Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015264.1 Kokia drynarioides strain JFW-HI SEQ_130309, 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: 18685
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.34
Warning! 352 characters in sequence are not A, C, G, or T
Found at i:10115 original size:96 final size:96
Alignment explanation
Indices: 9931--10122 Score: 230
Period size: 96 Copynumber: 2.0 Consensus size: 96
9921 ACTTTTGCAA
* ** *
9931 AAGGATATTCGATTATCTCGATTTGAAGAAAGGTCACACCTAGTAAGTTAAGGCGCAATATTTCA
1 AAGGATATTCAATTATCTCGATTTGAAGAAAAATCACACCTAGTAAGTTAAGGCACAATATTTCA
*
9996 GAATCGAAGATAAGGAAACATTGCCTCGATT
66 GAATCGAAGATAAAGAAACATTGCCTCGATT
* * * *
10027 AAGGGTATTCAATTATTTCGATTTGAAGAAAAATTACACCTAGTGAGTTAAGGCACAA-ATTTTC
1 AAGGATATTCAATTATCTCGATTTGAAGAAAAATCACACCTAGTAAGTTAAGGCACAATA-TTTC
*
10091 -GAAACTCGAA-ATAAA-AGAATATTGCCTCGATT
65 AG-AA-TCGAAGATAAAGA-AACATTGCCTCGATT
10123 TTTTAAAGCT
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
95 3 0.04
96 74 0.90
97 5 0.06
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.29
Consensus pattern (96 bp):
AAGGATATTCAATTATCTCGATTTGAAGAAAAATCACACCTAGTAAGTTAAGGCACAATATTTCA
GAATCGAAGATAAAGAAACATTGCCTCGATT
Found at i:10512 original size:30 final size:30
Alignment explanation
Indices: 10450--11117 Score: 503
Period size: 29 Copynumber: 22.8 Consensus size: 30
10440 ATTCGAGGCC
* ** *
10450 AAAAATGGGTTTTTTGGAAGTTCGATGG-T
1 AAAAATGGGATTTTTGGAAGTTTTAGGGTT
***
10479 AAAAATTAAATTTTTGGAAGTTTTAGGGTT
1 AAAAATGGGATTTTTGGAAGTTTTAGGGTT
** * *
10509 AAAAATGGGATTTTTAAAAG-TTCAGGGAT
1 AAAAATGGGATTTTTGGAAGTTTTAGGGTT
* * * * *
10538 AAAAATAGAATTTTTAGAAG-TTTCGAGGTC
1 AAAAATGGGATTTTTGGAAGTTTTAG-GGTT
* *
10568 AAAAATGGGATTTTTGGAAGTCTTAGGGTC
1 AAAAATGGGATTTTTGGAAGTTTTAGGGTT
* * **
10598 AAAAATGGGATTTTTAGAAATTCGAGGG-T
1 AAAAATGGGATTTTTGGAAGTTTTAGGGTT
* * *
10627 -AAAAT-AGAATTTTGGAAGTTTTGGGGTT
1 AAAAATGGGATTTTTGGAAGTTTTAGGGTT
* **
10655 -AAAATGGGATTTTTAGAAGTTCGAGGG-T
1 AAAAATGGGATTTTTGGAAGTTTTAGGGTT
* * *
10683 AAAAA-GGAGTTTTTTAGAAG-TTTCGAGGTT
1 AAAAATGG-GATTTTTGGAAGTTTTAG-GGTT
**
10713 AAAAATGGGATTTTTGGAAGTTCGA-GGTT
1 AAAAATGGGATTTTTGGAAGTTTTAGGGTT
* *
10742 AAAAATGGGATTTTTGGAAG-TTCAGGGGT
1 AAAAATGGGATTTTTGGAAGTTTTAGGGTT
* * * * * *
10771 AAAAATAGAATTTTTAGAAG-TTTCGAAGTC
1 AAAAATGGGATTTTTGGAAGTTTTAG-GGTT
* * *
10801 AAAAATGAGATTTTTGGAAG-TTTGGGGGT
1 AAAAATGGGATTTTTGGAAGTTTTAGGGTT
* * *
10830 -AAAATGGAATTTTTGGAAGTTTTGGGGTC
1 AAAAATGGGATTTTTGGAAGTTTTAGGGTT
*
10859 AAAAATGGGATTTTTGGAAGTTTTAGGGTA
1 AAAAATGGGATTTTTGGAAGTTTTAGGGTT
