Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006272.1 Kokia drynarioides strain JFW-HI SEQ_120843, 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: 17876
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2224 original size:208 final size:209
Alignment explanation
Indices: 1799--2603 Score: 1116
Period size: 208 Copynumber: 3.9 Consensus size: 209
1789 TCAAAAGGTA
* * ** * * * **
1799 ATCTTCCTGATGAGATACAGAGAAGCAGACCAAAACAATGATGAGAAGCTCAATACGAGTGAAAC
1 ATCTTCCTGATGAGATACAGAAAAGTAGACCAATTCAACGAAGTGAAGCTCAATGTGAGTGAAAC
* * * * * * *
1864 TTCGAAACCCCATCTTCTTGATGAGATATAAAGAAGTGGGTCAAAGCAATTAAGAGGTCATCTTC
66 TTCCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAATCAATAAAGTGGTCATCTTC
* ** * *
1929 CTGATGAGATATAGAGAAG-TAGAACAAATCCGTCTTTCTGATGAGATACAGAGAAGTGGATTAA
131 CTGACGAGATGCAGAGAAGTTA-ACCAAATCCGTCTTCCTGATGAGATACAGAGAAGTGGATTAA
1993 ATCAATGAAGC-AGTC
195 ATCAATGAAGCGA-TC
* *
2008 ATCTTCCTGATGAGATACAGAAAAGTAGACTAATTCAACGAAGTGAAGCTCAATGTGAATGAAAC
1 ATCTTCCTGATGAGATACAGAAAAGTAGACCAATTCAACGAAGTGAAGCTCAATGTGAGTGAAAC
* * *
2073 TTTCAAACCCCATCTTCCTGATGAGATATAGAGAAGT-GGTCAAATCAATAAAGTGGACATCTTC
66 TTCCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAATCAATAAAGTGGTCATCTTC
* * * *
2137 CTGACGAGATGCAGATAAGTTAACCAAATCCATCTTCTTGATGAGATACAGAGAAGGGGATTAAA
131 CTGACGAGATGCAGAGAAGTTAACCAAATCCGTCTTCCTGATGAGATACAGAGAAGTGGATTAAA
2202 TCAATGAAGCGATC
196 TCAATGAAGCGATC
* * *
2216 ATCTTCCTGATGAGATACAAAAAAGTAGACCAATTAAACGAAGTTAAGCTCAATGTGAGTG-AAC
1 ATCTTCCTGATGAGATACAGAAAAGTAGACCAATTCAACGAAGTGAAGCTCAATGTGAGTGAAAC
*
2280 TTCCAAACCCCATCTTCTTGATGAGATACAGAGAAGTGGGTCAAATCAATAAAGTGGTCATCTTC
66 TTCCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAATCAATAAAGTGGTCATCTTC
* * * * *
2345 CTAACGAGATGTAGAGAAGTGAACCAAATCCTTCTTCCTGATGAGATACATAGAAGTGGATTAAA
131 CTGACGAGATGCAGAGAAGTTAACCAAATCCGTCTTCCTGATGAGATACAGAGAAGTGGATTAAA
* *
2410 TCAATGAAGTGGTC
196 TCAATGAAGCGATC
* * *
2424 ATCGTCTTGATGAGATACA-AAGAAGTAGACCAAGTCAACGAAGTGAAGCTCAATGTGAGTGAAA
1 ATCTTCCTGATGAGATACAGAA-AAGTAGACCAATTCAACGAAGTGAAGCTCAATGTGAGTGAAA
*
2488 CTTCCAAACCCTATCTTCCTGATGAGATACAGAGAAGTGGGTCAAATCAATAAAGTGGTCATCTT
65 CTTCCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAATCAATAAAGTGGTCATCTT
* * *
2553 CCTGATGAGATGCAGAGAAATTAACCAAATTCGTCTTCCTGATGAGATACA
130 CCTGACGAGATGCAGAGAAGTTAACCAAATCCGTCTTCCTGATGAGATACA
2604 AACAAGTAGA
Statistics
Matches: 530, Mismatches: 61, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
207 39 0.07
208 292 0.55
209 199 0.38
