Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012141.1 Kokia drynarioides strain JFW-HI SEQ_127140, 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: 461594
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 104 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:448930 original size:28 final size:27
Alignment explanation
Indices: 448889--448975 Score: 77
Period size: 28 Copynumber: 3.0 Consensus size: 27
448879 TGAACTTGAC
*
448889 ATTTTTTACTAATTTGGTACGTAAACTT
1 ATTTTTTCCTAATTTGGTAC-TAAACTT
* *
448917 -TTTTTTGTCTAATTTCGTACTCAAACTT
1 ATTTTTT-CCTAATTTGGTACT-AAACTT
448945 GACATTTTTTCCTAATTTGGTACCTAAACTT
1 ---ATTTTTTCCTAATTTGGTA-CTAAACTT
448976 GACGCTTTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
27 7 0.15
28 17 0.35
31 16 0.33
32 8 0.17
ACGTcount: A:0.25, C:0.16, G:0.09, T:0.49
Consensus pattern (27 bp):
ATTTTTTCCTAATTTGGTACTAAACTT
Found at i:454158 original size:300 final size:300
Alignment explanation
Indices: 453504--454331 Score: 1181
Period size: 300 Copynumber: 2.8 Consensus size: 300
453494 AATCACAAAA
*
453504 TATTTCAATTAAAAAATTAATAATATTAACTATTTGAAGTAATTAATAACA-TTATAAAAAAATT
1 TATTT-AATTAAAAAATTAATAATATTAACTATTTGAAGTAATTAATAACACTT-TAAAAAATTT
*
453568 AGTGTTTAAAGACTCTATTTCAAATTTAATAAAAGTATAATATAACTACCTAACATGAGATTTTT
64 ATTGTTTAAAGACTCTATTTCAAATTTAATAAAAGTATAATATAACTACCTAACATGAGATTTTT
* * *
453633 TACAATAATAATAT---AAAAAAATTAAATACTAAAATAATACAC-TCCCCATTATTTACCAAAA
129 TACAATAATAATATAAAAAAAAAATTAAATACTAAAATAATGCACTTCCTCATTATTTTCCAAAA
* * * * * * *
453694 TGGTACATTTGAGGTAGTGATCCCTCTTAGATAGGCGGCATCATTTTAAAACTTTGACAATTTCT
194 TGGTACATTTGGGGTAGTGATGCCTCCTAGATAGACGACATCACTTTAAAACTTTAACAA--T-T
453759 TTTTTTTATTTAATAAAATATTGAAGGACTTGAGATGAAATTTTT
256 TTTTTTTATTTAATAAAATATTGAAGGACTTGAGATGAAATTTTT
* * *
453804 CATTTAATTAAAAAATTAATAGTATTAACTATTTGAAGTAATTAATATCACTTTAAAAAATTTAT
1 TATTTAATTAAAAAATTAATAATATTAACTATTTGAAGTAATTAATAACACTTTAAAAAATTTAT
* *
453869 TGTTTAAAGACTCTATTTCAAATTTAATAAAAGCATAATATAACTACTTAACATGAGATTTTTTA
66 TGTTTAAAGACTCTATTTCAAATTTAATAAAAGTATAATATAACTACCTAACATGAGATTTTTTA
453934 CAATAATAATATAAAAAAAAAATTAAATACTAAAATAATGCACTGTCCTCATTATTTTCCAAAAT
131 CAATAATAATATAAAAAAAAAATTAAATACTAAAATAATGCACT-TCCTCATTATTTTCCAAAAT
* *
453999 GGTACATTTGGGGTAGTGATGCTTCCTAGATAGACGACATTACTTTAAAA-TTCTAACAA-TTTT
195 GGTACATTTGGGGTAGTGATGCCTCCTAGATAGACGACATCACTTTAAAACTT-TAACAATTTTT
* * *
454062 TTTTATTTAATAAAATATTGAGGGATTTGAGATGTAATTTTT
259 TTTTATTTAATAAAATATTGAAGGACTTGAGATGAAATTTTT
* *
454104 TATTTAATTAAAAAATTAATAATATTAACTATTTGAAGTAATTAATACCACTTTAAAAATTTTAT
1 TATTTAATTAAAAAATTAATAATATTAACTATTTGAAGTAATTAATAACACTTTAAAAAATTTAT
* *
454169 TGTTTAAAGACTCTATCTCAAATTTAATAAAAGTATAATATAACTACCTAATATGAGATTTTTT-
66 TGTTTAAAGACTCTATTTCAAATTTAATAAAAGTATAATATAACTACCTAACATGAGATTTTTTA
* * * *
454233 CAATAATAATATAAAAAAAAAATTTAAAAACCAAAATAATAG-ACTCCCTTTATTATTTAT-CAA
131 CAATAATAATATAAAAAAAAAA-TTAAATACTAAAATAAT-GCACTTCC-TCATTATTT-TCCAA
