Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003877.1 Kokia drynarioides strain JFW-HI SEQ_116911, 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: 10041
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Found at i:596 original size:19 final size:20
Alignment explanation
Indices: 574--618 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
564 AAATAAAAGA
* *
574 AAAAAACAAAAGTAGA-AAT
1 AAAAAACAAAAGCAAATAAT
593 AAAAAACAAAAGCAAATAAT
1 AAAAAACAAAAGCAAATAAT
613 AAAAAA
1 AAAAAA
619 TTTCTATGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.78, C:0.07, G:0.07, T:0.09
Consensus pattern (20 bp):
AAAAAACAAAAGCAAATAAT
Found at i:2094 original size:12 final size:13
Alignment explanation
Indices: 2072--2112 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
2062 AAAGGGGTTT
2072 AATTAAAACTAAA
1 AATTAAAACTAAA
*
2085 AATT-AAACTAAGT
1 AATTAAAACTAA-A
2098 AATTAAAAC-AAA
1 AATTAAAACTAAA
2110 AAT
1 AAT
2113 AAATTCCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
12 10 0.42
13 10 0.42
14 4 0.17
ACGTcount: A:0.66, C:0.07, G:0.02, T:0.24
Consensus pattern (13 bp):
AATTAAAACTAAA
Found at i:8743 original size:51 final size:51
Alignment explanation
Indices: 8618--9007 Score: 487
Period size: 51 Copynumber: 7.6 Consensus size: 51
8608 TTTCATTTAA
** * * *
8618 TACTCACGATGACA-TGTAGTCATCGGACCTCTTGTTCCATATAGGAATTCATA
1 TACTCACGATGACACT-TAGTCATCGGACCT-TTAATCCGTAAAGG-ATTCATT
** * * * *
8671 TACTCACGATGACACAAAGTCATCGGACCCTTAATCCATCATGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
* * *
8722 TATTCACGATGACACTTAGTCATCAGACATTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
* * *
8773 TACTCACGATGACACTTAGTCATTGGACCTTT-CTCTGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
*
8823 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
* * *
8874 TACTCATGATGACTCTTAGTCATCGAACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
* * * *
8925 TACTTACGATGACACTTAATCATCAGACCTTTAATCCGTATAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
* * *
8976 TACTCACAATGACACTTAGACATCAGACCTTT
1 TACTCACGATGACACTTAGTCATCGGACCTTT
9008 TCGTTTATAG
Statistics
Matches: 292, Mismatches: 43, Indels: 6
0.86 0.13 0.02
Matches are distributed among these distances:
50 47 0.16
51 210 0.72
52 9 0.03
53 26 0.09
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.33
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
Found at i:8897 original size:152 final size:153
Alignment explanation
Indices: 8618--9007 Score: 516
Period size: 152 Copynumber: 2.5 Consensus size: 153
8608 TTTCATTTAA
** * *
8618 TACTCACGATGACA-TGTAGTCATCGGACCTCTTGTTCCATATAGGAATTCATATACTCACGATG
1 TACTCACGATGACACT-TAGTCATCGGACCT-TTAATCCGTATAGG-ATTCATTTACTCACGATG
** * * * *
8682 ACACAAAGTCATCGGACCCTTAATCCATCATGGATTCATTTATTCACGATGACACTTAGTCATC-
63 ACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATTTACTCACGATGACACTTAGTCATCG
8746 AGACATTTAATCCGTAAAGGATTCATT
128 A-ACATTTAATCCGTAAAGGATTCATT
* * * *
8773 TACTCACGATGACACTTAGTCATTGGACCTTT-CTCTGTAAAGGATTCATTTACTCACGATGACA
