Multiple sequence alignment - TraesCS4D01G302700

Loading Multiple Alignment...

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 TraesCS4D01G302700 chr4D 100.000 4090 0 0 1 4090 470505707 470509796 0.000000e+00 7553.0
1 TraesCS4D01G302700 chr4D 100.000 32 0 0 655 686 470506327 470506358 4.420000e-05 60.2
2 TraesCS4D01G302700 chr4D 100.000 32 0 0 621 652 470506361 470506392 4.420000e-05 60.2
3 TraesCS4D01G302700 chr4B 92.519 3382 139 44 685 3978 592819226 592822581 0.000000e+00 4739.0
4 TraesCS4D01G302700 chr4B 93.220 590 18 7 1 582 592818608 592819183 0.000000e+00 848.0
5 TraesCS4D01G302700 chr4A 91.642 2752 113 38 685 3346 678217458 678220182 0.000000e+00 3699.0
6 TraesCS4D01G302700 chr4A 91.837 588 36 2 3 590 678216853 678217428 0.000000e+00 809.0
7 TraesCS4D01G302700 chr4A 89.041 657 29 19 3346 3978 678220465 678221102 0.000000e+00 774.0
8 TraesCS4D01G302700 chr4A 91.089 101 5 4 3993 4090 678221089 678221188 2.560000e-27 134.0
9 TraesCS4D01G302700 chr4A 88.158 76 8 1 1479 1553 661320273 661320348 5.630000e-14 89.8
10 TraesCS4D01G302700 chr5A 88.172 186 22 0 1230 1415 462145388 462145573 5.320000e-54 222.0
11 TraesCS4D01G302700 chr5B 87.027 185 24 0 1230 1414 427238991 427239175 4.140000e-50 209.0
12 TraesCS4D01G302700 chr5D 87.931 174 21 0 1241 1414 361606659 361606832 5.360000e-49 206.0
13 TraesCS4D01G302700 chr5D 85.714 70 5 5 1496 1562 265665560 265665493 7.340000e-08 69.4
14 TraesCS4D01G302700 chr2D 84.940 166 22 2 1252 1414 557795287 557795122 9.100000e-37 165.0
15 TraesCS4D01G302700 chr2B 84.337 166 23 2 1252 1414 666089796 666089631 4.230000e-35 159.0
16 TraesCS4D01G302700 chr2B 84.337 166 23 2 1252 1414 666096234 666096069 4.230000e-35 159.0
17 TraesCS4D01G302700 chr2A 83.735 166 24 2 1252 1414 698134341 698134176 1.970000e-33 154.0
18 TraesCS4D01G302700 chr1B 83.562 73 9 3 1483 1554 648591808 648591878 9.490000e-07 65.8
19 TraesCS4D01G302700 chr3A 94.595 37 1 1 1488 1524 480156186 480156221 5.710000e-04 56.5


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 TraesCS4D01G302700 chr4D 470505707 470509796 4089 False 2557.8 7553 100.00000 1 4090 3 chr4D.!!$F1 4089
1 TraesCS4D01G302700 chr4B 592818608 592822581 3973 False 2793.5 4739 92.86950 1 3978 2 chr4B.!!$F1 3977
2 TraesCS4D01G302700 chr4A 678216853 678221188 4335 False 1354.0 3699 90.90225 3 4090 4 chr4A.!!$F2 4087

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
107 110 0.252696 TGGCCAAGGAGAAGGAGCTA 60.253 55.000 0.61 0.0 0.00 3.32 F
604 619 0.308376 TTTTCGCCGTTGTAACCAGC 59.692 50.000 0.00 0.0 0.00 4.85 F
610 625 0.322098 CCGTTGTAACCAGCCCATCA 60.322 55.000 0.00 0.0 0.00 3.07 F
709 724 0.393808 GGCCTTGCCCGATTCTGTTA 60.394 55.000 0.00 0.0 44.06 2.41 F
1332 1364 2.034066 AGGACCCACATTGCCGTG 59.966 61.111 0.00 0.0 36.61 4.94 F
2296 2371 1.304134 GGGTTCGCCTGGTTGGATT 60.304 57.895 0.00 0.0 38.35 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1019 1051 0.603975 GAAGTGGCCTTGCGAGAACT 60.604 55.0 3.32 0.25 0.00 3.01 R
2108 2177 0.250901 GAGAGTGCTGGCCCTCAAAA 60.251 55.0 0.00 0.00 0.00 2.44 R
