Multiple sequence alignment - TraesCS2D01G258100

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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 TraesCS2D01G258100 chr2D 100.000 3526 0 0 1 3526 314170541 314167016 0.000000e+00 6512.0
1 TraesCS2D01G258100 chr2B 93.556 2095 120 9 1 2090 382254288 382252204 0.000000e+00 3107.0
2 TraesCS2D01G258100 chr2B 95.162 1881 62 12 768 2620 381924686 381922807 0.000000e+00 2942.0
3 TraesCS2D01G258100 chr2B 92.008 513 28 9 2556 3064 382235144 382234641 0.000000e+00 708.0
4 TraesCS2D01G258100 chr2B 94.432 449 13 7 2622 3067 381922663 381922224 0.000000e+00 680.0
5 TraesCS2D01G258100 chr2B 90.698 473 33 7 3063 3526 533537133 533536663 1.390000e-173 619.0
6 TraesCS2D01G258100 chr2B 88.802 509 25 7 2080 2556 382246755 382246247 2.340000e-166 595.0
7 TraesCS2D01G258100 chr2B 86.542 483 46 14 3055 3523 235908641 235909118 6.750000e-142 514.0
8 TraesCS2D01G258100 chr2B 85.336 491 47 15 3055 3523 235065035 235065522 5.290000e-133 484.0
9 TraesCS2D01G258100 chr2B 97.619 42 1 0 2357 2398 382086850 382086809 4.880000e-09 73.1
10 TraesCS2D01G258100 chr2A 95.079 1524 50 4 716 2227 421566264 421567774 0.000000e+00 2375.0
11 TraesCS2D01G258100 chr2A 92.857 1274 67 3 716 1977 421910757 421912018 0.000000e+00 1827.0
12 TraesCS2D01G258100 chr2A 89.038 821 49 17 1979 2762 421914707 421915523 0.000000e+00 979.0
13 TraesCS2D01G258100 chr2A 88.551 559 35 12 2231 2762 421567873 421568429 0.000000e+00 651.0
14 TraesCS2D01G258100 chr2A 95.745 47 2 0 2351 2397 102692119 102692073 3.770000e-10 76.8
15 TraesCS2D01G258100 chr2A 97.561 41 1 0 2357 2397 369078082 369078042 1.760000e-08 71.3
16 TraesCS2D01G258100 chr4D 89.362 235 24 1 365 599 414044209 414044442 9.570000e-76 294.0
17 TraesCS2D01G258100 chr5D 92.647 204 12 3 3254 3454 487539158 487539361 1.240000e-74 291.0
18 TraesCS2D01G258100 chr5D 84.561 285 33 5 365 641 498464858 498465139 4.490000e-69 272.0
19 TraesCS2D01G258100 chr5D 84.211 285 36 6 365 641 438401014 438400731 5.800000e-68 268.0
20 TraesCS2D01G258100 chr5D 88.945 199 16 5 3057 3251 487537339 487537535 1.260000e-59 241.0
21 TraesCS2D01G258100 chr6A 84.859 284 34 6 365 641 608656275 608655994 9.640000e-71 278.0
22 TraesCS2D01G258100 chr3D 84.483 290 34 7 362 641 47748384 47748672 3.470000e-70 276.0
23 TraesCS2D01G258100 chr1B 84.806 283 34 7 365 641 661889867 661890146 3.470000e-70 276.0
