Multiple sequence alignment - TraesCS7D01G445800

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 TraesCS7D01G445800 chr7D 100.000 9090 0 0 1 9090 566530725 566521636 0.000000e+00 16787.0
1 TraesCS7D01G445800 chr7D 90.110 91 8 1 5898 5987 99461870 99461780 5.770000e-22 117.0
2 TraesCS7D01G445800 chr7B 96.463 4099 95 28 4531 8599 620672706 620676784 0.000000e+00 6721.0
3 TraesCS7D01G445800 chr7B 95.010 3547 103 17 859 4338 620668860 620672399 0.000000e+00 5502.0
4 TraesCS7D01G445800 chr7B 94.217 3130 123 20 44 3122 620668021 620671143 0.000000e+00 4724.0
5 TraesCS7D01G445800 chr7B 88.889 522 29 11 8598 9090 620676830 620677351 4.660000e-172 616.0
6 TraesCS7D01G445800 chr7A 97.103 2900 60 14 4511 7399 652707758 652704872 0.000000e+00 4868.0
7 TraesCS7D01G445800 chr7A 95.041 1714 64 11 7398 9090 652704820 652703107 0.000000e+00 2675.0
8 TraesCS7D01G445800 chr7A 95.366 1489 43 14 1625 3094 652710576 652709095 0.000000e+00 2344.0
9 TraesCS7D01G445800 chr7A 94.831 1335 45 8 3125 4436 652709094 652707761 0.000000e+00 2061.0
10 TraesCS7D01G445800 chr7A 96.811 784 19 4 862 1640 652711373 652710591 0.000000e+00 1304.0
11 TraesCS7D01G445800 chr7A 91.647 862 68 3 1 859 652712261 652711401 0.000000e+00 1190.0
12 TraesCS7D01G445800 chr7A 100.000 34 0 0 3595 3628 652708655 652708622 7.620000e-06 63.9
13 TraesCS7D01G445800 chr6B 83.359 637 76 18 5982 6605 143439189 143439808 6.160000e-156 562.0
14 TraesCS7D01G445800 chr6B 83.735 332 32 15 8769 9087 718595858 718596180 2.480000e-75 294.0
15 TraesCS7D01G445800 chr6A 83.683 619 73 17 5982 6587 85752031 85752634 7.970000e-155 558.0
16 TraesCS7D01G445800 chr6D 83.264 478 64 11 6114 6587 68334506 68334971 8.440000e-115 425.0
17 TraesCS7D01G445800 chr5D 83.607 366 50 7 4756 5121 14119118 14118763 1.460000e-87 335.0
18 TraesCS7D01G445800 chr5B 79.567 416 60 13 4729 5121 13430544 13430131 3.230000e-69 274.0
19 TraesCS7D01G445800 chr5B 82.006 339 40 19 3202 3529 13433699 13433371 1.500000e-67 268.0
20 TraesCS7D01G445800 chr5A 80.217 369 46 15 4777 5121 11062848 11062483 1.520000e-62 252.0
21 TraesCS7D01G445800 chr4A 94.048 84 5 0 5896 5979 724857590 724857673 2.660000e-25 128.0
22 TraesCS7D01G445800 chr4A 93.902 82 5 0 5900 5981 27643531 27643612 3.450000e-24 124.0
23 TraesCS7D01G445800 chr3D 92.045 88 7 0 5894 5981 477907444 477907357 3.450000e-24 124.0
24 TraesCS7D01G445800 chr3B 92.045 88 7 0 5894 5981 637089782 637089695 3.450000e-24 124.0
25 TraesCS7D01G445800 chr1D 92.045 88 7 0 5894 5981 101285147 101285234 3.450000e-24 124.0
26 TraesCS7D01G445800 chr1A 92.045 88 7 0 5894 5981 104216548 104216461 3.450000e-24 124.0
27 TraesCS7D01G445800 chr2D 100.000 29 0 0 4362 4390 10151666 10151638 5.000000e-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 TraesCS7D01G445800 chr7D 566521636 566530725 9089 True 16787.000000 16787 100.000000 1 9090 1 chr7D.!!$R2 9089
