Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011382.1 Kokia drynarioides strain JFW-HI SEQ_126364, 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: 36018
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.33
Warning! 230 characters in sequence are not A, C, G, or T
Found at i:315 original size:12 final size:12
Alignment explanation
Indices: 278--316 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
268 TAAAAGAATA
*
278 AAGAAAGAAAAA
1 AAGAAAGAAAAG
*
290 AAGAAACAAAAG
1 AAGAAAGAAAAG
*
302 AAGAAAGAACAG
1 AAGAAAGAAAAG
314 AAG
1 AAG
317 CTCAAACGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.74, C:0.05, G:0.21, T:0.00
Consensus pattern (12 bp):
AAGAAAGAAAAG
Found at i:2732 original size:11 final size:11
Alignment explanation
Indices: 2718--2763 Score: 65
Period size: 11 Copynumber: 4.2 Consensus size: 11
2708 TATGTTGTTG
*
2718 TTTTGTTATCA
1 TTTTGTTATTA
2729 TTTTGTTATTA
1 TTTTGTTATTA
*
2740 TATTGTTATTA
1 TTTTGTTATTA
*
2751 TTTTGTTGTTA
1 TTTTGTTATTA
2762 TT
1 TT
2764 GTTTGGATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.17, C:0.02, G:0.11, T:0.70
Consensus pattern (11 bp):
TTTTGTTATTA
Found at i:11610 original size:23 final size:23
Alignment explanation
Indices: 11580--11670 Score: 116
Period size: 23 Copynumber: 4.0 Consensus size: 23
11570 CGCTATCGGT
11580 CTTACTGTTTCGCACTTCATGTG
1 CTTACTGTTTCGCACTTCATGTG
**
11603 CTTACTGTTTCGCACTTTGTGTG
1 CTTACTGTTTCGCACTTCATGTG
* *
11626 CTTACTGTTTTGCACTTCGTGTG
1 CTTACTGTTTCGCACTTCATGTG
11649 CTTACTGATTT-GCA-TT-ATGTG
1 CTTACTG-TTTCGCACTTCATGTG
11670 C
1 C
11671 GCCTACTGAC
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
21 5 0.08
22 2 0.03
23 52 0.84
24 3 0.05
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (23 bp):
CTTACTGTTTCGCACTTCATGTG
Found at i:11649 original size:46 final size:45
Alignment explanation
Indices: 11580--11726 Score: 147
Period size: 46 Copynumber: 3.2 Consensus size: 45
11570 CGCTATCGGT
* *
11580 CTTACTGTTTCGCACTTCATGTGCTTACTGTTTCGCACTT-TGTGTG
1 CTTACTGTTTTGCACTTCGTGTGCTTACTGTTT-GCA-TTATGTGTG
*
11626 CTTACTGTTTTGCACTTCGTGTGCTTACTGATTTGCATTATGTGCG
1 CTTACTGTTTTGCACTTCGTGTGCTTACTG-TTTGCATTATGTGTG
* ** * * *
11672 CCTACTG-ACTGCACTGT-GTGTGCCTACTGGATTGCATTGTGTGTG
1 CTTACTGTTTTGCACT-TCGTGTGCTTACT-GTTTGCATTATGTGTG
11717 CTTACTGTTT
1 CTTACTGTTT
11727 CCCCAGCACT
Statistics
Matches: 83, Mismatches: 13, Indels: 10
0.78 0.12 0.09
Matches are distributed among these distances:
45 36 0.43
46 44 0.53
47 3 0.04
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (45 bp):
CTTACTGTTTTGCACTTCGTGTGCTTACTGTTTGCATTATGTGTG
Found at i:11677 original size:23 final size:22
Alignment explanation
Indices: 11644--11723 Score: 88
Period size: 23 Copynumber: 3.5 Consensus size: 22
11634 TTTGCACTTC
* *
11644 GTGTGCTTACTGATTTGCATTAT
1 GTGTGCCTACTGA-TTGCATTGT
* * *
11667 GTGCGCCTACTGACTGCACTGT
1 GTGTGCCTACTGATTGCATTGT
11689 GTGTGCCTACTGGATTGCATTGT
1 GTGTGCCTACT-GATTGCATTGT
*
11712 GTGTGCTTACTG
1 GTGTGCCTACTG
11724 TTTCCCCAGC
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
22 17 0.36
23 30 0.64
ACGTcount: A:0.14, C:0.20, G:0.28, T:0.39
Consensus pattern (22 bp):
GTGTGCCTACTGATTGCATTGT
