Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011378.1 Kokia drynarioides strain JFW-HI SEQ_126359, 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: 3664
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Found at i:103 original size:17 final size:17
Alignment explanation
Indices: 81--129 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
71 CGGTTTTCAT
81 AATATTTATTAATAATA
1 AATATTTATTAATAATA
**
98 AATATTTATTTTTAAT-
1 AATATTTATTAATAATA
*
114 AATA-ATATTAATAATA
1 AATATTTATTAATAATA
130 TTAATGAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
15 8 0.31
16 4 0.15
17 14 0.54
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AATATTTATTAATAATA
Found at i:127 original size:9 final size:9
Alignment explanation
Indices: 113--146 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
103 TTATTTTTAA
113 TAATAATAT
1 TAATAATAT
122 TAATAATAT
1 TAATAATAT
*
131 TAATGAATAA
1 TAAT-AATAT
141 TAATAA
1 TAATAA
147 AAAAATGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (9 bp):
TAATAATAT
Found at i:1244 original size:30 final size:29
Alignment explanation
Indices: 1199--1541 Score: 236
Period size: 30 Copynumber: 11.6 Consensus size: 29
1189 CCCTAGATTG
* * *
1199 TCCAAAAATCTCATTTTTGACCCAGAAACT
1 TCCAAAATTCCCATTTTT-ACCCCGAAACT
*
1229 TTCAAAATTCCCATTTTTACCCTCG-AACT
1 TCCAAAATTCCCATTTTTACCC-CGAAACT
* *
1258 TCCAAAAATCCCATTTTTGACCCCAAAACT
1 TCCAAAATTCCCATTTTT-ACCCCGAAACT
* *
1288 TTCAAAGTTCCCATTTTTACCCCTG-AACT
1 TCCAAAATTCCCATTTTTACCCC-GAAACT
* * ** *
1317 TCCAAAAATCTCATTTTTAACCTTGAACCTT
1 TCCAAAATTCCCATTTTT-ACCCCGAAAC-T
* *
1348 TCGAAAATTACCA-TTTTACCCTCG-AACT
1 TCCAAAATTCCCATTTTTACCC-CGAAACT
*
1376 TCCAAAAATT-TCATTTTTGACCCC-AAACCT
1 TCC-AAAATTCCCATTTTT-ACCCCGAAA-CT
* * *
1406 TCCAAAAATTACCA-TATTACCCCCAAACT
1 TCC-AAAATTCCCATTTTTACCCCGAAACT
* *
1435 TCCAAAAATCCCATTTTTGACCCCGAACCTT
1 TCCAAAATTCCCATTTTT-ACCCCGAAAC-T
* *
1466 TCAAAAATTACCA-TTTTACCCTCG-AACT
1 TCCAAAATTCCCATTTTTACCC-CGAAACT
* * *
1494 TCCAAAAATCCCATTTTTGACTCCGAACCT
1 TCCAAAATTCCCATTTTT-ACCCCGAAACT
* *
1524 TCCAAAACTACCATTTTT
1 TCCAAAATTCCCATTTTT
1542 CCCTCGTGCA
Statistics
Matches: 246, Mismatches: 45, Indels: 44
0.73 0.13 0.13
Matches are distributed among these distances:
28 24 0.10
29 92 0.37
30 107 0.43
31 23 0.09
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.32
Consensus pattern (29 bp):
TCCAAAATTCCCATTTTTACCCCGAAACT
Found at i:1291 original size:59 final size:59
Alignment explanation
Indices: 1199--1547 Score: 411