24 TraesCS2D01G258100 chr3A 84.375 288 33 8 365 643 711256898 711256614 4.490000e-69 272.0
25 TraesCS2D01G258100 chr3A 91.667 48 2 2 3056 3102 54576716 54576670 8.170000e-07 65.8
26 TraesCS2D01G258100 chr7D 82.562 281 43 6 365 641 22714820 22715098 3.520000e-60 243.0
27 TraesCS2D01G258100 chr7D 89.474 76 8 0 2324 2399 252560782 252560707 2.900000e-16 97.1
28 TraesCS2D01G258100 chr6D 89.655 58 5 1 3063 3119 460222614 460222557 4.880000e-09 73.1
29 TraesCS2D01G258100 chr6B 87.931 58 6 1 3063 3119 700658121 700658064 2.270000e-07 67.6
30 TraesCS2D01G258100 chr7B 95.122 41 2 0 2356 2396 658068833 658068793 8.170000e-07 65.8
31 TraesCS2D01G258100 chr7A 95.000 40 2 0 2357 2396 423277153 423277114 2.940000e-06 63.9
32 TraesCS2D01G258100 chr4B 85.484 62 5 4 3052 3109 580548697 580548758 1.060000e-05 62.1
33 TraesCS2D01G258100 chr1D 84.615 65 5 5 3033 3095 229077665 229077604 3.800000e-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 TraesCS2D01G258100 chr2D 314167016 314170541 3525 True 6512 6512 100.0000 1 3526 1 chr2D.!!$R1 3525
1 TraesCS2D01G258100 chr2B 382252204 382254288 2084 True 3107 3107 93.5560 1 2090 1 chr2B.!!$R4 2089
2 TraesCS2D01G258100 chr2B 381922224 381924686 2462 True 1811 2942 94.7970 768 3067 2 chr2B.!!$R6 2299
3 TraesCS2D01G258100 chr2B 382234641 382235144 503 True 708 708 92.0080 2556 3064 1 chr2B.!!$R2 508
4 TraesCS2D01G258100 chr2B 382246247 382246755 508 True 595 595 88.8020 2080 2556 1 chr2B.!!$R3 476
5 TraesCS2D01G258100 chr2A 421566264 421568429 2165 False 1513 2375 91.8150 716 2762 2 chr2A.!!$F1 2046
6 TraesCS2D01G258100 chr2A 421910757 421915523 4766 False 1403 1827 90.9475 716 2762 2 chr2A.!!$F2 2046
7 TraesCS2D01G258100 chr5D 487537339 487539361 2022 False 266 291 90.7960 3057 3454 2 chr5D.!!$F2 397

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
433 438 0.179045 GTGCGCTGGTCCTATTGGAT 60.179 55.0 9.73 0.0 45.29 3.41 F
559 564 0.669077 ATCGTCGCTAGGTGATCCAC 59.331 55.0 0.00 0.0 35.89 4.02 F
1785 1802 0.108615 CTGTCCTCGTGAAAGCGGAT 60.109 55.0 0.00 0.0 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1702 1719 0.033504 AGTTCCTGCGTGACGATGTT 59.966 50.0 10.10 0.00 0.00 2.71 R
1814 1831 0.176680 CAGGTAGAGCGTGCCATTCT 59.823 55.0 0.00 0.00 31.94 2.40 R
3268 7863 0.034186 TATGGGCCTTTGGACTGCAG 60.034 55.0 13.48 13.48 0.00 4.41 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
