Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009907.1 Kokia drynarioides strain JFW-HI SEQ_124645, 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, 676
Length: 1128
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Found at i:334 original size:29 final size:29
Alignment explanation
Indices: 289--697 Score: 365
Period size: 29 Copynumber: 14.0 Consensus size: 29
279 CCCTTAAGGT
*
289 CCCT-AAACTATCTAAAAATTCCATTTTTA
1 CCCTCAAACT-TCCAAAAATTCCATTTTTA
*
318 CCCTCGAACTTCCAAAAA-TCTCATTTTTAA
1 CCCTCAAACTTCCAAAAATTC-CATTTTT-A
*
348 CCC-CAAAACTTCCAAAAATTCCATTTTTGC
1 CCCTC-AAACTTCCAAAAATTCCATTTTT-A
*
378 CCCTCGAACTTCCAAAAA-TCACATTTTTGA
1 CCCTCAAACTTCCAAAAATTC-CATTTTT-A
* *
408 CCCTAAAACTTTCAAAAATTCCA-TTTTA
1 CCCTCAAACTTCCAAAAATTCCATTTTTA
* * * *
436 CCCTCGAACTTCCTAAAATCCCATTTTGA
1 CCCTCAAACTTCCAAAAATTCCATTTTTA
*
465 CCCTAAAACTTCCAAAAATTCCA-TTTTA
1 CCCTCAAACTTCCAAAAATTCCATTTTTA
* ** *
493 CCC-CTAAACTTCCTAAAACCCCATTTTAA
1 CCCTC-AAACTTCCAAAAATTCCATTTTTA
* *
522 CCCTAAAAGTTCCAAAAATTCCATTTTTA
1 CCCTCAAACTTCCAAAAATTCCATTTTTA
* **
551 CCCTTGAAA-TTCC-AAAAGCCTCATTTTTTA
1 CCC-TCAAACTTCCAAAAATTC-CA-TTTTTA
*
581 CCC-CAAAACTTCCAAAAATTCCAATTTTA
1 CCCTC-AAACTTCCAAAAATTCCATTTTTA
* *
610 CCCCCAAACTTCCAAAAA-TCATATTTTTAA
1 CCCTCAAACTTCCAAAAATTC-CATTTTT-A
* *
640 CCCTAAAAATTCCAAAAATTCCATTTTTA
1 CCCTCAAACTTCCAAAAATTCCATTTTTA
*
669 GCCC-CAAACTTCCAAAAATTACATTTTTA
1 -CCCTCAAACTTCCAAAAATTCCATTTTTA
698 ACCCCGAATT
Statistics
Matches: 309, Mismatches: 48, Indels: 46
0.77 0.12 0.11
Matches are distributed among these distances:
28 50 0.16
29 135 0.44
30 112 0.36
31 12 0.04
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.32
Consensus pattern (29 bp):
CCCTCAAACTTCCAAAAATTCCATTTTTA
Found at i:718 original size:59 final size:59
Alignment explanation
Indices: 293--702 Score: 465
Period size: 59 Copynumber: 7.0 Consensus size: 59
283 TAAGGTCCCT
* * *
293 AAACTATCTAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCTCATTTTTAACCCCA
1 AAACT-TCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCACATTTTTAACCCCA
* * * *
353 AAACTTCCAAAAATTCCATTTTTGCCCCTCGAACTTCCAAAAATCACATTTTTGACCCTA
1 AAACTTCCAAAAATTCCATTTTT-ACCCTCAAACTTCCAAAAATCACATTTTTAACCCCA
* * * * * *
413 AAACTTTCAAAAATTCCA-TTTTACCCTCGAACTTCCTAAAATCCCA-TTTTGACCCTA
1 AAACTTCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCACATTTTTAACCCCA
* * * *
470 AAACTTCCAAAAATTCCA-TTTTACCC-CTAAACTTCCTAAAACCCCA-TTTTAACCCTA
