Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011031.1 Kokia drynarioides strain JFW-HI SEQ_126002, 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: 34549
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Warning! 33 characters in sequence are not A, C, G, or T
Found at i:951 original size:26 final size:25
Alignment explanation
Indices: 896--957 Score: 63
Period size: 26 Copynumber: 2.5 Consensus size: 25
886 AATGAGAAAT
* ***
896 TAAAATTTAATTTATTTTCTTTTTC
1 TAAAATTTAATTTATTTTATTTAAA
*
921 CAAAATGTTAATTTATTTTATTTAAA
1 TAAAAT-TTAATTTATTTTATTTAAA
947 TAAAA-TTAATT
1 TAAAATTTAATT
958 GAATTATGTA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
24 6 0.20
25 5 0.17
26 19 0.63
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.55
Consensus pattern (25 bp):
TAAAATTTAATTTATTTTATTTAAA
Found at i:1800 original size:29 final size:30
Alignment explanation
Indices: 1745--1801 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
1735 TTAAGAAGAA
*
1745 TATGTCATTTTTAAAAAATAATTAGGGGTT
1 TATGTCAATTTTAAAAAATAATTAGGGGTT
*
1775 TATGTCAATTTT-AAAAATATTTAGGGG
1 TATGTCAATTTTAAAAAATAATTAGGGG
1802 AATAAGTCGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.37, C:0.04, G:0.18, T:0.42
Consensus pattern (30 bp):
TATGTCAATTTTAAAAAATAATTAGGGGTT
Found at i:1815 original size:29 final size:30
Alignment explanation
Indices: 1742--1815 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 30
1732 TTTTTAAGAA
1742 GAATATGTCATTTTTAAAAAATAATTAGGG
1 GAATATGTCATTTTTAAAAAATAATTAGGG
** * *
1772 GTTTATGTCAATTTT-AAAAATATTTAGGG
1 GAATATGTCATTTTTAAAAAATAATTAGGG
* *
1801 GAATAAGTCGTTTTT
1 GAATATGTCATTTTT
1816 GAGAAAATTG
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
29 23 0.66
30 12 0.34
ACGTcount: A:0.36, C:0.04, G:0.18, T:0.42
Consensus pattern (30 bp):
GAATATGTCATTTTTAAAAAATAATTAGGG
Found at i:1946 original size:4 final size:4
Alignment explanation
Indices: 1937--2082 Score: 166
Period size: 4 Copynumber: 36.0 Consensus size: 4
1927 TTAGAAATAT
* * * *
1937 TTTA TTTA TTTA TTTA TTTTA TTTA ATTA ATTA ATTA TTTT TTTA TTTA
1 TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * *
1986 TTTA ATTA TTTA CTTA TTTTA TTTA TTTA TTTA TTTA TTTA CTTA TTTA
1 TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * * *
2035 CTTA GTTA TTTA TTTA TTTA CTTA TTTA CTTA CTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
2083 CATTATAAAA
Statistics
Matches: 123, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
4 116 0.94
5 7 0.06
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.68
Consensus pattern (4 bp):
TTTA
Found at i:4285 original size:9 final size:9
Alignment explanation
Indices: 4261--4298 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
4251 GATTGTGTAT
4261 TTGAGAGAG
1 TTGAGAGAG
4270 TTTGAGAGAG
1 -TTGAGAGAG
4280 TTGAGAGAG
1 TTGAGAGAG
*
4289 TTTAGAGAG
1 TTGAGAGAG
4298 T
1 T
4299 ATAGTGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
9 18 0.67
10 9 0.33
ACGTcount: A:0.32, C:0.00, G:0.39, T:0.29
Consensus pattern (9 bp):
TTGAGAGAG
Found at i:4285 original size:19 final size:18
Alignment explanation
Indices: 4261--4298 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 18
4251 GATTGTGTAT
4261 TTGAGAGAGTTTGAGAGAG
1 TTGAGAGAGTTT-AGAGAG
4280 TTGAGAGAGTTTAGAGAG
1 TTGAGAGAGTTTAGAGAG
4298 T
1 T
4299 ATAGTGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.32, C:0.00, G:0.39, T:0.29
Consensus pattern (18 bp):
TTGAGAGAGTTTAGAGAG
Found at i:4982 original size:15 final size:15
Alignment explanation
Indices: 4962--5003 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
4952 ATTAATTGTG
*
4962 ATTAAGGTTTAATTA
1 ATTAAGGTTTAATGA
4977 ATTAAGGTTTAATGA
1 ATTAAGGTTTAATGA
*
4992 ATTAAGATTTAA
1 ATTAAGGTTTAA
5004 ACCAAGTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (15 bp):
ATTAAGGTTTAATGA
Found at i:7872 original size:20 final size:18
Alignment explanation
Indices: 7820--7873 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 18
7810 ATCCACAAGA
7820 TAATCATTAAATTAA-ATT
1 TAAT-ATTAAATTAATATT
7838 TAATATTAAGA-TAATCACTT
1 TAATATTAA-ATTAAT-A-TT
7858 TAATATTAAATTAATA
1 TAATATTAAATTAATA
7874 AATATTATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
17 8 0.26
18 5 0.16
19 3 0.10
20 15 0.48
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.43
Consensus pattern (18 bp):
TAATATTAAATTAATATT
Found at i:8760 original size:21 final size:21
Alignment explanation
