Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011170.1 Kokia drynarioides strain JFW-HI SEQ_126146, 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: 86994
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:6628 original size:25 final size:25
Alignment explanation
Indices: 6600--6660 Score: 122
Period size: 25 Copynumber: 2.4 Consensus size: 25
6590 AATCTCCTTT
6600 TTGTCGGTGCACACAAAAGCACGAC
1 TTGTCGGTGCACACAAAAGCACGAC
6625 TTGTCGGTGCACACAAAAGCACGAC
1 TTGTCGGTGCACACAAAAGCACGAC
6650 TTGTCGGTGCA
1 TTGTCGGTGCA
6661 TTTCTTTGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (25 bp):
TTGTCGGTGCACACAAAAGCACGAC
Found at i:10332 original size:37 final size:37
Alignment explanation
Indices: 10282--10416 Score: 144
Period size: 37 Copynumber: 3.5 Consensus size: 37
10272 AAATTCAAGT
10282 TTTGTGCCTAGTAGGCTTCGTGCTAGTGTTTTCAGGC
1 TTTGTGCCTAGTAGGCTTCGTGCTAGTGTTTTCAGGC
** **
10319 TTTGTGCCTAGTAGGCTTCGTGCCGGTGTTTTTTTTTTTTGGC
1 TTTGTGCCTAGTAGGCTTCGTGCTAGTG------TTTTCAGGC
* * *
10362 TTTGTACCTAGTAGGCTTCATGCTAATGTTTTCAGGC
1 TTTGTGCCTAGTAGGCTTCGTGCTAGTGTTTTCAGGC
*
10399 TATGTGCCTAGTAGGCTT
1 TTTGTGCCTAGTAGGCTT
10417 ATGCTGCTAT
Statistics
Matches: 79, Mismatches: 13, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
37 49 0.62
43 30 0.38
ACGTcount: A:0.12, C:0.18, G:0.27, T:0.44
Consensus pattern (37 bp):
TTTGTGCCTAGTAGGCTTCGTGCTAGTGTTTTCAGGC
Found at i:14954 original size:58 final size:58
Alignment explanation
Indices: 14892--15043 Score: 209
Period size: 58 Copynumber: 2.6 Consensus size: 58
14882 TAGCTCGATT
* *
14892 ACACCGACACGAAGCCTACTAGGCACATAGCCTGAAAACA-TGAGCACAAAGCTTA-AAA
1 ACACCGACACGAAGCCTACTAGGCACAAAGCCTGAAAACACTG-GCACAAAGC-CAGAAA
* * *
14950 ACACCGAAACGAAGCCTACTAGGCACAAAGCCTAAAAACACTGGCACGAAGCCAGAAA
1 ACACCGACACGAAGCCTACTAGGCACAAAGCCTGAAAACACTGGCACAAAGCCAGAAA
* *
15008 ACACCGGCACGAAGCTTACTAGGCACAAAGCCTGAA
1 ACACCGACACGAAGCCTACTAGGCACAAAGCCTGAA
15044 TTTTTAGATG
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
57 1 0.01
58 80 0.96
59 2 0.02
ACGTcount: A:0.42, C:0.29, G:0.19, T:0.10
Consensus pattern (58 bp):
ACACCGACACGAAGCCTACTAGGCACAAAGCCTGAAAACACTGGCACAAAGCCAGAAA
Found at i:15001 original size:21 final size:21
Alignment explanation
Indices: 14971--15022 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
14961 AAGCCTACTA
* *
14971 GGCACAAAGCCTA-AAAACACT
1 GGCACGAAGCC-AGAAAACACC
14992 GGCACGAAGCCAGAAAACACC
1 GGCACGAAGCCAGAAAACACC
15013 GGCACGAAGC
1 GGCACGAAGC
15023 TTACTAGGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 1 0.04
21 27 0.96
ACGTcount: A:0.42, C:0.31, G:0.23, T:0.04
Consensus pattern (21 bp):
GGCACGAAGCCAGAAAACACC
Found at i:17107 original size:18 final size:17
Alignment explanation
Indices: 17084--17138 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 17
17074 GGGGAACATC
17084 TTCTTCTTTTTCTTTCTT
1 TTCTTCTTTTTC-TTCTT
17102 TTCTTCTTTTTCTTCTT
1 TTCTTCTTTTTCTTCTT
* *
17119 TTTTTCCTTCTTCTTCTT
1 TTCTT-CTTTTTCTTCTT
17137 TT
1 TT
17139 GCCTCAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.26
18 25 0.74
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (17 bp):
