Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010373.1 Kokia drynarioides strain JFW-HI SEQ_125246, 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: 1722
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Found at i:886 original size:29 final size:28
Alignment explanation
Indices: 836--1081 Score: 222
Period size: 30 Copynumber: 8.8 Consensus size: 28
826 GAGGTCCCTA
836 AACTGTCCAAAAATTCCATTTTT-CCCCAG
1 AACT-TCCAAAAATTCCATTTTTACCCC-G
*
865 AACTTCCAAAAATTCCATTTTTGACCTCG
1 AACTTCCAAAAATTCCATTTTT-ACCCCG
* * **
894 AAACTTCAAAAAATTCCATTATTAACCTCAA
1 -AACTTCCAAAAATTCCATT-TTTACC-CCG
**
925 AACTTCCAAAAATTCCATTTATGCCCCCG
1 AACTTCCAAAAATTCCATTT-TTACCCCG
954 AACTTCCAAAAATTCCATTTTT------
1 AACTTCCAAAAATTCCATTTTTACCCCG
*
976 AAC--CCAAAAACTCCATTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTACCC-CG
*
1003 AACTTCCAAAAATTCCATTTTTAACCCTG
1 AACTTCCAAAAATTCCATTTTT-ACCCCG
* * *
1032 AAACTTCTAAAAATTCCATTTTTATCCCA
1 -AACTTCCAAAAATTCCATTTTTACCCCG
*
1061 AACTTCCAAAAATTTCATTTT
1 AACTTCCAAAAATTCCATTTT
1082 AAACCTCAAA
Statistics
Matches: 179, Mismatches: 21, Indels: 35
0.76 0.09 0.15
Matches are distributed among these distances:
20 16 0.09
22 3 0.02
27 3 0.02
28 38 0.21
29 47 0.26
30 70 0.39
31 2 0.01
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.33
Consensus pattern (28 bp):
AACTTCCAAAAATTCCATTTTTACCCCG
Found at i:999 original size:19 final size:20
Alignment explanation
Indices: 959--996 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
949 CCCCGAACTT
*
959 CCAAAAATTCCATTTTTAAC
1 CCAAAAACTCCATTTTTAAC
979 CCAAAAACTCCATTTTTA
1 CCAAAAACTCCATTTTTA
997 CCCTCGAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.26, G:0.00, T:0.34
Consensus pattern (20 bp):
CCAAAAACTCCATTTTTAAC
Found at i:1036 original size:49 final size:49
Alignment explanation
Indices: 930--1029 Score: 164
Period size: 49 Copynumber: 2.0 Consensus size: 49
920 CTCAAAACTT
* *
930 CCAAAAATTCCATTTATGCCCCCGAACTTCCAAAAATTCCATTTTTAAC
1 CCAAAAACTCCATTTATACCCCCGAACTTCCAAAAATTCCATTTTTAAC
* *
979 CCAAAAACTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAAC
1 CCAAAAACTCCATTTATACCCCCGAACTTCCAAAAATTCCATTTTTAAC
1028 CC
1 CC
1030 TGAAACTTCT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (49 bp):
CCAAAAACTCCATTTATACCCCCGAACTTCCAAAAATTCCATTTTTAAC
Found at i:1038 original size:108 final size:108
Alignment explanation
Indices: 870--1092 Score: 290
Period size: 108 Copynumber: 2.1 Consensus size: 108
860 CCCAGAACTT
*
870 CCAAAAATTCCATTTTTGACCTCGAAACTTCAAAAAATTCCATTATTAACCTCAAAACTTCCAAA
1 CCAAAAACTCCATTTTTGACCTCGAAACTTCAAAAAATTCCATTATTAACCTCAAAACTTCCAAA
* * *
935 AATTCCATTTATGCCCCCGAACTTCCAAAAATTCCATTTTTAAC
66 AATTCCATTT-TGACCCCAAACTTCCAAAAATTCCATTTTAAAC
* * * *
979 CCAAAAACTCCATTTTT-ACCCTCG-AACTTCCAAAAATTCCATTTTTAACC-CTGAAACTTCTA
1 CCAAAAACTCCATTTTTGA-CCTCGAAACTTCAAAAAATTCCATTATTAACCTC-AAAACTTCCA
* * *
1041 AAAATTCCATTTTTATCCCAAACTTCCAAAAATTTCATTTTAAAC
64 AAAATTCCATTTTGACCCCAAACTTCCAAAAATTCCATTTTAAAC
