Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010776.1 Kokia drynarioides strain JFW-HI SEQ_125739, 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: 34756
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Warning! 38 characters in sequence are not A, C, G, or T
Found at i:2349 original size:29 final size:29
Alignment explanation
Indices: 2250--2351 Score: 79
Period size: 29 Copynumber: 3.6 Consensus size: 29
2240 AATGCCCAAG
** *
2250 GTAAAATGGTAA-TTTTGGACACTCGGG-
1 GTAAAATGGTAATTTTTAAACATTCGGGT
*
2277 GTAAAATGGTAATTTTTGGAAA-GTTCGGAGT
1 GTAAAATGGTAATTTTT--AAACATTCGG-GT
*
2308 -TAAAAAT-GAAATTTTTAAACATTCGGGT
1 GT-AAAATGGTAATTTTTAAACATTCGGGT
*
2336 GTAAAATGGCAATTTT
1 GTAAAATGGTAATTTT
2352 GGAAAGTTTA
Statistics
Matches: 59, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
27 12 0.20
28 14 0.24
29 17 0.29
30 11 0.19
31 5 0.08
ACGTcount: A:0.35, C:0.07, G:0.24, T:0.34
Consensus pattern (29 bp):
GTAAAATGGTAATTTTTAAACATTCGGGT
Found at i:2350 original size:59 final size:58
Alignment explanation
Indices: 2262--2490 Score: 277
Period size: 59 Copynumber: 3.9 Consensus size: 58
2252 AAAATGGTAA
* *
2262 TTTTGGACACTCGGGGTAAAATGGTAATTTTTGGAAAG-TTCGGAGTTAAAAATGAAAT
1 TTTTAGACATTCGGGGTAAAATGGTAATTTTTGGAAAGTTTCGG-GTTAAAAATGAAAT
* * *
2320 TTTTAAACATTCGGGTGTAAAATGGCAA-TTTTGGAAAGTTTAGGGTTAAAAAT-AAAT
1 TTTTAGACATTCGGG-GTAAAATGGTAATTTTTGGAAAGTTTCGGGTTAAAAATGAAAT
* * *
2377 TTTTAGATATTCGAGGGTAAAATGGTGATTTTTGGAAAG-TTCGGGGTTAAAAATGGAAT
1 TTTTAGACATTCG-GGGTAAAATGGTAATTTTTGGAAAGTTTC-GGGTTAAAAATGAAAT
** * *
2436 TTTTAGACATTTAAGGGTAAAATGGTAATTTTTGGAAGGTTTCGGGTAAAAAATG
1 TTTTAGACA-TTCGGGGTAAAATGGTAATTTTTGGAAAGTTTCGGGTTAAAAATG
2491 GATTTTTTGG
Statistics
Matches: 146, Mismatches: 17, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
57 27 0.18
58 54 0.37
59 60 0.41
60 5 0.03
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (58 bp):
TTTTAGACATTCGGGGTAAAATGGTAATTTTTGGAAAGTTTCGGGTTAAAAATGAAAT
Found at i:2380 original size:29 final size:30
Alignment explanation
Indices: 2279--2527 Score: 153
Period size: 30 Copynumber: 8.4 Consensus size: 30
2269 CACTCGGGGT
*
2279 AAAATGGTAATTTTTGGAAAG-TTCGGAGTTA
1 AAAATGG-AATTTTTGGAAAGTTTAGG-GTTA
* ** *
2310 AAAATGAAATTTTT--AAACATTCGGGTGT-
1 AAAATGGAATTTTTGGAAAGTTTAGGGT-TA
2338 AAAATGGCAA-TTTTGGAAAGTTTAGGGTTA
1 AAAATGG-AATTTTTGGAAAGTTTAGGGTTA
* * * *
2368 AAAAT-AAATTTTTAGATA-TTCGAGGG-T-
1 AAAATGGAATTTTTGGAAAGTT-TAGGGTTA
* **
2395 AAAATGGTGATTTTTGGAAAGTTCGGGGTTA
1 AAAATGG-AATTTTTGGAAAGTTTAGGGTTA
* *
2426 AAAATGGAATTTTTAGACA-TTTAAGGG-T-
1 AAAATGGAATTTTTGGAAAGTTT-AGGGTTA
* * *
2454 AAAATGGTAATTTTTGGAAGGTTTCGGGTAA
1 AAAATGG-AATTTTTGGAAAGTTTAGGGTTA
* * *
2485 AAAATGGATTTTTTGGAAAATTTAGGGGTA
1 AAAATGGAATTTTTGGAAAGTTTAGGGTTA
*
2515 AAAATGTAATTTT
1 AAAATGGAATTTT
2528 GAAGACTTCA
Statistics
Matches: 166, Mismatches: 34, Indels: 37
0.70 0.14 0.16
Matches are distributed among these distances:
27 5 0.03
28 27 0.16
29 47 0.28
30 67 0.40
31 20 0.12
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.36
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAAGTTTAGGGTTA
Found at i:2401 original size:116 final size:117
Alignment explanation
Indices: 2275--2489 Score: 317
Period size: 116 Copynumber: 1.8 Consensus size: 117
2265 TGGACACTCG
**
2275 GGGTAAAATGGTAATTTTTGGAAAGTTCGGAGTTAAAAATGAAATTTTTAAACA-TTCGGGTGTA
