Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005987.1 Kokia drynarioides strain JFW-HI SEQ_120407, 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: 12298
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1020 original size:24 final size:24
Alignment explanation
Indices: 959--1021 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
949 TAGACTAATA
* *
959 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
* * *
983 AGAGTTTAATTGAAACAATTAAAT
1 AGAGTTTAACTGAAACAAATAAAC
1007 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
1022 GATTATTTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.27
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:2970 original size:24 final size:24
Alignment explanation
Indices: 2942--3028 Score: 77
Period size: 24 Copynumber: 3.7 Consensus size: 24
2932 TAGACTAATA
* * *
2942 AGAGTTTGACTCATACAAATAAAC
1 AGAGTTTAACTCAAAAAAATAAAC
* *
2966 AGAGTTTAATTGAAAAAAATAAAC
1 AGAGTTTAACTCAAAAAAATAAAC
* * * *
2990 AGAGTTTAATTGAAACAATTAAAC
1 AGAGTTTAACTCAAAAAAATAAAC
*
3014 AGAGCTTAACT-AAAA
1 AGAGTTTAACTCAAAA
3029 GATTATTTCT
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
23 3 0.06
24 50 0.94
ACGTcount: A:0.52, C:0.10, G:0.13, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTCAAAAAAATAAAC
Found at i:3876 original size:79 final size:79
Alignment explanation
Indices: 3745--3899 Score: 310
Period size: 79 Copynumber: 2.0 Consensus size: 79
3735 AGGCGAAATT
3745 ACTGTTTAAGAGATCAATGAGACTCATATTGTCCTAATCCCTAAGGTTAGTAATCCTCGTTCTAT
1 ACTGTTTAAGAGATCAATGAGACTCATATTGTCCTAATCCCTAAGGTTAGTAATCCTCGTTCTAT
3810 TACTCAATATCATC
66 TACTCAATATCATC
3824 ACTGTTTAAGAGATCAATGAGACTCATATTGTCCTAATCCCTAAGGTTAGTAATCCTCGTTCTAT
1 ACTGTTTAAGAGATCAATGAGACTCATATTGTCCTAATCCCTAAGGTTAGTAATCCTCGTTCTAT
3889 TACTCAATATC
66 TACTCAATATC
3900 GTCCCATTAG
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 76 1.00
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.35
Consensus pattern (79 bp):
ACTGTTTAAGAGATCAATGAGACTCATATTGTCCTAATCCCTAAGGTTAGTAATCCTCGTTCTAT
TACTCAATATCATC
Found at i:5342 original size:49 final size:49
Alignment explanation
Indices: 5284--5396 Score: 181
Period size: 49 Copynumber: 2.3 Consensus size: 49
5274 AGATTTGCCT
* * *
5284 TTGCGACTTCAATCTGCTTCTCCTTATCTTCAAAGTATAAGATTCGTCG
1 TTGCAACTTCAATCTGCTTCTCCTCATCTTCAAAGTATAAGATTCATCG
*
5333 TTGCAACTTCAATCTGCTTCTCCTCATCTTCAGAGTATAAGATTCATCG
1 TTGCAACTTCAATCTGCTTCTCCTCATCTTCAAAGTATAAGATTCATCG
*
5382 TTACAACTTCAATCT
1 TTGCAACTTCAATCT
5397 TTCCCTTCAC
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 59 1.00
ACGTcount: A:0.25, C:0.26, G:0.12, T:0.38
Consensus pattern (49 bp):
TTGCAACTTCAATCTGCTTCTCCTCATCTTCAAAGTATAAGATTCATCG
Found at i:5420 original size:49 final size:48
Alignment explanation
Indices: 5318--5573 Score: 212
Period size: 49 Copynumber: 5.2 Consensus size: 48
5308 TATCTTCAAA
* *
5318 GTATAAGATTCGTCGTTGCAACTTCAATCTGCTTCTCCT--CATCT-TCAGA
1 GTATAAGATTCGTCGTTACAACTTCAATCT--TTC-CCTCACATCTCT-AGG
* * *
5367 GTATAAGATTCATCGTTACAACTTCAATCTTTCCCTTCACGTCTATAGG
1 GTATAAGATTCGTCGTTACAACTTCAATCTTTCCC-TCACATCTCTAGG
* * * * * * *
5416 GTATAAGGTTTGTCATTTCAGCTTCAACCTTTCCCTCCATATCTCTAGG
1 GTATAAGATTCGTCGTTACAACTTCAATCTTTCCCT-CACATCTCTAGG
* * * * *
5465 GTACAAGATTCGTCATTACATCTTCAATCTTTCCCTCAACATTTCTAAG
1 GTATAAGATTCGTCGTTACAACTTCAATCTTTCCCTC-ACATCTCTAGG
* ****
