Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005155.1 Kokia drynarioides strain JFW-HI SEQ_119000, 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: 16341
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Found at i:1141 original size:96 final size:95
Alignment explanation
Indices: 977--1204 Score: 287
Period size: 96 Copynumber: 2.4 Consensus size: 95
967 TGAAGCGGTT
* * * * * * *
977 ATCTTTCTGATAAGATACAAAGAAGTGGACCAAAACAATGAAGTAGAGCTCAACATCCTTAAGGT
1 ATCTTCCTGATGAGATACAGAGAAGTGTATCAAAATAATGAAATAGAGCTCAACATCCTTAAGGT
1042 TACAGTGGAATAGAGCGAAACTTCAAAACCC
66 TACAGTGGAATAGAGCGAAACTTC-AAACCC
* ** *
1073 ATCTTCTTGATGAGATACAGAGAAGTGTATCAAAATAATGAAATAGAGCTCAATGT-CTATGAGG
1 ATCTTCCTGATGAGATACAGAGAAGTGTATCAAAATAATGAAATAGAGCTCAACATCCT-TAAGG
* *
1137 TTACAGTGGAGTAGAGCGATACTTCAAACCC
65 TTACAGTGGAATAGAGCGAAACTTCAAACCC
* * *
1168 ATCTTCCTGGTGAGATACAGAGAAATGTGTCAAAATA
1 ATCTTCCTGATGAGATACAGAGAAGTGTATCAAAATA
1205 GGTAGCAGAT
Statistics
Matches: 114, Mismatches: 17, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
95 41 0.36
96 73 0.64
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (95 bp):
ATCTTCCTGATGAGATACAGAGAAGTGTATCAAAATAATGAAATAGAGCTCAACATCCTTAAGGT
TACAGTGGAATAGAGCGAAACTTCAAACCC
Found at i:1479 original size:46 final size:45
Alignment explanation
Indices: 1355--1480 Score: 153
Period size: 45 Copynumber: 2.8 Consensus size: 45
1345 TACATCATCG
* *
1355 TCTAATCGTTTACCCCTAATCAAGAGGGGCAGATTGAAGCCACTA
1 TCTAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCCACCA
* * * * * * *
1400 TCCAATCTTTTACCCTTACTCAAGAGGAGCAGATTTAAGCTACCG
1 TCTAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCCACCA
*
1445 TTTAATCTTTTACCCCTAAGTCAAGAGGGGCAGATT
1 TCTAATCTTTTACCCCTAA-TCAAGAGGGGCAGATT
1481 AAAGTTGTAA
Statistics
Matches: 66, Mismatches: 14, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
45 51 0.77
46 15 0.23
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (45 bp):
TCTAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCCACCA
Found at i:3987 original size:45 final size:45
Alignment explanation
Indices: 3916--4175 Score: 239
Period size: 45 Copynumber: 5.9 Consensus size: 45
3906 AACGCTACCG
*
3916 TCCAATCTTTTA-CCCTAGTCAAGAGGGACAGATT-AAGGCCACCA
1 TCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAA-GCCACCA
* * * **
3960 TCCAATCTTTTACCCCTAGTCAAGAGGGGTAAATTGAATCCACGT
1 TCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGCCACCA
* *
4005 TCCAATCTTTTACCCCTAGTCAAGAAGGGCATATTGAAGCCA-CA
1 TCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGCCACCA
* * * * **