2256 2327 0.410270 TTTCATTAACCCGGGCCCTT 59.590 50.0 24.08 10.70 0.00 3.95 R
2257 2328 0.410270 TTTTCATTAACCCGGGCCCT 59.590 50.0 24.08 8.17 0.00 5.19 R
2419 2503 0.687920 TCACGTAGTTGATTGCCCCA 59.312 50.0 0.00 0.00 41.61 4.96 R
3430 3837 0.388520 TGGATTCGAGACACACAGCG 60.389 55.0 0.00 0.00 0.00 5.18 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
105 108 1.377856 GTGGCCAAGGAGAAGGAGC 60.378 63.158 7.24 0.00 0.00 4.70
106 109 1.539869 TGGCCAAGGAGAAGGAGCT 60.540 57.895 0.61 0.00 0.00 4.09
107 110 0.252696 TGGCCAAGGAGAAGGAGCTA 60.253 55.000 0.61 0.00 0.00 3.32
108 111 0.467804 GGCCAAGGAGAAGGAGCTAG 59.532 60.000 0.00 0.00 0.00 3.42
221 224 1.603326 GTCTAGCCAGTACTCCTACGC 59.397 57.143 0.00 0.00 0.00 4.42
258 261 4.447054 GCAGTGATGCTGTAGATGTATGTC 59.553 45.833 0.00 0.00 46.64 3.06
332 335 2.960170 CAGCAAGCTGGACAAGGC 59.040 61.111 14.10 0.00 40.17 4.35
390 393 2.828549 GCTGCATGTTACCCGGGG 60.829 66.667 27.92 12.73 0.00 5.73
542 551 3.810743 GCCGGGACCTATAGATTTGCAAT 60.811 47.826 2.18 0.00 0.00 3.56
551 561 1.386533 AGATTTGCAATCCTCTGCCG 58.613 50.000 0.00 0.00 41.90 5.69
553 563 0.813184 ATTTGCAATCCTCTGCCGTG 59.187 50.000 0.00 0.00 41.90 4.94
583 598 6.048732 CCATTGGGCCAAGTTTTTAGTATT 57.951 37.500 25.16 0.00 0.00 1.89
603 618 2.759538 TTTTTCGCCGTTGTAACCAG 57.240 45.000 0.00 0.00 0.00 4.00
604 619 0.308376 TTTTCGCCGTTGTAACCAGC 59.692 50.000 0.00 0.00 0.00 4.85
605 620 1.508808 TTTCGCCGTTGTAACCAGCC 61.509 55.000 0.00 0.00 0.00 4.85
607 622 2.281900 GCCGTTGTAACCAGCCCA 60.282 61.111 0.00 0.00 0.00 5.36
608 623 1.677633 GCCGTTGTAACCAGCCCAT 60.678 57.895 0.00 0.00 0.00 4.00
609 624 1.654023 GCCGTTGTAACCAGCCCATC 61.654 60.000 0.00 0.00 0.00 3.51
610 625 0.322098 CCGTTGTAACCAGCCCATCA 60.322 55.000 0.00 0.00 0.00 3.07
611 626 1.529226 CGTTGTAACCAGCCCATCAA 58.471 50.000 0.00 0.00 0.00 2.57
612 627 1.883275 CGTTGTAACCAGCCCATCAAA 59.117 47.619 0.00 0.00 0.00 2.69
613 628 2.095263 CGTTGTAACCAGCCCATCAAAG 60.095 50.000 0.00 0.00 0.00 2.77
614 629 2.214376 TGTAACCAGCCCATCAAAGG 57.786 50.000 0.00 0.00 0.00 3.11
615 630 1.427368 TGTAACCAGCCCATCAAAGGT 59.573 47.619 0.00 0.00 0.00 3.50
616 631 2.092323 GTAACCAGCCCATCAAAGGTC 58.908 52.381 0.00 0.00 0.00 3.85
617 632 0.482446 AACCAGCCCATCAAAGGTCA 59.518 50.000 0.00 0.00 0.00 4.02
618 633 0.482446 ACCAGCCCATCAAAGGTCAA 59.518 50.000 0.00 0.00 0.00 3.18
619 634 1.180029 CCAGCCCATCAAAGGTCAAG 58.820 55.000 0.00 0.00 0.00 3.02
620 635 1.548582 CCAGCCCATCAAAGGTCAAGT 60.549 52.381 0.00 0.00 0.00 3.16
621 636 2.242043 CAGCCCATCAAAGGTCAAGTT 58.758 47.619 0.00 0.00 0.00 2.66
622 637 2.029649 CAGCCCATCAAAGGTCAAGTTG 60.030 50.000 0.00 0.00 0.00 3.16
623 638 2.158475 AGCCCATCAAAGGTCAAGTTGA 60.158 45.455 0.08 0.08 38.09 3.18
624 639 2.827921 GCCCATCAAAGGTCAAGTTGAT 59.172 45.455 9.18 0.00 43.59 2.57
625 640 4.016444 GCCCATCAAAGGTCAAGTTGATA 58.984 43.478 9.18 0.00 41.44 2.15
626 641 4.462483 GCCCATCAAAGGTCAAGTTGATAA 59.538 41.667 9.18 0.00 41.44 1.75
627 642 5.127682 GCCCATCAAAGGTCAAGTTGATAAT 59.872 40.000 9.18 0.00 41.44 1.28
