Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011120.1 Kokia drynarioides strain JFW-HI SEQ_126093, 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: 58444
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 40 characters in sequence are not A, C, G, or T
Found at i:7801 original size:21 final size:22
Alignment explanation
Indices: 7776--7816 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
7766 AGTATAAAAA
7776 CTTTTTTAA-ATTTATTTTAAT
1 CTTTTTTAATATTTATTTTAAT
*
7797 CTTTTTTAATATTTTTTTTA
1 CTTTTTTAATATTTATTTTA
7817 TATATTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (22 bp):
CTTTTTTAATATTTATTTTAAT
Found at i:8184 original size:85 final size:85
Alignment explanation
Indices: 8076--8233 Score: 219
Period size: 85 Copynumber: 1.9 Consensus size: 85
8066 AAATTTTTTC
* * * *
8076 AAAAAAAGCAATTAAGCTTCTGCTTTTATTTTGCACTCATTTTGATATTTAAACTTTCAAAATGC
1 AAAAAAAGCAATTAAGCTCCTGCTTTTATTTTGCACTCAATTGGATACTTAAACTTTCAAAATGC
8141 ATAAAAAAATACCTTCAAAA
66 ATAAAAAAATACCTTCAAAA
* * *
8161 AAAAAAAGCAATTAAG-TCCCTGCTTTTGTTTTGCACTCAATTGGGTACTTGAACTTTCAAAATG
1 AAAAAAAGCAATTAAGCT-CCTGCTTTTATTTTGCACTCAATTGGATACTTAAACTTTCAAAATG
* *
8225 TATCAAAAA
65 CATAAAAAA
8234 GGCCCTCAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
84 1 0.02
85 62 0.98
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (85 bp):
AAAAAAAGCAATTAAGCTCCTGCTTTTATTTTGCACTCAATTGGATACTTAAACTTTCAAAATGC
ATAAAAAAATACCTTCAAAA
Found at i:9052 original size:18 final size:18
Alignment explanation
Indices: 9026--9061 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
9016 AATAATTTGA
*
9026 CGATTGATTAACCGAATT
1 CGATCGATTAACCGAATT
9044 CGATCGATTAACCGAATT
1 CGATCGATTAACCGAATT
9062 AATTAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (18 bp):
CGATCGATTAACCGAATT
Found at i:11466 original size:7 final size:7
Alignment explanation
Indices: 11456--11481 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
11446 AAATGGGAGA
11456 TGGTGGG
1 TGGTGGG
11463 TGGTGGG
1 TGGTGGG
11470 TGGTGGG
1 TGGTGGG
11477 TGGTG
1 TGGTG
11482 CACAATGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.69, T:0.31
Consensus pattern (7 bp):
TGGTGGG
Found at i:12041 original size:14 final size:14
Alignment explanation
Indices: 12022--12052 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
12012 AGAATAAATC
12022 TTTAATTAAATAAA
1 TTTAATTAAATAAA
*
12036 TTTAATTAATTAAA
1 TTTAATTAAATAAA
12050 TTT
1 TTT
12053 TTAAACTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTAATTAAATAAA
Found at i:12119 original size:6 final size:6
