Multiple sequence alignment - TraesCS5B01G256600

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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 TraesCS5B01G256600 chr5B 100.000 3413 0 0 1 3413 439243446 439240034 0.000000e+00 6303
1 TraesCS5B01G256600 chr5B 88.889 99 11 0 236 334 201895091 201895189 4.630000e-24 122
2 TraesCS5B01G256600 chr5D 93.522 2547 136 10 875 3413 370008010 370005485 0.000000e+00 3762
3 TraesCS5B01G256600 chr5D 83.173 208 18 5 685 877 370008267 370008062 1.260000e-39 174
4 TraesCS5B01G256600 chr5A 92.398 2473 150 21 959 3413 472435653 472433201 0.000000e+00 3491
5 TraesCS5B01G256600 chr7D 82.055 730 114 9 2697 3411 138286857 138286130 1.050000e-169 606
6 TraesCS5B01G256600 chr3D 80.658 729 124 10 2697 3411 355751996 355752721 1.790000e-152 549
7 TraesCS5B01G256600 chr3D 87.463 335 41 1 3 336 36535699 36536033 5.340000e-103 385
8 TraesCS5B01G256600 chr1D 80.786 687 114 11 2697 3368 419722175 419721492 3.900000e-144 521
9 TraesCS5B01G256600 chr4A 79.726 730 124 20 2697 3411 10219645 10220365 1.090000e-139 507
10 TraesCS5B01G256600 chr4A 92.192 333 26 0 4 336 581874382 581874050 3.990000e-129 472
11 TraesCS5B01G256600 chr4A 88.529 340 28 4 335 668 581873413 581873079 5.310000e-108 401
12 TraesCS5B01G256600 chr3A 79.589 730 128 14 2697 3411 329495819 329496542 1.410000e-138 503
13 TraesCS5B01G256600 chr1B 81.260 635 104 8 2697 3319 566830367 566829736 1.830000e-137 499
14 TraesCS5B01G256600 chr6D 90.936 342 29 2 1 341 10883272 10883612 3.100000e-125 459
15 TraesCS5B01G256600 chr6D 87.725 334 41 0 3 336 151943170 151943503 1.150000e-104 390
16 TraesCS5B01G256600 chr6D 85.163 337 44 5 335 670 151944142 151944473 1.170000e-89 340
17 TraesCS5B01G256600 chr6D 86.411 287 33 5 335 620 10884238 10884519 3.310000e-80 309
18 TraesCS5B01G256600 chr2B 84.366 339 46 6 335 671 606052788 606053121 3.280000e-85 326
19 TraesCS5B01G256600 chr2A 83.432 338 46 8 335 670 689637911 689638240 4.280000e-79 305
20 TraesCS5B01G256600 chr7B 84.342 281 40 3 335 614 747881947 747881670 4.340000e-69 272
21 TraesCS5B01G256600 chr7A 72.691 758 170 29 1021 1752 730764272 730765018 5.730000e-53 219
22 TraesCS5B01G256600 chr7A 87.417 151 14 5 522 670 673003674 673003821 5.860000e-38 169


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 TraesCS5B01G256600 chr5B 439240034 439243446 3412 True 6303.0 6303 100.0000 1 3413 1 chr5B.!!$R1 3412
1 TraesCS5B01G256600 chr5D 370005485 370008267 2782 True 1968.0 3762 88.3475 685 3413 2 chr5D.!!$R1 2728
