Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011915.1 Kokia drynarioides strain JFW-HI SEQ_126913, 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: 7767
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Found at i:627 original size:6 final size:6
Alignment explanation
Indices: 616--709 Score: 79
Period size: 6 Copynumber: 15.7 Consensus size: 6
606 GGCCCAACAG
* * * *
616 AATTTA AATTT- ATTTTA AAATTA AATTT- ATTTTA AGTTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
*
662 CTTAATTTA AATTT- -ATTATA AATTTA AGTTTA AATTTA AATTTA AATT
1 ---AATTTA AATTTA AATT-TA AATTTA AATTTA AATTTA AATTTA AATT
710 AATGTCCAAA
Statistics
Matches: 71, Mismatches: 9, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
4 3 0.04
5 9 0.13
6 50 0.70
7 3 0.04
9 6 0.08
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (6 bp):
AATTTA
Found at i:641 original size:17 final size:17
Alignment explanation
Indices: 616--709 Score: 111
Period size: 17 Copynumber: 5.6 Consensus size: 17
606 GGCCCAACAG
616 AATTTAAATTTATTTTA
1 AATTTAAATTTATTTTA
*
633 AAATTAAATTTATTTTA
1 AATTTAAATTTATTTTA
* *
650 AGTTTAAATTTA-CTT-
1 AATTTAAATTTATTTTA
*
665 AATTTAAATTTATTATA
1 AATTTAAATTTATTTTA
* *
682 AATTTAAGTTTAAATTTA
1 AATTTAAATTT-ATTTTA
700 AATTTAAATT
1 AATTTAAATT
710 AATGTCCAAA
Statistics
Matches: 63, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
15 11 0.17
16 3 0.05
17 36 0.57
18 13 0.21
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (17 bp):
AATTTAAATTTATTTTA
Found at i:757 original size:19 final size:20
Alignment explanation
Indices: 710--758 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
700 AATTTAAATT
710 AATGTCCAAATACAAACATA
1 AATGTCCAAATACAAACATA
*
730 AATGTCCAATTACAAA-ATCA
1 AATGTCCAAATACAAACAT-A
750 AA-GTCCAAA
1 AATGTCCAAA
759 ATGTTTACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.53, C:0.20, G:0.06, T:0.20
Consensus pattern (20 bp):
AATGTCCAAATACAAACATA
Found at i:1391 original size:3 final size:3
Alignment explanation
Indices: 1383--1479 Score: 59
Period size: 3 Copynumber: 32.0 Consensus size: 3
1373 CCTTTAGTCG
* * * * *
1383 TAA TAA TAA TAA TAA CAA CAA CAA TAA TAA TAA TAA TAA TAT TAC TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * * * * *
1431 TGA CAT TAG TAA TAC TAA TGA TAG TAA TAA TAG TAA TAAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA
1477 TAA
1 TAA
1480 ATATTATTAA
Statistics
Matches: 71, Mismatches: 22, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
3 68 0.96
4 3 0.04
ACGTcount: A:0.57, C:0.06, G:0.05, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1932 original size:60 final size:59
Alignment explanation
