Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003581.1 Kokia drynarioides strain JFW-HI SEQ_116454, 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: 54554
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 6 characters in sequence are not A, C, G, or T
Found at i:6387 original size:143 final size:143
Alignment explanation
Indices: 6129--6421 Score: 372
Period size: 143 Copynumber: 2.0 Consensus size: 143
6119 GAAAAGGAAG
* * *
6129 AGTTCAACATTAGTAAGGTTTGAACTTGTACATTAAACGAGGCATAAGTGTAAGTTGAATACTAT
1 AGTTCACCATTAGTAAGGTTTAAACTTGTACATTAAACGAGGCATAAGTGTAAGTTGAATACTAC
* * * * *
6194 TTAGGCTAACTCATCAACAAATGCCTTATACGTATATTATATGATATAGGTTCGATTCATACTAT
66 TTAGGCTAACTCATCAACAAATGCCATATACATATATTATAGGACATAGGTTCGATTCATACTAC
*
6259 GCGCTATGCGAAT
131 ACGCTATGCGAAT
* * * * *
6272 AGTTCACCATTAGTATGGTTTAAATTTGTACCTTAAATGAGGCATAAGTGTAAGTTGAGTACTAC
1 AGTTCACCATTAGTAAGGTTTAAACTTGTACATTAAACGAGGCATAAGTGTAAGTTGAATACTAC
** * * * *
6337 TTAGGCTAGTTCATCGACAAATGCCATAT-CTATATATTATGGGGCATAGGTTTGATTCATACTA
66 TTAGGCTAACTCATCAACAAATGCCATATAC-ATATATTATAGGACATAGGTTCGATTCATACTA
* *
6401 CACGCTGTGTGAAT
130 CACGCTATGCGAAT
6415 AGTTCAC
1 AGTTCAC
6422 ATATTAAGAC
Statistics
Matches: 127, Mismatches: 22, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
142 1 0.01
143 126 0.99
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (143 bp):
AGTTCACCATTAGTAAGGTTTAAACTTGTACATTAAACGAGGCATAAGTGTAAGTTGAATACTAC
TTAGGCTAACTCATCAACAAATGCCATATACATATATTATAGGACATAGGTTCGATTCATACTAC
ACGCTATGCGAAT
Found at i:10523 original size:18 final size:19
Alignment explanation
Indices: 10496--10541 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
10486 ACTTGATATA
10496 AAAAATATTA-ATAATGTAT
1 AAAAATATTATATAAT-TAT
*
10515 AAAAA-ATTATCTAATTAT
1 AAAAATATTATATAATTAT
10533 AAAAATATT
1 AAAAATATT
10542 TAAATAGGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (19 bp):
AAAAATATTATATAATTAT
Found at i:21889 original size:16 final size:16
Alignment explanation
Indices: 21868--21899 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
21858 GAAAAAAAAA
21868 ATCAAACTACACAAAG
1 ATCAAACTACACAAAG
*
21884 ATCAAACTACATAAAG
1 ATCAAACTACACAAAG
21900 TGTAAATGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.56, C:0.22, G:0.06, T:0.16
Consensus pattern (16 bp):
ATCAAACTACACAAAG
Found at i:22593 original size:13 final size:12
Alignment explanation
Indices: 22575--22622 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
22565 CAGTTCATGC
22575 AATAATTTAATCT
1 AATAATTTAAT-T
22588 AATAATTTAATT
1 AATAATTTAATT
* *
22600 ACTAAATTAATT
1 AATAATTTAATT
* *
22612 TAGAATTTAAT
1 AATAATTTAAT
22623 CTGATGATTA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
12 18 0.62
13 11 0.38
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (12 bp):
AATAATTTAATT
Found at i:23539 original size:17 final size:16
Alignment explanation
Indices: 23517--23548 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
23507 CGGTTAAAAT
23517 CATTAACTAATTATTTG
1 CATTAACTAA-TATTTG
23534 CATTAACTAATATTT
1 CATTAACTAATATTT
23549 TAAGAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.38, C:0.12, G:0.03, T:0.47
Consensus pattern (16 bp):
CATTAACTAATATTTG
Found at i:26887 original size:159 final size:155
Alignment explanation
Indices: 26570--26892 Score: 540
Period size: 159 Copynumber: 2.1 Consensus size: 155
26560 TTAAGTAAAG
* * * *
26570 AAAT-TAAAATGTAATCTGAATCTTAATACAAGAGCTTCTATGTTACTTTTACAAACATATAGTG
1 AAATCTAAAATGCAATCTGAATCTTAATACAAAAACTTCTATGTTACTTTCACAAACATATAGTG
26634 TATTTAGTACTAAGTGTATATATATACATGTGATTATTTATCAATATCTATCAATATATTATGAG
66 TATTTAGTACTAAGTGTATATATATACATGTGATTATTTATCAATATCTATCAATATATTATGAG
*
26699 ATTATAATGTTTGATTTTATTGTGA
