Multiple sequence alignment - TraesCS2D01G556700

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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 TraesCS2D01G556700 chr2D 100.000 4846 0 0 1 4846 630068923 630073768 0.000000e+00 8949.0
1 TraesCS2D01G556700 chr2D 87.794 467 34 12 1 450 87968993 87968533 4.300000e-145 525.0
2 TraesCS2D01G556700 chr2D 89.151 212 6 8 365 572 630069189 630069387 1.040000e-61 248.0
3 TraesCS2D01G556700 chr2D 89.151 212 6 8 267 465 630069287 630069494 1.040000e-61 248.0
4 TraesCS2D01G556700 chr5A 91.160 4751 337 55 156 4846 693855581 693850854 0.000000e+00 6370.0
5 TraesCS2D01G556700 chr5A 89.920 4772 382 69 149 4846 153562725 153567471 0.000000e+00 6056.0
6 TraesCS2D01G556700 chr5A 79.512 205 21 14 406 597 693855544 693855348 5.090000e-25 126.0
7 TraesCS2D01G556700 chr6A 90.292 4759 374 56 156 4846 602784836 602789574 0.000000e+00 6148.0
8 TraesCS2D01G556700 chr6A 89.964 4763 385 59 156 4846 555091809 555096550 0.000000e+00 6061.0
9 TraesCS2D01G556700 chr2A 90.031 4765 384 60 151 4846 30592977 30588235 0.000000e+00 6083.0
10 TraesCS2D01G556700 chr3A 90.053 4755 387 61 156 4846 17901232 17905964 0.000000e+00 6082.0
11 TraesCS2D01G556700 chr3A 89.722 4777 385 72 149 4846 38195965 38191216 0.000000e+00 6004.0
12 TraesCS2D01G556700 chr7A 89.914 4759 387 63 156 4846 15509113 15513846 0.000000e+00 6043.0
13 TraesCS2D01G556700 chr4B 92.108 4194 283 33 680 4846 15528712 15524540 0.000000e+00 5867.0
14 TraesCS2D01G556700 chr6D 94.761 859 27 10 1 846 305366106 305366959 0.000000e+00 1321.0
15 TraesCS2D01G556700 chr6D 92.045 352 22 6 1 349 258034480 258034132 1.570000e-134 490.0
16 TraesCS2D01G556700 chr6D 85.099 302 25 10 175 465 305366393 305366685 1.710000e-74 291.0
17 TraesCS2D01G556700 chr6D 85.027 187 22 3 175 360 305366500 305366681 8.280000e-43 185.0
18 TraesCS2D01G556700 chr6D 82.222 180 15 12 365 535 258034213 258034042 6.540000e-29 139.0
19 TraesCS2D01G556700 chr5B 86.929 482 37 14 1 465 447451548 447452020 7.190000e-143 518.0
20 TraesCS2D01G556700 chr5D 84.532 556 48 21 94 622 36575862 36575318 2.590000e-142 516.0
21 TraesCS2D01G556700 chr3B 92.151 344 24 3 1 343 43487764 43487423 2.620000e-132 483.0
22 TraesCS2D01G556700 chr3B 88.854 323 29 7 436 757 43486812 43486496 1.640000e-104 390.0
23 TraesCS2D01G556700 chr3B 89.888 89 6 2 362 450 43486778 43486693 1.430000e-20 111.0
24 TraesCS2D01G556700 chr2B 84.735 452 46 19 401 834 658211858 658212304 9.640000e-117 431.0
25 TraesCS2D01G556700 chr2B 86.111 144 8 5 801 935 717661736 717661876 1.410000e-30 145.0
26 TraesCS2D01G556700 chr2B 80.303 132 10 5 1 116 790116117 790116248 8.640000e-13 86.1
27 TraesCS2D01G556700 chr2B 86.207 58 5 3 62 116 670339860 670339803 5.240000e-05 60.2
28 TraesCS2D01G556700 chr1D 94.359 195 9 2 1 194 383329026 383329219 1.020000e-76 298.0
