Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007463.1 Kokia drynarioides strain JFW-HI SEQ_122084, 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: 63915
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 32 characters in sequence are not A, C, G, or T
Found at i:3121 original size:17 final size:18
Alignment explanation
Indices: 3086--3123 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
3076 TTTATCATGC
**
3086 TAATATTTTTATAGTAAT
1 TAATATTTTTATAAAAAT
3104 TAATATTTTT-TAAAAAT
1 TAATATTTTTATAAAAAT
3121 TAA
1 TAA
3124 GTTGTATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
TAATATTTTTATAAAAAT
Found at i:20701 original size:43 final size:44
Alignment explanation
Indices: 20615--20703 Score: 153
Period size: 44 Copynumber: 2.0 Consensus size: 44
20605 CAAAGTCAGA
*
20615 TTTTATAGCTCTTTAGTGCATTTCCCTGACCCACTAACTATTTT
1 TTTTATAACTCTTTAGTGCATTTCCCTGACCCACTAACTATTTT
*
20659 TTTTATAACTCTTTAGTGCATTT-GCTGACCCACTAACTATTTT
1 TTTTATAACTCTTTAGTGCATTTCCCTGACCCACTAACTATTTT
20702 TT
1 TT
20704 CTTTTATGAA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
43 21 0.49
44 22 0.51
ACGTcount: A:0.21, C:0.22, G:0.09, T:0.47
Consensus pattern (44 bp):
TTTTATAACTCTTTAGTGCATTTCCCTGACCCACTAACTATTTT
Found at i:21033 original size:15 final size:17
Alignment explanation
Indices: 21015--21046 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
21005 TAAATAATAC
21015 AAATTT-TTTT-TTTTG
1 AAATTTCTTTTATTTTG
21030 AAATTTCTTTTATTTTG
1 AAATTTCTTTTATTTTG
21047 TAAAAGATGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.22, C:0.03, G:0.06, T:0.69
Consensus pattern (17 bp):
AAATTTCTTTTATTTTG
Found at i:22310 original size:22 final size:23
Alignment explanation
Indices: 22282--22325 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
22272 AGCCTCTTGC
*
22282 TATTAAT-TTTTATAATATAAAA
1 TATTAATATTTAATAATATAAAA
22304 TATTAATATTTAATAATATAAA
1 TATTAATATTTAATAATATAAA
22326 TATGAGTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TATTAATATTTAATAATATAAAA
Found at i:22335 original size:22 final size:23
Alignment explanation
Indices: 22293--22336 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
22283 ATTAATTTTT
*
22293 ATAATATAAAATATTAATATTTA
1 ATAATATAAAATATGAATATTTA
*
22316 ATAATAT-AAATATGAGTATTT
1 ATAATATAAAATATGAATATTT
22337 GTTTAAATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (23 bp):
ATAATATAAAATATGAATATTTA
Found at i:44300 original size:12 final size:12
Alignment explanation
Indices: 44283--44319 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
44273 CACCCCTTTA
44283 TTATTATTATTC
1 TTATTATTATTC
44295 TTATTATTATTC
1 TTATTATTATTC
*
44307 TTATTCTTATTC
1 TTATTATTATTC
44319 T
1 T
44320 CTGACTTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.68
Consensus pattern (12 bp):
TTATTATTATTC
Found at i:44318 original size:6 final size:6
Alignment explanation
Indices: 44283--44319 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
44273 CACCCCTTTA
* *
44283 TTATTA TTATTC TTATTA TTATTC TTATTC TTATTC T
1 TTATTC TTATTC TTATTC TTATTC TTATTC TTATTC T
