Multiple sequence alignment - TraesCS3A01G296800

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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 TraesCS3A01G296800 chr3A 100.000 3582 0 0 1 3582 531453286 531456867 0.000000e+00 6615.0
1 TraesCS3A01G296800 chr3A 86.830 1678 187 18 935 2602 614239378 614237725 0.000000e+00 1844.0
2 TraesCS3A01G296800 chr3A 87.131 1422 171 6 1145 2558 614126310 614124893 0.000000e+00 1602.0
3 TraesCS3A01G296800 chr3A 85.246 427 47 8 749 1164 614126908 614126487 3.310000e-115 425.0
4 TraesCS3A01G296800 chr3D 95.841 2573 77 13 604 3154 419875610 419873046 0.000000e+00 4132.0
5 TraesCS3A01G296800 chr3D 84.515 1537 158 36 608 2124 471421405 471419929 0.000000e+00 1447.0
6 TraesCS3A01G296800 chr3D 90.536 317 29 1 1 316 419876069 419875753 5.530000e-113 418.0
7 TraesCS3A01G296800 chr3D 92.810 153 7 1 347 499 419875755 419875607 6.020000e-53 219.0
8 TraesCS3A01G296800 chr3B 85.526 2052 224 34 611 2632 626303326 626301318 0.000000e+00 2076.0
9 TraesCS3A01G296800 chr2A 92.483 439 29 2 3144 3578 89725791 89725353 3.040000e-175 625.0
10 TraesCS3A01G296800 chr2A 92.009 438 32 2 3148 3582 514713211 514713648 2.360000e-171 612.0
11 TraesCS3A01G296800 chr2A 91.572 439 33 2 3144 3578 89728049 89727611 1.420000e-168 603.0
12 TraesCS3A01G296800 chr2A 89.565 115 10 2 493 607 597465542 597465430 1.040000e-30 145.0
13 TraesCS3A01G296800 chr2A 90.000 110 10 1 498 607 597465430 597465538 1.340000e-29 141.0
14 TraesCS3A01G296800 chr6D 92.130 432 28 2 3154 3582 36286863 36286435 3.960000e-169 604.0
15 TraesCS3A01G296800 chr6D 91.879 431 31 3 3154 3581 456734906 456734477 1.840000e-167 599.0
16 TraesCS3A01G296800 chr1A 91.743 436 33 1 3150 3582 531929509 531929944 1.420000e-168 603.0
17 TraesCS3A01G296800 chr2D 91.917 433 29 4 3153 3582 417209264 417208835 5.120000e-168 601.0
18 TraesCS3A01G296800 chr2D 91.898 432 32 3 3154 3582 589515191 589514760 5.120000e-168 601.0
19 TraesCS3A01G296800 chr2D 91.667 432 33 1 3154 3582 538072846 538072415 2.380000e-166 595.0
20 TraesCS3A01G296800 chr2D 89.286 112 12 0 496 607 498317944 498317833 1.340000e-29 141.0
21 TraesCS3A01G296800 chr5A 91.892 111 9 0 498 608 387966874 387966764 4.790000e-34 156.0
22 TraesCS3A01G296800 chr5B 90.598 117 5 2 497 607 676276831 676276715 2.230000e-32 150.0
23 TraesCS3A01G296800 chr5B 76.087 138 29 4 1931 2066 448274677 448274542 6.420000e-08 69.4
24 TraesCS3A01G296800 chr5D 90.351 114 10 1 498 611 530638596 530638708 8.010000e-32 148.0
25 TraesCS3A01G296800 chr2B 88.235 119 11 2 493 609 731935945 731936062 4.820000e-29 139.0
26 TraesCS3A01G296800 chr2B 89.091 110 12 0 498 607 507408705 507408814 1.730000e-28 137.0
27 TraesCS3A01G296800 chr6B 88.034 117 10 2 498 614 452724318 452724206 6.240000e-28 135.0


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 TraesCS3A01G296800 chr3A 531453286 531456867 3581 False 6615.000000 6615 100.000000 1 3582 1 chr3A.!!$F1 3581
1 TraesCS3A01G296800 chr3A 614237725 614239378 1653 True 1844.000000 1844 86.830000 935 2602 1 chr3A.!!$R1 1667
