Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007848.1 Kokia drynarioides strain JFW-HI SEQ_122485, 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: 4832
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:2485 original size:17 final size:17
Alignment explanation
Indices: 2463--2504 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
2453 TTGGAAATTG
* *
2463 AATTTAAGTTTATTTTA
1 AATTTAAATTTATTATA
2480 AATTTAAATTTATTATA
1 AATTTAAATTTATTATA
*
2497 AAATTAAA
1 AATTTAAA
2505 ATTAGAAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
AATTTAAATTTATTATA
Found at i:2555 original size:15 final size:15
Alignment explanation
Indices: 2503--2556 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 15
2493 TATAAAATTA
*
2503 AAATTAGAAAAGTCC
1 AAATTACAAAAGTCC
*
2518 -AATTACAAAAAAATCC
1 AAATTAC--AAAAGTCC
2534 AAA--ACAAAAGTCC
1 AAATTACAAAAGTCC
2547 AAATTACAAA
1 AAATTACAAA
2557 TGGCCTAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
13 10 0.32
14 5 0.16
15 7 0.23
16 7 0.23
17 2 0.06
ACGTcount: A:0.61, C:0.17, G:0.06, T:0.17
Consensus pattern (15 bp):
AAATTACAAAAGTCC
Found at i:2614 original size:15 final size:15
Alignment explanation
Indices: 2548--2616 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
2538 CAAAAGTCCA
*
2548 AATTACAAATGGCCT
1 AATTACAAATGGCCC
*
2563 AATAACAAATGGCCC
1 AATTACAAATGGCCC
* *
2578 AGTTACAGATGGCCC
1 AATTACAAATGGCCC
*
2593 AAATACAAATGGCCC
1 AATTACAAATGGCCC
*
2608 GATTACAAA
1 AATTACAAA
2617 GTGCCCGAGA
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 44 1.00
ACGTcount: A:0.42, C:0.23, G:0.16, T:0.19
Consensus pattern (15 bp):
AATTACAAATGGCCC
Found at i:4087 original size:30 final size:29
Alignment explanation
Indices: 4053--4460 Score: 285
Period size: 30 Copynumber: 13.8 Consensus size: 29
4043 GGAGGTCCTT
*
4053 AAACTTTCTAAAAATTACCATTTTACCCCC
1 AAAC-TTCCAAAAATTACCATTTTACCCCC
* *
4083 AAACTTCCAAAAA-TCCCATTTTTTACCCCG
1 AAACTTCCAAAAATTACCA--TTTTACCCCC
* * *
4113 AACCTTCTAAAAATTACCATTTTATCCCC
1 AAACTTCCAAAAATTACCATTTTACCCCC
* *
4142 GAACTTCCAAAAA-TCCCATTTTTGA-CCCC
1 AAACTTCCAAAAATTACCA-TTTT-ACCCCC
* *
4171 GAACTTTCCAAAAATTACCATTTTACCCGC
1 AAAC-TTCCAAAAATTACCATTTTACCCCC
* * * *
4201 TAATTTCCAAAAA-TCCCATCTTTGA-CCTC
1 AAACTTCCAAAAATTACCAT-TTT-ACCCCC
4230 AAACTTTCCAAAAAGTTACCATTTTACCCCC
1 AAAC-TTCCAAAAA-TTACCATTTTACCCCC
* ** *
4261 AAACTTCCAAAAA-TCCCATTTTTGACTTCG
1 AAACTTCCAAAAATTACCA-TTTT-ACCCCC
** *
4291 AAACCTTTAAAAAATTACCATTTTACCCCT
1 AAA-CTTCCAAAAATTACCATTTTACCCCC
* * *
4321 GAACTTCCAAAAATT-TCATTTTTGACCCAC
1 AAACTTCCAAAAATTACCA-TTTT-ACCCCC
*
4351 AAACTTCCAAAAATTACCATTTTACCCTC
1 AAACTTCCAAAAATTACCATTTTACCCCC
* * * *
4380 GAACTTCCAAAAA-TCCCATTTTTGACTCCG
1 AAACTTCCAAAAATTACCA-TTTT-ACCCCC
* * * *
4410 AACCTTCAAAAAATTACCATTTTACTCCT
1 AAACTTCCAAAAATTACCATTTTACCCCC
* *
4439 GAACTTCCAAAAA-TCCCATTTT
1 AAACTTCCAAAAATTACCATTTT
4461 TGACCTTGAA
Statistics
Matches: 299, Mismatches: 55, Indels: 50
0.74 0.14 0.12
Matches are distributed among these distances:
28 31 0.10
29 110 0.37
30 113 0.38
31 36 0.12
32 9 0.03
ACGTcount: A:0.35, C:0.30, G:0.04, T:0.32
Consensus pattern (29 bp):
AAACTTCCAAAAATTACCATTTTACCCCC
Found at i:4150 original size:59 final size:58
Alignment explanation
Indices: 4062--4499 Score: 529
Period size: 59 Copynumber: 7.4 Consensus size: 58
4052 TAAACTTTCT
* * *
4062 AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTTACCCCGAACCTTCT
1 AAAAATTACCATTTTA-CCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCC
*
4121 AAAAATTACCATTTTATCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACTTTCC
1 AAAAATTACCATTTTA-CCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCC
* * * * * *
4180 AAAAATTACCATTTTACCCGCTAATTTCCAAAAATCCCATCTTTGACCTCAAACTTTCC
1 AAAAATTACCATTTTACCC-CGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCC
* ** **
4239 AAAAAGTTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACTTCGAAACCTTTA
1 AAAAA-TTACCATTTTA-CCCCGAACTTCCAAAAATCCCATTTTTGACCCCG-AACCTTCC
** *
4300 AAAAATTACCATTTTACCCCTGAACTTCCAAAAATTTCATTTTTGACCCAC-AAACTTCC
1 AAAAATTACCATTTTACCCC-GAACTTCCAAAAATCCCATTTTTGACCC-CGAACCTTCC
* *
4359 AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACTCCGAACCTTCA
1 AAAAATTACCATTTTACCC-CGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCC
* ** * *
4418 AAAAATTACCATTTTACTCCTGAACTTCCAAAAATCCCATTTTTGACCTTGAATCTGCC
1 AAAAATTACCATTTTAC-CCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCC
*
4477 -AAAATTACCCTTTTACCTCCGAA
1 AAAAATTACCATTTTACC-CCGAA
4500 TGCTTAAAAT
Statistics
Matches: 329, Mismatches: 40, Indels: 21
0.84 0.10 0.05
Matches are distributed among these distances:
57 1 0.00
58 23 0.07
59 217 0.66
60 74 0.22
61 14 0.04
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (58 bp):
AAAAATTACCATTTTACCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCC
Done.