Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009495.1 Kokia drynarioides strain JFW-HI SEQ_124205, 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: 60125
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 57 characters in sequence are not A, C, G, or T
Found at i:679 original size:45 final size:45
Alignment explanation
Indices: 615--751 Score: 175
Period size: 45 Copynumber: 3.0 Consensus size: 45
605 GCATAGCTTA
*
615 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCATCGTAATAC
1 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCATCGCAATAC
* * *
660 TCAAGTCAAGGATATCAGCCTCAATTTGATGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCATCGCAATAC
** ** * * *
705 TCAAGGGAAGGATATCAGGATGAGTTTGACGAGCCATCGCGATAC
1 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCATCGCAATAC
750 TC
1 TC
752 TATTCCTCCC
Statistics
Matches: 79, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 79 1.00
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.22
Consensus pattern (45 bp):
TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCATCGCAATAC
Found at i:1041 original size:28 final size:28
Alignment explanation
Indices: 1008--1061 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
998 TTTCATAACA
1008 TTAAACCCTAAAA-CCTAAATTATAAACC
1 TTAAA-CCTAAAACCCTAAATTATAAACC
* *
1036 TTAAACTTAAAACCCTAAATTGTAAA
1 TTAAACCTAAAACCCTAAATTATAAA
1062 GTTGGAAGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.50, C:0.20, G:0.02, T:0.28
Consensus pattern (28 bp):
TTAAACCTAAAACCCTAAATTATAAACC
Found at i:4207 original size:4 final size:4
Alignment explanation
Indices: 4187--4270 Score: 71
Period size: 4 Copynumber: 20.5 Consensus size: 4
4177 AACACATAAC
* * * *
4187 CTTT CTTT CCTT C-TT CTTT CTTT CCTCT CGTC CTTT CTTT CTTCT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTT-T CTTT
** *
4236 CTCC CTTT CTTT CCTT CTTTT CTTT CTTT CTTT CT
1 CTTT CTTT CTTT CTTT C-TTT CTTT CTTT CTTT CT
4271 CGTTTATTTG
Statistics
Matches: 63, Mismatches: 13, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
3 3 0.05
4 50 0.79
5 10 0.16
ACGTcount: A:0.00, C:0.35, G:0.01, T:0.64
Consensus pattern (4 bp):
CTTT
Found at i:4242 original size:21 final size:20
Alignment explanation
Indices: 4218--4270 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
4208 TTCCTCTCGT
4218 CCTTTCTTTCTTCTCTTTCTC
1 CCTTTCTTTCTTCT-TTTCTC
*
4239 CCTTTCTTTCCTTCTTTTCTT
1 CCTTTCTTT-CTTCTTTTCTC
*
4260 TCTTTCTTTCT
1 CCTTTCTTTCT
4271 CGTTTATTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 2 0.07
21 22 0.76
22 5 0.17
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (20 bp):
CCTTTCTTTCTTCTTTTCTC
Found at i:4260 original size:17 final size:17
Alignment explanation
Indices: 4187--4270 Score: 66
Period size: 17 Copynumber: 4.8 Consensus size: 17
4177 AACACATAAC
4187 CTTTCTTTCCTTC--TT
1 CTTTCTTTCCTTCTTTT
4202 CTTTCTTTCCTCTCGTCCTTT
1 CTTTCTTTCCT-TC-T--TTT
* **
4223 CTTTCTTCTCTTTC-TCC
1 CTTTCTT-TCCTTCTTTT
4240 CTTTCTTTCCTTCTTTT
1 CTTTCTTTCCTTCTTTT
*
4257 CTTTCTTTCTTTCT
1 CTTTCTTTCCTTCT
4271 CGTTTATTTG
Statistics
Matches: 54, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
15 11 0.20
16 7 0.13
17 22 0.41
21 11 0.20
22 3 0.06
ACGTcount: A:0.00, C:0.35, G:0.01, T:0.64
Consensus pattern (17 bp):
CTTTCTTTCCTTCTTTT
Found at i:9346 original size:23 final size:23
Alignment explanation
Indices: 9195--9346 Score: 119
Period size: 23 Copynumber: 6.5 Consensus size: 23
9185 GAACATTAGC
*
9195 GTGCTCTCTGTTTAGCAC-GTCT
1 GTGCTCTCTGTTTAGCACTGTGT
9217 CGTGCTCTCTGTTATTAGCACTGTGT
1 -GTGCTCTCTG-T-TTAGCACTGTGT
* * * *
9243 GTGCTCTTTGATT-GACACTTTAT
1 GTGCTCTCTGTTTAG-CACTGTGT
* * * * *
9266 GTGCTATTTGATTAACACTTTGT
1 GTGCTCTCTGTTTAGCACTGTGT
* * *
9289 GTGCTCTCTGATTAGTACTTTGT
1 GTGCTCTCTGTTTAGCACTGTGT
*
9312 GTACTCTCTGTTTAGCACTGTGT
