Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009894.1 Kokia drynarioides strain JFW-HI SEQ_124630, 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: 4318
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.25
Warning! 684 characters in sequence are not A, C, G, or T
Found at i:2729 original size:96 final size:96
Alignment explanation
Indices: 2545--2736 Score: 221
Period size: 96 Copynumber: 2.0 Consensus size: 96
2535 CTTTTGCGAA
**
2545 AAGGATATTTGATTATCTTGATTTGAAGAAAGGTTGCACCTAGTGAGTTAAGGCGCAATATTTCA
1 AAGGATATTTGATTATCTTGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGCGCAATATTTCA
**** * *
2610 GAATTGGAGATAAGGAAACATTGCCTCGATT
66 GAACCCAAAATAAAGAAACATTGCCTCGATT
*
2641 AAGGGTATTTGATTAT-TTCGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGCGCAA-AGTTT
1 AAGGATATTTGATTATCTT-GATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGCGCAATA-TTT
* *
2704 C-GAAACCCAAAATAAA-AGAATATTGCTTCGATT
64 CAG-AACCCAAAATAAAGA-AACATTGCCTCGATT
2737 TTAAAGTTTT
Statistics
Matches: 81, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
95 5 0.06
96 76 0.94
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (96 bp):
AAGGATATTTGATTATCTTGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGCGCAATATTTCA
GAACCCAAAATAAAGAAACATTGCCTCGATT
Found at i:3106 original size:29 final size:30
Alignment explanation
Indices: 3074--3432 Score: 241
Period size: 29 Copynumber: 12.2 Consensus size: 30
3064 CAAGAATGAG
*
3074 ATTTTTGGAAGTCCGGGGGT-AAAATGGTA
1 ATTTTTGGAAGTTCGGGGGTAAAAATGGTA
* * * *
3103 ATTTTTTGAAGGT-GTAGGGTAAAAATGG-G
1 ATTTTTGGAAGTTCG-GGGGTAAAAATGGTA
* * *
3132 ACTTTTGGAAGTTCGGGGGT-AAAATGTTC
1 ATTTTTGGAAGTTCGGGGGTAAAAATGGTA
* *
3161 ATTTTTGGAAGGCTC-GGGGTAAAAATGG-G
1 ATTTTTGGAA-GTTCGGGGGTAAAAATGGTA
* * * *
3190 A-CTTT-GAAGGCTC-GAGGTAAAAAATGGGA
1 ATTTTTGGAA-GTTCGGGGGT-AAAAATGGTA
* *
3219 CTTTTTGGAAGTTCGGGGCT-AAAATGGTA
1 ATTTTTGGAAGTTCGGGGGTAAAAATGGTA
* *
3248 ATTTTTGGAATGTTC-GAGGTAAAAAATCAG-A
1 ATTTTTGGAA-GTTCGGGGGT-AAAAAT-GGTA
* *
3279 CTTTTTGGAAGTTCGAGGGT-AAAATGGTA
1 ATTTTTGGAAGTTCGGGGGTAAAAATGGTA
* *
3308 AGTTTTGGAAGGTTCGGGGTTAAAAATGGGT-
1 ATTTTTGGAA-GTTCGGGGGTAAAAAT-GGTA
* **
3339 -TTTTTGGGAGTTCGATGGT-AAAATGGTA
1 ATTTTTGGAAGTTCGGGGGTAAAAATGGTA
* * *
3367 ATTTTTGGAAGGTTCGGAGTTAAAAATGG-G
1 ATTTTTGGAA-GTTCGGGGGTAAAAATGGTA
*
3397 ATTTTTGGAAGTTCGGGGGT-AAAATGGCA
1 ATTTTTGGAAGTTCGGGGGTAAAAATGGTA
3426 ATTTTTG
1 ATTTTTG
3433 AAAGGTTTAG
Statistics
Matches: 256, Mismatches: 49, Indels: 50
0.72 0.14 0.14
Matches are distributed among these distances:
27 15 0.06
28 31 0.12
29 107 0.42
30 63 0.25
31 36 0.14
32 4 0.02
ACGTcount: A:0.29, C:0.06, G:0.32, T:0.33
Consensus pattern (30 bp):
ATTTTTGGAAGTTCGGGGGTAAAAATGGTA
Found at i:3109 original size:30 final size:29
Alignment explanation
Indices: 3030--3432 Score: 235
Period size: 29 Copynumber: 13.8 Consensus size: 29
3020 TCAAACGTTT
3030 GGGGGTAAAATGGTAA-TTTTGGAAGGTT-
1 GGGGGTAAAATGGTAATTTTTGGAA-GTTC
** *
3058 TAGGGTCAAGAAT-G-AGATTTTTGGAAGTCC
1 GGGGGT-AA-AATGGTA-ATTTTTGGAAGTTC
* *
3088 GGGGGTAAAATGGTAATTTTTTGAAGGT-
1 GGGGGTAAAATGGTAATTTTTGGAAGTTC
* * *
3116 GTAGGGTAAAAATGG-GACTTTTGGAAGTTC
1 G-GGGGT-AAAATGGTAATTTTTGGAAGTTC
* * *
3146 GGGGGTAAAATGTTCATTTTTGGAAGGCTC
1 GGGGGTAAAATGGTAATTTTTGGAA-GTTC
* * *
3176 -GGGGTAAAAATGG-GA-CTTT-GAAGGCTC
1 GGGGGT-AAAATGGTAATTTTTGGAA-GTTC
* * *
3203 -GAGGTAAAAAATGGGACTTTTTGGAAGTTC
1 GGGGGT--AAAATGGTAATTTTTGGAAGTTC
*
