Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012362.1 Kokia drynarioides strain JFW-HI SEQ_127366, 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: 39360
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.31
Warning! 32 characters in sequence are not A, C, G, or T
Found at i:15183 original size:13 final size:14
Alignment explanation
Indices: 15149--15186 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
15139 CAATAAAATC
15149 TGCATAATTTTTTTA
1 TGCA-AATTTTTTTA
*
15164 TGTAAATTTTTTTA
1 TGCAAATTTTTTTA
15178 T-CAAATTTT
1 TGCAAATTTT
15187 ATCATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 7 0.33
14 11 0.52
15 3 0.14
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61
Consensus pattern (14 bp):
TGCAAATTTTTTTA
Found at i:21039 original size:28 final size:28
Alignment explanation
Indices: 21008--21069 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
20998 TGTTATTAAC
21008 AAATAAATA-TTATGGCAAACAAATAAAG
1 AAATAAA-AGTTATGGCAAACAAATAAAG
21036 AAATAAAAGTTATGGCAAACAAATAAAG
1 AAATAAAAGTTATGGCAAACAAATAAAG
21064 AAATAA
1 AAATAA
21070 TGTGATGGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
27 1 0.03
28 32 0.97
ACGTcount: A:0.63, C:0.06, G:0.11, T:0.19
Consensus pattern (28 bp):
AAATAAAAGTTATGGCAAACAAATAAAG
Found at i:22241 original size:21 final size:21
Alignment explanation
Indices: 22215--22258 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
22205 TCCAATGTGC
* *
22215 AAAATGTAATTAAA-ATATCTT
1 AAAATGCAACTAAACATA-CTT
22236 AAAATGCAACTAAACATACTT
1 AAAATGCAACTAAACATACTT
22257 AA
1 AA
22259 GTACAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.55, C:0.11, G:0.05, T:0.30
Consensus pattern (21 bp):
AAAATGCAACTAAACATACTT
Found at i:26138 original size:18 final size:18
Alignment explanation
Indices: 26098--26149 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
26088 TTTTTAGTTA
*
26098 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAATTTATT
*
26116 CAATTAATTAAATTTATT
1 TAATTAATTAAATTTATT
26134 TAATTAA--AAATTTATT
1 TAATTAATTAAATTTATT
26150 CTCATCCCAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 9 0.30
17 7 0.23
18 14 0.47
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
TAATTAATTAAATTTATT
Found at i:30861 original size:10 final size:10
Alignment explanation
Indices: 30826--30866 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
30816 CTTCTACTCA
*
30826 TTTTTTTCTT
1 TTTTTTTATT
* *
30836 TTCTTTTCTT
1 TTTTTTTATT
30846 TTTTTTTATT
1 TTTTTTTATT
30856 TTTTTTTATT
1 TTTTTTTATT
30866 T
1 T
30867 CTCTCTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.05, C:0.07, G:0.00, T:0.88
Consensus pattern (10 bp):
TTTTTTTATT
Found at i:31212 original size:17 final size:17
Alignment explanation
Indices: 31154--31282 Score: 150
Period size: 17 Copynumber: 7.4 Consensus size: 17
31144 CCAAACTCCC
31154 TTTAAATTTATTTTAAAA
1 TTTAAATTTATTTT-AAA
* * *
31172 ATTAAATTTGTTTAAAA
1 TTTAAATTTATTTTAAA
*
31189 TTTTAAATTTATTTTCAA
1 -TTTAAATTTATTTTAAA
*
31207 TTTAAATTTATTTTCAA
1 TTTAAATTTATTTTAAA
*
31224 TTTAAATTTAATTTAAA
1 TTTAAATTTATTTTAAA
