Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009538.1 Kokia drynarioides strain JFW-HI SEQ_124250, 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: 99327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 140 characters in sequence are not A, C, G, or T
Found at i:15550 original size:9 final size:9
Alignment explanation
Indices: 15532--15562 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
15522 TATTTTTTAA
15532 TTTC-TCTT
1 TTTCTTCTT
15540 TTTCTTCTT
1 TTTCTTCTT
15549 TTTCTTCTT
1 TTTCTTCTT
15558 TTTCT
1 TTTCT
15563 AATCCTTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 4 0.18
9 18 0.82
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTCTTCTT
Found at i:23506 original size:28 final size:29
Alignment explanation
Indices: 23434--23509 Score: 86
Period size: 28 Copynumber: 2.7 Consensus size: 29
23424 TATGAAATAT
* *
23434 TTTTTTTATTTTTTA-ATTTACATATGCA
1 TTTTTTTATTTTATATCTTTACATATGCA
*
23462 TTATTTTTATTTAATATCTTTA-ATAAT-CA
1 TT-TTTTTATTTTATATCTTTACAT-ATGCA
23491 TTTTTTTATTTTATATCTT
1 TTTTTTTATTTTATATCTT
23510 ATTTGTTGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 18 0.44
29 17 0.41
30 6 0.15
ACGTcount: A:0.26, C:0.07, G:0.01, T:0.66
Consensus pattern (29 bp):
TTTTTTTATTTTATATCTTTACATATGCA
Found at i:30206 original size:21 final size:21
Alignment explanation
Indices: 30177--30216 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
30167 ACACCTCTAA
*
30177 AATTAAAATAAATTTCATCTT
1 AATTAAAATAAATTGCATCTT
* *
30198 AATTTAAATTAATTGCATC
1 AATTAAAATAAATTGCATC
30217 AAATATCCTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (21 bp):
AATTAAAATAAATTGCATCTT
Found at i:36896 original size:5 final size:5
Alignment explanation
Indices: 36886--36911 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
36876 TTGAAAAATA
36886 CCCAT CCCAT CCCAT CCCAT CCCAT C
1 CCCAT CCCAT CCCAT CCCAT CCCAT C
36912 TAAACTAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.62, G:0.00, T:0.19
Consensus pattern (5 bp):
CCCAT
Found at i:37453 original size:5 final size:5
Alignment explanation
Indices: 37443--37485 Score: 86
Period size: 5 Copynumber: 8.6 Consensus size: 5
37433 AACATCAGCA
37443 TCTCC TCTCC TCTCC TCTCC TCTCC TCTCC TCTCC TCTCC TCT
1 TCTCC TCTCC TCTCC TCTCC TCTCC TCTCC TCTCC TCTCC TCT
37486 TCCTTTTCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (5 bp):
TCTCC
Found at i:38532 original size:22 final size:20
Alignment explanation
Indices: 38507--38554 Score: 51
Period size: 23 Copynumber: 2.2 Consensus size: 20
38497 CTTTAAATAT
38507 ATTTTACATAAATTAATTTATA
1 ATTTTA-ATAAATT-ATTTATA
*
38529 ATTTCTTAATAAATTATTTATT
1 A-TT-TTAATAAATTATTTATA
38551 ATTT
1 ATTT
38555 CGATAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
20 1 0.04
21 2 0.09
22 8 0.35
23 9 0.39
24 3 0.13
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTTTAATAAATTATTTATA
Found at i:43562 original size:59 final size:60
Alignment explanation
Indices: 43448--43568 Score: 154
Period size: 60 Copynumber: 2.0 Consensus size: 60
43438 ATTTTGGCCA
* * *
43448 ACACCCCCTTTTTTGTCAGATAAAAAATACAATTTTTTTGTGTTGGCCATACAATGATCG
