Multiple sequence alignment - TraesCS7A01G413800

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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 TraesCS7A01G413800 chr7A 100.000 2985 0 0 1 2985 604398288 604395304 0.000000e+00 5513
1 TraesCS7A01G413800 chr7A 85.178 506 67 6 3 502 695812838 695813341 2.050000e-141 512
2 TraesCS7A01G413800 chr7B 89.831 2311 154 27 710 2985 560533020 560530756 0.000000e+00 2891
3 TraesCS7A01G413800 chr7B 88.845 511 46 8 1 500 560558260 560558770 4.230000e-173 617
4 TraesCS7A01G413800 chr7D 90.296 2226 131 38 560 2744 524326767 524324586 0.000000e+00 2835
5 TraesCS7A01G413800 chr7D 92.614 176 6 3 2781 2952 524324612 524324440 2.300000e-61 246
6 TraesCS7A01G413800 chrUn 89.526 506 31 9 1 500 62218550 62218061 3.270000e-174 621
7 TraesCS7A01G413800 chr6D 86.588 507 61 2 1 501 428651512 428651007 1.210000e-153 553
8 TraesCS7A01G413800 chr6D 79.268 410 65 9 2108 2514 409770996 409770604 4.900000e-68 268
9 TraesCS7A01G413800 chr6B 91.123 383 31 3 118 500 708300260 708300639 1.590000e-142 516
10 TraesCS7A01G413800 chr5A 85.400 500 66 4 9 501 645486266 645486765 2.050000e-141 512
11 TraesCS7A01G413800 chr2A 84.221 507 68 7 1 499 726851308 726851810 1.610000e-132 483
12 TraesCS7A01G413800 chr3D 83.301 509 74 6 1 500 288555749 288555243 2.710000e-125 459
13 TraesCS7A01G413800 chr2D 86.650 397 49 4 103 498 159598172 159598565 1.270000e-118 436


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 TraesCS7A01G413800 chr7A 604395304 604398288 2984 True 5513.0 5513 100.000 1 2985 1 chr7A.!!$R1 2984
1 TraesCS7A01G413800 chr7A 695812838 695813341 503 False 512.0 512 85.178 3 502 1 chr7A.!!$F1 499
2 TraesCS7A01G413800 chr7B 560530756 560533020 2264 True 2891.0 2891 89.831 710 2985 1 chr7B.!!$R1 2275
3 TraesCS7A01G413800 chr7B 560558260 560558770 510 False 617.0 617 88.845 1 500 1 chr7B.!!$F1 499
4 TraesCS7A01G413800 chr7D 524324440 524326767 2327 True 1540.5 2835 91.455 560 2952 2 chr7D.!!$R1 2392
5 TraesCS7A01G413800 chr6D 428651007 428651512 505 True 553.0 553 86.588 1 501 1 chr6D.!!$R2 500
6 TraesCS7A01G413800 chr2A 726851308 726851810 502 False 483.0 483 84.221 1 499 1 chr2A.!!$F1 498
7 TraesCS7A01G413800 chr3D 288555243 288555749 506 True 459.0 459 83.301 1 500 1 chr3D.!!$R1 499

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
635 648 0.249784 CTCCATCGCTAGCTGTGCAT 60.250 55.0 13.93 4.3 0.0 3.96 F
1122 1157 0.584876 CCAAGAAACCCACGTCGTTC 59.415 55.0 0.00 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1437 1475 0.465278 TGCCAGCACTAGTTTGCACA 60.465 50.000 7.95 1.03 45.62 4.57 R
2616 2695 1.266989 CTTTTCCCTTGTCAGTTCCGC 59.733 52.381 0.00 0.00 0.00 5.54 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
68 75 2.093537 GAGCATGGGGAGCCGTAGAG 62.094 65.000 0.00 0.00 0.00 2.43
86 93 6.127338 CCGTAGAGCATGATGGGAGAATTATA 60.127 42.308 0.00 0.00 0.00 0.98