31241 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
* * *
31259 TTTAAAATTACTATAAA
1 TTTAAATTTATTTTAAA
31276 TTTAAAT
1 TTTAAAT
31283 AAGGCTAAAA
Statistics
Matches: 95, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
17 57 0.60
18 38 0.40
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:31214 original size:6 final size:6
Alignment explanation
Indices: 31190--31282 Score: 70
Period size: 6 Copynumber: 16.2 Consensus size: 6
31180 TGTTTAAAAT
* * * *
31190 TTTAAA TTT-AT TTTCAA TTTAAA TTT-AT TTTCAA TTTAAA TTT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * *
31235 TTTAAA TTTAAA TTT-AT TTTCAAA TTTAAA ATT-AC TATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA
31282 T
1 T
31283 AAGGCTAAAA
Statistics
Matches: 67, Mismatches: 14, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
5 19 0.28
6 44 0.66
7 4 0.06
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:31226 original size:35 final size:34
Alignment explanation
Indices: 31154--31282 Score: 150
Period size: 35 Copynumber: 3.7 Consensus size: 34
31144 CCAAACTCCC
* * **
31154 TTTAAATTTATTTTAAAAATTAAATTTGTTTAAAA
1 TTTAAATTTATTTT-AAATTTAAATTTATTTTCAA
*
31189 TTTTAAATTTATTTTCAATTTAAATTTATTTTCAA
1 -TTTAAATTTATTTTAAATTTAAATTTATTTTCAA
*
31224 TTTAAATTTAATTTAAATTTAAATTTATTTTCAAA
1 TTTAAATTTATTTTAAATTTAAATTTATTTTC-AA
* * *
31259 TTTAAAATTACTATAAATTTAAAT
1 TTTAAATTTATTTTAAATTTAAAT
31283 AAGGCTAAAA
Statistics
Matches: 82, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
34 30 0.37
35 38 0.46
36 14 0.17
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (34 bp):
TTTAAATTTATTTTAAATTTAAATTTATTTTCAA
Found at i:32082 original size:3 final size:3
Alignment explanation
Indices: 32076--32115 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
32066 AATATTTTTT
* *
32076 TAA TAA TAA TAA TAT TAA TAA TAT TAA TGAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
32116 AAAACGAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:32082 original size:21 final size:20
Alignment explanation
Indices: 32053--32091 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
32043 TTTCATAATA
*
32053 TTTATTAATAATAAATATTTT
1 TTTAATAATAAT-AATATTTT
32074 TTTAATAATAATAATATT
1 TTTAATAATAATAATATT
32092 AATAATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTAATAATAATAATATTTT
Found at i:33129 original size:29 final size:29
Alignment explanation
Indices: 33016--33387 Score: 219
Period size: 29 Copynumber: 13.0 Consensus size: 29
33006 AAGGTCCCTA
* * *
33016 AACTGTCCGAAAATTACCA-TTTAACCCCCA
1 AACT-TCC-AAAAATACCATTTTTACCCCCG
* * *
33046 AACATCCAAAAATCCCATTTTTGA-CCTCG
1 AACTTCCAAAAATACCATTTTT-ACCCCCG
*
33075 AACCTTCTAAAAATTACCA--TTTACCCCCG
1 AA-CTTCCAAAAA-TACCATTTTTACCCCCG
**
33104 AACTTCCAAAAAT-CCATTTTTGACCCCAA
1 AACTTCCAAAAATACCATTTTT-ACCCCCG
* * *
33133 AACTTCCAAAAATTCCAATTTTACCCTCG
1 AACTTCCAAAAATACCATTTTTACCCCCG
* *
33162 AACTTCCAAAAAATCCCATTTTTAACCCC-
1 AACTTCC-AAAAATACCATTTTTACCCCCG
* *
33191 -A-----AAAATTACCA-TTTTACCCCCA
1 AACTTCCAAAAATACCATTTTTACCCCCG
*
33213 AACTTCC-AAAATCCCATTTTTGA-CCCCG
1 AACTTCCAAAAATACCATTTTT-ACCCCCG
* * *
33241 AACCTTCTAAAATTACCA-TTTTACCCTCG