Indices: 8736--8776 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
8726 TTTTGGATAT
*
8736 AAACTAGCAAAGAAAATTGTA
1 AAACCAGCAAAGAAAATTGTA
* *
8757 AAACCATCAAAGCAAATTGT
1 AAACCAGCAAAGAAAATTGT
8777 GCCTAAATGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.54, C:0.15, G:0.12, T:0.20
Consensus pattern (21 bp):
AAACCAGCAAAGAAAATTGTA
Found at i:14193 original size:58 final size:58
Alignment explanation
Indices: 14060--14223 Score: 172
Period size: 58 Copynumber: 2.8 Consensus size: 58
14050 TTATAATATT
* * * * *
14060 TTATATTATAATTTTTATTAATTCATATTTTAATAATTATTATATTAAGAATGTTATTAAA
1 TTAT-TTATTATTTTTATTAAAT-ATA-TTTAATAATAATTATATTAAGAATATGATTAAA
* * *
14121 TTATATATTA-TTTTATTAAATGGTATTTAATAATAATTATGTTAA-AATATGATTAAA
1 TTATTTATTATTTTTATTAAAT-ATATTTAATAATAATTATATTAAGAATATGATTAAA
*
14178 TTATTTATTATTTTTAATAAAATATATTTAATAATAATGT-TATTAA
1 TTATTTATTATTTTT-ATTAAATATATTTAATAATAAT-TATATTAA
14224 AATTTAATAA
Statistics
Matches: 87, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
57 19 0.22
58 41 0.47
59 19 0.22
60 4 0.05
61 4 0.05
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (58 bp):
TTATTTATTATTTTTATTAAATATATTTAATAATAATTATATTAAGAATATGATTAAA
Found at i:14415 original size:16 final size:16
Alignment explanation
Indices: 14394--14460 Score: 82
Period size: 16 Copynumber: 4.2 Consensus size: 16
14384 TGAATTACTG
14394 ATTACAACTCTATTCC
1 ATTACAACTCTATTCC
*
14410 ATTACAACTCTGTTCC
1 ATTACAACTCTATTCC
* * *
14426 ATTATATCTCTATTAC
1 ATTACAACTCTATTCC
14442 ATTACAAC-CTTATTCC
1 ATTACAACTC-TATTCC
14458 ATT
1 ATT
14461 CTAGTAAACC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
15 1 0.02
16 41 0.98
ACGTcount: A:0.30, C:0.27, G:0.01, T:0.42
Consensus pattern (16 bp):
ATTACAACTCTATTCC
Found at i:17647 original size:24 final size:24
Alignment explanation
Indices: 17619--17669 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
17609 AGAAATAATC
* *
17619 TTTCAGTTAAACTCTTTTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
17643 TTTCAATTAAACTCTATTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
17667 TTT
1 TTT
17670 GAGTCAGACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.12, G:0.06, T:0.59
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTATTTG
Found at i:21536 original size:22 final size:22
Alignment explanation
Indices: 21486--21536 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 22
21476 TAATTGCTTA
*
21486 AAAATATTTAAAATTTATATATC
1 AAAATA-TTAAAATTTATATAAC
*
21509 -ATATATTAAAATATTA-ATAAC
1 AAAATATTAAAAT-TTATATAAC
21530 AAAATAT
1 AAAATAT
21537 AATAAATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAATATTAAAATTTATATAAC
Found at i:22584 original size:20 final size:20
Alignment explanation
Indices: 22555--22594 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
22545 ACTGATAGCA
*
22555 GATTGGGGGGACCAACGTTG
1 GATTGAGGGGACCAACGTTG
22575 GATTGAGGGGACCAACGTTG
1 GATTGAGGGGACCAACGTTG
22595 AGGAACGTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.15, G:0.42, T:0.20
Consensus pattern (20 bp):
GATTGAGGGGACCAACGTTG
Found at i:26942 original size:34 final size:34
Alignment explanation
Indices: 26904--26968 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
26894 GATACGTATT
26904 GGGCTAAAATATCAACAAACATAAAAGGGCGGCC
1 GGGCTAAAATATCAACAAACATAAAAGGGCGGCC
***
26938 GGGCTAAAATATCCGTAAACATAAAAGGGCG
1 GGGCTAAAATATCAACAAACATAAAAGGGCG
26969 ACTGAGACTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.43, C:0.18, G:0.25, T:0.14
Consensus pattern (34 bp):
GGGCTAAAATATCAACAAACATAAAAGGGCGGCC
Found at i:27384 original size:39 final size:39
Alignment explanation
Indices: 27330--27408 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
27320 AATATGCCTT
*
27330 AAAGTTTCCAAAAAATCTATTTTTCCGACAATCCCCCAC
1 AAAGTTTCCAAAAAATCTATTTTTCCAACAATCCCCCAC
27369 AAAGTTTCCAAAAAATCTATTTTTCCAACAATCCCCCAC
1 AAAGTTTCCAAAAAATCTATTTTTCCAACAATCCCCCAC
27408 A
1 A
27409 TGAATGAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.38, C:0.30, G:0.04, T:0.28
Consensus pattern (39 bp):
AAAGTTTCCAAAAAATCTATTTTTCCAACAATCCCCCAC
Found at i:32505 original size:17 final size:18
Alignment explanation
Indices: 32483--32519 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
32473 GGCCTATAAC
*
32483 AATATAAACATG-AATTA
1 AATATAAACAAGCAATTA
32500 AATATAAACAAGCAATTA
1 AATATAAACAAGCAATTA
32518 AA
1 AA
32520 CACAATCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.24
Consensus pattern (18 bp):
AATATAAACAAGCAATTA
Done.