628 643 6.351286 GCCCATCAAAGGTCAAGTTGATAATT 60.351 38.462 9.18 1.84 41.44 1.40
629 644 7.260603 CCCATCAAAGGTCAAGTTGATAATTC 58.739 38.462 9.18 0.00 41.44 2.17
630 645 7.093814 CCCATCAAAGGTCAAGTTGATAATTCA 60.094 37.037 9.18 0.00 41.44 2.57
631 646 8.306038 CCATCAAAGGTCAAGTTGATAATTCAA 58.694 33.333 9.18 0.00 41.44 2.69
642 657 5.484173 TTGATAATTCAACATCGGTGCTC 57.516 39.130 0.00 0.00 36.94 4.26
643 658 4.512484 TGATAATTCAACATCGGTGCTCA 58.488 39.130 0.00 0.00 0.00 4.26
644 659 4.332543 TGATAATTCAACATCGGTGCTCAC 59.667 41.667 0.00 0.00 0.00 3.51
645 660 2.183478 ATTCAACATCGGTGCTCACA 57.817 45.000 0.00 0.00 0.00 3.58
646 661 2.183478 TTCAACATCGGTGCTCACAT 57.817 45.000 0.00 0.00 0.00 3.21
647 662 2.183478 TCAACATCGGTGCTCACATT 57.817 45.000 0.00 0.00 0.00 2.71
648 663 2.503331 TCAACATCGGTGCTCACATTT 58.497 42.857 0.00 0.00 0.00 2.32
649 664 2.884012 TCAACATCGGTGCTCACATTTT 59.116 40.909 0.00 0.00 0.00 1.82
650 665 3.058293 TCAACATCGGTGCTCACATTTTC 60.058 43.478 0.00 0.00 0.00 2.29
651 666 2.783135 ACATCGGTGCTCACATTTTCT 58.217 42.857 0.00 0.00 0.00 2.52
652 667 3.937814 ACATCGGTGCTCACATTTTCTA 58.062 40.909 0.00 0.00 0.00 2.10
653 668 3.684788 ACATCGGTGCTCACATTTTCTAC 59.315 43.478 0.00 0.00 0.00 2.59
654 669 3.678056 TCGGTGCTCACATTTTCTACT 57.322 42.857 2.21 0.00 0.00 2.57
655 670 4.002906 TCGGTGCTCACATTTTCTACTT 57.997 40.909 2.21 0.00 0.00 2.24
656 671 3.745975 TCGGTGCTCACATTTTCTACTTG 59.254 43.478 2.21 0.00 0.00 3.16
657 672 3.745975 CGGTGCTCACATTTTCTACTTGA 59.254 43.478 2.21 0.00 0.00 3.02
658 673 4.393062 CGGTGCTCACATTTTCTACTTGAT 59.607 41.667 2.21 0.00 0.00 2.57
659 674 5.580691 CGGTGCTCACATTTTCTACTTGATA 59.419 40.000 2.21 0.00 0.00 2.15
660 675 6.092122 CGGTGCTCACATTTTCTACTTGATAA 59.908 38.462 2.21 0.00 0.00 1.75
661 676 7.201644 CGGTGCTCACATTTTCTACTTGATAAT 60.202 37.037 2.21 0.00 0.00 1.28
662 677 8.462016 GGTGCTCACATTTTCTACTTGATAATT 58.538 33.333 2.21 0.00 0.00 1.40
663 678 9.495754 GTGCTCACATTTTCTACTTGATAATTC 57.504 33.333 0.00 0.00 0.00 2.17
664 679 9.230122 TGCTCACATTTTCTACTTGATAATTCA 57.770 29.630 0.00 0.00 0.00 2.57
672 687 8.786826 TTTCTACTTGATAATTCAACATCGGT 57.213 30.769 0.00 0.00 36.94 4.69
673 688 7.770801 TCTACTTGATAATTCAACATCGGTG 57.229 36.000 0.00 0.00 36.94 4.94
674 689 5.235305 ACTTGATAATTCAACATCGGTGC 57.765 39.130 0.00 0.00 36.94 5.01
675 690 4.943705 ACTTGATAATTCAACATCGGTGCT 59.056 37.500 0.00 0.00 36.94 4.40
676 691 5.065218 ACTTGATAATTCAACATCGGTGCTC 59.935 40.000 0.00 0.00 36.94 4.26
677 692 4.512484 TGATAATTCAACATCGGTGCTCA 58.488 39.130 0.00 0.00 0.00 4.26
678 693 4.332543 TGATAATTCAACATCGGTGCTCAC 59.667 41.667 0.00 0.00 0.00 3.51
679 694 2.183478 ATTCAACATCGGTGCTCACA 57.817 45.000 0.00 0.00 0.00 3.58
680 695 2.183478 TTCAACATCGGTGCTCACAT 57.817 45.000 0.00 0.00 0.00 3.21
681 696 2.183478 TCAACATCGGTGCTCACATT 57.817 45.000 0.00 0.00 0.00 2.71
682 697 2.503331 TCAACATCGGTGCTCACATTT 58.497 42.857 0.00 0.00 0.00 2.32
683 698 2.884012 TCAACATCGGTGCTCACATTTT 59.116 40.909 0.00 0.00 0.00 1.82