3233 GGGGCTAAAATGGTAATTTTTGGAATGTTC
1 GGGGGTAAAATGGTAATTTTTGGAA-GTTC
* * *
3263 -GAGGTAAAAAATCAG-ACTTTTTGGAAGTTC
1 GGGGGT--AAAAT-GGTAATTTTTGGAAGTTC
* *
3293 GAGGGTAAAATGGTAAGTTTTGGAAGGTTC
1 GGGGGTAAAATGGTAATTTTTGGAA-GTTC
* *
3323 GGGGTTAAAAATGGGT--TTTTTGGGAGTTC
1 GGGGGT-AAAAT-GGTAATTTTTGGAAGTTC
**
3352 GATGGTAAAATGGTAATTTTTGGAAGGTTC
1 GGGGGTAAAATGGTAATTTTTGGAA-GTTC
* * *
3382 GGAGTTAAAAATGG-GATTTTTGGAAGTTC
1 GGGGGT-AAAATGGTAATTTTTGGAAGTTC
*
3411 GGGGGTAAAATGGCAATTTTTG
1 GGGGGTAAAATGGTAATTTTTG
3433 AAAGGTTTAG
Statistics
Matches: 289, Mismatches: 54, Indels: 63
0.71 0.13 0.16
Matches are distributed among these distances:
27 15 0.05
28 39 0.13
29 116 0.40
30 79 0.27
31 36 0.12
32 4 0.01
ACGTcount: A:0.29, C:0.06, G:0.33, T:0.32
Consensus pattern (29 bp):
GGGGGTAAAATGGTAATTTTTGGAAGTTC
Found at i:3208 original size:27 final size:28
Alignment explanation
Indices: 3168--3222 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
3158 TTCATTTTTG
*
3168 GAAGGCTCGGGGT-AAAAATGGGACTTT
1 GAAGGCTCGAGGTAAAAAATGGGACTTT
3195 GAAGGCTCGAGGTAAAAAATGGGACTTT
1 GAAGGCTCGAGGTAAAAAATGGGACTTT
3223 TTGGAAGTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 12 0.46
28 14 0.54
ACGTcount: A:0.33, C:0.11, G:0.35, T:0.22
Consensus pattern (28 bp):
GAAGGCTCGAGGTAAAAAATGGGACTTT
Found at i:3281 original size:60 final size:60
Alignment explanation
Indices: 3195--3439 Score: 318
Period size: 59 Copynumber: 4.1 Consensus size: 60
3185 ATGGGACTTT
*
3195 GAAGGCTCGAGGTAAAAAATGGGACTTTTTGGAAGTTCG-GGGCTAAAATGGTAATTTTTG
1 GAAGGTTCGAGGTAAAAAATGGGACTTTTTGGAAGTTCGAGGG-TAAAATGGTAATTTTTG
* ** *
3255 GAATGTTCGAGGTAAAAAATCAGACTTTTTGGAAGTTCGAGGGTAAAATGGTAAGTTTTG
1 GAAGGTTCGAGGTAAAAAATGGGACTTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTG
* * * * *
3315 GAAGGTTCGGGGTTAAAAATGGG-TTTTTTGGGAGTTCGATGGTAAAATGGTAATTTTTG
1 GAAGGTTCGAGGTAAAAAATGGGACTTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTG
* * *
3374 GAAGGTTCG-GAGTTAAAAATGGGA-TTTTTGGAAGTTCGGGGGTAAAATGGCAATTTTTG
1 GAAGGTTCGAG-GTAAAAAATGGGACTTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTG
*
3433 AAAGGTT
1 GAAGGTT
3440 TAGGGACCTT
Statistics
Matches: 163, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
58 1 0.01
59 90 0.55
60 69 0.42
61 3 0.02
ACGTcount: A:0.30, C:0.06, G:0.32, T:0.33
Consensus pattern (60 bp):
GAAGGTTCGAGGTAAAAAATGGGACTTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTG
Found at i:3284 original size:31 final size:29
Alignment explanation
Indices: 3201--3420 Score: 141
Period size: 30 Copynumber: 7.4 Consensus size: 29
3191 CTTTGAAGGC
3201 TCGAGGTAAAAAATGGGACTTTTTGGAAGT
1 TCGAGGTAAAAAAT-GGACTTTTTGGAAGT
* *
3231 TCGGGGCT--AAAATGGTAATTTTTGGAATGT
1 TCGAGG-TAAAAAATGG-ACTTTTTGGAA-GT
*
3261 TCGAGGTAAAAAATCAGACTTTTTGGAAGT
1 TCGAGGTAAAAAAT-GGACTTTTTGGAAGT
**
3291 TCGAGGGT--AAAATGGTAAGTTTTGGAAGGT
1 TCGA-GGTAAAAAATGG-ACTTTTTGGAA-GT
* * ** *
3321 TCGGGGTTAAAAATGGGTTTTTTGGGAGT
1 TCGAGGTAAAAAATGGACTTTTTGGAAGT
*
3350 TCGATGGT--AAAATGGTAATTTTTGGAAGGT
1 TCGA-GGTAAAAAATGG-ACTTTTTGGAA-GT
*
3380 TCG-GAGTTAAAAATGGGA-TTTTTGGAAGT
1 TCGAG-GTAAAAAAT-GGACTTTTTGGAAGT
*
3409 TCGGGGGTAAAA
1 TC-GAGGTAAAA
3421 TGGCAATTTT
Statistics
Matches: 152, Mismatches: 18, Indels: 40
0.72 0.09 0.19
Matches are distributed among these distances:
28 11 0.07
29 52 0.34
30 53 0.35
31 33 0.22
32 3 0.02
ACGTcount: A:0.30, C:0.05, G:0.32, T:0.33
Consensus pattern (29 bp):
TCGAGGTAAAAAATGGACTTTTTGGAAGT
Done.