131 ATTATAACGTTTGATTTTATTGTGA
*
26724 AAATCTAAAATGCAATCTGAATCTTAATACAAAAACTTCTATGTTACTTTCACTAACATATAGTG
1 AAATCTAAAATGCAATCTGAATCTTAATACAAAAACTTCTATGTTACTTTCACAAACATATAGTG
*
26789 TATTTAGTACTAAGTGTGTATATATATATATATGTGATTATTTATCAATATCTATCAATATATTA
66 TATTTAGTACTAA--GTG--TATATATATACATGTGATTATTTATCAATATCTATCAATATATTA
26854 TGAGATTATAACGTTTGATTTTATTGTGA
127 TGAGATTATAACGTTTGATTTTATTGTGA
26883 AAATCTAAAA
1 AAATCTAAAA
26893 ATTTTACAAA
Statistics
Matches: 157, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
154 4 0.03
155 68 0.43
157 3 0.02
159 82 0.52
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (155 bp):
AAATCTAAAATGCAATCTGAATCTTAATACAAAAACTTCTATGTTACTTTCACAAACATATAGTG
TATTTAGTACTAAGTGTATATATATACATGTGATTATTTATCAATATCTATCAATATATTATGAG
ATTATAACGTTTGATTTTATTGTGA
Found at i:28588 original size:31 final size:31
Alignment explanation
Indices: 28553--28621 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 31
28543 GAATATTAAT
28553 TTTTTTGAA-AAATTTAAATATAATTTTATTA
1 TTTTTTGAAGAAA-TTAAATATAATTTTATTA
* * *
28584 -TTTTTGAAGAGATTAAATATAATTTTCTTT
1 TTTTTTGAAGAAATTAAATATAATTTTATTA
28614 TTTTTTGA
1 TTTTTTGA
28622 GGGGCTAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 24 0.73
31 9 0.27
ACGTcount: A:0.35, C:0.01, G:0.07, T:0.57
Consensus pattern (31 bp):
TTTTTTGAAGAAATTAAATATAATTTTATTA
Found at i:29400 original size:17 final size:17
Alignment explanation
Indices: 29378--29436 Score: 57
Period size: 19 Copynumber: 3.3 Consensus size: 17
29368 TGTTTAAATT
29378 AAAATTTAAAAAATATA
1 AAAATTTAAAAAATATA
*
29395 AAAATTTATTAAAAA-GTA
1 AAAATTTA--AAAAATATA
*
29413 AAATTATTAAATAAATATA
1 AAAAT-TTAAA-AAATATA
29432 AAAAT
1 AAAAT
29437 ATACTTTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
17 10 0.30
18 9 0.27
19 14 0.42
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (17 bp):
AAAATTTAAAAAATATA
Found at i:29408 original size:20 final size:20
Alignment explanation
Indices: 29383--29436 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 20
29373 AAATTAAAAT
29383 TTAAAAAATATAAAAATTTA
1 TTAAAAAATATAAAAATTTA
*
29403 TT-AAAAA-GT-AAAA-TTA
1 TTAAAAAATATAAAAATTTA
29419 TTAAATAAATATAAAAAT
1 TTAAA-AAATATAAAAAT
29437 ATACTTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 9
0.71 0.05 0.24
Matches are distributed among these distances:
16 5 0.19
17 6 0.22
18 4 0.15
19 6 0.22
20 6 0.22
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
TTAAAAAATATAAAAATTTA
Found at i:29884 original size:8 final size:8
Alignment explanation
Indices: 29837--29889 Score: 58
Period size: 8 Copynumber: 6.6 Consensus size: 8
29827 GTTACATCAG
29837 TAAATAATT
1 TAAA-AATT
29846 TAAAAATT
1 TAAAAATT
29854 ATAAAAA--
1 -TAAAAATT
29861 TAAATAATT
1 TAAA-AATT
29870 T-AAAATT
1 TAAAAATT
29877 TAAAAATT
1 TAAAAATT
29885 TAAAA
1 TAAAA
29890 GTTAACATGT
Statistics
Matches: 39, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
6 4 0.10
7 7 0.18
8 17 0.44
9 11 0.28
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
TAAAAATT
Found at i:29888 original size:24 final size:24
Alignment explanation
Indices: 29837--29883 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
29827 GTTACATCAG
29837 TAAATAATTTAAAAATTATAAAAA
1 TAAATAATTTAAAAATTATAAAAA
29861 TAAATAATTT-AAAATT-TAAAAA
1 TAAATAATTTAAAAATTATAAAAA
29883 T
1 T
29884 TTAAAAGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 7 0.30
23 6 0.26
24 10 0.43
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (24 bp):
TAAATAATTTAAAAATTATAAAAA
Found at i:29894 original size:15 final size:14
Alignment explanation
Indices: 29845--29894 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 14
29835 AGTAAATAAT
29845 TTAAAAATTATAAAA
