Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008695.1 Kokia drynarioides strain JFW-HI SEQ_123377, 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: 61243
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Warning! 7 characters in sequence are not A, C, G, or T
Found at i:2029 original size:63 final size:62
Alignment explanation
Indices: 1954--2078 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 62
1944 GTGGTAACTC
1954 CAAATACTATAATAAAAT-ACACATTAATAATTTACGTACCACATTAAATAATTTATAAAAATA
1 CAAATACTATAAT-AAATCACACATTAATAATTTACGTACCACATT-AATAATTTATAAAAATA
* * * * * *
2017 CAAATA-TAATAATAAATCACATATTTATAATTTATGTACCATATTAATATTTTATGAAAATA
1 CAAATACT-ATAATAAATCACACATTAATAATTTACGTACCACATTAATAATTTATAAAAATA
2079 TATGTACCAA
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
62 20 0.37
63 34 0.63
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.36
Consensus pattern (62 bp):
CAAATACTATAATAAATCACACATTAATAATTTACGTACCACATTAATAATTTATAAAAATA
Found at i:15572 original size:18 final size:18
Alignment explanation
Indices: 15549--15605 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
15539 TATGTCAACA
15549 TTTAATTAATTTTTA-AAT
1 TTTAA-TAATTTTTATAAT
**
15567 TTTAATAATTTAAATAAT
1 TTTAATAATTTTTATAAT
*
15585 TTTAATAATTTTTTTAAT
1 TTTAATAATTTTTATAAT
15603 TTT
1 TTT
15606 TAAAAAAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
17 7 0.21
18 26 0.79
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTAATAATTTTTATAAT
Found at i:15576 original size:9 final size:9
Alignment explanation
Indices: 15549--15596 Score: 62
Period size: 9 Copynumber: 5.3 Consensus size: 9
15539 TATGTCAACA
15549 TTTAATTAAT
1 TTTAA-TAAT
*
15559 TTTTA-AAT
1 TTTAATAAT
15567 TTTAATAAT
1 TTTAATAAT
*
15576 TTAAATAAT
1 TTTAATAAT
15585 TTTAATAAT
1 TTTAATAAT
15594 TTT
1 TTT
15597 TTTAATTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
8 7 0.21
9 22 0.67
10 4 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
TTTAATAAT
Found at i:18821 original size:16 final size:15
Alignment explanation
Indices: 18770--18852 Score: 51
Period size: 15 Copynumber: 5.1 Consensus size: 15
18760 TTCATGCTAT
*
18770 TTTTTTTATTTATGAA
1 TTTTTTTATTT-TTAA
* *
18786 CTTTTCTTATATATT-A
1 -TTTTTTTAT-TTTTAA
*
18802 TTTTTTAATTTTTAA
1 TTTTTTTATTTTTAA
18817 TTTTTTTATTTTTGAA
1 TTTTTTTATTTTT-AA
*
18833 TATTTATATCATTTTTAA
1 T-TTT-T-TTATTTTTAA
18851 TT
1 TT
18853 ATTTATTGAT
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
14 3 0.06
15 20 0.38
16 4 0.08
17 13 0.25
18 5 0.10
19 7 0.13
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (15 bp):
TTTTTTTATTTTTAA
Found at i:25336 original size:43 final size:43
Alignment explanation
Indices: 25270--25355 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
25260 ATCTACGAGC
*
25270 TAGTATGTCCATATATCTGGTCAAGAAAACCAAAGTTCCATGG
1 TAGTATGTCCATATATCTAGTCAAGAAAACCAAAGTTCCATGG
* *
25313 TAGTATGTCTATTTATCTAGTCAAGAAAACCAAAGTTCCATGG
1 TAGTATGTCCATATATCTAGTCAAGAAAACCAAAGTTCCATGG
25356 ATAAGCAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (43 bp):
TAGTATGTCCATATATCTAGTCAAGAAAACCAAAGTTCCATGG
Found at i:29558 original size:23 final size:24
Alignment explanation
Indices: 29521--29568 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
29511 AGATTATTTT
29521 TATACAAAAATAAATT-TTAAAAA
1 TATACAAAAATAAATTATTAAAAA
29544 TATA-AAAAATCAAATTGATTAAAAA
1 TATACAAAAAT-AAATT-ATTAAAAA
29569 CATTAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 6 0.27
23 9 0.41
25 7 0.32
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (24 bp):
TATACAAAAATAAATTATTAAAAA
Found at i:29576 original size:25 final size:22
Alignment explanation
Indices: 29526--29581 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
29516 ATTTTTATAC
*
29526 AAAAATAAATTTTAAAAATATA
1 AAAAATAAATTTTAAAAACATA
29548 AAAAATCAAATTGATTAAAAACAT-
1 AAAAAT-AAATT--TTAAAAACATA
*
29572 TAAAATAAAT
1 AAAAATAAAT
29582 ATTTTGCAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 6 0.21
23 9 0.31
24 5 0.17