4049 TTCCAATCTTTTACCCTTAATCCAGAGGGGCAGATTAAAG---CTG
1 -TCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGCCACCA
** * *
4092 TCTGATCTTTTACCCCTAATCAAGAGGGGTAGATTGAAGCCACCA
1 TCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGCCACCA
* * *
4137 TCTAGTCTTTTACCTCT-GATCCAA-AGGGGCAGATTGAAG
1 TCCAATCTTTTACCCCTAG-T-CAAGAGGGGCAGATTGAAG
4176 TCAAACACAC
Statistics
Matches: 174, Mismatches: 33, Indels: 17
0.78 0.15 0.08
Matches are distributed among these distances:
42 33 0.19
44 12 0.07
45 124 0.71
46 5 0.03
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (45 bp):
TCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGCCACCA
Found at i:4130 original size:87 final size:87
Alignment explanation
Indices: 3920--4171 Score: 228
Period size: 87 Copynumber: 2.9 Consensus size: 87
3910 CTACCGTCCA
* * *
3920 ATCTTTTA-CCCTAGTCAAG-AGGGACAGATT-AAGGCCACCATCCAATCTTTTACCCCTAGT-C
1 ATCTTTTACCCCTAATCAAGAAGGG-CAGATTGAA-GCCACCATCCAATCTTTTACCTCTAATCC
* * ** * **
3981 AAGAGGGGTAAATTGAATCCACGTTCCA
64 AA-AGGGGCAGATT-AAAGC-TG-TCTG
* *
4009 ATCTTTTACCCCTAGTCAAGAAGGGCATATTGAAGCCA-CATTCCAATCTTTTACC-CTTAATCC
1 ATCTTTTACCCCTAATCAAGAAGGGCAGATTGAAGCCACCA-TCCAATCTTTTACCTC-TAATCC
*
4072 AGAGGGGCAGATTAAAGCTGTCTG
64 AAAGGGGCAGATTAAAGCTGTCTG
* * * * *
4096 ATCTTTTACCCCTAATCAAGAGGGGTAGATTGAAGCCACCATCTAGTCTTTTACCTCTGATCCAA
1 ATCTTTTACCCCTAATCAAGAAGGGCAGATTGAAGCCACCATCCAATCTTTTACCTCTAATCCAA
4161 AGGGGCAGATT
66 AGGGGCAGATT
4172 GAAGTCAAAC
Statistics
Matches: 137, Mismatches: 18, Indels: 18
0.79 0.10 0.10
Matches are distributed among these distances:
87 65 0.47
88 4 0.03
89 14 0.10
90 46 0.34
91 8 0.06
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.28
Consensus pattern (87 bp):
ATCTTTTACCCCTAATCAAGAAGGGCAGATTGAAGCCACCATCCAATCTTTTACCTCTAATCCAA
AGGGGCAGATTAAAGCTGTCTG
Found at i:5040 original size:23 final size:22
Alignment explanation
Indices: 5005--5056 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
4995 GTACTACTCT
*
5005 TTTTTA-TACATATACATATTTA
1 TTTTTATTACATATACAT-TCTA
* *
5027 TTTTTATTATATATTCATTCTA
1 TTTTTATTACATATACATTCTA
5049 TTTTTATT
1 TTTTTATT
5057 TTTTTTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 17 0.65
23 9 0.35
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTTTATTACATATACATTCTA
Found at i:5804 original size:10 final size:10
Alignment explanation
Indices: 5775--5807 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
5765 AAATTTACCT
*
5775 AATAATTTTA
1 AATAATTTTC
5785 AATAATTTTC
1 AATAATTTTC
5795 AATAATTTTC
1 AATAATTTTC
5805 AAT
1 AAT
5808 TTAGTCCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (10 bp):
