Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010953.1 Kokia drynarioides strain JFW-HI SEQ_125921, 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: 23273
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.35
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:433 original size:30 final size:28
Alignment explanation
Indices: 399--904 Score: 324
Period size: 30 Copynumber: 17.1 Consensus size: 28
389 ACTTGGAGGT
* *
399 CCCCGAAACTTTTAAAAATTTAGTTTTTA
1 CCCCGAAACTTCTAAAAATTCA-TTTTTA
*
428 CCCCCG-AACTTTTAAAAATCTCATTTTTAA
1 -CCCCGAAACTTCTAAAAAT-TCATTTTT-A
*
458 CCCCAAAACTTCTAAAAATTCCATTTTTA
1 CCCCGAAACTTCTAAAAATT-CATTTTTA
* *
487 CCCCTAAACTTCCAAAAATCTCATTTTTGA
1 CCCCGAAACTTCTAAAAAT-TCATTTTT-A
**
517 CCCCGAAACTTCTAAAAATTCCCCTTTTA
1 CCCCGAAACTTCTAAAAATT-CATTTTTA
** *
546 CCCTAAAACTTCTAAAAATCTCGTTTTTAA
1 CCCCGAAACTTCTAAAAAT-TCATTTTT-A
* *
576 CCTCGAAACTTCCAAAAATTCCATTTTTTA
1 CCCCGAAACTTCTAAAAATT-CA-TTTTTA
* *
606 CCCCCAAACTTCCAAAAATCTCATTTTTGA
1 CCCCGAAACTTCTAAAAAT-TCATTTTT-A
*
636 CCCCAAAACTTCTAAAAATTTCATTTTTA
1 CCCCGAAACTTCTAAAAA-TTCATTTTTA
** * * *
665 TCATCG-AACTTCCAAAAATCACATTCTTGA
1 -CCCCGAAACTTCTAAAAAT-TCATT-TTTA
** *
695 TTCCAAAACTTCTAAAAATTCCATTTTTA
1 CCCCGAAACTTCTAAAAATT-CATTTTTA
724 CCCCCG-AACTTCTAAAAATTTCATTTTTA
1 -CCCCGAAACTTCTAAAAA-TTCATTTTTA
** *
753 TCATCG-AACTTCTAAAAATCCCATTTTTAA
1 -CCCCGAAACTTCTAAAAAT-TCATTTTT-A
*** * *
783 CCTTAAAACTTC-CAAAATTCCCTTTTTTA
1 CCCCGAAACTTCTAAAAATT--CATTTTTA
*
812 CCCTCG-AACTTCCAAAAATATCATTTTTGA
1 CCC-CGAAACTTCTAAAAAT-TCATTTTT-A
** *
842 CCCTAAAACTTCAAAAAATTCCATTTTTGA
1 CCCCGAAACTTCTAAAAATT-CATTTTT-A
* *
872 CCCCGAAACCTCCAAAAATTACCA-TTTTA
1 CCCCGAAACTTCTAAAAATT--CATTTTTA
901 CCCC
1 CCCC
905 CGGGTATCCG
Statistics
Matches: 383, Mismatches: 60, Indels: 67
0.75 0.12 0.13
Matches are distributed among these distances:
28 2 0.01
29 168 0.44
30 202 0.53
31 11 0.03
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (28 bp):
CCCCGAAACTTCTAAAAATTCATTTTTA
Found at i:437 original size:29 final size:28
Alignment explanation
Indices: 399--781 Score: 174
Period size: 29 Copynumber: 13.0 Consensus size: 28
389 ACTTGGAGGT
*
399 CCCCGAAACTTTTAAAAATTTAGTTTTTAC
1 CCCCG-AACTTTTAAAAATTCA-TTTTTAC
429 CCCCGAACTTTTAAAAATCTCATTTTTAAC
1 CCCCGAACTTTTAAAAAT-TCATTTTT-AC
** *
459 CCCAAAACTTCTAAAAATTCCATTTTTAC
1 CCCCGAACTTTTAAAAATT-CATTTTTAC
** **
488 CCCTAAACTTCCAAAAATCTCATTTTTGA-
1 CCCCGAACTTTTAAAAAT-TCATTTTT-AC
* **
517 CCCCGAAACTTCTAAAAATTCCCCTTTTAC
1 CCCCG-AACTTTTAAAAATT-CATTTTTAC
*** * * *
547 CCTAAAACTTCTAAAAATCTCGTTTTTAA
1 CCCCGAACTTTTAAAAAT-TCATTTTTAC
* **
