Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010749.1 Kokia drynarioides strain JFW-HI SEQ_125707, 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: 56428
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 136 characters in sequence are not A, C, G, or T
Found at i:153 original size:4 final size:4
Alignment explanation
Indices: 134--202 Score: 77
Period size: 4 Copynumber: 17.0 Consensus size: 4
124 ACACATTATA
* * * *
134 TTTC TTTC CTTC -TTC TTTC TTTCC TCTC CTTC TTCC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTT-C TTTC TTTC TTTC TTTC TTTC TTTC
182 TTTTC TTTC TTTC TTTC TTTC
1 -TTTC TTTC TTTC TTTC TTTC
203 CCGTTTATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
3 3 0.05
4 45 0.82
5 7 0.13
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (4 bp):
TTTC
Found at i:167 original size:17 final size:15
Alignment explanation
Indices: 134--200 Score: 67
Period size: 13 Copynumber: 4.9 Consensus size: 15
124 ACACATTATA
134 TTTCTTTCCTTCTTC
1 TTTCTTTCCTTCTTC
149 TTTCTTTCC-TC-TC
1 TTTCTTTCCTTCTTC
*
162 CTTC-TTCC-T-TTC
1 TTTCTTTCCTTCTTC
174 TTTCTTT-CTT-TTC
1 TTTCTTTCCTTCTTC
*
187 TTTCTTTCTTTCTT
1 TTTCTTTCCTTCTT
201 TCCCGTTTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
12 11 0.25
13 18 0.41
14 4 0.09
15 11 0.25
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTCTTTCCTTCTTC
Found at i:180 original size:25 final size:22
Alignment explanation
Indices: 146--203 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 22
136 TCTTTCCTTC
146 TTCTTTCTTTCCTCTCCTTCTTCCT
1 TTCTTTCTTTCCT-T--TTCTTCCT
*
171 TTCTTTCTTT-CTTTTCTTTCT
1 TTCTTTCTTTCCTTTTCTTCCT
192 TTCTTTCTTTCC
1 TTCTTTCTTTCC
204 CGTTTATTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
21 17 0.55
22 1 0.03
23 1 0.03
24 2 0.06
25 10 0.32
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (22 bp):
TTCTTTCTTTCCTTTTCTTCCT
Found at i:2757 original size:17 final size:19
Alignment explanation
Indices: 2732--2772 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
2722 TAAATGAGTG
*
2732 TAAACTTATAAA-AATT-T
1 TAAAATTATAAATAATTAT
2749 TAAAATTATAAATAATTAT
1 TAAAATTATAAATAATTAT
2768 TAAAA
1 TAAAA
2773 ATATCTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 11 0.52
18 4 0.19
19 6 0.29
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (19 bp):
TAAAATTATAAATAATTAT
Found at i:3738 original size:15 final size:16
Alignment explanation
Indices: 3718--3747 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3708 TTAAACTCTA
3718 AAAATAAAT-ATAAAG
1 AAAATAAATCATAAAG
3733 AAAATAAATCATAAA
1 AAAATAAATCATAAA
3748 CATACGAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.20
Consensus pattern (16 bp):
AAAATAAATCATAAAG
Found at i:5276 original size:3 final size:3
Alignment explanation
Indices: 5268--5295 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5258 ATCCCTTTCT
5268 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
5296 GTATATGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:20503 original size:6 final size:6
Alignment explanation
Indices: 20492--20555 Score: 128
Period size: 6 Copynumber: 10.7 Consensus size: 6
20482 CATCTAACAT
20492 CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC
1 CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC
20540 CTTCTC CTTCTC CTTC
1 CTTCTC CTTCTC CTTC
20556 CGCTGCCGCG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 58 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (6 bp):
CTTCTC
Found at i:32842 original size:4 final size:4
Alignment explanation
Indices: 32833--32883 Score: 50
Period size: 4 Copynumber: 12.5 Consensus size: 4
32823 AAACACATTA
* * *
32833 TCTT TCTT TCTT TATT TCTT TCTT TCCTCT CCTT T-TT TCTT TCCT TCTT
1 TCTT TCTT TCTT TCTT TCTT TCTT T-CT-T TCTT TCTT TCTT TCTT TCTT
32882 TC
1 TC
32884 CCGTTTATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
3 3 0.08
4 30 0.79
5 4 0.11
6 1 0.03
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (4 bp):
TCTT
Found at i:34722 original size:18 final size:18
Alignment explanation
Indices: 34699--34752 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
34689 TTAATTTATT
34699 TTTTATTTTATGTTATAA
1 TTTTATTTTATGTTATAA
* *
34717 TTTTATTATA-GTATTTAA
1 TTTTATTTTATGT-TATAA
34735 TTTTATTATTATCGTTAT
1 TTTTATT-TTAT-GTTAT
34753 TTTTACGTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
17 2 0.07
18 20 0.71
19 2 0.07
20 2 0.07
21 2 0.07
ACGTcount: A:0.28, C:0.02, G:0.06, T:0.65
Consensus pattern (18 bp):
TTTTATTTTATGTTATAA
Found at i:34744 original size:13 final size:13
Alignment explanation
Indices: 34693--34744 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
34683 ATACGCTTAA
34693 TTTATTTT-TTAT
1 TTTATTTTATTAT
* *
34705 TTTATGTTATAAT
1 TTTATTTTATTAT
* *
34718 TTTATTATAGTAT
1 TTTATTTTATTAT
*
34731 TTAATTTTATTAT
1 TTTATTTTATTAT
34744 T
1 T
34745 ATCGTTATTT
Statistics
Matches: 30, Mismatches: 9, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
12 7 0.23
13 23 0.77
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (13 bp):
TTTATTTTATTAT
Found at i:36738 original size:23 final size:23
Alignment explanation
Indices: 36710--36762 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
36700 ATAAAAATAT
*
36710 TAAAATAAAA-TTTTAGCTTAATGG
1 TAAATTAAAAGTTTT-GC-TAATGG
36734 TAAATTAAAAGTTTTGCTAAT-G
1 TAAATTAAAAGTTTTGCTAATGG
36756 -AAATTAA
1 TAAATTAA
36763 CATGAATTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 7 0.26
22 1 0.04
23 4 0.15
24 11 0.41
25 4 0.15
ACGTcount: A:0.47, C:0.04, G:0.11, T:0.38
Consensus pattern (23 bp):
TAAATTAAAAGTTTTGCTAATGG
Found at i:38062 original size:65 final size:65
Alignment explanation
Indices: 37958--38086 Score: 240
Period size: 65 Copynumber: 2.0 Consensus size: 65
37948 AAGATCTTAT
37958 GAGCTTTGCTACTCAGACTCAGGTATAAGTATCAGTAAGGGTATGTTCAATTCTTTTTCAAGTTA
1 GAGCTTTGCTACTCAGACTCAGGTATAAGTATCAGTAAGGGTATGTTCAATTCTTTTTCAAGTTA
* *
38023 GAGCTTTGTTACTCAGACTCAGGTATAAGTGTCAGTAAGGGTATGTTCAATTCTTTTTCAAGTT
1 GAGCTTTGCTACTCAGACTCAGGTATAAGTATCAGTAAGGGTATGTTCAATTCTTTTTCAAGTT
38087 TTTCTATGTA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 62 1.00
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (65 bp):
GAGCTTTGCTACTCAGACTCAGGTATAAGTATCAGTAAGGGTATGTTCAATTCTTTTTCAAGTTA
Found at i:42220 original size:87 final size:91
Alignment explanation
Indices: 42068--42231 Score: 255
