Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013676.1 Kokia drynarioides strain JFW-HI SEQ_128704, 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: 11398
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.26
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:2187 original size:86 final size:86
Alignment explanation
Indices: 2081--2270 Score: 308
Period size: 86 Copynumber: 2.2 Consensus size: 86
2071 GGTTTATTCT
2081 TGATGAAATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAA
1 TGATGAAATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAA
* * *
2146 CAGACGACGCAGTTAGCTTCC
66 CAAACGACACAGTCAGCTTCC
* *
2167 TGATGAAATACTAAGAAGTGGACCAAATTTGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAA
1 TGATGAAATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAA
*
2232 CAAACGACACAGTCATCTTCC
66 CAAACGACACAGTCAGCTTCC
* *
2253 CGATGAGATACTGAGAAG
1 TGATGAAATACTGAGAAG
2271 AAAACCAAAT
Statistics
Matches: 95, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
86 95 1.00
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (86 bp):
TGATGAAATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAA
CAAACGACACAGTCAGCTTCC
Found at i:3005 original size:6 final size:6
Alignment explanation
Indices: 2994--3057 Score: 57
Period size: 6 Copynumber: 11.0 Consensus size: 6
2984 TTTAATTTAT
2994 TTTAAA TTTAAA -TT-AA TCTTAAA -TT-AA TCTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA T-TTAAA TTTAAA TTTAAA
*
3040 TTT-AA TTTCAAA GTTAAA
1 TTTAAA TTT-AAA TTTAAA
3058 AAGTCCAAAG
Statistics
Matches: 49, Mismatches: 1, Indels: 16
0.74 0.02 0.24
Matches are distributed among these distances:
4 4 0.08
5 9 0.18
6 27 0.55
7 9 0.18
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (6 bp):
TTTAAA
Found at i:3009 original size:11 final size:11
Alignment explanation
Indices: 2995--3057 Score: 58
Period size: 11 Copynumber: 5.5 Consensus size: 11
2985 TTAATTTATT
2995 TTAAATTTAAA
1 TTAAATTTAAA
3006 TT-AATCTTAAA
1 TTAAAT-TTAAA
3017 TT-AATCTTAAA
1 TTAAAT-TTAAA
3028 TTTAAATTTAAA
1 -TTAAATTTAAA
*
3040 TTTAATTTCAAA
1 TTAAATTT-AAA
3052 GTTAAA
1 -TTAAA
3058 AAGTCCAAAG
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
10 3 0.07
11 25 0.56
12 10 0.22
13 7 0.16
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.46
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:3015 original size:17 final size:17
Alignment explanation
Indices: 2994--3057 Score: 60
Period size: 17 Copynumber: 3.7 Consensus size: 17
2984 TTTAATTTAT
2994 TTTAAATTTAAATT-AA
1 TTTAAATTTAAATTAAA
*
3010 TCTTAAA-TTAATCTTAAA
1 T-TTAAATTTAA-ATTAAA
*
3028 TTTAAATTTAAATTTAA
1 TTTAAATTTAAATTAAA
*
3045 TTTCAAAGTTAAA
1 TTT-AAATTTAAA
3058 AAGTCCAAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
16 5 0.13
17 19 0.49
18 15 0.38
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (17 bp):
TTTAAATTTAAATTAAA
Found at i:4803 original size:29 final size:30
Alignment explanation
Indices: 4770--5168 Score: 296
Period size: 29 Copynumber: 13.5 Consensus size: 30
4760 CTAAACTGTT
4770 CAAAAATTACCATTTT-ACCCCCAAACTTC
1 CAAAAATTACCATTTTGACCCCCAAACTTC
* * *
4799 CAAAAA-TCCCATTTTTGACCCCGAAACTTT
1 CAAAAATTACCA-TTTTGACCCCCAAACTTC
* * *
4829 CAAAAATTACTATTTT-ACCCTCGAACTTC
1 CAAAAATTACCATTTTGACCCCCAAACTTC
4858 CAAAAA-T-CTCATTTTTGA-CCCCAAACCTTC
1 CAAAAATTAC-CA-TTTTGACCCCCAAA-CTTC
***
4888 CAAAAATTACCATTTT-ACCCTTGAACTTC
1 CAAAAATTACCATTTTGACCCCCAAACTTC
* *
4917 CAAAAA-T-CTCATTTTTGA-CCCCGAACTTT
1 CAAAAATTAC-CA-TTTTGACCCCCAAACTTC
* *
4946 CAAAAATT-CCAATTTTGA-CCTCGAACTTC
1 CAAAAATTACC-ATTTTGACCCCCAAACTTC
* *
4975 CAAAAATTACCATTTT-ATCCCCGAACTTC
1 CAAAAATTACCATTTTGACCCCCAAACTTC
* * * * *
5004 CAAAAA-TCCCATTTTTAACCTCGAACCTTC
