Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014516.1 Kokia drynarioides strain JFW-HI SEQ_129555, 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: 29864
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:11827 original size:201 final size:196
Alignment explanation
Indices: 11176--11870 Score: 771
Period size: 192 Copynumber: 3.5 Consensus size: 196
11166 AACCTTACTA
* * * * *
11176 CTGAGAAGTGGACCAAATTTGTCTTCCTAATGAGATACTGAGAAGCGGATTGAAACAAACGACGC
1 CTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTGAAACAAACGAGGC
* * * *
11241 GGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAATGCGAGCAAAT
66 GGTCATCTTCCTGATGAGACACT-AG-AGAAG--TATA-CTAA--CA-GCTCAATGCGAGCAAAT
* * * *
11306 CTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGGCAAAGCAACAAAAAGGTTAGCTTC
123 CTTCGAACCC-AGCTTCCTGATGAGATACTGAGAAGAAGGTCGAAGCAA-TAAAAGGTTAGCTTC
* *
11371 CTGATGAGATA
186 CTGATCAGATC
* * **
11382 CTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGTGGATTGAAACAAGTG-GGA
1 CTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTGAAACAAACGAGG-
* *
11446 CGGTCATCTTCCTGATGAGATAC-AGAGAAG--TA-TAACAACTCAATGCGA-CAAATCTTCGAA
65 CGGTCATCTTCCTGATGAGACACTAGAGAAGTATACTAACAGCTCAATGCGAGCAAATCTTCGAA
** * *
11506 CCCCAGCTTCCTGATGAGATACTGAGAAGTGGGGT-GAAGCAATAAAAGGTTAGTTTCCTGATTA
130 -CCCAGCTTCCTGATGAGATACTGAGAAG-AAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATCA
11570 GA-C
193 GATC
*
11573 ACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAAAGAAGCGGATTGAAACAAACGAGG
1 -CTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTGAAACAAACGAGG
* * * * *
11638 TGGTTATCTTCCTGATGAGACA-TAGAGAAGTATACTAACTTAGGGCTCGATGTGAGCAAATCCT
65 CGGTCATCTTCCTGATGAGACACTAGAGAAGTATACTAAC--A--GCTCAATGCGAGCAAATCTT
* * *
11702 CGAATCCCAGCTTCCTGATGAAATACCGAGAAGAAGGTCGAAGCAATAAAATGGTTAGCTTCTTG
126 CGAA-CCCAGCTTCCTGATGAGATACTGAGAAGAAGGTCGAAGCAATAAAA-GGTTAGCTTCCTG
*
11767 ATCAAATC
189 ATCAGATC
* * * * *
11775 CTGAGAAGTAGACCAAATTCGTCTTCCTGATAAGGTACAGAGAAGTGGATTGAAACAAGCGATGC
1 CTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTGAAACAAACGAGGC
*
11840 GGTCATCTTCCTGATAAGACACTA-AGAAGTA
66 GGTCATCTTCCTGATGAGACACTAGAGAAGTA
11871 GACCAAATCA
Statistics
Matches: 421, Mismatches: 50, Indels: 41
0.82 0.10 0.08
Matches are distributed among these distances:
192 103 0.24
193 45 0.11
194 17 0.04
195 6 0.01
197 3 0.01
199 12 0.03
200 49 0.12
201 99 0.24
202 3 0.01
203 5 0.01
204 2 0.00
205 1 0.00
206 76 0.18
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.23
Consensus pattern (196 bp):
CTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTGAAACAAACGAGGC
GGTCATCTTCCTGATGAGACACTAGAGAAGTATACTAACAGCTCAATGCGAGCAAATCTTCGAAC
