Multiple sequence alignment - TraesCS2B01G370200

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 TraesCS2B01G370200 chr2B 100.000 4189 0 0 1 4189 527871953 527876141 0.000000e+00 7736
1 TraesCS2B01G370200 chr2D 92.911 2934 106 41 645 3540 448120323 448123192 0.000000e+00 4172
2 TraesCS2B01G370200 chr2D 91.876 677 28 18 1 656 448119305 448119975 0.000000e+00 920
3 TraesCS2B01G370200 chr2D 87.500 680 33 22 3551 4189 448123238 448123906 0.000000e+00 737
4 TraesCS2B01G370200 chr2A 90.802 2555 115 59 376 2875 592689946 592692435 0.000000e+00 3306
5 TraesCS2B01G370200 chr2A 92.751 676 35 7 2886 3551 592692727 592693398 0.000000e+00 965
6 TraesCS2B01G370200 chr2A 86.598 679 36 19 3550 4189 592693427 592694089 0.000000e+00 699
7 TraesCS2B01G370200 chr2A 91.899 358 14 10 1 348 592689600 592689952 1.750000e-133 486
8 TraesCS2B01G370200 chr7A 89.844 896 58 14 1874 2769 10808980 10809842 0.000000e+00 1120
9 TraesCS2B01G370200 chr3B 90.932 397 23 6 1678 2073 275910387 275910771 4.800000e-144 521
10 TraesCS2B01G370200 chr4A 91.328 369 20 5 2308 2676 196611477 196611121 1.050000e-135 494
11 TraesCS2B01G370200 chr4A 93.793 145 8 1 1678 1821 196613218 196613074 2.540000e-52 217


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 TraesCS2B01G370200 chr2B 527871953 527876141 4188 False 7736.0 7736 100.000000 1 4189 1 chr2B.!!$F1 4188
1 TraesCS2B01G370200 chr2D 448119305 448123906 4601 False 1943.0 4172 90.762333 1 4189 3 chr2D.!!$F1 4188
2 TraesCS2B01G370200 chr2A 592689600 592694089 4489 False 1364.0 3306 90.512500 1 4189 4 chr2A.!!$F1 4188
3 TraesCS2B01G370200 chr7A 10808980 10809842 862 False 1120.0 1120 89.844000 1874 2769 1 chr7A.!!$F1 895
4 TraesCS2B01G370200 chr4A 196611121 196613218 2097 True 355.5 494 92.560500 1678 2676 2 chr4A.!!$R1 998

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
684 1070 0.035439 ACGGCATTCTCATCGGGTTT 60.035 50.0 0.0 0.0 0.0 3.27 F
820 1219 0.176680 ATTAGAGTGGAGCCAGCGTG 59.823 55.0 0.0 0.0 0.0 5.34 F
1104 1516 0.465097 ATTCGATTGGAGGGCAGCAG 60.465 55.0 0.0 0.0 0.0 4.24 F
2137 2864 0.467290 GGGTTGGTTTCTGTCCAGCA 60.467 55.0 0.0 0.0 37.8 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1553 1977 0.167470 CAGCCACGACTTGATTGCTG 59.833 55.0 0.00 0.0 40.05 4.41 R
2128 2855 0.461548 TAGAAGGCGATGCTGGACAG 59.538 55.0 0.00 0.0 0.00 3.51 R
2834 4441 0.241749 ATGAACGCGACCGACAGTAA 59.758 50.0 15.93 0.0 38.29 2.24 R
3453 5361 0.178924 AGCAACCAAAAGGCAGGGAT 60.179 50.0 0.00 0.0 0.00 3.85 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
54 56 5.642063 ACACAATACAAACTCTACCCGAATG 59.358 40.000 0.00 0.00 0.00 2.67
62 64 2.158900 ACTCTACCCGAATGAATGGCAG 60.159 50.000 0.00 0.00 0.00 4.85
129 131 4.143333 CCACTACGGCCGGTCTGG 62.143 72.222 31.76 24.45 42.50 3.86
