Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012721.1 Kokia drynarioides strain JFW-HI SEQ_127732, 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: 58983
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1837 original size:45 final size:45
Alignment explanation
Indices: 1773--1902 Score: 170
Period size: 45 Copynumber: 2.9 Consensus size: 45
1763 GCATAGCTCA
* *
1773 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGTCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCACAATAC
* * * *
1818 TCAAGCCAAGGATATCAGCCCCAATTTGACAAGCCACAACAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCACAATAC
** * *
1863 TCAAGGGAAGGATATCAGGCTAAGTTTGACGAGCCACCAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCAC
1903 GATAATCTAT
Statistics
Matches: 71, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 71 1.00
ACGTcount: A:0.35, C:0.28, G:0.20, T:0.18
Consensus pattern (45 bp):
TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCACAATAC
Found at i:2229 original size:28 final size:27
Alignment explanation
Indices: 2176--2251 Score: 64
Period size: 28 Copynumber: 2.8 Consensus size: 27
2166 TTAAACCCTA
* * * *
2176 AAACC-TAAATTATAAGCCCTAGACTT
1 AAACCTTAAACTATAAACACTAAACTT
2202 GAAACCTTAAACTATAAACACTAAACTT
1 -AAACCTTAAACTATAAACACTAAACTT
* **
2230 AAAACTCTAAACCGTAAACACT
1 AAACCT-TAAACTATAAACACT
2252 GGATTGATTA
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
27 10 0.25
28 30 0.75
ACGTcount: A:0.47, C:0.24, G:0.05, T:0.24
Consensus pattern (27 bp):
AAACCTTAAACTATAAACACTAAACTT
Found at i:6079 original size:4 final size:4
Alignment explanation
Indices: 6072--6132 Score: 68
Period size: 4 Copynumber: 14.8 Consensus size: 4
6062 TATTTTCTTC
* * *
6072 TTCT TTCT TTCCT CTCC TTCT TCCT TTCT TTCT TTCT TTCT TTCTT TTCT
1 TTCT TTCT TT-CT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTC-T TTCT
*
6122 TTCT GTCT TTC
1 TTCT TTCT TTC
6133 CCATTTATTT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
4 40 0.85
5 7 0.15
ACGTcount: A:0.00, C:0.31, G:0.02, T:0.67
Consensus pattern (4 bp):
TTCT
Found at i:6120 original size:21 final size:21
Alignment explanation
Indices: 6072--6132 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 21
6062 TATTTTCTTC
* *
6072 TTCTTTCTTTCCTCTCCTTCT
1 TTCTTTCTTTTCTCTCTTTCT
* *
6093 TCCTTTC-TTTCTTTCTTTCT
1 TTCTTTCTTTTCTCTCTTTCT
*
6113 TTCTTT-TCTTTCTGTCTTTC
1 TTCTTTCT-TTTCTCTCTTTC
6133 CCATTTATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.00, C:0.31, G:0.02, T:0.67
Consensus pattern (21 bp):
TTCTTTCTTTTCTCTCTTTCT
Found at i:7590 original size:19 final size:17
Alignment explanation
Indices: 7548--7591 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
7538 AACGTTTGAG
*
7548 TATCTGTAGTATATTTA
1 TATCTGTAGTATATCTA
*
7565 CATCTGTAGCTATATCCTA
1 TATCTGTAG-TATAT-CTA
7584 TATCTGTA
1 TATCTGTA
7592 TTTGGAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 8 0.36
18 5 0.23
19 9 0.41
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.45
Consensus pattern (17 bp):
TATCTGTAGTATATCTA
Found at i:8671 original size:27 final size:27
Alignment explanation
Indices: 8641--8731 Score: 173
Period size: 27 Copynumber: 3.4 Consensus size: 27
8631 TCTCCTTATC
*
8641 TTCATAATTTTAATTATGAAAAGGCAT
1 TTCATAATTTTAATTATGAAAGGGCAT
8668 TTCATAATTTTAATTATGAAAGGGCAT
1 TTCATAATTTTAATTATGAAAGGGCAT
8695 TTCATAATTTTAATTATGAAAGGGCAT
1 TTCATAATTTTAATTATGAAAGGGCAT
8722 TTCATAATTT
1 TTCATAATTT
8732 ATCTAATCGA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 63 1.00
ACGTcount: A:0.37, C:0.08, G:0.12, T:0.43
Consensus pattern (27 bp):
TTCATAATTTTAATTATGAAAGGGCAT
Found at i:10837 original size:29 final size:28
Alignment explanation
Indices: 10768--10825 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 28
10758 AATCTTTTTA
* *
10768 AAAAAAATAA-AATTGGGAATTTAAAAT
1 AAAAGAATAAGAATTAGGAATTTAAAAT
*
10795 AAAAGAATCGAGAATTAGGAATTTAAAAT
1 AAAAGAAT-AAGAATTAGGAATTTAAAAT
10824 AA
1 AA
10826 GAGTGATAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 7 0.27