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (209 bp):
ATCTTCCTGATGAGATACAGAAAAGTAGACCAATTCAACGAAGTGAAGCTCAATGTGAGTGAAAC
TTCCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAATCAATAAAGTGGTCATCTTC
CTGACGAGATGCAGAGAAGTTAACCAAATCCGTCTTCCTGATGAGATACAGAGAAGTGGATTAAA
TCAATGAAGCGATC
Found at i:2248 original size:85 final size:84
Alignment explanation
Indices: 2082--2241 Score: 205
Period size: 85 Copynumber: 1.9 Consensus size: 84
2072 CTTTCAAACC
* * *
2082 CCATCTTCCTGATGAGATATAGAGAAGTGGTCAAATCAATAAAGTGGACATCTTCCTGACGAGAT
1 CCATCTTCCTGATGAGATACAGAGAAGGGGTCAAATCAATAAAGTCGACATCTTCCTGACGAGAT
* * *
2147 GCAGATAAGTTAACCAAAT
66 ACAAAAAAGTTAACCAAAT
* * * *
2166 CCATCTTCTTGATGAGATACAGAGAAGGGGATTAAATCAATGAAG-CGATCATCTTCCTGATGAG
1 CCATCTTCCTGATGAGATACAGAGAAGGGG-TCAAATCAATAAAGTCGA-CATCTTCCTGACGAG
2230 ATACAAAAAAGT
64 ATACAAAAAAGT
2242 AGACCAATTA
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
84 29 0.45
85 35 0.55
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.25
Consensus pattern (84 bp):
CCATCTTCCTGATGAGATACAGAGAAGGGGTCAAATCAATAAAGTCGACATCTTCCTGACGAGAT
ACAAAAAAGTTAACCAAAT
Found at i:2456 original size:85 final size:85
Alignment explanation
Indices: 2292--2449 Score: 208
Period size: 85 Copynumber: 1.9 Consensus size: 85
2282 CCAAACCCCA
* * * **
2292 TCTTCTTGATGAGATACAGAGAAGTGGGTCAAATCAATAAAGTGGTCATCTTCCTAACGAGATGT
1 TCTTCCTGATGAGATACAGAGAAGTGGATCAAATCAATAAAGTGGTCATCGTCCTAACGAGATAC
*
2357 AGAGAAGTGAACCAAATCCT
66 AAAGAAGTGAACCAAATCCT
* * * * * *
2377 TCTTCCTGATGAGATACATAGAAGTGGATTAAATCAATGAAGTGGTCATCGTCTTGATGAGATAC
1 TCTTCCTGATGAGATACAGAGAAGTGGATCAAATCAATAAAGTGGTCATCGTCCTAACGAGATAC
2442 AAAGAAGT
66 AAAGAAGT
2450 AGACCAAGTC
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
85 61 1.00
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (85 bp):
TCTTCCTGATGAGATACAGAGAAGTGGATCAAATCAATAAAGTGGTCATCGTCCTAACGAGATAC
AAAGAAGTGAACCAAATCCT
Found at i:3588 original size:24 final size:24
Alignment explanation
Indices: 3561--3608 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
3551 AAAACAACCC
*
3561 TTCCATTGGAAGCTGTTTTTACCA
1 TTCCATTGGAAGCTGTCTTTACCA
3585 TTCCATTGGAAGCTGTCTTTACCA
1 TTCCATTGGAAGCTGTCTTTACCA
3609 ACAAAAGATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.40
Consensus pattern (24 bp):
TTCCATTGGAAGCTGTCTTTACCA
Found at i:7664 original size:203 final size:202
Alignment explanation
Indices: 7287--7693 Score: 681
Period size: 203 Copynumber: 2.0 Consensus size: 202
7277 CGTCCAATTC
* * *
