Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005998.1 Kokia drynarioides strain JFW-HI SEQ_120424, 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: 40856
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:398 original size:58 final size:59
Alignment explanation
Indices: 333--465 Score: 216
Period size: 58 Copynumber: 2.3 Consensus size: 59
323 TATTTTGTAC
*
333 TATTTTGGTAAATATTATGATGGA-GATATTATTTTCATAATTAATTA-TTTTTATATTA
1 TATTTTGGTAAATAATATGAT-GATGATATTATTTTCATAATTAATTATTTTTTATATTA
*
391 TATTTTGGTAAATAATATGATGATGATATTATTTTGATAATTAATTATTTTTTATATTA
1 TATTTTGGTAAATAATATGATGATGATATTATTTTCATAATTAATTATTTTTTATATTA
*
450 TATTTTGGTAATTAAT
1 TATTTTGGTAAATAAT
466 TAGCTAGGTT
Statistics
Matches: 70, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
57 2 0.03
58 42 0.60
59 26 0.37
ACGTcount: A:0.35, C:0.01, G:0.11, T:0.54
Consensus pattern (59 bp):
TATTTTGGTAAATAATATGATGATGATATTATTTTCATAATTAATTATTTTTTATATTA
Found at i:1759 original size:6 final size:6
Alignment explanation
Indices: 1749--1795 Score: 76
Period size: 6 Copynumber: 7.8 Consensus size: 6
1739 GTCTCAGGTG
* *
1749 AAATGG AAATGG AAATGA AAATGA AAATGA AAATGA AAATGA AAATG
1 AAATGA AAATGA AAATGA AAATGA AAATGA AAATGA AAATGA AAATG
1796 CAGGGTTAGG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.62, C:0.00, G:0.21, T:0.17
Consensus pattern (6 bp):
AAATGA
Found at i:7608 original size:17 final size:18
Alignment explanation
Indices: 7582--7615 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
7572 TATATTTTTG
7582 TAATTAAATTATTTAAAA
1 TAATTAAATTATTTAAAA
*
7600 TAATT-AATTTTTTAAA
1 TAATTAAATTATTTAAA
7616 TCATACATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATTAAATTATTTAAAA
Found at i:8637 original size:17 final size:17
Alignment explanation
Indices: 8592--8690 Score: 87
Period size: 17 Copynumber: 5.7 Consensus size: 17
8582 CTTTTGATTA
*
8592 AAAAAGTATTTTT-TTTC
1 AAAAA-TATTTTTATCTC
*
8609 AAACAT-TTTTTATCTC
1 AAAAATATTTTTATCTC
*
8625 AAAAATATTTTTAAAAAT-TT
1 AAAAATATTTTT----ATCTC
*
8645 AAAAATATTTTTATCAC
1 AAAAATATTTTTATCTC
*
8662 AAAAATATTTTTATCAC
1 AAAAATATTTTTATCTC
8679 AAAAATATTTTT
1 AAAAATATTTTT
8691 TTATCCATAA
Statistics
Matches: 69, Mismatches: 6, Indels: 14
0.78 0.07 0.16
Matches are distributed among these distances:
15 5 0.07
16 11 0.16
17 38 0.55
20 13 0.19
21 2 0.03
ACGTcount: A:0.44, C:0.08, G:0.01, T:0.46
Consensus pattern (17 bp):
AAAAATATTTTTATCTC
Found at i:8704 original size:19 final size:17
Alignment explanation
Indices: 8645--8690 Score: 92
Period size: 17 Copynumber: 2.7 Consensus size: 17
8635 TTAAAAATTT
8645 AAAAATATTTTTATCAC
1 AAAAATATTTTTATCAC
8662 AAAAATATTTTTATCAC
1 AAAAATATTTTTATCAC
8679 AAAAATATTTTT
1 AAAAATATTTTT
8691 TTATCCATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (17 bp):
AAAAATATTTTTATCAC
Found at i:9879 original size:18 final size:18
Alignment explanation
Indices: 9856--9894 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
9846 ATATATTTTT
*
9856 TATTTTTTATTAAAATAA
1 TATTTTTTACTAAAATAA
*
9874 TATTTTTTACTAAAATGA
1 TATTTTTTACTAAAATAA
9892 TAT
1 TAT
9895 AAATCCAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (18 bp):
TATTTTTTACTAAAATAA
Found at i:11516 original size:27 final size:28
Alignment explanation