1 AA-CTTCCAAAAATACCATTTTTACCCCCG
*
33270 AACTTCCAAAAATCCCATTTTTTA-CCCCG
1 AACTTCCAAAAATACCA-TTTTTACCCCCG
* * *
33299 AACCTTTCGAAAAGTACCA-TTTTACCCTCG
1 AA-C-TTCCAAAAATACCATTTTTACCCCCG
*
33329 AACTTCCAAAAAT-CTCATTTTTTGA-CCCCA
1 AACTTCCAAAAATAC-CA-TTTTT-ACCCCCG
*
33359 AACCTTCCAAAACTACCATTTTT-CCCCCG
1 AA-CTTCCAAAAATACCATTTTTACCCCCG
33388 TGCATCTGAA
Statistics
Matches: 263, Mismatches: 45, Indels: 69
0.70 0.12 0.18
Matches are distributed among these distances:
21 9 0.03
22 8 0.03
23 1 0.00
26 3 0.01
27 9 0.03
28 55 0.21
29 80 0.30
30 69 0.26
31 28 0.11
32 1 0.00
ACGTcount: A:0.34, C:0.33, G:0.04, T:0.29
Consensus pattern (29 bp):
AACTTCCAAAAATACCATTTTTACCCCCG
Found at i:33196 original size:21 final size:21
Alignment explanation
Indices: 33167--33214 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
33157 CCTCGAACTT
* *
33167 CCAAAAAATCCCATTTTTAACC
1 CCAAAAATTACCA-TTTTAACC
*
33189 CCAAAAATTACCATTTTACCC
1 CCAAAAATTACCATTTTAACC
33210 CCAAA
1 CCAAA
33215 CTTCCAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.42, C:0.33, G:0.00, T:0.25
Consensus pattern (21 bp):
CCAAAAATTACCATTTTAACC
Found at i:33223 original size:167 final size:167
Alignment explanation
Indices: 33025--33360 Score: 500
Period size: 167 Copynumber: 2.0 Consensus size: 167
33015 AAACTGTCCG
*
33025 AAAATTACCATTTAACCCCCAAACATCCAAAAATCCCATTTTTGACCTCGAACCTTCTAAAAATT
1 AAAATTACCATTTAACCCCCAAACATCC-AAAATCCCATTTTTGACCCCGAACCTTCT-AAAATT
*
33090 ACCA-TTTACCCCCGAACTTCCAAAAAT-CCATTTTTGACCCCAAAAC-TTCCAAAAATTCCAAT
64 ACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTTCCAAAAATACC-AT
33152 TTTACCCTCGAACTTCCAAAAAATCCCA-TTTTTAACCCCA
128 TTTACCCTCGAACTTCC-AAAAATCCCATTTTTTAACCCCA
* *
33192 AAAATTACCATTTTACCCCCAAACTTCCAAAATCCCATTTTTGACCCCGAACCTTCTAAAATTAC
1 AAAATTACCATTTAACCCCCAAACATCCAAAATCCCATTTTTGACCCCGAACCTTCTAAAATTAC
* * * * * *
33257 CATTTTACCCTCGAACTTCCAAAAATCCCATTTTTTACCCCGAACCTTTCGAAAAGTACCATTTT
66 CATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTTCCAAAAATACCATTTT
* *
33322 ACCCTCGAACTTCCAAAAATCTCATTTTTTGACCCCA
131 ACCCTCGAACTTCCAAAAATCCCATTTTTTAACCCCA
33359 AA
1 AA
33361 CCTTCCAAAA
Statistics
Matches: 153, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
165 10 0.07
166 59 0.39
167 74 0.48
168 10 0.07
ACGTcount: A:0.35, C:0.32, G:0.04, T:0.29
Consensus pattern (167 bp):
AAAATTACCATTTAACCCCCAAACATCCAAAATCCCATTTTTGACCCCGAACCTTCTAAAATTAC
CATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTTCCAAAAATACCATTTT
ACCCTCGAACTTCCAAAAATCCCATTTTTTAACCCCA
Found at i:33272 original size:108 final size:109
Alignment explanation
Indices: 33083--33380 Score: 363
Period size: 108 Copynumber: 2.7 Consensus size: 109
33073 CGAACCTTCT
*
33083 AAAAATTACCA-TTTACCCCCGAACTTCCAAAAAT-CCATTTTTGACCCCAAAACTTCCAAAAAT
1 AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAACCTT-CAAAAAT
33146 T-CCAATTTTACCCTCGAACTTCCAAAAAATCCCATTTTTAACCCC-
65 TACC-ATTTTACCCTCGAACTTCC-AAAAATCCCATTTTTAACCCCA
* * *
33191 AAAAATTACCATTTTACCCCCAAACTTCC-AAAATCCCATTTTTGACCCCGAACCTTCTAAAATT
1 AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAACCTTCAAAAATT
*
33255 ACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTTACCCCGA
66 ACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCC-A
* * *
33300 ACCTTTCGAAAAGTACCATTTTACCCTCGAACTTCCAAAAATCTCATTTTTTGACCCCAAACCTT
1 A-------AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCA-TTTTTGACCCCAAACCTT
* *
33365 CCAAAACTACCATTTT
58 CAAAAATTACCATTTT
33381 TCCCCCGTGC
Statistics
Matches: 164, Mismatches: 12, Indels: 18
0.85 0.06 0.09
Matches are distributed among these distances:
107 20 0.12
108 42 0.26
109 38 0.23
116 25 0.15
117 8 0.05
118 31 0.19
ACGTcount: A:0.34, C:0.32, G:0.04, T:0.30
Consensus pattern (109 bp):
AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAACCTTCAAAAATT
ACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCA
Found at i:33326 original size:59 final size:58
Alignment explanation
Indices: 33192--33380 Score: 272
Period size: 59 Copynumber: 3.2 Consensus size: 58
33182 TTTAACCCCA
* * * *
33192 AAAATTACCATTTTACCCCCAAACTTCC-AAAATCCCATTTTTGACCCCGAACCTTCT
1 AAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTTACCCCGAACCTTCC
*
33249 AAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTTACCCCGAACCTTTCG
1 AAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTTACCCCGAACC-TTCC
* * *
33308 AAAAGTACCATTTTACCCTCGAACTTCCAAAAATCTCATTTTTTGACCCCAAACCTTCC
1 AAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTT-ACCCCGAACCTTCC
*
33367 AAAACTACCATTTT
1 AAAATTACCATTTT
33381 TCCCCCGTGC
Statistics
Matches: 120, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
57 26 0.22
58 24 0.20
59 61 0.51
60 9 0.08
ACGTcount: A:0.32, C:0.32, G:0.04, T:0.31
Consensus pattern (58 bp):
AAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTTACCCCGAACCTTCC
Found at i:33778 original size:97 final size:97
Alignment explanation
Indices: 33586--33779 Score: 218
Period size: 97 Copynumber: 2.0 Consensus size: 97
33576 TTTTTTTAAA
* * **
33586 AATCGAGGCAATATTTCTTTATTTCGAGTTTCGAAAATTTGTGCCTTAACTCACTAGGTGCATTT
1 AATCGAGGCAATATTTCCTTATTTCGAGTTTCGAAAATTTGCGCCTTAACTCACTAGGTGCATAC
* * *
33651 TTTTCTTCAAATCGAAATAATTGAACACCTTT
66 CTTTCTTCAAATCGAAATAATCGAAAACCTTT
* *
33683 AATCGAGGCAATGTTTCCTTATCTTCGA--TTCTG-AAATATTGCGCCTTAACTTACTAGGTGCA
1 AATCGAGGCAATATTTCCTTAT-TTCGAGTTTC-GAAAAT-TTGCGCCTTAACTCACTAGGTGCA
*
33745 -ACCTTTCTTCGAATC-AAGATAATCGAATAACCTTT
63 TACCTTTCTTCAAATCGAA-ATAATCGAA-AACCTTT
33780 TCCCAAAAAT
Statistics
Matches: 82, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
95 2 0.02
96 26 0.32
97 49 0.60
98 5 0.06
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.38
Consensus pattern (97 bp):
AATCGAGGCAATATTTCCTTATTTCGAGTTTCGAAAATTTGCGCCTTAACTCACTAGGTGCATAC
CTTTCTTCAAATCGAAATAATCGAAAACCTTT
Found at i:36197 original size:13 final size:13
Alignment explanation
Indices: 36179--36206 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
36169 AGAAAAGCTG
36179 AAGGACTATAAAA
1 AAGGACTATAAAA
36192 AAGGACTATAAAA
1 AAGGACTATAAAA
36205 AA
1 AA
36207 CTTCAATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.07, G:0.14, T:0.14
Consensus pattern (13 bp):
AAGGACTATAAAA
Done.