529 557 0.179158 ACATGCATACACGTACGCGA 60.179 50.000 15.93 0.30 42.00 5.87
573 601 1.557099 TGTCCCTGCTCGTGTAATCT 58.443 50.000 0.00 0.00 0.00 2.40
684 1070 0.035439 ACGGCATTCTCATCGGGTTT 60.035 50.000 0.00 0.00 0.00 3.27
686 1072 2.285083 CGGCATTCTCATCGGGTTTAA 58.715 47.619 0.00 0.00 0.00 1.52
688 1074 3.058914 CGGCATTCTCATCGGGTTTAATC 60.059 47.826 0.00 0.00 0.00 1.75
689 1075 3.058914 GGCATTCTCATCGGGTTTAATCG 60.059 47.826 0.00 0.00 0.00 3.34
692 1078 4.475051 TTCTCATCGGGTTTAATCGGAA 57.525 40.909 0.00 0.00 0.00 4.30
693 1079 4.054780 TCTCATCGGGTTTAATCGGAAG 57.945 45.455 0.00 0.00 0.00 3.46
694 1080 2.544267 CTCATCGGGTTTAATCGGAAGC 59.456 50.000 0.00 0.00 0.00 3.86
695 1081 1.602377 CATCGGGTTTAATCGGAAGCC 59.398 52.381 0.00 0.00 40.40 4.35
696 1082 0.906775 TCGGGTTTAATCGGAAGCCT 59.093 50.000 3.92 0.00 41.36 4.58
697 1083 1.014352 CGGGTTTAATCGGAAGCCTG 58.986 55.000 3.92 2.22 41.36 4.85
698 1084 1.389555 GGGTTTAATCGGAAGCCTGG 58.610 55.000 0.00 0.00 40.58 4.45
699 1085 1.340697 GGGTTTAATCGGAAGCCTGGT 60.341 52.381 0.00 0.00 40.58 4.00
700 1086 2.092807 GGGTTTAATCGGAAGCCTGGTA 60.093 50.000 0.00 0.00 40.58 3.25
701 1087 3.203716 GGTTTAATCGGAAGCCTGGTAG 58.796 50.000 0.00 0.00 0.00 3.18
702 1088 3.370209 GGTTTAATCGGAAGCCTGGTAGT 60.370 47.826 0.00 0.00 0.00 2.73
703 1089 4.141869 GGTTTAATCGGAAGCCTGGTAGTA 60.142 45.833 0.00 0.00 0.00 1.82
704 1090 4.931661 TTAATCGGAAGCCTGGTAGTAG 57.068 45.455 0.00 0.00 0.00 2.57
705 1091 2.456073 ATCGGAAGCCTGGTAGTAGT 57.544 50.000 0.00 0.00 0.00 2.73
706 1092 3.589951 ATCGGAAGCCTGGTAGTAGTA 57.410 47.619 0.00 0.00 0.00 1.82
709 1095 3.455910 TCGGAAGCCTGGTAGTAGTAGTA 59.544 47.826 0.00 0.00 0.00 1.82
720 1106 7.070571 CCTGGTAGTAGTAGTAGTAGTAGGTGT 59.929 44.444 10.92 0.00 0.00 4.16
754 1143 5.048224 GGCCATGCTCGATTTACTACTACTA 60.048 44.000 0.00 0.00 0.00 1.82
766 1155 9.771915 GATTTACTACTACTACAGAACTGTGTC 57.228 37.037 16.37 0.00 44.63 3.67
820 1219 0.176680 ATTAGAGTGGAGCCAGCGTG 59.823 55.000 0.00 0.00 0.00 5.34
844 1243 3.291584 TCTGGTGGTAAACAAACATGCA 58.708 40.909 0.00 0.00 0.00 3.96
899 1299 1.040339 TGGAAAACCCGCTGCAAACT 61.040 50.000 0.00 0.00 37.93 2.66
918 1319 3.136123 CGGTGCAAGGATGGCTGG 61.136 66.667 0.00 0.00 34.64 4.85
920 1321 3.818787 GTGCAAGGATGGCTGGCG 61.819 66.667 0.00 0.00 34.64 5.69
1028 1437 0.588252 CAAGGACACCGCAACTTGAG 59.412 55.000 0.00 0.00 42.07 3.02
1029 1438 0.535102 AAGGACACCGCAACTTGAGG 60.535 55.000 9.83 9.83 43.39 3.86
1030 1439 1.966451 GGACACCGCAACTTGAGGG 60.966 63.158 15.22 7.05 41.96 4.30
1031 1440 1.070786 GACACCGCAACTTGAGGGA 59.929 57.895 15.22 0.00 41.96 4.20
1103 1515 0.749091 CATTCGATTGGAGGGCAGCA 60.749 55.000 0.00 0.00 0.00 4.41
1104 1516 0.465097 ATTCGATTGGAGGGCAGCAG 60.465 55.000 0.00 0.00 0.00 4.24
