Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002652.1 Kokia drynarioides strain JFW-HI SEQ_114890, 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: 6323
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Found at i:3138 original size:29 final size:30
Alignment explanation
Indices: 3106--3189 Score: 88
Period size: 29 Copynumber: 2.9 Consensus size: 30
3096 TTTGGGGAAC
3106 AAAATTGAATTTTTGGAAAATTTGAGATT-
1 AAAATTGAATTTTTGGAAAATTTGAGATTG
* *
3135 AAAATCGAACTTTCTT--AAAATTTGAGGTTG
1 AAAATTGAA-TTT-TTGGAAAATTTGAGATTG
3165 AAAATGTG-ATTTTTGG-AAATTTGAG
1 AAAAT-TGAATTTTTGGAAAATTTGAG
3190 GGAAAAATGG
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
28 2 0.04
29 32 0.70
30 9 0.20
31 3 0.07
ACGTcount: A:0.38, C:0.04, G:0.19, T:0.39
Consensus pattern (30 bp):
AAAATTGAATTTTTGGAAAATTTGAGATTG
Found at i:3237 original size:29 final size:29
Alignment explanation
Indices: 3165--3463 Score: 97
Period size: 29 Copynumber: 10.5 Consensus size: 29
3155 TTTGAGGTTG
* ** *
3165 AAAAT-GTGATTTTTGGAAATTTGAGGGA
1 AAAATGGTAATTTTTGGATGTTCGAGGGA
** *
3193 AAAATGGTAAAATTTGGATGTTCGAGGGC
1 AAAATGGTAATTTTTGGATGTTCGAGGGA
*
3222 AAAATGGTAATTTTTGGATG-T--A--TA
1 AAAATGGTAATTTTTGGATGTTCGAGGGA
* * * *
3246 AAAAT-GCAATTTTTGGACGTTCGTGGGT
1 AAAATGGTAATTTTTGGATGTTCGAGGGA
* * * * **
3274 AAAATGGTAATTTTAGAAAAGTTTG-GAGTC
1 AAAATGGTAATTTTTG-GATGTTCGAG-GGA
* * * *
3304 AAAATGATAATCTTTTTAGATATT--TGGGA
1 AAAATGGTAA--TTTTTGGATGTTCGAGGGA
* *
3333 TAAAATAGTAATTTTTGGATGTTTGAGGGTA
1 -AAAATGGTAATTTTTGGATGTTCGAGGG-A
* * *
3364 AAAAT-ATGATTTTTGGATGTTCG-GGTCTA
1 AAAATGGTAATTTTTGGATGTTCGAGG--GA
* * *
3393 AAAAT-GTGATTTTTAGAAGTTCGAGGGTA
1 AAAATGGTAATTTTTGGATGTTCGAGGG-A
* * * *
3422 AAAAT-TTAATTTTTTGAAGTTTGAGGGCA
1 AAAATGGTAATTTTTGGATGTTCGAGGG-A
3451 AAAAT-GTAATTTT
1 AAAATGGTAATTTT
3464 AAAGAAGTTT
Statistics
Matches: 201, Mismatches: 50, Indels: 39
0.69 0.17 0.13
Matches are distributed among these distances:
23 12 0.06
24 6 0.03
26 1 0.00
28 23 0.11
29 117 0.58
30 34 0.17
31 4 0.02
32 4 0.02
ACGTcount: A:0.34, C:0.04, G:0.24, T:0.38
Consensus pattern (29 bp):
AAAATGGTAATTTTTGGATGTTCGAGGGA
Found at i:3419 original size:58 final size:58
Alignment explanation
Indices: 3334--3542 Score: 188
Period size: 58 Copynumber: 3.6 Consensus size: 58
3324 TATTTGGGAT
* * * * *
3334 AAAATAGTAATTTTTGGATGTTTGAGGGTAAAAATATGATTTTTGGATGTTCG-GGTCTA
