Multiple sequence alignment - TraesCS2A01G478200

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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 TraesCS2A01G478200 chr2A 100.000 3521 0 0 656 4176 717143147 717139627 0.000000e+00 6503.0
1 TraesCS2A01G478200 chr2A 79.104 1675 333 6 1523 3181 716458587 716456914 0.000000e+00 1138.0
2 TraesCS2A01G478200 chr2A 100.000 153 0 0 1 153 717143802 717143650 2.460000e-72 283.0
3 TraesCS2A01G478200 chr2D 92.674 3126 189 25 1058 4176 579391909 579388817 0.000000e+00 4468.0
4 TraesCS2A01G478200 chr2D 82.604 1736 275 21 1463 3179 579187707 579185980 0.000000e+00 1507.0
5 TraesCS2A01G478200 chr2D 89.005 191 19 1 869 1059 579392129 579391941 6.980000e-58 235.0
6 TraesCS2A01G478200 chr2D 95.918 49 2 0 1 49 579392787 579392739 3.460000e-11 80.5
7 TraesCS2A01G478200 chr2B 92.190 3137 207 23 1058 4176 696675681 696672565 0.000000e+00 4401.0
8 TraesCS2A01G478200 chr2B 82.574 1733 281 13 1463 3179 696289764 696288037 0.000000e+00 1507.0
9 TraesCS2A01G478200 chr2B 79.191 1730 338 10 1523 3235 695842828 695841104 0.000000e+00 1181.0
10 TraesCS2A01G478200 chr2B 78.512 242 33 12 832 1059 696675949 696675713 1.570000e-29 141.0
11 TraesCS2A01G478200 chr2B 89.247 93 9 1 51 143 696676120 696676029 9.490000e-22 115.0
12 TraesCS2A01G478200 chr6B 80.212 753 130 16 3420 4167 68752234 68751496 7.890000e-152 547.0
13 TraesCS2A01G478200 chr6B 79.947 753 132 16 3420 4167 68779468 68780206 1.710000e-148 536.0
14 TraesCS2A01G478200 chr6B 86.364 352 44 4 3819 4167 67408654 67409004 8.470000e-102 381.0
15 TraesCS2A01G478200 chr6B 84.426 366 54 3 3805 4169 66989222 66989585 1.430000e-94 357.0
16 TraesCS2A01G478200 chr6B 86.084 309 41 2 3411 3718 66988840 66989147 8.650000e-87 331.0
17 TraesCS2A01G478200 chr6B 85.906 298 42 0 3412 3709 67128057 67128354 6.740000e-83 318.0
18 TraesCS2A01G478200 chr6B 85.235 298 44 0 3412 3709 67320579 67320876 1.460000e-79 307.0
19 TraesCS2A01G478200 chr6D 87.625 299 37 0 3412 3710 31767556 31767854 8.590000e-92 348.0
20 TraesCS2A01G478200 chr6D 87.291 299 38 0 3412 3710 23437435 23437733 4.000000e-90 342.0
21 TraesCS2A01G478200 chr6A 83.880 366 55 4 3805 4167 36250257 36250621 3.090000e-91 346.0
22 TraesCS2A01G478200 chr6A 82.952 393 55 7 3411 3793 36105966 36106356 1.110000e-90 344.0
23 TraesCS2A01G478200 chrUn 82.796 372 59 4 3806 4176 100622762 100622395 1.120000e-85 327.0
24 TraesCS2A01G478200 chrUn 82.880 368 60 3 3809 4176 344892394 344892030 1.120000e-85 327.0


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 TraesCS2A01G478200 chr2A 717139627 717143802 4175 True 3393.000000 6503 100.000000 1 4176 2 chr2A.!!$R2 4175
1 TraesCS2A01G478200 chr2A 716456914 716458587 1673 True 1138.000000 1138 79.104000 1523 3181 1 chr2A.!!$R1 1658
