Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011775.1 Kokia drynarioides strain JFW-HI SEQ_126770, 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: 23335
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 81 characters in sequence are not A, C, G, or T
Found at i:8 original size:3 final size:3
Alignment explanation
Indices: 1--46 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
47 ATTTTTTTCC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2408 original size:20 final size:20
Alignment explanation
Indices: 2383--2420 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2373 GGTTTTTCGA
2383 AAAAAGTCAACGGCCAACCC
1 AAAAAGTCAACGGCCAACCC
*
2403 AAAAAGTCAACGGTCAAC
1 AAAAAGTCAACGGCCAAC
2421 TATCAATGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.29, G:0.16, T:0.08
Consensus pattern (20 bp):
AAAAAGTCAACGGCCAACCC
Found at i:2501 original size:22 final size:21
Alignment explanation
Indices: 2471--2530 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
2461 TCAAATCTAG
*
2471 TTGGGTTTAAGGTTTTGGTGAT
1 TTGGTTTTAAGGTTTTGGT-AT
*
2493 TTGGTTTTAAGGTTTAGGTAT
1 TTGGTTTTAAGGTTTTGGTAT
* *
2514 TGGGTTTTCATGGTTTT
1 TTGGTTTT-AAGGTTTT
2531 TGGTTTACAC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 9 0.28
22 23 0.72
ACGTcount: A:0.13, C:0.02, G:0.32, T:0.53
Consensus pattern (21 bp):
TTGGTTTTAAGGTTTTGGTAT
Found at i:2521 original size:21 final size:22
Alignment explanation
Indices: 2471--2521 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
2461 TCAAATCTAG
*
2471 TTGGG-TTTAAGGTTTTGGTGA
1 TTGGGTTTTAAGGTTTAGGTGA
*
2492 TTTGGTTTTAAGGTTTAGGT-A
1 TTGGGTTTTAAGGTTTAGGTGA
2513 TTGGGTTTT
1 TTGGGTTTT
2522 CATGGTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 13 0.50
22 13 0.50
ACGTcount: A:0.14, C:0.00, G:0.33, T:0.53
Consensus pattern (22 bp):
TTGGGTTTTAAGGTTTAGGTGA
Found at i:18626 original size:76 final size:76
Alignment explanation
Indices: 18539--18697 Score: 257
Period size: 76 Copynumber: 2.1 Consensus size: 76
18529 CCTTCCGAAA
**
18539 TCCAATTCCACATAACAAAAAGGTTTTGAAACAAAACTGGTTAGATTACAACCAAAAGTTAAGGC
1 TCCAATTCCACATAACAAAAAGGTTTTGAAACAAAACCAGTTAGATTACAACCAAAAGTTAAGGC
18604 CAA-AATGGGGT
66 CAAGAA-GGGGT
* * *
18615 TCCAATTCCACATAATACAAAGGTTTTGAGACAAAACCAGTTAGATTACAACCAAAAGTTAAGGC
1 TCCAATTCCACATAACAAAAAGGTTTTGAAACAAAACCAGTTAGATTACAACCAAAAGTTAAGGC
18680 CAAGAAGGGGT
66 CAAGAAGGGGT
18691 TCCAATT
1 TCCAATT
18698 TTACAATACT
Statistics
Matches: 77, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
76 75 0.97
77 2 0.03
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.23
Consensus pattern (76 bp):
TCCAATTCCACATAACAAAAAGGTTTTGAAACAAAACCAGTTAGATTACAACCAAAAGTTAAGGC
CAAGAAGGGGT
Found at i:19242 original size:31 final size:31
Alignment explanation
Indices: 19207--19302 Score: 140
Period size: 31 Copynumber: 3.1 Consensus size: 31
19197 AAGAAACACC
19207 AAACATATCGAAAATTAATACAAAACCCACA
1 AAACATATCGAAAATTAATACAAAACCCACA
19238 AAACATATCGAAAATTAATACAAAACCCATC-
1 AAACATATCGAAAATTAATACAAAACCCA-CA
* ** *
19269 AGACATAGAGAAAATTAATACAAAACCCAAA
1 AAACATATCGAAAATTAATACAAAACCCACA
19300 AAA
1 AAA
19303 TAAAGAAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
31 57 0.98
32 1 0.02
ACGTcount: A:0.59, C:0.20, G:0.05, T:0.16
Consensus pattern (31 bp):