* * * *
454296 AATGGTACATTGGGGGTAATGATGTCTCATAGATAG
192 AATGGTACATTTGGGGTAGTGATGCCTCCTAGATAG
454332 GTTTAAAATT
Statistics
Matches: 478, Mismatches: 39, Indels: 22
0.89 0.07 0.04
Matches are distributed among these distances:
299 152 0.32
300 230 0.48
301 2 0.00
302 27 0.06
303 2 0.00
304 65 0.14
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.38
Consensus pattern (300 bp):
TATTTAATTAAAAAATTAATAATATTAACTATTTGAAGTAATTAATAACACTTTAAAAAATTTAT
TGTTTAAAGACTCTATTTCAAATTTAATAAAAGTATAATATAACTACCTAACATGAGATTTTTTA
CAATAATAATATAAAAAAAAAATTAAATACTAAAATAATGCACTTCCTCATTATTTTCCAAAATG
GTACATTTGGGGTAGTGATGCCTCCTAGATAGACGACATCACTTTAAAACTTTAACAATTTTTTT
TTATTTAATAAAATATTGAAGGACTTGAGATGAAATTTTT
Found at i:457432 original size:59 final size:59
Alignment explanation
Indices: 457287--457420 Score: 184
Period size: 58 Copynumber: 2.3 Consensus size: 59
457277 AAAAAAATTA
* * *
457287 GGGTGTTGGTCATGCAATGATTGACACCTCTTTTTTTCTGATAAAAAATATAATTTTTTT
1 GGGTGTTGGTCATGCAATG-TTGACACCCCTATTTATCTGATAAAAAATATAATTTTTTT
* *
457347 --GTGTTGGTCATACAATGGTTGACACCCCTATTTATCTGATAAAAAA-ATTATTTTTTT
1 GGGTGTTGGTCATGCAAT-GTTGACACCCCTATTTATCTGATAAAAAATATAATTTTTTT
457404 GGGTGTTGGTCATGCAA
1 GGGTGTTGGTCATGCAA
457421 ATGCCAACAC
Statistics
Matches: 65, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
57 10 0.15
58 40 0.62
59 15 0.23
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.42
Consensus pattern (59 bp):
GGGTGTTGGTCATGCAATGTTGACACCCCTATTTATCTGATAAAAAATATAATTTTTTT
Found at i:457573 original size:124 final size:122
Alignment explanation
Indices: 457288--457783 Score: 480
Period size: 124 Copynumber: 4.0 Consensus size: 122
457278 AAAAAATTAG
* * * *
457288 GGTGTTGGTCATGCAATGATTGACACCTCTTTTTTTCTGATAAAAAA---TATAATTTTTTTGTG
1 GGTGTTGGTCATGCAATGGTCGACACCTC-TTTTTTCAGATAAAAAATTTTAAAATTTTTTTGTG
* * * *
457350 TTGGTCATACAATGGTTGAC-ACCCCTATTTATCTGATAAAAAAATT----ATTTTTTT
65 TTGGTCATGCAATGGTCGACAACCCCT-TTTCTCGGATAAAAAAATTACAAATTTTTTT
* * * * *
457404 GGGTGTTGGTCATGCAAAT-GCCAACACC-CTTTTTTGAGAAAAAAAAATTTTAAAATTTTTTTA
1 -GGTGTTGGTCATGC-AATGGTCGACACCTCTTTTTTCAG-ATAAAAAATTTTAAAATTTTTTTG
*
457467 TGTTAGGTCATGCAATGGTCAACAACCCCTTTTCTCGGATTAAAAAAATTACAAATTTTTTT
63 TGTT-GGTCATGCAATGGTCGACAACCCCTTTTCTCGGA-TAAAAAAATTACAAATTTTTTT
* * *
457529 GGTGTTGATCATGTAATGGTCGACACTCTCTTTTTT-AGATAAAAAATTTTCAAAATTTTTTGGT
1 GGTGTTGGTCATGCAATGGTCGACAC-CTCTTTTTTCAGATAAAAAATTTT-AAAATTTTTTTGT
*
457593 GTTGGTCATGCAATGG-CTGACACCCCCTTTTCTCGGATAAAAAAATTACAAATTTTTTT
64 GTTGGTCATGCAATGGTC-GACAACCCCTTTTCTCGGATAAAAAAATTACAAATTTTTTT
* * * * **
457652 GGTGTTGGTCATGCAATGG-CTGACACCCCCTGTTATT-AGATAAAAAAATTCAATTTTTTTTTT
1 GGTGTTGGTCATGCAATGGTC-GACA-CCTCT-TTTTTCAGATAAAAAATTTTAA---AATTTTT
* * * * *
457715 TTGTGTTGGCCATGTAATGGCCGACACCCCCTTTTTCTCGGATAAAAAAATTACAATTTTTTTT
60 TTGTGTTGGTCATGCAATGGTCGACAACCCC-TTTTCTCGGATAAAAAAATTACAAATTTTTTT
457779 GGTGT
1 GGTGT
457784 CGGCCATATC
Statistics
