Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003123.1 Kokia drynarioides strain JFW-HI SEQ_115696, 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: 93302
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 62 characters in sequence are not A, C, G, or T
Found at i:7117 original size:13 final size:13
Alignment explanation
Indices: 7099--7127 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
7089 ATCTAATATA
7099 GCTAAACCATTAT
1 GCTAAACCATTAT
7112 GCTAAACCATTAT
1 GCTAAACCATTAT
7125 GCT
1 GCT
7128 CACTGCTAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.24, G:0.10, T:0.31
Consensus pattern (13 bp):
GCTAAACCATTAT
Found at i:11925 original size:19 final size:20
Alignment explanation
Indices: 11898--11938 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
11888 TTGAAAAACA
* *
11898 AAAATGAAAAAGAAAGAAAG
1 AAAATGAAAAAAAAAAAAAG
11918 AAAA-GAAAAAAAAAAAAAG
1 AAAATGAAAAAAAAAAAAAG
11937 AA
1 AA
11939 GAAATTACTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (20 bp):
AAAATGAAAAAAAAAAAAAG
Found at i:11926 original size:26 final size:22
Alignment explanation
Indices: 11892--11942 Score: 57
Period size: 26 Copynumber: 2.1 Consensus size: 22
11882 AGTCACTTGA
11892 AAAACAAAAATGAAAAAGAAAGAAAG
1 AAAACAAAAA--AAAAA-AAAG-AAG
*
11918 AAAAGAAAAAAAAAAAAAGAAG
1 AAAACAAAAAAAAAAAAAGAAG
11940 AAA
1 AAA
11943 TTACTGAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 6 0.25
23 4 0.17
24 5 0.21
26 9 0.38
ACGTcount: A:0.82, C:0.02, G:0.14, T:0.02
Consensus pattern (22 bp):
AAAACAAAAAAAAAAAAAGAAG
Found at i:25562 original size:19 final size:18
Alignment explanation
Indices: 25517--25585 Score: 54
Period size: 17 Copynumber: 3.8 Consensus size: 18
25507 TTTGTAGTGT
25517 TATTATTATATATTTTA-A
1 TATTATTAT-TATTTTATA
* *
25535 AAATATTTATGTATTTTATA
1 TATTA-TTAT-TATTTTATA
* *
25555 TATTTTTA-AATTTTATA
1 TATTATTATTATTTTATA
25572 TATTATTATT-TTTT
1 TATTATTATTATTTT
25586 GTCAACAATC
Statistics
Matches: 39, Mismatches: 9, Indels: 7
0.71 0.16 0.13
Matches are distributed among these distances:
17 19 0.49
18 3 0.08
19 14 0.36
20 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (18 bp):
TATTATTATTATTTTATA
Found at i:25569 original size:26 final size:29
Alignment explanation
Indices: 25517--25580 Score: 89
Period size: 28 Copynumber: 2.3 Consensus size: 29
25507 TTTGTAGTGT
*
25517 TATTATTATATATTTTAAAAATATTTATG
1 TATTATTATATATTTTAAAAATATTTATA
*
25546 TATT-TTATATATTTT-TAAAT-TTTATA
1 TATTATTATATATTTTAAAAATATTTATA
25572 TATTATTAT
1 TATTATTAT
25581 TTTTTGTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 9 0.28
27 8 0.25
28 11 0.34
29 4 0.12
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (29 bp):
TATTATTATATATTTTAAAAATATTTATA
Found at i:25585 original size:17 final size:17
Alignment explanation
Indices: 25547--25579 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
25537 ATATTTATGT
*
25547 ATTTTATATATTTTTAA
1 ATTTTATATATTATTAA
25564 ATTTTATATATTATTA
1 ATTTTATATATTATTA
25580 TTTTTTGTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTTATATATTATTAA
Found at i:25635 original size:50 final size:52
Alignment explanation
Indices: 25548--25652 Score: 178
Period size: 52 Copynumber: 2.1 Consensus size: 52
25538 TATTTATGTA
25548 TTTTATATATTTTTAAATTTTATATATTATTATTTTTTGTCAACAATCATTT
1 TTTTATATATTTTTAAATTTTATATATTATTATTTTTTGTCAACAATCATTT
* *