28 1 0.04
29 18 0.69
ACGTcount: A:0.60, C:0.02, G:0.14, T:0.24
Consensus pattern (28 bp):
AAAAGAATAAGAATTAGGAATTTAAAAT
Found at i:11122 original size:17 final size:16
Alignment explanation
Indices: 11091--11129 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
11081 TCATCCTTCT
11091 AATTTT-CCACCTTTCC
1 AATTTTCCCACCTTT-C
*
11107 AATTTTCCCTCCTTTC
1 AATTTTCCCACCTTTC
11123 AATTTTC
1 AATTTTC
11130 TTTCCATTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.18, C:0.33, G:0.00, T:0.49
Consensus pattern (16 bp):
AATTTTCCCACCTTTC
Found at i:14990 original size:16 final size:15
Alignment explanation
Indices: 14971--15000 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
14961 AGTTTTTACC
14971 ATTTTTTCAAAAAATT
1 ATTTTTT-AAAAAATT
14987 ATTTTTTAAAAAAT
1 ATTTTTTAAAAAAT
15001 GACATTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTTTTAAAAAATT
Found at i:15007 original size:17 final size:15
Alignment explanation
Indices: 14970--15013 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 15
14960 TAGTTTTTAC
14970 CATTTTTTCAAAAAAT
1 CATTTTTT-AAAAAAT
*
14986 TATTTTTTAAAAAAT
1 CATTTTTTAAAAAAT
15001 GACATTTTTTAAA
1 --CATTTTTTAAA
15014 TTGGTATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 7 0.29
16 7 0.29
17 10 0.42
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (15 bp):
CATTTTTTAAAAAAT
Found at i:18872 original size:15 final size:15
Alignment explanation
Indices: 18852--18890 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
18842 TAATAAAATT
*
18852 ATTATTTTCATTTTA
1 ATTATTTTAATTTTA
*
18867 ATTA-TTTAATTTTT
1 ATTATTTTAATTTTA
18881 ATTATTTTAA
1 ATTATTTTAA
18891 AGGTGTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTATTTTAATTTTA
Found at i:28715 original size:11 final size:11
Alignment explanation
Indices: 28701--28750 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
28691 ATATTCAAAC
*
28701 AATAACAACAA
1 AATAATAACAA
*
28712 AATAGTAACAA
1 AATAATAACAA
*
28723 AATAATAGCAA
1 AATAATAACAA
*
28734 AATAATAGCAA
1 AATAATAACAA
28745 AATAAT
1 AATAAT
28751 GAAAAATAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 35 1.00
ACGTcount: A:0.66, C:0.10, G:0.06, T:0.18
Consensus pattern (11 bp):
AATAATAACAA
Found at i:28771 original size:11 final size:11
Alignment explanation
Indices: 28709--28769 Score: 70
Period size: 11 Copynumber: 5.6 Consensus size: 11
28699 ACAATAACAA
* *
28709 CAAAATAGTAA
1 CAAAATAATAG
28720 CAAAATAATAG
1 CAAAATAATAG
28731 CAAAATAATAG
1 CAAAATAATAG
28742 CAAAATAAT-G
1 CAAAATAATAG
* * *
28752 AAAAATAGTGG
1 CAAAATAATAG
28763 CAAAATA
1 CAAAATA
28770 GTAAAAACAA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
10 8 0.18
11 36 0.82
ACGTcount: A:0.62, C:0.08, G:0.11, T:0.18
Consensus pattern (11 bp):
CAAAATAATAG
Found at i:28776 original size:21 final size:21
Alignment explanation
Indices: 28701--28776 Score: 62
Period size: 22 Copynumber: 3.5 Consensus size: 21
28691 ATATTCAAAC
* * *
28701 AATAACAACAAAATAGTAACAA
1 AATAATAA-AAAATAATAGCAA
*
28723 AATAATAGCAAAATAATAGCAA
1 AATAATA-AAAAATAATAGCAA
* * *
28745 AATAATGAAAAATAGTGGCAA
1 AATAATAAAAAATAATAGCAA
*
28766 AATAGTAAAAA
1 AATAATAAAAA
28777 CAACAACATT
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
21 20 0.47
22 23 0.53
ACGTcount: A:0.64, C:0.08, G:0.11, T:0.17
Consensus pattern (21 bp):
AATAATAAAAAATAATAGCAA
Found at i:29528 original size:12 final size:13
Alignment explanation
Indices: 29499--29531 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
29489 AATAGAATAA
*
29499 ATTTAATATTATT
1 ATTTAATTTTATT
29512 ATTTAATTTTA-T
1 ATTTAATTTTATT
29524 ATTTAATT
1 ATTTAATT
29532 ACTAATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
ATTTAATTTTATT
Found at i:36106 original size:41 final size:41
Alignment explanation
Indices: 36046--36141 Score: 138
Period size: 41 Copynumber: 2.3 Consensus size: 41
36036 TTGTTCGTAG
* * * *
36046 AGAATTATTGTCAAGGTGGAGATTGTTAGAATTGGGTGACT
1 AGAATTCTTGTTAAGGTGGAGATTATTAAAATTGGGTGACT
