Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008721.1 Kokia drynarioides strain JFW-HI SEQ_123403, 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: 15380
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Found at i:1267 original size:29 final size:29
Alignment explanation
Indices: 1217--1593 Score: 234
Period size: 29 Copynumber: 12.8 Consensus size: 29
1207 GAAGGTCCTT
* ** *
1217 GAACTGTCCAAAAATTATATTTTTACTCTC
1 GAACTTTCC-AAAATTCCATTTTTACCCTC
* * *
1247 AAACTTTCCAAAATTCCATTTTAACCCCC
1 GAACTTTCCAAAATTCCATTTTTACCCTC
* * * * *
1276 AAACTATCCAAAAATTACAATTTTACCCTT
1 GAACTTTCC-AAAATTCCATTTTTACCCTC
1306 GAACTTTCCAAAATTCCATATTTTGACCCT-
1 GAACTTTCCAAAATTCCAT-TTTT-ACCCTC
* * *
1336 GAACTTTTCAAAAATTACA-TTTTACCCAC
1 GAAC-TTTCCAAAATTCCATTTTTACCCTC
**
1365 GAACTTTCCAAAATTCTTTTTTTAACCC-C
1 GAACTTTCCAAAATTCCATTTTT-ACCCTC
* * *
1394 GAACTTTCCAAACATTGCATTTTCACCTTC
1 GAACTTTCCAAA-ATTCCATTTTTACCCTC
*
1424 GAACTTTCCAAAATTCCTTTTTTGA-CCTC
1 GAACTTTCCAAAATTCCATTTTT-ACCCTC
*
1453 GAACCTTCCAAAATTACCA-TTTTACCCTC
1 GAACTTTCCAAAATT-CCATTTTTACCCTC
* * *
1482 GAA-TGTCTAAAAATTCCATTTTTAACCTC
1 GAACTTTC-CAAAATTCCATTTTTACCCTC
* *
1511 -ATACCTTCCAAAAATTACCA-TTCTACCCTC
1 GA-ACTTTCC-AAAATT-CCATTTTTACCCTC
* * * *
1541 GGA-TATCTAAAAATTCCATTTTAAACCC-C
1 GAACTTTC-CAAAATTCCATTTT-TACCCTC
* *
1570 AAACCTTTCAAAAATTACCATTTT
1 GAA-CTTTCCAAAATT-CCATTTT
1594 ATTCTCGGAG
Statistics
Matches: 269, Mismatches: 53, Indels: 49
0.73 0.14 0.13
Matches are distributed among these distances:
28 24 0.09
29 123 0.46
30 92 0.34
31 30 0.11
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.36
Consensus pattern (29 bp):
GAACTTTCCAAAATTCCATTTTTACCCTC
Found at i:1315 original size:59 final size:57
Alignment explanation
Indices: 1218--1594 Score: 289
Period size: 59 Copynumber: 6.4 Consensus size: 57
1208 AAGGTCCTTG
* * *
1218 AACTGTCCAAAAATTA-TATTTTTACTCTCAAACTTTCCAAAATTCCATTTTAACCCCCA
1 AACT-TCCAAAAATTACCA-TTTTACCCTCGAACTTTCCAAAATTCCATTTTAA-CCCCA
* * * **
1277 AACTATCCAAAAATTACAATTTTACCCTTGAACTTTCCAAAATTCCATATTTTGACCCTG
1 AACT-TCCAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCC--ATTTTAACCCCA
* * ** *
1337 AACTTTTCAAAAATTA-CATTTTACCCACGAACTTTCCAAAATTCTTTTTTTAACCCCG
1 AAC-TTCCAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTC-CATTTTAACCCCA
* * * * * *
1395 AACTTTCCAAACATT-GCATTTTCACCTTCGAACTTTCCAAAATTCCTTTTTTGACCTCGA
1 AAC-TTCCAAAAATTACCATTTT-ACCCTCGAACTTTCCAAAATTCC-ATTTTAACC-CCA
* * * *
1455 ACCTTCC-AAAATTACCATTTTACCCTCGAA-TGTCTAAAAATTCCATTTTTAACCTCA
1 AACTTCCAAAAATTACCATTTTACCCTCGAACTTTC-CAAAATTCCA-TTTTAACCCCA
* * * * *
1512 TACCTTCCAAAAATTACCATTCTACCCTCGGA-TATCTAAAAATTCCATTTTAAACCCCA
