0.00 37.64 4.40
1788 4353 2.480555 GCTGATGGCGAAACACCG 59.519 61.111 0.00 0.00 0.00 4.94
2265 4830 2.582498 GACCTGCGCGCGTTCTAT 60.582 61.111 32.35 13.58 0.00 1.98
2329 4894 3.715097 GCAGCCTCCACAGCCTCT 61.715 66.667 0.00 0.00 0.00 3.69
2363 4928 1.522092 CCCATCAGCCAACGCTCTA 59.478 57.895 0.00 0.00 43.95 2.43
2696 5261 2.191641 GGGTCATCCTGCTGGAGC 59.808 66.667 18.00 10.14 46.91 4.70
2737 5302 1.303317 GGACGGCAAGGTGGACATT 60.303 57.895 0.00 0.00 0.00 2.71
3058 5623 1.703438 GCTCTTGATCCTGCGCACAG 61.703 60.000 5.66 0.00 44.05 3.66
3095 5663 1.598685 GCTCGTTTCCGGTTTCCCA 60.599 57.895 0.00 0.00 33.95 4.37
3136 5704 7.504403 TCTCTAGAGAAAAATATTGGCAGAGG 58.496 38.462 20.31 0.00 33.91 3.69
3143 5711 0.469917 ATATTGGCAGAGGACACGGG 59.530 55.000 0.00 0.00 0.00 5.28
3148 5716 0.322546 GGCAGAGGACACGGGATTTT 60.323 55.000 0.00 0.00 0.00 1.82
3221 5789 2.919328 AACCCAGCCTGGCTTTGC 60.919 61.111 20.79 0.00 36.40 3.68
3223 5791 3.379445 CCCAGCCTGGCTTTGCAG 61.379 66.667 20.79 7.27 36.40 4.41
3282 5850 2.025981 TGCCTGCATATGGACTTCTTGT 60.026 45.455 4.56 0.00 0.00 3.16
3329 5898 1.412079 TTGGTTGCCTGCATTGTCTT 58.588 45.000 0.00 0.00 0.00 3.01
3359 5929 2.032680 ACTACACGCTGTTTGGTTGT 57.967 45.000 0.00 0.00 0.00 3.32
3368 5938 1.682854 CTGTTTGGTTGTCTGCATGGT 59.317 47.619 0.00 0.00 0.00 3.55
3433 6003 1.691195 GCTAGCAGAGGAAGGGGGAC 61.691 65.000 10.63 0.00 0.00 4.46
3469 6039 2.261361 CGGACCATGACGACTGCA 59.739 61.111 0.00 0.00 0.00 4.41
3522 6100 2.982130 GAGCATGGAGTCGTGGGT 59.018 61.111 0.00 0.00 0.00 4.51
3771 6452 0.522180 AGTGCAGTAGAAGGACGACG 59.478 55.000 0.00 0.00 32.12 5.12
3913 6594 2.755876 AGGAGCTCGACATGGCGA 60.756 61.111 24.69 24.69 38.74 5.54
3932 6613 0.887836 ACGTCGGTGCAGTAGACTGA 60.888 55.000 13.87 0.00 46.59 3.41
3952 6633 6.767456 ACTGATGTTCAAAGAGAGATGAAGT 58.233 36.000 0.00 0.00 36.31 3.01
4013 6694 1.137086 GAGGAACTGCGAGATTAGGCA 59.863 52.381 0.00 0.00 41.55 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 1.004277 GGGGGATGCGAATATTGCCTA 59.996 52.381 0.00 0.00 0.00 3.93
29 30 0.883833 CTGGGGGATGCGAATATTGC 59.116 55.000 0.00 0.00 0.00 3.56
66 67 1.234615 GGAGCACTTTTGGCAGCGTA 61.235 55.000 0.00 0.00 0.00 4.42
80 81 1.540267 GATATACGAAGCGGAGGAGCA 59.460 52.381 0.00 0.00 40.15 4.26
89 90 5.378292 TCACTGATGGAGATATACGAAGC 57.622 43.478 0.00 0.00 0.00 3.86
109 110 1.794714 GATACTCCCTGGAAGCCTCA 58.205 55.000 0.00 0.00 0.00 3.86
140 141 0.595095 GCTGGTCTTTTGGCTGACAG 59.405 55.000 0.00 0.00 35.11 3.51
149 150 3.004752 AGCCGATAATGCTGGTCTTTT 57.995 42.857 0.00 0.00 37.76 2.27