Period size: 59 Copynumber: 5.9 Consensus size: 59
1189 CCCTAGATTG
* * *
1199 TCCAAAAATCTCATTTTTGA-CCCAGAAACTTTC-AAAATTCCCATTTTTACCCTCGAACT
1 TCCAAAAATCCCATTTTTGACCCCA-AACCTTTCAAAAATTACCA-TTTTACCCTCGAACT
* * *
1258 TCCAAAAATCCCATTTTTGACCCCAAAACTTTC-AAAGTTCCCATTTTTACCC-CTGAACT
1 TCCAAAAATCCCATTTTTGACCCCAAACCTTTCAAAAATTACCA-TTTTACCCTC-GAACT
* * *** *
1317 TCCAAAAATCTCATTTTTAACCTTGAACCTTTCGAAAATTACCATTTTACCCTCGAACT
1 TCCAAAAATCCCATTTTTGACCCCAAACCTTTCAAAAATTACCATTTTACCCTCGAACT
** * * * *
1376 TCCAAAAATTTCATTTTTGACCCCAAACCTTCCAAAAATTACCATATTACCCCCAAACT
1 TCCAAAAATCCCATTTTTGACCCCAAACCTTTCAAAAATTACCATTTTACCCTCGAACT
*
1435 TCCAAAAATCCCATTTTTGACCCCGAACCTTTCAAAAATTACCATTTTACCCTCGAACT
1 TCCAAAAATCCCATTTTTGACCCCAAACCTTTCAAAAATTACCATTTTACCCTCGAACT
* * * * *
1494 TCCAAAAATCCCATTTTTGACTCCGAACC-TTCCAAAACTACCATTTTTCCCTCG
1 TCCAAAAATCCCATTTTTGACCCCAAACCTTTCAAAAATTACCATTTTACCCTCG
1548 TGCATCCGAA
Statistics
Matches: 255, Mismatches: 31, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
58 23 0.09
59 219 0.86
60 13 0.05
ACGTcount: A:0.32, C:0.31, G:0.05, T:0.32
Consensus pattern (59 bp):
TCCAAAAATCCCATTTTTGACCCCAAACCTTTCAAAAATTACCATTTTACCCTCGAACT
Found at i:1426 original size:118 final size:118
Alignment explanation
Indices: 1199--1538 Score: 461
Period size: 118 Copynumber: 2.9 Consensus size: 118
1189 CCCTAGATTG
* *
1199 TCCAAAAATCTCATTTTTGACCCAGAAACTTTCAAAATTCCCATTTTTACCCTCGAACTTCCAAA
1 TCCAAAAATCTCATTTTTGACCCAGAACCTTTCAAAATTACCA-TTTTACCCTCGAACTTCCAAA
* * * * * **
1264 AATCCCATTTTTGACCCCAAAACTTTC-AAAGTTCCCATTTTTACCCCTGAACT
65 AATCCCATTTTTGACCCCAAACCTTCCAAAAATTACCATTATTACCCCCAAACT
* **
1317 TCCAAAAATCTCATTTTTAACCTTGAACCTTTCGAAAATTACCATTTTACCCTCGAACTTCCAAA
1 TCCAAAAATCTCATTTTTGACCCAGAACCTTTC-AAAATTACCATTTTACCCTCGAACTTCCAAA
**
1382 AATTTCATTTTTGACCCCAAACCTTCCAAAAATTACCA-TATTACCCCCAAACT
65 AATCCCATTTTTGACCCCAAACCTTCCAAAAATTACCATTATTACCCCCAAACT
* *
1435 TCCAAAAATCCCATTTTTGACCCCGAACCTTTCAAAAATTACCATTTTACCCTCGAACTTCCAAA
1 TCCAAAAATCTCATTTTTGACCCAGAACCTTTC-AAAATTACCATTTTACCCTCGAACTTCCAAA
* * *
1500 AATCCCATTTTTGACTCCGAACCTTCC-AAAACTACCATT
65 AATCCCATTTTTGACCCCAAACCTTCCAAAAATTACCATT
1539 TTTCCCTCGT
Statistics
Matches: 195, Mismatches: 24, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
117 9 0.05
118 169 0.87
119 17 0.09
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.32
Consensus pattern (118 bp):
TCCAAAAATCTCATTTTTGACCCAGAACCTTTCAAAATTACCATTTTACCCTCGAACTTCCAAAA
ATCCCATTTTTGACCCCAAACCTTCCAAAAATTACCATTATTACCCCCAAACT
Done.