Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001217.1 Kokia drynarioides strain JFW-HI SEQ_112570, 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: 35845
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:326 original size:32 final size:32
Alignment explanation
Indices: 290--352 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
280 GCCATCCATA
* *
290 CATGTACCTGAAATATATTAATCAGCTAATTG
1 CATGTACCTGAAACACATTAATCAGCTAATTG
322 CATGTACCTGAAACACATTAATCAGCTAATT
1 CATGTACCTGAAACACATTAATCAGCTAATT
353 AATTTCGGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (32 bp):
CATGTACCTGAAACACATTAATCAGCTAATTG
Found at i:441 original size:39 final size:39
Alignment explanation
Indices: 398--496 Score: 153
Period size: 39 Copynumber: 2.5 Consensus size: 39
388 TTAATTTGTC
* *
398 TCAAACTTAGACACCTTAAAAACAACTATTAAATATGTA
1 TCAAACTAAGACACATTAAAAACAACTATTAAATATGTA
* * *
437 TCAAAATAAGACACATTAAAAACAATTATTCAATATGTA
1 TCAAACTAAGACACATTAAAAACAACTATTAAATATGTA
476 TCAAACTAAGACACATTAAAA
1 TCAAACTAAGACACATTAAAA
497 CCCTATTTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.53, C:0.16, G:0.05, T:0.26
Consensus pattern (39 bp):
TCAAACTAAGACACATTAAAAACAACTATTAAATATGTA
Found at i:6838 original size:32 final size:32
Alignment explanation
Indices: 6802--6867 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 32
6792 AAGCCATCCA
* * *
6802 TACATGTACCTGAAATATATTAATCAGCTAAT
1 TACATGTACATGAAACACATTAATCAGCTAAT
*
6834 TACATGTACATGAAACACATTAATCAGTTAAT
1 TACATGTACATGAAACACATTAATCAGCTAAT
6866 TA
1 TA
6868 ATTTCGGCTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.33
Consensus pattern (32 bp):
TACATGTACATGAAACACATTAATCAGCTAAT
Found at i:6955 original size:39 final size:39
Alignment explanation
Indices: 6920--7049 Score: 188
Period size: 39 Copynumber: 3.3 Consensus size: 39
6910 TCTCAAACTT
* * *
6920 AGACACCTTAAAAACAATTATTAAACATGTATCAAAATA
1 AGACACATTAAAAACAACTATTAAATATGTATCAAAATA
* *
6959 AGACGCAGTAAAAACAACTATTAAATATGTATCAAAATA
1 AGACACATTAAAAACAACTATTAAATATGTATCAAAATA
* * *
6998 AGACACATTAAAAACAACTATTAAATACGTACCAAACTA
1 AGACACATTAAAAACAACTATTAAATATGTATCAAAATA
7037 AGACACATTAAAA
1 AGACACATTAAAA
7050 CCCTATTTAA
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 81 1.00
ACGTcount: A:0.55, C:0.16, G:0.07, T:0.22
Consensus pattern (39 bp):
AGACACATTAAAAACAACTATTAAATATGTATCAAAATA
Found at i:7866 original size:13 final size:12
Alignment explanation
Indices: 7845--7876 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
7835 TGAAAAGGAT
7845 AAAATAAAAGAG
1 AAAATAAAAGAG
7857 AAAATAAAA-AG
1 AAAATAAAAGAG
7868 -AAATAAAAG
1 AAAATAAAAG
7877 CAAGGTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 8 0.42
11 2 0.11
12 9 0.47
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.09
Consensus pattern (12 bp):
AAAATAAAAGAG
Found at i:9626 original size:16 final size:15
Alignment explanation
Indices: 9605--9634 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
9595 TGATTTGAGC
9605 ATGTGAATAATGTGAA
1 ATGTGAAT-ATGTGAA
9621 ATGTGAATATGTGA
1 ATGTGAATATGTGA
9635 TTATCAAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.40, C:0.00, G:0.27, T:0.33
Consensus pattern (15 bp):
ATGTGAATATGTGAA
Found at i:9963 original size:3 final size:3
Alignment explanation
Indices: 9950--9984 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
9940 AAAATCTCAA
*
9950 AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
9985 AACTTATGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:12076 original size:19 final size:19
Alignment explanation
Indices: 12048--12084 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
12038 CGACTTGTTG
*
12048 ACTTTGATCGTTGACTTTA
1 ACTTTAATCGTTGACTTTA
12067 ACTTTAATCGTTGACTTT
1 ACTTTAATCGTTGACTTT
12085 TTTTAACAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.14, T:0.49
Consensus pattern (19 bp):
