Multiple sequence alignment - TraesCS3D01G530200

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 TraesCS3D01G530200 chr3D 100.000 4909 0 0 1 4909 607059402 607064310 0.000000e+00 9066
1 TraesCS3D01G530200 chr3B 92.838 4119 198 54 827 4909 816515589 816519646 0.000000e+00 5882
2 TraesCS3D01G530200 chr3B 83.315 887 65 43 1 827 816514697 816515560 0.000000e+00 741
3 TraesCS3D01G530200 chr3A 88.250 2451 136 69 20 2390 739512860 739515238 0.000000e+00 2791
4 TraesCS3D01G530200 chr3A 92.977 1723 86 24 2400 4098 739515343 739517054 0.000000e+00 2479
5 TraesCS3D01G530200 chr3A 86.104 734 34 24 4146 4858 739517059 739517745 0.000000e+00 728
6 TraesCS3D01G530200 chr1A 92.771 83 6 0 3572 3654 12157751 12157669 2.400000e-23 121


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 TraesCS3D01G530200 chr3D 607059402 607064310 4908 False 9066.000000 9066 100.000000 1 4909 1 chr3D.!!$F1 4908
1 TraesCS3D01G530200 chr3B 816514697 816519646 4949 False 3311.500000 5882 88.076500 1 4909 2 chr3B.!!$F1 4908
2 TraesCS3D01G530200 chr3A 739512860 739517745 4885 False 1999.333333 2791 89.110333 20 4858 3 chr3A.!!$F1 4838

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
644 695 0.034756 TACCAGCACGCTCATGTTGT 59.965 50.000 0.00 0.00 0.00 3.32 F
2176 2316 0.040157 CCGGCATTTATGGTGCATCG 60.040 55.000 0.00 0.00 44.25 3.84 F
2994 3233 1.340114 ACCAAAAGAAGAGGGGATCGC 60.340 52.381 0.06 0.06 0.00 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2231 2371 0.108138 CTTGAAGGGTAGGTCCTGCG 60.108 60.0 0.00 0.00 35.11 5.18 R
3571 3826 0.106708 TTTTCTCGTGAGCAGGCTGT 59.893 50.0 17.16 2.59 0.00 4.40 R
3917 4172 0.308684 TAACAGCGGCGAGGTATACG 59.691 55.0 12.98 0.00 0.00 3.06 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
56 57 4.162690 ACCAGGGCGAGCGAATCC 62.163 66.667 0.00 0.00 0.00 3.01
106 107 4.825679 CTCCCACCCCCTCCTCCC 62.826 77.778 0.00 0.00 0.00 4.30
356 394 1.354368 TCAGCTTCCCCTTTCCGATTT 59.646 47.619 0.00 0.00 0.00 2.17
363 401 5.069119 GCTTCCCCTTTCCGATTTCATTATT 59.931 40.000 0.00 0.00 0.00 1.40
369 407 6.314784 CCTTTCCGATTTCATTATTATCGCC 58.685 40.000 0.00 0.00 39.71 5.54
384 422 2.188994 GCCAGAGCCCTAGTGCTG 59.811 66.667 3.78 0.00 42.95 4.41
407 445 7.333921 GCTGGATAGATAGATTGGTTCTTCATG 59.666 40.741 0.00 0.00 35.79 3.07
412 450 6.002704 AGATAGATTGGTTCTTCATGCCATC 58.997 40.000 0.00 0.00 35.79 3.51
429 471 4.839706 CCCATCCAAAGGCCGGGG 62.840 72.222 2.18 7.57 32.44 5.73
453 497 1.140652 TCCCCTACGTTTTGTTCCGTT 59.859 47.619 0.00 0.00 38.43 4.44
478 522 0.898320 GTTGACTAGGCAGGAGCAGA 59.102 55.000 0.00 0.00 44.61 4.26
511 555 1.202417 GCGTGACTAATCCTAGCAGCA 60.202 52.381 0.00 0.00 0.00 4.41
512 556 2.736978 CGTGACTAATCCTAGCAGCAG 58.263 52.381 0.00 0.00 0.00 4.24
513 557 2.478831 GTGACTAATCCTAGCAGCAGC 58.521 52.381 0.00 0.00 42.56 5.25
