Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005104.1 Kokia drynarioides strain JFW-HI SEQ_118927, 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: 11410
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:166 original size:16 final size:16
Alignment explanation
Indices: 144--180 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
134 AAATTTATTT
144 TAATAATAACTTTTAAA
1 TAATAATAA-TTTTAAA
161 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
176 TAATA
1 TAATA
181 TTCTTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:233 original size:15 final size:15
Alignment explanation
Indices: 213--269 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
203 ATTCAATATT
213 AATATTTTAATAATA
1 AATATTTTAATAATA
*
228 AATATTTATTAGAATTATA
1 AATA-TT-TT--AATAATA
*
247 AATATATTAATAATA
1 AATATTTTAATAATA
*
262 AATGTTTT
1 AATATTTT
270 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:767 original size:15 final size:15
Alignment explanation
Indices: 726--767 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
716 TTCCAAAAAA
726 GTAAATCATTTTTTC
1 GTAAATCATTTTTTC
* * *
741 ATAAATTATTTTCT-
1 GTAAATCATTTTTTC
755 GTAAATCATTTTT
1 GTAAATCATTTTT
768 AGTGAAACAA
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.31, C:0.10, G:0.05, T:0.55
Consensus pattern (15 bp):
GTAAATCATTTTTTC
Found at i:3481 original size:18 final size:18
Alignment explanation
Indices: 3458--3521 Score: 58
Period size: 18 Copynumber: 3.3 Consensus size: 18
3448 TACCATTGTT
3458 GAATTAATGGAGCTTTTG
1 GAATTAATGGAGCTTTTG
* *
3476 GAATTATTTGGACACCATTGTT-
1 GAATTA-ATGG--AGC-TT-TTG
3498 GAATTAATGGAGCTTTTG
1 GAATTAATGGAGCTTTTG
3516 GAATTA
1 GAATTA
3522 TTTGGACATA
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
17 2 0.06
18 14 0.39
19 5 0.14
21 5 0.14
22 8 0.22
23 2 0.06
ACGTcount: A:0.30, C:0.08, G:0.23, T:0.39
Consensus pattern (18 bp):
GAATTAATGGAGCTTTTG
Found at i:3493 original size:40 final size:40
Alignment explanation
Indices: 3449--3529 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
3439 TTTGAATGCT
3449 ACCATTGTTGAATTAATGGAGCTTTTGGAATTATTTGGAC
1 ACCATTGTTGAATTAATGGAGCTTTTGGAATTATTTGGAC
3489 ACCATTGTTGAATTAATGGAGCTTTTGGAATTATTTGGAC
1 ACCATTGTTGAATTAATGGAGCTTTTGGAATTATTTGGAC
3529 A
1 A
3530 TACATGACCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.28, C:0.10, G:0.22, T:0.40
Consensus pattern (40 bp):
ACCATTGTTGAATTAATGGAGCTTTTGGAATTATTTGGAC
Found at i:6001 original size:14 final size:13
Alignment explanation
Indices: 5983--6007 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5973 AATAATGTTT
