Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010512.1 Kokia drynarioides strain JFW-HI SEQ_125424, 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: 24776
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Found at i:372 original size:205 final size:204
Alignment explanation
Indices: 1--753 Score: 1092
Period size: 205 Copynumber: 3.7 Consensus size: 204
1 GCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTT
1 GCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTT
* * *
66 CCTGATGAGAT----A-TA-G-A--GAAACAAACGACGCAGTCATCTTCCAGATGAGATACTGAG
66 CCTGATGAGATACAGAGAAGGAATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAG
* *
122 AAGAAGACCAAATCAAACCCACGCTTGATGTAAGCAAATCTTCGAACCCCAGCTTCTTGATGAGA
131 AAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCTTGATGAGA
187 CACTGAGAA
196 CACTGAGAA
196 GCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTT
1 GCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTT
*
261 CCTGATGAGATACATAGAAGCGAATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGA
66 CCTGATGAGATACAGAGAAG-GAATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGA
*
326 GAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAACCCCTGCTTCTTGATGAG
130 GAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCTTGATGAG
391 ACACTGAGAA
195 ACACTGAGAA
*
401 GAAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTT
1 GCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTT
* *
466 CCTGATGAGATACAGAGAAGCGAATTGAAACAAACGACGCGATCATCTTCCTAATGAGATACTGA
66 CCTGATGAGATACAGAGAAG-GAATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGA
* *
531 GAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATCAG
130 GAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCTTGATGAG
* *
596 ATACTGAGGA
195 ACACTGAGAA
* * * * * ** *
606 GCAGGTCGAAGTAATAAAATGGTTAGCTTCCTGATGAAATACGGGGAAGTGAACCAAAACCATCT
1 GCAGGTCGAAGCAATAAAA-GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCT
* * * ** ** *** *
671 TCCTGATGAAACACAGAGAAGTAGATCAAAACAAGTGATATGGTCGTCTTCCTGATGAGATACTG
65 TCCTGATGAGATACAGAGAAGGA-ATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTG
* *
736 AGAAGAAGGCCAAGTCAA
129 AGAAGAAGACCAAATCAA
754 TGAAACCAGA
Statistics
Matches: 507, Mismatches: 39, Indels: 13
0.91 0.07 0.02
Matches are distributed among these distances:
195 76 0.15
199 1 0.00
200 1 0.00
202 1 0.00
203 1 0.00
205 323 0.64
206 104 0.21
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (204 bp):
GCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTT
CCTGATGAGATACAGAGAAGGAATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAG
AAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCTTGATGAGA
CACTGAGAA
Found at i:1104 original size:6 final size:6
Alignment explanation
Indices: 1066--1158 Score: 56
Period size: 6 Copynumber: 16.3 Consensus size: 6
1056 GGCCAACAGG
* * * *
1066 ATTTAA ATTT-A TTTTAA AATTAA ATTT-A TTTTAA GTTTAA ATTT--
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* * *
