Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006455.1 Kokia drynarioides strain JFW-HI SEQ_121038, 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: 29871
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 22 characters in sequence are not A, C, G, or T
Found at i:1390 original size:17 final size:17
Alignment explanation
Indices: 1354--1392 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1344 TAGTAAATAA
*
1354 AAATATATAAAATAATT
1 AAATATATAAAATAAAT
1371 AAATAT-TAAAATAAAAT
1 AAATATATAAAAT-AAAT
1388 AAATA
1 AAATA
1393 ATTTTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AAATATATAAAATAAAT
Found at i:1402 original size:21 final size:21
Alignment explanation
Indices: 1360--1401 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1350 ATAAAAATAT
*
1360 ATAAAATAATTAAATATTAAA
1 ATAAAATAAATAAATATTAAA
*
1381 ATAAAATAAAT-AATTTTAAA
1 ATAAAATAAATAAATATTAAA
1401 A
1 A
1402 AAATTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
ATAAAATAAATAAATATTAAA
Found at i:4799 original size:27 final size:26
Alignment explanation
Indices: 4708--4799 Score: 66
Period size: 27 Copynumber: 3.6 Consensus size: 26
4698 TACTCATTTT
* *
4708 ATTACTTAAAAAATATTTTTATTTAA
1 ATTAATTATAAAATATTTTTATTTAA
* ** **
4734 ATTTAATTATACAATGCTCGT-TTT--
1 A-TTAATTATAAAATATTTTTATTTAA
*
4758 ATTATTTA-AAAATATTTTTATTTAA
1 ATTAATTATAAAATATTTTTATTTAA
4783 ATCTAATTATAAAATAT
1 AT-TAATTATAAAATAT
4800 ATAAATGTTA
Statistics
Matches: 46, Mismatches: 14, Indels: 11
0.65 0.20 0.15
Matches are distributed among these distances:
22 6 0.13
23 9 0.20
24 1 0.02
25 2 0.04
26 9 0.20
27 19 0.41
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.50
Consensus pattern (26 bp):
ATTAATTATAAAATATTTTTATTTAA
Found at i:6232 original size:22 final size:21
Alignment explanation
Indices: 6202--6290 Score: 53
Period size: 21 Copynumber: 4.3 Consensus size: 21
6192 GTTTTGGTGT
*
6202 TGTTATTTTATTGTTTTGGTTA
1 TGTT-TTTTATTGTTTTAGTTA
** *
6224 CTGTTTTTTGCTGTATTAG-TA
1 -TGTTTTTTATTGTTTTAGTTA
*
6245 TTGTTTTTTATTGATTT-G--A
1 -TGTTTTTTATTGTTTTAGTTA
*
6264 T-TTTTTTACTGTTTTAGTTA
1 TGTTTTTTATTGTTTTAGTTA
6284 CTGTTTT
1 -TGTTTT
6291 GGTGATTTTT
Statistics
Matches: 50, Mismatches: 11, Indels: 11
0.69 0.15 0.15
Matches are distributed among these distances:
17 12 0.24
18 2 0.04
19 1 0.02
20 2 0.04
21 15 0.30
22 14 0.28
23 4 0.08
ACGTcount: A:0.13, C:0.04, G:0.16, T:0.66
Consensus pattern (21 bp):
TGTTTTTTATTGTTTTAGTTA
Found at i:6333 original size:26 final size:24
Alignment explanation
Indices: 6275--6350 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
6265 TTTTTTACTG
* *
6275 TTTTAGTTACTG-TTTTGGTG--A
1 TTTTTGTTACTGTTTTTGTTGCTA
*
6296 TTTTT-TTACTGTTTTGATGTTGTTA
1 TTTTTGTTACTGTTTT--TGTTGCTA
*
6321 TTTTTGTTGCTGTTTTTGTTGCTA
1 TTTTTGTTACTGTTTTTGTTGCTA
6345 TTTTTG
1 TTTTTG
6351 CTGTTATTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
20 6 0.13
21 7 0.16
23 4 0.09
24 13 0.29
25 6 0.13
26 9 0.20
ACGTcount: A:0.09, C:0.05, G:0.20, T:0.66
Consensus pattern (24 bp):
TTTTTGTTACTGTTTTTGTTGCTA
Found at i:6340 original size:24 final size:24
Alignment explanation
Indices: 6295--6367 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
6285 TGTTTTGGTG
*
6295 ATTTTT-TTACTGTTTTGATGTTGTT
1 ATTTTTGTTGCTGTTTT--TGTTGTT
*
6320 ATTTTTGTTGCTGTTTTTGTTGCT
1 ATTTTTGTTGCTGTTTTTGTTGTT
* * *
