Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003613.1 Kokia drynarioides strain JFW-HI SEQ_116502, 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: 19879
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Warning! 27 characters in sequence are not A, C, G, or T
Found at i:1003 original size:37 final size:37
Alignment explanation
Indices: 962--1047 Score: 172
Period size: 37 Copynumber: 2.3 Consensus size: 37
952 ATACCAGGGA
962 AAGGTGGTATTTTAAGTGGGTGATCAGAAGAAACTCG
1 AAGGTGGTATTTTAAGTGGGTGATCAGAAGAAACTCG
999 AAGGTGGTATTTTAAGTGGGTGATCAGAAGAAACTCG
1 AAGGTGGTATTTTAAGTGGGTGATCAGAAGAAACTCG
1036 AAGGTGGTATTT
1 AAGGTGGTATTT
1048 AACTAAAATT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.31, C:0.07, G:0.33, T:0.29
Consensus pattern (37 bp):
AAGGTGGTATTTTAAGTGGGTGATCAGAAGAAACTCG
Found at i:1653 original size:63 final size:64
Alignment explanation
Indices: 1499--1653 Score: 222
Period size: 63 Copynumber: 2.4 Consensus size: 64
1489 CTAAGTCCCG
* * * * *
1499 AAAATCCCCAAATCCAAGAACCCTAAAAATCTCAAAAATCCTTAAATTTTTTTAAAGCTAAACC
1 AAAATCCACAAACCCAAGAACCCTAAAAATCCCAAAAATCCTCAAATTTTTTTAAACCTAAACC
* *
1563 AAAATCCACAAACCCAAGAACCTTAAAAATCCCGAAAATCCTCAAA-TTTTTTAAACCTAAACC
1 AAAATCCACAAACCCAAGAACCCTAAAAATCCCAAAAATCCTCAAATTTTTTTAAACCTAAACC
* *
1626 AAAATCCTCAAACCCAATAACCCTAAAA
1 AAAATCCACAAACCCAAGAACCCTAAAA
1654 CTTAATCGAA
Statistics
Matches: 81, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
63 41 0.51
64 40 0.49
ACGTcount: A:0.48, C:0.28, G:0.03, T:0.21
Consensus pattern (64 bp):
AAAATCCACAAACCCAAGAACCCTAAAAATCCCAAAAATCCTCAAATTTTTTTAAACCTAAACC
Found at i:1871 original size:17 final size:18
Alignment explanation
Indices: 1845--1879 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1835 GGGTAAATAT
*
1845 TTTATTTTTTAA-TTTAA
1 TTTATGTTTTAACTTTAA
1862 TTTATGTTTTAACTTTAA
1 TTTATGTTTTAACTTTAA
1880 AAATTTTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (18 bp):
TTTATGTTTTAACTTTAA
Found at i:4156 original size:14 final size:14
Alignment explanation
Indices: 4132--4164 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
4122 ACTTTTTGTT
4132 TTTAA-ATTTAAAA
1 TTTAATATTTAAAA
4145 TTTAATATTTAAAA
1 TTTAATATTTAAAA
4159 TTTAAT
1 TTTAAT
4165 TTTGAGACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTAATATTTAAAA
Found at i:5790 original size:20 final size:20
Alignment explanation
Indices: 5765--5803 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5755 GAAATGCTAA
5765 CAGAGGCACCAAAGTGCAAG
1 CAGAGGCACCAAAGTGCAAG
* *
5785 CAGAGGCATCGAAGTGCAA
1 CAGAGGCACCAAAGTGCAA
5804 ACTCGTACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.31, T:0.08
Consensus pattern (20 bp):
CAGAGGCACCAAAGTGCAAG
Found at i:6219 original size:27 final size:26
Alignment explanation
Indices: 6189--6293 Score: 77
Period size: 27 Copynumber: 3.9 Consensus size: 26
6179 TCTTATACCC
6189 TAAATCTTAACTTTAAACCATAAGCCT
1 TAAATCTTAACTTTAAACCATAA-CCT
* * * *
6216 TAAATCATAAATCTT-AACCTTAAACCC
1 TAAATCTTAACT-TTAAACCAT-AACCT
* * *
6243 TAAATCTTAACCTTTAAGCCTTAACAT
1 TAAATCTTAA-CTTTAAACCATAACCT
* *
6270 TAAGTCTTAAACTCTAAACCATAA
1 TAAATCTT-AACTTTAAACCATAA
6294 TGCATAAGCC
Statistics
Matches: 60, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
27 48 0.80
28 12 0.20
ACGTcount: A:0.42, C:0.23, G:0.03, T:0.32
Consensus pattern (26 bp):
TAAATCTTAACTTTAAACCATAACCT
Found at i:6236 original size:20 final size:20
Alignment explanation
Indices: 6213--6256 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
6203 AAACCATAAG
*
6213 CCTTAAATCATAAATCTTAA
1 CCTTAAACCATAAATCTTAA
*
6233 CCTTAAACCCTAAATCTTAA
1 CCTTAAACCATAAATCTTAA
6253 CCTT
1 CCTT
6257 TAAGCCTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.39, C:0.27, G:0.00, T:0.34
Consensus pattern (20 bp):
CCTTAAACCATAAATCTTAA
Found at i:16117 original size:3 final size:3
Alignment explanation
Indices: 16109--16140 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
16099 ACATGTGATA
16109 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
