Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009128.1 Kokia drynarioides strain JFW-HI SEQ_123832, 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: 58183
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 198 characters in sequence are not A, C, G, or T
Found at i:6706 original size:31 final size:31
Alignment explanation
Indices: 6668--6728 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
6658 AATGGTTCAT
6668 TAAACTATTCGAAAA-TTTTCATTTAAGCCAC
1 TAAACTATTC-AAAAGTTTTCATTTAAGCCAC
*
6699 TAAACTATTCAAAAGTTTTTATTTAAGCCA
1 TAAACTATTCAAAAGTTTTCATTTAAGCCA
6729 TTGGGTTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 4 0.14
31 24 0.86
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.38
Consensus pattern (31 bp):
TAAACTATTCAAAAGTTTTCATTTAAGCCAC
Found at i:9262 original size:21 final size:20
Alignment explanation
Indices: 9238--9276 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
9228 TCAACAAATG
*
9238 ATTTTAAAATTATTAAATTTA
1 ATTTTAAAA-TATAAAATTTA
*
9259 ATTTTTAAATATAAAATT
1 ATTTTAAAATATAAAATT
9277 ATTAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTTAAAATATAAAATTTA
Found at i:9308 original size:16 final size:16
Alignment explanation
Indices: 9265--9310 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 16
9255 TTTAATTTTT
9265 AAATATAAAATTATT-
1 AAATATAAAATTATTA
9280 AAA-A-AAAA--A-TA
1 AAATATAAAATTATTA
9291 AAATATAAAATTATTA
1 AAATATAAAATTATTA
9307 AAAT
1 AAAT
9311 TATTTTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 11
0.69 0.00 0.31
Matches are distributed among these distances:
10 1 0.04
11 4 0.16
12 1 0.04
13 8 0.32
14 1 0.04
15 4 0.16
16 6 0.24
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATATAAAATTATTA
Found at i:10361 original size:30 final size:29
Alignment explanation
Indices: 10285--10362 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 29
10275 AAAATTATTT
10285 AATAATTTT-AATAATTTTATATTTCAAA
1 AATAATTTTAAATAATTTTATATTTCAAA
** *
10313 AA-AATAATATAATAATTTTATATTTTAAA
1 AATAATTTTA-AATAATTTTATATTTCAAA
10342 AATAATTTTAAATTAATTTTA
1 AATAATTTTAAA-TAATTTTA
10363 AAATTATTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
27 4 0.10
28 2 0.05
29 22 0.54
30 13 0.32
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (29 bp):
AATAATTTTAAATAATTTTATATTTCAAA
Found at i:10366 original size:12 final size:12
Alignment explanation
Indices: 10334--10368 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
10324 ATAATTTTAT
*
10334 ATTTTAAAAATA
1 ATTTTAAAATTA
10346 ATTTT-AAATTA
1 ATTTTAAAATTA
10357 ATTTTAAAATTA
1 ATTTTAAAATTA
10369 TTTGTTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
ATTTTAAAATTA
Found at i:14074 original size:63 final size:63
Alignment explanation
Indices: 13973--14101 Score: 249
Period size: 63 Copynumber: 2.0 Consensus size: 63
13963 ATATGTACAA
13973 TGCTGGTAGAGAAACTTGAGAAGGAGGATATGACTGAAGCAAAACAGAAGATTCAAGAATTGG
1 TGCTGGTAGAGAAACTTGAGAAGGAGGATATGACTGAAGCAAAACAGAAGATTCAAGAATTGG
*
