Multiple sequence alignment - TraesCS4D01G236600

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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 TraesCS4D01G236600 chr4D 100.000 3386 0 0 1 3386 398668293 398671678 0.000000e+00 6253.0
1 TraesCS4D01G236600 chr4A 91.518 2417 88 44 750 3106 56143734 56146093 0.000000e+00 3219.0
2 TraesCS4D01G236600 chr4A 87.500 648 28 26 62 672 56142814 56143445 0.000000e+00 699.0
3 TraesCS4D01G236600 chr4A 94.595 185 10 0 3114 3298 56146644 56146828 1.540000e-73 287.0
4 TraesCS4D01G236600 chr4B 93.162 1755 66 26 1572 3298 491465013 491466741 0.000000e+00 2527.0
5 TraesCS4D01G236600 chr4B 91.655 1390 45 25 193 1537 491463548 491464911 0.000000e+00 1858.0
6 TraesCS4D01G236600 chr4B 88.293 205 9 5 1 196 491463228 491463426 7.310000e-57 231.0
7 TraesCS4D01G236600 chr1B 89.928 139 11 2 2033 2168 418106021 418105883 3.470000e-40 176.0
8 TraesCS4D01G236600 chr1B 86.364 88 12 0 1314 1401 418106305 418106218 2.780000e-16 97.1
9 TraesCS4D01G236600 chr1A 89.928 139 11 2 2033 2168 387840975 387840837 3.470000e-40 176.0
10 TraesCS4D01G236600 chr1A 86.364 88 12 0 1314 1401 387841264 387841177 2.780000e-16 97.1
11 TraesCS4D01G236600 chr2D 89.706 136 13 1 2031 2166 527547519 527547653 4.490000e-39 172.0
12 TraesCS4D01G236600 chr2D 95.506 89 4 0 3298 3386 84745886 84745798 3.520000e-30 143.0
13 TraesCS4D01G236600 chr2B 89.706 136 13 1 2031 2166 624892074 624892208 4.490000e-39 172.0
14 TraesCS4D01G236600 chr1D 89.209 139 12 2 2033 2168 308459629 308459491 1.620000e-38 171.0
15 TraesCS4D01G236600 chr1D 87.500 88 11 0 1314 1401 308459917 308459830 5.980000e-18 102.0
16 TraesCS4D01G236600 chr2A 88.806 134 14 1 2033 2166 672415937 672416069 2.700000e-36 163.0
17 TraesCS4D01G236600 chr5D 91.228 114 10 0 2027 2140 344399992 344400105 4.520000e-34 156.0
18 TraesCS4D01G236600 chr5D 94.382 89 4 1 3298 3386 535499968 535499881 5.890000e-28 135.0
19 TraesCS4D01G236600 chr5D 83.962 106 17 0 1291 1396 344399599 344399704 5.980000e-18 102.0
20 TraesCS4D01G236600 chr3D 93.258 89 6 0 3298 3386 154184826 154184738 7.620000e-27 132.0
21 TraesCS4D01G236600 chr3D 85.870 92 13 0 1644 1735 3294616 3294525 7.730000e-17 99.0
22 TraesCS4D01G236600 chr7A 95.833 72 3 0 3298 3369 714823650 714823721 2.130000e-22 117.0
23 TraesCS4D01G236600 chr7A 96.825 63 2 0 3298 3360 727054659 727054721 4.620000e-19 106.0
24 TraesCS4D01G236600 chr7B 96.721 61 1 1 3298 3358 727116576 727116517 2.150000e-17 100.0
25 TraesCS4D01G236600 chr3B 85.870 92 13 0 1644 1735 213981 213890 7.730000e-17 99.0
