Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010552.1 Kokia drynarioides strain JFW-HI SEQ_125472, 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: 4675
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32
Warning! 52 characters in sequence are not A, C, G, or T
Found at i:2482 original size:70 final size:68
Alignment explanation
Indices: 2395--2532 Score: 249
Period size: 70 Copynumber: 2.0 Consensus size: 68
2385 TCCTCGATCC
2395 TTACCCATTACAGGCTCACATGGACGAGTTCAGTTTAGGGGGACGTATTACCCACATGTTTGCAC
1 TTACCCATTACAGGCTCACATGGACGAGTTCAGTTTA-GGGGACGTATTACCCACATGTTTGCAC
2460 GGAA
65 GGAA
*
2464 NTTACCCATTACAGGCTCACATGGACGAGTTCGGTTTAGGGGACGTATTACCCACATGTTTGCAC
1 -TTACCCATTACAGGCTCACATGGACGAGTTCAGTTTAGGGGACGTATTACCCACATGTTTGCAC
2529 GGAA
65 GGAA
2533 GTGAAAACTT
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
69 31 0.46
70 36 0.54
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.26
Consensus pattern (68 bp):
TTACCCATTACAGGCTCACATGGACGAGTTCAGTTTAGGGGACGTATTACCCACATGTTTGCACG
GAA
Found at i:3724 original size:30 final size:29
Alignment explanation
Indices: 3700--3763 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
3690 AAAATGAGAC
3700 TTTTCGGATACTCGGGGGCAAAAATGGTAA
1 TTTT-GGATACTCGGGGGCAAAAATGGTAA
* ** *
3730 TTTTGGATTCTCGGGGG-TGATATGGTAA
1 TTTTGGATACTCGGGGGCAAAAATGGTAA
3758 TTTTGG
1 TTTTGG
3764 GAAAATTTGG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 14 0.47
29 12 0.40
30 4 0.13
ACGTcount: A:0.22, C:0.09, G:0.33, T:0.36
Consensus pattern (29 bp):
TTTTGGATACTCGGGGGCAAAAATGGTAA
Found at i:3966 original size:59 final size:59
Alignment explanation
Indices: 3861--4303 Score: 357
Period size: 59 Copynumber: 7.5 Consensus size: 59
3851 GGACATCTGG
* * *
3861 GGGT-AAAATGGTAATTTTTGGAAG-TTCGAGGCTAAAAATGGAATTTTTGGAAGTTTGA
1 GGGTAAAAATGG-AATTTTTGGAAGTTTCGAGGGTAAAAATGGGATTTTTGGAAGTTCGA
** * **
3919 GGCCAAAAATTGAATTTTTGGAAG-TTCGAGGGGTAAAAATGGGATTTTTTAAAAGTTCGA
1 GGGTAAAAATGGAATTTTTGGAAGTTTCGA-GGGTAAAAATGGGA-TTTTTGGAAGTTCGA
* * * * *
3979 GGGTAAAAATGGAATTTATGGTAGTTTTG-GGGTTAAAAAAGGGATTTTTGGAAGTTCGG
1 GGGTAAAAATGGAATTTTTGGAAGTTTCGAGGG-TAAAAATGGGATTTTTGGAAGTTCGA
* * * *
4038 GGGTAAAAATGGAGTTTTTAGAAGTTTCGA-GGTCAAAAATAGGATTTTTGGAAGTTCGG
1 GGGTAAAAATGGAATTTTTGGAAGTTTCGAGGGT-AAAAATGGGATTTTTGGAAGTTCGA
* *** ** * * *
4097 GGGTAAATACAAAATTTTTAAAAGTTTCCA-GGTCAAAAATGGGATTTTTGGAAGTACGG
