Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008578.1 Kokia drynarioides strain JFW-HI SEQ_123256, 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: 4873
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Found at i:2972 original size:28 final size:28
Alignment explanation
Indices: 2949--3003 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
2939 ATTTTTGGAT
* *
2949 ACCCGGGGGCAAATTGGTAATTTTAGAC
1 ACCCGAGGGCAAAATGGTAATTTTAGAC
* *
2977 ACTCGAGGGTAAAATGGTAATTTTAGA
1 ACCCGAGGGCAAAATGGTAATTTTAGA
3004 AAAAATCGAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (28 bp):
ACCCGAGGGCAAAATGGTAATTTTAGAC
Found at i:3045 original size:59 final size:59
Alignment explanation
Indices: 2979--3108 Score: 188
Period size: 59 Copynumber: 2.2 Consensus size: 59
2969 TTTTAGACAC
* *
2979 TCGAGGGTAAAATGGTAATTTTAGAAAAAATCGAGGTCAAAAATGGGATTTTGGGAAGT
1 TCGAGGGTAAAATGGTAATTTTAGAAAAAATCGAGGTCAAAAATGGAATTTTGGAAAGT
* * *** *
3038 TTGAGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGTAATTTTGGAAAGT
1 TCGAGGGTAAAATGGTAATTTTAGAAAAAATCGAGGTCAAAAATGGAATTTTGGAAAGT
3097 TCGAGGGTAAAA
1 TCGAGGGTAAAA
3109 ATATATTTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.38, C:0.05, G:0.28, T:0.29
Consensus pattern (59 bp):
TCGAGGGTAAAATGGTAATTTTAGAAAAAATCGAGGTCAAAAATGGAATTTTGGAAAGT
Found at i:3049 original size:29 final size:29
Alignment explanation
Indices: 3009--3110 Score: 86
Period size: 29 Copynumber: 3.5 Consensus size: 29
2999 TTAGAAAAAA
*
3009 TCGA-GGTCAAAAATGGGATTTTGGGAAGT
1 TCGAGGGT-AAAAATGGAATTTTGGGAAGT
* *
3038 TTGAGGGT-AAAATGGTAATTTTTGGTGAA-A
1 TCGAGGGTAAAAATGG-AA-TTTTGG-GAAGT
* *
3068 TCGA-GGTCAAAAATGTAATTTTGGAAAGT
1 TCGAGGGT-AAAAATGGAATTTTGGGAAGT
3097 TCGAGGGTAAAAAT
1 TCGAGGGTAAAAAT
3111 ATATTTTTTG
Statistics
Matches: 58, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
28 9 0.16
29 23 0.40
30 17 0.29
31 9 0.16
ACGTcount: A:0.35, C:0.05, G:0.29, T:0.30
Consensus pattern (29 bp):
TCGAGGGTAAAAATGGAATTTTGGGAAGT
Found at i:3086 original size:30 final size:30
Alignment explanation
Indices: 3040--3352 Score: 100
Period size: 29 Copynumber: 10.7 Consensus size: 30
3030 TGGGAAGTTT
3040 GAGGGT-AAAATGGTAATTTTTGGTGAAA-TC
1 GAGGGTAAAAAT-GTAATTTTT-GTGAAAGTC
3070 GA-GGTCAAAAATGTAA-TTTTG-GAAAGTTC
1 GAGGGT-AAAAATGTAATTTTTGTGAAAG-TC
* *
3099 GAGGGTAAAAATAT-ATTTTT-TGAAAGTTT
1 GAGGGTAAAAATGTAATTTTTGTGAAAG-TC
* *
3128 AAGGGT-AAAATGGCAATTTTTGGTGAAA-TC
1 GAGGGTAAAAAT-GTAATTTTT-GTGAAAGTC
* * * *
3158 GA-GGTCAAAAATG-AAATTTTAT-AAAATT
1 GAGGGT-AAAAATGTAATTTTTGTGAAAGTC
* * *
3186 TAGGGGT-AAATTGTAA-TTTT-TGAAAGTTT
1 GA-GGGTAAAAATGTAATTTTTGTGAAAG-TC
*
3215 AAGGGT--AAATGGTAATTTTTGGTGAAA-TC
1 GAGGGTAAAAAT-GTAATTTTT-GTGAAAGTC
* * *
