Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009520.1 Kokia drynarioides strain JFW-HI SEQ_124231, 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: 4130
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:942 original size:30 final size:30
Alignment explanation
Indices: 908--968 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
898 GATTTTTTTC
* *
908 CGTTTACT-TTTTATATTTAATTTGTAATTT
1 CGTTT-CTATTTTAAATTTAATTTCTAATTT
*
938 CGTTTTTATTTTAAATTTAATTTCTAATTT
1 CGTTTCTATTTTAAATTTAATTTCTAATTT
968 C
1 C
969 CTGTATATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 1 0.04
30 26 0.96
ACGTcount: A:0.25, C:0.08, G:0.05, T:0.62
Consensus pattern (30 bp):
CGTTTCTATTTTAAATTTAATTTCTAATTT
Found at i:947 original size:23 final size:24
Alignment explanation
Indices: 916--961 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
906 TCCGTTTACT
*
916 TTTTATA-TTTAATTTGTAATTTCG
1 TTTTATATTTTAAATT-TAATTTCG
940 TTTT-TATTTTAAATTTAATTTC
1 TTTTATATTTTAAATTTAATTTC
962 TAATTTCCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.65
Consensus pattern (24 bp):
TTTTATATTTTAAATTTAATTTCG
Found at i:978 original size:30 final size:30
Alignment explanation
Indices: 916--1004 Score: 103
Period size: 30 Copynumber: 3.1 Consensus size: 30
906 TCCGTTTACT
* * * * *
916 TTTTATATTTAATTTGTAATTTCGTTTTTA
1 TTTTAAATTTAATTTCTAATTTCCTGTATA
946 TTTTAAATTTAATTTCTAATTTCCTGTATA
1 TTTTAAATTTAATTTCTAATTTCCTGTATA
*
976 TTTT-AATTT--TTTTTAATTTCCTGTATA
1 TTTTAAATTTAATTTCTAATTTCCTGTATA
1003 TT
1 TT
1005 CTAATTATTA
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
27 19 0.36
29 5 0.09
30 29 0.55
ACGTcount: A:0.25, C:0.07, G:0.04, T:0.64
Consensus pattern (30 bp):
TTTTAAATTTAATTTCTAATTTCCTGTATA
Found at i:2060 original size:42 final size:42
Alignment explanation
Indices: 2001--2081 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
1991 CAGCCATTGC
*
2001 ATGGCCAACACCAAAAAAATATGAAATTTTTTTATCTGAGAA
1 ATGGCCAACACCAAAAAAATATGAAATATTTTTATCTGAGAA
* * *
2043 ATGGCCGACACCAAAAAATTTTGAAATATTTTTATCTGA
1 ATGGCCAACACCAAAAAAATATGAAATATTTTTATCTGA
2082 AAAAAGGAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (42 bp):
ATGGCCAACACCAAAAAAATATGAAATATTTTTATCTGAGAA
Found at i:2096 original size:104 final size:103
Alignment explanation
Indices: 1834--2142 Score: 349
Period size: 104 Copynumber: 2.9 Consensus size: 103
1824 CGACAATTAC
* * ** * * *