TTCTTCTTTTTCTTCTT
Found at i:17119 original size:27 final size:27
Alignment explanation
Indices: 17084--17138 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
17074 GGGGAACATC
*
17084 TTCTTCTTTTTCTTTCTT-TTCTTCTTT
1 TTCTTCTTTTT-TTCCTTCTTCTTCTTT
17111 TTCTTCTTTTTTTCCTTCTTCTTCTTT
1 TTCTTCTTTTTTTCCTTCTTCTTCTTT
17138 T
1 T
17139 GCCTCAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (27 bp):
TTCTTCTTTTTTTCCTTCTTCTTCTTT
Found at i:17135 original size:21 final size:21
Alignment explanation
Indices: 17082--17136 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
17072 TCGGGGAACA
*
17082 TCTTCTTCTTTTTCTTTCTTT
1 TCTTCTTCTTCTTCTTTCTTT
*
17103 TCTTCTTTTTCTTCTTT-TTT
1 TCTTCTTCTTCTTCTTTCTTT
17123 TCCTTCTTCTTCTT
1 T-CTTCTTCTTCTT
17137 TTGCCTCAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 4 0.13
21 26 0.87
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (21 bp):
TCTTCTTCTTCTTCTTTCTTT
Found at i:22466 original size:12 final size:13
Alignment explanation
Indices: 22437--22495 Score: 50
Period size: 12 Copynumber: 4.4 Consensus size: 13
22427 GTCAGAACAA
*
22437 CTTCTTCTT-CTT
1 CTTCTTTTTCCTT
*
22449 TTTCTTTTTCCTT
1 CTTCTTTTTCCTT
22462 C-TCTTCTCTTCCTT
1 CTTCTT-T-TTCCTT
22476 CTTCTTTTTTCTCTT
1 CTTC-TTTTTC-CTT
22491 CTTCT
1 CTTCT
22496 GCAATACCCT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
12 11 0.29
13 4 0.11
14 11 0.29
15 10 0.26
16 2 0.05
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (13 bp):
CTTCTTTTTCCTT
Found at i:22467 original size:24 final size:25
Alignment explanation
Indices: 22439--22495 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
22429 CAGAACAACT
*
22439 TCTTCTTCTT-TTTCTT-TTTCCTTC
1 TCTTCTTCTTCCTTCTTCTTT-CTTC
*
22463 TCTTC-TCTTCCTTCTTCTTTTTTC
1 TCTTCTTCTTCCTTCTTCTTTCTTC
22487 TCTTCTTCT
1 TCTTCTTCT
22496 GCAATACCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
23 4 0.14
24 18 0.64
25 6 0.21
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (25 bp):
TCTTCTTCTTCCTTCTTCTTTCTTC
Found at i:29667 original size:24 final size:24
Alignment explanation
Indices: 29635--29682 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
29625 TACTTATTCG
29635 CTTATTCTTGGATTTAACCGCTCT
1 CTTATTCTTGGATTTAACCGCTCT
29659 CTTATTCTTGGATTTAACCGCTCT
1 CTTATTCTTGGATTTAACCGCTCT
29683 AAACACAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.17, C:0.25, G:0.12, T:0.46
Consensus pattern (24 bp):
CTTATTCTTGGATTTAACCGCTCT
Found at i:30838 original size:11 final size:11
Alignment explanation
Indices: 30811--30840 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
30801 AATTCATGCA
30811 TCCAAAAACAC
1 TCCAAAAACAC
30822 TCCCAAAAACAC
1 T-CCAAAAACAC
30834 TCCAAAA
1 TCCAAAA
30841 CCTTCATCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.53, C:0.37, G:0.00, T:0.10
Consensus pattern (11 bp):
TCCAAAAACAC
Found at i:47886 original size:17 final size:18
Alignment explanation
Indices: 47866--47901 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
47856 TAAATGAGTT
47866 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
47883 AATTAGGGTATAAATTGG
1 AATTAGGATATAAATTGG
47901 A
1 A