Found at i:11700 original size:45 final size:45
Alignment explanation
Indices: 11636--11723 Score: 108
Period size: 45 Copynumber: 2.0 Consensus size: 45
11626 CTTACTGTTT
*
11636 TGCACTTCGTGTGCTTACT-GATTTGCATTATGTGCGCCTACTGAC
1 TGCACTTCGTGTGCCTACTGGA-TTGCATTATGTGCGCCTACTGAC
* * *
11681 TGCACTGT-GTGTGCCTACTGGATTGCATTGTGTGTGCTTACTG
1 TGCACT-TCGTGTGCCTACTGGATTGCATTATGTGCGCCTACTG
11724 TTTCCCCAGC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
45 34 0.92
46 3 0.08
ACGTcount: A:0.14, C:0.22, G:0.26, T:0.39
Consensus pattern (45 bp):
TGCACTTCGTGTGCCTACTGGATTGCATTATGTGCGCCTACTGAC
Found at i:15638 original size:84 final size:84
Alignment explanation
Indices: 15549--15716 Score: 327
Period size: 84 Copynumber: 2.0 Consensus size: 84
15539 CAACATCATA
15549 AATGTATATAAATTTTTATGCTAATAATTTATTAATCTTGACACGTTTATGCATTCGTCGAATAT
1 AATGTATATAAATTTTTATGCTAATAATTTATTAATCTTGACACGTTTATGCATTCGTCGAATAT
15614 TGATATTACTTTCGTTTTT
66 TGATATTACTTTCGTTTTT
*
15633 AATGTATATAAATTTTTATGCTGATAATTTATTAATCTTGACACGTTTATGCATTCGTCGAATAT
1 AATGTATATAAATTTTTATGCTAATAATTTATTAATCTTGACACGTTTATGCATTCGTCGAATAT
15698 TGATATTACTTTCGTTTTT
66 TGATATTACTTTCGTTTTT
15717 TTATGGCATG
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 83 1.00
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (84 bp):
AATGTATATAAATTTTTATGCTAATAATTTATTAATCTTGACACGTTTATGCATTCGTCGAATAT
TGATATTACTTTCGTTTTT
Found at i:15909 original size:2 final size:2
Alignment explanation
Indices: 15902--15926 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15892 ATTATTAAAT
15902 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
15927 TTGATCATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17063 original size:2 final size:2
Alignment explanation
Indices: 17058--17086 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
17048 GAGGGGATAA
17058 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17087 AAATAAAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31556 original size:12 final size:12
Alignment explanation
Indices: 31539--31565 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
31529 GACTGTCGGT
31539 CACATGTCACAC
1 CACATGTCACAC
31551 CACATGTCACAC
1 CACATGTCACAC
31563 CAC
1 CAC
31566 TGCACAGTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.44, G:0.07, T:0.15
Consensus pattern (12 bp):
CACATGTCACAC
Found at i:35268 original size:58 final size:59
Alignment explanation
Indices: 35206--35330 Score: 162
Period size: 59 Copynumber: 2.1 Consensus size: 59
35196 GGGTAAAATA
* * *
35206 GTAATTTTGGGAAATTTGAGG-CTAAAAATGGAATTTTTTGACATTCAGGAGTAAAAGG
1 GTAATTTTGAGAAATTTGAGGTCGAAAAATGGAATTTTTGGACATTCAGGAGTAAAAGG
** * * * *
35264 GTAATTTTGAGAGTTTTGAGGTCGAAAAATGGAGTTTTTGGACATTCGGGGGTAAAATG
1 GTAATTTTGAGAAATTTGAGGTCGAAAAATGGAATTTTTGGACATTCAGGAGTAAAAGG
35323 GTAATTTT
1 GTAATTTT
35331 TAAAAGTTTC
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
58 18 0.32
59 39 0.68
ACGTcount: A:0.32, C:0.05, G:0.28, T:0.35
Consensus pattern (59 bp):
GTAATTTTGAGAAATTTGAGGTCGAAAAATGGAATTTTTGGACATTCAGGAGTAAAAGG
Found at i:35331 original size:29 final size:28
Alignment explanation
Indices: 35289--35543 Score: 183
Period size: 29 Copynumber: 8.8 Consensus size: 28
