Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013130.1 Kokia drynarioides strain JFW-HI SEQ_128149, 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: 6720
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Warning! 43 characters in sequence are not A, C, G, or T
Found at i:1081 original size:24 final size:26
Alignment explanation
Indices: 1034--1081 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
1024 TTTTATTATT
1034 ATTTATATTTACTTGTTTATTTTGGC
1 ATTTATATTTACTTGTTTATTTTGGC
1060 ATTTA-ATTTA-TTGATTT-TTTTG
1 ATTTATATTTACTTG-TTTATTTTG
1082 TTAATTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 8 0.38
26 5 0.24
ACGTcount: A:0.21, C:0.04, G:0.10, T:0.65
Consensus pattern (26 bp):
ATTTATATTTACTTGTTTATTTTGGC
Found at i:1160 original size:26 final size:25
Alignment explanation
Indices: 1128--1182 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 25
1118 TCCCAATTAT
1128 TTTTATTGTTTA-TATTTATTTGTTTA
1 TTTTATT-TTTATTATTT-TTTGTTTA
1154 TTTTATTTTTATTTATTTTTTGTTTA
1 TTTTATTTTTA-TTATTTTTTGTTTA
1180 TTT
1 TTT
1183 ATCTAGTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
25 4 0.15
26 18 0.67
27 5 0.19
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.78
Consensus pattern (25 bp):
TTTTATTTTTATTATTTTTTGTTTA
Found at i:1170 original size:15 final size:15
Alignment explanation
Indices: 1150--1202 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
1140 TATTTATTTG
1150 TTTATTTTATTTTTA
1 TTTATTTTATTTTTA
1165 TTTATTTT-TTGTTTA
1 TTTATTTTATT-TTTA
* *
1180 TTTA-TCTAGTTGTTA
1 TTTATTTTA-TTTTTA
1195 TTTATTTT
1 TTTATTTT
1203 CGTACCATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
14 4 0.13
15 23 0.74
16 4 0.13
ACGTcount: A:0.17, C:0.02, G:0.06, T:0.75
Consensus pattern (15 bp):
TTTATTTTATTTTTA
Found at i:1236 original size:15 final size:14
Alignment explanation
Indices: 1218--1278 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 14
1208 CATTTTAACG
1218 TTATCTTTTTTATTA
1 TTAT-TTTTTTATTA
*
1233 TTATTTATTTAATTA
1 TTATTT-TTTTATTA
1248 TTATTTATTGTTATTA
1 TTATTT-TT-TTATTA
*
1264 TCTTATTTATTTATT
1 --TTATTTTTTTATT
1279 TATTTACTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
14 2 0.05
15 20 0.51
16 10 0.26
17 1 0.03
18 6 0.15
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.70
Consensus pattern (14 bp):
TTATTTTTTTATTA
Found at i:1242 original size:4 final size:4
Alignment explanation
Indices: 1233--1289 Score: 55
Period size: 4 Copynumber: 14.0 Consensus size: 4
1223 TTTTTTATTA
*
1233 TTAT TTAT TTAA TTA- TTAT TTAT TGT-T ATTAT CTTAT TTAT TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT T-TAT -TTAT -TTAT TTAT TTAT TTAT
*
1282 TTAC TTAT
1 TTAT TTAT
1290 CATTAAATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
3 3 0.07
4 35 0.78
5 7 0.16
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (4 bp):
TTAT
Found at i:1254 original size:25 final size:26
Alignment explanation
Indices: 1226--1282 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
1216 CGTTATCTTT
1226 TTTATTATTATTTAT-TTAATTA-TTA
1 TTTATTATTA-TTATCTTAATTATTTA
* *
1251 TTTATTGTTATTATCTTATTTATTTA
1 TTTATTATTATTATCTTAATTATTTA
1277 TTTATT
1 TTTATT
1283 TACTTATCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 4 0.14
25 15 0.54
26 9 0.32
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (26 bp):
TTTATTATTATTATCTTAATTATTTA
Found at i:1289 original size:25 final size:23
Alignment explanation
Indices: 1218--1290 Score: 64
