Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002910.1 Kokia drynarioides strain JFW-HI SEQ_115339, 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: 17385
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Found at i:1456 original size:36 final size:36
Alignment explanation
Indices: 1416--1502 Score: 167
Period size: 36 Copynumber: 2.4 Consensus size: 36
1406 GATTTATGCA
1416 CCGGATTTTGTTTTATAGCCATAAGATACAACAGCG
1 CCGGATTTTGTTTTATAGCCATAAGATACAACAGCG
1452 CCGGATTTTGTTTTATAGCCATAAGATACAACAGCG
1 CCGGATTTTGTTTTATAGCCATAAGATACAACAGCG
1488 CCGGATTTT-TTTTAT
1 CCGGATTTTGTTTTAT
1503 TTATTTAACT
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 6 0.12
36 45 0.88
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (36 bp):
CCGGATTTTGTTTTATAGCCATAAGATACAACAGCG
Found at i:4024 original size:20 final size:21
Alignment explanation
Indices: 3999--4037 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
3989 TCAAAATAGA
3999 TATTAAAATTT-TATAAAAAT
1 TATTAAAATTTATATAAAAAT
4019 TATTAAAATTTATATAAAA
1 TATTAAAATTTATATAAAA
4038 TCATAAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TATTAAAATTTATATAAAAAT
Found at i:4038 original size:11 final size:11
Alignment explanation
Indices: 4002--4038 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
3992 AAATAGATAT
4002 TAAAATTT-TA
1 TAAAATTTATA
*
4012 TAAAAATTAT-
1 TAAAATTTATA
4022 TAAAATTTATA
1 TAAAATTTATA
4033 TAAAAT
1 TAAAAT
4039 CATAAAAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 16 0.70
11 7 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TAAAATTTATA
Found at i:4044 original size:19 final size:20
Alignment explanation
Indices: 4000--4045 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
3990 CAAAATAGAT
*
4000 ATTAAAATTTTATAAAAATT
1 ATTAAAATTTTATAAAAATC
4020 ATTAAAA-TTTATATAAAATC
1 ATTAAAATTTTATA-AAAATC
4040 A-TAAAA
1 ATTAAAA
4046 ACTTGAAGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
ATTAAAATTTTATAAAAATC
Found at i:4208 original size:24 final size:24
Alignment explanation
Indices: 4159--4208 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
4149 TGAATCAATT
* *
4159 TTTTTAATATTTTTTATCTTTTAA
1 TTTTTAATATTTTTTATCATTGAA
*
4183 TTTTTAATATTTTATT-TGATTGAA
1 TTTTTAATATTTT-TTATCATTGAA
4207 TT
1 TT
4209 GGATAATTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 20 0.91
25 2 0.09
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (24 bp):
TTTTTAATATTTTTTATCATTGAA
Found at i:4499 original size:9 final size:9
Alignment explanation
Indices: 4460--4511 Score: 52
Period size: 10 Copynumber: 5.6 Consensus size: 9
4450 TTTATGATTT
4460 TTTTTATAA
1 TTTTTATAA
*
4469 GTTTATATTAA
1 -TTTTTA-TAA
*
4480 TTTTAAT-A
1 TTTTTATAA
4488 TTTTTATAA
1 TTTTTATAA
4497 TTTTTTATAA
1 -TTTTTATAA
4507 TTTTT
1 TTTTT
4512 TTGTTATTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
8 7 0.20
9 7 0.20
10 18 0.51
11 3 0.09
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (9 bp):
TTTTTATAA
Found at i:5102 original size:21 final size:21
Alignment explanation
Indices: 5078--5121 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5068 ATTACTCGAA
*
5078 TTAA-ATATAATGTTATTTTAT
1 TTAATATATAAT-TAATTTTAT
*
5099 TTAATTTATAATTAATTTTAT
1 TTAATATATAATTAATTTTAT
5120 TT
1 TT
5122 TTTATGATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
TTAATATATAATTAATTTTAT
Found at i:5552 original size:62 final size:63
Alignment explanation
Indices: 5444--5561 Score: 157
Period size: 62 Copynumber: 1.9 Consensus size: 63
