Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011112.1 Kokia drynarioides strain JFW-HI SEQ_126085, 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: 26935
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 3 characters in sequence are not A, C, G, or T
Found at i:2425 original size:202 final size:202
Alignment explanation
Indices: 2074--2641 Score: 854
Period size: 202 Copynumber: 2.8 Consensus size: 202
2064 CCAACAAAAC
* * *
2074 GACGCGGTCATCTTCTTGATGAGG-TACTGAGAAGAAGACCAAACCAAACCGAGGCTCAAAGTGA
1 GACGCGGTCATCTTCTAGATG-GGACACCGAGAAGAAGA-C---CCAAACCGAGGCTCAAAGTGA
* *
2138 GCAAAGTCTTTGAACCCCAGCTTCCTTATGAGATACTAAGAAGCAGGTCGAAGCAATAAAAGGTT
61 GCAAAGTCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAGGTT
* *
2203 AGCTTCCTGATGAAATACTGAAAAGTGAACCAAACTCGTCTTCCTGATGAGATACAGAGAAGCGA
126 AGCTTCCTGATGAGATACTGAAAAGTGAACCAAACTCGTCTTCCTAATGAGATACAGAGAAGCGA
2268 GTTGAAACAAAT
191 GTTGAAACAAAT
2280 GACGCGGTCATCTTCTAGATGGGACACCGAGAAGAAGACCCAAACCGAGGCTCAAAGTGAGCAAA
1 GACGCGGTCATCTTCTAGATGGGACACCGAGAAGAAGACCCAAACCGAGGCTCAAAGTGAGCAAA
*
2345 GTCTTTGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTT
66 GTCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTT
* * *
2410 CCTGATGAGATACTGAGAAGTGAACCAAACTCGTTTTCTTAATGAGATACAGAGAAGCGAGTTGA
131 CCTGATGAGATACTGAAAAGTGAACCAAACTCGTCTTCCTAATGAGATACAGAGAAGCGAGTTGA
2475 AACAAAT
196 AACAAAT
* * *
2482 GACGCGGTCATCTTCTGGATGGGACACCGAGAAGAAGACCCAAACTGAGGCTCAAAGTAAGCAAA
1 GACGCGGTCATCTTCTAGATGGGACACCGAGAAGAAGACCCAAACCGAGGCTCAAAGTGAGCAAA
* * * *
2547 GTCTTTGAACCTCAGCTTCCTGAT-ATGACATTGAGAAGCAGGTCGAAGCAATAAAAAGATTAGC
66 GTCTTTGAACCCCAGCTTCCTGATGA-GATACTGAGAAGCAGGTCGAAGCAAT-AAAAGGTTAGC
* * *
2611 TTCCTGACGAGTTACT-AAGAAGTGAAGCAAA
129 TTCCTGATGAGATACTGAA-AAGTGAACCAAA
2642 TCCTGATGAA
Statistics
Matches: 335, Mismatches: 23, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
201 1 0.00
202 264 0.79
203 35 0.10
205 3 0.01
206 32 0.10
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.20
Consensus pattern (202 bp):
GACGCGGTCATCTTCTAGATGGGACACCGAGAAGAAGACCCAAACCGAGGCTCAAAGTGAGCAAA
GTCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTT
CCTGATGAGATACTGAAAAGTGAACCAAACTCGTCTTCCTAATGAGATACAGAGAAGCGAGTTGA
AACAAAT
Found at i:3078 original size:17 final size:17
Alignment explanation
Indices: 3056--3115 Score: 86
Period size: 17 Copynumber: 3.5 Consensus size: 17
3046 CATACTCCCT
3056 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
*
3073 TTAAATTT-GTTTAAAA
1 TTAAATTTATTTTAAAA
*
3089 TTTAAATTTATTTTAAAT
1 -TTAAATTTATTTTAAAA
3107 TTAAATTTA
1 TTAAATTTA
3116 AATTAAGTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
16 7 0.18
17 25 0.66
18 6 0.16
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:3121 original size:5 final size:6
Alignment explanation
Indices: 3055--3128 Score: 59
Period size: 6 Copynumber: 13.0 Consensus size: 6
3045 TCATACTCCC
* * * *
3055 TTTAAA TTT-AT TTTAAA ATTAAA TTT--G TTTAAAA TTTAAA TTT-AT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA
*
3100 TTTAAA TTTAAA TTTAAA -TTAAG TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
3129 ATTATTTCCA
Statistics
Matches: 52, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