2 TraesCS2A01G478200 chr2D 579388817 579392787 3970 True 1594.500000 4468 92.532333 1 4176 3 chr2D.!!$R2 4175
3 TraesCS2A01G478200 chr2D 579185980 579187707 1727 True 1507.000000 1507 82.604000 1463 3179 1 chr2D.!!$R1 1716
4 TraesCS2A01G478200 chr2B 696672565 696676120 3555 True 1552.333333 4401 86.649667 51 4176 3 chr2B.!!$R3 4125
5 TraesCS2A01G478200 chr2B 696288037 696289764 1727 True 1507.000000 1507 82.574000 1463 3179 1 chr2B.!!$R2 1716
6 TraesCS2A01G478200 chr2B 695841104 695842828 1724 True 1181.000000 1181 79.191000 1523 3235 1 chr2B.!!$R1 1712
7 TraesCS2A01G478200 chr6B 68751496 68752234 738 True 547.000000 547 80.212000 3420 4167 1 chr6B.!!$R1 747
8 TraesCS2A01G478200 chr6B 68779468 68780206 738 False 536.000000 536 79.947000 3420 4167 1 chr6B.!!$F4 747
9 TraesCS2A01G478200 chr6B 66988840 66989585 745 False 344.000000 357 85.255000 3411 4169 2 chr6B.!!$F5 758

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
709 738 0.250338 AAAGGGTTCTGGTCAGCGTC 60.250 55.0 0.0 0.0 0.00 5.19 F
936 1085 0.313987 CAACGGTTTCTTCTTGGGCC 59.686 55.0 0.0 0.0 0.00 5.80 F
1083 1266 0.544697 ACAAACGGTCCAAGGTCTGT 59.455 50.0 0.0 0.0 0.00 3.41 F
2198 2398 0.592637 CAACATCGCTTGCTTGGACA 59.407 50.0 0.0 0.0 0.00 4.02 F
2524 2724 0.690192 TCGAAGTGATTTCTGGCCCA 59.310 50.0 0.0 0.0 33.44 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2309 2509 1.074405 TGAAATGACCTCCAGCAGCTT 59.926 47.619 0.00 0.00 0.00 3.74 R
2512 2712 1.387539 GAGAGCTTGGGCCAGAAATC 58.612 55.000 6.23 4.13 39.73 2.17 R
2524 2724 1.668151 GTTTGCCGTCGGAGAGCTT 60.668 57.895 17.49 0.00 36.95 3.74 R
3126 3363 0.103026 CGCCTCAATCGTCCTGATGA 59.897 55.000 0.00 0.00 37.39 2.92 R
3671 3909 1.227089 CAGGGCTCGACGGATCTTG 60.227 63.158 0.00 0.00 0.00 3.02 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
41 42 2.034221 GGTTCAGGTCAGCACCCC 59.966 66.667 0.00 0.00 45.12 4.95
83 109 1.028868 GCTCTTTTCTGCCGCATCCT 61.029 55.000 0.00 0.00 0.00 3.24
86 112 0.677731 CTTTTCTGCCGCATCCTCCA 60.678 55.000 0.00 0.00 0.00 3.86
91 117 0.811616 CTGCCGCATCCTCCACTAAC 60.812 60.000 0.00 0.00 0.00 2.34
97 123 2.480416 CGCATCCTCCACTAACTCTGAC 60.480 54.545 0.00 0.00 0.00 3.51
101 127 3.165875 TCCTCCACTAACTCTGACCAAG 58.834 50.000 0.00 0.00 0.00 3.61
106 132 4.593206 TCCACTAACTCTGACCAAGAACAT 59.407 41.667 0.00 0.00 33.37 2.71
121 147 1.199789 GAACATCTTGCGGTGCATCAA 59.800 47.619 0.00 0.00 38.76 2.57
139 168 8.331022 GTGCATCAATAGTGTTATACAGACAAG 58.669 37.037 0.00 0.00 0.00 3.16
145 174 3.583086 AGTGTTATACAGACAAGGGTGCT 59.417 43.478 0.00 0.00 0.00 4.40
688 717 5.137551 AGGGCTAGTTACATTTGTGTTTGT 58.862 37.500 0.00 0.00 0.00 2.83
689 718 5.240844 AGGGCTAGTTACATTTGTGTTTGTC 59.759 40.000 0.00 0.00 0.00 3.18
709 738 0.250338 AAAGGGTTCTGGTCAGCGTC 60.250 55.000 0.00 0.00 0.00 5.19
710 739 1.407656 AAGGGTTCTGGTCAGCGTCA 61.408 55.000 0.00 0.00 0.00 4.35
