Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014923.1 Kokia drynarioides strain JFW-HI SEQ_129966, 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: 66226
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:4209 original size:29 final size:30
Alignment explanation
Indices: 4164--4225 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 30
4154 TTTTAATTTT
*
4164 AATATAGGGATTAAATTGAGT-AACTTGTG
1 AATATAGGGATTAAATTGAGTCAAATTGTG
4193 AATATAGGGACTT-AATTGAGTCAAATTGTG
1 AATATAGGGA-TTAAATTGAGTCAAATTGTG
4223 AAT
1 AAT
4226 TTTGAGGGCC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 18 0.60
30 12 0.40
ACGTcount: A:0.39, C:0.05, G:0.23, T:0.34
Consensus pattern (30 bp):
AATATAGGGATTAAATTGAGTCAAATTGTG
Found at i:5541 original size:12 final size:12
Alignment explanation
Indices: 5524--5548 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5514 GGTAATATCA
5524 TGATATTGAGAT
1 TGATATTGAGAT
5536 TGATATTGAGAT
1 TGATATTGAGAT
5548 T
1 T
5549 AAAACTGAGA
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:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (12 bp):
TGATATTGAGAT
Found at i:6079 original size:2 final size:2
Alignment explanation
Indices: 6074--6099 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6064 ATAATTTAAC
6074 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
6100 GAACGTGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11773 original size:21 final size:21
Alignment explanation
Indices: 11736--11775 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
11726 AGAGTGAATC
*
11736 TGGCAGTATTACTATATTTTT
1 TGGCAGTATTACAATATTTTT
11757 TGGCAGTA-TATCAATATTT
1 TGGCAGTATTA-CAATATTT
11776 GTCTGAGAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.28, C:0.10, G:0.15, T:0.47
Consensus pattern (21 bp):
TGGCAGTATTACAATATTTTT
Found at i:16825 original size:24 final size:24
Alignment explanation
Indices: 16769--16819 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
16759 AGCTTTTTCA
16769 AAAAAAAATAATTAAATGGTATAT
1 AAAAAAAATAATTAAATGGTATAT
*
16793 TAAAAAAATAATTAAATGGT-TA-
1 AAAAAAAATAATTAAATGGTATAT
16815 AAAAA
1 AAAAA
16820 TTAAATTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 4 0.16
23 2 0.08
24 19 0.76
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.27
Consensus pattern (24 bp):
AAAAAAAATAATTAAATGGTATAT
Found at i:24206 original size:21 final size:20
Alignment explanation
Indices: 24182--24221 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
24172 AACTTTTTAT
24182 ATTT-TTTTAATTTTAATTTTG
1 ATTTATTTT-ATTTT-ATTTTG
24203 ATTTATTTTATTTTATTTT
1 ATTTATTTTATTTTATTTT
24222 AATAAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.75
Consensus pattern (20 bp):
ATTTATTTTATTTTATTTTG
Found at i:29997 original size:21 final size:22
Alignment explanation
Indices: 29956--30004 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
29946 GTATCAGTTT
** *
29956 TTTTTTAAGTATTTAATATTTG
1 TTTTTTAAAAATTTAATATTTA
29978 TTTTTTAAAAATTTAA-ATTTA
1 TTTTTTAAAAATTTAATATTTA
29999 TTTTTT
1 TTTTTT
30005 GGAACCATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (22 bp):
TTTTTTAAAAATTTAATATTTA
Found at i:30166 original size:104 final size:105
Alignment explanation
Indices: 30009--30235 Score: 384
Period size: 104 Copynumber: 2.2 Consensus size: 105
29999 TTTTTTGGAA
* * *
30009 CCATTTTAAATTGCACCAACGAATTGATTTTTTGTTTTTTATTATTTATTATATAATATTTAAAT
1 CCATTTTAAATGGCGCCAACGAATTGATTTTTTGATTTTTATTATTTATTATATAATATTTAAAT
*
30074 ATATAATTTAATTTAAATGTATGTTTTATTTTTGGTAGAG
66 ATATAATTTAATTTAAATGTATATTTTATTTTTGGTAGAG
*
30114 CCATTTTAAATGGCGCCATCGAATTGATTTTTT-ATTTTTATTATTTATTATATAATATTTAAAT
1 CCATTTTAAATGGCGCCAACGAATTGATTTTTTGATTTTTATTATTTATTATATAATATTTAAAT
* *
30178 ATATAGTTTAATTTAAATGTATATTTTATTTTTGGTGGAG
66 ATATAATTTAATTTAAATGTATATTTTATTTTTGGTAGAG
30218 CCATTTTAAATGGCGCCA
1 CCATTTTAAATGGCGCCA
30236 CCAATTCCCG
Statistics