46 47 2.162716 GTGCTTGTGGCTAAGGACG 58.837 57.895 9.89 0.00 38.83 4.79
51 52 0.675083 TTGTGGCTAAGGACGAACGA 59.325 50.000 0.14 0.00 0.00 3.85
67 68 2.838693 GAGAGTAGGGGGCGGACC 60.839 72.222 0.00 0.00 39.11 4.46
78 79 2.665603 GCGGACCTGAGCCTTCTT 59.334 61.111 0.00 0.00 0.00 2.52
80 81 1.674057 CGGACCTGAGCCTTCTTGT 59.326 57.895 0.00 0.00 0.00 3.16
129 130 1.978617 CTGCCCCGAGTGCCATTTT 60.979 57.895 0.00 0.00 0.00 1.82
147 148 6.978080 GCCATTTTGGTCGTAATTATGATGTT 59.022 34.615 10.52 0.00 40.46 2.71
154 155 8.601845 TGGTCGTAATTATGATGTTCAATAGG 57.398 34.615 10.52 0.00 0.00 2.57
201 203 2.028125 TAAGGGGCTCGCAGGAATCG 62.028 60.000 0.00 0.00 0.00 3.34
205 207 3.267860 GCTCGCAGGAATCGCCAG 61.268 66.667 0.00 0.00 40.02 4.85
223 225 3.740764 GCCAGAATTGCCAAGTTTTGACA 60.741 43.478 0.00 0.00 0.00 3.58
225 227 5.058490 CCAGAATTGCCAAGTTTTGACAAT 58.942 37.500 0.00 0.00 44.07 2.71
258 260 5.747197 GCACTGCATTTTTGGATGATTCTAG 59.253 40.000 0.00 0.00 0.00 2.43
262 264 6.855836 TGCATTTTTGGATGATTCTAGACAC 58.144 36.000 0.00 0.00 0.00 3.67
273 275 7.279758 GGATGATTCTAGACACTTCCTGAAAAG 59.720 40.741 16.37 0.00 0.00 2.27
274 276 6.467677 TGATTCTAGACACTTCCTGAAAAGG 58.532 40.000 0.00 0.00 0.00 3.11
278 280 6.895782 TCTAGACACTTCCTGAAAAGGAAAA 58.104 36.000 8.47 0.00 46.16 2.29
280 282 6.456795 AGACACTTCCTGAAAAGGAAAAAG 57.543 37.500 8.47 0.32 46.16 2.27
328 333 9.551734 CAGACCATGATTCTTCATAATTGAGTA 57.448 33.333 0.00 0.00 40.70 2.59
362 367 7.716998 ACTGTCCCTTAATGCTTAATGTGATAG 59.283 37.037 0.00 0.00 0.00 2.08
433 438 0.179045 GTGCGCTGGTCCTATTGGAT 60.179 55.000 9.73 0.00 45.29 3.41
444 449 5.533903 TGGTCCTATTGGATCTTAGTACGAC 59.466 44.000 7.99 0.00 43.81 4.34
462 467 2.790468 CGACGATTTCCCGACTGTCTAC 60.790 54.545 6.21 0.00 0.00 2.59
496 501 2.363018 CGGCTCTGGTGAGGGAGA 60.363 66.667 0.00 0.00 40.53 3.71
506 511 2.121538 TGAGGGAGAGGCGATGACG 61.122 63.158 0.00 0.00 42.93 4.35
551 556 3.966154 AGTGATTGTAATCGTCGCTAGG 58.034 45.455 0.00 0.00 38.26 3.02
554 559 3.379057 TGATTGTAATCGTCGCTAGGTGA 59.621 43.478 0.00 0.00 38.26 4.02
559 564 0.669077 ATCGTCGCTAGGTGATCCAC 59.331 55.000 0.00 0.00 35.89 4.02
561 566 1.065928 GTCGCTAGGTGATCCACGG 59.934 63.158 0.00 0.00 34.83 4.94
570 575 5.279306 GCTAGGTGATCCACGGACATAATTA 60.279 44.000 0.00 0.00 34.83 1.40
573 578 7.496346 AGGTGATCCACGGACATAATTATAT 57.504 36.000 0.00 0.00 34.83 0.86
