Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000487.1 Kokia drynarioides strain JFW-HI SEQ_111362, 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: 32154
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 58 characters in sequence are not A, C, G, or T
Found at i:259 original size:4 final size:4
Alignment explanation
Indices: 252--290 Score: 60
Period size: 4 Copynumber: 9.5 Consensus size: 4
242 TTCTTCCTTC
*
252 TTCT TTCT TTCT TTCT TTCT TTCT CTTTT TTCT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TT
291 TTCCTTCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 29 0.91
5 3 0.09
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:302 original size:21 final size:21
Alignment explanation
Indices: 259--304 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
249 TTCTTCTTTC
* *
259 TTTCTTTCTTTCTTTCTCTTT
1 TTTCTTTCTTTCTTCCTCATT
280 TTTCTTTCTTT-TTCCTTCATT
1 TTTCTTTCTTTCTTCC-TCATT
301 TTTC
1 TTTC
305 GTTAGTCCCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTCTTTCTTTCTTCCTCATT
Found at i:1483 original size:24 final size:24
Alignment explanation
Indices: 1456--1505 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1446 ACATAAATCG
1456 TGTT-TTTTTCTCTCAATTAAACTT
1 TGTTATTTTTCTCT-AATTAAACTT
* *
1480 TGTTATTTTTTTCTAGTTAAACTT
1 TGTTATTTTTCTCTAATTAAACTT
1504 TG
1 TG
1506 ATTACTGTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.20, C:0.12, G:0.08, T:0.60
Consensus pattern (24 bp):
TGTTATTTTTCTCTAATTAAACTT
Found at i:11279 original size:17 final size:18
Alignment explanation
Indices: 11243--11280 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
11233 ATTTTAAAAA
*
11243 AAATATTTTTATACTTTT
1 AAATAATTTTATACTTTT
*
11261 AAATAATTTTA-ATTTTT
1 AAATAATTTTATACTTTT
11278 AAA
1 AAA
11281 GTTTTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (18 bp):
AAATAATTTTATACTTTT
Found at i:19567 original size:123 final size:123
Alignment explanation
Indices: 19349--19977 Score: 854
Period size: 123 Copynumber: 5.1 Consensus size: 123
19339 TCGATGGAGG
*
19349 ACCTTTAGGTAGCATCCCGAAGTTCAAAC-CTTTGAAATTGACAAAGATGTTGACT-TCAATGAT
1 ACCTTTAGGTAGCATCCCGAAGTTCAAACTTTTTGAAATTGACAAAGATGTTGA-TGTCAATGAT
* * * * * *
19412 AGTGAAGATGGAGGCGGATTTGATGTACGCGTACTAGGTCCTGACGAAAGG-ATAGGCGC
65 GGTGAAGGTGGAGGCAGATCTGATGTACGCGTACTAGGTCCTGACG-GAGGAATAGGCAC
* * *
19471 ACCTTTAGGTAGCAT-CCGAAAGTTCAAGCTTTTTGAAATTGACAAAGATCTTGATGTTAATGAT
1 ACCTTTAGGTAGCATCCCG-AAGTTCAAACTTTTTGAAATTGACAAAGATGTTGATGTCAATGAT
* * *
19535 GGTGAAGGTTGAGGCAGATCTGATGTACGCGTACTAGGTCCTGATGGAGGAATAGGTAC
65 GGTGAAGGTGGAGGCAGATCTGATGTACGCGTACTAGGTCCTGACGGAGGAATAGGCAC
* *
19594 ACTTTTAGGTAGCATCCCGAAGTTCAAGCTTTTTGAAATTGACAAAGATGTTGATGTCAATGATG
1 ACCTTTAGGTAGCATCCCGAAGTTCAAACTTTTTGAAATTGACAAAGATGTTGATGTCAATGATG
* * *
19659 GTGAAGGTGGAGGCAGATCAGATGTACGCGTACTAGGTCCTGATGGAGGAATAGGTAC
66 GTGAAGGTGGAGGCAGATCTGATGTACGCGTACTAGGTCCTGACGGAGGAATAGGCAC
