Multiple sequence alignment - TraesCS4D01G083000

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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 TraesCS4D01G083000 chr4D 100.000 4154 0 0 1 4154 56746153 56742000 0.000000e+00 7672.0
1 TraesCS4D01G083000 chr4D 86.463 2098 238 21 1292 3348 49937896 49935804 0.000000e+00 2259.0
2 TraesCS4D01G083000 chr4D 83.765 733 59 26 3414 4133 49935743 49935058 1.260000e-179 640.0
3 TraesCS4D01G083000 chr4D 85.813 578 74 2 2000 2574 50031868 50031296 1.280000e-169 606.0
4 TraesCS4D01G083000 chr4D 81.385 650 71 31 720 1349 49938360 49937741 6.240000e-133 484.0
5 TraesCS4D01G083000 chr4A 91.579 3028 165 24 398 3369 540414842 540417835 0.000000e+00 4096.0
6 TraesCS4D01G083000 chr4A 93.428 2115 115 17 1267 3369 540059187 540061289 0.000000e+00 3114.0
7 TraesCS4D01G083000 chr4A 86.735 1078 61 35 331 1349 540058308 540059362 0.000000e+00 1123.0
8 TraesCS4D01G083000 chr4A 94.110 747 26 7 3414 4154 540417844 540418578 0.000000e+00 1120.0
9 TraesCS4D01G083000 chr4A 93.566 746 29 6 3414 4154 540061298 540062029 0.000000e+00 1094.0
10 TraesCS4D01G083000 chr4A 88.667 300 23 5 3 300 540058022 540058312 5.110000e-94 355.0
11 TraesCS4D01G083000 chr4B 96.322 435 12 2 3721 4154 83312376 83311945 0.000000e+00 712.0
12 TraesCS4D01G083000 chr4B 82.143 364 45 11 3414 3771 242924218 242923869 1.130000e-75 294.0
13 TraesCS4D01G083000 chr3A 83.186 452 53 18 3417 3858 57010813 57010375 3.890000e-105 392.0
14 TraesCS4D01G083000 chr3A 82.787 244 26 5 3908 4151 18869701 18869928 1.960000e-48 204.0
15 TraesCS4D01G083000 chr5B 81.593 364 47 11 3414 3771 115862882 115862533 2.440000e-72 283.0
16 TraesCS4D01G083000 chr5A 83.607 244 25 4 3908 4151 708310368 708310596 9.040000e-52 215.0
17 TraesCS4D01G083000 chr5A 83.197 244 26 4 3908 4151 567943636 567943408 4.210000e-50 209.0
18 TraesCS4D01G083000 chr6D 94.958 119 6 0 1562 1680 454585291 454585173 1.970000e-43 187.0
19 TraesCS4D01G083000 chr6D 95.556 45 0 2 3368 3410 440594699 440594655 2.070000e-08 71.3
20 TraesCS4D01G083000 chr3D 94.118 119 7 0 1562 1680 571691627 571691509 9.170000e-42 182.0
21 TraesCS4D01G083000 chr2D 94.118 119 7 0 1562 1680 524269699 524269581 9.170000e-42 182.0
22 TraesCS4D01G083000 chr2D 90.323 62 4 2 3698 3759 161645486 161645427 3.440000e-11 80.5
23 TraesCS4D01G083000 chr6A 93.277 119 8 0 1562 1680 521552226 521552108 4.270000e-40 176.0
24 TraesCS4D01G083000 chr1D 93.966 116 7 0 1562 1677 14149004 14149119 4.270000e-40 176.0
25 TraesCS4D01G083000 chr7A 92.437 119 9 0 1562 1680 422485336 422485218 1.990000e-38 171.0
26 TraesCS4D01G083000 chr2A 91.935 62 4 1 3698 3759 172527393 172527333 7.400000e-13 86.1
27 TraesCS4D01G083000 chr3B 93.878 49 1 2 3368 3414 760671195 760671147 5.760000e-09 73.1
28 TraesCS4D01G083000 chr3B 95.556 45 0 2 3368 3410 648906005 648906049 2.070000e-08 71.3
29 TraesCS4D01G083000 chr5D 100.000 36 0 0 3375 3410 217445466 217445501 2.680000e-07 67.6
30 TraesCS4D01G083000 chr5D 91.111 45 4 0 3375 3419 377147893 377147849 1.250000e-05 62.1
31 TraesCS4D01G083000 chrUn 93.333 45 1 2 3375 3418 101229548 101229591 9.640000e-07 65.8
32 TraesCS4D01G083000 chr2B 95.122 41 2 0 3375 3415 694757106 694757146 9.640000e-07 65.8
33 TraesCS4D01G083000 chr6B 91.304 46 4 0 3375 3420 561640564 561640519 3.470000e-06 63.9