4 3 0.06
5 12 0.23
6 34 0.65
7 3 0.06
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:3121 original size:17 final size:17
Alignment explanation
Indices: 3055--3152 Score: 83
Period size: 17 Copynumber: 5.6 Consensus size: 17
3045 TCATACTCCC
*
3055 TTTAAATTTATTTTAAA
1 TTTAAATTTAATTTAAA
* *
3072 ATTAAATTT-GTTTAAAA
1 TTTAAATTTAATTT-AAA
*
3089 TTTAAATTTATTTTAAA
1 TTTAAATTTAATTTAAA
* *
3106 TTTAAATTTAAATTAAG
1 TTTAAATTTAATTTAAA
*
3123 TTTAAAATT-ATTTCCAAA
1 TTTAAATTTAATTT--AAA
3141 TTTAAAATTTAA
1 TTT-AAATTTAA
3153 AATAAATAAA
Statistics
Matches: 64, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
16 6 0.09
17 44 0.69
18 8 0.12
19 5 0.08
20 1 0.02
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (17 bp):
TTTAAATTTAATTTAAA
Found at i:3127 original size:34 final size:35
Alignment explanation
Indices: 3055--3158 Score: 113
Period size: 34 Copynumber: 3.0 Consensus size: 35
3045 TCATACTCCC
* **
3055 TTTAAATTTATTTTAAAATTAAATTT-GTTTAAAA
1 TTTAAATTTATTTTAAATTTAAATTTAAATTAAAA
*
3089 TTTAAATTTATTTTAAATTTAAATTTAAATT-AAG
1 TTTAAATTTATTTTAAATTTAAATTTAAATTAAAA
* * *
3123 TTTAAAATTATTTCCAAATTTAAAATTTAAAATAAA
1 TTTAAATTTATTT-TAAATTT-AAATTTAAATTAAA
3159 TAAAACCCAA
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
34 39 0.66
35 8 0.14
36 10 0.17
37 2 0.03
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (35 bp):
TTTAAATTTATTTTAAATTTAAATTTAAATTAAAA
Found at i:3896 original size:15 final size:16
Alignment explanation
Indices: 3872--3904 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3862 AAATGAAATT
*
3872 TATTATTATTAA-AAA
1 TATTAATATTAATAAA
3887 TATTAATATTAATAAA
1 TATTAATATTAATAAA
3903 TA
1 TA
3905 AAAAAACGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TATTAATATTAATAAA
Found at i:5169 original size:59 final size:58
Alignment explanation
Indices: 5009--5353 Score: 433
Period size: 59 Copynumber: 5.9 Consensus size: 58
4999 TAAACTGTCA
* * * *
5009 AAAAATCCCATTTTTTACCCCGAACCTTTTGAAAATTACCATTTTACACTCGAACTTCC
1 AAAAATCCCATTTTTGACCCCGAACCTTCT-AAAATTACCATTTTACCCCCGAACTTCC
* * *
5068 -AAAATCCCATTTTTGACCCTGAATCTTCTAAAAATAACCATTTTACCCCCGAACTTCC
1 AAAAATCCCATTTTTGACCCCGAACCTTCT-AAAATTACCATTTTACCCCCGAACTTCC
* *
5126 AAAAATCCCATTTTTGACCCCGAACCTTCTAACAATTATCATTTTACCCCCAAACTTCC
1 AAAAATCCCATTTTTGACCCCGAACCTTCTAA-AATTACCATTTTACCCCCGAACTTCC
* * * *
5185 AAAAATCCCATTTTTGACCTCAAACCTTTTGAAAATTACCATTTTACCCTCGAACTTCC
1 AAAAATCCCATTTTTGACCCCGAACCTTCT-AAAATTACCATTTTACCCCCGAACTTCC
* * * *
5244 AAAAATCTCATTTTTGACCCC-ATACCTTCCGAAAATTACCATTTTACCCTCGAACTTCT
1 AAAAATCCCATTTTTGACCCCGA-ACCTT-CTAAAATTACCATTTTACCCCCGAACTTCC
* * * *
5303 AAAAATCCCATTTTTGACTCCGAACCTTCCAAAACTACCATTTTGCCCCCG
1 AAAAATCCCATTTTTGACCCCGAACCTTCTAAAATTACCATTTTACCCCCG
5354 TGCATCCGAA
Statistics
Matches: 250, Mismatches: 30, Indels: 13
0.85 0.10 0.04
Matches are distributed among these distances:
58 72 0.29
59 175 0.70
60 3 0.01
ACGTcount: A:0.32, C:0.31, G:0.05, T:0.32
Consensus pattern (58 bp):
AAAAATCCCATTTTTGACCCCGAACCTTCTAAAATTACCATTTTACCCCCGAACTTCC
Found at i:5347 original size:29 final size:28
Alignment explanation
Indices: 5040--5353 Score: 185