Matches: 115, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
104 85 0.74
105 30 0.26
ACGTcount: A:0.31, C:0.07, G:0.11, T:0.50
Consensus pattern (105 bp):
CCATTTTAAATGGCGCCAACGAATTGATTTTTTGATTTTTATTATTTATTATATAATATTTAAAT
ATATAATTTAATTTAAATGTATATTTTATTTTTGGTAGAG
Found at i:30193 original size:18 final size:18
Alignment explanation
Indices: 30170--30205 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
30160 ATTATATAAT
30170 ATTTAAATATATAGTTTA
1 ATTTAAATATATAGTTTA
* *
30188 ATTTAAATGTATATTTTA
1 ATTTAAATATATAGTTTA
30206 TTTTTGGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (18 bp):
ATTTAAATATATAGTTTA
Found at i:33155 original size:22 final size:22
Alignment explanation
Indices: 33130--33184 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
33120 ATACATTTGT
33130 TTACATAACACTTGAAATTATA
1 TTACATAACACTTGAAATTATA
33152 TTACATAACACTTGAAATTATA
1 TTACATAACACTTGAAATTATA
*
33174 TGACATAACAC
1 TTACATAACAC
33185 ATAAATATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.33
Consensus pattern (22 bp):
TTACATAACACTTGAAATTATA
Found at i:35923 original size:13 final size:13
Alignment explanation
Indices: 35905--35930 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35895 ACCACATTTC
35905 CTTCTTCTCTTCT
1 CTTCTTCTCTTCT
35918 CTTCTTCTCTTCT
1 CTTCTTCTCTTCT
35931 AATTCAAAAT
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:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (13 bp):
CTTCTTCTCTTCT
Found at i:36712 original size:18 final size:18
Alignment explanation
Indices: 36666--36713 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
36656 CAACCCAAAA
*
36666 TTCATCAAAGAAAATAAC
1 TTCATCAAAGCAAATAAC
36684 TTCATCAAAGCAAATAA-
1 TTCATCAAAGCAAATAAC
36701 TGTCATCAAAGCA
1 T-TCATCAAAGCA
36714 TAAACAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
17 1 0.04
18 27 0.96
ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23
Consensus pattern (18 bp):
TTCATCAAAGCAAATAAC
Found at i:37801 original size:30 final size:30
Alignment explanation
Indices: 37729--37815 Score: 81
Period size: 30 Copynumber: 2.9 Consensus size: 30
37719 AATTTGATTT
* * **
37729 TAGGGATTAAATTGG-AATTTTAGTGACATT
1 TAGGGACTAAATTGGAAATTTT-GTGAAACC
*
37759 TATGGACT-AATTGGAAATTTTGTGAAACC
1 TAGGGACTAAATTGGAAATTTTGTGAAACC
*
37788 TAGGGACTAAATT-GAAATGTTAGTGAAA
1 TAGGGACTAAATTGGAAAT-TTTGTGAAA
37816 TTTGAGGGCC
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
29 23 0.49
30 24 0.51
ACGTcount: A:0.37, C:0.06, G:0.23, T:0.34
Consensus pattern (30 bp):
TAGGGACTAAATTGGAAATTTTGTGAAACC
Found at i:49124 original size:3 final size:3
Alignment explanation
Indices: 49116--49155 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
49106 TTGGTTAGTT
49116 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
49156 AATATTAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:50209 original size:14 final size:15
Alignment explanation
Indices: 50190--50218 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
50180 TCGAAAATTG
50190 CACAGTCG-GTGTCA
1 CACAGTCGTGTGTCA
50204 CACAGTCGTGTGTCA
1 CACAGTCGTGTGTCA
50219 GGCCGTGTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.21, C:0.28, G:0.28, T:0.24
Consensus pattern (15 bp):
CACAGTCGTGTGTCA
Found at i:51178 original size:23 final size:23
Alignment explanation
Indices: 51152--51226 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 23
51142 TTTTCTCAAT
51152 TAATTAAAATATGATGATTTTCG
1 TAATTAAAATATGATGATTTTCG
*** ** **
51175 TAATT-TTCTATTTTGGACTTTTAT
1 TAATTAAAATATGAT-GA-TTTTCG
51199 TAATTAAAATATGATGATTTTCG
1 TAATTAAAATATGATGATTTTCG
51222 TAATT
1 TAATT
51227 TTCTATTTTG
Statistics
Matches: 35, Mismatches: 14, Indels: 6
0.64 0.25 0.11
Matches are distributed among these distances:
22 4 0.11
23 16 0.46
24 11 0.31
25 4 0.11
ACGTcount: A:0.33, C:0.05, G:0.11, T:0.51
Consensus pattern (23 bp):
TAATTAAAATATGATGATTTTCG
Found at i:51219 original size:47 final size:47
Alignment explanation