1834 ATGGCCAACACAAAAAAATTT--AAT-TTTTTATCAAATAAAAAGGGGGTGCCAGCCGTTGCATG
1 ATGGCCGACACCAAAAAATTTGAAATATTTTTATCTGA-AAAAAGGAGGTGTCAGCCATTGCATG
* *
1896 ACCAACACCAAAAAAATTAATTTTTTTTTATATGAAAAAAGGGG
65 ACCAACACCAAAAAAATTAA-ATTTTTTTATCTG-AAAAA---G
* * * *
1940 ATGGCCGACACCAAAAAATTTGAAATTTTTTTATTTGAGAAAAGGAGGTGTCAGCCATTGCATGG
1 ATGGCCGACACCAAAAAATTTGAAATATTTTTATCTGAAAAAAGGAGGTGTCAGCCATTGCATGA
*
2005 CCAACACCAAAAAAATATGAAATTTTTTTATCTG-AGAA-
66 CCAACACCAAAAAAAT-T-AAATTTTTTTATCTGAAAAAG
*
2043 ATGGCCGACACCAAAAAATTTTGAAATATTTTTATCTGAAAAAAGGAGGTGTCAACCATTGCATG
1 ATGGCCGACACCAAAAAA-TTTGAAATATTTTTATCTGAAAAAAGGAGGTGTCAGCCATTGCATG
2108 ACCAACACCAAAAAAATTTAAAATTTTTTTATCTG
65 ACCAACACCAAAAAAA-TT-AAATTTTTTTATCTG
2143 TGAAGAGGGG
Statistics
Matches: 177, Mismatches: 19, Indels: 16
0.83 0.09 0.08
Matches are distributed among these distances:
103 18 0.10
104 73 0.41
105 1 0.01
106 19 0.11
107 3 0.02
108 41 0.23
109 20 0.11
110 2 0.01
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.29
Consensus pattern (103 bp):
ATGGCCGACACCAAAAAATTTGAAATATTTTTATCTGAAAAAAGGAGGTGTCAGCCATTGCATGA
CCAACACCAAAAAAATTAAATTTTTTTATCTGAAAAAG
Found at i:2120 original size:62 final size:61
Alignment explanation
Indices: 2043--2599 Score: 477
Period size: 62 Copynumber: 9.2 Consensus size: 61
2033 TATCTGAGAA
* * **
2043 ATGGCCGACACCAAAAAATTTTGAAATATTTTTATCTGAAAAAAGGAGGTGTCAACCATTGC
1 ATGGCCAACACCAAAAAA-TTTGAAATTTTTTTATCTGAAAAAAGGAGGTGTCGGCCATTGC
* * ** * * *
2105 ATGACCAACACCAAAAAAATTTAAAATTTTTTTATCTGTGAAGAGGGGGTGTCGGCCAGTGC
1 ATGGCCAACACC-AAAAAATTTGAAATTTTTTTATCTGAAAAAAGGAGGTGTCGGCCATTGC
* * *
2167 AT-GACAACACTC-AAAAATTTG-ATTTTTTTTATC-AAATAAATAGG-GGTGTCGGCCATTGC
1 ATGGCCAACAC-CAAAAAATTTGAAATTTTTTTATCTGAA-AAA-AGGAGGTGTCGGCCATTGC
* ** *
2226 ATGGCCAACACCAAAAAAATTTGAAAATTTTTTATCTGTGAATAGGAGGTGTCGGCCATTGC
1 ATGGCCAACACC-AAAAAATTTGAAATTTTTTTATCTGAAAAAAGGAGGTGTCGGCCATTGC
* * * *
2288 ATGGCTAACACCCAAAAATTT-AATTTTTTTTAATC-AAATAAATAGG-GGTGTCGGCCATTGC
1 ATGGCCAACACCAAAAAATTTGAAATTTTTTT-ATCTGAA-AAA-AGGAGGTGTCGGCCATTGC
* * *
2349 ATGACCAACACCAAAAAA-TT-AAA-TTTTTTATCTGATAAAAAAGAAGGTGTCGTCCATTGC
1 ATGGCCAACACCAAAAAATTTGAAATTTTTTTATCTG--AAAAAAGGAGGTGTCGGCCATTGC
* * * * * *
2409 ATGGCTAACACCCAAAAATTTG-ATTTTTTTTATCAGATAAATAGG-GGTGTCGGCCATTGT
1 ATGGCCAACACCAAAAAATTTGAAATTTTTTTATCTGA-AAAAAGGAGGTGTCGGCCATTGC
* * * *
2469 ATGGCCAACA-CAAAAAAATTG-TA-TTTTTTATCTGACAAAAAAGAGGTGTCGGCCATTAC
