Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001692.1 Kokia drynarioides strain JFW-HI SEQ_113371, 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: 49364
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 14 characters in sequence are not A, C, G, or T
Found at i:90 original size:18 final size:18
Alignment explanation
Indices: 67--130 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 18
57 TTTTTTTTCC
67 TCTCCTTCTTCCTCTTCT
1 TCTCCTTCTTCCTCTTCT
85 TCTCCTTCTTCCTTCTTCT
1 TCTCCTTCTTCC-TCTTCT
* *
104 T-TCTTTCTTTCT-TTCTT
1 TCTCCTTCTTCCTCTTC-T
*
121 TCTCTTTCTT
1 TCTCCTTCTT
131 TCTTTCTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
16 3 0.07
17 3 0.07
18 28 0.68
19 7 0.17
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (18 bp):
TCTCCTTCTTCCTCTTCT
Found at i:97 original size:7 final size:7
Alignment explanation
Indices: 69--108 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
59 TTTTTTCCTC
69 TCCTTCT
1 TCCTTCT
76 TCC-TCT
1 TCCTTCT
82 T-CTTC-
1 TCCTTCT
87 TCCTTCT
1 TCCTTCT
94 TCCTTCT
1 TCCTTCT
*
101 TCTTTCT
1 TCCTTCT
108 T
1 T
109 TCTTTCTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
5 2 0.07
6 10 0.34
7 17 0.59
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (7 bp):
TCCTTCT
Found at i:107 original size:4 final size:4
Alignment explanation
Indices: 100--143 Score: 67
Period size: 4 Copynumber: 11.8 Consensus size: 4
90 TTCTTCCTTC
100 TTCT TTCT TTCT TTCT TTCT TTC- -TCT TTCT TTCT TTCT TT-T TTC
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTC
144 CTTCATTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 2 0.05
3 3 0.08
4 32 0.86
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTCT
Found at i:115 original size:22 final size:22
Alignment explanation
Indices: 69--138 Score: 79
Period size: 22 Copynumber: 3.0 Consensus size: 22
59 TTTTTTCCTC
*
69 TCCTTCTTCCTCTTCTTCTCCTTCT
1 TCCTTCTT-CT-TTCTT-TCTTTCT
94 TCCTTCTTCTTTCTTTCTTTCT
1 TCCTTCTTCTTTCTTTCTTTCT
*
116 TTCTT-TCTCTTTCTTTCTTTCT
1 TCCTTCT-TCTTTCTTTCTTTCT
138 T
1 T
139 TTTTCCTTCA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
21 1 0.02
22 26 0.62
23 5 0.12
24 2 0.05
25 8 0.19
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (22 bp):
TCCTTCTTCTTTCTTTCTTTCT
Found at i:131 original size:18 final size:18
Alignment explanation
Indices: 105--139 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
95 CCTTCTTCTT
105 TCTTTCTTTCTTTCTTTC
1 TCTTTCTTTCTTTCTTTC
123 TCTTTCTTTCTTTCTTT
1 TCTTTCTTTCTTTCTTT
140 TTTCCTTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (18 bp):
TCTTTCTTTCTTTCTTTC
Found at i:139 original size:22 final size:21
Alignment explanation
Indices: 101--143 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 21
91 TCTTCCTTCT
101 TCTTTCTTTCTTTCTTTCTTTC
1 TCTTTCTTTCTTTCTTT-TTTC
123 TCTTTCTTTCTTTCTTTTTTC
1 TCTTTCTTTCTTTCTTTTTTC
144 CTTCATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (21 bp):
TCTTTCTTTCTTTCTTTTTTC
Found at i:5194 original size:32 final size:32
Alignment explanation
Indices: 5153--5263 Score: 100
Period size: 32 Copynumber: 3.4 Consensus size: 32
5143 TATAAAAAAA
*
5153 AAAGATAAAAAATAGATTTAATTATCAAGATG
1 AAAGATAAAAAATAAATTTAATTATCAAGATG
* * * *
