Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002005.1 Kokia drynarioides strain JFW-HI SEQ_113866, 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: 5929
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Found at i:558 original size:30 final size:30
Alignment explanation
Indices: 531--606 Score: 77
Period size: 30 Copynumber: 2.6 Consensus size: 30
521 TTTAACTTTT
531 TAAAAATTACAATTTT-ACCTCCGAACTTC
1 TAAAAATTACAATTTTAACCTCCGAACTTC
* * *
560 TAAAAATTCCATTTTTAACCT-CG-ATTTC
1 TAAAAATTACAATTTTAACCTCCGAACTTC
*
588 ATCAAAAATTACATTTTTA
1 -T-AAAAATTACAATTTTA
607 CCCTTGAACT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 4 0.10
29 17 0.43
30 19 0.47
ACGTcount: A:0.38, C:0.20, G:0.03, T:0.39
Consensus pattern (30 bp):
TAAAAATTACAATTTTAACCTCCGAACTTC
Found at i:595 original size:59 final size:57
Alignment explanation
Indices: 532--716 Score: 196
Period size: 59 Copynumber: 3.2 Consensus size: 57
522 TTAACTTTTT
532 AAAAATTACAATTTTACCTCCGAACTTCTAAAAATTCCATTTTTAACCTCGATTTCAT-C
1 AAAAATTACAATTTTACC-CCGAACTTCTAAAAATTCCATTTTT-ACCTCGATTTC-TCC
* * * * * *
591 AAAAATTACATTTTTACCCTTGAACTTTTCAAAATTTCATTTTTACC-CTATTTTCTCC
1 AAAAATTACAATTTTACCC-CGAACTTCTAAAAATTCCATTTTTACCTCGA-TTTCTCC
* * *
649 AAAAATTATC-ATTTTACCCCCTAACTTCCAAAAATTCCATTTTTGACCTCGATTTTTCC
1 AAAAATTA-CAATTTTA-CCCCGAACTTCTAAAAATTCCATTTTT-ACCTCGATTTCTCC
708 AAAAATTAC
1 AAAAATTAC
717 CATCCAAAAA
Statistics
Matches: 104, Mismatches: 15, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
57 3 0.03
58 41 0.39
59 58 0.56
60 2 0.02
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.40
Consensus pattern (57 bp):
AAAAATTACAATTTTACCCCGAACTTCTAAAAATTCCATTTTTACCTCGATTTCTCC
Found at i:623 original size:30 final size:30
Alignment explanation
Indices: 524--716 Score: 113
Period size: 29 Copynumber: 6.6 Consensus size: 30
514 TTTGACCTTT
* *
524 AACTTTTTAAAAATTACAATTTTA-CCTCCG
1 AACTTTTCAAAAATTACATTTTTACCCT-CG
* * *
554 AACTTCT-AAAAATTCCATTTTTAACCTCG
1 AACTTTTCAAAAATTACATTTTTACCCTCG
*
583 -A-TTTCATCAAAAATTACATTTTTACCCTTG
1 AACTTT--TCAAAAATTACATTTTTACCCTCG
*
613 AACTTTTC-AAAATTTCATTTTTACCCT--
1 AACTTTTCAAAAATTACATTTTTACCCTCG
* * *
640 -ATTTTCTCCAAAAATTATCA-TTTTACCCCCT
1 AACTTT-T-CAAAAATTA-CATTTTTACCCTCG
* *
671 AAC-TTCCAAAAATTCCATTTTTGA-CCTCG
1 AACTTTTCAAAAATTACATTTTT-ACCCTCG
*
700 -ATTTTTCCAAAAATTAC
1 AACTTTT-CAAAAATTAC
717 CATCCAAAAA
Statistics
Matches: 127, Mismatches: 19, Indels: 34
0.71 0.11 0.19
Matches are distributed among these distances:
26 4 0.03
27 3 0.02
28 5 0.04
29 66 0.52
30 42 0.33
31 3 0.02
32 4 0.03
ACGTcount: A:0.33, C:0.23, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTCAAAAATTACATTTTTACCCTCG
Found at i:625 original size:29 final size:29
Alignment explanation
Indices: 484--639 Score: 88
Period size: 29 Copynumber: 5.3 Consensus size: 29
474 AAAAATAATA
* * *
484 TTTTAGCCCTTAAACTATTCCAAATT-CAAT
1 TTTTA-CCCTTGAACTTTTCAAAATTAC-AT
