Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015354.1 Kokia drynarioides strain JFW-HI SEQ_130401, 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: 1324750
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 502 characters in sequence are not A, C, G, or T
File 4 of 4
Found at i:1302775 original size:114 final size:114
Alignment explanation
Indices: 1302575--1302804 Score: 424
Period size: 114 Copynumber: 2.0 Consensus size: 114
1302565 TATAGTGTAA
* *
1302575 TCAGCGTTTAATTCTTGAAATTGTTGCGTCTTCCATAATGTGAAGTTCCTACAAAAAGAATTAAA
1 TCAGCATTTAATGCTTGAAATTGTTGCGTCTTCCATAATGTGAAGTTCCTACAAAAAGAATTAAA
1302640 ACATATATACAAAGATAAATTCTAATCCTACTCCTACTAATTATATAAG
66 ACATATATACAAAGATAAATTCTAATCCTACTCCTACTAATTATATAAG
* *
1302689 TCAGCATTTAATGCTTGAAATTGTTGTGTCTTCCGTAATGTGAAGTTCCTACAAAAAGAATTAAA
1 TCAGCATTTAATGCTTGAAATTGTTGCGTCTTCCATAATGTGAAGTTCCTACAAAAAGAATTAAA
1302754 ACATATATACAAAGATAAATTCTAATCCTACTCCTACTAATTATATAAG
66 ACATATATACAAAGATAAATTCTAATCCTACTCCTACTAATTATATAAG
1302803 TC
1 TC
1302805 TAAAATAAAA
Statistics
Matches: 112, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
114 112 1.00
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (114 bp):
TCAGCATTTAATGCTTGAAATTGTTGCGTCTTCCATAATGTGAAGTTCCTACAAAAAGAATTAAA
ACATATATACAAAGATAAATTCTAATCCTACTCCTACTAATTATATAAG
Found at i:1302871 original size:75 final size:75
Alignment explanation
Indices: 1302756--1302915 Score: 277
Period size: 75 Copynumber: 2.1 Consensus size: 75
1302746 GAATTAAAAC
* *
1302756 ATATATACAAAGATAAATTCTAATCCTACTCCTACTAATTATATAAGTCTAAAATAAAAACAAAA
1 ATATATACAAAGATAAAATCTAATCCTACTCCTACAAATTATATAAGTCTAAAATAAAAACAAAA
1302821 AATTATCCAA
66 AATTATCCAA
*
1302831 ATATATACAAAGATAAAATCTAATCTTACTCCTACAAATTATATAAGTCTAAAATAAAAACAAAA
1 ATATATACAAAGATAAAATCTAATCCTACTCCTACAAATTATATAAGTCTAAAATAAAAACAAAA
1302896 AATTATCCAA
66 AATTATCCAA
*
1302906 AAAT-TACAAA
1 ATATATACAAA
1302916 ATGAAATTGT
Statistics
Matches: 81, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
74 6 0.07
75 75 0.93
ACGTcount: A:0.54, C:0.15, G:0.03, T:0.28
Consensus pattern (75 bp):
ATATATACAAAGATAAAATCTAATCCTACTCCTACAAATTATATAAGTCTAAAATAAAAACAAAA
AATTATCCAA
Found at i:1304660 original size:16 final size:17
Alignment explanation
Indices: 1304641--1304682 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
1304631 CAATTAAAAT
*
1304641 TAATAAAAT-AAACAAG
1 TAATAAAATAAAACAAA
1304657 TAATAAAATAAAACAAA
1 TAATAAAATAAAACAAA
1304674 TAATTAAAA
1 TAA-TAAAA
1304683 ACTAACAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.39
17 9 0.39
18 5 0.22
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.21
Consensus pattern (17 bp):
TAATAAAATAAAACAAA
