Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013694.1 Kokia drynarioides strain JFW-HI SEQ_128722, 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: 20049
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Warning! 127 characters in sequence are not A, C, G, or T
Found at i:11088 original size:85 final size:85
Alignment explanation
Indices: 10943--11107 Score: 213
Period size: 85 Copynumber: 1.9 Consensus size: 85
10933 AAACCCCATA
* * * * * * *
10943 TTCCTGATGAGATAGAGAGAAGTGGGTTGAAGCAATAAAGTGGTTATCTTCCTGACGAGATGCAG
1 TTCCTAATGAGATACAAAGAAGTGGATTAAAGCAATAAAGCGGTTATCTTCCTGACGAGATACAG
*
11008 AGAAGTGGACCAAATTCTTC
66 AGAAGTAGACCAAATTCTTC
* * * * *
11028 TTCCTAATGAGATACAAATAAGTGGATTAAATCAATGAAGCGGTTATCTTCCTGATGAGATATAG
1 TTCCTAATGAGATACAAAGAAGTGGATTAAAGCAATAAAGCGGTTATCTTCCTGACGAGATACAG
11093 AGAAGTAGACCAAAT
66 AGAAGTAGACCAAAT
11108 CAATGAAGTG
Statistics
Matches: 67, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
85 67 1.00
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (85 bp):
TTCCTAATGAGATACAAAGAAGTGGATTAAAGCAATAAAGCGGTTATCTTCCTGACGAGATACAG
AGAAGTAGACCAAATTCTTC
Found at i:11144 original size:15 final size:15
Alignment explanation
Indices: 11126--11155 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
11116 TGAAGCTCAA
*
11126 TACAAATGAGACTTC
1 TACAAATAAGACTTC
11141 TACAAATAAGACTTC
1 TACAAATAAGACTTC
11156 AAACCCCATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.27
Consensus pattern (15 bp):
TACAAATAAGACTTC
Found at i:11233 original size:48 final size:47
Alignment explanation
Indices: 11162--11415 Score: 213
Period size: 48 Copynumber: 5.5 Consensus size: 47
11152 CTTCAAACCC
*
11162 CATCTTCCTGATGAGATATAGAGAAGTGGGTCGAAGTAATAAAGTGGT
1 CATCTTCCTGATGAGATACAGAGAAGTGGGT-GAAGTAATAAAGTGGT
* * ** **
11210 CATCTTCCTGACGAGATGCAGAGAA----GTGAA-CCA-AATCT-GT
1 CATCTTCCTGATGAGATACAGAGAAGTGGGTGAAGTAATAAAGTGGT
* * * * * *
11250 --T-TTCTTGATGAGATACAGAGAAGTGGATTAAATCAATGAAGTGAT
1 CATCTTCCTGATGAGATACAGAGAAGTGGGTGAAGT-AATAAAGTGGT
* *
11295 CATCTTCCTGATAAGATACAGAGAAGTGGGTCGAAGTAATAAAGCGGT
1 CATCTTCCTGATGAGATACAGAGAAGTGGGT-GAAGTAATAAAGTGGT
* * *
11343 CATCTTCCTGATGAGATACAAACAAGTGGGTTGAAGTAATAAAGTGAT
1 CATCTTCCTGATGAGATACAGAGAAGTGGG-TGAAGTAATAAAGTGGT
** *
11391 CATCTTCCCAATGAGATTCAGAGAA
1 CATCTTCCTGATGAGATACAGAGAA
11416 TTAGACCAAG
Statistics
Matches: 157, Mismatches: 36, Indels: 26
0.72 0.16 0.12
Matches are distributed among these distances:
37 18 0.11
38 1 0.01
40 2 0.01
41 6 0.04
42 1 0.01
43 4 0.03
44 4 0.03
45 1 0.01
47 1 0.01
48 115 0.73
49 4 0.03
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.26
Consensus pattern (47 bp):
CATCTTCCTGATGAGATACAGAGAAGTGGGTGAAGTAATAAAGTGGT
Found at i:11805 original size:16 final size:17
Alignment explanation
Indices: 11765--11805 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
11755 AAATGTCAAT
*
11765 TTAC-AAAAGGCCCAAG
1 TTACAAAAAGACCCAAG
11781 TTACAAAAAAGACCCAA-
1 TTAC-AAAAAGACCCAAG
11798 TTACAAAA
1 TTACAAAA
11806 CAAGCCCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 8 0.36
17 4 0.18
18 10 0.45
ACGTcount: A:0.54, C:0.22, G:0.10, T:0.15
Consensus pattern (17 bp):
TTACAAAAAGACCCAAG
Found at i:11813 original size:17 final size:16
Alignment explanation
Indices: 11765--11815 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 16
11755 AAATGTCAAT
*
11765 TTAC-AAAAGGCCCAA
1 TTACAAAAAAGCCCAA
11780 GTTACAAAAAAGACCCAA
1 -TTACAAAAAAG-CCCAA
11798 TTACAAAACAAGCCCAA
1 TTACAAAA-AAGCCCAA
11815 T
1 T
11816 ACCCAAAACC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