CCAGCTTCCTGATGAGATACTGAGAAGAAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATCAGAT
C
Found at i:12227 original size:6 final size:6
Alignment explanation
Indices: 12218--12278 Score: 63
Period size: 6 Copynumber: 10.3 Consensus size: 6
12208 ATTGATTTTG
** *
12218 AATTTA AATTT- GTTTTA AAATTTA AATTT- AATTTA AATTTA TATTTA
1 AATTTA AATTTA AATTTA -AATTTA AATTTA AATTTA AATTTA AATTTA
*
12265 TATTTA AATTTA AA
1 AATTTA AATTTA AA
12279 ACTTATTATA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
5 8 0.17
6 34 0.74
7 4 0.09
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (6 bp):
AATTTA
Found at i:12243 original size:35 final size:35
Alignment explanation
Indices: 12185--12278 Score: 102
Period size: 35 Copynumber: 2.7 Consensus size: 35
12175 TTAAACCCAT
* * *
12185 TTTAAGATTTATTTTAAGA-TTAAATTGATTTTGAA
1 TTTAA-ATTTATTTTAAAATTTAAATTGAATTTAAA
* *
12220 TTTAAATTTGTTTTAAAATTTAAATTTAATTTAAA
1 TTTAAATTTATTTTAAAATTTAAATTGAATTTAAA
*
12255 TTTATATTTATATTT-AAATTTAAA
1 TTTAAATTTAT-TTTAAAATTTAAA
12279 ACTTATTATA
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
34 11 0.22
35 36 0.72
36 3 0.06
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.54
Consensus pattern (35 bp):
TTTAAATTTATTTTAAAATTTAAATTGAATTTAAA
Found at i:12269 original size:29 final size:29
Alignment explanation
Indices: 12218--12277 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
12208 ATTGATTTTG
*
12218 AATTTAAATTTGTTTTAAAATTTAAATTT
1 AATTTAAATTTATTTTAAAATTTAAATTT
*
12247 AATTTAAATTTATATTT-ATATTTAAATTT
1 AATTTAAATTTAT-TTTAAAATTTAAATTT
12276 AA
1 AA
12278 AACTTATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 25 0.89
30 3 0.11
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (29 bp):
AATTTAAATTTATTTTAAAATTTAAATTT
Found at i:12275 original size:18 final size:17
Alignment explanation
Indices: 12185--12278 Score: 82
Period size: 17 Copynumber: 5.4 Consensus size: 17
12175 TTAAACCCAT
*
12185 TTTAAGATTTATTTTAAGA
1 TTTAA-ATTTAATTTAA-A
* * *
12204 -TTAAATTGATTTTGAA
1 TTTAAATTTAATTTAAA
**
12220 TTTAAATTTGTTTTAAAA
1 TTTAAATTTAATTT-AAA
12238 TTTAAATTTAATTTAAA
1 TTTAAATTTAATTTAAA
*
12255 TTTATATTTATATTTAAA
1 TTTAAATTTA-ATTTAAA
12273 TTTAAA
1 TTTAAA
12279 ACTTATTATA
Statistics
Matches: 63, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
16 1 0.02
17 32 0.51
18 30 0.48
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.54
Consensus pattern (17 bp):
TTTAAATTTAATTTAAA
Found at i:12285 original size:23 final size:23
Alignment explanation
Indices: 12237--12291 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
12227 TTGTTTTAAA
**
12237 ATTTAAATTTAATTTAAATTTAT
1 ATTTAAATTTAATTTAAAACTAT