2 TraesCS5B01G256600 chr5A 472433201 472435653 2452 True 3491.0 3491 92.3980 959 3413 1 chr5A.!!$R1 2454
3 TraesCS5B01G256600 chr7D 138286130 138286857 727 True 606.0 606 82.0550 2697 3411 1 chr7D.!!$R1 714
4 TraesCS5B01G256600 chr3D 355751996 355752721 725 False 549.0 549 80.6580 2697 3411 1 chr3D.!!$F2 714
5 TraesCS5B01G256600 chr1D 419721492 419722175 683 True 521.0 521 80.7860 2697 3368 1 chr1D.!!$R1 671
6 TraesCS5B01G256600 chr4A 10219645 10220365 720 False 507.0 507 79.7260 2697 3411 1 chr4A.!!$F1 714
7 TraesCS5B01G256600 chr4A 581873079 581874382 1303 True 436.5 472 90.3605 4 668 2 chr4A.!!$R1 664
8 TraesCS5B01G256600 chr3A 329495819 329496542 723 False 503.0 503 79.5890 2697 3411 1 chr3A.!!$F1 714
9 TraesCS5B01G256600 chr1B 566829736 566830367 631 True 499.0 499 81.2600 2697 3319 1 chr1B.!!$R1 622
10 TraesCS5B01G256600 chr6D 10883272 10884519 1247 False 384.0 459 88.6735 1 620 2 chr6D.!!$F1 619
11 TraesCS5B01G256600 chr6D 151943170 151944473 1303 False 365.0 390 86.4440 3 670 2 chr6D.!!$F2 667
12 TraesCS5B01G256600 chr7A 730764272 730765018 746 False 219.0 219 72.6910 1021 1752 1 chr7A.!!$F2 731

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 1074 0.034896 GGTTTGCTTCCTCGGAGTCA 59.965 55.0 4.02 0.0 0.0 3.41 F
571 1212 0.038166 GGTTGCCCTGAAGATCACCA 59.962 55.0 0.00 0.0 0.0 4.17 F
693 1335 0.100861 CCTCTCGGTCGCCTCTAAAC 59.899 60.0 0.00 0.0 0.0 2.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2178 2925 1.971695 GCTTACCTGCCGGCAGTTT 60.972 57.895 44.92 35.24 42.15 2.66 R
2240 2987 2.283298 CCAGTGCAGCTATTTCATCGT 58.717 47.619 0.00 0.00 0.00 3.73 R
2661 3410 1.350071 TCTTGGCACGGTAGGGTTTA 58.650 50.000 0.00 0.00 0.00 2.01 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
24 25 2.358582 CACCAGTGTGCATTTTCTGTGA 59.641 45.455 0.00 0.00 35.31 3.58
224 225 0.176449 GGATGTTCCTTGCCATTGCC 59.824 55.000 0.00 0.00 32.49 4.52
227 228 0.899717 TGTTCCTTGCCATTGCCTCC 60.900 55.000 0.00 0.00 36.33 4.30
257 258 1.828660 CTCGACGATGCCCTACCCT 60.829 63.158 0.00 0.00 0.00 4.34
266 267 3.164269 CCCTACCCTGCGAGGCAT 61.164 66.667 0.00 0.00 38.13 4.40
270 271 2.671370 CTACCCTGCGAGGCATGCAT 62.671 60.000 21.36 13.78 42.32 3.96
303 304 1.079405 GCGACAAAGGATCCACCGA 60.079 57.895 15.82 0.00 44.74 4.69
317 318 2.306219 TCCACCGATGGGTCACAAATAA 59.694 45.455 0.00 0.00 46.01 1.40
354 995 1.617018 CCTCCGAGGTCTTGCCATCA 61.617 60.000 6.24 0.00 40.61 3.07
358 999 1.300963 GAGGTCTTGCCATCAGCCA 59.699 57.895 0.00 0.00 42.71 4.75
365 1006 1.483827 CTTGCCATCAGCCAGAGACTA 59.516 52.381 0.00 0.00 42.71 2.59
369 1010 2.288948 GCCATCAGCCAGAGACTATGAG 60.289 54.545 0.00 0.00 34.35 2.90