1 GGGTAAAATGGTAATTTTTGGAAAGTTCGGAGTTAAAAATGAAATTTTTAAACATTTAAGG-GTA
*
2339 AAATGGCAA-TTTTGGAAAGTTTAGGGTTAAAAATAAATTTTTAGATATTCGA
65 AAATGGCAATTTTTGGAAAGTTTAGGGTAAAAAATAAATTTTTAGATATTCGA
* * * *
2391 GGGTAAAATGGTGATTTTTGGAAAGTTCGGGGTTAAAAATGGAATTTTTAGACATTTAAGGGTAA
1 GGGTAAAATGGTAATTTTTGGAAAGTTCGGAGTTAAAAATGAAATTTTTAAACATTTAAGGGTAA
* * *
2456 AATGGTAATTTTTGGAAGGTTTCGGGTAAAAAAT
66 AATGGCAATTTTTGGAAAGTTTAGGGTAAAAAAT
2490 GGATTTTTTG
Statistics
Matches: 87, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
116 61 0.70
117 26 0.30
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.35
Consensus pattern (117 bp):
GGGTAAAATGGTAATTTTTGGAAAGTTCGGAGTTAAAAATGAAATTTTTAAACATTTAAGGGTAA
AATGGCAATTTTTGGAAAGTTTAGGGTAAAAAATAAATTTTTAGATATTCGA
Found at i:2491 original size:59 final size:58
Alignment explanation
Indices: 2275--2527 Score: 262
Period size: 59 Copynumber: 4.3 Consensus size: 58
2265 TGGACACTCG
* **
2275 GGGTAAAATGGTAATTTTTGGAAAGTTCGGAGTTAAAAATGAAATTTTTAAACA-TTCG
1 GGGTAAAATGGTAATTTTTGGAAAGTTCGG-GTTAAAAATGAAATTTTTAGACATTTAA
* * * **
2333 GGTGTAAAATGGCAA-TTTTGGAAAGTTTAGGGTTAAAAAT-AAATTTTTAGATATTCGA
1 GG-GTAAAATGGTAATTTTTGGAAAG-TTCGGGTTAAAAATGAAATTTTTAGACATTTAA
* *
2391 GGGTAAAATGGTGATTTTTGGAAAGTTCGGGGTTAAAAATGGAATTTTTAGACATTTAA
1 GGGTAAAATGGTAATTTTTGGAAAGTTC-GGGTTAAAAATGAAATTTTTAGACATTTAA
* * * * * * *
2450 GGGTAAAATGGTAATTTTTGGAAGGTTTCGGGTAAAAAATGGATTTTTTGGAAAATTTAG
1 GGGTAAAATGGTAATTTTTGGAAAG-TTCGGGTTAAAAATGAAATTTTTAG-ACATTTAA
2510 GGGTAAAAAT-GTAATTTT
1 GGGT-AAAATGGTAATTTT
2528 GAAGACTTCA
Statistics
Matches: 165, Mismatches: 21, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
57 23 0.14
58 45 0.27
59 71 0.43
60 21 0.13
61 5 0.03
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTTGGAAAGTTCGGGTTAAAAATGAAATTTTTAGACATTTAA
Found at i:3637 original size:6 final size:6
Alignment explanation
Indices: 3626--3664 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
3616 CCTTTTTTAT
**
3626 TTAATA TTAATA TTAATTA TTAATA TTTTTA TTAATA TT
1 TTAATA TTAATA TTAA-TA TTAATA TTAATA TTAATA TT
3665 TATTAATGCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (6 bp):
TTAATA
Found at i:3668 original size:10 final size:11
Alignment explanation
Indices: 3630--3671 Score: 50
Period size: 10 Copynumber: 3.6 Consensus size: 11
3620 TTTTATTTAA
3630 TATTAATATTAAT
1 TATTAATATT--T
3643 TATTAATATTTT
1 TATTAATA-TTT
3655 TATTAATA-TT
1 TATTAATATTT
3665 TATTAAT
1 TATTAAT
3672 GCTATTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 9 0.32
12 9 0.32
13 8 0.29
14 2 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATTAATATTT
Found at i:4459 original size:17 final size:17
Alignment explanation
Indices: 4437--4510 Score: 67
Period size: 17 Copynumber: 4.4 Consensus size: 17
4427 CACTTTTAAT
* *
4437 TAAATTTTAATTTAAAA
1 TAAATTTAAACTTAAAA
* *
4454 TAAATTTAAACTCAAAG
1 TAAATTTAAACTTAAAA
* * ***
4471 TAAGTTTAAATTTATTT
1 TAAATTTAAACTTAAAA
4488 TAAATTTAAACTTAAAA
1 TAAATTTAAACTTAAAA
4505 TAAATT
1 TAAATT
4511 AAAGTTTTAA
Statistics
Matches: 42, Mismatches: 15, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
17 42 1.00
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (17 bp):
TAAATTTAAACTTAAAA
Found at i:13675 original size:41 final size:41
Alignment explanation
Indices: 13630--13711 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