1 TraesCS7D01G445800 chr7B 620668021 620677351 9330 False 4390.750000 6721 93.644750 44 9090 4 chr7B.!!$F1 9046
2 TraesCS7D01G445800 chr7A 652703107 652712261 9154 True 2072.271429 4868 95.828429 1 9090 7 chr7A.!!$R1 9089
3 TraesCS7D01G445800 chr6B 143439189 143439808 619 False 562.000000 562 83.359000 5982 6605 1 chr6B.!!$F1 623
4 TraesCS7D01G445800 chr6A 85752031 85752634 603 False 558.000000 558 83.683000 5982 6587 1 chr6A.!!$F1 605
5 TraesCS7D01G445800 chr5B 13430131 13433699 3568 True 271.000000 274 80.786500 3202 5121 2 chr5B.!!$R1 1919

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
476 479 0.031994 ATGGTTTCCGTTGTTGCAGC 59.968 50.000 0.00 0.0 0.00 5.25 F
702 709 1.748493 GTTTGTTGAGTTGGCTGTGGA 59.252 47.619 0.00 0.0 0.00 4.02 F
1872 1939 2.351641 GCAAATGAAGACATCGGTTGCA 60.352 45.455 11.21 0.0 42.45 4.08 F
2620 2692 1.534595 GGTCAAGAGTACGTCGTCAGT 59.465 52.381 0.00 0.0 0.00 3.41 F
4493 6407 1.384643 TTTTTGGGTGGGTTGGGGG 60.385 57.895 0.00 0.0 0.00 5.40 F
4834 7145 0.533491 TGGCATTTGGATTGCTGCTC 59.467 50.000 0.00 0.0 40.03 4.26 F
5363 7697 0.394938 AGCGTGTTGGTATGTGGTCA 59.605 50.000 0.00 0.0 0.00 4.02 F
6888 9246 1.080705 AACTAGTGTCGTGAGCCGC 60.081 57.895 0.00 0.0 36.19 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1682 1749 1.665735 GCGGCATAATATTTGTGGGCG 60.666 52.381 15.10 15.1 45.44 6.13 R
2620 2692 2.410790 GGGGGACTACCTAGCCAATA 57.589 55.000 0.00 0.0 40.03 1.90 R
2912 2984 1.135286 GGCAGCAAATCAGTAACCTGC 60.135 52.381 0.00 0.0 43.52 4.85 R
4502 6416 0.396811 CGATCATAACACCCCTCCCC 59.603 60.000 0.00 0.0 0.00 4.81 R
5363 7697 3.243771 CGTCACCTCTAAGAACTGTTGGT 60.244 47.826 0.00 0.0 0.00 3.67 R
5881 8215 4.105057 CAGAGGTAGTAGGGAGACACCTAT 59.895 50.000 0.00 0.0 44.48 2.57 R
7056 9414 1.539827 GGACCGGAACCAAACAGAATG 59.460 52.381 9.46 0.0 46.00 2.67 R
8560 11004 0.968393 TGACCGATCATCGACACCCA 60.968 55.000 9.16 0.0 43.74 4.51 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
76 77 1.545841 GGGCTCTGTTCCGGAATTTT 58.454 50.000 22.04 0.00 0.00 1.82
80 81 2.820197 GCTCTGTTCCGGAATTTTCCTT 59.180 45.455 22.04 0.00 45.33 3.36
140 141 2.958355 CAGGCCATTATCCATTTTCCGT 59.042 45.455 5.01 0.00 0.00 4.69
165 166 4.111577 AGATCCTCCCCTGTTATGAAACA 58.888 43.478 0.00 0.00 43.32 2.83
166 167 4.728860 AGATCCTCCCCTGTTATGAAACAT 59.271 41.667 0.00 0.00 44.43 2.71
168 169 5.367945 TCCTCCCCTGTTATGAAACATAC 57.632 43.478 0.00 0.00 44.43 2.39
171 172 5.104527 CCTCCCCTGTTATGAAACATACAGA 60.105 44.000 15.57 0.00 44.43 3.41
180 181 7.817478 TGTTATGAAACATACAGACATCGAAGT 59.183 33.333 0.00 0.00 40.69 3.01
303 304 1.845809 CTGGTGACAACGAGCCAAGC 61.846 60.000 0.00 0.00 42.06 4.01
373 376 1.023513 GTAGCAGTGCTTGGAGGCTG 61.024 60.000 25.23 0.00 40.44 4.85
390 393 5.992217 GGAGGCTGTTGAATTAGACGATATT 59.008 40.000 0.00 0.00 0.00 1.28
432 435 3.119990 CCGTTGCCACCAAAGTAACATAG 60.120 47.826 0.00 0.00 31.68 2.23
433 436 3.669557 CGTTGCCACCAAAGTAACATAGC 60.670 47.826 0.00 0.00 31.68 2.97
