Multiple sequence alignment - TraesCS1A01G218800

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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 TraesCS1A01G218800 chr1A 100.000 3500 0 0 1 3500 387514523 387518022 0.000000e+00 6464
1 TraesCS1A01G218800 chr1D 91.948 3229 156 44 1 3166 308260405 308263592 0.000000e+00 4427
2 TraesCS1A01G218800 chr1D 87.647 340 24 8 3167 3500 308263625 308263952 2.550000e-101 379
3 TraesCS1A01G218800 chr1B 89.545 2965 163 67 604 3500 417399861 417402746 0.000000e+00 3622
4 TraesCS1A01G218800 chr5B 91.887 1060 52 17 843 1901 443697377 443698403 0.000000e+00 1450
5 TraesCS1A01G218800 chr3B 92.929 693 39 6 1210 1901 400612120 400611437 0.000000e+00 1000
6 TraesCS1A01G218800 chr3B 80.604 629 65 29 953 1570 22400972 22401554 1.930000e-117 433
7 TraesCS1A01G218800 chr4B 81.888 519 46 27 956 1463 626628964 626628483 9.110000e-106 394
8 TraesCS1A01G218800 chr4B 85.057 174 20 4 421 590 144074324 144074495 4.640000e-39 172
9 TraesCS1A01G218800 chr3D 84.158 202 30 2 1666 1866 62329618 62329818 9.910000e-46 195
10 TraesCS1A01G218800 chr3A 83.663 202 31 2 1666 1866 71224690 71224890 4.610000e-44 189
11 TraesCS1A01G218800 chr6D 86.047 172 18 4 428 595 323285865 323285696 2.780000e-41 180
12 TraesCS1A01G218800 chr6D 85.632 174 18 2 420 590 145462455 145462624 3.590000e-40 176
13 TraesCS1A01G218800 chr6D 84.916 179 18 6 421 594 41542480 41542654 4.640000e-39 172
14 TraesCS1A01G218800 chr5A 86.826 167 15 2 427 590 320214406 320214244 2.780000e-41 180
15 TraesCS1A01G218800 chr7D 85.311 177 20 4 423 595 620330091 620329917 9.980000e-41 178
16 TraesCS1A01G218800 chr7A 86.667 165 17 4 427 590 187107850 187107690 9.980000e-41 178
17 TraesCS1A01G218800 chr2D 86.747 166 15 2 428 590 134301488 134301649 9.980000e-41 178


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 TraesCS1A01G218800 chr1A 387514523 387518022 3499 False 6464 6464 100.0000 1 3500 1 chr1A.!!$F1 3499
1 TraesCS1A01G218800 chr1D 308260405 308263952 3547 False 2403 4427 89.7975 1 3500 2 chr1D.!!$F1 3499
2 TraesCS1A01G218800 chr1B 417399861 417402746 2885 False 3622 3622 89.5450 604 3500 1 chr1B.!!$F1 2896
3 TraesCS1A01G218800 chr5B 443697377 443698403 1026 False 1450 1450 91.8870 843 1901 1 chr5B.!!$F1 1058
4 TraesCS1A01G218800 chr3B 400611437 400612120 683 True 1000 1000 92.9290 1210 1901 1 chr3B.!!$R1 691
5 TraesCS1A01G218800 chr3B 22400972 22401554 582 False 433 433 80.6040 953 1570 1 chr3B.!!$F1 617

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
