Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008851.1 Kokia drynarioides strain JFW-HI SEQ_123537, 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: 55199
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:1175 original size:17 final size:16
Alignment explanation
Indices: 1136--1191 Score: 76
Period size: 17 Copynumber: 3.3 Consensus size: 16
1126 CTGGATTTTT
*
1136 TTAATTTTAAAATTAAA
1 TTAAATTTAAAA-TAAA
1153 TTTAAATTTAAAATAAA
1 -TTAAATTTAAAATAAA
1170 TCTAAATTTAAAATAAA
1 T-TAAATTTAAAATAAA
1187 TTAAA
1 TTAAA
1192 AAGGGGGGCC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
16 5 0.14
17 20 0.56
18 11 0.31
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (16 bp):
TTAAATTTAAAATAAA
Found at i:5632 original size:30 final size:32
Alignment explanation
Indices: 5573--5632 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
5563 TATATTTAAA
*
5573 AATATATTATATATCTTTTCATATATTTTAGG
1 AATATATTATATATCATTTCATATATTTTAGG
*
5605 AATATATTATATGT-ATTTCATAT-TTTTA
1 AATATATTATATATCATTTCATATATTTTA
5633 TGTGGTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 5 0.19
31 8 0.31
32 13 0.50
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (32 bp):
AATATATTATATATCATTTCATATATTTTAGG
Found at i:15718 original size:4 final size:4
Alignment explanation
Indices: 15711--15740 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
15701 AATTGAATGA
15711 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AA
1 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AA
15741 GCACTGCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:26413 original size:16 final size:15
Alignment explanation
Indices: 26392--26429 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
26382 AATGGAATGA
26392 AAATAAATATTTAATT
1 AAATAAA-ATTTAATT
26408 AAAT-AAATTTAATT
1 AAATAAAATTTAATT
*
26422 AATTAAAA
1 AAATAAAA
26430 ATTTTAAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 11 0.55
15 5 0.25
16 4 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAATAAAATTTAATT
Found at i:30827 original size:14 final size:14
Alignment explanation
Indices: 30795--30833 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
30785 TTATTTTATT
*
30795 AAAAATGATTTTCA
1 AAAAATAATTTTCA
*
30809 AAAAATAATTTTTA
1 AAAAATAATTTTCA
*
30823 GAAAATAATTT
1 AAAAATAATTT
30834 ATTTTTTTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (14 bp):
AAAAATAATTTTCA
Found at i:31264 original size:21 final size:21
Alignment explanation
Indices: 31234--31274 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
31224 TAACGGGATC
*
31234 GCTGATGTGGCCAGTTAACTA
1 GCTGACGTGGCCAGTTAACTA
31255 GCTGACGTGGCCAGTTAACT
1 GCTGACGTGGCCAGTTAACT
31275 TGCCACGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (21 bp):
GCTGACGTGGCCAGTTAACTA
Found at i:32524 original size:3 final size:3
Alignment explanation
Indices: 32516--32548 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
32506 CATTTGTTAT
32516 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
32549 CCCTTTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:35097 original size:10 final size:8