Alignment explanation
Indices: 12108--12136 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
12098 ACACCTCTCT
12108 TCTTCA TCTTCA TCTTCA TCTTCA TCTTC
1 TCTTCA TCTTCA TCTTCA TCTTCA TCTTC
12137 TTCCTTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.14, C:0.34, G:0.00, T:0.52
Consensus pattern (6 bp):
TCTTCA
Found at i:20949 original size:33 final size:33
Alignment explanation
Indices: 20911--21021 Score: 132
Period size: 33 Copynumber: 3.4 Consensus size: 33
20901 TTACAGGGGT
20911 ATCCCTGCTACTTGACCTGCTTATAGGGGCATC
1 ATCCCTGCTACTTGACCTGCTTATAGGGGCATC
* * *
20944 GTCCCTGCTACTTGACCTGCTTATGGGGGTATC
1 ATCCCTGCTACTTGACCTGCTTATAGGGGCATC
* * * ** *
20977 ATCCCAGCTGCTTAATATGCTTATAGGGGGATC
1 ATCCCTGCTACTTGACCTGCTTATAGGGGCATC
*
21010 ATCACTGCTACT
1 ATCCCTGCTACT
21022 CGGCCTCCTT
Statistics
Matches: 64, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 64 1.00
ACGTcount: A:0.19, C:0.27, G:0.23, T:0.32
Consensus pattern (33 bp):
ATCCCTGCTACTTGACCTGCTTATAGGGGCATC
Found at i:33237 original size:26 final size:25
Alignment explanation
Indices: 33206--33263 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 25
33196 TTTGTTTATT
* *
33206 TTTAATTTTATTTATT-TTAAATAAA
1 TTTAATTTTAATTATTCTGAAAT-AA
33231 TTCTAATTTTAATTATTCTGAAATAA
1 TT-TAATTTTAATTATTCTGAAATAA
33257 TTTAATT
1 TTTAATT
33264 AAAATTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 7 0.24
26 17 0.59
27 5 0.17
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (25 bp):
TTTAATTTTAATTATTCTGAAATAA
Found at i:40615 original size:5 final size:6
Alignment explanation
Indices: 40598--40622 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
40588 ACACTGTTGC
40598 TCTTTT TCTTTT TCTTTT TCTTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT T
40623 TAAATTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TCTTTT
Found at i:51665 original size:62 final size:60
Alignment explanation
Indices: 51558--52079 Score: 451
Period size: 62 Copynumber: 8.6 Consensus size: 60
51548 GAGATTGATT
* *
51558 AACACCAAAAAAATTT-AAATTTTTTTATCTGTTAACAAGA-GGTGTCAGTCATTGCATGACC
1 AACACCAAAAAAATTTGAAATTTTTTTATCTG--AAAAAGAGGGTGTC-GCCATTGCATGACC
** * * * * * *
51619 AACATAAAAAAAATTTGTAATTTTTTTATTTGAGAAAAGAGAGTGTCGGCCATTGTATAAGC
1 AACACCAAAAAAATTTGAAATTTTTTTATCTGA-AAAAGAGGGTGTC-GCCATTGCATGACC
* ** * *
51681 AACACCAAAAAATTTTGAAAACTTTTTATCTGAAAAAGAGGGTGTCGACCATTGTATGGCC
1 AACACCAAAAAAATTTGAAATTTTTTTATCTGAAAAAGAGGGTGTCG-CCATTGCATGACC
* * * *
51742 AACACCAAAAAAATTTGCAATTTTTTTATCCGAAAAAAGAGGGTGTCGGTCATTGCATGGCC
1 AACACCAAAAAAATTTGAAATTTTTTTATCTG-AAAAAGAGGGTGTC-GCCATTGCATGACC
