Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011222.1 Kokia drynarioides strain JFW-HI SEQ_126200, 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: 242829
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 140 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:225642 original size:21 final size:21
Alignment explanation
Indices: 225616--225662 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
225606 AGCTATGAAA
*
225616 TTCTACCAGTA-AAAGTGAGAC
1 TTCTACCAATACAAAGTG-GAC
*
225637 TTCTACCAATACAAATTGGAC
1 TTCTACCAATACAAAGTGGAC
225658 TTCTA
1 TTCTA
225663 TCGGTGGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (21 bp):
TTCTACCAATACAAAGTGGAC
Found at i:226318 original size:19 final size:17
Alignment explanation
Indices: 226294--226335 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
226284 TTTAAATTGG
*
226294 TTTAAATTTATTTTTTAAA
1 TTTAAATTTA--TCTTAAA
226313 TTTAAATTTATCTTAAA
1 TTTAAATTTATCTTAAA
226330 TTTAAA
1 TTTAAA
226336 AAGATAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 12 0.55
19 10 0.45
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTAAATTTATCTTAAA
Found at i:226439 original size:17 final size:18
Alignment explanation
Indices: 226417--226450 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
226407 ATTAAAAGCC
226417 CAAATA-AAAATCCAAAA
1 CAAATACAAAATCCAAAA
*
226434 CAAATACAAAGTCCAAA
1 CAAATACAAAATCCAAA
226451 TTACAATCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.65, C:0.21, G:0.03, T:0.12
Consensus pattern (18 bp):
CAAATACAAAATCCAAAA
Found at i:228226 original size:30 final size:29
Alignment explanation
Indices: 228190--228571 Score: 301
Period size: 29 Copynumber: 12.9 Consensus size: 29
228180 CCTCGAAAGT
*
228190 CCCTAAACTATCCAAAAATTACATTTTTAC
1 CCCTAAACT-TCCAAAAATTCCATTTTTAC
228220 CCCTAAACTTCCAAAAATTCCATTTTTGA-
1 CCCTAAACTTCCAAAAATTCCATTTTT-AC
* *
228249 CCCTCGAACTTCCACAAATTCCATTTTTAC
1 CCCT-AAACTTCCAAAAATTCCATTTTTAC
* **
228279 CCTTAAACTTCCAAAAATTATATTTTTAC
1 CCCTAAACTTCCAAAAATTCCATTTTTAC
* *
228308 ACTCT-AACTTCCAAAAATTTCATTTTTAAC
1 -CCCTAAACTTCCAAAAATTCCATTTTT-AC
* *
228338 CCTTAAACTTCTAAAAATTCCATTTTTGA-
1 CCCTAAACTTCCAAAAATTCCATTTTT-AC
* * * * *
228367 CCTTGAGACTCCCCAAAATTCAATTTTTA-
1 CCCT-AAACTTCCAAAAATTCCATTTTTAC
* * *
228396 CCCTCGAATTTCCAAAAAATCCATTTTTAAC
1 CCCT-AAACTTCCAAAAATTCCATTTTT-AC
* * *
228427 CCCAAAACTTCCAAAAATTCTATTTGTA-
1 CCCTAAACTTCCAAAAATTCCATTTTTAC
*
228455 CCCTCGAACTTCCAAAAATTCCATTTTTAAC
1 CCCT-AAACTTCCAAAAATTCCATTTTT-AC
* * *
228486 CTCAAAACTTCC-AAAATTGACATTTTTAC
1 CCCTAAACTTCCAAAAATT-CCATTTTTAC
* * * *
228515 CCTTGAACCTCTAAAAATTCCATTTTTGA-
1 CCCTAAACTTCCAAAAATTCCATTTTT-AC
* *
228544 TCCTGAAACTTTCAAAAATTACCATTTT
1 CCCT-AAACTTCCAAAAATT-CCATTTT
228572 GCCCCGGATG
Statistics
Matches: 277, Mismatches: 58, Indels: 33
0.75 0.16 0.09
Matches are distributed among these distances:
28 3 0.01
29 133 0.48
30 129 0.47
31 12 0.04
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (29 bp):
CCCTAAACTTCCAAAAATTCCATTTTTAC
Found at i:228297 original size:59 final size:59
Alignment explanation
Indices: 228195--228571 Score: 361
Period size: 59 Copynumber: 6.4 Consensus size: 59
