Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011105.1 Kokia drynarioides strain JFW-HI SEQ_126078, 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: 22448
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Warning! 82 characters in sequence are not A, C, G, or T
Found at i:4138 original size:7 final size:7
Alignment explanation
Indices: 4122--4152 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
4112 TCTATGGTCA
4122 TCCCGTT
1 TCCCGTT
*
4129 TCCTGTT
1 TCCCGTT
4136 TCCCGTT
1 TCCCGTT
4143 TCCCGTT
1 TCCCGTT
4150 TCC
1 TCC
4153 TCAGAGGGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.42, G:0.13, T:0.45
Consensus pattern (7 bp):
TCCCGTT
Found at i:8198 original size:16 final size:16
Alignment explanation
Indices: 8179--8224 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
8169 GAAATAGAAC
8179 TGTAATAAAATAAAAT
1 TGTAATAAAATAAAAT
** *
8195 TGTAATGTAATAGAAT
1 TGTAATAAAATAAAAT
*
8211 TGTAATAGAATAAA
1 TGTAATAAAATAAA
8225 GCTGAAATCA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.13, T:0.33
Consensus pattern (16 bp):
TGTAATAAAATAAAAT
Found at i:8207 original size:32 final size:32
Alignment explanation
Indices: 8161--8224 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
8151 CATTTGGTTT
*
8161 ATTGTGATGAAATAGAACTGTAATAAAATAAA
1 ATTGTAATGAAATAGAACTGTAATAAAATAAA
* * *
8193 ATTGTAATGTAATAGAATTGTAATAGAATAAA
1 ATTGTAATGAAATAGAACTGTAATAAAATAAA
8225 GCTGAAATCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.52, C:0.02, G:0.16, T:0.31
Consensus pattern (32 bp):
ATTGTAATGAAATAGAACTGTAATAAAATAAA
Found at i:10119 original size:24 final size:24
Alignment explanation
Indices: 10092--10143 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
10082 ATAAGTATTT
*
10092 AATAATAAAAATTTCATAATATGA
1 AATAATAAAAATTTAATAATATGA
* * * *
10116 AATATTAATATTTTAATAGTATGA
1 AATAATAAAAATTTAATAATATGA
10140 AATA
1 AATA
10144 TTATTAAATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (24 bp):
AATAATAAAAATTTAATAATATGA
Found at i:10132 original size:21 final size:21
Alignment explanation
Indices: 10108--10200 Score: 75
Period size: 21 Copynumber: 4.3 Consensus size: 21
10098 AAAAATTTCA
10108 TAATATGAAATATTAATATTT
1 TAATATGAAATATTAATATTT
*
10129 TAATAGTATGAAATATTATTAAATTT
1 T-A-A-TATGAAATATTA--ATATTT
*
10155 TATTAT--AATATTAATA-TT
1 TAATATGAAATATTAATATTT
**
10173 TAGATATTTAATATTAATATTT
1 TA-ATATGAAATATTAATATTT
10195 TAATAT
1 TAATAT
10201 TTTTACCGTA
Statistics
Matches: 59, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
18 4 0.07
19 5 0.08
21 22 0.37
22 5 0.08
23 4 0.07
24 12 0.20
25 1 0.02
26 6 0.10
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (21 bp):
TAATATGAAATATTAATATTT
Found at i:11467 original size:14 final size:14
Alignment explanation
Indices: 11421--11467 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
11411 GNGCGTGCGC
11421 GAGCCCCTTTAGTGT
1 GAGCCCC-TTAGTGT
* *
11436 GAG-CCCTTATCTGC
1 GAGCCCCTTA-GTGT
11450 GAGCCCCTTAGTGT
1 GAGCCCCTTAGTGT
11464 GAGC
1 GAGC
11468 GTCTATGTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
13 3 0.12
14 14 0.54
15 9 0.35
ACGTcount: A:0.15, C:0.30, G:0.28, T:0.28
Consensus pattern (14 bp):
GAGCCCCTTAGTGT
Found at i:11482 original size:97 final size:96
Alignment explanation
