Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011303.1 Kokia drynarioides strain JFW-HI SEQ_126283, 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: 9979
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34
Found at i:985 original size:24 final size:24
Alignment explanation
Indices: 934--985 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
924 TTATTAATCC
*
934 TTTTTTTTGTTTAAAACGTTTGAT
1 TTTTTTTTGTTTAAAACCTTTGAT
* *
958 TTTTTTTTTTTTAAAACCTCTTTAT
1 TTTTTTTTGTTTAAAACCT-TTGAT
983 TTT
1 TTT
986 ATATTCTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.19, C:0.08, G:0.06, T:0.67
Consensus pattern (24 bp):
TTTTTTTTGTTTAAAACCTTTGAT
Found at i:1183 original size:9 final size:9
Alignment explanation
Indices: 1171--1240 Score: 52
Period size: 9 Copynumber: 7.4 Consensus size: 9
1161 TATTGCGGTC
1171 ATTAATATT
1 ATTAATATT
1180 ATTAATGA-T
1 ATTAAT-ATT
* *
1189 ATTAGTAAT
1 ATTAATATT
*
1198 ATTATTATT
1 ATTAATATT
*
1207 ATTATTATT
1 ATTAATATT
*
1216 ATTACCATAATA
1 ATTA--AT-ATT
1228 ATTAATATT
1 ATTAATATT
1237 ATTA
1 ATTA
1241 TTAATGACAT
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
8 1 0.02
9 39 0.78
10 3 0.06
11 1 0.02
12 6 0.12
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (9 bp):
ATTAATATT
Found at i:1190 original size:12 final size:11
Alignment explanation
Indices: 1175--1245 Score: 54
Period size: 12 Copynumber: 6.0 Consensus size: 11
1165 GCGGTCATTA
1175 ATATTATTAAT
1 ATATTATTAAT
*
1186 GATATTAGTAAT
1 -ATATTATTAAT
*
1198 ATTATTATTATT
1 A-TATTATTAAT
1210 ATTATTATTACCAT
1 A-TATTATTA--AT
*
1224 A-ATAATTAAT
1 ATATTATTAAT
1234 ATTATTATTAAT
1 A-TATTATTAAT
1246 GACATTTATT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
10 3 0.06
11 1 0.02
12 42 0.88
14 2 0.04
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (11 bp):
ATATTATTAAT
Found at i:2012 original size:18 final size:17
Alignment explanation
Indices: 1989--2043 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
1979 TGTCTTGGAC
* *
1989 TTTTAATTTAATATTAAG
1 TTTTAATTCAAT-TTAAA
*
2007 TTTTAAGTCAATTTAAA
1 TTTTAATTCAATTTAAA
*
2024 TTTTAATTAAATTTAAA
1 TTTTAATTCAATTTAAA
2041 TTT
1 TTT
2044 AAACCAAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
17 22 0.69
18 10 0.31
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (17 bp):
TTTTAATTCAATTTAAA
Found at i:2027 original size:17 final size:17
Alignment explanation
Indices: 2002--2075 Score: 78
Period size: 17 Copynumber: 4.4 Consensus size: 17
1992 TAATTTAATA
* *
2002 TTAAGTTTTAAGTCAAT
1 TTAAATTTTAAGTAAAT
*
2019 TTAAATTTTAATTAAAT
1 TTAAATTTTAAGTAAAT
* **
2036 TTAAATTTAAACCAAAT
1 TTAAATTTTAAGTAAAT
2053 TTAAA-TTTAAGATAAAT
1 TTAAATTTTAAG-TAAAT
2070 TTAAAT
1 TTAAAT
2076 CAATTTAAAC
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
16 4 0.09
17 42 0.91
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (17 bp):
TTAAATTTTAAGTAAAT