*
12260 ATTTATATTTAAATTTAAAACT-T
1 ATTTAAATTT-AATTTAAAACTAT
12283 ATTATAAAT
1 ATT-TAAAT
12292 ATTGAATGTC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 13 0.50
24 13 0.50
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
ATTTAAATTTAATTTAAAACTAT
Found at i:13002 original size:12 final size:12
Alignment explanation
Indices: 12957--13004 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
12947 TTAATATCTT
**
12957 CATTAATAATTG
1 CATTAATAATAA
12969 CATTAATAATAA
1 CATTAATAATAA
* **
12981 TATTTCTAATAA
1 CATTAATAATAA
12993 CATTAATAATAA
1 CATTAATAATAA
13005 ACAGTAGTAA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (12 bp):
CATTAATAATAA
Found at i:13083 original size:16 final size:16
Alignment explanation
Indices: 13058--13100 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
13048 TCAATAATAA
*
13058 TAATAATAATATTAAT
1 TAATATTAATATTAAT
13074 TAATATTAATATTAAT
1 TAATATTAATATTAAT
* *
13090 AAATTTTAATA
1 TAATATTAATA
13101 AATAAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TAATATTAATATTAAT
Found at i:14249 original size:29 final size:29
Alignment explanation
Indices: 14188--14573 Score: 261
Period size: 29 Copynumber: 13.2 Consensus size: 29
14178 CCCTTGAGGT
* *
14188 CCCGAAACCGTCCAAAAATTCCATTTTTGAC
1 CCCGAAA-CTTCCAAAAATTACATTTTT-AC
* *
14219 CCCGAAACTACCAAAAATTATATTTTTAC
1 CCCGAAACTTCCAAAAATTACATTTTTAC
* * *
14248 CCTCG-AACATCCAAAAATTCCATTTTTGAT
1 CC-CGAAACTTCCAAAAATTACATTTTT-AC
** * * * *
14278 CTTGAAACTTTCAAAAATTATATATGTAC
1 CCCGAAACTTCCAAAAATTACATTTTTAC
*
14307 CCTCG-AACTTCCAAAAATTCCATTTTTAGC
1 CC-CGAAACTTCCAAAAATTACATTTTTA-C
* *
14337 CCCAAAACTTTCAAAAATTACATTTTTAC
1 CCCGAAACTTCCAAAAATTACATTTTTAC
*
14366 CCTCG-AACTTCCAAAAATTCCATTTTTAAC
1 CC-CGAAACTTCCAAAAATTACATTTTT-AC
*
14396 CCCAAAACTTCCAAAAATTACATTTTTAC
1 CCCGAAACTTCCAAAAATTACATTTTTAC
* * * *
14425 CTCTG-AACCTCCAAAAATTCCATTTTGAC
1 C-CCGAAACTTCCAAAAATTACATTTTTAC
**
14454 CTTGAAACTTCCAAAAATTACCA-TTTTAC
1 CCCGAAACTTCCAAAAATTA-CATTTTTAC
* * * * *
14483 CCCCAGA-TTCCAAAAACTCCATTTTGAC
1 CCCGAAACTTCCAAAAATTACATTTTTAC
* **
14511 CCCCAAAAGTCTC-AAAATTACCA-TTTTACC
1 CCCGAAACTTC-CAAAAATTA-CATTTTTA-C
* * *
14541 CCCG-AA-TGTCCAAAAATTCCGTTTTTAT
1 CCCGAAACT-TCCAAAAATTACATTTTTAC
14569 CCCGA
1 CCCGA
14574 TTTTTCTAAA
Statistics
Matches: 275, Mismatches: 59, Indels: 44
0.73 0.16 0.12
Matches are distributed among these distances:
27 2 0.01
28 29 0.11
29 140 0.51
30 97 0.35
31 7 0.03
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.31
Consensus pattern (29 bp):
CCCGAAACTTCCAAAAATTACATTTTTAC
Found at i:14293 original size:59 final size:59
Alignment explanation
Indices: 14198--14566 Score: 389
