Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005683.1 Kokia drynarioides strain JFW-HI SEQ_119874, 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: 38156
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Found at i:1348 original size:18 final size:18
Alignment explanation
Indices: 1325--1362 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1315 TAAAATGTTC
* *
1325 AACTCGAGTTATTCAAAT
1 AACTCGAATAATTCAAAT
1343 AACTCGAATAATTCAAAT
1 AACTCGAATAATTCAAAT
1361 AA
1 AA
1363 TTAAATATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.47, C:0.16, G:0.08, T:0.29
Consensus pattern (18 bp):
AACTCGAATAATTCAAAT
Found at i:1361 original size:9 final size:9
Alignment explanation
Indices: 1335--1377 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
1325 AACTCGAGTT
1335 ATTCAAATA
1 ATTCAAATA
* *
1344 ACTCGAATA
1 ATTCAAATA
1353 ATTCAAATA
1 ATTCAAATA
*
1362 ATTAAATATA
1 ATTCAA-ATA
1372 ATTCAA
1 ATTCAA
1378 CCCTACCTCT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.53, C:0.12, G:0.02, T:0.33
Consensus pattern (9 bp):
ATTCAAATA
Found at i:9631 original size:79 final size:79
Alignment explanation
Indices: 9500--9694 Score: 277
Period size: 79 Copynumber: 2.5 Consensus size: 79
9490 GTTTATAATC
* * * *
9500 TCCGTCAATTCATGGCACCCG-GTGCCTAGCGGATAAACCGCGAAAGTGAGCCCAGCTTTAGTTG
1 TCCGTCAAATCCTGGCA-CCGAGTGCCTAGCGGTTAAACCGCGAAAGTGAGCCCAGCTCTAGTTG
9564 GATTAACCAACAATG
65 GATTAACCAACAATG
* *
9579 TCCGTCAAATCCTGGCACCGAGTGCCTAGCGGTTAGACTGC-AAATGTGAGCCCAGCTCTAGTTG
1 TCCGTCAAATCCTGGCACCGAGTGCCTAGCGGTTAAACCGCGAAA-GTGAGCCCAGCTCTAGTTG
9643 GATTAACCAACAATG
65 GATTAACCAACAATG
* * *
9658 TCTGCCAAATCCTGGCACCTAGTGCCTAGCGGTTAAA
1 TCCGTCAAATCCTGGCACCGAGTGCCTAGCGGTTAAA
9695 TCGCAATTGT
Statistics
Matches: 104, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
78 6 0.06
79 98 0.94
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.23
Consensus pattern (79 bp):
TCCGTCAAATCCTGGCACCGAGTGCCTAGCGGTTAAACCGCGAAAGTGAGCCCAGCTCTAGTTGG
ATTAACCAACAATG
Found at i:13310 original size:196 final size:196
Alignment explanation
Indices: 12976--13519 Score: 912
Period size: 196 Copynumber: 2.8 Consensus size: 196
12966 ATGAAAATGT
* * *
12976 AACAATCTCT-TTTCGTCGTTTCTTCGAACAATTCATGTGCGATCAGTGATACAACCCATTAGTC
1 AACAATCTCTCGTT-GTCATTTCTTCGAACAATTCATGTGCGATCAGTGATACAACCCATTAGCC
*
13040 AAAACAGTTCCATGGCTTCTGAAGAAGGCACATCCATTGGCTCAATACCATTGCTTTTGCATCAC
65 AAAACAGTTCCATGGCTTCTGAAGAAGGCACATCCATTGGCTCAATACCATTGCTTTTGCATCTC
* *
13105 ATCAAGCAAATCCCATAGCCTCATTTATATTTGTATAAAGGGATGAATATGTAAATAACGGAAGA
130 ATCAAGCAAATCCCATAGCCTCATTTATATCTGTATAAAGGGATGAATATGTAAACAACGGAAGA
13170 AG
195 AG
*
13172 AACAATCTCTCGTTGTCATTTCTTCGAACAACTT-GTGTGCGATCAGTGATACAACCCATTAGCC
1 AACAATCTCTCGTTGTCATTTCTTCGAACAA-TTCATGTGCGATCAGTGATACAACCCATTAGCC
