Multiple sequence alignment - TraesCS4D01G313400

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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 TraesCS4D01G313400 chr4D 100.000 2369 0 0 1 2369 479524172 479526540 0.000000e+00 4375
1 TraesCS4D01G313400 chr4B 87.885 2435 143 70 1 2369 606754158 606756506 0.000000e+00 2723
2 TraesCS4D01G313400 chr4A 84.132 1670 131 74 22 1622 685825808 685827412 0.000000e+00 1493
3 TraesCS4D01G313400 chr4A 88.095 336 21 6 1821 2144 685827620 685827948 4.780000e-102 381
4 TraesCS4D01G313400 chr4A 87.500 200 22 2 2173 2369 685829759 685829958 6.590000e-56 228
5 TraesCS4D01G313400 chr6A 86.170 188 22 4 1023 1208 454934513 454934698 1.440000e-47 200
6 TraesCS4D01G313400 chr6D 85.484 186 23 4 1025 1208 317414363 317414546 8.640000e-45 191
7 TraesCS4D01G313400 chr1D 83.684 190 27 4 1027 1214 307420815 307420628 2.420000e-40 176
8 TraesCS4D01G313400 chr2D 83.708 178 27 2 1030 1206 498532612 498532436 1.460000e-37 167
9 TraesCS4D01G313400 chr2D 84.091 176 22 6 1028 1200 528635714 528635886 5.240000e-37 165
10 TraesCS4D01G313400 chr2A 84.091 176 22 6 1028 1200 673327382 673327554 5.240000e-37 165
11 TraesCS4D01G313400 chr1B 82.632 190 29 4 1027 1214 415744324 415744137 5.240000e-37 165


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 TraesCS4D01G313400 chr4D 479524172 479526540 2368 False 4375.000000 4375 100.000000 1 2369 1 chr4D.!!$F1 2368
1 TraesCS4D01G313400 chr4B 606754158 606756506 2348 False 2723.000000 2723 87.885000 1 2369 1 chr4B.!!$F1 2368
2 TraesCS4D01G313400 chr4A 685825808 685829958 4150 False 700.666667 1493 86.575667 22 2369 3 chr4A.!!$F1 2347

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
961 1048 0.179936 AGCTGCCTACTTGCTGATCC 59.82 55.0 0.0 0.0 35.54 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1975 2139 1.078143 ATTCTGAAGGCGGGTCTGC 60.078 57.895 0.0 0.0 0.0 4.26 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
84 85 0.736636 CCGTGACATGCATGCAGATT 59.263 50.000 26.69 12.33 31.94 2.40
85 86 1.533129 CCGTGACATGCATGCAGATTG 60.533 52.381 26.69 21.06 31.94 2.67
86 87 1.556564 GTGACATGCATGCAGATTGC 58.443 50.000 26.69 14.91 45.29 3.56
107 114 5.289595 TGCAACCTAGCTAATAGTCAATCG 58.710 41.667 0.00 0.00 34.99 3.34
108 115 4.686554 GCAACCTAGCTAATAGTCAATCGG 59.313 45.833 0.00 0.00 0.00 4.18
109 116 5.509163 GCAACCTAGCTAATAGTCAATCGGA 60.509 44.000 0.00 0.00 0.00 4.55
110 117 6.513180 CAACCTAGCTAATAGTCAATCGGAA 58.487 40.000 0.00 0.00 0.00 4.30
