Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006374.1 Kokia drynarioides strain JFW-HI SEQ_120950, 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: 12484
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36
Warning! 118 characters in sequence are not A, C, G, or T
Found at i:2398 original size:97 final size:97
Alignment explanation
Indices: 2232--2525 Score: 471
Period size: 97 Copynumber: 3.0 Consensus size: 97
2222 AACCTTGGAA
* *
2232 AAGGGTATTTGATTATCCTGATTTGAAGAAAAGTCGTGCCTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGGTATTCGATTATCCTGATTTGAAGAAAAATCGTGCCTAGTAAGTTAAGGCACAAATTTTCA
*
2297 AAACCAGAGATAAAGAAACATTACCTCTATTT
66 AAACCAGAGATAAAGAAACATTACCTCGATTT
* *
2329 AAGGGTATTCGATTATCCCGGTTTGAAGAAAAATCGTGCCTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGGTATTCGATTATCCTGATTTGAAGAAAAATCGTGCCTAGTAAGTTAAGGCACAAATTTTCA
*
2394 AAACCAGAGATAAAGAAACATTGCCTCGATTT
66 AAACCAGAGATAAAGAAACATTACCTCGATTT
**
2426 AAGGGTATTCGATTATCCTGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGGTATTCGATTATCCTGATTTGAAGAAAAATCGTGCCTAGTAAGTTAAGGCACAAATTTTCA
* * * *
2491 AAACCCGAGATAAAGGAATATTGCCTCGACTTT
66 AAACCAGAGATAAAGAAACATTACCTCGA-TTT
2524 AA
1 AA
2526 AGGTTTGTGA
Statistics
Matches: 183, Mismatches: 13, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
97 178 0.97
98 5 0.03
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (97 bp):
AAGGGTATTCGATTATCCTGATTTGAAGAAAAATCGTGCCTAGTAAGTTAAGGCACAAATTTTCA
AAACCAGAGATAAAGAAACATTACCTCGATTT
Found at i:2860 original size:30 final size:28
Alignment explanation
Indices: 2828--3098 Score: 110
Period size: 30 Copynumber: 9.4 Consensus size: 28
2818 AAAGTGTGAT
2828 TTTTTGGAAATTCGAGGGCAAAATGGTAA
1 TTTTTGGAAATTCGAGGGCAAAAT-GTAA
* ** * *
2857 -TTTTAGACGTCCGAGGGTAAAATTGTAA
1 TTTTTGGAAATTCGAGGGCAAAA-TGTAA
2885 -TTTTGG--ATCTC-A-GGCAAAAATGGTAA
1 TTTTTGGAAAT-TCGAGGGC-AAAAT-GTAA
** *
2911 -TTTTGGATGCTT-GAGGGTAAAATGGTAA
1 TTTTTGGA-AATTCGAGGGCAAAAT-GTAA
* **
2939 GTTTTGGAAAGTTC-AGAATCAAAATGGTAAA
1 TTTTTGGAAA-TTCGAG-GGCAAAAT-GT-AA
*** * * *
2970 TTTTTGGTTGTTTGAGGGAAAAAAATGTGA
1 TTTTTGGAAATTCGAGGG--CAAAATGTAA
** *
3000 TTTTTTTAAAGTTCGAGGGCAACATGTAA
1 TTTTTGGAAA-TTCGAGGGCAAAATGTAA
*
3029 TTTTTGAGAAGTTCGAGGGTCAAAATGTAA
1 TTTTTG-GAAATTCGAGGG-CAAAATGTAA
* *
3059 TTTTTAGAAAGTTTGAGGGTCAAAATGTAA
1 TTTTTGGAAA-TTCGAGGG-CAAAATGTAA
3089 TTTTTGGAAA
1 TTTTTGGAAA
3099 GTTTGGGTGT
Statistics
Matches: 179, Mismatches: 42, Indels: 41
0.68 0.16 0.16
Matches are distributed among these distances:
