Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012811.1 Kokia drynarioides strain JFW-HI SEQ_127824, 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: 60113
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1469 original size:22 final size:22
Alignment explanation
Indices: 1444--1493 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
1434 ATTATAATAC
1444 TTAAAAAAACAAACAT-AAAATT
1 TTAAAAAAACAAA-ATCAAAATT
**
1466 TTAAAAAAATTAAATCAAAATT
1 TTAAAAAAACAAAATCAAAATT
1488 TTAAAA
1 TTAAAA
1494 TAAAATATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 2 0.08
22 23 0.92
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (22 bp):
TTAAAAAAACAAAATCAAAATT
Found at i:1491 original size:13 final size:12
Alignment explanation
Indices: 1458--1512 Score: 62
Period size: 12 Copynumber: 4.7 Consensus size: 12
1448 AAAAACAAAC
1458 ATAAAATTTTAA
1 ATAAAATTTTAA
1470 A-AAAA--TTAA
1 ATAAAATTTTAA
1479 ATCAAAATTTTAAA
1 AT-AAAATTTT-AA
*
1493 ATAAAATATTAA
1 ATAAAATTTTAA
1505 ATAAAATT
1 ATAAAATT
1513 ATTATTATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
9 5 0.14
11 8 0.22
12 10 0.28
13 9 0.25
14 4 0.11
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (12 bp):
ATAAAATTTTAA
Found at i:1515 original size:13 final size:13
Alignment explanation
Indices: 1474--1516 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
1464 TTTTAAAAAA
1474 ATTAAATCAAAATT
1 ATTAAAT-AAAATT
1488 -TTAAAATAAAA-T
1 ATT-AAATAAAATT
1500 ATTAAATAAAATT
1 ATTAAATAAAATT
1513 ATTA
1 ATTA
1517 TTATTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
12 9 0.35
13 13 0.50
14 4 0.15
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (13 bp):
ATTAAATAAAATT
Found at i:7891 original size:8 final size:8
Alignment explanation
Indices: 7863--7903 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
7853 CGATTCAGGG
7863 TATA-TTA
1 TATACTTA
*
7870 TATACATA
1 TATACTTA
7878 TATACTTA
1 TATACTTA
7886 TATACTTA
1 TATACTTA
*
7894 CAT-CTTA
1 TATACTTA
7901 TAT
1 TAT
7904 TATTCTGTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
7 10 0.34
8 19 0.66
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.49
Consensus pattern (8 bp):
TATACTTA
Found at i:8114 original size:24 final size:24
Alignment explanation
Indices: 8087--8132 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
8077 ATTTAAAAAG
8087 GGGTTCATAGAAGACAGATTTTTA
1 GGGTTCATAGAAGACAGATTTTTA
8111 GGGTTCATAGAAGACAGATTTT
1 GGGTTCATAGAAGACAGATTTT
8133 AAAAAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.33, C:0.09, G:0.26, T:0.33
Consensus pattern (24 bp):
GGGTTCATAGAAGACAGATTTTTA
Found at i:21384 original size:14 final size:15
Alignment explanation
Indices: 21365--21394 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
21355 AGATGATTAT
21365 ATAAAAAAT-TATAA
1 ATAAAAAATATATAA
21379 ATAAAAAATATATAA
1 ATAAAAAATATATAA
21394 A
1 A
21395 ATTATTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
ATAAAAAATATATAA
Found at i:21411 original size:26 final size:27
Alignment explanation
Indices: 21362--21479 Score: 75
Period size: 26 Copynumber: 4.3 Consensus size: 27
21352 TTAAGATGAT
*
21362 TATATAAAA-AATTATAAATA--AAAAA
1 TATATAAAATTATTA-AAATATTAAAAA
21387 TATATAAAATTATT-AAATATTAAAATAA
1 TATATAAAATTATTAAAATATT-AAA-AA
* *
21415 TATAATATAATTATTTTTAAAATTTTAAAAA
1 TAT-ATA-AA--ATTATTAAAATATTAAAAA
* * *
21446 TATA-AATATTTTTAAAATTTTAAAAA
1 TATATAAAATTATTAAAATATTAAAAA
21472 TAATATAA
1 T-ATATAA
21480 GTGGGTTTGA
Statistics
Matches: 77, Mismatches: 4, Indels: 21
0.75 0.04 0.21
Matches are distributed among these distances:
24 5 0.06
25 9 0.12
26 23 0.30
27 6 0.08
28 8 0.10
29 4 0.05
30 3 0.04
31 5 0.06
32 8 0.10
33 6 0.08
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
TATATAAAATTATTAAAATATTAAAAA
Found at i:21955 original size:43 final size:44
Alignment explanation
