Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011194.1 Kokia drynarioides strain JFW-HI SEQ_126171, 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: 12054
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:8038 original size:218 final size:217
Alignment explanation
Indices: 7660--8447 Score: 1256
Period size: 218 Copynumber: 3.6 Consensus size: 217
7650 ATTATCCACA
* *
7660 AAACGATGCAGTCATCTTCCCGATGAGATACTGAGAAGAAGACAGAACCAAACCCATCCTCGATG
1 AAACGATCCAGTCATCTTCCCGATGAGATACTGAGAAGAAGACAGAACCAAACCCATGCTCGATG
*
7725 GGAGCAAATCTTCGAACCATAGCTTCCTGATGAGATACTGAGAAGCGTGCCGAAGTAATAAAACG
66 TGAGCAAATCTTCGAACCATAGCTTCCTGATGAGATACTGAGAAGCGTGCCGAAGTAATAAAACG
7790 GTTGGGTTCCTGACCATCTTCCTGATGAGGTACGGAGAAGTGGACCAAATTCGTTTTCCTGATGA
131 GTT-GGTTCCTGACCATCTTCCTGATGAGGTACGGAGAAGTGGACCAAATTCGTTTTCCTGATGA
7855 GATACAGAGAAGTGAATTGAAAC
195 GATACAGAGAAGTGAATTGAAAC
* ** * *
7878 AAACGATCCAATCATCTTCCTAATGAGATACTGAGAAGAAGACCGAACCAAACCCATGCTTGATA
1 AAACGATCCAGTCATCTTCCCGATGAGATACTGAGAAGAAGACAGAACCAAACCCATGCTCGAT-
*
7943 G-GAGTAAATCTTCGAACCATAGCTTCCTGATGAGATACTGAGAAGCGTGCCGAAGTAATAAAAC
65 GTGAGCAAATCTTCGAACCATAGCTTCCTGATGAGATACTGAGAAGCGTGCCGAAGTAATAAAAC
* * *
8007 GGTTAGGTTCCTGACCATCTTCCTAATGAGGTACAGAGAAGTGGACCAAATTCGTTTTCCTGATA
130 GGTT-GGTTCCTGACCATCTTCCTGATGAGGTACGGAGAAGTGGACCAAATTCGTTTTCCTGATG
8072 AGATACAGAGAAGTGAATTGAAAC
194 AGATACAGAGAAGTGAATTGAAAC
* *
8096 AAACGATGCAGCCATCTTCCCGATGAGATACTGAGAAGAAGACAGAACCAAACCCATGCTCGATG
1 AAACGATCCAGTCATCTTCCCGATGAGATACTGAGAAGAAGACAGAACCAAACCCATGCTCGATG
* * * * * *
8161 TGAGCAAATCTTCGAACCACAGCTTCTTGATGATATAC-GAAGAAGCATGCCAAAGTGATAAAAC
66 TGAGCAAATCTTCGAACCATAGCTTCCTGATGAGATACTG-AGAAGCGTGCCGAAGTAATAAAAC
** * *
8225 AATTGGCTTCCTGACCATCTTCCTGATGAGGTACGGAGAAGTGGACAAAATTCGTCTTCCTGATG
130 GGTTGG-TTCCTGACCATCTTCCTGATGAGGTACGGAGAAGTGGACCAAATTCGTTTTCCTGATG
8290 AGATACAGAGAAGTGAATTGAAAC
194 AGATACAGAGAAGTGAATTGAAAC
* * * *
8314 AAAACGACCCAGTCATCTTCCGGATGAAATACTGAGAAGAAGACCGAACCAAACCCATGCTCGAT
1 -AAACGATCCAGTCATCTTCCCGATGAGATACTGAGAAGAAGACAGAACCAAACCCATGCTCGAT
8379 GTGAGCAAATCTTCGAACCATAGCTTCCTGATGAGATACTGAGAAGCGTGCCGAAGTAATAAAAC
65 GTGAGCAAATCTTCGAACCATAGCTTCCTGATGAGATACTGAGAAGCGTGCCGAAGTAATAAAAC
8444 GGTT
130 GGTT
8448 NNNNNNNNNN
Statistics
Matches: 517, Mismatches: 47, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
217 4 0.01
218 394 0.76
219 118 0.23
220 1 0.00
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (217 bp):
AAACGATCCAGTCATCTTCCCGATGAGATACTGAGAAGAAGACAGAACCAAACCCATGCTCGATG
TGAGCAAATCTTCGAACCATAGCTTCCTGATGAGATACTGAGAAGCGTGCCGAAGTAATAAAACG
GTTGGTTCCTGACCATCTTCCTGATGAGGTACGGAGAAGTGGACCAAATTCGTTTTCCTGATGAG
ATACAGAGAAGTGAATTGAAAC