5514 GTAAAAGATTCGTCGTTGTGGCTTCAATCTTTCCCTCAACATCTCTAGG
1 GTATAAGATTCGTCGTTACAACTTCAATCTTTCCCTC-ACATCTCTAGG
*
5563 GTATATGATTC
1 GTATAAGATTC
5574 AACGTTTCCT
Statistics
Matches: 168, Mismatches: 33, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
46 2 0.01
47 4 0.02
48 2 0.01
49 159 0.95
50 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.14, T:0.37
Consensus pattern (48 bp):
GTATAAGATTCGTCGTTACAACTTCAATCTTTCCCTCACATCTCTAGG
Found at i:6191 original size:112 final size:112
Alignment explanation
Indices: 6013--6219 Score: 324
Period size: 112 Copynumber: 1.8 Consensus size: 112
6003 CCACTAATTG
*** *
6013 TTATTTCAATGCAAAAATGCTTAAACAAGATTGTAAGGTGGATAAAATTGAATTTTATTGGAGGC
1 TTATTTCAATGCAAAAATGCTTAAACAAGATCACAAGATGGATAAAATTGAATTTTATTGGAGGC
*
6078 AAAGCTCGCATGAATGATAAGATTAAAAATCATTGGTCCACTAACCA
66 AAAGCTCGCATGAATGAAAAGATTAAAAATCATTGGTCCACTAACCA
* * * *
6125 TTATTTCGATGCAAAAATGCTTGAACAGGGTCACAAGATGGATAAAATTGAATTTTATTGGAGGC
1 TTATTTCAATGCAAAAATGCTTAAACAAGATCACAAGATGGATAAAATTGAATTTTATTGGAGGC
*
6190 AAAGCTCGCATGAATTAAAAGATTAAAAAT
66 AAAGCTCGCATGAATGAAAAGATTAAAAAT
6220 GACCCACATT
Statistics
Matches: 85, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
112 85 1.00
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.29
Consensus pattern (112 bp):
TTATTTCAATGCAAAAATGCTTAAACAAGATCACAAGATGGATAAAATTGAATTTTATTGGAGGC
AAAGCTCGCATGAATGAAAAGATTAAAAATCATTGGTCCACTAACCA
Found at i:6548 original size:14 final size:13
Alignment explanation
Indices: 6529--6604 Score: 54
Period size: 14 Copynumber: 5.8 Consensus size: 13
6519 TCGACCACTC
6529 CTTTTTCTATTTCT
1 CTTTTTCT-TTTCT
*
6543 CTTTTTTTCTTTCTT
1 CTTTTTCT-TTTC-T
6558 CTTTTT-TTTTCT
1 CTTTTTCTTTTCT
*
6570 -TTTTTC-TCT-T
1 CTTTTTCTTTTCT
6580 CTTTTTC-TTTCTT
1 CTTTTTCTTTTC-T
6593 CTTCTTTCTTTT
1 CTT-TTTCTTTT
6605 TTTTTTTTGG
Statistics
Matches: 51, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
10 1 0.02
11 15 0.29
12 1 0.02
13 8 0.16
14 16 0.31
15 10 0.20
ACGTcount: A:0.01, C:0.21, G:0.00, T:0.78
Consensus pattern (13 bp):
CTTTTTCTTTTCT
Found at i:6569 original size:10 final size:10
Alignment explanation
Indices: 6556--6609 Score: 63
Period size: 10 Copynumber: 5.2 Consensus size: 10
6546 TTTTTCTTTC
6556 TTCTTTTTTT
1 TTCTTTTTTT
6566 TTCTTTTTTCT
1 TTCTTTTTT-T
*
6577 CTTCTTTTTCT
1 -TTCTTTTTTT
* *
6588 TTCTTCTTCT
1 TTCTTTTTTT
6598 TTCTTTTTTT
1 TTCTTTTTTT
6608 TT
1 TT
6610 TTTGGGTGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
10 28 0.74
11 2 0.05
12 8 0.21
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:6571 original size:25 final size:24
Alignment explanation
Indices: 6545--6612 Score: 88
Period size: 22 Copynumber: 3.0 Consensus size: 24
6535 CTATTTCTCT
6545 TTTTTTCTTTCTTCTTTTTTTTTC
1 TTTTTTCTTTCTTCTTTTTTTTTC
*
6569 TTTTTTC--TCTTCTTTTTCTTTC
1 TTTTTTCTTTCTTCTTTTTTTTTC
* *
6591 -TTCTTCTTTCTTTTTTTTTTTT
1 TTTTTTCTTTCTTCTTTTTTTTT
6613 GGGTGAAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
21 5 0.13
22 14 0.37
23 12 0.32
24 7 0.18
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (24 bp):
TTTTTTCTTTCTTCTTTTTTTTTC
Found at i:6591 original size:35 final size:35
Alignment explanation
Indices: 6530--6611 Score: 114
Period size: 35 Copynumber: 2.3 Consensus size: 35
6520 CGACCACTCC
*
6530 TTTTTC-TATTTCTCTTTTTTTCTTTCTTCTT-TT
1 TTTTTCTTTTTTCTCTTTTTTTCTTTCTTCTTCTT
6563 TTTTTCTTTTTTCTCTTCTTTTTCTTTCTTCTTCTT
1 TTTTTCTTTTTTCTCTT-TTTTTCTTTCTTCTTCTT
