Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001346.1 Kokia drynarioides strain JFW-HI SEQ_112793, 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: 29214
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:6124 original size:19 final size:19
Alignment explanation
Indices: 6092--6142 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
6082 TAGTCATTTG
* *
6092 AAAAAGAAACAAAATGAGAA
1 AAAAAGAAAGAAAAAGA-AA
6112 AAAAAG-AAGAAAAAGAAA
1 AAAAAGAAAGAAAAAGAAA
6130 AAAAAGAAAGAAA
1 AAAAAGAAAGAAA
6143 TTTTTTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 8 0.29
19 14 0.50
20 6 0.21
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (19 bp):
AAAAAGAAAGAAAAAGAAA
Found at i:8016 original size:26 final size:28
Alignment explanation
Indices: 7987--8047 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
7977 TGTAACATTT
*
7987 TTATGTTATAAA-ATT-TAACATATAGA
1 TTATGTTATAAAGATTATAACACATAGA
** *
8013 TTATGACATAAAGATTATGACACATAGA
1 TTATGTTATAAAGATTATAACACATAGA
8041 TTATGTT
1 TTATGTT
8048 TGAATGTAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
26 10 0.37
27 3 0.11
28 14 0.52
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (28 bp):
TTATGTTATAAAGATTATAACACATAGA
Found at i:8021 original size:14 final size:14
Alignment explanation
Indices: 8004--8045 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
7994 ATAAAATTTA
8004 ACATATAGATTATG
1 ACATATAGATTATG
*
8018 ACATAAAGATTATG
1 ACATATAGATTATG
*
8032 ACACATAGATTATG
1 ACATATAGATTATG
8046 TTTGAATGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (14 bp):
ACATATAGATTATG
Found at i:8485 original size:57 final size:57
Alignment explanation
Indices: 8333--8487 Score: 179
Period size: 57 Copynumber: 2.7 Consensus size: 57
8323 TATATTATGA
* * * *
8333 TTTTTATT-AATTCATATTTTAATAATAATTATATTAAGAATGTTATTAGATTATATACT
1 TTTTTATTAAATT-ATA-TTTAATAATAATTATATTAA-AATATGATTAAATTATATAAT
* * * * *
8392 ATTTTATTAAATTGTATTTAATAATAATTATGTTAAAATATGCTTAAATTATTTAAT
1 TTTTTATTAAATTATATTTAATAATAATTATATTAAAATATGATTAAATTATATAAT
8449 TTTTTATTAAATTATATTTAATAATAATCT-TATTAAAAT
1 TTTTTATTAAATTATATTTAATAATAAT-TATATTAAAAT
8488 TTAATAACAA
Statistics
Matches: 82, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
57 49 0.60
58 20 0.24
59 9 0.11
60 4 0.05
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.52
Consensus pattern (57 bp):
TTTTTATTAAATTATATTTAATAATAATTATATTAAAATATGATTAAATTATATAAT
Found at i:8624 original size:16 final size:16
Alignment explanation
Indices: 8603--8656 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
8593 TGAAATATTG
8603 ATTACAGCTCTATT-C
1 ATTACAGCTCTATTAC
*
8618 TATTACAACTCTATTAC
1 -ATTACAGCTCTATTAC
*
8635 ATTACAGTTCTATTAC
1 ATTACAGCTCTATTAC
8651 ATTACA
1 ATTACA
8657 ACGAATCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
16 33 0.97
17 1 0.03
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.41
Consensus pattern (16 bp):
ATTACAGCTCTATTAC
Found at i:8928 original size:20 final size:20
Alignment explanation
Indices: 8899--8937 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
8889 ACTCAATTTG
*
8899 AAAAATTTTCAAATCGAGTC
1 AAAAAATTTCAAATCGAGTC
8919 AAAAAATTTCAAATCGAGT
1 AAAAAATTTCAAATCGAGT
8938 AAGTCGAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.13, G:0.10, T:0.28
Consensus pattern (20 bp):
AAAAAATTTCAAATCGAGTC
