Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006794.1 Kokia drynarioides strain JFW-HI SEQ_121393, 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: 32920
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Warning! 124 characters in sequence are not A, C, G, or T
Found at i:558 original size:29 final size:29
Alignment explanation
Indices: 517--581 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
507 GTGCTTTATA
* *
517 AAACTTGAGAAACCAATTTAGTTGTCGAT
1 AAACTTGAAAAACCAATCTAGTTGTCGAT
*
546 AAACTTGAAAAACCGATCTAGTTGTCGAT
1 AAACTTGAAAAACCAATCTAGTTGTCGAT
575 AAACTTG
1 AAACTTG
582 TGAACTTGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.29
Consensus pattern (29 bp):
AAACTTGAAAAACCAATCTAGTTGTCGAT
Found at i:5113 original size:15 final size:16
Alignment explanation
Indices: 5084--5119 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
5074 CGCAATTGAA
5084 TTAATTTTTTCTATTT
1 TTAATTTTTTCTATTT
5100 TTAATTTTTT-TATTT
1 TTAATTTTTTCTATTT
*
5115 ATAAT
1 TTAAT
5120 GAATTATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (16 bp):
TTAATTTTTTCTATTT
Found at i:9775 original size:29 final size:29
Alignment explanation
Indices: 9739--9813 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
9729 AAAAAAAATC
9739 ATAA-TTTAATAATTATTAT-TTCAAAAAA
1 ATAATTTTAATAATT-TTATATTCAAAAAA
***
9767 ATAATTTTAATAATTTTATATTTTTAAAA
1 ATAATTTTAATAATTTTATATTCAAAAAA
*
9796 ATAATTTTAACAATTTTA
1 ATAATTTTAATAATTTTA
9814 AAATCATTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
28 8 0.20
29 33 0.80
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (29 bp):
ATAATTTTAATAATTTTATATTCAAAAAA
Found at i:9817 original size:20 final size:20
Alignment explanation
Indices: 9775--9816 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
9765 AAATAATTTT
* *
9775 AATAATTTTATATTTTTAAA
1 AATAATTTTACAATTTTAAA
9795 AATAATTTTAACAATTTTAAA
1 AATAATTTT-ACAATTTTAAA
9816 A
1 A
9817 TCATTTATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
AATAATTTTACAATTTTAAA
Found at i:10477 original size:20 final size:19
Alignment explanation
Indices: 10445--10489 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
10435 AAAGCAAAAA
*
10445 GAAAAATTACAAACATTAT
1 GAAAAATTACAAAAATTAT
*
10464 GAAAAATTTCCAAAAATTAT
1 GAAAAA-TTACAAAAATTAT
10484 GAAAAA
1 GAAAAA
10490 GAATATATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.60, C:0.09, G:0.07, T:0.24
Consensus pattern (19 bp):
GAAAAATTACAAAAATTAT
Found at i:10775 original size:15 final size:15
Alignment explanation
Indices: 10757--10803 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
10747 TGATTTTGAG
10757 TTTAATTATTTTAAA
1 TTTAATTATTTTAAA
*
10772 TTTAAATACTTTTAAA
1 TTTAATTA-TTTTAAA
*
10788 TTTAATTAATTTAAA
1 TTTAATTATTTTAAA
10803 T
1 T
10804 ATAAATAGAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 14 0.50
16 14 0.50
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTAATTATTTTAAA
Found at i:10786 original size:16 final size:15
Alignment explanation
Indices: 10757--10810 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
10747 TGATTTTGAG
*
10757 TTTAATTATTTTAAA
1 TTTAAATATTTTAAA
10772 TTTAAATACTTTTAAA
1 TTTAAATA-TTTTAAA
* *
10788 TTTAATTAATTTAAA
1 TTTAAATATTTTAAA
*
10803 TATAAATA
1 TTTAAATA
10811 GAGTGACGGG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