7287 CAATTCGAGAAGCTTATCTTGATCTGCTTTTTCTATGGTTGTCTGGGGCATGACAATGGGTTATA
1 CAATTCGAGAAGCTTACCCTGATCTACTTTTTCTATGGTTGTCTGGGGCATGACAATGGGTTATA
*
7352 TCCTATTTGGTTAAGGAGGAAGGTTTTTATTCTGATATGGGTTGAGATATCTCGCTCCAAGCAGT
66 TCCTATTTGGTTAAGGAGGAAGGTTTTTATTCTGATATGGGTTGAGATATCTCGCTCCAAGCAAT
* *
7417 GGGTAGACGGGTTGCAGTCGGTGAGAGCATCTAGTTACGAAAGGGGTCTGTTGGTGAGTCTCCTT
131 GGGTAGACGGGTAGCAGTCGGTGAGAGCATCTAGTTACGAAAGGGGTCTGTTGGTGAGTCTCATT
7482 GTATTGG
196 GTATTGG
* *
7489 CAATTCGAGAAGCTTACCCTGATCTACTTTTTCTATGGTTG-CTTGGGGCATGACGATGGGTTTT
1 CAATTCGAGAAGCTTACCCTGATCTACTTTTTCTATGGTTGTC-TGGGGCATGACAATGGGTTAT
*
7553 ATCCTATTTGGTTAAGGAGGGAGGTTTTTTATTCTGATATGGGTTGAGATATCTCGCTCCAAGCA
65 ATCCTATTTGGTTAAGGAGGAAGG-TTTTTATTCTGATATGGGTTGAGATATCTCGCTCCAAGCA
* * *
7618 ATGGGTAGACGGGTAGCAGTTGGTGAGAGCATCTAGTTGCGAAAGGGGTCTGTTGGTGAGTCTTA
129 ATGGGTAGACGGGTAGCAGTCGGTGAGAGCATCTAGTTACGAAAGGGGTCTGTTGGTGAGTCTCA
7683 TTGTATTGG
194 TTGTATTGG
7692 CA
1 CA
7694 TTTCTCATGG
Statistics
Matches: 191, Mismatches: 12, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
201 1 0.01
202 80 0.42
203 110 0.58
ACGTcount: A:0.21, C:0.14, G:0.30, T:0.35
Consensus pattern (202 bp):
CAATTCGAGAAGCTTACCCTGATCTACTTTTTCTATGGTTGTCTGGGGCATGACAATGGGTTATA
TCCTATTTGGTTAAGGAGGAAGGTTTTTATTCTGATATGGGTTGAGATATCTCGCTCCAAGCAAT
GGGTAGACGGGTAGCAGTCGGTGAGAGCATCTAGTTACGAAAGGGGTCTGTTGGTGAGTCTCATT
GTATTGG
Found at i:9994 original size:69 final size:69
Alignment explanation
Indices: 9900--10035 Score: 272
Period size: 69 Copynumber: 2.0 Consensus size: 69
9890 ATTGTGAATA
9900 GAAGCTAAAGCAAACAAAACACGAATAGTATAGATTTTAGTCACAGGAGAGTATGTATCAAAATA
1 GAAGCTAAAGCAAACAAAACACGAATAGTATAGATTTTAGTCACAGGAGAGTATGTATCAAAATA
9965 ATTG
66 ATTG
9969 GAAGCTAAAGCAAACAAAACACGAATAGTATAGATTTTAGTCACAGGAGAGTATGTATCAAAATA
1 GAAGCTAAAGCAAACAAAACACGAATAGTATAGATTTTAGTCACAGGAGAGTATGTATCAAAATA
10034 AT
66 AT
10036 CTACTCCAAA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 67 1.00
ACGTcount: A:0.47, C:0.12, G:0.18, T:0.23
Consensus pattern (69 bp):
GAAGCTAAAGCAAACAAAACACGAATAGTATAGATTTTAGTCACAGGAGAGTATGTATCAAAATA
ATTG
Found at i:16427 original size:21 final size:21
Alignment explanation
Indices: 16398--16439 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
16388 TCTTCTAAAG
16398 ATTAAATATCAAATCTAAGAT
1 ATTAAATATCAAATCTAAGAT
*
16419 ATTACATATCAAATCTAAGAT
1 ATTAAATATCAAATCTAAGAT
16440 TGTCAATCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.50, C:0.12, G:0.05, T:0.33
Consensus pattern (21 bp):
ATTAAATATCAAATCTAAGAT
Done.