Found at i:9981 original size:14 final size:15
Alignment explanation
Indices: 9953--9983 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
9943 AACATATCAA
9953 ATTTCTATGTATTTC
1 ATTTCTATGTATTTC
9968 ATTTCTAT-TATTTC
1 ATTTCTATGTATTTC
9982 AT
1 AT
9984 CCACATATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.23, C:0.13, G:0.03, T:0.61
Consensus pattern (15 bp):
ATTTCTATGTATTTC
Found at i:10557 original size:15 final size:14
Alignment explanation
Indices: 10525--10551 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
10515 CAAAAAAAAA
10525 AAAAATCATTTTCC
1 AAAAATCATTTTCC
10539 AAAAATCATTTTC
1 AAAAATCATTTTC
10552 TGAAAACTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.37
Consensus pattern (14 bp):
AAAAATCATTTTCC
Found at i:11302 original size:18 final size:19
Alignment explanation
Indices: 11261--11302 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
11251 TGGACAAACC
*
11261 AAATTTTAGATTTTAATTT
1 AAATTTTAGATTTAAATTT
* *
11280 TAATTTTA-CTTTAAATTT
1 AAATTTTAGATTTAAATTT
11298 AAATT
1 AAATT
11303 ATAAATCCAA
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (19 bp):
AAATTTTAGATTTAAATTT
Found at i:12639 original size:32 final size:29
Alignment explanation
Indices: 12552--12664 Score: 131
Period size: 32 Copynumber: 3.8 Consensus size: 29
12542 TTTTCAAAAA
* *
12552 TTTGACCCCTAAACTTCCTAAAATCTCAT
1 TTTGACCCCTAAACTTCCAAAAATCACAT
*
12581 TTTGA-CCC-AAACTTTCCTAAAATCACAT
1 TTTGACCCCTAAAC-TTCCAAAAATCACAT
*
12609 TTTAACCCCTAAACTTTTCCAAAAAATCACAT
1 TTTGACCCCTAAAC--TTCC-AAAAATCACAT
*
12641 TTTGGCCCCTAAACTTCCAAAAAT
1 TTTGACCCCTAAACTTCCAAAAAT
12665 TAAAATTTTC
Statistics
Matches: 74, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
27 4 0.05
28 21 0.28
29 14 0.19
30 8 0.11
31 5 0.07
32 22 0.30
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32
Consensus pattern (29 bp):
TTTGACCCCTAAACTTCCAAAAATCACAT
Found at i:12673 original size:30 final size:29
Alignment explanation
Indices: 12614--12721 Score: 92
Period size: 29 Copynumber: 3.6 Consensus size: 29
12604 CACATTTTAA
* * *
12614 CCCCTAAACTTTTCCAAAAAATCACATTTTGG
1 CCCCTAAAC--TTCCAAAAATTAAAATTTT-G
12646 CCCCTAAACTTCCAAAAATTAAAATTTT-
1 CCCCTAAACTTCCAAAAATTAAAATTTTG
* * * *
12674 CCCTTGAATCTTTCAAAAATTATAATTTTG
1 CCCCT-AAACTTCCAAAAATTAAAATTTTG
* *
12704 CCCCCAAACTTCTAAAAA
1 CCCCTAAACTTCCAAAAA
12722 AAAATCACAT
Statistics
Matches: 62, Mismatches: 12, Indels: 7
0.77 0.15 0.09
Matches are distributed among these distances:
28 4 0.06
29 30 0.48
30 19 0.31
32 9 0.15
ACGTcount: A:0.38, C:0.26, G:0.04, T:0.32
Consensus pattern (29 bp):
CCCCTAAACTTCCAAAAATTAAAATTTTG
Found at i:12720 original size:29 final size:30
Alignment explanation
Indices: 12688--12746 Score: 82
Period size: 32 Copynumber: 1.9 Consensus size: 30
12678 TGAATCTTTC
12688 AAAAATTATAATTTTGCCCCCAAACTTCTA
1 AAAAATTATAATTTTGCCCCCAAACTTCTA
**
12718 AAAAAAAATCACATTTTGCCCCCAAACTT
1 AAAAATTAT-A-ATTTTGCCCCCAAACTT
12747 TTCCAAAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 7 0.28
31 1 0.04
32 17 0.68
ACGTcount: A:0.42, C:0.25, G:0.03, T:0.29
Consensus pattern (30 bp):
AAAAATTATAATTTTGCCCCCAAACTTCTA
Found at i:12791 original size:91 final size:91
Alignment explanation
Indices: 12607--12802 Score: 213
Period size: 91 Copynumber: 2.2 Consensus size: 91
12597 CTAAAATCAC
