Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002810.1 Kokia drynarioides strain JFW-HI SEQ_115161, 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: 6140
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.32
Found at i:2212 original size:29 final size:29
Alignment explanation
Indices: 2173--2398 Score: 244
Period size: 29 Copynumber: 7.8 Consensus size: 29
2163 AATTTGGGGT
*
2173 TAAAAATGGGATTTTTGGAAGTTCGAGGG
1 TAAAAATGGAATTTTTGGAAGTTCGAGGG
* *
2202 TAAAAATGGGATTTTCGGAAGTT--AGGG
1 TAAAAATGGAATTTTTGGAAGTTCGAGGG
*** * *
2229 ATAAAAATGGAATTTTCAAAAGTTTGGGGG
1 -TAAAAATGGAATTTTTGGAAGTTCGAGGG
*
2259 TAAAAATGGAATTTTTGGAAGTTTCGA-GT
1 TAAAAATGGAATTTTTGGAAG-TTCGAGGG
* *
2288 TAAAAATGGGATTTTCGGAAGTTCGAGGG
1 TAAAAATGGAATTTTTGGAAGTTCGAGGG
* *
2317 TGAAAACGGAATTTTTGGAAGTTTCG-GGG
1 TAAAAATGGAATTTTTGGAAG-TTCGAGGG
* *
2346 TTAAAAATGGGATTTTTTGAAGTTCGAGGG
1 -TAAAAATGGAATTTTTGGAAGTTCGAGGG
*
2376 TAAAAACGGAATTTTTGGAAGTT
1 TAAAAATGGAATTTTTGGAAGTT
2399 TAAGGACTTT
Statistics
Matches: 164, Mismatches: 25, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
27 4 0.02
28 25 0.15
29 105 0.64
30 30 0.18
ACGTcount: A:0.33, C:0.04, G:0.30, T:0.32
Consensus pattern (29 bp):
TAAAAATGGAATTTTTGGAAGTTCGAGGG
Found at i:2328 original size:58 final size:58
Alignment explanation
Indices: 2169--2399 Score: 302
Period size: 59 Copynumber: 4.0 Consensus size: 58
2159 GGAAAATTTG
* * * * *
2169 GGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGGATTTTCGGAAG-TTA
1 GGGTTAAAAATGGGATTTTCGGAAGTTCGAGGGTAAAAACGGAATTTTTGGAAGTTTC
* * ** * * *
2226 GGGATAAAAATGGAATTTTCAAAAGTTTGGGGGTAAAAATGGAATTTTTGGAAGTTTC
1 GGGTTAAAAATGGGATTTTCGGAAGTTCGAGGGTAAAAACGGAATTTTTGGAAGTTTC
* *
2284 GAGTTAAAAATGGGATTTTCGGAAGTTCGAGGGTGAAAACGGAATTTTTGGAAGTTTC
1 GGGTTAAAAATGGGATTTTCGGAAGTTCGAGGGTAAAAACGGAATTTTTGGAAGTTTC
**
2342 GGGGTTAAAAATGGGATTTTTTGAAGTTCGAGGGTAAAAACGGAATTTTTGGAAGTTT
1 -GGGTTAAAAATGGGATTTTCGGAAGTTCGAGGGTAAAAACGGAATTTTTGGAAGTTT
2400 AAGGACTTTC
Statistics
Matches: 149, Mismatches: 23, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
57 45 0.30
58 51 0.34
59 53 0.36
ACGTcount: A:0.32, C:0.04, G:0.31, T:0.32
Consensus pattern (58 bp):
GGGTTAAAAATGGGATTTTCGGAAGTTCGAGGGTAAAAACGGAATTTTTGGAAGTTTC
Found at i:4238 original size:18 final size:17
Alignment explanation
Indices: 4203--4251 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
4193 GGCTTTATTT
**
4203 ATTTTAAATTTATGATA
1 ATTTTAAATTTAAAATA
4220 ATTTTAAATTTTAAAATA
1 ATTTTAAA-TTTAAAATA
*
4238 ATTTTAAACTTAAA
1 ATTTTAAATTTAAA
4252 TTAAATTTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (17 bp):
ATTTTAAATTTAAAATA
Found at i:4259 original size:18 final size:18
Alignment explanation
Indices: 4203--4251 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
4193 GGCTTTATTT
**
4203 ATTTTAAAT-TTATGATA
1 ATTTTAAATCTTAAAATA
*
4220 ATTTTAAATTTTAAAATA
1 ATTTTAAATCTTAAAATA
4238 ATTTTAAA-CTTAAA
1 ATTTTAAATCTTAAA
4252 TTAAATTTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 14 0.50
18 14 0.50
