Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010081.1 Kokia drynarioides strain JFW-HI SEQ_124860, 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: 29701
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Warning! 56 characters in sequence are not A, C, G, or T
Found at i:12907 original size:16 final size:16
Alignment explanation
Indices: 12858--12908 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
12848 AAAACATTTT
12858 TAATAAATACATAATAAA
1 TAAT-AATA-ATAATAAA
* **
12876 TAATTATAATTTTAAA
1 TAATAATAATAATAAA
12892 TAATAATAATAATAAA
1 TAATAATAATAATAAA
12908 T
1 T
12909 TTGAAAGGTC
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
16 20 0.74
17 3 0.11
18 4 0.15
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (16 bp):
TAATAATAATAATAAA
Found at i:13942 original size:30 final size:30
Alignment explanation
Indices: 13900--14243 Score: 209
Period size: 30 Copynumber: 11.6 Consensus size: 30
13890 TTTGACTTTC
* * * * *
13900 AAACTTTCCCAAAATTATATTTTTATCCCT
1 AAACTTTTCCAAAATTACATGTTGACCCCT
*
13930 AAGCTTTTCCAAAATTACATGTTGACCCCT
1 AAACTTTTCCAAAATTACATGTTGACCCCT
* * *
13960 AAACTTTTCCAAAA-T-CA--TTCATCCTT
1 AAACTTTTCCAAAATTACATGTTGACCCCT
* * * *
13986 AAAATTTTCTAAAATCACATTTTGACCCCT
1 AAACTTTTCCAAAATTACATGTTGACCCCT
* * * *
14016 AAACTTTCCCAAAATCACATTTTGACCCTT
1 AAACTTTTCCAAAATTACATGTTGACCCCT
* * * *
14046 AAACTTTCCCAAAATCACATTTTAACCCC-
1 AAACTTTTCCAAAATTACATGTTGACCCCT
* * * *
14075 AAAGATTTTCCAAAATTACATTTTAACCCCC
1 AAA-CTTTTCCAAAATTACATGTTGACCCCT
* * * * *
14106 AAACTTCTCCAAAATCAAATTTTAACCCCCT
1 AAACTTTTCCAAAATTACATGTTGA-CCCCT
* * * *
14137 AAAC-CTTCTCAAAATCACATTTTAACCCC-
1 AAACTTTTC-CAAAATTACATGTTGACCCCT
** * * *
14166 AAACTTAACCAAAATCACATTTTAACCCCT
1 AAACTTTTCCAAAATTACATGTTGACCCCT
* * *
14196 AAACTTTCCCAAAATTACATTTTTG-CCCTT
1 AAACTTTTCCAAAATTACA-TGTTGACCCCT
*
14226 AAATTTTTCCAAAATTAC
1 AAACTTTTCCAAAATTAC
14244 GTTCTAACAC
Statistics
Matches: 260, Mismatches: 43, Indels: 22
0.80 0.13 0.07
Matches are distributed among these distances:
26 18 0.07
28 4 0.02
29 28 0.11
30 180 0.69
31 30 0.12
ACGTcount: A:0.36, C:0.28, G:0.02, T:0.34
Consensus pattern (30 bp):
AAACTTTTCCAAAATTACATGTTGACCCCT
Found at i:13972 original size:60 final size:60
Alignment explanation
Indices: 13900--14240 Score: 320
Period size: 60 Copynumber: 5.8 Consensus size: 60
13890 TTTGACTTTC
* * * * *
13900 AAACTTTCCCAAAATTATATTTTTATCCCTAAGCTTTTCCAAAATTACATGTTGACCCCT
1 AAACTTTCCCAAAATTACATTTTTATCCCTAAACTTTTCCAAAATCACATTTTAACCCCT
* * * * * *
13960 AAACTTTTCCAAAA-T-CA--TTCATCCTTAAAATTTTCTAAAATCACATTTTGACCCCT
1 AAACTTTCCCAAAATTACATTTTTATCCCTAAACTTTTCCAAAATCACATTTTAACCCCT
* * *
14016 AAACTTTCCCAAAATCACATTTTGA-CCCTTAAACTTTCCCAAAATCACATTTTAACCCC-
1 AAACTTTCCCAAAATTACATTTTTATCCC-TAAACTTTTCCAAAATCACATTTTAACCCCT
* * * * * * *
14075 AAAGATTTTCCAAAATTACATTTTAACCCCCAAACTTCTCCAAAATCAAATTTTAACCCCCT