1 -AACTTCCAAAAATTACCATTTTACCCTCGAACTTTC-CAAAATTCCATTTT-AACCCCA
*
1571 AACCTTTCAAAAATTACCATTTTA
1 AA-CTTCCAAAAATTACCATTTTA
1595 TTCTCGGAGC
Statistics
Matches: 261, Mismatches: 41, Indels: 32
0.78 0.12 0.10
Matches are distributed among these distances:
57 4 0.02
58 68 0.26
59 162 0.62
60 20 0.08
61 7 0.03
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.36
Consensus pattern (57 bp):
AACTTCCAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTAACCCCA
Found at i:1622 original size:29 final size:28
Alignment explanation
Indices: 1580--1640 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
1570 AAACCTTTCA
** *
1580 AAAATTACCATTTTATTCTCGGAGCATCC
1 AAAATTACCATTTTACCCCCGG-GCATCC
**
1609 AAAATTACTGTTTTACCCCCGGGCATCC
1 AAAATTACCATTTTACCCCCGGGCATCC
1637 AAAA
1 AAAA
1641 ATCTCATTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 10 0.37
29 17 0.63
ACGTcount: A:0.33, C:0.26, G:0.11, T:0.30
Consensus pattern (28 bp):
AAAATTACCATTTTACCCCCGGGCATCC
Found at i:14025 original size:37 final size:37
Alignment explanation
Indices: 13967--14116 Score: 120
Period size: 37 Copynumber: 3.7 Consensus size: 37
13957 AAATGGTTAG
* *
13967 CTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGT
1 CTTCTTGATGAGATACAGAGAAGTGGACCAAATTCGT
* * *
14004 CTTCTTGATGAGATACAGAGAAGCGGATTGAAACAAATAAAATGGTT
1 CTTCTTGATGAGATACAGAGAA---G--TGGACCAAAT----TCG-T
*
14051 AGCTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGT
1 --CTTCTTGATGAGATACAGAGAAGTGGACCAAATTCGT
* *
14090 CTTCTTGATGAGATACAAAAAAGTGGA
1 CTTCTTGATGAGATACAGAGAAGTGGA
14117 TTGAAACAAG
Statistics
Matches: 89, Mismatches: 12, Indels: 24
0.71 0.10 0.19
Matches are distributed among these distances:
37 44 0.49
39 1 0.01
40 3 0.03
42 8 0.09
44 8 0.09
46 3 0.03
47 1 0.01
49 21 0.24
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (37 bp):
CTTCTTGATGAGATACAGAGAAGTGGACCAAATTCGT
Found at i:14068 original size:86 final size:86
Alignment explanation
Indices: 13953--14171 Score: 323
Period size: 86 Copynumber: 2.5 Consensus size: 86
13943 AGGTCGAAGC
*
13953 AATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGAGAT
1 AATAAAATGGTTAGCTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGAGAT
* *
14018 ACAGAGAAGCGGATTGAAACA
66 ACAAAAAAGCGGATTGAAACA
14039 AATAAAATGGTTAGCTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGAGAT
1 AATAAAATGGTTAGCTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGAGAT
*
14104 ACAAAAAAGTGGATTGAAACA
66 ACAAAAAAGCGGATTGAAACA
* * ** * * *
14125 AGTGATGTGGTCATCTT-TCTGATGAGATACTGAGAAGTAGACCAAAT
1 AATAAAATGGTTAGCTTCT-TGATGAGATACTGAGAAGTGGACCAAAT
14172 CAATGAAGCT
Statistics
Matches: 121, Mismatches: 11, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