1 ATGGCCAACACCAAAAAATTTGAAATTTTTTTATCTGA-AAAAAGGAGGTGTCGGCCATTGC
* ** *
2528 ATGGCCAACACCCAAAAATTTGATTTTTTTTTATCAGATTAAAAAGG-GGTG-CTGGCCA-TGC
1 ATGGCCAACACCAAAAAATTTGAAATTTTTTTATCTGA--AAAAAGGAGGTGTC-GGCCATTGC
2589 AATGGCCAACA
1 -ATGGCCAACA
2600 ACTCGAATTT
Statistics
Matches: 398, Mismatches: 69, Indels: 56
0.76 0.13 0.11
Matches are distributed among these distances:
58 19 0.05
59 70 0.18
60 94 0.24
61 75 0.19
62 128 0.32
63 12 0.03
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (61 bp):
ATGGCCAACACCAAAAAATTTGAAATTTTTTTATCTGAAAAAAGGAGGTGTCGGCCATTGC
Found at i:2196 original size:61 final size:58
Alignment explanation
Indices: 2071--2558 Score: 356
Period size: 60 Copynumber: 8.1 Consensus size: 58
2061 TTTTGAAATA
* * * ** * *
2071 TTTTTATCTGAAAAAAGGAGGTGTCAACCATTGCATGACCAACACCAAAAAAATTTAAAATT
1 TTTTTATCTGTAAATAGGGGGTGTCGGCCATTGCATGA-CAACACC--AAAAATTT-GATTT
* * *
2133 TTTTTATCTGTGAAGAGGGGGTGTCGGCCAGTGCATGACAACACTCAAAAATTTGATTT
1 TTTTTATCTGTAAATAGGGGGTGTCGGCCATTGCATGACAACAC-CAAAAATTTGATTT
** * **
2192 TTTTTATCAAATAAATA-GGGGTGTCGGCCATTGCATGGCCAACACCAAAAAAATTTGAAAAT
1 TTTTTATC-TGTAAATAGGGGGTGTCGGCCATTGCAT-GACAACACC--AAAAATTTG-ATTT
* * * *
2254 TTTTTATCTGTGAATAGGAGGTGTCGGCCATTGCATGGCTAACACCCAAAAATTTAATTT
1 TTTTTATCTGTAAATAGGGGGTGTCGGCCATTGCATGAC-AACA-CCAAAAATTTGATTT
** * **
2314 TTTTTAATCAAATAAATA-GGGGTGTCGGCCATTGCATGACCAACACCAAAAAATT-AAAT
1 TTTTT-ATC-TGTAAATAGGGGGTGTCGGCCATTGCATGA-CAACACCAAAAATTTGATTT
* ** * *
2373 TTTTTATCTGATAAAAAAGAAGGTGTCGTCCATTGCATGGCTAACACCCAAAAATTTGATTT
1 TTTTTATCTG-T-AAATAGGGGGTGTCGGCCATTGCATGAC-AACA-CCAAAAATTTGATTT
* * * * * *
2435 TTTTTATCAGATAAATA-GGGGTGTCGGCCATTGTATGGCCAACACAAAAAAATTG-TAT
1 TTTTTATCTG-TAAATAGGGGGTGTCGGCCATTGCAT-GACAACACCAAAAATTTGATTT
* * * * * *
2493 TTTTTATCTGACAAAAAAGAGGTGTCGGCCATTACATGGCCAACACCCAAAAATTTGATTT
1 TTTTTATCTG-TAAATAGGGGGTGTCGGCCATTGCAT-GACAACA-CCAAAAATTTGATTT
2554 TTTTT
1 TTTTT
2559 TATCAGATTA
Statistics
Matches: 342, Mismatches: 62, Indels: 45
0.76 0.14 0.10
Matches are distributed among these distances:
58 20 0.06
59 75 0.22
60 84 0.25
61 78 0.23
62 83 0.24
63 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (58 bp):
TTTTTATCTGTAAATAGGGGGTGTCGGCCATTGCATGACAACACCAAAAATTTGATTT
Found at i:2277 original size:121 final size:120
Alignment explanation
Indices: 2098--2599 Score: 640
Period size: 121 Copynumber: 4.1 Consensus size: 120
2088 GAGGTGTCAA
* * * *
