Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014811.1 Kokia drynarioides strain JFW-HI SEQ_129853, 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: 91032
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 65 characters in sequence are not A, C, G, or T
Found at i:19066 original size:418 final size:425
Alignment explanation
Indices: 18233--19068 Score: 1075
Period size: 425 Copynumber: 2.0 Consensus size: 425
18223 AGGAAAATGA
* *
18233 AATATGTTTTCCTTCACTTCCATCACTTGAAGCTGAGTATAGGGGATTATTCTTTTATCAAATAA
1 AATATGTTTTCCTTCACTTCCATCACTTGAAGCTGAGTATAGGAGATTATACTTTTATCAAATAA
* *
18298 ATCTCTAGGATAATATTTTATCTCAATTTAGTGAAGCACTCGACAACCTTATTACGAACATTCTT
66 ATCTCTACGATAATATTTTA-CT-AATTTAGTGAAGCACTCGACAACCTTACTACGAACATTCTT
* * * *
18363 CTTATTACATTCAATCTCACATGCAATATAATCACTTGTAATTTATCAATTTATCTCAAGTAATA
129 CTTATTACATCCAAGCTCACATGCAATATAACCACTTGTAATTTATAAATTTATCTCAAGTAATA
* * * * *
18428 TCTTATCACATCTTAGTAAAACACTCAATGATTATACTATCAAACCTATACAATGAAACCCCTGT
194 TATTATCACATC-TAATAAAACACTCAATGATTATACTATCAAACCTATACAATCAAACACCTGC
* * * *
18493 CTAGAATAACTCATGTCAAACACTTCTTTTATATAAATTTATTTCAATCACTAAAAGATTCTAAG
258 CTACAAGAACTCATGTCAAACACTTCTTTTATATAAATTTATTTCAATCACTAAAAAACTCTAA-
* *
18558 TTATTATTTCATTATCAATACTTTCCTCAAAACTCATCATAACTTTCTCACCACTTCCAAACCAC
322 -TA-TATTCCATTATCAATACTTTCCTCAAAACTCATCATAACTCTCTCACCACTTCCAAACCAC
18623 TAATAACTCTCAATAACCAACCTCTAGTGCTACATATGAGC
385 TAATAACTCTCAATAACCAACCTCTAGTGCTACATATGAGC
** * *
18664 AATATGTTTTTGTTCATTTCCATCACTTGAAGCTGAGTATA-GAGACTTATACTTTTATGAAATA
1 AATATGTTTTCCTTCACTTCCATCACTTGAAGCTGAGTATAGGAGA-TTATACTTTTATCAAATA
* * * ** *
18728 AATCTTTACGATAATATTTTA-T-A-TTAGTGAAGCACTCTATAATTTTACTATC-AGCATTCTT
65 AATCTCTACGATAATATTTTACTAATTTAGTGAAGCACTCGACAACCTTACTA-CGAACATTCTT
* * * *
18789 TTTATTATATCCAAGCTCACATGTAATATAACCCACTTGTAATTTATAAATTTATCTCGAGTAAT
129 CTTATTACATCCAAGCTCACATGCAATATAA-CCACTTGTAATTTATAAATTTATCTCAAGTAAT
** * * * * *
18854 ATATTATCACATC-AATAAAGTACTCCATGATTTTACTATCAAACCTATATAGTCAAACACGTGC
193 ATATTATCACATCTAATAAAACACTCAATGATTATACTATCAAACCTATACAATCAAACACCTGC
* * *
18918 CTACAAGAGCTCATGTCAAACTCTTCTTTTATATAAATTTCTTTCAATCACTAAAAAACTCT-A-
258 CTACAAGAACTCATGTCAAACACTTCTTTTATATAAATTTATTTCAATCACTAAAAAACTCTAAT
* * *
18981 A-A-TCCATTATCGATACTTTGCTC-AAACTTCATCATAACTCTCT-AGGCACTTCCAAACCACT
323 ATATTCCATTATCAATACTTTCCTCAAAAC-TCATCATAACTCTCTCA-CCACTTCCAAACCACT
19042 AATAACTCTCAATAACCAACCTCTAGT
386 AATAACTCTCAATAACCAACCTCTAGT
19069 ACAGGTGCAA
Statistics
Matches: 354, Mismatches: 46, Indels: 23
0.84 0.11 0.05
Matches are distributed among these distances:
417 5 0.01
418 74 0.21
419 1 0.00
421 1 0.00
424 1 0.00
425 95 0.27
426 56 0.16
427 44 0.12
429 1 0.00
430 3 0.01
431 73 0.21
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.36
Consensus pattern (425 bp):
AATATGTTTTCCTTCACTTCCATCACTTGAAGCTGAGTATAGGAGATTATACTTTTATCAAATAA
ATCTCTACGATAATATTTTACTAATTTAGTGAAGCACTCGACAACCTTACTACGAACATTCTTCT
TATTACATCCAAGCTCACATGCAATATAACCACTTGTAATTTATAAATTTATCTCAAGTAATATA
TTATCACATCTAATAAAACACTCAATGATTATACTATCAAACCTATACAATCAAACACCTGCCTA
CAAGAACTCATGTCAAACACTTCTTTTATATAAATTTATTTCAATCACTAAAAAACTCTAATATA
TTCCATTATCAATACTTTCCTCAAAACTCATCATAACTCTCTCACCACTTCCAAACCACTAATAA