364 383 1.600636 CGGCCACACACAAGGATGT 60.601 57.895 2.24 0.00 41.61 3.06
426 448 1.098050 GCCAATCTCCACGCATCTTT 58.902 50.000 0.00 0.00 0.00 2.52
444 466 0.899720 TTACTGTCGGGGTCATGTCC 59.100 55.000 0.00 0.00 0.00 4.02
453 479 1.349026 GGGGTCATGTCCATCGATCAT 59.651 52.381 11.23 0.00 0.00 2.45
488 514 5.723672 ACTGACTTAGTTTTCTCGATGGA 57.276 39.130 0.00 0.00 35.67 3.41
489 515 6.287589 ACTGACTTAGTTTTCTCGATGGAT 57.712 37.500 0.00 0.00 35.67 3.41
490 516 6.334202 ACTGACTTAGTTTTCTCGATGGATC 58.666 40.000 0.00 0.00 35.67 3.36
491 517 6.897842 ACTGACTTAGTTTTCTCGATGGATCG 60.898 42.308 2.50 2.50 43.69 3.69
492 518 8.968915 ACTGACTTAGTTTTCTCGATGGATCGA 61.969 40.741 11.08 11.08 46.51 3.59
520 551 4.964897 TCGATGGGAGAATATGCATATCCT 59.035 41.667 19.35 12.71 0.00 3.24
524 555 7.039152 CGATGGGAGAATATGCATATCCTATCT 60.039 40.741 29.55 23.67 33.47 1.98
596 631 3.313526 GTCGCGGTAGTAGAATGGTCTAA 59.686 47.826 6.13 0.00 38.11 2.10
604 639 5.145513 AGTAGAATGGTCTAAGGCCTAGT 57.854 43.478 5.16 0.00 38.11 2.57
608 643 5.033522 AGAATGGTCTAAGGCCTAGTTTCT 58.966 41.667 5.16 5.48 29.93 2.52
616 651 5.958380 TCTAAGGCCTAGTTTCTGAGAATGA 59.042 40.000 5.16 0.00 0.00 2.57
622 657 5.055812 CCTAGTTTCTGAGAATGATCAGCC 58.944 45.833 0.09 0.00 45.25 4.85
623 658 4.564782 AGTTTCTGAGAATGATCAGCCA 57.435 40.909 0.09 0.00 45.25 4.75
629 664 1.099879 AGAATGATCAGCCAAGCGCC 61.100 55.000 2.29 0.00 38.78 6.53
662 698 1.541147 TGCAACTATGACTTGCCTTGC 59.459 47.619 0.91 0.00 42.91 4.01
664 700 0.804989 AACTATGACTTGCCTTGCGC 59.195 50.000 0.00 0.00 38.31 6.09
665 701 1.349627 CTATGACTTGCCTTGCGCG 59.650 57.895 0.00 0.00 42.08 6.86
666 702 2.637715 CTATGACTTGCCTTGCGCGC 62.638 60.000 27.26 27.26 42.08 6.86
681 717 3.121030 CGCGCTTGCTAGCCAGTT 61.121 61.111 16.51 0.00 44.86 3.16
682 718 2.482374 GCGCTTGCTAGCCAGTTG 59.518 61.111 16.51 10.83 44.86 3.16
683 719 2.482374 CGCTTGCTAGCCAGTTGC 59.518 61.111 16.51 10.22 44.86 4.17
695 731 1.577922 CAGTTGCGCTGCTGATGTT 59.422 52.632 21.41 0.00 38.52 2.71
697 733 0.798776 AGTTGCGCTGCTGATGTTAC 59.201 50.000 9.73 0.00 0.00 2.50
726 779 0.658244 CATACGCCGCATGATGCAAC 60.658 55.000 18.47 7.40 45.36 4.17
735 796 1.476471 GCATGATGCAACCCTAGCTCT 60.476 52.381 13.36 0.00 44.26 4.09
738 799 3.032265 TGATGCAACCCTAGCTCTCTA 57.968 47.619 0.00 0.00 0.00 2.43
769 830 1.226773 GCATGCACCGCCAATTCTC 60.227 57.895 14.21 0.00 0.00 2.87
770 831 1.063006 CATGCACCGCCAATTCTCG 59.937 57.895 0.00 0.00 0.00 4.04
