Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007898.1 Kokia drynarioides strain JFW-HI SEQ_122539, 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: 46013
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 14 characters in sequence are not A, C, G, or T
Found at i:3695 original size:21 final size:22
Alignment explanation
Indices: 3671--3711 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
3661 AAACGAAGTA
3671 GTTTT-ACTTTTTAA-TTTAATG
1 GTTTTGAC-TTTTAACTTTAATG
3692 GTTTTGACTTTTAACTTTAA
1 GTTTTGACTTTTAACTTTAA
3712 AAAAAGTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.24, C:0.07, G:0.10, T:0.59
Consensus pattern (22 bp):
GTTTTGACTTTTAACTTTAATG
Found at i:3753 original size:71 final size:71
Alignment explanation
Indices: 3575--3752 Score: 261
Period size: 71 Copynumber: 2.5 Consensus size: 71
3565 AAACTTAATG
* * *
3575 AGTAAATATTTATCAAAACGGTGTAGTTTTACTTTTTAACTTAATGATTTTGACTTTTAACTTCA
1 AGTAAATATTTATCAAAACGATATAGTTTTACTTTTTAATTTAATGATTTTGACTTTTAACTTCA
3640 AAAAAA
66 AAAAAA
* *
3646 AGTAAACATTTATCAAAACGA-AGTAGTTTTACTTTTTAATTTAATGGTTTTGACTTTTAACTT-
1 AGTAAATATTTATCAAAACGATA-TAGTTTTACTTTTTAATTTAATGATTTTGACTTTTAACTTC
*
3709 TAAAAAA
65 AAAAAAA
* *
3716 AGTAAATATTTATCAAAACGATATAATTTTATTTTTT
1 AGTAAATATTTATCAAAACGATATAGTTTTACTTTTT
3753 TTATTTTGAT
Statistics
Matches: 96, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
70 38 0.40
71 58 0.60
ACGTcount: A:0.39, C:0.08, G:0.09, T:0.44
Consensus pattern (71 bp):
AGTAAATATTTATCAAAACGATATAGTTTTACTTTTTAATTTAATGATTTTGACTTTTAACTTCA
AAAAAA
Found at i:3881 original size:23 final size:21
Alignment explanation
Indices: 3850--3895 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3840 AATAACTTGA
*
3850 TTAACTCAAATAATTTGAATTAT
1 TTAACTC-AA-AATATGAATTAT
*
3873 TTAATTCAAAATATGAATTAT
1 TTAACTCAAAATATGAATTAT
3894 TT
1 TT
3896 TTAAAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 13 0.62
22 2 0.10
23 6 0.29
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (21 bp):
TTAACTCAAAATATGAATTAT
Found at i:5861 original size:19 final size:17
Alignment explanation
Indices: 5818--5863 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 17
5808 TAAAATATAA
5818 AATTAAATTTATAAATC
1 AATTAAATTTATAAATC
5835 ATATTTAAATTTAATAAACTC
1 A-A-TTAAATTT-ATAAA-TC
5856 AATTAAAT
1 AATTAAAT
5864 GTGTTATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 1 0.04
18 1 0.04
19 14 0.56
20 6 0.24
21 3 0.12
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (17 bp):
AATTAAATTTATAAATC
Found at i:8129 original size:28 final size:29
Alignment explanation
Indices: 8087--8142 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
8077 TAGTCCTCGT
*
8087 TTTTAATTGATTTTTCAATT-TCAAAATA
1 TTTTAATTGATTTTTAAATTATCAAAATA
8115 TTTTAATT-ATATTTTAAATTATCAAAAT
1 TTTTAATTGAT-TTTTAAATTATCAAAAT
8143 TATATCAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 2 0.08
28 16 0.64
29 7 0.28
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (29 bp):
TTTTAATTGATTTTTAAATTATCAAAATA
Found at i:15545 original size:29 final size:28
Alignment explanation
Indices: 15513--15569 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
15503 TTCTTATTTT
* **
15513 GAGTTAAATTTGATTTTTAACTTTTTAAA
1 GAGTTAAATTTAATCATTAA-TTTTTAAA
*
15542 GAGTTCAATTTAATCATTAATTTTTAAA
1 GAGTTAAATTTAATCATTAATTTTTAAA
15570 AAAAAATTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.49