15 19 0.58
16 14 0.42
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (15 bp):
TTTAAATATTTTAAA
Found at i:13118 original size:15 final size:15
Alignment explanation
Indices: 13076--13122 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
13066 AACGATAATG
*
13076 TAAATGATTAAAATA
1 TAAATAATTAAAATA
* *
13091 T-AATATTTCAAATA
1 TAAATAATTAAAATA
13105 TAAATAATTAAAATA
1 TAAATAATTAAAATA
13120 TAA
1 TAA
13123 TCTGAAACAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 11 0.42
15 15 0.58
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (15 bp):
TAAATAATTAAAATA
Found at i:14046 original size:6 final size:6
Alignment explanation
Indices: 14035--14068 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
14025 GCTTGTAAGT
14035 ATCACC ATCACC ATCACC ATCACC ATCACC ATCA
1 ATCACC ATCACC ATCACC ATCACC ATCACC ATCA
14069 ATATATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.35, C:0.47, G:0.00, T:0.18
Consensus pattern (6 bp):
ATCACC
Found at i:19244 original size:53 final size:53
Alignment explanation
Indices: 19123--19371 Score: 329
Period size: 53 Copynumber: 4.7 Consensus size: 53
19113 TTCACATTTG
* * * *
19123 ATAACTCACGATGACACAGAGTTATTGGACCTTTAATCCATGAT-GGATTCAT
1 ATAACTCACGATGACACATAGTCATCGGACCTTTAATCCATAATAGGATTCAT
* * * * * * *
19175 ATATCTCAAGATGACACAAAGTCATCGGACCCTTAATTCGTAATAAGATTCAT
1 ATAACTCACGATGACACATAGTCATCGGACCTTTAATCCATAATAGGATTCAT
* *
19228 ATAACTCACGATGACACATAGTAATCGGACCTTTAATCCATGATAGGATTCAT
1 ATAACTCACGATGACACATAGTCATCGGACCTTTAATCCATAATAGGATTCAT
* * * *
19281 ATAACTCATGATGACACATAGTCATCGAACCCTTAATCCGTAATAGGATTCAT
1 ATAACTCACGATGACACATAGTCATCGGACCTTTAATCCATAATAGGATTCAT
*
19334 ATAACTCACGATGACACATAGTCATTGGACCTTTAATC
1 ATAACTCACGATGACACATAGTCATCGGACCTTTAATC
19372 TTTGGCACAA
Statistics
Matches: 167, Mismatches: 29, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
52 35 0.21
53 132 0.79
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.29
Consensus pattern (53 bp):
ATAACTCACGATGACACATAGTCATCGGACCTTTAATCCATAATAGGATTCAT
Found at i:19316 original size:106 final size:105
Alignment explanation
Indices: 19123--19371 Score: 399
Period size: 106 Copynumber: 2.4 Consensus size: 105
19113 TTCACATTTG
* * *
19123 ATAACTCACGATGACACAGAGTTATTGGACCTTTAATCCATGATGGATTCATATATCTCAAGATG
1 ATAACTCACGATGACACATAGTAATTGGACCTTTAATCCATGATGGATTCATATAACTCAAGATG
* *
19188 ACACAAAGTCATCGGACCCTTAATTCGTAATAAGATTCAT
66 ACACAAAGTCATCGAACCCTTAATCCGTAATAAGATTCAT
* *
19228 ATAACTCACGATGACACATAGTAATCGGACCTTTAATCCATGATAGGATTCATATAACTCATGAT
1 ATAACTCACGATGACACATAGTAATTGGACCTTTAATCCATGAT-GGATTCATATAACTCAAGAT
* *
19293 GACACATAGTCATCGAACCCTTAATCCGTAATAGGATTCAT
65 GACACAAAGTCATCGAACCCTTAATCCGTAATAAGATTCAT
*
19334 ATAACTCACGATGACACATAGTCATTGGACCTTTAATC
1 ATAACTCACGATGACACATAGTAATTGGACCTTTAATC
19372 TTTGGCACAA
Statistics
Matches: 132, Mismatches: 11, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
105 41 0.31
106 91 0.69
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.29
Consensus pattern (105 bp):
ATAACTCACGATGACACATAGTAATTGGACCTTTAATCCATGATGGATTCATATAACTCAAGATG
ACACAAAGTCATCGAACCCTTAATCCGTAATAAGATTCAT
Found at i:20628 original size:28 final size:28
Alignment explanation
Indices: 20596--20683 Score: 79
Period size: 28 Copynumber: 3.1 Consensus size: 28
20586 GAAGGCATCT
*