26 TraesCS4D01G236600 chrUn 86.000 100 3 3 3298 3386 50935627 50935726 2.780000e-16 97.1
27 TraesCS4D01G236600 chrUn 100.000 50 0 0 3298 3347 15684071 15684022 3.600000e-15 93.5
28 TraesCS4D01G236600 chrUn 100.000 50 0 0 3298 3347 15815012 15814963 3.600000e-15 93.5
29 TraesCS4D01G236600 chr5B 84.848 99 12 3 1301 1396 407817614 407817516 2.780000e-16 97.1
30 TraesCS4D01G236600 chr5A 81.452 124 18 5 1278 1396 448090690 448090813 2.780000e-16 97.1


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 TraesCS4D01G236600 chr4D 398668293 398671678 3385 False 6253.000000 6253 100.000000 1 3386 1 chr4D.!!$F1 3385
1 TraesCS4D01G236600 chr4A 56142814 56146828 4014 False 1401.666667 3219 91.204333 62 3298 3 chr4A.!!$F1 3236
2 TraesCS4D01G236600 chr4B 491463228 491466741 3513 False 1538.666667 2527 91.036667 1 3298 3 chr4B.!!$F1 3297

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
29 30 0.391661 GTGGGTGCATGATGAGTCGT 60.392 55.000 0.00 0.0 0.0 4.34 F
1551 2003 1.684248 GCATGCCTCCTCAAATCTGGT 60.684 52.381 6.36 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1677 2191 0.480690 TGCCTTGGCCTGAGGTTTAA 59.519 50.0 21.9 7.64 36.63 1.52 R
3224 4332 0.095417 GACGATGAAGCAGAAACCGC 59.905 55.0 0.0 0.00 0.00 5.68 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
29 30 0.391661 GTGGGTGCATGATGAGTCGT 60.392 55.000 0.00 0.00 0.00 4.34
37 38 6.365839 GGTGCATGATGAGTCGTAATATTTG 58.634 40.000 0.00 0.00 0.00 2.32
39 40 6.847792 GTGCATGATGAGTCGTAATATTTGTG 59.152 38.462 0.00 0.00 0.00 3.33
46 47 5.121611 TGAGTCGTAATATTTGTGCCACAAG 59.878 40.000 10.58 0.00 39.53 3.16
102 119 7.672983 AATACCTAACAATTATCGAGCCATG 57.327 36.000 0.00 0.00 0.00 3.66
103 120 3.815401 ACCTAACAATTATCGAGCCATGC 59.185 43.478 0.00 0.00 0.00 4.06
104 121 3.814842 CCTAACAATTATCGAGCCATGCA 59.185 43.478 0.00 0.00 0.00 3.96
105 122 4.456911 CCTAACAATTATCGAGCCATGCAT 59.543 41.667 0.00 0.00 0.00 3.96
152 170 2.232941 TGTACTAGAACCAAAGCGGGAG 59.767 50.000 0.00 0.00 40.22 4.30
179 211 4.036498 CGTACCTGAACGGATGAGTCTATT 59.964 45.833 0.00 0.00 39.19 1.73
180 212 5.237996 CGTACCTGAACGGATGAGTCTATTA 59.762 44.000 0.00 0.00 39.19 0.98
244 406 2.523440 ACCCTCGGTGAACAGAACA 58.477 52.632 0.00 0.00 32.98 3.18
303 470 4.787598 CTGCATGTCTCACCTTTTGTAAC 58.212 43.478 0.00 0.00 0.00 2.50
518 686 5.163663 TGAGAACGGGATGAAAAATATGCAC 60.164 40.000 0.00 0.00 0.00 4.57
524 692 5.221106 CGGGATGAAAAATATGCACATCTGT 60.221 40.000 10.06 0.00 37.87 3.41
634 816 2.108566 CGATCTCCCTGCTGCCTG 59.891 66.667 0.00 0.00 0.00 4.85
635 817 2.729479 CGATCTCCCTGCTGCCTGT 61.729 63.158 0.00 0.00 0.00 4.00