21 22 0.249615 GTCAGAGCAGCACACACTCA 60.250 55.0 0.00 0.00 32.71 3.41 F
408 415 0.451783 CACCGTGCAATTTCTAGCCC 59.548 55.0 0.00 0.00 0.00 5.19 F
753 772 0.526739 AACAAAAACAAGGACGCGCC 60.527 50.0 5.73 9.03 0.00 6.53 F
844 882 1.051812 CACCCACCAAGAGTCAGTCT 58.948 55.0 0.00 0.00 36.94 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2018 2073 0.040067 GAGCAAGCTTGGTTCCAACG 60.040 55.000 30.17 1.29 39.30 4.10 R
2204 2259 1.458064 GCATCTGCATGTTGTTGTTGC 59.542 47.619 0.00 0.00 41.59 4.17 R
2283 2361 1.684450 CCCGGTTGGTGTAAAGCTTTT 59.316 47.619 18.47 1.58 0.00 2.27 R
2666 2749 2.100584 CCAACTTGTACCAAAGCAAGCA 59.899 45.455 4.45 0.00 44.12 3.91 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
18 19 1.300156 TCGTCAGAGCAGCACACAC 60.300 57.895 0.00 0.00 0.00 3.82
19 20 1.300465 CGTCAGAGCAGCACACACT 60.300 57.895 0.00 0.00 0.00 3.55
21 22 0.249615 GTCAGAGCAGCACACACTCA 60.250 55.000 0.00 0.00 32.71 3.41
22 23 0.683412 TCAGAGCAGCACACACTCAT 59.317 50.000 0.00 0.00 32.71 2.90
94 95 3.343617 GCAGAGGTTAGGCACAAATACA 58.656 45.455 0.00 0.00 0.00 2.29
108 109 3.290710 CAAATACATAGGTTGGGCAGCT 58.709 45.455 0.00 0.00 36.98 4.24
118 119 4.154347 GGGCAGCTGTCTCCGAGG 62.154 72.222 19.48 0.00 0.00 4.63
124 125 2.716017 GCTGTCTCCGAGGTGAGGG 61.716 68.421 0.00 0.00 33.04 4.30
131 132 1.231641 CCGAGGTGAGGGAGGAGAT 59.768 63.158 0.00 0.00 0.00 2.75
132 133 0.478942 CCGAGGTGAGGGAGGAGATA 59.521 60.000 0.00 0.00 0.00 1.98
133 134 1.076350 CCGAGGTGAGGGAGGAGATAT 59.924 57.143 0.00 0.00 0.00 1.63
134 135 2.309162 CCGAGGTGAGGGAGGAGATATA 59.691 54.545 0.00 0.00 0.00 0.86
140 142 5.561967 AGGTGAGGGAGGAGATATAACCTAT 59.438 44.000 0.00 0.00 36.57 2.57
166 168 7.556733 TTTTGTTACTGGAGTTATCGTTTGT 57.443 32.000 0.00 0.00 0.00 2.83
238 240 1.369625 GTATGAAGAGGCCAACGGTG 58.630 55.000 5.01 0.00 0.00 4.94
259 261 1.129251 GCAGTGTTGATGGTGATGTCG 59.871 52.381 0.00 0.00 0.00 4.35
262 264 0.676466 TGTTGATGGTGATGTCGGCC 60.676 55.000 0.00 0.00 0.00 6.13
289 291 3.066760 GGCGGGAAAATAAGAAGTGATGG 59.933 47.826 0.00 0.00 0.00 3.51
295 297 6.095377 GGAAAATAAGAAGTGATGGTGCTTG 58.905 40.000 0.00 0.00 0.00 4.01
327 330 6.690957 CAGTGAATAGACGAGAGAATGAGAAC 59.309 42.308 0.00 0.00 0.00 3.01
330 333 5.666969 ATAGACGAGAGAATGAGAACGAG 57.333 43.478 0.00 0.00 0.00 4.18
350 353 5.709631 ACGAGAGTGATGATCTATAGTGCAT 59.290 40.000 8.98 8.98 46.97 3.96
382 385 1.153449 CGGCGAGCATAACAAGGGA 60.153 57.895 0.00 0.00 0.00 4.20
383 386 0.532862 CGGCGAGCATAACAAGGGAT 60.533 55.000 0.00 0.00 0.00 3.85
385 388 1.604278 GGCGAGCATAACAAGGGATTC 59.396 52.381 0.00 0.00 0.00 2.52
