Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013539.1 Kokia drynarioides strain JFW-HI SEQ_128565, 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: 23660
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Found at i:4266 original size:27 final size:27
Alignment explanation
Indices: 4211--4267 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
4201 AGTGTGTGGG
* * *
4211 TTCAAATCCTCAGCTGGAGAGTGATGA
1 TTCAAAGCCTCAGCTGGACAGTGAAGA
*
4238 TTCAAAGCCTCAGCTGGACATTGAAGA
1 TTCAAAGCCTCAGCTGGACAGTGAAGA
4265 TTC
1 TTC
4268 GAAGGTGCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (27 bp):
TTCAAAGCCTCAGCTGGACAGTGAAGA
Found at i:9446 original size:10 final size:10
Alignment explanation
Indices: 9427--9459 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
9417 AACTTATATT
9427 AAAAAG-AAA
1 AAAAAGAAAA
9436 AAAAAGAAAA
1 AAAAAGAAAA
9446 AAAAAGAAAGA
1 AAAAAGAAA-A
9457 AAA
1 AAA
9460 TCAAATCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 6 0.27
10 12 0.55
11 4 0.18
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:11697 original size:6 final size:6
Alignment explanation
Indices: 11683--11797 Score: 84
Period size: 6 Copynumber: 20.0 Consensus size: 6
11673 TTTAATTTAT
* * * *
11683 TTTAAA TTTAGA TTT-AT TTTAAT TTTAAA -TT-AA TCTTAAA TTTAGA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
* *
11729 TTT-AT TTTAAA TTTAGA TTT--A TCTTAAA TTTAAA TTT-AA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAAA TTTAAA
*
11774 TTTAAA TTT-AA TTTCAAA GTTAAA
1 TTTAAA TTTAAA TTT-AAA TTTAAA
11798 AAGTCCAAAG
Statistics
Matches: 88, Mismatches: 10, Indels: 22
0.73 0.08 0.18
Matches are distributed among these distances:
4 4 0.05
5 20 0.23
6 55 0.62
7 9 0.10
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:11699 original size:17 final size:17
Alignment explanation
Indices: 11676--11797 Score: 145
Period size: 17 Copynumber: 7.1 Consensus size: 17
11666 GACCTTTTTT
11676 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
* *
11693 GATTTATTTTAATTTTA
1 AATTTATTTTAAATTTA
* *
11710 AATTAATCTTAAATTTA
1 AATTTATTTTAAATTTA
*
11727 GATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
* *
11744 GATTTATCTTAAATTTA
1 AATTTATTTTAAATTTA
*
11761 AATTTAATTTAAATTTA
1 AATTTATTTTAAATTTA
* *
11778 AATTTAATTTCAAAGTTA
1 AATTT-ATTTTAAATTTA
11796 AA
1 AA
11798 AAGTCCAAAG
Statistics
Matches: 88, Mismatches: 16, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
17 77 0.88
18 11 0.12
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.53
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:11783 original size:34 final size:34
Alignment explanation
Indices: 11676--11783 Score: 162
Period size: 34 Copynumber: 3.2 Consensus size: 34
11666 GACCTTTTTT
* *
11676 AATTTATTTTAAATTTAGATTTATTTTAATTTTA
