Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001756.1 Kokia drynarioides strain JFW-HI SEQ_113471, 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: 9401
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Found at i:928 original size:24 final size:24
Alignment explanation
Indices: 896--1034 Score: 172
Period size: 24 Copynumber: 5.8 Consensus size: 24
886 GCGTTTACGC
*
896 TTACGCTCGCCAGCTGATATGCGT
1 TTACGCTCGCCAGCTAATATGCGT
**
920 TTACGCTCGCCAGCTAATATATGT
1 TTACGCTCGCCAGCTAATATGCGT
*
944 TTACGCTCGCCAGCTAATATGTGT
1 TTACGCTCGCCAGCTAATATGCGT
* * * *
968 TTACGCTCGTCAGTTGATATACGT
1 TTACGCTCGCCAGCTAATATGCGT
* *
992 TTACGCTCGTCA-CTAATATGCAT
1 TTACGCTCGCCAGCTAATATGCGT
*
1015 TTACGCTCGCTAGCTAATAT
1 TTACGCTCGCCAGCTAATAT
1035 AATAAAAACA
Statistics
Matches: 99, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
23 17 0.17
24 82 0.83
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.34
Consensus pattern (24 bp):
TTACGCTCGCCAGCTAATATGCGT
Found at i:948 original size:48 final size:48
Alignment explanation
Indices: 891--1035 Score: 193
Period size: 48 Copynumber: 3.0 Consensus size: 48
881 AATATGCGTT
* *
891 TACGCTTACGCTCGCCAGCTGATATGCGTTTACGCTCGCCAGCTAATA
1 TACGTTTACGCTCGCCAGCTAATATGCGTTTACGCTCGCCAGCTAATA
* * * * *
939 TATGTTTACGCTCGCCAGCTAATATGTGTTTACGCTCGTCAGTTGATA
1 TACGTTTACGCTCGCCAGCTAATATGCGTTTACGCTCGCCAGCTAATA
* * *
987 TACGTTTACGCTCGTCA-CTAATATGCATTTACGCTCGCTAGCTAATA
1 TACGTTTACGCTCGCCAGCTAATATGCGTTTACGCTCGCCAGCTAATA
1034 TA
1 TA
1036 ATAAAAACAT
Statistics
Matches: 82, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
47 26 0.32
48 56 0.68
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.33
Consensus pattern (48 bp):
TACGTTTACGCTCGCCAGCTAATATGCGTTTACGCTCGCCAGCTAATA
Found at i:8788 original size:60 final size:58
Alignment explanation
Indices: 8702--9228 Score: 383
Period size: 59 Copynumber: 8.8 Consensus size: 58
8692 GAAAAAAAAA
*
8702 TTTGATGTTGGTCATTGC-ATGGCCGACACCCCTTTTTAATCTGATAAAAAAATCAAATT
1 TTTGGTGTTGGTCA-TGCAATGGCCGACACCCCTTTTT-ATCTGATAAAAAAATCAAATT
* * * *
8761 TTTGGATGTTGGTCATGCAATGACCGACACCTCCTTTTTGTC--A-AAAAAATTCAATTT
1 TTTGG-TGTTGGTCATGCAATGGCCGACACC-CCTTTTTATCTGATAAAAAAATCAAATT
* * *
8818 TTTGGTGTTGGTCATGCAATAGCGGACACCCCTATTTATCTGATAAAAAAAATCAAATT
1 TTTGGTGTTGGTCATGCAATGGCCGACACCCCTTTTTATCTGAT-AAAAAAATCAAATT
** *
8877 TTTGGGTGTTGGTCATGCCGTGGTCGACACTCCCTTTTT-T-TAGATAAAAAAATTTCAAAATTT
1 TTT-GGTGTTGGTCATGCAATGGCCGACAC-CCCTTTTTATCT-GATAAAAAAA--TC-AAA-TT