1 CAAAAATTACCA-TTTTGACCCCCAAACTTC
*
5034 CAAAAATTACCATTTT-ACCCTCAAACTTC
1 CAAAAATTACCATTTTGACCCCCAAACTTC
* **
5063 CAAAAA-TCCCATTTTTGACCCTAAAACTTC
1 CAAAAATTACCA-TTTTGACCCCCAAACTTC
**
5093 CAAAAATTACCATTTT-ACCCCTGAACTTC
1 CAAAAATTACCATTTTGACCCCCAAACTTC
* * *
5122 CAAAAA-T-CTCATTTTTGACCTCGATACTTC
1 CAAAAATTAC-CA-TTTTGACCCCCAAACTTC
5152 CAAAAAATTACCATTTT
1 C-AAAAATTACCATTTT
5169 ACTCATGGAT
Statistics
Matches: 299, Mismatches: 42, Indels: 56
0.75 0.11 0.14
Matches are distributed among these distances:
27 3 0.01
28 21 0.07
29 151 0.51
30 96 0.32
31 23 0.08
32 4 0.01
33 1 0.00
ACGTcount: A:0.35, C:0.30, G:0.04, T:0.32
Consensus pattern (30 bp):
CAAAAATTACCATTTTGACCCCCAAACTTC
Found at i:4835 original size:59 final size:59
Alignment explanation
Indices: 4770--5170 Score: 347
Period size: 59 Copynumber: 6.8 Consensus size: 59
4760 CTAAACTGTT
* * *
4770 CAAAAATTACCATTTT-ACCCCCAAACTTCCAAAAA-TCCCATTTTTGACCCCGAAACTTT
1 CAAAAATTACCATTTTGACCCTCAAACTTCCAAAAATTACCA-TTTT-ACCCCGAAACTTC
* *
4829 CAAAAATTACTATTTT-ACCCTCGAACTTCCAAAAA-T-CTCATTTTTGACCCC-AAACCTTC
1 CAAAAATTACCATTTTGACCCTCAAACTTCCAAAAATTAC-CA-TTTT-ACCCCGAAA-CTTC
** *
4888 CAAAAATTACCATTTT-ACCCTTGAACTTCCAAAAA-T-CTCATTTTTGACCCCG-AACTTT
1 CAAAAATTACCATTTTGACCCTCAAACTTCCAAAAATTAC-CA-TTTT-ACCCCGAAACTTC
*
4946 CAAAAATT-CCAATTTTGA-CCTCGAACTTCCAAAAATTACCATTTTATCCCCG-AACTTC
1 CAAAAATTACC-ATTTTGACCCTCAAACTTCCAAAAATTACCATTTTA-CCCCGAAACTTC
* * * *
5004 CAAAAA-TCCCATTTTTAACCTCGAACCTTCCAAAAATTACCATTTTACCCTC-AAACTTC
1 CAAAAATTACCATTTTGACCCTC-AAACTTCCAAAAATTACCATTTTACCC-CGAAACTTC
* *
5063 CAAAAA-TCCCATTTTTGACCCTAAAACTTCCAAAAATTACCATTTTACCCCTG-AACTTC
1 CAAAAATTACCA-TTTTGACCCTCAAACTTCCAAAAATTACCATTTTACCCC-GAAACTTC
*
5122 CAAAAA-T-CTCATTTTTGA-CCTCGATACTTCCAAAAAATTACCATTTTAC
1 CAAAAATTAC-CA-TTTTGACCCTC-AAACTTCC-AAAAATTACCATTTTAC
5171 TCATGGATAT
Statistics
Matches: 305, Mismatches: 18, Indels: 37
0.85 0.05 0.10
Matches are distributed among these distances:
57 10 0.03
58 70 0.23
59 199 0.65
60 26 0.09
ACGTcount: A:0.35, C:0.30, G:0.04, T:0.32
Consensus pattern (59 bp):
CAAAAATTACCATTTTGACCCTCAAACTTCCAAAAATTACCATTTTACCCCGAAACTTC
Found at i:5122 original size:205 final size:206
Alignment explanation
Indices: 4770--5157 Score: 643
Period size: 205 Copynumber: 1.9 Consensus size: 206
4760 CTAAACTGTT
* *
4770 CAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTTCAAAAA
1 CAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCGAAACTTCCAAAAA
* * * *
4835 TTACTATTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCCCAAACCTTCCAAAAATTACCA
66 TTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTACCA
* *
4900 TTTTACCCTTGAACTTCCAAAAATCTCATTTTTGACCCCGA-ACTTTCAAAAATTCCAATTTTGA
131 TTTTACCCCTGAACTTCCAAAAATCTCATTTTTGACCCCGATACTTCCAAAAATTCCAATTTTGA
4964 CCTCGAACTTC
196 CCTCGAACTTC
* * * *
4975 CAAAAATTACCATTTTATCCCCGAACTTCCAAAAATCCCATTTTTAACCTCGAACCTTCCAAAAA
1 CAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCGAAACTTCCAAAAA
*
5040 TTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCTAAAACTTCCAAAAATTACCA
66 TTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTACCA
*
5105 TTTTACCCCTGAACTTCCAAAAATCTCATTTTTGACCTCGATACTTCCAAAAA
131 TTTTACCCCTGAACTTCCAAAAATCTCATTTTTGACCCCGATACTTCCAAAAA
5158 ATTACCATTT
Statistics
Matches: 168, Mismatches: 14, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
205 158 0.94
206 10 0.06
ACGTcount: A:0.35, C:0.30, G:0.04, T:0.31
Consensus pattern (206 bp):
CAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCGAAACTTCCAAAAA
TTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTACCA
TTTTACCCCTGAACTTCCAAAAATCTCATTTTTGACCCCGATACTTCCAAAAATTCCAATTTTGA
CCTCGAACTTC
Done.