Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011342.1 Kokia drynarioides strain JFW-HI SEQ_126322, 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: 48828
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Warning! 44 characters in sequence are not A, C, G, or T
Found at i:143 original size:3 final size:3
Alignment explanation
Indices: 135--213 Score: 149
Period size: 3 Copynumber: 26.0 Consensus size: 3
125 TTTTTATTTT
135 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
183 TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
214 AGACAAAAAA
Statistics
Matches: 75, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 72 0.96
4 3 0.04
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:929 original size:17 final size:17
Alignment explanation
Indices: 907--980 Score: 94
Period size: 17 Copynumber: 4.4 Consensus size: 17
897 CACTTTTAAT
* *
907 TAAATTTTAATTTAAAA
1 TAAATTTAAACTTAAAA
* *
924 TAAATTTAAACTCAAAG
1 TAAATTTAAACTTAAAA
* *
941 TAAGTTTAAATTTAAAA
1 TAAATTTAAACTTAAAA
958 TAAATTTAAACTTAAAA
1 TAAATTTAAACTTAAAA
975 TAAATT
1 TAAATT
981 AAAATTTTAA
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 47 1.00
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (17 bp):
TAAATTTAAACTTAAAA
Found at i:954 original size:34 final size:34
Alignment explanation
Indices: 915--992 Score: 111
Period size: 34 Copynumber: 2.3 Consensus size: 34
905 ATTAAATTTT
* * *
915 AATTTAAAATAAATTTAAACTCAAAGTAAGTTTA
1 AATTTAAAATAAATTTAAACTCAAAATAAATTAA
*
949 AATTTAAAATAAATTTAAACTTAAAATAAATTAA
1 AATTTAAAATAAATTTAAACTCAAAATAAATTAA
983 AATTTTAAAA
1 AA-TTTAAAA
993 ACAATCCAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
34 32 0.82
35 7 0.18
ACGTcount: A:0.58, C:0.04, G:0.03, T:0.36
Consensus pattern (34 bp):
AATTTAAAATAAATTTAAACTCAAAATAAATTAA
Found at i:7831 original size:29 final size:30
Alignment explanation
Indices: 7748--7831 Score: 73
Period size: 30 Copynumber: 2.8 Consensus size: 30
7738 AATTTATTGT
* * *
7748 AAAATTACATTTTGATCTTTTAAAATGAAG
1 AAAATTATATTTTAATCTTTAAAAATGAAG
* * * *
7778 AAAATTAT-GTTTAACCCCTTAAAAATGATG
1 AAAATTATATTTTAA-TCTTTAAAAATGAAG
*
7808 -AAATTATATTTTAATCTTTCAAAA
1 AAAATTATATTTTAATCTTTAAAAA
7832 CTTTATTATT
Statistics
Matches: 41, Mismatches: 11, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
29 18 0.44
30 23 0.56
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.39
Consensus pattern (30 bp):
AAAATTATATTTTAATCTTTAAAAATGAAG
Found at i:12220 original size:21 final size:21
Alignment explanation
Indices: 12194--12233 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