* * * * *
8940 TTTTGTGTTTG-CTATGCAATGGCCAACACCCCTATTTATCTGATAAAAAAATTAAATT
1 TTTGGTGTTGGTC-ATGCAATGGCCGACACCCCTTTTTATCTGATAAAAAAATCAAATT
* * *
8998 TTTGAGTGTTGGTCATGCCATGGCTGACACCCCTTTTT-TCAGATAAAAAAATTTCAAAATTT
1 TTTG-GTGTTGGTCATGCAATGGCCGACACCCCTTTTTATCTGATAAAAAAA--TC-AAA-TT
* ** * * *
9060 TTTGGTGTTGGCCATGCAATGATCGACACCCTCTTTTTGT-AGATAAAAAAAAAT-AGATTTT
1 TTTGGTGTTGGTCATGCAATGGCCGACACCC-CTTTTTATCTGAT--AAAAAAATCA-A-ATT
* * * * * * * *
9121 TTTTGTGTTAGCCATGCAATGGTCGACACCCCTTTTTGT-TAAATAAAAAAATCGATTT
1 TTTGGTGTTGGTCATGCAATGGCCGACACCCCTTTTTATCT-GATAAAAAAATCAAATT
** * ** * * *
9179 TTTTATGTCGACCATGCAATGACCGACACCTCCTTTTTATTTGGTAAAAA
1 TTTGGTGTTGGTCATGCAATGGCCGACACC-CCTTTTTATCTGATAAAAA
9229 TTAAAATTTT
Statistics
Matches: 380, Mismatches: 55, Indels: 66
0.76 0.11 0.13
Matches are distributed among these distances:
55 8 0.02
56 22 0.06
57 18 0.05
58 45 0.12
59 82 0.22
60 60 0.16
61 82 0.22
62 49 0.13
63 7 0.02
64 7 0.02
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.37
Consensus pattern (58 bp):
TTTGGTGTTGGTCATGCAATGGCCGACACCCCTTTTTATCTGATAAAAAAATCAAATT
Found at i:9009 original size:181 final size:181
Alignment explanation
Indices: 8803--9153 Score: 449
Period size: 181 Copynumber: 1.9 Consensus size: 181
8793 CCTTTTTGTC
* *
8803 AAAAAAATTCAATTTTTTGGTGTTGGTCATGCAATAGCGGACACCCCTATTTATCTGATAAAAAA
1 AAAAAAATTCAAATTTTTGGTGTTGGTCATGCAATAGCGGACACCCCT-TTTATCAGATAAAAAA
* ** * * *
8868 A-ATC-AAATTTTTGGGTGTTGGTCATGCCGTGGTCGACACTCC-CTTTTTTTAGATAAAAAAAT
65 ATATCAAAATTTTTGGGTGTTGGCCATGCAATGATCGACAC-CCTCTTTTTGTAGATAAAAAAAA
* * *
8930 TTCAAAATTTTTTTGTGTTTGCTATGCAATGGCCAACACCCCTATTTATCTGAT
129 AT-AAAATTTTTTTGTGTTAGCCATGCAATGGCCAACACCCCTATTTATCTGAT
* * * *
8984 AAAAAAATT-AAATTTTTGAGTGTTGGTCATGCCATGGCTGACACCCCTTTTTTCAGATAAAAAA
1 AAAAAAATTCAAATTTTTG-GTGTTGGTCATGCAATAGCGGACACCCCTTTTATCAGATAAAAAA
* *
9048 ATTTCAAAATTTTTTGGTGTTGGCCATGCAATGATCGACACCCTCTTTTTGTAGATAAAAAAAAA
65 ATATCAAAATTTTTGGGTGTTGGCCATGCAATGATCGACACCCTCTTTTTGTAGATAAAAAAAAA
* * * *
9113 TAGATTTTTTTTGTGTTAGCCATGCAATGGTCGACACCCCT
130 TAAAATTTTTTTGTGTTAGCCATGCAATGGCCAACACCCCT
9154 TTTTGTTAAA
Statistics
Matches: 145, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
180 23 0.16
181 73 0.50
182 49 0.34
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.36
Consensus pattern (181 bp):
AAAAAAATTCAAATTTTTGGTGTTGGTCATGCAATAGCGGACACCCCTTTTATCAGATAAAAAAA
TATCAAAATTTTTGGGTGTTGGCCATGCAATGATCGACACCCTCTTTTTGTAGATAAAAAAAAAT
AAAATTTTTTTGTGTTAGCCATGCAATGGCCAACACCCCTATTTATCTGAT