475 478 2.126467 CAATGGTTTCCGTTGTTGCAG 58.874 47.619 11.30 0.00 43.37 4.41
476 479 0.031994 ATGGTTTCCGTTGTTGCAGC 59.968 50.000 0.00 0.00 0.00 5.25
541 548 2.739379 GTTCAGCCTTTCTTCTCCTTCG 59.261 50.000 0.00 0.00 0.00 3.79
570 577 5.476599 TGATGCACCTACTTGTTTTAATGCT 59.523 36.000 0.00 0.00 33.03 3.79
624 631 8.790718 ACAACATCCAATTCATAATAGCATCTC 58.209 33.333 0.00 0.00 0.00 2.75
673 680 4.943705 TGGCAAGATGGTTATTTCTGACTC 59.056 41.667 0.00 0.00 0.00 3.36
702 709 1.748493 GTTTGTTGAGTTGGCTGTGGA 59.252 47.619 0.00 0.00 0.00 4.02
1268 1301 4.922103 AGTCTTGCTAAGCTAACAACGTAC 59.078 41.667 0.00 0.00 0.00 3.67
1321 1354 3.798337 GGTGTTGTGATGCTTTTGTCTTG 59.202 43.478 0.00 0.00 0.00 3.02
1355 1388 5.291971 AGACGTTTAACTGACGGTGTATTT 58.708 37.500 3.47 0.00 44.34 1.40
1393 1426 7.962995 TGTGAAGTATCCTTCTATCTCTGTT 57.037 36.000 0.00 0.00 46.07 3.16
1649 1716 5.356751 GTCTTTGGGCAACATCATACACATA 59.643 40.000 0.00 0.00 39.74 2.29
1872 1939 2.351641 GCAAATGAAGACATCGGTTGCA 60.352 45.455 11.21 0.00 42.45 4.08
2000 2068 3.094386 AGTTTTGCTGAAGCGGACA 57.906 47.368 0.00 0.00 45.83 4.02
2088 2158 7.330900 AGTGATGCTTACTATACGTACAGTT 57.669 36.000 12.45 0.00 0.00 3.16
2090 2160 8.341173 AGTGATGCTTACTATACGTACAGTTAC 58.659 37.037 12.45 2.99 0.00 2.50
2253 2323 4.467795 TGTGCTATCTGCTTATCCCTATCC 59.532 45.833 0.00 0.00 43.37 2.59
2541 2613 4.201950 CCATGCTTTATGTGCCTTGTAGAC 60.202 45.833 0.00 0.00 34.87 2.59
2609 2681 2.427506 GAAATTCCGCTGGTCAAGAGT 58.572 47.619 0.00 0.00 0.00 3.24
2620 2692 1.534595 GGTCAAGAGTACGTCGTCAGT 59.465 52.381 0.00 0.00 0.00 3.41
2635 2707 3.881688 TCGTCAGTATTGGCTAGGTAGTC 59.118 47.826 0.00 0.00 0.00 2.59
2897 2969 7.348201 CACTTGCTAAGACTTTCAGTAACTTG 58.652 38.462 0.00 0.00 0.00 3.16
2912 2984 8.365399 TCAGTAACTTGTTCAACTCAGTATTG 57.635 34.615 0.00 0.00 0.00 1.90
2954 3040 3.973206 TTCGATATGGCGGGACATAAT 57.027 42.857 0.00 0.00 36.94 1.28
2959 3045 6.231951 TCGATATGGCGGGACATAATTTTTA 58.768 36.000 0.00 0.00 36.94 1.52
2961 3047 7.392113 TCGATATGGCGGGACATAATTTTTATT 59.608 33.333 0.00 0.00 36.94 1.40
2962 3048 8.670135 CGATATGGCGGGACATAATTTTTATTA 58.330 33.333 0.00 0.00 36.94 0.98
3108 3197 7.676893 TGGACTCTTATTTACCCTGTTTCTCTA 59.323 37.037 0.00 0.00 0.00 2.43
3122 3211 7.056635 CCTGTTTCTCTATCTCTCTCTCTCTT 58.943 42.308 0.00 0.00 0.00 2.85
3123 3212 7.012704 CCTGTTTCTCTATCTCTCTCTCTCTTG 59.987 44.444 0.00 0.00 0.00 3.02
3179 3294 5.402568 GCTAATCGATTTATGCTCGACTTCA 59.597 40.000 17.19 0.00 46.76 3.02
3194 3309 6.128254 GCTCGACTTCATATTTTAATAGCCCC 60.128 42.308 0.00 0.00 0.00 5.80
3201 3316 9.147732 CTTCATATTTTAATAGCCCCTTTTCCT 57.852 33.333 0.00 0.00 0.00 3.36
3468 3583 6.464465 CCCACATACCTAATTTCTAGGTCCTG 60.464 46.154 6.73 8.71 44.10 3.86
3780 3907 2.738846 CGTCCTGGCTATTGCATATGTC 59.261 50.000 4.29 0.00 41.91 3.06
3836 3963 7.483059 GCTTGCTGATTGTTTGATAGTTAGTTC 59.517 37.037 0.00 0.00 0.00 3.01
3941 5834 6.330250 AGCAGGTACATAAATTCCTAGTGGAT 59.670 38.462 0.00 0.00 42.81 3.41