709 724 0.393808 GGCCTTGCCCGATTCTGTTA 60.394 55.000 0.00 0.00 44.06 2.41
872 898 2.124996 CCCTCCCTCCCACCTCAA 59.875 66.667 0.00 0.00 0.00 3.02
1024 1056 2.282958 TGGAGGCCGTCGAGTTCT 60.283 61.111 0.00 0.00 0.00 3.01
1332 1364 2.034066 AGGACCCACATTGCCGTG 59.966 61.111 0.00 0.00 36.61 4.94
1442 1500 9.178758 ACTCGATTTTATCTGCCTTCTTATTTT 57.821 29.630 0.00 0.00 0.00 1.82
1752 1820 5.694995 TCCATTCCCCTTTTGCTATAAGAG 58.305 41.667 0.00 0.00 0.00 2.85
1905 1974 2.721906 TCTCTTTCCATTCCCCTTTGGT 59.278 45.455 0.00 0.00 34.48 3.67
1911 1980 2.929724 TCCATTCCCCTTTGGTTATCCA 59.070 45.455 0.00 0.00 42.66 3.41
1920 1989 4.586841 CCCTTTGGTTATCCACAAGAACAA 59.413 41.667 12.57 0.00 44.22 2.83
1933 2002 7.581476 TCCACAAGAACAAGTTATTTCGATTC 58.419 34.615 0.00 0.00 0.00 2.52
1946 2015 8.391106 AGTTATTTCGATTCAGCAACTAATGAC 58.609 33.333 0.00 0.00 0.00 3.06
1997 2066 6.515272 AAAATGGCAAGTTCAATCGTATCT 57.485 33.333 0.00 0.00 0.00 1.98
2008 2077 4.864633 TCAATCGTATCTGATGAGTGAGC 58.135 43.478 0.00 0.00 41.92 4.26
2070 2139 7.563888 TGATTGATTTTAGCATCTCTCAAGG 57.436 36.000 0.00 0.00 0.00 3.61
2118 2187 3.926058 TGTAGGAGTATTTTGAGGGCC 57.074 47.619 0.00 0.00 0.00 5.80
2138 2207 2.383527 GCACTCTCAGCGGGTTTCG 61.384 63.158 0.00 0.00 42.76 3.46
2158 2227 2.675032 CGTGCTAATGCTCCAACTCAGA 60.675 50.000 0.00 0.00 40.48 3.27
2182 2251 7.338703 AGAATATTTCTTACGGTTCCCCTTTTC 59.661 37.037 0.00 0.00 36.36 2.29
2246 2317 5.986501 ACCAAGGGTTAATAATTCGCAAA 57.013 34.783 0.00 0.00 27.29 3.68
2295 2370 2.355115 GGGTTCGCCTGGTTGGAT 59.645 61.111 0.00 0.00 38.35 3.41
2296 2371 1.304134 GGGTTCGCCTGGTTGGATT 60.304 57.895 0.00 0.00 38.35 3.01
2419 2503 0.038166 ACCAAGCATCCATCGTTGGT 59.962 50.000 12.19 4.78 46.32 3.67
2554 2638 3.192844 CACAGTACTCCACCTCGTGTAAT 59.807 47.826 0.00 0.00 0.00 1.89
2677 2761 3.123620 GCGAGCCTCAAGGTGCTG 61.124 66.667 0.00 0.00 38.11 4.41
2797 2881 2.239907 GGTCCTGTATTCCTTCAGCCTT 59.760 50.000 0.00 0.00 0.00 4.35
2956 3056 5.221880 TGGCATCGATCTTTCTTTGTTTTG 58.778 37.500 0.00 0.00 0.00 2.44
2957 3057 4.090498 GGCATCGATCTTTCTTTGTTTTGC 59.910 41.667 0.00 0.00 0.00 3.68
2958 3058 4.681025 GCATCGATCTTTCTTTGTTTTGCA 59.319 37.500 0.00 0.00 0.00 4.08
2994 3094 1.153005 GAGGATGGCTCCAAGCTGG 60.153 63.158 0.00 0.00 44.79 4.85
3143 3243 2.939022 GTCGTGCAAGCCTGTGAC 59.061 61.111 0.00 0.00 0.00 3.67
3146 3246 4.374702 GTGCAAGCCTGTGACGCG 62.375 66.667 3.53 3.53 0.00 6.01
3237 3342 3.870723 TGTACGTGAAACTGTGAATGC 57.129 42.857 0.00 0.00 31.75 3.56
3241 3346 1.398451 CGTGAAACTGTGAATGCGACC 60.398 52.381 0.00 0.00 31.75 4.79
3242 3347 0.865111 TGAAACTGTGAATGCGACCG 59.135 50.000 0.00 0.00 0.00 4.79
3256 3361 1.521681 GACCGCTGTACCCTGCATC 60.522 63.158 0.00 0.00 35.43 3.91
3358 3757 1.581934 TTGGCTCTGAACTGAACACG 58.418 50.000 0.00 0.00 0.00 4.49
3382 3789 2.505628 TTTTGGAGTGCGTACGTGTA 57.494 45.000 17.90 0.79 0.00 2.90
3430 3837 1.168407 ATGCACACAGACACACAGCC 61.168 55.000 0.00 0.00 0.00 4.85
3470 3885 3.607422 TTCACATGCTTCTGTTTCACG 57.393 42.857 0.00 0.00 0.00 4.35
3471 3886 1.872952 TCACATGCTTCTGTTTCACGG 59.127 47.619 0.00 0.00 0.00 4.94