1 AATTTATCTTAAATTTAGATTTATTTTAAATTTA
*
11710 AATTAATCTTAAATTTAGATTTATTTTAAATTTA
1 AATTTATCTTAAATTTAGATTTATTTTAAATTTA
* * *
11744 GATTTATCTTAAATTTAAATTTAATTTAAATTTA
1 AATTTATCTTAAATTTAGATTTATTTTAAATTTA
11778 AATTTA
1 AATTTA
11784 ATTTCAAAGT
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 66 1.00
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.56
Consensus pattern (34 bp):
AATTTATCTTAAATTTAGATTTATTTTAAATTTA
Found at i:13674 original size:30 final size:28
Alignment explanation
Indices: 13496--13835 Score: 208
Period size: 29 Copynumber: 11.6 Consensus size: 28
13486 AAACTATTCG
*
13496 AAAATTACCATTTTATCCCTGAAA-TTCCA
1 AAAATTACCATTTTA-CCC-CAAACTTCCA
* *
13525 AAAA-TCCCATTTTTTGACCCCAAAACTTCTA
1 AAAATTACCA--TTTT-ACCCC-AAACTTCCA
* * ***
13556 GAAATTATCATTTTACTCTTGAACTTCCA
1 AAAATTACCATTTTAC-CCCAAACTTCCA
* * *
13585 AAAA-TCCCATTCTGA-CCCAAACCTTCTA
1 AAAATTACCATT-TTACCCCAAA-CTTCCA
13613 AAAATTACCATTTTACCCCTAAACTTCCA
1 AAAATTACCATTTTACCCC-AAACTTCCA
* * *
13642 AAAA-TCCCATTTTTGACCTCAAAACTTTCA
1 AAAATTACCA-TTTT-ACC-CCAAACTTCCA
13672 AAAATTACCATTTTACCCCTAAACTTCCA
1 AAAATTACCATTTTACCCC-AAACTTCCA
* ** *
13701 AAAATT-CCATTTTTGA-CTCGTACATTCTA
1 AAAATTACCA-TTTT-ACCCCAAAC-TTCCA
*
13730 AAAATTACCATTTTACCCCCAAACTTTCA
1 AAAATTACCATTTTA-CCCCAAACTTCCA
* * * *
13759 AAAAATCCCATTTTTAACCTCGAACCTTCCA
1 AAAATTACCA-TTTT-ACC-CCAAACTTCCA
*
13790 AAAATTACCATTTTACCCCCGAACTTCCAA
1 AAAATTACCATTTTA-CCCCAAACTTCC-A
13820 AAAATTACCATTTTAC
1 AAAATTACCATTTTAC
13836 TTCCGGATGT
Statistics
Matches: 237, Mismatches: 46, Indels: 56
0.70 0.14 0.17
Matches are distributed among these distances:
27 3 0.01
28 31 0.13
29 97 0.41
30 73 0.31
31 30 0.13
32 3 0.01
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.33
Consensus pattern (28 bp):
AAAATTACCATTTTACCCCAAACTTCCA
Found at i:13737 original size:117 final size:117
Alignment explanation
Indices: 13496--13833 Score: 421
Period size: 117 Copynumber: 2.9 Consensus size: 117
13486 AAACTATTCG
* * *
13496 AAAATTACCATTTTATCCCTGAAA-TTCCAAAAATCCCATTTTTTGACCCCAAAAC-TTCTAGAA
1 AAAATTACCATTTTACCCCT-AAACTTCCAAAAATCCCA-TTTTTGACCTCAAAACTTTC-AAAA
* * * * * *
13559 ATTATCATTTTACTCTTGAACTTCCAAAAATCCCA-TTCTGACCCAAACCTTCTA
63 ATTACCATTTTACCCCTGAACTTCCAAAAATTCCATTTTTGACCCAAACATTCTA
13613 AAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCTCAAAACTTTCAAAAATT
1 AAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCTCAAAACTTTCAAAAATT
* * **
13678 ACCATTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACTCGTACATTCTA
66 ACCATTTTACCCCTGAACTTCCAAAAATTCCATTTTTGACCCAAACATTCTA
* * * * * *
13730 AAAATTACCATTTTACCCCCAAACTTTCAAAAAATCCCATTTTTAACCTCGAACCTTCCAAAAAT
1 AAAATTACCATTTTACCCCTAAAC-TTCCAAAAATCCCATTTTTGACCTCAAAACTTTCAAAAAT
*
13795 TACCATTTTACCCCCGAACTTCCAAAAAATTACCATTTT