6344 ATTTTTGCTGTTATTTTTGTTGTT
1 ATTTTTGTTGCTGTTTTTGTTGTT
6368 TTGCTTTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
24 26 0.63
25 6 0.15
26 9 0.22
ACGTcount: A:0.08, C:0.05, G:0.18, T:0.68
Consensus pattern (24 bp):
ATTTTTGTTGCTGTTTTTGTTGTT
Found at i:6367 original size:12 final size:12
Alignment explanation
Indices: 6313--6367 Score: 74
Period size: 12 Copynumber: 4.6 Consensus size: 12
6303 ACTGTTTTGA
6313 TGTTGTTATTTT
1 TGTTGTTATTTT
* *
6325 TGTTGCTGTTTT
1 TGTTGTTATTTT
*
6337 TGTTGCTATTTT
1 TGTTGTTATTTT
*
6349 TGCTGTTATTTT
1 TGTTGTTATTTT
6361 TGTTGTT
1 TGTTGTT
6368 TTGCTTTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.05, C:0.05, G:0.20, T:0.69
Consensus pattern (12 bp):
TGTTGTTATTTT
Found at i:6570 original size:27 final size:25
Alignment explanation
Indices: 6540--6595 Score: 60
Period size: 27 Copynumber: 2.2 Consensus size: 25
6530 TACAATTATC
6540 TTAATATAAAAT-TTTTTTAATGTATTT
1 TTAAT-TAAAATATTTTTTAA--TATTT
**
6567 TTAATTAATTTATTTTTTAATATTT
1 TTAATTAAAATATTTTTTAATATTT
6592 TTAA
1 TTAA
6596 GTTTATTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 9 0.35
26 4 0.15
27 13 0.50
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (25 bp):
TTAATTAAAATATTTTTTAATATTT
Found at i:7080 original size:18 final size:18
Alignment explanation
Indices: 7049--7083 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
7039 ATAAAGATTT
7049 TGTTTTTTTGAGTTTGAG
1 TGTTTTTTTGAGTTTGAG
7067 TGTTTGTTTT-AGTTTGA
1 TGTTT-TTTTGAGTTTGA
7084 AAGTGAGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.11, C:0.00, G:0.26, T:0.63
Consensus pattern (18 bp):
TGTTTTTTTGAGTTTGAG
Found at i:11502 original size:29 final size:28
Alignment explanation
Indices: 11461--11519 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
11451 CTATGAGAGA
*
11461 AATGATCGATTTAGTCCCT-TAACTATTG
1 AATGATCAATTTAGTCCCTGT-ACTATTG
*
11489 AATGAATCAATTTAGTTCCTGTACTATTG
1 AATG-ATCAATTTAGTCCCTGTACTATTG
11518 AA
1 AA
11520 AAAAATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 4 0.15
29 22 0.81
30 1 0.04
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (28 bp):
AATGATCAATTTAGTCCCTGTACTATTG
Found at i:12748 original size:16 final size:16
Alignment explanation
Indices: 12714--12748 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
12704 ATTCGTACAT
*
12714 TTTGATTCGAATTTCA
1 TTTGATTCGAATTTAA
*
12730 TTTGATTCGATTTTAA
1 TTTGATTCGAATTTAA
12746 TTT
1 TTT
12749 TTACGGTACG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.23, C:0.09, G:0.11, T:0.57
Consensus pattern (16 bp):
TTTGATTCGAATTTAA
Found at i:13093 original size:21 final size:20
Alignment explanation
Indices: 13062--13100 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
13052 AATTTACATT
13062 TTTTAAAGAATTTAAATCGA
1 TTTTAAAGAATTTAAATCGA
*
13082 TTTTAAATGAATTTGAATC
1 TTTTAAA-GAATTTAAATC
13101 CAACTGTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (20 bp):
TTTTAAAGAATTTAAATCGA
Found at i:13737 original size:31 final size:31
Alignment explanation
Indices: 13694--13754 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
13684 ATCAATTTAG
* *
13694 TTTATATATTTTAATTTGATCAATTTTAGTT
1 TTTATATATTTTAAATTGATCAACTTTAGTT
*
13725 TTTATATTTTTTAAATTGATCAACTTTAGT
1 TTTATATATTTTAAATTGATCAACTTTAGT
13755 CCATTGTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.59
Consensus pattern (31 bp):