44320 CTGACTTTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.68
Consensus pattern (6 bp):
TTATTC
Found at i:55913 original size:173 final size:172
Alignment explanation
Indices: 55692--56325 Score: 908
Period size: 173 Copynumber: 3.7 Consensus size: 172
55682 GTCAAAGAAT
** * ** * * *
55692 TAAGGAAGAAGGAAAATGAAATTCAAAATATAATCTGAGCTCGGGTTCGAATCGGGGACCTCTGG
1 TAAGGAAGTCGGAGAATGAAATTCAAAATATTGTCTGAGCCCGGGTTCGAACCGGGGACCTCTAG
*
55757 TGAGTGAGACTAGCGTGATAACCAACTACACCACCCAGACATTACATTTGAGATGTTTAATAATG
66 TGTGTGAGACTAGCGTGATAACCAACTACACCACCCAGACATTACATTTGAGATGTTTAATAATG
*
55822 ATAATTGTTTACAATTACAGATATAACCCTGAGAGAGCCAAG
131 ATAATTGTTTAAAATTACAGATATAACCCTGAGAGAGCCAAG
55864 TAAGGAAGTCGGAGAATGAAATTCAAAAATATTGTCTGAGCCCGGGTTCGAACCGGGGACCTCTA
1 TAAGGAAGTCGGAGAATGAAATTC-AAAATATTGTCTGAGCCCGGGTTCGAACCGGGGACCTCTA
* * * *
55929 GTGTGTGAGACTAGCGTGATAACCAACTACACCACCCAGACATCACATTAGAGTTGTTTAATAGT
65 GTGTGTGAGACTAGCGTGATAACCAACTACACCACCCAGACATTACATTTGAGATGTTTAATAAT
*
55994 GATAATTGTTTAAAATTACTGATATAACCCTGAGAGAGCCAAG
130 GATAATTGTTTAAAATTACAGATATAACCCTGAGAGAGCCAAG
* * * ** *
56037 TAAGAAAATCGGAGAATGAAATTCAAAATACTGTAAGAGCCCGGTTTCGAACCGGGG------A-
1 TAAGGAAGTCGGAGAATGAAATTCAAAATATTGTCTGAGCCCGGGTTCGAACCGGGGACCTCTAG
* * *
56095 -GTGTGAGACTAGTGAGATAACCAACTACACCACCCAGACATTACATTTGAGATGTTCAATAATG
66 TGTGTGAGACTAGCGTGATAACCAACTACACCACCCAGACATTACATTTGAGATGTTTAATAATG
*
56159 ATAATTGTTTATAATTACAGATATAACCCTGAGAGAGCCAAG
131 ATAATTGTTTAAAATTACAGATATAACCCTGAGAGAGCCAAG
* *
56201 TAAGGAAGTCGGA-AATAAAATTCAAAAATATTGTCTGAGCCCGGGTTCGAACTGGGGACCTCTA
1 TAAGGAAGTCGGAGAATGAAATTC-AAAATATTGTCTGAGCCCGGGTTCGAACCGGGGACCTCTA
* * * *
56265 GTGTGTGAGACTAGCGTGATAACCAACTACACCACCCAGACAATATACTTGAGTTGTTTAA
65 GTGTGTGAGACTAGCGTGATAACCAACTACACCACCCAGACATTACATTTGAGATGTTTAA
56326 AAATTACAAT
Statistics
Matches: 407, Mismatches: 45, Indels: 20
0.86 0.10 0.04
Matches are distributed among these distances:
163 9 0.02
164 136 0.33
166 1 0.00
170 1 0.00
172 102 0.25
173 158 0.39
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (172 bp):
TAAGGAAGTCGGAGAATGAAATTCAAAATATTGTCTGAGCCCGGGTTCGAACCGGGGACCTCTAG
TGTGTGAGACTAGCGTGATAACCAACTACACCACCCAGACATTACATTTGAGATGTTTAATAATG
ATAATTGTTTAAAATTACAGATATAACCCTGAGAGAGCCAAG
Found at i:58708 original size:21 final size:22
Alignment explanation
Indices: 58670--58729 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 22
58660 CTTGAATTTT
* *
58670 AAAATTTAAAAAATAAAAATAG
1 AAAAATTAAAATATAAAAATAG
* * *
58692 AAACATT-TAATATAAAAATAT
1 AAAAATTAAAATATAAAAATAG
58713 AAAAATTAAAATATAAA
1 AAAAATTAAAATATAAA
58730 TTTATGAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
21 17 0.57
22 13 0.43
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.27
Consensus pattern (22 bp):
AAAAATTAAAATATAAAAATAG
Found at i:61229 original size:17 final size:17
Alignment explanation
Indices: 61207--61239 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
61197 CAACACCATC
*
61207 AATAAAAATAATATTTT
1 AATAAAAAAAATATTTT
61224 AATAAAAAAAATATTT
1 AATAAAAAAAATATTT
61240 AAAATTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AATAAAAAAAATATTTT
Done.