AATAATTTTC
Found at i:5941 original size:30 final size:29
Alignment explanation
Indices: 5905--6064 Score: 112
Period size: 30 Copynumber: 5.4 Consensus size: 29
5895 TTCATTTCAA
5905 CCCCAAACTTTCTAAAAATTATGTTTTAGC
1 CCCCAAACTTTCTAAAAATTATGTTTT-GC
*
5935 CCCCAAACTTGTC-AAAAATTATTTTTTGGC
1 CCCCAAACTT-TCTAAAAATTATGTTTT-GC
* * *
5965 CCTCGAACTTT-TCAAAAATT-TGAATTTGAC
1 CCCCAAACTTTCT-AAAAATTATG-TTTTG-C
* * *
5995 TCTCAAACTTTCTAAAAAATATGTTTTGAC
1 CCCCAAACTTTCTAAAAATTATGTTTTG-C
* * ** *
6025 CCCTAAACTTTC-CAAAATTCAAATTTAGC
1 CCCCAAACTTTCTAAAAATT-ATGTTTTGC
6054 CCCCAAACTTT
1 CCCCAAACTTT
6065 AAATTTTTTT
Statistics
Matches: 103, Mismatches: 19, Indels: 17
0.74 0.14 0.12
Matches are distributed among these distances:
29 19 0.18
30 79 0.77
31 5 0.05
ACGTcount: A:0.34, C:0.24, G:0.07, T:0.36
Consensus pattern (29 bp):
CCCCAAACTTTCTAAAAATTATGTTTTGC
Found at i:6368 original size:17 final size:17
Alignment explanation
Indices: 6338--6381 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
6328 TTACATGCTC
*
6338 ATTTTTTAA-AAAAAAT
1 ATTTTTTAATTAAAAAT
*
6354 ATTTTTTAATTAAAATT
1 ATTTTTTAATTAAAAAT
*
6371 GTTTTTTAATT
1 ATTTTTTAATT
6382 TTCTTCAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 9 0.38
17 15 0.62
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
ATTTTTTAATTAAAAAT
Found at i:8865 original size:184 final size:182
Alignment explanation
Indices: 8494--9450 Score: 1111
Period size: 178 Copynumber: 5.3 Consensus size: 182
8484 GCAATAGAAT
* *
8494 AAAACTTTAGGTACCAAAATGGGAAAAATTGCATAGTTTAAGTACCTAAAGTGGTAATAGATTAA
1 AAAACTTTAGGTACCTAAATGGGAAAAGTTGCATAGTTTAAGTACCTAAAGTGGTAATAGATTAA
* * *
8559 AAAT-TCATGTGTCATAATTTGATTGGTTTGAATTCCTTTTTCTTTTTTTTTAATGTGAGTTAAT
66 AAATGTCATGTGTCATAATTTGATTGGTTTGGATT-C---TT-TTTTTTTTTAACGTGAGTTAAC
* * ** * * **
8623 AGCTGATACCTAAAGTGGTAGCAAAATAAAACTTTAAGT-TCCTACTTT-G-ATTAAA
126 AGTTGGTACCTAAAGTGGTAATAGAATAAAACTTTAGGTAT-CTACTTTGGTAAAAAA
* * * *
8678 AAAACTTTAGGCACCTAACTGGGAAAAGTTGCTTAGTTTAAGTACCTAAAGTGGGAATAGATTAA
1 AAAACTTTAGGTACCTAAATGGGAAAAGTTGCATAGTTTAAGTACCTAAAGTGGTAATAGATTAA
** * *
8743 AAATGTCACATGTCATAATTTGATTGGTTTGAATTCTTTTTTTTTTGGTAACGTGAGTTAACCGT
66 AAATGTCATGTGTCATAATTTGATTGGTTTGGATTCTTTTTTTTTT--TAACGTGAGTTAACAGT
* * * *
8808 TGCTACCTAAAGTGGCAACAGGATAAAACTTTAGGTATCTACTTTGGTAAAAAA
129 TGGTACCTAAAGTGGTAATAGAATAAAACTTTAGGTATCTACTTTGGTAAAAAA
* * * * *
8862 AAAACTTTAAGTACTTAAATGAGAAAAGTTGCATAGTTTAAATACCTAAAGTGATAATAGATTAA
1 AAAACTTTAGGTACCTAAATGGGAAAAGTTGCATAGTTTAAGTACCTAAAGTGGTAATAGATTAA
* * * * *
8927 AAATGTCATGTGTCATGATTCGATTGGTTCGGATTC----TTTTTTAAACATGAGTTAACAGTTG