5185 AAAGGTAAAAAAT-TATGTT-ATCCTATAAAAAATG
1 AAAGATAAAAAATAAAT-TTAAT--TAT-CAAGATG
* *
5219 AAAGGTAAAAAATAAATTTAATTGTCAAGATG
1 AAAGATAAAAAATAAATTTAATTATCAAGATG
*
5251 AAAAATAAAAAAT
1 AAAGATAAAAAAT
5264 TATATTATCC
Statistics
Matches: 63, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
31 4 0.06
32 30 0.48
33 5 0.08
34 20 0.32
35 4 0.06
ACGTcount: A:0.58, C:0.04, G:0.12, T:0.27
Consensus pattern (32 bp):
AAAGATAAAAAATAAATTTAATTATCAAGATG
Found at i:5223 original size:34 final size:34
Alignment explanation
Indices: 5117--5231 Score: 132
Period size: 34 Copynumber: 3.5 Consensus size: 34
5107 AATTGTTAAG
5117 ATGAAAGGTAAAAAATTATGTTATCCTATAAAAA
1 ATGAAAGGTAAAAAATTATGTTATCCTATAAAAA
* * * * *
5151 A-AAAAGATAAAAAATAGAT-TTAAT--TAT-CAAG
1 ATGAAAGGTAAAAAAT-TATGTT-ATCCTATAAAAA
5182 ATGAAAGGTAAAAAATTATGTTATCCTATAAAAA
1 ATGAAAGGTAAAAAATTATGTTATCCTATAAAAA
5216 ATGAAAGGTAAAAAAT
1 ATGAAAGGTAAAAAAT
5232 AAATTTAATT
Statistics
Matches: 64, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
31 7 0.11
32 17 0.27
33 17 0.27
34 23 0.36
ACGTcount: A:0.57, C:0.04, G:0.12, T:0.27
Consensus pattern (34 bp):
ATGAAAGGTAAAAAATTATGTTATCCTATAAAAA
Found at i:5238 original size:66 final size:65
Alignment explanation
Indices: 5096--5283 Score: 270
Period size: 66 Copynumber: 2.9 Consensus size: 65
5086 TTTAATGATC
* *
5096 AAAAA-AAACTTAATTGTTAAGATGAAAGGTAAAAAATTATGTTATCCTATAAAAAAAAAAGATA
1 AAAAATAAATTTAATTGTCAAGATGAAAGGTAAAAAATTATGTTATCCTATAAAAAAAAAAGATA
* * * *
5160 AAAAATAGATTTAATTATCAAGATGAAAGGTAAAAAATTATGTTATCCTATAAAAAATGAAAGGT
1 AAAAATAAATTTAATTGTCAAGATGAAAGGTAAAAAATTATGTTATCCTATAAAAAA-AAAAGAT
5225 A
65 A
** * *
5226 AAAAATAAATTTAATTGTCAAGATGAAAAATAAAAAATTATATTATCCTACAAAAAAA
1 AAAAATAAATTTAATTGTCAAGATGAAAGGTAAAAAATTATGTTATCCTATAAAAAAA
5284 TAATCAAGCT
Statistics
Matches: 109, Mismatches: 13, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
64 5 0.05
65 47 0.43
66 57 0.52
ACGTcount: A:0.57, C:0.05, G:0.10, T:0.28
Consensus pattern (65 bp):
AAAAATAAATTTAATTGTCAAGATGAAAGGTAAAAAATTATGTTATCCTATAAAAAAAAAAGATA
Found at i:23906 original size:159 final size:159
Alignment explanation
Indices: 23611--24075 Score: 576
Period size: 159 Copynumber: 2.9 Consensus size: 159
23601 TTACTCCTCG
* * * *
23611 CAGTGGTCTTCATGGAATGCTTTCTTCAGAAATCTTTGAACAACGCAGCATTCAGAGATCTGGAT
1 CAGTGGCCTTCATAGAATGCTTTCTTCAGAAATCTTTGAACAACGCAGCATTGAGAGACCTGGAT
** *
23676 TTTCTGGAAGAAGTGATGAAAGAGATTCAGGAAACAGTTATGGGGAAAGAAGAAATAATGGAAAC
66 TTAGTGGAAGAAGTGATGAAAGAGATTCAGGAAACAGTTATGGGGAAAGAAGAAATAATGGAAAT
* *
23741 GGTAAAGAATCTGAAAAACATGGTGGTCA
131 GGTAAAGAATCTAAAAAACATGGTGATCA
* ** *
23770 CAGTGGCCTT-ATCAGAATGCTTTCTTCTGAAATCTTTGAACAACGCAGTGTTGAGAGCCCTGGA
1 CAGTGGCCTTCAT-AGAATGCTTTCTTCAGAAATCTTTGAACAACGCAGCATTGAGAGACCTGGA
* * ** * * * *
23834 TTTAGTGGAAGAAATGATGAAAGAGATTCAGGGAATGGTTATTGTGAAAGGAGAAATATTGGAAA
65 TTTAGTGGAAGAAGTGATGAAAGAGATTCAGGAAACAGTTATGGGGAAAGAAGAAATAATGGAAA
* **
23899 TGCTAAAGAATCTAAAAAACATGGTGATTG
130 TGGTAAAGAATCTAAAAAACATGGTGATCA
* * * * * * *
23929 CAGTGGCCTTCATAAAATGCGTTCTTCAGATACCTATGAACAATGCAGCACTGAGAGATCC-GGA
1 CAGTGGCCTTCATAGAATGCTTTCTTCAGAAATCTTTGAACAACGCAGCATTGAGAGA-CCTGGA
* *
23993 TTTAGTGGAACAAGTGATGAAA-AGGATTCAGGAAACAATTATGGGGAAAGAAGAAATAATGGAA
