Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005774.1 Kokia drynarioides strain JFW-HI SEQ_120041, 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: 40101
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Found at i:138 original size:9 final size:9
Alignment explanation
Indices: 121--150 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
111 ATTATTTTTC
121 CTTCTCCTT
1 CTTCTCCTT
*
130 CTTCCCCTT
1 CTTCTCCTT
139 CTTCTCCTT
1 CTTCTCCTT
148 CTT
1 CTT
151 TCTTTCTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (9 bp):
CTTCTCCTT
Found at i:161 original size:18 final size:18
Alignment explanation
Indices: 117--176 Score: 61
Period size: 17 Copynumber: 3.4 Consensus size: 18
107 CATTATTATT
* *
117 TTTCCTTCTCCTTCTTCCC
1 TTTCTTTCTCCTTCTT-TC
*
136 CTTC-TTCTCCTTCTTTC
1 TTTCTTTCTCCTTCTTTC
*
153 TTTCTTTCT-CTTTTTTC
1 TTTCTTTCTCCTTCTTTC
170 TTTCTTT
1 TTTCTTT
177 TTTCCTTCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
17 18 0.50
18 15 0.42
19 3 0.08
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTCTTTCTCCTTCTTTC
Found at i:169 original size:13 final size:13
Alignment explanation
Indices: 147--179 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
137 TTCTTCTCCT
147 TCTTTCTTTCTTTC
1 TCTTT-TTTCTTTC
161 TCTTTTTTCTTTC
1 TCTTTTTTCTTTC
174 T-TTTTT
1 TCTTTTT
180 CCTTCAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 5 0.26
13 9 0.47
14 5 0.26
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TCTTTTTTCTTTC
Found at i:1620 original size:19 final size:19
Alignment explanation
Indices: 1596--1634 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1586 AAGTATTTGA
*
1596 TAAAATCGTGTTAA-AAAAT
1 TAAAATCAT-TTAACAAAAT
1615 TAAAATCATTTAACAAAAT
1 TAAAATCATTTAACAAAAT
1634 T
1 T
1635 CAATCAAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.33
Consensus pattern (19 bp):
TAAAATCATTTAACAAAAT
Found at i:6791 original size:20 final size:21
Alignment explanation
Indices: 6766--6805 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
6756 TTCATAAGTG
*
6766 AAATAA-CTATTGATATTATT
1 AAATAATCTAATGATATTATT
*
6786 AAATAATCTAATGGTATTAT
1 AAATAATCTAATGATATTAT
6806 AAAAAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.42
Consensus pattern (21 bp):
AAATAATCTAATGATATTATT
Found at i:10470 original size:2 final size:2
Alignment explanation
Indices: 10465--10506 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
10455 CTAAAAAATA
10465 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10507 TCAGTCGTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10714 original size:21 final size:21
Alignment explanation
Indices: 10692--10738 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
10682 TTTTTATGAT
10692 TTTTAAT-AATTTTTATACAA
1 TTTTAATCAATTTTTATACAA
* *
10712 TTTTAATCTATTTTTATAAAA
1 TTTTAATCAATTTTTATACAA
*
10733 TCTTAA
1 TTTTAA
10739 ATATTATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTTAATCAATTTTTATACAA
Found at i:12293 original size:17 final size:18
Alignment explanation
Indices: 12268--12301 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
12258 ATAACAATTA
*
12268 TGAAGATTTTGG-ATATG
1 TGAAAATTTTGGCATATG
12285 TGAAAATTTTGGCATAT
1 TGAAAATTTTGGCATAT
12302 TCTCTGAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.32, C:0.03, G:0.24, T:0.41
Consensus pattern (18 bp):
TGAAAATTTTGGCATATG
Found at i:14817 original size:9 final size:9
Alignment explanation
Indices: 14805--14975 Score: 84
Period size: 9 Copynumber: 18.6 Consensus size: 9
14795 GCTTTATTAA
14805 TTTTATAAT