20596 TTTAAAAGGTTCACCACAAAGGCTTACC
1 TTTAAAAGGTTCGCCACAAAGGCTTACC
* * * * *
20624 TTTAACAAAGTTTTGCTACAAAGGC-AATCA
1 TTT-A-AAAGGTTCGCCACAAAGGCTTA-CC
*
20654 TTTAAAAGGTTCGCCACAAAGGCTTTCC
1 TTTAAAAGGTTCGCCACAAAGGCTTACC
20682 TT
1 TT
20684 GACTGGTGTT
Statistics
Matches: 44, Mismatches: 12, Indels: 8
0.69 0.19 0.12
Matches are distributed among these distances:
28 22 0.50
29 3 0.07
30 19 0.43
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.30
Consensus pattern (28 bp):
TTTAAAAGGTTCGCCACAAAGGCTTACC
Found at i:23155 original size:18 final size:19
Alignment explanation
Indices: 23132--23177 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
23122 ATGAAAACTT
* *
23132 TATTATTAAATTCT-TATA
1 TATTATTAAACTATATATA
*
23150 TATTA-TAAACTATATATT
1 TATTATTAAACTATATATA
23168 TATTATTAAA
1 TATTATTAAA
23178 ATAGTAGCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 6 0.26
18 13 0.57
19 4 0.17
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.52
Consensus pattern (19 bp):
TATTATTAAACTATATATA
Found at i:24018 original size:23 final size:23
Alignment explanation
Indices: 23990--24039 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
23980 TTAACAAGTT
23990 TCAATATAAAAAAATGATAGATG
1 TCAATATAAAAAAATGATAGATG
* *
24013 TCAATATAAAATAATGATAGGTG
1 TCAATATAAAAAAATGATAGATG
24036 TCAA
1 TCAA
24040 CCCTTGAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.52, C:0.06, G:0.14, T:0.28
Consensus pattern (23 bp):
TCAATATAAAAAAATGATAGATG
Found at i:29709 original size:21 final size:20
Alignment explanation
Indices: 29679--29722 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
29669 AGTAATATGG
29679 TAAAAAAAATATTAAAATAT
1 TAAAAAAAATATTAAAATAT
* *
29699 TAAAAATAAATATTTAAATGT
1 TAAAAA-AAATATTAAAATAT
29720 TAA
1 TAA
29723 TATTATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (20 bp):
TAAAAAAAATATTAAAATAT
Found at i:30610 original size:23 final size:23
Alignment explanation
Indices: 30580--30631 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
30570 ATTTAACAAG
30580 TGTCAATATAACA-GAATGATAGA
1 TGTCAATATAACAGGAA-GATAGA
* *
30603 TGTCAATATAAGAGGAAGATAGG
1 TGTCAATATAACAGGAAGATAGA
30626 TGTCAA
1 TGTCAA
30632 AGTTAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 23 0.88
24 3 0.12
ACGTcount: A:0.44, C:0.08, G:0.23, T:0.25
Consensus pattern (23 bp):
TGTCAATATAACAGGAAGATAGA
Found at i:32697 original size:101 final size:101
Alignment explanation
Indices: 32579--32791 Score: 417
Period size: 101 Copynumber: 2.1 Consensus size: 101
32569 CGCTTTAAAA
*
32579 ACCGTTTTGAAAACACGTAGGTCTTCGAAATCCAGAAAAACAAATTCGGGAGTCGGTTACGCATG
1 ACCGTTTTGATAACACGTAGGTCTTCGAAATCCAGAAAAACAAATTCGGGAGTCGGTTACGCATG
32644 AGGAAGGATTAGCACCCTCATACGCTCAAAATTGGT
66 AGGAAGGATTAGCACCCTCATACGCTCAAAATTGGT
32680 ACCGTTTTGATAACACGTAGGTCTTCGAAATCCAGAAAAACAAATTCGGGAGTCGGTTACGCATG
1 ACCGTTTTGATAACACGTAGGTCTTCGAAATCCAGAAAAACAAATTCGGGAGTCGGTTACGCATG
32745 AGGAAGGATTAGCACCCTCATACGCTCAAAATTGGT
66 AGGAAGGATTAGCACCCTCATACGCTCAAAATTGGT
32781 ACCGTTTTGAT
1 ACCGTTTTGAT
32792 TATTTTCGTG
Statistics
Matches: 111, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
101 111 1.00
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (101 bp):
ACCGTTTTGATAACACGTAGGTCTTCGAAATCCAGAAAAACAAATTCGGGAGTCGGTTACGCATG
AGGAAGGATTAGCACCCTCATACGCTCAAAATTGGT
Done.