Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005443.1 Kokia drynarioides strain JFW-HI SEQ_119475, 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: 57720
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Warning! 94 characters in sequence are not A, C, G, or T
Found at i:1100 original size:232 final size:231
Alignment explanation
Indices: 682--1135 Score: 802
Period size: 232 Copynumber: 2.0 Consensus size: 231
672 CTTCATGTCA
*
682 AATTTATGGTCCATGTTTGAGAATTGTAATTACCTCTCCCAACGATGTCATCTCCAAGGTTTAAA
1 AATTTATGGTCCATGTTTGAGAATTGTAATTACCCCTCCCAACGATGTCATCTCCAAGGTTTAAA
747 CTTGTGTCTCCCGTTGAGAGTAAATTATAATATTATATATTTAACTATAATATATATAGATTATA
66 CTTGTGTCTCCCGTTGAGAGTAAATTATAATATTATATATTTAACTATAATATATATAGATTATA
* *
812 TAAAGTAAATGAGCTGAGCTGGGTTCAAGCTTTGAATGTAGAAGCCTGCGCTAGGCCCACTTAAA
131 TAAAGTAAATGAGCTGAGCTGGGTTCAAGCTTTGAATGTAAAAACCTGCGCTAGGCCCACTTAAA
*
877 CGGATTTATTTATTTATTTTCTAAGCCTTACCATTCC
196 AGGATTTATTT-TTTATTTTCTAAGCCTTACCATTCC
914 AATTTATGGTCCATGTTTGAGAATTGTAATTACCCCTCCCAACGATGTCATCTCCAAGGTTTAAA
1 AATTTATGGTCCATGTTTGAGAATTGTAATTACCCCTCCCAACGATGTCATCTCCAAGGTTTAAA
* *
979 CTTGTGTCTCCTGTTGGGAGTAAATTATAATATTATATATTTAACTATAATATATATAGATTATA
66 CTTGTGTCTCCCGTTGAGAGTAAATTATAATATTATATATTTAACTATAATATATATAGATTATA
* *
1044 TAACGTAAATGAGCTGAGCTGGGTTCAGGCTTTGAATGTAAAAACCTG-GTCTAGGCCCACTTAA
131 TAAAGTAAATGAGCTGAGCTGGGTTCAAGCTTTGAATGTAAAAACCTGCG-CTAGGCCCACTTAA
*
1108 AAGGATTTATTTTTTTTTTTCTAAGCCT
195 AAGGATTTATTTTTTATTTTCTAAGCCT
1136 AAAGGCTAGG
Statistics
Matches: 212, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
231 16 0.08
232 196 0.92
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.37
Consensus pattern (231 bp):
AATTTATGGTCCATGTTTGAGAATTGTAATTACCCCTCCCAACGATGTCATCTCCAAGGTTTAAA
CTTGTGTCTCCCGTTGAGAGTAAATTATAATATTATATATTTAACTATAATATATATAGATTATA
TAAAGTAAATGAGCTGAGCTGGGTTCAAGCTTTGAATGTAAAAACCTGCGCTAGGCCCACTTAAA
AGGATTTATTTTTTATTTTCTAAGCCTTACCATTCC
Found at i:8152 original size:20 final size:22
Alignment explanation
Indices: 8108--8152 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
8098 TGTTTGATTG
*
8108 TTGAGGATTTAGTGAGGGAATA
1 TTGAGGATTTAGTGAGAGAATA
8130 TTGAGGATTTAGT-AGAG-ATA
1 TTGAGGATTTAGTGAGAGAATA
8150 TTG
1 TTG
8153 TTATGGGTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.27
21 3 0.14
22 13 0.59
ACGTcount: A:0.31, C:0.00, G:0.33, T:0.36
Consensus pattern (22 bp):
TTGAGGATTTAGTGAGAGAATA
Found at i:11475 original size:22 final size:21
Alignment explanation
Indices: 11435--11495 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 21
11425 TTAGAAGGAA
11435 CTAATCATAAAAAAAAACAAG
1 CTAATCATAAAAAAAAACAAG
11456 CTAATCATAAAAAAATAACAAG
1 CTAATCATAAAAAAA-AACAAG
** *
11478 GAAATTATATAAAAAAAA
1 CTAATCATA-AAAAAAAA
11496 ATGAAAACCC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 15 0.43
22 14 0.40
23 6 0.17
ACGTcount: A:0.67, C:0.10, G:0.05, T:0.18
Consensus pattern (21 bp):
CTAATCATAAAAAAAAACAAG
Found at i:12153 original size:27 final size:28
Alignment explanation
Indices: 12114--12167 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
12104 AGTTTTAGAA