* * * *
514 TTTGA-CCTTTAACTTTTTAAAAATTACAA
1 TTTTACCCTTGAAC-TTTTCAAAATTACAT
* * * *
543 TTTTA-CCTCCGAACTTCTAAAAATTCCAT
1 TTTTACCCT-TGAACTTTTCAAAATTACAT
* *
572 TTTTAACCTCG-A-TTTCATCAAAAATTACAT
1 TTTTACCCTTGAACTTT--TC-AAAATTACAT
*
602 TTTTACCCTTGAACTTTTCAAAATTTCAT
1 TTTTACCCTTGAACTTTTCAAAATTACAT
631 TTTTACCCT
1 TTTTACCCT
640 ATTTTCTCCA
Statistics
Matches: 99, Mismatches: 18, Indels: 19
0.73 0.13 0.14
Matches are distributed among these distances:
27 2 0.02
28 8 0.08
29 54 0.55
30 31 0.31
31 1 0.01
32 3 0.03
ACGTcount: A:0.32, C:0.22, G:0.03, T:0.43
Consensus pattern (29 bp):
TTTTACCCTTGAACTTTTCAAAATTACAT
Found at i:725 original size:44 final size:44
Alignment explanation
Indices: 675--763 Score: 142
Period size: 44 Copynumber: 2.0 Consensus size: 44
665 CCCCCTAACT
* *
675 TCCAAAAATTCCATTTTTGACCTCGATTTTTCCAAAAATTACCA
1 TCCAAAAATTCCATTTTTGACCCCAATTTTTCCAAAAATTACCA
* *
719 TCCAAAAATTCCATTTTTGACCCCAATTTTTTCTAAAATTACCA
1 TCCAAAAATTCCATTTTTGACCCCAATTTTTCCAAAAATTACCA
763 T
1 T
764 TTTACCCCCG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (44 bp):
TCCAAAAATTCCATTTTTGACCCCAATTTTTCCAAAAATTACCA
Found at i:784 original size:28 final size:28
Alignment explanation
Indices: 753--871 Score: 96
Period size: 28 Copynumber: 4.1 Consensus size: 28
743 AATTTTTTCT
* *
753 AAAATTACCATTTTACCCCCGAATGTCTA
1 AAAATTACCATTTTACCCCCGAATATC-C
* * *
782 AAAATT-CCATTTTAGACCTCGAATTTTCAC
1 AAAATTACCATTTTA-CCCCCGAA-TATC-C
* * * *
812 AAAATTATCATTTTGCCCTCGAGTATCC
1 AAAATTACCATTTTACCCCCGAATATCC
* *
840 AAAATTACTATTTTACCCCCGAGTATCC
1 AAAATTACCATTTTACCCCCGAATATCC
868 AAAA
1 AAAA
872 ATCACATTTT
Statistics
Matches: 73, Mismatches: 14, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
28 37 0.51
29 15 0.21
30 15 0.21
31 6 0.08
ACGTcount: A:0.34, C:0.25, G:0.08, T:0.33
Consensus pattern (28 bp):
AAAATTACCATTTTACCCCCGAATATCC
Found at i:880 original size:28 final size:27
Alignment explanation
Indices: 811--881 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 27
801 CGAATTTTCA
* * *
811 CAAAATTATCATTTTGCCCTCGAGTATC
1 CAAAATCA-CATTTTACCCCCGAGTATC
*
839 CAAAATTACTATTTTACCCCCGAGTATC
1 CAAAATCAC-ATTTTACCCCCGAGTATC
867 CAAAAATCACATTTT
1 C-AAAATCACATTTT
882 CAACTTCGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 1 0.03
28 30 0.79
29 7 0.18
ACGTcount: A:0.34, C:0.25, G:0.07, T:0.34
Consensus pattern (27 bp):
CAAAATCACATTTTACCCCCGAGTATC
Found at i:1408 original size:27 final size:25
Alignment explanation
Indices: 1378--1439 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
1368 TGGGACTTCC
*
1378 AAATAAAAATCGATTTCTTTTTAAAAT
1 AAATAAAAATAGA-TT-TTTTTAAAAT
*
1405 AAATAAATATAGATTTTTTTAAAAT
1 AAATAAAAATAGATTTTTTTAAAAT
1430 AAATATAAAA
1 AAATA-AAAA
1440 AACAATTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 15 0.48
26 5 0.16
27 11 0.35
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (25 bp):
AAATAAAAATAGATTTTTTTAAAAT
Done.