TTTATATATTTTAAATTGATCAACTTTAGTT
Found at i:13770 original size:32 final size:31
Alignment explanation
Indices: 13684--13771 Score: 92
Period size: 31 Copynumber: 2.9 Consensus size: 31
13674 TCCATCTAAT
* *
13684 ATCAA-TTTAGT--TTATATATTTTAATTTG
1 ATCAACTTTAGTCATTATATTTTTTAAATTG
* **
13712 ATCAATTTTAGTTTTTATATTTTTTAAATTG
1 ATCAACTTTAGTCATTATATTTTTTAAATTG
*
13743 ATCAACTTTAGTCCATTGTATTTTTTAAA
1 ATCAACTTTAGT-CATTATATTTTTTAAA
13772 CATAAAAGTT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
28 5 0.10
29 6 0.12
31 26 0.52
32 13 0.26
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.56
Consensus pattern (31 bp):
ATCAACTTTAGTCATTATATTTTTTAAATTG
Found at i:15132 original size:193 final size:193
Alignment explanation
Indices: 14911--15279 Score: 485
Period size: 194 Copynumber: 1.9 Consensus size: 193
14901 AAAATGATTT
* ** * *
14911 TTTTTTTCGTTTAAACTTTTTATAATTTATAAAATTTTAAATTAGTAATGGT-AAGTTACACTTT
1 TTTTTTTCATTTAAACCCTTTATAATTTATAAAATTTTAAATTAGTAATGGTAAAATTACACTCT
* * * * *
14975 AAT-CCTCTAAAAATAAT-AAAAATTTGATTTAATCTTTTAAAAAATATAAATATATAGACTATT
66 -ATCCCCCTAAAAATAATAAAAAATTAG-TTTAATCCTTTAAAAAATATAAAGATATAGACCATT
* * *
15038 AAAGTGGTGAACTTGCATTTTTACT-ATCATAAAAATATACAATTTAATTCTGCCCCTAAAATGA
129 AAAATGATGAAATTGCATTTTTA-TAATCAT-AAAATATACAATTTAATTCTGCCCCTAAAATGA
15102 AA
192 AA
* * *
15104 TTTTTTTCATTTAGACCCTTTATAATTTATAAAATTTTGAATTAGTAATGGTAAAATTGCACTCT
1 TTTTTTTCATTTAAACCCTTTATAATTTATAAAATTTTAAATTAGTAATGGTAAAATTACACTCT
* * * *
15169 GTCCCCCTCAAAATAATAAAAAATTAGTTTTATCCTTTAAAAATTATAAAGATATAGACCATTAA
66 ATCCCCCTAAAAATAATAAAAAATTAGTTTAATCCTTTAAAAAATATAAAGATATAGACCATTAA
*
15234 AATGATGAAATTGCATTTTTATAATCGTAAAATATACAATTTAATT
131 AATGATGAAATTGCATTTTTATAATCATAAAATATACAATTTAATT
15280 ATGTCCTCCC
Statistics
Matches: 151, Mismatches: 21, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
193 67 0.44
194 76 0.50
195 8 0.05
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.41
Consensus pattern (193 bp):
TTTTTTTCATTTAAACCCTTTATAATTTATAAAATTTTAAATTAGTAATGGTAAAATTACACTCT
ATCCCCCTAAAAATAATAAAAAATTAGTTTAATCCTTTAAAAAATATAAAGATATAGACCATTAA
AATGATGAAATTGCATTTTTATAATCATAAAATATACAATTTAATTCTGCCCCTAAAATGAAA
Found at i:20722 original size:24 final size:24
Alignment explanation
Indices: 20695--20744 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
20685 ATTATTTTTA
20695 ATTTAATAT-TTAATAATATTATAT
1 ATTTAATATATTAA-AATATTATAT
* * *
20719 ATTTTATTTATTAAAATTTTATAT
1 ATTTAATATATTAAAATATTATAT
20743 AT
1 AT
20745 AATCATCTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
ATTTAATATATTAAAATATTATAT
Found at i:20741 original size:22 final size:22
Alignment explanation
Indices: 20701--20742 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
20691 TTTAATTTAA
*
20701 TATTTAATAATATTATATATTT
1 TATTTAATAAAATTATATATTT
* *
20723 TATTTATTAAAATTTTATAT
1 TATTTAATAAAATTATATAT
20743 ATAATCATCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TATTTAATAAAATTATATATTT
Found at i:29061 original size:22 final size:21
Alignment explanation
Indices: 29016--29059 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
29006 TTTAACTATT
29016 AATTTTTTTAAAAAATAATTA
1 AATTTTTTTAAAAAATAATTA
29037 AATTATTTTTAAAAAA-AATTA
1 AATT-TTTTTAAAAAATAATTA
29058 AA
1 AA
29060 ATATCAACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AATTTTTTTAAAAAATAATTA
Done.