5983 TTTTTTTCTTTTG
1 TTTTTTTCTTTTG
5996 TTTTTTTCTTTT
1 TTTTTTTCTTTT
6008 AAAACATGTT
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:0.00, C:0.08, G:0.04, T:0.88
Consensus pattern (13 bp):
TTTTTTTCTTTTG
Found at i:7295 original size:49 final size:49
Alignment explanation
Indices: 7242--7873 Score: 342
Period size: 49 Copynumber: 13.1 Consensus size: 49
7232 ATGTTTATGA
* * * *
7242 GGTACAAGGTTCACCATTGCGACTTCAACCTTTCCCTCCATATCTTCGT
1 GGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTCCATATCTTCGT
* * * ** * * *
7291 GGTACCAGATAT-GCCGTTGCGACTTCAATCTTTCCCAACATGT-TCCTT
1 GGTACAAGGT-TCGCCGTTGCGACTTAAATCTTTCCCTCCATATCTTCGT
* * **
7339 AGGTACCATGTTCGCCGTTGTAACTTAAATCTTTCCCTCCATATCTTCGT
1 -GGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTCCATATCTTCGT
* * * * * * * * * * * * *
7389 GATACTAGATTCTCCATTG-TAGCTTAAATATTTTCCTTCATGTTTTTGA
1 GGTACAAGGTTCGCCGTTGCGA-CTTAAATCTTTCCCTCCATATCTTCGT
* *
7438 GGTACAAGGTTCGTCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGT
1 GGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTCCATATCTTCGT
* * * ** * *
7487 GATACTAGATTCGCCACTG-TAGCTTAAATCTTT---TCC-T-TCAT-GCT
1 GGTACAAGGTTCGCCGTTGCGA-CTTAAATCTTTCCCTCCATATCTTCG-T
* * * * *
7531 --T-C-AGGTTCGCTGTTGCGACTTAAACCTTTGCCTCTATATCTTAGT
1 GGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTCCATATCTTCGT
* * * * * * * *
7576 GGTACTAA-ATTCACCGTTGTGGCTTAAATCTTTCCCTTCATATTTTTGA
1 GGTAC-AAGGTTCGCCGTTGCGACTTAAATCTTTCCCTCCATATCTTCGT
* * * *
7625 GGTACAAGGTTAGCCATTACGACTTAAA-CATTTCCCTACATATCTTCGT
1 GGTACAAGGTTCGCCGTTGCGACTTAAATC-TTTCCCTCCATATCTTCGT
* * *** * * ** * * *
7674 GGTACTAGATTTATCATTGCGGCTTAAATCTTTCCCTTTATATTTTTGA
1 GGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTCCATATCTTCGT
* * *
7723 GGTACAAGGTTCGCCATTGCAACTTAAACCTTTCCCTCCATATCTTCGT
1 GGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTCCATATCTTCGT
* * * * * * * * * *
7772 GGTACTAGATTCGCCGTTGCGGCTGAAATCTTTTCCTTCATGTTTTTGA
1 GGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTCCATATCTTCGT
* * *
7821 GGTACAAAGTTCACCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGT
1 GGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTCCATATCTTCGT
7870 GGTA
1 GGTA
7874 ATGAAACCTA
Statistics
Matches: 420, Mismatches: 140, Indels: 46
0.69 0.23 0.08
Matches are distributed among these distances:
40 19 0.05
41 2 0.00
42 1 0.00
43 3 0.01
44 5 0.01
45 5 0.01
46 4 0.01
47 1 0.00
48 10 0.02
49 363 0.86
50 7 0.02
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.38
Consensus pattern (49 bp):
GGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTCCATATCTTCGT
