Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014389.1 Kokia drynarioides strain JFW-HI SEQ_129427, 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: 4766
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.32
Found at i:3034 original size:19 final size:19
Alignment explanation
Indices: 3010--3047 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3000 CGTCCTTCTT
3010 GCTGTCTTTGAAATCCAGA
1 GCTGTCTTTGAAATCCAGA
3029 GCTGTCTTTGAAATCCAGA
1 GCTGTCTTTGAAATCCAGA
3048 AAAACAGGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (19 bp):
GCTGTCTTTGAAATCCAGA
Found at i:3062 original size:23 final size:23
Alignment explanation
Indices: 3032--3097 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 23
3022 ATCCAGAGCT
3032 GTCTTTGAAATCCAGAAAAACAG
1 GTCTTTGAAATCCAGAAAAACAG
*
3055 GTCTTTGAAA-ACACG-----CAG
1 GTCTTTGAAATCCA-GAAAAACAG
3073 GTCTTTGAAATCCAGAAAAACAG
1 GTCTTTGAAATCCAGAAAAACAG
3096 GT
1 GT
3098 TCGGGAGTCG
Statistics
Matches: 34, Mismatches: 2, Indels: 14
0.68 0.04 0.28
Matches are distributed among these distances:
18 14 0.41
19 2 0.06
22 2 0.06
23 16 0.47
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23
Consensus pattern (23 bp):
GTCTTTGAAATCCAGAAAAACAG
Found at i:3578 original size:97 final size:96
Alignment explanation
Indices: 3388--3580 Score: 214
Period size: 97 Copynumber: 2.0 Consensus size: 96
3378 TTTTTGGGAA
** *
3388 AAGGATATTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGACGCAATATTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGACACAATATTTCA
* **
3453 GAATCGAAGATAAGGAAACATTGTCTCGATT
66 GAATCGAAGATAAAGAAACATTACCTCGATT
* * * * *
3484 AAGGGTATTCGATTATTTCGATTTGAGGAAAAAATTGCACCTAGTGAGTTAAGGCACAA-ATTTT
1 AAGGATATTCGATTATCTCGATTTGAAG-AAAAATTGCACCTAGTAAGTTAAGACACAATA-TTT
3548 C-GAAACTCGAA-ATAAAAGAAA-ATTACCTCGATT
64 CAG-AA-TCGAAGAT-AAAGAAACATTACCTCGATT
3581 TTAAAGTTTT
Statistics
Matches: 81, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
96 27 0.33
97 43 0.53
98 11 0.14
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGACACAATATTTCA
GAATCGAAGATAAAGAAACATTACCTCGATT
Found at i:3952 original size:30 final size:30
Alignment explanation
Indices: 3840--4273 Score: 353
Period size: 29 Copynumber: 14.9 Consensus size: 30
3830 ATTCAAGGTT
*
3840 AAAATGGGATTTTTGGAAG-TTCGAGGGT-
1 AAAATGGGATTTTTGGAAGTTTCGGGGGTA
* * * *
3868 AAAATGGAATCTTTGGAAGTTTC-GAGGTC
1 AAAATGGGATTTTTGGAAGTTTCGGGGGTA
3897 AAAATGGGATTTTTGGAAG-TTCGGGGGTA
1 AAAATGGGATTTTTGGAAGTTTCGGGGGTA
*
3926 AAAATGGAATTTTTGGAAGTTTC-GGGGTAA
1 AAAATGGGATTTTTGGAAGTTTCGGGGGT-A
* *
3956 AAAATGGGATTTTAGAAAGTTT-GGGGGTA
1 AAAATGGGATTTTTGGAAGTTTCGGGGGTA
* * *
3985 AAAATGGAATTTTTGGAAGTTT-TGAGGTCA
1 AAAATGGGATTTTTGGAAGTTTCGGGGGT-A
* ***
4015 AAAATGGGGTTTTCAAAAG-TTCGGGGGT-
1 AAAATGGGATTTTTGGAAGTTTCGGGGGTA
* *
4043 AAAATGGGATTTTTGGTAG-TT--GTGGTCA
1 AAAATGGGATTTTTGGAAGTTTCGGGGGT-A
* *
4071 AAAATGGGATTTTTGAAAG-TTCGAGGGTA
1 AAAATGGGATTTTTGGAAGTTTCGGGGGTA
* *
4100 AAAATGGGATTTTTGAAAGTTTC-GTGGTCA
1 AAAATGGGATTTTTGGAAGTTTCGGGGGT-A
* * *
4130 AAAATGGGATTTTCGAAAG-TTCGAGGGTA
1 AAAATGGGATTTTTGGAAGTTTCGGGGGTA
* * *
4159 AAAATGGAATTTTTGAAAGTTT-TGGGGTAA
1 AAAATGGGATTTTTGGAAGTTTCGGGGGT-A
* * * *
4189 AAAATAGGATTTTTGGAAATTTTGGGGTTA
1 AAAATGGGATTTTTGGAAGTTTCGGGGGTA
* * * *
4219 AAAATTGGATTTTTAGTAG-TTCGAGGGTA
1 AAAATGGGATTTTTGGAAGTTTCGGGGGTA
* ***