2098 CCATTGCATGACCAACACCAAAAAAATTTAAAATTTTTTTATCTG-TGAAGAGGGGGTGTCGGCC
1 CCATTGCATGGCCAACACCAAAAAAA-TT-AAA-TTTTTTATCTGATAAAAAGGAGGTGTCGGCC
* * *
2162 AGTGCATGAC-AACACTCAAAAATTTGATTTTTTTTATCAAATAAATAGGGGTGTCGG
63 ATTGCATGGCTAACACCCAAAAATTTGATTTTTTTTATCAAATAAATAGGGGTGTCGG
* *
2219 CCATTGCATGGCCAACACCAAAAAAATTTGAAAATTTTTTATCTG-TGAATAGGAGGTGTCGGCC
1 CCATTGCATGGCCAACACCAAAAAAA-TT--AAATTTTTTATCTGATAAAAAGGAGGTGTCGGCC
*
2283 ATTGCATGGCTAACACCCAAAAATTTAATTTTTTTTAATCAAATAAATAGGGGTGTCGG
63 ATTGCATGGCTAACACCCAAAAATTTGATTTTTTTT-ATCAAATAAATAGGGGTGTCGG
* * *
2342 CCATTGCATGACCAACACC-AAAAAATTAAATTTTTTATCTGATAAAAAAGAAGGTGTCGTCCAT
1 CCATTGCATGGCCAACACCAAAAAAATTAAATTTTTTATCTGAT-AAAAAGGAGGTGTCGGCCAT
*
2406 TGCATGGCTAACACCCAAAAATTTGATTTTTTTTATCAGATAAATAGGGGTGTCGG
65 TGCATGGCTAACACCCAAAAATTTGATTTTTTTTATCAAATAAATAGGGGTGTCGG
* ** * *
2462 CCATTGTATGGCCAACA-CAAAAAAATTGTATTTTTTATCTGACAAAAAAGAGGTGTCGGCCATT
1 CCATTGCATGGCCAACACCAAAAAAATTAAATTTTTTATCTGATAAAAAGGAGGTGTCGGCCATT
* * * *
2526 ACATGGCCAACACCCAAAAATTTGATTTTTTTTTATCAGATTAAAAAGGGGTG-CTGG
66 GCATGGCTAACACCCAAAAATTTGA-TTTTTTTTATCA-AATAAATAGGGGTGTC-GG
2583 CCA-TGCAATGGCCAACA
1 CCATTGC-ATGGCCAACA
2600 ACTCGAATTT
Statistics
Matches: 343, Mismatches: 28, Indels: 20
0.88 0.07 0.05
Matches are distributed among these distances:
119 56 0.16
120 73 0.21
121 141 0.41
122 33 0.10
123 40 0.12
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (120 bp):
CCATTGCATGGCCAACACCAAAAAAATTAAATTTTTTATCTGATAAAAAGGAGGTGTCGGCCATT
GCATGGCTAACACCCAAAAATTTGATTTTTTTTATCAAATAAATAGGGGTGTCGG
Found at i:3289 original size:62 final size:61
Alignment explanation
Indices: 2967--3412 Score: 389
Period size: 61 Copynumber: 7.4 Consensus size: 61
2957 AAAAAATTTG
* * * * * *
2967 GGTGTTGGTCATGCAATGGTCGACACCCATTTTTGTCAGAT--AAAAAGTAC-AATTTTTT
1 GGTGTTGGCCATGCAATGGCCGACACCCCTTTTTATCAGATAAAAAAAATTCAAATTTTTT
* * * * * *
3025 -GTGTTGGTCAT-AAATGGCCAATACCCCTATTTATCTGATAAAAAAAA-TCAAATTTTTT
1 GGTGTTGGCCATGCAATGGCCGACACCCCTTTTTATCAGATAAAAAAAATTCAAATTTTTT
* ** *
3083 TGTGTTGGCCATGCAATGGCAAACACCCCCTTGTTTATCAGAT--AAAAAATT-TAATTTTTT
1 GGTGTTGGCCATGCAATGGCCGACA-CCCCTT-TTTATCAGATAAAAAAAATTCAAATTTTTT
* * * ** * * *
3143 GGTGTTGGCCGTGCAATGACCGACACCCCTATTTATTTGATAAAAAAAAATCAAAATTTTG
1 GGTGTTGGCCATGCAATGGCCGACACCCCTTTTTATCAGATAAAAAAAATTCAAATTTTTT
* * * * *
3204 GGTTTTGACCATGCAATGACCGACACCCCTTCTTCA-CAGATAAAAAAATTTCAAATTTTTCT
1 GGTGTTGGCCATGCAATGGCCGACACCCCTT-TTTATCAGATAAAAAAAATTCAAATTTTT-T