408 415 0.451783 CACCGTGCAATTTCTAGCCC 59.548 55.000 0.00 0.00 0.00 5.19
415 422 4.754618 CGTGCAATTTCTAGCCCATGTATA 59.245 41.667 0.00 0.00 0.00 1.47
453 460 7.724287 ACTCCCTTCGTTCCTAATTATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
473 480 6.787085 AGTCGTTTTAGAGATTTCAACAGG 57.213 37.500 0.00 0.00 0.00 4.00
481 488 7.496346 TTAGAGATTTCAACAGGGACTACAT 57.504 36.000 0.00 0.00 36.02 2.29
482 489 8.603898 TTAGAGATTTCAACAGGGACTACATA 57.396 34.615 0.00 0.00 36.02 2.29
483 490 6.879400 AGAGATTTCAACAGGGACTACATAC 58.121 40.000 0.00 0.00 36.02 2.39
484 491 5.661458 AGATTTCAACAGGGACTACATACG 58.339 41.667 0.00 0.00 36.02 3.06
496 503 9.419614 CAGGGACTACATACGTACGGATGTATG 62.420 48.148 39.66 33.63 46.96 2.39
535 542 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
536 543 5.412594 GTGTAGATTCACTCATTTTGCTCCA 59.587 40.000 0.00 0.00 35.68 3.86
539 546 6.690194 AGATTCACTCATTTTGCTCCATAC 57.310 37.500 0.00 0.00 0.00 2.39
540 547 6.182627 AGATTCACTCATTTTGCTCCATACA 58.817 36.000 0.00 0.00 0.00 2.29
543 550 7.558161 TTCACTCATTTTGCTCCATACATAG 57.442 36.000 0.00 0.00 0.00 2.23
545 552 6.763135 TCACTCATTTTGCTCCATACATAGTC 59.237 38.462 0.00 0.00 0.00 2.59
552 559 2.738846 GCTCCATACATAGTCCGCATTG 59.261 50.000 0.00 0.00 0.00 2.82
553 560 3.329386 CTCCATACATAGTCCGCATTGG 58.671 50.000 0.00 0.00 40.09 3.16
630 648 2.159043 CGAGGCAGAAGATTAAGGAGCA 60.159 50.000 0.00 0.00 0.00 4.26
693 711 6.404844 GGAATTAAAAGCCTACTCCAGAAAGC 60.405 42.308 0.00 0.00 0.00 3.51
710 729 3.692791 AAGCAAGTCGTGGAGAAAAAC 57.307 42.857 0.00 0.00 0.00 2.43
715 734 4.207019 GCAAGTCGTGGAGAAAAACAAATG 59.793 41.667 0.00 0.00 0.00 2.32
753 772 0.526739 AACAAAAACAAGGACGCGCC 60.527 50.000 5.73 9.03 0.00 6.53
844 882 1.051812 CACCCACCAAGAGTCAGTCT 58.948 55.000 0.00 0.00 36.94 3.24
983 1021 4.856801 CAACCCCCGGCTCCATCG 62.857 72.222 0.00 0.00 0.00 3.84
1036 1074 2.436824 GGAAGGCGGTGCTCTTCC 60.437 66.667 17.32 17.32 43.21 3.46
1332 1373 4.601084 TCTTCTACCCTCCTGTCTTGTAG 58.399 47.826 0.00 0.00 0.00 2.74
1333 1374 4.044317 TCTTCTACCCTCCTGTCTTGTAGT 59.956 45.833 0.00 0.00 32.64 2.73
1334 1375 3.965694 TCTACCCTCCTGTCTTGTAGTC 58.034 50.000 0.00 0.00 32.64 2.59
1397 1438 7.468084 GCGGTTTACAGATTCCTGCAATTATTA 60.468 37.037 0.00 0.00 44.16 0.98
1407 1448 8.776376 ATTCCTGCAATTATTAAGGTGTTTTG 57.224 30.769 5.96 0.00 0.00 2.44
1411 1452 5.182487 GCAATTATTAAGGTGTTTTGGGGG 58.818 41.667 0.00 0.00 0.00 5.40
1412 1453 5.046231 GCAATTATTAAGGTGTTTTGGGGGA 60.046 40.000 0.00 0.00 0.00 4.81
1506 1559 6.763355 TCAAGAAACTGAGTTCAAGCTATCT 58.237 36.000 0.00 0.00 0.00 1.98