2 TraesCS3A01G296800 chr3A 614124893 614126908 2015 True 1013.500000 1602 86.188500 749 2558 2 chr3A.!!$R2 1809
3 TraesCS3A01G296800 chr3D 419873046 419876069 3023 True 1589.666667 4132 93.062333 1 3154 3 chr3D.!!$R2 3153
4 TraesCS3A01G296800 chr3D 471419929 471421405 1476 True 1447.000000 1447 84.515000 608 2124 1 chr3D.!!$R1 1516
5 TraesCS3A01G296800 chr3B 626301318 626303326 2008 True 2076.000000 2076 85.526000 611 2632 1 chr3B.!!$R1 2021
6 TraesCS3A01G296800 chr2A 89725353 89728049 2696 True 614.000000 625 92.027500 3144 3578 2 chr2A.!!$R2 434

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
603 605 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.0 13.64 4.95 46.06 4.20 F
1038 1096 0.538584 CCTGCTCTGCCTGTGTATCA 59.461 55.0 0.00 0.00 0.00 2.15 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2368 2626 0.034337 TAACAGACTGACCAACCGCC 59.966 55.000 10.08 0.0 0.00 6.13 R
2991 3255 1.205655 TGTATGCCAGTGAGCTGAGAC 59.794 52.381 0.00 0.0 45.28 3.36 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
47 48 3.151710 TCCAGCCCCGGTCGTATG 61.152 66.667 0.00 0.00 0.00 2.39
49 50 2.129146 CCAGCCCCGGTCGTATGTA 61.129 63.158 0.00 0.00 0.00 2.29
88 89 4.796495 GTGAAAGCCGGCGGGGAT 62.796 66.667 29.48 6.48 38.47 3.85
178 180 2.722201 GGAGCGGATCCCTCACGTT 61.722 63.158 23.61 5.23 43.01 3.99
225 227 3.431725 CCGCCCTTGTCGCCTTTC 61.432 66.667 0.00 0.00 0.00 2.62
255 257 1.153765 GGCGGACCGTACTGTTACC 60.154 63.158 16.73 1.08 0.00 2.85
256 258 1.586028 GCGGACCGTACTGTTACCA 59.414 57.895 16.73 0.00 0.00 3.25
260 262 3.328505 CGGACCGTACTGTTACCATTTT 58.671 45.455 5.48 0.00 0.00 1.82
318 320 3.790437 CCGGAGCTCAGCCCATGT 61.790 66.667 17.19 0.00 0.00 3.21
320 322 2.827642 GGAGCTCAGCCCATGTGC 60.828 66.667 17.19 0.00 46.50 4.57
323 325 3.819188 GCTCAGCCCATGTGCTAC 58.181 61.111 1.17 0.00 43.53 3.58
324 326 1.078214 GCTCAGCCCATGTGCTACA 60.078 57.895 1.17 0.00 43.53 2.74
327 329 1.140452 CTCAGCCCATGTGCTACAGAT 59.860 52.381 1.17 0.00 40.32 2.90
329 331 1.134310 CAGCCCATGTGCTACAGATGA 60.134 52.381 1.17 0.00 40.32 2.92
330 332 1.561076 AGCCCATGTGCTACAGATGAA 59.439 47.619 0.00 0.00 40.56 2.57
331 333 2.174210 AGCCCATGTGCTACAGATGAAT 59.826 45.455 0.00 0.00 40.56 2.57
332 334 2.551459 GCCCATGTGCTACAGATGAATC 59.449 50.000 6.31 0.00 37.32 2.52
333 335 2.804527 CCCATGTGCTACAGATGAATCG 59.195 50.000 6.31 0.00 37.32 3.34
334 336 2.804527 CCATGTGCTACAGATGAATCGG 59.195 50.000 6.31 0.00 37.32 4.18
335 337 3.461061 CATGTGCTACAGATGAATCGGT 58.539 45.455 0.00 1.77 37.32 4.69
336 338 3.610040 TGTGCTACAGATGAATCGGTT 57.390 42.857 1.43 0.00 36.61 4.44
338 340 2.866762 GTGCTACAGATGAATCGGTTCC 59.133 50.000 5.84 0.00 36.61 3.62
339 341 2.158957 TGCTACAGATGAATCGGTTCCC 60.159 50.000 5.84 0.00 36.61 3.97
354 356 0.326595 TTCCCGCAGTGCCAGATAAA 59.673 50.000 10.11 0.00 0.00 1.40
359 361 1.098050 GCAGTGCCAGATAAACAGGG 58.902 55.000 2.85 0.00 0.00 4.45
363 365 0.991146 TGCCAGATAAACAGGGCTCA 59.009 50.000 0.00 0.00 46.53 4.26
365 367 1.656652 CCAGATAAACAGGGCTCACG 58.343 55.000 0.00 0.00 0.00 4.35