*
19717 ACCTTTAGGTAGCATCCCGAAGTTCAAACTTTTTGAAATTGACAAAGATGTCGATGTCAATGATG
1 ACCTTTAGGTAGCATCCCGAAGTTCAAACTTTTTGAAATTGACAAAGATGTTGATGTCAATGATG
* * *
19782 GTGGAGGTGGAGGC-GAATCTGATGTACGGGTACTAGGTCCCGACGGAGGAATAGGCAC
66 GTGAAGGTGGAGGCAG-ATCTGATGTACGCGTACTAGGTCCTGACGGAGGAATAGGCAC
** ** *
19840 ACCTTTAGGTAGCATCCCGAAGTTCAAACTTTTTGAAATTGACACTGATGTCAATATCAATGATG
1 ACCTTTAGGTAGCATCCCGAAGTTCAAACTTTTTGAAATTGACAAAGATGTTGATGTCAATGATG
** * *
19905 GTGATGGTGGAGGTGGAGGTGGATCTGATGTACGCGTACTAGGTCCCGACGGAGGAATAGGAAC
66 GTGA------AGGTGGAGGCAGATCTGATGTACGCGTACTAGGTCCTGACGGAGGAATAGGCAC
19969 ACCTTTAGG
1 ACCTTTAGG
19978 CAACATCTCG
Statistics
Matches: 459, Mismatches: 35, Indels: 19
0.89 0.07 0.04
Matches are distributed among these distances:
121 3 0.01
122 29 0.06
123 365 0.80
124 3 0.01
129 58 0.13
130 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.27
Consensus pattern (123 bp):
ACCTTTAGGTAGCATCCCGAAGTTCAAACTTTTTGAAATTGACAAAGATGTTGATGTCAATGATG
GTGAAGGTGGAGGCAGATCTGATGTACGCGTACTAGGTCCTGACGGAGGAATAGGCAC
Found at i:22093 original size:123 final size:123
Alignment explanation
Indices: 21874--22386 Score: 857
Period size: 123 Copynumber: 4.2 Consensus size: 123
21864 CTGACGAAGG
* * ** * * * * *
21874 ACCTTTAGCCAACATCGTGAAGTTCAAATTTTTTGAAATCGACAAAGATGTCGATGCCAATGGTG
1 ACCTTTAGGCAGCATCCCGAAGTTTAAACTTTTTGAAATCGACAGAGATGTCGATGTCAATGATG
*
21939 GTGGAGGTGGAGGCGGATCTGATGTACGCGTACTAGGACCCGATGGAGGAATAGGGAC
66 GTGGAGGTGGAGGCGAATCTGATGTACGCGTACTAGGACCCGATGGAGGAATAGGGAC
21997 ACCTTTAGGCAGCATCCCGAAGTTTAAACTTTTTGAAATCGACAGAGATGTCGATGTCAATGATG
1 ACCTTTAGGCAGCATCCCGAAGTTTAAACTTTTTGAAATCGACAGAGATGTCGATGTCAATGATG
* *
22062 GTGAAGGTGGAGGCGGATCTGATGTACGCGTACTAGGACCCGATGGAGGAATAGGGAC
66 GTGGAGGTGGAGGCGAATCTGATGTACGCGTACTAGGACCCGATGGAGGAATAGGGAC
22120 ACCTTTAGGCAGCATCCCGAAGTTTAAACTTTTTGAAATCGACAGAGATGTCGATGTCAATGATG
1 ACCTTTAGGCAGCATCCCGAAGTTTAAACTTTTTGAAATCGACAGAGATGTCGATGTCAATGATG
*
22185 GTGGAGGTGGAGGCGAATCTGATGTACGCGTACTAGGACTCGATGGAGGAATAGGGAC
66 GTGGAGGTGGAGGCGAATCTGATGTACGCGTACTAGGACCCGATGGAGGAATAGGGAC
*
22243 ACCTTTAGGCAGCATCCCGAAGTTTAAACTTTTTGAAATCGACAGAGATGTCGATGTCAATGGTG
1 ACCTTTAGGCAGCATCCCGAAGTTTAAACTTTTTGAAATCGACAGAGATGTCGATGTCAATGATG
* * *
22308 GTGGAGGTGGAGGC-AATTATGATGTATGCGTACTAGGACCCGACGGAGGAATAGGGAC
66 GTGGAGGTGGAGGCGAA-TCTGATGTACGCGTACTAGGACCCGATGGAGGAATAGGGAC
22366 ACCTTTAGGCAGCATCCCGAA
1 ACCTTTAGGCAGCATCCCGAA
22387 TCGAAGGGTT
Statistics
Matches: 371, Mismatches: 18, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
122 2 0.01
123 369 0.99
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.24
Consensus pattern (123 bp):
ACCTTTAGGCAGCATCCCGAAGTTTAAACTTTTTGAAATCGACAGAGATGTCGATGTCAATGATG
GTGGAGGTGGAGGCGAATCTGATGTACGCGTACTAGGACCCGATGGAGGAATAGGGAC
Found at i:26953 original size:6 final size:6
Alignment explanation
Indices: 26942--26969 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
26932 GAAGGTGGGA