711 740 1.194781 AGGGTTCTGGTCAGCGTCAT 61.195 55.000 0.00 0.00 0.00 3.06
712 741 1.021390 GGGTTCTGGTCAGCGTCATG 61.021 60.000 0.00 0.00 0.00 3.07
713 742 1.639298 GGTTCTGGTCAGCGTCATGC 61.639 60.000 0.00 0.00 46.98 4.06
727 756 2.627945 GTCATGCTTCGGATTGTGGTA 58.372 47.619 0.00 0.00 0.00 3.25
729 758 3.063997 GTCATGCTTCGGATTGTGGTAAG 59.936 47.826 0.00 0.00 0.00 2.34
730 759 2.107950 TGCTTCGGATTGTGGTAAGG 57.892 50.000 0.00 0.00 0.00 2.69
749 778 3.571590 AGGGTTAGGTTGCACATTTTGA 58.428 40.909 0.00 0.00 0.00 2.69
754 783 3.216147 AGGTTGCACATTTTGATACGC 57.784 42.857 0.00 0.00 0.00 4.42
761 790 1.323534 ACATTTTGATACGCGCTCGAC 59.676 47.619 5.73 0.00 39.41 4.20
767 796 3.538028 ATACGCGCTCGACCGATGG 62.538 63.158 5.73 0.00 39.41 3.51
791 820 2.589720 AGGTTTGAACTTAAACGGGGG 58.410 47.619 0.00 0.00 40.56 5.40
792 821 2.175284 AGGTTTGAACTTAAACGGGGGA 59.825 45.455 0.00 0.00 40.56 4.81
795 824 4.321452 GGTTTGAACTTAAACGGGGGAATC 60.321 45.833 0.00 0.00 40.56 2.52
796 825 4.376225 TTGAACTTAAACGGGGGAATCT 57.624 40.909 0.00 0.00 0.00 2.40
797 826 3.681593 TGAACTTAAACGGGGGAATCTG 58.318 45.455 0.00 0.00 0.00 2.90
799 828 2.271777 ACTTAAACGGGGGAATCTGGA 58.728 47.619 0.00 0.00 0.00 3.86
801 830 3.279434 CTTAAACGGGGGAATCTGGAAG 58.721 50.000 0.00 0.00 0.00 3.46
802 831 0.323451 AAACGGGGGAATCTGGAAGC 60.323 55.000 0.00 0.00 0.00 3.86
803 832 1.497309 AACGGGGGAATCTGGAAGCA 61.497 55.000 0.00 0.00 0.00 3.91
806 835 0.332972 GGGGGAATCTGGAAGCAAGT 59.667 55.000 0.00 0.00 0.00 3.16
807 836 1.683319 GGGGGAATCTGGAAGCAAGTC 60.683 57.143 0.00 0.00 0.00 3.01
808 837 1.283321 GGGGAATCTGGAAGCAAGTCT 59.717 52.381 0.00 0.00 0.00 3.24
826 862 2.924290 GTCTTTGTAGCGAGCAGGTAAG 59.076 50.000 0.00 0.00 34.24 2.34
827 863 2.823747 TCTTTGTAGCGAGCAGGTAAGA 59.176 45.455 0.00 0.00 34.24 2.10
860 896 8.348285 TGAATTTATTTTGGTCCTTCAGTAGG 57.652 34.615 0.00 0.00 46.27 3.18
862 898 5.853572 TTATTTTGGTCCTTCAGTAGGGT 57.146 39.130 0.00 0.00 44.86 4.34
863 899 6.956102 TTATTTTGGTCCTTCAGTAGGGTA 57.044 37.500 0.00 0.00 44.86 3.69
864 900 4.903045 TTTTGGTCCTTCAGTAGGGTAG 57.097 45.455 0.00 0.00 44.86 3.18
866 902 2.005350 TGGTCCTTCAGTAGGGTAGGA 58.995 52.381 0.00 0.00 44.86 2.94
867 903 2.024273 TGGTCCTTCAGTAGGGTAGGAG 60.024 54.545 0.00 0.00 44.86 3.69
900 1049 7.148355 TGGTTGGGTATTAAATCGAAAAGTC 57.852 36.000 0.00 0.00 0.00 3.01
921 1070 4.322804 GTCTGTTCTTGTACGGATACAACG 59.677 45.833 0.00 0.00 44.62 4.10
936 1085 0.313987 CAACGGTTTCTTCTTGGGCC 59.686 55.000 0.00 0.00 0.00 5.80
956 1105 1.734465 CGAAATGTGGCCACTTCTCTC 59.266 52.381 34.75 22.48 0.00 3.20
977 1127 1.134788 GTACTGAACGGAGGTGGGATG 60.135 57.143 0.00 0.00 0.00 3.51
1012 1162 1.878088 GTGTAGCCATGGAGCATCATG 59.122 52.381 18.40 11.02 42.92 3.07
1013 1163 1.491754 TGTAGCCATGGAGCATCATGT 59.508 47.619 18.40 4.03 42.02 3.21