4351 6251 3.438434 GCATCCCTTCTCTCAGTTTTCAC 59.562 47.826 0.00 0.00 0.00 3.18
4359 6259 5.959618 TCTCTCAGTTTTCACGTCTCATA 57.040 39.130 0.00 0.00 0.00 2.15
4360 6260 5.700846 TCTCTCAGTTTTCACGTCTCATAC 58.299 41.667 0.00 0.00 0.00 2.39
4385 6299 9.653287 ACGTATACCATACATAAATGATGGAAG 57.347 33.333 19.51 11.84 40.18 3.46
4386 6300 9.869757 CGTATACCATACATAAATGATGGAAGA 57.130 33.333 19.51 10.29 40.18 2.87
4436 6350 4.523083 TGTGGTAGTTTGCTCAAAGAAGT 58.477 39.130 0.00 0.00 0.00 3.01
4438 6352 5.417580 TGTGGTAGTTTGCTCAAAGAAGTTT 59.582 36.000 0.00 0.00 0.00 2.66
4439 6353 6.071616 TGTGGTAGTTTGCTCAAAGAAGTTTT 60.072 34.615 0.00 0.00 0.00 2.43
4440 6354 6.811665 GTGGTAGTTTGCTCAAAGAAGTTTTT 59.188 34.615 0.00 0.00 0.00 1.94
4475 6389 6.882678 TCCTTTAGTTATTCTTAGCGGCTTTT 59.117 34.615 8.26 0.00 0.00 2.27
4476 6390 7.392393 TCCTTTAGTTATTCTTAGCGGCTTTTT 59.608 33.333 8.26 0.00 0.00 1.94
4492 6406 4.401657 TTTTTGGGTGGGTTGGGG 57.598 55.556 0.00 0.00 0.00 4.96
4493 6407 1.384643 TTTTTGGGTGGGTTGGGGG 60.385 57.895 0.00 0.00 0.00 5.40
4575 6714 6.127619 GGTTTTCCATGGTCTCTTTATTCCAG 60.128 42.308 12.58 0.00 40.31 3.86
4646 6880 8.621532 TGTTAGCTTGAATTGAACTCTGTTAT 57.378 30.769 0.00 0.00 0.00 1.89
4657 6891 6.822667 TGAACTCTGTTATTGTGATTGCAT 57.177 33.333 0.00 0.00 0.00 3.96
4761 7072 6.684686 TCTTCGTGTTGTAGTAGCACTTATT 58.315 36.000 0.00 0.00 38.25 1.40
4834 7145 0.533491 TGGCATTTGGATTGCTGCTC 59.467 50.000 0.00 0.00 40.03 4.26
4845 7156 3.622612 GGATTGCTGCTCTTTCTCTCTTC 59.377 47.826 0.00 0.00 0.00 2.87
5363 7697 0.394938 AGCGTGTTGGTATGTGGTCA 59.605 50.000 0.00 0.00 0.00 4.02
5900 8234 4.801164 TCAATAGGTGTCTCCCTACTACC 58.199 47.826 0.00 0.00 39.86 3.18
5901 8235 4.481280 TCAATAGGTGTCTCCCTACTACCT 59.519 45.833 0.00 0.00 43.69 3.08
5903 8237 2.575713 AGGTGTCTCCCTACTACCTCT 58.424 52.381 0.00 0.00 37.15 3.69
6182 8530 8.949421 AGTTTTATGGAAGATGGATGTAGGTAT 58.051 33.333 0.00 0.00 0.00 2.73
6185 8533 8.609617 TTATGGAAGATGGATGTAGGTATAGG 57.390 38.462 0.00 0.00 0.00 2.57
6186 8534 5.977533 TGGAAGATGGATGTAGGTATAGGT 58.022 41.667 0.00 0.00 0.00 3.08
6187 8535 7.111136 TGGAAGATGGATGTAGGTATAGGTA 57.889 40.000 0.00 0.00 0.00 3.08
6514 8870 9.874195 TGTATAGGATGCTATATATTCTGCTCT 57.126 33.333 16.01 0.00 0.00 4.09
6545 8902 4.592485 AACGGGCACATATTTTGTTTGA 57.408 36.364 0.00 0.00 36.00 2.69
6620 8978 3.213249 AGCTCGGTAGTGTTCGTAAAG 57.787 47.619 0.00 0.00 0.00 1.85
6888 9246 1.080705 AACTAGTGTCGTGAGCCGC 60.081 57.895 0.00 0.00 36.19 6.53
6968 9326 3.485947 TTTTGAACTGGATATGTGCGC 57.514 42.857 0.00 0.00 0.00 6.09
7056 9414 0.109132 CCAATCGCCAAACCTTGCTC 60.109 55.000 0.00 0.00 0.00 4.26
7198 9556 8.953313 TCCACATGATATTTGCATGAATCTATC 58.047 33.333 10.22 0.00 44.49 2.08
7317 9675 4.585581 GGGAGGACTACATAGGAGTTCTTC 59.414 50.000 0.00 0.00 32.58 2.87
7375 9733 3.775261 AGAAGCCATTTTTGCACCATT 57.225 38.095 0.00 0.00 0.00 3.16