29 TraesCS2D01G556700 chr1D 84.068 295 26 10 190 468 383338422 383338711 1.030000e-66 265.0
30 TraesCS2D01G556700 chr4A 80.303 132 10 5 1 116 713747281 713747412 8.640000e-13 86.1


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 TraesCS2D01G556700 chr2D 630068923 630073768 4845 False 8949 8949 100.000000 1 4846 1 chr2D.!!$F1 4845
1 TraesCS2D01G556700 chr5A 153562725 153567471 4746 False 6056 6056 89.920000 149 4846 1 chr5A.!!$F1 4697
2 TraesCS2D01G556700 chr5A 693850854 693855581 4727 True 3248 6370 85.336000 156 4846 2 chr5A.!!$R1 4690
3 TraesCS2D01G556700 chr6A 602784836 602789574 4738 False 6148 6148 90.292000 156 4846 1 chr6A.!!$F2 4690
4 TraesCS2D01G556700 chr6A 555091809 555096550 4741 False 6061 6061 89.964000 156 4846 1 chr6A.!!$F1 4690
5 TraesCS2D01G556700 chr2A 30588235 30592977 4742 True 6083 6083 90.031000 151 4846 1 chr2A.!!$R1 4695
6 TraesCS2D01G556700 chr3A 17901232 17905964 4732 False 6082 6082 90.053000 156 4846 1 chr3A.!!$F1 4690
7 TraesCS2D01G556700 chr3A 38191216 38195965 4749 True 6004 6004 89.722000 149 4846 1 chr3A.!!$R1 4697
8 TraesCS2D01G556700 chr7A 15509113 15513846 4733 False 6043 6043 89.914000 156 4846 1 chr7A.!!$F1 4690
9 TraesCS2D01G556700 chr4B 15524540 15528712 4172 True 5867 5867 92.108000 680 4846 1 chr4B.!!$R1 4166
10 TraesCS2D01G556700 chr6D 305366106 305366959 853 False 599 1321 88.295667 1 846 3 chr6D.!!$F1 845
11 TraesCS2D01G556700 chr5D 36575318 36575862 544 True 516 516 84.532000 94 622 1 chr5D.!!$R1 528
12 TraesCS2D01G556700 chr3B 43486496 43487764 1268 True 328 483 90.297667 1 757 3 chr3B.!!$R1 756

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
306 310 0.249447 GTTGCCCCTGTTTTGTGAGC 60.249 55.000 0.00 0.0 0.0 4.26 F
1360 1941 0.584876 CGTCGACCAACCTCCAAAAC 59.415 55.000 10.58 0.0 0.0 2.43 F
1764 2354 1.808512 CGTAGGATATGCGGTTTGCCA 60.809 52.381 0.00 0.0 45.6 4.92 F
2369 2968 0.178068 GGCTCCAAGAGAATACGGCA 59.822 55.000 0.00 0.0 0.0 5.69 F
3028 3656 0.523072 CCACAAGATTGCCCGAGTTG 59.477 55.000 0.00 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1764 2354 0.261696 ACACCTTCTTGCCCCTGTTT 59.738 50.0 0.00 0.00 0.00 2.83 R
2365 2964 0.179174 GAGTTACCCGCAATTTGCCG 60.179 55.0 15.45 9.09 41.12 5.69 R
3363 3994 0.533032 GCTAAGCTGTCTCTTCCGGT 59.467 55.0 0.00 0.00 0.00 5.28 R
3443 4074 0.542938 TATCCCTGCCATCTCCCTCG 60.543 60.0 0.00 0.00 0.00 4.63 R
4616 5247 0.250640 ACAGCTGGTCTTGCTTCCTG 60.251 55.0 19.93 0.00 38.92 3.86 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
96 98 2.716217 AGCCTTGGTGCTGTAGATTTC 58.284 47.619 0.00 0.00 40.90 2.17
100 102 4.074970 CCTTGGTGCTGTAGATTTCTGTT 58.925 43.478 0.00 0.00 0.00 3.16
239 243 1.165270 GCCTACGCAGGTGTTTTGAT 58.835 50.000 3.02 0.00 44.68 2.57
306 310 0.249447 GTTGCCCCTGTTTTGTGAGC 60.249 55.000 0.00 0.00 0.00 4.26
323 328 2.621763 GCGACTTGCCTGATATGGG 58.378 57.895 0.00 0.00 37.76 4.00
360 367 0.960364 ATGTGTTTAGCGCCAGTGGG 60.960 55.000 12.15 2.02 37.18 4.61