166 174 1.041447 TGCCTAGAAGGACTACGGGC 61.041 60.000 0.00 0.00 40.58 6.13
244 252 3.417330 AGGCACTTGACCCCTCATA 57.583 52.632 0.00 0.00 27.25 2.15
275 283 2.844946 TCGGAAATCAGAGTGTTTGCA 58.155 42.857 0.00 0.00 0.00 4.08
289 297 3.037549 TGTTTGCAAAGGAATTCCAGGT 58.962 40.909 26.22 8.33 38.89 4.00
322 330 7.415206 GCAAGGAAACAGAGAAGTTAAAGTTCA 60.415 37.037 0.00 0.00 30.04 3.18
323 331 7.555306 AGGAAACAGAGAAGTTAAAGTTCAC 57.445 36.000 0.00 0.00 30.04 3.18
363 375 7.862675 AGTCAATAGTTTAGCCCATAGTCTTT 58.137 34.615 0.00 0.00 0.00 2.52
364 376 7.770897 AGTCAATAGTTTAGCCCATAGTCTTTG 59.229 37.037 0.00 0.00 0.00 2.77
368 380 3.730215 TTAGCCCATAGTCTTTGCCAA 57.270 42.857 0.00 0.00 0.00 4.52
372 384 4.609301 AGCCCATAGTCTTTGCCAATTTA 58.391 39.130 0.00 0.00 0.00 1.40
421 434 3.726790 TGTAAGGGACATAGCCAACCTA 58.273 45.455 0.00 0.00 31.20 3.08
521 534 8.697507 AAAAATGTCATTCTAGGACTTGAACT 57.302 30.769 0.00 0.00 36.26 3.01
522 535 9.793259 AAAAATGTCATTCTAGGACTTGAACTA 57.207 29.630 0.00 0.00 36.26 2.24
523 536 9.965902 AAAATGTCATTCTAGGACTTGAACTAT 57.034 29.630 0.00 0.00 36.26 2.12
524 537 9.606631 AAATGTCATTCTAGGACTTGAACTATC 57.393 33.333 0.00 0.00 36.26 2.08
525 538 7.718334 TGTCATTCTAGGACTTGAACTATCA 57.282 36.000 0.00 0.00 36.26 2.15
526 539 8.311395 TGTCATTCTAGGACTTGAACTATCAT 57.689 34.615 0.00 0.00 36.26 2.45
527 540 8.200120 TGTCATTCTAGGACTTGAACTATCATG 58.800 37.037 0.00 0.00 36.26 3.07
528 541 7.655328 GTCATTCTAGGACTTGAACTATCATGG 59.345 40.741 0.00 0.00 35.57 3.66
529 542 6.485830 TTCTAGGACTTGAACTATCATGGG 57.514 41.667 0.00 0.00 35.57 4.00
530 543 3.567478 AGGACTTGAACTATCATGGGC 57.433 47.619 0.00 0.00 35.57 5.36
531 544 3.118531 AGGACTTGAACTATCATGGGCT 58.881 45.455 0.00 0.00 35.57 5.19
532 545 4.298626 AGGACTTGAACTATCATGGGCTA 58.701 43.478 0.00 0.00 35.57 3.93
533 546 4.721776 AGGACTTGAACTATCATGGGCTAA 59.278 41.667 0.00 0.00 35.57 3.09
534 547 5.370880 AGGACTTGAACTATCATGGGCTAAT 59.629 40.000 0.00 0.00 35.57 1.73
535 548 6.064717 GGACTTGAACTATCATGGGCTAATT 58.935 40.000 0.00 0.00 35.57 1.40
536 549 6.205658 GGACTTGAACTATCATGGGCTAATTC 59.794 42.308 0.00 0.00 35.57 2.17
537 550 6.064717 ACTTGAACTATCATGGGCTAATTCC 58.935 40.000 0.00 0.00 35.57 3.01
538 551 5.645056 TGAACTATCATGGGCTAATTCCA 57.355 39.130 0.00 0.00 38.82 3.53
539 552 5.376625 TGAACTATCATGGGCTAATTCCAC 58.623 41.667 0.00 0.00 37.08 4.02
540 553 4.373156 ACTATCATGGGCTAATTCCACC 57.627 45.455 0.00 0.00 37.08 4.61
541 554 3.721575 ACTATCATGGGCTAATTCCACCA 59.278 43.478 0.00 0.00 37.08 4.17
542 555 2.435372 TCATGGGCTAATTCCACCAC 57.565 50.000 0.00 0.00 37.08 4.16
543 556 1.638070 TCATGGGCTAATTCCACCACA 59.362 47.619 0.00 0.00 37.08 4.17
544 557 2.042297 TCATGGGCTAATTCCACCACAA 59.958 45.455 0.00 0.00 37.08 3.33
545 558 2.685106 TGGGCTAATTCCACCACAAA 57.315 45.000 0.00 0.00 0.00 2.83
546 559 3.182887 TGGGCTAATTCCACCACAAAT 57.817 42.857 0.00 0.00 0.00 2.32
547 560 4.323569 TGGGCTAATTCCACCACAAATA 57.676 40.909 0.00 0.00 0.00 1.40