14036 TGCTGGTAGAGAAACTTGAGAAGGAGGATATGATTGAAGCAAAACAGAAGATTCAAGAATTGG
1 TGCTGGTAGAGAAACTTGAGAAGGAGGATATGACTGAAGCAAAACAGAAGATTCAAGAATTGG
14099 TGC
1 TGC
14102 CAAATGTGAA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.40, C:0.09, G:0.30, T:0.20
Consensus pattern (63 bp):
TGCTGGTAGAGAAACTTGAGAAGGAGGATATGACTGAAGCAAAACAGAAGATTCAAGAATTGG
Found at i:16407 original size:27 final size:27
Alignment explanation
Indices: 16376--16428 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
16366 TTCAATTTAG
*
16376 TTCAATTCACAGTAATTAAGGGTTTTC
1 TTCAATTCACAATAATTAAGGGTTTTC
*
16403 TTCAATTCACAATCATTAAGGGTTTT
1 TTCAATTCACAATAATTAAGGGTTTT
16429 TTCTTCAGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (27 bp):
TTCAATTCACAATAATTAAGGGTTTTC
Found at i:22046 original size:28 final size:28
Alignment explanation
Indices: 22014--22071 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
22004 TTTTTCGTAA
*
22014 ATTTATTTATTTATTTTAGGGTTTTCTT
1 ATTTATTTATTTATTTAAGGGTTTTCTT
*
22042 ATTTATTTATTTATTTAAGGGTTTTTTT
1 ATTTATTTATTTATTTAAGGGTTTTCTT
22070 AT
1 AT
22072 GGTTTTCTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.21, C:0.02, G:0.10, T:0.67
Consensus pattern (28 bp):
ATTTATTTATTTATTTAAGGGTTTTCTT
Found at i:22099 original size:42 final size:42
Alignment explanation
Indices: 22043--22139 Score: 117
Period size: 42 Copynumber: 2.3 Consensus size: 42
22033 GGTTTTCTTA
* * *
22043 TTTATTTATTTATTTA-AGGGTTTTTTTATGGTTT-TCTTAAGG
1 TTTATTTATTTATTTATA-AGTTTGTTTAGGGTTTAT-TTAAGG
* *
22085 TTTATTTATTTATTTATAAGTTTGTTTAGGGTTTATTTATGT
1 TTTATTTATTTATTTATAAGTTTGTTTAGGGTTTATTTAAGG
22127 TTTATTTATTTAT
1 TTTATTTATTTAT
22140 AAAATAATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
42 46 0.96
43 2 0.04
ACGTcount: A:0.21, C:0.01, G:0.13, T:0.65
Consensus pattern (42 bp):
TTTATTTATTTATTTATAAGTTTGTTTAGGGTTTATTTAAGG
Found at i:22123 original size:11 final size:11
Alignment explanation
Indices: 22051--22134 Score: 50
Period size: 11 Copynumber: 7.7 Consensus size: 11
22041 TATTTATTTA
22051 TTTATTTAAGGG
1 TTTATTTAA-GG
* *
22063 TTTTTTTATGG
1 TTTATTTAAGG
22074 TTT-TCTTAAGG
1 TTTAT-TTAAGG
22085 TTTATTT-A--
1 TTTATTTAAGG
*
22093 TTTATTTATAAG
1 TTTATTTA-AGG
* *
22105 TTTGTTTAGGG
1 TTTATTTAAGG
* *
22116 TTTATTTATGT
1 TTTATTTAAGG
22127 TTTATTTA
1 TTTATTTA
22135 TTTATAAAAT
Statistics
Matches: 57, Mismatches: 9, Indels: 13
0.72 0.11 0.16
Matches are distributed among these distances:
8 7 0.12
10 3 0.05
11 32 0.56
12 15 0.26
ACGTcount: A:0.20, C:0.01, G:0.15, T:0.63
Consensus pattern (11 bp):
TTTATTTAAGG
Found at i:31658 original size:308 final size:310
Alignment explanation
Indices: 31300--31921 Score: 1099
Period size: 318 Copynumber: 2.0 Consensus size: 310
31290 CTTTCATTTC
31300 TTAGACTTGACCAGTCAACAATTATTATTATTATTTTATCTTTTATCACATTTTCTTTTTCTGAA
1 TTAGACTTGACCAGTCAACAATTATTATTATTATTTTATCTTTTATCACATTTTCTTTTTCTGAA
* *
31365 ATTTAAGAATATT-A-A-TCATA-TCTCTCTTTCTAAATATATAATATAACCGTTACTAAATGCT
66 ATTTAAAAATATTAATATTCATACACTCTCTTTCTAAATATATAATATAACCGTTACTAAATGCT