Indices: 11476--11546 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
11466 ATCGGAATTG
* *
11476 AAAATGAGATTTTTGGATA-CCGGGGGC
1 AAAATGATAATTTTGGATATCCGGGGGC
*
11503 AAAATGATAATTTTGGATATTCGGGGGC
1 AAAATGATAATTTTGGATATCCGGGGGC
*
11531 AAAATGGTAATTTTGG
1 AAAATGATAATTTTGG
11547 GAAAGTTCGG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 17 0.44
28 22 0.56
ACGTcount: A:0.32, C:0.07, G:0.30, T:0.31
Consensus pattern (28 bp):
AAAATGATAATTTTGGATATCCGGGGGC
Found at i:11636 original size:60 final size:59
Alignment explanation
Indices: 11561--11784 Score: 260
Period size: 60 Copynumber: 3.8 Consensus size: 59
11551 GTTCGGGGTA
* * * * *
11561 AAAAATGGAACTTTTATACA-TTTGGGGGTAAAATGGTAATTTTTGGAAAAAATAAAGGTC
1 AAAAATGGAATTTTTATA-AGTTCGAGGGTAAAATGGTAATTTTTGG-AAAAATTAAGGTT
* *
11621 AAAAATGGAATTTTTAGAAGTTCGAGGGTAAAATGGTAATTTTTTGGAAAAATTGAGGTT
1 AAAAATGGAATTTTTATAAGTTCGAGGGTAAAATGGTAA-TTTTTGGAAAAATTAAGGTT
* *
11681 AAAAATGGAA-TTTTATGAAGTTCAAGAGTAAAATGGTAATTTTTGGAAAAATTAAGGTT
1 AAAAATGGAATTTTTAT-AAGTTCGAGGGTAAAATGGTAATTTTTGGAAAAATTAAGGTT
* *
11740 AAAAATGGAATTTTGGA-AAGTTTGAGGGTAAAAAT-GT-ATTTTTGG
1 AAAAATGGAATTTT-TATAAGTTCGAGGGT-AAAATGGTAATTTTTGG
11785 GACAGTTTAG
Statistics
Matches: 143, Mismatches: 15, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
58 8 0.06
59 46 0.32
60 81 0.57
61 8 0.06
ACGTcount: A:0.41, C:0.02, G:0.23, T:0.34
Consensus pattern (59 bp):
AAAAATGGAATTTTTATAAGTTCGAGGGTAAAATGGTAATTTTTGGAAAAATTAAGGTT
Found at i:11655 original size:119 final size:117
Alignment explanation
Indices: 11522--11791 Score: 296
Period size: 119 Copynumber: 2.3 Consensus size: 117
11512 ATTTTGGATA
* * * **
11522 TTCGGGGGCAAAATGGTAATTTTGGGAAAGTTCGGGGTAAAAAATGGAACTTTTAT-ACA-TTTG
1 TTCGAGGGTAAAATGGTAATTTTGGGAAAGTT-GAGGTAAAAAATGGAA-TTTTATGA-AGTTCA
* *
11585 GGGGTAAAATGGTAATTTTTGGAAAAAATAAAGGTCAAAAATGGAATTTTTAG-AAG
63 AGAGTAAAATGGTAATTTTTGG-AAAAATAAAGGTCAAAAATGGAA-TTTTAGAAAG
* * *
11641 TTCGAGGGTAAAATGGTAATTTTTTGGAAAAATTGAGGTTAAAAATGGAATTTTATGAAGTTCAA
1 TTCGAGGGTAAAATGGTAA--TTTTGGGAAAGTTGAGGTAAAAAATGGAATTTTATGAAGTTCAA
* * *
11706 GAGTAAAATGGTAATTTTTGGAAAAATTAAGGTTAAAAATGGAATTTTGGAAAG
64 GAGTAAAATGGTAATTTTTGGAAAAATAAAGGTCAAAAATGGAATTTTAGAAAG
* * *
11760 TTTGAGGGTAAAAAT-GTATTTTTGGGACAGTT
1 TTCGAGGGT-AAAATGGTAATTTTGGGAAAGTT
11792 TAGGGACCTT
Statistics
Matches: 127, Mismatches: 18, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
117 10 0.08
118 5 0.04
119 59 0.46
120 42 0.33
121 11 0.09
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.33
Consensus pattern (117 bp):
TTCGAGGGTAAAATGGTAATTTTGGGAAAGTTGAGGTAAAAAATGGAATTTTATGAAGTTCAAGA
GTAAAATGGTAATTTTTGGAAAAATAAAGGTCAAAAATGGAATTTTAGAAAG
Found at i:11661 original size:29 final size:28
Alignment explanation
Indices: 11622--11724 Score: 84
Period size: 28 Copynumber: 3.5 Consensus size: 28
11612 ATAAAGGTCA
11622 AAAATGGAATTTTTAGAAGTTCGAGGGT
1 AAAATGGAATTTTTAGAAGTTCGAGGGT
* * *
11650 AAAATGGTAATTTTTTGGAAAAATT-GAGGTT
1 AAAATGG-AA-TTTTT--AGAAGTTCGAGGGT
* *
11681 AAAAATGGAA-TTTTATGAAGTTCAAGAGT
1 -AAAATGGAATTTTTA-GAAGTTCGAGGGT
11710 AAAATGGTAATTTTT
1 AAAATGG-AATTTTT
11725 GGAAAAATTA
Statistics
Matches: 58, Mismatches: 8, Indels: 16
0.71 0.10 0.20
Matches are distributed among these distances:
27 1 0.02
28 18 0.31
29 11 0.19
30 9 0.16
31 7 0.12