401 1042 2.685380 CTTGTCTCCCGCCTCCCT 60.685 66.667 0.00 0.00 0.00 4.20
402 1043 2.203938 TTGTCTCCCGCCTCCCTT 60.204 61.111 0.00 0.00 0.00 3.95
433 1074 0.034896 GGTTTGCTTCCTCGGAGTCA 59.965 55.000 4.02 0.00 0.00 3.41
434 1075 1.433534 GTTTGCTTCCTCGGAGTCAG 58.566 55.000 4.02 0.52 0.00 3.51
436 1077 1.471829 TTGCTTCCTCGGAGTCAGCA 61.472 55.000 19.19 19.19 34.79 4.41
468 1109 1.151908 CCTCCCTCCCCTACTCGAG 59.848 68.421 11.84 11.84 0.00 4.04
501 1142 1.374758 CACCTCGTCAAGCAGGGTC 60.375 63.158 0.00 0.00 33.57 4.46
507 1148 2.281484 TCAAGCAGGGTCGCCAAC 60.281 61.111 0.00 0.00 0.00 3.77
530 1171 0.915364 AGGAGGACCAAGCCAAGATC 59.085 55.000 0.00 0.00 38.94 2.75
571 1212 0.038166 GGTTGCCCTGAAGATCACCA 59.962 55.000 0.00 0.00 0.00 4.17
621 1263 2.415843 CGCCTTCCGATCGCCTTA 59.584 61.111 10.32 0.00 40.02 2.69
624 1266 1.742768 CCTTCCGATCGCCTTAGCT 59.257 57.895 10.32 0.00 36.60 3.32
642 1284 3.769369 TATCGCCTCTCGGTCGCCT 62.769 63.158 0.00 0.00 39.05 5.52
651 1293 0.941542 CTCGGTCGCCTCTTAGAGAG 59.058 60.000 11.32 4.67 41.96 3.20
670 1312 4.309950 GAACGTGGTGGACCCGCT 62.310 66.667 0.00 0.00 41.91 5.52
671 1313 4.619227 AACGTGGTGGACCCGCTG 62.619 66.667 0.00 0.00 41.91 5.18
690 1332 2.516460 GCCTCTCGGTCGCCTCTA 60.516 66.667 0.00 0.00 0.00 2.43
691 1333 2.119655 GCCTCTCGGTCGCCTCTAA 61.120 63.158 0.00 0.00 0.00 2.10
692 1334 1.664321 GCCTCTCGGTCGCCTCTAAA 61.664 60.000 0.00 0.00 0.00 1.85
693 1335 0.100861 CCTCTCGGTCGCCTCTAAAC 59.899 60.000 0.00 0.00 0.00 2.01
694 1336 0.248134 CTCTCGGTCGCCTCTAAACG 60.248 60.000 0.00 0.00 0.00 3.60
695 1337 1.226603 CTCGGTCGCCTCTAAACGG 60.227 63.158 0.00 0.00 0.00 4.44
696 1338 1.651240 CTCGGTCGCCTCTAAACGGA 61.651 60.000 0.00 0.00 0.00 4.69
697 1339 1.515736 CGGTCGCCTCTAAACGGAC 60.516 63.158 0.00 0.00 0.00 4.79
698 1340 1.515736 GGTCGCCTCTAAACGGACG 60.516 63.158 0.00 0.00 0.00 4.79
699 1341 1.515736 GTCGCCTCTAAACGGACGG 60.516 63.158 0.00 0.00 0.00 4.79
700 1342 1.675310 TCGCCTCTAAACGGACGGA 60.675 57.895 0.00 0.00 0.00 4.69
750 1392 2.259204 CACGCACCTTGGCCATTG 59.741 61.111 6.09 5.62 0.00 2.82
785 1435 3.676291 TTGTGTGGTCTCGAATCATCA 57.324 42.857 0.00 0.00 0.00 3.07
798 1455 1.275666 ATCATCAGGGTCCGTGTTCA 58.724 50.000 11.26 0.00 0.00 3.18
824 1481 1.207089 TCTTGTGAACGGCCTATGGAG 59.793 52.381 0.00 0.00 0.00 3.86
828 1485 1.069935 GAACGGCCTATGGAGCTCC 59.930 63.158 26.78 26.78 0.00 4.70
830 1487 3.996124 CGGCCTATGGAGCTCCCG 61.996 72.222 29.95 20.11 37.93 5.14
1008 1719 1.213094 CGCGTCGTCATATGGGTTCC 61.213 60.000 2.13 0.00 0.00 3.62