66 AAATGTCATGTGTCATAATTTGATTGGTTTGGATTCTTTTTTTTTTTAACGTGAGTTAACAGTTG
* *
8988 GTTCCTAAAGTGGTAATAGAATAAAACTTTGGGTATCTACTTTGGTAAAAAA
131 GTACCTAAAGTGGTAATAGAATAAAACTTTAGGTATCTACTTTGGTAAAAAA
* *
9040 AAAACTTTAGGTACCTAAATGGGAGAAA-TTGCATAGTTTAAGTACCTAAAGTGGTAACAAATTA
1 AAAACTTTAGGTACCTAAATGGGA-AAAGTTGCATAGTTTAAGTACCTAAAGTGGTAATAGATTA
* * * *
9104 AAAATATAATGTGTCATAATTTGATTGGTTTGGATTC----TTTTTTTAACATGAGTTAACTGTT
65 AAAATGTCATGTGTCATAATTTGATTGGTTTGGATTCTTTTTTTTTTTAACGTGAGTTAACAGTT
* *
9165 GGTACCTAAAGTGGTAATAAAATAAAACTTTAGGTATCTACTTTGGT-TAAAA
130 GGTACCTAAAGTGGTAATAGAATAAAACTTTAGGTATCTACTTTGGTAAAAAA
* * * * *
9217 AAAA-TATTAGGTACTTAAATGGGAAAAGTTGCATAGTTTAATTATCTAAAGTGGTAATAAAATA
1 AAAACT-TTAGGTACCTAAATGGGAAAAGTTGCATAGTTTAAGTACCTAAAGTGGTAATAGATTA
* *
9281 AAATTGTCATTTGTCATAATTT-ATTTGGTTTGGATTCTTTTTTTTTTTTAAACGTGAGTTAACA
65 AAAATGTCATGTGTCATAATTTGA-TTGGTTTGGATTC-TTTTTTTTTTT-AACGTGAGTTAACA
* * * *
9345 ATTGGTACCTAAAGTGGTAATAGAATAAAACTTTAGGCACCTACTTTGATAAAAAAAAA
127 GTTGGTACCTAAAGTGGTAATAGAATAAAACTTTAGGTATCTACTTTGGT---AAAAAA
* * * *
9404 AAAAATTTAGATACCTAAATGAGAAAGGTT-CATAGTTTAAGTACCTA
1 AAAACTTTAGGTACCTAAATGGGAAAAGTTGCATAGTTTAAGTACCTA
9451 TTTTGATATT
Statistics
Matches: 667, Mismatches: 85, Indels: 40
0.84 0.11 0.05
Matches are distributed among these distances:
176 5 0.01
177 88 0.13
178 213 0.32
179 3 0.00
180 14 0.02
181 2 0.00
182 57 0.09
183 59 0.09
184 154 0.23
185 28 0.04
186 15 0.02
187 28 0.04
188 1 0.00
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (182 bp):
AAAACTTTAGGTACCTAAATGGGAAAAGTTGCATAGTTTAAGTACCTAAAGTGGTAATAGATTAA
AAATGTCATGTGTCATAATTTGATTGGTTTGGATTCTTTTTTTTTTTAACGTGAGTTAACAGTTG
GTACCTAAAGTGGTAATAGAATAAAACTTTAGGTATCTACTTTGGTAAAAAA
Found at i:13357 original size:27 final size:27
Alignment explanation
Indices: 13196--13355 Score: 117
Period size: 27 Copynumber: 5.9 Consensus size: 27
13186 CTTATAACCC
* * *
13196 CGTGTTTA-TGGTCCCGATGGACTATCT
1 CGTGTTTACT-GTCTCGACGGACTACCT
* * **
13223 CATGTTTACTATCTCGGTGGACTACCT
1 CGTGTTTACTGTCTCGACGGACTACCT
* * *
13250 CGTGTTTACTGTTTCAATGGACTACCT
1 CGTGTTTACTGTCTCGACGGACTACCT
* * * * *
13277 TGTGTTTATTGTCTTGACAGACTATCT
1 CGTGTTTACTGTCTCGACGGACTACCT
* * * *
13304 CATGTTTACTATCTCGGCGAACTACAC-
1 CGTGTTTACTGTCTCGACGGACTAC-CT
13331 CGTGTTTACTGTCTCGACGGACTAC
1 CGTGTTTACTGTCTCGACGGACTAC
13356 ACTAGTTGCC
Statistics
Matches: 100, Mismatches: 31, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
27 98 0.98
28 2 0.02
ACGTcount: A:0.19, C:0.24, G:0.20, T:0.38
Consensus pattern (27 bp):
CGTGTTTACTGTCTCGACGGACTACCT
Done.