548 561 4.678256 TGGGCTAATTCCACCACAAATAA 58.322 39.130 0.00 0.00 0.00 1.40
549 562 4.464597 TGGGCTAATTCCACCACAAATAAC 59.535 41.667 0.00 0.00 0.00 1.89
550 563 4.142026 GGGCTAATTCCACCACAAATAACC 60.142 45.833 0.00 0.00 0.00 2.85
551 564 4.464597 GGCTAATTCCACCACAAATAACCA 59.535 41.667 0.00 0.00 0.00 3.67
552 565 5.128663 GGCTAATTCCACCACAAATAACCAT 59.871 40.000 0.00 0.00 0.00 3.55
553 566 6.042143 GCTAATTCCACCACAAATAACCATG 58.958 40.000 0.00 0.00 0.00 3.66
554 567 6.350949 GCTAATTCCACCACAAATAACCATGT 60.351 38.462 0.00 0.00 0.00 3.21
555 568 4.862902 TTCCACCACAAATAACCATGTG 57.137 40.909 0.00 0.00 45.06 3.21
566 579 0.537188 AACCATGTGAGCTACCCTCG 59.463 55.000 0.00 0.00 43.82 4.63
584 597 3.057806 CCTCGGTTCCCAATGTTTAACAC 60.058 47.826 0.00 0.00 0.00 3.32
589 602 4.261867 GGTTCCCAATGTTTAACACTGTCC 60.262 45.833 5.82 0.05 0.00 4.02
590 603 4.447138 TCCCAATGTTTAACACTGTCCT 57.553 40.909 5.82 0.00 0.00 3.85
591 604 4.798882 TCCCAATGTTTAACACTGTCCTT 58.201 39.130 5.82 0.00 0.00 3.36
626 639 3.606662 GCTCCGCCTCCATCGCTA 61.607 66.667 0.00 0.00 0.00 4.26
627 640 2.647875 CTCCGCCTCCATCGCTAG 59.352 66.667 0.00 0.00 0.00 3.42
628 641 3.565910 CTCCGCCTCCATCGCTAGC 62.566 68.421 4.06 4.06 0.00 3.42
629 642 3.610669 CCGCCTCCATCGCTAGCT 61.611 66.667 13.93 0.00 0.00 3.32
635 648 0.249784 CTCCATCGCTAGCTGTGCAT 60.250 55.000 13.93 4.30 0.00 3.96
637 650 0.812811 CCATCGCTAGCTGTGCATGT 60.813 55.000 13.93 0.00 0.00 3.21
652 665 3.998911 ATGTGCCGATGTGCGCGTA 62.999 57.895 8.43 0.00 44.60 4.42
703 716 3.715097 GGAGGCAGCTGCTGTCCT 61.715 66.667 34.96 31.71 36.67 3.85
708 721 4.340246 CAGCTGCTGTCCTGGCCA 62.340 66.667 21.21 4.71 0.00 5.36
806 822 2.731571 GCGTCTCCCTGCCCATACA 61.732 63.158 0.00 0.00 0.00 2.29
848 867 3.938112 GTCTGTGGCTGTGACGAC 58.062 61.111 0.00 0.00 0.00 4.34
865 884 2.196382 GACCGCGGCGAGATATAGCA 62.196 60.000 28.58 0.00 34.54 3.49
898 921 0.620556 ACGCACTTCCATCCCATTCT 59.379 50.000 0.00 0.00 0.00 2.40
917 947 4.422073 TCTACCATCTCATTCCGCATTT 57.578 40.909 0.00 0.00 0.00 2.32
925 955 3.001228 TCTCATTCCGCATTTCGATTTCG 59.999 43.478 0.00 0.00 41.67 3.46
979 1011 3.423154 CCGGTGAACCAAGCGCTC 61.423 66.667 12.06 0.00 39.65 5.03
980 1012 2.357517 CGGTGAACCAAGCGCTCT 60.358 61.111 12.06 0.00 33.92 4.09
981 1013 2.383527 CGGTGAACCAAGCGCTCTC 61.384 63.158 12.06 6.08 33.92 3.20
982 1014 1.004440 GGTGAACCAAGCGCTCTCT 60.004 57.895 12.06 0.00 35.64 3.10
983 1015 0.603975 GGTGAACCAAGCGCTCTCTT 60.604 55.000 12.06 0.96 35.64 2.85
1101 1136 1.153489 CACGCTGCTGCATCCTACT 60.153 57.895 16.29 0.00 39.64 2.57
1114 1149 1.440618 TCCTACTGCCAAGAAACCCA 58.559 50.000 0.00 0.00 0.00 4.51
1116 1151 1.156736 CTACTGCCAAGAAACCCACG 58.843 55.000 0.00 0.00 0.00 4.94
1121 1156 1.441732 GCCAAGAAACCCACGTCGTT 61.442 55.000 0.00 0.00 0.00 3.85
1122 1157 0.584876 CCAAGAAACCCACGTCGTTC 59.415 55.000 0.00 0.00 0.00 3.95