34 TraesCS4D01G083000 chr1B 97.222 36 1 0 3375 3410 16863199 16863234 1.250000e-05 62.1


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 TraesCS4D01G083000 chr4D 56742000 56746153 4153 True 7672.000000 7672 100.0000 1 4154 1 chr4D.!!$R2 4153
1 TraesCS4D01G083000 chr4D 49935058 49938360 3302 True 1127.666667 2259 83.8710 720 4133 3 chr4D.!!$R3 3413
2 TraesCS4D01G083000 chr4D 50031296 50031868 572 True 606.000000 606 85.8130 2000 2574 1 chr4D.!!$R1 574
3 TraesCS4D01G083000 chr4A 540414842 540418578 3736 False 2608.000000 4096 92.8445 398 4154 2 chr4A.!!$F2 3756
4 TraesCS4D01G083000 chr4A 540058022 540062029 4007 False 1421.500000 3114 90.5990 3 4154 4 chr4A.!!$F1 4151

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
574 580 0.027455 CCGAACGCCGTATACGTACA 59.973 55.0 22.87 0.0 44.3 2.90 F
1224 1342 0.178975 CGCCCTACCTCCTCTCAGAT 60.179 60.0 0.00 0.0 0.0 2.90 F
2178 2356 0.846693 AAGTTGCCCAGTTGAGGTCT 59.153 50.0 0.00 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2202 2380 0.111446 TTTTGATCCACGGCCAAGGA 59.889 50.0 14.98 14.98 38.5 3.36 R
2511 2689 0.178981 AATGGTCCACTGCAGCAAGT 60.179 50.0 15.27 0.00 0.0 3.16 R
3183 3363 0.770499 TTCCCATCCTTGTCAGTGCA 59.230 50.0 0.00 0.00 0.0 4.57 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
41 42 4.400251 CCTCCACCGTCCTCCCCT 62.400 72.222 0.00 0.00 0.00 4.79
77 78 2.182030 CACGACCTCCCTCGCTTC 59.818 66.667 0.00 0.00 37.15 3.86
80 81 3.471806 GACCTCCCTCGCTTCCCC 61.472 72.222 0.00 0.00 0.00 4.81
99 100 3.733960 CGACGACCTCGACAGCCA 61.734 66.667 0.78 0.00 46.14 4.75
142 144 2.279784 CTCCGGCGATCTGAAGGC 60.280 66.667 9.30 1.00 0.00 4.35
148 150 1.817099 GCGATCTGAAGGCACCTGG 60.817 63.158 0.00 0.00 0.00 4.45
259 261 3.185203 ACCTGGCCCTGCTCCAAA 61.185 61.111 0.00 0.00 32.41 3.28
262 264 1.676967 CTGGCCCTGCTCCAAAGAC 60.677 63.158 0.00 0.00 32.41 3.01
289 291 3.379445 CCGGTACTGTCACGCCCT 61.379 66.667 0.00 0.00 0.00 5.19
290 292 2.126071 CGGTACTGTCACGCCCTG 60.126 66.667 0.00 0.00 0.00 4.45
291 293 2.927580 CGGTACTGTCACGCCCTGT 61.928 63.158 0.00 0.00 0.00 4.00
292 294 1.080025 GGTACTGTCACGCCCTGTC 60.080 63.158 0.00 0.00 0.00 3.51
295 297 2.725127 TACTGTCACGCCCTGTCCCT 62.725 60.000 0.00 0.00 0.00 4.20
296 298 3.596066 CTGTCACGCCCTGTCCCTG 62.596 68.421 0.00 0.00 0.00 4.45
303 305 3.644606 CCCTGTCCCTGCTGTGCT 61.645 66.667 0.00 0.00 0.00 4.40
304 306 2.359602 CCTGTCCCTGCTGTGCTG 60.360 66.667 0.00 0.00 0.00 4.41
305 307 3.054503 CTGTCCCTGCTGTGCTGC 61.055 66.667 0.00 0.00 0.00 5.25
306 308 3.548306 CTGTCCCTGCTGTGCTGCT 62.548 63.158 0.00 0.00 0.00 4.24
307 309 2.282040 GTCCCTGCTGTGCTGCTT 60.282 61.111 0.00 0.00 0.00 3.91
308 310 1.900498 GTCCCTGCTGTGCTGCTTT 60.900 57.895 0.00 0.00 0.00 3.51
309 311 1.152694 TCCCTGCTGTGCTGCTTTT 60.153 52.632 0.00 0.00 0.00 2.27
310 312 0.756442 TCCCTGCTGTGCTGCTTTTT 60.756 50.000 0.00 0.00 0.00 1.94
374 376 8.810652 TTTTTGGTATTGAAATGTGCTAAGTC 57.189 30.769 0.00 0.00 0.00 3.01
375 377 5.794687 TGGTATTGAAATGTGCTAAGTCG 57.205 39.130 0.00 0.00 0.00 4.18
376 378 5.242434 TGGTATTGAAATGTGCTAAGTCGT 58.758 37.500 0.00 0.00 0.00 4.34
400 402 3.484229 GCGTGATTCAGTCAATTCCTTCG 60.484 47.826 0.00 0.00 38.90 3.79
547 553 4.686554 CGTTTTTAATCGAAAATTGGGGCA 59.313 37.500 0.00 0.00 36.89 5.36
574 580 0.027455 CCGAACGCCGTATACGTACA 59.973 55.000 22.87 0.00 44.30 2.90
