Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010041.1 Kokia drynarioides strain JFW-HI SEQ_124809, 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: 39264
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Warning! 26 characters in sequence are not A, C, G, or T
Found at i:5028 original size:31 final size:30
Alignment explanation
Indices: 4993--5117 Score: 107
Period size: 31 Copynumber: 4.2 Consensus size: 30
4983 TTGGTATTTG
4993 AACTTGACACTTTTTTTTAATTTGGTACCTA
1 AACTTGACA-TTTTTTTTAATTTGGTACCTA
*
5024 AACTT----TTTTTGGTTCAATTTGGTA-CTCA
1 AACTTGACATTTTT--TTTAATTTGGTACCT-A
** *
5052 AACTTGACACTTTTTCCTAATTTGTTACCTA
1 AACTTGACA-TTTTTTTTAATTTGGTACCTA
* * *
5083 AACTTGACATTTTTTTAAAGTTGGTACTTA
1 AACTTGACATTTTTTTTAATTTGGTACCTA
5113 AACTT
1 AACTT
5118 TTTGGGGTCC
Statistics
Matches: 74, Mismatches: 11, Indels: 19
0.71 0.11 0.18
Matches are distributed among these distances:
26 5 0.07
27 2 0.03
28 17 0.23
30 20 0.27
31 23 0.31
32 2 0.03
33 5 0.07
ACGTcount: A:0.26, C:0.16, G:0.10, T:0.47
Consensus pattern (30 bp):
AACTTGACATTTTTTTTAATTTGGTACCTA
Found at i:5116 original size:89 final size:90
Alignment explanation
Indices: 4993--5164 Score: 229
Period size: 89 Copynumber: 1.9 Consensus size: 90
4983 TTGGTATTTG
* * ** * *
4993 AACTTGACACTTTTTTTTAATTTGGTACCTAAACTTTTTTTGGTTCAATTTGGTACTCAAACTTG
1 AACTTGACACTTTTTTTAAAGTTGGTACCTAAACTTTTTGGGGTCCAATTTAGTACTCAAACTTG
5058 ACACTTTTTCCTAATTTGTTACCTA
66 ACACTTTTTCCTAATTTGTTACCTA
* ** *
5083 AACTTGACA-TTTTTTTAAAGTTGGTACTTAAACTTTTTGGGGTCCAATTTAGTACTTGACCTTG
1 AACTTGACACTTTTTTTAAAGTTGGTACCTAAACTTTTTGGGGTCCAATTTAGTACTCAAACTTG
**
5147 ATTCTTTTTCCTAATTTG
66 ACACTTTTTCCTAATTTG
5165 GCACTTAATC
Statistics
Matches: 70, Mismatches: 12, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
89 61 0.87
90 9 0.13
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (90 bp):
AACTTGACACTTTTTTTAAAGTTGGTACCTAAACTTTTTGGGGTCCAATTTAGTACTCAAACTTG
ACACTTTTTCCTAATTTGTTACCTA
Found at i:6057 original size:31 final size:31
Alignment explanation
Indices: 6022--6092 Score: 117
Period size: 31 Copynumber: 2.3 Consensus size: 31
6012 TTAATATAAT
*
6022 ATTTGGTACTTGA-ACTTGACACTTTTTCTTA
1 ATTTGGTACTT-ACACTTGACACTTTTTCCTA
6053 ATTTGGTACTTACACTTGACACTTTTTCCTA
1 ATTTGGTACTTACACTTGACACTTTTTCCTA
6084 ATTTGGTAC
1 ATTTGGTAC
6093 CAAAACCTGA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
30 1 0.03
31 37 0.97
ACGTcount: A:0.23, C:0.18, G:0.13, T:0.46
Consensus pattern (31 bp):
ATTTGGTACTTACACTTGACACTTTTTCCTA
Found at i:6121 original size:31 final size:31
Alignment explanation
Indices: 6038--6122 Score: 100