1 TTTTATAAT
*
14814 TTTTATCAT
1 TTTTATAAT
*
14823 TTATTAGAAT
1 TT-TTATAAT
*
14833 TTATTAAAATT
1 TT-TTATAA-T
14844 TTTTATAA-
1 TTTTATAAT
* *
14852 TATTAAAATT
1 TTTTATAA-T
14862 TTTTATAAT
1 TTTTATAAT
14871 TTTTATAAGT
1 TTTTATAA-T
** *
14881 TCATATCAAA
1 TTTTAT-AAT
*
14891 TTTCAT-A-
1 TTTTATAAT
14898 TTTT-TAAT
1 TTTTATAAT
*
14906 ATTTAATAAT
1 -TTTTATAAT
14916 TTTTAT-AT
1 TTTTATAAT
14924 TTGTTGAT-AT
1 TT-TT-ATAAT
*
14934 TTTTGTAAT
1 TTTTATAAT
* *
14943 TTTCATTAT
1 TTTTATAAT
14952 TTTTATAAT
1 TTTTATAAT
*
14961 TTGTTATGAT
1 TT-TTATAAT
14971 TTTTA
1 TTTTA
14976 ATCAATTTAT
Statistics
Matches: 123, Mismatches: 25, Indels: 28
0.70 0.14 0.16
Matches are distributed among these distances:
6 1 0.01
7 4 0.03
8 12 0.10
9 51 0.41
10 50 0.41
11 5 0.04
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.60
Consensus pattern (9 bp):
TTTTATAAT
Found at i:14855 original size:28 final size:27
Alignment explanation
Indices: 14824--14878 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
14814 TTTTATCATT
*
14824 TATTAGAATTTATTAAAATTTTTTATAA
1 TATTAAAATTTATTAAAA-TTTTTATAA
* *
14852 TATTAAAATTTTTTATAATTTTTATAA
1 TATTAAAATTTATTAAAATTTTTATAA
14879 GTTCATATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 9 0.38
28 15 0.62
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (27 bp):
TATTAAAATTTATTAAAATTTTTATAA
Found at i:14873 original size:10 final size:10
Alignment explanation
Indices: 14805--14878 Score: 57
Period size: 10 Copynumber: 7.8 Consensus size: 10
14795 GCTTTATTAA
14805 TTTTATAA-T
1 TTTTATAATT
*
14814 TTTTATCATT
1 TTTTATAATT
* *
14824 TATTAGAATT
1 TTTTATAATT
* *
14834 TATTAAAATT
1 TTTTATAATT
14844 TTTTATAA--
1 TTTTATAATT
* *
14852 TATTAAAATT
1 TTTTATAATT
14862 TTTTATAA-T
1 TTTTATAATT
14871 TTTTATAA
1 TTTTATAA
14879 GTTCATATCA
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
8 6 0.12
9 16 0.31
10 29 0.57
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (10 bp):
TTTTATAATT
Found at i:18212 original size:18 final size:18
Alignment explanation
Indices: 18191--18241 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 18
18181 AATAATTATT
18191 ATAAAATACAA-TAAATTA
1 ATAAAATA-AATTAAATTA
*
18209 ATAAATTAAATTAAATTAA
1 ATAAAATAAATTAAATT-A
18228 ATTAAAATTAAATT
1 A-TAAAA-TAAATT
18242 GAACAGACCA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 2 0.07
18 13 0.48
19 2 0.07
20 4 0.15
21 6 0.22
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (18 bp):
ATAAAATAAATTAAATTA
Found at i:18218 original size:5 final size:5
Alignment explanation
Indices: 18202--18241 Score: 57
Period size: 5 Copynumber: 8.2 Consensus size: 5
18192 TAAAATACAA
18202 TAAAT T-AA- TAAAT TAAAT TAAAT TAAAT TAAAAT TAAAT T
1 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT T-AAAT TAAAT T
18242 GAACAGACCA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
3 1 0.03
4 4 0.12
5 22 0.69
6 5 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAAAT
Found at i:18218 original size:23 final size:21
Alignment explanation
Indices: 18193--18239 Score: 51
Period size: 23 Copynumber: 2.1 Consensus size: 21
18183 TAATTATTAT
18193 AAAATACAA-TAAATTAATAAATT
1 AAAATA-AATTAAATT-A-AAATT
*
18216 AAATTAAATTAAATTAAAATT
1 AAAATAAATTAAATTAAAATT
18237 AAA
1 AAA
18240 TTGAACAGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 8 0.36
22 3 0.14
23 11 0.50
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (21 bp):
AAAATAAATTAAATTAAAATT
Found at i:18549 original size:18 final size:16
Alignment explanation
