Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001710.1 Kokia drynarioides strain JFW-HI SEQ_113404, 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: 25208
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Found at i:16077 original size:16 final size:15
Alignment explanation
Indices: 16052--16082 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
16042 TTAATTAATT
16052 TTAATTTTTTTAAAA
1 TTAATTTTTTTAAAA
16067 TTAATTTTTTTTAAAA
1 TTAA-TTTTTTTAAAA
16083 AATATTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTAATTTTTTTAAAA
Found at i:19535 original size:17 final size:16
Alignment explanation
Indices: 19507--19554 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
19497 TTCGATTTTA
19507 TTTTTT-AAATTAATT
1 TTTTTTAAAATTAATT
*
19522 TTTATTTAAAATTAAAT
1 TTT-TTTAAAATTAATT
19539 TTTTTTAAAATGTAAT
1 TTTTTTAAAAT-TAAT
19555 ATACTAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 3 0.11
16 11 0.39
17 14 0.50
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (16 bp):
TTTTTTAAAATTAATT
Found at i:19548 original size:16 final size:16
Alignment explanation
Indices: 19507--19549 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
19497 TTCGATTTTA
*
19507 TTTTTT-AAATTAATT
1 TTTTTTAAAATTAAAT
19522 TTTATTTAAAATTAAAT
1 TTT-TTTAAAATTAAAT
19539 TTTTTTAAAAT
1 TTTTTTAAAAT
19550 GTAATATACT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 3 0.12
16 11 0.44
17 11 0.44
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTTTTAAAATTAAAT
Found at i:19661 original size:39 final size:39
Alignment explanation
Indices: 19611--19697 Score: 124
Period size: 39 Copynumber: 2.3 Consensus size: 39
19601 TTAAAATTAT
*
19611 TTATATT-AAAAACTAC-CATAAATATAATAAATATTTTA
1 TTATATTAAAAAAC-ACAAATAAATATAATAAATATTTTA
*
19649 TTATATTAAAAAACACAAATAAATATAATAAATGTTTTA
1 TTATATTAAAAAACACAAATAAATATAATAAATATTTTA
*
19688 TTTTATTAAA
1 TTATATTAAA
19698 TATAAATTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
38 9 0.20
39 35 0.80
ACGTcount: A:0.53, C:0.06, G:0.01, T:0.40
Consensus pattern (39 bp):
TTATATTAAAAAACACAAATAAATATAATAAATATTTTA
Found at i:20817 original size:18 final size:18
Alignment explanation
Indices: 20794--20843 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
20784 ATAGGTTAAG
20794 GCATTAGCGGCGCTATCA
1 GCATTAGCGGCGCTATCA
20812 GCATTAGCGGCGCTATCA
1 GCATTAGCGGCGCTATCA
*
20830 GCATTAGCGACGCT
1 GCATTAGCGGCGCT
20844 TTCCCACAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.22, C:0.28, G:0.28, T:0.22
Consensus pattern (18 bp):
GCATTAGCGGCGCTATCA
Found at i:20942 original size:41 final size:41
Alignment explanation
Indices: 20830--20943 Score: 133
Period size: 40 Copynumber: 2.8 Consensus size: 41
20820 GGCGCTATCA
* * *
20830 GCATTAGCGACGCTTTCCCACAAACGCCACTAAAGGTCAGG
1 GCATTAGCGGCGCTTTCTCACAAACGCCGCTAAAGGTCAGG
* * **
20871 TCA-TAGCGGCGCTTT-TCCACAAGCATCGCTAAAGGTCAGG
1 GCATTAGCGGCGCTTTCT-CACAAACGCCGCTAAAGGTCAGG
*
20911 GCATTAGCGGCGCTTTCTCATAAACGCCGCTAA
1 GCATTAGCGGCGCTTTCTCACAAACGCCGCTAA
20944 TGCTCTGACT
Statistics
Matches: 58, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
40 32 0.55
41 25 0.43
42 1 0.02
