Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006924.1 Kokia drynarioides strain JFW-HI SEQ_121527, 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: 80711
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Warning! 44 characters in sequence are not A, C, G, or T
Found at i:2466 original size:16 final size:16
Alignment explanation
Indices: 2445--2476 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2435 TTTGGATTAA
2445 TTTTTTACAAATATAT
1 TTTTTTACAAATATAT
2461 TTTTTTACAAATATAT
1 TTTTTTACAAATATAT
2477 GACTAGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTTTTACAAATATAT
Found at i:18384 original size:19 final size:19
Alignment explanation
Indices: 18351--18394 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
18341 TTTAGATAAG
*
18351 ATTTTTTATATTTTAATTT
1 ATTTTTTATATTTTAATTA
*
18370 ATTTTTTA-ATATTTAGTTA
1 ATTTTTTATAT-TTTAATTA
18389 ATTTTT
1 ATTTTT
18395 CATTGTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 2 0.09
19 20 0.91
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (19 bp):
ATTTTTTATATTTTAATTA
Found at i:24065 original size:151 final size:151
Alignment explanation
Indices: 23838--24140 Score: 606
Period size: 151 Copynumber: 2.0 Consensus size: 151
23828 ATGATTATTA
23838 CTGGGTTTTAGTTCTCATTGCTTGGTTGTTTCAAAGTGTTTTTTCTTTGTTTTAATTTTCCCCTT
1 CTGGGTTTTAGTTCTCATTGCTTGGTTGTTTCAAAGTGTTTTTTCTTTGTTTTAATTTTCCCCTT
23903 TAGGCATCTGAGCTAATAGTAAGTTTACTTACCTCTATCTAATGAATTTTCTCTTTAAGGTCGTT
66 TAGGCATCTGAGCTAATAGTAAGTTTACTTACCTCTATCTAATGAATTTTCTCTTTAAGGTCGTT
23968 TGGAGGTGCTGCCTCTCCTAT
131 TGGAGGTGCTGCCTCTCCTAT
23989 CTGGGTTTTAGTTCTCATTGCTTGGTTGTTTCAAAGTGTTTTTTCTTTGTTTTAATTTTCCCCTT
1 CTGGGTTTTAGTTCTCATTGCTTGGTTGTTTCAAAGTGTTTTTTCTTTGTTTTAATTTTCCCCTT
24054 TAGGCATCTGAGCTAATAGTAAGTTTACTTACCTCTATCTAATGAATTTTCTCTTTAAGGTCGTT
66 TAGGCATCTGAGCTAATAGTAAGTTTACTTACCTCTATCTAATGAATTTTCTCTTTAAGGTCGTT
24119 TGGAGGTGCTGCCTCTCCTAT
131 TGGAGGTGCTGCCTCTCCTAT
24140 C
1 C
24141 CCTGCTTTCT
Statistics
Matches: 152, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
151 152 1.00
ACGTcount: A:0.17, C:0.18, G:0.18, T:0.47
Consensus pattern (151 bp):
CTGGGTTTTAGTTCTCATTGCTTGGTTGTTTCAAAGTGTTTTTTCTTTGTTTTAATTTTCCCCTT
TAGGCATCTGAGCTAATAGTAAGTTTACTTACCTCTATCTAATGAATTTTCTCTTTAAGGTCGTT
TGGAGGTGCTGCCTCTCCTAT
Found at i:39869 original size:136 final size:136
Alignment explanation
Indices: 39698--39965 Score: 310
Period size: 136 Copynumber: 2.0 Consensus size: 136
39688 TATATTCATA
* * * * **
39698 TGATATTGTCAATATTAGTTTTCTTTATGAATGAATTGTTTTAGAAATTTAGCTCCAAATCATGG
1 TGATATTATCAATAGTAGTTTTCTTTATGAATGAATAGTTTCAGAAATCCAGCTCCAAATCATGG
** * * *
39763 TGTCTTGATT-CTACAA-CAAATGGTGATATGGAATTTTTACATACT-TTCAGGTTTCTCAGCAT
66 TGTCTAAATTGC-ACAACCAAA-GCTGATATGGAATTATTACATA-TATTCAGATTTCTCAGCAT
39825 GGAAACATG
128 GGAAACATG
* * * *
39834 TGATATTATCATTAGTAGTTGTT-TTTATGAATGAATAGTTTCAGAAATCCCGGTCCAAATTATG
1 TGATATTATCAATAGTAGTT-TTCTTTATGAATGAATAGTTTCAGAAATCCAGCTCCAAATCATG
* * *
39898 GTGTCTAAATTGCAGAACCAAAGCTGCTATGGAATTATTACATATATTCAGATTTCTCAGTATGG
65 GTGTCTAAATTGCACAACCAAAGCTGATATGGAATTATTACATATATTCAGATTTCTCAGCATGG
39963 AAA
130 AAA
39966 GCTTCCTACA
Statistics
Matches: 110, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
135 1 0.01
136 102 0.93
137 7 0.06