Period size: 59 Copynumber: 6.3 Consensus size: 59
14188 CCCGAAACCG
* * *
14198 TCCAAAAATTCCATTTTTGACCCCGAAACTACCAAAAATTATATTTTTACCCTCGAACA
1 TCCAAAAATTCCATTTTTGACCCCGAAACTTCCAAAAATTACATTTTTACCCTCGAACT
* ** * * * *
14257 TCCAAAAATTCCATTTTTGATCTTGAAACTTTCAAAAATTATATATGTACCCTCGAACT
1 TCCAAAAATTCCATTTTTGACCCCGAAACTTCCAAAAATTACATTTTTACCCTCGAACT
* *
14316 TCCAAAAATTCCATTTTT-AGCCCCAAAACTTTCAAAAATTACATTTTTACCCTCGAACT
1 TCCAAAAATTCCATTTTTGA-CCCCGAAACTTCCAAAAATTACATTTTTACCCTCGAACT
* * *
14375 TCCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTACATTTTTA-CCTCTGAACC
1 TCCAAAAATTCCATTTTTGACCCCGAAACTTCCAAAAATTACATTTTTACCCTC-GAACT
** *
14434 TCCAAAAATTCCA-TTTTGACCTTGAAACTTCCAAAAATTACCA-TTTTACCC-CCAGA-T
1 TCCAAAAATTCCATTTTTGACCCCGAAACTTCCAAAAATTA-CATTTTTACCCTCGA-ACT
* * ** *
14491 TCCAAAAACTCCA-TTTTGACCCCCAAAAGTCTC-AAAATTACCA-TTTTACCCCCGAA-T
1 TCCAAAAATTCCATTTTTGACCCCGAAACTTC-CAAAAATTA-CATTTTTACCCTCGAACT
*
14548 GTCCAAAAATTCCGTTTTT
1 -TCCAAAAATTCCATTTTT
14567 ATCCCGATTT
Statistics
Matches: 268, Mismatches: 32, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
57 46 0.17
58 49 0.18
59 172 0.64
60 1 0.00
ACGTcount: A:0.36, C:0.27, G:0.05, T:0.33
Consensus pattern (59 bp):
TCCAAAAATTCCATTTTTGACCCCGAAACTTCCAAAAATTACATTTTTACCCTCGAACT
Found at i:14565 original size:28 final size:28
Alignment explanation
Indices: 14463--14687 Score: 110
Period size: 28 Copynumber: 7.9 Consensus size: 28
14453 CCTTGAAACT
14463 TCCAAAAATTACCATTTTACCCCCAGAT-
1 TCCAAAAATTACCATTTTACCCCCA-ATG
* *
14491 TCCAAAAACT-CCATTTTGACCCCCAAAAG
1 TCCAAAAATTACCATTTT-ACCCCC-AATG
14520 TCTC-AAAATTACCATTTTACCCCCGAATG
1 TC-CAAAAATTACCATTTTACCCCC-AATG
* * * * *
14549 TCCAAAAATT-CCGTTTTTATCCCGATTTT
1 TCCAAAAATTACC-ATTTTACCCCCA-ATG
* * * * *
14578 TCTAAAAATTATCGTTTTAACCTCGAATG
1 TCCAAAAATTACCATTTT-ACCCCCAATG
* *
14607 T--ATAAAATT-CCATTTTAAACCCCAAATTTT
1 TCCA-AAAATTACCATTTT--ACCCCCAA--TG
*
14637 TCC-AAAATTACCATTTTGCCCCCAA-G
1 TCCAAAAATTACCATTTTACCCCCAATG
14663 AATCC-AAAATTACCATTTTACCCCC
1 --TCCAAAAATTACCATTTTACCCCC
14688 GGGTATCCAA
Statistics
Matches: 152, Mismatches: 26, Indels: 38
0.70 0.12 0.18
Matches are distributed among these distances:
27 13 0.09
28 55 0.36
29 55 0.36
30 22 0.14
31 7 0.05
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.32
Consensus pattern (28 bp):
TCCAAAAATTACCATTTTACCCCCAATG
Found at i:22325 original size:18 final size:18
Alignment explanation
Indices: 22287--22321 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
22277 TGTAACATTT
*
22287 TTATTATTTTATTTATAA
1 TTATTATTTTATTTAAAA
22305 TTATTATTTT-TTTAAAA
1 TTATTATTTTATTTAAAA
22322 ATTAAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTATTATTTTATTTAAAA
Done.