Found at i:7431 original size:98 final size:98
Alignment explanation
Indices: 7223--7873 Score: 703
Period size: 98 Copynumber: 6.7 Consensus size: 98
7213 AGTTTTAGTC
* * * *
7223 TTTCCTTTCATGTTTATGAGGTACAAGGTTCACCATTGCGACTTCAACCTTTCCCTCCATATCTT
1 TTTCC-TTCATGTTTTTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTT
* * * * *
7288 CGTGGTACCAGATAT-GCCGTTGCGACTTCAATCT
65 CGTGGTACTAGAT-TCGCCATTGTGGCTTAAATCT
* ** * * * ** *
7322 TTCCCAACATGTTCCTT-AGGTACCATGTTCGCCGTTGTAACTTAAATCTTTCCCTCCATATCTT
1 TTTCCTTCATGTT-TTTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTT
* * * *
7386 CGTGATACTAGATTCTCCATTGTAGCTTAAATAT
65 CGTGGTACTAGATTCGCCATTGTGGCTTAAATCT
*
7420 TTTCCTTCATGTTTTTGAGGTACAAGGTTCGTCGTTGCGACTTAAACCTTTCCCTCCATATCTTC
1 TTTCCTTCATGTTTTTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTC
* * *
7485 GTGATACTAGATTCGCCACTGTAGCTTAAATCT
66 GTGGTACTAGATTCGCCATTGTGGCTTAAATCT
* * * * *
7518 TTTCCTTCATG---CT----T-C-AGGTTCGCTGTTGCGACTTAAACCTTTGCCTCTATATCTTA
1 TTTCCTTCATGTTTTTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTC
* * *
7574 GTGGTACTAAATTCACCGTTGTGGCTTAAATCT
66 GTGGTACTAGATTCGCCATTGTGGCTTAAATCT
* * * * * * *
7607 TTCCCTTCATATTTTTGAGGTACAAGGTTAGCCATTACGACTTAAACATTTCCCTACATATCTTC
1 TTTCCTTCATGTTTTTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTC
*** *
7672 GTGGTACTAGATTTATCATTGCGGCTTAAATCT
66 GTGGTACTAGATTCGCCATTGTGGCTTAAATCT
* * * * *
7705 TTCCCTTTATATTTTTGAGGTACAAGGTTCGCCATTGCAACTTAAACCTTTCCCTCCATATCTTC
1 TTTCCTTCATGTTTTTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTC
* * *
7770 GTGGTACTAGATTCGCCGTTGCGGCTGAAATCT
66 GTGGTACTAGATTCGCCATTGTGGCTTAAATCT
* *
7803 TTTCCTTCATGTTTTTGAGGTACAAAGTTCACCGTTGCGACTTAAACCTTTCCCTCCATATCTTC
1 TTTCCTTCATGTTTTTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTC
7868 GTGGTA
66 GTGGTA
7874 ATGAAACCTA
Statistics
Matches: 458, Mismatches: 82, Indels: 25
0.81 0.15 0.04
Matches are distributed among these distances:
89 72 0.16
90 1 0.00
91 1 0.00
92 1 0.00
95 1 0.00
96 1 0.00
97 4 0.01
98 372 0.81
99 5 0.01
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.38
Consensus pattern (98 bp):
TTTCCTTCATGTTTTTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTC
GTGGTACTAGATTCGCCATTGTGGCTTAAATCT
Found at i:7601 original size:89 final size:89
Alignment explanation
Indices: 7444--7616 Score: 240
Period size: 89 Copynumber: 1.9 Consensus size: 89
7434 TTGAGGTACA
* * *
7444 AGGTTCGTCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGATACTAGATTCGCCACTGTAG
1 AGGTTCGTCGTTGCGACTTAAACCTTTCCCTCCATATCTTAGTGATACTAAATTCACCACTGTAG