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (136 bp):
TGATATTATCAATAGTAGTTTTCTTTATGAATGAATAGTTTCAGAAATCCAGCTCCAAATCATGG
TGTCTAAATTGCACAACCAAAGCTGATATGGAATTATTACATATATTCAGATTTCTCAGCATGGA
AACATG
Found at i:50163 original size:61 final size:62
Alignment explanation
Indices: 50062--50226 Score: 182
Period size: 61 Copynumber: 2.8 Consensus size: 62
50052 TGGATTTGGT
* * * * *
50062 AATTATTTTTATATT-GAG-TTTAA-TTTT-TTTTTGTTTAAGTTAAGTCA-TGAACTTGAC
1 AATTATTTTTATATTGGAGCCTAAACTTTTATTTTTGTTCAAGTTAAGGCACTGAACTTAAC
* * * * *
50119 AATTGTTTTTATGTTGGAGCTTGAATTTTTATTTTTGTTCAAGTT-AGGCACTGAACTTAAC
1 AATTATTTTTATATTGGAGCCTAAACTTTTATTTTTGTTCAAGTTAAGGCACTGAACTTAAC
50180 AATTATTTTTATATTGGAGCCTAAACTTTTATTTTTG-TCTAAGTTAA
1 AATTATTTTTATATTGGAGCCTAAACTTTTATTTTTGTTC-AAGTTAA
50227 TCTCTGATAT
Statistics
Matches: 90, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
57 13 0.14
58 3 0.03
59 4 0.04
60 10 0.11
61 59 0.66
62 1 0.01
ACGTcount: A:0.27, C:0.08, G:0.14, T:0.51
Consensus pattern (62 bp):
AATTATTTTTATATTGGAGCCTAAACTTTTATTTTTGTTCAAGTTAAGGCACTGAACTTAAC
Found at i:54200 original size:14 final size:14
Alignment explanation
Indices: 54183--54216 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
54173 TGTAATTTTT
54183 TTATTTTATTGCTA
1 TTATTTTATTGCTA
*
54197 TTATTTTATTGTTA
1 TTATTTTATTGCTA
54211 TTATTT
1 TTATTT
54217 GAATATTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.21, C:0.03, G:0.06, T:0.71
Consensus pattern (14 bp):
TTATTTTATTGCTA
Found at i:58402 original size:22 final size:21
Alignment explanation
Indices: 58363--58404 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
58353 AATTATTGAA
* *
58363 TTTAAATGTAAATTTTTAAAT
1 TTTAAAAGTAAATATTTAAAT
58384 TTTAAAAGTAAAATATTTAAA
1 TTTAAAAGT-AAATATTTAAA
58405 GGATAATGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (21 bp):
TTTAAAAGTAAATATTTAAAT
Found at i:62149 original size:16 final size:15
Alignment explanation
Indices: 62125--62158 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
62115 ATTTTTTTTA
*
62125 AAATTTTAAAATTAT
1 AAATTTTAAAATAAT
62140 AAATTATTAAAATAAT
1 AAATT-TTAAAATAAT
62156 AAA
1 AAA
62159 ATTGTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAATTTTAAAATAAT
Found at i:62830 original size:22 final size:22
Alignment explanation
Indices: 62805--62847 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
62795 TATTCAAACA
62805 ATAACAATAAAAT-AGTAACAAC
1 ATAACAATAAAATGA-TAACAAC
*
62827 ATAATAATAAAATGATAACAA
1 ATAACAATAAAATGATAACAA
62848 AATCGTGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.65, C:0.09, G:0.05, T:0.21
Consensus pattern (22 bp):
ATAACAATAAAATGATAACAAC
Found at i:66191 original size:183 final size:182
Alignment explanation
Indices: 65883--66425 Score: 917
Period size: 183 Copynumber: 3.0 Consensus size: 182
65873 CAGCATTGTT
* * * * *
65883 CACTGTTGAATTCTTATTTAACTCTACCAGTTCAGCAGTTGAAGACTCCTTCTGAGCTTCGATAC
1 CACTGTTGAATTCTTATTTAACTCTACCGGTTCAGCAGTCGAAGACTCCTTCCGAGCTTTGGTAC
* * *
65948 CTTCATTC-AATGTTGAAGATTTATTCAAGCCCACATCTGTTTCTGTTATAACATCAGTATCTAT
66 CTTCA-TCGAATGTAGAAGATTTATTCAACCCCACATCTGCTTCTGTTATAACATCAGTATCTAT
*
66012 GTCTCTCCCTTCAAAGATCTCATCATCATGAGCTGTCTCATTACCGGCGCTGTC
130 GTCT-TCCCTTCGAAGATCTCATCATCATGAGCTGTCTCATTACCGGCGCTGTC
*