* **
51804 AACA-CAAAAAAATTTTGAAATTTTTTTTTCTGAAAAAG-GAATGTCGACCATTGCATGACC
1 AACACCAAAAAAA-TTTGAAATTTTTTTATCTGAAAAAGAGGGTGTCG-CCATTGCATGACC
* * * * *
51864 AACACC-CAAAAA---GTAATTTTTTTATCCGAGAAAAGAGGGTGTTGGCCATTGCATGGCC
1 AACACCAAAAAAATTTGAAATTTTTTTATCTGA-AAAAGAGGGTG-TCGCCATTGCATGACC
* * *
51922 AACA-CAAAAAAATTTTGAAATTTTTTTTTCTGAAAAAAAGGGTGTCGATCATTGCATGACC
1 AACACCAAAAAAA-TTTGAAATTTTTTTATCTGAAAAAGAGGGTGTCG-CCATTGCATGACC
* * * *
51983 AACACTC--AAAAA---GTAATTTTTTTATCTGAGAAAAGGGGGTGTCCGTCATTGCATGGCC
1 AACAC-CAAAAAAATTTGAAATTTTTTTATCTGA-AAAAGAGGGTGT-CGCCATTGCATGACC
* * *
52041 AACGCCAAAAAAATTTGAAAATTTTTTTTTCTAAAAAAG
1 AACACCAAAAAAATTTG-AAATTTTTTTATCTGAAAAAG
52080 GGCCCAAAAA
Statistics
Matches: 372, Mismatches: 61, Indels: 55
0.76 0.12 0.11
Matches are distributed among these distances:
56 14 0.04
57 22 0.06
58 50 0.13
59 10 0.03
60 29 0.08
61 113 0.30
62 119 0.32
63 15 0.04
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (60 bp):
AACACCAAAAAAATTTGAAATTTTTTTATCTGAAAAAGAGGGTGTCGCCATTGCATGACC
Found at i:51780 original size:123 final size:123
Alignment explanation
Indices: 51558--52079 Score: 572
Period size: 123 Copynumber: 4.3 Consensus size: 123
51548 GAGATTGATT
* *
51558 AACACCAAAAAAA-TTT-AAATTTTTTTATCTGTTAACAAGA-GGTGTC-AGTCATTGCATGACC
1 AACA-CAAAAAAATTTTGAAATTTTTTTATCTG--AAAAAGAGGGTGTCGA-CCATTGCATGACC
** ** * * *
51619 AACATAAAAAAAATTTGTAATTTTTTTATTTGAGAAAAGAGAGTGTCGGCCATTGTATAAG-C
62 AACACCAAAAAAATTTGTAATTTTTTTATCCGAGAAAAGAGGGTGTCGGCCATTGCAT-GGCC
* ** * *
51681 AACACCAAAAAATTTTGAAAACTTTTTATCTGAAAAAGAGGGTGTCGACCATTGTATGGCCAACA
1 AACACAAAAAAATTTTGAAATTTTTTTATCTGAAAAAGAGGGTGTCGACCATTGCATGACCAACA
* * *
51746 CCAAAAAAATTTGCAATTTTTTTATCCGAAAAAAGAGGGTGTCGGTCATTGCATGGCC
66 CCAAAAAAATTTGTAATTTTTTTATCCGAGAAAAGAGGGTGTCGGCCATTGCATGGCC
* **
51804 AACACAAAAAAATTTTGAAATTTTTTTTTCTGAAAAAG-GAATGTCGACCATTGCATGACCAACA
1 AACACAAAAAAATTTTGAAATTTTTTTATCTGAAAAAGAGGGTGTCGACCATTGCATGACCAACA
* *
51868 CC-CAAAAA---GTAATTTTTTTATCCGAGAAAAGAGGGTGTTGGCCATTGCATGGCC
66 CCAAAAAAATTTGTAATTTTTTTATCCGAGAAAAGAGGGTGTCGGCCATTGCATGGCC
* * *
51922 AACACAAAAAAATTTTGAAATTTTTTTTTCTGAAAAAAAGGGTGTCGATCATTGCATGACCAACA
1 AACACAAAAAAATTTTGAAATTTTTTTATCTGAAAAAGAGGGTGTCGACCATTGCATGACCAACA
* * * *
51987 CTC--AAAAA---GTAATTTTTTTATCTGAGAAAAGGGGGTGTCCGTCATTGCATGGCC
66 C-CAAAAAAATTTGTAATTTTTTTATCCGAGAAAAGAGGGTGTCGGCCATTGCATGGCC
* * *
52041 AACGCCAAAAAAA-TTTGAAAATTTTTTTTTCTAAAAAAG
1 AAC-ACAAAAAAATTTTG-AAATTTTTTTATCTGAAAAAG
52080 GGCCCAAAAA
Statistics
Matches: 348, Mismatches: 42, Indels: 21