1 AAACTTCCAAAAATTCCATTTTTACCCTC-AAACTTCCAAAAATCACATTTTTAACCCCA
* * ** * *
527 AAAGTTCCAAAAATTCCATTTTTACCCTTGAAA-TTCCAAAAGCCTCATTTTTTACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCC-TCAAACTTCCAAAAATCACATTTTTAACCCCA
* * * *
586 AAACTTCCAAAAATTCCAATTTTACCCCCAAACTTCCAAAAATCATATTTTTAACCCTA
1 AAACTTCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCACATTTTTAACCCCA
* *
645 AAAATTCCAAAAATTCCATTTTTAGCCC-CAAACTTCCAAAAATTACATTTTTAACCCC
1 AAACTTCCAAAAATTCCATTTTTA-CCCTCAAACTTCCAAAAATCACATTTTTAACCCC
703 GAATTTTCCC
Statistics
Matches: 307, Mismatches: 35, Indels: 17
0.86 0.10 0.05
Matches are distributed among these distances:
56 1 0.00
57 79 0.26
58 43 0.14
59 127 0.41
60 57 0.19
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.32
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCACATTTTTAACCCCA
Found at i:719 original size:30 final size:29
Alignment explanation
Indices: 293--721 Score: 259
Period size: 30 Copynumber: 14.6 Consensus size: 29
283 TAAGGTCCCT
* *
293 AAACTATCTAAAAATTCCATTTTT-ACCCTC
1 AAACT-TCCAAAAATTACATTTTTAACCC-C
*
323 GAACTTCCAAAAATCT-CATTTTTAACCCC
1 AAACTTCCAAAAAT-TACATTTTTAACCCC
* **
352 AAAACTTCCAAAAATTCCATTTTTGCCCCTC
1 -AAACTTCCAAAAATTACATTTTTAACCC-C
* * * *
383 GAACTTCCAAAAATCACATTTTTGACCCTA
1 AAACTTCCAAAAATTACATTTTTAACCC-C
* *
413 AAACTTTCAAAAATTCCA-TTTT-ACCCTC
1 AAACTTCCAAAAATTACATTTTTAACCC-C
* * ** * *
441 GAACTTCCTAAAATCCCA-TTTTGACCCTA
1 AAACTTCCAAAAATTACATTTTTAACCC-C
*
470 AAACTTCCAAAAATTCCA-TTTT-ACCCC
1 AAACTTCCAAAAATTACATTTTTAACCCC
* *** *
497 TAAACTTCCTAAAACCCCA-TTTTAACCCTA
1 -AAACTTCCAAAAATTACATTTTTAACCC-C
* * *
527 AAAGTTCCAAAAATTCCATTTTT-ACCCTTG
1 AAACTTCCAAAAATTACATTTTTAACCC--C
** *
557 AAA-TTCCAAAAGCCT-CATTTTTTACCCC
1 AAACTTCCAAAA-ATTACATTTTTAACCCC
* * *
585 AAAACTTCCAAAAATTCCAATTTTACCCCC
1 -AAACTTCCAAAAATTACATTTTTAACCCC
* * *
615 AAACTTCCAAAAATCATATTTTTAACCCTA
1 AAACTTCCAAAAATTACATTTTTAACCC-C
* * *
645 AAAATTCCAAAAATTCCATTTTTAGCCCC
1 AAACTTCCAAAAATTACATTTTTAACCCC
674 AAACTTCCAAAAATTACATTTTTAACCCC
1 AAACTTCCAAAAATTACATTTTTAACCCC
** *
703 GAATTTTCCCAAAATTACA
1 -AAACTTCCAAAAATTACA
722 ATTTCACGCT
Statistics
Matches: 322, Mismatches: 59, Indels: 36
0.77 0.14 0.09
Matches are distributed among these distances:
28 46 0.14
29 135 0.42
30 140 0.43
31 1 0.00
ACGTcount: A:0.37, C:0.29, G:0.03, T:0.32
Consensus pattern (29 bp):
AAACTTCCAAAAATTACATTTTTAACCCC
Done.