*
10889 AAAAATGGGA-TTTTGGAAGTTTTAGGGTA
1 AAAAATGGGATTTTTGGAAGTTTTAGGGTT
* **
10918 AAAAATGGGATTTTTAGAAGTTCGAGGG-T
1 AAAAATGGGATTTTTGGAAGTTTTAGGGTT
* * **
10947 AAAAATGGAGTTTTTTAGAAGTTTCGGGGTT
1 AAAAATGG-GATTTTTGGAAGTTTTAGGGTT
* * *
10978 AAAAATGAGATTTTTGGAAG-TTTGGGGTC
1 AAAAATGGGATTTTTGGAAGTTTTAGGGTT
**
11007 AAAAATGGGATTTTTGGAAGTTCAAGGG-T
1 AAAAATGGGATTTTTGGAAGTTTTAGGGTT
* * * *
11036 AAAAATGGAATTTTTAGAAGTTTTGGGGTC
1 AAAAATGGGATTTTTGGAAGTTTTAGGGTT
** * * *
11066 AAAAATGGGATTTTT-TTATTTTTGGGGGT
1 AAAAATGGGATTTTTGGAAGTTTTAGGGTT
* *
11095 AAAAATGGAATTTTTAGAAGTTT
1 AAAAATGGGATTTTTGGAAGTTT
11118 CGGGGACCTT
Statistics
Matches: 504, Mismatches: 114, Indels: 41
0.76 0.17 0.06
Matches are distributed among these distances:
27 14 0.03
28 35 0.07
29 244 0.48
30 197 0.39
31 14 0.03
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.36
Consensus pattern (30 bp):
AAAAATGGGATTTTTGGAAGTTTTAGGGTT
Found at i:11117 original size:59 final size:58
Alignment explanation
Indices: 10420--11122 Score: 527
Period size: 59 Copynumber: 12.0 Consensus size: 58
10410 AATTAAGGGT
* * ** ** * *
10420 TAAAAATGGAATTTTTAGACA-TTCGAGGCCAAAAATGGGTTTTTTGGAAG-TTCGATGG
1 TAAAAATGGGATTTTTGGA-AGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTG-GGG
*** ** * ** ** *
10478 TAAAAATTAAATTTTTGGAAGTTTTAGGGTTAAAAATGGGATTTTTAAAAGTTCAGGGA
1 TAAAAATGGGATTTTTGGAAGTTCGAGGG-TAAAAATGGAATTTTTGGAAGTTTTGGGG
* * * * * *
10537 TAAAAATAGAATTTTTAGAAGTTTCGA-GGTCAAAAATGGGATTTTTGGAAGTCTTAGGG
1 TAAAAATGGGATTTTTGGAAG-TTCGAGGGT-AAAAATGGAATTTTTGGAAGTTTTGGGG
* * *
10596 TCAAAAATGGGATTTTTAGAAATTCGAGGGT-AAAATAGAA-TTTTGGAAGTTTTGGGG
1 T-AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGG
* * * * * *
10653 TTAAAATGGGATTTTTAGAAGTTCGAGGGTAAAAA-GGAGTTTTTTAGAAGTTTCGAGGT
1 TAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGA-ATTTTTGGAAGTTTTG-GGG
* * **
10712 TAAAAATGGGATTTTTGGAAGTTCGAGGTTAAAAATGGGATTTTTGGAAGTTCAGGGG
1 TAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGG
* * * * *
10770 TAAAAATAGAATTTTTAGAAGTTTCGA-AGTCAAAAAT-GAGATTTTTGGAAGTTTGGGGG
1 TAAAAATGGGATTTTTGGAAG-TTCGAGGGT-AAAAATGGA-ATTTTTGGAAGTTTTGGGG
* * * *
10829 T-AAAATGGAATTTTTGGAAGTTTTG-GGGTCAAAAATGGGATTTTTGGAAGTTTTAGGG
1 TAAAAATGGGATTTTTGGAAG-TTCGAGGGT-AAAAATGGAATTTTTGGAAGTTTTGGGG
** * * *
10887 TAAAAAATGGGA-TTTTGGAAGTTTTAGGGTAAAAAATGGGATTTTTAGAAG-TTCGAGGG
1 T-AAAAATGGGATTTTTGGAAGTTCGAGGGT-AAAAATGGAATTTTTGGAAGTTTTG-GGG
* *
10946 TAAAAATGGAGTTTTTTAGAAGTTTCG-GGGTTAAAAAT-GAGATTTTTGGAAG-TTTGGGG
1 TAAAAATGG-GATTTTTGGAAG-TTCGAGGG-TAAAAATGGA-ATTTTTGGAAGTTTTGGGG