Indices: 18519--18552 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
18509 CAAGTTATCC
18519 AATTTTTTTCATGTTA
1 AATTTTTTTCATGTTA
18535 AATTATTTTTCCATGTTA
1 AATT-TTTTT-CATGTTA
18553 GCTTCTAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 5 0.31
18 7 0.44
ACGTcount: A:0.26, C:0.09, G:0.06, T:0.59
Consensus pattern (16 bp):
AATTTTTTTCATGTTA
Found at i:21199 original size:43 final size:43
Alignment explanation
Indices: 21142--21227 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
21132 TGCAATGCCA
21142 GACGAGGTATCACATACTAATAATACCCATTGTTGTTCACAAT
1 GACGAGGTATCACATACTAATAATACCCATTGTTGTTCACAAT
21185 GACGAGGTATCACATACTAATAATACCCATTGTTGTTCACAAT
1 GACGAGGTATCACATACTAATAATACCCATTGTTGTTCACAAT
21228 TAGATTTACC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (43 bp):
GACGAGGTATCACATACTAATAATACCCATTGTTGTTCACAAT
Found at i:28653 original size:30 final size:29
Alignment explanation
Indices: 28619--28707 Score: 90
Period size: 30 Copynumber: 3.0 Consensus size: 29
28609 AATTTATAAG
28619 AATTGAATC-AAATCAAAATTTAATATATAC
1 AATTGAA-CAAAATCAAAATTT-ATATATAC
* * *
28649 AATTGCACAAAATCAAAGTTTATGTATAC
1 AATTGAACAAAATCAAAATTTATATATAC
* *
28678 AATTGAACACCAAATCATAGTTTATATATA
1 AATTGAACA--AAATCAAAATTTATATATA
28708 GTTTTAATAT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 16 0.32
30 17 0.34
31 17 0.34
ACGTcount: A:0.48, C:0.12, G:0.07, T:0.33
Consensus pattern (29 bp):
AATTGAACAAAATCAAAATTTATATATAC
Found at i:28700 original size:31 final size:29
Alignment explanation
Indices: 28628--28707 Score: 97
Period size: 31 Copynumber: 2.7 Consensus size: 29
28618 GAATTGAATC
*
28628 AAATCAAAATTTAATATATACAATTGCACA
1 AAATCAAAGTTT-ATATATACAATTGCACA
* *
28658 AAATCAAAGTTTATGTATACAATTGAACACC
1 AAATCAAAGTTTATATATACAATTG--CACA
*
28689 AAATCATAGTTTATATATA
1 AAATCAAAGTTTATATATA
28708 GTTTTAATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 12 0.28
30 11 0.26
31 20 0.47
ACGTcount: A:0.49, C:0.12, G:0.06, T:0.33
Consensus pattern (29 bp):
AAATCAAAGTTTATATATACAATTGCACA
Found at i:36494 original size:19 final size:19
Alignment explanation
Indices: 36472--36509 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
36462 ACATATAAAA
36472 TTTTAAATATTTTATATATT
1 TTTTAAA-ATTTTATATATT
*
36492 TTTTACAATTTTATATAT
1 TTTTAAAATTTTATATAT
36510 ATATATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTAAAATTTTATATATT
Found at i:37177 original size:25 final size:24
Alignment explanation
Indices: 37137--37210 Score: 87
Period size: 25 Copynumber: 3.0 Consensus size: 24
37127 ATCGACTCAA
*
37137 ATTTTAAATAATTAAAAAAAATAT
1 ATTTTAAATATTTAAAAAAAATAT
* *
37161 -TTATTATATATTATAAAATAAATAT
1 ATT-TTAAATATT-TAAAAAAAATAT
*
37186 ATTTTAAATATTTAAAAATAATAT
1 ATTTTAAATATTTAAAAAAAATAT
37210 A
1 A
37211 ATATAAGTCA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
23 2 0.05
24 18 0.44
25 19 0.46
26 2 0.05
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
ATTTTAAATATTTAAAAAAAATAT
Found at i:37201 original size:24 final size:23
Alignment explanation
Indices: 37137--37210 Score: 78
Period size: 24 Copynumber: 3.0 Consensus size: 23
37127 ATCGACTCAA
*
37137 ATTTTAAATAATTAAAAAAA-AT
1 ATTTTAAATATTTAAAAAAATAT
*
37159 ATTTATTATATATTATAAAATAAATAT
1 A-TT-TTAAATATT-TAAAA-AAATAT
37186 ATTTTAAATATTTAAAAATAATAT
1 ATTTTAAATATTTAAAAA-AATAT
37210 A
1 A
37211 ATATAAGTCA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
22 1 0.02
23 3 0.07
24 18 0.42
25 13 0.30
26 5 0.12
27 3 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
ATTTTAAATATTTAAAAAAATAT
Done.