416 418 2.930040 GTGATTCGTCGACATGGTCATT 59.070 45.455 17.16 0.00 32.09 2.57
452 454 4.980434 CGAGGTACGGGATAAAATGTACTG 59.020 45.833 0.00 0.00 37.80 2.74
454 456 6.238731 CGAGGTACGGGATAAAATGTACTGTA 60.239 42.308 0.00 0.00 37.80 2.74
455 457 6.809869 AGGTACGGGATAAAATGTACTGTAC 58.190 40.000 10.98 10.98 41.08 2.90
500 502 9.884814 AGATGTGGTTAATCCTTCTATAGTACT 57.115 33.333 0.00 0.00 37.07 2.73
502 504 8.474710 TGTGGTTAATCCTTCTATAGTACTCC 57.525 38.462 0.00 0.00 37.07 3.85
503 505 7.508296 TGTGGTTAATCCTTCTATAGTACTCCC 59.492 40.741 0.00 0.00 37.07 4.30
504 506 7.729431 GTGGTTAATCCTTCTATAGTACTCCCT 59.271 40.741 0.00 0.00 37.07 4.20
505 507 7.949006 TGGTTAATCCTTCTATAGTACTCCCTC 59.051 40.741 0.00 0.00 37.07 4.30
506 508 7.396907 GGTTAATCCTTCTATAGTACTCCCTCC 59.603 44.444 0.00 0.00 0.00 4.30
507 509 4.637387 TCCTTCTATAGTACTCCCTCCG 57.363 50.000 0.00 0.00 0.00 4.63
508 510 3.979347 TCCTTCTATAGTACTCCCTCCGT 59.021 47.826 0.00 0.00 0.00 4.69
510 512 4.325972 CTTCTATAGTACTCCCTCCGTCC 58.674 52.174 0.00 0.00 0.00 4.79
511 513 2.301296 TCTATAGTACTCCCTCCGTCCG 59.699 54.545 0.00 0.00 0.00 4.79
515 517 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
518 520 1.117150 CTCCCTCCGTCCGGAAATAA 58.883 55.000 5.23 0.00 44.66 1.40
519 521 1.692519 CTCCCTCCGTCCGGAAATAAT 59.307 52.381 5.23 0.00 44.66 1.28
520 522 2.104281 CTCCCTCCGTCCGGAAATAATT 59.896 50.000 5.23 0.00 44.66 1.40
521 523 2.158871 TCCCTCCGTCCGGAAATAATTG 60.159 50.000 5.23 0.00 44.66 2.32
522 524 2.420967 CCCTCCGTCCGGAAATAATTGT 60.421 50.000 5.23 0.00 44.66 2.71
524 526 3.527533 CTCCGTCCGGAAATAATTGTCA 58.472 45.455 5.23 0.00 44.66 3.58
525 527 4.127171 CTCCGTCCGGAAATAATTGTCAT 58.873 43.478 5.23 0.00 44.66 3.06
526 528 4.124238 TCCGTCCGGAAATAATTGTCATC 58.876 43.478 5.23 0.00 42.05 2.92
527 529 3.874543 CCGTCCGGAAATAATTGTCATCA 59.125 43.478 5.23 0.00 37.50 3.07
528 530 4.334203 CCGTCCGGAAATAATTGTCATCAA 59.666 41.667 5.23 0.00 37.50 2.57
531 533 6.972328 CGTCCGGAAATAATTGTCATCAAAAT 59.028 34.615 5.23 0.00 37.11 1.82
532 534 7.044117 CGTCCGGAAATAATTGTCATCAAAATG 60.044 37.037 5.23 0.00 37.11 2.32
533 535 7.222611 GTCCGGAAATAATTGTCATCAAAATGG 59.777 37.037 5.23 0.00 37.11 3.16
534 536 7.123397 TCCGGAAATAATTGTCATCAAAATGGA 59.877 33.333 0.00 0.00 37.11 3.41
535 537 7.222611 CCGGAAATAATTGTCATCAAAATGGAC 59.777 37.037 0.00 0.00 37.11 4.02
536 538 7.758980 CGGAAATAATTGTCATCAAAATGGACA 59.241 33.333 0.00 0.00 37.11 4.02
537 539 9.434420 GGAAATAATTGTCATCAAAATGGACAA 57.566 29.630 8.64 8.64 37.34 3.18
544 546 8.783833 TTGTCATCAAAATGGACAAAAAGAAA 57.216 26.923 4.15 0.00 33.71 2.52
545 547 8.961294 TGTCATCAAAATGGACAAAAAGAAAT 57.039 26.923 0.00 0.00 33.42 2.17
546 548 8.828644 TGTCATCAAAATGGACAAAAAGAAATG 58.171 29.630 0.00 0.00 33.42 2.32
547 549 8.829612 GTCATCAAAATGGACAAAAAGAAATGT 58.170 29.630 0.00 0.00 33.42 2.71
582 584 9.206870 ACATACATTTTTGTCCATTTTGATGAC 57.793 29.630 0.00 0.00 0.00 3.06
584 586 9.775854 ATACATTTTTGTCCATTTTGATGACAA 57.224 25.926 0.00 0.00 34.47 3.18
585 587 8.145316 ACATTTTTGTCCATTTTGATGACAAG 57.855 30.769 0.00 0.00 37.13 3.16