Matches: 319, Mismatches: 35, Indels: 40
0.81 0.09 0.10
Matches are distributed among these distances:
115 7 0.02
116 8 0.03
117 19 0.06
118 3 0.01
119 15 0.05
120 22 0.07
121 16 0.05
122 1 0.00
123 52 0.16
124 76 0.24
125 25 0.08
126 38 0.12
127 37 0.12
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (122 bp):
GGTGTTGGTCATGCAATGGTCGACACCTCTTTTTTCAGATAAAAAATTTTAAAATTTTTTTGTGT
TGGTCATGCAATGGTCGACAACCCCTTTTCTCGGATAAAAAAATTACAAATTTTTTT
Found at i:457633 original size:62 final size:61
Alignment explanation
Indices: 457288--457783 Score: 356
Period size: 62 Copynumber: 8.1 Consensus size: 61
457278 AAAAAATTAG
** * * * * *
457288 GGTGTTGGTCATGCAATGATTGACACCTCTTTTTTTCTGATAAAAAATAT--AATTTTTTT
1 GGTGTTGGTCATGCAATGGCTGACACCCCCTTTTCTCGGATAAAAAATTTCAAATTTTTTT
* * * * *
457347 -GTGTTGGTCATACAATGGTTGACA-CCCCTATTTATCTGATAAAAAAATT---ATTTTTTT
1 GGTGTTGGTCATGCAATGGCTGACACCCCCT-TTTCTCGGATAAAAAATTTCAAATTTTTTT
* * * * *
457404 GGGTGTTGGTCATGCAAAT-GC-CA-ACACCCTTTT-TTGAGAAAAAAAAATTTTAAAATTTTTT
1 -GGTGTTGGTCATGC-AATGGCTGACACCCCCTTTTCTCG-G-ATAAAAAA-TTTCAAATTTTTT
457465 T
61 T
* * * *
457466 -ATGTTAGGTCATGCAATGG-TCAACAACCCCTTTTCTCGGATTAAAAAAATTACAAATTTTTTT
1 GGTGTT-GGTCATGCAATGGCT-GACACCCCCTTTTCTCGGA-T-AAAAAATTTCAAATTTTTTT
* * * * ** *
457529 GGTGTTGATCATGTAATGG-TCGACACTCTCTTTT-TTAGATAAAAAATTTTCAAAATTTTTT
1 GGTGTTGGTCATGCAATGGCT-GACACCCCCTTTTCTCGGATAAAAAA-TTTCAAATTTTTTT
*
457590 GGTGTTGGTCATGCAATGGCTGACACCCCCTTTTCTCGGATAAAAAAATTACAAATTTTTTT
1 GGTGTTGGTCATGCAATGGCTGACACCCCCTTTTCTCGGAT-AAAAAATTTCAAATTTTTTT
* * ** * *
457652 GGTGTTGGTCATGCAATGGCTGACACCCCCTGTTATTAGATAAAAAAATTCAATTTTTTTTTTT
1 GGTGTTGGTCATGCAATGGCTGACACCCCCTTTTCTCGGATAAAAAATTTCAA---ATTTTTTT
* * * * * *
457716 TGTGTTGGCCATGTAATGGCCGACACCCCCTTTTTCTCGGATAAAAAAATTACAATTTTTTTT
1 GGTGTTGGTCATGCAATGGCTGACACCCCC-TTTTCTCGGAT-AAAAAATTTCAAATTTTTTT
457779 GGTGT
1 GGTGT
457784 CGGCCATATC
Statistics
Matches: 348, Mismatches: 60, Indels: 54
0.75 0.13 0.12
Matches are distributed among these distances:
56 1 0.00
57 16 0.05
58 50 0.14
59 15 0.04
60 16 0.05
61 60 0.17
62 67 0.19
63 61 0.18
64 45 0.13
65 7 0.02
66 10 0.03
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (61 bp):
GGTGTTGGTCATGCAATGGCTGACACCCCCTTTTCTCGGATAAAAAATTTCAAATTTTTTT
Found at i:458701 original size:2 final size:2
Alignment explanation
Indices: 458694--458726 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
458684 CCAGCACCAG
458694 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
458727 ACCGTTAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:459554 original size:12 final size:12
Alignment explanation
Indices: 459537--459562 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
459527 CACAGATGCA
459537 AACAAACCGACG
1 AACAAACCGACG
459549 AACAAACCGACG
1 AACAAACCGACG
459561 AA
1 AA
459563 GAAGACTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.31, G:0.15, T:0.00
Consensus pattern (12 bp):
AACAAACCGACG
Done.