Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009391.1 Kokia drynarioides strain JFW-HI SEQ_124098, 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: 14419
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:607 original size:6 final size:6
Alignment explanation
Indices: 598--661 Score: 73
Period size: 6 Copynumber: 11.2 Consensus size: 6
588 TTGAAATTAT
598 ATTTAA ATTTAA A-TTAA ATTTAA ATTTAA GA-TT-A ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA -ATTTAA ATTTAA ATTTAA
* *
644 A-ATAA ATCTAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA A
662 ATAAATTAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
4 1 0.02
5 12 0.24
6 36 0.72
7 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (6 bp):
ATTTAA
Found at i:613 original size:17 final size:17
Alignment explanation
Indices: 581--668 Score: 106
Period size: 17 Copynumber: 5.1 Consensus size: 17
571 TTTTGGACTT
* *
581 TTTAATTTTGAAATTATA
1 TTTAAATTT-AAATTAAA
599 TTTAAATTTAAATTAAA
1 TTTAAATTTAAATTAAA
616 TTTAAATTTAAGATT-AA
1 TTTAAATTTAA-ATTAAA
*
633 TTTAAATTTAAAATAAA
1 TTTAAATTTAAATTAAA
* *
650 TCTAAATTTAAAATAAA
1 TTTAAATTTAAATTAAA
667 TT
1 TT
669 AAAAAGGGGC
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
16 2 0.03
17 50 0.79
18 11 0.17
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (17 bp):
TTTAAATTTAAATTAAA
Found at i:614 original size:11 final size:11
Alignment explanation
Indices: 600--671 Score: 67
Period size: 11 Copynumber: 6.5 Consensus size: 11
590 GAAATTATAT
600 TTAAATTTAAA
1 TTAAATTTAAA
611 TTAAATTTAAA
1 TTAAATTTAAA
*
622 TTTAAGA-TTAAT
1 -TTAA-ATTTAAA
634 TTAAATTTAAA
1 TTAAATTTAAA
* *
645 ATAAATCTAAA
1 TTAAATTTAAA
*
656 TTTAAA-ATAAA
1 -TTAAATTTAAA
667 TTAAA
1 TTAAA
672 AAGGGGCCTG
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
10 6 0.12
11 32 0.63
12 12 0.24
13 1 0.02
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:1253 original size:205 final size:206
Alignment explanation
Indices: 920--1507 Score: 911
Period size: 205 Copynumber: 2.9 Consensus size: 206
910 TGTTCTCAGT
* * * *
920 ATCTCATCTGGAAGCTAATCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTG
1 ATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATTTCATCAGGAAGCTG
* * * *
985 GGGTTCGAAGATTTGCTCATGTCGAG-CATGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCA
66 GGGTTCGAAGATTTGCTCGTATTGAGCCCTGGG-TTGATTTGGTCTTCTTCTCAGTATCTCATCA
*
1049 GGAAGATGACTGCATCGTTTGTTTCAATTCGCTTCTC-GTATCTGATCAGGAAGACGAATTTGGT
130 GGAAGATGACTGCATCGTTTGTTTCAATTCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGT
1113 CCACTTCTTAGA
195 CCACTTCTTAGA
1125 ATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATTTCATCAGGAAGCTG
1 ATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATTTCATCAGGAAGCTG
1190 GGGTTCGAAGATTTGCTCGTATTGAGCCCTGGGTTGATTTGGTCTTCTTCTCAGTATCTCATCAG
66 GGGTTCGAAGATTTGCTCGTATTGAGCCCTGGGTTGATTTGGTCTTCTTCTCAGTATCTCATCAG
*
1255 GAAGATGACTGCATCGTTCGTTTCAATTCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTC
131 GAAGATGACTGCATCGTTTGTTTCAATTCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTC
*
1320 CACTTCTTAGT
196 CACTTCTTAGA
*
1331 ATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATTTCATCAGGAAGTTG
1 ATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATTTCATCAGGAAGCTG
* * * * *
1396 GGGTTCGAAGATTTGCTCGCATTGAGCCC-----TGAGTTGGTATACTTCTCTGTATCTCATCAG
66 GGGTTCGAAGATTTGCTCGTATTGAGCCCTGGGTTGATTTGGTCTTCTTCTCAGTATCTCATCAG
* * ** * *
1456 GAAGATGACCGCCTCACTTGTTTCAATCCGCTTCTCTGTACCTCATCAGGAA
131 GAAGATGACTGCATCGTTTGTTTCAATTCGCTTCTCTGTATCTCATCAGGAA
1508 ACTAAGATTC
Statistics
Matches: 357, Mismatches: 24, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
201 72 0.20
205 151 0.42
206 134 0.38
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.35
Consensus pattern (206 bp):
ATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATTTCATCAGGAAGCTG
GGGTTCGAAGATTTGCTCGTATTGAGCCCTGGGTTGATTTGGTCTTCTTCTCAGTATCTCATCAG
GAAGATGACTGCATCGTTTGTTTCAATTCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTC
CACTTCTTAGA
Found at i:12868 original size:29 final size:29
Alignment explanation
Indices: 12826--13115 Score: 252
Period size: 29 Copynumber: 9.9 Consensus size: 29
12816 ATTTTGAGAG
*
12826 TTCGGTGGTAAAAATGGAATTTTGGGAAGT
1 TTCGG-GGTAAAAATGGAATTTTTGGAAGT
* *
12856 TTTGGGGTTAAAAT-GAGATTTTTGGAAG-
1 TTCGGGGTAAAAATGGA-ATTTTTGGAAGT
* * * *
12884 TTCAGTGGTAAAAATGAAAGTTTGGGAAGT
1 TTC-GGGGTAAAAATGGAATTTTTGGAAGT
* **
12914 TTCGGGGTCAAAAAT-AAGATTTTTGGGTGT
1 TTCGGGGT-AAAAATGGA-ATTTTTGGAAGT
* * *
12944 TTGGGGGTAAAAATGGAATTTTTAGAAAT
1 TTCGGGGTAAAAATGGAATTTTTGGAAGT
*
12973 TTCGGTGTTAAAAATGG-ATTTTTGGAAGT
1 TTCGG-GGTAAAAATGGAATTTTTGGAAGT
* *
13002 TT-GGGAGTAAAAATGGAATTTTTAGAAATT
1 TTCGGG-GTAAAAATGGAATTTTT-GGAAGT
* * *
13032 TTAGGGTTAAAAATGGGATTTTTGGAAG-
1 TTCGGGGTAAAAATGGAATTTTTGGAAGT
*
13060 TTCGGTGGTAAAAATGGAATTTTTTGAAG-
1 TTCGG-GGTAAAAATGGAATTTTTGGAAGT
*
13089 TTCGGGGGTAAAAATGGAATTTATGGA
1 TTC-GGGGTAAAAATGGAATTTTTGGA
13116 CGGTTTAGGG
Statistics
Matches: 209, Mismatches: 37, Indels: 29
0.76 0.13 0.11
Matches are distributed among these distances:
27 1 0.00
28 19 0.09
29 123 0.59
30 63 0.30
31 3 0.01
ACGTcount: A:0.32, C:0.02, G:0.30, T:0.36
Consensus pattern (29 bp):
TTCGGGGTAAAAATGGAATTTTTGGAAGT
Found at i:12886 original size:58 final size:59
Alignment explanation
Indices: 12824--13104 Score: 300
Period size: 58 Copynumber: 4.8 Consensus size: 59
12814 TAATTTTGAG
* * *
12824 AGTTCGGTGGTAAAAATGGAATTTTGGGAAGTTTTGGGGTT-AAAATGAGATTTTTGGA
1 AGTTCGGTGGTAAAAATGGAATTTTGAGAAATTTCGGGGTTAAAAATGAGATTTTTGGA
* * * * * * * *
12882 AGTTCAGTGGTAAAAATGAAAGTTTGGGAAGTTTCGGGGTCAAAAATAAGATTTTTGGG
1 AGTTCGGTGGTAAAAATGGAATTTTGAGAAATTTCGGGGTTAAAAATGAGATTTTTGGA
* * * * *
12941 TGTTTGGGGGTAAAAATGGAATTTTTAGAAATTTCGGTGTTAAAAATG-GATTTTTGGA
1 AGTTCGGTGGTAAAAATGGAATTTTGAGAAATTTCGGGGTTAAAAATGAGATTTTTGGA
* * ** *
12999 AGTTTGG-GAGTAAAAATGGAATTTTTAGAAATTTTAGGGTTAAAAATGGGATTTTTGGA
1 AGTTCGGTG-GTAAAAATGGAATTTTGAGAAATTTCGGGGTTAAAAATGAGATTTTTGGA
** * *
13058 AGTTCGGTGGTAAAAATGGAATTTTTTG-AAGTTCGGGGGTAAAAATG
1 AGTTCGGTGGTAAAAATGGAATTTTGAGAAATTTCGGGGTTAAAAATG