85 1 0.01
86 120 0.99
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (86 bp):
AATAAAATGGTTAGCTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGAGAT
ACAAAAAAGCGGATTGAAACA
Found at i:14071 original size:209 final size:209
Alignment explanation
Indices: 13685--14085 Score: 631
Period size: 209 Copynumber: 1.9 Consensus size: 209
13675 TAATGAAACC
* *
13685 AAGTGAGTAAATCTTTGAACCCCAACTTCCTGATGAGATACTAAGAAGCAGGTCGAAACAATAAA
1 AAGTAAGTAAATCTTTGAACCCCAACTTCCTGATGAGAGACTAAGAAGCAGGTCGAAACAATAAA
13750 ATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGAG
66 ATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGAG
* * * ** *
13815 AAGTGGATTGAAACAAGTGATGCGGTCATCTTCCTGATGAAATACTGAGAAGTAGACCAAATCAA
131 AAGCGGATTGAAACAAATAAAACGGTCAGCTTCCTGATGAAATACTGAGAAGTAGACCAAATCAA
13880 TGAAGCCAGACTCA
196 TGAAGCCAGACTCA
* * *
13894 AAGTAAGTAAATCTTTGAACCCCAGCTTCCTGATGAGAGACTAAGAAGTAGGTCGAAGCAATAAA
1 AAGTAAGTAAATCTTTGAACCCCAACTTCCTGATGAGAGACTAAGAAGCAGGTCGAAACAATAAA
* * *
13959 ATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGAGATACAGAG
66 ATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGAG
* * * * *
14024 AAGCGGATTGAAACAAATAAAATGGTTAGCTTCTTGATGAGATACTGAGAAGTGGACCAAAT
131 AAGCGGATTGAAACAAATAAAACGGTCAGCTTCCTGATGAAATACTGAGAAGTAGACCAAAT
14086 TCGTCTTCTT
Statistics
Matches: 173, Mismatches: 19, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
209 173 1.00
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.24
Consensus pattern (209 bp):
AAGTAAGTAAATCTTTGAACCCCAACTTCCTGATGAGAGACTAAGAAGCAGGTCGAAACAATAAA
ATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGAG
AAGCGGATTGAAACAAATAAAACGGTCAGCTTCCTGATGAAATACTGAGAAGTAGACCAAATCAA
TGAAGCCAGACTCA
Found at i:14274 original size:295 final size:295
Alignment explanation
Indices: 13710--14381 Score: 1017
Period size: 295 Copynumber: 2.3 Consensus size: 295
13700 TGAACCCCAA
*
13710 CTTCCTGATGAGATACTA-AGAAGCAGG-TCGAAAC-AATAAAATGGTTAGCTTCCTGATGAGAT
1 CTTCCTGATGAGATAC-AGAGAAGC-GGATTGAAACAAATAAAATGGTTAGCTTCCTGATGAGAT
* * *
13772 ACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGAGAAGTGGATTGAAACAAGTGATG
64 ACTGAGAAGTGGACCAAATTCATCTTCCTGATGAGATACAAAAAAGTGGATTGAAACAAGTGATG
*
13837 CGGTCATCTTCCTGATGAAATACTGAGAAGTAGACCAAATCAATGAAGCCAGACTCAAAGTAAGT
129 CGGTCATCTTCCTGATGAAATACTGAGAAGTAGACCAAATCAATGAAGCCAGACTCAAAGTAAGC
*
13902 AAATCTTTGAACCCCAGCTTCCTGATGAGAGACTAAGAAGTAGGTCGAAGCAATAAAATGGTTAG
194 AAATCTTTGAACCCCAGCTTCCTGATGAGAGACTAAGAAGCAGGTCGAAGCAATAAAATGGTTAG
* *
13967 CTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGT
259 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCAT
* *
14004 CTTCTTGATGAGATACAGAGAAGCGGATTGAAACAAATAAAATGGTTAGCTTCTTGATGAGATAC