Found at i:8538 original size:73 final size:73
Alignment explanation
Indices: 8385--8530 Score: 195
Period size: 73 Copynumber: 2.0 Consensus size: 73
8375 CGATGTGAGC
**
8385 AAATCTTCGAACCATAGCTTCCTGATGAGATACTGAGAAGCGTGCCGAAGTAATAAAACGGTTNN
1 AAATCTTCGAACCATAGCTTCCTGATGAGATACTGAGAAGCGTGCCGAAGTAATAAAACGGTTAA
********
8450 NNNNNNNN
66 GCTTCCGG
8458 AAATCTTCGAACCATAGCTTCCTGATGAGATACTGAGAAGCGTGCCGAAGTAATAAAACGGTT-A
1 AAATCTTCGAACCATAGCTTCCTGATGAGATACTGAGAAGCGTGCCGAAGTAATAAAACGGTTAA
8522 GCTTCCGG
66 GCTTCCGG
8530 A
1 A
8531 CCATCTTCCT
Statistics
Matches: 64, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
72 1 0.02
73 63 0.98
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.22
Consensus pattern (73 bp):
AAATCTTCGAACCATAGCTTCCTGATGAGATACTGAGAAGCGTGCCGAAGTAATAAAACGGTTAA
GCTTCCGG
Found at i:9203 original size:17 final size:18
Alignment explanation
Indices: 9180--9241 Score: 74
Period size: 17 Copynumber: 3.6 Consensus size: 18
9170 CAAGCTCCCC
*
9180 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAAAA
* *
9198 -TTAAATTTGTTTAAAAA
1 TTTAAATTTATTTTAAAA
9215 TTTAAATTTATTTT-AAA
1 TTTAAATTTATTTTAAAA
*
9232 TTTAAGTTTA
1 TTTAAATTTA
9242 AATTTATTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
17 26 0.70
18 11 0.30
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (18 bp):
TTTAAATTTATTTTAAAA
Found at i:9242 original size:23 final size:24
Alignment explanation
Indices: 9215--9260 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
9205 TGTTTAAAAA
*
9215 TTTAAATTTATT-TTAAATTTAAG
1 TTTAAATTTATTATCAAATTTAAG
9238 TTTAAATTTATTATCAAATTTAA
1 TTTAAATTTATTATCAAATTTAA
9261 AATTATTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (24 bp):
TTTAAATTTATTATCAAATTTAAG
Found at i:9243 original size:12 final size:12
Alignment explanation
Indices: 9215--9247 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
9205 TGTTTAAAAA
*
9215 TTTAAATTT-AT
1 TTTAAATTTAAG
9226 TTTAAATTTAAG
1 TTTAAATTTAAG
9238 TTTAAATTTA
1 TTTAAATTTA
9248 TTATCAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (12 bp):
TTTAAATTTAAG
Found at i:11113 original size:30 final size:30
Alignment explanation
Indices: 11029--11485 Score: 378
Period size: 30 Copynumber: 15.4 Consensus size: 30
11019 ATTGTTCAAC
* * * *
11029 AATCCCATTATTAACCCAAAAAATTGCCAAA
1 AATCCCATTTTTAACCCCAAAACTT-CTAAA
* **
11060 AATCCTATTTTT-ACCCCTGAACTTCTAAA
1 AATCCCATTTTTAACCCCAAAACTTCTAAA
11089 AATCCCATTTTTAACCCCAAAACTT-TAAAA
1 AATCCCATTTTTAACCCCAAAACTTCT-AAA
* *
11119 AATCCCATTTTTAACCTCAAAACTTCCAAA
1 AATCCCATTTTTAACCCCAAAACTTCTAAA
* ** *
11149 AATTCCATTTTT-ACCCCCGACCTTCTAAA
1 AATCCCATTTTTAACCCCAAAACTTCTAAA
* * * *