1560 1613 2.783828 AGCAGTCGATGGATCTTACG 57.216 50.000 0.00 0.00 0.00 3.18
1593 1646 8.624776 CCTCCTGAATAACAATTTGATTAGTCC 58.375 37.037 2.79 0.00 0.00 3.85
1594 1647 9.401058 CTCCTGAATAACAATTTGATTAGTCCT 57.599 33.333 2.79 0.00 0.00 3.85
1623 1676 6.376581 GTGTTGCTTCCTAGTAGTAGTCCTAA 59.623 42.308 3.91 0.00 0.00 2.69
1639 1692 6.101650 AGTCCTAATACGATGAATCATGCA 57.898 37.500 0.00 0.00 0.00 3.96
1929 1984 1.891919 GTCCAGTTCACGCCAAGCA 60.892 57.895 0.00 0.00 0.00 3.91
1930 1985 1.891919 TCCAGTTCACGCCAAGCAC 60.892 57.895 0.00 0.00 0.00 4.40
1931 1986 1.893808 CCAGTTCACGCCAAGCACT 60.894 57.895 0.00 0.00 0.00 4.40
1976 2031 3.181523 CGCAGCAGCTAATATATGCAGTG 60.182 47.826 0.00 0.00 42.45 3.66
1981 2036 6.309980 CAGCAGCTAATATATGCAGTGTACTC 59.690 42.308 0.00 0.00 42.45 2.59
2018 2073 1.744741 GCTGCCAAGTCCTCAGAGC 60.745 63.158 0.00 0.00 0.00 4.09
2060 2115 3.165071 TGCTGAGAAGATACTCCACACA 58.835 45.455 0.00 0.00 36.22 3.72
2204 2259 3.414193 TGGAGGCATCAGGGGCAG 61.414 66.667 0.00 0.00 35.46 4.85
2283 2361 3.339141 TGTAACAACAACAGTGTGAGCA 58.661 40.909 0.00 0.00 38.27 4.26
2339 2417 1.565305 GCTGATGAGCTAACTGACCG 58.435 55.000 0.00 0.00 42.52 4.79
2504 2582 1.662629 CATCAAGGTGCTGTGATCGAC 59.337 52.381 0.00 0.00 32.06 4.20
2575 2658 1.063166 GCTTAGCTTCATGTGGCGC 59.937 57.895 0.00 0.00 0.00 6.53
2585 2668 3.628646 ATGTGGCGCCCCTGTTCTC 62.629 63.158 26.77 4.61 0.00 2.87
2784 2867 1.354506 GCTTGCATCGCATGGAGAC 59.645 57.895 3.85 0.00 38.76 3.36
2851 2934 2.369600 CATCGCGCTCATGAATTGAAC 58.630 47.619 5.56 0.00 32.78 3.18
2881 2967 0.249280 GGGTTGGTTTCTTGTTGCCG 60.249 55.000 0.00 0.00 0.00 5.69
2896 2982 4.154347 CCGTCTGAGGAGGCAGCC 62.154 72.222 1.84 1.84 35.86 4.85
2913 2999 1.142748 CCATGACAGGAGAGGACGC 59.857 63.158 0.00 0.00 0.00 5.19
2988 3074 1.138247 GCCTGCATTTTGCTCCTCG 59.862 57.895 0.75 0.00 45.31 4.63
3081 3178 1.117994 TGTGATGCTAGCAGAGGGAG 58.882 55.000 23.89 0.00 0.00 4.30
3201 3333 1.255600 GATCGCAAAATCTCGTCCGTC 59.744 52.381 0.00 0.00 0.00 4.79
3207 3339 3.262420 CAAAATCTCGTCCGTCCATTCT 58.738 45.455 0.00 0.00 0.00 2.40
3216 3348 3.615496 CGTCCGTCCATTCTAAACGAAAT 59.385 43.478 0.00 0.00 38.65 2.17
3243 3375 1.053424 ACCCGGTTGACAGCTAAAGA 58.947 50.000 0.00 0.00 0.00 2.52
3256 3388 5.312079 ACAGCTAAAGAAAACTGAGATGCT 58.688 37.500 0.00 0.00 34.25 3.79
3259 3391 7.609532 ACAGCTAAAGAAAACTGAGATGCTTAT 59.390 33.333 0.00 0.00 34.25 1.73
3261 3393 8.046107 AGCTAAAGAAAACTGAGATGCTTATCT 58.954 33.333 0.00 0.00 0.00 1.98
3312 3444 1.153349 GGAACAGCCCGATCCTCAC 60.153 63.158 0.00 0.00 33.76 3.51