1158 1193 0.737715 CGAGTAGCACAAGCCAGGAC 60.738 60.000 0.00 0.00 43.56 3.85
1159 1194 0.737715 GAGTAGCACAAGCCAGGACG 60.738 60.000 0.00 0.00 43.56 4.79
1160 1195 1.741770 GTAGCACAAGCCAGGACGG 60.742 63.158 0.00 0.00 43.56 4.79
1161 1196 2.214216 TAGCACAAGCCAGGACGGT 61.214 57.895 0.00 0.00 43.56 4.83
1162 1197 2.167398 TAGCACAAGCCAGGACGGTC 62.167 60.000 0.00 0.00 43.56 4.79
1163 1198 2.358737 CACAAGCCAGGACGGTCC 60.359 66.667 19.61 19.61 36.97 4.46
1254 1289 4.851214 GCCGGCTCCTCCTCCTCT 62.851 72.222 22.15 0.00 0.00 3.69
1409 1447 1.869767 GGCTCGATCGATCAGCAAAAT 59.130 47.619 31.97 1.28 34.69 1.82
1410 1448 2.289002 GGCTCGATCGATCAGCAAAATT 59.711 45.455 31.97 0.60 34.69 1.82
1431 1469 3.821421 AGCCATGCCTTGTACTAGTAC 57.179 47.619 23.58 23.58 36.63 2.73
1433 1471 3.133003 AGCCATGCCTTGTACTAGTACTG 59.867 47.826 28.56 21.26 37.00 2.74
1437 1475 5.303078 CCATGCCTTGTACTAGTACTGATCT 59.697 44.000 28.56 10.52 37.00 2.75
1438 1476 5.836821 TGCCTTGTACTAGTACTGATCTG 57.163 43.478 28.56 14.67 37.00 2.90
1447 1496 6.835819 ACTAGTACTGATCTGTGCAAACTA 57.164 37.500 19.90 14.93 0.00 2.24
1453 1513 3.069289 TGATCTGTGCAAACTAGTGCTG 58.931 45.455 0.00 0.00 45.17 4.41
1641 1702 0.601558 TGCTCCTACCAGAACACGAC 59.398 55.000 0.00 0.00 0.00 4.34
1651 1712 5.401531 ACCAGAACACGACACTTACATAT 57.598 39.130 0.00 0.00 0.00 1.78
1653 1714 7.108841 ACCAGAACACGACACTTACATATAT 57.891 36.000 0.00 0.00 0.00 0.86
1655 1716 8.857098 ACCAGAACACGACACTTACATATATAT 58.143 33.333 0.00 0.00 0.00 0.86
1682 1750 5.766222 ACTGTTTGACTGCAATTTCATCTC 58.234 37.500 0.00 0.00 33.25 2.75
1703 1771 6.877236 TCTCATTTCTATCACTGTATGTGCA 58.123 36.000 0.00 0.00 45.81 4.57
1747 1815 3.173240 GAAGAGCGCGGTCGACAC 61.173 66.667 30.16 18.90 38.10 3.67
1757 1825 0.314302 CGGTCGACACCTTCAACTCT 59.686 55.000 18.91 0.00 41.17 3.24
1839 1908 5.711976 CACTGGAAGAATTAGGAAATGGTGT 59.288 40.000 0.00 0.00 37.43 4.16
1840 1909 5.946377 ACTGGAAGAATTAGGAAATGGTGTC 59.054 40.000 0.00 0.00 37.43 3.67
1841 1910 5.261216 TGGAAGAATTAGGAAATGGTGTCC 58.739 41.667 0.00 0.00 35.17 4.02
1842 1911 6.804935 CTGGAAGAATTAGGAAATGGTGTCCT 60.805 42.308 0.00 0.00 42.52 3.85
1843 1912 5.590663 GGAAGAATTAGGAAATGGTGTCCTC 59.409 44.000 0.00 0.00 42.02 3.71
1844 1913 5.779241 AGAATTAGGAAATGGTGTCCTCA 57.221 39.130 0.00 0.00 42.02 3.86
1845 1914 6.139679 AGAATTAGGAAATGGTGTCCTCAA 57.860 37.500 0.00 0.00 42.02 3.02
1846 1915 5.946377 AGAATTAGGAAATGGTGTCCTCAAC 59.054 40.000 0.00 0.00 42.02 3.18
2096 2172 1.878088 CTCCATGCCACTGATACATGC 59.122 52.381 0.00 0.00 39.86 4.06
2218 2296 3.061006 CGTGTCAAGAAATTGTTTGCAGC 60.061 43.478 0.00 0.00 0.00 5.25
2318 2397 1.766143 GCACCGAGATTCCGATGTGC 61.766 60.000 0.00 0.00 39.25 4.57
2320 2399 1.143838 CCGAGATTCCGATGTGCCA 59.856 57.895 0.00 0.00 0.00 4.92
2386 2465 4.401022 AGCCATCACAAATCAAACTCTCA 58.599 39.130 0.00 0.00 0.00 3.27
2388 2467 4.217118 GCCATCACAAATCAAACTCTCACT 59.783 41.667 0.00 0.00 0.00 3.41