388 497 5.964958 ATGTTTCTTCCATGTCGATGTTT 57.035 34.783 0.00 0.00 0.00 2.83
430 957 2.300433 TGCCTGATATGGTTCATGTGC 58.700 47.619 0.00 0.00 0.00 4.57
431 958 1.265095 GCCTGATATGGTTCATGTGCG 59.735 52.381 0.00 0.00 0.00 5.34
493 1028 5.547465 ACAGTAATGTTTCTTCCATGTCGA 58.453 37.500 0.00 0.00 0.00 4.20
545 1081 3.694926 TGATATGGTTCATGTGTTGCCA 58.305 40.909 0.00 0.00 0.00 4.92
546 1082 3.443329 TGATATGGTTCATGTGTTGCCAC 59.557 43.478 0.00 0.00 42.19 5.01
547 1083 0.597568 ATGGTTCATGTGTTGCCACG 59.402 50.000 0.00 0.00 44.92 4.94
553 1089 2.720605 TGTGTTGCCACGCATGTG 59.279 55.556 4.30 4.30 44.92 3.21
591 1133 7.084486 GGTTTTGATTTACTGCAGGAAAGTAG 58.916 38.462 27.31 0.00 31.96 2.57
737 1300 6.463995 TTCAGTGATTTTGTTTTAGGTGCT 57.536 33.333 0.00 0.00 0.00 4.40
753 1318 5.192327 AGGTGCTTTGATTTGTTTCAGAG 57.808 39.130 0.00 0.00 32.47 3.35
796 1361 3.154710 GGGTAATAGGGCCAATTGTAGC 58.845 50.000 6.18 1.21 0.00 3.58
1037 1612 5.940470 GTCATAAGTCAAAACAGGATGGACT 59.060 40.000 0.00 0.00 43.62 3.85
1040 1615 4.170468 AGTCAAAACAGGATGGACTTGT 57.830 40.909 0.00 0.00 43.62 3.16
1141 1717 9.744468 GTTTTATGTTCTTCCTGTACAAAACAT 57.256 29.630 17.13 17.13 39.75 2.71
1186 1767 8.472413 CATTGATTTATGTGGTTTCCATCTTCT 58.528 33.333 0.00 0.00 35.28 2.85
1194 1775 2.093658 GGTTTCCATCTTCTAGCCACGA 60.094 50.000 0.00 0.00 0.00 4.35
1225 1806 2.676342 CCAATAACTGGGTACAAGCGTC 59.324 50.000 0.00 0.00 42.17 5.19
1226 1807 3.331150 CAATAACTGGGTACAAGCGTCA 58.669 45.455 0.00 0.00 0.00 4.35
1260 1841 2.472414 TTATTGCACGGGGGAAGCGT 62.472 55.000 0.00 0.00 0.00 5.07
1360 1941 0.584876 CGTCGACCAACCTCCAAAAC 59.415 55.000 10.58 0.00 0.00 2.43
1376 1957 3.516615 CAAAACCAAAACGCCAGAAGAA 58.483 40.909 0.00 0.00 0.00 2.52
1394 1975 3.379452 AGAAGGGAGGAACTGAGGTATG 58.621 50.000 0.00 0.00 41.55 2.39
1623 2213 3.716431 AGAATTTGGTGGCATTCTGGAT 58.284 40.909 0.00 0.00 38.16 3.41
1630 2220 1.820519 GTGGCATTCTGGATCTTGCAA 59.179 47.619 0.00 0.00 36.82 4.08
1683 2273 4.102524 TGGATAATGAAGCATTACGACCCT 59.897 41.667 2.29 0.00 38.83 4.34
1764 2354 1.808512 CGTAGGATATGCGGTTTGCCA 60.809 52.381 0.00 0.00 45.60 4.92
2096 2686 1.896660 GGCGTGCCAACAAGAAGGA 60.897 57.895 5.89 0.00 35.81 3.36
2213 2809 9.624697 TGCAATCATTAGCTAACTTAAACTTTG 57.375 29.630 8.70 0.00 0.00 2.77
2232 2831 6.993079 ACTTTGTGTTCTTTTTCCTTGTCTT 58.007 32.000 0.00 0.00 0.00 3.01
2365 2964 3.198853 ACAGGAAGGCTCCAAGAGAATAC 59.801 47.826 5.90 0.00 45.24 1.89
2369 2968 0.178068 GGCTCCAAGAGAATACGGCA 59.822 55.000 0.00 0.00 0.00 5.69
2401 3000 7.593644 CGGGTAACTCAATTTTTCTGTTTTAGG 59.406 37.037 0.00 0.00 0.00 2.69
2402 3001 8.635328 GGGTAACTCAATTTTTCTGTTTTAGGA 58.365 33.333 0.00 0.00 0.00 2.94
2442 3042 8.512138 GTCATATTGTTTTTAGGCAACACTACT 58.488 33.333 0.00 0.00 33.81 2.57
2473 3077 6.205658 AGAGTAGGCAATTCACTTTGAAAGAC 59.794 38.462 12.53 0.00 40.12 3.01