66066 CACTGTTGAATTCTTATTTAACACTACCGGTTCAGCAGTCGAAGACTCCTTCCGAGCTTTGGTAC
1 CACTGTTGAATTCTTATTTAACTCTACCGGTTCAGCAGTCGAAGACTCCTTCCGAGCTTTGGTAC
66131 CTTCATCGAATGTAGAAGATTTATTCAACCCCACATCTGCTTCTGTTATAACATCAGTATCTATG
66 CTTCATCGAATGTAGAAGATTTATTCAACCCCACATCTGCTTCTGTTATAACATCAGTATCTATG
*
66196 TCTTCCCCTTCGAAGATCTCATCATCATGAGCTGTCTCATTACCGGCGTTGTC
131 TCTT-CCCTTCGAAGATCTCATCATCATGAGCTGTCTCATTACCGGCGCTGTC
66249 CACTGTTGAATTCTTATTTAACTCTACCGGTTCAGCAGTCGAAGACTCCTTCCGAGCTTTGGTAC
1 CACTGTTGAATTCTTATTTAACTCTACCGGTTCAGCAGTCGAAGACTCCTTCCGAGCTTTGGTAC
66314 CTTCATCGAATGTAGAAGATTTATTCAACCCCACATCTGCTTCTGTTATAACATCAGTATCTATG
66 CTTCATCGAATGTAGAAGATTTATTCAACCCCACATCTGCTTCTGTTATAACATCAGTATCTATG
* * *
66379 TTTTTCCCTTCGAAGATCTCATCATCGTGAACTGTCTCATTACCGGC
131 -TCTTCCCTTCGAAGATCTCATCATCATGAGCTGTCTCATTACCGGC
66426 ATTTGTACCA
Statistics
Matches: 342, Mismatches: 15, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
182 3 0.01
183 336 0.98
184 3 0.01
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.35
Consensus pattern (182 bp):
CACTGTTGAATTCTTATTTAACTCTACCGGTTCAGCAGTCGAAGACTCCTTCCGAGCTTTGGTAC
CTTCATCGAATGTAGAAGATTTATTCAACCCCACATCTGCTTCTGTTATAACATCAGTATCTATG
TCTTCCCTTCGAAGATCTCATCATCATGAGCTGTCTCATTACCGGCGCTGTC
Found at i:68740 original size:28 final size:28
Alignment explanation
Indices: 68704--68760 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
68694 AATAATAATG
* *
68704 GTTTGAATATTAATATTAAT-TTATTATA
1 GTTTAAATAATAATATTAATGTT-TTATA
*
68732 GTTTAAATAATATTATTAATGTTTTATA
1 GTTTAAATAATAATATTAATGTTTTATA
68760 G
1 G
68761 GTTATTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 23 0.92
29 2 0.08
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.53
Consensus pattern (28 bp):
GTTTAAATAATAATATTAATGTTTTATA
Found at i:72672 original size:53 final size:53
Alignment explanation
Indices: 72587--72700 Score: 183
Period size: 53 Copynumber: 2.2 Consensus size: 53
72577 GTCTTATCCG
* * * *
72587 ATGTACTGTCAGTTTAGTCAATCACATTTATGTTTCAATCTTCTGGGAATCAT
1 ATGTTCTGTCAGTCTAGTCAATCACATTTATGTTTCAATCCTCTGAGAATCAT
72640 ATGTTCTGTCAGTCTAGTCAATCACATTTATGTTTCAATCCTCTGAGAATCAT
1 ATGTTCTGTCAGTCTAGTCAATCACATTTATGTTTCAATCCTCTGAGAATCAT
*
72693 ATGCTCTG
1 ATGTTCTG
72701 ATGTTGAAGA
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.40
Consensus pattern (53 bp):
ATGTTCTGTCAGTCTAGTCAATCACATTTATGTTTCAATCCTCTGAGAATCAT
Found at i:77393 original size:19 final size:18
Alignment explanation
Indices: 77368--77410 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 18
77358 AAATACTATC
77368 AATTTAAATTTAATTTAA
1 AATTTAAATTTAATTTAA
*
77386 ATATTTAAATTTTATTTAA
1 A-ATTTAAATTTAATTTAA
77405 AATTTA
1 AATTTA
77411 CCATATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AATTTAAATTTAATTTAA
Found at i:77399 original size:26 final size:27
Alignment explanation
Indices: 77341--77399 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 27
77331 AAAATGGTTT
* *
77341 AATTTTAAATGTATTTTAAATACTATC
1 AATTTTAAATGTAATTTAAATACTATA
* *
77368 AA-TTTAAATTTAATTTAAATA-TTTA
1 AATTTTAAATGTAATTTAAATACTATA
77393 AATTTTA
1 AATTTTA
77400 TTTAAAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 4 0.15
26 21 0.78
27 2 0.07
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (27 bp):
AATTTTAAATGTAATTTAAATACTATA
Done.