1105 1517 3.207669 CGATTGGAGGGCAGCAGC 61.208 66.667 0.00 0.00 41.10 5.25
1106 1518 2.044650 GATTGGAGGGCAGCAGCA 60.045 61.111 2.65 0.00 44.61 4.41
1107 1519 2.044252 ATTGGAGGGCAGCAGCAG 60.044 61.111 2.65 0.00 44.61 4.24
1108 1520 3.657038 ATTGGAGGGCAGCAGCAGG 62.657 63.158 2.65 0.00 44.61 4.85
1204 1620 2.046314 ACCGCCAATCTTGTCCGG 60.046 61.111 14.08 14.08 42.85 5.14
1473 1897 2.401766 CGCCTTCCACTGCATCACC 61.402 63.158 0.00 0.00 0.00 4.02
1551 1975 4.202305 TGCGGATTTTTGGTCTGGATTTTT 60.202 37.500 0.00 0.00 0.00 1.94
1553 1977 4.929211 CGGATTTTTGGTCTGGATTTTTCC 59.071 41.667 0.00 0.00 0.00 3.13
1554 1978 5.510520 CGGATTTTTGGTCTGGATTTTTCCA 60.511 40.000 0.00 0.00 38.25 3.53
1568 1994 3.624326 TTTTCCAGCAATCAAGTCGTG 57.376 42.857 0.00 0.00 0.00 4.35
1571 1997 0.957395 CCAGCAATCAAGTCGTGGCT 60.957 55.000 0.00 0.00 0.00 4.75
1601 2027 1.064654 GATCCGGAATGCTTCTTGTGC 59.935 52.381 9.01 0.00 0.00 4.57
1679 2109 1.338655 GAGAAGAGATCCTACGTGGCC 59.661 57.143 0.00 0.00 35.26 5.36
1739 2169 3.771160 ATGGTCGGCTGGTCGTCC 61.771 66.667 4.14 4.14 38.48 4.79
1847 2277 4.353437 AACAGGACCGTCGCCGTC 62.353 66.667 0.00 0.00 0.00 4.79
2042 2476 7.001674 ACATCCATTATTAATTCCACCGCTAA 58.998 34.615 0.00 0.00 0.00 3.09
2089 2806 3.322828 AGCAGTGGTAAGAGAAACGGTAA 59.677 43.478 0.00 0.00 0.00 2.85
2128 2855 2.437413 GAGGATCTGTGGGTTGGTTTC 58.563 52.381 0.00 0.00 0.00 2.78
2137 2864 0.467290 GGGTTGGTTTCTGTCCAGCA 60.467 55.000 0.00 0.00 37.80 4.41
2143 2870 0.674895 GTTTCTGTCCAGCATCGCCT 60.675 55.000 0.00 0.00 0.00 5.52
2218 3062 2.487532 GCTGCTGTCCATGATGGGC 61.488 63.158 9.60 9.60 43.98 5.36
2466 4065 5.045872 GCAGCACAGAATTTTTCTTGAGTT 58.954 37.500 0.00 0.00 38.11 3.01
2467 4066 5.174579 GCAGCACAGAATTTTTCTTGAGTTC 59.825 40.000 0.00 0.00 38.11 3.01
2468 4067 5.397534 CAGCACAGAATTTTTCTTGAGTTCG 59.602 40.000 0.00 0.00 38.11 3.95
2469 4068 5.296780 AGCACAGAATTTTTCTTGAGTTCGA 59.703 36.000 0.00 0.00 38.11 3.71
2794 4398 2.228582 CCGTGATTTGTTGCCATCAGAA 59.771 45.455 0.00 0.00 29.85 3.02
2795 4399 3.119388 CCGTGATTTGTTGCCATCAGAAT 60.119 43.478 0.00 0.00 29.85 2.40
2796 4400 4.096231 CCGTGATTTGTTGCCATCAGAATA 59.904 41.667 0.00 0.00 29.85 1.75
2797 4401 5.268544 CGTGATTTGTTGCCATCAGAATAG 58.731 41.667 0.00 0.00 29.85 1.73
2807 4411 5.731591 TGCCATCAGAATAGATAGATGCTG 58.268 41.667 0.00 0.00 37.21 4.41
2826 4433 1.374252 CCGTTCGTTGACTCCCAGG 60.374 63.158 0.00 0.00 0.00 4.45
2834 4441 3.053842 TCGTTGACTCCCAGGATAGTACT 60.054 47.826 0.00 0.00 0.00 2.73
2835 4442 3.700038 CGTTGACTCCCAGGATAGTACTT 59.300 47.826 0.00 0.00 0.00 2.24
2910 4802 5.419155 AGAGAGAGTTGAAACCACGATGATA 59.581 40.000 0.00 0.00 0.00 2.15
2932 4824 4.648626 TGTGCTCACCCTGCTGCC 62.649 66.667 0.00 0.00 0.00 4.85