771 832 1.377202 ATGCACCGCCAATTCTCGT 60.377 52.632 0.00 0.00 0.00 4.18
783 844 5.405571 CGCCAATTCTCGTGTATAAATAGCT 59.594 40.000 0.00 0.00 0.00 3.32
784 845 6.593978 GCCAATTCTCGTGTATAAATAGCTG 58.406 40.000 0.00 0.00 0.00 4.24
785 846 6.593978 CCAATTCTCGTGTATAAATAGCTGC 58.406 40.000 0.00 0.00 0.00 5.25
786 847 6.347725 CCAATTCTCGTGTATAAATAGCTGCC 60.348 42.308 0.00 0.00 0.00 4.85
787 848 5.531122 TTCTCGTGTATAAATAGCTGCCT 57.469 39.130 0.00 0.00 0.00 4.75
818 879 0.800631 CATATGCCGGCAGCTACATG 59.199 55.000 35.36 24.69 44.23 3.21
821 882 0.397941 ATGCCGGCAGCTACATGTAT 59.602 50.000 35.36 11.04 44.23 2.29
884 971 3.452474 CTCCTTCTAGATTGCAACCTCG 58.548 50.000 0.00 0.00 0.00 4.63
886 973 2.621338 CTTCTAGATTGCAACCTCGCA 58.379 47.619 0.00 0.00 41.03 5.10
907 994 4.325119 CAAAGATATAGCTGCATCTGCCT 58.675 43.478 11.42 0.00 41.18 4.75
917 1004 1.437573 CATCTGCCTTGCCTGCATG 59.562 57.895 0.00 0.00 38.22 4.06
918 1005 2.423898 ATCTGCCTTGCCTGCATGC 61.424 57.895 11.82 11.82 38.22 4.06
919 1006 3.378602 CTGCCTTGCCTGCATGCA 61.379 61.111 21.29 21.29 38.22 3.96
920 1007 3.642778 CTGCCTTGCCTGCATGCAC 62.643 63.158 18.46 9.02 41.88 4.57
942 1029 1.645034 GAGCTGATTAAGTGAGCGCA 58.355 50.000 11.47 0.00 42.42 6.09
956 1043 2.435586 CGCAGCTGCCTACTTGCT 60.436 61.111 32.07 0.00 37.91 3.91
961 1048 0.179936 AGCTGCCTACTTGCTGATCC 59.820 55.000 0.00 0.00 35.54 3.36
962 1049 0.817229 GCTGCCTACTTGCTGATCCC 60.817 60.000 0.00 0.00 32.50 3.85
963 1050 0.835941 CTGCCTACTTGCTGATCCCT 59.164 55.000 0.00 0.00 32.50 4.20
964 1051 1.211457 CTGCCTACTTGCTGATCCCTT 59.789 52.381 0.00 0.00 32.50 3.95
966 1053 1.488393 GCCTACTTGCTGATCCCTTCT 59.512 52.381 0.00 0.00 0.00 2.85
967 1054 2.484594 GCCTACTTGCTGATCCCTTCTC 60.485 54.545 0.00 0.00 0.00 2.87
969 1056 1.963985 ACTTGCTGATCCCTTCTCCT 58.036 50.000 0.00 0.00 0.00 3.69
995 1085 4.336889 AGCTAGCAATACCGAATTAGCA 57.663 40.909 18.83 0.00 31.65 3.49
996 1086 4.899502 AGCTAGCAATACCGAATTAGCAT 58.100 39.130 18.83 0.00 31.65 3.79
997 1087 4.932200 AGCTAGCAATACCGAATTAGCATC 59.068 41.667 18.83 0.00 31.65 3.91
998 1088 4.690748 GCTAGCAATACCGAATTAGCATCA 59.309 41.667 10.63 0.00 30.26 3.07
999 1089 5.352569 GCTAGCAATACCGAATTAGCATCAT 59.647 40.000 10.63 0.00 30.26 2.45
1202 1292 1.452108 CCATCCTCAACTTCCCCGC 60.452 63.158 0.00 0.00 0.00 6.13
1358 1448 1.135333 GGAGGACTACTACAGCAGCAC 59.865 57.143 0.00 0.00 0.00 4.40
1395 1485 2.356553 TAGCACGCACACCCGAAC 60.357 61.111 0.00 0.00 0.00 3.95
