Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013695.1 Kokia drynarioides strain JFW-HI SEQ_128723, 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: 6460
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Warning! 51 characters in sequence are not A, C, G, or T
Found at i:2886 original size:26 final size:28
Alignment explanation
Indices: 2830--2887 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
2820 ACAATTTTCA
*
2830 TTTAATGATTGTTTTCTGTGACCCTCTT
1 TTTAATGATTGTTTCCTGTGACCCTCTT
*
2858 TTTAAT-ATTGTTTCCT-TCGATCCTCTT
1 TTTAATGATTGTTTCCTGT-GACCCTCTT
2885 TTT
1 TTT
2888 TTAATAGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 1 0.04
27 20 0.74
28 6 0.22
ACGTcount: A:0.14, C:0.19, G:0.10, T:0.57
Consensus pattern (28 bp):
TTTAATGATTGTTTCCTGTGACCCTCTT
Found at i:3844 original size:146 final size:146
Alignment explanation
Indices: 3580--3869 Score: 490
Period size: 146 Copynumber: 2.0 Consensus size: 146
3570 ATGAGATACA
3580 GAGAAGCGAATTGAAACAAACGACGCAATCATCTTCCCGATGAGATACTAAGAAGAAGACCAAAT
1 GAGAAGCGAATTGAAACAAACGACGCAATCATCTTCCCGATGAGATACTAAGAAGAAGACCAAAT
*
3645 CAAACTCACACCCGATGTGAGCAAATCTTCAAACCCCAGCTTCCTGATGAGACACTGAGAAGCAA
66 CAAACTCACACCCGATGTGAGCAAATCTTCAAACCCCAACTTCCTGATGAGACACTGAGAAGCAA
3710 GTCGAAGTAATAAAAT
131 GTCGAAGTAATAAAAT
* * * * *
3726 GAGAAGCGAATTGAAACAGACGACGCAGTCATTTTCCCGATGAGATACTGAGAAGAAGATCAAAT
1 GAGAAGCGAATTGAAACAAACGACGCAATCATCTTCCCGATGAGATACTAAGAAGAAGACCAAAT
** * *
3791 CAAACTCACGTCCGATGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGACACTGAGAAGCAG
66 CAAACTCACACCCGATGTGAGCAAATCTTCAAACCCCAACTTCCTGATGAGACACTGAGAAGCAA
3856 GTCGAAGTAATAAA
131 GTCGAAGTAATAAA
3870 GCGGTTAGCT
Statistics
Matches: 134, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
146 134 1.00
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.18
Consensus pattern (146 bp):
GAGAAGCGAATTGAAACAAACGACGCAATCATCTTCCCGATGAGATACTAAGAAGAAGACCAAAT
CAAACTCACACCCGATGTGAGCAAATCTTCAAACCCCAACTTCCTGATGAGACACTGAGAAGCAA
GTCGAAGTAATAAAAT
Found at i:4344 original size:18 final size:18
Alignment explanation
Indices: 4320--4448 Score: 124
Period size: 17 Copynumber: 7.4 Consensus size: 18
4310 CCAAACTCCC
4320 TTTAAATTTATTTTAAAA
1 TTTAAATTTATTTTAAAA
* *
4338 ATTAAATTT-GTTTAAAA
1 TTTAAATTTATTTTAAAA
4355 TTTTAAATTTATTTT-AAA
1 -TTTAAATTTATTTTAAAA
*
4373 TTTAAATTTATTTT-GAA
1 TTTAAATTTATTTTAAAA
* * * *
4390 TTTAATTTTA-ATTCAAG
1 TTTAAATTTATTTTAAAA
*
4407 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTTAAAA
* *
4425 TTTAAAATTATTAT-AAA
1 TTTAAATTTATTTTAAAA
4442 TTTAAAT
1 TTTAAAT
4449 AAAGCTAAAA
Statistics
Matches: 92, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
16 2 0.02
17 51 0.55
18 36 0.39
19 3 0.03
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (18 bp):
TTTAAATTTATTTTAAAA
Found at i:4368 original size:11 final size:11
Alignment explanation
Indices: 4354--4428 Score: 54
Period size: 11 Copynumber: 7.1 Consensus size: 11
4344 TTTGTTTAAA
4354 ATTTTAAATTT
1 ATTTTAAATTT
4365 ATTTT-AA---
1 ATTTTAAATTT
4372 A-TTTAAATTT
1 ATTTTAAATTT
*
