Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001930.1 Kokia drynarioides strain JFW-HI SEQ_113732, 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, 915
Length: 1526
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.38
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:638 original size:29 final size:29
Alignment explanation
Indices: 606--982 Score: 260
Period size: 29 Copynumber: 12.8 Consensus size: 29
596 AAATTTATCA
* *
606 TTTTACCCCCGAACTTCCAAAGATCCCAT
1 TTTTACCCCCAAACTTCCAAAAATCCCAT
* * * *
635 TTTTGA-CCCCGAACTCCCTAAAATACCATT
1 TTTT-ACCCCCAAACTTCCAAAAATCCCA-T
* * **
665 TTTTACCTCAAAACTTCCAAAAATTATCA-
1 TTTTACCCCCAAACTTCCAAAAA-TCCCAT
* * *
694 TTTTACCCTCGAACTTCTAAAAATCCCAT
1 TTTTACCCCCAAACTTCCAAAAATCCCAT
* *** *
723 TTTTGACCCCAAAACTTCCAAAAATTATAA
1 TTTT-ACCCCCAAACTTCCAAAAATCCCAT
* * **
753 TTTTATCCCTAAACTTCTTAAAATCCC-T
1 TTTTACCCCCAAACTTCCAAAAATCCCAT
* *
781 TTTTGACCCCAAAACTTCCAAAAATTACCA-
1 TTTT-ACCCCCAAACTTCCAAAAA-TCCCAT
* *
811 TTTTACCCTCAAACTTCTAAAAATCCCAT
1 TTTTACCCCCAAACTTCCAAAAATCCCAT
* * *
840 TTTTAACCCCAAAACTTCCCAAAATTCCAT
1 TTTT-ACCCCCAAACTTCCAAAAATCCCAT
**
870 TTTTACCCTTAAACTTCCAAAAATCCCACT
1 TTTTACCCCCAAACTTCCAAAAATCCCA-T
* * * * *
900 TTTAACCCCAAAACTTCAAAAAAAT-CTAC
1 TTTTACCCCCAAACTTC-CAAAAATCCCAT
* * *
929 TTTTACCCTCAAACTTTCAAAAATCTCAT
1 TTTTACCCCCAAACTTCCAAAAATCCCAT
* *
958 TTTTAACCCCAAAACTTCTAAAAAT
1 TTTT-ACCCCCAAACTTCCAAAAAT
983 TTGATTTTTG
Statistics
Matches: 264, Mismatches: 69, Indels: 29
0.73 0.19 0.08
Matches are distributed among these distances:
28 17 0.06
29 134 0.51
30 103 0.39
31 10 0.04
ACGTcount: A:0.36, C:0.30, G:0.02, T:0.32
Consensus pattern (29 bp):
TTTTACCCCCAAACTTCCAAAAATCCCAT
Found at i:707 original size:59 final size:59
Alignment explanation
Indices: 646--983 Score: 393
Period size: 59 Copynumber: 5.7 Consensus size: 59
636 TTTGACCCCG
* * * * *
646 AACTCCCTAAAATACCATTTTTTACCTCAAAACTTCCAAAAATTATCATTTTACCCTCG
1 AACTTCCTAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTATCATTTTACCCTCA
* *
705 AACTT-CTAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTATAATTTTATCCCT-A
1 AACTTCCT-AAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTATCATTTTA-CCCTCA
* * *
764 AACTTCTTAAAATCCC-TTTTTGACCCCAAAACTTCCAAAAATTACCATTTTACCCTCA
1 AACTTCCTAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTATCATTTTACCCTCA
* * *
822 AACTT-CTAAAAATCCCATTTTTAACCCCAAAACTTCCCAAAATT-CCATTTTTACCCTTA
1 AACTTCCT-AAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTATCA-TTTTACCCTCA
* * *
881 AACTTCCAAAAATCCCACTTTTAACCCCAAAACTT-CAAAAA-AATCTACTTTTACCCTCA
1 AACTTCCTAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTATC-A-TTTTACCCTCA
* * * *
940 AACTTTCAAAAATCTCATTTTTAACCCCAAAACTTCTAAAAATT
1 AACTTCCTAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATT
984 TGATTTTTGA
Statistics
Matches: 242, Mismatches: 25, Indels: 22
0.84 0.09 0.08
Matches are distributed among these distances:
57 5 0.02
58 59 0.24
59 167 0.69
60 11 0.05
ACGTcount: A:0.38, C:0.29, G:0.01, T:0.33
