Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002363.1 Kokia drynarioides strain JFW-HI SEQ_114437, 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: 28090
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Warning! 65 characters in sequence are not A, C, G, or T
Found at i:828 original size:17 final size:17
Alignment explanation
Indices: 803--863 Score: 95
Period size: 17 Copynumber: 3.6 Consensus size: 17
793 TAAATTTAGT
* *
803 TTTATAATAAATTTAAA
1 TTTAAAATAAACTTAAA
*
820 TTTCAAATAAACTTAAA
1 TTTAAAATAAACTTAAA
837 TTTAAAATAAACTTAAA
1 TTTAAAATAAACTTAAA
854 TTTAAAATAA
1 TTTAAAATAA
864 GTTCAATTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (17 bp):
TTTAAAATAAACTTAAA
Found at i:4211 original size:20 final size:21
Alignment explanation
Indices: 4181--4219 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
4171 AATATATAAA
4181 ATTTCAAAATTCAAAGTTTTT
1 ATTTCAAAATTCAAAGTTTTT
*
4202 ATTT-AAAATTTAAAGTTT
1 ATTTCAAAATTCAAAGTTT
4220 AATTAATAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (21 bp):
ATTTCAAAATTCAAAGTTTTT
Found at i:4459 original size:2 final size:2
Alignment explanation
Indices: 4454--4487 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
4444 TTACACACAC
*
4454 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4488 TCTTGTTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9471 original size:30 final size:28
Alignment explanation
Indices: 9397--9484 Score: 81
Period size: 30 Copynumber: 3.1 Consensus size: 28
9387 CAAATGCCTC
*
9397 TAAAATAATAGCAAAATTAACAATAAAA
1 TAAAATAATAGCAATATTAACAATAAAA
* * *
9425 CAAGAATTATA-TAATATTCAAACAATAAAA
1 TAA-AATAATAGCAATATT--AACAATAAAA
* *
9455 TAAAATAATAGCAATA-TAATAACAAAA
1 TAAAATAATAGCAATATTAACAATAAAA
9482 TAA
1 TAA
9485 CAGGAAAAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
27 11 0.23
28 7 0.15
29 13 0.28
30 16 0.34
ACGTcount: A:0.65, C:0.08, G:0.03, T:0.24
Consensus pattern (28 bp):
TAAAATAATAGCAATATTAACAATAAAA
Found at i:10700 original size:190 final size:188
Alignment explanation
Indices: 10370--10832 Score: 460
Period size: 190 Copynumber: 2.5 Consensus size: 188
10360 AAATATCCCC
*
10370 CATTCAACCTAAATTTTCTTTGCACCCAATTTTCATTCTATACA-AG-TTA--TAT-TT-TAAGT
1 CATTCAACCT-AATTTACTTTGCACCCAATTTTCATTCTATACACAGTTTAGTTATATTCTAAGT
* * * ** * * * *
10429 CGATT-AACTCTTAACTCGATTGGTATAAGTATAGTTGTTCGTGTGGGAGGATATAAATTTGAGT
65 CGATTGAA-TCTTAGCTCGATTAGTATAAGCATAGTTGTTAATATAGAAGGATATAAATTCGAGT
** * *
10493 ACGTTGAAATGCATTATCCTCTTATTTATG-GATTGAGAAGGGATTACGGA-TAGTTTTAGG
129 ACGTTGAAACACATTATCCTCTTATTTATGAG-TTGAGAAGGGACTA-GGAGTAGTTCTAGG
* *
10553 TATTCAACCTAATTCTACTTTGCACCCAATTTTCATTCTATACACAGTTTGAGTTATATTCTATG
1 CATTCAACCTAATT-TACTTTGCACCCAATTTTCATTCTATACACAGTTT-AGTTATATTCTAAG
** * **
10618 TCGATTGAATCTTAGCTCGATTAGTATGGGCATTGTTGTTAATATAGAAGGATATGGATTCGAGT
64 TCGATTGAATCTTAGCTCGATTAGTATAAGCATAGTTGTTAATATAGAAGGATATAAATTCGAGT
* * * * * *
10683 GCGTTGAAGCACATTATCCTCTTATTTATGAGTTGGGGAGGGGCTATGAGTAGTTCTAGG
129 ACGTTGAAACACATTATCCTCTTATTTATGAGTTGAGAAGGGACTAGGAGTAGTTCTAGG
* * *
10743 CGTTCAACCCAATTATACTTTGCACCCAATTTTCATTCTATACACAATTTATAAGTTGATATTCT
1 CATTCAACCTAATT-TACTTTGCACCCAATTTTCATTCTATACAC-AGTT-T-AGTT-ATATTCT
* *
10808 AAG-CTGATTGAGTCTTAGCTTGATT
