Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007638.1 Kokia drynarioides strain JFW-HI SEQ_122269, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 6938
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Found at i:727 original size:30 final size:30
Alignment explanation
Indices: 663--917 Score: 236
Period size: 30 Copynumber: 8.6 Consensus size: 30
653 CTCTATTTTC
* * *
663 TTTCAAAAATCACATTTTAACCCC-AAAAT
1 TTTCTAAAATTACATTTTAACCCCTAAACT
692 TTTCTAAAATTACATTTTAACCCCTAAACT
1 TTTCTAAAATTACATTTTAACCCCTAAACT
722 TTTCTAAAATTACATTTTAACCCCTAAACT
1 TTTCTAAAATTACATTTTAACCCCTAAACT
*
752 TTTCTAAAATTACATTTTAGCCCCTAAA-T
1 TTTCTAAAATTACATTTTAACCCCTAAACT
* * * *
781 ATTGTAAAAATTACATTTTGACCCTTAAAC-
1 TTTCT-AAAATTACATTTTAACCCCTAAACT
* * *
811 TTTCTAAAAAATATATTTTGACCCCTAAA-T
1 TTTCT-AAAATTACATTTTAACCCCTAAACT
* * * **
841 TGCTCCAAAA-TCCATTTCGACCCC-AAACT
1 T-TTCTAAAATTACATTTTAACCCCTAAACT
* *
870 TCTCTAAAATTATGATTTT-ACCCCTAAACT
1 TTTCTAAAATTA-CATTTTAACCCCTAAACT
* * *
900 TCTCAAAAAATACATTTT
1 TTTCTAAAATTACATTTT
918 TGCCCTCGAA
Statistics
Matches: 191, Mismatches: 26, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
28 10 0.05
29 50 0.26
30 129 0.68
31 2 0.01
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.37
Consensus pattern (30 bp):
TTTCTAAAATTACATTTTAACCCCTAAACT
Found at i:923 original size:29 final size:29
Alignment explanation
Indices: 713--1090 Score: 86
Period size: 30 Copynumber: 12.9 Consensus size: 29
703 ACATTTTAAC
* * * **
713 CCCTAAACTTTTCTAAAATTACATTTTAAC
1 CCCTAAACTTCTCAAAAAATACATTTT-TG
* * * *
743 CCCTAAACTTTTCTAAAATTACATTTTAG
1 CCCTAAACTTCTCAAAAAATACATTTTTG
* * *
772 CCCCTAAATATTGT-AAAAATTACA-TTTTG
1 -CCCTAAA-CTTCTCAAAAAATACATTTTTG
*
801 ACCCTTAAACTT-TCTAAAAAATATA-TTTTG
1 -CCC-TAAACTTCTC-AAAAAATACATTTTTG
* * *
831 ACCCCTAAA-TTGCTC-CAAAATCCA-TTTCG
1 --CCCTAAACTT-CTCAAAAAATACATTTTTG
* * * * **
860 ACCCCAAACTTCTCTAAAATTATGATTTTAC
1 -CCCTAAACTTCTCAAAAAATA-CATTTTTG
891 CCCTAAACTTCTCAAAAAATACATTTTTG
1 CCCTAAACTTCTCAAAAAATACATTTTTG
* * *
920 CCCTCGAACTT-AC-AAAAATCACATTTTTTA
1 CCCT-AAACTTCTCAAAAAAT-ACA-TTTTTG
* * * * *
950 CCCTCGAACTTAT-AAAAATTATATTTTTA
1 CCCT-AAACTTCTCAAAAAATACATTTTTG
* *
979 CCCTCGAA-TATC-C-AAAAATCACATTTTTA
1 CCCT-AAACT-TCTCAAAAAAT-ACATTTTTG
* * * * *
1008 CCCCAAATTTCTCAAACACTACATTTTTT
1 CCCTAAACTTCTCAAAAAATACATTTTTG
* * *
1037 CCTTGAACTTC-C-AAAAATCACATTTTTA
1 CCCTAAACTTCTCAAAAAAT-ACATTTTTG
* * *
1065 CCCCAAACTT-TCCAAAATTACATTTT
1 CCCTAAACTTCTCAAAAAATACATTTT
1091 AACCTCGAAC
Statistics
Matches: 269, Mismatches: 53, Indels: 54
0.72 0.14 0.14
Matches are distributed among these distances:
27 4 0.01
28 50 0.19
29 89 0.33
30 110 0.41
31 16 0.06
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (29 bp):
CCCTAAACTTCTCAAAAAATACATTTTTG
Found at i:930 original size:30 final size:29
Alignment explanation
Indices: 896--1118 Score: 153
Period size: 29 Copynumber: 7.7 Consensus size: 29
886 TTTACCCCTA
*
896 AACTTCTCAAAAAATACATTTTTGCCCTCG
1 AACTTCTC-AAAAATACATTTTTACCCTCG
*
926 AACTT-ACAAAAATCACATTTTTTACCCTCG
1 AACTTCTCAAAAAT-ACA-TTTTTACCCTCG
* *
956 AACTTAT-AAAAATTATATTTTTACCCTCG
1 AACTTCTCAAAAA-TACATTTTTACCCTCG
*
985 AA-TATC-CAAAAATCACATTTTTACCC-CA
1 AACT-TCTCAAAAAT-ACATTTTTACCCTCG
* * * *
1013 AATTTCTCAAACACTACATTTTT-TCCTTG
1 AACTTCTCAAA-AATACATTTTTACCCTCG
*
