Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011591.1 Kokia drynarioides strain JFW-HI SEQ_126581, 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: 412326
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 224 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:355979 original size:19 final size:19
Alignment explanation
Indices: 355955--356001 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
355945 GCATGAAACT
355955 ACTAAGT-TCTATATGTTAC
1 ACTAAGTAT-TATATGTTAC
355974 ACTAAGTATTATATGTTAC
1 ACTAAGTATTATATGTTAC
355993 ACTAAGTAT
1 ACTAAGTAT
356002 AGATAGAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 26 0.96
20 1 0.04
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (19 bp):
ACTAAGTATTATATGTTAC
Found at i:357632 original size:70 final size:70
Alignment explanation
Indices: 357519--357659 Score: 239
Period size: 70 Copynumber: 2.0 Consensus size: 70
357509 TTGTTGATAC
* * *
357519 ATGCAGGACAGTAACCAAAGTTCAAATTCTCTATACTTCTATTGATACATGCAAGAGTTCTACCG
1 ATGCAAGACAGTAACCAAAGTGCAAATTCTCTATACTTCTATTGATACATGAAAGAGTTCTACCG
357584 AAACA
66 AAACA
357589 ATGCAAGACAGTAACCAAAGTGCAAATTC-CTTATACTTCTATTGATACATGAAAGAGTTCTACC
1 ATGCAAGACAGTAACCAAAGTGCAAATTCTC-TATACTTCTATTGATACATGAAAGAGTTCTACC
357653 GAAACA
65 GAAACA
357659 A
1 A
357660 GTGTGCAGAA
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
69 1 0.01
70 66 0.99
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.26
Consensus pattern (70 bp):
ATGCAAGACAGTAACCAAAGTGCAAATTCTCTATACTTCTATTGATACATGAAAGAGTTCTACCG
AAACA
Found at i:358419 original size:33 final size:33
Alignment explanation
Indices: 358382--358459 Score: 86
Period size: 33 Copynumber: 2.4 Consensus size: 33
358372 TGGCCCGAGC
* **
358382 ATGGTCTTACATTCATAATGACATAACCCAGTT
1 ATGGTCTTACATTCAAAATGACATAACCCAACT
** *
358415 ATGGTCTTAGCA-TCAAAATGTTATAGCCCAACT
1 ATGGTCTTA-CATTCAAAATGACATAACCCAACT
358448 ATGGTCTTACAT
1 ATGGTCTTACAT
358460 CTATATACAC
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
32 2 0.05
33 33 0.89
34 2 0.05
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (33 bp):
ATGGTCTTACATTCAAAATGACATAACCCAACT
Found at i:358519 original size:69 final size:69
Alignment explanation
Indices: 358415--358703 Score: 328
Period size: 69 Copynumber: 4.3 Consensus size: 69
358405 TAACCCAGTT
* ** *
358415 ATGGTCTTAGCATCAAAATGTTATAGCCCAACTATGGTCTTACATCTATATACACTGTCATGGTC
1 ATGGTCTTA-CATCAGAATGCCATAGCCCAGCTATGGTCTTACATCTATATACACTGTCATGGTC
*
358480 CAACA
65 CAACC
* * * * *
358485 ATGGTCTTACGTCAGAATGTCATAGCCTAGCTATGGTCTTA-A-C-ATCAGA-A-TG-CCT--T-
1 ATGGTCTTACATCAGAATGCCATAGCCCAGCTATGGTCTTACATCTAT-ATACACTGTCATGGTC
*
358541 -AACT
65 CAACC
* * * *
358545 ATGGTCTTAACATCAGAATGCCCTAGCCCAGCTATGGTTTTATATCTATATATACTGTCATGGTC
1 ATGGTCTT-ACATCAGAATGCCATAGCCCAGCTATGGTCTTACATCTATATACACTGTCATGGTC
358610 CAACC
65 CAACC
*
358615 ATGGTCTTACATCAGAATGCCATAGCCCAGCTATGGTCTTACATCTATAAACACTGTCATGGTCC
1 ATGGTCTTACATCAGAATGCCATAGCCCAGCTATGGTCTTACATCTATATACACTGTCATGGTCC
358680 AACC
66 AACC
*
358684 ATGGTCTTACATTAGAATGC
1 ATGGTCTTACATCAGAATGC
358704 AGCTTATCTC
Statistics
Matches: 185, Mismatches: 22, Indels: 25
0.80 0.09 0.11
Matches are distributed among these distances:
60 11 0.06
61 28 0.15
62 2 0.01
63 3 0.02
64 5 0.03
65 4 0.02
66 5 0.03
67 3 0.02
68 2 0.01
69 102 0.55
70 20 0.11
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (69 bp):
ATGGTCTTACATCAGAATGCCATAGCCCAGCTATGGTCTTACATCTATATACACTGTCATGGTCC
AACC
Found at i:358580 original size:130 final size:129
Alignment explanation
Indices: 358334--358659 Score: 366
Period size: 130 Copynumber: 2.5 Consensus size: 129
358324 TTTCTTATTG
* * ** * * *
358334 TGTCATAGTCCAACTATGGTCTTACATGTGCATTGCCATGGCCCGAGC-ATGGTCTTACATTCAT
1 TGTCATGGTCCAACAATGGTCTTACATCAG-AATGCCATAGCCC-AGCTATGGTCTTACA-TCAG
* * * **
358398 AATGACATAACCCAGTTATGGTCTTAGCATCAAAATGTTATAGCCCAACTATGGTCTTACATCTA