599 604 2.285827 TTGCCCGTTGTTGTTCTTTG 57.714 45.000 0.00 0.00 0.00 2.77
623 628 4.811024 CGCTGCCAAAGACTAATAGATTGA 59.189 41.667 0.00 0.00 0.00 2.57
672 677 3.459828 TGGAAGAGGACCCATATGTGAA 58.540 45.455 1.24 0.00 0.00 3.18
710 715 3.321968 TCAGGATTGATATCACAGGACCG 59.678 47.826 4.48 2.79 32.09 4.79
829 834 2.239201 GTTAAAATCACGCGCCAACTC 58.761 47.619 5.73 0.00 0.00 3.01
835 840 2.746277 ACGCGCCAACTCATTCCC 60.746 61.111 5.73 0.00 0.00 3.97
1114 1131 4.393778 TCCCTCCAGACGACCCCC 62.394 72.222 0.00 0.00 0.00 5.40
1242 1259 1.542547 GGCTTCGTCCTCAACCTGAAA 60.543 52.381 0.00 0.00 0.00 2.69
1682 1699 2.490217 CTGCGACCCGTACCTCAG 59.510 66.667 0.00 0.00 0.00 3.35
1702 1719 4.956700 TCAGTTTCAAAATGTTGGGGTACA 59.043 37.500 0.00 0.00 35.29 2.90
1712 1729 2.172851 TTGGGGTACAACATCGTCAC 57.827 50.000 0.00 0.00 33.18 3.67
1785 1802 0.108615 CTGTCCTCGTGAAAGCGGAT 60.109 55.000 0.00 0.00 0.00 4.18
1833 1850 0.176680 AGAATGGCACGCTCTACCTG 59.823 55.000 0.00 0.00 0.00 4.00
1911 1928 1.738099 GCACAAGACGATGCTCCGT 60.738 57.895 3.76 3.76 46.43 4.69
1956 1973 2.813908 GTCGTTGGCTTCGCGGAT 60.814 61.111 6.13 0.00 0.00 4.18
1959 1976 2.746277 GTTGGCTTCGCGGATGGT 60.746 61.111 6.13 0.00 0.00 3.55
1966 1983 2.629050 CTTCGCGGATGGTCACGGAT 62.629 60.000 6.13 0.00 0.00 4.18
2031 4735 0.981183 AGTCAGGCCATGTCCGTAAA 59.019 50.000 5.01 0.00 0.00 2.01
2227 4931 6.888105 TGTAATCTTGTATGCATCTCCTTGA 58.112 36.000 0.19 0.00 0.00 3.02
2339 5144 6.069331 TGGCTTAGATATACTTTCTCCGTCT 58.931 40.000 0.00 0.00 0.00 4.18
2391 5198 5.667626 GGCTCTTATATTATGGGATGGAGGA 59.332 44.000 0.00 0.00 0.00 3.71
2502 5328 3.503363 GCAGACTGCCATCGCCAC 61.503 66.667 17.01 0.00 37.42 5.01
2567 5393 2.671130 TGTTGCATAGATGACGCTCA 57.329 45.000 0.00 0.00 0.00 4.26
2572 5398 4.385358 TGCATAGATGACGCTCAAAGTA 57.615 40.909 0.00 0.00 0.00 2.24
2581 5407 5.181690 TGACGCTCAAAGTATTTTGCTTT 57.818 34.783 5.86 0.00 42.71 3.51
2586 5412 5.117592 CGCTCAAAGTATTTTGCTTTCAAGG 59.882 40.000 5.86 0.00 42.71 3.61
2595 5421 2.435372 TGCTTTCAAGGTGGACTGTT 57.565 45.000 0.00 0.00 0.00 3.16
2620 5446 6.817765 AAGTAGTTACCATGGTCAATGTTG 57.182 37.500 23.76 0.00 34.11 3.33
2732 5704 4.026356 AGCTTAAGCAAGACTGATGGTT 57.974 40.909 28.39 0.58 45.16 3.67
2828 5800 3.390135 TCTGGTTTTCTTAGTGTCTGCG 58.610 45.455 0.00 0.00 0.00 5.18
2841 5813 3.753272 AGTGTCTGCGTATTTCATGCTTT 59.247 39.130 0.00 0.00 40.09 3.51