158 159 2.663602 CAGACGTGATAGCCGATAATGC 59.336 50.000 0.00 0.00 0.00 3.56
175 176 2.769095 AGACCAGATTAAGGCTCCAGAC 59.231 50.000 0.00 0.00 0.00 3.51
179 180 2.700897 TGCTAGACCAGATTAAGGCTCC 59.299 50.000 0.00 0.00 0.00 4.70
198 199 1.076705 GGAGGATTGGGGGACTTGC 60.077 63.158 0.00 0.00 0.00 4.01
201 202 2.136026 GTATTGGAGGATTGGGGGACT 58.864 52.381 0.00 0.00 0.00 3.85
216 217 7.756395 ATGGCTGATATCTTTTGGAGTATTG 57.244 36.000 3.98 0.00 0.00 1.90
218 219 9.866655 TTTTATGGCTGATATCTTTTGGAGTAT 57.133 29.630 3.98 0.00 0.00 2.12
219 220 9.120538 GTTTTATGGCTGATATCTTTTGGAGTA 57.879 33.333 3.98 0.00 0.00 2.59
221 222 7.999679 TGTTTTATGGCTGATATCTTTTGGAG 58.000 34.615 3.98 0.00 0.00 3.86
233 234 9.360901 TGCCTATATAAAATGTTTTATGGCTGA 57.639 29.630 23.83 12.34 43.26 4.26
234 235 9.630098 CTGCCTATATAAAATGTTTTATGGCTG 57.370 33.333 23.83 21.35 43.26 4.85
247 248 7.807198 TGGTAATGACACCTGCCTATATAAAA 58.193 34.615 0.00 0.00 39.50 1.52
256 257 1.539827 GTGTTGGTAATGACACCTGCC 59.460 52.381 0.00 0.00 40.11 4.85
257 258 2.504367 AGTGTTGGTAATGACACCTGC 58.496 47.619 3.26 0.00 45.54 4.85
263 264 7.490079 TCATATCGTTGTAGTGTTGGTAATGAC 59.510 37.037 0.00 0.00 0.00 3.06
293 294 4.463891 GGGAGAGGAAAATGCAGAAATTGA 59.536 41.667 0.00 0.00 0.00 2.57
349 352 7.510549 AAAATATAGAAATGGGGTCATGTCG 57.489 36.000 0.00 0.00 41.41 4.35
375 380 9.342308 TGAAGTTCAAAGATGAAAACAGATAGT 57.658 29.630 2.20 0.00 46.66 2.12
457 465 2.969950 CCATGCATTCAATTGGGATCCT 59.030 45.455 12.58 0.00 0.00 3.24
465 473 5.049954 GCGAATAATTGCCATGCATTCAATT 60.050 36.000 26.66 26.66 41.56 2.32
531 539 8.204836 AGTACAGAAGTTACATGAGACTTTGTT 58.795 33.333 21.83 13.11 36.31 2.83
579 587 8.817092 ATTCGTGGGGATTTTCTCTTTTATTA 57.183 30.769 0.00 0.00 0.00 0.98
580 588 7.718334 ATTCGTGGGGATTTTCTCTTTTATT 57.282 32.000 0.00 0.00 0.00 1.40
612 620 0.958382 TCCTGCCCCGTTCGATTTTG 60.958 55.000 0.00 0.00 0.00 2.44
619 627 0.108281 GTCTAACTCCTGCCCCGTTC 60.108 60.000 0.00 0.00 0.00 3.95
625 633 1.174783 TGTCTCGTCTAACTCCTGCC 58.825 55.000 0.00 0.00 0.00 4.85
627 635 5.821516 AACTATGTCTCGTCTAACTCCTG 57.178 43.478 0.00 0.00 0.00 3.86
638 646 6.796426 TGAGACCAGAAATAACTATGTCTCG 58.204 40.000 10.94 0.00 43.25 4.04
639 647 8.637986 AGATGAGACCAGAAATAACTATGTCTC 58.362 37.037 9.23 9.23 42.14 3.36
673 681 6.919115 GCCGTTTTAAACACAGGATAGAAAAA 59.081 34.615 8.61 0.00 0.00 1.94
674 682 6.440436 GCCGTTTTAAACACAGGATAGAAAA 58.560 36.000 8.61 0.00 0.00 2.29
675 683 5.334260 CGCCGTTTTAAACACAGGATAGAAA 60.334 40.000 8.61 0.00 0.00 2.52