47902 TAGAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:51701 original size:18 final size:15
Alignment explanation
Indices: 51678--51720 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 15
51668 ATAATCTTAC
51678 CAAATAAATACAATAA
1 CAAATAAATA-AATAA
51694 TTCAAATATAATAAATAA
1 --CAAATA-AATAAATAA
51712 CAAATAAAT
1 CAAATAAAT
51721 CTTTGTCCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 3 0.12
16 6 0.25
18 11 0.46
19 4 0.17
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (15 bp):
CAAATAAATAAATAA
Found at i:51857 original size:27 final size:27
Alignment explanation
Indices: 51819--51960 Score: 124
Period size: 27 Copynumber: 5.3 Consensus size: 27
51809 ACAATAACAA
* *
51819 AATATTGCTCATTCAAGCTAGCTACAG
1 AATATCGCTCATTCAAGCTAGATACAG
* * * *
51846 GATATCGATCATTCAAGCAAGATATAGG
1 AATATCGCTCATTCAAGCTAGATACA-G
* * * *
51874 AA-ATAGTTCATTCGAGCCAGATACAG
1 AATATCGCTCATTCAAGCTAGATACAG
* *
51900 AATATCGCTCATTCGAGCTAGATATAG
1 AATATCGCTCATTCAAGCTAGATACAG
** * *
51927 AATATCGCTCATTTGAGCCAGATACAA
1 AATATCGCTCATTCAAGCTAGATACAG
51954 AATATCG
1 AATATCG
51961 TTAATTGCTC
Statistics
Matches: 93, Mismatches: 20, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
26 3 0.03
27 88 0.95
28 2 0.02
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.27
Consensus pattern (27 bp):
AATATCGCTCATTCAAGCTAGATACAG
Found at i:51905 original size:54 final size:54
Alignment explanation
Indices: 51819--51960 Score: 160
Period size: 54 Copynumber: 2.6 Consensus size: 54
51809 ACAATAACAA
* * * * *
51819 AATATTGCTCATTCAAGCTAGCTACAGGATATCGATCATTCAAGCAAGATATAGG
1 AATATAGCTCATTCGAGCCAGATACAGAATATCGATCATTCAAGCAAGATATA-G
* * * *
51874 AA-ATAGTTCATTCGAGCCAGATACAGAATATCGCTCATTCGAGCTAGATATAG
1 AATATAGCTCATTCGAGCCAGATACAGAATATCGATCATTCAAGCAAGATATAG
* * *
51927 AATATCGCTCATTTGAGCCAGATACAAAATATCG
1 AATATAGCTCATTCGAGCCAGATACAGAATATCG
51961 TTAATTGCTC
Statistics
Matches: 73, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
53 3 0.04
54 68 0.93
55 2 0.03
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.27
Consensus pattern (54 bp):
AATATAGCTCATTCGAGCCAGATACAGAATATCGATCATTCAAGCAAGATATAG
Found at i:67356 original size:111 final size:110
Alignment explanation
Indices: 67155--67372 Score: 364
Period size: 111 Copynumber: 2.0 Consensus size: 110
67145 TCTTCAAGCC
* *
67155 AAGGAATTTTTGAGAAGGGAATTATAATCAGTACCAACAAAATTTCAATCAAAGTCCTCAGATGC
1 AAGGAATTTTTGACAAGGGAATTATAATCAGTACCAACAAAATTTCAATCAAAGTCCCCAGATGC
* *
67220 ATGTACATCAAGATCAGTTGTAGCCACATACTCGTGTGCAGCCAT
66 ATGTACATCAAGATCAGTTGCAGCCACATACTCGTATGCAGCCAT
* * *
67265 AAGGAAATTTTTTACAAGGGAATTATAATCAGTAGCAACAAAATTTCAATGAAAGTCCCCAGATG
1 AAGG-AATTTTTGACAAGGGAATTATAATCAGTACCAACAAAATTTCAATCAAAGTCCCCAGATG
67330 CATGTACATCAAGATCAGTTGCAGCCACATACTCGTATGCAGC
65 CATGTACATCAAGATCAGTTGCAGCCACATACTCGTATGCAGC
67373 TACAACAATC
Statistics
Matches: 100, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
110 4 0.04
111 96 0.96
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (110 bp):
AAGGAATTTTTGACAAGGGAATTATAATCAGTACCAACAAAATTTCAATCAAAGTCCCCAGATGC
ATGTACATCAAGATCAGTTGCAGCCACATACTCGTATGCAGCCAT
Done.