*
6599 TCTTTTTTTTTTT
1 T-TTTTCTTTTTT
6612 TGGGTGAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
33 6 0.14
34 9 0.21
35 15 0.35
36 3 0.07
37 10 0.23
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.80
Consensus pattern (35 bp):
TTTTTCTTTTTTCTCTTTTTTTCTTTCTTCTTCTT
Found at i:7533 original size:10 final size:10
Alignment explanation
Indices: 7513--7549 Score: 56
Period size: 10 Copynumber: 3.5 Consensus size: 10
7503 TTCATCTTAA
7513 TTTTCTTTTTC
1 TTTT-TTTTTC
7524 TTTTTTTTTC
1 TTTTTTTTTC
7534 TTTTTTTTTC
1 TTTTTTTTTC
7544 TCTTTT
1 T-TTTT
7550 CCTTTTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 17 0.68
11 8 0.32
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:7534 original size:16 final size:16
Alignment explanation
Indices: 7513--7558 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
7503 TTCATCTTAA
7513 TTTTCTTTTTCTTTTT-
1 TTTTCTTTTT-TTTTTC
7529 TTTTCTTTTTTTTTCTC
1 TTTTCTTTTTTTTT-TC
7546 TTTTCCTTTTTTT
1 TTTT-CTTTTTTT
7559 GGGTTTCAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 4 0.15
16 11 0.41
17 4 0.15
18 8 0.30
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (16 bp):
TTTTCTTTTTTTTTTC
Found at i:10883 original size:12 final size:14
Alignment explanation
Indices: 10829--10892 Score: 53
Period size: 13 Copynumber: 4.5 Consensus size: 14
10819 ACAAAATAAA
*
10829 TAAATAAAAACAAT
1 TAAATAAATACAAT
10843 ATATGAATAAAATA-AAT
1 -TA--AAT-AAATACAAT
10860 TAAATAAATACAAT
1 TAAATAAATACAAT
10874 T-AAT-AATACAAT
1 TAAATAAATACAAT
*
10886 AAAATAA
1 TAAATAA
10893 TAATGACAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
12 8 0.20
13 11 0.27
14 8 0.20
15 2 0.05
16 2 0.05
17 6 0.15
18 4 0.10
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.27
Consensus pattern (14 bp):
TAAATAAATACAAT
Found at i:10887 original size:35 final size:30
Alignment explanation
Indices: 10821--10892 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 30
10811 CAATAATGAC
*
10821 AAAATAAATAAATAAAAACAATATATGAAT
1 AAAATAAATAAATAAAAACAATATATCAAT
*
10851 AAAATAAATTAAATAAATACAATTAATAATACAAT
1 AAAATAAA-TAAATAAAAACAA-T-AT-AT-CAAT
10886 AAAATAA
1 AAAATAA
10893 TAATGACAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 8 0.23
31 12 0.34
32 1 0.03
33 2 0.06
34 2 0.06
35 10 0.29
ACGTcount: A:0.69, C:0.04, G:0.01, T:0.25
Consensus pattern (30 bp):
AAAATAAATAAATAAAAACAATATATCAAT
Found at i:10893 original size:16 final size:17
Alignment explanation
Indices: 10874--10905 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
10864 TAAATACAAT
10874 TAATAAT-ACAATAAAA
1 TAATAATGACAATAAAA
10890 TAATAATGACAATAAA
1 TAATAATGACAATAAA
10906 TGTCAATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.66, C:0.06, G:0.03, T:0.25
Consensus pattern (17 bp):
TAATAATGACAATAAAA
Found at i:11120 original size:24 final size:23
Alignment explanation
Indices: 11084--11166 Score: 107
Period size: 23 Copynumber: 3.6 Consensus size: 23
11074 AATAATAAAT
11084 AAAATAAAT-AATTAAAATCATG
1 AAAATAAATAAATTAAAATCATG
*
11106 AAAACTAAACAAATTAAAATCATG
1 AAAA-TAAATAAATTAAAATCATG
*
11130 CAAATTAAATAAA-TAAAATCATG
1 -AAAATAAATAAATTAAAATCATG
11153 CAAAATAAATAAAT
1 -AAAATAAATAAAT
11167 AAATAAAATA
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
22 4 0.08
23 26 0.49
24 20 0.38
25 3 0.06
ACGTcount: A:0.64, C:0.08, G:0.04, T:0.24
Consensus pattern (23 bp):
AAAATAAATAAATTAAAATCATG
Done.