Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000141.1 Kokia drynarioides strain JFW-HI SEQ_110795, 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: 2181
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.38
Found at i:648 original size:29 final size:29
Alignment explanation
Indices: 616--873 Score: 225
Period size: 29 Copynumber: 8.8 Consensus size: 29
606 ATTTGGCCCC
*
616 AAACTTCCCAAAATTACATTTTGAACCC-T
1 AAACTTCCAAAAATTACATTTT-AACCCTT
* *
645 AAACTTTTCAAAAAATACATTTTAACCCTT
1 AAAC-TTCCAAAAATTACATTTTAACCCTT
** *
675 AAACTTCCAAATTTTACATTTTGACCCTT
1 AAACTTCCAAAAATTACATTTTAACCCTT
*
704 AAACTTCTCAAAAATTATATTTTAACCCTT
1 AAACTTC-CAAAAATTACATTTTAACCCTT
* * *
734 AAAATT-TATAAAATATACATTTTAACCCCT
1 AAACTTCCA-AAAAT-TACATTTTAACCCTT
* *
764 AAACTTCTTAAAATTTACATTTT-ACCCTT
1 AAACTTC-CAAAAATTACATTTTAACCCTT
* * * *
793 GAACTTCCAAAAATCACATTTTTACCCCT
1 AAACTTCCAAAAATTACATTTTAACCCTT
* * * * *
822 AAATTTTCAAAAATTATATTTTTACCCTC
1 AAACTTCCAAAAATTACATTTTAACCCTT
* *
851 GAACTTCTCAAAAATTACTTTTT
1 AAACTTC-CAAAAATTACATTTT
874 TTCCCCCGAA
Statistics
Matches: 184, Mismatches: 36, Indels: 17
0.78 0.15 0.07
Matches are distributed among these distances:
28 13 0.07
29 83 0.45
30 82 0.45
31 4 0.02
32 2 0.01
ACGTcount: A:0.38, C:0.22, G:0.02, T:0.39
Consensus pattern (29 bp):
AAACTTCCAAAAATTACATTTTAACCCTT
Found at i:666 original size:30 final size:30
Alignment explanation
Indices: 625--873 Score: 217
Period size: 30 Copynumber: 8.4 Consensus size: 30
615 CAAACTTCCC
625 AAAATTACATTTTGAACCC-TAAACTTTTCA
1 AAAATTACATTTT-AACCCTTAAACTTTTCA
* *
655 AAAAATACATTTTAACCCTTAAAC-TTCCA
1 AAAATTACATTTTAACCCTTAAACTTTTCA
** * *
684 AATTTTACATTTTGACCCTTAAACTTCTCA
1 AAAATTACATTTTAACCCTTAAACTTTTCA
* *
714 AAAATTATATTTTAACCCTTAAA-ATTT-A
1 AAAATTACATTTTAACCCTTAAACTTTTCA
*
742 TAAAATATACATTTTAACCCCTAAACTTCTT-A
1 -AAAAT-TACATTTTAACCCTTAAACTT-TTCA
* * *
774 AAATTTACATTTT-ACCCTTGAAC-TTCCA
1 AAAATTACATTTTAACCCTTAAACTTTTCA
* * *
802 AAAATCACATTTTTACCCCTAAA-TTTTCA
1 AAAATTACATTTTAACCCTTAAACTTTTCA
* * ** *
831 AAAATTATATTTTTACCCTCGAACTTCTCA
1 AAAATTACATTTTAACCCTTAAACTTTTCA
*
861 AAAATTACTTTTT
1 AAAATTACATTTT
874 TTCCCCCGAA
Statistics
Matches: 175, Mismatches: 34, Indels: 20
0.76 0.15 0.09
Matches are distributed among these distances:
27 1 0.01
28 14 0.08
29 73 0.42
30 79 0.45
31 5 0.03
32 3 0.02
ACGTcount: A:0.38, C:0.21, G:0.02, T:0.39
Consensus pattern (30 bp):
AAAATTACATTTTAACCCTTAAACTTTTCA
Found at i:680 original size:59 final size:59
Alignment explanation
Indices: 588--873 Score: 262
Period size: 59 Copynumber: 4.9 Consensus size: 59
578 AAGGTCCTTG
* * ** * *
588 AACTTATCAAAAATTACAATTTGGCCC-CAAACTTCCCAAAATTACATTTTGAACCCTA
1 AACTTTTCAAAAATTACATTTTAACCCTTAAACTTCCAAAAATTACATTTTGAACCCTA
* **
646 AACTTTTCAAAAAATACATTTTAACCCTTAAACTTCCAAATTTTACATTTTG-ACCCTTA
1 AACTTTTCAAAAATTACATTTTAACCCTTAAACTTCCAAAAATTACATTTTGAACCC-TA
* * * *
705 AACTTCTCAAAAATTATATTTTAACCCTTAAAATT-TATAAAATATACATTTT-AACCCCTA
1 AACTTTTCAAAAATTACATTTTAACCCTTAAACTTCCA-AAAAT-TACATTTTGAA-CCCTA
* * * * *
765 AACTTCTT-AAAATTTACATTTT-ACCCTTGAACTTCCAAAAATCACATTTTTACCCCTA
1 AACTT-TTCAAAAATTACATTTTAACCCTTAAACTTCCAAAAATTACATTTTGAACCCTA