555 599 1.525619 GTTCAGTTCGGAGTTGGAACG 59.474 52.381 0.00 0.00 46.40 3.95
564 609 4.240096 TCGGAGTTGGAACGTCTTTAATC 58.760 43.478 0.00 0.00 0.00 1.75
579 624 5.066505 GTCTTTAATCAATCCGGCACTTCAT 59.933 40.000 0.00 0.00 0.00 2.57
615 666 3.673173 GCCATGGCCATGTGAAATC 57.327 52.632 37.30 18.50 37.11 2.17
642 693 1.806542 CTTTACCAGCACGCTCATGTT 59.193 47.619 0.00 0.00 0.00 2.71
643 694 1.155889 TTACCAGCACGCTCATGTTG 58.844 50.000 0.00 0.00 0.00 3.33
644 695 0.034756 TACCAGCACGCTCATGTTGT 59.965 50.000 0.00 0.00 0.00 3.32
645 696 0.819259 ACCAGCACGCTCATGTTGTT 60.819 50.000 0.00 0.00 0.00 2.83
646 697 0.110056 CCAGCACGCTCATGTTGTTC 60.110 55.000 0.00 0.00 0.00 3.18
647 698 0.587768 CAGCACGCTCATGTTGTTCA 59.412 50.000 0.00 0.00 0.00 3.18
648 699 0.588252 AGCACGCTCATGTTGTTCAC 59.412 50.000 0.00 0.00 0.00 3.18
649 700 0.307453 GCACGCTCATGTTGTTCACA 59.693 50.000 0.00 0.00 40.71 3.58
650 701 1.921573 GCACGCTCATGTTGTTCACAC 60.922 52.381 0.00 0.00 38.61 3.82
651 702 1.330213 CACGCTCATGTTGTTCACACA 59.670 47.619 0.00 0.00 38.61 3.72
652 703 1.599071 ACGCTCATGTTGTTCACACAG 59.401 47.619 0.00 0.00 38.61 3.66
653 704 1.599071 CGCTCATGTTGTTCACACAGT 59.401 47.619 0.00 0.00 38.61 3.55
654 705 2.600556 CGCTCATGTTGTTCACACAGTG 60.601 50.000 0.00 0.00 38.61 3.66
700 755 4.324402 GTGCTGCATCAAAATTAGGAAACG 59.676 41.667 5.27 0.00 0.00 3.60
717 772 0.529378 ACGAACCAGTAACCGGCTAG 59.471 55.000 0.00 0.00 0.00 3.42
733 788 0.381801 CTAGCCGCCGCATCAAAATT 59.618 50.000 0.00 0.00 37.52 1.82
739 794 1.843992 GCCGCATCAAAATTAGGCAG 58.156 50.000 0.00 0.00 43.65 4.85
751 806 2.018542 TTAGGCAGGCGTGTGTAATC 57.981 50.000 8.40 0.00 0.00 1.75
762 828 0.812549 TGTGTAATCGGCAGCGACTA 59.187 50.000 0.00 0.00 0.00 2.59
763 829 1.197910 GTGTAATCGGCAGCGACTAC 58.802 55.000 0.00 0.00 0.00 2.73
766 832 2.032550 TGTAATCGGCAGCGACTACTAC 59.967 50.000 5.77 0.00 0.00 2.73
768 834 1.783031 ATCGGCAGCGACTACTACCG 61.783 60.000 0.00 0.00 46.11 4.02
792 866 1.468736 CGGAGTTAGGGAAGCGTGTAC 60.469 57.143 0.00 0.00 0.00 2.90
793 867 1.134877 GGAGTTAGGGAAGCGTGTACC 60.135 57.143 0.00 0.00 0.00 3.34
814 888 1.725641 TTGGCAGCGAGTAATGACTG 58.274 50.000 0.00 0.00 35.45 3.51
870 985 0.461961 ACTACAGCCGCCTGATTCTC 59.538 55.000 0.00 0.00 41.77 2.87
875 990 1.525535 GCCGCCTGATTCTCATGCT 60.526 57.895 3.52 0.00 36.14 3.79
880 995 2.286294 CGCCTGATTCTCATGCTAACAC 59.714 50.000 3.52 0.00 36.14 3.32
881 996 2.615912 GCCTGATTCTCATGCTAACACC 59.384 50.000 0.00 0.00 35.54 4.16
888 1007 2.094700 TCTCATGCTAACACCGACTGTC 60.095 50.000 0.00 0.00 30.29 3.51
972 1091 1.941734 CGCTCGCAAGACTCGATCC 60.942 63.158 0.00 0.00 45.01 3.36
998 1117 4.742201 CGCGCTGGTGTGCTAGGT 62.742 66.667 5.56 0.00 46.58 3.08
1094 1214 0.991146 TATGCTGCCCTGTTCCTTGA 59.009 50.000 0.00 0.00 0.00 3.02