2490 3094 6.065374 TGAAAGACCAAGCAAGGTAATGTAA 58.935 36.000 0.00 0.00 43.38 2.41
2492 3096 4.980573 AGACCAAGCAAGGTAATGTAACA 58.019 39.130 0.00 0.00 43.38 2.41
2507 3111 2.697751 TGTAACATTTTGGGCAAGTGCT 59.302 40.909 2.85 0.00 41.70 4.40
2508 3112 3.133721 TGTAACATTTTGGGCAAGTGCTT 59.866 39.130 2.85 0.00 41.70 3.91
2509 3113 2.531522 ACATTTTGGGCAAGTGCTTC 57.468 45.000 2.85 0.00 41.70 3.86
2525 3130 7.219535 GCAAGTGCTTCACATATATTTCAAGTG 59.780 37.037 0.00 0.00 36.74 3.16
2548 3153 5.187186 TGGGTCCAAGTAGTTATCAGACTTC 59.813 44.000 0.00 0.00 31.04 3.01
2550 3155 6.406065 GGGTCCAAGTAGTTATCAGACTTCTC 60.406 46.154 0.00 0.00 31.04 2.87
2551 3156 6.378848 GGTCCAAGTAGTTATCAGACTTCTCT 59.621 42.308 0.00 0.00 31.04 3.10
2592 3198 5.472148 CATGCACACAGTTGGATAATGTTT 58.528 37.500 0.00 0.00 0.00 2.83
2611 3218 6.783708 TGTTTACAAGAAGGATTTGTTGGT 57.216 33.333 0.00 0.00 40.74 3.67
2642 3250 8.647796 TGTATTTAATGGTAGCTGCTGTAGTAT 58.352 33.333 13.43 0.00 0.00 2.12
2693 3307 8.216453 GCAATTTACATGTTGAAAAGTAGCAAG 58.784 33.333 2.30 0.00 0.00 4.01
2730 3344 6.974622 ACACAAGCAACTTATGTTCTGAAAAG 59.025 34.615 0.00 0.00 25.22 2.27
2817 3436 2.220653 AGTGGCATAATGGTTGCAGT 57.779 45.000 0.00 0.00 41.95 4.40
2829 3448 6.403866 AATGGTTGCAGTAATTTTCAGACA 57.596 33.333 0.00 0.00 0.00 3.41
2943 3571 4.455606 GCTATAAACCACCAGCTCAAGAT 58.544 43.478 0.00 0.00 0.00 2.40
3011 3639 3.464907 CACATCACCAAATTTGTTGCCA 58.535 40.909 16.73 0.00 0.00 4.92
3027 3655 1.244019 GCCACAAGATTGCCCGAGTT 61.244 55.000 0.00 0.00 0.00 3.01
3028 3656 0.523072 CCACAAGATTGCCCGAGTTG 59.477 55.000 0.00 0.00 0.00 3.16
3038 3666 2.852449 TGCCCGAGTTGTATGACAAAA 58.148 42.857 0.00 0.00 40.15 2.44
3073 3703 3.631250 AGCACTTGTTTTTCCCTCTCAA 58.369 40.909 0.00 0.00 0.00 3.02
3102 3732 3.194542 TCCCCTTTTTATCGCCATTTGTG 59.805 43.478 0.00 0.00 0.00 3.33
3109 3739 2.572191 ATCGCCATTTGTGCATTCAG 57.428 45.000 0.00 0.00 0.00 3.02
3172 3803 5.939883 TCATGTTCTCTACCATCCACTTTTG 59.060 40.000 0.00 0.00 0.00 2.44
3363 3994 1.774894 AAGGGGCAAGCGAGTACCAA 61.775 55.000 0.00 0.00 0.00 3.67
3381 4012 2.611518 CAACCGGAAGAGACAGCTTAG 58.388 52.381 9.46 0.00 0.00 2.18
3395 4026 2.027745 CAGCTTAGCAAGTGAGGAGGAA 60.028 50.000 7.07 0.00 0.00 3.36
3443 4074 0.462759 AGGCAGCCGATAGTGAAAGC 60.463 55.000 5.55 0.00 0.00 3.51
3482 4113 5.992217 GGATAAAGGTAGTGATGAAAGCGAT 59.008 40.000 0.00 0.00 0.00 4.58
3502 4133 2.327343 GCGATGGCAGTGCAGACAA 61.327 57.895 18.61 0.00 39.62 3.18
3513 4144 2.233676 AGTGCAGACAACGATGATGGTA 59.766 45.455 0.00 0.00 0.00 3.25
3541 4172 2.044793 TCAAGTGGAGTTCAGGGGAT 57.955 50.000 0.00 0.00 0.00 3.85
3624 4255 1.546961 GAGGGAAGACGGAACTGAGA 58.453 55.000 0.00 0.00 0.00 3.27
3629 4260 2.498078 GGAAGACGGAACTGAGAGGAAT 59.502 50.000 0.00 0.00 0.00 3.01
3641 4272 4.533707 ACTGAGAGGAATGAGGACAATGAA 59.466 41.667 0.00 0.00 0.00 2.57
3722 4353 0.104855 CGATGAAGAAGGCGATGGGA 59.895 55.000 0.00 0.00 0.00 4.37