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (18 bp):
ATTTTAAATCTTAAAATA
Found at i:5542 original size:29 final size:29
Alignment explanation
Indices: 5504--5613 Score: 107
Period size: 29 Copynumber: 3.8 Consensus size: 29
5494 TTTAGGGTTT
5504 AAAAAA-GGAATTTTTAGACA-TTCGGGGG
1 AAAAAATGGAATTTTTAGA-AGTTCGGGGG
* * **
5532 AAAAAATGGAATTTTTAGAAATTTTGGGAT
1 AAAAAATGGAATTTTTAG-AAGTTCGGGGG
* *
5562 AAAAAATGGCATTTTTGGAAGTTCGGGGG
1 AAAAAATGGAATTTTTAGAAGTTCGGGGG
* * *
5591 TAAAAATGAAATTTTTGGAAGTT
1 AAAAAATGGAATTTTTAGAAGTT
5614 TCAAGGTCAA
Statistics
Matches: 67, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
28 6 0.09
29 39 0.58
30 22 0.33
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.32
Consensus pattern (29 bp):
AAAAAATGGAATTTTTAGAAGTTCGGGGG
Found at i:5554 original size:59 final size:60
Alignment explanation
Indices: 5473--5606 Score: 148
Period size: 59 Copynumber: 2.2 Consensus size: 60
5463 ACCCGAGGGG
** *
5473 AAAATGGTAATTTTGGGAAAATTTAGGGTTTAAAAAA-GGAATTTTTAGACA-TTCGGGGGAA
1 AAAATGG-AATTTTTAGAAAATTTAGGG-ATAAAAAATGGAATTTTTAGA-AGTTCGGGGGAA
* * * *
5534 AAAATGGAATTTTTAG-AAATTTTGGGATAAAAAATGGCATTTTTGGAAGTTCGGGGGTA
1 AAAATGGAATTTTTAGAAAATTTAGGGATAAAAAATGGAATTTTTAGAAGTTCGGGGGAA
*
5593 AAAATGAAATTTTT
1 AAAATGGAATTTTT
5607 GGAAGTTTCA
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
58 8 0.13
59 41 0.65
60 7 0.11
61 7 0.11
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.34
Consensus pattern (60 bp):
AAAATGGAATTTTTAGAAAATTTAGGGATAAAAAATGGAATTTTTAGAAGTTCGGGGGAA
Found at i:5625 original size:29 final size:29
Alignment explanation
Indices: 5572--5674 Score: 86
Period size: 29 Copynumber: 3.5 Consensus size: 29
5562 AAAAAATGGC
**
5572 ATTTTTGGAAG-TTCGGGGGTAAAAATGAA
1 ATTTTTGGAAGTTTCGAAGGT-AAAATGAA
**
5601 ATTTTTGGAAGTTTC-AAGGTCAAAATTGGG
1 ATTTTTGGAAGTTTCGAAGGT-AAAA-TGAA
* *
5631 ATTTTTGGAAG-TTCGAGGGTAAAATGGTA
1 ATTTTTGGAAGTTTCGAAGGTAAAAT-GAA
5660 ATTTTTGGACAGTTT
1 ATTTTTGGA-AGTTT
5675 AGGGACCTCC
Statistics
Matches: 60, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
28 1 0.02
29 35 0.58
30 22 0.37
31 2 0.03
ACGTcount: A:0.30, C:0.05, G:0.28, T:0.37
Consensus pattern (29 bp):
ATTTTTGGAAGTTTCGAAGGTAAAATGAA
Found at i:5678 original size:29 final size:29
Alignment explanation
Indices: 5533--5678 Score: 91
Period size: 30 Copynumber: 4.9 Consensus size: 29
5523 ATTCGGGGGA
* * * * *
5533 AAAAATGGAATTTTTAGAAATTTTGGGATA
1 AAAATTGGAATTTTTGGAAGTTTAGGG-TC
* * **
5563 AAAAATGGCATTTTTGGAAGTTCGGGGGT-
1 AAAATTGGAATTTTTGGAAGTT-TAGGGTC
* * *
5592 AAAAATGAAATTTTTGGAAGTTTCAAGGTC
1 AAAATTGGAATTTTTGGAAGTTT-AGGGTC
* *
5622 AAAATTGGGATTTTTGGAAGTTCGAGGGT-
1 AAAATTGGAATTTTTGGAAGTT-TAGGGTC
5651 AAAA-TGGTAATTTTTGGACAGTTTAGGG
1 AAAATTGG-AATTTTTGGA-AGTTTAGGG
5679 ACCTCCAGGG
Statistics
Matches: 93, Mismatches: 17, Indels: 13
0.76 0.14 0.11
Matches are distributed among these distances:
28 3 0.03
29 40 0.43
30 47 0.51
31 3 0.03
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.34
Consensus pattern (29 bp):
AAAATTGGAATTTTTGGAAGTTTAGGGTC
Done.