Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003857.1 Kokia drynarioides strain JFW-HI SEQ_116885, 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: 11127
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.36
Found at i:133 original size:22 final size:23
Alignment explanation
Indices: 93--136 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
83 ACGCATTACT
*
93 TTTTTTTCATTCTCCTTCTTCCCC
1 TTTTTCTCATTCT-CTTCTTCCCC
117 TTTTTCTCATTCT-TTCTTCC
1 TTTTTCTCATTCTCTTCTTCC
137 TTCTTTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
24 12 0.63
ACGTcount: A:0.05, C:0.34, G:0.00, T:0.61
Consensus pattern (23 bp):
TTTTTCTCATTCTCTTCTTCCCC
Found at i:147 original size:25 final size:24
Alignment explanation
Indices: 117--171 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
107 CTTCTTCCCC
117 TTTTTCTCAT-TCTTTCTTCCTTCT
1 TTTTTCT-ATCTCTTTCTTCCTTCT
* *
141 TTCTTTCTTTCTCTTTTTTCCTTCT
1 TT-TTTCTATCTCTTTCTTCCTTCT
166 TTTTTC
1 TTTTTC
172 CTTCAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 7 0.26
25 20 0.74
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (24 bp):
TTTTTCTATCTCTTTCTTCCTTCT
Found at i:1064 original size:15 final size:15
Alignment explanation
Indices: 1046--1079 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
1036 TTAAATTTTT
1046 TCGAATCAAATCGAC
1 TCGAATCAAATCGAC
1061 TCGAATCAAATCGAC
1 TCGAATCAAATCGAC
1076 TCGA
1 TCGA
1080 GTTAACGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.38, C:0.26, G:0.15, T:0.21
Consensus pattern (15 bp):
TCGAATCAAATCGAC
Found at i:1830 original size:33 final size:33
Alignment explanation
Indices: 1777--1843 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 33
1767 AGATAATATA
*
1777 TTTTGATGTTTGAATGTA-TTTGAGTAAAATATTT
1 TTTTGATGTTTGAA-GTATTTTCAG-AAAATATTT
1811 TTTTGATGTTTGACA-TATTTTCAGAAAATATTT
1 TTTTGATGTTTGA-AGTATTTTCAGAAAATATTT
1844 CATAAAAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
33 11 0.37
34 18 0.60
35 1 0.03
ACGTcount: A:0.30, C:0.03, G:0.15, T:0.52
Consensus pattern (33 bp):
TTTTGATGTTTGAAGTATTTTCAGAAAATATTT
Found at i:4246 original size:29 final size:29
Alignment explanation
Indices: 4212--4276 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
4202 AATTTTATAC
**
4212 TTTTTAAATAATTT-TAATGATTTTTATTT
1 TTTTTAAATAATTTATAAT-ATTTTTAAAT
* *
4241 TTTTTAAATAGTTTATTATATTTTTAAAT
1 TTTTTAAATAATTTATAATATTTTTAAAT
4270 TTTTTAA
1 TTTTTAA
4277 TTTAAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 28 0.90
30 3 0.10
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (29 bp):
TTTTTAAATAATTTATAATATTTTTAAAT
Found at i:4275 original size:20 final size:18
Alignment explanation
Indices: 4232--4275 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
4222 ATTTTAATGA
4232 TTTTTATTTTTTTTAAAT
1 TTTTTATTTTTTTTAAAT
**
4250 AGTTTATTATATTTTTAAAT
1 TTTTTATT-T-TTTTTAAAT
4270 TTTTTA
1 TTTTTA
4276 ATTTAAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
18 6 0.30
19 1 0.05
20 13 0.65
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTTTATTTTTTTTAAAT
Found at i:4517 original size:33 final size:33
Alignment explanation
Indices: 4475--4542 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
4465 AAGAATGGTG
4475 TAGGGGATAATGTGGAATATAATAATGTTGAGT
1 TAGGGGATAATGTGGAATATAATAATGTTGAGT
4508 TAGGGGATAATGTGGAATATAATAATGTTGAGT
1 TAGGGGATAATGTGGAATATAATAATGTTGAGT
4541 TA
1 TA
4543 TGTAATTGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.37, C:0.00, G:0.29, T:0.34
