Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000552.1 Kokia drynarioides strain JFW-HI SEQ_111458, 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: 1770
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.34
Found at i:697 original size:29 final size:28
Alignment explanation
Indices: 665--762 Score: 74
Period size: 29 Copynumber: 3.4 Consensus size: 28
655 CTCAAATTTA
665 ATTTTTACCTTCTAACTTTTTAAAATTCC
1 ATTTTTACC-TCTAACTTTTTAAAATTCC
* **
694 ATTTTAACCT-TAA-TTTTTCCAAAAATTAT
1 ATTTTTACCTCTAACTTTTT---AAAATTCC
* **
723 AATTTTACCTCTAAACTTTCCAAAATTCC
1 ATTTTTACCTCT-AACTTTTTAAAATTCC
752 ATTTTTGACCT
1 ATTTTT-ACCT
763 TGATTTTCCA
Statistics
Matches: 52, Mismatches: 10, Indels: 13
0.69 0.13 0.17
Matches are distributed among these distances:
26 5 0.10
27 3 0.06
28 1 0.02
29 33 0.63
30 5 0.10
31 2 0.04
32 3 0.06
ACGTcount: A:0.32, C:0.20, G:0.01, T:0.47
Consensus pattern (28 bp):
ATTTTTACCTCTAACTTTTTAAAATTCC
Found at i:776 original size:29 final size:28
Alignment explanation
Indices: 686--789 Score: 102
Period size: 29 Copynumber: 3.6 Consensus size: 28
676 CTAACTTTTT
* *
686 AAAATTCCATTTTAACCTTAATTTTTCCA
1 AAAATTACATTTTTACCTTAA-TTTTCCA
* * *
715 AAAATTATAATTTTACCTCTAAACTTTCC-
1 AAAATTACATTTTTACCT-T-AATTTTCCA
* *
744 AAAATTCCATTTTTGACCTTGATTTTCCA
1 AAAATTACATTTTT-ACCTTAATTTTCCA
773 AAAATTACATTTTTACC
1 AAAATTACATTTTTACC
790 CACGAACTTT
Statistics
Matches: 60, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
28 9 0.15
29 39 0.65
30 10 0.17
31 2 0.03
ACGTcount: A:0.35, C:0.20, G:0.02, T:0.43
Consensus pattern (28 bp):
AAAATTACATTTTTACCTTAATTTTCCA
Found at i:1013 original size:30 final size:30
Alignment explanation
Indices: 739--1016 Score: 96
Period size: 29 Copynumber: 9.3 Consensus size: 30
729 ACCTCTAAAC
* *
739 TTTCC-AAAATTCCATTTTTGACCTTGA-T
1 TTTCCAAAAATTTCATTTTTGACCTCGATT
* * **
767 TTTCCAAAAATTACATTTTT-ACCCACGAAC
1 TTTCCAAAAATTTCATTTTTGA-CCTCGATT
* *
797 TTT-CAAAAA-TTCTATTTTTTATCCT-AATT
1 TTTCCAAAAATTTC-ATTTTTGA-CCTCGATT
* * * * **
826 TTTCAAAAAAATTT-ATATTTTTACCCCCAAAC
1 TTTC-CAAAAATTTCAT-TTTTGA-CCTCGATT
* * * *
858 TTT-CTAAAATTTCATTTTTTACCTAGTTTTT
1 TTTCCAAAAATTTCATTTTTGACCTCG--ATT
** * * **
889 TTTCCAAAAATCACATTTTTGCCCTCAAAC
1 TTTCCAAAAATTTCATTTTTGACCTCGATT
*
919 TTTCC-AAAATTTCATTTTTAACC-CTGATT
1 TTTCCAAAAATTTCATTTTTGACCTC-GATT
* * * * *
948 TTTCCATAAATTACCA-TTCT-ACCCCCGA-A
1 TTTCCAAAAATT-TCATTTTTGA-CCTCGATT
977 TTTCCAAAAATTTCATTTTTGACCTCGATT
1 TTTCCAAAAATTTCATTTTTGACCTCGATT
1007 TTTCCAAAAA
1 TTTCCAAAAA
1017 CTACCATTTT
Statistics
Matches: 179, Mismatches: 49, Indels: 42
0.66 0.18 0.16
Matches are distributed among these distances:
28 11 0.06
29 75 0.42
30 49 0.27
31 21 0.12
32 23 0.13
ACGTcount: A:0.31, C:0.22, G:0.03, T:0.43
Consensus pattern (30 bp):
TTTCCAAAAATTTCATTTTTGACCTCGATT
Found at i:1055 original size:29 final size:28
Alignment explanation
Indices: 889--1144 Score: 112
Period size: 30 Copynumber: 8.6 Consensus size: 28
879 CCTAGTTTTT
* * *