CTCTCAATAACCAACCTCTAGTGCTACATATGAGC
Found at i:20708 original size:27 final size:29
Alignment explanation
Indices: 20665--20728 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 29
20655 AGCTTATATC
*
20665 TTATCATTTTTTAAAAAGTAAATTA-AATT
1 TTATCA-TTTTTAAAAAGTAAAGTATAATT
* *
20694 TTCTCATTTTT-AAAATTAAAGTATAATT
1 TTATCATTTTTAAAAAGTAAAGTATAATT
20722 TTATCAT
1 TTATCAT
20729 ACATTAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 10 0.33
28 15 0.50
29 5 0.17
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.50
Consensus pattern (29 bp):
TTATCATTTTTAAAAAGTAAAGTATAATT
Found at i:24188 original size:114 final size:114
Alignment explanation
Indices: 23988--24216 Score: 449
Period size: 114 Copynumber: 2.0 Consensus size: 114
23978 ATTTATCAAA
23988 TAACATTTGAATGCATGAAGCTATAAAAGAACAGCAATAATCTTTGGATTGGCTTACTTGTTGCT
1 TAACATTTGAATGCATGAAGCTATAAAAGAACAGCAATAATCTTTGGATTGGCTTACTTGTTGCT
*
24053 GTGGCTGAGATACTAGGAAAGAAAGGCTCATTGTATGAATTCAATCGCG
66 GTGGATGAGATACTAGGAAAGAAAGGCTCATTGTATGAATTCAATCGCG
24102 TAACATTTGAATGCATGAAGCTATAAAAGAACAGCAATAATCTTTGGATTGGCTTACTTGTTGCT
1 TAACATTTGAATGCATGAAGCTATAAAAGAACAGCAATAATCTTTGGATTGGCTTACTTGTTGCT
24167 GTGGATGAGATACTAGGAAAGAAAGGCTCATTGTATGAATTCAATCGCG
66 GTGGATGAGATACTAGGAAAGAAAGGCTCATTGTATGAATTCAATCGCG
24216 T
1 T
24217 CCATAGTCGC
Statistics
Matches: 114, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
114 114 1.00
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.30
Consensus pattern (114 bp):
TAACATTTGAATGCATGAAGCTATAAAAGAACAGCAATAATCTTTGGATTGGCTTACTTGTTGCT
GTGGATGAGATACTAGGAAAGAAAGGCTCATTGTATGAATTCAATCGCG
Found at i:31081 original size:30 final size:30
Alignment explanation
Indices: 31046--31107 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
31036 TATTTTATTA
* * *
31046 TTAATTTTGTTATTACTTTCGAGGTATTTG
1 TTAATTTTATTACTACTTTAGAGGTATTTG
*
31076 TTAATTTTATTACTATTTTAGAGGTATTTG
1 TTAATTTTATTACTACTTTAGAGGTATTTG
31106 TT
1 TT
31108 TATTAAGTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.23, C:0.05, G:0.15, T:0.58
Consensus pattern (30 bp):
TTAATTTTATTACTACTTTAGAGGTATTTG
Found at i:48707 original size:22 final size:20
Alignment explanation
Indices: 48668--48707 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
48658 TTTATTAAAA
*
48668 TAATAAAATTATATTTTACT
1 TAATAAAATTATAATTTACT
48688 TAATAAAAATATATAATTTA
1 TAAT-AAAAT-TATAATTTA
48708 ATTTTAACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 5 0.29
22 8 0.47
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
TAATAAAATTATAATTTACT
Found at i:61634 original size:7 final size:8
Alignment explanation
Indices: 61607--61632 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
61597 TTTATTATAT
61607 AAATTTAA
1 AAATTTAA
61615 AAATTTAA
1 AAATTTAA
61623 AAATTTAA
1 AAATTTAA
61631 AA
1 AA
61633 TTAAATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
AAATTTAA
Found at i:79780 original size:6 final size:6
Alignment explanation
Indices: 79769--79794 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
79759 AAAAAGAATT
79769 TGCAAG TGCAAG TGCAAG TGCAAG TG
1 TGCAAG TGCAAG TGCAAG TGCAAG TG
79795 GGGCGTGTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.15, G:0.35, T:0.19