31426 TTAATTTATTTTTTTCCTTTTCTTAATTTTTTATAAATTATTATAAATTCAATAATTAAAAAAAT
131 TTAATTTATTTTTTTCCTTTTCTTAATTTTTTATAAATTATTATAAATTCAATAATTAAAAAAAT
*
31491 TTAATTAAAGCATAGTATAAAAAAAAAAACTAATGTACACGTTATGATTTAATAGAACTCTCAAT
196 TTAATTAAAGCATAGTAT--AAAAAAAAACTAATGTACACGTTATGATTTAATAGAACTCCCAAT
31556 CGAGTTAATACCATAAATTAATAGATTTATAAACAAATTGCATCAATAATTA
259 CGAGTTAATACCATAAATTAATAGATTTATAAACAAATTGCATCAATAATTA
31608 TTAGACTTGACCAGTCAACAATTATTATTATTATTTTATCTTTTATCACATTTTCTTTTTCTGAA
1 TTAGACTTGACCAGTCAACAATTATTATTATTATTTTATCTTTTATCACATTTTCTTTTTCTGAA
31673 ATTTAAAAATATTAACCATATCTTCATACCACTCTCTTTCTAAATATATAATATAACCGTTACTA
66 ATTTAAAAATATT-A--ATA--TTCATA-CACTCTCTTTCTAAATATATAATATAACCGTTACTA
*
31738 AATGCTTTAATTTTTTTTTTTCCTTTTCTTAATTTTTTATAAATTATTATAAATTCAATAATTAA
125 AATGCTTTAATTTATTTTTTTCCTTTTCTTAATTTTTTATAAATTATTATAAATTCAATAATTAA
*
31803 AAAAATTTAATTAAAGCATAGTATAAAAAAAAACTAATGTACTCGTTATGATTTAATAGAACTCC
190 AAAAATTTAATTAAAGCATAGTATAAAAAAAAACTAATGTACACGTTATGATTTAATAGAACTCC
31868 CAATCGAGTTAATACCATAAATTAATAGATTTATAAACAAATTGCATCAATAAT
255 CAATCGAGTTAATACCATAAATTAATAGATTTATAAACAAATTGCATCAATAAT
31922 AGATCTTGAG
Statistics
Matches: 299, Mismatches: 5, Indels: 12
0.95 0.02 0.04
Matches are distributed among these distances:
308 77 0.26
312 1 0.00
313 1 0.00
316 98 0.33
318 122 0.41
ACGTcount: A:0.40, C:0.13, G:0.05, T:0.42
Consensus pattern (310 bp):
TTAGACTTGACCAGTCAACAATTATTATTATTATTTTATCTTTTATCACATTTTCTTTTTCTGAA
ATTTAAAAATATTAATATTCATACACTCTCTTTCTAAATATATAATATAACCGTTACTAAATGCT
TTAATTTATTTTTTTCCTTTTCTTAATTTTTTATAAATTATTATAAATTCAATAATTAAAAAAAT
TTAATTAAAGCATAGTATAAAAAAAAACTAATGTACACGTTATGATTTAATAGAACTCCCAATCG
AGTTAATACCATAAATTAATAGATTTATAAACAAATTGCATCAATAATTA
Found at i:36155 original size:16 final size:15
Alignment explanation
Indices: 36131--36164 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
36121 TAATAAGCAT
36131 ATTTA-AAAAATAAA
1 ATTTATAAAAATAAA
*
36145 ATTTATAAAAATTAA
1 ATTTATAAAAATAAA
36160 ATTTA
1 ATTTA
36165 GTAATTATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATTTATAAAAATAAA
Found at i:51531 original size:21 final size:20
Alignment explanation
Indices: 51506--51547 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
51496 TTTTACTTTC
51506 ATATA-AAAAAAATTACAAAAT
1 ATATATAAAAAAA-TA-AAAAT
*
51527 ATATATAATAAAATAAAAAT
1 ATATATAAAAAAATAAAAAT
51547 A
1 A
51548 ACATATCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 7 0.37
22 6 0.32
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (20 bp):
ATATATAAAAAAATAAAAAT
Found at i:53518 original size:21 final size:21
Alignment explanation
Indices: 53489--53538 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
53479 TCAAATCGAA
*
53489 TTGGGTTTAAGGTTT-GGTGAT
1 TTGGTTTTAAGGTTTAGGT-AT
*
53510 TTGGTTTTAGGGTTTAGGTAT
1 TTGGTTTTAAGGTTTAGGTAT
*
53531 TGGGTTTT
1 TTGGTTTT
53539 TATGGTTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.12, C:0.00, G:0.36, T:0.52
Consensus pattern (21 bp):
TTGGTTTTAAGGTTTAGGTAT
Done.