Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006642.1 Kokia drynarioides strain JFW-HI SEQ_121232, 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: 8734
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Found at i:961 original size:60 final size:58
Alignment explanation
Indices: 748--1143 Score: 275
Period size: 59 Copynumber: 6.7 Consensus size: 58
738 TACTAGATAA
* * * * *
748 AAAAAGGGGTGTCGGCCA-TGACATGACCAACACAAAAAAAAAATTAATTTTTTTATTTGAC
1 AAAAAGGGATGTCGGCCATTG-CATGACCAACAC---CAAAAATTTAAATTTTTTATCTGAC
* * * * *
809 AAAAAGGGGATATCGGCCATGGCATGACCAACACCCAAAAATTT-GATTTTTTATTTAGAT
1 AAAAA-GGGATGTCGGCCATTGCATGACCAACA-CCAAAAATTTAAATTTTTTATCT-GAC
** * *
869 AAAAAGGGATGTTAGCCA-TGCAATGGCAAACACCAGAAAATTTTAAAATTTTTTATCTGA-
1 AAAAAGGGATGTCGGCCATTGC-ATGACCAACACCA-AAAA-TTT-AAATTTTTTATCTGAC
* * * *
929 AAAAAGGGATGTCGACCATTGCATGACCAACACCCAAAAATTTAATTTTTTTATCAGAT
1 AAAAAGGGATGTCGGCCATTGCATGACCAACA-CCAAAAATTTAAATTTTTTATCTGAC
** * * * * * *
988 AATTAGGGGTGTCGGCCATGGCATGGCTAACACCAAAAAATTGAATTTTTTATCTGAC
1 AAAAAGGGATGTCGGCCATTGCATGACCAACACCAAAAATTTAAATTTTTTATCTGAC
* * * * * *
1046 AAAAAGGGGGTGTCGGCCATTGCATGGCCAACATCGAAAAATCT-GATTTTTTATCAT-AT
1 AAAAA-GGGATGTCGGCCATTGCATGACCAACA-CCAAAAATTTAAATTTTTTATC-TGAC
* * *
1105 TAAAAGGGAGTGTCGGCCA-TGCAAAGGCCAACACCAAAA
1 AAAAAGGGA-TGTCGGCCATTGC-ATGACCAACACCAAAA
1144 TTTTTTTTTC
Statistics
Matches: 270, Mismatches: 48, Indels: 37
0.76 0.14 0.10
Matches are distributed among these distances:
58 53 0.20
59 118 0.44
60 52 0.19
61 13 0.05
62 32 0.12
63 2 0.01
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.27
Consensus pattern (58 bp):
AAAAAGGGATGTCGGCCATTGCATGACCAACACCAAAAATTTAAATTTTTTATCTGAC
Found at i:970 original size:119 final size:119
Alignment explanation
Indices: 722--1148 Score: 411
Period size: 119 Copynumber: 3.6 Consensus size: 119
712 GTCAACACAA
* * * **
722 AAAAATTTGATTTTTT-TACTAGATAAAAAAAGGGGTGTCGGCCATG-ACATGACCAACACAAAA
1 AAAAATTTGATTTTTTATTC-AGAT--AAAAAGGGATGTCGGCCATGCA-ATG-GCAA-ACACCA
** * * * *
785 AAAAAATTAATTTTTTTATTTGACAAAAAGGGGATATCGGCCATGGCATGACCAACACCC
60 AAAATTTTAAATTTTTTATCTGACAAAAAGGGGATGTCGGCCATTGCATGACCAACACCC
* **
845 AAAAATTTGATTTTTTATTTAGATAAAAAGGGATGTTAGCCATGCAATGGCAAACACCAGAAAAT
1 AAAAATTTGATTTTTTATTCAGATAAAAAGGGATGTCGGCCATGCAATGGCAAACACCA-AAAAT
*
910 TTTAAAATTTTTTATCTGA-AAAAA-GGGATGTCGACCATTGCATGACCAACACCC
65 TTT-AAATTTTTTATCTGACAAAAAGGGGATGTCGGCCATTGCATGACCAACACCC
* ** * *
964 AAAAATTTAATTTTTT-TATCAGATAATTAGGGGTGTCGGCCATGGC-ATGGCTAACACCAAAAA
1 AAAAATTTGATTTTTTAT-TCAGATAAAAAGGGATGTCGGCCAT-GCAATGGCAAACACCAAAAA
* * * * * *
1027 -ATTGAATTTTTTATCTGACAAAAAGGGGGTGTCGGCCATTGCATGGCCAACATCG
64 TTTTAAATTTTTTATCTGACAAAAAGGGGATGTCGGCCATTGCATGACCAACACCC
* * * * * *
1082 AAAAATCTGATTTTTTA-TCATATTAAAAGGGAGTGTCGGCCATGCAAAGGCCAACACCAAAATT
1 AAAAATTTGATTTTTTATTCAGATAAAAAGGGA-TGTCGGCCATGCAATGGCAAACACCAAAAAT
1146 TTT
65 TTT
1149 TTTTCTGTCA
Statistics
Matches: 251, Mismatches: 41, Indels: 28
0.78 0.13 0.09
Matches are distributed among these distances:
116 14 0.06
117 19 0.08
118 68 0.27
119 79 0.31
120 16 0.06
121 33 0.13
122 1 0.00
123 20 0.08
124 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (119 bp):