4248 AAATTATAATTTTTGGAAGTTTCGGG
1 AAAATGGGATTTTTGGAAGTTTCGGG
4274 ACCTCCGGGG
Statistics
Matches: 324, Mismatches: 63, Indels: 36
0.77 0.15 0.09
Matches are distributed among these distances:
26 4 0.01
28 58 0.18
29 141 0.44
30 117 0.36
31 4 0.01
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (30 bp):
AAAATGGGATTTTTGGAAGTTTCGGGGGTA
Found at i:3982 original size:59 final size:59
Alignment explanation
Indices: 3840--4250 Score: 449
Period size: 59 Copynumber: 7.0 Consensus size: 59
3830 ATTCAAGGTT
* * * * *
3840 AAAATGGGATTTTTGGAAGTTCGAGGGT-AAAATGGAATCTTTGGAAGTTTCGAGGT-C
1 AAAATGGGATTTTTGAAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTAA
*
3897 AAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTAA
1 AAAATGGGATTTTTGAAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTAA
* * * * *
3956 AAAATGGGATTTTAGAAAGTTTGGGGGTAAAAATGGAATTTTTGGAAGTTTTGAGGTCA
1 AAAATGGGATTTTTGAAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTAA
* ** * * * *
4015 AAAATGGGGTTTTCAAAAGTTCGGGGGT-AAAATGGGATTTTTGGTAG-TT-GTGGTCA
1 AAAATGGGATTTTTGAAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTAA
* * * * *
4071 AAAATGGGATTTTTGAAAGTTCGAGGGTAAAAATGGGATTTTTGAAAGTTTCGTGGTCA
1 AAAATGGGATTTTTGAAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTAA
* * * *
4130 AAAATGGGATTTTCGAAAGTTCGAGGGTAAAAATGGAATTTTTGAAAGTTTTGGGGTAA
1 AAAATGGGATTTTTGAAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTAA
* * * * * *
4189 AAAATAGGATTTTTGGAAATTTTGGGGTTAAAAATTGG-ATTTTTAGTAG-TTCGAGGGTAA
1 AAAATGGGATTTTT-GAAAGTTCGGGGGTAAAAA-TGGAATTTTTGGAAGTTTCG-GGGTAA
4249 AA
1 AA
4251 TTATAATTTT
Statistics
Matches: 308, Mismatches: 38, Indels: 13
0.86 0.11 0.04
Matches are distributed among these distances:
56 30 0.10
57 46 0.15
58 45 0.15
59 153 0.50
60 31 0.10
61 3 0.01
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (59 bp):
AAAATGGGATTTTTGAAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTAA
Found at i:4101 original size:174 final size:175
Alignment explanation
Indices: 3856--4193 Score: 500
Period size: 174 Copynumber: 1.9 Consensus size: 175
3846 GGATTTTTGG
* *
3856 AAGTTCGAGGGTAAAATGGAATCTTTGGAAGTTTCGAGGTCAAAATGGGATTTTTGGAAGTTCGG
1 AAGTTCGAGGGTAAAATGGAATCTTTGGAAGTTTCGAGGTCAAAATGGGATTTTTGAAAGTTCGA
* * *
3921 GGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTAAAAAATGGGATTTTAGAAAGTTTGGGGGTAA
66 GGGTAAAAATGGAATTTTTGAAAGTTTCGGGGTAAAAAATGGGATTTTAGAAAGTTCGAGGGTAA
* *
3986 AAATGGAATTTTTGGAAGTTTTGAGGTCAAAAATGGGGTTTTCAA
131 AAATGGAATTTTTGAAAGTTTTGAGGTAAAAAATGGGGTTTTCAA
* * * * *
4031 AAGTTCGGGGGTAAAATGGGATTTTTGGTAG-TT-GTGGTCAAAAATGGGATTTTTGAAAGTTCG
1 AAGTTCGAGGGTAAAATGGAATCTTTGGAAGTTTCGAGGTC-AAAATGGGATTTTTGAAAGTTCG
* * * *
4094 AGGGTAAAAATGGGATTTTTGAAAGTTTCGTGGTCAAAAATGGGATTTTCGAAAGTTCGAGGGTA
65 AGGGTAAAAATGGAATTTTTGAAAGTTTCGGGGTAAAAAATGGGATTTTAGAAAGTTCGAGGGTA
*
4159 AAAATGGAATTTTTGAAAGTTTTGGGGTAAAAAAT
130 AAAATGGAATTTTTGAAAGTTTTGAGGTAAAAAAT
4194 AGGATTTTTG
Statistics
Matches: 145, Mismatches: 17, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
173 5 0.03
174 113 0.78
175 27 0.19
ACGTcount: A:0.32, C:0.04, G:0.31, T:0.33
Consensus pattern (175 bp):
AAGTTCGAGGGTAAAATGGAATCTTTGGAAGTTTCGAGGTCAAAATGGGATTTTTGAAAGTTCGA
GGGTAAAAATGGAATTTTTGAAAGTTTCGGGGTAAAAAATGGGATTTTAGAAAGTTCGAGGGTAA
AAATGGAATTTTTGAAAGTTTTGAGGTAAAAAATGGGGTTTTCAA
Done.