3329 3462 4.043310 TCCTCACAGGAATGGACAAGATTT 59.957 41.667 0.00 0.00 42.51 2.17
3330 3463 4.768968 CCTCACAGGAATGGACAAGATTTT 59.231 41.667 0.00 0.00 37.67 1.82
3331 3464 5.945784 CCTCACAGGAATGGACAAGATTTTA 59.054 40.000 0.00 0.00 37.67 1.52
3367 3509 1.068921 AAACCGGTTTGGCACATGC 59.931 52.632 31.17 0.00 43.94 4.06
3395 3537 3.813166 CACATCATGTGCATGCTCATAGA 59.187 43.478 29.16 26.12 41.89 1.98
3396 3538 4.065789 ACATCATGTGCATGCTCATAGAG 58.934 43.478 29.16 22.86 38.65 2.43
3397 3539 3.832615 TCATGTGCATGCTCATAGAGT 57.167 42.857 29.16 10.45 38.65 3.24
3398 3540 3.725490 TCATGTGCATGCTCATAGAGTC 58.275 45.455 29.16 6.29 38.65 3.36
3399 3541 3.133362 TCATGTGCATGCTCATAGAGTCA 59.867 43.478 29.16 10.80 38.65 3.41
3400 3542 3.832615 TGTGCATGCTCATAGAGTCAT 57.167 42.857 20.33 0.00 30.78 3.06
3401 3543 4.942761 TGTGCATGCTCATAGAGTCATA 57.057 40.909 20.33 0.00 30.06 2.15
3402 3544 4.879598 TGTGCATGCTCATAGAGTCATAG 58.120 43.478 20.33 0.00 30.06 2.23
3417 3559 3.316588 AGTCATAGTCCACATCTACAGCG 59.683 47.826 0.00 0.00 0.00 5.18
3421 3563 2.184322 CCACATCTACAGCGGCGT 59.816 61.111 9.37 0.00 0.00 5.68
3455 3598 1.842562 AGAAGGATGGGTGTGATGGAG 59.157 52.381 0.00 0.00 0.00 3.86
3471 3614 1.202842 TGGAGTCGCGGATAGGATGTA 60.203 52.381 6.13 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.520494 AATGAGTGTGTGCTGCTCTG 58.480 50.000 0.00 0.00 0.00 3.35
18 19 3.126858 CACCACCGAACCACATAAATGAG 59.873 47.826 0.00 0.00 0.00 2.90
19 20 3.078097 CACCACCGAACCACATAAATGA 58.922 45.455 0.00 0.00 0.00 2.57
21 22 3.078837 GTCACCACCGAACCACATAAAT 58.921 45.455 0.00 0.00 0.00 1.40
22 23 2.496111 GTCACCACCGAACCACATAAA 58.504 47.619 0.00 0.00 0.00 1.40
75 76 5.428783 ACCTATGTATTTGTGCCTAACCTCT 59.571 40.000 0.00 0.00 0.00 3.69
85 86 3.181487 GCTGCCCAACCTATGTATTTGTG 60.181 47.826 0.00 0.00 0.00 3.33
94 95 0.543749 GAGACAGCTGCCCAACCTAT 59.456 55.000 15.27 0.00 0.00 2.57
108 109 3.177291 TCCCTCACCTCGGAGACA 58.823 61.111 6.58 0.00 37.05 3.41
118 119 7.800300 AAATAGGTTATATCTCCTCCCTCAC 57.200 40.000 2.42 0.00 35.51 3.51
160 162 1.742831 CATGTACCCCCATCACAAACG 59.257 52.381 0.00 0.00 0.00 3.60
166 168 1.212375 CTCCACATGTACCCCCATCA 58.788 55.000 0.00 0.00 0.00 3.07
215 217 0.252197 GTTGGCCTCTTCATACCCGT 59.748 55.000 3.32 0.00 0.00 5.28
238 240 1.470098 GACATCACCATCAACACTGCC 59.530 52.381 0.00 0.00 0.00 4.85
262 264 5.588648 TCACTTCTTATTTTCCCGCCTATTG 59.411 40.000 0.00 0.00 0.00 1.90
289 291 5.292101 GTCTATTCACTGTATCCACAAGCAC 59.708 44.000 0.00 0.00 33.22 4.40
295 297 5.527951 TCTCTCGTCTATTCACTGTATCCAC 59.472 44.000 0.00 0.00 0.00 4.02
311 314 3.372822 ACTCTCGTTCTCATTCTCTCGTC 59.627 47.826 0.00 0.00 0.00 4.20