1095 1215 0.610232 ATGCTGCCCTGTTCCTTGAC 60.610 55.000 0.00 0.00 0.00 3.18
1096 1216 1.973812 GCTGCCCTGTTCCTTGACC 60.974 63.158 0.00 0.00 0.00 4.02
1097 1217 1.763770 CTGCCCTGTTCCTTGACCT 59.236 57.895 0.00 0.00 0.00 3.85
1284 1407 2.400399 TCAACGTAGTGCTGCAGTAAC 58.600 47.619 18.12 14.10 45.00 2.50
1448 1571 1.648467 CTGCTAGAAACGCAAGGGGC 61.648 60.000 0.00 0.00 46.39 5.80
1452 1575 1.133025 CTAGAAACGCAAGGGGCAATG 59.867 52.381 0.00 0.00 45.17 2.82
1583 1708 9.807921 TCCTAACTTTTTGATCTAACCTTGATT 57.192 29.630 0.00 0.00 0.00 2.57
1730 1855 9.381038 AGGTAGCTATTCTTTTCTGTATATCCA 57.619 33.333 0.00 0.00 0.00 3.41
1731 1856 9.425577 GGTAGCTATTCTTTTCTGTATATCCAC 57.574 37.037 0.00 0.00 0.00 4.02
1732 1857 9.425577 GTAGCTATTCTTTTCTGTATATCCACC 57.574 37.037 0.00 0.00 0.00 4.61
1743 1878 5.604231 TCTGTATATCCACCTTTCAGCTCAT 59.396 40.000 0.00 0.00 0.00 2.90
1747 1882 0.682209 CCACCTTTCAGCTCATGGGG 60.682 60.000 0.00 0.00 0.00 4.96
1755 1890 0.901580 CAGCTCATGGGGTGCCTTTT 60.902 55.000 12.63 0.00 36.68 2.27
1804 1939 5.984725 TGTATTCCGCCTCAAAGAGAATAA 58.015 37.500 0.00 0.00 32.75 1.40
1811 1946 5.106157 CCGCCTCAAAGAGAATAATGTGTTT 60.106 40.000 0.00 0.00 0.00 2.83
1870 2005 6.006449 ACCTCAAAAAGCTGACTATGATGTT 58.994 36.000 0.00 0.00 0.00 2.71
1892 2027 5.885230 TTTCTGCCTATCACATTGTTCTG 57.115 39.130 0.00 0.00 0.00 3.02
1929 2068 4.835678 TGCTTGCTCTTGTCATCTGATAA 58.164 39.130 0.00 0.00 0.00 1.75
2015 2154 0.179140 CTGTTGTGCACTGGCGTTTT 60.179 50.000 19.41 0.00 45.35 2.43
2042 2181 6.604171 TGTGCTCCTGTGAATTCCATATATT 58.396 36.000 2.27 0.00 0.00 1.28
2087 2227 6.309737 GTCCTGCATTTCTTTGCTGATTTTAG 59.690 38.462 5.08 0.00 42.27 1.85
2088 2228 6.209192 TCCTGCATTTCTTTGCTGATTTTAGA 59.791 34.615 5.08 0.00 42.27 2.10
2092 2232 5.371115 TTTCTTTGCTGATTTTAGACCCG 57.629 39.130 0.00 0.00 0.00 5.28
2176 2316 0.040157 CCGGCATTTATGGTGCATCG 60.040 55.000 0.00 0.00 44.25 3.84
2231 2371 8.389603 TCACAAAATTTGCTTGACTTTGAATTC 58.610 29.630 5.52 0.00 32.57 2.17
2295 2435 3.499338 TGTTGGAATTGCACAGAAGGAT 58.501 40.909 0.00 0.00 0.00 3.24
2323 2463 7.291182 ACATAAATAGAGCAGTCCAGAAGGTAT 59.709 37.037 0.00 0.00 35.89 2.73
2369 2512 5.014123 TCAATTATCTGAGTGTCCCAGGTTT 59.986 40.000 0.00 0.00 32.73 3.27
2370 2513 4.993705 TTATCTGAGTGTCCCAGGTTTT 57.006 40.909 0.00 0.00 32.73 2.43
2371 2514 3.884037 ATCTGAGTGTCCCAGGTTTTT 57.116 42.857 0.00 0.00 32.73 1.94
2418 2657 3.561143 AGTACAGGGCATTGTTTTGTCA 58.439 40.909 0.00 0.00 32.56 3.58
2426 2665 4.562394 GGGCATTGTTTTGTCATGTTATCG 59.438 41.667 0.00 0.00 0.00 2.92
2695 2934 7.997482 ACAGCGAATCTAGAAGTTGACTAATA 58.003 34.615 13.86 0.00 0.00 0.98
2790 3029 2.307098 CTGGGATGAAGACCTTGGAGTT 59.693 50.000 0.00 0.00 0.00 3.01
2814 3053 7.199167 TGATCATTTCAATGGAGAGGAGTAA 57.801 36.000 0.00 0.00 37.03 2.24
2994 3233 1.340114 ACCAAAAGAAGAGGGGATCGC 60.340 52.381 0.06 0.06 0.00 4.58