16141 ATTCTTGCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:16248 original size:29 final size:28
Alignment explanation
Indices: 16191--16248 Score: 64
Period size: 29 Copynumber: 2.0 Consensus size: 28
16181 GTCTTTTAGG
* *
16191 TTTAATTTTAAATTAAATATCTTGATTAT
1 TTTAATTTTAAATAAAATATCAT-ATTAT
16220 TTTAATTTTAATGATAAAATATCAT-TTAT
1 TTTAATTTTAA--ATAAAATATCATATTAT
16249 CCTTTCCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
29 15 0.60
31 10 0.40
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.53
Consensus pattern (28 bp):
TTTAATTTTAAATAAAATATCATATTAT
Found at i:16280 original size:32 final size:32
Alignment explanation
Indices: 16235--16295 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
16225 TTTTAATGAT
16235 AAAATATCATTTATCCTTTCCA-AAAATTTAAA
1 AAAATATCATTTAT-CTTTCCATAAAATTTAAA
** *
16267 AAAATATTTTTTATCTTTTCATAAAATTT
1 AAAATATCATTTATCTTTCCATAAAATTT
16296 TAAGATTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 6 0.24
32 19 0.76
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (32 bp):
AAAATATCATTTATCTTTCCATAAAATTTAAA
Found at i:16352 original size:42 final size:42
Alignment explanation
Indices: 16286--16379 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 42
16276 TTTATCTTTT
*
16286 CATAAAATTTTAAGATTTTAACTGTTTAAATATCAAGGATAA
1 CATAATATTTTAAGATTTTAACTGTTTAAATATCAAGGATAA
* * * * *
16328 -ATAATATTTTAAATATTTTTACTGTTTTAATTTTAAGGATAA
1 CATAATATTTT-AAGATTTTAACTGTTTAAATATCAAGGATAA
*
16370 CATATTATTT
1 CATAATATTT
16380 ATCCTCCAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
41 9 0.21
42 26 0.60
43 8 0.19
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.47
Consensus pattern (42 bp):
CATAATATTTTAAGATTTTAACTGTTTAAATATCAAGGATAA
Found at i:16810 original size:8 final size:8
Alignment explanation
Indices: 16797--16824 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
16787 CTTTTCATAT
16797 AAAATGTG
1 AAAATGTG
16805 AAAATGTG
1 AAAATGTG
16813 AAAATGTG
1 AAAATGTG
16821 AAAA
1 AAAA
16825 CTTAACAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.21, T:0.21
Consensus pattern (8 bp):
AAAATGTG
Found at i:18341 original size:25 final size:25
Alignment explanation
Indices: 18288--18341 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 25
18278 AATTAAATAG
*
18288 AAAATTAAGCAGATAAGTAAATGCAA
1 AAAATTAAGCA-ATAAGTAAATACAA
18314 AAAATTAAGC-ATAAGATAAAATACAA
1 AAAATTAAGCAATAAG-T-AAATACAA
18340 AA
1 AA
18342 TATGATAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 5 0.20
25 1 0.04
26 19 0.76
ACGTcount: A:0.63, C:0.07, G:0.11, T:0.19
Consensus pattern (25 bp):
AAAATTAAGCAATAAGTAAATACAA
Found at i:18520 original size:30 final size:30
Alignment explanation
Indices: 18482--18822 Score: 282
Period size: 30 Copynumber: 11.5 Consensus size: 30
18472 GTAAAAATAC
18482 AATTTTGGAAAAGTTTA-GGGTCAAAATGT
1 AATTTTGGAAAAGTTTAGGGGTCAAAATGT
* * * *
18511 GATTTTTGG-AAAGTTTAAGGGTTAAAAATGC
1 -AATTTTGGAAAAGTTT-AGGGGTCAAAATGT
* * *
18542 AATTTT-GTAAA-TTTTGGGATCAAAATGT
1 AATTTTGGAAAAGTTTAGGGGTCAAAATGT
* *
18570 GATTTTGG-GAAGTTTAGGGGTCAAAATGT
1 AATTTTGGAAAAGTTTAGGGGTCAAAATGT
* * *
18599 GATTTTGG-AAAGTTTAGGGGTTAAAATAT
1 AATTTTGGAAAAGTTTAGGGGTCAAAATGT
* * * * *
18628 AATTTTTGATAAGATTAGGGGT-TAAATAT
1 AATTTTGGAAAAGTTTAGGGGTCAAAATGT
** *
18657 AATTTTAAAAAAGTTTAGGGGTCAAAATAT
1 AATTTTGGAAAAGTTTAGGGGTCAAAATGT
* *
18687 AATTTTAGAAAAGTTTAGGGGTTAAAATGT
1 AATTTTGGAAAAGTTTAGGGGTCAAAATGT
** * * *
18717 AATTTTTAAAAAGATTAGGGGTTATAATGT
1 AATTTTGGAAAAGTTTAGGGGTCAAAATGT
* * * * *
18747 AATTTTGGAGAAGTTTATGGGTGAAGATAT
1 AATTTTGGAAAAGTTTAGGGGTCAAAATGT
** * *
18777 AATTTTAAAAAAGTTTAAGGGCCAAAATGT
1 AATTTTGGAAAAGTTTAGGGGTCAAAATGT
*
18807 AATTTTAGAAAAGTTT
1 AATTTTGGAAAAGTTT
18823 TTGAGTTAAA
Statistics
Matches: 253, Mismatches: 51, Indels: 14
0.80 0.16 0.04
Matches are distributed among these distances:
28 17 0.07
29 83 0.33
30 144 0.57
31 9 0.04
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (30 bp):
AATTTTGGAAAAGTTTAGGGGTCAAAATGT
Done.