Consensus pattern (59 bp):
AACTTCCTAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTATCATTTTACCCTCA
Found at i:757 original size:88 final size:87
Alignment explanation
Indices: 589--982 Score: 274
Period size: 88 Copynumber: 4.5 Consensus size: 87
579 AGGTCTCTAG
* * * * * *
589 ACTTCCAAAATTTATCATTTTACCCCCGAACTTCCAAAGATCCCATTTTTGACCCCGAACTCCCT
1 ACTTCCAAAAATTATCATTTTA-CCCCAAACTTCCAAAAATCCCATTTTTGACCCCAAACTTCCA
654 AAAA-TACCATTTTTTA-CCTCAAA
65 AAAATTA-CA-TTTTTACCCTCAAA
* *
677 ACTTCCAAAAATTATCATTTTACCCTCGAACTTCTAAAAATCCCATTTTTGACCCCAAAACTTCC
1 ACTTCCAAAAATTATCATTTTACCC-CAAACTTCCAAAAATCCCATTTTTGACCCC-AAACTTCC
* *
742 AAAAATTATAATTTTATCCCT--AA
64 AAAAATTACATTTTTA-CCCTCAAA
** ** * *
765 ACTTCTTAAAA-TCCCTTTTTGACCCCAAAACTTCCAAAAATTACCA-TTTT-ACCCTCAAACTT
1 ACTTCCAAAAATTATCATTTT-ACCCC-AAACTTCCAAAAA-TCCCATTTTTGACCC-CAAACTT
* **
827 CTAAAAATCCCATTTTTAACCC-CAAA
62 CCAAAAATTACATTTTT-ACCCTCAAA
* * * * *
853 ACTTCCCAAAATT-CCATTTTTACCCTTAAACTTCCAAAAATCCCACTTTTAACCCCAAAACTTC
1 ACTTCCAAAAATTATCA-TTTTACCC-CAAACTTCCAAAAATCCCATTTTTGACCCC-AAACTTC
*
917 AAAAAAATCTAC--TTTTACCCTC-AA
63 -CAAAAAT-TACATTTTTACCCTCAAA
* * *
941 ACTTTCAAAAA-TCTCATTTTTAACCCCAAAACTTCTAAAAAT
1 ACTTCCAAAAATTATCA-TTTT-ACCCC-AAACTTCCAAAAAT
983 TTGATTTTTG
Statistics
Matches: 248, Mismatches: 34, Indels: 47
0.75 0.10 0.14
Matches are distributed among these distances:
87 40 0.16
88 143 0.58
89 53 0.21
90 11 0.04
91 1 0.00
ACGTcount: A:0.37, C:0.29, G:0.02, T:0.32
Consensus pattern (87 bp):
ACTTCCAAAAATTATCATTTTACCCCAAACTTCCAAAAATCCCATTTTTGACCCCAAACTTCCAA
AAATTACATTTTTACCCTCAAA
Found at i:805 original size:117 final size:117
Alignment explanation
Indices: 646--983 Score: 432
Period size: 117 Copynumber: 2.9 Consensus size: 117
636 TTTGACCCCG
* * * * *
646 AACTCCCTAAAATACCATTTTTTACCTCAAAACTTCCAAAAATTATCATTTTACCCTCGAACTTC
1 AACTTCCTAAAAT-CCCTTTTTAACCCCAAAACTTCCAAAAATTATCATTTTACCCTCAAACTTC
* *
711 TAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTATAATTTTATCCC-TA
65 TAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTACAATTTTA-CCCTTA
* * *
764 AACTTCTTAAAATCCCTTTTTGACCCCAAAACTTCCAAAAATTACCATTTTACCCTCAAACTTCT
1 AACTTCCTAAAATCCCTTTTTAACCCCAAAACTTCCAAAAATTATCATTTTACCCTCAAACTTCT
* * *
829 AAAAATCCCATTTTTAACCCCAAAACTTCCCAAAATTCCATTTTTACCCTTA
66 AAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTACAATTTTACCCTTA
* * *
881 AACTTCCAAAAATCCCACTTTTAACCCCAAAACTT-CAAAAA-AATCTACTTTTACCCTCAAACT
1 AACTTCCTAAAATCCC-TTTTTAACCCCAAAACTTCCAAAAATTATC-A-TTTTACCCTCAAACT
* *
944 T-TCAAAAATCTCATTTTTAACCCCAAAACTTCTAAAAATT
63 TCT-AAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATT
984 TGATTTTTGA
Statistics
Matches: 194, Mismatches: 21, Indels: 10
0.86 0.09 0.04
Matches are distributed among these distances:
116 5 0.03
117 112 0.58
118 77 0.40
ACGTcount: A:0.38, C:0.29, G:0.01, T:0.33
Consensus pattern (117 bp):
AACTTCCTAAAATCCCTTTTTAACCCCAAAACTTCCAAAAATTATCATTTTACCCTCAAACTTCT
AAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTACAATTTTACCCTTA
Done.