Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003546.1 Kokia drynarioides strain JFW-HI SEQ_116394, 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: 3505
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1661 original size:242 final size:243
Alignment explanation
Indices: 1213--1704 Score: 844
Period size: 242 Copynumber: 2.0 Consensus size: 243
1203 TTCTACTAAA
* *
1213 CCAAACTTAATTACGTTGAAAATGAGAATTTGAAAAGAAAAAGATATTTGAATTGCCTTTTAATA
1 CCAAACTTAATTACATTGAAAATGAGAATTTGAAAAGAAAAAGATATTTGAATTGCCTTCTAATA
*
1278 TGTTAAATTAAAATATTAGTGAGAAACAAAAAGAATCAAATTAAACAATTTTTTATGAACAAACA
66 TGTTAAATTAAAATATTAGTGAGAAACAAAAAGAATCAAATTAAACAAATTTTTATGAACAAACA
* * *
1343 ATACTAGTGAGAAACAAAAAGAATCAAATAACATCTTCCCTCACCATGTTTTTTTATTCTTTGCT
131 ATACTAGTGAAAAACAAAAAGAATCAAATAACATCTTCCCCCACCATGTTTTTTAATTCTTTGCT
*
1408 CCTCCACCCAAATTAAAACTTATCATATTATTTGCCATCTTACAAAGT
196 CCTCCACCCAAAGTAAAACTTATCATATTATTTGCCATCTTACAAAGT
*
1456 CCAAACTTAATTACATTGAAAATGAGAATTTGAAAAGAAAGAGATATTTGAATTGCCTTCTAATA
1 CCAAACTTAATTACATTGAAAATGAGAATTTGAAAAGAAAAAGATATTTGAATTGCCTTCTAATA
* **
1521 TGTTAGATTAAAATATTAGTGAGAAAC-AAAAGAATCAAATCT-AACAAATTTTTATGATTAAAC
66 TGTTAAATTAAAATATTAGTGAGAAACAAAAAGAATCAAAT-TAAACAAATTTTTATGAACAAAC
*
1584 AATACTAGTGAAAAACAAAAAGAATCAAATTACATCTTCCCCCACCATGTTTTTTAATTCTTTGC
130 AATACTAGTGAAAAACAAAAAGAATCAAATAACATCTTCCCCCACCATGTTTTTTAATTCTTTGC
*
1649 TTCTCCACCCAAAGTAAAACTTATCATATTATTTGCCATCTTACAAAGT
195 TCCTCCACCCAAAGTAAAACTTATCATATTATTTGCCATCTTACAAAGT
1698 CCAAACT
1 CCAAACT
1705 GTTCCCTAAC
Statistics
Matches: 235, Mismatches: 13, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
242 146 0.62
243 89 0.38
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (243 bp):
CCAAACTTAATTACATTGAAAATGAGAATTTGAAAAGAAAAAGATATTTGAATTGCCTTCTAATA
TGTTAAATTAAAATATTAGTGAGAAACAAAAAGAATCAAATTAAACAAATTTTTATGAACAAACA
ATACTAGTGAAAAACAAAAAGAATCAAATAACATCTTCCCCCACCATGTTTTTTAATTCTTTGCT
CCTCCACCCAAAGTAAAACTTATCATATTATTTGCCATCTTACAAAGT
Found at i:2831 original size:87 final size:87
Alignment explanation
Indices: 2722--2986 Score: 329
Period size: 88 Copynumber: 3.1 Consensus size: 87
2712 CTGCTAAAAA
* *
2722 TAGCGACGTTTATGAGGAAAAACTCCGCTATAGAACATGGTCTTTAGCGGCGCTATTCCCACAAA
1 TAGCGGCGTTTATGAGGAAAAACTCCGCTATAGAACATGGTCTTTAGCGGCGCTATCCCCACAAA
*
2787 CTCCGCTATAGAAAATGGTCTT
66 CTCCGCTATAGAACATGGTCTT
* * * * **** *