3023 3262 7.065923 GGTTCACAAGTAAGTTGAAGAACTCTT 59.934 37.037 20.56 0.00 44.68 2.85
3041 3280 2.235650 TCTTGTCTGCCCTTCTGAGATG 59.764 50.000 0.00 0.00 0.00 2.90
3055 3294 6.480981 CCTTCTGAGATGCACAAATTTGTTTT 59.519 34.615 21.10 8.89 39.91 2.43
3080 3320 8.792830 TTTTCTTACCTTTCATCTCATACCTG 57.207 34.615 0.00 0.00 0.00 4.00
3083 3323 2.173569 ACCTTTCATCTCATACCTGCCC 59.826 50.000 0.00 0.00 0.00 5.36
3205 3446 3.248602 CAGCTGACTTGTGTTACTTGGTC 59.751 47.826 8.42 0.00 0.00 4.02
3216 3457 5.105675 TGTGTTACTTGGTCGCTGATATACA 60.106 40.000 0.00 0.00 0.00 2.29
3235 3477 2.102578 CATGGAAAAGGGCCTAACTGG 58.897 52.381 6.41 0.00 39.35 4.00
3277 3519 3.426615 TGTTGAAATTATGGCTCCGGTT 58.573 40.909 0.00 0.00 0.00 4.44
3468 3720 2.590575 AACCACACGCCCTTGTCG 60.591 61.111 0.00 0.00 0.00 4.35
3549 3804 5.060506 TCTCGACCATCTTATCTCTGTCTC 58.939 45.833 0.00 0.00 0.00 3.36
3551 3806 3.885901 CGACCATCTTATCTCTGTCTCCA 59.114 47.826 0.00 0.00 0.00 3.86
3583 3838 2.464157 ACTCTTTACAGCCTGCTCAC 57.536 50.000 0.00 0.00 0.00 3.51
3713 3968 4.142315 CCCATCATAGAACAGCAAAACCTG 60.142 45.833 0.00 0.00 38.78 4.00
3744 3999 3.565307 ACCAAACTCATTCCTGCTTTCA 58.435 40.909 0.00 0.00 0.00 2.69
3911 4166 3.007614 ACGTAACATTTGTCCACTAGGCT 59.992 43.478 0.00 0.00 33.74 4.58
3917 4172 0.601558 TTGTCCACTAGGCTGTCGTC 59.398 55.000 0.00 0.00 33.74 4.20
3918 4173 1.136984 GTCCACTAGGCTGTCGTCG 59.863 63.158 0.00 0.00 33.74 5.12
3919 4174 1.303074 TCCACTAGGCTGTCGTCGT 60.303 57.895 0.00 0.00 33.74 4.34
3924 4179 2.032204 CACTAGGCTGTCGTCGTATACC 60.032 54.545 0.00 0.00 0.00 2.73
4098 4355 2.421619 CTCTGTGTGCTTCTCCCTTTC 58.578 52.381 0.00 0.00 0.00 2.62
4111 4368 5.957771 TCTCCCTTTCTGCTGTGTATATT 57.042 39.130 0.00 0.00 0.00 1.28
4130 4387 8.998814 TGTATATTCTTCTCCCATTTTACTCCA 58.001 33.333 0.00 0.00 0.00 3.86
4133 4390 5.843019 TCTTCTCCCATTTTACTCCAGTT 57.157 39.130 0.00 0.00 0.00 3.16
4135 4392 5.548056 TCTTCTCCCATTTTACTCCAGTTCT 59.452 40.000 0.00 0.00 0.00 3.01
4136 4393 5.843019 TCTCCCATTTTACTCCAGTTCTT 57.157 39.130 0.00 0.00 0.00 2.52
4140 4397 7.664318 TCTCCCATTTTACTCCAGTTCTTTTAC 59.336 37.037 0.00 0.00 0.00 2.01
4165 4422 9.280174 ACTTTACTATTCGTTTCCTTGAATTGA 57.720 29.630 3.99 0.00 36.32 2.57
4213 4470 5.049167 TCGCAAGCAAATGAAAATCAGTTT 58.951 33.333 0.00 0.00 31.77 2.66
4241 4498 5.909621 AATCTCAATGGAACACTGATTGG 57.090 39.130 0.00 0.00 45.92 3.16
4265 4522 7.092891 TGGTGTTCATGTTAATCCTCTCAGTAT 60.093 37.037 0.00 0.00 0.00 2.12
4266 4523 7.225538 GGTGTTCATGTTAATCCTCTCAGTATG 59.774 40.741 0.00 0.00 37.54 2.39
4335 4612 6.578020 CAAAGTATGCAAATGCTGTATTGG 57.422 37.500 6.97 0.00 42.66 3.16
4413 4697 3.007398 ACTGCTCAAGAAACCCTAGACAG 59.993 47.826 0.00 0.00 0.00 3.51
4575 4860 6.969473 GCTTAGCCATTGTAAATCTCTGAAAC 59.031 38.462 0.00 0.00 0.00 2.78
