Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013525.1 Kokia drynarioides strain JFW-HI SEQ_128551, 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: 40483
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Warning! 63 characters in sequence are not A, C, G, or T
Found at i:2684 original size:19 final size:19
Alignment explanation
Indices: 2662--2707 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
2652 CAATAATATG
*
2662 TTAAAAATTAAATAAAATT
1 TTAAAAATAAAATAAAATT
**
2681 TTAATAAATAAAATACGATT
1 TTAA-AAATAAAATAAAATT
2701 TTAAAAA
1 TTAAAAA
2708 GATATCATAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (19 bp):
TTAAAAATAAAATAAAATT
Found at i:2767 original size:4 final size:4
Alignment explanation
Indices: 2747--2813 Score: 59
Period size: 4 Copynumber: 17.2 Consensus size: 4
2737 AACACATTAC
* * * *
2747 CTTT CTTT CATT C-TT CTTT CTTT CCTCT CCTT CTTC CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT
*
2795 -TTT -TTT CTTT CTTT TTTT C
1 CTTT CTTT CTTT CTTT CTTT C
2814 CGTTTATTTG
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
3 9 0.18
4 39 0.76
5 3 0.06
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.70
Consensus pattern (4 bp):
CTTT
Found at i:2803 original size:14 final size:14
Alignment explanation
Indices: 2784--2812 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2774 TCCTTCTTCC
2784 TTTCTTTCTTTTTT
1 TTTCTTTCTTTTTT
2798 TTTCTTTCTTTTTT
1 TTTCTTTCTTTTTT
2812 T
1 T
2813 CCGTTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTCTTTCTTTTTT
Found at i:4955 original size:19 final size:19
Alignment explanation
Indices: 4933--4978 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
4923 CAATAATATG
*
4933 TTAAAAATTAAATAAAATT
1 TTAAAAATAAAATAAAATT
**
4952 TTAATAAATAAAATACGATT
1 TTAA-AAATAAAATAAAATT
4972 TTAAAAA
1 TTAAAAA
4979 GATATCATAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (19 bp):
TTAAAAATAAAATAAAATT
Found at i:5038 original size:4 final size:4
Alignment explanation
Indices: 5018--5084 Score: 59
Period size: 4 Copynumber: 17.2 Consensus size: 4
5008 AACACATTAC
* * * *
5018 CTTT CTTT CATT C-TT CTTT CTTT CCTCT CCTT CTTC CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT
*
5066 -TTT -TTT CTTT CTTT TTTT C
1 CTTT CTTT CTTT CTTT CTTT C
5085 CGTTTATTTG
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
3 9 0.18
4 39 0.76
5 3 0.06
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.70
Consensus pattern (4 bp):
CTTT
Found at i:5074 original size:14 final size:14
Alignment explanation
Indices: 5055--5083 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5045 TCCTTCTTCC
5055 TTTCTTTCTTTTTT
1 TTTCTTTCTTTTTT
5069 TTTCTTTCTTTTTT
1 TTTCTTTCTTTTTT
5083 T
1 T
5084 CCGTTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTCTTTCTTTTTT
Found at i:8519 original size:23 final size:23
Alignment explanation
Indices: 8471--8615 Score: 147
Period size: 23 Copynumber: 6.4 Consensus size: 23
8461 TATACGAAAC
* * *
8471 AAACAGAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACACAGTGCT
8493 -AACAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACACAGTGCT
* * *
8515 AAACAGAGAGTACACAAAGTACT
1 AAACAGAGAGCACACACAGTGCT
*
8538 AATCAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACACAGTGCT
*
8561 AATCAGAGAG--CACACAGTGCT
1 AAACAGAGAGCACACACAGTGCT
*
8582 ACTAACAGAGAGCACGAGAC-GTGCT
1 A--AACAGAGAGCAC-ACACAGTGCT
8607 AAACAGAGA
1 AAACAGAGA
8616 ACGCGCTAGT
Statistics
Matches: 104, Mismatches: 12, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
21 23 0.22
22 7 0.07
23 64 0.62
25 7 0.07
26 3 0.03
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACACAGTGCT
Found at i:8559 original size:46 final size:45
Alignment explanation
Indices: 8471--8615 Score: 204
Period size: 46 Copynumber: 3.2 Consensus size: 45
8461 TATACGAAAC
8471 AAACAGAGAGTAC-CAAAGTACTAACAGAGAGCACACACAGTGCT
1 AAACAGAGAGTACACAAAGTACTAACAGAGAGCACACACAGTGCT
8515 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACACAGTGCT
1 AAACAGAGAGTACACAAAGTACTAA-CAGAGAGCACACACAGTGCT
* * ** *
8561 AATCAGAGAGCACACAGTGCTACTAACAGAGAGCACGAGAC-GTGCT
1 AAACAGAGAGTACACAAAG-TACTAACAGAGAGCAC-ACACAGTGCT
8607 AAACAGAGA
1 AAACAGAGA
8616 ACGCGCTAGT
Statistics
Matches: 91, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
44 13 0.14
45 11 0.12
46 58 0.64
47 9 0.10
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (45 bp):
AAACAGAGAGTACACAAAGTACTAACAGAGAGCACACACAGTGCT
Found at i:19498 original size:21 final size:21
Alignment explanation
Indices: 19456--19499 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
19446 AAAATTATTT
*
19456 AATAATTTTATTATTTAAAAA
1 AATAATTTTATAATTTAAAAA
*
19477 AATAATTTTAATAATTTTAAAA
1 AATAATTTT-ATAATTTAAAAA
19499 A
1 A
19500 CAATTTCTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AATAATTTTATAATTTAAAAA
Found at i:24731 original size:18 final size:16
Alignment explanation
Indices: 24708--24743 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
24698 CTTAGTAAAT
24708 ATTAAATTGAGGAATGAA
1 ATTAAATTGA--AATGAA
24726 ATTAAATTGAAATGAA
1 ATTAAATTGAAATGAA
24742 AT
1 AT
24744 GGTATTGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
18 10 0.56
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (16 bp):
ATTAAATTGAAATGAA
Found at i:25352 original size:52 final size:52
Alignment explanation
Indices: 25268--25399 Score: 210
Period size: 52 Copynumber: 2.5 Consensus size: 52
25258 TAAATGCAAA
* * *
25268 AGGTTCGATGACTATGTGTCATCGCGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATG
* *
25320 AGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTTCAGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATG
*
25372 AGGTCCGATGACTATATGTCATCGTGAG
1 AGGTCCGATGACTATGTGTCATCGTGAG
25400 AATTAAATGA
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATG
Found at i:26774 original size:15 final size:15
Alignment explanation
Indices: 26751--26780 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
26741 GACCTTTTTG
26751 CAAAACAGCAATGAA
1 CAAAACAGCAATGAA
*
26766 CAAATCAGCAATGAA
1 CAAAACAGCAATGAA
26781 AATATTACTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.20, G:0.13, T:0.10
Consensus pattern (15 bp):
CAAAACAGCAATGAA
Found at i:28037 original size:27 final size:27
Alignment explanation
Indices: 27994--28125 Score: 153
Period size: 27 Copynumber: 5.0 Consensus size: 27
27984 TCATTATCAT
* *
27994 TATCTACCTCTGGAACAACTTCCTCCC
1 TATCTCCCTCTGAAACAACTTCCTCCC
* *
28021 CATCTCCCTCTGAAACAATTTCCTCCC
1 TATCTCCCTCTGAAACAACTTCCTCCC
* *
28048 TATCTCCCTCTAAAACAACTTCCTCAC