2809 TAGCGGCGTTTATGAGGAAAAACTCTGCAATAGAACATGGTCTTTAGTGGCGTTTATGAGGAAAA
1 TAGCGGCGTTTATGAGGAAAAACTCCGCTATAGAACATGGTCTTTAGCGGCG-CTATCCCCACAA
*
2874 ACTCTGCTATAGAACATGGTCTT
65 ACTCCGCTATAGAACATGGTCTT
* *
2897 TAGTGGCGTTTATGAGGAAAAACTCCGTTATAGAACATGGTCTTTAGC-G-GCT-TCCCTCACAA
1 TAGCGGCGTTTATGAGGAAAAACTCCGCTATAGAACATGGTCTTTAGCGGCGCTATCCC-CACAA
* * *
2959 GCGCCGCTAAAGAACATGGTCTT
65 ACTCCGCTATAGAACATGGTCTT
2982 TAGCG
1 TAGCG
2987 ACACTTCCCT
Statistics
Matches: 148, Mismatches: 28, Indels: 6
0.81 0.15 0.03
Matches are distributed among these distances:
84 1 0.01
85 27 0.18
86 1 0.01
87 49 0.33
88 70 0.47
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (87 bp):
TAGCGGCGTTTATGAGGAAAAACTCCGCTATAGAACATGGTCTTTAGCGGCGCTATCCCCACAAA
CTCCGCTATAGAACATGGTCTT
Found at i:2849 original size:44 final size:44
Alignment explanation
Indices: 2722--2947 Score: 319
Period size: 44 Copynumber: 5.2 Consensus size: 44
2712 CTGCTAAAAA
*
2722 TAGCGACGTTTATGAGGAAAAACTCCGCTATAGAACATGGTCTT
1 TAGCGGCGTTTATGAGGAAAAACTCCGCTATAGAACATGGTCTT
* **** * *
2766 TAGCGGCG-CTATTCCCACAAACTCCGCTATAGAAAATGGTCTT
1 TAGCGGCGTTTATGAGGAAAAACTCCGCTATAGAACATGGTCTT
* *
2809 TAGCGGCGTTTATGAGGAAAAACTCTGCAATAGAACATGGTCTT
1 TAGCGGCGTTTATGAGGAAAAACTCCGCTATAGAACATGGTCTT
* *
2853 TAGTGGCGTTTATGAGGAAAAACTCTGCTATAGAACATGGTCTT
1 TAGCGGCGTTTATGAGGAAAAACTCCGCTATAGAACATGGTCTT
* *
2897 TAGTGGCGTTTATGAGGAAAAACTCCGTTATAGAACATGGTCTT
1 TAGCGGCGTTTATGAGGAAAAACTCCGCTATAGAACATGGTCTT
2941 TAGCGGC
1 TAGCGGC
2948 TTCCCTCACA
Statistics
Matches: 159, Mismatches: 22, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
43 36 0.23
44 123 0.77
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (44 bp):
TAGCGGCGTTTATGAGGAAAAACTCCGCTATAGAACATGGTCTT
Found at i:3035 original size:43 final size:42
Alignment explanation
Indices: 2928--3035 Score: 164
Period size: 43 Copynumber: 2.5 Consensus size: 42
2918 ACTCCGTTAT
* *
2928 AGAACATGGTCTTTAGCG-GCTTCCCTCACAAGCGCCGCTAA
1 AGAACATGGTCTTTAGCGCACTTCCCTCAAAAGCGCCGCTAA
2969 AGAACATGGTCTTTAGCGACACTTCCCTCAAAAGCGCCGCTAA
1 AGAACATGGTCTTTAGCG-CACTTCCCTCAAAAGCGCCGCTAA
*
3012 AGAACATGGTTTTTAGCAGCACTT
1 AGAACATGGTCTTTAGC-GCACTT
3036 TTTCTACAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
41 18 0.30
43 42 0.69
44 1 0.02
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (42 bp):
AGAACATGGTCTTTAGCGCACTTCCCTCAAAAGCGCCGCTAA
Done.