Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009727.1 Kokia drynarioides strain JFW-HI SEQ_124446, 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: 29602
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:11800 original size:119 final size:119
Alignment explanation
Indices: 11585--11822 Score: 449
Period size: 119 Copynumber: 2.0 Consensus size: 119
11575 TGTTTGGCAC
11585 ACCAAAATCGACAAACTACCAAATGGGTTCTAATTTTAACCCAGAAAATAACCCTGTCGACTTTG
1 ACCAAAATCGACAAACTACCAAATGGGTTCTAATTTTAACCCAGAAAATAACCCTGTCGACTTTG
11650 ACATACCAGATTTAAATGAGGTGATGAAGCTAGAGAAAACAAGAGCCGAACTTT
66 ACATACCAGATTTAAATGAGGTGATGAAGCTAGAGAAAACAAGAGCCGAACTTT
*
11704 ACCAAAATCGACAAACTACCAAATGGGTTCTAATTTTAACCCAGGAAATAACCCTGTCGACTTTG
1 ACCAAAATCGACAAACTACCAAATGGGTTCTAATTTTAACCCAGAAAATAACCCTGTCGACTTTG
* *
11769 GCATACCAGATTTAAATGAGGTGATGGAGCTAGAGAAAACAAGAGCCGAACTTT
66 ACATACCAGATTTAAATGAGGTGATGAAGCTAGAGAAAACAAGAGCCGAACTTT
11823 CTAACCAGTT
Statistics
Matches: 116, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
119 116 1.00
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (119 bp):
ACCAAAATCGACAAACTACCAAATGGGTTCTAATTTTAACCCAGAAAATAACCCTGTCGACTTTG
ACATACCAGATTTAAATGAGGTGATGAAGCTAGAGAAAACAAGAGCCGAACTTT
Found at i:16325 original size:15 final size:15
Alignment explanation
Indices: 16288--16329 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
16278 TATCTTTTAT
*
16288 TTCTTCTTCATTCTCT
1 TTCTTCTTC-TTCTCC
*
16304 TTC-TCTTCTTGTCC
1 TTCTTCTTCTTCTCC
16318 TTCTTCTTCTTC
1 TTCTTCTTCTTC
16330 AACTTTCTCC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 7 0.32
15 12 0.55
16 3 0.14
ACGTcount: A:0.02, C:0.33, G:0.02, T:0.62
Consensus pattern (15 bp):
TTCTTCTTCTTCTCC
Found at i:22189 original size:17 final size:17
Alignment explanation
Indices: 22169--22201 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
22159 TTTAAGGACT
22169 TTTTAATTTTA-TTTAAG
1 TTTT-ATTTTAGTTTAAG
22186 TTTTATTTTAGTTTAA
1 TTTTATTTTAGTTTAA
22202 TAAGTGTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTTATTTTAGTTTAAG
Found at i:22473 original size:50 final size:50
Alignment explanation
Indices: 22396--22516 Score: 136
Period size: 50 Copynumber: 2.4 Consensus size: 50
22386 TGGAATCCAT
* * *
22396 TAACTCTCATGATTAGTTAAGTTTGCATCATAAATAATGA-CATGCATTAAG
1 TAACTCACATG-TTAGTTAAATATGCATCATAAATAAT-ATCATGCATTAAG
* ** *
22447 TAACTTACATGTTAGTTAAATATGCATCATAAATCCTATCATGCATTATG
1 TAACTCACATGTTAGTTAAATATGCATCATAAATAATATCATGCATTAAG
* *
22497 TAACTCCCATATTAGTTAAA
1 TAACTCACATGTTAGTTAAA
22517 GTTTACACCA
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
49 1 0.02
50 49 0.83
51 9 0.15
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (50 bp):
TAACTCACATGTTAGTTAAATATGCATCATAAATAATATCATGCATTAAG
Found at i:23834 original size:26 final size:27
Alignment explanation
Indices: 23805--23856 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
23795 ACGAAGTTTG
23805 TAAAAAAAGAAGAAAAAA-ATT-AAAAT
1 TAAAAAAAGAA-AAAAAAGATTCAAAAT
23831 TAAAAAAAGAAAAAAAAGATTCAAAA
1 TAAAAAAAGAAAAAAAAGATTCAAAA