2477 2556 4.624024 CCAGCAAATTTAACATCACAGCTG 59.376 41.667 13.48 13.48 44.65 4.24
2616 2695 7.348080 TCCCATACTCTACATTACAAGACAG 57.652 40.000 0.00 0.00 0.00 3.51
2727 2806 5.747675 CAGACACAGCATGAGACATTAGTAG 59.252 44.000 0.00 0.00 39.69 2.57
2784 2863 3.618507 GCACAAGACTAGCCAGACAAGAT 60.619 47.826 0.00 0.00 0.00 2.40
2923 3002 1.066929 ACACATCGAGCATGCACAGTA 60.067 47.619 21.98 2.22 35.65 2.74
2976 3059 9.434420 CCTTTTCTTCTCCTGCTAATAGATATG 57.566 37.037 0.00 0.00 0.00 1.78
2977 3060 9.434420 CTTTTCTTCTCCTGCTAATAGATATGG 57.566 37.037 0.00 0.00 0.00 2.74
2981 3064 4.158579 TCTCCTGCTAATAGATATGGCACG 59.841 45.833 0.00 0.00 0.00 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 2.072487 GGCTCCCCATGCTCCACTA 61.072 63.158 0.00 0.00 0.00 2.74
68 75 6.183360 CCGACAATATAATTCTCCCATCATGC 60.183 42.308 0.00 0.00 0.00 4.06
86 93 0.907704 TGTAGTCCCAGGCCGACAAT 60.908 55.000 11.28 0.00 32.41 2.71
149 157 1.033574 CTGCCCGTAGTCCTTCTAGG 58.966 60.000 0.00 0.00 36.46 3.02
166 174 3.190849 CTGTGCCCGACATCGCTG 61.191 66.667 0.00 0.00 38.18 5.18
244 252 3.889538 TCTGATTTCCGATCTATCCACGT 59.110 43.478 0.00 0.00 0.00 4.49
275 283 3.766051 GCTTGATGACCTGGAATTCCTTT 59.234 43.478 24.73 9.23 36.82 3.11
289 297 4.356405 TCTCTGTTTCCTTGCTTGATGA 57.644 40.909 0.00 0.00 0.00 2.92
368 380 3.887621 TGCAACTCTCTACGCCTAAAT 57.112 42.857 0.00 0.00 0.00 1.40
372 384 0.176680 CCATGCAACTCTCTACGCCT 59.823 55.000 0.00 0.00 0.00 5.52
411 424 1.337447 GCTCAACACGTAGGTTGGCTA 60.337 52.381 16.14 0.22 46.29 3.93
412 425 0.602905 GCTCAACACGTAGGTTGGCT 60.603 55.000 16.14 0.00 46.29 4.75
421 434 3.750373 AAGGCCACGCTCAACACGT 62.750 57.895 5.01 0.00 46.42 4.49
502 515 7.655328 CCATGATAGTTCAAGTCCTAGAATGAC 59.345 40.741 0.00 0.00 34.96 3.06
503 516 7.202038 CCCATGATAGTTCAAGTCCTAGAATGA 60.202 40.741 0.00 0.00 34.96 2.57
504 517 6.933521 CCCATGATAGTTCAAGTCCTAGAATG 59.066 42.308 0.00 0.00 34.96 2.67
505 518 6.465035 GCCCATGATAGTTCAAGTCCTAGAAT 60.465 42.308 0.00 0.00 34.96 2.40
506 519 5.163301 GCCCATGATAGTTCAAGTCCTAGAA 60.163 44.000 0.00 0.00 34.96 2.10
507 520 4.345257 GCCCATGATAGTTCAAGTCCTAGA 59.655 45.833 0.00 0.00 34.96 2.43
508 521 4.346418 AGCCCATGATAGTTCAAGTCCTAG 59.654 45.833 0.00 0.00 34.96 3.02
509 522 4.298626 AGCCCATGATAGTTCAAGTCCTA 58.701 43.478 0.00 0.00 34.96 2.94
510 523 3.118531 AGCCCATGATAGTTCAAGTCCT 58.881 45.455 0.00 0.00 34.96 3.85
511 524 3.567478 AGCCCATGATAGTTCAAGTCC 57.433 47.619 0.00 0.00 34.96 3.85
512 525 6.205658 GGAATTAGCCCATGATAGTTCAAGTC 59.794 42.308 0.00 0.00 32.54 3.01
513 526 6.064717 GGAATTAGCCCATGATAGTTCAAGT 58.935 40.000 0.00 0.00 32.54 3.16
514 527 6.016777 GTGGAATTAGCCCATGATAGTTCAAG 60.017 42.308 0.00 0.00 32.54 3.02
515 528 5.827797 GTGGAATTAGCCCATGATAGTTCAA 59.172 40.000 0.00 0.00 32.54 2.69
516 529 5.376625 GTGGAATTAGCCCATGATAGTTCA 58.623 41.667 0.00 0.00 32.54 3.18
517 530 4.762251 GGTGGAATTAGCCCATGATAGTTC 59.238 45.833 0.00 0.00 35.91 3.01