25 3 0.02
26 16 0.09
27 1 0.01
28 38 0.21
29 38 0.21
30 59 0.33
31 19 0.11
32 5 0.03
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.35
Consensus pattern (28 bp):
TTTTTGGAAATTCGAGGGCAAAATGTAA
Found at i:2910 original size:26 final size:28
Alignment explanation
Indices: 2875--2946 Score: 85
Period size: 26 Copynumber: 2.6 Consensus size: 28
2865 GTCCGAGGGT
*
2875 AAAATTGTAATTTTGGAT-C-TCAGGCA
1 AAAATGGTAATTTTGGATGCTTCAGGCA
* **
2901 AAAATGGTAATTTTGGATGCTTGAGGGT
1 AAAATGGTAATTTTGGATGCTTCAGGCA
2929 AAAATGGTAAGTTTTGGA
1 AAAATGGTAA-TTTTGGA
2947 AAGTTCAGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
26 17 0.44
27 1 0.03
28 14 0.36
29 7 0.18
ACGTcount: A:0.33, C:0.06, G:0.26, T:0.35
Consensus pattern (28 bp):
AAAATGGTAATTTTGGATGCTTCAGGCA
Found at i:3054 original size:59 final size:59
Alignment explanation
Indices: 2991--3182 Score: 205
Period size: 59 Copynumber: 3.2 Consensus size: 59
2981 TTGAGGGAAA
* * *
2991 AAAATGTGATTTTTTTAAAGTTCGAGGG-CAACATGTAATTTTTGAGAAGTTCGAGGGTC
1 AAAATGT-ATTTTTTAAAAGTTCGAGGGTCAAAATGTAATTTTTGAGAAGTTTGAGGGTC
* * *
3050 AAAATGTAATTTTTAGAAAGTTTGAGGGTCAAAATGTAATTTTTG-GAAAGTTTG-GGTGTT
1 AAAATGTATTTTTTA-AAAGTTCGAGGGTCAAAATGTAATTTTTGAG-AAGTTTGAGG-GTC
* * * *
3110 AAAATGTA-ATTTTAAGAAG-TCTAAGGGTTAAAATGTAATTTTTGAGAAGTTTAAGGGTC
1 AAAATGTATTTTTTAA-AAGTTC-GAGGGTCAAAATGTAATTTTTGAGAAGTTTGAGGGTC
3169 AAAATGTATTTTTT
1 AAAATGTATTTTTT
3183 GAGAAGTTTA
Statistics
Matches: 111, Mismatches: 13, Indels: 17
0.79 0.09 0.12
Matches are distributed among these distances:
58 8 0.07
59 65 0.59
60 38 0.34
ACGTcount: A:0.34, C:0.04, G:0.23, T:0.39
Consensus pattern (59 bp):
AAAATGTATTTTTTAAAAGTTCGAGGGTCAAAATGTAATTTTTGAGAAGTTTGAGGGTC
Found at i:3093 original size:89 final size:88
Alignment explanation
Indices: 2991--3190 Score: 228
Period size: 89 Copynumber: 2.2 Consensus size: 88
2981 TTGAGGGAAA
* * * *
2991 AAAATGTGATTTTTTTAAAGTTCGAGG-G-CAACATGTAATTTTTGAGAAGT-TCGAGGGTCAAA
1 AAAATGT-ATTTTTTGAAAGTTCG-GGTGTCAAAATGTAA-TTTTAAGAAGTCT-AAGGGTCAAA
*
3053 ATGTAATTTTT-AGAAAGTTTGAGGGTC
62 ATGTAATTTTTGAG-AAGTTTAAGGGTC
* * * *
3080 AAAATGTAATTTTTGGAAAGTTTGGGTGTTAAAATGTAATTTTAAGAAGTCTAAGGGTTAAAATG
1 AAAATGT-ATTTTTTGAAAGTTCGGGTGTCAAAATGTAATTTTAAGAAGTCTAAGGGTCAAAATG
3145 TAATTTTTGAGAAGTTTAAGGGTC
65 TAATTTTTGAGAAGTTTAAGGGTC
3169 AAAATGTATTTTTTGAGAAGTT
1 AAAATGTATTTTTTGA-AAGTT
3191 TAGGGGTCAA
Statistics
Matches: 95, Mismatches: 11, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
88 10 0.11