1428 1530 7.209471 AGCTACTATACTACTAAAGCTGCTG 57.791 40.000 1.35 0.00 37.44 4.41
1454 1556 2.840651 TGAAGGAGGAGAATGGTCTTCC 59.159 50.000 0.00 0.00 41.93 3.46
1469 1575 1.202722 TCTTCCTTGGTTTGGTCGGTC 60.203 52.381 0.00 0.00 0.00 4.79
1499 1605 0.176680 AGGACTAGTCATGGCTTGCG 59.823 55.000 23.91 0.00 0.00 4.85
1574 1689 2.180017 CCCATGCAGCGTGCTTTC 59.820 61.111 9.34 0.00 45.31 2.62
1684 1828 5.804692 ACGTAAAATGGTCGCATCAAATA 57.195 34.783 0.00 0.00 0.00 1.40
1763 1907 8.560355 AAAAATGGTGCCTATAAATTTTGTCC 57.440 30.769 0.00 0.00 32.36 4.02
1782 1926 5.852827 TGTCCTGGATTTTTCACCAATTTC 58.147 37.500 0.00 0.00 35.67 2.17
1786 1930 6.780031 TCCTGGATTTTTCACCAATTTCTACA 59.220 34.615 0.00 0.00 35.67 2.74
1812 1957 8.442660 AGTATATATCTTCTGGGAAGAAAGGG 57.557 38.462 12.94 0.00 0.00 3.95
1975 2139 5.438761 AAAAGAAGTGAATCCTCGGTTTG 57.561 39.130 0.00 0.00 0.00 2.93
2109 2283 7.065923 GCCTCTCTGATTTTTATAGGTTTTCGT 59.934 37.037 0.00 0.00 0.00 3.85
2121 2295 2.812011 AGGTTTTCGTTTCGAGGATTGG 59.188 45.455 0.00 0.00 37.14 3.16
2238 4195 8.192774 TCATGTTCAAGAGAAATTATGCATTCC 58.807 33.333 3.54 0.00 35.08 3.01
2361 4319 9.710900 GATAGACACCATATTGTAATCATGTGA 57.289 33.333 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 1.752498 GATGCATGCACTGGGAATCAA 59.248 47.619 25.37 0.00 0.00 2.57
84 85 5.289595 CGATTGACTATTAGCTAGGTTGCA 58.710 41.667 0.00 0.00 34.99 4.08
85 86 4.686554 CCGATTGACTATTAGCTAGGTTGC 59.313 45.833 0.00 0.00 0.00 4.17
86 87 6.085555 TCCGATTGACTATTAGCTAGGTTG 57.914 41.667 0.00 0.00 0.00 3.77
88 89 6.069331 TCTTCCGATTGACTATTAGCTAGGT 58.931 40.000 0.00 0.00 0.00 3.08
107 114 2.090195 GTCGTCGTCGTCATTTTCTTCC 59.910 50.000 1.33 0.00 38.33 3.46
108 115 2.722629 TGTCGTCGTCGTCATTTTCTTC 59.277 45.455 1.33 0.00 38.33 2.87
109 116 2.734670 TGTCGTCGTCGTCATTTTCTT 58.265 42.857 1.33 0.00 38.33 2.52
110 117 2.410785 TGTCGTCGTCGTCATTTTCT 57.589 45.000 1.33 0.00 38.33 2.52
112 119 4.087510 TCTATGTCGTCGTCGTCATTTT 57.912 40.909 17.61 0.62 41.31 1.82
194 207 2.043980 GGAGAATTTTCGCGGGCCA 61.044 57.895 6.13 0.00 0.00 5.36
198 211 1.713830 GGACGGAGAATTTTCGCGG 59.286 57.895 6.13 1.18 34.44 6.46
199 212 1.343821 CGGACGGAGAATTTTCGCG 59.656 57.895 0.00 0.00 0.00 5.87
261 278 0.739813 GAATCTCGGTTCACGTGGGG 60.740 60.000 17.00 0.00 44.69 4.96
275 294 4.256180 GCGGGGGCATCGGAATCT 62.256 66.667 1.29 0.00 0.00 2.40
353 372 3.264193 TGAGCTCCATTACATCCTTGTGT 59.736 43.478 12.15 0.00 36.53 3.72
407 428 1.098050 AAAGATGCGTGGAGATTGGC 58.902 50.000 0.00 0.00 0.00 4.52