61 AAGTC-GATTGAATCTTAGCTCGATT
10833 GATATGAACA
Statistics
Matches: 229, Mismatches: 36, Indels: 20
0.80 0.13 0.07
Matches are distributed among these distances:
182 4 0.02
183 37 0.16
184 2 0.01
185 2 0.01
186 1 0.00
188 3 0.01
189 4 0.02
190 137 0.60
191 6 0.03
192 6 0.03
193 27 0.12
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (188 bp):
CATTCAACCTAATTTACTTTGCACCCAATTTTCATTCTATACACAGTTTAGTTATATTCTAAGTC
GATTGAATCTTAGCTCGATTAGTATAAGCATAGTTGTTAATATAGAAGGATATAAATTCGAGTAC
GTTGAAACACATTATCCTCTTATTTATGAGTTGAGAAGGGACTAGGAGTAGTTCTAGG
Found at i:26941 original size:11 final size:11
Alignment explanation
Indices: 26922--26977 Score: 60
Period size: 11 Copynumber: 5.0 Consensus size: 11
26912 GACTGGGCCC
*
26922 TTTTTAATTTA
1 TTTTAAATTTA
26933 TTTTAAATTTGA
1 TTTTAAATTT-A
26945 -TTTAAATTTAA
1 TTTTAAATTT-A
*
26956 TTTTAAATTAA
1 TTTTAAATTTA
*
26967 TCTTAAATTTA
1 TTTTAAATTTA
26978 AATTAAATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
11 29 0.76
12 9 0.24
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (11 bp):
TTTTAAATTTA
Found at i:26955 original size:6 final size:6
Alignment explanation
Indices: 26934--27001 Score: 65
Period size: 6 Copynumber: 12.0 Consensus size: 6
26924 TTTAATTTAT
* *
26934 TTTAAA TTT-GA TTTAAA TTTAAT TTTAAA -TT-AA TCTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
*
26980 -TTAAA -TTAAA TTTAAA ATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
27002 AAGTCCAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
4 2 0.04
5 16 0.31
6 31 0.60
7 3 0.06
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:26966 original size:17 final size:17
Alignment explanation
Indices: 26946--27001 Score: 69
Period size: 17 Copynumber: 3.3 Consensus size: 17
26936 TAAATTTGAT
26946 TTAAATTTAATTTTAAA
1 TTAAATTTAATTTTAAA
*
26963 TT-AATCTTAAATTTAAA
1 TTAAAT-TTAATTTTAAA
* *
26980 TTAAATTAAATTTAAAA
1 TTAAATTTAATTTTAAA
26997 TTAAA
1 TTAAA
27002 AAGTCCAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 3 0.09
17 27 0.82
18 3 0.09
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
TTAAATTTAATTTTAAA
Found at i:26983 original size:11 final size:11
Alignment explanation
Indices: 26934--27001 Score: 59
Period size: 11 Copynumber: 6.0 Consensus size: 11
26924 TTTAATTTAT
**
26934 TTTAAATTTGA
1 TTTAAATTAAA
*
26945 TTTAAATTTAAT
1 TTTAAA-TTAAA
26957 TTTAAATT-AA
1 TTTAAATTAAA
26967 TCTTAAATTTAAA
1 T-TTAAA-TTAAA
26980 -TTAAATTAAA
1 TTTAAATTAAA
26990 TTTAAAATTAAA
1 TTT-AAATTAAA
27002 AAGTCCAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
10 7 0.15
11 20 0.43
12 18 0.38
13 2 0.04
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:27634 original size:21 final size:21
Alignment explanation
Indices: 27608--27683 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 21
27598 ATGTTTCGAA
*
27608 AATATCATTAATAATATTACT
1 AATATCATTAATAATATTAAT
* *
27629 AATATCATTAACAATATTATT
1 AATATCATTAATAATATTAAT
* * * *
27650 GACAACAATAATAATATTTAAT
1 AATATCATTAATAATA-TTAAT
*
27672 AATAGCATTAAT
1 AATATCATTAAT
27684 TAAAAAAAAA
Statistics
Matches: 42, Mismatches: 12, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
21 30 0.71
22 12 0.29
ACGTcount: A:0.50, C:0.09, G:0.03, T:0.38
Consensus pattern (21 bp):
AATATCATTAATAATATTAAT
Done.