0.85 0.10 0.05
Matches are distributed among these distances:
118 79 0.23
119 77 0.22
120 28 0.08
121 5 0.01
122 38 0.11
123 107 0.31
124 14 0.04
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (123 bp):
AACACAAAAAAATTTTGAAATTTTTTTATCTGAAAAAGAGGGTGTCGACCATTGCATGACCAACA
CCAAAAAAATTTGTAATTTTTTTATCCGAGAAAAGAGGGTGTCGGCCATTGCATGGCC
Found at i:52117 original size:96 final size:93
Alignment explanation
Indices: 51999--52172 Score: 233
Period size: 96 Copynumber: 1.8 Consensus size: 93
51989 CAAAAAGTAA
* * * * *
51999 TTTTTTTATCTGAGAAAAGGGGGTGTCCG-TCATTGCATGGCCAACGCCAAAAAAATTTGAAAAT
1 TTTTTTTATCCGAAAAAAGGGGGTATCGGCT-ATTGCATGGCCAACACCAAAAAAATTTG--AA-
52063 TTTTTTTTCTAAAAAAGGGCCCAAAAATACAT
62 TTTTTTTTCTAAAAAAGGGCCCAAAAATACAT
* *
52095 TTTTTTTATCCGAAAAAAGGGGGTATTGGCTATTGCATGGCCAACACCAAAAAATTTTGAATTTT
1 TTTTTTTATCCGAAAAAAGGGGGTATCGGCTATTGCATGGCCAACACCAAAAAAATTTGAATTTT
*
52160 TTTTCTCAAAAAG
66 TTTTCTAAAAAAG
52173 AGAGTGTCGA
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
93 16 0.23
94 2 0.03
96 50 0.72
97 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.33
Consensus pattern (93 bp):
TTTTTTTATCCGAAAAAAGGGGGTATCGGCTATTGCATGGCCAACACCAAAAAAATTTGAATTTT
TTTTCTAAAAAAGGGCCCAAAAATACAT
Found at i:52239 original size:59 final size:58
Alignment explanation
Indices: 52126--52319 Score: 171
Period size: 59 Copynumber: 3.3 Consensus size: 58
52116 GGTATTGGCT
* * * *
52126 ATTGCATGGCCAACACCAAAAAATTTTGAATTTTTTTTCTCAAAAAGAGAGTGTCGATC
1 ATTGCATGGTCAACACCAAAAAATTGT-AATTTTTTTTCACAAAAAGAGAGTGTCGACC
* * *
52185 ATTGCATGGTCAACACCAAAAAA-TGTAATTTTTTTATCAGATAAATAG-GGGTGTCGGCC
1 ATTGCATGGTCAACACCAAAAAATTGTAATTTTTTT-TCACA-AAA-AGAGAGTGTCGACC
** * * *
52244 ATTATATGGTCAACACAAAAAAATTGT-ATTTTTTATCTCACAAAAA-AGGGATGTCGGCC
1 ATTGCATGGTCAACACCAAAAAATTGTAATTTTTT-T-TCACAAAAAGAGAG-TGTCGACC
**
52303 ATTGCATGACCAACACC
1 ATTGCATGGTCAACACC
52320 TCAAAATTTT
Statistics
Matches: 111, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
57 9 0.08
58 9 0.08
59 83 0.75
60 10 0.09
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (58 bp):
ATTGCATGGTCAACACCAAAAAATTGTAATTTTTTTTCACAAAAAGAGAGTGTCGACC
Found at i:56537 original size:130 final size:130
Alignment explanation
Indices: 56375--56739 Score: 488
Period size: 130 Copynumber: 2.8 Consensus size: 130
56365 ATTTCTGAAG
* *
56375 TTTTTTTTATTGCACTT-AAATAAATAAAATAATAATGATTGAAAATATTGAATCGTATTAACTC
1 TTTTTTTTATTTCA-TTAAAATAAATAAAATAATAATGATTGAAAATATTGAATCGTGTTAACTC
* * *
56439 ACAATAAATTAAAACTCGAACTCAATTAATCTTATTAAAA-ATACCATTC-GATAGTTTTTATGT