25 9 0.31
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.29
Consensus pattern (22 bp):
AAAAATAAATTTTAAAAACATA
Found at i:40119 original size:20 final size:19
Alignment explanation
Indices: 40091--40149 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
40081 TTAAAATATA
40091 AAAAATATAGAAATTTTTT
1 AAAAATATAGAAATTTTTT
** * **
40110 AAATGTTATAAAAATTTTAG
1 AAA-AATATAGAAATTTTTT
40130 AAAAATATAGAAATTTTTT
1 AAAAATATAGAAATTTTTT
40149 A
1 A
40150 TACATTTTTT
Statistics
Matches: 29, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.41
Consensus pattern (19 bp):
AAAAATATAGAAATTTTTT
Found at i:40283 original size:19 final size:17
Alignment explanation
Indices: 40254--40303 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 17
40244 AGATTTATAT
40254 AAAAA-TATAAAATTAA
1 AAAAATTATAAAATTAA
*
40270 AGAAAAGTTATAAAAATAA
1 A-AAAA-TTATAAAATTAA
40289 AAAAATTACTAAAAT
1 AAAAATTA-TAAAAT
40304 ATTTTTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
16 1 0.04
17 7 0.25
18 9 0.32
19 11 0.39
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (17 bp):
AAAAATTATAAAATTAA
Found at i:43340 original size:28 final size:28
Alignment explanation
Indices: 43300--43363 Score: 128
Period size: 28 Copynumber: 2.3 Consensus size: 28
43290 GAGGTCCAAC
43300 TATTTGGAAATTCCATAAAAAAACTTAG
1 TATTTGGAAATTCCATAAAAAAACTTAG
43328 TATTTGGAAATTCCATAAAAAAACTTAG
1 TATTTGGAAATTCCATAAAAAAACTTAG
43356 TATTTGGA
1 TATTTGGA
43364 TATTAGTAGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.34
Consensus pattern (28 bp):
TATTTGGAAATTCCATAAAAAAACTTAG
Found at i:51623 original size:11 final size:11
Alignment explanation
Indices: 51607--51632 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
51597 AAAAAATTAG
51607 AAATCATTAAA
1 AAATCATTAAA
51618 AAATCATTAAA
1 AAATCATTAAA
51629 AAAT
1 AAAT
51633 AATAAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (11 bp):
AAATCATTAAA
Found at i:51650 original size:18 final size:18
Alignment explanation
Indices: 51623--51667 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
51613 TTAAAAAATC
51623 ATTA-AAAAATAATAAAA
1 ATTATAAAAATAATAAAA
* * *
51640 ATTGTAAAAATATTTAAA
1 ATTATAAAAATAATAAAA
51658 ATTATAAAAA
1 ATTATAAAAA
51668 ATTTAAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 3 0.13
18 20 0.87
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (18 bp):
ATTATAAAAATAATAAAA
Found at i:51674 original size:9 final size:9
Alignment explanation
Indices: 51613--51724 Score: 61
Period size: 10 Copynumber: 11.9 Consensus size: 9
51603 TTAGAAATCA
51613 TTAAAAAAT
1 TTAAAAAAT
51622 CATTAAAAAA-
1 --TTAAAAAAT
*
51632 TAATAAAAAT
1 TTA-AAAAAT
51642 TGTAAAAATAT
1 T-TAAAAA-AT
51653 TT--AAAAT
1 TTAAAAAAT
51660 TATAAAAAAT
1 T-TAAAAAAT
* *
51670 TTAAATAAC
1 TTAAAAAAT
*
51679 TGAAAAAA-
1 TTAAAAAAT
51687 TTAAAAAAT
1 TTAAAAAAT
*
51696 GTAAATAAAT
1 TTAAA-AAAT
*
51706 ATTTAAAAAT
1 -TTAAAAAAT
51716 TATAAAAAA
1 T-TAAAAAA
51725 AAACCAAGAT
Statistics
Matches: 79, Mismatches: 11, Indels: 23
0.70 0.10 0.20
Matches are distributed among these distances:
7 3 0.04
8 13 0.16
9 22 0.28
10 26 0.33
11 15 0.19
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (9 bp):
TTAAAAAAT
Found at i:54945 original size:72 final size:72
Alignment explanation
Indices: 54818--54972 Score: 283
Period size: 72 Copynumber: 2.1 Consensus size: 72
54808 TATAATTTAT
*
54818 AAAATTTTAAATTATTAATGATAAAATTACATTTTGACCTCTCAAAAATGATAAAAATTTGATTT
1 AAAA-TTTATATTATTAATGATAAAATTACATTTTGACCTCTCAAAAATGATAAAAATTTGATTT
54883 AATCCTTC
65 AATCCTTC
*
54891 AAAATTTATATTATTAATGATAAAATTGCATTTTGACCTCTCAAAAATGATAAAAATTTGATTTA
1 AAAATTTATATTATTAATGATAAAATTACATTTTGACCTCTCAAAAATGATAAAAATTTGATTTA
54956 ATCCTTC
66 ATCCTTC
54963 AAAATTTATA
1 AAAATTTATA
54973 AAGATGTAGA
Statistics
Matches: 80, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
72 76 0.95
73 4 0.05
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (72 bp):
AAAATTTATATTATTAATGATAAAATTACATTTTGACCTCTCAAAAATGATAAAAATTTGATTTA
ATCCTTC
Done.