Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001322.1 Kokia drynarioides strain JFW-HI SEQ_112754, 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: 45265
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:1358 original size:21 final size:22
Alignment explanation
Indices: 1304--1368 Score: 64
Period size: 21 Copynumber: 3.0 Consensus size: 22
1294 TTGGATCTTA
1304 GTATTCTAAAAATAAT-AATAAT
1 GTATT-TAAAAATAATAAATAAT
* *
1326 -CATATTAGAAATAATAAAT-AT
1 GTAT-TTAAAAATAATAAATAAT
*
1347 GTATTTAAAAATAATATATAAT
1 GTATTTAAAAATAATAAATAAT
1369 AAGTAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
21 26 0.76
22 8 0.24
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (22 bp):
GTATTTAAAAATAATAAATAAT
Found at i:2829 original size:9 final size:9
Alignment explanation
Indices: 2811--2855 Score: 81
Period size: 9 Copynumber: 5.0 Consensus size: 9
2801 TTGCCCTCAG
2811 TGTTGCGAC
1 TGTTGCGAC
*
2820 TGTTGTGAC
1 TGTTGCGAC
2829 TGTTGCGAC
1 TGTTGCGAC
2838 TGTTGCGAC
1 TGTTGCGAC
2847 TGTTGCGAC
1 TGTTGCGAC
2856 ATGCCTCCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.11, C:0.20, G:0.33, T:0.36
Consensus pattern (9 bp):
TGTTGCGAC
Found at i:8735 original size:10 final size:10
Alignment explanation
Indices: 8722--8752 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
8712 AAAAGACAAT
8722 AAAAA-ATGA
1 AAAAATATGA
8731 AAAAATATGA
1 AAAAATATGA
8741 AAAAATATGA
1 AAAAATATGA
8751 AA
1 AA
8753 GAGAAGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.24
10 16 0.76
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.16
Consensus pattern (10 bp):
AAAAATATGA
Found at i:16071 original size:19 final size:21
Alignment explanation
Indices: 16039--16077 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
16029 GCCTTATTTA
*
16039 ATTTTATTTATTTAT-TGTTC
1 ATTTAATTTATTTATATGTTC
16059 ATTTAATTT-TTTATATGTT
1 ATTTAATTTATTTATATGTT
16078 GTTTTTTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (21 bp):
ATTTAATTTATTTATATGTTC
Found at i:16079 original size:23 final size:25
Alignment explanation
Indices: 16034--16080 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 25
16024 TTTATGCCTT
*
16034 ATTTAATTTTATTTATTTATTGTTC
1 ATTTAATTTTATTTATATATTGTTC
*
16059 ATTTAA-TTT-TTTATATGTTGTT
1 ATTTAATTTTATTTATATATTGTT
16081 TTTTATGCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 11 0.55
24 3 0.15
25 6 0.30
ACGTcount: A:0.23, C:0.02, G:0.06, T:0.68
Consensus pattern (25 bp):
ATTTAATTTTATTTATATATTGTTC
Found at i:21393 original size:10 final size:10
Alignment explanation
Indices: 21378--21411 Score: 68
Period size: 10 Copynumber: 3.4 Consensus size: 10
21368 ATAATATATA
21378 TTCTTTCTTT
1 TTCTTTCTTT
21388 TTCTTTCTTT
1 TTCTTTCTTT
21398 TTCTTTCTTT
1 TTCTTTCTTT
21408 TTCT
1 TTCT
21412 CTTTCTCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (10 bp):
TTCTTTCTTT
Found at i:22465 original size:15 final size:15
Alignment explanation
Indices: 22445--22478 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
22435 TGTGGGGGCA
22445 TCTTCATCCTTCTCC
1 TCTTCATCCTTCTCC
*
22460 TCTTCATCCTTCTTC
1 TCTTCATCCTTCTCC
22475 TCTT
1 TCTT
22479 TAGTTCCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.06, C:0.41, G:0.00, T:0.53
Consensus pattern (15 bp):
TCTTCATCCTTCTCC
Found at i:36792 original size:49 final size:49
Alignment explanation
Indices: 36735--37409 Score: 499
Period size: 49 Copynumber: 13.8 Consensus size: 49
36725 AAAGTTGAAG
* * *
36735 AGGGACAGATTAAAGCCGTAATGGTGAATCTTACACCTTAAAATCGAAA
1 AGGGACAGATTAAAGCCGTAACGATGAATCTTACACCTCAAAATCGAAA
* *
36784 AGGGACAGATTAAAGCCGCAACAATGAATCTTACACC-CTAAAATCGAATA
1 AGGGACAGATTAAAGCCGTAACGATGAATCTTACACCTC-AAAATCGAA-A
* ***
36834 A-GGACAAATTAAAGCCGTAGTAATGAATCTTACACCTCAAAA-CAGAAA
1 AGGGACAGATTAAAGCCGTAACGATGAATCTTACACCTCAAAATC-GAAA
* * *** *
36882 AAGGACATATTAAAGCTACAACGGTGAATCTTACACCTCAAAA-CAGAAA