**
3266 GGTGTTGGCCATGCAATGGCCGACACTCCCTTTTT-TCAGATAAAAAAAATTCATTTTTTTT
1 GGTGTTGGCCATGCAATGGCCGACAC-CCCTTTTTATCAGATAAAAAAAATTCAAATTTTTT
* ** * *
3327 TGTGTTGGCCATGCAATGGCCGACACCCCTTTTTTATTTGGT--AAAAAATT-AATTTTTTT
1 GGTGTTGGCCATGCAATGGCCGACACCCC-TTTTTATCAGATAAAAAAAATTCAAATTTTTT
* * *
3386 GGTGTTCGCCATGTAATGGCCAACACC
1 GGTGTTGGCCATGCAATGGCCGACACC
3413 AACTTCCTCT
Statistics
Matches: 315, Mismatches: 56, Indels: 33
0.78 0.14 0.08
Matches are distributed among these distances:
56 20 0.06
57 12 0.04
58 21 0.07
59 46 0.15
60 61 0.19
61 89 0.28
62 61 0.19
63 5 0.02
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (61 bp):
GGTGTTGGCCATGCAATGGCCGACACCCCTTTTTATCAGATAAAAAAAATTCAAATTTTTT
Found at i:3339 original size:123 final size:119
Alignment explanation
Indices: 2968--3412 Score: 402
Period size: 123 Copynumber: 3.7 Consensus size: 119
2958 AAAAATTTGG
* * * ** * **
2968 GTGTTGGTCATGCAATGGTCGACACCCATT-TTTGTCAGATAAAAAGTACAATTTTTT-GTGTTG
1 GTGTTGGCCATGCAATGGCCGACACCCCTTCTTCATCAGATAAAAAATTTAATTTTTTGGTGTTG
* * * * *
3031 GTCAT-AAATGGCCAATACCCCTATTTATCT-GATAAAAAAAATCAAATTTTTTT
66 GCCATGCAATGACCGACACCCCTATTTAT-TAGATAAAAAAAATCAAATTTTTTT
** * *
3084 GTGTTGGCCATGCAATGGCAAACACCCCCTTGTTTATCAGATAAAAAATTTAATTTTTTGGTGTT
1 GTGTTGGCCATGCAATGGCCGACA-CCCCTTCTTCATCAGATAAAAAATTTAATTTTTTGGTGTT
* * * **
3149 GGCCGTGCAATGACCGACACCCCTATTTATTTGATAAAAAAAAATCAAAATTTTGG
65 GGCCATGCAATGACCGACACCCCTATTTATTAGAT-AAAAAAAATCAAATTTTTTT
* * *
3205 GTTTTGACCATGCAATGACCGACACCCCTTCTTCA-CAGATAAAAAAATTTCAAATTTTTCTGGT
1 GTGTTGGCCATGCAATGGCCGACACCCCTTCTTCATCAGAT-AAAAAATTT--AATTTTT-TGGT
* **
3269 GTTGGCCATGCAATGGCCGACACTCCCT-TTT-TTCAGATAAAAAAAATTCATTTTTTTTT
62 GTTGGCCATGCAATGACCGACAC-CCCTATTTATT-AGATAAAAAAAA-TCAAATTTTTTT
* * ** *
3328 GTGTTGGCCATGCAATGGCCGACACCCCTTTTTTATTTGGTAAAAAA-TTAATTTTTTTGGTGTT
1 GTGTTGGCCATGCAATGGCCGACACCCCTTCTTCATCAGATAAAAAATTTAA-TTTTTTGGTGTT
* * * *
3392 CGCCATGTAATGGCCAACACC
65 GGCCATGCAATGACCGACACC
3413 AACTTCCTCT
Statistics
Matches: 270, Mismatches: 44, Indels: 27
0.79 0.13 0.08
Matches are distributed among these distances:
116 20 0.07
117 5 0.02
118 23 0.09
119 16 0.06
120 66 0.24
121 41 0.15
122 19 0.07
123 74 0.27
124 6 0.02
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (119 bp):
GTGTTGGCCATGCAATGGCCGACACCCCTTCTTCATCAGATAAAAAATTTAATTTTTTGGTGTTG
GCCATGCAATGACCGACACCCCTATTTATTAGATAAAAAAAATCAAATTTTTTT
Done.