576 CCTCGAAACTTCCAAAAATTCCATTTTTTAC
1 CCCCG-AACTTTTAAAAATT-CA-TTTTTAC
* **
607 CCCCAAACTTCCAAAAATCTCATTTTTGAC
1 CCCCGAACTTTTAAAAAT-TCATTTTT-AC
** * *
637 CCCAAAACTTCTAAAAATTTCATTTTTAT
1 CCCCGAACTTTTAAAAA-TTCATTTTTAC
** ** * * *
666 CATCGAACTTCCAAAAATCACATTCTTGAT
1 CCCCGAACTTTTAAAAAT-TCATT-TTTAC
* ** *
696 TCCAAAACTTCTAAAAATTCCATTTTTAC
1 CCCCGAACTTTTAAAAATT-CATTTTTAC
* *
725 CCCCGAACTTCTAAAAATTTCATTTTTAT
1 CCCCGAACTTTTAAAAA-TTCATTTTTAC
** * *
754 CATCGAACTTCTAAAAATCCCATTTTTA
1 CCCCGAACTTTTAAAAAT-TCATTTTTA
782 ACCTTAAAAC
Statistics
Matches: 283, Mismatches: 50, Indels: 41
0.76 0.13 0.11
Matches are distributed among these distances:
28 2 0.01
29 142 0.50
30 128 0.45
31 11 0.04
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (28 bp):
CCCCGAACTTTTAAAAATTCATTTTTAC
Found at i:477 original size:59 final size:59
Alignment explanation
Indices: 399--905 Score: 425
Period size: 59 Copynumber: 8.6 Consensus size: 59
389 ACTTGGAGGT
* * * * **
399 CCCCGAAACTTTTAAAAATT-TAGTTTTTACCCCCGAACTTTTAAAAATCTCATTTTTAA
1 CCCCAAAACTTCTAAAAATTCCA-TTTTTACCCCCAAACTTCCAAAAATCTCATTTTTAA
* *
458 CCCCAAAACTTCTAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCTCATTTTTGA
1 CCCCAAAACTTCTAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCTCATTTTTAA
* ** ** * *
517 CCCCGAAACTTCTAAAAATTCCCCTTTTACCCTAAAACTTCTAAAAATCTCGTTTTTAA
1 CCCCAAAACTTCTAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCTCATTTTTAA
* * * *
576 CCTCGAAACTTCCAAAAATTCCATTTTTTACCCCCAAACTTCCAAAAATCTCATTTTTGA
1 CCCCAAAACTTCTAAAAATTCCA-TTTTTACCCCCAAACTTCCAAAAATCTCATTTTTAA
* * ** * * * *
636 CCCCAAAACTTCTAAAAATTTCATTTTTATCATCGAACTTCCAAAAATCACATTCTTGA
1 CCCCAAAACTTCTAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCTCATTTTTAA
** * * * *
695 TTCCAAAACTTCTAAAAATTCCATTTTTACCCCCGAACTTCTAAAAATTTCATTTTTAT
1 CCCCAAAACTTCTAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCTCATTTTTAA
** * * *** * * *
754 CATC-GAACTTCTAAAAATCCCATTTTTAACCTTAAAACTTCCAAAATTC-CCTTTTTTA
1 CCCCAAAACTTCTAAAAATTCCATTTTT-ACCCCCAAACTTCCAAAAATCTCATTTTTAA
* * ** * *
812 CCCTC-GAACTTCCAAAAATAT-CATTTTTGACCCTAAAACTTCAAAAAAT-TCCATTTTTGA
1 CCC-CAAAACTTCTAAAAAT-TCCATTTTT-ACCCCCAAACTTCCAAAAATCT-CATTTTTAA
* * *
872 CCCCGAAACCTCCAAAAATTACCA-TTTTACCCCC
1 CCCCAAAACTTCTAAAAATT-CCATTTTTACCCCC
906 GGGTATCCGA
Statistics
Matches: 362, Mismatches: 76, Indels: 20
0.79 0.17 0.04
Matches are distributed among these distances:
58 28 0.08
59 256 0.71
60 76 0.21
61 2 0.01
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (59 bp):
CCCCAAAACTTCTAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCTCATTTTTAA
Found at i:4904 original size:33 final size:33
Alignment explanation
Indices: 4860--4924 Score: 105
Period size: 34 Copynumber: 2.0 Consensus size: 33
4850 TTGAATGCAT
4860 GAAAAAATTAATGCAA-TTTATAATTTCAATAA
1 GAAAAAATTAATGCAATTTTATAATTTCAATAA
*
4892 GAAAAAACTTAATGCAATTTTATAGTTTCAATA
1 GAAAAAA-TTAATGCAATTTTATAATTTCAATA
4925 GCAACACAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 7 0.23
33 9 0.30
34 14 0.47
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (33 bp):
GAAAAAATTAATGCAATTTTATAATTTCAATAA
Found at i:15503 original size:9 final size:9
Alignment explanation
Indices: 15472--15509 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
15462 ATTAATTTTT
15472 TTTTTTAAA
1 TTTTTTAAA
*
15481 -TTTATAAA
1 TTTTTTAAA
*
15489 TCTTTTAAA
1 TTTTTTAAA
15498 TTTTTTAAA
1 TTTTTTAAA
15507 TTT
1 TTT
15510 AAAAGAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
8 7 0.29
9 17 0.71
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:20712 original size:150 final size:150
Alignment explanation
Indices: 20440--20723 Score: 480
Period size: 150 Copynumber: 1.9 Consensus size: 150
20430 AAACCCATTT
*
20440 CCACACACCTCTCTTTTTCATCTTCATCTTCTTCCCTTTTGATTCCAATATCTTTAGTTACAAAT
1 CCACACACCTCTCTTCTTCATCTTCATCTTCTTCCCTTTTGATTCCAATATCTTTAGTTACAAAT
* * * *
20505 CCGTCTCAAAGCTTGAATATTTGAAATCCATTAATCCAAAAAAACTTAACGGGAAGAAGATATTG
66 CCGTCTCAAAGCTTGAATATTTAAAACCCATTAACCCAAAAAAACTCAACGGGAAGAAGATATT-
20570 GAATCAAAGATATTGAATCTC
130 GAATCAAAGATATTGAATCTC
* *
20591 CCACACACCTCTCTTCTTCTTCTTCATCTTCTTCCCTTTTGATTCCAATA-CTTTAGTTATAAAT
1 CCACACACCTCTCTTCTTCATCTTCATCTTCTTCCCTTTTGATTCCAATATCTTTAGTTACAAAT
*
20655 CTGTCTCAAAGCTTGAATATTTAAAACCCATTAACCCAAAAAAACTCAACGGGAAGAAGATATTG
66 CCGTCTCAAAGCTTGAATATTTAAAACCCATTAACCCAAAAAAACTCAACGGGAAGAAGATATTG
20720 AATC
131 AATC
20724 TTTGGGTTAA
Statistics
Matches: 125, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
149 5 0.04
150 72 0.58
151 48 0.38
ACGTcount: A:0.33, C:0.24, G:0.09, T:0.34
Consensus pattern (150 bp):
CCACACACCTCTCTTCTTCATCTTCATCTTCTTCCCTTTTGATTCCAATATCTTTAGTTACAAAT
CCGTCTCAAAGCTTGAATATTTAAAACCCATTAACCCAAAAAAACTCAACGGGAAGAAGATATTG
AATCAAAGATATTGAATCTC
Found at i:23236 original size:25 final size:23
Alignment explanation
Indices: 23208--23253 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
23198 GTTTGATCCA
23208 AATTAAATTCTAAAAAAATAATTAG
1 AATTAAA-TCT-AAAAAATAATTAG
*
23233 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
23254 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
24 3 0.15
25 7 0.35
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Done.