Consensus pattern (28 bp):
GAGTTAAATTTAATCATTAATTTTTAAA
Found at i:16179 original size:21 final size:22
Alignment explanation
Indices: 16149--16190 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
16139 TTTAAATGTT
*
16149 TAATTGAAA-TTTAAAAAAATC
1 TAATTAAAATTTTAAAAAAATC
*
16170 TAATTAAAATTTTTAAAAAAT
1 TAATTAAAATTTTAAAAAAAT
16191 TTAAACAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (22 bp):
TAATTAAAATTTTAAAAAAATC
Found at i:16469 original size:23 final size:23
Alignment explanation
Indices: 16443--16491 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
16433 TTTTGTAATC
*
16443 TAATATTTTTATTTTTAAGAATT
1 TAATATCTTTATTTTTAAGAATT
* * *
16466 TAATCTCTTTATTTTTTAGATTT
1 TAATATCTTTATTTTTAAGAATT
16489 TAA
1 TAA
16492 AATTAATGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (23 bp):
TAATATCTTTATTTTTAAGAATT
Found at i:29422 original size:57 final size:57
Alignment explanation
Indices: 29343--29457 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
29333 AAATTCAGAT
29343 TATGAACAGGCAGAAATAAATATACAAATCTAAACATTATGTGATGTAAGATTAGAG
1 TATGAACAGGCAGAAATAAATATACAAATCTAAACATTATGTGATGTAAGATTAGAG
29400 TATGAACAGGCAGAAATAAATATACAAATCTAAACATTATGTGATGTAAGATTAGAG
1 TATGAACAGGCAGAAATAAATATACAAATCTAAACATTATGTGATGTAAGATTAGAG
29457 T
1 T
29458 TGGTCCAAGG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.47, C:0.09, G:0.17, T:0.27
Consensus pattern (57 bp):
TATGAACAGGCAGAAATAAATATACAAATCTAAACATTATGTGATGTAAGATTAGAG
Found at i:34285 original size:17 final size:17
Alignment explanation
Indices: 34263--34298 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
34253 ATTAGGAAAT
34263 GAGGGTCTTGCATTCTA
1 GAGGGTCTTGCATTCTA
34280 GAGGGTCTTGCATTCTA
1 GAGGGTCTTGCATTCTA
34297 GA
1 GA
34299 ATTAAAGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.19, C:0.17, G:0.31, T:0.33
Consensus pattern (17 bp):
GAGGGTCTTGCATTCTA
Found at i:36853 original size:7 final size:7
Alignment explanation
Indices: 36841--36866 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
36831 CAATTCAACT
36841 CCTAAAC
1 CCTAAAC
36848 CCTAAAC
1 CCTAAAC
36855 CCTAAAC
1 CCTAAAC
36862 CCTAA
1 CCTAA
36867 TACAAGAGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.15
Consensus pattern (7 bp):
CCTAAAC
Found at i:42140 original size:94 final size:94
Alignment explanation
Indices: 41879--42146 Score: 342
Period size: 95 Copynumber: 2.8 Consensus size: 94
41869 TGTTTTAAGC
* * *
41879 AAAATAGTTATATATCTTATAATTTAATTACTATGTCAAATTGATAAATATTGATGGAAAATATT
1 AAAATAGTTATATATTTTATAATTTAATTAC-ATGTCAAATTGATAAATGTTGATGGAAAATACT
*
41944 TATAATCTTAATGATTATAAACCAAGTCAG
65 TATAATTTTAATGATTATAAACCAAGTCAG
* *
41974 AAAATAGTTATATATTTTATAATTTAATCAACATGTCAAATTGATAGATGTTGATGGAAAATACT
1 AAAATAGTTATATATTTTATAATTTAAT-TACATGTCAAATTGATAAATGTTGATGGAAAATACT
* * *
42039 TATAATTTTAATGATTATAAATCGAGT-GG
65 TATAATTTTAATGATTATAAACCAAGTCAG
* * * * *
42068 AAAAATAGTTATATATTTTAT-ACTTGATTAGCATGCCAATTTGATAAATGTTGATGGATAATAC
1 -AAAATAGTTATATATTTTATAATTTAATTA-CATGTCAAATTGATAAATGTTGATGGAAAATAC
* *
42132 TTGTAATTTTCATGA
64 TTATAATTTTAATGA
42147 ATGGACAGAG
Statistics
Matches: 152, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
93 1 0.01
94 48 0.32
95 101 0.66
96 2 0.01
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.40
Consensus pattern (94 bp):
AAAATAGTTATATATTTTATAATTTAATTACATGTCAAATTGATAAATGTTGATGGAAAATACTT
ATAATTTTAATGATTATAAACCAAGTCAG
Done.