3727 4358 2.173356 TGAAGAAGGCGATGGGAATGAT 59.827 45.455 0.00 0.00 0.00 2.45
3784 4415 6.099990 AGGATGAAGATGATGAAGATGACAGT 59.900 38.462 0.00 0.00 0.00 3.55
3952 4583 2.765699 GGATGAGGCAGATAGGATCTCC 59.234 54.545 0.00 0.00 37.58 3.71
3985 4616 5.922544 CCTTGTGATGACAGAATTCAAAACC 59.077 40.000 8.44 0.00 32.26 3.27
4011 4642 1.530655 CCCCAAAACCACGCTTCCT 60.531 57.895 0.00 0.00 0.00 3.36
4097 4728 3.812156 TGTTCGAAGAGTTGTTGAGGA 57.188 42.857 0.00 0.00 38.43 3.71
4098 4729 4.131649 TGTTCGAAGAGTTGTTGAGGAA 57.868 40.909 0.00 0.00 38.43 3.36
4111 4742 5.110814 TGTTGAGGAAGAAAGACTTGGAA 57.889 39.130 0.00 0.00 39.13 3.53
4123 4754 4.713792 AGACTTGGAAATGGTCTTCACT 57.286 40.909 0.00 0.00 37.04 3.41
4131 4762 4.537015 GAAATGGTCTTCACTTTCAACCG 58.463 43.478 0.00 0.00 32.50 4.44
4132 4763 2.702592 TGGTCTTCACTTTCAACCGT 57.297 45.000 0.00 0.00 32.50 4.83
4154 4785 2.586425 AGGAAATATGTCCAATGCCGG 58.414 47.619 14.67 0.00 40.48 6.13
4159 4790 1.092921 TATGTCCAATGCCGGTTCGC 61.093 55.000 1.90 0.00 0.00 4.70
4178 4809 6.128007 GGTTCGCCAGAAAATAATGAGAGAAA 60.128 38.462 0.00 0.00 38.23 2.52
4180 4811 7.019774 TCGCCAGAAAATAATGAGAGAAATG 57.980 36.000 0.00 0.00 0.00 2.32
4206 4837 4.268884 CGCTCTAAATGAAGCTACAGAACC 59.731 45.833 0.00 0.00 0.00 3.62
4207 4838 5.178797 GCTCTAAATGAAGCTACAGAACCA 58.821 41.667 0.00 0.00 0.00 3.67
4212 4843 6.959639 AAATGAAGCTACAGAACCAAAGAA 57.040 33.333 0.00 0.00 0.00 2.52
4217 4848 4.006319 AGCTACAGAACCAAAGAATGCTC 58.994 43.478 0.00 0.00 0.00 4.26
4224 4855 1.880027 ACCAAAGAATGCTCGTCCAAC 59.120 47.619 0.00 0.00 0.00 3.77
4282 4913 8.651391 TGAAGAAAACTGTCAGTTTCGTATTA 57.349 30.769 27.01 12.36 46.78 0.98
4446 5077 6.040729 TCTGAAACAAAAGAGGCAATTCATGA 59.959 34.615 0.00 0.00 0.00 3.07
4452 5083 6.209986 ACAAAAGAGGCAATTCATGAGAATGA 59.790 34.615 0.00 0.00 43.52 2.57
4494 5125 0.399454 ACACCATCAAGCTCAGCAGT 59.601 50.000 0.00 0.00 0.00 4.40
4514 5145 1.602323 CCCCCGTGCAGCAAAGTTA 60.602 57.895 0.00 0.00 0.00 2.24
4616 5247 0.250467 TCTGGCAACTCAGTCCAAGC 60.250 55.000 0.00 0.00 36.25 4.01
4639 5270 2.287849 GGAAGCAAGACCAGCTGTTTTC 60.288 50.000 13.81 6.05 42.53 2.29
4699 5330 4.164843 AGTAAGGCCAGTTCAACTCAAA 57.835 40.909 5.01 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 98 1.181786 AACCCCAACACACACAACAG 58.818 50.000 0.00 0.00 0.00 3.16
100 102 1.214217 TCCTAACCCCAACACACACA 58.786 50.000 0.00 0.00 0.00 3.72
169 171 2.124570 CATCAGGAGCAACCCCCG 60.125 66.667 0.00 0.00 40.05 5.73
306 310 1.138859 TGACCCATATCAGGCAAGTCG 59.861 52.381 0.00 0.00 0.00 4.18
360 367 4.391830 TCGACATGGAAGAAACATTACTGC 59.608 41.667 0.00 0.00 0.00 4.40
388 497 2.241176 AGTCACTCACAAAAACAGGGGA 59.759 45.455 0.00 0.00 0.00 4.81
450 977 1.455383 CCTCAAAAACCACTGGCGCT 61.455 55.000 7.64 0.00 0.00 5.92
452 979 0.310854 GTCCTCAAAAACCACTGGCG 59.689 55.000 0.00 0.00 0.00 5.69
493 1028 2.102925 CTCACAAAACAGGGGCAACATT 59.897 45.455 0.00 0.00 39.74 2.71