2856 5828 3.806591 CTTTGCAAGCTCATGTGGG 57.193 52.632 0.00 0.00 0.00 4.61
2891 5863 7.611467 TCCAGAGTGAGTTATAATGCACATTTT 59.389 33.333 17.52 0.00 33.85 1.82
2892 5864 7.912250 CCAGAGTGAGTTATAATGCACATTTTC 59.088 37.037 17.52 9.68 33.85 2.29
3096 6069 2.995938 GCACGTTGTTGCGGAATAC 58.004 52.632 0.00 0.00 35.98 1.89
3097 6070 0.236187 GCACGTTGTTGCGGAATACA 59.764 50.000 0.00 0.00 35.98 2.29
3098 6071 1.135803 GCACGTTGTTGCGGAATACAT 60.136 47.619 0.00 0.00 35.98 2.29
3099 6072 2.504868 CACGTTGTTGCGGAATACATG 58.495 47.619 0.00 0.00 35.98 3.21
3100 6073 1.135803 ACGTTGTTGCGGAATACATGC 60.136 47.619 0.00 0.00 35.98 4.06
3101 6074 1.135831 CGTTGTTGCGGAATACATGCA 60.136 47.619 0.00 0.00 36.72 3.96
3109 6083 5.611796 TGCGGAATACATGCATAAATCTC 57.388 39.130 0.00 0.00 32.86 2.75
3114 6088 7.959651 GCGGAATACATGCATAAATCTCTAAAG 59.040 37.037 0.00 0.00 0.00 1.85
3204 6178 2.603560 GCTAAGTACCTAGTGCTTTGCG 59.396 50.000 13.73 2.19 43.16 4.85
3234 6209 7.961351 TGAATCCCATTTACAAATTGACAGTT 58.039 30.769 0.00 0.00 0.00 3.16
3285 7881 1.422977 TACTGCAGTCCAAAGGCCCA 61.423 55.000 25.56 0.00 0.00 5.36
3288 7884 0.323360 TGCAGTCCAAAGGCCCATAC 60.323 55.000 0.00 0.00 0.00 2.39
3365 7962 9.030301 GCTTAGCACTCTTTTTATGAACAAAAA 57.970 29.630 0.00 0.00 36.31 1.94
3406 8004 7.855784 AGATGTCATCCATACCATTACAGTA 57.144 36.000 9.29 0.00 32.56 2.74
3441 8039 7.335422 AGAGGATTTTTGACACACATTAGCTAG 59.665 37.037 0.00 0.00 0.00 3.42
3446 8044 4.655762 TGACACACATTAGCTAGCCTAG 57.344 45.455 12.13 1.57 0.00 3.02
3454 8052 1.414158 TAGCTAGCCTAGGTTGCTGG 58.586 55.000 25.07 14.27 41.41 4.85
3455 8053 4.865865 CTAGCCTAGGTTGCTGGC 57.134 61.111 11.31 0.00 46.42 4.85
3459 8057 3.569873 GCCTAGGTTGCTGGCTTAA 57.430 52.632 11.31 0.00 43.05 1.85
3460 8058 1.095600 GCCTAGGTTGCTGGCTTAAC 58.904 55.000 11.31 0.00 43.05 2.01
3461 8059 1.613255 GCCTAGGTTGCTGGCTTAACA 60.613 52.381 11.31 0.00 43.05 2.41
3462 8060 2.084546 CCTAGGTTGCTGGCTTAACAC 58.915 52.381 0.00 0.00 0.00 3.32
3463 8061 2.290323 CCTAGGTTGCTGGCTTAACACT 60.290 50.000 0.00 0.00 0.00 3.55
3464 8062 1.897560 AGGTTGCTGGCTTAACACTC 58.102 50.000 0.00 0.00 0.00 3.51
3465 8063 1.421646 AGGTTGCTGGCTTAACACTCT 59.578 47.619 0.00 0.00 0.00 3.24
3466 8064 2.158608 AGGTTGCTGGCTTAACACTCTT 60.159 45.455 0.00 0.00 0.00 2.85
3467 8065 2.623416 GGTTGCTGGCTTAACACTCTTT 59.377 45.455 0.00 0.00 0.00 2.52
3468 8066 3.068165 GGTTGCTGGCTTAACACTCTTTT 59.932 43.478 0.00 0.00 0.00 2.27