833 1226 2.040359 CTTCCTCCCCTCCCCTCC 60.040 72.222 0.00 0.00 0.00 4.30
834 1227 3.707189 TTCCTCCCCTCCCCTCCC 61.707 72.222 0.00 0.00 0.00 4.30
837 1230 4.179599 CTCCCCTCCCCTCCCCTC 62.180 77.778 0.00 0.00 0.00 4.30
838 1231 4.761304 TCCCCTCCCCTCCCCTCT 62.761 72.222 0.00 0.00 0.00 3.69
839 1232 4.179599 CCCCTCCCCTCCCCTCTC 62.180 77.778 0.00 0.00 0.00 3.20
840 1233 4.179599 CCCTCCCCTCCCCTCTCC 62.180 77.778 0.00 0.00 0.00 3.71
841 1234 3.039526 CCTCCCCTCCCCTCTCCT 61.040 72.222 0.00 0.00 0.00 3.69
842 1235 2.612251 CTCCCCTCCCCTCTCCTC 59.388 72.222 0.00 0.00 0.00 3.71
854 1247 2.131854 CCTCTCCTCTCCTCACCTCTA 58.868 57.143 0.00 0.00 0.00 2.43
884 1277 1.995991 CGTGAATACACTTCCGCGG 59.004 57.895 22.12 22.12 43.99 6.46
993 1403 2.099062 CTCTGCCGATTTGTGCGC 59.901 61.111 0.00 0.00 0.00 6.09
1239 1664 4.821589 GCGGTGAAGAGGGAGCGG 62.822 72.222 0.00 0.00 33.75 5.52
1242 1667 4.475135 GTGAAGAGGGAGCGGGCC 62.475 72.222 0.00 0.00 0.00 5.80
1269 1694 1.760875 GGACCTGGGCGAGATGGTA 60.761 63.158 0.00 0.00 32.30 3.25
1450 1885 2.456989 GTTCGAATCGATTCACCGCTA 58.543 47.619 31.57 11.88 36.61 4.26
1460 1895 4.083271 TCGATTCACCGCTACTGATAGATG 60.083 45.833 0.00 0.00 0.00 2.90
1488 1923 5.240891 CGGATACCTAACATGCATCATCTT 58.759 41.667 0.00 0.00 0.00 2.40
1496 1931 6.262496 CCTAACATGCATCATCTTTCATCTGT 59.738 38.462 0.00 0.00 0.00 3.41
1531 1969 2.407026 TCTATTTATGCATGCGCGTACG 59.593 45.455 14.09 11.84 39.36 3.67
1541 1979 4.873129 CGCGTACGCATGCCTCCT 62.873 66.667 36.44 0.00 42.06 3.69
1551 2003 1.684248 GCATGCCTCCTCAAATCTGGT 60.684 52.381 6.36 0.00 0.00 4.00
1552 2004 2.731572 CATGCCTCCTCAAATCTGGTT 58.268 47.619 0.00 0.00 0.00 3.67
1581 2091 7.215789 ACTTTCTTGATCCATAGTATGAGCTG 58.784 38.462 11.91 0.00 0.00 4.24
1602 2112 8.611654 AGCTGCTGAATCAAAAATAAAAATGT 57.388 26.923 0.00 0.00 0.00 2.71
1735 2249 2.569404 AGAACAGAAGAGCCAGGTTAGG 59.431 50.000 0.00 0.00 0.00 2.69
1737 2251 2.183679 ACAGAAGAGCCAGGTTAGGAG 58.816 52.381 0.00 0.00 0.00 3.69
1751 2265 6.042781 CCAGGTTAGGAGCCTTGTATTATACA 59.957 42.308 0.29 0.29 33.31 2.29
1850 2368 9.838339 CCTTGTATTATACACCTCTTCATCTTT 57.162 33.333 4.35 0.00 38.63 2.52
1946 2473 4.107363 TGCATGCATGAAAAATTAGCGA 57.893 36.364 30.64 0.01 0.00 4.93
1947 2474 4.106909 TGCATGCATGAAAAATTAGCGAG 58.893 39.130 30.64 0.00 0.00 5.03
1954 2482 5.503194 GCATGAAAAATTAGCGAGACCTCTC 60.503 44.000 0.00 0.00 39.55 3.20
1980 2508 4.477302 AAATTACGGGTCGTTTCAGTTG 57.523 40.909 0.00 0.00 41.54 3.16
1983 2511 0.108041 ACGGGTCGTTTCAGTTGTGT 60.108 50.000 0.00 0.00 36.35 3.72
2277 2812 3.390521 ATCTGCCCGTCCTGCGAA 61.391 61.111 0.00 0.00 44.77 4.70