13620 GGAATGAGTA
*
13630 AAAATTTATTAACTTTCGCAATACGAAATTTCAATAGAAAC
1 AAAATTTACTAACTTTCGCAATACGAAATTTCAATAGAAAC
*
13671 AAAATTTACTAACTTTCGCAATACGAAATTTCAGTAGAAAC
1 AAAATTTACTAACTTTCGCAATACGAAATTTCAATAGAAAC
13712 CTAACATTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.45, C:0.16, G:0.09, T:0.30
Consensus pattern (41 bp):
AAAATTTACTAACTTTCGCAATACGAAATTTCAATAGAAAC
Found at i:23938 original size:23 final size:24
Alignment explanation
Indices: 23882--23948 Score: 91
Period size: 23 Copynumber: 2.8 Consensus size: 24
23872 TCATTAACAT
* *
23882 TGTTCGTGAACATGTTCAATTATA
1 TGTTCGTGAACATGTTCGATGATA
* *
23906 TGTTCATGAACATGTTCGCTGA-A
1 TGTTCGTGAACATGTTCGATGATA
23929 TGTTCGTGAACATGTTCGAT
1 TGTTCGTGAACATGTTCGAT
23949 TAAGTTAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
23 19 0.51
24 18 0.49
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.39
Consensus pattern (24 bp):
TGTTCGTGAACATGTTCGATGATA
Found at i:23946 original size:12 final size:12
Alignment explanation
Indices: 23877--23946 Score: 56
Period size: 12 Copynumber: 5.8 Consensus size: 12
23867 ATTATTCATT
23877 AACATTGTTCGTG
1 AACA-TGTTCGTG
*
23890 AACATGTTCAAT-
1 AACATGTTC-GTG
* * *
23902 TATATGTTCATG
1 AACATGTTCGTG
23914 AACATGTTCGCTG
1 AACATGTTCG-TG
23927 -A-ATGTTCGTG
1 AACATGTTCGTG
23937 AACATGTTCG
1 AACATGTTCG
23947 ATTAAGTTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
10 2 0.04
11 10 0.22
12 27 0.59
13 7 0.15
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (12 bp):
AACATGTTCGTG
Found at i:23979 original size:23 final size:23
Alignment explanation
Indices: 23935--23980 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
23925 TGAATGTTCG
* *
23935 TGAACATGTTCGATTAAGTTAAA
1 TGAACATGTTCGATGAAATTAAA
23958 TGAACATGTTCG-TGAACATTAAA
1 TGAACATGTTCGATGAA-ATTAAA
23981 CAAACAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (23 bp):
TGAACATGTTCGATGAAATTAAA
Found at i:30007 original size:56 final size:57
Alignment explanation
Indices: 29938--30058 Score: 147
Period size: 56 Copynumber: 2.1 Consensus size: 57
29928 CAAATTAAGG
** *
29938 AAAAAAAAGTCAAGTTCAAGTACCAAATT-AGACCTAAAAAA-TTTAACTACCAACTT
1 AAAAAAAAGTCAAGTTCAAGTACCAAATTGA-ACAAAAAAAATTTTAACTACCAAATT
* * * **
29994 AAAAAAATGTCAAGTTTAAGTATCAAATTGAACAAAAAAAATTTTATGTACCAAATT
1 AAAAAAAAGTCAAGTTCAAGTACCAAATTGAACAAAAAAAATTTTAACTACCAAATT
30051 AAAAAAAA
1 AAAAAAAA
30059 ATGTGTCAAT
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
56 34 0.63
57 20 0.37
ACGTcount: A:0.55, C:0.12, G:0.07, T:0.25
Consensus pattern (57 bp):
AAAAAAAAGTCAAGTTCAAGTACCAAATTGAACAAAAAAAATTTTAACTACCAAATT
Found at i:30048 original size:28 final size:26
Alignment explanation
Indices: 29955--30059 Score: 68
Period size: 28 Copynumber: 3.8 Consensus size: 26
29945 AGTCAAGTTC
**
29955 AAGTACCAAATTAGACCTAAAAAA-TTT
1 AAGTACCAAATTA-A-AAAAAAAATTTT
* * * *
29982 AACTACCAACTTAAAAAAATGTCAAGTTT
1 AAGTACCAAATTAAAAAAA---AAATTTT
*
30011 AAGTATCAAATTGAACAAAAAAAATTTT
1 AAGTACCAAATT-AA-AAAAAAAATTTT
*
30039 ATGTACCAAATTAAAAAAAAA
1 AAGTACCAAATTAAAAAAAAA
30060 TGTGTCAATT
Statistics
Matches: 60, Mismatches: 12, Indels: 13
0.71 0.14 0.15
Matches are distributed among these distances:
25 3 0.05
26 8 0.13
27 13 0.22
28 17 0.28
29 12 0.20
30 2 0.03
31 5 0.08
ACGTcount: A:0.55, C:0.12, G:0.07, T:0.26
Consensus pattern (26 bp):
AAGTACCAAATTAAAAAAAAAATTTT
Done.