3469 8067 4.441495 GGTTGCTGGCTTAACACTCTTTTT 60.441 41.667 0.00 0.00 0.00 1.94
3470 8068 5.221165 GGTTGCTGGCTTAACACTCTTTTTA 60.221 40.000 0.00 0.00 0.00 1.52
3471 8069 6.447162 GTTGCTGGCTTAACACTCTTTTTAT 58.553 36.000 0.00 0.00 0.00 1.40
3472 8070 6.012658 TGCTGGCTTAACACTCTTTTTATG 57.987 37.500 0.00 0.00 0.00 1.90
3473 8071 5.767665 TGCTGGCTTAACACTCTTTTTATGA 59.232 36.000 0.00 0.00 0.00 2.15
3474 8072 6.264292 TGCTGGCTTAACACTCTTTTTATGAA 59.736 34.615 0.00 0.00 0.00 2.57
3475 8073 6.582672 GCTGGCTTAACACTCTTTTTATGAAC 59.417 38.462 0.00 0.00 0.00 3.18
3476 8074 7.575414 TGGCTTAACACTCTTTTTATGAACA 57.425 32.000 0.00 0.00 0.00 3.18
3477 8075 7.422399 TGGCTTAACACTCTTTTTATGAACAC 58.578 34.615 0.00 0.00 0.00 3.32
3478 8076 7.067615 TGGCTTAACACTCTTTTTATGAACACA 59.932 33.333 0.00 0.00 0.00 3.72
3479 8077 7.378728 GGCTTAACACTCTTTTTATGAACACAC 59.621 37.037 0.00 0.00 0.00 3.82
3480 8078 7.913297 GCTTAACACTCTTTTTATGAACACACA 59.087 33.333 0.00 0.00 0.00 3.72
3481 8079 9.950680 CTTAACACTCTTTTTATGAACACACAT 57.049 29.630 0.00 0.00 0.00 3.21
3499 8097 9.859427 AACACACATAATTCAGAAATGTTATGG 57.141 29.630 15.08 9.20 38.32 2.74
3500 8098 9.241919 ACACACATAATTCAGAAATGTTATGGA 57.758 29.630 15.08 0.00 38.32 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 2.783288 CCGCCCCCTACTCTCGTTC 61.783 68.421 0.00 0.00 0.00 3.95
51 52 3.357082 AGGTCCGCCCCCTACTCT 61.357 66.667 0.00 0.00 34.57 3.24
67 68 3.539604 CCTATCCAACAAGAAGGCTCAG 58.460 50.000 0.00 0.00 0.00 3.35
78 79 2.432444 CCAAAACGAGCCTATCCAACA 58.568 47.619 0.00 0.00 0.00 3.33
80 81 1.953311 GCCCAAAACGAGCCTATCCAA 60.953 52.381 0.00 0.00 0.00 3.53
129 130 7.659799 CCCTATTGAACATCATAATTACGACCA 59.340 37.037 0.00 0.00 0.00 4.02
182 184 1.830145 GATTCCTGCGAGCCCCTTA 59.170 57.895 0.00 0.00 0.00 2.69
183 185 2.592308 GATTCCTGCGAGCCCCTT 59.408 61.111 0.00 0.00 0.00 3.95
201 203 3.740764 TGTCAAAACTTGGCAATTCTGGC 60.741 43.478 0.00 0.00 43.24 4.85
242 244 7.391554 CAGGAAGTGTCTAGAATCATCCAAAAA 59.608 37.037 16.59 0.00 0.00 1.94
302 307 8.447924 ACTCAATTATGAAGAATCATGGTCTG 57.552 34.615 1.69 0.00 45.82 3.51
334 339 6.374333 TCACATTAAGCATTAAGGGACAGTTC 59.626 38.462 0.00 0.00 45.75 3.01
337 342 6.949352 ATCACATTAAGCATTAAGGGACAG 57.051 37.500 0.00 0.00 45.75 3.51
350 355 7.930325 TCAGAAGGATCAAGCTATCACATTAAG 59.070 37.037 0.00 0.00 0.00 1.85
433 438 3.063997 GTCGGGAAATCGTCGTACTAAGA 59.936 47.826 0.00 0.00 0.00 2.10