35279 TTGAGGTCGA
*
35289 AAAATGGAGTTTTTGGACA-TTCGGGGGT
1 AAAATGGAATTTTTGGA-AGTTCGGGGGT
** * *
35317 AAAATGGTAATTTTTAAAAGTTTCGGTGTT
1 AAAATGG-AATTTTTGGAAG-TTCGGGGGT
* *
35347 AAAAATGTAAATTTTGG-AGATTCGGGCGGT
1 -AAAATGGAATTTTTGGAAG-TTCGGG-GGT
* * * *
35377 AAAAATGGTATTTGTGTAAGTTTC-GAGGT
1 -AAAATGGAATTTTTGGAAG-TTCGGGGGT
* **
35406 CAAAATGGATTTTTTGGAAGTTTAGGGGT
1 -AAAATGGAATTTTTGGAAGTTCGGGGGT
* *
35435 AAAAATGGAATTTTTGGAAGTTTCGAGGTT
1 -AAAATGGAATTTTTGGAAG-TTCGGGGGT
* * *
35465 AAAATGGAAATTTTGGAAGTTCAGGTGT
1 AAAATGGAATTTTTGGAAGTTCGGGGGT
35493 AAAATTGGAATTTTTGGAAGTTCGGGGGT
1 AAAA-TGGAATTTTTGGAAGTTCGGGGGT
* *
35522 AAAATGAAATTTTCGGACAGTT
1 AAAATGGAATTTTTGGA-AGTT
35544 TAGGGACCTC
Statistics
Matches: 175, Mismatches: 42, Indels: 19
0.74 0.18 0.08
Matches are distributed among these distances:
28 30 0.17
29 101 0.58
30 33 0.19
31 11 0.06
ACGTcount: A:0.32, C:0.05, G:0.28, T:0.35
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAAGTTCGGGGGT
Found at i:35351 original size:59 final size:58
Alignment explanation
Indices: 35172--35514 Score: 256
Period size: 58 Copynumber: 5.8 Consensus size: 58
35162 ACCCAGGGGC
* * * * *
35172 AAAATGGCAA-TTTTGGATTCTCGGGGGTAAAATAGTAATTTTGGGAAA-TTT-GAGGCTA
1 AAAATGG-AATTTTTGGAAT-TCAGGGGTAAAATGGTAATTTT-TGAAAGTTTCGAGGTTA
* * * * * *
35230 AAAATGGAATTTTTTGACATTCAGGAGTAAAAGGGTAA-TTTTGAGAGTTTTGAGGTCGA
1 AAAATGGAATTTTTGGA-ATTCAGGGGTAAAATGGTAATTTTTGAAAGTTTCGAGGT-TA
* * *
35289 AAAATGGAGTTTTTGGACATTCGGGGGTAAAATGGTAATTTTTAAAAGTTTCG-GTGTTA
1 AAAATGGAATTTTTGGA-ATTCAGGGGTAAAATGGTAATTTTTGAAAGTTTCGAG-GTTA
* * * * * *
35348 AAAATGTAAATTTTGGAGATTCGGGCGGTAAAAATGGT-ATTTGTGTAAGTTTCGAGG-TC
1 AAAATGGAATTTTTGGA-ATTCAGG-GGT-AAAATGGTAATTTTTGAAAGTTTCGAGGTTA
* * *
35407 AAAATGGATTTTTTGGAAGTTTAGGGGTAAAAATGG-AATTTTTGGAAGTTTCGAGGTT-
1 AAAATGGAATTTTTGGAA-TTCAGGGGT-AAAATGGTAATTTTTGAAAGTTTCGAGGTTA
* * *
35465 AAAATGGAAATTTTGGAAGTTCAGGTGTAAAATTGG-AATTTTTGGAAGTT
1 AAAATGGAATTTTTGGAA-TTCAGGGGTAAAA-TGGTAATTTTTGAAAGTT
35515 CGGGGGTAAA
Statistics
Matches: 233, Mismatches: 38, Indels: 28
0.78 0.13 0.09
Matches are distributed among these distances:
56 3 0.01
57 12 0.05
58 101 0.43
59 78 0.33
60 30 0.13
61 9 0.04
ACGTcount: A:0.32, C:0.05, G:0.28, T:0.35
Consensus pattern (58 bp):
AAAATGGAATTTTTGGAATTCAGGGGTAAAATGGTAATTTTTGAAAGTTTCGAGGTTA
Found at i:35456 original size:58 final size:57
Alignment explanation
Indices: 35374--35548 Score: 208
Period size: 58 Copynumber: 3.0 Consensus size: 57
35364 AGATTCGGGC
* * * *
35374 GGTAAAAATGGTATTTGTGTAAGTTTCGAGGTCAAAATGGATTTTTTGGAAGTTTAGG
1 GGTAAAAATGGAATTTTTGGAAGTTTCGAGGT-AAAATGGAATTTTTGGAAGTTTAGG
* *
35432 GGTAAAAATGGAATTTTTGGAAGTTTCGAGGTTAAAATGGAAATTTTGGAAGTTCAGG
1 GGTAAAAATGGAATTTTTGGAAGTTTCGAGG-TAAAATGGAATTTTTGGAAGTTTAGG
* * * * *
35490 TGTAAAATTGGAATTTTTGGAAG-TTCGGGGGTAAAATGAAATTTTCGGACAGTTTAGG
1 GGTAAAAATGGAATTTTTGGAAGTTTC-GAGGTAAAATGGAATTTTTGGA-AGTTTAGG
35548 G
1 G
35549 ACCTCCAATG
Statistics
Matches: 100, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
57 18 0.18
58 81 0.81
59 1 0.01
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.35
Consensus pattern (57 bp):
GGTAAAAATGGAATTTTTGGAAGTTTCGAGGTAAAATGGAATTTTTGGAAGTTTAGG
Done.