Found at i:2039 original size:6 final size:6
Alignment explanation
Indices: 2016--2075 Score: 56
Period size: 6 Copynumber: 10.5 Consensus size: 6
2006 GTTTTAAGTC
* **
2016 AATTTA AATTTT AA-TTA AATTTA AATTTA AA-CCA AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
2062 AGA--TA AATTTA AAT
1 A-ATTTA AATTTA AAT
2076 CAATTTAAAC
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
4 1 0.02
5 10 0.23
6 31 0.72
7 1 0.02
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (6 bp):
AATTTA
Found at i:6125 original size:30 final size:30
Alignment explanation
Indices: 6085--6283 Score: 258
Period size: 30 Copynumber: 6.6 Consensus size: 30
6075 CACTTATGCC
* *
6085 TTTTGAAAAAGTTTAGGGGTCAAAATATGA
1 TTTTGGAAAAGTTTAGGGGTCAAAATGTGA
*
6115 TTTTGGAAAAGTTTGAGGGGTCAAAACGTGA
1 TTTTGGAAAAGTTT-AGGGGTCAAAATGTGA
*
6146 TTTTGGAAAAGTTTAAGGGTCAAAATGTGA
1 TTTTGGAAAAGTTTAGGGGTCAAAATGTGA
*
6176 TTTTGGAAAAGTTTA-GGGTCAAAATGTAA
1 TTTTGGAAAAGTTTAGGGGTCAAAATGTGA
* *
6205 TTTTGGATAAGTTTAGGGGTCAAAATGTAA
1 TTTTGGAAAAGTTTAGGGGTCAAAATGTGA
*
6235 TTTTGGAAAAAGTTT-GAGGGTCAAAATGTAA
1 TTTTGG-AAAAGTTTAG-GGGTCAAAATGTGA
** *
6266 TTTTTTAAAAATTTAGGG
1 TTTTGGAAAAGTTTAGGG
6284 ACCTCTTGAG
Statistics
Matches: 153, Mismatches: 11, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
29 27 0.18
30 72 0.47
31 54 0.35
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.35
Consensus pattern (30 bp):
TTTTGGAAAAGTTTAGGGGTCAAAATGTGA
Found at i:6180 original size:61 final size:60
Alignment explanation
Indices: 6085--6283 Score: 283
Period size: 61 Copynumber: 3.3 Consensus size: 60
6075 CACTTATGCC
* * * *
6085 TTTTGAAAAAGTTTAGGGGTCAAAATATGATTTTGGAAAAGTTTGAGGGGTCAAAACGTGA
1 TTTTGGAAAAGTTTAGGGGTCAAAATGTGATTTTGGAAAAGTTTGA-GGGTCAAAATGTAA
*
6146 TTTTGGAAAAGTTTAAGGGTCAAAATGTGATTTTGGAAAAGTTT-AGGGTCAAAATGTAA
1 TTTTGGAAAAGTTTAGGGGTCAAAATGTGATTTTGGAAAAGTTTGAGGGTCAAAATGTAA
* *
6205 TTTTGGATAAGTTTAGGGGTCAAAATGTAATTTTGGAAAAAGTTTGAGGGTCAAAATGTAA
1 TTTTGGAAAAGTTTAGGGGTCAAAATGTGATTTTGG-AAAAGTTTGAGGGTCAAAATGTAA
** *
6266 TTTTTTAAAAATTTAGGG
1 TTTTGGAAAAGTTTAGGG
6284 ACCTCTTGAG
Statistics
Matches: 124, Mismatches: 12, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
59 45 0.36
60 9 0.07
61 70 0.56
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.35
Consensus pattern (60 bp):
TTTTGGAAAAGTTTAGGGGTCAAAATGTGATTTTGGAAAAGTTTGAGGGTCAAAATGTAA
Found at i:9279 original size:78 final size:78
Alignment explanation
Indices: 9183--9420 Score: 370
Period size: 78 Copynumber: 3.1 Consensus size: 78
9173 TGGAGGGCTC
* * *
9183 GGTTTAGGCACTGCTGGTGGTTGCGGTTTCGATTGAGAAGGAGGATTTGGTTTAGGCATTGGTGC
1 GGTTTAGACATTGGTGGTGGTTGCGGTTTCGATTGAGAAGGAGGATTTGGTTTAGGCATTGGTGC
9248 TGGATTCGGTTTT
66 TGGATTCGGTTTT
*
9261 GGTTTAGACATTGGTGGTGGTGGCGGTTTCGATTGAGAAGGAGGATTTGGTTTAGGCATTGGTGC
1 GGTTTAGACATTGGTGGTGGTTGCGGTTTCGATTGAGAAGGAGGATTTGGTTTAGGCATTGGTGC