1039 1189 2.163390 CAGCACGAGCAGGATGACG 61.163 63.158 7.77 0.00 45.49 4.35
1043 1193 2.887568 CGAGCAGGATGACGGCAC 60.888 66.667 0.00 0.00 43.19 5.01
1083 1266 0.544697 ACAAACGGTCCAAGGTCTGT 59.455 50.000 0.00 0.00 0.00 3.41
1093 1276 1.611977 CCAAGGTCTGTGACGTACTGA 59.388 52.381 0.00 0.00 35.23 3.41
1129 1312 3.181440 TGGAGACTGAATGTGGCTTCTTT 60.181 43.478 0.00 0.00 0.00 2.52
1192 1386 2.793288 TGGAGCATTCTGATGAGCAA 57.207 45.000 0.00 0.00 35.16 3.91
1215 1409 1.211212 CAAGGAGGATGACAGCATGGA 59.789 52.381 0.00 0.00 43.62 3.41
1216 1410 1.588239 AGGAGGATGACAGCATGGAA 58.412 50.000 0.00 0.00 43.62 3.53
1217 1411 1.489649 AGGAGGATGACAGCATGGAAG 59.510 52.381 0.00 0.00 43.62 3.46
1281 1475 2.040813 ACAAGCACCAGATTCAGTCCAT 59.959 45.455 0.00 0.00 0.00 3.41
1354 1548 2.033141 TGCCTGAGCTGCCACTTC 59.967 61.111 0.00 0.00 40.80 3.01
1365 1559 0.767375 TGCCACTTCCTCTTCAGCTT 59.233 50.000 0.00 0.00 0.00 3.74
1406 1600 2.356278 GGCACCTGGAATCCTGCA 59.644 61.111 13.00 0.00 0.00 4.41
1444 1638 1.333636 CGGAGAGGCCACAGAAGGAT 61.334 60.000 5.01 0.00 35.94 3.24
1473 1667 1.065926 CACAGATGGTAGCAGCTCCAA 60.066 52.381 10.23 0.00 37.27 3.53
1618 1818 3.494398 GCAAGTTTAGTCAGGAGTCACCA 60.494 47.826 0.00 0.00 42.04 4.17
2004 2204 1.073897 GCAAGGAGGCCTGTGTTCT 59.926 57.895 12.00 0.00 32.13 3.01
2044 2244 4.996758 TCTTACAATGTCATATGGGATGCG 59.003 41.667 2.13 0.00 0.00 4.73
2074 2274 8.152246 AGAGATTGGAATCTTGATCAGAAGATC 58.848 37.037 9.79 4.96 45.39 2.75
2155 2355 2.775911 TGCTCATGGAGAAGAAGTGG 57.224 50.000 0.00 0.00 0.00 4.00
2167 2367 1.366319 AGAAGTGGCTTCCCATCAGT 58.634 50.000 5.38 0.00 44.51 3.41
2198 2398 0.592637 CAACATCGCTTGCTTGGACA 59.407 50.000 0.00 0.00 0.00 4.02
2199 2399 0.877071 AACATCGCTTGCTTGGACAG 59.123 50.000 0.00 0.00 0.00 3.51
2300 2500 2.536365 CACATGCATCTTCACCATTGC 58.464 47.619 0.00 0.00 35.67 3.56
2341 2541 5.123027 GGAGGTCATTTCACAGATGAGTTTC 59.877 44.000 0.00 0.00 35.83 2.78
2427 2627 7.523293 TGCAATTCAAGAAGTTATTTCCTGA 57.477 32.000 0.00 0.00 35.07 3.86
2498 2698 8.641499 TTGCAAGATTTTGAGAACGTTTTATT 57.359 26.923 0.46 0.00 36.36 1.40
2512 2712 3.845775 CGTTTTATTGTGCCATCGAAGTG 59.154 43.478 0.00 0.00 0.00 3.16
2524 2724 0.690192 TCGAAGTGATTTCTGGCCCA 59.310 50.000 0.00 0.00 33.44 5.36
2684 2885 1.336517 ACTCATACGTGTGGTTGTCGG 60.337 52.381 12.66 0.00 0.00 4.79
3016 3253 1.140134 ATGCCACCAAGTACCCCACT 61.140 55.000 0.00 0.00 40.05 4.00
3151 3388 1.063649 GACGATTGAGGCGCTCGTA 59.936 57.895 19.64 3.43 44.89 3.43
3191 3428 4.573607 TGAGATGAAATGGCGAAGATTCTG 59.426 41.667 0.00 0.00 0.00 3.02
3205 3442 0.530744 ATTCTGTAAGCCGCTCGACA 59.469 50.000 7.62 7.62 0.00 4.35
3269 3506 7.503521 TGTAGAACTTTTGCATGTTCATGTA 57.496 32.000 21.48 7.01 43.38 2.29
3271 3508 7.860373 TGTAGAACTTTTGCATGTTCATGTAAC 59.140 33.333 21.48 14.25 43.38 2.50
