Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015047.1 Kokia drynarioides strain JFW-HI SEQ_130091, 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: 39564
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:5463 original size:16 final size:16
Alignment explanation
Indices: 5444--5475 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5434 GAAATTTCAA
*
5444 ATATATACATACATAG
1 ATATATAAATACATAG
5460 ATATATAAATACATAG
1 ATATATAAATACATAG
5476 CAGTTATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.09, G:0.06, T:0.31
Consensus pattern (16 bp):
ATATATAAATACATAG
Found at i:17261 original size:18 final size:18
Alignment explanation
Indices: 17238--17272 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
17228 GAATTCTTGT
*
17238 TAAAATAAAATACAATTG
1 TAAAATAAAATAAAATTG
17256 TAAAATAAAATAAAATT
1 TAAAATAAAATAAAATT
17273 AAAGTCCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (18 bp):
TAAAATAAAATAAAATTG
Found at i:20209 original size:23 final size:23
Alignment explanation
Indices: 20135--20344 Score: 134
Period size: 23 Copynumber: 9.3 Consensus size: 23
20125 TAAACGGAAC
* *
20135 AAACAGAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
* *
20157 GAACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
20179 GGGCAACAGAGCGCACACAAAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
* **
20205 AAACAGAGAGTATGCAAA--G-T
1 AAACAGAGAGCACACAAAGTGCT
*
20225 --AC--TGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
20244 AATCAGAGAGCACACGAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
20267 AATAACAGAGAGCACGA-GACGTGCT
1 -A-AACAGAGAGCAC-ACAAAGTGCT
*
20292 AAACAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * *
20315 GAACATAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
20338 AAACAGA
1 AAACAGA
20345 AAGCGTGCTA
Statistics
Matches: 144, Mismatches: 28, Indels: 31
0.71 0.14 0.15
Matches are distributed among these distances:
16 8 0.06
18 3 0.02
19 1 0.01
20 1 0.01
21 2 0.01
22 18 0.12
23 71 0.49
24 2 0.01
25 30 0.21
26 8 0.06
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:20299 original size:48 final size:46
Alignment explanation
Indices: 20228--20344 Score: 139
Period size: 48 Copynumber: 2.5 Consensus size: 46
20218 GCAAAGTACT
* * *
20228 GAGCACACAAAGTGCTAATCAGAGAGCACACGA-AGTGCTAATAACAGA
1 GAGCACACACAGTGCTAAACAGAGAGCACAC-ACAGTGCT--GAACAGA
* *
20276 GAGCACGAGAC-GTGCTAAACAGAGAGCACACACAGTGCTGAACATA
1 GAGCAC-ACACAGTGCTAAACAGAGAGCACACACAGTGCTGAACAGA
20322 GAGCACACACAGTGCTAAACAGA
1 GAGCACACACAGTGCTAAACAGA
20345 AAGCGTGCTA
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
45 3 0.05
46 23 0.38
47 1 0.02
48 31 0.52
49 2 0.03
ACGTcount: A:0.42, C:0.23, G:0.24, T:0.11
Consensus pattern (46 bp):
GAGCACACACAGTGCTAAACAGAGAGCACACACAGTGCTGAACAGA
Found at i:23493 original size:112 final size:112
Alignment explanation
Indices: 23296--23527 Score: 455
Period size: 112 Copynumber: 2.1 Consensus size: 112
23286 GTAAGGGTAT
23296 TTCATTTAGATATAATTGTGGCTATAATTTTCAAGTAAAAATAATGGAAATAGAAGATGGTGGGA
1 TTCATTTAGATATAATTGTGGCTATAATTTTCAAGTAAAAATAATGGAAATAGAAGATGGTGGGA
23361 TTAGGTGGAGAAGGCATGAGCAATGTCATGATGAAAAACCATTCAAA
66 TTAGGTGGAGAAGGCATGAGCAATGTCATGATGAAAAACCATTCAAA
23408 TTCATTTAGATATAATTGTGGCTATAATTTTCAAGTAAAAATAATGGAAATAGAAGATGGTGGGA
1 TTCATTTAGATATAATTGTGGCTATAATTTTCAAGTAAAAATAATGGAAATAGAAGATGGTGGGA
23473 TTAGGTGGAGAAGGCATGAGCAATGTCATGATGAAAAACCATTCAAA
66 TTAGGTGGAGAAGGCATGAGCAATGTCATGATGAAAAACCATTCAAA
*
23520 TTGATTTA
1 TTCATTTA
23528 TAAAGGAAAA
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
112 119 1.00
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.30
Consensus pattern (112 bp):
TTCATTTAGATATAATTGTGGCTATAATTTTCAAGTAAAAATAATGGAAATAGAAGATGGTGGGA