65 TACCATTTTACCCCTGAACTTCC-AAAAATT-CCATTTT
13834 ACTTCCGGAT
Statistics
Matches: 194, Mismatches: 21, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
116 51 0.26
117 73 0.38
118 56 0.29
119 7 0.04
120 7 0.04
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.33
Consensus pattern (117 bp):
AAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCTCAAAACTTTCAAAAATT
ACCATTTTACCCCTGAACTTCCAAAAATTCCATTTTTGACCCAAACATTCTA
Found at i:13834 original size:60 final size:59
Alignment explanation
Indices: 13496--13822 Score: 394
Period size: 59 Copynumber: 5.6 Consensus size: 59
13486 AAACTATTCG
* * *
13496 AAAATTACCATTTTATCCCTGAAA-TTCCAAAAATCCCATTTTTTGACCCCAAAACTTCTA
1 AAAATTACCATTTTACCCCT-AAACTTCCAAAAATCCCA-TTTTTGACCTCAAACCTTCTA
* * * * * *
13556 GAAATTATCATTTTACTCTTGAACTTCCAAAAATCCCA-TTCTGACC-CAAACCTTCTA
1 AAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCTCAAACCTTCTA
*
13613 AAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCTCAAAACTT-TCA
1 AAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCTCAAACCTTCT-A
* ** *
13672 AAAATTACCATTTTACCCCTAAACTTCCAAAAATTCCATTTTTGA-CTCGTACATTCTA
1 AAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCTCAAACCTTCTA
* * * * *
13730 AAAATTACCATTTTACCCCCAAACTTTCAAAAAATCCCATTTTTAACCTCGAACCTTCCA
1 AAAATTACCATTTTACCCCTAAAC-TTCCAAAAATCCCATTTTTGACCTCAAACCTTCTA
**
13790 AAAATTACCATTTTACCCCCGAACTTCCAAAAA
1 AAAATTACCATTTTACCCCTAAACTTCCAAAAA
13823 ATTACCATTT
Statistics
Matches: 231, Mismatches: 29, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
57 43 0.19
58 45 0.19
59 81 0.35
60 62 0.27
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.32
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCTCAAACCTTCTA
Found at i:13850 original size:30 final size:30
Alignment explanation
Indices: 13612--13835 Score: 167
Period size: 30 Copynumber: 7.6 Consensus size: 30
13602 CAAACCTTCT
**
13612 AAAAATTACCATTTTACCCCTAAACTTCC-
1 AAAAATTACCATTTTACCCCCGAACTTCCA
* * ** *
13641 AAAAA-TCCCATTTTTGACCTCAAAACTTTC-
1 AAAAATTACCA-TTTT-ACCCCCGAACTTCCA
**
13671 AAAAATTACCATTTTACCCCTAAACTTCC-
1 AAAAATTACCATTTTACCCCCGAACTTCCA
*** * * *
13700 AAAAATT-CCATTTTTGACTCGTACATT-CT
1 AAAAATTACCATTTTACCCCCGAAC-TTCCA
* *
13729 AAAAATTACCATTTTACCCCCAAACTTTCA
1 AAAAATTACCATTTTACCCCCGAACTTCCA
* * *
13759 AAAAA-TCCCATTTTTAACCTCGAACCTTCC-
1 AAAAATTACCA-TTTTACCCCCGAA-CTTCCA
13789 AAAAATTACCATTTTACCCCCGAACTTCCA
1 AAAAATTACCATTTTACCCCCGAACTTCCA
13819 AAAAATTACCATTTTAC
1 AAAAATTACCATTTTAC
13836 TTCCGGATGT
Statistics
Matches: 154, Mismatches: 30, Indels: 21
0.75 0.15 0.10
Matches are distributed among these distances:
28 15 0.10
29 47 0.31
30 80 0.52
31 12 0.08
ACGTcount: A:0.37, C:0.29, G:0.02, T:0.32
Consensus pattern (30 bp):
AAAAATTACCATTTTACCCCCGAACTTCCA
Done.