Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014929.1 Kokia drynarioides strain JFW-HI SEQ_129972, 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: 61900
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Warning! 72 characters in sequence are not A, C, G, or T
Found at i:9395 original size:35 final size:37
Alignment explanation
Indices: 9321--9396 Score: 93
Period size: 39 Copynumber: 2.1 Consensus size: 37
9311 GGGGTCATTA
* *
9321 AAGTAATTTTATTTTATTAGTAGTAGTTTATACGTAAGT
1 AAGTAATTTTATTTTATTAGTAGAAG-TTAAACG-AAGT
*
9360 AAGTAATTTTATTTTGTTAGTAGAAG-TAAAC-AAGT
1 AAGTAATTTTATTTTATTAGTAGAAGTTAAACGAAGT
9395 AA
1 AA
9397 TATAAATGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
35 6 0.18
37 4 0.12
39 24 0.71
ACGTcount: A:0.38, C:0.03, G:0.16, T:0.43
Consensus pattern (37 bp):
AAGTAATTTTATTTTATTAGTAGAAGTTAAACGAAGT
Found at i:9559 original size:47 final size:46
Alignment explanation
Indices: 9508--9598 Score: 137
Period size: 47 Copynumber: 2.0 Consensus size: 46
9498 GTGTGGATAC
* *
9508 CATTTTGGTATATAAATATTTATTTTATATCATTTTCGTAAATAATT
1 CATTTTGGTATATAAATATTT-GTTTATACCATTTTCGTAAATAATT
* *
9555 CATTTTGGTATATAAATATTTGTTTGTACCATTTTGGTAAATAA
1 CATTTTGGTATATAAATATTTGTTTATACCATTTTCGTAAATAA
9599 CCTATTTTAG
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
46 19 0.47
47 21 0.52
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.51
Consensus pattern (46 bp):
CATTTTGGTATATAAATATTTGTTTATACCATTTTCGTAAATAATT
Found at i:9606 original size:46 final size:46
Alignment explanation
Indices: 9508--9629 Score: 138
Period size: 46 Copynumber: 2.6 Consensus size: 46
9498 GTGTGGATAC
* * *
9508 CATTTTGGTATATAAATATTTATTTTATATCATTTTCGTAAATAATT
1 CATTTTGGTATATAAATATTT-TTTTGTACCATTTTCGTAAATAACT
* *
9555 CATTTTGGTATATAAATATTTGTTTGTACCATTTTGGTAAATAAC-
1 CATTTTGGTATATAAATATTTTTTTGTACCATTTTCGTAAATAACT
* * *
9600 CTATTTTAGTATTTAATTATTATTTTTGTA
1 C-ATTTTGGTATATAAATATT-TTTTTGTA
9630 TTATATTGGT
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
45 1 0.02
46 35 0.55
47 28 0.44
ACGTcount: A:0.31, C:0.07, G:0.09, T:0.53
Consensus pattern (46 bp):
CATTTTGGTATATAAATATTTTTTTGTACCATTTTCGTAAATAACT
Found at i:9881 original size:27 final size:27
Alignment explanation
Indices: 9822--9873 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
9812 AACACTCCTT
* *
9822 GGTGCCGCCACTTGATATCCTTCCAAG
1 GGTGTCGCCACTTGATATCCCTCCAAG
9849 GGTGTCGCCACTTGATATCCCTCCA
1 GGTGTCGCCACTTGATATCCCTCCA
9874 CTTGTGTCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.17, C:0.35, G:0.21, T:0.27
Consensus pattern (27 bp):
GGTGTCGCCACTTGATATCCCTCCAAG
Found at i:13171 original size:2 final size:2
Alignment explanation
Indices: 13164--13188 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13154 TTCTGATAAT
13164 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
13189 TTTTTTTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:26239 original size:39 final size:39
Alignment explanation
Indices: 26184--26259 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
26174 ATCGGAAGTG
*
26184 TATTGAATCGACAGTGACATTGTAAACATTGCGTTGTTA
1 TATTGAATCGACAGTGACATTGTAAACACTGCGTTGTTA
*
26223 TATTGAATCGATAGTGACATTGTAAACACTGCGTTGT
1 TATTGAATCGACAGTGACATTGTAAACACTGCGTTGT
26260 CCTTAACAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (39 bp):
TATTGAATCGACAGTGACATTGTAAACACTGCGTTGTTA
Found at i:29985 original size:18 final size:18