418 439 0.108329 ACCCCGACAGTAAAGATGCG 60.108 55.000 0.00 0.00 0.00 4.73
419 440 1.066430 TGACCCCGACAGTAAAGATGC 60.066 52.381 0.00 0.00 0.00 3.91
426 448 0.251877 TGGACATGACCCCGACAGTA 60.252 55.000 11.80 0.00 0.00 2.74
491 517 4.047822 GCATATTCTCCCATCGATCGATC 58.952 47.826 27.20 15.68 31.62 3.69
492 518 3.448660 TGCATATTCTCCCATCGATCGAT 59.551 43.478 24.60 24.60 34.81 3.59
493 519 2.825532 TGCATATTCTCCCATCGATCGA 59.174 45.455 21.86 21.86 0.00 3.59
494 520 3.236632 TGCATATTCTCCCATCGATCG 57.763 47.619 9.36 9.36 0.00 3.69
495 521 5.931146 GGATATGCATATTCTCCCATCGATC 59.069 44.000 20.00 4.84 0.00 3.69
502 528 7.609097 TGAGATAGGATATGCATATTCTCCC 57.391 40.000 27.53 19.39 31.20 4.30
520 551 2.938451 CCGCAATCAAGCAGTTGAGATA 59.062 45.455 0.00 0.00 45.96 1.98
524 555 0.890542 AGCCGCAATCAAGCAGTTGA 60.891 50.000 0.00 0.00 46.81 3.18
596 631 4.718774 TGATCATTCTCAGAAACTAGGCCT 59.281 41.667 11.78 11.78 0.00 5.19
604 639 3.693085 GCTTGGCTGATCATTCTCAGAAA 59.307 43.478 0.00 0.00 44.48 2.52
608 643 1.660167 CGCTTGGCTGATCATTCTCA 58.340 50.000 0.00 0.00 0.00 3.27
646 682 1.361668 CGCGCAAGGCAAGTCATAGT 61.362 55.000 8.75 0.00 43.84 2.12
668 704 2.037136 AGCGCAACTGGCTAGCAAG 61.037 57.895 18.06 18.06 39.39 4.01
669 705 2.032528 AGCGCAACTGGCTAGCAA 59.967 55.556 18.24 3.74 39.39 3.91
670 706 2.743538 CAGCGCAACTGGCTAGCA 60.744 61.111 18.24 1.68 43.19 3.49
678 714 0.798776 GTAACATCAGCAGCGCAACT 59.201 50.000 11.47 2.49 0.00 3.16
679 715 0.179189 GGTAACATCAGCAGCGCAAC 60.179 55.000 11.47 0.00 0.00 4.17
680 716 1.634757 CGGTAACATCAGCAGCGCAA 61.635 55.000 11.47 0.00 0.00 4.85
681 717 2.100031 CGGTAACATCAGCAGCGCA 61.100 57.895 11.47 0.00 0.00 6.09
682 718 0.804544 TACGGTAACATCAGCAGCGC 60.805 55.000 0.00 0.00 36.69 5.92
683 719 1.588404 CTTACGGTAACATCAGCAGCG 59.412 52.381 0.00 0.00 38.99 5.18
684 720 1.933853 CCTTACGGTAACATCAGCAGC 59.066 52.381 0.00 0.00 0.00 5.25
685 721 1.933853 GCCTTACGGTAACATCAGCAG 59.066 52.381 0.00 0.00 0.00 4.24
688 724 2.967362 TGTGCCTTACGGTAACATCAG 58.033 47.619 0.00 0.00 0.00 2.90
695 731 3.646650 GCGTATGTGCCTTACGGTA 57.353 52.632 16.53 0.00 41.99 4.02
704 740 1.082561 CATCATGCGGCGTATGTGC 60.083 57.895 31.53 5.36 0.00 4.57
705 741 1.082561 GCATCATGCGGCGTATGTG 60.083 57.895 31.53 27.39 31.71 3.21
813 874 4.179926 GCTAGCTAGCTGCATACATGTA 57.820 45.455 33.71 8.27 45.62 2.29
876 963 3.059325 CAGCTATATCTTTGCGAGGTTGC 60.059 47.826 0.00 0.00 0.00 4.17
877 964 3.059325 GCAGCTATATCTTTGCGAGGTTG 60.059 47.826 0.00 0.00 0.00 3.77