3189 5089 1.073964 CTACGAGGACGACGACTGAA 58.926 55.000 0.00 0.00 42.66 3.02
3193 5093 1.158434 GAGGACGACGACTGAAGACT 58.842 55.000 0.00 0.00 0.00 3.24
3256 5159 6.203530 CGCATAGAGAGAATTAATTTGGAGCA 59.796 38.462 1.43 0.00 0.00 4.26
3275 5178 2.740580 GCAGCTACTACCAAACGGCATA 60.741 50.000 0.00 0.00 0.00 3.14
3292 5195 3.600388 GCATAGTTTGTGGTAGCTCACT 58.400 45.455 7.05 0.00 38.40 3.41
3299 5202 0.038159 GTGGTAGCTCACTTCGCAGT 60.038 55.000 0.00 0.00 34.98 4.40
3331 5234 4.584874 TGGCGAATTTGAGGATTCTGTTA 58.415 39.130 0.00 0.00 34.58 2.41
3453 5361 9.386010 GTACATGGTGTTATAATTCTTGTACCA 57.614 33.333 18.29 0.00 40.78 3.25
3486 5396 2.224744 TGGTTGCTTGGTAGATTGCTCA 60.225 45.455 0.00 0.00 0.00 4.26
3488 5398 3.366374 GGTTGCTTGGTAGATTGCTCAAC 60.366 47.826 0.00 0.00 33.78 3.18
3500 5410 5.629125 AGATTGCTCAACTTTTCTTCCTCT 58.371 37.500 0.00 0.00 0.00 3.69
3568 5515 1.079127 CATCCCTTCGGCTTCACGT 60.079 57.895 0.00 0.00 34.94 4.49
3583 5530 1.004918 ACGTCTGAGCTTTTCCCCG 60.005 57.895 0.00 0.00 0.00 5.73
3591 5538 2.402572 GCTTTTCCCCGCTGAGAGC 61.403 63.158 0.00 0.00 38.02 4.09
3592 5539 1.003355 CTTTTCCCCGCTGAGAGCA 60.003 57.895 0.00 0.00 42.58 4.26
3593 5540 1.003355 TTTTCCCCGCTGAGAGCAG 60.003 57.895 0.00 0.00 42.58 4.24
3594 5541 1.768684 TTTTCCCCGCTGAGAGCAGT 61.769 55.000 0.00 0.00 42.58 4.40
3600 5547 2.675056 CGCTGAGAGCAGTGGCAAC 61.675 63.158 0.00 0.00 46.38 4.17
3602 5549 0.959372 GCTGAGAGCAGTGGCAACAT 60.959 55.000 0.00 0.00 46.14 2.71
3603 5550 3.134888 GCTGAGAGCAGTGGCAACATG 62.135 57.143 0.00 0.00 46.14 3.21
3627 5574 0.963962 ACTGGAAGGCTGCAAATGTG 59.036 50.000 0.50 0.00 39.30 3.21
3686 5654 7.568199 TCTACCAAGCAAAATTTAGGCTATC 57.432 36.000 15.27 0.00 36.76 2.08
3688 5656 5.272402 ACCAAGCAAAATTTAGGCTATCCT 58.728 37.500 15.27 0.00 46.57 3.24
3689 5657 6.431722 ACCAAGCAAAATTTAGGCTATCCTA 58.568 36.000 15.27 0.00 43.91 2.94
3691 5659 7.565029 ACCAAGCAAAATTTAGGCTATCCTATT 59.435 33.333 15.27 0.00 44.09 1.73
3695 5663 9.868160 AGCAAAATTTAGGCTATCCTATTTAGT 57.132 29.630 13.80 0.00 44.09 2.24
3724 5694 2.514458 AAAGGTGCACCCAGAATAGG 57.486 50.000 32.29 0.00 36.42 2.57
3788 5759 2.568090 GCCAAGCCGACATGGTTG 59.432 61.111 0.00 0.00 41.21 3.77
3816 5787 5.565509 TCAACTATCAGTCTCTCACTCTGT 58.434 41.667 0.00 0.00 30.26 3.41
3817 5788 6.007076 TCAACTATCAGTCTCTCACTCTGTT 58.993 40.000 0.00 0.00 30.26 3.16
3818 5789 6.150307 TCAACTATCAGTCTCTCACTCTGTTC 59.850 42.308 0.00 0.00 30.26 3.18
3820 5791 6.245408 ACTATCAGTCTCTCACTCTGTTCTT 58.755 40.000 0.00 0.00 30.26 2.52
3843 5814 4.764823 TGCACCATATTCGAGAAAGGTTTT 59.235 37.500 5.59 0.00 0.00 2.43
3894 5870 2.040939 TGGAACACTCCGTCTGGTAAA 58.959 47.619 0.00 0.00 45.85 2.01
3896 5872 3.064931 GGAACACTCCGTCTGGTAAAAG 58.935 50.000 0.00 0.00 36.30 2.27