577 583 2.633299 GAACGCCGTATACGTACAGAG 58.367 52.381 22.87 12.04 44.30 3.35
594 600 4.305769 ACAGAGCTCTACCGTATACGTAG 58.694 47.826 22.87 21.09 37.74 3.51
595 601 4.038522 ACAGAGCTCTACCGTATACGTAGA 59.961 45.833 22.87 23.37 37.74 2.59
616 622 7.062605 CGTAGACGGAAGCAGACTAAATAAAAA 59.937 37.037 0.00 0.00 35.37 1.94
693 724 2.034878 AGCCTGATCTTGATAGCGTGA 58.965 47.619 0.00 0.00 0.00 4.35
696 727 3.491619 GCCTGATCTTGATAGCGTGAGAA 60.492 47.826 0.00 0.00 0.00 2.87
699 730 5.582269 CCTGATCTTGATAGCGTGAGAAAAA 59.418 40.000 0.00 0.00 0.00 1.94
700 731 6.238049 CCTGATCTTGATAGCGTGAGAAAAAG 60.238 42.308 0.00 0.00 0.00 2.27
795 848 1.722636 GGTCGGTCGGTAGCCTGTAG 61.723 65.000 0.00 0.00 0.00 2.74
796 849 1.028868 GTCGGTCGGTAGCCTGTAGT 61.029 60.000 0.00 0.00 0.00 2.73
797 850 0.541392 TCGGTCGGTAGCCTGTAGTA 59.459 55.000 0.00 0.00 0.00 1.82
806 879 4.389374 GGTAGCCTGTAGTACACCGTATA 58.611 47.826 0.00 0.00 0.00 1.47
857 930 4.280461 CGAACAAGCTACCATCTACGTAG 58.720 47.826 16.73 16.73 36.97 3.51
860 933 3.089117 GCTACCATCTACGTAGCGC 57.911 57.895 18.00 0.00 46.59 5.92
928 1001 2.987404 GCAAAAGCTTTTCCGCGCG 61.987 57.895 25.67 25.67 34.40 6.86
955 1028 1.007336 GGAAGAGTTCTCGCGCGAAA 61.007 55.000 33.99 25.16 0.00 3.46
1107 1180 2.428925 CCATACCTACGCCCACGGT 61.429 63.158 0.00 0.00 46.04 4.83
1111 1184 2.769652 TACCTACGCCCACGGTCAGT 62.770 60.000 0.00 0.00 46.04 3.41
1127 1200 2.509561 GTTCTTCTCGCCGGGCTC 60.510 66.667 18.34 0.00 0.00 4.70
1224 1342 0.178975 CGCCCTACCTCCTCTCAGAT 60.179 60.000 0.00 0.00 0.00 2.90
1225 1343 1.627864 GCCCTACCTCCTCTCAGATC 58.372 60.000 0.00 0.00 0.00 2.75
1363 1505 1.971695 CAGCCGGAAACCAACCTCC 60.972 63.158 5.05 0.00 0.00 4.30
1431 1573 3.394836 GGCTTGGACTCGGAGGCT 61.395 66.667 11.32 0.00 33.61 4.58
1441 1583 3.893763 CGGAGGCTGATCGCTCGT 61.894 66.667 0.00 0.00 39.13 4.18
1704 1873 2.126346 GGCCGCACATTGCTGAAC 60.126 61.111 0.00 0.00 42.25 3.18
1710 1879 1.242076 GCACATTGCTGAACTGGACT 58.758 50.000 0.00 0.00 40.96 3.85
1814 1983 0.940126 GTCCAATGCCTGTATCGCTG 59.060 55.000 0.00 0.00 0.00 5.18
2066 2244 5.063944 GCACTATGATTCACAACGTCTCAAT 59.936 40.000 0.00 0.00 0.00 2.57
2178 2356 0.846693 AAGTTGCCCAGTTGAGGTCT 59.153 50.000 0.00 0.00 0.00 3.85
2202 2380 4.189231 CCGGAATCAAAATCTCTACCGTT 58.811 43.478 0.00 0.00 37.87 4.44
2341 2519 1.203994 GGGAACGATCTGAGAAACCGA 59.796 52.381 8.75 0.00 0.00 4.69
2482 2660 1.594862 GATACACATGCCGTCTGAAGC 59.405 52.381 0.00 0.00 0.00 3.86
2511 2689 2.156891 GCGTCACAAATCGCTTGTTCTA 59.843 45.455 2.35 0.00 46.49 2.10
2613 2791 1.196808 CAGGCACGTGTGAACCATTAC 59.803 52.381 18.38 0.00 0.00 1.89
2619 2797 4.153475 GCACGTGTGAACCATTACAAGTAT 59.847 41.667 18.38 0.00 37.40 2.12
2629 2807 3.254166 CCATTACAAGTATCAGGCATGGC 59.746 47.826 12.14 12.14 0.00 4.40
2665 2843 1.135527 AGTTCAAACGACGAGTGTCCA 59.864 47.619 0.00 0.00 42.37 4.02
2706 2884 3.370104 AGATCCGATCAACCTTCAGTCT 58.630 45.455 11.01 0.00 0.00 3.24
2753 2931 0.739813 GATGGAGTCGAACCGGTTGG 60.740 60.000 27.87 24.68 42.84 3.77
2811 2989 0.241749 TTCAGCAATTGAGCGCAAGG 59.758 50.000 11.47 4.71 37.45 3.61
2822 3000 2.388232 GCGCAAGGTGGTTCGGTAG 61.388 63.158 0.30 0.00 38.28 3.18
2837 3015 1.553248 CGGTAGTGGATTGGGAAGTCA 59.447 52.381 0.00 0.00 0.00 3.41
2953 3131 0.035630 CTTGTCTCCTTGCCTCCCAG 60.036 60.000 0.00 0.00 0.00 4.45
