Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013673.1 Kokia drynarioides strain JFW-HI SEQ_128701, 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: 11635
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1066 original size:117 final size:115
Alignment explanation
Indices: 799--1104 Score: 354
Period size: 117 Copynumber: 2.7 Consensus size: 115
789 CCGGTGTCCC
* * * * * * * * *
799 AACACCTAAAAAAATATTTTTAAATATAG-AAATGTGATGTCAACCATTGGATGCCAAATACCTA
1 AACACCCAAAAAAATATTTTTAAATCTAGAAAAAGTGGTGTCGATCATTGGGTGCCAAACACCCA
*
863 AAAAA-ATTTTTTTATTCGTATTCTTTTAGGTGTTGGTCATTGCTTACCA
66 AAAAATATTTTTTTATTCGTATTCTTTTAGGTGTCGGTCATTGCTTACCA
* *
912 AACACCCAAAAAAATATTTTTAAATCTA-AAAAGGTGGTGTCGATCATTGGGTGTCAAACACCCA
1 AACACCCAAAAAAATATTTTTAAATCTAGAAAAAGTGGTGTCGATCATTGGGTGCCAAACACCCA
* * * **
976 AAAAATTATTTTTTTATTTGTTTTTTTTTTTCA-GTGTCGGTCATTGCTTGTCA
66 AAAAA-TATTTTTTTATTCG--TATTCTTTT-AGGTGTCGGTCATTGCTTACCA
* *
1029 AACACCC-AAAAAATATTTTTAAATCTAGAAAAAGTGGTGTATG-TCATTGGGTGGCAAACACCC
1 AACACCCAAAAAAATATTTTTAAATCTAGAAAAAGTGGTGT-CGATCATTGGGTGCCAAACACCC
1092 AAAAAATATTTTT
65 AAAAAATATTTTT
1105 AAATATGAGA
Statistics
Matches: 166, Mismatches: 19, Indels: 13
0.84 0.10 0.07
Matches are distributed among these distances:
113 58 0.35
115 12 0.07
116 27 0.16
117 67 0.40
118 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (115 bp):
AACACCCAAAAAAATATTTTTAAATCTAGAAAAAGTGGTGTCGATCATTGGGTGCCAAACACCCA
AAAAATATTTTTTTATTCGTATTCTTTTAGGTGTCGGTCATTGCTTACCA
Found at i:1094 original size:56 final size:56
Alignment explanation
Indices: 1027--1160 Score: 180
Period size: 56 Copynumber: 2.4 Consensus size: 56
1017 CATTGCTTGT
* * * ** *
1027 CAAACACCCAAAAAATATTTTTAAATCT-AGAAAAAGTGGTGTATGTCATTGGGTGG
1 CAAACACCCAAAAAATATTTTTAAATATGAG-AAAAGTGGTGTAGGCCATTAAGTGA
*
1083 CAAACACCCAAAAAATATTTTTAAATATGAGAAAGGTGGTGTAGGCCATTAAGTGA
1 CAAACACCCAAAAAATATTTTTAAATATGAGAAAAGTGGTGTAGGCCATTAAGTGA
*
1139 TAAACACCCAAAAAATATTTTT
1 CAAACACCCAAAAAATATTTTT
1161 TATTCGTATT
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
56 67 0.97
57 2 0.03
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (56 bp):
CAAACACCCAAAAAATATTTTTAAATATGAGAAAAGTGGTGTAGGCCATTAAGTGA
Found at i:1208 original size:112 final size:111
Alignment explanation
Indices: 1082--1328 Score: 266
Period size: 112 Copynumber: 2.2 Consensus size: 111
1072 TCATTGGGTG
* * * * *
1082 GCAAACACCCAAAAAATATTTTTAA-A-TATGAGAAAG-GTGGTGTAGGCCATTAAGTGATAAAC
1 GCAAACACTCAAAAAATATTTTTAAGACT-TAAAAAAGAG-GGTGTAGGCCATGAAGTGACAAAC
* * * *
1144 ACCCAAAAAATATTTTTTATTCGTATTTTTGGGTGTCGATCATGATTTA
64 A-CCAAAAAAAAATTTTTATTCGTATTTTTGGGTGTCGACCATGACTTA
* * * *** *
1193 GCAAACATTCAAAAAATATTTTTAAGGACTTAAAAAAGAGGGTGTCGGTCATGGCTTGACAGACA
1 GCAAACACTCAAAAAATATTTTTAA-GACTTAAAAAAGAGGGTGTAGGCCATGAAGTGACAAACA
* *
1258 CCAAAAAAAAATTTTTATTCGTATTTTTGGGTGTCGACCATGGCTTG
65 CCAAAAAAAAATTTTTATTCGTATTTTTGGGTGTCGACCATGACTTA
1305 GCAAACACTCAAAAAAATATTTTT
1 GCAAACACTC-AAAAAATATTTTT
1329 TAATGTAAAA