3897 5873 3.493873 GGAACACTCCGTCTGGTAAAAGT 60.494 47.826 0.00 0.00 36.30 2.66
3898 5874 4.262164 GGAACACTCCGTCTGGTAAAAGTA 60.262 45.833 0.00 0.00 36.30 2.24
3899 5875 4.248691 ACACTCCGTCTGGTAAAAGTAC 57.751 45.455 0.00 0.00 36.30 2.73
3900 5876 3.893813 ACACTCCGTCTGGTAAAAGTACT 59.106 43.478 0.00 0.00 36.30 2.73
3901 5877 4.022503 ACACTCCGTCTGGTAAAAGTACTC 60.023 45.833 0.00 0.00 36.30 2.59
3902 5878 3.190118 ACTCCGTCTGGTAAAAGTACTCG 59.810 47.826 0.00 0.00 36.30 4.18
3903 5879 2.095059 TCCGTCTGGTAAAAGTACTCGC 60.095 50.000 0.00 0.00 36.30 5.03
3904 5880 2.094854 CCGTCTGGTAAAAGTACTCGCT 60.095 50.000 0.00 0.00 0.00 4.93
3905 5881 3.169733 CGTCTGGTAAAAGTACTCGCTC 58.830 50.000 0.00 0.00 0.00 5.03
3914 5893 0.171455 AGTACTCGCTCCGCTTTCAG 59.829 55.000 0.00 0.00 0.00 3.02
4033 6017 2.936912 GCCACTCGACTCAGGCAGT 61.937 63.158 7.56 0.00 46.26 4.40
4127 6111 4.483243 GCGGCCATCGAAAGGGGA 62.483 66.667 2.24 0.00 42.43 4.81
4128 6112 2.513897 CGGCCATCGAAAGGGGAC 60.514 66.667 2.24 0.97 42.43 4.46
4129 6113 2.513897 GGCCATCGAAAGGGGACG 60.514 66.667 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 56 1.202867 GGAGGGATCTTCCTGCCATTC 60.203 57.143 8.89 0.00 39.05 2.67
138 140 1.962306 GCTTGCCAAACCGTCCGTA 60.962 57.895 0.00 0.00 0.00 4.02
223 227 3.976490 AACGGGGAGGAGATGCCGA 62.976 63.158 0.00 0.00 41.29 5.54
406 420 2.438614 GAGGAAGGGGAAAGCCGC 60.439 66.667 0.00 0.00 46.91 6.53
473 492 1.418334 ATCAGTGGGCTAGCCAGTAG 58.582 55.000 34.09 20.45 37.98 2.57
474 493 1.486310 CAATCAGTGGGCTAGCCAGTA 59.514 52.381 34.09 17.50 37.98 2.74
475 494 0.254178 CAATCAGTGGGCTAGCCAGT 59.746 55.000 34.09 19.74 37.98 4.00
573 601 2.089980 GTCGCTTGTCCTGTAGAGGTA 58.910 52.381 5.71 0.00 40.76 3.08
684 1070 3.907221 ACTACTACCAGGCTTCCGATTA 58.093 45.455 0.00 0.00 0.00 1.75
686 1072 2.456073 ACTACTACCAGGCTTCCGAT 57.544 50.000 0.00 0.00 0.00 4.18
688 1074 2.652590 ACTACTACTACCAGGCTTCCG 58.347 52.381 0.00 0.00 0.00 4.30
689 1075 4.790937 ACTACTACTACTACCAGGCTTCC 58.209 47.826 0.00 0.00 0.00 3.46
692 1078 6.269769 CCTACTACTACTACTACTACCAGGCT 59.730 46.154 0.00 0.00 0.00 4.58
693 1079 6.042666 ACCTACTACTACTACTACTACCAGGC 59.957 46.154 0.00 0.00 0.00 4.85
694 1080 7.070571 ACACCTACTACTACTACTACTACCAGG 59.929 44.444 0.00 0.00 0.00 4.45
695 1081 8.017418 ACACCTACTACTACTACTACTACCAG 57.983 42.308 0.00 0.00 0.00 4.00
696 1082 7.201830 CGACACCTACTACTACTACTACTACCA 60.202 44.444 0.00 0.00 0.00 3.25
697 1083 7.142680 CGACACCTACTACTACTACTACTACC 58.857 46.154 0.00 0.00 0.00 3.18
698 1084 7.708998 ACGACACCTACTACTACTACTACTAC 58.291 42.308 0.00 0.00 0.00 2.73
699 1085 7.254829 CGACGACACCTACTACTACTACTACTA 60.255 44.444 0.00 0.00 0.00 1.82
700 1086 6.459024 CGACGACACCTACTACTACTACTACT 60.459 46.154 0.00 0.00 0.00 2.57