**
12114 AAATATAGTAAATTTATTTTC-TTTTAC
1 AAATATAGTAAATCGATTTTCGTTTTAC
12141 AAATACTAG-AAATCGATTTTCGTTTTA
1 AAATA-TAGTAAATCGATTTTCGTTTTA
12168 GAAAATATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 15 0.65
28 8 0.35
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.46
Consensus pattern (28 bp):
AAATATAGTAAATCGATTTTCGTTTTAC
Found at i:18725 original size:15 final size:16
Alignment explanation
Indices: 18705--18738 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
18695 AATTTTTTAA
18705 AAATTATAAAAAT-AT
1 AAATTATAAAAATGAT
*
18720 AAATTATTAAAATGAT
1 AAATTATAAAAATGAT
18736 AAA
1 AAA
18739 ATTGTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
AAATTATAAAAATGAT
Found at i:21355 original size:31 final size:31
Alignment explanation
Indices: 21287--21356 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 31
21277 GATTGATGAG
** *
21287 AATTTTCAAAAAATTTAAGAGAGTCTAATTAA
1 AATTTTCAAAAAATTTAAGAGAG-AAAATCAA
21319 AATTTTCTAAAAAATTTAAGAGA-AAAATCAA
1 AATTTTC-AAAAAATTTAAGAGAGAAAATCAA
21350 AATTTTC
1 AATTTTC
21357 CAATTTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 12 0.35
32 7 0.21
33 15 0.44
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.34
Consensus pattern (31 bp):
AATTTTCAAAAAATTTAAGAGAGAAAATCAA
Found at i:25152 original size:7 final size:7
Alignment explanation
Indices: 25140--25172 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
25130 AACATAGTGG
25140 CATGTGC
1 CATGTGC
25147 CATGTGC
1 CATGTGC
25154 CATGTGC
1 CATGTGC
25161 CATGTGC
1 CATGTGC
25168 CATGT
1 CATGT
25173 ATTTTACCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.15, C:0.27, G:0.27, T:0.30
Consensus pattern (7 bp):
CATGTGC
Found at i:29714 original size:23 final size:22
Alignment explanation
Indices: 29704--29751 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
29694 TAGAGATATA
29704 AATTATTAAAATAATAAAATTAT
1 AATTATTAAAAT-ATAAAATTAT
* *
29727 AATCATTAAAATATATAATT-T
1 AATTATTAAAATATAAAATTAT
29748 AATT
1 AATT
29752 CGGGTTCTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 4 0.18
22 7 0.32
23 11 0.50
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
AATTATTAAAATATAAAATTAT
Found at i:50656 original size:16 final size:17
Alignment explanation
Indices: 50628--50666 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
50618 TATGAAATTC
*
50628 AAAGAACCAAAAAAGAA
1 AAAGAACCAAAAAAAAA
50645 AAAGAA-CAAAAAAAAA
1 AAAGAACCAAAAAAAAA
50661 AAAGAA
1 AAAGAA
50667 AGTTATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.82, C:0.08, G:0.10, T:0.00
Consensus pattern (17 bp):
AAAGAACCAAAAAAAAA
Found at i:55512 original size:17 final size:17
Alignment explanation
Indices: 55490--55541 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
55480 TAAAATTTAT
*
55490 AAAAATATTTAAAAATA
1 AAAAATATTAAAAAATA
55507 AAAAATA-TAAAAAATTA
1 AAAAATATTAAAAAA-TA
55524 AAAAGA-ATTAAAAAATA
1 AAAA-ATATTAAAAAATA
55541 A
1 A
55542 GTACACGTGG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
16 6 0.19
17 17 0.55
18 8 0.26
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (17 bp):
AAAAATATTAAAAAATA
Done.