884 971 3.119919 GGCAGATGCAGCTATATCTTTGC 60.120 47.826 3.06 1.47 44.36 3.68
886 973 4.637387 AGGCAGATGCAGCTATATCTTT 57.363 40.909 3.06 0.00 44.36 2.52
890 977 2.434428 GCAAGGCAGATGCAGCTATAT 58.566 47.619 3.06 0.00 43.29 0.86
917 1004 0.025513 CACTTAATCAGCTCGCGTGC 59.974 55.000 24.56 24.56 0.00 5.34
918 1005 1.585668 CTCACTTAATCAGCTCGCGTG 59.414 52.381 5.77 4.44 0.00 5.34
919 1006 1.914634 CTCACTTAATCAGCTCGCGT 58.085 50.000 5.77 0.00 0.00 6.01
920 1007 0.574454 GCTCACTTAATCAGCTCGCG 59.426 55.000 0.00 0.00 0.00 5.87
929 1016 1.372087 GGCAGCTGCGCTCACTTAAT 61.372 55.000 31.19 0.00 43.26 1.40
942 1029 0.179936 GGATCAGCAAGTAGGCAGCT 59.820 55.000 0.00 0.00 39.63 4.24
950 1037 1.963985 AGGAGAAGGGATCAGCAAGT 58.036 50.000 0.00 0.00 0.00 3.16
952 1039 1.765314 GCTAGGAGAAGGGATCAGCAA 59.235 52.381 0.00 0.00 0.00 3.91
954 1041 1.715785 AGCTAGGAGAAGGGATCAGC 58.284 55.000 0.00 0.00 0.00 4.26
956 1043 2.448961 AGCTAGCTAGGAGAAGGGATCA 59.551 50.000 17.69 0.00 0.00 2.92
958 1045 3.563479 GCTAGCTAGCTAGGAGAAGGGAT 60.563 52.174 39.60 11.07 45.62 3.85
959 1046 2.224917 GCTAGCTAGCTAGGAGAAGGGA 60.225 54.545 39.60 13.88 45.62 4.20
985 1075 5.089970 TCCTCCATATGATGCTAATTCGG 57.910 43.478 3.65 0.00 0.00 4.30
987 1077 7.108194 TGTCATCCTCCATATGATGCTAATTC 58.892 38.462 3.65 0.00 38.57 2.17
988 1078 7.024345 TGTCATCCTCCATATGATGCTAATT 57.976 36.000 3.65 0.00 38.57 1.40
989 1079 6.631763 TGTCATCCTCCATATGATGCTAAT 57.368 37.500 3.65 0.00 38.57 1.73
990 1080 6.270695 TCTTGTCATCCTCCATATGATGCTAA 59.729 38.462 3.65 0.00 38.57 3.09
991 1081 5.781818 TCTTGTCATCCTCCATATGATGCTA 59.218 40.000 3.65 0.00 38.57 3.49
992 1082 4.596212 TCTTGTCATCCTCCATATGATGCT 59.404 41.667 3.65 0.00 38.57 3.79
993 1083 4.903054 TCTTGTCATCCTCCATATGATGC 58.097 43.478 3.65 0.00 38.57 3.91
994 1084 5.938710 CCTTCTTGTCATCCTCCATATGATG 59.061 44.000 3.65 0.00 39.75 3.07
995 1085 5.848369 TCCTTCTTGTCATCCTCCATATGAT 59.152 40.000 3.65 0.00 35.87 2.45
996 1086 5.218959 TCCTTCTTGTCATCCTCCATATGA 58.781 41.667 3.65 0.00 0.00 2.15
997 1087 5.512749 CCTCCTTCTTGTCATCCTCCATATG 60.513 48.000 0.00 0.00 0.00 1.78
998 1088 4.596643 CCTCCTTCTTGTCATCCTCCATAT 59.403 45.833 0.00 0.00 0.00 1.78
999 1089 3.969976 CCTCCTTCTTGTCATCCTCCATA 59.030 47.826 0.00 0.00 0.00 2.74
1202 1292 3.457625 CTCATCCTGCCAGCCTCGG 62.458 68.421 0.00 0.00 0.00 4.63
1428 1530 1.488393 CCATTCTCCTCCTTCACTCCC 59.512 57.143 0.00 0.00 0.00 4.30