1 AAAAT-GTAATTTTTAGAAGTTTGAGGGTAAAAATATAATTTTTGGAAGTTCGAGGGC-A
* * * * *
3393 AAAATGTGATTTTTAGAAGTTCGAGGGTAAAAATTTAATTTTTTGAAGTTTGAGGGCA
1 AAAATGTAATTTTTAGAAGTTTGAGGGTAAAAATATAATTTTTGGAAGTTCGAGGGCA
* * * * *
3451 AAAATGTAATTTTAAAGAAGTTTGGGGGTAAAAATGTAATTTTTGAAAAGATTAGAGGGC-
1 AAAATGTAATTTT-TAGAAGTTTGAGGGTAAAAATATAATTTTTG-GAAG-TTCGAGGGCA
* * * *
3511 AAAATGTAATTTTGAAAAGTTTAAGGGGAAAA
1 AAAATGTAATTTTTAGAAGTTTGAGGGTAAAA
3543 TGAAATTTTG
Statistics
Matches: 123, Mismatches: 23, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
58 51 0.41
59 48 0.39
60 16 0.13
61 8 0.07
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.35
Consensus pattern (58 bp):
AAAATGTAATTTTTAGAAGTTTGAGGGTAAAAATATAATTTTTGGAAGTTCGAGGGCA
Found at i:3473 original size:30 final size:29
Alignment explanation
Indices: 3392--3551 Score: 130
Period size: 29 Copynumber: 5.5 Consensus size: 29
3382 GTTCGGGTCT
* * * *
3392 AAAAATGTGATTTTTAGAAGTTCGAGGGT
1 AAAAATGTAATTTTAAGAAGTTTGAGGGC
* **
3421 AAAAATTTAATTTTTTGAAGTTTGAGGGC
1 AAAAATGTAATTTTAAGAAGTTTGAGGGC
* *
3450 AAAAATGTAATTTTAAAGAAGTTTGGGGGT
1 AAAAATGTAATTTT-AAGAAGTTTGAGGGC
*
3480 AAAAATGTAATTTTTGAA-AAGATTAGAGGGC
1 AAAAATGTAA-TTTT-AAGAAG-TTTGAGGGC
*
3511 -AAAATGTAATTTTGAA-AAGTTTAAGGG-
1 AAAAATGTAATTTT-AAGAAGTTTGAGGGC
* *
3538 GAAAATGAAATTTT
1 AAAAATGTAATTTT
3552 GGAAAAGTTT
Statistics
Matches: 110, Mismatches: 17, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
28 18 0.16
29 47 0.43
30 33 0.30
31 12 0.11
ACGTcount: A:0.41, C:0.02, G:0.23, T:0.34
Consensus pattern (29 bp):
AAAAATGTAATTTTAAGAAGTTTGAGGGC
Found at i:3543 original size:88 final size:89
Alignment explanation
Indices: 3451--3622 Score: 215
Period size: 88 Copynumber: 1.9 Consensus size: 89
3441 TTTGAGGGCA
* * * *
3451 AAAATGTAATTTT-AAAGAAGTTTGGGGGTAAAAATGTAATTTTTGAAAAGATTAGAGGGC-AAA
1 AAAATGAAATTTTGAAA-AAGTTTAGGGGTAAAAATGCAATTTTGGAAAAGATTAG-GGGCTAAA
3514 ATGT-AATTTTGAAAAGTTTAAGGGG
64 ATGTGAATTTTGAAAAGTTTAAGGGG
* * * *
3539 AAAATGAAATTTTGGAAAAGTTTAGTGGTTAAAATGCAATTTTGGAAAAGTTTAGGGGCTAAAAT
1 AAAATGAAATTTTGAAAAAGTTTAGGGGTAAAAATGCAATTTTGGAAAAGATTAGGGGCTAAAAT
* *
3604 GTGATTTTTGGAAAGTTTA
66 GTGAATTTTGAAAAGTTTA
3623 GGGACCTTTT
Statistics
Matches: 71, Mismatches: 10, Indels: 5
0.83 0.12 0.06
Matches are distributed among these distances:
87 4 0.06
88 51 0.72
89 16 0.23