63 AATGCCTTAA--C---TATGGTCTTAACATCAAAATGCCATAGCCCAACTATGGTCTTACATCTA
358463 TATACAC
123 TATACAC
* * *
358470 TGTCATGGTCCAACAATGGTCTTACGTCAGAATGTCATAGCCTAGCTATGGTCTTAACATCAGAA
1 TGTCATGGTCCAACAATGGTCTTACATCAGAATGCCATAGCCCAGCTATGGTCTT-ACATCAGAA
* * * * * *
358535 TGCCTTAACTATGGTCTTAACATCAGAATGCCCTAGCCCAGCTATGGTTTTATATCTATATATAC
65 TGCCTTAACTATGGTCTTAACATCAAAATGCCATAGCCCAACTATGGTCTTACATCTATATACAC
*
358600 TGTCATGGTCCAACCATGGTCTTACATCAGAATGCCATAGCCCAGCTATGGTCTTACATC
1 TGTCATGGTCCAACAATGGTCTTACATCAGAATGCCATAGCCCAGCTATGGTCTTACATC
358660 TATAAACACT
Statistics
Matches: 163, Mismatches: 25, Indels: 11
0.82 0.13 0.06
Matches are distributed among these distances:
129 5 0.03
130 98 0.60
133 1 0.01
134 3 0.02
135 28 0.17
136 28 0.17
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (129 bp):
TGTCATGGTCCAACAATGGTCTTACATCAGAATGCCATAGCCCAGCTATGGTCTTACATCAGAAT
GCCTTAACTATGGTCTTAACATCAAAATGCCATAGCCCAACTATGGTCTTACATCTATATACAC
Found at i:362429 original size:18 final size:17
Alignment explanation
Indices: 362380--362429 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 17
362370 GTTATGTTTC
362380 TTCCTTC-TCTTCTTCTT
1 TTCCTTCATCTTC-TCTT
362397 TTCCTTCAT-TT-TCTT
1 TTCCTTCATCTTCTCTT
*
362412 TTTCTTCATCCTTCTCTT
1 TTCCTTCAT-CTTCTCTT
362430 GGTCACCTCC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 12 0.43
17 11 0.39
18 5 0.18
ACGTcount: A:0.04, C:0.32, G:0.00, T:0.64
Consensus pattern (17 bp):
TTCCTTCATCTTCTCTT
Found at i:372441 original size:21 final size:22
Alignment explanation
Indices: 372407--372447 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
372397 GTATTGCGTT
*
372407 CAGGAGTCTATGTCACGACACA
1 CAGGAGTCCATGTCACGACACA
*
372429 CAGGA-TCCATGTCGCGACA
1 CAGGAGTCCATGTCACGACA
372448 TTTAAGGCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.17
Consensus pattern (22 bp):
CAGGAGTCCATGTCACGACACA
Found at i:377298 original size:57 final size:57
Alignment explanation
Indices: 377211--377324 Score: 219
Period size: 57 Copynumber: 2.0 Consensus size: 57
377201 GGAGAGTGAG
*
377211 TTAAGATCCTTTAATTCTTCTATGGTCGTCACCTTTGGTTCCCAAGATGTTGGGAGA
1 TTAAGATCCTTTAATTCTTCTATGGCCGTCACCTTTGGTTCCCAAGATGTTGGGAGA
377268 TTAAGATCCTTTAATTCTTCTATGGCCGTCACCTTTGGTTCCCAAGATGTTGGGAGA
1 TTAAGATCCTTTAATTCTTCTATGGCCGTCACCTTTGGTTCCCAAGATGTTGGGAGA
377325 CTATTCAACA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (57 bp):
TTAAGATCCTTTAATTCTTCTATGGCCGTCACCTTTGGTTCCCAAGATGTTGGGAGA
Found at i:378870 original size:20 final size:20
Alignment explanation
Indices: 378845--378898 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
378835 AGTCTTCAAG
378845 ATATCGGTAGAAGTGGAGTT
1 ATATCGGTAGAAGTGGAGTT
*
378865 ATATCGGTAGAAGTGGTGTT
1 ATATCGGTAGAAGTGGAGTT
* *
378885 CTACCGGTAGAAGT
1 ATATCGGTAGAAGT
378899 CTCACAGGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.28, C:0.09, G:0.33, T:0.30
Consensus pattern (20 bp):
ATATCGGTAGAAGTGGAGTT
Found at i:394142 original size:17 final size:17
Alignment explanation
Indices: 394120--394165 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 17
394110 TTAGTTTTCA
394120 TGCATTCTTTTTGTGC-C
1 TGCATTCTTTTTGT-CAC
394137 TGCATT-TTTATTGTCAC
1 TGCATTCTTT-TTGTCAC
394154 TGCATTCCTTTT
1 TGCATT-CTTTT
394166 AGTTTAGTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
16 4 0.16
17 17 0.68
18 1 0.04
19 3 0.12
ACGTcount: A:0.11, C:0.22, G:0.13, T:0.54
Consensus pattern (17 bp):
TGCATTCTTTTTGTCAC
Found at i:399908 original size:21 final size:21
Alignment explanation
Indices: 399882--399924 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
399872 AATATATATT
399882 TTTTC-TGCTTTTCTCTTCTTC
1 TTTTCTTGCTTTT-TCTTCTTC
*
399903 TTTTCTTTCTTTTTCTTCTTC
1 TTTTCTTGCTTTTTCTTCTTC
399924 T
1 T
399925 CTATTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.00, C:0.26, G:0.02, T:0.72
Consensus pattern (21 bp):
TTTTCTTGCTTTTTCTTCTTC
Done.