7421 9832 9.952188 TTTAGATATCACTCGAAACACTGATAG 57.048 33.333 5.32 0.00 30.93 2.08
7427 9838 5.863935 TCACTCGAAACACTGATAGAATGTG 59.136 40.000 0.00 0.00 37.67 3.21
7543 9954 3.822735 CGGTCCAGAAATCATATGGCAAT 59.177 43.478 2.13 0.00 33.92 3.56
7681 10092 3.427368 CCTCACGTGAAGATCAGAGAGTG 60.427 52.174 20.49 2.67 0.00 3.51
7945 10356 2.173569 ACCTGGCCTGGAAGATAACATC 59.826 50.000 33.43 0.00 34.07 3.06
8059 10470 1.611491 GAGGTTGGTTCATTGCCGAAA 59.389 47.619 0.00 0.00 0.00 3.46
8239 10650 3.658351 AATGCTATTTGTCGCGTCTTC 57.342 42.857 5.77 0.00 0.00 2.87
8240 10651 1.355971 TGCTATTTGTCGCGTCTTCC 58.644 50.000 5.77 0.00 0.00 3.46
8241 10652 1.337354 TGCTATTTGTCGCGTCTTCCA 60.337 47.619 5.77 0.00 0.00 3.53
8282 10706 1.915141 CTGATGCCTCCTTGTTTGGT 58.085 50.000 0.00 0.00 0.00 3.67
8323 10747 9.851686 TTCATAAAATGTAGCCTAGTCATTGAT 57.148 29.630 0.00 0.00 33.04 2.57
8333 10757 4.505566 GCCTAGTCATTGATTATGCTCCCA 60.506 45.833 8.53 0.00 34.06 4.37
8335 10759 4.785346 AGTCATTGATTATGCTCCCAGT 57.215 40.909 0.00 0.00 34.06 4.00
8347 10771 1.272769 GCTCCCAGTGTACGGATATCC 59.727 57.143 12.14 12.14 0.00 2.59
8390 10831 5.895636 TCAAACATAAATTGAGCCGACAT 57.104 34.783 0.00 0.00 33.15 3.06
8392 10833 5.182950 TCAAACATAAATTGAGCCGACATGT 59.817 36.000 0.00 0.00 33.15 3.21
8414 10856 4.273480 GTGTCGGCTGTTGCATATTATCTT 59.727 41.667 0.00 0.00 41.91 2.40
8511 10955 1.634702 GCTGTAGAGTGTAGTGCAGC 58.365 55.000 0.00 0.00 43.67 5.25
8535 10979 4.574421 GCTTGGTTTTGTTTGGCATAAGTT 59.426 37.500 0.00 0.00 0.00 2.66
8539 10983 5.128827 TGGTTTTGTTTGGCATAAGTTGGTA 59.871 36.000 0.00 0.00 0.00 3.25
8560 11004 0.331278 TTTCTTGGCCGGATCATGGT 59.669 50.000 5.05 0.00 0.00 3.55
8671 11162 2.177888 GGGCAGGAAGGGATAAAGGATT 59.822 50.000 0.00 0.00 0.00 3.01
8896 11413 3.138884 TGTCCATGCACTCAAAGCTTA 57.861 42.857 0.00 0.00 0.00 3.09
8910 11429 4.825085 TCAAAGCTTACCCATCTTTTCGTT 59.175 37.500 0.00 0.00 0.00 3.85
8983 11505 1.241315 CCTTTTGGGTACAGGGCACG 61.241 60.000 0.00 0.00 35.46 5.34
9000 11522 2.665519 GCACGGCTACAACATTTGACTG 60.666 50.000 0.00 0.00 0.00 3.51
9006 11528 3.730715 GCTACAACATTTGACTGTGCAAC 59.269 43.478 0.00 0.00 37.35 4.17
9065 11587 0.460459 GCCCGAGGAGAACACTAAGC 60.460 60.000 0.00 0.00 0.00 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 2.536997 AATTCCGGAACAGAGCCCCG 62.537 60.000 21.56 0.00 42.64 5.73
76 77 1.681780 GGATTTGGATCGTGGCAAGGA 60.682 52.381 0.00 0.00 32.84 3.36
80 81 1.077068 GGGGATTTGGATCGTGGCA 60.077 57.895 0.00 0.00 32.84 4.92
124 125 7.390027 AGGATCTAGACGGAAAATGGATAATG 58.610 38.462 0.00 0.00 0.00 1.90
125 126 7.310734 GGAGGATCTAGACGGAAAATGGATAAT 60.311 40.741 0.00 0.00 33.73 1.28
140 141 5.418692 TTCATAACAGGGGAGGATCTAGA 57.581 43.478 0.00 0.00 33.73 2.43
165 166 7.438459 GGCTAACAAATACTTCGATGTCTGTAT 59.562 37.037 7.29 0.00 0.00 2.29
166 167 6.755141 GGCTAACAAATACTTCGATGTCTGTA 59.245 38.462 7.29 0.00 0.00 2.74
168 169 5.276395 CGGCTAACAAATACTTCGATGTCTG 60.276 44.000 7.29 6.85 0.00 3.51