4613 4898 0.191064 TTCCTCACCTCTGGACACCT 59.809 55.000 0.00 0.00 31.24 4.00
4616 4901 1.152247 TCACCTCTGGACACCTGCT 60.152 57.895 0.00 0.00 0.00 4.24
4626 4911 2.821366 CACCTGCTGCCGGATGAC 60.821 66.667 17.38 0.00 0.00 3.06
4721 5009 1.134461 CAGATGAACTGGGAGAGCAGG 60.134 57.143 0.00 0.00 42.39 4.85
4775 5063 2.171448 GCTCATCATGTAGGGGTTCACT 59.829 50.000 0.00 0.00 0.00 3.41
4790 5078 2.042686 TCACTTCATATGCAGGTGGC 57.957 50.000 7.30 0.00 45.13 5.01
4845 5133 1.892819 CGAAGGCTTCCTCCTCTGCA 61.893 60.000 20.97 0.00 34.82 4.41
4860 5148 3.753797 CCTCTGCAATGATCAGATGATGG 59.246 47.826 13.84 6.66 39.56 3.51
4861 5149 4.390264 CTCTGCAATGATCAGATGATGGT 58.610 43.478 13.84 0.00 39.56 3.55
4862 5150 4.134563 TCTGCAATGATCAGATGATGGTG 58.865 43.478 13.84 0.00 35.81 4.17
4892 5180 1.974343 TTTTTCGTGCCGGGATGGG 60.974 57.895 15.88 0.00 38.63 4.00
4893 5181 2.413211 TTTTTCGTGCCGGGATGGGA 62.413 55.000 15.88 2.66 38.63 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 4.162690 GTGGGATTCGCTCGCCCT 62.163 66.667 0.00 0.00 42.52 5.19
56 57 0.523072 CCAAATCTTCTGGTGCGTGG 59.477 55.000 0.00 0.00 0.00 4.94
94 95 3.369388 GAGAGGGGAGGAGGGGGT 61.369 72.222 0.00 0.00 0.00 4.95
95 96 4.179599 GGAGAGGGGAGGAGGGGG 62.180 77.778 0.00 0.00 0.00 5.40
100 101 1.093408 TGAAGAAGGAGAGGGGAGGA 58.907 55.000 0.00 0.00 0.00 3.71
106 107 4.165758 AGATTGGGATTGAAGAAGGAGAGG 59.834 45.833 0.00 0.00 0.00 3.69
288 326 2.508439 ATCGGCGTACCTGTTGCG 60.508 61.111 6.85 0.00 0.00 4.85
356 394 2.906389 AGGGCTCTGGCGATAATAATGA 59.094 45.455 0.00 0.00 39.81 2.57
363 401 1.464376 GCACTAGGGCTCTGGCGATA 61.464 60.000 10.54 0.00 39.81 2.92
369 407 1.617850 CTATCCAGCACTAGGGCTCTG 59.382 57.143 18.99 11.81 43.68 3.35
384 422 6.597280 GGCATGAAGAACCAATCTATCTATCC 59.403 42.308 0.00 0.00 37.42 2.59
407 445 2.136229 GGCCTTTGGATGGGATGGC 61.136 63.158 0.00 0.00 39.61 4.40
412 450 4.839706 CCCCGGCCTTTGGATGGG 62.840 72.222 0.00 1.10 38.08 4.00
429 471 2.030540 GGAACAAAACGTAGGGGAAAGC 60.031 50.000 0.00 0.00 0.00 3.51
430 472 2.224784 CGGAACAAAACGTAGGGGAAAG 59.775 50.000 0.00 0.00 0.00 2.62
453 497 0.320374 CCTGCCTAGTCAACCGACAA 59.680 55.000 0.00 0.00 45.23 3.18
512 556 1.825474 TCAACCTAGGAGTAGTGCTGC 59.175 52.381 17.98 0.00 35.61 5.25
513 557 4.021016 ACTTTCAACCTAGGAGTAGTGCTG 60.021 45.833 17.98 0.00 0.00 4.41
555 599 4.394920 TGAAGTGCCGGATTGATTAAAGAC 59.605 41.667 5.05 0.00 0.00 3.01
564 609 2.417243 GGGAAAATGAAGTGCCGGATTG 60.417 50.000 5.05 0.00 0.00 2.67
597 648 1.068127 GAGATTTCACATGGCCATGGC 59.932 52.381 41.25 29.47 42.91 4.40
598 649 1.684983 GGAGATTTCACATGGCCATGG 59.315 52.381 41.25 30.98 42.91 3.66
599 650 2.380941 TGGAGATTTCACATGGCCATG 58.619 47.619 38.53 38.53 44.15 3.66
600 651 2.832643 TGGAGATTTCACATGGCCAT 57.167 45.000 14.09 14.09 0.00 4.40
642 693 1.543208 GCCAGGATCACTGTGTGAACA 60.543 52.381 7.79 0.00 45.96 3.18
