Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013154.1 Kokia drynarioides strain JFW-HI SEQ_128173, 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: 2527
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Found at i:361 original size:98 final size:98
Alignment explanation
Indices: 189--475 Score: 434
Period size: 98 Copynumber: 2.9 Consensus size: 98
179 TCTTGAAAAG
* * * * *
189 GGGTATTCGATTATCCCGGATTGAAG-AAAAGTCGCGCCTAGTAAGTTAAGGCACAACTTTTCAA
1 GGGTACTCGATTATTCCGGTTTGAAGAAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTCAA
* *
253 GACTCGAAATAATGGAATATTGCCTCGGTTTAA
66 GACCCGAAATAAAGGAATATTGCCTCGGTTTAA
*
286 GGGTACTCGATTATTCCGGTTTGAAGAAAAAATCGCGCCTAGTGAGTTAAGGCACAAATTTTCAA
1 GGGTACTCGATTATTCCGGTTTGAAGAAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTCAA
*
351 GACCCAAAATAAAGGAATATTGCCTCGGTTTAA
66 GACCCGAAATAAAGGAATATTGCCTCGGTTTAA
* * * *
384 GGGTACTCGATTATTTCGGTTTGAAGAAAAAATAGCACCTAGTAAGTTAAGACACAAATTTTCAT
1 GGGTACTCGATTATTCCGGTTTGAAGAAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTCA-
449 A-ACCCGAAATAAAGGAATATTGCCTCG
65 AGACCCGAAATAAAGGAATATTGCCTCG
476 ATTTTAAATA
Statistics
Matches: 173, Mismatches: 15, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
97 23 0.13
98 149 0.86
99 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (98 bp):
GGGTACTCGATTATTCCGGTTTGAAGAAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTCAA
GACCCGAAATAAAGGAATATTGCCTCGGTTTAA
Found at i:922 original size:30 final size:29
Alignment explanation
Indices: 751--959 Score: 87
Period size: 29 Copynumber: 7.2 Consensus size: 29
741 CTAAAATGCA
* *
751 ATTTTGGAAAGTTTTA-GGACAAAAATGTG
1 ATTTTTGAAAG-TTTAGGGGCAAAAATGTG
* * * * *
780 AATTTTGGAAA--TTCGCGAGCAGAAATGTA
1 -ATTTTTGAAAGTTTAG-GGGCAAAAATGTG
* ** *
809 ATTTTTGAAAGTTCAGGGTTAAAATTG-G
1 ATTTTTGAAAGTTTAGGGGCAAAAATGTG
* * *
837 AATTTTTGGAAG-TTCGAGGGAAAAAATG-G
1 -ATTTTTGAAAGTTTAG-GGGCAAAAATGTG
*
866 AATTTTTGGAAA-TTT-GAAGG-AAAAATGTG
1 -ATTTTT-GAAAGTTTAG-GGGCAAAAATGTG
* *
895 ATTTTTGAAAGTTTTGGGGGTAAAAATG-G
1 ATTTTTGAAAG-TTTAGGGGCAAAAATGTG
* *
924 AATTTTTGGAAGTTTAGGGGCAAAAATGTA
1 -ATTTTTGAAAGTTTAGGGGCAAAAATGTG
954 ATTTTT
1 ATTTTT
960 TAGAATTTGG
Statistics
Matches: 137, Mismatches: 27, Indels: 31
0.70 0.14 0.16
Matches are distributed among these distances:
27 6 0.04
28 24 0.18
29 72 0.53
30 35 0.26
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (29 bp):
ATTTTTGAAAGTTTAGGGGCAAAAATGTG
Found at i:959 original size:87 final size:87
Alignment explanation
Indices: 743--959 Score: 228
Period size: 87 Copynumber: 2.5 Consensus size: 87
733 GTTTGGGACT
* * * *
743 AAAATGCAA-TTTTGGAAAGTTTTA-GGACAAAAATGTGAA-TTTTGGAAATTCGCGAGCAGAAA
1 AAAATGGAATTTTTGG-AAG-TTTAGGGGCAAAAATGT-AATTTTTGGAAATTCGCAAGCAAAAA
*
805 TGTAATTTTTGAAAGTTCAGGGTTA
63 TGTAATTTTTGAAAGTTCAGGGGTA
* * * * * *
830 AAATTGGAATTTTTGGAAG-TTCGAGGGAAAAAATGGAATTTTTGGAAATTTG-AAGGAAAAATG
1 AAAATGGAATTTTTGGAAGTTTAG-GGGCAAAAATGTAATTTTTGGAAATTCGCAAGCAAAAATG
* **
893 TGATTTTTGAAAGTTTTGGGGGTA
65 TAATTTTTGAAAG-TTCAGGGGTA
917 AAAATGGAATTTTTGGAAGTTTAGGGGCAAAAATGTAATTTTT
1 AAAATGGAATTTTTGGAAGTTTAGGGGCAAAAATGTAATTTTT
960 TAGAATTTGG
Statistics
Matches: 106, Mismatches: 18, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
85 2 0.02
86 22 0.21
87 73 0.69
88 9 0.08
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.34
Consensus pattern (87 bp):
AAAATGGAATTTTTGGAAGTTTAGGGGCAAAAATGTAATTTTTGGAAATTCGCAAGCAAAAATGT