1110 ATTATAA ATTT-A CTTAAA ATTTAA ATTT-- ATTATAA ATTTAA GTTTAA
1 ATT-TAA ATTTAA ATTTAA ATTTAA ATTTAA ATT-TAA ATTTAA ATTTAA
1157 AT
1 AT
1159 CTATTTAAAT
Statistics
Matches: 65, Mismatches: 13, Indels: 18
0.68 0.14 0.19
Matches are distributed among these distances:
4 6 0.09
5 13 0.20
6 40 0.62
7 6 0.09
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (6 bp):
ATTTAA
Found at i:1117 original size:11 final size:10
Alignment explanation
Indices: 1101--1168 Score: 61
Period size: 11 Copynumber: 6.7 Consensus size: 10
1091 TTATTTTAAG
1101 TTTAAATTTA
1 TTTAAATTTA
1111 TTATAAATTTA
1 TT-TAAATTTA
*
1122 CTTAAA---A
1 TTTAAATTTA
1129 TTTAAATTTA
1 TTTAAATTTA
1139 TTATAAATTTAA
1 TT-TAAATTT-A
*
1151 GTTTAAATCTA
1 -TTTAAATTTA
1162 TTTAAAT
1 TTTAAAT
1169 CAAAGTCCAA
Statistics
Matches: 48, Mismatches: 3, Indels: 14
0.74 0.05 0.22
Matches are distributed among these distances:
7 6 0.12
10 16 0.33
11 17 0.35
12 7 0.15
13 2 0.04
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.51
Consensus pattern (10 bp):
TTTAAATTTA
Found at i:1117 original size:28 final size:28
Alignment explanation
Indices: 1086--1149 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 28
1076 ATTTTAAAAT
* * *
1086 TAAATTTATTTTAAGTTTAAATTTATTA
1 TAAATTTACTTAAAATTTAAATTTATTA
1114 TAAATTTACTTAAAATTTAAATTTATTA
1 TAAATTTACTTAAAATTTAAATTTATTA
1142 TAAATTTA
1 TAAATTTA
1150 AGTTTAAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (28 bp):
TAAATTTACTTAAAATTTAAATTTATTA
Found at i:1118 original size:45 final size:45
Alignment explanation
Indices: 1069--1155 Score: 122
Period size: 45 Copynumber: 1.9 Consensus size: 45
1059 CAACAGGATT
* * *
1069 TAAATTTATTTTAAAA-TTAAATTTATTTTAAGTTTAAATTTATTA
1 TAAATTTA-CTTAAAATTTAAATTTATTATAAATTTAAATTTATTA
*
1114 TAAATTTACTTAAAATTTAAATTTATTATAAATTTAAGTTTA
1 TAAATTTACTTAAAATTTAAATTTATTATAAATTTAAATTTA
1156 AATCTATTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
44 6 0.16
45 31 0.84
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (45 bp):
TAAATTTACTTAAAATTTAAATTTATTATAAATTTAAATTTATTA
Found at i:1121 original size:17 final size:17
Alignment explanation
Indices: 1066--1155 Score: 84
Period size: 17 Copynumber: 5.6 Consensus size: 17
1056 GGCCAACAGG
*
1066 ATTTAAATTTATTTTAA
1 ATTTAAATTTATTATAA
* *
1083 AATTAAATTTATTTTAA
1 ATTTAAATTTATTATAA
*
1100 GTTTAAATTTATTATAA
1 ATTTAAATTTATTATAA
*
1117 ATTT--A---CTTA-AA
1 ATTTAAATTTATTATAA
1128 ATTTAAATTTATTATAA
1 ATTTAAATTTATTATAA
*
1145 ATTTAAGTTTA
1 ATTTAAATTTA
1156 AATCTATTTA
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
11 6 0.10
12 3 0.05
13 1 0.02
15 1 0.02
16 3 0.05
17 45 0.76
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.53
Consensus pattern (17 bp):
ATTTAAATTTATTATAA
Found at i:2826 original size:23 final size:24
Alignment explanation
Indices: 2778--2826 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
2768 CATTTGGTCC
* *
2778 TTTCGTTTTTTTTTATTGTTTCAA
1 TTTCGTTTTTTTCTACTGTTTCAA
2802 TTTCGTTCTTTTTCTACT-TTT-AA
1 TTTCGTT-TTTTTCTACTGTTTCAA