2392 2927 2.733301 CCGCCTGCTGATCGATCT 59.267 61.111 25.02 0.00 0.00 2.75
2445 2980 0.532573 ACGCTCATCAACATCGACCT 59.467 50.000 0.00 0.00 0.00 3.85
2458 2993 4.722700 GACCTGCACCACCGCCAT 62.723 66.667 0.00 0.00 0.00 4.40
2459 2994 3.323758 GACCTGCACCACCGCCATA 62.324 63.158 0.00 0.00 0.00 2.74
2460 2995 2.514592 CCTGCACCACCGCCATAG 60.515 66.667 0.00 0.00 0.00 2.23
2461 2996 3.204827 CTGCACCACCGCCATAGC 61.205 66.667 0.00 0.00 0.00 2.97
2538 3078 4.511454 TCGCAAGTAACATATGATCCTTGC 59.489 41.667 28.15 28.15 46.87 4.01
2541 3081 5.755813 CAAGTAACATATGATCCTTGCAGC 58.244 41.667 10.38 0.00 0.00 5.25
2648 3190 5.869579 TCAGTTTAGCTAATCCATCCATCC 58.130 41.667 7.08 0.00 0.00 3.51
2649 3191 5.369404 TCAGTTTAGCTAATCCATCCATCCA 59.631 40.000 7.08 0.00 0.00 3.41
2650 3192 6.044754 TCAGTTTAGCTAATCCATCCATCCAT 59.955 38.462 7.08 0.00 0.00 3.41
2651 3193 6.373774 CAGTTTAGCTAATCCATCCATCCATC 59.626 42.308 7.08 0.00 0.00 3.51
2694 3240 2.829720 ACGATAGGTAGTCAAACAGCCA 59.170 45.455 0.00 0.00 43.77 4.75
2695 3241 3.187700 CGATAGGTAGTCAAACAGCCAC 58.812 50.000 0.00 0.00 0.00 5.01
2696 3242 3.532542 GATAGGTAGTCAAACAGCCACC 58.467 50.000 0.00 0.00 0.00 4.61
2697 3243 1.435256 AGGTAGTCAAACAGCCACCT 58.565 50.000 0.00 0.00 0.00 4.00
2698 3244 1.072331 AGGTAGTCAAACAGCCACCTG 59.928 52.381 0.00 0.00 44.80 4.00
3015 3580 3.613193 CGGGCCTTAAACTTTACTTTGCC 60.613 47.826 0.84 0.00 35.65 4.52
3224 4332 2.967362 TGCCTGGTAATTAGTGACGTG 58.033 47.619 0.00 0.00 0.00 4.49
3241 4349 0.179215 GTGCGGTTTCTGCTTCATCG 60.179 55.000 2.33 0.00 0.00 3.84
3283 4391 8.922058 TTCAGTTAGATCGTTGAGTAATTACC 57.078 34.615 12.05 4.78 0.00 2.85
3284 4392 8.289939 TCAGTTAGATCGTTGAGTAATTACCT 57.710 34.615 12.05 2.48 0.00 3.08
3308 4416 6.954232 TGGTAACCAGAAAATAAGTCCTAGG 58.046 40.000 0.82 0.82 0.00 3.02
3309 4417 6.731919 TGGTAACCAGAAAATAAGTCCTAGGA 59.268 38.462 7.62 7.62 0.00 2.94
3310 4418 7.046652 GGTAACCAGAAAATAAGTCCTAGGAC 58.953 42.308 31.29 31.29 44.86 3.85
3338 4446 6.956102 TTTAGTCCCAACTTATAAGTCCCA 57.044 37.500 18.28 1.06 38.57 4.37
3339 4447 6.956102 TTAGTCCCAACTTATAAGTCCCAA 57.044 37.500 18.28 3.05 38.57 4.12
3340 4448 5.437191 AGTCCCAACTTATAAGTCCCAAG 57.563 43.478 18.28 6.66 38.57 3.61
3341 4449 4.850386 AGTCCCAACTTATAAGTCCCAAGT 59.150 41.667 18.28 5.74 38.57 3.16
3342 4450 5.045797 AGTCCCAACTTATAAGTCCCAAGTC 60.046 44.000 18.28 6.78 38.57 3.01
3343 4451 4.226620 TCCCAACTTATAAGTCCCAAGTCC 59.773 45.833 18.28 0.00 38.57 3.85
3344 4452 4.524053 CCAACTTATAAGTCCCAAGTCCC 58.476 47.826 18.28 0.00 38.57 4.46
3345 4453 4.227527 CCAACTTATAAGTCCCAAGTCCCT 59.772 45.833 18.28 0.00 38.57 4.20