1454 1556 1.227734 ACCGACCGACCAAACCAAG 60.228 57.895 0.00 0.00 0.00 3.61
1469 1575 1.522355 CTAGTCCTGCCATGCACCG 60.522 63.158 0.00 0.00 33.79 4.94
1499 1605 0.459585 ACGTGTGTGAGTGTGTCCAC 60.460 55.000 0.00 0.00 42.17 4.02
1574 1689 2.675844 TCCATCTTCGCGGTAACAAATG 59.324 45.455 6.13 1.12 0.00 2.32
1684 1828 7.405292 ACATGGGTAAATGCAGCATACTATAT 58.595 34.615 8.75 0.00 0.00 0.86
1693 1837 3.019564 AGAGAACATGGGTAAATGCAGC 58.980 45.455 0.00 0.00 0.00 5.25
1721 1865 3.748645 TTTTAGCCATAGCCAAGGGAA 57.251 42.857 0.00 0.00 41.25 3.97
1722 1866 3.748645 TTTTTAGCCATAGCCAAGGGA 57.251 42.857 0.00 0.00 41.25 4.20
1723 1867 3.070015 CCATTTTTAGCCATAGCCAAGGG 59.930 47.826 0.00 0.00 41.25 3.95
1724 1868 3.706086 ACCATTTTTAGCCATAGCCAAGG 59.294 43.478 0.00 0.00 41.25 3.61
1725 1869 4.685924 CACCATTTTTAGCCATAGCCAAG 58.314 43.478 0.00 0.00 41.25 3.61
1726 1870 3.118811 GCACCATTTTTAGCCATAGCCAA 60.119 43.478 0.00 0.00 41.25 4.52
1727 1871 2.430332 GCACCATTTTTAGCCATAGCCA 59.570 45.455 0.00 0.00 41.25 4.75
1728 1872 2.224042 GGCACCATTTTTAGCCATAGCC 60.224 50.000 0.00 0.00 46.26 3.93
1729 1873 3.097877 GGCACCATTTTTAGCCATAGC 57.902 47.619 0.00 0.00 46.26 2.97
1763 1907 8.143835 ACTTGTAGAAATTGGTGAAAAATCCAG 58.856 33.333 0.00 0.00 35.05 3.86
1786 1930 8.885346 CCCTTTCTTCCCAGAAGATATATACTT 58.115 37.037 7.81 0.00 40.28 2.24
1807 1952 3.139397 TGGAGTGGACATTGTTACCCTTT 59.861 43.478 0.00 0.00 0.00 3.11
1812 1957 3.127548 CAGCATGGAGTGGACATTGTTAC 59.872 47.826 0.00 0.00 0.00 2.50
1974 2138 1.841302 ATTCTGAAGGCGGGTCTGCA 61.841 55.000 4.06 0.00 36.28 4.41
1975 2139 1.078143 ATTCTGAAGGCGGGTCTGC 60.078 57.895 0.00 0.00 0.00 4.26
2020 2194 5.450688 GGTCGATCAATAGAGTGCTGTTACT 60.451 44.000 0.00 0.00 0.00 2.24
2109 2283 3.618019 CGTAAGGGTTCCAATCCTCGAAA 60.618 47.826 0.00 0.00 39.03 3.46
2121 2295 6.073980 GGCAAAGAAAATTTTCGTAAGGGTTC 60.074 38.462 21.98 8.17 41.92 3.62
2211 4166 9.577110 GAATGCATAATTTCTCTTGAACATGAA 57.423 29.630 0.00 0.00 31.02 2.57
2213 4168 7.437267 GGGAATGCATAATTTCTCTTGAACATG 59.563 37.037 0.00 0.00 31.02 3.21
2214 4169 7.343833 AGGGAATGCATAATTTCTCTTGAACAT 59.656 33.333 0.00 0.00 31.02 2.71
2215 4170 6.664816 AGGGAATGCATAATTTCTCTTGAACA 59.335 34.615 0.00 0.00 31.02 3.18
2216 4171 7.105241 AGGGAATGCATAATTTCTCTTGAAC 57.895 36.000 0.00 0.00 31.02 3.18
2218 4173 8.821686 TTTAGGGAATGCATAATTTCTCTTGA 57.178 30.769 5.52 0.00 0.00 3.02
2238 4195 9.565090 TGATGATTCATTCCAAGAGTATTTAGG 57.435 33.333 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.