1 CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAATAAAATGGTTAGCTTCCTGATGAGATAC
* * *
14069 TGAGAAGTGGACCAAATTCGTCTTCTTGATGAGATACAAAAAAGTGGATTGAAACAAGTGATGTG
66 TGAGAAGTGGACCAAATTCATCTTCCTGATGAGATACAAAAAAGTGGATTGAAACAAGTGATGCG
* * *
14134 GTCATCTTTCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAGCTAGACTCAAAGTAAGCAA
131 GTCATCTTCCTGATGAAATACTGAGAAGTAGACCAAATCAATGAAGCCAGACTCAAAGTAAGCAA
* * * *
14199 ATCTTTGAATCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTTGAAGCAATAAAATGGTTAGCT
196 ATCTTTGAACCCCAGCTTCCTGATGAGAGACTAAGAAGCAGGTCGAAGCAATAAAATGGTTAGCT
*
14264 TCTTGATGAGATACTGAGAAGTGAACCAAATTCAT
261 TCCTGATGAGATACTGAGAAGTGAACCAAATTCAT
* * * * **** * *
14299 CTTCCTGATGAGATACAGGGAAGCAGATTGAAATAAATGAGGCAGTCATCTTCCTGATGAGATAC
1 CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAATAAAATGGTTAGCTTCCTGATGAGATAC
*
14364 TGAGAAGTAGACCAAATT
66 TGAGAAGTGGACCAAATT
14382 AATAACACCA
Statistics
Matches: 341, Mismatches: 34, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
293 3 0.01
294 27 0.08
295 311 0.91
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (295 bp):
CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAATAAAATGGTTAGCTTCCTGATGAGATAC
TGAGAAGTGGACCAAATTCATCTTCCTGATGAGATACAAAAAAGTGGATTGAAACAAGTGATGCG
GTCATCTTCCTGATGAAATACTGAGAAGTAGACCAAATCAATGAAGCCAGACTCAAAGTAAGCAA
ATCTTTGAACCCCAGCTTCCTGATGAGAGACTAAGAAGCAGGTCGAAGCAATAAAATGGTTAGCT
TCCTGATGAGATACTGAGAAGTGAACCAAATTCAT
Found at i:14697 original size:17 final size:16
Alignment explanation
Indices: 14675--14767 Score: 69
Period size: 17 Copynumber: 5.6 Consensus size: 16
14665 GCCTAACAGG
*
14675 ATTTAAATTTATTTTAA
1 ATTTAAATTTA-TATAA
*
14692 ATTTAAGTTTATATAA
1 ATTTAAATTTATATAA
* *
14708 AGTTTAAATCTATTTAGA
1 A-TTTAAATTTATATA-A
14726 ATTTAAATTTATTATAA
1 ATTTAAATTTA-TATAA
* * * **
14743 AATTAAGTTTAAATTT
1 ATTTAAATTTATATAA
14759 ATTTAAATT
1 ATTTAAATT
14768 ACAAACTCAA
Statistics
Matches: 59, Mismatches: 14, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
16 14 0.24
17 40 0.68
18 5 0.08
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (16 bp):
ATTTAAATTTATATAA
Found at i:14715 original size:34 final size:35
Alignment explanation
Indices: 14676--14743 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 35
14666 CCTAACAGGA
* *
14676 TTTAAATTTATTTTA-AATTTAAGTTTA-TATAAAG
1 TTTAAATCTA-TTTAGAATTTAAATTTATTATAAAG
14710 TTTAAATCTATTTAGAATTTAAATTTATTATAAA
1 TTTAAATCTATTTAGAATTTAAATTTATTATAAA
14744 ATTAAGTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 4 0.13
34 20 0.67
35 6 0.20
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (35 bp):
TTTAAATCTATTTAGAATTTAAATTTATTATAAAG
Done.