676 684 4.152759 CGCCGTTTTAAACACAGGATAGAA 59.847 41.667 8.61 0.00 0.00 2.10
677 685 3.680937 CGCCGTTTTAAACACAGGATAGA 59.319 43.478 8.61 0.00 0.00 1.98
680 688 1.538075 CCGCCGTTTTAAACACAGGAT 59.462 47.619 8.61 0.00 0.00 3.24
681 689 0.945813 CCGCCGTTTTAAACACAGGA 59.054 50.000 8.61 0.00 0.00 3.86
682 690 0.662077 GCCGCCGTTTTAAACACAGG 60.662 55.000 8.61 8.08 0.00 4.00
684 692 1.009900 CGCCGCCGTTTTAAACACA 60.010 52.632 8.61 0.00 0.00 3.72
685 693 1.726672 CCGCCGCCGTTTTAAACAC 60.727 57.895 8.61 0.00 0.00 3.32
686 694 1.890979 TCCGCCGCCGTTTTAAACA 60.891 52.632 8.61 0.00 0.00 2.83
687 695 1.440850 GTCCGCCGCCGTTTTAAAC 60.441 57.895 0.00 0.00 0.00 2.01
688 696 2.945206 GTCCGCCGCCGTTTTAAA 59.055 55.556 0.00 0.00 0.00 1.52
689 697 3.413023 CGTCCGCCGCCGTTTTAA 61.413 61.111 0.00 0.00 0.00 1.52
690 698 4.661246 ACGTCCGCCGCCGTTTTA 62.661 61.111 0.00 0.00 41.42 1.52
710 3264 4.326548 ACGCTCTCTGTTTAAAATCTACGC 59.673 41.667 0.00 0.00 0.00 4.42
713 3267 5.100259 CGGACGCTCTCTGTTTAAAATCTA 58.900 41.667 0.00 0.00 0.00 1.98
786 3340 1.225854 GCGACGTGAGCTCATTTGC 60.226 57.895 21.47 20.21 0.00 3.68
843 3399 4.467107 AGGGGAGAGAGGTCCGGC 62.467 72.222 0.00 0.00 37.50 6.13
890 3452 2.190170 TTGATTGTGCAACGGCCGT 61.190 52.632 28.70 28.70 42.39 5.68
959 3524 1.524849 GCTTGGATCGAGGAAGGCC 60.525 63.158 0.00 0.00 0.00 5.19
990 3555 3.429085 GCGTAGTGCCATGAAAAAGATG 58.571 45.455 0.00 0.00 37.76 2.90
1207 3772 2.829458 GGAGGAGGAGGACGACCG 60.829 72.222 0.00 0.00 41.83 4.79
1261 3826 4.115199 ATCCCCAGCAAGGCCGAC 62.115 66.667 0.00 0.00 35.39 4.79
1302 3867 0.391263 ACGAAAGCGAAGGGACATCC 60.391 55.000 0.00 0.00 41.64 3.51
1306 3871 0.320508 AGGAACGAAAGCGAAGGGAC 60.321 55.000 0.00 0.00 41.64 4.46
1317 3882 3.070446 TGTTCTTGAGGCTAAGGAACGAA 59.930 43.478 18.84 3.17 0.00 3.85
1579 4144 4.079850 CAGAGAGCTGGGCACGCT 62.080 66.667 4.97 4.97 41.15 5.07
1599 4164 0.935898 CAGCTAGCTTTGGCATCGAG 59.064 55.000 16.46 0.00 41.70 4.04
1651 4216 1.534729 GCGAGGTGGTTTGGAATCTT 58.465 50.000 0.00 0.00 0.00 2.40
1760 4325 3.842126 CATCAGCGTCGGTGTGCG 61.842 66.667 22.58 9.65 35.87 5.34
1779 4344 2.938823 CTGTCCGTGCGGTGTTTCG 61.939 63.158 10.60 0.00 36.47 3.46
1780 4345 2.604174 CCTGTCCGTGCGGTGTTTC 61.604 63.158 10.60 0.00 36.47 2.78
1781 4346 2.590575 CCTGTCCGTGCGGTGTTT 60.591 61.111 10.60 0.00 36.47 2.83
1782 4347 4.619227 CCCTGTCCGTGCGGTGTT 62.619 66.667 10.60 0.00 36.47 3.32
1787 4352 3.649277 CTTCTCCCCTGTCCGTGCG 62.649 68.421 0.00 0.00 0.00 5.34
1788 4353 2.266055 CTTCTCCCCTGTCCGTGC 59.734 66.667 0.00 0.00 0.00 5.34