13105 GAATTTATGG
Statistics
Matches: 189, Mismatches: 30, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
57 1 0.01
58 102 0.54
59 85 0.45
60 1 0.01
ACGTcount: A:0.32, C:0.02, G:0.30, T:0.35
Consensus pattern (59 bp):
AGTTCGGTGGTAAAAATGGAATTTTGAGAAATTTCGGGGTTAAAAATGAGATTTTTGGA
Found at i:12956 original size:117 final size:117
Alignment explanation
Indices: 12824--13115 Score: 293
Period size: 117 Copynumber: 2.5 Consensus size: 117
12814 TAATTTTGAG
* * * *
12824 AGTTCGGTGGTAAAAATGGAATTTTGGGAAGTTTTGGGGTT-AAAATGAGATTTTTGGAAGTTCA
1 AGTTCGGGGGTAAAAATGGAATTTTGAGAAATTTCGGGGTTAAAAATG-GATTTTTGGAAGTT-A
* * * * *
12888 GTG-GTAAAAATGAAAGTTTGGGAAGTTTCGGGGTCAAAAATAAGATTTTTGGG
64 GGGAGTAAAAATGAAAGTTTGAGAAATTTCAGGGTCAAAAATAAGATTTTTGGA
* * * * *
12941 TGTTTGGGGGTAAAAATGGAATTTTTAGAAATTTCGGTGTTAAAAATGGATTTTTGGAAGTTTGG
1 AGTTCGGGGGTAAAAATGGAATTTTGAGAAATTTCGGGGTTAAAAATGGATTTTTGGAAGTTAGG
* * * * * **
13006 GAGTAAAAATGGAATTTTTAGAAATTTTAGGGTTAAAAATGGGATTTTTGGA
66 GAGTAAAAATGAAAGTTTGAGAAATTTCAGGGTCAAAAATAAGATTTTTGGA
* ** * * *
13058 AGTTCGGTGGTAAAAATGGAATTTTTTG-AAGTTCGGGGGTAAAAATGGAATTTATGGA
1 AGTTCGGGGGTAAAAATGGAATTTTGAGAAATTTCGGGGTTAAAAATGG-ATTTTTGGA
13116 CGGTTTAGGG
Statistics
Matches: 143, Mismatches: 29, Indels: 6
0.80 0.16 0.03
Matches are distributed among these distances:
116 19 0.13
117 118 0.83
118 6 0.04
ACGTcount: A:0.33, C:0.02, G:0.30, T:0.35
Consensus pattern (117 bp):
AGTTCGGGGGTAAAAATGGAATTTTGAGAAATTTCGGGGTTAAAAATGGATTTTTGGAAGTTAGG
GAGTAAAAATGAAAGTTTGAGAAATTTCAGGGTCAAAAATAAGATTTTTGGA
Found at i:12957 original size:59 final size:57
Alignment explanation
Indices: 12832--13103 Score: 249
Period size: 59 Copynumber: 4.7 Consensus size: 57
12822 AGAGTTCGGT
* * ** *
12832 GGTAAAAATGGAATTTTGGGAAGTTTTGGGGTTAAAATGAGATTTTTGGAAGTTCAGT
1 GGTAAAAATGGAATTTTGGGAAGTTTCGGGGTAAAAAT-AGATTTTTGGAAGTTTGGG
* * **
12890 GGTAAAAATGAAAGTTTGGGAAGTTTCGGGGTCAAAAATAAGATTTTTGGGTGTTTGGG
1 GGTAAAAATGGAATTTTGGGAAGTTTCGGGGT-AAAAAT-AGATTTTTGGAAGTTTGGG
** * * *
12949 GGTAAAAATGGAATTTTTAGAAATTTCGGTGTTAAAAATGGATTTTTGGAAGTTTGGG
1 GGTAAAAATGGAATTTTGGGAAGTTTCGG-GGTAAAAATAGATTTTTGGAAGTTTGGG
* * * * * * * * *
13007 AGTAAAAATGGAATTTTTAGAAATTTTAGGGTTAAAAATGGGATTTTTGGAAGTTCGGT
1 GGTAAAAATGGAA-TTTTGGGAAGTTTCGGGGTAAAAAT-AGATTTTTGGAAGTTTGGG
**
13066 GGTAAAAATGGAATTTTTTGAAG-TTCGGGGGTAAAAAT
1 GGTAAAAATGGAATTTTGGGAAGTTTC-GGGGTAAAAAT
13104 GGAATTTATG
Statistics
Matches: 175, Mismatches: 34, Indels: 10
0.80 0.16 0.05
Matches are distributed among these distances:
57 2 0.01
58 82 0.47
59 89 0.51
60 2 0.01
ACGTcount: A:0.33, C:0.02, G:0.29, T:0.35
Consensus pattern (57 bp):
GGTAAAAATGGAATTTTGGGAAGTTTCGGGGTAAAAATAGATTTTTGGAAGTTTGGG
Found at i:14110 original size:19 final size:20
Alignment explanation
Indices: 14086--14124 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
14076 GTTTTATTAT
14086 TATTATTAATTA-TTAATAA
1 TATTATTAATTATTTAATAA
14105 TATTATTAATTATTTAATAA
1 TATTATTAATTATTTAATAA
14125 ATATCATCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TATTATTAATTATTTAATAA
Done.