65 TTTAGTGGAAGAAGTGATGAAAGA-GATTCAGGAAACAGTTATGGGGAAAGAAGAAATAATGGAA
*
24057 ATGGTAAAGAATCTCAAAA
129 ATGGTAAAGAATCTAAAAA
24076 GAATGTTGAT
Statistics
Matches: 255, Mismatches: 47, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
158 3 0.01
159 248 0.97
160 4 0.02
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (159 bp):
CAGTGGCCTTCATAGAATGCTTTCTTCAGAAATCTTTGAACAACGCAGCATTGAGAGACCTGGAT
TTAGTGGAAGAAGTGATGAAAGAGATTCAGGAAACAGTTATGGGGAAAGAAGAAATAATGGAAAT
GGTAAAGAATCTAAAAAACATGGTGATCA
Found at i:26081 original size:72 final size:72
Alignment explanation
Indices: 25917--26119 Score: 248
Period size: 72 Copynumber: 2.8 Consensus size: 72
25907 GTAGCAACCC
* * * * * **
25917 ATTCATCAGCTACTGCACAATCCCCGGGGTGGCAAGCACTTCAAGCTCATGTCACGGGGCCTGGC
1 ATTCATCAGCTACAGCACAATCCCCTGGGTGGCAAGCACTTCAAGCCCATGTCATGGGTCAAGGC
25982 TTGCAGT
66 TTGCAGT
* * ** *
25989 ATTCA-CTGGC-GCCTCTACAATCCCCTGGGTGGCAAGCAGTTCAAGCCCATGTCATGGGTCAAG
1 ATTCATC-AGCTACAGC-ACAATCCCCTGGGTGGCAAGCACTTCAAGCCCATGTCATGGGTCAAG
26052 GCTTGCAGT
64 GCTTGCAGT
* *
26061 ATTCATCAGCTACAGCACAATCCCCTGGGTGGCAAGTACTTCAAGACCATGTCATGGGT
1 ATTCATCAGCTACAGCACAATCCCCTGGGTGGCAAGCACTTCAAGCCCATGTCATGGGT
26120 TATGCAGTGG
Statistics
Matches: 109, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
71 3 0.03
72 103 0.94
73 3 0.03
ACGTcount: A:0.23, C:0.29, G:0.25, T:0.23
Consensus pattern (72 bp):
ATTCATCAGCTACAGCACAATCCCCTGGGTGGCAAGCACTTCAAGCCCATGTCATGGGTCAAGGC
TTGCAGT
Found at i:30932 original size:21 final size:21
Alignment explanation
Indices: 30908--30949 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
30898 TATACATGAT
30908 AAAAGGTATCGATACGTTTTG
1 AAAAGGTATCGATACGTTTTG
* *
30929 AAAATGTATCGATACTTTTTG
1 AAAAGGTATCGATACGTTTTG
30950 TCATTGTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (21 bp):
AAAAGGTATCGATACGTTTTG
Found at i:32442 original size:25 final size:25
Alignment explanation
Indices: 32386--32456 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 25
32376 GCTTTAAGAT
*
32386 CTGCGAGCTCAA-CAAGATGTGTGAG
1 CTGCGAGCT-AAGCAAGATGTGCGAG
* *
32411 CTCCGAGCTTAGCAAGATGTGCGAG
1 CTGCGAGCTAAGCAAGATGTGCGAG
* *
32436 GTGCGAGCTAAGCAACATGTG
1 CTGCGAGCTAAGCAAGATGTG
32457 GAAGCTCAGT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
24 1 0.03
25 37 0.97
ACGTcount: A:0.27, C:0.21, G:0.32, T:0.20
Consensus pattern (25 bp):
CTGCGAGCTAAGCAAGATGTGCGAG
Found at i:32501 original size:17 final size:17
Alignment explanation
Indices: 32475--32509 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
32465 GTGCAAGTTA
32475 TAAAGGTGCAAGCCTAT
1 TAAAGGTGCAAGCCTAT
*
32492 TAAAGTTGCAAGCCTAT
1 TAAAGGTGCAAGCCTAT
32509 T
1 T
32510 GAATATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (17 bp):
TAAAGGTGCAAGCCTAT
Found at i:35276 original size:20 final size:21
Alignment explanation
Indices: 35251--35306 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 21
35241 TCTAGAACTC
35251 AGGTATCGATACTTTTT-CAA
1 AGGTATCGATACTTTTTGCAA
* * *
35271 AGGTATCAATATTTTTTGTAA
1 AGGTATCGATACTTTTTGCAA
*
35292 A-ATATCGATACTTTT
1 AGGTATCGATACTTTT
35307 GCTTAAAACG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
20 26 0.90
21 3 0.10
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (21 bp):