444 449 3.376234 TGTAGTAGACAGTCGGGAAATCG 59.624 47.826 0.00 0.00 32.86 3.34
462 467 1.268625 GCCGGGAAAACCTTGTTGTAG 59.731 52.381 2.18 0.00 36.97 2.74
599 604 2.550978 TCTATTAGTCTTTGGCAGCGC 58.449 47.619 0.00 0.00 0.00 5.92
645 650 1.573108 TGGGTCCTCTTCCAAGCTAG 58.427 55.000 0.00 0.00 0.00 3.42
672 677 0.539051 CTGATCCGTCTTCCAAGCCT 59.461 55.000 0.00 0.00 0.00 4.58
710 715 0.613260 TCAGGGCACACCAGTACATC 59.387 55.000 0.00 0.00 43.89 3.06
1242 1259 0.322816 CCATGCCTTGGTAGTGCTGT 60.323 55.000 0.00 0.00 40.99 4.40
1429 1446 4.189188 GAAGCCGAGCGCGTAGGA 62.189 66.667 20.07 0.00 44.76 2.94
1702 1719 0.033504 AGTTCCTGCGTGACGATGTT 59.966 50.000 10.10 0.00 0.00 2.71
1712 1729 0.526524 GATCACCGAGAGTTCCTGCG 60.527 60.000 0.00 0.00 0.00 5.18
1785 1802 1.304381 GAACCCCAGCTTGCCATCA 60.304 57.895 0.00 0.00 0.00 3.07
1814 1831 0.176680 CAGGTAGAGCGTGCCATTCT 59.823 55.000 0.00 0.00 31.94 2.40
1833 1850 1.810030 GCCGTCCTTCATCGACCAC 60.810 63.158 0.00 0.00 0.00 4.16
1861 1878 0.747644 CGCTGCACCCATTCCACATA 60.748 55.000 0.00 0.00 0.00 2.29
1911 1928 2.104859 CGTCGAGAGGCCACGAGTA 61.105 63.158 17.29 0.00 39.16 2.59
1956 1973 2.773487 ACGAAAATGAATCCGTGACCA 58.227 42.857 0.00 0.00 33.69 4.02
1966 1983 2.151202 GCCTGTCCTCACGAAAATGAA 58.849 47.619 0.00 0.00 0.00 2.57
2182 4886 1.315257 CCTTGCGCAACCTGCCTATT 61.315 55.000 21.02 0.00 41.12 1.73
2227 4931 7.669722 ACAAACAACCTGAAGATTACATATGGT 59.330 33.333 7.80 0.00 0.00 3.55
2331 5136 8.873186 TGGTGTATTATATTATGAGACGGAGA 57.127 34.615 0.00 0.00 0.00 3.71
2367 5172 5.667626 TCCTCCATCCCATAATATAAGAGCC 59.332 44.000 0.00 0.00 0.00 4.70
2465 5291 2.880890 GCCCATAGCACGATCTGAAAAT 59.119 45.455 0.00 0.00 42.97 1.82
2502 5328 0.972983 AGGATGACAGTGGGTCCTCG 60.973 60.000 7.24 0.00 46.38 4.63
2567 5393 6.098266 AGTCCACCTTGAAAGCAAAATACTTT 59.902 34.615 0.00 0.00 39.99 2.66
2572 5398 3.706086 ACAGTCCACCTTGAAAGCAAAAT 59.294 39.130 0.00 0.00 32.73 1.82
2581 5407 5.881923 ACTACTTAAACAGTCCACCTTGA 57.118 39.130 0.00 0.00 36.88 3.02
2586 5412 6.370718 CCATGGTAACTACTTAAACAGTCCAC 59.629 42.308 2.57 0.00 36.88 4.02
2595 5421 7.392113 CCAACATTGACCATGGTAACTACTTAA 59.608 37.037 19.80 3.81 37.17 1.85
2620 5446 5.470777 TGCCACACTGTAAACTAAACATACC 59.529 40.000 0.00 0.00 0.00 2.73
2668 5637 7.553334 ACATACTAAACTGACCGTGATTACAT 58.447 34.615 0.00 0.00 0.00 2.29