ACGTcount: A:0.26, C:0.30, G:0.23, T:0.21
Consensus pattern (41 bp):
GCATTAGCGGCGCTTTCTCACAAACGCCGCTAAAGGTCAGG
Found at i:20959 original size:41 final size:42
Alignment explanation
Indices: 20914--21010 Score: 117
Period size: 42 Copynumber: 2.3 Consensus size: 42
20904 GGTCAGGGCA
* * *
20914 TTAGCGGCGCTTTCTCATA-AA-CGCCGCTAATGCTCTGACTT
1 TTAGCGGCG-TTTATCATAGAAGCGCCGCTAATGATCTGACCT
**
20955 TTAGCGGCGTTTATTGTAGAAGCGCCGCTAATGATCTGACCT
1 TTAGCGGCGTTTATCATAGAAGCGCCGCTAATGATCTGACCT
*
20997 TTAGCTGCGTTTAT
1 TTAGCGGCGTTTAT
21011 TTTTAAAAAC
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
40 6 0.12
41 11 0.23
42 31 0.65
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.34
Consensus pattern (42 bp):
TTAGCGGCGTTTATCATAGAAGCGCCGCTAATGATCTGACCT
Found at i:21775 original size:168 final size:168
Alignment explanation
Indices: 21490--21825 Score: 512
Period size: 168 Copynumber: 2.0 Consensus size: 168
21480 AACAGGGGGA
* * * * *
21490 ACAGTAACAATTAAAATGGTGGCCTCTTTAGTGAGATTATATGAACAAATGTCCGAACTTAAATA
1 ACAGTAACAATGAAAATGGCGCCCTCTTTAGTGAGATTATATGAACAAATGCCCGAACCTAAATA
* *
21555 TGTTATTGCTATGGGCGCGTGTACAATTGAGGGAGGGATGTTCAGCACTGATTCTTATAGTACCG
66 TGTTATTGCTATGGGCGCATGTACAATTGAAGGAGGGATGTTCAGCACTGATTCTTATAGTACCG
* * *
21620 TTCGGGGGGTCGATAAGCTAATTCCTGTGGATGTCTAT
131 TTCGGGGGATCGATAAGCTAATTCCCGTAGATGTCTAT
*
21658 ACAGTAACAATGAAAATGGCGCCCTCTTTAGTGAGATTATATGAACAAATGCCCGAACCTGAATA
1 ACAGTAACAATGAAAATGGCGCCCTCTTTAGTGAGATTATATGAACAAATGCCCGAACCTAAATA
* * *
21723 TGTTATTGCTATGGGTGCATGTACAATT-ACAGGAGGGATGTTCAGTACTGATTCTTATAGTACT
66 TGTTATTGCTATGGGCGCATGTACAATTGA-AGGAGGGATGTTCAGCACTGATTCTTATAGTACC
* *
21787 GTTCGGGGGATGGATAAGCTAGTTCCCGTAGATGTCTAT
130 GTTCGGGGGATCGATAAGCTAATTCCCGTAGATGTCTAT
21826 TTGTCGGGCT
Statistics
Matches: 151, Mismatches: 16, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
167 1 0.01
168 150 0.99
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (168 bp):
ACAGTAACAATGAAAATGGCGCCCTCTTTAGTGAGATTATATGAACAAATGCCCGAACCTAAATA
TGTTATTGCTATGGGCGCATGTACAATTGAAGGAGGGATGTTCAGCACTGATTCTTATAGTACCG
TTCGGGGGATCGATAAGCTAATTCCCGTAGATGTCTAT
Found at i:24762 original size:6 final size:6
Alignment explanation
Indices: 24751--24775 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
24741 CATCTCAACA
24751 ATAAAT ATAAAT ATAAAT ATAAAT A
1 ATAAAT ATAAAT ATAAAT ATAAAT A
24776 CATTGATAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
ATAAAT
Found at i:24912 original size:8 final size:8
Alignment explanation
Indices: 24901--25024 Score: 60
Period size: 8 Copynumber: 15.4 Consensus size: 8
24891 AAATTAACAA
24901 ATTTAATT
1 ATTTAATT
24909 ATTTAATT
1 ATTTAATT
*
24917 ATTTAAAT
1 ATTTAATT
*
24925 GTTTAATT
1 ATTTAATT
*
24933 A-CTAATAT
1 ATTTAAT-T
24941 CATTTAATT
1 -ATTTAATT
24950 A---AA-T
1 ATTTAATT
*
24954 ATTTAAAT
1 ATTTAATT
24962 ATTTAAATT
1 ATTT-AATT
* **
24971 ATTAAAACA
1 ATT-TAATT
* *
24980 ATTCAAAT
1 ATTTAATT
24988 ATTTAATT
1 ATTTAATT
*
24996 AGTTAATT
1 ATTTAATT
*
25004 GTTTAATTAT
1 ATTTAA-T-T
25014 ATTTAATT
1 ATTTAATT
25022 ATT
1 ATT
25025 AAAAATAACC
Statistics
Matches: 86, Mismatches: 19, Indels: 22
0.68 0.15 0.17