Period size: 31 Copynumber: 2.7 Consensus size: 31
6028 TACTTGAACT
** * *
6038 TGACACTTTTTCTTAATTTGGTACTTACACT
1 TGACACTTTTTCTTAATTTGGTACCAAAACC
*
6069 TGACACTTTTTCCTAATTTGGTACCAAAACC
1 TGACACTTTTTCTTAATTTGGTACCAAAACC
*
6100 TGACACTTGTTT-TTAAGTTGGTA
1 TGACACTT-TTTCTTAATTTGGTA
6123 GTTAAACTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
31 43 0.93
32 3 0.07
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.44
Consensus pattern (31 bp):
TGACACTTTTTCTTAATTTGGTACCAAAACC
Found at i:6746 original size:17 final size:17
Alignment explanation
Indices: 6724--6782 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
6714 AAGAATATGA
6724 AAGGTTAAGGAAGATAG
1 AAGGTTAAGGAAGATAG
6741 AAGGTTAAAGGTCAAG--AG
1 AAGGTT-AAGG--AAGATAG
*
6759 -AGGTTAAGGAAGATGG
1 AAGGTTAAGGAAGATAG
6775 AAGGTTAA
1 AAGGTTAA
6783 AAGTCAAGGG
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
14 3 0.09
16 5 0.14
17 18 0.51
18 6 0.17
20 3 0.09
ACGTcount: A:0.44, C:0.02, G:0.36, T:0.19
Consensus pattern (17 bp):
AAGGTTAAGGAAGATAG
Found at i:6768 original size:34 final size:34
Alignment explanation
Indices: 6725--6799 Score: 123
Period size: 34 Copynumber: 2.2 Consensus size: 34
6715 AGAATATGAA
*
6725 AGGTTAAGGAAGATAGAAGGTTAAAGGTCAAGAG
1 AGGTTAAGGAAGATAGAAGGTTAAAAGTCAAGAG
* *
6759 AGGTTAAGGAAGATGGAAGGTTAAAAGTCAAGGG
1 AGGTTAAGGAAGATAGAAGGTTAAAAGTCAAGAG
6793 AGGTTAA
1 AGGTTAA
6800 AGGTTGAACA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.43, C:0.03, G:0.36, T:0.19
Consensus pattern (34 bp):
AGGTTAAGGAAGATAGAAGGTTAAAAGTCAAGAG
Found at i:12174 original size:17 final size:17
Alignment explanation
Indices: 12154--12212 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
12144 AGATAGAAGA
12154 TTAAAGGTCAAGGGAGG
1 TTAAAGGTCAAGGGAGG
12171 TT-AAGG--AAGATGGAAGG
1 TTAAAGGTCAAG--GG-AGG
*
12188 TTAAAAGTCAAGGGAGG
1 TTAAAGGTCAAGGGAGG
12205 TTAAAGGT
1 TTAAAGGT
12213 TGAACATCCA
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
14 3 0.09
16 6 0.18
17 17 0.50
18 5 0.15
20 3 0.09
ACGTcount: A:0.39, C:0.03, G:0.37, T:0.20
Consensus pattern (17 bp):
TTAAAGGTCAAGGGAGG
Found at i:12177 original size:34 final size:34
Alignment explanation
Indices: 12134--12208 Score: 123
Period size: 34 Copynumber: 2.2 Consensus size: 34
12124 AGAATATGAA
*
12134 AGGTTAAGGAAGATAGAAGATTAAAGGTCAAGGG
1 AGGTTAAGGAAGATAGAAGATTAAAAGTCAAGGG
* *
12168 AGGTTAAGGAAGATGGAAGGTTAAAAGTCAAGGG
1 AGGTTAAGGAAGATAGAAGATTAAAAGTCAAGGG
12202 AGGTTAA
1 AGGTTAA
12209 AGGTTGAACA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.43, C:0.03, G:0.36, T:0.19
Consensus pattern (34 bp):
AGGTTAAGGAAGATAGAAGATTAAAAGTCAAGGG