9326 TGGATTCGGTTTT
66 TGGATTCGGTTTT
* * * * *
9339 GGTTTAGACATTGGTGGTGGTTGCAGTTTCGATTCAGAAGGTGGATTTGGTTTAGGCACTGGTGT
1 GGTTTAGACATTGGTGGTGGTTGCGGTTTCGATTGAGAAGGAGGATTTGGTTTAGGCATTGGTGC
*
9404 TGG-TTGCGGTTTA
66 TGGATT-CGGTTTT
9417 GGTT
1 GGTT
9421 CTACGGGCGG
Statistics
Matches: 148, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
77 2 0.01
78 146 0.99
ACGTcount: A:0.15, C:0.09, G:0.39, T:0.38
Consensus pattern (78 bp):
GGTTTAGACATTGGTGGTGGTTGCGGTTTCGATTGAGAAGGAGGATTTGGTTTAGGCATTGGTGC
TGGATTCGGTTTT
Found at i:9288 original size:30 final size:30
Alignment explanation
Indices: 9228--9289 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
9218 AGAAGGAGGA
* *
9228 TTTGGTTTAGGCATTGGTGCTGGATTCGGT
1 TTTGGTTTAGACATTGGTGCTGGATGCGGT
*
9258 TTTGGTTTAGACATTGGTGGTGG-TGGCGGT
1 TTTGGTTTAGACATTGGTGCTGGAT-GCGGT
9288 TT
1 TT
9290 CGATTGAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 1 0.04
30 27 0.96
ACGTcount: A:0.10, C:0.08, G:0.39, T:0.44
Consensus pattern (30 bp):
TTTGGTTTAGACATTGGTGCTGGATGCGGT
Found at i:9472 original size:132 final size:125
Alignment explanation
Indices: 9336--9685 Score: 393
Period size: 132 Copynumber: 2.7 Consensus size: 125
9326 TGGATTCGGT
*
9336 TTTGGTTTAGACATTGGTGGTGGTTGCAGTTTCGATTCAGAAGGTGGATTTGGTTTAGGCACTGG
1 TTTGGTTTAGACATTGGTGGTGGTTGCGGTTTCGATTCAGAAGGTGGATTTGGTTTAGGCACTGG
* *
9401 TGTTGGTTGCGGTTTAGGTTCT-ACGGGCGGGTTAGGTTCAGCAACTTGTGGTGGTGATGGTTGT
66 TGCTGGTTGCGGTTT-GGTTCTGA-GGGAGGGTTAGGTTCAGCAAC---TGGT-G-G-TGGTTGT
9465 GGA
123 GGA
* * *
9468 TTTGGTCTAGGCATTGGTGGTGGTTGCGGTTTCGATTCAGAAGGTGGACTTGGTTTAGGCACTGG
1 TTTGGTTTAGACATTGGTGGTGGTTGCGGTTTCGATTCAGAAGGTGGATTTGGTTTAGGCACTGG
* * *
9533 TGCTGGTTGTGGTTTTGGTTCTGAGGGAGGGTTAGGTTTAGCTACTGGTGGTGGTTGTGGA
66 TGCTGGTTGCGG-TTTGGTTCTGAGGGAGGGTTAGGTTCAGCAACTGGTGGTGGTTGTGGA
* * * * * * *
9594 TTTGGTTTATGA-ATTGGTGGAGGTTGTGGTTTTGGTTCAG-AGG-GCAAGTTAGGTTTAGGCAT
1 TTTGGTTTA-GACATTGGTGGTGGTTGCGGTTTCGATTCAGAAGGTG-GA-TTTGGTTTAGGCAC
* *
9656 TGGTGGTGGTTGCGGCTTTGGTTCAGAGGG
63 TGGTGCTGGTTGCGG-TTTGGTTCTGAGGG
9686 CGAGTTTAGT
Statistics
Matches: 190, Mismatches: 23, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
124 1 0.01
125 4 0.02
126 79 0.42
127 2 0.01
128 1 0.01
129 4 0.02
132 95 0.50
133 4 0.02
ACGTcount: A:0.13, C:0.09, G:0.40, T:0.37
Consensus pattern (125 bp):
TTTGGTTTAGACATTGGTGGTGGTTGCGGTTTCGATTCAGAAGGTGGATTTGGTTTAGGCACTGG
TGCTGGTTGCGGTTTGGTTCTGAGGGAGGGTTAGGTTCAGCAACTGGTGGTGGTTGTGGA
Found at i:9593 original size:78 final size:78
Alignment explanation
Indices: 9511--9667 Score: 201
Period size: 78 Copynumber: 2.0 Consensus size: 78
9501 GATTCAGAAG
* * * *
9511 GTGGACTTGGTTTAGGCACTGGTGCTGGTTGTGGTTTTGGTTCTGAGGG-AGGGTTAGGTTTA-G
1 GTGGACTTGGTTTAGGAACTGGTGCAGGTTGTGGTTTTGGTTCAGAGGGCA-AGTTAGGTTTAGG
9574 CTACTGGTGGTGGTT
65 C-ACTGGTGGTGGTT
* * * *
9589 GTGGATTTGGTTTATGAATTGGTGGAGGTTGTGGTTTTGGTTCAGAGGGCAAGTTAGGTTTAGGC