Alignment explanation
Indices: 35070--35115 Score: 56
Period size: 8 Copynumber: 5.5 Consensus size: 8
35060 TTTATGGATA
*
35070 AAAATAAA
1 AAAATAAT
*
35078 AAAATCAT
1 AAAATAAT
35086 AAAATCATAT
1 AAAAT-A-AT
35096 AAAATAAT
1 AAAATAAT
35104 AAAATAAT
1 AAAATAAT
35112 AAAA
1 AAAA
35116 GGTATTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
8 25 0.76
9 1 0.03
10 7 0.21
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (8 bp):
AAAATAAT
Found at i:37045 original size:134 final size:130
Alignment explanation
Indices: 36827--37231 Score: 487
Period size: 134 Copynumber: 3.2 Consensus size: 130
36817 TGTTTGTAAA
* * * *
36827 TTGTAATGCTTTT-GAGTGTGTGGGG-T---T-TCTTTTTTATCTGCATACAACAGTGGCTTCCG
1 TTGTATTGCTTTTCGAGTGTGTGGGGTTCACTCTCTTTTTTATTTGCAAACAACAGTGGCTTTCG
* * * *
36886 TTTGCTATGC-GTTTGGGTGTATAGGGTCTCATTGCTCTCTCATTGAAGACAACGGTGGTCTTTG
66 TTTG-TATGCTCTTTGGGTGTATAGGGTTTCATTGCTTTCTCATTGAAGACAACAGTGGTCTTTG
36950 T
130 T
* * *
36951 TTGTAATGCTTTTCGAGTGTGTGGGGTTTACTCTCTTTTTTTGTTATTTGCAGACAACAGTGGCT
1 TTGTATTGCTTTTCGAGTGTGTGGGGTTCACTCTC---TTTT-TTATTTGCAAACAACAGTGGCT
* * *
37016 TTCGTTTGT-TGCTCCTTTGGGTGTTTAGGGTTTCATTGCTTTCTCATTGAA-AGCAGCAGCGGT
62 TTCGTTTGTATGCT-CTTTGGGTGTATAGGGTTTCATTGCTTTCTCATTGAAGA-CAACAGTGGT
37079 CTTTGT
125 CTTTGT
* *
37085 TTGTATTGCTTTT-GAGTGTTTGGGGTTCACTCTCTTTTTTATTTGCAAAC-ACAGTGGCTTTCC
1 TTGTATTGCTTTTCGAGTGTGTGGGGTTCACTCTCTTTTTTATTTGCAAACAACAGTGGCTTTCG
*
37148 TTTGTCATGCT-TTTGGGTG-ATAGGGTTTCATTGCTTTCTCATTGAAGGCAACAGTGGTCTTTG
66 TTTGT-ATGCTCTTTGGGTGTATAGGGTTTCATTGCTTTCTCATTGAAGACAACAGTGGTCTTTG
37211 T
130 T
37212 TTGTATTGCTTTTCG-GTGTG
1 TTGTATTGCTTTTCGAGTGTG
37232 GCCTGGTGGT
Statistics
Matches: 244, Mismatches: 20, Indels: 31
0.83 0.07 0.11
Matches are distributed among these distances:
124 13 0.05
125 12 0.05
126 1 0.00
127 57 0.23
128 26 0.11
129 12 0.05
130 10 0.04
132 3 0.01
133 25 0.10
134 85 0.35
ACGTcount: A:0.14, C:0.16, G:0.25, T:0.45
Consensus pattern (130 bp):
TTGTATTGCTTTTCGAGTGTGTGGGGTTCACTCTCTTTTTTATTTGCAAACAACAGTGGCTTTCG
TTTGTATGCTCTTTGGGTGTATAGGGTTTCATTGCTTTCTCATTGAAGACAACAGTGGTCTTTGT
Found at i:37104 original size:64 final size:63
Alignment explanation
Indices: 37007--37230 Score: 205
Period size: 64 Copynumber: 3.5 Consensus size: 63
36997 TTTGCAGACA
37007 ACAGTGG-CTTTCGTTTG--TTGCTCCTTTGGGTGTTTAGGGTTTCATTGCTTTCTCATTGAAAG
1 ACAGTGGTCTTT-GTTTGTATTGCT--TTTGGGTGTTTAGGGTTTCATTGCTTTCTCATTGAAAG
37069 C
63 C
* * * * *
37070 AGCAGCGGTCTTTGTTTGTATTGCTTTTGAGTGTTT-GGGGTTCACTCT-CTTTTTTATTTGCAA
1 A-CAGTGGTCTTTGTTTGTATTGCTTTTGGGTGTTTAGGGTTTCA-T-TGCTTTCTCA-TTG-AA
37133 A-C
61 AGC
* * *
37135 ACAGTGG-CTTTCCTTTGTCA-TGCTTTTGGGTG-ATAGGGTTTCATTGCTTTCTCATTGAAGGC
1 ACAGTGGTCTTT-GTTTGT-ATTGCTTTTGGGTGTTTAGGGTTTCATTGCTTTCTCATTGAAAGC
*
37197 AACAGTGGTCTTTGTTTGTATTGCTTTTCGGTGT
1 -ACAGTGGTCTTTGTTTGTATTGCTTTTGGGTGT
37231 GGCCTGGTGG
Statistics
Matches: 129, Mismatches: 15, Indels: 33
0.73 0.08 0.19
Matches are distributed among these distances:
61 2 0.02
62 6 0.05
63 43 0.33
64 59 0.46
65 11 0.09
66 8 0.06
ACGTcount: A:0.13, C:0.16, G:0.25, T:0.46
