Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012463.1 Kokia drynarioides strain JFW-HI SEQ_127467, 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: 69573
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:59 original size:23 final size:23
Alignment explanation
Indices: 29--118 Score: 78
Period size: 23 Copynumber: 3.9 Consensus size: 23
19 TGTGCTCAGT
29 ACTTTGTGTACTCTCTGTTTAGC
1 ACTTTGTGTACTCTCTGTTTAGC
* *
52 ACTTTGTGTGCTCTCTGTTGCCCAGC
1 ACTTTGTGTACTCTCTGTT---TAGC
* *
78 AC-TTATG-AGCTCTCTGTTTAGT
1 ACTTTGTGTA-CTCTCTGTTTAGC
*
100 ACTTCG-GTACTCTCTGTTT
1 ACTTTGTGTACTCTCTGTTT
119 GTTCCGTTTA
Statistics
Matches: 53, Mismatches: 8, Indels: 13
0.72 0.11 0.18
Matches are distributed among these distances:
22 15 0.28
23 20 0.38
25 13 0.25
26 5 0.09
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.44
Consensus pattern (23 bp):
ACTTTGTGTACTCTCTGTTTAGC
Found at i:3624 original size:39 final size:39
Alignment explanation
Indices: 3440--3615 Score: 298
Period size: 39 Copynumber: 4.5 Consensus size: 39
3430 TGGCATCAAG
*
3440 GACTCCGGACCAAGCCCTGGAACGGGAAATAAGTTTACC
1 GACTCCGGTCCAAGCCCTGGAACGGGAAATAAGTTTACC
3479 GACTCCGGTCCAAGCCCTGGAACGGGAAATAAGTTTACC
1 GACTCCGGTCCAAGCCCTGGAACGGGAAATAAGTTTACC
*
3518 GACTCTGGTCCAAGCCCTGGAACGGGAAATAAGTTTACC
1 GACTCCGGTCCAAGCCCTGGAACGGGAAATAAGTTTACC
* *
3557 GACTCCGGTCCGAGCCCTGGAACGGGAAATAGGTTTACC
1 GACTCCGGTCCAAGCCCTGGAACGGGAAATAAGTTTACC
* *
3596 AACTCCGGTCCGAGCCCTGG
1 GACTCCGGTCCAAGCCCTGG
3616 TGTGGGAAAC
Statistics
Matches: 131, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 131 1.00
ACGTcount: A:0.26, C:0.29, G:0.27, T:0.18
Consensus pattern (39 bp):
GACTCCGGTCCAAGCCCTGGAACGGGAAATAAGTTTACC
Found at i:11863 original size:5 final size:5
Alignment explanation
Indices: 11853--11879 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
11843 AAACACAAAT
11853 ATTGA ATTGA ATTGA ATTGA ATTGA AT
1 ATTGA ATTGA ATTGA ATTGA ATTGA AT
11880 CATCAACCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (5 bp):
ATTGA
Found at i:15346 original size:17 final size:20
Alignment explanation
Indices: 15324--15360 Score: 53
Period size: 17 Copynumber: 2.0 Consensus size: 20
15314 TTTATCAGAT
15324 AAAAA-GAAA-AAAA-AAAA
1 AAAAAGGAAAGAAAACAAAA
15341 AAAAAGGAAAGAAAACAAAA
1 AAAAAGGAAAGAAAACAAAA
15361 GATTAACACA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.29
18 4 0.24
19 4 0.24
20 4 0.24
ACGTcount: A:0.86, C:0.03, G:0.11, T:0.00
Consensus pattern (20 bp):
AAAAAGGAAAGAAAACAAAA
Found at i:22557 original size:29 final size:28
Alignment explanation
Indices: 22502--22561 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
22492 CGTTTGGGTG
* **
22502 TTTGGTCACTTTGGCCCTTATGGTTTTT
1 TTTGGTCACTTTGGCCCCTAACGTTTTT
*
22530 TTTGGCTCACTTTGGCCCCTAACTTTTTT
1 TTTGG-TCACTTTGGCCCCTAACGTTTTT
22559 TTT
1 TTT
22562 TGTTCAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 5 0.19
29 22 0.81
ACGTcount: A:0.08, C:0.22, G:0.17, T:0.53
Consensus pattern (28 bp):
TTTGGTCACTTTGGCCCCTAACGTTTTT
Found at i:22692 original size:25 final size:25
Alignment explanation
Indices: 22662--22710 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
22652 AAGTCCACAT
*
22662 ATGCAACTGCTGACGTGGCACTATG
1 ATGCAACTGCTGACGTGACACTATG
*
22687 ATGCAACTTCTGACGTGACACTAT
1 ATGCAACTGCTGACGTGACACTAT
22711 TTTATCTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (25 bp):
ATGCAACTGCTGACGTGACACTATG
Found at i:22750 original size:11 final size:11
Alignment explanation
Indices: 22734--22771 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
22724 CTATGTCAGC
22734 AAATAATTTTA
1 AAATAATTTTA
22745 AAATAATTTTA
1 AAATAATTTTA
22756 AAATTAA-TTTA
1 AAA-TAATTTTA
22767 AAATA
1 AAATA
22772 TAAAATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 2 0.08
11 21 0.81
12 3 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