* * ** *
823 AA-TTTTCAAAAATTATATTTTTACCCTCGAACTTCTCAAAAATTACTTTTT
1 AACTTTTCAAAAATTACATTTTAACCCTTAAACTTC-CAAAAATTACATTTT
874 TTCCCCCGAA
Statistics
Matches: 187, Mismatches: 29, Indels: 23
0.78 0.12 0.10
Matches are distributed among these distances:
56 2 0.01
57 14 0.07
58 53 0.28
59 85 0.45
60 29 0.16
61 4 0.02
ACGTcount: A:0.38, C:0.22, G:0.02, T:0.38
Consensus pattern (59 bp):
AACTTTTCAAAAATTACATTTTAACCCTTAAACTTCCAAAAATTACATTTTGAACCCTA
Found at i:874 original size:30 final size:30
Alignment explanation
Indices: 765--894 Score: 117
Period size: 29 Copynumber: 4.5 Consensus size: 30
755 TTAACCCCTA
* * * *
765 AACTTCTTAAAATTTAC-ATTTTACCCTTG
1 AACTTCTCAAAAATTACTTTTTTACCCTCG
* * *
794 AACTTC-CAAAAATCACATTTTTACCC-CT
1 AACTTCTCAAAAATTACTTTTTTACCCTCG
* *
822 AAATTTTCAAAAATTA-TATTTTTACCCTCG
1 AACTTCTCAAAAATTACT-TTTTTACCCTCG
* *
852 AACTTCTCAAAAATTACTTTTTTTCCCCCG
1 AACTTCTCAAAAATTACTTTTTTACCCTCG
882 AAC-TCTCAAAAAT
1 AACTTCTCAAAAAT
895 CACCATTTTG
Statistics
Matches: 81, Mismatches: 15, Indels: 10
0.76 0.14 0.09
Matches are distributed among these distances:
28 11 0.14
29 41 0.51
30 28 0.35
31 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.38
Consensus pattern (30 bp):
AACTTCTCAAAAATTACTTTTTTACCCTCG
Found at i:888 original size:29 final size:30
Alignment explanation
Indices: 705--894 Score: 115
Period size: 30 Copynumber: 6.5 Consensus size: 30
695 TTGACCCTTA
* ***
705 AACTTCTCAAAAATTATATTTTAACCCTTA
1 AACTTCTCAAAAATTATATTTTTACCCCCG
* * * **
735 AAATT-T-ATAAAATATACATTTTAACCCCTA
1 AACTTCTCA-AAAAT-TATATTTTTACCCCCG
* * * **
765 AACTTCTTAAAATTTACA-TTTTACCCTTG
1 AACTTCTCAAAAATTATATTTTTACCCCCG
* * *
794 AACTTC-CAAAAATCACATTTTTA-CCCCT
1 AACTTCTCAAAAATTATATTTTTACCCCCG
* * *
822 AAATTTTCAAAAATTATATTTTTACCCTCG
1 AACTTCTCAAAAATTATATTTTTACCCCCG
*
852 AACTTCTCAAAAATTACT-TTTTTTCCCCCG
1 AACTTCTCAAAAATTA-TATTTTTACCCCCG
882 AAC-TCTCAAAAAT
1 AACTTCTCAAAAAT
895 CACCATTTTG
Statistics
Matches: 128, Mismatches: 24, Indels: 17
0.76 0.14 0.10
Matches are distributed among these distances:
28 15 0.12
29 50 0.39
30 56 0.44
31 6 0.05
32 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.38
Consensus pattern (30 bp):
AACTTCTCAAAAATTATATTTTTACCCCCG
Found at i:950 original size:30 final size:30
Alignment explanation
Indices: 781--950 Score: 113
Period size: 29 Copynumber: 5.8 Consensus size: 30
771 TTAAAATTTA
*
781 CATTTTACCCTTGAAC-TTCCAAAAATCA-
1 CATTTTACCCTCGAACTTTCCAAAAATCAC
* * * *
809 CATTTTTACCC-CTAAATTTTCAAAAATTA-
1 CA-TTTTACCCTCGAACTTTCCAAAAATCAC
* *
838 TATTTTTACCCTCGAAC-TTCTCAAAAATTAC
1 CA-TTTTACCCTCGAACTTTC-CAAAAATCAC
** * * *
869 TTTTTTTCCCCCGAACTCT-CAAAAATCAC
1 CATTTTACCCTCGAACTTTCCAAAAATCAC
* * *
898 CATTTT-GCCTCG-AGTATCCAAAAATCAC
1 CATTTTACCCTCGAACTTTCCAAAAATCAC
*
926 CATTTTACCCTCAAACTTTCCAAAA
1 CATTTTACCCTCGAACTTTCCAAAA
951 GTTTGATTTT
Statistics
Matches: 109, Mismatches: 24, Indels: 16
0.73 0.16 0.11
Matches are distributed among these distances:
27 3 0.03
28 24 0.22
29 47 0.43
30 33 0.30
31 2 0.02
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.35
Consensus pattern (30 bp):
CATTTTACCCTCGAACTTTCCAAAAATCAC
Done.