315 318 4.946772 TCATCACTCTCGTTCTCATTCTCT 59.053 41.667 0.00 0.00 0.00 3.10
317 320 5.593909 AGATCATCACTCTCGTTCTCATTCT 59.406 40.000 0.00 0.00 0.00 2.40
327 330 5.619625 TGCACTATAGATCATCACTCTCG 57.380 43.478 6.78 0.00 0.00 4.04
330 333 7.277539 GCCTTAATGCACTATAGATCATCACTC 59.722 40.741 6.78 0.00 0.00 3.51
335 338 6.827251 CCATGCCTTAATGCACTATAGATCAT 59.173 38.462 7.63 6.24 45.48 2.45
338 341 4.946157 GCCATGCCTTAATGCACTATAGAT 59.054 41.667 7.63 0.00 45.48 1.98
365 368 1.604278 GAATCCCTTGTTATGCTCGCC 59.396 52.381 0.00 0.00 0.00 5.54
369 372 2.238646 TGGACGAATCCCTTGTTATGCT 59.761 45.455 0.00 0.00 45.59 3.79
372 375 3.277142 GGTGGACGAATCCCTTGTTAT 57.723 47.619 0.00 0.00 45.59 1.89
415 422 6.481434 ACGAAGGGAGTATTACTTTATGCT 57.519 37.500 0.00 0.00 0.00 3.79
453 460 5.701290 AGTCCCTGTTGAAATCTCTAAAACG 59.299 40.000 0.00 0.00 0.00 3.60
470 477 2.564771 TCCGTACGTATGTAGTCCCTG 58.435 52.381 15.21 0.00 0.00 4.45
472 479 2.880890 ACATCCGTACGTATGTAGTCCC 59.119 50.000 22.93 0.00 34.61 4.46
473 480 5.625251 CATACATCCGTACGTATGTAGTCC 58.375 45.833 29.33 0.00 40.78 3.85
481 488 8.552083 AATATGTCTACATACATCCGTACGTA 57.448 34.615 15.21 0.00 41.15 3.57
482 489 7.444629 AATATGTCTACATACATCCGTACGT 57.555 36.000 15.21 0.00 41.15 3.57
483 490 8.738199 AAAATATGTCTACATACATCCGTACG 57.262 34.615 8.69 8.69 41.15 3.67
516 523 6.182627 TGTATGGAGCAAAATGAGTGAATCT 58.817 36.000 0.00 0.00 0.00 2.40
532 539 3.006859 TCCAATGCGGACTATGTATGGAG 59.993 47.826 0.00 0.00 39.64 3.86
535 542 5.240891 AGATTCCAATGCGGACTATGTATG 58.759 41.667 0.00 0.00 46.36 2.39
536 543 5.489792 AGATTCCAATGCGGACTATGTAT 57.510 39.130 0.00 0.00 46.36 2.29
539 546 5.505173 AAAAGATTCCAATGCGGACTATG 57.495 39.130 0.00 0.00 46.36 2.23
540 547 6.483640 GTCTAAAAGATTCCAATGCGGACTAT 59.516 38.462 0.00 0.00 46.36 2.12
543 550 4.636206 AGTCTAAAAGATTCCAATGCGGAC 59.364 41.667 0.00 0.00 46.36 4.79
545 552 5.567138 AAGTCTAAAAGATTCCAATGCGG 57.433 39.130 0.00 0.00 0.00 5.69
559 566 9.467258 CCGTCCATTCGTAAATATAAGTCTAAA 57.533 33.333 0.00 0.00 0.00 1.85
561 568 8.394971 TCCGTCCATTCGTAAATATAAGTCTA 57.605 34.615 0.00 0.00 0.00 2.59
597 614 6.817765 TCTTCTGCCTCGTTTCAATATTTT 57.182 33.333 0.00 0.00 0.00 1.82
598 615 7.396540 AATCTTCTGCCTCGTTTCAATATTT 57.603 32.000 0.00 0.00 0.00 1.40
643 661 8.711457 CCAAAATTTTCCATACTTTTAGCACAG 58.289 33.333 0.00 0.00 0.00 3.66
693 711 4.207019 GCATTTGTTTTTCTCCACGACTTG 59.793 41.667 0.00 0.00 0.00 3.16
710 729 3.853831 TCCTTGCTGTATGTGCATTTG 57.146 42.857 0.00 0.00 40.34 2.32
