Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009670.1 Kokia drynarioides strain JFW-HI SEQ_124388, 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: 3030
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.24
Found at i:1384 original size:27 final size:28
Alignment explanation
Indices: 1345--1403 Score: 93
Period size: 27 Copynumber: 2.1 Consensus size: 28
1335 AACTTTCAAC
*
1345 TAATGATTGTTTCCTTTGATCCTCTTTT
1 TAATGATTGTTTCCTTTGATCCTCTTCT
*
1373 TAAT-ATTGTTTCTTTTGATCCTCTTCT
1 TAATGATTGTTTCCTTTGATCCTCTTCT
1400 TAAT
1 TAAT
1404 TATTTTGGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 25 0.86
28 4 0.14
ACGTcount: A:0.17, C:0.17, G:0.08, T:0.58
Consensus pattern (28 bp):
TAATGATTGTTTCCTTTGATCCTCTTCT
Found at i:2360 original size:206 final size:205
Alignment explanation
Indices: 1880--2550 Score: 794
Period size: 204 Copynumber: 3.3 Consensus size: 205
1870 TCCCAACTTA
*
1880 AAGCAGATCGGAGCAATAAACA-GTTAGCTTCCTGATGAGATACGGAGAAGTGAACCAAATTCGT
1 AAGCAGATCGAAGCAATAAA-AGGTTAGCTTCCTGATGAGATACGGAGAAGTGAACCAAATTCGT
* * *
1944 CTTCCTGGTGAGATACAGAGAAGCG-GATTGAAACAAGCTATACGGTCATCTTCCTAATGAGATA
65 CTTCCTGGTGAGATACAAAGAAGCGAG-TTGAAACAAGCGATACGGTCATCTTCCTGATGAGATA
* * * * *
2008 CTGACAAGA-AGACCAAGTCAAACCCACGCTCGAAGTGAGCAAGTCTTCGAATCCCAGC-TCCTG
129 CTGACAAGAGA-ACCAAATCGAACCCACGCTCAAAGCGAGCAAATCTTCGAATCCCAGCTTCCTG
*
2071 ATGAGACACCGAG
193 ATGAGACACTGAG
* * * *
2084 AAGCAGATGGGAGCAATAAACGGTTAGCTTCCTGATGAGATACGGAGAAGTAAACCAAATTCGTC
1 AAGCAGATCGAAGCAATAAAAGGTTAGCTTCCTGATGAGATACGGAGAAGTGAACCAAATTCGTC
* * * *
2149 TTCCTGGTAAGATACAAAGAGGCGAGTTGAAACAAGCGATACGGTCATCTTCCTGACGAGATATT
66 TTCCTGGTGAGATACAAAGAAGCGAGTTGAAACAAGCGATACGGTCATCTTCCTGATGAGATACT
* *
2214 GGA-AAGAGAACCAAATCGAACCCACGCTCAAAGCGAACAAAATCTTCGAATCCCATCTTCCT-A
131 -GACAAGAGAACCAAATCGAACCCACGCTCAAAGCGAGC-AAATCTTCGAATCCCAGCTTCCTGA
* *
2277 AGAAGATACTGAG
194 TG-AGACACTGAG
* * *
2290 AAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGCC
1 AAGCAGATCGAAGCAATAAAAGGTTAGCTTCCTGATGAGATACGGAGAAGTGAACCAAATTCGTC
* * ** *
2355 TTCCTGATGAGATACAAAGAAGCGAGTTGAAACAAACGACGCGGTCATCTTCCTGATGAGACACT
66 TTCCTGGTGAGATACAAAGAAGCGAGTTGAAACAAGCGATACGGTCATCTTCCTGATGAGATACT
* * * *
2420 GAGAAGAAGACCCAAA-CG-----AGGCTCAAAACGAGCAAATCTTCGAA-CCCTAGCTTCCTGA
131 GACAAG-AGAACCAAATCGAACCCACGCTCAAAGCGAGCAAATCTTCGAATCCC-AGCTTCCTGA
*
2478 TGAGACGCTGAG
194 TGAGACACTGAG
* * * * *
2490 AAGTAGGTCGAAGCCAT-AAAGTAGTTAGCTCCCTGATGAGATACAGAGAAGTGAACCAAAT
1 AAGCAGATCGAAGCAATAAAAG--GTTAGCTTCCTGATGAGATACGGAGAAGTGAACCAAAT
2551 CCTGATGAAA
Statistics
Matches: 406, Mismatches: 48, Indels: 29
0.84 0.10 0.06
Matches are distributed among these distances:
199 7 0.02
200 41 0.10
201 50 0.12
204 145 0.36
205 24 0.06
206 131 0.32
207 8 0.02
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.19
Consensus pattern (205 bp):
AAGCAGATCGAAGCAATAAAAGGTTAGCTTCCTGATGAGATACGGAGAAGTGAACCAAATTCGTC
TTCCTGGTGAGATACAAAGAAGCGAGTTGAAACAAGCGATACGGTCATCTTCCTGATGAGATACT
GACAAGAGAACCAAATCGAACCCACGCTCAAAGCGAGCAAATCTTCGAATCCCAGCTTCCTGATG
AGACACTGAG
Found at i:2985 original size:17 final size:17
Alignment explanation
Indices: 2963--3029 Score: 89
Period size: 17 Copynumber: 3.9 Consensus size: 17
2953 CAAACTCCCT
2963 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
* *
2980 TTAAATTTGTTTAAAAA
1 TTAAATTTATTTTAAAA
*
2997 TTTAAATTTATTTTAAAT
1 -TTAAATTTATTTTAAAA
*
3015 TTAAATTTAATTTAA
1 TTAAATTTATTTTAA
3030 G
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
17 29 0.67
18 14 0.33
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Done.