*** *
12607 ATTTTAACCCCTAAACTT-TTCCAAAAAATCACATTTTGGCCCCTAAACTTCCAAAAATTAAAAT
1 ATTTTAACCCC-AAACTTCTAAAAAAAAATCACATTTTGGCCCCCAAACTTCCAAAAATTAAAAT
*
12671 TTTCCCTTGAATCTTTCAAAAATTATA
65 TTTACCTTGAATCTTTCAAAAATTATA
** * *
12698 ATTTTGCCCCCAAACTTCTAAAAAAAAATCACATTTT-GCCCCCAAACTTTTCCAAAAGTT-CAA
1 ATTTTAACCCCAAACTTCTAAAAAAAAATCACATTTTGGCCCCCAAAC--TTCCAAAAATTAAAA
* *
12761 TTTTGACCTTGAAT-TTTCCGAAAGTT-TA
64 TTTT-ACCTTGAATCTTT-CAAAAATTATA
12789 ATTTTAACCCCAAA
1 ATTTTAACCCCAAA
12803 ATTTCCAAAA
Statistics
Matches: 87, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
90 15 0.17
91 48 0.55
92 24 0.28
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (91 bp):
ATTTTAACCCCAAACTTCTAAAAAAAAATCACATTTTGGCCCCCAAACTTCCAAAAATTAAAATT
TTACCTTGAATCTTTCAAAAATTATA
Found at i:12807 original size:29 final size:29
Alignment explanation
Indices: 12775--12843 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
12765 GACCTTGAAT
**
12775 TTTCCGAAAGTTTAATTTTAACCCCAAAA
1 TTTCCGAAAGCCTAATTTTAACCCCAAAA
* * *
12804 TTTCCAAAAAGCCTAATTTTGACCCTAAAA
1 TTTCC-GAAAGCCTAATTTTAACCCCAAAA
12834 TTTCTCGAAA
1 TTTC-CGAAA
12844 ATTACGTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
29 5 0.16
30 26 0.81
31 1 0.03
ACGTcount: A:0.38, C:0.22, G:0.07, T:0.33
Consensus pattern (29 bp):
TTTCCGAAAGCCTAATTTTAACCCCAAAA
Found at i:21725 original size:25 final size:25
Alignment explanation
Indices: 21693--21745 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
21683 TGAATAATAT
21693 ATATTTAATAAAGTTACTTTATAAA
1 ATATTTAATAAAGTTACTTTATAAA
* * *
21718 ATATTTAATAGATTTATTTTATAAA
1 ATATTTAATAAAGTTACTTTATAAA
21743 ATA
1 ATA
21746 ATTGAAGTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (25 bp):
ATATTTAATAAAGTTACTTTATAAA
Found at i:21984 original size:20 final size:20
Alignment explanation
Indices: 21947--21984 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
21937 TAATATTTTA
*
21947 AAATATTTATTTTGAAACTC
1 AAATATTTATATTGAAACTC
21967 AAATATATTATATT-AAAC
1 AAATAT-TTATATTGAAAC
21985 CTAAAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (20 bp):
AAATATTTATATTGAAACTC
Found at i:21991 original size:21 final size:20
Alignment explanation
Indices: 21945--21991 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
21935 GTTAATATTT
*
21945 TAAAATATTTATTTTGAAAC
1 TAAAATATTTATATTGAAAC
*
21965 TCAAATATATTATATT-AAACC
1 TAAAATAT-TTATATTGAAA-C
21986 TAAAAT
1 TAAAAT
21992 TAAATGACAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (20 bp):
TAAAATATTTATATTGAAAC
Found at i:24473 original size:24 final size:24
Alignment explanation
Indices: 24428--24474 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
24418 ATTTAGTAGT
*
24428 ATAATATATTTAGCATTTATTAGC
1 ATAATATATTTAGCATTGATTAGC
* *
24452 ATAATATATTTTGTATTGATTAG
1 ATAATATATTTAGCATTGATTAG
24475 AATTAGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.49
Consensus pattern (24 bp):
ATAATATATTTAGCATTGATTAGC
Found at i:28884 original size:24 final size:24
Alignment explanation
Indices: 28839--28885 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
28829 ATTTAGTAGT
* *
28839 ATAATTTATTTAGAATTTATTAGC
1 ATAATATATTTAGAATTGATTAGC
* *
28863 ATAATATATTTTGTATTGATTAG
1 ATAATATATTTAGAATTGATTAG
28886 AATTAGGCTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.51
Consensus pattern (24 bp):
ATAATATATTTAGAATTGATTAGC
Done.