Found at i:19019 original size:69 final size:69
Alignment explanation
Indices: 18891--19039 Score: 194
Period size: 69 Copynumber: 2.2 Consensus size: 69
18881 AGTGTTGGGG
* * * * *
18891 AAACAATAAGCACACACAGTGCAAATCAGTAGGCACAAGCAGTGCAAATTAGTAGGCACACGCAG
1 AAACAGTAAGCACACACAGTGCAAATCAGTAAGCACAAGCAGTGCAAATCAGTAAGCACACACAG
18956 TGCA
66 TGCA
*
18960 AAACAGTAAGCACACACAGTGCAAATCAGTAAGCACATA-TAGTG-AGAATCAGTAAGCACACAC
1 AAACAGTAAGCACACACAGTGCAAATCAGTAAGCACA-AGCAGTGCA-AATCAGTAAGCACACAC
*
19023 AGTGCT
64 AGTGCA
*
19029 GAACAGTAAGC
1 AAACAGTAAGC
19040 GCGCTAATGT
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
68 1 0.01
69 68 0.97
70 1 0.01
ACGTcount: A:0.43, C:0.22, G:0.21, T:0.14
Consensus pattern (69 bp):
AAACAGTAAGCACACACAGTGCAAATCAGTAAGCACAAGCAGTGCAAATCAGTAAGCACACACAG
TGCA
Found at i:19039 original size:23 final size:23
Alignment explanation
Indices: 18897--19027 Score: 167
Period size: 23 Copynumber: 5.7 Consensus size: 23
18887 GGGGAAACAA
18897 TAAGCACACACAGTGCAAATCAG
1 TAAGCACACACAGTGCAAATCAG
* *
18920 TAGGCACA-AGCAGTGCAAATTAG
1 TAAGCACACA-CAGTGCAAATCAG
* * *
18943 TAGGCACACGCAGTGCAAAACAG
1 TAAGCACACACAGTGCAAATCAG
18966 TAAGCACACACAGTGCAAATCAG
1 TAAGCACACACAGTGCAAATCAG
* *
18989 TAAGCACATATAGTG-AGAATCAG
1 TAAGCACACACAGTGCA-AATCAG
19012 TAAGCACACACAGTGC
1 TAAGCACACACAGTGC
19028 TGAACAGTAA
Statistics
Matches: 92, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
22 2 0.02
23 90 0.98
ACGTcount: A:0.41, C:0.23, G:0.21, T:0.15
Consensus pattern (23 bp):
TAAGCACACACAGTGCAAATCAG
Found at i:22521 original size:11 final size:11
Alignment explanation
Indices: 22505--22539 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
22495 ATAATTTACG
22505 ATTAACAAATA
1 ATTAACAAATA
22516 ATTAACAAATA
1 ATTAACAAATA
**
22527 ATGCACAAATA
1 ATTAACAAATA
22538 AT
1 AT
22540 GCACAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.60, C:0.11, G:0.03, T:0.26
Consensus pattern (11 bp):
ATTAACAAATA
Found at i:22540 original size:11 final size:11
Alignment explanation
Indices: 22509--22546 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
22499 TTTACGATTA
**
22509 ACAAATAATTA
1 ACAAATAATGC
22520 ACAAATAATGC
1 ACAAATAATGC
22531 ACAAATAATGC
1 ACAAATAATGC
22542 ACAAA
1 ACAAA
22547 AAAACAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.61, C:0.16, G:0.05, T:0.18
Consensus pattern (11 bp):
ACAAATAATGC
Found at i:22732 original size:11 final size:10
Alignment explanation
Indices: 22704--22750 Score: 51
Period size: 11 Copynumber: 4.6 Consensus size: 10
22694 ACGGATATGT
22704 AAATAAA-AA
1 AAATAAATAA
*
22713 AAATGAATAA