16 4 0.13
17 19 0.61
18 8 0.26
ACGTcount: A:0.51, C:0.25, G:0.10, T:0.14
Consensus pattern (16 bp):
TTACAAAAAAGCCCAA
Found at i:13200 original size:30 final size:30
Alignment explanation
Indices: 13160--13407 Score: 208
Period size: 30 Copynumber: 8.5 Consensus size: 30
13150 GCTTTATTTA
* * *
13160 AAAATTACATTTTGACCCTTAAACTTTCCT
1 AAAATCACATTTTGACCCTCAAACTTTCCC
* * *
13190 AAAATCACATTTTGACCCTTAATCTTTTCC
1 AAAATCACATTTTGACCCTCAAACTTTCCC
* * * **
13220 AAAATCACATTTTTA-CCTCGATCTTTCGT
1 AAAATCACATTTTGACCCTCAAACTTTCCC
* *
13249 AAAATCACATTTTGACCC-CAATCTTTCTC
1 AAAATCACATTTTGACCCTCAAACTTTCCC
* *
13278 AAAATCACATTTTGACTCC-CGATCTTTCCC
1 AAAATCACATTTTGAC-CCTCAAACTTTCCC
* * *
13308 CAAATCAAATTTTG----TTAAACTTTCCC
1 AAAATCACATTTTGACCCTCAAACTTTCCC
*
13334 AAAATCACATTTTGACCCCTCGAAC-TTCCC
1 AAAATCACATTTTGA-CCCTCAAACTTTCCC
* * *
13364 AAAATCACATTTTTA-CCTCAAAATTTCCA
1 AAAATCACATTTTGACCCTCAAACTTTCCC
*
13393 AAAATTACATTTTGA
1 AAAATCACATTTTGA
13408 ACCCGTAATT
Statistics
Matches: 178, Mismatches: 31, Indels: 19
0.78 0.14 0.08
Matches are distributed among these distances:
26 20 0.11
28 6 0.03
29 64 0.36
30 84 0.47
31 4 0.02
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.36
Consensus pattern (30 bp):
AAAATCACATTTTGACCCTCAAACTTTCCC
Found at i:13348 original size:56 final size:56
Alignment explanation
Indices: 13271--13376 Score: 151
Period size: 56 Copynumber: 1.9 Consensus size: 56
13261 TGACCCCAAT
* * * *
13271 CTTTCTCAAAATCACATTTTGACTCC-CGATCTTTCCCCAAATCAAATTTTGTTAAA
1 CTTTCCCAAAATCACATTTTGACCCCTCGAAC-TTCCCAAAATCAAATTTTGTTAAA
*
13327 CTTTCCCAAAATCACATTTTGACCCCTCGAACTTCCCAAAATCACATTTT
1 CTTTCCCAAAATCACATTTTGACCCCTCGAACTTCCCAAAATCAAATTTT
13377 TACCTCAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
56 40 0.91
57 4 0.09
ACGTcount: A:0.30, C:0.30, G:0.05, T:0.35
Consensus pattern (56 bp):
CTTTCCCAAAATCACATTTTGACCCCTCGAACTTCCCAAAATCAAATTTTGTTAAA
Found at i:13405 original size:59 final size:58
Alignment explanation
Indices: 13160--13407 Score: 220
Period size: 59 Copynumber: 4.3 Consensus size: 58
13150 GCTTTATTTA
* ** * * *
13160 AAAATTACATTTTGACCCTTAAACTTTCCTAAAATCACATTTTGACCCTTAATCTTTTCC
1 AAAATCACATTTTGACCCTCGAACTTTCCCAAAATCACATTTTGA-CCTCAAAC-TTTCC
* * ** * *
13220 AAAATCACATTTTTA-CCTCGATCTTTCGTAAAATCACATTTTGACCCCAATCTTTCTC
1 AAAATCACATTTTGACCCTCGAACTTTCCCAAAATCACATTTTGACCTCAAACTTTC-C
* * * *
13278 AAAATCACATTTTGACTCC-CGATCTTTCCCCAAATCAAATTTTG---TTAAACTTTCCC
1 AAAATCACATTTTGAC-CCTCGAACTTTCCCAAAATCACATTTTGACCTCAAACTTT-CC
* *
13334 AAAATCACATTTTGACCCCTCGAAC-TTCCCAAAATCACATTTTTACCTCAAAATTTCC
1 AAAATCACATTTTGA-CCCTCGAACTTTCCCAAAATCACATTTTGACCTCAAACTTTCC
*
13392 AAAAATTACATTTTGA
1 -AAAATCACATTTTGA
13408 ACCCGTAATT
Statistics
Matches: 155, Mismatches: 23, Indels: 21
0.78 0.12 0.11
Matches are distributed among these distances:
56 40 0.26
57 10 0.06
58 23 0.15
59 67 0.43
60 15 0.10
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.36
Consensus pattern (58 bp):
AAAATCACATTTTGACCCTCGAACTTTCCCAAAATCACATTTTGACCTCAAACTTTCC
Found at i:16325 original size:14 final size:13
Alignment explanation
Indices: 16285--16327 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
16275 ATATTGAGTT
16285 TATGCATGATATA
1 TATGCATGATATA
* *
16298 AATGCATGACATA
1 TATGCATGATATA
*
16311 TTTGCTATGATATA
1 TATGC-ATGATATA
16325 TAT
1 TAT
16328 ATATTGAAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
13 14 0.61
14 9 0.39
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (13 bp):
TATGCATGATATA
Done.