3244 G-GGGTCAAAAATAG-AA-TTATG-GTAAGTT
1 GAGGGT-AAAAAT-GTAATTTTTGTGAAAGTC
* *
3272 TAGGGGTAAAAATGT-ATTTTT-TGAAAGTT
1 GA-GGGTAAAAATGTAATTTTTGTGAAAGTC
* ** *
3301 TAGGGGTAAAAATGTAATTTTTAAG-AAGTTT
1 GA-GGGTAAAAATGTAATTTTTGTGAAAG-TC
*
3332 TAGGGTAAAAATGTAATTTTT
1 GAGGGTAAAAATGTAATTTTT
3353 AGGAAGTATA
Statistics
Matches: 223, Mismatches: 25, Indels: 70
0.70 0.08 0.22
Matches are distributed among these distances:
27 14 0.06
28 38 0.17
29 86 0.39
30 55 0.25
31 25 0.11
32 5 0.02
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.36
Consensus pattern (30 bp):
GAGGGTAAAAATGTAATTTTTGTGAAAGTC
Found at i:3118 original size:29 final size:29
Alignment explanation
Indices: 3026--3137 Score: 79
Period size: 29 Copynumber: 3.8 Consensus size: 29
3016 CAAAAATGGG
* * *
3026 ATTTTGGGAAGTTTGAGGGT-AAAATGGTA
1 ATTTTGGAAAGTTCGAGGGTAAAAAT-ATA
*
3055 ATTTTTGGTGAAA--TCGA-GGTCAAAAATGTA
1 A-TTTT-G-GAAAGTTCGAGGGT-AAAAATATA
3085 ATTTTGGAAAGTTCGAGGGTAAAAATATA
1 ATTTTGGAAAGTTCGAGGGTAAAAATATA
* * **
3114 TTTTTTGAAAGTTTAAGGGTAAAA
1 ATTTTGGAAAGTTCGAGGGTAAAA
3138 TGGCAATTTT
Statistics
Matches: 68, Mismatches: 7, Indels: 16
0.75 0.08 0.18
Matches are distributed among these distances:
27 4 0.06
28 1 0.01
29 40 0.59
30 14 0.21
31 6 0.09
32 3 0.04
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.35
Consensus pattern (29 bp):
ATTTTGGAAAGTTCGAGGGTAAAAATATA
Found at i:3133 original size:88 final size:87
Alignment explanation
Indices: 3034--3322 Score: 388
Period size: 88 Copynumber: 3.3 Consensus size: 87
3024 GGATTTTGGG
*
3034 AAGTTTGAGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGTAATTTTGGAAAG-TT
1 AAGTTTAAGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATG-AATTTTGGAAAGTTT
* *
3098 CGAGGGTAAAAATATATTTTTTGA
65 AG-GGGTAAAAATGTATTTTTTGA
* ** *
3122 AAGTTTAAGGGTAAAATGGCAATTTTTGGTGAAATCGAGGTCAAAAATGAAATTTTATAAAATTT
1 AAGTTTAAGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATG-AATTTTGGAAAGTTT
* *
3187 AGGGGT-AAATTGTAATTTTTGA
65 AGGGGTAAAAATGTATTTTTTGA
* * *
3209 AAGTTTAAGGGT-AAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATAGAATTATGGTAAGTTT
1 AAGTTTAAGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAAT-GAATTTTGGAAAGTTT
3273 AGGGGTAAAAATGTATTTTTTGA
65 AGGGGTAAAAATGTATTTTTTGA
*
3296 AAGTTTAGGGGTAAAAAT-GTAATTTTT
1 AAGTTTAAGGGT-AAAATGGTAATTTTT
3323 AAGAAGTTTT
Statistics
Matches: 176, Mismatches: 20, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
86 49 0.28
87 51 0.29
88 69 0.39
89 7 0.04
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.36
Consensus pattern (87 bp):
AAGTTTAAGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGAATTTTGGAAAGTTTA
GGGGTAAAAATGTATTTTTTGA
Found at i:3177 original size:29 final size:29
Alignment explanation