1086 CTCAAAA
1 C-CAAAA
1093 CTCTCAAAAT
Statistics
Matches: 100, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
107 29 0.29
108 50 0.50
109 21 0.21
ACGTcount: A:0.38, C:0.27, G:0.03, T:0.32
Consensus pattern (108 bp):
CCAAAAACTCCATTTTTGACCTCGAAACTTCAAAAAATTCCATTATTAACCTCAAAACTTCCAAA
AATTCCATTTTGACCCCAAACTTCCAAAAATTCCATTTTAAAC
Found at i:1094 original size:58 final size:58
Alignment explanation
Indices: 981--1103 Score: 151
Period size: 58 Copynumber: 2.1 Consensus size: 58
971 TTTTTAACCC
* * * *
981 AAAAACTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCCTGAAACTTCT
1 AAAAATTCCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTAAACCCTAAAAC-TCT
* *
1040 AAAAATTCCATTTTTATCC-CAAACTTCCAAAAATTTCATTTTAAA-CCTCAAAACTCT
1 AAAAATTCCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTAAACCCT-AAAACTCT
*
1097 CAAAATT
1 AAAAATT
1104 ACCCTTTTAC
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
57 12 0.21
58 27 0.48
59 17 0.30
ACGTcount: A:0.38, C:0.26, G:0.02, T:0.34
Consensus pattern (58 bp):
AAAAATTCCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTAAACCCTAAAACTCT
Found at i:1174 original size:29 final size:28
Alignment explanation
Indices: 979--1174 Score: 128
Period size: 29 Copynumber: 6.8 Consensus size: 28
969 CATTTTTAAC
* *
979 CCAAAAACTCCATTTTTACCCTCGAACTT
1 CCAAAAATTCCATTTTAACCC-CGAACTT
*
1008 CCAAAAATTCCATTTTTAACCCTGAAACTT
1 CCAAAAATTCCA-TTTTAACCCCG-AACTT
* * * *
1038 CTAAAAATTCCATTTTTATCCCAAACTT
1 CCAAAAATTCCATTTTAACCCCGAACTT
* **
1066 CCAAAAATTTCATTTTAAACCTCAAAAC-T
1 CCAAAAATTCCATTTT-AACC-CCGAACTT
* *
1095 CTC-AAAATTACCCTTTTACCCCCGAA-TAT
1 C-CAAAAATT-CCATTTTAACCCCGAACT-T
* * *
1124 CTAAGAATTTCATATTTAACCCCGAACTT
1 CCAAAAATTCCAT-TTTAACCCCGAACTT
* *
1153 CCCAAAATTACCATTTTGACCC
1 CCAAAAATT-CCATTTTAACCC
1175 TGAGAATTGA
Statistics
Matches: 127, Mismatches: 28, Indels: 24
0.71 0.16 0.13
Matches are distributed among these distances:
28 24 0.19
29 64 0.50
30 39 0.31
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (28 bp):
CCAAAAATTCCATTTTAACCCCGAACTT
Found at i:1583 original size:95 final size:95
Alignment explanation
Indices: 1430--1615 Score: 250
Period size: 95 Copynumber: 1.9 Consensus size: 95
1420 AAAACTTTAA
* * * **
1430 AATCGAGGCAATATTCCTTTATTTCGAGTTTCAAAAATTTGCGTCTTAACTTACTAGGTGCAATT
1 AATCGAGGCAATATTCCTTTATTTCGAG-TTCAAAAATTTACGCCTTAACGTACTAGGTGCAACC
1495 TTTCTTCAAATCGAAATAATCGAATACCCTT
65 TTTCTTCAAATCGAAATAATCGAATACCCTT
** *
1526 AATCGAGGCAATATTTCC-TTATCTTCGA-TTCTGAAATTTACGCCTTAACGTATTAGGTGCAAC
1 AATCGAGGCAATA-TTCCTTTAT-TTCGAGTTCAAAAATTTACGCCTTAACGTACTAGGTGCAAC
*
1589 CTTTCTTCAAATCGAGATAATCGAATA
64 CTTTCTTCAAATCGAAATAATCGAATA
1616 TCTTTTTCCC
Statistics
Matches: 79, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
95 53 0.67
96 17 0.22
97 9 0.11
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.36
Consensus pattern (95 bp):
AATCGAGGCAATATTCCTTTATTTCGAGTTCAAAAATTTACGCCTTAACGTACTAGGTGCAACCT
TTCTTCAAATCGAAATAATCGAATACCCTT
Done.