171 172 4.751060 TCGGCTAACAAATACTTCGATGT 58.249 39.130 9.12 9.12 0.00 3.06
180 181 5.164954 GCCACAAATTTCGGCTAACAAATA 58.835 37.500 17.35 0.00 42.78 1.40
205 206 1.811266 CTCACGCCCCACAGAATCG 60.811 63.158 0.00 0.00 0.00 3.34
261 262 3.117512 CCCTAGTAATGCCCTGGTCATTT 60.118 47.826 8.41 0.00 35.87 2.32
303 304 3.119029 CCCCATTACAAACTGAGGCAATG 60.119 47.826 0.00 0.00 0.00 2.82
365 368 2.565391 TCGTCTAATTCAACAGCCTCCA 59.435 45.455 0.00 0.00 0.00 3.86
367 370 7.329717 CCTAATATCGTCTAATTCAACAGCCTC 59.670 40.741 0.00 0.00 0.00 4.70
373 376 5.347907 CGCCCCTAATATCGTCTAATTCAAC 59.652 44.000 0.00 0.00 0.00 3.18
412 415 3.506067 AGCTATGTTACTTTGGTGGCAAC 59.494 43.478 0.00 0.00 0.00 4.17
432 435 5.924254 TGCGATACCATTAGTACATTACAGC 59.076 40.000 0.00 0.00 32.46 4.40
433 436 7.940178 TTGCGATACCATTAGTACATTACAG 57.060 36.000 0.00 0.00 32.46 2.74
475 478 2.678336 GACCACCTGTTTACAGCTATGC 59.322 50.000 4.34 0.00 42.47 3.14
476 479 3.935203 CTGACCACCTGTTTACAGCTATG 59.065 47.826 4.34 2.97 42.47 2.23
488 491 0.625849 ATTTAGGGGCTGACCACCTG 59.374 55.000 0.00 0.00 42.21 4.00
494 497 4.164843 TCCACAATATTTAGGGGCTGAC 57.835 45.455 3.70 0.00 0.00 3.51
495 498 4.871871 TTCCACAATATTTAGGGGCTGA 57.128 40.909 3.70 0.00 0.00 4.26
541 548 2.636830 ACAAGTAGGTGCATCATGAGC 58.363 47.619 0.00 5.90 0.00 4.26
570 577 2.308722 GGGGATCCTTCTGCACCCA 61.309 63.158 12.58 0.00 42.03 4.51
673 680 0.381801 ACTCAACAAACGCCAAGCAG 59.618 50.000 0.00 0.00 0.00 4.24
702 709 2.819284 GCGCAACCCCTAGCCCTAT 61.819 63.158 0.30 0.00 0.00 2.57
1298 1331 3.290710 AGACAAAAGCATCACAACACCT 58.709 40.909 0.00 0.00 0.00 4.00
1321 1354 3.746492 AGTTAAACGTCTTCCAGTGATGC 59.254 43.478 0.00 0.00 0.00 3.91
1393 1426 8.868522 TTAACAAGTACTAGCTTACACTAGGA 57.131 34.615 0.00 0.00 43.34 2.94
1449 1482 6.944557 TTCTGTCTGACATACATTTGTACG 57.055 37.500 11.45 0.00 32.72 3.67
1682 1749 1.665735 GCGGCATAATATTTGTGGGCG 60.666 52.381 15.10 15.10 45.44 6.13
1692 1759 5.375417 CATTCAAATGGAGCGGCATAATA 57.625 39.130 1.45 0.00 32.78 0.98
1853 1920 4.487948 CAATGCAACCGATGTCTTCATTT 58.512 39.130 0.00 0.00 34.06 2.32
2088 2158 6.547880 ACAACAAACATTATGGAAGTGTGGTA 59.452 34.615 0.00 0.00 0.00 3.25
2090 2160 5.691305 CACAACAAACATTATGGAAGTGTGG 59.309 40.000 0.00 0.00 0.00 4.17
2401 2473 4.002316 GGTATACAGTACCGGCACAAAAA 58.998 43.478 7.75 0.00 0.00 1.94
2609 2681 2.615447 CCTAGCCAATACTGACGACGTA 59.385 50.000 0.00 0.00 0.00 3.57
2620 2692 2.410790 GGGGGACTACCTAGCCAATA 57.589 55.000 0.00 0.00 40.03 1.90
2763 2835 8.972127 CCACCAGCAGTATATAGTGTAGATAAT 58.028 37.037 17.04 0.00 0.00 1.28
2825 2897 5.771666 ACCACTGAACAAATCATCTGATTGT 59.228 36.000 6.20 4.69 43.41 2.71
2897 2969 5.701290 AGTAACCTGCAATACTGAGTTGAAC 59.299 40.000 0.00 0.00 31.35 3.18
2912 2984 1.135286 GGCAGCAAATCAGTAACCTGC 60.135 52.381 0.00 0.00 43.52 4.85
3108 3197 6.040842 GCAATAACCTCAAGAGAGAGAGAGAT 59.959 42.308 0.00 0.00 44.98 2.75