587 589 9.258826 CATTTTTGTCCATTTTGATGACAAGTA 57.741 29.630 0.00 0.00 37.13 2.24
589 591 9.829507 TTTTTGTCCATTTTGATGACAAGTATT 57.170 25.926 0.00 0.00 37.13 1.89
590 592 9.829507 TTTTGTCCATTTTGATGACAAGTATTT 57.170 25.926 0.00 0.00 37.13 1.40
591 593 9.474920 TTTGTCCATTTTGATGACAAGTATTTC 57.525 29.630 0.00 0.00 37.13 2.17
592 594 7.601856 TGTCCATTTTGATGACAAGTATTTCC 58.398 34.615 0.00 0.00 37.32 3.13
594 596 6.035843 CCATTTTGATGACAAGTATTTCCGG 58.964 40.000 0.00 0.00 37.32 5.14
596 598 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
597 599 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
598 600 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
599 601 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
600 602 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
601 603 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
602 604 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
603 605 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
744 748 6.582295 AGTTGATCATACAAATTGCAACGAAC 59.418 34.615 0.00 0.00 39.14 3.95
790 803 7.124448 ACTCTTACATAGAAAAGGAATCTCGGT 59.876 37.037 0.00 0.00 30.91 4.69
792 805 8.974238 TCTTACATAGAAAAGGAATCTCGGTAA 58.026 33.333 0.00 0.00 30.97 2.85
793 806 9.765795 CTTACATAGAAAAGGAATCTCGGTAAT 57.234 33.333 0.00 0.00 31.19 1.89
843 891 4.365514 TTCAATGCACTTACCTTCCTCA 57.634 40.909 0.00 0.00 0.00 3.86
892 940 4.034510 CGAGCAGATCACTTGGGATTTAAC 59.965 45.833 0.00 0.00 0.00 2.01
1021 1079 1.660560 GCCATTGCGTGATTCTGCCT 61.661 55.000 0.16 0.00 0.00 4.75
1038 1096 0.538584 CCTGCTCTGCCTGTGTATCA 59.461 55.000 0.00 0.00 0.00 2.15
1113 1171 5.067283 GGAAACACTAGGCTTGAAACAGAAA 59.933 40.000 2.20 0.00 0.00 2.52
1270 1524 4.844349 AATAGTTGGCTCCAGAAAGCTA 57.156 40.909 0.00 0.00 42.13 3.32
1311 1565 1.946768 GTCACACTTTTGCTGCCTACA 59.053 47.619 0.00 0.00 0.00 2.74
2112 2368 3.369471 GCAAAGGTGTCTAGTATCTGCCA 60.369 47.826 0.00 0.00 0.00 4.92
2462 2726 3.138884 TGGAAGCACATAAAGCACTCA 57.861 42.857 0.00 0.00 0.00 3.41
2518 2782 6.231211 TCCCTCTTCAGTCAAGTTAAATGTC 58.769 40.000 0.00 0.00 33.27 3.06
2618 2882 4.499183 AGATGTTGTCCTTCGTCTTCATC 58.501 43.478 0.00 0.00 0.00 2.92
2620 2884 1.390463 GTTGTCCTTCGTCTTCATCGC 59.610 52.381 0.00 0.00 0.00 4.58
2648 2912 2.833794 TGTTCTCTGCTGTGTTGGTAC 58.166 47.619 0.00 0.00 0.00 3.34
2704 2968 5.283294 CACACATGTGCTTTCATTTCTTGA 58.717 37.500 25.68 0.00 39.39 3.02
2727 2991 6.770785 TGACAAGTTACCAGTTTTTCTATGCT 59.229 34.615 0.00 0.00 0.00 3.79
2732 2996 6.546034 AGTTACCAGTTTTTCTATGCTTGTGT 59.454 34.615 0.00 0.00 0.00 3.72
2866 3130 9.672086 CTGTTTCTTCAATTAAATCGTTGGTAA 57.328 29.630 0.00 0.00 0.00 2.85
2906 3170 5.111989 CAAATGGTGACGATGACTATCACT 58.888 41.667 3.83 0.00 42.00 3.41
2910 3174 4.036852 TGGTGACGATGACTATCACTGATC 59.963 45.833 0.00 0.00 42.00 2.92
2911 3175 4.541779 GTGACGATGACTATCACTGATCC 58.458 47.826 0.00 0.00 39.72 3.36
2912 3176 3.570125 TGACGATGACTATCACTGATCCC 59.430 47.826 0.00 0.00 32.67 3.85
2913 3177 3.566351 ACGATGACTATCACTGATCCCA 58.434 45.455 0.00 0.00 32.67 4.37