32 12 0.21
ACGTcount: A:0.40, C:0.02, G:0.22, T:0.36
Consensus pattern (28 bp):
AAAATGGAATTTTTAGAAGTTCGAGGGT
Found at i:11796 original size:29 final size:29
Alignment explanation
Indices: 11531--11784 Score: 108
Period size: 29 Copynumber: 8.5 Consensus size: 29
11521 ATTCGGGGGC
*
11531 AAAATGGTAATTTTGGGAAAGTTCG-GGGTAA
1 AAAATGG-AATTTT-GGAAAGTTTGAGGGT-A
** * *
11562 AAAATGGAACTTTTATACA-TTTGGGGGT-
1 AAAATGGAA-TTTTGGAAAGTTTGAGGGTA
*** * *
11590 AAAATGGTAATTTTTGGAAAAAATAAAGGTCA
1 AAAATGG-AA-TTTTGGAAAGTTTGAGGGT-A
* *
11622 AAAATGGAATTTT-TAGAAGTTCGAGGGT-
1 AAAATGGAATTTTGGA-AAGTTTGAGGGTA
** *
11650 AAAATGGTAATTTTTTGGAAAAATTGAGGTTA
1 AAAATGG-AA--TTTTGGAAAGTTTGAGGGTA
* ** *
11682 AAAATGGAATTTTATG-AAGTTCAAGAGT-
1 AAAATGGAATTTT-GGAAAGTTTGAGGGTA
** * *
11710 AAAATGGTAATTTTTGGAAAAATTAAGGTTA
1 AAAATGG-AA-TTTTGGAAAGTTTGAGGGTA
11741 AAAATGGAATTTTGGAAAGTTTGAGGGTA
1 AAAATGGAATTTTGGAAAGTTTGAGGGTA
* *
11770 AAAATGTATTTTTGG
1 AAAATGGAATTTTGG
11785 GACAGTTTAG
Statistics
Matches: 162, Mismatches: 44, Indels: 36
0.67 0.18 0.15
Matches are distributed among these distances:
28 21 0.13
29 56 0.35
30 36 0.22
31 34 0.21
32 15 0.09
ACGTcount: A:0.40, C:0.02, G:0.24, T:0.33
Consensus pattern (29 bp):
AAAATGGAATTTTGGAAAGTTTGAGGGTA
Found at i:12909 original size:22 final size:22
Alignment explanation
Indices: 12881--12923 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
12871 GATTTTTCTT
12881 TTTTTATTAATAGTAATTAATA
1 TTTTTATTAATAGTAATTAATA
* *
12903 TTTTTATTAATATTTATTAAT
1 TTTTTATTAATAGTAATTAAT
12924 GCTATTCATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
TTTTTATTAATAGTAATTAATA
Found at i:12965 original size:3 final size:3
Alignment explanation
Indices: 12959--12986 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
12949 TAACATCATC
12959 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
12987 AATATATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:13671 original size:6 final size:6
Alignment explanation
Indices: 13662--13732 Score: 67
Period size: 6 Copynumber: 12.2 Consensus size: 6
13652 ATTTTTATTT
* ** *
13662 ATTTAA ATTTATA A--TAA TTTTAA ATTTAA AAATAA ATTTAA ACTTAA
1 ATTTAA ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
*
13709 ATTTAA A-ATAA ATTTAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA ATTTAA A
13733 ACAAATTTAA
Statistics
Matches: 51, Mismatches: 10, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
4 1 0.02
5 6 0.12
6 42 0.82
7 2 0.04
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (6 bp):
ATTTAA
Found at i:13685 original size:17 final size:18
Alignment explanation
Indices: 13662--13760 Score: 80
Period size: 17 Copynumber: 5.4 Consensus size: 18
13652 ATTTTTATTT
*
13662 ATTTAAATTT-ATAATAA
1 ATTTAAATTTAAAAATAA
*
13679 TTTTAAATTTAAAAATAA
1 ATTTAAATTTAAAAATAA
*
13697 ATTTAAACTTAAATTTAAAATAA
1 ATTTAAA--T---TTAAAAATAA
*
13720 ATTTAAATTT-AAAACAA
1 ATTTAAATTTAAAAATAA
13737 ATTT-AATCTT-AAAATAA
1 ATTTAAAT-TTAAAAATAA
13754 ATTTAAA
1 ATTTAAA
13761 AAGGATCCAA
Statistics
Matches: 68, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
16 3 0.04
17 31 0.46
18 16 0.24
20 1 0.01
21 1 0.01
23 16 0.24
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTTAAATTTAAAAATAA
Found at i:13713 original size:41 final size:40
Alignment explanation