* *
11005 TCAAAAATGGGATTTTTGGAAGTTCAAGGGTAAAAATGGAATTTTTAGAAGTTTTGGGG
1 T-AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGG
** ** * * * *
11064 TCAAAAATGGGATTTTTTTATTTTTGGGGGTAAAAATGGAATTTTTAGAAGTTTCGGGG
1 T-AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGG
11123 ACCTTTAGGG
Statistics
Matches: 526, Mismatches: 89, Indels: 59
0.78 0.13 0.09
Matches are distributed among these distances:
56 29 0.06
57 21 0.04
58 144 0.27
59 256 0.49
60 73 0.14
61 3 0.01
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.35
Consensus pattern (58 bp):
TAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGG
Found at i:13018 original size:17 final size:17
Alignment explanation
Indices: 12960--13029 Score: 79
Period size: 17 Copynumber: 4.1 Consensus size: 17
12950 TTTGGACTTT
* *
12960 TTTAATTTTGAAATTAAA
1 TTTAAATTT-AAAATAAA
* *
12978 TTTAAATTT-AGATTAA
1 TTTAAATTTAAAATAAA
12994 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
13011 TCTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
13028 TT
1 TT
13030 AAAAAGAGGG
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
16 13 0.30
17 22 0.51
18 8 0.19
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:13024 original size:7 final size:6
Alignment explanation
Indices: 12960--13022 Score: 53
Period size: 6 Copynumber: 11.0 Consensus size: 6
12950 TTTGGACTTT
* *
12960 TTTAAT TTTGAAA -TTAAA TTTAAA TTTAGA -TT-AA TTTAAA TTTAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
13006 -ATAAA TCTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA
13023 ATAAATTAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
4 1 0.02
5 11 0.24
6 32 0.70
7 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:15844 original size:92 final size:92
Alignment explanation
Indices: 15743--15918 Score: 289
Period size: 92 Copynumber: 1.9 Consensus size: 92
15733 TGGTAGTGAG
* * * * *
15743 TTTTTTTATTAAGTGTTGTTAGTTTGGGTTAAGATGCAATTGTTTGATAGGTGGATTATGGTTCG
1 TTTTTTTATTAAGTGTTGTTAGTTTGAGTTAAGATGCAATTGTTTGATAGATGAATTATAGTTCA
15808 AGTGTTTGCTGCAATTTGATGGTAAAT
66 AGTGTTTGCTGCAATTTGATGGTAAAT
* *
15835 TTTTTTTATTAGGTGTTGTTAGTTTGAGTTAAGATGCAATTGTTTGATAGATGAATTATAGTTTA
1 TTTTTTTATTAAGTGTTGTTAGTTTGAGTTAAGATGCAATTGTTTGATAGATGAATTATAGTTCA
15900 AGTGTTTGCTGCAATTTGA
66 AGTGTTTGCTGCAATTTGA
15919 CACCTGGTTT
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
92 77 1.00
ACGTcount: A:0.23, C:0.04, G:0.25, T:0.48
Consensus pattern (92 bp):
TTTTTTTATTAAGTGTTGTTAGTTTGAGTTAAGATGCAATTGTTTGATAGATGAATTATAGTTCA
AGTGTTTGCTGCAATTTGATGGTAAAT
Done.