1 ACACCCCCTTTTTTATCAGATAAAAAATACAATTTTTTGGTGTTGACCATACAATGATCG
* ** * * *
43508 ACACCCTCTTTTTTATCAGATAAAAAATTTAATTTTTTGGTGTT-ATCATGCAATGGTCG
1 ACACCCCCTTTTTTATCAGATAAAAAATACAATTTTTTGGTGTTGACCATACAATGATCG
43567 AC
1 AC
43569 TCCTATTTAT
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
59 13 0.25
60 39 0.75
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (60 bp):
ACACCCCCTTTTTTATCAGATAAAAAATACAATTTTTTGGTGTTGACCATACAATGATCG
Found at i:43756 original size:62 final size:62
Alignment explanation
Indices: 43618--43743 Score: 200
Period size: 62 Copynumber: 2.0 Consensus size: 62
43608 AGGCCATTGC
*
43618 TCTCAGATAAAAAAATTTCAAAATTTTTTTGTGTTGGCCATGTCATGGCCGACACCCCCTTT
1 TCTCAGATAAAAAAATTTCAAAATTTTTTTGTGTTGGCCATGTAATGGCCGACACCCCCTTT
* *
43680 TCTCAGATAAAAAAATTTCAAAATTTTTTTGGTGTTGGCCATGTAAAT-GTCGACATCCCCTTT
1 TCTCAGATAAAAAAATTTCAAAATTTTTTT-GTGTTGGCCATGT-AATGGCCGACACCCCCTTT
43743 T
1 T
43744 TATTTGGTAA
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
62 30 0.51
63 27 0.46
64 2 0.03
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (62 bp):
TCTCAGATAAAAAAATTTCAAAATTTTTTTGTGTTGGCCATGTAATGGCCGACACCCCCTTT
Found at i:43756 original size:63 final size:62
Alignment explanation
Indices: 43620--43795 Score: 191
Period size: 62 Copynumber: 2.9 Consensus size: 62
43610 GCCATTGCTC
* *
43620 TCAGATAAAAAAATTTCAAAATTTTTTTGTGTTGGCCATGTCATGGCCGACACCCCCTTTTC
1 TCAGATAAAAAAATTTCAAAATTTTTTTGTGTTGGCCATGTAATGGCCGACACCCCCTTTTA
* *
43682 TCAGATAAAAAAATTTCAAAATTTTTTTGGTGTTGGCCATGTAAAT-GTCGACATCCCCTTTTTA
1 TCAGATAAAAAAATTTCAAAATTTTTTT-GTGTTGGCCATGT-AATGGCCGACA-CCCCCTTTTA
** * ** * *
43746 TTTGGT-AAAAAA-TT--AAATTTTTTAATGTTGACTATGTAATGGCCGACACC
1 TCAGATAAAAAAATTTCAAAATTTTTTTGTGTTGGCCATGTAATGGCCGACACC
43796 AACTTCTCCT
Statistics
Matches: 98, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
58 5 0.05
59 16 0.16
60 9 0.09
62 30 0.31
63 25 0.26
64 13 0.13
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.38
Consensus pattern (62 bp):
TCAGATAAAAAAATTTCAAAATTTTTTTGTGTTGGCCATGTAATGGCCGACACCCCCTTTTA
Found at i:44516 original size:121 final size:119
Alignment explanation
Indices: 44349--44637 Score: 395
Period size: 120 Copynumber: 2.4 Consensus size: 119
44339 GCCATTTGAA
* * **
44349 ATTTTTTTATCTGA-AAAAGAGGGTGTCGATCATTGCATGGCCAACACAAAAAAATTTTGAAATT
1 ATTTTTTTATCAGATAAAAG-GGGTGTCGGTCATTGCATGGCCAACACAAAAAAAAATT-AAA-T
* * *
44413 TTTTTATCTGA-GAAAAGGGGGTGTCGGCCATTGCATGACCAACA-TCCAAAAATTTG
63 TTTTTATCTGACAAAAAAGAGGTGTCGGCCATTGCATGACCAACACT-CAAAAATTTG
* * * *
44469 ATTTTTTTATCAGATAAATAGGGGTGTCGGCCATTGTATGGTCAACACAAAAAAAAATTATATTT
1 ATTTTTTTATCAGATAAA-AGGGGTGTCGGTCATTGCATGGCCAACACAAAAAAAAATTAAATTT
44534 TTTATCTGACAAAAAAGAGGTGTCGGCCATTGCATGACCAACACTCAAAAATTTG
65 TTTATCTGACAAAAAAGAGGTGTCGGCCATTGCATGACCAACACTCAAAAATTTG
44589 ATTTTTTTATCAGATTAAGAAGGGGTGTCGGTCATTGCATGGCCAACAC
1 ATTTTTTTATCAGA-TAA-AAGGGGTGTCGGTCATTGCATGGCCAACAC
44638 CCAATTTTTT
Statistics
Matches: 149, Mismatches: 14, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
119 12 0.08
120 69 0.46
121 65 0.44
122 3 0.02