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTATAGGATTCATTTACTCACGATGACA
* *
8837 CTTAGTCATCGGACCTTTAATCCATAAAGGATTCATTTACTCATGATGACTCTTAGTCATCGAAC
66 CTTAGTCATCGGACCTTTAATCCATAAAGGATTCATTTACTCACGATGACACTTAGTCATCGAAC
*
8902 CTTTAATCCGTAAAGGATTCATT
131 ATTTAATCCGTAAAGGATTCATT
* * * *
8925 TACTTACGATGACACTTAATCATCAGACCTTTAATCCGTATAGGATTCATTTACTCACAATGACA
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTATAGGATTCATTTACTCACGATGACA
* *
8990 CTTAGACATCAGACCTTT
66 CTTAGTCATCGGACCTTT
9008 TCGTTTATAG
Statistics
Matches: 207, Mismatches: 25, Indels: 8
0.86 0.10 0.03
Matches are distributed among these distances:
152 125 0.60
153 52 0.25
154 2 0.01
155 27 0.13
156 1 0.00
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.33
Consensus pattern (153 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTATAGGATTCATTTACTCACGATGACA
CTTAGTCATCGGACCTTTAATCCATAAAGGATTCATTTACTCACGATGACACTTAGTCATCGAAC
ATTTAATCCGTAAAGGATTCATT
Found at i:8972 original size:203 final size:205
Alignment explanation
Indices: 8618--8994 Score: 555
Period size: 203 Copynumber: 1.8 Consensus size: 205
8608 TTTCATTTAA
** *
8618 TACTCACGATGACATGTAGTCATCGGACCTCTTGTTCCATATAGGAATTCATATACTCACGATGA
1 TACTCACGATGACATGTAGTCATCGGACCTCTTAATCCATAAAGGAATTCATATACTCACGATGA
* * * *
8683 CACAAAGTCATCGGACCCTTAATCCATCATGGATTCATTTATTCACGATGACACTTAGTCATCAG
66 CACAAAGTCATCGAACCCTTAATCCATAAAGGATTCATTTATTCACGATGACACTTAATCATCAG
*
8748 ACATTTAATCCGTAAAGGATTCATTTACTCACGATGACACTTAGTCATTGGACCTTTCTCTGTAA
131 ACATTTAATCCGTAAAGGATTCATTTACTCACAATGACACTTAGTCATTGGACCTTTCTCTGTAA
8813 AGGATTCATT
196 AGGATTCATT
* *
8823 TACTCACGATGACACT-TAGTCATCGGACCT-TTAATCCATAAAGG-ATTCATTTACTCATGATG
1 TACTCACGATGACA-TGTAGTCATCGGACCTCTTAATCCATAAAGGAATTCATATACTCACGATG
* ** * *
8885 ACTCTTAGTCATCGAACCTTTAATCCGTAAAGGATTCATTTACTT-ACGATGACACTTAATCATC
65 ACACAAAGTCATCGAACCCTTAATCCATAAAGGATTCATTTA-TTCACGATGACACTTAATCATC
* *
8949 AGACCTTTAATCCGTATAGGATTCATTTACTCACAATGACACTTAG
129 AGACATTTAATCCGTAAAGGATTCATTTACTCACAATGACACTTAG
8995 ACATCAGACC
Statistics
Matches: 153, Mismatches: 17, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
203 111 0.73
204 13 0.08
205 28 0.18
206 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.33
Consensus pattern (205 bp):
TACTCACGATGACATGTAGTCATCGGACCTCTTAATCCATAAAGGAATTCATATACTCACGATGA
CACAAAGTCATCGAACCCTTAATCCATAAAGGATTCATTTATTCACGATGACACTTAATCATCAG
ACATTTAATCCGTAAAGGATTCATTTACTCACAATGACACTTAGTCATTGGACCTTTCTCTGTAA
AGGATTCATT
Found at i:9907 original size:22 final size:23
Alignment explanation
Indices: 9864--9916 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
9854 TTCATCATTA
* *
9864 AACTTAATTAAT-C-CTTTCTTTT
1 AACTTAATTAATACACTAT-TTTC
9886 AACTTAATTAATACACTATTTTC
1 AACTTAATTAATACACTATTTTC
*
9909 ACCTTAAT
1 AACTTAAT
9917 ATCATATCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 12 0.46
23 11 0.42
24 3 0.12
ACGTcount: A:0.34, C:0.19, G:0.00, T:0.47
Consensus pattern (23 bp):
AACTTAATTAATACACTATTTTC
Done.