701 1087 5.683743 CGACGACACCTACTACTACTACTAC 59.316 48.000 0.00 0.00 0.00 2.73
702 1088 5.221067 CCGACGACACCTACTACTACTACTA 60.221 48.000 0.00 0.00 0.00 1.82
703 1089 4.440802 CCGACGACACCTACTACTACTACT 60.441 50.000 0.00 0.00 0.00 2.57
704 1090 3.799420 CCGACGACACCTACTACTACTAC 59.201 52.174 0.00 0.00 0.00 2.73
705 1091 3.738281 GCCGACGACACCTACTACTACTA 60.738 52.174 0.00 0.00 0.00 1.82
706 1092 2.898705 CCGACGACACCTACTACTACT 58.101 52.381 0.00 0.00 0.00 2.57
709 1095 1.364626 CGCCGACGACACCTACTACT 61.365 60.000 0.00 0.00 43.93 2.57
742 1128 7.175641 GGGACACAGTTCTGTAGTAGTAGTAAA 59.824 40.741 5.11 0.00 0.00 2.01
820 1219 2.303175 TGTTTGTTTACCACCAGAGCC 58.697 47.619 0.00 0.00 0.00 4.70
824 1223 3.724508 TGCATGTTTGTTTACCACCAG 57.275 42.857 0.00 0.00 0.00 4.00
844 1243 4.704057 GCAGAAATGAGAAAGAAGACCCAT 59.296 41.667 0.00 0.00 0.00 4.00
899 1299 4.349503 AGCCATCCTTGCACCGCA 62.350 61.111 0.00 0.00 36.47 5.69
918 1319 1.732474 GCGCACATGCATTTACACGC 61.732 55.000 0.30 11.84 42.21 5.34
920 1321 0.171007 AGGCGCACATGCATTTACAC 59.829 50.000 10.83 0.00 42.21 2.90
1028 1437 2.041405 CCTGACTCCCTCCCTCCC 60.041 72.222 0.00 0.00 0.00 4.30
1029 1438 2.041405 CCCTGACTCCCTCCCTCC 60.041 72.222 0.00 0.00 0.00 4.30
1030 1439 1.075600 CTCCCTGACTCCCTCCCTC 60.076 68.421 0.00 0.00 0.00 4.30
1031 1440 2.641746 CCTCCCTGACTCCCTCCCT 61.642 68.421 0.00 0.00 0.00 4.20
1079 1491 0.748005 CCCTCCAATCGAATGGCGTT 60.748 55.000 15.04 0.00 40.46 4.84
1083 1495 1.450531 GCTGCCCTCCAATCGAATGG 61.451 60.000 13.67 13.67 42.12 3.16
1103 1515 2.754658 GATGCTTGCTGCCCTGCT 60.755 61.111 0.00 0.00 42.00 4.24
1104 1516 3.834799 GGATGCTTGCTGCCCTGC 61.835 66.667 0.00 0.00 42.00 4.85
1105 1517 2.044252 AGGATGCTTGCTGCCCTG 60.044 61.111 0.00 0.00 42.00 4.45
1106 1518 2.274760 GAGGATGCTTGCTGCCCT 59.725 61.111 0.00 0.00 42.00 5.19
1107 1519 2.119655 CAGAGGATGCTTGCTGCCC 61.120 63.158 0.00 0.00 42.00 5.36
1108 1520 1.077930 TCAGAGGATGCTTGCTGCC 60.078 57.895 0.00 0.00 42.00 4.85
1109 1521 1.375098 GGTCAGAGGATGCTTGCTGC 61.375 60.000 0.00 0.00 43.25 5.25
1110 1522 0.252479 AGGTCAGAGGATGCTTGCTG 59.748 55.000 0.00 0.00 0.00 4.41
1111 1523 0.252479 CAGGTCAGAGGATGCTTGCT 59.748 55.000 0.00 0.00 0.00 3.91
1112 1524 1.375098 GCAGGTCAGAGGATGCTTGC 61.375 60.000 0.00 0.00 35.78 4.01
1113 1525 0.747283 GGCAGGTCAGAGGATGCTTG 60.747 60.000 0.00 0.00 38.71 4.01
1114 1526 1.203441 TGGCAGGTCAGAGGATGCTT 61.203 55.000 0.00 0.00 38.71 3.91
1154 1570 2.225791 GAAATGGCCAAGGTTCCGCC 62.226 60.000 10.96 0.00 43.32 6.13
1156 1572 0.611896 AGGAAATGGCCAAGGTTCCG 60.612 55.000 27.65 0.00 43.60 4.30
1157 1573 1.186200 GAGGAAATGGCCAAGGTTCC 58.814 55.000 27.25 27.25 39.94 3.62
1158 1574 1.186200 GGAGGAAATGGCCAAGGTTC 58.814 55.000 10.96 13.97 0.00 3.62
