Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011555.1 Kokia drynarioides strain JFW-HI SEQ_126543, 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: 135577
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Warning! 52 characters in sequence are not A, C, G, or T
Found at i:7940 original size:26 final size:26
Alignment explanation
Indices: 7903--7976 Score: 105
Period size: 26 Copynumber: 2.8 Consensus size: 26
7893 CAATAGCGTG
* *
7903 AAGCCTACTAGGCACATA-CCATGAGC
1 AAGCCTATTAGGCACATAGCC-TGACC
*
7929 AAGCCTATTAGGGACATAGCCTGACC
1 AAGCCTATTAGGCACATAGCCTGACC
7955 AAGCCTATTAGGCACATAGCCT
1 AAGCCTATTAGGCACATAGCCT
7977 AAATACATCG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 41 0.95
27 2 0.05
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.19
Consensus pattern (26 bp):
AAGCCTATTAGGCACATAGCCTGACC
Found at i:22348 original size:23 final size:25
Alignment explanation
Indices: 22322--22367 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
22312 GCAATGAGGA
*
22322 CTTAAATTG-CAATTA-ACCATAGG
1 CTTAAAATGACAATTAGACCATAGG
22345 CTTAAAATGACAATTAGACCATA
1 CTTAAAATGACAATTAGACCATA
22368 ATAAAATGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 8 0.40
24 6 0.30
25 6 0.30
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.28
Consensus pattern (25 bp):
CTTAAAATGACAATTAGACCATAGG
Found at i:46680 original size:31 final size:29
Alignment explanation
Indices: 46642--46717 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 29
46632 CACTCACGAA
46642 TTTTTTCTTTGTTTGTTTCTACTCGTCTCTT
1 TTTTTTCTTT-TTT-TTTCTACTCGTCTCTT
* **
46673 TTTTTTCTTTTTTTTTTTTNTCGTCTCTT
1 TTTTTTCTTTTTTTTTCTACTCGTCTCTT
46702 TTTTTTCTTTTTTTTT
1 TTTTTTCTTTTTTTTT
46718 TTGGATCTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
29 29 0.69
30 3 0.07
31 10 0.24
ACGTcount: A:0.01, C:0.14, G:0.05, T:0.78
Consensus pattern (29 bp):
TTTTTTCTTTTTTTTTCTACTCGTCTCTT
Found at i:46730 original size:29 final size:29
Alignment explanation
Indices: 46642--46735 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 29
46632 CACTCACGAA
* *
46642 TTTTTTCTTTGTTTGTTTCT-ACTCGTCTCTT
1 TTTTTTCTTT-TTT-TTTTTGA-TCGTATCTT
** *
46673 TTTTTTCTTTTTTTTTTTTNTCGTCTCTT
1 TTTTTTCTTTTTTTTTTTGATCGTATCTT
46702 TTTTTTCTTTTTTTTTTTGGATC-TATCTT
1 TTTTTTCTTTTTTTTTTT-GATCGTATCTT
*
46731 GTTTT
1 TTTTT
46736 CATAATTCTG
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
29 40 0.73
30 5 0.09
31 10 0.18
ACGTcount: A:0.03, C:0.14, G:0.07, T:0.74
Consensus pattern (29 bp):
TTTTTTCTTTTTTTTTTTGATCGTATCTT
Found at i:49134 original size:21 final size:21
Alignment explanation
Indices: 49106--49145 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
49096 AACCTCATCA
49106 ATTTCA-TTATGGCACGACAC
1 ATTTCATTTATGGCACGACAC
*
49126 ATTTACATTTATGTCACGAC
1 ATTT-CATTTATGGCACGAC
49146 GTCGTCCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 2 0.12
22 11 0.65
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (21 bp):
ATTTCATTTATGGCACGACAC
Found at i:51887 original size:37 final size:37
Alignment explanation
Indices: 51833--51907 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
51823 GGTGTTCACG
*
51833 AATGGGAAATACCAATTTTGGGTTAATTGCCACCTAA
1 AATGGGAAATACCAATTTTGGGTTAATTACCACCTAA
*
51870 AATGGGAAATACTAATTTTGGGTTAATTACCACCTAA
1 AATGGGAAATACCAATTTTGGGTTAATTACCACCTAA
51907 A
1 A
51908 TGACTTTCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (37 bp):
AATGGGAAATACCAATTTTGGGTTAATTACCACCTAA
Found at i:72981 original size:26 final size:26
Alignment explanation
Indices: 72949--73001 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