547 1083 1.330306 CACTTGCGCTAAACACATGC 58.670 50.000 9.73 0.00 0.00 4.06
550 1086 1.384525 AACCACTTGCGCTAAACACA 58.615 45.000 9.73 0.00 0.00 3.72
552 1088 2.423892 TCAAAACCACTTGCGCTAAACA 59.576 40.909 9.73 0.00 0.00 2.83
553 1089 3.073144 TCAAAACCACTTGCGCTAAAC 57.927 42.857 9.73 0.00 0.00 2.01
562 1101 4.892934 TCCTGCAGTAAATCAAAACCACTT 59.107 37.500 13.81 0.00 0.00 3.16
656 1216 1.132689 AGCCCTATTACCCTCCCTCTG 60.133 57.143 0.00 0.00 0.00 3.35
753 1318 5.246429 CCCTCCCTCTACATGTCCTATAAAC 59.754 48.000 0.00 0.00 0.00 2.01
796 1361 8.773645 TCTGATTTTCACTATGTTACAACTGTG 58.226 33.333 8.60 8.60 0.00 3.66
953 1526 6.243900 AGGACAAACAGTGAGATTCATCATT 58.756 36.000 0.00 0.00 0.00 2.57
1037 1612 4.701651 GGTCATCATGACTTGATCCAACAA 59.298 41.667 17.46 0.00 46.19 2.83
1040 1615 4.849813 AGGTCATCATGACTTGATCCAA 57.150 40.909 17.46 0.00 46.19 3.53
1141 1717 9.883142 AATCAATGAAAAGTGGAAAACAAACTA 57.117 25.926 0.00 0.00 0.00 2.24
1155 1736 8.830201 TGGAAACCACATAAATCAATGAAAAG 57.170 30.769 0.00 0.00 0.00 2.27
1160 1741 8.472413 AGAAGATGGAAACCACATAAATCAATG 58.528 33.333 0.00 0.00 35.80 2.82
1186 1767 1.667830 GTGCACTGCTTCGTGGCTA 60.668 57.895 10.32 0.00 35.47 3.93
1194 1775 1.888512 CCAGTTATTGGTGCACTGCTT 59.111 47.619 17.98 2.16 42.41 3.91
1360 1941 0.598065 CCCTTCTTCTGGCGTTTTGG 59.402 55.000 0.00 0.00 0.00 3.28
1376 1957 2.472029 CACATACCTCAGTTCCTCCCT 58.528 52.381 0.00 0.00 0.00 4.20
1414 1996 0.690192 TGCTGGGCAACTGCTTAGTA 59.310 50.000 1.06 0.00 43.66 1.82
1505 2094 2.963101 TCCTACGACCCTATTGGACATG 59.037 50.000 0.00 0.00 38.00 3.21
1510 2099 2.102588 CCTGTTCCTACGACCCTATTGG 59.897 54.545 0.00 0.00 41.37 3.16
1551 2140 2.427095 ACCAAGTCCTTGTTCAACTTGC 59.573 45.455 8.57 0.00 45.39 4.01
1585 2174 6.296030 CCAAATTCTTTTCCAATGATGACCCT 60.296 38.462 0.00 0.00 0.00 4.34
1596 2186 4.347583 AGAATGCCACCAAATTCTTTTCCA 59.652 37.500 0.00 0.00 39.55 3.53
1623 2213 1.078709 GCATGCTACTCGTTGCAAGA 58.921 50.000 11.37 0.00 43.72 3.02
1630 2220 2.758327 TCCGGGCATGCTACTCGT 60.758 61.111 18.92 0.00 0.00 4.18
1683 2273 5.163416 TGGAATGACTATCTGCGAAATCTCA 60.163 40.000 0.00 0.00 0.00 3.27
1755 2345 2.733945 CCCCTGTTTGGCAAACCG 59.266 61.111 33.31 27.98 40.67 4.44
1764 2354 0.261696 ACACCTTCTTGCCCCTGTTT 59.738 50.000 0.00 0.00 0.00 2.83
1775 2365 2.672478 CGATTCTCGAAGCACACCTTCT 60.672 50.000 2.11 0.00 46.29 2.85
2056 2646 2.411547 CCGAAGTGAACGCAAGCTTTAG 60.412 50.000 0.00 0.00 45.62 1.85
2213 2809 5.454554 GCGTAAAGACAAGGAAAAAGAACAC 59.545 40.000 0.00 0.00 0.00 3.32
2232 2831 2.821378 TCTAGGTACAACAGCTGCGTAA 59.179 45.455 15.27 0.40 36.15 3.18
2323 2922 6.003950 CCTGTCCTTCTTGATAACTTTGGAA 58.996 40.000 0.00 0.00 0.00 3.53
2328 2927 5.804771 GCCTTCCTGTCCTTCTTGATAACTT 60.805 44.000 0.00 0.00 0.00 2.66
2365 2964 0.179174 GAGTTACCCGCAATTTGCCG 60.179 55.000 15.45 9.09 41.12 5.69
2442 3042 9.733556 TCAAAGTGAATTGCCTACTCTAAAATA 57.266 29.630 0.00 0.00 0.00 1.40