2984 3163 4.258702 AGATACCAATCTGTACATCGCC 57.741 45.455 0.00 0.00 41.08 5.54
3016 3195 7.352739 GTTCGGCACCTATAAATAAACATCAG 58.647 38.462 0.00 0.00 0.00 2.90
3136 3315 0.612744 GAGCTCTTCCTCCAGCTGTT 59.387 55.000 13.81 0.00 46.31 3.16
3137 3316 1.003003 GAGCTCTTCCTCCAGCTGTTT 59.997 52.381 13.81 0.00 46.31 2.83
3146 3325 1.808945 CTCCAGCTGTTTCGCTTCATT 59.191 47.619 13.81 0.00 38.41 2.57
3155 3334 1.896339 TTCGCTTCATTGACACCGCG 61.896 55.000 0.00 0.00 41.69 6.46
3219 3399 1.881973 GGAAGCAGCACTGACAAATCA 59.118 47.619 0.81 0.00 0.00 2.57
3244 3424 3.010027 TCATAAGGTTCACAGGATGGCAA 59.990 43.478 0.00 0.00 43.62 4.52
3297 3478 3.254892 GGTTTCTTACTCTTCGGCTCTG 58.745 50.000 0.00 0.00 0.00 3.35
3381 3594 9.755804 TCAAGAACTATAATTGTCTATGCAGAG 57.244 33.333 0.69 0.69 0.00 3.35
3382 3595 8.986847 CAAGAACTATAATTGTCTATGCAGAGG 58.013 37.037 8.78 0.00 0.00 3.69
3383 3596 7.158021 AGAACTATAATTGTCTATGCAGAGGC 58.842 38.462 5.87 5.87 41.68 4.70
3384 3597 5.799213 ACTATAATTGTCTATGCAGAGGCC 58.201 41.667 10.99 0.00 40.13 5.19
3385 3598 1.959042 AATTGTCTATGCAGAGGCCG 58.041 50.000 10.99 0.00 40.13 6.13
3386 3599 0.107456 ATTGTCTATGCAGAGGCCGG 59.893 55.000 10.99 0.00 40.13 6.13
3387 3600 1.971505 TTGTCTATGCAGAGGCCGGG 61.972 60.000 10.99 0.00 40.13 5.73
3388 3601 2.844362 TCTATGCAGAGGCCGGGG 60.844 66.667 8.78 0.00 40.13 5.73
3389 3602 3.946201 CTATGCAGAGGCCGGGGG 61.946 72.222 2.18 0.00 40.13 5.40
3390 3603 4.815973 TATGCAGAGGCCGGGGGT 62.816 66.667 2.18 0.00 40.13 4.95
3391 3604 3.398365 TATGCAGAGGCCGGGGGTA 62.398 63.158 2.18 0.00 40.13 3.69
3392 3605 2.900269 TATGCAGAGGCCGGGGGTAA 62.900 60.000 2.18 0.00 40.13 2.85
3393 3606 3.489513 GCAGAGGCCGGGGGTAAT 61.490 66.667 2.18 0.00 0.00 1.89
3394 3607 2.829592 CAGAGGCCGGGGGTAATC 59.170 66.667 2.18 0.00 0.00 1.75
3395 3608 2.447959 AGAGGCCGGGGGTAATCC 60.448 66.667 2.18 0.00 0.00 3.01
3396 3609 2.447959 GAGGCCGGGGGTAATCCT 60.448 66.667 2.18 0.00 35.33 3.24
3397 3610 2.447959 AGGCCGGGGGTAATCCTC 60.448 66.667 2.18 0.00 35.33 3.71
3406 3619 3.750501 GGGGTAATCCTCCTTTTCCAA 57.249 47.619 0.00 0.00 35.33 3.53
3407 3620 4.055710 GGGGTAATCCTCCTTTTCCAAA 57.944 45.455 0.00 0.00 35.33 3.28
3408 3621 4.422057 GGGGTAATCCTCCTTTTCCAAAA 58.578 43.478 0.00 0.00 35.33 2.44
3409 3622 4.841813 GGGGTAATCCTCCTTTTCCAAAAA 59.158 41.667 0.00 0.00 35.33 1.94
3410 3623 5.046591 GGGGTAATCCTCCTTTTCCAAAAAG 60.047 44.000 5.40 5.40 35.33 2.27
3411 3624 5.778241 GGGTAATCCTCCTTTTCCAAAAAGA 59.222 40.000 12.53 0.00 0.00 2.52
3412 3625 6.269077 GGGTAATCCTCCTTTTCCAAAAAGAA 59.731 38.462 12.53 0.00 0.00 2.52
3470 3683 7.416664 GCCTCTTCAACAATCTATTGGCATAAA 60.417 37.037 7.56 0.00 41.96 1.40
3471 3684 7.917505 CCTCTTCAACAATCTATTGGCATAAAC 59.082 37.037 7.56 0.00 41.96 2.01
3472 3685 8.579850 TCTTCAACAATCTATTGGCATAAACT 57.420 30.769 7.56 0.00 41.96 2.66
3473 3686 8.677300 TCTTCAACAATCTATTGGCATAAACTC 58.323 33.333 7.56 0.00 41.96 3.01
3474 3687 8.579850 TTCAACAATCTATTGGCATAAACTCT 57.420 30.769 7.56 0.00 41.96 3.24
3475 3688 8.579850 TCAACAATCTATTGGCATAAACTCTT 57.420 30.769 7.56 0.00 41.96 2.85
3476 3689 9.679661 TCAACAATCTATTGGCATAAACTCTTA 57.320 29.630 7.56 0.00 41.96 2.10
3585 3802 3.069586 CGCTGTCCACTTATCCAGGATTA 59.930 47.826 7.44 0.00 33.33 1.75
3699 3916 1.421268 TCTTTGAGCAGGACACCATGT 59.579 47.619 0.00 0.00 0.00 3.21