1042 AACTTC-CAAAAATCACATTTTTACCC-CA
1 AACTTCTCAAAAAT-ACATTTTTACCCTCG
* *
1070 AACTT-TCCAAAATTACA-TTTTAACCTCG
1 AACTTCT-CAAAAATACATTTTTACCCTCG
* *
1098 AAC-TCTCCAAAACTTCATTTT
1 AACTTCT-CAAAAATACATTTT
1119 CAACCTCTTT
Statistics
Matches: 154, Mismatches: 21, Indels: 37
0.73 0.10 0.17
Matches are distributed among these distances:
27 10 0.06
28 49 0.32
29 64 0.42
30 30 0.19
31 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (29 bp):
AACTTCTCAAAAATACATTTTTACCCTCG
Found at i:1065 original size:57 final size:59
Alignment explanation
Indices: 885--1109 Score: 248
Period size: 57 Copynumber: 3.9 Consensus size: 59
875 AAAATTATGA
* * *
885 TTTTACCCCTAAACTTCTCAAAAAATACATTTTTGCCCTCGAACT-TACAAAAATCACATT
1 TTTTACCCC-AAACTTCTCAAAAATTACATTTTTACCCTCGAACTATCCAAAAATCACA-T
* * *
945 TTTTACCCTCGAACTTAT-AAAAATTATATTTTTACCCTCGAA-TATCCAAAAATCACAT
1 TTTTACCC-CAAACTTCTCAAAAATTACATTTTTACCCTCGAACTATCCAAAAATCACAT
* * * * *
1003 TTTTACCCCAAATTTCTCAAACACTACATTTTT-TCCTTGAACT-TCCAAAAATCACAT
1 TTTTACCCCAAACTTCTCAAAAATTACATTTTTACCCTCGAACTATCCAAAAATCACAT
* * *
1060 TTTTACCCCAAACTT-TCCAAAATTACA-TTTTAACCTCGAACTCTCCAAAA
1 TTTTACCCCAAACTTCTCAAAAATTACATTTTTACCCTCGAACTATCCAAAA
1110 CTTCATTTTC
Statistics
Matches: 139, Mismatches: 20, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
55 4 0.03
56 17 0.12
57 47 0.34
58 23 0.17
59 33 0.24
60 14 0.10
61 1 0.01
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.35
Consensus pattern (59 bp):
TTTTACCCCAAACTTCTCAAAAATTACATTTTTACCCTCGAACTATCCAAAAATCACAT
Found at i:1116 original size:28 final size:29
Alignment explanation
Indices: 1070--1125 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
1060 TTTTACCCCA
*
1070 AACTTTCCAAAATTACATTTT-AACCTCG
1 AACTCTCCAAAATTACATTTTCAACCTCG
1098 AACTCTCCAAAACTT-CATTTTCAACCTC
1 AACTCTCCAAAA-TTACATTTTCAACCTC
1126 TTTTTTCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 17 0.68
29 8 0.32
ACGTcount: A:0.34, C:0.30, G:0.02, T:0.34
Consensus pattern (29 bp):
AACTCTCCAAAATTACATTTTCAACCTCG
Found at i:2874 original size:75 final size:75
Alignment explanation
Indices: 2751--2901 Score: 293
Period size: 75 Copynumber: 2.0 Consensus size: 75
2741 AGATATCAGT
2751 ACTTTATTTATTTAGTAGTGAATAAAGAATAATAAAAGCATGAAACAGAATGGCAGTGGATACAC
1 ACTTTATTTATTTAGTAGTGAATAAAGAATAATAAAAGCATGAAACAGAATGGCAGTGGATACAC
2816 CTAATTGCGC
66 CTAATTGCGC
*
2826 ACTTTATTTATTTGGTAGTGAATAAAGAATAATAAAAGCATGAAACAGAATGGCAGTGGATACAC
1 ACTTTATTTATTTAGTAGTGAATAAAGAATAATAAAAGCATGAAACAGAATGGCAGTGGATACAC
2891 CTAATTGCGC
66 CTAATTGCGC
2901 A
1 A
2902 AAGGAGTCAA
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (75 bp):
ACTTTATTTATTTAGTAGTGAATAAAGAATAATAAAAGCATGAAACAGAATGGCAGTGGATACAC
CTAATTGCGC
Found at i:5170 original size:5 final size:5
Alignment explanation
Indices: 5160--5184 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
5150 GACATGTGTC
5160 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
5185 TTGAGTGAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:5995 original size:6 final size:6
Alignment explanation
Indices: 5984--6016 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
5974 TAAGACAAAA
5984 GGAAAG GGAAAG GGAAAG GGAAAG GGAAAG GGA
1 GGAAAG GGAAAG GGAAAG GGAAAG GGAAAG GGA
6017 GAATGTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (6 bp):
GGAAAG
Done.