Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010145.1 Kokia drynarioides strain JFW-HI SEQ_124945, 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: 18127
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:1457 original size:26 final size:27
Alignment explanation
Indices: 1424--1515 Score: 89
Period size: 26 Copynumber: 3.3 Consensus size: 27
1414 ATTAAAAATG
1424 TTATTAAATTATATTTAATAATAATTA
1 TTATTAAATTATATTTAATAATAATTA
* * * *
1451 TT-TTAAAATATAATTAAATTATTTATTATTT
1 TTATTAAATTAT-ATTTAA-TA---ATAATTA
1482 TTATTAAATTATATTTAATAATAA-TA
1 TTATTAAATTATATTTAATAATAATTA
1508 TTATTAAA
1 TTATTAAA
1516 ATTTAATAAC
Statistics
Matches: 51, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
26 17 0.33
27 10 0.20
28 2 0.04
30 2 0.04
31 12 0.24
32 8 0.16
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
TTATTAAATTATATTTAATAATAATTA
Found at i:1460 original size:14 final size:16
Alignment explanation
Indices: 1430--1506 Score: 51
Period size: 16 Copynumber: 5.2 Consensus size: 16
1420 AATGTTATTA
1430 AATTATATTTAATAAT
1 AATTATATTTAATAAT
1446 AATTAT-TTTAA-AAT
1 AATTATATTTAATAAT
* *
1460 -A-TA-ATTAAATTATT
1 AATTATATTTAA-TAAT
* * *
1474 TATTAT-TTTTATTA-
1 AATTATATTTAATAAT
1488 AATTATATTTAATAAT
1 AATTATATTTAATAAT
1504 AAT
1 AAT
1507 ATTATTAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 16
0.64 0.13 0.23
Matches are distributed among these distances:
12 6 0.14
13 1 0.02
14 10 0.23
15 13 0.30
16 14 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AATTATATTTAATAAT
Found at i:1468 original size:37 final size:39
Alignment explanation
Indices: 1390--1472 Score: 116
Period size: 37 Copynumber: 2.2 Consensus size: 39
1380 AAATTTTACT
* *
1390 AATTCATATTTTAATAATAATTATATTAAAAATGTTATTA
1 AATT-ATATTTTAATAATAATTATATTAAAAATATAATTA
*
1430 AATTATA-TTTAATAATAATTAT-TTTAAAATATAATTA
1 AATTATATTTTAATAATAATTATATTAAAAATATAATTA
1467 AATTAT
1 AATTAT
1473 TTATTATTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
37 18 0.45
38 15 0.38
39 3 0.08
40 4 0.10
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (39 bp):
AATTATATTTTAATAATAATTATATTAAAAATATAATTA
Found at i:1510 original size:32 final size:32
Alignment explanation
Indices: 1424--1512 Score: 93
Period size: 32 Copynumber: 3.0 Consensus size: 32
1414 ATTAAAAATG
1424 TTATTAAATTATATTTAATAAT-A-ATTA-TT
1 TTATTAAATTATATTTAATAATAATATTATTT
* * *
1453 TTA--AAA-TATAATTAA-ATTATTTATTATTT
1 TTATTAAATTATATTTAATAATA-ATATTATTT
1482 TTATTAAATTATATTTAATAATAATATTATT
1 TTATTAAATTATATTTAATAATAATATTATT
1513 AAAATTTAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
25 2 0.04
26 8 0.17
27 3 0.07
28 4 0.09
29 8 0.17
31 3 0.07
32 15 0.33
33 3 0.07
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (32 bp):
TTATTAAATTATATTTAATAATAATATTATTT
Found at i:1694 original size:46 final size:44
Alignment explanation
Indices: 1604--1697 Score: 111
Period size: 44 Copynumber: 2.1 Consensus size: 44
1594 ATTATAACAT
*
1604 CATTCCATTCAACCAAACACAAGAATATTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACACAAGAATATGATTACAGTTCTATTC
* *
1648 CATTTCATTCAACCAAACA-ACTGAATTACTGATTACAG-TCTTATTC
1 CATTCCATTCAACCAAACACA-AGAA-TA-TGATTACAGTTC-TATTC
1694 CATT
1 CATT
1698 ACAATTCTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
43 1 0.02
44 21 0.49
45 4 0.09
46 17 0.40
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.34
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAAGAATATGATTACAGTTCTATTC
Found at i:1700 original size:16 final size:17
Alignment explanation
Indices: 1679--1749 Score: 69
Period size: 16 Copynumber: 4.4 Consensus size: 17
1669 TGAATTACTG
1679 ATTACAGTCT-TATTCC
1 ATTACAGTCTCTATTCC
* *
1695 ATTACAAT-TCTATTCT
1 ATTACAGTCTCTATTCC
*
1711 ATTACA-ACTCTATTCC
1 ATTACAGTCTCTATTCC
* *
1727 ATTACAGT-TTTATTCT
1 ATTACAGTCTCTATTCC
1743 ATTACAG
1 ATTACAG
1750 CGAACCCAAC
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
15 1 0.02
16 44 0.98
ACGTcount: A:0.30, C:0.21, G:0.04, T:0.45
Consensus pattern (17 bp):
ATTACAGTCTCTATTCC
Found at i:1715 original size:32 final size:33
Alignment explanation
Indices: 1679--1749 Score: 101
Period size: 32 Copynumber: 2.2 Consensus size: 33
1669 TGAATTACTG
*
1679 ATTACAGTCT-TATTCCATTACAATTCTATTCT
1 ATTACAGACTCTATTCCATTACAATTCTATTCT
* *
1711 ATTACA-ACTCTATTCCATTACAGTTTTATTCT
1 ATTACAGACTCTATTCCATTACAATTCTATTCT
1743 ATTACAG
1 ATTACAG
1750 CGAACCCAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 2 0.06
32 32 0.94
ACGTcount: A:0.30, C:0.21, G:0.04, T:0.45
Consensus pattern (33 bp):
ATTACAGACTCTATTCCATTACAATTCTATTCT
Found at i:2256 original size:40 final size:41
Alignment explanation
Indices: 2204--2283 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 41
2194 CTCACCCGAT
* * *
2204 TATAAAAGAAAAAATCCCCACT-ACCCTTTAGCTTCTTTTA
1 TATAAAAAAAAAAATCCCCACTCACCCTTTAACTTATTTTA
*
2244 TATAAAAAAAAAAATCTCCACTCACCCTTTAACTTATTTT
1 TATAAAAAAAAAAATCCCCACTCACCCTTTAACTTATTTT
2284 CTTCTTTTGG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
40 20 0.57
41 15 0.43
ACGTcount: A:0.40, C:0.24, G:0.03, T:0.34
Consensus pattern (41 bp):
TATAAAAAAAAAAATCCCCACTCACCCTTTAACTTATTTTA
Found at i:8733 original size:20 final size:20
Alignment explanation
Indices: 8708--8748 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
8698 GGACTTTAGA
*
8708 TATATAAAACATATTGGGTT
1 TATATAAAACAGATTGGGTT
* *
8728 TATATATAATAGATTGGGTT
1 TATATAAAACAGATTGGGTT
8748 T
1 T
8749 GGGCTTGTAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.02, G:0.17, T:0.44
Consensus pattern (20 bp):
TATATAAAACAGATTGGGTT
Found at i:10215 original size:14 final size:14
Alignment explanation
Indices: 10196--10230 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
10186 GGGGGTTTAT
10196 TAGAAATATAATTG
1 TAGAAATATAATTG
10210 TAGAAATATAATTG
1 TAGAAATATAATTG
10224 TAGAAAT
1 TAGAAAT
10231 CTCATAGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.34
Consensus pattern (14 bp):
TAGAAATATAATTG
Found at i:14806 original size:18 final size:18
Alignment explanation
Indices: 14783--14817 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
14773 ATATTTGAAA
14783 TAATTTAATATAAAATAT
1 TAATTTAATATAAAATAT
* *
14801 TAATTTTATTTAAAATA
1 TAATTTAATATAAAATA
14818 AAACGTTATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TAATTTAATATAAAATAT
Found at i:16960 original size:40 final size:40
Alignment explanation
Indices: 16905--16987 Score: 166
Period size: 40 Copynumber: 2.1 Consensus size: 40
16895 AAAGAATAGC
16905 TTTTTCCTTTTGTTTTCTTTTTTAAAAATGTTTATGTTGG
1 TTTTTCCTTTTGTTTTCTTTTTTAAAAATGTTTATGTTGG
16945 TTTTTCCTTTTGTTTTCTTTTTTAAAAATGTTTATGTTGG
1 TTTTTCCTTTTGTTTTCTTTTTTAAAAATGTTTATGTTGG
16985 TTT
1 TTT
16988 CATTATATAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.14, C:0.07, G:0.12, T:0.66
Consensus pattern (40 bp):
TTTTTCCTTTTGTTTTCTTTTTTAAAAATGTTTATGTTGG
Done.