Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013240.1 Kokia drynarioides strain JFW-HI SEQ_128259, 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: 8913
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.34
Warning! 99 characters in sequence are not A, C, G, or T
Found at i:691 original size:11 final size:12
Alignment explanation
Indices: 667--737 Score: 62
Period size: 11 Copynumber: 6.3 Consensus size: 12
657 TGGACTTTTT
667 AATTTAAAT-TA
1 AATTTAAATATA
* *
678 AATAT-AATTTA
1 AATTTAAATATA
*
689 AATTT-AATATC
1 AATTTAAATATA
*
700 AATTTAAATTTA
1 AATTTAAATATA
*
712 AATTTAAAT-CA
1 AATTTAAATATA
723 AATTTAAA-ATA
1 AATTTAAATATA
734 AATT
1 AATT
738 AAAAAAAAAG
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
10 3 0.06
11 33 0.67
12 13 0.27
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (12 bp):
AATTTAAATATA
Found at i:692 original size:6 final size:6
Alignment explanation
Indices: 667--730 Score: 64
Period size: 6 Copynumber: 11.3 Consensus size: 6
657 TGGACTTTTT
* * *
667 AATTTA AA-TTA AATAT- AATTTA AATTT- AATATC AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
*
712 AATTTA AA-TCA AATTTA AA
1 AATTTA AATTTA AATTTA AA
731 ATAAATTAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
5 17 0.36
6 30 0.64
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (6 bp):
AATTTA
Found at i:703 original size:17 final size:16
Alignment explanation
Indices: 666--740 Score: 78
Period size: 16 Copynumber: 4.6 Consensus size: 16
656 TTGGACTTTT
*
666 TAATTTAAATTAAATA
1 TAATTTAAATTTAATA
682 TAATTTAAATTTAATA
1 TAATTTAAATTTAATA
*
698 TCAATTTAAATTTAAATT
1 T-AATTTAAATTT-AATA
* * *
716 TAAATCAAATTTAAAA
1 TAATTTAAATTTAATA
*
732 TAAATTAAA
1 TAATTTAAA
741 AAAAAAGCCC
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
16 26 0.52
17 20 0.40
18 4 0.08
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATTTAAATTTAATA
Found at i:712 original size:23 final size:23
Alignment explanation
Indices: 667--730 Score: 87
Period size: 23 Copynumber: 2.8 Consensus size: 23
657 TGGACTTTTT
* *
667 AATTTAAATTAAATAT-AATTTA
1 AATTTAAATCAAATTTAAATTTA
689 AATTTAATATC-AATTTAAATTTA
1 AATTTAA-ATCAAATTTAAATTTA
712 AATTTAAATCAAATTTAAA
1 AATTTAAATCAAATTTAAA
731 ATAAATTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
22 14 0.38
23 23 0.62
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (23 bp):
AATTTAAATCAAATTTAAATTTA
Found at i:1651 original size:206 final size:206
Alignment explanation
Indices: 1297--2013 Score: 1117
Period size: 206 Copynumber: 3.5 Consensus size: 206
1287 NNNNNNNNNN
*
1297 AAGATGACCGCATCGCTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTTC
1 AAGATGACCGCATCGCTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGGCGAATTTGGTTC
* * * * *
1362 ACTCCTCAATATATCATCTGGAAGCTAATCGTTTATTGCTTCGACCTGCTTCTCGGTGTCTTATC
66 ACTCCTCAGTATCTCATCTGGAAGCTAACCGTTTACTGCTTCGACCTGCTTCTCGGTGTCTCATC
*
1427 AGGAAGTTGGGGTTCGAAGATTTTACTCGCTTTGAGAGTGGGCTTGATTTGGTCTTCTTCTCAGT
131 AGGAAGCTGGGGTTCGAAGATTTTACTCGCTTTGAGAGTGGGCTTGATTTGGTCTTCTTCTCAGT
1492 ATCTCATCGGG
196 ATCTCATCGGG
1503 AAGATGACCGCATCGCTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGGCGAATTTGGTTC
1 AAGATGACCGCATCGCTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGGCGAATTTGGTTC
*
1568 ACTCCTCAGTATCTCATCTGGAAGCTAACCGTTTACTGCTTCGACCTGCTTCTCAGTGTCTCATC
66 ACTCCTCAGTATCTCATCTGGAAGCTAACCGTTTACTGCTTCGACCTGCTTCTCGGTGTCTCATC
*
1633 AGGAAGCTGGGGTTCGAAGATTTTACTCGCTTTGAGCGTGGGCTTGATTTGGTCTTCTTCTCAGT
131 AGGAAGCTGGGGTTCGAAGATTTTACTCGCTTTGAGAGTGGGCTTGATTTGGTCTTCTTCTCAGT
*
1698 ATCTCATCGGA
196 ATCTCATCGGG
1709 AAGATGACCGCATCGCTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGGCGAATTTGGTTC
1 AAGATGACCGCATCGCTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGGCGAATTTGGTTC
* *
1774 ACTCCTCAGTATCTCATCTGAAAGCTAACCGTTTACTGCTTCGACCTGCTTCTTGGTGTCTCATC
66 ACTCCTCAGTATCTCATCTGGAAGCTAACCGTTTACTGCTTCGACCTGCTTCTCGGTGTCTCATC
* * * * *
1839 AGGAAGCTGGGGCTCGAAGA-TTTGCTCG-TTT-TGA---GCCTCG-TTTGGGTCTTCTTCTCAG
131 AGGAAGCTGGGGTTCGAAGATTTTACTCGCTTTGAGAGTGGGCTTGATTT-GGTCTTCTTCTCAG
* *
1897 TGTCTCATCAGG
195 TATCTCATCGGG
* * * * *
1909 AAGATAACCGCGTCGTTTGTTTCAA-CTAGCTTCTCTGTATCTCATTAGGAAGGCGAATTTGGTT
1 AAGATGACCGCATCGCTTGTTTCAATC-CGCTTCTCTGTATCTCATCAGGAAGGCGAATTTGGTT
* * *
1973 CACTTCTCAGTATCTCATCAGGAAGCTAACCGTTTATTGCT
65 CACTCCTCAGTATCTCATCTGGAAGCTAACCGTTTACTGCT
2014 CCAATCTGCT
Statistics
Matches: 478, Mismatches: 31, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
199 4 0.01
200 121 0.25
203 1 0.00
204 3 0.01
205 7 0.01
206 342 0.72
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.35
Consensus pattern (206 bp):
AAGATGACCGCATCGCTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGGCGAATTTGGTTC
ACTCCTCAGTATCTCATCTGGAAGCTAACCGTTTACTGCTTCGACCTGCTTCTCGGTGTCTCATC
AGGAAGCTGGGGTTCGAAGATTTTACTCGCTTTGAGAGTGGGCTTGATTTGGTCTTCTTCTCAGT
ATCTCATCGGG
Found at i:2655 original size:27 final size:28
Alignment explanation
Indices: 2607--2664 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
2597 AAGAATTCTA
* * *
2607 TAAAAAGAGGATCGAAGGAAACAAT-AT
1 TAAAAACAGGATCAAAGAAAACAATCAT
*
2634 TAAAAACAGGTTCAAAGAAAACAATCAT
1 TAAAAACAGGATCAAAGAAAACAATCAT
2662 TAA
1 TAA
2665 TTGAAAATTG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 21 0.81
28 5 0.19
ACGTcount: A:0.57, C:0.10, G:0.16, T:0.17
Consensus pattern (28 bp):
TAAAAACAGGATCAAAGAAAACAATCAT
Done.