1233 1956 4.459089 GGGCTGTCGCTGGAGTCC 62.459 72.222 0.73 0.73 36.09 3.85
1599 2346 2.738521 CCGACCTTCTGCCACACG 60.739 66.667 0.00 0.00 0.00 4.49
1600 2347 2.738521 CGACCTTCTGCCACACGG 60.739 66.667 0.00 0.00 0.00 4.94
1653 2400 3.112075 CACCAGATGCGCGTCGTT 61.112 61.111 23.15 9.23 0.00 3.85
1941 2688 3.000727 CGCCGACAAGATAAAGGAGTTT 58.999 45.455 0.00 0.00 0.00 2.66
1975 2722 2.760385 GGTGCGGCTCTCCCTACT 60.760 66.667 0.00 0.00 0.00 2.57
1989 2736 0.320374 CCTACTTGTGGGTTCTGCGA 59.680 55.000 0.00 0.00 0.00 5.10
2001 2748 4.899239 CTGCGATCCGACCTGGCC 62.899 72.222 0.00 0.00 37.80 5.36
2178 2925 1.675552 TGATATCCGAGCAGACGACA 58.324 50.000 0.00 0.00 35.09 4.35
2489 3237 4.827835 AGTGAACTAGCACAAGTCAGTAGA 59.172 41.667 3.72 0.00 41.19 2.59
2510 3258 8.572828 GTAGAATGAACTACTGATGAGTGATG 57.427 38.462 0.00 0.00 39.44 3.07
2511 3259 7.415592 AGAATGAACTACTGATGAGTGATGA 57.584 36.000 0.00 0.00 33.21 2.92
2512 3260 7.845037 AGAATGAACTACTGATGAGTGATGAA 58.155 34.615 0.00 0.00 33.21 2.57
2513 3261 7.763528 AGAATGAACTACTGATGAGTGATGAAC 59.236 37.037 0.00 0.00 33.21 3.18
2534 3283 6.256539 TGAACGAGCTTCTAATAATCTGCAAG 59.743 38.462 0.00 0.00 0.00 4.01
2626 3375 2.051334 TTGGCTAATGGGGTTGATCG 57.949 50.000 0.00 0.00 0.00 3.69
2641 3390 3.627395 TGATCGGTGCCTCTAACAATT 57.373 42.857 0.00 0.00 0.00 2.32
2711 3460 8.447924 TGTACTATACTTCGAGCAGTTATCTT 57.552 34.615 0.00 0.00 0.00 2.40
2790 3541 7.596749 AATGAGAATCCGTACAAACAACTAG 57.403 36.000 0.00 0.00 0.00 2.57
2793 3544 7.660112 TGAGAATCCGTACAAACAACTAGTTA 58.340 34.615 8.04 0.00 40.26 2.24
2809 3560 3.951775 AGTTAGTTCTGAGTCTGGCTG 57.048 47.619 0.00 0.00 0.00 4.85
2917 3668 6.280643 AGAAAAAGCTGGGTTGTTGAATTAC 58.719 36.000 0.00 0.00 0.00 1.89
3007 3760 9.490663 GTTCATGGTATCTTTCTTTGAAATACG 57.509 33.333 0.00 0.00 0.00 3.06
3020 3773 6.372381 TCTTTGAAATACGTAAAGGGGTAAGC 59.628 38.462 0.00 0.00 33.41 3.09
3032 3786 3.365472 AGGGGTAAGCAAATGATTGGAC 58.635 45.455 0.00 0.00 37.02 4.02
3190 3952 9.547753 TGAGAAAATGGCTATACAAGATACTTC 57.452 33.333 0.00 0.00 0.00 3.01
3199 3961 6.717540 GCTATACAAGATACTTCCTGAGGAGA 59.282 42.308 0.00 0.00 31.21 3.71
3201 3964 4.941713 ACAAGATACTTCCTGAGGAGAGT 58.058 43.478 16.62 16.62 31.21 3.24
3277 4041 0.310854 GAGGCCAAACAAACGGACTG 59.689 55.000 5.01 0.00 42.31 3.51
3345 4112 0.743345 GGGGCGTTTGTAGTAGGCAG 60.743 60.000 0.00 0.00 0.00 4.85
3370 4137 7.390718 AGTTGTCTAACTAATAGGTTTTGGCAG 59.609 37.037 0.00 0.00 45.07 4.85
3379 4146 6.391227 AATAGGTTTTGGCAGTATACATGC 57.609 37.500 15.03 15.03 43.09 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
224 225 1.946768 GTCGAGTCATCAGGAGAGGAG 59.053 57.143 0.00 0.00 34.87 3.69