2825 TT
1 TT
2827 ATTTTTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 4 0.18
24 10 0.45
25 8 0.36
ACGTcount: A:0.12, C:0.12, G:0.06, T:0.69
Consensus pattern (24 bp):
TTTCGTTTTTTTCTACTGTTTCAA
Found at i:3176 original size:30 final size:28
Alignment explanation
Indices: 3118--3219 Score: 123
Period size: 29 Copynumber: 3.5 Consensus size: 28
3108 AACTACTTTT
* *
3118 AAAAATTACATTTTTACCCTTGAACTTCC
1 AAAAATTCCATTTTTA-CCTCGAACTTCC
3147 AAAAATTCCATTTTTGACCTCGAAACTTCC
1 AAAAATTCCATTTTT-ACCTCG-AACTTCC
* * *
3177 AAATATTCCAATTTTACATTCGAACTTCC
1 AAAAATTCCATTTTTAC-CTCGAACTTCC
3206 AAAAATTCCATTTT
1 AAAAATTCCATTTT
3220 AACCAAAAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
29 39 0.62
30 24 0.38
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.37
Consensus pattern (28 bp):
AAAAATTCCATTTTTACCTCGAACTTCC
Found at i:3315 original size:108 final size:108
Alignment explanation
Indices: 3118--3327 Score: 255
Period size: 108 Copynumber: 1.9 Consensus size: 108
3108 AACTACTTTT
* * * * *
3118 AAAAATTACATTTTTACCCTTGAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTCCAAATAT
1 AAAAATTACATATTTACCCTCGAACCTCCAAAAATTCCATTTTTGACCCCGAAACTTCCAAAAAT
**
3183 TCCAATTTTACATTCGAACTTCCAAAAA-TTCCATTTTAACCAA
66 TCCAATTTTACACCCGAACTTCCAAAAACTT-CATTTTAACCAA
* * *
3226 AAAAATTACATATTTACCCTCGAACCTCCAAAATTTCTATTTTTGACCCCGAAACTTTCAAAAAT
1 AAAAATTACATATTTACCCTCGAACCTCCAAAAATTCCATTTTTGACCCCGAAACTTCCAAAAAT
* * *
3291 TACC-ATTTTGCCCCCGGA-TGTCCAAAAACTTCATTTT
66 T-CCAATTTTACACCCGAACT-TCCAAAAACTTCATTTT
3328 CGACCTCTAA
Statistics
Matches: 86, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
107 1 0.01
108 81 0.94
109 4 0.05
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.34
Consensus pattern (108 bp):
AAAAATTACATATTTACCCTCGAACCTCCAAAAATTCCATTTTTGACCCCGAAACTTCCAAAAAT
TCCAATTTTACACCCGAACTTCCAAAAACTTCATTTTAACCAA
Found at i:3317 original size:59 final size:57
Alignment explanation
Indices: 3252--3424 Score: 177
Period size: 59 Copynumber: 2.9 Consensus size: 57
3242 CCCTCGAACC
* *
3252 TCCAAAATTTCTATTTTTGACCCCGAAACTTTCAAAAATTACCATTTTGCCCCCGGATG
1 TCCAAAAATTC-ATTTTTGACCCCGAAACTTTC-AAAATTACCATTTTGCCCCCGAATG
* * * * * *
3311 TCCAAAAACTTCATTTTCGACCTCTAAACTCTCAAAATTACCCTTTTACCCCCGAATG
1 TCCAAAAA-TTCATTTTTGACCCCGAAACTTTCAAAATTACCATTTTGCCCCCGAATG
* * * *
3369 TCTAAAAATTCCATTTTTAACCCTG-AACTTTCCCAAAATTGCCATTTTGCCCCCGA
1 TCCAAAAATT-CATTTTTGACCCCGAAACTTT--CAAAATTACCATTTTGCCCCCGA
3425 GAATCTAAAA
Statistics
Matches: 92, Mismatches: 18, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
57 7 0.08
58 38 0.41
59 44 0.48
60 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (57 bp):
TCCAAAAATTCATTTTTGACCCCGAAACTTTCAAAATTACCATTTTGCCCCCGAATG
Found at i:3385 original size:28 final size:28
Alignment explanation
Indices: 3344--3451 Score: 76
Period size: 28 Copynumber: 3.8 Consensus size: 28
3334 CTAAACTCTC
* *
3344 AAAATTACCCTTTTACCCCCGAATGTCT
1 AAAATTACCATTTTACCCCCGAATATCT
* * * *
3372 AAAAATT-CCATTTTTAACCCTGAACTTTCCC