3805 4023 7.542130 AGACATTTTCTGTGTTCTTGTTTTGTC 59.458 33.333 0.00 0.00 38.54 3.18
3893 4114 8.092687 AGCTTCATCTGATTTTGCTAAATGTTT 58.907 29.630 10.91 0.00 34.16 2.83
3981 4204 6.509418 TCATTGCAGGTTTGGTACTAATTC 57.491 37.500 0.00 0.00 0.00 2.17
3982 4205 6.245408 TCATTGCAGGTTTGGTACTAATTCT 58.755 36.000 0.00 0.00 0.00 2.40
3984 4207 5.957842 TGCAGGTTTGGTACTAATTCTTG 57.042 39.130 0.00 0.00 0.00 3.02
3985 4208 5.626142 TGCAGGTTTGGTACTAATTCTTGA 58.374 37.500 9.52 0.00 0.00 3.02
4085 4308 6.032956 TGTTTACGGATCACTACATGTTCT 57.967 37.500 2.30 0.00 0.00 3.01
4090 4313 4.245660 CGGATCACTACATGTTCTGTTGT 58.754 43.478 2.30 0.00 43.30 3.32
4137 4360 6.371809 TTTTCAGTAACCATCTGAACACAC 57.628 37.500 7.69 0.00 46.88 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.038490 GGGTCGGTGTAGGAGGGT 59.962 66.667 0.00 0.00 0.00 4.34
1 2 2.762875 GGGGTCGGTGTAGGAGGG 60.763 72.222 0.00 0.00 0.00 4.30
13 14 4.717313 GTGGAGGTTGCGGGGGTC 62.717 72.222 0.00 0.00 0.00 4.46
83 84 2.126424 GTGGCTGTCGAGGTCGTC 60.126 66.667 0.00 0.00 40.80 4.20
84 85 2.597805 AGTGGCTGTCGAGGTCGT 60.598 61.111 0.00 0.00 40.80 4.34
85 86 2.126307 CAGTGGCTGTCGAGGTCG 60.126 66.667 0.00 0.00 41.45 4.79
86 87 2.433318 GCAGTGGCTGTCGAGGTC 60.433 66.667 0.00 0.00 36.96 3.85
134 136 2.583441 CCGACCAGGTGCCTTCAGA 61.583 63.158 0.00 0.00 34.51 3.27
242 244 3.185203 TTTGGAGCAGGGCCAGGT 61.185 61.111 6.18 2.08 36.64 4.00
243 245 2.362120 CTTTGGAGCAGGGCCAGG 60.362 66.667 6.18 0.00 36.64 4.45
248 250 1.078848 CTCGGTCTTTGGAGCAGGG 60.079 63.158 0.00 0.00 39.68 4.45
267 269 2.431942 GTGACAGTACCGGCGTGG 60.432 66.667 6.01 0.00 46.41 4.94
289 291 2.629424 AAAGCAGCACAGCAGGGACA 62.629 55.000 0.00 0.00 36.85 4.02
290 292 1.458639 AAAAGCAGCACAGCAGGGAC 61.459 55.000 0.00 0.00 36.85 4.46
291 293 0.756442 AAAAAGCAGCACAGCAGGGA 60.756 50.000 0.00 0.00 36.85 4.20
292 294 1.744014 AAAAAGCAGCACAGCAGGG 59.256 52.632 0.00 0.00 36.85 4.45
310 312 2.915137 GCAGGGACCCCGCAAAAA 60.915 61.111 14.29 0.00 41.95 1.94
311 313 3.897122 AGCAGGGACCCCGCAAAA 61.897 61.111 21.10 0.00 41.95 2.44
312 314 4.659172 CAGCAGGGACCCCGCAAA 62.659 66.667 21.10 0.00 41.95 3.68
317 319 4.729918 CAGCACAGCAGGGACCCC 62.730 72.222 7.00 1.17 0.00 4.95
319 321 3.857309 AAGCAGCACAGCAGGGACC 62.857 63.158 0.00 0.00 36.85 4.46
320 322 2.282040 AAGCAGCACAGCAGGGAC 60.282 61.111 0.00 0.00 36.85 4.46
321 323 2.281970 CAAGCAGCACAGCAGGGA 60.282 61.111 0.00 0.00 36.85 4.20
322 324 2.596631 ACAAGCAGCACAGCAGGG 60.597 61.111 0.00 0.00 36.85 4.45
323 325 1.731433 AACACAAGCAGCACAGCAGG 61.731 55.000 0.00 0.00 36.85 4.85
324 326 0.594028 CAACACAAGCAGCACAGCAG 60.594 55.000 0.00 0.00 36.85 4.24
325 327 1.434287 CAACACAAGCAGCACAGCA 59.566 52.632 0.00 0.00 36.85 4.41
326 328 1.947642 GCAACACAAGCAGCACAGC 60.948 57.895 0.00 0.00 0.00 4.40
327 329 0.594028 CAGCAACACAAGCAGCACAG 60.594 55.000 0.00 0.00 0.00 3.66
328 330 1.031029 TCAGCAACACAAGCAGCACA 61.031 50.000 0.00 0.00 0.00 4.57
329 331 0.313043 ATCAGCAACACAAGCAGCAC 59.687 50.000 0.00 0.00 0.00 4.40
362 364 1.194547 CACGCAACGACTTAGCACATT 59.805 47.619 0.00 0.00 0.00 2.71
363 365 0.790207 CACGCAACGACTTAGCACAT 59.210 50.000 0.00 0.00 0.00 3.21
364 366 0.249114 TCACGCAACGACTTAGCACA 60.249 50.000 0.00 0.00 0.00 4.57
365 367 1.068474 ATCACGCAACGACTTAGCAC 58.932 50.000 0.00 0.00 0.00 4.40