518 531 4.167892 TGGTGGAATTAGCCCATGATAGTT 59.832 41.667 0.00 0.00 35.91 2.24
519 532 3.721575 TGGTGGAATTAGCCCATGATAGT 59.278 43.478 0.00 0.00 35.91 2.12
520 533 4.074970 GTGGTGGAATTAGCCCATGATAG 58.925 47.826 0.00 0.00 35.91 2.08
521 534 3.461458 TGTGGTGGAATTAGCCCATGATA 59.539 43.478 0.00 0.00 35.91 2.15
522 535 2.244510 TGTGGTGGAATTAGCCCATGAT 59.755 45.455 0.00 0.00 35.91 2.45
523 536 1.638070 TGTGGTGGAATTAGCCCATGA 59.362 47.619 0.00 0.00 35.91 3.07
524 537 2.142356 TGTGGTGGAATTAGCCCATG 57.858 50.000 0.00 0.00 35.91 3.66
525 538 2.917713 TTGTGGTGGAATTAGCCCAT 57.082 45.000 0.00 0.00 35.91 4.00
526 539 2.685106 TTTGTGGTGGAATTAGCCCA 57.315 45.000 0.00 0.00 0.00 5.36
527 540 4.142026 GGTTATTTGTGGTGGAATTAGCCC 60.142 45.833 0.00 0.00 0.00 5.19
528 541 4.464597 TGGTTATTTGTGGTGGAATTAGCC 59.535 41.667 0.00 0.00 0.00 3.93
529 542 5.652994 TGGTTATTTGTGGTGGAATTAGC 57.347 39.130 0.00 0.00 0.00 3.09
530 543 7.035004 CACATGGTTATTTGTGGTGGAATTAG 58.965 38.462 0.00 0.00 39.61 1.73
531 544 6.721668 TCACATGGTTATTTGTGGTGGAATTA 59.278 34.615 0.00 0.00 42.72 1.40
532 545 5.541868 TCACATGGTTATTTGTGGTGGAATT 59.458 36.000 0.00 0.00 42.72 2.17
533 546 5.083122 TCACATGGTTATTTGTGGTGGAAT 58.917 37.500 0.00 0.00 42.72 3.01
534 547 4.474394 TCACATGGTTATTTGTGGTGGAA 58.526 39.130 0.00 0.00 42.72 3.53
535 548 4.078537 CTCACATGGTTATTTGTGGTGGA 58.921 43.478 0.00 0.00 42.72 4.02
536 549 3.367292 GCTCACATGGTTATTTGTGGTGG 60.367 47.826 0.00 0.00 42.72 4.61
537 550 3.507233 AGCTCACATGGTTATTTGTGGTG 59.493 43.478 0.00 0.00 42.72 4.17
538 551 3.766545 AGCTCACATGGTTATTTGTGGT 58.233 40.909 0.00 0.00 42.72 4.16
539 552 4.096382 GGTAGCTCACATGGTTATTTGTGG 59.904 45.833 0.00 0.00 42.72 4.17
540 553 4.096382 GGGTAGCTCACATGGTTATTTGTG 59.904 45.833 0.00 0.00 43.61 3.33
541 554 4.018415 AGGGTAGCTCACATGGTTATTTGT 60.018 41.667 0.00 0.00 0.00 2.83
542 555 4.526970 AGGGTAGCTCACATGGTTATTTG 58.473 43.478 0.00 0.00 0.00 2.32
543 556 4.683400 CGAGGGTAGCTCACATGGTTATTT 60.683 45.833 0.00 0.00 0.00 1.40
544 557 3.181465 CGAGGGTAGCTCACATGGTTATT 60.181 47.826 0.00 0.00 0.00 1.40
545 558 2.365617 CGAGGGTAGCTCACATGGTTAT 59.634 50.000 0.00 0.00 0.00 1.89
546 559 1.754803 CGAGGGTAGCTCACATGGTTA 59.245 52.381 0.00 0.00 0.00 2.85
547 560 0.537188 CGAGGGTAGCTCACATGGTT 59.463 55.000 0.00 0.00 0.00 3.67
548 561 1.330655 CCGAGGGTAGCTCACATGGT 61.331 60.000 0.00 0.00 0.00 3.55
549 562 1.330655 ACCGAGGGTAGCTCACATGG 61.331 60.000 0.00 0.00 32.11 3.66
550 563 0.537188 AACCGAGGGTAGCTCACATG 59.463 55.000 0.00 0.00 33.12 3.21
551 564 0.824759 GAACCGAGGGTAGCTCACAT 59.175 55.000 0.00 0.00 33.12 3.21
552 565 1.255667 GGAACCGAGGGTAGCTCACA 61.256 60.000 0.00 0.00 33.12 3.58
553 566 1.516423 GGAACCGAGGGTAGCTCAC 59.484 63.158 0.00 0.00 33.12 3.51
554 567 1.684734 GGGAACCGAGGGTAGCTCA 60.685 63.158 0.00 0.00 40.86 4.26
555 568 3.218227 GGGAACCGAGGGTAGCTC 58.782 66.667 0.00 0.00 40.86 4.09