3478 3893 0.534203 TTCTGTTTCACGGTGAGGCC 60.534 55.000 11.14 0.00 0.00 5.19
3606 4021 6.676237 TTATCTGTTGCGCAATAAATCTCA 57.324 33.333 27.79 16.08 0.00 3.27
3770 4187 4.293494 AGAGGCTAGAGATTCCATTGACA 58.707 43.478 0.00 0.00 0.00 3.58
3835 4252 2.736192 GCTTGTTGCAGTTGTGTTGTTT 59.264 40.909 0.00 0.00 42.31 2.83
3836 4253 3.186205 GCTTGTTGCAGTTGTGTTGTTTT 59.814 39.130 0.00 0.00 42.31 2.43
3841 4258 5.574830 TGTTGCAGTTGTGTTGTTTTATGAC 59.425 36.000 0.00 0.00 0.00 3.06
3842 4259 5.574891 TGCAGTTGTGTTGTTTTATGACT 57.425 34.783 0.00 0.00 0.00 3.41
3846 4263 5.971202 CAGTTGTGTTGTTTTATGACTGTCC 59.029 40.000 5.17 0.00 0.00 4.02
3883 4300 6.404623 CCCACACGACATGATTTCATAAATGT 60.405 38.462 0.00 0.00 36.00 2.71
3930 4363 2.227089 CTAGATGATACCCCGGGCGC 62.227 65.000 17.73 0.00 0.00 6.53
3980 4413 8.463930 TTCCAATGAGATTTGGTTATATGTCC 57.536 34.615 3.36 0.00 45.32 4.02
3981 4414 7.004086 TCCAATGAGATTTGGTTATATGTCCC 58.996 38.462 3.36 0.00 45.32 4.46
3982 4415 6.072508 CCAATGAGATTTGGTTATATGTCCCG 60.073 42.308 0.00 0.00 41.09 5.14
3983 4416 4.385825 TGAGATTTGGTTATATGTCCCGC 58.614 43.478 0.00 0.00 0.00 6.13
3984 4417 4.141597 TGAGATTTGGTTATATGTCCCGCA 60.142 41.667 0.00 0.00 0.00 5.69
3985 4418 4.787551 AGATTTGGTTATATGTCCCGCAA 58.212 39.130 0.00 0.00 0.00 4.85
3986 4419 5.197451 AGATTTGGTTATATGTCCCGCAAA 58.803 37.500 0.00 0.00 0.00 3.68
3987 4420 5.654650 AGATTTGGTTATATGTCCCGCAAAA 59.345 36.000 0.00 0.00 0.00 2.44
3988 4421 5.723672 TTTGGTTATATGTCCCGCAAAAA 57.276 34.783 0.00 0.00 0.00 1.94
4086 4521 1.202879 TGGGGTGCTTTGTACTTCTGG 60.203 52.381 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 108 1.202417 ACCGTTCATGCATCGACCTAG 60.202 52.381 7.77 0.00 0.00 3.02
106 109 0.821517 ACCGTTCATGCATCGACCTA 59.178 50.000 7.77 0.00 0.00 3.08
107 110 0.740868 CACCGTTCATGCATCGACCT 60.741 55.000 7.77 0.00 0.00 3.85
108 111 0.739462 TCACCGTTCATGCATCGACC 60.739 55.000 7.77 0.00 0.00 4.79
150 153 2.104928 CAGCCAGCTGCATGCATG 59.895 61.111 22.97 22.70 45.94 4.06
151 154 3.147595 CCAGCCAGCTGCATGCAT 61.148 61.111 22.97 3.95 45.94 3.96
154 157 2.124445 TAGCCAGCCAGCTGCATG 60.124 61.111 14.26 8.82 44.67 4.06
155 158 2.192443 CTAGCCAGCCAGCTGCAT 59.808 61.111 14.26 7.05 44.67 3.96
156 159 3.320879 GACTAGCCAGCCAGCTGCA 62.321 63.158 14.26 0.87 44.67 4.41
221 224 3.429141 CTGCAGCGCCAACTCCTG 61.429 66.667 2.29 0.00 0.00 3.86
258 261 2.468831 CTAAGCTAGCTCAAAGCCTCG 58.531 52.381 19.65 0.00 43.77 4.63
332 335 0.377554 AGCACTAGCGCTAGTACACG 59.622 55.000 41.19 31.00 43.98 4.49
530 539 3.144506 CGGCAGAGGATTGCAAATCTAT 58.855 45.455 1.71 0.00 45.86 1.98
532 541 1.340405 ACGGCAGAGGATTGCAAATCT 60.340 47.619 1.71 4.72 45.86 2.40
542 551 1.891919 GCAAACACACGGCAGAGGA 60.892 57.895 0.00 0.00 0.00 3.71
590 605 1.654023 GATGGGCTGGTTACAACGGC 61.654 60.000 0.00 0.00 0.00 5.68
591 606 0.322098 TGATGGGCTGGTTACAACGG 60.322 55.000 0.00 0.00 0.00 4.44
595 610 1.427368 ACCTTTGATGGGCTGGTTACA 59.573 47.619 0.00 0.00 0.00 2.41
596 611 2.092323 GACCTTTGATGGGCTGGTTAC 58.908 52.381 0.00 0.00 30.82 2.50