2978 3242 4.713946 TCCATCCTGTTGGAACGC 57.286 55.556 0.00 0.00 46.80 4.84
2991 3255 1.000385 TGGAACGCCTCAATTGCAAAG 60.000 47.619 1.71 0.00 34.31 2.77
2993 3257 2.319472 GAACGCCTCAATTGCAAAGTC 58.681 47.619 1.71 0.00 0.00 3.01
3082 3350 6.598457 GGTCTAGGCGAGTATTGTCAGATATA 59.402 42.308 0.00 0.00 0.00 0.86
3156 3430 1.672881 CGAAGATCAATCACTTGGGGC 59.327 52.381 0.00 0.00 32.95 5.80
3160 3434 0.038166 ATCAATCACTTGGGGCGTGT 59.962 50.000 0.00 0.00 34.14 4.49
3194 3468 1.945387 CTACAGTTCCTGCATCGCAT 58.055 50.000 0.00 0.00 38.13 4.73
3210 3484 2.037902 TCGCATACACTTCTCAACCCAA 59.962 45.455 0.00 0.00 0.00 4.12
3211 3485 3.009723 CGCATACACTTCTCAACCCAAT 58.990 45.455 0.00 0.00 0.00 3.16
3237 3511 2.238521 TGAGCAAAAACAGGCCCTAAG 58.761 47.619 0.00 0.00 0.00 2.18
3248 3522 1.522569 GCCCTAAGACGCCATCTGT 59.477 57.895 0.00 0.00 37.88 3.41
3263 3537 4.202111 GCCATCTGTAAGTTGTTTGGTTGT 60.202 41.667 0.00 0.00 31.74 3.32
3294 3568 7.016914 TCTAGTGTCCCTGCATTAGGTAATAT 58.983 38.462 0.00 0.00 45.80 1.28
3321 3595 1.405391 GCACTTTGTTTGGTTGCCTGT 60.405 47.619 0.00 0.00 0.00 4.00
3334 3608 1.682005 GCCTGTATTGGCCCAAGCA 60.682 57.895 1.16 2.82 46.82 3.91
3349 3623 0.819259 AAGCAGCACATGAACACGGT 60.819 50.000 0.00 0.00 0.00 4.83
3365 3639 0.109964 CGGTGTTTGGTTGCATACGG 60.110 55.000 0.00 0.00 0.00 4.02
3424 3701 2.487625 GCTTACCCACACCTACACCAAA 60.488 50.000 0.00 0.00 0.00 3.28
3426 3703 1.218844 ACCCACACCTACACCAAAGT 58.781 50.000 0.00 0.00 0.00 2.66
3431 3708 2.872245 CACACCTACACCAAAGTCACAG 59.128 50.000 0.00 0.00 0.00 3.66
3468 3745 2.787473 ACTGGGCGAAGATGATGAAA 57.213 45.000 0.00 0.00 0.00 2.69
3534 3811 1.488812 ACCTTGCCACTGTCAACACTA 59.511 47.619 0.00 0.00 0.00 2.74
3551 3828 1.078759 CTACTGCCTCCGTGCTTTCG 61.079 60.000 0.00 0.00 0.00 3.46
3572 3849 1.476891 CAGCCAGTCGGAGTAAGCTTA 59.523 52.381 0.86 0.86 0.00 3.09
3578 3855 4.142138 CCAGTCGGAGTAAGCTTATTCTGT 60.142 45.833 27.55 13.78 30.43 3.41
3579 3856 5.411781 CAGTCGGAGTAAGCTTATTCTGTT 58.588 41.667 27.55 18.45 30.43 3.16
3580 3857 5.289675 CAGTCGGAGTAAGCTTATTCTGTTG 59.710 44.000 27.55 23.23 30.43 3.33
3581 3858 4.033014 GTCGGAGTAAGCTTATTCTGTTGC 59.967 45.833 27.55 18.64 30.43 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 1.170919 GGAGGCGCTCCTACATACGA 61.171 60.000 7.64 0.00 46.41 3.43
158 160 4.593864 GTGAGGGATCCGCTCCGC 62.594 72.222 20.96 13.35 46.01 5.54
233 235 3.066190 CAGTACGGTCCGCCTCCA 61.066 66.667 12.28 0.00 0.00 3.86
255 257 2.223641 CGATCTGGTGATGGGCAAAATG 60.224 50.000 0.00 0.00 32.19 2.32
256 258 2.026641 CGATCTGGTGATGGGCAAAAT 58.973 47.619 0.00 0.00 32.19 1.82
260 262 0.977627 AGTCGATCTGGTGATGGGCA 60.978 55.000 0.00 0.00 35.82 5.36
313 315 2.804527 CCGATTCATCTGTAGCACATGG 59.195 50.000 0.00 0.00 0.00 3.66
314 316 3.461061 ACCGATTCATCTGTAGCACATG 58.539 45.455 0.00 0.00 0.00 3.21
315 317 3.827008 ACCGATTCATCTGTAGCACAT 57.173 42.857 0.00 0.00 0.00 3.21
316 318 3.521560 GAACCGATTCATCTGTAGCACA 58.478 45.455 0.00 0.00 34.70 4.57
317 319 2.866762 GGAACCGATTCATCTGTAGCAC 59.133 50.000 0.00 0.00 36.46 4.40
