Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011712.1 Kokia drynarioides strain JFW-HI SEQ_126706, 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: 28536
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:14071 original size:29 final size:29
Alignment explanation
Indices: 14038--14134 Score: 113
Period size: 29 Copynumber: 3.3 Consensus size: 29
14028 CACGAGCTAG
* * * *
14038 ACACATGGGAGTGTGATAGGCTGTGTGTT
1 ACACACGGGCGTGTGACAGGCTGTGTGTC
* *
14067 ACACACGGGCGTGTGACATGCCGTGTGTC
1 ACACACGGGCGTGTGACAGGCTGTGTGTC
* *
14096 ACACACGAGCGTGTGACAGGCTATGTGTC
1 ACACACGGGCGTGTGACAGGCTGTGTGTC
*
14125 ACAAACGGGC
1 ACACACGGGC
14135 TAGCACATGA
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 56 1.00
ACGTcount: A:0.23, C:0.22, G:0.34, T:0.22
Consensus pattern (29 bp):
ACACACGGGCGTGTGACAGGCTGTGTGTC
Found at i:21063 original size:21 final size:21
Alignment explanation
Indices: 21031--21081 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
21021 GGAGTTTTTA
* *
21031 GTATCAGTAGAAG-CATGACTT
1 GTATCGGTAGAAGTC-TCACTT
*
21052 GTTTCGGTAGAAGTCTCACTT
1 GTATCGGTAGAAGTCTCACTT
21073 GTATCGGTA
1 GTATCGGTA
21082 AAACTATCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.33
Consensus pattern (21 bp):
GTATCGGTAGAAGTCTCACTT
Found at i:22418 original size:20 final size:21
Alignment explanation
Indices: 22379--22418 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
22369 TCTAACCATG
*
22379 AAAAAGCTTTATCAGTTAGTAA
1 AAAAAGCATTATCAG-TAGTAA
22401 AAAAAGCATTATCA-TAGT
1 AAAAAGCATTATCAGTAGT
22419 CGTTTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
22 13 0.76
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.30
Consensus pattern (21 bp):
AAAAAGCATTATCAGTAGTAA
Found at i:22977 original size:5 final size:5
Alignment explanation
Indices: 22967--22991 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
22957 AAAGACTTGG
22967 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
22992 AAATAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:24007 original size:59 final size:58
Alignment explanation
Indices: 23941--24173 Score: 159
Period size: 59 Copynumber: 4.0 Consensus size: 58
23931 GGATACCAGG
* **
23941 GGGTAAAATGGTAATTTTGGGAAAATTAGAGGTTAAAAATGAGATTTTTGGAAGTTCAA
1 GGGTAAAAT-GTAATTTTGGGAAAATTAGAGGTCAAAAATGAGATTTTCAGAAGTTCAA
* ** * * *
24000 GGGTAAAAATGTAATTTTTGGAAGTTTCGAGGTCAAAAATGGGATTTTCAGAAGTTCGA
1 GGGT-AAAATGTAATTTTGGGAAAATTAGAGGTCAAAAATGAGATTTTCAGAAGTTCAA
* * * * * *
24059 GGGTAAAAAATG-AATTTT-TGAAAGTTTCGAGGT-AAAAATGGGATTTT-AGGGAGTTCGA
1 GGGT--AAAATGTAATTTTGGGAAA-ATTAGAGGTCAAAAATGAGATTTTCA-GAAGTTCAA
** * ** * * * *
24117 GGGTAAAAACATAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTAGAAGTTC
1 GGGT-AAAATGTAATTTTGGGAAAATTAGAGGTCAAAAATGAGATTTTCAGAAGTTC
24174 GGGGATAGAA
Statistics
Matches: 148, Mismatches: 18, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
57 6 0.04
58 43 0.29
59 86 0.58
60 13 0.09
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.32
Consensus pattern (58 bp):
GGGTAAAATGTAATTTTGGGAAAATTAGAGGTCAAAAATGAGATTTTCAGAAGTTCAA
Found at i:24016 original size:29 final size:29
Alignment explanation
Indices: 23941--24320 Score: 249
Period size: 29 Copynumber: 12.9 Consensus size: 29