584 597 3.443037 CAGCAGATACGAAGAAGGACAG 58.557 50.000 0.00 0.00 0.00 3.51
618 631 0.812811 ACATGCACAGCTAGCGATGG 60.813 55.000 19.08 9.54 33.85 3.51
619 632 0.303796 CACATGCACAGCTAGCGATG 59.696 55.000 9.55 12.71 33.85 3.84
620 633 1.434622 GCACATGCACAGCTAGCGAT 61.435 55.000 9.55 0.00 41.59 4.58
621 634 2.102438 GCACATGCACAGCTAGCGA 61.102 57.895 9.55 0.00 41.59 4.93
622 635 2.402388 GCACATGCACAGCTAGCG 59.598 61.111 9.55 7.05 41.59 4.26
623 636 2.796651 GGCACATGCACAGCTAGC 59.203 61.111 6.62 6.62 44.36 3.42
624 637 0.812811 ATCGGCACATGCACAGCTAG 60.813 55.000 6.15 0.00 44.36 3.42
625 638 1.091197 CATCGGCACATGCACAGCTA 61.091 55.000 6.15 0.00 44.36 3.32
626 639 2.045634 ATCGGCACATGCACAGCT 60.046 55.556 6.15 0.00 44.36 4.24
627 640 2.101575 CATCGGCACATGCACAGC 59.898 61.111 6.15 0.00 44.36 4.40
628 641 1.135939 CACATCGGCACATGCACAG 59.864 57.895 6.15 0.00 44.36 3.66
629 642 2.980378 GCACATCGGCACATGCACA 61.980 57.895 6.15 0.00 44.36 4.57
635 648 3.998911 ATACGCGCACATCGGCACA 62.999 57.895 5.73 0.00 38.94 4.57
637 650 3.261216 CATACGCGCACATCGGCA 61.261 61.111 5.73 0.00 38.94 5.69
652 665 1.026182 TAGTACGTCACGTCCCGCAT 61.026 55.000 5.85 0.00 41.54 4.73
692 705 4.341783 GTGGCCAGGACAGCAGCT 62.342 66.667 5.11 0.00 0.00 4.24
784 800 4.475135 GGGCAGGGAGACGCTTCC 62.475 72.222 0.00 0.00 36.46 3.46
848 867 1.073216 CTTGCTATATCTCGCCGCGG 61.073 60.000 24.05 24.05 0.00 6.46
865 884 0.252197 GTGCGTGTCCCCTTATCCTT 59.748 55.000 0.00 0.00 0.00 3.36
898 921 3.130633 CGAAATGCGGAATGAGATGGTA 58.869 45.455 0.00 0.00 36.03 3.25
962 992 3.423154 GAGCGCTTGGTTCACCGG 61.423 66.667 13.26 0.00 39.43 5.28
963 993 2.357517 AGAGCGCTTGGTTCACCG 60.358 61.111 13.26 0.00 39.43 4.94
964 994 0.603975 AAGAGAGCGCTTGGTTCACC 60.604 55.000 13.26 0.00 0.00 4.02
966 996 1.070758 AGAAAGAGAGCGCTTGGTTCA 59.929 47.619 13.26 0.00 0.00 3.18
969 999 0.972883 AGAGAAAGAGAGCGCTTGGT 59.027 50.000 13.26 0.00 0.00 3.67
978 1010 1.934525 CGATCGACGGAGAGAAAGAGA 59.065 52.381 10.26 0.00 38.46 3.10
979 1011 2.376915 CGATCGACGGAGAGAAAGAG 57.623 55.000 10.26 0.00 38.46 2.85
1084 1119 1.153489 CAGTAGGATGCAGCAGCGT 60.153 57.895 11.15 11.15 46.23 5.07
1085 1120 2.532256 GCAGTAGGATGCAGCAGCG 61.532 63.158 3.51 0.00 45.77 5.18
1101 1136 1.890041 CGACGTGGGTTTCTTGGCA 60.890 57.895 0.00 0.00 0.00 4.92
1114 1149 2.050351 CACCGCTCTGAACGACGT 60.050 61.111 1.43 0.00 0.00 4.34
1116 1151 3.112709 GCCACCGCTCTGAACGAC 61.113 66.667 1.43 0.00 0.00 4.34
1137 1172 2.432456 TGGCTTGTGCTACTCGCG 60.432 61.111 0.00 0.00 43.27 5.87
1143 1178 2.167398 GACCGTCCTGGCTTGTGCTA 62.167 60.000 0.00 0.00 43.94 3.49
1147 1182 3.637273 GGGACCGTCCTGGCTTGT 61.637 66.667 17.27 0.00 43.94 3.16
1287 1325 2.282251 AGCTCCAGGTCGTCGTCA 60.282 61.111 0.00 0.00 0.00 4.35
1350 1388 1.418334 CGGAGGAGTTGATGATCCCT 58.582 55.000 0.00 0.00 36.14 4.20
1395 1433 4.558095 GCATGGCTAATTTTGCTGATCGAT 60.558 41.667 0.00 0.00 32.41 3.59
1409 1447 4.960469 AGTACTAGTACAAGGCATGGCTAA 59.040 41.667 29.87 8.50 38.48 3.09