3294 3531 4.438472 CGTTAGTAGCCTAGTTCCACAGTC 60.438 50.000 0.00 0.00 0.00 3.51
3325 3563 6.486253 TCAGTTTCATGTTTGACTAGATGC 57.514 37.500 0.00 0.00 0.00 3.91
3381 3619 1.807742 CAAAACCCCATTGCAATGCAG 59.192 47.619 30.15 24.32 40.61 4.41
3534 3772 1.569493 CAAAGTTGAGTGACGCCCG 59.431 57.895 0.00 0.00 0.00 6.13
3559 3797 4.682787 TGAAGGTATGCGATAGTGTTGAG 58.317 43.478 0.00 0.00 39.35 3.02
3604 3842 3.726557 TTCAGATCCTGCCATTCACTT 57.273 42.857 0.00 0.00 0.00 3.16
3615 3853 2.357009 GCCATTCACTTGCGATCATCTT 59.643 45.455 0.00 0.00 0.00 2.40
3671 3909 2.037251 TCTCTGTGGTACAACTCCTTGC 59.963 50.000 1.23 0.00 44.16 4.01
3689 3927 1.227089 CAAGATCCGTCGAGCCCTG 60.227 63.158 0.00 0.00 0.00 4.45
3758 4012 0.959867 TTGATGTGGATGCACACCCG 60.960 55.000 23.18 0.00 40.62 5.28
3818 4073 7.499321 TTTTTACGTGGAATTCATGTACAGT 57.501 32.000 7.93 6.12 44.78 3.55
3819 4074 7.499321 TTTTACGTGGAATTCATGTACAGTT 57.501 32.000 7.93 0.00 44.78 3.16
3827 4082 9.120538 GTGGAATTCATGTACAGTTATTGGTAT 57.879 33.333 7.93 0.00 0.00 2.73
3865 4120 9.653287 CAGTCTTATGTGATAAAGTTCTTGGTA 57.347 33.333 0.00 0.00 0.00 3.25
3908 4163 0.400213 TGTCGTCCCAAAGCCTCATT 59.600 50.000 0.00 0.00 0.00 2.57
3962 4217 1.338674 CGGTCATTGTTGCCCTCTGTA 60.339 52.381 0.00 0.00 0.00 2.74
4103 4358 4.454847 CCCTCGATCATGAATCCATCAAAG 59.545 45.833 0.00 0.00 42.54 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.874019 CTGAACCGATCGCCGACTG 60.874 63.158 10.32 0.00 41.76 3.51
41 42 3.474806 CTAACGAGCAAGGCCACG 58.525 61.111 5.01 5.11 35.71 4.94
83 109 3.964688 TGTTCTTGGTCAGAGTTAGTGGA 59.035 43.478 0.00 0.00 31.12 4.02
86 112 6.426646 AAGATGTTCTTGGTCAGAGTTAGT 57.573 37.500 0.00 0.00 34.98 2.24
101 127 0.804364 TGATGCACCGCAAGATGTTC 59.196 50.000 0.00 0.00 43.62 3.18
106 132 2.009051 CACTATTGATGCACCGCAAGA 58.991 47.619 0.00 0.00 43.62 3.02
121 147 5.425539 AGCACCCTTGTCTGTATAACACTAT 59.574 40.000 0.00 0.00 0.00 2.12
655 684 0.620700 AACTAGCCCTTCCGTCCCAT 60.621 55.000 0.00 0.00 0.00 4.00
656 685 0.041535 TAACTAGCCCTTCCGTCCCA 59.958 55.000 0.00 0.00 0.00 4.37
657 686 0.463204 GTAACTAGCCCTTCCGTCCC 59.537 60.000 0.00 0.00 0.00 4.46
658 687 1.188863 TGTAACTAGCCCTTCCGTCC 58.811 55.000 0.00 0.00 0.00 4.79
659 688 3.538634 AATGTAACTAGCCCTTCCGTC 57.461 47.619 0.00 0.00 0.00 4.79
660 689 3.008704 ACAAATGTAACTAGCCCTTCCGT 59.991 43.478 0.00 0.00 0.00 4.69
661 690 3.374058 CACAAATGTAACTAGCCCTTCCG 59.626 47.826 0.00 0.00 0.00 4.30
662 691 4.332828 ACACAAATGTAACTAGCCCTTCC 58.667 43.478 0.00 0.00 37.26 3.46
663 692 5.959618 AACACAAATGTAACTAGCCCTTC 57.040 39.130 0.00 0.00 38.45 3.46
664 693 5.596772 ACAAACACAAATGTAACTAGCCCTT 59.403 36.000 0.00 0.00 38.45 3.95
665 694 5.137551 ACAAACACAAATGTAACTAGCCCT 58.862 37.500 0.00 0.00 38.45 5.19
666 695 5.009210 TGACAAACACAAATGTAACTAGCCC 59.991 40.000 0.00 0.00 38.45 5.19