Indices: 21907--21989 Score: 116
Period size: 42 Copynumber: 1.9 Consensus size: 44
21897 AAATGATGGT
* *
21907 ATTTAATAATTTTTTTTAATTTGGTACCT-AA-TTTTTTTGTCTA
1 ATTTAAT-ATATTTTTTAATTTGATACCTAAACTTTTTTTGTCTA
*
21950 ATTTAATATATTTTTTAATTTGATATCTAAACTTTTTTTG
1 ATTTAATATATTTTTTAATTTGATACCTAAACTTTTTTTG
21990 GATTCAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
42 18 0.51
43 9 0.26
44 8 0.23
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.60
Consensus pattern (44 bp):
ATTTAATATATTTTTTAATTTGATACCTAAACTTTTTTTGTCTA
Found at i:22073 original size:61 final size:60
Alignment explanation
Indices: 21960--22073 Score: 174
Period size: 60 Copynumber: 1.9 Consensus size: 60
21950 ATTTAATATA
** * *
21960 TTTTTTAATTTGATATCTAAACTTTTTTTGGATTCAATTTGATACTTGAATTTGGCTTTT
1 TTTTTTAATTTGATATCTAAACTTTTTTTAAATTCAATTTGATACATAAATTTGGCTTTT
*
22020 TTTTTTAATTTGGTATCTAAACTTTTTTTAAAATTCAATTTGATACATAAATTT
1 TTTTTTAATTTGATATCTAAACTTTTTTT-AAATTCAATTTGATACATAAATTT
22074 ATTAAATATT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
60 28 0.58
61 20 0.42
ACGTcount: A:0.28, C:0.08, G:0.09, T:0.55
Consensus pattern (60 bp):
TTTTTTAATTTGATATCTAAACTTTTTTTAAATTCAATTTGATACATAAATTTGGCTTTT
Found at i:22330 original size:31 final size:32
Alignment explanation
Indices: 22288--22349 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
22278 ACCAACTTAA
*
22288 AAAAAAGTGTCAAGTTTAAGTA-TCAAATTAGG
1 AAAAAAGTGTCAAATTTAAGTACT-AAATTAGG
*
22320 AAAAAA-TGTCAAATTTGAGTACTAAATTAG
1 AAAAAAGTGTCAAATTTAAGTACTAAATTAG
22350 ACTAAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 20 0.74
32 7 0.26
ACGTcount: A:0.48, C:0.06, G:0.16, T:0.29
Consensus pattern (32 bp):
AAAAAAGTGTCAAATTTAAGTACTAAATTAGG
Found at i:27479 original size:18 final size:17
Alignment explanation
Indices: 27458--27491 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
27448 AACAAAACAC
27458 TTTAAGCAAAGCTAATGT
1 TTTAAGCAAAGC-AATGT
*
27476 TTTAGGCAAAGCAATG
1 TTTAAGCAAAGCAATG
27492 AATAAGACCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (17 bp):
TTTAAGCAAAGCAATGT
Found at i:30367 original size:31 final size:32
Alignment explanation
Indices: 30309--30372 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 32
30299 TATACACGTG
30309 AAACTTTAATTATGATTCAAATCTATAC-TTA
1 AAACTTTAATTATGATTCAAATCTATACATTA
* *
30340 AAACTTTAATTTTGATT-TAATCATATACATTA
1 AAACTTTAATTATGATTCAAATC-TATACATTA
30372 A
1 A
30373 GAAATAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 4 0.14
31 21 0.72
32 4 0.14
ACGTcount: A:0.42, C:0.11, G:0.03, T:0.44
Consensus pattern (32 bp):
AAACTTTAATTATGATTCAAATCTATACATTA
Found at i:55221 original size:7 final size:7
Alignment explanation
Indices: 55205--55247 Score: 77
Period size: 7 Copynumber: 6.1 Consensus size: 7
55195 GCAACTTGAA
*
55205 TTTCCCT
1 TTTCCTT
55212 TTTCCTT
1 TTTCCTT
55219 TTTCCTT
1 TTTCCTT
55226 TTTCCTT
1 TTTCCTT
55233 TTTCCTT
1 TTTCCTT
55240 TTTCCTT
1 TTTCCTT
55247 T
1 T
55248 GTAACTCTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (7 bp):
TTTCCTT
Found at i:55492 original size:17 final size:17
Alignment explanation
Indices: 55467--55500 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
55457 AAGGGTATGC
55467 TTTTCTTTCTGTGTTTT
1 TTTTCTTTCTGTGTTTT
*
55484 TTTTTTTTCTGTGTTTT
1 TTTTCTTTCTGTGTTTT
55501 AATTTTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.09, G:0.12, T:0.79
Consensus pattern (17 bp):
TTTTCTTTCTGTGTTTT
Found at i:55506 original size:17 final size:17
Alignment explanation
Indices: 55472--55508 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
55462 TATGCTTTTC
**
55472 TTTCTGTGTTTTTTTTT
1 TTTCTGTGTTTTAATTT
55489 TTTCTGTGTTTTAATTT
1 TTTCTGTGTTTTAATTT
55506 TTT
1 TTT
55509 AAGATTTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.05, C:0.05, G:0.11, T:0.78
Consensus pattern (17 bp):
TTTCTGTGTTTTAATTT
Done.