643 694 1.160137 GCCAGGATCACTGTGTGAAC 58.840 55.000 7.79 2.22 45.96 3.18
644 695 1.059098 AGCCAGGATCACTGTGTGAA 58.941 50.000 7.79 0.00 45.96 3.18
645 696 0.322648 CAGCCAGGATCACTGTGTGA 59.677 55.000 7.79 2.77 46.90 3.58
646 697 1.303799 GCAGCCAGGATCACTGTGTG 61.304 60.000 7.79 0.00 46.06 3.82
647 698 1.002868 GCAGCCAGGATCACTGTGT 60.003 57.895 7.79 0.00 46.06 3.72
648 699 1.748122 GGCAGCCAGGATCACTGTG 60.748 63.158 6.55 0.17 46.06 3.66
649 700 2.673523 GGCAGCCAGGATCACTGT 59.326 61.111 6.55 0.00 46.06 3.55
651 702 2.233566 TTGGGCAGCCAGGATCACT 61.234 57.895 15.19 0.00 0.00 3.41
652 703 2.048603 GTTGGGCAGCCAGGATCAC 61.049 63.158 15.19 0.00 0.00 3.06
653 704 2.356278 GTTGGGCAGCCAGGATCA 59.644 61.111 15.19 0.00 0.00 2.92
654 705 2.440980 GGTTGGGCAGCCAGGATC 60.441 66.667 15.19 0.00 0.00 3.36
676 731 4.454728 TTCCTAATTTTGATGCAGCACC 57.545 40.909 2.94 0.00 0.00 5.01
700 755 0.461516 GGCTAGCCGGTTACTGGTTC 60.462 60.000 20.16 0.00 0.00 3.62
717 772 0.594796 CCTAATTTTGATGCGGCGGC 60.595 55.000 9.78 9.68 40.52 6.53
733 788 0.179121 CGATTACACACGCCTGCCTA 60.179 55.000 0.00 0.00 0.00 3.93
739 794 3.089784 CTGCCGATTACACACGCC 58.910 61.111 0.00 0.00 0.00 5.68
768 834 0.876342 CGCTTCCCTAACTCCGATGC 60.876 60.000 0.00 0.00 0.00 3.91
769 835 0.460311 ACGCTTCCCTAACTCCGATG 59.540 55.000 0.00 0.00 0.00 3.84
771 837 0.896940 ACACGCTTCCCTAACTCCGA 60.897 55.000 0.00 0.00 0.00 4.55
772 838 0.813184 TACACGCTTCCCTAACTCCG 59.187 55.000 0.00 0.00 0.00 4.63
792 866 1.331756 GTCATTACTCGCTGCCAATGG 59.668 52.381 0.00 0.00 0.00 3.16
793 867 2.031314 CAGTCATTACTCGCTGCCAATG 59.969 50.000 0.00 0.00 31.97 2.82
814 888 6.572167 ATCCACGCTAGAGTATTTACTACC 57.428 41.667 0.00 0.00 36.50 3.18
870 985 2.370281 AGACAGTCGGTGTTAGCATG 57.630 50.000 0.00 0.00 40.56 4.06
875 990 2.696707 ACCTGAAAGACAGTCGGTGTTA 59.303 45.455 0.00 0.00 44.40 2.41
880 995 1.937108 GCAGACCTGAAAGACAGTCGG 60.937 57.143 0.47 0.00 44.40 4.79
881 996 1.423395 GCAGACCTGAAAGACAGTCG 58.577 55.000 0.47 0.00 44.40 4.18
998 1117 2.238646 ACTATCGGGAGTTTTGCCATCA 59.761 45.455 0.00 0.00 33.71 3.07
1056 1175 7.700656 GCAGCATAATTAAAAACAGATAACCGT 59.299 33.333 0.00 0.00 0.00 4.83
1057 1176 7.167468 GGCAGCATAATTAAAAACAGATAACCG 59.833 37.037 0.00 0.00 0.00 4.44
1094 1214 1.353358 GGCACCAAGTTAAGGGTAGGT 59.647 52.381 0.00 0.00 35.09 3.08
1095 1215 2.124277 GGCACCAAGTTAAGGGTAGG 57.876 55.000 0.00 0.00 35.09 3.18
1128 1248 4.117685 CGTTGGGTTTCCTACTACTATGC 58.882 47.826 0.00 0.00 36.78 3.14
1129 1249 5.359009 TCTCGTTGGGTTTCCTACTACTATG 59.641 44.000 0.00 0.00 36.78 2.23
1130 1250 5.513233 TCTCGTTGGGTTTCCTACTACTAT 58.487 41.667 0.00 0.00 36.78 2.12
1131 1251 4.922206 TCTCGTTGGGTTTCCTACTACTA 58.078 43.478 0.00 0.00 36.78 1.82
1132 1252 3.762823 CTCTCGTTGGGTTTCCTACTACT 59.237 47.826 0.00 0.00 36.78 2.57