*
36087 AGAATTCTTGTTAATGTGGAGATTATTAAAATTGGGTGACT
1 AGAATTCTTGTTAAGGTGGAGATTATTAAAATTGGGTGACT
*
36128 AGAATTCTTATTAA
1 AGAATTCTTGTTAA
36142 AATAAAATTC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.32, C:0.05, G:0.25, T:0.38
Consensus pattern (41 bp):
AGAATTCTTGTTAAGGTGGAGATTATTAAAATTGGGTGACT
Found at i:41954 original size:2 final size:2
Alignment explanation
Indices: 41947--41982 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
41937 TTTAAACAAC
41947 TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA GTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
41983 AGAGATGAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 29 0.91
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41967 original size:13 final size:13
Alignment explanation
Indices: 41949--41974 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41939 TAAACAACTA
41949 TATATATATATAT
1 TATATATATATAT
41962 TATATATATATAT
1 TATATATATATAT
41975 AGTATATAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATATATATAT
Found at i:41967 original size:15 final size:15
Alignment explanation
Indices: 41947--41982 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
41937 TTTAAACAAC
*
41947 TATATATATATATAT
1 TATATATATATATAG
41962 TATATATATATATAG
1 TATATATATATATAG
41977 TATATA
1 TATATA
41983 AGAGATGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
TATATATATATATAG
Found at i:41980 original size:13 final size:12
Alignment explanation
Indices: 41947--41982 Score: 56
Period size: 11 Copynumber: 3.0 Consensus size: 12
41937 TTTAAACAAC
41947 TATATATATATA
1 TATATATATATA
41959 TAT-TATATATA
1 TATATATATATA
41970 TATATAGTATATA
1 TATATA-TATATA
41983 AGAGATGAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.50
12 5 0.23
13 6 0.27
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (12 bp):
TATATATATATA
Found at i:46480 original size:142 final size:142
Alignment explanation
Indices: 46224--46495 Score: 413
Period size: 142 Copynumber: 1.9 Consensus size: 142
46214 TTATTCCTTT
* * **
46224 TATCAGTTTTCATTCATATATCTTCTGTTTCATATAATAATCGAGTCTCGGGGGAGATAGTAGGT
1 TATCAATTTTCATTCATATATCTTCCGTTTCATATAATAATCGAGTCTCGAAGGAGATAGTAGGT
* * **
46289 GATGAGAATGATAGACTGTTGTTCCCTTTTAAAATGGTTTTGTTTTAGATGCCCGGGTTTTCCTC
66 GATGAGAATGAAAGACTGTTGTTCCCTTTTAAAATGGTTTTGCTTTAGATGCCCAAGTTTTCCTC
46354 ATATTTGTTTTG
131 ATATTTGTTTTG
* *
46366 TATCAATTTTCATTCATATATCTTCCGTTTCCTA-ACATAATCGAGTCTCGAAGGAGATGGTAGG
1 TATCAATTTTCATTCATATATCTTCCGTTTCATATA-ATAATCGAGTCTCGAAGGAGATAGTAGG
*
46430 TGATGAGAGTGAAAGACTGTTGTTCCCTTTT-AAATCGGTTTTGCTTTAGATGCCCAAGTTTTCC
65 TGATGAGAATGAAAGACTGTTGTTCCCTTTTAAAAT-GGTTTTGCTTTAGATGCCCAAGTTTTCC
46494 TC
129 TC
46496 TTGTCTATAT
Statistics
Matches: 117, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
141 5 0.04
142 112 0.96
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (142 bp):
TATCAATTTTCATTCATATATCTTCCGTTTCATATAATAATCGAGTCTCGAAGGAGATAGTAGGT
GATGAGAATGAAAGACTGTTGTTCCCTTTTAAAATGGTTTTGCTTTAGATGCCCAAGTTTTCCTC
ATATTTGTTTTG
Found at i:53001 original size:21 final size:20
Alignment explanation
Indices: 52976--53035 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
52966 GTGTTTAATC
52976 AATATTGAAAATTTAAAAACT
1 AATATT-AAAATTTAAAAACT
** *
52997 AATA-TAAAATATTATATTATT
1 AATATTAAAAT-TTA-AAAACT
53018 AATATTAAAATTTAAAAA
1 AATATTAAAATTTAAAAA
53036 TAAATAATCT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
19 5 0.16
20 6 0.19
21 14 0.45
22 6 0.19
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (20 bp):
AATATTAAAATTTAAAAACT
Found at i:53442 original size:17 final size:16
Alignment explanation
Indices: 53422--53459 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
53412 CAAAAAATCT
53422 AAAAAAT-TAAAATTAAA
1 AAAAAATATAAAA--AAA
53439 AAAAAATATAAAAAAA
1 AAAAAATATAAAAAAA
53455 AAAAA
1 AAAAA
53460 GCATGAAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 8 0.40
17 7 0.35
18 5 0.25
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAAAATATAAAAAAA
Done.