5434 TCCCCACCCA
* * *
5444 AAAATTTTGGGATATTTTGATTTCTCCCTTGAAATTTTTAGCAAA-TTTTAATTAAATTCTCC
1 AAAATTTTGGGAAATTTTGATTTCTCCCTTAAAAGTTTTAGCAAATTTTTAATTAAATTCTCC
* * * * *
5506 AAAATTTTTGGAAATTTTTATTTCTCTCTTAAAAGTTTTCGGAAATTTTTAATTAA
1 AAAATTTTGGGAAATTTTGATTTCTCCCTTAAAAGTTTTAGCAAATTTTTAATTAA
5562 GCTCTCTTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
62 37 0.79
63 10 0.21
ACGTcount: A:0.32, C:0.10, G:0.09, T:0.48
Consensus pattern (63 bp):
AAAATTTTGGGAAATTTTGATTTCTCCCTTAAAAGTTTTAGCAAATTTTTAATTAAATTCTCC
Found at i:6342 original size:3 final size:3
Alignment explanation
Indices: 6334--6364 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
6324 GTGTGGCAAT
*
6334 GTA GTA GTA GTA GTA GTA GCA GTA GTA GTA G
1 GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA G
6365 GCATTTGCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.03, G:0.35, T:0.29
Consensus pattern (3 bp):
GTA
Found at i:7876 original size:16 final size:16
Alignment explanation
Indices: 7821--7876 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 16
7811 TAATGACCTT
* *
7821 TATATTTTCATAAATA
1 TATATTTACTTAAATA
* *
7837 AATA-TTATTTAAAT-
1 TATATTTACTTAAATA
*
7851 TATTTTTACTTAAATA
1 TATATTTACTTAAATA
7867 TATATTTACT
1 TATATTTACT
7877 AAAACTAAAT
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
14 2 0.07
15 16 0.53
16 12 0.40
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (16 bp):
TATATTTACTTAAATA
Found at i:9569 original size:30 final size:29
Alignment explanation
Indices: 9533--9602 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
9523 ATAATTTATA
*
9533 AAAATTGGATCAA-ATCAAAATTTCATGTAT
1 AAAATTGCA-CAATATCAAAA-TTCATGTAT
9563 AAAATTGCACAATATCAAAATTCATGTAT
1 AAAATTGCACAATATCAAAATTCATGTAT
* *
9592 ACAATTACACA
1 AAAATTGCACA
9603 TTAAATCATT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 21 0.58
30 15 0.42
ACGTcount: A:0.49, C:0.14, G:0.07, T:0.30
Consensus pattern (29 bp):
AAAATTGCACAATATCAAAATTCATGTAT
Found at i:9597 original size:29 final size:30
Alignment explanation
Indices: 9546--9602 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
9536 ATTGGATCAA
*
9546 ATCAAAATTTCATGTATAAAATTGCACAAT
1 ATCAAAATTTCATGTATAAAATTACACAAT
*
9576 ATCAAAA-TTCATGTATACAATTACACA
1 ATCAAAATTTCATGTATAAAATTACACA
9603 TTAAATCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.32
Consensus pattern (30 bp):
ATCAAAATTTCATGTATAAAATTACACAAT
Found at i:10009 original size:7 final size:7
Alignment explanation
Indices: 9997--10022 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
9987 ATTGGAAGGT
9997 ATAATAA
1 ATAATAA
10004 ATAATAA
1 ATAATAA
10011 ATAATAA
1 ATAATAA
10018 ATAAT
1 ATAAT
10023 GGTTGGGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
ATAATAA
Found at i:12228 original size:15 final size:16
Alignment explanation
Indices: 12199--12228 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12189 TAAAATGTTA
12199 TTATAAAAGATAATTG
1 TTATAAAAGATAATTG
12215 TTATAAAA-ATAATT
1 TTATAAAAGATAATT
12229 ATTGACAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (16 bp):
TTATAAAAGATAATTG
Found at i:14672 original size:23 final size:22
Alignment explanation
Indices: 14634--14702 Score: 81
Period size: 22 Copynumber: 3.2 Consensus size: 22
14624 AAATTTTAAC
* *
14634 TTTTAATATAATTTTTTAAATT
1 TTTTAATATAAATTTTTGAATT
14656 TTTTAAATATAAA-TTTTGAATT
1 TTTT-AATATAAATTTTTGAATT
14678 TTTT--TATAAATATTTTGAATT
1 TTTTAATATAAAT-TTTTGAATT
14699 TTTT
1 TTTT