Found at i:9076 original size:61 final size:59
Alignment explanation
Indices: 8702--9172 Score: 353
Period size: 60 Copynumber: 7.9 Consensus size: 59
8692 GAAAAAAAAA
* * *
8702 TTTGATGTTGGTCATTGC-ATGGCCGACACCCCTTTTTAATCTGATAAAAAAA-TCAAA-TT
1 TTTGGTGTTGGTCA-TGCAATGGCTGACACCCCTTTTT--TCAGATAAAAAAATTCAAATTT
* *
8761 TTTGGATGTTGGTCATGCAATGACCGACACCTCC-TTTTT--G-TCAAAAAAATTC-AATTT
1 TTTGG-TGTTGGTCATGCAATGGCTGACACC-CCTTTTTTCAGAT-AAAAAAATTCAAATTT
* * * * *
8818 TTTGGTGTTGGTCATGCAATAGCGGACACCCCTATTTATCTGATAAAAAAAATCAAATTT
1 TTTGGTGTTGGTCATGCAATGGCTGACACCCCT-TTTTTCAGATAAAAAAATTCAAATTT
* ** *
8878 TTGGGTGTTGGTCATGCCGTGG-TCGACACTCCCTTTTTTTAGATAAAAAAATTTCAAAATTT
1 TTTGGTGTTGGTCATGCAATGGCT-GACAC-CCCTTTTTTCAGATAAAAAAA-TTC-AAATTT
* * ** * *
8940 TTTTGTGTTTG-CTATGCAATGGCCAACACCCCTATTTATCTGATAAAAAAATT-AAA-TT
1 TTTGGTGTTGGTC-ATGCAATGGCTGACACCCCT-TTTTTCAGATAAAAAAATTCAAATTT
*
8998 TTTGAGTGTTGGTCATGCCATGGCTGACACCCCTTTTTTCAGATAAAAAAATTTCAAAATTT
1 TTTG-GTGTTGGTCATGCAATGGCTGACACCCCTTTTTTCAGATAAAAAAA-TTC-AAATTT
* * * *
9060 TTTGGTGTTGGCCATGCAAT-GATCGACACCCTCTTTTTGT-AGATAAAAAAAAAT-AGATTTT
1 TTTGGTGTTGGTCATGCAATGGCT-GACACCC-CTTTTT-TCAGAT-AAAAAAATTCA-AATTT
* * * * *
9121 TTTTGTGTTAGCCATGCAATGG-TCGACACCCCTTTTTGTTAAATAAAAAAAT
1 TTTGGTGTTGGTCATGCAATGGCT-GACACCCCTTTTT-TCAGATAAAAAAAT
9173 CGATTTTTTT
Statistics
Matches: 338, Mismatches: 42, Indels: 63
0.76 0.09 0.14
Matches are distributed among these distances:
55 3 0.01
56 32 0.09
57 13 0.04
58 21 0.06
59 45 0.13
60 86 0.25
61 73 0.22
62 57 0.17
63 8 0.02
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (59 bp):
TTTGGTGTTGGTCATGCAATGGCTGACACCCCTTTTTTCAGATAAAAAAATTCAAATTT
Found at i:9089 original size:120 final size:118
Alignment explanation
Indices: 8702--9090 Score: 445
Period size: 116 Copynumber: 3.3 Consensus size: 118
8692 GAAAAAAAAA
* * * *
8702 TTTGATGTTGGTCATTGC-ATGGCCGACACCCCTTTTTAATCTGATAAAAAAATCAAATTTTTGG
1 TTTGGTGTTGGCCA-TGCAATGACCGACACCCCTATTT-ATCTGATAAAAAAATCAAATTTTTGG
* * *
8766 ATGTTGGTCATGCAATGACCGACACCTCC-TTTTT-G-TCAAAAAAA-TTC--AATTT
64 -TGTTGGTCATGCCATGGCTGACACC-CCTTTTTTAGAT-AAAAAAATTTCAAAATTT
* *
8818 TTTGGTGTTGGTCATGCAAT-AGCGGACACCCCTATTTATCTGATAAAAAAAATCAAATTTTTGG
1 TTTGGTGTTGGCCATGCAATGA-CCGACACCCCTATTTATCTGAT-AAAAAAATCAAATTTTT-G
*
8882 GTGTTGGTCATGCCGTGG-TCGACACTCCCTTTTTTTAGATAAAAAAATTTCAAAATTT
63 GTGTTGGTCATGCCATGGCT-GACAC-CCC-TTTTTTAGATAAAAAAATTTCAAAATTT
* * * * * *
8940 TTTTGTGTTTGCTATGCAATGGCCAACACCCCTATTTATCTGATAAAAAAATTAAATTTTTGAGT