AATTTTTGAAAGTTCAGGGGTA
Found at i:967 original size:87 final size:86
Alignment explanation
Indices: 802--978 Score: 214
Period size: 87 Copynumber: 2.0 Consensus size: 86
792 TCGCGAGCAG
* * *
802 AAATGTAATTTTTGAAAGTTCAGGGTTAAAATTGGAATTTTTGGAAGTTCGAGGGAAAAAATGGA
1 AAATGTAATTTTTGAAAGTTCAGGGGTAAAAATGGAATTTTTGGAAGTTAGAGGGAAAAAATGGA
*
867 ATTTTTGGAAATTTGAAGGAA
66 ATTTTTAGAAATTTGAAGGAA
* ** *
888 AAATGTGATTTTTGAAAGTTTTGGGGGTAAAAATGGAATTTTTGGAAGTTTAG-GGGCAAAAATG
1 AAATGTAATTTTTGAAAG-TTCAGGGGTAAAAATGGAATTTTTGGAAG-TTAGAGGGAAAAAATG
* **
952 TAATTTTTTAG-AATTTGGGGGAA
64 GAA-TTTTTAGAAATTTGAAGGAA
975 AAAT
1 AAAT
979 TCTAATTTGA
Statistics
Matches: 77, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
86 17 0.22
87 51 0.66
88 9 0.12
ACGTcount: A:0.37, C:0.02, G:0.27, T:0.35
Consensus pattern (86 bp):
AAATGTAATTTTTGAAAGTTCAGGGGTAAAAATGGAATTTTTGGAAGTTAGAGGGAAAAAATGGA
ATTTTTAGAAATTTGAAGGAA
Found at i:971 original size:28 final size:29
Alignment explanation
Indices: 802--1049 Score: 156
Period size: 29 Copynumber: 8.6 Consensus size: 29
792 TCGCGAGCAG
* **
802 AAATGTAATTTTTGA-AAGTTCAGGGTTAA
1 AAATGTAATTTTTGAGAA-TTTAGGGGGAA
* * * * *
831 AATTGGAATTTTTG-GAAGTTCGAGGGAAA
1 AAATGTAATTTTTGAGAATTTAG-GGGGAA
* **
860 AAATGGAATTTTTG-GAAATTT-GAAGGAA
1 AAATGTAATTTTTGAG-AATTTAGGGGGAA
* *
888 AAATGTGATTTTTGA-AAGTTTTGGGGGTAA
1 AAATGTAATTTTTGAGAA-TTTAGGGGG-AA
* *
918 AAATGGAATTTTTG-GAAGTTTAGGGGCAA
1 AAATGTAATTTTTGAGAA-TTTAGGGGGAA
*
947 AAATGTAATTTTTTAGAATTT-GGGGGAA
1 AAATGTAATTTTTGAGAATTTAGGGGGAA
* *
975 AAATTCTAA--TTTGAGAATTT-GGGGGGA
1 AAA-TGTAATTTTTGAGAATTTAGGGGGAA
* * *
1002 AATTGTAATTTTTGAGAAATTTAGAGGTAA
1 AAATGTAATTTTTGAG-AATTTAGGGGGAA
*
1032 ACATGTAATTTTTGAGAA
1 AAATGTAATTTTTGAGAA
1050 GTTCGAGGGT
Statistics
Matches: 172, Mismatches: 33, Indels: 28
0.74 0.14 0.12
Matches are distributed among these distances:
26 4 0.02
27 20 0.12
28 35 0.20
29 64 0.37
30 49 0.28
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.36
Consensus pattern (29 bp):
AAATGTAATTTTTGAGAATTTAGGGGGAA
Found at i:972 original size:29 final size:28
Alignment explanation
Indices: 858--1049 Score: 151
Period size: 30 Copynumber: 6.7 Consensus size: 28
848 GTTCGAGGGA
* **
858 AAAAATGGAATTTTTG-GAAATTTGAAGG
1 AAAAATGTAATTTTTGAG-AATTTGGGGG
*
886 AAAAATGTGATTTTTGA-AAGTTTTGGGGG
1 AAAAATGTAATTTTTGAGAA--TTTGGGGG
* *
915 TAAAAATGGAATTTTTG-GAAGTTTAGGGGC
1 -AAAAATGTAATTTTTGAGAA-TTT-GGGGG
*
945 AAAAATGTAATTTTTTAGAATTTGGGGG
1 AAAAATGTAATTTTTGAGAATTTGGGGG
*
973 AAAAATTCTAA--TTTGAGAATTTGGGGG
1 AAAAA-TGTAATTTTTGAGAATTTGGGGG
* * * *
1000 GAAATTGTAATTTTTGAGAAATTTAGAGGT
1 AAAAATGTAATTTTTGAG-AATTT-GGGGG
*
1030 AAACATGTAATTTTTGAGAA
1 AAAAATGTAATTTTTGAGAA
1050 GTTCGAGGGT
Statistics
Matches: 131, Mismatches: 21, Indels: 23
0.75 0.12 0.13
Matches are distributed among these distances:
26 4 0.03
27 20 0.15
28 29 0.22
29 37 0.28
30 41 0.31
ACGTcount: A:0.37, C:0.02, G:0.26, T:0.36
Consensus pattern (28 bp):
AAAAATGTAATTTTTGAGAATTTGGGGG
Found at i:1005 original size:26 final size:27
Alignment explanation
Indices: 961--1012 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
951 GTAATTTTTT
961 AGAATTTGGGGGAAAAATTCTAATTTG
1 AGAATTTGGGGGAAAAATTCTAATTTG
* *
988 AGAATTTGGGGG-GAAATTGTAATTT
1 AGAATTTGGGGGAAAAATTCTAATTT
1013 TTGAGAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.35, C:0.02, G:0.29, T:0.35
Consensus pattern (27 bp):
AGAATTTGGGGGAAAAATTCTAATTTG
Done.