Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007861.1 Kokia drynarioides strain JFW-HI SEQ_122500, 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: 6855
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Found at i:3406 original size:10 final size:10
Alignment explanation
Indices: 3383--3454 Score: 51
Period size: 10 Copynumber: 7.4 Consensus size: 10
3373 CTAGTTTAAG
*
3383 TTTTTATGATT
1 TTTTTAT-AAT
3394 TTTTTATAA-
1 TTTTTATAAT
*
3403 TTTTTATAAG
1 TTTTTATAAT
*
3413 TTTATATAA-
1 TTTTTATAAT
* *
3422 -TTTTAAAAC
1 TTTTTATAAT
3431 TTTTTATAAT
1 TTTTTATAAT
* *
3441 TATTTATTAT
1 TTTTTATAAT
3451 TTTT
1 TTTT
3455 AAGAATTCTA
Statistics
Matches: 49, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
8 6 0.12
9 9 0.18
10 27 0.55
11 7 0.14
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:3438 original size:18 final size:18
Alignment explanation
Indices: 3394--3441 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
3384 TTTTATGATT
* *
3394 TTTTTATAATTTTTATAAG
1 TTTTTATAA-TTTTAAAAC
*
3413 TTTATATAATTTTAAAAC
1 TTTTTATAATTTTAAAAC
3431 TTTTTATAATT
1 TTTTTATAATT
3442 ATTTATTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (18 bp):
TTTTTATAATTTTAAAAC
Found at i:3564 original size:16 final size:15
Alignment explanation
Indices: 3539--3587 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
3529 CTAGAAGTTA
*
3539 TTATATTTTATAATAT
1 TTATAATTTA-AATAT
3555 TTATAATTTAAATAT
1 TTATAATTTAAATAT
*
3570 ATATCAATTTAAATAT
1 TTAT-AATTTAAATAT
3586 TT
1 TT
3588 TTATAAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 8 0.28
16 21 0.72
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (15 bp):
TTATAATTTAAATAT
Found at i:3637 original size:18 final size:19
Alignment explanation
Indices: 3606--3642 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
3596 TTTCTCTAAT
*
3606 TTTTATAATGTTTTTATGA
1 TTTTATAATATTTTTATGA
3625 TTTT-TAATATTTTTATGA
1 TTTTATAATATTTTTATGA
3643 GAAAAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (19 bp):
TTTTATAATATTTTTATGA
Found at i:3941 original size:21 final size:20
Alignment explanation
Indices: 3917--3959 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
3907 TTTCTTTTTC
3917 AAAACTAATAATTATTAATAA
1 AAAACTAATAATT-TTAATAA
* * *
3938 AAAATTAATGATTTTCATAA
1 AAAACTAATAATTTTAATAA
3958 AA
1 AA
3960 TAATTAGCAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (20 bp):
AAAACTAATAATTTTAATAA
Found at i:6052 original size:59 final size:58
Alignment explanation
Indices: 5984--6186 Score: 171
Period size: 59 Copynumber: 3.4 Consensus size: 58
5974 TGCATTTTAA
*
5984 ACATTCGAGGGTAAAACGGTAATTTTTAGAAAAATCGAGATAAAAAATAAAATTTTTGG
1 ACATTCGAGGGTAAAA-GGTAATTTTTAGAAAAATCGAGATCAAAAATAAAATTTTTGG
* * * ** * **
6043 ACATCCGAGGATAAAATGATAATTTTTAGAAAAAT-GAGGATCAAAAACGAATTTTTTAA
1 ACATTCGAGGGTAAAA-GGTAATTTTTAGAAAAATCGA-GATCAAAAATAAAATTTTTGG
** *
6102 ACATTCG-GGAGTAAAAGTGTAATTTTT-GAAAGTTTCGAGGTCAAAAATAAAATTTTTGGG
1 ACATTCGAGG-GTAAAAG-GTAATTTTTAGAAA-AATCGAGATCAAAAATAAAATTTTT-GG
** *
6162 AGTTTAG-GGGTAAAATGGTAATTTT
1 ACATTCGAGGGTAAAA-GGTAATTTT
6187 CGAAAGTTTC
Statistics
Matches: 113, Mismatches: 24, Indels: 14
0.75 0.16 0.09
Matches are distributed among these distances:
58 9 0.08