366 368 1.724623 GAATCACGCAACGACTTAGCA 59.275 47.619 0.00 0.00 0.00 3.49
368 370 2.987149 ACTGAATCACGCAACGACTTAG 59.013 45.455 0.00 0.00 0.00 2.18
369 371 2.984471 GACTGAATCACGCAACGACTTA 59.016 45.455 0.00 0.00 0.00 2.24
370 372 1.792949 GACTGAATCACGCAACGACTT 59.207 47.619 0.00 0.00 0.00 3.01
371 373 1.269569 TGACTGAATCACGCAACGACT 60.270 47.619 0.00 0.00 29.99 4.18
372 374 1.136690 TGACTGAATCACGCAACGAC 58.863 50.000 0.00 0.00 29.99 4.34
373 375 1.859383 TTGACTGAATCACGCAACGA 58.141 45.000 0.00 0.00 36.92 3.85
374 376 2.880822 ATTGACTGAATCACGCAACG 57.119 45.000 0.00 0.00 36.92 4.10
375 377 3.189287 AGGAATTGACTGAATCACGCAAC 59.811 43.478 0.00 0.00 36.92 4.17
376 378 3.411446 AGGAATTGACTGAATCACGCAA 58.589 40.909 0.00 0.00 36.92 4.85
400 402 5.796935 CGTCAAATTGGTGATGAAATCTGAC 59.203 40.000 0.00 0.00 45.81 3.51
487 493 3.244596 GGGACAAAACAGAAGAGCTACCT 60.245 47.826 0.00 0.00 0.00 3.08
488 494 3.075148 GGGACAAAACAGAAGAGCTACC 58.925 50.000 0.00 0.00 0.00 3.18
520 526 7.063662 GCCCCAATTTTCGATTAAAAACGTATT 59.936 33.333 0.00 0.00 40.37 1.89
521 527 6.532302 GCCCCAATTTTCGATTAAAAACGTAT 59.468 34.615 0.00 0.00 40.37 3.06
547 553 1.229315 TACGGCGTTCGGCATGTTTT 61.229 50.000 21.24 0.00 46.16 2.43
574 580 4.555262 GTCTACGTATACGGTAGAGCTCT 58.445 47.826 27.62 22.17 44.95 4.09
577 583 3.696711 CGTCTACGTATACGGTAGAGC 57.303 52.381 27.62 20.14 44.95 4.09
594 600 7.130303 ACTTTTTATTTAGTCTGCTTCCGTC 57.870 36.000 0.00 0.00 0.00 4.79
595 601 7.227910 TCAACTTTTTATTTAGTCTGCTTCCGT 59.772 33.333 0.00 0.00 0.00 4.69
616 622 8.433421 TTCTTTCTTCGACAATAAAGTCAACT 57.567 30.769 0.00 0.00 38.43 3.16
648 679 5.822519 GGTTCTATGTCATGTTGCTGGATTA 59.177 40.000 0.00 0.00 0.00 1.75
649 680 4.641989 GGTTCTATGTCATGTTGCTGGATT 59.358 41.667 0.00 0.00 0.00 3.01
660 691 3.972638 AGATCAGGCTGGTTCTATGTCAT 59.027 43.478 15.73 0.00 0.00 3.06
795 848 6.085068 GCGTATTTTCTACGTATACGGTGTAC 59.915 42.308 27.62 17.23 44.29 2.90
796 849 6.133392 GCGTATTTTCTACGTATACGGTGTA 58.867 40.000 27.62 11.40 44.29 2.90
797 850 4.970003 GCGTATTTTCTACGTATACGGTGT 59.030 41.667 27.62 10.85 44.29 4.16
806 879 3.764885 ACGGTAGCGTATTTTCTACGT 57.235 42.857 19.91 0.00 42.35 3.57
850 923 1.297451 GTCCGACTGCGCTACGTAG 60.297 63.158 18.47 18.47 44.55 3.51
877 950 3.182372 CGTCGACGACCTGTATTATACGA 59.818 47.826 33.35 0.00 43.02 3.43
928 1001 2.911120 CGAGAACTCTTCCGATCGATC 58.089 52.381 18.66 15.68 32.13 3.69
937 1010 0.782384 TTTTCGCGCGAGAACTCTTC 59.218 50.000 32.74 0.00 0.00 2.87
945 1018 0.234884 AGGTTTCTTTTTCGCGCGAG 59.765 50.000 32.74 21.09 0.00 5.03
955 1028 0.405973 GGGGAGCTGGAGGTTTCTTT 59.594 55.000 0.00 0.00 0.00 2.52
1107 1180 2.970639 CCCGGCGAGAAGAACTGA 59.029 61.111 9.30 0.00 0.00 3.41
1111 1184 4.129737 CGAGCCCGGCGAGAAGAA 62.130 66.667 9.30 0.00 0.00 2.52
1312 1454 1.066908 GTCGGCCTCTGAATCTGAGAG 59.933 57.143 17.14 4.85 37.33 3.20
1407 1549 1.374947 CGAGTCCAAGCCCAGGAAA 59.625 57.895 0.00 0.00 36.80 3.13
1431 1573 3.784746 TCGTCGTACGAGCGATCA 58.215 55.556 27.12 13.88 46.73 2.92
1441 1583 3.502455 AGCATCCGCGTCGTCGTA 61.502 61.111 4.92 0.00 45.49 3.43
1704 1873 4.899239 GCGATCCGGCCAGTCCAG 62.899 72.222 2.24 0.00 34.01 3.86
1710 1879 4.812476 CTGAACGCGATCCGGCCA 62.812 66.667 15.93 0.00 42.52 5.36
1897 2072 2.303022 TGTTCCTGGAGTTCAGATGGAC 59.697 50.000 0.00 0.00 46.18 4.02
