Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012012.1 Kokia drynarioides strain JFW-HI SEQ_127010, 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: 5116
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:4004 original size:205 final size:206
Alignment explanation
Indices: 3393--4160 Score: 1082
Period size: 205 Copynumber: 3.7 Consensus size: 206
3383 CACAAACAGT
* *
3393 GATGTGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACACACGCTCAAAGCGAG
1 GATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAAAGCGAG
* ** *
3458 CAAAATCTTCGAACCTCAGCTTCCTGCGGAGATACTAAGAAGCAGGTCGAAGCAATAAAATGGTT
66 CAAAATCTTCGAACCCCAGCTTCCTGATGAGACACTAAGAAGCAGGTCGAAGCAATAAAA-GGTT
*
3523 AGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTTGTCTTCCTGATGAGATACAGAGAAGCGG
130 AGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGG
*
3588 ATTGAAACAAGA
195 ATTGAAACAAGC
3600 GATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATC-AA---ACGCTCAAAGCGAG
1 GATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAAAGCGAG
* * * * * * *
3661 CAAAATCTTCGAACTCCAGCTTCTTGACGAGACATTGAGAAGCAGGTCGAAGTAATAGAACGGTT
66 CAAAATCTTCGAACCCCAGCTTCCTGATGAGACACTAAGAAGCAGGTCGAAGCAATA-AAAGGTT
*
3726 AGCTTCCTGATGAGATACTGAGAAGTGAACCTAATTCGTCTTCCTGATGAGATACAGAGAAGCGG
130 AGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGG
3791 ATTGAAACAAGC
195 ATTGAAACAAGC
** * *** *
3803 GATGCGGTCATCTTCCCNATGAAATACTGAGAAGAAGACCAAATCAAACCCACGCTCTGCGTGAG
1 GATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAAAGCGAG
* *
3868 C-AAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCAAAGCAATAAAAGGTTA
66 CAAAATCTTCGAACCCCAGCTTCCTGATGAGACACTAAGAAGCAGGTCGAAGCAATAAAAGGTTA
* * * * * * *
3932 ACTTCCTGAAGAGATACTGAGAAATGGACCAAATTCGTCTTCCTGACGAAATATAGAGAAGCGGA
131 GCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGA
*
3997 TTGAAACAAAC
196 TTGAAACAAGC
* * * ** * *
4008 GACGCGGTCATCTTCCTTATGAGATACTGAGAAGAAGACCAAATCAAACCCACTCTTGACGTGAG
1 GATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAAAGCGAG
* *
4073 C-AAATCTTCGAATCCCAGCTTCCTGATGAGACACCAAGAAGCAGGTCGAAGCAATAAACA-GTT
66 CAAAATCTTCGAACCCCAGCTTCCTGATGAGACACTAAGAAGCAGGTCGAAGCAATAAA-AGGTT
4136 AGCTTCCTGATGAGATACTGAGAAG
130 AGCTTCCTGATGAGATACTGAGAAG
4161 AAGGCCAAGT
Statistics
Matches: 503, Mismatches: 52, Indels: 14
0.88 0.09 0.02
Matches are distributed among these distances:
203 182 0.36
204 4 0.01
205 210 0.42
206 52 0.10
207 55 0.11
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (206 bp):
GATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAAAGCGAG
CAAAATCTTCGAACCCCAGCTTCCTGATGAGACACTAAGAAGCAGGTCGAAGCAATAAAAGGTTA
GCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGA
TTGAAACAAGC
Found at i:4491 original size:11 final size:11
Alignment explanation
Indices: 4475--4543 Score: 51
Period size: 11 Copynumber: 6.6 Consensus size: 11
4465 GCCCAACAAA
4475 TTTAAATTTAT
1 TTTAAATTTAT
4486 TTTAAA---A-
1 TTTAAATTTAT
*
4493 -TTAAGTTTAT
1 TTTAAATTTAT
*
4503 TTAAAATTTAT
1 TTTAAATTTAT
4514 TTTAAATTTAAAT
1 TTTAAATTT--AT
*
4527 TTAAAATTTA-
1 TTTAAATTTAT
4537 TTTAAAT
1 TTTAAAT
4544 AATGCCCAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 15
0.68 0.09 0.23
Matches are distributed among these distances:
6 4 0.09
8 1 0.02
9 1 0.02
10 6 0.13
11 23 0.51
13 10 0.22
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:4512 original size:28 final size:24
Alignment explanation
Indices: 4472--4539 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 24
4462 TGGGCCCAAC
4472 AAATTT-AAATTTATTTTAAAATT
1 AAATTTAAAATTTATTTTAAAATT
*
4495 AAGTTTATTTAAAATTTATTTTAAATTT
1 AA----ATTTAAAATTTATTTTAAAATT
4523 AAATTTAAAATTTATTT
1 AAATTTAAAATTTATTT
4540 AAATAATGCC
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
23 2 0.05
24 15 0.38
27 4 0.10
28 18 0.46
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (24 bp):
AAATTTAAAATTTATTTTAAAATT
Found at i:4543 original size:17 final size:16
Alignment explanation
Indices: 4472--4543 Score: 65
Period size: 17 Copynumber: 4.2 Consensus size: 16
4462 TGGGCCCAAC
4472 AAATTTAAATTTATTTT
1 AAATTTAAATTTA-TTT
* *
4489 AAAATTAAGTTTATTT
1 AAATTTAAATTTATTT
*
4505 AAAATTT-ATTTTAAATTT
1 -AAATTTAAATTT--ATTT
4523 AAATTTAAAATTTATTT
1 AAATTT-AAATTTATTT
4540 AAAT
1 AAAT
4544 AATGCCCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
16 7 0.16
17 30 0.67
18 4 0.09
19 4 0.09
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (16 bp):
AAATTTAAATTTATTT
Done.