Period size: 87 Copynumber: 1.8 Consensus size: 91
42058 TCGTCTATTG
42068 TCATAATTATGAATTTTAATCTCTTAATATTTTCTTTTTTTAACAAACGATAAAGATCGTAAAAG
1 TCATAATTATGAATTTTAATCTCTTAATA-TTTCTTTTTTTAACAAACGATAAAGATCGTAAAAG
42133 ACCCACGTTGAAAAATCGAATCTTTTT
65 ACCCACGTTGAAAAATCGAATCTTTTT
* *
42160 TCATAATTATGAATTTTAATCTCTT-A-A-TT-TTTTTTTAACAAATGATAAAGATCGTGAAAGA
1 TCATAATTATGAATTTTAATCTCTTAATATTTCTTTTTTTAACAAACGATAAAGATCGTAAAAGA
* *
42221 CCGACTTTGAA
66 CCCACGTTGAA
42232 CAGCCAAAAA
Statistics
Matches: 68, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
87 39 0.57
88 2 0.03
90 1 0.01
91 1 0.01
92 25 0.37
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (91 bp):
TCATAATTATGAATTTTAATCTCTTAATATTTCTTTTTTTAACAAACGATAAAGATCGTAAAAGA
CCCACGTTGAAAAATCGAATCTTTTT
Found at i:44153 original size:3 final size:3
Alignment explanation
Indices: 44145--44195 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
44135 CAAGCCTGTT
* * * *
44145 TCA TCA TCA ACA TCA TCA TCG TCCA -CA CCA TTA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA T-CA TCA TCA TCA TCA TCA TCA TCA
44190 TCA TCA
1 TCA TCA
44196 CTGTCATCTC
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
2 2 0.05
3 36 0.92
4 1 0.03
ACGTcount: A:0.33, C:0.35, G:0.02, T:0.29
Consensus pattern (3 bp):
TCA
Found at i:49156 original size:22 final size:22
Alignment explanation
Indices: 49131--49172 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
49121 TAAAAACTAG
49131 AAAAAAAACAAAATATAAAAGA
1 AAAAAAAACAAAATATAAAAGA
* **
49153 AAAAAGAACTGAATATAAAA
1 AAAAAAAACAAAATATAAAA
49173 AAGAAAAGGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.76, C:0.05, G:0.07, T:0.12
Consensus pattern (22 bp):
AAAAAAAACAAAATATAAAAGA
Found at i:50191 original size:20 final size:20
Alignment explanation
Indices: 50166--50214 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
50156 TAAAAATATT
50166 TTTATATTTACTTTTTAAAA
1 TTTATATTTACTTTTTAAAA
* * *
50186 TTTATATTTATTTTTTATAC
1 TTTATATTTACTTTTTAAAA
50206 TTTATATTT
1 TTTATATTT
50215 GTATTTATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTATATTTACTTTTTAAAA
Found at i:50194 original size:6 final size:6
Alignment explanation
Indices: 50166--50226 Score: 50
Period size: 6 Copynumber: 9.5 Consensus size: 6
50156 TAAAAATATT
* * * *
50166 TTTATA TTTACTT TTTAAAA TTTATA TTTATTT TTTATA CTTTATA TTTGTA
1 TTTATA TTTA-TA TTT-ATA TTTATA TTTA-TA TTTATA -TTTATA TTTATA
50218 TTTATA TTT
1 TTTATA TTT
50227 TCTCATCAAC
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
6 24 0.56
7 18 0.42
8 1 0.02
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (6 bp):
TTTATA
Found at i:53887 original size:32 final size:32
Alignment explanation
Indices: 53842--53914 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
53832 TTTATATATA
* *
53842 ATCATTATTTTTATATGTAAAATGTTTCAAAT
1 ATCATTATGTTTATATGTAAAATATTTCAAAT
* *
53874 ATCATTATGTTTATATGTGAAATATTTTAAAT
1 ATCATTATGTTTATATGTAAAATATTTCAAAT
53906 A-CA-TATGTT
1 ATCATTATGTT
53915 AAAATATATA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
30 6 0.16
31 2 0.05
32 29 0.78
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.49
Consensus pattern (32 bp):
ATCATTATGTTTATATGTAAAATATTTCAAAT
Done.