ACTTTAATCGTTGACTTTA
Found at i:20922 original size:38 final size:39
Alignment explanation
Indices: 20880--20969 Score: 128
Period size: 38 Copynumber: 2.3 Consensus size: 39
20870 TAAAGATTTC
* *
20880 AAAATATTATATAAAAATTAAAGAAGTATATGACTTTT-
1 AAAATATTATATAAAAATTAAAGAAATATATAACTTTTA
* *
20918 AAAATTTTATATAAAAATTAAAGAAATATTTAACTTTTA
1 AAAATATTATATAAAAATTAAAGAAATATATAACTTTTA
20957 AACAATATTATAT
1 AA-AATATTATAT
20970 TTAGGAAAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
38 34 0.76
39 2 0.04
40 9 0.20
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.39
Consensus pattern (39 bp):
AAAATATTATATAAAAATTAAAGAAATATATAACTTTTA
Found at i:21073 original size:30 final size:31
Alignment explanation
Indices: 21017--21075 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
21007 AAATTTAAAG
* *
21017 TCTAAAATTTCAAAATTAACATATCTAAAAA
1 TCTAAAAATTCAAAATCAACATATCTAAAAA
*
21048 TCTAAAAATTCAAAA-CAAGATATCTAAA
1 TCTAAAAATTCAAAATCAACATATCTAAA
21076 TTTTACTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 11 0.44
31 14 0.56
ACGTcount: A:0.56, C:0.14, G:0.02, T:0.29
Consensus pattern (31 bp):
TCTAAAAATTCAAAATCAACATATCTAAAAA
Found at i:21157 original size:21 final size:22
Alignment explanation
Indices: 21133--21185 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 22
21123 TTTTGGGGTT
21133 TTTTAAATTAGAGTTT-TGGTA
1 TTTTAAATTAGAGTTTATGGTA
* *
21154 TTTTAAATAAGGGTTTATGGTA
1 TTTTAAATTAGAGTTTATGGTA
21176 TTTTAAATTA
1 TTTTAAATTA
21186 ATAGTTATAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 14 0.50
22 14 0.50
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (22 bp):
TTTTAAATTAGAGTTTATGGTA
Found at i:21193 original size:22 final size:22
Alignment explanation
Indices: 21133--21193 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
21123 TTTTGGGGTT
*
21133 TTTTAAATT-AGAGTTTTGGTA
1 TTTTAAATTAAGAGTTATGGTA
*
21154 TTTTAAA-TAAGGGTTTATGGTA
1 TTTTAAATTAAGAG-TTATGGTA
*
21176 TTTTAAATTAATAGTTAT
1 TTTTAAATTAAGAGTTAT
21194 AGAAAATATT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
20 1 0.03
21 10 0.30
22 18 0.55
23 4 0.12
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (22 bp):
TTTTAAATTAAGAGTTATGGTA
Found at i:22359 original size:2 final size:2
Alignment explanation
Indices: 22354--22405 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
22344 TATATATATA
* *
22354 TG TG TG TG TG CG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TT
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
22396 TG TG TG TG TG
1 TG TG TG TG TG
22406 ATTACTTTGA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.02, G:0.48, T:0.50
Consensus pattern (2 bp):
TG
Found at i:26975 original size:28 final size:27
Alignment explanation
Indices: 26921--26975 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
26911 ACATCAAAAT
* *
26921 AATTTTTTTCAAAACCCATCTTCTCAA
1 AATTTTTTTCAAAACACATCATCTCAA
* *
26948 AATTATTTTTCAGAACACATCATGTCAA
1 AATT-TTTTTCAAAACACATCATCTCAA
26976 TTATTTAGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.36, C:0.22, G:0.04, T:0.38
Consensus pattern (27 bp):
AATTTTTTTCAAAACACATCATCTCAA
Found at i:34229 original size:19 final size:18
Alignment explanation
Indices: 34198--34233 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
34188 GGTTTTATTT
34198 AAAAAATTATTATTTTTC
1 AAAAAATTATTATTTTTC
*
34216 AAAACAATTTTTATTTTT
1 AAAA-AATTATTATTTTT
34234 TTAACAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.53
Consensus pattern (18 bp):
AAAAAATTATTATTTTTC
Found at i:34388 original size:15 final size:16
Alignment explanation
Indices: 34364--34396 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
34354 AATTTTAATA
*
34364 TAATTAAAACTGATTT
1 TAATTAAAACTAATTT
34380 TAATT-AAACTAATTT
1 TAATTAAAACTAATTT
34395 TA
1 TA
34397 TTCAATTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (16 bp):
TAATTAAAACTAATTT
Done.