Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005596.1 Kokia drynarioides strain JFW-HI SEQ_119724, 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, 839
Length: 1399
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Found at i:470 original size:30 final size:30
Alignment explanation
Indices: 425--764 Score: 213
Period size: 30 Copynumber: 11.6 Consensus size: 30
415 CCCTATATTC
*
425 TCCAAAAATCTCATTTTTGACCCCGAAACT
1 TCCAAAAATCCCATTTTTGACCCCGAAACT
* * *
455 TTCAAAATTCCCATTTTT-ACCCTTG-AACT
1 TCCAAAAATCCCATTTTTGACCC-CGAAACT
*
484 TCCAAAAATCCCATTTTTGACCCCAAAACT
1 TCCAAAAATCCCATTTTTGACCCCGAAACT
* * *
514 TTCAAAATTCCCA-TTTTAACCCCCG-AACT
1 TCCAAAAATCCCATTTTTGA-CCCCGAAACT
* * * *
543 TCCAAAAAT-CTAATTTTGACCTCGAACCT
1 TCCAAAAATCCCATTTTTGACCCCGAAACT
* * *
572 T-TAAAAATACCA-TTTT-ACCCCTAAACT
1 TCCAAAAATCCCATTTTTGACCCCGAAACT
** *
599 TCCAAAAATCATATTTTTGACCCTCGAACCTT
1 TCCAAAAATCCCATTTTTGACCC-CGAAAC-T
** * * *
631 TTGAAAATTACCA-TTTT-ACACTCG-AACT
1 TCCAAAAATCCCATTTTTGAC-CCCGAAACT
* *
659 TCCAAAAATCTCATTTTTGACCCCGAACCTT
1 TCCAAAAATCCCATTTTTGACCCCGAAAC-T
* * *
690 TCGAAAATTACCA-TTTT-ACCCTCG-AACT
1 TCCAAAAATCCCATTTTTGACCC-CGAAACT
* * * *
718 TCCAAAAATTCTATTTTTGACTCCGAACCT
1 TCCAAAAATCCCATTTTTGACCCCGAAACT
* *
748 TCCAAAACTACCATTTT
1 TCCAAAAATCCCATTTT
765 GCCCTCGTGC
Statistics
Matches: 231, Mismatches: 58, Indels: 42
0.70 0.18 0.13
Matches are distributed among these distances:
27 9 0.04
28 42 0.18
29 76 0.33
30 77 0.33
31 19 0.08
32 8 0.03
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (30 bp):
TCCAAAAATCCCATTTTTGACCCCGAAACT
Found at i:471 original size:29 final size:29
Alignment explanation
Indices: 425--765 Score: 203
Period size: 29 Copynumber: 11.6 Consensus size: 29
415 CCCTATATTC
*
425 TCCAAAAATCTCATTTTTGACCCCGAAACT
1 TCCAAAAATCCCA-TTTTGACCCCGAAACT
* * * *
455 TTCAAAATTCCCATTTTTACCCTTG-AACT
1 TCCAAAAATCCCATTTTGACCC-CGAAACT
*
484 TCCAAAAATCCCATTTTTGACCCCAAAACT
1 TCCAAAAATCCCA-TTTTGACCCCGAAACT
* * *
514 TTCAAAATTCCCATTTTAACCCCCG-AACT
1 TCCAAAAATCCCATTTTGA-CCCCGAAACT
** * *
543 TCCAAAAATCTAATTTTGACCTCGAACCT
1 TCCAAAAATCCCATTTTGACCCCGAAACT
* * *
572 T-TAAAAATACCATTTT-ACCCCTAAACT
1 TCCAAAAATCCCATTTTGACCCCGAAACT
** *
599 TCCAAAAATCATATTTTTGACCCTCGAACCTT
1 TCCAAAAATCCCA-TTTTGACCC-CGAAAC-T
** * * *
631 TTGAAAATTACCATTTT-ACACTCG-AACT
1 TCCAAAAATCCCATTTTGAC-CCCGAAACT
* *
659 TCCAAAAATCTCATTTTTGACCCCGAACCTT
1 TCCAAAAATCCCA-TTTTGACCCCGAAAC-T
* * *
690 TCGAAAATTACCATTTT-ACCCTCG-AACT
1 TCCAAAAATCCCATTTTGACCC-CGAAACT
* * * *
718 TCCAAAAATTCTATTTTTGACTCCGAACCT
1 TCCAAAAATCCCA-TTTTGACCCCGAAACT