Found at i:1306170 original size:3 final size:3
Alignment explanation
Indices: 1306162--1306205 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1306152 CTATGGCCTA
1306162 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1306206 ACAAAATAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1310130 original size:18 final size:18
Alignment explanation
Indices: 1310107--1310141 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1310097 AATAGTTAGA
1310107 AAAAATCAAAACTTTTTT
1 AAAAATCAAAACTTTTTT
**
1310125 AAAAATTTAAACTTTTT
1 AAAAATCAAAACTTTTT
1310142 CTTTAAAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (18 bp):
AAAAATCAAAACTTTTTT
Found at i:1310150 original size:51 final size:51
Alignment explanation
Indices: 1310071--1310302 Score: 142
Period size: 51 Copynumber: 4.6 Consensus size: 51
1310061 CACTATTTTG
** *
1310071 TTTAAAAATCCAAACTTTTAT-TTCAAAATAGTTAGAAAAAATCAAAACTTT
1 TTTAAAAATTTAAACTTTT-TCTTTAAAATAGTTAGAAAAAATCAAAACTTT
** * **** *
1310122 TTTAAAAATTTAAACTTTTTCTTTAAAATAACTACAAAAAGATTTTTATTTT
1 TTTAAAAATTTAAACTTTTTCTTTAAAATAGTTAGAAAAA-ATCAAAACTTT
* * **
1310174 TTTAAAAAATCTT-AACTTTCTCTTT----T-TTTA-AAGAAAATCATTA-TTT
1 TTT-AAAAAT-TTAAACTTTTTCTTTAAAATAGTTAGAA-AAAATCAAAACTTT
* * **
1310220 TGCTCAAAAATCTAAACTTTTAT-TTCGAAATAGTTAGAAAAAATCAAAACTTT
1 T--TTAAAAATTTAAACTTTT-TCTTTAAAATAGTTAGAAAAAATCAAAACTTT
*
1310273 GTTAAAAATTTAAACTTTTTCTTTAAAATA
1 TTTAAAAATTTAAACTTTTTCTTTAAAATA
1310303 ACAAAAAAAT
Statistics
Matches: 136, Mismatches: 28, Indels: 34
0.69 0.14 0.17
Matches are distributed among these distances:
46 5 0.04
47 21 0.15
48 7 0.05
49 1 0.01
50 2 0.01
51 56 0.41
52 20 0.15
53 22 0.16
54 2 0.01
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.42
Consensus pattern (51 bp):
TTTAAAAATTTAAACTTTTTCTTTAAAATAGTTAGAAAAAATCAAAACTTT
Found at i:1310229 original size:151 final size:151
Alignment explanation
Indices: 1310015--1310425 Score: 517
Period size: 151 Copynumber: 2.7 Consensus size: 151
1310005 AAAATAACTA
* * *
1310015 ATTTTTTTTAAAATCTAAACTTTCGCTTTTTTTTTATTAAGAAAATCACTATTTTGTTTAAAAAT
1 ATTTTTTTAAAAATCTAAACTTT--CTTTTTTTTTA--AAGAAAATCACTATTTTGCTAAAAAAT
* *
1310080 CCAAACTTTTATTTCAAAATAGTTAGAAAAAATCAAAACTTTTTTAAAAATTTAAACTTTTTCTT
62 CCAAACTTTTATTTCGAAATAGTTAGAAAAAATCAAAACTTTGTTAAAAATTTAAACTTTTTCTT
* *
1310145 TAAAATAACTACAAAA-AGATTTTT
127 TAAAATAACAAAAAAATAGATTTTT
* * * * *
1310169 ATTTTTTTAAAAAATCTTAACTTTCTCTTTTTTTAAAGAAAATCATTATTTTGCTCAAAAATCTA
1 ATTTTTTT-AAAAATCTAAACTTTCTTTTTTTTTAAAGAAAATCACTATTTTGCTAAAAAATCCA
1310234 AACTTTTATTTCGAAATAGTTAGAAAAAATCAAAACTTTGTTAAAAATTTAAACTTTTTCTTTAA
65 AACTTTTATTTCGAAATAGTTAGAAAAAATCAAAACTTTGTTAAAAATTTAAACTTTTTCTTTAA
*