1 GTGCTCTCTGTTTAGCACTGTGT
*
9335 GTGCTCTTTGTT
1 GTGCTCTCTGTT
9347 GCCCAGCACT
Statistics
Matches: 106, Mismatches: 18, Indels: 10
0.79 0.13 0.07
Matches are distributed among these distances:
22 1 0.01
23 85 0.80
24 1 0.01
25 16 0.15
26 3 0.03
ACGTcount: A:0.13, C:0.20, G:0.21, T:0.46
Consensus pattern (23 bp):
GTGCTCTCTGTTTAGCACTGTGT
Found at i:18215 original size:16 final size:17
Alignment explanation
Indices: 18196--18227 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
18186 TTTTGCTTCT
18196 TAATTC-ATTATATTTC
1 TAATTCAATTATATTTC
18212 TAATTCAATTATATTT
1 TAATTCAATTATATTT
18228 AAAGTAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.56
Consensus pattern (17 bp):
TAATTCAATTATATTTC
Found at i:58173 original size:18 final size:18
Alignment explanation
Indices: 58126--58173 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
58116 TCAGGCTTAA
*
58126 AGACTTCACCA-AGCTCAG
1 AGACTTCACTAGA-CTCAG
58144 AGACTTCACTAGACTCAG
1 AGACTTCACTAGACTCAG
*
58162 AGACTTCGCTAG
1 AGACTTCACTAG
58174 GCTTATAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 26 0.96
19 1 0.04
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (18 bp):
AGACTTCACTAGACTCAG
Found at i:58208 original size:18 final size:19
Alignment explanation
Indices: 58172--58274 Score: 92
Period size: 18 Copynumber: 5.7 Consensus size: 19
58162 AGACTTCGCT
* *
58172 AGGCTTATA-ATCTTTACC
1 AGGCTTATAGAGCTTCACC
58190 AGGCTTATAGAGC-TCACC
1 AGGCTTATAGAGCTTCACC
*
58208 AAGCTTATAGA-CTTCGA-C
1 AGGCTTATAGAGCTTC-ACC
**
58226 AGGCTTATAGA-CTTTTCC
1 AGGCTTATAGAGCTTCACC
* *
58244 AAGCTTATAGAG-TTCACT
1 AGGCTTATAGAGCTTCACC
58262 AGGCTTATAGAGC
1 AGGCTTATAGAGC
58275 GCGTTAACTT
Statistics
Matches: 68, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
17 1 0.01
18 64 0.94
19 3 0.04
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.31
Consensus pattern (19 bp):
AGGCTTATAGAGCTTCACC
Found at i:58229 original size:36 final size:36
Alignment explanation
Indices: 58117--58274 Score: 119
Period size: 36 Copynumber: 4.4 Consensus size: 36
58107 GTGAGTTCGT
* * *
58117 CAGGCTTAAAGA-CTTCACCAAGCTCAGAGACTTCA
1 CAGGCTTATAGAGCTTCACCAAGCTTATAGACTTCA
* * * * * * *
58152 CTAGACTCAGAGA-CTTCGCTAGGCTTATA-ATCTTTA
1 C-AGGCTTATAGAGCTTCACCAAGCTTATAGA-CTTCA
58188 CCAGGCTTATAGAGC-TCACCAAGCTTATAGACTTCGA
1 -CAGGCTTATAGAGCTTCACCAAGCTTATAGACTTC-A
** *
58225 CAGGCTTATAGA-CTTTTCCAAGCTTATAGAGTTCA
1 CAGGCTTATAGAGCTTCACCAAGCTTATAGACTTCA
58260 CTAGGCTTATAGAGC
1 C-AGGCTTATAGAGC
58275 GCGTTAACTT
Statistics
Matches: 95, Mismatches: 19, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
35 5 0.05
36 85 0.89
37 5 0.05
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (36 bp):
CAGGCTTATAGAGCTTCACCAAGCTTATAGACTTCA
Found at i:58230 original size:54 final size:54
Alignment explanation
Indices: 58162--58272 Score: 145
Period size: 54 Copynumber: 2.1 Consensus size: 54
58152 CTAGACTCAG
*
58162 AGACTTCGCTAGGCTTATA-ATCTTTACCAGGCTTATAGAGCTCACCAAGCTTAT
1 AGACTTCGCTAGGCTTATAGA-CTTTACCAAGCTTATAGAGCTCACCAAGCTTAT
* * * *
58216 AGACTTCGAC-AGGCTTATAGACTTTTCCAAGCTTATAGAGTTCACTAGGCTTAT
1 AGACTTCG-CTAGGCTTATAGACTTTACCAAGCTTATAGAGCTCACCAAGCTTAT
58270 AGA
1 AGA
58273 GCGCGTTAAC
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
54 48 0.96
55 2 0.04
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.32
Consensus pattern (54 bp):
AGACTTCGCTAGGCTTATAGACTTTACCAAGCTTATAGAGCTCACCAAGCTTAT
Found at i:60108 original size:14 final size:14
Alignment explanation
Indices: 60089--60118 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
60079 TAGGGCTCGA
60089 TTTAGGGTTTAGGT
1 TTTAGGGTTTAGGT
*
60103 TTTAGGTTTTAGGT
1 TTTAGGGTTTAGGT
60117 TT
1 TT
60119 GGGGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.13, C:0.00, G:0.30, T:0.57
Consensus pattern (14 bp):
TTTAGGGTTTAGGT
Done.