89 74 0.78
90 11 0.12
ACGTcount: A:0.34, C:0.04, G:0.23, T:0.38
Consensus pattern (88 bp):
AAAATGTATTTTTTGAAAGTTCGGGTGTCAAAATGTAATTTTAAGAAGTCTAAGGGTCAAAATGT
AATTTTTGAGAAGTTTAAGGGTC
Found at i:3099 original size:30 final size:30
Alignment explanation
Indices: 2921--3201 Score: 204
Period size: 30 Copynumber: 9.4 Consensus size: 30
2911 TTTTGGATGC
*
2921 TTGAGGGT-AAAATGGTAAGTTTTGGAAAG-
1 TTGAGGGTCAAAAT-GTAATTTTTGGAAAGT
* ** **
2950 TTCAGAATCAAAATGGTAAATTTTTGG-TTGT
1 TTGAGGGTCAAAAT-GT-AATTTTTGGAAAGT
** * **
2981 TTGAGGGAAAAAAATGTGATTTTTTTAAAGT
1 TTGAGGG-TCAAAATGTAATTTTTGGAAAGT
* *
3012 TCGAGGG-CAACATGTAATTTTT-GAGAAGT
1 TTGAGGGTCAAAATGTAATTTTTGGA-AAGT
* *
3041 TCGAGGGTCAAAATGTAATTTTTAGAAAGT
1 TTGAGGGTCAAAATGTAATTTTTGGAAAGT
3071 TTGAGGGTCAAAATGTAATTTTTGGAAAGT
1 TTGAGGGTCAAAATGTAATTTTTGGAAAGT
* **
3101 TTG-GGTGTTAAAATGTAATTTTAAG-AAGT
1 TTGAGG-GTCAAAATGTAATTTTTGGAAAGT
* * *
3130 CTAAGGGTTAAAATGTAATTTTT-GAGAAGT
1 TTGAGGGTCAAAATGTAATTTTTGGA-AAGT
* *
3160 TTAAGGGTCAAAATGT-ATTTTTTGAGAAGT
1 TTGAGGGTCAAAATGTAATTTTTGGA-AAGT
3190 TT-AGGGGTCAAA
1 TTGA-GGGTCAAA
3202 CGTGATTTTT
Statistics
Matches: 206, Mismatches: 32, Indels: 27
0.78 0.12 0.10
Matches are distributed among these distances:
28 2 0.01
29 58 0.28
30 117 0.57
31 24 0.12
32 5 0.02
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (30 bp):
TTGAGGGTCAAAATGTAATTTTTGGAAAGT
Found at i:3210 original size:59 final size:57
Alignment explanation
Indices: 3023--3221 Score: 181
Period size: 59 Copynumber: 3.4 Consensus size: 57
3013 CGAGGGCAAC
**
3023 ATGTAATTTTTGAGAAGTTCGAGGGTCAAAATGTAATTTTTAGAAAGTTT-GAGGGTCAAA
1 ATGTAATTTTTGAGAAGTTTAAGGGTCAAAATGT-ATTTTTAG-AAGTTTAG-GGGTC-AA
* * * * * *
3083 ATGTAATTTTTG-GAAAGTTT-GGGTGTTAAAATGTAATTTTAAGAAGTCTAAGGGTTAAA
1 ATGTAATTTTTGAG-AAGTTTAAGG-GTCAAAATGT-ATTTTTAGAAGT-TTAGGGGTCAA
3142 ATGTAATTTTTGAGAAGTTTAAGGGTCAAAATGTATTTTTTGAGAAGTTTAGGGGTCAA
1 ATGTAATTTTTGAGAAGTTTAAGGGTCAAAATGTA-TTTTT-AGAAGTTTAGGGGTCAA
* *
3201 ACGTGATTTTT-AGACAGTTTA
1 ATGTAATTTTTGAGA-AGTTTA
3222 GGGACCTTTT
Statistics
Matches: 115, Mismatches: 15, Indels: 19
0.77 0.10 0.13
Matches are distributed among these distances:
58 4 0.03
59 63 0.55
60 47 0.41
61 1 0.01
ACGTcount: A:0.34, C:0.04, G:0.24, T:0.38
Consensus pattern (57 bp):
ATGTAATTTTTGAGAAGTTTAAGGGTCAAAATGTATTTTTAGAAGTTTAGGGGTCAA
Found at i:3211 original size:29 final size:29
Alignment explanation
Indices: 3023--3224 Score: 166
Period size: 30 Copynumber: 6.8 Consensus size: 29
3013 CGAGGGCAAC
*