3346 4454 5.427481 CCAACTTATAAGTCCCAAGTCCCTA 59.573 44.000 18.28 0.00 38.57 3.53
3347 4455 6.346896 CAACTTATAAGTCCCAAGTCCCTAC 58.653 44.000 18.28 0.00 38.57 3.18
3348 4456 4.967442 ACTTATAAGTCCCAAGTCCCTACC 59.033 45.833 12.50 0.00 32.86 3.18
3349 4457 3.797671 ATAAGTCCCAAGTCCCTACCT 57.202 47.619 0.00 0.00 0.00 3.08
3350 4458 4.913154 ATAAGTCCCAAGTCCCTACCTA 57.087 45.455 0.00 0.00 0.00 3.08
3351 4459 3.797671 AAGTCCCAAGTCCCTACCTAT 57.202 47.619 0.00 0.00 0.00 2.57
3352 4460 3.797671 AGTCCCAAGTCCCTACCTATT 57.202 47.619 0.00 0.00 0.00 1.73
3353 4461 4.090027 AGTCCCAAGTCCCTACCTATTT 57.910 45.455 0.00 0.00 0.00 1.40
3354 4462 3.780850 AGTCCCAAGTCCCTACCTATTTG 59.219 47.826 0.00 0.00 0.00 2.32
3355 4463 3.118000 GTCCCAAGTCCCTACCTATTTGG 60.118 52.174 0.00 0.00 42.93 3.28
3373 4481 8.893727 CCTATTTGGTTCCTAAGACTTAACATG 58.106 37.037 0.00 0.00 0.00 3.21
3374 4482 7.703058 ATTTGGTTCCTAAGACTTAACATGG 57.297 36.000 0.00 0.00 0.00 3.66
3375 4483 6.442541 TTGGTTCCTAAGACTTAACATGGA 57.557 37.500 0.00 0.00 0.00 3.41
3376 4484 5.801380 TGGTTCCTAAGACTTAACATGGAC 58.199 41.667 0.00 0.00 0.00 4.02
3377 4485 5.546499 TGGTTCCTAAGACTTAACATGGACT 59.454 40.000 0.00 0.00 0.00 3.85
3378 4486 6.727231 TGGTTCCTAAGACTTAACATGGACTA 59.273 38.462 0.00 0.00 0.00 2.59
3379 4487 7.236019 TGGTTCCTAAGACTTAACATGGACTAA 59.764 37.037 0.00 0.00 0.00 2.24
3380 4488 8.098912 GGTTCCTAAGACTTAACATGGACTAAA 58.901 37.037 0.00 0.00 0.00 1.85
3381 4489 9.498176 GTTCCTAAGACTTAACATGGACTAAAA 57.502 33.333 0.00 0.00 0.00 1.52
3382 4490 9.720769 TTCCTAAGACTTAACATGGACTAAAAG 57.279 33.333 0.00 0.00 0.00 2.27
3383 4491 9.096823 TCCTAAGACTTAACATGGACTAAAAGA 57.903 33.333 0.00 0.00 0.00 2.52
3384 4492 9.152595 CCTAAGACTTAACATGGACTAAAAGAC 57.847 37.037 0.00 0.00 0.00 3.01
3385 4493 7.981102 AAGACTTAACATGGACTAAAAGACC 57.019 36.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 2.489722 TGCGCTTGTGGCACAAATATTA 59.510 40.909 30.66 15.18 44.16 0.98
37 38 2.603135 GATGGATGCGCTTGTGGCAC 62.603 60.000 11.55 11.55 44.23 5.01
39 40 2.056481 GAGATGGATGCGCTTGTGGC 62.056 60.000 9.73 0.00 37.64 5.01
46 47 2.182842 GTGGTGGAGATGGATGCGC 61.183 63.158 0.00 0.00 0.00 6.09
127 144 4.322198 CCCGCTTTGGTTCTAGTACAAGTA 60.322 45.833 1.69 0.00 35.15 2.24
128 145 3.556423 CCCGCTTTGGTTCTAGTACAAGT 60.556 47.826 1.69 0.00 35.15 3.16
180 212 4.997905 ACGCACGTACGTGTATAGATAT 57.002 40.909 39.56 19.14 46.28 1.63
242 404 2.839486 TTGCTTGCTGCTACTACTGT 57.161 45.000 0.00 0.00 43.37 3.55
243 405 4.488126 TTTTTGCTTGCTGCTACTACTG 57.512 40.909 0.00 0.00 43.37 2.74