* * * *
13236 AAAACAGTTACATGGCTTCTGAGGAAGGCACATCCCTTGGCTCAATACCATTGCTTTTTCATCTC
65 AAAACAGTTCCATGGCTTCTGAAGAAGGCACATCCATTGGCTCAATACCATTGCTTTTGCATCTC
*
13301 ATGAAGCAAATCCCATAGCCTCATTTATATCTGTATAAAGGGATGAATATGTAAACAACGGAAGA
130 ATCAAGCAAATCCCATAGCCTCATTTATATCTGTATAAAGGGATGAATATGTAAACAACGGAAGA
13366 AG
195 AG
* *
13368 AACGATCTCTCGTTGTCATTTCTTCGAACAATTCATGTCCGATCAGTGATACAACCCATTAGCCA
1 AACAATCTCTCGTTGTCATTTCTTCGAACAATTCATGTGCGATCAGTGATACAACCCATTAGCCA
* *
13433 AGACAATTCCATGGCTTCTGAAGAAGGCACATCCATTGGCTCAATACCATTGCTTTTGCATCTCA
66 AAACAGTTCCATGGCTTCTGAAGAAGGCACATCCATTGGCTCAATACCATTGCTTTTGCATCTCA
13498 TCAAGCAAATCCCATAGCCTCA
131 TCAAGCAAATCCCATAGCCTCA
13520 ATTGAATAAC
Statistics
Matches: 323, Mismatches: 22, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
195 2 0.01
196 317 0.98
197 4 0.01
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (196 bp):
AACAATCTCTCGTTGTCATTTCTTCGAACAATTCATGTGCGATCAGTGATACAACCCATTAGCCA
AAACAGTTCCATGGCTTCTGAAGAAGGCACATCCATTGGCTCAATACCATTGCTTTTGCATCTCA
TCAAGCAAATCCCATAGCCTCATTTATATCTGTATAAAGGGATGAATATGTAAACAACGGAAGAA
G
Found at i:19781 original size:15 final size:15
Alignment explanation
Indices: 19763--19803 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
19753 TGATGAAGTT
19763 GAAAGAGATGAGGTG
1 GAAAGAGATGAGGTG
* *
19778 GAAAGAGATGATGTT
1 GAAAGAGATGAGGTG
19793 GAAAGAGATGA
1 GAAAGAGATGA
19804 AGACTCTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.44, C:0.00, G:0.39, T:0.17
Consensus pattern (15 bp):
GAAAGAGATGAGGTG
Found at i:24606 original size:21 final size:18
Alignment explanation
Indices: 24582--24681 Score: 73
Period size: 18 Copynumber: 5.3 Consensus size: 18
24572 AAAAAATCAT
*
24582 TAAAAATATCTATAAAAATTG
1 TAAAAATAT-T-T-AAAATTA
24603 TAAAAATATTTAAAATTA
1 TAAAAATATTTAAAATTA
*
24621 TAAAAA-ATTT-AAATAA
1 TAAAAATATTTAAAATTA
*
24637 CTAAAAA-ATTAAAAAATGTA
1 -TAAAAATATT-TAAAAT-TA
24657 -AACAAATATTTAAAAATTA
1 TAA-AAATATTT-AAAATTA
24676 TAAAAA
1 TAAAAA
24682 AATCTAAGAT
Statistics
Matches: 66, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
16 5 0.08
17 13 0.20
18 14 0.21
19 13 0.20
20 12 0.18
21 9 0.14
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (18 bp):
TAAAAATATTTAAAATTA
Found at i:24684 original size:21 final size:21
Alignment explanation
Indices: 24645--24684 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
24635 AACTAAAAAA
* *
24645 TTAAAAAATGTAAACAAATAT
1 TTAAAAAATATAAAAAAATAT
*
24666 TTAAAAATTATAAAAAAAT
1 TTAAAAAATATAAAAAAAT
24685 CTAAGATCCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (21 bp):
TTAAAAAATATAAAAAAATAT
Found at i:26177 original size:32 final size:32
Alignment explanation
Indices: 26136--26204 Score: 129
Period size: 32 Copynumber: 2.2 Consensus size: 32