2669 5638 6.927416 ACATACTAAACTGACCGTGATTACA 58.073 36.000 0.00 0.00 0.00 2.41
2676 5646 5.979288 AGAGAACATACTAAACTGACCGT 57.021 39.130 0.00 0.00 0.00 4.83
2841 5813 1.179152 CAATCCCACATGAGCTTGCA 58.821 50.000 0.00 0.00 0.00 4.08
2891 5863 7.441760 GTCACTAATAACTGGAGAGTAGATCGA 59.558 40.741 0.00 0.00 0.00 3.59
2892 5864 7.442969 AGTCACTAATAACTGGAGAGTAGATCG 59.557 40.741 0.00 0.00 0.00 3.69
2932 5905 9.230122 TCAGTATCATAATCACTTTCTTTTGCA 57.770 29.630 0.00 0.00 0.00 4.08
3165 6139 9.562583 GTACTTAGCGAGATATCATCCTTTTAG 57.437 37.037 5.32 0.00 0.00 1.85
3171 6145 6.824704 ACTAGGTACTTAGCGAGATATCATCC 59.175 42.308 11.69 0.00 41.75 3.51
3175 6149 5.644636 AGCACTAGGTACTTAGCGAGATATC 59.355 44.000 11.69 0.00 41.75 1.63
3178 6152 3.822940 AGCACTAGGTACTTAGCGAGAT 58.177 45.455 11.69 0.00 41.75 2.75
3204 6178 6.822676 TCAATTTGTAAATGGGATTCATTGCC 59.177 34.615 0.00 0.00 44.68 4.52
3234 6209 9.575868 TGGTACAGGATTACATTTTTACTTCAA 57.424 29.630 0.00 0.00 0.00 2.69
3267 7862 2.085343 ATGGGCCTTTGGACTGCAGT 62.085 55.000 21.88 21.88 0.00 4.40
3268 7863 0.034186 TATGGGCCTTTGGACTGCAG 60.034 55.000 13.48 13.48 0.00 4.41
3269 7864 0.323360 GTATGGGCCTTTGGACTGCA 60.323 55.000 4.53 0.00 0.00 4.41
3270 7865 1.037579 GGTATGGGCCTTTGGACTGC 61.038 60.000 4.53 0.00 0.00 4.40
3271 7866 0.331278 TGGTATGGGCCTTTGGACTG 59.669 55.000 4.53 0.00 0.00 3.51
3272 7867 1.308877 ATGGTATGGGCCTTTGGACT 58.691 50.000 4.53 0.00 0.00 3.85
3273 7868 2.174854 ACTATGGTATGGGCCTTTGGAC 59.825 50.000 4.53 0.00 0.00 4.02
3288 7884 9.184523 CAAGATCCTCTAATCTACCTACTATGG 57.815 40.741 0.00 0.00 34.90 2.74
3314 7910 0.320697 ACTTGGGCTAACGTGAGACC 59.679 55.000 19.25 19.25 46.08 3.85
3318 7914 0.107831 AGCAACTTGGGCTAACGTGA 59.892 50.000 0.00 0.00 40.47 4.35
3366 7963 9.512588 GGATGACATCTATACCATTTCTGATTT 57.487 33.333 14.95 0.00 0.00 2.17
3406 8004 7.824779 GTGTGTCAAAAATCCTCTAATCTACCT 59.175 37.037 0.00 0.00 0.00 3.08
3446 8044 1.897560 AGAGTGTTAAGCCAGCAACC 58.102 50.000 0.00 0.00 0.00 3.77
3454 8052 7.913297 TGTGTGTTCATAAAAAGAGTGTTAAGC 59.087 33.333 0.00 0.00 0.00 3.09
3455 8053 9.950680 ATGTGTGTTCATAAAAAGAGTGTTAAG 57.049 29.630 0.00 0.00 0.00 1.85
3473 8071 9.859427 CCATAACATTTCTGAATTATGTGTGTT 57.141 29.630 15.63 10.02 33.10 3.32
3474 8072 9.241919 TCCATAACATTTCTGAATTATGTGTGT 57.758 29.630 15.63 3.71 33.10 3.72


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

AutoCloner maintained by Alex Coulton.