318 320 2.158957 GGGAACCGATTCATCTGTAGCA 60.159 50.000 0.00 0.00 40.86 3.49
334 336 0.392461 TTATCTGGCACTGCGGGAAC 60.392 55.000 0.00 0.00 0.00 3.62
335 337 0.326595 TTTATCTGGCACTGCGGGAA 59.673 50.000 0.00 0.00 0.00 3.97
336 338 0.392461 GTTTATCTGGCACTGCGGGA 60.392 55.000 0.00 0.00 0.00 5.14
338 340 0.729116 CTGTTTATCTGGCACTGCGG 59.271 55.000 0.00 0.00 0.00 5.69
339 341 0.729116 CCTGTTTATCTGGCACTGCG 59.271 55.000 0.00 0.00 0.00 5.18
340 342 1.098050 CCCTGTTTATCTGGCACTGC 58.902 55.000 0.00 0.00 34.39 4.40
341 343 1.098050 GCCCTGTTTATCTGGCACTG 58.902 55.000 0.00 0.00 34.39 3.66
342 344 0.995024 AGCCCTGTTTATCTGGCACT 59.005 50.000 1.86 0.00 34.39 4.40
343 345 1.340017 TGAGCCCTGTTTATCTGGCAC 60.340 52.381 1.86 0.00 34.39 5.01
344 346 0.991146 TGAGCCCTGTTTATCTGGCA 59.009 50.000 1.86 0.00 34.39 4.92
345 347 1.383523 GTGAGCCCTGTTTATCTGGC 58.616 55.000 0.00 0.00 34.39 4.85
363 365 1.089920 GATCATCTTGTTGGCAGCGT 58.910 50.000 0.00 0.00 0.00 5.07
365 367 3.129813 TGAATGATCATCTTGTTGGCAGC 59.870 43.478 9.06 0.00 0.00 5.25
416 418 0.031917 TACCTCGGGTAGATTGGGCA 60.032 55.000 0.00 0.00 37.09 5.36
496 498 0.967380 TTTCCGGACGGAGGGAGTAC 60.967 60.000 13.64 0.00 46.06 2.73
497 499 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
498 500 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
499 501 1.117150 TTATTTCCGGACGGAGGGAG 58.883 55.000 13.64 0.00 46.06 4.30
500 502 1.797320 ATTATTTCCGGACGGAGGGA 58.203 50.000 13.64 4.95 46.06 4.20
502 504 2.870411 GACAATTATTTCCGGACGGAGG 59.130 50.000 13.64 0.00 46.06 4.30
503 505 3.527533 TGACAATTATTTCCGGACGGAG 58.472 45.455 13.64 3.15 46.06 4.63
504 506 3.613494 TGACAATTATTTCCGGACGGA 57.387 42.857 1.83 9.76 43.52 4.69
505 507 3.874543 TGATGACAATTATTTCCGGACGG 59.125 43.478 1.83 3.96 0.00 4.79
506 508 5.478233 TTGATGACAATTATTTCCGGACG 57.522 39.130 1.83 0.00 0.00 4.79
507 509 7.222611 CCATTTTGATGACAATTATTTCCGGAC 59.777 37.037 1.83 0.00 35.85 4.79
508 510 7.123397 TCCATTTTGATGACAATTATTTCCGGA 59.877 33.333 0.00 0.00 35.85 5.14
510 512 7.758980 TGTCCATTTTGATGACAATTATTTCCG 59.241 33.333 0.00 0.00 35.85 4.30
511 513 9.434420 TTGTCCATTTTGATGACAATTATTTCC 57.566 29.630 0.00 0.00 35.85 3.13
518 520 8.961294 TTCTTTTTGTCCATTTTGATGACAAT 57.039 26.923 5.27 0.00 35.96 2.71
519 521 8.783833 TTTCTTTTTGTCCATTTTGATGACAA 57.216 26.923 0.00 0.00 34.47 3.18
520 522 8.828644 CATTTCTTTTTGTCCATTTTGATGACA 58.171 29.630 0.00 0.00 0.00 3.58
521 523 8.829612 ACATTTCTTTTTGTCCATTTTGATGAC 58.170 29.630 0.00 0.00 0.00 3.06
522 524 8.961294 ACATTTCTTTTTGTCCATTTTGATGA 57.039 26.923 0.00 0.00 0.00 2.92
556 558 9.206870 GTCATCAAAATGGACAAAAATGTATGT 57.793 29.630 0.00 0.00 33.42 2.29
557 559 9.205719 TGTCATCAAAATGGACAAAAATGTATG 57.794 29.630 0.00 0.00 33.42 2.39
558 560 9.775854 TTGTCATCAAAATGGACAAAAATGTAT 57.224 25.926 4.15 0.00 33.71 2.29
559 561 9.258826 CTTGTCATCAAAATGGACAAAAATGTA 57.741 29.630 7.70 0.00 34.98 2.29
560 562 7.769970 ACTTGTCATCAAAATGGACAAAAATGT 59.230 29.630 7.70 0.64 34.98 2.71
564 566 9.829507 AAATACTTGTCATCAAAATGGACAAAA 57.170 25.926 7.70 0.84 34.98 2.44
