Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005658.1 Kokia drynarioides strain JFW-HI SEQ_119828, 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: 38380
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:9897 original size:21 final size:21
Alignment explanation
Indices: 9881--9922 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
9871 TGAGATTGGT
*
9881 TATTGTACTGATGAGATTAAA
1 TATTGTACTAATGAGATTAAA
9902 TATTGTACTAATGAGATTAAA
1 TATTGTACTAATGAGATTAAA
9923 ATTAGTGGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.17, T:0.38
Consensus pattern (21 bp):
TATTGTACTAATGAGATTAAA
Found at i:17110 original size:21 final size:21
Alignment explanation
Indices: 17081--17123 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
17071 TAAAATGGAA
*
17081 ATTATTTTTAAAAATATTTTT
1 ATTAATTTTAAAAATATTTTT
* *
17102 ATTAATTTTTAATATATTTTT
1 ATTAATTTTAAAAATATTTTT
17123 A
1 A
17124 GATTATGACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
ATTAATTTTAAAAATATTTTT
Found at i:25438 original size:4 final size:4
Alignment explanation
Indices: 25429--25464 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
25419 TCATATTTAT
25429 CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA
25465 TACACACACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:27133 original size:21 final size:22
Alignment explanation
Indices: 27108--27153 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
27098 GAAAAACTCA
27108 AAATAATTCAA-AATTTGAGTT
1 AAATAATTCAAGAATTTGAGTT
* *
27129 AAATAGTTCAAGTTATTTGAGTT
1 AAATAATTCAAG-AATTTGAGTT
27152 AA
1 AA
27154 TCAAGTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 10 0.48
23 11 0.52
ACGTcount: A:0.43, C:0.04, G:0.13, T:0.39
Consensus pattern (22 bp):
AAATAATTCAAGAATTTGAGTT
Found at i:27670 original size:19 final size:19
Alignment explanation
Indices: 27597--27670 Score: 73
Period size: 19 Copynumber: 3.9 Consensus size: 19
27587 AAGTAAATAA
* *
27597 TATT-AAAATATTAAAATC
1 TATTAAAAATATAAAAAAC
*
27615 TATTAAAAATATAGAAAA-
1 TATTAAAAATATAAAAAAC
*
27633 T-TTAAAAATTTATACAAAAC
1 TATTAAAAA--TATAAAAAAC
27653 TATTAAAAATATAAAAAA
1 TATTAAAAATATAAAAAA
27671 GTAAAATTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
17 7 0.15
18 5 0.11
19 26 0.57
20 1 0.02
21 7 0.15
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.32
Consensus pattern (19 bp):
TATTAAAAATATAAAAAAC
Found at i:27997 original size:18 final size:17
Alignment explanation
Indices: 27968--28035 Score: 57
Period size: 18 Copynumber: 3.9 Consensus size: 17
27958 CTATATATAT
*
27968 TTTTTAATTTTTATAAA
1 TTTTAAATTTTTATAAA
* **
27985 TTTTAAATATTTTCTACT
1 TTTTAAAT-TTTTATAAA
*
28003 TTTTATATTTTATAATAAA
1 TTTTAAATTTT-T-ATAAA
28022 TTTT-AATTTTTATA
1 TTTTAAATTTTTATA
28036 TTTTTAAGAA
Statistics
Matches: 39, Mismatches: 9, Indels: 7
0.71 0.16 0.13
Matches are distributed among these distances:
16 3 0.08
17 11 0.28
18 19 0.49
19 6 0.15
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTAAATTTTTATAAA
Found at i:28040 original size:27 final size:27
Alignment explanation
Indices: 27937--28041 Score: 81
Period size: 27 Copynumber: 3.8 Consensus size: 27
27927 TATATTTTTT
* *
27937 ATTTTAATTTTTAAAAGTTTTCTATATATAT
1 ATTTTAATTTTT-ATA-TTTT-TATA-ATAA
* *
27968 TTTTTAATTTTTATAAATTTTA-AAT-A
1 ATTTTAATTTTTAT-ATTTTTATAATAA
* *
27994 TTTTCTACTTTTTATA-TTTTATAATAA
1 ATTT-TAATTTTTATATTTTTATAATAA
28021 ATTTTAATTTTTATATTTTTA
1 ATTTTAATTTTTATATTTTTA
28042 AGAATTTTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
25 5 0.08
26 18 0.29
27 20 0.32
28 1 0.02
29 2 0.03
30 4 0.06
31 12 0.19
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (27 bp):
ATTTTAATTTTTATATTTTTATAATAA
Found at i:28050 original size:19 final size:19
Alignment explanation
Indices: 28028--28077 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
28018 TAAATTTTAA
28028 TTTTTATATTTTTAAGAA-T
1 TTTTTATATTTTT-AGAAGT
* *
28047 TTTTTTTAATTTTAGAAGT
1 TTTTTATATTTTTAGAAGT
*
28066 TTTCTATATTTT
1 TTTTTATATTTT
28078 GTTATTAATG
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.26, C:0.02, G:0.06, T:0.66
Consensus pattern (19 bp):
TTTTTATATTTTTAGAAGT
Found at i:28051 original size:26 final size:25
Alignment explanation
Indices: 27966--28051 Score: 84
Period size: 26 Copynumber: 3.3 Consensus size: 25
27956 TTCTATATAT
*
27966 ATTTTTTAATTTTTATAAATTTTAAA
1 ATTTTTTAATTTTTAT-ATTTTTAAA
* *
27992 TATTTTCTACTTTTTATATTTTATAATA
1 -ATTTTTTAATTTTTATATTTT-TAA-A
*
28020 A-ATTTTAATTTTTATATTTTTAAGA
1 ATTTTTTAATTTTTATATTTTTAA-A
28045 ATTTTTT
1 ATTTTTT
28052 TTAATTTTAG
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
25 5 0.10
26 24 0.50
27 18 0.38
28 1 0.02
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (25 bp):
ATTTTTTAATTTTTATATTTTTAAA
Found at i:32780 original size:2 final size:2
Alignment explanation
Indices: 32773--32808 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
32763 GCAAAAGATT
32773 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
32809 GGGCCGATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:36773 original size:3 final size:3
Alignment explanation
Indices: 36765--36790 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
36755 AATCATTCAT
36765 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
36791 TGTAACTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Done.