Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004922.1 Kokia drynarioides strain JFW-HI SEQ_118621, 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: 3820
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.37
Found at i:787 original size:29 final size:28
Alignment explanation
Indices: 755--920 Score: 99
Period size: 29 Copynumber: 5.6 Consensus size: 28
745 ACCCCCAAAC
755 TTTCCAAAATTCAATTTTTGACCTCGAAT
1 TTTCCAAAATTC-ATTTTTGACCTCGAAT
* * *
784 TTTCTAAAAAAATTACATTTCT-ACCCTCGAAC
1 TTTC---CAAAATT-CATTTTTGA-CCTCGAAT
* *
816 TTCCCAAAATTCATTATTTGACCTCGTA-
1 TTTCCAAAATTCATT-TTTGACCTCGAAT
* * *
844 TGTCTAAAAATTTCATTTTTAACCTCGAAT
1 TTTC-CAAAA-TTCATTTTTGACCTCGAAT
874 TTTCCAAAATTACA-TTTT-ACC-CGTAAAT
1 TTTCCAAAATT-CATTTTTGACCTCG--AAT
*
902 TTTCGAAAATTCTATTTTT
1 TTTCCAAAATTC-ATTTTT
921 AATCCCGAAC
Statistics
Matches: 107, Mismatches: 15, Indels: 30
0.70 0.10 0.20
Matches are distributed among these distances:
26 2 0.02
27 4 0.04
28 26 0.24
29 42 0.39
30 10 0.09
31 1 0.01
32 21 0.20
33 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.05, T:0.42
Consensus pattern (28 bp):
TTTCCAAAATTCATTTTTGACCTCGAAT
Found at i:977 original size:58 final size:57
Alignment explanation
Indices: 721--1124 Score: 261
Period size: 58 Copynumber: 6.9 Consensus size: 57
711 TTTGAACCCT
* * * * *
721 AATGTTTTCAAAAATTACATTTTTACCCCCAAACTTTCC-AAAATT-CAATTTTTGACCTCG
1 AATG-TTT-AAAAATTCCATTTTTA-ACCCGAACCTTCCAAAAATTACCA-TTTT-ACCTCG
* * * * * ** *
781 AATTTTCTAAAAAAATTACATTTCTACCCTCGAA-CTTCCCAAAATTCATTATTTGACCTCG
1 AATGTT-T--AAAAATTCCATTTTTAACC-CGAACCTTCCAAAAATT-ACCATTTTACCTCG
* * * **
842 TATGTCTAAAAATTTCATTTTTAACCTCGAATTTTCC-AAAATTA-CATTTTACC-CG
1 AATGTTTAAAAATTCCATTTTTAACC-CGAACCTTCCAAAAATTACCATTTTACCTCG
* * * *
897 TAAAT-TTTCGAAAATTCTATTTTTAATCCCGAACCTTCCAAAAATTACCATTTCACCTTG
1 --AATGTTT-AAAAATTCCATTTTTAA-CCCGAACCTTCCAAAAATTACCATTTTACCTCG
* * *
957 AATGTTTAAAAATTCCA-TTTTGACCTCGAACCTTCAAAAAATTACCATTTTACTCCCG
1 AATGTTTAAAAATTCCATTTTTAACC-CGAACCTTCCAAAAATTACCATTTTAC-CTCG
* * ** *
1015 AATGTCTAAAAATT-TAGTTTTTAACCCCGAATATTCCAAAAATTATCATTTTACCTCCG
1 AATGTTTAAAAATTCCA-TTTTTAA-CCCGAACCTTCCAAAAATTACCATTTTACCT-CG
* *
1074 AATG-TTAAAAATTTCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTT
1 AATGTTTAAAAATTCCATTTTT-AACCCGAACCTTCCAAAAATTACCATTTT
1125 GCCCCCGAGT
Statistics
Matches: 274, Mismatches: 47, Indels: 48
0.74 0.13 0.13
Matches are distributed among these distances:
55 2 0.01
56 11 0.04
57 56 0.20
58 100 0.36
59 53 0.19
60 15 0.05
61 33 0.12
62 3 0.01
63 1 0.00
ACGTcount: A:0.34, C:0.23, G:0.06, T:0.38