59 95 0.84
60 9 0.08
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (58 bp):
ACATTCGAGGGTAAAAGGTAATTTTTAGAAAAATCGAGATCAAAAATAAAATTTTTGG
Found at i:6216 original size:59 final size:59
Alignment explanation
Indices: 6112--6245 Score: 141
Period size: 59 Copynumber: 2.3 Consensus size: 59
6102 ACATTCGGGA
* * * *
6112 GTAAAA-GTGTAATTTTTGAAAGTTTCGAGGTCAAAAATAAAATTTTTGGGAGTTTAG-GG
1 GTAAAATG-GTAATTTTCGAAAGTTTCAACGTCAAAAATAAAATTTTTGGAAG-TTAGAGG
* * *
6171 GTAAAATGGTAATTTTCGAAAGTTTCAACGT-AAAAATCGAGATTTTTGGAAGTTCGAGG
1 GTAAAATGGTAATTTTCGAAAGTTTCAACGTCAAAAAT-AAAATTTTTGGAAGTTAGAGG
6230 GTAAAAAT-GTAATTTT
1 GT-AAAATGGTAATTTT
6246 TTGGAAGTTT
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
58 9 0.14
59 49 0.77
60 6 0.09
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.35
Consensus pattern (59 bp):
GTAAAATGGTAATTTTCGAAAGTTTCAACGTCAAAAATAAAATTTTTGGAAGTTAGAGG
Found at i:6356 original size:31 final size:30
Alignment explanation
Indices: 6112--6435 Score: 176
Period size: 30 Copynumber: 10.8 Consensus size: 30
6102 ACATTCGGGA
* *
6112 GTAAAAGTGTAATTTTT-GAAAGTTTCGA-G
1 GTAAAAATGGAATTTTTGGAAAG-TTCGAGG
** * *
6141 GTCAAAAATAAAATTTTTGG-GAGTT-TAGGG
1 GT-AAAAATGGAATTTTTGGAAAGTTCGA-GG
* **
6171 GT-AAAATGGTAA-TTTTCGAAAGTTTC-AAC
1 GTAAAAATGG-AATTTTTGGAAAG-TTCGAGG
*
6200 GTAAAAATCGAGATTTTTGG-AAGTTCGAGG
1 GTAAAAATGGA-ATTTTTGGAAAGTTCGAGG
* * *
6230 GTAAAAATGTAATTTTTTGG-AAGTTTTG-GA
1 GTAAAAATGGAA-TTTTTGGAAAG-TTCGAGG
* * *
6260 ATAAAAAATGGAAGTTTTGG-AAGTTTTG-GG
1 GT-AAAAATGGAATTTTTGGAAAG-TTCGAGG
** *
6290 GTAAAAATATAATTTTTGGAAAAATT-GA-G
1 GTAAAAATGGAATTTTTGG-AAAGTTCGAGG
*
6319 GTCAAAAATGGATTTTTTGGAAAGTTCGAGG
1 GT-AAAAATGGAATTTTTGGAAAGTTCGAGG
*
6350 GTCAAAAATGGATTTTTTGGAAAGTTCGAGG
1 GT-AAAAATGGAATTTTTGGAAAGTTCGAGG
* *
6381 GTCAAAAATGGAA-TTTTGAAAAGTT-TAGG
1 GT-AAAAATGGAATTTTTGGAAAGTTCGAGG
* *
6410 GATAAAAATGTAATTTTTGAAAAGTT
1 G-TAAAAATGGAATTTTTGGAAAGTT
6436 TAAGTGTCAA
Statistics
Matches: 236, Mismatches: 36, Indels: 45
0.74 0.11 0.14
Matches are distributed among these distances:
28 11 0.05
29 51 0.22
30 110 0.47
31 64 0.27
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.35
Consensus pattern (30 bp):
GTAAAAATGGAATTTTTGGAAAGTTCGAGG
Found at i:6434 original size:60 final size:59
Alignment explanation
Indices: 6263--6471 Score: 185
Period size: 60 Copynumber: 3.5 Consensus size: 59
6253 TTTTGGAATA
* * * * *
6263 AAAAATGGAAGTTTTG-GAAGTTTTGGGGTAAAAATATAATTTTTGGAAAAATTGA-GGTC
1 AAAAATGGAA-TTTTGAAAAGTTTAGGGATAAAAATGTAATTTTT-GAAAAGTTGAGGGTC
* * * * * *
6322 AAAAATGGATTTTTTGGAAAGTTCGAGGG-TCAAAAATGGATTTTTTGGAAAGTTCGAGGGTC
1 AAAAATGGA-ATTTTGAAAAGTT-TAGGGAT-AAAAATGTAATTTTTGAAAAGTT-GAGGGTC
* *
6384 AAAAATGGAATTTTGAAAAGTTTAGGGATAAAAATGTAATTTTTGAAAAGTTTAAGTGTC
1 AAAAATGGAATTTTGAAAAGTTTAGGGATAAAAATGTAATTTTTGAAAAG-TTGAGGGTC
6444 AAAATAT--AATTTTGGAAAAGTTTAGGGA
1 AAAA-ATGGAATTTT-GAAAAGTTTAGGGA
6472 CCTTCAAGGT
Statistics
Matches: 123, Mismatches: 17, Indels: 19
0.77 0.11 0.12
Matches are distributed among these distances:
59 20 0.16
60 57 0.46
61 33 0.27
62 13 0.11
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.33
Consensus pattern (59 bp):
AAAAATGGAATTTTGAAAAGTTTAGGGATAAAAATGTAATTTTTGAAAAGTTGAGGGTC
Done.