Indices: 13664--13749 Score: 127
Period size: 41 Copynumber: 2.1 Consensus size: 40
13654 TTTTATTTAT
* * *
13664 TTAAATTTATAATAATTTTAAATTTAAAAATAAATTTAAAC
1 TTAAATTTAAAATAAATTTAAATTT-AAAACAAATTTAAAC
*
13705 TTAAATTTAAAATAAATTTAAATTTAAAACAAATTTAATC
1 TTAAATTTAAAATAAATTTAAATTTAAAACAAATTTAAAC
13745 TTAAA
1 TTAAA
13750 ATAAATTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 18 0.44
41 23 0.56
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (40 bp):
TTAAATTTAAAATAAATTTAAATTTAAAACAAATTTAAAC
Found at i:14440 original size:132 final size:132
Alignment explanation
Indices: 14202--14457 Score: 327
Period size: 132 Copynumber: 1.9 Consensus size: 132
14192 GGAATGGGTT
* * ** * * *
14202 TGCTCACACGAGTTGTGAGTCGAGATGTTAAGCTACACGATGTTGCTCACACGAGCTGTGGAGAA
1 TGCTCACACGAGCTGTGAGTCAAGATGTTAAGCTACACGATACTGCTCACACAAGCTATGAAGAA
* * * * * *
14267 TCCGCAATATATGTCGGATCTCAATCATCAGTAGGATATCTAAGACCAACACCTATATATCATGT
66 TCCGCAACATATGCCAGATCTCAACCATCAGTAGGACATCTAAAACCAACACCTATATATCATGT
14332 AA
131 AA
* *
14334 TGCTCACACGAGCTGT-AGGTCAAGATGTTAGGTTACACGATACTGCTCACACAAGCTATGAAGA
1 TGCTCACACGAGCTGTGA-GTCAAGATGTTAAGCTACACGATACTGCTCACACAAGCTATGAAGA
* *
14398 ATCCGCAACATATGCCAGATCTCAGCCATC-GATAGGACATCTAAAACCAACACTTATATA
65 ATCCGCAACATATGCCAGATCTCAACCATCAG-TAGGACATCTAAAACCAACACCTATATA
14458 ACCTGTAAAT
Statistics
Matches: 105, Mismatches: 17, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
131 2 0.02
132 103 0.98
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.25
Consensus pattern (132 bp):
TGCTCACACGAGCTGTGAGTCAAGATGTTAAGCTACACGATACTGCTCACACAAGCTATGAAGAA
TCCGCAACATATGCCAGATCTCAACCATCAGTAGGACATCTAAAACCAACACCTATATATCATGT
AA
Found at i:16312 original size:23 final size:24
Alignment explanation
Indices: 16286--16344 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
16276 TAATCAAAAG
* *
16286 TGTTCACAAACAT-TAAACGGACA
1 TGTTCACGAACATATAAACGAACA
**
16309 TGTTCACGAACATATAATTGAACA
1 TGTTCACGAACATATAAACGAACA
16333 TGTTCACGAACA
1 TGTTCACGAACA
16345 ATGTTAATGA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 12 0.39
24 19 0.61
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (24 bp):
TGTTCACGAACATATAAACGAACA
Found at i:27415 original size:2 final size:2
Alignment explanation
Indices: 27408--27432 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
27398 CAGTGGCTTT
27408 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
27433 TTCTTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29890 original size:25 final size:23
Alignment explanation
Indices: 29862--29907 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
29852 GTTGGATTCA
29862 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
29887 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
29908 CTCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:36671 original size:30 final size:30
Alignment explanation
Indices: 36635--36693 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
36625 CGACTAACAG
*
36635 TGGTGTCACCT-GACAAGAGCCCTCCTCCCT
1 TGGTGTCACCTAG-CAAAAGCCCTCCTCCCT
* *
36665 TGGTGTCGCCTAGCAAAAGCCTTCCTCCC
1 TGGTGTCACCTAGCAAAAGCCCTCCTCCC
36694 CTTAAAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.17, C:0.39, G:0.20, T:0.24
Consensus pattern (30 bp):
TGGTGTCACCTAGCAAAAGCCCTCCTCCCT
Done.