493 661 5.066375 TGCATATTTTTCATCCCGTTCTCAG 59.934 40.000 0.00 0.00 0.00 3.35
518 686 1.471676 GCGTGTTCCCTCCTACAGATG 60.472 57.143 0.00 0.00 0.00 2.90
524 692 1.987855 CTGGGCGTGTTCCCTCCTA 60.988 63.158 0.12 0.00 46.67 2.94
634 816 0.675633 ATGTTTGACAAGCCCAGCAC 59.324 50.000 0.00 0.00 0.00 4.40
635 817 1.340889 GAATGTTTGACAAGCCCAGCA 59.659 47.619 0.00 0.00 0.00 4.41
833 1226 0.106217 GAGGTGAGGAGAGGAGAGGG 60.106 65.000 0.00 0.00 0.00 4.30
834 1227 0.926293 AGAGGTGAGGAGAGGAGAGG 59.074 60.000 0.00 0.00 0.00 3.69
835 1228 2.777692 AGTAGAGGTGAGGAGAGGAGAG 59.222 54.545 0.00 0.00 0.00 3.20
836 1229 2.853430 AGTAGAGGTGAGGAGAGGAGA 58.147 52.381 0.00 0.00 0.00 3.71
837 1230 3.456644 TGTAGTAGAGGTGAGGAGAGGAG 59.543 52.174 0.00 0.00 0.00 3.69
838 1231 3.200385 GTGTAGTAGAGGTGAGGAGAGGA 59.800 52.174 0.00 0.00 0.00 3.71
839 1232 3.054287 TGTGTAGTAGAGGTGAGGAGAGG 60.054 52.174 0.00 0.00 0.00 3.69
840 1233 4.080807 TCTGTGTAGTAGAGGTGAGGAGAG 60.081 50.000 0.00 0.00 0.00 3.20
841 1234 3.844804 TCTGTGTAGTAGAGGTGAGGAGA 59.155 47.826 0.00 0.00 0.00 3.71
842 1235 3.942748 GTCTGTGTAGTAGAGGTGAGGAG 59.057 52.174 0.00 0.00 0.00 3.69
854 1247 2.227149 TGTATTCACGCGTCTGTGTAGT 59.773 45.455 9.86 0.00 40.74 2.73
898 1291 1.554392 CGACTTGAATCCTCTCGCAG 58.446 55.000 0.00 0.00 0.00 5.18
993 1403 4.758251 TCCTGCGACATGGCGTGG 62.758 66.667 24.28 23.66 35.06 4.94
1332 1757 2.435059 GCGGACTGCTCCTTGGTC 60.435 66.667 0.00 0.00 41.73 4.02
1450 1885 1.188219 ATCCGCGGCCATCTATCAGT 61.188 55.000 23.51 0.00 0.00 3.41
1460 1895 0.949105 CATGTTAGGTATCCGCGGCC 60.949 60.000 23.51 16.99 0.00 6.13
1488 1923 7.479352 AGAGAAGAAGATCTCAACAGATGAA 57.521 36.000 0.00 0.00 46.73 2.57
1531 1969 1.030457 CCAGATTTGAGGAGGCATGC 58.970 55.000 9.90 9.90 0.00 4.06
1537 1975 8.171164 AGAAAGTAAAAACCAGATTTGAGGAG 57.829 34.615 0.00 0.00 0.00 3.69
1539 1977 8.413229 TCAAGAAAGTAAAAACCAGATTTGAGG 58.587 33.333 0.00 0.00 0.00 3.86
1541 1979 9.965824 GATCAAGAAAGTAAAAACCAGATTTGA 57.034 29.630 0.00 0.00 0.00 2.69
1676 2190 1.077005 TGCCTTGGCCTGAGGTTTAAT 59.923 47.619 21.90 0.00 36.63 1.40
1677 2191 0.480690 TGCCTTGGCCTGAGGTTTAA 59.519 50.000 21.90 7.64 36.63 1.52
1735 2249 9.504710 CATATACTCGTGTATAATACAAGGCTC 57.495 37.037 18.31 0.00 42.70 4.70
1737 2251 9.286946 GACATATACTCGTGTATAATACAAGGC 57.713 37.037 18.31 6.22 42.70 4.35
1776 2290 2.436115 GACCGTAAGCTGGGGTGC 60.436 66.667 8.21 0.00 33.28 5.01
1865 2385 2.060284 CACAAAATGATTGCCCGTGTG 58.940 47.619 0.00 0.00 0.00 3.82
1980 2508 7.646446 AGTTTTACAAAAAGTTCACCAACAC 57.354 32.000 0.00 0.00 34.60 3.32
1983 2511 8.081025 ACGTTAGTTTTACAAAAAGTTCACCAA 58.919 29.630 0.00 0.00 0.00 3.67