3023 ATGTAATTTTTGAGAAG-TTCGAGGGTCAAA
1 ATGT-ATTTTTGAGAAGTTTAG-GGGTCAAA
3053 ATGTAATTTTT-AGAAAGTTT-GAGGGTCAAA
1 ATGT-ATTTTTGAG-AAGTTTAG-GGGTCAAA
*
3083 ATGTAATTTTTG-GAAAGTTT-GGGTGTTAAA
1 ATGT-ATTTTTGAG-AAGTTTAGGG-GTCAAA
* * * * *
3113 ATGTAATTTTAAGAAGTCTAAGGGTTAAA
1 ATGTATTTTTGAGAAGTTTAGGGGTCAAA
*
3142 ATGTAATTTTTGAGAAGTTTAAGGGTCAAA
1 ATGT-ATTTTTGAGAAGTTTAGGGGTCAAA
3172 ATGTATTTTTTGAGAAGTTTAGGGGTC-AA
1 ATGTA-TTTTTGAGAAGTTTAGGGGTCAAA
*
3201 ACGTGATTTTT-AGACAGTTTAGGG
1 ATGT-ATTTTTGAGA-AGTTTAGGG
3225 ACCTTTTAGG
Statistics
Matches: 151, Mismatches: 11, Indels: 21
0.83 0.06 0.11
Matches are distributed among these distances:
28 3 0.02
29 44 0.29
30 102 0.68
31 2 0.01
ACGTcount: A:0.33, C:0.04, G:0.25, T:0.38
Consensus pattern (29 bp):
ATGTATTTTTGAGAAGTTTAGGGGTCAAA
Found at i:7140 original size:13 final size:12
Alignment explanation
Indices: 7121--7154 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
7111 AATATATTTT
*
7121 TAAAATTAATTA
1 TAAAATTAATCA
7133 TAACAATTAATCA
1 TAA-AATTAATCA
7146 TAAAATTAA
1 TAAAATTAA
7155 ATATGCTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (12 bp):
TAAAATTAATCA
Found at i:7811 original size:29 final size:30
Alignment explanation
Indices: 7726--7811 Score: 86
Period size: 31 Copynumber: 2.9 Consensus size: 30
7716 ACCAAATATT
* * *
7726 TTTTCCAGCTTTTAAGGGGTC-AAAAAATTG
1 TTTTCCAACTTTTAAGGGATCTAAAAAA-TA
* * *
7756 TTTTACTAACTTTTAAGGGCT-TAAAAAAAA
1 TTTT-CCAACTTTTAAGGGATCTAAAAAATA
7786 TTTTCCAACTTTTAAGGGATCTAAAA
1 TTTTCCAACTTTTAAGGGATCTAAAA
7812 TTCAATTTAT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
29 14 0.30
30 13 0.28
31 19 0.41
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (30 bp):
TTTTCCAACTTTTAAGGGATCTAAAAAATA
Found at i:8830 original size:23 final size:23
Alignment explanation
Indices: 8779--8824 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
8769 GAGCCTCTCC
8779 TATATTGATCCCAATTATATGTG
1 TATATTGATCCCAATTATATGTG
8802 TATATTGATCCCAATTATATGTG
1 TATATTGATCCCAATTATATGTG
8825 CTTATTAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.43
Consensus pattern (23 bp):
TATATTGATCCCAATTATATGTG
Found at i:8959 original size:22 final size:22
Alignment explanation
Indices: 8914--8959 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
8904 TATTAAATTA
*
8914 ATTTAAATAAAATAATTTTCCT
1 ATTTAAATAAAATAATTTTACT
*
8936 ATTTAAAT-AAATATTATTTACT
1 ATTTAAATAAAATAAT-TTTACT
8958 AT
1 AT
8960 AAAAGAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTTAAATAAAATAATTTTACT
Done.