667 696 6.067263 TGACAAACACAAATGTAACTAGCC 57.933 37.500 0.00 0.00 38.45 3.93
668 697 7.167468 CCTTTGACAAACACAAATGTAACTAGC 59.833 37.037 0.00 0.00 38.45 3.42
688 717 0.250295 CGCTGACCAGAACCCTTTGA 60.250 55.000 0.47 0.00 0.00 2.69
689 718 0.535102 ACGCTGACCAGAACCCTTTG 60.535 55.000 0.47 0.00 0.00 2.77
709 738 2.355756 CCTTACCACAATCCGAAGCATG 59.644 50.000 0.00 0.00 0.00 4.06
710 739 2.643551 CCTTACCACAATCCGAAGCAT 58.356 47.619 0.00 0.00 0.00 3.79
711 740 1.339631 CCCTTACCACAATCCGAAGCA 60.340 52.381 0.00 0.00 0.00 3.91
712 741 1.339727 ACCCTTACCACAATCCGAAGC 60.340 52.381 0.00 0.00 0.00 3.86
713 742 2.781681 ACCCTTACCACAATCCGAAG 57.218 50.000 0.00 0.00 0.00 3.79
714 743 3.054948 CCTAACCCTTACCACAATCCGAA 60.055 47.826 0.00 0.00 0.00 4.30
715 744 2.502538 CCTAACCCTTACCACAATCCGA 59.497 50.000 0.00 0.00 0.00 4.55
727 756 3.964031 TCAAAATGTGCAACCTAACCCTT 59.036 39.130 0.00 0.00 34.36 3.95
729 758 4.535526 ATCAAAATGTGCAACCTAACCC 57.464 40.909 0.00 0.00 34.36 4.11
730 759 5.092781 CGTATCAAAATGTGCAACCTAACC 58.907 41.667 0.00 0.00 34.36 2.85
749 778 2.051256 CATCGGTCGAGCGCGTAT 60.051 61.111 30.70 17.17 38.98 3.06
761 790 3.611766 AGTTCAAACCTAGACCATCGG 57.388 47.619 0.00 0.00 0.00 4.18
767 796 4.453478 CCCCGTTTAAGTTCAAACCTAGAC 59.547 45.833 0.00 0.00 35.42 2.59
791 820 5.391416 GCTACAAAGACTTGCTTCCAGATTC 60.391 44.000 0.00 0.00 35.24 2.52
792 821 4.457257 GCTACAAAGACTTGCTTCCAGATT 59.543 41.667 0.00 0.00 35.24 2.40
795 824 2.158449 CGCTACAAAGACTTGCTTCCAG 59.842 50.000 0.00 0.00 35.24 3.86
796 825 2.143122 CGCTACAAAGACTTGCTTCCA 58.857 47.619 0.00 0.00 35.24 3.53
797 826 2.413453 CTCGCTACAAAGACTTGCTTCC 59.587 50.000 0.00 0.00 35.24 3.46
799 828 1.801178 GCTCGCTACAAAGACTTGCTT 59.199 47.619 0.00 0.00 38.88 3.91
801 830 1.127582 CTGCTCGCTACAAAGACTTGC 59.872 52.381 0.00 0.00 35.84 4.01
802 831 1.728971 CCTGCTCGCTACAAAGACTTG 59.271 52.381 0.00 0.00 38.61 3.16
803 832 1.344763 ACCTGCTCGCTACAAAGACTT 59.655 47.619 0.00 0.00 0.00 3.01
806 835 2.823747 TCTTACCTGCTCGCTACAAAGA 59.176 45.455 0.00 0.00 0.00 2.52
807 836 3.232213 TCTTACCTGCTCGCTACAAAG 57.768 47.619 0.00 0.00 0.00 2.77
808 837 3.006537 ACTTCTTACCTGCTCGCTACAAA 59.993 43.478 0.00 0.00 0.00 2.83
860 896 6.429151 ACCCAACCAAAAATATACTCCTACC 58.571 40.000 0.00 0.00 0.00 3.18
921 1070 1.324383 TTTCGGCCCAAGAAGAAACC 58.676 50.000 0.00 0.00 0.00 3.27
936 1085 1.734465 GAGAGAAGTGGCCACATTTCG 59.266 52.381 36.39 0.00 45.03 3.46
966 1116 6.890268 AGTAAAGAAAATAACATCCCACCTCC 59.110 38.462 0.00 0.00 0.00 4.30
970 1120 7.882179 ACACAGTAAAGAAAATAACATCCCAC 58.118 34.615 0.00 0.00 0.00 4.61
977 1127 7.968405 CCATGGCTACACAGTAAAGAAAATAAC 59.032 37.037 0.00 0.00 0.00 1.89
1012 1162 1.061711 CTGCTCGTGCTGCTCATAAAC 59.938 52.381 11.19 0.00 40.48 2.01
1013 1163 1.362768 CTGCTCGTGCTGCTCATAAA 58.637 50.000 11.19 0.00 40.48 1.40