12184 CAAAACAACG
12194 TAGTTTTGCCTTTTAACTTAA
1 TAGTTTTGCCTTTTAACTTAA
12215 TAGTTTTGCCTTTTAACTT
1 TAGTTTTGCCTTTTAACTT
12234 TTAAAAAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.55
Consensus pattern (21 bp):
TAGTTTTGCCTTTTAACTTAA
Found at i:27154 original size:18 final size:18
Alignment explanation
Indices: 27087--27157 Score: 54
Period size: 18 Copynumber: 3.9 Consensus size: 18
27077 TGTCACTATG
*
27087 TATTTTAAAATTAAAAAA
1 TATTTTAAAAATAAAAAA
* ** *
27105 TATATTAAATGTAAAAATG
1 TATTTTAAAAATAAAAA-A
**
27124 TGATTTT-TTAATAAAAAA
1 T-ATTTTAAAAATAAAAAA
27142 TATTTTAAAAATAAAA
1 TATTTTAAAAATAAAA
27158 TATGAAATTG
Statistics
Matches: 38, Mismatches: 12, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
17 5 0.13
18 22 0.58
19 7 0.18
20 4 0.11
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.39
Consensus pattern (18 bp):
TATTTTAAAAATAAAAAA
Found at i:27815 original size:18 final size:18
Alignment explanation
Indices: 27792--27828 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
27782 ATTATAGTTT
* *
27792 AATATTTGATTTATTCAA
1 AATATTCGAGTTATTCAA
27810 AATATTCGAGTTATTCAA
1 AATATTCGAGTTATTCAA
27828 A
1 A
27829 TTCGAAAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (18 bp):
AATATTCGAGTTATTCAA
Found at i:34230 original size:22 final size:23
Alignment explanation
Indices: 34189--34235 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
34179 TATATTAAGT
34189 ATAAATAGATTTAATTAAGATTA
1 ATAAATAGATTTAATTAAGATTA
34212 ATAAAT-GA-TTAATTAAAGATTA
1 ATAAATAGATTTAATT-AAGATTA
34234 AT
1 AT
34236 GATGAAAGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 6 0.26
22 11 0.48
23 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (23 bp):
ATAAATAGATTTAATTAAGATTA
Found at i:42356 original size:41 final size:43
Alignment explanation
Indices: 42284--42372 Score: 137
Period size: 41 Copynumber: 2.1 Consensus size: 43
42274 ATTTTGATAC
* *
42284 TTAAATTTGACATTTTTTTTTTAAATTTGGTATCTAAGCTTTTT
1 TTAAATTTGACA-TTTTTTTCTAAATTTGGTACCTAAGCTTTTT
42328 TTAAATTTGACA-TTTTTTCT-AATTTGGTACCTAAGCTTTTT
1 TTAAATTTGACATTTTTTTCTAAATTTGGTACCTAAGCTTTTT
42369 TTAA
1 TTAA
42373 GGTTCAATTG
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
41 24 0.56
42 7 0.16
44 12 0.28
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.56
Consensus pattern (43 bp):
TTAAATTTGACATTTTTTTCTAAATTTGGTACCTAAGCTTTTT
Found at i:44191 original size:69 final size:68
Alignment explanation
Indices: 44103--44243 Score: 264
Period size: 69 Copynumber: 2.1 Consensus size: 68
44093 ACAAATTGAA