14703 TTTTTTTTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
19 6 0.14
21 13 0.31
22 16 0.38
23 7 0.17
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (22 bp):
TTTTAATATAAATTTTTGAATT
Found at i:16276 original size:11 final size:11
Alignment explanation
Indices: 16262--16292 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
16252 TACAAAAATC
16262 AAAGAAAAAAA
1 AAAGAAAAAAA
16273 AAAGAAAAAAA
1 AAAGAAAAAAA
16284 AAAGAAAAA
1 AAAGAAAAA
16293 GGGGGGTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAAA
Found at i:16391 original size:29 final size:29
Alignment explanation
Indices: 16326--16704 Score: 271
Period size: 29 Copynumber: 13.1 Consensus size: 29
16316 GAGAATTCGA
*
16326 GGTTAAAATGTAATTTTG-GAAATGTTTAAG
1 GGTTAAAATATAATTTTGAGAAA-GTTT-AG
* * **
16356 GG-CAAAATATAATTATGAGAAAGTTCGG
1 GGTTAAAATATAATTTTGAGAAAGTTTAG
* * *
16384 GGTTAAAATGTAATATT-AGAGAAGTTTGG
1 GGTTAAAATATAATTTTGAGA-AAGTTTAG
* *
16413 GGTTAAAATATAATTTT-AGGAAGGTTTGGG
1 GGTTAAAATATAATTTTGA-GAAAGTTT-AG
* * *
16443 GGTCAAAATGTAATTTTG-GATAAGTTTTG
1 GGTTAAAATATAATTTTGAGA-AAGTTTAG
* *
16472 GAGTTAAAATGA-AATTTTGAAAAAATTTAG
1 G-GTTAAAAT-ATAATTTTGAGAAAGTTTAG
* *
16502 GGTAAAAAATATAATTTTGGGAAAGTTTAG
1 GGT-TAAAATATAATTTTGAGAAAGTTTAG
*
16532 GGTTAAAATATAATTTT-AGAAAAGTTTAA
1 GGTTAAAATATAATTTTGAG-AAAGTTTAG
*
16561 GGTCAAAATATAATTTTG-GAAAAGTTTAG
1 GGTTAAAATATAATTTTGAG-AAAGTTTAG
* * * *
16590 GGTCAAAATATAATTTTCAAAAAGTTTAT
1 GGTTAAAATATAATTTTGAGAAAGTTTAG
*
16619 GGTCAAAATATAATTTT-AGAAAAGTTT-G
1 GGTTAAAATATAATTTTGAG-AAAGTTTAG
* * * * * *
16647 GGGT-CAATGTAATTTT-AAAAAATTTAA
1 GGTTAAAATATAATTTTGAGAAAGTTTAG
*
16674 GGTTAAAATATGATTTCT-AGAAAGTTTAG
1 GGTTAAAATATAATTT-TGAGAAAGTTTAG
16703 GG
1 GG
16705 ACCTACTAAG
Statistics
Matches: 280, Mismatches: 50, Indels: 39
0.76 0.14 0.11
Matches are distributed among these distances:
26 6 0.02
27 14 0.05
28 18 0.06
29 167 0.60
30 74 0.26
31 1 0.00
ACGTcount: A:0.41, C:0.02, G:0.21, T:0.36
Consensus pattern (29 bp):
GGTTAAAATATAATTTTGAGAAAGTTTAG
Found at i:16651 original size:58 final size:57
Alignment explanation
Indices: 16330--16704 Score: 310
Period size: 58 Copynumber: 6.5 Consensus size: 57
16320 ATTCGAGGTT
* * * * ** *
16330 AAAATGTAATTTTGGAAATGTTTAAGGG-CAAAATATAATTATGAGAAAGTTCGGGGTT
1 AAAATATAATTTTGGAAAAGTTT-AGGGTCAAAATATAATT-TTAAAAAGTTTAGGGTC
* * * * * * * * *
16388 AAAATGTAATATTAGAGAAGTTTGGGGTTAAAATATAATTTTAGGAAGGTTTGGGGGTC
1 AAAATATAATTTTGGAAAAGTTTAGGGTCAAAATATAATTTTA-AAAAGTTT-AGGGTC
* * * * * *
16447 AAAATGTAATTTTGGATAAGTTTTGGAGTTAAAATGA-AATTTTGAAAAAATTTAGGGTAA
1 AAAATATAATTTTGGAAAAGTTTAGG-GTCAAAAT-ATAATTTT-AAAAAGTTTAGGGT-C
* * *
16507 AAAATATAATTTTGGGAAAGTTTAGGGTTAAAATATAATTTTAGAAAAGTTTAAGGTC
1 AAAATATAATTTTGGAAAAGTTTAGGGTCAAAATATAATTTTA-AAAAGTTTAGGGTC
*
16565 AAAATATAATTTTGGAAAAGTTTAGGGTCAAAATATAATTTTCAAAAAGTTTATGGTC
1 AAAATATAATTTTGGAAAAGTTTAGGGTCAAAATATAATTTT-AAAAAGTTTAGGGTC
* * * * * *
16623 AAAATATAATTTTAGAAAAGTTTGGGGTC--AATGTAATTTTAAAAAATTTAAGGTT
1 AAAATATAATTTTGGAAAAGTTTAGGGTCAAAATATAATTTTAAAAAGTTTAGGGTC
* *
16678 AAAATATGATTTCTAG-AAAGTTTAGGG
1 AAAATATAATTT-TGGAAAAGTTTAGGG
16705 ACCTACTAAG
Statistics
Matches: 269, Mismatches: 37, Indels: 25
0.81 0.11 0.08
Matches are distributed among these distances:
55 33 0.12
56 13 0.05
57 5 0.02
58 118 0.44
59 57 0.21
60 41 0.15
61 2 0.01
ACGTcount: A:0.41, C:0.02, G:0.21, T:0.35
Consensus pattern (57 bp):
AAAATATAATTTTGGAAAAGTTTAGGGTCAAAATATAATTTTAAAAAGTTTAGGGTC
Done.