* *
748 TCCAAAACTACCATTTTG
1 TCCAAAAATCCCATTTTG
766 CCCTCGTGCA
Statistics
Matches: 229, Mismatches: 63, Indels: 39
0.69 0.19 0.12
Matches are distributed among these distances:
27 9 0.04
28 41 0.18
29 80 0.35
30 72 0.31
31 19 0.08
32 8 0.03
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (29 bp):
TCCAAAAATCCCATTTTGACCCCGAAACT
Found at i:517 original size:59 final size:58
Alignment explanation
Indices: 425--771 Score: 403
Period size: 59 Copynumber: 5.9 Consensus size: 58
415 CCCTATATTC
* * * *
425 TCCAAAAATCTCATTTTTGACCCCGAAACTTTCAAAATTCCCATTTTTACCCTTGAACT
1 TCCAAAAATCCCATTTTTGACCCCGAACCTTTCAAAATTACCA-TTTTACCCTCGAACT
* * * *
484 TCCAAAAATCCCATTTTTGACCCCAAAACTTTCAAAATTCCCATTTTAACCCCCGAACT
1 TCCAAAAATCCCATTTTTGACCCCGAACCTTTCAAAATTACCATTTT-ACCCTCGAACT
* * * * *
543 TCCAAAAAT-CTAATTTTGACCTCGAACCTTT-AAAAATACCATTTTACCC-CTAAACT
1 TCCAAAAATCCCATTTTTGACCCCGAACCTTTCAAAATTACCATTTTACCCTC-GAACT
** * *
599 TCCAAAAATCATATTTTTGACCCTCGAACCTTTTGAAAATTACCATTTTACACTCGAACT
1 TCCAAAAATCCCATTTTTGACCC-CGAACC-TTTCAAAATTACCATTTTACCCTCGAACT
*
659 TCCAAAAATCTCATTTTTGACCCCGAACCTTTCGAAAATTACCATTTTACCCTCGAACT
1 TCCAAAAATCCCATTTTTGACCCCGAACCTTTC-AAAATTACCATTTTACCCTCGAACT
* * * * * *
718 TCCAAAAATTCTATTTTTGACTCCGAACCTTCCAAAACTACCATTTTGCCCTCG
1 TCCAAAAATCCCATTTTTGACCCCGAACCTTTCAAAATTACCATTTTACCCTCG
772 TGCATCCGAA
Statistics
Matches: 251, Mismatches: 29, Indels: 17
0.85 0.10 0.06
Matches are distributed among these distances:
55 1 0.00
56 17 0.07
57 22 0.09
58 49 0.20
59 120 0.48
60 41 0.16
61 1 0.00
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.33
Consensus pattern (58 bp):
TCCAAAAATCCCATTTTTGACCCCGAACCTTTCAAAATTACCATTTTACCCTCGAACT
Found at i:1133 original size:96 final size:96
Alignment explanation
Indices: 987--1168 Score: 253
Period size: 96 Copynumber: 1.9 Consensus size: 96
977 AATTTAAAAA
* **
987 AATCGAGGCAATATTCCTTTATTTCGAGTTTTGAAAATTTATGCCTTAACTCACTAGGTGCATTC
1 AATCGAGGCAATATTCCTTTATTTCGAGTTCTGAAAATTTATGCCTTAACTCACTAGGTGCAACC
1052 TTTCTTCAAATCGAAATAATCGAACACCCTT
66 TTTCTTCAAATCGAAATAATCGAACACCCTT
* *
1083 AATCGAGGCAATGTTTCC-TTATCTTCGA-TTCTGAAATATTT-TGCCTTAACTTACTAGGTGCA
1 AATCGAGGCAAT-ATTCCTTTAT-TTCGAGTTCTGAAA-ATTTATGCCTTAACTCACTAGGTGCA
* *
1145 ACCTTTCTTCGAATCGAGATAATC
63 ACCTTTCTTCAAATCGAAATAATC
1169 AAATATCCTT
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
96 63 0.83
97 13 0.17
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.37
Consensus pattern (96 bp):
AATCGAGGCAATATTCCTTTATTTCGAGTTCTGAAAATTTATGCCTTAACTCACTAGGTGCAACC
TTTCTTCAAATCGAAATAATCGAACACCCTT
Done.