1959 2134 1.244019 AAGTTGCAAGTGCGGGGATC 61.244 55.000 7.73 0.00 45.83 3.36
1966 2141 1.804151 TGGACGATAAGTTGCAAGTGC 59.196 47.619 7.73 3.13 42.50 4.40
2066 2244 0.871722 CACCCATTCGCGAAGAAACA 59.128 50.000 27.20 2.47 42.91 2.83
2178 2356 3.541632 GGTAGAGATTTTGATTCCGGCA 58.458 45.455 0.00 0.00 0.00 5.69
2202 2380 0.111446 TTTTGATCCACGGCCAAGGA 59.889 50.000 14.98 14.98 38.50 3.36
2316 2494 3.594603 TTCTCAGATCGTTCCCAGTTC 57.405 47.619 0.00 0.00 0.00 3.01
2341 2519 1.131126 CGCCTCAAGCATCGATTTTGT 59.869 47.619 15.37 0.00 44.04 2.83
2482 2660 3.030475 CGATTTGTGACGCAGAATCTG 57.970 47.619 5.78 5.78 34.12 2.90
2505 2683 1.416030 TCCACTGCAGCAAGTAGAACA 59.584 47.619 15.27 0.00 33.69 3.18
2511 2689 0.178981 AATGGTCCACTGCAGCAAGT 60.179 50.000 15.27 0.00 0.00 3.16
2544 2722 4.739046 CTTCAGTGTGAAGTGGTGAATC 57.261 45.455 8.27 0.00 46.50 2.52
2629 2807 3.334691 TGAACTTATGCTTGAACTCGGG 58.665 45.455 0.00 0.00 0.00 5.14
2665 2843 1.228769 TCCAGTCAGCCACGTAGGT 60.229 57.895 0.00 0.00 40.61 3.08
2731 2909 0.898789 ACCGGTTCGACTCCATCAGT 60.899 55.000 0.00 0.00 38.45 3.41
2732 2910 0.246635 AACCGGTTCGACTCCATCAG 59.753 55.000 15.86 0.00 0.00 2.90
2753 2931 0.735978 GCAATACCTTTGCGCCCAAC 60.736 55.000 4.18 0.00 35.58 3.77
2811 2989 1.677820 CCCAATCCACTACCGAACCAC 60.678 57.143 0.00 0.00 0.00 4.16
2822 3000 0.991920 TCCCTGACTTCCCAATCCAC 59.008 55.000 0.00 0.00 0.00 4.02
2837 3015 3.404425 AGCCTAAGTATCCTGAGATCCCT 59.596 47.826 0.00 0.00 33.67 4.20
2953 3131 8.807118 TGTACAGATTGGTATCTAGATTGATCC 58.193 37.037 11.25 9.29 39.11 3.36
3136 3315 1.866237 GCGGTGTCAATGAAGCGAA 59.134 52.632 16.55 0.00 39.55 4.70
3137 3316 3.561429 GCGGTGTCAATGAAGCGA 58.439 55.556 16.55 0.00 39.55 4.93
3155 3334 1.668101 ATTCCTCAGAGACGGCGGTC 61.668 60.000 16.09 16.09 43.76 4.79
3166 3345 1.280133 TGCAGGACAGGAATTCCTCAG 59.720 52.381 24.67 16.43 46.65 3.35
3183 3363 0.770499 TTCCCATCCTTGTCAGTGCA 59.230 50.000 0.00 0.00 0.00 4.57
3219 3399 4.646492 GCCATCCTGTGAACCTTATGAAAT 59.354 41.667 0.00 0.00 0.00 2.17
3284 3465 1.840737 TAAGAGCAGAGCCGAAGAGT 58.159 50.000 0.00 0.00 0.00 3.24
3297 3478 3.275999 TCCGGCCAAGTATTTTAAGAGC 58.724 45.455 2.24 0.00 0.00 4.09
3362 3575 4.867047 CGGCCTCTGCATAGACAATTATAG 59.133 45.833 0.00 0.00 40.13 1.31
3369 3582 2.434843 CCCGGCCTCTGCATAGACA 61.435 63.158 0.00 0.00 40.13 3.41
3371 3584 2.844362 CCCCGGCCTCTGCATAGA 60.844 66.667 0.00 0.00 40.13 1.98
3372 3585 3.946201 CCCCCGGCCTCTGCATAG 61.946 72.222 0.00 0.00 40.13 2.23
3376 3589 3.477578 GATTACCCCCGGCCTCTGC 62.478 68.421 0.00 0.00 0.00 4.26
3377 3590 2.819284 GGATTACCCCCGGCCTCTG 61.819 68.421 0.00 0.00 0.00 3.35
3378 3591 2.447959 GGATTACCCCCGGCCTCT 60.448 66.667 0.00 0.00 0.00 3.69
3379 3592 2.447959 AGGATTACCCCCGGCCTC 60.448 66.667 0.00 0.00 36.73 4.70
3380 3593 2.447959 GAGGATTACCCCCGGCCT 60.448 66.667 0.00 0.00 36.73 5.19
3381 3594 3.567209 GGAGGATTACCCCCGGCC 61.567 72.222 0.00 0.00 36.73 6.13
3382 3595 1.642513 AAAGGAGGATTACCCCCGGC 61.643 60.000 0.00 0.00 36.73 6.13
3383 3596 0.924090 AAAAGGAGGATTACCCCCGG 59.076 55.000 0.00 0.00 36.73 5.73
3384 3597 1.133884 GGAAAAGGAGGATTACCCCCG 60.134 57.143 0.00 0.00 36.73 5.73
3385 3598 1.927371 TGGAAAAGGAGGATTACCCCC 59.073 52.381 0.00 0.00 36.73 5.40
3386 3599 3.750501 TTGGAAAAGGAGGATTACCCC 57.249 47.619 0.00 0.00 36.73 4.95