23931 GGATACCAGG
* * *
23941 GGGT-AAAATGGTAATTTTGGGAAAATTAGA
1 GGGTAAAAATGG-AATTTTTGG-AAGTTCGA
* *
23971 GGTTAAAAAT-GAGATTTTTGGAAGTTCAA
1 GGGTAAAAATGGA-ATTTTTGGAAGTTCGA
*
24000 GGGTAAAAATGTAATTTTTGGAAGTTTCGA
1 GGGTAAAAATGGAATTTTTGGAAG-TTCGA
* **
24030 -GGTCAAAAATGGGATTTTCAGAAGTTCGA
1 GGGT-AAAAATGGAATTTTTGGAAGTTCGA
*
24059 GGGTAAAAAAT-GAATTTTTGAAAGTTTCGA
1 GGGT-AAAAATGGAATTTTTGGAAG-TTCGA
* * *
24089 -GGTAAAAATGGGATTTTAGGGAGTTCGA
1 GGGTAAAAATGGAATTTTTGGAAGTTCGA
***
24117 GGGTAAAAACATAATTTTTGGAAGTTTCG-
1 GGGTAAAAATGGAATTTTTGGAAG-TTCGA
* *
24146 GGGTCAAAAATGGGATTTTTAGAAGTTCG-
1 GGGT-AAAAATGGAATTTTTGGAAGTTCGA
* * *
24175 GGGATAGAAATAGAATTTTTGGAAGTTTTG-
1 GGG-TAAAAATGGAATTTTTGGAAG-TTCGA
* * *
24205 GGGTCAAAAATGGGATTTTTGAAAGTT-TA
1 GGGT-AAAAATGGAATTTTTGGAAGTTCGA
* *
24234 GGGGTAAAAATGAAATTTATGGAAGTTTC-A
1 -GGGTAAAAATGGAATTTTTGGAAG-TTCGA
* *** * *
24264 GGGTCAAAAATGGGATTTTAAAAAATTTGA
1 GGGT-AAAAATGGAATTTTTGGAAGTTCGA
*
24294 GGGTAAAAACGGAATTTTTGGACAGTT
1 GGGTAAAAATGGAATTTTTGGA-AGTT
24321 TAGGGACCTC
Statistics
Matches: 269, Mismatches: 60, Indels: 42
0.73 0.16 0.11
Matches are distributed among these distances:
28 11 0.04
29 137 0.51
30 116 0.43
31 5 0.02
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.32
Consensus pattern (29 bp):
GGGTAAAAATGGAATTTTTGGAAGTTCGA
Found at i:24192 original size:59 final size:58
Alignment explanation
Indices: 23975--24321 Score: 355
Period size: 59 Copynumber: 5.9 Consensus size: 58
23965 ATTAGAGGTT
* * * *
23975 AAAAATGAGATTTTTGGAAGTTCAAGGGTAAAAAT-GTAATTTTTGGAAGTTTCGAGGTC
1 AAAAATGGGATTTTTAGAAGTTC-GGGGTAAAAATAG-AATTTTTGGAAGTTTCGGGGTC
* * *
24034 AAAAATGGGATTTTCAGAAGTTCGAGGGTAAAAA-ATGAATTTTTGAAAGTTTCGAGGT-
1 AAAAATGGGATTTTTAGAAGTTCG-GGGTAAAAATA-GAATTTTTGGAAGTTTCGGGGTC
* * *
24092 AAAAATGGGA-TTTTAGGGAGTTCGAGGGTAAAAACATAATTTTTGGAAGTTTCGGGGTC
1 AAAAATGGGATTTTTA-GAAGTTCG-GGGTAAAAATAGAATTTTTGGAAGTTTCGGGGTC
* *
24151 AAAAATGGGATTTTTAGAAGTTCGGGGATAGAAATAGAATTTTTGGAAGTTTTGGGGTC
1 AAAAATGGGATTTTTAGAAGTTCGGGG-TAAAAATAGAATTTTTGGAAGTTTCGGGGTC
* * *
24210 AAAAATGGGATTTTT-GAAAGTTTAGGGGTAAAAAT-GAAATTTATGGAAGTTTCAGGGTC
1 AAAAATGGGATTTTTAG-AAG-TTCGGGGTAAAAATAG-AATTTTTGGAAGTTTCGGGGTC
* * * * **
24269 AAAAATGGGATTTTAAAAAATTTGAGGGTAAAAACGGAATTTTTGGACAGTTT
1 AAAAATGGGATTTTTAGAAGTTCG-GGGTAAAAATAGAATTTTTGGA-AGTTT
24322 AGGGACCTCT
Statistics
Matches: 247, Mismatches: 26, Indels: 29
0.82 0.09 0.10
Matches are distributed among these distances:
57 4 0.02
58 54 0.22
59 171 0.69
60 18 0.07
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.32
Consensus pattern (58 bp):
AAAAATGGGATTTTTAGAAGTTCGGGGTAAAAATAGAATTTTTGGAAGTTTCGGGGTC
Found at i:25450 original size:9 final size:9
Alignment explanation
Indices: 25379--25466 Score: 50
Period size: 9 Copynumber: 9.6 Consensus size: 9
25369 TTAATAACAT
25379 TTATTAATA
1 TTATTAATA
*
25388 TTAATAATTA
1 TTATTAA-TA
* *
25398 TTATTACTG
1 TTATTAATA
*
25407 TCATTAATA
1 TTATTAATA
* *
25416 TTACTAATG
1 TTATTAATA
*
25425 TTATTAGTA
1 TTATTAATA
* *
25434 ATATTTATTA
1 TTA-TTAATA
* *
25444 TTATTATTT
1 TTATTAATA
*
25453 TTATTAAGA
1 TTATTAATA
25462 TTATT
1 TTATT
25467 GCTGTTATTG
Statistics
Matches: 57, Mismatches: 20, Indels: 4
0.70 0.25 0.05