Alignment explanation
Indices: 29962--29996 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
29952 TAATAAATTA
29962 TTTAATAATAAAATGTAT
1 TTTAATAATAAAATGTAT
*
29980 TTTAATAATAAATTGTA
1 TTTAATAATAAAATGTA
29997 ATATATTTAT
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:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (18 bp):
TTTAATAATAAAATGTAT
Found at i:30077 original size:18 final size:19
Alignment explanation
Indices: 30054--30104 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
30044 ATGTTTAAAA
*
30054 TTTATTATTAAA-ATTTAT
1 TTTATTATTAAATAATTAT
30072 TTTATTATTAAATAATTAT
1 TTTATTATTAAATAATTAT
* *
30091 TATATTAATAAATA
1 TTTATTATTAAATA
30105 TACATAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 12 0.41
19 17 0.59
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTATTATTAAATAATTAT
Found at i:30078 original size:15 final size:13
Alignment explanation
Indices: 30048--30072 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30038 AAGAATATGT
30048 TTAAAATTTATTA
1 TTAAAATTTATTA
30061 TTAAAATTTATT
1 TTAAAATTTATT
30073 TTATTATTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAAAATTTATTA
Found at i:33071 original size:26 final size:26
Alignment explanation
Indices: 33022--33071 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
33012 TCTGTCTAAA
* **
33022 TTTGAATTTATTTAATAATTTTTATG
1 TTTGAATTTATTTAACAAGATTTATG
*
33048 TTTGAATTTATTTAACGAGATTTA
1 TTTGAATTTATTTAACAAGATTTA
33072 GCAAATGACA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.32, C:0.02, G:0.10, T:0.56
Consensus pattern (26 bp):
TTTGAATTTATTTAACAAGATTTATG
Found at i:33148 original size:6 final size:6
Alignment explanation
Indices: 33137--33177 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
33127 ATATTTGCAT
*
33137 ACATAA ACATAA ATA-AGA ACATAA ACATAA ACATAA ACATA
1 ACATAA ACATAA ACATA-A ACATAA ACATAA ACATAA ACATA
33178 TTTAATTCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 1 0.03
6 29 0.94
7 1 0.03
ACGTcount: A:0.66, C:0.15, G:0.02, T:0.17
Consensus pattern (6 bp):
ACATAA
Found at i:37697 original size:12 final size:12
Alignment explanation
Indices: 37680--37704 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
37670 TACTTTTAAA
37680 AATTTATAAAAG
1 AATTTATAAAAG
37692 AATTTATAAAAG
1 AATTTATAAAAG
37704 A
1 A
37705 GTGAGAGTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (12 bp):
AATTTATAAAAG
Found at i:39968 original size:43 final size:43
Alignment explanation
Indices: 39906--40014 Score: 193
Period size: 43 Copynumber: 2.5 Consensus size: 43
39896 TCTGGTACTA
39906 GTCTATTTCGAAAATAATGATGCACATGAAGTGTGCAACCATT
1 GTCTATTTCGAAAATAATGATGCACATGAAGTGTGCAACCATT
*
39949 GTCTATTTCGAAAACAATGATGCACATGAAGTGTGCAACCATT
1 GTCTATTTCGAAAATAATGATGCACATGAAGTGTGCAACCATT
39992 GTCTATTTC-AACAATAATGATGC
1 GTCTATTTCGAA-AATAATGATGC
40015 TATACAAAAG
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
42 2 0.03
43 61 0.97
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (43 bp):
GTCTATTTCGAAAATAATGATGCACATGAAGTGTGCAACCATT
Found at i:44651 original size:25 final size:23
Alignment explanation
Indices: 44614--44664 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 23
44604 TTTTAAAGAT
44614 AAAAAAATATTTTT-AATTTTTCA
1 AAAAAAATATTTTTAAATTTTT-A
44637 AAAAAAATACTTTTTTAAATTTTTA
1 AAAAAAATA--TTTTTAAATTTTTA
44662 AAA
1 AAA
44665 TTTAAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 9 0.36