Indices: 1839--2208 Score: 302
Period size: 60 Copynumber: 6.2 Consensus size: 59
1829 AAATTTCCTG
* * * * ***
1839 AAAATTATATTTTTACCCCTAAACTTTCTAAAATTCCATTTTTGACCTTGATTTTTCCA
1 AAAATTACATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTCCA
* * *
1898 AAAATTACATTTATTACCCCTAAACTTCCCAAAATTCTATTATTGACAC-CGAAACTTCCA
1 AAAATTACATTT-TTACCCCTAAACTTCCAAAAATTCCATTTTTGAC-CTCGAAACTTCCA
* *
1958 AAAATTACATTTTTACCCCCAAACTTCCAAAAATTCCA-TTTTAACCTCGAAACTTCCA
1 AAAATTACATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTCCA
* * * * * ***
2016 AAAATTCCATTTTTA-CCCTCGAACTTCTAAAAATTACATTTTT-ACC-CCAAACTTTTG
1 AAAATTACATTTTTACCCCT-AAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTCCA
* * * * * * *
2073 AAAATTCCATTTTTACCTCAAAACTTCAAAAAATTCCATTTTTGACCCCAAAATTTCCAAAAAA
1 AAAATTACATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTCC-----A
* * * * * * *
2137 AAAAATACATTTTGACCTCGAAACTTCCAAAAATTCTATTTTTGATCC-CGAAATTTGCA
1 AAAATTACATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTGA-CCTCGAAACTTCCA
2196 AAAATTACCATTT
1 AAAATTA-CATTT
2209 CGCCCCAGAG
Statistics
Matches: 254, Mismatches: 42, Indels: 29
0.78 0.13 0.09
Matches are distributed among these distances:
57 46 0.18
58 53 0.21
59 51 0.20
60 54 0.21
61 1 0.00
64 47 0.19
65 2 0.01
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (59 bp):
AAAATTACATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTCCA
Found at i:2016 original size:58 final size:57
Alignment explanation
Indices: 1839--2208 Score: 281
Period size: 58 Copynumber: 6.2 Consensus size: 57
1829 AAATTTCCTG
* * * * * ***
1839 AAAATTATATTTTTACCCCTAAACTTTCTAAAATTCCATTTTTGACCTTGATTTTTCCA
1 AAAATTACATTTTTACCCCCAAACTTCCAAAAATTCCA-TTTTGACC-CGAAACTTCCA
* * *
1898 AAAATTACATTTATTACCCCTAAACTTCCCAAAATTCTATTATTGACACCGAAACTTCCA
1 AAAATTACATTT-TTACCCCCAAACTTCCAAAAATTCCATT-TTGAC-CCGAAACTTCCA
*
1958 AAAATTACATTTTTACCCCCAAACTTCCAAAAATTCCATTTTAACCTCGAAACTTCCA
1 AAAATTACATTTTTACCCCCAAACTTCCAAAAATTCCATTTTGACC-CGAAACTTCCA
* * * * * * * ***
2016 AAAATTCCATTTTTACCCTCGAACTTCTAAAAATTACATTTTTACCCCAAACTTTTG
1 AAAATTACATTTTTACCCCCAAACTTCCAAAAATTCCATTTTGACCCGAAACTTCCA
* * * * * *
2073 AAAATTCCATTTTTACCTCAAAACTTCAAAAAATTCCATTTTTGACCCCAAAATTTCCAAAAAA
1 AAAATTACATTTTTACCCCCAAACTTCCAAAAATTCCA-TTTTGA-CCCGAAACTTCC-----A
* * * * * * *
2137 AAAAATACATTTTGACCTCGAAACTTCCAAAAATTCTATTTTTGATCCCGAAATTTGCA
1 AAAATTACATTTTTACCCCCAAACTTCCAAAAATTCCA-TTTTGA-CCCGAAACTTCCA
2196 AAAATTACCATTT
1 AAAATTA-CATTT
2209 CGCCCCAGAG
Statistics
Matches: 255, Mismatches: 44, Indels: 23
0.79 0.14 0.07
Matches are distributed among these distances:
57 40 0.16
58 60 0.24
59 53 0.21
60 52 0.20
61 1 0.00
64 49 0.19