597 612 1.707989 TGACCTTTGATGGGCTGGTTA 59.292 47.619 0.00 0.00 35.73 2.85
598 613 0.482446 TGACCTTTGATGGGCTGGTT 59.518 50.000 0.00 0.00 35.73 3.67
600 615 1.180029 CTTGACCTTTGATGGGCTGG 58.820 55.000 0.00 0.00 35.73 4.85
602 617 2.158475 TCAACTTGACCTTTGATGGGCT 60.158 45.455 0.00 0.00 35.73 5.19
603 618 2.238521 TCAACTTGACCTTTGATGGGC 58.761 47.619 0.00 0.00 35.14 5.36
604 619 6.780457 ATTATCAACTTGACCTTTGATGGG 57.220 37.500 7.01 0.00 41.51 4.00
605 620 7.829725 TGAATTATCAACTTGACCTTTGATGG 58.170 34.615 7.01 0.00 41.51 3.51
620 635 4.940654 TGAGCACCGATGTTGAATTATCAA 59.059 37.500 0.00 0.00 43.18 2.57
621 636 4.332543 GTGAGCACCGATGTTGAATTATCA 59.667 41.667 0.00 0.00 0.00 2.15
622 637 4.332543 TGTGAGCACCGATGTTGAATTATC 59.667 41.667 0.00 0.00 0.00 1.75
623 638 4.260985 TGTGAGCACCGATGTTGAATTAT 58.739 39.130 0.00 0.00 0.00 1.28
624 639 3.669536 TGTGAGCACCGATGTTGAATTA 58.330 40.909 0.00 0.00 0.00 1.40
625 640 2.503331 TGTGAGCACCGATGTTGAATT 58.497 42.857 0.00 0.00 0.00 2.17
626 641 2.183478 TGTGAGCACCGATGTTGAAT 57.817 45.000 0.00 0.00 0.00 2.57
627 642 2.183478 ATGTGAGCACCGATGTTGAA 57.817 45.000 0.00 0.00 0.00 2.69
628 643 2.183478 AATGTGAGCACCGATGTTGA 57.817 45.000 0.00 0.00 0.00 3.18
629 644 2.995466 AAATGTGAGCACCGATGTTG 57.005 45.000 0.00 0.00 0.00 3.33
630 645 3.149196 AGAAAATGTGAGCACCGATGTT 58.851 40.909 0.00 0.00 0.00 2.71
631 646 2.783135 AGAAAATGTGAGCACCGATGT 58.217 42.857 0.00 0.00 0.00 3.06
632 647 3.935203 AGTAGAAAATGTGAGCACCGATG 59.065 43.478 0.00 0.00 0.00 3.84
633 648 4.207891 AGTAGAAAATGTGAGCACCGAT 57.792 40.909 0.00 0.00 0.00 4.18
634 649 3.678056 AGTAGAAAATGTGAGCACCGA 57.322 42.857 0.00 0.00 0.00 4.69
635 650 3.745975 TCAAGTAGAAAATGTGAGCACCG 59.254 43.478 0.00 0.00 0.00 4.94
636 651 5.886960 ATCAAGTAGAAAATGTGAGCACC 57.113 39.130 0.00 0.00 0.00 5.01
637 652 9.495754 GAATTATCAAGTAGAAAATGTGAGCAC 57.504 33.333 0.00 0.00 0.00 4.40
638 653 9.230122 TGAATTATCAAGTAGAAAATGTGAGCA 57.770 29.630 0.00 0.00 30.99 4.26
646 661 9.226606 ACCGATGTTGAATTATCAAGTAGAAAA 57.773 29.630 0.00 0.00 45.88 2.29
647 662 8.664798 CACCGATGTTGAATTATCAAGTAGAAA 58.335 33.333 0.00 0.00 45.88 2.52
648 663 7.201609 GCACCGATGTTGAATTATCAAGTAGAA 60.202 37.037 0.00 0.00 45.88 2.10
649 664 6.257849 GCACCGATGTTGAATTATCAAGTAGA 59.742 38.462 0.00 0.00 45.88 2.59
650 665 6.258727 AGCACCGATGTTGAATTATCAAGTAG 59.741 38.462 0.00 0.00 45.88 2.57
651 666 6.112734 AGCACCGATGTTGAATTATCAAGTA 58.887 36.000 0.00 0.00 45.88 2.24
652 667 4.943705 AGCACCGATGTTGAATTATCAAGT 59.056 37.500 0.00 0.00 45.88 3.16
653 668 5.065090 TGAGCACCGATGTTGAATTATCAAG 59.935 40.000 0.00 0.00 45.88 3.02
654 669 4.940654 TGAGCACCGATGTTGAATTATCAA 59.059 37.500 0.00 0.00 43.18 2.57
655 670 4.332543 GTGAGCACCGATGTTGAATTATCA 59.667 41.667 0.00 0.00 0.00 2.15
656 671 4.332543 TGTGAGCACCGATGTTGAATTATC 59.667 41.667 0.00 0.00 0.00 1.75
657 672 4.260985 TGTGAGCACCGATGTTGAATTAT 58.739 39.130 0.00 0.00 0.00 1.28
658 673 3.669536 TGTGAGCACCGATGTTGAATTA 58.330 40.909 0.00 0.00 0.00 1.40