1 GGGTAAAAATGGAATTTTTGGAAGTTTCGAGGGT-AAAAATGGGATTTTTGGAAGTTCGA
* * * * *
4156 GGGTAAAAATGGTATTTTTAGAAGTTTTG-GGGTTAAAAATAGGATTTTTGGAAGTT-TA
1 GGGTAAAAATGGAATTTTTGGAAGTTTCGAGGG-TAAAAATGGGATTTTTGGAAGTTCGA
* * * * *
4214 GGGGTAAAAATGAAATTTTTAGAAGTTTTG-GGGTCAAAAAATGCGATTTTTGGAAGTATTG-
1 -GGGTAAAAATGGAATTTTTGGAAGTTTCGAGGGT--AAAAATGGGATTTTTGGAAGT-TCGA
* *
4275 GGGTAAAAACGAAATTTTTTGGATAGTTT
1 GGGTAAAAATGGAA-TTTTTGGA-AGTTT
4304 AGGGACCTCA
Statistics
Matches: 316, Mismatches: 53, Indels: 28
0.80 0.13 0.07
Matches are distributed among these distances:
58 21 0.07
59 205 0.65
60 74 0.23
61 11 0.03
62 5 0.02
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (59 bp):
GGGTAAAAATGGAATTTTTGGAAGTTTCGAGGGTAAAAATGGGATTTTTGGAAGTTCGA
Found at i:4241 original size:29 final size:29
Alignment explanation
Indices: 3860--4307 Score: 282
Period size: 29 Copynumber: 15.1 Consensus size: 29
3850 TGGACATCTG
*
3860 GGGGT-AAAATGGTAATTTTTGGAAG-TTC
1 GGGGTAAAAATGG-AATTTTTGGAAGTTTA
*
3888 GAGGCTAAAAATGGAATTTTTGGAAGTTT-
1 G-GGGTAAAAATGGAATTTTTGGAAGTTTA
** * *
3917 GAGGCCAAAAATTGAATTTTTGGAAGTTCGA
1 G-GGGTAAAAATGGAATTTTTGGAAGTT-TA
* ** *
3948 GGGGTAAAAATGGGATTTTTTAAAAG-TTC
1 GGGGTAAAAAT-GGAATTTTTGGAAGTTTA
* * *
3977 GAGGGTAAAAATGGAATTTATGGTAGTTTT
1 G-GGGTAAAAATGGAATTTTTGGAAGTTTA
* * **
4007 GGGGTTAAAAAAGGGATTTTTGGAAGTTCG
1 GGGG-TAAAAATGGAATTTTTGGAAGTTTA
* * *
4037 GGGGTAAAAATGGAGTTTTTAGAAGTTTC
1 GGGGTAAAAATGGAATTTTTGGAAGTTTA
* **
4066 GAGGTCAAAAATAGG-ATTTTTGGAAGTTCG
1 GGGGT-AAAAAT-GGAATTTTTGGAAGTTTA
* *** ** *
4096 GGGGTAAATACAAAATTTTTAAAAGTTTC
1 GGGGTAAAAATGGAATTTTTGGAAGTTTA
** * ***
4125 CAGGTCAAAAATGGGATTTTTGGAAGTACG
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTA
* * *
4155 GGGGTAAAAATGGTATTTTTAGAAGTTTT
1 GGGGTAAAAATGGAATTTTTGGAAGTTTA
4184 GGGGTTAAAAATAGG-ATTTTTGGAAGTTTA
1 GGGG-TAAAAAT-GGAATTTTTGGAAGTTTA
* * *
4214 GGGGTAAAAATGAAATTTTTAGAAGTTTT
1 GGGGTAAAAATGGAATTTTTGGAAGTTTA
4243 GGGGTCAAAAAATGCG-ATTTTTGGAAGTATT-
1 GGGGT--AAAAATG-GAATTTTTGGAAGT-TTA
* *
4274 GGGGTAAAAACGAAATTTTTTGGATAGTTTA
1 GGGGTAAAAATGGAA-TTTTTGGA-AGTTTA
4305 GGG
1 GGG
4308 ACCTCAAGGG
Statistics
Matches: 324, Mismatches: 72, Indels: 45
0.73 0.16 0.10
Matches are distributed among these distances:
28 2 0.01
29 150 0.46
30 126 0.39
31 44 0.14
32 2 0.01
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34
Consensus pattern (29 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTTA
Done.