1 -AAAATTACCA-TTTTACCCCCGAA-TAT-CT
* *
3403 AAAATTGCCATTTTGCCCCCGAGA-ATCT
1 AAAATTACCATTTTACCCCCGA-ATATCT
*
3431 AAAATTACCATTTTGCCCCCG
1 AAAATTACCATTTTACCCCCG
3452 GGTATCCAAA
Statistics
Matches: 63, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
28 23 0.37
29 18 0.29
30 17 0.27
31 5 0.08
ACGTcount: A:0.30, C:0.31, G:0.08, T:0.31
Consensus pattern (28 bp):
AAAATTACCATTTTACCCCCGAATATCT
Found at i:3462 original size:28 final size:28
Alignment explanation
Indices: 3401--3462 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
3391 CTGAACTTTC
*
3401 CCAAAATTGCCATTTTGCCCCCGAGAAT
1 CCAAAATTACCATTTTGCCCCCGAGAAT
* * *
3429 CTAAAATTACCATTTTGCCCCCGGGTAT
1 CCAAAATTACCATTTTGCCCCCGAGAAT
3457 CCAAAA
1 CCAAAA
3463 AGTCTCATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.31, C:0.31, G:0.13, T:0.26
Consensus pattern (28 bp):
CCAAAATTACCATTTTGCCCCCGAGAAT
Found at i:4363 original size:13 final size:13
Alignment explanation
Indices: 4345--4373 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
4335 TACTATTAAT
4345 TTTGGATTTATTA
1 TTTGGATTTATTA
4358 TTTGGATTTATTA
1 TTTGGATTTATTA
4371 TTT
1 TTT
4374 AATTTTTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.14, T:0.66
Consensus pattern (13 bp):
TTTGGATTTATTA
Found at i:10287 original size:113 final size:113
Alignment explanation
Indices: 10140--10365 Score: 353
Period size: 113 Copynumber: 2.0 Consensus size: 113
10130 TAACCCTAAA
* * *
10140 AAACTTAATGGGAAGAAAATATTGAAACCAAAGATATTGAATCTTTTGGTTAATAGGTTTTGAAG
1 AAACTTAACGGAAAGAAAATATTGAAACCAAAGATATTGAATCTTTTGGTTAATAGGTTTTAAAG
* *
10205 ATTCAAACTTTGAGACAGATTTGTAACTAAAGATATTAGAATCAAAAG
66 ATTCAAACTTTGAGAAAAATTTGTAACTAAAGATATTAGAATCAAAAG
* * *
10253 AAACTTAACGGAAAGAAGATATTGAAACCAAAGATATTGAATCTTTTGGTTAATGGGTTTTAAAT
1 AAACTTAACGGAAAGAAAATATTGAAACCAAAGATATTGAATCTTTTGGTTAATAGGTTTTAAAG
* * *
10318 ATTCAAGCTTTGGGAAAAATTTGTAACTAAAGATATTGGAATCAAAAG
66 ATTCAAACTTTGAGAAAAATTTGTAACTAAAGATATTAGAATCAAAAG
10366 GGGAGAAGAT
Statistics
Matches: 102, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
113 102 1.00
ACGTcount: A:0.43, C:0.08, G:0.18, T:0.31
Consensus pattern (113 bp):
AAACTTAACGGAAAGAAAATATTGAAACCAAAGATATTGAATCTTTTGGTTAATAGGTTTTAAAG
ATTCAAACTTTGAGAAAAATTTGTAACTAAAGATATTAGAATCAAAAG
Found at i:11107 original size:24 final size:24
Alignment explanation
Indices: 11075--11121 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
11065 TGATTACAAG
11075 GTCTTCTCATGGCTTCCAAAATTT
1 GTCTTCTCATGGCTTCCAAAATTT
11099 GTCTTCTCATGGCTTCCAAAATT
1 GTCTTCTCATGGCTTCCAAAATT
11122 AACTTTCTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.21, C:0.26, G:0.13, T:0.40
Consensus pattern (24 bp):
GTCTTCTCATGGCTTCCAAAATTT
Found at i:16060 original size:2 final size:2
Alignment explanation
Indices: 16053--16084 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
16043 GGTTGAATGA
16053 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16085 GCTTGATGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.