1410 1448 4.341235 CAGTACTAGTACAAGGCATGGCTA 59.659 45.833 29.87 3.83 38.48 3.93
1431 1469 3.124806 CAGCACTAGTTTGCACAGATCAG 59.875 47.826 7.95 0.00 45.62 2.90
1433 1471 2.417933 CCAGCACTAGTTTGCACAGATC 59.582 50.000 7.95 0.00 45.62 2.75
1437 1475 0.465278 TGCCAGCACTAGTTTGCACA 60.465 50.000 7.95 1.03 45.62 4.57
1438 1476 0.667993 TTGCCAGCACTAGTTTGCAC 59.332 50.000 7.95 0.00 45.62 4.57
1447 1496 4.402474 GGTTAAGGATTAATTGCCAGCACT 59.598 41.667 0.00 0.00 43.30 4.40
1453 1513 4.099419 CCCTGTGGTTAAGGATTAATTGCC 59.901 45.833 0.00 0.00 43.30 4.52
1627 1687 4.233123 TGTAAGTGTCGTGTTCTGGTAG 57.767 45.455 0.00 0.00 0.00 3.18
1653 1714 8.389779 TGAAATTGCAGTCAAACAGTTCTATA 57.610 30.769 0.00 0.00 35.56 1.31
1655 1716 6.691754 TGAAATTGCAGTCAAACAGTTCTA 57.308 33.333 0.00 0.00 35.56 2.10
1656 1717 5.581126 TGAAATTGCAGTCAAACAGTTCT 57.419 34.783 0.00 0.00 35.56 3.01
1657 1718 6.211515 AGATGAAATTGCAGTCAAACAGTTC 58.788 36.000 0.00 0.00 35.56 3.01
1660 1721 5.765176 TGAGATGAAATTGCAGTCAAACAG 58.235 37.500 0.00 0.00 35.56 3.16
1661 1722 5.771153 TGAGATGAAATTGCAGTCAAACA 57.229 34.783 0.00 0.00 35.56 2.83
1662 1723 7.597743 AGAAATGAGATGAAATTGCAGTCAAAC 59.402 33.333 5.55 2.01 35.56 2.93
1703 1771 1.945394 CTGCTTGAGCTGAACTGTTGT 59.055 47.619 0.00 0.00 41.71 3.32
1747 1815 1.001406 AGGACAGCGAAGAGTTGAAGG 59.999 52.381 0.00 0.00 34.92 3.46
1757 1825 2.565391 TGTGAATAAGGAGGACAGCGAA 59.435 45.455 0.00 0.00 0.00 4.70
1790 1858 7.663081 TGCTAGAGTGAAAAACTGATGAAGAAT 59.337 33.333 0.00 0.00 40.07 2.40
1808 1876 5.273208 TCCTAATTCTTCCAGTGCTAGAGT 58.727 41.667 0.00 0.00 0.00 3.24
1839 1908 3.525537 GAAAGCGAGATGATGTTGAGGA 58.474 45.455 0.00 0.00 0.00 3.71
1840 1909 2.611292 GGAAAGCGAGATGATGTTGAGG 59.389 50.000 0.00 0.00 0.00 3.86
1841 1910 3.264947 TGGAAAGCGAGATGATGTTGAG 58.735 45.455 0.00 0.00 0.00 3.02
1842 1911 3.333029 TGGAAAGCGAGATGATGTTGA 57.667 42.857 0.00 0.00 0.00 3.18
1843 1912 4.334759 AGAATGGAAAGCGAGATGATGTTG 59.665 41.667 0.00 0.00 0.00 3.33
1844 1913 4.521146 AGAATGGAAAGCGAGATGATGTT 58.479 39.130 0.00 0.00 0.00 2.71
1845 1914 4.148128 AGAATGGAAAGCGAGATGATGT 57.852 40.909 0.00 0.00 0.00 3.06
1846 1915 4.334759 ACAAGAATGGAAAGCGAGATGATG 59.665 41.667 0.00 0.00 0.00 3.07
1924 1993 2.753966 CCATTTCTCCAGCGCCGTG 61.754 63.158 2.29 0.00 0.00 4.94
2616 2695 1.266989 CTTTTCCCTTGTCAGTTCCGC 59.733 52.381 0.00 0.00 0.00 5.54
2681 2760 3.774528 CTGAGCAGCTACCCGCCA 61.775 66.667 0.00 0.00 40.39 5.69
2727 2806 4.858140 GGCTTCTTGTAGTTACTTCTCGTC 59.142 45.833 0.00 0.00 0.00 4.20
2784 2863 7.554959 ACTGAAGTTCTTCTCCCTTGTATTA 57.445 36.000 12.74 0.00 0.00 0.98
2890 2969 6.827641 TGCTCGATGTGTATTTTTCAGTTAC 58.172 36.000 0.00 0.00 0.00 2.50
2923 3002 1.937546 GCATTAGTTTGGCGCCTGCT 61.938 55.000 29.70 23.09 42.25 4.24
2930 3013 2.164422 GGTCCTCTTGCATTAGTTTGGC 59.836 50.000 0.00 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.