AGGTATCGATACTTTTTGCAA
Found at i:35805 original size:2 final size:2
Alignment explanation
Indices: 35798--35825 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35788 ACATATCTTT
35798 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
35826 TATCATTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:36145 original size:23 final size:23
Alignment explanation
Indices: 36117--36216 Score: 157
Period size: 23 Copynumber: 4.3 Consensus size: 23
36107 TGCTGAGCAA
*
36117 CAGTAAGCACACACAGTGC-AAT
1 CAGTAAGCACACACAGTGCTGAT
36139 CCAGTAAGCACACACAGTGCTGAT
1 -CAGTAAGCACACACAGTGCTGAT
36163 CAGTAAGCACACACAGTGCTGAT
1 CAGTAAGCACACACAGTGCTGAT
* *
36186 CAGTAAGCACAAACAGTGCTGAA
1 CAGTAAGCACACACAGTGCTGAT
36209 CAGTAAGC
1 CAGTAAGC
36217 GCGCTAGTGT
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
23 71 0.97
24 2 0.03
ACGTcount: A:0.38, C:0.26, G:0.21, T:0.15
Consensus pattern (23 bp):
CAGTAAGCACACACAGTGCTGAT
Found at i:43352 original size:25 final size:25
Alignment explanation
Indices: 43318--43403 Score: 93
Period size: 25 Copynumber: 3.5 Consensus size: 25
43308 GGTTAACCAT
43318 TCTGGGCTCGTAAGAGCTAATGTTG
1 TCTGGGCTCGTAAGAGCTAATGTTG
* * ***
43343 TCTGTGCTCGTATGAGCTAACCAT-
1 TCTGGGCTCGTAAGAGCTAATGTTG
* *
43367 CCTGGGCTCGTGAGAGCTAATGTTG
1 TCTGGGCTCGTAAGAGCTAATGTTG
*
43392 TCTGTGCTCGTA
1 TCTGGGCTCGTA
43404 TGAGATAAAA
Statistics
Matches: 45, Mismatches: 15, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
24 17 0.38
25 28 0.62
ACGTcount: A:0.17, C:0.21, G:0.29, T:0.33
Consensus pattern (25 bp):
TCTGGGCTCGTAAGAGCTAATGTTG
Found at i:43383 original size:24 final size:23
Alignment explanation
Indices: 43311--43386 Score: 71
Period size: 24 Copynumber: 3.1 Consensus size: 23
43301 GCATAATGGT
43311 TAACCATTCTGGGCTCGTAAGAGC
1 TAACCATTCTGGGCTCGT-AGAGC
*** *
43335 TAATGTTGTCTGTGCTCGTATGAGC
1 TAACCAT-TCTGGGCTCGTA-GAGC
*
43360 TAACCATCCTGGGCTCGTGAGAGC
1 TAACCATTCTGGGCTCGT-AGAGC
43384 TAA
1 TAA
43387 TGTTGTCTGT
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
24 21 0.52
25 19 0.47
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.29
Consensus pattern (23 bp):
TAACCATTCTGGGCTCGTAGAGC
Found at i:43383 original size:49 final size:49
Alignment explanation
Indices: 43311--43407 Score: 176
Period size: 49 Copynumber: 2.0 Consensus size: 49
43301 GCATAATGGT
*
43311 TAACCATTCTGGGCTCGTAAGAGCTAATGTTGTCTGTGCTCGTATGAGC
1 TAACCATCCTGGGCTCGTAAGAGCTAATGTTGTCTGTGCTCGTATGAGC
*
43360 TAACCATCCTGGGCTCGTGAGAGCTAATGTTGTCTGTGCTCGTATGAG
1 TAACCATCCTGGGCTCGTAAGAGCTAATGTTGTCTGTGCTCGTATGAG
43408 ATAAAATCTG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.20, C:0.21, G:0.28, T:0.32
Consensus pattern (49 bp):
TAACCATCCTGGGCTCGTAAGAGCTAATGTTGTCTGTGCTCGTATGAGC
Found at i:44077 original size:21 final size:21
Alignment explanation
Indices: 44029--44080 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
44019 GGAGTTTTTA
*
44029 GTATCGGTAGAAGCATGACAT
1 GTATCGGTAGAAGCATCACAT
* *
44050 GTTTCGGTAGAAGTC-TCACTT
1 GTATCGGTAGAAG-CATCACAT
44071 GTATCGGTAG
1 GTATCGGTAG
44081 TACTGTCTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 25 0.96
22 1 0.04
ACGTcount: A:0.25, C:0.15, G:0.29, T:0.31
Consensus pattern (21 bp):
GTATCGGTAGAAGCATCACAT
Done.