Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011551.1 Kokia drynarioides strain JFW-HI SEQ_126537, 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: 33335
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1479 original size:43 final size:43
Alignment explanation
Indices: 1410--1571 Score: 227
Period size: 43 Copynumber: 3.8 Consensus size: 43
1400 AAAACTTGGT
* * ** * *
1410 AAAGGAAGACTCATGTCTCGGATAGAGCATGTGATTATTTACA
1 AAAGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTATA
*
1453 AATGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTATA
1 AAAGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTATA
1496 AAAGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTATA
1 AAAGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTATA
* *
1539 AAAGGAAAACTTATGTCTTGG-TAGGAGCATAAG
1 AAAGGAAGACTTATGTCTCGGTTA-GAGCATAAG
1572 GTTATTTGTA
Statistics
Matches: 108, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
42 2 0.02
43 106 0.98
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.30
Consensus pattern (43 bp):
AAAGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTATA
Found at i:11748 original size:41 final size:41
Alignment explanation
Indices: 11654--11841 Score: 150
Period size: 41 Copynumber: 4.5 Consensus size: 41
11644 TATGCTCTAT
* * * *
11654 TGAGTCATAAGTCTTCCTTTCAAACATAATCTCATGCTCAATTC
1 TGAGACATGAGTCTTCCTTT-ATACA-AATCTCATGCTC-ATCC
* *
11698 -GAGATATGAGTCTTCCTTTAATA-AAATCTCATTCTCATCC
1 TGAGACATGAGTCTTCCTTT-ATACAAATCTCATGCTCATCC
* * *
11738 TGAGACATGAGTCTTCCTTTAT-CATATTCTCATGCTTAT-T
1 TGAGACATGAGTCTTCCTTTATACA-AATCTCATGCTCATCC
* * * * *
11778 TCGAGTCACGAGTCTTCCAATTATACAATTTCTCATGCTCAACC
1 T-GAGACATGAGTCTTCC-TTTATACAA-ATCTCATGCTCATCC
11822 TGAGACATGAGTCTTCCTTT
1 TGAGACATGAGTCTTCCTTT
11842 TTATACGTCG
Statistics
Matches: 115, Mismatches: 21, Indels: 18
0.75 0.14 0.12
Matches are distributed among these distances:
40 7 0.06
41 54 0.47
42 8 0.07
43 45 0.39
44 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.38
Consensus pattern (41 bp):
TGAGACATGAGTCTTCCTTTATACAAATCTCATGCTCATCC
Found at i:25972 original size:50 final size:50
Alignment explanation
Indices: 25832--25989 Score: 156
Period size: 50 Copynumber: 3.2 Consensus size: 50
25822 CCTATATCCT
* ** ** * *
25832 TAAAGATGTAGAGGAACAGATTGAAGCTACAATG-GCAAATCTCATACACC
1 TAAAGCTGTAGAGGGGCAGATTGAAGCCGCAA-GAGCGAATCTTATACACC
* * *
25882 TAAAGCTGTAGAGGGGCAGATTGAAGCCGCAATAGTGAATCTTATTCACC
1 TAAAGCTGTAGAGGGGCAGATTGAAGCCGCAAGAGCGAATCTTATACACC
* * * * *
25932 TAAAGCTGTAGAGGGGTATATTGAAGTCGCAAGGGCGAATCTTATACTCC
1 TAAAGCTGTAGAGGGGCAGATTGAAGCCGCAAGAGCGAATCTTATACACC
*
25982 TGAAGCTG
1 TAAAGCTG
25990 AAAAAGGTTG
Statistics
Matches: 88, Mismatches: 19, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
50 88 1.00
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.23
Consensus pattern (50 bp):
TAAAGCTGTAGAGGGGCAGATTGAAGCCGCAAGAGCGAATCTTATACACC
Found at i:27814 original size:60 final size:60
Alignment explanation
Indices: 27750--27909 Score: 259
Period size: 60 Copynumber: 2.7 Consensus size: 60
27740 AAAATTTCAA
* *
27750 ATTTGACCCCTAAACTTTCTAAAAATTTGGATTTGACCCTCAAACTTTCCAAAAATTTGT
1 ATTTGACCCCTAAACTTTCCAAAAATTTGGATTTGACCCTCAAACTTTCCAAAAATTTGG
* *
27810 ATTTGACCCCCAAACTTTCCAAAAATTTGGATTTGACCCTCGAACTTTCCAAAAATTTGG
1 ATTTGACCCCTAAACTTTCCAAAAATTTGGATTTGACCCTCAAACTTTCCAAAAATTTGG
*
27870 ATTTGACCCCTAAACTTTCCAAAAATTCT-AATTTGACCCT
1 ATTTGACCCCTAAACTTTCCAAAAATT-TGGATTTGACCCT
27910 ATTTTATTTT
Statistics
Matches: 93, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
60 92 0.99
61 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.09, T:0.34
Consensus pattern (60 bp):
ATTTGACCCCTAAACTTTCCAAAAATTTGGATTTGACCCTCAAACTTTCCAAAAATTTGG
Found at i:27908 original size:30 final size:30
Alignment explanation
Indices: 27750--27896 Score: 226
Period size: 30 Copynumber: 4.9 Consensus size: 30
27740 AAAATTTCAA
*
27750 ATTTGACCCCTAAACTTTCTAAAAATTTGG
1 ATTTGACCCCTAAACTTTCCAAAAATTTGG
*
27780 ATTTGA-CCCTCAAACTTTCCAAAAATTTGT
1 ATTTGACCCCT-AAACTTTCCAAAAATTTGG
*
27810 ATTTGACCCCCAAACTTTCCAAAAATTTGG
1 ATTTGACCCCTAAACTTTCCAAAAATTTGG
*
27840 ATTTGA-CCCTCGAACTTTCCAAAAATTTGG
1 ATTTGACCCCT-AAACTTTCCAAAAATTTGG
27870 ATTTGACCCCTAAACTTTCCAAAAATT
1 ATTTGACCCCTAAACTTTCCAAAAATT
27897 CTAATTTGAC
Statistics
Matches: 106, Mismatches: 7, Indels: 8
0.88 0.06 0.07
Matches are distributed among these distances:
29 7 0.07
30 92 0.87
31 7 0.07
ACGTcount: A:0.33, C:0.24, G:0.09, T:0.34
Consensus pattern (30 bp):
ATTTGACCCCTAAACTTTCCAAAAATTTGG
Found at i:31475 original size:17 final size:17
Alignment explanation
Indices: 31453--31491 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
31443 AATAACAAGT
31453 TTTATTTGATTATTT-TA
1 TTTATTT-ATTATTTATA
31470 TTTATTTATTATTTATA
1 TTTATTTATTATTTATA
31487 TTTAT
1 TTTAT
31492 AAAATAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (17 bp):
TTTATTTATTATTTATA
Done.