72939 TTAGATGTGC
*
72949 TCATGTAGCGACAACTCTGGACATGT
1 TCATGTAGCGACAACTCTAGACATGT
*
72975 TCATGTAGTGACAACTCTAGACATGT
1 TCATGTAGCGACAACTCTAGACATGT
73001 T
1 T
73002 AATGCAGTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (26 bp):
TCATGTAGCGACAACTCTAGACATGT
Found at i:73010 original size:26 final size:26
Alignment explanation
Indices: 72958--73010 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
72948 CTCATGTAGC
* * *
72958 GACAACTCTGGACATGTTCATGTAGT
1 GACAACTCTAGACATGTTAATGCAGT
72984 GACAACTCTAGACATGTTAATGCAGT
1 GACAACTCTAGACATGTTAATGCAGT
73010 G
1 G
73011 GCAATAGTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (26 bp):
GACAACTCTAGACATGTTAATGCAGT
Found at i:85066 original size:17 final size:18
Alignment explanation
Indices: 85044--85080 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
85034 GGCCTATAAC
*
85044 AATATAAACATG-AATTA
1 AATATAAACAAGCAATTA
85061 AATATAAACAAGCAATTA
1 AATATAAACAAGCAATTA
85079 AA
1 AA
85081 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
Found at i:88095 original size:21 final size:21
Alignment explanation
Indices: 88071--88110 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
88061 TTGAATTATG
88071 TTTAATATTT-TGTATGAGTTA
1 TTTAA-ATTTATGTATGAGTTA
88092 TTTAAATTTATGTATGAGT
1 TTTAAATTTATGTATGAGT
88111 CGAGTTGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (21 bp):
TTTAAATTTATGTATGAGTTA
Found at i:93755 original size:18 final size:17
Alignment explanation
Indices: 93732--93772 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
93722 TTTTGAGAGC
93732 ATAAAATAAAAAGATAAA
1 ATAAAATAAAAAG-TAAA
*
93750 ATAAAATATAAAGTAAA
1 ATAAAATAAAAAGTAAA
*
93767 AGAAAA
1 ATAAAA
93773 ACTTGAGATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (17 bp):
ATAAAATAAAAAGTAAA
Found at i:102950 original size:21 final size:21
Alignment explanation
Indices: 102921--102963 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
102911 GGTTTAAAGA
* * *
102921 ACAAGAAGAGGAAGCGCAAGG
1 ACAAAAAGAAGAAGCACAAGG
102942 ACAAAAAGAAGAAGCACAAGG
1 ACAAAAAGAAGAAGCACAAGG
102963 A
1 A
102964 GGAAGGAGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.56, C:0.14, G:0.30, T:0.00
Consensus pattern (21 bp):
ACAAAAAGAAGAAGCACAAGG
Found at i:107677 original size:19 final size:20
Alignment explanation
Indices: 107655--107693 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
107645 ATCAAAAAGT
*
107655 CGAGAAAAA-AAGAAAAATA
1 CGAGAAAAATAAAAAAAATA
107674 CGAGAAAAATAAAAAAAATA
1 CGAGAAAAATAAAAAAAATA
107694 TTCTGTGGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.74, C:0.05, G:0.13, T:0.08
Consensus pattern (20 bp):
CGAGAAAAATAAAAAAAATA
Found at i:107682 original size:20 final size:19
Alignment explanation
Indices: 107655--107693 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
107645 ATCAAAAAGT
107655 CGAGAAAA-AAAGAAAAATA
1 CGAGAAAATAAA-AAAAATA
107674 CGAGAAAAATAAAAAAAATA
1 CGAG-AAAATAAAAAAAATA
107694 TTCTGTGGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 11 0.61
21 3 0.17
ACGTcount: A:0.74, C:0.05, G:0.13, T:0.08
Consensus pattern (19 bp):
CGAGAAAATAAAAAAAATA
Found at i:110265 original size:18 final size:18
Alignment explanation
Indices: 110242--110280 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
110232 TTTAGATTAG
110242 TTAGAGTTCTAGTTTA-AT
1 TTAGAGTTCTA-TTTATAT
*
110260 TTAGAGTTTTATTTATAT
1 TTAGAGTTCTATTTATAT
110278 TTA
1 TTA
110281 TTTAGTTTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.28, C:0.03, G:0.13, T:0.56
Consensus pattern (18 bp):
TTAGAGTTCTATTTATAT
Found at i:118583 original size:24 final size:24