228185 AAAGTCCCTA
* *
228195 AACTATCCAAAAATTACATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCCTCG
1 AACT-TCCAAAAATTCCATTTTTACCCTTAAACTTCCAAAAATTCCATTTTTGACCCTCG
* ** * *
228255 AACTTCCACAAATTCCATTTTTACCCTTAAACTTCCAAAAATTATATTTTT-ACACTCT
1 AACTTCCAAAAATTCCATTTTTACCCTTAAACTTCCAAAAATTCCATTTTTGACCCTCG
* * *
228313 AACTTCCAAAAATTTCATTTTTAACCCTTAAACTTCTAAAAATTCCATTTTTGA-CCTTG
1 AACTTCCAAAAATTCCATTTTT-ACCCTTAAACTTCCAAAAATTCCATTTTTGACCCTCG
* * * ** * * * *
228372 AGACTCCCCAAAATTCAATTTTTACCCTCGAATTTCCAAAAAATCCATTTTTAACCC-CAA
1 A-ACTTCCAAAAATTCCATTTTTACCCTTAAACTTCCAAAAATTCCATTTTTGACCCTC-G
* * ** * *
228432 AACTTCCAAAAATTCTATTTGTACCCTCGAACTTCCAAAAATTCCATTTTT-AACCTCAA
1 AACTTCCAAAAATTCCATTTTTACCCTTAAACTTCCAAAAATTCCATTTTTGACCCTC-G
* * * * *
228491 AACTTCC-AAAATTGACATTTTTACCCTTGAACCTCTAAAAATTCCATTTTTGATCCT-G
1 AACTTCCAAAAATT-CCATTTTTACCCTTAAACTTCCAAAAATTCCATTTTTGACCCTCG
*
228549 AAACTTTCAAAAATTACCATTTT
1 -AACTTCCAAAAATT-CCATTTT
228572 GCCCCGGATG
Statistics
Matches: 262, Mismatches: 45, Indels: 20
0.80 0.14 0.06
Matches are distributed among these distances:
58 34 0.13
59 187 0.71
60 41 0.16
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (59 bp):
AACTTCCAAAAATTCCATTTTTACCCTTAAACTTCCAAAAATTCCATTTTTGACCCTCG
Found at i:239220 original size:46 final size:47
Alignment explanation
Indices: 239145--239235 Score: 132
Period size: 46 Copynumber: 1.9 Consensus size: 47
239135 ACTTCGCCTA
* *
239145 AAAAAAACAAAAGGGGAATTGAGATGAAAACTCGCAAAGGGCGTCTCG
1 AAAAAAACAAAAGGGG-ATTCAGATGAAAACCCGCAAAGGGCGTCTCG
239193 AAAAAAA-AAAAGGGG-TTCAGGATGAAAACCCGCAAAGGGCGTC
1 AAAAAAACAAAAGGGGATTCA-GATGAAAACCCGCAAAGGGCGTC
239236 CTGGAACCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
45 3 0.08
46 22 0.55
47 8 0.20
48 7 0.17
ACGTcount: A:0.46, C:0.15, G:0.27, T:0.11
Consensus pattern (47 bp):
AAAAAAACAAAAGGGGATTCAGATGAAAACCCGCAAAGGGCGTCTCG
Found at i:240346 original size:205 final size:205
Alignment explanation
Indices: 239989--241200 Score: 1908
Period size: 205 Copynumber: 5.9 Consensus size: 205
239979 GCAATTATGC
* *
239989 ACAAACGACGCGGTCATCTTCCTGATGAGTTACTGAGAAGAAGACCAAATCAAACCCACGCTCAA
1 ACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGA
* *
240054 TGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGACACTGAGAAGCAGGTTGAAGCAATAAAA
66 TGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAA
* * *
240119 GGTTAGCTTCCTGATAAGATACTGAGCAGTGGACCAAATTCATCTTCCTGATGAGATACAGAGAA
131 GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAA
240184 GCGAATTGAA
196 GCGAATTGAA
* * *
240194 ACAAACGACGCTGTCATCTTCCTGATGAGATACTGAGAAGAAAACCAAATCAAACCAACGCTCGA
1 ACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGA
*
240259 TGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTTGAAGCAATAAAA
66 TGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAA
*
240324 GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAGAGAA
131 GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAA
240389 GCGAATTGAA
196 GCGAATTGAA
* * *
240399 ACAAACGACGGGGTCATCTTCCTGATGAGATACTAAGAAGAAGACCAAATCAAATCCACGCTCGA
1 ACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGA
*