Period size: 22 Copynumber: 3.2 Consensus size: 23
1208 CATTTTAACG
*
1218 TTATCTTTTTTA-TTATTATTTA
1 TTATCTTATTTATTTATTATTTA
* *
1240 TT-TAATTA-TTATTTATT-GTTA
1 TTAT-CTTATTTATTTATTATTTA
1261 TTATCTTATTTATTTATTTATTTA
1 TTATCTTATTTATTTA-TTATTTA
1285 CTTATC
1 -TTATC
1291 ATTAAATTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
21 12 0.31
22 17 0.44
23 2 0.05
24 3 0.08
25 5 0.13
ACGTcount: A:0.25, C:0.05, G:0.01, T:0.68
Consensus pattern (23 bp):
TTATCTTATTTATTTATTATTTA
Found at i:3096 original size:20 final size:19
Alignment explanation
Indices: 3050--3143 Score: 100
Period size: 19 Copynumber: 4.8 Consensus size: 19
3040 AGTCTTTAGA
* *
3050 TTAAAGATTTTGGTATCTG
1 TTAAAGATTTTGATATTTG
3069 TTAAAGATTTTGATATTTGG
1 TTAAAGATTTTGATATTT-G
* *
3089 TTATAGATTTTGTTATCTT-
1 TTAAAGATTTTGATAT-TTG
*
3108 TTAAAAATTTTGATATTTG
1 TTAAAGATTTTGATATTTG
*
3127 ATTACAGATTTTGATAT
1 -TTAAAGATTTTGATAT
3144 CCAATCACAA
Statistics
Matches: 62, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
18 2 0.03
19 29 0.47
20 29 0.47
21 2 0.03
ACGTcount: A:0.30, C:0.03, G:0.15, T:0.52
Consensus pattern (19 bp):
TTAAAGATTTTGATATTTG
Found at i:3112 original size:39 final size:39
Alignment explanation
Indices: 3048--3144 Score: 131
Period size: 39 Copynumber: 2.5 Consensus size: 39
3038 AGAGTCTTTA
* * *
3048 GATTAAAGATTTTGGTATCTGTTAAAGATTTTGATATTT
1 GATTACAGATTTTGATATCTGTTAAAAATTTTGATATTT
* * * *
3087 GGTTATAGATTTTGTTATCTTTTAAAAATTTTGATATTT
1 GATTACAGATTTTGATATCTGTTAAAAATTTTGATATTT
3126 GATTACAGATTTTGATATC
1 GATTACAGATTTTGATATC
3145 CAATCACAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.30, C:0.04, G:0.15, T:0.51
Consensus pattern (39 bp):
GATTACAGATTTTGATATCTGTTAAAAATTTTGATATTT
Found at i:3784 original size:24 final size:27
Alignment explanation
Indices: 3756--3805 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
3746 TATTTTTAAA
3756 AATTTTT-TAAA-ATAT-AAAATTTAG
1 AATTTTTATAAATATATGAAAATTTAG
*
3780 AATTTTTATAAATATTTGAAAATTTA
1 AATTTTTATAAATATATGAAAATTTA
3806 AAAATTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 7 0.32
25 4 0.18
26 3 0.14
27 8 0.36
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (27 bp):
AATTTTTATAAATATATGAAAATTTAG
Found at i:3785 original size:34 final size:34
Alignment explanation
Indices: 3741--3808 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
3731 CTTTAGATTT
* * *
3741 TTTAGTATTTTTAAAAATTTTTTAAAATATAAAA
1 TTTAGAATTTTTAAAAATATTTGAAAATATAAAA
* *
3775 TTTAGAATTTTTATAAATATTTGAAAATTTAAAA
1 TTTAGAATTTTTAAAAATATTTGAAAATATAAAA
3809 ATTATTTTGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (34 bp):
TTTAGAATTTTTAAAAATATTTGAAAATATAAAA
Found at i:4555 original size:26 final size:26
Alignment explanation
Indices: 4513--4575 Score: 99
Period size: 26 Copynumber: 2.4 Consensus size: 26
4503 TCTCTTACTA
* *
4513 ATTTAATTAATTAGAGATAAAATAATT
1 ATTTAA-TATTTAGAGATAAAAAAATT
4540 ATTTAATATTTAGAGATAAAAAAATT
1 ATTTAATATTTAGAGATAAAAAAATT
4566 ATTTAATATT
1 ATTTAATATT
4576 ATCAGCTAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
26 28 0.82
27 6 0.18
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (26 bp):
ATTTAATATTTAGAGATAAAAAAATT
Found at i:6151 original size:13 final size:13
Alignment explanation
Indices: 6133--6158 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6123 TTTAAATAAT
6133 GTCCAATTACAAA
1 GTCCAATTACAAA
6146 GTCCAATTACAAA
1 GTCCAATTACAAA
6159 TCAAGCCCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (13 bp):
GTCCAATTACAAA
Done.