*
7509 CTTAAATCTTTTCCTTCATGCTTC
66 CTTAAATCTTTCCCTTCATGCTTC
* * * ** *
7533 AGGTTCG-CTGTTGCGACTTAAACCTTTGCCTCTATATCTTAGTGGTACTAAATTCACCGTTGTG
1 AGGTTCGTC-GTTGCGACTTAAACCTTTCCCTCCATATCTTAGTGATACTAAATTCACCACTGTA
7597 GCTTAAATCTTTCCCTTCAT
65 GCTTAAATCTTTCCCTTCAT
7617 ATTTTTGAGG
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
88 1 0.01
89 72 0.99
ACGTcount: A:0.20, C:0.26, G:0.16, T:0.39
Consensus pattern (89 bp):
AGGTTCGTCGTTGCGACTTAAACCTTTCCCTCCATATCTTAGTGATACTAAATTCACCACTGTAG
CTTAAATCTTTCCCTTCATGCTTC
Found at i:8368 original size:20 final size:20
Alignment explanation
Indices: 8343--8381 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
8333 TGATTGAGAC
8343 GCGAGTCCCTCCTTCGGTCG
1 GCGAGTCCCTCCTTCGGTCG
8363 GCGAGTCCCTCCTTCGGTC
1 GCGAGTCCCTCCTTCGGTC
8382 AGATCCTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.05, C:0.41, G:0.28, T:0.26
Consensus pattern (20 bp):
GCGAGTCCCTCCTTCGGTCG
Found at i:9129 original size:107 final size:109
Alignment explanation
Indices: 8958--9170 Score: 349
Period size: 108 Copynumber: 2.0 Consensus size: 109
8948 TTCTTTTAAA
* *
8958 ACCTGTTTCATTATTTTGTGTTACTGTTTCTCTTTATTTTATTTTATTTAATTTATACGTTT-AA
1 ACCTGTTTCATTATTTTGTGTTACTATTTCCCTTTATTTTATTTTATTTAATTTATACGTTTAAA
9022 AAATCTGTTTATAAATAAAAATAATACAATAATAGTAAATAGGT
66 AAATCTGTTTATAAATAAAAATAATACAATAATAGTAAATAGGT
* *
9066 ACCTGTTTCATTGTTTTGTGTTACTATTTCCCTTT-TTTTGTTTTATTTAATTTATACGTTTAAA
1 ACCTGTTTCATTATTTTGTGTTACTATTTCCCTTTATTTTATTTTATTTAATTTATACGTTTAAA
* * *
9130 AAATTTGTTTATGAATAAAAATAATACAGTAATAGTAAATA
66 AAATCTGTTTATAAATAAAAATAATACAATAATAGTAAATA
9171 CGTAATATAT
Statistics
Matches: 97, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
107 25 0.26
108 72 0.74
ACGTcount: A:0.33, C:0.08, G:0.09, T:0.49
Consensus pattern (109 bp):
ACCTGTTTCATTATTTTGTGTTACTATTTCCCTTTATTTTATTTTATTTAATTTATACGTTTAAA
AAATCTGTTTATAAATAAAAATAATACAATAATAGTAAATAGGT
Found at i:10370 original size:49 final size:49
Alignment explanation
Indices: 10317--10738 Score: 269
Period size: 49 Copynumber: 8.6 Consensus size: 49
10307 TTCGTCATTA
* * *
10317 CGACTTCAACCTTTCCCTCCATATGTTCGTGGTACCAGATTTACCGTTG
1 CGACTTAAACCTTTCCCTCCATATCTTCGTGGTACCAGATTCACCGTTG
* * ** * * * **
10366 CGACTTCAATCTTTCCCAACATGTTCTT-GAGGTACCAGGTTTGCCGTTG
1 CGACTTAAACCTTTCCCTCCAT-ATCTTCGTGGTACCAGATTCACCGTTG
** * * *
10415 TAACTTAAACCTTTCCTTCTATATCTTTGTGGTACCAGATTCACCGTTG
1 CGACTTAAACCTTTCCCTCCATATCTTCGTGGTACCAGATTCACCGTTG
* * * * * * * *
10464 CGGCTTCAATCC-TTCCCTTCATGT-TTCTGAGGTACAAGGTTCACCATTG
1 CGACTT-AAACCTTTCCCTCCATATCTTC-GTGGTACCAGATTCACCGTTG