Consensus pattern (6 bp):
TGCAAG
Found at i:86737 original size:6 final size:6
Alignment explanation
Indices: 86715--86753 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
86705 TCTTTAAAAA
* *
86715 AATTAT AAATA- AATTAT AATTAT AATCAT AATTAT AATT
1 AATTAT AATTAT AATTAT AATTAT AATTAT AATTAT AATT
86754 GAACAATATG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
5 4 0.14
6 24 0.86
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (6 bp):
AATTAT
Found at i:86866 original size:20 final size:19
Alignment explanation
Indices: 86843--86887 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
86833 CACATCAATA
*
86843 ATTTTATTCTGAATTTTATT
1 ATTTTATT-TGAATTTGATT
86863 ATTTTCATTTGAATTTGATT
1 ATTTT-ATTTGAATTTGATT
86883 -TTTTA
1 ATTTTA
86888 AAAATAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 1 0.04
19 4 0.17
20 15 0.65
21 3 0.13
ACGTcount: A:0.24, C:0.04, G:0.07, T:0.64
Consensus pattern (19 bp):
ATTTTATTTGAATTTGATT
Found at i:87032 original size:132 final size:134
Alignment explanation
Indices: 86830--87102 Score: 451
Period size: 132 Copynumber: 2.0 Consensus size: 134
86820 TATTTTTTAA
*
86830 AATCACATCAATAATTTTATTCTGAATTTTATTATTTTCATTTGAATTTGATTTTTTAAAAATAA
1 AATCACATCAATAATTTTATTCTGAATTTTAATATTTTCATTTGAATTTGATTTTTTAAAAATAA
* *
86895 AAATATTAAAATTTAGAATAAAAATATTTATCTGACATTAAATTATT-AAAA-AAATATAAATAA
66 AAATATTAAAATTCAGAATAAAAATATTTATCTGACATTAAATTATTAAAAAGAAATACAAATAA
86958 TATG
131 TATG
*
86962 AATCACATCAATAATTTTATTCTGAATTTTAATATTTTCATTTGAATTTGATTTTTTTAAAATAA
1 AATCACATCAATAATTTTATTCTGAATTTTAATATTTTCATTTGAATTTGATTTTTTAAAAATAA
* * *
87027 AAATATTAAAATTCAGAATAAAATTATTTATTTGATATTAAATTATTAAAAAAGAAATACAAATA
66 AAATATTAAAATTCAGAATAAAAATATTTATCTGACATTAAATTATT-AAAAAGAAATACAAATA
87092 ATATG
130 ATATG
87097 ACATCA
1 A-ATCA
87103 TTATTTCATT
Statistics
Matches: 130, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
132 106 0.82
134 4 0.03
135 16 0.12
136 4 0.03
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (134 bp):
AATCACATCAATAATTTTATTCTGAATTTTAATATTTTCATTTGAATTTGATTTTTTAAAAATAA
AAATATTAAAATTCAGAATAAAAATATTTATCTGACATTAAATTATTAAAAAGAAATACAAATAA
TATG
Found at i:87926 original size:4 final size:4
Alignment explanation
Indices: 87911--87976 Score: 62
Period size: 4 Copynumber: 16.2 Consensus size: 4
87901 AAATAAACGG
* * * *
87911 GAAA GGAA GAAA GAAAA GAAA GAAA GAAA GGAA GAAG GAGAG GAAA GAAA
1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
*
87961 G-AA GAAG GAAA GAAA G
1 GAAA GAAA GAAA GAAA G
87977 GTAATGTGTT
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
3 3 0.06
4 40 0.78
5 8 0.16
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:87940 original size:25 final size:25
Alignment explanation
Indices: 87911--87975 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 25
87901 AAATAAACGG
87911 GAAAGGAAGAAAGAAAAGAAAGAAA
1 GAAAGGAAGAAAGAAAAGAAAGAAA
* * *
87936 GAAAGGAAGAAGGAGAGGAAAGAAA
1 GAAAGGAAGAAAGAAAAGAAAGAAA
87961 G-AA-GAAGGAAAGAAA
1 GAAAGGAA-GAAAGAAA
87976 GGTAATGTGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
23 3 0.09
24 8 0.24
25 23 0.68
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (25 bp):
GAAAGGAAGAAAGAAAAGAAAGAAA
Done.