Consensus pattern (33 bp):
TAGGGGATAATGTGGAATATAATAATGTTGAGT
Found at i:4600 original size:6 final size:6
Alignment explanation
Indices: 4567--4599 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
4557 ATTCATTCCG
*
4567 TTGTCA TTGTCA TTGTCA TTGTCA TTGCCA TTG
1 TTGTCA TTGTCA TTGTCA TTGTCA TTGTCA TTG
4600 CTATCATGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.15, C:0.18, G:0.18, T:0.48
Consensus pattern (6 bp):
TTGTCA
Found at i:5170 original size:28 final size:28
Alignment explanation
Indices: 5126--5212 Score: 93
Period size: 34 Copynumber: 2.9 Consensus size: 28
5116 GAAATCACTA
*
5126 TATATATATATATTAAAAATTAATTCATT
1 TATATAGATA-ATTAAAAATTAATTCATT
5155 TATATAGATAATTAAAAATAAAAATTAATTCATT
1 TATATAGATAA-T-----TAAAAATTAATTCATT
*
5189 TATATAGATAATTAAAAATAAATT
1 TATATAGATAATTAAAAATTAATT
5213 ATATATCTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
28 12 0.24
29 10 0.20
33 1 0.02
34 27 0.54
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (28 bp):
TATATAGATAATTAAAAATTAATTCATT
Found at i:5177 original size:34 final size:34
Alignment explanation
Indices: 5139--5210 Score: 144
Period size: 34 Copynumber: 2.1 Consensus size: 34
5129 ATATATATAT
5139 TAAAAATTAATTCATTTATATAGATAATTAAAAA
1 TAAAAATTAATTCATTTATATAGATAATTAAAAA
5173 TAAAAATTAATTCATTTATATAGATAATTAAAAA
1 TAAAAATTAATTCATTTATATAGATAATTAAAAA
5207 TAAA
1 TAAA
5211 TTATATATCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (34 bp):
TAAAAATTAATTCATTTATATAGATAATTAAAAA
Found at i:6783 original size:21 final size:22
Alignment explanation
Indices: 6740--6780 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
6730 ATGGGATGAG
*
6740 TAACTTTAAACTCCATGACAAT
1 TAACTTGAAACTCCATGACAAT
6762 TAACTTGAAA-TCCAT-ACAA
1 TAACTTGAAACTCCATGACAA
6781 ATTTATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 5 0.28
22 9 0.50
ACGTcount: A:0.44, C:0.22, G:0.05, T:0.29
Consensus pattern (22 bp):
TAACTTGAAACTCCATGACAAT
Found at i:7087 original size:19 final size:19
Alignment explanation
Indices: 7041--7091 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
7031 TGCGTATCGA
* *
7041 TATAATATAGTTTTCTCATG
1 TATAA-ATAATTTACTCATG
* *
7061 TGTTAATAATTTACTCATG
1 TATAAATAATTTACTCATG
7080 TATAAAT-ATTTA
1 TATAAATAATTTA
7092 TAGTTTATAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
18 5 0.20
19 17 0.68
20 3 0.12
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.49
Consensus pattern (19 bp):
TATAAATAATTTACTCATG
Found at i:10211 original size:20 final size:21
Alignment explanation
Indices: 10186--10235 Score: 66
Period size: 24 Copynumber: 2.3 Consensus size: 21
10176 ATAAAATACA
10186 CTCTTT-TTTACTCTCTCATT
1 CTCTTTCTTTACTCTCTCATT
10206 CTCTTTGTTCTTTACTCTCTCATT
1 CTC--T-TTCTTTACTCTCTCATT
10230 CTCTTT
1 CTCTTT
10236 GTTTTTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
20 3 0.12
21 2 0.08
22 2 0.08
23 2 0.08
24 17 0.65
ACGTcount: A:0.08, C:0.30, G:0.02, T:0.60
Consensus pattern (21 bp):
CTCTTTCTTTACTCTCTCATT
Found at i:10222 original size:24 final size:24
Alignment explanation
Indices: 10192--10238 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
10182 TACACTCTTT
10192 TTTACTCTCTCATTCTCTTTGTTC
1 TTTACTCTCTCATTCTCTTTGTTC
10216 TTTACTCTCTCATTCTCTTTGTT
1 TTTACTCTCTCATTCTCTTTGTT
10239 TTTTTATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.09, C:0.28, G:0.04, T:0.60
Consensus pattern (24 bp):
TTTACTCTCTCATTCTCTTTGTTC
Done.