23857 GAAGAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 6 0.25
26 14 0.58
27 4 0.17
ACGTcount: A:0.77, C:0.02, G:0.08, T:0.13
Consensus pattern (27 bp):
TAAAAAAAGAAAAAAAAGATTCAAAAT
Found at i:23864 original size:26 final size:26
Alignment explanation
Indices: 23806--23865 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
23796 CGAAGTTTGT
**
23806 AAAAAAAGAAGAAAAAAATTAAAATT
1 AAAAAAAGAAGAAAAAAATTAAAAAG
*
23832 AAAAAAAGAA-AAAAAAGATTCAAAAG
1 AAAAAAAGAAGAAAAAA-ATTAAAAAG
23858 AAGAAAAA
1 AA-AAAAA
23866 AATTCGAGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 6 0.21
26 18 0.62
27 5 0.17
ACGTcount: A:0.78, C:0.02, G:0.10, T:0.10
Consensus pattern (26 bp):
AAAAAAAGAAGAAAAAAATTAAAAAG
Found at i:23870 original size:18 final size:18
Alignment explanation
Indices: 23835--23870 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
23825 TAAAATTAAA
23835 AAAAGAAAAAAAAGATTC
1 AAAAGAAAAAAAAGATTC
23853 AAAAGAAGAAAAAA-ATTC
1 AAAAGAA-AAAAAAGATTC
23871 GAGTATTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.72, C:0.06, G:0.11, T:0.11
Consensus pattern (18 bp):
AAAAGAAAAAAAAGATTC
Found at i:24829 original size:28 final size:29
Alignment explanation
Indices: 24798--24853 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
24788 TGAAAGGAAA
*
24798 GAAAAAGAAATT-GAAAAAAAAAAAGAAT
1 GAAAAAGAAATTCCAAAAAAAAAAAGAAT
**
24826 GAAAGTGAAATTCCAAAAAAAAAAAGAA
1 GAAAAAGAAATTCCAAAAAAAAAAAGAA
24854 AGTGTGAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 10 0.42
29 14 0.58
ACGTcount: A:0.71, C:0.04, G:0.14, T:0.11
Consensus pattern (29 bp):
GAAAAAGAAATTCCAAAAAAAAAAAGAAT
Found at i:26316 original size:16 final size:17
Alignment explanation
Indices: 26295--26326 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
26285 TTAAGGACTT
26295 TTTAATTTTA-TTTAAG
1 TTTAATTTTAGTTTAAG
26311 TTTAATTTTAGTTTAA
1 TTTAATTTTAGTTTAA
26327 TAAGTGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.62
Consensus pattern (17 bp):
TTTAATTTTAGTTTAAG
Found at i:26598 original size:50 final size:50
Alignment explanation
Indices: 26521--26641 Score: 136
Period size: 50 Copynumber: 2.4 Consensus size: 50
26511 TGACATCCAT
* * * *
26521 TAACTCTCATGATTAGTTAAGTTTGCATCATAAATAATGA-CATGCTTTAAG
1 TAACTCACATG-TTAGTTAAATATGCATCATAAATAAT-ATCATGCATTAAG
* ** *
26572 TAACTTACATGTTAGTTAAATATGCATCATAAATCCTATCATGCATTATG
1 TAACTCACATGTTAGTTAAATATGCATCATAAATAATATCATGCATTAAG
*
26622 TAACTCCCATGTTAGTTAAA
1 TAACTCACATGTTAGTTAAA
26642 GTTTACACCA
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
49 1 0.02
50 49 0.83
51 9 0.15
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.37
Consensus pattern (50 bp):
TAACTCACATGTTAGTTAAATATGCATCATAAATAATATCATGCATTAAG
Found at i:28683 original size:18 final size:18
Alignment explanation
Indices: 28660--28696 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
28650 ACAATTAATG
28660 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
28678 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
28696 T
1 T
28697 TGATCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Done.