3150 3265 7.189693 TCGAGCATAAATCGATTAGCATTTT 57.810 32.000 23.44 7.73 43.79 1.82
3179 3294 7.837191 AGGAGGAAAAGGGGCTATTAAAATAT 58.163 34.615 0.00 0.00 0.00 1.28
3468 3583 3.126073 CAAAGAAGCAAAGGTTGAAGGC 58.874 45.455 0.00 0.00 0.00 4.35
3836 3963 7.065443 TGACTCTAGTGAAATGCTGATTCATTG 59.935 37.037 0.00 0.00 38.89 2.82
3941 5834 2.367894 TGTGTCATTGGGGTTACGTACA 59.632 45.455 0.00 0.00 0.00 2.90
4359 6259 9.653287 CTTCCATCATTTATGTATGGTATACGT 57.347 33.333 14.93 0.00 37.08 3.57
4360 6260 9.869757 TCTTCCATCATTTATGTATGGTATACG 57.130 33.333 14.93 0.00 37.08 3.06
4380 6294 4.019681 CCCACCTGTTTAGTATGTCTTCCA 60.020 45.833 0.00 0.00 0.00 3.53
4381 6295 4.514401 CCCACCTGTTTAGTATGTCTTCC 58.486 47.826 0.00 0.00 0.00 3.46
4382 6296 3.939592 GCCCACCTGTTTAGTATGTCTTC 59.060 47.826 0.00 0.00 0.00 2.87
4383 6297 3.308188 GGCCCACCTGTTTAGTATGTCTT 60.308 47.826 0.00 0.00 0.00 3.01
4384 6298 2.238898 GGCCCACCTGTTTAGTATGTCT 59.761 50.000 0.00 0.00 0.00 3.41
4385 6299 2.640184 GGCCCACCTGTTTAGTATGTC 58.360 52.381 0.00 0.00 0.00 3.06
4386 6300 1.065709 CGGCCCACCTGTTTAGTATGT 60.066 52.381 0.00 0.00 0.00 2.29
4387 6301 1.663695 CGGCCCACCTGTTTAGTATG 58.336 55.000 0.00 0.00 0.00 2.39
4388 6302 0.544697 CCGGCCCACCTGTTTAGTAT 59.455 55.000 0.00 0.00 0.00 2.12
4389 6303 0.544833 TCCGGCCCACCTGTTTAGTA 60.545 55.000 0.00 0.00 0.00 1.82
4390 6304 1.838073 CTCCGGCCCACCTGTTTAGT 61.838 60.000 0.00 0.00 0.00 2.24
4445 6359 8.833493 GCCGCTAAGAATAACTAAAGGAAATAA 58.167 33.333 0.00 0.00 0.00 1.40
4446 6360 8.208903 AGCCGCTAAGAATAACTAAAGGAAATA 58.791 33.333 0.00 0.00 0.00 1.40
4447 6361 7.054751 AGCCGCTAAGAATAACTAAAGGAAAT 58.945 34.615 0.00 0.00 0.00 2.17
4475 6389 1.384643 CCCCCAACCCACCCAAAAA 60.385 57.895 0.00 0.00 0.00 1.94
4476 6390 2.287251 CCCCCAACCCACCCAAAA 59.713 61.111 0.00 0.00 0.00 2.44
4501 6415 0.771755 GATCATAACACCCCTCCCCC 59.228 60.000 0.00 0.00 0.00 5.40
4502 6416 0.396811 CGATCATAACACCCCTCCCC 59.603 60.000 0.00 0.00 0.00 4.81
4503 6417 1.129058 ACGATCATAACACCCCTCCC 58.871 55.000 0.00 0.00 0.00 4.30
4504 6418 1.760613 TCACGATCATAACACCCCTCC 59.239 52.381 0.00 0.00 0.00 4.30
4505 6419 3.536956 TTCACGATCATAACACCCCTC 57.463 47.619 0.00 0.00 0.00 4.30
4506 6420 3.992943 TTTCACGATCATAACACCCCT 57.007 42.857 0.00 0.00 0.00 4.79
4507 6421 5.236478 CACTATTTCACGATCATAACACCCC 59.764 44.000 0.00 0.00 0.00 4.95
4508 6422 5.815740 ACACTATTTCACGATCATAACACCC 59.184 40.000 0.00 0.00 0.00 4.61
4509 6423 6.903883 ACACTATTTCACGATCATAACACC 57.096 37.500 0.00 0.00 0.00 4.16
4646 6880 8.196771 ACTGAGAAGTTTAAAATGCAATCACAA 58.803 29.630 0.00 0.00 0.00 3.33
4727 7038 9.199982 CTACTACAACACGAAGAAAATTAAGGA 57.800 33.333 0.00 0.00 0.00 3.36
4740 7051 6.016213 TCAATAAGTGCTACTACAACACGA 57.984 37.500 0.00 0.00 39.31 4.35
4834 7145 4.392445 CAGCAACTCCATGAAGAGAGAAAG 59.608 45.833 6.04 0.00 37.33 2.62
4845 7156 0.250858 TGACACCCAGCAACTCCATG 60.251 55.000 0.00 0.00 0.00 3.66
5363 7697 3.243771 CGTCACCTCTAAGAACTGTTGGT 60.244 47.826 0.00 0.00 0.00 3.67