1 AAA-CTTTCCCAAAATTACATTTTTATCCCTAAACTTTTCCAAAATCACATTTTAA-CCCCT
* * * * * **
14137 AAACCTTCTCAAAATCACA-TTTTAACCCCAAACTTAACCAAAATCACATTTTAACCCCT
1 AAACTTTCCCAAAATTACATTTTTATCCCTAAACTTTTCCAAAATCACATTTTAACCCCT
* *
14196 AAACTTTCCCAAAATTACATTTTT-GCCCTTAAATTTTTCCAAAAT
1 AAACTTTCCCAAAATTACATTTTTATCCC-TAAACTTTTCCAAAAT
14241 TACGTTCTAA
Statistics
Matches: 227, Mismatches: 43, Indels: 22
0.78 0.15 0.08
Matches are distributed among these distances:
56 45 0.20
58 3 0.01
59 30 0.13
60 128 0.56
61 18 0.08
62 3 0.01
ACGTcount: A:0.36, C:0.28, G:0.02, T:0.34
Consensus pattern (60 bp):
AAACTTTCCCAAAATTACATTTTTATCCCTAAACTTTTCCAAAATCACATTTTAACCCCT
Found at i:14118 original size:90 final size:89
Alignment explanation
Indices: 13899--14240 Score: 334
Period size: 90 Copynumber: 3.9 Consensus size: 89
13889 TTTTGACTTT
* * * * * * * * * *
13899 CAAACTTTCCCAAAATTATATTTTTATCCCTAAGCTTTTCCAAAATTACATGTTGACCCCTAAAC
1 CAAAATTTTCCAAAATCACATTTTAACCCCTAAACTTTCCCAAAATCACATTTTGACCCCTAAAC
* * * *
13964 TTTTCCAAAAT--CA-TTCATCCT
66 TTTCCCAAAATCACATTTTAACCC
* * * *
13985 TAAAATTTTCTAAAATCACATTTTGACCCCTAAACTTTCCCAAAATCACATTTTGACCCTTAAAC
1 CAAAATTTTCCAAAATCACATTTTAACCCCTAAACTTTCCCAAAATCACATTTTGACCCCTAAAC
14050 TTTCCCAAAATCACATTTTAACCC
66 TTTCCCAAAATCACATTTTAACCC
* * * *
14074 CAAAGATTTTCCAAAATTACATTTTAACCCCCAAAC-TTCTCCAAAATCAAATTTTAACCCCCTA
1 CAAA-ATTTTCCAAAATCACATTTTAACCCCTAAACTTTC-CCAAAATCACATTTTGA-CCCCTA
* *
14138 AACCTTCTCAAAATCACATTTTAACCC
63 AACTTTCCCAAAATCACATTTTAACCC
* ** * *
14165 CAAACTTAACCAAAATCACATTTTAACCCCTAAACTTTCCCAAAATTACATTTTTG-CCCTTAAA
1 CAAAATTTTCCAAAATCACATTTTAACCCCTAAACTTTCCCAAAATCACA-TTTTGACCCCTAAA
* *
14229 TTTTTCCAAAAT
65 CTTTCCCAAAAT
14241 TACGTTCTAA
Statistics
Matches: 208, Mismatches: 40, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
86 62 0.30
88 2 0.01
89 26 0.12
90 77 0.37
91 41 0.20
ACGTcount: A:0.36, C:0.28, G:0.02, T:0.34
Consensus pattern (89 bp):
CAAAATTTTCCAAAATCACATTTTAACCCCTAAACTTTCCCAAAATCACATTTTGACCCCTAAAC
TTTCCCAAAATCACATTTTAACCC
Found at i:26287 original size:37 final size:37
Alignment explanation
Indices: 26246--26349 Score: 181
Period size: 37 Copynumber: 2.8 Consensus size: 37
26236 ATAAAACGGT
*
26246 TGTCTTCCTGATGAGATATAGAGAAGTGGACGAAATC
1 TGTCTTCCTGATGAGATATAGAGAAGTGGACCAAATC
*
26283 TGTCTTCTTGATGAGATATAGAGAAGTGGACCAAATC
1 TGTCTTCCTGATGAGATATAGAGAAGTGGACCAAATC
*
26320 TGTCTTCCTGATGAGATACAGAGAAGTGGA
1 TGTCTTCCTGATGAGATATAGAGAAGTGGA
26350 TTAAAACAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 63 1.00
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.28
Consensus pattern (37 bp):
TGTCTTCCTGATGAGATATAGAGAAGTGGACCAAATC
Found at i:26660 original size:209 final size:209
Alignment explanation
Indices: 26284--26776 Score: 783
Period size: 209 Copynumber: 2.4 Consensus size: 209
26274 GACGAAATCT
* *
26284 GTCTTCTTGATGAGATATAGAGAAGTGGACCAAATCTGTCTTCCTGATGAGATACAGAGAAGTGG
1 GTCTTCCTGATGAGATATAGAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAGAGAAGTGG
* *
26349 ATTAAAACAAATGAGGCAGTCATCTTTCTGATGAGATACAAAGAAGTAAACCAAATCAATGAAGC
66 ATTAAAACAAATGAGGCAGCCATCTTCCTGATGAGATACAAAGAAGTAAACCAAATCAATGAAGC
* * *
26414 AAAGCTCAATGTGAGTGAAAACTCAAACCTTATCTTCCTTATGAGATACTGAAAAAAGGGTTAAA
131 AAAGCTCAATGTGAGTGAAAACTCAAACCTCATCTTCCTGATGAGATACTGAAAAAAGGGTCAAA
26479 GCAATAAAGTGGTC
196 GCAATAAAGTGGTC
* *
26493 GTCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAGAGGAGTGG
1 GTCTTCCTGATGAGATATAGAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAGAGAAGTGG
*
26558 ATTAAAACAAATGAGGCAGCCATCTTCCTGATGAGATACAGAGAAGTAAACCAAATCAATGAAGC
66 ATTAAAACAAATGAGGCAGCCATCTTCCTGATGAGATACAAAGAAGTAAACCAAATCAATGAAGC
* * **
26623 AAAGCTCAATGTTAGTG-AAACTTCAAATCC-CATCTTCCTGATGAGATACTGAGAAGTGGGTCA
131 AAAGCTCAATGTGAGTGAAAAC-TCAAA-CCTCATCTTCCTGATGAGATACTGAAAAAAGGGTCA
*
26686 AAGCAATAAAGTGGTT
194 AAGCAATAAAGTGGTC
* * * *
26702 GTCTTCCTAATGAGATATAGAGAAGTGGACCAAATTCGTCTTCATGACGAGATACAGAGAAGTGG
1 GTCTTCCTGATGAGATATAGAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAGAGAAGTGG
26767 ATTAAAACAA
66 ATTAAAACAA
26777 GTGATGCGTG
Statistics
Matches: 261, Mismatches: 21, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
208 4 0.02
209 255 0.98
210 2 0.01
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (209 bp):
GTCTTCCTGATGAGATATAGAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAGAGAAGTGG
ATTAAAACAAATGAGGCAGCCATCTTCCTGATGAGATACAAAGAAGTAAACCAAATCAATGAAGC
AAAGCTCAATGTGAGTGAAAACTCAAACCTCATCTTCCTGATGAGATACTGAAAAAAGGGTCAAA
GCAATAAAGTGGTC
Found at i:27684 original size:29 final size:28
Alignment explanation
Indices: 27652--27713 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
27642 AAAATGAGAC
* *
27652 TTTTCGAATACCCGGGGAGAAAATGGTAA
1 TTTT-GAATACCCGGGAACAAAATGGTAA
* * *
27681 TTTTGGATTCTCGGGAACAAAATGGTAA
1 TTTTGAATACCCGGGAACAAAATGGTAA
27709 TTTTG
1 TTTTG
27714 GGAAAATTTG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 24 0.86
29 4 0.14
ACGTcount: A:0.31, C:0.11, G:0.26, T:0.32
Consensus pattern (28 bp):
TTTTGAATACCCGGGAACAAAATGGTAA
Found at i:27799 original size:29 final size:29
Alignment explanation
Indices: 27754--28107 Score: 341
Period size: 29 Copynumber: 12.1 Consensus size: 29
27744 GGACATCCGG
*
27754 GGGT-AAAATGGTAATTTTTGGAAGTTCGA
1 GGGTAAAAATGG-AATTTTTGGAAGTTTGA
*
27783 GGATAAAAATGGAA-TTTTGGAAAGTTTTGA
1 GGGTAAAAATGGAATTTTTGG-AAG-TTTGA
*
27813 -GGTCAAAAATGGGATTTTTGGAAGTTTG-
1 GGGT-AAAAATGGAATTTTTGGAAGTTTGA
* *
27841 GTGGAAAAAATGGAATTTTTGGAAGTTTTA
1 G-GGTAAAAATGGAATTTTTGGAAGTTTGA
*
27871 GGGTTAAAAATGGGATTTTTGGAAGTTT-A
1 GGG-TAAAAATGGAATTTTTGGAAGTTTGA
*
27900 GGGGTAAAAATGGAATTTTTGGAAGTTTTA
1 -GGGTAAAAATGGAATTTTTGGAAGTTTGA
* *
27930 GGGTCAAAATGGGATTTTTGGAAGTTTTG-
1 GGGTAAAAATGGAATTTTTGGAAG-TTTGA
*
27959 GGGTAAAAAAT-GAATTTTTGGAAGTTTCA
1 GGGT-AAAAATGGAATTTTTGGAAGTTTGA