889 TTTCCAAAAATCACATTTTTGCCCTCAAA
1 TTTCCAAAATTC-CATTTTTACCCTCGAA
* *
918 CTTTCCAAAATTTCATTTTTAACCCT-GATT
1 -TTTCCAAAATTCCATTTTT-ACCCTCGA-A
* *
948 TTTCCATAAATTACCA-TTCTACCCCCGAA
1 TTTCCA-AAATT-CCATTTTTACCCTCGAA
* *
977 TTTCCAAAAATTTCATTTTTGA-CCTCGATT
1 TTTCC-AAAATTCCATTTTT-ACCCTCGA-A
*
1007 TTTCCAAAAACTACCA-TTTTACCCTCGAA
1 TTTCC-AAAA-TTCCATTTTTACCCTCGAA
* *
1036 CTTCCAAAATTCCATTTTTTTTA-CCTCGAT
1 TTTCCAAAATTCCA---TTTTTACCCTCGAA
**
1066 TCTTCCAAAAGTAGCA-TTTTACCCTCGAA
1 T-TTCCAAAA-TTCCATTTTTACCCTCGAA
* * * *
1095 TGTCTAGAAA-TCTCATTTTTGACCCCCGAC
1 TTTCCA-AAATTC-CATTTTT-ACCCTCGAA
1125 TTTCCCAAAATTACCATTTT
1 TTT-CCAAAATT-CCATTTT
1145 GCCTCTCGAG
Statistics
Matches: 170, Mismatches: 31, Indels: 49
0.68 0.12 0.20
Matches are distributed among these distances:
27 4 0.02
28 16 0.09
29 55 0.32
30 64 0.38
31 27 0.16
32 4 0.02
ACGTcount: A:0.29, C:0.27, G:0.05, T:0.38
Consensus pattern (28 bp):
TTTCCAAAATTCCATTTTTACCCTCGAA
Found at i:1084 original size:59 final size:57
Alignment explanation
Indices: 686--1153 Score: 216
Period size: 59 Copynumber: 7.9 Consensus size: 57
676 CTAACTTTTT
* ** * ** *
686 AAAATTCCA-TTTTAACCTTAATTTTTCCAAAAATTATAATTTTA-CCTCTAAACTTTCC
1 AAAATTTCATTTTTAACCTCGATTTTTCC-AAAACTACCATTTTACCCTC-GAAC-TTCC
* * * * * *
744 AAAATTCCATTTTTGACCTTGA-TTTTCCAAAAATTA-CATTTTTACCCACGAACTTTC
1 AAAATTTCATTTTTAACCTCGATTTTTCC-AAAACTACCA-TTTTACCCTCGAACTTCC
* * * * * * * * *
801 AAAAATTCTATTTTTTATCCT-AATTTTTCAAAAAAATTTA-TATTTTTACCCCCAAACTTTCT
1 AAAATTTC-A-TTTTTAACCTCGATTTTTC--CAAAA-CTACCA-TTTTACCCTCGAAC-TTCC
* * * * * *
863 AAAATTTCATTTTTTACCTAGTTTTTTTTCCAAAAAT-CACATTTTTGCCCTCAAACTTTCC
1 AAAATTTCATTTTTAACCTCG--ATTTTTCCAAAACTAC-CA-TTTTACCCTCGAAC-TTCC
* * * *
924 AAAATTTCATTTTTAACC-CTGATTTTTCCATAAATTACCATTCTACCCCCGAATTTCC
1 AAAATTTCATTTTTAACCTC-GATTTTTCCA-AAACTACCATTTTACCCTCGAACTTCC
*
982 AAAAATTTCATTTTTGACCTCGATTTTTCCAAAAACTACCATTTTACCCTCGAACTTCC
1 -AAAATTTCATTTTTAACCTCGATTTTTCC-AAAACTACCATTTTACCCTCGAACTTCC
* * * * * *
1041 AAAATTCCATTTTTTTTACCTCGATTCTTCCAAAAGTAGCATTTTACCCTCGAA-TGTCT
1 AAAATTTCA--TTTTTAACCTCGATTTTTCCAAAACTACCATTTTACCCTCGAACT-TCC
* * * * * * *
1100 AGAAATCTCATTTTTGACCCCCGACTTTCCCAAAATTACCATTTTGCCTCTCGA
1 A-AAATTTCATTTTT-AACCTCGATTTTTCCAAAACTACCATTTTACC-CTCGA
1154 GTGACCAAAA
Statistics
Matches: 324, Mismatches: 59, Indels: 52
0.74 0.14 0.12
Matches are distributed among these distances:
57 10 0.03
58 51 0.16
59 139 0.43
60 50 0.15
61 59 0.18
62 9 0.03
63 6 0.02
ACGTcount: A:0.31, C:0.24, G:0.04, T:0.41
Consensus pattern (57 bp):
AAAATTTCATTTTTAACCTCGATTTTTCCAAAACTACCATTTTACCCTCGAACTTCC
Found at i:1697 original size:31 final size:30
Alignment explanation
Indices: 1640--1697 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
1630 AGGAAAATTC
**
1640 AATCGAAAGTTTTTTTTAAATCATTAATCA
1 AATCGAAAGTTTTTTTTAAAAAATTAATCA
1670 AATCGAAAGTTTTTTTTAAAAAAATTAA
1 AATCGAAAGTTTTTTTT-AAAAAATTAA
1698 CCGAACATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (30 bp):
AATCGAAAGTTTTTTTTAAAAAATTAATCA
Done.