Indices: 11316--11508 Score: 368
Period size: 97 Copynumber: 2.0 Consensus size: 96
11306 AGAACACCTA
11316 GCGTGCGCGAGCCCCTTTAGTGTGAGCCCTTATCTGCAAGCCCCTTAGTGTGAGCGTCTATGTGT
1 GCGTGCGCGAGCCCCTTTAGTGTGAGCCCTTATCTGCAAGCCCCTTAGTGTGAGCGTCTATGTGT
11381 GAACCCCTAGGTGCGAACTTACATGTGCAAG
66 GAACCCCTAGGTGCGAACTTACATGTGCAAG
*
11412 NGCGTGCGCGAGCCCCTTTAGTGTGAGCCCTTATCTGCGAGCCCCTTAGTGTGAGCGTCTATGTG
1 -GCGTGCGCGAGCCCCTTTAGTGTGAGCCCTTATCTGCAAGCCCCTTAGTGTGAGCGTCTATGTG
11477 TGAACCCCTAGGTGCGAACTTACATGTGCAAG
65 TGAACCCCTAGGTGCGAACTTACATGTGCAAG
11509 CCCTACATGC
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
97 95 1.00
ACGTcount: A:0.18, C:0.27, G:0.28, T:0.26
Consensus pattern (96 bp):
GCGTGCGCGAGCCCCTTTAGTGTGAGCCCTTATCTGCAAGCCCCTTAGTGTGAGCGTCTATGTGT
GAACCCCTAGGTGCGAACTTACATGTGCAAG
Found at i:12735 original size:2 final size:2
Alignment explanation
Indices: 12728--12756 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12718 TCAATCGTTT
12728 TA TA 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 TA TA T
12757 TAATTTTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18311 original size:16 final size:16
Alignment explanation
Indices: 18265--18311 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
18255 AAAAAATATT
18265 TATATTGTTTTATTTTA
1 TATATT-TTTTATTTTA
* *
18282 -ATATTTAATAATTTTA
1 TATATTT-TTTATTTTA
18298 TATATTTTTTATTT
1 TATATTTTTTATTT
18312 ATTGAAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
15 1 0.04
16 17 0.71
17 6 0.25
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (16 bp):
TATATTTTTTATTTTA
Found at i:18803 original size:25 final size:25
Alignment explanation
Indices: 18765--18830 Score: 62
Period size: 25 Copynumber: 2.6 Consensus size: 25
18755 AATTATTATT
* *
18765 TTTAAAATAATTTAATAAG-AATAGA
1 TTTAGAATTATTTAATAAGTAATA-A
* * *
18790 TTTAGAATTTTTTAAAAAGTTATAA
1 TTTAGAATTATTTAATAAGTAATAA
*
18815 TTTATAATTATTTAAT
1 TTTAGAATTATTTAAT
18831 TTTTATAATT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
25 29 0.91
26 3 0.09
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (25 bp):
TTTAGAATTATTTAATAAGTAATAA
Found at i:20426 original size:40 final size:40
Alignment explanation
Indices: 20382--20461 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 40
20372 AATGAGTTTA
20382 TGATTTAT-ATGCTTATGATTAATGACATGAAA-TTGTGAAT
1 TGATTTATGAT-CTTATGATTAATGACAT-AAACTTGTGAAT
* *
20422 TGATTTATGATTTTATGATTAATGGCATAAACTTGTGAAT
1 TGATTTATGATCTTATGATTAATGACATAAACTTGTGAAT
20462 GATATCATGA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
39 3 0.08
40 31 0.86
41 2 0.06
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.44
Consensus pattern (40 bp):
TGATTTATGATCTTATGATTAATGACATAAACTTGTGAAT
Found at i:20472 original size:40 final size:40
Alignment explanation
Indices: 20394--20472 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
20384 ATTTATATGC
*
20394 TTATGATTAATGACATGAAATTGTGAATTGATTTATGATT
1 TTATGATTAATGACATGAAATTGTGAATTGATTCATGATT
*
20434 TTATGATTAATGGCAT-AAACTTGTGAA-TGATATCATGAT
1 TTATGATTAATGACATGAAA-TTGTGAATTGAT-TCATGAT
20473 CATCGATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 7 0.20
40 28 0.80
ACGTcount: A:0.35, C:0.05, G:0.18, T:0.42
Consensus pattern (40 bp):
TTATGATTAATGACATGAAATTGTGAATTGATTCATGATT
Done.