240464 TGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACATTGAGAAGCAGGTCGAAGCAATAAAA
66 TGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAA
* * * * *
240529 GGTTAGGTTCTTGATGAGATATTGAGAAATGGACCAAATTCGTCCTCCTGATGAGATACAGAGAA
131 GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAA
* *
240594 GCAAATTAAA
196 GCGAATTGAA
*
240604 ACAAACGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGA
1 ACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGA
240669 TGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAA
66 TGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAA
* *
240734 GGTTAGCTTCCTGATGAGATATTGAGAAGTGGACCAAATTCGTCCTCCTGATGAGATACAGAGAA
131 GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAA
240799 GCGAATTGAA
196 GCGAATTGAA
* * * * *
240809 ACAAACGATGCGATCATCTTCCAGATGAGATACTGAGAAGAAGACCAAATCAAACCCATGTTCGA
1 ACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGA
* * * * *
240874 TGTGAGCAAATCCTCGAACCCCAGCTTCTTGATGAGATACTGAGAAGCAGGTTGAAGTAATAAAA
66 TGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAA
*
240939 TGGTTAAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCT-ATTGAGATACAGA
131 -GGTT-AGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGA-TGAGATACAGA
*
241003 GAAGCGGATTGAA
193 GAAGCGAATTGAA
* * *
241016 ACAAACGACGTGGTCATCTTCCTGATGAGACACAGA-AGAGAAGACCAAATCAAACCCACGCTCG
1 ACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGA-AGAAGACCAAATCAAACCCACGCTCG
* * *
241080 ATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGTAATAAA
65 ATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAA
* * ** *
241145 ACGGTTAGCTTCCTGATGAAATAC-GAGGAAGTGAACCAAAACCATCTTCCTGATGA
130 A-GGTTAGCTTCCTGATGAGATACTGA-GAAGTGGACCAAATTCGTCTTCCTGATGA
241201 ATCACGGAGA
Statistics
Matches: 935, Mismatches: 66, Indels: 11
0.92 0.07 0.01
Matches are distributed among these distances:
205 702 0.75
206 47 0.05
207 186 0.20
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (205 bp):
ACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGA
TGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAA
GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAA
GCGAATTGAA
Found at i:241631 original size:19 final size:19
Alignment explanation
Indices: 241607--241671 Score: 98
Period size: 19 Copynumber: 3.5 Consensus size: 19
241597 TTTAAATTGG
241607 TTTAAATTTATTTTTTAAA
1 TTTAAATTTATTTTTTAAA
*
241626 TTTAAATTTA--TCTTAAA
1 TTTAAATTTATTTTTTAAA
*
241643 TTTAAATTTATTTTTTTAA
1 TTTAAATTTATTTTTTAAA
241662 TTTAAATTTA
1 TTTAAATTTA
241672 ATCAAATTTG
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
17 16 0.39
19 25 0.61
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTAAATTTATTTTTTAAA
Found at i:241643 original size:17 final size:17
Alignment explanation
Indices: 241607--241653 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 17
241597 TTTAAATTGG
*
241607 TTTAAATTTATTTTTTAAA
1 TTTAAATTTA--TCTTAAA
241626 TTTAAATTTATCTTAAA
1 TTTAAATTTATCTTAAA
241643 TTTAAATTTAT
1 TTTAAATTTAT
241654 TTTTTTAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 17 0.63
19 10 0.37
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTAAATTTATCTTAAA
Done.