Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001734.1 Kokia drynarioides strain JFW-HI SEQ_113439, 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: 4342
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Found at i:1837 original size:49 final size:49
Alignment explanation
Indices: 1778--2198 Score: 330
Period size: 49 Copynumber: 8.6 Consensus size: 49
1768 GTACCGTGAA
* * *
1778 ACATGAAGGGAAATATTTAACCCGCAACGGCGAATCTAGTACCACCAAG
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAG
* ** * * * * * *
1827 ACATGGAGGGAAAGGCTTAAGTCACAATGACGAACCGT-GTACCTCAGAAG
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATC-TAGTACCAC-GAAG
* *
1877 ACACGAAGGGAAAGATTTAAGCCGCAACGACGAAT-TCAGTACCAC-AGAG
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCT-AGTACCACGA-AG
* * * * * * *
1926 ACGT-ACAAGGAAAGATTTAGGCCACAATGGCGAATCTAATACCACAAAG
1 ACATGA-AGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAG
* * * *
1975 ACACGAATGGAAAGATTTAAGCCGCAACGGCAAATCCAGTACCACGAAG
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAG
* *
2024 ACATGAAGGGAAAGATATAAGCCGCAACGGC-AGATCCAGTACCACGAAG
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGA-ATCTAGTACCACGAAG
* * * * * * * * **
2073 ACATAAAGGGAAAGGTTTAAGTCACAACGGCAAACCCAATACCTTGAAG
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAG
* * * * *
2122 ACATAAAGGGAAAGATTTAAGCCGCAATGGCGAATCCAGTACCATGAAA
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAG
* * * * *
2171 ATACGAGGGGAAAGATTGAAGCGGCAAC
1 ACATGAAGGGAAAGATTTAAGCCGCAAC
2199 AACAAATCTA
Statistics
Matches: 294, Mismatches: 67, Indels: 22
0.77 0.17 0.06
Matches are distributed among these distances:
48 4 0.01
49 249 0.85
50 41 0.14
ACGTcount: A:0.41, C:0.21, G:0.24, T:0.14
Consensus pattern (49 bp):
ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAG
Found at i:1953 original size:99 final size:97
Alignment explanation
Indices: 1782--2027 Score: 262
Period size: 99 Copynumber: 2.5 Consensus size: 97
1772 CGTGAAACAT
* * ** * *
1782 GAAGGGAAATATTTAACCCGCAACGGCGAA-TCTAGTACCACCAAGACATGGAGGGAAAGGCTTA
1 GAAGGGAAAGATTTAAGCCGCAACGGCGAATTC-AGTACCA-CAAGACATACAAGGAAAGACTTA
* * *
1846 AGTCACAATGACGAACCGT-GTACCTCAGAAGACAC
64 AGCCACAATGACGAACC-TAATACCACA-AAGACAC
* * * *
1881 GAAGGGAAAGATTTAAGCCGCAACGACGAATTCAGTACCACAGAGACGTACAAGGAAAGATTTAG
1 GAAGGGAAAGATTTAAGCCGCAACGGCGAATTCAGTACCACA-AGACATACAAGGAAAGACTTAA
* *
1946 GCCACAATGGCGAATCTAATACCACAAAGACAC
65 GCCACAATGACGAACCTAATACCACAAAGACAC
* * *
1979 GAATGGAAAGATTTAAGCCGCAACGGCAAATCCAGTACCACGAAGACAT
1 GAAGGGAAAGATTTAAGCCGCAACGGCGAATTCAGTACCAC-AAGACAT
2028 GAAGGGAAAG
Statistics
Matches: 123, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
98 52 0.42
99 69 0.56
100 2 0.02
ACGTcount: A:0.40, C:0.22, G:0.23, T:0.15
Consensus pattern (97 bp):
GAAGGGAAAGATTTAAGCCGCAACGGCGAATTCAGTACCACAAGACATACAAGGAAAGACTTAAG