1310299 AATAACAAAAAAATAGTTTTTT
130 AATAACAAAAAAATAGATTTTT
* *
1310321 A-TTTTTTAAAAATCTAAACTTTTTTTTTATTTATTTAAAGAATATCACTATTTTGCTTAAAAAA
1 ATTTTTTTAAAAATCTAAAC--TTTCTTT-TTT-TTTAAAGAAAATCACTATTTTGC-T--AAAA
*
1310385 AAT-CAAAGCTTTTATTTCGAAATTGTTTA-AAAAAA-CAAAAC
59 AATCCAAA-CTTTTATTTCGAAATAG-TTAGAAAAAATCAAAAC
1310426 ATTTCCCAAA
Statistics
Matches: 226, Mismatches: 20, Indels: 20
0.85 0.08 0.08
Matches are distributed among these distances:
150 11 0.05
151 106 0.47
152 13 0.06
153 13 0.06
154 29 0.13
155 14 0.06
156 9 0.04
157 28 0.12
158 3 0.01
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.44
Consensus pattern (151 bp):
ATTTTTTTAAAAATCTAAACTTTCTTTTTTTTTAAAGAAAATCACTATTTTGCTAAAAAATCCAA
ACTTTTATTTCGAAATAGTTAGAAAAAATCAAAACTTTGTTAAAAATTTAAACTTTTTCTTTAAA
ATAACAAAAAAATAGATTTTT
Found at i:1310374 original size:29 final size:28
Alignment explanation
Indices: 1310315--1310374 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
1310305 AAAAAAATAG
* *
1310315 TTTTTTATTTTTTAAAAATCTAAACTTT
1 TTTTTTATTTTTTAAAAATATAAACTAT
*
1310343 TTTTTTATTTATTTAAAGAATAT-CACTAT
1 TTTTTTATTT-TTTAAA-AATATAAACTAT
1310372 TTT
1 TTT
1310375 GCTTAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 10 0.37
29 13 0.48
30 4 0.15
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.60
Consensus pattern (28 bp):
TTTTTTATTTTTTAAAAATATAAACTAT
Found at i:1310860 original size:3 final size:3
Alignment explanation
Indices: 1310854--1310898 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
1310844 AAAAAATTAA
*
1310854 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1310899 TTGGGTCCAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1310938 original size:11 final size:11
Alignment explanation
Indices: 1310924--1310948 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1310914 CCCAAAAAGG
1310924 AAAGAAAAATA
1 AAAGAAAAATA
1310935 AAAGAAAAATA
1 AAAGAAAAATA
1310946 AAA
1 AAA
1310949 ACCTCTACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAGAAAAATA
Found at i:1311322 original size:42 final size:42
Alignment explanation
Indices: 1311274--1311387 Score: 176
Period size: 42 Copynumber: 2.7 Consensus size: 42
1311264 CCTTTACTCA
* *
1311274 TAGGCCTCTAAATGCAATAAAAAGTAAATGAGCCTCCACACC
1 TAGGCCTCTAAATGCAATGAAAAGTAAATGAACCTCCACACC
* *
1311316 TAGGCCTCTAAATGCAATGAAAAGTAAACGAACCTCCGCACC
1 TAGGCCTCTAAATGCAATGAAAAGTAAATGAACCTCCACACC
1311358 T-GGACCTCTAAATGCAATGAAAAGTAAATG
1 TAGG-CCTCTAAATGCAATGAAAAGTAAATG
1311388 CCTCAACAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
41 2 0.03
42 64 0.97
ACGTcount: A:0.40, C:0.24, G:0.17, T:0.19
Consensus pattern (42 bp):
TAGGCCTCTAAATGCAATGAAAAGTAAATGAACCTCCACACC
Done.