753 772 7.680310 TCCCCTCCTTCTCCATTTATAAGATAG 59.320 40.741 0.00 0.00 0.00 2.08
754 773 7.553655 TCCCCTCCTTCTCCATTTATAAGATA 58.446 38.462 0.00 0.00 0.00 1.98
755 774 6.402442 TCCCCTCCTTCTCCATTTATAAGAT 58.598 40.000 0.00 0.00 0.00 2.40
756 775 5.799536 TCCCCTCCTTCTCCATTTATAAGA 58.200 41.667 0.00 0.00 0.00 2.10
757 776 5.846714 TCTCCCCTCCTTCTCCATTTATAAG 59.153 44.000 0.00 0.00 0.00 1.73
844 882 2.246874 ACGAGGGGAAGGAGGGAGA 61.247 63.158 0.00 0.00 0.00 3.71
980 1018 3.606662 CCTCGCCCGATGGTCGAT 61.607 66.667 0.22 0.00 43.74 3.59
983 1021 2.808206 ATTCCCTCGCCCGATGGTC 61.808 63.158 10.93 0.00 32.73 4.02
984 1022 2.768344 ATTCCCTCGCCCGATGGT 60.768 61.111 10.93 0.00 32.73 3.55
1332 1373 0.456628 GAGCTCTCTACGGGTTGGAC 59.543 60.000 6.43 0.00 0.00 4.02
1333 1374 0.331954 AGAGCTCTCTACGGGTTGGA 59.668 55.000 11.45 0.00 38.35 3.53
1334 1375 2.054232 TAGAGCTCTCTACGGGTTGG 57.946 55.000 22.17 0.00 40.93 3.77
1397 1438 4.757692 TGATTATTCCCCCAAAACACCTT 58.242 39.130 0.00 0.00 0.00 3.50
1407 1448 3.054802 AGCGATCAGATGATTATTCCCCC 60.055 47.826 0.00 0.00 34.37 5.40
1506 1559 8.862325 ACACTTTGATGATACATAAAGGTCAA 57.138 30.769 0.00 0.00 35.13 3.18
1539 1592 3.498777 TCGTAAGATCCATCGACTGCTAG 59.501 47.826 0.00 0.00 45.01 3.42
1560 1613 4.503714 TTGTTATTCAGGAGGTGGGATC 57.496 45.455 0.00 0.00 0.00 3.36
1568 1621 9.401058 AGGACTAATCAAATTGTTATTCAGGAG 57.599 33.333 0.00 0.00 0.00 3.69
1569 1622 9.753674 AAGGACTAATCAAATTGTTATTCAGGA 57.246 29.630 0.00 0.00 0.00 3.86
1593 1646 2.457366 ACTAGGAAGCAACACGGAAG 57.543 50.000 0.00 0.00 0.00 3.46
1594 1647 2.895404 ACTACTAGGAAGCAACACGGAA 59.105 45.455 0.00 0.00 0.00 4.30
1623 1676 4.024302 CACTTGCTGCATGATTCATCGTAT 60.024 41.667 20.66 0.00 0.00 3.06
1639 1692 4.458295 CAGAATCTCAATCAACCACTTGCT 59.542 41.667 0.00 0.00 0.00 3.91
1789 1844 0.613853 AGTACTTCTGGGCGTGGCTA 60.614 55.000 0.00 0.00 0.00 3.93
1920 1975 0.107831 TTTGGAGTAGTGCTTGGCGT 59.892 50.000 0.00 0.00 0.00 5.68
1929 1984 3.104512 TCCGATGGATGTTTGGAGTAGT 58.895 45.455 0.00 0.00 0.00 2.73
1930 1985 3.819564 TCCGATGGATGTTTGGAGTAG 57.180 47.619 0.00 0.00 0.00 2.57
1931 1986 3.243737 CGATCCGATGGATGTTTGGAGTA 60.244 47.826 2.43 0.00 43.27 2.59
1976 2031 7.653311 AGCTGAAACCAAATTGAAATTGAGTAC 59.347 33.333 0.00 0.00 0.00 2.73
1981 2036 5.445845 GCAGCTGAAACCAAATTGAAATTG 58.554 37.500 20.43 0.00 0.00 2.32
2018 2073 0.040067 GAGCAAGCTTGGTTCCAACG 60.040 55.000 30.17 1.29 39.30 4.10
2097 2152 6.240894 TCTAGCAGGAAACAAGATGAAACAT 58.759 36.000 0.00 0.00 0.00 2.71
2204 2259 1.458064 GCATCTGCATGTTGTTGTTGC 59.542 47.619 0.00 0.00 41.59 4.17