2020 2549 2.707529 TTCGTCCTGCATGCACGTGA 62.708 55.000 22.23 15.07 35.05 4.35
2140 2672 2.046314 CGGGGCGAACTTGATGGT 60.046 61.111 0.00 0.00 0.00 3.55
2337 2872 1.150536 GAAGAAGTGGTGGGTGGCA 59.849 57.895 0.00 0.00 0.00 4.92
2445 2980 2.310327 CTAGCTATGGCGGTGGTGCA 62.310 60.000 0.00 0.00 44.37 4.57
2494 3029 2.963101 ACGTGAGGTATTAGCTATGGCA 59.037 45.455 3.10 0.00 41.70 4.92
2648 3190 2.815503 TGGATTGCGCCTATGATTGATG 59.184 45.455 4.18 0.00 0.00 3.07
2649 3191 3.144657 TGGATTGCGCCTATGATTGAT 57.855 42.857 4.18 0.00 0.00 2.57
2650 3192 2.636647 TGGATTGCGCCTATGATTGA 57.363 45.000 4.18 0.00 0.00 2.57
2651 3193 4.093998 GTCTATGGATTGCGCCTATGATTG 59.906 45.833 4.18 0.00 0.00 2.67
2694 3240 9.523974 GAGTACTAGCTACTGCCTACTACAGGT 62.524 48.148 0.00 0.00 40.21 4.00
2695 3241 7.236984 GAGTACTAGCTACTGCCTACTACAGG 61.237 50.000 0.00 0.00 40.67 4.00
2696 3242 5.613329 AGTACTAGCTACTGCCTACTACAG 58.387 45.833 0.00 0.00 40.80 2.74
2697 3243 5.609423 GAGTACTAGCTACTGCCTACTACA 58.391 45.833 0.00 0.00 35.66 2.74
2698 3244 4.685628 CGAGTACTAGCTACTGCCTACTAC 59.314 50.000 0.00 0.00 35.66 2.73
2699 3245 4.586421 TCGAGTACTAGCTACTGCCTACTA 59.414 45.833 0.00 0.00 35.66 1.82
2700 3246 3.387374 TCGAGTACTAGCTACTGCCTACT 59.613 47.826 0.00 0.00 35.66 2.57
2701 3247 3.726607 TCGAGTACTAGCTACTGCCTAC 58.273 50.000 0.00 0.00 35.66 3.18
2703 3249 3.207778 CTTCGAGTACTAGCTACTGCCT 58.792 50.000 0.00 0.00 35.66 4.75
2704 3250 2.287129 GCTTCGAGTACTAGCTACTGCC 60.287 54.545 8.59 0.00 35.66 4.85
2705 3251 2.600320 CGCTTCGAGTACTAGCTACTGC 60.600 54.545 12.99 5.43 35.66 4.40
2706 3252 2.032722 CCGCTTCGAGTACTAGCTACTG 60.033 54.545 12.99 0.00 35.66 2.74
2707 3253 2.211806 CCGCTTCGAGTACTAGCTACT 58.788 52.381 12.99 5.12 38.52 2.57
2816 3368 7.201696 GCTTAGTCTATTATCTCCTCTCCGATG 60.202 44.444 0.00 0.00 0.00 3.84
3115 4223 2.874086 AGGTTACAACTTACAACGGTGC 59.126 45.455 0.00 0.00 0.00 5.01
3224 4332 0.095417 GACGATGAAGCAGAAACCGC 59.905 55.000 0.00 0.00 0.00 5.68
3241 4349 2.996621 CTGAAAACGACCTCTGATGGAC 59.003 50.000 0.00 0.00 0.00 4.02
3284 4392 6.731919 TCCTAGGACTTATTTTCTGGTTACCA 59.268 38.462 7.62 3.29 0.00 3.25
3313 4421 7.757611 TGGGACTTATAAGTTGGGACTAAAAA 58.242 34.615 18.96 0.00 39.88 1.94
3314 4422 7.332433 TGGGACTTATAAGTTGGGACTAAAA 57.668 36.000 18.96 0.00 39.88 1.52
3315 4423 6.956102 TGGGACTTATAAGTTGGGACTAAA 57.044 37.500 18.96 0.00 39.88 1.85
3316 4424 6.502863 ACTTGGGACTTATAAGTTGGGACTAA 59.497 38.462 18.96 10.32 39.88 2.24
3317 4425 6.027482 ACTTGGGACTTATAAGTTGGGACTA 58.973 40.000 18.96 3.96 39.88 2.59