44103 AATACATTAAAATTATATTTAAATAACACTAAGATAGTTGCAACTTAGCAAGCAAATACCTCTAA
1 AATACATTAAAATTATATTTAAATAACACTAAGATAGTTGCAACTTAGCAAGCAAATACCTCTAA
44168 AAT
66 AAT
*
44171 AATACATTAAAAATTATATTTAAATAACACTAAGATAGTTGCAACTTAGCAAGCAAATACCTTTA
1 AATACATT-AAAATTATATTTAAATAACACTAAGATAGTTGCAACTTAGCAAGCAAATACCTCTA
44236 AAAT
65 AAAT
44240 AATA
1 AATA
44244 GTAAAGTTAA
Statistics
Matches: 71, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
68 8 0.11
69 63 0.89
ACGTcount: A:0.50, C:0.13, G:0.07, T:0.30
Consensus pattern (68 bp):
AATACATTAAAATTATATTTAAATAACACTAAGATAGTTGCAACTTAGCAAGCAAATACCTCTAA
AAT
Found at i:48096 original size:43 final size:43
Alignment explanation
Indices: 48034--48117 Score: 123
Period size: 43 Copynumber: 2.0 Consensus size: 43
48024 GCATAGGGGC
* *
48034 AAAATGGTAGTTTTGGAAGGTTCGGAATCAAAAAAGGGATTGT
1 AAAATGGTAATTTTAGAAGGTTCGGAATCAAAAAAGGGATTGT
** *
48077 AAAATGGTAATTTTAGAAGGTTCGGGGTCAAAAATGGGATT
1 AAAATGGTAATTTTAGAAGGTTCGGAATCAAAAAAGGGATT
48118 TTTGGACATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.37, C:0.05, G:0.30, T:0.29
Consensus pattern (43 bp):
AAAATGGTAATTTTAGAAGGTTCGGAATCAAAAAAGGGATTGT
Found at i:48118 original size:29 final size:29
Alignment explanation
Indices: 48077--48435 Score: 189
Period size: 29 Copynumber: 12.2 Consensus size: 29
48067 AAGGGATTGT
* *
48077 AAAATGGTAATTTTAGAAGGTTCGGGGTCA
1 AAAATGGGATTTTTAGAAGGTTCGGGGT-A
*
48107 AAAATGGGATTTTTGGACA--TTCGGGGTTA
1 AAAATGGGATTTTTAGA-AGGTTCGGGG-TA
* *
48136 AAATTCGGATTTTTGAGAA--TTCGGGGGT-
1 AAAATGGGATTTTT-AGAAGGTTC-GGGGTA
* * *
48164 AAAATGGTAATTTTTAGAAGGTTCGTGGTT
1 AAAATGG-GATTTTTAGAAGGTTCGGGGTA
* * *
48194 AAAATGGGATTTTTGGGAA-TTTAGGGGT-
1 AAAATGGGATTTTT-AGAAGGTTCGGGGTA
* *
48222 AAAATGGTATTTTTTAGAAGGTTCGTGGTTA
1 AAAATGGGA-TTTTTAGAAGGTTCG-GGGTA
* * * * * * *
48253 AAATTTGGATTTTTGGAAGTTTTGATGTTA
1 AAAATGGGATTTTTAGAAGGTTCG-GGGTA
* * ** *
48283 AAATTGGGATTTTTAGAGGGTTTAGGGTT
1 AAAATGGGATTTTTAGAAGGTTCGGGGTA
*
48312 AAAATGGGATTTTT-GAAAGTTTCGGGGTTA
1 AAAATGGGATTTTTAG-AAGGTTCGGGG-TA
* * *
48342 AAATTGGGATTTTTAGAGGGTTCGGGGTT
1 AAAATGGGATTTTTAGAAGGTTCGGGGTA
* * *
48371 AAAATGAGATTTTTGGAA-ATTCGAGGGT-
1 AAAATGGGATTTTTAGAAGGTTCG-GGGTA
* * * *
48399 AAAATGGTAATTTTCGAAAGTTTCGGGGTTA
1 AAAATGGGATTTTTAG-AAGGTTCGGGG-TA
48430 AAAATG
1 AAAATG
48436 TAATTTTTGG
Statistics
Matches: 252, Mismatches: 56, Indels: 41
0.72 0.16 0.12
Matches are distributed among these distances:
28 37 0.15
29 101 0.40
30 100 0.40
31 14 0.06
ACGTcount: A:0.29, C:0.04, G:0.30, T:0.37
Consensus pattern (29 bp):
AAAATGGGATTTTTAGAAGGTTCGGGGTA