565 567 9.474920 GAAATACTTGTCATCAAAATGGACAAA 57.525 29.630 7.70 0.00 34.98 2.83
566 568 8.087750 GGAAATACTTGTCATCAAAATGGACAA 58.912 33.333 0.00 0.00 34.59 3.18
567 569 7.574779 CGGAAATACTTGTCATCAAAATGGACA 60.575 37.037 0.00 0.00 33.42 4.02
568 570 6.747280 CGGAAATACTTGTCATCAAAATGGAC 59.253 38.462 0.00 0.00 33.42 4.02
570 572 6.035843 CCGGAAATACTTGTCATCAAAATGG 58.964 40.000 0.00 0.00 33.42 3.16
573 575 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
574 576 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
575 577 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
576 578 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
577 579 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
578 580 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
579 581 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
580 582 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
582 584 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
584 586 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
585 587 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
587 589 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
588 590 0.682209 CTACTCCCTCCGTCCGGAAA 60.682 60.000 5.23 0.00 44.66 3.13
589 591 1.077212 CTACTCCCTCCGTCCGGAA 60.077 63.158 5.23 0.00 44.66 4.30
590 592 1.856539 AACTACTCCCTCCGTCCGGA 61.857 60.000 0.00 0.00 42.90 5.14
591 593 1.379576 AACTACTCCCTCCGTCCGG 60.380 63.158 0.00 0.00 0.00 5.14
592 594 1.664321 CCAACTACTCCCTCCGTCCG 61.664 65.000 0.00 0.00 0.00 4.79
594 596 0.971447 AGCCAACTACTCCCTCCGTC 60.971 60.000 0.00 0.00 0.00 4.79
596 598 0.745468 GTAGCCAACTACTCCCTCCG 59.255 60.000 0.00 0.00 44.61 4.63
714 718 7.087409 TGCAATTTGTATGATCAACTACTGG 57.913 36.000 0.00 0.00 0.00 4.00
715 719 7.216881 CGTTGCAATTTGTATGATCAACTACTG 59.783 37.037 0.59 0.00 32.59 2.74
790 803 9.905713 ATTTTGGTAGATAAGTTCAGCTCATTA 57.094 29.630 0.00 0.00 0.00 1.90
792 805 8.814038 AATTTTGGTAGATAAGTTCAGCTCAT 57.186 30.769 0.00 0.00 0.00 2.90
793 806 9.162764 GTAATTTTGGTAGATAAGTTCAGCTCA 57.837 33.333 0.00 0.00 0.00 4.26
929 977 4.728772 AGTTGATCACTGGGATTGAACAA 58.271 39.130 14.52 3.85 36.00 2.83
1021 1079 0.108662 CGTGATACACAGGCAGAGCA 60.109 55.000 0.00 0.00 33.40 4.26
1038 1096 2.478894 CCAAGAACGTAGAAATGTGCGT 59.521 45.455 0.00 0.00 40.76 5.24
1113 1171 6.711277 TGCTATATCGATATTTTGGCCTTCT 58.289 36.000 22.37 0.00 0.00 2.85
1270 1524 3.331889 ACTTCTTCAATCCCTGGTGTGAT 59.668 43.478 0.00 0.00 0.00 3.06
1333 1588 0.889306 AGTAGAGCTGAACACGGGAC 59.111 55.000 0.00 0.00 0.00 4.46
2112 2368 5.716228 TGCCAGTCAAATTAAATGTCTCCAT 59.284 36.000 0.00 0.00 0.00 3.41
2236 2494 2.027377 CACCTTCTTGAGCCTCTCATGT 60.027 50.000 8.81 0.00 40.39 3.21
2288 2546 7.437748 AGGATATGACATGTTAGCTCAACTAC 58.562 38.462 0.00 0.00 38.05 2.73
2368 2626 0.034337 TAACAGACTGACCAACCGCC 59.966 55.000 10.08 0.00 0.00 6.13
2378 2642 2.417719 GGCAGAACACCTAACAGACTG 58.582 52.381 0.00 0.00 0.00 3.51
2462 2726 2.101582 GGATGTATCTCTTGACGGCACT 59.898 50.000 0.00 0.00 0.00 4.40