25600 TTTTATATTTTTTTTAATTTTATATATTA-TATTTTTT-TCAACAATCATTT
1 TTTTATATATTTTTAAATTTTATATATTATTATTTTTTGTCAACAATCATTT
25650 TTT
1 TTT
25653 ATTTTTATAT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
50 16 0.31
51 8 0.16
52 27 0.53
ACGTcount: A:0.29, C:0.06, G:0.01, T:0.65
Consensus pattern (52 bp):
TTTTATATATTTTTAAATTTTATATATTATTATTTTTTGTCAACAATCATTT
Found at i:35545 original size:35 final size:33
Alignment explanation
Indices: 35471--35546 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 33
35461 TTTGAACTAT
35471 ATAAAAAAAGTAAATTATAATGTTAATTGAAAA
1 ATAAAAAAAGTAAATTATAATGTTAATTGAAAA
* *
35504 A-AAAAAAATGTAGCAATTATAATAGTTCA-TGATAA
1 ATAAAAAAA-GTA--AATTATAAT-GTTAATTGAAAA
35539 ATAAAAAA
1 ATAAAAAA
35547 GATATTTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
32 7 0.19
33 4 0.11
35 15 0.42
36 10 0.28
ACGTcount: A:0.61, C:0.03, G:0.09, T:0.28
Consensus pattern (33 bp):
ATAAAAAAAGTAAATTATAATGTTAATTGAAAA
Found at i:41576 original size:25 final size:25
Alignment explanation
Indices: 41542--41599 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
41532 TAACGTCGAT
*
41542 AATAATAATAAAACGATCGCAAAAC
1 AATAACAATAAAACGATCGCAAAAC
* * *
41567 AATAACAATAGAACGATCGTAAAAT
1 AATAACAATAAAACGATCGCAAAAC
41592 AATAACAA
1 AATAACAA
41600 AAGAAAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.60, C:0.14, G:0.09, T:0.17
Consensus pattern (25 bp):
AATAACAATAAAACGATCGCAAAAC
Found at i:41604 original size:25 final size:25
Alignment explanation
Indices: 41540--41604 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
41530 ACTAACGTCG
*
41540 ATAATAATAATAA-AACGATCGCAAA
1 ATAATAACAA-AAGAACGATCGCAAA
* * *
41565 ACAATAACAATAGAACGATCGTAAA
1 ATAATAACAAAAGAACGATCGCAAA
41590 ATAATAACAAAAGAA
1 ATAATAACAAAAGAA
41605 AAATAATACA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
24 1 0.03
25 32 0.97
ACGTcount: A:0.62, C:0.12, G:0.09, T:0.17
Consensus pattern (25 bp):
ATAATAACAAAAGAACGATCGCAAA
Found at i:44766 original size:21 final size:21
Alignment explanation
Indices: 44740--44789 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
44730 CTTTCGGAAT
44740 ATTTTACTTAGTAAAACATGC
1 ATTTTACTTAGTAAAACATGC
44761 ATTTTACTTAGTAAAACATGC
1 ATTTTACTTAGTAAAACATGC
44782 ATTTTACT
1 ATTTTACT
44790 GATCATATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.42
Consensus pattern (21 bp):
ATTTTACTTAGTAAAACATGC
Found at i:45436 original size:19 final size:20
Alignment explanation
Indices: 45409--45446 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
45399 AGAAATGAGA
45409 GAATAGAAGAGATGATTGAT
1 GAATAGAAGAGATGATTGAT
*
45429 GAAT-GAAGGGATGATTGA
1 GAATAGAAGAGATGATTGA
45447 GAAGTGAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.42, C:0.00, G:0.34, T:0.24
Consensus pattern (20 bp):
GAATAGAAGAGATGATTGAT
Found at i:45920 original size:22 final size:23
Alignment explanation
Indices: 45890--45932 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
45880 TACATGTCCA
45890 TTAAATAATATAATTT-CATGCT
1 TTAAATAATATAATTTGCATGCT
* *
45912 TTAATTAATTTAATTTGCATG
1 TTAAATAATATAATTTGCATG
45933 ATCCACTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (23 bp):
TTAAATAATATAATTTGCATGCT
Found at i:50766 original size:15 final size:12
Alignment explanation
Indices: 50732--50756 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
50722 ATTAAAGAAT
50732 TAATAACATTCA
1 TAATAACATTCA
50744 TAATAACATTCA