* * * *
27988 TGGTCAAAATGGGATTTTTGGAAGTTCGA
1 GGGTAAAAATGGAATTTTTGGAAGTTTGA
*
28017 GGGTAAAAATGGAATTTTTGGATA-TTTTA
1 GGGTAAAAATGGAATTTTTGGA-AGTTTGA
* * * *
28046 GGGGTCCAAAATGGGATTTTTAGAAGTTCG-
1 -GGGT-AAAAATGGAATTTTTGGAAGTTTGA
*
28076 GGATAAAAATGGAATTTTTGGATAGTTT-A
1 GGGTAAAAATGGAATTTTTGGA-AGTTTGA
28105 GGG
1 GGG
28108 ACCTTCGGGG
Statistics
Matches: 267, Mismatches: 37, Indels: 42
0.77 0.11 0.12
Matches are distributed among these distances:
28 29 0.11
29 149 0.56
30 66 0.25
31 23 0.09
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.36
Consensus pattern (29 bp):
GGGTAAAAATGGAATTTTTGGAAGTTTGA
Found at i:27801 original size:88 final size:87
Alignment explanation
Indices: 27663--27824 Score: 199
Period size: 88 Copynumber: 1.9 Consensus size: 87
27653 TTTCGAATAC
*
27663 CCGGGGAGAAAATGGTAATTTTGGATTCTCGGGAACAAAATGGTAATTTTGGGAAA-ATTTGAGG
1 CCGGGGAGAAAATGGTAATTTTGGAGTCTCGGGAACAAAATGGTAATTTT-GGAAAGATTTGAGG
**
27727 TTTAAAATGGAGTCTTCGGACAT
65 TCAAAAATGGAGTCTTCGGACAT
*
27750 CCGGGG-GTAAAATGGTAATTTTTGGAAGT-TCGAGGATA-AAAATGG-AATTTTGGAAAGTTTT
1 CCGGGGAG-AAAATGGTAA-TTTTGG-AGTCTCG-GGA-ACAAAATGGTAATTTTGGAAAGATTT
27811 GAGGTCAAAAATGG
61 GAGGTCAAAAATGG
27825 GATTTTTGGA
Statistics
Matches: 65, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
86 1 0.02
87 21 0.32
88 30 0.46
89 12 0.18
90 1 0.02
ACGTcount: A:0.33, C:0.07, G:0.30, T:0.30
Consensus pattern (87 bp):
CCGGGGAGAAAATGGTAATTTTGGAGTCTCGGGAACAAAATGGTAATTTTGGAAAGATTTGAGGT
CAAAAATGGAGTCTTCGGACAT
Found at i:27849 original size:58 final size:57
Alignment explanation
Indices: 27754--28107 Score: 432
Period size: 59 Copynumber: 6.1 Consensus size: 57
27744 GGACATCCGG
* * *
27754 GGGT-AAAATGGTAATTTTTGGAAGTTCGAGGATAAAAATGGAA-TTTTGGAAAGTTTT-
1 GGGTCAAAATGG-GATTTTTGGAAGTTTG-GGGTAAAAATGGAATTTTTGG-AAGTTTTA
*
27811 GAGGTCAAAAATGGGATTTTTGGAAGTTTGGTGGAAAAAATGGAATTTTTGGAAGTTTTA
1 G-GGTC-AAAATGGGATTTTTGGAAGTTTGG-GGTAAAAATGGAATTTTTGGAAGTTTTA
*
27871 GGGTTAAAAATGGGATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTTTGGAAGTTTTA
1 GGG-TCAAAATGGGATTTTTGGAAGTTT-GGGGTAAAAATGGAATTTTTGGAAGTTTTA
*
27930 GGGTCAAAATGGGATTTTTGGAAGTTTTGGGGTAAAAAAT-GAATTTTTGGAAGTTTCA
1 GGGTCAAAATGGGATTTTTGGAAG-TTTGGGGT-AAAAATGGAATTTTTGGAAGTTTTA
* *
27988 TGGTCAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGATA-TTTTA
1 GGGTCAAAATGGGATTTTTGGAAGTTTG-GGGTAAAAATGGAATTTTTGGA-AGTTTTA
* * *
28046 GGGGTCCAAAATGGGATTTTTAGAAGTTCGGGATAAAAATGGAATTTTTGGATAG-TTTA
1 -GGGT-CAAAATGGGATTTTTGGAAGTTTGGGGTAAAAATGGAATTTTTGGA-AGTTTTA
28105 GGG
1 GGG
28108 ACCTTCGGGG
Statistics
Matches: 267, Mismatches: 14, Indels: 31
0.86 0.04 0.10
Matches are distributed among these distances:
57 10 0.04
58 91 0.34
59 126 0.47
60 40 0.15
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.36
Consensus pattern (57 bp):
GGGTCAAAATGGGATTTTTGGAAGTTTGGGGTAAAAATGGAATTTTTGGAAGTTTTA
Done.