26942 GGAGAG GGAGAG GGAGAG GGAGAG GGAG
1 GGAGAG GGAGAG GGAGAG GGAGAG GGAG
26970 GCCGACGGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (6 bp):
GGAGAG
Found at i:27152 original size:17 final size:18
Alignment explanation
Indices: 27132--27175 Score: 63
Period size: 20 Copynumber: 2.4 Consensus size: 18
27122 TTTGTCAATA
27132 TAAAAA-TGTTGTTAGAT
1 TAAAAACTGTTGTTAGAT
27149 TAAAAACCGTGTTGTTAGAT
1 TAAAAA-C-TGTTGTTAGAT
27169 TAAAAAC
1 TAAAAAC
27176 CGTTTCTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.25
19 1 0.04
20 17 0.71
ACGTcount: A:0.43, C:0.07, G:0.16, T:0.34
Consensus pattern (18 bp):
TAAAAACTGTTGTTAGAT
Found at i:27163 original size:20 final size:20
Alignment explanation
Indices: 27138--27178 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
27128 AATATAAAAA
27138 TGTTGTTAGATTAAAAACCG
1 TGTTGTTAGATTAAAAACCG
27158 TGTTGTTAGATTAAAAACCG
1 TGTTGTTAGATTAAAAACCG
27178 T
1 T
27179 TTCTGAAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.37
Consensus pattern (20 bp):
TGTTGTTAGATTAAAAACCG
Found at i:28221 original size:26 final size:25
Alignment explanation
Indices: 28176--28228 Score: 79
Period size: 26 Copynumber: 2.1 Consensus size: 25
28166 AAATAATAAA
* *
28176 TTTATTTTTTAATAAATATCAAGAT
1 TTTATTTTATAATAAATATCAAAAT
28201 TTTATTTTATAACTAAATATCAAAAT
1 TTTATTTTATAA-TAAATATCAAAAT
28227 TT
1 TT
28229 ACCCTATCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 11 0.44
26 14 0.56
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.51
Consensus pattern (25 bp):
TTTATTTTATAATAAATATCAAAAT
Found at i:28229 original size:25 final size:24
Alignment explanation
Indices: 28173--28229 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 24
28163 CACAAATAAT
*
28173 AAATTTATTTTTTAATAAATATCA
1 AAATTTATTTTATAATAAATATCA
*
28197 AGATTTTATTTTATAACTAAATATCA
1 A-AATTTATTTTATAA-TAAATATCA
28223 AAATTTA
1 AAATTTA
28230 CCCTATCTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 1 0.04
25 17 0.61
26 10 0.36
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.47
Consensus pattern (24 bp):
AAATTTATTTTATAATAAATATCA
Found at i:28993 original size:20 final size:20
Alignment explanation
Indices: 28968--29010 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
28958 TCACCTAGTT
28968 CCAACTGTCCACCTAAGACC
1 CCAACTGTCCACCTAAGACC
28988 CCAACTGTCCACCTAAGACC
1 CCAACTGTCCACCTAAGACC
29008 CCA
1 CCA
29011 CTTGAATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.47, G:0.09, T:0.14
Consensus pattern (20 bp):
CCAACTGTCCACCTAAGACC
Found at i:29707 original size:5 final size:5
Alignment explanation
Indices: 29697--29728 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
29687 TTCAAGGGCC
29697 CAGGG CAGGG CAGGG CAGGG CAGGG CAGGG CA
1 CAGGG CAGGG CAGGG CAGGG CAGGG CAGGG CA
29729 ATATTGGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.22, C:0.22, G:0.56, T:0.00
Consensus pattern (5 bp):
CAGGG
Done.