1 TATCTCCCTCTGAAACAACTTCCTCCC
** *
28075 TATCTCCCTCTG--A-AACGGCCTCCT
1 TATCTCCCTCTGAAACAACTTCCTCCC
*
28099 TATCTCCCTCTGGAACAACTTCCTCCC
1 TATCTCCCTCTGAAACAACTTCCTCCC
28126 CTCCCTCTCG
Statistics
Matches: 86, Mismatches: 16, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
24 19 0.22
25 1 0.01
26 1 0.01
27 65 0.76
ACGTcount: A:0.22, C:0.42, G:0.06, T:0.30
Consensus pattern (27 bp):
TATCTCCCTCTGAAACAACTTCCTCCC
Found at i:28065 original size:54 final size:51
Alignment explanation
Indices: 28007--28126 Score: 150
Period size: 51 Copynumber: 2.3 Consensus size: 51
27997 CTACCTCTGG
**
28007 AACAACTTCCTCCCCATCTCCCTCTGAAACAATTTCCTCCCTATCTCCCTCTAA
1 AACAACTTCCTCCCCATCTCCCTCTGAAAC---GGCCTCCCTATCTCCCTCTAA
* * * **
28061 AACAACTTCCTCACTATCTCCCTCTGAAACGGCCTCCTTATCTCCCTCTGG
1 AACAACTTCCTCCCCATCTCCCTCTGAAACGGCCTCCCTATCTCCCTCTAA
28112 AACAACTTCCTCCCC
1 AACAACTTCCTCCCC
28127 TCCCTCTCGA
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
51 29 0.51
54 28 0.49
ACGTcount: A:0.23, C:0.44, G:0.05, T:0.28
Consensus pattern (51 bp):
AACAACTTCCTCCCCATCTCCCTCTGAAACGGCCTCCCTATCTCCCTCTAA
Found at i:28144 original size:24 final size:25
Alignment explanation
Indices: 28102--28150 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
28092 GCCTCCTTAT
*
28102 CTCCCTCTGGAACAACTTC-CTCCC
1 CTCCCTCTCGAACAACTTCACTCCC
28126 CTCCCTCTCGAA-AAGCTTCACTCCC
1 CTCCCTCTCGAACAA-CTTCACTCCC
28151 ACACTGATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 2 0.09
24 15 0.68
25 5 0.23
ACGTcount: A:0.18, C:0.49, G:0.08, T:0.24
Consensus pattern (25 bp):
CTCCCTCTCGAACAACTTCACTCCC
Found at i:29564 original size:183 final size:184
Alignment explanation
Indices: 29239--29569 Score: 445
Period size: 183 Copynumber: 1.8 Consensus size: 184
29229 AAATTTTAAT
* * *
29239 ATTTTTTAAGATTATTTACAGATTTATTCATATTTTCAATTTTTGACACATGTTTCAATATTTGG
1 ATTTTTTAAGATTATTTACAGATTTATTCATATTTTCAATTTTTGACACATGCTTCAATATGTGC
* * *
29304 AATTCTTTAACAATTTTAGCAAATTCTCAAATTTTTAATACCTTAAACCTTATTGAAATATGTTA
66 AATTCTTTAACAATTTCAACAAATTCTCAAATTTTTAATACCTTAAACCTTATTGAAATATATTA
29369 AATCTGTAATTTT-CACTTTTCTTCATATAAACTTTACCTTGTTAAATTCTCAA
131 AATCTGTAATTTTACACTTTTCTTCATATAAACTTTACCTTGTTAAATTCTCAA
* * * *
29422 ATTTTTTAATATTATTTATAGTTTTATTCATATTTTCAATTTTTGATACATGCTTCAATATGTGC
1 ATTTTTTAAGATTATTTACAGATTTATTCATATTTTCAATTTTTGACACATGCTTCAATATGTGC
* * * * * * *
29487 AATTTTTTAACAGTTTCAATAAATT-TCCACATTTTTCAT-TCTTATCAACCTTATTGAAATCTA
66 AATTCTTTAACAATTTCAACAAATTCT-CAAATTTTTAATACCTTA--AACCTTATTGAAATATA
*
29550 TTAAAT-TTTAATTTTACACT
128 TTAAATCTGTAATTTTACACT
29570 GTAATTGTTT
Statistics
Matches: 126, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
182 5 0.04
183 96 0.76
184 25 0.20
ACGTcount: A:0.32, C:0.13, G:0.05, T:0.49
Consensus pattern (184 bp):
ATTTTTTAAGATTATTTACAGATTTATTCATATTTTCAATTTTTGACACATGCTTCAATATGTGC
AATTCTTTAACAATTTCAACAAATTCTCAAATTTTTAATACCTTAAACCTTATTGAAATATATTA
AATCTGTAATTTTACACTTTTCTTCATATAAACTTTACCTTGTTAAATTCTCAA
Found at i:39782 original size:2 final size:2
Alignment explanation
Indices: 39775--39812 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
39765 AAATTAAAGT
39775 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39813 AACTATAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.