ACGTcount: A:0.40, C:0.02, G:0.24, T:0.34
Consensus pattern (89 bp):
AAAATGAAATTTTGAAAAAGTTTAGGGGTAAAAATGCAATTTTGGAAAAGATTAGGGGCTAAAAT
GTGAATTTTGAAAAGTTTAAGGGG
Found at i:3580 original size:30 final size:28
Alignment explanation
Indices: 3451--3625 Score: 149
Period size: 30 Copynumber: 6.0 Consensus size: 28
3441 TTTGAGGGCA
* *
3451 AAAATGTAATTTT-AAAGAAGTTTGGGGGT
1 AAAATGTAATTTTGGAA-AAGTTT-AGGGT
* * *
3480 AAAAATGTAATTTTTGAAAAGATTAGAGGGC
1 -AAAATGTAATTTTGGAAAAG-TT-TAGGGT
*
3511 AAAATGTAATTTT-GAAAAGTTTAAGGGG
1 AAAATGTAATTTTGGAAAAGTTT-AGGGT
*
3539 AAAATGAAATTTTGGAAAAGTTTAGTGGTT
1 AAAATGTAATTTTGGAAAAGTTTAG-GG-T
*
3569 AAAATGCAATTTTGGAAAAGTTTAGGGGCT
1 AAAATGTAATTTTGGAAAAGTTTA-GGG-T
*
3599 AAAATGTGATTTTTGG-AAAGTTTAGGG
1 AAAATGT-AATTTTGGAAAAGTTTAGGG
3626 ACCTTTTAAG
Statistics
Matches: 124, Mismatches: 12, Indels: 19
0.80 0.08 0.12
Matches are distributed among these distances:
28 20 0.16
29 20 0.16
30 69 0.56
31 15 0.12
ACGTcount: A:0.39, C:0.02, G:0.26, T:0.33
Consensus pattern (28 bp):
AAAATGTAATTTTGGAAAAGTTTAGGGT
Found at i:4069 original size:36 final size:36
Alignment explanation
Indices: 4021--4123 Score: 134
Period size: 36 Copynumber: 2.8 Consensus size: 36
4011 TAAAAATGGG
* * **
4021 TAAGGCTCAAAACGGCGTCATTTTTAGGCCTGGGCAC
1 TAAGGC-CAAAACGGCGTCGTTTTGAGGCCCAGGCAC
4058 TAAGGCCAAAACGGCGTCGTTTTGAGGCCCAGGCAC
1 TAAGGCCAAAACGGCGTCGTTTTGAGGCCCAGGCAC
* * *
4094 CAAGGCCAAAACGACGTCGTTTTGATGCCC
1 TAAGGCCAAAACGGCGTCGTTTTGAGGCCC
4124 TATAAATACC
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
36 53 0.90
37 6 0.10
ACGTcount: A:0.25, C:0.27, G:0.27, T:0.20
Consensus pattern (36 bp):
TAAGGCCAAAACGGCGTCGTTTTGAGGCCCAGGCAC
Found at i:5512 original size:6 final size:6
Alignment explanation
Indices: 5501--5584 Score: 70
Period size: 6 Copynumber: 14.7 Consensus size: 6
5491 TAATTTTTAA
* * * *
5501 TTAAAT TTAAAT TTATAA- -TGAAT TTAAAT TCAAA- ATAAAT TTATAT
1 TTAAAT TTAAAT TTA-AAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
5547 TTAAA- CTAAAT TTAAAC TTAAA- TTAAAT TTAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAA
5585 CAAATGGGTC
Statistics
Matches: 61, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
4 2 0.03
5 13 0.21
6 44 0.72
7 2 0.03
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (6 bp):
TTAAAT
Found at i:5526 original size:17 final size:17
Alignment explanation