1159 1575 0.252239 GGGAGGAAATGGCCAAGGTT 60.252 55.000 10.96 4.08 0.00 3.50
1160 1576 1.149133 AGGGAGGAAATGGCCAAGGT 61.149 55.000 10.96 0.00 0.00 3.50
1227 1647 2.023673 TGCTGTGTCTTTCTTGGGTTG 58.976 47.619 0.00 0.00 0.00 3.77
1551 1975 0.955428 GCCACGACTTGATTGCTGGA 60.955 55.000 0.00 0.00 0.00 3.86
1553 1977 0.167470 CAGCCACGACTTGATTGCTG 59.833 55.000 0.00 0.00 40.05 4.41
1554 1978 1.580845 GCAGCCACGACTTGATTGCT 61.581 55.000 0.00 0.00 33.79 3.91
1555 1979 1.154150 GCAGCCACGACTTGATTGC 60.154 57.895 0.00 0.00 0.00 3.56
1556 1980 0.957395 AGGCAGCCACGACTTGATTG 60.957 55.000 15.80 0.00 0.00 2.67
1568 1994 1.301558 CGGATCAGATCAGGCAGCC 60.302 63.158 12.66 1.84 0.00 4.85
1571 1997 1.071228 CATTCCGGATCAGATCAGGCA 59.929 52.381 21.60 13.64 43.28 4.75
1601 2027 0.319211 TGTTCTTGTACTGGCGACGG 60.319 55.000 0.00 0.00 44.60 4.79
1679 2109 4.367023 TTGCCCGAGAACCCGACG 62.367 66.667 0.00 0.00 0.00 5.12
2042 2476 7.390027 TCTCTCGAGGAGAAAAGAAAATGAAT 58.610 34.615 13.56 0.00 46.85 2.57
2089 2806 6.117975 TCCTCCTCGGTTAGTAAAAATGTT 57.882 37.500 0.00 0.00 0.00 2.71
2101 2828 0.978146 CCCACAGATCCTCCTCGGTT 60.978 60.000 0.00 0.00 0.00 4.44
2128 2855 0.461548 TAGAAGGCGATGCTGGACAG 59.538 55.000 0.00 0.00 0.00 3.51
2466 4065 5.122554 GGCTAATCTAATGAGACTCGATCGA 59.877 44.000 18.32 18.32 33.41 3.59
2467 4066 5.123186 AGGCTAATCTAATGAGACTCGATCG 59.877 44.000 9.36 9.36 33.41 3.69
2468 4067 6.509418 AGGCTAATCTAATGAGACTCGATC 57.491 41.667 0.00 0.00 33.41 3.69
2469 4068 6.909550 AAGGCTAATCTAATGAGACTCGAT 57.090 37.500 0.00 0.00 33.41 3.59
2527 4126 1.303724 CAACCACCGCCCCATGTTA 60.304 57.895 0.00 0.00 0.00 2.41
2710 4313 7.119407 TCACAGTCAACATCTACTACAGTACTC 59.881 40.741 0.00 0.00 0.00 2.59
2794 4398 2.558795 ACGAACGGCAGCATCTATCTAT 59.441 45.455 0.00 0.00 0.00 1.98
2795 4399 1.954382 ACGAACGGCAGCATCTATCTA 59.046 47.619 0.00 0.00 0.00 1.98
2796 4400 0.747255 ACGAACGGCAGCATCTATCT 59.253 50.000 0.00 0.00 0.00 1.98
2797 4401 1.258982 CAACGAACGGCAGCATCTATC 59.741 52.381 0.00 0.00 0.00 2.08
2807 4411 2.027625 CTGGGAGTCAACGAACGGC 61.028 63.158 0.00 0.00 0.00 5.68
2826 4433 3.603401 CGCGACCGACAGTAAGTACTATC 60.603 52.174 0.00 0.00 33.68 2.08
2834 4441 0.241749 ATGAACGCGACCGACAGTAA 59.758 50.000 15.93 0.00 38.29 2.24
2835 4442 0.455464 CATGAACGCGACCGACAGTA 60.455 55.000 15.93 0.00 38.29 2.74
2932 4824 1.881973 CCTGTCCATCAACCAACACAG 59.118 52.381 0.00 0.00 0.00 3.66
3189 5089 2.837947 TGAAGGGTGATGGATGAGTCT 58.162 47.619 0.00 0.00 0.00 3.24
3193 5093 2.780414 AGGATGAAGGGTGATGGATGA 58.220 47.619 0.00 0.00 0.00 2.92
3256 5159 2.764572 ACTATGCCGTTTGGTAGTAGCT 59.235 45.455 0.35 0.00 37.67 3.32
3275 5178 2.755650 CGAAGTGAGCTACCACAAACT 58.244 47.619 8.15 0.00 39.42 2.66