CCACAATGACGAACCTAATACCACAAAGACAC
Found at i:2036 original size:98 final size:98
Alignment explanation
Indices: 1782--2198 Score: 367
Period size: 98 Copynumber: 4.2 Consensus size: 98
1772 CGTGAAACAT
* * * * * * **
1782 GAAGGGAAATATTTAACCCGCAACGGCGAATCTAGTACCACCAAGACATGGAGGGAAAGGCTTAA
1 GAAGGGAAAGATTTAAGCCGCAACGGCAAATCCAGTACCACGAAGACATGAAGGGAAAGATTTAA
* * * *
1847 GTCACAATGACGAACCGT-GTACCTCAGAAGACAC
66 GCCACAATGGCGAATC-TAGTACCACA-AAGACAC
* * * * *
1881 GAAGGGAAAGATTTAAGCCGCAACGACGAATTCAGTACCAC-AGAGACGT-ACAAGGAAAGATTT
1 GAAGGGAAAGATTTAAGCCGCAACGGCAAATCCAGTACCACGA-AGACATGA-AGGGAAAGATTT
* *
1944 AGGCCACAATGGCGAATCTAATACCACAAAGACAC
64 AAGCCACAATGGCGAATCTAGTACCACAAAGACAC
* *
1979 GAATGGAAAGATTTAAGCCGCAACGGCAAATCCAGTACCACGAAGACATGAAGGGAAAGATATAA
1 GAAGGGAAAGATTTAAGCCGCAACGGCAAATCCAGTACCACGAAGACATGAAGGGAAAGATTTAA
* * * * *
2044 GCCGCAACGGC-AGATCCAGTACCACGAAGACAT
66 GCCACAATGGCGA-ATCTAGTACCACAAAGACAC
* * * * * * ** *
2077 AAAGGGAAAGGTTTAAGTCACAACGGCAAACCCAATACCTTGAAGACATAAAGGGAAAGATTTAA
1 GAAGGGAAAGATTTAAGCCGCAACGGCAAATCCAGTACCACGAAGACATGAAGGGAAAGATTTAA
* * * *
2142 GCCGCAATGGCGAATCCAGTACCATGAAA-ATAC
66 GCCACAATGGCGAATCTAGTACCA-CAAAGACAC
* * *
2175 GAGGGGAAAGATTGAAGCGGCAAC
1 GAAGGGAAAGATTTAAGCCGCAAC
2199 AACAAATCTA
Statistics
Matches: 257, Mismatches: 53, Indels: 17
0.79 0.16 0.05
Matches are distributed among these distances:
97 1 0.00
98 181 0.70
99 75 0.29
ACGTcount: A:0.41, C:0.21, G:0.24, T:0.14
Consensus pattern (98 bp):
GAAGGGAAAGATTTAAGCCGCAACGGCAAATCCAGTACCACGAAGACATGAAGGGAAAGATTTAA
GCCACAATGGCGAATCTAGTACCACAAAGACAC
Found at i:2086 original size:147 final size:147
Alignment explanation
Indices: 1873--2186 Score: 364
Period size: 147 Copynumber: 2.1 Consensus size: 147
1863 GTGTACCTCA
* * *
1873 GAAGACACGAAGGGAAAGATTTAAGCCGCAACGACGAATTCAGTACCACAGAGACGTACAAGGAA
1 GAAGACACGAAGGGAAAGATATAAGCCGCAACGACGAATCCAGTACCACAGAGACATACAAGGAA
* * * * * * *
1938 AGATTTAGGCCACAATGGCGAATCTAATACCACAAAGACACGAATGGAAAGATTTAAGCCGCAAC
66 AGATTTAAGCCACAACGGCAAACCCAATACCACAAAGACACAAAGGGAAAGATTTAAGCCGCAAC
2003 GGCAAATCCAGTACCAC
131 GGCAAATCCAGTACCAC
* *
2020 GAAGACATGAAGGGAAAGATATAAGCCGCAACGGC-AGATCCAGTACCAC-GAAGACATA-AAGG
1 GAAGACACGAAGGGAAAGATATAAGCCGCAACGACGA-ATCCAGTACCACAG-AGACATACAA-G
* * *** *
2082 GAAAGGTTTAAGTCACAACGGCAAACCCAATACCTTGAAGACATAAAGGGAAAGATTTAAGCCGC
63 GAAAGATTTAAGCCACAACGGCAAACCCAATACCACAAAGACACAAAGGGAAAGATTTAAGCCGC
* * *
2147 AATGGCGAATCCAGTACCAT
128 AACGGCAAATCCAGTACCAC
* * *
2167 GAAAATACGAGGGGAAAGAT
1 GAAGACACGAAGGGAAAGAT
2187 TGAAGCGGCA
Statistics
Matches: 139, Mismatches: 25, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
146 4 0.03
147 135 0.97
ACGTcount: A:0.42, C:0.20, G:0.24, T:0.14
Consensus pattern (147 bp):
GAAGACACGAAGGGAAAGATATAAGCCGCAACGACGAATCCAGTACCACAGAGACATACAAGGAA
