Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007591.1 Kokia drynarioides strain JFW-HI SEQ_122222, 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: 1729
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Found at i:270 original size:21 final size:23
Alignment explanation
Indices: 241--283 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
231 AAGTTAAATA
*
241 AAAAGGTTTTC-AA-AAAAAGGG
1 AAAACGTTTTCTAACAAAAAGGG
262 AAAACGTTTTCTAACAAAAAGG
1 AAAACGTTTTCTAACAAAAAGG
284 AGGACTGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
22 2 0.11
23 7 0.37
ACGTcount: A:0.51, C:0.09, G:0.19, T:0.21
Consensus pattern (23 bp):
AAAACGTTTTCTAACAAAAAGGG
Found at i:1132 original size:29 final size:29
Alignment explanation
Indices: 1081--1413 Score: 203
Period size: 29 Copynumber: 11.3 Consensus size: 29
1071 AAAATCCCTT
* ** *
1081 TTTTAA-CCCAAAGCTTTTAAAAAACCTAA
1 TTTTAACCCCAAAACTTCCAAAAATCC-AA
*
1110 TTTTAACCCTAAAACTTCCAAAAATTCC-A
1 TTTTAACCCCAAAACTTCCAAAAA-TCCAA
* * *
1139 TTTTTACCCTC-AAACTACCAAAAATCCCAT
1 TTTTAACCC-CAAAACTTCCAAAAAT-CCAA
* * **
1169 TTTTAACCCCGAAGCTTTAAAAAATTCCAA
1 TTTTAACCCCAAAACTTCCAAAAA-TCCAA
1199 TTTTAACCCCAAAACTTCCAAAAATTCC-A
1 TTTTAACCCCAAAACTTCCAAAAA-TCCAA
* * * *
1228 TTTTTACCCTC-GAACTACCAAAAATCCCAT
1 TTTTAACCC-CAAAACTTCCAAAAAT-CCAA
* *
1258 TTTTAACCCCAAAGCTTTCAAAAATTCC-A
1 TTTTAACCCCAAAACTTCCAAAAA-TCCAA
* * * * *
1287 TTTTTACCCCCAAACCTCCAAACATCCCA
1 TTTTAACCCCAAAACTTCCAAAAATCCAA
* * * * *
1316 TTTTTACCCTAAAACTACAAAAAATCCCAT
1 TTTTAACCCCAAAACTTCCAAAAAT-CCAA
* *
1346 TTTTAACCCCAAAACTTTCAAAAGGTCC-A
1 TTTTAACCCCAAAACTTCCAAAA-ATCCAA
* * * *
1375 TTTTTACCCCCAAACTTCTAAAAATCCAT
1 TTTTAACCCCAAAACTTCCAAAAATCCAA
*
1404 TTTTGACCCC
1 TTTTAACCCC
1414 GAATTTTCTC
Statistics
Matches: 231, Mismatches: 57, Indels: 32
0.72 0.18 0.10
Matches are distributed among these distances:
28 8 0.03
29 119 0.52
30 99 0.43
31 5 0.02
ACGTcount: A:0.38, C:0.30, G:0.02, T:0.30
Consensus pattern (29 bp):
TTTTAACCCCAAAACTTCCAAAAATCCAA
Found at i:1347 original size:88 final size:89
Alignment explanation
Indices: 1069--1412 Score: 455
Period size: 88 Copynumber: 3.9 Consensus size: 89
1059 CTAAATTGTT
* * * *
1069 CAAAAATCCCTTTTTTAA-CCCAAAGCTTTTAAAAA-ACCTAATTTTAACCCTAAAACTTCCAAA