1 TTTGGTGTTGGCCATGCAATGACCGACACCCCTATTTATCTGATAAAAAAATCAAATTTTTG-GT
9005 GTTGGTCATGCCATGGCTGACACCCCTTTTTTCAGATAAAAAAATTTCAAAATTT
65 GTTGGTCATGCCATGGCTGACACCCCTTTTTT-AGATAAAAAAATTTCAAAATTT
*
9060 TTTGGTGTTGGCCATGCAATGATCGACACCC
1 TTTGGTGTTGGCCATGCAATGACCGACACCC
9091 TCTTTTTGTA
Statistics
Matches: 233, Mismatches: 23, Indels: 30
0.81 0.08 0.10
Matches are distributed among these distances:
115 10 0.04
116 66 0.28
117 3 0.01
118 5 0.02
119 14 0.06
120 55 0.24
121 38 0.16
122 42 0.18
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (118 bp):
TTTGGTGTTGGCCATGCAATGACCGACACCCCTATTTATCTGATAAAAAAATCAAATTTTTGGTG
TTGGTCATGCCATGGCTGACACCCCTTTTTTAGATAAAAAAATTTCAAAATTT
Found at i:9179 original size:59 final size:58
Alignment explanation
Indices: 8720--9216 Score: 289
Period size: 61 Copynumber: 8.3 Consensus size: 58
8710 TGGTCATTGC
* * * *
8720 ATGGCCGACACCCCTTTTTAATCT-GATAAAAAAATCAAA-TTTTTGGATGTTGGTCATGCA
1 ATGGTCGACACCCCTTTTT--T-TAGATAAAAAAATCAAATTTTTTTG-TGTTAGCCATGCA
** * * * * * *
8780 ATGACCGACACCTCCTTTTTGT-CA-AAAAAATTC-AATTTTTTGGTGTTGGTCATGCA
1 ATGGTCGACACC-CCTTTTTTTAGATAAAAAAATCAAATTTTTTTGTGTTAGCCATGCA
* * ** * * *
8836 ATAG-CGGACACCCCTATTTATCT-GATAAAAAAAATCAAATTTTTGGGTGTTGGTCATGCC
1 ATGGTC-GACACCCCT-TTT-TTTAGAT-AAAAAAATCAAATTTTTTTGTGTTAGCCATGCA
* * *
8896 GTGGTCGACACTCCCTTTTTTTAGATAAAAAAATTTCAAAATTTTTTTGTGTTTGCTATGCA
1 ATGGTCGACAC-CCCTTTTTTTAGATAAAAAAA--TC-AAATTTTTTTGTGTTAGCCATGCA
* * * * ** * * *
8958 ATGGCCAACACCCCTATTTATCT-GATAAAAAAATTAAATTTTTGAGTGTTGGTCATGCC
1 ATGGTCGACACCCCT-TTT-TTTAGATAAAAAAATCAAATTTTTTTGTGTTAGCCATGCA
* * *
9017 ATGG-CTGACACCCCTTTTTTCAGATAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATGCA
1 ATGGTC-GACACCCCTTTTTTTAGATAAAAAAA--TC-AAATTTTTTTGTGTTAGCCATGCA
* * *
9078 ATGATCGACACCCTCTTTTTGTAGATAAAAAAAAAT-AGATTTTTTTTGTGTTAGCCATGCA
1 ATGGTCGACACCC-CTTTTTTTAGAT--AAAAAAATCA-AATTTTTTTGTGTTAGCCATGCA
* * * *
9139 ATGGTCGACACCCCTTTTTGTTAAATAAAAAAATC-GATTTTTTTATG-TCGACCATGCA
1 ATGGTCGACACCCCTTTTT-TTAGATAAAAAAATCAAATTTTTTTGTGTTAG-CCATGCA
**
9197 ATGACCGACACCTCCTTTTT
1 ATGGTCGACACC-CCTTTTT
9217 ATTTGGTAAA
Statistics
Matches: 353, Mismatches: 54, Indels: 61
0.75 0.12 0.13
Matches are distributed among these distances:
55 4 0.01
56 26 0.07
57 21 0.06
58 42 0.12
59 62 0.18
60 54 0.15
61 84 0.24
62 51 0.14
63 2 0.01
64 7 0.02
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.36
Consensus pattern (58 bp):
ATGGTCGACACCCCTTTTTTTAGATAAAAAAATCAAATTTTTTTGTGTTAGCCATGCA
Done.