Matches are distributed among these distances:
4 2 0.02
5 2 0.02
7 6 0.07
8 51 0.59
9 15 0.17
10 10 0.12
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (8 bp):
ATTTAATT
Found at i:25086 original size:30 final size:29
Alignment explanation
Indices: 25038--25182 Score: 95
Period size: 30 Copynumber: 4.9 Consensus size: 29
25028 AATAACCCAA
25038 ATATTTAATTAAAAATATTTTATTATTTAATT
1 ATATTTAATT--AAATATTTTATTA-TTAATT
25070 ATATTTAATTAAATA-TTTA--A-TAATT
1 ATATTTAATTAAATATTTTATTATTAATT
* *** * * *
25095 AAAAACAATCCAAATATTTAAATAATTAA-T
1 ATATTTAAT-TAAATATTT-TATTATTAATT
25125 -TATTTAATTAAAAATATTTTATTAGTTAATT
1 ATATTTAATT--AAATATTTTATTA-TTAATT
* *
25156 ATATTTAATTAAATATTTAATAATTAA
1 ATATTTAATTAAATATTTTATTATTAA
25183 AAACAATCCA
Statistics
Matches: 87, Mismatches: 15, Indels: 25
0.69 0.12 0.20
Matches are distributed among these distances:
25 10 0.11
26 5 0.06
27 3 0.03
28 1 0.01
29 15 0.17
30 30 0.34
31 4 0.05
32 19 0.22
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (29 bp):
ATATTTAATTAAATATTTTATTATTAATT
Found at i:25099 original size:70 final size:66
Alignment explanation
Indices: 24984--25134 Score: 176
Period size: 70 Copynumber: 2.2 Consensus size: 66
24974 AAAACAATTC
* * *
24984 AAATATTTAATTAGTTAATTGTTTAATTATATTTAATTATTAAAAATAACCCAAATATTTAATTA
1 AAATATTTAATTAGTTAATTATTTAATTATATTTAATAATTAAAAACAACCCAAATATTTAATTA
25049 A
66 A
* * *
25050 AAATATTTTATTATTTAATTATATTTAATTAAATATTTAATAATTAAAAACAATCCAAATATTTA
1 AAATATTTAATTAGTTAA-T-TATTTAATT--ATATTTAATAATTAAAAACAACCCAAATATTTA
*
25115 AATAA
62 ATTAA
*
25120 TTAATTATTTAATTA
1 --AAATATTTAATTA
25135 AAAATATTTT
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
66 16 0.23
67 1 0.01
68 8 0.11
70 34 0.49
72 11 0.16
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.46
Consensus pattern (66 bp):
AAATATTTAATTAGTTAATTATTTAATTATATTTAATAATTAAAAACAACCCAAATATTTAATTA
A
Found at i:25129 original size:86 final size:86
Alignment explanation
Indices: 25039--25204 Score: 323
Period size: 86 Copynumber: 1.9 Consensus size: 86
25029 ATAACCCAAA
*
25039 TATTTAATTAAAAATATTTTATTATTTAATTATATTTAATTAAATATTTAATAATTAAAAACAAT
1 TATTTAATTAAAAATATTTTATTAGTTAATTATATTTAATTAAATATTTAATAATTAAAAACAAT
25104 CCAAATATTTAAATAATTAAT
66 CCAAATATTTAAATAATTAAT
25125 TATTTAATTAAAAATATTTTATTAGTTAATTATATTTAATTAAATATTTAATAATTAAAAACAAT
1 TATTTAATTAAAAATATTTTATTAGTTAATTATATTTAATTAAATATTTAATAATTAAAAACAAT
25190 CCAAATATTTAAATA
66 CCAAATATTTAAATA
25205 TTTA
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 79 1.00
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.46
Consensus pattern (86 bp):
TATTTAATTAAAAATATTTTATTAGTTAATTATATTTAATTAAATATTTAATAATTAAAAACAAT
CCAAATATTTAAATAATTAAT
Found at i:25140 original size:22 final size:22
Alignment explanation
Indices: 25114--25176 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 22
25104 CCAAATATTT
25114 AAATAATTAATTATTTAATTAA
1 AAATAATTAATTATTTAATTAA
* * * *
25136 AAATATTTTATTAGTTAATTAT
1 AAATAATTAATTATTTAATTAA
** *
25158 ATTTAATTAAATATTTAAT
1 AAATAATTAATTATTTAAT
25177 AATTAAAAAC
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
AAATAATTAATTATTTAATTAA
Done.