Consensus pattern (63 bp):
ACAGTGGTCTTTGTTTGTATTGCTTTTGGGTGTTTAGGGTTTCATTGCTTTCTCATTGAAAGC
Found at i:39204 original size:3 final size:3
Alignment explanation
Indices: 39196--39223 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
39186 ATTAAAAATA
39196 AAC AAC AAC AAC AAC AAC AAC AAC AAC A
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC A
39224 TAATAATAAT
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:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:39229 original size:3 final size:3
Alignment explanation
Indices: 39223--39248 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
39213 CAACAACAAC
39223 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
39249 CCTAAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:39557 original size:12 final size:12
Alignment explanation
Indices: 39540--39564 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39530 CCACATAAGC
39540 TTAATGACATCA
1 TTAATGACATCA
39552 TTAATGACATCA
1 TTAATGACATCA
39564 T
1 T
39565 CAAAATAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (12 bp):
TTAATGACATCA
Found at i:42344 original size:28 final size:27
Alignment explanation
Indices: 42280--42344 Score: 67
Period size: 29 Copynumber: 2.3 Consensus size: 27
42270 ATTTAGTCCT
* *
42280 TAAAAGAAAATTTTGACCTATAAAAAT
1 TAAAAAAAAATTTTGACCTATAAAAAG
* * *
42307 TAAAAGAAAAATTTTGGGCCTCTTAAAAG
1 TAAAA-AAAAATTTT-GACCTATAAAAAG
42336 TAAAAAAAA
1 TAAAAAAAA
42345 TTAGACCCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
27 5 0.16
28 12 0.39
29 14 0.45
ACGTcount: A:0.55, C:0.08, G:0.11, T:0.26
Consensus pattern (27 bp):
TAAAAAAAAATTTTGACCTATAAAAAG
Found at i:42906 original size:12 final size:12
Alignment explanation
Indices: 42889--42914 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42879 AAAAAATATT
42889 TTGATGATGTCA
1 TTGATGATGTCA
42901 TTGATGATGTCA
1 TTGATGATGTCA
42913 TT
1 TT
42915 ATGCTTATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (12 bp):
TTGATGATGTCA
Found at i:49445 original size:18 final size:18
Alignment explanation
Indices: 49424--49458 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
49414 GCTGTTGTCT
* *
49424 TTTTTTTTTTTTAATTTG
1 TTTTTCTTTTTCAATTTG
49442 TTTTTCTTTTTCAATTT
1 TTTTTCTTTTTCAATTT
49459 ATTGTCCTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.11, C:0.06, G:0.03, T:0.80
Consensus pattern (18 bp):
TTTTTCTTTTTCAATTTG
Found at i:49745 original size:3 final size:3
Alignment explanation
Indices: 49737--49775 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
49727 TCACCTTGCT
*
49737 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
49776 TTAAACAAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:51755 original size:17 final size:17
Alignment explanation
Indices: 51733--51768 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
51723 TAGCAAATTC
51733 TAATGAAGTTAATCGAT
1 TAATGAAGTTAATCGAT
51750 TAATGAAGTTAATCGAT
1 TAATGAAGTTAATCGAT
51767 TA
1 TA
51769 GCTTTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.36
Consensus pattern (17 bp):
TAATGAAGTTAATCGAT
Done.