1 GTGGACTTGGTTTAGGAACTGGTGCAGGTTGTGGTTTTGGTTCAGAGGGCAAGTTAGGTTTAGGC
*
9654 ATTGGTGGTGGTT
66 ACTGGTGGTGGTT
9667 G
1 G
9668 CGGCTTTGGT
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
78 65 0.96
79 3 0.04
ACGTcount: A:0.13, C:0.06, G:0.42, T:0.39
Consensus pattern (78 bp):
GTGGACTTGGTTTAGGAACTGGTGCAGGTTGTGGTTTTGGTTCAGAGGGCAAGTTAGGTTTAGGC
ACTGGTGGTGGTT
Found at i:9658 original size:48 final size:48
Alignment explanation
Indices: 9597--9691 Score: 136
Period size: 48 Copynumber: 2.0 Consensus size: 48
9587 TTGTGGATTT
* * *
9597 GGTTTATGAATTGGTGGAGGTTGTGGTTTTGGTTCAGAGGGCAAGTTA
1 GGTTTAGGAATTGGTGGAGGTTGCGGCTTTGGTTCAGAGGGCAAGTTA
* * *
9645 GGTTTAGGCATTGGTGGTGGTTGCGGCTTTGGTTCAGAGGGCGAGTT
1 GGTTTAGGAATTGGTGGAGGTTGCGGCTTTGGTTCAGAGGGCAAGTT
9692 TAGTGGTGGT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.15, C:0.07, G:0.42, T:0.36
Consensus pattern (48 bp):
GGTTTAGGAATTGGTGGAGGTTGCGGCTTTGGTTCAGAGGGCAAGTTA
Found at i:9676 original size:78 final size:79
Alignment explanation
Indices: 9537--9764 Score: 241
Period size: 84 Copynumber: 2.8 Consensus size: 79
9527 CACTGGTGCT
* *
9537 GGTTGTGGTTTTGGTTCTGAGGG-AGGGTTAGGTTTA-GCTACTGGTGGTGGTTGTGGATTTGGT
1 GGTTGTGGTTTTGGTTCAGAGGGCA-GGTTAGGTTTAGGC-ACTGGTGGTGGTTGCGGATTTGGT
* *
9600 TTATGA-A-TTGGTGGA
64 TCA-GAGAGTTAGTGGA
* * *
9615 GGTTGTGGTTTTGGTTCAGAGGGCAAGTTAGGTTTAGGCATTGGTGGTGGTTGCGGCTTTGGTTC
1 GGTTGTGGTTTTGGTTCAGAGGGCAGGTTAGGTTTAGGCACTGGTGGTGGTTGCGGATTTGGTTC
*
9680 AGAGGGCGAGTTTAGTGGT
66 AGA----GAG-TTAGTGGA
* * *
9699 GGTTGTGGTCTTGGTTCAGAGGGC-GGATTAGGTTTAGGCACTGGTAGTGGTTGCGGTTTTGGTT
1 GGTTGTGGTTTTGGTTCAGAGGGCAGG-TTAGGTTTAGGCACTGGTGGTGGTTGCGGATTTGGTT
9763 CA
65 CA
9765 AGGGCGGATT
Statistics
Matches: 127, Mismatches: 13, Indels: 14
0.82 0.08 0.09
Matches are distributed among these distances:
77 2 0.02
78 55 0.43
79 3 0.02
82 1 0.01
83 1 0.01
84 65 0.51
ACGTcount: A:0.13, C:0.07, G:0.42, T:0.38
Consensus pattern (79 bp):
GGTTGTGGTTTTGGTTCAGAGGGCAGGTTAGGTTTAGGCACTGGTGGTGGTTGCGGATTTGGTTC
AGAGAGTTAGTGGA
Found at i:9730 original size:84 final size:83
Alignment explanation
Indices: 9610--9770 Score: 243
Period size: 84 Copynumber: 1.9 Consensus size: 83
9600 TTATGAATTG
* * *
9610 GTGGAGGTTGTGGTTTTGGTTCAGAGGGCAAGTTAGGTTTAGGCATTGGTGGTGGTTGCGGCTTT
1 GTGGAGGTTGTGGTCTTGGTTCAGAGGGCAAGTTAGGTTTAGGCACTGGTAGTGGTTGCGGCTTT
9675 GGTTCAGAGGGCGAGTTTA
66 GGTTCA-AGGGCGAGTTTA
* * *
9694 GTGGTGGTTGTGGTCTTGGTTCAGAGGGC-GGATTAGGTTTAGGCACTGGTAGTGGTTGCGGTTT
1 GTGGAGGTTGTGGTCTTGGTTCAGAGGGCAAG-TTAGGTTTAGGCACTGGTAGTGGTTGCGGCTT
9758 TGGTTCAAGGGCG
65 TGGTTCAAGGGCG
9771 GATTTGGTTT
Statistics
Matches: 70, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
83 7 0.10
84 63 0.90
ACGTcount: A:0.13, C:0.09, G:0.43, T:0.34
Consensus pattern (83 bp):
GTGGAGGTTGTGGTCTTGGTTCAGAGGGCAAGTTAGGTTTAGGCACTGGTAGTGGTTGCGGCTTT
GGTTCAAGGGCGAGTTTA
Done.