2473 3077 6.368516 CCAAAATGTTACATTACCTTGCTTGG 59.631 38.462 11.23 14.25 0.00 3.61
2490 3094 1.761784 TGAAGCACTTGCCCAAAATGT 59.238 42.857 0.00 0.00 43.38 2.71
2492 3096 1.761784 TGTGAAGCACTTGCCCAAAAT 59.238 42.857 0.00 0.00 43.38 1.82
2507 3111 6.726379 TGGACCCACTTGAAATATATGTGAA 58.274 36.000 2.53 0.00 0.00 3.18
2508 3112 6.320434 TGGACCCACTTGAAATATATGTGA 57.680 37.500 2.53 0.00 0.00 3.58
2509 3113 6.603201 ACTTGGACCCACTTGAAATATATGTG 59.397 38.462 0.00 0.00 0.00 3.21
2525 3130 5.422650 AGAAGTCTGATAACTACTTGGACCC 59.577 44.000 0.00 0.00 33.72 4.46
2548 3153 3.181491 TGGCAAACGAAAAAGGTTCAGAG 60.181 43.478 0.00 0.00 0.00 3.35
2550 3155 3.157932 TGGCAAACGAAAAAGGTTCAG 57.842 42.857 0.00 0.00 0.00 3.02
2551 3156 3.452474 CATGGCAAACGAAAAAGGTTCA 58.548 40.909 0.00 0.00 0.00 3.18
2592 3198 6.783708 ACAAACCAACAAATCCTTCTTGTA 57.216 33.333 0.00 0.00 35.98 2.41
2611 3218 7.040062 ACAGCAGCTACCATTAAATACAACAAA 60.040 33.333 0.00 0.00 0.00 2.83
2626 3234 7.873505 AGCTAAAAATATACTACAGCAGCTACC 59.126 37.037 0.00 0.00 34.08 3.18
2663 3276 7.232945 ACTTTTCAACATGTAAATTGCACAC 57.767 32.000 0.00 0.00 0.00 3.82
2693 3307 7.749539 AAGTTGCTTGTGTTGTTGTATAAAC 57.250 32.000 0.00 0.00 0.00 2.01
2730 3344 4.003648 AGAACTGGTATGCAAGTTGCTAC 58.996 43.478 27.17 23.07 45.31 3.58
2920 3545 2.710096 TGAGCTGGTGGTTTATAGCC 57.290 50.000 0.00 0.00 36.86 3.93
2943 3571 1.440938 CGCACACCGGAAAAACTCCA 61.441 55.000 9.46 0.00 45.74 3.86
3011 3639 2.851263 TACAACTCGGGCAATCTTGT 57.149 45.000 0.00 0.00 0.00 3.16
3038 3666 8.904099 AAAACAAGTGCTAGATAACTTACTGT 57.096 30.769 0.00 0.00 34.90 3.55
3073 3703 3.194755 GGCGATAAAAAGGGGAACAACAT 59.805 43.478 0.00 0.00 0.00 2.71
3172 3803 7.060600 AGCTTCTTTTGCTTTTGTAAAACAC 57.939 32.000 0.00 0.00 38.68 3.32
3182 3813 2.363359 CCCTGTGAGCTTCTTTTGCTTT 59.637 45.455 0.00 0.00 41.30 3.51
3316 3947 4.704833 GCCGCCTGCTTGTCTCCA 62.705 66.667 0.00 0.00 36.87 3.86
3341 3972 0.822164 GTACTCGCTTGCCCCTTCTA 59.178 55.000 0.00 0.00 0.00 2.10
3363 3994 0.533032 GCTAAGCTGTCTCTTCCGGT 59.467 55.000 0.00 0.00 0.00 5.28
3381 4012 2.100605 AACGATTCCTCCTCACTTGC 57.899 50.000 0.00 0.00 0.00 4.01
3395 4026 2.601763 GTCGCTGTCGGAATTAAACGAT 59.398 45.455 0.00 0.00 41.53 3.73
3443 4074 0.542938 TATCCCTGCCATCTCCCTCG 60.543 60.000 0.00 0.00 0.00 4.63
3482 4113 1.153568 GTCTGCACTGCCATCGCTA 60.154 57.895 0.00 0.00 35.36 4.26
3495 4126 3.871006 TCATTACCATCATCGTTGTCTGC 59.129 43.478 0.00 0.00 0.00 4.26
3502 4133 5.488262 TGATCCATCATTACCATCATCGT 57.512 39.130 0.00 0.00 0.00 3.73
3513 4144 5.183530 TGAACTCCACTTGATCCATCATT 57.816 39.130 0.00 0.00 36.56 2.57
3541 4172 1.762957 GTGCTCCCTGGCTACTTGATA 59.237 52.381 0.00 0.00 0.00 2.15
3624 4255 5.705397 TCATCTTCATTGTCCTCATTCCT 57.295 39.130 0.00 0.00 0.00 3.36
3629 4260 6.243216 TCATCATCATCTTCATTGTCCTCA 57.757 37.500 0.00 0.00 0.00 3.86