25 9 0.36
26 7 0.28
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (23 bp):
AAAAAAATATTTTTAAATTTTTA
Found at i:49582 original size:5 final size:5
Alignment explanation
Indices: 49572--49597 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
49562 AGTGAGAAAC
49572 CTGCA CTGCA CTGCA CTGCA CTGCA C
1 CTGCA CTGCA CTGCA CTGCA CTGCA C
49598 CCTTTTCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.42, G:0.19, T:0.19
Consensus pattern (5 bp):
CTGCA
Found at i:52356 original size:2 final size:2
Alignment explanation
Indices: 52349--52381 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
52339 ATAAAACATG
52349 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
52382 GGTATTAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53420 original size:208 final size:208
Alignment explanation
Indices: 53062--53589 Score: 930
Period size: 208 Copynumber: 2.5 Consensus size: 208
53052 CCCATAAACT
* * *
53062 CATTTCCACACATCTTTCGTCTTCATCTTCATCCTCTTCCCTTTTGATTTCAATATTTTTAGTTA
1 CATTTCCACACATCTCTCTTCTTCATCTTCATCCTCTTCCCTTTTGATTTCAATATCTTTAGTTA
* *
53127 CAAATCTGTCTCAAAGCTTGAATCTTTGAAACCCATTAACCCAAAGATTCAATATCTTTGATTTC
66 CAAATCTATCTCAAAGCTTGAATCTTTGAAACCCATTAACCCAAAGATTCAATATCTTTGATTCC
*
53192 AATATTTTCTTCCCGTTAAGTTTCTAAATCTTTAATTAAATAAATTTAATTAATTAAAATTTTTA
131 AATATTTTCTTCCCGTTAAGTTTCTAAATCTTTAATTAAATAAATTTAATTAATTAAAAATTTTA
53257 AACCCTAAATACC
196 AACCCTAAATACC
* *
53270 CATTTCCACACACCTCTCTTCTTCATCTTCATCCTCTTCCCTTTTAATTTCAATATCTTTAGTTA
1 CATTTCCACACATCTCTCTTCTTCATCTTCATCCTCTTCCCTTTTGATTTCAATATCTTTAGTTA
*
53335 CAAATCCATCTCAAAGCTTGAATCTTTGAAACCCATTAACCCAAAGATTCAATATCTTTGATTCC
66 CAAATCTATCTCAAAGCTTGAATCTTTGAAACCCATTAACCCAAAGATTCAATATCTTTGATTCC
53400 AATATTTTCTTCCCGTTAAGTTTCTAAATCTTTAATTAAATAAATTTAATTAATTAAAAATTTTA
131 AATATTTTCTTCCCGTTAAGTTTCTAAATCTTTAATTAAATAAATTTAATTAATTAAAAATTTTA
*
53465 AACCCTAAATACT
196 AACCCTAAATACC
* *
53478 CATTTCCACACATCTCTCTTCTTCTTCTTCATCCTCTTCCCTTTTGATTCCAATATCTTTAGTTA
1 CATTTCCACACATCTCTCTTCTTCATCTTCATCCTCTTCCCTTTTGATTTCAATATCTTTAGTTA
* *
53543 CAAATCTATCTCAAAGCTTGAATCTTTGAAACTCATTAACCTAAAGA
66 CAAATCTATCTCAAAGCTTGAATCTTTGAAACCCATTAACCCAAAGA
53590 AACTTAACGG
Statistics
Matches: 303, Mismatches: 17, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
208 303 1.00
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.41
Consensus pattern (208 bp):
CATTTCCACACATCTCTCTTCTTCATCTTCATCCTCTTCCCTTTTGATTTCAATATCTTTAGTTA
CAAATCTATCTCAAAGCTTGAATCTTTGAAACCCATTAACCCAAAGATTCAATATCTTTGATTCC
AATATTTTCTTCCCGTTAAGTTTCTAAATCTTTAATTAAATAAATTTAATTAATTAAAAATTTTA
AACCCTAAATACC
Found at i:55350 original size:75 final size:73
Alignment explanation
Indices: 55261--55406 Score: 231
Period size: 75 Copynumber: 2.0 Consensus size: 73
55251 ATTCATACGG
55261 AATGCCTGTTTTTAATTAATAATTATCATTCTGGCCAAATGCTATTTATTTATTTTTCTTAAG-A
1 AATGCCTGTTTTTAATTAATAATTATCATTCTGGCCAAATGCTATTTA-TTA-TTTTC-TAAGTA
55325 AAATTATTTCT
63 AAATTATTTCT
* * *
55336 AATGCTTGTTTTTAATTAATAATTATCTTTCTGGCCAAATGCTATTTATTATTTTCTCAGTAAAA
1 AATGCCTGTTTTTAATTAATAATTATCATTCTGGCCAAATGCTATTTATTATTTTCTAAGTAAAA
55401 TTATTT
66 TTATTT
55407 TTTAATTAAA
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
72 3 0.04
73 15 0.22
74 3 0.04
75 46 0.69
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.50
Consensus pattern (73 bp):
AATGCCTGTTTTTAATTAATAATTATCATTCTGGCCAAATGCTATTTATTATTTTCTAAGTAAAA
TTATTTCT
Done.