Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014374.1 Kokia drynarioides strain JFW-HI SEQ_129412, 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: 7608
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.26
Warning! 78 characters in sequence are not A, C, G, or T
Found at i:1003 original size:30 final size:30
Alignment explanation
Indices: 945--1180 Score: 259
Period size: 29 Copynumber: 8.0 Consensus size: 30
935 GAAGGTCCCT
*
945 AAACTGTCCAAAAATTTCATTTTT-ACCCCC
1 AAACT-TCCAAAAATTCCATTTTTAACCCCC
*
975 AAACTTCCAAAAA-TCACATTTTTAACCCCA
1 AAACTTCCAAAAATTC-CATTTTTAACCCCC
*
1005 AAACTTCCAAAAATTCCA-TTTTACCCCCC
1 AAACTTCCAAAAATTCCATTTTTAACCCCC
* * * *
1034 GAACTTCCTAAAATCCCATTTTTGAA-CCCA
1 AAACTTCCAAAAATTCCATTTTT-AACCCCC
* *
1064 AAACTTCCAAAAATTCCGTTTTTAA-CCTC
1 AAACTTCCAAAAATTCCATTTTTAACCCCC
* * **
1093 GAACTTCCAAAAATCCCATTTTTAACCCTA
1 AAACTTCCAAAAATTCCATTTTTAACCCCC
* *
1123 AAACTTCCAAAAATTCCATTTTT-AGCCTC
1 AAACTTCCAAAAATTCCATTTTTAACCCCC
*
1152 GAACTTCCAAAAATTCCATTTTTAACCCC
1 AAACTTCCAAAAATTCCATTTTTAACCCC
1181 AAATTTTCCC
Statistics
Matches: 173, Mismatches: 26, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
28 1 0.01
29 91 0.53
30 78 0.45
31 3 0.02
ACGTcount: A:0.36, C:0.31, G:0.03, T:0.31
Consensus pattern (30 bp):
AAACTTCCAAAAATTCCATTTTTAACCCCC
Found at i:1196 original size:59 final size:59
Alignment explanation
Indices: 945--1183 Score: 338
Period size: 59 Copynumber: 4.0 Consensus size: 59
935 GAAGGTCCCT
* * *
945 AAACTGTCCAAAAATTTCATTTTTACCCCCAAACTTCCAAAAATCACATTTTTAACCCCA
1 AAACT-TCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCA
*
1005 AAACTTCCAAAAATTCCA-TTTTACCCCCCGAACTTCCTAAAATCCCATTTTTGAA-CCCA
1 AAACTTCCAAAAATTCCATTTTTA-CCCCCGAACTTCCAAAAATCCCATTTTT-AACCCCA
* * * *
1064 AAACTTCCAAAAATTCCGTTTTTAACCTCGAACTTCCAAAAATCCCATTTTTAACCCTA
1 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCA
* * *
1123 AAACTTCCAAAAATTCCATTTTTAGCCTCGAACTTCCAAAAATTCCATTTTTAACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCA
1182 AA
1 AA
1184 TTTTCCCAAA
Statistics
Matches: 162, Mismatches: 13, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
58 7 0.04
59 143 0.88
60 12 0.07
ACGTcount: A:0.36, C:0.30, G:0.03, T:0.31
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCA
Found at i:1220 original size:118 final size:117
Alignment explanation
Indices: 980--1233 Score: 291
Period size: 118 Copynumber: 2.2 Consensus size: 117
970 CCCCCAAACT
* *
980 TCCAAAAATCACATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTACCCCCCGAACTTCCTAA
1 TCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTACCCCCCGAACTTCCAAA
* * *
1045 AATCCCATTTTTGAACCCAAAACTTCCAAAAATTCCGTTTTTAACCTCGAACT
66 AATCCCATTTTTGAACCCAAAACTTCCAAAAATTACG-ATTTAACCTCGAACA
* * *
1098 TCCAAAAATCCCATTTTTAACCCTAAAACTTCCAAAAATTCCATTTTTA-GCCTCGAACTTCCAA
1 TCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCCA-TTTTACCCCCCGAACTTCCAA
* ** * *
1162 AAATTCCATTTTT-AACCCCAAATTTTCCCAAAATTAAC-ATTTCACCTACGAGA-A
65 AAATCCCATTTTTGAA-CCCAAAACTTCCAAAAATT-ACGATTTAACCT-CGA-ACA
* *
1216 TCCAAAATTACCATTTTT
1 TCCAAAAATCCCATTTTT
1234 CCCCTGAGTA
Statistics
Matches: 116, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
117 9 0.08
118 100 0.86
119 7 0.06
ACGTcount: A:0.36, C:0.29, G:0.03, T:0.31
Consensus pattern (117 bp):
TCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTACCCCCCGAACTTCCAAA
AATCCCATTTTTGAACCCAAAACTTCCAAAAATTACGATTTAACCTCGAACA
Done.