3641 4272 6.517027 CGTCATCCTCTTCTTCATCATCATCT 60.517 42.308 0.00 0.00 0.00 2.90
3672 4303 4.227073 CCTCCTTTCCTTCATCCTCTTCTT 59.773 45.833 0.00 0.00 0.00 2.52
3673 4304 3.779738 CCTCCTTTCCTTCATCCTCTTCT 59.220 47.826 0.00 0.00 0.00 2.85
3679 4310 1.831736 TCGTCCTCCTTTCCTTCATCC 59.168 52.381 0.00 0.00 0.00 3.51
3722 4353 7.504911 CCCATCATCTTCCTTGTCTTTATCATT 59.495 37.037 0.00 0.00 0.00 2.57
3727 4358 4.018506 TGCCCATCATCTTCCTTGTCTTTA 60.019 41.667 0.00 0.00 0.00 1.85
3784 4415 4.263572 CCACCGTTGCCACCTCCA 62.264 66.667 0.00 0.00 0.00 3.86
3952 4583 4.081807 TCTGTCATCACAAGGTCTCTGATG 60.082 45.833 10.20 10.20 41.78 3.07
4011 4642 8.502387 CCAACATTTCTTTCACTTCAAAAACAA 58.498 29.630 0.00 0.00 0.00 2.83
4111 4742 3.551846 ACGGTTGAAAGTGAAGACCATT 58.448 40.909 0.00 0.00 0.00 3.16
4123 4754 6.239396 TGGACATATTTCCTTACGGTTGAAA 58.761 36.000 9.30 0.00 36.51 2.69
4131 4762 4.023193 CCGGCATTGGACATATTTCCTTAC 60.023 45.833 9.30 0.00 36.51 2.34
4132 4763 4.141287 CCGGCATTGGACATATTTCCTTA 58.859 43.478 9.30 0.00 36.51 2.69
4151 4782 2.680841 TCATTATTTTCTGGCGAACCGG 59.319 45.455 0.00 0.00 44.63 5.28
4154 4785 6.422776 TTCTCTCATTATTTTCTGGCGAAC 57.577 37.500 0.00 0.00 0.00 3.95
4159 4790 6.510536 GCCCATTTCTCTCATTATTTTCTGG 58.489 40.000 0.00 0.00 0.00 3.86
4178 4809 1.133976 AGCTTCATTTAGAGCGCCCAT 60.134 47.619 2.29 0.00 0.00 4.00
4180 4811 1.867865 GTAGCTTCATTTAGAGCGCCC 59.132 52.381 2.29 0.00 0.00 6.13
4206 4837 1.200020 GGGTTGGACGAGCATTCTTTG 59.800 52.381 0.00 0.00 0.00 2.77
4207 4838 1.202879 TGGGTTGGACGAGCATTCTTT 60.203 47.619 0.00 0.00 0.00 2.52
4212 4843 0.981183 TAGTTGGGTTGGACGAGCAT 59.019 50.000 0.00 0.00 0.00 3.79
4217 4848 0.604511 GGTGGTAGTTGGGTTGGACG 60.605 60.000 0.00 0.00 0.00 4.79
4224 4855 1.683441 GGGAGTGGTGGTAGTTGGG 59.317 63.158 0.00 0.00 0.00 4.12
4282 4913 4.498894 TTCATTCATCACAGATGGCTCT 57.501 40.909 7.11 0.00 0.00 4.09
4348 4979 1.660019 TTGACTTTCCCCCTTGGCCA 61.660 55.000 0.00 0.00 0.00 5.36
4391 5022 2.555757 GTTGTTGCTGCTGAGAAGGAAT 59.444 45.455 0.00 0.00 0.00 3.01
4392 5023 1.949525 GTTGTTGCTGCTGAGAAGGAA 59.050 47.619 0.00 0.00 0.00 3.36
4446 5077 3.631250 ACCACCTGTGTTTTGTCATTCT 58.369 40.909 0.00 0.00 0.00 2.40
4452 5083 4.595986 ACTCTTTACCACCTGTGTTTTGT 58.404 39.130 0.00 0.00 0.00 2.83
4494 5125 2.033448 CTTTGCTGCACGGGGGTA 59.967 61.111 0.00 0.00 0.00 3.69
4514 5145 3.561143 CTGTAGGTACTGCCTCATCTCT 58.439 50.000 0.00 0.00 46.96 3.10
4616 5247 0.250640 ACAGCTGGTCTTGCTTCCTG 60.251 55.000 19.93 0.00 38.92 3.86
4658 5289 5.061721 ACTTTTATGGGGTCAAGTGTTCT 57.938 39.130 0.00 0.00 0.00 3.01
4659 5290 6.072119 CCTTACTTTTATGGGGTCAAGTGTTC 60.072 42.308 0.00 0.00 31.83 3.18
4666 5297 2.650322 TGGCCTTACTTTTATGGGGTCA 59.350 45.455 3.32 0.00 0.00 4.02
4699 5330 0.693049 CTAGCACTGTGGGTCCCTTT 59.307 55.000 10.00 0.00 0.00 3.11


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

AutoCloner maintained by Alex Coulton.