Alignment explanation
Indices: 118556--118731 Score: 237
Period size: 24 Copynumber: 7.4 Consensus size: 24
118546 TAGCCCACAT
*
118556 GAGCCCAGAATGATTAGCTCTTAC
1 GAGCCCAGAATGGTTAGCTCTTAC
118580 GAGCCCAGAATGGTTAGCTCTTAC
1 GAGCCCAGAATGGTTAGCTCTTAC
* *
118604 GAGCCCAGAATGATTAGCTCTTAT
1 GAGCCCAGAATGGTTAGCTCTTAC
**
118628 GA-CTTAGAATGGTTAGCTCTTAC
1 GAGCCCAGAATGGTTAGCTCTTAC
* * * *
118651 TAGCCTAGAATGATTAGCTCTTAT
1 GAGCCCAGAATGGTTAGCTCTTAC
*
118675 AAGCCCAGAATGGTTAGCTCTTAC
1 GAGCCCAGAATGGTTAGCTCTTAC
*
118699 GAGCCCAGAATGGTTACCTCTTAC
1 GAGCCCAGAATGGTTAGCTCTTAC
*
118723 AAGCCCAGA
1 GAGCCCAGA
118732 CAAAGTTTAA
Statistics
Matches: 133, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
23 18 0.14
24 115 0.86
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.27
Consensus pattern (24 bp):
GAGCCCAGAATGGTTAGCTCTTAC
Found at i:123108 original size:47 final size:47
Alignment explanation
Indices: 123020--123147 Score: 123
Period size: 47 Copynumber: 2.7 Consensus size: 47
123010 TAGCCCACAC
* * * ** *
123020 GAGCCCAGAATGATCAGCTCTTACGAGCCCGAAATGATTAGCTCTTA-
1 GAGCCCAGAATGGTTAACTCTTACGAGCTAG-AATGATTAGCTCATAT
*
123067 GAGCCCAGAATGGTTAACTCTTACGAGCTTAGAATGGTTAGCTCATAT
1 GAGCCCAGAATGGTTAACTCTTACGAGC-TAGAATGATTAGCTCATAT
** * *
123115 GAGCATAGAATGGTTACCTCTTATGAGCCTAGA
1 GAGCCCAGAATGGTTAACTCTTACGAG-CTAGA
123148 CAGAGTTTAA
Statistics
Matches: 67, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
47 38 0.57
48 28 0.42
49 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.27
Consensus pattern (47 bp):
GAGCCCAGAATGGTTAACTCTTACGAGCTAGAATGATTAGCTCATAT
Found at i:123147 original size:24 final size:24
Alignment explanation
Indices: 123020--123147 Score: 116
Period size: 24 Copynumber: 5.4 Consensus size: 24
123010 TAGCCCACAC
* * * *
123020 GAGCCCAGAATGATCAGCTCTTAC
1 GAGCCTAGAATGGTTAGCTCTTAT
* *
123044 GAGCC-CGAAATGATTAGCTCTTA-
1 GAGCCTAG-AATGGTTAGCTCTTAT
* * *
123067 GAGCCCAGAATGGTTAACTCTTAC
1 GAGCCTAGAATGGTTAGCTCTTAT
* *
123091 GAGCTTAGAATGGTTAGCTCATAT
1 GAGCCTAGAATGGTTAGCTCTTAT
* *
123115 GAGCATAGAATGGTTACCTCTTAT
1 GAGCCTAGAATGGTTAGCTCTTAT
123139 GAGCCTAGA
1 GAGCCTAGA
123148 CAGAGTTTAA
Statistics
Matches: 87, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
23 19 0.22
24 68 0.78
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.27
Consensus pattern (24 bp):
GAGCCTAGAATGGTTAGCTCTTAT
Found at i:130174 original size:19 final size:19
Alignment explanation
Indices: 130150--130188 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
130140 AAGTTAAGAA
130150 AGTAAAACTAATTGCAACT
1 AGTAAAACTAATTGCAACT
130169 AGTAAAACTAATTGCAACT
1 AGTAAAACTAATTGCAACT
130188 A
1 A
130189 CAAAAGTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.15, G:0.10, T:0.26
Consensus pattern (19 bp):
AGTAAAACTAATTGCAACT
Found at i:133861 original size:48 final size:48
Alignment explanation
Indices: 133717--133846 Score: 197
Period size: 48 Copynumber: 2.7 Consensus size: 48
133707 ATTATGCTTC
* *
133717 ATTAAGTGTTTTGTTGGTTAAATGCATCTTTGTTTAATAATCTACATC
1 ATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATCTACATT
* * *
133765 ATTAAGTGTTCTGTCTGTTAAATGCATCTTTGTTTAGTAATCTACATT
1 ATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATCTACATT
* *
133813 ATTAAATGTTTTGTTTGTTAAATGCATCTCTGTT
1 ATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTT
133847 AAATGTCTTG
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 73 1.00
ACGTcount: A:0.25, C:0.11, G:0.15, T:0.49
Consensus pattern (48 bp):
ATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATCTACATT
Done.