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (57 bp):
AAAATTACATTTTTACCCCCAAACTTCCAAAAATTCCATTTTGACCCGAAACTTCCA
Found at i:2105 original size:86 final size:88
Alignment explanation
Indices: 1893--2120 Score: 273
Period size: 86 Copynumber: 2.6 Consensus size: 88
1883 ACCTTGATTT
* * * * ** * * *
1893 TTCCAAAAATTACATTTATTACCCCTAAACTTCCCAAAATTCTATTATTGACAC-CGAAACTTCC
1 TTCCAAAAATTCCATTT-TAACCTCAAAACTTCAAAAAATTCCATTTTTGACCCTCG-AACTTCC
1957 AAAAATTACATTTTTACCCCCAAAC
64 AAAAATTACATTTTTACCCCCAAAC
* * *
1982 TTCCAAAAATTCCATTTTAACCTCGAAACTTCCAAAAATTCCATTTTT-ACCCTCGAACTTCTAA
1 TTCCAAAAATTCCATTTTAACCTCAAAACTTCAAAAAATTCCATTTTTGACCCTCGAACTTCCAA
2046 AAATTACATTTTTA-CCCCAAAC
66 AAATTACATTTTTACCCCCAAAC
*** *
2068 TTTTGAAAATTCCATTTTTACCTCAAAACTTCAAAAAATTCCATTTTTGACCC
1 TTCCAAAAATTCCATTTTAACCTCAAAACTTCAAAAAATTCCATTTTTGACCC
2121 CAAAATTTCC
Statistics
Matches: 122, Mismatches: 15, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
86 50 0.41
87 29 0.24
88 27 0.22
89 16 0.13
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (88 bp):
TTCCAAAAATTCCATTTTAACCTCAAAACTTCAAAAAATTCCATTTTTGACCCTCGAACTTCCAA
AAATTACATTTTTACCCCCAAAC
Found at i:2178 original size:64 final size:64
Alignment explanation
Indices: 2080--2199 Score: 177
Period size: 64 Copynumber: 1.9 Consensus size: 64
2070 TTGAAAATTC
*
2080 CATTTTTACCTCAAAACTTCAAAAAATTCCATTTTTGACCCCAAAATTTCCAAAAAAAAAAATA
1 CATTTTGACCTCAAAACTTCAAAAAATTCCATTTTTGACCCCAAAATTTCCAAAAAAAAAAATA
* * * * * *
2144 CATTTTGACCTCGAAACTTCCAAAAATTCTATTTTTGATCCCGAAATTTGCAAAAA
1 CATTTTGACCTCAAAACTTCAAAAAATTCCATTTTTGACCCCAAAATTTCCAAAAA
2200 TTACCATTTC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
64 49 1.00
ACGTcount: A:0.42, C:0.22, G:0.05, T:0.32
Consensus pattern (64 bp):
CATTTTGACCTCAAAACTTCAAAAAATTCCATTTTTGACCCCAAAATTTCCAAAAAAAAAAATA
Found at i:2180 original size:30 final size:29
Alignment explanation
Indices: 1847--2208 Score: 255
Period size: 29 Copynumber: 12.1 Consensus size: 29
1837 TGAAAATTAT
* * * *
1847 ATTTTTACCCCTAAACTTTCTAAAATTCC
1 ATTTTTACCTCGAAACTTCCAAAAATTCC
* *** *
1876 ATTTTTGACCTTGATTTTTCCAAAAATTAC
1 ATTTTT-ACCTCGAAACTTCCAAAAATTCC
* * * *
1906 ATTTATTACCCCTAAACTTCCCAAAATTCT
1 ATTT-TTACCTCGAAACTTCCAAAAATTCC
* *
1936 ATTATTGACAC-CGAAACTTCCAAAAATTAC
1 ATT-TTTAC-CTCGAAACTTCCAAAAATTCC
* *
1966 ATTTTTACCCCCAAACTTCCAAAAATTCC
1 ATTTTTACCTCGAAACTTCCAAAAATTCC
*
1995 ATTTTAACCTCGAAACTTCCAAAAATTCC
1 ATTTTTACCTCGAAACTTCCAAAAATTCC
* *
2024 ATTTTTACCCTCG-AACTTCTAAAAATTAC
1 ATTTTTA-CCTCGAAACTTCCAAAAATTCC
* ***
2053 ATTTTTACC-CCAAACTTTTGAAAATTCC
1 ATTTTTACCTCGAAACTTCCAAAAATTCC
* *
2081 ATTTTTACCTCAAAACTTCAAAAAATTCC
1 ATTTTTACCTCGAAACTTCCAAAAATTCC