2283 2361 1.684450 CCCGGTTGGTGTAAAGCTTTT 59.316 47.619 18.47 1.58 0.00 2.27
2339 2417 5.180304 GGGAACTTTGATCTCTTCTTCACAC 59.820 44.000 0.00 0.00 0.00 3.82
2666 2749 2.100584 CCAACTTGTACCAAAGCAAGCA 59.899 45.455 4.45 0.00 44.12 3.91
2708 2791 9.781633 ACATTACAAACAAACCTACTACACATA 57.218 29.630 0.00 0.00 0.00 2.29
2784 2867 4.083110 GCCAATTCCAATATCTCGGTGATG 60.083 45.833 2.94 0.00 36.65 3.07
2881 2967 1.153208 CATGGCTGCCTCCTCAGAC 60.153 63.158 21.03 0.00 42.43 3.51
2896 2982 1.142748 GGCGTCCTCTCCTGTCATG 59.857 63.158 0.00 0.00 0.00 3.07
2913 2999 2.149578 CACACAGGCAGAGAAAGAAGG 58.850 52.381 0.00 0.00 0.00 3.46
2988 3074 2.094659 CGTGCCATGGACTGACGAC 61.095 63.158 18.40 0.00 31.71 4.34
3081 3178 1.518903 GCTGGTTGCTTCTGTCCACC 61.519 60.000 0.00 0.00 38.95 4.61
3126 3223 2.228582 CCAACATGATCCGACAGCAAAA 59.771 45.455 0.00 0.00 0.00 2.44
3158 3258 2.035321 TGATTATCGCGAGGTATGCACA 59.965 45.455 16.66 3.88 0.00 4.57
3191 3323 2.159476 CGTTTAGAATGGACGGACGAGA 60.159 50.000 0.00 0.00 33.45 4.04
3216 3348 1.346479 TGTCAACCGGGTGGAAAGGA 61.346 55.000 21.90 0.00 39.21 3.36
3243 3375 7.001073 GGGGATTAGATAAGCATCTCAGTTTT 58.999 38.462 0.00 0.00 40.81 2.43
3302 3434 1.123077 TCCATTCCTGTGAGGATCGG 58.877 55.000 0.00 0.00 45.34 4.18
3312 3444 7.417612 CCGTAATAAAATCTTGTCCATTCCTG 58.582 38.462 0.00 0.00 0.00 3.86
3319 3451 5.501897 CGAGTGCCGTAATAAAATCTTGTCC 60.502 44.000 0.00 0.00 0.00 4.02
3329 3462 1.415288 GCGTGCGAGTGCCGTAATAA 61.415 55.000 0.00 0.00 41.78 1.40
3330 3463 1.874915 GCGTGCGAGTGCCGTAATA 60.875 57.895 0.00 0.00 41.78 0.98
3331 3464 3.186047 GCGTGCGAGTGCCGTAAT 61.186 61.111 0.00 0.00 41.78 1.89
3395 3537 3.316588 CGCTGTAGATGTGGACTATGACT 59.683 47.826 0.00 0.00 0.00 3.41
3396 3538 3.551046 CCGCTGTAGATGTGGACTATGAC 60.551 52.174 0.00 0.00 37.26 3.06
3397 3539 2.623416 CCGCTGTAGATGTGGACTATGA 59.377 50.000 0.00 0.00 37.26 2.15
3398 3540 2.864097 GCCGCTGTAGATGTGGACTATG 60.864 54.545 0.00 0.00 37.26 2.23
3399 3541 1.341531 GCCGCTGTAGATGTGGACTAT 59.658 52.381 0.00 0.00 37.26 2.12
3400 3542 0.744874 GCCGCTGTAGATGTGGACTA 59.255 55.000 0.00 0.00 37.26 2.59
3401 3543 1.517832 GCCGCTGTAGATGTGGACT 59.482 57.895 0.00 0.00 37.26 3.85
3402 3544 1.878522 CGCCGCTGTAGATGTGGAC 60.879 63.158 0.00 0.00 37.26 4.02
3417 3559 2.379030 CTATCCTTTCCCCCGACGCC 62.379 65.000 0.00 0.00 0.00 5.68
3421 3563 1.292849 TCCTTCTATCCTTTCCCCCGA 59.707 52.381 0.00 0.00 0.00 5.14
3455 3598 1.816835 TCCATACATCCTATCCGCGAC 59.183 52.381 8.23 0.00 0.00 5.19
3471 3614 3.948473 CGTCACCCTATCGAGATATCCAT 59.052 47.826 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.