AAATAATTTTA
Found at i:23621 original size:29 final size:31
Alignment explanation
Indices: 23583--23652 Score: 108
Period size: 32 Copynumber: 2.3 Consensus size: 31
23573 TTAAAATATT
23583 AAAATAATTTT-AATAATTTTATA-TTTTAA
1 AAAATAATTTTAAATAATTTTATATTTTTAA
*
23612 AAAATAATTTTAAAATAATTTTATATTTTTTA
1 AAAATAATTTT-AAATAATTTTATATTTTTAA
23644 AAAATAATT
1 AAAATAATT
23653 AATTTTTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
29 11 0.30
31 12 0.32
32 14 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (31 bp):
AAAATAATTTTAAATAATTTTATATTTTTAA
Found at i:23660 original size:20 final size:20
Alignment explanation
Indices: 23619--23660 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
23609 TAAAAAATAA
*
23619 TTTTAAAATAATTTTATATT
1 TTTTAAAATAATTTAATATT
23639 TTTTAAAAATAA-TTAAT-TT
1 TTTT-AAAATAATTTAATATT
23658 TTT
1 TTT
23661 ATTGACGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 5 0.25
20 8 0.40
21 7 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTAAAATAATTTAATATT
Found at i:35881 original size:17 final size:18
Alignment explanation
Indices: 35853--35889 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
35843 AAACTTGAAC
35853 CAATTCACAAAGCAATCT
1 CAATTCACAAAGCAATCT
*
35871 CAATT-ACAAAGTAATCT
1 CAATTCACAAAGCAATCT
35888 CA
1 CA
35890 TCAAAAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.46, C:0.24, G:0.05, T:0.24
Consensus pattern (18 bp):
CAATTCACAAAGCAATCT
Found at i:38291 original size:25 final size:23
Alignment explanation
Indices: 38250--38295 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
38240 CCAATTAGGG
38250 AATTATTGTTTAGATTTAATTCA
1 AATTATTGTTTAGATTTAATTCA
*
38273 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TGTTTAG-ATTTAATT
38296 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (23 bp):
AATTATTGTTTAGATTTAATTCA
Found at i:47472 original size:34 final size:31
Alignment explanation
Indices: 47434--47520 Score: 99
Period size: 28 Copynumber: 2.8 Consensus size: 31
47424 TTCTAAAATT
47434 TTTTAAATATATTAAATATATATTTATATTTACG
1 TTTTAAAT-T-TT-AATATATATTTATATTTACG
*
47468 TTTTAAATTTT--TATA-ATTTATATTTACT
1 TTTTAAATTTTAATATATATTTATATTTACG
*
47496 TTTTAAATTTTTAATTTATATTTAT
1 TTTTAAA-TTTTAATATATATTTAT
47521 TTTTTCTCAT
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
28 19 0.40
29 8 0.17
31 3 0.06
32 8 0.17
33 1 0.02
34 8 0.17
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.61
Consensus pattern (31 bp):
TTTTAAATTTTAATATATATTTATATTTACG
Found at i:47517 original size:26 final size:28
Alignment explanation
Indices: 47450--47525 Score: 111
Period size: 28 Copynumber: 2.8 Consensus size: 28
47440 ATATATTAAA
*
47450 TATATATTTATATTTACGTTTTAAATTTT
1 TATA-ATTTATATTTACTTTTTAAATTTT
47479 TATAATTTATATTTACTTTTTAAA-TTT
1 TATAATTTATATTTACTTTTTAAATTTT
*
47506 T-TAATTTATATTTATTTTTT
1 TATAATTTATATTTACTTTTT
47526 CTCATCAATC
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
26 18 0.40
27 4 0.09
28 19 0.42
29 4 0.09
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (28 bp):
TATAATTTATATTTACTTTTTAAATTTT
Found at i:52866 original size:21 final size:22
Alignment explanation
Indices: 52831--52872 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
52821 CAAGGCCAAA
* *
52831 ATAATTTTTTATTTATTTTTTT
1 ATAATTTTATATTTACTTTTTT
52853 ATAA-TTTATATTTACTTTTT
1 ATAATTTTATATTTACTTTTT
52873 CTCATTAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (22 bp):
ATAATTTTATATTTACTTTTTT
Found at i:68520 original size:25 final size:25
Alignment explanation
Indices: 68482--68530 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
68472 AAAATTTTTA
**
68482 TTTTACATTTATTTGTATTTAATAT
1 TTTTACATTTATTTAAATTTAATAT
68507 TTTTA-ATTTAATTTAAATTTAATA
1 TTTTACATTT-ATTTAAATTTAATA
68531 AATTACAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (25 bp):
TTTTACATTTATTTAAATTTAATAT
Done.