Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006628.1 Kokia drynarioides strain JFW-HI SEQ_121218, 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: 18808
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Warning! 69 characters in sequence are not A, C, G, or T
Found at i:3916 original size:14 final size:13
Alignment explanation
Indices: 3882--3922 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
3872 TGCTTTTGAG
*
3882 AAGTATTTTTAAA
1 AAGTATTTTGAAA
*
3895 AAATATTTTGAAA
1 AAGTATTTTGAAA
3908 AAGTAATTTTGAAA
1 AAGT-ATTTTGAAA
3922 A
1 A
3923 GTTTGGTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
13 14 0.58
14 10 0.42
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (13 bp):
AAGTATTTTGAAA
Found at i:4882 original size:28 final size:27
Alignment explanation
Indices: 4850--4907 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
4840 ACTTTCAAAC
*
4850 AAAATTATAAATTAAAATGATTAATT-TT
1 AAAATGATAAATTAAAAT-ATT-ATTGTT
**
4878 AAAATGATTGATTAAAATATTATTGTT
1 AAAATGATAAATTAAAATATTATTGTT
4905 AAA
1 AAA
4908 TATTTAATGC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 3 0.12
27 8 0.31
28 15 0.58
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (27 bp):
AAAATGATAAATTAAAATATTATTGTT
Found at i:13612 original size:142 final size:142
Alignment explanation
Indices: 13356--13640 Score: 561
Period size: 142 Copynumber: 2.0 Consensus size: 142
13346 TCATAATAAT
13356 TATTATACTGAATAAATCATTGCAAACAAAACTCTCCAACCCCACAATTCATATTTCTAATTAAT
1 TATTATACTGAATAAATCATTGCAAACAAAACTCTCCAACCCCACAATTCATATTTCTAATTAAT
13421 GATAAAAATTAAATTTTAAGAGAGTCAGTCCCCCACCCTTGCAATTTGACAATGCCAGGGGCCAC
66 GATAAAAATTAAATTTTAAGAGAGTCAGTCCCCCACCCTTGCAATTTGACAATGCCAGGGGCCAC
13486 CAAACATCAATA
131 CAAACATCAATA
*
13498 TATTATACTGAATAAATCATTGCAAATAAAACTCTCCAACCCCACAATTCATATTTCTAATTAAT
1 TATTATACTGAATAAATCATTGCAAACAAAACTCTCCAACCCCACAATTCATATTTCTAATTAAT
13563 GATAAAAATTAAATTTTAAGAGAGTCAGTCCCCCACCCTTGCAATTTGACAATGCCAGGGGCCAC
66 GATAAAAATTAAATTTTAAGAGAGTCAGTCCCCCACCCTTGCAATTTGACAATGCCAGGGGCCAC
13628 CAAACATCAATA
131 CAAACATCAATA
13640 T
1 T
13641 TTGACTATGA
Statistics
Matches: 142, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
142 142 1.00
ACGTcount: A:0.39, C:0.24, G:0.10, T:0.27
Consensus pattern (142 bp):
TATTATACTGAATAAATCATTGCAAACAAAACTCTCCAACCCCACAATTCATATTTCTAATTAAT
GATAAAAATTAAATTTTAAGAGAGTCAGTCCCCCACCCTTGCAATTTGACAATGCCAGGGGCCAC
CAAACATCAATA
Found at i:17362 original size:32 final size:32
Alignment explanation
Indices: 17326--17429 Score: 95
Period size: 32 Copynumber: 3.2 Consensus size: 32
17316 AATATTATTC
*
17326 ATTTTTAATTTAGTATATGAATCTGAATCCTA
1 ATTTTTAATTTAGTATATGAATCTGAATCTTA
** * * * *
17358 ATTTTTCTTTTAG-AGA-GATTATGTAATATTA
1 ATTTTTAATTTAGTATATGAATCTG-AATCTTA
17389 TTCATTTTTAATTTAGTATATGAATCTGAATCTTA
1 ---ATTTTTAATTTAGTATATGAATCTGAATCTTA
17424 ATTTTT
1 ATTTTT
17430 CTTTTAGAGA
Statistics
Matches: 53, Mismatches: 13, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
30 5 0.09
31 7 0.13
32 17 0.32
34 11 0.21
35 8 0.15
36 5 0.09
ACGTcount: A:0.32, C:0.07, G:0.10, T:0.52
Consensus pattern (32 bp):
ATTTTTAATTTAGTATATGAATCTGAATCTTA
Found at i:17393 original size:66 final size:66
Alignment explanation
Indices: 17316--17448 Score: 257
Period size: 66 Copynumber: 2.0 Consensus size: 66
17306 TTTGACTAAG
17316 AATATTATTCATTTTTAATTTAGTATATGAATCTGAATCCTAATTTTTCTTTTAGAGAGATTATG
1 AATATTATTCATTTTTAATTTAGTATATGAATCTGAATCCTAATTTTTCTTTTAGAGAGATTATG
17381 T
66 T
*
17382 AATATTATTCATTTTTAATTTAGTATATGAATCTGAATCTTAATTTTTCTTTTAGAGAGATTATG
1 AATATTATTCATTTTTAATTTAGTATATGAATCTGAATCCTAATTTTTCTTTTAGAGAGATTATG
17447 T
66 T
17448 A
1 A
17449 CATGTTAATG
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.32, C:0.07, G:0.11, T:0.50
Consensus pattern (66 bp):
AATATTATTCATTTTTAATTTAGTATATGAATCTGAATCCTAATTTTTCTTTTAGAGAGATTATG
T
Found at i:17457 original size:32 final size:31
Alignment explanation
Indices: 17356--17457 Score: 80
Period size: 32 Copynumber: 3.1 Consensus size: 31
17346 ATCTGAATCC
17356 TAATTTTTCTTTTAGAGAGATTATGTAATAT
1 TAATTTTTCTTTTAGAGAGATTATGTAATAT
** * * * *
17387 TATTCATTTTTAATTTAGTATATGAATCTG-AATCT
1 TA---ATTTTTCTTTTAG-AGA-GATTATGTAATAT
*
17422 TAATTTTTCTTTTAGAGAGATTATGTACATGT
1 TAATTTTTCTTTTAGAGAGATTATGTA-ATAT
17454 TAAT
1 TAAT
17458 GATCAAGGTT
Statistics
Matches: 52, Mismatches: 12, Indels: 13
0.68 0.16 0.17
Matches are distributed among these distances:
30 5 0.10
31 5 0.10
32 18 0.35
34 11 0.21
35 8 0.15
36 5 0.10
ACGTcount: A:0.31, C:0.06, G:0.12, T:0.51
Consensus pattern (31 bp):
TAATTTTTCTTTTAGAGAGATTATGTAATAT
Done.