Indices: 51150--51244 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
51140 TGTTTTCTCA
51150 ATTAATTAAAATATGATGATTTTCGTAATTTTCTATTTTGGACTTTT
1 ATTAATTAAAATATGATGATTTTCGTAATTTTCTATTTTGGACTTTT
51197 ATTAATTAAAATATGATGATTTTCGTAATTTTCTATTTTGGACTTTT
1 ATTAATTAAAATATGATGATTTTCGTAATTTTCTATTTTGGACTTTT
51244 A
1 A
51245 GGATTATAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.31, C:0.06, G:0.11, T:0.53
Consensus pattern (47 bp):
ATTAATTAAAATATGATGATTTTCGTAATTTTCTATTTTGGACTTTT
Found at i:52112 original size:22 final size:22
Alignment explanation
Indices: 52084--52128 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
52074 TTTGATTTTT
52084 TATATTTTTTCGAATTTTT-AAA
1 TATATTTTTT-GAATTTTTCAAA
*
52106 TATATTTTTTTAATTTTTCAAA
1 TATATTTTTTGAATTTTTCAAA
52128 T
1 T
52129 GATGGTGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (22 bp):
TATATTTTTTGAATTTTTCAAA
Found at i:52211 original size:47 final size:47
Alignment explanation
Indices: 52113--52213 Score: 116
Period size: 47 Copynumber: 2.1 Consensus size: 47
52103 AAATATATTT
* ***
52113 TTTTAATTTTTCAAATGATGGTGTCATTGAAACATGAATAAATATTT
1 TTTTAATTTTTCAAATGATGGTGTCATTGAAACATGAACAAATAAAA
* *
52160 TTTTAATTTTTCAAATGATGGTGTCATT-CAA-ATGGACAGAATGAAAA
1 TTTTAATTTTTCAAATGATGGTGTCATTGAAACATGAACA-AAT-AAAA
52207 TTTTAAT
1 TTTTAAT
52214 AACTTGGGAT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
45 5 0.11
46 5 0.11
47 36 0.78
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.43
Consensus pattern (47 bp):
TTTTAATTTTTCAAATGATGGTGTCATTGAAACATGAACAAATAAAA
Found at i:54210 original size:26 final size:25
Alignment explanation
Indices: 54185--54307 Score: 99
Period size: 25 Copynumber: 4.8 Consensus size: 25
54175 CTAGACAGAG
*
54185 TTTA-GCTCTTACGAACCCAAATAGA
1 TTTACGCTCTTACG-AGCCAAATAGA
*
54210 GTATT--GCTCTTACGAGCCAGATAGA
1 -T-TTACGCTCTTACGAGCCAAATAGA
*
54235 ATTACGCTCTTACGAGCCAGAATTAGA
1 TTTACGCTCTTACGAGCCA-AA-TAGA
* *
54262 TTTACGCTCTTACGAGCCAGACAGA
1 TTTACGCTCTTACGAGCCAAATAGA
* ** *
54287 ATTGTGCTCTTACAAGCCAAA
1 TTTACGCTCTTACGAGCCAAA
54308 ATCAGATTAT
Statistics
Matches: 80, Mismatches: 12, Indels: 11
0.78 0.12 0.11
Matches are distributed among these distances:
23 2 0.03
25 42 0.52
26 12 0.15
27 24 0.30
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.27
Consensus pattern (25 bp):
TTTACGCTCTTACGAGCCAAATAGA
Found at i:54243 original size:25 final size:25
Alignment explanation
Indices: 54215--54305 Score: 119
Period size: 25 Copynumber: 3.6 Consensus size: 25
54205 ATAGAGTATT
54215 GCTCTTACGAGCCAGATAGAATTAC
1 GCTCTTACGAGCCAGATAGAATTAC
*
54240 GCTCTTACGAGCCAGAATTAGATTTAC
1 GCTCTTACGAGCCAG-A-TAGAATTAC
* **
54267 GCTCTTACGAGCCAGACAGAATTGT
1 GCTCTTACGAGCCAGATAGAATTAC
*
54292 GCTCTTACAAGCCA
1 GCTCTTACGAGCCA
54306 AAATCAGATT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
25 33 0.57
26 2 0.03
27 23 0.40
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (25 bp):
GCTCTTACGAGCCAGATAGAATTAC
Found at i:54276 original size:52 final size:52
Alignment explanation
Indices: 54215--54315 Score: 148
Period size: 52 Copynumber: 1.9 Consensus size: 52
54205 ATAGAGTATT
* * * *
54215 GCTCTTACGAGCCAGATAGAATTACGCTCTTACGAGCCAGAATTAGATTTAC
1 GCTCTTACGAGCCAGACAGAATTACGCTCTTACAAGCCAAAATCAGATTTAC
**
54267 GCTCTTACGAGCCAGACAGAATTGTGCTCTTACAAGCCAAAATCAGATT
1 GCTCTTACGAGCCAGACAGAATTACGCTCTTACAAGCCAAAATCAGATT
54316 ATCTTCGTCA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.26
Consensus pattern (52 bp):
GCTCTTACGAGCCAGACAGAATTACGCTCTTACAAGCCAAAATCAGATTTAC
Found at i:63050 original size:20 final size:20
Alignment explanation
Indices: 63025--63064 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
63015 ATATATCATC
*
63025 CACATGTATGTCATGTCACT
1 CACATGTATATCATGTCACT
63045 CACATGTATATCATGTCACT
1 CACATGTATATCATGTCACT
63065 AAAATTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (20 bp):
CACATGTATATCATGTCACT
Done.