Indices: 5502--5584 Score: 96
Period size: 17 Copynumber: 4.9 Consensus size: 17
5492 AATTTTTAAT
5502 TAAATTTAAATTTATAA-
1 TAAATTTAAATTTA-AAC
* * *
5519 TGAATTTAAATTCAAAA
1 TAAATTTAAATTTAAAC
*
5536 TAAATTTATATTTAAAC
1 TAAATTTAAATTTAAAC
* *
5553 TAAATTTAAACTTAAAT
1 TAAATTTAAATTTAAAC
5570 TAAATTTAAATTTAA
1 TAAATTTAAATTTAA
5585 CAAATGGGTC
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
16 2 0.04
17 53 0.96
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTTAAAC
Found at i:5549 original size:34 final size:34
Alignment explanation
Indices: 5502--5584 Score: 107
Period size: 34 Copynumber: 2.4 Consensus size: 34
5492 AATTTTTAAT
*
5502 TAAATTTAAATTTATAA-TGAATTTAAA-TTCAAAA
1 TAAATTTAAATTTA-AACTAAATTTAAACTT-AAAA
* *
5536 TAAATTTATATTTAAACTAAATTTAAACTTAAAT
1 TAAATTTAAATTTAAACTAAATTTAAACTTAAAA
5570 TAAATTTAAATTTAA
1 TAAATTTAAATTTAA
5585 CAAATGGGTC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
33 2 0.05
34 39 0.91
35 2 0.05
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (34 bp):
TAAATTTAAATTTAAACTAAATTTAAACTTAAAA
Found at i:6301 original size:78 final size:79
Alignment explanation
Indices: 5998--6318 Score: 283
Period size: 78 Copynumber: 4.1 Consensus size: 79
5988 CTTTATTGCT
* * * * * **
5998 TCGAATGCCTGCAATCTGCCCCATGATC-GAGGTAAGAGATTGGCTGATGGTGATCTACCCCCAG
1 TCGAATGGCTGCAATCTACCCGAAGCTCGGA-GTAAGAGATTGGCTGATGGTGATCTGTCCCCAG
*
6062 GCTCGGGGTAATAGA
65 GCTCGGGGTAAGAGA
* * * * *
6077 TCGAATGGCTGCAATTTGCCCTAAGATC-GAGGTAAGAGATTGGCTGATGATGATCTGT-CCCAG
1 TCGAATGGCTGCAATCTACCCGAAGCTCGGA-GTAAGAGATTGGCTGATGGTGATCTGTCCCCAG
* ** *
6140 GGTAAGGGTAAAAGA
65 GCTCGGGGTAAGAGA
* * * * * * * * * **
6155 TCGAAAGGCTGTAATCTACTCGAGGCTTGGGGTAAGAGATTAGCTGATGGAGATC-GACCCCAAA
1 TCGAATGGCTGCAATCTACCCGAAGCTCGGAGTAAGAGATTGGCTGATGGTGATCTGTCCCCAGG
6219 CTCGGGGTAAGAGA
66 CTCGGGGTAAGAGA
* * * * *
6233 TTGAATGGCTGCAATCTACCCGAAGCTCGGAGTAAGAGATTGGCTGACGGTGAT-TTTCTCTAGG
1 TCGAATGGCTGCAATCTACCCGAAGCTCGGAGTAAGAGATTGGCTGATGGTGATCTGTCCCCAGG
6297 CTCGGGGTAAGAGA
66 CTCGGGGTAAGAGA
*
6311 TTGAATGG
1 TCGAATGG
6319 TTACA
Statistics
Matches: 192, Mismatches: 47, Indels: 7
0.78 0.19 0.03
Matches are distributed among these distances:
77 1 0.01
78 139 0.72
79 52 0.27
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (79 bp):
TCGAATGGCTGCAATCTACCCGAAGCTCGGAGTAAGAGATTGGCTGATGGTGATCTGTCCCCAGG
CTCGGGGTAAGAGA
Done.