11178 AAT-CCAATTTTAACCTCGAAACTTCCAAA
1 AATCCCATTTTTAACCCCAAAACTTCTAAA
* * *
11207 AATCCCATTTTTAACCTCAAAGCTTTTAAA
1 AATCCCATTTTTAACCCCAAAACTTCTAAA
* * * ** *
11237 AATCCCAATTTAAACCCTAAAACACCCAAAA
1 AATCCCATTTTTAACCCCAAAAC-TTCTAAA
11268 AATCCCATTTTT-ACCCTC-AAACTTCTAAA
1 AATCCCATTTTTAACCC-CAAAACTTCTAAA
* * *
11297 AATCCAATTTTTAACCCCAAAAATTCCAAA
1 AATCCCATTTTTAACCCCAAAACTTCTAAA
* * * *
11327 AATCCCAATTTTAACCCCGAAGCTTTTAAA
1 AATCCCATTTTTAACCCCAAAACTTCTAAA
* * *
11357 AATCCCAATTTTAACCTCAAAACCTCT-AA
1 AATCCCATTTTTAACCCCAAAACTTCTAAA
* * *
11386 AATCCCA-TTTTGACCCCAAAACTACCAAA
1 AATCCCATTTTTAACCCCAAAACTTCTAAA
*
11415 AATCTCATTTTTAACCCCAAAACTT-TCAAA
1 AATCCCATTTTTAACCCCAAAACTTCT-AAA
* ** *
11445 AGGT-CCATTTTT-ACCCCTGAACTTCTAAT
1 A-ATCCCATTTTTAACCCCAAAACTTCTAAA
*
11474 GATCCCATTTTT
1 AATCCCATTTTT
11486 TAGCCCGAAT
Statistics
Matches: 336, Mismatches: 75, Indels: 32
0.76 0.17 0.07
Matches are distributed among these distances:
28 22 0.07
29 99 0.29
30 191 0.57
31 24 0.07
ACGTcount: A:0.39, C:0.29, G:0.03, T:0.30
Consensus pattern (30 bp):
AATCCCATTTTTAACCCCAAAACTTCTAAA
Found at i:11457 original size:88 final size:89
Alignment explanation
Indices: 11029--11445 Score: 299
Period size: 88 Copynumber: 4.7 Consensus size: 89
11019 ATTGTTCAAC
* * * * * * **
11029 AATCCCATTATTAACCCAAAAAATTGCCAAAAAT-CCTATTTTTACCCCTGAAC-TTCTAAAAAT
1 AATCCAATTTTTAACCCCAAAAA-TACCAAAAATCCCAATTTTAACCCCAAAACTTTC-AAAAAT
* * *
11092 CCCATTTTTAACCCCAAAACTTTAAAA
64 CCCATTTTTAACCTCAAACCTCT-AAA
* * * * * * ** *
11119 AATCCCATTTTTAACCTCAAAACTTCCAAAAATTCC-ATTTTTACCCC-CGACCTTCTAAAAAT-
1 AATCCAATTTTTAACCCCAAAAATACCAAAAATCCCAATTTTAACCCCAAAACTTTC-AAAAATC
* * *
11181 CCAATTTTAACCTCGAAACTTCCAAA
65 CCATTTTTAACCTC-AAACCTCTAAA
* * ** *** * * ***
11207 AATCCCATTTTTAACCTCAAAGCTTTTAAAAATCCCAATTTAAACCCTAAAACACCCAAAAAATC
1 AATCCAATTTTTAACCCCAAAAATACCAAAAATCCCAATTTTAACCCCAAAACTTTC-AAAAATC
* *
11272 CCATTTTTACCCTCAAACTTCTAAA
65 CCATTTTTAACCTCAAACCTCTAAA
* * * *
11297 AATCCAATTTTTAACCCCAAAAATTCCAAAAATCCCAATTTTAACCCCGAAGCTTTTAAAAATCC
1 AATCCAATTTTTAACCCCAAAAATACCAAAAATCCCAATTTTAACCCCAAAACTTTCAAAAATCC
*
11362 CAATTTTAACCTCAAAACCTCT-AA
66 CATTTTTAACCTC-AAACCTCTAAA
* * * * *
11386 AATCCCA-TTTTGACCCCAAAACTACCAAAAATCTCATTTTTAACCCCAAAACTTTCAAAA
1 AATCCAATTTTTAACCCCAAAAATACCAAAAATCCCAATTTTAACCCCAAAACTTTCAAAA
11446 GGTCCATTTT
Statistics
Matches: 265, Mismatches: 55, Indels: 16
0.79 0.16 0.05
Matches are distributed among these distances:
88 94 0.35
89 69 0.26
90 90 0.34
91 12 0.05
ACGTcount: A:0.40, C:0.29, G:0.02, T:0.29
Consensus pattern (89 bp):
AATCCAATTTTTAACCCCAAAAATACCAAAAATCCCAATTTTAACCCCAAAACTTTCAAAAATCC
CATTTTTAACCTCAAACCTCTAAA
Done.