1 TTAAAAATT-TAAAA
*
29860 ATAAATAATTTAAAA
1 TTAAA-AATTTAAAA
29875 TTTAAAAATTTAAAA
1 -TTAAAAATTTAAAA
29890 GTTAA
1 -TTAA
29895 CATGTAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 22 0.73
16 8 0.27
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (14 bp):
TTAAAAATTTAAAA
Found at i:35209 original size:28 final size:28
Alignment explanation
Indices: 35176--35231 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
35166 GAGTGTAAGC
35176 CCAACGTACTAGCTCGAAAAGATATTCA
1 CCAACGTACTAGCTCGAAAAGATATTCA
35204 CCAACGTACTAGCTCGAAAAGATATTCA
1 CCAACGTACTAGCTCGAAAAGATATTCA
35232 TCAGTCCAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.25, G:0.14, T:0.21
Consensus pattern (28 bp):
CCAACGTACTAGCTCGAAAAGATATTCA
Found at i:41752 original size:23 final size:23
Alignment explanation
Indices: 41724--41775 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
41714 GAAAATATCA
*
41724 CCAAGGAAGGGGTATTGCAATAT
1 CCAAGGAAGGGGTATTACAATAT
** *
41747 CCAAGGTTGGGGTATTACGATAT
1 CCAAGGAAGGGGTATTACAATAT
41770 CCAAGG
1 CCAAGG
41776 TCATCTACAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.23
Consensus pattern (23 bp):
CCAAGGAAGGGGTATTACAATAT
Found at i:41776 original size:23 final size:23
Alignment explanation
Indices: 41732--41776 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
41722 CACCAAGGAA
*
41732 GGGGTATTGCAATATCCAAGGTT
1 GGGGTATTACAATATCCAAGGTT
*
41755 GGGGTATTACGATATCCAAGGT
1 GGGGTATTACAATATCCAAGGT
41777 CATCTACAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.13, G:0.31, T:0.29
Consensus pattern (23 bp):
GGGGTATTACAATATCCAAGGTT
Found at i:42521 original size:68 final size:68
Alignment explanation
Indices: 42327--42530 Score: 290
Period size: 68 Copynumber: 3.0 Consensus size: 68
42317 TTTTTTTTCA
* * *
42327 TCTTCTTCGATTCTCTCTTTTGAGAAACAAAAGCTCTAGAGATCTTTAGAGAAATAAT-T-GT-T
1 TCTTCTTCGATTCTCTCTTTTGAGAAACAAAAACTCTAGAGATTTTTAGAGAAATAATCTCTTCT
*
42389 TAT
66 TCT
* * *
42392 TCTTCTTTGATTCTCTCTTTTGAAAAACAAAAAACTCTAAAGATTTTTAGAGAAATAATCTCTTC
1 TCTTCTTCGATTCTCTCTTTTGAGAAAC-AAAAACTCTAGAGATTTTTAGAGAAATAATCTCTTC
42457 TTCT
65 TTCT
*
42461 TCTTCTTCGATTC-CTTCTTTTGAGAAACAAAAACTCTAGAGATTTTTAGAGAAATTATCTCTTC
1 TCTTCTTCGATTCTC-TCTTTTGAGAAACAAAAACTCTAGAGATTTTTAGAGAAATAATCTCTTC
42525 TTCT
65 TTCT
42529 TC
1 TC
42531 AATATTGTCC
Statistics
Matches: 123, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
65 26 0.21
66 27 0.22
67 1 0.01
68 42 0.34
69 27 0.22
ACGTcount: A:0.30, C:0.18, G:0.10, T:0.42
Consensus pattern (68 bp):
TCTTCTTCGATTCTCTCTTTTGAGAAACAAAAACTCTAGAGATTTTTAGAGAAATAATCTCTTCT
TCT
Found at i:45291 original size:16 final size:15
Alignment explanation
Indices: 45265--45323 Score: 59
Period size: 17 Copynumber: 3.8 Consensus size: 15
45255 TGAAATTTAT
45265 TAATCATTTTATTGAAA
1 TAAT-ATTTTATT-AAA
45282 TAATATTTTAATTAAGA
1 TAATATTTT-ATTAA-A
*
45299 TAAT-TTTTATTTAA
1 TAATATTTTATTAAA
45313 TAA-ATTTTATT
1 TAATATTTTATT
45324 TAAAAATTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
14 11 0.29
15 4 0.11
16 11 0.29
17 12 0.32
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (15 bp):
TAATATTTTATTAAA
Found at i:45332 original size:13 final size:14
Alignment explanation
Indices: 45270--45332 Score: 56
Period size: 14 Copynumber: 4.3 Consensus size: 14
45260 TTTATTAATC
*
45270 ATTTTATTGAAATAA
1 ATTTTATT-TAATAA
*
45285 TATTTTAATTAAGATAA
1 -ATTTT-ATTTA-ATAA
*
45302 TTTTTATTTAATAA
1 ATTTTATTTAATAA
45316 ATTTTATTTAA-AA
1 ATTTTATTTAATAA
45329 ATTT
1 ATTT
45333 AGACAATATA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
13 6 0.14
14 14 0.33
15 4 0.10
16 11 0.26
17 7 0.17
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (14 bp):
ATTTTATTTAATAA
Done.