1043 1193 3.191539 GCTCTGCCTCCGCTTTCG 61.192 66.667 0.00 0.00 35.36 3.46
1083 1266 1.166129 GAGGCTCTGTCAGTACGTCA 58.834 55.000 7.40 0.00 0.00 4.35
1192 1386 1.059098 TGCTGTCATCCTCCTTGTGT 58.941 50.000 0.00 0.00 0.00 3.72
1215 1409 2.039084 ACGAATTCTGCCTCCACTTCTT 59.961 45.455 3.52 0.00 0.00 2.52
1216 1410 1.625818 ACGAATTCTGCCTCCACTTCT 59.374 47.619 3.52 0.00 0.00 2.85
1217 1411 2.100605 ACGAATTCTGCCTCCACTTC 57.899 50.000 3.52 0.00 0.00 3.01
1281 1475 1.003580 GCTCAAACTCATCCCAGACCA 59.996 52.381 0.00 0.00 0.00 4.02
1354 1548 1.273606 TCTCCGTTGAAGCTGAAGAGG 59.726 52.381 0.00 0.00 0.00 3.69
1365 1559 1.135139 GCAGACAGCTATCTCCGTTGA 59.865 52.381 0.00 0.00 41.15 3.18
1444 1638 2.355108 GCTACCATCTGTGAAGCAGGAA 60.355 50.000 0.00 0.00 45.08 3.36
1604 1804 4.614475 TCTTGATATGGTGACTCCTGACT 58.386 43.478 0.00 0.00 37.07 3.41
1618 1818 6.551975 TGATCATTTTGGCCACATCTTGATAT 59.448 34.615 3.88 0.00 0.00 1.63
1788 1988 4.097892 AGGTAAGCGCAATTTTATCCTTGG 59.902 41.667 11.47 0.00 0.00 3.61
2004 2204 6.911250 TGTAAGATCCACTTTCAGACTGTA 57.089 37.500 1.59 0.00 39.72 2.74
2044 2244 7.443477 TCTGATCAAGATTCCAATCTCTGATC 58.557 38.462 25.43 25.43 44.67 2.92
2074 2274 2.149578 CCAACTGAAGTCAAGCTCAGG 58.850 52.381 4.27 0.00 34.77 3.86
2198 2398 4.152402 GTCGACAACACTGTTTATCATGCT 59.848 41.667 11.55 0.00 35.30 3.79
2199 2399 4.394795 GTCGACAACACTGTTTATCATGC 58.605 43.478 11.55 0.00 35.30 4.06
2309 2509 1.074405 TGAAATGACCTCCAGCAGCTT 59.926 47.619 0.00 0.00 0.00 3.74
2314 2514 2.479566 TCTGTGAAATGACCTCCAGC 57.520 50.000 0.00 0.00 0.00 4.85
2341 2541 1.442769 CATCTTCCCGTGGACACTTG 58.557 55.000 0.56 0.00 0.00 3.16
2498 2698 2.743664 CAGAAATCACTTCGATGGCACA 59.256 45.455 3.12 0.00 40.65 4.57
2512 2712 1.387539 GAGAGCTTGGGCCAGAAATC 58.612 55.000 6.23 4.13 39.73 2.17
2524 2724 1.668151 GTTTGCCGTCGGAGAGCTT 60.668 57.895 17.49 0.00 36.95 3.74
2651 2852 3.510360 ACGTATGAGTTCTGCCAGTACTT 59.490 43.478 5.42 0.00 0.00 2.24
2684 2885 5.259632 TCTAGGGTCTAGAACAACAGGTAC 58.740 45.833 10.60 0.00 0.00 3.34
3126 3363 0.103026 CGCCTCAATCGTCCTGATGA 59.897 55.000 0.00 0.00 37.39 2.92
3151 3388 5.303845 TCATCTCATCCAATCTCGAGAACAT 59.696 40.000 20.91 6.06 37.99 2.71
3191 3428 0.666577 AGTTGTGTCGAGCGGCTTAC 60.667 55.000 2.97 6.71 0.00 2.34
3205 3442 5.770663 ACGCTACTGGATCTATGATAGTTGT 59.229 40.000 0.00 0.00 0.00 3.32
3269 3506 3.828451 TGTGGAACTAGGCTACTAACGTT 59.172 43.478 5.88 5.88 38.04 3.99
3271 3508 3.442977 ACTGTGGAACTAGGCTACTAACG 59.557 47.826 0.00 0.00 38.04 3.18
3294 3531 3.996150 AACATGAAACTGAACAGCCTG 57.004 42.857 0.00 0.00 0.00 4.85
3308 3546 5.939764 AGGTAGCATCTAGTCAAACATGA 57.060 39.130 0.00 0.00 0.00 3.07
3359 3597 2.369860 TGCATTGCAATGGGGTTTTGTA 59.630 40.909 34.23 9.99 34.76 2.41
3534 3772 4.258702 ACACTATCGCATACCTTCATCC 57.741 45.455 0.00 0.00 0.00 3.51