4382 ATTTTGAATTT
1 ATTTTAAATTT
*
4393 AATTTT-AATTCA
1 -ATTTTAAATT-T
*
4405 AGTTTAAATTT
1 ATTTTAAATTT
4416 ATTTTCAAATTT
1 ATTTT-AAATTT
4428 A
1 A
4429 AAATTATTAT
Statistics
Matches: 50, Mismatches: 5, Indels: 17
0.69 0.07 0.24
Matches are distributed among these distances:
6 3 0.06
7 3 0.06
10 3 0.06
11 25 0.50
12 16 0.32
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (11 bp):
ATTTTAAATTT
Found at i:4376 original size:6 final size:6
Alignment explanation
Indices: 4356--4448 Score: 54
Period size: 6 Copynumber: 16.2 Consensus size: 6
4346 TGTTTAAAAT
* * * *
4356 TTTAAA TTT-AT TTTAAA TTTAAA TTT-AT TTTGAA TTT-AA TTTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * *
4401 TTCAAG TTTAAA TTT-AT TTTCAAA TTTAAA ATT--A TTATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TT-TAAA TTTAAA
4448 T
1 T
4449 AAAGCTAAAA
Statistics
Matches: 66, Mismatches: 13, Indels: 16
0.69 0.14 0.17
Matches are distributed among these distances:
4 2 0.03
5 18 0.27
6 39 0.59
7 7 0.11
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:4392 original size:35 final size:34
Alignment explanation
Indices: 4320--4448 Score: 141
Period size: 35 Copynumber: 3.7 Consensus size: 34
4310 CCAAACTCCC
* * *
4320 TTTAAATTTATTTTAAAAATTAAATTTGTTTAAAA
1 TTTAAATTTATTTT-AAATTTAAATTTATTTTAAA
*
4355 TTTTAAATTTATTTTAAATTTAAATTTATTTTGAA
1 -TTTAAATTTATTTTAAATTTAAATTTATTTTAAA
* * * *
4390 TTTAATTTTAATTCAAGTTTAAATTTATTTTCAAA
1 TTTAAATTTATTTTAAATTTAAATTTATTTT-AAA
* *
4425 TTTAAAATTATTATAAATTTAAAT
1 TTTAAATTTATTTTAAATTTAAAT
4449 AAAGCTAAAA
Statistics
Matches: 77, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
34 27 0.35
35 36 0.47
36 14 0.18
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (34 bp):
TTTAAATTTATTTTAAATTTAAATTTATTTTAAA
Found at i:5164 original size:3 final size:3
Alignment explanation
Indices: 5158--5198 Score: 55
Period size: 3 Copynumber: 13.0 Consensus size: 3
5148 ATAAATGCTT
*
5158 TAA TAA TAA TAA TAA TAA TAA TATT TAA TAA TTAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA -TAA TAA TAA
5199 AAAAGGAGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 29 0.85
4 5 0.15
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:6311 original size:93 final size:92
Alignment explanation
Indices: 6152--6340 Score: 362
Period size: 93 Copynumber: 2.1 Consensus size: 92
6142 AAAACGGTTT
6152 TAAAAAGGGATTTTCTAAAATCTGTTAAAAAAGATCGGGGTTTTATCTCACCGGATTTAAACTCG
1 TAAAAAGGGATTTTCTAAAATCTGTTAAAAAAGATCGGGGTTTTATCTCACCGGATTTAAACTCG
6217 ATCTCCGTTTAAAAGAGTATACAAAAG
66 ATCTCCGTTTAAAAGAGTATACAAAAG
6244 NTAAAAAGGGATTTTCTAAAATCTGTTAAAAAAGATCGGGGTTTTATCTCACCGGATTTAAACTC
1 -TAAAAAGGGATTTTCTAAAATCTGTTAAAAAAGATCGGGGTTTTATCTCACCGGATTTAAACTC
6309 GATCTCCGTTTAAAAGAGTATACAAAAG
65 GATCTCCGTTTAAAAGAGTATACAAAAG
6337 -AAAA
1 TAAAA
6341 GGCAGTAAGA
Statistics
Matches: 96, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
91 4 0.04
93 92 0.96
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (92 bp):
TAAAAAGGGATTTTCTAAAATCTGTTAAAAAAGATCGGGGTTTTATCTCACCGGATTTAAACTCG
ATCTCCGTTTAAAAGAGTATACAAAAG
Done.