AGATTTAAGCCACAACGGCAAACCCAATACCACAAAGACACAAAGGGAAAGATTTAAGCCGCAAC
GGCAAATCCAGTACCAC
Found at i:2614 original size:10 final size:10
Alignment explanation
Indices: 2585--2618 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
2575 GATCAAGCCT
2585 TTGGTTTTAAA
1 TTGG-TTTAAA
2596 TTAGGTTTAAA
1 TT-GGTTTAAA
2607 TTGGTTTAAA
1 TTGGTTTAAA
2617 TT
1 TT
2619 TATTTTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.45
11 10 0.45
12 2 0.09
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (10 bp):
TTGGTTTAAA
Found at i:2646 original size:20 final size:20
Alignment explanation
Indices: 2621--2658 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2611 TTTAAATTTA
2621 TTTTTAAATTAAAATTTATC
1 TTTTTAAATTAAAATTTATC
*
2641 TTTTTAAATTTAAATTTA
1 TTTTTAAATTAAAATTTA
2659 CTCTAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTTAAATTAAAATTTATC
Found at i:3432 original size:3 final size:3
Alignment explanation
Indices: 3417--3517 Score: 58
Period size: 3 Copynumber: 32.0 Consensus size: 3
3407 GGTTATATAT
* * ** * *
3417 TAA TAA TAT TAA TAA TGA TAAA TAA TAAA TAA TGG TAA TAAA TAA CAT
1 TAA TAA TAA TAA TAA TAA T-AA TAA T-AA TAA TAA TAA T-AA TAA TAA
* * * * *
3465 TAA TAA TTAT TAA TAA AAA CAT TAA TAA TAA TAA TAA TTAA TAT TAA
1 TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA
3512 TAA TAA
1 TAA TAA
3518 ATAAAAATGA
Statistics
Matches: 72, Mismatches: 21, Indels: 10
0.70 0.20 0.10
Matches are distributed among these distances:
3 59 0.82
4 13 0.18
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3485 original size:22 final size:22
Alignment explanation
Indices: 3452--3521 Score: 79
Period size: 22 Copynumber: 3.1 Consensus size: 22
3442 TAAATAATGG
*
3452 TAATAAATAACATTAATAATTAT
1 TAATAAA-AACATTAATAATTAA
3475 TAATAAAAACATTAATAA-TAA
1 TAATAAAAACATTAATAATTAA
* * *
3496 TAATAATTAATATTAATAATAAA
1 TAATAA-AAACATTAATAATTAA
3519 TAA
1 TAA
3522 AAATGAAGCC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.20
22 21 0.51
23 12 0.29
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (22 bp):
TAATAAAAACATTAATAATTAA
Found at i:3512 original size:13 final size:13
Alignment explanation
Indices: 3417--3521 Score: 51
Period size: 13 Copynumber: 8.2 Consensus size: 13
3407 GGTTATATAT
3417 TAATAAT-ATTAA
1 TAATAATAATTAA
* *
3429 TAATGATAAATAA
1 TAATAATAATTAA
3442 T-A-AATAATGGTAA
1 TAATAATAAT--TAA
*
3455 TAAATAA-CATTAA
1 T-AATAATAATTAA
*
3468 TAATTATTAA-TAA
1 TAA-TAATAATTAA
* * *
3481 AAACATTAA-TAA
1 TAATAATAATTAA
3493 TAATAATAATTAA
1 TAATAATAATTAA
* *
3506 TATTAATAATAAA
1 TAATAATAATTAA
3519 TAA
1 TAA
3522 AAATGAAGCC
Statistics
Matches: 69, Mismatches: 15, Indels: 17
0.68 0.15 0.17
Matches are distributed among these distances:
11 4 0.06
12 23 0.33
13 36 0.52
14 1 0.01
15 3 0.04
16 2 0.03
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (13 bp):
TAATAATAATTAA
Done.