227 228 1.657822 TCGTCGAGTCATCAGGAGAG 58.342 55.000 0.00 0.00 0.00 3.20
257 258 1.449726 GAATGGATGCATGCCTCGCA 61.450 55.000 16.68 14.67 44.86 5.10
266 267 2.030571 GCAATGGGGAGAATGGATGCA 61.031 52.381 0.00 0.00 33.00 3.96
270 271 0.107214 GTCGCAATGGGGAGAATGGA 60.107 55.000 0.00 0.00 36.56 3.41
303 304 4.671831 TGTGGATGTTATTTGTGACCCAT 58.328 39.130 0.00 0.00 0.00 4.00
317 318 2.169352 GAGGACTAGTGCATGTGGATGT 59.831 50.000 17.34 0.00 31.50 3.06
354 995 3.500289 GGAGATCCTCATAGTCTCTGGCT 60.500 52.174 0.00 0.00 38.68 4.75
358 999 3.650942 AGTCGGAGATCCTCATAGTCTCT 59.349 47.826 0.00 0.00 40.67 3.10
365 1006 1.175983 GGCGAGTCGGAGATCCTCAT 61.176 60.000 15.52 0.00 40.67 2.90
369 1010 1.066587 CAAGGCGAGTCGGAGATCC 59.933 63.158 15.52 6.34 40.67 3.36
401 1042 2.197324 AAACCCCGCTGAAGGCAA 59.803 55.556 0.00 0.00 41.91 4.52
402 1043 2.597217 CAAACCCCGCTGAAGGCA 60.597 61.111 0.00 0.00 41.91 4.75
433 1074 2.997897 GACTCCTCCCGTGGTGCT 60.998 66.667 0.00 0.00 0.00 4.40
434 1075 4.083862 GGACTCCTCCCGTGGTGC 62.084 72.222 0.00 0.00 0.00 5.01
436 1077 2.037527 GAGGACTCCTCCCGTGGT 59.962 66.667 13.65 0.00 44.36 4.16
460 1101 2.288702 CCATGGCATCTTCCTCGAGTAG 60.289 54.545 12.31 8.50 0.00 2.57
507 1148 4.785453 GGCTTGGTCCTCCTGCGG 62.785 72.222 0.00 0.00 35.80 5.69
514 1155 1.078143 GCGATCTTGGCTTGGTCCT 60.078 57.895 0.00 0.00 0.00 3.85
515 1156 1.372087 CTGCGATCTTGGCTTGGTCC 61.372 60.000 0.00 0.00 0.00 4.46
516 1157 1.986575 GCTGCGATCTTGGCTTGGTC 61.987 60.000 0.00 0.00 0.00 4.02
517 1158 2.042831 GCTGCGATCTTGGCTTGGT 61.043 57.895 0.00 0.00 0.00 3.67
554 1195 0.770499 TGTGGTGATCTTCAGGGCAA 59.230 50.000 0.00 0.00 0.00 4.52
571 1212 1.491754 AGGGTTTTGAACGTAGGGTGT 59.508 47.619 0.00 0.00 0.00 4.16
642 1284 3.082548 CCACCACGTTCTCTCTCTAAGA 58.917 50.000 0.00 0.00 0.00 2.10
651 1293 2.048503 CGGGTCCACCACGTTCTC 60.049 66.667 0.00 0.00 40.22 2.87
653 1295 4.309950 AGCGGGTCCACCACGTTC 62.310 66.667 0.00 0.00 40.22 3.95
675 1317 0.248134 CGTTTAGAGGCGACCGAGAG 60.248 60.000 0.00 0.00 0.00 3.20
676 1318 1.651240 CCGTTTAGAGGCGACCGAGA 61.651 60.000 0.00 0.00 0.00 4.04
677 1319 1.226603 CCGTTTAGAGGCGACCGAG 60.227 63.158 0.00 0.00 0.00 4.63
678 1320 1.675310 TCCGTTTAGAGGCGACCGA 60.675 57.895 0.00 0.00 0.00 4.69
679 1321 1.515736 GTCCGTTTAGAGGCGACCG 60.516 63.158 0.00 0.00 0.00 4.79
680 1322 1.515736 CGTCCGTTTAGAGGCGACC 60.516 63.158 0.00 0.00 32.73 4.79
681 1323 1.515736 CCGTCCGTTTAGAGGCGAC 60.516 63.158 0.00 0.00 32.73 5.19
682 1324 1.651240 CTCCGTCCGTTTAGAGGCGA 61.651 60.000 0.00 0.00 32.73 5.54