1 TAATAACATTCA
50756 T
1 T
50757 CATGATAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (12 bp):
TAATAACATTCA
Found at i:69402 original size:17 final size:18
Alignment explanation
Indices: 69382--69421 Score: 66
Period size: 16 Copynumber: 2.3 Consensus size: 18
69372 CTGTCCTTCT
69382 TTAAACTTCAGCCTT-AA
1 TTAAACTTCAGCCTTGAA
69399 TT-AACTTCAGCCTTGAA
1 TTAAACTTCAGCCTTGAA
69416 TTAAAC
1 TTAAAC
69422 AACAACACCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 12 0.57
17 6 0.29
18 3 0.14
ACGTcount: A:0.35, C:0.23, G:0.07, T:0.35
Consensus pattern (18 bp):
TTAAACTTCAGCCTTGAA
Found at i:75160 original size:23 final size:23
Alignment explanation
Indices: 75134--75182 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
75124 TTGTTTAATT
75134 CTTTGATATGAGTTCACATAGTG
1 CTTTGATATGAGTTCACATAGTG
75157 CTTTGATATGAGTTCACATAGTG
1 CTTTGATATGAGTTCACATAGTG
75180 CTT
1 CTT
75183 CCCATAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.41
Consensus pattern (23 bp):
CTTTGATATGAGTTCACATAGTG
Found at i:76241 original size:30 final size:30
Alignment explanation
Indices: 76173--76241 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
76163 CATTGCACAA
* *
76173 TCCAAATGACATATGTCGGAAGGCAAAGGT
1 TCCAAATGGCATACGTCGGAAGGCAAAGGT
76203 TCCAAATGGCATACGTCGGAAGGCAAAGGT
1 TCCAAATGGCATACGTCGGAAGGCAAAGGT
76233 TCCAAATGG
1 TCCAAATGG
76242 GCATGTGAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.35, C:0.19, G:0.28, T:0.19
Consensus pattern (30 bp):
TCCAAATGGCATACGTCGGAAGGCAAAGGT
Found at i:80246 original size:14 final size:14
Alignment explanation
Indices: 80227--80253 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
80217 AATAAATAAG
80227 AATCAAAGTAATCT
1 AATCAAAGTAATCT
80241 AATCAAAGTAATC
1 AATCAAAGTAATC
80254 AAAGTAATCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.15, G:0.07, T:0.26
Consensus pattern (14 bp):
AATCAAAGTAATCT
Found at i:89922 original size:22 final size:23
Alignment explanation
Indices: 89891--89934 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
89881 GGGGGTTCTG
89891 TTTTTAAATTTCTA-GGTTTTTA
1 TTTTTAAATTTCTAGGGTTTTTA
* *
89913 TTTTTTAATTTGTAGGGTTTTT
1 TTTTTAAATTTCTAGGGTTTTT
89935 TTAAATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.18, C:0.02, G:0.14, T:0.66
Consensus pattern (23 bp):
TTTTTAAATTTCTAGGGTTTTTA
Found at i:90435 original size:16 final size:16
Alignment explanation
Indices: 90416--90468 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
90406 ATGTTTAGGT
90416 TGGTTTATGGTGGTGA
1 TGGTTTATGGTGGTGA
*
90432 TGGTGTTATGTTTAGGT--
1 TGGT-TTATG-GT-GGTGA
90449 TGGTTTATGGTGGTGA
1 TGGTTTATGGTGGTGA
90465 TGGT
1 TGGT
90469 GTTGAGACTC
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
14 3 0.10
15 1 0.03
16 13 0.43
17 9 0.30
18 1 0.03
19 3 0.10
ACGTcount: A:0.11, C:0.00, G:0.42, T:0.47
Consensus pattern (16 bp):
TGGTTTATGGTGGTGA
Found at i:90445 original size:33 final size:33
Alignment explanation
Indices: 90403--90471 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
90393 TGTTAATGAG
90403 GTTATGTTTAGGTTGGTTTATGGTGGTGATGGT
1 GTTATGTTTAGGTTGGTTTATGGTGGTGATGGT
90436 GTTATGTTTAGGTTGGTTTATGGTGGTGATGGT
1 GTTATGTTTAGGTTGGTTTATGGTGGTGATGGT
90469 GTT
1 GTT
90472 GAGACTCAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.12, C:0.00, G:0.39, T:0.49
Consensus pattern (33 bp):
GTTATGTTTAGGTTGGTTTATGGTGGTGATGGT
Done.