3387 3600 5.778241 TCTTTTTGGAAAAGGAGGATTACCC 59.222 40.000 11.87 0.00 36.73 3.69
3388 3601 6.911250 TCTTTTTGGAAAAGGAGGATTACC 57.089 37.500 11.87 0.00 31.48 2.85
3389 3602 9.424319 GAATTCTTTTTGGAAAAGGAGGATTAC 57.576 33.333 11.87 0.00 35.76 1.89
3390 3603 9.379770 AGAATTCTTTTTGGAAAAGGAGGATTA 57.620 29.630 0.88 0.00 35.76 1.75
3391 3604 8.267620 AGAATTCTTTTTGGAAAAGGAGGATT 57.732 30.769 0.88 8.18 35.76 3.01
3392 3605 7.862274 AGAATTCTTTTTGGAAAAGGAGGAT 57.138 32.000 0.88 0.00 35.76 3.24
3393 3606 7.451566 CCTAGAATTCTTTTTGGAAAAGGAGGA 59.548 37.037 14.36 0.00 35.76 3.71
3394 3607 7.233553 ACCTAGAATTCTTTTTGGAAAAGGAGG 59.766 37.037 14.36 11.39 35.76 4.30
3395 3608 8.183104 ACCTAGAATTCTTTTTGGAAAAGGAG 57.817 34.615 14.36 0.00 35.76 3.69
3396 3609 8.421002 CAACCTAGAATTCTTTTTGGAAAAGGA 58.579 33.333 14.36 5.19 32.98 3.36
3397 3610 8.204160 ACAACCTAGAATTCTTTTTGGAAAAGG 58.796 33.333 14.36 12.81 0.00 3.11
3398 3611 9.249457 GACAACCTAGAATTCTTTTTGGAAAAG 57.751 33.333 14.36 1.17 0.00 2.27
3399 3612 8.977412 AGACAACCTAGAATTCTTTTTGGAAAA 58.023 29.630 14.36 0.00 0.00 2.29
3400 3613 8.533569 AGACAACCTAGAATTCTTTTTGGAAA 57.466 30.769 14.36 0.00 0.00 3.13
3401 3614 8.413229 CAAGACAACCTAGAATTCTTTTTGGAA 58.587 33.333 14.36 0.00 0.00 3.53
3402 3615 7.777910 TCAAGACAACCTAGAATTCTTTTTGGA 59.222 33.333 14.36 5.04 0.00 3.53
3403 3616 7.940850 TCAAGACAACCTAGAATTCTTTTTGG 58.059 34.615 14.36 12.93 0.00 3.28
3404 3617 9.617975 GATCAAGACAACCTAGAATTCTTTTTG 57.382 33.333 14.36 15.56 0.00 2.44
3405 3618 9.579932 AGATCAAGACAACCTAGAATTCTTTTT 57.420 29.630 14.36 1.79 0.00 1.94
3407 3620 9.883142 CTAGATCAAGACAACCTAGAATTCTTT 57.117 33.333 14.36 0.00 31.06 2.52
3408 3621 9.261035 TCTAGATCAAGACAACCTAGAATTCTT 57.739 33.333 14.36 0.00 34.60 2.52
3409 3622 8.830915 TCTAGATCAAGACAACCTAGAATTCT 57.169 34.615 13.56 13.56 34.60 2.40
3410 3623 7.651704 GCTCTAGATCAAGACAACCTAGAATTC 59.348 40.741 0.00 0.00 36.42 2.17
3411 3624 7.344352 AGCTCTAGATCAAGACAACCTAGAATT 59.656 37.037 0.00 0.00 36.42 2.17
3412 3625 6.838612 AGCTCTAGATCAAGACAACCTAGAAT 59.161 38.462 0.00 0.00 36.42 2.40
3470 3683 5.470437 GCAGCTTCAGGTAAAAGTTAAGAGT 59.530 40.000 0.00 0.00 0.00 3.24
3471 3684 5.106515 GGCAGCTTCAGGTAAAAGTTAAGAG 60.107 44.000 0.00 0.00 0.00 2.85
3472 3685 4.760204 GGCAGCTTCAGGTAAAAGTTAAGA 59.240 41.667 0.00 0.00 0.00 2.10
3473 3686 4.082733 GGGCAGCTTCAGGTAAAAGTTAAG 60.083 45.833 0.00 0.00 0.00 1.85
3474 3687 3.824443 GGGCAGCTTCAGGTAAAAGTTAA 59.176 43.478 0.00 0.00 0.00 2.01
3475 3688 3.418047 GGGCAGCTTCAGGTAAAAGTTA 58.582 45.455 0.00 0.00 0.00 2.24
3476 3689 2.239400 GGGCAGCTTCAGGTAAAAGTT 58.761 47.619 0.00 0.00 0.00 2.66
3542 3759 3.302434 CGTACCAAACAGTATGCAGTACG 59.698 47.826 12.89 12.89 42.70 3.67
3585 3802 3.774766 TCCACTATTACTGCAGACCATGT 59.225 43.478 23.35 10.44 0.00 3.21
3637 3854 9.362151 AGAAGTGATACCAAACCTGAAAAATAA 57.638 29.630 0.00 0.00 0.00 1.40
3762 3980 8.958119 AAAATGTCTGACACTCAAGTAACTAA 57.042 30.769 13.50 0.00 0.00 2.24
3764 3982 7.275920 AGAAAATGTCTGACACTCAAGTAACT 58.724 34.615 13.50 1.23 34.29 2.24
3958 4181 6.245408 AGAATTAGTACCAAACCTGCAATGA 58.755 36.000 0.00 0.00 0.00 2.57
4085 4308 5.432645 TCTCACATTGTTCCACTTACAACA 58.567 37.500 0.00 0.00 38.23 3.33
4090 4313 4.536090 AGGGATCTCACATTGTTCCACTTA 59.464 41.667 7.39 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.