26126 TGGTTTTACC
*
26136 ACTTAATCAATATTTATTATATATATTATTCA
1 ACTTAATCAATATCTATTATATATATTATTCA
26168 ACTTAATCAATATCTATTATATATATTATTCA
1 ACTTAATCAATATCTATTATATATATTATTCA
26200 ACTTA
1 ACTTA
26205 GTATCACGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.48
Consensus pattern (32 bp):
ACTTAATCAATATCTATTATATATATTATTCA
Found at i:27405 original size:58 final size:54
Alignment explanation
Indices: 27315--27536 Score: 219
Period size: 58 Copynumber: 3.9 Consensus size: 54
27305 AATTTTGAAA
* *
27315 TTTTTTTCTCGAAAAGAGAGTATCGACCATTGCATGCCCAACACCCAAAAATGCAATT
1 TTTTTTTCTC-AAAAAAGAGTGTCGACCATTGCATG-CCAACACCCAAAAATGC-A-T
* * * *
27373 TTTTTTTCTCTAAAAAAGAGTGTCGTCCATTGCATAGCCAATACCAAAAAATACAT
1 TTTTTTTCTC-AAAAAAGAGTGTCGACCATTGCAT-GCCAACACCCAAAAATGCAT
* * ** *
27429 TTTTTTTCTCAAAAAGGAGATGTCGACCATTACATGGCCAACACATAAAAATTGTAT
1 TTTTTTTCTCAAAAAAGAG-TGTCGACCATTGCAT-GCCAACACCCAAAAA-TGCAT
*
27486 TTTTTATCTGACAAAAAAGAAGTGTCGACCATTGCATGACCAACACCCAAA
1 TTTTTTTCT--CAAAAAAG-AGTGTCGACCATTGCATG-CCAACACCCAAA
27537 TTTTTTTTTT
Statistics
Matches: 136, Mismatches: 21, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
55 8 0.06
56 36 0.26
57 12 0.09
58 46 0.34
59 32 0.24
60 2 0.01
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (54 bp):
TTTTTTTCTCAAAAAAGAGTGTCGACCATTGCATGCCAACACCCAAAAATGCAT
Found at i:27459 original size:56 final size:56
Alignment explanation
Indices: 27278--27532 Score: 214
Period size: 59 Copynumber: 4.4 Consensus size: 56
27268 AAATGGGGTA
* * * * * *
27278 TCGATCATTGCATGACCAACACAAAAAAATTTTGAAATTTTTTTCTC-GAAAAGAGAGTA
1 TCGACCATTGCATG-CCAACACCAAAAAA---TGCATTTTTTTTCTCAAAAAAGAGAGTG
* *
27337 TCGACCATTGCATGCCCAACACCCAAAAATGCAATTTTTTTTTCTCTAAAAA-AGAGTG
1 TCGACCATTGCATG-CCAACACCAAAAAATGC-A-TTTTTTTTCTCAAAAAAGAGAGTG
* * * *
27395 TCGTCCATTGCATAGCCAATACCAAAAAATACATTTTTTTTCTCAAAAAGGAGA-TG
1 TCGACCATTGCAT-GCCAACACCAAAAAATGCATTTTTTTTCTCAAAAAAGAGAGTG
* * *
27451 TCGACCATTACATGGCCAACA-CATAAAAATTGTATTTTTTATCTGACAAAAAAGA-AGTG
1 TCGACCATTGCAT-GCCAACACCA-AAAAA-TGCATTTTTTTTCT--CAAAAAAGAGAGTG
27510 TCGACCATTGCATGACCAACACC
1 TCGACCATTGCATG-CCAACACC
27533 CAAATTTTTT
Statistics
Matches: 161, Mismatches: 23, Indels: 23
0.78 0.11 0.11
Matches are distributed among these distances:
55 2 0.01
56 41 0.25
57 16 0.10
58 43 0.27
59 58 0.36
60 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.29
Consensus pattern (56 bp):
TCGACCATTGCATGCCAACACCAAAAAATGCATTTTTTTTCTCAAAAAAGAGAGTG
Found at i:27479 original size:114 final size:114
Alignment explanation
Indices: 27315--27522 Score: 262
Period size: 114 Copynumber: 1.8 Consensus size: 114
27305 AATTTTGAAA
* * * *
27315 TTTTTTTCTCGAAAAGAGAGTATCGACCATTGCATGCCCAACACCCAAAAA-TGCAATTTTTTTT
1 TTTTTTTCTCAAAAAGAGAGTATCGACCATTACATGCCCAACACACAAAAATTG-AA-TTTTTTA