2571 2835 5.350365 ACAACGTCGCAAATCTACATATTGT 59.650 36.000 0.00 0.00 0.00 2.71
2618 2882 1.802960 AGCAGAGAACAACAATGAGCG 59.197 47.619 0.00 0.00 0.00 5.03
2620 2884 3.562973 ACACAGCAGAGAACAACAATGAG 59.437 43.478 0.00 0.00 0.00 2.90
2648 2912 3.055819 ACCTACACAGTGAACAGCTATGG 60.056 47.826 7.81 0.00 0.00 2.74
2704 2968 7.068226 ACAAGCATAGAAAAACTGGTAACTTGT 59.932 33.333 0.00 0.00 38.32 3.16
2727 2991 3.068560 GTGACGCCAATAAGGTACACAA 58.931 45.455 0.00 0.00 40.61 3.33
2732 2996 4.463539 TGTTCTAGTGACGCCAATAAGGTA 59.536 41.667 0.00 0.00 40.61 3.08
2776 3040 3.964031 AGTCTTAGCTCTAATCCAGGTGG 59.036 47.826 0.00 0.00 0.00 4.61
2866 3130 5.885912 ACCATTTGCGTTGATAAAGATAGGT 59.114 36.000 0.00 0.00 0.00 3.08
2941 3205 4.248908 TGGAACAGATGGGGAGCA 57.751 55.556 0.00 0.00 0.00 4.26
2978 3242 2.818432 AGCTGAGACTTTGCAATTGAGG 59.182 45.455 10.34 0.00 0.00 3.86
2991 3255 1.205655 TGTATGCCAGTGAGCTGAGAC 59.794 52.381 0.00 0.00 45.28 3.36
2993 3257 2.277969 CTTGTATGCCAGTGAGCTGAG 58.722 52.381 0.00 0.00 45.28 3.35
3030 3298 2.030958 GCAATTGCTTGGTGCCTGC 61.031 57.895 23.21 0.00 42.00 4.85
3045 3313 2.436417 GCCTAGACCAAATCACAGCAA 58.564 47.619 0.00 0.00 0.00 3.91
3082 3350 2.525368 GCCTTTTCCACACCCTACATT 58.475 47.619 0.00 0.00 0.00 2.71
3156 3430 1.747686 GCAAACGGCAACCAAACACG 61.748 55.000 0.00 0.00 43.97 4.49
3194 3468 3.650942 ACCAGATTGGGTTGAGAAGTGTA 59.349 43.478 0.00 0.00 43.37 2.90
3210 3484 2.036346 GCCTGTTTTTGCTCAACCAGAT 59.964 45.455 0.00 0.00 0.00 2.90
3211 3485 1.408702 GCCTGTTTTTGCTCAACCAGA 59.591 47.619 0.00 0.00 0.00 3.86
3237 3511 3.364964 CCAAACAACTTACAGATGGCGTC 60.365 47.826 0.00 0.00 0.00 5.19
3245 3519 4.142491 TGCAGACAACCAAACAACTTACAG 60.142 41.667 0.00 0.00 0.00 2.74
3248 3522 4.887071 AGATGCAGACAACCAAACAACTTA 59.113 37.500 0.00 0.00 0.00 2.24
3263 3537 0.826715 GCAGGGACACTAGATGCAGA 59.173 55.000 0.00 0.00 36.88 4.26
3301 3575 1.289276 CAGGCAACCAAACAAAGTGC 58.711 50.000 0.00 0.00 37.17 4.40
3304 3578 4.057432 CCAATACAGGCAACCAAACAAAG 58.943 43.478 0.00 0.00 37.17 2.77
3321 3595 0.324552 ATGTGCTGCTTGGGCCAATA 60.325 50.000 21.25 11.19 37.74 1.90
3334 3608 1.065401 CAAACACCGTGTTCATGTGCT 59.935 47.619 17.11 0.00 40.14 4.40
3349 3623 1.167155 ACGCCGTATGCAACCAAACA 61.167 50.000 0.00 0.00 41.33 2.83
3365 3639 3.824414 AGGTAAGCAAAACATGTACGC 57.176 42.857 0.00 1.99 0.00 4.42
3374 3648 5.571791 ACTAGGGTACAAGGTAAGCAAAA 57.428 39.130 0.00 0.00 0.00 2.44
3376 3650 4.263156 CCAACTAGGGTACAAGGTAAGCAA 60.263 45.833 0.00 0.00 0.00 3.91
3424 3701 0.670162 GCCATTGTTGTGCTGTGACT 59.330 50.000 0.00 0.00 0.00 3.41
3426 3703 0.817229 TCGCCATTGTTGTGCTGTGA 60.817 50.000 0.00 0.00 0.00 3.58
3431 3708 1.068333 AGTTCATCGCCATTGTTGTGC 60.068 47.619 0.00 0.00 0.00 4.57
3468 3745 2.560105 GTTTGGGCTGAAGCTGAAGAAT 59.440 45.455 1.74 0.00 41.70 2.40
3534 3811 2.357517 CGAAAGCACGGAGGCAGT 60.358 61.111 0.00 0.00 35.83 4.40
3551 3828 1.811679 GCTTACTCCGACTGGCTGC 60.812 63.158 0.00 0.00 34.14 5.25
3555 3832 4.142138 ACAGAATAAGCTTACTCCGACTGG 60.142 45.833 11.17 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.