1789 4354 1.608717 CTCCTTCTCCCCTGTCCGTG 61.609 65.000 0.00 0.00 0.00 4.94
1790 4355 1.305381 CTCCTTCTCCCCTGTCCGT 60.305 63.158 0.00 0.00 0.00 4.69
2265 4830 4.742649 AGCTCCTCCTCCGACGCA 62.743 66.667 0.00 0.00 0.00 5.24
2329 4894 1.682005 GGGGCTGCTTACCATGCAA 60.682 57.895 0.00 0.00 40.13 4.08
2360 4925 2.473760 GGCTGACGAGCTCGCTAGA 61.474 63.158 34.83 15.46 45.44 2.43
2696 5261 4.189188 CGACCGGCCCGTGAGTAG 62.189 72.222 0.00 0.00 0.00 2.57
2956 5521 1.601171 AGCTTGCGATGGAGAAGCT 59.399 52.632 8.14 8.14 45.99 3.74
3016 5581 0.251922 AGGCGGTGGTAGACTTGGTA 60.252 55.000 0.00 0.00 0.00 3.25
3058 5623 1.672356 ATGCAACTCGCTGGTGACC 60.672 57.895 0.00 0.00 43.06 4.02
3122 5690 2.643551 CCGTGTCCTCTGCCAATATTT 58.356 47.619 0.00 0.00 0.00 1.40
3128 5696 1.488705 AAATCCCGTGTCCTCTGCCA 61.489 55.000 0.00 0.00 0.00 4.92
3148 5716 2.423892 TGCAACCAAACACGCTCTTAAA 59.576 40.909 0.00 0.00 0.00 1.52
3154 5722 0.944386 CTACTGCAACCAAACACGCT 59.056 50.000 0.00 0.00 0.00 5.07
3221 5789 4.256110 TGTCACATATGAGGCTGTTTCTG 58.744 43.478 10.38 0.00 34.75 3.02
3223 5791 5.007430 CAGATGTCACATATGAGGCTGTTTC 59.993 44.000 6.56 0.32 34.75 2.78
3282 5850 4.871871 TGCCAAAGTTGATCCCCTAATA 57.128 40.909 0.00 0.00 0.00 0.98
3329 5898 1.355796 GCGTGTAGTTGTATGCGCCA 61.356 55.000 4.18 0.00 39.11 5.69
3359 5929 5.059161 GCTCTTAATCATACACCATGCAGA 58.941 41.667 0.00 0.00 34.35 4.26
3368 5938 5.755375 GCAAGTGCTAGCTCTTAATCATACA 59.245 40.000 26.76 0.00 38.21 2.29
3404 5974 1.414550 CCTCTGCTAGCTCTTAACCCC 59.585 57.143 17.23 0.00 0.00 4.95
3433 6003 1.005294 GGCGCACACTGCATTTCTTG 61.005 55.000 10.83 0.00 45.36 3.02
3461 6031 0.532573 CCACTATCCACTGCAGTCGT 59.467 55.000 18.64 8.39 0.00 4.34
3469 6039 3.031417 GCCACGGCCACTATCCACT 62.031 63.158 2.24 0.00 34.56 4.00
3738 6419 0.034756 TGCACTGACGCTGTAATGGT 59.965 50.000 0.00 0.00 0.00 3.55
3771 6452 1.243902 CTCATCTCGGCCTACTCTCC 58.756 60.000 0.00 0.00 0.00 3.71
3913 6594 0.887836 TCAGTCTACTGCACCGACGT 60.888 55.000 5.21 0.00 43.46 4.34
3918 6599 3.319137 TGAACATCAGTCTACTGCACC 57.681 47.619 5.21 0.00 43.46 5.01
3932 6613 7.378966 TCGTAACTTCATCTCTCTTTGAACAT 58.621 34.615 0.00 0.00 0.00 2.71
3952 6633 4.507388 AGTTTTTGGTTTCGACGATCGTAA 59.493 37.500 22.79 10.29 41.35 3.18
4013 6694 5.514274 TTTGAAATTTCCTTTGACGAGCT 57.486 34.783 15.48 0.00 0.00 4.09
4017 6698 6.801377 TCGATCATTTGAAATTTCCTTTGACG 59.199 34.615 15.48 16.93 0.00 4.35


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

AutoCloner maintained by Alex Coulton.