Period size: 29 Copynumber: 10.8 Consensus size: 28
5030 GAACCTTTTG
* *
5040 AAAATTACCATTTT-ACACTCGAACTTCC
1 AAAAATACCATTTTGAC-CCCGAACTTCC
* * *
5068 -AAAATCCCATTTTTGACCCTGAATCTTCT
1 AAAAATACCA-TTTTGACCCCGAA-CTTCC
5097 AAAAATAACCATTTT-ACCCCCGAACTTCC
1 AAAAAT-ACCATTTTGA-CCCCGAACTTCC
* *
5126 AAAAATCCCATTTTTGACCCCGAACCTTCT
1 AAAAATACCA-TTTTGACCCCGAA-CTTCC
* * *
5156 AACAATTATCATTTT-ACCCCCAAACTTCC
1 AA-AAATACCATTTTGA-CCCCGAACTTCC
* * * **
5185 AAAAATCCCATTTTTGACCTCAAACCTTTTG
1 AAAAATACCA-TTTTGACCCCGAA-C-TTCC
*
5216 AAAATTACCATTTT-ACCCTCGAACTTCC
1 AAAAATACCATTTTGACCC-CGAACTTCC
5244 AAAAAT-CTCATTTTTGACCCC-ATACCTTCC
1 AAAAATAC-CA-TTTTGACCCCGA-A-CTTCC
* *
5274 GAAAATTACCATTTT-ACCCTCGAACTTCT
1 -AAAAATACCATTTTGACCC-CGAACTTCC
* *
5303 AAAAATCCCATTTTTGACTCCGAACCTTCC
1 AAAAATACCA-TTTTGACCCCGAA-CTTCC
* *
5333 AAAACTACCATTTTGCCCCCG
1 AAAAATACCATTTTGACCCCG
5354 TGCATCCGAA
Statistics
Matches: 220, Mismatches: 38, Indels: 55
0.70 0.12 0.18
Matches are distributed among these distances:
27 8 0.04
28 34 0.15
29 80 0.36
30 71 0.32
31 26 0.12
32 1 0.00
ACGTcount: A:0.32, C:0.32, G:0.05, T:0.32
Consensus pattern (28 bp):
AAAAATACCATTTTGACCCCGAACTTCC
Found at i:5698 original size:97 final size:96
Alignment explanation
Indices: 5559--5740 Score: 235
Period size: 97 Copynumber: 1.9 Consensus size: 96
5549 AAAAAAAATT
* **
5559 GAGGCAATATTCCTTTATTTCGAGTTTCGAAAATTTGTGCCTTAACTCACTAGGTGCAATTTTTT
1 GAGGCAATATTCCTTTATTTCGAGTTTCGAAAATTTGCGCCTTAACTCACTAGGTGCAA-CCTTT
5624 CTTCAAATCGAAATAATCGAACACCCTTAATC
65 CTTCAAATCGAAATAATCGAACACCCTTAATC
* * *
5656 GAGGCAATGTTTCC-TTATCTTCGA-TTTTG-AAATATTGCGCCTTAACTTACTAGGTGCAACCT
1 GAGGCAAT-ATTCCTTTAT-TTCGAGTTTCGAAAAT-TTGCGCCTTAACTCACTAGGTGCAACCT
* *
5718 TTCTTCGAATCGAGATAATCGAA
63 TTCTTCAAATCGAAATAATCGAA
5741 TATATTTTTC
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
96 26 0.35
97 39 0.53
98 9 0.12
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (96 bp):
GAGGCAATATTCCTTTATTTCGAGTTTCGAAAATTTGCGCCTTAACTCACTAGGTGCAACCTTTC
TTCAAATCGAAATAATCGAACACCCTTAATC
Found at i:10796 original size:11 final size:11
Alignment explanation
Indices: 10770--10798 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
10760 GATTTTACAT
10770 TTTTTG-TTTA
1 TTTTTGTTTTA
10780 TTTTTGTTTTA
1 TTTTTGTTTTA
10791 TTTTTGTT
1 TTTTTGTT
10799 GGGTCCAGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.33
11 12 0.67
ACGTcount: A:0.07, C:0.00, G:0.10, T:0.83
Consensus pattern (11 bp):
TTTTTGTTTTA
Found at i:15792 original size:15 final size:16
Alignment explanation
Indices: 15772--15804 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
15762 TATTCAATAA
15772 ATTTA-TAAATTTTTT
1 ATTTATTAAATTTTTT
*
15787 ATTTATTGAATTTTTT
1 ATTTATTAAATTTTTT
15803 AT
1 AT
15805 ATAGTTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (16 bp):
ATTTATTAAATTTTTT
Found at i:24562 original size:15 final size:15
Alignment explanation
Indices: 24542--24575 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
24532 TTTCCTACTC
24542 AAATTTTCAACCTAT
1 AAATTTTCAACCTAT
24557 AAATTTTCAACCTAT
1 AAATTTTCAACCTAT
24572 AAAT
1 AAAT
24576 AGGCCTTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (15 bp):
AAATTTTCAACCTAT
Done.