3559 3797 2.489722 GGAATGCTTCTCTGGGACAAAC 59.510 50.000 0.00 0.00 38.70 2.93
3604 3842 1.937899 CACATGCTGAAGATGATCGCA 59.062 47.619 0.00 0.00 34.89 5.10
3671 3909 1.227089 CAGGGCTCGACGGATCTTG 60.227 63.158 0.00 0.00 0.00 3.02
3689 3927 2.223735 CCATGCAGGATGAATCACAAGC 60.224 50.000 0.00 0.00 39.69 4.01
3718 3956 4.127566 ACATTGACCAAATTAGGCATGC 57.872 40.909 9.90 9.90 0.00 4.06
3794 4049 7.499321 ACTGTACATGAATTCCACGTAAAAA 57.501 32.000 0.00 0.00 0.00 1.94
3795 4050 7.499321 AACTGTACATGAATTCCACGTAAAA 57.501 32.000 0.00 0.00 0.00 1.52
3796 4051 8.780846 ATAACTGTACATGAATTCCACGTAAA 57.219 30.769 0.00 0.00 0.00 2.01
3797 4052 8.661257 CAATAACTGTACATGAATTCCACGTAA 58.339 33.333 0.00 0.00 0.00 3.18
3798 4053 7.279090 CCAATAACTGTACATGAATTCCACGTA 59.721 37.037 0.00 0.00 0.00 3.57
3799 4054 6.093495 CCAATAACTGTACATGAATTCCACGT 59.907 38.462 0.00 0.00 0.00 4.49
3800 4055 6.093495 ACCAATAACTGTACATGAATTCCACG 59.907 38.462 0.00 0.00 0.00 4.94
3801 4056 7.391148 ACCAATAACTGTACATGAATTCCAC 57.609 36.000 0.00 0.00 0.00 4.02
3802 4057 9.693739 AATACCAATAACTGTACATGAATTCCA 57.306 29.630 0.00 0.00 0.00 3.53
3803 4058 9.950680 CAATACCAATAACTGTACATGAATTCC 57.049 33.333 0.00 0.00 0.00 3.01
3804 4059 9.450807 GCAATACCAATAACTGTACATGAATTC 57.549 33.333 0.00 0.00 0.00 2.17
3805 4060 9.189156 AGCAATACCAATAACTGTACATGAATT 57.811 29.630 0.00 0.00 0.00 2.17
3806 4061 8.752005 AGCAATACCAATAACTGTACATGAAT 57.248 30.769 0.00 0.00 0.00 2.57
3807 4062 9.674068 TTAGCAATACCAATAACTGTACATGAA 57.326 29.630 0.00 0.00 0.00 2.57
3808 4063 9.845740 ATTAGCAATACCAATAACTGTACATGA 57.154 29.630 0.00 0.00 0.00 3.07
3810 4065 9.284968 GGATTAGCAATACCAATAACTGTACAT 57.715 33.333 0.00 0.00 0.00 2.29
3811 4066 8.491134 AGGATTAGCAATACCAATAACTGTACA 58.509 33.333 0.00 0.00 0.00 2.90
3812 4067 8.774586 CAGGATTAGCAATACCAATAACTGTAC 58.225 37.037 0.00 0.00 0.00 2.90
3813 4068 7.444183 GCAGGATTAGCAATACCAATAACTGTA 59.556 37.037 0.00 0.00 0.00 2.74
3814 4069 6.263168 GCAGGATTAGCAATACCAATAACTGT 59.737 38.462 0.00 0.00 0.00 3.55
3815 4070 6.262944 TGCAGGATTAGCAATACCAATAACTG 59.737 38.462 0.00 0.00 39.39 3.16
3816 4071 6.364701 TGCAGGATTAGCAATACCAATAACT 58.635 36.000 0.00 0.00 39.39 2.24
3817 4072 6.263168 ACTGCAGGATTAGCAATACCAATAAC 59.737 38.462 19.93 0.00 42.17 1.89
3818 4073 6.364701 ACTGCAGGATTAGCAATACCAATAA 58.635 36.000 19.93 0.00 42.17 1.40
3819 4074 5.940617 ACTGCAGGATTAGCAATACCAATA 58.059 37.500 19.93 0.00 42.17 1.90
3827 4082 4.877823 CACATAAGACTGCAGGATTAGCAA 59.122 41.667 19.93 0.00 42.17 3.91
3865 4120 3.447229 GGGCAGTGCAAAGGTTATAACAT 59.553 43.478 18.61 7.49 0.00 2.71
3908 4163 3.198417 TCATCTCCTGCACTGCAAAGATA 59.802 43.478 20.42 8.83 38.33 1.98
4103 4358 2.079925 CTCTTACAGTGGGCAGCTTTC 58.920 52.381 0.00 0.00 0.00 2.62


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

AutoCloner maintained by Alex Coulton.