3299 5202 1.254284 AAATTCGCCATCCGCCCAAA 61.254 50.000 0.00 0.00 36.73 3.28
3453 5361 0.178924 AGCAACCAAAAGGCAGGGAT 60.179 50.000 0.00 0.00 0.00 3.85
3454 5362 0.398381 AAGCAACCAAAAGGCAGGGA 60.398 50.000 0.00 0.00 0.00 4.20
3553 5500 3.996757 CTCAGACGTGAAGCCGAAGGG 62.997 61.905 0.00 0.00 39.77 3.95
3559 5506 1.195674 GAAAAGCTCAGACGTGAAGCC 59.804 52.381 0.00 0.00 31.08 4.35
3560 5507 1.195674 GGAAAAGCTCAGACGTGAAGC 59.804 52.381 0.00 0.00 30.14 3.86
3568 5515 1.003355 CAGCGGGGAAAAGCTCAGA 60.003 57.895 0.00 0.00 42.52 3.27
3583 5530 0.959372 ATGTTGCCACTGCTCTCAGC 60.959 55.000 0.00 0.00 44.10 4.26
3591 5538 1.536766 CAGTACCACATGTTGCCACTG 59.463 52.381 14.19 14.19 32.38 3.66
3592 5539 1.545428 CCAGTACCACATGTTGCCACT 60.545 52.381 0.00 0.00 0.00 4.00
3593 5540 0.881118 CCAGTACCACATGTTGCCAC 59.119 55.000 0.00 0.00 0.00 5.01
3594 5541 0.767998 TCCAGTACCACATGTTGCCA 59.232 50.000 0.00 0.00 0.00 4.92
3595 5542 1.812571 CTTCCAGTACCACATGTTGCC 59.187 52.381 0.00 0.00 0.00 4.52
3596 5543 1.812571 CCTTCCAGTACCACATGTTGC 59.187 52.381 0.00 0.00 0.00 4.17
3597 5544 1.812571 GCCTTCCAGTACCACATGTTG 59.187 52.381 0.00 0.00 0.00 3.33
3600 5547 1.742761 CAGCCTTCCAGTACCACATG 58.257 55.000 0.00 0.00 0.00 3.21
3602 5549 1.374947 GCAGCCTTCCAGTACCACA 59.625 57.895 0.00 0.00 0.00 4.17
3603 5550 0.250727 TTGCAGCCTTCCAGTACCAC 60.251 55.000 0.00 0.00 0.00 4.16
3605 5552 1.474077 CATTTGCAGCCTTCCAGTACC 59.526 52.381 0.00 0.00 0.00 3.34
3627 5574 2.843701 AGATCGAATGATTGCTGACCC 58.156 47.619 0.00 0.00 34.09 4.46
3660 5607 6.456795 AGCCTAAATTTTGCTTGGTAGATC 57.543 37.500 8.61 0.00 29.17 2.75
3663 5610 6.547510 AGGATAGCCTAAATTTTGCTTGGTAG 59.452 38.462 16.94 0.00 44.74 3.18
3664 5611 6.431722 AGGATAGCCTAAATTTTGCTTGGTA 58.568 36.000 16.94 4.99 44.74 3.25
3665 5612 5.272402 AGGATAGCCTAAATTTTGCTTGGT 58.728 37.500 16.94 7.08 44.74 3.67
3724 5694 6.866010 AAATGCTTGGTGGAAAGAAAATTC 57.134 33.333 0.00 0.00 0.00 2.17
3788 5759 5.125417 AGTGAGAGACTGATAGTTGAAGCTC 59.875 44.000 0.00 0.00 31.75 4.09
3816 5787 4.635765 CCTTTCTCGAATATGGTGCAAGAA 59.364 41.667 0.00 0.00 0.00 2.52
3817 5788 4.191544 CCTTTCTCGAATATGGTGCAAGA 58.808 43.478 0.00 0.00 0.00 3.02
3818 5789 3.941483 ACCTTTCTCGAATATGGTGCAAG 59.059 43.478 0.00 0.00 0.00 4.01
3820 5791 3.627395 ACCTTTCTCGAATATGGTGCA 57.373 42.857 3.94 0.00 0.00 4.57
3843 5814 1.133325 ACCATAAACAGTTGGTGCCCA 60.133 47.619 0.00 0.00 44.49 5.36
3855 5826 7.973944 GTGTTCCATCTGGATTTAACCATAAAC 59.026 37.037 0.00 0.00 44.98 2.01
3867 5843 1.573108 ACGGAGTGTTCCATCTGGAT 58.427 50.000 0.00 0.00 42.16 3.41
3886 5862 2.163010 CGGAGCGAGTACTTTTACCAGA 59.837 50.000 0.00 0.00 0.00 3.86
4033 6017 9.726232 CAGTAATAATAGACTTGCGTTGTACTA 57.274 33.333 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.