*
27379 TCT-CTAAAAAAG-AGTGTCGTCCATTGCATAGCCAATACCAAAAAATACAT
64 TCTAC-AAAAAAGAAGTGTCGACCATTGCATAGCCAATACCAAAAAATACAT
* * * *
27429 TTTTTTTCTCAAAAAG-GAGATGTCGACCATTACATGGCCAACACATAAAAATTGTATTTTTTAT
1 TTTTTTTCTCAAAAAGAGAG-TATCGACCATTACATGCCCAACACACAAAAATTGAATTTTTTAT
27493 CTGACAAAAAAGAAGTGTCGACCATTGCAT
65 CT-ACAAAAAAGAAGTGTCGACCATTGCAT
27523 GACCAACACC
Statistics
Matches: 80, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
113 12 0.15
114 49 0.61
115 19 0.24
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (114 bp):
TTTTTTTCTCAAAAAGAGAGTATCGACCATTACATGCCCAACACACAAAAATTGAATTTTTTATC
TACAAAAAAGAAGTGTCGACCATTGCATAGCCAATACCAAAAAATACAT
Found at i:29175 original size:127 final size:130
Alignment explanation
Indices: 28939--29238 Score: 430
Period size: 127 Copynumber: 2.3 Consensus size: 130
28929 AACACTGCAC
* *
28939 CCAAATTTCACATTTGCACTGACAAAAATAAAGAAACAAAGATTTATTTGGTATTGTTCATTTCC
1 CCAAA-TTCACACTTGCACTAAC-AAAATAAAGAAACAAAGATTTATTTGGTATTGTTCATTTCC
*
29004 ATTTTACAGTTCATGTTTGGAGCTTATGGAACCTATGTTCGAAACTCAATC-TGCCTTACCACCG
64 ATTTTACAGTTCATGTTCGGAGCTTATGGAACCTATGTTCGAAACTCAA-CGTGCCTTACCACCG
*
29068 CAT
128 CAA
* **
29071 CCAAATTCACACTTGCACTAACAAAA-AAA-AAA-AGAGATTTATTTGGTATTGTTCATTTCTGT
1 CCAAATTCACACTTGCACTAACAAAATAAAGAAACAAAGATTTATTTGGTATTGTTCATTTCCAT
* *
29133 TTTTCAGTTCATGTTCGGAGCTTATGGAACCTATGTTCGAAACTCAACGTGTCTTACCACCGCAA
66 TTTACAGTTCATGTTCGGAGCTTATGGAACCTATGTTCGAAACTCAACGTGCCTTACCACCGCAA
* *
29198 CCAAATTCACACTTGCACTAAC-AAGTAACAAAAACAAAGAT
1 CCAAATTCACACTTGCACTAACAAAATAA-AGAAACAAAGAT
29239 ATCATAAAAA
Statistics
Matches: 152, Mismatches: 11, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
126 3 0.02
127 110 0.72
128 4 0.03
129 6 0.04
130 9 0.06
131 15 0.10
132 5 0.03
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.31
Consensus pattern (130 bp):
CCAAATTCACACTTGCACTAACAAAATAAAGAAACAAAGATTTATTTGGTATTGTTCATTTCCAT
TTTACAGTTCATGTTCGGAGCTTATGGAACCTATGTTCGAAACTCAACGTGCCTTACCACCGCAA
Found at i:37953 original size:4 final size:4
Alignment explanation
Indices: 37940--37978 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
37930 AAAATTGAAG
*
37940 GAAA -AAA GAAA GAAA AAAGA GAAA GAAA GAAA GAAA GAA
1 GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAA
37979 GAAGGGGAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 3 0.10
4 25 0.81
5 3 0.10
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:37970 original size:21 final size:20
Alignment explanation
Indices: 37940--37980 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
37930 AAAATTGAAG
37940 GAAAAAAGAAAGAAAAAAGA
1 GAAAAAAGAAAGAAAAAAGA
*
37960 GAAAGAAAGAAAGAAAGAAGA
1 GAAA-AAAGAAAGAAAAAAGA
37981 AGGGGAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (20 bp):
GAAAAAAGAAAGAAAAAAGA
Done.