659 674 2.503331 TGTGAGCACCGATGTTGAATT 58.497 42.857 0.00 0.00 0.00 2.17
660 675 2.183478 TGTGAGCACCGATGTTGAAT 57.817 45.000 0.00 0.00 0.00 2.57
661 676 2.183478 ATGTGAGCACCGATGTTGAA 57.817 45.000 0.00 0.00 0.00 2.69
662 677 2.183478 AATGTGAGCACCGATGTTGA 57.817 45.000 0.00 0.00 0.00 3.18
663 678 2.995466 AAATGTGAGCACCGATGTTG 57.005 45.000 0.00 0.00 0.00 3.33
664 679 3.149196 AGAAAATGTGAGCACCGATGTT 58.851 40.909 0.00 0.00 0.00 2.71
665 680 2.783135 AGAAAATGTGAGCACCGATGT 58.217 42.857 0.00 0.00 0.00 3.06
666 681 3.058016 ACAAGAAAATGTGAGCACCGATG 60.058 43.478 0.00 0.00 30.82 3.84
667 682 3.149196 ACAAGAAAATGTGAGCACCGAT 58.851 40.909 0.00 0.00 30.82 4.18
668 683 2.571212 ACAAGAAAATGTGAGCACCGA 58.429 42.857 0.00 0.00 30.82 4.69
669 684 3.044986 CAACAAGAAAATGTGAGCACCG 58.955 45.455 0.00 0.00 32.81 4.94
670 685 3.383761 CCAACAAGAAAATGTGAGCACC 58.616 45.455 0.00 0.00 32.81 5.01
671 686 2.796593 GCCAACAAGAAAATGTGAGCAC 59.203 45.455 0.00 0.00 34.19 4.40
672 687 2.224018 GGCCAACAAGAAAATGTGAGCA 60.224 45.455 0.00 0.00 35.15 4.26
673 688 2.036346 AGGCCAACAAGAAAATGTGAGC 59.964 45.455 5.01 0.00 32.81 4.26
674 689 4.053295 CAAGGCCAACAAGAAAATGTGAG 58.947 43.478 5.01 0.00 32.81 3.51
675 690 3.740764 GCAAGGCCAACAAGAAAATGTGA 60.741 43.478 5.01 0.00 32.81 3.58
676 691 2.545106 GCAAGGCCAACAAGAAAATGTG 59.455 45.455 5.01 0.00 32.81 3.21
677 692 2.837498 GCAAGGCCAACAAGAAAATGT 58.163 42.857 5.01 0.00 34.24 2.71
709 724 1.061324 TCCCACCCAACGGTTTAGGT 61.061 55.000 6.54 6.54 42.04 3.08
1019 1051 0.603975 GAAGTGGCCTTGCGAGAACT 60.604 55.000 3.32 0.25 0.00 3.01
1101 1133 2.600439 CTGATCCCAGCAGTCCTCA 58.400 57.895 0.00 0.00 33.07 3.86
1546 1606 6.985188 TTAGAGCTTATGATGCTTTTTCGT 57.015 33.333 0.00 0.00 41.30 3.85
1597 1665 6.341316 AGAGATGCTAAAATCGAGTAAAGCA 58.659 36.000 19.93 19.93 43.43 3.91
1752 1820 1.862806 GTTGAGAGCGTTGACAGGC 59.137 57.895 0.00 0.00 0.00 4.85
1755 1823 3.179433 CTCGTTGAGAGCGTTGACA 57.821 52.632 0.00 0.00 40.54 3.58
1905 1974 8.610248 TCGAAATAACTTGTTCTTGTGGATAA 57.390 30.769 0.00 0.00 0.00 1.75
1911 1980 7.078228 GCTGAATCGAAATAACTTGTTCTTGT 58.922 34.615 0.00 0.00 0.00 3.16
1920 1989 8.391106 GTCATTAGTTGCTGAATCGAAATAACT 58.609 33.333 0.00 0.00 0.00 2.24
1933 2002 4.479619 GCCTTTTCAGTCATTAGTTGCTG 58.520 43.478 0.00 0.00 33.44 4.41
1978 2047 4.200838 TCAGATACGATTGAACTTGCCA 57.799 40.909 0.00 0.00 0.00 4.92
1979 2048 4.811024 TCATCAGATACGATTGAACTTGCC 59.189 41.667 0.00 0.00 0.00 4.52
2046 2115 7.114754 ACCTTGAGAGATGCTAAAATCAATCA 58.885 34.615 0.00 0.00 0.00 2.57
2047 2116 7.255070 GGACCTTGAGAGATGCTAAAATCAATC 60.255 40.741 0.00 0.00 0.00 2.67
2096 2165 4.972568 TGGCCCTCAAAATACTCCTACATA 59.027 41.667 0.00 0.00 0.00 2.29
2106 2175 1.635487 AGAGTGCTGGCCCTCAAAATA 59.365 47.619 0.00 0.00 0.00 1.40
2107 2176 0.407139 AGAGTGCTGGCCCTCAAAAT 59.593 50.000 0.00 0.00 0.00 1.82
2108 2177 0.250901 GAGAGTGCTGGCCCTCAAAA 60.251 55.000 0.00 0.00 0.00 2.44
2112 2181 2.583520 CTGAGAGTGCTGGCCCTC 59.416 66.667 0.00 0.00 0.00 4.30
2118 2187 1.294659 GAAACCCGCTGAGAGTGCTG 61.295 60.000 0.00 0.00 0.00 4.41