3318 4426 4.850386 ACTTGGGACTTATAAGTTGGGACT 59.150 41.667 18.96 0.00 39.88 3.85
3319 4427 5.175388 ACTTGGGACTTATAAGTTGGGAC 57.825 43.478 18.96 6.19 39.88 4.46
3320 4428 4.226620 GGACTTGGGACTTATAAGTTGGGA 59.773 45.833 18.96 6.15 39.88 4.37
3321 4429 4.524053 GGACTTGGGACTTATAAGTTGGG 58.476 47.826 18.96 10.37 39.88 4.12
3322 4430 4.227527 AGGGACTTGGGACTTATAAGTTGG 59.772 45.833 18.96 10.07 34.84 3.77
3323 4431 5.437191 AGGGACTTGGGACTTATAAGTTG 57.563 43.478 18.96 9.81 34.84 3.16
3324 4432 5.427806 GGTAGGGACTTGGGACTTATAAGTT 59.572 44.000 18.96 2.29 38.78 2.66
3325 4433 4.967442 GGTAGGGACTTGGGACTTATAAGT 59.033 45.833 18.05 18.05 40.66 2.24
3326 4434 5.217400 AGGTAGGGACTTGGGACTTATAAG 58.783 45.833 11.05 11.05 41.75 1.73
3327 4435 5.230746 AGGTAGGGACTTGGGACTTATAA 57.769 43.478 0.00 0.00 41.75 0.98
3328 4436 4.913154 AGGTAGGGACTTGGGACTTATA 57.087 45.455 0.00 0.00 41.75 0.98
3329 4437 3.797671 AGGTAGGGACTTGGGACTTAT 57.202 47.619 0.00 0.00 41.75 1.73
3330 4438 4.913154 ATAGGTAGGGACTTGGGACTTA 57.087 45.455 0.00 0.00 41.75 2.24
3331 4439 3.797671 ATAGGTAGGGACTTGGGACTT 57.202 47.619 0.00 0.00 41.75 3.01
3332 4440 3.780850 CAAATAGGTAGGGACTTGGGACT 59.219 47.826 0.00 0.00 41.75 3.85
3333 4441 3.118000 CCAAATAGGTAGGGACTTGGGAC 60.118 52.174 0.00 0.00 41.75 4.46
3334 4442 3.120108 CCAAATAGGTAGGGACTTGGGA 58.880 50.000 0.00 0.00 41.75 4.37
3335 4443 3.577805 CCAAATAGGTAGGGACTTGGG 57.422 52.381 0.00 0.00 41.75 4.12
3347 4455 8.893727 CATGTTAAGTCTTAGGAACCAAATAGG 58.106 37.037 0.00 0.00 45.67 2.57
3348 4456 8.893727 CCATGTTAAGTCTTAGGAACCAAATAG 58.106 37.037 0.00 0.00 0.00 1.73
3349 4457 8.607713 TCCATGTTAAGTCTTAGGAACCAAATA 58.392 33.333 0.00 0.00 0.00 1.40
3350 4458 7.393515 GTCCATGTTAAGTCTTAGGAACCAAAT 59.606 37.037 0.99 0.00 0.00 2.32
3351 4459 6.713450 GTCCATGTTAAGTCTTAGGAACCAAA 59.287 38.462 0.99 0.00 0.00 3.28
3352 4460 6.043938 AGTCCATGTTAAGTCTTAGGAACCAA 59.956 38.462 0.99 0.00 0.00 3.67
3353 4461 5.546499 AGTCCATGTTAAGTCTTAGGAACCA 59.454 40.000 0.99 0.00 0.00 3.67
3354 4462 6.051179 AGTCCATGTTAAGTCTTAGGAACC 57.949 41.667 0.99 0.00 0.00 3.62
3355 4463 9.498176 TTTTAGTCCATGTTAAGTCTTAGGAAC 57.502 33.333 0.99 0.00 0.00 3.62
3356 4464 9.720769 CTTTTAGTCCATGTTAAGTCTTAGGAA 57.279 33.333 0.99 0.00 0.00 3.36
3357 4465 9.096823 TCTTTTAGTCCATGTTAAGTCTTAGGA 57.903 33.333 0.00 0.00 0.00 2.94
3358 4466 9.152595 GTCTTTTAGTCCATGTTAAGTCTTAGG 57.847 37.037 0.00 0.00 0.00 2.69
3359 4467 9.152595 GGTCTTTTAGTCCATGTTAAGTCTTAG 57.847 37.037 0.00 0.00 0.00 2.18
3361 4469 7.981102 GGTCTTTTAGTCCATGTTAAGTCTT 57.019 36.000 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.