Indices: 3006--3177 Score: 67
Period size: 29 Copynumber: 5.9 Consensus size: 29
2996 ATTTTAGAAA
**
3006 AAATCGA-GGTCAAAAATGGGATTTTGG-G
1 AAATCGAGGGT-AAAAATGAAATTTTGGTG
* * *
3034 AAGTTTGAGGGT-AAAATGGTAATTTTTGGTG
1 AA-ATCGAGGGTAAAAAT-G-AAATTTTGGTG
*
3065 AAATCGA-GGTCAAAAATGTAATTTT-G-G
1 AAATCGAGGGT-AAAAATGAAATTTTGGTG
* *
3092 AAAGTTCGAGGGTAAAAAT-ATATTTT-TTG
1 AAA--TCGAGGGTAAAAATGAAATTTTGGTG
** *
3121 AAAGTTTAAGGGT-AAAATGGCAATTTTTGGTG
1 AAA--TCGAGGGTAAAAAT-G-AAATTTTGGTG
3153 AAATCGA-GGTCAAAAATGAAATTTT
1 AAATCGAGGGT-AAAAATGAAATTTT
3178 ATAAAATTTA
Statistics
Matches: 107, Mismatches: 20, Indels: 33
0.67 0.12 0.21
Matches are distributed among these distances:
27 4 0.04
28 18 0.17
29 43 0.40
30 19 0.18
31 18 0.17
32 5 0.05
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.33
Consensus pattern (29 bp):
AAATCGAGGGTAAAAATGAAATTTTGGTG
Found at i:3203 original size:28 final size:28
Alignment explanation
Indices: 3172--3235 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
3162 TCAAAAATGA
* *
3172 AATTTTAT-AAAATTTAGGGGTAAATTGT
1 AATTTT-TGAAAATTTAAGGGTAAATGGT
*
3200 AATTTTTGAAAGTTTAAGGGTAAATGGT
1 AATTTTTGAAAATTTAAGGGTAAATGGT
3228 AATTTTTG
1 AATTTTTG
3236 GTGAAATCGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
27 1 0.03
28 31 0.97
ACGTcount: A:0.36, C:0.00, G:0.20, T:0.44
Consensus pattern (28 bp):
AATTTTTGAAAATTTAAGGGTAAATGGT
Found at i:3353 original size:30 final size:30
Alignment explanation
Indices: 3267--3424 Score: 162
Period size: 30 Copynumber: 5.3 Consensus size: 30
3257 GAATTATGGT
* *
3267 AAGTTTAGGGGTAAAAATGTATTTTTTGA-
1 AAGTTTAGGGGTAAAAATGTAATTTTTAAG
3296 AAGTTTAGGGGTAAAAATGTAATTTTTAAG
1 AAGTTTAGGGGTAAAAATGTAATTTTTAAG
*
3326 AAGTTTTA-GGGTAAAAATGTAATTTTTAGG
1 AAG-TTTAGGGGTAAAAATGTAATTTTTAAG
* * * * *
3356 AAGTATATGGTTAAAAATGTAATTTTCAAA
1 AAGTTTAGGGGTAAAAATGTAATTTTTAAG
* * * *
3386 AAGTTT-GAGGTCAAAATATAATTTTT-TG
1 AAGTTTAGGGGTAAAAATGTAATTTTTAAG
3414 ATAGTTTAGGG
1 A-AGTTTAGGG
3425 ACCTTCAAGG
Statistics
Matches: 106, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
28 1 0.01
29 49 0.46
30 52 0.49
31 4 0.04
ACGTcount: A:0.38, C:0.01, G:0.22, T:0.39
Consensus pattern (30 bp):
AAGTTTAGGGGTAAAAATGTAATTTTTAAG
Found at i:4500 original size:3 final size:3
Alignment explanation
Indices: 4487--4545 Score: 66
Period size: 3 Copynumber: 19.3 Consensus size: 3
4477 TTTTATTTTC
* *
4487 ATT ACT ATT ATT ATT ATT ATT A-T ATT AATT ATT ATT GAAT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT -ATT ATT ATT
*
4533 AAT ATT ATT ATT A
1 ATT ATT ATT ATT A
4546 AATACGTTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
2 2 0.04
3 40 0.85
4 5 0.11
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (3 bp):
ATT
Done.