Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004581.1 Kokia drynarioides strain JFW-HI SEQ_118069, 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: 50606
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:38 original size:24 final size:24
Alignment explanation
Indices: 6--63 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
1 ATATG
*
6 AAAT-ATTAATTTTAAATATTTCT
1 AAATAATTAATTTTAAATATTTAT
* *
29 AAATAATTAATATTAATTATTTAT
1 AAATAATTAATTTTAAATATTTAT
*
53 AAA-ATTTAATT
1 AAATAATTAATT
64 AGAATATATA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
23 10 0.34
24 19 0.66
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
AAATAATTAATTTTAAATATTTAT
Found at i:107 original size:20 final size:21
Alignment explanation
Indices: 61--113 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 21
51 ATAAAATTTA
*
61 ATTAGAATATATAAACTATATT
1 ATTA-AATATTTAAACTATATT
*
83 -TTTAATATTTAAA-TATAATT
1 ATTAAATATTTAAACTAT-ATT
103 ATTAAATATTT
1 ATTAAATATTT
114 GTAATTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 3 0.12
20 12 0.46
21 11 0.42
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
ATTAAATATTTAAACTATATT
Found at i:1536 original size:14 final size:14
Alignment explanation
Indices: 1513--1544 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1503 AAATCATCTC
1513 AAAA-AGGCTATTG
1 AAAAGAGGCTATTG
1526 AAAAGAGGCTATTG
1 AAAAGAGGCTATTG
1540 AAAAG
1 AAAAG
1545 TACTTTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.50, C:0.06, G:0.25, T:0.19
Consensus pattern (14 bp):
AAAAGAGGCTATTG
Found at i:3871 original size:146 final size:143
Alignment explanation
Indices: 3684--3944 Score: 380
Period size: 146 Copynumber: 1.8 Consensus size: 143
3674 TTCTTAATGC
* ** *
3684 ATAGGATTTATGTATTAATAATGCATCAAATGTAATATCTAATTTTAACTACATTTAAATAAAAT
1 ATAGGATTCATGTACCAAAAATGCATCAAATGTAATATCTAATTTTAACTACATTTAAAT-AAA-
*
3749 TTAAGTATTTATTAAAAA-TCTTTCCACTTTTTATTTATTTATTCATTAATGATGAGATGAGTTA
64 TTAAGTATTTATTAAAAAGTCTTTCAAC-TTTT-TTTATTTATTCATTAATGATGAGATGAGTTA
3813 TACTGTATTGATGGTGA
127 TACTGTATTGATGGTGA
* * * * *
3830 ATAGGATTCATGTACCAAAAATGGATCAATTGTAATCTCTAATTTTAATTATATTTAAATAAATT
1 ATAGGATTCATGTACCAAAAATGCATCAAATGTAATATCTAATTTTAACTACATTTAAATAAATT
*
3895 AAGTATTTATTAAAAAGTCTTTCAACTTTTTTTCTTTATTCATTAATGAT
66 AAGTATTTATTAAAAAGTCTTTCAACTTTTTTTATTTATTCATTAATGAT
3945 CTAGCGAATT
Statistics
Matches: 103, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
143 19 0.18
144 22 0.21
145 11 0.11
146 51 0.50
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.45
Consensus pattern (143 bp):
ATAGGATTCATGTACCAAAAATGCATCAAATGTAATATCTAATTTTAACTACATTTAAATAAATT
AAGTATTTATTAAAAAGTCTTTCAACTTTTTTTATTTATTCATTAATGATGAGATGAGTTATACT
GTATTGATGGTGA
Found at i:15472 original size:23 final size:24
Alignment explanation
Indices: 15433--15477 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
15423 CTTTTTGAAT
*
15433 TTTCAGAAATTGTTTTG-TTTTCA
1 TTTCAGAAATTGATTTGATTTTCA
15456 TTTCA-AAATTTGATTTGATTTT
1 TTTCAGAAA-TTGATTTGATTTT
15478 TAAAAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 3 0.16
23 12 0.63
24 4 0.21
ACGTcount: A:0.24, C:0.07, G:0.11, T:0.58
Consensus pattern (24 bp):
TTTCAGAAATTGATTTGATTTTCA
Found at i:16775 original size:13 final size:14
Alignment explanation
Indices: 16741--16784 Score: 54
Period size: 16 Copynumber: 3.0 Consensus size: 14
16731 ATTCTATCAA
16741 ATAAAAAATAATTAT
1 ATAAAAAATAA-TAT
16756 ATTAAAAAATAATAT
1 A-TAAAAAATAATAT
16771 A-AAAAAATCAATAT
1 ATAAAAAAT-AATAT
16785 TAGTATCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 7 0.26
14 5 0.19
15 5 0.19
16 10 0.37
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (14 bp):
ATAAAAAATAATAT
Found at i:17625 original size:2 final size:2
Alignment explanation
Indices: 17618--17642 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17608 TCTTGTCTTT
17618 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
17643 TAAAAAAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23502 original size:20 final size:21
Alignment explanation
Indices: 23477--23518 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
23467 TTTACAAAAG
* *
23477 TAATTTTATTTATTA-AATAT
1 TAATTTCATTTAATATAATAT
23497 TAATTTCATTTAATATAATAT
1 TAATTTCATTTAATATAATAT
23518 T
1 T
23519 TGATTAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TAATTTCATTTAATATAATAT
Found at i:45141 original size:18 final size:17
Alignment explanation
Indices: 45099--45141 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
45089 TAAGATTGAA
*
45099 TTTATTATAAAAATAAG
1 TTTATTTTAAAAATAAG
*
45116 TTTATTTTAAAAATGAG
1 TTTATTTTAAAAATAAG
45133 TTTAGTTTT
1 TTTA-TTTT
45142 TGCTCAACTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (17 bp):
TTTATTTTAAAAATAAG
Found at i:45388 original size:16 final size:18
Alignment explanation
Indices: 45340--45406 Score: 63
Period size: 16 Copynumber: 4.0 Consensus size: 18
45330 ATTTTATTTC
45340 ATTA-AATATAATT--TT
1 ATTATAATATAATTAATT
* * *
45355 AATATAAAATATTTAATT
1 ATTATAATATAATTAATT
45373 ATTAT-ATA-AATTAATT
1 ATTATAATATAATTAATT
*
45389 TTTATAATATAATTAATT
1 ATTATAATATAATTAATT
45407 TAAGTGAATA
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
15 3 0.08
16 18 0.45
17 5 0.12
18 14 0.35
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTATAATATAATTAATT
Found at i:45407 original size:18 final size:18
Alignment explanation
Indices: 45357--45407 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
45347 ATAATTTTAA
* * *
45357 TATAAAATATTTAATTAT
1 TATAATATAATTAATTTT
45375 TAT-ATA-AATTAATTTT
1 TATAATATAATTAATTTT
45391 TATAATATAATTAATTT
1 TATAATATAATTAATTT
45408 AAGTGAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 11 0.39
17 5 0.18
18 12 0.43
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TATAATATAATTAATTTT
Done.