Found at i:48199 original size:30 final size:29
Alignment explanation
Indices: 48076--48443 Score: 206
Period size: 30 Copynumber: 12.5 Consensus size: 29
48066 AAAGGGATTG
48076 TAAAATGGTAA-TTTTAGAAGGTTCGGGGT
1 TAAAATGG-AATTTTTAGAAGGTTCGGGGT
* * *
48105 CAAAAATGGGATTTTTGGACA--TTCGGGGT
1 -TAAAATGGAATTTTTAGA-AGGTTCGGGGT
*
48134 TAAAATTCGG-ATTTTTGAGAA--TTCGGGGG
1 TAAAA-T-GGAATTTTT-AGAAGGTTCGGGGT
*
48163 TAAAATGGTAATTTTTAGAAGGTTCGTGGT
1 TAAAATGG-AATTTTTAGAAGGTTCGGGGT
* * * *
48193 TAAAATGGGATTTTTGGGAA-TTTAGGGG-
1 TAAAATGGAATTTTT-AGAAGGTTCGGGGT
* *
48221 TAAAATGGTATTTTTTAGAAGGTTCGTGGT
1 TAAAATGG-AATTTTTAGAAGGTTCGGGGT
* * * **
48251 TAAAATTTGG-ATTTTTGGAAGTTTTGATGT
1 TAAAA--TGGAATTTTTAGAAGGTTCGGGGT
* * **
48281 TAAAATTGGGATTTTTAGAGGGTTTAGGGT
1 TAAAA-TGGAATTTTTAGAAGGTTCGGGGT
* *
48311 TAAAATGGGATTTTT-GAAAGTTTCGGGGT
1 TAAAATGGAATTTTTAG-AAGGTTCGGGGT
* *
48340 TAAAATTGGGATTTTTAGAGGGTTCGGGGT
1 TAAAA-TGGAATTTTTAGAAGGTTCGGGGT
* *
48370 TAAAAT-GAGATTTTTGGAA-ATTCGAGGG-
1 TAAAATGGA-ATTTTTAGAAGGTTCG-GGGT
* *
48398 TAAAATGGTAA-TTTTCGAAAGTTTCGGGGT
1 TAAAATGG-AATTTTTAG-AAGGTTCGGGGT
*
48428 TAAAAATGTAATTTTT
1 T-AAAATGGAATTTTT
48444 GGACAATCCA
Statistics
Matches: 266, Mismatches: 44, Indels: 55
0.73 0.12 0.15
Matches are distributed among these distances:
27 2 0.01
28 37 0.14
29 102 0.38
30 110 0.41
31 12 0.05
32 3 0.01
ACGTcount: A:0.29, C:0.04, G:0.29, T:0.38
Consensus pattern (29 bp):
TAAAATGGAATTTTTAGAAGGTTCGGGGT
Found at i:48326 original size:59 final size:58
Alignment explanation
Indices: 48173--48388 Score: 249
Period size: 59 Copynumber: 3.7 Consensus size: 58
48163 TAAAATGGTA
* *
48173 ATTTTTAGAAGGTTCGTGGTTAAAATGGGATTTTTGGGAA-TTTAGGGGTAAAA-TGGT
1 ATTTTTAGAAGGTTCGTGGTTAAAATGGGATTTTT-GGAAGTTTAGGGTTAAAATTGGG
* * *
48230 ATTTTTTAGAAGGTTCGTGGTTAAAATTTGGATTTTTGGAAGTTTTGATGTTAAAATTGGG
1 A-TTTTTAGAAGGTTCGTGGTTAAAA-TGGGATTTTTGGAAGTTTAG-GGTTAAAATTGGG
* * * *
48291 ATTTTTAGAGGGTTTAG-GGTTAAAATGGGATTTTTGAAAGTTTCGGGGTTAAAATTGGG
1 ATTTTTAGAAGG-TTCGTGGTTAAAATGGGATTTTTGGAAGTTT-AGGGTTAAAATTGGG
* * *
48350 ATTTTTAGAGGGTTCGGGGTTAAAATGAGATTTTTGGAA
1 ATTTTTAGAAGGTTCGTGGTTAAAATGGGATTTTTGGAA
48389 ATTCGAGGGT
Statistics
Matches: 137, Mismatches: 14, Indels: 14
0.83 0.08 0.08
Matches are distributed among these distances:
57 1 0.01
58 31 0.23
59 73 0.53
60 25 0.18
61 7 0.05
ACGTcount: A:0.27, C:0.02, G:0.30, T:0.41
Consensus pattern (58 bp):
ATTTTTAGAAGGTTCGTGGTTAAAATGGGATTTTTGGAAGTTTAGGGTTAAAATTGGG
Found at i:48422 original size:88 final size:87
Alignment explanation
Indices: 48087--48432 Score: 319