AAAAATTTGATTTTTTATTCAGATAAAAAGGGATGTCGGCCATGCAATGGCAAACACCAAAAATT
TTAAATTTTTTATCTGACAAAAAGGGGATGTCGGCCATTGCATGACCAACACCC
Found at i:1126 original size:237 final size:238
Alignment explanation
Indices: 696--1148 Score: 556
Period size: 237 Copynumber: 1.9 Consensus size: 238
686 GGAAAGTTAG
** *
696 TGTCGACCATTACATGGTCAACACAAAAAAATTTGATTTTTTTACTAGATAAAAAAAGGGGTGTC
1 TGTCGACCATTACATGACCAACACAAAAAAATTTAATTTTTTTACTAGAT-AAAAAAGGGGTGTC
*
761 GGCCATGACATGACCAACACAAAAAAAAAATTAATTTTTTTATTTGACAAAAAGGGGATATCGGC
65 GGCCATGACATGACCAACAC--AAAAAAAATTAATTTTTTTATCTGACAAAAAGGGGATATCGGC
* * *
826 CATGGCATGACCAACACCCAAAAATTTGATTTTTTATTTAGATAAAAAGGGATGTTAGCCATGCA
128 CATGGCATGACCAACACCCAAAAATCTGATTTTTTATTCAGATAAAAAGGGATGTCAGCCATGCA
*
891 ATGGCAAACACCAGAAAATTTTAAAATTTTTTATCTGAAAAAAGGGA
193 AAGGCAAACACCA-AAAATTTTAAAATTTTTTATCTGAAAAAAGGGA
* ** **
938 TGTCGACCATTGCATGACCAACACCCAAAAATTTAATTTTTTTA-TCAGAT-AATTAGGGGTGTC
1 TGTCGACCATTACATGACCAACACAAAAAAATTTAATTTTTTTACT-AGATAAAAAAGGGGTGTC
* * * * * *
1001 GGCCATGGCATGGCTAACAC-CAAAAAATTGAA-TTTTTTATCTGACAAAAAGGGGGTGTCGGCC
65 GGCCATGACATGACCAACACAAAAAAAATT-AATTTTTTTATCTGACAAAAAGGGGATATCGGCC
* * * * * * *
1064 ATTGCATGGCCAACATCGAAAAATCTGATTTTTTA-TCATATTAAAAGGGAGTGTCGGCCATGCA
129 ATGGCATGACCAACACCCAAAAATCTGATTTTTTATTCAGATAAAAAGGGA-TGTCAGCCATGCA
* *
1128 AAGGCCAACACCAAAATTTTT
193 AAGGCAAACACCAAAAATTTT
1149 TTTTCTGTCA
Statistics
Matches: 180, Mismatches: 28, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
236 19 0.11
237 88 0.49
238 2 0.01
240 28 0.16
241 1 0.01
242 42 0.23
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (238 bp):
TGTCGACCATTACATGACCAACACAAAAAAATTTAATTTTTTTACTAGATAAAAAAGGGGTGTCG
GCCATGACATGACCAACACAAAAAAAATTAATTTTTTTATCTGACAAAAAGGGGATATCGGCCAT
GGCATGACCAACACCCAAAAATCTGATTTTTTATTCAGATAAAAAGGGATGTCAGCCATGCAAAG
GCAAACACCAAAAATTTTAAAATTTTTTATCTGAAAAAAGGGA
Found at i:7845 original size:24 final size:24
Alignment explanation
Indices: 7813--7866 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
7803 ATAATAAAAA
* *
7813 TATAATTTTATCATTTTGATAGT-T
1 TATATTTTTAT-ATTTTGAAAGTAT
*
7837 TATATTTTTATATTTTTAAAGTAT
1 TATATTTTTATATTTTGAAAGTAT
7861 TATATT
1 TATATT
7867 AAATTTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 9 0.35
24 17 0.65
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (24 bp):
TATATTTTTATATTTTGAAAGTAT
Found at i:8424 original size:21 final size:19
Alignment explanation
Indices: 8381--8425 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
8371 AATGTTATGC
*
8381 TTTTGTTGTTTTCTTACTG
1 TTTTGTTGTTTTCTTACTA
*
8400 TTTTGTTGCTATTTTTTACTA
1 TTTTGTTG-T-TTTCTTACTA
8421 TTTTG
1 TTTTG
8426 CTAACGTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 8 0.36
20 1 0.05
21 13 0.59
ACGTcount: A:0.09, C:0.09, G:0.13, T:0.69
Consensus pattern (19 bp):
TTTTGTTGTTTTCTTACTA
Found at i:8611 original size:8 final size:9
Alignment explanation
Indices: 8588--8621 Score: 68
Period size: 9 Copynumber: 3.8 Consensus size: 9
8578 AAAAAATATT
8588 TATTTTTAA
1 TATTTTTAA
8597 TATTTTTAA
1 TATTTTTAA
8606 TATTTTTAA
1 TATTTTTAA
8615 TATTTTT
1 TATTTTT
8622 GATGTATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (9 bp):
TATTTTTAA
Done.