1 AAATAAATAA
22723 CAAATAAATAA
1 -AAATAAATAA
*
22734 TAAATAAATTA
1 -AAATAAATAA
22745 AAATAA
1 AAATAA
22751 TGGCAATTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
9 6 0.19
10 8 0.25
11 18 0.56
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (10 bp):
AAATAAATAA
Found at i:24606 original size:50 final size:51
Alignment explanation
Indices: 24503--24620 Score: 123
Period size: 50 Copynumber: 2.3 Consensus size: 51
24493 TATGCCCCTC
* * * *
24503 TTAGGTGTATAAGATTCGCCATTGCAAGCTTCAATCTGCTCCTTTATAGCT
1 TTAGGTATATAAGATTCGCCATTACAAGCTTCAATCTGCTCCTCTACAGCT
* * * * *
24554 TTAGGTATATGAGATTTGCCATTAC-GGCTTCAATTTGCTCCTCTACATCT
1 TTAGGTATATAAGATTCGCCATTACAAGCTTCAATCTGCTCCTCTACAGCT
*
24604 TTACAG-ATATAAGATTC
1 TTA-GGTATATAAGATTC
24621 AGGGTTGTAA
Statistics
Matches: 54, Mismatches: 12, Indels: 3
0.78 0.17 0.04
Matches are distributed among these distances:
50 32 0.59
51 22 0.41
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.38
Consensus pattern (51 bp):
TTAGGTATATAAGATTCGCCATTACAAGCTTCAATCTGCTCCTCTACAGCT
Found at i:28330 original size:30 final size:30
Alignment explanation
Indices: 28294--28386 Score: 116
Period size: 30 Copynumber: 3.1 Consensus size: 30
28284 TACGCTTTAA
28294 CCCCAAAATTTCCAAAAATTTGAATTTGAC
1 CCCCAAAATTTCCAAAAATTTGAATTTGAC
* * *
28324 CCCCAAACTTTCTAAAAATTGGAATTTGAC
1 CCCCAAAATTTCCAAAAATTTGAATTTGAC
** *
28354 CCTTAAATTTTCCAAAAATTCT-AATTTGAC
1 CCCCAAAATTTCCAAAAATT-TGAATTTGAC
28384 CCC
1 CCC
28387 AAACTTTTCG
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.37, C:0.25, G:0.06, T:0.32
Consensus pattern (30 bp):
CCCCAAAATTTCCAAAAATTTGAATTTGAC
Found at i:28395 original size:30 final size:29
Alignment explanation
Indices: 28293--28409 Score: 112
Period size: 30 Copynumber: 4.0 Consensus size: 29
28283 TTACGCTTTA
*
28293 ACCCCAAAATTTCCAAAAATT-TGAATTTG
1 ACCCCAAATTTTCCAAAAATTCT-AATTTG
* * **
28322 ACCCCCAAACTTTCTAAAAATTGGAATTTG
1 A-CCCCAAATTTTCCAAAAATTCTAATTTG
*
28352 ACCCTTAAATTTTCCAAAAATTCTAATTTG
1 ACCC-CAAATTTTCCAAAAATTCTAATTTG
* *
28382 ACCCCAAACTTTT-CGAAAATTCAAATTT
1 ACCCCAAA-TTTTCCAAAAATTCTAATTT
28410 AACCTGATTT
Statistics
Matches: 73, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
29 20 0.27
30 53 0.73
ACGTcount: A:0.38, C:0.22, G:0.06, T:0.33
Consensus pattern (29 bp):
ACCCCAAATTTTCCAAAAATTCTAATTTG
Found at i:28494 original size:3 final size:3
Alignment explanation
Indices: 28488--28516 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
28478 TTTATGTTGT
28488 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
28517 TAATCCCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Done.