683 1325 1.226603 CTCCGTCCGTTTAGAGGCG 60.227 63.158 0.00 0.00 0.00 5.52
684 1326 1.065251 CTACTCCGTCCGTTTAGAGGC 59.935 57.143 0.00 0.00 0.00 4.70
685 1327 2.363683 ACTACTCCGTCCGTTTAGAGG 58.636 52.381 0.00 0.00 0.00 3.69
686 1328 3.190118 ACAACTACTCCGTCCGTTTAGAG 59.810 47.826 0.00 0.00 0.00 2.43
687 1329 3.149196 ACAACTACTCCGTCCGTTTAGA 58.851 45.455 0.00 0.00 0.00 2.10
688 1330 3.565905 ACAACTACTCCGTCCGTTTAG 57.434 47.619 0.00 0.00 0.00 1.85
689 1331 4.615912 GCTAACAACTACTCCGTCCGTTTA 60.616 45.833 0.00 0.00 0.00 2.01
690 1332 2.896745 AACAACTACTCCGTCCGTTT 57.103 45.000 0.00 0.00 0.00 3.60
691 1333 2.352127 GCTAACAACTACTCCGTCCGTT 60.352 50.000 0.00 0.00 0.00 4.44
692 1334 1.200948 GCTAACAACTACTCCGTCCGT 59.799 52.381 0.00 0.00 0.00 4.69
693 1335 1.471684 AGCTAACAACTACTCCGTCCG 59.528 52.381 0.00 0.00 0.00 4.79
694 1336 3.251571 CAAGCTAACAACTACTCCGTCC 58.748 50.000 0.00 0.00 0.00 4.79
695 1337 2.666994 GCAAGCTAACAACTACTCCGTC 59.333 50.000 0.00 0.00 0.00 4.79
696 1338 2.036733 TGCAAGCTAACAACTACTCCGT 59.963 45.455 0.00 0.00 0.00 4.69
697 1339 2.683968 TGCAAGCTAACAACTACTCCG 58.316 47.619 0.00 0.00 0.00 4.63
698 1340 3.181506 GCATGCAAGCTAACAACTACTCC 60.182 47.826 14.21 0.00 0.00 3.85
699 1341 3.436704 TGCATGCAAGCTAACAACTACTC 59.563 43.478 20.30 0.00 34.99 2.59
700 1342 3.189287 GTGCATGCAAGCTAACAACTACT 59.811 43.478 24.58 0.00 34.99 2.57
710 1352 2.595463 ACACGGTGCATGCAAGCT 60.595 55.556 24.58 3.98 34.99 3.74
755 1405 0.798776 GACCACACAATTCGCTGGAG 59.201 55.000 0.00 0.00 0.00 3.86
762 1412 4.631377 TGATGATTCGAGACCACACAATTC 59.369 41.667 0.00 0.00 0.00 2.17
763 1413 4.578871 TGATGATTCGAGACCACACAATT 58.421 39.130 0.00 0.00 0.00 2.32
766 1416 2.094026 CCTGATGATTCGAGACCACACA 60.094 50.000 0.00 0.00 0.00 3.72
768 1418 1.482182 CCCTGATGATTCGAGACCACA 59.518 52.381 0.00 0.00 0.00 4.17
798 1455 0.953960 GGCCGTTCACAAGACCGATT 60.954 55.000 0.00 0.00 30.42 3.34
843 1500 1.578206 GGGAGCGGAGACAAAAGTGC 61.578 60.000 0.00 0.00 0.00 4.40
888 1599 1.335697 GCTTGTCGACGACGTTCCTC 61.336 60.000 22.06 5.33 40.69 3.71
903 1614 1.400846 GACTGATGTGCTGATGGCTTG 59.599 52.381 0.00 0.00 42.39 4.01
998 1709 1.202698 GCTTCTGCTCGGAACCCATAT 60.203 52.381 0.00 0.00 36.03 1.78
1008 1719 2.816958 ACATGCGGCTTCTGCTCG 60.817 61.111 0.00 0.00 39.59 5.03
1197 1920 2.050350 GTCCGGGATGACCTCGACA 61.050 63.158 0.00 0.00 35.66 4.35
1263 1986 2.126149 CAGTTCTGCTCGAGCGCT 60.126 61.111 30.75 21.90 45.83 5.92
1975 2722 4.713946 GGATCGCAGAACCCACAA 57.286 55.556 0.00 0.00 44.30 3.33
2161 2908 2.427453 AGTTTGTCGTCTGCTCGGATAT 59.573 45.455 0.00 0.00 0.00 1.63
