Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014864.1 Kokia drynarioides strain JFW-HI SEQ_129907, 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: 40504
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.30
Warning! 369 characters in sequence are not A, C, G, or T
Found at i:5206 original size:18 final size:18
Alignment explanation
Indices: 5183--5223 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
5173 TCTTAAGGAA
5183 AATACATGTTCTACATAG
1 AATACATGTTCTACATAG
5201 AATACATGTTCTACATAG
1 AATACATGTTCTACATAG
5219 AATAC
1 AATAC
5224 TAAACCATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (18 bp):
AATACATGTTCTACATAG
Found at i:27029 original size:3 final size:3
Alignment explanation
Indices: 27002--27047 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
26992 GATCAAGGTT
* * *
27002 CTC CTTC CTC CGC CTC CGC CGC CTC CTC CTC CTC CTC CTC CTC CTC
1 CTC C-TC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
27048 ATCCCAAAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.00, C:0.65, G:0.07, T:0.28
Consensus pattern (3 bp):
CTC
Found at i:30227 original size:29 final size:29
Alignment explanation
Indices: 30160--30249 Score: 105
Period size: 28 Copynumber: 3.2 Consensus size: 29
30150 ATGAAAGTAC
* * *
30160 TAAATATTATTTGATTAA-TAGAAATACT
1 TAAATATTATTTGATAAATTAAAAAAACT
30188 TAAATATTATTTGATAAATTAAAAAAACT
1 TAAATATTATTTGATAAATTAAAAAAACT
* **
30217 TAAAAATTATTTGAT-AATTTGAAAAA-T
1 TAAATATTATTTGATAAATTAAAAAAACT
30244 TAAATA
1 TAAATA
30250 CTAAAAGAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
27 6 0.11
28 26 0.48
29 22 0.41
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (29 bp):
TAAATATTATTTGATAAATTAAAAAAACT
Found at i:30669 original size:16 final size:16
Alignment explanation
Indices: 30650--30796 Score: 76
Period size: 16 Copynumber: 9.1 Consensus size: 16
30640 TAATTAAATT
30650 ATTTAATAAATATAAA
1 ATTTAATAAATATAAA
*
30666 ATTT-A-AATTATAAA
1 ATTTAATAAATATAAA
* * * **
30680 AATT-AT-ATTCTACC
1 ATTTAATAAATATAAA
30694 ATTTAATTAAATTTATAAA
1 ATTTAA-TAAA--TATAAA
30713 ATTTAATAAATATAAA
1 ATTTAATAAATATAAA
* *
30729 AATT-ATAAA-AT-CA
1 ATTTAATAAATATAAA
*
30742 ATTACAAGATATAAT-TAAA
1 ATT--TA-ATA-AATATAAA
30761 TTATTTAATAAATATAAA
1 --ATTTAATAAATATAAA
30779 ATTTAATAAATATAAA
1 ATTTAATAAATATAAA
30795 AT
1 AT
30797 GTAAATTTTT
Statistics
Matches: 99, Mismatches: 16, Indels: 32
0.67 0.11 0.22
Matches are distributed among these distances:
13 3 0.03
14 22 0.22
15 7 0.07
16 32 0.32
17 7 0.07
18 14 0.14
19 11 0.11
21 3 0.03
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.39
Consensus pattern (16 bp):
ATTTAATAAATATAAA
Found at i:30718 original size:19 final size:17
Alignment explanation
Indices: 30694--30732 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
30684 ATATTCTACC
*
30694 ATTTAATTAAATTTATAAA
1 ATTTAA-TAAATATA-AAA
30713 ATTTAATAAATATAAAA
1 ATTTAATAAATATAAAA
30730 ATT
1 ATT
30733 ATAAAATCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 7 0.37
19 6 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTTAATAAATATAAAA
Found at i:30842 original size:113 final size:112
Alignment explanation
Indices: 30621--30836 Score: 260
Period size: 113 Copynumber: 1.9 Consensus size: 112
30611 TCATAACACT
* *
30621 TAAAATCAATTAAAAGATATAATTAAATTATTTAATAAATATAAAATTTAAATTATAAAAATTAT
1 TAAAATCAATTAAAAGATATAATTAAATTATTTAATAAATATAAAATTTAAAATATAAAAATTAA
* ** *
30686 ATTCTACCATTTAATTAAATTTATAAAATTTAATAAATATAAAAATTA
66 ATTCTACAAGATAATTAAA-TTATAAAATTAAATAAATATAAAAATTA
*
30734 TAAAATCAATTACAAGATATAATTAAATTATTTAATAAATATAAAATTTAATAA-ATATAAAATG
1 TAAAATCAATTAAAAGATATAATTAAATTATTTAATAAATATAAAATTTAA-AATATA-AAAAT-
* *
30798 TAAATTTTTATAAGATAATGTAACA-T-TAAAA-TAAATAAA
63 TAAA-TTCTACAAGATAAT-TAA-ATTATAAAATTAAATAAA
30837 CTAAAATTGA
Statistics
Matches: 88, Mismatches: 9, Indels: 11
0.81 0.08 0.10
Matches are distributed among these distances:
113 53 0.60
114 13 0.15
115 8 0.09
116 10 0.11
117 3 0.03
118 1 0.01
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.38
Consensus pattern (112 bp):
TAAAATCAATTAAAAGATATAATTAAATTATTTAATAAATATAAAATTTAAAATATAAAAATTAA
ATTCTACAAGATAATTAAATTATAAAATTAAATAAATATAAAAATTA
Found at i:31172 original size:20 final size:20
Alignment explanation
Indices: 31149--31186 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
31139 TTTAAACAAT
31149 TAAAA-ATTATATATAATACC
1 TAAAATATTAT-TATAATACC
31169 TAAAATATTATTATAATA
1 TAAAATATTATTATAATA
31187 GAAAAATACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (20 bp):
TAAAATATTATTATAATACC
Found at i:32501 original size:10 final size:9
Alignment explanation
Indices: 32487--32514 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
32477 ATGTTTTAGG
32487 ATTTTTTTT
1 ATTTTTTTT
32496 ATTTTTTTT
1 ATTTTTTTT
32505 ATTTTTTTT
1 ATTTTTTTT
32514 A
1 A
32515 CAAAGAGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (9 bp):
ATTTTTTTT
Done.