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (119 bp):
ATTTTTTTATCAGATAAAAGGGGTGTCGGTCATTGCATGGCCAACACAAAAAAAAATTAAATTTT
TTATCTGACAAAAAAGAGGTGTCGGCCATTGCATGACCAACACTCAAAAATTTG
Found at i:44535 original size:60 final size:58
Alignment explanation
Indices: 44349--44637 Score: 296
Period size: 60 Copynumber: 4.8 Consensus size: 58
44339 GCCATTTGAA
**
44349 ATTTTTTTATCTGA-AAAAGAGGGTGTCGATCATTGCATGGCCAACACAAAAAAATTTTG
1 ATTTTTTTATCTGATAAAAG-GGGTGTCGGCCATTGCATGGCCAACACAAAAAAA-TTTG
* * *
44408 AAATTTTTTTATCTGAGAAAAGGGGGTGTCGGCCATTGCATGACCAACATC-CAAAAATTTG
1 --ATTTTTTTATCTGATAAAA-GGGGTGTCGGCCATTGCATGGCCAACA-CAAAAAAATTTG
* * * *
44469 ATTTTTTTATCAGATAAATAGGGGTGTCGGCCATTGTATGGTCAACACAAAAAAAAATT-
1 ATTTTTTTATCTGATAAA-AGGGGTGTCGGCCATTGCATGGCCAACAC-AAAAAAATTTG
* * * **
44528 ATATTTTTTATCTGACAAAAAAGAGGTGTCGGCCATTGCATGACCAACACTCAAAAATTTG
1 AT-TTTTTTATCTG--ATAAAAGGGGTGTCGGCCATTGCATGGCCAACACAAAAAAATTTG
* *
44589 ATTTTTTTATCAGATTAAGAAGGGGTGTCGGTCATTGCATGGCCAACAC
1 ATTTTTTTATCTGA-TAA-AAGGGGTGTCGGCCATTGCATGGCCAACAC
44638 CCAATTTTTT
Statistics
Matches: 191, Mismatches: 25, Indels: 25
0.79 0.10 0.10
Matches are distributed among these distances:
58 2 0.01
59 44 0.23
60 62 0.32
61 45 0.24
62 36 0.19
63 2 0.01
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (58 bp):
ATTTTTTTATCTGATAAAAGGGGTGTCGGCCATTGCATGGCCAACACAAAAAAATTTG
Found at i:51232 original size:26 final size:25
Alignment explanation
Indices: 51195--51251 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 25
51185 GATATACTCA
*
51195 TTTTTCTATTTTGGTA-TTTAATTT
1 TTTTTCTATTTTGGTACTTGAATTT
51219 TTTTATCTCATTTTGGTACTTGAATTT
1 TTTT-TCT-ATTTTGGTACTTGAATTT
51246 TGTTTT
1 T-TTTT
51252 ATTACCCGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 4 0.14
25 3 0.11
26 9 0.32
27 9 0.32
28 3 0.11
ACGTcount: A:0.16, C:0.07, G:0.11, T:0.67
Consensus pattern (25 bp):
TTTTTCTATTTTGGTACTTGAATTT
Found at i:51572 original size:20 final size:20
Alignment explanation
Indices: 51539--51584 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 20
51529 AAAATTATTT
51539 AAAAATTATGAAAATCATAAAA
1 AAAAATTA-GAAAAT-ATAAAA
*
51561 AAAAATTA-AAAATGTAAAA
1 AAAAATTAGAAAATATAAAA
51580 AAAAA
1 AAAAA
51585 AATTATAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 10 0.43
20 5 0.22
22 8 0.35
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (20 bp):
AAAAATTAGAAAATATAAAA
Found at i:58349 original size:24 final size:24
Alignment explanation
Indices: 58322--58368 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
58312 CGATTACGAG
*
58322 AAATGAGTGATAATATGTAAATGT
1 AAATGAGTGATAAGATGTAAATGT
58346 AAATGAGTGATAAGATGTAAATG
1 AAATGAGTGATAAGATGTAAATG
58369 AGTAGTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.23, T:0.30
Consensus pattern (24 bp):
AAATGAGTGATAAGATGTAAATGT
Found at i:60014 original size:23 final size:22
Alignment explanation
Indices: 59929--60008 Score: 115
Period size: 23 Copynumber: 3.5 Consensus size: 22
59919 GCTGGGGAAA
59929 CAGTAGGCACACACAGTGCAAT
1 CAGTAGGCACACACAGTGCAAT
59951 CTAGTAGGCACACACAGTGCAAT
1 C-AGTAGGCACACACAGTGCAAT
* *
59974 CAGTAGGCGCACATAGTGCAAAT
1 CAGTAGGCACACACAGTGC-AAT