2178 2925 1.971695 GCTTACCTGCCGGCAGTTT 60.972 57.895 44.92 35.24 42.15 2.66
2240 2987 2.283298 CCAGTGCAGCTATTTCATCGT 58.717 47.619 0.00 0.00 0.00 3.73
2489 3237 6.533012 CGTTCATCACTCATCAGTAGTTCATT 59.467 38.462 0.00 0.00 0.00 2.57
2505 3253 7.568497 GCAGATTATTAGAAGCTCGTTCATCAC 60.568 40.741 0.00 0.00 37.67 3.06
2507 3255 6.422100 TGCAGATTATTAGAAGCTCGTTCATC 59.578 38.462 0.00 0.00 37.67 2.92
2508 3256 6.283694 TGCAGATTATTAGAAGCTCGTTCAT 58.716 36.000 0.00 0.00 37.67 2.57
2509 3257 5.660460 TGCAGATTATTAGAAGCTCGTTCA 58.340 37.500 0.00 0.00 37.67 3.18
2510 3258 6.256757 ACTTGCAGATTATTAGAAGCTCGTTC 59.743 38.462 0.00 0.00 35.08 3.95
2511 3259 6.109359 ACTTGCAGATTATTAGAAGCTCGTT 58.891 36.000 0.00 0.00 0.00 3.85
2512 3260 5.665459 ACTTGCAGATTATTAGAAGCTCGT 58.335 37.500 0.00 0.00 0.00 4.18
2513 3261 6.256539 TCAACTTGCAGATTATTAGAAGCTCG 59.743 38.462 0.00 0.00 0.00 5.03
2534 3283 8.585189 AAAATGAAGCTCAATTTCTCTTCAAC 57.415 30.769 13.64 0.00 45.20 3.18
2626 3375 8.000780 AGAATTAATCAATTGTTAGAGGCACC 57.999 34.615 5.13 0.00 34.44 5.01
2660 3409 1.698532 TCTTGGCACGGTAGGGTTTAA 59.301 47.619 0.00 0.00 0.00 1.52
2661 3410 1.350071 TCTTGGCACGGTAGGGTTTA 58.650 50.000 0.00 0.00 0.00 2.01
2776 3527 7.646922 ACTCAGAACTAACTAGTTGTTTGTACG 59.353 37.037 18.56 10.55 45.84 3.67
2790 3541 3.669251 ACAGCCAGACTCAGAACTAAC 57.331 47.619 0.00 0.00 0.00 2.34
2793 3544 3.471680 GAAAACAGCCAGACTCAGAACT 58.528 45.455 0.00 0.00 0.00 3.01
2845 3596 7.771826 TCCATTCCTTATTAAGAAGTTTACGGG 59.228 37.037 8.91 3.44 0.00 5.28
2934 3685 5.654603 TTGATTAGAACGAGCCTTGTCTA 57.345 39.130 0.00 0.00 0.00 2.59
2937 3688 4.579869 ACATTGATTAGAACGAGCCTTGT 58.420 39.130 0.00 0.00 0.00 3.16
2946 3697 8.778358 ACTTGTGAGAAGAACATTGATTAGAAC 58.222 33.333 0.00 0.00 0.00 3.01
3007 3760 5.420739 TCCAATCATTTGCTTACCCCTTTAC 59.579 40.000 0.00 0.00 0.00 2.01
3020 3773 9.650539 CTGGATCTATAGTAGTCCAATCATTTG 57.349 37.037 18.25 7.48 36.36 2.32
3097 3859 4.224370 TCCTTGGTCTTTAGGGACACATAC 59.776 45.833 0.00 0.00 37.91 2.39
3190 3952 2.630098 TCTTGTCAACACTCTCCTCAGG 59.370 50.000 0.00 0.00 0.00 3.86
3256 4020 0.310854 GTCCGTTTGTTTGGCCTCAG 59.689 55.000 3.32 0.00 0.00 3.35
3322 4088 2.355007 GCCTACTACAAACGCCCCTTAA 60.355 50.000 0.00 0.00 0.00 1.85
3345 4112 7.174426 ACTGCCAAAACCTATTAGTTAGACAAC 59.826 37.037 0.00 0.00 34.67 3.32
3370 4137 4.010349 GGCAATCCCTTAGGCATGTATAC 58.990 47.826 0.00 0.00 0.00 1.47
3379 4146 2.938956 CCTAGTGGCAATCCCTTAGG 57.061 55.000 0.00 0.00 36.20 2.69


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

AutoCloner maintained by Alex Coulton.