Statistics
Matches: 112, Mismatches: 19, Indels: 8
0.81 0.14 0.06
Matches are distributed among these distances:
111 23 0.21
112 50 0.45
113 37 0.33
114 2 0.02
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (111 bp):
GCAAACACTCAAAAAATATTTTTAAGACTTAAAAAAGAGGGTGTAGGCCATGAAGTGACAAACAC
CAAAAAAAAATTTTTATTCGTATTTTTGGGTGTCGACCATGACTTA
Found at i:1503 original size:125 final size:124
Alignment explanation
Indices: 1279--1530 Score: 468
Period size: 125 Copynumber: 2.0 Consensus size: 124
1269 TTTTTATTCG
*
1279 TATTTTTGGGTGTCGACCATGGCTTGGCAAACACTCAAAAAAATATTTTTTAATGTAAAAAGATG
1 TATTTTTGGGTGTCGACCATGGCTTGACAAACACTCAAAAAAATATTTTTTAATGTAAAAAGATG
*
1344 GTGTCGACTATGGGATGTCAGGAACCCAAGTTTTTTTTTAAAAATCAAGTATTTTCGTA
66 GTGTCGACTATGGGATGTCAGGAACCCAAGTTTTTTTTAAAAAATCAAGTATTTTCGTA
1403 TANTTTTTGGGTGTCGACCATGGCTTGACAAACACTCAAAAAAATATTTTTTAATGTAAAAAGAT
1 TA-TTTTTGGGTGTCGACCATGGCTTGACAAACACTCAAAAAAATATTTTTTAATGTAAAAAGAT
*
1468 GGTGTCGGCTATGGGATGTCAGGAACCCAAGTTTTTTTTAAAAAATCAAGTATTTTCGTA
65 GGTGTCGACTATGGGATGTCAGGAACCCAAGTTTTTTTTAAAAAATCAAGTATTTTCGTA
1528 TAT
1 TAT
1531 CAATATAATA
Statistics
Matches: 124, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
124 3 0.02
125 121 0.98
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (124 bp):
TATTTTTGGGTGTCGACCATGGCTTGACAAACACTCAAAAAAATATTTTTTAATGTAAAAAGATG
GTGTCGACTATGGGATGTCAGGAACCCAAGTTTTTTTTAAAAAATCAAGTATTTTCGTA
Found at i:1896 original size:19 final size:18
Alignment explanation
Indices: 1874--1957 Score: 73
Period size: 17 Copynumber: 4.6 Consensus size: 18
1864 TTATGAATTC
1874 TATATTTCTTTACATTTTT
1 TATATTT-TTTACATTTTT
*
1893 TATATTTTTTTTACA-ATTT
1 TATA--TTTTTTACATTTTT
** *
1912 TATAAAATTTTATATTTTT
1 TAT-ATTTTTTACATTTTT
*
1931 TATA-TTTTTATATTTTT
1 TATATTTTTTACATTTTT
1948 TATATTTTTT
1 TATATTTTTT
1958 CCTAATTTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
17 16 0.30
18 12 0.22
19 16 0.30
20 7 0.13
21 3 0.06
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (18 bp):
TATATTTTTTACATTTTT
Found at i:1899 original size:9 final size:9
Alignment explanation
Indices: 1874--1957 Score: 80
Period size: 9 Copynumber: 9.1 Consensus size: 9
1864 TTATGAATTC
1874 TATATTTCTT
1 TATATTT-TT
*
1884 TACATTTTT
1 TATATTTTT
1893 TATATTTTT
1 TATATTTTT
* **
1902 TTTACAATTT
1 TATA-TTTTT
**
1912 TATAAAATTT
1 TAT-ATTTTT
1922 TATATTTTT
1 TATATTTTT
1931 TATA-TTTT
1 TATATTTTT
1939 TATATTTTT
1 TATATTTTT
1948 TATATTTTT
1 TATATTTTT
1957 T
1 T
1958 CCTAATTTTT
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
8 8 0.13
9 35 0.56
10 19 0.30
11 1 0.02
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (9 bp):
TATATTTTT
Found at i:1939 original size:17 final size:17
Alignment explanation
Indices: 1919--1956 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
1909 TTTTATAAAA
1919 TTTTATATTTTTTATAT
1 TTTTATATTTTTTATAT
1936 TTTTATATTTTTTATAT
1 TTTTATATTTTTTATAT
1953 TTTT
1 TTTT
1957 TCCTAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTATATTTTTTATAT
Done.