1133 1253 3.675502 GCTCTCGTTGGGTTTCCTACTAC 60.676 52.174 0.00 0.00 36.78 2.73
1170 1293 1.601703 CACCCCGATGATGGTCACA 59.398 57.895 0.00 0.00 30.70 3.58
1412 1535 8.276950 TTCTAGCAGAAATCCAGGCATGGTTA 62.277 42.308 18.43 0.00 38.36 2.85
1489 1612 4.134563 TGGAGTAGAAGAACAAAGGCAAC 58.865 43.478 0.00 0.00 0.00 4.17
1731 1856 1.318158 GCACCCCATGAGCTGAAAGG 61.318 60.000 0.00 0.00 0.00 3.11
1732 1857 1.318158 GGCACCCCATGAGCTGAAAG 61.318 60.000 0.00 0.00 0.00 2.62
1743 1878 2.091333 AGAAAGAAGAAAAGGCACCCCA 60.091 45.455 0.00 0.00 0.00 4.96
1747 1882 5.520288 GTGGAAAAGAAAGAAGAAAAGGCAC 59.480 40.000 0.00 0.00 0.00 5.01
1755 1890 8.109634 AGCATATAAGGTGGAAAAGAAAGAAGA 58.890 33.333 0.00 0.00 0.00 2.87
1804 1939 7.509546 TCTAGTGGAGAAAGAAAGAAACACAT 58.490 34.615 0.00 0.00 0.00 3.21
1811 1946 9.702253 ATAGTACATCTAGTGGAGAAAGAAAGA 57.298 33.333 0.00 0.00 37.85 2.52
1870 2005 5.559770 TCAGAACAATGTGATAGGCAGAAA 58.440 37.500 0.00 0.00 0.00 2.52
1929 2068 8.845227 TGACAACAATAGACACACATAACAATT 58.155 29.630 0.00 0.00 0.00 2.32
1939 2078 8.227119 CGAAATTATGTGACAACAATAGACACA 58.773 33.333 0.00 0.00 43.70 3.72
1940 2079 8.440059 TCGAAATTATGTGACAACAATAGACAC 58.560 33.333 0.00 0.00 40.46 3.67
2015 2154 3.295093 TGGAATTCACAGGAGCACAAAA 58.705 40.909 7.93 0.00 0.00 2.44
2053 2192 4.240881 AGAAATGCAGGACATACCACAT 57.759 40.909 0.00 0.00 38.34 3.21
2087 2227 3.616821 GCTAAAAATGCAAATTCCGGGTC 59.383 43.478 0.00 0.00 0.00 4.46
2088 2228 3.260632 AGCTAAAAATGCAAATTCCGGGT 59.739 39.130 0.00 0.00 0.00 5.28
2092 2232 7.809665 ACATGAAAGCTAAAAATGCAAATTCC 58.190 30.769 0.00 0.00 0.00 3.01
2176 2316 4.618965 ACTCGAACACTGAGGTTAACTTC 58.381 43.478 10.63 10.63 37.79 3.01
2231 2371 0.108138 CTTGAAGGGTAGGTCCTGCG 60.108 60.000 0.00 0.00 35.11 5.18
2295 2435 7.125811 ACCTTCTGGACTGCTCTATTTATGTTA 59.874 37.037 0.00 0.00 37.04 2.41
2393 2537 5.381757 ACAAAACAATGCCCTGTACTAGAA 58.618 37.500 0.00 0.00 0.00 2.10
2397 2636 3.561143 TGACAAAACAATGCCCTGTACT 58.439 40.909 0.00 0.00 0.00 2.73
2456 2695 8.292448 GGCAGATAACCAAGTTACAATATCATG 58.708 37.037 0.00 0.00 30.49 3.07
2668 2907 4.926238 AGTCAACTTCTAGATTCGCTGTTG 59.074 41.667 0.00 3.60 35.89 3.33
2790 3029 5.705397 ACTCCTCTCCATTGAAATGATCA 57.295 39.130 0.00 0.00 38.70 2.92
2814 3053 4.342862 TGCTAAGTGAAGACTGAAAGCT 57.657 40.909 0.00 0.00 37.60 3.74
2994 3233 5.047847 TCTTCAACTTACTTGTGAACCTCG 58.952 41.667 0.00 0.00 0.00 4.63
3023 3262 0.251354 GCATCTCAGAAGGGCAGACA 59.749 55.000 0.00 0.00 0.00 3.41
3055 3294 7.336931 GCAGGTATGAGATGAAAGGTAAGAAAA 59.663 37.037 0.00 0.00 0.00 2.29
3080 3320 3.611674 CCAAACCACCAACGGGGC 61.612 66.667 0.00 0.00 42.05 5.80
3083 3323 3.188492 GTTAAAACCAAACCACCAACGG 58.812 45.455 0.00 0.00 0.00 4.44
3178 3418 0.463654 AACACAAGTCAGCTGCGGAA 60.464 50.000 9.47 0.00 0.00 4.30