* * * * *
2110 ATTTTTGACCCCAAAATTTCCAAAAAAAAAAATAC
1 ATTTTT-ACCTCGAAACTTCC-----AAAAATTCC
* *
2145 ATTTTGACCTCGAAACTTCCAAAAATTCT
1 ATTTTTACCTCGAAACTTCCAAAAATTCC
* *
2174 ATTTTTGATCC-CGAAATTTGCAAAAATTACC
1 ATTTTT-A-CCTCGAAACTTCCAAAAATT-CC
2205 ATTT
1 ATTT
2209 CGCCCCAGAG
Statistics
Matches: 260, Mismatches: 56, Indels: 32
0.75 0.16 0.09
Matches are distributed among these distances:
27 1 0.00
28 25 0.10
29 112 0.43
30 88 0.34
31 11 0.04
34 11 0.04
35 12 0.05
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (29 bp):
ATTTTTACCTCGAAACTTCCAAAAATTCC
Found at i:4163 original size:6 final size:6
Alignment explanation
Indices: 4152--4239 Score: 62
Period size: 6 Copynumber: 15.2 Consensus size: 6
4142 TGTGCCCAAC
* * * *
4152 AAATTT AAATTT -ATTTT AAAATT AAGTTT -ATTTT AAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
*
4198 --ATTT GAAATTT AAGTTT --ATTAT AAATTT AAATTT AAAATTT A
1 AAATTT -AAATTT AAATTT AAATT-T AAATTT AAATTT -AAATTT A
4240 TTTATAATGT
Statistics
Matches: 64, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
4 6 0.09
5 9 0.14
6 36 0.56
7 13 0.20
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:4195 original size:34 final size:34
Alignment explanation
Indices: 4152--4232 Score: 135
Period size: 34 Copynumber: 2.4 Consensus size: 34
4142 TGTGCCCAAC
* *
4152 AAATTTAAATTTATTTTAAAATTAAGTTTATTTT
1 AAATTTAAATTTATTTGAAAATTAAGTTTATTAT
*
4186 AAATTTAAATTTATTTGAAATTTAAGTTTATTAT
1 AAATTTAAATTTATTTGAAAATTAAGTTTATTAT
4220 AAATTTAAATTTA
1 AAATTTAAATTTA
4233 AAATTTATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (34 bp):
AAATTTAAATTTATTTGAAAATTAAGTTTATTAT
Found at i:4239 original size:24 final size:25
Alignment explanation
Indices: 4198--4246 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
4188 ATTTAAATTT
*
4198 ATTTGAAATTTAAGTTTA-TTATAA
1 ATTTGAAATTTAAATTTATTTATAA
4222 ATTT-AAATTTAAAATTTATTTATAA
1 ATTTGAAATTT-AAATTTATTTATAA
4247 TGTCCAAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 6 0.27
24 10 0.45
25 6 0.27
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (25 bp):
ATTTGAAATTTAAATTTATTTATAA
Found at i:4243 original size:17 final size:17
Alignment explanation
Indices: 4152--4232 Score: 117
Period size: 17 Copynumber: 4.8 Consensus size: 17
4142 TGTGCCCAAC
4152 AAATTTAAATTTATTTT
1 AAATTTAAATTTATTTT
* *
4169 AAAATTAAGTTTATTTT
1 AAATTTAAATTTATTTT
*
4186 AAATTTAAATTTATTTG
1 AAATTTAAATTTATTTT
* *
4203 AAATTTAAGTTTATTAT
1 AAATTTAAATTTATTTT
4220 AAATTTAAATTTA
1 AAATTTAAATTTA
4233 AAATTTATTT
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 55 1.00
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (17 bp):
AAATTTAAATTTATTTT
Done.