*
59997 CAGAAGGCACAC
1 CAGTAGGCACAC
60009 GAAGTGTGAA
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
22 17 0.33
23 35 0.67
ACGTcount: A:0.36, C:0.26, G:0.24, T:0.14
Consensus pattern (22 bp):
CAGTAGGCACACACAGTGCAAT
Found at i:61461 original size:35 final size:34
Alignment explanation
Indices: 61422--61498 Score: 118
Period size: 34 Copynumber: 2.2 Consensus size: 34
61412 GGCCCAAAAC
61422 TTTGCCTCCAAAAATATCTTCCATCAAATTACTCT
1 TTTGCC-CCAAAAATATCTTCCATCAAATTACTCT
** *
61457 TTTGCCCCTTAAATATCTTCCATCAAATTACTTT
1 TTTGCCCCAAAAATATCTTCCATCAAATTACTCT
61491 TTTGCCCC
1 TTTGCCCC
61499 TCCTCAATCA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
34 33 0.85
35 6 0.15
ACGTcount: A:0.26, C:0.30, G:0.04, T:0.40
Consensus pattern (34 bp):
TTTGCCCCAAAAATATCTTCCATCAAATTACTCT
Found at i:61472 original size:34 final size:34
Alignment explanation
Indices: 61433--61499 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
61423 TTGCCTCCAA
61433 AAATATCTTCCATCAAATTACTCTTTTGCCCCTT
1 AAATATCTTCCATCAAATTACTCTTTTGCCCCTT
*
61467 AAATATCTTCCATCAAATTACTTTTTTGCCCCT
1 AAATATCTTCCATCAAATTACTCTTTTGCCCCT
61500 CCTCAATCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.27, C:0.28, G:0.03, T:0.42
Consensus pattern (34 bp):
AAATATCTTCCATCAAATTACTCTTTTGCCCCTT
Found at i:66381 original size:19 final size:20
Alignment explanation
Indices: 66354--66392 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
66344 GCTTGTAGGT
66354 TTTAAAAAAATA-TATTTTA
1 TTTAAAAAAATATTATTTTA
* *
66373 TTTATAAAAGTATTATTTTA
1 TTTAAAAAAATATTATTTTA
66393 ATAAATAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (20 bp):
TTTAAAAAAATATTATTTTA
Found at i:72369 original size:2 final size:2
Alignment explanation
Indices: 72364--72405 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
72354 TTTTATTCGA
72364 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
72406 CAATAAGCAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:74196 original size:24 final size:23
Alignment explanation
Indices: 74164--74210 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
74154 CCCGGCCTAG
74164 ATTTATAATAATAATTTTATTTTT
1 ATTTATAATAATAATTTT-TTTTT
* *
74188 ATTTTTAATACTAATTTTTTTTT
1 ATTTATAATAATAATTTTTTTTT
74211 GCTTGTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (23 bp):
ATTTATAATAATAATTTTTTTTT
Found at i:83340 original size:25 final size:25
Alignment explanation
Indices: 83312--83359 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
83302 TTTTTTTATC
83312 AAAAAT-TTAGATGACATAATTTTAA
1 AAAAATATTA-ATGACATAATTTTAA
**
83337 AAAAATATTAATGATTTAATTTT
1 AAAAATATTAATGACATAATTTT
83360 TTTTAAATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 17 0.85
26 3 0.15
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (25 bp):
AAAAATATTAATGACATAATTTTAA
Found at i:84671 original size:2 final size:2
Alignment explanation
Indices: 84664--84688 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
84654 ACCCACAATG
84664 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
84689 GTAAGTTCGT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Done.