1 CAAAAATCCCATTTTTAACCCCAAAGCTTTCAAAAATTCC-AATTTTAACCCCAAAACTTCCAAA
1132 AATTCCATTTTTACCCTCAAACTAC
65 AATTCCATTTTTACCCTCAAACTAC
* *
1157 CAAAAATCCCATTTTTAACCCCGAAGCTTTAAAAAATTCCAATTTTAACCCCAAAACTTCCAAAA
1 CAAAAATCCCATTTTTAACCCCAAAGCTTTCAAAAATTCCAATTTTAACCCCAAAACTTCCAAAA
*
1222 ATTCCATTTTTACCCTCGAACTAC
66 ATTCCATTTTTACCCTCAAACTAC
* * * *
1246 CAAAAATCCCATTTTTAACCCCAAAGCTTTCAAAAATTCC-ATTTTTACCCCCAAACCTCCAAAC
1 CAAAAATCCCATTTTTAACCCCAAAGCTTTCAAAAATTCCAATTTTAACCCCAAAACTTCCAAAA
* *
1310 ATCCCATTTTTACCCTAAAACTAC
66 ATTCCATTTTTACCCTCAAACTAC
* * ** * * *
1334 AAAAAATCCCATTTTTAACCCCAAAACTTTCAAAAGGTCC-ATTTTTACCCCCAAACTTCTAAAA
1 CAAAAATCCCATTTTTAACCCCAAAGCTTTCAAAAATTCCAATTTTAACCCCAAAACTTCCAAAA
1398 A-TCCATTTTTGACCC
66 ATTCCATTTTT-ACCC
1413 CGAATTTTCT
Statistics
Matches: 230, Mismatches: 23, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
87 8 0.03
88 120 0.52
89 100 0.43
90 2 0.01
ACGTcount: A:0.38, C:0.30, G:0.02, T:0.30
Consensus pattern (89 bp):
CAAAAATCCCATTTTTAACCCCAAAGCTTTCAAAAATTCCAATTTTAACCCCAAAACTTCCAAAA
ATTCCATTTTTACCCTCAAACTAC
Found at i:1426 original size:59 final size:56
Alignment explanation
Indices: 1121--1428 Score: 223
Period size: 59 Copynumber: 5.2 Consensus size: 56
1111 TTTAACCCTA
* *
1121 AAACTTC-CAAAAATTCCATTTTTACCCTCAAACTACCAAAAATCCCATTTTTAACCCCG
1 AAACTTCTC-AAAA-TCCATTTTTACCCCCAAACTTCCAAAAAT-CCATTTTT-ACCCCG
* * * *
1180 AAGCTT-TAAAAAATTCCAATTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCTCG
1 AAACTTCT-CAAAA-TCC-ATTTTTACCCCCAAACTTCCAAAAA-TCCATTTTTACCC-CG
* * * *
1240 -AACTAC-CAAAAATCCCATTTTTAACCCCAAAGCTTTCAAAAATTCCATTTTTACCCCC
1 AAACTTCTC-AAAAT-CCATTTTTACCCCCAAA-CTTCCAAAAA-TCCATTTTTACCCCG
* ** * * *
1298 AAACCTC-CAAACATCCCATTTTTACCCTAAAACTACAAAAAATCCCATTTTTAACCCCA
1 AAACTTCTCAAA-AT-CCATTTTTACCCCCAAACTTCCAAAAAT-CCATTTTT-ACCCCG
*
1357 AAACTT-TCAAAAGGTCCATTTTTACCCCCAAACTTCTAAAAATCCATTTTTGACCCCG
1 AAACTTCTCAAAA--TCCATTTTTACCCCCAAACTTCCAAAAATCCATTTTT-ACCCCG
**
1415 AATTTTCTCAAAAT
1 AAACTTCTCAAAAT
1429 TATCACTTTT
Statistics
Matches: 200, Mismatches: 32, Indels: 36
0.75 0.12 0.13
Matches are distributed among these distances:
57 2 0.01
58 50 0.25
59 115 0.57
60 32 0.16
61 1 0.00
ACGTcount: A:0.37, C:0.30, G:0.03, T:0.30
Consensus pattern (56 bp):
AAACTTCTCAAAATCCATTTTTACCCCCAAACTTCCAAAAATCCATTTTTACCCCG
Done.