TTAGGTGGAGAAGGCATGAGCAATGTCATGATGAAAAACCATTCAAA
Found at i:24231 original size:158 final size:158
Alignment explanation
Indices: 23943--24232 Score: 465
Period size: 158 Copynumber: 1.8 Consensus size: 158
23933 ATTTTGGGAT
* **
23943 TTACATGTTATATAGGTGTTGGTCCTAGATGTCCTACCGATGGCTGAAATCCAGCATATGTTGTT
1 TTACATGTTATATAGGTGCTGGTCCTAGATGTCCTACCGATGGCTGAAATCCAGCATATGTTGAG
* * *
24008 GATTCTCCACAGCTCGTGTAAGCAGCATCTTGTAGTCTAACATCTCGACCCGCAGCTTGTGTGAG
66 GATTCTCCACAGCTCGTGTAAGCAGCATCGTGTAGTCTAACATCTCGACCCACAGCTCGTGTGAG
24073 CAGGCCCATTTCACAGCTCGTCTGAGCA
131 CAGGCCCATTTCACAGCTCGTCTGAGCA
* *
24101 TTACATGTTATATGGGTGCTGGTCCTAGATGTCCTACCGATGGCT-AAGATCCGGCATATGTTGA
1 TTACATGTTATATAGGTGCTGGTCCTAGATGTCCTACCGATGGCTGAA-ATCCAGCATATGTTGA
* * *
24165 GGATTCTCCATAGCTCGTGTGAGCAGCATCGTGTAGTGTAACATCTCGACCCACAGCTCGTGTGA
65 GGATTCTCCACAGCTCGTGTAAGCAGCATCGTGTAGTCTAACATCTCGACCCACAGCTCGTGTGA
24230 GCA
130 GCA
24233 CTACATGATA
Statistics
Matches: 120, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
157 2 0.02
158 118 0.98
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.30
Consensus pattern (158 bp):
TTACATGTTATATAGGTGCTGGTCCTAGATGTCCTACCGATGGCTGAAATCCAGCATATGTTGAG
GATTCTCCACAGCTCGTGTAAGCAGCATCGTGTAGTCTAACATCTCGACCCACAGCTCGTGTGAG
CAGGCCCATTTCACAGCTCGTCTGAGCA
Found at i:24823 original size:24 final size:24
Alignment explanation
Indices: 24796--24865 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
24786 TTGTATCGAT
24796 AGTACTCTTGTGACTACCGGTATA
1 AGTACTCTTGTGACTACCGGTATA
*
24820 AGTA-TACTTGT-A-T---TG-AT-
1 AGTACT-CTTGTGACTACCGGTATA
24837 AGTACTCTTGTGACTACCGGTATA
1 AGTACTCTTGTGACTACCGGTATA
24861 AGTAC
1 AGTAC
24866 AGGGCAAGTG
Statistics
Matches: 35, Mismatches: 2, Indels: 18
0.64 0.04 0.33
Matches are distributed among these distances:
17 9 0.26
18 4 0.11
19 2 0.06
22 2 0.06
23 4 0.11
24 14 0.40
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (24 bp):
AGTACTCTTGTGACTACCGGTATA
Found at i:24838 original size:41 final size:41
Alignment explanation
Indices: 24780--24864 Score: 161
Period size: 41 Copynumber: 2.1 Consensus size: 41
24770 TATGAAACCT
24780 GTATACTTGTATCGATAGTACTCTTGTGACTACCGGTATAA
1 GTATACTTGTATCGATAGTACTCTTGTGACTACCGGTATAA
*
24821 GTATACTTGTATTGATAGTACTCTTGTGACTACCGGTATAA
1 GTATACTTGTATCGATAGTACTCTTGTGACTACCGGTATAA
24862 GTA
1 GTA
24865 CAGGGCAAGT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (41 bp):
GTATACTTGTATCGATAGTACTCTTGTGACTACCGGTATAA
Found at i:29814 original size:16 final size:16
Alignment explanation
Indices: 29793--29827 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
29783 AACTGTTATG
29793 TATGTATATATA-TATA
1 TATGTATAT-TAGTATA
29809 TATGTATATTAGTATA
1 TATGTATATTAGTATA
29825 TAT
1 TAT
29828 TTGAAATTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 2 0.11
16 16 0.89
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (16 bp):
TATGTATATTAGTATA
Found at i:31356 original size:18 final size:18
Alignment explanation
Indices: 31333--31382 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
31323 ACAGGGTAAA
***
31333 GATGATGATGATGACTCT
1 GATGATGATGATGACGAG
* *
31351 GATGATGATCAAGACGAG
1 GATGATGATGATGACGAG
31369 GATGATGATGATGA
1 GATGATGATGATGA
31383 TGAAGACGAG
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.34, C:0.08, G:0.32, T:0.26
Consensus pattern (18 bp):
GATGATGATGATGACGAG
Found at i:31382 original size:24 final size:24
Alignment explanation
Indices: 31350--31395 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
31340 ATGATGACTC
31350 TGATGATGATCAAGACGAGGATGA
1 TGATGATGATCAAGACGAGGATGA
*
31374 TGATGATGATGAAGACGAGGAT
1 TGATGATGATCAAGACGAGGAT
31396 TGAATCACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.07, G:0.35, T:0.22
Consensus pattern (24 bp):
TGATGATGATCAAGACGAGGATGA
Done.