* * *
10513 CGACTTAAACATTTCCCTCGATATCTTCGTGGTACTAGATTCACCGTTG
1 CGACTTAAACCTTTCCCTCCATATCTTCGTGGTACCAGATTCACCGTTG
* ** * * * * * * *
10562 CGGCTTAAATATTTCCCTTCATGT-TTATGAGGTACAATG-TTCGCTGTTG
1 CGACTTAAACCTTTCCCTCCATATCTT-CGTGGTACCA-GATTCACCGTTG
* * * *
10611 CGACTTAAACCTTTCCCTCGATATCTTCGTGGTACTAGATTCGCTGTTG
1 CGACTTAAACCTTTCCCTCCATATCTTCGTGGTACCAGATTCACCGTTG
* * * * * * * * * * *
10660 TGACTTAAATCATTCCCTTCATGTTTTTGAGGTACAAGGTTCGCCGTTG
1 CGACTTAAACCTTTCCCTCCATATCTTCGTGGTACCAGATTCACCGTTG
* *
10709 CGACTTAAATCTTTTCCTCCATATCTTCGT
1 CGACTTAAACCTTTCCCTCCATATCTTCGT
10739 CGTAATGAAA
Statistics
Matches: 280, Mismatches: 83, Indels: 20
0.73 0.22 0.05
Matches are distributed among these distances:
48 12 0.04
49 255 0.91
50 13 0.05
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.37
Consensus pattern (49 bp):
CGACTTAAACCTTTCCCTCCATATCTTCGTGGTACCAGATTCACCGTTG
Found at i:10426 original size:98 final size:98
Alignment explanation
Indices: 10255--10738 Score: 556
Period size: 98 Copynumber: 4.9 Consensus size: 98
10245 TCGAGGTAGG
* * * * * * * * *
10255 AGATTCACCGTTGTGATTTAAATATTTCCTTTCACGTTTTTGAGGTACAAGGTTCGTCATTACGA
1 AGATTCACCGTTGCGACTTAAATCTTTCCCTTCATGTTTATGAGGTACAAGGTTCGCCGTTGCGA
* *
10320 CTTCAACCTTTCCCTCCATATGTTCGTGGTACC
66 CTTAAACCTTTCCCTCCATATCTTCGTGGTACC
* * ** * * **
10353 AGATTTACCGTTGCGACTTCAATCTTTCCCAACATGTTCT-TGAGGTACCAGGTTTGCCGTTGTA
1 AGATTCACCGTTGCGACTTAAATCTTTCCCTTCATGTT-TATGAGGTACAAGGTTCGCCGTTGCG
* * *
10417 ACTTAAACCTTTCCTTCTATATCTTTGTGGTACC
65 ACTTAAACCTTTCCCTCCATATCTTCGTGGTACC
* * * * * *
10451 AGATTCACCGTTGCGGCTTCAATCCTTCCCTTCATGTTTCTGAGGTACAAGGTTCACCATTGCGA
1 AGATTCACCGTTGCGACTTAAATCTTTCCCTTCATGTTTATGAGGTACAAGGTTCGCCGTTGCGA
* * *
10516 CTTAAACATTTCCCTCGATATCTTCGTGGTACT
66 CTTAAACCTTTCCCTCCATATCTTCGTGGTACC
* * * *
10549 AGATTCACCGTTGCGGCTTAAATATTTCCCTTCATGTTTATGAGGTACAATGTTCGCTGTTGCGA
1 AGATTCACCGTTGCGACTTAAATCTTTCCCTTCATGTTTATGAGGTACAAGGTTCGCCGTTGCGA
* *
10614 CTTAAACCTTTCCCTCGATATCTTCGTGGTACT
66 CTTAAACCTTTCCCTCCATATCTTCGTGGTACC
* * * * *
10647 AGATTCGCTGTTGTGACTTAAATCATTCCCTTCATGTTTTTGAGGTACAAGGTTCGCCGTTGCGA
1 AGATTCACCGTTGCGACTTAAATCTTTCCCTTCATGTTTATGAGGTACAAGGTTCGCCGTTGCGA
* *
10712 CTTAAATCTTTTCCTCCATATCTTCGT
66 CTTAAACCTTTCCCTCCATATCTTCGT
10739 CGTAATGAAA
Statistics
Matches: 326, Mismatches: 58, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
97 1 0.00
98 324 0.99
99 1 0.00
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.38
Consensus pattern (98 bp):
AGATTCACCGTTGCGACTTAAATCTTTCCCTTCATGTTTATGAGGTACAAGGTTCGCCGTTGCGA
CTTAAACCTTTCCCTCCATATCTTCGTGGTACC
Done.