Period size: 88 Copynumber: 3.9 Consensus size: 87
48077 AAAATGGTAA
* *
48087 TTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGACATTCG-GGGTTAAAATTCGGATTTTTG
1 TTTTAGAAGGTTCGGGGT-TAAAATGGGATTTTTGGAAATT-GAGGGTTAAAA-T-GGATTTTTG
* *
48151 AGAA--TTCGGGGGTAAAA-TGGTAAT
62 AGAAGTTTCGGGGTTAAAATTGG-GAT
* * * * *
48175 TTTTAGAAGGTTCGTGGTTAAAATGGGATTTTTGGGAATTTAGGGGTAAAATGGTATTTTTTAGA
1 TTTTAGAAGGTTCGGGGTTAAAATGGGATTTTTGGAAATTGAGGGTTAAAATGG-ATTTTTGAGA
* * *
48240 AGGTTCGTGGTTAAAATTTGGAT
65 AGTTTCGGGGTTAAAATTGGGAT
* * * ** * ** *
48263 TTTTGGAAGTTTTGATGTTAAAATTGGGATTTTTAGAGGGTTTAGGGTTAAAATGGGATTTTTGA
1 TTTTAGAAGGTTCGGGGTTAAAA-TGGGATTTTTGGA-AATTGAGGGTTAAAAT-GGATTTTTGA
48328 -AAGTTTCGGGGTTAAAATTGGGAT
63 GAAGTTTCGGGGTTAAAATTGGGAT
* * *
48352 TTTTAGAGGGTTCGGGGTTAAAATGAGATTTTTGGAAATTCGAGGG-TAAAATGGTAATTTTCGA
1 TTTTAGAAGGTTCGGGGTTAAAATGGGATTTTTGGAAATT-GAGGGTTAAAATGG--ATTTTTGA
48416 -AAGTTTCGGGGTTAAAA
63 GAAGTTTCGGGGTTAAAA
48433 ATGTAATTTT
Statistics
Matches: 210, Mismatches: 37, Indels: 22
0.78 0.14 0.08
Matches are distributed among these distances:
85 2 0.01
86 13 0.06
87 35 0.17
88 87 0.41
89 51 0.24
90 20 0.10
91 2 0.01
ACGTcount: A:0.28, C:0.04, G:0.30, T:0.38
Consensus pattern (87 bp):
TTTTAGAAGGTTCGGGGTTAAAATGGGATTTTTGGAAATTGAGGGTTAAAATGGATTTTTGAGAA
GTTTCGGGGTTAAAATTGGGAT
Found at i:48434 original size:59 final size:57
Alignment explanation
Indices: 48126--48446 Score: 226
Period size: 59 Copynumber: 5.4 Consensus size: 57
48116 TTTTTGGACA
*
48126 TTCGGGGTTAAAATTCGGATTTTT-GAGAATTCGGGGGTAAAATGGTAATTTTTAG-AAGG
1 TTCGGGGTTAAAA-T-GGATTTTTGGA-AATTCGAGGGTAAAATGGTAA-TTTTAGAAAGG
* * * *
48185 TTCGTGGTTAAAATGGGATTTTTGGGAATT-TAGGGGTAAAATGGTATTTTTTAG-AAGG
1 TTCGGGGTTAAAAT-GGATTTTTGGAAATTCGA-GGGTAAAATGGTA-ATTTTAGAAAGG
* * * * * * * *
48243 TTCGTGGTTAAAATTTGGATTTTTGGAAGTTTTGATGTTAAAATTGGGATTTTTAG-AGGG
1 TTCGGGGTTAAAA--TGGATTTTTGGAA-ATTCGAGGGTAAAA-TGGTAATTTTAGAAAGG
** * * *
48303 TTTAGGGTTAAAATGGGATTTTT-GAAAGTTTCG-GGGTTAAAATTGGGATTTTTAG-AGGG
1 TTCGGGGTTAAAAT-GGATTTTTGGAAA--TTCGAGGG-TAAAA-TGGTAATTTTAGAAAGG
* *
48362 TTCGGGGTTAAAATGAGATTTTTGGAAATTCGAGGGTAAAATGGTAATTTTCGAAAGT
1 TTCGGGGTTAAAATG-GATTTTTGGAAATTCGAGGGTAAAATGGTAATTTTAGAAAGG
*
48420 TTCGGGGTTAAAAATGTAATTTTTGGA
1 TTCGGGGTT-AAAATG-GATTTTTGGA
48447 CAATCCAGGG
Statistics
Matches: 216, Mismatches: 29, Indels: 34
0.77 0.10 0.12
Matches are distributed among these distances:
57 9 0.04
58 75 0.35
59 94 0.44
60 33 0.15
61 5 0.02
ACGTcount: A:0.28, C:0.03, G:0.30, T:0.39
Consensus pattern (57 bp):
TTCGGGGTTAAAATGGATTTTTGGAAATTCGAGGGTAAAATGGTAATTTTAGAAAGG
Done.