5881 8215 4.105057 CAGAGGTAGTAGGGAGACACCTAT 59.895 50.000 0.00 0.00 44.48 2.57
6212 8561 9.594478 TGAAAATAGAAAGGAAAAGAAACAACC 57.406 29.630 0.00 0.00 0.00 3.77
6514 8870 8.349245 CAAAATATGTGCCCGTTATCTATTGAA 58.651 33.333 0.00 0.00 0.00 2.69
6515 8871 7.500892 ACAAAATATGTGCCCGTTATCTATTGA 59.499 33.333 0.00 0.00 41.93 2.57
6620 8978 8.887717 AGAATGTTTTGTACAGCTGATTCTATC 58.112 33.333 23.35 6.46 40.83 2.08
7056 9414 1.539827 GGACCGGAACCAAACAGAATG 59.460 52.381 9.46 0.00 46.00 2.67
7198 9556 5.219343 TGGAGTAATCACTGATGCTATGG 57.781 43.478 0.00 0.00 34.21 2.74
7228 9586 1.630369 TGAACAGATCAGGGGTTCAGG 59.370 52.381 14.35 0.00 44.14 3.86
7298 9656 6.487299 AATGGAAGAACTCCTATGTAGTCC 57.513 41.667 0.00 0.00 45.64 3.85
7317 9675 8.755018 GTCAAACTTCATCTACAAACAAAATGG 58.245 33.333 0.00 0.00 0.00 3.16
7421 9832 7.144661 TGTGTATTGGAACATCAAACACATTC 58.855 34.615 14.91 0.00 39.95 2.67
7427 9838 5.920273 CCTGTTGTGTATTGGAACATCAAAC 59.080 40.000 0.00 0.00 39.30 2.93
7543 9954 7.067372 CCAAAAGGAATGTTATCTATGTCTGCA 59.933 37.037 0.00 0.00 0.00 4.41
7681 10092 2.103042 AGCCGATGCGCTTGTCTTC 61.103 57.895 9.73 0.00 44.33 2.87
7945 10356 1.148310 CAAGTGCTACACCCAGAACG 58.852 55.000 0.00 0.00 34.49 3.95
8059 10470 6.264067 GCATATGGCTTTGACCTTTCTTATCT 59.736 38.462 4.56 0.00 40.25 1.98
8282 10706 8.107095 ACATTTTATGAACTAACAGGCTCCTTA 58.893 33.333 0.00 0.00 0.00 2.69
8288 10712 6.318900 AGGCTACATTTTATGAACTAACAGGC 59.681 38.462 0.00 0.00 0.00 4.85
8323 10747 1.855295 TCCGTACACTGGGAGCATAA 58.145 50.000 0.00 0.00 0.00 1.90
8333 10757 3.813443 ACGTACAGGATATCCGTACACT 58.187 45.455 32.42 23.05 41.54 3.55
8335 10759 4.696877 CCATACGTACAGGATATCCGTACA 59.303 45.833 32.42 23.64 41.54 2.90
8347 10771 2.273370 ACGCTTCACCATACGTACAG 57.727 50.000 0.00 0.00 36.91 2.74
8390 10831 1.819928 AATATGCAACAGCCGACACA 58.180 45.000 0.00 0.00 0.00 3.72
8392 10833 4.071961 AGATAATATGCAACAGCCGACA 57.928 40.909 0.00 0.00 0.00 4.35
8511 10955 1.580815 ATGCCAAACAAAACCAAGCG 58.419 45.000 0.00 0.00 0.00 4.68
8535 10979 2.025793 TGATCCGGCCAAGAAATTACCA 60.026 45.455 2.24 0.00 0.00 3.25
8539 10983 2.034124 CCATGATCCGGCCAAGAAATT 58.966 47.619 2.24 0.00 0.00 1.82
8560 11004 0.968393 TGACCGATCATCGACACCCA 60.968 55.000 9.16 0.00 43.74 4.51
8671 11162 7.414208 CGTGAAGACTCAGTATAACTGCTCTTA 60.414 40.741 14.64 6.32 45.54 2.10
8910 11429 1.270785 TGATTGCTCTCAACTTCGGCA 60.271 47.619 0.00 0.00 34.60 5.69
8917 11436 5.659463 ACACTAGAGATGATTGCTCTCAAC 58.341 41.667 0.00 0.00 41.58 3.18
8922 11441 6.974932 TTGAAACACTAGAGATGATTGCTC 57.025 37.500 0.00 0.00 0.00 4.26
8983 11505 2.293122 TGCACAGTCAAATGTTGTAGCC 59.707 45.455 0.00 0.00 0.00 3.93
9006 11528 0.804989 GAAGGTCGGTGCTTGGAATG 59.195 55.000 0.00 0.00 0.00 2.67
9065 11587 2.766828 CCTAGTAACCTTCTCCTGGGTG 59.233 54.545 0.00 0.00 35.81 4.61


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

AutoCloner maintained by Alex Coulton.