3205 3446 3.189287 GCCCTTTTCCATGTATATCAGCG 59.811 47.826 0.00 0.00 0.00 5.18
3216 3457 1.007118 CCCAGTTAGGCCCTTTTCCAT 59.993 52.381 0.00 0.00 35.39 3.41
3235 3477 5.288804 ACAAAACTGCACATCAAACATACC 58.711 37.500 0.00 0.00 0.00 2.73
3549 3804 9.698617 GCTGTAAAGAGTAAATACGTTAATTGG 57.301 33.333 0.00 0.00 0.00 3.16
3551 3806 9.662947 AGGCTGTAAAGAGTAAATACGTTAATT 57.337 29.630 0.00 0.00 0.00 1.40
3571 3826 0.106708 TTTTCTCGTGAGCAGGCTGT 59.893 50.000 17.16 2.59 0.00 4.40
3583 3838 3.833265 GTCGACGACACCGATTTTCTCG 61.833 54.545 22.66 0.00 38.57 4.04
3713 3968 4.395231 GGAATGAGTTTGGTAGTAAGTGCC 59.605 45.833 0.00 0.00 0.00 5.01
3744 3999 1.172812 GCCTGTCCCTGCGAGTTTTT 61.173 55.000 0.00 0.00 0.00 1.94
3911 4166 2.016961 GGCGAGGTATACGACGACA 58.983 57.895 19.30 0.00 33.43 4.35
3917 4172 0.308684 TAACAGCGGCGAGGTATACG 59.691 55.000 12.98 0.00 0.00 3.06
3918 4173 2.497107 TTAACAGCGGCGAGGTATAC 57.503 50.000 12.98 0.00 0.00 1.47
3919 4174 2.029649 GGATTAACAGCGGCGAGGTATA 60.030 50.000 12.98 0.00 0.00 1.47
3924 4179 0.876342 GGAGGATTAACAGCGGCGAG 60.876 60.000 12.98 4.29 0.00 5.03
4098 4355 5.282055 TGGGAGAAGAATATACACAGCAG 57.718 43.478 0.00 0.00 0.00 4.24
4111 4368 5.548056 AGAACTGGAGTAAAATGGGAGAAGA 59.452 40.000 0.00 0.00 0.00 2.87
4165 4422 9.233232 GACGTCAAATAATTTCAGTTCAAACTT 57.767 29.630 11.55 0.00 37.08 2.66
4167 4424 7.614499 GCGACGTCAAATAATTTCAGTTCAAAC 60.614 37.037 17.16 0.00 0.00 2.93
4213 4470 4.523943 CAGTGTTCCATTGAGATTTTCCCA 59.476 41.667 0.00 0.00 0.00 4.37
4241 4498 7.766278 ACATACTGAGAGGATTAACATGAACAC 59.234 37.037 0.00 0.00 0.00 3.32
4265 4522 6.892658 ATTAATGTGCTTCTTTGGTGTACA 57.107 33.333 0.00 0.00 0.00 2.90
4266 4523 7.865385 TCAAATTAATGTGCTTCTTTGGTGTAC 59.135 33.333 0.22 0.00 0.00 2.90
4327 4604 5.745312 TGGCTATCCATCTACCAATACAG 57.255 43.478 0.00 0.00 37.47 2.74
4335 4612 9.203163 ACTATATAACCTTGGCTATCCATCTAC 57.797 37.037 0.00 0.00 43.05 2.59
4378 4662 1.082690 GAGCAGTTCTAAGCCTGTGC 58.917 55.000 0.00 0.00 37.95 4.57
4413 4697 9.704098 GTTAACTATAAGCTCTAATTGTGTTGC 57.296 33.333 0.00 0.00 0.00 4.17
4478 4762 0.760189 AGGAGAGGCTGCAGAGGATC 60.760 60.000 20.43 9.32 0.00 3.36
4514 4798 2.419990 GCCTTTTGTTTTCAGGCCTGTT 60.420 45.455 31.58 0.00 39.57 3.16
4575 4860 1.742761 AGATGATGGTCGCCTGTTTG 58.257 50.000 0.00 0.00 0.00 2.93
4721 5009 3.403558 GACCCTGAGCCTGACCCC 61.404 72.222 0.00 0.00 0.00 4.95
4775 5063 1.596603 CATCGCCACCTGCATATGAA 58.403 50.000 6.97 0.00 41.33 2.57
4845 5133 6.779860 TCATCATCACCATCATCTGATCATT 58.220 36.000 0.00 0.00 31.21 2.57
4860 5148 4.790140 GCACGAAAAACTCATCATCATCAC 59.210 41.667 0.00 0.00 0.00 3.06
4861 5149 4.142622 GGCACGAAAAACTCATCATCATCA 60.143 41.667 0.00 0.00 0.00 3.07
4862 5150 4.346129 GGCACGAAAAACTCATCATCATC 58.654 43.478 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.