AAACATATCGAAAATTAATACAAAACCCACA
Found at i:19322 original size:20 final size:20
Alignment explanation
Indices: 19290--19333 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
19280 AAATTAATAC
19290 AAAACCCAAAAAAT-AAAGA
1 AAAACCCAAAAAATGAAAGA
* *
19309 AAAATCCAACAAAATGAAATA
1 AAAACCCAA-AAAATGAAAGA
19330 AAAA
1 AAAA
19334 AAGGGGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.38
20 5 0.24
21 8 0.38
ACGTcount: A:0.73, C:0.14, G:0.05, T:0.09
Consensus pattern (20 bp):
AAAACCCAAAAAATGAAAGA
Found at i:20220 original size:30 final size:29
Alignment explanation
Indices: 20142--20222 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 29
20132 ATACTAAAAC
* *
20142 TATACATGAACTATGGTTTAATGTGCAATTG
1 TATACATGAACTTTGATTT--TGTGCAATTG
*
20173 TATACATGAACTTTGATTTTGTGCAATTT
1 TATACATGAACTTTGATTTTGTGCAATTG
*
20202 TATACATGAAATTTTGATTTT
1 TATACATG-AACTTTGATTTT
20223 ATCCAATTCT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
29 17 0.38
30 11 0.24
31 17 0.38
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.46
Consensus pattern (29 bp):
TATACATGAACTTTGATTTTGTGCAATTG
Found at i:20230 original size:30 final size:29
Alignment explanation
Indices: 20167--20230 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 29
20157 GTTTAATGTG
* *
20167 CAATTGTATACATGAACTTTGATTTTGTG
1 CAATTGTATACATGAACTTTGATTTTATC
* *
20196 CAATTTTATACATGAAATTTTGATTTTATC
1 CAATTGTATACATG-AACTTTGATTTTATC
20226 CAATT
1 CAATT
20231 CTTGTAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 13 0.43
30 17 0.57
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.47
Consensus pattern (29 bp):
CAATTGTATACATGAACTTTGATTTTATC
Found at i:21299 original size:10 final size:10
Alignment explanation
Indices: 21245--21303 Score: 61
Period size: 10 Copynumber: 6.1 Consensus size: 10
21235 NNNNNNNNNN
21245 TTTTTTTGAA
1 TTTTTTTGAA
**
21255 TTTTTACGAA
1 TTTTTTTGAA
*
21265 TTTTTTTAAA
1 TTTTTTTGAA
21275 TCTTTTTTGAA
1 T-TTTTTTGAA
21286 ---TTTTGAA
1 TTTTTTTGAA
21293 TTTTTTTGAA
1 TTTTTTTGAA
21303 T
1 T
21304 ACTTTTATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
7 7 0.18
10 24 0.62
11 8 0.21
ACGTcount: A:0.24, C:0.03, G:0.08, T:0.64
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:21323 original size:29 final size:28
Alignment explanation
Indices: 21263--21323 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
21253 AATTTTTACG
* *
21263 AATTTTTTTAAATCTTTTTTGAATTTTG
1 AATTTTTTTAAATCTTTTATGAATTTTA
*
21291 AATTTTTTTGAATACTTTTAT-AATTTTCA
1 AATTTTTTTAAAT-CTTTTATGAATTTT-A
21320 AATT
1 AATT
21324 ATCTATTAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 18 0.64
29 10 0.36
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.61
Consensus pattern (28 bp):
AATTTTTTTAAATCTTTTATGAATTTTA
Found at i:23082 original size:33 final size:30
Alignment explanation
Indices: 23036--23095 Score: 84
Period size: 33 Copynumber: 1.9 Consensus size: 30
23026 CATTTAATCA
*
23036 GATAAATTAATGATATTAACTATTTAAACTT
1 GATAAATTAATGATATTAAAT-TTTAAACTT
23067 GATAAGATTAAATGATATTAAATTTTAAA
1 GATAA-ATT-AATGATATTAAATTTTAAA
23096 TTTAAATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 5 0.19
32 9 0.35
33 12 0.46
ACGTcount: A:0.48, C:0.03, G:0.08, T:0.40
Consensus pattern (30 bp):
GATAAATTAATGATATTAAATTTTAAACTT
Done.