Consensus pattern (57 bp):
AATGTTTAAAAATTCCATTTTTAACCCGAACCTTCCAAAAATTACCATTTTACCTCG
Found at i:995 original size:28 final size:29
Alignment explanation
Indices: 926--1007 Score: 87
Period size: 28 Copynumber: 2.8 Consensus size: 29
916 TTTTTAATCC
926 CGAACCTTCCAAAAATTACCA-TTTCACCT
1 CGAACCTT-CAAAAATTACCATTTTCACCT
* ** * *
955 TGAATGTTTAAAAATT-CCATTTTGACCT
1 CGAACCTTCAAAAATTACCATTTTCACCT
983 CGAACCTTCAAAAAATTACCATTTT
1 CGAACCTTC-AAAAATTACCATTTT
1008 ACTCCCGAAT
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
27 3 0.07
28 19 0.46
29 12 0.29
30 7 0.17
ACGTcount: A:0.35, C:0.24, G:0.06, T:0.34
Consensus pattern (29 bp):
CGAACCTTCAAAAATTACCATTTTCACCT
Found at i:1007 original size:30 final size:30
Alignment explanation
Indices: 924--1132 Score: 125
Period size: 30 Copynumber: 7.2 Consensus size: 30
914 TATTTTTAAT
*
924 CCCGAACCTTCCAAAAATTACCA-TTTCAC
1 CCCGAACCTTCCAAAAATTACCATTTTGAC
** ** *
953 CTTGAATGTT-TAAAAATT-CCATTTTGAC
1 CCCGAACCTTCCAAAAATTACCATTTTGAC
* *
981 CTCGAACCTTCAAAAAATTACCATTTT-AC
1 CCCGAACCTTCCAAAAATTACCATTTTGAC
* ** *
1010 TCCCGAA--TGTCTAAAAATTTA-GTTTTTAAC
1 -CCCGAACCT-TCCAAAAA-TTACCATTTTGAC
** *
1040 CCCGAATATTCCAAAAATTATCATTTT-AC
1 CCCGAACCTTCCAAAAATTACCATTTTGAC
** *
1069 CTCCGAATGTT--AAAAATT-TCATTTTTGAC
1 C-CCGAACCTTCCAAAAATTACCA-TTTTGAC
*
1098 CCCGAACCTTCCAAAAATTACCATTTTGCC
1 CCCGAACCTTCCAAAAATTACCATTTTGAC
1128 CCCGA
1 CCCGA
1133 GTGTCCAAAA
Statistics
Matches: 142, Mismatches: 22, Indels: 31
0.73 0.11 0.16
Matches are distributed among these distances:
27 6 0.04
28 38 0.27
29 41 0.29
30 54 0.38
31 3 0.02
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.33
Consensus pattern (30 bp):
CCCGAACCTTCCAAAAATTACCATTTTGAC
Found at i:1143 original size:58 final size:58
Alignment explanation
Indices: 843--1153 Score: 265
Period size: 58 Copynumber: 5.4 Consensus size: 58
833 TTGACCTCGT
* ** ***
843 ATGTCTAAAAATTTCATTTTTAACCTCGAATTTTCC-AAAATTA-CATTTTACCCGTAA
1 ATGTC-AAAAATTTCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCCGA
* * * * **
900 ATTTTCGAAAA-TTCTATTTTTAATCCCGAACCTTCCAAAAATTACCATTTCA-CCTTGA
1 A-TGTCAAAAATTTC-ATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCCGA
* * * * * *
958 ATGTTTAAAAATTCCA-TTTTGACCTCGAACCTTCAAAAAATTACCATTTTACTCCCGA
1 ATG-TCAAAAATTTCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCCGA
** * *
1016 ATGTCTAAAAATTT-AGTTTTTAACCCCGAATATTCCAAAAATTATCATTTTACCTCCGA
1 ATGTC-AAAAATTTCA-TTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCCGA
* * *
1075 ATGTTAAAAATTTCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTGCCCCCGA
1 ATGTCAAAAATTTCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCCGA
* * * *
1133 GTGTCCAAAATTACCTTTTTA
1 ATGTCAAAAATTTCATTTTTA
1154 CTCCCGAGCA
Statistics
Matches: 199, Mismatches: 44, Indels: 21
0.75 0.17 0.08
Matches are distributed among these distances:
56 3 0.02
57 55 0.28
58 94 0.47
59 47 0.24
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (58 bp):
ATGTCAAAAATTTCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCCGA
Found at i:1152 original size:28 final size:28
Alignment explanation
Indices: 1111--1170 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
1101 GAACCTTCCA
* **
1111 AAAATTACCATTTTGCCCCCGAGTGTCC
1 AAAATTACCATTTTACCCCCGAGCATCC
* *
1139 AAAATTACCTTTTTACTCCCGAGCATCC
1 AAAATTACCATTTTACCCCCGAGCATCC
1167 AAAA
1 AAAA
1171 ATCACATTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.32, C:0.30, G:0.10, T:0.28
Consensus pattern (28 bp):
AAAATTACCATTTTACCCCCGAGCATCC
Found at i:1160 original size:116 final size:116
Alignment explanation
Indices: 907--1172 Score: 310
Period size: 116 Copynumber: 2.3 Consensus size: 116
897 TAAATTTTCG
* * *
907 AAAATTCTA-TTTTTAATCCCGAACCTTCCAAAAATTACCATTTCACCTTGAATGTTTAAAAATT
1 AAAATT-TACTTTTTACTCCCGAACATTCCAAAAATTACCATTTCACCTCGAATGTTTAAAAATT
* *
971 CCATTTTGACCTCGAACCTTCAAAAAATTACCATTTTACTCCCGAATGTCTA
65 CCATTTTGACCCCGAACCTTCAAAAAATTACCATTTTACCCCCGAATGTCTA
* * * *
1023 AAAATTTAGTTTTTAAC-CCCGAATATTCCAAAAATTATCATTTTACCTCCGAATG-TTAAAAAT
1 AAAATTTACTTTTT-ACTCCCGAACATTCCAAAAATTACCATTTCACCT-CGAATGTTTAAAAAT
* * * * *
1086 TTCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTGCCCCCGAGTGTC-C
64 TCCA-TTTTGACCCCGAACCTTCAAAAAATTACCATTTTACCCCCGAATGTCTA
*
1139 AAAA-TTACCTTTTTACTCCCGAGCA-TCCAAAAAT
1 AAAATTTA-CTTTTTACTCCCGAACATTCCAAAAAT
1173 CACATTTTGA
Statistics
Matches: 128, Mismatches: 16, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
115 16 0.12
116 64 0.50
117 48 0.38
ACGTcount: A:0.34, C:0.25, G:0.07, T:0.34
Consensus pattern (116 bp):
AAAATTTACTTTTTACTCCCGAACATTCCAAAAATTACCATTTCACCTCGAATGTTTAAAAATTC
CATTTTGACCCCGAACCTTCAAAAAATTACCATTTTACCCCCGAATGTCTA
Found at i:3323 original size:15 final size:14
Alignment explanation
Indices: 3282--3332 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 14
3272 ATTTTGGTTA
3282 TTAAAATTAATTATTT
1 TTAAAATT--TTATTT
*
3298 TTAAGATTTTATTT
1 TTAAAATTTTATTT
3312 TATAAAATTTTATTT
1 T-TAAAATTTTATTT
3327 TTAAAA
1 TTAAAA
3333 AACTTTCACA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 12 0.38
15 13 0.41
16 7 0.22
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (14 bp):
TTAAAATTTTATTT
Done.