1 AGGGACAGATTAAAGCCGTAACGATGAATCTTACACCTCAAAATC-GAAA
* * *** * * * * *
36931 AAGGACATATTAAAGCTACAACGGTGAATCTTATACCCCAAAACCAAAA
1 AGGGACAGATTAAAGCCGTAACGATGAATCTTACACCTCAAAATCGAAA
* * * * * *
36980 AGGAACAGATTAAAGCTGTAATGGTGAATCTTACACCCCAAAA-CTAAA
1 AGGGACAGATTAAAGCCGTAACGATGAATCTTACACCTCAAAATCGAAA
* * ** * *
37028 TAGGGATAGATTAAAGTCGTAACGAAAAATCTTACA--TCGTAAATCCGAAG
1 -AGGGACAGATTAAAGCCGTAACGATGAATCTTACACCTC-AAAAT-CGAAA
* * ** * *
37078 AGGGATAGATTAAAGCCGCAATAATGAATCTTACACCTCAAAATTGAAT
1 AGGGACAGATTAAAGCCGTAACGATGAATCTTACACCTCAAAATCGAAA
* * ** * *
37127 AGGGACAAATTAAAGCCGTAATGGCGAATCTTACACCCCAAAATCGAAG
1 AGGGACAGATTAAAGCCGTAACGATGAATCTTACACCTCAAAATCGAAA
* * ** * * *
37176 ACGGATAGATTAAAGTTGTAACGGTAAATCTTACACCGT-AAAA-CTGAAT
1 AGGGACAGATTAAAGCCGTAACGATGAATCTTACACC-TCAAAATC-GAAA
* * ** *
37225 AGGGATAGATTAAAGTCACAACGATGAATCTTACACCATAAAAAT-GAAA
1 AGGGACAGATTAAAGCCGTAACGATGAATCTTACACC-TCAAAATCGAAA
* * *
37274 AGGGACAGATTAAAGCCATAATGATGAATCTTACACC-CTAAAATCGAAT
1 AGGGACAGATTAAAGCCGTAACGATGAATCTTACACCTC-AAAATCGAAA
* * * * * *
37323 AGAGACAAATTAAAGTCGCAACGATGAATCTTACACCCTTAAAATTGAAA
1 AGGGACAGATTAAAGCCGTAACGATGAATCTTACA-CCTCAAAATCGAAA
* * * *
37373 AGGGACAAATTAAAGCTGTAATGACGAATCTTACACC
1 AGGGACAGATTAAAGCCGTAACGATGAATCTTACACC
37410 CCTAAACCCG
Statistics
Matches: 509, Mismatches: 97, Indels: 40
0.79 0.15 0.06
Matches are distributed among these distances:
47 1 0.00
48 16 0.03
49 436 0.86
50 54 0.11
51 2 0.00
ACGTcount: A:0.44, C:0.18, G:0.17, T:0.21
Consensus pattern (49 bp):
AGGGACAGATTAAAGCCGTAACGATGAATCTTACACCTCAAAATCGAAA
Found at i:37483 original size:100 final size:100
Alignment explanation
Indices: 37202--37512 Score: 270
Period size: 100 Copynumber: 3.1 Consensus size: 100
37192 TGTAACGGTA
* * * * * * * * * * *
37202 AATCTTACA-CCGTAAAACTGAATAGGGATAGATTAAAGTCACAACGATGAATCTTACA-CCATA
1 AATCTTACACCCCTAAAACCGAAGAGAGACAAATTAAAGTCGCAAAGATGAACCGTACACCCCTA
* * * *
37265 AAAATGAAAAGGGACAGATTAAAGCCATAATGATG
66 AAACTGAAAAGGGACAAATTAAAGCCGTAATGACG
* * * * * *
37300 AATCTTACA-CCCTAAAATCGAATAGAGACAAATTAAAGTCGCAACGATGAATCTTACACCCTTA
1 AATCTTACACCCCTAAAACCGAAGAGAGACAAATTAAAGTCGCAAAGATGAACCGTACACCCCTA
* *
37364 AAATTGAAAAGGGACAAATTAAAGCTGTAATGACG
66 AAACTGAAAAGGGACAAATTAAAGCCGTAATGACG
* * * * *
37399 AATCTTACACCCCTAAACCCGAAGAGAGACAAATTGAATTCGTAAAGGTGAACCGTACACCCCTA
1 AATCTTACACCCCTAAAACCGAAGAGAGACAAATTAAAGTCGCAAAGATGAACCGTACACCCCTA
* * * * * *
37464 AAACTGTAGAA-GGATAAATTGAAGCCGCAAAGGCG
66 AAACTG-AAAAGGGACAAATTAAAGCCGTAATGACG
*
37499 AATCTTATACCCCT
1 AATCTTACACCCCT
37513 GAAGTTGCAG
Statistics
Matches: 177, Mismatches: 33, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
98 51 0.29
99 43 0.24
100 80 0.45
101 3 0.02
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.21
Consensus pattern (100 bp):
AATCTTACACCCCTAAAACCGAAGAGAGACAAATTAAAGTCGCAAAGATGAACCGTACACCCCTA
AAACTGAAAAGGGACAAATTAAAGCCGTAATGACG
Found at i:39244 original size:14 final size:14
Alignment explanation
Indices: 39225--39271 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
39215 TTATTGTCAT
39225 TATTACTATGATTA
1 TATTACTATGATTA
*
39239 TATTACTAT-TTTA
1 TATTACTATGATTA
39252 TTTATTACTATGATTA
1 --TATTACTATGATTA
39268 TATT
1 TATT
39272 TTATTTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
13 3 0.11
14 13 0.46
15 9 0.32
16 3 0.11
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.57
Consensus pattern (14 bp):
TATTACTATGATTA
Found at i:39256 original size:29 final size:28
Alignment explanation
Indices: 39224--39281 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 28
39214 TTTATTGTCA
39224 TTATTACTATGATTATATTACTATTTTAT
1 TTATTACTATGATTATATT-CTATTTTAT
*
39253 TTATTACTATGATTATATTTTATTTTAT
1 TTATTACTATGATTATATTCTATTTTAT
39281 T
1 T
39282 GTGTTATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.62
Consensus pattern (28 bp):
TTATTACTATGATTATATTCTATTTTAT
Done.