Matches are distributed among these distances:
9 43 0.75
10 14 0.25
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (9 bp):
TTATTAATA
Found at i:26198 original size:17 final size:16
Alignment explanation
Indices: 26180--26271 Score: 85
Period size: 17 Copynumber: 5.4 Consensus size: 16
26170 CTTTATTTAT
* *
26180 TTTAAATTTATCATAAT
1 TTTAAATTTA-AATAAA
*
26197 TTTAAACTTAAATTAAA
1 TTTAAATTTAAA-TAAA
26214 TTTAAATTTAAAATAAA
1 TTTAAATTT-AAATAAA
*
26231 TTTAAATTTTTAAACAAA
1 TTTAAA--TTTAAATAAA
*
26249 TTTAATTTTATAATAAA
1 TTTAAATTTA-AATAAA
26266 TTTAAA
1 TTTAAA
26272 GGGAGTTTGG
Statistics
Matches: 62, Mismatches: 8, Indels: 10
0.77 0.10 0.12
Matches are distributed among these distances:
16 5 0.08
17 40 0.65
18 14 0.23
19 3 0.05
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTAAATTTAAATAAA
Found at i:26207 original size:6 final size:6
Alignment explanation
Indices: 26197--26239 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
26187 TTATCATAAT
* *
26197 TTTAAA CTTAAA -TTAAA TTTAAA TTTAAA -ATAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
26240 TTAAACAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
5 9 0.28
6 23 0.72
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (6 bp):
TTTAAA
Found at i:27002 original size:204 final size:200
Alignment explanation
Indices: 26682--27182 Score: 661
Period size: 204 Copynumber: 2.5 Consensus size: 200
26672 TTTCATCAGG
* * *
26682 ATTTGGTTCACTTCTCTGTATCTCATCATGG-AGCTAACCACTTTATGGCTTCGACCTGCTTCTC
1 ATTTGGTTCACTTCTCAGTATCTCATCA-GGAAGCTAACC-TTTTATTGCTTCGACCTGCTTCTC
** **
26746 AACGTCTCATCAGGAAGCTGGGGTTCAAAGATTTGCTCGTTTTGAGCCTCGTTTGGGTCTTCTTC
64 AGTGTCTCATCAGGAAGCTGGGGTTCAAAGATTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTC
* *
26811 TCAGTGCCTCATCAGGAAGATGATTACATCGC-T-GTTTGTTTCAATTTGCTCCTCCGTATCTCA
129 TCAGTGCCTCATCAGGAAGATG---AC--CGCGTCGTTTGTTTCAACTCGCTCCTCCGTATCTCA
* *
26874 TCCGGAAGACTA
189 TCAGGAAGACAA
* *
26886 ATTTGGATCACTTCTCAGTACCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAG
1 ATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAG
*
26951 TGTCTCATCAGGAAGCTGGGGTTCAAATATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCT
66 TGTCTCATCAGGAAGCTGGGGTTCAAAGA-TTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCT
* * *
27016 CAGTGTCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGA
130 CAGTGCCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAACTCGCTCCTCCGTATCTCATCAGGA
*
27081 AGGCAA
195 AGACAA
* * *
27087 ATTTGGTTCACTTCTCAGT-TCTCATCAGGAAGCTAACCTTTTATTGCTTTGACTTGCTTCTAAG
1 ATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAG
* * **
27151 TATCTTC-TAAGGAAGCTGGGGTTTGAAGATTT
66 TGTC-TCATCAGGAAGCTGGGGTTCAAAGATTT
27183 TATTTTCTTT
Statistics
Matches: 264, Mismatches: 28, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
199 6 0.02
200 63 0.24
201 57 0.22
203 52 0.20
204 86 0.33
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.36
Consensus pattern (200 bp):
ATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAG
TGTCTCATCAGGAAGCTGGGGTTCAAAGATTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCTC
AGTGCCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAACTCGCTCCTCCGTATCTCATCAGGAA
GACAA
Done.