2138 2207 2.977914 TCTGAGTTGGAGCATTAGCAC 58.022 47.619 0.00 0.00 45.49 4.40
2182 2251 4.504858 ACCGGTTCTTACAGATAGCAAAG 58.495 43.478 0.00 0.00 0.00 2.77
2205 2274 7.364585 CCCTTGGTTAATTGCTCAATGGAAATA 60.365 37.037 0.00 0.00 30.06 1.40
2256 2327 0.410270 TTTCATTAACCCGGGCCCTT 59.590 50.000 24.08 10.70 0.00 3.95
2257 2328 0.410270 TTTTCATTAACCCGGGCCCT 59.590 50.000 24.08 8.17 0.00 5.19
2258 2329 0.821517 CTTTTCATTAACCCGGGCCC 59.178 55.000 24.08 13.57 0.00 5.80
2259 2330 0.821517 CCTTTTCATTAACCCGGGCC 59.178 55.000 24.08 0.00 0.00 5.80
2260 2331 0.821517 CCCTTTTCATTAACCCGGGC 59.178 55.000 24.08 0.00 0.00 6.13
2261 2332 1.272816 ACCCCTTTTCATTAACCCGGG 60.273 52.381 22.25 22.25 35.30 5.73
2262 2333 2.225382 ACCCCTTTTCATTAACCCGG 57.775 50.000 0.00 0.00 0.00 5.73
2419 2503 0.687920 TCACGTAGTTGATTGCCCCA 59.312 50.000 0.00 0.00 41.61 4.96
2509 2593 2.035442 GGTGAAGGAGCTGGCGAAC 61.035 63.158 0.00 0.00 0.00 3.95
2956 3056 1.153706 ACCTACCGTACGTGCATGC 60.154 57.895 11.82 11.82 0.00 4.06
2957 3057 0.804544 CCACCTACCGTACGTGCATG 60.805 60.000 15.21 3.82 0.00 4.06
2958 3058 0.966875 TCCACCTACCGTACGTGCAT 60.967 55.000 15.21 0.00 0.00 3.96
2994 3094 1.869767 CGCAATATCTTCCACAGAGCC 59.130 52.381 0.00 0.00 33.87 4.70
3112 3212 2.436292 CGACGACGGTCTCCTCCT 60.436 66.667 6.57 0.00 41.16 3.69
3213 3313 3.936902 TCACAGTTTCACGTACAAAGC 57.063 42.857 0.00 0.00 0.00 3.51
3237 3342 3.371097 ATGCAGGGTACAGCGGTCG 62.371 63.158 0.00 0.00 33.60 4.79
3241 3346 1.078497 TTGGATGCAGGGTACAGCG 60.078 57.895 0.00 0.00 33.60 5.18
3242 3347 1.032114 GGTTGGATGCAGGGTACAGC 61.032 60.000 0.00 0.00 0.00 4.40
3256 3361 1.604593 CTGGACTGGGCAAGGTTGG 60.605 63.158 0.00 0.00 0.00 3.77
3358 3757 1.193874 CGTACGCACTCCAAAAAGGAC 59.806 52.381 0.52 0.00 43.07 3.85
3382 3789 5.643379 AAAGTAAATCCGTGAATGCATGT 57.357 34.783 0.00 0.00 0.00 3.21
3430 3837 0.388520 TGGATTCGAGACACACAGCG 60.389 55.000 0.00 0.00 0.00 5.18
3478 3893 1.809619 CAGATGTACCACACGGCCG 60.810 63.158 26.86 26.86 34.57 6.13
3606 4021 0.882474 GCCGAGCTCTATACACGGAT 59.118 55.000 12.85 0.00 45.31 4.18
3770 4187 1.739067 GCAGCGACAACTATTTCCCT 58.261 50.000 0.00 0.00 0.00 4.20
3800 4217 2.730550 ACAAGCAGCAATTTACCAGC 57.269 45.000 0.00 0.00 0.00 4.85
3801 4218 2.733026 GCAACAAGCAGCAATTTACCAG 59.267 45.455 0.00 0.00 44.79 4.00
3802 4219 2.753296 GCAACAAGCAGCAATTTACCA 58.247 42.857 0.00 0.00 44.79 3.25
3832 4249 6.496338 CCTACAAAGGGACAGTCATAAAAC 57.504 41.667 2.17 0.00 39.48 2.43
3883 4300 6.988622 TCCGTCAAAGAAAACAAGAAAGTA 57.011 33.333 0.00 0.00 0.00 2.24
3903 4320 4.142227 CCGGGGTATCATCTAGTATTTCCG 60.142 50.000 0.00 0.00 0.00 4.30
3930 4363 3.940209 TGTAAGCAAATTCCCAAGCAG 57.060 42.857 0.00 0.00 0.00 4.24
4052 4485 9.158097 ACAAAGCACCCCAATAATAATAATCAT 57.842 29.630 0.00 0.00 0.00 2.45
4053 4486 8.546083 ACAAAGCACCCCAATAATAATAATCA 57.454 30.769 0.00 0.00 0.00 2.57
4054 4487 9.908152 GTACAAAGCACCCCAATAATAATAATC 57.092 33.333 0.00 0.00 0.00 1.75


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

AutoCloner maintained by Alex Coulton.