65 ACAATAGATTAAAACTCGAACTCAATTAATATTATTAAAAGATACCATTCAG-TAGTTTTTATGC
56502 AA
129 AA
* *
56504 -TTTTTTTATTTCATTAAAAATAAATAAAAATAATAATGATTGAAAATATTGATTCGTGTAAACT
1 TTTTTTTTATTTCATT-AAAATAAAT-AAAATAATAATGATTGAAAATATTGAATCGTGTTAACT
* * *
56568 CACAATAGATTAAAACTCGAACTCAATGAATATTATTAAAAGTTACCCTTCAGTAGTTTTTATGC
64 CACAATAGATTAAAACTCGAACTCAATTAATATTATTAAAAGATACCATTCAGTAGTTTTTATGC
56633 AA
129 AA
* * * * *
56635 TTTTTTTTTAATTCACTGAAAATATATAAAATAATAATGATTGAAAACATT-AGATTGTGTTAAC
1 -TTTTTTTTATTTCA-TTAAAATAAATAAAATAATAATGATTGAAAATATTGA-ATCGTGTTAAC
*
56699 TCACAATAGATTAAAACTCGAATTCAATTAATATTATTAAA
63 TCACAATAGATTAAAACTCGAACTCAATTAATATTATTAAA
56740 GACTATCATT
Statistics
Matches: 208, Mismatches: 19, Indels: 15
0.86 0.08 0.06
Matches are distributed among these distances:
127 2 0.01
128 12 0.06
129 8 0.04
130 73 0.35
131 21 0.10
132 71 0.34
133 20 0.10
134 1 0.00
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (130 bp):
TTTTTTTTATTTCATTAAAATAAATAAAATAATAATGATTGAAAATATTGAATCGTGTTAACTCA
CAATAGATTAAAACTCGAACTCAATTAATATTATTAAAAGATACCATTCAGTAGTTTTTATGCAA
Found at i:56756 original size:132 final size:128
Alignment explanation
Indices: 56375--56758 Score: 484
Period size: 132 Copynumber: 2.9 Consensus size: 128
56365 ATTTCTGAAG
* * *
56375 TTTTTTTT-ATTGCACTTAAATAAATAAAATAATAATGATTGAAAATATTGAATCGTATTAACTC
1 TTTTTTTTAATT-CACTAAAATAAATAAAATAATAATGATTGAAAATATTG-ATTGTGTTAACTC
* * * *
56439 ACAATAAATTAAAACTCGAACTCAATTAATCTTATTAAAAATACCATTCGATAGTTTTTATGTAA
64 ACAATAGATTAAAACTCGAACTCAATTAATATTATTAAAAATACCATTCGGTAGTTTTTATGCAA
* * *
56504 -TTTTTTTATTTCATTAAAAATAAATAAAAATAATAATGATTGAAAATATTGATTCGTGTAAACT
1 TTTTTTTTAATTCACT-AAAATAAAT-AAAATAATAATGATTGAAAATATTGATT-GTGTTAACT
* * * *
56568 CACAATAGATTAAAACTCGAACTCAATGAATATTATTAAAAGTTACCCTTCAGTAGTTTTTATGC
63 CACAATAGATTAAAACTCGAACTCAATTAATATTATTAAAA-ATACCATTCGGTAGTTTTTATGC
56633 AA
127 AA
* *
56635 TTTTTTTTTAATTCACTGAAAATATATAAAATAATAATGATTGAAAACATTAGATTGTGTTAACT
1 -TTTTTTTTAATTCACT-AAAATAAATAAAATAATAATGATTGAAAATATT-GATTGTGTTAACT
* * * *
56700 CACAATAGATTAAAACTCGAATTCAATTAATATTATTAAAGACTATCATTGGGTAGTTT
63 CACAATAGATTAAAACTCGAACTCAATTAATATTATTAAA-AATACCATTCGGTAGTTT
56759 ACATTGAAAA
Statistics
Matches: 219, Mismatches: 27, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
128 10 0.05
129 12 0.05
130 70 0.32
131 20 0.09
132 81 0.37
133 26 0.12
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.39
Consensus pattern (128 bp):
TTTTTTTTAATTCACTAAAATAAATAAAATAATAATGATTGAAAATATTGATTGTGTTAACTCAC
AATAGATTAAAACTCGAACTCAATTAATATTATTAAAAATACCATTCGGTAGTTTTTATGCAA
Done.